Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022633.1 Corchorus olitorius cultivar O-4 contig22666, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 163261
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:612 original size:19 final size:18
Alignment explanation
Indices: 579--614 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
569 TGGAAATAAT
579 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
597 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
615 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:4365 original size:21 final size:21
Alignment explanation
Indices: 4339--4380 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4329 GCACAAAGAA
4339 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
4360 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
4381 TCTAAGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:13061 original size:14 final size:14
Alignment explanation
Indices: 13042--13068 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13032 GTAACATTAG
13042 TTTATTTTTTTTAT
1 TTTATTTTTTTTAT
13056 TTTATTTTTTTTA
1 TTTATTTTTTTTA
13069 GTTTGATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTATTTTTTTTAT
Found at i:13566 original size:2 final size:2
Alignment explanation
Indices: 13559--13600 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
13549 AATCAATTAA
13559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13601 GCTAGGAGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14227 original size:17 final size:17
Alignment explanation
Indices: 14181--14233 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
14171 AACCCATGTA
*
14181 ATCTTTGATCACCGGTG
1 ATCTTTGATCACTGGTG
14198 AT-TTTGCATCACTGGTG
1 ATCTTTG-ATCACTGGTG
* *
14215 ATCTTAGATCACTAGTG
1 ATCTTTGATCACTGGTG
14232 AT
1 AT
14234 GATCCTAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 4 0.13
17 24 0.77
18 3 0.10
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (17 bp):
ATCTTTGATCACTGGTG
Found at i:17055 original size:12 final size:12
Alignment explanation
Indices: 17038--17065 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17028 CGAGTTGGTC
17038 TCAGGAGTTAAT
1 TCAGGAGTTAAT
17050 TCAGGAGTTAAT
1 TCAGGAGTTAAT
17062 TCAG
1 TCAG
17066 AGACAAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (12 bp):
TCAGGAGTTAAT
Found at i:19663 original size:16 final size:15
Alignment explanation
Indices: 19626--19665 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
19616 GATTAAATAG
19626 AACAATTATAAAGAA
1 AACAATTATAAAGAA
*
19641 ACGCAATTATAAAGGAA
1 A-ACAATTATAAA-GAA
19658 AACAATTA
1 AACAATTA
19666 AAATAAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (15 bp):
AACAATTATAAAGAA
Found at i:21049 original size:19 final size:18
Alignment explanation
Indices: 21012--21051 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
21002 TTCTTGAAAT
*
21012 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
21030 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
21049 AAT
1 AAT
21052 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:27690 original size:21 final size:21
Alignment explanation
Indices: 27652--27692 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27642 AAACAATAGG
**
27652 AAAGATTGAAAATGGAAGAAA
1 AAAGATTGAAAAAAGAAGAAA
*
27673 AAAGGTTGAAAAAAGAAGAA
1 AAAGATTGAAAAAAGAAGAA
27693 GAGAGCGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAGATTGAAAAAAGAAGAAA
Found at i:34601 original size:246 final size:246
Alignment explanation
Indices: 34285--34777 Score: 887
Period size: 246 Copynumber: 2.0 Consensus size: 246
34275 TCTCTATCAT
* *
34285 AAACAATGGTTTTAGGCATTCCATGCAATCTAACAATCTCCCTAAATAACAAGTTAGCTACATTA
1 AAACAATGGTTCTAGGCATTCCATGCAATCTAACAATCTCCCTAAAGAACAAGTTAGCTACATTA
*
34350 ATGGCATCATCAGTCTTAGAACATGCAATAAAGTGTGCCATTTTAGAAAACCTGTCAACAACAAC
66 ATGGCATCATCAGTCTTAGAACATGCAATAAAGTGTGCCATCTTAGAAAACCTGTCAACAACAAC
* * *
34415 AAAAACAGAATCTTTACCTCTCCTAGAATGAGGCAAACCTAACACAAAATCCATGCTAATGTGTG
131 AAAAACAAAATCATTACCTCTCCTAGAACGAGGCAAACCTAACACAAAATCCATGCTAATGTGTG
* *
34480 TCTATGGTTCATGAGGTATAGGCAAAGGTGTATACAATCCATGAGGTTTAG
196 TCCATGGTTCATGAGGTATAGGCAAAGATGTATACAATCCATGAGGTTTAG
*
34531 AAACAATGGTTCTAGGCATTCCATGCAATCTAACAATTTCCCTAAAGAACAAGTTAGCTACATTA
1 AAACAATGGTTCTAGGCATTCCATGCAATCTAACAATCTCCCTAAAGAACAAGTTAGCTACATTA
* *
34596 ATGGCATCATCGGTCTTAGAACATGCAATAAAGTGTGCCATCTTAGAAAACCTGTCAACCACAAC
66 ATGGCATCATCAGTCTTAGAACATGCAATAAAGTGTGCCATCTTAGAAAACCTGTCAACAACAAC
34661 AAAAACAAAATCATTACCTCTCCTAGAACGAGGCAAACCTAACACAAAATCCATGCTAATGTGTG
131 AAAAACAAAATCATTACCTCTCCTAGAACGAGGCAAACCTAACACAAAATCCATGCTAATGTGTG
34726 TCCATGGTTCATGAGGTATAGGCAAAGATGTATACAATCCATGAGGTTTAG
196 TCCATGGTTCATGAGGTATAGGCAAAGATGTATACAATCCATGAGGTTTAG
34777 A
1 A
34778 TATAGATTTA
Statistics
Matches: 236, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
246 236 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (246 bp):
AAACAATGGTTCTAGGCATTCCATGCAATCTAACAATCTCCCTAAAGAACAAGTTAGCTACATTA
ATGGCATCATCAGTCTTAGAACATGCAATAAAGTGTGCCATCTTAGAAAACCTGTCAACAACAAC
AAAAACAAAATCATTACCTCTCCTAGAACGAGGCAAACCTAACACAAAATCCATGCTAATGTGTG
TCCATGGTTCATGAGGTATAGGCAAAGATGTATACAATCCATGAGGTTTAG
Found at i:38560 original size:138 final size:138
Alignment explanation
Indices: 38312--38611 Score: 573
Period size: 138 Copynumber: 2.2 Consensus size: 138
38302 ATCTTTCAAG
*
38312 CTCACATGAGACACTCCCGTGTCATTCTCCTCCGGTTGAAAAAGAAAAATGGGCATCTCCTCATG
1 CTCACATGGGACACTCCCGTGTCATTCTCCTCCGGTTGAAAAAGAAAAATGGGCATCTCCTCATG
* *
38377 ATAGGGCAACGCATGGGCAAACTCTTGTAGCATGGGAAACTCTAATGGATGGATGTCCATGAGAT
66 ATAGGGCAACACATGGGCAAACTCTTGTAGCATGGGAAACTCTAATGGATGGATGTCCATGAAAT
38442 ATGATGAA
131 ATGATGAA
38450 CTCACATGGGACACTCCCGTGTCATTCTCCTCCGGTTGAAAAAGAAAAATGGGCATCTCCTCATG
1 CTCACATGGGACACTCCCGTGTCATTCTCCTCCGGTTGAAAAAGAAAAATGGGCATCTCCTCATG
38515 ATAGGGCAACACATGGGCAAACTCTTGTAGCATGGGAAACTCTAATGGATGGATGTCCATGAAAT
66 ATAGGGCAACACATGGGCAAACTCTTGTAGCATGGGAAACTCTAATGGATGGATGTCCATGAAAT
38580 ATGATGAA
131 ATGATGAA
38588 CTCACATGGGACACTCCCGTGTCA
1 CTCACATGGGACACTCCCGTGTCA
38612 ACTCTCAATT
Statistics
Matches: 159, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 159 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (138 bp):
CTCACATGGGACACTCCCGTGTCATTCTCCTCCGGTTGAAAAAGAAAAATGGGCATCTCCTCATG
ATAGGGCAACACATGGGCAAACTCTTGTAGCATGGGAAACTCTAATGGATGGATGTCCATGAAAT
ATGATGAA
Found at i:39542 original size:21 final size:21
