Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010364.1 Corchorus olitorius cultivar O-4 contig10396, 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: 3464
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:785 original size:329 final size:329
Alignment explanation
Indices: 13--845 Score: 1022
Period size: 329 Copynumber: 2.5 Consensus size: 329
3 TCCGGCTCGG
* * * * *
13 TTTTGCATGATTTTTTGCGTAAAGACTTCTTGAAATATGTATATTCATCGATCCAAATCGCAACC
1 TTTTGCATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAGCC
* * *
78 ACAGTGGATTTAAGGATTTGTTTTCACAAGCATCTGAATCTTGTTTCGATTT-ATTAAAAATAAA
66 ACA-TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
* * *
142 TTTGGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCGTAATTTTTTTTTGGTGTTG
130 TTT-GGGAAAAAA-GGAAAAACGATATTAGAAGCGTG-AAAACCCATAATTTTTTTTTGGCGTTA
* * * *
207 AATTGCATATTTTTCTGACTAATGTGGCAAAAAATTTAAGAAAAATTTTTTTGATTAGTTTTTGC
192 AATTACATATTTTTCTGACTAATATGGCAAAAAATTTAAGAAAAATTTTTTGGATAAGTTTTTGC
* * * *
272 AAAATTTTAGCCGAAATCTCGTGTATTAACCTTCACTGTTTTAGGCTAAAAACGCGTTCTGAAAC
257 AAAATTTTAGCCGAAA-CTCGTGTACT-A-CATCACGGTTTTAGGCTAAAAACGCGTTCCGAAAC
337 CCCGACCCAAT
319 CCCGACCCAAT
* * * *
348 TTTTG-ATGATTTTTGG-GATAAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC
1 TTTTGCATGATTTTTGGCG-TAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAGC
* * * *
411 GACTTTGGATTTAAAGATTTATTTTTACGAGCATCT-AATTCTTGTTTCGATTTAATTAGATAAT
65 CAC-ATGGATTTAAGGATTTGTTTTTACGAGCATCTGAA-TCTTGTTTCGATTTAATTAGA-AAT
* *
475 AAATTTGGGAAAAAAGGAAAAACAATATTAGAAGCATGAAAACCCATCAA-TTTTTTTT-GCGTT
127 AAATTTGGGAAAAAAGGAAAAACGATATTAGAAGCGTGAAAACCCAT-AATTTTTTTTTGGCGTT
* * *
538 AAATTACATATTTTTTCTGACTATTATGGCAAAAAATTTGAGGAAAAATTTTTTGGGTAAGTTTT
191 AAATTACATA-TTTTTCTGACTAATATGGCAAAAAATTT-AAGAAAAATTTTTTGGATAAGTTTT
* * * **
603 TGCAAAATTTTAGCCGAAA-TGGTGTACT-CATCACGGTATTT-TGCTAAAAATGCGTTCCGGGA
254 TGCAAAATTTTAGCCGAAACTCGTGTACTACATCACGGT-TTTAGGCTAAAAACGCGTTCCGAAA
*
665 CCCCGACTCAA-
318 CCCCGACCCAAT
676 TTTTGCATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAGCC
1 TTTTGCATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAGCC
* * * *
741 ACATCGGA-TTATAGGACTTGTTTTTACGAGCATTTGAATCTTGTTTCAATTTAATTAGAATTAA
66 ACAT-GGATTTA-AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
* * *
805 ATTCGGGGAAAAATGGAAAAATGATATTAGAAGCGTGAAAA
129 ATT-TGGGAAAAAAGGAAAAACGATATTAGAAGCGTGAAAA
846 ACAATATTTA
Statistics
Matches: 429, Mismatches: 54, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
328 16 0.04
329 161 0.38
330 6 0.01
332 19 0.04
333 45 0.10
334 154 0.36
335 19 0.04
336 9 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (329 bp):
TTTTGCATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAGCC
ACATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT
TTGGGAAAAAAGGAAAAACGATATTAGAAGCGTGAAAACCCATAATTTTTTTTTGGCGTTAAATT
ACATATTTTTCTGACTAATATGGCAAAAAATTTAAGAAAAATTTTTTGGATAAGTTTTTGCAAAA
TTTTAGCCGAAACTCGTGTACTACATCACGGTTTTAGGCTAAAAACGCGTTCCGAAACCCCGACC
