Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010129.1 Corchorus capsularis cultivar CVL-1 contig10150, 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: 79744
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:7569 original size:440 final size:439
Alignment explanation
Indices: 6736--7908 Score: 1515
Period size: 440 Copynumber: 2.7 Consensus size: 439
6726 TGTAATCATT
* * * * *
6736 AATTATACAATATTAAATAGACCCGCAATCAAAACCACAAAATTTTAAAA-TCATGTTTTAGAAT
1 AATTATACAATATTAAATAGACCGGCAATCGAGACCACAAAATTTCAAAAGT-ATTTTTTAGAAT
** * * * **
6800 TGAAACATT--ATTTGGCTTCTAAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTCATAAT
65 CAAAACATTAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAAT
* * * * * * * *
6863 ATACACTTGAATCACCTTGATCAGACAAATAGAACAGAAAATACAAAAATAAAAGTC-AAAGCGT
130 AGACACTTGAATCACCTTCATCGGACAAACAAAACAAAAAATA-AAAAATTAAAGCCGAAA-CGT
* * * *
6927 TAAATCGTCCAACCTATAATTT-T-AGAGGATTAAATAGCATAAAACATAAAAGTAT-GAGGATC
193 TCAATCGTCCAACCCAAAATTTGTGAG-GGACTAAATAGCATAAAACATAAAAGTATAGA-GATC
* * * * *
6989 ATTTGATAGATAATCCAGCAAAAAAAAAATATTTGCTTATTGAGACCAAATATAAAAATTCTCTC
256 ATTTGATAAATAATCCAGC--AAAAAAATTATTTGTTTATGGAGACCAAATATAAAAATTCCCTC
* * * **
7054 TTGAACATTCCACGAAACTCATTAATCAAATTCAGTTTTTAAGGCCTTAACGAAAGTTGTAGATC
319 TTGAACACTCCACGAAACTCATCAATCAAATTCAGTCTTTAAGGCCTTAACGAAAGTCATAGATC
* * * *
7119 ATACAATAACCTTTTAATCGACACTTGTACAACCTCAACCGGACAAGTTGACCAAA
384 ACACAATAACCTTTTAACCGACACTTGAACAACCTCAACCGGACAAGTGGACCAAA
* *
7175 AATTATACAATATTAAATAGACCGGCAATGGAGACCAGAAAATTTCAAAAGTATTTTTTAGAATC
1 AATTATACAATATTAAATAGACCGGCAATCGAGACCACAAAATTTCAAAAGTATTTTTTAGAATC
* *
7240 AAAACATTAAAATTGGCTTTTG-GATCCTTCATGAAAGTTATAGATCATGAAATTACCTTTTAAC
66 AAAACATTAAAATTGGCTTTTGAG-TCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAAT
*
7304 AGACACTTGAATCACCTTCATCGGACAAGA-AAAATAAAAAATAAAAGAATTAAAGCCGAAACGT
130 AGACACTTGAATCACCTTCATCGGACAA-ACAAAACAAAAAATAAAA-AATTAAAGCCGAAACGT
* ** *
7368 TCAATCGTCCAACCCAGAATTTGTGAGGGACTAAATAGCATAAATTACAAAAGTATAGAGATCAT
193 TCAATCGTCCAACCCAAAATTTGTGAGGGACTAAATAGCATAAAACATAAAAGTATAGAGATCAT
7433 TTGATAAATAATCCAGCAAAAAAATTATTTGTTTATGGAGACCAAATATAAAAATTCCCTCTTGA
258 TTGATAAATAATCCAGCAAAAAAATTATTTGTTTATGGAGACCAAATATAAAAATTCCCTCTTGA
* * * *
7498 ACCCTCCACGAAACTCATCAATCAAATTCAG-CTTTCAGTCTCTTAACGAAAGTCATAGATTACA
323 ACACTCCACGAAACTCATCAATCAAATTCAGTCTTTAAGGC-CTTAACGAAAGTCATAGATCACA
* * * *
7562 TAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGATCGAA
387 CAATAACCTTTTAACCGACACTTGAACAACCTCAACCGGACAAGTGGACCAAA
* * * * * *
7615 ATTTATACGATATCAAATAGACCGGCAATCGAGACCACCAAATTTCAGAAGCATTTTTTTA-AAT
1 AATTATACAATATTAAATAGACCGGCAATCGAGACCACAAAATTTCAAAAGTA-TTTTTTAGAAT
*
7679 CAAAACATTAAAATTGACTTTTGAGTCCTTCAT-AGAAGTTGTAGATCATGAAATTACCTTTTAA
65 CAAAACATTAAAATTGGCTTTTGAGTCCTTCATGA-AAGTTGTAGATCATGAAATTACCTTTTAA
*
7743 TAGACACTTGAATCACCTTCATCGGACAAACAAAACAAAAAACAAAATAATTAAAGCCGAAACGT
129 TAGACACTTGAATCACCTTCATCGGACAAACAAAACAAAAAATAAAA-AATTAAAGCCGAAACGT
* * * *
7808 TCCATCGTCCAACCCAAAAATTGTGAAGGACTAAATAGCATAAAACATAAAAGTATAGGGATCAT
193 TCAATCGTCCAACCCAAAATTTGTGAGGGACTAAATAGCATAAAACATAAAAGTATAGAGATCAT
* *
7873 TTGATAAATAAACCAGCAAAAAAATGATTTGTTTAT
258 TTGATAAATAATCCAGCAAAAAAATTATTTGTTTAT
7909 TATAAGCGGA
Statistics
Matches: 642, Mismatches: 77, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
439 70 0.11
440 398 0.62
441 118 0.18
442 52 0.08
443 4 0.01
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (439 bp):
AATTATACAATATTAAATAGACCGGCAATCGAGACCACAAAATTTCAAAAGTATTTTTTAGAATC
AAAACATTAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATA
GACACTTGAATCACCTTCATCGGACAAACAAAACAAAAAATAAAAAATTAAAGCCGAAACGTTCA
ATCGTCCAACCCAAAATTTGTGAGGGACTAAATAGCATAAAACATAAAAGTATAGAGATCATTTG
ATAAATAATCCAGCAAAAAAATTATTTGTTTATGGAGACCAAATATAAAAATTCCCTCTTGAACA
CTCCACGAAACTCATCAATCAAATTCAGTCTTTAAGGCCTTAACGAAAGTCATAGATCACACAAT
AACCTTTTAACCGACACTTGAACAACCTCAACCGGACAAGTGGACCAAA
Found at i:8227 original size:2 final size:2
Alignment explanation
Indices: 8222--8247 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8212 GTATTCACTG
8222 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
8248 TCTACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8465 original size:20 final size:20
Alignment explanation
Indices: 8440--8480 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
8430 TTAATTATTG
8440 ATATGTTAAGTGGATTTTTA
1 ATATGTTAAGTGGATTTTTA
*
8460 ATATGTTAAGTGGGTTTTTA
1 ATATGTTAAGTGGATTTTTA
8480 A
1 A
8481 GACATCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (20 bp):
ATATGTTAAGTGGATTTTTA
Found at i:12400 original size:14 final size:13
Alignment explanation
Indices: 12359--12406 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
12349 GTCAAAAATT
12359 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
**
12372 AAAAAGAAACGGAA
1 AAAAA-AAAAAGAA
12386 AAAACAAAAAAGAA
1 AAAA-AAAAAAGAA
12400 AATAAAA
1 AA-AAAA
12407 GGATTTCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 5 0.18
14 20 0.71
15 3 0.11
ACGTcount: A:0.83, C:0.04, G:0.10, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:12607 original size:26 final size:24
Alignment explanation
Indices: 12571--12652 Score: 96
Period size: 24 Copynumber: 3.4 Consensus size: 24
12561 GTCCCTCCAT
*
12571 TCGATCTCTCTCTCTCATCTAGTTAA
1 TCGATCTCTCTCTC-C-TCAAGTTAA
* *
12597 TCGATCTCTCTCTCCTCCAGTCAA
1 TCGATCTCTCTCTCCTCAAGTTAA
*
12621 TTGATCTCTCTCTCC-CAAGTTAA
1 TCGATCTCTCTCTCCTCAAGTTAA
12644 TC-ATCTCTC
1 TCGATCTCTC
12653 ACTCTCCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.14
