Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006189.1 Corchorus capsularis cultivar CVL-1 contig06207, 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: 61054
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:179 original size:26 final size:25
Alignment explanation
Indices: 150--199 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
140 TATGATTAAA
150 ATGCAAC-AATACTAAGCTAAATGAAG
1 ATGCAACTAATA-TAA-CTAAATGAAG
*
176 ATGCAACTAATATTACTAAATGAA
1 ATGCAACTAATATAACTAAATGAA
200 AATATGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 9 0.41
27 4 0.18
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (25 bp):
ATGCAACTAATATAACTAAATGAAG
Found at i:2249 original size:70 final size:69
Alignment explanation
Indices: 2162--2746 Score: 477
Period size: 70 Copynumber: 8.6 Consensus size: 69
2152 TGCAAAAATA
** * *
2162 TGACAAAACTAATCCTTTGTCTGGAAGGGTATTTTGGGAATCGAAAACGCTGAACTTAGATGCTA
1 TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGGAAT-GAAAATGCTGAACTTAGATGCTA
2227 GAATG
65 GAATG
* ** * * *
2232 TGACAAAACTAGCCCTTTGTCTGAATGGGCGTTTT-GG---GAAAA--CTAGAACCTAAATGCAA
1 TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGGAATGAAAATGCT-GAACTTAGATGCTA
*
2291 AAATG
65 GAATG
* * * * *
2296 TGACAAAACTAACCCTTTGTCTGAAAGGGTATTTTGGGAATAAAAAATGCTAAACTTAGATACTG
1 TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGGAAT-GAAAATGCTGAACTTAGATGCTA
2361 GAATG
65 GAATG
* * * * * *
2366 TGACAAAACTAGGCCTTTGTCTGAAAGGGCATTTTTGG---GAAAA--CTAGAACGTAAATGCAA
1 TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGGAATGAAAATGCT-GAACTTAGATGCTA
*
2426 AAATG
65 GAATG
* * * * * *
2431 TGGCAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATAAAAAATGCTAAACTTAGATACT-
1 TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGGAAT-GAAAATGCTGAACTTAGATGCTA
2495 GCAATG
65 G-AATG
* ** * * *
2501 TGACAAAACTAGCCCTTTGTCTAAAAGGGCGTTTTTGG---GAAAA--CTAGAACTTAAATGCAA
1 TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGGAATGAAAATGCT-GAACTTAGATGCTA
*
2561 AAATG
65 GAATG
* * * * * * *
2566 TGGCAAAACTAACCCTTTGTCCGAAAGGGTATTTTGAGAATCAAAAATGCTGAACTTAGATACTG
1 TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGGAAT-GAAAATGCTGAACTTAGATGCTA
2631 GAATG
65 GAATG
* ** *
2636 TGACAAAACTAGCTCTTTGTCTGAAAGGGCGTTTTGGGAAATTGAAAATGCTAAACTTAGA-GAC
1 TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGG-AA-TGAAAATGCTGAACTTAGATG-C
*
2700 TGGAATG
63 TAGAATG
* * * *
2707 TGACAAAACTAGCCATTTATCCGAAAGGGTGTTTTGGGAA
1 TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGGAA
2747 AACTAGAACC
Statistics
Matches: 399, Mismatches: 89, Indels: 54
0.74 0.16 0.10
Matches are distributed among these distances:
63 2 0.01
64 50 0.13
65 94 0.24
66 8 0.02
69 14 0.04
70 165 0.41
71 65 0.16
72 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (69 bp):
TGACAAAACTAGCCCTTTGTCTGAAAGGGTATTTTGGGAATGAAAATGCTGAACTTAGATGCTAG
AATG
Found at i:2457 original size:135 final size:134
Alignment explanation
Indices: 2077--2676 Score: 894
Period size: 135 Copynumber: 4.5 Consensus size: 134
2067 TTTAGGACTA
* * * * * * *
2077 CTAAACTTAAATGCAGGAATGTGACGAAACTAGCCCCTTGTCCGAAAGGGCGTTTTGGGAAAACC
1 CTAAACTTAGATACTGGAATGTGACAAAACTAGCCCTTTGTCTGAAAGGGCGTTTTGGGAAAACT
* * * * * **
2142 AGATCCTAAATGCAAAAATATGACAAAACTAATCCTTTGTCTGGAAGGGTATTTTGGGAATCGAA
66 AGAACCTAAATGCAAAAATGTGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATAAAA
*
2207 AACG
131 AATG
* * * *
2211 CTGAACTTAGATGCTAGAATGTGACAAAACTAGCCCTTTGTCTGAATGGGCGTTTTGGGAAAACT
1 CTAAACTTAGATACTGGAATGTGACAAAACTAGCCCTTTGTCTGAAAGGGCGTTTTGGGAAAACT
*
2276 AGAACCTAAATGCAAAAATGTGACAAAACTAACCCTTTGTCTGAAAGGGTATTTTGGGAATAAAA
66 AGAACCTAAATGCAAAAATGTGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATAAAA
2341 AATG
131 AATG
* *
2345 CTAAACTTAGATACTGGAATGTGACAAAACTAGGCCTTTGTCTGAAAGGGCATTTTTGGGAAAAC
1 CTAAACTTAGATACTGGAATGTGACAAAACTAGCCCTTTGTCTGAAAGGGC-GTTTTGGGAAAAC
* *
2410 TAGAACGTAAATGCAAAAATGTGGCAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATAAA
65 TAGAACCTAAATGCAAAAATGTGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATAAA
2475 AAATG
130 AAATG
* *
2480 CTAAACTTAGATACTGCAATGTGACAAAACTAGCCCTTTGTCTAAAAGGGCGTTTTTGGGAAAAC
