Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 1 of 126
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 4--454 Score: 282
Period size: 7 Copynumber: 63.4 Consensus size: 7
1 AAA
*
4 CCCCAAA
1 CCCCAAG
*
11 CCCCAAA
1 CCCCAAG
*
18 CCCCAAA
1 CCCCAAG
*
25 CCCCAAA
1 CCCCAAG
* *
32 CCCGAAA
1 CCCCAAG
* *
39 CCCGAAA
1 CCCCAAG
* *
46 CCCGAAA
1 CCCCAAG
* *
53 CCCGAAA
1 CCCCAAG
60 CCCCAAG
1 CCCCAAG
67 -CCCAAG
1 CCCCAAG
73 CCCCAAG
1 CCCCAAG
80 CCCCAAG
1 CCCCAAG
87 CCCCAAG
1 CCCCAAG
94 CCCCAAG
1 CCCCAAG
101 CCCCAAG
1 CCCCAAG
108 CCCCAAG
1 CCCCAAG
115 CCCCAAG
1 CCCCAAG
122 CCCCAAG
1 CCCCAAG
129 CCCCAAG
1 CCCCAAG
136 CCCCAAG
1 CCCCAAG
143 CCCCAAG
1 CCCCAAG
150 CCCCAAG
1 CCCCAAG
*
157 CCCGAAG
1 CCCCAAG
*
164 CCCGAAG
1 CCCCAAG
*
171 CCCGAAG
1 CCCCAAG
*
178 CCCGAAG
1 CCCCAAG
* *
185 CCCGAAA
1 CCCCAAG
192 CCCCAAG
1 CCCCAAG
*
199 CCCGAAG
1 CCCCAAG
206 CCCCCGAAG
1 -CCCC-AAG
215 CCCCCGAAG
1 -CCCC-AAG
224 CCCCCGAAG
1 -CCCC-AAG
*
233 CCCGAAG
1 CCCCAAG
*
240 CCCGAAG
1 CCCCAAG
*
247 CCCGAAG
1 CCCCAAG
*
254 CCCCGA-
1 CCCCAAG
260 CCCCGAA-
1 CCCC-AAG
* *
267 ACCCGAG
1 CCCCAAG
*
274 CCCCGAG
1 CCCCAAG
*
281 CCCCGAG
1 CCCCAAG
*
288 CCCCGAG
1 CCCCAAG
*
295 CCCCGAG
1 CCCCAAG
*
302 -CCCGAG
1 CCCCAAG
*
308 CCCCGAG
1 CCCCAAG
*
315 CCCCGAG
1 CCCCAAG
*
322 CCCCGAG
1 CCCCAAG
*
329 CCCCGAG
1 CCCCAAG
*
336 -CCCGAG
1 CCCCAAG
*
342 CCCCGAG
1 CCCCAAG
*
349 CCCCGAG
1 CCCCAAG
*
356 CCCCCGAG
1 -CCCCAAG
*
364 CCCCCGAG
1 -CCCCAAG
*
372 CCCCCGAG
1 -CCCCAAG
*
380 CCCCCGAG
1 -CCCCAAG
*
388 CCCCCAG
1 CCCCAAG
*
395 CCCCTAG
1 CCCCAAG
* *
402 ACCCTAG
1 CCCCAAG
* *
409 ACCCTAG
1 CCCCAAG
* *
416 ACCCTAG
1 CCCCAAG
*
423 ACCCGAAG
1 -CCCCAAG
*
431 CCCGAAG
1 CCCCAAG
*
438 CCCGAAG
1 CCCCAAG
*
445 CCCGAAG
1 CCCCAAG
452 CCC
1 CCC
455 GAACCCTAAA
Statistics
Matches: 413, Mismatches: 22, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
6 23 0.06
7 328 0.79
8 41 0.10
9 21 0.05
ACGTcount: A:0.26, C:0.53, G:0.20, T:0.01
Consensus pattern (7 bp):
CCCCAAG
Found at i:600 original size:7 final size:7
Alignment explanation
Indices: 456--840 Score: 136
Period size: 7 Copynumber: 55.6 Consensus size: 7
446 CCGAAGCCCG
*
456 AACCCTA
1 AACCCCA
*
463 AACCCTA
1 AACCCCA
*
470 AACCCTA
1 AACCCCA
*
477 AACCCTA
1 AACCCCA
*
484 AACCCCG
1 AACCCCA
* *
491 GACCCCG
1 AACCCCA
*
498 GACCCCA
1 AACCCCA
* *
505 GACCCTA
1 AACCCCA
*
512 AACCCTA
1 AACCCCA
*
519 AACCCTA
1 AACCCCA
*
526 AA-CCCT
1 AACCCCA
**
532 AA-CCTT
1 AACCCCA
*
538 AACCCTA
1 AACCCCA
*
545 AACCCGA
1 AACCCCA
552 AACCCCCA
1 AA-CCCCA
*
560 AA-CCGA
1 AACCCCA
566 AA-CCCA
1 AACCCCA
572 AACCCCA
1 AACCCCA
579 AACCCCA
1 AACCCCA
586 AACCCCA
1 AACCCCA
*
593 AACACCA
1 AACCCCA
* *
600 AACTCGA
1 AACCCCA
* *
607 GACCCGA
1 AACCCCA
* *
614 GACCCGA
1 AACCCCA
* *
621 GACCCGA
1 AACCCCA
* *
628 GA-CCCG
1 AACCCCA
*
634 AACCCCG
1 AACCCCA
*
641 AACCCCG
1 AACCCCA
* *
648 AAGCCCG
1 AACCCCA
* *
655 AAGCCCG
1 AACCCCA
* *
662 AAGCCCG
1 AACCCCA
* *
669 AAGCCCG
1 AACCCCA
* *
676 AAGCCCT
1 AACCCCA
* *
683 AAGCCCT
1 AACCCCA
* *
690 AAGCCCT
1 AACCCCA
* *
697 AAGCCCT
1 AACCCCA
* *
704 AAGCCCG
1 AACCCCA
* *
711 AACCTCG
1 AACCCCA
*
718 AACCCCG
1 AACCCCA
*
725 AACCCCG
1 AACCCCA
*
732 AACCCCG
1 AACCCCA
739 AA-CCCA
1 AACCCCA
*
745 ACCCCCA
1 AACCCCA
752 AACCCC-
1 AACCCCA
*
758 AACCCCC
1 AACCCCA
*
765 AACCCCC
1 AACCCCA
*
772 AACCCCC
1 AACCCCA
*
779 AACCCCC
1 AACCCCA
786 AACCCCA
1 AACCCCA
* *
793 AGCCCTTA
1 AACCC-CA
801 AACCCCA
1 AACCCCA
*
808 AACCCTTA
1 AACCC-CA
816 AACCCCA
1 AACCCCA
823 AACCCCA
1 AACCCCA
830 AACCCCA
1 AACCCCA
837 AACC
1 AACC
841 TTAAATCTCT
Statistics
Matches: 332, Mismatches: 38, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
6 32 0.10
7 283 0.85
8 17 0.05
ACGTcount: A:0.35, C:0.50, G:0.10, T:0.05
Consensus pattern (7 bp):
AACCCCA
Found at i:804 original size:15 final size:15
Alignment explanation
Indices: 786--845 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 15
776 CCCAACCCCC
*
786 AACCCCAAGCCCTTA
1 AACCCCAAACCCTTA
801 AACCCCAAACCCTTA
1 AACCCCAAACCCTTA
*
816 AACCCCAAACCC-CA
1 AACCCCAAACCCTTA
830 AACCCCAAA-CCTTA
1 AACCCCAAACCCTTA
844 AA
1 AA
846 TCTCTAACCT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
13 2 0.05
14 13 0.32
15 26 0.63
ACGTcount: A:0.42, C:0.47, G:0.02, T:0.10
Consensus pattern (15 bp):
AACCCCAAACCCTTA
Found at i:832 original size:29 final size:29
Alignment explanation
Indices: 713--840 Score: 104
Period size: 27 Copynumber: 4.6 Consensus size: 29
703 TAAGCCCGAA
* * * *
713 CCTCGAACCCCGAACCCCGAACCCCGAA-
1 CCTCAAACCCCAAACCCCAAACCCCAAAC
* *
741 CC-CAACCCCCAAACCCC-AACCCCCAAC
1 CCTCAAACCCCAAACCCCAAACCCCAAAC
* * * *
768 CC-CCAACCCCCAACCCCCAACCCCAAGC
1 CCTCAAACCCCAAACCCCAAACCCCAAAC
* *
796 CCTTAAACCCCAAACCCTTAAACCCCAAAC
1 CCTCAAACCCCAAACCC-CAAACCCCAAAC
826 CC-CAAACCCCAAACC
1 CCTCAAACCCCAAACC
841 TTAAATCTCT
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
26 8 0.10
27 26 0.32
28 12 0.15
29 23 0.29
30 11 0.14
ACGTcount: A:0.34, C:0.59, G:0.04, T:0.04
Consensus pattern (29 bp):
CCTCAAACCCCAAACCCCAAACCCCAAAC
Found at i:865 original size:13 final size:13
Alignment explanation
Indices: 847--878 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
837 AACCTTAAAT
847 CTCTAACCTCAAC
1 CTCTAACCTCAAC
860 CTCTAACCTCAAC
1 CTCTAACCTCAAC
*
873 CCCTAA
1 CTCTAA
879 ATCCCAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (13 bp):
CTCTAACCTCAAC
Found at i:5654 original size:14 final size:14
Alignment explanation
Indices: 5632--5674 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
5622 AAACATCAAG
5632 CCCTAAACCCCAAA
1 CCCTAAACCCCAAA
** *
5646 CCCTAAACCTTATA
1 CCCTAAACCCCAAA
*
5660 CCCCAAACCCCAAA
1 CCCTAAACCCCAAA
5674 C
1 C
5675 ATCGACCTCT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.49, G:0.00, T:0.12
Consensus pattern (14 bp):
CCCTAAACCCCAAA
Found at i:5781 original size:21 final size:21
Alignment explanation
Indices: 5757--5799 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5747 TTAGACCCTC
*
5757 AACCCTAAACCCCAAACTTTA
1 AACCCTAAACCCCAAACATTA
* *
5778 AACCTTAAACCCTAAACATTA
1 AACCCTAAACCCCAAACATTA
5799 A
1 A
5800 CCCATAACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (21 bp):
AACCCTAAACCCCAAACATTA
Found at i:6022 original size:21 final size:21
Alignment explanation
Indices: 5973--6023 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
5963 CCCCTAACCC
5973 AAACCTT--ACCCTAAACCTT
1 AAACCTTAAACCCTAAACCTT
* *
5992 -AACTTCTAAACCCTAAGCCTT
1 AAACCT-TAAACCCTAAACCTT
6013 AAACCTTAAAC
1 AAACCTTAAAC
6024 TCGAGCCCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
18 4 0.16
19 1 0.04
21 16 0.64
22 4 0.16
ACGTcount: A:0.39, C:0.33, G:0.02, T:0.25
Consensus pattern (21 bp):
AAACCTTAAACCCTAAACCTT
Found at i:6073 original size:14 final size:14
Alignment explanation
Indices: 6056--6103 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
6046 TTAAACCTTA
*
6056 AACCCCAAACCTCT
1 AACCCCAAACCTCG
* *
6070 AACCCCTAATCTCG
1 AACCCCAAACCTCG
*
6084 AGCCCCAAACCTCG
1 AACCCCAAACCTCG
6098 AACCCC
1 AACCCC
6104 GACCCTCAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.31, C:0.50, G:0.06, T:0.12
Consensus pattern (14 bp):
AACCCCAAACCTCG
Found at i:11981 original size:15 final size:15
Alignment explanation
Indices: 11961--11991 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11951 AGAATAAGCA
11961 AAATTGGCAGAGTCC
1 AAATTGGCAGAGTCC
11976 AAATTGGCAGAGTCC
1 AAATTGGCAGAGTCC
11991 A
1 A
11992 TTGTTCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (15 bp):
AAATTGGCAGAGTCC
Found at i:22890 original size:22 final size:22
Alignment explanation
Indices: 22862--22953 Score: 148
Period size: 22 Copynumber: 4.2 Consensus size: 22
22852 CTGCTGGGGA
*
22862 AACAGAAGCACTCACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
22884 AACAGAAGCACACACAGTACTG
1 AACAGAAGCACACACAGTGCTG
*
22906 AACAGAAGCACACATAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
22928 AACAGAAGCACACACAGTGTTG
1 AACAGAAGCACACACAGTGCTG
22950 AACA
1 AACA
22954 ATAAGCGCGC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.42, C:0.25, G:0.21, T:0.12
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:26691 original size:23 final size:23
Alignment explanation
Indices: 26665--26743 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
26655 ACACTAGCGC
*
26665 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* * *
26688 GCTCTCTGATCAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
26711 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
26734 GCTCTCTGTT
1 GCTCTCTGTT
26744 GCCCAGCACT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.46
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:28365 original size:15 final size:15
Alignment explanation
Indices: 28347--28403 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
28337 ATTCAATATT
28347 AATATTTTAATAATA
1 AATATTTTAATAATA
*
28362 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
28381 AATATATTAATAATA
1 AATATTTTAATAATA
28396 AATATTTT
1 AATATTTT
28404 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:29165 original size:59 final size:59
Alignment explanation
Indices: 29082--29765 Score: 598
Period size: 59 Copynumber: 11.5 Consensus size: 59
29072 AAAAAAAAAA
* * *
29082 TTGGTGTTGGTCATTG-CATAGCCGACACCCCTTTTAATCTGATAAAAAAATCAAATTTT
1 TTGGTGTTGGCCA-TGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTT
* * * * * * *
29141 TGGGTGTTGGTCATGCAATGGCCGACGCCCTCTTTTTATCAGATAAAAAAATTAATTTTT
1 TTGGTGTTGGCCATGCCATGGCCGACACCC-CTTTTTATCTGATAAAAAAATCAAATTTT
* * * *
29201 TTGGTGTTGGTCATGCTATGGCCGACACCCCTATTTATCTGATAAAAAAATTAAATTTTT
1 TTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAA-TTTT
** * * * * *
29261 TTGGTGTTGGCCATTACATAGTCGACAGCCCATTTTATCTGA-ATAAAAAATCAAA-CTT
1 TTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTATCTGATA-AAAAAATCAAATTTT
* * * **
29319 TTGAGTGTTGGCCATGCCATGGCCGACACCCCTTTTTGTCAGATAAAAAATTTGAATTTT
1 TTG-GTGTTGGCCATGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTT
* ** *
29379 TTTGTGTTGGTTATGCCATGGCCGACATCCCCTTTTTTATCTGGTAAAAAAAT--AATTTT
1 TTGGTGTTGGCCATGCCATGGCCGACA-CCCC-TTTTTATCTGATAAAAAAATCAAATTTT
* * * * * * *
29438 TTTGTGTTGGTCATGCAATGGTCGACACCCTCTTTTTGTCAGATAAAAAATTCAAA-TTT
1 TTGGTGTTGGCCATGCCATGGCCGACACCC-CTTTTTATCTGATAAAAAAATCAAATTTT
** * * * * *
29497 TTGGCATTAGCCATTG-CATTGCTGACACCCCTTTTTTATCTGGTAAAAAAATTTGAAATTTTT
1 TTGGTGTTGGCCA-TGCCATGGCCGACACCCC-TTTTTATCTGATAAAAAAA--TCAAA-TTTT
* *
29560 TTGATGTTGGCCATTG-CATGACCGACACCCCTTTTTATCTGA-ATAAAAAATCAAATTTT
1 TTGGTGTTGGCCA-TGCCATGGCCGACACCCCTTTTTATCTGATA-AAAAAATCAAATTTT
* * * * * * *
29619 TGGGTGTT-GCTCATGCCATGGTCGACACCTTCTTTTTGTCAGATAAAAAAATTAATTTTT
1 TTGGTGTTGGC-CATGCCATGGCCGACACC-CCTTTTTATCTGATAAAAAAATCAAATTTT
* * * *
29679 TTGGTGTTGGCCATACCATGGCTGACATCCCTATTTATCTGAT-AAAAAATCAAATTTT
1 TTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTT
* * *
29737 TTTGTGTTGGCCATGCTATGACCGACACC
1 TTGGTGTTGGCCATGCCATGGCCGACACC
29766 AATTTTCTCT
Statistics
Matches: 501, Mismatches: 100, Indels: 49
0.77 0.15 0.08
Matches are distributed among these distances:
58 67 0.13
59 207 0.41
60 160 0.32
61 24 0.05
62 16 0.03
63 27 0.05
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (59 bp):
TTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTT
Found at i:29228 original size:119 final size:117
Alignment explanation
Indices: 29082--29765 Score: 614
Period size: 119 Copynumber: 5.7 Consensus size: 117
29072 AAAAAAAAAA
* * * *
29082 TTGGTGTTGGTCATTGCATAGCCGACACCCCTTTTAATCTGATAAAAAAATCAAATTTTTGGGTG
1 TTGGTGTTGGCCA-TGCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTTTTGGTG
* * *
29147 TTGGTCATGCAATGGCCGACGCCCTCTTTTTATCAGATAAAAAAATTAATTTTT
65 TTGGCCATGCAATGGCCGACACCC-CTTTTTATCTGATAAAAAAATTAATTTTT
* * *
29201 TTGGTGTTGGTCATGCTATGGCCGACACCCCTATTTATCTGATAAAAAAATTAAATTTTTTTGGT
1 TTGGTGTTGGCCATGC-ATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAA-TTTTTTGGT
* * * * * * **
29266 GTTGGCCAT-TACATAGTCGACAGCCCATTTTATCTGA-ATAAAAAATCAA-ACTT
64 GTTGGCCATGCA-ATGGCCGACACCCCTTTTTATCTGATA-AAAAAATTAATTTTT
* * * ** *
29319 TTGAGTGTTGGCCATGCCATGGCCGACACCCCTTTTTGTCAGATAAAAAATTTGAATTTTTTTGT
1 TTG-GTGTTGGCCATG-CATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTTTTGGT
** * *
29384 GTTGGTTATGCCATGGCCGACATCCCCTTTTTTATCTGGTAAAAAAA-TAATTTTT
64 GTTGGCCATGCAATGGCCGACA-CCCC-TTTTTATCTGATAAAAAAATTAATTTTT
* * * * * *
29439 TT-GTGTTGGTCATGCAATGGTCGACACCCTCTTTTTGTCAGATAAAAAATTCAAA-TTTTTGGC
1 TTGGTGTTGGCCATGC-ATGGCCGACACCC-CTTTTTATCTGATAAAAAAATCAAATTTTTTGGT
* * * * *
29502 ATTAGCCATTGC-ATTGCTGACACCCCTTTTTTATCTGGTAAAAAAATTTGAAATTTTT
64 GTTGGCCA-TGCAATGGCCGACACCCC-TTTTTATCTGATAAAAAAA-TT--AATTTTT
* * *
29560 TTGATGTTGGCCATTGCATGACCGACACCCCTTTTTATCTGA-ATAAAAAATCAAATTTTTGGGT
1 TTGGTGTTGGCCA-TGCATGGCCGACACCCCTTTTTATCTGATA-AAAAAATCAAATTTTTTGGT
* * * * *
29624 GTT-GCTCATGCCATGGTCGACACCTTCTTTTTGTCAGATAAAAAAATTAATTTTT
64 GTTGGC-CATGCAATGGCCGACACC-CCTTTTTATCTGATAAAAAAATTAATTTTT
* * * * *
29679 TTGGTGTTGGCCATACCATGGCTGACATCCCTATTTATCTGAT-AAAAAATCAAATTTTTTTGTG
1 TTGGTGTTGGCCAT-GCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTTTTGGTG
* *
29743 TTGGCCATGCTATGACCGACACC
65 TTGGCCATGCAATGGCCGACACC
29766 AATTTTCTCT
Statistics
Matches: 462, Mismatches: 75, Indels: 57
0.78 0.13 0.10
Matches are distributed among these distances:
117 25 0.05
118 110 0.24
119 186 0.40
120 46 0.10
121 37 0.08
122 54 0.12
123 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (117 bp):
TTGGTGTTGGCCATGCATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTTTTGGTGT
TGGCCATGCAATGGCCGACACCCCTTTTTATCTGATAAAAAAATTAATTTTT
Found at i:30548 original size:7 final size:6
Alignment explanation
Indices: 30535--30617 Score: 51
Period size: 6 Copynumber: 12.7 Consensus size: 6
30525 GAATATACAG
*
30535 AAAATT AGAAATT AAAATT AAAATAT ACAGGAAATT ATAAATT AAATTT
1 AAAATT A-AAATT AAAATT AAAAT-T --A--AAATT A-AAATT AAAATT
** *
30584 AAAA-T AAAAAC AAAATT ACAAATT AAACTT AAAA
