Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 1 of 135
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--69 Score: 138
Period size: 7 Copynumber: 9.9 Consensus size: 7
1 AAGCCCT
1 AAGCCCT
8 AAGCCCT
1 AAGCCCT
15 AAGCCCT
1 AAGCCCT
22 AAGCCCT
1 AAGCCCT
29 AAGCCCT
1 AAGCCCT
36 AAGCCCT
1 AAGCCCT
43 AAGCCCT
1 AAGCCCT
50 AAGCCCT
1 AAGCCCT
57 AAGCCCT
1 AAGCCCT
64 AAGCCC
1 AAGCCC
70 CGAGCCCCGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.29, C:0.43, G:0.14, T:0.13
Consensus pattern (7 bp):
AAGCCCT
Found at i:75 original size:7 final size:7
Alignment explanation
Indices: 65--561 Score: 493
Period size: 7 Copynumber: 71.9 Consensus size: 7
55 CTAAGCCCTA
65 AGCCCCG
1 AGCCCCG
72 AGCCCCG
1 AGCCCCG
*
79 AACCCCG
1 AGCCCCG
*
86 A-ACCCG
1 AGCCCCG
*
92 AACCCCG
1 AGCCCCG
*
99 AACCCCG
1 AGCCCCG
*
106 AACCCCG
1 AGCCCCG
*
113 AACCCCG
1 AGCCCCG
*
120 AACCCCG
1 AGCCCCG
*
127 AACCCCG
1 AGCCCCG
*
134 AACCCCG
1 AGCCCCG
*
141 AACCCCG
1 AGCCCCG
*
148 AACCCCG
1 AGCCCCG
*
155 AACCCCG
1 AGCCCCG
*
162 AACCCCG
1 AGCCCCG
*
169 ACCCCCCCG
1 A--GCCCCG
*
178 ACCCCCG
1 AGCCCCG
*
185 ACCCCCG
1 AGCCCCG
*
192 ACCCCCG
1 AGCCCCG
199 A-CCCC-
1 AGCCCCG
204 AGACCCC-
1 AG-CCCCG
211 AGACCCC-
1 AG-CCCCG
218 AGACCCC-
1 AG-CCCCG
225 AGACCCC-
1 AG-CCCCG
*
232 AGACCCG
1 AGCCCCG
239 AGACCCC-
1 AG-CCCCG
*
246 AGACCCG
1 AGCCCCG
*
253 AGACCCG
1 AGCCCCG
260 AGCCCCG
1 AGCCCCG
267 AG-CCCG
1 AGCCCCG
273 AGCCCCG
1 AGCCCCG
280 AG-CCCG
1 AGCCCCG
286 AGCCCCG
1 AGCCCCG
293 AGCCCCG
1 AGCCCCG
300 AGCCCCG
1 AGCCCCG
307 AGCCCCG
1 AGCCCCG
314 AG-CCCG
1 AGCCCCG
320 AGCCCCG
1 AGCCCCG
327 AGCCCCG
1 AGCCCCG
334 AGCCCCG
1 AGCCCCG
341 AGCCCCG
1 AGCCCCG
348 AGCCCCG
1 AGCCCCG
355 AGCCCCG
1 AGCCCCG
362 AGCCCCG
1 AGCCCCG
369 AGCCCCG
1 AGCCCCG
376 AGCCCCG
1 AGCCCCG
383 AGCCCCG
1 AGCCCCG
390 AGCCCCG
1 AGCCCCG
397 AGCCCCG
1 AGCCCCG
404 AGCCCCG
1 AGCCCCG
411 AGCCCCG
1 AGCCCCG
418 AGCCCCG
1 AGCCCCG
425 AGCCCCG
1 AGCCCCG
432 AGCCCCG
1 AGCCCCG
439 AGCCCCG
1 AGCCCCG
**
446 AGCCCTA
1 AGCCCCG
*
453 AACCCC-
1 AGCCCCG
459 AGACCCC-
1 AG-CCCCG
466 AGACCCC-
1 AG-CCCCG
*
473 AGACCCG
1 AGCCCCG
*
480 AACCCCG
1 AGCCCCG
* *
487 A-ACCCT
1 AGCCCCG
** *
493 AAACCCT
1 AGCCCCG
** *
500 AAACCCT
1 AGCCCCG
**
507 AAACCCG
1 AGCCCCG
514 AGCCCCG
1 AGCCCCG
521 AGCCCCG
1 AGCCCCG
528 AGCCCCG
1 AGCCCCG
535 AGCCCCG
1 AGCCCCG
542 AGCCCCG
1 AGCCCCG
549 AGCCCCG
1 AGCCCCG
556 AGCCCC
1 AGCCCC
562 AAAACCCGAA
Statistics
Matches: 455, Mismatches: 21, Indels: 28
0.90 0.04 0.06
Matches are distributed among these distances:
5 1 0.00
6 41 0.09
7 404 0.89
8 3 0.01
9 6 0.01
ACGTcount: A:0.21, C:0.57, G:0.21, T:0.01
Consensus pattern (7 bp):
AGCCCCG
Found at i:114 original size:21 final size:21
Alignment explanation
Indices: 67--658 Score: 326
Period size: 21 Copynumber: 28.5 Consensus size: 21
57 AAGCCCTAAG
*
67 CCCCGAGCCCCGAACCCCGAA
1 CCCCGAACCCCGAACCCCGAA
88 -CCCGAACCCCGAACCCCGAA
1 CCCCGAACCCCGAACCCCGAA
108 CCCCGAACCCCGAACCCCGAA
1 CCCCGAACCCCGAACCCCGAA
129 CCCCGAACCCCGAACCCCGAA
1 CCCCGAACCCCGAACCCCGAA
*
150 CCCCGAACCCCGAACCCCGACCC
1 CCCCGAACCCCGAACCCCGA--A
* * *
173 CCCCGACCCCCGACCCCCGAC
1 CCCCGAACCCCGAACCCCGAA
194 CCCCG-ACCCC-AGACCCC-AGA
1 CCCCGAACCCCGA-ACCCCGA-A
214 CCCC-AGACCCC-AGACCCC-AGA
1 CCCCGA-ACCCCGA-ACCCCGA-A
235 -CCCGAGACCCC-AGA-CCCGAGA
1 CCCCGA-ACCCCGA-ACCCCGA-A
* * *
256 -CCCGAGCCCCG-AGCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* * *
275 CCCCG-AGCCCGAGCCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* *
295 CCCCGAGCCCCGAGCCCCG-A
1 CCCCGAACCCCGAACCCCGAA
* * * *
315 GCCCGAGCCCCGAGCCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* * *
336 CCCCGAGCCCCGAGCCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* * *
357 CCCCGAGCCCCGAGCCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* * *
378 CCCCGAGCCCCGAGCCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* * *
399 CCCCGAGCCCCGAGCCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* * *
420 CCCCGAGCCCCGAGCCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* **
441 CCCCGAGCCCTAAACCCC-AGA
1 CCCCGAACCCCGAACCCCGA-A
462 CCCC-AGACCCC-AGA-CCCGAA
1 CCCCGA-ACCCCGA-ACCCCGAA
* * *
482 CCCCGAA-CCCTAAACCCTAA
1 CCCCGAACCCCGAACCCCGAA
* * * * *
502 ACCCTAAACCCGAGCCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* * *
523 CCCCGAGCCCCGAGCCCCGAG
1 CCCCGAACCCCGAACCCCGAA
* * *
544 CCCCGAGCCCCGAGCCCCAAA
1 CCCCGAACCCCGAACCCCGAA
* *
565 ACCCGAAACCCGAAGCCCC-AA
1 CCCCGAACCCCGAA-CCCCGAA
* ** * *
586 GCCC-AAAACCAAACCCCTAA
1 CCCCGAACCCCGAACCCCGAA
* * * * *
606 ACCCTAAACCCTAACCCCTAA
1 CCCCGAACCCCGAACCCCGAA
* * *
627 CCCCTAACCCCTAACCCCTAA
1 CCCCGAACCCCGAACCCCGAA
*
648 CCCCTAACCCC
1 CCCCGAACCCC
659 AGACCCCAGA
Statistics
Matches: 494, Mismatches: 51, Indels: 52
0.83 0.09 0.09
Matches are distributed among these distances:
19 15 0.03
20 114 0.23
21 343 0.69
22 4 0.01
23 18 0.04
ACGTcount: A:0.24, C:0.56, G:0.18, T:0.02
Consensus pattern (21 bp):
CCCCGAACCCCGAACCCCGAA
Found at i:612 original size:7 final size:7
Alignment explanation
Indices: 600--838 Score: 106
Period size: 7 Copynumber: 34.4 Consensus size: 7
590 AAAACCAAAC
600 CCCTAAA
1 CCCTAAA
607 CCCTAAA
1 CCCTAAA
*
614 CCCTAAC
1 CCCTAAA
*
621 CCCTAAC
1 CCCTAAA
*
628 CCCTAAC
1 CCCTAAA
*
635 CCCTAAC
1 CCCTAAA
*
642 CCCTAAC
1 CCCTAAA
649 CCCT-AA
1 CCCTAAA
* *
655 CCCCAGA
1 CCCTAAA
* *
662 CCCCAGA
1 CCCTAAA
* *
669 CCCCAGA
1 CCCTAAA
* *
676 CCCCAGA
1 CCCTAAA
* *
683 CCCCAGA
1 CCCTAAA
* *
690 CCCCAGA
1 CCCTAAA
* *
697 CCCCAGA
1 CCCTAAA
* *
704 CCCCAGA
1 CCCTAAA
711 CCCTAAA
1 CCCTAAA
718 CCCTAAA
1 CCCTAAA
725 CCCTAAA
1 CCCTAAA
*
732 ACCTAAA
1 CCCTAAA
739 CCCTAAA
1 CCCTAAA
* *
746 CCC-GAG
1 CCCTAAA
752 CCCTAAAA
1 CCCT-AAA
*
760 CCC-GAA
1 CCCTAAA
**
766 CCCCGAA
1 CCCTAAA
*
773 CCCTAGA
1 CCCTAAA
*
780 CCCTAGA
1 CCCTAAA
*
787 CCCTAGA
1 CCCTAAA
* *
794 CCCCAAG
1 CCCTAAA
* *
801 CCCCAAG
1 CCCTAAA
808 CCCTAAA
1 CCCTAAA
* *
815 CCCCAGA
1 CCCTAAA
**
822 CCCCGAA
1 CCCTAAA
829 CCCTAAA
1 CCCTAAA
836 CCC
1 CCC
839 CGGACCCCGG
Statistics
Matches: 201, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
6 13 0.06
7 184 0.92
8 4 0.02
ACGTcount: A:0.33, C:0.51, G:0.08, T:0.08
Consensus pattern (7 bp):
CCCTAAA
Found at i:720 original size:21 final size:21
Alignment explanation
Indices: 649--882 Score: 125
Period size: 21 Copynumber: 11.6 Consensus size: 21
639 AACCCCTAAC
649 CCCT-AACCCCAGACCCCAGA
1 CCCTAAACCCCAGACCCCAGA
* *
669 CCCCAGACCCCAGACCCCAGA
1 CCCTAAACCCCAGACCCCAGA
* *
690 CCCCAGACCCCAGACCCCAGA
1 CCCTAAACCCCAGACCCCAGA
* * * *
711 CCCTAAACCCTAAACCCTAAA
1 CCCTAAACCCCAGACCCCAGA
* * * *
732 ACCTAAACCCTAAACCCGAG-
1 CCCTAAACCCCAGACCCCAGA
*
752 CCCTAAAACCC-GAACCCC-G-
1 CCCTAAACCCCAG-ACCCCAGA
* *
771 -----AACCCTAGACCCTAGA
1 CCCTAAACCCCAGACCCCAGA
*
787 CCCTAGACCCCAAG-CCCCAAG-
1 CCCTAAACCCC-AGACCCC-AGA
808 CCCTAAACCCCAGACCCC-GAA
1 CCCTAAACCCCAGACCCCAG-A
* *
829 CCCTAAACCCCGGACCCCGGA
1 CCCTAAACCCCAGACCCCAGA
* * * *
850 CCCGAGACCCGAGACCCGAGA
1 CCCTAAACCCCAGACCCCAGA
* *
871 CCCGAGACCCCA
1 CCCTAAACCCCA
883 AGCCCCCAAG
Statistics
Matches: 167, Mismatches: 31, Indels: 31
0.73 0.14 0.14
Matches are distributed among these distances:
14 8 0.05
15 2 0.01
19 2 0.01
20 17 0.10
21 133 0.80
22 5 0.03
ACGTcount: A:0.32, C:0.50, G:0.13, T:0.05
Consensus pattern (21 bp):
CCCTAAACCCCAGACCCCAGA
Found at i:858 original size:7 final size:7
Alignment explanation
Indices: 844--880 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
834 AACCCCGGAC
844 CCCG-GA
1 CCCGAGA
850 CCCGAGA
1 CCCGAGA
857 CCCGAGA
1 CCCGAGA
864 CCCGAGA
1 CCCGAGA
871 CCCGAGA
1 CCCGAGA
878 CCC
1 CCC
881 CAAGCCCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.24, C:0.49, G:0.27, T:0.00
Consensus pattern (7 bp):
CCCGAGA
Found at i:858 original size:14 final size:15
Alignment explanation
Indices: 837--880 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
827 AACCCTAAAC
837 CCCG-GACCCCG-GA
1 CCCGAGACCCCGAGA
850 CCCGAGA-CCCGAGA
1 CCCGAGACCCCGAGA
864 CCCGAGA-CCCGAGA
1 CCCGAGACCCCGAGA
878 CCC
1 CCC
881 CAAGCCCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.28
14 21 0.72
ACGTcount: A:0.23, C:0.50, G:0.27, T:0.00
Consensus pattern (15 bp):
CCCGAGACCCCGAGA
Found at i:891 original size:8 final size:8
Alignment explanation
Indices: 878--910 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
868 AGACCCGAGA
878 CCCCAAGC
1 CCCCAAGC
886 CCCCAAGC
1 CCCCAAGC
894 CCCCAAG-
1 CCCCAAGC
901 CCCCAAGC
1 CCCCAAGC
909 CC
1 CC
911 AAATCTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.24, C:0.64, G:0.12, T:0.00
Consensus pattern (8 bp):
CCCCAAGC
Found at i:904 original size:15 final size:16
Alignment explanation
Indices: 878--910 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
868 AGACCCGAGA
878 CCCCAAGCCCCCAAGC
1 CCCCAAGCCCCCAAGC
894 CCCCAAG-CCCCAAGC
1 CCCCAAGCCCCCAAGC
909 CC
1 CC
911 AAATCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.24, C:0.64, G:0.12, T:0.00
Consensus pattern (16 bp):
CCCCAAGCCCCCAAGC
Found at i:927 original size:7 final size:7
Alignment explanation
Indices: 917--1045 Score: 85
Period size: 7 Copynumber: 19.0 Consensus size: 7
907 GCCCAAATCT
917 AAAACCC
1 AAAACCC
924 AAAACCTC
1 AAAACC-C
*
932 -AACCCC
1 AAAACCC
938 AAAACCC
1 AAAACCC
945 -AAACCC
1 AAAACCC
*
951 TAAACCC
1 AAAACCC
*
958 TAAACCCCC
1 -AAA-ACCC
*
967 TAAACCC
1 AAAACCC
974 -AAACCC
1 AAAACCC