1 CTAAACTTAGATACTGGAATGTGACAAAACTAGCCCTTTGTCTGAAAGGGCG-TTTTGGGAAAAC
* * * *
2545 TAGAACTTAAATGCAAAAATGTGGCAAAACTAACCCTTTGTCCGAAAGGGTATTTTGAGAATCAA
65 TAGAACCTAAATGCAAAAATGTGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATAAA
2610 AAATG
130 AAATG
* *
2615 CTGAACTTAGATACTGGAATGTGACAAAACTAGCTCTTTGTCTGAAAGGGCGTTTTGGGAAA
1 CTAAACTTAGATACTGGAATGTGACAAAACTAGCCCTTTGTCTGAAAGGGCGTTTTGGGAAA
2677 TTGAAAATGC
Statistics
Matches: 428, Mismatches: 36, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
134 174 0.41
135 254 0.59
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (134 bp):
CTAAACTTAGATACTGGAATGTGACAAAACTAGCCCTTTGTCTGAAAGGGCGTTTTGGGAAAACT
AGAACCTAAATGCAAAAATGTGACAAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATAAAA
AATG
Found at i:3608 original size:52 final size:51
Alignment explanation
Indices: 3547--3646 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 51
3537 TATCACCAAT
* * * *
3547 TCACCAAAATTGAAACTTTTTAAGGCTACA-GATTGTATTTTTTATTTTAATC
1 TCACCAAAATTAAAACTTTTCAAGACTA-ATGATTGTA-TTGTTATTTTAATC
3599 TCACCAAAATTAAAACTTTTCAAGACTAATGATTGTATTGTTATTTTA
1 TCACCAAAATTAAAACTTTTCAAGACTAATGATTGTATTGTTATTTTA
3647 TTATTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 11 0.26
52 32 0.74
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (51 bp):
TCACCAAAATTAAAACTTTTCAAGACTAATGATTGTATTGTTATTTTAATC
Found at i:3950 original size:53 final size:51
Alignment explanation
Indices: 3882--4001 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 51
3872 TCAAAATTCT
* * *
3882 AATCTTTAAGCTAAAAG-TTCTTACTTTTTACACAT-TATATGAACAAAAGATTC
1 AATCTTTAAACTAAAAGATT-TTACTCTTT--ACATGT-TATGAACAAAAGATCC
* *
3935 AATTTTTAAATTAAAAGATTTTACTCTTTACATGTTATGAACAAAAGATCC
1 AATCTTTAAACTAAAAGATTTTACTCTTTACATGTTATGAACAAAAGATCC
3986 AATCTTTAAACTAAAA
1 AATCTTTAAACTAAAA
4002 AGCTTGTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
51 33 0.57
52 1 0.02
53 22 0.38
54 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (51 bp):
AATCTTTAAACTAAAAGATTTTACTCTTTACATGTTATGAACAAAAGATCC
Found at i:5451 original size:32 final size:32
Alignment explanation
Indices: 5415--5502 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
5405 TCCGAACCCG
* *
5415 AACCCAAAAAAACACGAACTCGAAAAAGCTTA
1 AACCCAAAAAAACACGAACCCGAAAAAGCTGA
* *
5447 AACCCGAAAAAATCA-GAACCCGAAAAATCTGA
1 AACCC-AAAAAAACACGAACCCGAAAAAGCTGA
* *
5479 AACCCGAAAAAACCCGAACCCGAA
1 AACCCAAAAAAACACGAACCCGAA
5503 CCTGAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 33 0.70
33 8 0.17
ACGTcount: A:0.53, C:0.28, G:0.11, T:0.07
Consensus pattern (32 bp):
AACCCAAAAAAACACGAACCCGAAAAAGCTGA
Found at i:5498 original size:16 final size:16
Alignment explanation
Indices: 5409--5502 Score: 73
Period size: 16 Copynumber: 5.9 Consensus size: 16
5399 AACCCGTCCG
*
5409 AACCCGAACCCAAAAA
1 AACCCGAACCCGAAAA
* *
5425 AACACGAACTCGAAAA
1 AACCCGAACCCGAAAA
* ***
5441 AGCTTAAACCCGAAAA
1 AACCCGAACCCGAAAA
* *
5457 AATCAGAACCCG-AAA
1 AACCCGAACCCGAAAA
* *
5472 AATCTGAAACCCGAAAA
1 AACCCG-AACCCGAAAA
5489 AACCCGAACCCGAA
1 AACCCGAACCCGAA
5503 CCTGAAAAAA
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
15 8 0.13
16 45 0.75
17 7 0.12
ACGTcount: A:0.52, C:0.30, G:0.12, T:0.06
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:5789 original size:17 final size:16
Alignment explanation
Indices: 5763--5794 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5753 CAATCTAAAT
5763 TTAACCCGAACCCGAC
1 TTAACCCGAACCCGAC
5779 TTAAGCCCGAACCCGA
1 TTAA-CCCGAACCCGA
5795 AAATAGACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.31, C:0.41, G:0.16, T:0.12
Consensus pattern (16 bp):
TTAACCCGAACCCGAC
Found at i:6834 original size:2 final size:2
Alignment explanation
Indices: 6827--6858 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6817 TTCATTAGTA
6827 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
6859 CACTCATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10290 original size:62 final size:62
Alignment explanation
Indices: 10086--10499 Score: 289
Period size: 63 Copynumber: 6.6 Consensus size: 62
10076 TATGTTCGGT
** * * *
10086 TTTCCCAAAATACCCTTTCGGATGAAGCGTCAGTTTTGTCACATTCTCTCATATAGTTTCAG
