Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012755.1 Corchorus olitorius cultivar O-4 contig12788, 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: 52624
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:3179 original size:63 final size:63
Alignment explanation
Indices: 3080--3211 Score: 246
Period size: 63 Copynumber: 2.1 Consensus size: 63
3070 TATTTTCTAC
3080 TTCAATTTAATCCTTTCCTTTCTATTTCAATAAACTTCCACTAAAAATCAATAATAATTATAA
1 TTCAATTTAATCCTTTCCTTTCTATTTCAATAAACTTCCACTAAAAATCAATAATAATTATAA
* *
3143 TTCAATTTAATCCTTTCCTTTCTATTTCAATCAACTTCCGCTAAAAATCAATAATAATTATAA
1 TTCAATTTAATCCTTTCCTTTCTATTTCAATAAACTTCCACTAAAAATCAATAATAATTATAA
3206 TTCAAT
1 TTCAAT
3212 AGATTCTTTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.38, C:0.20, G:0.01, T:0.42
Consensus pattern (63 bp):
TTCAATTTAATCCTTTCCTTTCTATTTCAATAAACTTCCACTAAAAATCAATAATAATTATAA
Found at i:5157 original size:124 final size:123
Alignment explanation
Indices: 5029--5292 Score: 268
Period size: 124 Copynumber: 2.1 Consensus size: 123
5019 CTTGGTGGAA
* * *
5029 TGACACGTCA-ATAGTGTTGTACCACAG-TAGTCACGCTAATGGCCTCCTTTGTTGATAAAGAAC
1 TGACACGTCACA-AG-GTTGCACCA-AGTTAGCCACGCTAATGACCTCCTTTGTTGATAAAGAAC
* * *
5092 AGGACTTCGGTTG-AAGTGCCC-AGTAGCACTTCTC-GTCAGCGGAACCTCCTCCTCGGCAGAG
63 AAGACTTCGG-TGAAAGTGCCCGA-CAACACTTCTCAG-CAGCGGAACCTCCTCCTCGGCAGAG
* * * ** * *
5153 TGACATGTCAGCAAGGTTGCACCAGGTTAGCCATGCTGCTGACCTCCTTTGTTGATGAAGGACAA
1 TGACACGTCA-CAAGGTTGCACCAAGTTAGCCACGCTAATGACCTCCTTTGTTGATAAAGAACAA
* * *
5218 GACTTTGGTGAAAGTGCCCGACAACACTTTTCAGCGGCGGAACCTCCTCCTCGGCAGAG
65 GACTTCGGTGAAAGTGCCCGACAACACTTCTCAGCAGCGGAACCTCCTCCTCGGCAGAG
*
5277 TGACACATCAGCAAGG
1 TGACACGTCA-CAAGG
5293 CATTCCCACA
Statistics
Matches: 116, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
123 3 0.03
124 108 0.93
125 4 0.03
126 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (123 bp):
TGACACGTCACAAGGTTGCACCAAGTTAGCCACGCTAATGACCTCCTTTGTTGATAAAGAACAAG
ACTTCGGTGAAAGTGCCCGACAACACTTCTCAGCAGCGGAACCTCCTCCTCGGCAGAG
Found at i:7108 original size:147 final size:147
Alignment explanation
Indices: 6824--7139 Score: 452
Period size: 147 Copynumber: 2.1 Consensus size: 147
6814 ACAGGACCTT
* * ** *
6824 CCAGCAGGGGTCGACGAACAGTGACCTTCCAGTCGAGGCTGAGAACAATAAACTCACCTATTAGT
1 CCAGCAGGGGTC-ATGAACAGTGACCTTCCAGTAGAGGCCAAAAACAATAAACTCACCTATTAGT
*
6889 GAACCCCACCATCAGCATGTCTCGGGTGTTGCCACGTCAGCTTGCTATGGGTCCCAACAATGCCG
65 GAACCCCACCATCAGCATGTCTCGGGTGTTGCCACGTCAGCTTGCTATGGATCCCAACAATGCCG
*
6954 GATAGTGGGTCCGACATC
130 GACAGTGGGTCCGACATC
* * *
6972 CCAGCAGAGGTCATGAACAGTGACCTTCCAGTAGGGGCCAAAAACAATAAACTCATCTATTAGTG
1 CCAGCAGGGGTCATGAACAGTGACCTTCCAGTAGAGGCCAAAAACAATAAACTCACCTATTAGTG
* * * * * **
7037 AGCCCCACCATTAGCATGTCTCGGGTGTTGCCACGTTAGCTTGCTGTGGATCCCAACAGTGCTTG
66 AACCCCACCATCAGCATGTCTCGGGTGTTGCCACGTCAGCTTGCTATGGATCCCAACAATGCCGG
* *
7102 ACAGTGGGTTCGGCATC
131 ACAGTGGGTCCGACATC
7119 CCAGCAGGGGTCATGAACAGT
1 CCAGCAGGGGTCATGAACAGT
7140 AGCTTTCCAG
Statistics
