Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 181 of 213
Found at i:54585989 original size:35 final size:35
Alignment explanation
Indices: 54585801--54586071 Score: 179
Period size: 40 Copynumber: 7.3 Consensus size: 35
54585791 TGATATTGTC
* *
54585801 GGTTCATCCGACTAGCGCTGGGCGC-AATCATCGTT
1 GGTTTATCCAACTAGCGCTGGGCGCAAAT-ATCGTT
* * *
54585836 -GTTCATCCAACTAGAGCTGGGCTCACAATTATAATCGTT
1 GGTTTATCCAACTAGCGCTGGG--CGCAA--AT-ATCGTT
* * * * * *
54585875 GGTATA-CTCGACTAGCACTAGGTGCAAATATCGGT
1 GGTTTATC-CAACTAGCGCTGGGCGCAAATATCGTT
* * * *
54585910 GGTTTATCCAACTAGAGCTGGGCTCACTTTTTATATCGTC
1 GGTTTATCCAACTAGCGCTGGGCGCA-----AATATCGTT
*
54585950 GGTTTATCCGACTAGCGCTGGGCGCAAATATCGTT
1 GGTTTATCCAACTAGCGCTGGGCGCAAATATCGTT
* * * *
54585985 GGTTTATCCAACTAGAGCTGGGCTCACTATTTATATTGTC
1 GGTTTATCCAACTAGCGCTGGGCGCA--A---ATATCGTT
*
54586025 GGTTTATCCAACTAGCGCTGGGCGCAAATATCATT
1 GGTTTATCCAACTAGCGCTGGGCGCAAATATCGTT
54586060 GGTTTATCCAAC
1 GGTTTATCCAAC
54586072 CAGAGTTGGG
Statistics
Matches: 180, Mismatches: 38, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
34 19 0.11
35 69 0.38
36 5 0.03
37 2 0.01
38 4 0.02
39 9 0.05
40 72 0.40
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (35 bp):
GGTTTATCCAACTAGCGCTGGGCGCAAATATCGTT
Found at i:54586773 original size:23 final size:24
Alignment explanation
Indices: 54586725--54586774 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
54586715 TATTTGATAT
**
54586725 TATTAGAATAAGGAGTTTCACTCC
1 TATTAGAATAAGGAGTTTCAAGCC
*
54586749 TATTAGAATAAGG-TTTTCAAGCC
1 TATTAGAATAAGGAGTTTCAAGCC
54586772 TAT
1 TAT
54586775 AAATAGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (24 bp):
TATTAGAATAAGGAGTTTCAAGCC
Found at i:54592275 original size:69 final size:69
Alignment explanation
Indices: 54592164--54592302 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
54592154 AGCCACACTA
54592164 CCGTGTGAACCCTGTAGTCAAAAATTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
1 CCGTGTGAACCCTGTAGTCAAAAATTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
54592229 GTCC
66 GTCC
* *
54592233 CCGTGTGAACCTTGTAGTCAAAAATTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTTTTA
1 CCGTGTGAACCCTGTAGTCAAAAATTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
54592298 GTCC
66 GTCC
54592302 C
1 C
54592303 AAAGTGTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.42
Consensus pattern (69 bp):
CCGTGTGAACCCTGTAGTCAAAAATTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
GTCC
Found at i:54596415 original size:35 final size:35
Alignment explanation
Indices: 54596368--54596437 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
54596358 TGAACCACTG
*
54596368 ATCCAACTGACTAACCTGAATAACTTTAACCCCAA
1 ATCCAACCGACTAACCTGAATAACTTTAACCCCAA
*
54596403 ATCCAACCGACTAACCTGAATAATTTTAACCCCAA
1 ATCCAACCGACTAACCTGAATAACTTTAACCCCAA
54596438 TTTTGGGGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.23
Consensus pattern (35 bp):
ATCCAACCGACTAACCTGAATAACTTTAACCCCAA
Found at i:54599108 original size:17 final size:17
Alignment explanation
Indices: 54599056--54599108 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
54599046 TATGGAAACA
* *
54599056 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
54599073 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
54599092 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
54599109 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:54599108 original size:22 final size:23
Alignment explanation
Indices: 54599080--54599124 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
54599070 ATGCAATCTT
54599080 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
54599102 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
54599125 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:54599134 original size:22 final size:23
Alignment explanation
Indices: 54599090--54599134 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
54599080 AGATATGATA
*
54599090 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
54599113 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
54599135 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:54599320 original size:19 final size:21
Alignment explanation
Indices: 54599296--54599334 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
54599286 GTTTTCTTTT
*
54599296 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
54599315 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
54599335 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:54599562 original size:15 final size:15
Alignment explanation
Indices: 54599538--54599575 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
54599528 GTTTTTAGCC
54599538 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
54599552 TGTTATTATTATTTT
1 TATTATTATTAATTT
54599567 TATTATTAT
1 TATTATTAT
54599576 ATTATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:54599569 original size:12 final size:12
Alignment explanation
Indices: 54599540--54599590 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
54599530 TTTTAGCCTA
54599540 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
54599552 TGTTATTATTAT
1 TTTTATTATTAT
54599564 TTTTATTATTAT
1 TTTTATTATTAT
54599576 ATTATATATTATTAT
1 -TT-T-TATTATTAT
54599591 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 3 0.09
12 18 0.55
13 2 0.06
14 1 0.03
15 9 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:54599585 original size:15 final size:13
Alignment explanation
Indices: 54599554--54599591 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
54599544 ATTAATTTTG
54599554 TTATTATTAT-TT
1 TTATTATTATATT
54599566 TTATTATTATATT
1 TTATTATTATATT
54599579 ATATATTATTATA
1 -T-TATTATTATA
54599592 CCTACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTATATT
Found at i:54606254 original size:88 final size:87
Alignment explanation
Indices: 54606103--54606324 Score: 327
Period size: 88 Copynumber: 2.5 Consensus size: 87
54606093 AGCAGATCGG
* *
54606103 TAAAAATAGCAGATCTTGCCTTACTGCACCGACAGCGAAGCAGATCGAAGACACCAGCTTTGCCT
1 TAAAAATAGCAGATCTTGCCTT-CTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCT
* *
54606168 CCCTAGGTTGCAGTGGAGCAGGT
65 CCCTAGGTTGCAGCGGAGCACGT
* *
54606191 TAAAAATAGCAGATCTTGCCTTCTTGCACTGACAGCGAAGTAGATCAAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTC-TGCACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCT
* *
54606256 CCCTGGGTTGCAGCGGCGCACGT
65 CCCTAGGTTGCAGCGGAGCACGT
* *
54606279 TAAAAATAGCAGATCTTGCCTTCCTACACCGATAGCGAAGCAGATC
1 TAAAAATAGCAGATCTTGCCTT-CTGCACCGACAGCGAAGCAGATC
54606325 GATGACCTCA
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
87 1 0.01
88 118 0.98
89 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (87 bp):
TAAAAATAGCAGATCTTGCCTTCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTC
CCTAGGTTGCAGCGGAGCACGT
Found at i:54606403 original size:44 final size:44
Alignment explanation
Indices: 54606336--54606800 Score: 570
Period size: 44 Copynumber: 10.7 Consensus size: 44
54606326 ATGACCTCAG
* ** * *
54606336 TCCTATCTCCCTGGTCAATAGTGGAATAGTTTGAAGATTGAGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
*
54606380 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
54606424 TCCTATCTCCTTGGACAGCAGTGGAATAGGTTAAAGATTGTGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
54606468 TCCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGATTGAGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* * *
54606512 TTCTATCTCCCTGGGCAGCAGTGGAATAGATT--A-A---AGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
*
54606550 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
54606594 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* * *
54606638 TCCCATCTCCCTTGACAGCAGTGGAATAGGTTGAAGATTGAGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* * * *
54606682 TTCTATCTCCCTAGG-TAGCAGTGGAATAGATTAAAGATTGTAG-G
1 TCCTATCTCCCT-GGACAGCAGTGGAATAGGTTAAAGATTG-AGAA
* * * * *
54606726 TCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATCGTGAA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
* *
54606770 CCCTATCTCCCT-GAGCAGCAGTGGAGTAGGT
1 TCCTATCTCCCTGGA-CAGCAGTGGAATAGGT
54606801 GGAAAATAGC
Statistics
Matches: 366, Mismatches: 44, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
38 33 0.09
40 1 0.00
41 2 0.01
42 1 0.00
43 4 0.01
44 322 0.88
45 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGAA
Found at i:54606606 original size:214 final size:214
Alignment explanation
Indices: 54606336--54606754 Score: 628
Period size: 214 Copynumber: 2.0 Consensus size: 214
54606326 ATGACCTCAG
* * * *
54606336 TCCTATCTCCCTGGTCAATAGTGGAATAGTTTGAAGATTGAGAATCCTATCTCCCTGGACAGCAG
1 TCCTATCTCCCTGGACAACAGTGGAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGACAGCAG
* * *
54606401 TGGAATAGGTTAAAGATTGTGAATCCTATCT-CCTTGGACAGCAGTGGAATAGGTTAAAGATTGT
66 TGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTT-GACAGCAGTGGAATAGGTTAAAGATTGA
* *
54606465 GAATCCTATCTCCCTA-GTCAGCAGTGGAATAGGTTAAAGATTG-AGAATTCTATCTCCCTGGGC
130 GAATCCTATCTCCCTAGGT-AGCAGTGGAATAGATTAAAGATTGTAG-ATCCTATCTCCCTGGGC
54606528 AGCAGTGGAATAGATTAAAGAA
193 AGCAGTGGAATAGATTAAAGAA
* * *
54606550 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAG
1 TCCTATCTCCCTGGACAACAGTGGAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGACAGCAG
* *
54606615 TGGAATAGGTTGAAGATTGAGAATCCCATCTCCCTTGACAGCAGTGGAATAGGTTGAAGATTGAG
66 TGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTTGACAGCAGTGGAATAGGTTAAAGATTGAG
* * * *
54606680 AATTCTATCTCCCTAGGTAGCAGTGGAATAGATTAAAGATTGTAGGTCCTATCTCCCTGGTCAGT
131 AATCCTATCTCCCTAGGTAGCAGTGGAATAGATTAAAGATTGTAGATCCTATCTCCCTGGGCAGC
54606745 AGTGGAATAG
196 AGTGGAATAG
54606755 GTTGAAGATC
Statistics
Matches: 184, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
214 176 0.96
215 8 0.04
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (214 bp):
TCCTATCTCCCTGGACAACAGTGGAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGACAGCAG
TGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTTGACAGCAGTGGAATAGGTTAAAGATTGAG
AATCCTATCTCCCTAGGTAGCAGTGGAATAGATTAAAGATTGTAGATCCTATCTCCCTGGGCAGC
AGTGGAATAGATTAAAGAA
Found at i:54606633 original size:170 final size:169
Alignment explanation
Indices: 54606376--54606800 Score: 634
Period size: 170 Copynumber: 2.5 Consensus size: 169
54606366 TTGAAGATTG
*
54606376 AGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCTTGGACA
1 AGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGG-CA
* * *
54606441 GCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTAAAGAT
65 GCAGTGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTAGACAGCAGTGGAATAGGTTAAAGAT
*
54606506 TGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAA
130 TGAGAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTAA
54606546 AGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCA
1 AGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGG-CA
* * *