980 -AAACCC
1 AAAACCC
986 -AAA-CC
1 AAAACCC
*
991 TAAA-CC
1 AAAACCC
*
997 TAAACCC
1 AAAACCC
*
1004 AAACCCC
1 AAAACCC
1011 AAAACCC
1 AAAACCC
1018 AAAACCTC
1 AAAACC-C
*
1026 GAAA-CC
1 AAAACCC
1032 AAAACCC
1 AAAACCC
*
1039 CAAACCC
1 AAAACCC
1046 TTTAACCTAC
Statistics
Matches: 101, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
5 2 0.02
6 35 0.35
7 52 0.51
8 9 0.09
9 3 0.03
ACGTcount: A:0.48, C:0.46, G:0.01, T:0.05
Consensus pattern (7 bp):
AAAACCC
Found at i:940 original size:14 final size:13
Alignment explanation
Indices: 918--1045 Score: 109
Period size: 14 Copynumber: 9.5 Consensus size: 13
908 CCCAAATCTA
918 AAACCCAAAACCTC
1 AAACCCAAAACC-C
*
932 AACCCCAAAACCC
1 AAACCCAAAACCC
*
945 AAACCCTAAACCC
1 AAACCCAAAACCC
*
958 TAAACCCCCTAAACCC
1 -AAA--CCCAAAACCC
974 AAACCC-AAACCC
1 AAACCCAAAACCC
* *
986 AAA-CCTAAACCT
1 AAACCCAAAACCC
*
998 AAACCCAAACCCC
1 AAACCCAAAACCC
1011 AAAACCCAAAACCTC
1 -AAACCCAAAACC-C
1026 GAAA-CCAAAACCCC
1 -AAACCCAAAA-CCC
1040 AAACCC
1 AAACCC
1046 TTTAACCTAC
Statistics
Matches: 96, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
11 2 0.02
12 17 0.18
13 24 0.25
14 34 0.35
15 9 0.09
16 10 0.10
ACGTcount: A:0.48, C:0.46, G:0.01, T:0.05
Consensus pattern (13 bp):
AAACCCAAAACCC
Found at i:948 original size:6 final size:6
Alignment explanation
Indices: 918--1045 Score: 94
Period size: 6 Copynumber: 19.0 Consensus size: 6
908 CCCAAATCTA
*
918 AAACCC AAAACCTC AACCCC AAAACCC AAACCC TAAACCC TAAACCCCC
1 AAACCC -AAACC-C AAACCC -AAACCC AAACCC -AAACCC -AAA--CCC
* *
967 TAAACCC AAACCC AAACCC AAACCT AAACCT AAACCC AAACCCC AAAACCC
1 -AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAA-CCC -AAACCC
*
1018 AAAACCTC GAAACCA AAACCCC AAACCC
1 -AAACC-C -AAACCC AAA-CCC AAACCC
1046 TTTAACCTAC
Statistics
Matches: 105, Mismatches: 7, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
6 44 0.42
7 44 0.42
8 10 0.10
9 7 0.07
ACGTcount: A:0.48, C:0.46, G:0.01, T:0.05
Consensus pattern (6 bp):
AAACCC
Found at i:969 original size:16 final size:15
Alignment explanation
Indices: 934--1039 Score: 71
Period size: 15 Copynumber: 7.2 Consensus size: 15
924 AAAACCTCAA
*
934 CCCCAAAACCCAAA-
1 CCCCTAAACCCAAAC
948 -CCCTAAACCCTAAAC
1 CCCCTAAACCC-AAAC
963 CCCCTAAACCCAAA-
1 CCCCTAAACCCAAAC
977 -CCC-AAACCCAAAC
1 CCCCTAAACCCAAAC
*
990 CTAAACCTAAACCCAAA-
1 C---CCCTAAACCCAAAC
* *
1007 CCCCAAAACCCAAAA
1 CCCCTAAACCCAAAC
* * *
1022 CCTCGAAACCAAAAC
1 CCCCTAAACCCAAAC
1037 CCC
1 CCC
1040 AAACCCTTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
12 9 0.12
13 12 0.16
14 14 0.19
15 16 0.22
16 10 0.14
17 3 0.04
18 9 0.12
ACGTcount: A:0.46, C:0.47, G:0.01, T:0.06
Consensus pattern (15 bp):
CCCCTAAACCCAAAC
Found at i:2462 original size:14 final size:14
Alignment explanation
Indices: 2443--2472 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2433 TAGATAGGTT
2443 CAATTATATATTCC
1 CAATTATATATTCC
2457 CAATTATATATTCC
1 CAATTATATATTCC
2471 CA
1 CA
2473 TTCAACAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (14 bp):
CAATTATATATTCC
Found at i:3316 original size:12 final size:12
Alignment explanation
Indices: 3299--3336 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
3289 TTACACTACC
3299 AATGAAAGAAGT
1 AATGAAAGAAGT
3311 AATGAAAGAAGT
1 AATGAAAGAAGT
3323 AATGAAAGAAGT
1 AATGAAAGAAGT
3335 AA
1 AA
3337 CAGATTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AATGAAAGAAGT
Found at i:4072 original size:19 final size:20
Alignment explanation
Indices: 4045--4088 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
4035 ATGAGCAGTA
4045 AATGCAACGGTCAA-TTTTT
1 AATGCAACGGTCAATTTTTT
*
4064 AATGTAACGGTCAATTTTTT
1 AATGCAACGGTCAATTTTTT
4084 AATGC
1 AATGC
4089 TACTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (20 bp):
AATGCAACGGTCAATTTTTT
Found at i:7331 original size:17 final size:17
Alignment explanation
Indices: 7311--7344 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7301 AAAAAATTTT
*
7311 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
7328 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
7345 TTATTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:8140 original size:17 final size:17
Alignment explanation
Indices: 8107--8139 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
8097 AATTCAATTG
8107 ATATATTTAAATATTTT
1 ATATATTTAAATATTTT
8124 ATATA-TTAAATATTTT
1 ATATATTTAAATATTTT
8140 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTTAAATATTTT
Found at i:8159 original size:12 final size:13
Alignment explanation
Indices: 8131--8158 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8121 TTTATATATT
8131 AAATATTTTTTAA
1 AAATATTTTTTAA
8144 AAATATTTTTTAA
1 AAATATTTTTTAA
8157 AA
1 AA
8159 TGACAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:9564 original size:122 final size:123
Alignment explanation
Indices: 9347--9591 Score: 474
Period size: 122 Copynumber: 2.0 Consensus size: 123
9337 ACAATCGTGG
*
9347 ACCCTATATCGGATGCCTTTCTTAGCTAATATCAAACACCTGCCATACGTTTTCTCACTCGTGAA
1 ACCCTATATCGGATGCCTTTCTTAGCTAATATCAAACACCTGCCATACGTTTTCTCACTCATGAA
9412 CAGGTGATAACATCTAATCTTTGTCCATAATTATTTGA-TTTTTTATGTAAATTTGAT
66 CAGGTGATAACATCTAATCTTTGTCCATAATTATTTGATTTTTTTATGTAAATTTGAT
9469 ACCCTATATCGGATGCCTTTCTTAGCTAATATCAAACACCTGCCATACGTTTTCTCACTCATGAA
1 ACCCTATATCGGATGCCTTTCTTAGCTAATATCAAACACCTGCCATACGTTTTCTCACTCATGAA
9534 CAGGTGATAACATCTAATCTTTGTCCATAATTATTTGATTTTTTTATGTAAATTTGAT
66 CAGGTGATAACATCTAATCTTTGTCCATAATTATTTGATTTTTTTATGTAAATTTGAT
9592 GTAATAAGTT
Statistics
Matches: 121, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
122 102 0.84
123 19 0.16
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (123 bp):
ACCCTATATCGGATGCCTTTCTTAGCTAATATCAAACACCTGCCATACGTTTTCTCACTCATGAA
CAGGTGATAACATCTAATCTTTGTCCATAATTATTTGATTTTTTTATGTAAATTTGAT
Found at i:10027 original size:6 final size:6
Alignment explanation
Indices: 10016--10045 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
10006 TAGAATTAAA
10016 TATGTT TATGTT TATGTT TATGTT TATGTT
1 TATGTT TATGTT TATGTT TATGTT TATGTT
10046 CATGCATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (6 bp):
TATGTT
Found at i:10179 original size:26 final size:26
Alignment explanation
Indices: 10124--10199 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
10114 GCTAAACCTC
**
10124 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
10150 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
10176 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
10200 TTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:11401 original size:21 final size:21
Alignment explanation
Indices: 11350--11441 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 21
11340 TAAAGCCCTA
* * *
11350 AACCCTTAAACCCTAAACTTT
1 AACCCCTAAACCCCAAACCTT
*
11371 ATA-CCTTAAACCCCAAACCTT
1 A-ACCCCTAAACCCCAAACCTT
**
11392 AACCCCTAAACCTTAAACCTT
1 AACCCCTAAACCCCAAACCTT
* *
11413 AACCTCT-AA-TCCAAACC-T
1 AACCCCTAAACCCCAAACCTT
*
11431 AACCACTAAAC
1 AACCCCTAAAC
11442 TGAACCTCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
18 7 0.12
19 7 0.12
20 3 0.05
21 39 0.68
22 1 0.02
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCCTAAACCCCAAACCTT
Found at i:11411 original size:7 final size:7
Alignment explanation
Indices: 11284--11414 Score: 72
Period size: 7 Copynumber: 18.6 Consensus size: 7
11274 GCCTCGAGCT
11284 TTAAACC
1 TTAAACC
*
11291 CTAAATCC
1 TTAAA-CC
*
11299 -TATACC
1 TTAAACC
11305 TTAAA-C
1 TTAAACC
11311 TCTAAACC
1 T-TAAACC
**
11319 TCGAACC
1 TTAAACC
*
11326 TCAAACC
1 TTAAACC
11333 -TAAA-C
1 TTAAACC
11338 TATAAAGCC
1 T-TAAA-CC
*
11347 CTAAACCC
1 TTAAA-CC
11355 TTAAACC
1 TTAAACC
* *
11362 CTAAACT
1 TTAAACC
*
11369 TTATACC
1 TTAAACC
11376 TTAAACC
1 TTAAACC
**
11383 CCAAACC
1 TTAAACC
*
11390 TTAACCC
1 TTAAACC
*
11397 CTAAACC
1 TTAAACC
11404 TTAAACC
1 TTAAACC
11411 TTAA
1 TTAA
11415 CCTCTAATCC
Statistics
Matches: 92, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
5 1 0.01
6 7 0.08
7 69 0.75
8 14 0.15
9 1 0.01
ACGTcount: A:0.40, C:0.34, G:0.02, T:0.24
Consensus pattern (7 bp):
TTAAACC
Found at i:11497 original size:7 final size:7
Alignment explanation
Indices: 11487--11515 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
11477 GAGCCCTTAG
11487 CCTAGAC
1 CCTAGAC
11494 CCTAGAC
1 CCTAGAC
11501 CCTAGAC
1 CCTAGAC
11508 CCTAGAC
1 CCTAGAC
11515 C
1 C
11516 TTAAGATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.45, G:0.14, T:0.14
Consensus pattern (7 bp):
CCTAGAC
Found at i:12435 original size:23 final size:23
Alignment explanation
Indices: 12409--12469 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 23
12399 TTTTTATCTG
*
12409 CCTTTGTGCACGCTTTTCCTTTA
1 CCTTTGTGCACGCTTTTCCTCTA
* *
12432 CC-TTGTCCCATGCTTTTCCTCTA
1 CCTTTGT-GCACGCTTTTCCTCTA
*
12455 CATTATG-GCACGCTT
1 CCTT-TGTGCACGCTT
12470 CTGCTTTATG
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
22 4 0.14
23 22 0.76
24 1 0.03
25 2 0.07
ACGTcount: A:0.11, C:0.33, G:0.13, T:0.43
Consensus pattern (23 bp):
CCTTTGTGCACGCTTTTCCTCTA
Found at i:13574 original size:20 final size:20
Alignment explanation
Indices: 13535--13595 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
13525 CCTTTTACTT
13535 AACAG-CATTTATTATTAATGC
1 AACAGTCATTT-TT-TTAATGC
*
13556 AACGGTCATTTTTTTAATGC
1 AACAGTCATTTTTTTAATGC
13576 AACAGTCATTTTTTTAATGC
1 AACAGTCATTTTTTTAATGC