Matches: 148, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
147 137 0.93
148 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.22
Consensus pattern (147 bp):
CCAGCAGGGGTCATGAACAGTGACCTTCCAGTAGAGGCCAAAAACAATAAACTCACCTATTAGTG
AACCCCACCATCAGCATGTCTCGGGTGTTGCCACGTCAGCTTGCTATGGATCCCAACAATGCCGG
ACAGTGGGTCCGACATC
Found at i:7470 original size:72 final size:72
Alignment explanation
Indices: 7353--7500 Score: 278
Period size: 72 Copynumber: 2.1 Consensus size: 72
7343 CTTAATGAAG
* *
7353 CCTTTGTAAATAATAAAGATAAGGTGAGAGCTATAGATTGCTACAATCACCAATGCCTTGCCACA
1 CCTTTGTAAATAATAAAGACAAGGTGAGAGCTATAGATCGCTACAATCACCAATGCCTTGCCACA
7418 TAGTGGA
66 TAGTGGA
7425 CCTTTGTAAATAATAAAGACAAGGTGAGAGCTATAGATCGCTACAATCACCAATGCCTTGCCACA
1 CCTTTGTAAATAATAAAGACAAGGTGAGAGCTATAGATCGCTACAATCACCAATGCCTTGCCACA
7490 TAGTGGA
66 TAGTGGA
7497 CCTT
1 CCTT
7501 GAGATGAACC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (72 bp):
CCTTTGTAAATAATAAAGACAAGGTGAGAGCTATAGATCGCTACAATCACCAATGCCTTGCCACA
TAGTGGA
Found at i:7828 original size:143 final size:143
Alignment explanation
Indices: 7570--7855 Score: 437
Period size: 143 Copynumber: 2.0 Consensus size: 143
7560 AAGGAGAAGG
* ** * *
7570 AAACCATGGGGTATTTACCATTCTAGGCCGGTGACCATGATTTAAGCTACCTCTTGATATACAAG
1 AAACCATGGGGGATTTACCATTCTAGGCCGGCCACCATGATTCAAGCTACCTCTTAATATACAAG
* * *
7635 TTCTTTATAATCAAATGTTGACCACCATTGTTGGAGTTACCACCACAATGGTAGCCTTCAAGAAG
66 TTCTTTATAATCAAATGGTAACCACCATAGTTGGAGTTACCACCACAATGGTAGCCTTCAAGAAG
7700 AATAAAGACACTT
131 AATAAAGACACTT
* * ***
7713 AAACCATGGGGGATTTACCATTCTAGGTCGGCCACCATGATTCATGCTACCTCTTAATATATGGG
1 AAACCATGGGGGATTTACCATTCTAGGCCGGCCACCATGATTCAAGCTACCTCTTAATATACAAG
* *
7778 TTCTTTATAATCAAATGGTAACCACCCTAGTTGGAGTTACCACCACAATGGTAGCCTTCAAGAGG
66 TTCTTTATAATCAAATGGTAACCACCATAGTTGGAGTTACCACCACAATGGTAGCCTTCAAGAAG
7843 AATAAAGACACTT
131 AATAAAGACACTT
7856 CTTGGAGGCT
Statistics
Matches: 128, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
143 128 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (143 bp):
AAACCATGGGGGATTTACCATTCTAGGCCGGCCACCATGATTCAAGCTACCTCTTAATATACAAG
TTCTTTATAATCAAATGGTAACCACCATAGTTGGAGTTACCACCACAATGGTAGCCTTCAAGAAG
AATAAAGACACTT
Found at i:17216 original size:15 final size:14
Alignment explanation
Indices: 17196--17225 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
17186 ATCTTTTTAA
17196 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
17211 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
17225 T
1 T
17226 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:29001 original size:18 final size:18
Alignment explanation
Indices: 28978--29041 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
28968 TAATCATTTG
28978 TGAATAATGGGCTTTTAA
1 TGAATAATGGGCTTTTAA
* *
28996 TGAATAGTGGACTTTTAA
1 TGAATAATGGGCTTTTAA
* * * *
29014 TGAGTAATAGGATTTTGA
1 TGAATAATGGGCTTTTAA
29032 TGAAGTAATG
1 TGAA-TAATG
29042 CCTTTTAAGA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
18 31 0.89
19 4 0.11
