Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 52 of 150
Found at i:15488742 original size:2 final size:2
Alignment explanation
Indices: 15488737--15488779 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
15488727 TGTATATACG
15488737 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
15488779 T
1 T
15488780 TCATGCTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15491492 original size:11 final size:11
Alignment explanation
Indices: 15491476--15491500 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15491466 AAACACAAGA
15491476 GAGTATCTATT
1 GAGTATCTATT
15491487 GAGTATCTATT
1 GAGTATCTATT
15491498 GAG
1 GAG
15491501 GTTACCTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (11 bp):
GAGTATCTATT
Found at i:15494369 original size:24 final size:23
Alignment explanation
Indices: 15494345--15494390 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
15494335 AAACTACTTC
15494345 TGAAGAAAACTCAAGAGAGAATTCT
1 TGAAG-AAACTCAA-AGAGAATTCT
*
15494370 TGGAGAAACTCAAAGAGAATT
1 TGAAGAAACTCAAAGAGAATT
15494391 TTCACTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 8 0.40
25 4 0.20
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.20
Consensus pattern (23 bp):
TGAAGAAACTCAAAGAGAATTCT
Found at i:15498938 original size:14 final size:14
Alignment explanation
Indices: 15498919--15498949 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
15498909 TCTATTGAGC
*
15498919 GAGAAAAAGAAAAA
1 GAGAAAAACAAAAA
15498933 GAGAAAAACAAAAA
1 GAGAAAAACAAAAA
15498947 GAG
1 GAG
15498950 TGAAAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (14 bp):
GAGAAAAACAAAAA
Found at i:15505148 original size:19 final size:19
Alignment explanation
Indices: 15505124--15505162 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
15505114 AATAAATTAC
*
15505124 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
15505143 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
15505162 T
1 T
15505163 GCTGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:15505168 original size:54 final size:54
Alignment explanation
Indices: 15505105--15505226 Score: 208
Period size: 54 Copynumber: 2.3 Consensus size: 54
15505095 ATAAGTATTT
* * *
15505105 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATATTAGTTAATTAAATTCATCTTAGTTAATTA
*
15505159 AGTTGCTGGAATAAATTACTCATATTAGTTAATTAAATTCATCTTAGTTAATTT
1 AGTTGCTGGAATAAATTACTCATATTAGTTAATTAAATTCATCTTAGTTAATTA
15505213 AGTTGCTGGAATAA
1 AGTTGCTGGAATAA
15505227 TTTATTGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (54 bp):
AGTTGCTGGAATAAATTACTCATATTAGTTAATTAAATTCATCTTAGTTAATTA
Found at i:15505576 original size:45 final size:44
Alignment explanation
Indices: 15505521--15505606 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 44
15505511 CGGTTACATA
* *
15505521 CAAAGGGTTGTTACATCAATTGAAGGAGAGCATTATACATCATT
1 CAAAGGGTTGTTACATCAATTAAAGGAAAGCATTATACATCATT
* *
15505565 CAAAGGAGTTGTTACATTATTTAAAGGAAAGCATTATACATC
1 CAAAGG-GTTGTTACATCAATTAAAGGAAAGCATTATACATC
15505607 CTTTAAATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 6 0.16
45 31 0.84
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (44 bp):
CAAAGGGTTGTTACATCAATTAAAGGAAAGCATTATACATCATT
Found at i:15507382 original size:36 final size:36
Alignment explanation
Indices: 15507339--15507419 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
15507329 AAAAGAAGCG
*
15507339 AGAAAAAGAAATTG-AGAA-AAAAAGAAAAGAAAAGAA
1 AGAAAAAGAAATTGAAAAAGAAAAAG-AAAGAAAA-AA
* **
15507375 AGAAAAAGCAATTGAAAAAGAAAAAGAAAGTGAAAA
1 AGAAAAAGAAATTGAAAAAGAAAAAGAAAGAAAAAA
15507411 AGAAAAAGA
1 AGAAAAAGA
15507420 GAGCGAGAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
36 23 0.61
37 9 0.24
38 6 0.16
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (36 bp):
AGAAAAAGAAATTGAAAAAGAAAAAGAAAGAAAAAA
Found at i:15507394 original size:18 final size:18
Alignment explanation
Indices: 15507373--15507419 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
15507363 AAAAGAAAAG
* *
15507373 AAAGAAAAAGCAATTGAA
1 AAAGAAAAAGAAAGTGAA
15507391 AAAGAAAAAGAAAGTGAA
1 AAAGAAAAAGAAAGTGAA
15507409 AAAGAAAAAGA
1 AAAGAAAAAGA
15507420 GAGCGAGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAGAAAAAGAAAGTGAA
Found at i:15507416 original size:5 final size:6
Alignment explanation
Indices: 15507357--15507419 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
15507347 AAATTGAGAA
* * ** **
15507357 AAAAAG AAAAGAA AAGAAAG AAAAAG CAATTG AAAAAG AAAAAG AAAGTG
1 AAAAAG AAAA-AG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
15507407 AAAAAG AAAAAG A
1 AAAAAG AAAAAG A
15507420 GAGCGAGAGT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
6 35 0.81
7 6 0.14
8 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:15509182 original size:19 final size:19
Alignment explanation
Indices: 15509158--15509194 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15509148 TAAATTACTT
*
15509158 ATCTTAGTTAATTGAGTTC
1 ATCTTAGTTAATTAAGTTC
15509177 ATCTTAGTTAATTAAGTT
1 ATCTTAGTTAATTAAGTT
15509195 ACTGGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (19 bp):
ATCTTAGTTAATTAAGTTC
Found at i:15513496 original size:40 final size:40
Alignment explanation
Indices: 15513436--15513624 Score: 200
Period size: 40 Copynumber: 4.8 Consensus size: 40
15513426 AATTTTTAAA
* * *
15513436 TGATTGCACTTGCGTGCCCCTGTTTGTACTTTGGTACTCC
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
15513476 TGATTGCATTTACGTACCCCTATTTGTACTTCGGTACCCT
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * *
15513516 TGATTACACCTACATGGCCCTGTTTGTACTT-TGTACCCC
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
15513555 TGATTACACTTACATGCCCCAGTTTGTACTCCGGTACCCC
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
** *
15513595 TGATTGCACTTTTGTGCCCCTGTTTATACT
1 TGATTGCACTTACGTGCCCCTGTTTGTACT
15513625 CGAGTAACTC
Statistics
Matches: 121, Mismatches: 27, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
39 33 0.27
40 88 0.73
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (40 bp):
TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:15513616 original size:79 final size:80
Alignment explanation
Indices: 15513436--15513624 Score: 220
Period size: 79 Copynumber: 2.4 Consensus size: 80
15513426 AATTTTTAAA
* * * * *
15513436 TGATTGCACTTGCGTGCCCCTGTTTGTACTTTGGTACTCCTGATTGCATTTACGTACCCCTATTT
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTACACTTACATACCCCTATTT
* *
15513501 GTACTTCGGTACCCT
66 GTACTCCGGTACCCC
* * * * *
15513516 TGATTACACCTACATGGCCCTGTTTGTACTTT-GTACCCCTGATTACACTTACATGCCCC-AGTT
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTACACTTACATACCCCTA-TT
15513579 TGTACTCCGGTACCCC
65 TGTACTCCGGTACCCC
** *
15513595 TGATTGCACTTTTGTGCCCCTGTTTATACT
1 TGATTGCACTTACGTGCCCCTGTTTGTACT
15513625 CGAGTAACTC
Statistics
Matches: 89, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
78 1 0.01
79 61 0.69
80 27 0.30
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (80 bp):
TGATTGCACTTACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTACACTTACATACCCCTATTT
GTACTCCGGTACCCC
Found at i:15525726 original size:18 final size:19
Alignment explanation
Indices: 15525699--15525745 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
15525689 CAATTTAATT
15525699 AATA-AAATAAAATTTTAA
1 AATATAAATAAAATTTTAA
* **
15525717 CAT-TAAATAATTTTTTAA
1 AATATAAATAAAATTTTAA
15525735 AATATAAATAA
1 AATATAAATAA
15525746 TTAAGTATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATAAATAAAATTTTAA
Found at i:15525742 original size:19 final size:18
Alignment explanation
Indices: 15525711--15525747 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
15525701 TAAAATAAAA
*
15525711 TTTTAACATTAAATAATT
1 TTTTAAAATTAAATAATT
15525729 TTTTAAAATATAAATAATT
1 TTTTAAAAT-TAAATAATT
15525748 AAGTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTAAAATTAAATAATT
Found at i:15527677 original size:13 final size:13
Alignment explanation
Indices: 15527659--15527683 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15527649 TTTATTTCAA
15527659 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
15527672 AAAAAAGAAAAA
1 AAAAAAGAAAAA
15527684 CCTTAATCCC
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:15529073 original size:22 final size:22
Alignment explanation
Indices: 15529042--15529084 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
15529032 TTCATAATTT
15529042 TTAAAATCCAAATT-ATTTTTC
1 TTAAAATCCAAATTAATTTTTC
*
15529063 TTAAATATCCAATTTAATTTTT
1 TTAAA-ATCCAAATTAATTTTT
15529085 AAAACCGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAAATCCAAATTAATTTTTC
Found at i:15529566 original size:19 final size:19
Alignment explanation
Indices: 15529542--15529580 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
15529532 CTTAATTTCG
*
15529542 TCCCATTATATGTTTATTA
1 TCCCATCATATGTTTATTA
* *
15529561 TCCCATCCTATTTTTATTA
1 TCCCATCATATGTTTATTA
15529580 T
1 T
15529581 TTACTTCACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.03, T:0.54
Consensus pattern (19 bp):
TCCCATCATATGTTTATTA
Found at i:15530087 original size:2 final size:2
Alignment explanation
Indices: 15530080--15530110 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15530070 TATGTGTATG
15530080 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15530111 TAAGTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15531719 original size:52 final size:52
Alignment explanation
Indices: 15531658--15531757 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
15531648 CCACACAGCC
* * * *
15531658 GTGTACTCCAACCGTGTACAAGACTGATGTCGTGTAATGCAAAGTCACGACT
1 GTGTACTCCAACCATGTACAAGACTAATCTCATGTAATGCAAAGTCACGACT
* *