Alignment explanation
Indices: 39516--39558 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
39506 TTTCCCGCAA
*
39516 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGACTTGT
*
39537 CAAGTCTTGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGACTTGT
39558 C
1 C
39559 TTGTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.35, T:0.26
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGACTTGT
Found at i:48544 original size:407 final size:409
Alignment explanation
Indices: 47862--48596 Score: 1063
Period size: 407 Copynumber: 1.8 Consensus size: 409
47852 TAAAAATAGT
* * *
47862 TAGGGCAAGTAGGGGTCGAACCCACAGAGAGATAGTTTATTATTCTTTTTCTTAAAACAATCAAA
1 TAGGGCAAGTAGGGGTCGAACCCACAGAGAGAAAGGTTATTATTCTTTTTCTTAAAACAAGCAAA
*
47927 CAAAATAAAGAGAATTTTTTAAAAGTAAAATTAAATCAAATCAAATTAACAATTAAAATTAACTA
66 CAAAATAAAGAGAATTTTTTAAAAGTAAAATTAAATCAAATCAAACTAACAATTAAAATTAACTA
* * * *
47992 AGAAAACAATCAAGAAAATTTAGGAAAACAATCAATCAGAAAGCAGTGAAAAAGTTAAGAAAATA
131 AGAAAACAATCAAGAAAATTAAAGAAAACAATCAATCAGAAAGCAGTGAAAAAGTCAAGAAAACA
* *
48057 ATTAAGAAAATCCTCCAAGATAGAATTAATATCCCTCTTGACAAGAATAACATGGATCATTGATA
196 ATTAAGAAAAACCTCCAACATAGAATTAATATCCCTCTTGACAAGAATAACATGGATCATTGATA
* *
48122 TCTAAGAATTATGAAAACA-ATGGATAGTTTGTTTGGAATTAAATCCTAAATTACC-TAGATTAA
261 TCTAAGAATTATGAAAACATA-GAATAGCTTG-TTGGAATTAAATCCTAAATTACCTTA-ATTAA
48185 ATAAGACTCTTGATCCGGTGTGAATTATTGATTGGTCGTCAGCAAATCATAAAAATAAAATCCCA
323 ATAAGACTCTTGATCCGGTGTGAATTATTGATTGGTCGTCAGCAAATCATAAAAATAAAATCCCA
48250 ACAAAATCCTAACTAGAGCAAA
388 ACAAAATCCTAACTAGAGCAAA
* *
48272 TAGGGTAAGTAGGGGTCGAACCCACAGAGAGAAAGGTTATT-TATCTTTTTCTTAAAACAGGCAA
1 TAGGGCAAGTAGGGGTCGAACCCACAGAGAGAAAGGTTATTAT-TCTTTTTCTTAAAACAAGCAA
* * * * * * * *
48336 AGAAATTAAAGAGAA-TTTTT-ATAGTGAAATTAAATCTAATCTAACTAACAATTAGAGTTAACT
65 ACAAAATAAAGAGAATTTTTTAAAAGTAAAATTAAATCAAATCAAACTAACAATTAAAATTAACT
* * ** * *
48399 AAGAAAGCAATCAAGAAAATTAAAGAAATCAATTGATTATG-AAGCA-TTAAATAA-TCAAGAAA
130 AAGAAAACAATCAAGAAAATTAAAGAAAACAATCAATCA-GAAAGCAGTGAAA-AAGTCAAGAAA
* **
48461 ACAATTAATAAAAACCTCCAACATAGAATTAATATCCCTCTTGACAATTATAACATGGATCATTG
193 ACAATTAAGAAAAACCTCCAACATAGAATTAATATCCCTCTTGACAAGAATAACATGGATCATTG
* *
48526 ATATCTAATAATTATGAAATCATAGAATAGCTTGTTGGAATTAAATCCTAAATTACCTTAATTAA
258 ATATCTAAGAATTATGAAAACATAGAATAGCTTGTTGGAATTAAATCCTAAATTACCTTAATTAA
48591 ATAAGA
323 ATAAGA
48597 TTACCGGTTA
Statistics
Matches: 287, Mismatches: 33, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
406 34 0.12
407 100 0.35
408 76 0.26
409 7 0.02
410 70 0.24
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (409 bp):
TAGGGCAAGTAGGGGTCGAACCCACAGAGAGAAAGGTTATTATTCTTTTTCTTAAAACAAGCAAA
CAAAATAAAGAGAATTTTTTAAAAGTAAAATTAAATCAAATCAAACTAACAATTAAAATTAACTA
AGAAAACAATCAAGAAAATTAAAGAAAACAATCAATCAGAAAGCAGTGAAAAAGTCAAGAAAACA
ATTAAGAAAAACCTCCAACATAGAATTAATATCCCTCTTGACAAGAATAACATGGATCATTGATA
TCTAAGAATTATGAAAACATAGAATAGCTTGTTGGAATTAAATCCTAAATTACCTTAATTAAATA
AGACTCTTGATCCGGTGTGAATTATTGATTGGTCGTCAGCAAATCATAAAAATAAAATCCCAACA
AAATCCTAACTAGAGCAAA
Found at i:51683 original size:9 final size:9
Alignment explanation
Indices: 51669--51698 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
51659 AATTTCGGAT
51669 TTGCTTTGA
1 TTGCTTTGA
51678 TTGCTTTGA
1 TTGCTTTGA
51687 TTGCTTTGA
1 TTGCTTTGA
51696 TTG
1 TTG
51699 TTGGCTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.57
Consensus pattern (9 bp):
TTGCTTTGA
Found at i:56415 original size:36 final size:36
Alignment explanation
Indices: 56364--56468 Score: 124
Period size: 36 Copynumber: 2.9 Consensus size: 36
56354 AATCAAAGCT
* *
56364 CTTTCATCATTCAACACTTGGGGTCTCCAGCAACCC
1 CTTTCATCATTCAACACTTGGGGGCTCCAACAACCC
* **
56400 CTTTCATCATACAACA-TTCGGGGGCTCCAACAATTC
1 CTTTCATCATTCAACACTT-GGGGGCTCCAACAACCC
* *
56436 C-TTCATCATTCAACGCTTGGGGGCTTCAACAAC
1 CTTTCATCATTCAACACTTGGGGGCTCCAACAAC
56469 AAAAAGTTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
35 27 0.47
36 31 0.53
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (36 bp):
CTTTCATCATTCAACACTTGGGGGCTCCAACAACCC
Found at i:59526 original size:12 final size:11
Alignment explanation
Indices: 59498--59523 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59488 TGAAAAATTC
59498 AAAATTTTCAA
1 AAAATTTTCAA
59509 AAAATTTTCAA
1 AAAATTTTCAA
59520 AAAA
1 AAAA
59524 ATTATGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTTTCAA
Found at i:60366 original size:21 final size:21
Alignment explanation
Indices: 60342--60395 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
60332 AATGACCGGT
* *
60342 GATGGCCGGGCTTGGTGTGAG
1 GATGGCCGGGCCTGGTGCGAG
* *
60363 GATGGTCGGGCCTGGTGCGCG
1 GATGGCCGGGCCTGGTGCGAG
60384 GATGGCCGGGCC
1 GATGGCCGGGCC
60396 ATAGCCGGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (21 bp):
GATGGCCGGGCCTGGTGCGAG
Found at i:63729 original size:41 final size:41
Alignment explanation
Indices: 63670--63762 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
63660 TTTGCTTCAT
* *
63670 TTTATTCCCTGATTTAGGATTCTATTTACTATTTGATGCAA
1 TTTAGTCCCTGATTTAGGATTCTAGTTACTATTTGATGCAA
* *
63711 TTTAGTCCCTGATTTAGGATTTTAGTTACTATTTGATTCAA
1 TTTAGTCCCTGATTTAGGATTCTAGTTACTATTTGATGCAA
*
63752 TTTGGTCCCTG
1 TTTAGTCCCTG
63763 GTTTTAGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (41 bp):
TTTAGTCCCTGATTTAGGATTCTAGTTACTATTTGATGCAA
Found at i:64527 original size:26 final size:29
Alignment explanation
Indices: 64466--64541 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 29
64456 CTTAAGCAAA
64466 TCCAAAAGAAGATTTTGGAAAAGAAGGTAAC
1 TCCAAAAGAAGATTTTGGAAAAGAA-G-AAC
*
64497 TCCAAAAGAAGATTTTGGAAAA-TA-AAC
1 TCCAAAAGAAGATTTTGGAAAAGAAGAAC
64524 -CCAAAAGAAGATTTTGGA
1 TCCAAAAGAAGATTTTGGA
64542 GGTTAATAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 18 0.41
27 3 0.07
30 1 0.02
31 22 0.50
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.21
Consensus pattern (29 bp):
TCCAAAAGAAGATTTTGGAAAAGAAGAAC
Found at i:69914 original size:16 final size:15
Alignment explanation
Indices: 69876--69917 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
69866 ACAGAGATTG
*
69876 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
69891 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
69906 ACTAGAAAACAA
1 AC-AGAAAACAA
69918 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:72802 original size:14 final size:15
Alignment explanation
Indices: 72783--72812 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
