Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021775.1 Corchorus olitorius cultivar O-4 contig21808, 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: 23297
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:283 original size:170 final size:170
Alignment explanation
Indices: 1--391 Score: 612
Period size: 170 Copynumber: 2.3 Consensus size: 170
1 TTTTGTTTTACTCAAAACAGATAAAGTAAGATACATAATTGTTTTATATTTTGATCTCATTAGTT
1 TTTTGTTTTACTCAAAACAGATAAAGTAAGATACATAATTGTTTTATATTTTGATCT-ATTAGTT
* *
66 CATTAGTCTTTTCATAGCCACGCGTGAGTAATGGTTGTTACATGCAACTTACGTGTACGTTCCAC
65 CATTAGTCTTTTCATAGCCACGCGTGAGTAATGGTTGTTACATGCAACTTACATGTACATTCCAC
*
131 GTTGAATGATGTTGTTACAG-GGACGTAAAATCCATAAAAT
130 GTTGAATGATGTTGTTACAGTGGATGTAAAATCCATAAAAT
*
171 TTTTGTTTTACTCAAAACAAATAAAGTAAGATACATAATTGTTTTATATTTTGATCTTATTAGTT
1 TTTTGTTTTACTCAAAACAGATAAAGTAAGATACATAATTGTTTTATATTTTGATC-TATTAGTT
* * *
236 CATTACTCTTTTCATAGCCACGCGTGAGTAATGATTGTTACATGCAACTTACATGCACATT-CAC
65 CATTAGTCTTTTCATAGCCACGCGTGAGTAATGGTTGTTACATGCAACTTACATGTACATTCCAC
*
300 GTTGAATGATGTTG-TACAG-GGACGTAAAATCCATAAAAT
130 GTTGAATGATGTTGTTACAGTGGATGTAAAATCCATAAAAT
* * * * *
339 TTTTGTTTTGCTCAAAACAGATAAAGTAATATATATAA-TCTTTAATATTTTGA
1 TTTTGTTTTACTCAAAACAGATAAAGTAAGATACATAATTGTTTTATATTTTGA
392 CCTCATTTGT
Statistics
Matches: 208, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
167 13 0.06
168 59 0.28
169 17 0.08
170 118 0.57
171 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.39
Consensus pattern (170 bp):
TTTTGTTTTACTCAAAACAGATAAAGTAAGATACATAATTGTTTTATATTTTGATCTATTAGTTC
ATTAGTCTTTTCATAGCCACGCGTGAGTAATGGTTGTTACATGCAACTTACATGTACATTCCACG
TTGAATGATGTTGTTACAGTGGATGTAAAATCCATAAAAT
Found at i:1779 original size:111 final size:112
Alignment explanation
Indices: 1492--2040 Score: 480
Period size: 111 Copynumber: 4.9 Consensus size: 112
1482 GTCATACTTT
* * *
1492 TTTTTTGTGGCTAAAACAAAAGCATA-CAGATTCCAAGTCCACGTGACAACATCATTAAATGTGG
1 TTTTTTG-GG-TAAAACAAAAGCGTATGA-ATTCCATGTCCACGTGACAACATCATTAAATGTGG
* * * * * *
1556 AATGCACACATATGGTGCTTGTAACAATCATTACTTATGCGTGAATACGT-
63 AATGTACACATAAGGCGCTTGTAACAACCATTACTTACGCGTGGATAC-TA
* * * *
1606 TTTTTTGGGTAAAATAGAAGCGTATGAATTCCACGTCCACGTGACAACATCATTAAACGTGGAAT
1 TTTTTTGGGTAAAACAAAAGCGTATGAATTCCATGTCCACGTGACAACATCATTAAATGTGGAAT
* *
1671 GTACGCATAAGGCGCTTGTAACAACCATTACTTATGCGTGGATA-TA
66 GTACACATAAGGCGCTTGTAACAACCATTACTTACGCGTGGATACTA
* * * * * *
1717 TTTTTTGGGTAAAATAAAAGTGTATGGATTTCATGTTCACGTGACAACATCATTAAATGTGGAGT
1 TTTTTTGGGTAAAACAAAAGCGTATGAATTCCATGTCCACGTGACAACATCATTAAATGTGGAAT
** * * * *
1782 GTACATGT-AGGCACTTGTAACGACCATTATTTACGCGTGGATACGA
66 GTACACATAAGGCGCTTGTAACAACCATTACTTACGCGTGGATACTA
* * * * * **
1828 TTTTTT-GGTAAAACAAAAGCATATAAATTCCATATCCGA-GTGACAATATCACTAAACATGGAA
1 TTTTTTGGGTAAAACAAAAGCGTATGAATTCCATGTCC-ACGTGACAACATCATTAAATGTGGAA
* * * * ** * * *
1891 CGTACACGTATGACATTTGTAACAACCATTAATTACACGTGGATATGTACA
65 TGTACACATAAGGCGCTTGTAACAACCATTACTTACGCGTGGATA-CT--A
** * * * * *
1942 CTTTTTTGGGTAAATACAAAAGTTTATGGATTCCATGTCCACATGACAACATCATTCAATATGAA
1 -TTTTTTGGGTAAA-ACAAAAGCGTATGAATTCCATGTCCACGTGACAACATCATTAAATGTGGA