1 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACATTCTCGCATATAGTTTCAA
* * * * * * *
10148 TTTCCC--AATACCCTTTCAGACAAAGGGTCAGTTTTGTTACATTTATAGCATCTATTTTCGA
1 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACA-TTCTCGCATATAGTTTCAA
* *
10209 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGCCACATCCTCGCATATAGTTTCAA
1 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACATTCTCGCATATAGTTTCAA
* * * ** * * * * * **
10271 TTTCCCAGAATACCCTTTCGGATAAAGGGTCAGCTCAGTCACACTCCCGCATTTAATCTCTGG
1 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACATTCTCGCATATAGTTTC-AA
* * * ** * * * *
10334 TTTCGCTAAATGCCCTTTTAGACAAAGGGTCAATTTTCTCACAAATCT-GCATACAAGTTT-AA
1 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCAC-ATTCTCGCATA-TAGTTTCAA
* * ** * * *
10396 TCTTGGATTCCTAGAATACCCTTTCGGACAAAGGGTCAACTTTGTCACTCTTCTTGCATTTAGAT
1 ---T---TTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCAC-ATTCTCGCATATAG-T
*
10461 TT-TA
58 TTCAA
*
10465 CTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTT
1 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTT
10500 CTATCATGTT
Statistics
Matches: 263, Mismatches: 75, Indels: 27
0.72 0.21 0.07
Matches are distributed among these distances:
60 30 0.11
61 18 0.07
62 67 0.25
63 96 0.37
64 6 0.02
65 1 0.00
68 37 0.14
69 8 0.03
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (62 bp):
TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTTGTCACATTCTCGCATATAGTTTCAA
Found at i:13732 original size:41 final size:40
Alignment explanation
Indices: 13654--13925 Score: 373
Period size: 40 Copynumber: 6.7 Consensus size: 40
13644 CTAAAGGCTT
*
13654 AATTAAGTCTATGCTTACTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
*
13694 AATTAAGTCTGTGCTTACATTTACCTAATTTCCATCCTTGA
1 AATTAAGTCTGTGCTTAC-TTTACCTAATTTCCTTCCTTGA
* *
13735 AATTAAGTATGTGTTTTACTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTG-CTTACTTTACCTAATTTCCTTCCTTGA
*
13776 AATTAAGTATGTGCTTACTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
* * * *
13816 AATTAAGTCTATGCTTACTTTTCTTAATTTCCCTCCTTGA
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
* * * * *
13856 AATTAAGTCTATGCTTACTTTTCTTAAATTCCCTCCTTGA
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
* *
13896 AATTAAGTTTGTGCTTATCTTTACTTAATT
1 AATTAAGTCTGTGCTTA-CTTTACCTAATT
13926 ACCATGAATT
Statistics
Matches: 213, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
40 132 0.62
41 77 0.36
42 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (40 bp):
AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGA
Found at i:13964 original size:37 final size:37
Alignment explanation
Indices: 13915--14208 Score: 394
Period size: 37 Copynumber: 7.9 Consensus size: 37
13905 TGTGCTTATC
*
13915 TTTACTTAATTACCATGAATTAACTCCTTTTACTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTTACTGCT
* *
13952 TTTATTTAATTACCATGAATAAAGT-CTTTTAACTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTT-ACTGCT
* *
13989 TTTACTTAATTACCCTGAATTAAGTCATTTTACTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTTACTGCT
*
14026 TTTACTTAATTACCATGAATTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTTACTGCT
* *
14063 TTTACTTAATTACCATGAATTAAGTCCTTTAATTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTTACTGCT
* * * * *
14100 TTTACTTAATTTCCCTAAATTAAGTCCTATAACTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTTACTGCT
* *
14137 TTTACTTAATTTCCCTGAATTAAGTCC-TTTAGCTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTTA-CTGCT
* * *
14174 TTTACTTAATTTCCTTGGATTAAGTCCTTTTACTG
1 TTTACTTAATTACCATGAATTAAGTCCTTTTACTG
14209 ACTGCGTTCT
Statistics
Matches: 232, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
36 7 0.03
37 217 0.94
38 8 0.03
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (37 bp):
TTTACTTAATTACCATGAATTAAGTCCTTTTACTGCT
Found at i:14313 original size:42 final size:43
Alignment explanation
Indices: 14258--14341 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
14248 ACCGTGTTTA
14258 CTTAATTACCCTGAATTAAG-TTCT-TTGACTGCGTTTTCTTTT
1 CTTAATTACCCTGAATTAAGATT-TGTTGACTGCGTTTTCTTTT
*
14300 CTTAATTGA-CCTGAATTAAGACTTTGTTGACTGTGTTTTCTT
1 CTTAATT-ACCCTGAATTAAGA-TTTGTTGACTGCGTTTTCTT