15531710 GTGTACTCCAACCATGTACAAGACTAATCTCATGTAATGTAGAGTCAC
1 GTGTACTCCAACCATGTACAAGACTAATCTCATGTAATGCAAAGTCAC
15531758 ACAACCGTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (52 bp):
GTGTACTCCAACCATGTACAAGACTAATCTCATGTAATGCAAAGTCACGACT
Found at i:15539478 original size:28 final size:27
Alignment explanation
Indices: 15539445--15539584 Score: 92
Period size: 27 Copynumber: 5.1 Consensus size: 27
15539435 AATGGGCCAT
*
15539445 AAATGACCAAAATACCC-AAGGATGGGTA
1 AAATGACTAAAATACCCTAA--ATGGGTA
*
15539473 AAATGA-TAGAAATACCCTCAATGGGTA
1 AAATGACTA-AAATACCCTAAATGGGTA
* *
15539500 AAATGACTGAAATACCCTCAATGGGTA
1 AAATGACTAAAATACCCTAAATGGGTA
* * * **
15539527 ACATGA-TCGAAATAACCTCGATGGGTA
1 AAATGACT-AAAATACCCTAAATGGGTA
* *
15539554 AAATGA-TCGAAATACCCTCGAA-GGGTA
1 AAATGACT-AAAATACCCT-AAATGGGTA
15539581 AAAT
1 AAAT
15539585 TATCGAAAAG
Statistics
Matches: 97, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
26 1 0.01
27 79 0.81
28 16 0.16
29 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (27 bp):
AAATGACTAAAATACCCTAAATGGGTA
Found at i:15539496 original size:27 final size:26
Alignment explanation
Indices: 15539468--15539827 Score: 257
Period size: 27 Copynumber: 13.3 Consensus size: 26
15539458 ACCCAAGGAT
* *
15539468 GGGTAAAATGATAGAAATACCCTCAA
1 GGGTAAAATTATCGAAATACCCTCAA
*
15539494 TGGGTAAAATGA-CTGAAATACCCTCAA
1 -GGGTAAAATTATC-GAAATACCCTCAA
* * * *
15539521 TGGGTAACATGATCGAAATAACCTCGAT
1 -GGGTAAAATTATCGAAATACCCTC-AA
*
15539549 GGGTAAAATGATCGAAATACCCTCGAA
1 GGGTAAAATTATCGAAATACCCTC-AA
15539576 GGGTAAAATTATCGAAA-AGCCCTCGAA
1 GGGTAAAATTATCGAAATA-CCCTC-AA
* *
15539603 GGATAAAATTATCCAAATACCCTCGAA
1 GGGTAAAATTATCGAAATACCCTC-AA
* *
15539630 GGATAAAATTATCGAAATACCCTTGAA
1 GGGTAAAATTATCGAAATACCC-TCAA
* * *
15539657 AGGTAAAAATTATTGAAA-GCCCTCAAA
1 GGGT-AAAATTATCGAAATACCCTC-AA
* * *
15539684 GGATAAAATTA-CTAAAATACCCTTGAA
1 GGGTAAAATTATC-GAAATACCC-TCAA
**
15539711 GGGTAAAATTATCGAAATACTGTCGAA
1 GGGTAAAATTATCGAAATACCCTC-AA
* * *
15539738 GGGTAAAATT-GCTAAAATACCCTTGAA
1 GGGTAAAATTATC-GAAATACCC-TCAA
*
15539765 GGGTAAAATTA-CAGAAATACCCCCAAA
1 GGGTAAAATTATC-GAAATACCCTC-AA
* *
15539792 GGGTAAAATTACCGGAATACTCC-CGAA
1 GGGTAAAATTATCGAAATAC-CCTC-AA
15539819 GGGTAAAAT
1 GGGTAAAAT
15539828 GACTGTTATA
Statistics
Matches: 275, Mismatches: 39, Indels: 38
0.78 0.11 0.11
Matches are distributed among these distances:
26 14 0.05
27 239 0.87
28 22 0.08
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (26 bp):
GGGTAAAATTATCGAAATACCCTCAA
Found at i:15539621 original size:81 final size:80
Alignment explanation
Indices: 15539468--15539827 Score: 304
Period size: 81 Copynumber: 4.5 Consensus size: 80
15539458 ACCCAAGGAT
* * * *
15539468 GGGTAAAATGATAGAAATACCCTC-AATGGGTAAAATGA-CTGAAATA-CCCTCAATGGGTAACA
1 GGGTAAAATGATCGAAATACCCTCGAA-GGGTAAAATTATC-GAAA-AGCCCTCAA-GGATAAAA
* * * *
15539530 TGATCGAAATAACCTCGAT
62 TTATCAAAATACCCTCGAA
15539549 GGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATTATCGAAAAGCCCTCGAAGGATAAAATTA
1 GGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATTATCGAAAAGCCCTC-AAGGATAAAATTA
*
15539614 TCCAAATACCCTCGAA
65 TCAAAATACCCTCGAA
* * * * *
15539630 GGATAAAATTATCGAAATACCCTTGAAAGGTAAAAATTATTG-AAAGCCCTCAAAGGATAAAATT
1 GGGTAAAATGATCGAAATACCCTCGAAGGGT-AAAATTATCGAAAAGCCCTC-AAGGATAAAATT
*
15539694 A-CTAAAATACCCTTGAA
64 ATC-AAAATACCCTCGAA
* ** * * * * *
15539711 GGGTAAAATTATCGAAATACTGTCGAAGGGTAAAATT-GCTAAAATACCCTTGAAGGGTAAAATT
1 GGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATTATCGAAAA-GCCC-TCAAGGATAAAATT
* *
15539775 A-CAGAAATACCCCCAAA
64 ATCA-AAATACCCTCGAA
* * *
15539792 GGGTAAAATTACCGGAATACTCC-CGAAGGGTAAAAT
1 GGGTAAAATGATCGAAATAC-CCTCGAAGGGTAAAAT
15539828 GACTGTTATA
Statistics
Matches: 234, Mismatches: 34, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
80 12 0.05
81 207 0.88
82 15 0.06
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (80 bp):
GGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATTATCGAAAAGCCCTCAAGGATAAAATTAT
CAAAATACCCTCGAA
Found at i:15539811 original size:54 final size:54
Alignment explanation
Indices: 15539481--15539827 Score: 310
Period size: 54 Copynumber: 6.4 Consensus size: 54
15539471 TAAAATGATA
* * * * *
15539481 GAAATACCCTC-AATGGGTAAAATGA-CTGAAATACCCTCAATGGGTAACATGATC
1 GAAATACCCTCGAA-GGGTAAAATTATC-GAAATACCCTCAAAGGGTAAAATTACC
* * * * *
15539535 GAAATAACCTCGATGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATTATC
1 GAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACC
* * * * *
15539589 GAAA-AGCCCTCGAAGGATAAAATTATCCAAATACCCTCGAAGGATAAAATTATC
1 GAAATA-CCCTCGAAGGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACC
* * * * * *
15539643 GAAATACCCTTGAAAGGTAAAAATTATTGAAA-GCCCTCAAAGGATAAAATTACT
1 GAAATACCCTCGAAGGGT-AAAATTATCGAAATACCCTCAAAGGGTAAAATTACC
* * ** * * *
15539697 AAAATACCCTTGAAGGGTAAAATTATCGAAATACTGTCGAAGGGTAAAATTGCT
1 GAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACC
* * *
15539751 AAAATACCCTTGAAGGGTAAAATTA-CAGAAATACCCCCAAAGGGTAAAATTACC
1 GAAATACCCTCGAAGGGTAAAATTATC-GAAATACCCTCAAAGGGTAAAATTACC
*
15539805 GGAATACTCC-CGAAGGGTAAAAT
1 GAAATAC-CCTCGAAGGGTAAAAT
15539828 GACTGTTATA
Statistics
Matches: 246, Mismatches: 39, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
53 14 0.06
54 216 0.88
55 16 0.07
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (54 bp):
GAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACC
Found at i:15540202 original size:28 final size:28
Alignment explanation
Indices: 15540161--15540255 Score: 102
Period size: 28 Copynumber: 3.4 Consensus size: 28
15540151 TATGCACTGT
*
15540161 ATTGATTACTGTATTGGGTTAAGGCCCAC
1 ATTGA-TACTGTATTGGGCTAAGGCCCAC
* * *
15540190 ATTGATACTGTATTGGGCAAATGCCTAC
1 ATTGATACTGTATTGGGCTAAGGCCCAC
* * * *
15540218 ATTGCTATTGAATTGGGCTAAGGCCCTC
1 ATTGATACTGTATTGGGCTAAGGCCCAC
15540246 ATTG-TACTGT
1 ATTGATACTGT
15540256 CACTGAATAG
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
27 4 0.08
28 44 0.83
29 5 0.09
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (28 bp):
ATTGATACTGTATTGGGCTAAGGCCCAC
Found at i:15541349 original size:25 final size:25
Alignment explanation
Indices: 15541333--15541421 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
15541323 CAAAGGTGAG
15541333 ATACATA-A-TACGCCACAAAGGCA
1 ATACATAGAGTACGCCACAAAGGCA
15541356 ATACATAGAGTACGCCACAAAGGC-
1 ATACATAGAGTACGCCACAAAGGCA
*
15541380 -TAGC--AGA--ATGCCACAAAGGCA
1 ATA-CATAGAGTACGCCACAAAGGCA
* *
15541401 ATACACAGAGTACACCACAAA
1 ATACATAGAGTACGCCACAAA
15541422 TGCTAGTAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
20 12 0.22
21 1 0.02
22 5 0.09
23 12 0.22
24 2 0.04
25 22 0.41
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (25 bp):
ATACATAGAGTACGCCACAAAGGCA
Found at i:15541394 original size:20 final size:20
Alignment explanation
Indices: 15541369--15541453 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
15541359 CATAGAGTAC
*
15541369 GCCACAAAGGCTAGCAGAAT
1 GCCACAAAGGCTAACAGAAT
*
15541389 GCCACAAAGGCAATACACAGAGTAC
1 GCCACAAAGGC--TA-ACAGA--AT
* * **
15541414 ACCACAAATGCTAGTAGAAT
1 GCCACAAAGGCTAACAGAAT
15541434 GCCACAAAGGCTAACAGAAT
1 GCCACAAAGGCTAACAGAAT
15541454 ATGCCATAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
20 28 0.57
22 5 0.10
23 6 0.12
25 10 0.20
ACGTcount: A:0.44, C:0.25, G:0.20, T:0.12
Consensus pattern (20 bp):
GCCACAAAGGCTAACAGAAT
Found at i:15541395 original size:45 final size:45
Alignment explanation
Indices: 15541344--15541444 Score: 166
Period size: 45 Copynumber: 2.2 Consensus size: 45
15541334 TACATAATAC
* *
15541344 GCCACAAAGGCAATACATAGAGTACGCCACAAAGGCTAGCAGAAT
1 GCCACAAAGGCAATACACAGAGTACACCACAAAGGCTAGCAGAAT
* *
15541389 GCCACAAAGGCAATACACAGAGTACACCACAAATGCTAGTAGAAT
1 GCCACAAAGGCAATACACAGAGTACACCACAAAGGCTAGCAGAAT
15541434 GCCACAAAGGC
1 GCCACAAAGGC
15541445 TAACAGAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.43, C:0.26, G:0.21, T:0.11
Consensus pattern (45 bp):
GCCACAAAGGCAATACACAGAGTACACCACAAAGGCTAGCAGAAT
Found at i:15541479 original size:20 final size:21
Alignment explanation
Indices: 15541431--15541480 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
15541421 ATGCTAGTAG
*
15541431 AATGCCACAAAGGCTAACAGA
1 AATGCCATAAAGGCTAACAGA
* *
15541452 ATATGCCATAAAGGTTATC-GA
1 A-ATGCCATAAAGGCTAACAGA
15541473 AATGCCAT
1 AATGCCAT
15541481 CTAGGCACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 7 0.28
21 4 0.16
22 14 0.56
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (21 bp):
AATGCCATAAAGGCTAACAGA
Found at i:15543894 original size:24 final size:26
Alignment explanation
Indices: 15543867--15543916 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
15543857 ATATAATTTT
15543867 CAAATCA-TGT-ATATATATCATGTA
1 CAAATCATTGTCATATATATCATGTA
* *
15543891 CAAATCATTTTCATATATCTCATGTA
1 CAAATCATTGTCATATATATCATGTA
15543917 AATACCTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 2 0.09
26 13 0.59
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (26 bp):
CAAATCATTGTCATATATATCATGTA
Found at i:15544168 original size:50 final size:50
Alignment explanation
Indices: 15544074--15544168 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
15544064 ACGAGCTGTA
* * *
15544074 AATGGTAAGCTCCTCTTAGCTGAATAACGGTAAGCTCTTCCGAGTCAAAT
1 AATGGCAAGCTCCTCTTAGCTGAATAACGGTAAGCTCATACGAGTCAAAT
* *
15544124 AATGGCAAGCT-CTTTTGAGCTGAATAATGGTAAGCTCATACGAGT
1 AATGGCAAGCTCCTCTT-AGCTGAATAACGGTAAGCTCATACGAGT
15544169 TGAGTATCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 4 0.10
50 35 0.90
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (50 bp):
AATGGCAAGCTCCTCTTAGCTGAATAACGGTAAGCTCATACGAGTCAAAT
