Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 1 of 171
Found at i:480 original size:7 final size:7
Alignment explanation
Indices: 42--630 Score: 381
Period size: 7 Copynumber: 82.0 Consensus size: 7
32 GAGCCCCGAG
*
42 ACCCCAG
1 ACCCCAA
* *
49 ACCCGAG
1 ACCCCAA
*
56 ACCCCAG
1 ACCCCAA
*
63 ACCCCAG
1 ACCCCAA
70 ACCCCAGA
1 ACCCCA-A
* *
78 CCCCCAG
1 ACCCCAA
*
85 ACCCGAA
1 ACCCCAA
*
92 ACCCGAA
1 ACCCCAA
*
99 A-CCCGA
1 ACCCCAA
*
105 ACCCCGA
1 ACCCCAA
112 ACCCCGAA
1 ACCCC-AA
*
120 A-CCCGA
1 ACCCCAA
*
126 ACCCCGA
1 ACCCCAA
*
133 ACCCCGA
1 ACCCCAA
*
140 ACCCCGA
1 ACCCCAA
*
147 ACCCCGA
1 ACCCCAA
*
154 ACCCTAAA
1 ACCC-CAA
*
162 ACCCTAAA
1 ACCC-CAA
*
170 ACCCGAA
1 ACCCCAA
*
177 ACCCGAA
1 ACCCCAA
*
184 ACCCGAA
1 ACCCCAA
*
191 ACCCGAA
1 ACCCCAA
*
198 ACCCGAA
1 ACCCCAA
*
205 ACCCGAA
1 ACCCCAA
*
212 ACCCGAA
1 ACCCCAA
*
219 ACCCGAA
1 ACCCCAA
*
226 ACCCGAA
1 ACCCCAA
*
233 ACCCGAA
1 ACCCCAA
*
240 ACCCGAA
1 ACCCCAA
*
247 ACCCGAA
1 ACCCCAA
254 ACCCCAA
1 ACCCCAA
261 ACCCCAA
1 ACCCCAA
*
268 ACCCGAA
1 ACCCCAA
275 ACCCCAA
1 ACCCCAA
282 ACCCCAA
1 ACCCCAA
289 ACCCCAA
1 ACCCCAA
296 ACCCCAA
1 ACCCCAA
*
303 GCCCCAA
1 ACCCCAA
*
310 GCCCCAA
1 ACCCCAA
*
317 GCCCCAA
1 ACCCCAA
*
324 GCCCCAA
1 ACCCCAA
*
331 GCCCCAA
1 ACCCCAA
*
338 GCCCCAAA
1 ACCCC-AA
346 ACCCCAAA
1 ACCCC-AA
354 ACCCCAAA
1 ACCCC-AA
*
362 ACCCCGA
1 ACCCCAA
*
369 ACCCTAA
1 ACCCCAA
*
376 ACCCTAA
1 ACCCCAA
*
383 ACCCTAAA
1 ACCC-CAA
*
391 ACCCCCTA
1 A-CCCCAA
399 ACCCCAA
1 ACCCCAA
406 ACCCCAA
1 ACCCCAA
413 ACCCCAA
1 ACCCCAA
*
420 ACCCTAAA
1 ACCC-CAA
428 ACCCCAA
1 ACCCCAA
*
435 ACCCCGA
1 ACCCCAA
*
442 ACCCTAAA
1 ACCC-CAA
450 ACCCCAA
1 ACCCCAA
*
457 ACCCCGA
1 ACCCCAA
464 ACCCCAAA
1 ACCCC-AA
*
472 ACCCTAA
1 ACCCCAA
*
479 ACCCTAA
1 ACCCCAA
*
486 ACCCTAAA
1 ACCC-CAA
**
494 ACCCTGA
1 ACCCCAA
*
501 ACCCTAA
1 ACCCCAA
* *
508 AACCCGA
1 ACCCCAA
*
515 ACCCCGA
1 ACCCCAA
*
522 GCCCCTAAA
1 ACCCC--AA
*
531 ACCCTAA
1 ACCCCAA
* *
538 AACCCTA
1 ACCCCAA
*
545 ACCCTTAA
1 ACCC-CAA
553 AGCCCCAA
1 A-CCCCAA
*
561 GCCCCAA
1 ACCCCAA
*
568 GCCCCAA
1 ACCCCAA
*
575 GCCCCAA
1 ACCCCAA
*
582 GCCCCAA
1 ACCCCAA
*
589 GCCCCAA
1 ACCCCAA
*
596 GCCCCAA
1 ACCCCAA
*
603 GCCCCAA
1 ACCCCAA
*
610 GCCCCAA
1 ACCCCAA
*
617 GCCCCAA
1 ACCCCAA
*
624 GCCCCAA
1 ACCCCAA
631 TATAAATACT
Statistics
Matches: 510, Mismatches: 56, Indels: 32
0.85 0.09 0.05
Matches are distributed among these distances:
6 6 0.01
7 421 0.83
8 73 0.14
9 10 0.02
ACGTcount: A:0.38, C:0.50, G:0.09, T:0.03
Consensus pattern (7 bp):
ACCCCAA
Found at i:549 original size:22 final size:22
Alignment explanation
Indices: 352--549 Score: 113
Period size: 22 Copynumber: 9.0 Consensus size: 22
342 CAAAACCCCA
* *
352 AAACCCCAAAACCCCGAACCCT-
1 AAACCCTAAAA-CCCTAACCCTC
*
374 AAACCCT-AAACCCTAAAACCCCC
1 AAACCCTAAAACCCT--AACCCTC
* * * *
397 TAACCCCAAACCCCAAACCC-C
1 AAACCCTAAAACCCTAACCCTC
*
418 AAACCCTAAAACCCCAAACCC-C
1 AAACCCTAAAA-CCCTAACCCTC
* *
440 GAACCCTAAAACCCCAAACCC-C
1 AAACCCTAAAA-CCCTAACCCTC
* *
462 GAACCCCAAAACCCTAAACCCT-
1 AAACCCTAAAACCCT-AACCCTC
*
484 AAACCCTAAAACCCTGAACCCTA
1 AAACCCTAAAACCCT-AACCCTC
* * * * *
507 AAACCC-GAACCCCGAGCCCCTA
1 AAACCCTAAAACCCTA-ACCCTC
529 AAACCCTAAAACCCTAACCCT
1 AAACCCTAAAACCCTAACCCT
550 TAAAGCCCCA
Statistics
Matches: 142, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.02
21 16 0.11
22 101 0.71
23 17 0.12
24 5 0.04
ACGTcount: A:0.41, C:0.48, G:0.04, T:0.08
Consensus pattern (22 bp):
AAACCCTAAAACCCTAACCCTC
Found at i:1222 original size:173 final size:170
Alignment explanation
Indices: 936--1278 Score: 494
Period size: 173 Copynumber: 2.0 Consensus size: 170
926 TTTCGACATC
* *
936 TGATTCTTGAATGAGACTTCCTAACAGTTAATAAAGAAAATGACAAAAAACACGATCCACCGAGT
1 TGATTCTTGAAGGAGACTTCCTAACAGTTAATAAAAAAAATGACAAAAAACACGATCCACCGAGT
* *
1001 ATTTCTGTAATTATACAAGAAATCAAACAAAGATCTTCAAGGTTTGAGAGCTTTACCTGTTCATT
66 ATATCTGTAATTATACAAGAAATCAAACAAAGATCTTCAAGGTTTGAGAGCTTTACCTGTTCATC
* *
1066 TGCAAGGAA-AACGGCGAACCAAGCAGCCTATGAAGCACGG
131 TGCAA-GAAGAAAGGCGAACCAAGCAACCTATGAAGCACGG
* * * * *
1106 TGATTCTTGAAGGAGACTTGCTAACAG-TAATAAAAAATATCAATGACAAATAACCCGATCGATC
1 TGATTCTTGAAGGAGACTTCCTAACAGTTAAT-AAAAA-A--AATGACAAAAAACACGATCCACC
*
1170 GAGTATATCTGTAATTATACAAGAAATCAAACAAAGATCTT-TAGAGTTTGAGAGCTTTACCTGT
62 GAGTATATCTGTAATTATACAAGAAATCAAACAAAGATCTTCAAG-GTTTGAGAGCTTTACCTGT
*
1234 TCATCTGCGAGAAGAAAGGCGAACCAAGCAACCTATGAAGCACGG
126 TCATCTGCAAGAAGAAAGGCGAACCAAGCAACCTATGAAGCACGG
1279 ACCAGTGTCG
Statistics
Matches: 154, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
169 4 0.03
170 29 0.19
171 1 0.01
172 5 0.03
173 115 0.75
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (170 bp):
TGATTCTTGAAGGAGACTTCCTAACAGTTAATAAAAAAAATGACAAAAAACACGATCCACCGAGT
ATATCTGTAATTATACAAGAAATCAAACAAAGATCTTCAAGGTTTGAGAGCTTTACCTGTTCATC
TGCAAGAAGAAAGGCGAACCAAGCAACCTATGAAGCACGG
Found at i:1818 original size:26 final size:26
Alignment explanation
Indices: 1782--1832 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1772 AACGAATTTA
1782 TGAACAAGAAGACTTCCAAGATGTGC
1 TGAACAAGAAGACTTCCAAGATGTGC
*
1808 TGAACAAGAAGAGTTCCAAGATGTG
1 TGAACAAGAAGACTTCCAAGATGTG
1833 TTGTATTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (26 bp):
TGAACAAGAAGACTTCCAAGATGTGC
Found at i:3529 original size:7 final size:7
Alignment explanation
Indices: 3519--3555 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
3509 CCCAAGCCCC
3519 AAGCTTT
1 AAGCTTT
3526 AAGCTTT
1 AAGCTTT
3533 AAGCTTT
1 AAGCTTT
3540 AAGCTTT
1 AAGCTTT
3547 AAGCTTT
1 AAGCTTT
3554 AA
1 AA
3556 ACCTTAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (7 bp):
AAGCTTT
Found at i:3536 original size:21 final size:21
Alignment explanation
Indices: 3512--3555 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3502 CTTAAATCCC
3512 AAGCCCCAAGCTTTAAGCTTT
1 AAGCCCCAAGCTTTAAGCTTT
***
3533 AAGCTTTAAGCTTTAAGCTTT
1 AAGCCCCAAGCTTTAAGCTTT
3554 AA
1 AA
3556 ACCTTAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (21 bp):
AAGCCCCAAGCTTTAAGCTTT
Found at i:3562 original size:7 final size:7
Alignment explanation
Indices: 3553--3621 Score: 120
Period size: 7 Copynumber: 9.9 Consensus size: 7
3543 CTTTAAGCTT
*
3553 TAAACCT
1 TAAACCC
3560 TAAACCC
1 TAAACCC
3567 TAAACCC
1 TAAACCC
3574 TAAACCC
1 TAAACCC
3581 TAAACCC
1 TAAACCC
3588 TAAACCC
1 TAAACCC
3595 TAAACCC
1 TAAACCC
*
3602 TAAACCT
1 TAAACCC
3609 TAAACCC
1 TAAACCC
3616 TAAACC
1 TAAACC
3622 TCAAATCTCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:3562 original size:21 final size:21
Alignment explanation
Indices: 3519--3562 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3509 CCCAAGCCCC
* *
3519 AAGCTTTAAGCTTTAAGCTTT
1 AAGCTTTAAGCTTTAAACCTT
3540 AAGCTTTAAGCTTTAAACCTT
1 AAGCTTTAAGCTTTAAACCTT
3561 AA
1 AA
3563 ACCCTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (21 bp):
AAGCTTTAAGCTTTAAACCTT
Found at i:3642 original size:7 final size:7
Alignment explanation
Indices: 3632--3657 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3622 TCAAATCTCA
3632 AGCCTCG
1 AGCCTCG
3639 AGCCTCG
1 AGCCTCG
3646 AGCCTCG
1 AGCCTCG
3653 AGCCT
1 AGCCT
3658 TAAACCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.42, G:0.27, T:0.15
Consensus pattern (7 bp):
AGCCTCG
Found at i:3791 original size:22 final size:21
Alignment explanation
Indices: 3721--3791 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
3711 TCTCAAACCT
3721 TAAAC-ATTAAATCCTAAATCC
1 TAAACTATTAAATCCTAAAT-C
* *
3742 TAAACCATTAAACCCTTAAATC
1 TAAACTATTAAATCC-TAAATC
* *
3764 TTAACTTTTAAATCCTAAACTC
1 TAAACTATTAAATCCTAAA-TC
3786 TAAACT
1 TAAACT
3792 CTAGACCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
21 9 0.22
22 27 0.66
23 5 0.12
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAACTATTAAATCCTAAATC
Found at i:3885 original size:21 final size:21
Alignment explanation
Indices: 3861--3925 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
3851 ACCCCTACCT
*
3861 CTTGACCTCGAACCCCGAACC
1 CTTGACCTCGAGCCCCGAACC
* *
3882 CTTGAGCTCCGAGCCCCGAGCC
1 CTTGACCT-CGAGCCCCGAACC
*
3904 C-CGAGCCTCGAGCCCCGAACC
1 CTTGA-CCTCGAGCCCCGAACC
3925 C
1 C
3926 AGTCTATCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.11
Consensus pattern (21 bp):
CTTGACCTCGAGCCCCGAACC
Found at i:3895 original size:7 final size:7
Alignment explanation
Indices: 3885--3921 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
3875 CCGAACCCTT
*
3885 GAGCTCC
1 GAGCCCC
3892 GAGCCCC
1 GAGCCCC
3899 GAGCCCC
1 GAGCCCC
*
3906 GAGCCTC
1 GAGCCCC
3913 GAGCCCC
1 GAGCCCC
3920 GA
1 GA
