Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008048.1 Corchorus capsularis cultivar CVL-1 contig08069, 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: 88399
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1312 original size:16 final size:17
Alignment explanation
Indices: 1276--1312 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1266 AGGAGTGATC
1276 TGCAAAGCAAAACAGAA
1 TGCAAAGCAAAACAGAA
*
1293 -GCAAA-CAAAATAGAA
1 TGCAAAGCAAAACAGAA
1308 TGCAA
1 TGCAA
1313 TTAACATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.08
Consensus pattern (17 bp):
TGCAAAGCAAAACAGAA
Found at i:10008 original size:11 final size:11
Alignment explanation
Indices: 9988--10021 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
9978 GGATAAGTGG
*
9988 AAAAATGAAAA
1 AAAAAAGAAAA
9999 AAAAAAGAAAA
1 AAAAAAGAAAA
*
10010 AAGAAAGAAAA
1 AAAAAAGAAAA
10021 A
1 A
10022 GAGAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:10010 original size:18 final size:19
Alignment explanation
Indices: 9987--10031 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
9977 AGGATAAGTG
*
9987 GAAAAATGAAA-AAAAAAA
1 GAAAAAAGAAAGAAAAAAA
*
10005 GAAAAAAGAAAGAAAAAGA
1 GAAAAAAGAAAGAAAAAAA
10024 GAAAAAAG
1 GAAAAAAG
10032 CAACGATGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
GAAAAAAGAAAGAAAAAAA
Found at i:10026 original size:12 final size:11
Alignment explanation
Indices: 9994--10027 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
9984 GTGGAAAAAT
*
9994 GAAAAAAAAAA
1 GAAAAAAGAAA
10005 GAAAAAAGAAA
1 GAAAAAAGAAA
10016 GAAAAAGAGAAA
1 GAAAAA-AGAAA
10028 AAAGCAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:10059 original size:19 final size:19
Alignment explanation
Indices: 10037--10099 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
10027 AAAAGCAACG
10037 ATGGTTTTCAAAAAGAGTC
1 ATGGTTTTCAAAAAGAGTC
10056 ATGGTTTTC--AAA-A---
1 ATGGTTTTCAAAAAGAGTC
10069 AT-GTTTTCAAAAAGAGTC
1 ATGGTTTTCAAAAAGAGTC
10087 ATGGTTTTCAAAA
1 ATGGTTTTCAAAA
10100 GGTTTTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
12 6 0.16
13 2 0.05
14 3 0.08
15 1 0.03
16 1 0.03
17 3 0.08
18 2 0.05
19 19 0.51
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (19 bp):
ATGGTTTTCAAAAAGAGTC
Found at i:10078 original size:31 final size:31
Alignment explanation
Indices: 10040--10099 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
10030 AGCAACGATG
10040 GTTTTCAAAAAGAGTCATGGTTTTCAAAAAT
1 GTTTTCAAAAAGAGTCATGGTTTTCAAAAAT
10071 GTTTTCAAAAAGAGTCATGGTTTTCAAAA
1 GTTTTCAAAAAGAGTCATGGTTTTCAAAA
10100 GGTTTTGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (31 bp):
GTTTTCAAAAAGAGTCATGGTTTTCAAAAAT
Found at i:10583 original size:27 final size:27
Alignment explanation
Indices: 10544--10596 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
10534 ATAAAGATCC
**
10544 AAAAAAAAGTGAAAATTGAAAGTGAAG
1 AAAAAAAAGTGAAAAAAGAAAGTGAAG
**
10571 AAAAAAATTTGAAAAAAGAAAGTGAA
1 AAAAAAAAGTGAAAAAAGAAAGTGAA
10597 AGGAAAGGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (27 bp):
AAAAAAAAGTGAAAAAAGAAAGTGAAG
Found at i:10930 original size:17 final size:17
Alignment explanation
Indices: 10904--10939 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
10894 ACTGAAAAAG
10904 AAAAGAAAAGAAAAGAAA
1 AAAAGAAAAG-AAAGAAA
10922 AAAAG-AAAGAAAGAAA
1 AAAAGAAAAGAAAGAAA
10938 AA
1 AA
10940 GAAAAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGAAAGAAA
Found at i:10930 original size:22 final size:23
Alignment explanation
Indices: 10898--10945 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
