Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011730.1 Corchorus olitorius cultivar O-4 contig11763, 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: 1764
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:643 original size:334 final size:328
Alignment explanation
Indices: 4--1593 Score: 1723
Period size: 334 Copynumber: 4.9 Consensus size: 328
1 AAG
* *
4 GGTTTTTCATGCTTCGAATATCATTTTTCCTATGCTTTTCCGAATTAATTTCCAATTAAATCGAA
1 GGTTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTAATTTCCAATTAAATCGAA
* * * * *
69 ACTAGATTATGATGCTTGTAAAAAAAAATCTTTAAATCCTATGTGGCTGAGATTTGGGTAAATGA
66 ACTGGATTCTGATGCTCGT-AAAAAAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGATGA
* * * * * * *
134 ATATAGAAATTCCAAAGAGTCTT--TGCCGAAAATCATACAAAATGGAGCCGAGGCACCAGAACG
130 ATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAAT-GAGCCGGGGCCCCGGAACG
* * * *
197 CATTTTTAGCCGAAAACTGTGATGGTAACACAAACACGATTTCGGTCAAGATTTTGCAAAAATTG
194 CGTTTTTAGCCGAAAACTGTGATGGTTA-GC--ACACGATTTCAGTCAAGATTTTGCAAAAATTG
* * * *
262 TCCCGAATAATTTTTCCTCAATGTTTGGCCAAAATACTCATAAAATATATATCAATCATAGCCAA
256 ACCAGAATAATTTTTCCTCAATATTTGGCCAAAATACTCA-AAAA-ATATATAAATCATAGCCAA
*
327 AAATGTTGAAA
319 AAATATTG-AA
* *
338 GGTTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTAGTTTCCATTTAAATCGAA
1 GGTTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTAATTTCCAATTAAATCGAA
*
403 ACTGGATTCTGATGCTCGT-AAAAAAATCTTTAAATATTATGTGGCTGAGATTTGGGTAGATGAA
66 ACTGGATTCTGATGCTCGTAAAAAAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGATGAA
* *
467 TATAGATATTCCACGGAGTCTTGGCGCCAAAAATCATACAAAACTGAACCGGGGCCCCGGAACGC
131 TATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAA-TGAGCCGGGGCCCCGGAACGC
* * *
532 GTTTTTAGCCGAAAATTGTGATTGTTAGCACACGATTTCAGTCAAGATTTTGCGAAAATTGACCA
195 GTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCAGTCAAGATTTTGCAAAAATTGACCA
* * * *
597 GAATAATTTTTTTCTCAATTTTTGGCTAAAATACTCCTAAAAAATATATAAATCATCGCCAAAAA
260 GAATAA-TTTTTCCTCAATATTTGGCCAAAATACT-C-AAAAAATATATAAATCATAGCCAAAAA
662 TATTGAA
322 TATTGAA
* *
669 GGCTTTTTCACGCTTCGAATA-CTGTTTTTCCTATGTTTTTCCGAATTAATTTCCAATTAAATTG
1 GG-TTTTTCACGCTTCGAATATC-GTTTTTCCTATGCTTTTCCGAATTAATTTCCAATTAAATCG
* *
733 AAACTGGATTCTGATACTCGTAAAAACAAATCATTAAATCTTATGTGGCTGAGATTTGGGTAGAT
64 AAACTGGATTCTGATGCTCGTAAAAA-AAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGAT
* * *
798 GAATATAGATATTCCAAGGAGTTTTGGCGCCAAAAATCATACAAAAATGAGCAGGGGCCTCGGAA
128 GAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATAC-AAAATGAGCCGGGGCCCCGGAA
*
863 CGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCAGTCAAGATTTTGCAAAAATTAA
192 CGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCAGTCAAGATTTTGCAAAAATTGA
* ** *** * * * * *
928 CGCA-AATGATTTTTCCTCAATATTTGGCCAAAAATA-TTGAAGGGTTTTTAAAGC-T--TC-GA
257 C-CAGAATAATTTTTCCTCAATATTTGGCC-AAAATACTCAAAAAATATATAAATCATAGCCAAA
987 AA-A-T---
320 AATATTGAA
* * * *
991 CGTTTTT----C--C---TAT-G--CTT-C--T------CGGAATTAATTTACAATTAAAATCGA
1 GGTTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTAATTTCCAATT-AAATCGA
* ** * * *
1035 AACTGGATTCTGATGCTCGTAATAACAAATCTTTAAAAATCATGGGGCTGAGATTTGGGCAGATG
65 AACTGGATTCTGATGCTCGTAA-AAAAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGATG
* * * * * * * *