Found at i:15544974 original size:27 final size:26
Alignment explanation
Indices: 15544944--15545013 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 26
15544934 CGTTCTGACC
15544944 CATAGCTCGTGTGAGCAGACCCATTTT
1 CATAGCTCGTGTGAGCAGACCC-TTTT
* * *
15544971 CATAGCTCGTGTAAGCATACTCTTTT
1 CATAGCTCGTGTGAGCAGACCCTTTT
* * *
15544997 CACAACTCATGTGAGCA
1 CATAGCTCGTGTGAGCA
15545014 TATATGTAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 17 0.47
27 19 0.53
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (26 bp):
CATAGCTCGTGTGAGCAGACCCTTTT
Found at i:15550066 original size:23 final size:24
Alignment explanation
Indices: 15550040--15550093 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 24
15550030 TCTCGCTCTT
15550040 TTTCTTTTTCAATCTCATTTT-GC
1 TTTCTTTTTCAATCTCATTTTAGC
* *
15550063 TTTC--TCTCACTCTCATTTTCAGC
1 TTTCTTTTTCAATCTCATTTT-AGC
15550086 TTTCTTTT
1 TTTCTTTT
15550094 CTTGTTCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
21 13 0.54
23 10 0.42
25 1 0.04
ACGTcount: A:0.11, C:0.26, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTCTTTTTCAATCTCATTTTAGC
Found at i:15551169 original size:20 final size:20
Alignment explanation
Indices: 15551146--15551192 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
15551136 CTTTCAAGAC
15551146 TTTTTTTTA-ACTTCGTAAAA
1 TTTTTTTTATACTTCG-AAAA
*
15551166 -TTTTTTTATACTTCGAATA
1 TTTTTTTTATACTTCGAAAA
15551185 TTTTTTTT
1 TTTTTTTT
15551193 TCAATTACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTTTTTATACTTCGAAAA
Found at i:15551171 original size:19 final size:19
Alignment explanation
Indices: 15551147--15551191 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
15551137 TTTCAAGACT
15551147 TTTTTTTA-ACTTCGTAAAA
1 TTTTTTTATACTTCG-AAAA
*
15551166 TTTTTTTATACTTCGAATA
1 TTTTTTTATACTTCGAAAA
15551185 TTTTTTT
1 TTTTTTT
15551192 TTCAATTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTTTTATACTTCGAAAA
Found at i:15554583 original size:28 final size:28
Alignment explanation
Indices: 15554546--15554623 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
15554536 AAATTTGAAG
15554546 GGGGTTGCTAAGTGCTGATTCCCCCGAA
1 GGGGTTGCTAAGTGCTGATTCCCCCGAA
* *
15554574 GGGGTTGCTAAATGTTGATTCCCCCGAA
1 GGGGTTGCTAAGTGCTGATTCCCCCGAA
15554602 GGGGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATTCC
15554624 ACCATATCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.28
Consensus pattern (28 bp):
GGGGTTGCTAAGTGCTGATTCCCCCGAA
Found at i:15565724 original size:24 final size:24
Alignment explanation
Indices: 15565686--15565749 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
15565676 AAAGAATTTG
* *
15565686 AGAAAGAAGATAGTGAGCGAGAACA
1 AGAAA-AAGAGAGTGAGCAAGAACA
* *
15565711 AGAACAAGAGAGTGAGCAAGAATA
1 AGAAAAAGAGAGTGAGCAAGAACA
15565735 AGAAAAAGAGAGTGA
1 AGAAAAAGAGAGTGA
15565750 TATTTTAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 30 0.88
25 4 0.12
ACGTcount: A:0.55, C:0.06, G:0.31, T:0.08
Consensus pattern (24 bp):
AGAAAAAGAGAGTGAGCAAGAACA
Found at i:15575041 original size:27 final size:28
Alignment explanation
Indices: 15574989--15575042 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
15574979 GACAAGGGAA
**
15574989 GAAAGAAAATTAGAAAGCAACTAGAAAG
1 GAAAGAAAATTAGAAAGCAAAGAGAAAG
15575017 GAAAGAAAA-TAGAAAG-ATAAGAGAAA
1 GAAAGAAAATTAGAAAGCA-AAGAGAAA
15575043 AGATGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.04
27 13 0.57
28 9 0.39
ACGTcount: A:0.65, C:0.04, G:0.22, T:0.09
Consensus pattern (28 bp):
GAAAGAAAATTAGAAAGCAAAGAGAAAG
Found at i:15580341 original size:27 final size:27
Alignment explanation
Indices: 15580311--15580762 Score: 490
Period size: 27 Copynumber: 16.7 Consensus size: 27
15580301 GGTATTACGA
*
15580311 TAATTTTACCCTTCGGGGGTATTTTAG
1 TAATTTTACCCTTCGAGGGTATTTTAG
*
15580338 TAATTTTACCCTTC-AGGGGTATTTCAG
1 TAATTTTACCCTTCGA-GGGTATTTTAG
* * *
15580365 TAATTTTACCCATCGAAGGTATTTTGG
1 TAATTTTACCCTTCGAGGGTATTTTAG
* * *
15580392 TAATTTTACCCATCGAGGCTATTTTGG
1 TAATTTTACCCTTCGAGGGTATTTTAG
* *
15580419 TAATTTTTACCCATCGAGGGTATTTCAG
1 TAA-TTTTACCCTTCGAGGGTATTTTAG
* * *
15580447 TAATTTTACCCATTAG-GGGTATTTCAA
1 TAATTTTACCC-TTCGAGGGTATTTTAG
15580474 TAATTTTACCC-TCGAGGGTATTTTAG
1 TAATTTTACCCTTCGAGGGTATTTTAG
* *
15580500 TAATTTTACCCATCGAGGGTATTTCAG
1 TAATTTTACCCTTCGAGGGTATTTTAG
** * *
15580527 TAACCTTACCCATCGGGGGTATTTTAG
1 TAATTTTACCCTTCGAGGGTATTTTAG
15580554 TAATTTTACCCTTC-AGGGGTATTTTAG
1 TAATTTTACCCTTCGA-GGGTATTTTAG
*
15580581 TAATTTTACCTATTC-AGGGTATTTTAG
1 TAATTTTACC-CTTCGAGGGTATTTTAG
*
15580608 TAATTTTACCCATCGAGGGTATTTT-G
1 TAATTTTACCCTTCGAGGGTATTTTAG
* *
15580634 ATAATTTTTACCCATCGAGGGTA-TTTCG
1 -TAA-TTTTACCCTTCGAGGGTATTTTAG
* *
15580662 ATAATTTTACCCTTTGAGGGTA-TTTCG
1 -TAATTTTACCCTTCGAGGGTATTTTAG
* * *
15580689 ATAATTTTACCCTTTGAGGGTATTTCAA
1 -TAATTTTACCCTTCGAGGGTATTTTAG
*
15580717 TAATTTTACCCATT-AAGGGTATTTTAG
1 TAATTTTACCC-TTCGAGGGTATTTTAG
15580744 TAATTTTACCCTTCGAGGG
1 TAATTTTACCCTTCGAGGG
15580763 GTAAGCCTCT
Statistics
Matches: 372, Mismatches: 38, Indels: 30
0.85 0.09 0.07
Matches are distributed among these distances:
25 2 0.01
26 25 0.07
27 287 0.77
28 58 0.16
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (27 bp):
TAATTTTACCCTTCGAGGGTATTTTAG
Found at i:15581456 original size:40 final size:40
Alignment explanation
Indices: 15581407--15581522 Score: 196
Period size: 40 Copynumber: 2.9 Consensus size: 40
15581397 AGGATGATAT
* *
15581407 TCGGCTAGAGAAGAAGAAGAGAAAGGAAAAAGAAGGTTTGG
1 TCGG-TAGAGAAAAAGAAGAGAAAGGAAGAAGAAGGTTTGG
15581448 TCGGTAGAGAAAAAGAAGAGAAAGGAAGAAGAAGGTTTGG
1 TCGGTAGAGAAAAAGAAGAGAAAGGAAGAAGAAGGTTTGG
*
15581488 TCGGCAGAGAAAAAGAAGAGAAAGGAAGAAGAAGG
1 TCGGTAGAGAAAAAGAAGAGAAAGGAAGAAGAAGG
15581523 GAAAACTCGG
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 68 0.94
41 4 0.06
ACGTcount: A:0.49, C:0.04, G:0.37, T:0.09
Consensus pattern (40 bp):
TCGGTAGAGAAAAAGAAGAGAAAGGAAGAAGAAGGTTTGG
Found at i:15581848 original size:22 final size:22
Alignment explanation
Indices: 15581820--15581868 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
15581810 TCCTAAAATC
*
15581820 AATCCTCCA-ATCCTCTCCTTGA
1 AATCCTCCAGATCCACTCCTT-A
15581842 AATCCTCCATGATCCACTCCTTA
1 AATCCTCCA-GATCCACTCCTTA
15581865 AATC
1 AATC
15581869 ACTCATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 9 0.38
23 5 0.21
24 10 0.42
ACGTcount: A:0.27, C:0.39, G:0.04, T:0.31
Consensus pattern (22 bp):
AATCCTCCAGATCCACTCCTTA
Found at i:15592601 original size:43 final size:41
Alignment explanation
Indices: 15592470--15592809 Score: 317
Period size: 43 Copynumber: 8.0 Consensus size: 41
15592460 ATGCCGCTAG
* * * * *
15592470 AGAACATGACCTTTAGCGACTTTCTCACAAAAATGCCGCTAT
1 AGAACATGACCTTTAGCGACTTT-TCCCACAAACGCCACTAA
* * * *
15592512 AGAACATGACC-TTAGTGGTTCTTTTCCCATAAACGCCGCTAA
1 AGAACATGACCTTTAG-CG-ACTTTTCCCACAAACGCCACTAA
* *
15592554 AGAACATGACCTTTAGCCGCACTTTTCCCACAAACACCACTAT
1 AGAACATGACCTTTAG-CG-ACTTTTCCCACAAACGCCACTAA
** *
15592597 AGAACATGACCTTTAGTGGCG-CTTTTCCCACAAATTCCATTAA
1 AGAACATGACCTTTA---GCGACTTTTCCCACAAACGCCACTAA
*
15592640 AGAACATGACCTTTAGCGGTGCTTTTCCCACAAACGCCACTAA
1 AGAACATGACCTTTAGC-G-ACTTTTCCCACAAACGCCACTAA
** *
15592683 AGAACATGACCTTTAGCAGTGTTTTTCCACAAACGCCACTAA
1 AGAACATGACCTTTAGC-GACTTTTCCCACAAACGCCACTAA
*
15592725 AGAACATGATCTTTAGCGACTCTTTCCCCACAAACGCC-CTAA
1 AGAACATGACCTTTAGCGACT-TTT-CCCACAAACGCCACTAA
* * * *
15592767 AGAATATGACTTTTAGCGACGCTTTTCTCACAAATGCCACTAA
1 AGAACATGACCTTTAGCGA--CTTTTCCCACAAACGCCACTAA
15592810 CTTTAGCAAA
Statistics
Matches: 250, Mismatches: 34, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
40 2 0.01
41 7 0.03
42 106 0.42
43 130 0.52
44 2 0.01
45 2 0.01
46 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.26
Consensus pattern (41 bp):
AGAACATGACCTTTAGCGACTTTTCCCACAAACGCCACTAA
Found at i:15592641 original size:86 final size:84
Alignment explanation
Indices: 15592470--15592809 Score: 346
Period size: 85 Copynumber: 4.0 Consensus size: 84
15592460 ATGCCGCTAG
* * * * * **
15592470 AGAACATGACCTTTAGCGAC-TTTCTCACAAAAATGCCGCTATAGAACATGACC-TTAGTGGTTC
1 AGAACATGACCTTTAGCGACTTTTCCCACAAACA--CCACTAAAGAACATGACCTTTAGCGGCGC
* *
15592533 TTTTCCCATAAACGCCGCTAA
64 TTTTCCCACAAACGCCACTAA
* *
15592554 AGAACATGACCTTTAGCCGCACTTTTCCCACAAACACCACTATAGAACATGACCTTTAGTGGCGC
1 AGAACATGACCTTTAG-CG-ACTTTTCCCACAAACACCACTAAAGAACATGACCTTTAGCGGCGC
** *
15592619 TTTTCCCACAAATTCCATTAA
64 TTTTCCCACAAACGCCACTAA
* * * *
15592640 AGAACATGACCTTTAGCGGTGCTTTTCCCACAAACGCCACTAAAGAACATGACCTTTAGCAGTG-
1 AGAACATGACCTTTAGC-G-ACTTTTCCCACAAACACCACTAAAGAACATGACCTTTAGCGGCGC
*
15592704 TTTTTCCACAAACGCCACTAA
64 TTTTCCCACAAACGCCACTAA
* * * * *
15592725 AGAACATGATCTTTAGCGACTCTTTCCCCACAAACGCC-CTAAAGAATATGACTTTTAGCGACGC
1 AGAACATGACCTTTAGCGACT-TTT-CCCACAAACACCACTAAAGAACATGACCTTTAGCGGCGC
* *
15592789 TTTTCTCACAAATGCCACTAA
64 TTTTCCCACAAACGCCACTAA
15592810 CTTTAGCAAA
Statistics
Matches: 217, Mismatches: 31, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
83 2 0.01
84 40 0.18
85 83 0.38
86 81 0.37
87 11 0.05
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.26
Consensus pattern (84 bp):
AGAACATGACCTTTAGCGACTTTTCCCACAAACACCACTAAAGAACATGACCTTTAGCGGCGCTT
TTCCCACAAACGCCACTAA
Found at i:15598643 original size:9 final size:9
Alignment explanation
Indices: 15598629--15598755 Score: 67
Period size: 9 Copynumber: 15.0 Consensus size: 9
15598619 TAAGTATAAT
15598629 TAAGTTATG
1 TAAGTTATG
15598638 TAAGTTATG
1 TAAGTTATG
* * *
15598647 ATATGATATA
1 -TAAGTTATG
*
15598657 T-ATTTATG
1 TAAGTTATG
*
15598665 -CA-TTATG
1 TAAGTTATG
15598672 TAAGTTATG
1 TAAGTTATG
*
15598681 TAAGTTATA
1 TAAGTTATG
*
15598690 TAGGTTATG
1 TAAGTTATG