** * *
2007 ATGTACATGTAAGGTGTTTGTAACAACCATTACT
64 ATGTACACATAAGGCGCTTGTAACAACCATTACT
2041 CACATGTGGT
Statistics
Matches: 354, Mismatches: 69, Indels: 21
0.80 0.16 0.05
Matches are distributed among these distances:
110 81 0.23
111 99 0.28
112 86 0.24
113 3 0.01
114 8 0.02
115 6 0.02
116 7 0.02
117 64 0.18
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (112 bp):
TTTTTTGGGTAAAACAAAAGCGTATGAATTCCATGTCCACGTGACAACATCATTAAATGTGGAAT
GTACACATAAGGCGCTTGTAACAACCATTACTTACGCGTGGATACTA
Found at i:1916 original size:221 final size:227
Alignment explanation
Indices: 1520--2040 Score: 570
Period size: 221 Copynumber: 2.3 Consensus size: 227
1510 AAAGCATACA
* * ** ** *
1520 GATTCCAAGTCCACGTGACAACATCATTAAATGTGGAATGCACACATATGGTGCTTGTAACAATC
1 GATTCCATGTCCACGTGACAACATCATTAAATGTGGAATGTACATGTATGGCACTTGTAACAACC
* * * * * * *
1585 ATTACTTATGCGTGAATACGTTTTTTTGGGTAAAATAGAAGCGTATGAATTCCACGTCCACGTGA
66 ATTACTTACGCGTGAATACGATTTTTTGGGTAAAACAAAAGCATATAAATTCCACATCCACGTGA
* * * * * * * **
1650 CAACATCATTAAACGTGGAATGTACGCATAAGGCGCTTGTAACAACCATTACTTATGCGTGGATA
131 CAACATCACTAAACATGGAACGTACACATAAGACACTTGTAACAACCATTAATTACACGTGGATA
*
1715 -T-A-TTTTTTGGGTAAA-ATAAAAGTGTATG
196 GTAACTTTTTTGGGTAAATACAAAAGTGTATG
* * * *
1743 GATTTCATGTTCACGTGACAACATCATTAAATGTGGAGTGTACATGTA-GGCACTTGTAACGACC
1 GATTCCATGTCCACGTGACAACATCATTAAATGTGGAATGTACATGTATGGCACTTGTAACAACC
* * *
1807 ATTATTTACGCGTGGATACGATTTTTT-GGTAAAACAAAAGCATATAAATTCCATATCCGA-GTG
66 ATTACTTACGCGTGAATACGATTTTTTGGGTAAAACAAAAGCATATAAATTCCACATCC-ACGTG
* * * *
1870 ACAATATCACTAAACATGGAACGTACACGTATGACATTTGTAACAACCATTAATTACACGTGGAT
130 ACAACATCACTAAACATGGAACGTACACATAAGACACTTGTAACAACCATTAATTACACGTGGAT
*
1935 ATGTACACTTTTTTGGGTAAATACAAAAGTTTATG
195 A-GTA-ACTTTTTTGGGTAAATACAAAAGTGTATG
* * * * * ***
1970 GATTCCATGTCCACATGACAACATCATTCAATATGAAATGTACATGTAAGGTGTTTGTAACAACC
1 GATTCCATGTCCACGTGACAACATCATTAAATGTGGAATGTACATGTATGGCACTTGTAACAACC
2035 ATTACT
66 ATTACT
2041 CACATGTGGT
Statistics
Matches: 242, Mismatches: 48, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
221 81 0.33
222 36 0.15
223 42 0.17
225 1 0.00
226 13 0.05
227 52 0.21
228 17 0.07
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (227 bp):
GATTCCATGTCCACGTGACAACATCATTAAATGTGGAATGTACATGTATGGCACTTGTAACAACC
ATTACTTACGCGTGAATACGATTTTTTGGGTAAAACAAAAGCATATAAATTCCACATCCACGTGA
CAACATCACTAAACATGGAACGTACACATAAGACACTTGTAACAACCATTAATTACACGTGGATA
GTAACTTTTTTGGGTAAATACAAAAGTGTATG
Found at i:4059 original size:14 final size:13
Alignment explanation
Indices: 4023--4061 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
4013 TATATATTAG
4023 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
4036 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
4050 AATTTTTTAAAT
1 AATTTTTTAAAT
4062 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:5645 original size:2 final size:2
Alignment explanation
Indices: 5633--5664 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5623 AGTGAGAAAC
5633 TA TA T- TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5665 ATAAGAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:19991 original size:2 final size:2
