Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009530.1 Corchorus olitorius cultivar O-4 contig09562, 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: 6035
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:948 original size:321 final size:319
Alignment explanation
Indices: 1--3607 Score: 2825
Period size: 321 Copynumber: 11.0 Consensus size: 319
* * * *
1 TTAGAAACGTG-AAAATCCTTCAATTTTTTTGGCGTTGAACTATATATTTTTTCTGAGTATTGTG
1 TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATATTTTCTGAGTATT-TG
** * ** * *
65 GCAAAAAAATTGAGGAAACTACTTTTTGAGTCAGTTTTTTGCAAAATTTTAGTTGAAATTGTGTA
65 GC-AAAAAATTGA-GAAAAAAC-TTTTGGGTCAG-----T------TTTTAGCCGAAATCGGGTA
* * * * *
130 TTAACCAATCACAGTGTTTT-GCTAAAAACGCGTTCCGGAGGCCCGGCTCAATTTTGCGTGATTT
116 CTAACC-ATCACGGT-TTTTGGCTAAAAACGCGTTCCGG-GCCCCGGCTCAGTTTTGCATGATTT
* * * *
194 TT-TCCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATGTCAGCCACATTGGATATA
178 TTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTA
* * *
258 AGGATTTGTTTTTACGAGTATTTGAATCTTGTTTCGATTTAATTACAAATTAATTC-GAAAAAAA
242 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAA
* *
322 AAGGAAAAACGATT
307 TA-GAAAAACGATA
* ** * * * * *
336 TTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGCGTTGAATTATATATTTTTTTTTGAATATTTT
1 TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATA-TATTTTCTGAGTATTTG
* * * ** *
401 GCGAAAAATAGAGAAAAAGAAGTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACA
65 GCAAAAAATTGAG-AAAA-AACTTTTGGGTCAGTTTTTAGCCGAAATCGGGTACTAACCATCAC-
* *
466 GG-TTTTGGCCAAAAACGCGTTTCGGGTCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGAC
127 GGTTTTTGGCTAAAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGAC
* * * *
530 TCCTTGAAAGATCTATATTCATCTAACCAAATCCCAGCCACATTCGATTTAAGGATTTGTTTTTA
191 TCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * *
595 CGAGCATCTGAATCTTCTTTCGGTTTAATTAAAAATTAATTCGGAAAAAAATAGAAAAACGATA
256 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGAAAAACGATA
* * * *
659 TTAGAAACGTGAAAAAACCCTTC-CTTTTTTTGGCTTTGAATTATATATATTTTATGAGTATTGT
1 TTAGAAGCGTG-AAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATATTTTCTGAGTATT-T
* * * *
723 AGCAAAAATTTGAGAAAAAACTTTTATGGTCAGTTTTTACCCGAAATCGGGTACTAACCATCACG
64 GGCAAAAAATTGAGAAAAAACTTTT-GGGTCAGTTTTTAGCCGAAATCGGGTACTAACCATCACG
* * * * * * ** *** *
788 GTTTTTGGCTAAAAATGCGTTCCGAGACTCGACTTAGTTTTGCATGGCTTTTGGTTTAAGGACTC
128 GTTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
* * ** * *
853 CATGAAATATCTATATTCATCTAAAGAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACA
193 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* * * * * *
918 AGCAT-TGGAATCTTGTTTTGATTTAATTAAAAATAAATTCGGAAAAAAA-AGGAAAACTATC
258 AGCATCT-GAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGAAAAACGATA
* * *
979 TTAGAAGCGTGAAAACCCCTTCAATTTTTTTGGCGTTAAATTATATATTTTTTTCTGAGTATTCT
1 TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATA-TATTTTCTGAGTATT-T
* * * ** * *
1044 GGCAAAAAATTGAGGGAAAAA-TTTTCGTGTCAGTTTTT-G-CAAAATTTTAGCTAAAATCGTCT
64 GGCAAAAAATTGA-GAAAAAACTTTT-GGGTCAGTTTTTAGCCGAAA--TCGGGT---A-C-T-A