10888 AAGTGCACTG
10898 AAAAAGAAAAGAAA-AGAAAAGAA
1 AAAAAGAAAAGAAAGA-AAAAGAA
10921 AAAAAG-AAAGAAAGAAAAAGAA
1 AAAAAGAAAAGAAAGAAAAAGAA
10943 AAA
1 AAA
10946 TGAATGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAGAAAGAAAAAGAA
Found at i:10963 original size:5 final size:5
Alignment explanation
Indices: 10899--10944 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
10889 AGTGCACTGA
10899 AAAAG AAAAG AAAAG AAAAG -AAA- AAAAG -AAAG -AAAG AAAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAA
10945 ATGAATGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 14 0.38
5 19 0.51
6 4 0.11
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:12103 original size:36 final size:36
Alignment explanation
Indices: 12062--12169 Score: 137
Period size: 36 Copynumber: 3.0 Consensus size: 36
12052 CAGTTGACCT
*
12062 AGGGTGGTTTTTCTTCAGTTTATGTCGGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
* * * * *
12098 AGGGTGGTCTTTCTTTAGTTTATTTCGG-TTGACCT
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
* *
12133 AGGGCGGTCTTTCTTCAGTTTATGTCAGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
12169 A
1 A
12170 TTAAGTCGAC
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
35 28 0.48
36 30 0.52
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.42
Consensus pattern (36 bp):
AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
Found at i:12153 original size:35 final size:35
Alignment explanation
Indices: 12049--12155 Score: 133
Period size: 35 Copynumber: 3.0 Consensus size: 35
12039 CTTCAATGCG
* *
12049 TTTCAGTTGACCTAGGGTGGTTTTTCTTCAGTTTA
1 TTTCGGTTGACCTAGGGTGGTCTTTCTTCAGTTTA
* * * * *
12084 TGTCGGAATGATCGAGGGTGGTCTTTCTTTAGTTTA
1 TTTCGG-TTGACCTAGGGTGGTCTTTCTTCAGTTTA
*
12120 TTTCGGTTGACCTAGGGCGGTCTTTCTTCAGTTTA
1 TTTCGGTTGACCTAGGGTGGTCTTTCTTCAGTTTA
12155 T
1 T
12156 GTCAGAATGA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
35 29 0.50
36 29 0.50
ACGTcount: A:0.14, C:0.15, G:0.26, T:0.45
Consensus pattern (35 bp):
TTTCGGTTGACCTAGGGTGGTCTTTCTTCAGTTTA
Found at i:12224 original size:71 final size:70
Alignment explanation
Indices: 12149--12571 Score: 605
Period size: 71 Copynumber: 6.0 Consensus size: 70
12139 GTCTTTCTTC
* *
12149 AGTTTATGTCAGAATGATCGATTAAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
12214 ATTCGA
66 A-TCCA
* * *
12220 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGCTATTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
12285 ATCCA
66 ATCCA
* ** * * *
12290 AGTTTGTGTCAGAAATGATCGATTTGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTT
1 AGTTTATGTCAG-AATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
12355 TATCCA
65 TATCCA
* * *
12361 AGTTTATGTCAAAATGATCGGTTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTACAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
12426 ATTCCA
66 A-TCCA
* * * *
12432 AGTTTATGTAAGAATGATCGATTCAGTCGACCTAGGGTGGTCTTTCTTCAGTAT-TTTCCACGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGT-TGTTTCCAAGTT
12496 TATCCA
65 TATCCA
* * *
12502 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTTTTTCATCAGTTGTTTCCAAGTTG
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
12567 ATCCA
66 ATCCA
12572 GGGTGGTCTT
Statistics
Matches: 312, Mismatches: 36, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
69 1 0.00
70 126 0.40
71 184 0.59
72 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATCCA
Found at i:12403 original size:141 final size:140
Alignment explanation
Indices: 12149--12571 Score: 630
Period size: 141 Copynumber: 3.0 Consensus size: 140
12139 GTCTTTCTTC
