Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008736.1 Hibiscus syriacus cultivar Beakdansim tig00111810_pilon, whole genome shotgun sequence
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: 2478687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 13
Found at i:1986 original size:24 final size:23
Alignment explanation
Indices: 1941--1993 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1931 CTGAATGATT
*
1941 CCATTAAGAGTCAAACCAACAGTC
1 CCATTAAGAGGCAAACCAACAG-C
1965 CCATTAAGAGGCAAA-CAGACAGC
1 CCATTAAGAGGCAAACCA-ACAGC
1988 CC-TTAA
1 CCATTAA
1994 ATCGAGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 5 0.19
24 18 0.67
ACGTcount: A:0.42, C:0.28, G:0.15, T:0.15
Consensus pattern (23 bp):
CCATTAAGAGGCAAACCAACAGC
Found at i:5664 original size:27 final size:26
Alignment explanation
Indices: 5634--5690 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
5624 AATGTTCAGT
5634 TTGACTCAAAATAAAAAAAATGGAAGC
1 TTGACTCAAAATAAAAAAAATGGAA-C
* * *
5661 TTGACTCAAACTCAAAAAAATTGAAC
1 TTGACTCAAAATAAAAAAAATGGAAC
5687 TTGA
1 TTGA
5691 AACATTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (26 bp):
TTGACTCAAAATAAAAAAAATGGAAC
Found at i:6594 original size:16 final size:16
Alignment explanation
Indices: 6573--6633 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
6563 TTATGGGATG
6573 AAAATAATATTATTAT
1 AAAATAATATTATTAT
6589 AAAAT-ATAATTATT-T
1 AAAATAAT-ATTATTAT
6604 AAAATAATATT-TTATT
1 AAAATAATATTATTA-T
**
6620 ACCATAATATTATT
1 AAAATAATATTATT
6634 TTTATATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 2 0.05
15 11 0.29
16 23 0.61
17 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATAATATTATTAT
Found at i:6815 original size:25 final size:26
Alignment explanation
Indices: 6769--6821 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
6759 ATAACGATTA
* * *
6769 AAATATTTTTTATGAATTTTAA-TTT
1 AAATATTTATAATGAATATTAAGTTT
*
6794 AAATATTTATAATTAATATTAAGTTT
1 AAATATTTATAATGAATATTAAGTTT
6820 AA
1 AA
6822 CTTTAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
AAATATTTATAATGAATATTAAGTTT
Found at i:9491 original size:31 final size:31
Alignment explanation
Indices: 9431--9503 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
9421 TTAAGATATT
* ** *
9431 TTAAAAAATATATTTTTAAGTGATGATAAAG
1 TTAAAATATATATTTTTAAGTGAAAATAAAA
9462 TTAAAATATATATTTTTACA-TGAAAATAAAA
1 TTAAAATATATATTTTTA-AGTGAAAATAAAA
*
9493 ATAAAATATAT
1 TTAAAATATAT
9504 TTAATAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.38
Consensus pattern (31 bp):
TTAAAATATATATTTTTAAGTGAAAATAAAA
Found at i:9820 original size:21 final size:20
Alignment explanation
Indices: 9783--9822 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
9773 TAATTAGTAG
* *
9783 AAAATAAATATATTAAATTA
1 AAAATAAATAAAATAAATTA
9803 AAAATAAAATAAAATAAATT
1 AAAAT-AAATAAAATAAATT
9823 TACTCTTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATAAATAAAATAAATTA
Found at i:10032 original size:33 final size:33
Alignment explanation
Indices: 9990--10065 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
9980 ATTCGGGTAA
9990 GCCTGTTAACAGTCCACGTGTGTTTTTCGTCAT
1 GCCTGTTAACAGTCCACGTGTGTTTTTCGTCAT
10023 GCCTGTTAACAGTCCACGTGTGTTTTTCGTCAT
1 GCCTGTTAACAGTCCACGTGTGTTTTTCGTCAT
10056 GCCTGTTAAC
1 GCCTGTTAAC
10066 GACGAGTGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (33 bp):
GCCTGTTAACAGTCCACGTGTGTTTTTCGTCAT
Found at i:14462 original size:23 final size:24
Alignment explanation
Indices: 14428--14480 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
14418 AGAATAAGTT
14428 TGTC-TTATTGGCAAGTTTATCTA
1 TGTCTTTATTGGCAAGTTTATCTA
*
14451 TGTCTTTA-TGGCAAGTTTATCTC
1 TGTCTTTATTGGCAAGTTTATCTA
14474 TGTCTTT
1 TGTCTTT
14481 TTAGTACGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (24 bp):
TGTCTTTATTGGCAAGTTTATCTA
Found at i:19488 original size:40 final size:39
Alignment explanation
Indices: 19436--19540 Score: 99
Period size: 40 Copynumber: 2.7 Consensus size: 39
19426 AAACAAGTGC
* *
19436 AATAAATAAAATAAGT-TAAAGAAAAAAATGAAAGTAAAAA
1 AATAAA-AAAATAAATATAAAGAAAAAAAT-AAAGGAAAAA
* **
19476 ACATAAAAAAATAAATATAAGGAAATGAATAAAGGAAAAA
1 A-ATAAAAAAATAAATATAAAGAAAAAAATAAAGGAAAAA
* *
19516 AAT-AAAAATTAAA-ATAAATAAAAAA
1 AATAAAAAAATAAATATAAAGAAAAAA
19541 TGAAATAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
37 8 0.15
38 9 0.17
39 2 0.04
40 19 0.36
41 15 0.28
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (39 bp):
AATAAAAAAATAAATATAAAGAAAAAAATAAAGGAAAAA
Found at i:19520 original size:13 final size:13
Alignment explanation
Indices: 19452--19521 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 13
19442 TAAAATAAGT
19452 TAAA-GAAAAAAA
1 TAAAGGAAAAAAA
*
19464 TGAAAGTAAAAAACA
1 T-AAAGGAAAAAA-A
19479 TAAA--AAAATAAA
1 TAAAGGAAAA-AAA
**
19491 TATAAGGAAATGAA
1 TA-AAGGAAAAAAA
19505 TAAAGGAAAAAAA
1 TAAAGGAAAAAAA
19518 TAAA
1 TAAA
19522 AATTAAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
12 8 0.17
13 20 0.43
14 13 0.28
15 5 0.11
ACGTcount: A:0.73, C:0.01, G:0.11, T:0.14
Consensus pattern (13 bp):
TAAAGGAAAAAAA
Found at i:19531 original size:25 final size:26
Alignment explanation
Indices: 19436--19588 Score: 79
Period size: 27 Copynumber: 5.8 Consensus size: 26
19426 AAACAAGTGC
**
19436 AATAAATAAAATAAGTTAAA-GAAAAA
1 AATAAAT-AAATAAAATAAAGGAAAAA
19462 AATGAAAGTAAA-AAACATAAA--AAAATA
1 AAT-AAA-TAAATAAA-ATAAAGGAAAA-A
* *
19489 AATATAAGGAAAT-GAATAAAGGAAAAA
1 AATA-AA-TAAATAAAATAAAGGAAAAA
* *
19516 AATAAA-AATTAAAATAAA--TAAAA
1 AATAAATAAATAAAATAAAGGAAAAA
*
19539 AATGAAATAAATAAGATAAAGGTAAAAA
1 AAT-AAATAAATAAAATAAAGG-AAAAA
*
19567 AATAAACGAAAATAAAATAAAG
1 AATAAA--TAAATAAAATAAAG
19589 AAGATAAAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 29
0.71 0.09 0.21
Matches are distributed among these distances:
23 7 0.07
24 6 0.06
25 16 0.16
26 17 0.17
27 29 0.29
28 12 0.12
29 12 0.12
ACGTcount: A:0.72, C:0.01, G:0.10, T:0.17
Consensus pattern (26 bp):
AATAAATAAATAAAATAAAGGAAAAA
Found at i:19536 original size:16 final size:16
Alignment explanation
Indices: 19511--19552 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
19501 TGAATAAAGG
*
19511 AAAA-AAATAAAAATT
1 AAAATAAATAAAAAAT
19526 AAAATAAATAAAAAAT
1 AAAATAAATAAAAAAT
*
19542 GAAATAAATAA
1 AAAATAAATAA
19553 GATAAAGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAATAAATAAAAAAT
Found at i:19597 original size:14 final size:15
Alignment explanation
Indices: 19547--19597 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
19537 AAAATGAAAT
* * *
19547 AAATAAGATAAAGGT
1 AAATAAAATAAACGA
19562 AAA-AAAATAAACGA
1 AAATAAAATAAACGA
19576 AAATAAAATAAA-GA
1 AAATAAAATAAACGA
*
19590 AGATAAAA
1 AAATAAAA
19598 ACAAAGTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.14
Consensus pattern (15 bp):
AAATAAAATAAACGA
Found at i:20102 original size:19 final size:18
Alignment explanation
Indices: 20080--20130 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
20070 AACAATAACT
20080 AAATAAAAGTAGAAA-TAAA
1 AAATAAAA-TA-AAATTAAA
*
20099 AAATAAGATAAAATTAAA
1 AAATAAAATAAAATTAAA
*
20117 AGAATAAAACAAAA
1 A-AATAAAATAAAA
20131 AAATGAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.11
18 7 0.26
19 17 0.63
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (18 bp):
AAATAAAATAAAATTAAA
Found at i:20265 original size:3 final size:3
Alignment explanation
Indices: 20257--20296 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
20247 TGTAGGTAGT
20257 ATA ATA ATA ATA A-A ATA TATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A
20297 AGACAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20387 original size:38 final size:38
Alignment explanation
Indices: 20262--20388 Score: 99
Period size: 38 Copynumber: 3.4 Consensus size: 38
20252 GTAGTATAAT
* *
20262 AATAATA-AAATATAT-AATAATAATAATAATAATAAAGA
1 AATAATAGAAATAAATAAATAA-AATAAAAATAATAAA-A
* * *