* * * * * * *
1106 ACGTTATCATGGTTTTTGGCTAAAAACGCGTTCCAGAGTCTCGGCTCATTTTTGCATGATTTTTT
119 AC--CATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTTG
* * * * * *
1171 ACACAAAAACTCCTTGAAATATCTAGATTCATCGAACCAAATCTC-GACCACATTGTATATAAGG
181 GCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAG-CCACATTGGATTTAAGG
* * * * * *
1235 TTTTTTTTTTACGAGCATCTGAATCTTTTTTCCATTTAATTAGAAATTTATTCGGAAAAAAATGG
245 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAG
1300 AAAAATC-ATA
310 AAAAA-CGATA
* * * * * *
1310 TTAGAAGCATG-AAAAGCCTGTCAATCTTTTTGGCGTTAAATTATATATGTTTTCTGAATAATTT
1 TTAGAAGCGTGAAAAACCCT-TCAATTTTTTTGGCGTTGAATTATATATATTTTCTGAGT-ATTT
**
1374 -GCAAATAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCC-AAATCATGTACGT----ATCA
64 GGCAAA-AAATTGAGAAAAAACTTTT-GGGTCAGTTTTTAGCCGAAATCGGGTAC-TAACCATCA
* * * * **
1433 TGGTTTTTGGCTAAAAACGCGTTTCGGGACCCGGCTTAGTTTTGCATGCGTTTTGGCAGAAAGAC
126 CGGTTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGAC
* * * * * * *
1498 TCCGTGGAATATCTATATTCATCTAAGCAAATCTCAGCAACAATAGATTTAAGGATTTGTTTTTT
191 TCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTT
* *
1563 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTGAGAAAAAAA-AGGAAAAACGA
255 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG-GAAAAAAATA-GAAAAACGA
1627 TA
318 TA
* * * *
1629 TTAGAAGCGT-ATAAAACCCTTCAATTTGTTTTTGCATTGAATTAAATA-ATTTTTATGAGTATT
1 TTAGAAGCGTGA-AAAACCCTTCAATTT-TTTTGGCGTTGAATTATATATA-TTTTCTGAGTATT
* * ** ***** *
1692 ATGGAAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTT-GCAAAAAAAATTTAGCCGAAATCA
63 -TGGCAAAAAATTGAGAAAAAACTTTT-GGGTCAGTTTTTAGCCGAAATCGGGTA--C-TAA-C-
* * * * * ***
1756 CATCACGGTTTTTTGCTAAAAACGTGTTCCGGGGCCCCGTCTCCGTTTTGCATAATTTTT-TTTG
121 CATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
* ** * *
1820 TAAAGACTTCTCAAAATATCTATATTCATCGAACCAAATCCCAACCACATTGGATTTAAGGATTT
185 -AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTT
* * * * *
1885 GTTTTTAC-ATGTATCTTATTCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATGGAAA
249 GTTTTTACGA-GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGAAA
1949 AACGATA
313 AACGATA
* * * * *
1956 TTAAAAGCGTGAAAAACCCTT-TATTTTTTCGGCGTTAAATTATATATTTTTTCTGAGTATTATG
1 TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATATTTTCTGAGTATT-TG
* ** * * * *
2020 GAAAAAAATTGAGGGAAAACTTTTTGGGTCATTTTTTTGCAAAATTTAGCCGAAATCGTGTTCTT
65 GCAAAAAATTGAGAAAAAAC-TTTTGGGTCA----GTT------TTTAGCCGAAATCGGGTACTA
** ** * * * * * *
2085 ATTATCACGACTTTTGGCTAAAAACGCTTTCCAGAGCCCCAGCTTAATTTTGCATAATTTTTAGC
119 ACCATCACGGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTT-G-
* * * * *
2150 GCA-AAA-ACGCCTTGAAATATCTTTATTCAACGAACCAAATCTGAGCCACATTGGATATAAGGA
181 GCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGA
* * *
2213 TTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCGG-AAAAAATGGA
246 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGA
**
2277 AAATTGATA
311 AAAACGATA
* * * * ** * * * *
2286 CTGGAAGCGTGAAAAGCCCGTCAAACTTATTGTCGTTGAATTATATA-ATTTTTCTGAATATTTT
1 TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATA-TTTTCTGAGTATTTG