54606611 GCAGTGGAATAGGTTGAAGATTGAGAATCCCATCTCCCTTGACAGCAGTGGAATAGGTTGAAGAT
65 GCAGTGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTAGACAGCAGTGGAATAGGTTAAAGAT
*
54606676 TGAGAATTCTATCTCCCTAGGTAGCAGTGGAATAGATTAA
130 TGAGAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTAA
* * * * *
54606716 AGATTGTAGGTCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATCGTGAACCCTATCTCCC
1 AGA----A--TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCC
*
54606781 TGAGCAGCAGTGGAGTAGGT
60 TG-GCAGCAGTGGAATAGGT
54606801 GGAAAATAGC
Statistics
Matches: 232, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
170 163 0.70
174 1 0.00
176 67 0.29
177 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (169 bp):
AGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGCAG
CAGTGGAATAGGTTAAAGATTGAGAATCCCATCTCCCTAGACAGCAGTGGAATAGGTTAAAGATT
GAGAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTAA
Found at i:54607200 original size:44 final size:44
Alignment explanation
Indices: 54607107--54607222 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 44
54607097 ATGGCAAATT
* *
54607107 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATC
1 TTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCGATAATC
* * * *
54607151 CTATCTCCCTGAAATTGCAGTGAAGC-GAATTAAAACC-TTGGATC
1 TTATCTCCCTGAAGTTGCAGTGAAGCAG-ATTAAAACCGAT-AATC
* *
54607195 TTATCTCTCTGAAGTTGCAGAG-AGCAGA
1 TTATCTCCCTGAAGTTGCAGTGAAGCAGA
54607223 ATGCATCTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
43 6 0.10
44 53 0.90
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCGATAATC
Found at i:54607683 original size:17 final size:17
Alignment explanation
Indices: 54607631--54607683 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
54607621 TATGGAAACA
* *
54607631 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
54607648 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
54607667 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
54607684 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:54607683 original size:22 final size:23
Alignment explanation
Indices: 54607655--54607699 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
54607645 ATGCAATCTT
54607655 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
54607677 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
54607700 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:54607709 original size:22 final size:23
Alignment explanation
Indices: 54607665--54607709 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
54607655 AGATATGATA
*
54607665 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
54607688 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
54607710 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:54613616 original size:15 final size:15
Alignment explanation
Indices: 54613596--54613627 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54613586 CATTTCACTA
*
54613596 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
54613611 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
54613626 TT
1 TT
54613628 TGCATGCATA
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:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:54621142 original size:21 final size:21
Alignment explanation
Indices: 54621102--54621143 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54621092 CAAACAATTA
*
54621102 CAAAAAGTAACAATATCTTTT
1 CAAAAAGTAACAATACCTTTT
* *
54621123 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTAACAATACCTTTT
54621144 ACCAGGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (21 bp):
CAAAAAGTAACAATACCTTTT
Found at i:54625465 original size:55 final size:55
Alignment explanation
Indices: 54625401--54625513 Score: 172
Period size: 55 Copynumber: 2.1 Consensus size: 55
54625391 TCTTCTTAAT
* *
54625401 TGTTGGAATACTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTATTA
1 TGTTGGAATACTACTTCTTTTGAATCGATTATTTATATGTTTAAATCGATTATTA
* * * *
54625456 TGTTGGAATATTACTTCTTTTGAATCGATTATTTATATGTTTACATTGATTGTTA
1 TGTTGGAATACTACTTCTTTTGAATCGATTATTTATATGTTTAAATCGATTATTA
54625511 TGT
1 TGT
54625514 AGCACATCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (55 bp):
TGTTGGAATACTACTTCTTTTGAATCGATTATTTATATGTTTAAATCGATTATTA
Found at i:54641146 original size:26 final size:27
Alignment explanation
Indices: 54641114--54641222 Score: 91
Period size: 26 Copynumber: 4.0 Consensus size: 27
54641104 TTATATATTT
54641114 TTATTAAATTATATTTAATAATAATTA
1 TTATTAAATTATATTTAATAATAATTA
* *
54641141 TT-TTAAATTAT-TTTTATAGT-ATTA
1 TTATTAAATTATATTTAATAATAATTA
* * * * *
54641165 TATATTATGATTTTAGTAAATTCATATATT-
1 T-TATTA-AATTATATTTAA-TAATA-ATTA
54641195 TTATTAAATTATATTTAATAATAATTA
1 TTATTAAATTATATTTAATAATAATTA
54641222 T
1 T
54641223 GTTAAAATAT
Statistics
Matches: 60, Mismatches: 14, Indels: 16
0.67 0.16 0.18
Matches are distributed among these distances:
24 5 0.08
25 8 0.13
26 15 0.25
27 11 0.18
28 10 0.17
29 7 0.12
30 1 0.02
31 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (27 bp):
TTATTAAATTATATTTAATAATAATTA
Found at i:54641197 original size:18 final size:17
Alignment explanation
Indices: 54641174--54641208 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54641164 ATATATTATG
54641174 ATTTTAGTAAATTCATAT
1 ATTTTAGTAAATT-ATAT
*
54641192 ATTTTATTAAATTATAT
1 ATTTTAGTAAATTATAT
54641209 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTAGTAAATTATAT
Found at i:54641399 original size:39 final size:41
Alignment explanation
Indices: 54641354--54641459 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
54641344 TTTCCTTATG
* * *
54641354 CTATTACACCTCTATTCCATTCAACCAAACATAAGAA-TAT
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
54641394 C-ATTACGCCTCTATTTCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTC----T-ATTCCATTCAACCAAACAAAAGAATTAC
54641439 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
54641460 ACGCATCTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 9 0.16
40 1 0.02
41 8 0.14
42 1 0.02
43 1 0.02
44 23 0.41
45 3 0.05
46 10 0.18
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:54641434 original size:44 final size:46
Alignment explanation
Indices: 54641367--54641459 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
54641357 TTACACCTCT
* * *
54641367 ATTCCATTCAACCAAACATAAGAA-TATC-ATTACGCCTCTATTTC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
54641411 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
54641457 ATT
1 ATT
54641460 ACGCATCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.52
45 3 0.07
46 18 0.41
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:54641462 original size:16 final size:16
Alignment explanation
Indices: 54641441--54641493 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
54641431 AGAATTACCT
54641441 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
54641457 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
** *
54641473 ATTATACCTCTATTCT
1 ATTACGCCTCTATTCC
54641489 ATTAC
1 ATTAC
54641494 AGCGAACCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:54642619 original size:11 final size:11
Alignment explanation
Indices: 54642598--54642644 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
54642588 GTGTAGTTTG
54642598 TTTATTGTTATT
1 TTTA-TGTTATT
54642610 TTTATGTTATT
1 TTTATGTTATT
54642621 TTTAAT-TTATT
1 TTT-ATGTTATT
* *
54642632 TTAAAGTTATT
1 TTTATGTTATT
54642643 TT
1 TT
54642645 GTTAGCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 1 0.03
11 24 0.77
12 6 0.19
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.70
Consensus pattern (11 bp):
TTTATGTTATT
Found at i:54646812 original size:3 final size:3
Alignment explanation
Indices: 54646799--54646835 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
54646789 TTTGTTGTTA
54646799 TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54646836 ACTTACACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:54647003 original size:18 final size:19
Alignment explanation
Indices: 54646975--54647012 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
54646965 ATAGTTTATA
*
54646975 TATATATACATTTACATTT
1 TATATATACATATACATTT
54646994 TATA-ATACATATACATTT
1 TATATATACATATACATTT
54647012 T
1 T
54647013 TCCATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATACATATACATTT
Found at i:54647007 original size:24 final size:25
Alignment explanation
Indices: 54646969--54647030 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
54646959 TTATATATAG
*
54646969 TTTAT-ATATATATACA-TTTACAT
1 TTTATAATACATATACATTTTACAT
*
54646992 TTTATAATACATATACATTTTTCCAT
1 TTTATAATACATATACA-TTTTACAT
*
54647018 TTTATAATTCATA
1 TTTATAATACATA
54647031 CATATTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.15
24 10 0.30
26 18 0.55
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTATAATACATATACATTTTACAT
Found at i:54647037 original size:26 final size:26
Alignment explanation
Indices: 54646989--54647038 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
54646979 TATACATTTA
*
54646989 CATTTTATAATACATATACATTTTTC
1 CATTTTATAATACATACACATTTTTC
* *
54647015 CATTTTATAATTCATACATATTTT
1 CATTTTATAATACATACACATTTT
54647039 CACATACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (26 bp):
CATTTTATAATACATACACATTTTTC
Found at i:54648863 original size:15 final size:15
Alignment explanation
Indices: 54648843--54648894 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
54648833 CCTTAGCCTC
54648843 TCCATTTTT-ACTTTT
1 TCCATTTTTCA-TTTT
54648858 TCCATTTTTCATTTT
1 TCCATTTTTCATTTT
54648873 T-C-TTTTTCATTTT
1 TCCATTTTTCATTTT
*
54648886 TTCATTTTT
1 TCCATTTTT
54648895 TTCACATCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.35
14 2 0.06
15 19 0.56
16 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (15 bp):
TCCATTTTTCATTTT
Found at i:54648865 original size:7 final size:7
Alignment explanation
Indices: 54648845--54648894 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
54648835 TTAGCCTCTC
54648845 CATTTTT
1 CATTTTT
54648852 -ACTTTTT
1 CA-TTTTT
54648859 CCATTTTT
1 -CATTTTT
54648867 CATTTTT
1 CATTTTT
54648874 C-TTTTT
1 CATTTTT
54648880 CATTTTTT
1 CA-TTTTT
54648888 CATTTTT
1 CATTTTT
54648895 TTCACATCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.18
7 18 0.47
8 12 0.32
9 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (7 bp):
CATTTTT
Found at i:54648880 original size:13 final size:13
Alignment explanation
Indices: 54648862--54648886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54648852 ACTTTTTCCA
54648862 TTTTTCATTTTTC
1 TTTTTCATTTTTC
54648875 TTTTTCATTTTT
1 TTTTTCATTTTT
54648887 TCATTTTTTT
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCATTTTTC
Found at i:54649417 original size:23 final size:23
Alignment explanation
Indices: 54649382--54649447 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 23
54649372 CCTAGTGGAG
54649382 GTTTTTT-GTTTCTTTTTATTTTT
1 GTTTTTTCG-TTCTTTTTATTTTT
*
54649405 GTTTTTTCGTTC-TTCT-TTTTT
1 GTTTTTTCGTTCTTTTTATTTTT