14342 AGCCCTTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 18 0.49
43 2 0.05
44 17 0.46
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (43 bp):
CTTAATTACCCTGAATTAAGATTTGTTGACTGCGTTTTCTTTT
Found at i:15458 original size:18 final size:18
Alignment explanation
Indices: 15435--15473 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
15425 AATGACATGG
15435 CATTTA-ATAACATATAAA
1 CATTTAGATAA-ATATAAA
*
15453 CATTTAGGTAAATATAAA
1 CATTTAGATAAATATAAA
15471 CAT
1 CAT
15474 GGATGCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (18 bp):
CATTTAGATAAATATAAA
Found at i:27633 original size:16 final size:16
Alignment explanation
Indices: 27600--27653 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
27590 GGCAATTGGG
***
27600 CGGGTTCGGGTGGGTT
1 CGGGTTCGGGTTATTT
*
27616 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTTATTT
*
27632 CGGCTTCGGG-TATTT
1 CGGGTTCGGGTTATTT
27647 CGGGTTC
1 CGGGTTC
27654 AGGCTCGGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 10 0.31
16 22 0.69
ACGTcount: A:0.02, C:0.17, G:0.43, T:0.39
Consensus pattern (16 bp):
CGGGTTCGGGTTATTT
Found at i:28479 original size:12 final size:12
Alignment explanation
Indices: 28447--28496 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
28437 TATTTTGATC
*
28447 TCGGGCTCAGG-
1 TCGGGCTCGGGT
28458 TCGGGCTCGGGT
1 TCGGGCTCGGGT
*
28470 TCGGGTTCGGGT
1 TCGGGCTCGGGT
*
28482 T--GTCTCGGGT
1 TCGGGCTCGGGT
28492 TCGGG
1 TCGGG
28497 TATTTTCGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.26
11 10 0.32
12 13 0.42
ACGTcount: A:0.02, C:0.22, G:0.48, T:0.28
Consensus pattern (12 bp):
TCGGGCTCGGGT
Found at i:28491 original size:16 final size:16
Alignment explanation
Indices: 28470--28529 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
28460 GGGCTCGGGT
28470 TCGGGTTCGGGT-TGTC
1 TCGGGTTCGGGTAT-TC
*
28486 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTATTC
28502 TCGGGTTCGGGTAATT-
1 TCGGGTTCGGGT-ATTC
*
28518 TTGGGTTCGGGT
1 TCGGGTTCGGGT
28530 TCGGGATGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
16 36 0.90
17 4 0.10
ACGTcount: A:0.05, C:0.13, G:0.42, T:0.40
Consensus pattern (16 bp):
TCGGGTTCGGGTATTC
Found at i:28524 original size:32 final size:32
Alignment explanation
Indices: 28469--28529 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
28459 CGGGCTCGGG
**
28469 TTCGGGTTCGGGTTGTCTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTAATCTCGGGTTCGGGTATT
* *
28501 TTCGGGTTCGGGTAATTTTGGGTTCGGGT
1 TTCGGGTTCGGGTAATCTCGGGTTCGGGT
28530 TCGGGATGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.05, C:0.13, G:0.41, T:0.41
Consensus pattern (32 bp):
TTCGGGTTCGGGTAATCTCGGGTTCGGGTATT
Found at i:28593 original size:17 final size:17
Alignment explanation
Indices: 28567--28600 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28557 CGGGTAATTT
28567 CGGGTTCGGG-TTCGGG
1 CGGGTTCGGGTTTCGGG
28583 CGGGTTTCGGGTTTCGGG
1 CGGG-TTCGGGTTTCGGG
28601 TTCATTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (17 bp):
CGGGTTCGGGTTTCGGG
Found at i:37941 original size:124 final size:124
Alignment explanation
Indices: 37721--37963 Score: 414
Period size: 124 Copynumber: 2.0 Consensus size: 124
37711 ATGAGGTTGG
*
37721 CCCCACAAATATTAAATGGGCTTTTACAAACAAATTAGAATAAACAAAGTGGTTACAACCCCAAT
1 CCCCACAAATATTAAATGGGCTTTTACAAACAAATTACAATAAACAAAGTGGTTACAACCCCAAT
* * *
37786 AAAAATAAAGTTTAAGAGGTCAAATGTAATAAAGGGTATTGCTAAACACCGCCCCTTGA
66 AAAAATAAAATTTAAGAGGCCAAAAGTAATAAAGGGTATTGCTAAACACCGCCCCTTGA
* *
37845 CCCCACAAATATTAAATGGGCTTTTATAAACAAATTACAATAAACAAAGTGGTTCCAACCCCAAT
1 CCCCACAAATATTAAATGGGCTTTTACAAACAAATTACAATAAACAAAGTGGTTACAACCCCAAT
* *
37910 AAACATAAAATTTAAGAGGCCAAAAGTAATAAAGGGTGTTGCTAAACACCGCCC
66 AAAAATAAAATTTAAGAGGCCAAAAGTAATAAAGGGTATTGCTAAACACCGCCC
37964 GTAAAAGTGT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
124 111 1.00
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.23
Consensus pattern (124 bp):
CCCCACAAATATTAAATGGGCTTTTACAAACAAATTACAATAAACAAAGTGGTTACAACCCCAAT
AAAAATAAAATTTAAGAGGCCAAAAGTAATAAAGGGTATTGCTAAACACCGCCCCTTGA
Found at i:38750 original size:9 final size:9
Alignment explanation
Indices: 38734--38773 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