* * * * *
2350 GCAAAAAAATGAGCAAAAAACTTTTCGGATTAGTTTTTAACCGAAAT-GGTGTACTAACTATCAC
65 GCAAAAAATTGAG-AAAAAACTTTT-GGGTCAGTTTTTAGCCGAAATCGG-GTACTAACCATCAC
* * *
2414 GGTTTTTGGCTAAAAACGGGTTTCGGGGCCCCGGCTCAGTTTTTCATGATTTTTGGCAGAAAGAC
127 GGTTTTTGGCTAAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGAC
* * *
2479 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTAA
191 TCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * *
2544 CGAGCATCTGAATCTTGCTTCGATTTAATT-GAAAATAAATTCTTGAAAAAAA-AGGAAAAACGA
256 CGAGCATCTGAATCTTGTTTCGATTTAATTAG-AAATTAATTC-GGAAAAAAATA-GAAAAACGA
2607 TA
318 TA
* ** * * * * * *
2609 TTAGAAGCGTGAAAATCCCTTCAA-TTTTTTGATGTTAAAATATTTAT-TTTATCTAAGGACTAT
1 TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATATTT-TCTGAGTA-TTT
* * * *
2672 GGCAAGAAATTTGAG-GAAAACTTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAAT-GGTATA
64 GGCAA-AAAATTGAGAAAAAAC-TTTTGGGTC-A-----G----TTTTTAGCCGAAATCGG-GTA
* * * *
2735 CTAACCATCACGGTTTTTGGCTAAAAACACGTTACGGAGCCCCGGCTAAATTTTGCATGATTTTT
116 CTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGG-GCCCCGGCTCAGTTTTGCATGATTTTT
* * *
2800 GGC-GCAAAGACTTCTTGAAATACCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAG
180 GGCAG-AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAG
* * * * * ** * *
2864 AATTTGTTTTTACGAGAATTTTAATCTTTTTTTTATTTAATTAGCAATTAATTCGGAAAAAAATG
244 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATA
2929 GAAAAACGATA
309 GAAAAACGATA
* * * ** * * * *
2940 TAAGAAGCGTGCAAAAGCCCGTCAACATTTTTGGTGTTGAATTATATAATTTTTTTTGAATATGT
1 TTAGAAGCGTG-AAAAACCCTTCAATTTTTTTGGCGTTGAATTATAT-ATATTTTCTGAGTAT-T
*
3005 T-GCAAAAAATTGAGAAAAAAACTTTTCGGGTTAGTTTTTAGCCGAAAT--GGTAAACTAACCAT
63 TGGCAAAAAATTGAG-AAAAAACTTTT-GGGTCAGTTTTTAGCCGAAATCGGGT--ACTAACCAT
* * * ** * *
3067 CACGGTTTTTGG-TAAAAAACGCATTTCGGGGCCCTGGCTCAGTTTTAAATAATTTTTGGTAGAA
124 CACGGTTTTTGGCT-AAAAACGC-GTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAA
* ** * * *
3131 AGACTCCTTGAAATATCTATATTCATCTAAATAAATCTCAGCCACAATGGATTTAAGAATTTATT
187 AGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* * * *
3196 TTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATAAATTTAGGGAAAAAAATGGAAAAA
252 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TT-CGGAAAAAAATAGAAAAA
3261 CGATA
315 CGATA
* * * * * *
3266 TTCGAAGCGTGAAAACCCCTTCAA-TTTTTTGACGTTGAATTATATAT-TTTATCTAAATACTGT
1 TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATATTT-TCTGAGTA-TTT
** * * *
3329 GGCAAAAAATTGAGGCAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAAT-GGTGTAC
64 GGCAAAAAATTGAGAAAAAACTTTT-GGGTC-A-----G----TTTTTAGCCGAAATCGG-GTAC
* * *
3393 T---TATCACGGTTTTTGGTTAAAAACGCGTTTCGGGTCCCCGGCTCAGTTTTGCATGATATTTT
117 TAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCATG--ATTTT
* ** * ** ** * *
3455 TTGTTGAAAGA-TGCCTTGAAATATCTATATTCATCTAATTAAATCTCAATCACAATAGATTTAA
179 TGGCAGAAAGACT-CCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAA
** * * * * * *
3519 TTATTTGTTTTTACAAGTC-TCTAAATCTTGTTTCGATTAAATTACAAATAAATTCGAAAAAAAA