1 AAAATT AAAATT AAAATT A-AAATT AAAATT AAAA
30618 AGTAAACGGA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
5 5 0.08
6 30 0.49
7 19 0.31
8 1 0.02
9 1 0.02
10 1 0.02
11 4 0.07
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:30553 original size:13 final size:12
Alignment explanation
Indices: 30535--30617 Score: 51
Period size: 13 Copynumber: 6.3 Consensus size: 12
30525 GAATATACAG
30535 AAAATTAGAAATT
1 AAAATTA-AAATT
30548 AAAATTAAAATAT
1 AAAATTAAAAT-T
30561 ACAGGAAATTATAAATT
1 --A--AAATTA-AAATT
*
30578 AAATTTAAAA-T
1 AAAATTAAAATT
**
30589 AAAAACAAAATT
1 AAAATTAAAATT
*
30601 ACAAATTAAACTT
1 A-AAATTAAAATT
30614 AAAA
1 AAAA
30618 AGTAAACGGA
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
11 8 0.15
12 12 0.22
13 22 0.40
15 2 0.04
17 7 0.13
18 4 0.07
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.28
Consensus pattern (12 bp):
AAAATTAAAATT
Found at i:30554 original size:30 final size:30
Alignment explanation
Indices: 30520--30617 Score: 115
Period size: 30 Copynumber: 3.3 Consensus size: 30
30510 AAAAAATAAT
* *
30520 AATTAGAATATACAGAAAATTAGAAATTAA
1 AATTAAAATATACAGAAAATTACAAATTAA
* *
30550 AATTAAAATATACAGGAAATTATAAATTAA
1 AATTAAAATATACAGAAAATTACAAATTAA
* * * *
30580 ATTTAAAATAAAAACAAAATTACAAATTAA
1 AATTAAAATATACAGAAAATTACAAATTAA
*
30610 ACTTAAAA
1 AATTAAAA
30618 AGTAAACGGA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (30 bp):
AATTAAAATATACAGAAAATTACAAATTAA
Found at i:31949 original size:60 final size:60
Alignment explanation
Indices: 31878--32251 Score: 204
Period size: 59 Copynumber: 6.3 Consensus size: 60
31868 ATCATCTCCT
* *
31878 CCATACAATGGCCAACACAAAAAAAATT-AATTTTTTACCAGATAAAAAAAGGGGTGTCGA
1 CCATGCAATGGCCAACACAAAAAAAATTAAATTTTTTATCAGAT-AAAAAAGGGGTGTCGA
* * * * * *
31938 CCATGCAATGGCCAACAC-AAAAAATTTGAATTTTTTATCTGA-CAAAAAGAAGGTGTCGG
1 CCATGCAATGGCCAACACAAAAAAAATTAAATTTTTTATCAGATAAAAAAG-GGGTGTCGA
* ** * ** * * *
31997 CCATGGC-ATGGTCAACAC-CCAAAATTTTGATTTTTTATTCAGAT-AAAAAGGAGTGTTGG
1 CCAT-GCAATGGCCAACACAAAAAAAATTAAATTTTTTA-TCAGATAAAAAAGGGGTGTCGA
* * * *
32056 CCATGCAAT-GACAACACCAAAAAAATTTAAAATTTTTTTATCTG--AAGAAAGGGAGTGTC-A
1 CCATGCAATGGCCAACA-CAAAAAAAATT-AAA-TTTTTTATCAGATAAAAAAGGG-GTGTCGA
* * * * * * * *
32116 GCCATTGC-ATGACGAACAC--AAAAAATTGATTTTTTTATTAGAT-AAATAGGGGTATCGG
1 -CCA-TGCAATGGCCAACACAAAAAAAATTAAATTTTTTATCAGATAAAAAAGGGGTGTCGA
* * * * * *
32174 CAATGGC-ATGACCAACACCAAAAAAAA-TGATTTTTTTATCAGATTAAAAGGGGGTGTCGA
1 CCAT-GCAATGGCCAACA-CAAAAAAAATTAAATTTTTTATCAGATAAAAAAGGGGTGTCGA
*
32234 TCATGCAATGGCCAACAC
1 CCATGCAATGGCCAACAC
32252 CAAATTTTTT
Statistics
Matches: 242, Mismatches: 48, Indels: 49
0.71 0.14 0.14
Matches are distributed among these distances:
56 1 0.00
57 26 0.11
58 22 0.09
59 83 0.34
60 82 0.34
61 14 0.06
62 14 0.06
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (60 bp):
CCATGCAATGGCCAACACAAAAAAAATTAAATTTTTTATCAGATAAAAAAGGGGTGTCGA
Found at i:32252 original size:60 final size:59
Alignment explanation
Indices: 31878--32255 Score: 222
Period size: 60 Copynumber: 6.4 Consensus size: 59
31868 ATCATCTCCT
* * * * *
31878 CCATACAATGGCCAACA-CAAAAAAAATTAATTTTTTACCAGATAAAAAAAGGGGTGTCGA
1 CCATGCAATGGCCAACACCAAAAAAAATGATTTTTTTATCAGAT--AAAAGGGGGTGTCGA
** * * * ** *
31938 CCATGCAATGGCCAACA-CAAAAAATTTGAATTTTTTATCTGACAAAAAGAAGGTGTCGG
1 CCATGCAATGGCCAACACCAAAAAAAATGATTTTTTTATCAGA-TAAAAGGGGGTGTCGA
* * *** * * * *
31997 CCATGGC-ATGGTCAACACCCAAAATTTTGA-TTTTTTATTCAGATAAAAAGGAGTGTTGG
1 CCAT-GCAATGGCCAACACCAAAAAAAATGATTTTTTTA-TCAGATAAAAGGGGGTGTCGA
* ** * *
32056 CCATGCAAT-GACAACACCAAAAAAATTTAAAATTTTTTTATCTGA-AGAAAGGGAGTGTC-A
1 CCATGCAATGGCCAACACCAAAAAAA---ATGATTTTTTTATCAGATA-AAAGGGGGTGTCGA
* * * * * *
32116 GCCATTGC-ATGACGAACA-C-AAAAAATTGATTTTTTTATTAGATAAATA-GGGGTATCGG
1 -CCA-TGCAATGGCCAACACCAAAAAAAATGATTTTTTTATCAGATAAA-AGGGGGTGTCGA
* *
32174 CAATGGC-ATGACCAACACCAAAAAAAATGATTTTTTTATCAGATTAAAAGGGGGTGTCGA
1 CCAT-GCAATGGCCAACACCAAAAAAAATGATTTTTTTATCAGA-TAAAAGGGGGTGTCGA
*
32234 TCATGCAATGGCCAACACCAAA
1 CCATGCAATGGCCAACACCAAA
32256 TTTTTTTTTT
Statistics
Matches: 244, Mismatches: 52, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
56 1 0.00
57 33 0.14
58 17 0.07
59 71 0.29
60 87 0.36
61 21 0.09
62 14 0.06
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (59 bp):
CCATGCAATGGCCAACACCAAAAAAAATGATTTTTTTATCAGATAAAAGGGGGTGTCGA
Found at i:32890 original size:21 final size:21
Alignment explanation
Indices: 32847--32891 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
32837 TTACCTCAAA
* ** *
32847 CCCCAAAACTTTTTTTCTTCT
1 CCCCAAAACTCTTACTCTACT
32868 CCCCAAAACTCTTACTCTACT
1 CCCCAAAACTCTTACTCTACT
32889 CCC
1 CCC
32892 ATCTATCCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.42, G:0.00, T:0.36
Consensus pattern (21 bp):
CCCCAAAACTCTTACTCTACT
Found at i:34152 original size:21 final size:21
Alignment explanation
Indices: 34126--34176 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
34116 ATTTTATTAT
* *
34126 TTAATTAATAATTTAAAGTGA
1 TTAATTAATAATTAAAAGTAA
*
34147 TTAATTAA-AATTAAAATTAA
1 TTAATTAATAATTAAAAGTAA
34167 TTAAATTAAT
1 TT-AATTAAT
34177 TGATTAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
TTAATTAATAATTAAAAGTAA
Found at i:34167 original size:16 final size:15
Alignment explanation
Indices: 34146--34175 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
34136 ATTTAAAGTG
34146 ATTAATTAAAATTAAA
1 ATTAATT-AAATTAAA
34162 ATTAATTAAATTAA
1 ATTAATTAAATTAA
34176 TTGATTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTAATTAAATTAAA
Found at i:36310 original size:18 final size:18
Alignment explanation
Indices: 36289--36329 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
36279 ATATTAGTTA
36289 AAATAAAAATATATATTT
1 AAATAAAAATATATATTT
* *
36307 AAATTAAATTATATATTT
1 AAATAAAAATATATATTT
36325 AAATA
1 AAATA
36330 TTATATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATAAAAATATATATTT
Found at i:41834 original size:8 final size:7
Alignment explanation
Indices: 41823--41877 Score: 60
Period size: 8 Copynumber: 7.7 Consensus size: 7
41813 AAAAAAATTA
41823 AAAAAAGG
1 AAAAAA-G
41831 AAAAAAG
1 AAAAAAG
41838 AGAAAAAG
1 A-AAAAAG
*
41846 -AAAAGG
1 AAAAAAG
41852 AAAAAAG
1 AAAAAAG
41859 AAGAAAAG
1 AA-AAAAG
41867 -AAAAAG
1 AAAAAAG
41873 AAAAA
1 AAAAA
41878 GGGAGGTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
6 10 0.24
7 14 0.34
8 17 0.41
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:41834 original size:18 final size:19
Alignment explanation
Indices: 41791--41836 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
41781 GGATTCGGTG
*
41791 AGGAAAAAATTTTAAAAAA
1 AGGAAAAAATATTAAAAAA
* *
41810 A-TAAAAAAAATTAAAAAA
1 AGGAAAAAATATTAAAAAA
41828 AGGAAAAAA
1 AGGAAAAAA
41837 GAGAAAAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (19 bp):
AGGAAAAAATATTAAAAAA
Found at i:41836 original size:21 final size:21
Alignment explanation
Indices: 41822--41877 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
41812 AAAAAAAATT
41822 AAAAAAAGGAAAAAAGAGAAA
1 AAAAAAAGGAAAAAAGAGAAA
*
41843 AAGAAAAGGAAAAAAGAAGAAA
1 AAAAAAAGGAAAAAAG-AGAAA
*
41865 AGAAAAA-GAAAAA
1 AAAAAAAGGAAAAA
41878 GGGAGGTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAAAGGAAAAAAGAGAAA
Found at i:41855 original size:27 final size:27
Alignment explanation
Indices: 41823--41876 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 27
41813 AAAAAAATTA
41823 AAAAAAGGAAAAAAGAGAAAAAGAAAAGG
1 AAAAAA-GAAAAAA-AGAAAAAGAAAAGG
*
41852 AAAAAAGAAGAAAAGAAAAAGAAAA
1 AAAAAAGAAAAAAAGAAAAAGAAAA
41877 AGGGAGGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 12 0.50
28 6 0.25
29 6 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (27 bp):
AAAAAAGAAAAAAAGAAAAAGAAAAGG
Found at i:42936 original size:98 final size:98
Alignment explanation
Indices: 42762--42944 Score: 253
Period size: 98 Copynumber: 1.9 Consensus size: 98
42752 CGTGTTTTAA
*
42762 GGGAAAGATTGAAACCGTAACGGTAAATCTAATACCCTAGAGATATGAAGAGAAAGGTTGAAGTC
1 GGGAAAAATTGAAACCGTAACGGTAAATCTAATACCCTAGAGATATGAAGAGAAAGGTTGAAGTC
*
42827 GCAACGGCGAACCTTGTACCTTAGGGACGTGAT
66 GCAACGACGAACCTTGTACCTTAGGGACGTGAT
* * ** * * *
42860 GGGAAAAATTGAAACC-TCGACGGTGAATCTTGTACCCTAGAGTTATGGAGGGAAAGGTTGAAG-
1 GGGAAAAATTGAAACCGT-AACGGTAAATCTAATACCCTAGAGATATGAAGAGAAAGGTTGAAGT
42923 CTGCAACGACGAACCTTGTACC
65 C-GCAACGACGAACCTTGTACC
42945 CTAGAGATGT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
97 2 0.03
98 72 0.97
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (98 bp):
GGGAAAAATTGAAACCGTAACGGTAAATCTAATACCCTAGAGATATGAAGAGAAAGGTTGAAGTC
GCAACGACGAACCTTGTACCTTAGGGACGTGAT
Found at i:42964 original size:49 final size:49
Alignment explanation
Indices: 42794--42964 Score: 132
Period size: 49 Copynumber: 3.5 Consensus size: 49
42784 GTAAATCTAA
42794 TACCCTAGAGATATG-AAGAGAAAGGTTGAAG-TCGCAACGGCGAACCTTG
1 TACCCTAGAGATATGAAAG-GAAAGGTTGAAGCT-GCAACGGCGAACCTTG
* * ** ** ** * * * *
42843 TACCTTAGGGACGTGATGGGAAAAATTGAAACCT-CGACGGTGAATCTTG
1 TACCCTAGAGATATGAAAGGAAAGGTTG-AAGCTGCAACGGCGAACCTTG
* * * *
42892 TACCCTAGAGTTATGGAGGGAAAGGTTGAAGCTGCAACGACGAACCTTG
1 TACCCTAGAGATATGAAAGGAAAGGTTGAAGCTGCAACGGCGAACCTTG
* *
42941 TACCCTAGAGATGTGAAATGAAAG
1 TACCCTAGAGATATGAAAGGAAAG
42965 ATTGGGGTTG
Statistics
Matches: 87, Mismatches: 31, Indels: 8
0.69 0.25 0.06
Matches are distributed among these distances:
48 4 0.05
49 79 0.91
50 3 0.03
51 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (49 bp):
TACCCTAGAGATATGAAAGGAAAGGTTGAAGCTGCAACGGCGAACCTTG
Found at i:43325 original size:40 final size:39
Alignment explanation
Indices: 43262--44803 Score: 892
Period size: 40 Copynumber: 39.1 Consensus size: 39
43252 AAGTTACAAT
* * * * *
43262 CATCCAAACTTTTGCCCTAATCAGAGGACAAATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
* * * *
43302 TATTCAATCTTTTACCCTAATCAGAGGGTAGATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
* *
43342 CATCCAATCTCTTAACCC-AACCATAGGGCAGATTGAAG-
1 CATCCAATCT-TTTACCCTAACCAGAGGGCAGATTGAAGC
* * *
43380 TAGTCCAATCTTTTAACCC-AATCATG-GGGCAAATTGAAG-
1 CA-TCCAATCTTTT-ACCCTAACCA-GAGGGCAGATTGAAGC
* * *
43419 TAGTCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGT
1 CA-TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
* * * * **
43459 CATTCAATCTCTTACCTCGATCGTG-GGGCAGATTGAAGC
1 CATCCAATCTTTTACC-CTAACCAGAGGGCAGATTGAAGC
* * *
43498 AATCCAATCTTTTACACC-AACCATGA-GGCAGATTAAAGT
1 CATCCAATCTTTTAC-CCTAACCA-GAGGGCAGATTGAAGC
* ** * * * *
43537 AATTAAGATCTTTTTCCCTAACCAGAGGGTAAATTGAAGT
1 CATCCA-ATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
* *
43577 GATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
* * * * * * *
43616 AATCCAATCTCTTACCTTGACCATG-GGGCAAATT-ATGT
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGC
* * * **
43654 AATCTAATCTTTTACCCTAGCCAGAGGAAAGATTGAAGGC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAA-GC
* * ** *
43694 AATCTAATCTTTTACCCCGACCATG-GGGCAGATTAAAGC
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGC
* * * **
43733 AATCCAATCTTTTACCCTAACCATAGGGTAGATTGAAAT
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
* * ** *
43772 CATCTAATCTTTTACCCTAATCAGAGAACAGATTAAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
* * *
43812 CATTCAATCTTTTACCCTAATCAGAGGGCAAATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
* * * * *
43852 CATCCAATCTCTTACCTTGACCATG-GGGCAAATTAAAG-
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGC
* * * * * *
43890 TAGTCTAATCTTTTACCCTCACTAGAAGGCAGATTGAAGT
1 CA-TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
* * *
43930 CATGCAATCTCTTA-CCTCGACCATG-GGGCAGATTGAAGC
1 CATCCAATCTTTTACCCT-AACCA-GAGGGCAGATTGAAGC
* * *
43969 AATCCAATCTTTTA-CCTAACCAAAGGGCATATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
*
44008 CATCCAATCTTTTACCATAACCAGAGGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
* * * *
44048 CAT-CAGATCTTTTACCTTAACCAGAGGACAAATTGAAAAC
1 CATCCA-ATCTTTTACCCTAACCAGAGGGCAGATTG-AAGC
* ** *
44088 CATCCAATCTCTTACCC-CGCTCATG-GGGCAAATTGAAGC
1 CATCCAATCTTTTACCCTAAC-CA-GAGGGCAGATTGAAGC
* * * * *
44127 AATTCAATCTTTTACCCTAATCATG-GGGCAAATTGAAGT
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGC
* * * *
44166 AATTCAGATCTTTTACCCTAACAAGAGGGCAGATTGAAGT
1 CATCCA-ATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
* * *
44206 AATCCAATCTTTTACCCCAACCAGAGAGCAGATTGAAGC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
* * ** *
44245 CATCTAATCTCTTACCCCGATCATG-GGGCAGATTGAAGC
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGC
* * *
44284 TATCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
* * ** * *
44324 CATCCGATCTCTTACCCCGATCATG-GGGCAAATT-ACAGC
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGA-AGC
* * ** *
44363 AATCCAATCTTTTACCTTAATTAGAGGGCAGATTTAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
* * * * *
44403 CATCCGATCTCTTACTCTGAA-CAGAGGGCAGACTGAAAAC
1 CATCCAATCTTTTACCCT-AACCAGAGGGCAGATTG-AAGC
* * ** * *
44443 CATCCGATCTCTTACCCCGACCATGA-GGAAAATTGAAGAC
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG-C
*** * *
44483 CATTTGATCTTTTACCCTAACTAGAGGGCAGATTAAAGC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
* * * * *
44522 CATCTAATCTCTTACCCTGACCTTG-GGGCAAATTGAAGC
1 CATCCAATCTTTTACCCTAACC-AGAGGGCAGATTGAAGC
* * *
44561 AATACAATCTTTTACCCTAACCAGAGGACAGATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
** * * * *
44601 CATCTGATCTCTTACCCCAACTATG-GGGCAAATTGAAGAC
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG-C
* ** * * *
44641 CATCCGATCTTTTACCCCGACTAGAGGGCAAATTGAAGAT
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-C
* * * * * *
44681 CACCCGATCTCTTACCCCAATCATGA-GGCAGATTGAAGT
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGC
* * * * * *
44720 AATTCAAATCTTTTACCCTAACTAGAGGGTAAATTGAAGT
1 CA-TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
* * ** *
44760 AATCCAGATCTCTTACCCCGACCATGA-GACAGATTGAAGC
1 CATCCA-ATCTTTTACCCTAACCA-GAGGGCAGATTGAAGC
44800 CATC
