Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015984.1 Corchorus olitorius cultivar O-4 contig16017, 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: 3212
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Found at i:63 original size:21 final size:21
Alignment explanation
Indices: 37--84 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
27 TATTAATTTC
37 TTTTTCCTGCATCCCATTTTT
1 TTTTTCCTGCATCCCATTTTT
*
58 TTTTTCCTGCATCTCATTTTT
1 TTTTTCCTGCATCCCATTTTT
*
79 TCTTTC
1 TTTTTC
85 TCATGTGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.08, C:0.27, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTTCCTGCATCCCATTTTT
Found at i:500 original size:17 final size:17
Alignment explanation
Indices: 478--517 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
468 AGATTACCAT
*
478 TGATCTT-GCATCACTGG
1 TGATCTTAG-ATCACTAG
495 TGATCTTAGATCACTAG
1 TGATCTTAGATCACTAG
512 TGATCT
1 TGATCT
518 GGGGGGTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (17 bp):
TGATCTTAGATCACTAG
Found at i:1125 original size:53 final size:53
Alignment explanation
Indices: 1067--1176 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
1057 TCTTTAAATC
1067 CAATAGTTCATTGCATCTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATCTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
*
1120 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATCTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1173 CAAT
1 CAAT
1177 TGAATAAACA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.49
Consensus pattern (53 bp):
CAATAGTTCATTGCATCTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
Found at i:2003 original size:324 final size:322
Alignment explanation
Indices: 1297--3208 Score: 2735
Period size: 324 Copynumber: 6.0 Consensus size: 322
1287 TGCATTTTGT
* *
1297 ATTTTTTGCAGAAAGATTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGAT
1 ATTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACGTTGGAT
* *
1362 TT-AGCGATTTATTAATACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAA
66 TTGAG-GATTTATTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAA
* * * *
1426 AAAGTGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATCTTGTTGACTTTGAATTTTATAT
130 AAAGTGGAAAAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATAT
* * * * ** *
1491 TCTTTATAAGTATTGCGGGAAAAAATTGAGAAAAAAAAATTTGGGTCTGTTTTAAGCCGAAATCG
195 TCTTTATGACTATTGCGGGAAAAAATGGAGAAAAAAAATTTTGGGTAAGTTTTTAGCCGAAATCG
1556 TGTACGT-----T-ACGGTTTTTAGCTAAAAACGCGTTTTGGGGCCCCGGCTCAGTTTTGAATG
260 TGTAC-TAACCCTCACGGTTTTTAGCTAAAAACGCGTTTTGGGGCCCCGGCTCAGTTTTGAATG
* *
1614 ATTTTTTGCAGAAAGACTCCTTGCAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGAT
1 ATTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACGTTGGAT
* *
1679 TTAAGGATTTATTTATACGACCATCTGAATC-TGTTTTCGATTTAATTAGAAATTAATTCGGAAA
66 TTGAGGATTTATTTATACGAGCATCTGAATCTTG-TTTCGATTTAATTAGAAATTAATTCGG-AA
** *
1743 AAAAGTGGAAAAACGATATTAGAAGTATGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATA
129 AAAAGTGGAAAAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATA
* * * * * ** **
1808 TTATTTATGAGTATTGTGGGAAAAAATTGAGAAAACAAATTTTTGGGCCAGTTTTTAGCAAAAAT
194 TTCTTTATGACTATTGCGGGAAAAAATGGAGAAAA-AAAATTTTGGGTAAGTTTTTAGCCGAAAT
* * * * *
1873 CGTGTACTAACCCACACGGTTTTTAGCTAAACACGCATTTTGGGGACTCGGCTCAGTTTTGAATG
258 CGTGTACTAACCCTCACGGTTTTTAGCTAAAAACGCGTTTTGGGGCCCCGGCTCAGTTTTGAATG
* *
1938 ATTTTTTGTAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTTAGCCACGTTGGAT
1 ATTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACGTTGGAT
* * * *