15598699 TAAGTTA--
1 TAAGTTATG
15598706 TAA--TATG
1 TAAGTTATG
* * *
15598713 ATATGATATA
1 -TAAGTTATG
*
15598723 T-ATTTATG
1 TAAGTTATG
15598731 T-A-TTATG
1 TAAGTTATG
15598738 TAAGTTATG
1 TAAGTTATG
15598747 TAAGTTATG
1 TAAGTTATG
15598756 ATCCAAAGTT
Statistics
Matches: 89, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
5 2 0.02
7 14 0.16
8 13 0.15
9 51 0.57
10 9 0.10
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:15598824 original size:13 final size:13
Alignment explanation
Indices: 15598806--15598832 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15598796 TGATTATCAT
15598806 CTTTAAATTTTAA
1 CTTTAAATTTTAA
15598819 CTTTAAATTTTAA
1 CTTTAAATTTTAA
15598832 C
1 C
15598833 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:15604171 original size:77 final size:75
Alignment explanation
Indices: 15604076--15604275 Score: 237
Period size: 77 Copynumber: 2.6 Consensus size: 75
15604066 ACGCGCTTTG
* *
15604076 GGGAAAAGAATTAGGGATTTC-GGAGAGGGGGAAC-GAATTTGGGGAAAAGAAGTTGGGG-AAAA
1 GGGAAAAAAATTAGGGATTTCAGG-GAGGGGGAACTG-ATTTGGGGAAAAGAAATTGGGGAAAAA
*
15604138 AGGAAAGGGAATT
64 AAGAAAGGG-ATT
* *
15604151 GGGAAAAAAAAGTTAGGGATTTCAGGGAGGGGGAACTGATTTGGTGAAAATAAATTGGGGAAAAA
1 GGG-AAAAAAA-TTAGGGATTTCAGGGAGGGGGAACTGATTTGGGGAAAAGAAATTGGGGAAAAA
15604216 AAGAAAGGGATT
64 AAGAAAGGGATT
* * * *
15604228 GGGAAAACAATTAGGGATTTTAGGG-GGTGGAACTGATTTAAGGGAAAA
1 GGGAAAAAAATTAGGGATTTCAGGGAGGGGGAACTGATTT-GGGGAAAA
15604276 ATTAGGGATT
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
74 13 0.12
75 23 0.21
76 12 0.11
77 46 0.42
78 15 0.14
ACGTcount: A:0.41, C:0.03, G:0.38, T:0.19
Consensus pattern (75 bp):
GGGAAAAAAATTAGGGATTTCAGGGAGGGGGAACTGATTTGGGGAAAAGAAATTGGGGAAAAAAA
GAAAGGGATT
Found at i:15614649 original size:10 final size:9
Alignment explanation
Indices: 15614626--15614682 Score: 53
Period size: 10 Copynumber: 5.9 Consensus size: 9
15614616 AGCTAATAAC
*
15614626 GAGCTCAAT
1 GAGCTGAAT
15614635 GAGCTGAATT
1 GAGCTGAA-T
15614645 GAGCTCGAAT
1 GAGCT-GAAT
15614655 GAGCT-AACTT
1 GAGCTGAA--T
15614665 GAGCTCGAAT
1 GAGCT-GAAT
15614675 GAGCTGAA
1 GAGCTGAA
15614683 CCACATGAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
8 2 0.05
9 10 0.24
10 24 0.59
11 3 0.07
12 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.23
Consensus pattern (9 bp):
GAGCTGAAT
Found at i:15614655 original size:20 final size:21
Alignment explanation
Indices: 15614626--15614683 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
15614616 AGCTAATAAC
15614626 GAGCTC-AATGAGCTGAA-TT
1 GAGCTCGAATGAGCTGAACTT
15614645 GAGCTCGAATGAGCT-AACTT
1 GAGCTCGAATGAGCTGAACTT
15614665 GAGCTCGAATGAGCTGAAC
1 GAGCTCGAATGAGCTGAAC
15614684 CACATGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.22
20 25 0.69
21 3 0.08
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (21 bp):
GAGCTCGAATGAGCTGAACTT
Found at i:15616380 original size:48 final size:48
Alignment explanation
Indices: 15616324--15616419 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
15616314 CAGAAATAGA
15616324 TAATGCTCCTAAGAGCTAATCAGATACAAATTAAATGTGTCAGGTTAC
1 TAATGCTCCTAAGAGCTAATCAGATACAAATTAAATGTGTCAGGTTAC
15616372 TAATGCTCCTAAGAGCTAATCAGATACAAATTAAATGTGTCAGGTTAC
1 TAATGCTCCTAAGAGCTAATCAGATACAAATTAAATGTGTCAGGTTAC
15616420 CCGTCCAAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (48 bp):
TAATGCTCCTAAGAGCTAATCAGATACAAATTAAATGTGTCAGGTTAC
Found at i:15620082 original size:43 final size:43
Alignment explanation
Indices: 15620021--15620103 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
15620011 GTGTTCCAAC
* *
15620021 CTGTGTGTCTACCCATGTGTATATTCGAAATAGGGTCACACGG
1 CTGTGTGTCAAACCATGTGTATATTCGAAATAGGGTCACACGG
* * *
15620064 CTGTGTGTCAAACCATGTGTGTATTCGAAGTTGGGTCACA
1 CTGTGTGTCAAACCATGTGTATATTCGAAATAGGGTCACA
15620104 TAGTCGAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (43 bp):
CTGTGTGTCAAACCATGTGTATATTCGAAATAGGGTCACACGG
Found at i:15620612 original size:91 final size:91
Alignment explanation
Indices: 15620457--15620644 Score: 376
Period size: 91 Copynumber: 2.1 Consensus size: 91
15620447 CAATCCACAC
15620457 ACCAAATTCAATTTAAGAATAAAGTTACAAATAAGAAATAAGTTTTATCATTAGTTAATCATTCA
1 ACCAAATTCAATTTAAGAATAAAGTTACAAATAAGAAATAAGTTTTATCATTAGTTAATCATTCA
15620522 TGCCTAAACCCATCAATAAAAAAATT
66 TGCCTAAACCCATCAATAAAAAAATT
15620548 ACCAAATTCAATTTAAGAATAAAGTTACAAATAAGAAATAAGTTTTATCATTAGTTAATCATTCA
1 ACCAAATTCAATTTAAGAATAAAGTTACAAATAAGAAATAAGTTTTATCATTAGTTAATCATTCA
15620613 TGCCTAAACCCATCAATAAAAAAATT
66 TGCCTAAACCCATCAATAAAAAAATT
15620639 ACCAAA
1 ACCAAA
15620645 GATATGGCCA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 97 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (91 bp):
ACCAAATTCAATTTAAGAATAAAGTTACAAATAAGAAATAAGTTTTATCATTAGTTAATCATTCA
TGCCTAAACCCATCAATAAAAAAATT
Found at i:15622409 original size:29 final size:28
Alignment explanation
Indices: 15622371--15622433 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
15622361 CGACCAATGA
*
15622371 AAAAGGATAGCTTCGGCAATCAAATATG
1 AAAAGGATAGCTTCGACAATCAAATATG
* * *
15622399 AAAAGGTATAGCTTCGACTATCGATTATG
1 AAAAGG-ATAGCTTCGACAATCAAATATG
15622428 AAAAGG
1 AAAAGG
15622434 GATGGTGACG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (28 bp):
AAAAGGATAGCTTCGACAATCAAATATG
Found at i:15622509 original size:32 final size:29
Alignment explanation
Indices: 15622413--15622530 Score: 155
Period size: 29 Copynumber: 3.9 Consensus size: 29
15622403 GGTATAGCTT
* *
15622413 CGACTATCGATTATGAAAAGGGATGGTGA
1 CGACCATCAATTATGAAAAGGGATGGTGA
15622442 CGACCATCAATTATGAAAAGGGATGGTGA
1 CGACCATCAATTATGAAAAGGGATGGTGA
* *
15622471 CGACCATCAACTATGAAAATGGATGGTGATGA
1 CGACCATCAATTATGAAAAGGGAT-G-G-TGA
*
15622503 CGACCATCGATTAATGAAAAGGGATGGT
1 CGACCATCAATT-ATGAAAAGGGATGGT
15622531 TCTTACCATT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
29 49 0.63
30 2 0.03
31 2 0.03
32 14 0.18
33 11 0.14
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (29 bp):
CGACCATCAATTATGAAAAGGGATGGTGA
Found at i:15625958 original size:109 final size:109
Alignment explanation
Indices: 15625759--15625992 Score: 342
Period size: 109 Copynumber: 2.1 Consensus size: 109
15625749 AGGCTGTGTG
* * *
15625759 GCCAGGCCGTGTAACAATCAAAAGAGGGACACATGGCCATGTCTCAGCCCGTGTCTGTGCCCGTG
1 GCCAGGCAGTGTAACAATCAAAAGAGGGACACATGGCCATGTCCCAGCCCGTGTCTGTACCCGTG
*
15625824 CAACTCTTTAAGTTGGGCCACATGGCCAAGCCACAAGACCGTCT
66 CAACACTTTAAGTTGGGCCACATGGCCAAGCCACAAGACCGTCT
* * * *
15625868 GCTAGGCTGTGTAACAATCAAAATAGGGACACATGGCCGTGTCCCAGCCCGTGTCTGTACCCGTG
1 GCCAGGCAGTGTAACAATCAAAAGAGGGACACATGGCCATGTCCCAGCCCGTGTCTGTACCCGTG
* * * * *
15625933 TAACACTTTGAGTTGGGTCACATGGCCAAGCCACAAGCCCGTGT
66 CAACACTTTAAGTTGGGCCACATGGCCAAGCCACAAGACCGTCT
*
15625977 GCCAGGCAATGTAACA
1 GCCAGGCAGTGTAACA
15625993 CTAAAAAATG
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.25, C:0.29, G:0.26, T:0.20
Consensus pattern (109 bp):
GCCAGGCAGTGTAACAATCAAAAGAGGGACACATGGCCATGTCCCAGCCCGTGTCTGTACCCGTG
CAACACTTTAAGTTGGGCCACATGGCCAAGCCACAAGACCGTCT
Found at i:15626907 original size:41 final size:41
Alignment explanation
Indices: 15626860--15627026 Score: 154
Period size: 41 Copynumber: 4.1 Consensus size: 41
15626850 ATTTTACTCG
* ** * *
15626860 ATTCAAGGTTACCGGAGTATAAACAAGGGCACATATGTGCT
1 ATTCAAGGGTACCAAAGTACAAACAAGGGCACATATGTGCA
* * *
15626901 ATTCAAGGGTATCAAAGTACAAACATGGGCACGTATGTGCA
1 ATTCAAGGGTACCAAAGTACAAACAAGGGCACATATGTGCA
* ** * * **
15626942 ATTCAGGGGTACTGAAGTACAAACAGGGGTATGTATGTGCA
1 ATTCAAGGGTACCAAAGTACAAACAAGGGCACATATGTGCA
** * * *
15626983 ATTCAAGGGTACTGAAGTACAAATAGGGGCACGTATGTGCA
1 ATTCAAGGGTACCAAAGTACAAACAAGGGCACATATGTGCA
15627024 ATT
1 ATT
15627027 TAGGGAATAA
Statistics
Matches: 107, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (41 bp):
ATTCAAGGGTACCAAAGTACAAACAAGGGCACATATGTGCA
Found at i:15626993 original size:21 final size:22
Alignment explanation
Indices: 15626933--15627031 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 22
15626923 ACATGGGCAC
15626933 GTATGTGCAATTCAGGGGTACT
1 GTATGTGCAATTCAGGGGTACT
* * *
15626955 G-AAGTACAA-ACAGGGGTA-T
1 GTATGTGCAATTCAGGGGTACT
*
15626974 GTATGTGCAATTCAAGGGTACT
1 GTATGTGCAATTCAGGGGTACT
* * * *
15626996 G-AAGTACAAAT-AGGGGCAC-
1 GTATGTGCAATTCAGGGGTACT
*
15627015 GTATGTGCAATTTAGGG
1 GTATGTGCAATTCAGGG
15627032 AATAATTTAG
Statistics
Matches: 57, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
19 3 0.05
20 27 0.47
21 24 0.42
22 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.25
Consensus pattern (22 bp):
GTATGTGCAATTCAGGGGTACT
Found at i:15631479 original size:19 final size:19
Alignment explanation
Indices: 15631455--15631500 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
15631445 AAGCATGATT
*
15631455 GTGCAATTGAGGCACCGAA
1 GTGCAATAGAGGCACCGAA
* *
15631474 GTGCAAATAGTGGCACTGAA
1 GTGC-AATAGAGGCACCGAA
15631494 GTGCAAT
1 GTGCAAT
15631501 CCCGTACAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (19 bp):
GTGCAATAGAGGCACCGAA
Found at i:15639456 original size:60 final size:60
Alignment explanation
Indices: 15639357--15639486 Score: 179
Period size: 60 Copynumber: 2.2 Consensus size: 60
15639347 ATACCCACAA
* * * *
15639357 TAAGCTTGAATAACACTGGCACTAAGCCTAAATAACACCGGCACTAAGCTTGCTAGACTC
1 TAAGCTTGAACAACACCGGCACTAAGCCTAAATAACACCGGCACTAAGCCTGCTAGACAC
* * * * *
15639417 TAAGCCTGAACAACACCGGCACTAAGCCTGAATAGCACCGGTACTAAGCCTGCTAGGCAC
1 TAAGCTTGAACAACACCGGCACTAAGCCTAAATAACACCGGCACTAAGCCTGCTAGACAC
15639477 TAAGCTTGAA
1 TAAGCTTGAA
15639487 TAATAGTATG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (60 bp):
TAAGCTTGAACAACACCGGCACTAAGCCTAAATAACACCGGCACTAAGCCTGCTAGACAC
Found at i:15639476 original size:22 final size:22