CAAT
Found at i:3221 original size:331 final size:332
Alignment explanation
Indices: 1475--3464 Score: 2831
Period size: 331 Copynumber: 6.0 Consensus size: 332
1465 CCCTTCAATT
* ** * *
1475 TTTTAGGACTAATGTGGCAAAAAATTGAGGAAATTTTTTTTGCGTCAGCTTTT-GCAAAATTTTA
1 TTTTAGGACTAATGTGGCCAAAAATTGAGGAAAAATTTTTTGGGTCAGTTTTTGGCAAAATTTTA
* * * * *
1539 GACGAAATCATGTATTAACCACCACGGATTCAGACTAAAAACGCGTTCCGGAACCCCAACTCAAT
66 GCCGAAATCGTGTATTAACCATCACGGATTCAGGCTAAAAACGCGTTCCGGAACCCCGACTCAAT
* *
1604 TTCTCATGATTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACTAAATCCCAGCCA
131 TTTTCATGATTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACCAAATCCCAGCCA
* *
1669 CAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTTTTTCGATTTAATTAGTAATAAAT
196 CAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTGTTTCGATTTAATTAGAAATAAAT
* *
1734 TCGGGAAAGAAATGAACAAACGATATTAGAAGCGTGAAAAACCCTTA-TTTTTTTGCGATTGAAT
261 TCGGGAAAAAAATGAACAAACGATATTAGAAGCGTGAAAAACCATTATTTTTTTTGCG-TTGAAT
1798 TACATATC
325 TACATATC
1806 TTTTAGGACTAATGTGGCCAAAAATTGAGGAAAAATTTTTTGGGTCAGTTTTT-GCAAAATTTTA
1 TTTTAGGACTAATGTGGCCAAAAATTGAGGAAAAATTTTTTGGGTCAGTTTTTGGCAAAATTTTA
* *
1870 GCCGAAATCGTGTATTAACCATCACGGATTCAGGCTAAAAAAGCGTTCCGGAACCCCCACTCAAT
66 GCCGAAATCGTGTATTAACCATCACGGATTCAGGCTAAAAACGCGTTCCGGAACCCCGACTCAAT
* *
1935 TTTTCAT-ATTTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCAAACCAAATCCAAGCC
131 TTTTCATGA-TTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACCAAATCCCAGCC
* * * *
1999 ACACTGGATTTAAGGATTTGTTTTTACAGGCATCTGAATCTTGTTTCGACTT-ATTAGAAATAAA
195 ACAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTGTTTCGATTTAATTAGAAATAAA
** * * * *
2063 TTCAAGAAAAAAGATGAAAAAAACGTTATTACAAGCGTGAAAAACCATTCAATTTTTTTTGTGTT
260 TTCGGGAAAAAA-ATG-AACAAACGATATTAGAAGCGTGAAAAACCATT--ATTTTTTTTGCGTT
2128 GAATTACATATC
321 GAATTACATATC
* **
2140 TTTTAGGACTAATGTGGCCAAAAATTGAGAAAAAAAATTTTGGGTCAGTTTTTGG-AAAATTTTA
1 TTTTAGGACTAATGTGGCCAAAAATTGAGGAAAAATTTTTTGGGTCAGTTTTTGGCAAAATTTTA
* * *
2204 GCCGAAATCATGTACTAACCATCACGGATTTAGGCTAAAAACGCGTTCCGGAACCCCGACTCAAT
66 GCCGAAATCGTGTATTAACCATCACGGATTCAGGCTAAAAACGCGTTCCGGAACCCCGACTCAAT
* * *
2269 TTTTCATGATTTTTGGTATAAAGACACCTTGAAATATTTATATTCATCGAACTAAATCCCAGCCA
131 TTTTCATGATTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACCAAATCCCAGCCA
*
2334 CAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTGTTTCGATTTAATTAGTAATAAAT
196 CAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTGTTTCGATTTAATTAGAAATAAAT
*
2399 TCGGGAAAAAAATGAACAAACGATATTAGAAGCGTGAAAAACCCTTATTTTTTTTTGCGATTGAA
261 TCGGGAAAAAAATGAACAAACGATATTAGAAGCGTGAAAAACCATTA-TTTTTTTTGCG-TTGAA
2464 TTACATATC
324 TTACATATC
2473 TTTTAGGACTAATGTGGCCAAAAATTGAGGAAAAATTTTTTGGGTCAGTTTTT--CAAAATTTTA
1 TTTTAGGACTAATGTGGCCAAAAATTGAGGAAAAATTTTTTGGGTCAGTTTTTGGCAAAATTTTA
*
2536 GCCGAAATC--G------------CGGATTCAGGCTAAAATA-GCGTTCCGGAACTCCGACTCAA
66 GCCGAAATCGTGTATTAACCATCACGGATTCAGGCTAAAA-ACGCGTTCCGGAACCCCGACTCAA
