Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000794.1 Corchorus capsularis cultivar CVL-1 contig00794, 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: 9865
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Found at i:2830 original size:14 final size:14
Alignment explanation
Indices: 2786--2832 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2776 TAAAAAATAG
2786 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
* * * *
2800 TAAACT-TTTAAAT
1 TAAAATGGTAAAAA
2813 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
2827 TAAAAT
1 TAAAAT
2833 AATTATAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (14 bp):
TAAAATGGTAAAAA
Found at i:2961 original size:152 final size:150
Alignment explanation
Indices: 2704--3104 Score: 653
Period size: 151 Copynumber: 2.7 Consensus size: 150
2694 TTATAAAAAT
* *
2704 ATTAAATGAAAATAGAGTTTTTAGAAGAATCAAAGC-ATATATTAAAAAATTTTAATATAACCAA
1 ATTAAATGAAAATAGAGTTTTTAGTAGAATCAAA-CTATATATTAAAAAATTTTAATATATCCAA
*
2768 GTTTTTAATAAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAATAAAAT
65 GTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGG-AAAAATAAAAT
*
2833 AATTATAAAAATATTGAATTTA
129 AATCATAAAAATATTGAATTTA
* * *
2855 ATTAAATAAAAATAGATTTTTTAGTAGAATCAAACTATATATTAAAAAAAACTTT-ATATATCCA
1 ATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATT--AAAAAATTTTAATATATCCA
*
2919 AGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGGAAAATAAAAT
64 AGTTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGAAAAATAAAAT
2984 AATCATAAAAATATTGAATTTA
129 AATCATAAAAATATTGAATTTA
* * *
3006 ATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAGAAAATTTTAATAAATCGAAG
1 ATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAG
3071 TTTTTAATGAAAAATAGTAAAATGGTAAAAATAA
66 TTTTTAATGAAAAATAGTAAAATGGTAAAAATAA
3105 GTAATTTTAA
Statistics
Matches: 232, Mismatches: 14, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
149 8 0.03
150 44 0.19
151 110 0.47
152 61 0.26
153 9 0.04
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (150 bp):
ATTAAATGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAG
TTTTTAATGAAAAATAGTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGAAAAATAAAATAA
TCATAAAAATATTGAATTTA
Found at i:3171 original size:151 final size:146
Alignment explanation
Indices: 2657--3104 Score: 576
Period size: 151 Copynumber: 3.0 Consensus size: 146
2647 GGTCAATAAC
* *
2657 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAAT-T-ATAA-A--AA--T-ATTAAATGAA
1 AATAAACTTTTAAA-TAAAAT-GT-AAAATAAAATAATATAAAAATATGAATTTAATTAAATAAA
*
2714 AATAGAGTTTTTAGAAGAATCAAAGC-ATATATTAAAAAATTTTAATATAA-CCAAGTTTTTAAT
63 AATAGAGTTTTTAGTAGAATCAAA-CTATATATTAAAAAATTTTAATA-AATCCAAGTTTTTAAT
*
2777 AAAAAATAGTAAAATGGTAAA
126 GAAAAATAGTAAAATGGTAAA
2798 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATA
1 AATAAACTTTTAAA-TAAAAT-GT-AAAATAAAATAA-TATAAAAATA-TGAATTTAATTAAATA
* * *
2863 AAAATAGATTTTTTAGTAGAATCAAACTATATATTAAAAAAAACTTT-ATATATCCAAGTTTTTA
61 AAAATAGAGTTTTTAGTAGAATCAAACTATATATT--AAAAAATTTTAATAAATCCAAGTTTTTA
2927 ATGAAAAATAGTAAAATGGTAAA
124 ATGAAAAATAGTAAAATGGTAAA
* *
2950 AATAAACTTTTAAATTAAAATGGGAAAATAAAATAATCATAAAAATATTGAATTTAATTAAATGA
1 AATAAACTTTTAAA-TAAAAT-GTAAAATAAAATAAT-ATAAAAATA-TGAATTTAATTAAATAA