1 CATC
44804 AGATTTAAAA
Statistics
Matches: 1174, Mismatches: 266, Indels: 124
0.75 0.17 0.08
Matches are distributed among these distances:
37 1 0.00
38 59 0.05
39 541 0.46
40 549 0.47
41 24 0.02
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (39 bp):
CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGC
Found at i:43396 original size:39 final size:38
Alignment explanation
Indices: 43306--44777 Score: 572
Period size: 39 Copynumber: 37.3 Consensus size: 38
43296 GAAGACTATT
* * *
43306 CAATCTTTTACCCTAATCAGAGGGTAGATTGAAG-ACCATC
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTA--ATC
* *
43346 CAATCTCTTAACCCAACCATAGGGCAGATTGAAGTAGTC
1 CAATCT-TTTACCCAACCATAGGGCAGATTGAAGTAATC
* * * *
43385 CAATCTTTTAACCCAATCATGGGGCAAATTGAAGTAGTC
1 CAATCTTTT-ACCCAACCATAGGGCAGATTGAAGTAATC
* * * *
43424 CAATCTTTTACCCTAACTAGAGGGCAGATTGAAGTCATT
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
* * * * * *
43463 CAATCTCTTACCTCGATCGTGGGGCAGATTGAAGCAATC
1 CAATCTTTTACC-CAACCATAGGGCAGATTGAAGTAATC
* *
43502 CAATCTTTTACACCAACCAT-GAGGCAGATTAAAGTAATT
1 CAATCTTTTAC-CCAACCATAG-GGCAGATTGAAGTAATC
* * * * * *
43541 AAGATCTTTTTCCCTAACCAGAGGGTAAATTGAAGTGATC
1 CA-ATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
* * *
43581 CAATCTTTTACCCTAACTAGAGGGCAGATTGAAGCAATC
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
* ** * * *
43620 CAATCTCTTACCTTGACCATGGGGCAAATT-ATGTAATC
1 CAATCTTTTACC-CAACCATAGGGCAGATTGAAGTAATC
* * * ** *
43658 TAATCTTTTACCCTAGCCAGAGGAAAGATTGAAGGCAATC
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAA-GTAATC
* * * * *
43698 TAATCTTTTACCCCGACCATGGGGCAGATTAAAGCAATC
1 CAATCTTTTA-CCCAACCATAGGGCAGATTGAAGTAATC
* * *
43737 CAATCTTTTACCCTAACCATAGGGTAGATTGAAATCATC
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
* * * ** * *
43776 TAATCTTTTACCCTAATCAGAGAACAGATTAAAG-ACCATT
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTA--ATC
* * *
43816 CAATCTTTTACCCTAATCAGAGGGCAAATTGAAG-ACCATC
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTA--ATC
* ** * * * *
43856 CAATCTCTTACCTTGACCATGGGGCAAATTAAAGTAGTC
1 CAATCTTTTACC-CAACCATAGGGCAGATTGAAGTAATC
* * * * * * *
43895 TAATCTTTTACCCTCACTAGAAGGCAGATTGAAGTCATG
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
* * * *
43934 CAATCTCTTACCTCGACCATGGGGCAGATTGAAGCAATC
1 CAATCTTTTACC-CAACCATAGGGCAGATTGAAGTAATC
* * *
43973 CAATCTTTTACCTAACCAAAGGGCATATTGAAG-ACCATC
1 CAATCTTTTACCCAACCATAGGGCAGATTGAAGTA--ATC
* *
44012 CAATCTTTTACCATAACCAGAGGGCAGATTGAAG-ACCAT-
1 CAATCTTTTACC-CAACCATAGGGCAGATTGAAGTA--ATC
* * * * *
44051 CAGATCTTTTACCTTAACCAGAGGACAAATTGAA-AACCATC
1 CA-ATCTTTTACC-CAACCATAGGGCAGATTGAAGTA--ATC
* ** * * * *
44092 CAATCTCTTACCCCGCTCATGGGGCAAATTGAAGCAATT
1 CAATCTTTTACCCAAC-CATAGGGCAGATTGAAGTAATC
* * * *
44131 CAATCTTTTACCCTAATCATGGGGCAAATTGAAGTAATT
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
* *
44170 CAGATCTTTTACCCTAACAAGAGGGCAGATTGAAGTAATC
1 CA-ATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
* * **
44210 CAATCTTTTACCCCAACCAGAGAGCAGATTGAAGCCATC
1 CAATCTTTTA-CCCAACCATAGGGCAGATTGAAGTAATC
* * * * *
44249 TAATCTCTTACCCCGATCATGGGGCAGATTGAAGCT-ATC
1 CAATCTTTTA-CCCAACCATAGGGCAGATTGAAG-TAATC
* *
44288 CAATCTTTTACCCTAACCAAAGGGCAAATTGAAG-ACCATC
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTA--ATC
* * * * * * *
44328 CGATCTCTTACCCCGATCATGGGGCAAATT-ACAGCAATC
1 CAATCTTTTA-CCCAACCATAGGGCAGATTGA-AGTAATC
* ** * *
44367 CAATCTTTTACCTTAATTAGAGGGCAGATTTAAG-ACCATC
1 CAATCTTTTACC-CAACCATAGGGCAGATTGAAGTA--ATC
* * * * * *
44407 CGATCTCTTACTCTGAA-CAGAGGGCAGACTGAA-AACCATC
1 CAATCTTTTAC-C-CAACCATAGGGCAGATTGAAGTA--ATC
* * * * * *
44447 CGATCTCTTACCCCGACCAT-GAGGAAAATTGAAG-ACCATT
1 CAATCTTTTA-CCCAACCATAG-GGCAGATTGAAGTA--ATC
** * * * **
44487 TGATCTTTTACCCTAACTAGAGGGCAGATTAAAGCCATC
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
* * * * * * * *
44526 TAATCTCTTACCCTGACCTTGGGGCAAATTGAAGCAATA
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
* *
44565 CAATCTTTTACCCTAACCAGAGGACAGATTGAAG-ACCATC
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTA--ATC
** * * * *
44605 TGATCTCTTACCCCAACTATGGGGCAAATTGAAG-ACCATC
1 CAATCTTTTA-CCCAACCATAGGGCAGATTGAAGTA--ATC
* * * * * * *
44645 CGATCTTTTACCCCGACTAGAGGGCAAATTGAAGATCACC
1 CAATCTTTTA-CCCAACCATAGGGCAGATTGAAG-TAATC
* * *
44685 CGATCTCTTACCCCAATCAT-GAGGCAGATTGAAGTAATTC
1 CAATCTTTTA-CCCAACCATAG-GGCAGATTGAAGTAA-TC
* * * * *
44725 AAATCTTTTACCCTAACTAGAGGGTAAATTGAAGTAATC
1 CAATCTTTTACCC-AACCATAGGGCAGATTGAAGTAATC
*
44764 CAGATCTCTTACCC
1 CA-ATCTTTTACCC
44778 CGACCATGAG
Statistics
Matches: 1096, Mismatches: 272, Indels: 128
0.73 0.18 0.09
Matches are distributed among these distances:
37 1 0.00
38 58 0.05
39 528 0.48
40 480 0.44
41 29 0.03
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (38 bp):
CAATCTTTTACCCAACCATAGGGCAGATTGAAGTAATC
Found at i:43556 original size:118 final size:115
Alignment explanation
Indices: 43307--44799 Score: 804
Period size: 118 Copynumber: 12.6 Consensus size: 115
43297 AAGACTATTC
* * * * *
43307 AATCTTTTACCCTAA-TCAGAGGGTAGATTGAAGACCATCCAATCTCTTAACCCAACCATAGGGC
1 AATCTTTTACCCTAACT-AGAGGGCAGATTGAAG-TCATTCAATCTCTT-ACCCGACCATGGGGC
* * * * * *
43371 AGATTGAAGTAGTCCAATCTTTTAACCCAATCATGGGGCAAATTGAAGTAGTCC
63 AGATTGAAGCAATCCAATCTTTT-ACCCAACCATGGGGCAAATTAAAGTAATCT
* *
43425 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGTCATTCAATCTCTTACCTCGATCGTGGGGCAG
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGTCATTCAATCTCTTACC-CGACCATGGGGCAG
* *
43490 ATTGAAGCAATCCAATCTTTTACACCAACCATGAGGCAGATTAAAGTAAT-T
65 ATTGAAGCAATCCAATCTTTTAC-CCAACCATGGGGCAAATTAAAGTAATCT
* * * * * * * * *
43541 AAGATCTTTTTCCCTAACCAGAGGGTAAATTGAAGTGATCCAATCTTTTACCCTAAC-TAGAGGG
1 -A-ATCTTTTACCCTAACTAGAGGGCAGATTGAAGTCATTCAATCTCTTACCCGACCAT-G-GGG
* ** *
43605 CAGATTGAAGCAATCCAATCTCTTACCTTGACCATGGGGCAAATT-ATGTAATCT
62 CAGATTGAAGCAATCCAATCTTTTACC-CAACCATGGGGCAAATTAAAGTAATCT
* * ** * * *
43659 AATCTTTTACCCTAGCCAGAGGAAAGATTGAAGGCAATCTAATCTTTTACCCCGACCATGGGGCA
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGTCATTC-AATCTCTTA-CCCGACCATGGGGCA
* * * * *
43724 GATTAAAGCAATCCAATCTTTTACCCTAACCATAGGGTAGATTGAAA-TCATCT
64 GATTGAAGCAATCCAATCTTTTACCC-AACCATGGGGCAAATT-AAAGTAATCT
** * * * * *
43777 AATCTTTTACCCTAA-TCAGAGAACAGATTAAAGACCATTCAATCTTTTACCCTAATCA-GAGGG
1 AATCTTTTACCCTAACT-AGAGGGCAGATTGAAG-TCATTCAATCTCTTACCC-GACCATG-GGG
* * * ** *
43840 CAAATTGAAGACCATCCAATCTCTTACCTTGACCATGGGGCAAATTAAAGTAGTCT
62 CAGATTGAAG-CAATCCAATCTTTTACC-CAACCATGGGGCAAATTAAAGTAATCT
* * *
43896 AATCTTTTACCCTCACTAGAAGGCAGATTGAAGTCATGCAATCTCTTACCTCGACCATGGGGCAG
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGTCATTCAATCTCTTACC-CGACCATGGGGCAG
* ** * * *
43961 ATTGAAGCAATCCAATCTTTTACCTAACCAAAGGGCATATTGAAG-ACCATCC
65 ATTGAAGCAATCCAATCTTTTACCCAACCATGGGGCAAATTAAAGTA--ATCT
* * * * ** *
44013 AATCTTTTACCATAACCAGAGGGCAGATTGAAGACCA-TCAGATCTTTTACCTTAACCA-GAGGA
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAG-TCATTCA-ATCTCTTACC-CGACCATG-GGG
* * * * ** * *
44076 CAAATTGAAAACCATCCAATCTCTTACCCCGCTCATGGGGCAAATTGAAGCAAT-T
62 CAGATTG-AAGCAATCCAATCTTTTACCCAAC-CATGGGGCAAATTAAAGTAATCT
* * * * * *
44131 CAATCTTTTACCCTAA-TCATG-GGGCAAATTGAAGTAATTCAGATCTTTTACCCTAACAAGAGG
1 -AATCTTTTACCCTAACT-A-GAGGGCAGATTGAAGTCATTCA-ATCTCTTACCCGACCATG-GG
* * * * **
44194 GCAGATTGAAGTAATCCAATCTTTTACCCCAACCA-GAGAGCAGATTGAAGCCATCT
61 GCAGATTGAAGCAATCCAATCTTTTA-CCCAACCATG-GGGCAAATTAAAGTAATCT
* ** * * * **
44250 AATCTCTTACCCCGA-TCATG-GGGCAGATTGAAG-CTATCCAATCTTTTACCCTAACCAAAGGG
1 AATCTTTTACCCTAACT-A-GAGGGCAGATTGAAGTC-ATTCAATCTCTTACCC-GACCATGGGG
* * * * * * * * *
44312 CAAATTGAAGACCATCCGATCTCTTACCCCGATCATGGGGCAAATTACAGCAATCC
62 CAGATTGAAG-CAATCCAATCTTTTA-CCCAACCATGGGGCAAATTAAAGTAATCT
* * * * * * * *
44368 AATCTTTTACCTTAATTAGAGGGCAGATTTAAGACCATCCGATCTCTTACTCTGAACA-GAGGGC
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAG-TCATTCAATCTCTTAC-CCGACCATG-GGGC
* * * * * * * * * *
44432 AGACTGAAAACCATCCGATCTCTTACCCCGACCATGAGGAAAATTGAAG-ACCATTT
63 AGATTG-AAGCAATCCAATCTTTTA-CCCAACCATGGGGCAAATTAAAGTA--ATCT
* * * *
44488 GATCTTTTACCCTAACTAGAGGGCAGATTAAAGCCA-TCTAATCTCTTACCCTGACCTTGGGGCA
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGTCATTC-AATCTCTTACCC-GACCATGGGGCA
* * * * *
44552 AATTGAAGCAATACAATCTTTTACCCTAACCA-GAGGACAGATTGAAG-ACCATCT
64 GATTGAAGCAATCCAATCTTTTACCC-AACCATG-GGGCAAATTAAAGTA--ATCT
* * * * * * * * *
44606 GATCTCTTACCCCAACTATG-GGGCAAATTGAAGACCATCCGATCTTTTACCCCGACTA-GAGGG
1 AATCTTTTACCCTAACTA-GAGGGCAGATTGAAG-TCATTCAATCTCTTA-CCCGACCATG-GGG
* * * * * * * * *
44669 CAAATTGAAG-ATCACCCGATCTCTTACCCCAATCATGAGGCAGATTGAAGTAATTCA
62 CAGATTGAAGCA--ATCCAATCTTTTA-CCCAACCATGGGGCAAATTAAAGTAA-TCT
* * * * * *
44726 AATCTTTTACCCTAACTAGAGGGTAAATTGAAGTAATCCAGATCTCTTACCCCGACCATGAGACA
1 AATCTTTTACCCTAACTAGAGGGCAGATTGAAGTCATTCA-ATCTCTTA-CCCGACCATGGGGCA
44791 GATTGAAGC
64 GATTGAAGC
44800 CATCAGATTT
Statistics
Matches: 1077, Mismatches: 224, Indels: 145
0.74 0.15 0.10
Matches are distributed among these distances:
115 1 0.00
116 51 0.05
117 206 0.19
118 421 0.39
119 257 0.24
120 134 0.12
121 7 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (115 bp):
AATCTTTTACCCTAACTAGAGGGCAGATTGAAGTCATTCAATCTCTTACCCGACCATGGGGCAGA
TTGAAGCAATCCAATCTTTTACCCAACCATGGGGCAAATTAAAGTAATCT
Found at i:43962 original size:236 final size:235
Alignment explanation
Indices: 43263--44577 Score: 1152
Period size: 236 Copynumber: 5.6 Consensus size: 235
43253 AGTTACAATC
* * * * * * *
43263 ATCCAAACTTTTGCCCTAATCAGAGGACAAATTGAAGACTAT-TCAATCTTTTACCCTAATCAGA
1 ATCCAATCTTTTACCCTAACCATAGGGCAGATTGAA-ACCATCT-AATCTTTTACCCTAATCAGA
* * * * *
43327 GGGTAGATTGAAGACCATCCAATCTCTTAACCC-AACCATAGGGCAGATTGAAGTA--GTCCAAT
64 GGGCAGATTGAAGACCATCCAATCT-TTTACCCTAACCAGAGGGCAAATTGAAG-ACCATCCAAT
* * * * * * *
43389 CTTTTAACCCAATCATGGGGCAAATTGAAGTAGTCCAATCTTTTACCCTAACTAGAGGGCAGATT
127 CTCTTACCCCGACCATGGGGCAAATTAAAGTAATCTAATCTTTTACCCT-ACTAGAGGGCAGATT
* *
43454 GAAGTCATTCAATCTCTTACCTCGATCGTGGGGCAGATTGAAGCA
191 GAAGTCATTCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCA
** * *
43499 ATCCAATCTTTTACACC-AACCAT-GAGGCAGATT-AAAGTAAT-TAAGATCTTTTTCCCTAACC
1 ATCCAATCTTTTAC-CCTAACCATAG-GGCAGATTGAAA-CCATCT-A-ATCTTTTACCCTAATC
* * ** * * *
43560 AGAGGGTAAATTGAAG-TGATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAG-CAATCCAA
61 AGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAA
** * * **
43623 TCTCTTACCTTGACCATGGGGCAAATT-ATGTAATCTAATCTTTTACCCTAGCCAGAGGAAAGAT
126 TCTCTTACCCCGACCATGGGGCAAATTAAAGTAATCTAATCTTTTACCCTA-CTAGAGGGCAGAT
* * * * *
43687 TGAAGGCAATCTAATCTTTTACCCCGACCATGGGGCAGATTAAAGCA
190 TGAAGTCATTC-AATCTCTTACCTCGACCATGGGGCAGATTGAAGCA
* * *
43734 ATCCAATCTTTTACCCTAACCATAGGGTAGATTGAAATCATCTAATCTTTTACCCTAATCAGAGA
1 ATCCAATCTTTTACCCTAACCATAGGGCAGATTGAAACCATCTAATCTTTTACCCTAATCAGAGG
* * * *
43799 ACAGATTAAAGACCATTCAATCTTTTACCCTAATCAGAGGGCAAATTGAAGACCATCCAATCTCT
66 GCAGATTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCT
** * *
43864 TACCTTGACCATGGGGCAAATTAAAGTAGTCTAATCTTTTACCCTCACTAGAAGGCAGATTGAAG
131 TACCCCGACCATGGGGCAAATTAAAGTAATCTAATCTTTTACCCT-ACTAGAGGGCAGATTGAAG
*
43929 TCATGCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCA
195 TCATTCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCA
* * * * *
43970 ATCCAATCTTTTA-CCTAACCAAAGGGCATATTGAAGACCATCCAATCTTTTACCATAACCAGAG
1 ATCCAATCTTTTACCCTAACCATAGGGCAGATTGAA-ACCATCTAATCTTTTACCCTAATCAGAG
* * *
44034 GGCAGATTGAAGACCAT-CAGATCTTTTACCTTAACCAGAGGACAAATTGAAAACCATCCAATCT
65 GGCAGATTGAAGACCATCCA-ATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCT
* * * *
44098 CTTACCCCG-CTCATGGGGCAAATTGAAGCAAT-TCAATCTTTTACCCTAATCATG-GGGCAAAT
129 CTTACCCCGAC-CATGGGGCAAATTAAAGTAATCT-AATCTTTTACCCTACT-A-GAGGGCAGAT
* * * * * *
44160 TGAAGTAATTCAGATCTTTTACC-CTAACAAGAGGGCAGATTGAAGTA
190 TGAAGTCATTCA-ATCTCTTACCTCGACCATG-GGGCAGATTGAAGCA
* * * * * **
44207 ATCCAATCTTTTACCCCAACCAGAGAGCAGATTGAAGCCATCTAATCTCTTACCCCGATCATG-G
1 ATCCAATCTTTTACCCTAACCATAGGGCAGATTGAAACCATCTAATCTTTTACCCTAATCA-GAG
* * *
44271 GGCAGATTGAAG-CTATCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAGACCATCCGATCTC
65 GGCAGATTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTC
* * * * * * *
44335 TTACCCCGATCATGGGGCAAATTACAGCAATCCAATCTTTTACCTTAATTAGAGGGCAGATTTAA
130 TTACCCCGACCATGGGGCAAATTAAAGTAATCTAATCTTTTACCCT-ACTAGAGGGCAGATTGAA
* * * * * * *
44400 GACCATCCGATCTCTTA-CTCTGAACA-GAGGGCAGACTGAAAACC
194 G-TCATTCAATCTCTTACCTC-GACCATG-GGGCAGATTG-AAGCA
* * ** * * * *
44444 ATCCGATCTCTTACCCCGACCAT-GAGGAAAATTGAAGACCATTTGATCTTTTACCCTAA-CTAG
1 ATCCAATCTTTTACCCTAACCATAG-GGCAGATTGAA-ACCATCTAATCTTTTACCCTAATC-AG
* * * * * * *
44507 AGGGCAGATTAAAG-CCATCTAATCTCTTACCCTGACCTTG-GGGCAAATTGAAG-CAATACAAT
63 AGGGCAGATTGAAGACCATCCAATCTTTTACCCTAACC-AGAGGGCAAATTGAAGACCATCCAAT
*
44569 CTTTTACCC
127 CTCTTACCC
44578 TAACCAGAGG
Statistics
Matches: 885, Mismatches: 153, Indels: 81
0.79 0.14 0.07
Matches are distributed among these distances:
233 1 0.00
234 72 0.08
235 181 0.20
236 387 0.44
237 163 0.18
238 81 0.09
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (235 bp):
ATCCAATCTTTTACCCTAACCATAGGGCAGATTGAAACCATCTAATCTTTTACCCTAATCAGAGG
GCAGATTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCT
TACCCCGACCATGGGGCAAATTAAAGTAATCTAATCTTTTACCCTACTAGAGGGCAGATTGAAGT
CATTCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCA
Found at i:44407 original size:79 final size:79
Alignment explanation
Indices: 43263--44417 Score: 875
Period size: 79 Copynumber: 14.7 Consensus size: 79
43253 AGTTACAATC
* * * * * * * * ** *
43263 ATCCAAACTTTTGCCCTAATCAGAGGACAAATTGAAGACTATTCAATCTTTTACCCTAATCA-GA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATG-
* *
43327 GGGTAGATTGAAGACC
65 GGGCAGATTGAAG-CA
* * * * * * *
43343 ATCCAATCTCTTAACCC-AACCATAGGGCAGATTGAAGTA--GTCCAATCTTTTAACCCAATCAT
1 ATCCAATCT-TTTACCCTAACCAGAGGGCAGATTGAAG-ACCATCCAATCTCTTACCCCGACCAT
* *
