Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005007.1 Corchorus capsularis cultivar CVL-1 contig05025, 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: 24026
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:43 original size:32 final size:33
Alignment explanation
Indices: 2--63 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1 G
**
2 GGGCGGCCTG-CTGTGGCGAAGCCGCCCCATGA
1 GGGCGGCCTGCCCATGGCGAAGCCGCCCCATGA
*
34 GGGCGGCCTGCCCATGGTGAAGCCGCCCCA
1 GGGCGGCCTGCCCATGGCGAAGCCGCCCCA
64 GTGGGAAGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.13, C:0.37, G:0.39, T:0.11
Consensus pattern (33 bp):
GGGCGGCCTGCCCATGGCGAAGCCGCCCCATGA
Found at i:107 original size:33 final size:33
Alignment explanation
Indices: 63--141 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
53 AAGCCGCCCC
* *
63 AGTGGGAAGGCTCCGCCGTGGTTGAACC-TCCCT
1 AGTGGGGAGGCTCCGCCGTGGCTGAACCGT-CCT
*
96 AGTGGGGAGGCTCCGCCGTGGCTGAGCCGTCCT
1 AGTGGGGAGGCTCCGCCGTGGCTGAACCGTCCT
129 AGTGGGGAGGCTC
1 AGTGGGGAGGCTC
142 AGTGTAAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
33 41 0.98
34 1 0.02
ACGTcount: A:0.13, C:0.28, G:0.41, T:0.19
Consensus pattern (33 bp):
AGTGGGGAGGCTCCGCCGTGGCTGAACCGTCCT
Found at i:842 original size:22 final size:21
Alignment explanation
Indices: 817--1380 Score: 279
Period size: 22 Copynumber: 25.9 Consensus size: 21
807 ATGATCCCGT
817 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* ** *
839 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAA-CCTCC
* **
861 TAT-AGAATTTCGATAACCTTTT
1 TATGA-AATTTTGATAACC-TCC
** *
883 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACC-TCC
*
904 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
926 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTC-C
*
948 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCT-CC
* *
970 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
*
993 TAT-AAGATGTTGATAACCTCC
1 TATGAA-ATTTTGATAACCTCC
* * * * *
1014 ATATGATATATCGATAACCACGT
1 -TATGAAATTTTGATAACCTC-C
* * *
1037 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
1058 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTC-C
* *
1081 TCTGAAATTTTAATAATCAC-CC
1 TATGAAATTTTGATAA-C-CTCC
**
1103 TATGAAATTGAGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
*
1125 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CCTCC
*
1148 TATAAAATTTTGATAAACCTCTC
1 TATGAAATTTTGAT-AACCTC-C
* * *
1171 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAAC-CTCC
*
1193 TATGAAATCTTGATAA----C
1 TATGAAATTTTGATAACCTCC
*
1210 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
** *
1231 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTC-C
* *
1253 TATGAAATTTTGGTAACCATAC
1 TATGAAATTTTGATAACC-TCC
* *
1275 TATGAAATTTTGATAACTTTCA
1 TATGAAATTTTGATAAC-CTCC
* * *
1297 TATGAAATTTTGGTGACCACAC
1 TATGAAATTTTGATAACCTC-C
1319 TATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* * *
1340 TCATGAAATTATAATAACCATCT
1 T-ATGAAATTTTGATAACC-TCC
1363 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
1381 ACATAGAGAC
Statistics
Matches: 410, Mismatches: 91, Indels: 82
0.70 0.16 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
20 1 0.00
21 34 0.08
22 294 0.72
23 64 0.16