3922 ACCCAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.16, C:0.49, G:0.30, T:0.05
Consensus pattern (7 bp):
GAGCCCC
Found at i:4359 original size:13 final size:13
Alignment explanation
Indices: 4343--4368 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4333 AATTTTAATT
4343 GTTTCATTTATTG
1 GTTTCATTTATTG
4356 GTTTCATTTATTG
1 GTTTCATTTATTG
4369 TCTACCGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
GTTTCATTTATTG
Found at i:10084 original size:23 final size:23
Alignment explanation
Indices: 10058--10178 Score: 163
Period size: 23 Copynumber: 5.2 Consensus size: 23
10048 ACACTAGCGC
10058 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
10081 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
10104 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* *
10129 GCTCTCCGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
10152 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
10175 GCTC
1 GCTC
10179 AGTACTTTGT
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
22 3 0.03
23 65 0.75
25 16 0.18
26 3 0.03
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:10127 original size:48 final size:46
Alignment explanation
Indices: 10058--10178 Score: 163
Period size: 48 Copynumber: 2.6 Consensus size: 46
10048 ACACTAGCGC
* *
10058 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCAC-TCTGCGT
* *
10104 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACTCTGCGT
*
10152 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
10179 AGTACTTTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
46 26 0.39
47 2 0.03
48 39 0.58
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACTCTGCGT
Found at i:10197 original size:39 final size:39
Alignment explanation
Indices: 10143--10217 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
10133 TCCGATTAGC
*
10143 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
*
10182 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTC
10218 TCTGTTGCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (39 bp):
ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:10212 original size:23 final size:23
Alignment explanation
Indices: 10177--10270 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
10167 CTTTGTGTGC
*
10177 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
10200 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
10223 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
10248 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
10270 T
1 T
10271 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:17080 original size:12 final size:13
Alignment explanation
Indices: 17046--17081 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
17036 GTTTAACGAT
*
17046 ATTTTAAAAAGTG
1 ATTTTAAAAAGTA
*
17059 TTTTTAAAAAGTA
1 ATTTTAAAAAGTA
17072 ATTTTAAAAA
1 ATTTTAAAAA
17082 ATTTAGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (13 bp):
ATTTTAAAAAGTA
Found at i:17457 original size:20 final size:20
Alignment explanation
Indices: 17420--17457 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17410 TCCATTTGAA
*
17420 AAAAAATATTTTTGAAAAGC
1 AAAAAATATTTTTCAAAAGC
17440 AAAAAAT-TTTCTTCAAAA
1 AAAAAATATTT-TTCAAAA
17458 ATTACTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAAAATATTTTTCAAAAGC
Found at i:18074 original size:30 final size:30
Alignment explanation
Indices: 18027--18084 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
18017 AAAATGATAT
*
18027 ATTTACTATTTTATTTAATATACATAAATTA
1 ATTTACTATTTTATTTAATAAACA-AAATTA
18058 ATTTACT-TATTT-TTTAATAAACAAAAT
1 ATTTACTAT-TTTATTTAATAAACAAAAT
18085 AATAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 4 0.16
30 11 0.44
31 10 0.40
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTACTATTTTATTTAATAAACAAAATTA
Found at i:23713 original size:58 final size:58
Alignment explanation
Indices: 23646--23773 Score: 172
Period size: 58 Copynumber: 2.2 Consensus size: 58
23636 TAATTCATAT
* *
23646 TTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACATATTATTTTATTAAACTGTA
1 TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-ATA-T-TTTTATTAAACTATA
* *
23704 TTTAATAATAATTATGTTAAAATATAATTAAATAAATTAATATTTTTATTAAATTATA
1 TTTAATAATAATTATATTAAAATATAATTAAATAAATTAATATTTTTATTAAACTATA
23762 TTTAATAATAAT
1 TTTAATAATAAT
23774 CATTAAAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
58 46 0.73
59 3 0.05
60 6 0.10
61 8 0.13
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (58 bp):
TTTAATAATAATTATATTAAAATATAATTAAATAAATTAATATTTTTATTAAACTATA
Found at i:23965 original size:16 final size:16
Alignment explanation
Indices: 23944--24015 Score: 101
Period size: 16 Copynumber: 4.5 Consensus size: 16
23934 TGAATTACTG
23944 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTTC
23960 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTTC
* *
23976 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTTC
*
23992 ATTACACCTCTA-TTC
1 ATTACAGCTCTATTTC
24007 TATTACAGC
1 -ATTACAGC
24016 GAACCAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
15 2 0.04
16 47 0.96
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTTC
Found at i:25435 original size:24 final size:26
Alignment explanation
Indices: 25408--25455 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
25398 CAAAAATAAT
25408 ATTGAT-TGTGAAT-TATATTATTAA
1 ATTGATATGTGAATCTATATTATTAA
* *
25432 ATTGATATTTGAATCTATTTTATT
1 ATTGATATGTGAATCTATATTATT
25456 TTATTCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 6 0.30
26 8 0.40
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTGATATGTGAATCTATATTATTAA
Found at i:25669 original size:17 final size:18
Alignment explanation
Indices: 25649--25686 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
25639 ATATCATATC
*
25649 TATTAAAACAACTAA-AA
1 TATTAAAAAAACTAATAA
25666 TATTAAAAAAACTAATAA
1 TATTAAAAAAACTAATAA
25684 TAT
1 TAT
25687 ACATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (18 bp):
TATTAAAAAAACTAATAA
Found at i:27100 original size:31 final size:31
Alignment explanation
Indices: 27065--27141 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
27055 ATAGAGTTAA
27065 AATTGTATAAAATGTATACACCAAAAAAAAG
1 AATTGTATAAAATGTATACACCAAAAAAAAG
27096 AATTGTATAAAATGTATACACCAAAAAAAAG
1 AATTGTATAAAATGTATACACCAAAAAAAAG
27127 AATTGTATAAAATGT
1 AATTGTATAAAATGT
27142 CTTCTAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (31 bp):
AATTGTATAAAATGTATACACCAAAAAAAAG
Found at i:27744 original size:22 final size:23
Alignment explanation
Indices: 27718--27777 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
27708 TATAAATGAT
* * *
27718 AAAATTTTAATTTAATTCT-TTA
1 AAAATTATAATTTAATTATCGTA
* *
27740 AAAATTATATTTTTATTATCGTA
1 AAAATTATAATTTAATTATCGTA
27763 AAAATTATAATTTAA
1 AAAATTATAATTTAA
27778 CTTCGATCCT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (23 bp):
AAAATTATAATTTAATTATCGTA
Found at i:28619 original size:26 final size:27
Alignment explanation
Indices: 28590--28650 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
28580 ACTTGAAATT
28590 TAATAT-ATATACTTTAATTTT-TACCA
1 TAATATAATATA-TTTAATTTTATACCA
* * *
28616 TAATTTAATCTATTTAATTTTATATCA
1 TAATATAATATATTTAATTTTATACCA
28643 TAAT-TAAT
1 TAATATAAT
28651 CTGAATAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATATAATATATTTAATTTTATACCA
Found at i:28651 original size:26 final size:26
Alignment explanation
Indices: 28602--28652 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
28592 ATATATATAC
28602 TTTAATTTTTACCATAATTTAATCTA
1 TTTAATTTTTACCATAATTTAATCTA
*
28628 TTTAATTTTATATCATAA-TTAATCT
1 TTTAATTTT-TACCATAATTTAATCT
28653 GAATAGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTAATTTTTACCATAATTTAATCTA
Found at i:35561 original size:22 final size:22
Alignment explanation
Indices: 35516--35562 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
35506 CAAAATGCTG
* *
35516 TAAGAGAAATTATGAAGAATTC
1 TAAGAGAAATTAAGAAGAACTC
*
35538 TAAGAGAAATTAAGATGAACTC
1 TAAGAGAAATTAAGAAGAACTC
35560 TAA
1 TAA
35563 TGTAGCTGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (22 bp):
TAAGAGAAATTAAGAAGAACTC
Found at i:59742 original size:24 final size:26
Alignment explanation
Indices: 59705--59756 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
59695 ATATATTTCT
59705 TATTATATGAAATA-ATCAAACATAAA
1 TATTATATGAAATATATCAAA-ATAAA
*
59731 TATTA-AT-AAATATATTAAAATAAA
1 TATTATATGAAATATATCAAAATAAA
59755 TA
1 TA
59757 AAATACAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 12 0.50
25 7 0.29