20300 CA-AA-AG-ATTAAA-AAATAAAATAAAAATAATATAA
1 AATAATAGAAATAAATAAATAAAATAAAAATAATAAAA
* *
20334 TATAATAGTAATAAATAAA-AAAACTAAAAATAATAAAA
1 AATAATAGAAATAAATAAATAAAA-TAAAAATAATAAAA
20372 AAT-ATAGAAAGTAAATA
1 AATAATAGAAA-TAAATA
20389 TATTTATATA
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
34 2 0.03
35 15 0.21
36 12 0.17
37 17 0.24
38 25 0.35
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (38 bp):
AATAATAGAAATAAATAAATAAAATAAAAATAATAAAA
Found at i:21216 original size:150 final size:150
Alignment explanation
Indices: 21035--21306 Score: 499
Period size: 150 Copynumber: 1.8 Consensus size: 150
21025 AAAAAACAAA
* * *
21035 AAAAAAAATATTAGAAAAGCAACATGCAAAAGGCTAAAACACCGAATCAAGGTAAAATATACCTT
1 AAAAAAAAGATGAGAAAAACAACATGCAAAAGGCTAAAACACCGAATCAAGGTAAAATATACCTT
21100 CTTATTTCTTTCTGCTTTCGAATGTTACAAGCTTTGAGTACTTAGATCTTACTATTTTTTCATCG
66 CTTATTTCTTTCTGCTTTCGAATGTTACAAGCTTTGAGTACTTAGATCTTACTATTTTTTCATCG
21165 GCCATCTCGAAGCAAAATCG
131 GCCATCTCGAAGCAAAATCG
*
21185 AAAAAAAAGATGAGAAAAACAACATGCAAAAGGCTAAAACACCGAATCAAGGTAAAATATATCTT
1 AAAAAAAAGATGAGAAAAACAACATGCAAAAGGCTAAAACACCGAATCAAGGTAAAATATACCTT
*
21250 TTTATTTCTTTCTGCTTTCGAATGTTACAAGCTTTGAGTACTTAGATCTTACTATTT
66 CTTATTTCTTTCTGCTTTCGAATGTTACAAGCTTTGAGTACTTAGATCTTACTATTT
21307 GCTACGTATT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 117 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (150 bp):
AAAAAAAAGATGAGAAAAACAACATGCAAAAGGCTAAAACACCGAATCAAGGTAAAATATACCTT
CTTATTTCTTTCTGCTTTCGAATGTTACAAGCTTTGAGTACTTAGATCTTACTATTTTTTCATCG
GCCATCTCGAAGCAAAATCG
Found at i:22568 original size:116 final size:119
Alignment explanation
Indices: 22327--22618 Score: 403
Period size: 116 Copynumber: 2.5 Consensus size: 119
22317 AAAGCTCCTC
* * * * *
22327 CGTTGTGAAGTTG-GGCTTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGAGTTGCAT
1 CGTTGTGAAGTTGAGTC-TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAAAGATGCAA
* **
22391 TGCTGCTTGTGGGCACGATATCCTTCATTGTGAAGTTGAAATCGTGGATGACCCATT
65 TGCTGC-T-TGGGAACGATATCCTTCATCATGAAGTTGAAATCGTGGATGACCCATT
* *
22448 CGTTGTGAAATTGAGTCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCTAAAAGATG-AAT
1 CGTTGTGAAGTTGAGTCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAAAGATGCAAT
* * *
22512 GTTGC-T-GGAACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGACCCCTT
66 GCTGCTTGGGAACGATATCCTTCATCATGAAGTTGAAATCGTGGATGACCCATT
*
22564 CGTTGTGAAGTTGAGTCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAA
1 CGTTGTGAAGTTGAGTCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
22619 GTATTGTTTG
Statistics
Matches: 154, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
116 93 0.60
117 1 0.01
120 6 0.04
121 52 0.34
122 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.34
Consensus pattern (119 bp):
CGTTGTGAAGTTGAGTCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAAAGATGCAAT
GCTGCTTGGGAACGATATCCTTCATCATGAAGTTGAAATCGTGGATGACCCATT
Found at i:33620 original size:14 final size:13
Alignment explanation
Indices: 33603--33654 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
33593 AAACATAAAA
33603 AAATAAATATAAGG
1 AAATAAATA-AAGG
*
33617 AAATGAATAAAGG
1 AAATAAATAAAGG
* *
33630 AAAAAAATTAAAATG
1 AAATAAA-T-AAAGG
33645 AAATAAATAA
1 AAATAAATAA
33655 GATAAAGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.35
14 10 0.32
15 10 0.32
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (13 bp):
AAATAAATAAAGG
Found at i:33631 original size:13 final size:14
Alignment explanation
Indices: 33603--33653 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
33593 AAACATAAAA
33603 AAATAAATATAAGG
1 AAATAAATATAAGG
*
33617 AAATGAATA-AAGG
1 AAATAAATATAAGG
* * *
33630 AAAAAAATTAAAATG
1 AAATAAA-TATAAGG
33645 AAATAAATA
1 AAATAAATA
33654 AGATAAAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 9 0.30
14 12 0.40
15 9 0.30
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.20
Consensus pattern (14 bp):
AAATAAATATAAGG
Found at i:34105 original size:13 final size:13
Alignment explanation
Indices: 34087--34112 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34077 TATAATAACG
34087 TTAAAACAAAATA
1 TTAAAACAAAATA
34100 TTAAAACAAAATA
1 TTAAAACAAAATA
34113 ATAATAGGAA
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
TTAAAACAAAATA
Found at i:34364 original size:3 final size:3
Alignment explanation
Indices: 34352--34426 Score: 52
Period size: 3 Copynumber: 26.0 Consensus size: 3
34342 AGTGTGTAGG
* * *
34352 TAA T-A TAA TAA TAA TAA T-A TAA TAA GAA AAA TAA AAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* *
34396 T-A TAA TAG TAA T-A TAA AAA CTAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
34427 AAAATATAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
2 10 0.18
3 41 0.73
4 5 0.09
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:34371 original size:14 final size:14
Alignment explanation
Indices: 34352--34408 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
34342 AGTGTGTAGG
34352 TAATATAATAATAA
1 TAATATAATAATAA
*
34366 TAATATAATAAGAA
1 TAATATAATAATAA
*
34380 -AA-ATAAAAATATA
1 TAATATAATAATA-A
*
34393 TAATATAATAGTAA
1 TAATATAATAATAA
34407 TA
1 TA
34409 TAAAAACTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 7 0.20
13 3 0.09
14 18 0.51
15 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:34459 original size:2 final size:2
Alignment explanation
Indices: 34452--34508 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
34442 AATAAAATAG
34452 AT AT 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 AT AT
34494 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
34509 AATTATAGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45233 original size:30 final size:32
Alignment explanation
Indices: 45179--45260 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 32
45169 AAAAGTAATT
45179 TAAACTTTGAGTTATTAA-AAAATA-T-TAAAA
1 TAAA-TTTGAGTTATTAATAAAATATTATAAAA
45209 TAAATTTGAGTTATTAATAAAATATTAATAAAA
1 TAAATTTGAGTTATTAATAAAATATT-ATAAAA
*
45242 TAAATTTGAATTATTAATA
1 TAAATTTGAGTTATTAATA
45261 GATGTCATGT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
29 13 0.28
30 10 0.21
31 1 0.02
33 23 0.49
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (32 bp):
TAAATTTGAGTTATTAATAAAATATTATAAAA
Found at i:54054 original size:20 final size:20
Alignment explanation
Indices: 54025--54063 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54015 ATTCCACCAT
*
54025 ATGCAACTATATGTTCCTAA
1 ATGCAACTATATGATCCTAA
*
54045 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
54064 CATGGGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:56503 original size:33 final size:34
Alignment explanation
Indices: 56430--56511 Score: 132
Period size: 33 Copynumber: 2.4 Consensus size: 34
56420 TAATTTAGAC
*
56430 TTTGAGTTATTAA-AAAGTATTAATAAAATAAAAA
1 TTTGAGTTATTAATAAAATATTAATAAAAT-AAAA
56464 TTTGAGTTATTAATAAAATATTAATAAAAT-AAA
1 TTTGAGTTATTAATAAAATATTAATAAAATAAAA
56497 TTTGAGTTATTAATA
1 TTTGAGTTATTAATA
56512 GATGCCATGT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 18 0.39
34 13 0.28
35 15 0.33
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (34 bp):
TTTGAGTTATTAATAAAATATTAATAAAATAAAA
Found at i:57254 original size:23 final size:22
Alignment explanation
Indices: 57203--57254 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
57193 GATTGGACTC
*
57203 ATTTCTTTTATTTATAACATAT
1 ATTTATTTTATTTATAACATAT
*
57225 TTATTATTTTATTTTAATAA-ATAT
1 AT-TTATTTTA-TTT-ATAACATAT
57249 ATTTAT
1 ATTTAT
57255 ATAAAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.04
23 11 0.46
24 8 0.33
25 4 0.17
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTATTTTATTTATAACATAT
Found at i:57286 original size:16 final size:16
Alignment explanation
Indices: 57265--57297 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
57255 ATAAAGAAAA
*
57265 AATATAAATTTATAAT