43405 GGGGCAAATTGAAGTA
64 GGGGCAGATTGAAGCA
* * * * * * *
43421 GTCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAG-TCATTCAATCTCTTACCTCGATCGTGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGG
43485 GGCAGATTGAAGCA
66 GGCAGATTGAAGCA
* ** * * **
43499 ATCCAATCTTTTACACC-AACCATGA-GGCAGATTAAAGTA--ATTAAGATCTTTTTCCCTAACC
1 ATCCAATCTTTTAC-CCTAACCA-GAGGGCAGATTGAAG-ACCATCCA-ATCTCTTACCCCGACC
* * **
43560 A-GAGGGTAAATTGAAGTG
62 ATG-GGGCAGATTGAAGCA
* * **
43578 ATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAG-CAATCCAATCTCTTACCTTGACCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGG
* * *
43642 GGCAAATT-ATGTA
66 GGCAGATTGAAGCA
* * ** * * * *
43655 ATCTAATCTTTTACCCTAGCCAGAGGAAAGATTGAAGGCAATCTAATCTTTTACCCCGACCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGG
*
43720 GGCAGATTAAAGCA
66 GGCAGATTGAAGCA
* * * * * ** *
43734 ATCCAATCTTTTACCCTAACCATAGGGTAGATTGAA-ATCATCTAATCTTTTACCCTAATCA-GA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATG-
** * *
43797 GAACAGATTAAAGACC
65 GGGCAGATTGAAG-CA
* * * **
43813 ATTCAATCTTTTACCCTAATCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCTTGACCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGG
* * *
43878 GGCAAATTAAAGTA
66 GGCAGATTGAAGCA
* * * * * * * *
43892 GTCTAATCTTTTACCCTCACTAGAAGGCAGATTGAAG-TCATGCAATCTCTTACCTCGACCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGG
43956 GGCAGATTGAAGCA
66 GGCAGATTGAAGCA
* * * ***
43970 ATCCAATCTTTTA-CCTAACCAAAGGGCATATTGAAGACCATCCAATCTTTTACCATAACCA-GA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATG-
*
44033 GGGCAGATTGAAGACC
65 GGGCAGATTGAAG-CA
* * * *
44049 AT-CAGATCTTTTACCTTAACCAGAGGACAAATTGAAAACCATCCAATCTCTTACCCCG-CTCAT
1 ATCCA-ATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGAC-CAT
*
44112 GGGGCAAATTGAAGCA
64 GGGGCAGATTGAAGCA
* * * * * * *
44128 ATTCAATCTTTTACCCTAATCATG-GGGCAAATTGAAGTA--ATTCAGATCTTTTA-CCCTAACA
1 ATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG-ACCATCCA-ATCTCTTACCCCGACCA
* *
44189 AGAGGGCAGATTGAAGTA
63 TG-GGGCAGATTGAAGCA
* * * *
44207 ATCCAATCTTTTACCCCAACCAGAGAGCAGATTGAAG-CCATCTAATCTCTTACCCCGATCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGG
*
44271 GGCAGATTGAAGCT
66 GGCAGATTGAAGCA
* * * *
44285 ATCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAGACCATCCGATCTCTTACCCCGATCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGG
*
44350 GGCAAATT-ACAGCA
66 GGCAGATTGA-AGCA
* ** * *
44364 ATCCAATCTTTTACCTTAATTAGAGGGCAGATTTAAGACCATCCGATCTCTTAC
1 ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTAC
44418 TCTGAACAGA
Statistics
Matches: 860, Mismatches: 173, Indels: 85
0.77 0.15 0.08
Matches are distributed among these distances:
77 61 0.07
78 318 0.37
79 366 0.43
80 107 0.12
81 8 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (79 bp):
ATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGG
GGCAGATTGAAGCA
Found at i:44432 original size:79 final size:79
Alignment explanation
Indices: 43263--44657 Score: 858
Period size: 79 Copynumber: 17.7 Consensus size: 79
43253 AGTTACAATC
* * * * * * *
43263 ATCCAAACTTTTGCCCTAATCAGAGGACAAATTGAAGACTATTCAATCTTTTACCCT-AATCA-G
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAA-CATG
* *
43326 AGGGTAGATTGAAGACC
65 -GGGCAGATTGAAG-CA
* * * * *
43343 ATCCAATCTCTTAACCC-AACCATAGGGCAGATTGAAGTA--GTCCAATCTTTTAACCC--AATC
1 ATCCAATCT-TTTACCCTAACCAGAGGGCAAATTGAAG-ACCATCCAATCTCTT-ACCCTGAA-C
* *
43403 ATGGGGCAAATTGAAGTA
62 ATGGGGCAGATTGAAGCA
* * * * * * *
43421 GTCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAG-TCATTCAATCTCTTA-CCTCGATCGTG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCT-GAACATG
43484 GGGCAGATTGAAGCA
65 GGGCAGATTGAAGCA
* * ** * *
43499 ATCCAATCTTTTACACC-AACCATGA-GGCAGATTAAAGTA--ATTAAGATCTTTTTCCCT-AAC
1 ATCCAATCTTTTAC-CCTAACCA-GAGGGCAAATTGAAG-ACCATCCA-ATCTCTTACCCTGAA-
* * **
43559 CA-GAGGGTAAATTGAAGTG
61 CATG-GGGCAGATTGAAGCA
* * * * *
43578 ATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAG-CAATCCAATCTCTTACCTTGACCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAACATGG
* * *
43642 GGCAAATT-ATGTA
66 GGCAGATTGAAGCA
* * * * * * * * *
43655 ATCTAATCTTTTACCCTAGCCAGA-GGAAAGATTGAAGGCAATCTAATCTTTTACCCCGACCATG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAA-ATTGAAGACCATCCAATCTCTTACCCTGAACATG
*
43719 GGGCAGATTAAAGCA
65 GGGCAGATTGAAGCA
* * * * * *
43734 ATCCAATCTTTTACCCTAACCATAGGGTAGATTGAA-ATCATCTAATCTTTTACCCT-AATCA-G
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAA-CATG
** * *
43796 AGAACAGATTAAAGACC
65 -GGGCAGATTGAAG-CA
* * * *
43813 ATTCAATCTTTTACCCTAATCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCTTGACCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAACATGG
* * *
43878 GGCAAATTAAAGTA
66 GGCAGATTGAAGCA
* * * * * * * * *
43892 GTCTAATCTTTTACCCTCACTAGAAGGCAGATTGAAG-TCATGCAATCTCTTA-CCTCGACCATG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCT-GAACATG
43955 GGGCAGATTGAAGCA
65 GGGCAGATTGAAGCA
* * * *
43970 ATCCAATCTTTTA-CCTAACCAAAGGGCATATTGAAGACCATCCAATCTTTTACCAT-AACCA-G
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAA-CATG
*
44032 AGGGCAGATTGAAGACC
65 -GGGCAGATTGAAG-CA
* * * * **
44049 AT-CAGATCTTTTACCTTAACCAGAGGACAAATTGAAAACCATCCAATCTCTTACCCCGCTCATG
1 ATCCA-ATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAACATG
*
44113 GGGCAAATTGAAGCA
65 GGGCAGATTGAAGCA
* * * *
44128 ATTCAATCTTTTACCCTAATCATG-GGGCAAATTGAAGTA--ATTCAGATCTTTTACCCT-AACA
1 ATCCAATCTTTTACCCTAACCA-GAGGGCAAATTGAAG-ACCATCCA-ATCTCTTACCCTGAACA
* *
44189 AGAGGGCAGATTGAAGTA
63 TG-GGGCAGATTGAAGCA
* * * * * *
44207 ATCCAATCTTTTACCCCAACCAGAGAGCAGATTGAAG-CCATCTAATCTCTTACCCCGATCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAACATGG
*
44271 GGCAGATTGAAGCT
66 GGCAGATTGAAGCA
* * * *
44285 ATCCAATCTTTTACCCTAACCAAAGGGCAAATTGAAGACCATCCGATCTCTTACCCCGATCATGG
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAACATGG
*
44350 GGCAAATT-ACAGCA
66 GGCAGATTGA-AGCA
* ** * * * *
44364 ATCCAATCTTTTACCTTAATTAGAGGGCAGATTTAAGACCATCCGATCTCTTACTCTGAACA-GA
1 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAACATG-
* * *
44428 GGGCAGACTGAAAACC
65 GGGCAGATTG-AAGCA
* * ** * *** *
44444 ATCCGATCTCTTACCCCGACCATGA-GGAAAATTGAAGACCATTTGATCTTTTACCCT-AAC-TA
1 ATCCAATCTTTTACCCTAACCA-GAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAACAT-
* *
44506 GAGGGCAGATTAAAGCC
64 G-GGGCAGATTGAAGCA
* * * * * * *
44523 ATCTAATCTCTTACCCTGACCTTG-GGGCAAATTGAAG-CAATACAATCTTTTACCCT-AACCA-
1 ATCCAATCTTTTACCCTAACC-AGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAA-CAT
* *
44584 GAGGACAGATTGAAGACC
64 G-GGGCAGATTGAAG-CA
** * * * * *
44602 ATCTGATCTCTTACCCCAACTATG-GGGCAAATTGAAGACCATCCGATCTTTTACCC
1 ATCCAATCTTTTACCCTAACCA-GAGGGCAAATTGAAGACCATCCAATCTCTTACCC
44658 CGACTAGAGG
Statistics
Matches: 1039, Mismatches: 208, Indels: 136
0.75 0.15 0.10
Matches are distributed among these distances:
76 5 0.00
77 62 0.06
78 335 0.32
79 442 0.43
80 183 0.18
81 12 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (79 bp):
ATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCTGAACATGG
GGCAGATTGAAGCA
Found at i:44650 original size:158 final size:160
Alignment explanation
Indices: 44424--44747 Score: 391
Period size: 158 Copynumber: 2.0 Consensus size: 160
44414 TTACTCTGAA
* * **
44424 CAGAGGGCAGACTGAAAACCATCCGATCTCTTACCCCGACCATGAGGAAAATTGAAGACCATTTG
1 CAGAGGACAGACTGAAAACCATCCGATCTCTTACCCCAACCATGAGGAAAATTGAAGACCATCCG
* * * * ** * *
44489 ATCTTTTACCCTAACTAGAGGGCAGATTAAAG-CCATCTAATCTCTTACCCTGACCTTGGGGCAA
66 ATCTTTTACCCCAACTAGAGGGCAAATTAAAGACCACCCAATCTCTTACCCCAACCATGAGGCAA
44553 ATTGAAGCAATAC-AATCTTTTACCCTAAC
131 ATTGAAGCAATACAAATCTTTTACCCTAAC
* * * * * *
44582 CAGAGGACAGATTGAAGACCATCTGATCTCTTACCCCAACTATGGGGCAAATTGAAGACCATCCG
1 CAGAGGACAGACTGAAAACCATCCGATCTCTTACCCCAACCATGAGGAAAATTGAAGACCATCCG
* * * * * *
44647 ATCTTTTACCCCGACTAGAGGGCAAATTGAAGATCACCCGATCTCTTACCCCAATCATGAGGCAG
66 ATCTTTTACCCCAACTAGAGGGCAAATTAAAGACCACCCAATCTCTTACCCCAACCATGAGGCAA
* *
44712 ATTGAAGTAATTCAAATCTTTTACCCTAAC
131 ATTGAAGCAATACAAATCTTTTACCCTAAC
*
44742 TAGAGG
1 CAGAGG
44748 GTAAATTGAA
Statistics
Matches: 137, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
158 83 0.61
159 33 0.24
160 21 0.15
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (160 bp):
CAGAGGACAGACTGAAAACCATCCGATCTCTTACCCCAACCATGAGGAAAATTGAAGACCATCCG
ATCTTTTACCCCAACTAGAGGGCAAATTAAAGACCACCCAATCTCTTACCCCAACCATGAGGCAA
ATTGAAGCAATACAAATCTTTTACCCTAAC
Found at i:44905 original size:40 final size:39
Alignment explanation
Indices: 44845--44948 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 39
44835 CATGAGGCAA
*
44845 ATTGAAGCAATCCAATCTTTTACCCTAACTAAAGGGTAG
1 ATTGAAGCAATCCAATCTTTTACCCTAACCAAAGGGTAG
* * * * **
44884 ATTGAAGACCATCCGATCTTTTACCTTGACCATGGGGTAG
1 ATTGAAG-CAATCCAATCTTTTACCCTAACCAAAGGGTAG
*
44924 ATTGAAGCAATCTAATCTTTTACCC
1 ATTGAAGCAATCCAATCTTTTACCC
44949 CTAAAGTTAC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 21 0.40
40 32 0.60
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (39 bp):
ATTGAAGCAATCCAATCTTTTACCCTAACCAAAGGGTAG
Found at i:45494 original size:11 final size:12
Alignment explanation
Indices: 45470--45499 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
45460 CAATCCAAAT
45470 TTTATTATTTTA
1 TTTATTATTTTA
45482 TTTATTA-TTTA
1 TTTATTATTTTA
45493 TTTATTA
1 TTTATTA
45500 AATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:49736 original size:14 final size:13
Alignment explanation
Indices: 49727--49763 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
49717 TTTAATATTG
49727 TAATTATAATTTA
1 TAATTATAATTTA
49740 TAATTTATAATTTA
1 TAA-TTATAATTTA
*
49754 TAATGATAAT
1 TAATTATAAT
49764 GATAATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (13 bp):
TAATTATAATTTA
Found at i:49740 original size:7 final size:7
Alignment explanation
Indices: 49730--49757 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
49720 AATATTGTAA
49730 TTATAAT
1 TTATAAT
49737 TTATAAT
1 TTATAAT
49744 TTATAAT
1 TTATAAT
49751 TTATAAT
1 TTATAAT
49758 GATAATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATAAT
Found at i:51410 original size:59 final size:59
Alignment explanation
Indices: 51323--51490 Score: 196
Period size: 59 Copynumber: 2.8 Consensus size: 59
51313 GAAAAAAAAA
* * * * *
51323 ATTTAATCTGATAAAAAAATCAAATTTTTGGGTGTTGGCCATGCAATGGCCTATACCCCCT
1 ATTT-ATCTAATAAAAAAATTAAATTTTTGAGTGTTGGCCATGCAATGGCCGACA-CCCCT
* * * * *
51384 TTTTATC-AGAT-AAAATATTCAATTTTTTAGTGTTGGTCATGCAATGGCCGACACCCCT
1 ATTTATCTA-ATAAAAAAATTAAATTTTTGAGTGTTGGCCATGCAATGGCCGACACCCCT
*
51442 ATTTATCTAATAAAAAAATTAAATTTTTGAGTGTTGGCCATACAATGGC
1 ATTTATCTAATAAAAAAATTAAATTTTTGAGTGTTGGCCATGCAATGGC
51491 TGCCACTCTC
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
58 13 0.15
59 67 0.76
60 5 0.06
61 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (59 bp):
ATTTATCTAATAAAAAAATTAAATTTTTGAGTGTTGGCCATGCAATGGCCGACACCCCT
Found at i:51550 original size:61 final size:60
Alignment explanation
Indices: 51451--51656 Score: 181
Period size: 61 Copynumber: 3.4 Consensus size: 60
51441 TATTTATCTA
* * * *
51451 ATAAAAAAA-TT--AAA-TTTTTGAGTGTTGGCCATACAATGGCTGCCACTCTCTTTTCTTAG
1 ATAAAAAAATTTCAAAATTTTTTG-GCGTTGGACATGCAATGG-TGCCACCCTCTTTT-TTAG
51510 ATAAAAAAATTTCAAAATTTTTTGGCGTT-GACATGCAATGGT-CAACACCCTCTTTTTTCAG
1 ATAAAAAAATTTCAAAATTTTTTGGCGTTGGACATGCAATGGTGC--CACCCTCTTTTTT-AG
* * * ** ** * *
51571 ATAAAAAAATTTTAAAATTTTTTTGTGTTGGTTATGCAATAATCGACACCCTCTTTTTCAG
1 ATAAAAAAATTTCAAAATTTTTTGGCGTTGGACATGCAATGGT-GCCACCCTCTTTTTTAG
*
51632 ATAAAAAATTTTCAAAATTTTTTGG
1 ATAAAAAAATTTCAAAATTTTTTGG
51657 TGTTAGCCAT
Statistics
Matches: 121, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
59 10 0.08
60 5 0.04
61 72 0.60
62 28 0.23
63 6 0.05
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (60 bp):
ATAAAAAAATTTCAAAATTTTTTGGCGTTGGACATGCAATGGTGCCACCCTCTTTTTTAG
Found at i:51610 original size:62 final size:62
Alignment explanation
Indices: 51344--51660 Score: 248
Period size: 59 Copynumber: 5.2 Consensus size: 62
51334 TAAAAAAATC
** * * * * * *
51344 AAATTTTTGGGTGTTGGCCATGCAATGGCCTATACCCCCTTTTTATCAGAT---AAAATATT-
1 AAATTTTTTAGTGTTGGTCATGCAATGGTCGACACCCTCTTTTT-TCAGATAAAAAAATTTTA
* * *
51403 CAATTTTTTAGTGTTGGTCATGCAATGGCCGACACCC-CTATTTATCTA-ATAAAAAAA--TT-
1 AAATTTTTTAGTGTTGGTCATGCAATGGTCGACACCCTCT-TTTTTC-AGATAAAAAAATTTTA
* * * * * *
51462 AAATTTTTGAGTGTTGGCCATACAATGG-CTGCCACTCTCTTTTCTT-AGATAAAAAAATTTCA
1 AAATTTTTTAGTGTTGGTCATGCAATGGTC-GACACCCTCTTTT-TTCAGATAAAAAAATTTTA
* * * *
51524 AAATTTTTTGGCGTT-GACATGCAATGGTCAACACCCTCTTTTTTCAGATAAAAAAATTTTA
1 AAATTTTTTAGTGTTGGTCATGCAATGGTCGACACCCTCTTTTTTCAGATAAAAAAATTTTA
* * **
51585 AAATTTTTTTGTGTTGGTTATGCAATAATCGACACCCTC-TTTTTCAGAT-AAAAAATTTTCA
1 AAATTTTTTAGTGTTGGTCATGCAATGGTCGACACCCTCTTTTTTCAGATAAAAAAATTTT-A
*
51646 AAATTTTTTGGTGTT
1 AAATTTTTTAGTGTT
51661 AGCCATGTCA
Statistics
Matches: 210, Mismatches: 32, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
58 8 0.04
59 78 0.37
60 15 0.07
61 78 0.37
62 31 0.15
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (62 bp):
AAATTTTTTAGTGTTGGTCATGCAATGGTCGACACCCTCTTTTTTCAGATAAAAAAATTTTA
Found at i:51689 original size:61 final size:60
Alignment explanation
Indices: 51498--51660 Score: 202
Period size: 61 Copynumber: 2.7 Consensus size: 60
51488 GGCTGCCACT
* * * * *
51498 CTCTTTTCTTAGATAAAAAAATTTCAAAATTTTTTGGCGTTGACATGCAATGGTCAACACC
1 CTCTTTT-TCAGATAAAAAATTTTCAAAATTTTTTGGTGTTGACATGCAATGATCGACACC
* ** *
51559 CTCTTTTTTCAGATAAAAAAATTTT-AAAATTTTTTTGTGTTGGTTATGCAATAATCGACACC
1 CTC-TTTTTCAGAT-AAAAAATTTTCAAAATTTTTTGGTGTT-GACATGCAATGATCGACACC
51621 CTCTTTTTCAGATAAAAAATTTTCAAAATTTTTTGGTGTT
1 CTCTTTTTCAGATAAAAAATTTTCAAAATTTTTTGGTGTT
51661 AGCCATGTCA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
60 10 0.11
61 47 0.53
62 31 0.35
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (60 bp):
CTCTTTTTCAGATAAAAAATTTTCAAAATTTTTTGGTGTTGACATGCAATGATCGACACC