** *
54649426 CCTTTTTCCTT-TTTTTATTTTT
1 GTTTTTTCGTTCTTTTTATTTTT
54649448 TTATATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 16 0.46
22 8 0.23
23 10 0.29
24 1 0.03
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (23 bp):
GTTTTTTCGTTCTTTTTATTTTT
Found at i:54653667 original size:18 final size:19
Alignment explanation
Indices: 54653644--54653681 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
54653634 ATAAAATGGA
*
54653644 AAAATGTATATGTAT-TAT
1 AAAATGTAAATGTATATAT
54653662 AAAATGTAAATGTATATAT
1 AAAATGTAAATGTATATAT
54653681 A
1 A
54653682 TATAAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (19 bp):
AAAATGTAAATGTATATAT
Found at i:54653680 original size:26 final size:26
Alignment explanation
Indices: 54653618--54653667 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
54653608 TATGTATGTG
*
54653618 AAAATATGTATGAATTATAAAATGGA
1 AAAATATATATGAATTATAAAATGGA
* *
54653644 AAAATGTATATGTATTATAAAATG
1 AAAATATATATGAATTATAAAATG
54653668 TAAATGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (26 bp):
AAAATATATATGAATTATAAAATGGA
Found at i:54655776 original size:48 final size:48
Alignment explanation
Indices: 54655699--54655818 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
54655689 AATGTACTCT
* * * * *
54655699 AATGTATCTAATTTATATTGCAAAGTTTGTTCCGCA-TTTTAATATTGC
1 AATGAATCTAATTTAAATTACAAACTTTGTTCC-AAGTTTTAATATTGC
* *
54655747 AATTAATCTAATTTAAATTACAAACTTTGTTCCAAGTTTTAATGTTGC
1 AATGAATCTAATTTAAATTACAAACTTTGTTCCAAGTTTTAATATTGC
54655795 AATGAATCTCAA-TTAAATTACAAA
1 AATGAATCT-AATTTAAATTACAAA
54655819 GTTATTCTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
47 1 0.02
48 59 0.95
49 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (48 bp):
AATGAATCTAATTTAAATTACAAACTTTGTTCCAAGTTTTAATATTGC
Found at i:54658115 original size:21 final size:22
Alignment explanation
Indices: 54658085--54658148 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 22
54658075 ATTATCAAGA
* * *
54658085 TACATTAATATTATACATACAG
1 TACAATAATAATATAAATACAG
** *
54658107 TA-AATAATACGATAAATATAG
1 TACAATAATAATATAAATACAG
*
54658128 TACAATAATAATATAAGTACA
1 TACAATAATAATATAAATACA
54658149 ATAAAAAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.31
Consensus pattern (22 bp):
TACAATAATAATATAAATACAG
Found at i:54658146 original size:17 final size:16
Alignment explanation
Indices: 54658121--54658152 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54658111 TAATACGATA
54658121 AATATAGTACAATAAT
1 AATATAGTACAATAAT
54658137 AATATAAGTACAATAA
1 AATAT-AGTACAATAA
54658153 AAAATTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (16 bp):
AATATAGTACAATAAT
Found at i:54658466 original size:109 final size:113
Alignment explanation
Indices: 54658353--54658863 Score: 369
Period size: 106 Copynumber: 4.8 Consensus size: 113
54658343 ACATTTCAAT
* * * *
54658353 AAATAAAAAAATTCAAATAA-ATCAAAAACAA-ATAAAA-TTACATT-ATAACAAATCACAATAC
1 AAAT-AAAAAATTAAAATAATATCAAAAA-AATAAAAAATTTACATTCATAAAAAATCACAATAA
* *
54658414 ACATTAAACT-AA-ACAAATAATTTATAACCTAATCATAAATTACTAACA
64 ACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACA
** * * * *
54658462 AAAT--AACTTTAAAATAATTTTAAAAAAATAAAAAATTTATATTCATAAAAAATCACAATAAAT
1 AAATAAAAAATTAAAATAATATCAAAAAAATAAAAAATTTACATTCATAAAAAATCACAATAAAC
54658525 ACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACA
66 ACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACA
** * * * * *
54658573 AAAT--AACTTTAAAATAATTTTAAAAAACAAAAAAAAAATTACATTAATAAAAAAT--C-----
1 AAATAAAAAATTAAAATAA-TATCAAAAA-AATAAAAAATTTACATTCATAAAAAATCACAATAA
* *
54658629 ACACTAAACTAAACACAAACAATTTA-ACACCTAATCATAAATAATTAA-A
64 ACACTAAACTAAACACAAACAATTTATA-ACCTAATCATAAATTACTAACA
** *** **
54658678 AAAT--AACTTTAAAATAAT-T-----TTTTTTAAAATTTACATTCATAAAAAATCACAATAAAC
1 AAATAAAAAATTAAAATAATATCAAAAAAATAAAAAATTTACATTCATAAAAAATCACAATAAAC
* * *
54658735 ACTAAGCTAAACACAAACAATATATAACCTAATCATATATTACTAACA
66 ACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACA
** * * ** *
54658783 AAAT--AACTTTAAAATGATTTTTAAAAAAT-TAAAA---A-ATT--T--AAAATCACAATAAAC
1 AAATAAAAAATTAAAATAATATCAAAAAAATAAAAAATTTACATTCATAAAAAATCACAATAAAC
54658837 ACTAAACTAAACACAAACAATTTATAA
66 ACTAAACTAAACACAAACAATTTATAA
54658864 TAATTATTAA
Statistics
Matches: 339, Mismatches: 39, Indels: 55
0.78 0.09 0.13
Matches are distributed among these distances:
97 20 0.06
99 1 0.00
102 40 0.12
103 1 0.00
104 43 0.13
105 38 0.11
106 59 0.17
107 12 0.04
108 6 0.02
109 27 0.08
110 7 0.02
111 54 0.16
112 8 0.02
113 23 0.07
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (113 bp):
AAATAAAAAATTAAAATAATATCAAAAAAATAAAAAATTTACATTCATAAAAAATCACAATAAAC
ACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACA
Found at i:54658570 original size:111 final size:111
Alignment explanation
Indices: 54658376--54658863 Score: 553
Period size: 111 Copynumber: 4.6 Consensus size: 111
54658366 CAAATAAATC
* * * * * *
54658376 AAAAACAAATAAAATTACATT-ATAACAAATCACAATACACATTAAACT-AA-ACAAATAATTTA
1 AAAAATAAA-AAATTTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
54658438 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTAA
65 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTAA
* *
54658485 AAAAATAAAAAATTTATATTCATAAAAAATCACAATAAATACTAAACTAAACACAAACAATTTAT
1 AAAAATAAAAAATTTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTAT
54658550 AACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTAAA
66 AACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTT-AA
* * *
54658597 AAACAAAAAAAAAATTACATTAATAAAAAAT--C-----ACACTAAACTAAACACAAACAATTTA
1 AAA-AATAAAAAATTTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
* *
54658655 -ACACCTAATCATAAATAATTAA-AAAATAACTTTAAAATAATTTT--
65 TA-ACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTAA
* ** * *
54658699 ----TTTTAAAATTTACATTCATAAAAAATCACAATAAACACTAAGCTAAACACAAACAATATAT
1 AAAAATAAAAAATTTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTAT
* * *
54658760 AACCTAATCATATATTACTAACAAAATAACTTTAAAATGATTTTTA
66 AACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTAA
*
54658806 AAAAAT-TAAAA---A-ATT--T--AAAATCACAATAAACACTAAACTAAACACAAACAATTTAT
1 AAAAATAAAAAATTTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTAT
54658862 AA
66 AA
54658864 TAATTATTAA
Statistics
Matches: 328, Mismatches: 30, Indels: 49
0.81 0.07 0.12
Matches are distributed among these distances:
97 20 0.06
99 1 0.00
102 40 0.12
104 42 0.13
105 45 0.14
106 46 0.14
107 1 0.00
108 9 0.03
109 31 0.09
110 7 0.02
111 58 0.18
112 5 0.02
113 23 0.07
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (111 bp):
AAAAATAAAAAATTTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTAT
AACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTAA
Found at i:54658765 original size:104 final size:102
Alignment explanation
Indices: 54658629--54658863 Score: 303
Period size: 102 Copynumber: 2.3 Consensus size: 102
54658619 ATAAAAAATC
*
54658629 ACACTAAACTAAACACAAACAATTTA-ACACCTAATCATAAATAATTAA-AAAATAACTTTAAAA
1 ACACTAAACTAAACACAAACAATTTATA-ACCTAATCATAAATAACTAACAAAATAACTTTAAAA
* * ***
54658692 TAATTTTTTTTAAAATTTACATTCATAAAAAATCACAATAA
65 TAA--TTTTTAAAAAATTA-AAAAATAAAAAATCACAATAA
* * * *
54658733 ACACTAAGCTAAACACAAACAATATATAACCTAATCATATATTACTAACAAAATAACTTTAAAAT
1 ACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATAACTAACAAAATAACTTTAAAAT
* **
54658798 GATTTTTAAAAAATTAAAAAATTTAAAATCACAATAA
66 AATTTTTAAAAAATTAAAAAATAAAAAATCACAATAA
54658835 ACACTAAACTAAACACAAACAATTTATAA
1 ACACTAAACTAAACACAAACAATTTATAA
54658864 TAATTATTAA
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
102 43 0.38
103 12 0.11
104 41 0.36
105 18 0.16
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.29
Consensus pattern (102 bp):
ACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATAACTAACAAAATAACTTTAAAAT
AATTTTTAAAAAATTAAAAAATAAAAAATCACAATAA
Found at i:54658997 original size:4 final size:4
Alignment explanation
Indices: 54658990--54659042 Score: 58
Period size: 4 Copynumber: 13.5 Consensus size: 4
54658980 CATACCTTCC
*
54658990 CTTT CTTT -TTT CTTT -TTT TTTT CTTT CTTT CTTCT CATTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT-T C-TTT CTTT CTTT
54659038 -TTT CT
1 CTTT CT
54659043 CCTTCTATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
3 9 0.21
4 28 0.65
5 4 0.09
6 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (4 bp):
CTTT
Found at i:54659003 original size:7 final size:8
Alignment explanation
Indices: 54658990--54659042 Score: 58
Period size: 7 Copynumber: 6.8 Consensus size: 8
54658980 CATACCTTCC
54658990 CTTTCTTT
1 CTTTCTTT
54658998 -TTTCTTT
1 CTTTCTTT
*
54659005 -TTTTTTT
1 CTTTCTTT
54659012 CTTTCTTT
1 CTTTCTTT
54659020 CTTCTCATTT
1 CTT-TC-TTT
54659030 CTTTCTTT
1 CTTTCTTT
54659038 -TTTCT
1 CTTTCT
54659043 CCTTCTATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
7 18 0.45
8 12 0.30
9 4 0.10
10 6 0.15
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (8 bp):
CTTTCTTT
Found at i:54659014 original size:18 final size:20
Alignment explanation
Indices: 54658990--54659042 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
54658980 CATACCTTCC
54658990 CTTTCTTTTTTCTT-T-TTT
1 CTTTCTTTTTTCTTCTATTT
*
54659008 TTTTCTTTCTTTCTTCTCATTT
1 CTTTCTTT-TTTCTTCT-ATTT
54659030 CTTTCTTTTTTCT
1 CTTTCTTTTTTCT
54659043 CCTTCTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 7 0.24
19 6 0.21
20 1 0.03
21 5 0.17
22 10 0.34
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (20 bp):
CTTTCTTTTTTCTTCTATTT
Found at i:54659041 original size:11 final size:12
Alignment explanation
Indices: 54658990--54659042 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 12
54658980 CATACCTTCC
54658990 CTTTCTTT-TTT
1 CTTTCTTTCTTT
*
54659001 CTTT-TTTTTTT
1 CTTTCTTTCTTT
54659012 CTTTCTTTCTTCT
1 CTTTCTTTCTT-T
54659025 CATTTCTTTCTTT
1 C-TTTCTTTCTTT
54659038 -TTTCT
1 CTTTCT
54659043 CCTTCTATTC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 3 0.08
11 16 0.43
12 5 0.14
13 3 0.08
14 10 0.27
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTTCTTTCTTT
Found at i:54659236 original size:27 final size:27
Alignment explanation
Indices: 54659198--54659260 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
54659188 ACTGGCACCA
54659198 GTGCCGCCTGTCAAGGAAGCGTGACTG
1 GTGCCGCCTGTCAAGGAAGCGTGACTG
54659225 GTGCCGCCTGTCAAGGAAGCGTGACTG
1 GTGCCGCCTGTCAAGGAAGCGTGACTG
54659252 GTGCCGCCT
1 GTGCCGCCT
54659261 ACCAATGTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.16, C:0.29, G:0.37, T:0.19
Consensus pattern (27 bp):
GTGCCGCCTGTCAAGGAAGCGTGACTG
Found at i:54665447 original size:34 final size:35
Alignment explanation
Indices: 54665403--54665469 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54665393 CAGTAAAATA
*
54665403 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
54665437 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
54665470 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:54667488 original size:14 final size:15