13596 TACTTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 26 0.70
21 6 0.16
22 5 0.14
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (20 bp):
AACAGTCATTTTTTTAATGC
Found at i:25067 original size:17 final size:18
Alignment explanation
Indices: 25045--25078 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25035 GCTTCCTTGC
*
25045 ATCTTCA-AGTTTAAATA
1 ATCTTCATAGATTAAATA
25062 ATCTTCATAGATTAAAT
1 ATCTTCATAGATTAAAT
25079 CAAATCAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (18 bp):
ATCTTCATAGATTAAATA
Found at i:25915 original size:211 final size:211
Alignment explanation
Indices: 25548--26184 Score: 1044
Period size: 211 Copynumber: 3.0 Consensus size: 211
25538 TAAAGCACAT
* * *
25548 GTTGAGGTTTGAGTTCATAAGTAGCTTCAAAAGTTATCTTCTTAATTGTTCTATTCACAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCACAGAGTTG
* *
25613 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACCTCATTCCAAA-CAGGACACC
66 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCA-GACACC
25677 TAAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTG
130 TAAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTG
*
25742 CTAGAAAATTTCAATTG
195 CTAGAAAATTTCAATCG
*
25759 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGGGTCTTCTTAATTGTTCTATTCACAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCACAGAGTTG
* * * *
25824 AATGTAAACTCATTTTGAGGACTAACCAAAGCCTAACTCTTCACATGATTCCAAACCAGACACCT
66 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
* * * *
25889 AAGCATATTTCCTAAACTTCGGTTAACAACCTCTATTTTCCCATCTATTTGTGGATGAAATGTGC
131 AAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
*
25954 TA-AAATATTTCAGTCG
196 TAGAAA-ATTTCAATCG
* *
25970 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTATTCTTAATTGTTCTATTCATAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCACAGAGTTG
*
26035 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACAAGACACCT
66 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
*
26100 AAGCATATTTCCTAAACTTTGATTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
131 AAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
*
26165 TAGGAAATTTCAATCAG
196 TAGAAAATTTCAATC-G
26182 GTT
1 GTT
26185 CCCATTTCCT
Statistics
Matches: 391, Mismatches: 31, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
210 3 0.01
211 380 0.97
212 8 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (211 bp):
GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCACAGAGTTG
TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
AAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
TAGAAAATTTCAATCG
Found at i:30759 original size:95 final size:95
Alignment explanation
Indices: 30551--30741 Score: 332
Period size: 95 Copynumber: 2.0 Consensus size: 95
30541 GAAATTGAAT
30551 ATATAATTATAATTATTTAAATGCTCCTAGCTCTTATTACCATTGTAAAAGTTTTACTTGTGTTA
1 ATATAATTATAATTATTTAAATGCTCCTAGCTCTTATTACCATTGTAAAAGTTTTACTTGTGTTA
*
30616 TAAAGTTATATATATAATTTTTTTTCCAAA
66 TAAACTTATATATATAATTTTTTTTCCAAA
*
30646 ATATAATTATAATTATTTAAATGCTCCTAGCTTTTATTACCATTGTAAAAGTTTTACTTGTGTTA
1 ATATAATTATAATTATTTAAATGCTCCTAGCTCTTATTACCATTGTAAAAGTTTTACTTGTGTTA
*
30711 TAAACTTATATA-A-ATTTTATTTTTCCAAA
66 TAAACTTATATATATAATTT-TTTTTCCAAA
30740 AT
1 AT
30742 GAGTTTTTTA
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
93 4 0.04
94 13 0.14
95 75 0.82
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (95 bp):
ATATAATTATAATTATTTAAATGCTCCTAGCTCTTATTACCATTGTAAAAGTTTTACTTGTGTTA
TAAACTTATATATATAATTTTTTTTCCAAA
Found at i:34143 original size:22 final size:22
Alignment explanation
Indices: 34098--34143 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
34088 ACATTAGAGT
* *
34098 ATTTATCTCTAATTTCATCTTG
1 ATTTATCTCTAATTTCAACATG
34120 ATTTATCTCTAATTTCAACATG
1 ATTTATCTCTAATTTCAACATG
34142 AT
1 AT
34144 ATCAATGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTATCTCTAATTTCAACATG
Found at i:36073 original size:211 final size:210
Alignment explanation
Indices: 35691--36327 Score: 1022
Period size: 211 Copynumber: 3.0 Consensus size: 210
35681 AGAAAATGGG
* *
35691 AACCTGATTGAAATTTCCTAGCACATTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAATC
1 AACC-GATTGAAATTT-TTAGCACATTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACC
35756 AAAGTTTAGGAAATATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATT
64 AAAGTTTAGGAAATATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATT
* * *
35821 CCTCAAGATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAATACACCTTCTGAAGCTAC
129 CCTCAAGATGAGTTTACATACAACTCTGTGAATAGAACAATTAAGAAGACACCTTTTGAAGCTAC
35886 TTATGGACTCAAACCTC
194 TTATGGACTCAAACCTC
* * *
35903 AACCGATTGAAATATTTTAGCACATTTCATCCACAAATAGATGGGAAAATAGAGGTTGTTAACCG
1 AACCGATTGAAAT-TTTTAGCACATTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACCA
* * *
35968 AAGTTTAGGAAATATGCTTAGGTGCCTGGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTAGTC
65 AAGTTTAGGAAATATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATTC
* * *
36033 CTCAAAATGAGTTTACATTCAACTCTGTGAATAAAACAATTAAGAAGACACCTTTTGAAGCTACT
130 CTCAAGATGAGTTTACATACAACTCTGTGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACT
*
36098 TACGGACTCAAACCTC
195 TATGGACTCAAACCTC
* * *
36114 AACCAATTGAAATTTTCTAGCACTTTTCAGCCACAAATAGATGGGCAAATAGAGGCTGTTAACCA
1 AACCGATTGAAATTTT-TAGCACATTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACCA
* *
36179 AAGTTTAGGAAATATGCTTAAGTGTCTTGTTTGGAATCAGGTGAAGAGTTAGGATTTGGTTATTC
65 AAGTTTAGGAAATATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATTC
* *
36244 CTCAAGATGAGTTTACATACAACTCTGTGAATAGAACAATTAAGAGGATACCTTTTGAAGCTACT
130 CTCAAGATGAGTTTACATACAACTCTGTGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACT
* *
36309 TATGAACCCAAACCTC
195 TATGGACTCAAACCTC
36325 AAC
1 AAC
36328 ATGTGCTTTA
Statistics
Matches: 389, Mismatches: 34, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
210 3 0.01
211 380 0.98
212 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (210 bp):
AACCGATTGAAATTTTTAGCACATTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACCAA
AGTTTAGGAAATATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATTCC
TCAAGATGAGTTTACATACAACTCTGTGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTT
ATGGACTCAAACCTC
Found at i:37497 original size:12 final size:12
Alignment explanation
Indices: 37480--37510 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
37470 CGACTTCTTA
37480 AAGAAAATCGAG
1 AAGAAAATCGAG
37492 AAGAAAATCGAG
1 AAGAAAATCGAG
37504 AAGAAAA
1 AAGAAAA
37511 CTATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.06, G:0.23, T:0.06
Consensus pattern (12 bp):
AAGAAAATCGAG
Found at i:39558 original size:21 final size:21
Alignment explanation
Indices: 39519--39558 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39509 AATGATTTTA
*
39519 ATCTTATCACTATAATATTCG
1 ATCTTATCACTACAATATTCG
*
39540 ATCTTATCACTACACTATT
1 ATCTTATCACTACAATATT
39559 TAATTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (21 bp):
ATCTTATCACTACAATATTCG
Found at i:39567 original size:21 final size:21
Alignment explanation
Indices: 39515--39567 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
39505 TACCAATGAT
*
39515 TTTAATCTTATCACTATAATA
1 TTTAATCTTATCACTACAATA
** *
39536 TTCGATCTTATCACTACACTA
1 TTTAATCTTATCACTACAATA
*
39557 TTTAATTTTAT
1 TTTAATCTTAT
39568 TGCGGCCATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTAATCTTATCACTACAATA
Found at i:55266 original size:14 final size:14
Alignment explanation
Indices: 55247--55294 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
55237 CAGCAAATGA
55247 TTTTAAAATTATTT
1 TTTTAAAATTATTT
**
55261 TTTTAAAATATAAAAT
1 TTTTAAAAT-T-ATTT
*
55277 TATTAAAATTATTT
1 TTTTAAAATTATTT
55291 TTTT
1 TTTT
55295 TGAAATAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 14 0.54
15 2 0.08
16 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAAAATTATTT
Found at i:55285 original size:30 final size:32
Alignment explanation
Indices: 55249--55315 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
55239 GCAAATGATT
55249 TTAAAATTA-TTTTTTTAAAAT-ATAAAATTA
1 TTAAAATTATTTTTTTTAAAATAATAAAATTA
*
55279 TTAAAATTATTTTTTTTGAAATAATAAAATTA
1 TTAAAATTATTTTTTTTAAAATAATAAAATTA
55311 TTAAA
1 TTAAA
55316 TAATTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 9 0.26
31 11 0.32
32 14 0.41
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
TTAAAATTATTTTTTTTAAAATAATAAAATTA
Found at i:55322 original size:31 final size:31
Alignment explanation
Indices: 55249--55322 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
55239 GCAAATGATT
*
55249 TTAAAATTA-TTTTTTTAAAATATAAAATTA
1 TTAAAATAATTTTTTTTAAAATATAAAATTA
* *
55279 TTAAAATTATTTTTTTTGAAATAATAAAATTA
1 TTAAAATAATTTTTTTTAAAAT-ATAAAATTA
55311 TT-AAATAATTTT
1 TTAAAATAATTTT
55323 AATTTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 9 0.22
31 20 0.50
32 11 0.28
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
TTAAAATAATTTTTTTTAAAATATAAAATTA
Found at i:56404 original size:9 final size:9
Alignment explanation
Indices: 56390--56458 Score: 62
Period size: 9 Copynumber: 8.2 Consensus size: 9
56380 ATTTCAAAAA
56390 AATAATTTT
1 AATAATTTT
56399 AATAATTTT
1 AATAATTTT
56408 AAAATAATTTT
1 --AATAATTTT
56419 AATAATTTT
1 AATAATTTT
56428 -AT-A-TTT
1 AATAATTTT
*
56434 AA-AA---A
1 AATAATTTT
56439 AATAATTTT
1 AATAATTTT
56448 AATAATTTT
1 AATAATTTT
56457 AA
