Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008240.1 Corchorus capsularis cultivar CVL-1 contig08261, 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: 52302
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:1597 original size:23 final size:22
Alignment explanation
Indices: 1554--1599 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1544 TCGAAAAAAT
*
1554 TGATTTTTATTGAAAATTTTGA
1 TGATTTTTATTCAAAATTTTGA
* *
1576 TGATTTTTTTTCAAACTCTTTGA
1 TGATTTTTATTCAAAAT-TTTGA
1599 T
1 T
1600 TTTTTCAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.57
Consensus pattern (22 bp):
TGATTTTTATTCAAAATTTTGA
Found at i:7000 original size:16 final size:16
Alignment explanation
Indices: 6975--7005 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6965 TCTTTAGTTT
*
6975 AATTGCTTTCTTTTTC
1 AATTGATTTCTTTTTC
6991 AATTGATTTCTTTTT
1 AATTGATTTCTTTTT
7006 AATCCCCTGT
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:0.16, C:0.13, G:0.06, T:0.65
Consensus pattern (16 bp):
AATTGATTTCTTTTTC
Found at i:7269 original size:22 final size:23
Alignment explanation
Indices: 7241--7290 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
7231 CGTTTTTTCT
7241 AAAAAAAAAAAAAA-TTGCGTCG
1 AAAAAAAAAAAAAATTTGCGTCG
7263 AAAAAAAAAAAAAATTTTGCGTCG
1 AAAAAAAAAAAAAA-TTTGCGTCG
7287 AAAA
1 AAAA
7291 TAAATTTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 14 0.54
24 12 0.46
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (23 bp):
AAAAAAAAAAAAAATTTGCGTCG
Found at i:7273 original size:24 final size:24
Alignment explanation
Indices: 7241--7290 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
7231 CGTTTTTTCT
7241 AAAAAAAAAAAAAATTGCGTCGAA
1 AAAAAAAAAAAAAATTGCGTCGAA
**
7265 AAAAAAAAAAAATTTTGCGTCGAA
1 AAAAAAAAAAAAAATTGCGTCGAA
7289 AA
1 AA
7291 TAAATTTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (24 bp):
AAAAAAAAAAAAAATTGCGTCGAA
Found at i:8388 original size:15 final size:15
Alignment explanation
Indices: 8368--8408 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
8358 CCTTGCCAAG
8368 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
8383 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
*
8398 CAAGAAGATGA
1 CCAGAAGATGA
8409 ACAACTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.44, C:0.22, G:0.27, T:0.07
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:11340 original size:11 final size:11
Alignment explanation
Indices: 11324--11355 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
11314 GAAGTTCGTG
11324 TTTGAAGATTA
1 TTTGAAGATTA
*
11335 TTTGAAGATAA
1 TTTGAAGATTA
11346 TTTGAAGATT
1 TTTGAAGATT
11356 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:11352 original size:22 final size:22
Alignment explanation
Indices: 11324--11383 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
11314 GAAGTTCGTG
*
11324 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
11346 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
11365 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
11384 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:11358 original size:19 final size:18
Alignment explanation
Indices: 11334--11371 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
11324 TTTGAAGATT
*
11334 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
11353 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
11371 A
1 A
11372 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:11598 original size:87 final size:87
Alignment explanation
Indices: 11452--11625 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
11442 GCCCGGAAGT
11452 TAAGGATTTTTGGATAATTTATATGGGATTATATTCAGCATATATAAGTCCATAATTGGAGTTAA
1 TAAGGATTTTTGGATAATTTATATGGGATTATATTCAGCATATATAAGTCCATAATTGGAGTTAA
11517 AATTCCAATTAATGCCGATTGG
66 AATTCCAATTAATGCCGATTGG
11539 TAAGGATTTTTGGATAATTTATATGGGATTATATTCAGCATATATAAGTCCATAATTGGAGTTAA
1 TAAGGATTTTTGGATAATTTATATGGGATTATATTCAGCATATATAAGTCCATAATTGGAGTTAA
11604 AATTCCAATTAATGCCGATTGG
66 AATTCCAATTAATGCCGATTGG
11626 ACCCTCCAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (87 bp):
TAAGGATTTTTGGATAATTTATATGGGATTATATTCAGCATATATAAGTCCATAATTGGAGTTAA
AATTCCAATTAATGCCGATTGG
Found at i:12807 original size:16 final size:18
Alignment explanation
Indices: 12773--12807 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12763 AGAAGAAGTA
12773 TGCTTTATAATTACTGTT
1 TGCTTTATAATTACTGTT
12791 TGCTTTAT-ATT-CTGTT
1 TGCTTTATAATTACTGTT
12807 T
1 T
12808 TAGATTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.60
Consensus pattern (18 bp):
TGCTTTATAATTACTGTT
Found at i:12878 original size:16 final size:16
Alignment explanation
Indices: 12853--12883 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12843 TCTTTAGTTT
*
12853 AATTGCTTTCTTTTTC