Alignment explanation
Indices: 54667469--54667499 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
54667459 ATTCTATGCA
54667469 TTTTCTTTA-AATTT
1 TTTTCTTTATAATTT
54667483 TTTTCTTTATAATTT
1 TTTTCTTTATAATTT
54667498 TT
1 TT
54667500 ATATATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCTTTATAATTT
Found at i:54668231 original size:28 final size:29
Alignment explanation
Indices: 54668194--54668278 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
54668184 TCTTACAACT
54668194 TATAAAATTTTATAATTTTTTTATATTTC
1 TATAAAATTTTATAATTTTTTTATATTTC
* * * *
54668223 TGT-ATATTTTATACTTTTTTTACTATTTT
1 TATAAAATTTTATAATTTTTTTA-TATTTC
*
54668252 TATAAAATTTTACAATTTTTTGTATAT
1 TATAAAATTTTATAATTTTTT-TATAT
54668279 ATTTTTTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
28 17 0.38
29 9 0.20
30 17 0.38
31 2 0.04
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (29 bp):
TATAAAATTTTATAATTTTTTTATATTTC
Found at i:54675042 original size:15 final size:16
Alignment explanation
Indices: 54675024--54675062 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
54675014 GAAAACTGAA
54675024 AGAAAG-AAGAAAAAT
1 AGAAAGAAAGAAAAAT
*
54675039 AGAAAGAAAGAAAAAG
1 AGAAAGAAAGAAAAAT
54675055 A-AAAGAAA
1 AGAAAGAAA
54675063 CCAAGGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AGAAAGAAAGAAAAAT
Found at i:54675061 original size:19 final size:19
Alignment explanation
Indices: 54675010--54675062 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
54675000 ATAAACACAG
54675010 AAAAGAAAACTGAAAGAAAGA
1 AAAAGAAAA--GAAAGAAAGA
*
54675031 AGAAA-AATAGAAAGAAAGA
1 A-AAAGAAAAGAAAGAAAGA
54675050 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
54675063 CCAAGGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 3 0.11
19 18 0.64
21 4 0.14
22 3 0.11
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (19 bp):
AAAAGAAAAGAAAGAAAGA
Found at i:54682334 original size:17 final size:17
Alignment explanation
Indices: 54682314--54682389 Score: 50
Period size: 17 Copynumber: 4.4 Consensus size: 17
54682304 AGTAATAAAG
54682314 TGTGAAATAATATAATA
1 TGTGAAATAATATAATA
* *
54682331 TGTG-AATAAGGAAAATA
1 TGTGAAATAA-TATAATA
* *
54682348 TGGTAAAAGTTTAATA-AA-G
1 T-GTGAAA---TAATATAATA
54682367 TGTGAAATAATATAATA
1 TGTGAAATAATATAATA
54682384 TGTGAA
1 TGTGAA
54682390 TAAGGAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
15 5 0.11
16 7 0.16
17 16 0.36
18 7 0.16
19 3 0.07
20 2 0.05
21 1 0.02
22 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
TGTGAAATAATATAATA
Found at i:54682363 original size:53 final size:53
Alignment explanation
Indices: 54682306--54682415 Score: 220
Period size: 53 Copynumber: 2.1 Consensus size: 53
54682296 GGTAAATTAG
54682306 TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
1 TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
54682359 TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
1 TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
54682412 TAAT
1 TAAT
54682416 GAGTGTGTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (53 bp):
TAATAAAGTGTGAAATAATATAATATGTGAATAAGGAAAATATGGTAAAAGTT
Found at i:54684283 original size:16 final size:18
Alignment explanation
Indices: 54684262--54684297 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
54684252 TTTTAATTTT
54684262 TTAAAAAAC-A-ATAAAA
1 TTAAAAAACTATATAAAA
54684278 TTAAAAAACTATATAAAA
1 TTAAAAAACTATATAAAA
54684296 TT
1 TT
54684298 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
TTAAAAAACTATATAAAA
Found at i:54684549 original size:13 final size:13
Alignment explanation
Indices: 54684531--54684564 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
54684521 TTTTGTTGAG
*
54684531 AAGTGCTTTTAAA
1 AAGTGCTTTGAAA
54684544 AAGTGCTTTGAAA
1 AAGTGCTTTGAAA
54684557 AAGTGCTT
1 AAGTGCTT
54684565 CACAAGTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (13 bp):
AAGTGCTTTGAAA
Found at i:54700787 original size:52 final size:51
Alignment explanation
Indices: 54700730--54700832 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 51
54700720 ACTTTACTTG
* * * *
54700730 AAAAAGAAGGGACCAAAGTGAAAACCTGCAAAGGGCGCTTTGATTCCTAAAA
1 AAAAAGAAGAGACCAAAGTGAAAACCCGCAAAAGGCGCTTTGAGT-CTAAAA
*
54700782 AAAAAGGAGAGACCAAAGTGAAAACCCGCAAAAGGCGCTTTGAGTCTAAAA
1 AAAAAGAAGAGACCAAAGTGAAAACCCGCAAAAGGCGCTTTGAGTCTAAAA
54700833 TAATAATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 6 0.13
52 40 0.87
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (51 bp):
AAAAAGAAGAGACCAAAGTGAAAACCCGCAAAAGGCGCTTTGAGTCTAAAA
Found at i:54702185 original size:44 final size:44
Alignment explanation
Indices: 54702103--54702226 Score: 126
Period size: 44 Copynumber: 2.8 Consensus size: 44
54702093 TGAAGATGGC
* * * *
54702103 AGATCTTATATCCCTGAAGTTGCAGT-GAAGCAGATTAAAGCCAAT
1 AGATCCTATCTCCCTGAAGTTGCAGTAG-AGTAGATTAAA-ACAAT
* * *
54702148 A-ATCCTATCTCCCTGAAGTTGCAGTAGAGTGGTTTAAAATAAT
1 AGATCCTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAACAAT
* * *
54702191 AGATCTTATCTCTCTGAAGTTGCAGCAGAGTAGATT
1 AGATCCTATCTCCCTGAAGTTGCAGTAGAGTAGATT
54702227 GCATTAGGTC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
43 4 0.06
44 59 0.91
45 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (44 bp):
AGATCCTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAACAAT
Found at i:54702303 original size:44 final size:45
Alignment explanation
Indices: 54702255--54702350 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
54702245 TTGAGGTTTT
* *
54702255 AGTGGAGCAGACTG-AG-TAAGCAGGTCTTATCCCCCTAAAGTTAC
1 AGTGGAGCAAACTGAAGAT-AGCAGATCTTATCCCCCTAAAGTTAC
* * * *
54702299 AGTGGGGCAAACTGAAGATGGCAGATCTTATCTCCCTAAAGTTGC
1 AGTGGAGCAAACTGAAGATAGCAGATCTTATCCCCCTAAAGTTAC
54702344 AGTGGAG
1 AGTGGAG
54702351 TAGATTAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
44 12 0.28
45 30 0.70
46 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (45 bp):
AGTGGAGCAAACTGAAGATAGCAGATCTTATCCCCCTAAAGTTAC
Found at i:54702386 original size:43 final size:44
Alignment explanation
Indices: 54702321--54702442 Score: 158
Period size: 43 Copynumber: 2.8 Consensus size: 44
54702311 TGAAGATGGC
* * *
54702321 AGATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCAAT
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAA-ACAAT
*
54702366 A-ATCCTATC-CCCTGAAGTTGCAGTGGAGCAGATTAAAACAAT
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACAAT
* * *
54702408 AGATCTTATCTCTCTGAATTTGCAGTGGAGTAGAT
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
54702443 CGCATTAGGT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
42 5 0.07
43 33 0.49
44 28 0.42
45 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACAAT
Found at i:54702436 original size:44 final size:45
Alignment explanation
Indices: 54702321--54703140 Score: 179
Period size: 44 Copynumber: 18.7 Consensus size: 45
54702311 TGAAGATGGC
* *
54702321 AGATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCAAT
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
* *
54702366 A-ATCCTATC-CCCTGAAGTTGCAGTGGAGCAGATTAAA-ACAAT
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
* * * *
54702408 AGATCTTATCTCTCTGAATTTGCAGTGGAGTAGA-T--CG-CATT
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
* * * * * **
54702449 AGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACT-GAGTA-AGC
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAG-ACAAT
* * * * * ****
54702493 AGGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGC
1 AGATCTTATCTC-CCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
* * * * **
54702538 AGGTCTTATCTCCCTG-AG-CGACAGTGGAGTAGGTTGAAA-ATAGC
1 AGATCTTATCTCCCTGAAGTTG-CAGTGGAGTAGATT-AAAGACAAT
* * * ** * * ** * **
54702582 AGATATTGTCTTCCTG-TTTTGGCAGCGAAGTAGATCGAAGATACC
1 AGATCTTATCTCCCTGAAGTT-GCAGTGGAGTAGATTAAAGACAAT
* * ** * **
54702627 AG-CCTTGTCTCCCTG-AGCAGCAGTGGAGCAGGTAAAAAAGAGCAGATCAT
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTA-G-ATTAAAGA-C--A--AT
* * * *
54702677 ATTCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGA-TAGAAGA-AACC
1 A---GATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA-AAGACAA-T
* * ** * * *
54702725 A-ATCCTATCTCCCTAAAGTTATAGTGGAGCAGATTAAA-ACCAC
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
* * * * *
54702768 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T--CG-CATCT
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACA-AT
* * * * *
54702810 AG-TCTTATCTCCCGGAAGTTACAGTGGAGCAGA-CAGAAGA-AACC
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA-AAGACAA-T
* * * * *
54702854 AG-TCCTATCTCCCTGAAGTTGCTGTGGAGCAGATTAAA-ACCAC
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
* * * *
54702897 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T--CG-C-AT
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
** * *
54702937 CCAG-TCTTATCTCCCTGAAGTTGCAGTGGAACAGA-CAGAAGA-AACC
1 --AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA-AAGACAA-T
* ** *
54702983 A-ATCTTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAA-ACCAT
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
** * * *
54703026 AGATCTTATCTTTCTGAAGTTGCAGTAGAGCAGA-T--CG-C-AT
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
* * * *
54703066 CCAG-TCTTATCTCCCTGATGTTGCAGTGGAGCAGA-CAGAAGA-AACC
1 --AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA-AAGACAA-T
*
54703112 A-ATCCTATCTCCCTGAAGTTGCAGTGGAG
1 AGATCTTATCTCCCTGAAGTTGCAGTGGAG
54703141 CGGATCAAAA
Statistics
Matches: 582, Mismatches: 127, Indels: 133
0.69 0.15 0.16
Matches are distributed among these distances:
40 3 0.01
41 117 0.20
42 12 0.02
43 57 0.10
44 308 0.53
45 48 0.08
46 2 0.00
47 1 0.00
48 2 0.00
49 1 0.00
50 1 0.00
52 1 0.00
53 5 0.01
54 12 0.02
55 12 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
AGATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGACAAT
Found at i:54702490 original size:217 final size:218
Alignment explanation
Indices: 54702058--54702552 Score: 785
Period size: 217 Copynumber: 2.3 Consensus size: 218
54702048 TAAAATCATA
* *
54702058 AGGTCTTATCCCCCTAAAGTTACAGTGGGGCAGACTGAAGATGGCAGATCTTATATCCCTGAAGT
1 AGGTCTTATCCCCCTAAAGTTACAGTGGGGCAGACTGAAGATGGCAGATCTTATCTCCCTAAAGT
** * *
54702123 TGCAGTGAAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTAGAGTGGTTTAAAAT
66 TGCAGTGAAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAC
* *
54702188 AATAGATCTTATCTCTCTGAAGTTGCAGCAGAGTAGATTGCATTAGGTCTTATCTCATTGAGGTT
131 AATAGATCTTATCTCTCTGAAGTTGCAGCAGAGTAGATCGCATTAGGTCTTATCTCACTGAGGTT
**
54702253 TTAGTGGAGCAGACTGAGTAAGC
196 GCAGTGGAGCAGACTGAGTAAGC
*
54702276 AGGTCTTATCCCCCTAAAGTTACAGTGGGGCAAACTGAAGATGGCAGATCTTATCTCCCTAAAGT
1 AGGTCTTATCCCCCTAAAGTTACAGTGGGGCAGACTGAAGATGGCAGATCTTATCTCCCTAAAGT
* * *
54702341 TGCAGTGGAGTAGATTAAAGCCAATAATCCTATC-CCCTGAAGTTGCAGTGGAGCAGATTAAAAC
66 TGCAGTGAAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAC
* ** *
54702405 AATAGATCTTATCTCTCTGAATTTGCAGTGGAGTAGATCGCATTAGGTCTTATCTCCCTGAGGTT