23 7 0.14
24 21 0.42
25 1 0.02
26 14 0.28
ACGTcount: A:0.18, C:0.35, G:0.07, T:0.39
Consensus pattern (24 bp):
TCGATCTCTCTCTCCTCAAGTTAA
Found at i:12649 original size:22 final size:22
Alignment explanation
Indices: 12577--12662 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 22
12567 CCATTCGATC
* *
12577 TCTCTCTCTCATCTAGTTAATCGA
1 TCTCTCTCTC-CCAAGTTAATC-A
* * *
12601 TCTCTCTCTCCTCCAGTCAATTGA
1 TCTCTCTCTCC-CAAGTTAA-TCA
12625 TCTCTCTCTCCCAAGTTAATCA
1 TCTCTCTCTCCCAAGTTAATCA
12647 TCTCTCACTCTCCCAA
1 TCTCT--CTCTCCCAA
12663 TTTCTTAACT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 7 0.14
23 6 0.12
24 37 0.73
25 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.06, T:0.37
Consensus pattern (22 bp):
TCTCTCTCTCCCAAGTTAATCA
Found at i:12853 original size:33 final size:33
Alignment explanation
Indices: 12789--12853 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
12779 AGTACAATAT
* *
12789 TTGGGTTAAAAATGAGTTTCTAATTTGTTCTTA
1 TTGGGTTAAAAATGAATTTCTAATTTATTCTTA
12822 TTGGGTTAAAAAT-AATCTTCTTAA-TTATTCTT
1 TTGGGTTAAAAATGAAT-TTC-TAATTTATTCTT
12854 TTTCTTCAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.07
33 23 0.82
34 3 0.11
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (33 bp):
TTGGGTTAAAAATGAATTTCTAATTTATTCTTA
Found at i:14693 original size:13 final size:11
Alignment explanation
Indices: 14655--14691 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
14645 TATAAAATTA
14655 ATATGTAGTAT
1 ATATGTAGTAT
14666 ATATGTAGTAT
1 ATATGTAGTAT
14677 ATATGTAGTAT
1 ATATGTAGTAT
14688 ATAT
1 ATAT
14692 ATCTATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (11 bp):
ATATGTAGTAT
Found at i:14800 original size:32 final size:31
Alignment explanation
Indices: 14736--14802 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
14726 AACTTTATGT
*
14736 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
14767 TTTCCAATTGTACCCTT-TTTTTAAAAAACATA
1 TTTCCAATTGTACCCTTATTTTT--AAAACATA
14799 TTTC
1 TTTC
14803 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 5 0.15
31 16 0.48
32 12 0.36
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:15197 original size:22 final size:22
Alignment explanation
Indices: 15077--15417 Score: 137
Period size: 22 Copynumber: 15.6 Consensus size: 22
15067 TGGTCCAATT
* *
15077 TCAAAATTTCAAAGCGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
** * *
15099 TCAAAATTAT-ATAATGTGATTA
1 TCAAAATT-TCATAGGGAGGTTA
**
15121 T-AAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
*
15142 TCAAAATTT-GTA---A--TTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
15158 TCAAGATTTCAAAAGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* *
15180 TCAAAATTTTATAGGGAGATTTA
1 TCAAAATTTCATAGGGAG-GTTA
**
15203 TCAAAATTTCATAGCAAGGTTTA
1 TCAAAATTTCATAGGGAGG-TTA
* *
15226 TCACAATTTCATAGTGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
15248 TCAAAATTTCATAGTGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
* * * * *
15270 CTGACAA-TTCATATGAAGGTTT
1 -TCAAAATTTCATAGGGAGGTTA
* * ** *
15292 TTAAATTTTCATAACGTGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
15314 TCAATATATCATATGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* ** *
15336 TCAACATCTT-ATAGTGCTGATTA
1 TCAAAAT-TTCATAG-GGAGGTTA
* *
15359 TCAAAATTTCATAGTGAGATCT-
1 TCAAAATTTCATAGGGAGGT-TA
* *
15381 TCAAAATTCCTTACGGAGAGGTTA
1 TCAAAATTTCATA-GG-GAGGTTA
*
15405 ACAAAATTTCATA
1 TCAAAATTTCATA
15418 AGAAGGTCAA
Statistics
Matches: 227, Mismatches: 72, Indels: 38
0.67 0.21 0.11
Matches are distributed among these distances:
16 11 0.05
17 1 0.00
18 1 0.00
20 2 0.01
21 18 0.08
22 119 0.52
23 61 0.27
24 14 0.06
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAGGGAGGTTA
Found at i:15207 original size:23 final size:22
Alignment explanation
Indices: 15155--15261 Score: 99
Period size: 23 Copynumber: 4.8 Consensus size: 22
15145 AAATTTGTAA
* * *
15155 TTATCAAGATTTCAAAAG-GAGG
1 TTATCAAAATTTC-ATAGCGAGT
* *
15177 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTCATAGCGAG-T
*
15200 TTATCAAAATTTCATAGCAAGGT
1 TTATCAAAATTTCATAGCGA-GT
* * *
15223 TTATCACAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGCGAGT
15245 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
15262 TGTGATTACT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
21 3 0.04
22 31 0.44
23 35 0.50
24 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGT
Found at i:15552 original size:22 final size:22
Alignment explanation
Indices: 15506--15558 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
15496 AATAGTGTAA
* *
15506 TTATCATAATTTCATAAGAATG
1 TTATCAAAATTTCATAAGAACG
*
15528 TTATCAAAATTTCATAAGGACG
1 TTATCAAAATTTCATAAGAACG
*
15550 TTATAAAAA
1 TTATCAAAA
15559 ATAGTGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGAACG
Found at i:15556 original size:62 final size:60
Alignment explanation
Indices: 15474--15602 Score: 186
Period size: 62 Copynumber: 2.1 Consensus size: 60
15464 ATTGTTATTG
* *
15474 AAATTTCATAGACGTCATAAAAAATAGTGTAATTATCATAATTTCATAAGAATGTTATCA
1 AAATTTCATAGACGTCATAAAAAATAGTGTAATTATCATAATTTAATAAGAAGGTTATCA
* * *
15534 AAATTTCATAAGGACGTTATAAAAAATAGTGTAATTATCATTATTTAATAGGAAGGTTATCA
1 AAATTTCAT-A-GACGTCATAAAAAATAGTGTAATTATCATAATTTAATAAGAAGGTTATCA
*
15596 TAATTTC
1 AAATTTC
15603 GTATGAGTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 9 0.15
61 1 0.02
62 51 0.84
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (60 bp):
AAATTTCATAGACGTCATAAAAAATAGTGTAATTATCATAATTTAATAAGAAGGTTATCA
