Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009663.1 Corchorus olitorius cultivar O-4 contig09695, 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, 891
Length: 1485
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:801 original size:325 final size:324
Alignment explanation
Indices: 195--1481 Score: 1153
Period size: 332 Copynumber: 3.8 Consensus size: 324
185 CGTCAAGACT
* *
195 CATTGGATTTAAGGAAATGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATCGGAAATTAAT
1 CATTGGATTTAAGGAAATG-TTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
** * * * * *** ** ** *
260 TTGGAAAAAATAGGAAAAACGGTATTAGAAACGTGAAAAGCCCGCCAATCTTTTTGGGGTTCAAT
65 TTGG---AAA-A--AAAAACCATATTTGAAGCATGAAAAACCCTTAAATAGTTTTGGCATTGAAT
* * * * * * * ** *
325 TATATATTTTTTATGCA-TATTTTGGGCAAAGATTGATGATAAA-TAATTAGGGTCAATTTT-TG
124 TATATATTTTTTATG-AGTATTGTGGCCAAA-ATTAACGAAAAACT-TTTCGTTTCAGTTTTAT-
* * * * *
387 CAAAATTTTAG-TCAAAATCATGTACTAACCATCAAGGTTTCTGACTGAAAACGCATTCCAGGGC
185 CAAAATTTTAGCT-GAAATCATGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGC
* * * *
451 TCCGACTCAGTTTTGCATTATTTTTGGCGCAGAGAGTCATTGAAATATCTATATTCATCTAATCA
249 CCCGGCTCAGTTTTGCATGATTTTTGGCGCAGAGACTCATTGAAATATCTATATTCATCTAATCA
516 AATCTCAGCCA
314 AATCTCAGCCA
* * * *
527 CATTGGATTTAAGGAAATGTTTTGACAAGCATCTAAATTTTGTTTCGATTTAATCAGAACTTAAT
1 CATTGGATTTAAGGAAATGTTTT-ACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
*
592 TTGG-AAAAAAAACCATATTTGAAGCATGAAAAACCCTTAAATAGTTTTGGCCTTGAATTATATA
65 TTGGAAAAAAAAACCATATTTGAAGCATGAAAAACCCTTAAATAGTTTTGGCATTGAATTATATA
656 TTTTTTATGAGTATTGTGGCCTAAAATTAACGAAAAACTTTTCGTTTCAGTTTTATC-AAATATT
130 TTTTTTATGAGTATTGTGGCC-AAAATTAACGAAAAACTTTTCGTTTCAGTTTTATCAAAAT-TT
* * ** * * *
720 CAGTTGAAATTGTGTATTAACCATCACGGTTTCTGGCTGAAAATGCGTTCCGGGGCCCCAGCTCA
193 TAGCTGAAATCATGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCA
* *
785 GTTTTGCATGATTTTTGGCGCCGAGACTCATTGAAATATCTATAATT-ATCTAATCAAATCTCGG
258 GTTTTGCATGATTTTTGGCGCAGAGACTCATTGAAATATCTAT-ATTCATCTAATCAAATCTCAG
849 CCA
322 CCA
*
852 CATTGGATTTAAGGAAATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCGGAAATTAAT
1 CATTGGATTTAAGGAAATG-TTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
* * * * * ** * *
917 TTGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCGCT-AATCTTTTTGGCGTTCAA
65 TTGG---AAA-A--AAAAACCATATTTGAAGCATGAAAAACCC-TTAAATAGTTTTGGCATTGAA
* * * * * * * * *
981 TTATATATTATTTAGGCA-TATTTTGGGCAGAAGTTGAGGAAAAA-TATTTCAG-GTCAATTTT-
123 TTATATATTTTTTATG-AGTATTGTGGCCA-AAATTAACGAAAAACT-TTTC-GTTTCAGTTTTA
* * *
1042 TGCAAAATTTTAGCAGAAATCATGTACTAACCATCACCGTTTCTGGCTGAAAACGAGTTCCGGGG
184 T-CAAAATTTTAGCTGAAATCATGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGG
* *
1107 CTCCGGCTCAGTTTTGCATGATTTTTGGCGCAGAGACTCATTAAAATATCTATATTCATCTAATC