Alignment explanation
Indices: 19984--20017 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19974 CTTAACATAG
*
19984 AT AT AT AT AT AT AT AT AT GT 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
20018 TATGTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21340 original size:36 final size:35
Alignment explanation
Indices: 21300--21410 Score: 84
Period size: 37 Copynumber: 3.1 Consensus size: 35
21290 CCTTGGATAT
*
21300 TCTTCAAGAATAATAATAATTCTCCACATACATGGA
1 TCTTCAA-AATAATAATAATCCTCCACATACATGGA
** * *
21336 TCTTC--TTTGATAATAATCCTCCACATACGTGGA
1 TCTTCAAAATAATAATAATCCTCCACATACATGGA
** * *
21369 TCTTCAATCTTTGAA-AATAATCCTCCACATACGTGAA
1 TCTTCAA--AAT-AATAATAATCCTCCACATACATGGA
21406 TCTTC
1 TCTTC
21411 TTTCAATAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
33 28 0.44
36 5 0.08
37 29 0.46
38 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (35 bp):
TCTTCAAAATAATAATAATCCTCCACATACATGGA
Found at i:21349 original size:33 final size:33
Alignment explanation
Indices: 21312--21413 Score: 132
Period size: 37 Copynumber: 3.0 Consensus size: 33
21302 TTCAAGAATA
* *
21312 ATAATAATTCTCCACATACATGGATCTTCTTTG
1 ATAATAATCCTCCACATACGTGGATCTTCTTTG
21345 ATAATAATCCTCCACATACGTGGATCTTCAATCTTTG
1 ATAATAATCCTCCACATACGTGGATC-T---TCTTTG
* *
21382 AAAATAATCCTCCACATACGTGAATCTTCTTT
1 ATAATAATCCTCCACATACGTGGATCTTCTTT
21414 CAATAATTCT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
33 29 0.48
34 1 0.02
36 1 0.02
37 30 0.49
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (33 bp):
ATAATAATCCTCCACATACGTGGATCTTCTTTG
Found at i:22691 original size:333 final size:332
Alignment explanation
Indices: 21810--23297 Score: 1770
Period size: 333 Copynumber: 4.5 Consensus size: 332
21800 TTGCTCTACA
* ** * * *
21810 GCTCGTAAAAACAAATCCTTAAATCCAATGTGTTTAAGATTAGGTTAGAT-AACTATAGATATTT
1 GCTCGTAAAAACAAATCCTTAAATGCAATGTGACTGAGATTTGATTAGATGAA-TATAGATATTT
* * * * * * * ** * *
21874 AAAGGAGTTTTGCCACAAAAAATTATGCAAAACTGACCCGG-GACCCCGGAACGCGTTTTTAGCC
65 CAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGTCGGAG-CCCTGAAACGCGTTTTTA-CC
* * *
21938 AAAAAA-CTTGATGG-TA-T--ACGATTT-CGGCTAAAATTTTGC-AAAAATAGACCCGAAATAT
128 AAAAAACCGTGATGGTTACTACACGATTTCCAGCTAAAATTTTGCAAAAAAT-GACCCGAAAAAT
* * * *
21996 TTTTCCTCAATTTTTAGCCACAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGGAG
192 TTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAAAAAGATTGGAG
*
22061 GACTTTTCACGCTTTTAATATCGTTTTCCATATTTTTCTGAATTAATTTCTAATTAAATCAAAAC
257 GACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCAAAAC
*
22126 AAGATTCAGAT
322 AAGATTCAAAT
* * * * *
22137 GCTCGTAAAAACAAATCATTAAATTCAAATATGATTGAGATTTGATTAAAT-AAGTATAGATATT
1 GCTCGTAAAAACAAATCCTTAAATGC-AATGTGACTGAGATTTGATTAGATGAA-TATAGATATT
* * * * * * ** ***
22201 TCAAGGAGTCTCGGCGCAAAAAATAATGCAAAACTAAGCCGGGGCCCCAAAACATATTTTTAGCC
64 TCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGTCGGAGCCCTGAAACGCGTTTTTA-CC
** * *
22266 -AAAAACCGTGATGACCCGACACCCTACACGA-TTCCAGCTTAAATTTTGCAGAAAATGACCCGA
128 AAAAAACCGTGATG----GTTA--CTACACGATTTCCAGCTAAAATTTTGCAAAAAATGACCCGA
* * * *