Alignment explanation
Indices: 15639357--15639468 Score: 83
Period size: 22 Copynumber: 5.4 Consensus size: 22
15639347 ATACCCACAA
* * *
15639357 TAAGCTTGAATAACACTGGCAC
1 TAAGCCTGAATAGCACCGGCAC
* *
15639379 TAAGCCTAAATAACACCGGCAC
1 TAAGCCTGAATAGCACCGGCAC
* * *
15639401 TAAGCTTG-CTAG-A----CTC
1 TAAGCCTGAATAGCACCGGCAC
* *
15639417 TAAGCCTGAACAACACCGGCAC
1 TAAGCCTGAATAGCACCGGCAC
*
15639439 TAAGCCTGAATAGCACCGGTAC
1 TAAGCCTGAATAGCACCGGCAC
15639461 TAAGCCTG
1 TAAGCCTG
15639469 CTAGGCACTA
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.13
17 1 0.01
18 1 0.01
20 1 0.01
21 2 0.03
22 54 0.79
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.19
Consensus pattern (22 bp):
TAAGCCTGAATAGCACCGGCAC
Found at i:15640544 original size:16 final size:16
Alignment explanation
Indices: 15640523--15640556 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
15640513 AATCTCGTAG
15640523 AAAATAAATAAATAAT
1 AAAATAAATAAATAAT
15640539 AAAATAAATAAATAAT
1 AAAATAAATAAATAAT
15640555 AA
1 AA
15640557 TTCACTCGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAAATAAATAAT
Found at i:15643748 original size:27 final size:27
Alignment explanation
Indices: 15643688--15643859 Score: 177
Period size: 27 Copynumber: 6.4 Consensus size: 27
15643678 CCCTAAAATA
* *
15643688 GGTAAAATGACCAAAATACCTCTATAA
1 GGTAAAATGACCAAAATACCCCTATAG
*
15643715 GATAAAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCCTATAG
* * ** *
15643742 GGAAAAATGTCTGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCTATAG
* * * *
15643769 GGTAGAATGACTAAAATGCCCCCATAG
1 GGTAAAATGACCAAAATACCCCTATAG
* *
15643796 GGTAAAATAATCAAAATACCCC-ATAG
1 GGTAAAATGACCAAAATACCCCTATAG
* *
15643822 GGTAAAATGA-CAGTAACACCCCTATAG
1 GGTAAAATGACCA-AAATACCCCTATAG
15643849 GGTAAAATGAC
1 GGTAAAATGAC
15643860 TGTAATGCCC
Statistics
Matches: 120, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
25 2 0.02
26 20 0.17
27 98 0.82
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.19
Consensus pattern (27 bp):
GGTAAAATGACCAAAATACCCCTATAG
Found at i:15643930 original size:23 final size:23
Alignment explanation
Indices: 15643900--15643946 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
15643890 TTCCTCCCAA
* *
15643900 GGTTAAATGATTGTTTTATTTGT
1 GGTTAAATGACTGATTTATTTGT
*
15643923 GGTTAAATGACTGATTTGTTTGT
1 GGTTAAATGACTGATTTATTTGT
15643946 G
1 G
15643947 TTTGGTATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.02, G:0.26, T:0.51
Consensus pattern (23 bp):
GGTTAAATGACTGATTTATTTGT
Found at i:15643964 original size:24 final size:25
Alignment explanation
Indices: 15643929--15643975 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
15643919 TTGTGGTTAA
*
15643929 ATGACTGATTTGTTTGTG-TTTGGT
1 ATGACTGATTTGTCTGTGATTTGGT
*
15643953 ATGACTGGTTTGTCTGTGATTTG
1 ATGACTGATTTGTCTGTGATTTG
15643976 AATGATTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.13, C:0.06, G:0.30, T:0.51
Consensus pattern (25 bp):
ATGACTGATTTGTCTGTGATTTGGT
Found at i:15643980 original size:24 final size:24
Alignment explanation
Indices: 15643928--15643986 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
15643918 TTTGTGGTTA
*
15643928 AATGACTGATTTGTTTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTTGG
* *
15643952 TATGACTGGTTTGTCTGTGATTT-G
1 AATGACTGATTTGTCTGTG-TTTGG
*
15643976 AATGATTGATT
1 AATGACTGATT
15643987 CTGAGCATGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.19, C:0.05, G:0.27, T:0.49
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGTTTGG
Found at i:15644089 original size:27 final size:27
Alignment explanation
Indices: 15644050--15644114 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
15644040 ATGGAGGAAG
*
15644050 TACTG-TATTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
15644075 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
*
15644103 TACTGTTGCTGG
1 TACTGTTACTGG
15644115 CAACTTTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 26 0.76
28 2 0.06
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:15644188 original size:32 final size:32
Alignment explanation
Indices: 15644132--15644365 Score: 204
Period size: 32 Copynumber: 7.4 Consensus size: 32
15644122 GCTGCGATGC
* * *
15644132 TACTGATGGCTTTGTTCCGGTCATAGT-ACCGT
1 TACTGATGGCTTTGTGCCGATCATA-TCACTGT
* * * *
15644164 TACTAATGGCTTTGTGCTGATCATATTACTAT
1 TACTGATGGCTTTGTGCCGATCATATCACTGT
* * *
15644196 TACTGGTGGCTATGTGCCGATCATTTCACTGT
1 TACTGATGGCTTTGTGCCGATCATATCACTGT
* * * *
15644228 TACTGATGGCTGTGTACTGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATCACTGT
* * * *
15644260 TACT-ATGGCTTTGTACCGATCATGTTACCGT
1 TACTGATGGCTTTGTGCCGATCATATCACTGT
* * * *
15644291 TGCTGATGGCTGTGTGCCAATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATCACTGT
* * *
15644323 TACTGATGGCTTTGTGCCAATCACATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATCACTGT
*
15644354 TACTTATGGCTT
1 TACTGATGGCTT
15644366 GTAGCCATTC
Statistics
Matches: 162, Mismatches: 38, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
31 36 0.22
32 126 0.78
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATCACTGT
Found at i:15644362 original size:95 final size:96
Alignment explanation
Indices: 15644129--15644365 Score: 253
Period size: 95 Copynumber: 2.5 Consensus size: 96
15644119 TTTGCTGCGA
* * * * * * * * *
15644129 TGCTACTGATGGCTTTGTTCCGGTCATAGTACCGTTACTAATGGCTTTGTGCTGATCATATTACT
1 TGCTACTGATGGCTTTGTACCGATCATATTACTGCTACTTATGGCTTTGTACCGATCATATTACC
* * *
15644194 ATTACTGGTGGCTATGTGCCGATCATTTCAC
66 ATTACTGATGGCTATGTGCCAATCATATCAC
* * * * *
15644225 TGTTACTGATGGCTGTGTACTGATCATATCACTGCTAC-TATGGCTTTGTACCGATCATGTTACC
1 TGCTACTGATGGCTTTGTACCGATCATATTACTGCTACTTATGGCTTTGTACCGATCATATTACC
* * *
15644289 GTTGCTGATGGCTGTGTGCCAATCATATCAC
66 ATTACTGATGGCTATGTGCCAATCATATCAC
* * *
15644320 TGCTACTGATGGCTTTGTGCCAATCACATTACTG-TACTTATGGCTT
1 TGCTACTGATGGCTTTGTACCGATCATATTACTGCTACTTATGGCTT
15644366 GTAGCCATTC
Statistics
Matches: 113, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
94 3 0.03
95 81 0.72
96 29 0.26
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (96 bp):
TGCTACTGATGGCTTTGTACCGATCATATTACTGCTACTTATGGCTTTGTACCGATCATATTACC
ATTACTGATGGCTATGTGCCAATCATATCAC
Found at i:15648508 original size:22 final size:22
Alignment explanation
Indices: 15648480--15648534 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
15648470 GCTTGCTAGG
*
15648480 CACTAAGCCTGAATAACATCGA
1 CACTAAGCCTGAATAACACCGA
*
15648502 CACTAAGCCTGACTAACACCGA
1 CACTAAGCCTGAATAACACCGA
15648524 CACTAAGCCTG
1 CACTAAGCCTG
15648535 CTAGGCATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.33, G:0.15, T:0.16
Consensus pattern (22 bp):
CACTAAGCCTGAATAACACCGA
Found at i:15652374 original size:39 final size:37
Alignment explanation
Indices: 15652302--15652450 Score: 133
Period size: 38 Copynumber: 3.9 Consensus size: 37
15652292 TAAAGGCATG
*
15652302 TATTAAAGATG-TCTAAACTAGGACAT-ATATAAAACAT
1 TATTAAAGATGTTC-AAACTATGACATAAT-TAAAACAT
* * *
15652339 GTATTTAAGATGTCCTAAACTATGACATAATTAAAAACCCT
1 -TATTAAAGATGTTC-AAACTATGACATAATT-AAAA-CAT
* *
15652380 TATTAAAGATGTTCAGATTATGACATAATTAAAAC-T
1 TATTAAAGATGTTCAAACTATGACATAATTAAAACAT
* *
15652416 CATATTAATGATGTTCAAATTATGACATAATTAAA
1 --TATTAAAGATGTTCAAACTATGACATAATTAAA
15652451 GACTTAAACT
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 45 0.47
39 28 0.29
40 18 0.19
41 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (37 bp):
TATTAAAGATGTTCAAACTATGACATAATTAAAACAT
Found at i:15652423 original size:38 final size:38
Alignment explanation
Indices: 15652340--15652450 Score: 141
Period size: 38 Copynumber: 2.9 Consensus size: 38
15652330 ATAAAACATG
* * * *
15652340 TATTTAAGATGTCCTAAACTATGACATAATTAAAAACCCT
1 TATTAAAGATGTTC-AAATTATGACATAATT-AAAACCCA
* *
15652380 TATTAAAGATGTTCAGATTATGACATAATTAAAACTCA
1 TATTAAAGATGTTCAAATTATGACATAATTAAAACCCA
*
15652418 TATTAATGATGTTCAAATTATGACATAATTAAA
1 TATTAAAGATGTTCAAATTATGACATAATTAAA
15652451 GACTTAAACT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 37 0.59
39 14 0.22
40 12 0.19
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (38 bp):
TATTAAAGATGTTCAAATTATGACATAATTAAAACCCA
Found at i:15655845 original size:29 final size:29
Alignment explanation
Indices: 15655789--15655845 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
15655779 ATGTATTTGA
*
15655789 CCCTTAACTTTTCATTAATTACACATTTT
1 CCCTAAACTTTTCATTAATTACACATTTT
*
15655818 CCCTAAACTTTTACATTTATTACA-ATTT
1 CCCTAAACTTTT-CATTAATTACACATTT
15655846 AGTCCCTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (29 bp):
CCCTAAACTTTTCATTAATTACACATTTT
Found at i:15656799 original size:23 final size:23
Alignment explanation
Indices: 15656771--15656817 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
15656761 AGAATGATCA
15656771 TGAAAATGAAGAATAGAGGTGGG
1 TGAAAATGAAGAATAGAGGTGGG
15656794 TGAAAATGAAGAATAGAGGTGGG
1 TGAAAATGAAGAATAGAGGTGGG
15656817 T
1 T
15656818 ATTTATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.19
Consensus pattern (23 bp):
TGAAAATGAAGAATAGAGGTGGG
Found at i:15657740 original size:17 final size:18
Alignment explanation
Indices: 15657707--15657756 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
15657697 CATTCCATAA
*
15657707 CATTTTCTAGTTT-AATAC
1 CATTTTCCA-TTTCAATAC
*
15657725 CA-TTTCCATTTCAATAT
1 CATTTTCCATTTCAATAC
15657742 CATTTTCCATTTCAA
1 CATTTTCCATTTCAA
15657757 AATCATGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
18 14 0.50
ACGTcount: A:0.28, C:0.22, G:0.02, T:0.48
Consensus pattern (18 bp):
CATTTTCCATTTCAATAC
Found at i:15657748 original size:18 final size:18
Alignment explanation
Indices: 15657727--15657762 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