1 AATTGATTTCTTTTTC
12869 AATTGATTTCTTTTT
1 AATTGATTTCTTTTT
12884 AATCCCCTGT
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:0.16, C:0.13, G:0.06, T:0.65
Consensus pattern (16 bp):
AATTGATTTCTTTTTC
Found at i:13138 original size:22 final size:22
Alignment explanation
Indices: 13041--13395 Score: 123
Period size: 22 Copynumber: 16.1 Consensus size: 22
13031 AGTTTTTAAG
*
13041 AGGGATGTTATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * * *
13063 TGTGG-GGTAATCTAAATTTCTT
1 AG-GGAGGTTATCAAAATTTCAT
* * ** *
13085 AGTGTGGTTAAAAAAAATTTGAT
1 AGGGAGGTT-ATCAAAATTTCAT
*** *
13108 AGTTTGGTTATCAAAATTACAT
1 AGGGAGGTTATCAAAATTTCAT
**
13130 AGGGAGGTTATCGTAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** ** *
13152 A-ATATAATTATCAAAATTTAAT
1 AGGGA-GGTTATCAAAATTTCAT
* * ***
13174 A-GTATGGTTTTCAAAATTTTGC
1 AGGGA-GGTTATCAAAATTTCAT
* * * *
13196 AGGGAGATTAACAAAATTCCTT
1 AGGGAGGTTATCAAAATTTCAT
* * *
13218 AAGGATGTTATCAAAAATTCAT
1 AGGGAGGTTATCAAAATTTCAT
13240 AGGGAGGTTATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
*
13262 AGAGTA-GTTATC-AAATTTCAT
1 AG-GGAGGTTATCAAAATTTCAT
* *
13283 -GAGGTGGTTATCGAAATTTCAT
1 AG-GGAGGTTATCAAAATTTCAT
* *
13305 -GAGGAGATTATCAAAATTTTA-
1 AG-GGAGGTTATCAAAATTTCAT
** * * *
13326 AAAGAGGGTTATAAAAATTTTAC
1 AGGGA-GGTTATCAAAATTTCAT
* * *
13349 AGAGAGATTTATCAAAATTTTAT
1 AGGGAG-GTTATCAAAATTTCAT
** * *
13372 AATGAGGTTATCACAATTTGAT
1 AGGGAGGTTATCAAAATTTCAT
13394 AG
1 AG
13396 TGATTACCAA
Statistics
Matches: 244, Mismatches: 77, Indels: 24
0.71 0.22 0.07
Matches are distributed among these distances:
20 3 0.01
21 19 0.08
22 179 0.73
23 43 0.18
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (22 bp):
AGGGAGGTTATCAAAATTTCAT
Found at i:13533 original size:22 final size:23
Alignment explanation
Indices: 13484--13545 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
13474 TATTATTGTG
13484 TGCTTATC-AAATTTCATAAGAA
1 TGCTTATCAAAATTTCATAAGAA
*
13506 TG-TTATCAAAATTTCATAAGCA
1 TGCTTATCAAAATTTCATAAGAA
* *
13528 -GCTTATTAAATTTTCATA
1 TGCTTATCAAAATTTCATA
13546 GTTTCGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.17
22 29 0.83
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (23 bp):
TGCTTATCAAAATTTCATAAGAA
Found at i:13716 original size:22 final size:22
Alignment explanation
Indices: 13683--13761 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
13673 TTTTGATGTC
*
13683 ATTATCAGAATTTCATAGTGTG
1 ATTATCAAAATTTCATAGTGTG
*
13705 ATTAGCAAAATTTCATA-TG-G
1 ATTATCAAAATTTCATAGTGTG
* * *
13725 ATGTCATTAAAATTTTATGGTGTG
1 AT-T-ATCAAAATTTCATAGTGTG
13749 ATTATCAAAATTT
1 ATTATCAAAATTT
13762 AATATAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
20 3 0.07
21 3 0.07
22 34 0.74
23 3 0.07
24 3 0.07
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGTGTG
Found at i:13748 original size:44 final size:46
Alignment explanation
Indices: 13677--13766 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 46
13667 TCGAAATTTT
*
13677 GATGTCATTATCAGAATTTCATAGTGTGATTAGCAAAATTTCATATG
1 GATGTCATTA-CAGAATTTCATAGTGTGATTAGCAAAATTTAATATG
* * *
13724 GATGTCATTA-A-AATTTTATGGTGTGATTATCAAAATTTAATAT
1 GATGTCATTACAGAATTTCATAGTGTGATTAGCAAAATTTAATAT
13767 AAATTTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
44 28 0.72
45 1 0.03
47 10 0.26
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.41
Consensus pattern (46 bp):
GATGTCATTACAGAATTTCATAGTGTGATTAGCAAAATTTAATATG
Found at i:16540 original size:8 final size:8
Alignment explanation
Indices: 16529--16586 Score: 75
Period size: 8 Copynumber: 7.4 Consensus size: 8
16519 CCAAAATTAC
16529 AAAAA-AA
1 AAAAAGAA
16536 AAAAAGAA
1 AAAAAGAA
16544 AAAAAG-A
1 AAAAAGAA
*
16551 AAAGAGAAA
1 AAAAAG-AA
*
16560 AAAAAGGA
1 AAAAAGAA
16568 AAAAAGAA
1 AAAAAGAA
16576 AAAAAGAA
1 AAAAAGAA
16584 AAA
1 AAA
16587 GTGTTTCAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
7 11 0.25
8 27 0.61
9 6 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:16560 original size:24 final size:25
Alignment explanation
Indices: 16529--16586 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
16519 CCAAAATTAC
16529 AAAA-AAAAAAAAGAAAAAAAG-AA
1 AAAAGAAAAAAAAGAAAAAAAGAAA
* *
16552 AAGAGAAAAAAAAGGAAAAAAGAAA
1 AAAAGAAAAAAAAGAAAAAAAGAAA
16577 AAAAGAAAAA
1 AAAAGAAAAA
16587 GTGTTTCAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 16 0.53
25 11 0.37
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (25 bp):
AAAAGAAAAAAAAGAAAAAAAGAAA
Found at i:16562 original size:17 final size:17
Alignment explanation
Indices: 16529--16580 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
16519 CCAAAATTAC
16529 AAAAAA-AAAAAAG--A
1 AAAAAAGAAAAAAGAAA
*
16543 AAAAAAGAAAAGAGAAA
1 AAAAAAGAAAAAAGAAA
*
16560 AAAAAGGAAAAAAGAAA
1 AAAAAAGAAAAAAGAAA
16577 AAAA
1 AAAA