243 GGATTTGTTTTTACGAG-CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG-GAAAAAA
* *
3583 ATTGGAAAACGATA
306 ATAGAAAAACGATA
3597 TTAGAAGCGTG
1 TTAGAAGCGTG
3608 TCAGTTTTTG
Statistics
Matches: 2639, Mismatches: 485, Indels: 300
0.77 0.14 0.09
Matches are distributed among these distances:
317 74 0.03
318 74 0.03
319 54 0.02
320 116 0.04
321 342 0.13
322 120 0.05
323 268 0.10
324 241 0.09
325 77 0.03
326 41 0.02
327 42 0.02
328 70 0.03
329 124 0.05
330 252 0.10
331 296 0.11
332 295 0.11
333 44 0.02
334 19 0.01
335 37 0.01
336 40 0.02
337 13 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (319 bp):
TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATATTTTCTGAGTATTTGG
CAAAAAATTGAGAAAAAACTTTTGGGTCAGTTTTTAGCCGAAATCGGGTACTAACCATCACGGTT
TTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTT
GAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGAAAAACGATA
Found at i:3802 original size:248 final size:251
Alignment explanation
Indices: 3357--3856 Score: 573
Period size: 248 Copynumber: 2.0 Consensus size: 251
3347 AATTTTTCGG
* * * *
3357 GTCAATTTTTGCAAAATTTTAGCCAAAATGGTGTACTTATCACGGTTTTTGGTTAAAAACGCGTT
1 GTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACTCATCACGGTTTTTGGCTAAAAACGCCTT
* * *
3422 TCGGGTCCCCGGCTCAGTTTTGCATGATATTTTTTGTTGAAAGATGCCTTGAAATATCTATATTC
66 CCGGGTCCCCGACTCAGTATTGCATGATATTTTTTGTTGAAAGATGCCTTGAAATATCTATATTC
* ** * * * **
3487 ATCTAATTAAATCTCAATCACAATAGATTTAATTATTTGTTTTTACAAGTCTCTAAATCTTGTTT
131 ATCCAACCAAACCCCAACCACAATAGATTTAACGATTTGTTTTTACAAGTCTCTAAATCTTGTTT
* *
3552 CGATTAAATTACAAATAAA-TTCGAAAAAAAAATTGG-AAAACGATATTAGAAGCGT
196 CGATTAAATTACAAATAAATTTCGAAAAAAAAA-GGGAAAAACGATATTAGAAACGT
* * * * *
3607 GTCAGTTTTTGCAAAATTTTAGCCGAAATCGTTTTCTCATCACTGTTTTTGGCTAAAAACGCCTT
1 GTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACTCATCACGGTTTTTGGCTAAAAACGCCTT
* * **
3672 CCTGGG-CCCCGACTCAGTATTGGATGATTTTTTTTG-T-AAAGACT-TTTTGAAATATCTATAT
66 CC-GGGTCCCCGACTCAGTATTGCATGATATTTTTTGTTGAAAGA-TGCCTTGAAATATCTATAT
* * * * * *
3733 TCATCCAACCAAACCCCAGCCACATTGGATTTAACGATTTGTTTTTTCGAG-CATCTGAATCTTG
129 TCATCCAACCAAACCCCAACCACAATAGATTTAACGATTTGTTTTTACAAGTC-TCTAAATCTTG
* ** * * *
3797 TTTCGATTTAATTAGTAATAAATTTGGTAAAAAAGAGGGAAAAACGATATTAGAAACGT
193 TTTCGATTAAATTACAAATAAATTTCGAAAAAAAAAGGGAAAAACGATATTAGAAACGT
3856 G
1 G
3857 AAAATCCTTC
Statistics
Matches: 207, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
247 1 0.00
248 89 0.43
249 31 0.15
250 83 0.40
251 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (251 bp):
GTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACTCATCACGGTTTTTGGCTAAAAACGCCTT
CCGGGTCCCCGACTCAGTATTGCATGATATTTTTTGTTGAAAGATGCCTTGAAATATCTATATTC
ATCCAACCAAACCCCAACCACAATAGATTTAACGATTTGTTTTTACAAGTCTCTAAATCTTGTTT
CGATTAAATTACAAATAAATTTCGAAAAAAAAAGGGAAAAACGATATTAGAAACGT
Found at i:5397 original size:2 final size:2
Alignment explanation
Indices: 5385--5419 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
5375 ATTGACTACC
5385 AT AT GAT 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 AT
5420 GAAATGTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.