1 AA
56459 AATCATTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
5 2 0.04
6 5 0.10
7 3 0.06
8 2 0.04
9 29 0.58
11 9 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATAATTTT
Found at i:56442 original size:20 final size:21
Alignment explanation
Indices: 56368--56448 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 21
56358 AAAATTATTT
*
56368 AATAATTTTATTATTTCAAAAA
1 AATAATTTTA-TATTTAAAAAA
56390 AATAATTTTAATAATTTTAAAATAA
1 AATAATTTT-AT-A-TTTAAAA-AA
56415 TTTTAATAATTTTATATTT-AAAAA
1 ----AATAATTTTATATTTAAAAAA
56439 AATAATTTTA
1 AATAATTTTA
56449 ATAATTTTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
20 10 0.20
22 10 0.20
23 2 0.04
24 8 0.16
25 5 0.10
26 3 0.06
27 1 0.02
28 2 0.04
29 9 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (21 bp):
AATAATTTTATATTTAAAAAA
Found at i:56452 original size:49 final size:51
Alignment explanation
Indices: 56356--56466 Score: 183
Period size: 49 Copynumber: 2.2 Consensus size: 51
56346 AAATTAGAAA
*
56356 TTAAAATTA-TTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATT
1 TTAAAATAATTTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATT
56406 TTAAAATAATTTTAATAATTTTA-TATTT-AAAAAAATAATTTTAATAATT
1 TTAAAATAATTTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATT
*
56455 TTAAAATCATTT
1 TTAAAATAATTT
56467 ATTAACGTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
49 32 0.55
50 13 0.22
51 13 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (51 bp):
TTAAAATAATTTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATT
Found at i:56461 original size:20 final size:20
Alignment explanation
Indices: 56388--56428 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
56378 TTATTTCAAA
56388 AAAATAATTTTAATAATTTT
1 AAAATAATTTTAATAATTTT
56408 AAAATAATTTTAATAATTTT
1 AAAATAATTTTAATAATTTT
56428 A
1 A
56429 TATTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATAATTTTAATAATTTT
Found at i:58637 original size:24 final size:23
Alignment explanation
Indices: 58588--58642 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
58578 ATATATGATA
* *
58588 AAAATAAAATAACAGAAATAATT
1 AAAATAAAATAACAGAAAAAAAT
58611 AAAATCAAAATAACA-ATAAAAAAT
1 AAAAT-AAAATAACAGA-AAAAAAT
*
58635 AAATTAAA
1 AAAATAAA
58643 TTGAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAATAAAATAACAGAAAAAAAT
Found at i:59071 original size:7 final size:7
Alignment explanation
Indices: 59059--59097 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
59049 TTACTGTAGT
59059 GAAAGTA
1 GAAAGTA
59066 GAAAGTA
1 GAAAGTA
59073 GAAAGTA
1 GAAAGTA
59080 GAAAGTA
1 GAAAGTA
59087 GAAAGTA
1 GAAAGTA
59094 GAAA
1 GAAA
59098 CTAAAGCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (7 bp):
GAAAGTA
Found at i:59195 original size:6 final size:6
Alignment explanation
Indices: 59186--59213 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
59176 GATACGGATA
59186 CGGGTG CGGGTG CGGGTG CGGGTG CGGG
1 CGGGTG CGGGTG CGGGTG CGGGTG CGGG
59214 CGGAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.68, T:0.14
Consensus pattern (6 bp):
CGGGTG
Found at i:64987 original size:6 final size:6
Alignment explanation
Indices: 64976--65012 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
64966 CCCACCTGTA
64976 TCAATT TCAATT TCAATT TCAATT TCAATT TCAATT T
1 TCAATT TCAATT TCAATT TCAATT TCAATT TCAATT T
65013 ATTAGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.51
Consensus pattern (6 bp):
TCAATT
Found at i:71370 original size:12 final size:12
Alignment explanation
Indices: 71353--71379 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
71343 GGCTGTTAGC
71353 GGCATGGGCTGG
1 GGCATGGGCTGG
71365 GGCATGGGCTGG
1 GGCATGGGCTGG
71377 GGC
1 GGC
71380 TGGAATTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.19, G:0.59, T:0.15
Consensus pattern (12 bp):
GGCATGGGCTGG
Found at i:71429 original size:36 final size:36
Alignment explanation
Indices: 71370--71511 Score: 250
Period size: 36 Copynumber: 4.0 Consensus size: 36
71360 GCTGGGGCAT
71370 GGGCTGGGGCTG-GAATTCGAGGCGGACTTGGACTG
1 GGGCTGGGGCTGCGAATTCGAGGCGGACTTGGACTG
*
71405 GGGCTGGGGCTGCGAATTCGAGGCGGACTTAGACTG
1 GGGCTGGGGCTGCGAATTCGAGGCGGACTTGGACTG
*
71441 GGGCTGGGGCTGCGAATTCGAGGCTGACTTGGACTG
1 GGGCTGGGGCTGCGAATTCGAGGCGGACTTGGACTG
*
71477 GGGCTGGGGCTGCGAATTCGAGGCTGACTTGGACT
1 GGGCTGGGGCTGCGAATTCGAGGCGGACTTGGACT
71512 AGAAGAAGGG
Statistics
Matches: 103, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 12 0.12
36 91 0.88
ACGTcount: A:0.15, C:0.19, G:0.45, T:0.21
Consensus pattern (36 bp):
GGGCTGGGGCTGCGAATTCGAGGCGGACTTGGACTG
Found at i:79933 original size:12 final size:12
Alignment explanation
Indices: 79909--79950 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
79899 TTAATTATTT
79909 TTTTAAAA-T-A
1 TTTTAAAATTAA
79919 TTTTAAAATTAA
1 TTTTAAAATTAA
79931 -TTTAAAATTAA
1 TTTTAAAATTAA
*
79942 TTTTTAAAT
1 TTTTAAAAT
79951 ATGAAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 8 0.29
11 12 0.43
12 8 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTAAAATTAA
Found at i:80257 original size:30 final size:29
Alignment explanation
Indices: 80194--80249 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
80184 CTCATTTCAA
* *
80194 AATAAA-TAAAAATTTTGCTGAAGAACAG
1 AATAAATTTAAAACTTTGCTGAAGAACAG
*
80222 AATAAATTTAAAACTTTGTTGAAGAACA
1 AATAAATTTAAAACTTTGCTGAAGAACA
80250 TGGATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (29 bp):
AATAAATTTAAAACTTTGCTGAAGAACAG
Found at i:80357 original size:15 final size:16
Alignment explanation
Indices: 80323--80363 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
80313 GATAAAAAAA
80323 ATTTAATAATTGTGAT
1 ATTTAATAATTGTGAT
*
80339 -TTTAATAATT-TTAT
1 ATTTAATAATTGTGAT
*
80353 ATTTAAAAATT
1 ATTTAATAATT
80364 AATTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTTAATAATTGTGAT
Found at i:88943 original size:27 final size:26
Alignment explanation
Indices: 88912--88966 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 26
88902 TTCTTCCTTT
88912 TTCATCCACTACCACTTATTCCTCATC
1 TTCATCCACTACCACTT-TTCCTCATC
*
88939 TTCATCCACTACCACTTTTTCTCATC
1 TTCATCCACTACCACTTTTCCTCATC
88965 TT
1 TT
88967 TTTTCTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (26 bp):
TTCATCCACTACCACTTTTCCTCATC
Found at i:90502 original size:30 final size:31
Alignment explanation
Indices: 90437--90503 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
90427 TGTTAATCAA
* *
90437 TGACTATTTTGTCACTTTTTAATAACGTTAG
1 TGACTGTTTTGTCACATTTTAATAACGTTAG
*
90468 TGACTGTTTTGTCACATTTTCA-AA-GTTGAG
1 TGACTGTTTTGTCACATTTTAATAACGTT-AG
90498 TGACTG
1 TGACTG
90504 AAATGTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 10 0.31
31 19 0.59
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (31 bp):
TGACTGTTTTGTCACATTTTAATAACGTTAG
Found at i:91689 original size:637 final size:637
Alignment explanation
Indices: 90548--91724 Score: 2192
Period size: 637 Copynumber: 1.8 Consensus size: 637
90538 TGAAAGTTGA
90548 GTGACTGTTGGTGTAATTTAACCTAAATTTTTGTCAGTCACTCGATTATGAAAAATTACAAAATT
1 GTGACTGTTGGTGTAATTTAACCTAAATTTTTGTCAGTCACTCGATTATGAAAAATTACAAAATT
* *
90613 GTCATTCAACTATTTGATTTTGTCTTTTTCTATCACTAGCCATTAAATGTTTAACATAAAGGTGA
66 GTCATTCAACTATTTGATTTTGTCTTTTTCTATCACTAGCCATTAAAAGTTTAACAGAAAGGTGA
* * * *
90678 CGCGATAACTTTTAAATTTAGCATAATAGCAACTTTAACCTTCAATATTTATATTTTATATCAAT
131 CGCGATAACTTTTAAATTTAGCATAACAACAACTTTAACCCTCAATATTTATATATTATATCAAT
*
90743 TTAGTCTTGATTCTAAAAAATTTAACATTTATTTATGCTTTGTGTAATTTAATCGTTTTTTTATA
196 TTAGTCTTGATTCTAAAAAATTTAACATTTATTTATACTTTGTGTAATTTAATCGTTTTTTTATA
90808 GTTTGTTTTTCTTTGTAACATTTTCACCTAAAAAGTTAAATAACAGAGTTATCAGGTAAATTTTA
261 GTTTGTTTTTCTTTGTAACATTTTCACCTAAAAAGTTAAATAACAGAGTTATCAGGTAAATTTTA
90873 TTGAAAATATGCCTAAAATAAAAACATTCAAAAATTCAAGATAATTATTATTTTTTATCTTTTCT
326 TTGAAAATATGCCTAAAATAAAAACATTCAAAAATTCAAGATAATTATTATTTTTTATCTTTTCT
* *
90938 TATTCTTTTAAAATTAACTCTCAATGTTACAAAGAAAAGAAAAACCACAAAAGAGACCAAGTTAT
391 CATTCTTTTAAAATTAACTCTCAATGTTACAAAAAAAAGAAAAACCACAAAAGAGACCAAGTTAT
*
91003 ACAATGTGTAAATGTTGAGGGTTAATTTTTTTTAAATGAAAACTAAATTGACACAATATATAAAT
456 ACAATGTGTAAATGTTAAGGGTTAATTTTTTTTAAATGAAAACTAAATTGACACAATATATAAAT
*
91068 GTTGGGAATTGAAGTTTCTAATAAAACTGTTAATCAATGACTATTTTGTCACTTTTTGATAACGT
521 GTTGGGAATTAAAGTTTCTAATAAAACTGTTAATCAATGACTATTTTGTCACTTTTTGATAACGT
91133 TAGTGACTGTTTTGTCACATTTTCAAAATTGAGTGACTGAAATGTAAATCAG
586 TAGTGACTGTTTTGTCACATTTTCAAAATTGAGTGACTGAAATGTAAATCAG
*
91185 GTGACTGTTGGTGTAATTTAACCTAAATTTTTTTCAGTCACTCGATTATGAAAAATTACAAAATT
1 GTGACTGTTGGTGTAATTTAACCTAAATTTTTGTCAGTCACTCGATTATGAAAAATTACAAAATT
* *
91250 GTTATTCAACTATTTGATTTTGTTTTTTTCTATCACTAGCCATTAAAAGTTTAACAGAAAGGTGA
66 GTCATTCAACTATTTGATTTTGTCTTTTTCTATCACTAGCCATTAAAAGTTTAACAGAAAGGTGA
*
91315 CGTGATAACTTTTAAATTTAGCATAACAACAACTTTAACCCTCAATATTTATATATTATATCAAT
131 CGCGATAACTTTTAAATTTAGCATAACAACAACTTTAACCCTCAATATTTATATATTATATCAAT
* *
91380 TTAGTCTTGATTCTAAAAAATTTAACCTTTATTTATACTTTGTGTAATTTGATCGTTTTTTTATA
196 TTAGTCTTGATTCTAAAAAATTTAACATTTATTTATACTTTGTGTAATTTAATCGTTTTTTTATA
*
91445 GTTTGTTTTTCTTTGTAACATTTTCACCTAAAAAGTTAAATGACAGAGTTATCAGGTAAATTTTA
261 GTTTGTTTTTCTTTGTAACATTTTCACCTAAAAAGTTAAATAACAGAGTTATCAGGTAAATTTTA
91510 TTGAAAATATGCCTAAAATAAAAACATTCAAAAATTCAAGATAATTATTATTTTTTATCTTTTCT
326 TTGAAAATATGCCTAAAATAAAAACATTCAAAAATTCAAGATAATTATTATTTTTTATCTTTTCT
91575 CATTCTTTTAAAATTAACTCTCAATGTTACAAAAAAAAGAAAAACCACAAAAGAGACCAAGTTAT