38724 TTACAAATAC
38734 AAATGTTAT
1 AAATGTTAT
*
38743 ACATGTTAT
1 AAATGTTAT
*
38752 AAATGTTCT
1 AAATGTTAT
*
38761 AAATGTTAA
1 AAATGTTAT
38770 AAAT
1 AAAT
38774 ACAAATCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (9 bp):
AAATGTTAT
Found at i:44473 original size:27 final size:26
Alignment explanation
Indices: 44442--44515 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
44432 TAGTGGACCT
44442 AAAATGACCGAAATGCCCCTGAATGTGC
1 AAAATGACCGAAATGCCCCT-AA-GTGC
** * *
44470 -AAATGACTAAAATG-CCATTAGTGC
1 AAAATGACCGAAATGCCCCTAAGTGC
44494 AAAAATGACCGAAATGCCCCTA
1 -AAAATGACCGAAATGCCCCTA
44516 TGTGACCCTG
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
24 4 0.11
25 1 0.03
26 15 0.43
27 15 0.43
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.19
Consensus pattern (26 bp):
AAAATGACCGAAATGCCCCTAAGTGC
Found at i:49682 original size:22 final size:21
Alignment explanation
Indices: 49657--49726 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
49647 ATTATGTATC
49657 ATTCTCACTCTTGCATTACATG
1 ATTCTCA-TCTTGCATTACATG
* * * *
49679 ATTCTTAT-GTCCATTATATG
1 ATTCTCATCTTGCATTACATG
*
49699 TCATTCTCATTCTTGCATTACATA
1 --ATTCTCA-TCTTGCATTACATG
49723 ATTC
1 ATTC
49727 ATAATGCCAG
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
20 9 0.26
21 1 0.03
22 16 0.46
23 1 0.03
24 8 0.23
ACGTcount: A:0.24, C:0.23, G:0.07, T:0.46
Consensus pattern (21 bp):
ATTCTCATCTTGCATTACATG
Found at i:52950 original size:13 final size:13
Alignment explanation
Indices: 52920--52983 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
52910 AGAGTCATGG
*
52920 TTTTCAAAAATGTTT
1 TTTTCAAAAA--TAT
52935 TTTTCAAAAATAT
1 TTTTCAAAAATAT
* *
52948 TTTTCAAAATGTCT
1 TTTTCAAAA-ATAT
*
52962 TTTTCAAAAATGT
1 TTTTCAAAAATAT
52975 TTTTCAAAA
1 TTTTCAAAA
52984 GAGAGTCATG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
13 22 0.51
14 11 0.26
15 10 0.23
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (13 bp):
TTTTCAAAAATAT
Found at i:52958 original size:27 final size:27
Alignment explanation
Indices: 52920--52983 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
52910 AGAGTCATGG
*
52920 TTTTCAAAAATGTTTTTTTCAAAAATAT
1 TTTTC-AAAATGTCTTTTTCAAAAATAT
*
52948 TTTTCAAAATGTCTTTTTCAAAAATGT
1 TTTTCAAAATGTCTTTTTCAAAAATAT
52975 TTTTCAAAA
1 TTTTCAAAA
52984 GAGAGTCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (27 bp):
TTTTCAAAATGTCTTTTTCAAAAATAT
Found at i:53026 original size:12 final size:13
Alignment explanation
Indices: 53011--53044 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
53001 AAAAAGTTTC
53011 TTTTCAAAAATG-
1 TTTTCAAAAATGT
53023 TTTTCAAAAATGT
1 TTTTCAAAAATGT
53036 TTTTCAAAA
1 TTTTCAAAA
53045 GTAATTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTTCAAAAATGT
Found at i:53027 original size:17 final size:16
Alignment explanation
Indices: 52995--53025 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52985 AGAGTCATGG
52995 TTTTCAAAAAAGTTTC
1 TTTTCAAAAAAGTTTC
*
53011 TTTTCAAAAATGTTT
1 TTTTCAAAAAAGTTT
53026 TCAAAAATGT
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:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTTCAAAAAAGTTTC
Found at i:53039 original size:13 final size:13
Alignment explanation
Indices: 52920--53044 Score: 83
Period size: 15 Copynumber: 8.7 Consensus size: 13
52910 AGAGTCATGG
52920 TTTTCAAAAATGTTT
1 TTTTCAAAAATG--T
*
52935 TTTTCAAAAATAT
1 TTTTCAAAAATGT
52948 TTTTC-AAAATGTCT
1 TTTTCAAAAATG--T
52962 TTTTCAAAAATGT
1 TTTTCAAAAATGT
*
52975 TTTTCAAAAGAGAGTCATGG
1 TTTTC--AA-A-A---ATGT
*
52995 TTTTCAAAAAAGTTT
1 TTTTC-AAAAA-TGT
53010 CTTTTCAAAAATG-
1 -TTTTCAAAAATGT
53023 TTTTCAAAAATGT
1 TTTTCAAAAATGT
53036 TTTTCAAAA
1 TTTTCAAAA
53045 GTAATTTTCG
Statistics
Matches: 91, Mismatches: 6, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
12 17 0.19
13 21 0.23
14 8 0.09
15 25 0.27
16 6 0.07
17 2 0.02
18 1 0.01
19 3 0.03
20 8 0.09
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTTCAAAAATGT
Found at i:53702 original size:21 final size:21
Alignment explanation
Indices: 53648--53703 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
53638 TTCCAAGTGC
*
53648 AATG-AAAAAAATAATGAAAA
1 AATGAAAAAAAAAAATGAAAA
* **