24 4 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:1150 original size:23 final size:23
Alignment explanation
Indices: 1124--1208 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
1114 GATAACCTCG
*
1124 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
*
1147 CTATAAAATTTTGATAAA-CCTC
1 CTATAAAATTTTGATAAATCTTC
*
1169 TCTATAAAATTTTGATAACT-TTC
1 -CTATAAAATTTTGATAAATCTTC
* * *
1192 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
1209 CTACAAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
22 17 0.32
23 36 0.68
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:1183 original size:46 final size:45
Alignment explanation
Indices: 1117--1208 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 45
1107 AAATTGAGAT
* *
1117 AACCTCGCTATGAAATTTTGATAAATCTTCCTATAAAATTTTGATA
1 AACCTCGCTATAAAATTTTGATAAAT-TTCCTATAAAATCTTGATA
* * * *
1163 AACCTCTCTATAAAATTTTGATAACTTTCTTATGAAATCTTGATA
1 AACCTCGCTATAAAATTTTGATAAATTTCCTATAAAATCTTGATA
1208 A
1 A
1209 CTACAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 17 0.43
46 23 0.57
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (45 bp):
AACCTCGCTATAAAATTTTGATAAATTTCCTATAAAATCTTGATA
Found at i:1243 original size:60 final size:61
Alignment explanation
Indices: 1152--1269 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 61
1142 TCTTCCTATA
* *
1152 AAATTTTGATAAACCTCTCTATAAAATTTTGATAACTTTC-TTATGAAATCTTGATAACTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAC-CTCATTATGAAATCTTGATAACTAC
* ** * *
1213 AAATTTTGAT-AACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGGTAAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATCTTGATAAC
1270 CATACTATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 2 0.04
60 37 0.76
61 10 0.20
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATCTTGATAACTAC
Found at i:2784 original size:37 final size:37
Alignment explanation
Indices: 2692--2787 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 37
2682 ATCTAAGCTC
*
2692 AAATAGGACGTTGGAGACAAAGACTAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACTAAAAGCAAAATT
** *
2729 AAATACAACGATTAGAAACAAAGAC-AAAAGGCAAAATT
1 AAATAGGACG-TTGGAAACAAAGACTAAAA-GCAAAATT
*
2767 AAATAGGATGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
2788 AAATCAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 22 0.45
38 27 0.55
ACGTcount: A:0.55, C:0.10, G:0.19, T:0.16
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACTAAAAGCAAAATT
Found at i:2946 original size:31 final size:31
Alignment explanation
Indices: 2911--2975 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2901 GGCAATTTAT
* *
2911 AAATATGTTTTTTAAAA-AAGGGTACAATTGG
1 AAATATG-TTTTAAAAATAAGGGTACAATCGG
*
2942 AAATATGTTTTAAAAATAAGGGTATAATCGG
1 AAATATGTTTTAAAAATAAGGGTACAATCGG
2973 AAA
1 AAA
2976 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.32
Consensus pattern (31 bp):
AAATATGTTTTAAAAATAAGGGTACAATCGG
Found at i:5991 original size:322 final size:327
Alignment explanation
Indices: 5306--6345 Score: 927
Period size: 317 Copynumber: 3.2 Consensus size: 327
5296 ATTTTTTTAG
* * * *
5306 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAATAAATCCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAT
* * ** * * * * * *
5371 GTCGCTAAGACTTT-ATTTGATGAATATAGATATTTCAAGGAGTGTCGGCGCCAAAAATCATGCA