26 5 0.21
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (26 bp):
TATTATATGAAATATATCAAAATAAA
Found at i:66513 original size:57 final size:57
Alignment explanation
Indices: 66425--66538 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
66415 CCATGTATTT
66425 GTATAGATGGAACACATGGGTTTTATATGATTAAAGATCCGTGCATGTTATTAATTC
1 GTATAGATGGAACACATGGGTTTTATATGATTAAAGATCCGTGCATGTTATTAATTC
66482 GTATAGATGGAACACATGGGTTTTATATGATTAAAGATCCGTGCATGTTATTAATTC
1 GTATAGATGGAACACATGGGTTTTATATGATTAAAGATCCGTGCATGTTATTAATTC
66539 TCCCTGTTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (57 bp):
GTATAGATGGAACACATGGGTTTTATATGATTAAAGATCCGTGCATGTTATTAATTC
Found at i:82142 original size:19 final size:18
Alignment explanation
Indices: 82118--82169 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 18
82108 ACTTCTTATC
82118 TGTTAAATATTATTAAAA
1 TGTTAAATATTATTAAAA
*
82136 TTGTTAAA-ATT-TT-ATA
1 -TGTTAAATATTATTAAAA
*
82152 TGTTAAATACTATTAAAA
1 TGTTAAATATTATTAAAA
82170 ATGCTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
15 7 0.26
16 4 0.15
17 4 0.15
18 5 0.19
19 7 0.26
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (18 bp):
TGTTAAATATTATTAAAA
Found at i:107053 original size:18 final size:17
Alignment explanation
Indices: 107016--107065 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
107006 ACAGTCAAAA
*
107016 TATTTATAAACTATATG
1 TATTTATAATCTATATG
*
107033 TATTTATAATGTATGATG
1 TATTTATAATCTAT-ATG
*
107051 TATGTATAATCTATA
1 TATTTATAATCTATA
107066 AATTAGATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (17 bp):
TATTTATAATCTATATG
Found at i:107633 original size:58 final size:58
Alignment explanation
Indices: 107504--107663 Score: 171
Period size: 58 Copynumber: 2.7 Consensus size: 58
107494 CCGATGTGGG
* * * * * *
107504 AACATTTGTCAAG-TTCAAGTCTTAACTTGAACAAAAAAAAGTTCCGGCCCCAATGTGAA
1 AACAATTGTCAAGTTTAAAG-CTTAACTTGGACCAAAAAAA-TTCCGGACCCAATATGAA
* *
107563 AACAATTATCAAGTTTAAAGCTTAACTTGGACCAAAAAAATT-GGAGACCCAATATGAA
1 AACAATTGTCAAGTTTAAAGCTTAACTTGGACCAAAAAAATTCCG-GACCCAATATGAA
* * *
107621 AATAATTGTCAAGTTTGAAGCCTAACTTGGATCCAAAAAAATT
1 AACAATTGTCAAGTTTAAAGCTTAACTTGGA-CCAAAAAAATT
107664 TAAGCCACAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
57 1 0.01
58 40 0.47
59 40 0.47
60 5 0.06
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.26
Consensus pattern (58 bp):
AACAATTGTCAAGTTTAAAGCTTAACTTGGACCAAAAAAATTCCGGACCCAATATGAA
Found at i:107880 original size:30 final size:31
Alignment explanation
Indices: 107846--107921 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
107836 CTTTAACTTA
* *
107846 AAGTTCAAGCCTTAATGTGAG-ATATTTGTC
1 AAGTTCAAGCCTTAATGTGAGAACAATTGTC
** *
107876 AAGTTCAAGCCCCAATGTGTGAACAATTGTC
1 AAGTTCAAGCCTTAATGTGAGAACAATTGTC
*
107907 AAGTTCAAGGCTTAA
1 AAGTTCAAGCCTTAA
107922 CTTGAACTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 18 0.49
31 19 0.51
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (31 bp):
AAGTTCAAGCCTTAATGTGAGAACAATTGTC
Found at i:112420 original size:6 final size:6
Alignment explanation
Indices: 112414--112470 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
112404 CGTCCTCCGC
* * *
112414 CATCGC CATCGC CATCGC CATCGT CATCGT CATCGT CATCGT CATCGT
1 CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT
112462 CATCGT CAT
1 CATCGT CAT
112471 GGCCTTTAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.18, C:0.39, G:0.16, T:0.28
Consensus pattern (6 bp):
CATCGT
Found at i:113517 original size:6 final size:6
Alignment explanation
Indices: 113509--113542 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
113499 CAACGATGGG
* *
113509 TCCGGG TCCGGT TCTGGT TCCGGT TCCGGT TCCG
1 TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCG
113543 TCGGTTCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.35, T:0.32
Consensus pattern (6 bp):
TCCGGT
Found at i:116112 original size:13 final size:13
Alignment explanation
Indices: 116094--116118 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
116084 AATAATTAAG
116094 ATGGAGAAAAGAA
1 ATGGAGAAAAGAA
116107 ATGGAGAAAAGA
1 ATGGAGAAAAGA
116119 GAAACGAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.32, T:0.08
Consensus pattern (13 bp):
ATGGAGAAAAGAA
Found at i:122467 original size:28 final size:26
Alignment explanation
Indices: 122408--122458 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
122398 GGATTTCGAA
*
122408 AATATTATTATATTTTTATTTTAATT
1 AATATTATTATATATTTATTTTAATT
122434 AATATTATTATATATTT-TTTTAATT
1 AATATTATTATATATTTATTTTAATT
122459 TTTTATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
AATATTATTATATATTTATTTTAATT
Found at i:123224 original size:17 final size:17
Alignment explanation
Indices: 123199--123245 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
123189 AATAATATAG
* *
123199 TTATCATATTATTTTTA
1 TTATTATATTATTTTGA
123216 TTATTATATT-TTTTGA
1 TTATTATATTATTTTGA
* *
123232 ATAATATATTATTT
1 TTATTATATTATTT
123246 GAATATGTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTATTATATTATTTTGA
Found at i:123239 original size:16 final size:16
Alignment explanation
Indices: 123220--123250 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
123210 TTTTTATTAT
*
123220 TATATTTTTTGAATAA
1 TATATTATTTGAATAA
123236 TATATTATTTGAATA
1 TATATTATTTGAATA
123251 TGTGGAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TATATTATTTGAATAA
Found at i:133302 original size:79 final size:79
Alignment explanation
Indices: 133171--133330 Score: 241
Period size: 79 Copynumber: 2.0 Consensus size: 79
133161 TACTGATGAT
* *
133171 AAAGGTGTGAATACATTGACCAAAGCCTTACCAAGAAGAAAGTTTGAAGCTTGTTATGGCGAACA
1 AAAGGTGTGAATACATTGACCAAAGCCTTACCAAAAAGAAAGTTTGAAGCTTGTTATAGCGAACA
*
133236 -TCTCCACCTAGTAG
66 TTC-CCACCTAATAG
* * * *
133250 AAAGGTGTGAATATATTGACCAAAGTCTTTCCAAAAAGGAAGTTTGAAGCTTGTTATAGCGAACA
1 AAAGGTGTGAATACATTGACCAAAGCCTTACCAAAAAGAAAGTTTGAAGCTTGTTATAGCGAACA
133315 TTCCCACCTAATAG
66 TTCCCACCTAATAG
133329 AA
1 AA
133331 GGGGGAGATT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 71 0.97
80 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (79 bp):
AAAGGTGTGAATACATTGACCAAAGCCTTACCAAAAAGAAAGTTTGAAGCTTGTTATAGCGAACA
TTCCCACCTAATAG
Found at i:151264 original size:2 final size:2
Alignment explanation
Indices: 151257--151283 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
151247 CTTTTCCAAC
151257 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 T
151284 CTTAGTTCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:152866 original size:3 final size:3
Alignment explanation
Indices: 152860--152908 Score: 53
Period size: 3 Copynumber: 15.0 Consensus size: 3
152850 TTTTATTAAA
*
152860 AAG AAG AAG AAG AAG AAG AATA AAG AAAG AAAG AAAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AA-G AAG -AAG -AAG -AAG AAG AAG AAG AAG
152909 TGAACTGACC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 29 0.69
4 13 0.31
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:154089 original size:60 final size:57
Alignment explanation
Indices: 153724--154307 Score: 402
Period size: 58 Copynumber: 10.1 Consensus size: 57
153714 GATATCAATA
* * *
153724 TTTTTTATCAGA-AAAATAA-AA-TTTTTTGGTGTTGATCAATGCTTGGCCGACACTAC
1 TTTTTTATCAGATAAAA-AATAATTTTTTTGGTGTTGGTC-ATGCTTGGCTGACACCAC
* * ** * *
153780 CTTTTTATAAGATAAAAAA-AA---AATTGGTGTTAGTCATGCATT-GATCGACACCACC
1 TTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCATGC-TTGGCT-GACACCA-C
* ** *
153835 TTTTTTATCTGATAAAAAATAATTTTTTTGGTGTTGACCATGTATTGGCTGACACCAC
1 TTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCATG-CTTGGCTGACACCAC
* * * *
153893 TTTTTTATCAGATGAAAAAT-TTTTTTTTAGTTTTGG-CTATTGCTTGG-TCGACACCATC
1 TTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTC-A-TGCTTGGCT-GACACCA-C
* * * * *
153951 TTTTTTATCTGATAAAAAATTCAAAATTTTTT-GTGTTGATCATGCATTGG-TCAACACTAGC
1 TTTTTTATCAGATAAAAAA-T--AATTTTTTTGGTGTTGGTCATGC-TTGGCT-GACACCA-C
* *
154012 ATTTTTTATCATATAAAAAAT-ATTTTTTTGGTGTTGGCCATTGCTTGGCTGACACCAGC
1 -TTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCA-TGCTTGGCTGACACCA-C
* *
154071 ATTATTTTATCAGAT-AAAAAT-A-TTTTTTGGTGTT--TCATTGCTTGGCCGACACCAT
1 -TT-TTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCA-TGCTTGGCTGACACCAC
* *
154126 TTTTTTATCTA-ATAAAAAATTCAAATTTTTTTTGTGTTGGTCATGCATT-GATCGACACCAC
1 TTTTTTATC-AGATAAAAAA-T--AATTTTTTTGGTGTTGGTCATGC-TTGGCT-GACACCAC
* * *
154187 CTTTTTATCAGATAAAAAAT-ATTTTTTTGGTGTTGGTAATTGCTTGGCCGACACCAC
1 TTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCA-TGCTTGGCTGACACCAC