Found at i:55531 original size:23 final size:22
Alignment explanation
Indices: 55501--55544 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
55491 AATGAACATG
55501 TTTAAATTTAAATAA-TTTAAAC
1 TTTAAA-TTAAATAAGTTTAAAC
*
55523 TTTATAATTATATAAGTTTAAA
1 TTTA-AATTAAATAAGTTTAAA
55545 TCTAAAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTAAATTAAATAAGTTTAAAC
Found at i:55754 original size:59 final size:60
Alignment explanation
Indices: 55631--55754 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 60
55621 AATTATTATT
** * **
55631 ATATTACAATTTATATCAAATATTGTGTTCATTTGACAATACGTTATTTATCAAATTTTC
1 ATATTACAATTTATATCAAATAACGTGTTCATTTGACAATACATTATTTATCAAATTTAA
* * * *
55691 ATATT-CAATTTTTATCAAATAACGTGTTGATTTGATAATACATTATTTA-CTAACTTTAA
1 ATATTACAATTTATATCAAATAACGTGTTCATTTGACAATACATTATTTATC-AAATTTAA
55750 ATATT
1 ATATT
55755 TAAATAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
58 1 0.02
59 48 0.89
60 5 0.09
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.47
Consensus pattern (60 bp):
ATATTACAATTTATATCAAATAACGTGTTCATTTGACAATACATTATTTATCAAATTTAA
Found at i:55878 original size:84 final size:85
Alignment explanation
Indices: 55697--56046 Score: 578
Period size: 85 Copynumber: 4.1 Consensus size: 85
55687 TTTCATATTC
* * *
55697 AATTTTTATCAAATAACGTGTTGATTTGATAATACATTATTTACTAACTTTAAATATTTAAATAA
1 AATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAAT-A
*
55762 AAAAGATTATTATTATATTAT
65 AAAATATTATTATTATATTAT
55783 AATTTTTATCAAATAATGTGTTGATTTGACAAT-CATTATTTACTAAATTTAAATATTTAAATAA
1 AATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAA
55847 AAATATTATTATTATATTAT
66 AAATATTATTATTATATTAT
55867 AATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAA
1 AATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAA
* *
55932 AATTATTATTATTATATTAC
66 AAATATTATTATTATATTAT
* * * *
55952 AATTTTTATCAAATAATATGTTGATTTGATAATATATTATTTATTAAATTTAAATATTTAAATAA
1 AATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAA
*
56017 AAA-AATATTATTATATTAT
66 AAATATTATTATTATATTAT
56036 AATTTTTATCA
1 AATTTTTATCA
56047 GATTTTAAAT
Statistics
Matches: 250, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
84 79 0.32
85 140 0.56
86 31 0.12
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (85 bp):
AATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAA
AAATATTATTATTATATTAT
Found at i:56169 original size:22 final size:22
Alignment explanation
Indices: 56141--56201 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
56131 TGGATCGCCC
*
56141 AAATTCCAGCTCACCTAAACCG
1 AAATTCCAGCTCACCAAAACCG
* *
56163 AAATTCCAACTCAGCAAAACCG
1 AAATTCCAGCTCACCAAAACCG
56185 AAATTCCAGCTCACCAA
1 AAATTCCAGCTCACCAA
56202 CACCTCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.41, C:0.34, G:0.08, T:0.16
Consensus pattern (22 bp):
AAATTCCAGCTCACCAAAACCG
Found at i:58462 original size:27 final size:29
Alignment explanation
Indices: 58404--58465 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
58394 TCCGTTTACT
* * *
58404 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTTAAATTTAA-TTGTAATTTCCTATATA
58434 TTTTAAATTTAA-T-TAATTTCCTATATA
1 TTTTAAATTTAATTGTAATTTCCTATATA
58461 TTTTA
1 TTTTA
58466 TTTTTTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 16 0.55
28 1 0.03
30 12 0.41
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTTAAATTTAATTGTAATTTCCTATATA
Found at i:59559 original size:59 final size:61
Alignment explanation
Indices: 59427--59573 Score: 203
Period size: 61 Copynumber: 2.4 Consensus size: 61
59417 AAAAAAGGGG
*
59427 AATTTGAAATTTTTTTATCTTAGAAAAAGGGGTGTCGGCCATTACATGGCCAACACCAAAAA
1 AATTT-AAATTTTTTTATCTGAGAAAAAGGGGTGTCGGCCATTACATGGCCAACACCAAAAA
* * *
59489 AATTTAAATTTTTTTATCTGAG-ACAAGGGAGTGTCGGCTATTGCATGGCCAACACC-AAAA
1 AATTTAAATTTTTTTATCTGAGAAAAAGGG-GTGTCGGCCATTACATGGCCAACACCAAAAA
*
59549 AA-TTAAA-TTTTTTATCTGATAAAAA
1 AATTTAAATTTTTTTATCTGAGAAAAA
59574 AGGACCCAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
58 12 0.16
59 8 0.10
60 12 0.16
61 40 0.52
62 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (61 bp):
AATTTAAATTTTTTTATCTGAGAAAAAGGGGTGTCGGCCATTACATGGCCAACACCAAAAA
Found at i:62232 original size:5 final size:6
Alignment explanation
Indices: 62215--62241 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
62205 TCTTTTGCTT
62215 CTCCCC CTCCCC CTCCCC CTCCCC CTC
1 CTCCCC CTCCCC CTCCCC CTCCCC CTC
62242 ATTTTACAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.81, G:0.00, T:0.19
Consensus pattern (6 bp):
CTCCCC
Found at i:90997 original size:62 final size:62
Alignment explanation
Indices: 90738--91187 Score: 325
Period size: 62 Copynumber: 7.5 Consensus size: 62
90728 AAAAAATTAG
* * * *
90738 ATTTTTTGGTATTGGCTATCAAATGGACGACACCCCT-TTTTCTCGA-AAAAAAATTT--AA
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCTTTTCCCGAGAAAAAAATTTCAAA
*** ** * * *
90796 ATTTTTTGGTGTTGGCCATTGCATGGTTGATACCCCT-TTTT--TGAGAAAAAAAATTTTAAA
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCTTTTCCCGAG-AAAAAAATTTCAAA
* * * * * * * *
90856 ATTTTTTGATGTTGGTCATCAAATGGTCGACACCTCT-TTTTCTC-AAAAAAAAAATT--AC
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCTTTTCCCGAGAAAAAAATTTCAAA
* *
90914 ATTTTTGGGTGTTGGCCATCAAATGGCCGACACTCCC-CTTTTCCCGAGAAAAAAATTTCAGA
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACAC-CCCTCTTTTCCCGAGAAAAAAATTTCAAA
* * * * * * *
90976 TTTTTTTTGTGTTGGCTATCAAATGCCCAATACCCCTCTTTTCTCGAGAAAAAAATTTCAAA
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCTTTTCCCGAGAAAAAAATTTCAAA
* *
91038 ATTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCT-TATTT----A-AAAAAAATTGC---
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCT-TTTCCCGAGAAAAAAATTTCAAA
* *** * * *
91092 ATTTTTGGGTGTTGGCCATTGCATGGCCGACA-CCCTTTTTTCTCGGATAAAAAAATTGT-AAA
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCTTTTC-CCGAGAAAAAAATT-TCAAA
* **
91154 TTTTTTTGGTGTTGGCCATGTAATGGCCGACACC
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACC
91188 AACTTCCCCT
Statistics
Matches: 308, Mismatches: 59, Indels: 45
0.75 0.14 0.11
Matches are distributed among these distances:
53 7 0.02
54 28 0.09
56 2 0.01
57 10 0.03
58 75 0.24
59 17 0.06
60 54 0.18
61 5 0.02
62 109 0.35
63 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (62 bp):
ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTCTTTTCCCGAGAAAAAAATTTCAAA
Found at i:98125 original size:30 final size:30
Alignment explanation
Indices: 98089--98145 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
98079 TCTCAATTAT
98089 TTAAATGAAAATTTTT-AAATAATTTAAGAC
1 TTAAATGAAAATTTTTCAAA-AATTTAAGAC
*
98119 TTAAATGAAATTTTTTCAAAAATTTAA
1 TTAAATGAAAATTTTTCAAAAATTTAA
98146 TGATTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (30 bp):
TTAAATGAAAATTTTTCAAAAATTTAAGAC
Found at i:107657 original size:23 final size:23
Alignment explanation
Indices: 107627--107672 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
107617 ACTAGGTGTT
107627 AGATTGCATTTTGCCTCCTCTAC
1 AGATTGCATTTTGCCTCCTCTAC
107650 AGATTGCATTTTGCCTCCTCTAC
1 AGATTGCATTTTGCCTCCTCTAC
107673 TTAAATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.39
Consensus pattern (23 bp):
AGATTGCATTTTGCCTCCTCTAC
Found at i:134484 original size:114 final size:105
Alignment explanation
Indices: 134298--134607 Score: 344
Period size: 114 Copynumber: 2.9 Consensus size: 105
134288 TAATTCTAGC
* * * * *
134298 CACACTAGTATTTTACAATGAACAAAATAAAATAGCTGCA-AGTGAATTCTAGTAGATATTAAAC
1 CACA-TAGGATTTTACAATGAATAAAATAAAATAACTGCATA-TAAATTCTAGTAAATATTAAAC
*
134362 TCTTAATTTGAGCCAATAAAATAAATAAATTCTAGTAACATAATTCAACT
64 TCTCAATTTG-GCCAATAAAATAAATAAATTCTAGT---A-AA--C-ACT
* * *
134412 CACAGTAGGATTTTACAATGAATAAAATAAAATAATTGCATATAAATTCTAATAAATACTAAACT
1 CACA-TAGGATTTTACAATGAATAAAATAAAATAACTGCATATAAATTCTAGTAAATATTAAACT
134477 CTCAATTTGGGCCAATAAAATAAATAAATTCTAGTAAACACT
65 CTCAATTT-GGCCAATAAAATAAATAAATTCTAGTAAACACT
* * *
134519 ---A-A-GATTTTACAATGAATAAAATAAAATAAGTGCATGTAAATTCTAGTAAATATTAAAATC
1 CACATAGGATTTTACAATGAATAAAATAAAATAACTGCATATAAATTCTAGTAAATATTAAACTC
*
134579 TCAATTTTGGCTAATAAAATAAATAAATT
66 TCAA-TTTGGCCAATAAAATAAATAAATT
134608 TCATCTCTCT
Statistics
Matches: 177, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
101 77 0.44
102 4 0.02
104 1 0.01
107 3 0.02
108 1 0.01
110 2 0.01
111 1 0.01
114 86 0.49
115 2 0.01
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (105 bp):
CACATAGGATTTTACAATGAATAAAATAAAATAACTGCATATAAATTCTAGTAAATATTAAACTC
TCAATTTGGCCAATAAAATAAATAAATTCTAGTAAACACT
Found at i:134595 original size:101 final size:101
Alignment explanation
Indices: 134420--134607 Score: 313
Period size: 101 Copynumber: 1.9 Consensus size: 101
134410 CTCACAGTAG
* *
134420 GATTTTACAATGAATAAAATAAAATAATTGCATATAAATTCTAATAAATACTAAACTCTCAATTT
1 GATTTTACAATGAATAAAATAAAATAAGTGCATATAAATTCTAATAAATACTAAAATCTCAATTT
134485 GGGCCAATAAAATAAATAAATTCTAGTAAACACTAA
66 GGGCCAATAAAATAAATAAATTCTAGTAAACACTAA
* * *
134521 GATTTTACAATGAATAAAATAAAATAAGTGCATGTAAATTCTAGTAAATATTAAAATCTCAATTT
1 GATTTTACAATGAATAAAATAAAATAAGTGCATATAAATTCTAATAAATACTAAAATCTCAATTT
* *
134586 TGGCTAATAAAATAAATAAATT
66 GGGCCAATAAAATAAATAAATT
134608 TCATCTCTCT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 80 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (101 bp):
GATTTTACAATGAATAAAATAAAATAAGTGCATATAAATTCTAATAAATACTAAAATCTCAATTT
GGGCCAATAAAATAAATAAATTCTAGTAAACACTAA
Found at i:147913 original size:11 final size:11
Alignment explanation
Indices: 147897--147957 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
147887 GAATGAAAAC
147897 TTAATAATAAT
1 TTAATAATAAT
147908 TTAATAATAAT
1 TTAATAATAAT
**
147919 TTAATAATTTT
1 TTAATAATAAT
*
147930 TTAA-AATTCAAA
1 TTAATAA-T-AAT
*
147942 TTACTAATAAT
1 TTAATAATAAT
147953 TTAAT
1 TTAAT
147958 GATTTTAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
10 2 0.05
11 31 0.79
12 4 0.10
13 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATAATAAT
Found at i:149397 original size:63 final size:63
Alignment explanation
Indices: 149278--149408 Score: 158
Period size: 63 Copynumber: 2.1 Consensus size: 63
149268 ATGCACTTAA
* * *
149278 AAAATTGGCATGAACAAATCAATACCTAAATCCCACTTCGACCTGACTTTCAAAAATTATCTT
1 AAAATCGGCATGAACAAATCAACACCTAAATCCCACTTCGACCTAACTTTCAAAAATTATCTT
* * ** *
149341 AAAATCGGCATGAATAAATCAACACTTAACATCTGACTTCGACAC-AAC-TTCCAAAATTATCTT
1 AAAATCGGCATGAACAAATCAACACCTAA-ATCCCACTTCGAC-CTAACTTTCAAAAATTATCTT
149404 AAAAT
1 AAAAT
149409 TTGTTGACCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 44 0.76
64 13 0.22
65 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (63 bp):
AAAATCGGCATGAACAAATCAACACCTAAATCCCACTTCGACCTAACTTTCAAAAATTATCTT
Found at i:158160 original size:27 final size:26
Alignment explanation
Indices: 158130--158182 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
158120 TTACGAAAGT
* *
158130 TTTTATATTAGAAATTAATTTAAATTA
1 TTTTATATTAAAAAATAA-TTAAATTA
*
158157 TTTTTTATTAAAAAATAATTAAATTA
1 TTTTATATTAAAAAATAATTAAATTA
158183 ATCTTCCTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTTATATTAAAAAATAATTAAATTA
Found at i:168018 original size:15 final size:17
Alignment explanation
Indices: 167982--168022 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
167972 GAGCTAAAAT
167982 ATAATTT-TATTATATA
1 ATAATTTATATTATATA
*
167998 AAAATTTATATT-T-TA
1 ATAATTTATATTATATA
168013 ATAATTTATA
1 ATAATTTATA
168023 AAGGGACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
16 7 0.32
17 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAATTTATATTATATA
Found at i:170872 original size:19 final size:19
Alignment explanation
Indices: 170850--170887 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
170840 ACAAATCATA
170850 CAAAAAAAAAAAAAGTAAG
1 CAAAAAAAAAAAAAGTAAG
* *
170869 CAAAAAAAAGATAAGTAAG
1 CAAAAAAAAAAAAAGTAAG
170888 ATTTCTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (19 bp):
CAAAAAAAAAAAAAGTAAG
Found at i:173045 original size:31 final size:31
Alignment explanation
Indices: 173003--173097 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
172993 TTACAAAATG
*
173003 GTTATTGAACTATTTGAAAATTTTCATTGAA
1 GTTATTGAACTATTTGAAAGTTTTCATTGAA
* * *
173034 TTTATTAAACTATTCT-AAAGTTTTCATTTAA
1 GTTATTGAACTATT-TGAAAGTTTTCATTGAA
* * * *
173065 GTTATTGAATTATTCGAAAGTTTTTATTTAA
1 GTTATTGAACTATTTGAAAGTTTTCATTGAA
173096 GT
1 GT
173098 CACTAAGTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 52 0.98
32 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (31 bp):
GTTATTGAACTATTTGAAAGTTTTCATTGAA
Found at i:195274 original size:172 final size:172
Alignment explanation
Indices: 194975--195284 Score: 471
Period size: 172 Copynumber: 1.8 Consensus size: 172
194965 AATGTCACCG
* * *
194975 ACAATACATGACATAACAACCAAATAATGCTTGTACTGAAATAAATACTAAATCTTAAAATATCC
1 ACAATACATGACATAACAACCAAAGAATGCTTGTACTGAAATAAAGACTAAATCTTAAAATAACC
* *
195040 TACTGTCTTTCGATTTCCCAATCTGTGAAACTAAAGAACTATGGAACTCAAAACCAAGATAACTG
66 AACTGTCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAAACCAAGATAACTG
195105 CAGACATGGACGAGAAACATGAACACAACATCTATGCCACTA
131 CAGACATGGACGAGAAACATGAACACAACATCTATGCCACTA
* * * *
195147 ACAATACATGACA-ATACAATCAAAGAATGTTTGTACTGAAATAAAGACTAAATCTTCACATAAC
1 ACAATACATGACATA-ACAACCAAAGAATGCTTGTACTGAAATAAAGACTAAATCTTAAAATAAC
* * * *
195211 CAACTGTCTTTCTATTATCCCAATTTGTGAAACTAAATAAATATGGAACTC-AAACCCAGATAAC
65 CAACTGTCTTTCGATT-TCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAAACCAAGATAAC
195275 TGCAGACATG
129 TGCAGACATG
195285 TCATAGAAAC
Statistics
Matches: 123, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
171 1 0.01
172 91 0.74
173 31 0.25
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (172 bp):
ACAATACATGACATAACAACCAAAGAATGCTTGTACTGAAATAAAGACTAAATCTTAAAATAACC
AACTGTCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAAACCAAGATAACTG
CAGACATGGACGAGAAACATGAACACAACATCTATGCCACTA
Found at i:195429 original size:147 final size:151
Alignment explanation