131 AATAGATCTTATCTCTCTGAAGTTGCAGCAGAGTAGATCGCATTAGGTCTTATCTCACTGAGGTT
54702470 GCAGTGGAGCAGACTGAGTAAGC
196 GCAGTGGAGCAGACTGAGTAAGC
* * * *
54702493 AGGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAGGTCTTATCTCCCT
1 AGGTCTTATCCCCCTAAAGTTACAGTGGGGCAGACTGAAGATGGCAGATCTTATCTCCCT
54702553 GAGCGACAGT
Statistics
Matches: 254, Mismatches: 23, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
217 160 0.63
218 94 0.37
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (218 bp):
AGGTCTTATCCCCCTAAAGTTACAGTGGGGCAGACTGAAGATGGCAGATCTTATCTCCCTAAAGT
TGCAGTGAAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAC
AATAGATCTTATCTCTCTGAAGTTGCAGCAGAGTAGATCGCATTAGGTCTTATCTCACTGAGGTT
GCAGTGGAGCAGACTGAGTAAGC
Found at i:54702836 original size:85 final size:83
Alignment explanation
Indices: 54702683--54703141 Score: 337
Period size: 85 Copynumber: 5.3 Consensus size: 83
54702673 TCATATTCAA
* * * * * * **
54702683 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATAGAAGAAACCAATCCTATCTCCCTAAAGTTATA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT---AGAATCCAGTCTTATCTCCCTGAAGTTGCA
54702748 GTGGAGCAGATTAAAACCACAG
63 GTGGAGCAGATTAAAACC-CAG
* * * * * *
54702770 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCCCGGAAGTTACAGT
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCCAGTCTTATCTCCCTGAAGTTGCAGT
** *
54702835 GGAGCAGACAGAAGAAACCAG
65 GGAGCAGA-TTAA-AACCCAG
* * * * * *
54702856 TCCTATCTCCCTGAAGTTGCTGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TAGAATC-CAG-TCTTATCTCCCTGAAGTTGCA
* *** *
54702921 GTAGAGCAGA-TCGCATCCAG
63 GTGGAGCAGATTAAAACCCAG
* * * *
54702941 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGA-AGAAACCAATCTTATCTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGT---AGAG-CAGATAGAATCCAGTCTTATCTCCCTGAAGTTGC
* *
54703005 AGTGGAGCGGATTAAAACCATAG
62 AGTGGAGCAGATTAAAACC-CAG
** * * *
54703028 ATCTTATCTTTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGATGTTGCAGT
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCCAGTCTTATCTCCCTGAAGTTGCAGT
** * *
54703093 GGAGCAGACAGAAGAAACCAA
65 GGAGCAGA-TTAA-AACCCAG
* *
54703114 TCCTATCTCCCTGAAGTTGCAGTGGAGC
1 TCTTATCTCCCTGAAGTTGCAGTAGAGC
54703142 GGATCAAAAT
Statistics
Matches: 288, Mismatches: 68, Indels: 33
0.74 0.17 0.08
Matches are distributed among these distances:
84 4 0.01
85 171 0.59
86 16 0.06
87 14 0.05
88 79 0.27
89 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (83 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCCAGTCTTATCTCCCTGAAGTTGCAGTG
GAGCAGATTAAAACCCAG
Found at i:54702895 original size:129 final size:129
Alignment explanation
Indices: 54702665--54703190 Score: 791
Period size: 129 Copynumber: 4.1 Consensus size: 129
54702655 CAGGTAAAAA
** * * * *
54702665 AGAGCAGATCATATTCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATAGAAGAAACCAATCC
1 AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
**
54702730 TATCTCCCTAAAGTTATAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
66 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
* * * *
54702794 AGAGCAGATCGCATCTAGTCTTATCTCCCGGAAGTTACAGTGGAGCAGACAGAAGAAACCAGTCC
1 AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
* *
54702859 TATCTCCCTGAAGTTGCTGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
66 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
* *
54702923 AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAACCAATCT
1 AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
* * *
54702988 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCATAGATCTTATCTTTCTGAAGTTGCAGT
66 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
*
54703052 AGAGCAGATCGCATCCAGTCTTATCTCCCTGATGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
1 AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
* * * ** ** * *
54703117 TATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAATGATGGATCTCATCTCTCTAAAGTTGCAGT
66 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
54703181 AGAGCAGATC
1 AGAGCAGATC
54703191 ATATCAGACT
Statistics
Matches: 361, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 361 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (129 bp):
AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT
Found at i:54703141 original size:44 final size:44
Alignment explanation
Indices: 54702680--54703141 Score: 332
Period size: 44 Copynumber: 10.7 Consensus size: 44
54702670 AGATCATATT
* *
54702680 CAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATAGAAGAAAC
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC
* * ** ** *
54702724 CAATCCTATCTCCCTAAAGTTATAGTGGAGCAGA-TTAA-AACC
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC
* * * *
54702766 ACAGATCTTATCTCTCTGAAGTTGCAGT--AG-AG-CAGATCGCATC
1 -CA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAC
* * * *
54702809 TAGTCTTATCTCCCGGAAGTTACAGTGGAGCAGACAGAAGAAAC
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC
* * * ** *
54702853 CAGTCCTATCTCCCTGAAGTTGCTGTGGAGCAGA-TTAA-AACC
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC
* * * *
54702895 ACAGATCTTATCTCTCTGAAGTTGCAGT--AG-AG-CAGATCGCATC
1 -CA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAC
* *
54702938 CAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACAGAAGAAAC
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC
* * **
54702982 CAATCTTATCTCCCTAAAGTTGCAGTGGAGC-G-GATTA-AAAC
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC
** * * *
54703023 CATAGATCTTATCTTTCTGAAGTTGCAGT--AG-AG-CAGATCGCATC
1 C--A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAC
* *
54703067 CAGTCTTATCTCCCTGATGTTGCAGTGGAGCAGACAGAAGAAAC
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC
*
54703111 CAATCCTATCTCCCTGAAGTTGCAGTGGAGC
1 CAATCTTATCTCCCTGAAGTTGCAGTGGAGC
54703142 GGATCAAAAT
Statistics
Matches: 318, Mismatches: 72, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
41 73 0.23
42 20 0.06
43 19 0.06
44 194 0.61
45 12 0.04
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (44 bp):
CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC
Found at i:54703640 original size:18 final size:18
Alignment explanation
Indices: 54703617--54703668 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
54703607 GCTTAAATTA
54703617 AATACCCAAACCCAATAC
1 AATACCCAAACCCAATAC
* * *
54703635 AATACCTAAACCCGATTC
1 AATACCCAAACCCAATAC
*
54703653 AATGCCCAAAACCCAA
1 AATACCC-AAACCCAA
54703669 CTCAGCCTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.46, C:0.37, G:0.04, T:0.13
Consensus pattern (18 bp):
AATACCCAAACCCAATAC
Found at i:54706316 original size:41 final size:40
Alignment explanation
Indices: 54706271--54706348 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
54706261 TTAAAGTGTG
*
54706271 AATTAGGTTAAACAGTAA-AGAATCGATTCAAACAGAAAAAC
1 AATTAGGTTAAACA-TAAGACAATCGATTCAAA-AGAAAAAC
*
54706312 AATTAGTTTAAACATAATGACAATCGATTCAAAAGAA
1 AATTAGGTTAAACATAA-GACAATCGATTCAAAAGAA
54706349 GAAGTACTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 3 0.09
41 17 0.52
42 13 0.39
ACGTcount: A:0.53, C:0.12, G:0.13, T:0.23
Consensus pattern (40 bp):
AATTAGGTTAAACATAAGACAATCGATTCAAAAGAAAAAC
Found at i:54708528 original size:10 final size:10
Alignment explanation
Indices: 54708486--54708528 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
54708476 GAAAATAGTC
*
54708486 AAAATTAATC
1 AAAATTAATT
54708496 AAAATTAACTAT
1 AAAATTAA-T-T
54708508 AAAATTAATT
1 AAAATTAATT
*
54708518 AAAATTTATT
1 AAAATTAATT
54708528 A
1 A
54708529 TGTTCATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 19 0.66
11 2 0.07
12 8 0.28
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATTAATT
Found at i:54713900 original size:62 final size:62
Alignment explanation
Indices: 54713803--54713924 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 62
54713793 TAGAATTATA
* *
54713803 AAGTCAGCAAGAAAGATAAACTTATCTAAATGTACCAATACGTCCTCGATTTTTCCTTCTAG
1 AAGTCAGCAAGAAAGATAAACTTACCTAAATGTACCAATACGTCCTCAATTTTTCCTTCTAG
* *
54713865 AAGTCAGCAGGAAAGATAAACTTACCTACATGTACCAATACGTCCTCAATTTTTCCTTCT
1 AAGTCAGCAAGAAAGATAAACTTACCTAAATGTACCAATACGTCCTCAATTTTTCCTTCT
54713925 GGATGTGCTA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.30
Consensus pattern (62 bp):
AAGTCAGCAAGAAAGATAAACTTACCTAAATGTACCAATACGTCCTCAATTTTTCCTTCTAG
Found at i:54721349 original size:4 final size:4
Alignment explanation
Indices: 54721340--54721403 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
54721330 ATTTGTTTTA
* * *
54721340 AAAT AAAT AAAT AAAT AAAT AAAA ACAAC AAAT ATATAT AAAT AAA- AACT
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT A-A-AT AAAT AAAT AAAT
*
54721390 AATT AAA- AAAT AAA
1 AAAT AAAT AAAT AAA
54721404 AGAAATAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
3 5 0.10
4 36 0.73
5 5 0.10
6 3 0.06
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:54721836 original size:19 final size:21
Alignment explanation
Indices: 54721798--54721836 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
54721788 CCTTTTTTAA
*
54721798 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
54721819 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
54721837 AAACAGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:54722044 original size:23 final size:22
Alignment explanation
Indices: 54722001--54722058 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
54721991 AAAGGGTATC
* *
54722001 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
54722022 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
54722045 TACATATCATATCT
1 TACAAATCATATCT
54722059 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:54722061 original size:19 final size:19
Alignment explanation
Indices: 54722014--54722111 Score: 97
Period size: 19 Copynumber: 4.8 Consensus size: 19
54722004 AAATTAAATC
*
54722014 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
54722034 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
54722056 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
* *
54722077 TCTAATATTGCATATCATA
1 TCTAAGATTACATATCATA
*
54722096 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
54722112 CTCGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
19 32 0.48
21 17 0.25
22 7 0.10
23 11 0.16
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:54722074 original size:21 final size:21
Alignment explanation
Indices: 54722048--54722110 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
54722038 CTAAGATTAC
54722048 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
54722069 ATATCATATCTAATATTGC--
1 ATATCATATCTAAGATTGCAT
54722088 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
54722109 AT
1 AT
54722111 CCTCGAAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.47
21 20 0.53
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:54724221 original size:14 final size:15
Alignment explanation
Indices: 54724188--54724262 Score: 64