* * * *
154244 TTTTTTTATCTGATAAAAAAATAAATTTTTTGGTGTAGGTCATGCATTGGCCGACACCAAC
1 -TTTTTTATCAGAT-AAAAAATAATTTTTTTGGTGTTGGTCATGC-TTGGCTGACACC-AC
154305 TTT
1 TTT
154308 CCCTCCTTTC
Statistics
Matches: 424, Mismatches: 60, Indels: 84
0.75 0.11 0.15
Matches are distributed among these distances:
53 14 0.03
54 26 0.06
55 18 0.04
56 36 0.08
57 55 0.13
58 74 0.17
59 72 0.17
60 56 0.13
61 49 0.12
62 24 0.06
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (57 bp):
TTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGGTCATGCTTGGCTGACACCAC
Found at i:154183 original size:117 final size:116
Alignment explanation
Indices: 153725--154307 Score: 360
Period size: 117 Copynumber: 5.0 Consensus size: 116
153715 ATATCAATAT
* * *
153725 TTTTTATCAGA-AAAATAA-AATTTTTTGGTGTTGATCAA-TGCTTGGCCGACACTAC-CTTTTT
1 TTTTTATCAGATAAAA-AATATTTTTTTGGTGTTG-T-AATTGCTTGGCCGACACCACTTTTTTT
* *
153786 AT-AAGATAAAAAAA-AAA----TTGGTGTTA-GTCATGCATTGATCGACACCACC
63 ATCTA-ATAAAAAAATAAATTTTTTGGTG-TAGGTCATGCATTGACCGACACCACC
* * *
153835 TTTTTTATCTGATAAAAAATAATTTTTTTGGTGTTG-ACCA-TGTATTGGCTGACACCAC-TTTT
1 -TTTTTATCAGATAAAAAAT-ATTTTTTTGGTGTTGTA--ATTG-CTTGGCCGACACCACTTTTT
* ** * * * ** *
153897 TTATC-AGAT-GAAAAAT-TTTTTTTTAGTTTTGG-CTATTGC-TTGGTCGACACCATCT
61 TTATCTA-ATAAAAAAATAAATTTTTTGGTGTAGGTC-A-TGCATTGACCGACACCA-CC
* * * * * * *
153952 TTTTTATCTGATAAAAAATTCAAAATTTTTT-GTGTTGATCA-TGCATTGGTCAACACTAGCATT
1 TTTTTATCAGATAAAAAA-T---ATTTTTTTGGTGTTG-TAATTGC-TTGGCCGACACCA-CTTT
* * * * * *
154015 TTTTATC--ATATAAAAAAT-ATTTTTTTGGTGTTGGCCATTGC-TTGGCTGACACCAGCAT
59 TTTTATCTAATA-AAAAAATAAATTTTTTGGTGTAGGTCA-TGCATTGACCGACACCA-C-C
*
154073 TATTTTATCAGAT-AAAAATA-TTTTTTGGTGTT-TCATTGCTTGGCCGACACCA-TTTTTTTAT
1 T-TTTTATCAGATAAAAAATATTTTTTTGGTGTTGTAATTGCTTGGCCGACACCACTTTTTTTAT
* * * *
154134 CTAATAAAAAATTCAAATTTTTTTTGTGTTGGTCATGCATTGATCGACACCACC
65 CTAATAAAAAAAT-AAA-TTTTTTGGTGTAGGTCATGCATTGACCGACACCACC
154188 TTTTTATCAGATAAAAAATATTTTTTTGGTGTTGGTAATTGCTTGGCCGACACCACTTTTTTTAT
1 TTTTTATCAGATAAAAAATATTTTTTTGGTGTT-GTAATTGCTTGGCCGACACCACTTTTTTTAT
* * *
154253 CTGATAAAAAAATAAATTTTTTGGTGTAGGTCATGCATTGGCCGACACCAAC
65 CTAATAAAAAAATAAATTTTTTGGTGTAGGTCATGCATTGACCGACACCACC
154305 TTT
1 TTT
154308 CCCTCCTTTC
Statistics
Matches: 381, Mismatches: 49, Indels: 78
0.75 0.10 0.15
Matches are distributed among these distances:
110 1 0.00
111 12 0.03
112 12 0.03
113 46 0.12
114 17 0.04
115 26 0.07
116 62 0.16
117 70 0.18
118 42 0.11
119 29 0.08
120 46 0.12
121 8 0.02
122 10 0.03
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (116 bp):
TTTTTATCAGATAAAAAATATTTTTTTGGTGTTGTAATTGCTTGGCCGACACCACTTTTTTTATC
TAATAAAAAAATAAATTTTTTGGTGTAGGTCATGCATTGACCGACACCACC
Found at i:154935 original size:60 final size:59
Alignment explanation
Indices: 154836--155225 Score: 266
Period size: 60 Copynumber: 6.6 Consensus size: 59
154826 GAGAAAGGAG
* * * ** *
154836 AAAAAGTTGATGTCGGCCAATGC-ATGGCCAACATAAAAAAATTTAAATTTTTATCAGATA
1 AAAAAGGTGGTGTCGGCCAA-GCAATGACCAACACCAAAAAA-TTAATTTTTTATCAGATA
* * *
154896 AAAAAGGTGGTGTCGGCCAAGCAATGGCCAACACCAAAAAA-AATATTTTTTATCTGATA
1 AAAAAGGTGGTGTCGGCCAAGCAATGACCAACACCAAAAAATTA-ATTTTTTATCAGATA
** * *
154955 AAAAATACTGGTGTTGGCCAA-TACATGACCAACACCAAAAAAAATTTGAATTTTTTATCAGATA
1 AAAAA-GGTGGTGTCGGCCAAGCA-ATGACCAACACC--AAAAAA-TT-AATTTTTTATCAGATA
* * * **
155019 AAAAAAGTGGTGTCGACCAAGCAATAACCAACACCAAAAAA-T-ATTTTTTATTTGAT-
1 AAAAAGGTGGTGTCGGCCAAGCAATGACCAACACCAAAAAATTAATTTTTTATCAGATA
* ** * * * *
155075 AAAAAGATGGTGTCAACCAATG-TATGACCAACACCAAAAAATCATTTTTTTATCAAATA
1 AAAAAGGTGGTGTCGGCCAA-GCAATGACCAACACCAAAAAATTAATTTTTTATCAGATA
** **** * *
155134 AAAAAGGTGGTGTCGATCAATGC-ATGGTTGACATC--AAAATT--TTTTTTATCTGAT-
1 AAAAAGGTGGTGTCGGCCAA-GCAATGACCAACACCAAAAAATTAATTTTTTATCAGATA
* * *
155188 AAAAAGGTGATGTCGGCTAAGCATTGACCAACACCAAA
1 AAAAAGGTGGTGTCGGCCAAGCAATGACCAACACCAAA
155226 TTTTTTTTCA
Statistics
Matches: 260, Mismatches: 52, Indels: 40
0.74 0.15 0.11
Matches are distributed among these distances:
53 2 0.01
54 22 0.08
55 11 0.04
56 35 0.13
57 18 0.07
58 11 0.04
59 48 0.18
60 57 0.22
61 6 0.02
62 6 0.02
63 23 0.09
64 20 0.08
65 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (59 bp):
AAAAAGGTGGTGTCGGCCAAGCAATGACCAACACCAAAAAATTAATTTTTTATCAGATA
Found at i:154955 original size:59 final size:59
Alignment explanation
Indices: 154883--155148 Score: 265
Period size: 59 Copynumber: 4.5 Consensus size: 59
154873 AAAATTTAAA
*
154883 TTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGGCCAACACCAAAAAAAATAT
1 TTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGACCAACACCAAAAAAAATAT
* ** * *
154942 TTTTTATCTGATAAAAAATACTGGTGTTGGCCAA-TACATGACCAACACCAAAAAAAATTTGAAT
1 TTTTTATCAGATAAAAAA-GGTGGTGTCGGCCAAGCA-ATGACCAACACCAAAAAAAA--T--AT
* * *
155006 TTTTTATCAGATAAAAAAAGTGGTGTCGACCAAGCAATAACCAACACC--AAAAAATAT
1 TTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGACCAACACCAAAAAAAATAT
** * ** * *
155063 TTTTTATTTGAT-AAAAAGATGGTGTCAACCAATG-TATGACCAACACCAAAAAATCAT-T
1 TTTTTATCAGATAAAAAAGGTGGTGTCGGCCAA-GCAATGACCAACACCAAAAAA-AATAT
*
155121 TTTTTATCAAATAAAAAAGGTGGTGTCG
1 TTTTTATCAGATAAAAAAGGTGGTGTCG
155149 ATCAATGCAT
Statistics
Matches: 170, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
56 28 0.16
57 13 0.08
58 14 0.08
59 34 0.20
60 31 0.18
61 6 0.04
62 1 0.01
63 23 0.14
64 20 0.12
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (59 bp):
TTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGACCAACACCAAAAAAAATAT
Found at i:155021 original size:123 final size:117
Alignment explanation
Indices: 154852--155149 Score: 359
Period size: 123 Copynumber: 2.5 Consensus size: 117
154842 TTGATGTCGG
* * * * *
154852 CCAATGCATGGCCAACA-TAAAAAAATTTAAATTTTTATCAGATAAAAAAGGTGGTGTCGGCCAA
1 CCAATACATGACCAACACCAAAAAAATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGACCAA
** * ***
154916 GCAATGGCCAACACCAAAAAAAATATTTTTTATCTGATAAAAAATACTGGTGTTGG
66 GCAATAACCAACACC--AAAAAATATTTTTTATCTGAT-AAAAAGA-TGGTGTCAA
*
154972 CCAATACATGACCAACACCAAAAAAAATTTGAATTTTTTATCAGATAAAAAAAGTGGTGTCGACC
1 CCAATACATGACCAACACC-AAAAAAATTT-AATTTTTTATCAGATAAAAAAGGTGGTGTCGACC
*
155037 AAGCAATAACCAACACCAAAAAATATTTTTTATTTGATAAAAAGATGGTGTCAA
64 AAGCAATAACCAACACCAAAAAATATTTTTTATCTGATAAAAAGATGGTGTCAA
** * * *
155091 CCAATGTATGACCAACACC-AAAAAA-TCATTTTTTTATCAAATAAAAAAGGTGGTGTCGA
1 CCAATACATGACCAACACCAAAAAAATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGA
155150 TCAATGCATG
Statistics
Matches: 156, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
115 29 0.19
116 1 0.01
117 6 0.04
119 23 0.15
120 21 0.13
121 20 0.13
122 10 0.06
123 46 0.29
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (117 bp):
CCAATACATGACCAACACCAAAAAAATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGACCAA
GCAATAACCAACACCAAAAAATATTTTTTATCTGATAAAAAGATGGTGTCAA
Found at i:155094 original size:56 final size:59
Alignment explanation
Indices: 154883--155124 Score: 203
Period size: 56 Copynumber: 4.1 Consensus size: 59
154873 AAAATTTAAA
* * * *
154883 TTTTTATCAGATAAAAA-AGGTGGTGTCGGCCAAGCAATGGCCAACACCAAAAAAA-ATAT
1 TTTTTATCTGATAAAAAGA-CTGGTGTCGACCAAGCAATGACCAACACCAAAAAAATA-AT
* * * *
154942 TTTTTATCTGATAAAAAATACTGGTGTTGGCCAA-TACATGACCAACACCAAAAAAAATTTGAAT
1 TTTTTATCTGAT-AAAAAGACTGGTGTCGACCAAGCA-ATGACCAACACC-AAAAAAA--T-AAT
* * * *
155006 TTTTTATCAGATAAAAAAAGTGGTGTCGACCAAGCAATAACCAACACC-AAAAAAT-AT
1 TTTTTATCTGATAAAAAGACTGGTGTCGACCAAGCAATGACCAACACCAAAAAAATAAT
* * * *
155063 TTTTTATTTGATAAAAAGA-TGGTGTCAACCAATG-TATGACCAACACC-AAAAAATCAT
1 TTTTTATCTGATAAAAAGACTGGTGTCGACCAA-GCAATGACCAACACCAAAAAAATAAT
155120 TTTTT
1 TTTTT
155125 TATCAAATAA
Statistics
Matches: 154, Mismatches: 18, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
56 30 0.19
57 26 0.17
59 13 0.08
60 28 0.18
61 14 0.09
63 28 0.18
64 14 0.09
65 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (59 bp):
TTTTTATCTGATAAAAAGACTGGTGTCGACCAAGCAATGACCAACACCAAAAAAATAAT
Found at i:155524 original size:6 final size:6
Alignment explanation
Indices: 155513--155537 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
155503 CATGCGCCTG
155513 CCTCAC CCTCAC CCTCAC CCTCAC C
1 CCTCAC CCTCAC CCTCAC CCTCAC C
155538 ATTGAAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CCTCAC
Found at i:167773 original size:19 final size:18
Alignment explanation
Indices: 167717--167778 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
167707 ATATACATTT
* *
167717 TATAAAAAAATAATAAAA
1 TATAAATAAATATTAAAA
*
167735 TATACATAATATAATT-AAA