1 AATATAAATTTACAAT
57281 AATATAAATTTACAAT
1 AATATAAATTTACAAT
57297 A
1 A
57298 TAATTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATAAATTTACAAT
Found at i:59158 original size:11 final size:11
Alignment explanation
Indices: 59124--59160 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
59114 GTTGAAACAT
59124 AATTC-AAAAC
1 AATTCAAAAAC
*
59134 AACTCAAAAAC
1 AATTCAAAAAC
59145 AATTCAAAAAC
1 AATTCAAAAAC
59156 AATTC
1 AATTC
59161 TTTTATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (11 bp):
AATTCAAAAAC
Found at i:59953 original size:45 final size:45
Alignment explanation
Indices: 59903--60054 Score: 171
Period size: 45 Copynumber: 3.4 Consensus size: 45
59893 TATGCCAAAG
59903 CTTTTGATTATTGGGTTGCCAAAAGTAAAATCAAA-GTATTAATTC
1 CTTTTGATTATTGGGTTGCCAAAAGTAAAATCAAATG-ATTAATTC
* * * * * **
59948 CTTTTGGTTATTGTGTCGTCAAGAGTAAAATCAAATGATTGGTTC
1 CTTTTGATTATTGGGTTGCCAAAAGTAAAATCAAATGATTAATTC
* * * * *
59993 CTTTTAAATATTGGGTTGCCAAAATTAGAATCAAATGATTAATTT
1 CTTTTGATTATTGGGTTGCCAAAAGTAAAATCAAATGATTAATTC
*
60038 CTTTCGATTATTGGGTT
1 CTTTTGATTATTGGGTT
60055 ACGAAAATTA
Statistics
Matches: 84, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
45 83 0.99
46 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.41
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGCCAAAAGTAAAATCAAATGATTAATTC
Found at i:61421 original size:26 final size:26
Alignment explanation
Indices: 61388--61439 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
61378 AGAACCTTTC
61388 CAGATATTATGAAAGAATTTAGCAAA
1 CAGATATTATGAAAGAATTTAGCAAA
61414 CAGATATTATGAAAGAATTTAGCAAA
1 CAGATATTATGAAAGAATTTAGCAAA
61440 TTGATGCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (26 bp):
CAGATATTATGAAAGAATTTAGCAAA
Found at i:65389 original size:73 final size:73
Alignment explanation
Indices: 65224--65389 Score: 226
Period size: 73 Copynumber: 2.3 Consensus size: 73
65214 GTTAAATGAC
* * * * * *
65224 TAAGGGTATCGTTACCTCTAGGGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGTCAA
1 TAAGGGTATCGATACCTATGGGGGGTATCGATACCCATTGGGCATTCTGTTTTTCTCAGAGCCAA
*
65289 AATTAACA
66 AATCAACA
* *
65297 CAAGGGTATCGATACCTATGGGGGGTATCGATA-CCAGTTTGGCATTCTGTTTTTCTCAGAGCCA
1 TAAGGGTATCGATACCTATGGGGGGTATCGATACCCA-TTGGGCATTCTGTTTTTCTCAGAGCCA
65361 AAATCAACA
65 AAATCAACA
*
65370 TAAGGGTATCGGTACCTATG
1 TAAGGGTATCGATACCTATG
65390 ATTTAGGTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 3 0.04
73 78 0.96
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (73 bp):
TAAGGGTATCGATACCTATGGGGGGTATCGATACCCATTGGGCATTCTGTTTTTCTCAGAGCCAA
AATCAACA
Found at i:65724 original size:13 final size:13
Alignment explanation
Indices: 65706--65741 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
65696 GATTTTCTTA
65706 TTGAAAATCATTT
1 TTGAAAATCATTT
65719 TTG-AAATCAATTT
1 TTGAAAATC-ATTT
65732 TTGAAAATCA
1 TTGAAAATCA
65742 CTCCCCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (13 bp):
TTGAAAATCATTT
Found at i:67293 original size:12 final size:12
Alignment explanation
Indices: 67276--67310 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
67266 GGTTGAATAG
67276 GAGGTGGATTTA
1 GAGGTGGATTTA
*
67288 GAGGTGGGTTTA
1 GAGGTGGATTTA
*
67300 GAGGTCGATTT
1 GAGGTGGATTT
67311 GAACGACTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.20, C:0.03, G:0.43, T:0.34
Consensus pattern (12 bp):
GAGGTGGATTTA
Found at i:67604 original size:25 final size:24
Alignment explanation
Indices: 67548--67596 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
67538 CAACTTAATT
*
67548 AAAT-AAAAAACAATAATTTAAAA
1 AAATCAAAAAAAAATAATTTAAAA
* *
67571 AAATCAAAAAAAAATTATTTCAAA
1 AAATCAAAAAAAAATAATTTAAAA
67595 AA
1 AA
67597 TCTCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (24 bp):
AAATCAAAAAAAAATAATTTAAAA
Found at i:68100 original size:21 final size:21
Alignment explanation
Indices: 67979--68101 Score: 103
Period size: 21 Copynumber: 5.8 Consensus size: 21
67969 AAAACCCGAC
*
67979 GGGGGTATCGATACCCT-TATA
1 GGGGGTATCGATA-CCTATAAA
68000 -GGGGTATCGATACAC-ATTCAAA
1 GGGGGTATCGATAC-CTA-T-AAA
* *
68022 GAGGGTATCGATACACGT-TGAA
1 GGGGGTATCGATAC-C-TATAAA
* **
68044 -GGAGTATCGATACCTAGCAA
1 GGGGGTATCGATACCTATAAA
68064 GGGGGTATCGATACCTATAAA
1 GGGGGTATCGATACCTATAAA
68085 GGGGGTATCGATACCTA
1 GGGGGTATCGATACCTA
68102 GTGCACAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
19 2 0.02
20 16 0.19
21 46 0.55
22 4 0.05
23 15 0.18
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (21 bp):
GGGGGTATCGATACCTATAAA
Found at i:70159 original size:63 final size:63
Alignment explanation
Indices: 70043--70164 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 63
70033 CCCTAAGGGA
* * ** * *
70043 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTATCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
70106 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAA
70165 AAGTCACATT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
62 1 0.02
63 45 0.92
64 3 0.06
ACGTcount: A:0.26, C:0.29, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:71067 original size:22 final size:22
Alignment explanation
Indices: 71042--71084 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
71032 GAAAGTCAAC
71042 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
71064 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
71085 AGACTGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:71127 original size:10 final size:10
Alignment explanation
Indices: 71114--71169 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
71104 AGACCGGTCA
71114 AACCGGTTCG
1 AACCGGTTCG
71124 AACCGGTT-G
1 AACCGGTTCG
*
71133 AAACCGG-TCA
1 -AACCGGTTCG
71143 AACCGGTTCG
1 AACCGGTTCG
71153 AACCGGTT-G
1 AACCGGTTCG
71162 AAACCGGT
1 -AACCGGT
71170 CAAACCCGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 9 0.22
10 31 0.77
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.18
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:71128 original size:19 final size:19
Alignment explanation
Indices: 71090--71188 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
71080 GGGTCAGACT
*
71090 GGTCAAACCGATTC-AGACC
1 GGTCAAACCGGTTCGA-ACC
71109 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCGAACC
* *
71128 GGTTGAAACCGG-TCAAACC
1 GG-TCAAACCGGTTCGAACC
*
71147 GGTTCGAACCGGTT-GAAACC
1 GG-TCAAACCGGTTCG-AACC
*
71167 GGTCAAACCCG-TCAGAACC
1 GGTCAAACCGGTTC-GAACC
71186 GGT
1 GGT
71189 TGAAAACTGG
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.02
19 48 0.73
20 17 0.26
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGTTCGAACC
Found at i:71128 original size:29 final size:29
Alignment explanation
Indices: 71106--71209 Score: 165
Period size: 29 Copynumber: 3.6 Consensus size: 29
71096 ACCGATTCAG
71106 ACCGGTCAAACCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCGAACCGGTTGAA
71135 ACCGGTCAAACCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCGAACCGGTTGAA
*
71164 ACCGGTCAAACCCG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
*
71194 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
71210 TCCAGCAGCC
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
28 2 0.03
29 52 0.75
30 14 0.20
31 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (29 bp):
ACCGGTCAAACCGGTTCGAACCGGTTGAA
Found at i:77364 original size:32 final size:31
Alignment explanation
Indices: 77328--77404 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
77318 CGGGGCCGTG
*
77328 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
77360 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
77391 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
77405 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:77387 original size:63 final size:63
Alignment explanation
Indices: 77281--77404 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
77271 CCCTAAGGGA
* * ** *