15657717 TTTAATACCA
*
15657727 TTTCCATTTCAATATCAT
1 TTTCCATTTCAAAATCAT
15657745 TTTCCATTTCAAAATCAT
1 TTTCCATTTCAAAATCAT
15657763 GATTTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTCCATTTCAAAATCAT
Found at i:15667034 original size:21 final size:19
Alignment explanation
Indices: 15666991--15667035 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
15666981 GAGCTCAAAT
* *
15666991 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
15667010 GAGCTGGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
15667031 GAGCT
1 GAGCT
15667036 CAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:15670010 original size:51 final size:51
Alignment explanation
Indices: 15669890--15670073 Score: 167
Period size: 51 Copynumber: 3.6 Consensus size: 51
15669880 AAAGTGATGG
* * *** * * *
15669890 TCACATGTGTAGTACTATGTGTAAGCTACTACGTGTACCGGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATACGTACCAGATAGTAAT-GA
* * *
15669940 TCGCATGTGTAGTACTATGTGCAGCCTACTATACGTACCAGATAGT-TTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATACGTACCAGATAGTAAT-GA
* *** * * *
15669991 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATACGTACCAGATAGTAATGA
15670042 TCACATGTGTAGTACTATGTGCAGGCTACTAT
1 TCACATGTGTAGTACTATGTGCAGGCTACTAT
15670074 GTGAACTGAA
Statistics
Matches: 108, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
50 34 0.31
51 72 0.67
52 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATACGTACCAGATAGTAATGA
Found at i:15670076 original size:26 final size:26
Alignment explanation
Indices: 15669996--15670076 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
15669986 TTCGATCACG
15669996 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
15670022 CGTGTA-T-CAGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
15670047 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
15670073 TGTG
1 TGTG
15670077 AACTGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:15670169 original size:45 final size:45
Alignment explanation
Indices: 15670083--15670170 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
15670073 TGTGAACTGA
* * *
15670083 ACATCGTTGATTAGTAAGGTGGTTGCTATGTGCTAATTCCACCGG
1 ACATCCTTGATTAATAAGGTGGTTGCTATGTACTAATTCCACCGG
15670128 ACATCCTTGATTAATAAGGTGGTTGCTATGTACTGAA-TCCACC
1 ACATCCTTGATTAATAAGGTGGTTGCTATGTACT-AATTCCACC
15670171 AAGTATCTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 37 0.95
46 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (45 bp):
ACATCCTTGATTAATAAGGTGGTTGCTATGTACTAATTCCACCGG
Found at i:15676862 original size:14 final size:14
Alignment explanation
Indices: 15676843--15676878 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
15676833 TTTTTGTTTT
15676843 TTTCTTTCTTTTAC
1 TTTCTTTCTTTTAC
* *
15676857 TTTCTTTATTTTCC
1 TTTCTTTCTTTTAC
15676871 TTTCTTTC
1 TTTCTTTC
15676879 ACCACCACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTCTTTCTTTTAC
Found at i:15679234 original size:35 final size:35
Alignment explanation
Indices: 15679186--15679284 Score: 126
Period size: 35 Copynumber: 2.8 Consensus size: 35
15679176 ATTTGTTGAT
*
15679186 ATTCTGATTCACATGTTAAGCATGCCATTATTTTG
1 ATTCTGATTCACATGTTAAGCATGCCACTATTTTG
* * **
15679221 ATTCTGATACACATGTTAACCATGTTACTATTTTG
1 ATTCTGATTCACATGTTAAGCATGCCACTATTTTG
** *
15679256 ATTCTGATTCGTATGTTAAGTATGCCACT
1 ATTCTGATTCACATGTTAAGCATGCCACT
15679285 GTGTTAAATC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (35 bp):
ATTCTGATTCACATGTTAAGCATGCCACTATTTTG
Found at i:15680881 original size:22 final size:22
Alignment explanation
Indices: 15680829--15680881 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
15680819 TGGACAAGCC
* *
15680829 ACCACTAATTTGCAGTTAAACT
1 ACCACTGATTTGCAGATAAACT
** * *
15680851 GTCATTGATTTGTAGATAAACT
1 ACCACTGATTTGCAGATAAACT
15680873 ACCACTGAT
1 ACCACTGAT
15680882 AACACTAATG
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (22 bp):
ACCACTGATTTGCAGATAAACT
Found at i:15685940 original size:26 final size:26
Alignment explanation
Indices: 15685911--15685961 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
15685901 CTTGAACTCA
* * *
15685911 AAATTCAAACTCAAGCCCTGAACCTT
1 AAATCCAAACCCAAACCCTGAACCTT
*
15685937 AAATCCAAACCCAAACCTTGAACCT
1 AAATCCAAACCCAAACCCTGAACCT
15685962 CGAGGTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.33, G:0.06, T:0.20
Consensus pattern (26 bp):
AAATCCAAACCCAAACCCTGAACCTT
Found at i:15688745 original size:43 final size:43
Alignment explanation
Indices: 15688682--15688858 Score: 189
Period size: 43 Copynumber: 4.1 Consensus size: 43
15688672 AAATAGGACT
* * *
15688682 TCGATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGATTTGAGATTTAGTGTAAGACCATGTCTGGGACATTGGCA
* **
15688725 TCGATTTGAGAATTT-GTGTAAGACCACGTCTGGGATGTTGGCA
1 TCGATTTGAG-ATTTAGTGTAAGACCATGTCTGGGACATTGGCA
* *
15688768 TCAATTTGAGATTTACGTGTAAGACCATGTTTGGGACATTGGCA
1 TCGATTTGAGATTTA-GTGTAAGACCATGTCTGGGACATTGGCA
* * * * *
15688812 TCG-TAT-ATGATTTAATGTAAGACCCTGTTTGGGACAGTGGCA
1 TCGATTTGA-GATTTAGTGTAAGACCATGTCTGGGACATTGGCA
15688854 TCGAT
1 TCGAT
15688859 AGTTGATTAC
Statistics
Matches: 114, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
42 33 0.29
43 51 0.45
44 30 0.26
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (43 bp):
TCGATTTGAGATTTAGTGTAAGACCATGTCTGGGACATTGGCA
Found at i:15688841 original size:42 final size:42
Alignment explanation
Indices: 15688682--15688879 Score: 134
Period size: 43 Copynumber: 4.6 Consensus size: 42
15688672 AAATAGGACT
* * * *
15688682 TCGATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGATA-GTGATTACATGTAAGACCATGTTTGGGACAGTGGCA
* * ** * * *
15688725 TCGATTTGAGAATT-TGTGTAAGACCACGTCTGGGA-TGTTGGCA
1 TCGA-TAGTG-ATTACATGTAAGACCATGTTTGGGACAG-TGGCA
* * * * *
15688768 TCAATTTGAGATTTACGTGTAAGACCATGTTTGGGACATTGGCA
1 TCGA-TAGTGA-TTACATGTAAGACCATGTTTGGGACAGTGGCA
*
15688812 TCGTATA-TGATTTA-ATGTAAGACCCTGTTTGGGACAGTGGCA
1 TCG-ATAGTGA-TTACATGTAAGACCATGTTTGGGACAGTGGCA
15688854 TCGATAGTTGATTACATGTAAGACCA
1 TCGATAG-TGATTACATGTAAGACCA
15688880 CGTCCGAGAC
Statistics
Matches: 126, Mismatches: 19, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
41 3 0.02
42 32 0.25
43 60 0.48
44 30 0.24
45 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (42 bp):
TCGATAGTGATTACATGTAAGACCATGTTTGGGACAGTGGCA
Found at i:15688866 original size:43 final size:42
Alignment explanation
Indices: 15688780--15688879 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
15688770 AATTTGAGAT
* *
15688780 TTACGTGTAAGACCATGTTTGGGACATTGGCATCGTATATGA
1 TTACATGTAAGACCATGTTTGGGACAGTGGCATCGTATATGA
*
15688822 TTTA-ATGTAAGACCCTGTTTGGGACAGTGGCATCG-ATAGTTGA
1 -TTACATGTAAGACCATGTTTGGGACAGTGGCATCGTATA--TGA
15688865 TTACATGTAAGACCA
1 TTACATGTAAGACCA
15688880 CGTCCGAGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
41 3 0.06
42 31 0.62
43 16 0.32
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (42 bp):
TTACATGTAAGACCATGTTTGGGACAGTGGCATCGTATATGA
Found at i:15691393 original size:14 final size:14
Alignment explanation
Indices: 15691374--15691403 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15691364 ATCACAATCA
*
15691374 TTAAAATCCCAAAT
1 TTAAAATCCAAAAT
15691388 TTAAAATCCAAAAT
1 TTAAAATCCAAAAT
15691402 TT
1 TT
15691404 TTGAGGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAATCCAAAAT
Found at i:15692041 original size:32 final size:32
Alignment explanation
Indices: 15691986--15692156 Score: 204
Period size: 32 Copynumber: 5.4 Consensus size: 32
15691976 GAATGGCTAC
* * *
15691986 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
15692017 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
15692049 CAA-CCATCAATAATGGTAATATGATCGGCACA
1 -AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
15692081 AAGCCA-CTAGTAATGGTAATATGATCGACACA
1 AAGCCATC-AGTAACGGTAATATGATCGGCACA
*
15692113 AAGCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
15692145 AAGCCATCAGTA
1 AAGCCATCAGTA
15692157 GAATCGCAGC
Statistics
Matches: 123, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
31 13 0.11
32 107 0.87
33 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:15692354 original size:11 final size:11
Alignment explanation
Indices: 15692338--15692380 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
15692328 AATCAGTCAT
15692338 ACAAATCACAG
1 ACAAATCACAG
*
15692349 ACAAATCAATCAT
1 ACAAATC-A-CAG
*
15692362 ACCAATCACAG
1 ACAAATCACAG
15692373 ACAAATCA
1 ACAAATCA
15692381 GTCATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 16 0.62
12 2 0.08
13 8 0.31
ACGTcount: A:0.53, C:0.28, G:0.05, T:0.14
Consensus pattern (11 bp):
ACAAATCACAG
Found at i:15692355 original size:24 final size:24
Alignment explanation
Indices: 15692328--15692433 Score: 122
Period size: 24 Copynumber: 4.4 Consensus size: 24
15692318 CCATGCTCAG
15692328 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
* *
15692352 AATCAATCATACCAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
**
15692376 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
* ** * *
15692400 AATTAGTCATTTACATCACGGACA
1 AATCAGTCATACAAATCACAGACA
*
15692424 AATCAATCAT
1 AATCAGTCAT
15692434 TTACACTCGA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.23
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:15692484 original size:26 final size:28
Alignment explanation
Indices: 15692455--15692570 Score: 97
Period size: 27 Copynumber: 4.4 Consensus size: 28
15692445 GGGAAAAATA
15692455 GTCA-TTTACCCTCTA-GGGG-CATTACG
1 GTCATTTTACCCT-TACGGGGTCATTACG
15692481 GTCATTTTA-CCTTACGGGGTCATTACG
1 GTCATTTTACCCTTACGGGGTCATTACG
* * *
15692508 GTCATTTTACCC-TATGGGGGT--TTTCA