1 TATAAATAA-AT-ATTAAAA
167754 TATAAATATAATATTAAAA
1 TATAAATA-AATATTAAAA
167773 TA-AAAT
1 TATAAAT
167779 TTTTGTTTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 14 0.39
19 19 0.53
20 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TATAAATAAATATTAAAA
Found at i:187277 original size:8 final size:8
Alignment explanation
Indices: 187264--187294 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
187254 TCTTATATTC
187264 AAAAAATA
1 AAAAAATA
187272 AAAAAATA
1 AAAAAATA
187280 AAAAAATA
1 AAAAAATA
187288 AAAAAAT
1 AAAAAAT
187295 TAGCAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:187753 original size:17 final size:17
Alignment explanation
Indices: 187731--187765 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
187721 ACAAGGGTAA
187731 TTCACTCAATCACCCAC
1 TTCACTCAATCACCCAC
187748 TTCACTCAATCACCCAC
1 TTCACTCAATCACCCAC
187765 T
1 T
187766 ACTGAGCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.46, G:0.00, T:0.26
Consensus pattern (17 bp):
TTCACTCAATCACCCAC
Found at i:193081 original size:23 final size:23
Alignment explanation
Indices: 193030--193084 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
193020 TATTTTTTTT
193030 CGTTTTTATCTATCTTTGTGACA
1 CGTTTTTATCTATCTTTGTGACA
* *
193053 CATTTTTCTTCTATC-TTGT-AGCA
1 CGTTTTT-ATCTATCTTTGTGA-CA
193076 CGTTTTTAT
1 CGTTTTTAT
193085 TTTATGACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
22 2 0.08
23 18 0.69
24 6 0.23
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.55
Consensus pattern (23 bp):
CGTTTTTATCTATCTTTGTGACA
Found at i:197624 original size:6 final size:6
Alignment explanation
Indices: 197613--197643 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
197603 GAAAAATGCA
197613 GGATAT GGATAT GGATAT GGATAT GGATAT G
1 GGATAT GGATAT GGATAT GGATAT GGATAT G
197644 ACAGTGTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (6 bp):
GGATAT
Found at i:197765 original size:6 final size:6
Alignment explanation
Indices: 197754--197792 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
197744 CTTACTTGCT
* *
197754 CAACAA CAACAA CAACAC CAACAC CAACAC CAACAC CAA
1 CAACAC CAACAC CAACAC CAACAC CAACAC CAACAC CAA
197793 ATGATGATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (6 bp):
CAACAC
Found at i:204329 original size:20 final size:20
Alignment explanation
Indices: 204291--204330 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
204281 TTTTTTTTTC
**
204291 CTTTTATTTTTCCTCCAAAA
1 CTTTTATTTCCCCTCCAAAA
*
204311 CTTTTATTTCCCCTTCAAAA
1 CTTTTATTTCCCCTCCAAAA
204331 AAATTTCTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (20 bp):
CTTTTATTTCCCCTCCAAAA
Found at i:207722 original size:6 final size:6
Alignment explanation
Indices: 207710--207781 Score: 117
Period size: 6 Copynumber: 12.0 Consensus size: 6
207700 ATCGATCTCT
* * *
207710 CTTGCC TTTGCC TTTGCC TTTGCC CTTGCC CTTGCC CTTGCC CTTGCC
1 CTTGCC CTTGCC CTTGCC CTTGCC CTTGCC CTTGCC CTTGCC CTTGCC
207758 CTTGCC CTTGCC CTTGCC CTTGCC
1 CTTGCC CTTGCC CTTGCC CTTGCC
207782 TATTTTAGTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.00, C:0.46, G:0.17, T:0.38
Consensus pattern (6 bp):
CTTGCC
Found at i:208090 original size:6 final size:6
Alignment explanation
Indices: 208081--208118 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
208071 AATAAAAATA
208081 GGCGTG GGCGTG GGCGTG GGCGTG GGCGTG GGCGTG GG
1 GGCGTG GGCGTG GGCGTG GGCGTG GGCGTG GGCGTG GG
208119 GTTGGGGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.16, G:0.68, T:0.16
Consensus pattern (6 bp):
GGCGTG
Found at i:228746 original size:16 final size:15
Alignment explanation
Indices: 228720--228749 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
228710 AACCATACTT
228720 TTCATTTATAATTTG
1 TTCATTTATAATTTG
228735 TTCATCTTATAATTT
1 TTCAT-TTATAATTT
228750 AAAATTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.60
Consensus pattern (15 bp):
TTCATTTATAATTTG
Found at i:229203 original size:2 final size:2
Alignment explanation
Indices: 229196--229233 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
229186 ATCATTGAAC
229196 AT AT AT AT AT AT 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 AT AT AT AT AT AT
229234 GCATCCCAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:233197 original size:48 final size:49
Alignment explanation
Indices: 233134--233233 Score: 148
Period size: 48 Copynumber: 2.1 Consensus size: 49
233124 CACCTCGGCT
* * *
233134 TCTTTTATCCCTATCATGATCGTCATCACTTTCAGCTCTCCGGTGCC-A
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGCTCTCCGATGCCTA
* *
233182 TCTTCTATCTCTATCATGATCATCATCACTTTCAGTTCTCCGATGCCTA
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGCTCTCCGATGCCTA
233231 TCT
1 TCT
233234 ATCCGTTCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 42 0.91
49 4 0.09
ACGTcount: A:0.18, C:0.32, G:0.10, T:0.40
Consensus pattern (49 bp):
TCTTCTATCCCTATCATGATCATCATCACTTTCAGCTCTCCGATGCCTA
Found at i:240611 original size:21 final size:21
Alignment explanation
Indices: 240587--240626 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
240577 ATAAGCAGCA
240587 ACAAAG-TGGTTACCATAATGG
1 ACAAAGCT-GTTACCATAATGG
*
240608 ACAAAGCTGTTATCATAAT
1 ACAAAGCTGTTACCATAAT
240627 AAACTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
ACAAAGCTGTTACCATAATGG
Found at i:246415 original size:10 final size:10
Alignment explanation
Indices: 246400--246424 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
246390 CAAATCCATT
246400 CTGCTAGTCA
1 CTGCTAGTCA
246410 CTGCTAGTCA
1 CTGCTAGTCA
246420 CTGCT
1 CTGCT
246425 CAATAAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.32, G:0.20, T:0.32
Consensus pattern (10 bp):
CTGCTAGTCA
Found at i:250774 original size:1 final size:1
Alignment explanation
Indices: 250768--250792 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
250758 AACAAACACC
250768 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
250793 AGGAATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:256302 original size:2 final size:2
Alignment explanation
Indices: 256297--256332 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
256287 AAAAAAGGAA
256297 AT AT AT AT AT 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 AT AT AT AT AT
256333 TCTACTGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:262581 original size:30 final size:29
Alignment explanation
Indices: 262514--262582 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
262504 TTATTTTTTT
*
262514 AATTATAAAATATTTTTAAAATTTTGAAA
1 AATTATAAAATATTTTTAAAATTTTCAAA
** *
262543 AAAAATAAAA-ATTATTTAAAGTATTTCAAA
1 AATTATAAAATATT-TTTAAAAT-TTTCAAA
262573 AATTATAAAA
1 AATTATAAAA
262583 GCATTTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.09
29 15 0.47
30 14 0.44
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (29 bp):
AATTATAAAATATTTTTAAAATTTTCAAA
Found at i:262637 original size:30 final size:30
Alignment explanation
Indices: 262595--262652 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
262585 ATTTAATTTA
262595 TTTAAAAGTTTTA-AAAATAATTAATAAATAT
1 TTTAAAAGTTTTAGAAAAT-ATTAA-AAATAT
262626 TTTAAAA-TTTTAGAAAATATTAAAAAT
1 TTTAAAAGTTTTAGAAAATATTAAAAAT
262653 TATAAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 10 0.38
31 12 0.46
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
TTTAAAAGTTTTAGAAAATATTAAAAATAT
Found at i:263422 original size:66 final size:66
Alignment explanation
Indices: 263299--263691 Score: 277
Period size: 66 Copynumber: 6.0 Consensus size: 66
263289 ATCGCAACCA
** * * * ** * * * *
263299 AAATTATTTGGGTTCGTTGACCTAAGATCACAACCCAT-ACAGCTCGCTGGCCAAAGATCGCGGT
1 AAATTATTCAGGTTCGCTGACATAAGATCACAACCTATGTGA-CTCGCCGACCTAAGATCGCAGT
263363 TG
65 TG
* * * * * ** **
263365 AAATTATTCACGTTCGCTGACATAAGATCACAACCTATGTGGCTTGTCAACCTAAGATCATAGCC
1 AAATTATTCAGGTTCGCTGACATAAGATCACAACCTATGTGACTCGCCGACCTAAGATCGCAGTT
*
263430 A
66 G
* * * * *** * * *
263431 AAATTATTCGGGTTCACTGACCTAAGATCACAACCCATACAACTCACCGACCTAAAATCTCAGTT
1 AAATTATTCAGGTTCGCTGACATAAGATCACAACCTATGTGACTCGCCGACCTAAGATCGCAGTT
263496 G
66 G
** * * * *
263497 AAATTATTC-GAGTTCGCTGACATAAGATCATGACCTATGTGTCTTGCCGACCCAAGATCGTAGT
1 AAATTATTCAG-GTTCGCTGACATAAGATCACAACCTATGTGACTCGCCGACCTAAGATCGCAGT
**
263561 CA
65 TG
* * * * * * * * * *
263563 AAATCATTCAGGTTCGCTGACCTAAGATCACAACCCATATAACTCACCGACCTAAAATCACGGCT
1 AAATTATTCAGGTTCGCTGACATAAGATCACAACCTATGTGACTCGCCGACCTAAGATCGCAGTT
263628 G
66 G
* * * *
263629 AAATTATTCGGGTTCGCTGACATAAGATCGCAACCTATGTGGCTCGCCGAACTAAGATCGCAG