77281 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
77344 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
77405 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:78285 original size:7 final size:7
Alignment explanation
Indices: 78273--78345 Score: 128
Period size: 7 Copynumber: 10.4 Consensus size: 7
78263 GTCAAAGAAA
78273 GTCAACG
1 GTCAACG
78280 GTCAACG
1 GTCAACG
78287 GTCAACG
1 GTCAACG
78294 GTCAACG
1 GTCAACG
78301 GTCAACG
1 GTCAACG
*
78308 ATCAACG
1 GTCAACG
*
78315 ATCAACG
1 GTCAACG
78322 GTCAACG
1 GTCAACG
78329 GTCAACG
1 GTCAACG
78336 GTCAACG
1 GTCAACG
78343 GTC
1 GTC
78346 GGGTCGGGTC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 64 1.00
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:78363 original size:22 final size:22
Alignment explanation
Indices: 78335--78377 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
78325 AACGGTCAAC
78335 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
78357 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
78378 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:78392 original size:9 final size:9
Alignment explanation
Indices: 78374--78472 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
78364 GGTCGGGTCG
*
78374 GGTCAGACC
1 GGTCAAACC
78383 GGTCAAACC
1 GGTCAAACC
* *
78392 GATTCAGACC
1 G-GTCAAACC
78402 GGTCAAACC
1 GGTCAAACC
*
78411 GGTTCGAACC
1 GG-TCAAACC
*
78421 GGTTGAAACC
1 GG-TCAAACC
78431 GGTCAAACC
1 GGTCAAACC
*
78440 GATCAGAACC
1 GGTCA-AACC
*
78450 GGTTGAAAACC
1 GG-T-CAAACC
78461 GGTCAAACC
1 GGTCAAACC
78470 GGT
1 GGT
78473 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
9 35 0.49
10 29 0.40
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:78421 original size:19 final size:19
Alignment explanation
Indices: 78380--78473 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
78370 GTCGGGTCAG
*
78380 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
78398 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
* *
78418 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCGA
*
78437 ACCGATCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGGTTCG--A
78458 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
78474 TCCAGCAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.03
19 34 0.55
20 18 0.29
21 8 0.13
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:78431 original size:29 final size:31
Alignment explanation
Indices: 78399--78473 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
78389 ACCGATTCAG
78399 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
78428 ACCGGTCAAACC-GATCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
78458 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
78474 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 3 0.07
29 22 0.54
30 14 0.34
31 2 0.05
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:79783 original size:18 final size:18
Alignment explanation
Indices: 79760--79800 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
79750 CTTATGCTTC
79760 TTCTTGGATTGACCATTT
1 TTCTTGGATTGACCATTT
* *
79778 TTCTTGGATTTACCCTTT
1 TTCTTGGATTGACCATTT
79796 TTCTT
1 TTCTT
79801 TAATTGTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.56
Consensus pattern (18 bp):
TTCTTGGATTGACCATTT
Found at i:81642 original size:73 final size:75
Alignment explanation
Indices: 81485--81650 Score: 239
Period size: 73 Copynumber: 2.3 Consensus size: 75
81475 TAAATGACTT
* * * *
81485 AGGGTATCGGTACCTCT-AGGGGGTATCGGTACCCATTGGGCATTCTGCTTTTTCTCGGAGCCAA
1 AGGGTATCGGTACCTATGAGGGGGTATCGGTACCCATTGGACAATCTGCTTTTTCTCAGAGCCAA
*
81549 AATTAACACA
66 AATCAACACA
* *
81559 AGGGTATCGGTACCTATGA-GGGGTATCGGTACCCGTTTGACAATCTG-TTTTTCTCAGAGCCAA
1 AGGGTATCGGTACCTATGAGGGGGTATCGGTACCCATTGGACAATCTGCTTTTTCTCAGAGCCAA
*
81622 AATCAACATA
66 AATCAACACA
81632 AGGGTATCGGTACCTATGA
1 AGGGTATCGGTACCTATGA
81651 CTTAGGTATC
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
73 42 0.51
74 40 0.48
75 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (75 bp):
AGGGTATCGGTACCTATGAGGGGGTATCGGTACCCATTGGACAATCTGCTTTTTCTCAGAGCCAA
AATCAACACA
Found at i:83698 original size:21 final size:19
Alignment explanation
Indices: 83674--83715 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
83664 AGTTTTCATG
83674 AAAACAACATAATTAAATAAA
1 AAAACAACA-AATTAAA-AAA
*
83695 AAAACAACAATTTAAAAAA
1 AAAACAACAAATTAAAAAA
83714 AA
1 AA
83716 TCAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 9 0.45
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAACAACAAATTAAAAAA
Found at i:84213 original size:21 final size:21
Alignment explanation
Indices: 84184--84242 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
84174 ATACATGTTG
*
84184 AAGGA-GTATCGATACCTAGC
1 AAGGAGGTATCGATACCTAGA
* *
84204 AAGGGGGTATCGATACCTATA
1 AAGGAGGTATCGATACCTAGA
84225 AAGGAGGTATCGATACCT
1 AAGGAGGTATCGATACCT
84243 GGTGCACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (21 bp):
AAGGAGGTATCGATACCTAGA
Found at i:89245 original size:54 final size:54
Alignment explanation
Indices: 89160--89280 Score: 163
Period size: 54 Copynumber: 2.2 Consensus size: 54
89150 GTACCTCTAG
* *
89160 GGGTATCGGTACCCTTTGGGCATTCTATTTTTCTCGGAGCCAAAATTAACACAA
1 GGGTATCGGTACCCTTTGGGCATTATATTTTTCTCGGAGCCAAAATCAACACAA
* * * *
89214 GGTTATCGGTACCCGTTT-GTCATTATGTTTTTCTCGGAGCCAAAATCAACATAA
1 GGGTATCGGTACCC-TTTGGGCATTATATTTTTCTCGGAGCCAAAATCAACACAA
*
89268 GGGTATTGGTACC
1 GGGTATCGGTACC
89281 TATGACTTAG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 55 0.95
55 3 0.05
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (54 bp):
GGGTATCGGTACCCTTTGGGCATTATATTTTTCTCGGAGCCAAAATCAACACAA
Found at i:92897 original size:25 final size:25
Alignment explanation
Indices: 92824--92918 Score: 97
Period size: 25 Copynumber: 3.8 Consensus size: 25
92814 TTTTTGATAA
* *
92824 GAATAA-AAAATATATTT-TTAAAT
1 GAATAATAAAATATATTTAATAAGT
* *
92847 TAA-AATAAAAATATTTTTAAATTAAGT
1 GAATAAT-AAAATATATTT-AA-TAAGT
92874 GAATAATAAAATATATTTAATAAGT
1 GAATAATAAAATATATTTAATAAGT
*
92899 GAATAATAAAATATTTTTAA
1 GAATAATAAAATATATTTAA
92919 AGTTAATATA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
22 2 0.03
23 2 0.03
24 10 0.17
25 24 0.41
26 2 0.03
27 16 0.27
28 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (25 bp):
GAATAATAAAATATATTTAATAAGT
Found at i:92908 original size:53 final size:50
Alignment explanation
Indices: 92824--92924 Score: 132
Period size: 52 Copynumber: 2.0 Consensus size: 50
92814 TTTTTGATAA
* *
92824 GAATAAAAAATATATTTTTAAATTAAAATAAAAATATTTTTAAA-TTAAGT
1 GAATAAAAAATATATTTATAAATGAAAAT-AAAATATTTTTAAAGTTAAGT
*
92874 GAATAATAAAATATATTTAATAAGTGAATAATAAAATATTTTTAAAGTTAA
1 GAATAA-AAAATATATTT-ATAAATGAA-AATAAAATATTTTTAAAGTTAA
92925 TATATATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
50 6 0.14
51 11 0.25
52 20 0.45
53 7 0.16
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (50 bp):
GAATAAAAAATATATTTATAAATGAAAATAAAATATTTTTAAAGTTAAGT
Found at i:93107 original size:27 final size:27
Alignment explanation
Indices: 93061--93118 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
93051 GGAGGATTAA
* *
93061 TTAAATTAAATTAAAAATAAAACATTT
1 TTAAATTAAATGAAAAATAAAACATAT
* * *
93088 TTAAATTAAGTGAAAGATAAAATATAT
1 TTAAATTAAATGAAAAATAAAACATAT
93115 TTAA
1 TTAA
93119 TAAGTTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (27 bp):
TTAAATTAAATGAAAAATAAAACATAT
Found at i:93147 original size:24 final size:27
Alignment explanation
Indices: 93106--93164 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
93096 AGTGAAAGAT
*
93106 AAAATATATTTAATAAGTT-A-ATATA
1 AAAATATTTTTAATAAGTTAATATATA
*
93131 AAAATATTTTTTA-AAGTTAATATATA
1 AAAATATTTTTAATAAGTTAATATATA
93157 AAAATATT
1 AAAATATT
93165 ATGAATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 5 0.17
25 12 0.40
26 13 0.43
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
AAAATATTTTTAATAAGTTAATATATA