Indices: 195157--195591 Score: 565
Period size: 162 Copynumber: 2.8 Consensus size: 151
195147 ACAATACATG
* * * **
195157 ACAATACAATCAAAGAATGTTTGTACTGAAATAAAGACTAAATCTTCACATAACCAACTGTCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCATCTTT
** *
195222 CTATTATCCCAATTTGTGAAACTAAATAAATATGGAACTCAAACCCAGATAACTGCAGACATGTC
66 C-ATTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAGACATGTC
195287 AT-A-GAA-AC-AC-GCCACCA
130 ATAACGAATACGACAGCCACCA
* *
195304 ACAACACAATCAAAGAATGTCTGTACTGAAATGAAGACTGTATCTTCACATAACCAACCATCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCATCTTT
* *
195369 CAGTTATCCCAATCAGTGAAACTAAAGAAATATGGGACTCAAGCCCAGATAACTGCAGACATGTC
66 CA-TTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAGACATGTC
195434 ATAGAAACACGAATACGACATATATGCCACCA
130 AT----A-ACGAATACGAC----A-GCCACCA
* * * *
195466 ACAATACAATCAAAGAAAGTCTGTACTGAAATGAAGACTGCATCTTCACATAACCACCCATCTCT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCATCTTT
*
195531 CAATTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCAAACCCGGATAACTGCAGACA
66 C-ATTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAGACA
195592 ACTGAGACAA
Statistics
Matches: 251, Mismatches: 20, Indels: 19
0.87 0.07 0.07
Matches are distributed among these distances:
146 1 0.00
147 118 0.47
153 1 0.00
154 3 0.01
155 2 0.01
156 2 0.01
162 123 0.49
163 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (151 bp):
ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCATCTTT
CATTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAGACATGTCA
TAACGAATACGACAGCCACCA
Found at i:196030 original size:326 final size:332
Alignment explanation
Indices: 195630--196309 Score: 858
Period size: 326 Copynumber: 2.1 Consensus size: 332
195620 CACATGAACA
** * * *
195630 ATGCCACCAACAATACATGATAATAAAATCAAAGAATGCCCATACTGCAATAAAGACTAAATCTT
1 ATGCCACCAACAATACACAAAAATAAAATCAAAGAAAGCCCATACTACAATAAAGACTAAATCTT
* ** *
195695 CACACATCCATCTGACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAA-ACAAC
66 CACACATCCAACCAACTTCCAATCAGTCAAACTAAAGTACTACAGAACACAAACCC-AAGACAAC
* * *
195759 CAGCGACTTGTCGGAGGAACAT-G-A-ACACA-A-CATATATGCCACCAACAATACACAACAATA
130 CACCAACTTGTCGGAGGAACATGGAAGACACATACCATATATGCCACCAACAATACACAACAACA
*
195819 AAATCAAAGAATGCCTATACT-ACAATAAAGACT-ATCTTCACACATCCAACCAACTTTCAATCA
195 AAATCAAAGAATGCCTAT-CTAACAATAAAGACTAATCTCCACACATCCAACCAACTTTCAATCA
** * * *
195882 GTCAAACTAAAGTACTATGGAACACAAACCCGAGACAACCGCAGACAT-GTTGGAGAGACACGGA
259 GTCAAACTAAAGTACTACAGAACACAAACCCGAGACAACCACAGAC-TGGTTGGAGAAACACGAA
195946 CATGACATAT
323 CATGACATAT
*
195956 ATGCCACCAACAATACACAAAAATAAAATCAAAGAAAGCCTATACTACAATAAAGACTAAAT-TT
1 ATGCCACCAACAATACACAAAAATAAAATCAAAGAAAGCCCATACTACAATAAAGACTAAATCTT
* * *
196020 CCATACATCCAACCAACTTCCAATCAGTCAAACTAAAGTACTACGGAGCACAAACCCAAGACAAC
66 -CACACATCCAACCAACTTCCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCAAGACAAC
* * * *
196085 CACCAACTTGTCGGAGGAACATGGACATGACATATATGCCATATATGCCACTAACAATATATAAC
130 CACCAACTTGTCGGAGGAACATGGA-A-GACACATA--CCATATATGCCACCAACAATACACAAC
* * * ** *
196150 AACACAATCAAAGAATGCCTGTGTAACAATAAAGACTAAATCTCCACTTATCTAACCAACTTTCA
191 AACAAAATCAAAGAATGCCTATCTAACAATAAAGACT-AATCTCCACACATCCAACCAACTTTCA
* * * * *
196215 ATCAGTCAAACTAAAGTCCTACAGAAGACAAACCCGAGACAACCACCGACTGGTTGGAGAAATAT
255 ATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAGACAACCACAGACTGGTTGGAGAAACAC
196280 GAACATGACATAT
320 GAACATGACATAT
* *
196293 ATGACACTAACAATACA
1 ATGCCACCAACAATACA
196310 TGACAACACA
Statistics
Matches: 300, Mismatches: 39, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
325 4 0.01
326 130 0.43
327 1 0.00
329 1 0.00
331 4 0.01
332 1 0.00
334 1 0.00
335 54 0.18
336 1 0.00
337 103 0.34
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (332 bp):
ATGCCACCAACAATACACAAAAATAAAATCAAAGAAAGCCCATACTACAATAAAGACTAAATCTT
CACACATCCAACCAACTTCCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCAAGACAACC
ACCAACTTGTCGGAGGAACATGGAAGACACATACCATATATGCCACCAACAATACACAACAACAA
AATCAAAGAATGCCTATCTAACAATAAAGACTAATCTCCACACATCCAACCAACTTTCAATCAGT
CAAACTAAAGTACTACAGAACACAAACCCGAGACAACCACAGACTGGTTGGAGAAACACGAACAT
GACATAT
Found at i:196114 original size:164 final size:164
Alignment explanation
Indices: 195630--196309 Score: 762
Period size: 164 Copynumber: 4.1 Consensus size: 164
195620 CACATGAACA
** * * *
195630 ATGCCACCAACAATACATGATAATAAAATCAAAGAATGCCCATACTGCAATAAAGACTAAATCTT
1 ATGCCACCAACAATACACAACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
* ** *
195695 CACACATCCATCTGACTTTCAATCAGTCAAACTAAAGTACTACAGAACACAAACCCGAA-ACAAC
66 CACACATCCAACCAACTTTCAATCAGTCAAACTAAAGTACTACGGAACACAAACCC-AAGACAAC
* * **
195759 CAGCGACTTGTCGGAGGAACATGAACACAACATAT
130 CACCAACTTGTCGGAGGAACATGAACATGACATAT
195794 ATGCCACCAACAATACACAACAATAAAATCAAAGAATGCCTATACTACAATAAAGACT--ATCTT
1 ATGCCACCAACAATACACAACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
* *
195857 CACACATCCAACCAACTTTCAATCAGTCAAACTAAAGTACTATGGAACACAAACCCGAGACAACC
66 CACACATCCAACCAACTTTCAATCAGTCAAACTAAAGTACTACGGAACACAAACCCAAGACAACC
* * * * *
195922 -GCAGACATGTTGGA-GAGACACGGACATGACATAT
131 ACCA-ACTTGTCGGAGGA-ACATGAACATGACATAT
* *
195956 ATGCCACCAACAATACACAAAAATAAAATCAAAGAAAGCCTATACTACAATAAAGACTAAAT-TT
1 ATGCCACCAACAATACACAACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
* * *
196020 CCATACATCCAACCAACTTCCAATCAGTCAAACTAAAGTACTACGGAGCACAAACCCAAGACAAC
66 -CACACATCCAACCAACTTTCAATCAGTCAAACTAAAGTACTACGGAACACAAACCCAAGACAAC
*
196085 CACCAACTTGTCGGAGGAACATGGACATGACATAT
130 CACCAACTTGTCGGAGGAACATGAACATGACATAT
* * * * * *
196120 ATGCCATATATGCCACTAACAATATATAACAACACAATCAAAGAATGCCTGT-GTAACAATAAAG
1 ATGCC----A---C-C-AACAATACACAACAATAAAATCAAAGAATGCCTATACT-ACAATAAAG
* ** * * * *
196184 ACTAAATCTCCACTTATCTAACCAACTTTCAATCAGTCAAACTAAAGTCCTACAGAAGACAAACC
56 ACTAAATCTTCACACATCCAACCAACTTTCAATCAGTCAAACTAAAGTACTACGGAACACAAACC
* * * * * *
196249 CGAGACAACCACCGACTGGTTGGAGAAATATGAACATGACATAT
121 CAAGACAACCACCAACTTGTCGGAGGAACATGAACATGACATAT
* *
196293 ATGACACTAACAATACA
1 ATGCCACCAACAATACA
196310 TGACAACACA
Statistics
Matches: 440, Mismatches: 57, Indels: 38
0.82 0.11 0.07
Matches are distributed among these distances:
161 5 0.01
162 139 0.32
163 2 0.00
164 152 0.35
165 4 0.01
166 1 0.00
168 1 0.00
169 1 0.00
171 1 0.00
172 2 0.00
173 131 0.30
174 1 0.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (164 bp):
ATGCCACCAACAATACACAACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
CACACATCCAACCAACTTTCAATCAGTCAAACTAAAGTACTACGGAACACAAACCCAAGACAACC
ACCAACTTGTCGGAGGAACATGAACATGACATAT
Found at i:196219 original size:173 final size:173
Alignment explanation
Indices: 195951--196295 Score: 444
Period size: 173 Copynumber: 2.0 Consensus size: 173
195941 ACGGACATGA
*
195951 CATATATGCCACCAACAATACACAAAAATAAAATCAAAGAAAGCCTATACTACAATAAAGACTAA
1 CATATATGCCACCAACAATACACAAAAACAAAATCAAAGAAAGCCTATACTACAATAAAGACTAA
* *
196016 ATTTCCATACATCCAACCAACTTCCAATCAGTCAAACTAAAGTACTAC-GGAGCACAAACCCAAG
66 ATCTCCATACATCCAACCAACTTCCAATCAGTCAAACTAAAGTACTACAGAAG-ACAAACCCAAG
* * *
196080 ACAACCACCAACTTGTCGGAGGAACATGGACATGACATATATGC
130 ACAACCACCAACTGGTCGGAGAAACATGAACATGACATATATGC
* * * * * * * *
196124 CATATATGCCACTAACAATATATAACAACACAATCAAAGAATGCCTGT-GTAACAATAAAGACTA
1 CATATATGCCACCAACAATACACAAAAACAAAATCAAAGAAAGCCTATACT-ACAATAAAGACTA
* * * * *
196188 AATCTCCACT-TATCTAACCAACTTTCAATCAGTCAAACTAAAGTCCTACAGAAGACAAACCCGA
65 AATCTCCA-TACATCCAACCAACTTCCAATCAGTCAAACTAAAGTACTACAGAAGACAAACCCAA
* * *
196252 GACAACCACCGACTGGTTGGAGAAATATGAACATGACATATATG
129 GACAACCACCAACTGGTCGGAGAAACATGAACATGACATATATG
196296 ACACTAACAA
Statistics
Matches: 147, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
172 1 0.01
173 142 0.97
174 4 0.03
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.20
Consensus pattern (173 bp):
CATATATGCCACCAACAATACACAAAAACAAAATCAAAGAAAGCCTATACTACAATAAAGACTAA
ATCTCCATACATCCAACCAACTTCCAATCAGTCAAACTAAAGTACTACAGAAGACAAACCCAAGA
CAACCACCAACTGGTCGGAGAAACATGAACATGACATATATGC
Found at i:202909 original size:113 final size:114
Alignment explanation
Indices: 202779--203053 Score: 365
Period size: 113 Copynumber: 2.4 Consensus size: 114
202769 ATAGAGTGAT
* *
202779 GAAATTTATTTATTTTATTGGCTCAAATTGAGAATTTAGTATTTACTAGAATTTACATGAACTTA
1 GAAA-TTATTTATTTTATTGGCTCAAATTGAGAGTTTAATATTTACTAGAATTTACATGAACTTA
*
202844 TTTTATTTTATTAACTGTAAAATTCTAGTGTGAGTAGAATGAAGTTACTA
65 TTTTATTTTATTAACTGTAAAATTCTAGAGTGAGTAGAATGAAGTTACTA
* * * *
202894 -AAATTATTTATTTTATTGGTTCAAATTGAGAGTTTAATATTTACTATAATTTACATGCAGTTAT
1 GAAATTATTTATTTTATTGGCTCAAATTGAGAGTTTAATATTTACTAGAATTTACATGAACTTAT
* * * * * *
202958 TTTATTTTATTCATTGTAAAATTTTAGAGTGAGTTGAATTATGTTACTA
66 TTTATTTTATTAACTGTAAAATTCTAGAGTGAGTAGAATGAAGTTACTA
* ** *
203007 GAATTTATTTATTTTACCGGC-CTAAATTGAGAGTTTAATATCTACTA
1 GAAATTATTTATTTTATTGGCTC-AAATTGAGAGTTTAATATTTACTA
203054 TTTATTGTAA
Statistics
Matches: 140, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
113 98 0.70
114 42 0.30
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (114 bp):
GAAATTATTTATTTTATTGGCTCAAATTGAGAGTTTAATATTTACTAGAATTTACATGAACTTAT
TTTATTTTATTAACTGTAAAATTCTAGAGTGAGTAGAATGAAGTTACTA
Found at i:208299 original size:22 final size:21
Alignment explanation
Indices: 208265--208306 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
208255 AATATTGTCT
* *
208265 ATTTTTCAAATAACTTCATAA
1 ATTTTTAAAATAACTACATAA
208286 ATTTTTAAAGATAACTACATA
1 ATTTTTAAA-ATAACTACATA
208307 TATCTTTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTTTAAAATAACTACATAA
Found at i:208689 original size:2 final size:2
Alignment explanation
Indices: 208682--208716 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
208672 TACGGTCACT
208682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
208717 TAATTGTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:211517 original size:267 final size:267
Alignment explanation
Indices: 211042--211575 Score: 822
Period size: 267 Copynumber: 2.0 Consensus size: 267
211032 TGGTTGTCAT
* *
211042 CCCACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACATTCAAGTCGGGTTTAAGTTGGATTC
1 CCCACATCAGTTAAATCCGGGATTGCGTATGCTCTTTACATTCAAGTCAGGTTTAAGTTGGATTC
*
211107 CGTTATATTGTTATTGTTGTTATTGCATGTTCAAGTTTATCACACGATAGGCTATTATATTATCT
66 CGTTATATTGTTATTATTGTTATTGCATGTTCAAGTTTATCACACGATAGGCTATTATATTATCT
211172 GCCTACGGAGTTATTTACTGCAGCCAATTGGTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGTAG
131 GCCTACGGAGTTATTTACTGCAGCCAATTGGTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGTAG
* * *
211237 TTTCCAGGGGATAAGCTTGCTCATTTGGAGGAACTC-GGGTGTCAACCGGTTGATCCAAATGATG
196 TTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCAGGTTG-CAACCGGTTGATCCAAATGATA
211301 TAAGGAAG
260 TAAGGAAG
** * * * * **
211309 CCCACATCAGTTAAATCCTTGATTGTGTATGCTCTTTATATTCGAGTCAGTTTTGGGTTGGATTC
1 CCCACATCAGTTAAATCCGGGATTGCGTATGCTCTTTACATTCAAGTCAGGTTTAAGTTGGATTC
* * *
211374 TGTTGTATTGTTATTATTGTTATTGCATGTTCGAGTTTATCACAC-ATAGGCTATTATATTATCT
66 CGTTATATTGTTATTATTGTTATTGCATGTTCAAGTTTATCACACGATAGGCTATTATATTATCT
* *
211438 GCCTATGGAGGTT-TTTTCTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGT
131 GCCTACGGA-GTTATTTACTGCAGCCAATTGG-TTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGT
* **
211502 AGTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCAGGTTGCAGCCGGTTGATCTGAATGAT
194 AGTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCAGGTTGCAACCGGTTGATCCAAATGAT
211567 ATAAGGAAG
259 ATAAGGAAG
211576 GACCAGAAAT
Statistics
Matches: 242, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
266 44 0.18
267 194 0.80
268 4 0.02
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (267 bp):
CCCACATCAGTTAAATCCGGGATTGCGTATGCTCTTTACATTCAAGTCAGGTTTAAGTTGGATTC
CGTTATATTGTTATTATTGTTATTGCATGTTCAAGTTTATCACACGATAGGCTATTATATTATCT
GCCTACGGAGTTATTTACTGCAGCCAATTGGTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGTAG
TTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCAGGTTGCAACCGGTTGATCCAAATGATAT
AAGGAAG
Found at i:221000 original size:20 final size:21
Alignment explanation
Indices: 220975--221029 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
220965 TAGTTATTCT
220975 TTAAATACTATATTATA-TAA
1 TTAAATACTATATTATATTAA
*
220995 TTAAATAC-ATAATTTTATTAA
1 TTAAATACTAT-ATTATATTAA
*
221016 TTAATTACTATATT
1 TTAAATACTATATT
221030 GTGATTACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.07
20 13 0.43
21 13 0.43
22 2 0.07
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAATACTATATTATATTAA
Found at i:221125 original size:17 final size:17
Alignment explanation
Indices: 221099--221133 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
221089 ACAGGTGTGT
221099 TTTTAGTTTAAATTTTA
1 TTTTAGTTTAAATTTTA
* *
221116 TTTTATTTTAAGTTTTA
1 TTTTAGTTTAAATTTTA
221133 T
1 T
221134 CATGTATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTTAGTTTAAATTTTA
Found at i:223164 original size:267 final size:268
Alignment explanation
Indices: 222689--223218 Score: 821
Period size: 267 Copynumber: 2.0 Consensus size: 268
222679 GTTGTCATCC
*
222689 CACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACATTCGAATCGGCTTTAAGTTGGATTCCG
1 CACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACATTCGAATCAGCTTTAAGTTGGATTCCG
* *
222754 TTATATTGTTATTGTTGTTATTGCATGTTCGAGTTTATCACATGATAGGCTATTATATTATCTGC
66 TTATATTGTTATTGCTGTTATTGCATGTTCGAGTTTATCACATGATAGGCGATTATATTATCTGC
* * ** *
222819 CTATGGAGGTTTTTAGTGCATCCAGTTGGTTTTAGCCTGCCAAAGTTCTTCCACTTTGTTGTAGT
131 CTATGGAGGTTTTTACTGCAGCCAAATGGTTTTAGCCTGCCAAAGTTCTTCCACATTGTTGTAGT
* *
222884 TTCCAGGGGATAAGCCTGCTCATTTGGATGAACTTGGGTTGCAACCGGTTGA-CCAAATGATGTA
196 TTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGATGTA
222948 AGGAAGCT
261 AGGAAGCT
* * * * * ** *
222956 CACATCGGTTAAATCCTGGATTGCGTTTGCTCTTTATATTCGAGTCAGTTTTGGGTTGGATTCTG
1 CACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACATTCGAATCAGCTTTAAGTTGGATTCCG
*
223021 TTGTATTGTTATTGCTGTTATTGCATGTTCGAGTTTATCACACT-ATAGGCGATTATATTATCTG