Found at i:15941 original size:16 final size:16
Alignment explanation
Indices: 15871--15979 Score: 98
Period size: 15 Copynumber: 6.8 Consensus size: 16
15861 GCGGGTCAGG
* *
15871 TTGGGTTCGGGTCATT
1 TTGGGTTCGGGTTAAT
**
15887 TTCGGGTTCGGGCTGGAT
1 TT-GGGTTCGGG-TTAAT
*
15905 TTGGGTTAGGG-TAAT
1 TTGGGTTCGGGTTAAT
*
15920 TCGGGTTCGGGTTAAT
1 TTGGGTTCGGGTTAAT
*
15936 TTGGG-TCAGGTTAAT
1 TTGGGTTCGGGTTAAT
*
15951 TCGGGTTC-GGTTGAAT
1 TTGGGTTCGGGTT-AAT
15967 TTGGGTTCGGGTT
1 TTGGGTTCGGGTT
15980 CTGTTTAGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
15 28 0.37
16 22 0.29
17 21 0.28
18 4 0.05
ACGTcount: A:0.11, C:0.10, G:0.39, T:0.39
Consensus pattern (16 bp):
TTGGGTTCGGGTTAAT
Found at i:15941 original size:31 final size:31
Alignment explanation
Indices: 15887--15978 Score: 114
Period size: 31 Copynumber: 2.9 Consensus size: 31
15877 TCGGGTCATT
**
15887 TTCGGGTTCGGGCTGGATTTGGGTTAGGGTAA
1 TTCGGGTTCGGG-TTAATTTGGGTTAGGGTAA
* *
15919 TTCGGGTTCGGGTTAATTTGGGTCAGGTTAA
1 TTCGGGTTCGGGTTAATTTGGGTTAGGGTAA
*
15950 TTCGGGTTC-GGTTGAATTTGGGTTCGGGT
1 TTCGGGTTCGGGTT-AATTTGGGTTAGGGT
15979 TCTGTTTAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 4 0.08
31 36 0.69
32 12 0.23
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (31 bp):
TTCGGGTTCGGGTTAATTTGGGTTAGGGTAA
Found at i:16156 original size:16 final size:16
Alignment explanation
Indices: 16135--16222 Score: 106
Period size: 16 Copynumber: 5.5 Consensus size: 16
16125 AATTTTCGGA
16135 TTCGGGTTTGAGCTTT
1 TTCGGGTTTGAGCTTT
* * *
16151 TTCGGGTTCGGGTTTT
1 TTCGGGTTTGAGCTTT
16167 TTCGGGTTTGAGCTTTT
1 TTCGGGTTTGAGC-TTT
* * *
16184 TTCGGGTTCGTGTTTT
1 TTCGGGTTTGAGCTTT
16200 TTCGGG-TTGAGCTTT
1 TTCGGGTTTGAGCTTT
16215 TTCGGGTT
1 TTCGGGTT
16223 CGGGTTCAGG
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
15 12 0.21
16 33 0.57
17 13 0.22
ACGTcount: A:0.03, C:0.12, G:0.33, T:0.51
Consensus pattern (16 bp):
TTCGGGTTTGAGCTTT
Found at i:16190 original size:33 final size:32
Alignment explanation
Indices: 16135--16228 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 32
16125 AATTTTCGGA
16135 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
*
16167 TTCGGGTTTGAGCTTTTTTCGGGTTCGTGTTTT
1 TTCGGGTTTGAGC-TTTTTCGGGTTCGGGTTTT
16200 TTCGGG-TTGAGCTTTTTCGGGTTCGGGTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTT
16229 CAGGCGGGTT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 16 0.27
32 19 0.32
33 24 0.41
ACGTcount: A:0.03, C:0.13, G:0.34, T:0.50
Consensus pattern (32 bp):
TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
Found at i:17523 original size:18 final size:17
Alignment explanation
Indices: 17500--17533 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
17490 ATTGTGAAGG
17500 TCTTTTCCAAAGAATATA
1 TCTTTTCCAAA-AATATA
17518 TCTTTTCCAAAAATAT
1 TCTTTTCCAAAAATAT
17534 CACTTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (17 bp):
TCTTTTCCAAAAATATA
Found at i:20933 original size:21 final size:21
Alignment explanation
Indices: 20909--20958 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
20899 GCACGGACAA
20909 GGCCGGACTTCGCGCGGATAT
1 GGCCGGACTTCGCGCGGATAT
* * *
20930 GGCCGGTCTTGGTGCGGATAT
1 GGCCGGACTTCGCGCGGATAT
20951 GGCCGGAC
1 GGCCGGAC
20959 ATGGCATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.26, G:0.42, T:0.20
Consensus pattern (21 bp):
GGCCGGACTTCGCGCGGATAT
Found at i:23111 original size:21 final size:21
Alignment explanation
Indices: 23087--23135 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
23077 CAGCTGGGGG
* * *
23087 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
23108 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
23129 CCCATGT
1 CCCATGT
23136 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:26640 original size:13 final size:13
Alignment explanation
Indices: 26619--26648 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
26609 GGTAAGTACG
*
26619 GCATGGCATGGGT
1 GCATAGCATGGGT
26632 GCATAGCATGGGT
1 GCATAGCATGGGT
26645 GCAT
1 GCAT
26649 GGATGTTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.40, T:0.23
Consensus pattern (13 bp):
GCATAGCATGGGT
Found at i:29038 original size:21 final size:21
Alignment explanation
Indices: 29005--29053 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
28995 AAGAATTGTA
**
29005 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
29025 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
29046 GCATTCCT
1 GC-TTCCT
29054 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:31639 original size:12 final size:12
Alignment explanation
Indices: 31622--31647 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31612 TTGTAGATCT
31622 TGGCTACTCATA
1 TGGCTACTCATA
31634 TGGCTACTCATA
1 TGGCTACTCATA
31646 TG
1 TG
31648 CCTCAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (12 bp):
TGGCTACTCATA
Found at i:31814 original size:21 final size:21
Alignment explanation
Indices: 31788--31828 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31778 CGACTCCCCC
* *
31788 TGTGCGCCCATGTGGTTGGCT
1 TGTGCGCCCAGGTCGTTGGCT
31809 TGTGCGCCCAGGTCGTTGGC
1 TGTGCGCCCAGGTCGTTGGC
31829 CTCAGCACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.27, G:0.39, T:0.29
Consensus pattern (21 bp):
TGTGCGCCCAGGTCGTTGGCT
Found at i:31917 original size:21 final size:21
Alignment explanation
Indices: 31893--31941 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31883 CAGCTGGGGG
* * *
31893 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
31914 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
31935 CCCATGT