72773 CAATCAAAGC
72783 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
72797 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
72812 A
1 A
72813 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:75709 original size:32 final size:30
Alignment explanation
Indices: 75646--75734 Score: 87
Period size: 32 Copynumber: 3.0 Consensus size: 30
75636 AAAATAAAGG
* *
75646 AAATATTTTTTTTTCTAAAAACGCAGGAAC
1 AAATTTTTTTTTTTCTAAAAACGCAGAAAC
* *
75676 AAGAATTTTTTTTTTTTTAGAAAATGCA-AAAC
1 -A-AATTTTTTTTTTTCTA-AAAACGCAGAAAC
75708 AAA-TTTTTTTTTTC-AAAAACGCA-AAAC
1 AAATTTTTTTTTTTCTAAAAACGCAGAAAC
75735 TAATAAATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 11 0.22
28 1 0.02
29 10 0.20
30 2 0.04
31 2 0.04
32 17 0.34
33 7 0.14
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (30 bp):
AAATTTTTTTTTTTCTAAAAACGCAGAAAC
Found at i:75789 original size:26 final size:27
Alignment explanation
Indices: 75744--75797 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
75734 CTAATAAATT
**
75744 AAAAACGCAAGAAATTTTTTTTTTATG
1 AAAAACGCAAGAAACCTTTTTTTTATG
75771 AAAAACGCAA-AAACCTTTTTTTTATG
1 AAAAACGCAAGAAACCTTTTTTTTATG
75797 A
1 A
75798 CGCAAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (27 bp):
AAAAACGCAAGAAACCTTTTTTTTATG
Found at i:76241 original size:16 final size:15
Alignment explanation
Indices: 76203--76244 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
76193 ACAGAGATTG
*
76203 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
76218 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
76233 ACTAGAAAACAA
1 AC-AGAAAACAA
76245 AGTAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:82101 original size:67 final size:66
Alignment explanation
Indices: 81992--82210 Score: 294
Period size: 67 Copynumber: 3.3 Consensus size: 66
81982 TTTTAGAAGT
*
81992 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAGGA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTC-AAAGTTGATTGGAAGACAATCTCATTAAGGA
82057 AC
65 AC
* *
82059 ACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAGGGA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAA-GTTGATTGGAAGACAATCTCATTAAGGA
82124 AC
65 AC
** * * * **
82126 ACATTGGAAGACGGTTTGCTAGAAAGAATTCTCAGAAGTTGGTTGGAAGACGATCTCATTAAAAA
1 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCA-AAGTTGATTGGAAGACAATCTCATTAAGGA
*
82191 AGT
65 A-C
*
82194 ACACCGGAAGATGGTTT
1 ACACCGGAAGACGGTTT
82211 CTCAACAATT
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
66 3 0.02
67 114 0.86
68 16 0.12
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (66 bp):
ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAGTTGATTGGAAGACAATCTCATTAAGGAA
C
Found at i:82275 original size:64 final size:64
Alignment explanation
Indices: 82152--82571 Score: 445
Period size: 64 Copynumber: 6.5 Consensus size: 64
82142 TGCTAGAAAG
* * * * *
82152 AATTCTCAGAAGTTGGTTGGAAGACGATCTCAT-TAAAAAAGTACACCGGAAGATGGTTTCTCAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCT--TGTCAAAAAGTACACCAGAAGATGGTTTCTCAA
82216 C
64 C
*
82217 AATTTTCAGAAGATGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAAC
* * * * *
82281 AGTTTTCAGAAGTTGATCGAAAGACGATCTTGTTAAGGAA-TACACCAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAA-AAAGTACACCAGAAGATGGTTTCTCAAC
* * * *
82345 AATTTTCAGAAGTTGATCGGAAGACGATCTTATGAAGAAGTACATCCA-AAGATGGTTTTCCCAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACA-CCAGAAGATGG-TTTCTCAA
*
82409 G
64 C
* * * * * * * * * *
82410 AGTGTTCAGAAATTGATCGGAAGACGAACTTGTCAAAAA-TACGCTAGAAGATAGTCTCTTAGC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAAC
* * * * *
82473 AACTTTCAGATGTTGATCGGAAGACAATCTTGTCAAAAGGTACACCAGAAGATAGTTTCTCGAA-
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTC-AAC
*
82537 AAGGTTTCAGAAGTTGATTCGGAAGACGATCTTGT
1 AA-TTTTCAGAAGTTGA-TCGGAAGACGATCTTGT
82572 TAAGAGATGC
Statistics
Matches: 296, Mismatches: 49, Indels: 19
0.81 0.13 0.05
Matches are distributed among these distances:
63 41 0.14
64 156 0.53
65 83 0.28
66 16 0.05
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAAC
Found at i:82349 original size:128 final size:128
Alignment explanation
Indices: 82157--82590 Score: 494
Period size: 128 Copynumber: 3.4 Consensus size: 128
82147 GAAAGAATTC
* * ** * *
82157 TCAGAAGTTGGTTGGAAGACGATCTCATTAAAAAAGTACACCGGAAGATGGTTTCTCAACAATTT
1 TCAGAAGTTGATCGGAAGACGATCTTGTTAAGAAA-TACACCAGAAGATGGTTTCTCAACAATTT
* *
82222 TCAGAAGATGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAACAGTTT
65 TCAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAAAAGTTT
* * *
82286 TCAGAAGTTGATCGAAAGACGATCTTGTTAAGGAATACACCAGAAGATGGTTTCTCAAAAATTTT
1 TCAGAAGTTGATCGGAAGACGATCTTGTTAAGAAATACACCAGAAGATGGTTTCTCAACAATTTT
* * * * * *
82351 CAGAAGTTGATCGGAAGACGATCTTATGAAGAAGTACATCCA-AAGATGGTTTTCCCAAGAGTGT
66 CAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACA-CCAGAAGATGG-TTTCTCAAAAGTTT
* * * * * * * * * *
82415 TCAGAAATTGATCGGAAGACGAACTTGTCAA-AAATACGCTAGAAGATAGTCTCTTAGCAACTTT
1 TCAGAAGTTGATCGGAAGACGATCTTGTTAAGAAATACACCAGAAGATGGTTTCTCAACAATTTT
* * * * *
82479 CAGATGTTGATCGGAAGACAATCTTGTCAAAAGGTACACCAGAAGATAGTTTCTCGAAAAGGTT
66 CAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTC-AAAAGTTT
* * *
82543 TCAGAAGTTGATTCGGAAGACGATCTTGTTAAGAGATGCACCGGAAGA
1 TCAGAAGTTGA-TCGGAAGACGATCTTGTTAAGAAATACACCAGAAGA
82591 CGGCTATTTA
Statistics
Matches: 251, Mismatches: 48, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
127 8 0.03
128 146 0.58
129 87 0.35
130 10 0.04
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (128 bp):
TCAGAAGTTGATCGGAAGACGATCTTGTTAAGAAATACACCAGAAGATGGTTTCTCAACAATTTT
CAGAAGTTGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTCTCAAAAGTTT
Found at i:82420 original size:193 final size:192
Alignment explanation
Indices: 82147--82574 Score: 488
Period size: 193 Copynumber: 2.2 Consensus size: 192
82137 CGGTTTGCTA
* * * * *
82147 GAAAGAATTCTCAGAAGTTGGTTGGAAGACGATCTCATTAAAAAAGTACACCGGAAGATGGTTTC
1 GAAA-AATTTTCAGAAGTTGATCGGAAGACGATCTTATTAAAAAAGTACACCGAAAGATGGTTTC
* * * * *
82212 TCAACAATTTTCAGAAGA-TGATCGGAAGACGATCTTGTCAAAAAGTACACCAGAAGATGGTTTC
65 CCAACAATGTTCAGAA-ATTGATCGGAAGACGAACTTGTCAAAAA-TACACCAGAAGATAGTCTC
** * * *
82276 TCAACAGTTTTCAGAAGTTGATCGAAAGACGATCTTGTTAAGGAA-TACACCAGAAGATGGTTTC
128 TCAACAACTTTCAGAAGTTGATCGAAAGACAATCTTGTCAA--AAGTACACCAGAAGATAGTTTC
82340 TC
191 TC
* *
82342 -AAAAATTTTCAGAAGTTGATCGGAAGACGATCTTA-TGAAGAAGTACATCC-AAAGATGGTTTT