Period size: 14 Copynumber: 5.0 Consensus size: 15
54724178 TCTTTTTTTG
54724188 AATAATATTAATAAAT
1 AATAATA-TAATAAAT
*
54724204 AATAATATAAT-TAT
1 AATAATATAATAAAT
54724218 AATAATATAA-AAAT
1 AATAATATAATAAAT
* * *
54724232 GATAATAACAAAAAAT
1 AATAAT-ATAATAAAT
* *
54724248 TATAAAATAATAAAT
1 AATAATATAATAAAT
54724263 TTAAACTCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
14 19 0.40
15 14 0.29
16 15 0.31
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (15 bp):
AATAATATAATAAAT
Found at i:54725347 original size:19 final size:18
Alignment explanation
Indices: 54725312--54725348 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
54725302 TTTTTTAAAA
54725312 TATAAATTTTGAAATTTT
1 TATAAATTTTGAAATTTT
*
54725330 TATAAATATTTTAAATTTT
1 TATAAAT-TTTGAAATTTT
54725349 AACAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATAAATTTTGAAATTTT
Found at i:54725348 original size:18 final size:17
Alignment explanation
Indices: 54725285--54725349 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
54725275 TTATATAATT
*
54725285 TTTTTAAATTATTATAAT
1 TTTTTAAATT-TTATAAA
*
54725303 TTTTTAAA--ATATAAA
1 TTTTTAAATTTTATAAA
*
54725318 TTTTGAAATTTTTATAAA
1 TTTTTAAA-TTTTATAAA
54725336 TATTTTAAATTTTA
1 T-TTTTAAATTTTA
54725350 ACAATTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
15 12 0.32
18 20 0.53
19 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTTTAAATTTTATAAA
Found at i:54725358 original size:19 final size:20
Alignment explanation
Indices: 54725317--54725362 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
54725307 TAAAATATAA
* *
54725317 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAATTTTAACAAAT
*
54725337 ATTTT-AAATTTTAACAATT
1 ATTTTGAAATTTTAACAAAT
54725356 ATTTTGA
1 ATTTTGA
54725363 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
ATTTTGAAATTTTAACAAAT
Found at i:54725924 original size:19 final size:19
Alignment explanation
Indices: 54725900--54726012 Score: 156
Period size: 19 Copynumber: 5.8 Consensus size: 19
54725890 AATTTTTTAG
54725900 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
54725919 GATATGCAAT-TCAAGATAT
1 GATATGCAATCT-TAGATAT
54725938 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
54725959 GATATGCAATATTAGATAT
1 GATATGCAATCTTAGATAT
**
54725978 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
54725997 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
54726013 ATATATGATT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.01
19 64 0.78
21 16 0.20
22 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:54725945 original size:40 final size:40
Alignment explanation
Indices: 54725901--54726006 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
54725891 ATTTTTTAGG
54725901 ATATGCAATCTTAGATATGATATGCAAT-TCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATAT-AAGATATGAT
*
54725941 ATATGCAATCTTAGATATGATATGCAATATTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATATAAGATATGAT
54725981 ATAT--AATCTTAGATATGATATGCAAT
1 ATATGCAATCTTAGATATGATATGCAAT
54726007 CTTAGAATAT
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
38 22 0.34
40 41 0.64
41 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATATAAGATATGAT
Found at i:54726572 original size:18 final size:17
Alignment explanation
Indices: 54726529--54726572 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
54726519 TTGCAATTCA
*
54726529 ATTTAGTTTTTCTTTTC
1 ATTTATTTTTTCTTTTC
* *
54726546 TTTTCTTTTGTTCTTTTC
1 ATTTATTTT-TTCTTTTC
54726564 ATTTATTTT
1 ATTTATTTT
54726573 ATTAATTAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.75
Consensus pattern (17 bp):
ATTTATTTTTTCTTTTC
Found at i:54726822 original size:25 final size:26
Alignment explanation
Indices: 54726778--54726828 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
54726768 TGTACATGTA
54726778 TATATTTTTTTAAAACGAATATTTTCC
1 TATATTTTTTT-AAACGAATATTTTCC
*
54726805 TATATTTTTTT-AATGAATATTTTC
1 TATATTTTTTTAAACGAATATTTTC
54726829 ATATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
27 11 0.48
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (26 bp):
TATATTTTTTTAAACGAATATTTTCC
Found at i:54727627 original size:98 final size:98
Alignment explanation
Indices: 54727504--54727698 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
54727494 AAAAATCATG
*
54727504 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
54727569 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
* *
54727602 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
54727667 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
54727699 TTTATTGTAT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:54728645 original size:98 final size:98
Alignment explanation
Indices: 54728466--54728662 Score: 324
Period size: 98 Copynumber: 2.0 Consensus size: 98
54728456 GTACAATAAA
* *
54728466 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCGCGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * *
54728531 CCTTTAGAATCTCAAACTTGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
*
54728564 ACTTTAAAAGAACATCTCA-TTTTCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAAT
1 ACTTTAAAAGAACATC-CACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAAT
54728628 TCCTTTAAAATCCCAAACTCGGAATATTTCCTTT
65 TCCTTTAAAATCCCAAACTCGGAATATTTCCTTT
54728662 A
1 A
54728663 TTATTTTTAA
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 90 0.98
99 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:54729358 original size:22 final size:23
Alignment explanation
Indices: 54729333--54729381 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
54729323 ATATACATAT
54729333 AAATAT-GAAAATATTCA-TTAAA
1 AAATATAGAAAATATT-AGTTAAA
54729355 AAATATAGGAAAATATTAGTTAAA
1 AAATATA-GAAAATATTAGTTAAA
54729379 AAA
1 AAA
54729382 ATATTAGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.25
23 1 0.04
24 17 0.71
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (23 bp):
AAATATAGAAAATATTAGTTAAA
Found at i:54729384 original size:15 final size:15
Alignment explanation
Indices: 54729364--54729399 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54729354 AAAATATAGG
*
54729364 AAAATATTAGTTAAA
1 AAAATATTAGCTAAA
*
54729379 AAAATATTAGCTGAA
1 AAAATATTAGCTAAA
54729394 AAAATA
1 AAAATA
54729400 AGTATGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (15 bp):
AAAATATTAGCTAAA
Found at i:54729882 original size:10 final size:9
Alignment explanation
Indices: 54729866--54729892 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
54729856 CCTCCTCCTC
54729866 CTTTTTTTT
1 CTTTTTTTT
54729875 CTTTTTTTT
1 CTTTTTTTT
54729884 CTTTTTTTT
1 CTTTTTTTT
54729893 GTCACAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:54730057 original size:19 final size:19
Alignment explanation
Indices: 54730001--54730136 Score: 128
Period size: 19 Copynumber: 6.8 Consensus size: 19
54729991 AAATTAAATC
*
54730001 TCTAAGATTACAAAATCATATA
1 TCTAAGATTAC-ATATC--ATA
* *
54730023 TTCTAATATTGCATATCATA
1 -TCTAAGATTACATATCATA
*
54730043 TCTAAGATTATATATCATA
1 TCTAAGATTACATATCATA
*
54730062 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
54730081 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
** *
54730102 TCTTGGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
54730121 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
54730137 CTCAAAAATT
Statistics
Matches: 95, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
19 64 0.67
20 3 0.03
21 15 0.16
22 4 0.04
23 9 0.09
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:54730111 original size:40 final size:40
Alignment explanation
Indices: 54730024--54730135 Score: 183
Period size: 40 Copynumber: 2.9 Consensus size: 40
54730014 AATCATATAT
*
54730024 TCTAATATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
54730062 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
**
54730102 TCTTGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
54730136 CCTCAAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
38 27 0.39
40 42 0.61
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:54730368 original size:44 final size:44
Alignment explanation
Indices: 54730314--54730735 Score: 294
Period size: 44 Copynumber: 9.8 Consensus size: 44
54730304 CCATCTTCAG
* * *
54730314 TCTGCCCCACTGCAACTTCAGGAG-GATAGGACTTGCTTACTTAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTT-CTTAA
* * * *
54730358 TCTGCTCCACTGCAACTTCAGG-GAGATAAGACTAGATGC--GA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTCTTAA
* * *
54730399 TCTGCT-CTCTGCAACTTCA-GAGAGATAAGATCTGAGGTT-TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CT-TGCTTCTTAA
* * *
54730442 TCCGCTCCACTGCAACTTCAGG-GAGATAGGATTATCGGC-T-TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACT-T--GCTTCTTAA
* * * * *
54730486 TCTGCTCCACTGCAACTTCAAG-GAGATAAGACTAGATGC--GA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTCTTAA
* * *
54730527 TCTGCT-CTCTGCAACTTCA-GAGAGATAAGATCTGAGGTT-TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CT-TGCTTCTTAA
* * * * *
54730570 TCCGCTCTAATGCAACTTCAGG-GAGATAGGATTATCGGC-T-TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACT-T--GCTTCTTAA
* *
54730614 TCTGCTCCACTGCAACTTCAGG-GAGATAAGACTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTG-CTTCTT-AA
* *
54730659 TCTGCCCCACTGCAACTTCAGGAG-GATAAGACTTGCTTACTTAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTT-CTTAA
54730703 TCTGCTCCACTGCAACTTCAGG-GAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACT
54730736 AGATGCGATA
Statistics
Matches: 302, Mismatches: 48, Indels: 56
0.74 0.12 0.14
Matches are distributed among these distances:
39 2 0.01
40 42 0.14
41 19 0.06
42 7 0.02
43 19 0.06
44 172 0.57
45 40 0.13
46 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTCTTAA
Found at i:54730548 original size:128 final size:128
Alignment explanation
Indices: 54730358--54730646 Score: 551
Period size: 128 Copynumber: 2.3 Consensus size: 128
54730348 GCTTACTTAG
54730358 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
*
54730423 ATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
66 ATAAGATCTGAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
*
54730486 TCTGCTCCACTGCAACTTCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
*
54730551 ATAAGATCTGAGGTTTTAATCCGCTCTAATGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
66 ATAAGATCTGAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
54730614 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT
54730647 TGCCATCTTC
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 157 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (128 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
ATAAGATCTGAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
Found at i:54730946 original size:44 final size:44
Alignment explanation
Indices: 54730898--54731342 Score: 176
Period size: 44 Copynumber: 10.2 Consensus size: 44
54730888 TATCTTGGAA
* *