16581 GAAAAAGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 6 0.19
15 6 0.19
17 20 0.62
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAA
Found at i:16569 original size:25 final size:25
Alignment explanation
Indices: 16532--16586 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
16522 AAATTACAAA
*
16532 AAAAAAAAAGAAAAAA-AGAAAAGAG
1 AAAAAAAAAGAAAAAAGA-AAAAAAG
*
16557 AAAAAAAAGGAAAAAAGAAAAAAAG
1 AAAAAAAAAGAAAAAAGAAAAAAAG
16582 AAAAA
1 AAAAA
16587 GTGTTTCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAGAAAAAAGAAAAAAAG
Found at i:22041 original size:30 final size:30
Alignment explanation
Indices: 22007--22068 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
21997 AATTCTCTGC
22007 CTTGCTCTTATTTGGGGCTACCTCTCGGAG
1 CTTGCTCTTATTTGGGGCTACCTCTCGGAG
*
22037 CTTGCTCTTATTTGGGGCTGCCTCTCGGAG
1 CTTGCTCTTATTTGGGGCTACCTCTCGGAG
22067 CT
1 CT
22069 AGGCCTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.08, C:0.27, G:0.27, T:0.37
Consensus pattern (30 bp):
CTTGCTCTTATTTGGGGCTACCTCTCGGAG
Found at i:22746 original size:30 final size:30
Alignment explanation
Indices: 22710--22784 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
22700 AGAGGATGCC
* **
22710 ATCGCACAAGACCGGCCATTGCATGGAG-GG
1 ATCGCACAAGACCGGCCATGGCATGG-GCCA
* *
22740 ATCGCACATGACCGGCTATGGCATGGGCCA
1 ATCGCACAAGACCGGCCATGGCATGGGCCA
22770 ATCGCACAAGACCGG
1 ATCGCACAAGACCGG
22785 GCACAACCGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 1 0.03
30 37 0.97
ACGTcount: A:0.27, C:0.29, G:0.31, T:0.13
Consensus pattern (30 bp):
ATCGCACAAGACCGGCCATGGCATGGGCCA
Found at i:28759 original size:26 final size:26
Alignment explanation
Indices: 28730--28791 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
28720 AATAATATGG
**
28730 AATATAAGTTCCATCTTAACATATAT
1 AATATAAGTTCCATCCCAACATATAT
28756 AATATAAGTTCCATCCCAACATATAT
1 AATATAAGTTCCATCCCAACATATAT
28782 AATATAAGTT
1 AATATAAGTT
28792 AATACCCTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (26 bp):
AATATAAGTTCCATCCCAACATATAT
Found at i:31373 original size:11 final size:11
Alignment explanation
Indices: 31349--31392 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
31339 GAAGGAGGAG
*
31349 GAAGAAGAAGAA
1 GAAG-AGAAAAA
31361 GAAGAGAAAAA
1 GAAGAGAAAAA
31372 GAAG-GCAAAAA
1 GAAGAG-AAAAA
31383 GAAGAGAAAA
1 GAAGAGAAAA
31393 GGAAAAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 1 0.03
11 23 0.79
12 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (11 bp):
GAAGAGAAAAA
Found at i:32197 original size:35 final size:35
Alignment explanation
Indices: 32141--32384 Score: 260
Period size: 35 Copynumber: 6.9 Consensus size: 35
32131 AAGAAGTAAG
* * *
32141 GTAATTAACTTAATTTAAGGTAATTAAGTAAGTCA
1 GTAATCAACTTAATTCAGGGTAATTAAGTAAGTCA
* * * *
32176 GTTATTGAA-TTAATTCCA-GGTAATTAAGTCAGTCG
1 G-TAATCAACTTAATT-CAGGGTAATTAAGTAAGTCA
*
32211 GTAATCAACTTAATTCAGGGTAATTAAGTGAGTCA
1 GTAATCAACTTAATTCAGGGTAATTAAGTAAGTCA
* *
32246 GTAATCAACTTAATTCAGGGTAATTAAGTGAGTCT
1 GTAATCAACTTAATTCAGGGTAATTAAGTAAGTCA
*
32281 GTAATCAACTTAAATCCAGGGTAATTAAGTAAGTCA
1 GTAATCAACTT-AATTCAGGGTAATTAAGTAAGTCA
* *
32317 ATAAGT-AATTTAATTCAGGGTAATTAAGTAAGTCA
1 GTAA-TCAACTTAATTCAGGGTAATTAAGTAAGTCA
* * * * * *
32352 TTAATCGACTTAATGCAGGATAATCAATTAAGT
1 GTAATCAACTTAATTCAGGGTAATTAAGTAAGT
32385 AAGAAGCAAA
Statistics
Matches: 179, Mismatches: 23, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
34 8 0.04
35 136 0.76
36 34 0.19
37 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (35 bp):
GTAATCAACTTAATTCAGGGTAATTAAGTAAGTCA
Found at i:32234 original size:19 final size:19
Alignment explanation
Indices: 32210--32269 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
32200 TAAGTCAGTC
32210 GGTAATCAACTTAATTCAG
1 GGTAATCAACTTAATTCAG
* * * *
32229 GGTAATTAA-GTGAGTCA-
1 GGTAATCAACTTAATTCAG
32246 -GTAATCAACTTAATTCAG
1 GGTAATCAACTTAATTCAG
32264 GGTAAT
1 GGTAAT
32270 TAAGTGAGTC
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 7 0.23
17 5 0.17
18 5 0.17
19 13 0.43
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (19 bp):
GGTAATCAACTTAATTCAG
Found at i:32331 original size:71 final size:70
Alignment explanation
Indices: 32159--32364 Score: 249
Period size: 71 Copynumber: 2.9 Consensus size: 70
32149 CTTAATTTAA
* * * *
32159 GGTAATTAAGTAAGTCAGTTATTGAATTAATTCCA-GGTAATTAAGTCAGTCGGTAATCAACTT-
1 GGTAATTAAGTAAGTCAG-TAATCAATTAATT-CAGGGTAATTAAGTAAGTCTGTAATCAACTTA
*
32222 AATTCAG
64 AATCCAG
* *
32229 GGTAATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTAATTAAGTGAGTCTGTAATCAACTTAA
1 GGTAATTAAGTAAGTCAGTAATCAA-TTAATTCAGGGTAATTAAGTAAGTCTGTAATCAACTTAA
32294 ATCCAG
65 ATCCAG
* *
32300 GGTAATTAAGTAAGTCAATAAGT-AATTTAATTCAGGGTAATTAAGTAAGTCAT-TAATCGACTT
1 GGTAATTAAGTAAGTCAGTAA-TCAA-TTAATTCAGGGTAATTAAGTAAGTC-TGTAATCAACTT