* * * *
12149 AGTTTATGTCAGAATGATCGATTAAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTAAGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
* * * *
12214 ATTCGAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGCTATTTCC
66 A-TCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCC
12279 AAGTTTATCCA
130 AAGTTTATCCA
* **
12290 AGTTTGTGTCAGAAATGATCGATTTGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTT
1 AGTTTATGTCAG-AATGATCGATTAAGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTT
* * *
12355 TATCCAAGTTTATGTCAAAATGATCGGTTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTAC
65 TATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCC
12420 AAGTTTATTCCA
130 AAGTTTA-TCCA
* * * *
12432 AGTTTATGTAAGAATGATCGATTCAGTCGACCTAGGGTGGTCTTTCTTCAGTATTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTAAGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
* *
12497 ATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTTTTTCATCAGTTGTTTCCA
66 ATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCA
*
12562 AGTTGATCCA
131 AGTTTATCCA
12572 GGGTGGTCTT
Statistics
Matches: 254, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
140 4 0.02
141 188 0.74
142 62 0.24
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (140 bp):
AGTTTATGTCAGAATGATCGATTAAGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
ATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCA
AGTTTATCCA
Found at i:21889 original size:17 final size:17
Alignment explanation
Indices: 21867--21910 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
21857 CATATCACAT
21867 GACTAGTAATGTTTTAG
1 GACTAGTAATGTTTTAG
* *
21884 GACTAGTCATGTTTTAT
1 GACTAGTAATGTTTTAG
*
21901 TACTAGTAAT
1 GACTAGTAAT
21911 ATTTCTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (17 bp):
GACTAGTAATGTTTTAG
Found at i:23428 original size:19 final size:19
Alignment explanation
Indices: 23404--23440 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23394 CTAAATTATC
*
23404 CTAATTATAGGGATACAAA
1 CTAATTATAGGAATACAAA
*
23423 CTAATTCTAGGAATACAA
1 CTAATTATAGGAATACAA
23441 TCTGTTATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (19 bp):
CTAATTATAGGAATACAAA
Found at i:25340 original size:12 final size:12
Alignment explanation
Indices: 25323--25347 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25313 AGATTCTTTG
25323 GGTTCAAGTTCA
1 GGTTCAAGTTCA
25335 GGTTCAAGTTCA
1 GGTTCAAGTTCA
25347 G
1 G
25348 TTATGGGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (12 bp):
GGTTCAAGTTCA
Found at i:25392 original size:39 final size:39
Alignment explanation
Indices: 25349--25453 Score: 210
Period size: 39 Copynumber: 2.7 Consensus size: 39
25339 CAAGTTCAGT
25349 TATGGGTTCAAGAGGATTTTCAGGCATAATGGGTTCAAC
1 TATGGGTTCAAGAGGATTTTCAGGCATAATGGGTTCAAC
25388 TATGGGTTCAAGAGGATTTTCAGGCATAATGGGTTCAAC
1 TATGGGTTCAAGAGGATTTTCAGGCATAATGGGTTCAAC
25427 TATGGGTTCAAGAGGATTTTCAGGCAT
1 TATGGGTTCAAGAGGATTTTCAGGCAT
25454 GATGCAGCAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (39 bp):
TATGGGTTCAAGAGGATTTTCAGGCATAATGGGTTCAAC
Found at i:41689 original size:20 final size:20
Alignment explanation
Indices: 41664--41706 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
41654 AGCAATTAAA
41664 TTAAATGAAAGTAAATATTG
1 TTAAATGAAAGTAAATATTG
41684 TTAAATGAAAGTAAATATTG
1 TTAAATGAAAGTAAATATTG
41704 TTA
1 TTA
41707 GTATTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (20 bp):
TTAAATGAAAGTAAATATTG
Found at i:42229 original size:35 final size:35
Alignment explanation