66 TTATATTGTTATTGCTGTTATTGCATGTTCGAGTTTATCACA-TGATAGGCGATTATATTATCTG
* *
223085 CCTATGGTGGTTTTTACTGCAGCCAAATGGTTTTAGCCTGCCAAAGTTCTTCCCCATTGTTGTAG
130 CCTATGGAGGTTTTTACTGCAGCCAAATGGTTTTAGCCTGCCAAAGTTCTTCCACATTGTTGTAG
* **
223150 TTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACTGGTTGATCTGAATGATGT
195 TTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGATGT
223215 AAGG
260 AAGG
223219 GAGGACCAGA
Statistics
Matches: 237, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
267 223 0.94
268 14 0.06
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (268 bp):
CACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACATTCGAATCAGCTTTAAGTTGGATTCCG
TTATATTGTTATTGCTGTTATTGCATGTTCGAGTTTATCACATGATAGGCGATTATATTATCTGC
CTATGGAGGTTTTTACTGCAGCCAAATGGTTTTAGCCTGCCAAAGTTCTTCCACATTGTTGTAGT
TTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGATGTA
AGGAAGCT
Found at i:225710 original size:16 final size:16
Alignment explanation
Indices: 225690--225744 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
225680 GTTTGGTTCG
225690 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
*
225706 GTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
225722 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
225738 CTGTAAT
1 CTGTAAT
225745 CAGTAATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.27
Consensus pattern (16 bp):
CTGTAATGGAATAGAA
Found at i:225983 original size:58 final size:56
Alignment explanation
Indices: 225914--226059 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 56
225904 AATTTTAATG
*
225914 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
225972 ATTATTATTAAATACAATTTAATAAAATAGTATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAA-A-TATGTAATTTAATAATATTTTTAACATA
*
226030 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
226060 TATAATAATA
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 1 0.01
58 45 0.58
59 17 0.22
60 8 0.10
61 7 0.09
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:230639 original size:26 final size:26
Alignment explanation
Indices: 230610--230666 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
230600 AGCTTTGAAT
* *
230610 TTTATAGTCTAGTTAGTATGATTATA
1 TTTATAGTATAGTTAGTACGATTATA
*
230636 TTTATATTATAGTTAGTACGATTATA
1 TTTATAGTATAGTTAGTACGATTATA
230662 TTTAT
1 TTTAT
230667 GAATCTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.53
Consensus pattern (26 bp):
TTTATAGTATAGTTAGTACGATTATA
Found at i:230878 original size:3 final size:3
Alignment explanation
Indices: 230870--230895 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
230860 TGACACAAGT
230870 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
230896 CCTCAACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:230931 original size:21 final size:21
Alignment explanation
Indices: 230907--230946 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
230897 CTCAACCTCC
*
230907 TTAATTAAGAGAGTGTTAGAG
1 TTAATTAAGAGAGTATTAGAG
230928 TTAATTAAGAGAGTATTAG
1 TTAATTAAGAGAGTATTAG
230947 GGTACTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (21 bp):
TTAATTAAGAGAGTATTAGAG
Found at i:231936 original size:14 final size:13
Alignment explanation
Indices: 231912--231942 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
231902 CTGTCAATAA
231912 TTTGTTTATTCGT
1 TTTGTTTATTCGT
231925 TTTGTATTATTCGT
1 TTTGT-TTATTCGT
231939 TTTG
1 TTTG
231943 CTTTGCCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.68
Consensus pattern (13 bp):
TTTGTTTATTCGT
Found at i:238053 original size:18 final size:18
Alignment explanation
Indices: 238030--238064 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
238020 CAAAATACAT
238030 AGTTTTAGAATCGAATCA
1 AGTTTTAGAATCGAATCA
238048 AGTTTTAGAATCGAATC
1 AGTTTTAGAATCGAATC
238065 TTCAAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (18 bp):
AGTTTTAGAATCGAATCA
Found at i:239956 original size:202 final size:201
Alignment explanation
Indices: 239604--240074 Score: 542
Period size: 202 Copynumber: 2.3 Consensus size: 201
239594 GTTCTATTTG
* * ** * *
239604 TTTATGTTCATTTATCAAGCTAAATAAATGAACATGAACAAGATTTAGAGGCTCGTTTCTT-AAT
1 TTTATGCTCATTTATCAAGCTAAATAAATGAACATGAACAAGATTTTGAGGCTCACTTATTAAAC
* * *
239668 TGAACCAAACACGAACCTAACAAGAACAAGTTTGAAAATAAACTAATATGAACAAAGATTCCTTT
66 TGAACCAAACACGAACCTAACAAGAACAAGTTTGAAAATAAACGAACATGAACAAAGATTCCTTA
* * * ** *
239733 GTCTAAGCTCAGTTCATTTACAGCCGTGAATATATTGATAAACAGTTCATAAATCATTCTGATCC
131 GTCTAACCTCAGTTAATTTACAGCCATGAATATATCCATAAACAGTTCATAAATCATTCAGATCC
*
239798 TGTTCA
196 AGTTCA
* *
239804 TTTATGCTCATTTATCAAACTAAATAAATGAATATGAACAAGATTTTGAAGG-TCAACTTATTAA
1 TTTATGCTCATTTATCAAGCTAAATAAATGAACATGAACAAGATTTTG-AGGCTC-ACTTATTAA
* * *
239868 ACTGAACCAAACACGGACCTAGCACA-AACAAGTTT-AAACATAAACGAACAT-AACCAGAGATT
64 ACTGAACCAAACACGAACCTAACA-AGAACAAGTTTGAAA-ATAAACGAACATGAA-CAAAGATT
* * * *
239930 CCTTAGT-TCAACCTCGGTTAATTTACAGCCATGAATATATCCATGAATAGTTCATAAATCGTTC
126 CCTTAGTCT-AACCTCAGTTAATTTACAGCCATGAATATATCCATAAACAGTTCATAAATCATTC
* * **
239994 AGTTTCAGTTTG
190 AGATCCAGTTCA
* * *
240006 TTTA-GCTTCGTTTATCAAGCTAAATAAATGAACATGAACAATATTTTGAGGCTCACTCATTAAA
1 TTTATGC-TCATTTATCAAGCTAAATAAATGAACATGAACAAGATTTTGAGGCTCACTTATTAAA
240070 CTGAA
65 CTGAA
240075 TCGAACATGA
Statistics
Matches: 228, Mismatches: 34, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
200 46 0.20
201 32 0.14
202 149 0.65
203 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (201 bp):
TTTATGCTCATTTATCAAGCTAAATAAATGAACATGAACAAGATTTTGAGGCTCACTTATTAAAC
TGAACCAAACACGAACCTAACAAGAACAAGTTTGAAAATAAACGAACATGAACAAAGATTCCTTA
GTCTAACCTCAGTTAATTTACAGCCATGAATATATCCATAAACAGTTCATAAATCATTCAGATCC
AGTTCA
Found at i:241950 original size:27 final size:24
Alignment explanation
Indices: 241880--241961 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 24
241870 AATACCAAAC
241880 TTTAATATCAATTTTAAAAAACTAATTTA
1 TTTAATATCAATTTT--AAAA--AA-TTA
241909 TTTAATATCAATTTT-AAAAATTA
1 TTTAATATCAATTTTAAAAAATTA
241932 TTTATATATCAAACTTTTTAAAAAATTA
1 TTTA-ATATC-AA--TTTTAAAAAATTA
241960 TT
1 TT
241962 AAAAAAGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
23 7 0.15
24 7 0.15
25 2 0.04
26 3 0.06
27 4 0.08
28 10 0.21
29 15 0.31
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTAATATCAATTTTAAAAAATTA
Found at i:241955 original size:28 final size:23
Alignment explanation
Indices: 241906--241961 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 23
241896 AAAAACTAAT
241906 TTATTTAATATCAATTTTAAAAA
1 TTATTTAATATCAATTTTAAAAA
241929 TTATTTATATATCAAACTTTTTAAAAAA
1 TTATTTA-ATATC-AA--TTTT-AAAAA
241957 TTATT
1 TTATT
241962 AAAAAAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.25
24 5 0.18
25 2 0.07
27 4 0.14
28 10 0.36
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATTTAATATCAATTTTAAAAA
Found at i:246533 original size:18 final size:18
Alignment explanation
Indices: 246510--246545 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
246500 TGGAAGCTGG
*
246510 TGTTGAGTAGTCTACTGA
1 TGTTGAGCAGTCTACTGA
*
246528 TGTTGAGCAGTCTGCTGA
1 TGTTGAGCAGTCTACTGA
246546 AATGATTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.36
Consensus pattern (18 bp):
TGTTGAGCAGTCTACTGA
Found at i:248820 original size:247 final size:248
Alignment explanation
Indices: 248368--248862 Score: 877
Period size: 247 Copynumber: 2.0 Consensus size: 248
248358 GTATCAGACT
* *
248368 AGTATAAATGAGCATTACTGGCTCAAGATAAGATAGCTTTTGATTACTCAACACTGTTATCTTTT
1 AGTATAAATGAGCATTAATGGCTCAAGATAAGATAGCTTTTGATTACTCAACAATGTTATCTTTT
* *
248433 ATCATTTAGTTCTCTTATTGTTATTCTGATGCTATACCTAAGATCACTGAAAAGTTTTCATGTAA
66 ATCATTTAGTTCTCTTACTGTTATTCTGATACTATACCTAAGATCACTGAAAAGTTTTCATGTAA
* *
248498 TTTGATTCTTAGAATCATTTATGTACGGCCTTTTTTTGTTACTATCGCTTGCACCAATCAAAAAA
131 TTTGATTCTTAGAATCATTTATGTACAGCCTTTCTTTGTTACTATCGCTTGCACCAATCAAAAAA
248563 CTTATTTCTAGGGGTGAAGTTAGAAATTTGCTTTTGGG-AGGGGGAAATTGAG
196 CTTATTTCTAGGGGTGAAGTTAGAAATTTGCTTTTGGGAAGGGGGAAATTGAG
248615 AGTATAAATGAGCATTAATGGCTCAAGATAAGATAGCTTTTGATTACTCAACAATGTTATCTTTT
1 AGTATAAATGAGCATTAATGGCTCAAGATAAGATAGCTTTTGATTACTCAACAATGTTATCTTTT
* * *
248680 ATCATTTGGTTTTCTTGCTGTTATTCTGATACTATACCTAAGATCACTGAAAAGTTTTCATGTAA
66 ATCATTTAGTTCTCTTACTGTTATTCTGATACTATACCTAAGATCACTGAAAAGTTTTCATGTAA
*
248745 TTTGATTGTTAGAATCATTTATGTACAG-CTTTCTTTGTTACTATCGCTTGCACCAATCAAAAAA
131 TTTGATTCTTAGAATCATTTATGTACAGCCTTTCTTTGTTACTATCGCTTGCACCAATCAAAAAA
248809 CTTATTTTCTAGGGGTGAAGTTAGAAATTTGCTTTTGGGAAGGGGGAAATTGAG
196 CTTA-TTTCTAGGGGTGAAGTTAGAAATTTGCTTTTGGGAAGGGGGAAATTGAG
248863 TTATATATTT
Statistics
Matches: 236, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
246 39 0.17
247 183 0.78
248 14 0.06
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (248 bp):
AGTATAAATGAGCATTAATGGCTCAAGATAAGATAGCTTTTGATTACTCAACAATGTTATCTTTT
ATCATTTAGTTCTCTTACTGTTATTCTGATACTATACCTAAGATCACTGAAAAGTTTTCATGTAA
TTTGATTCTTAGAATCATTTATGTACAGCCTTTCTTTGTTACTATCGCTTGCACCAATCAAAAAA
CTTATTTCTAGGGGTGAAGTTAGAAATTTGCTTTTGGGAAGGGGGAAATTGAG
Found at i:250065 original size:16 final size:16
Alignment explanation
Indices: 250052--250088 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
250042 TATCTAAAGT
250052 TGAAA-TGTAATAAAA
1 TGAAATTGTAATAAAA
250067 TGAAATTGTAATAAAAA
1 TGAAATTGTAAT-AAAA
250084 TGAAA
1 TGAAA
250089 ATGAAATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 6 0.30
17 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (16 bp):
TGAAATTGTAATAAAA
Found at i:250212 original size:15 final size:16
Alignment explanation
Indices: 250182--250214 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
250172 TATAATATAT
250182 ATTTTTAAAAATATTA
1 ATTTTTAAAAATATTA
*
250198 ATTTTTAATAA-ATTA
1 ATTTTTAAAAATATTA
250213 AT
1 AT
250215 GCGAAACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTTAAAAATATTA
Found at i:250352 original size:46 final size:47
Alignment explanation
Indices: 250280--250372 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 47
250270 TCGGGCGATC
*
250280 ATTGTTGTGTTTCTTTTATTTTTCCAAGCCTACA-GACCAGCAAGCT
1 ATTGATGTGTTTCTTTTATTTTTCCAAGCCTACAGGACCAGCAAGCT
*
250326 ATTGATGTGTTTCTTTTATTTTTCCAAGCCTACAGGACTAGCAAGCT
1 ATTGATGTGTTTCTTTTATTTTTCCAAGCCTACAGGACCAGCAAGCT
250373 TAGGATACTG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 33 0.75
47 11 0.25
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (47 bp):
ATTGATGTGTTTCTTTTATTTTTCCAAGCCTACAGGACCAGCAAGCT
Found at i:253492 original size:20 final size:20
Alignment explanation
Indices: 253467--253507 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
253457 GTCTACGTAT
*
253467 GTATATATAGTAGGAGAAAG
1 GTATATATACTAGGAGAAAG
253487 GTATATATACTAGGAGAAAG
1 GTATATATACTAGGAGAAAG
253507 G
1 G
253508 ATTGTATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.29, T:0.24
Consensus pattern (20 bp):
GTATATATACTAGGAGAAAG
Found at i:253695 original size:11 final size:10
Alignment explanation
Indices: 253665--253693 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
253655 ACTCCTAATC
253665 CCTTCTTTTT
1 CCTTCTTTTT
253675 CCTTCTTTTT
1 CCTTCTTTTT
253685 CCTT-TTTTT
1 CCTTCTTTTT
253694 TTGTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
CCTTCTTTTT
Found at i:254168 original size:135 final size:134
Alignment explanation
Indices: 253832--254175 Score: 408
Period size: 133 Copynumber: 2.6 Consensus size: 134
253822 CTTTGAGCTA
* * *
253832 ACCCATCAGAAATGCTCATCAACTTAATATTCGTATGAATTCGTGTGAACCTCACTCTTTAACTA
1 ACCCATCAGAAATGTTCATCAACTTAATATTCGTATGAATCCGTGTGAACCTCACTCCTTAACTA
* * * ** ** *
253897 TTTGATATTGAATTCTTGGAATACTAATAGATTTACGGCTCATAAGAGCTTTATTTATTCCTTGA
66 TTTGACATTGAATTCTGGGAATACTAATAAATTTACAACTCATAAGAGCTCCATTTATTCCTCGA
253962 ACCG
131 ACCG
* *
253966 ACCCATTAG-AATGTTCATCAACTTAATATTC--ATGAATCCATGTGAACCTCACTCCTTAACTA
1 ACCCATCAGAAATGTTCATCAACTTAATATTCGTATGAATCCGTGTGAACCTCACTCCTTAACTA
* * ** * *
254028 CTTGACATTGAATTCTCGGGGATACTTGTAAATTTGCAACTTATAAGAGCTCCATTTATTCCTCG
66 TTTGACATTGAATTCT-GGGAATACTAATAAATTTACAACTCATAAGAGCTCCATTTATTCCTCG
* *
254093 AGCTG
130 AACCG
* * * * *
254098 ATCTC-TCAGAAATGTTTATCAACTTAATATTCGTATGAGTCCGTGTGAACATCACTCCTTAACC
1 A-CCCATCAGAAATGTTCATCAACTTAATATTCGTATGAATCCGTGTGAACCTCACTCCTTAACT
254162 ATTTGACATTGAAT
65 ATTTGACATTGAAT
254176 ATTCGGATAT
Statistics
Matches: 176, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
131 42 0.24
132 43 0.24
133 44 0.25
134 8 0.05
135 39 0.22
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (134 bp):
ACCCATCAGAAATGTTCATCAACTTAATATTCGTATGAATCCGTGTGAACCTCACTCCTTAACTA
TTTGACATTGAATTCTGGGAATACTAATAAATTTACAACTCATAAGAGCTCCATTTATTCCTCGA
ACCG
Found at i:254203 original size:135 final size:135
Alignment explanation
Indices: 253760--254228 Score: 437
Period size: 135 Copynumber: 3.5 Consensus size: 135
253750 TTTTTTTTCT
* * * * * * * * *
253760 TATTTGACATTGAATTTTCGGAGATACCCACATATTTACAATTTATACGGGTTTCATTTATTCTT
1 TATTTGACATTGAATTCTCGGAGATACCCACAGATTTACAACTCATAAGAGCTCCATTTATTCCT
* * * * *
253825 TGAGCTAACCCATCAGAAATGCTCATCAACTTAATATTCGTATGAATTCGTGTGAACCTCACTCT
66 CGAGCTGACCCATCAGAAATGTTCATCAACTTAATATTCGTATGAATCCGTGTGAACCTCACTCC
253890 TTAAC
131 TTAAC
* * ** * ** **
253895 TATTTGATATTGAATTCTTGGA-ATACTAATAGATTTACGGCTCATAAGAGCTTTATTTATTCCT
1 TATTTGACATTGAATTCTCGGAGATACCCACAGATTTACAACTCATAAGAGCTCCATTTATTCCT
* * * * *
253959 TGAACCGACCCATTAG-AATGTTCATCAACTTAATATTC--ATGAATCCATGTGAACCTCACTCC
66 CGAGCTGACCCATCAGAAATGTTCATCAACTTAATATTCGTATGAATCCGTGTGAACCTCACTCC
254021 TTAAC
131 TTAAC
* * **** * * *
254026 TACTTGACATTGAATTCTCGGGGATACTTGTAAATTTGCAACTTATAAGAGCTCCATTTATTCCT
1 TATTTGACATTGAATTCTCGGAGATACCCACAGATTTACAACTCATAAGAGCTCCATTTATTCCT
* * * *
254091 CGAGCTGATCTC-TCAGAAATGTTTATCAACTTAATATTCGTATGAGTCCGTGTGAACATCACTC
66 CGAGCTGA-CCCATCAGAAATGTTCATCAACTTAATATTCGTATGAATCCGTGTGAACCTCACTC
254155 CTTAAC
130 CTTAAC
* * * * * ** *
254161 CATTTGACATTGAATAT-TCGGATATACCCGCAGATCTACAACTCATAAAAATTCCATTTATTTC
