Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021778.1 Corchorus olitorius cultivar O-4 contig21811, 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: 48295
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--41 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42 CATTTCATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18897 original size:6 final size:6
Alignment explanation
Indices: 18881--18912 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
18871 CCCTGAACCC
*
18881 TCCCAA ACCCAA TCCCAA TCCCAA TCCCAA TC
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TC
18913 AGTTCCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (6 bp):
TCCCAA
Found at i:29260 original size:35 final size:35
Alignment explanation
Indices: 29214--29283 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
29204 ATAAGGTGAC
29214 GGTTAAATTACCAGTAACTGTAGGAGGGGGCCAAG
1 GGTTAAATTACCAGTAACTGTAGGAGGGGGCCAAG
29249 GGTTAAATTACCAGTAACTGTAGGAGGGGGCCAAG
1 GGTTAAATTACCAGTAACTGTAGGAGGGGGCCAAG
29284 TGAGATGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.20
Consensus pattern (35 bp):
GGTTAAATTACCAGTAACTGTAGGAGGGGGCCAAG
Found at i:34797 original size:58 final size:57
Alignment explanation
Indices: 34703--34816 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 57
34693 ATTAATCAAA
*
34703 TATCAAGTGACATGGTCTTTATTAGATGCATAAAAAAGACGTTTTCGGACCGAGGCT
1 TATCAAGTGACATGGTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAGGCT
* * * *
34760 TATCGAGTGACATGTTTTTTTATTAGATGTC-TAAAAAAGATGTTTTAGGACCGAGGC
1 TATCAAGTGACATG-GTCTTTATTAGATG-CATAAAAAAGACGTTTTAGGACCGAGGC
34817 ATGATGCTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 13 0.26
58 36 0.72
59 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (57 bp):
TATCAAGTGACATGGTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAGGCT
Found at i:36126 original size:36 final size:36
Alignment explanation
Indices: 36079--36148 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
36069 TTCAATAACC
* *
36079 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
36115 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
36149 CCAAAATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:37064 original size:208 final size:201
Alignment explanation
Indices: 36659--37072 Score: 668
Period size: 208 Copynumber: 2.0 Consensus size: 201
36649 GCTTAATAAC
* *
36659 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
36724 GATACAATACATTATTATTATATATAAAACTATACCAAAAAGAAAGTTGAACATTTAGTACTTGA
66 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAAGTTGAACATTTAGTACTTGA
36789 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
36854 GATTTA
196 GATTTA
* *
36860 TTTATCAATGATGAACGTTGTTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGTATAA
1 TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
36925 GATACAACACATTACTATTATATATATATATAGAACTATACCAAAAAAAAATAGTTGAATA-TTA
66 GATACAACACA-T--TATTAT-TATATATA-A-AACTATACC-AAAAAAAA-AGTTGAACATTTA
**
36989 GTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT
123 GTACTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT
37054 AAAGATCCGATTTA
188 AAAGATCCGATTTA
37068 TTTAT
1 TTTAT
37073 TATTAAGGAA
Statistics
Matches: 196, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
201 71 0.36
202 1 0.01
204 6 0.03
205 8 0.04
206 1 0.01
207 9 0.05
208 92 0.47
209 8 0.04
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAAGTTGAACATTTAGTACTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
GATTTA
Found at i:37176 original size:24 final size:23
Alignment explanation
Indices: 37143--37188 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
37133 ACGTTTGCAC
37143 AAATACCTAAGAATTTGAATTAAA
1 AAATACCTAAGAATTT-AATTAAA
*
37167 AAATATCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
37189 TATAAGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.33
Consensus pattern (23 bp):
AAATACCTAAGAATTTAATTAAA
Found at i:37244 original size:39 final size:40
Alignment explanation
Indices: 37179--37259 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
37169 ATATCTAAGA
*
37179 ATTTAATTAATATAAGGATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAGGATTTCAGTTATTATATATATTAC
* * *
37218 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAGGATTTCAGTTATTATATATATTAC
37258 AT
1 AT
37260 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATATAAGGATTTCAGTTATTATATATATTAC
Found at i:39036 original size:330 final size:331
Alignment explanation
Indices: 38211--39391 Score: 1307
Period size: 332 Copynumber: 3.6 Consensus size: 331
38201 CTTTGTTACA
* * * * * * * * *
38211 AAAAATCGTGATGGCTAATACACGATTTCGGTTAAACTTTTGCAAAAATTTACCCGAGAGAATTT
1 AAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC-AAAAAATTT
* * *
38276 -TCCTA-AATTTTTTTGCCATGATACTCATAAAAAATATATAATTAAACACCAAAAAGATTGAAA
65 CTCC-ACAA-TTTTTGGCCATCATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAA
* *
38339 GGCTTT-TCACGCTTCTAATATCGGTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGAA
128 GGCTTTCTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAA
** * *
38403 ACATGATTCAAATGCTCGTGAAAGCAAATCCTTAAATACAATGTGGTTGAGATTTGGTTAGATGG
193 ACATGATTCAAATGCTCGT-AAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGG
*