248 CCCCGGCTCAGTTTTGCATGATTTTTGGCGCAGAGACTCATTGAAATATCTATATTCATCTAATC
* *
1172 ATATCTCATCCA
313 AAATCTCAGCCA
* * * *
1184 CATTGGATTTAAGGAAATATTTCTACGGGTATCTGAATCTTGTTTCGATTAAATCAGAAATTAAT
1 CATTGGATTTAAGGAAATGTTT-TACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
* * *
1249 TTCGAAAAAGAATAAAAAAAAATCATATTTGAGGCAGGAAATATTTGAGGCATGAAATGCCCTAA
65 TT-G-----G---AAAAAAAAACCATATTTGA---A-G---CA--TGA---A--AAA--CCCTTA
*
1314 AATAGTATT-GCATTGAA-TATATATTTTTTATGAGTATTGTGGCCAAAAATTAACGAAAAACTT
105 AATAGTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGGCC-AAAATTAACGAAAAACTT
* * * * *
1377 TTCATTTCAGTTTTATCAAAATTTTAGCTGAAAATCATGTATTAACCAACACGGGTTCTGGTTGA
169 TTCGTTTCAGTTTTATCAAAATTTTAGCTG-AAATCATGTACTAACCATCACGGTTTCTGGCTGA
*
1442 AAACGCGTTCCGGGGCCCCGGCTCAGTTTTTCATGTATTT
233 AAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATG-ATTT
1482 GTGG
Statistics
Matches: 776, Mismatches: 124, Indels: 91
0.78 0.13 0.09
Matches are distributed among these distances:
324 5 0.01
325 250 0.32
326 13 0.02
327 1 0.00
328 2 0.00
329 2 0.00
330 1 0.00
331 13 0.02
332 314 0.40
333 8 0.01
335 12 0.02
337 1 0.00
338 7 0.01
339 1 0.00
344 3 0.00
347 1 0.00
348 1 0.00
349 58 0.07
350 70 0.09
351 13 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (324 bp):
CATTGGATTTAAGGAAATGTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAATT
TGGAAAAAAAAACCATATTTGAAGCATGAAAAACCCTTAAATAGTTTTGGCATTGAATTATATAT
TTTTTATGAGTATTGTGGCCAAAATTAACGAAAAACTTTTCGTTTCAGTTTTATCAAAATTTTAG
CTGAAATCATGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTT
TTGCATGATTTTTGGCGCAGAGACTCATTGAAATATCTATATTCATCTAATCAAATCTCAGCCA
Found at i:1156 original size:332 final size:331
Alignment explanation
Indices: 195--1257 Score: 1341
Period size: 332 Copynumber: 3.2 Consensus size: 331
185 CGTCAAGACT
* *
195 CATTGGATTTAAGGAAATGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATCGGAAATTAAT
1 CATTGGATTTAAGGAAATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
* * * *
260 TTGGAAAAAATAGGAAAAACGGTATTAGAAACGTGAAAAGCCCGCCAATCTTTTTGGGGTTCAAT
66 TTGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCGCTAATCTTTTTGGCGTTCAAT
* * *
325 TATATATTTTTTATGCATATTTTGGGCAAAGATTGATGATAAATAATT-AGGGTCAATTTTTGCA
131 TATATATTTTTTATGCATATTTTGGGCAAAG-TTGACGAAAAATATTTCA-GGTCAATTTTTGCA
* * *
389 AAATTTTAGTCA-AAATCATGTACTAACCATCAAGGTTTCTGACTGAAAACGCA-TTCCAGGGCT
194 AAATTTTAG-CAGAAATCATGTACTAACCATCACGGTTTCTGGCTGAAAACG-AGTTCCGGGGCT
* * *
452 CCGACTCAGTTTTGCATTATTTTTGGCGCAGAGAGTCATTGAAATATCTATATTCATCTAATCAA
257 CCGGCTCAGTTTTGCATGATTTTTGGCGCAGAGACTCATTGAAATATCTATATTCATCTAATCAA
517 ATCTCAGCCA
322 ATCTCAGCCA
* * * * *
527 CATTGGATTTAAGGAAATGTTTTGACAAGCATCTAAATTTTGTTTCGATTTAATCAGAACTTAAT
1 CATTGGATTTAAGGAAATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