66 GTGGCTAA-AATTTGATTAAATAAATATAGACATCTCAAGGAGTCTCGGAGTCAAAAATCATGC-
* * * * ** *
5435 AAACTAAGTCGGGGTTCGA-AACGCGTTTTTAGCCAAAAACC------GTG--A-TACA--ATTT
129 AAATTGAGCCAGGGCCCTAGAACGCGTTTTTAGCCAAAAACCGTGATGGTGTTAGTACACGATTT
* * * * * * **
5488 TGGCTAAAATTTTGCAAAAAATGAC-C-CAA-ATTTTTCCTCAATTTTTGGATAAAATTTTCATA
194 CGGCTAAAATTTTACAAAAATTGACACGAAAGATTTCTCCTCAATTTTTGGCTAAAATAATCATA
* ** * * * * * * *
5550 AAATATATATAATTTAACGGCAAAAATATTGGA-GGACTTTTCACGCT-TTAATATCATTTTTCA
259 AAA-ATATATAATTCAACACCAAAAAGATTAGAGGGCCTTTT-ACACTGTT-ATCT-A-ATATC-
*
5613 TATTTTT-CA
318 TGTTTTTCCA
* * *
5622 GAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTGAATCCAA
1 -AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAA
* *
5687 TGTGGCTAAAATTTGATTAAATAAATATAGACATCTCAAGGAGTCTTGGCGTCAAAAATCATGCA
65 TGTGGCTAAAATTTGATTAAATAAATATAGACATCTCAAGGAGTCTCGGAGTCAAAAATCATGC-
* * * **
5752 AAATTGAGCCAGGGCCCTAGAATC-C-TCTTTTATCCAAAAAACTGTGAT-G-GTTATTACTTGA
129 AAATTGAGCCAGGGCCCTAGAA-CGCGT-TTTTAGCC-AAAAACCGTGATGGTGTTAGTACACGA
* * * *
5813 TTTCGGCTAAAATTTTA-TAAAATTGACCCGAAAGATATT-TCCTCATTTTTTGGCTAAAATACT
191 TTTCGGCTAAAATTTTACAAAAATTGACACGAAAGAT-TTCTCCTCAATTTTTGGCTAAAATAAT
* * *
5876 GATAAAAAATATATAATTCAACACTAAAAAGATT-GAAGGG-CTTTT-GAC-GTT-TCTAATATC
255 CAT-AAAAATATATAATTCAACACCAAAAAGATTAG-AGGGCCTTTTACACTGTTATCTAATATC
5936 -GTTTTTCCA
318 TGTTTTTCCA
* *
5945 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAT
* * * ** * * * *
6010 GTGGGTAAGATTTGATTAGATGTATATAGATATTTCAAGTAGTCTCGTAGTCAAAAATCATGCAA
66 GTGGCTAAAATTTGATTAAATAAATATAGACATCTCAAGGAGTCTCGGAGTCAAAAATCATGCAA
* *
6075 ATTGAGCCAGGTCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTTGTTAGTACACGATTT
131 ATTGAGCCAGGGCCCTAGAACGCGTTTTTAGCCAAAAACCGTGATGG--TGTTAGTACACGATTT
*
6140 CGGCTAAAATTTTACAAAAATTGACACGAAAGATTTCTTCTCAATTTTTGGCTAAAATAATCATA
194 CGGCTAAAATTTTACAAAAATTGACACGAAAGATTTCTCCTCAATTTTTGGCTAAAATAATCATA
* * * *
6205 AAAATATATAATTCAACGCCAAAAAGATTAGAGGGCCTTTTACACTTTTAACCTCTTATTTCTTA
259 AAAATATATAATTCAACACCAAAAAGATTAGAGGGCCTTTTACACTGTT-A--TCTAATATC-T-
* *
6270 TTTTTTCTA
319 GTTTTTCCA
* * * *
6279 AAATAATTTCTAATTAAATCGAAACAAGATTCAGATGGTCGTGAAAATAAATTCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAT
6344 GT
66 GT
6346 TGCTGAGAAT
Statistics
Matches: 591, Mismatches: 89, Indels: 69
0.79 0.12 0.09
Matches are distributed among these distances:
316 4 0.01
317 122 0.21
318 10 0.02
319 7 0.01
320 12 0.02
321 29 0.05
322 118 0.20
323 3 0.01
324 64 0.11
325 48 0.08
326 7 0.01
327 10 0.02
328 20 0.03
329 3 0.01
330 51 0.09
331 15 0.03
334 68 0.12
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (327 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAT
GTGGCTAAAATTTGATTAAATAAATATAGACATCTCAAGGAGTCTCGGAGTCAAAAATCATGCAA
ATTGAGCCAGGGCCCTAGAACGCGTTTTTAGCCAAAAACCGTGATGGTGTTAGTACACGATTTCG
GCTAAAATTTTACAAAAATTGACACGAAAGATTTCTCCTCAATTTTTGGCTAAAATAATCATAAA
AATATATAATTCAACACCAAAAAGATTAGAGGGCCTTTTACACTGTTATCTAATATCTGTTTTTC
CA
Found at i:20570 original size:1 final size:1
Alignment explanation
Indices: 20564--20598 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
20554 TAGCCTCATC
20564 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20599 CCCTGCTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.