391 CATTCTTTTAAAATTAACTCTCAATGTTACAAAAAAAAGAAAAACCACAAAAGAGACCAAGTTAT
91640 ACAATGTGTAAATGTTAAGGGTTAATTTTTTTTAAATGAAAACTAAATTGACACAATATATAAAT
456 ACAATGTGTAAATGTTAAGGGTTAATTTTTTTTAAATGAAAACTAAATTGACACAATATATAAAT
91705 GTTGGGAATTAAAGTTTCTA
521 GTTGGGAATTAAAGTTTCTA
91725 TTATACCAAA
Statistics
Matches: 522, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
637 522 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (637 bp):
GTGACTGTTGGTGTAATTTAACCTAAATTTTTGTCAGTCACTCGATTATGAAAAATTACAAAATT
GTCATTCAACTATTTGATTTTGTCTTTTTCTATCACTAGCCATTAAAAGTTTAACAGAAAGGTGA
CGCGATAACTTTTAAATTTAGCATAACAACAACTTTAACCCTCAATATTTATATATTATATCAAT
TTAGTCTTGATTCTAAAAAATTTAACATTTATTTATACTTTGTGTAATTTAATCGTTTTTTTATA
GTTTGTTTTTCTTTGTAACATTTTCACCTAAAAAGTTAAATAACAGAGTTATCAGGTAAATTTTA
TTGAAAATATGCCTAAAATAAAAACATTCAAAAATTCAAGATAATTATTATTTTTTATCTTTTCT
CATTCTTTTAAAATTAACTCTCAATGTTACAAAAAAAAGAAAAACCACAAAAGAGACCAAGTTAT
ACAATGTGTAAATGTTAAGGGTTAATTTTTTTTAAATGAAAACTAAATTGACACAATATATAAAT
GTTGGGAATTAAAGTTTCTAATAAAACTGTTAATCAATGACTATTTTGTCACTTTTTGATAACGT
TAGTGACTGTTTTGTCACATTTTCAAAATTGAGTGACTGAAATGTAAATCAG
Found at i:97521 original size:164 final size:164
Alignment explanation
Indices: 97250--97582 Score: 666
Period size: 164 Copynumber: 2.0 Consensus size: 164
97240 TCAAATGGTG
97250 AATATCTGGGTTTCTTTTTATTCCTCTTGGTATCTGGTTGATGACTCTAAACAAAAAGATTATTT
1 AATATCTGGGTTTCTTTTTATTCCTCTTGGTATCTGGTTGATGACTCTAAACAAAAAGATTATTT
97315 ATTTAGTCTCCAATAGTTTACTTGACAATGAACCATCTTAACATAGATGGGGTCCAAATGGTATT
66 ATTTAGTCTCCAATAGTTTACTTGACAATGAACCATCTTAACATAGATGGGGTCCAAATGGTATT
97380 CTATAACATGCTTTAAGAGCAGAAATCTTTGCTC
131 CTATAACATGCTTTAAGAGCAGAAATCTTTGCTC
97414 AATATCTGGGTTTCTTTTTATTCCTCTTGGTATCTGGTTGATGACTCTAAACAAAAAGATTATTT
1 AATATCTGGGTTTCTTTTTATTCCTCTTGGTATCTGGTTGATGACTCTAAACAAAAAGATTATTT
97479 ATTTAGTCTCCAATAGTTTACTTGACAATGAACCATCTTAACATAGATGGGGTCCAAATGGTATT
66 ATTTAGTCTCCAATAGTTTACTTGACAATGAACCATCTTAACATAGATGGGGTCCAAATGGTATT
97544 CTATAACATGCTTTAAGAGCAGAAATCTTTGCTC
131 CTATAACATGCTTTAAGAGCAGAAATCTTTGCTC
97578 AATAT
1 AATAT
97583 AATGACTATC
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 169 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (164 bp):
AATATCTGGGTTTCTTTTTATTCCTCTTGGTATCTGGTTGATGACTCTAAACAAAAAGATTATTT
ATTTAGTCTCCAATAGTTTACTTGACAATGAACCATCTTAACATAGATGGGGTCCAAATGGTATT
CTATAACATGCTTTAAGAGCAGAAATCTTTGCTC
Found at i:99706 original size:23 final size:23
Alignment explanation
Indices: 99687--99730 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
99677 TTTTAAATAT
99687 TAATTTTGTTAAACAGTAAATTA
1 TAATTTTGTTAAACAGTAAATTA
* * *
99710 TAATTTTTTTAATCAGCAAAT
1 TAATTTTGTTAAACAGTAAAT
99731 GTTGATTTAA
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:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (23 bp):
TAATTTTGTTAAACAGTAAATTA
Found at i:100312 original size:41 final size:41
Alignment explanation
Indices: 100255--100337 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
100245 GATTAGAAAT
*
100255 TTAACCCCGATTTTTTAAAATTTTGAAAAGGACCAATTTGA
1 TTAACCCCGATGTTTTAAAATTTTGAAAAGGACCAATTTGA
*
100296 TTAACCTCGATGTTTTAAAATTTTGAAAAGGACCAATTTGA
1 TTAACCCCGATGTTTTAAAATTTTGAAAAGGACCAATTTGA
100337 T
1 T
100338 CAATATCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (41 bp):
TTAACCCCGATGTTTTAAAATTTTGAAAAGGACCAATTTGA
Found at i:110987 original size:21 final size:21
Alignment explanation
Indices: 110963--111004 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
110953 AACAATAATG
110963 AATGTTATTAATCAAATAGAA
1 AATGTTATTAATCAAATAGAA
110984 AATGTTATTAATCAAATAGAA
1 AATGTTATTAATCAAATAGAA
111005 TCCACCCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
AATGTTATTAATCAAATAGAA
Found at i:115607 original size:3 final size:3
Alignment explanation
Indices: 115599--115627 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
115589 AATGCATCTT
115599 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
115628 TACAACATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:120563 original size:30 final size:31
Alignment explanation
Indices: 120528--120585 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
120518 AGACTTGACA
*
120528 ATTTTTTC-TAAGTTGGTACTTAAACTTGAT
1 ATTTTTTCTTAAATTGGTACTTAAACTTGAT
120558 ATTTTTTCTTAAATTGGTACTTAAACTT
1 ATTTTTTCTTAAATTGGTACTTAAACTT
120586 TTTGGGGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
ATTTTTTCTTAAATTGGTACTTAAACTTGAT
Found at i:120564 original size:31 final size:31
Alignment explanation
Indices: 120520--120585 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
120510 TGATACCCAG
*
120520 ACTTGACAATTTTTTC-TAAGTTGGTACTTAA
1 ACTTGAC-ATTTTTTCTTAAATTGGTACTTAA
*
120551 ACTTGATATTTTTTCTTAAATTGGTACTTAA
1 ACTTGACATTTTTTCTTAAATTGGTACTTAA
120582 ACTT
1 ACTT
120586 TTTGGGGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (31 bp):
ACTTGACATTTTTTCTTAAATTGGTACTTAA
Found at i:123093 original size:45 final size:45
Alignment explanation
Indices: 123042--123134 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
123032 CTTCTTCATG
123042 CTAAGCTTAAGGTTATTGTTGCGGGAAGATTGATTGGTGCCTTGC
1 CTAAGCTTAAGGTTATTGTTGCGGGAAGATTGATTGGTGCCTTGC
* *
123087 CTAAGCTTAAGGTTTTTGTTGCGGGAAGATTGATTGGTGTCTTGC
1 CTAAGCTTAAGGTTATTGTTGCGGGAAGATTGATTGGTGCCTTGC
123132 CTA
1 CTA
123135 TCTTGCTACT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (45 bp):
CTAAGCTTAAGGTTATTGTTGCGGGAAGATTGATTGGTGCCTTGC
Found at i:127004 original size:4 final size:4
Alignment explanation
Indices: 126995--127019 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
126985 ATGTGCAAGA
126995 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
127020 AGGAGTAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:130845 original size:2 final size:2
Alignment explanation
Indices: 130838--130862 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
130828 GTTCATCTTC
130838 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 T
130863 GTAATTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:143138 original size:3 final size:3
Alignment explanation
Indices: 143130--143157 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
143120 AAAGTTTTGA
143130 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
143158 GAGTAGGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:144150 original size:15 final size:14
Alignment explanation
Indices: 144130--144177 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
144120 ATAACACTTT
144130 AATATAAGTAATTAA
1 AATATAA-TAATTAA
*
144145 AATATAATATTTTAA
1 AATATAATA-ATTAA
144160 ACATA-AATAATTAA
1 A-ATATAATAATTAA
144174 AATA
1 AATA
144178 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 7 0.24
15 16 0.55
16 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (14 bp):
AATATAATAATTAA
Found at i:144173 original size:14 final size:13
Alignment explanation
Indices: 144128--144194 Score: 55
Period size: 13 Copynumber: 5.0 Consensus size: 13
144118 TTATAACACT
* *
144128 TTAATATAAGTAA
1 TTAAAATAAATAA
*
144141 TTAAAATATAATATT
1 TTAAAATA-AATA-A
144156 TTAAACATAAATAA
1 TTAAA-ATAAATAA
*
144170 TTAAAATAAA-AT
1 TTAAAATAAATAA
*
144182 TTAAAATCAATAA
1 TTAAAATAAATAA
144195 AAATAATTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
12 10 0.23
13 13 0.30
14 8 0.19
15 9 0.21
16 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (13 bp):
TTAAAATAAATAA
Found at i:144195 original size:29 final size:29
Alignment explanation
Indices: 144133--144187 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
144123 ACACTTTAAT
* *
144133 ATAAGTAATTAAAATATAATATTTTAAAC
1 ATAAATAATTAAAATATAATATTTAAAAC
144162 ATAAATAATTAAAATA-AA-ATTTAAAA
1 ATAAATAATTAAAATATAATATTTAAAA
144188 TCAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 2 0.08
29 15 0.62
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (29 bp):
ATAAATAATTAAAATATAATATTTAAAAC
Found at i:145123 original size:110 final size:110
Alignment explanation
Indices: 144995--145201 Score: 387
Period size: 110 Copynumber: 1.9 Consensus size: 110
144985 TAACGGGAAG
144995 AAGATATTGGAACCAAAGATATTGAATCTTTTGGTTAATGGATTTTAAAGATTCAAGCTTTGAGA
1 AAGATATTGGAACCAAAGATATTGAATCTTTTGGTTAATGGATTTTAAAGATTCAAGCTTTGAGA
145060 CAGATTTGTAACTAAAGATATTGGAATAAAAAAAACTTAACTTGA
66 CAGATTTGTAACTAAAGATATTGGAATAAAAAAAACTTAACTTGA
*
145105 AAGATATTGGAACCAAAGATATTGAATCTTTTGGTTAATGGGTTTTAAAGATTCAAGCTTTGAGA
1 AAGATATTGGAACCAAAGATATTGAATCTTTTGGTTAATGGATTTTAAAGATTCAAGCTTTGAGA
* *
145170 TAGATTTGTAACTAAAGATATTGGAATCAAAA
66 CAGATTTGTAACTAAAGATATTGGAATAAAAA
145202 GGGAAGAAGA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 94 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (110 bp):
AAGATATTGGAACCAAAGATATTGAATCTTTTGGTTAATGGATTTTAAAGATTCAAGCTTTGAGA
CAGATTTGTAACTAAAGATATTGGAATAAAAAAAACTTAACTTGA
Found at i:145294 original size:16 final size:16
Alignment explanation
Indices: 145277--145306 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
145267 TTAGGGTTTA
145277 AAAATT-TTAATTAAT
1 AAAATTATTAATTAAT
145292 AAAATTATTAATTAA
1 AAAATTATTAATTAA
145307 ATATTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTATTAATTAAT
Found at i:145847 original size:21 final size:20
Alignment explanation
Indices: 145823--145870 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
145813 GATATTTTCT
*
145823 AAAAGAAAAAACGAAAAACAA
1 AAAAGAAAAAA-GAAAAAAAA
145844 AAAAGAAAAAAGAAAAAAAA