Found at i:110863 original size:20 final size:19
Alignment explanation
Indices: 110831--110868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
110821 AACTTGTATT
*
110831 TAAAATTTTATATAAATAC
1 TAAAATTTAATATAAATAC
110850 TAAATATTTAATATAAATA
1 TAAA-ATTTAATATAAATA
110869 TTATTAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAATTTAATATAAATAC
Found at i:110952 original size:12 final size:12
Alignment explanation
Indices: 110937--110967 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
110927 ATACAAGTAT
110937 ATTAATACTATA
1 ATTAATACTATA
*
110949 ATTAATATTATA
1 ATTAATACTATA
110961 ATTAATA
1 ATTAATA
110968 ATTAATGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTAATACTATA
Found at i:111926 original size:16 final size:15
Alignment explanation
Indices: 111901--111938 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
111891 TTGCTCTCTG
111901 TCTCTTGTGTGTCTC
1 TCTCTTGTGTGTCTC
*
111916 TCTCGTTGTGTGTTTC
1 TCTC-TTGTGTGTCTC
111932 TCTCTTG
1 TCTCTTG
111939 CAGGATCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.00, C:0.24, G:0.21, T:0.55
Consensus pattern (15 bp):
TCTCTTGTGTGTCTC
Found at i:112397 original size:2 final size:2
Alignment explanation
Indices: 112385--112424 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
112375 TATAATAATA
112385 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112425 CTATCATAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:113215 original size:20 final size:20
Alignment explanation
Indices: 113190--113234 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
113180 AAACTGACAG
113190 ATGACCCAAAGGATTTACAA
1 ATGACCCAAAGGATTTACAA
* *
113210 ATGACCCGAAGGTTTTACAA
1 ATGACCCAAAGGATTTACAA
113230 ATGAC
1 ATGAC
113235 TCGGAGGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (20 bp):
ATGACCCAAAGGATTTACAA
Found at i:113246 original size:20 final size:20
Alignment explanation
Indices: 113190--113246 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
113180 AAACTGACAG
* *
113190 ATGACCCAAAGGATTTACAA
1 ATGACCCGAAGGCTTTACAA
*
113210 ATGACCCGAAGGTTTTACAA
1 ATGACCCGAAGGCTTTACAA
* *
113230 ATGACTCGGAGGCTTTA
1 ATGACCCGAAGGCTTTA
113247 ATTTTCTAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (20 bp):
ATGACCCGAAGGCTTTACAA
Found at i:113340 original size:20 final size:20
Alignment explanation
Indices: 113312--113365 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
113302 AAAACATCCT
* *
113312 ACCCTGAGGCTTTACAGATG
1 ACCCGGAGGCTTTACAAATG
* *
113332 ACCCGGAGGTTTTACAAATT
1 ACCCGGAGGCTTTACAAATG
*
113352 ACCTGGAGGCTTTA
1 ACCCGGAGGCTTTA
113366 ATTTTCTAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (20 bp):
ACCCGGAGGCTTTACAAATG
Found at i:119932 original size:20 final size:19
Alignment explanation
Indices: 119903--119940 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
119893 AACTTGTATT
119903 TAAAATTTAATATAAATAC
1 TAAAATTTAATATAAATAC
119922 TAAATATTTAATATAAATA
1 TAAA-ATTTAATATAAATA
119941 TTATTAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTTAATATAAATAC
Found at i:120797 original size:18 final size:17
Alignment explanation
Indices: 120770--120807 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
120760 TTGGTCTCTG
120770 TCTCTTGTGTGTGTCTC
1 TCTCTTGTGTGTGTCTC
*
120787 TCTCGTTGTGTGTTTCTC
1 TCTC-TTGTGTGTGTCTC
120805 TCT
1 TCT
120808 TGCAGGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.00, C:0.24, G:0.21, T:0.55
Consensus pattern (17 bp):
TCTCTTGTGTGTGTCTC
Found at i:121253 original size:10 final size:11
Alignment explanation
Indices: 121241--121292 Score: 62
Period size: 10 Copynumber: 5.3 Consensus size: 11
121231 TCTTGTAATA
121241 ATAATATATA-
1 ATAATATATAT
121251 ATAAT-TA-AT
1 ATAATATATAT
121260 AT-ATATATAT
1 ATAATATATAT
121270 AT-ATATATAT
1 ATAATATATAT
121280 AT-ATATATAT
1 ATAATATATAT
121290 ATA
1 ATA
121293 CTAATTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
8 3 0.08
9 6 0.16
10 29 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATAATATATAT
Found at i:121261 original size:14 final size:13
Alignment explanation
Indices: 121236--121297 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 13
121226 CATCCTCTTG
121236 TAATAATAATATA
1 TAATAATAATATA
121249 TAATAATTAATATA
1 TAATAA-TAATATA
121263 T-AT-ATATATATA
1 TAATAATA-ATATA
121275 TATATATATATATATA
1 TA-ATA-ATA-ATATA
*
121291 TACTAAT
1 TAATAAT
121298 TATAACACTC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
11 2 0.05
12 7 0.17
13 8 0.19
14 12 0.29
15 2 0.05
16 11 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATAATAATATA
Found at i:121263 original size:2 final size:2
Alignment explanation
Indices: 121258--121292 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
121248 ATAATAATTA
121258 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
121293 CTAATTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:123999 original size:22 final size:21
Alignment explanation
Indices: 123952--124012 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
123942 CACAATAAAC
* *
123952 AATATTGTTTTTAAAAAATAAT
1 AATATT-TTTTTAAAATATAAG
*
123974 AATATTATTTTTAAAATATTAG
1 AATATT-TTTTTAAAATATAAG
*
123996 AATAATTTATTTAAAAT
1 AAT-ATTTTTTTAAAAT
124013 TATTTATATC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 30 0.91
23 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
AATATTTTTTTAAAATATAAG
Found at i:124172 original size:17 final size:19
Alignment explanation
Indices: 124139--124180 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
124129 ATTATTACTT
124139 ATATTAGTTACTTATTAAA
1 ATATTAGTTACTTATTAAA
124158 ATATTA-TTA-TTATTAAA
1 ATATTAGTTACTTATTAAA
124175 ATATTA
1 ATATTA
124181 AAAATATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 14 0.61
18 3 0.13
19 6 0.26
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATTAGTTACTTATTAAA
Found at i:124212 original size:24 final size:25
Alignment explanation
Indices: 124154--124213 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
124144 AGTTACTTAT
124154 TAAAATATTAT-TATTATTAAAATA
1 TAAAATATTATATATTATTAAAATA
*
124178 TTAAAA-A-TATATGTTATTAAAATA
1 -TAAAATATTATATATTATTAAAATA
124202 -AAAATATTATAT
1 TAAAATATTATAT
124214 TATATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.13
23 4 0.13
24 18 0.58
25 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAAATATTATATATTATTAAAATA
Found at i:133062 original size:29 final size:29
Alignment explanation
Indices: 133017--133086 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
133007 TTGTTAACCT
*
133017 TGTAATAATGCATGCATACTTATGTTGAA
1 TGTAATAATGCACGCATACTTATGTTGAA
133046 TGTAATAATGCACGCATACTTATGTTGAA
1 TGTAATAATGCACGCATACTTATGTTGAA
133075 TGTAATAATGCA
1 TGTAATAATGCA
133087 TTATTAACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (29 bp):
TGTAATAATGCACGCATACTTATGTTGAA
Found at i:135228 original size:24 final size:26
Alignment explanation
Indices: 135196--135256 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 26
135186 AAACAATTTT
*
135196 AAAAAAAATA-TCAAACAAAAA-AAC
1 AAAAAAAATAGTAAAACAAAAACAAC
*
135220 AAAAAAAATAGTAAAATAAAAACAAC
1 AAAAAAAATAGTAAAACAAAAACAAC
135246 ATAAAATAAAT
1 A-AAAA-AAAT
135257 TAAAATAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 10 0.32
25 9 0.29
26 4 0.13
27 4 0.13
28 4 0.13
ACGTcount: A:0.77, C:0.08, G:0.02, T:0.13
Consensus pattern (26 bp):
AAAAAAAATAGTAAAACAAAAACAAC
Found at i:135241 original size:26 final size:25
Alignment explanation
Indices: 135196--135265 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
135186 AAACAATTTT
* *
135196 AAAAAAAATATCAAA-CAAAAAAAC
1 AAAAAAAATATAAAATAAAAAAAAC
*
135220 AAAAAAAATAGTAAAATAAAAACAAC
1 AAAAAAAATA-TAAAATAAAAAAAAC
135246 ATAAAATAAAT-TAAAATAAA
1 A-AAAA-AAATATAAAATAAA
135266 CATAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 10 0.26
25 4 0.10
26 17 0.44
27 4 0.10
28 4 0.10