1 GAAAAATTTTCAGAAGTTGATCGGAAGACGATCTTATTAAAAAAGTACA-CCGAAAGATGG-TTT
* * * *
82404 CCCAAGAGTGTTCAGAAATTGATCGGAAGACGAACTTGTCAAAAATACGCTAGAAGATAGTCTCT
64 CCCAACAATGTTCAGAAATTGATCGGAAGACGAACTTGTCAAAAATACACCAGAAGATAGTCTCT
* * * *
82469 TAGCAACTTTCAGATGTTGATCGGAAGACAATCTTGTCAAAAGGTACACCAGAAGATAGTTTCTC
129 CAACAACTTTCAGAAGTTGATCGAAAGACAATCTTGTCAAAA-GTACACCAGAAGATAGTTTCTC
** *
82534 GAAAAGGTTTCAGAAGTTGATTCGGAAGACGATCTTGTTAA
1 GAAAAATTTTCAGAAGTTGA-TCGGAAGACGATCTTATTAA
82575 GAGATGCACC
Statistics
Matches: 196, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
190 2 0.01
192 86 0.44
193 88 0.45
194 18 0.09
195 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (192 bp):
GAAAAATTTTCAGAAGTTGATCGGAAGACGATCTTATTAAAAAAGTACACCGAAAGATGGTTTCC
CAACAATGTTCAGAAATTGATCGGAAGACGAACTTGTCAAAAATACACCAGAAGATAGTCTCTCA
ACAACTTTCAGAAGTTGATCGAAAGACAATCTTGTCAAAAGTACACCAGAAGATAGTTTCTC
Found at i:84399 original size:15 final size:15
Alignment explanation
Indices: 84381--84410 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
84371 TTTTTCAGTT
84381 TAATTGCTTTCTTTC
1 TAATTGCTTTCTTTC
*
84396 TAATTGTTTTCTTTC
1 TAATTGCTTTCTTTC
84411 AACCTCTGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (15 bp):
TAATTGCTTTCTTTC
Found at i:84706 original size:50 final size:50
Alignment explanation
Indices: 84648--84789 Score: 248
Period size: 50 Copynumber: 2.8 Consensus size: 50
84638 GATGATTTTC
84648 TTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTT
1 TTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTT
*
84698 TTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTT
1 TTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTT
* * *
84748 TTGAGATTGAATTGGAAGACAGTTCAAAAGATAAGTGGAAGA
1 TTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGA
84790 TGACTCTTTG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (50 bp):
TTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTT
Found at i:85192 original size:27 final size:29
Alignment explanation
Indices: 85119--85195 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
85109 TTAGGATCAC
* *
85119 CTAGGGGCATTTTGGTCATTTTCAAGAAT
1 CTAGGGGCATTTTGGTCATTTGCAACAAT
* *
85148 CTAGGGGCATTTTAGTCATTTGC-ACATT
1 CTAGGGGCATTTTGGTCATTTGCAACAAT
85176 C-AGGGGCATTTTGGTCATTT
1 CTAGGGGCATTTTGGTCATTT
85196 TAAGTTAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 18 0.42
28 4 0.09
29 21 0.49
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.39
Consensus pattern (29 bp):
CTAGGGGCATTTTGGTCATTTGCAACAAT
Found at i:96180 original size:16 final size:16
Alignment explanation
Indices: 96159--96189 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
96149 TCAATTTTTC
*
96159 AAAATTTATTTTTGAA
1 AAAATTGATTTTTGAA
96175 AAAATTGATTTTTGA
1 AAAATTGATTTTTGA
96190 TGGTTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (16 bp):
AAAATTGATTTTTGAA
Found at i:97374 original size:11 final size:10
Alignment explanation
Indices: 97358--97404 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
97348 AACCTCGTGT
97358 TTGAAGACTCA
1 TTGAAGA-TCA
*
97369 TTGAAGATAA
1 TTGAAGATCA
97379 TTTGAAGAT--
1 -TTGAAGATCA
97388 TTGAAGATCA
1 TTGAAGATCA
97398 TTGAAGA
1 TTGAAGA
97405 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:97393 original size:19 final size:18
Alignment explanation
Indices: 97369--97404 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
97359 TGAAGACTCA
97369 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
97388 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
97405 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:100707 original size:9 final size:9
Alignment explanation
Indices: 100680--100717 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
100670 TTCCCACCTG
100680 AAAAG-GAA
1 AAAAGAGAA
100688 AAAAGAAGAA
1 AAAAG-AGAA
*
100698 AAAAGTGAA
1 AAAAGAGAA
100707 AAAAGAGAA
1 AAAAGAGAA
100716 AA
1 AA
100718 TAGAAAAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 5 0.19
9 13 0.50
10 8 0.31
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (9 bp):
AAAAGAGAA
Found at i:100725 original size:16 final size:18
Alignment explanation
Indices: 100680--100717 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
100670 TTCCCACCTG
100680 AAAAGGAAAAAAGAAGAA
1 AAAAGGAAAAAAGAAGAA
100698 AAAAGTGAAAAAAG-AGAA
1 AAAAG-GAAAAAAGAAGAA
100716 AA
1 AA
100718 TAGAAAAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (18 bp):
AAAAGGAAAAAAGAAGAA
Found at i:100816 original size:14 final size:13
Alignment explanation
Indices: 100788--100838 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
100778 CGAGATACAT
*
100788 TTTTCAAAAATTG
1 TTTTCAAAAAATG
100801 TTTTCAAGAAAATG
1 TTTTCAA-AAAATG
100815 TTTT-AAAAAATGAG
1 TTTTCAAAAAAT--G
100829 TTTTCAAAAA
1 TTTTCAAAAA
100839 GGTTTTGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.15
13 9 0.27
14 14 0.42
15 5 0.15
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (13 bp):
TTTTCAAAAAATG
Found at i:101518 original size:22 final size:20
Alignment explanation
Indices: 101493--101532 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
101483 GGATTGTCCA
*
101493 AAAAGAAGAAATTGATTTTTGC
1 AAAAG-AGAAAGTG-TTTTTGC
101515 AAAAGAGAAAGTGTTTTT
1 AAAAGAGAAAGTGTTTTT
101533 CTCAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (20 bp):
AAAAGAGAAAGTGTTTTTGC
Found at i:105024 original size:17 final size:17
Alignment explanation
Indices: 104956--105024 Score: 50
Period size: 17 Copynumber: 3.8 Consensus size: 17
104946 TGCCCAAATA
*
104956 AAATGTAAAACCCAACAG
1 AAAT-TAAAACCCAACAT
*
104974 AAATTAAAGCCC-ACTAT
1 AAATTAAAACCCAAC-AT
* *
104991 AAAAGAATAAGACCCAACAT
1 --AA-ATTAAAACCCAACAT
105011 AAATTAAAACCCAA
1 AAATTAAAACCCAA
105025 TAGATATGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 11
0.68 0.12 0.19
Matches are distributed among these distances:
16 2 0.05
17 18 0.46
18 6 0.15
19 2 0.05
20 9 0.23
21 2 0.05
ACGTcount: A:0.57, C:0.22, G:0.07, T:0.14
Consensus pattern (17 bp):
AAATTAAAACCCAACAT
Found at i:107382 original size:8 final size:8
Alignment explanation
Indices: 107369--108044 Score: 183
Period size: 8 Copynumber: 88.8 Consensus size: 8
107359 CATGGGAGAG
107369 TTGAAGAA
1 TTGAAGAA
*
107377 TTGAAGCAT
1 TTGAAG-AA
*
107386 TTGAATAA
1 TTGAAGAA
107394 TTGAAGAA
1 TTGAAGAA
107402 TTGAAGCAA
1 TTGAAG-AA
* *
107411 -TAAATAA
1 TTGAAGAA
107418 TTGAAGAA
1 TTGAAGAA
107426 TTGAAGAA
1 TTGAAGAA