1 AAATTATTCAGGTTCGCTGACATAAGATCACAACCTATGTGACTCGCCGACCTAAGATCGCAG
263692 CCAAAATCTC
Statistics
Matches: 236, Mismatches: 88, Indels: 6
0.72 0.27 0.02
Matches are distributed among these distances:
65 1 0.00
66 234 0.99
67 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (66 bp):
AAATTATTCAGGTTCGCTGACATAAGATCACAACCTATGTGACTCGCCGACCTAAGATCGCAGTT
G
Found at i:263497 original size:132 final size:131
Alignment explanation
Indices: 263285--263698 Score: 517
Period size: 132 Copynumber: 3.1 Consensus size: 131
263275 TTCGTCGACA
* * * * * * *
263285 TAAGATCGCAACCAAAATTATTTGGGTTCGTTGACCTAAGATCACAACCCATACAGCTCGCTGGC
1 TAAGATCGCAGCCAAAATTATTCGGGTTCGCTGACCTAAGATCACAACCCATACAACTCACCGAC
* *
263350 C-AAAGATCGCGGTTGAAATTATTCACGTTCGCTGACATAAGATCACAACCTATGTGGCTTGTCA
66 CTAAA-ATCACGGTTGAAATTATTCA-GTTCGCTGACATAAGATCACAACCTATGTGGCTTGCCA
263414 ACC
129 ACC
** *
263417 TAAGATCATAGCCAAAATTATTCGGGTTCACTGACCTAAGATCACAACCCATACAACTCACCGAC
1 TAAGATCGCAGCCAAAATTATTCGGGTTCGCTGACCTAAGATCACAACCCATACAACTCACCGAC
* * ** * *
263482 CTAAAATCTCAGTTGAAATTATTCGAGTTCGCTGACATAAGATCATGACCTATGTGTCTTGCCGA
66 CTAAAATCACGGTTGAAATTATTC-AGTTCGCTGACATAAGATCACAACCTATGTGGCTTGCCAA
263547 CC
130 CC
* * * * * *
263549 CAAGATCGTAGTCAAAATCATTCAGGTTCGCTGACCTAAGATCACAACCCATATAACTCACCGAC
1 TAAGATCGCAGCCAAAATTATTCGGGTTCGCTGACCTAAGATCACAACCCATACAACTCACCGAC
* * * *
263614 CTAAAATCACGGCTGAAATTATTCGGGTTCGCTGACATAAGATCGCAACCTATGTGGCTCGCCGA
66 CTAAAATCACGGTTGAAATTATTC-AGTTCGCTGACATAAGATCACAACCTATGTGGCTTGCC-A
263679 A-C
129 ACC
263681 TAAGATCGCAGCCAAAAT
1 TAAGATCGCAGCCAAAAT
263699 CTCGTGGCTA
Statistics
Matches: 242, Mismatches: 37, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
132 237 0.98
133 5 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (131 bp):
TAAGATCGCAGCCAAAATTATTCGGGTTCGCTGACCTAAGATCACAACCCATACAACTCACCGAC
CTAAAATCACGGTTGAAATTATTCAGTTCGCTGACATAAGATCACAACCTATGTGGCTTGCCAAC
C
Found at i:266407 original size:17 final size:18
Alignment explanation
Indices: 266385--266418 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
266375 ATTTTTTAAA
*
266385 AATTAAATTA-AATTTTT
1 AATTAAAGTATAATTTTT
266402 AATTAAAGTATAATTTT
1 AATTAAAGTATAATTTT
266419 ACTTTTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTAAAGTATAATTTTT
Found at i:273290 original size:5 final size:5
Alignment explanation
Indices: 273280--273304 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
273270 TTAAACTTGG
273280 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
273305 AATATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:273356 original size:30 final size:28
Alignment explanation
Indices: 273285--273360 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
273275 CTTGGTTTTA
* *
273285 TTTTATTT-TATTTTATTTTAAATATAT
1 TTTTATTTGTATTTAATTTTAAAGATAT
*
273312 TTTTATTAAG-ATTTAATATTTAAAGATAT
1 TTTTATT-TGTATTTAAT-TTTAAAGATAT
273341 TATTTATTTGTATTTAATTT
1 T-TTTATTTGTATTTAATTT
273361 ATGTTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 7 0.17
28 6 0.15
29 14 0.35
30 13 0.32
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTATTTGTATTTAATTTTAAAGATAT
Found at i:274171 original size:22 final size:22
Alignment explanation
Indices: 274145--274193 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
274135 TCGACTTTCT
*
274145 TATTTTATATT-TCTTTTAATTC
1 TATTTTATTTTATC-TTTAATTC
*
274167 TATTTTCTTTTATCTTTAATTC
1 TATTTTATTTTATCTTTAATTC
274189 TATTT
1 TATTT
274194 CTTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTTATTTTATCTTTAATTC
Found at i:274177 original size:27 final size:25
Alignment explanation
Indices: 274147--274205 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 25
274137 GACTTTCTTA
274147 TTTTATATTTCTTTTAATTCTATTT-
1 TTTTATATTTC-TTTAATTCTATTTC
274172 TCTTT-TA--TCTTTAATTCTATTTC
1 T-TTTATATTTCTTTAATTCTATTTC
*
274195 TTTTATTTTTC
1 TTTTATATTTC
274206 CTCAGATCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
22 16 0.57
23 4 0.14
25 5 0.18
26 3 0.11
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTTATATTTCTTTAATTCTATTTC
Found at i:274196 original size:21 final size:22
Alignment explanation
Indices: 274159--274200 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
274149 TTATATTTCT
274159 TTTAATTCTATTTTCTTTTATC
1 TTTAATTCTATTTTCTTTTATC
274181 TTTAATTCTA-TTTCTTTTAT
1 TTTAATTCTATTTTCTTTTAT
274201 TTTTCCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTAATTCTATTTTCTTTTATC
Found at i:276924 original size:12 final size:12
Alignment explanation
Indices: 276907--276962 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
276897 AGCAACCTAA
276907 TTATTTTTATTT
1 TTATTTTTATTT
276919 TTATTTTTATTT
1 TTATTTTTATTT
*
276931 TT-TTCTCTA-TT
1 TTATT-TTTATTT
276942 TTATTTATTTATTT
1 TTA-TT-TTTATTT
276956 ATTATTT
1 -TTATTT
276963 GTCCAGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
11 6 0.17
12 17 0.47
13 6 0.17
14 4 0.11
15 3 0.08
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:279132 original size:15 final size:16
Alignment explanation
Indices: 279112--279141 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
279102 CTTTCTTATT
279112 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
279127 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
279142 TCTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:279134 original size:22 final size:22
Alignment explanation
Indices: 279108--279163 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
279098 TTGACTTTCT
*
279108 TATTTTCTATTTCT-TTTAATTC
1 TATTTTCT-TTTATCTTTAATTC
279130 TATTTTCTTTTATCTTTAATTC
1 TATTTTCTTTTATCTTTAATTC
*
279152 -AGTTTCTTTTAT
1 TATTTTCTTTTAT
279164 TTTTCCTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.18, C:0.12, G:0.02, T:0.68
Consensus pattern (22 bp):
TATTTTCTTTTATCTTTAATTC
Found at i:279159 original size:21 final size:22
Alignment explanation
Indices: 279122--279163 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
279112 TTCTATTTCT
*
279122 TTTAATTCTATTTTCTTTTATC
1 TTTAATTCTAGTTTCTTTTATC
279144 TTTAATTC-AGTTTCTTTTAT
1 TTTAATTCTAGTTTCTTTTAT
279164 TTTTCCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTAATTCTAGTTTCTTTTATC
Found at i:286081 original size:6 final size:6
Alignment explanation
Indices: 286070--286099 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
286060 GTGACCAACT
*
286070 CCAGCC CCAGCC CCAGCC CCAGCC CTAGCC
1 CCAGCC CCAGCC CCAGCC CCAGCC CCAGCC
286100 ACCCAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.63, G:0.17, T:0.03
Consensus pattern (6 bp):
CCAGCC
Found at i:287037 original size:2 final size:2
Alignment explanation
Indices: 287030--287078 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
287020 TTTATATCAT
287030 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA
287072 TA TA TA T
1 TA TA TA T
287079 GAAATTTTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:287118 original size:51 final size:51
Alignment explanation
Indices: 287075--287179 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
287065 ATATATATAT
* * *
287075 ATATGAAATTTTAGTTTTGATT-TAATTTGACACATTTAAATATATGAATAC
1 ATATAAAATTTTAATTTTGATTCT-ATTTAACACATTTAAATATATGAATAC
*
287126 ATATAAAATTTTAATTTTGATTCTATTTAACACATTTAAATATATGAGTAC
1 ATATAAAATTTTAATTTTGATTCTATTTAACACATTTAAATATATGAATAC
287177 ATA
1 ATA
287180 AATTTAACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
51 48 0.98
52 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (51 bp):
ATATAAAATTTTAATTTTGATTCTATTTAACACATTTAAATATATGAATAC
Found at i:297519 original size:21 final size:22
Alignment explanation
Indices: 297482--297529 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
297472 AGATTTATCT
* *
297482 ATTTTTATTATATTC-AAATA-
1 ATTTTTATTAAAATCAAAATAG
297502 ATTTTTATTTAAAATCAAAATAG
1 ATTTTTA-TTAAAATCAAAATAG
297525 ATTTT
1 ATTTT
297530 GAATATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 5 0.22
23 5 0.22
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTTTATTAAAATCAAAATAG
Found at i:300925 original size:20 final size:20
Alignment explanation
Indices: 300888--300940 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
300878 AACATTATAA
*
300888 AAAAATCATAAAACTATTAT
1 AAAAATTATAAAACTATTAT
* *
300908 ATAAATTATTAAAA-TATTTT
1 AAAAATTA-TAAAACTATTAT
300928 AAAAATTATAAAA
1 AAAAATTATAAAA
300941 GTGCAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.18
20 18 0.64
21 5 0.18
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTATAAAACTATTAT
Found at i:300949 original size:18 final size:18