1 GTCATTTTACCCTTA-CGGGGTCATTACG
* *
15692534 GTTATTTTACCC-TACAGGGGT-ATTATG
1 GTCATTTTACCCTTAC-GGGGTCATTACG
15692561 GTCATTTTAC
1 GTCATTTTAC
15692571 AAATATCGGG
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
25 2 0.03
26 32 0.43
27 33 0.45
28 7 0.09
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.39
Consensus pattern (28 bp):
GTCATTTTACCCTTACGGGGTCATTACG
Found at i:15692504 original size:27 final size:26
Alignment explanation
Indices: 15692470--15692570 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 26
15692460 TTACCCTCTA
* *
15692470 GGGGCATTACGGTCATTTTACCTTAC
1 GGGGTATTACGGTCATTTTACCCTAC
*
15692496 GGGGTCATTACGGTCATTTTACCCTATG
1 GGGGT-ATTACGGTCATTTTACCCTA-C
* * *
15692524 GGGGT-TTTCAGTTATTTTACCCTAC
1 GGGGTATTACGGTCATTTTACCCTAC
*
15692549 AGGGGTATTATGGTCATTTTAC
1 -GGGGTATTACGGTCATTTTAC
15692571 AAATATCGGG
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
26 25 0.42
27 30 0.50
28 5 0.08
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (26 bp):
GGGGTATTACGGTCATTTTACCCTAC
Found at i:15694795 original size:97 final size:97
Alignment explanation
Indices: 15694682--15694890 Score: 337
Period size: 97 Copynumber: 2.2 Consensus size: 97
15694672 TTAAATTTTT
* *
15694682 GTTATGAAATTTTAATGTTTAAATGGTTAATTAAATGAAAAGGATTAAATCGTAAAAATAGAAAA
1 GTTATGAAATTTTAATGTTTAAATGGTTAATTAAATGAAAAGGACTAAATCATAAAAATAGAAAA
* * *
15694747 AGTTAAGTTCTGTTAGTTAAAAGGGTCAAGTG
66 AGTTAAGTTCTATTAGTTAAAAGAGTCAAATG
* * *
15694779 GTTATGAAATTTTAATGTTTAAATGGTTAATTAAATTAAAAGGACTAAATCATAAAAATGGTAAA
1 GTTATGAAATTTTAATGTTTAAATGGTTAATTAAATGAAAAGGACTAAATCATAAAAATAGAAAA
15694844 AGTTAAGTTCTATTAGTTAAAAGAGTCAAATG
66 AGTTAAGTTCTATTAGTTAAAAGAGTCAAATG
*
15694876 GCTATGAAATTTTAA
1 GTTATGAAATTTTAA
15694891 ACTAAGGGAC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 103 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (97 bp):
GTTATGAAATTTTAATGTTTAAATGGTTAATTAAATGAAAAGGACTAAATCATAAAAATAGAAAA
AGTTAAGTTCTATTAGTTAAAAGAGTCAAATG
Found at i:15698630 original size:16 final size:17
Alignment explanation
Indices: 15698607--15698644 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
15698597 AATAAACAAT
15698607 TAAA-TAAATT-GGAAA
1 TAAATTAAATTGGGAAA
15698622 TAAATTAAATTGGGAAA
1 TAAATTAAATTGGGAAA
15698639 TAAATT
1 TAAATT
15698645 TGGGTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (17 bp):
TAAATTAAATTGGGAAA
Found at i:15701351 original size:45 final size:45
Alignment explanation
Indices: 15701301--15701386 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
15701291 TCTTCGTTCT
* *
15701301 TCAATTTCTTTTTCAATTTTCTCCTTTTCATTTCCTTTTTCAATA
1 TCAATTTCCTTTTCAATCTTCTCCTTTTCATTTCCTTTTTCAATA
* * *
15701346 TCAATTTCCTTTTCAATCTTCTCTTTTTCGTTTTCTTTTTC
1 TCAATTTCCTTTTCAATCTTCTCCTTTTCATTTCCTTTTTC
15701387 TCTCACTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.14, C:0.23, G:0.01, T:0.62
Consensus pattern (45 bp):
TCAATTTCCTTTTCAATCTTCTCCTTTTCATTTCCTTTTTCAATA
Found at i:15703923 original size:5 final size:5
Alignment explanation
Indices: 15703913--15703943 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
15703903 TGCATGAGAT
15703913 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
15703944 CTAACTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:15714443 original size:50 final size:50
Alignment explanation
Indices: 15714348--15714468 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
15714338 TAAGGTTATC
* ** * *
15714348 AGAGGTCCCAC-GTGAGACCATGTCTGGGACATGGTGTTGGTACCGAGATG
1 AGAGGTCCC-CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
*
15714398 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
** * *
15714448 AGAACTCTCATGTAAGACCAT
1 AGAGGTCCCCTGTAAGACCAT
15714469 ATCTAGGATA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 1 0.02
50 59 0.98
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:15714544 original size:18 final size:18
Alignment explanation
Indices: 15714521--15714563 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
15714511 AGACCATGTC
15714521 TGATGTGAATCGACTTGG
1 TGATGTGAATCGACTTGG
* * *
15714539 TGATGTGAGTCGAGTTGT
1 TGATGTGAATCGACTTGG
15714557 TGATGTG
1 TGATGTG
15714564 TCCGATCGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.07, G:0.37, T:0.37
Consensus pattern (18 bp):
TGATGTGAATCGACTTGG
Found at i:15719493 original size:22 final size:21
Alignment explanation
Indices: 15719468--15719510 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
15719458 CGTATAGAAT
15719468 ATGGAT-ATGATCTCTAAGATGA
1 ATGGATAATG-TCTCTAA-ATGA
*
15719490 ATGGCTAATGTCTCTAAATGA
1 ATGGATAATGTCTCTAAATGA
15719511 GTAAAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 12 0.63
23 3 0.16
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (21 bp):
ATGGATAATGTCTCTAAATGA
Found at i:15719844 original size:29 final size:29
Alignment explanation
Indices: 15719811--15720054 Score: 235
Period size: 29 Copynumber: 8.5 Consensus size: 29
15719801 CCAATTTTTG
* * * * *
15719811 TAAAAGGATGCCTTTGTAGCTTTTTCTTT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
*
15719840 TAAAAAGAACGCCTTTGTGGCTATCTCTAT
1 TAAAAGGAA-GCCTTTGTGGCTATCTCTAT
*
15719870 TAAAAGGAAACCTTTGTGGCTATCTCTAT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
*
15719899 TAAAAGGAAGCCATTGTGGCTATCT-T-T
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* *
15719926 GTAAAAGGAAGCCTTTGTGACGATCTCTAT
1 -TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * *
15719956 T-AAAGGAAGCTTTTGTGGCTATCTTTGT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * * *
15719984 TAAAAGGATGCC-TTATGGCAAACTCTAT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * * * *
15720012 TTAAAGGATGCCTTTATGTCTATCTCTGT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
*
15720041 TAAAAGGATGCCTT
1 TAAAAGGAAGCCTT
15720055 AAGGTAAACT
Statistics
Matches: 178, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
27 1 0.01
28 68 0.38
29 84 0.47
30 25 0.14
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (29 bp):
TAAAAGGAAGCCTTTGTGGCTATCTCTAT
Found at i:15719944 original size:57 final size:57
Alignment explanation
Indices: 15719807--15720054 Score: 250
Period size: 57 Copynumber: 4.3 Consensus size: 57
15719797 AACACCAATT
* * * * *
15719807 TTTGTAAAAGGATGCCTTTGTAGCTTTTTCTTTTAAAAAGAACGCCTTTGTGGCTATC
1 TTTGTAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGAA-GCCTTTGTGGCTATC
** *
15719865 TCTAT-TAAAAGGAAACCTTTGTGGCTATCTCTATTAAAAGGAAGCCATTGTGGCTATC
1 T-T-TGTAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCTATC
* * * *
15719923 TTTGTAAAAGGAAGCCTTTGTGACGATCTCTATT-AAAGGAAGCTTTTGTGGCTATC
1 TTTGTAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCTATC
* * * * * * *
15719979 TTTGTTAAAAGGATGCC-TTATGGCAAACTCTATTTAAAGGATGCCTTTATGTCTATC
1 TTTG-TAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCTATC
*
15720036 TCTGTTAAAAGGATGCCTT
1 TTTG-TAAAAGGATGCCTT
15720055 AAGGTAAACT
Statistics
Matches: 161, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
56 38 0.24
57 73 0.45
58 17 0.11
59 32 0.20
60 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (57 bp):
TTTGTAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCTATC
Found at i:15720055 original size:57 final size:57
Alignment explanation
Indices: 15719839--15720087 Score: 234
Period size: 57 Copynumber: 4.4 Consensus size: 57
15719829 GCTTTTTCTT
* * * * * *
15719839 TTAAAAAGAACGCCTTTGTGGCTATCTCTATTAAAAGGAAACCTTTGTGGCTATCTCTA
1 TTAAAAGGAA-GCCTTTGTGGCTATCTCTGTTAAAAGGAAGCC-TTATGGCAAACTCTA
* * * *
15719898 TTAAAAGGAAGCCATTGTGGCTATCTTTG-TAAAAGGAAGCCTT-TGTGACGATCTCTA
1 TTAAAAGGAAGCCTTTGTGGCTATCTCTGTTAAAAGGAAGCCTTATG-G-CAAACTCTA
* * *
15719955 TT-AAAGGAAGCTTTTGTGGCTATCTTTGTTAAAAGGATGCCTTATGGCAAACTCTA
1 TTAAAAGGAAGCCTTTGTGGCTATCTCTGTTAAAAGGAAGCCTTATGGCAAACTCTA
* * * * * * * *
15720011 TTTAAAGGATGCCTTTATGTCTATCTCTGTTAAAAGGATGCCTTAAGGTAAACTCTG
1 TTAAAAGGAAGCCTTTGTGGCTATCTCTGTTAAAAGGAAGCCTTATGGCAAACTCTA
* *
15720068 TTAAAAGGATGCCTTCGTGG
1 TTAAAAGGAAGCCTTTGTGG
15720088 TGAGACTATG
Statistics
Matches: 162, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
55 2 0.01
56 36 0.22
57 97 0.60
58 18 0.11
59 9 0.06
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (57 bp):
TTAAAAGGAAGCCTTTGTGGCTATCTCTGTTAAAAGGAAGCCTTATGGCAAACTCTA
Found at i:15720066 original size:28 final size:28
Alignment explanation
Indices: 15719981--15720082 Score: 123
Period size: 28 Copynumber: 3.6 Consensus size: 28
15719971 TGGCTATCTT
* *
15719981 TGTTAAAAGGATGCCTTATGGCAAACTC
1 TGTTAAAAGGATGCCTTAAGGTAAACTC
* * * * * *
15720009 TATTTAAAGGATGCCTTTATGTCTATCTC
1 TGTTAAAAGGATGCCTTAAGGT-AAACTC
15720038 TGTTAAAAGGATGCCTTAAGGTAAACTC
1 TGTTAAAAGGATGCCTTAAGGTAAACTC
15720066 TGTTAAAAGGATGCCTT
1 TGTTAAAAGGATGCCTT
15720083 CGTGGTGAGA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
28 37 0.63
29 22 0.37
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (28 bp):
TGTTAAAAGGATGCCTTAAGGTAAACTC
Found at i:15730839 original size:42 final size:41
Alignment explanation
Indices: 15730787--15730926 Score: 134
Period size: 42 Copynumber: 3.6 Consensus size: 41
15730777 ACCAATGATT
*
15730787 CGGGAAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATA
1 CGGGGAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATA
* * *
15730828 CGGAGGAATCAGCACTTAGCAACCAC-----CA-AT-A-ATT
1 CGG-GGAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATA
* * *
15730862 CAGGGAATCAGTACTTAGCAGCCCCTTTTTCATTTAAGATA
1 CGGGGAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATA
*
15730903 TGGTGGAATCAGCACTTAGCAACC
1 CGG-GGAATCAGCACTTAGCAACC
15730927 ACCAATGATT
Statistics
Matches: 75, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