53668 AATGAAAAGAAAAAATGATGA
1 AATGAAAAAAAAAAATGAAAA
53689 AATGAAAAAAAAAAA
1 AATGAAAAAAAAAAA
53704 GAGCTCTAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (21 bp):
AATGAAAAAAAAAAATGAAAA
Found at i:54841 original size:38 final size:37
Alignment explanation
Indices: 54793--54876 Score: 116
Period size: 38 Copynumber: 2.3 Consensus size: 37
54783 TCACCTCTTA
* * * *
54793 ACAATCATCAAAGTTGACTAGAAACATGTCATCTTTC
1 ACAATTATCAAAGTTCACTAGAAACAGGTCATCTATC
54830 AGCAATTATCAAAGTTCACTAGAAACAGGTCATCTATC
1 A-CAATTATCAAAGTTCACTAGAAACAGGTCATCTATC
54868 A-AATTATCA
1 ACAATTATCA
54877 GAGGTCATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 8 0.19
37 1 0.02
38 33 0.79
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (37 bp):
ACAATTATCAAAGTTCACTAGAAACAGGTCATCTATC
Found at i:54884 original size:22 final size:22
Alignment explanation
Indices: 54856--54898 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
54846 CACTAGAAAC
54856 AGGTCATCTATC-AAATTATCAG
1 AGGTCATCT-TCAAAATTATCAG
54878 AGGTCATCTTCAAAATTATCA
1 AGGTCATCTTCAAAATTATCA
54899 AAGTTGACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (22 bp):
AGGTCATCTTCAAAATTATCAG
Found at i:54949 original size:36 final size:37
Alignment explanation
Indices: 54904--55158 Score: 286
Period size: 38 Copynumber: 6.9 Consensus size: 37
54894 TATCAAAGTT
54904 GACTGGAAACAGGTCATCTTTCAGCAATTATC-TTTC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCATTTC
* *
54940 GACTTGAAACAAGTCATCTTTCAGCAATTATC-TTTC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCATTTC
* * * * **
54976 GACTGGAAACATGTCGTCTTTCAACAGTTATCAAGATC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATC-ATTTC
* * * *
55014 GACTGGAAACAGGCCATCTTTCAACAGTTATCAAGGTT-
1 GACTGGAAACAGGTCATCTTTCAGCAATTATC-A-TTTC
*
55052 GACTGGAAACAGGTCATCTTTCAGCAATTATCAAGATT-
1 GACTGGAAACAGGTCATCTTTCAGCAATTATC-A-TTTC
*
55090 GACTGGAAACATGTCATCTTTCAGCAATTATC-TTTC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCATTTC
* *
55126 GACTGGAAACAGGTCATCTTTCAACAGTTATCA
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCA
55159 AGACCGATTG
Statistics
Matches: 192, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
35 2 0.01
36 90 0.47
38 98 0.51
39 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (37 bp):
GACTGGAAACAGGTCATCTTTCAGCAATTATCATTTC
Found at i:55023 original size:38 final size:38
Alignment explanation
Indices: 54878--55186 Score: 276
Period size: 38 Copynumber: 8.3 Consensus size: 38
54868 AAATTATCAG
* *
54878 AGGTCATC-TTCAA-AATTATCAA-AGTTGACTGGAAAC
1 AGGTCATCTTTCAACAGTTATCAAGA-TCGACTGGAAAC
* * ** *
54914 AGGTCATCTTTCAGCAATTATC--TTTCGACTTGAAAC
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAAC
* * * **
54950 AAGTCATCTTTCAGCAATTATC--TTTCGACTGGAAAC
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAAC
* *
54986 ATGTCGTCTTTCAACAGTTATCAAGATCGACTGGAAAC
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAAC
* * *
55024 AGGCCATCTTTCAACAGTTATCAAGGTTGACTGGAAAC
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAAC
* * *
55062 AGGTCATCTTTCAGCAATTATCAAGATTGACTGGAAAC
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAAC
* * * **
55100 ATGTCATCTTTCAGCAATTATC--TTTCGACTGGAAAC
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAAC
* * *
55136 AGGTCATCTTTCAACAGTTATCAAGACCGATTGAAAAC
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAAC
* *
55174 GGGTCATTTTTCA
1 AGGTCATCTTTCA
55187 GTGGTTTTCG
Statistics
Matches: 231, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
36 100 0.43
37 4 0.02
38 127 0.55
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (38 bp):
AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAAC
Found at i:55179 original size:112 final size:110
Alignment explanation
Indices: 54880--55187 Score: 322
Period size: 112 Copynumber: 2.8 Consensus size: 110
54870 ATTATCAGAG
* * * * **
54880 GTCATC-TTCAA-AATTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATC--TTTCG
1 GTCATCTTTCAACAATTATCAGA-TCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGATCG
* *
54941 ACTTGAAACAAGTCATCTTTCAGCAATTATCTTTCGACTGGAAACAT
65 A-TTGAAACAGGTCATCTTTCAGCAATTATCATTCGACTGGAAACAT
* * * * *
54988 GTCGTCTTTCAACAGTTATCAAGATCGACTGGAAACAGGCCATCTTTCAACAGTTATCAAGGTTG