*
107434 AT--A-AA
1 TTGAAGAA
*
107439 TTAAAGAA
1 TTGAAGAA
107447 TTGAAGAA
1 TTGAAGAA
* **
107455 -AG-ACCA
1 TTGAAGAA
* **
107461 TCCTGGATCA
1 T--TGAAGAA
107471 TTGAAGTAAA
1 TTGAAG--AA
107481 TTGAA-ACA
1 TTGAAGA-A
* *
107489 ATGAATAA
1 TTGAAGAA
107497 TTGAAGAA
1 TTGAAGAA
*
107505 TTGAAGCA
1 TTGAAGAA
*
107513 TTGAATAA
1 TTGAAGAA
107521 TTGAAGAA
1 TTGAAGAA
107529 TTGAAGAA
1 TTGAAGAA
** *
107537 -ACACGACCA
1 TTGAAGA--A
* **
107546 -TGGATCA
1 TTGAAGAA
107553 TTGAAGTAAA
1 TTGAAG--AA
*
107563 TTGAAGCA
1 TTGAAGAA
*
107571 TTGTAGAA
1 TTGAAGAA
107579 TTG-A-AA
1 TTGAAGAA
* *
107585 TTCAAGCA
1 TTGAAGAA
107593 TTGAAGAA
1 TTGAAGAA
107601 TTG--GAA
1 TTGAAGAA
107607 TTGAA-ATA
1 TTGAAGA-A
107615 TTGAAGAA
1 TTGAAGAA
107623 TTG-A-AA
1 TTGAAGAA
*
107629 TTGAAGCA
1 TTGAAGAA
*
107637 TTGAA-ACG
1 TTGAAGA-A
107645 TTG-A-AA
1 TTGAAGAA
*
107651 TTGAAGCA
1 TTGAAGAA
107659 TTGAAGAA
1 TTGAAGAA
107667 -TG--GAA
1 TTGAAGAA
*
107672 CTTGAAGCA
1 -TTGAAGAA
107681 TTGAAGAA
1 TTGAAGAA
107689 TTG-A-AA
1 TTGAAGAA
*
107695 TTGAAGCA
1 TTGAAGAA
107703 TTGAAGAA
1 TTGAAGAA
*
107711 -TGGA-AA
1 TTGAAGAA
107717 TTGAAGAA
1 TTGAAGAA
*
107725 TTGAAGCA
1 TTGAAGAA
107733 TTGAA-ATA
1 TTGAAGA-A
*
107741 CTG-A-AA
1 TTGAAGAA
**
107747 TTGAATCA
1 TTGAAGAA
107755 TTGAAGAA
1 TTGAAGAA
*
107763 TTG--GAC
1 TTGAAGAA
**
107769 TTGAATCA
1 TTGAAGAA
107777 TTGAAGAA
1 TTGAAGAA
107785 TTG-A-AA
1 TTGAAGAA
107791 TTGAAGCAA
1 TTGAAG-AA
*
107800 -TGACA-TA
1 TTGA-AGAA
107807 TTG-A-AA
1 TTGAAGAA
107813 TTGAA-ACA
1 TTGAAGA-A
*
107821 TTGAAGGA
1 TTGAAGAA
*
107829 TTG-A-AT
1 TTGAAGAA
*
107835 TTGAGGAA
1 TTGAAGAA
107843 TTG-A-AA
1 TTGAAGAA
*
107849 TTGAAGCA
1 TTGAAGAA
*
107857 CTGAA-ATA
1 TTGAAGA-A
107865 TTG-A-AA
1 TTGAAGAA
*
107871 TTGAAGCA
1 TTGAAGAA
*
107879 CTGAA-ATA
1 TTGAAGA-A
107887 TTG-A-AA
1 TTGAAGAA
*
107893 TTGAAGCA
1 TTGAAGAA
*
107901 CTGAA-ATA
1 TTGAAGA-A
107909 TTG-A-AA
1 TTGAAGAA
107915 TTGAA-ACA
1 TTGAAGA-A
107923 TTGAAGAA
1 TTGAAGAA
107931 TTG-A-AA
1 TTGAAGAA
*
107937 TTG-AGCCA
1 TTGAAG-AA
107945 TTGAA-ATA
1 TTGAAGA-A
107953 TTG-A-AA
1 TTGAAGAA
107959 TTGAA-ACA
1 TTGAAGA-A
107967 TTGAAGAA
1 TTGAAGAA
107975 TTGAAGAA
1 TTGAAGAA
*
107983 TTGAGGAA
1 TTGAAGAA
* *
107991 TTGGATAA
1 TTGAAGAA
107999 TTGAAGAA
1 TTGAAGAA
* *
108007 TTGGAGCA
1 TTGAAGAA
* *
108015 TTGGATAA
1 TTGAAGAA
*
108023 TTAAAGAA
1 TTGAAGAA
*
108031 TTGAAAAA
1 TTGAAGAA
108039 TTGAAG
1 TTGAAG
108045 CTAATTGAAC
Statistics
Matches: 488, Mismatches: 108, Indels: 144
0.66 0.15 0.19
Matches are distributed among these distances:
5 6 0.01
6 76 0.16
7 54 0.11
8 315 0.65
9 20 0.04
10 17 0.03
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (8 bp):
TTGAAGAA
Found at i:107557 original size:82 final size:82
Alignment explanation
Indices: 107393--107611 Score: 253
Period size: 82 Copynumber: 2.8 Consensus size: 82
107383 CATTTGAATA
* *
107393 ATTGAAG--AATTGAAGCAATAAATAATTGAAGAATTGAAG-A---AATAAATTAAAGAATTGAA
1 ATTGAAGTAAATTGAAGCAATGAATAATTGAAGAATTGAAGCATTGAAT-AATTGAAGAATTGAA
*
107452 GAAAGACCATCCTGGATC
65 GAAACACCATCCTGGATC
*
107470 ATTGAAGTAAATTGAAACAATGAATAATTGAAGAATTGAAGCATTGAATAATTGAAGAATTGAAG
1 ATTGAAGTAAATTGAAGCAATGAATAATTGAAGAATTGAAGCATTGAATAATTGAAGAATTGAAG
*
107535 AAACACGA-CCATGGATC
66 AAACACCATCC-TGGATC
* * * * *
107552 ATTGAAGTAAATTGAAGCATTGTAGAATTG-A-AATTCAAGCATTGAAGAATTG--GAATTGAA
1 ATTGAAGTAAATTGAAGCAATGAATAATTGAAGAATTGAAGCATTGAATAATTGAAGAATTGAA
107612 ATATTGAAGA
Statistics
Matches: 124, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
77 7 0.06
78 8 0.06
79 30 0.24
80 20 0.16
81 3 0.02
82 53 0.43
83 3 0.02
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.26
Consensus pattern (82 bp):
ATTGAAGTAAATTGAAGCAATGAATAATTGAAGAATTGAAGCATTGAATAATTGAAGAATTGAAG
AAACACCATCCTGGATC
Found at i:107591 original size:22 final size:22
Alignment explanation
Indices: 107560--107979 Score: 345
Period size: 22 Copynumber: 19.1 Consensus size: 22
107550 TCATTGAAGT
*
107560 AAATTGAAGCATTGTAGAATTG
1 AAATTGAAGCATTGAAGAATTG
*
107582 AAATTCAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* **
107604 GAATTGAAATATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
*
107626 AAATTGAAGCATTGAA-ACGTTG
1 AAATTGAAGCATTGAAGA-ATTG
*
107648 AAATTGAAGCATTGAAGAATGG
1 AAATTGAAGCATTGAAGAATTG
*
107670 AACTTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
*
107692 AAATTGAAGCATTGAAGAATGG
1 AAATTGAAGCATTGAAGAATTG
* *
107714 AAATTGAAGAATTGAAGCATTG
1 AAATTGAAGCATTGAAGAATTG
**
107736 AAATACTGAA--ATTGAATCATTG
1 AAAT--TGAAGCATTGAAGAATTG
* **
107758 AAGAATTGGA-C-TTGAATCATTG
1 -A-AATTGAAGCATTGAAGAATTG
107780 AAGAATTGAA--ATTGAAGCAA-TG
1 -A-AATTGAAGCATTGAAG-AATTG
107802 ACATATTGAA--ATTGAA-ACATTG
1 A-A-ATTGAAGCATTGAAGA-ATTG
* *
107824 AAGGATTGAA--TTTGAGGAATTG
1 AA--ATTGAAGCATTGAAGAATTG
*
107846 AAATTGAAGCACTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
*
107868 AAATTGAAGCACTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
*
107890 AAATTGAAGCACTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
*
107912 AAATTGAAACATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
107934 AAATTG-AGCCATTGAA-ATATTG
1 AAATTGAAG-CATTGAAGA-ATTG
*
107956 AAATTGAAACATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
107978 AA
1 AA
107980 GAATTGAGGA
Statistics
Matches: 341, Mismatches: 35, Indels: 44
0.81 0.08 0.10
Matches are distributed among these distances:
20 7 0.02
21 8 0.02
22 312 0.91
23 7 0.02
24 7 0.02
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGAATTG
Found at i:107684 original size:52 final size:50
Alignment explanation
Indices: 107628--107940 Score: 198
Period size: 52 Copynumber: 6.4 Consensus size: 50
107618 AAGAATTGAA
107628 ATTGAAGCATTGAAACGTTGAAATTGAAGCATTGAAGAATGGAACTTGAAGC
1 ATTGAAGCATTGAAA--TTGAAATTGAAGCATTGAAGAATGGAACTTGAAGC
* *
107680 ATTG-A--A--G-AATTGAAATTGAAGCATTGAAGAATGGAAATTGAAGA
1 ATTGAAGCATTGAAATTGAAATTGAAGCATTGAAGAATGGAACTTGAAGC
* *
107724 ATTGAAGCATTGAAATACTGAAATTGAATCATTGAAGAATTGG-ACTTGAATC
1 ATTGAAGCATTGAAAT--TGAAATTGAAGCATTGAAGAA-TGGAACTTGAAGC
* * * * * *
107776 ATTGAAGAATTGAAATTGAAGCAATGACA-TATTGAA-ATTGAAACATTGAAGG
1 ATTGAAGCATTGAAATTGAA--ATTGA-AGCATTGAAGAATGGAAC-TTGAAGC
* *
107828 ATTGAA--TTTGAGGAATTGAAATTGAAGCACTG-A-AAT---A-TTGAA--
1 ATTGAAGCATTGA--AATTGAAATTGAAGCATTGAAGAATGGAACTTGAAGC
* * * * *
107870 ATTGAAGCACTGAAATATTGAAATTGAAGCACTGAA-ATATTGAAATTGAAAC
1 ATTGAAGCATTG-AA-ATTGAAATTGAAGCATTGAAGA-ATGGAACTTGAAGC
*
