Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022427.1 Corchorus olitorius cultivar O-4 contig22460, 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: 5190
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:381 original size:131 final size:128
Alignment explanation
Indices: 132--393 Score: 318
Period size: 131 Copynumber: 2.0 Consensus size: 128
122 ATTATATATT
* * *
132 TTTCCGAGTATTGCGGCAAAAATTTCAGAAAAAATTTTTCGGGTCACTTTTTAGTCGAAATCGTG
1 TTTCCGAGTATTGCGGCAAAAATTTCAGAAAAAATTTTTCGAGTCACTCTTTAGCCGAAATCGTG
* * *
197 TACCAATCATCACGGTTTTTTGGTTAAAAATGCGTCTGGTGAACCCGGCTCAGTTTTGCATGA
66 TACCAACCATCACGGTTTTTTGGCTAAAAATGCGTCTGGTGAACCCGACTCAGTTTTGCATGA
* * *
260 TTTCTGAGTATTGTGGCAAAGAA-TTCAGAAAATA-TTTTCGAGTCACTCTTTAGCCGAAATCGT
1 TTTCCGAGTATTGCGGCAAA-AATTTCAGAAAAAATTTTTCGAGTCACTCTTTAGCCGAAATCGT
* *
323 GTACTAACTAACCATCACGG-TTTTTGCGCTAAAAACT-CGTTTCGG-GGACCCGACTCAGTTTT
65 GTAC---C-AACCATCACGGTTTTTTG-GCTAAAAA-TGCGTCT-GGTGAACCCGACTCAGTTTT
385 GCATGA
123 GCATGA
391 TTT
1 TTT
394 TTGGCAGAAA
Statistics
Matches: 115, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
127 30 0.26
128 28 0.24
129 2 0.02
130 7 0.06
131 45 0.39
132 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (128 bp):
TTTCCGAGTATTGCGGCAAAAATTTCAGAAAAAATTTTTCGAGTCACTCTTTAGCCGAAATCGTG
TACCAACCATCACGGTTTTTTGGCTAAAAATGCGTCTGGTGAACCCGACTCAGTTTTGCATGA
Found at i:648 original size:16 final size:15
Alignment explanation
Indices: 610--651 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
600 GCAGAGATTG
*
610 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
625 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
640 ACTAGAAAACAA
1 AC-AGAAAACAA
652 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:3537 original size:323 final size:323
Alignment explanation
Indices: 2290--4652 Score: 2694
Period size: 323 Copynumber: 7.4 Consensus size: 323
2280 CAATCAATGG
* * * *
2290 AGGATATGGTTTTACGAGCATCGGAATTTAGTTTTGATTTAATTGGAAATAAATTCGG-AAAAAA
1 AGGATATGTTTTTACGAGCATCTGAATTT-GTTTCGATTTAATTAGAAATAAATTCGGAAAAAAA
* * * *
2354 TGGAAAAACGATATTGCAAGCGTGAAAAACCCATCAAATTTTTTTTGTGTTGAATTATATATTTT
65 TGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTT
* * * *
2419 TTCCGAGCATTGTGGCAAAAATATCAGAAAAAATTTTTCGAGTCACTTTTTAGCCGAAATCGTGT
130 TTCCGAGTATTGTGGCAAAAATTTCAGAAAAATTTTTTCGAGTCACTTTTTAGCCGAAATCGTTT
* * *
2484 ACTAACCATTACGGTTTTTGAGCTAAAAACGCGTTTCGGGGACCTGACTCAGTTTTGCATGATTT
195 ACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGACCCGACTCAGTTTTGCATGATTT
* * *
2549 TTGCCAGAAAGCATCCATGAAATATCTGTATTCATAGAACCAAATCTCAGCCACAATGGATTTA
260 TTGGCAGAAAGCCTCCATGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTA
* * * * * *
2613 AAGATTTGTTTTTTACGAGCTTTTGAATTTGTTTCGGTTTAATTAGAATTAAATTCGGAAAAAAA
1 AGGATATG-TTTTTACGAGCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAA
* *
2678 TGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAA-TTTTTTTTGCGTT-ATAATAAATATTT