* *
3015 AAATAGAGTTTTTAGTAGAATCAAACTATATATTAGAAAATTTTAATAAATCGAAGTTTTTAATG
62 AAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATAAATCCAAGTTTTTAATG
3080 AAAAATAGTAAAATGGTAAA
127 AAAAATAGTAAAATGGTAAA
3100 AATAA
1 AATAA
3105 GTAATTTTAA
Statistics
Matches: 277, Mismatches: 14, Indels: 23
0.88 0.04 0.07
Matches are distributed among these distances:
141 37 0.13
142 1 0.00
143 1 0.00
144 3 0.01
145 1 0.00
148 2 0.01
149 8 0.03
150 46 0.17
151 110 0.40
152 59 0.21
153 9 0.03
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (146 bp):
AATAAACTTTTAAATAAAATGTAAAATAAAATAATATAAAAATATGAATTTAATTAAATAAAAAT
AGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATAAATCCAAGTTTTTAATGAAAA
ATAGTAAAATGGTAAA
Found at i:5239 original size:1 final size:1
Alignment explanation
Indices: 5233--5260 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
5223 GATTCAATGG
5233 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
5261 ATATTTACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5372 original size:40 final size:40
Alignment explanation
Indices: 5317--5394 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
5307 TAAAATTATG
*
5317 CCAACAATGGTTTTCTCTATTCACAAGACTCGAACCTGTA
1 CCAACAATGGTTTTCTCCATTCACAAGACTCGAACCTGTA
5357 CCAACAATGGTTTTCTCCATTCACAAGACTCGAACCTG
1 CCAACAATGGTTTTCTCCATTCACAAGACTCGAACCTG
5395 AGACCTTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.28
Consensus pattern (40 bp):
CCAACAATGGTTTTCTCCATTCACAAGACTCGAACCTGTA
Found at i:8077 original size:39 final size:42
Alignment explanation
Indices: 8033--8125 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 42
8023 TTATGTCAAG
*
8033 TTTTGATAACCATACAA-TGAAA-T-ATAACCT-CCTATAAAA
1 TTTTGATAACCACACAACT-AAATTCATAACCTACCTATAAAA
* *
8072 TTTTGAAAACCACACAACTAAATTTCGATAACCTACCTATATAA
1 TTTTGATAACCACACAACTAAA-TTC-ATAACCTACCTATAAAA
8116 TTTTGATAAC
1 TTTTGATAAC
8126 TTCGTCATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
39 18 0.41
40 1 0.02
41 1 0.02
43 7 0.16
44 17 0.39
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.32
Consensus pattern (42 bp):
TTTTGATAACCACACAACTAAATTCATAACCTACCTATAAAA
Found at i:8211 original size:23 final size:22
Alignment explanation
Indices: 8056--8679 Score: 220
Period size: 22 Copynumber: 28.2 Consensus size: 22
8046 ACAATGAAAT
*
8056 ATAACCTC-CTATAAAATTTTG
1 ATAACCTCACTATGAAATTTTG
* * * *
8077 AAAACCACACAACT-AAATTTCG
1 ATAACCTCACTA-TGAAATTTTG
8099 ATAACCT-ACCTAT-ATAATTTTG
1 ATAACCTCA-CTATGA-AATTTTG
* *
8121 ATAACTTC-GTCATGAAATTTT-
1 ATAACCTCACT-ATGAAATTTTG
** * * *
8142 ATTAACCAGATTA-CAAAATTTG
1 A-TAACCTCACTATGAAATTTTG
* * *
8164 ATAACCGCACTACGAAATTTCG
1 ATAACCTCACTATGAAATTTTG
*
8186 ATAAACTCACTATGTAAATTTTG
1 ATAACCTCACTATG-AAATTTTG
*
8209 ATAACCTCCCTATGAAATTTTG
1 ATAACCTCACTATGAAATTTTG
*
8231 ATAACCTTC-CTATAAAATTTTG
1 ATAACC-TCACTATGAAATTTTG
* *
8253 ATAA-TTATACTAT-AAGATTTTG
1 ATAACCT-CACTATGAA-ATTTTG
* * * *
8275 ATAATCTCCCTATGAAA-TATC
1 ATAACCTCACTATGAAATTTTG
* *
8296 AGTAACCACACTATAAAATTTTG
1 A-TAACCTCACTATGAAATTTTG
* * *
8319 ATAA-TTACATTATG-AATTGTG
1 ATAACCT-CACTATGAAATTTTG
* *
8340 ATAACTCTC-TTATGAAATTTTC
1 ATAAC-CTCACTATGAAATTTTG
* *
8362 ATAACCTTACTATGAAGTTTTGG
1 ATAACCTCACTATGAAATTTT-G