1 CCCATGT
31942 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:35154 original size:18 final size:17
Alignment explanation
Indices: 35131--35164 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
35121 ATTGTGAAGG
35131 TCTTTTCCAAAGAATATA
1 TCTTTTCCAAA-AATATA
35149 TCTTTTCCAAAAATAT
1 TCTTTTCCAAAAATAT
35165 CACTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (17 bp):
TCTTTTCCAAAAATATA
Found at i:43039 original size:35 final size:35
Alignment explanation
Indices: 42948--43059 Score: 118
Period size: 35 Copynumber: 3.1 Consensus size: 35
42938 TTAATATTTT
* *
42948 ACTCTTTACCATTTTTTTTCTTTACTGGACTACTCTTT
1 ACTCTTTACCA--TTTTTTCTTTACT-GACTACCCTTC
* * *
42986 ACTCTTCACCA-TTCTTCTTTACTGACTTCCCTTC
1 ACTCTTTACCATTTTTTCTTTACTGACTACCCTTC
* * *
43020 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTT
1 ACTCTTTACCATTTTTTCTTTACTGACTACCCTTC
43055 ACTCT
1 ACTCT
43060 ACTCTTTACC
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
34 18 0.29
35 34 0.55
38 10 0.16
ACGTcount: A:0.16, C:0.29, G:0.04, T:0.52
Consensus pattern (35 bp):
ACTCTTTACCATTTTTTCTTTACTGACTACCCTTC
Found at i:43056 original size:7 final size:7
Alignment explanation
Indices: 43036--43412 Score: 133
Period size: 7 Copynumber: 56.0 Consensus size: 7
43026 TACCATTTTT
43036 TCTTTAC
1 TCTTTAC
**
43043 TGATTAC
1 TCTTTAC
43050 TCTTTAC
1 TCTTTAC
43057 TC--TAC
1 TCTTTAC
43062 TCTTTAC
1 TCTTTAC
*
43069 CCTTTAC
1 TCTTTAC
**
43076 -CATTTTTT
1 TC--TTTAC
43084 TCTTTAC
1 TCTTTAC
**
43091 TGATTAC
1 TCTTTAC
43098 TC-TT-C
1 TCTTTAC
43103 TCTTTAC
1 TCTTTAC
43110 TCTTTAC
1 TCTTTAC
* *
43117 CCTTT-T
1 TCTTTAC
43123 TCTTTAC
1 TCTTTAC
**
43130 TGATTAC
1 TCTTTAC
43137 TCTTTTAC
1 TC-TTTAC
*
43145 TTTTTAC
1 TCTTTAC
43152 -CATTT--
1 TC-TTTAC
*
43157 TACTTTGC
1 T-CTTTAC
**
43165 TGATTAC
1 TCTTTAC
43172 TCTTTA-
1 TCTTTAC
43178 -CTTTAC
1 TCTTTAC
43184 TCTTTAC
1 TCTTTAC
43191 TCTTTAC
1 TCTTTAC
*
43198 -CATTT-T
1 TC-TTTAC
43204 TCTTTAC
1 TCTTTAC
**
43211 TGATTAC
1 TCTTTAC
43218 TCTTTAC
1 TCTTTAC
43225 TC--TAC
1 TCTTTAC
43230 TCTTTAC
1 TCTTTAC
* *
43237 CCTTT-T
1 TCTTTAC
43243 TCTTTAC
1 TCTTTAC
**
43250 TGATTAC
1 TCTTTAC
43257 TCTTTTAC
1 TC-TTTAC
*
43265 TTTTTAC
1 TCTTTAC
43272 -CATTT--
1 TC-TTTAC
*
43277 TACTTTGC
1 T-CTTTAC
**
43285 TGATTAC
1 TCTTTAC
43292 TCTTTA-
1 TCTTTAC
43298 -CTTTAC
1 TCTTTAC
43304 TCTTTAC
1 TCTTTAC
43311 TCTTTAC
1 TCTTTAC
*
43318 -CATTT-T
1 TC-TTTAC
43324 TCTTTAC
1 TCTTTAC
**
43331 TGATTAC
1 TCTTTAC
43338 TCTTTAC
1 TCTTTAC
43345 TC--TAC
1 TCTTTAC
43350 TCTTTAC
1 TCTTTAC
*
43357 CCTTTACC
1 TCTTTA-C
* **
43365 ATTTTTTT
1 -TCTTTAC
*
43373 TCTTTTC
1 TCTTTAC
**
43380 TGATTAC
1 TCTTTAC
43387 TC-TT-C
1 TCTTTAC
43392 TCTTTAC
1 TCTTTAC
43399 TCTTTAC
1 TCTTTAC
43406 TCTTTAC
1 TCTTTAC
43413 CATTTTTTTC
Statistics
Matches: 266, Mismatches: 65, Indels: 78
0.65 0.16 0.19
Matches are distributed among these distances:
5 31 0.12
6 31 0.12
7 184 0.69
8 16 0.06
9 4 0.02
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (7 bp):
TCTTTAC
Found at i:43065 original size:81 final size:80
Alignment explanation
Indices: 42977--43347 Score: 345
Period size: 81 Copynumber: 4.6 Consensus size: 80
42967 CTTTACTGGA
* *
42977 CTACTCTTTACTCTTCACCATTCTTCTTTACTGACTT-CCCTTCACTCTTTACCATTTTTTCTTT
1 CTACTCTTTACTCTTCACCATTTTTCTTTACTGA-TTACCCTTTACTCTTTACCA-TTTTTCTTT
43041 ACTGATTACTCTTTACT
64 ACTGATTACTCTTTACT
* * *
43058 CTACTCTTTACCCTTTACCATTTTTTTCTTTACTGATTACTCTTCTCTTTACTCTTTACCCTTTT
1 CTACTCTTTACTCTTCACCA--TTTTTCTTTACTGATTA--C--C-CTTTACTCTTTACCATTTT
43123 TCTTTACTGATTACTCTTTTACTTT
59 TCTTTACTGATTACTC-TTTAC--T
* ** ** *
43148 TTAC-CATTTTACT-TTGC-TGATTACTCTTTACT--TTACTCTTTACTCTTTACCATTTTTCTT
1 CTACTC--TTTACTCTT-CACCATTTTTCTTTACTGATTACCCTTTACTCTTTACCATTTTTCTT
43208 TACTGATTACTCTTTACT
63 TACTGATTACTCTTTACT
* * * *
43226 CTACTCTTTA-----C-CC-TTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTG
1 CTACTCTTTACTCTTCACCATTTTTCTTTACTGATTAC-CCTTTACTCTTTACCATTTTTCTTTA
43284 CTGATTACTCTTTACT
65 CTGATTACTCTTTACT
* * *
43300 TTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCT
1 CTACTCTTTACTCTTCACCATTTTTCTTTACTGATTACCCTTTACTCT
43348 ACTCTTTACC
Statistics
Matches: 236, Mismatches: 29, Indels: 51
0.75 0.09 0.16
Matches are distributed among these distances:
71 10 0.04
72 1 0.00
73 4 0.02
74 46 0.19
77 4 0.02
78 4 0.02
79 1 0.00
80 14 0.06
81 70 0.30
82 2 0.01
83 13 0.06
84 1 0.00
85 1 0.00
86 3 0.01
87 21 0.09
88 28 0.12
89 1 0.00
90 7 0.03
91 5 0.02
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.55
Consensus pattern (80 bp):
CTACTCTTTACTCTTCACCATTTTTCTTTACTGATTACCCTTTACTCTTTACCATTTTTCTTTAC
TGATTACTCTTTACT
Found at i:43068 original size:19 final size:19
Alignment explanation
Indices: 43046--43197 Score: 54
Period size: 19 Copynumber: 7.6 Consensus size: 19
43036 TCTTTACTGA
43046 TTACTCTTTACTCTACTCT
1 TTACTCTTTACTCTACTCT
* * **
43065 TTACCCTTTACCATTTTTTTCT
1 TTACTCTTTA-C--TCTACTCT
** *
43087 TTACTGATTACTCTTCTCT
1 TTACTCTTTACTCTACTCT
* **
43106 TTACTCTTTACCCTTTTTCT
1 TTACTCTTTACTC-TACTCT
** *
43126 TTACTGATTACTCTTTTACTTT
1 TTACTCTTTACTC---TACTCT
* * **
43148 TTAC-CATTTTACTTTGCTGA
1 TTACTC--TTTACTCTACTCT
*
43168 TTACTCTTTACTTTACTCT
1 TTACTCTTTACTCTACTCT
43187 TTACTCTTTAC
1 TTACTCTTTAC
43198 CATTTTTCTT
Statistics
Matches: 96, Mismatches: 28, Indels: 18
0.68 0.20 0.13
Matches are distributed among these distances:
19 46 0.48
20 23 0.24
21 2 0.02
22 20 0.21
23 5 0.05
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.56
Consensus pattern (19 bp):
TTACTCTTTACTCTACTCT