* * * * * ** * *
592 TTGG----AA-A--AAAAACCATATTTGAAGCATGAAAAACCC-TTAAATAGTTTTGGCCTTGAA
66 TTGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCGCT-AATCTTTTTGGCGTTCAA
* * * * * *
649 TTATATATTTTTTATG-AGTATTGTGGCCTAAAATTAACGAAAAACT-TTTC-GTTTCAGTTTTA
130 TTATATATTTTTTATGCA-TATTTTGGGC-AAAGTTGACGAAAAA-TATTTCAG-GTCAATTTT-
* ** ** * * *
711 T-C-AAATATTCAGTTGAAATTGTGTATTAACCATCACGGTTTCTGGCTGAAAATGCGTTCCGGG
190 TGCAAAAT-TTTAGCAGAAATCATGTACTAACCATCACGGTTTCTGGCTGAAAACGAGTTCCGGG
* * *
774 GCCCCAGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCATTGAAATATCTATAATT-ATCTAA
254 GCTCCGGCTCAGTTTTGCATGATTTTTGGCGCAGAGACTCATTGAAATATCTAT-ATTCATCTAA
*
838 TCAAATCTCGGCCA
318 TCAAATCTCAGCCA
*
852 CATTGGATTTAAGGAAATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCGGAAATTAAT
1 CATTGGATTTAAGGAAATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
917 TTGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCGCTAATCTTTTTGGCGTTCAAT
66 TTGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCGCTAATCTTTTTGGCGTTCAAT
* * *
982 TATATATTATTTAGGCATATTTTGGGCAGAAGTTGAGGAAAAATATTTCAGGTCAATTTTTGCAA
131 TATATATTTTTTATGCATATTTTGGGCA-AAGTTGACGAAAAATATTTCAGGTCAATTTTTGCAA
*
1047 AATTTTAGCAGAAATCATGTACTAACCATCACCGTTTCTGGCTGAAAACGAGTTCCGGGGCTCCG
195 AATTTTAGCAGAAATCATGTACTAACCATCACGGTTTCTGGCTGAAAACGAGTTCCGGGGCTCCG
* *
1112 GCTCAGTTTTGCATGATTTTTGGCGCAGAGACTCATTAAAATATCTATATTCATCTAATCATATC
260 GCTCAGTTTTGCATGATTTTTGGCGCAGAGACTCATTGAAATATCTATATTCATCTAATCAAATC
*
1177 TCATCCA
325 TCAGCCA
* * * * *
1184 CATTGGATTTAAGGAAATATTTCTACGGGTATCTGAATCTTGTTTCGATTAAATCAGAAATTAAT
1 CATTGGATTTAAGGAAATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
*
1249 TTCGAAAAA
66 TTGGAAAAA
1258 GAATAAAAAA
Statistics
Matches: 611, Mismatches: 94, Indels: 52
0.81 0.12 0.07
Matches are distributed among these distances:
324 6 0.01
325 251 0.41
326 8 0.01
327 1 0.00
328 2 0.00
329 2 0.00
330 1 0.00
331 6 0.01
332 327 0.54
333 7 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (331 bp):
CATTGGATTTAAGGAAATGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
TTGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCGCTAATCTTTTTGGCGTTCAAT
TATATATTTTTTATGCATATTTTGGGCAAAGTTGACGAAAAATATTTCAGGTCAATTTTTGCAAA
ATTTTAGCAGAAATCATGTACTAACCATCACGGTTTCTGGCTGAAAACGAGTTCCGGGGCTCCGG
CTCAGTTTTGCATGATTTTTGGCGCAGAGACTCATTGAAATATCTATATTCATCTAATCAAATCT
CAGCCA
Found at i:1294 original size:16 final size:16
Alignment explanation
Indices: 1273--1306 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1263 AAAAAAAATC
1273 ATATTTGAGGCAGGAA
1 ATATTTGAGGCAGGAA
*
1289 ATATTTGAGGCATGAA
1 ATATTTGAGGCAGGAA
1305 AT
1 AT
1307 GCCCTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.29
Consensus pattern (16 bp):
ATATTTGAGGCAGGAA
Done.