Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008511.1 Corchorus capsularis cultivar CVL-1 contig08532, 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: 54752
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:14914 original size:29 final size:30
Alignment explanation
Indices: 14865--14926 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
14855 ACTTGTAGCG
* * *
14865 TTTGGACGTTTTGTCCTTTGAA-TTTCAAT
1 TTTGGACATTTTATCCTTTGAACTCTCAAT
14894 TTTGGACATTTTAT-CTCTTGAACTCTCAAT
1 TTTGGACATTTTATCCT-TTGAACTCTCAAT
14924 TTT
1 TTT
14927 TAACGTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.07
29 17 0.61
30 9 0.32
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (30 bp):
TTTGGACATTTTATCCTTTGAACTCTCAAT
Found at i:15105 original size:30 final size:29
Alignment explanation
Indices: 15066--15138 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 29
15056 ATCGTTTGAG
* *
15066 GGGGGCAAAACGTCCAAAATTGAGAGTTTA
1 GGGGACAAAACGTCCAAAATTGA-AGTTCA
* *
15096 GGGGACAAAATGTCTAAAATTGAAGTTCA
1 GGGGACAAAACGTCCAAAATTGAAGTTCA
* *
15125 TGGAACAAAACGTC
1 GGGGACAAAACGTC
15139 GAAACGCTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 16 0.44
30 20 0.56
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (29 bp):
GGGGACAAAACGTCCAAAATTGAAGTTCA
Found at i:15133 original size:29 final size:30
Alignment explanation
Indices: 15071--15138 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
15061 TTGAGGGGGG
* *
15071 CAAAACGTCCAAAATTGAGAGTTTAGGGGA
1 CAAAACGTCCAAAATTGAGAGTTCAGGGAA
* * *
15101 CAAAATGTCTAAAATTGA-AGTTCATGGAA
1 CAAAACGTCCAAAATTGAGAGTTCAGGGAA
15130 CAAAACGTC
1 CAAAACGTC
15139 GAAACGCTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.22
Consensus pattern (30 bp):
CAAAACGTCCAAAATTGAGAGTTCAGGGAA
Found at i:19395 original size:77 final size:77
Alignment explanation
Indices: 19288--19431 Score: 288
Period size: 77 Copynumber: 1.9 Consensus size: 77
19278 CCATAATAAC
19288 AATTATCATATAAACTCAAAAGTAGCCAATATTTGTGAGCAAAATATACATCCAATTACAAACAT
1 AATTATCATATAAACTCAAAAGTAGCCAATATTTGTGAGCAAAATATACATCCAATTACAAACAT
19353 TTACATTGCTCA
66 TTACATTGCTCA
19365 AATTATCATATAAACTCAAAAGTAGCCAATATTTGTGAGCAAAATATACATCCAATTACAAACAT
1 AATTATCATATAAACTCAAAAGTAGCCAATATTTGTGAGCAAAATATACATCCAATTACAAACAT
19430 TT
66 TT
19432 CCATAAGCTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 67 1.00
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (77 bp):
AATTATCATATAAACTCAAAAGTAGCCAATATTTGTGAGCAAAATATACATCCAATTACAAACAT
TTACATTGCTCA
Found at i:30630 original size:44 final size:44
Alignment explanation
Indices: 30589--30716 Score: 229
Period size: 44 Copynumber: 2.9 Consensus size: 44
30579 TCCTCTTTGG
*
30589 ATCTTCTTTGATAATAATCCTCCACATACGTGGATTTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
*
30633 ATCTTCTATGATAATAATCCTCCACATACGTGGATCTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
*
30677 ATCTTCTTTGATAATAATCCTCCACATATGTGGATCTTCT
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCT
30717 AGAGACTCTG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 80 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.41
Consensus pattern (44 bp):
ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
Found at i:32783 original size:15 final size:15
Alignment explanation
Indices: 32763--32792 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
32753 ATCAGGCTAC
32763 CACGATACACAATAT
1 CACGATACACAATAT
32778 CACGATACACAATAT
1 CACGATACACAATAT
32793 TTCAACCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:40797 original size:44 final size:44
Alignment explanation
Indices: 40666--40800 Score: 207
Period size: 44 Copynumber: 3.1 Consensus size: 44
40656 TTAATAATCC
* *
40666 TCTTTGAATCTTCTTTGATAATAATCCTCCACATACGTGGATTT
1 TCTTTCAATCTTCTTTGATAATAATCCTCCACATACGTGGATCT
* * *
40710 TCTTTCAATCTTCTATGATAATAATCCTCCACCTACGCGGATCT
1 TCTTTCAATCTTCTTTGATAATAATCCTCCACATACGTGGATCT
* *
40754 TCTTTCAATCTTCTTTGATAATAATCCTCCACATATGTAGATCT
1 TCTTTCAATCTTCTTTGATAATAATCCTCCACATACGTGGATCT
40798 TCT
1 TCT
40801 AGAGACTCTG
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 81 1.00