32363 AA
63 AA
32365 TGCAGGATAA
Statistics
Matches: 120, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
69 7 0.06
70 49 0.41
71 62 0.52
72 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (70 bp):
GGTAATTAAGTAAGTCAGTAATCAATTAATTCAGGGTAATTAAGTAAGTCTGTAATCAACTTAAA
TCCAG
Found at i:32345 original size:106 final size:105
Alignment explanation
Indices: 32141--32384 Score: 276
Period size: 106 Copynumber: 2.3 Consensus size: 105
32131 AAGAAGTAAG
* * * * * * *
32141 GTAATTAACTTAATTTAAGGTAATTAAGTAAGTCAGTTATTGAATTAATTCCAGGTAATTAAGTC
1 GTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAATCAATTAAATCCAGGTAATTAAGTA
** *
32206 AGTCGGTAATCAACTTAATTCAGGGTAATTAAGTGAGTCA
66 AGTCAATAATCAACTTAATTCAGGGTAATTAAGTAAGTCA
* *
32246 GTAATCAACTTAATTCAGGGTAATTAAGTGAGTCTG-TAATCAACTTAAATCCAGGGTAATTAAG
1 GTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAATCAA-TTAAATCCA-GGTAATTAAG
*
32310 TAAGTCAATAAGT-AATTTAATTCAGGGTAATTAAGTAAGTCA
64 TAAGTCAATAA-TCAACTTAATTCAGGGTAATTAAGTAAGTCA
* * * * * *
32352 TTAATCGACTTAATGCAGGATAATCAATTAAGT
1 GTAATCAACTTAATTCAGGGTAATTAAGTAAGT
32385 AAGAAGCAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
104 5 0.04
105 39 0.34
106 71 0.61
107 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (105 bp):
GTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTTAATCAATTAAATCCAGGTAATTAAGTA
AGTCAATAATCAACTTAATTCAGGGTAATTAAGTAAGTCA
Found at i:33418 original size:24 final size:24
Alignment explanation
Indices: 33381--33427 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
33371 CTGCTTGCAT
*
33381 TTTATTATTCTTTATTCATGCCTG
1 TTTATCATTCTTTATTCATGCCTG
* *
33405 TTTATCATTGTTTATTCTTGCCT
1 TTTATCATTCTTTATTCATGCCT
33428 ATCTTTATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTATCATTCTTTATTCATGCCTG
Found at i:35464 original size:20 final size:20
Alignment explanation
Indices: 35427--35488 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
35417 TTCCCACCTG
35427 AAAAG-GAAAAAGAAGAAAA
1 AAAAGTGAAAAAGAAGAAAA
* *
35446 AAAAGTGAAAAGGATGAAAA
1 AAAAGTGAAAAAGAAGAAAA
* *
35466 AAAAATGAAGAAAAAAGAGAAA
1 AAAAGTGAA-AAAGAAGA-AAA
35488 A
1 A
35489 GAGAAAGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 5 0.15
20 20 0.59
21 5 0.15
22 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (20 bp):
AAAAGTGAAAAAGAAGAAAA
Found at i:37548 original size:35 final size:35
Alignment explanation
Indices: 37483--37549 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
37473 GGTTTCAAAT
* **
37483 TGATCCAGGGTGATCTTTGTTCAGTGAATTTCGGC
1 TGATCCAGGGTGATCTTTCTTCAGCAAATTTCGGC
*
37518 TGATCTAGGGTGATCTTTCTAT-AGCAAATTTC
1 TGATCCAGGGTGATCTTTCT-TCAGCAAATTTC
37550 AATTAACCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 26 0.96
36 1 0.04
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (35 bp):
TGATCCAGGGTGATCTTTCTTCAGCAAATTTCGGC
Found at i:37837 original size:64 final size:63
Alignment explanation
Indices: 37769--37950 Score: 192
Period size: 64 Copynumber: 2.8 Consensus size: 63
37759 AATTTCCACC
*
37769 TGACCCAAGGCGGTCCATTTTAAGTTAATTGATCCAGGGCGATCTTTCTTTAGATT-A-TTT-CA
1 TGACCCAGGGCGGTCCATTTT-AGTTAATTGATCCAGGGCGATCTTTCTTTAG-TTAAGTTTAC-
37831 G
63 G
* * * * *
37832 TTGACCCGGGGCGGTCCATTATTAGTTAATTGATCCAGGGTGGTCATTCTTCAGTTAAGGTTTAC
1 -TGACCCAGGGCGGTCCATT-TTAGTTAATTGATCCAGGGCGATCTTTCTTTAGTTAA-GTTTAC
37897 G
63 G
* * *
37898 -GACCCAGGGCGGTCCATCTTCAGTTAATTGGTCCAGGGCGATCTCTCTTTAGT
1 TGACCCAGGGCGGTCCAT-TTTAGTTAATTGATCCAGGGCGATCTTTCTTTAGT
37951 GAATTTCAAT
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
63 2 0.02
64 88 0.90
65 3 0.03
66 4 0.04
67 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (63 bp):
TGACCCAGGGCGGTCCATTTTAGTTAATTGATCCAGGGCGATCTTTCTTTAGTTAAGTTTACG
Found at i:38450 original size:14 final size:14
Alignment explanation
Indices: 38431--38458 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38421 GCGTATTAAT
38431 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
38445 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
38459 ACTACTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:38673 original size:20 final size:20
Alignment explanation
Indices: 38648--38686 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38638 AAATACAAGG
38648 CATTTGATTTACAAATTGGA
1 CATTTGATTTACAAATTGGA
*
38668 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
38687 TGCTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:41771 original size:55 final size:55
Alignment explanation
Indices: 41708--42177 Score: 690
Period size: 55 Copynumber: 8.5 Consensus size: 55
41698 TCAGTCCGAA
* * * **
41708 CAGT-AATCAGTAATTAAGTAAAAAGAGATTAATCGGAATTATGGTAATAGTAAT
1 CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
* * * *