* *
8385 ATAAATCTTC-CTATAAAATTTTG
1 AT-AA-CCTCACTATGAAATTTTG
** *
8408 ATAACCTCTTTATAAAATTTT-
1 ATAACCTCACTATGAAATTTTG
* *
8429 ATTAA-CTATACTACGAAATTTTG
1 A-TAACCT-CACTATGAAATTTTG
* * *
8452 ATAACCTCCTCCCTACGAAATGTTG
1 ATAA---CCTCACTATGAAATTTTG
* ** *
8477 ATAACTTC-CTTATGATTTTTTT
1 ATAACCTCAC-TATGAAATTTTG
*
8499 ATAACTTTC-CTATGAAATTTTG
1 ATAAC-CTCACTATGAAATTTTG
*** * **
8521 ATAAGAACACAATGAAATTTCA
1 ATAACCTCACTATGAAATTTTG
**
8543 AT-ACCTTGCTTATGAAATTTTG
1 ATAACCTCAC-TATGAAATTTTG
* *
8565 ATAACCACATTAT-AAAGTTTTG
1 ATAACCTCACTATGAAA-TTTTG
*
8587 GT-ACCTC-CTAATGAAATTTTTG
1 ATAACCTCACT-ATGAAA-TTTTG
* *
8609 ATAACCAT-ACTATTAAAATTTG
1 ATAACC-TCACTATGAAATTTTG
* * *
8631 ATAGCTTTACTATGAAATTTTG
1 ATAACCTCACTATGAAATTTTG
*
8653 ATAA--TCACAAAGTGAAATTTTG
1 ATAACCTCAC-TA-TGAAATTTTG
8675 ATAAC
1 ATAAC
8680 GTCCTTAGAA
Statistics
Matches: 443, Mismatches: 109, Indels: 100
0.68 0.17 0.15
Matches are distributed among these distances:
20 5 0.01
21 68 0.15
22 283 0.64
23 52 0.12
24 15 0.03
25 18 0.04
26 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
ATAACCTCACTATGAAATTTTG
Found at i:8248 original size:88 final size:86
Alignment explanation
Indices: 8055--8256 Score: 212
Period size: 87 Copynumber: 2.3 Consensus size: 86
8045 TACAATGAAA
* * *
8055 TATAACCTCCTATAAAATTTTGAAAACCACACAACTAAATTTCGATAACCTACCTATATAATTTT
1 TATAACCTCCTATAAAATTTTGATAACCACACAACGAAATTTCGATAAACTACCTATATAATTTT
* *
8120 GATAACTTCGTCATGAAATTT
66 GATAACTCCCTCATGAAATTT
*** * * * *
8141 TATTAACCAGAT-TACAAAATTTGATAACCGCACTACGAAATTTCGATAAACT-CACTATGTAAA
1 TA-TAACCTCCTATA-AAATTTTGATAACCACACAACGAAATTTCGATAAACTAC-CTATAT-AA
8204 TTTTGATAACCTCCCT-ATGAAATTT
62 TTTTGATAA-CTCCCTCATGAAATTT
8229 TGATAACCTTCCTATAAAATTTTGATAA
1 T-ATAACC-TCCTATAAAATTTTGATAA
8257 TTATACTATA
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
86 5 0.05
87 42 0.46
88 26 0.28
89 17 0.18
90 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (86 bp):
TATAACCTCCTATAAAATTTTGATAACCACACAACGAAATTTCGATAAACTACCTATATAATTTT
GATAACTCCCTCATGAAATTT
Found at i:8477 original size:25 final size:25
Alignment explanation
Indices: 8439--8486 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
8429 ATTAACTATA
*
8439 CTACGAAATTTTGATAACCTCCTCC
1 CTACGAAATGTTGATAACCTCCTCC
*
8464 CTACGAAATGTTGATAACTTCCT
1 CTACGAAATGTTGATAACCTCCT
8487 TATGATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (25 bp):
CTACGAAATGTTGATAACCTCCTCC
Found at i:8871 original size:22 final size:22
Alignment explanation
Indices: 8846--8899 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
8836 TAACCACATC
* *
8846 ATGAAATTTTGATAA-TATTCCT
1 ATGAAATTTTGATAAGT-TCCCA
8868 ATGAAATTTTGATAAGTTCCCA
1 ATGAAATTTTGATAAGTTCCCA
8890 ATGAAATTTT
1 ATGAAATTTT
8900 TGTTTTTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (22 bp):
ATGAAATTTTGATAAGTTCCCA
Found at i:9074 original size:22 final size:22
Alignment explanation
Indices: 9025--9076 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
9015 AGATAAACAC
9025 ACTATGAAATTACGATAACCTT
1 ACTATGAAATTACGATAACCTT
* **
9047 AGTATGAAATTTTGATAACCTT
1 ACTATGAAATTACGATAACCTT
*
9069 CCTATGAA
1 ACTATGAA
9077 TGCATAACCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
ACTATGAAATTACGATAACCTT
Done.