65 TGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGA-ATTATATATTT
* * * * *
2741 TTTCCGAGTACTGTGGCAAAAATTTCAGATTAGA-TTTTTC-AGGTAATTTTTTA---G----C-
129 TTTCCGAGTATTGTGGCAAAAATTTCAGA-AAAATTTTTTCGA-GTCACTTTTTAGCCGAAATCG
* * * * * *
2796 -TTA--AATCGTCACGGTTTTTGGGCTAAAATCGTGTTTCAGGGACCCGACCCAGTTTTGCATGA
192 TTTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGACCCGACTCAGTTTTGCATGA
* * * *
2858 TTTTTGACAGAAAGCCTCCTTGAAATATCTGTACTCATCGAACCAAATCTCAGCCACAATAGATT
257 TTTTTGGCAGAAAGCCTCCATGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATT
2923 TA
322 TA
* * * *
2925 AGGATTTGCTTTTACAAGCATCTGAATTTTGTTTCGATTTAGTTAGAAATAAATTCGTG-AAAAA
1 AGGATATGTTTTTACGAGCATCTGAA-TTTGTTTCGATTTAATTAGAAATAAATTCG-GAAAAAA
* * * *
2989 ATGGAAAACCGATATTGGAAACGTGAAAAACCCTTC-A-TTTGTTTTGCGTTGCATTATATATTT
64 ATGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTT
* ** ** * * * * * * * * *
3052 TTACTTAGTATTAAGGTAAAAAATTCCGAAAAAATTTTTCGGGTTACTTTTTAGCCG-ACTTGTG
129 TTTCCGAGTATTGTGGCAAAAATTTCAGAAAAATTTTTTCGAGTCACTTTTTAGCCGAAATCGTT
* * * * *
3116 TACTAATCATCACGGTTTTTGGGCTAAAAATGCCTTTCGGGGACCCGGCTCAGTTTTGCATGAAT
194 TACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGACCCGACTCAGTTTTGCATGATT
* * * * *
3181 TTTGGCAGAAAGCCTCCTTGAAATATCTGTATTTATCGAACCAAATATCAGCCACAATGAAGTTA
259 TTTGGCAGAAAGCCTCCATGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTA
* * *
3246 AGGATAT-TTTTTACGAGCAT-TGGAATTTAGTTTTGATTTTATTAGATATAAATTCGGAAAAAA
1 AGGATATGTTTTTACGAGCATCT-GAATTT-GTTTCGATTTAATTAGAAATAAATTCGGAAAAAA
* * *
3309 ATGGAAAAACAATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGTGTAGAATTATATATTT
64 ATGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTT
*
3374 TTTCCGAGTATTGTGGCAAAAATTTCAGAAAATTTTTTTCGAGTCACTTTTTAGCCGAAATCGTT
129 TTTCCGAGTATTGTGGCAAAAATTTCAGAAAAATTTTTTCGAGTCACTTTTTAGCCGAAATCGTT
* *
3439 TACTAACCATCACTGTTTTTGGGCTAAAAACGCGTTTCGGGGACCTGACTCAGTTTTGCATGATT
194 TACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGACCCGACTCAGTTTTGCATGATT
* * *
3504 TTTGGTAGAAAGCCTCCATGAAATATATGTATTTATCGAACCAAATCTCAGCCACAATGGATTTA
259 TTTGGCAGAAAGCCTCCATGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTA
* * *
3569 AGGATTTGTTTTTACGAGCATCTGAATTTGTTTCGGTTTAATTAGAAATAAATTCGAAAAAAAAT
1 AGGATATGTTTTTACGAGCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAT
* *
3634 GGAAAAGCGATATTGGAAGTGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATATTT
66 GGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATAT-TTT
* * * * * * *
3699 TTTCGAGTGTTTTGGCAAAAAATTCAGGAAAAACTTTTTTTGGGTCACTTTTTTGCCGAAATC--
130 TTCCGAGTATTGTGGCAAAAATTTCA-GAAAAA-TTTTTTCGAGTCACTTTTTAGCCGAAATCGT
* * ** * *
3762 TT-GT-ACGATCACAATTTTTGGGCTATAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATGAT
193 TTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGACCCGACTCAGTTTTGCATGAT
* * * *
3825 TTTTGGCAGAAAGCCTACTC-T-AATTATCTATATTCATCGAATCAAATCTCAGACACAATGGAT