107922 ATTGAAGAATTGAAATTGA
1 ATTGAAGCATTGAAATTGA
107941 GCCATTGAAA
Statistics
Matches: 210, Mismatches: 22, Indels: 60
0.72 0.08 0.21
Matches are distributed among these distances:
42 6 0.03
43 1 0.00
44 62 0.30
45 4 0.02
46 5 0.02
47 2 0.01
49 7 0.03
50 30 0.14
51 6 0.03
52 83 0.40
53 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (50 bp):
ATTGAAGCATTGAAATTGAAATTGAAGCATTGAAGAATGGAACTTGAAGC
Found at i:107920 original size:36 final size:36
Alignment explanation
Indices: 107804--107927 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 36
107794 AAGCAATGAC
* * ** * *
107804 ATATTGAAATTGAAACATTGAAGGATTGAATTTGAGG
1 ATATTGAAATTGAAGCACTGAAATATTGAAATTGA-A
107841 A-ATTGAAATTGAAGCACTGAAATATTGAAATTGAAGCACTGAA
1 ATATTGAAATTGAAGCACTGAAATATTGAAA-T-------TGAA
107884 ATATTGAAATTGAAGCACTGAAATATTGAAATTGAA
1 ATATTGAAATTGAAGCACTGAAATATTGAAATTGAA
*
107920 ACATTGAA
1 ATATTGAA
107928 GAATTGAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
36 35 0.49
37 2 0.03
43 2 0.03
44 32 0.45
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (36 bp):
ATATTGAAATTGAAGCACTGAAATATTGAAATTGAA
Found at i:117149 original size:21 final size:21
Alignment explanation
Indices: 117125--117166 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
117115 ACACAAAGAA
* *
117125 GTTTTAAGCTCATCAGAGTTG
1 GTTTCAAGCCCATCAGAGTTG
*
117146 GTTTCAAGCCCATCGGAGTTG
1 GTTTCAAGCCCATCAGAGTTG
117167 CCTAAGGTGC
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:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCCCATCAGAGTTG
Found at i:123910 original size:40 final size:40
Alignment explanation
Indices: 123855--123937 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
123845 ATTTAGGCTT
123855 CAAAAGTTAGTTAAATGAATTTGATCTTACCTAACTAATC
1 CAAAAGTTAGTTAAATGAATTTGATCTTACCTAACTAATC
123895 CAAAAGTTAGTTAAATGAATTTGATCTTACCTAACTAATC
1 CAAAAGTTAGTTAAATGAATTTGATCTTACCTAACTAATC
123935 CAA
1 CAA
123938 TTTAAGCCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34
Consensus pattern (40 bp):
CAAAAGTTAGTTAAATGAATTTGATCTTACCTAACTAATC
Found at i:124186 original size:21 final size:19
Alignment explanation
Indices: 124162--124211 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
124152 ACTTTTCTAG
* *
124162 GCCCAATTCGGATGTCTTATA
1 GCCCAATTAGGA-GTCTCA-A
*
124183 GCCCAAATAGGAGTCTCAA
1 GCCCAATTAGGAGTCTCAA
124202 GCCCAATTAG
1 GCCCAATTAG
124212 CAATTATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 5 0.20
21 10 0.40
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (19 bp):
GCCCAATTAGGAGTCTCAA
Found at i:126289 original size:36 final size:36
Alignment explanation
Indices: 126249--126340 Score: 143
Period size: 36 Copynumber: 2.6 Consensus size: 36
126239 AGAACGACTC
*
126249 AGGGTGGTCTTTCATT-AGTTCA-TGCCGGAATGATTG
1 AGGGTGGTCGTTC-TTCAGTTCAGT-CCGGAATGATTG
126285 AGGGTGGTCGTTCTTCAGTTCAGTCCGGAATGATTG
1 AGGGTGGTCGTTCTTCAGTTCAGTCCGGAATGATTG
126321 AGGGTGGTCGTTCTTCAGTT
1 AGGGTGGTCGTTCTTCAGTT
126341 TATTCTAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
35 2 0.04
36 50 0.94
37 1 0.02
ACGTcount: A:0.16, C:0.15, G:0.33, T:0.36
Consensus pattern (36 bp):
AGGGTGGTCGTTCTTCAGTTCAGTCCGGAATGATTG
Found at i:128420 original size:6 final size:6
Alignment explanation
Indices: 128387--128414 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
128377 TATTCTTTCA
128387 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
128415 GAAAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:130257 original size:19 final size:20
Alignment explanation
Indices: 130220--130257 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
130210 AGAATACAGT
*
130220 CCAATTCAATAGAGTAATTC
1 CCAATTCAATAGAGCAATTC
*
130240 CCAATTCCA-AGAGCAATT
1 CCAATTCAATAGAGCAATT
130258 AAACAAAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (20 bp):
CCAATTCAATAGAGCAATTC
Found at i:130646 original size:9 final size:9
Alignment explanation
Indices: 130629--130663 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
130619 ATAGCAACAC
*
130629 AAAAAAAAA
1 AAAAAAAAT
130638 AACAAAAAAT
1 AA-AAAAAAT
130648 AAAAAAAAT
1 AAAAAAAAT
130657 AAAAAAA
1 AAAAAAA
130664 TACAGACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.91, C:0.03, G:0.00, T:0.06
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:130653 original size:16 final size:16
Alignment explanation
Indices: 130632--130662 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
130622 GCAACACAAA
130632 AAAAAAAACAAAAAAT
1 AAAAAAAACAAAAAAT
*
130648 AAAAAAAATAAAAAA
1 AAAAAAAACAAAAAA
130663 ATACAGACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAAAAAACAAAAAAT
Found at i:131861 original size:38 final size:37
Alignment explanation
Indices: 131803--131988 Score: 217
Period size: 35 Copynumber: 5.2 Consensus size: 37
131793 AAAAGGTGAA
131803 TCAGTAATAAGCAACTTAATTCAGGGTAATTAAGTAAT
1 TCAGT-ATAAGCAACTTAATTCAGGGTAATTAAGTAAT
* * *
131841 TTAGTATTAAGCAGCTTAATTCAGGGTAATTAAGTAAA
1 TCAGTA-TAAGCAACTTAATTCAGGGTAATTAAGTAAT
*
131879 TCAGTA-AAG-AACTTAATTCA-GGTAATTAAGTAAG
1 TCAGTATAAGCAACTTAATTCAGGGTAATTAAGTAAT
* * *
131913 TCAGT-TAA-AAACTTAATTTAGGGTAGTTAAGTAAT
1 TCAGTATAAGCAACTTAATTCAGGGTAATTAAGTAAT
*
131948 TCAG--TAAGCAACTTAATTCTA-GGTAATTAAGTAAG
1 TCAGTATAAGCAACTTAATTC-AGGGTAATTAAGTAAT
131983 TCAGTA
1 TCAGTA
131989 AGTAACTTTG
Statistics
Matches: 127, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
34 33 0.26
35 51 0.40
36 4 0.03
37 1 0.01
38 38 0.30
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (37 bp):
TCAGTATAAGCAACTTAATTCAGGGTAATTAAGTAAT
Found at i:131937 original size:69 final size:71
Alignment explanation
Indices: 131801--131996 Score: 238
Period size: 69 Copynumber: 2.7 Consensus size: 71
131791 AGAAAAGGTG
* * * *
131801 AATCAGTAATAAGCAACTTAATTCAGGGTAATTAAGTAATTTAGTATTAAGCAGCTTAATTCAGG
1 AATCAGT-A-AAGCAACTTAATTCA-GGTAATTAAGTAAGTCAG--TTAAGAAACTTAATTCAGG
131866 GTAATTAAGTA
61 GTAATTAAGTA
* *
131877 AATCAGTAAAG-AACTTAATTCAGGTAATTAAGTAAGTCAGTTAA-AAACTTAATTTAGGGTAGT
1 AATCAGTAAAGCAACTTAATTCAGGTAATTAAGTAAGTCAGTTAAGAAACTTAATTCAGGGTAAT
131940 TAAGTA
66 TAAGTA
* *
131946 ATTCAGT-AAGCAACTTAATTCTAGGTAATTAAGTAAGTCAG-TAAGTAACTT
1 AATCAGTAAAGCAACTTAATTC-AGGTAATTAAGTAAGTCAGTTAAGAAACTT
131997 TGTTTAGTAA
Statistics
Matches: 109, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
68 3 0.03
69 40 0.37
70 28 0.26
72 16 0.15
73 11 0.10
74 3 0.03
75 1 0.01
76 7 0.06
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (71 bp):