Indices: 42178--42248 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
42168 TTCAAATGTC
*
42178 TACTAATGAGTGATAGACTCA-TCGAATACAGAAGT
1 TACTAATGAGTAATAGACTCACT-GAATACAGAAGT
*
42213 TACTGATGAGTAATAGACTCACTGAATACAGAAGT
1 TACTAATGAGTAATAGACTCACTGAATACAGAAGT
42248 T
1 T
42249 TCTATATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (35 bp):
TACTAATGAGTAATAGACTCACTGAATACAGAAGT
Found at i:42606 original size:13 final size:13
Alignment explanation
Indices: 42588--42613 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42578 TTGAATTTTT
42588 ATTAATTTAATTA
1 ATTAATTTAATTA
42601 ATTAATTTAATTA
1 ATTAATTTAATTA
42614 TAATATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTAATTTAATTA
Found at i:42664 original size:36 final size:39
Alignment explanation
Indices: 42613--42687 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 39
42603 TAATTTAATT
*
42613 ATAATATTTATTAATT-GT-TA-AATTAAATTAAGTGTA
1 ATAAAATTTATTAATTAGTGTAGAATTAAATTAAGTGTA
42649 ATAAAATTTATTAATTAAGTGTAGTAATTAAATTAAGTG
1 ATAAAATTTATTAATT-AGTGTAG-AATTAAATTAAGTG
42688 AATGATTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 15 0.45
38 2 0.06
39 2 0.06
41 14 0.42
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.44
Consensus pattern (39 bp):
ATAAAATTTATTAATTAGTGTAGAATTAAATTAAGTGTA
Found at i:42911 original size:36 final size:36
Alignment explanation
Indices: 42864--42936 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
42854 ATAGGGAATT
42864 ATGTTTAACCTTACACTAGACATAGGAAAATGATAG
1 ATGTTTAACCTTACACTAGACATAGGAAAATGATAG
42900 ATGTTTAACCTTACACTAGACATAGGAAAATGATAG
1 ATGTTTAACCTTACACTAGACATAGGAAAATGATAG
42936 A
1 A
42937 CCATTACACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (36 bp):
ATGTTTAACCTTACACTAGACATAGGAAAATGATAG
Found at i:43323 original size:31 final size:31
Alignment explanation
Indices: 43248--43326 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
43238 ACGGTGTCCA
*
43248 ACGTGGCATGCCACGTGGATCAAAAAGTAAC
1 ACGTGGCACGCCACGTGGATCAAAAAGTAAC
* * * *
43279 ACATGACAGGCCACGTGGATCAAAAAGTGAC
1 ACGTGGCACGCCACGTGGATCAAAAAGTAAC
*
43310 ATGTGGCACGCCACGTG
1 ACGTGGCACGCCACGTG
43327 TGCCAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.33, C:0.24, G:0.28, T:0.15
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGGATCAAAAAGTAAC
Found at i:43334 original size:31 final size:30
Alignment explanation
Indices: 43299--43410 Score: 92
Period size: 31 Copynumber: 3.8 Consensus size: 30
43289 CCACGTGGAT
* *
43299 CAAAAAGTGACATGTGGCACGCCACGTGTGC
1 CAAAAAGTGACA-GTGGCACGCCACATGTAC
**
43330 C-AAAA---A-A-TGGCACATCACATGTAC
1 CAAAAAGTGACAGTGGCACGCCACATGTAC
*
43354 CAAAAAGTGATACGTGGCACGCCACATGTAC
1 CAAAAAGTGACA-GTGGCACGCCACATGTAC
* *
43385 CAAAAAGTGACACGCGGCATGCCACA
1 CAAAAAGTGACA-GTGGCACGCCACA
43411 CCGATTCGTT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
24 14 0.22
25 4 0.06
26 1 0.02
27 1 0.02
28 1 0.02
29 1 0.02
30 4 0.06
31 39 0.60
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (30 bp):
CAAAAAGTGACAGTGGCACGCCACATGTAC
Found at i:48303 original size:31 final size:33
Alignment explanation
Indices: 48235--48313 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
48225 CCCCTACTCA
* *
48235 GGGGTAAAATGTCC--AGAATTTGGAAAGTTTAG
1 GGGGCAAAATGTCCTTA-AATTTGGAAAGTTCAG
48267 GGGGCAAAATG-CCTTAAATTTGGAAA-TTCAG
1 GGGGCAAAATGTCCTTAAATTTGGAAAGTTCAG
48298 GGGGCAAAATGTCCTT
1 GGGGCAAAATGTCCTT
48314 GACGCAATAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 17 0.40
32 24 0.57
33 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (33 bp):
GGGGCAAAATGTCCTTAAATTTGGAAAGTTCAG