1 GTCATCTTTCAACAATTATC-AGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGATCG
*
55053 ACTGGAAACAGGTCATCTTTCAGCAATTATCAAGATT-GACTGGAAACAT
65 A-TTGAAACAGGTCATCTTTCAGCAATTATC---ATTCGACTGGAAACAT
* ** *
55102 GTCATCTTTCAGCAATTATC-TTTCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGACCGA
1 GTCATCTTTCAACAATTATCAGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGATCGA
* *
55166 TTGAAAACGGGTCATTTTTCAG
66 TTG-AAACAGGTCATCTTTCAG
55188 TGGTTTTCGG
Statistics
Matches: 166, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
108 5 0.03
109 5 0.03
110 36 0.22
111 4 0.02
112 85 0.51
114 29 0.17
115 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (110 bp):
GTCATCTTTCAACAATTATCAGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGATCGA
TTGAAACAGGTCATCTTTCAGCAATTATCATTCGACTGGAAACAT
Found at i:55186 original size:150 final size:148
Alignment explanation
Indices: 54893--55173 Score: 447
Period size: 150 Copynumber: 1.9 Consensus size: 148
54883 ATCTTCAAAA
* *
54893 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTTCGACTTGAAACAAGTCATC
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCATTCGACTGGAAACAAGTCATC
* * * *
54958 TTTCAGCAATTATCTTTCGACTGGAAACATGTCGTCTTTCAACAGTTATCAAGATCGACTGGAAA
66 TTTCAGCAATTATCTTTCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGACCGACTGAAAA
55023 CAGGCCATCTTTCAACAG
131 CAGGCCATCTTTCAACAG
* *
55041 TTATCAAGGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCAAGATT-GACTGGAAACATGTC
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATC---ATTCGACTGGAAACAAGTC
*
55105 ATCTTTCAGCAATTATCTTTCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGACCGATTGA
63 ATCTTTCAGCAATTATCTTTCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGACCGACTGA
55170 AAAC
128 AAAC
55174 GGGTCATTTT
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
148 42 0.35
150 77 0.64
151 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (148 bp):
TTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCATTCGACTGGAAACAAGTCATC
TTTCAGCAATTATCTTTCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGACCGACTGAAAA
CAGGCCATCTTTCAACAG
Found at i:55286 original size:62 final size:59
Alignment explanation
Indices: 55190--55311 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 59
55180 TTTTTCAGTG
* * *
55190 GTTTTCGGTTGCTCCCAAGGAGGGCATTCCAACAACTTTTCAGCATTCCAACAACTTTACA
1 GTTTTCAGCTGCTCCCAAGGAGGGCATTCCAACAACTTTTCAGAATT--AACAACTTTACA
*
55251 GTTTTCAGCTGCTCCCCGAAGGA-GGCATTCCAACAACTTTTCAGAATTAATAACTTTACA
1 GTTTTCAGCTGCT-CCC-AAGGAGGGCATTCCAACAACTTTTCAGAATTAACAACTTTACA
55311 G
1 G
55312 CATTTCAACA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
60 12 0.22
61 11 0.20
62 27 0.49
63 5 0.09
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (59 bp):
GTTTTCAGCTGCTCCCAAGGAGGGCATTCCAACAACTTTTCAGAATTAACAACTTTACA
Found at i:55348 original size:34 final size:35
Alignment explanation
Indices: 55275--55497 Score: 215
Period size: 34 Copynumber: 6.3 Consensus size: 35
55265 CCCGAAGGAG
* * *
55275 GCATTCCAACAACTTTTCAGAATTAATAACTTTACA
1 GCATTTCAACAACTTTTCA-AATTTACAACTTTACA
* **
55311 GCATTTCAACAACTTTTC-AATCTACAACTTTTTA
1 GCATTTCAACAACTTTTCAAATTTACAACTTTACA
* * *
55345 GCATTTCAATTTACAACTTTACAGCATTTTAACAACTTTTCA
1 GCATTTC-A---ACAACTTTTCA--AATTT-ACAACTTTACA
55387 --ATTT--ACAACTTTTCAGAATTTACAACTTTACA
1 GCATTTCAACAACTTTTCA-AATTTACAACTTTACA
*
55419 ACATTTCAACAACTTTTC-AATTTACAACTTTACA
1 GCATTTCAACAACTTTTCAAATTTACAACTTTACA
*
55453 GCATTTCAACAACTTTTCAGAATTTACAACTTTTCA
1 GCATTTCAACAACTTTTCA-AATTTACAACTTTACA
55489 GCATTTCAA
1 GCATTTCAA
55498 TTCACAACTT
Statistics
Matches: 157, Mismatches: 16, Indels: 28
0.78 0.08 0.14
Matches are distributed among these distances:
32 10 0.06
33 4 0.03
34 65 0.41
35 1 0.01
36 51 0.32
38 9 0.06
40 4 0.03
41 3 0.02
42 10 0.06
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (35 bp):
GCATTTCAACAACTTTTCAAATTTACAACTTTACA
Found at i:55351 original size:23 final size:23
Alignment explanation
Indices: 55325--55373 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
55315 TTCAACAACT
**
55325 TTTCAATCTACAACTTTTTAGCA
1 TTTCAATCTACAACTTTACAGCA
*
55348 TTTCAATTTACAACTTTACAGCA