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.41
Consensus pattern (44 bp):
TCTTTCAATCTTCTTTGATAATAATCCTCCACATACGTGGATCT
Found at i:41712 original size:63 final size:63
Alignment explanation
Indices: 41590--41714 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
41580 TTATTTTTGT
* * * ** * **
41590 GCTCTAAGTTTTGTCTAAGCCGCCCTTTTTAGGATTTTCAACTTAGCGAGACTTTTTTTTTTC
1 GCTCTAACTTTTGCCCAAGCCGCCCTTTACAGGATTTTCAACTTAGCAAGACTGGTTTTTTTC
*
41653 GCTCTAACTTTTGCCCAAGCCGTCCTTTACAGGATTTTCAACTTAGCAAG-CTCGGTTTTTTT
1 GCTCTAACTTTTGCCCAAGCCGCCCTTTACAGGATTTTCAACTTAGCAAGACT-GGTTTTTTT
41715 TTTTGGGTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.42
Consensus pattern (63 bp):
GCTCTAACTTTTGCCCAAGCCGCCCTTTACAGGATTTTCAACTTAGCAAGACTGGTTTTTTTC
Found at i:43671 original size:44 final size:44
Alignment explanation
Indices: 43623--43750 Score: 229
Period size: 44 Copynumber: 2.9 Consensus size: 44
43613 TCCTCTTTGG
*
43623 ATCTTCTTTGATAATAATCCTCCACATACGTGGATTTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
*
43667 ATCTTCTATGATAATAATCCTCCACATACGTGGATCTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
*
43711 ATCTTCTTTGATAATAATCCTCCACATATGTGGATCTTCT
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCT
43751 AGAGGCTCTG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 80 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.41
Consensus pattern (44 bp):
ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
Found at i:46651 original size:44 final size:44
Alignment explanation
Indices: 46601--46719 Score: 175
Period size: 44 Copynumber: 2.7 Consensus size: 44
46591 GTAATCCTCC
* * * **
46601 TTGATAATAATCCCCCACATAAGTTGATCTTCTTTCAATCTTTT
1 TTGATAATAATCCTCCACATACGTGGATCTTCTTTCAATCTTCA
*
46645 TTGATAATAAGCCTCCACATACGTGGATCTTCTTTCAATCTTCA
1 TTGATAATAATCCTCCACATACGTGGATCTTCTTTCAATCTTCA
*
46689 TTGATAATAATCCTCCAAATACGTGGATCTT
1 TTGATAATAATCCTCCACATACGTGGATCTT
46720 TTGGAGACTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (44 bp):
TTGATAATAATCCTCCACATACGTGGATCTTCTTTCAATCTTCA
Found at i:48293 original size:291 final size:291
Alignment explanation
Indices: 47764--48345 Score: 1083
Period size: 291 Copynumber: 2.0 Consensus size: 291
47754 TCAACCATTA
*
47764 TTGCATATACATTTATAGCACCAATCCTTTGGAATTCCGGCAGAGGAGTTGAACCAATAAATCCT
1 TTGCATATACATTTATAGCACCAATCCTTTGGAATTCCGACAGAGGAGTTGAACCAATAAATCCT
47829 AATATCCACACACAATTAATATGTAATTAAAACACACTTAATTATAAATATAAAAATAGTAAATT
66 AATATCCACACACAATTAATATGTAATTAAAACACACTTAATTATAAATATAAAAATAGTAAATT
*
47894 ACAAAAAAGGACAGTAGGAAAACTAAGGGAGGAAATTCGTTAAGGGTCTTTTAGTCACCCGAAAA
131 ACAAAAAAGGACAGTAGGAAAACTAAGGGAGGAAATTCATTAAGGGTCTTTTAGTCACCCGAAAA
* *
47959 GTGAGAAAAGACCAAAAAAAGCCAAAAGAAGGCACCGCATTAATCCTCAATTTGGCCTTTAAGTA
196 ATGAGAAAAGACCAAAAAAAGCCAAAAGAAGGCACCACATTAATCCTCAATTTGGCCTTTAAGTA
*
48024 ATTTCCATAGTCATTAAAAATAATATATAGT
261 ATTTCCAGAGTCATTAAAAATAATATATAGT
48055 TTGCATATACATTTATAGCACCAATCCTTTGGAATTCCGACAGAGGAGTTGAACCAATAAATCCT
1 TTGCATATACATTTATAGCACCAATCCTTTGGAATTCCGACAGAGGAGTTGAACCAATAAATCCT
48120 AATATCCACACACAATTAATATGTAATTAAAACACACTTAATTATAAATATAAAAATAGTAAATT
66 AATATCCACACACAATTAATATGTAATTAAAACACACTTAATTATAAATATAAAAATAGTAAATT
* * *
48185 ACAAAAAAGGACAGTAGGAAAAGTAAGGGAGGAAATTCATTGAGGGTCTTTTAGTGACCCGAAAA
131 ACAAAAAAGGACAGTAGGAAAACTAAGGGAGGAAATTCATTAAGGGTCTTTTAGTCACCCGAAAA
*
48250 ATGAGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATTTGGCCTTTAAGTA
196 ATGAGAAAAGACCAAAAAAAGCCAAAAGAAGGCACCACATTAATCCTCAATTTGGCCTTTAAGTA
48315 ATTTCCAGAGTCATTAAAAATAATATATAGT
261 ATTTCCAGAGTCATTAAAAATAATATATAGT
48346 ACAAGTTATA
Statistics
Matches: 282, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
291 282 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.26
Consensus pattern (291 bp):
TTGCATATACATTTATAGCACCAATCCTTTGGAATTCCGACAGAGGAGTTGAACCAATAAATCCT
AATATCCACACACAATTAATATGTAATTAAAACACACTTAATTATAAATATAAAAATAGTAAATT
ACAAAAAAGGACAGTAGGAAAACTAAGGGAGGAAATTCATTAAGGGTCTTTTAGTCACCCGAAAA
ATGAGAAAAGACCAAAAAAAGCCAAAAGAAGGCACCACATTAATCCTCAATTTGGCCTTTAAGTA
ATTTCCAGAGTCATTAAAAATAATATATAGT
Done.