54730898 AGATAAGATTCGTCGTCTTCGATCTGCTTCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54730942 AGATAAGA-TC-TACAATCTTCAACCTTCTCCGCTGCTGCTGAGGG
1 AGATAAGATTCGT-C-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54730986 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
54731030 AGATAAGATT-G-CGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54731072 AGATAAGA-TC-TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGG
1 AGATAAGATTCGT-C-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
54731116 AGACAAGCTTGGT-GGCTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTCGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
54731159 AGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * *
54731203 AGATAAGA-TC-TACAATCTTCTA-CTTATCCGCTGCTGCTGAGGG
1 AGATAAGATTCGT-C-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
54731246 AGACAAGGCTTGGT-GGCTTAAATATGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
** *
54731290 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
54731334 AGATAAGAT
1 AGATAAGAT
54731343 CTACAATCTT
Statistics
Matches: 279, Mismatches: 84, Indels: 76
0.64 0.19 0.17
Matches are distributed among these distances:
40 6 0.02
41 3 0.01
42 38 0.14
43 68 0.24
44 137 0.49
45 15 0.05
46 11 0.04
47 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (44 bp):
AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:54730986 original size:132 final size:132
Alignment explanation
Indices: 54730806--54731448 Score: 1123
Period size: 132 Copynumber: 4.9 Consensus size: 132
54730796 TTGCAACTTC
* * *
54730806 AGGGAGATAGGATTTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
* *
54730871 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTTCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54730936 TT
131 TT
*
54730938 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
54731003 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATT-G-CGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54731066 TT
131 TT
54731068 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAA-GCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
* *
54731132 TTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54731197 TT
131 TT
* * *
54731199 AGGGAGATAAGATCTACAATCTTCTA-CTTATCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
* *
54731263 TTAAATATGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54731328 TT
131 TT
**
54731330 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAATCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
54731395 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGC
54731449 NNNNNNNNNN
Statistics
Matches: 486, Mismatches: 21, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
129 46 0.09
130 105 0.22
131 151 0.31
132 184 0.38
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
TT
Found at i:54742118 original size:74 final size:75
Alignment explanation
Indices: 54741982--54742126 Score: 274
Period size: 74 Copynumber: 1.9 Consensus size: 75
54741972 CGACACTTTA
54741982 TCCACCTTCCAAAAGTGACTGTGAAACCACGTGAGTAGAAGCTGTGCACATCCAATAAATCTACC
1 TCCACCTTCCAAAAGTGACTGTGAAACCACG-GAGTAGAAGCTGTGCACATCCAATAAATCTACC
54742047 TTCACCTGTCC
65 TTCACCTGTCC
54742058 TCCACCTTCCAAAAGTGACTGTGAAACCAC-GAGTAGAAGCTGTGCACATCCAATAAATCTACCT
1 TCCACCTTCCAAAAGTGACTGTGAAACCACGGAGTAGAAGCTGTGCACATCCAATAAATCTACCT
54742122 TCACC
66 TCACC
54742127 GTCTTCCGGC
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 39 0.57
76 30 0.43
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (75 bp):
TCCACCTTCCAAAAGTGACTGTGAAACCACGGAGTAGAAGCTGTGCACATCCAATAAATCTACCT
TCACCTGTCC
Found at i:54744099 original size:98 final size:97
Alignment explanation
Indices: 54743842--54744034 Score: 323
Period size: 97 Copynumber: 2.0 Consensus size: 97
54743832 GTACAATAAA
* * *
54743842 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGAATCAAGAAATCACACCCAATACGTTAGGGCACAATT
*
54743907 CCTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTAAAATCCCAAACTCGGAATATTTCCTTT
* *
54743939 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGAATCAAGAAATCACACCCAATACGTTAGGGCACAATT
54744004 CCTTTAAAATCCCAAACTCGGAATATTTCCT
66 CC-TTAAAATCCCAAACTCGGAATATTTCCT
54744035 ATTATTTTTA
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
97 66 0.71
98 27 0.29
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.27
Consensus pattern (97 bp):
ACTTTAAAAGAACATCCACTTATCCAAGAATCAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:54744711 original size:23 final size:23
Alignment explanation
Indices: 54744680--54744726 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
54744670 ATATACATAT
*
54744680 AATATGAAAATATTCATTAAAAA
1 AATAGGAAAATATTCATTAAAAA
* *
54744703 AATAGGAAAATATTCGTTTAAAA
1 AATAGGAAAATATTCATTAAAAA
54744726 A
1 A
54744727 TTTAAAAAAT
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:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (23 bp):
AATAGGAAAATATTCATTAAAAA
Found at i:54745408 original size:21 final size:19
Alignment explanation
Indices: 54745333--54745444 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
54745323 AATCATATAT
54745333 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
54745352 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
54745371 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54745390 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
54745411 TCTTGGATTGCATAT-ATA
1 TCTAAGATTGCATATCATA
54745429 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
54745445 CTCAAAAATT
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
18 16 0.20
19 49 0.60
21 17 0.21
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54769972 original size:45 final size:44
Alignment explanation
Indices: 54769877--54770030 Score: 185
Period size: 44 Copynumber: 3.5 Consensus size: 44
54769867 TCCGCTCTAA
* *
54769877 TGCAACTTCAGGGAGAT-AGA-TT--ATCGCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGACTTGCAT-AC-TTAGTCTGCTCCAC
*
54769919 TGCAACTTCAGGGAGATAAGACTTGCCAT-CTTCAGTCTGCCCCAC
1 TGCAACTTCAGGGAGATAAGACTTG-CATACTT-AGTCTGCTCCAC
*
54769964 TGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTGCTCCAC
1 TGCAACTTCAGGGA-GATAAGACTTGCATACTTAGTCTGCTCCAC
54770008 TGCAACTTCAGGGAGATAAGACT
1 TGCAACTTCAGGGAGATAAGACT
54770031 AGATGCGATA
Statistics
Matches: 99, Mismatches: 4, Indels: 16
0.83 0.03 0.13
Matches are distributed among these distances:
42 17 0.17
43 3 0.03
44 39 0.39
45 38 0.38
47 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGACTTGCATACTTAGTCTGCTCCAC
Found at i:54770015 original size:44 final size:45
Alignment explanation
Indices: 54769909--54770030 Score: 187
Period size: 45 Copynumber: 2.7 Consensus size: 45
54769899 ATCGCTTTAA
54769909 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAG
* *
54769954 TCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTG-CTTACTT-AG
1 TCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCCAT-CTTCAG
54769998 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT
54770031 AGATGCGATA
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
44 35 0.49
45 36 0.51
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAG
Found at i:54770241 original size:44 final size:44
Alignment explanation
Indices: 54770193--54770641 Score: 214
Period size: 44 Copynumber: 10.2 Consensus size: 44
54770183 TATCTTGGAA
* *
54770193 AGATAAGATTCGTCGTCTTCGATCTGCTTCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54770237 AGATAAGA-TC-TACAATCTTCAACCTTCTCCGCTACTACTGAGGG
1 AGATAAGATTCGT-C-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54770281 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
54770325 AGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54770369 AGATAAGA-TC-TACAATCTTCAACCTTCTCCGCTGCTGCTGAGGG
1 AGATAAGATTCGT-C-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54770413 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
54770457 AGATAAGATTCGCCGTCTTCTATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54770501 AGATAAGA-TC-TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGG
1 AGATAAGATTCGT-C-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
54770545 AGACAAGTCTTGGT-GGCTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATAAG-ATTCGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
54770589 AGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
54770633 AGATAAGAT
1 AGATAAGAT
54770642 CTACAATCTT
Statistics
Matches: 287, Mismatches: 82, Indels: 72
0.65 0.19 0.16
Matches are distributed among these distances:
42 20 0.07
43 33 0.11
44 201 0.70
45 14 0.05
46 16 0.06
47 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (44 bp):
AGATAAGATTCGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:54770281 original size:132 final size:132
Alignment explanation
Indices: 54770101--54770885 Score: 1363
Period size: 132 Copynumber: 5.9 Consensus size: 132
54770091 TTGCAACTTC
* * *
54770101 AGGGAGATAGGATTTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
* *
54770166 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTTCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54770231 TT
131 TT
* * *
54770233 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTACTACTGAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
* *
54770298 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54770363 TT
131 TT
*
54770365 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
*
54770430 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCTATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54770495 TT
131 TT
*
54770497 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGTCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
* *
54770562 TTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54770627 TT
131 TT
* * * *
54770629 AGGGAGATAAGATCTACAATCTTCTACTTTATCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
* *
54770694 TTAAATATGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54770759 TT
131 TT
**
54770761 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAATCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
54770826 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
54770886 GTCAACGCAG
Statistics
Matches: 618, Mismatches: 35, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 618 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
TT
Found at i:54770652 original size:44 final size:43
Alignment explanation
Indices: 54770193--54770811 Score: 191
Period size: 44 Copynumber: 14.1 Consensus size: 43
54770183 TATCTTGGAA
* *
54770193 AGATAAGATTCGTC-GTCTTCGATCTGCTTCACTACTGCTTAGGG
1 AGATAAGA-TC-TCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54770237 AGATAAGATCTACAATCTTCAACCTTCTCCGCTACTACTGAGGG
1 AGATAAGATCT-CAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * *
54770281 AGACAAG-GCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATCTCAGT--CTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