Found at i:51524 original size:12 final size:12
Alignment explanation
Indices: 51507--51532 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
51497 TGTATAAAAT
51507 AAAAAAAAATTA
1 AAAAAAAAATTA
51519 AAAAAAAAATTA
1 AAAAAAAAATTA
51531 AA
1 AA
51533 TTTATTAGCA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:52092 original size:148 final size:148
Alignment explanation
Indices: 51824--52113 Score: 580
Period size: 148 Copynumber: 2.0 Consensus size: 148
51814 CTGATATTGA
51824 AGCTTAGTCTAAATAGATACACATCTTCCAACAATAAATCAATCATTCTGGTCAATTTGCCAATT
1 AGCTTAGTCTAAATAGATACACATCTTCCAACAATAAATCAATCATTCTGGTCAATTTGCCAATT
51889 TTTAATGGAAAAAATCATTAATTAGATGATGGCCAATATACCTTAGGACGAGTAAACCCTTGATC
66 TTTAATGGAAAAAATCATTAATTAGATGATGGCCAATATACCTTAGGACGAGTAAACCCTTGATC
51954 AAGATGACCATCTTGATC
131 AAGATGACCATCTTGATC
51972 AGCTTAGTCTAAATAGATACACATCTTCCAACAATAAATCAATCATTCTGGTCAATTTGCCAATT
1 AGCTTAGTCTAAATAGATACACATCTTCCAACAATAAATCAATCATTCTGGTCAATTTGCCAATT
52037 TTTAATGGAAAAAATCATTAATTAGATGATGGCCAATATACCTTAGGACGAGTAAACCCTTGATC
66 TTTAATGGAAAAAATCATTAATTAGATGATGGCCAATATACCTTAGGACGAGTAAACCCTTGATC
52102 AAGATGACCATC
131 AAGATGACCATC
52114 ACCTGGAAGC
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 142 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (148 bp):
AGCTTAGTCTAAATAGATACACATCTTCCAACAATAAATCAATCATTCTGGTCAATTTGCCAATT
TTTAATGGAAAAAATCATTAATTAGATGATGGCCAATATACCTTAGGACGAGTAAACCCTTGATC
AAGATGACCATCTTGATC
Found at i:60038 original size:2 final size:2
Alignment explanation
Indices: 60033--60059 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60023 TGTGTGTGTG
60033 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
60060 CTTTAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61542 original size:12 final size:11
Alignment explanation
Indices: 61525--61577 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 11
61515 TAGAGAGAGG
61525 TAAATAAATTAA
1 TAAATAAA-TAA
61537 TAAATAAATAA
1 TAAATAAATAA
61548 T-AAT-AATAA
1 TAAATAAATAA
61557 T-AAT-AATAA
1 TAAATAAATAA
61566 T-AAT-AATAA
1 TAAATAAATAA
61575 TAA
1 TAA
61578 TCTTGCTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
9 24 0.60
10 4 0.10
11 4 0.10
12 8 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:61551 original size:3 final size:3
Alignment explanation
Indices: 61543--61578 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
61533 TTAATAAATA
61543 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61579 CTTGCTGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:64521 original size:15 final size:15
Alignment explanation
Indices: 64501--64538 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
64491 CTGGCTATTG
64501 TCATTTGTTATG-TAT
1 TCATTT-TTATGCTAT
*
64516 TCATTTTTATGCTCT
1 TCATTTTTATGCTAT
64531 TCATTTTT
1 TCATTTTT
64539 TAGCCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.16, C:0.13, G:0.08, T:0.63
Consensus pattern (15 bp):
TCATTTTTATGCTAT
Found at i:69035 original size:24 final size:25
Alignment explanation
Indices: 68987--69035 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
68977 GTCATTTCCT
* *
68987 TCAAACTTCAAAATTTTCAATTCTC
1 TCAAACTTCAAAACTTTCAAATCTC
*
69012 TCAACCTTC-AAACTTTCAAATCTC
1 TCAAACTTCAAAACTTTCAAATCTC
69036 AATCATTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37
Consensus pattern (25 bp):
TCAAACTTCAAAACTTTCAAATCTC
Found at i:70866 original size:32 final size:29
Alignment explanation
Indices: 70830--70889 Score: 93
Period size: 32 Copynumber: 2.0 Consensus size: 29
70820 ATCGAATTTG
70830 TCGAGCCGAGCTCGAGTAGCTCGATACTCGAT
1 TCGAGCCGAGCTCGA-T--CTCGATACTCGAT