41762 CAATAAATCAGTAATTAAGTAAAAAGAGACTAATCAGAGTTAAGGTAATAGTAAT
1 CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
* * *
41817 CAGTAAATCAGTAATTAAGTGAACAGAGATTAATCAAAGTCAAAGTAATAGTAAT
1 CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
* * *
41872 CAGTAAATTAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAAT
1 CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
* * *
41927 CAGTAAATCAGTAATTAAGTGAACAGAGATTAATCAAAGTCAAAGTAATAGTAAT
1 CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
41982 CAGTAAATCAGTAATTAAAGTAAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
1 CAGTAAATCAGTAATT-AAGT-AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
* *
42039 CAGTAAATTAGTAATTAAAGTAAAAAAAAGATTAATCAGAGTCAAAGTAATAGTAAT
1 CAGTAAATCAGTAATT-AAGT-AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
* *
42096 CAGTAAATCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAAGGTAATAGTAAT
1 CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
*
42151 CAGTAAATCAGTAATCAAGTAAAAAGA
1 CAGTAAATCAGTAATTAAGTAAAAAGA
42178 TAGTAATTAG
Statistics
Matches: 378, Mismatches: 35, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
54 3 0.01
55 265 0.70
56 8 0.02
57 102 0.27
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (55 bp):
CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAAT
Found at i:41981 original size:21 final size:20
Alignment explanation
Indices: 41957--42097 Score: 54
Period size: 21 Copynumber: 7.3 Consensus size: 20
41947 GAACAGAGAT
41957 TAATCAAAGTCAAAGTAATAG
1 TAATCAAAGT-AAAGTAATAG
*
41978 TAATC--AGTAAA-T--CAG
1 TAATCAAAGTAAAGTAATAG
* * *
41993 TAATTAAAGTAAA-AAAGAG
1 TAATCAAAGTAAAGTAATAG
*
42012 ATTAATCAGAGTCAAAGTAATAG
1 --TAATCAAAGT-AAAGTAATAG
42035 TAATC--AGTAAA-T--TAG
1 TAATCAAAGTAAAGTAATAG
* * *
42050 TAATTAAAGTAAA-AAAAAG
1 TAATCAAAGTAAAGTAATAG
*
42069 ATTAATCAGAGTCAAAGTAATAG
1 --TAATCAAAGT-AAAGTAATAG
42092 TAATCA
1 TAATCA
42098 GTAAATCAGT
Statistics
Matches: 89, Mismatches: 15, Indels: 32
0.65 0.11 0.24
Matches are distributed among these distances:
15 13 0.15
17 14 0.16
18 6 0.07
19 10 0.11
21 32 0.36
22 6 0.07
23 8 0.09
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TAATCAAAGTAAAGTAATAG
Found at i:42127 original size:224 final size:220
Alignment explanation
Indices: 41708--42177 Score: 710
Period size: 224 Copynumber: 2.1 Consensus size: 220
41698 TCAGTCCGAA
* * **
41708 CAGT-AATCAGTAATTAAGTAAAAAGAGATTAATCGGAATTATGGTAATAGTAATCAATAAATCA
1 CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCGAAATCAAAGTAATAGTAATCAATAAATCA
* *
41772 GTAATTAAGTAAAAAGAGACTAATCAGAGTTAAGGTAATAGTAATCAGTAAATCAGTAATTAAGT
66 GTAATTAAGTAAAAAGAGACTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGT
* * * *
41837 GAACAGAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAATTAGTAATTAAGTAAAAAGAGAT
131 AAAAAAAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
*
41902 TAATCAGAGTTAAGGTAATAGTAAT
196 TAATCAGAGTCAAGGTAATAGTAAT
* * *
41927 CAGTAAATCAGTAATTAAGTGAACAGAGATTAATC-AAAGTCAAAGTAATAGTAATCAGTAAATC
1 CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCGAAA-TCAAAGTAATAGTAATCAATAAATC
* *
41991 AGTAATTAAAGTAAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATTAGTAATTA
65 AGTAATT-AAGT-AAAAAGAGACTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATT-
* *
42056 AAGTAAAAAAAAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAG
127 AAGT-AAAAAAAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAA
42121 GAGATTAATCAGAGTCAAGGTAATAGTAAT
191 GAGATTAATCAGAGTCAAGGTAATAGTAAT
*
42151 CAGTAAATCAGTAATCAAGTAAAAAGA
1 CAGTAAATCAGTAATTAAGTAAAAAGA
42178 TAGTAATTAG
Statistics
Matches: 224, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
219 6 0.03
220 56 0.25
221 4 0.02
222 47 0.21
223 4 0.02
224 107 0.48
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (220 bp):
CAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCGAAATCAAAGTAATAGTAATCAATAAATCA
GTAATTAAGTAAAAAGAGACTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGT
AAAAAAAGATTAATCAAAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
TAATCAGAGTCAAGGTAATAGTAAT
Found at i:42559 original size:43 final size:42
Alignment explanation
Indices: 42511--42623 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 42
42501 GTAATCAGTA
* * *
42511 AAAGAGTAAAATAGTAATCAGTAAGAAGTAAGAAGGTAATCA-
1 AAAGAGTAAAATAGTAATCAGTAAAAAGCAA-AAGGCAATCAG
*
42553 ACAAGAGTAAAATAGTAGTCAGTAAAAAGCAAAAGGCAATCAG
1 A-AAGAGTAAAATAGTAATCAGTAAAAAGCAAAAGGCAATCAG
* *
42596 TAAAAAGTAAAAGAGTAATCAGTAAAAA
1 -AAAGAGTAAAATAGTAATCAGTAAAAA
42624 AAAGGAGCAG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
42 10 0.16
43 50 0.82
44 1 0.02
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (42 bp):
AAAGAGTAAAATAGTAATCAGTAAAAAGCAAAAGGCAATCAG