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (18 bp):
TGAATAATGGGCTTTTAA
Found at i:29890 original size:18 final size:18
Alignment explanation
Indices: 29867--29901 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29857 CGCACAAGGT
29867 CACCCCACCAATTATGGG
1 CACCCCACCAATTATGGG
29885 CACCCCACCAATTATGG
1 CACCCCACCAATTATGG
29902 TAGGGTAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.40, G:0.14, T:0.17
Consensus pattern (18 bp):
CACCCCACCAATTATGGG
Found at i:31496 original size:31 final size:31
Alignment explanation
Indices: 31460--31577 Score: 155
Period size: 31 Copynumber: 3.8 Consensus size: 31
31450 CTGACATGGT
*
31460 ACGCCACGTGTACCAAAAAGCGACATGTGGC
1 ACGCCACATGTACCAAAAAGCGACATGTGGC
* *
31491 ACGCCACGTATACCAAAAAGCGACATGTGGC
1 ACGCCACATGTACCAAAAAGCGACATGTGGC
* * * *
31522 ATGCCACATGTACCAAAAAGTGACACGTGAC
1 ACGCCACATGTACCAAAAAGCGACATGTGGC
* *
31553 ACGTCACATGTACCAAAAAGTGACA
1 ACGCCACATGTACCAAAAAGCGACA
31578 CGTGTTACAC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.14
Consensus pattern (31 bp):
ACGCCACATGTACCAAAAAGCGACATGTGGC
Found at i:33692 original size:17 final size:16
Alignment explanation
Indices: 33654--33695 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
33644 TTTGGTAGGG
33654 AGGAAA-GAAATAGTA
1 AGGAAAGGAAATAGTA
33669 AGGAAAGGAAATAGTA
1 AGGAAAGGAAATAGTA
33685 AGGGAAAGGAA
1 A-GGAAAGGAA
33696 TTAGGGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.24
16 10 0.40
17 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (16 bp):
AGGAAAGGAAATAGTA
Found at i:33706 original size:16 final size:16
Alignment explanation
Indices: 33649--33712 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
33639 GTCCGTTTGG
*
33649 TAGGGAGGAAA-GAAA
1 TAGGAAGGAAAGGAAA
*
33664 TAGTAAGGAAAGGAAA
1 TAGGAAGGAAAGGAAA
* *
33680 TAGTAAGGGAAAGGAAT
1 TAGGAA-GGAAAGGAAA
* *
33697 TAGGGAGGAAGGGAAA
1 TAGGAAGGAAAGGAAA
33713 GGAAATCACA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 9 0.22
16 18 0.45
17 13 0.32
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (16 bp):
TAGGAAGGAAAGGAAA
Found at i:34170 original size:30 final size:32
Alignment explanation
Indices: 34136--34199 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
34126 GCAGGTTAGA
34136 AGCCCATTTCA-C-AAAAAAAAAAAGAGTAGC
1 AGCCCATTTCACCAAAAAAAAAAAAGAGTAGC
34166 AGCCCATTTCACCTAAAAAAAAAAAAGAGTAGC
1 AGCCCATTTCACC-AAAAAAAAAAAAGAGTAGC
34199 A
1 A
34200 ATCCATTCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 11 0.35
31 1 0.03
33 19 0.61
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.14
Consensus pattern (32 bp):
AGCCCATTTCACCAAAAAAAAAAAAGAGTAGC
Found at i:35752 original size:16 final size:16
Alignment explanation
Indices: 35718--35750 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35708 GAATTATATG
*
35718 AACAATAAAATACATA
1 AACAAGAAAATACATA
35734 AACAAGAAAATA-ATA
1 AACAAGAAAATACATA
35749 AA
1 AA
35751 ACTAAGCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (16 bp):
AACAAGAAAATACATA
Done.