Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006692.1 Corchorus capsularis cultivar CVL-1 contig06713, 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: 18761
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:92 original size:2 final size:2
Alignment explanation
Indices: 79--110 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
69 ATTACACTTT
79 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
111 TATTGGCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:276 original size:22 final size:22
Alignment explanation
Indices: 196--425 Score: 75
Period size: 22 Copynumber: 10.8 Consensus size: 22
186 GAAATATTCA
*
196 TATGAAATTATGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * * *
218 TATTAAATTGTGATAA-TTACAC
1 TATGAAATTTTGATAACCT-CCC
* *
240 TAT----TTTTTATGACCTCCC
1 TATGAAATTTTGATAACCTCCC
*
258 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTCCC
* * * *
280 TATAAAATTTTAATAACGAT-AC
1 TATGAAATTTTGATAAC-CTCCC
* * * ***
302 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTCCC
* * **
324 TATTAATTTTTTTTAACCT---
1 TATGAAATTTTGATAACCTCCC
* *
343 TATGAAATTTTGTTAACCTCGC
1 TATGAAATTTTGATAACCTCCC
* * **
365 TAAGGAATTTTGA-ACACCTAAC
1 TATGAAATTTTGATA-ACCTCCC
* *
387 TATGAAATTTTAATAACTTCCC
1 TATGAAATTTTGATAACCTCCC
* *
409 AATGAAATTTTAATAAC
1 TATGAAATTTTGATAAC
426 TAACACTATG
Statistics
Matches: 149, Mismatches: 46, Indels: 26
0.67 0.21 0.12
Matches are distributed among these distances:
18 11 0.07
19 17 0.11
21 3 0.02
22 116 0.78
23 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:9843 original size:13 final size:13
Alignment explanation
Indices: 9808--9848 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
9798 TGCGCAGACA
* *
9808 GCACCCATGACAA
1 GCACCCATGCCAT
9821 GCACCCATGCCAT
1 GCACCCATGCCAT
9834 GCACCCATGCCAT
1 GCACCCATGCCAT
9847 GC
1 GC
9849 CGATGTCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.27, C:0.44, G:0.17, T:0.12
Consensus pattern (13 bp):
GCACCCATGCCAT
Found at i:15233 original size:22 final size:19
Alignment explanation
Indices: 15205--15248 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
15195 CGAACCCGAT
15205 TATGAAAATATATATAATAATA
1 TATGAAAATAT-T-TAAT-ATA
15227 TATGAAAATATTTAATATA
1 TATGAAAATATTTAATATA
15246 TAT
1 TAT
15249 TTATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.27
20 4 0.18
21 1 0.05
22 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TATGAAAATATTTAATATA
Found at i:16471 original size:22 final size:22
Alignment explanation
Indices: 16416--16471 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
16406 CCTCCATATG
* **
16416 AATTGTTAGTAATCACACTCTGA
1 AATTG-TAATAATCACACAATGA
* *
16439 AATTTTCATAATCACACAATGA
1 AATTGTAATAATCACACAATGA
16461 AATTGTAATAA
1 AATTGTAATAA
16472 CCTCGTTATG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (22 bp):
AATTGTAATAATCACACAATGA
Found at i:16508 original size:23 final size:23
Alignment explanation
Indices: 16482--16560 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 23
16472 CCTCGTTATG
* *
16482 AAATTTTAATAAACCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
16505 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
* *
16528 AAATTTTGAT-AACCTCCTTATT
1 AAATTTTGATAAACCTCCCTATA
*
16550 AAATCTTGATA
1 AAATTTTGATA
16561 GCTACAAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 19 0.38
23 31 0.62
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:16544 original size:22 final size:22
Alignment explanation
Indices: 16468--16560 Score: 96
Period size: 23 Copynumber: 4.1 Consensus size: 22
16458 TGAAATTGTA
** * *
16468 ATAACCTCGTTATGAAATTTTA
1 ATAACCTCCCTATAAAATTTTG
*
16490 ATAAACCTTCCTATAAAATTTTG
1 AT-AACCTCCCTATAAAATTTTG
16513 ATAAACCTCCCTATAAAATTTTG
1 AT-AACCTCCCTATAAAATTTTG
* * *
16536 ATAACCTCCTTATTAAATCTTG
1 ATAACCTCCCTATAAAATTTTG
16558 ATA
1 ATA
16561 GCTACAAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 22 0.36
23 39 0.64
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (22 bp):
ATAACCTCCCTATAAAATTTTG
Found at i:16770 original size:64 final size:66
Alignment explanation
Indices: 16651--16774 Score: 155
Period size: 64 Copynumber: 1.9 Consensus size: 66
16641 TCTACATACT
* *
16651 ATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAACTATAAAATTTTAATAACTTTCA
1 ATGAAATTTTGATAACCCTCCTATGAAATTTTGAAAACTAAACTATAAAAGTTTAATAACTTTCA
16716 A
66 A
* ** **
16717 ATGAAATTTTGAT-ATCCTCCT-TGAAATTTTGATTACTCCA-TAATAAAAGTTTAATAAC
1 ATGAAATTTTGATAACCCTCCTATGAAATTTTGAAAACTAAACT-ATAAAAGTTTAATAAC