Found at i:42595 original size:21 final size:22
Alignment explanation
Indices: 42571--42623 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
42561 AAAATAGTAG
42571 TCAGTAAAAAGCAAAAG-GCAA
1 TCAGTAAAAAGCAAAAGAGCAA
* *
42592 TCAGTAAAAAGTAAAAGAGTAA
1 TCAGTAAAAAGCAAAAGAGCAA
42614 TCAGTAAAAA
1 TCAGTAAAAA
42624 AAAGGAGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.58, C:0.09, G:0.17, T:0.15
Consensus pattern (22 bp):
TCAGTAAAAAGCAAAAGAGCAA
Found at i:42686 original size:21 final size:21
Alignment explanation
Indices: 42640--42757 Score: 84
Period size: 21 Copynumber: 5.5 Consensus size: 21
42630 GCAGAAAATA
42640 GTAATCAGTAAAAGAGTAA-AATG
1 GTAATCAGT-AAA-AGTAAGAA-G
42663 GTAATCAGTAAAAGTAAGAAG
1 GTAATCAGTAAAAGTAAGAAG
** * *
42684 GTAATCAACAAGAGTAA-AATA
1 GTAATCAGTAAAAGTAAGAA-G
42705 GTAATCAGTACAAAGTAAAGAA-
1 GTAATCAGTA-AAAGT-AAGAAG
*
42727 -TAATCAGTAAAA-TAATGATG
1 GTAATCAGTAAAAGTAA-GAAG
*
42747 GTAGTCAGTAA
1 GTAATCAGTAA
42758 TTCACTAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
18 2 0.03
19 3 0.04
20 5 0.06
21 46 0.59
22 9 0.12
23 11 0.14
24 2 0.03
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (21 bp):
GTAATCAGTAAAAGTAAGAAG
Found at i:42731 original size:42 final size:41
Alignment explanation
Indices: 42651--42732 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 41
42641 TAATCAGTAA
*
42651 AAGAGTAAAATGGTAATCAGTAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAGTAAGAA-GTAATCAAC
42693 AAGAGTAAAATAGTAATCAGTACAAAGTAAAGAA-TAATCA
1 AAGAGTAAAATAGTAATCAGTA-AAAGT-AAGAAGTAATCA
42733 GTAAAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 27 0.73
43 5 0.14
44 5 0.14
ACGTcount: A:0.55, C:0.07, G:0.18, T:0.20
Consensus pattern (41 bp):
AAGAGTAAAATAGTAATCAGTAAAAGTAAGAAGTAATCAAC
Found at i:46882 original size:3 final size:3
Alignment explanation
Indices: 46876--46945 Score: 113
Period size: 3 Copynumber: 23.3 Consensus size: 3
46866 TTGGATGATG
* * *
46876 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATG GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46924 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
46946 GGAATAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:47219 original size:76 final size:76
Alignment explanation
Indices: 47087--47232 Score: 229
Period size: 76 Copynumber: 1.9 Consensus size: 76
47077 CTAGACTATG
** * *
47087 AGCAAAGGAATGATGAGTTTTAATCAAAAAGCTATTTTAAAATCAGTTTTAATCAAAGCAATGAT
1 AGCAAAGGAATGATGAGTTTTAATCAAAAAAATATTTCAAAATCAGTTTCAATCAAAGCAATGAT
47152 TTCGAGGTGTA
66 TTCGAGGTGTA
* * *
47163 AGCAAAGGAATGATGAGTTTTAATCAAAAAAATGTTTCAAAATCAGTTTCAGTCAAAGTAATGAT
1 AGCAAAGGAATGATGAGTTTTAATCAAAAAAATATTTCAAAATCAGTTTCAATCAAAGCAATGAT
47228 TTCGA
66 TTCGA
47233 AGGGACTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 63 1.00
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.31
Consensus pattern (76 bp):
AGCAAAGGAATGATGAGTTTTAATCAAAAAAATATTTCAAAATCAGTTTCAATCAAAGCAATGAT
TTCGAGGTGTA
Found at i:47649 original size:24 final size:23
Alignment explanation
Indices: 47614--47717 Score: 83
Period size: 23 Copynumber: 4.6 Consensus size: 23
47604 AATTTCCCAA
* *
47614 AAAAAAACAAAAAAAATGAAATG
1 AAAAAAAGAAAAAAAATGAAAAG
47637 AAAAAAATG--AAAAAATGAAAAG
1 AAAAAAA-GAAAAAAAATGAAAAG
* *
47659 AGAAAAAGAAAGATAAATGAAAA-
1 AAAAAAAGAAA-AAAAATGAAAAG
* * *
47682 AAAAAGAG-AAAAAGAGGAAATAG
1 AAAAAAAGAAAAAAAATGAAA-AG
47705 AAAAAAA-AAAAAA
1 AAAAAAAGAAAAAA
47718 GAGAAAACGC
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
21 8 0.12
22 21 0.33
23 25 0.39
24 10 0.16
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (23 bp):
AAAAAAAGAAAAAAAATGAAAAG
Found at i:47687 original size:29 final size:30
Alignment explanation
Indices: 47654--47724 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
47644 TGAAAAAATG
**
47654 AAAAGAGAAAAAGA-AAGATA-AATGAAAAA
1 AAAAGAGAAAAAGAGAA-ATAGAAAAAAAAA
47683 AAAAGAGAAAAAGAGGAAATAGAAAAAAAAA
1 AAAAGAGAAAAAGA-GAAATAGAAAAAAAAA
47714 AAAAGAGAAAA
1 AAAAGAGAAAA
47725 CGCAACGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 14 0.38
30 3 0.08
31 20 0.54
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.04
Consensus pattern (30 bp):
AAAAGAGAAAAAGAGAAATAGAAAAAAAAA
Found at i:47788 original size:45 final size:45
Alignment explanation
Indices: 47732--47833 Score: 179
Period size: 45 Copynumber: 2.3 Consensus size: 45
47722 AAACGCAACG
*
47732 ATGG-TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTCGATAAA
47776 ATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTCGATAAA
1 ATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTCGATAAA
*
47821 ATGGTTTTCCAAA
1 ATGGTTTTTCAAA
47834 TTTGTGTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
44 4 0.07
45 51 0.93
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (45 bp):
ATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTCGATAAA
Found at i:49018 original size:17 final size:17
Alignment explanation
Indices: 48996--49088 Score: 104
Period size: 17 Copynumber: 5.5 Consensus size: 17
48986 AAAAATGTAA
*
48996 AAAAAATGAAAG-AGAAG
1 AAAAAA-GAAAGAAAAAG
*
49013 AAAAAAGAGAGAAAAAG
1 AAAAAAGAAAGAAAAAG
49030 AAAAAAGAAAGAAAAAG
1 AAAAAAGAAAGAAAAAG
*
49047 AAAGAAA-AAAG--AGAG
1 AAA-AAAGAAAGAAAAAG
49062 AAAAAATGAAAGAAAAAG
1 AAAAAA-GAAAGAAAAAG
49080 AAAAAAGAA
1 AAAAAAGAA
49089 TGAAGAAAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.05
15 6 0.09
16 8 0.12
17 36 0.55
18 12 0.18
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAAGAAAAAG
Found at i:49027 original size:11 final size:11
Alignment explanation
Indices: 48996--49082 Score: 83
Period size: 11 Copynumber: 7.9 Consensus size: 11
48986 AAAAATGTAA
48996 AAAAAATGAAAG
1 AAAAAA-GAAAG
49008 AGAAGAAA-AAAG
1 A-AA-AAAGAAAG
* *
49020 AGAGAA-AAAG
1 AAAAAAGAAAG
49030 AAAAAAGAAAG
1 AAAAAAGAAAG
49041 -AAAAAGAAAG
1 AAAAAAGAAAG
*
49051 AAAAAAGAGAG
1 AAAAAAGAAAG
49062 AAAAAATGAAAG
1 AAAAAA-GAAAG
49074 -AAAAAGAAA
1 AAAAAAGAAA
49083 AAAGAATGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
10 24 0.38
11 25 0.39
12 10 0.16
13 2 0.03
14 3 0.05
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:49027 original size:38 final size:36
Alignment explanation
Indices: 48985--49100 Score: 126
Period size: 38 Copynumber: 3.0 Consensus size: 36
48975 CAAGTGCATG
*
48985 GAAAAATGTAAAAAAAATGAAAGAGAAGAAAAAAGAGA
1 GAAAAATG-AAAAAAAA-GAAAAAGAAGAAAAAAGAGA
49023 GAAAAA-GAAAAAAGAAAGAAAAAGAAAGAAAAAAGAGA
1 GAAAAATG-AAAAA-AAAGAAAAAG-AAGAAAAAAGAGA
49061 GAAAAAATGAAAGAAAAAGAAAAAAGAATGAAGAAAAGAG
1 G-AAAAATGAAA-AAAAAG-AAAAAGAA-GAA-AAAAGAG
49101 GCTCTAGGGT
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
37 12 0.18
38 23 0.34
39 14 0.21
40 12 0.18
41 7 0.10
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (36 bp):
GAAAAATGAAAAAAAAGAAAAAGAAGAAAAAAGAGA
Found at i:49099 original size:12 final size:10
Alignment explanation
Indices: 49008--49097 Score: 66
Period size: 11 Copynumber: 8.9 Consensus size: 10
48998 AAAATGAAAG
49008 AGAAGAAAAA
1 AGAAGAAAAA
*
49018 AG-AG-AGAA
1 AGAAGAAAAA
49026 A-AAGAAAAA
1 AGAAGAAAAA
49035 AGAA-AGAAAA
1 AGAAGA-AAAA
49045 AGAAAGAAAAA
1 AG-AAGAAAAA
49056 AGAGAGAAAAA
1 AGA-AGAAAAA
49067 ATGAA-AGAAAA
1 A-GAAGA-AAAA
49078 AGAA-AAAAGA
1 AGAAGAAAA-A
49088 ATGAAGAAAA
1 A-GAAGAAAA
49098 GAGGCTCTAG
Statistics
Matches: 66, Mismatches: 2, Indels: 22
0.73 0.02 0.24
Matches are distributed among these distances:
8 6 0.09
9 10 0.15
10 18 0.27
11 25 0.38
12 7 0.11
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (10 bp):
AGAAGAAAAA
Found at i:49431 original size:51 final size:51
Alignment explanation
Indices: 49372--49469 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
49362 AGTGTTATAA
* *
49372 ATAAGATTGCATTTCATTTGTGAGTCCAATATCAAAATTCGATTTTCGAAG
1 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCGAAG
*
49423 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTC
1 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTC
49470 AAAGGGCATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (51 bp):
ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCGAAG
Found at i:49977 original size:69 final size:69
Alignment explanation
Indices: 49888--50541 Score: 865
Period size: 69 Copynumber: 9.6 Consensus size: 69
49878 AATGCTTTGA
* *
49888 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
49953 GCGG
66 GGGG
* *
49957 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGATCAAGCCTTGGTTCCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
50022 AGGGG
65 AGGGG
* * *
50027 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTGAGTTCAAGCCTTGGTTCCATCCAAACAGTA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
50092 GGGG
66 GGGG
* *
50096 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCA-ATCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
50160 GCGG
66 GGGG
* *
50164 CTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
50229 AGGGG
65 AGGGG
* * *
50234 CTTTTCCACTAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCAGTA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
50299 GGGG
66 GGGG
* * * *
50303 CTTTTCCACAAGCCAATCTCGTTTCCACACGAGTCA-ATCAAGCCTTGGTTCTATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
50367 AGGG
66 GGGG
* * * * * * *
50371 C--TTCCACCAGCCAAACTCGATTCCACATGAGTCAATT-TAGCTTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
50433 AGGG
66 GGGG
* ** * * *
50437 CCTTTCCATTAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCCAAGCAG--
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
50499 GGGG
66 GGGG
* ** * *