Found at i:43139 original size:27 final size:27
Alignment explanation
Indices: 43106--43224 Score: 86
Period size: 27 Copynumber: 4.4 Consensus size: 27
43096 ACTCTTCTCT
43106 TTACTCTTTACCCTTTTTCTTTACTGA
1 TTACTCTTTACCCTTTTTCTTTACTGA
43133 TTACTCTTTTA--CTTTTTACCATTTTACT--
1 TTACTC-TTTACCCTTTTT--C--TTTACTGA
* ** * * **
43161 TTGCTGATTACTC-TTTACTTTACTCT
1 TTACTCTTTACCCTTTTTCTTTACTGA
*
43187 TTACTCTTTACCATTTTTCTTTACTGA
1 TTACTCTTTACCCTTTTTCTTTACTGA
43214 TTACTCTTTAC
1 TTACTCTTTAC
43225 TCTACTCTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 20
0.69 0.12 0.20
Matches are distributed among these distances:
24 6 0.09
26 15 0.21
27 30 0.43
28 12 0.17
29 1 0.01
30 6 0.09
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.56
Consensus pattern (27 bp):
TTACTCTTTACCCTTTTTCTTTACTGA
Found at i:43197 original size:46 final size:46
Alignment explanation
Indices: 43123--43241 Score: 166
Period size: 46 Copynumber: 2.5 Consensus size: 46
43113 TTACCCTTTT
* *
43123 TCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTAC
1 TCTTTACT--TTACTC-TTTACTCTTTACCATTTTACTTTACTGATTAC
*
43172 TCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTAC
1 TCTTTACTTTACTCTTTACTCTTTACCATTTTACTTTACTGATTAC
* *
43218 TCTTTACTCTACTCTTTACCCTTT
1 TCTTTACTTTACTCTTTACTCTTT
43242 TTCTTTACTG
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
46 51 0.78
47 6 0.09
49 8 0.12
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.55
Consensus pattern (46 bp):
TCTTTACTTTACTCTTTACTCTTTACCATTTTACTTTACTGATTAC
Found at i:43254 original size:120 final size:121
Alignment explanation
Indices: 42945--43361 Score: 602
Period size: 120 Copynumber: 3.5 Consensus size: 121
42935 TGATTAATAT
* * *
42945 TTTACTCTTTACCATTTTTTTTCTTTACTGGACTACTCTTTACTCT--TC---ACCATTCTTCTT
1 TTTACTCTTTACCA--TTTTTTCTTTACT-GATTACTCTTTACTCTACTCTTTACCCTTTTTCTT
* * * * * *
43005 TACTGACTT-C-CCTTCACTCTTTACCATTTTTTCTTTACTGATTACTCTTTACTCTACTC
63 TACTGA-TTACTCTTTTACTTTTTACCA-TTTTACTTTGCTGATTACTCTTTACTTTACTC
* *
43064 TTTACCCTTTACCATTTTTTTCTTTACTGATTACTCTTCT-CTTTACTCTTTACCCTTTTTCTTT
1 TTTACTCTTTACCA-TTTTTTCTTTACTGATTACTCTT-TACTCTACTCTTTACCCTTTTTCTTT
43128 ACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTACTC
64 ACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTACTC
43186 TTTACTCTTTACCA-TTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTTTTCTTTAC
1 TTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTTTTCTTTAC
43250 TGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTACTC
66 TGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTACTC
43306 TTTACTCTTTACCA-TTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTT
1 TTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTT
43362 ACCATTTTTT
Statistics
Matches: 276, Mismatches: 13, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
117 12 0.04
118 15 0.05
119 16 0.06
120 159 0.58
121 2 0.01
122 59 0.21
123 13 0.05
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.55
Consensus pattern (121 bp):
TTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTTTTCTTTAC
TGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTACTC
Found at i:43257 original size:46 final size:46
Alignment explanation
Indices: 43207--43435 Score: 118
Period size: 49 Copynumber: 5.1 Consensus size: 46
43197 CCATTTTTCT
*
43207 TTACTGATTACTCTTTACTC-TACTCTTTACCCTTTTTCTTTACTGA
1 TTACT-ATTACTCTTTACTCTTACTCTTTACCATTTTTCTTTACTGA
* * * **
43253 TTACTCTTTTACTTTTTAC-C--A-T-TTTA-C--TTTGCTGATTACTCT
1 TTA--CTATTACTCTTTACTCTTACTCTTTACCATTTTTCT--TTACTGA
43295 TTACT-TTACTCTTTA--C-T-C--TTTACCATTTTTCTTTACTGA
1 TTACTATTACTCTTTACTCTTACTCTTTACCATTTTTCTTTACTGA
* * *
43334 TTACTCTTTACTC--TACTCTTTACCCTTTACCATTTTTTTTCTTTTCTGA
1 TTACT-ATTACTCTTTACTC-TTACTCTTTACCA---TTTTTCTTTACTGA
*
43383 TTACTCTT-CTCTTTACTCTTTACTCTTTACCATTTTTTTCTTTACTGA
1 TTACTATTACTCTTTACTC-TTACTCTTTACCA--TTTTTCTTTACTGA
43431 TTACT
1 TTACT
43436 CTTTTACTTT
Statistics
Matches: 147, Mismatches: 13, Indels: 44
0.72 0.06 0.22
Matches are distributed among these distances:
38 5 0.03
39 22 0.15
40 7 0.05
41 12 0.08
42 9 0.06
43 5 0.03
44 2 0.01
45 1 0.01
46 11 0.07
47 13 0.09
48 24 0.16
49 36 0.24
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.56
Consensus pattern (46 bp):
TTACTATTACTCTTTACTCTTACTCTTTACCATTTTTCTTTACTGA
Found at i:43299 original size:19 final size:19
Alignment explanation
Indices: 43275--43317 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
43265 TTTTTACCAT
* *
43275 TTTACTTTGCTGATTACTC
1 TTTACTTTACTCATTACTC
*
43294 TTTACTTTACTCTTTACTC
1 TTTACTTTACTCATTACTC
43313 TTTAC
1 TTTAC
43318 CATTTTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTACTTTACTCATTACTC
Found at i:43377 original size:81 final size:81
Alignment explanation
Indices: 42945--43398 Score: 295
Period size: 81 Copynumber: 5.6 Consensus size: 81
42935 TGATTAATAT
* * *
42945 TTTACTCTTTACCATTTTTTTTCTTTACTGGACTACTCTTTACTCTTCACCATTCTTCTTTACTG
1 TTTACTCTTTACC-TTTTTTTTCTTTACT-G-TTACTCTTTACTCTTTACCATTTTTCTTTACTG
* *
43010 ACTT-CCCTTCACTCTTTAC-C
63 A-TTACTCTTTACTC--TACTC
** ** ** * *
43030 ATTTTTTCTTTA-CTGATTACTCTTTACT-CTACTCTTTACCCTTTACCA-TTTT-TTT-CT--T
1 -TTTACTCTTTACCTTTTTTTTCTTTACTGTTACTCTTTACTCTTTACCATTTTTCTTTACTGAT
** *
43088 TACTGATTACTCTTCTC
65 TACTCTTTACTCTACTC
* * * *
43105 TTTACTCTTTACC--CTTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGA
1 TTTACTCTTTACCTTTTTTTTCTTTACTG-TTACTC-TTTACTCTTTACCATTTTTCTTTACTGA
*
43168 TTACTCTTTACTTTACTC
64 TTACTCTTTACTCTACTC
* *