ACGTcount: A:0.77, C:0.07, G:0.01, T:0.14
Consensus pattern (25 bp):
AAAAAAAATATAAAATAAAAAAAAC
Found at i:135260 original size:21 final size:21
Alignment explanation
Indices: 135231--135274 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
135221 AAAAAAATAG
135231 TAAAATAAAA-ACAACATAAAA
1 TAAAATAAAATA-AACATAAAA
*
135252 TAAATTAAAATAAACATAAAA
1 TAAAATAAAATAAACATAAAA
135273 TA
1 TA
135275 TAAGGACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAAATAAAATAAACATAAAA
Found at i:136897 original size:3 final size:3
Alignment explanation
Indices: 136889--136961 Score: 75
Period size: 3 Copynumber: 25.7 Consensus size: 3
136879 TATAATTATT
* * *
136889 TAA TAA TAA TAA -AA -AA T-A TAA TAA AAA TAA TAA TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
136934 TAA TAA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
136962 TTCAAATGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
2 10 0.17
3 47 0.80
4 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:137264 original size:36 final size:35
Alignment explanation
Indices: 137167--137271 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 35
137157 TGTCTCAAGG
**
137167 GTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTT
1 GTTTTAAGAAAAACCATCTCAAGTGAGATAAA-AAT
* ** ** * *
137203 GTTTAAAGGGAAACTGTCTCCAGTGAGACAAAAAT
1 GTTTTAAGAAAAACCATCTCAAGTGAGATAAAAAT
137238 GATTTTAAGAAAAACCATCTCAAGTGAGATAAAA
1 G-TTTTAAGAAAAACCATCTCAAGTGAGATAAAA
137272 TTTCTTATTT
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
35 2 0.04
36 50 0.96
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (35 bp):
GTTTTAAGAAAAACCATCTCAAGTGAGATAAAAAT
Found at i:137302 original size:39 final size:40
Alignment explanation
Indices: 137249--137434 Score: 218
Period size: 39 Copynumber: 4.8 Consensus size: 40
137239 ATTTTAAGAA
* *
137249 AAACCATCTCAAGTGAGATAAAAT-TTCTTATTTCAAGGG
1 AAACTATCTCAAGTGAGATAAAATCTTCTTATTTCGAGGG
* * * *
137288 AAACTATATCAAGTGAGACAAAATCTTC-TGTTTCGAGGA
1 AAACTATCTCAAGTGAGATAAAATCTTCTTATTTCGAGGG
* * *
137327 AAACTATCTCAAGTGAGATAAAATCTT-ATGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTTATTTCGAGGG
** * *
137366 AAACTATCTCAAGCAAGATAAAATCTTC-TGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTTATTTCGAGGG
*
137405 AAACTATCTTAAGTGAGATAAAATCTTCTT
1 AAACTATCTCAAGTGAGATAAAATCTTCTT
137435 TTAAGAAAAA
Statistics
Matches: 128, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
39 124 0.97
40 4 0.03
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (40 bp):
AAACTATCTCAAGTGAGATAAAATCTTCTTATTTCGAGGG
Found at i:137348 original size:78 final size:77
Alignment explanation
Indices: 137176--137428 Score: 259
Period size: 78 Copynumber: 3.3 Consensus size: 77
137166 GGTTTTAAGA
* * * * *
137176 AAAACCATCTCAAGTGAGAT-AAATT-TTGTTTAAAGGGAAACTGTCTCCAGTGAGACAAAA-AT
1 AAAACCATCTCAAGTGAGATAAAATTCTTATTTCAAGGGAAACTATCTCAAGTGAGACAAAATCT
** * *
137238 GAT-TTT-AAGA
66 TCTGTTTCGAGG
*
137248 AAAACCATCTCAAGTGAGATAAAATTTCTTATTTCAAGGGAAACTATATCAAGTGAGACAAAATC
1 AAAACCATCTCAAGTGAGATAAAA-TTCTTATTTCAAGGGAAACTATCTCAAGTGAGACAAAATC
137313 TTCTGTTTCGAGG
65 TTCTGTTTCGAGG
* * * ** *
137326 AAAACTATCTCAAGTGAGATAAAA-TCTTATGTTTCGAGTGAAACTATCTCAAGCAAGATAAAAT
1 AAAACCATCTCAAGTGAGATAAAATTCTTA--TTTCAAGGGAAACTATCTCAAGTGAGACAAAAT
137390 CTTCTGTTTCGAGTG
64 CTTCTGTTTCGAG-G
* *
137405 -AAACTATCTTAAGTGAGATAAAAT
1 AAAACCATCTCAAGTGAGATAAAAT
137429 CTTCTTTTAA
Statistics
Matches: 153, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
72 20 0.13
73 3 0.02
74 2 0.01
75 30 0.20
76 7 0.05
77 3 0.02
78 87 0.57
79 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (77 bp):
AAAACCATCTCAAGTGAGATAAAATTCTTATTTCAAGGGAAACTATCTCAAGTGAGACAAAATCT
TCTGTTTCGAGG
Found at i:140246 original size:149 final size:149
Alignment explanation
Indices: 139972--140250 Score: 346
Period size: 149 Copynumber: 1.9 Consensus size: 149
139962 TTCAAAGTTT
* * * * ***
139972 CTACTTCATCTTCTACTTCCAGAAATCTTTCGAGCTGGTTCGCGATCTTCAACTGTTGGCTTTGG
1 CTACTTCATCTTCTACTTCCAGAAATCCTTCGAGCTGGTTCACGATCTTCAACAGTTAGCTTCAA
* *
140037 CGTTGAATCATCTCAGGTCCAACTTGTTACCTCAGCAAGCAAATGTCTGGATCGTCTCCTTGGTA
66 CGTTGAATCATCTCAGGTCCAACTTGTTACCTCAGCAAGCAAATGTCTGGATCATATCCTTGGTA
140102 GATAAACTTCCTCTAGCTC
131 GATAAACTTCCTCTAGCTC
* * ** *
140121 CTACTTCCTTTTCTACTTCCAGAAATCCTTCGAGCTGGTTCATTATTTTCAACAGTTAGCTTCAA
1 CTACTTCATCTTCTACTTCCAGAAATCCTTCGAGCTGGTTCACGATCTTCAACAGTTAGCTTCAA
* * * * * *
140186 TGTTGAATCGTCT-TGAGTCCAACTTGTTACCTCAGC-AGGAAGATGTCTGGCTTATATCCTTGG
66 CGTTGAATCATCTCAG-GTCCAACTTGTTACCTCAGCAAGCAA-ATGTCTGGATCATATCCTTGG
140249 TA
129 TA
140251 AGTAGACTCC
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
148 5 0.05
149 103 0.95
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.36
Consensus pattern (149 bp):
CTACTTCATCTTCTACTTCCAGAAATCCTTCGAGCTGGTTCACGATCTTCAACAGTTAGCTTCAA
CGTTGAATCATCTCAGGTCCAACTTGTTACCTCAGCAAGCAAATGTCTGGATCATATCCTTGGTA
GATAAACTTCCTCTAGCTC
Found at i:143050 original size:28 final size:28
Alignment explanation
Indices: 143019--143086 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
143009 AATTTAAAGA
*
143019 CTAAGTGTAATTCTATCTAAAATGGAGG
1 CTAAGTGTAATTCTATCTAAAATGAAGG
143047 CTAAGTGTAATTCTATCTAAAATGAAGG
1 CTAAGTGTAATTCTATCTAAAATGAAGG
*
143075 CTAAGTCTAATT
1 CTAAGTGTAATT
143087 AACCTAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.34
Consensus pattern (28 bp):
CTAAGTGTAATTCTATCTAAAATGAAGG
Found at i:148754 original size:28 final size:28
Alignment explanation
Indices: 148722--148793 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
148712 TGATTCTGAC
* *
148722 CATTGGTTTAAAAAAAAGTTATTTTGAT
1 CATTGGTTTAAAAAAAAGTGATCTTGAT
*
148750 CATTGGTTTAAAAAAGAGTGATCTTGAT
1 CATTGGTTTAAAAAAAAGTGATCTTGAT
*
148778 CATTGATTTAAAAAAA
1 CATTGGTTTAAAAAAA
148794 GAATGGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (28 bp):
CATTGGTTTAAAAAAAAGTGATCTTGAT
Found at i:148805 original size:29 final size:28
Alignment explanation
Indices: 148712--148807 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 28
148702 TTAAGTTGTC
* * *
148712 TGATTCTGACCATTGGTTTAAAAAA-AA
1 TGATTTTGATCATTGATTTAAAAAAGAA
* * *
148739 GTTATTTTGATCATTGGTTTAAAAAAGAG
1 -TGATTTTGATCATTGATTTAAAAAAGAA
*
148768 TGATCTTGATCATTGATTTAAAAAAAGAA
1 TGATTTTGATCATTGATTT-AAAAAAGAA
*
148797 TGGTTTTGATC
1 TGATTTTGATC
148808 CCTTACGTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
28 38 0.68
29 18 0.32
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (28 bp):
TGATTTTGATCATTGATTTAAAAAAGAA
Found at i:149033 original size:21 final size:21
Alignment explanation
Indices: 148990--149034 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
148980 CATTTCGGTG
* *
148990 TTGTTCTTACCAATAGAGGGC
1 TTGTTCTTACCAATAAAGAGC
*
149011 TTGTTCTTACCAGTAAAGAGC
1 TTGTTCTTACCAATAAAGAGC
149032 TTG
1 TTG
149035 ACAATGAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (21 bp):
TTGTTCTTACCAATAAAGAGC
Found at i:151526 original size:17 final size:17
Alignment explanation
Indices: 151494--151536 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
151484 ATTCCCTTTC
* * *
151494 TTTGAGAGAAATTCTCT
1 TTTGAGAAAAACTCTCA
151511 TTTGAGAAAAACTCTCA
1 TTTGAGAAAAACTCTCA
*
151528 TTCGAGAAA
1 TTTGAGAAA
151537 TAAACACTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (17 bp):
TTTGAGAAAAACTCTCA
Found at i:155931 original size:28 final size:28
Alignment explanation
Indices: 155900--155956 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
155890 ATAATTAACA
155900 AATAATTTGTGATATCTCATATAAACTT
1 AATAATTTGTGATATCTCATATAAACTT
155928 AATAATTTGTGATATCTCATATAAACTT
1 AATAATTTGTGATATCTCATATAAACTT
155956 A
1 A
155957 CTCGAGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (28 bp):
AATAATTTGTGATATCTCATATAAACTT
Found at i:159625 original size:18 final size:18
Alignment explanation
Indices: 159602--159639 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