1 TATTTGACATTGAAT-TCTCGGAGATACCCACAGATTTACAACTCATAAGAGCTCCATTTATTCC
254225 TCGA
65 TCGA
254229 TCCATAAAAA
Statistics
Matches: 267, Mismatches: 61, Indels: 12
0.79 0.18 0.04
Matches are distributed among these distances:
131 44 0.16
132 41 0.15
133 44 0.16
134 41 0.15
135 96 0.36
136 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (135 bp):
TATTTGACATTGAATTCTCGGAGATACCCACAGATTTACAACTCATAAGAGCTCCATTTATTCCT
CGAGCTGACCCATCAGAAATGTTCATCAACTTAATATTCGTATGAATCCGTGTGAACCTCACTCC
TTAAC
Found at i:254875 original size:133 final size:135
Alignment explanation
Indices: 254620--254885 Score: 367
Period size: 133 Copynumber: 2.0 Consensus size: 135
254610 TTTTTTTCCT
*** * **
254620 TATTTGACATTGAATTATCGGGGGTACCCGCAGATTTACAGCTCATAAGGGTTCTGTTTATTCCT
1 TATTTGACATTGAATTATCGGGAAAACCCGCAAATTTACAGCTCATAAGGGTTCCATTTATTCCT
* *
254685 TGGGTCGACACATCAAAAATGTTTGTCAACTTAATATTCGTATGAATCCGTGTGGACCTCAATCC
66 TGGGTCGACACATCAAAAATGTTTATCAACTTAATATTCGTATGAATCCATGTGGACCTCAATCC
254750 TTAAC
131 TTAAC
* *
254755 TATTTG-CATTGAATTTTCGGGAAAACCCTCAAATTTACAGCTCATAAGGGTTCCATTTATTCCT
1 TATTTGACATTGAATTATCGGGAAAACCCGCAAATTTACAGCTCATAAGGGTTCCATTTATTCCT
* * * * *
254819 T-GGTCGATC-CATCAGAAATGTTTATCAACTTAATATTCGTATGAGTCTATGTGGACCTTACTC
66 TGGGTCGA-CACATCAAAAATGTTTATCAACTTAATATTCGTATGAATCCATGTGGACCTCAATC
254882 CTTA
130 CTTA
254886 TCCGCCATCT
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
133 57 0.50
134 52 0.45
135 6 0.05
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (135 bp):
TATTTGACATTGAATTATCGGGAAAACCCGCAAATTTACAGCTCATAAGGGTTCCATTTATTCCT
TGGGTCGACACATCAAAAATGTTTATCAACTTAATATTCGTATGAATCCATGTGGACCTCAATCC
TTAAC
Found at i:256512 original size:25 final size:24
Alignment explanation
Indices: 256470--256520 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
256460 CTAGAAAAAA
256470 AATATTGTTTTAATTTTAATATTG
1 AATATTGTTTTAATTTTAATATTG
256494 AATATT-TTTATATATTTTAATATTG
1 AATATTGTTT-TA-ATTTTAATATTG
256519 AA
1 AA
256521 CTTGACTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 3 0.12
24 8 0.32
25 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (24 bp):
AATATTGTTTTAATTTTAATATTG
Found at i:259012 original size:14 final size:15
Alignment explanation
Indices: 258995--259039 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
258985 GTAATTTTAA
258995 TATATTTTAATAT-T
1 TATATTTTAATATAT
*
259009 TATATTTAAATAGTAT
1 TATATTTTAATA-TAT
259025 TATATATTTAATATA
1 TATAT-TTTAATATA
259040 AATTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 11 0.42
15 1 0.04
16 8 0.31
17 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TATATTTTAATATAT
Found at i:260074 original size:23 final size:23
Alignment explanation
Indices: 260043--260086 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
260033 AGTCTGTTTA
**
260043 TTTTAATTTTTTGTAATTTAATT
1 TTTTAATTTTTTAAAATTTAATT
*
260066 TTTTTATTTTTTAAAATTTAA
1 TTTTAATTTTTTAAAATTTAA
260087 AATTTAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTAATTTTTTAAAATTTAATT
Found at i:263325 original size:35 final size:36
Alignment explanation
Indices: 263254--263325 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
263244 CGTCAAGCTT
263254 AATAAATTTTATCCATAAGATATGAGTGTTGGATAA
1 AATAAATTTTATCCATAAGATATGAGTGTTGGATAA
* *
263290 AATAGATTTTATCCATAAGAT-TGAGTGTTGTATAA
1 AATAAATTTTATCCATAAGATATGAGTGTTGGATAA
263325 A
1 A
263326 GATCGTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 14 0.41
36 20 0.59
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (36 bp):
AATAAATTTTATCCATAAGATATGAGTGTTGGATAA
Found at i:273639 original size:23 final size:23
Alignment explanation
Indices: 273608--273670 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
273598 TTTGTATTTT
*
273608 TGTTGTGATGCTGTTTTTTTTAC
1 TGTTTTGATGCTGTTTTTTTTAC
273631 TGTTTTGATGCTG-TTTTTTTAC
1 TGTTTTGATGCTGTTTTTTTTAC
* *
273653 TGTTTTGGTGTTGTTTTT
1 TGTTTTGATGCTGTTTTT
273671 GCTGTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.65
Consensus pattern (23 bp):
TGTTTTGATGCTGTTTTTTTTAC
Found at i:273647 original size:20 final size:21
Alignment explanation
Indices: 273608--273678 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
273598 TTTGTATTTT
*
273608 TGTTGTGATGCTGTTTTTTTTAC
1 TGTTTTGATGCTG--TTTTTTAC
273631 TGTTTTGATGCTGTTTTTTTAC
1 TGTTTTGATGCTG-TTTTTTAC
* * *
273653 TGTTTTGGTGTTG-TTTTTGC
1 TGTTTTGATGCTGTTTTTTAC
273673 TGTTTT
1 TGTTTT
273679 TTTTGTTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 12 0.27
22 20 0.45
23 12 0.27
ACGTcount: A:0.06, C:0.07, G:0.23, T:0.65
Consensus pattern (21 bp):
TGTTTTGATGCTGTTTTTTAC
Found at i:273680 original size:11 final size:11
Alignment explanation
Indices: 273616--273741 Score: 69
Period size: 12 Copynumber: 11.2 Consensus size: 11
273606 TTTGTTGTGA
273616 TGCTGTTTTTTT
1 TGCTG-TTTTTT
* **
273628 TACTGTTTTGA
1 TGCTGTTTTTT
273639 TGCTGTTTTTT
1 TGCTGTTTTTT
*
273650 TACTG---TTT
1 TGCTGTTTTTT
*
273658 TGGTGTTGTTTT
1 TGCTGTT-TTTT
273670 TGCTGTTTTTTT
1 TGCTG-TTTTTT
*
273682 TGTTGTTATTTT
1 TGCTGTT-TTTT
273694 TGCTGTTATTTT
1 TGCTGTT-TTTT
* **
273706 TGTTGCCGTTTT
1 TGCTG-TTTTTT
* *
273718 TGTTGTTATTT
1 TGCTGTTTTTT
*
273729 TGCTGTTGTTT
1 TGCTGTTTTTT
273740 TG
1 TG
273742 GTTGTTTGGA
Statistics
Matches: 87, Mismatches: 20, Indels: 15
0.71 0.16 0.12
Matches are distributed among these distances:
8 6 0.07
11 32 0.37
12 47 0.54
13 2 0.02
ACGTcount: A:0.05, C:0.07, G:0.21, T:0.67
Consensus pattern (11 bp):
TGCTGTTTTTT
Found at i:273688 original size:24 final size:24
Alignment explanation
Indices: 273655--273740 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 24
273645 TTTTTTACTG
*
273655 TTTTGGTGTTGTTTTTGCTGTTTT
1 TTTTGTTGTTGTTTTTGCTGTTTT
* *
273679 TTTTGTTGTTATTTTTGCTGTTAT
1 TTTTGTTGTTGTTTTTGCTGTTTT
** * *
273703 TTTTGTTGCCGTTTTTGTTG-TTA
1 TTTTGTTGTTGTTTTTGCTGTTTT
*
273726 TTTTGCTGTTGTTTT
1 TTTTGTTGTTGTTTT
273741 GGTTGTTTGG
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 13 0.26
24 37 0.74
ACGTcount: A:0.03, C:0.06, G:0.21, T:0.70
Consensus pattern (24 bp):
TTTTGTTGTTGTTTTTGCTGTTTT
Found at i:273706 original size:36 final size:35
Alignment explanation
Indices: 273655--273740 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 35
273645 TTTTTTACTG
* ***
273655 TTTTGGTGTTGTTTTTGCTGTTTTTTTTGTTGTTA
1 TTTTGCTGTTGTTTTTGCTGCCGTTTTTGTTGTTA
* *
273690 TTTTTGCTGTTATTTTTGTTGCCGTTTTTGTTGTTA
1 -TTTTGCTGTTGTTTTTGCTGCCGTTTTTGTTGTTA
273726 TTTTGCTGTTGTTTT
1 TTTTGCTGTTGTTTT
273741 GGTTGTTTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 14 0.33
36 29 0.67
ACGTcount: A:0.03, C:0.06, G:0.21, T:0.70
Consensus pattern (35 bp):
TTTTGCTGTTGTTTTTGCTGCCGTTTTTGTTGTTA
Found at i:273747 original size:12 final size:12
Alignment explanation
Indices: 273655--273747 Score: 80
Period size: 12 Copynumber: 7.8 Consensus size: 12
273645 TTTTTTACTG
*
273655 TTTTGGTGTTGT
1 TTTTGTTGTTGT
* *
273667 TTTTGCTGTTTT
1 TTTTGTTGTTGT
*
273679 TTTTGTTGTTAT
1 TTTTGTTGTTGT
* *
273691 TTTTGCTGTTAT
1 TTTTGTTGTTGT
**
273703 TTTTGTTGCCGT
1 TTTTGTTGTTGT
*
273715 TTTTGTTGTT-A
1 TTTTGTTGTTGT
*
273726 TTTTGCTGTTGT
1 TTTTGTTGTTGT
*
273738 TTTGGTTGTT
1 TTTTGTTGTT
273748 TGGATGTTAT
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
11 9 0.14
12 55 0.86
ACGTcount: A:0.03, C:0.05, G:0.23, T:0.69
Consensus pattern (12 bp):
TTTTGTTGTTGT
Found at i:279516 original size:16 final size:16
Alignment explanation
Indices: 279495--279530 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
279485 AGAGATGGGG
279495 TATCTATACTCAATTT
1 TATCTATACTCAATTT
279511 TATCTATACTCAATTT
1 TATCTATACTCAATTT
279527 TATC
1 TATC
279531 ATTCAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (16 bp):
TATCTATACTCAATTT
Found at i:286079 original size:17 final size:17
Alignment explanation
Indices: 286052--286094 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
286042 AAATTTAAAC
286052 ATTTT-ATTAAAATAAT
1 ATTTTAATTAAAATAAT
*
286068 ATTTTAATTAAAATCAT
1 ATTTTAATTAAAATAAT
*
286085 -TTTTATTTAA
1 ATTTTAATTAA
286095 TAAATTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAATTAAAATAAT
Found at i:286094 original size:16 final size:16
Alignment explanation
Indices: 286052--286091 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
286042 AAATTTAAAC
286052 ATTTTATTAAAATAAT
1 ATTTTATTAAAATAAT
*
286068 ATTTTAATTAAAATCAT
1 ATTTT-ATTAAAATAAT
286085 -TTTTATT
1 ATTTTATT
286092 TAATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 9 0.41
17 10 0.45
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATTAAAATAAT
Found at i:286865 original size:1 final size:1
Alignment explanation
Indices: 286859--286885 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
286849 TTCTCTTTCT
286859 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
286886 GACACTGCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:294510 original size:26 final size:27
Alignment explanation
Indices: 294475--294527 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
294465 TAAATTAGTC
*
294475 TTTCTGTT-AAAATATAATCTAAAATT
1 TTTCTATTAAAAATATAATCTAAAATT
* *
294501 TTTCTATTAAAAATGTAATTTAAAATT
1 TTTCTATTAAAAATATAATCTAAAATT
294528 CATAGTACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (27 bp):
TTTCTATTAAAAATATAATCTAAAATT
Found at i:298027 original size:21 final size:20
Alignment explanation
Indices: 298003--298065 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
297993 AAAACGCATA
*
298003 AAAAAATAACATTCAAACAAT
1 AAAAAATAACA-ACAAACAAT
298024 -AAAAATAACAACCAAAACAAT
1 AAAAAATAACAA-C-AAACAAT
298045 AGCAAAAATAACAACAAACAA
1 A--AAAAATAACAACAAACAA
298066 CATTAAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 11 0.31
21 7 0.19
22 6 0.17
23 1 0.03
24 11 0.31
ACGTcount: A:0.70, C:0.17, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAAATAACAACAAACAAT
Found at i:298158 original size:22 final size:21
Alignment explanation
Indices: 298126--298215 Score: 96
Period size: 22 Copynumber: 4.3 Consensus size: 21
298116 AGTAACAACT
*
298126 AAAACAATAAAAAAAAGTCACC
1 AAAACAGTAAAAAAAAG-CACC
*
298148 AAAACAGT---AAAAAGCACA
1 AAAACAGTAAAAAAAAGCACC
* *
298166 AAAACAGCAAAAAATAGCAACC
1 AAAACAGTAAAAAAAAGC-ACC
298188 AAAACAGTAAAAAAATAGCACC
1 AAAACAGTAAAAAAA-AGCACC
298210 AAAACA
1 AAAACA
298216 ACAATATAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
18 10 0.18
19 6 0.11
21 6 0.11
22 31 0.55
23 3 0.05
ACGTcount: A:0.67, C:0.19, G:0.08, T:0.07
Consensus pattern (21 bp):
AAAACAGTAAAAAAAAGCACC
Found at i:298169 original size:18 final size:19
Alignment explanation
Indices: 298137--298178 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
298127 AAACAATAAA
* *
298137 AAAAAGTCACCAAAACAGT
1 AAAAAGTCACAAAAACAGC
298156 AAAAAG-CACAAAAACAGC
1 AAAAAGTCACAAAAACAGC
298174 AAAAA
1 AAAAA
298179 ATAGCAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.05
Consensus pattern (19 bp):
AAAAAGTCACAAAAACAGC
Found at i:310749 original size:8 final size:8
Alignment explanation
Indices: 310736--310773 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
310726 TCAATTAAAT
310736 TAATTTTA
1 TAATTTTA
310744 TAATTTT-
1 TAATTTTA
*
310751 TAATATTA
1 TAATTTTA
*
310759 TTATTTTA
1 TAATTTTA
310767 TAATTTT
1 TAATTTT
310774 TTATTATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TAATTTTA
Found at i:310787 original size:21 final size:22
Alignment explanation
Indices: 310738--310786 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
310728 AATTAAATTA
310738 ATTTTATAATTTTTAATATTATT
1 ATTTTATAATTTTT-ATATTATT
310761 ATTTTATAATTTTT-TATTATTT
1 ATTTTATAATTTTTATATTA-TT
310783 ATTT
1 ATTT
310787 AATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 5 0.20
22 6 0.24
23 14 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTTTATAATTTTTATATTATT
Found at i:311653 original size:3 final size:3
Alignment explanation
Indices: 311647--311677 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
311637 TGATTAGCAC
311647 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
311678 GTCAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:325634 original size:24 final size:24
Alignment explanation
Indices: 325581--325645 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
325571 AATAATTTAT
325581 GTATCAAATTAAAA-AAATTTAAA
1 GTATCAAATTAAAATAAATTTAAA
* *
325604 GTGTCAAATTAAAATTAAA-TTCAA
1 GTATCAAATTAAAA-TAAATTTAAA
*
325628 GTATCAAATTGAAATAAA
1 GTATCAAATTAAAATAAA
325646 AAATTTCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.47
24 16 0.44
25 3 0.08
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (24 bp):
GTATCAAATTAAAATAAATTTAAA
Found at i:328841 original size:3 final size:3
Alignment explanation
Indices: 328833--328866 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
328823 AGTCTTAAAA
328833 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
328867 CATGGCCGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:336523 original size:32 final size:35
Alignment explanation
Indices: 336477--336544 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 35
336467 ATTTTCTTTT
*
336477 AAAAATTTTAATTAAACC-C-T-AATTTTTTAAAA
1 AAAAATTTTAATTAAACCTCTTAAAATTTTTAAAA
336509 AAAAATTCTT-ATTAAACCTCTTAAAATTTTTAAAA
1 AAAAATT-TTAATTAAACCTCTTAAAATTTTTAAAA
336544 A
1 A
336545 TTTCAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 15 0.48
33 3 0.10
34 1 0.03
35 12 0.39
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (35 bp):
AAAAATTTTAATTAAACCTCTTAAAATTTTTAAAA
Found at i:337405 original size:20 final size:20
Alignment explanation
Indices: 337355--337405 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
337345 AAACTTACAC
337355 TCGAAACCT-AATATAAAGT
1 TCGAAACCTAAATATAAAGT
*
337374 T-TAAACCCTAAATCATAAA-T
1 TCGAAA-CCTAAAT-ATAAAGT
337394 TCGAAACCTAAA
1 TCGAAACCTAAA
337406 CTTGAGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 3 0.12
19 4 0.15
20 11 0.42
21 8 0.31
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.25
Consensus pattern (20 bp):
TCGAAACCTAAATATAAAGT
Done.