16775 CTTCCTAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
63 1 0.02
64 30 0.60
65 6 0.12
66 13 0.26
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (66 bp):
ATGAAATTTTGATAACCCTCCTATGAAATTTTGAAAACTAAACTATAAAAGTTTAATAACTTTCA
A
Found at i:16868 original size:22 final size:22
Alignment explanation
Indices: 16797--16896 Score: 89
Period size: 22 Copynumber: 4.5 Consensus size: 22
16787 TTAACCATAC
16797 TATGAAATTTTGATAATACCAC--
1 TATGAAATTTTGAT-A-ACCACTT
* *
16819 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCAC-TT
*
16842 T-TGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCACTT
* * *
16863 TATGAAATTTCGATAACCTCTC
1 TATGAAATTTTGATAACCACTT
*
16885 TATAAAATTTTG
1 TATGAAATTTTG
16897 TTGATCCCTC
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
20 4 0.06
21 4 0.06
22 56 0.86
23 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACTT
Found at i:17351 original size:22 final size:22
Alignment explanation
Indices: 17233--17396 Score: 101
Period size: 22 Copynumber: 7.5 Consensus size: 22
17223 ATTCTAAGCC
*
17233 CTCTATGAAATTTTGATAATAA
1 CTCTATGAAATTTTGATAATCA
* *
17255 CAT-TATGTAATTTTGATAATCT
1 C-TCTATGAAATTTTGATAATCA
* * *
17277 CGCTTTGAAATTTTAATAATC-
1 CTCTATGAAATTTTGATAATCA
* *
17298 TTCCTAT-AAACTTTGATAATCCGA
1 CT-CTATGAAATTTTGATAAT-C-A
*
17322 TCTCTATGAAATTTCGATAATCA
1 -CTCTATGAAATTTTGATAATCA
*
17345 CTCTATGAGA-TTTGATAA-C-
1 CTCTATGAAATTTTGATAATCA
* * *
17364 CTTCTATCAAATTTTGGTACTC-
1 C-TCTATGAAATTTTGATAATCA
17386 CTC-ATGAAATT
1 CTCTATGAAATT
17397 GAGACTTTTA
Statistics
Matches: 109, Mismatches: 22, Indels: 24
0.70 0.14 0.15
Matches are distributed among these distances:
19 1 0.01
20 15 0.14
21 26 0.24
22 48 0.44
23 2 0.02
24 5 0.05
25 12 0.11
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
CTCTATGAAATTTTGATAATCA
Found at i:17470 original size:22 final size:22
Alignment explanation
Indices: 17445--17562 Score: 73
Period size: 22 Copynumber: 5.4 Consensus size: 22
17435 CATAAAAAAA
17445 TTTGATAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
* * *
17467 TTTGATAA-CATCCCCATGATAT
1 TTTGATAACCA-CACTATGAAAT
* **
17489 ATT-AGTAACTTC-CTTATGAAAT
1 TTTGA-TAACCACAC-TATGAAAT
* *
17511 TTTGTTAACCACACTATAAAAT
1 TTTGATAACCACACTATGAAAT
* * *
17533 TCTT-ATAACCTCGCTATGACAT
1 T-TTGATAACCACACTATGAAAT
17555 TTTGATAA
1 TTTGATAA
17563 TCTCTTTGAT
Statistics
Matches: 70, Mismatches: 18, Indels: 16
0.67 0.17 0.15
Matches are distributed among these distances:
21 6 0.09
22 61 0.87
23 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (22 bp):
TTTGATAACCACACTATGAAAT
Found at i:17670 original size:67 final size:65
Alignment explanation
Indices: 17598--17745 Score: 154
Period size: 67 Copynumber: 2.2 Consensus size: 65
17588 TTGTGATAAG
*
17598 CACACTATGAAATTTCAATAACATTCCTAAGAAATTTTAATAACCTATCC-CACGAAATTTTGGT
1 CACACTATGAAATTT-AATAACATTCCCAAGAAATTTTAATAA-CT-TCCACACGAAATTTTGGT
17662 AAC
63 AAC
* * * * * * * *
17665 CACACTGTGAACTTGTGATAACTTTCCCATGAAATTTTGATAACTTCCATATGAAATTTTGGTAA
1 CACACTATGAAATT-TAATAACATTCCCAAGAAATTTTAATAACTTCCACACGAAATTTTGGTAA
17730 C
65 C
* *
17731 CATACTATGGAATTT
1 CACACTATGAAATTT
17746 TGATTACCAC
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
65 4 0.06
66 27 0.41
67 34 0.52
68 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (65 bp):
CACACTATGAAATTTAATAACATTCCCAAGAAATTTTAATAACTTCCACACGAAATTTTGGTAAC
Found at i:17739 original size:22 final size:22
Alignment explanation
Indices: 17567--17798 Score: 101
Period size: 22 Copynumber: 10.5 Consensus size: 22
17557 TGATAATCTC
* * *
17567 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCATACTATGAAAT
* * *
17589 TGTGATAAGCACACTATGAAAT
1 TTTGATAACCATACTATGAAAT
** * *
17611 TTCAATAA-CATTCCTAAGAAAT
1 TTTGATAACCA-TACTATGAAAT
* * * *
17633 TTTAATAACCTATCCCACGAAAT
1 TTTGATAACC-ATACTATGAAAT
* * * *
17656 TTTGGTAACCACACTGTGAACT
1 TTTGATAACCATACTATGAAAT
* ** * *
17678 TGTGATAACTTTCCCATGAAAT
1 TTTGATAACCATACTATGAAAT
* *
17700 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCATAC-TATGAAAT
* *
17722 TTTGGTAACCATACTATGGAAT
1 TTTGATAACCATACTATGAAAT
* *
17744 TTTGATTACCA-CCTCATGAAAT
1 TTTGATAACCATACT-ATGAAAT
* * **
17766 TATAATAACCATTTTATGAAAT
1 TTTGATAACCATACTATGAAAT
*
17788 TTCGATAACCA
1 TTTGATAACCA
17799 CACAGAGACA
Statistics
Matches: 152, Mismatches: 51, Indels: 14
0.70 0.24 0.06
Matches are distributed among these distances:
21 8 0.05
22 121 0.80
23 22 0.14
24 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
TTTGATAACCATACTATGAAAT
Done.