70862 TCGAGCCGAGCTCGATCTCGATACTCGA
1 TCGAGCCGAGCTCGATCTCGATACTCGA
70890 AACTCGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.43
31 1 0.04
32 15 0.54
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.22
Consensus pattern (29 bp):
TCGAGCCGAGCTCGATCTCGATACTCGAT
Found at i:80899 original size:93 final size:92
Alignment explanation
Indices: 80779--80963 Score: 361
Period size: 93 Copynumber: 2.0 Consensus size: 92
80769 TAAAAAAAAA
80779 ACTCTATTTCGTCGTGTATACTTTTTTTTGACTTCAAGAAACACTTAGCCAAATATATATATTAT
1 ACTCTATTTCGTCGTGTATACTTTTTTTTGACTTCAAGAAACACTTAGCCAAATATATATATTAT
80844 AAAGTCCGTTAAATATACAAATTATATG
66 AAAGTCCGTTAAATATACAAATT-TATG
80872 ACTCTATTTCGTCGTGTATACTTTTTTTTGACTTCAAGAAACACTTAGCCAAATATATATATTAT
1 ACTCTATTTCGTCGTGTATACTTTTTTTTGACTTCAAGAAACACTTAGCCAAATATATATATTAT
80937 AAAGTCCGTTAAATATACAAATTTATG
66 AAAGTCCGTTAAATATACAAATTTATG
80964 GGTAATTTCA
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 4 0.04
93 88 0.96
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (92 bp):
ACTCTATTTCGTCGTGTATACTTTTTTTTGACTTCAAGAAACACTTAGCCAAATATATATATTAT
AAAGTCCGTTAAATATACAAATTTATG
Found at i:80983 original size:17 final size:17
Alignment explanation
Indices: 80963--81015 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
80953 ACAAATTTAT
80963 GGGTAATTTCAATTTTG
1 GGGTAATTTCAATTTTG
80980 GGG---TTTCAAATTTAT-
1 GGGTAATTTC-AATTT-TG
80995 GGGTAATTTCAATTTTG
1 GGGTAATTTCAATTTTG
81012 GGGT
1 GGGT
81016 TTCAATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
14 4 0.13
15 8 0.27
16 2 0.07
17 12 0.40
18 4 0.13
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (17 bp):
GGGTAATTTCAATTTTG
Found at i:80988 original size:14 final size:14
Alignment explanation
Indices: 80969--81024 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
80959 TTATGGGTAA
80969 TTTCAATTTTGGGG
1 TTTCAATTTTGGGG
*
80983 TTTCAAATTTATGGGTAA
1 TTTC-AATTT-TGGG--G
81001 TTTCAATTTTGGGG
1 TTTCAATTTTGGGG
81015 TTTCAATTTT
1 TTTCAATTTT
81025 ATGGGGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 14 0.39
15 5 0.14
16 8 0.22
17 5 0.14
18 4 0.11
ACGTcount: A:0.21, C:0.07, G:0.20, T:0.52
Consensus pattern (14 bp):
TTTCAATTTTGGGG
Found at i:80990 original size:32 final size:32
Alignment explanation
Indices: 80954--81029 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
80944 GTTAAATATA
80954 CAAATTTATGGGTAATTTCAATTTTGGGGTTT
1 CAAATTTATGGGTAATTTCAATTTTGGGGTTT
80986 CAAATTTATGGGTAATTTCAATTTTGGGGTTT
1 CAAATTTATGGGTAATTTCAATTTTGGGGTTT
*
81018 CAATTTTATGGG
1 CAAATTTATGGG
81030 GTTTTAATGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (32 bp):
CAAATTTATGGGTAATTTCAATTTTGGGGTTT
Found at i:80997 original size:16 final size:16
Alignment explanation
Indices: 80954--81033 Score: 69
Period size: 16 Copynumber: 5.0 Consensus size: 16
80944 GTTAAATATA
*
80954 CAAATTTATGGGTAATTT
1 CAAATTTATGGG--GTTT
80972 C-AATTT-TGGGGTTT
1 CAAATTTATGGGGTTT
*
80986 CAAATTTATGGGTAATTT
1 CAAATTTATGGG--GTTT
81004 C-AATTT-TGGGGTTT
1 CAAATTTATGGGGTTT
*
81018 CAATTTTATGGGGTTT
1 CAAATTTATGGGGTTT
81034 TAATGAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
14 8 0.15
15 9 0.17
16 20 0.38
17 10 0.19
18 5 0.10
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.47
Consensus pattern (16 bp):
CAAATTTATGGGGTTT
Found at i:81598 original size:19 final size:19
Alignment explanation
Indices: 81576--81613 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
81566 GGATTTGTCC
81576 TTTTAATTTGGTCAATTAA
1 TTTTAATTTGGTCAATTAA
81595 TTTTAATTTGGTCAATTAA
1 TTTTAATTTGGTCAATTAA