2003 TTAAGTATTTATTTATATGAGCATCTGAATCTTGTTTCG-TTTAAATTA-CAATTAATTCGGAAA
66 TTGAGGATTTATTTATACGAGCATCTGAATCTTGTTTCGATTT-AATTAGAAATTAATTCGGAAA
* * *
2066 AAAGTGGAAAAACGATATTAAAAGTGTGAAAAACCCTGCAATCTTTTTGGCTTTGAATTATATAT
130 AAAGTGGAAAAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATAT
* * * *
2131 TCTTCATGACTATTGCGAGAAAAAATTGAGAAAAAAAAGATTTTGGGTCAGTTTTTAGCCGAAAT
195 TCTTTATGACTATTGCGGGAAAAAATGGAG-AAAAAAA-ATTTTGGGTAAGTTTTTAGCCGAAAT
* * * * * * *
2196 CGTGTACAAACCCTCACAGTTTTTAGCTTAAAATGCGTTTTTGGGGTCCCAGCTCAGTTTAGAAT
258 CGTGTACTAACCCTCACGGTTTTTAGCTAAAAACGCG-TTTTGGGGCCCCGGCTCAGTTTTGAAT
*
2261 A
322 G
* * *
2262 ATTTTTTGCAGAAAGACTCTTTGAAATGTCTTTATTCATCGAACCAAATCTCAGCCACGTTGGAT
1 ATTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACGTTGGAT
* * *
2327 TTGAGGATTTATTTATACGGGCTTCTGAATCTTGATTCGATTTAATTAGAAATTAATTCGGAAAA
66 TTGAGGATTTATTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
2392 AAGTGGAAAAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATATT
131 AAGTGGAAAAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATATT
* *
2457 CTTTATTACTATTGCGGGAAAAAAATGGAGAAAAAAAAATTTTGGGTAATTTTTTAGCCGAAATC
196 CTTTATGACTATTGCGGG-AAAAAATGGAG-AAAAAAAATTTTGGGTAAGTTTTTAGCCGAAATC
* * * * **
2522 GTGTATTAACTCTCACGGTTTTTAGCTAAAAACGCGTTTTTTGAGGTCCCGGCTCAAATTTGAAT
259 GTGTACTAACCCTCACGGTTTTTAGCTAAAAACGCG--TTTTGGGGCCCCGGCTCAGTTTTGAAT
2587 -
322 G
*
2587 ATTTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACGTTGGA
1 A-TTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACGTTGGA
* *
2652 TTTGAGGATTTATTTATATGAGCTTCTG-ATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAA
65 TTTGAGGATTTATTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAA
* *
2715 ATAGTGGAAAAACGATATTAGAAGGGGGAAAAACCCTTCAATC-TTTTGGCTTTGAATTATATAT
130 AAAGTGGAAAAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATAT
* *** * * *
2779 TCTTTATAACTATTGCATAAAAAAATGGAG-AAAAAAAGTTTGGGTAATTTTTTAGCCGAAATGG
195 TCTTTATGACTATTGCGGGAAAAAATGGAGAAAAAAAATTTTGGGTAAGTTTTTAGCCGAAATCG
* * *
2843 TGTACTAACCCTCACGG-TTTTAGCTAAAAACGCGTTTCGGGGCCCCTGCTCAGTTTTGAATT
260 TGTACTAACCCTCACGGTTTTTAGCTAAAAACGCGTTTTGGGGCCCCGGCTCAGTTTTGAATG
*
2905 ATTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACGTTCGAT
1 ATTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACGTTGGAT
* * *
2970 TTGAGGATTTATTTATGCGAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGATAA
66 TTGAGGATTTATTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
3035 AAGTGGAAAAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATATT
131 AAGTGGAAAAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATATT
* * *
3100 CTTTATGACTATTGCAGGAAAAAATGGAGAAAAAAAAATTTGGGTAATTTTTTAGCCGAAATCGT
196 CTTTATGACTATTGCGGGAAAAAATGGAGAAAAAAAATTTTGGGTAAGTTTTTAGCCGAAATCGT
3165 GTACTAACCCTCACGGTTTTT-GCTAAAAACGCGTTTT-GGGCCCC
261 GTACTAACCCTCACGGTTTTTAGCTAAAAACGCGTTTTGGGGCCCC
3209 TGCT
Statistics
Matches: 1444, Mismatches: 125, Indels: 49
0.89 0.08 0.03
Matches are distributed among these distances:
316 2 0.00
317 223 0.15
318 130 0.09
319 90 0.06
320 102 0.07
321 64 0.04
322 107 0.07
323 106 0.07
324 311 0.22
325 183 0.13
326 126 0.09
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (322 bp):
ATTTTTTGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACGTTGGAT
TTGAGGATTTATTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
AAGTGGAAAAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTTTGGCTTTGAATTATATATT
CTTTATGACTATTGCGGGAAAAAATGGAGAAAAAAAATTTTGGGTAAGTTTTTAGCCGAAATCGT
GTACTAACCCTCACGGTTTTTAGCTAAAAACGCGTTTTGGGGCCCCGGCTCAGTTTTGAATG
Done.