258 TTTTGGCAGAAAGCCT-C-CATGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGAT
3888 TTA
321 TTA
* * * * *
3891 AGGATTTG-TTTTATTGAGCGTCTGAATTTTGTTTCGATTTAATTATAAATAAATTCGTTAAAAA
1 AGGATATGTTTTTA-CGAGCATCTGAA-TTTGTTTCGATTTAATTAGAAATAAATTCG--GAAAA
* * * *
3955 AAATGGAAAAACGATATTGTAAGCGTGAAAAACCCTTCAATTTTTTTTTTCAGTTGAATCAGATA
62 AAATGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGC-GTTGAATTATATA
* ** * * * * *
4020 TTCTTTGTGAGTATTGTGGCAAAAAATTCTG-AAAATATTTTCGAGTCTCTTTTTAGCCGATATC
126 TTTTTTCCGAGTATTGTGGCAAAAATTTCAGAAAAATTTTTTCGAGTCACTTTTTAGCCGAAATC
* * ** * * *
4084 G-TAACTAACCATCATGGTTTTTAAGCTAAAAACGCGTTTCGGTGACCCGCCTCAGTTTCGCATG
191 GTTTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGACCCGACTCAGTTTTGCATG
* * * *
4148 ATTTTTGGCAAAAAGTCTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAATGGAT
256 ATTTTTGGCAGAAAGCCTCCATGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGAT
4213 TTA
321 TTA
* * *
4216 AGGATATGTATTTACGAGCATCGGAATTTAGTTTTGATTTAATTAGAAATAAATTCGG-AAAAAA
1 AGGATATGTTTTTACGAGCATCTGAATTT-GTTTCGATTTAATTAGAAATAAATTCGGAAAAAAA
4280 TGG---AA-G----T------GTGAAAAACCCTTCAA---TTTTTT---TTGAATTATATATTTT
65 TGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTT
** * * * * ** * *
4325 TTCCGAGTATTGTGGTGAAAATTTCAGAAAAGTATTTCCGAGTCACTTTTTAACAAAAAACGTGT
130 TTCCGAGTATTGTGGCAAAAATTTCAGAAAAATTTTTTCGAGTCACTTTTTAGCCGAAATCGTTT
* * * * *
4390 AC---CCATCACGATTTTTGGGCTAAAAACGCGTGTCAGGAACCCGGCTCAGTTTTGCATGATTT
195 ACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGACCCGACTCAGTTTTGCATGATTT
* * *
4452 TTGGCAGAAATCCTCCATGAAATATCTGTATTCATCGAACCAAATCCCAGCCTCAATGGATTTA
260 TTGGCAGAAAGCCTCCATGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTA
*
4516 AGGATTTGTTTTTACGAGCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAT
1 AGGATATGTTTTTACGAGCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAT
* * * * *
4581 GGATAAACAATATTGGAAGCGTGAAAAATCCTTCAATTTTTTTTTCCGTTGAATTATATATATTT
66 GGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTTT
*
4646 TCAGAGT
131 TCCGAGT
4653 GTTTTGGAAA
Statistics
Matches: 1722, Mismatches: 250, Indels: 139
0.82 0.12 0.07
Matches are distributed among these distances:
299 27 0.02
300 142 0.08
301 34 0.02
302 26 0.02
303 4 0.00
305 6 0.00
308 17 0.01
310 2 0.00
311 71 0.04
312 184 0.11
313 1 0.00
314 19 0.01
316 1 0.00
317 6 0.00
318 1 0.00
319 9 0.01
320 98 0.06
321 122 0.07
322 226 0.13
323 343 0.20
324 114 0.07
325 227 0.13
326 42 0.02
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (323 bp):
AGGATATGTTTTTACGAGCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAT
GGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTTT
TCCGAGTATTGTGGCAAAAATTTCAGAAAAATTTTTTCGAGTCACTTTTTAGCCGAAATCGTTTA
CTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGACCCGACTCAGTTTTGCATGATTTT
TGGCAGAAAGCCTCCATGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTA
Done.