43186 TTTACTCTTTACC--ATTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCCTTTTTCTTTA
1 TTTACTCTTTACCTTTTTTTTCTTTACTG-TTACTC--T--T-TACTCTTTACCATTTTTCTTTA
*
43249 CTGATTACTC-TT--T-TACTT
60 CTGATTACTCTTTACTCTACTC
*
43267 TTTAC-CATTTTA-CTTTGCTGATTACTCTTTACT-TTACTCTTTACTCTTTACCATTTTTCTTT
1 TTTACTC--TTTACCTTT--T--TT-TTCTTTACTGTTACTCTTTACTCTTTACCATTTTTCTTT
43329 ACTGATTACTCTTTACTCTACTC
59 ACTGATTACTCTTTACTCTACTC
* *
43352 TTTACCCTTTACCATTTTTTTTCTTTTCTGATTACTC-TT-CTCTTTAC
1 TTTACTCTTTACC-TTTTTTTTCTTTACTG-TTACTCTTTACTCTTTAC
43399 TCTTTACTCT
Statistics
Matches: 296, Mismatches: 39, Indels: 71
0.73 0.10 0.17
Matches are distributed among these distances:
73 10 0.03
74 11 0.04
75 9 0.03
76 18 0.06
77 3 0.01
78 5 0.02
79 5 0.02
80 4 0.01
81 121 0.41
82 14 0.05
83 6 0.02
84 21 0.07
85 40 0.14
86 19 0.06
87 2 0.01
88 8 0.03
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.55
Consensus pattern (81 bp):
TTTACTCTTTACCTTTTTTTTCTTTACTGTTACTCTTTACTCTTTACCATTTTTCTTTACTGATT
ACTCTTTACTCTACTC
Found at i:43434 original size:22 final size:22
Alignment explanation
Indices: 43399--43662 Score: 150
Period size: 22 Copynumber: 12.3 Consensus size: 22
43389 TTCTCTTTAC
** *
43399 TCTTTACTCTTTACCATTTTTT
1 TCTTTACTGATTACCATTTTCT
43421 TCTTTACTGATTACTC-TTTTACT
1 TCTTTACTGATTAC-CATTTT-CT
43444 T-TTTACTGATTACCATTTTAC-
1 TCTTTACTGATTACCATTTT-CT
* * * *
43465 TCTTTTCTAATTACTATTTTACC
1 TCTTTACTGATTACCATTTT-CT
43488 T-TTTACTGATTACC-TTTGTACT
1 TCTTTACTGATTACCATTT-T-CT
*
43510 T-TTTACTGATTACCA-TTGCT
1 TCTTTACTGATTACCATTTTCT
*
43530 TC-TTACTGATTACCA-TTACT
1 TCTTTACTGATTACCATTTTCT
* * *
43550 TC-TTACTGATCACTA-TTAC-
1 TCTTTACTGATTACCATTTTCT
* *
43569 TCTTTACTGACTACTC-TTTTAAT
1 TCTTTACTGATTAC-CATTTT-CT
*
43592 T-TTCACTGATTACCATTTTACT
1 TCTTTACTGATTACCATTTT-CT
*
43614 T-TTTACTAATTACCATTTTAC-
1 TCTTTACTGATTACCATTTT-CT
*
43635 CCTTTACTGATTACC-TTTTACT
1 TCTTTACTGATTACCATTTT-CT
43657 T-TTTAC
1 TCTTTAC
43663 CATTTTACCT
Statistics
Matches: 199, Mismatches: 27, Indels: 33
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.01
20 46 0.23
21 19 0.10
22 127 0.64
23 5 0.03
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.53
Consensus pattern (22 bp):
TCTTTACTGATTACCATTTTCT
Found at i:43484 original size:66 final size:66
Alignment explanation
Indices: 43480--43662 Score: 120
Period size: 62 Copynumber: 2.9 Consensus size: 66
43470 TCTAATTACT
* *
43480 ATTTTACCTTTTACTGATTACCTTTGTACTTTTTACTGATTACCA--TTGCT-TCTTACTGATTA
1 ATTTTACCTTTTACTGATTACCTTTGTACTTTTTACTGATTACCATTTTACTCT-TTACTAATTA
43542 CC
65 CC
* * * * * *
43544 A--TTA-CTTCTTACTGATCA-CTAT-TACTCTTTACTGACTACTC-TTTTAAT-TTTCACTGAT
1 ATTTTACCTT-TTACTGATTACCTTTGTACTTTTTACTGATTAC-CATTTTACTCTTT-ACTAAT
43602 TACC
63 TACC
* * ** *
43606 ATTTTACTTTTTACTAATTACCATTT-TACCCTTTACTGATTACC-TTTTACTTTTTAC
1 ATTTTACCTTTTACTGATTACC-TTTGTACTTTTTACTGATTACCATTTTACTCTTTAC
43663 CATTTTACCT
Statistics
Matches: 95, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
60 15 0.16
61 9 0.09
62 27 0.28
64 12 0.13
65 12 0.13
66 20 0.21
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.50
Consensus pattern (66 bp):
ATTTTACCTTTTACTGATTACCTTTGTACTTTTTACTGATTACCATTTTACTCTTTACTAATTAC
C
Found at i:43576 original size:40 final size:41
Alignment explanation
Indices: 43487--43578 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 41
43477 ACTATTTTAC
* * * *
43487 CTTTTACTGATTACCTTTGTACTTTTTACTGATTACCATTG
1 CTTTTACTGATTACCTATGTACTTCTTACTGATCACCATTA
*
43528 CTTCTTACTGATTACC-AT-TACTTCTTACTGATCACTATTA
1 CTT-TTACTGATTACCTATGTACTTCTTACTGATCACCATTA
43568 CTCTTTACTGA
1 CT-TTTACTGA
43579 CTACTCTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
40 27 0.61
41 5 0.11
42 12 0.27
ACGTcount: A:0.22, C:0.23, G:0.08, T:0.48
Consensus pattern (41 bp):
CTTTTACTGATTACCTATGTACTTCTTACTGATCACCATTA
Found at i:43699 original size:126 final size:127
Alignment explanation
Indices: 43545--43925 Score: 363
Period size: 126 Copynumber: 3.0 Consensus size: 127
43535 CTGATTACCA
* * *
43545 TTACTTCTTACTGATCACTATTACTCTTTACTGACTACTCTTTTAAT-TTTCACTGATTACCATT
1 TTACTTCTTACTGATTACTATT--TCTTTACTGACTACTCTATTACTCTTTCACTGATTA-CATT
* * * *
43609 TTACTTTTTACTAATTACCATTTTACCCTTTACTGATTACC-TTTTACTTTTTACCAT-TTTACC
63 TTACTCTTTACTAATTACCATTTTACCCTTT-CAGA-TACCTTTTTACTTTTTACC-TGATTACA
43672 TTT
125 TTT
* * * *
43675 TTAC-TCTTACT-ATTACTCTTTCTTTATCATTTTTGTCTTTACT-GATTACTCTTCCACTGATT
1 TTACTTCTTACTGATTACTATTTCTTTA-C-----TGAC--TACTCTATTACTCTTTCACTGATT
43737 AC-TCTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTTTTACTTTTTA-CTGATT
58 ACAT-TTTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTTTTACTTTTTACCTGATT
43800 ACATTT
122 ACATTT
* * * * *
43806 TTACTTTTTACTGTTTACTATTACTTCTTACTGA-T-TTCTATTACTCTTT-ACTGATTATCACT
1 TTACTTCTTACTGATTACTATTTC-T-TTACTGACTACTCTATTACTCTTTCACTGATTA-CATT
*
43868 TTACTCTTTACTAATTACCATTTTACCCTTTCGGATACCTTTTTACTTTTTA-CTGATT
63 TTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTTTTACTTTTTACCTGATT
43926 GCCCTTTTTA
Statistics
Matches: 211, Mismatches: 21, Indels: 42
0.77 0.08 0.15
Matches are distributed among these distances:
125 9 0.04
126 75 0.36
127 1 0.00
128 7 0.03
129 9 0.04
130 5 0.02
131 16 0.08
132 25 0.12
133 44 0.21
134 17 0.08
135 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.52
Consensus pattern (127 bp):
TTACTTCTTACTGATTACTATTTCTTTACTGACTACTCTATTACTCTTTCACTGATTACATTTTA
CTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTTTTACTTTTTACCTGATTACATTT
Found at i:43766 original size:22 final size:22
Alignment explanation
Indices: 43720--43925 Score: 130