81614 GGACAATACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTAATTTGGTCAATTAA
Found at i:82249 original size:24 final size:24
Alignment explanation
Indices: 82217--82273 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
82207 CTGGTAAAAT
82217 GAACCCGAAATCCGAAACCAGCTC
1 GAACCCGAAATCCGAAACCAGCTC
*
82241 GAACCCGAAATCCGAAACCCGCTC
1 GAACCCGAAATCCGAAACCAGCTC
*
82265 GAATCCGAA
1 GAACCCGAA
82274 CCCGAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.37, C:0.37, G:0.18, T:0.09
Consensus pattern (24 bp):
GAACCCGAAATCCGAAACCAGCTC
Found at i:82340 original size:16 final size:16
Alignment explanation
Indices: 82321--82362 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
82311 CCGAACCCGT
*
82321 CCGAACCCGAAATTAC
1 CCGAACCCGAAAATAC
82337 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
82353 CCGAACCCGA
1 CCGAACCCGA
82363 GACAACCCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.40, G:0.14, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:82370 original size:16 final size:15
Alignment explanation
Indices: 82321--82378 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
82311 CCGAACCCGT
*
82321 CCGAACCCGAAATTAC
1 CCGAACCCGAAA-AAC
82337 CCGAACCCGAAAATAC
1 CCGAACCCGAAAA-AC
*
82353 CCGAACCCGAGACAAC
1 CCGAACCCGA-AAAAC
*
82369 CCGACCCCGA
1 CCGAACCCGA
82379 CCCGAGCCCG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 35 0.95
17 2 0.05
ACGTcount: A:0.36, C:0.43, G:0.16, T:0.05
Consensus pattern (15 bp):
CCGAACCCGAAAAAC
Found at i:83184 original size:15 final size:16
Alignment explanation
Indices: 83153--83226 Score: 107
Period size: 15 Copynumber: 4.8 Consensus size: 16
83143 CCGATCCGAG
83153 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
83169 CCCAAACCCG-AAATA
1 CCCGAACCCGAAAATA
83184 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
83200 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
*
83215 CCCGAATCCGAA
1 CCCGAACCCGAA
83227 CCCGCCTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
15 27 0.52
16 25 0.48
ACGTcount: A:0.41, C:0.39, G:0.14, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:83190 original size:31 final size:31
Alignment explanation
Indices: 83153--83226 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
83143 CCGATCCGAG
83153 CCCGAACCCGAAAATACCCAAACCCGAAATA
1 CCCGAACCCGAAAATACCCAAACCCGAAATA
* *
83184 CCCGAACCCGAAAATACCCGAACCCGAAGTA
1 CCCGAACCCGAAAATACCCAAACCCGAAATA
*
83215 CCCGAATCCGAA
1 CCCGAACCCGAA
83227 CCCGCCTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.41, C:0.39, G:0.14, T:0.07
Consensus pattern (31 bp):
CCCGAACCCGAAAATACCCAAACCCGAAATA
Found at i:83243 original size:16 final size:16
Alignment explanation
Indices: 83216--83256 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
83206 CCCGAAGTAC
*
83216 CCGAATCCGAACCCG-
1 CCGAACCCGAACCCGT
83231 CCTGAACCCGAACCCGT
1 CC-GAACCCGAACCCGT
83248 CCGAACCCG
1 CCGAACCCG
83257 CCCAATTGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.24, C:0.49, G:0.20, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAACCCGT
Found at i:83435 original size:41 final size:41
Alignment explanation
Indices: 83378--83462 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
83368 TCTACTGTTG
83378 ACCACTCTTTTTGTTGGTGATCTTCCCTATGTTGATAAGAT
1 ACCACTCTTTTTGTTGGTGATCTTCCCTATGTTGATAAGAT
83419 ACCACTCTTTTTGTTGGTGATCTTCCCTATGTTGATAAGAT
1 ACCACTCTTTTTGTTGGTGATCTTCCCTATGTTGATAAGAT
83460 ACC
1 ACC
83463 TTCAGCTCGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.42
Consensus pattern (41 bp):
ACCACTCTTTTTGTTGGTGATCTTCCCTATGTTGATAAGAT
Done.