1 AAAAGAAAAAAGAAAAAAAA
145864 ACAAAGA
1 A-AAAGA
145871 GTTATAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAGAAAAAAAA
Found at i:145862 original size:8 final size:7
Alignment explanation
Indices: 145823--145870 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
145813 GATATTTTCT
145823 AAAAGAA
1 AAAAGAA
145830 AAAACG-A
1 AAAA-GAA
*
145837 AAAACAA
1 AAAAGAA
145844 AAAAGAA
1 AAAAGAA
145851 AAAAGAA
1 AAAAGAA
145858 AAAA-AA
1 AAAAGAA
145864 ACAAAGA
1 A-AAAGA
145871 GTTATAGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
6 3 0.09
7 30 0.86
8 2 0.06
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:151189 original size:57 final size:56
Alignment explanation
Indices: 151128--151290 Score: 145
Period size: 58 Copynumber: 2.9 Consensus size: 56
151118 AAAATACGAA
* * *
151128 TAAAAAATATTTTTTGAGTGTTTACAA-CTTAATGGCTTATACCACCTTTCTCAAATT
1 TAAAAAATATTTTTTGAGCGTTTACAATC-CAATGGCTTACACCACCTTTCTCAAA-T
* * * * *
151185 TAAAAATATTTTTTTTGAGCGTTTGCCATCCAATGGCTTACACTACCTTTTTCAAAT
1 TAAAAA-ATATTTTTTGAGCGTTTACAATCCAATGGCTTACACCACCTTTCTCAAAT
** *
151242 T-AAAAATATTTATTTTTGTGTTTATC-ATCCAATGG-TCTACACCACCTTT
1 TAAAAAATATTT-TTTGAGCGTTTA-CAATCCAATGGCT-TACACCACCTTT
151291 TCTAAGAGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
55 6 0.07
56 32 0.37
57 9 0.10
58 39 0.45
59 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (56 bp):
TAAAAAATATTTTTTGAGCGTTTACAATCCAATGGCTTACACCACCTTTCTCAAAT
Found at i:151289 original size:56 final size:57
Alignment explanation
Indices: 151158--151291 Score: 166
Period size: 56 Copynumber: 2.4 Consensus size: 57
151148 TTTACAACTT
* * *
151158 AATGGCTTATACCACCTTTCTCAAATTTAAAAATATTTTTTTTGAGCGTTTGCCATCC
1 AATGGCTTACACCACCTTTTTCAAATTTAAAAATATTTTTTTT-AGCGTTTACCATCC
* * *
151216 AATGGCTTACACTACCTTTTTCAAA-TTAAAAATATTTATTTTT-GTGTTTATCATCC
1 AATGGCTTACACCACCTTTTTCAAATTTAAAAATATTT-TTTTTAGCGTTTACCATCC
151272 AATGG-TCTACACCACCTTTT
1 AATGGCT-TACACCACCTTTT
151292 CTAAGAGAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
55 1 0.01
56 27 0.40
57 12 0.18
58 27 0.40
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (57 bp):
AATGGCTTACACCACCTTTTTCAAATTTAAAAATATTTTTTTTAGCGTTTACCATCC
Found at i:151643 original size:39 final size:39
Alignment explanation
Indices: 151573--151665 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
151563 TTAAAACAAA
* * *
151573 AATTAAATTTTAAATAATTAAACCATAATTTAAA-AATTAT
1 AATTAAA-TTAAAATAATTAAACAAAAATTTAAATAATT-T
151613 AATTAAATTAAAATAATTAAA-AAAAGATTTAAATAATTT
1 AATTAAATTAAAATAATTAAACAAAA-ATTTAAATAATTT
*
151652 -TTTAAATTAAAATA
1 AATTAAATTAAAATA
151666 TTACAATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
38 15 0.32
39 21 0.45
40 11 0.23
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (39 bp):
AATTAAATTAAAATAATTAAACAAAAATTTAAATAATTT
Found at i:151845 original size:57 final size:57
Alignment explanation
Indices: 151776--152079 Score: 257
Period size: 56 Copynumber: 5.4 Consensus size: 57
151766 TTTGGATGAT
* *
151776 AAACACTCAAAAAAATATTTTTAAATCTGAAAAA-GATAATGTAAGTCATTGGGTTGC
1 AAACACTCAAAAAAATATTTTTAAATCTGAAAAATG-TAATGTAAGCCATTGGGTGGC
* * *
151833 AAACACTTAAAAAAATATTTTTTAAAATTTGAAAAATGTAGTGTAAGCCATTGGGTGGC
1 AAACACTCAAAAAAATA-TTTTT-AAATCTGAAAAATGTAATGTAAGCCATTGGGTGGC
* * *
151892 AAACA---AAAAAAATATTTTTAAATTTGAAAAATGTAGTG-CAGCCCATTGGGTGGC
1 AAACACTCAAAAAAATATTTTTAAATCTGAAAAATGTAATGTAAG-CCATTGGGTGGC
** * * * * * * *
151946 AAACA-AAAAAAAAATATTTTTCAAT-TTAAGAAATGTGATGTAGGTCATTAGGTGAC
1 AAACACTCAAAAAAATATTTTTAAATCTGAA-AAATGTAATGTAAGCCATTGGGTGGC
* ** * * * *
152002 AAAAACTCAAAAAAATATTTTTAAATCTGAGAAAA-GTGGTATAAGCCATTAGATGAC
1 AAACACTCAAAAAAATATTTTTAAATCTGA-AAAATGTAATGTAAGCCATTGGGTGGC
* *
152059 GAACA-TCCAAAAAATATTTTT
1 AAACACTCAAAAAAATATTTTT
152080 TGGGGACTTG
Statistics
Matches: 208, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
53 2 0.01
54 36 0.17
55 8 0.04
56 62 0.30
57 54 0.26
58 10 0.05
59 35 0.17
60 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (57 bp):
AAACACTCAAAAAAATATTTTTAAATCTGAAAAATGTAATGTAAGCCATTGGGTGGC
Found at i:152014 original size:113 final size:114
Alignment explanation
Indices: 151780--152037 Score: 280
Period size: 113 Copynumber: 2.3 Consensus size: 114
151770 GATGATAAAC
* * **
151780 ACTCAAAAAAATATTTTTAAATCTGAAAAAGATAATGTAAGTCATTGGGTTGCAAACACTTAAAA
1 ACTCAAAAAAATATTTTTAAATCTGAAAAAGATAATGTAAGCCATTGGGTGGCAAACACAAAAAA
* *
151845 AAATATTTTTTAAAATTTGAAAAATGTAGTGTAAGCCATTGGGTGGCAA
66 AAATATTTTTTAAAATTTGAAAAATGTAGTGTAAGCCATTAGGTGACAA
* * * *
151894 AC-AAAAAAAATATTTTTAAATTTGAAAAATG-TAGTG-CAGCCCATTGGGTGGCAAACA-AAAA
1 ACTCAAAAAAATATTTTTAAATCTGAAAAA-GATAATGTAAG-CCATTGGGTGGCAAACACAAAA
* * *
151955 AAAAATA-TTTTT-CAATTT-AAGAAATGT-GATGTAGGTCATTAGGTGACAAAA
64 AAAAATATTTTTTAAAATTTGAA-AAATGTAG-TGTAAGCCATTAGGTGAC--AA
152006 ACTCAAAAAAATATTTTTAAATCTGAGAAAAG
1 ACTCAAAAAAATATTTTTAAATCTGA-AAAAG
152038 TGGTATAAGC
Statistics
Matches: 121, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
109 3 0.02
110 25 0.21
111 5 0.04
112 15 0.12
113 66 0.55
114 7 0.06
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.30
Consensus pattern (114 bp):
ACTCAAAAAAATATTTTTAAATCTGAAAAAGATAATGTAAGCCATTGGGTGGCAAACACAAAAAA
AAATATTTTTTAAAATTTGAAAAATGTAGTGTAAGCCATTAGGTGACAA
Found at i:158638 original size:12 final size:11
Alignment explanation
Indices: 158597--158649 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
158587 TTATCTTATT
*
158597 ATTATAAAAAA
1 ATTATATAAAA
*
158608 ATTATATAATGA
1 ATTATATAA-AA
158620 ATT-TATAAAA
1 ATTATATAAAA
*
158630 ATTGATATAGAA
1 ATT-ATATAAAA
158642 ATTATATA
1 ATTATATA
158650 TGATTTCTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 13 0.37
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (11 bp):
ATTATATAAAA
Found at i:158646 original size:21 final size:22
Alignment explanation
Indices: 158604--158647 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
158594 ATTATTATAA
*
158604 AAAAATTATATAATGAATTTAT
1 AAAAATTATATAATGAAATTAT
158626 AAAAATTGATAT-A-GAAATTAT
1 AAAAATT-ATATAATGAAATTAT
158647 A
1 A
158648 TATGATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 8 0.40
23 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAAATTATATAATGAAATTAT
Found at i:164638 original size:41 final size:41
Alignment explanation
Indices: 164581--164665 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
164571 CAAAATGCAA
164581 TCTAACACTTAGTACAGAGGCCTCCGTAGTATTTTAACCTT
1 TCTAACACTTAGTACAGAGGCCTCCGTAGTATTTTAACCTT
164622 TCTAACACTTAGTACAGAGGCCTCCGTAGTATTTTAACCTT
1 TCTAACACTTAGTACAGAGGCCTCCGTAGTATTTTAACCTT
164663 TCT
1 TCT
164666 TGGGGTACTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (41 bp):
TCTAACACTTAGTACAGAGGCCTCCGTAGTATTTTAACCTT
Found at i:181559 original size:2 final size:2
Alignment explanation
Indices: 181548--181578 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
181538 TCTATAATAC
181548 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
181579 AGATTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:190263 original size:12 final size:13
Alignment explanation
Indices: 190232--190263 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
190222 GGTGAGTCTT
190232 GTGTGTTATTTGC
1 GTGTGTTATTTGC
190245 GTGTGTTATTTGC
1 GTGTGTTATTTGC
190258 -TGTGTT
1 GTGTGTT
190264 TAGATTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.06, C:0.06, G:0.31, T:0.56
Consensus pattern (13 bp):
GTGTGTTATTTGC
Found at i:192635 original size:11 final size:11
Alignment explanation
Indices: 192619--192653 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
192609 GAAGTAATTG
192619 GAAACAAAAAA
1 GAAACAAAAAA
192630 GAAACAAAAAA
1 GAAACAAAAAA
*
192641 -AAAAAAAAAA
1 GAAACAAAAAA
192651 GAA
1 GAA
192654 GAGGTGGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.86, C:0.06, G:0.09, T:0.00
Consensus pattern (11 bp):
GAAACAAAAAA
Found at i:200496 original size:20 final size:18
Alignment explanation
Indices: 200471--200512 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
200461 GAAAATTTTA
200471 AAATTAATTATAAATCAAAT
1 AAATTAATTA-AAAT-AAAT
200491 AAATTAATTAAAATAAAT
1 AAATTAATTAAAATAAAT
200509 AAAT
1 AAAT
200513 ATTTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.36
19 4 0.18
20 10 0.45
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTAATTAAAATAAAT
Found at i:203060 original size:6 final size:6
Alignment explanation
Indices: 203051--203098 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
203041 CTCTTATACA
* * *
203051 TGTATG TGTATG TGTATG TTTATG TGTATA TGTGTG T-TATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
203098 T
1 T
203099 TTCAATCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (6 bp):
TGTATG
Found at i:215418 original size:2 final size:2
Alignment explanation
Indices: 215411--215435 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
215401 TGCACCAAAG
215411 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
215436 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:215441 original size:2 final size:2
Alignment explanation
Indices: 215436--215461 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
215426 CACACACACA
215436 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
215462 TCTAAATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:215901 original size:1 final size:1
Alignment explanation