Alignment explanation
Indices: 300928--300962 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
300918 AAAATATTTT
300928 AAAAAT-TATAAAAGTGC
1 AAAAATATATAAAAGTGC
300945 AAAAATATATAAAAGTGC
1 AAAAATATATAAAAGTGC
300963 TAGAAAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (18 bp):
AAAAATATATAAAAGTGC
Found at i:301610 original size:16 final size:16
Alignment explanation
Indices: 301575--301617 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
301565 TGCTATTTTA
*
301575 AATATTTTTATAATTTTC
1 AATA-TTTT-TAACTTTC
301593 AATATTTTTAACTTTC
1 AATATTTTTAACTTTC
301609 AA-ATTTTTA
1 AATATTTTTA
301618 TAATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 9 0.38
17 4 0.17
18 4 0.17
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (16 bp):
AATATTTTTAACTTTC
Found at i:324339 original size:27 final size:27
Alignment explanation
Indices: 324297--324352 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
324287 TGCCGTCTAT
*
324297 GCCGTGAAAGACTTGGAAAAGAAAGCA
1 GCCGTGAAAGAATTGGAAAAGAAAGCA
*
324324 GCCGTGAAAGAATTGGAAGAGAAAGCA
1 GCCGTGAAAGAATTGGAAAAGAAAGCA
324351 GC
1 GC
324353 GATAGTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.43, C:0.14, G:0.32, T:0.11
Consensus pattern (27 bp):
GCCGTGAAAGAATTGGAAAAGAAAGCA
Found at i:330310 original size:2 final size:2
Alignment explanation
Indices: 330303--330333 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
330293 GCCGGCAACG
330303 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
330334 GACCCAGTTT
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):
AT
Found at i:331289 original size:3 final size:3
Alignment explanation
Indices: 331281--331306 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
331271 CAACTTGAAA
331281 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
331307 GGGACAACAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:335492 original size:18 final size:18
Alignment explanation
Indices: 335469--335540 Score: 126
Period size: 18 Copynumber: 4.0 Consensus size: 18
335459 CATATGTGTC
335469 TATTGAAGATACAAATGA
1 TATTGAAGATACAAATGA
*
335487 TATTGAAGATGCAAATGA
1 TATTGAAGATACAAATGA
*
335505 TGTTGAAGATACAAATGA
1 TATTGAAGATACAAATGA
335523 TATTGAAGATACAAATGA
1 TATTGAAGATACAAATGA
335541 AACACAAGAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (18 bp):
TATTGAAGATACAAATGA
Found at i:344201 original size:19 final size:19
Alignment explanation
Indices: 344177--344215 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
344167 AATTGAATAG
344177 AGAACTAGTGATCTGACCA
1 AGAACTAGTGATCTGACCA
344196 AGAACTAGTGATCTGACCA
1 AGAACTAGTGATCTGACCA
344215 A
1 A
344216 TTCAACGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
AGAACTAGTGATCTGACCA
Found at i:348589 original size:3 final size:3
Alignment explanation
Indices: 348581--348612 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
348571 AGGGTGAAAT
348581 ATG ATG ATG ATG ATG ATG AT- ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
348613 GGAATAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:348752 original size:19 final size:21
Alignment explanation
Indices: 348728--348768 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
348718 CTTCTCAATA
*
348728 ATAAA-TAAATAAATAA-AAT
1 ATAAATTAAACAAATAATAAT
348747 ATAAATTAAACAAATAATAAT
1 ATAAATTAAACAAATAATAAT
348768 A
1 A
348769 ATGTACACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAAATTAAACAAATAATAAT
Found at i:353049 original size:17 final size:19
Alignment explanation
Indices: 353015--353049 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
353005 TACGCATGAC
353015 AAATTCAAATATATTAAAA
1 AAATTCAAATATATTAAAA
353034 AAATTC-AATA-ATTAAA
1 AAATTCAAATATATTAAA
353050 TTACTAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATTCAAATATATTAAAA
Found at i:354404 original size:6 final size:6
Alignment explanation
Indices: 354395--354421 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
354385 TGATGAAGGG
354395 ATCCAA ATCCAA ATCCAA ATCCAA ATC
1 ATCCAA ATCCAA ATCCAA ATCCAA ATC
354422 TTTGAGTGTA
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:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (6 bp):
ATCCAA
Found at i:354619 original size:30 final size:29
Alignment explanation
Indices: 354575--354654 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 29
354565 TATGTAATTA
354575 TATACATG-AATTTTAATTTGGTGT-AAT-
1 TATACATGAAATTTTAATTTGGT-TAAATC
354602 TATACATGTAAAATTTTAATTATGGTTCAAATC
1 TATACATG--AAATTTTAATT-TGGTT-AAATC
354635 TATACATGAAATTTTAATTT
1 TATACATGAAATTTTAATTT
354655 TGATATAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
27 8 0.17
30 12 0.26
31 15 0.33
32 3 0.07
33 8 0.17
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (29 bp):
TATACATGAAATTTTAATTTGGTTAAATC
Found at i:359270 original size:55 final size:55
Alignment explanation
Indices: 359186--359290 Score: 183
Period size: 55 Copynumber: 1.9 Consensus size: 55
359176 AGACAGAGCG
*
359186 TTAAGAATATGAACTATCATCAGTTTTGCTCTAAAGCTGAACCAAAAGTACAGTA
1 TTAAGAATATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAAAAGTACAGTA
* *
359241 TTAAGACTATGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAAAAGTA
1 TTAAGAATATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAAAAGTA
359291 AAGCAAGATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (55 bp):
TTAAGAATATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAAAAGTACAGTA
Found at i:359308 original size:55 final size:55
Alignment explanation
Indices: 359194--359320 Score: 173
Period size: 55 Copynumber: 2.3 Consensus size: 55
359184 CGTTAAGAAT
* * * ** *
359194 ATGAACTATCATCAGTTTTGCTCTAAAGCTGAACCAAAAGTACAGTATTAAGACT
1 ATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAAAAGTAAAGCAAGAAGACA
* *
359249 ATGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAAAAGTAAAGCAAGATGACA
1 ATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAAAAGTAAAGCAAGAAGACA
*
359304 ATGAAATAACATCAGTT
1 ATGAACTAACATCAGTT
359321 CAACTCCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.26
Consensus pattern (55 bp):
ATGAACTAACATCAGTTTTGCTCTAAAGCTGAACCAAAAGTAAAGCAAGAAGACA
Found at i:364232 original size:58 final size:59
Alignment explanation
Indices: 364162--364302 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 59
364152 GGGTTGTTAT
* *
364162 AATTA-TCACACATAGGGGCCTAAACTTTT-TTTGACCAAGTTAGGCATTAAACTTGAC
1 AATTATTCTCACATTGGGGCCTAAACTTTTGTTTGACCAAGTTAGGCATTAAACTTGAC
* * *** * *
364219 AATTATTCTCACATTGGGGCTTGAACTTTTGTTTTTTCAAGTTAGTCATTGAACTTGAC
1 AATTATTCTCACATTGGGGCCTAAACTTTTGTTTGACCAAGTTAGGCATTAAACTTGAC
* * *
364278 AATTGTTCTTACATTGGAGCCTAAA
1 AATTATTCTCACATTGGGGCCTAAA
364303 ATTTAGGGTT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
57 5 0.07
58 20 0.29
59 43 0.63
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (59 bp):
AATTATTCTCACATTGGGGCCTAAACTTTTGTTTGACCAAGTTAGGCATTAAACTTGAC
Found at i:364808 original size:10 final size:9
Alignment explanation
Indices: 364786--364854 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
364776 CACGTGGTAA
*
364786 AAAAATGAT
1 AAAAATTAT
364795 -AAAATTAAT
1 AAAAATT-AT
364804 AAAAAATTAT
1 -AAAAATTAT
364814 AAATAA-TAT
1 AAA-AATTAT
364823 AGAAAATTAT
1 A-AAAATTAT
364833 AAAAA-TAT
1 AAAAATTAT
* *
364841 TAAAATCAT
1 AAAAATTAT
364850 AAAAA
1 AAAAA
364855 AAGTACTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
8 12 0.24
9 21 0.43
10 10 0.20
11 6 0.12
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:364828 original size:21 final size:18
Alignment explanation
Indices: 364787--364854 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
364777 ACGTGGTAAA
* * *
364787 AAAATGATAAAATTAATAA
1 AAAATTATAAAAAT-ATAG
364806 AAAATTATAAATAATATAG
1 AAAATTATAAA-AATATAG
*
364825 AAAATTATAAAAATAT-T
1 AAAATTATAAAAATATAG
*
364842 AAAATCATAAAAA
1 AAAATTATAAAAA
364855 AAGTACTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
17 12 0.28
18 5 0.12
19 24 0.56
20 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATTATAAAAATATAG
Found at i:365781 original size:27 final size:27
Alignment explanation
Indices: 365749--365824 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
365739 TTGTATTTTA
*
365749 TTTTATTTATTAAAAAAATAAATTAAT
1 TTTTATTTATTAAAAAAATAAATAAAT
* *
365776 TTTTATATATTAAATTAAA-AAATAAAT
1 TTTTATTTATTAAA-AAAATAAATAAAT
*
365803 TTATCATTTCTATTAAAAAAAT
1 TT-TTA-TT-TATTAAAAAAAT
365825 TATCCATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
27 22 0.58
28 5 0.13
29 4 0.11
30 7 0.18