Period size: 22 Copynumber: 9.7 Consensus size: 22
43710 TCTTTACTGA
*
43720 TTACTCTTCCACTGATTA-C-TCT
1 TTACTCTT-TACTGATTACCAT-T
*
43742 TTACTCTTTACTAATTACCATT
1 TTACTCTTTACTGATTACCATT
* * *
43764 TTACCCTTT-CAGA-TACCTTT
1 TTACTCTTTACTGATTACCATT
*
43784 TTACTTTTTACTGATTA-CATTT
1 TTACTCTTTACTGATTACCA-TT
* * *
43806 TTACTTTTTACTGTTTA-C-TA
1 TTACTCTTTACTGATTACCATT
* *
43826 TTACT-TCTTACTGATT-TC-TA
1 TTACTCT-TTACTGATTACCATT
* *
43846 TTACTCTTTACTGATTATCACT
1 TTACTCTTTACTGATTACCATT
*
43868 TTACTCTTTACTAATTACCATT
1 TTACTCTTTACTGATTACCATT
* * *
43890 TTACCCTTT-CGGA-TACCTTT
1 TTACTCTTTACTGATTACCATT
*
43910 TTACTTTTTACTGATT
1 TTACTCTTTACTGATT
43926 GCCCTTTTTA
Statistics
Matches: 147, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
19 1 0.01
20 57 0.39
21 21 0.14
22 67 0.46
23 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.52
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCATT
Found at i:43792 original size:7 final size:7
Alignment explanation
Indices: 43780--43837 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
43770 TTTCAGATAC
43780 CTTTTTA
1 CTTTTTA
43787 CTTTTTA
1 CTTTTTA
**
43794 CTGATTA
1 CTTTTTA
43801 CATTTTTA
1 C-TTTTTA
43809 CTTTTTA
1 CTTTTTA
*
43816 CTGTTTA
1 CTTTTTA
*
43823 C-TATTA
1 CTTTTTA
*
43829 CTTCTTA
1 CTTTTTA
43836 CT
1 CT
43838 GATTTCTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 4 0.10
7 32 0.78
8 5 0.12
ACGTcount: A:0.19, C:0.17, G:0.03, T:0.60
Consensus pattern (7 bp):
CTTTTTA
Found at i:43801 original size:42 final size:43
Alignment explanation
Indices: 43394--43925 Score: 193
Period size: 44 Copynumber: 12.4 Consensus size: 43
43384 TACTCTTCTC
* ** ***
43394 TTTACTCTTTACTCTTTACCATTTTTTTCTTTACTGATTA-CTCT
1 TTTACTTTTTACTGATTACCATTTTACCCTTTACTGA-TACCT-T
* * *
43438 TTTACTTTTTACTGATTACCATTTTACTCTTTTCTAATTA-CTAT
1 TTTACTTTTTACTGATTACCATTTTACCCTTTACTGA-TACCT-T
* **
43482 TTTACCTTTTACTGATTACC-TTTGTACTTTTTACTGATTACC--
1 TTTACTTTTTACTGATTACCATTT-TACCCTTTACTGA-TACCTT
* * * *
43524 ATTGCTTCTTACTGATTACCA--TTA-CTTCTTACTGAT-CAC-T
1 TTTACTTTTTACTGATTACCATTTTACCCT-TTACTGATAC-CTT
* * * ** *
43564 ATTACTCTTTACTGACTACTC-TTTTA-ATTTTCACTGATTACCAT
1 TTTACTTTTTACTGATTAC-CATTTTACCCTTT-ACTGA-TACCTT
*
43608 TTTACTTTTTACTAATTACCATTTTACCCTTTACTGATTACC-T
1 TTTACTTTTTACTGATTACCATTTTACCCTTTACTGA-TACCTT
* * *
43651 TTTACTTTTTACCAT-TTTACCTTTTTACTC-TTACT-ATTACTCTTT
1 TTTACTTTTTA-C-TGATTACCATTTTACCCTTTACTGA-TAC-C-TT
* * * * *
43696 CTTTATCATTTTTGTCT--TTA-C-TGATTACTCTTCCACTGATTA-CTC
1 -TTTA-C-TTTTT-ACTGATTACCAT-TTTACCCTT-TACTGA-TACCTT
* * *
43741 TTTACTCTTTACTAATTACCATTTTACCCTTT-CAGATACCTT
1 TTTACTTTTTACTGATTACCATTTTACCCTTTACTGATACCTT
** *
43783 TTTACTTTTTACTGATTA-CATTTTTACTTTTTACTGTTTA-C-T
1 TTTACTTTTTACTGATTACCA-TTTTACCCTTTACTG-ATACCTT
* * * * * * **
43825 ATTACTTCTTACTGATT-TC-TATTACTCTTTACTGATTATCAC
1 TTTACTTTTTACTGATTACCATTTTACCCTTTACTGA-TACCTT
* * *
43867 TTTACTCTTTACTAATTACCATTTTACCCTTT-CGGATACCTT
1 TTTACTTTTTACTGATTACCATTTTACCCTTTACTGATACCTT
43909 TTTACTTTTTACTGATT
1 TTTACTTTTTACTGATT
43926 GCCCTTTTTA
Statistics
Matches: 379, Mismatches: 67, Indels: 86
0.71 0.13 0.16
Matches are distributed among these distances:
38 1 0.00
39 4 0.01
40 39 0.10
41 11 0.03
42 113 0.30
43 35 0.09
44 137 0.36
45 15 0.04
46 9 0.02
47 5 0.01
48 10 0.03
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.53
Consensus pattern (43 bp):
TTTACTTTTTACTGATTACCATTTTACCCTTTACTGATACCTT
Found at i:43815 original size:29 final size:27
Alignment explanation
Indices: 43780--43837 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
43770 TTTCAGATAC
* *
43780 CTTTTTACTTTTTACTGATTACATTTTTA
1 CTTTTTACTGTTTACT-ATTAC-TTCTTA
43809 CTTTTTACTGTTTACTATTACTTCTTA
1 CTTTTTACTGTTTACTATTACTTCTTA
43836 CT
1 CT
43838 GATTTCTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 7 0.26
28 5 0.19
29 15 0.56
ACGTcount: A:0.19, C:0.17, G:0.03, T:0.60
Consensus pattern (27 bp):
CTTTTTACTGTTTACTATTACTTCTTA
Found at i:43831 original size:20 final size:20
Alignment explanation
Indices: 43784--43858 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
43774 AGATACCTTT
* *
43784 TTACTTTTTACTGATTACATTT
1 TTACTTTTTACTGTTTAC--TA
43806 TTACTTTTTACTGTTTACTA
1 TTACTTTTTACTGTTTACTA
*
43826 TTACTTCTTACTGATTT-CTA
1 TTACTTTTTACTG-TTTACTA
*
43846 TTACTCTTTACTG
1 TTACTTTTTACTG
43859 ATTATCACTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 27 0.57
21 3 0.06
22 17 0.36
ACGTcount: A:0.20, C:0.17, G:0.05, T:0.57
Consensus pattern (20 bp):
TTACTTTTTACTGTTTACTA
Found at i:43859 original size:20 final size:20
Alignment explanation
Indices: 43806--43879 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
43796 GATTACATTT
*
43806 TTACTTTTTACTG-TTTACTA
1 TTACTCTTTACTGATTT-CTA
43826 TTACT-TCTTACTGATTTCTA
1 TTACTCT-TTACTGATTTCTA
43846 TTACTCTTTACTGATTATC-A
1 TTACTCTTTACTGATT-TCTA
43866 CTTTACTCTTTACT
1 --TTACTCTTTACT
43880 AATTACCATT
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.02
20 29 0.60
21 6 0.12
22 12 0.25
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.55
Consensus pattern (20 bp):
TTACTCTTTACTGATTTCTA
Found at i:43985 original size:126 final size:124
Alignment explanation
Indices: 43719--43975 Score: 293
Period size: 126 Copynumber: 2.0 Consensus size: 124
43709 GTCTTTACTG
* *
43719 ATTACTCTTCCACTGATTACTCTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTT
1 ATTACTCTT-GACTGATTACACTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTT
** * * * ** *
43784 TTACTTTTTACTGATTACATTTTTACTTTTTACTGTTTACTATTACTTCTTACTGATTTCT