Indices: 215868--215894 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
215858 AATACATGTT
215868 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
215895 GGAAAAAGAA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:224009 original size:23 final size:24
Alignment explanation
Indices: 223969--224013 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
223959 GCGCACATGA
*
223969 TTTATTTATTATTTAATAATAATT
1 TTTATTTATAATTTAATAATAATT
223993 TTTATTTA-AATTTAATAATAA
1 TTTATTTATAATTTAATAATAA
224014 ATAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTATTTATAATTTAATAATAATT
Found at i:224028 original size:23 final size:24
Alignment explanation
Indices: 223971--224028 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
223961 GCACATGATT
* * **
223971 TATTTATTATTTAATAATAATTTT
1 TATTTAATATTTAATAATAAATAA
223995 TATTTAA-ATTTAATAATAAATAA
1 TATTTAATATTTAATAATAAATAA
224018 TA-TTAATATTT
1 TATTTAATATTT
224029 TTAACGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 4 0.14
23 19 0.66
24 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTAATATTTAATAATAAATAA
Found at i:230552 original size:16 final size:16
Alignment explanation
Indices: 230522--230572 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
230512 TTTTTAAAAA
*
230522 TATTT-ATATTGTTTT
1 TATTTAATATTTTTTT
230537 TATTTAATATTTTTTT
1 TATTTAATATTTTTTT
* *
230553 CATTTATTAATTTTTGTT
1 TATTTAAT-ATTTTT-TT
230571 TA
1 TA
230573 GTGAAATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 5 0.17
16 15 0.52
17 6 0.21
18 3 0.10
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (16 bp):
TATTTAATATTTTTTT
Found at i:231515 original size:29 final size:29
Alignment explanation
Indices: 231473--231529 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
231463 TCCTCCTCTC
231473 TATACGTTGGATTGAAATGAATAAAATTT
1 TATACGTTGGATTGAAATGAATAAAATTT
*
231502 TATATGTTGGATTGAAATGAATAAAATT
1 TATACGTTGGATTGAAATGAATAAAATT
231530 AAAAAAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.39
Consensus pattern (29 bp):
TATACGTTGGATTGAAATGAATAAAATTT
Found at i:238300 original size:24 final size:23
Alignment explanation
Indices: 238267--238316 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
238257 TTTAAGTAGG
*
238267 ATTAATTAAAGTTA-AAATGACTTA
1 ATTAAGTAAA-TTAGAAA-GACTTA
238291 ATTAAGTAAATTATGAAAGACTTA
1 ATTAAGTAAATTA-GAAAGACTTA
238315 AT
1 AT
238317 ATTTACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 3 0.13
24 17 0.74
25 3 0.13
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (23 bp):
ATTAAGTAAATTAGAAAGACTTA
Found at i:239237 original size:53 final size:53
Alignment explanation
Indices: 239155--239347 Score: 262
Period size: 53 Copynumber: 3.6 Consensus size: 53
239145 GTAAATGTAA
* * *
239155 AAAGGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCCTATTACTGATT
1 AAAGGTCCGATGACTCTGTATCATCGTGAGTTATATGAATCCTATTACAGATT
* ** *
239208 AAAGGTCAC-ATGACTCTGTATCATTGTGAGTTATATGAATCCTAACACGGATT
1 AAAGGTC-CGATGACTCTGTATCATCGTGAGTTATATGAATCCTATTACAGATT
* * *
239261 AAAGGTCTGATGACTCTGTATCATCGTGAGTTATACGAATCCTATTCCAGATT
1 AAAGGTCCGATGACTCTGTATCATCGTGAGTTATATGAATCCTATTACAGATT
* *
239314 AAAAGTCCGATGACTCTGTGTCATCGTGAGTTAT
1 AAAGGTCCGATGACTCTGTATCATCGTGAGTTAT
239348 CAAATGTGAA
Statistics
Matches: 122, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 121 0.99
54 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (53 bp):
AAAGGTCCGATGACTCTGTATCATCGTGAGTTATATGAATCCTATTACAGATT
Found at i:239343 original size:106 final size:106
Alignment explanation
Indices: 239155--239347 Score: 289
Period size: 106 Copynumber: 1.8 Consensus size: 106
239145 GTAAATGTAA
* * * *
239155 AAAGGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCCTATTACTGATTAAAGGTCACATG
1 AAAGGTCCGATGACTCTATATCATCGTGAGTTATACGAATCCTATTACAGATTAAAAGTCACATG
*
239220 ACTCTGTATCATTGTGAGTTATATGAATCCTAACACGGATT
66 ACTCTGTATCATCGTGAGTTATATGAATCCTAACACGGATT
* * *
239261 AAAGGTCTGATGACTCTGTATCATCGTGAGTTATACGAATCCTATTCCAGATTAAAAGTC-CGAT
1 AAAGGTCCGATGACTCTATATCATCGTGAGTTATACGAATCCTATTACAGATTAAAAGTCAC-AT
*
239325 GACTCTGTGTCATCGTGAGTTAT
65 GACTCTGTATCATCGTGAGTTAT
239348 CAAATGTGAA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
105 1 0.01
106 76 0.99
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (106 bp):
AAAGGTCCGATGACTCTATATCATCGTGAGTTATACGAATCCTATTACAGATTAAAAGTCACATG
ACTCTGTATCATCGTGAGTTATATGAATCCTAACACGGATT
Found at i:240031 original size:21 final size:21
Alignment explanation
Indices: 240005--240051 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
239995 TTAGTATTGA
*
240005 TAGAAGTAAT-ACTTGTTTCGG
1 TAGAAG-AATCACTTGTATCGG
*
240026 TAGAAGAGTCACTTGTATCGG
1 TAGAAGAATCACTTGTATCGG
240047 TAGAA
1 TAGAA
240052 CTGTCACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (21 bp):
TAGAAGAATCACTTGTATCGG
Found at i:240057 original size:21 final size:21
Alignment explanation
Indices: 240015--240072 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
240005 TAGAAGTAAT
* *
240015 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
240036 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
* *
240057 ACTTATATCGATAGAA
1 ACTTGTATCGGTAGAA
240073 GTCTTCACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:253022 original size:29 final size:28
Alignment explanation
Indices: 252914--253029 Score: 99
Period size: 29 Copynumber: 3.9 Consensus size: 28
252904 ATTTGAGGGC
* *
252914 TTTTGAAAAGGTGTGGCCCTTATTTGACCA
1 TTTTGAAAA-GTTTGGCCCTTATATGA-CA
* *
252944 TTTTGAAAAGTTT-GACCTTCATTTGAGCA
1 TTTTGAAAAGTTTGGCCCTT-ATATGA-CA
* **
252973 CTTTTGTAAAGGTTAAGCCCTTATATGACTA
1 -TTTTG-AAAAGTTTGGCCCTTATATGAC-A
253004 TTTTGAAAAGTTTGGCCCTTATATGA
1 TTTTGAAAAGTTTGGCCCTTATATGA
253030 GCTACCCCTA
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
28 5 0.07
29 29 0.41
30 20 0.28
31 12 0.17
32 5 0.07
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (28 bp):
TTTTGAAAAGTTTGGCCCTTATATGACA
Found at i:253031 original size:60 final size:59
Alignment explanation
Indices: 252898--253031 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 59
252888 CATATGAGAA
** * *
252898 GCCCTTATTTGAGGGCTTTTGAAAAGGTGTGGCCCTTATTTGACCATTTTGAAAAGTTT
1 GCCCTTATTTGAGCACTTTTGAAAAGGTGTAGCCCTTATATGACCATTTTGAAAAGTTT
* * *
252957 GACCTTCATTTGAGCACTTTTGTAAAGGT-TAAGCCCTTATATGACTATTTTGAAAAGTTT
1 GCCCTT-ATTTGAGCACTTTTGAAAAGGTGT-AGCCCTTATATGACCATTTTGAAAAGTTT
*
253017 GGCCCTTATATGAGC
1 -GCCCTTATTTGAGC
253032 TACCCCTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
59 6 0.10
60 52 0.83
61 5 0.08
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (59 bp):
GCCCTTATTTGAGCACTTTTGAAAAGGTGTAGCCCTTATATGACCATTTTGAAAAGTTT
Found at i:255405 original size:29 final size:29
Alignment explanation
Indices: 255335--255404 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
255325 GGATTTTAAT
255335 TTGTAATTTGGGGCTTATTCAAAAAAAAA
1 TTGTAATTTGGGGCTTATTCAAAAAAAAA
255364 TTGTAATTTGGGGCTTATTCAAAAAAAAA
1 TTGTAATTTGGGGCTTATTCAAAAAAAAA
255393 -TGTAATTTGGGG
1 TTGTAATTTGGGG
255405 GGGGGGGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 12 0.29
29 29 0.71
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.36
Consensus pattern (29 bp):
TTGTAATTTGGGGCTTATTCAAAAAAAAA
Found at i:255839 original size:17 final size:18
Alignment explanation
Indices: 255814--255857 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
255804 TTTATTTAAT
255814 AATAC-TTTTATCTCAAA
1 AATACTTTTTATCTCAAA
* *
255831 AATATTTTTTATTTCAAA
1 AATACTTTTTATCTCAAA
255849 AATACTTTT
1 AATACTTTT
255858 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
AATACTTTTTATCTCAAA
Found at i:262659 original size:29 final size:30
Alignment explanation
Indices: 262612--262696 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 30
262602 TTGATTTAAT
* *
262612 GTGCAATTATATATATAAACTTTAATT-TG
1 GTGCAATTATACATGTAAACTTTAATTGTG
*
262641 GTGCAATTATACATGTAAAATTTTAATTGTG
1 GTGCAATTATACATGT-AAACTTTAATTGTG
*
262672 GTTCGAATCTATACATG-AAACTTTA
1 GTGC-AAT-TATACATGTAAACTTTA
262697 GTTTTGATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 14 0.30
30 10 0.21
31 12 0.26
32 3 0.06
33 8 0.17
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.41
Consensus pattern (30 bp):
GTGCAATTATACATGTAAACTTTAATTGTG
Found at i:264083 original size:31 final size:31
Alignment explanation
Indices: 264045--264107 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
264035 AATTTCGCTT
264045 TTCTCGAGCATTTTTTCTCTTCTTTGATCAG
1 TTCTCGAGCATTTTTTCTCTTCTTTGATCAG
264076 TTCTCGAGCATTTTTTCTCTTCTTTGATCAG
1 TTCTCGAGCATTTTTTCTCTTCTTTGATCAG
264107 T
1 T
264108 AAGTTTACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.13, C:0.22, G:0.13, T:0.52
Consensus pattern (31 bp):
TTCTCGAGCATTTTTTCTCTTCTTTGATCAG
Found at i:266817 original size:17 final size:18
Alignment explanation
Indices: 266792--266842 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
266782 GTTTATATTA
*
266792 ATTTCATATTTTTTAAT-
1 ATTTTATATTTTTTAATG
266809 ATTTTATA-TTTTTAATG
1 ATTTTATATTTTTTAATG
* *
266826 ATTTTTTATGTTTTAAT
1 ATTTTATATTTTTTAAT
266843 TTATATGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 8 0.28
17 14 0.48
18 7 0.24
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
ATTTTATATTTTTTAATG
Found at i:268702 original size:21 final size:21
Alignment explanation
Indices: 268641--268697 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