22329 CAAATTTTTCCTCAATTTTTAACTAAAATACTCATAAAATATATTTATAATTTAACCCCAAAACG
187 AAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATA--TATAATTTAACGCCAAAAAG
* *
22394 ATTGGAGGACTTATCACGCTTTTAATATCGTTTTTCATA-TTTTCTGAATTAATTTTTAATTAAA
250 ATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAA
* *
22458 TCGAAACAAAATTCAAAT
315 TCAAAACAAGATTCAAAT
* * * * *
22476 GCTCGTATAATCAAATCCTTAAATGCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTC
1 GCTCGTAAAAACAAATCCTTAAATGCAATGTGACTGAGATTTGATTAGATGAATATAGATATTTC
*
22541 AAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGTCGGAGCCCTGAAATGCGTTTTTACCAAA
66 AAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGTCGGAGCCCTGAAACGCGTTTTTACC-AA
**
22606 AAAACCGTGATGGTTACTACACGATTTTGA-CTAAAATTTTGCAAAAAATGACCCGAAAAATTTT
130 AAAACCGTGATGGTTACTACACGATTTCCAGCTAAAATTTTGCAAAAAATGACCCGAAAAATTTT
* * * * * *
22670 TCTTCAATTTTTGGCTAAAATATTCATGAAATATATATAATTTAACGCCAAAAAGGTTGAAGGAC
195 TCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGAC
*
22735 TTTTCGA-GCTTTTAATATCATTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCAAAACAA
260 TTTTC-ACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCAAAACAA
*
22799 GATTCAGAT
324 GATTCAAAT
* * * *
22808 GCTCGTAAAAACAAATCATTAAATTCAAATGTGGCTGAGATTTGATTAGATGAGTATAGATATTT
1 GCTCGTAAAAACAAATCCTTAAATGC-AATGTGACTGAGATTTGATTAGATGAATATAGATATTT
* * * * * * *
22873 CAAGGAGTTTCGGCGCCAAAAATCATGCAAAACTAAGT-GGGGTCCTCGAAACGCGTTATTAGCG
65 CAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGTCGGAGCCCT-GAAACGCGTTTTTA-CC
* * * * * *
22937 AAAAACCCGTGATGGTTAATACACGA-TTCCAGCTTAAATTTTGCAGAAAATGACCAGACAAATT
128 AAAAAACCGTGATGGTTACTACACGATTTCCAGCTAAAATTTTGCAAAAAATGACCCGAAAAATT
*
23001 TTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATTTATAATTTTACGCCAAAAAGATTGGA
193 TTTCCTCAATTTTTAGCTAAAATACTCATAAAATATA--TATAATTTAACGCCAAAAAGATTGGA
* * *
23066 GGACTTTTCACGCTTTTAATACCGTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAA
256 GGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCAAAA
23131 CAAGATTCAAAT
321 CAAGATTCAAAT
* *
23143 GCTCGTATAAACAAATCCTTAAATGCAATCTGACTGAGATTTGATTAGATGAATATAGATATTTC
1 GCTCGTAAAAACAAATCCTTAAATGCAATGTGACTGAGATTTGATTAGATGAATATAGATATTTC
* * * * *
23208 AAGGATTCTCGATGCCAGAAATTATGCAAAATTGAGTCGGAGCCCTGAAACGCGTTTTT-CCAAA
66 AAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGTCGGAGCCCTGAAACGCGTTTTTACCAAA
23272 AAACCGTGATGGTTACTACACGATTT
131 AAACCGTGATGGTTACTACACGATTT
Statistics
Matches: 989, Mismatches: 140, Indels: 58
0.83 0.12 0.05
Matches are distributed among these distances:
327 29 0.03
328 86 0.09
329 1 0.00
331 51 0.05
332 97 0.10
333 239 0.24
334 82 0.08
335 124 0.13
336 1 0.00
337 4 0.00
338 140 0.14
339 81 0.08
340 54 0.05
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (332 bp):
GCTCGTAAAAACAAATCCTTAAATGCAATGTGACTGAGATTTGATTAGATGAATATAGATATTTC
AAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGTCGGAGCCCTGAAACGCGTTTTTACCAAA
AAACCGTGATGGTTACTACACGATTTCCAGCTAAAATTTTGCAAAAAATGACCCGAAAAATTTTT
CCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGACT
TTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGA
TTCAAAT
Done.