1100 AATATAGATATTCAAAAGAATATCT-GCGCCAAAAATAACACAAAACTGAGCCAGGGCCCTGGAA
129 AATATAGATATTCCAAGGAGTCT-TGGCGCCAAAAATCATACAAAA-TGAGCCGGGGCCCCGGAA
* * * *
1164 CGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGAATTTGCAAAAATTGA
192 CGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCAGTCAAGATTTTGCAAAAATTGA
* * * * * *
1229 CCCGAATGATTTTTCATCAATTTTTGGCCAAAATACACATAAAAATATATAAATCATCGCCAAAA
257 CCAGAATAATTTTTCCTCAATATTTGGCCAAAATACTCA-AAAAATATATAAATCATAGCCAAAA
*
1294 ATATTGTAG
321 ATATTG-AA
* * * * *
1303 GGTTTTCCATGTTTCGATTATCGTTTTTCCTATGATTTTCCGAATTAATTTCCAATTAAATCGAA
1 GGTTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTAATTTCCAATTAAATCGAA
* * * * *
1368 ACTAGATTCGGATGCTCGTAAAAAAAAATCTTTAAATCTTATGTGGCCGAGATTTTGGTAGATTA
66 ACTGGATTCTGATGCTCGT-AAAAAAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGATGA
* * *
1433 ATATAGATATTCCAAGGAGTCTCT-GCGCCAAAAATCACACAAAA-CAG-TGTTGGGCCCCGGAA
130 ATATAGATATTCCAAGGAGTCT-TGGCGCCAAAAATCATACAAAATGAGCCG--GGGCCCCGGAA
* *
1495 CGCGTTTTTAGCCGAAACCTGTGATGGTTAGCACACGATTTCGGTCAAGATTTTGCAAAAATTGA
192 CGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCAGTCAAGATTTTGCAAAAATTGA
* * *
1560 TGCA-AATGATTTTTCCTCAATTTTTGGCCAAAAT
257 -CCAGAATAATTTTTCCTCAATATTTGGCCAAAAT
1594 TCACACAAAA
Statistics
Matches: 1061, Mismatches: 139, Indels: 115
0.81 0.11 0.09
Matches are distributed among these distances:
300 27 0.03
301 191 0.18
302 12 0.01
303 1 0.00
305 1 0.00
306 4 0.00
307 1 0.00
308 2 0.00
309 2 0.00
311 1 0.00
312 7 0.01
315 1 0.00
317 1 0.00
318 1 0.00
321 8 0.01
322 2 0.00
324 2 0.00
325 2 0.00
326 1 0.00
327 4 0.00
328 1 0.00
330 3 0.00
331 152 0.14
332 284 0.27
333 46 0.04
334 297 0.28
335 7 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (328 bp):
GGTTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTAATTTCCAATTAAATCGAA
ACTGGATTCTGATGCTCGTAAAAAAAATCTTTAAATCTTATGTGGCTGAGATTTGGGTAGATGAA
TATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAATGAGCCGGGGCCCCGGAACGCG
TTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCAGTCAAGATTTTGCAAAAATTGACCAG
AATAATTTTTCCTCAATATTTGGCCAAAATACTCAAAAAATATATAAATCATAGCCAAAAATATT
GAA
Found at i:1196 original size:301 final size:300
Alignment explanation
Indices: 654--1261 Score: 853
Period size: 301 Copynumber: 2.0 Consensus size: 300
644 ATAAATCATC
* * * * *
654 GCCAAAAATATTGAAGGCTTTTTCACGCTTCGAATACTGTTTTTCCTATGTTTTTCCGAATTAAT
1 GCCAAAAATATTGAAGGCTTTTTAAAGCTTCGAAAACTGTTTTTCCTATGCTTCTCCGAATTAAT
* * ** * *
719 TTCCAATTAAATTGAAACTGGATTCTGATACTCGTAAAAACAAATCATTAAATCTTATGTGGCTG
66 TTACAATTAAATCGAAACTGGATTCTGATACTCGTAAAAACAAATCATTAAAAATCATGGGGCTG
* * * * * * *
784 AGATTTGGGTAGATGAATATAGATATTCCAAGGAGTTTTGGCGCCAAAAATCATACAAAAATGAG
131 AGATTTGGGCAGATGAATATAGATATTCAAAAGAATTCTGGCGCCAAAAATAACACAAAAATGAG
* * * *
849 CAGGGGCCTCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCAGTCAAGAT
196 CAGGGCCCTCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCAGTCAAGAA
* *
914 TTTGCAAAAATTAACGCAAATGATTTTTCCTCAATATTTG
261 TTTGCAAAAATTAACCCAAATGATTTTTCATCAATATTTG
* *
954 GCCAAAAATATTGAAGGGTTTTTAAAGCTTCGAAAA-TCGTTTTTCCTATGCTTCTCGGAATTAA
1 GCCAAAAATATTGAAGGCTTTTTAAAGCTTCGAAAACT-GTTTTTCCTATGCTTCTCCGAATTAA
* * *
1018 TTTACAATTAAAATCGAAACTGGATTCTGATGCTCGTAATAACAAATCTTTAAAAATCATGGGGC
65 TTTACAATT-AAATCGAAACTGGATTCTGATACTCGTAAAAACAAATCATTAAAAATCATGGGGC