54770325 AGATAAGATTTGTC-GTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGA--TCTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54770369 AGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGG
1 AGATAAGATCT-CAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * *
54770413 AGACAAG-GCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATCTCAGT--CTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * *
54770457 AGATAAGATTCGCCGTCTTCTATCTGCTCCACTACTGCTTAGGG
1 AGATAAGA-TCTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54770501 AGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGG
1 AGATAAGATCT-CAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * *
54770545 AGACAAG-TCTTGGTGGCTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATAAGATCTCAGT--CTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
54770589 AGATAAGATTCGTC-GTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGA-TC-TCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * *
54770633 AGATAAGATCTACAATCTTCTA-CTTTATCCGCTGCTGCTGAGGG
1 AGATAAGATCT-CAGTCTTCAATC-TGCTCCACTACTGCTTAGGG
* * ** * * *
54770677 AGACAAG-GCTTGGTGGCTTAAATATGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATCTCAGT--CTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
54770721 AGATAAGAT-TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATCTCA--GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
54770765 AGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGG
1 AGATAAGATCT-CAGTCTTCAATCTGCTCCACTACTGCTTAGGG
54770809 AGA
1 AGA
54770812 CAAATCTTGG
Statistics
Matches: 405, Mismatches: 116, Indels: 108
0.64 0.18 0.17
Matches are distributed among these distances:
42 32 0.08
43 35 0.09
44 289 0.71
45 17 0.04
46 30 0.07
47 2 0.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (43 bp):
AGATAAGATCTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:54775703 original size:13 final size:13
Alignment explanation
Indices: 54775685--54775709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54775675 GAATTTACTT
54775685 GTGTGAAAATTTC
1 GTGTGAAAATTTC
54775698 GTGTGAAAATTT
1 GTGTGAAAATTT
54775710 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:54777372 original size:41 final size:41
Alignment explanation
Indices: 54777327--54777486 Score: 223
Period size: 41 Copynumber: 3.9 Consensus size: 41
54777317 ATTATTCAGA
*
54777327 CTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCGGG
1 CTATACGTCTAGCAGGCTAAATGCCGGTGAACTGAATCGGG
* *
54777368 CTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCGGA
1 CTATACGTCTAGCAGGCTAAATGCCGGTGAACTGAATCGGG
* * *
54777409 CTATACGTCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGG
1 CTATACGTCTAGCAGGCTAAATGCCGGTGAACTGAATCGGG
* * *
54777450 CTACAAG-CTTAGCAGGCTAAGTGCCGGTGAACTGAAT
1 CTATACGTC-TAGCAGGCTAAATGCCGGTGAACTGAAT
54777487 TAAACTATAA
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 1 0.01
41 108 0.99
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CTATACGTCTAGCAGGCTAAATGCCGGTGAACTGAATCGGG
Found at i:54783351 original size:13 final size:13
Alignment explanation
Indices: 54783333--54783357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54783323 GAATTTACTT
54783333 GTGTGAAAATTTC
1 GTGTGAAAATTTC
54783346 GTGTGAAAATTT
1 GTGTGAAAATTT
54783358 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:54785103 original size:41 final size:41
Alignment explanation
Indices: 54784974--54785094 Score: 215
Period size: 41 Copynumber: 3.0 Consensus size: 41
54784964 AAATTATTCA
54784974 GACTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCG
*
54785015 GGCTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCG
* *
54785056 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAAT
1 GACTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAAT
54785095 TAAACTATAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (41 bp):
GACTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCG
Found at i:54785129 original size:82 final size:81
Alignment explanation
Indices: 54784956--54785130 Score: 199
Period size: 82 Copynumber: 2.1 Consensus size: 81
54784946 TCGGATTTAT
* * ***
54784956 TGCCAGTGAAATTATTCAGACTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCGGGCTAT
1 TGCCAGTG-AATTAATCAGACTATACGTCTAGCAGGCTAAATGCCGGTGAACTGAATCAAACTAT
* *
54785021 ACGTCTAGCAGGCTAAA
65 AAGCCTAGCAGGCTAAA
* * * *
54785038 TGCCGGTGAATTGAATCGGACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATTAAACTAT
1 TGCCAGTGAATT-AATCAGACTATACGTCTAGCAGGCTAAATGCCGGTGAACTGAATCAAACTAT
* *
54785103 AAGCCTATCAGG-TGAAG
65 AAGCCTAGCAGGCT-AAA
54785120 TGCCAGTGAAT
1 TGCCAGTGAAT
54785131 CTGTTTAAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
81 5 0.06
82 72 0.94
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (81 bp):
TGCCAGTGAATTAATCAGACTATACGTCTAGCAGGCTAAATGCCGGTGAACTGAATCAAACTATA
AGCCTAGCAGGCTAAA
Found at i:54786678 original size:76 final size:76
Alignment explanation
Indices: 54786552--54786706 Score: 310
Period size: 76 Copynumber: 2.0 Consensus size: 76
54786542 CGACACTTTA
54786552 TCCACCTTCCAAAAGTGACTGTGAAACCACGTGAGTAGAAGCTGTGCACATCCAATAAATCTACC
1 TCCACCTTCCAAAAGTGACTGTGAAACCACGTGAGTAGAAGCTGTGCACATCCAATAAATCTACC
54786617 TTCACCTGTCC
66 TTCACCTGTCC
54786628 TCCACCTTCCAAAAGTGACTGTGAAACCACGTGAGTAGAAGCTGTGCACATCCAATAAATCTACC
1 TCCACCTTCCAAAAGTGACTGTGAAACCACGTGAGTAGAAGCTGTGCACATCCAATAAATCTACC
54786693 TTCACCTGTCC
66 TTCACCTGTCC
54786704 TCC
1 TCC
54786707 GGCATGCACT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (76 bp):
TCCACCTTCCAAAAGTGACTGTGAAACCACGTGAGTAGAAGCTGTGCACATCCAATAAATCTACC
TTCACCTGTCC
Found at i:54789330 original size:25 final size:25
Alignment explanation
Indices: 54789300--54789348 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
54789290 ATATAAATAT
54789300 GAAAATATTCA-TTAAAAAAATATAG
1 GAAAATATT-AGTTAAAAAAATATAG
54789325 GAAAATATTAGTTTAAAAAAATAT
1 GAAAATATTAG-TTAAAAAAATAT
54789349 TAGCTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 1 0.05
25 9 0.41
26 12 0.55
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (25 bp):
GAAAATATTAGTTAAAAAAATATAG
Found at i:54789358 original size:16 final size:16
Alignment explanation
Indices: 54789326--54789360 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54789316 AAAATATAGG
* *
54789326 AAAATATTAGTTTAAA
1 AAAATATTAGCTGAAA
54789342 AAAATATTAGCTGAAA
1 AAAATATTAGCTGAAA
54789358 AAA
1 AAA
54789361 TAAGTATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (16 bp):
AAAATATTAGCTGAAA
Found at i:54790008 original size:19 final size:19
Alignment explanation
Indices: 54789984--54790096 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
54789974 AATCATATAT
54789984 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
54790003 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
54790022 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54790041 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
** *
54790062 TCTTGGATTGCATATTATA
1 TCTAAGATTGCATATCATA
54790081 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
54790097 CTCAAAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 65 0.79
21 17 0.21
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54790071 original size:40 final size:40
Alignment explanation
Indices: 54789984--54790095 Score: 183
Period size: 40 Copynumber: 2.9 Consensus size: 40
54789974 AATCATATAT
54789984 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
54790022 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
** *
54790062 TCTTGGATTGCATATTATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
54790096 CCTCAAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
38 28 0.41
40 41 0.59
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:54801798 original size:24 final size:27
Alignment explanation
Indices: 54801756--54801804 Score: 77
Period size: 24 Copynumber: 1.9 Consensus size: 27
54801746 ACATCGATCT
54801756 ATTCACATTATAAATAACA-TAATAAC
1 ATTCACATTATAAATAACATTAATAAC
54801782 ATTCA-ATT-TAAATAACATTAATA
1 ATTCACATTATAAATAACATTAATA
54801805 CGATAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 8 0.36
26 5 0.23
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTCACATTATAAATAACATTAATAAC
Found at i:54807623 original size:98 final size:98
Alignment explanation
Indices: 54807454--54807648 Score: 336
Period size: 98 Copynumber: 2.0 Consensus size: 98
54807444 ATACAATAAA
* * *
54807454 ACTTTAAAAGAACATTCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACAATC
54807519 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
54807552 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACAATC
*
54807617 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
54807649 CATGATTTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:54808347 original size:25 final size:25
Alignment explanation
Indices: 54808317--54808365 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
54808307 ATATAAATAT
54808317 GAAAATATTCATTAAAAAAATATAG
1 GAAAATATTCATTAAAAAAATATAG
* **
54808342 GAAAATATTCGTTTTAAAAATATA
1 GAAAATATTCATTAAAAAAATATA
54808366 TATATACGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (25 bp):
GAAAATATTCATTAAAAAAATATAG
Found at i:54809126 original size:19 final size:19
Alignment explanation
Indices: 54809102--54809195 Score: 152
Period size: 19 Copynumber: 4.8 Consensus size: 19
54809092 AATCATATAT
54809102 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54809121 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
54809142 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
54809161 TCTAGGATTGTATATCATA
1 TCTAAGATTGCATATCATA
54809180 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
54809196 CTCAAAAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 50 0.72
21 19 0.28
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54809150 original size:40 final size:38
Alignment explanation
Indices: 54809102--54809195 Score: 161
Period size: 40 Copynumber: 2.4 Consensus size: 38
54809092 AATCATATAT
54809102 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTG--TATATCATA
*
54809142 TCTAAGATTGCATATCATATCTAGGATTGTATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGTATATCATA
54809180 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
54809196 CTCAAAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
38 25 0.47
40 28 0.53
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTGTATATCATA
Found at i:54813137 original size:14 final size:14
Alignment explanation
Indices: 54813120--54813174 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
54813110 ACAACGAAGT
54813120 AAAAGAAAGAAAGG
1 AAAAGAAAGAAAGG
*
54813134 AAAAAAAAGAAAGG
1 AAAAGAAAGAAAGG
*
54813148 AAAAGAAA-AGAGG
1 AAAAGAAAGAAAGG
54813161 AAAAAGAAGAGAAA
1 -AAAAGAA-AGAAA
54813175 CGAACGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 4 0.12
14 27 0.79
15 1 0.03
16 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAGG
Done.