50503 CTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTCAGT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACG-AGTCAGT
50542 CTTCCAAGAC
Statistics
Matches: 522, Mismatches: 56, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
66 85 0.16
67 7 0.01
68 143 0.27
69 159 0.30
70 128 0.25
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GGGG
Found at i:50049 original size:139 final size:137
Alignment explanation
Indices: 49888--50518 Score: 869
Period size: 139 Copynumber: 4.6 Consensus size: 137
49878 AATGCTTTGA
* *
49888 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* *
49953 GCGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGATCAAGCCTTGGTTCCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCA-ATCAAGCCTTGGTTCCATCCAAGC
*
50018 ATTCAGGGG
130 A-GCAGGGG
* * *
50027 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTGAGTTCAAGCCTTGGTTCCATCCAAACAGTA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
50092 GGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCA
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCA
*
50157 GCAGCGG
131 GCAGGGG
* *
50164 CTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
* * * *
50229 AGGGGCTTTTCCACTAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAG
65 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCA-ATCAAGCCTTGGTTCCATCCAAG
*
50294 CAGTAGGGG
129 CAGCAGGGG
* * * *
50303 CTTTTCCACAAGCCAATCTCGTTTCCACACGAGTCA-ATCAAGCCTTGGTTCTATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* * * * ** *
50367 AGGGC--TTCCACCAGCCAAACTCGATTCCACATGAGTCAATTTAGCTTTGGTTCCATCCAAGCA
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCA
*
50430 GCAAGGG
131 GCAGGGG
* ** * * *
50437 CCTTTCCATTAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCCAAGCAG--
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
50499 GGGGCTTTTCCATAAGCCAA
66 GGGGCTTTTCCACAAGCCAA
50519 GTTCATTTCC
Statistics
Matches: 436, Mismatches: 51, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
132 4 0.01
134 87 0.20
135 29 0.07
137 70 0.16
138 86 0.20
139 160 0.37
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (137 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCA
GCAGGGG
Found at i:50222 original size:207 final size:207
Alignment explanation
Indices: 49888--50518 Score: 963
Period size: 207 Copynumber: 3.1 Consensus size: 207
49878 AATGCTTTGA
* * * *
49888 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCA-ATCAAGCCTTGGTTCCATCCAAGCAGCA
*
49953 GCGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGATCAAGCCTTGGTTCCATCCAAGC
65 GCGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
* *
50018 ATTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTGAGTTCAAGCCTTGGTTCCATC
130 ATTCAGGGGCTTTTCCACTAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATC
*
50083 CAAACAGTAGGGG
195 CAAGCAGTAGGGG
50096 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAG
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAG
*
50161 CGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA
66 CGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA
50226 TTCAGGGGCTTTTCCACTAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCC
131 TTCAGGGGCTTTTCCACTAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCC
50291 AAGCAGTAGGGG
196 AAGCAGTAGGGG
* *
50303 CTTTTCCACAAGCCAATCTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCTATCCAAGCAGCAA
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGC-A
* * * * * * *
50368 G-GGC--TTCCACCAGCCAAACTCGATTCCACATGAGTCAATT-TAGCTTTGGTTCCATCCAAGC
65 GCGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
* * * * * *
50429 A-GCAAGGGCCTTTCCATTAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATC
130 ATTCAGGGGCTTTTCCACTAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATC
50492 CAAGCAG--GGGG
195 CAAGCAGTAGGGG
*
50503 CTTTTCCATAAGCCAA
1 CTTTTCCACAAGCCAA
50519 GTTCATTTCC
Statistics
Matches: 396, Mismatches: 26, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
200 19 0.05
202 22 0.06
203 41 0.10
204 20 0.05
205 30 0.08
207 227 0.57
208 37 0.09
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (207 bp):
CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATCAAGCCTTGGTTCCATCCAAGCAGCAG
CGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA
TTCAGGGGCTTTTCCACTAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCC
AAGCAGTAGGGG
Found at i:52132 original size:18 final size:19
Alignment explanation
Indices: 52095--52132 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
52085 ACTTTGCAGC
52095 ATGGATTTTACAATAGGAG
1 ATGGATTTTACAATAGGAG
52114 ATGGATTTTACAA-AGGAG
1 ATGGATTTTACAATAGGAG
52132 A
1 A
52133 AAAGGGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (19 bp):
ATGGATTTTACAATAGGAG
Done.