268631 TAAATATAAA
* *
268641 TAAAATTATTTTATTTTAATTAT
1 TAAAAATATTTTA-ATT-ATTAT
*
268664 TAAAAATGTTTTAATTATTATT
1 TAAAAATATTTTAATTATTA-T
268686 TAAAAATATTTT
1 TAAAAATATTTT
268698 GTTATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 4 0.14
22 14 0.48
23 11 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAAAAATATTTTAATTATTAT
Found at i:269200 original size:3 final size:3
Alignment explanation
Indices: 269192--269219 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
269182 GTTGGTTTAG
269192 GGC GGC GGC GGC GGC GGC GGC GGC GGC G
1 GGC GGC GGC GGC GGC GGC GGC GGC GGC G
269220 ACCTAAAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.68, T:0.00
Consensus pattern (3 bp):
GGC
Found at i:270009 original size:42 final size:42
Alignment explanation
Indices: 269962--270056 Score: 174
Period size: 42 Copynumber: 2.3 Consensus size: 42
269952 AGTGTCTGTT
*
269962 ATAGATGGAAACTGTTAATAAGGCTTAATAGTTGTTGTAGAA
1 ATAGATGGAAACTGTTAATAAGGCTTAATAGTTGTTATAGAA
270004 ATAGATGGAAACTGTTAATAAGGCTTAATAGTTGTTATAGAA
1 ATAGATGGAAACTGTTAATAAGGCTTAATAGTTGTTATAGAA
270046 ATAGAT-GAAAC
1 ATAGATGGAAAC
270057 CTCGGTTCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 5 0.10
42 47 0.90
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (42 bp):
ATAGATGGAAACTGTTAATAAGGCTTAATAGTTGTTATAGAA
Found at i:302771 original size:18 final size:17
Alignment explanation
Indices: 302748--302786 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
302738 TATTTTTAAG
302748 AATATTAATTAATATAAA
1 AATATTAATTAA-ATAAA
* *
302766 AATATTAGTTTAATAAA
1 AATATTAATTAAATAAA
302783 AATA
1 AATA
302787 ATTTCTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AATATTAATTAAATAAA
Found at i:304340 original size:31 final size:31
Alignment explanation
Indices: 304304--304366 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
304294 GCAATTATAC
304304 ACATGAAACTTGAATTGTGATTCATA-TGTAT
1 ACATGAAACTTGAATTGTGATTCA-ACTGTAT
* *
304335 ACATGAAACTTTAATTTTGATTCAACTGTAT
1 ACATGAAACTTGAATTGTGATTCAACTGTAT
304366 A
1 A
304367 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.40
Consensus pattern (31 bp):
ACATGAAACTTGAATTGTGATTCAACTGTAT
Found at i:305648 original size:14 final size:14
Alignment explanation
Indices: 305629--305657 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
305619 TTACTGCTAT
305629 TTATTTTTACATAC
1 TTATTTTTACATAC
305643 TTATTTTTACATAC
1 TTATTTTTACATAC
305657 T
1 T
305658 ACTCATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTTTACATAC
Found at i:306827 original size:18 final size:20
Alignment explanation
Indices: 306792--306832 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
306782 GTGGTGGTGT
*
306792 TTTTTTTCATGGTGTTTG-G
1 TTTTTTTCATGGTCTTTGAG
*
306811 TTTTTTTC-TTGTCTTTGAG
1 TTTTTTTCATGGTCTTTGAG
306830 TTT
1 TTT
306833 GTAAAACCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.05, C:0.07, G:0.20, T:0.68
Consensus pattern (20 bp):
TTTTTTTCATGGTCTTTGAG
Found at i:317375 original size:58 final size:57
Alignment explanation
Indices: 317301--317480 Score: 195
Period size: 56 Copynumber: 3.1 Consensus size: 57
317291 TCAGATAATT
*
317301 TTTTTTCTGGTGTTGGCCA-TGCATTGGCTGACACCACCTTTTTTATCTGATAAAAAATAA
1 TTTTTT-T-GTGTTGGCCATTGCA-TGGCTGACACC-CCTTTTTTATCTGAAAAAAAATAA
* * * * *
317361 TTTTTTTGTGTTGGCCATTGCATGG-TCGATACTCCTTTTTTCTC-AAAAAAAAATAT
1 TTTTTTTGTGTTGGCCATTGCATGGCT-GACACCCCTTTTTTATCTGAAAAAAAATAA
* * * *
317417 TTTTTTTGTGTTGGCCATTGCATGACCGACATCCCATTTTTTATCTGAAAAAAAATTA
1 TTTTTTTGTGTTGGCCATTGCATGGCTGACA-CCCCTTTTTTATCTGAAAAAAAATAA
317475 TTTTTT
1 TTTTTT
317481 ATCTGACAAC
Statistics
Matches: 100, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
56 36 0.36
57 21 0.21
58 32 0.32
59 5 0.05
60 6 0.06
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (57 bp):
TTTTTTTGTGTTGGCCATTGCATGGCTGACACCCCTTTTTTATCTGAAAAAAAATAA
Found at i:317678 original size:60 final size:60
Alignment explanation
Indices: 317579--317718 Score: 192
Period size: 60 Copynumber: 2.4 Consensus size: 60
317569 TACAATGGCA
* * ** *
317579 TTGATGTTTTTATCAGATAAATAGGTGGTGTCGGTCATGCAATGGCCAACACAAAAAAAT
1 TTGATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATGACCAACACAAAAAAAT
* *
317639 TTGATTTTTTTATTAGATAAAAAGGTGGTGTCGACCATGCAATGACCAACACCAAAAAAT
1 TTGATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATGACCAACACAAAAAAAT
* *
317699 TT-AATTTTTTATCAAATAAA
1 TTGATTTTTTTATCAGATAAA
317719 TAGCATGACC
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
59 15 0.21
60 55 0.79
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (60 bp):
TTGATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATGACCAACACAAAAAAAT
Found at i:317839 original size:60 final size:58
Alignment explanation
Indices: 317727--318040 Score: 273
Period size: 59 Copynumber: 5.3 Consensus size: 58
317717 AATAGCATGA
* * * * * *
317727 CCAACACCAAAAAAATATTTTTTATCAGA-CAAAAAGGGGGTATCGGCTATGCAATGA
1 CCAACACAAAAAAAATATTTTTTATCAGATAAAAAAGAGGGTGTCGGCCATGCAATGG
* * *
317784 CCAACATAAAAAAAACTGATTTTTTACCAGATAAAAAAGATGGTGTCGGCCATGCAATGG
1 CCAACACAAAAAAAA-T-ATTTTTTATCAGATAAAAAAGAGGGTGTCGGCCATGCAATGG
* * * ** *
317844 CCAACATAAAAAAATTAATTTTTT-TCCAGATAAAAAAGAGAGTGTCAACCATGTAATGG
1 CCAACACAAAAAAAAT-ATTTTTTAT-CAGATAAAAAAGAGGGTGTCGGCCATGCAATGG
* * * * *
317903 TCAACACCAAAAAAAATATTTTTTATCTGA-CAAAAAG-GGAGTGTCGGTCGTGCAATGG
1 CCAACA-CAAAAAAAATATTTTTTATCAGATAAAAAAGAGG-GTGTCGGCCATGCAATGG
* * *
317961 CCAACACAAAAAAATTGA-TTTTTATCAGATAAAAAAG-GTGGTGTCGACCAATAC-ATGG
1 CCAACACAAAAAAAAT-ATTTTTTATCAGATAAAAAAGAG-GGTGTCGGCC-ATGCAATGG
318019 CCAACACCAAAAAAAATTATTT
1 CCAACA-CAAAAAAAA-TATTT
318041 GACAAAAAAG
Statistics
Matches: 206, Mismatches: 37, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
57 33 0.16
58 50 0.24
59 75 0.36
60 48 0.23
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (58 bp):
CCAACACAAAAAAAATATTTTTTATCAGATAAAAAAGAGGGTGTCGGCCATGCAATGG
Found at i:317938 original size:117 final size:117
Alignment explanation
Indices: 317826--318040 Score: 301
Period size: 117 Copynumber: 1.8 Consensus size: 117
317816 AAAAAAGATG
* *
317826 GTGTCGGCCATGCAATGGCCAACATAAAAAAATTAATTTTTTTCCAGATAAAAAAGAG-AGTGTC
1 GTGTCGGCCATGCAATGGCCAACACAAAAAAATTAATTTTTAT-CAGATAAAAAAG-GTAGTGTC
* *
317890 AACCATGTA-ATGGTCAACACCAAAAAAAA-TATTTTTTATCTGACAAAAAGGGA
64 AACCA-ATACATGGCCAACACCAAAAAAAATTATTTTTTATCTGACAAAAAGGGA
* * * * *
317943 GTGTCGGTCGTGCAATGGCCAACACAAAAAAATTGATTTTTATCAGATAAAAAAGGTGGTGTCGA
1 GTGTCGGCCATGCAATGGCCAACACAAAAAAATTAATTTTTATCAGATAAAAAAGGTAGTGTCAA
318008 CCAATACATGGCCAACACCAAAAAAAATTATTT
66 CCAATACATGGCCAACACCAAAAAAAATTATTT
318041 GACAAAAAAG
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
115 3 0.03
116 40 0.47
117 43 0.50
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (117 bp):
GTGTCGGCCATGCAATGGCCAACACAAAAAAATTAATTTTTATCAGATAAAAAAGGTAGTGTCAA
CCAATACATGGCCAACACCAAAAAAAATTATTTTTTATCTGACAAAAAGGGA
Found at i:320257 original size:2 final size:2
Alignment explanation
Indices: 320250--320288 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
320240 ATTAGTGGAG
320250 TA TA 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 TA TA T
320289 CACTCGTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:320613 original size:33 final size:33
Alignment explanation
Indices: 320576--320642 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
320566 TTGGTTTGGG
*
320576 GTCGGGTATGAGTTTTATATCTTTTAATTTTGA
1 GTCGGGTATGAGTTTTATATCTTTTAACTTTGA
320609 GTCGGGTATGAGTTTTATATCTTTTAACTTTGA
1 GTCGGGTATGAGTTTTATATCTTTTAACTTTGA
320642 G
1 G
320643 CTAATTTGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.07, G:0.22, T:0.49
Consensus pattern (33 bp):
GTCGGGTATGAGTTTTATATCTTTTAACTTTGA
Found at i:321033 original size:9 final size:9
Alignment explanation
Indices: 321019--321102 Score: 67
Period size: 9 Copynumber: 9.8 Consensus size: 9
321009 GCAAATGATT
321019 TTAAAATTA
1 TTAAAATTA
321028 TTAAAATTA
1 TTAAAATTA
321037 TT----TT-
1 TTAAAATTA
*
321041 TTAAAAATA
1 TTAAAATTA
321050 -TAAAATTA
1 TTAAAATTA
321058 TTAAAATTA
1 TTAAAATTA
321067 TTTTAAAATTAAA
1 --TTAAAATT--A
321080 TTAAAA-TA
1 TTAAAATTA
321088 -TAAAATTA
1 TTAAAATTA
321096 TTAAAAT
1 TTAAAAT
321103 AATCATCATT
Statistics
Matches: 61, Mismatches: 2, Indels: 24
0.70 0.02 0.28
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 5 0.08
8 11 0.18
9 25 0.41
10 1 0.02
11 14 0.23
13 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAAATTA
Found at i:321053 original size:21 final size:22
Alignment explanation
Indices: 321017--321059 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
321007 CAGCAAATGA
*
321017 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATTATT
321039 TTTTAAAAATA-TAAAATTATT
1 TTTTAAAAATATTAAAATTATT
321060 AAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:321098 original size:16 final size:16
Alignment explanation
Indices: 321044--321103 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 16
321034 TTATTTTTTA
321044 AAAATATAAAATTATT
1 AAAATATAAAATTATT
321060 AAAATTATTTTAAAATTAAATT
1 AAAA-TA---TAAAATT--ATT
321082 AAAATATAAAATTATT
1 AAAATATAAAATTATT
321098 AAAATA
1 AAAATA
321104 ATCATCATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 13 0.34
17 2 0.05
18 7 0.18
20 7 0.18
21 2 0.05
22 7 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATATAAAATTATT
Done.