33 19 0.25
34 4 0.05
35 1 0.01
36 1 0.01
37 2 0.03
38 2 0.03
39 1 0.01
40 1 0.01
41 6 0.08
42 38 0.51
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (41 bp):
CGGGGAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATA
Found at i:15730887 original size:75 final size:74
Alignment explanation
Indices: 15730763--15730963 Score: 321
Period size: 75 Copynumber: 2.7 Consensus size: 74
15730753 CGATGGATTT
15730763 AGCACTTAGCAACCACCAATGATTCGGGAAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATA
1 AGCACTTAGCAACCACCAATGATTCGGG-AATCAGCACTTAGCAACCCCTTTTTCATTTAAGATA
15730828 CGGAGGAATC
65 CGGAGGAATC
* * *
15730838 AGCACTTAGCAACCACCAATAATTCAGGGAATCAGTACTTAGCAGCCCCTTTTTCATTTAAGATA
1 AGCACTTAGCAACCACCAATGATTC-GGGAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATA
* *
15730903 TGGTGGAATC
65 CGGAGGAATC
*
15730913 AGCACTTAGCAACCACCAATGATTTGGGGAATCAGCACTTAGCAACCCCTT
1 AGCACTTAGCAACCACCAATGA-TTCGGGAATCAGCACTTAGCAACCCCTT
15730964 GGGGGGATCA
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
75 110 0.96
76 5 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (74 bp):
AGCACTTAGCAACCACCAATGATTCGGGAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATAC
GGAGGAATC
Found at i:15730949 original size:33 final size:33
Alignment explanation
Indices: 15730907--15731059 Score: 120
Period size: 33 Copynumber: 4.5 Consensus size: 33
15730897 AAGATATGGT
15730907 GGAATCAGCACTTAGCAACCACCAATGATTTGG
1 GGAATCAGCACTTAGCAACCACCAATGATTTGG
*
15730940 GGAATCAGCACTTAGCAACC-CC-----TTGGG
1 GGAATCAGCACTTAGCAACCACCAATGATTTGG
* * * * **
15730967 GGGATCAGCAGTTAGCAACCCCTTTTTCATTTAAGATAAGG
1 GGAATCAGCACTTAGCAACCAC-----CA---ATGATTTGG
15731008 TGGAATCAGCACTTAGCAACCACCAATGATTTGG
1 -GGAATCAGCACTTAGCAACCACCAATGATTTGG
15731042 GGAATCAGCACTTAGCAA
1 GGAATCAGCACTTAGCAA
15731060 ACCCTTGGGG
Statistics
Matches: 94, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
27 22 0.23
28 1 0.01
32 2 0.02
33 39 0.41
34 6 0.06
37 2 0.02
41 3 0.03
42 19 0.20
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGATTTGG
Found at i:15730975 original size:27 final size:27
Alignment explanation
Indices: 15730938--15730990 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
15730928 CCAATGATTT
15730938 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
* *
15730965 GGGGGATCAGCAGTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
15730991 TTTCATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTG
Found at i:15731014 original size:102 final size:102
Alignment explanation
Indices: 15730864--15731092 Score: 404
Period size: 102 Copynumber: 2.2 Consensus size: 102
15730854 CAATAATTCA
* * *
15730864 GGGAATCAGTACTTAGCAGCCCCTTTTTCATTTAAGATATGGTGGAATCAGCACTTAGCAACCAC
1 GGGAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATAAGGTGGAATCAGCACTTAGCAACCAC
*
15730929 CAATGATTTGGGGAATCAGCACTTAGCAACCCCTTGG
66 CAATGATTTGGGGAATCAGCACTTAGCAAACCCTTGG
* *
15730966 GGGGATCAGCAGTTAGCAACCCCTTTTTCATTTAAGATAAGGTGGAATCAGCACTTAGCAACCAC
1 GGGAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATAAGGTGGAATCAGCACTTAGCAACCAC
15731031 CAATGATTTGGGGAATCAGCACTTAGCAAACCCTTGG
66 CAATGATTTGGGGAATCAGCACTTAGCAAACCCTTGG
15731068 GGGAATCAGCACTTAGCAACCCCTT
1 GGGAATCAGCACTTAGCAACCCCTT
15731093 GTATATTCAA
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 119 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (102 bp):
GGGAATCAGCACTTAGCAACCCCTTTTTCATTTAAGATAAGGTGGAATCAGCACTTAGCAACCAC
CAATGATTTGGGGAATCAGCACTTAGCAAACCCTTGG
Found at i:15731076 original size:27 final size:27
Alignment explanation
Indices: 15731040--15731093 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
15731030 CCAATGATTT
15731040 GGGGAATCAGCACTTAGCAAACCCTTG
1 GGGGAATCAGCACTTAGCAAACCCTTG
*
15731067 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAAACCCTTG
15731094 TATATTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAAACCCTTG
Found at i:15736219 original size:49 final size:49
Alignment explanation
Indices: 15736161--15736260 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
15736151 CTTATAAAGC
* * *
15736161 ACATATGGAAAGCATTAAACATGTTATATTCTTTCCAAAAAGAAATATA
1 ACATATGGAAAGCACTAAAAAAGTTATATTCTTTCCAAAAAGAAATATA
* *
15736210 ACATATGGAAAGTACTAAAAAAGTTATATTCTTTCCAAAAAGAATTATA
1 ACATATGGAAAGCACTAAAAAAGTTATATTCTTTCCAAAAAGAAATATA
15736259 AC
1 AC
15736261 CACCATGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (49 bp):
ACATATGGAAAGCACTAAAAAAGTTATATTCTTTCCAAAAAGAAATATA
Found at i:15741679 original size:3 final size:3
Alignment explanation
Indices: 15741673--15741713 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
15741663 AAACATAAAA
15741673 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
15741714 GGGAACTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:15746297 original size:20 final size:19
Alignment explanation
Indices: 15746261--15746321 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
15746251 TATAAACGCA
*
15746261 ATTGAGCTTAAAATGAGCTG
1 ATTGAGC-TAAAGTGAGCTG
15746281 ATTGAGCTAAGAGTGAGCTCG
1 ATTGAGCTAA-AGTGAGCT-G
15746302 A-TGAGCTAAAGTTGAGCTG
1 ATTGAGCTAAAG-TGAGCTG
15746321 A
1 A
15746322 ATGAACTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 7 0.19
20 28 0.76
21 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (19 bp):
ATTGAGCTAAAGTGAGCTG
Found at i:15754286 original size:15 final size:15
Alignment explanation
Indices: 15754262--15754293 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15754252 AGAAAATAAA
15754262 AACAAAAACAAGAAG
1 AACAAAAACAAGAAG
*
15754277 AACAAGAACAAGAAG
1 AACAAAAACAAGAAG
15754292 AA
1 AA
15754294 GTGTCAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (15 bp):
AACAAAAACAAGAAG
Found at i:15762163 original size:20 final size:20
Alignment explanation
Indices: 15762138--15762202 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
15762128 GTAAATATTT
15762138 GTAAAGGAAAAAAAAAGTAA
1 GTAAAGGAAAAAAAAAGTAA
**
15762158 GTAAAGGAAAGGAAAAG-AA
1 GTAAAGGAAAAAAAAAGTAA
*
15762177 -T---GGAAAAAAATAGT-A
1 GTAAAGGAAAAAAAAAGTAA
15762192 GTAAAGGAAAA
1 GTAAAGGAAAA
15762203 GAATTGAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
15 10 0.29
16 1 0.03
18 1 0.03
19 8 0.23
20 15 0.43
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.11
Consensus pattern (20 bp):
GTAAAGGAAAAAAAAAGTAA
Found at i:15769479 original size:2 final size:2
Alignment explanation
Indices: 15769472--15769506 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15769462 TCCTCCACAT
15769472 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
15769507 ATTTTCACTT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:15773764 original size:9 final size:9
Alignment explanation
Indices: 15773721--15773783 Score: 63
Period size: 9 Copynumber: 6.3 Consensus size: 9
15773711 TATTTAGATA
15773721 AAAAGAAGAG
1 AAAAGAA-AG
15773731 AAAAGAAATG
1 AAAAGAAA-G
15773741 AAACGAAGAAGAG
1 -AA--AAGAA-AG
*
15773754 AAAAGAGAG
1 AAAAGAAAG
15773763 AAAAGAAAG
1 AAAAGAAAG
15773772 AAAAGAAAG
1 AAAAGAAAG
15773781 AAA
1 AAA
15773784 GATTAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
9 23 0.50
10 12 0.26
11 2 0.04
12 2 0.04
13 6 0.13
14 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:15773771 original size:13 final size:13
Alignment explanation
Indices: 15773722--15773785 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 13
15773712 ATTTAGATAA
15773722 AAAGAAGAGAAAAG
1 AAAGAA-AGAAAAG
15773736 AAATGAAACGAAGAAG
1 AAA-GAAA-GAA-AAG
* *
15773752 AGA-AAAG-AGAG
1 AAAGAAAGAAAAG
15773763 AAAAGAAAGAAAAG
1 -AAAGAAAGAAAAG
15773777 AAAGAAAGA
1 AAAGAAAGA
15773786 TTAAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
11 2 0.05
12 3 0.08
13 14 0.35
14 10 0.25
15 6 0.15
16 5 0.12
ACGTcount: A:0.70, C:0.02, G:0.27, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAAAG
Found at i:15773772 original size:23 final size:24
Alignment explanation
Indices: 15773722--15773783 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
15773712 ATTTAGATAA
*
15773722 AAAGAAGAGAAAAGAAATGAAACG
1 AAAGAAGAGAAAAGAAATGAAAAG
*
15773746 -AAGAAGAGAAAAGAGA-GAAAAG
1 AAAGAAGAGAAAAGAAATGAAAAG
*
15773768 AAAGAAAAG-AAAGAAA
1 AAAGAAGAGAAAAGAAA
15773784 GATTAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.02
Consensus pattern (24 bp):
AAAGAAGAGAAAAGAAATGAAAAG
Found at i:15782671 original size:15 final size:15
Alignment explanation
Indices: 15782651--15782680 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15782641 GTCATTGAAA
15782651 AACCACTTCCTAATG
1 AACCACTTCCTAATG
*
15782666 AACCACTTGCTAATG
1 AACCACTTCCTAATG
15782681 CCTCGAGGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (15 bp):
AACCACTTCCTAATG
Found at i:15786416 original size:22 final size:22
Alignment explanation
Indices: 15786391--15786435 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
15786381 TTGATCCCCT
15786391 GATATATGACTGATTGGTATTA
1 GATATATGACTGATTGGTATTA
* *
15786413 GATATATGAGTGATTGGTCTTA
1 GATATATGACTGATTGGTATTA
15786435 G
1 G
15786436 TGCTAGTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (22 bp):
GATATATGACTGATTGGTATTA
Found at i:15790387 original size:12 final size:12
Alignment explanation
Indices: 15790370--15790417 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
15790360 ATAGTAGTTT
15790370 CTCGAAAAAAAA
1 CTCGAAAAAAAA
15790382 CTCGAAAAAAAA
1 CTCGAAAAAAAA
15790394 -TC-AAAAAAAA
1 CTCGAAAAAAAA
*
15790404 TTCGAAAAAAAA
1 CTCGAAAAAAAA
15790416 CT
1 CT
15790418 AGTTTCCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 8 0.24
11 4 0.12
12 21 0.64
ACGTcount: A:0.67, C:0.15, G:0.06, T:0.12
Consensus pattern (12 bp):
CTCGAAAAAAAA
Done.