AATCAGTAAAGCAACTTAATTCAGGTAATTAAGTAAGTCAGTTAAGAAACTTAATTCAGGGTAAT
TAAGTA
Found at i:132054 original size:31 final size:31
Alignment explanation
Indices: 132008--132107 Score: 103
Period size: 31 Copynumber: 3.1 Consensus size: 31
131998 GTTTAGTAAT
* *
132008 TAACTTAATTCAGGGTAATTAAGTCAGTTAG
1 TAACTGAATTCAGGGTAATTAAGTAAGTTAG
*
132039 TAACTGAATTTAGGGTAATTAAGTAAGTTAG
1 TAACTGAATTCAGGGTAATTAAGTAAGTTAG
* *
132070 TAAATAACTTAATTCAGGATAATTAAGTAA-TTCAG
1 ----TAACTGAATTCAGGGTAATTAAGTAAGTT-AG
132105 TAA
1 TAA
132108 GCAAAAGTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
31 31 0.53
34 2 0.03
35 25 0.43
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (31 bp):
TAACTGAATTCAGGGTAATTAAGTAAGTTAG
Found at i:132066 original size:35 final size:35
Alignment explanation
Indices: 132027--132107 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
132017 TCAGGGTAAT
* * * *
132027 TAAGTCAGTTAGTAACTGAATTTAGGGTAATTAAG
1 TAAGTCAGTAAATAACTGAATTCAGGATAATTAAG
* *
132062 TAAGTTAGTAAATAACTTAATTCAGGATAATTAAG
1 TAAGTCAGTAAATAACTGAATTCAGGATAATTAAG
*
132097 TAATTCAGTAA
1 TAAGTCAGTAA
132108 GCAAAAGTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (35 bp):
TAAGTCAGTAAATAACTGAATTCAGGATAATTAAG
Found at i:132149 original size:88 final size:83
Alignment explanation
Indices: 131941--132187 Score: 232
Period size: 88 Copynumber: 2.9 Consensus size: 83
131931 TAGGGTAGTT
* * ** *
131941 AAGTAATTCAGTAAGCAACTTAATTCTAGGTAATTAAGTAAGTCAGTAAGTAACTTTGTTTA-GT
1 AAGTAATTCAGTAATCAACTTAATTCTAGGTAATTAAGTAAGTCAGTAAATAACTTAATTCAGGT
* **
132005 AATTAACTTAATTCAGGGT
66 AATTAA-GTAATTCAGGAA
* * * * *
132024 AATTAAGTCAGTTAGT-AACTGAATT-TAGGGTAATTAAGTAAGTTAGTAAATAACTTAATTCAG
1 AAGTAATTCAG-TAATCAACTTAATTCTA-GGTAATTAAGTAAGTCAGTAAATAACTTAATTCAG
132087 GATAATTAAGTAATTCAGTAAGCAA
64 G-TAATTAAGTAATTCAG---G-AA
* * *
132112 AAGTAATTCAGTAATCAACTTAATTCGAGGTAATTAAGTAAGTCGGT-AATCAACTTAATTCCTG
1 AAGTAATTCAGTAATCAACTTAATTCTAGGTAATTAAGTAAGTCAGTAAAT-AACTTAATT-CAG
132176 GTAATTAAGTAA
64 GTAATTAAGTAA
132188 GATATTAAGT
Statistics
Matches: 131, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
82 2 0.02
83 46 0.35
84 11 0.08
85 7 0.05
87 7 0.05
88 54 0.41
89 4 0.03
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (83 bp):
AAGTAATTCAGTAATCAACTTAATTCTAGGTAATTAAGTAAGTCAGTAAATAACTTAATTCAGGT
AATTAAGTAATTCAGGAA
Found at i:132179 original size:35 final size:35
Alignment explanation
Indices: 132112--132188 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
132102 CAGTAAGCAA
* *
132112 AAGTAATTCAGTAATCAACTTAATTCGAGGTAATT
1 AAGTAAGTCAGTAATCAACTTAATTCCAGGTAATT
* *
132147 AAGTAAGTCGGTAATCAACTTAATTCCTGGTAATT
1 AAGTAAGTCAGTAATCAACTTAATTCCAGGTAATT
132182 AAGTAAG
1 AAGTAAG
132189 ATATTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (35 bp):
AAGTAAGTCAGTAATCAACTTAATTCCAGGTAATT
Found at i:132180 original size:19 final size:18
Alignment explanation
Indices: 132122--132180 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 18
132112 AAGTAATTCA
*
132122 GTAATCAACTTAATTCGAG
1 GTAATCAACTTAATTC-CG
* * *
132141 GTAATTAA-GTAAGT-CG
1 GTAATCAACTTAATTCCG
132157 GTAATCAACTTAATTCCTG
1 GTAATCAACTTAATTCC-G
132176 GTAAT
1 GTAAT
132181 TAAGTAAGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
16 8 0.27
17 4 0.13
18 5 0.17
19 13 0.43
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
GTAATCAACTTAATTCCG
Found at i:132202 original size:35 final size:33
Alignment explanation
Indices: 132123--132245 Score: 103
Period size: 35 Copynumber: 3.6 Consensus size: 33
132113 AGTAATTCAG
*
132123 TAATCAACTTAATTCGA-GGTAATTAAGTAAG-TCGG
1 TAAT-AACTTAATTC-ATGGTAATTAAGTAAGAT--A
*
132158 TAATCAACTTAATTCCTGGTAATTAAGTAAGATA
1 TAAT-AACTTAATTCATGGTAATTAAGTAAGATA
*
132192 TTAAGTAACTTAA-TCATGGGTAATTAAATAA-ATA
1 -TAA-TAACTTAATTCAT-GGTAATTAAGTAAGATA
*
132226 -AATAACTTAATTCAGGGTAA
1 TAATAACTTAATTCATGGTAA
132246 ATTGAGTCAG
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
31 13 0.17
32 5 0.06
34 6 0.08
35 51 0.66
36 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (33 bp):
TAATAACTTAATTCATGGTAATTAAGTAAGATA
Found at i:136629 original size:24 final size:24
Alignment explanation
Indices: 136597--136669 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 24
136587 TAATATATAG
136597 CGGCGTCTAGACGCCACTATTTAA
1 CGGCGTCTAGACGCCACTATTTAA
136621 CGGCGTCTAGACGCCACGCAACTATTTAA
1 CGGCGTCTAGACG---C-C-ACTATTTAA
*
136650 CGGCGTCTAGACGCCGCTAT
1 CGGCGTCTAGACGCCACTAT
136670 CTGGACACGT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
24 17 0.40
25 1 0.02
26 1 0.02
27 1 0.02
28 1 0.02
29 22 0.51
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (24 bp):
CGGCGTCTAGACGCCACTATTTAA
Found at i:136649 original size:29 final size:29
Alignment explanation
Indices: 136607--136664 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
136597 CGGCGTCTAG
*
136607 ACGCCACTATTTAACGGCGTCTAGACGCC
1 ACGCAACTATTTAACGGCGTCTAGACGCC
136636 ACGCAACTATTTAACGGCGTCTAGACGCC
1 ACGCAACTATTTAACGGCGTCTAGACGCC
136665 GCTATCTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (29 bp):
ACGCAACTATTTAACGGCGTCTAGACGCC
Found at i:136889 original size:32 final size:32
Alignment explanation
Indices: 136818--136968 Score: 225
Period size: 32 Copynumber: 4.8 Consensus size: 32
136808 CTTTATCTGC
*
136818 AGACGCCGCTAAATAAGGGCG-TTT-TCCTTT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTCTTT
*
136848 AGACGCCGCTAAATAAGGGTGTTTTGTTCTTT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTCTTT
* *
136880 AGACACCGCTAAATAAGGGCGTTTTGTTCTCT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTCTTT
* * *
136912 AGACGCCGCCAAATAAGGGTGTTTTGTTCTGT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTCTTT
136944 AGACGCCGCTAAATAAGGGCGTTTT
1 AGACGCCGCTAAATAAGGGCGTTTT
136969 CTTTTCACAC
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
30 20 0.19
31 3 0.03
32 85 0.79
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (32 bp):
AGACGCCGCTAAATAAGGGCGTTTTGTTCTTT
Found at i:136995 original size:96 final size:94
Alignment explanation
Indices: 136818--136995 Score: 214
Period size: 96 Copynumber: 1.9 Consensus size: 94
136808 CTTTATCTGC
* * * * * *
136818 AGACGCCGCTAAATAAGGGCGTTTTCCTTTAGACGCCGCTAAATAAGGGTGTTTTGTTCTTTAGA
1 AGACGCCGCCAAATAAGGGCGTTTTCCTGTAGACGCCGCTAAATAAGGGCGTTTTCTTCTTCACA
* *
136883 CACCGCTAAATAAGGGCGTTTTGTTCTCT
66 CAACGCCAAATAAGGGCGTTTTGTTCTCT
* *