65 TTACTTTTTACTGATTACATTTTTACTTTTTA-TGTGAACTATCACTTATAACCCATTTCA
* *
43845 ATTACTCTTTACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTCGGATACCTTT
1 ATTACTCTTGACTGATTA-CACTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTT
* * *
43910 TTACTTTTTACTGATTGCCCTTTTTACTTTTT-TG-GAACTTAATCACTTAAATAACCCTTTTCA
65 TTACTTTTTACTGATT-ACATTTTTACTTTTTATGTGAAC-T-ATCACTT--ATAACCCATTTCA
43973 ATT
1 ATT
43976 TTCTGACTGA
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
124 2 0.02
125 11 0.10
126 75 0.68
127 13 0.12
128 10 0.09
ACGTcount: A:0.23, C:0.22, G:0.05, T:0.51
Consensus pattern (124 bp):
ATTACTCTTGACTGATTACACTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTTT
TACTTTTTACTGATTACATTTTTACTTTTTATGTGAACTATCACTTATAACCCATTTCA
Found at i:45597 original size:21 final size:20
Alignment explanation
Indices: 45555--45598 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
45545 CTCTAAAAAA
*
45555 TCCTCTCTAAAACTCTTGCC
1 TCCTCTCTAAAACTCCTGCC
45575 TCCTCTCTTAAAACCTCCT-CC
1 TCCTCTC-TAAAA-CTCCTGCC
45596 TCC
1 TCC
45599 AGAAACCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 10 0.48
22 4 0.19
ACGTcount: A:0.18, C:0.45, G:0.02, T:0.34
Consensus pattern (20 bp):
TCCTCTCTAAAACTCCTGCC
Found at i:46668 original size:2 final size:2
Alignment explanation
Indices: 46661--46693 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
46651 TGATCACTAG
46661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46694 CTGCTGAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46942 original size:3 final size:3
Alignment explanation
Indices: 46930--46968 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
46920 CCAAGTATGG
46930 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
46969 GTATTTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:47299 original size:27 final size:26
Alignment explanation
Indices: 47269--47328 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
47259 TGACTAAAAC
47269 GCCCCTGAATGTGCA-AATGACCAAAGT
1 GCCCCT-AATGT-CAGAATGACCAAAGT
*
47296 GCCCCTAATGTTAGAATGACCAAAGT
1 GCCCCTAATGTCAGAATGACCAAAGT
47322 GCCCCTA
1 GCCCCTA
47329 TGTGACCCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 1 0.03
26 24 0.77
27 6 0.19
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (26 bp):
GCCCCTAATGTCAGAATGACCAAAGT
Found at i:47827 original size:20 final size:20
Alignment explanation
Indices: 47802--47841 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
47792 GGAAGCCATT
47802 GGAACTTGAAAAGTTGCTGA
1 GGAACTTGAAAAGTTGCTGA
47822 GGAACTTGAAAAGTTGCTGA
1 GGAACTTGAAAAGTTGCTGA
47842 AAATTTCGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (20 bp):
GGAACTTGAAAAGTTGCTGA
Found at i:50472 original size:94 final size:94
Alignment explanation
Indices: 50349--50537 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
50339 TAGATTAAGA
50349 TAGAACTTGTAAATAACTAAGTATTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATCC
1 TAGAACTTGTAAATAACTAAGTATTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATCC
50414 AAATAAGAAAATGTTTGTTAATGAAGATC
66 AAATAAGAAAATGTTTGTTAATGAAGATC
50443 TAGAACTTGTAAATAACTAAGTATTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATCC
1 TAGAACTTGTAAATAACTAAGTATTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATCC
50508 AAATAAGAAAATGTTTGTTAATGAAGATC
66 AAATAAGAAAATGTTTGTTAATGAAGATC
50537 T
1 T
50538 TGAAATATAA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (94 bp):
TAGAACTTGTAAATAACTAAGTATTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATCC
AAATAAGAAAATGTTTGTTAATGAAGATC
Found at i:52644 original size:2 final size:2
Alignment explanation
Indices: 52637--52666 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52627 GATAATTTTC
52637 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
52667 TGTCATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58162 original size:14 final size:13
Alignment explanation
Indices: 58139--58168 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
58129 CCATTTTCTC
58139 AAAAAAAAAAAAT
1 AAAAAAAAAAAAT
58152 AAAATAAAAAAAAT
1 AAAA-AAAAAAAAT
58166 AAA
1 AAA
58169 CAAACCATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:60071 original size:19 final size:19
Alignment explanation
Indices: 60047--60088 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
60037 ACTGGCTATG
*
60047 GAAAATGGAAATGGACATT
1 GAAAATGAAAATGGACATT
60066 GAAAATGAAAATGGACATT
1 GAAAATGAAAATGGACATT
60085 GAAA
1 GAAA
60089 CTGGCGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.24, T:0.19
Consensus pattern (19 bp):
GAAAATGAAAATGGACATT
Found at i:75023 original size:54 final size:54
Alignment explanation
Indices: 74946--75054 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
74936 TAGGAAAATA
74946 TAATGACCTTGTCAAGTTAATTTGGATTTAGTTATAATTTGGTCAGATTTAATG
1 TAATGACCTTGTCAAGTTAATTTGGATTTAGTTATAATTTGGTCAGATTTAATG
75000 TAATGACCTTGTCAAGTTAATTTGGATTTAGTTATAATTTGGTCAGATTTAATG
1 TAATGACCTTGTCAAGTTAATTTGGATTTAGTTATAATTTGGTCAGATTTAATG
75054 T
1 T
75055 TTATAGATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.45
Consensus pattern (54 bp):
TAATGACCTTGTCAAGTTAATTTGGATTTAGTTATAATTTGGTCAGATTTAATG
Found at i:77629 original size:2 final size:2
Alignment explanation
Indices: 77624--77667 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
77614 AAGAGCACAC
*
77624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT CT 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
77667 A
1 A
77668 GGTACCATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.