*
2586 TTTTTCATGATTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACCAAATCCAAGCC
130 TTTTTCATGATTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACCAAATCCCAGCC
* * * *
2651 ACAGTGGATTTAAGGATTTGTTTTTACAGGAATCTGAATCTTGTTTCGACTT-ATTAGAAATAAA
195 ACAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTGTTTCGATTTAATTAGAAATAAA
* * * * * * * *
2715 TTCAAGAAAAAAAATGAAAAAAACGTTATTACAAGCGTGATAAACCATTCA-ATTTTTTGTGTTG
260 TTC-GGGAAAAAAATG-AACAAACGATATTAGAAGCGTGAAAAACCATT-ATTTTTTTTGCGTTG
2779 AATTACATATC
322 AATTACATATC
2790 TTTTAGGACTAATGTGGCCAAAAATTGAGGGAAAAA--TTTTGGGTCAGTTTTTGG-AAAATTTT
1 TTTTAGGACTAATGTGGCCAAAAATTGA-GGAAAAATTTTTTGGGTCAGTTTTTGGCAAAATTTT
* * * *
2852 AGCCGAAATCGTGTACTAACCATCACGGATTTAGGCTAAAAACGCGTTCCGCAACTCCGACTCAA
65 AGCCGAAATCGTGTATTAACCATCACGGATTCAGGCTAAAAACGCGTTCCGGAACCCCGACTCAA
* *
2917 TTTTTCATGA-TTTTGGTATAAAGACACCTTGAAATATTTATATTCATCGAACCAAATCCCAGCC
130 TTTTTCATGATTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACCAAATCCCAGCC
* * *
2981 ACAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTTTTTCGATTT-TTTAAAAAGTAA
195 ACAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTGTTTCGATTTAATTAGAAA-TAA
* *
3045 ATTCGGGAAAAAAATGAACAAATGATATTAGAAGCGTGAAAAACCCTTATTTTTGTTTGCGTTGA
259 ATTCGGGAAAAAAATGAACAAACGATATTAGAAGCGTGAAAAACCATTATTTTT-TTTGCGTTGA
3110 ATTTA-ATATC
323 A-TTACATATC
* * *
3120 TTTTAGGACTAATGTGGCGAGAAATTGAGGAAAAACTTTTTGGGTCAG-TTTTGGCAAAATTTTA
1 TTTTAGGACTAATGTGGCCAAAAATTGAGGAAAAATTTTTTGGGTCAGTTTTTGGCAAAATTTTA
* * * * *
3184 GCCGAAATCGTGAATTAACCATCACAGATTCAGGCTAAAAACGCGTTCCGGACCCCCGACTGAAC
66 GCCGAAATCGTGTATTAACCATCACGGATTCAGGCTAAAAACGCGTTCCGGAACCCCGACTCAAT
*
3249 TTTTCATGATTTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACTAAATCCCAGCC
131 TTTTCATGA-TTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACCAAATCCCAGCC
* * * * **
3314 ACAGTGGATTTAAGGATTTGTTTTTACAAGTATCTGAATCTTGTTTCGATTTAATGACAAATATT
195 ACAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTGTTTCGATTTAATTAGAAATAAA
* * *
3379 TTC-GGAAAAAAATGAACAAACGATATTAGAAGCGTGAAAAAACCATCAATTTTGTTGCGTTGAA
260 TTCGGGAAAAAAATGAACAAACGATATTAGAAGCGTG-AAAAACCATTATTTTTTTTGCGTTGAA
3443 TTACATATC
324 TTACATATC
3452 TTTTAGGACTAAT
1 TTTTAGGACTAAT
Statistics
Matches: 1487, Mismatches: 126, Indels: 91
0.87 0.07 0.05
Matches are distributed among these distances:
316 16 0.01
317 74 0.05
318 170 0.11
319 29 0.02
320 1 0.00
328 1 0.00
329 36 0.02
330 184 0.12
331 371 0.25
332 116 0.08
333 210 0.14
334 247 0.17
335 32 0.02
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (332 bp):
TTTTAGGACTAATGTGGCCAAAAATTGAGGAAAAATTTTTTGGGTCAGTTTTTGGCAAAATTTTA
GCCGAAATCGTGTATTAACCATCACGGATTCAGGCTAAAAACGCGTTCCGGAACCCCGACTCAAT
TTTTCATGATTTTTGGCATAAAGACACCTTGAAATATCTATATTCATCGAACCAAATCCCAGCCA
CAGTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCTTGTTTCGATTTAATTAGAAATAAAT
TCGGGAAAAAAATGAACAAACGATATTAGAAGCGTGAAAAACCATTATTTTTTTTGCGTTGAATT
ACATATC
Done.