159592 TTGACTTACC
159602 CTATATAAATATTCCACT
1 CTATATAAATATTCCACT
* *
159620 CTATATAAATGTTTCACT
1 CTATATAAATATTCCACT
159638 CT
1 CT
159640 TGGAGGCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (18 bp):
CTATATAAATATTCCACT
Found at i:163434 original size:17 final size:17
Alignment explanation
Indices: 163409--163443 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
163399 ATTACCTGTG
*
163409 TTAGTTTTTAATTATTT
1 TTAGCTTTTAATTATTT
*
163426 TTAGCTTTTATTTATTT
1 TTAGCTTTTAATTATTT
163443 T
1 T
163444 AACAATTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TTAGCTTTTAATTATTT
Found at i:166664 original size:19 final size:19
Alignment explanation
Indices: 166607--166664 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
166597 TGAATCAGAA
* * *
166607 CTTATTTCCATATTCATAA
1 CTTATTTTCAAATTCATAG
* *
166626 CTTATTTTCAAACTCGTAG
1 CTTATTTTCAAATTCATAG
166645 CTTATTTTCAAATTCATAG
1 CTTATTTTCAAATTCATAG
166664 C
1 C
166665 CCAATGCATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (19 bp):
CTTATTTTCAAATTCATAG
Found at i:170986 original size:29 final size:29
Alignment explanation
Indices: 170951--171016 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
170941 CTTAAGCTCA
170951 CCTAAGAGTCTATTTTCCTTCCCATTGAC
1 CCTAAGAGTCTATTTTCCTTCCCATTGAC
170980 CCTAAGAGTCTATTTTCCTTCCCATTGAC
1 CCTAAGAGTCTATTTTCCTTCCCATTGAC
171009 CCTAAGAG
1 CCTAAGAG
171017 CTTTCACCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (29 bp):
CCTAAGAGTCTATTTTCCTTCCCATTGAC
Found at i:175025 original size:21 final size:21
Alignment explanation
Indices: 174996--175040 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
174986 GATTTCTGGG
* *
174996 CAAGAGGAATCGGTACCCATT
1 CAAGAGGAACCGATACCCATT
* *
175017 CAAGGGGAACCGATACCCCTT
1 CAAGAGGAACCGATACCCATT
175038 CAA
1 CAA
175041 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGAGGAACCGATACCCATT
Found at i:176463 original size:31 final size:31
Alignment explanation
Indices: 176376--176503 Score: 129
Period size: 31 Copynumber: 4.1 Consensus size: 31
176366 AGAGTCGAGG
176376 GTTTACCTATGTTCTACA-GAACATATGGACA
1 GTTTACCTATGTTCTA-AGGAACATATGGACA
**
176407 GTTTTACCTATGTAT-T-TCGAGACATATGGACA
1 G-TTTACCTATGT-TCTAAGGA-ACATATGGACA
*
176439 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* * *
176470 GTTTACCTAGGTTCTTCAGG-ACCTATGGACA
1 GTTTACCTATGTTC-TAAGGAACATATGGACA
176501 GTT
1 GTT
176504 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
30 1 0.01
31 50 0.61
32 30 0.37
33 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:176523 original size:30 final size:30
Alignment explanation
Indices: 176462--176558 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
176452 CTAAGGAACA
* * * *
176462 TATGGACAGTTTACCTAGGTTCTTCAGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
176493 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * * *
176523 TCTGGATAGTTACTGAGGATCTTTATAACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
176553 TCTGGA
1 TATGGA
176559 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 49 0.84
31 9 0.16
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:176559 original size:30 final size:30
Alignment explanation
Indices: 176490--176561 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
176480 GTTCTTCAGG
* * *
176490 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
*
176520 ACCTCTGGATAGTTACTGAGGATCTTTATA
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
176550 ACCTCTGGATAG
1 ACCTCTGGATAG
176562 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATA
Found at i:178333 original size:21 final size:21
Alignment explanation
Indices: 178304--178348 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
178294 GATTTCTGGG
* *
178304 CAAGAGGAATCGGTACCCATT
1 CAAGAGGAACCGATACCCATT
* *
178325 CAAGGGGAACCGATACCCCTT
1 CAAGAGGAACCGATACCCATT
178346 CAA
1 CAA
178349 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGAGGAACCGATACCCATT
Found at i:179767 original size:31 final size:31
Alignment explanation
Indices: 179680--179807 Score: 129
Period size: 31 Copynumber: 4.1 Consensus size: 31
179670 AGAGTCGAGG
179680 GTTTACCTATGTTCTACA-GAACATATGGACA
1 GTTTACCTATGTTCTA-AGGAACATATGGACA
**
179711 GTTTTACCTATGTAT-T-TCGAGACATATGGACA
1 G-TTTACCTATGT-TCTAAGGA-ACATATGGACA
*
179743 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* * *
179774 GTTTACCTAGGTTCTTCAGG-ACCTATGGACA
1 GTTTACCTATGTTC-TAAGGAACATATGGACA
179805 GTT
1 GTT
179808 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
30 1 0.01
31 50 0.61
32 30 0.37
33 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:179827 original size:30 final size:30
Alignment explanation
Indices: 179766--179862 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
179756 CTAAGGAACA
* * * *
179766 TATGGACAGTTTACCTAGGTTCTTCAGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
179797 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * * *
179827 TCTGGATAGTTACTGAGGATCTTTATAACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
179857 TCTGGA
1 TATGGA
179863 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 49 0.84
31 9 0.16
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:179863 original size:30 final size:30
Alignment explanation
Indices: 179794--179865 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
179784 GTTCTTCAGG
* * *
179794 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
*
179824 ACCTCTGGATAGTTACTGAGGATCTTTATA
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
179854 ACCTCTGGATAG
1 ACCTCTGGATAG
179866 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATA
Found at i:183174 original size:21 final size:21
Alignment explanation
Indices: 183148--183192 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
183138 GATTTCTGGG
* *
183148 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
183169 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
183190 CAA
1 CAA
183193 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:184612 original size:31 final size:31
Alignment explanation
Indices: 184525--184652 Score: 129
Period size: 31 Copynumber: 4.1 Consensus size: 31
184515 AGAGTCGAGG
184525 GTTTACCTATGTTCTACA-GAACATATGGACA
1 GTTTACCTATGTTCTA-AGGAACATATGGACA
**
184556 GTTTTACCTATGTAT-T-TCGAGACATATGGACA
1 G-TTTACCTATGT-TCTAAGGA-ACATATGGACA
*
184588 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* * *
184619 GTTTACCTAGGTTCTTCAGG-ACCTATGGACA
1 GTTTACCTATGTTC-TAAGGAACATATGGACA
184650 GTT
1 GTT
184653 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
30 1 0.01
31 50 0.61
32 30 0.37
33 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:184672 original size:30 final size:30
Alignment explanation
Indices: 184611--184707 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
184601 CTAAGGAACA
* * * *
184611 TATGGACAGTTTACCTAGGTTCTTCAGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
184642 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * *
184672 TCTGGATAGTTACCGAGGATCTTTATAACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
184702 TCTGGA
1 TATGGA
184708 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:184708 original size:30 final size:30
Alignment explanation
Indices: 184639--184710 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
184629 GTTCTTCAGG
* * *
184639 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
184669 ACCTCTGGATAGTTACCGAGGATCTTTATA
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
184699 ACCTCTGGATAG
1 ACCTCTGGATAG
184711 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATA
Found at i:189122 original size:21 final size:21
Alignment explanation
Indices: 189098--189159 Score: 52
Period size: 24 Copynumber: 2.8 Consensus size: 21
189088 TCGGTGCATC
189098 TTCATGATGTATCGATGAACA
1 TTCATGATGTATCGATGAACA
* * *
189119 TTCAAAGGGATGCATCGATGCACA