1 TTTCAATCTACAACTTTACAGCA
55371 TTT
1 TTT
55374 TAACAACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (23 bp):
TTTCAATCTACAACTTTACAGCA
Found at i:55367 original size:8 final size:8
Alignment explanation
Indices: 55354--55485 Score: 79
Period size: 8 Copynumber: 15.4 Consensus size: 8
55344 AGCATTTCAA
55354 TTTACAAC
1 TTTACAAC
*
55362 TTTACAGCAT
1 TTTACA--AC
55372 TTTAACAAC
1 TTT-ACAAC
*
55381 TTTTCAA-
1 TTTACAAC
55388 TTTACAAC
1 TTTACAAC
* *
55396 TTTTCAGAA
1 TTTACA-AC
55405 TTTACAAC
1 TTTACAAC
55413 TTTACAAC
1 TTTACAAC
55421 ATTTCAACAAC
1 -TTT--ACAAC
*
55432 TTTTCAA-
1 TTTACAAC
55439 TTTACAAC
1 TTTACAAC
*
55447 TTTACAGC
1 TTTACAAC
55455 ATTTCAACAAC
1 -TTT--ACAAC
* *
55466 TTTTCAGAA
1 TTTACA-AC
55475 TTTACAAC
1 TTTACAAC
55483 TTT
1 TTT
55486 TCAGCATTTC
Statistics
Matches: 95, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
7 12 0.13
8 39 0.41
9 22 0.23
10 10 0.11
11 12 0.13
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (8 bp):
TTTACAAC
Found at i:55424 original size:51 final size:51
Alignment explanation
Indices: 55283--55488 Score: 220
Period size: 51 Copynumber: 3.9 Consensus size: 51
55273 AGGCATTCCA
* * * *
55283 ACAACTTTTCAGAATTAATAACTTTACAGCATTTCAACAACTTTTCAATCT
1 ACAACTTTTCAGAATTTACAACTTTACAACATTTCAACAACTTTTCAATTT
* * *
55334 ACAACTTTTTAGCATTTCAATTTACAACTTTACAGCATTTTAACAACTTTTCAATTT
1 ACAAC-TTTT--CA---GAATTTACAACTTTACAACATTTCAACAACTTTTCAATTT
55391 ACAACTTTTCAGAATTTACAACTTTACAACATTTCAACAACTTTTCAATTT
1 ACAACTTTTCAGAATTTACAACTTTACAACATTTCAACAACTTTTCAATTT
* * *
55442 ACAACTTTACAGCATTTCAACAACTTTTCAGA-ATTT--ACAACTTTTCA
1 ACAACTTTTCAGAATTT--ACAACTTTACA-ACATTTCAACAACTTTTCA
55489 GCATTTCAAT
Statistics
Matches: 135, Mismatches: 11, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
51 68 0.50
52 4 0.03
53 14 0.10
54 5 0.04
56 4 0.03
57 40 0.30
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (51 bp):
ACAACTTTTCAGAATTTACAACTTTACAACATTTCAACAACTTTTCAATTT
Found at i:55504 original size:23 final size:23
Alignment explanation
Indices: 55473--55518 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
55463 AACTTTTCAG
*
55473 AATTTACAACTTTTCAGCATTTC
1 AATTCACAACTTTTCAGCATTTC
*
55496 AATTCACAACTTTTGAGCATTTC
1 AATTCACAACTTTTCAGCATTTC
55519 CAACAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (23 bp):
AATTCACAACTTTTCAGCATTTC
Found at i:55505 original size:85 final size:85
Alignment explanation
Indices: 55348--55505 Score: 257
Period size: 85 Copynumber: 1.9 Consensus size: 85
55338 CTTTTTAGCA
*
55348 TTTCAATTTACAACTTTACAGCATTTTAACAACTTTTCAATTTACAACTTTTCAGAATTTACAAC
1 TTTCAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAAC
*
55413 TTTACAACATTTCAACAACT
66 TTCACAACATTTCAACAACT
*
55433 TTTCAATTTACAACTTTACAGCATTTCAACAACTTTTCAGAATTTACAACTTTTCAGCATTT-CA
1 TTTCAATTTACAACTTTACAGCATTTCAACAACTTTTC--AATTTACAACTTTTCAGAATTTACA
55497 A-TTCACAAC
64 ACTTCACAAC
55506 TTTTGAGCAT
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
85 44 0.65
86 3 0.04
87 21 0.31
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.39
Consensus pattern (85 bp):
TTTCAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTTACAAC
TTCACAACATTTCAACAACT
Found at i:56328 original size:13 final size:14
Alignment explanation
Indices: 56310--56355 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
56300 TTGTGTGAGC
56310 ATTAGTTGA-GCAT
1 ATTAGTTGACGCAT
56323 ATTAGTT-ACGCAT
1 ATTAGTTGACGCAT
*
56336 ATTTAGTTGCATGCAT
1 A-TTAGTTG-ACGCAT
56352 ATTA
1 ATTA
56356 CTGCCATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 1 0.04
13 12 0.43
14 6 0.21
15 3 0.11
16 6 0.21
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (14 bp):
ATTAGTTGACGCAT
Found at i:60894 original size:42 final size:42
Alignment explanation
Indices: 60835--60915 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
60825 ATCGTTTCGT
60835 ACTCCCTAAAATTAATAAATGAATTAATAACTAAATTAAACG
1 ACTCCCTAAAATTAATAAATGAATTAATAACTAAATTAAACG
*
60877 ACTCCCTATAATTAATAAATGAATTAATAACTAAATTAA
1 ACTCCCTAAAATTAATAAATGAATTAATAACTAAATTAA
60916 TTTACTAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.31
Consensus pattern (42 bp):
ACTCCCTAAAATTAATAAATGAATTAATAACTAAATTAAACG
Done.