136912 AGACGCCGCCAAATAAGGGTGTTTTGTTCTGTAGACGCCGCTAAATAAGGGCGTTTTCTT-TTCA
1 AGACGCCGCCAAATAAGGGCG-TTT-TCCTGTAGACGCCGCTAAATAAGGGCGTTTTCTTCTTCA
* *
136976 CACATACTCCAAATCAGGGC
64 CACA-ACGCCAAATAAGGGC
136996 TTTCATTTAT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
94 19 0.28
95 9 0.13
96 41 0.59
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (94 bp):
AGACGCCGCCAAATAAGGGCGTTTTCCTGTAGACGCCGCTAAATAAGGGCGTTTTCTTCTTCACA
CAACGCCAAATAAGGGCGTTTTGTTCTCT
Found at i:144862 original size:156 final size:157
Alignment explanation
Indices: 144659--144944 Score: 424
Period size: 156 Copynumber: 1.8 Consensus size: 157
144649 CAAGGAAAGG
144659 AAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAG-GGGGAGGGGGGAA
1 AAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGTGGGGA---GGGAA
* *
144723 TTTTTCCCTCC-AAAAAAAAG-GGAAAAAAATCTCTTC-CTCCATATATTGAA-ATGGTGGCGT-
63 TTTTTCCCTCCAAAAAAAAAGAGAAAAAAAATCTC-TCACTCCATATATT-AATATGGCGGCGTC
144783 TTCCTTTCCCAGACGCCGCTAGTCTGATGTCA
126 TTCCTTTCCCAGACGCCGCTAGTCTGATGTCA
* * *
144815 AAACGCTGCTATATATTATAGGTGTAGAGTT-GAAAACTTTTTTTGTTTTAGTGGGGAGGGAATT
1 AAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAA-TTTCTTTGTTTTAGTGGGGAGGGAATT
144879 TTTCCCTCCAAAAAAAAAGAGAAAAAAAATCTCTCACTCCATATATTAATATGGCGGCGTCTTCC
65 TTTCCCTCCAAAAAAAAAGAGAAAAAAAATCTCTCACTCCATATATTAATATGGCGGCGTCTTCC
144944 T
130 T
144945 ATCAAAACGT
Statistics
Matches: 118, Mismatches: 5, Indels: 13
0.87 0.04 0.10
Matches are distributed among these distances:
154 16 0.14
155 18 0.15
156 74 0.63
157 10 0.08
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (157 bp):
AAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGTGGGGAGGGAATTT
TTCCCTCCAAAAAAAAAGAGAAAAAAAATCTCTCACTCCATATATTAATATGGCGGCGTCTTCCT
TTCCCAGACGCCGCTAGTCTGATGTCA
Found at i:145839 original size:21 final size:20
Alignment explanation
Indices: 145815--145879 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
145805 TTGGAGCTCA
145815 TTGAATTCAAAATTAGGGTTC
1 TTGAATTC-AAATTAGGGTTC
*
145836 TTGAGTTCATAATTAGGGTTC
1 TTGAATTCA-AATTAGGGTTC
*
145857 TTGAGTTTC-AATTAGGGTTC
1 TTGA-ATTCAAATTAGGGTTC
145877 TTG
1 TTG
145880 GTTGATTGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 15 0.38
21 22 0.55
22 3 0.08
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGAATTCAAATTAGGGTTC
Found at i:145871 original size:20 final size:20
Alignment explanation
Indices: 145824--145879 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
145814 ATTGAATTCA
145824 AAATTAGGGTTCTTGAGTTC
1 AAATTAGGGTTCTTGAGTTC
145844 ATAATTAGGGTTCTTGAGTTTC
1 A-AATTAGGGTTCTTGAG-TTC
145866 -AATTAGGGTTCTTG
1 AAATTAGGGTTCTTG
145880 GTTGATTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.44
21 16 0.47
22 3 0.09
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (20 bp):
AAATTAGGGTTCTTGAGTTC
Found at i:147538 original size:22 final size:22
Alignment explanation
Indices: 147510--147554 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
147500 AGTGTTTTAA
147510 GTGTCAAGGATTTGGTCACTAT
1 GTGTCAAGGATTTGGTCACTAT
147532 GTGTCAAGGATTTGGTCACTAT
1 GTGTCAAGGATTTGGTCACTAT
147554 G
1 G
147555 CTAAAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (22 bp):
GTGTCAAGGATTTGGTCACTAT
Found at i:154653 original size:21 final size:21
Alignment explanation
Indices: 154629--154668 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
154619 CTCTTGTCAT
154629 TGGACCAATAT-GCATCTTTAA
1 TGGACCAA-ATGGCATCTTTAA
*
154650 TGGATCAAATGGCATCTTT
1 TGGACCAAATGGCATCTTT
154669 TTTGTGCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
TGGACCAAATGGCATCTTTAA
Found at i:157400 original size:36 final size:38
Alignment explanation
Indices: 157332--157412 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 38
157322 GTTATCATAA
* * *
157332 CATTCATTTGTATATGTCATGCATCCATCATGCATTGTC
1 CATTCATTTGTATA-GTCATGCATCAACCATGCATTATC
*
157371 CATTCCTTTGTATA-T-ATGCATCAACCATGCATTATC
1 CATTCATTTGTATAGTCATGCATCAACCATGCATTATC
157407 CATTCA
1 CATTCA
157413 CTAGTATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 23 0.62
37 1 0.03
39 13 0.35
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.40
Consensus pattern (38 bp):
CATTCATTTGTATAGTCATGCATCAACCATGCATTATC
Found at i:157420 original size:36 final size:36
Alignment explanation
Indices: 157350--157422 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
157340 TGTATATGTC
* * * *
157350 ATGCATCCATCATGCATTGTCCATTCCTTTGTATAT
1 ATGCATCAACCATGCATTATCCATTCCTTAGTATAT
157386 ATGCATCAACCATGCATTATCCATTCAC-TAGTATAT
1 ATGCATCAACCATGCATTATCCATTC-CTTAGTATAT
157422 A
1 A
157423 CATCCATCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.37
Consensus pattern (36 bp):
ATGCATCAACCATGCATTATCCATTCCTTAGTATAT
Found at i:158509 original size:22 final size:22
Alignment explanation
Indices: 158484--158536 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
158474 AAAGCAAACT
158484 AACAATTAA-AATTAACT-AAGAA
1 AACAATTAAGAA--AACTAAAGAA
* *
158506 AACAATCAAGAAAATTAAAGAA
1 AACAATTAAGAAAACTAAAGAA
158528 AACAATTAA
1 AACAATTAA
158537 TAAGAAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 21 0.81
23 2 0.08
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (22 bp):
AACAATTAAGAAAACTAAAGAA
Found at i:159791 original size:19 final size:18
Alignment explanation
Indices: 159758--159793 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
159748 TTGAAATAAT
159758 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
159776 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
159794 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:160667 original size:20 final size:19
Alignment explanation
Indices: 160642--160679 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
160632 CTCCTCTATC
*
160642 ATGAAAACACTTTTCTTTTT
1 ATGAAAACAATTTT-TTTTT
160662 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTTTTTTT
160680 AATTACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (19 bp):
ATGAAAACAATTTTTTTTT
Found at i:162745 original size:34 final size:34
Alignment explanation
Indices: 162702--162770 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
162692 GCCGCGGCAT
*
162702 CAAGGCAGCAACACTGCCTTGT-GCGTGGGCTGGC
1 CAAGGCAGCAACACTGCCTAGTCGCGT-GGCTGGC
* *
162736 CAAGGCAGCAGCGCTGCCTAGTCGCGTGGCTGGC
1 CAAGGCAGCAACACTGCCTAGTCGCGTGGCTGGC
162770 C
1 C
162771 TGGTTGCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (34 bp):
CAAGGCAGCAACACTGCCTAGTCGCGTGGCTGGC
Done.