*
1083 TGAGATTTGGGCAGATGAATATAGATATTCAAAAGAATATCT-GCGCCAAAAATAACACAAAACT
129 TGAGATTTGGGCAGATGAATATAGATATTCAAAAGAAT-TCTGGCGCCAAAAATAACACAAAAAT
*
1147 GAGCCAGGGCCCT-GGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCA
193 GAG-CAGGGCCCTCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCAGTCA
* * *
1211 AGAATTTGCAAAAATTGACCCGAATGATTTTTCATCAATTTTTG
257 AGAATTTGCAAAAATTAACCCAAATGATTTTTCATCAATATTTG
1255 GCCAAAA
1 GCCAAAA
1262 TACACATAAA
Statistics
Matches: 270, Mismatches: 34, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
299 1 0.00
300 63 0.23
301 196 0.73
302 10 0.04
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (300 bp):
GCCAAAAATATTGAAGGCTTTTTAAAGCTTCGAAAACTGTTTTTCCTATGCTTCTCCGAATTAAT
TTACAATTAAATCGAAACTGGATTCTGATACTCGTAAAAACAAATCATTAAAAATCATGGGGCTG
AGATTTGGGCAGATGAATATAGATATTCAAAAGAATTCTGGCGCCAAAAATAACACAAAAATGAG
CAGGGCCCTCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCAGTCAAGAA
TTTGCAAAAATTAACCCAAATGATTTTTCATCAATATTTG
Found at i:1574 original size:331 final size:333
Alignment explanation
Indices: 954--1603 Score: 899
Period size: 331 Copynumber: 2.0 Consensus size: 333
944 TCAATATTTG
* * *
954 GCCAAAAATATTGAAGGGTTTTTAAAGCTTCGAAAATCGTTTTTCCTATGCTTCTCGGAATTAAT
1 GCCAAAAATATTGAAGGGTTTTCAAAGCTTCGAAAATCGTTTTTCCTATGATTCTCCGAATTAAT
* * * * *
1019 TTACAATTAAAATCGAAACTGGATTCTGATGCTCGTAATAACAAATCTTTAAAAATCATGGGGCT
66 TTACAATTAAAATCGAAACTAGATTCGGATGCTCGTAAAAAAAAATCTTTAAAAATCATGGGGCC
*
1084 GAGATTTGGGCAGATGAATATAGATATTCAAAAGAATATCTGCGCCAAAAATAACACAAAACTGA
131 GAGATTTGGGCAGATGAATATAGATATTCAAAAGAATATCTGCGCCAAAAATAACACAAAACAGA
*
1149 GCCAGGGCCCTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGA
196 GCCAGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGA
* *
1214 ATTTGCAAAAATTGACCCGAATGATTTTTCATCAATTTTTGGCCAAAATACACATAAAAATATAT
261 ATTTGCAAAAATTGACCCAAATGATTTTTCATCAATTTTTGGCCAAAATACACACAAAAATATAT
1279 AAATCATC
326 AAATCATC
* * * * ** *
1287 GCCAAAAATATTGTAGGGTTTTCCATGTTTCGATTATCGTTTTTCCTATGATTTTCCGAATTAAT
1 GCCAAAAATATTGAAGGGTTTTCAAAGCTTCGAAAATCGTTTTTCCTATGATTCTCCGAATTAAT
* ** * *
1352 TTCCAATT-AAATCGAAACTAGATTCGGATGCTCGTAAAAAAAAATCTTTAAATCTTATGTGGCC
66 TTACAATTAAAATCGAAACTAGATTCGGATGCTCGTAAAAAAAAATCTTTAAAAATCATGGGGCC
* * * * * * * * *
1416 GAGATTTTGGTAGATTAATATAGATATTCCAAGGAGTCTCTGCGCCAAAAATCACACAAAACAGT
131 GAGATTTGGGCAGATGAATATAGATATTCAAAAGAATATCTGCGCCAAAAATAACACAAAACAGA
** * * *
1481 G-TTGGGCCCCGGAACGCGTTTTTAGCCGAAACCTGTGATGGTTAGCACACGATTTCGGTCAAGA
196 GCCAGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGA
* ** * *
1545 TTTTGCAAAAATTGATGCAAATGATTTTTCCTCAATTTTTGGCCAAAATTCACACAAAA
261 ATTTGCAAAAATTGACCCAAATGATTTTTCATCAATTTTTGGCCAAAATACACACAAAA
1604 CTAAGTTGAA
Statistics
Matches: 274, Mismatches: 43, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
331 109 0.40
332 103 0.38
333 62 0.23
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (333 bp):
GCCAAAAATATTGAAGGGTTTTCAAAGCTTCGAAAATCGTTTTTCCTATGATTCTCCGAATTAAT
TTACAATTAAAATCGAAACTAGATTCGGATGCTCGTAAAAAAAAATCTTTAAAAATCATGGGGCC
GAGATTTGGGCAGATGAATATAGATATTCAAAAGAATATCTGCGCCAAAAATAACACAAAACAGA
GCCAGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACAAGATTTCGGTCAAGA
ATTTGCAAAAATTGACCCAAATGATTTTTCATCAATTTTTGGCCAAAATACACACAAAAATATAT
AAATCATC
Done.