38468 ATATAGATATTTCAATGA-TACTTGGCGCCAAAAATCATGCAAAA-TAGAGCCGG-GACCCCGAA
257 ATATAGATATTTCAATGAGT-CTTGGCGCCAAAAATCATGCAAAACT-GAGCCGGAG-CCCGGAA
38530 TCGCATTTTTAGTC
319 -CGCATTTTTAGTC
** * * * * *
38544 AAAAACTATGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAAATGACACAAAACATTTC
1 AAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAAATTTC
* ** * * * * * * *
38609 TCCTCAATTTCCGGCCACCATATTTATAAAAAAAAATATAAATCAACGCCAAAAAAATT-AAAGG
66 TCCACAATTTTTGGCCATCATACTCAT-AAAAAATATATAATTCAACACCAAAAAGATTGAAA-G
* * *
38673 GC-TTCTCACACTTCTAATAT--TTTTTTCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAA
129 GCTTTCTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAA
** * * * * **
38735 CCGGACTGAGATGCTCGTAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATAAAT
194 CATGATTCAAATGCTCGTAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGGAT
* *
38800 ATAGATATTTCAATGAGTCTTGACGCCAAAAAT-ATGCAAAACTGAGTCGGAGCCACGGAACGCA
259 ATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGAGCC-CGGAACGCA
*
38864 TTTTTAGCC
323 TTTTTAGTC
* *
38873 AAAAACCGTGATAGTTTGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCAAAAGAATTT
1 AAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAA-AATTT
* * *
38938 -TCCACAATTTTTGGCCATGATACTCATAAAAAATTTATAATTCAATACCAAAAAGATTGAAAGG
65 CTCCACAATTTTTGGCCATCATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGG
* * * * * *
39002 CTAT-TCACGCTTCAAATATCATTTTTCATATTTTTTCCGAATTAA-TTCATAATTGAACCGAAA
130 CTTTCTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTC-TAATTAAATCGAAA
* * * *
39065 CATGATTCATATGCTCGTAAAAACAAA-CCATTAAATCTAATGTGGGTAAGATTTGGTTAGATGG
194 CATGATTCAAATGCTCGTAAAAA-AAATCC-TTAAATCCAATGTGGCTGAGATTTGGTTAGATGG
* * *
39129 ATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCCGGAGCTCCGAAACG
257 ATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGAGC-CCGGAACG
*
39194 CGTTTTTAGTC
321 CATTTTTAGTC
* * * * * *
39205 AAAAACCGTGATTGTTAGTACACGATTTCAGCTAAAATTTTACAAAAATTTACCCGATAAATTTC
1 AAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAAATTTC
* * * * * *
39270 TCCTCAATTTTGGGCCA-CACTACTAATAAGAAATATATAACTCAACGCCAAAAAGATTG-AAGG
66 TCCACAATTTTTGGCCATCA-TACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGG
* * * * *
39333 GTTTCTCATGCTTCTAATATCGCTTTTCCTACCTTTTCCCGAATTAATTTCTAATTAAA
130 CTTTCTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTCCGAATTAATTTCTAATTAAA
39392 AAAATTATAT
Statistics
Matches: 703, Mismatches: 121, Indels: 48
0.81 0.14 0.06
Matches are distributed among these distances:
328 41 0.06
329 108 0.15
330 133 0.19
331 128 0.18
332 177 0.25
333 113 0.16
334 3 0.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (331 bp):
AAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAAATTTC
TCCACAATTTTTGGCCATCATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGC
TTTCTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
TGATTCAAATGCTCGTAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGGATAT
AGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGAGCCCGGAACGCATTT
TTAGTC
Found at i:39484 original size:27 final size:27
Alignment explanation
Indices: 39449--39514 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
39439 AAAAGTACAC
* *
39449 AAAATTATATTTTAATAATGGCATAGTT
1 AAAAATATATTTTAATAATGACA-AGTT
*
39477 -AAAATATATTTTAATAATGACAATTT
1 AAAAATATATTTTAATAATGACAAGTT
39503 AAAAATATATTT
1 AAAAATATATTT
39515 GAAAAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.09
27 31 0.91
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (27 bp):
AAAAATATATTTTAATAATGACAAGTT
Found at i:39610 original size:94 final size:97
Alignment explanation
Indices: 39437--39614 Score: 299
Period size: 94 Copynumber: 1.9 Consensus size: 97
39427 TATATTTGAA
* *
39437 AAAAAAGTACACAAAATTATATTTTAATAATGGCATAGTTAAAATATATTTTAATAATGACAATT
1 AAAAAAGTACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAATAATGACAATT
39502 TAAAAATATATTTGAAAAAATAGTAAAATCGG
66 TAAAAATATATTTGAAAAAATAGTAAAATCGG
*
39534 AAAAAA-TACATAAAATTATATTTTAATAATGACATAATT-AAA-ATATTTTAATAATGACAATT
1 AAAAAAGTACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAATAATGACAATT
*
39596 TAGAAATATATTTGAAAAA
66 TAAAAATATATTTGAAAAA
39615 GGGGTATAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
94 38 0.49
95 3 0.04
96 30 0.39
97 6 0.08
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.34
Consensus pattern (97 bp):
AAAAAAGTACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAATAATGACAATT
TAAAAATATATTTGAAAAAATAGTAAAATCGG
Found at i:43719 original size:6 final size:6
Alignment explanation
Indices: 43708--43748 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
43698 AAACATACAA
43708 ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGA
1 ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGAT ACAGA
43749 GTAGCATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (6 bp):
ACAGAT
Found at i:46924 original size:21 final size:21
Alignment explanation
Indices: 46898--46947 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
46888 CAACTTCTTC
* *
46898 ATGAGATGGCAACTTTCAGGA
1 ATGAGATGACAACTTCCAGGA
46919 ATGAGATGACAACTTCCAGGA
1 ATGAGATGACAACTTCCAGGA
*
46940 AAGAGATG
1 ATGAGATG
46948 CTTCCTCCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (21 bp):
ATGAGATGACAACTTCCAGGA
Done.