1 TTC--A-TGATGTATCGATGAACA
**
189143 TTCATGGCGTATCGATG
1 TTCATGATGTATCGATG
189160 CATTATGCAC
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
21 12 0.39
22 1 0.03
23 1 0.03
24 17 0.55
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (21 bp):
TTCATGATGTATCGATGAACA
Found at i:189148 original size:45 final size:44
Alignment explanation
Indices: 189064--189159 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
189054 GGCATTGTGC
* * *
189064 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
1 ATCGATGAACATTCAAGGAGTGCATCGATGCATCTTCATGACGT
*
189108 ATCGATGAACATTCAAAGG-GATGCATCGATGCA-CATTCATGGCGT
1 ATCGATGAACATTC-AAGGAG-TGCATCGATGCATC-TTCATGACGT
189153 ATCGATG
1 ATCGATG
189160 CATTATGCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
44 15 0.33
45 30 0.67
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (44 bp):
ATCGATGAACATTCAAGGAGTGCATCGATGCATCTTCATGACGT
Found at i:192893 original size:21 final size:22
Alignment explanation
Indices: 192859--192899 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
192849 TAAGTTATGC
* *
192859 AAATCAT-TATTTTTATTTTCA
1 AAATCATCAATTTTGATTTTCA
192880 AAATCATCAATTTTGATTTT
1 AAATCATCAATTTTGATTTT
192900 TAATTCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (22 bp):
AAATCATCAATTTTGATTTTCA
Found at i:192997 original size:22 final size:21
Alignment explanation
Indices: 192955--192994 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
192945 AAGACTGTTT
192955 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
192976 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
192995 ATAGAGTCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:195060 original size:18 final size:18
Alignment explanation
Indices: 195037--195087 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
195027 TAAAAAACTG
* *
195037 AGTGCATCGATTCATGGC
1 AGTGCATCGATGCATGAC
195055 AGTGCATCGATGCATGAC
1 AGTGCATCGATGCATGAC
195073 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
195088 AAAATGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (18 bp):
AGTGCATCGATGCATGAC
Found at i:195084 original size:64 final size:64
Alignment explanation
Indices: 194928--195069 Score: 216
Period size: 64 Copynumber: 2.2 Consensus size: 64
194918 TGCACTAAGG
* * *
194928 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCTTGAGTGCATCGATGCATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAAAACTTGAGTGCATCGATGCATGGTCA
*
194992 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAAAC-TGAGTGCATCGATTCATGG-C
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAAAAACTTGAGTGCATCGATGCATGGTC
195055 A
64 A
195056 GTGCATCGATGCAT
1 GTGCATCGATGCAT
195070 GACAGTGCAT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
64 44 0.61
65 23 0.32
66 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAAAACTTGAGTGCATCGATGCATGGTCA
Found at i:195100 original size:18 final size:18
Alignment explanation
Indices: 195057--195096 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
195047 TTCATGGCAG
* *
195057 TGCATCGATGCATGACAG
1 TGCATCGATGCATGAAAA
195075 TGCATCGATGCAT-AAAA
1 TGCATCGATGCATGAAAA
195092 TGCAT
1 TGCAT
195097 TCGAAATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (18 bp):
TGCATCGATGCATGAAAA
Found at i:196167 original size:34 final size:34
Alignment explanation
Indices: 196124--196190 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
196114 TGTAAAAGGA
* *
196124 AAGGTTCTAGCTGAGCCCTTGAAAAGCTAGGGAT
1 AAGGTTCTAGCTGAGCCCGTGAAAAACTAGGGAT
* *
196158 AAGGTTCTAGTTTAGCCCGTGAAAAACTAGGGA
1 AAGGTTCTAGCTGAGCCCGTGAAAAACTAGGGA
196191 GTTGTAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (34 bp):
AAGGTTCTAGCTGAGCCCGTGAAAAACTAGGGAT
Found at i:197032 original size:17 final size:17
Alignment explanation
Indices: 197002--197047 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
196992 GAAACGAGTA
* *
197002 ATTAATCCACTTGGATT
1 ATTAACCCAATTGGATT
197019 ATTAACCCAATTGGATT
1 ATTAACCCAATTGGATT
197036 ATTAACCCAATT
1 ATTAACCCAATT
197048 TTAATGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.37
Consensus pattern (17 bp):
ATTAACCCAATTGGATT
Found at i:197210 original size:34 final size:33
Alignment explanation
Indices: 197171--197246 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 33
197161 ATTGAAAAAG
*
197171 ATATTATTTTTTATTAATTTATTGACAACATAC
1 ATATTATTTTTGATTAATTTATTGACAACATAC
197204 AATATTATTTTTGATTAATTTATTGACAACATAC
1 -ATATTATTTTTGATTAATTTATTGACAACATAC
197238 ATACTTATT
1 ATA-TTATT
197247 ATGTAGATAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 3 0.08
34 37 0.93
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (33 bp):
ATATTATTTTTGATTAATTTATTGACAACATAC
Found at i:217779 original size:24 final size:24
Alignment explanation
Indices: 217747--217814 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
217737 TTGATGGTGA
217747 ATGATGTTGTCGTGGCAAGTAGAG
1 ATGATGTTGTCGTGGCAAGTAGAG
*
217771 ATGACGTTGTCGTGGCAAGTAGAG
1 ATGATGTTGTCGTGGCAAGTAGAG
*
217795 ATGATGTTGTCGTGACAAGT
1 ATGATGTTGTCGTGGCAAGT
217815 GAAGTTGTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.29
Consensus pattern (24 bp):
ATGATGTTGTCGTGGCAAGTAGAG
Found at i:217835 original size:42 final size:43
Alignment explanation
Indices: 217776--217877 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 43
217766 TAGAGATGAC
**
217776 GTTGTCGTGGCAAGTAGAG-ATGATGTTGTCGTGACAAGTGAA
1 GTTGTCGTGGCAAGTAGAGTATGATGTTACCGTGACAAGTGAA
* *
217818 GTTGTCGAGGCAAGTAGAGTTAATGATGTTACCGTGGCAAGTGAA
1 GTTGTCGTGGCAAGTAGAG-T-ATGATGTTACCGTGACAAGTGAA
217863 GTTGTCGTGGCAAGT
1 GTTGTCGTGGCAAGT
217878 GTATGATCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
42 18 0.35
45 34 0.65
ACGTcount: A:0.25, C:0.11, G:0.35, T:0.28
Consensus pattern (43 bp):
GTTGTCGTGGCAAGTAGAGTATGATGTTACCGTGACAAGTGAA
Found at i:222026 original size:14 final size:14
Alignment explanation
Indices: 222007--222056 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
221997 AATATGTTTG
*
222007 TTTATGCTCGTTCA
1 TTTATGTTCGTTCA
*
222021 TTTATGTTCGTTCG
1 TTTATGTTCGTTCA
*
222035 TTTATGTTTGTTCA
1 TTTATGTTCGTTCA
222049 TTTATGTT
1 TTTATGTT
222057 TAGTCCAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.60
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:223288 original size:20 final size:21
Alignment explanation
Indices: 223263--223355 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
223253 TTTTCCCAAT
*
223263 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
223283 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
223304 TTGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
223324 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
223345 TCGCAATGCGA
1 TCGCAATGCGA
223356 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:223310 original size:41 final size:41
Alignment explanation
Indices: 223260--223355 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
223250 CGATTTTCCC
223260 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1 AATT-GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
223302 AATTGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1 AATTGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
*
223343 AATCGCAATGCGA
1 AATTGCAATGCGA
223356 TACTGACTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 49 0.92
42 4 0.08
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
Found at i:223368 original size:41 final size:41
Alignment explanation
Indices: 223282--223416 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
223272 GAATAAGTAA
* * *
223282 ATCGCAACGCGAATTGGGAAAATTGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
223323 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
223364 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
223405 TTCGCAACGCGA
1 ATCGCAACGCGA
223417 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Done.