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTTATTTATTAAAAAAATAAATAAAT
Found at i:370159 original size:5 final size:5
Alignment explanation
Indices: 370149--370186 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
370139 TAGGTAACCC
370149 AACAA AACAA AACAA AACAA AACAA AACAA AACAA AAC
1 AACAA AACAA AACAA AACAA AACAA AACAA AACAA AAC
370187 CTCCTGTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:372084 original size:6 final size:6
Alignment explanation
Indices: 372075--372115 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
372065 AAACAAGAAA
*
372075 AAGAGG AAGATG AAGATG AAGATG AAGA-G AAGATG AA-ATG A
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG A
372116 TAGCATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.54, C:0.00, G:0.34, T:0.12
Consensus pattern (6 bp):
AAGATG
Found at i:376351 original size:2 final size:2
Alignment explanation
Indices: 376344--376381 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
376334 AAAATACAAA
376344 AT AT AT AT AT AT 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 AT AT AT AT AT AT
376382 TGTTACTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:380584 original size:32 final size:32
Alignment explanation
Indices: 380548--380610 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
380538 TTTTTTTTGT
*
380548 CTAATTTGGTA-CTCAAACTTGACACTTTTTTC
1 CTAATTTGCTACCT-AAACTTGACACTTTTTTC
*
380580 CTAATTTGCTACCTAAACTTGACGCTTTTTT
1 CTAATTTGCTACCTAAACTTGACACTTTTTT
380611 TGAATTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (32 bp):
CTAATTTGCTACCTAAACTTGACACTTTTTTC
Found at i:380610 original size:33 final size:34
Alignment explanation
Indices: 380539--380612 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 34
380529 GTATTTAAAT
* *
380539 TTTTTTTGTCTAATTTGGTACTCAAACTTGACAC
1 TTTTTTTGCCTAATTTGCTACTCAAACTTGACAC
*
380573 -TTTTTT-CCTAATTTGCTAC-CTAAACTTGACGC
1 TTTTTTTGCCTAATTTGCTACTC-AAACTTGACAC
380605 TTTTTTTG
1 TTTTTTTG
380613 AATTTGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
31 1 0.03
32 21 0.62
33 12 0.35
ACGTcount: A:0.20, C:0.19, G:0.11, T:0.50
Consensus pattern (34 bp):
TTTTTTTGCCTAATTTGCTACTCAAACTTGACAC
Found at i:380647 original size:90 final size:89
Alignment explanation
Indices: 380491--380684 Score: 209
Period size: 90 Copynumber: 2.2 Consensus size: 89
380481 AGTTTTAATA
* * *** *
380491 TAATTTGGTACCTGAACTTGACATTTTTTCTTAATTTAGTATTTAAATTTTTTTTGTCTAATTTG
1 TAATTTGGTACCTAAACTTGACATTTTTTCTGAATTTAGTATTTAAATTTTTGGGGTCCAATTTG
380556 GTA-CTCAAACTTGACACTTTTT-T
66 GTACCT-AAACTTGACACTTTTTAT
* *
380579 CCTAATTTGCTACCTAAACTTGACGCTTTTTT-TGAATTT-GTATTTAAACTTTTTGGGGTCC-A
1 --TAATTTGGTACCTAAACTTGAC-ATTTTTTCTGAATTTAGTATTTAAA-TTTTTGGGGTCCAA
* *
380641 TATTGGTACCTGAACTTGACTCTTTTTAT
62 T-TTGGTACCTAAACTTGACACTTTTTAT
380670 TAATTTGGTACCTAA
1 TAATTTGGTACCTAA
380685 TAATTTTTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
89 25 0.28
90 54 0.61
91 9 0.10
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (89 bp):
TAATTTGGTACCTAAACTTGACATTTTTTCTGAATTTAGTATTTAAATTTTTGGGGTCCAATTTG
GTACCTAAACTTGACACTTTTTAT
Found at i:380904 original size:31 final size:31
Alignment explanation
Indices: 380867--380991 Score: 106
Period size: 31 Copynumber: 4.2 Consensus size: 31
380857 AAGTTTAAAC
* *
380867 ACCAAATTAGGAAAAAAT-TCCAAATTCAAGT
1 ACCAAATTAAGAAAAAATGT-CAAATTCAAAT
*
380898 ACCAAATTAAGAAAAAATGTCAAGTTCAAAT
1 ACCAAATTAAGAAAAAATGTCAAATTCAAAT
*
380929 ACCAAATT-A-AATAAA----AAATT-AAAT
1 ACCAAATTAAGAAAAAATGTCAAATTCAAAT
* *
380953 ACCAAATTAA-AAAATATATATCAAATTCAAGT
1 ACCAAATTAAGAAAA-A-ATGTCAAATTCAAAT
380985 ACCAAAT
1 ACCAAAT
380992 ATTATATTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
24 12 0.15
25 8 0.10
26 1 0.01
27 1 0.01
29 5 0.06
30 1 0.01
31 39 0.50
32 11 0.14
ACGTcount: A:0.57, C:0.14, G:0.06, T:0.24
Consensus pattern (31 bp):
ACCAAATTAAGAAAAAATGTCAAATTCAAAT
Found at i:382614 original size:20 final size:20
Alignment explanation
Indices: 382584--382630 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
382574 AATTTTAGAG
382584 TTAATTTAATAAAA-TATATAA
1 TTAA-TTAATAAAATTA-ATAA
*
382605 TTAATTAATAATATTAATAA
1 TTAATTAATAAAATTAATAA
382625 TTAATT
1 TTAATT
382631 TTCATAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATTAATAAAATTAATAA
Found at i:382618 original size:16 final size:16
Alignment explanation
Indices: 382596--382629 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
382586 AATTTAATAA
382596 AATATATAATTAATTAAT
1 AATAT-TAA-TAATTAAT
382614 AATATTAATAATTAAT
1 AATATTAATAATTAAT
382630 TTTCATAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATTAATAATTAAT
Found at i:383431 original size:12 final size:12
Alignment explanation
Indices: 383414--383448 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
383404 AAGGTAGAGT
383414 AAAAAGAAAAAA
1 AAAAAGAAAAAA
383426 AAAAAGGAAAAAA
1 AAAAA-GAAAAAA
383439 AAAAAGAAAA
1 AAAAAGAAAA
383449 CCCAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:384120 original size:45 final size:46
Alignment explanation
Indices: 384042--384155 Score: 144
Period size: 45 Copynumber: 2.5 Consensus size: 46
384032 AGTTTGTACA
* * *
384042 AAGTTTCAGGC-TC-AACATTATTTAAAATGGGTTTTTGTTTATAAG
1 AAGTTTCA-GCTTCAAACATTCTTGAAAATGGGTTTATGTTTATAAG
* *
384087 AAGTTTTAGCTTCAAATATTCTTGAAAAT-GGTTTATGTTTATAAG
1 AAGTTTCAGCTTCAAACATTCTTGAAAATGGGTTTATGTTTATAAG
*
384132 TAGTTTCAGCTTCAAACATTCTTG
1 AAGTTTCAGCTTCAAACATTCTTG
384156 TCAATACTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 2 0.03
45 45 0.76
46 12 0.20
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.43
Consensus pattern (46 bp):
AAGTTTCAGCTTCAAACATTCTTGAAAATGGGTTTATGTTTATAAG
Found at i:386701 original size:145 final size:143
Alignment explanation
Indices: 386440--386717 Score: 418
Period size: 145 Copynumber: 1.9 Consensus size: 143
386430 ACTGTTTTAA
* *
386440 TAAACTATTTTCTAAATTGTAATAATTTATATACATTATATATGTAAATCTAAAAGCAGCACCCA
1 TAAACTATTTTCTAAATTATAATAATTTATATACATTATATATGTAAATCTAAAAGCAGCACCAA
386505 TGGCCTAATGGATAAGGCGCTTGACTTCTAATCAAGCGATTGTGGGTTCGAGTCCCACTGGGTGT
66 TGGCCTAATGGATAAGGCGCTTGACTTCTAATCAAGCGATTGTGGGTTCGAGTCCCACTGGGTGT
386570 GATAGTGCTTTTG
131 GATAGTGCTTTTG
* * * *
386583 TAAACTATTTTC-AAACTTAT-ATAAGTTTATATATATTTTATATGTTAAAT-TCACAGCAAAGC
1 TAAACTATTTTCTAAA-TTATAATAA-TTTATATACATTATATATG-TAAATCTAAAAGC--AGC
* *
386645 ACCAATGGCCTACTGGATAAGGCGCTTGACTTCTATTCAAGCGATTGTGGGTTCGAGTCCCACTG
61 ACCAATGGCCTAATGGATAAGGCGCTTGACTTCTAATCAAGCGATTGTGGGTTCGAGTCCCACTG
386710 GGTGTGAT
126 GGTGTGAT
386718 TGTTTTTGGT
Statistics
Matches: 122, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
142 7 0.06
143 37 0.30
144 5 0.04
145 73 0.60
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (143 bp):
TAAACTATTTTCTAAATTATAATAATTTATATACATTATATATGTAAATCTAAAAGCAGCACCAA
TGGCCTAATGGATAAGGCGCTTGACTTCTAATCAAGCGATTGTGGGTTCGAGTCCCACTGGGTGT
GATAGTGCTTTTG
Found at i:407288 original size:23 final size:22
Alignment explanation
Indices: 407255--407301 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
407245 TTAGTGCTTG
407255 AATTTTTATTTTTAAGAAT-TTA
1 AATTTTTATTTTTAA-AATATTA
407277 AATTTTTAATTTTTAAAATATTA
1 AATTTTT-ATTTTTAAAATATTA
407300 AA
1 AA
407302 ATTTAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATTTTTATTTTTAAAATATTA
Found at i:407785 original size:21 final size:20
Alignment explanation
Indices: 407760--407816 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
407750 GCAACGTGTT
407760 TTTATATATTTATACGTTA-TA
1 TTTATATATTTATA--TTATTA
*
407781 TTTATTTATTTATATTATTA
1 TTTATATATTTATATTATTA
*
407801 TTTAAATATTT-TATTA
1 TTTATATATTTATATTA
407817 ATTGATATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 8 0.25
20 11 0.34
21 13 0.41
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTATATATTTATATTATTA
Found at i:414630 original size:8 final size:8
Alignment explanation
Indices: 414617--414641 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
414607 TTTAAGAGGC
414617 GGGGTTTT
1 GGGGTTTT
414625 GGGGTTTT
1 GGGGTTTT
414633 GGGGTTTT
1 GGGGTTTT
414641 G
1 G
414642 CCGGTTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (8 bp):
GGGGTTTT
Found at i:415069 original size:13 final size:14
Alignment explanation
Indices: 415040--415072 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
415030 TGAATTAAAA
415040 TTTATATTTCCATTT
1 TTTATATTT-CATTT
415055 TTTATATTT-ATTT
1 TTTATATTTCATTT
415068 TTTAT
1 TTTAT
415073 TGATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATATTTCATTT
Done.