Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010604.1 Corchorus capsularis cultivar CVL-1 contig10625, 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: 35897
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:106 original size:22 final size:22
Alignment explanation
Indices: 81--641 Score: 213
Period size: 22 Copynumber: 25.7 Consensus size: 22
71 ATGATCACAT
81 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
103 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
125 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
147 TAT-AAATTTTTTTAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* * *
168 TATGAAATTTGGTTAACC-TCTT
1 TATGAAATTTTGATAACCTTC-C
* * * *
190 TAAGGAATTTTGAAAACC-TCAA
1 TATGAAATTTTGATAACCTTC-C
*
212 TATGAAATTTTGAT-AGCTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
234 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* * *
257 TATGAGATGTTGATAAAC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * * *
278 ATGTGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
301 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * * *
322 ATATG-AATTGCTAATAATC-ACAA
1 -TATGAAATT-TTGATAACCTTC-C
* * *
345 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
367 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
389 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
412 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
435 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
457 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
474 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * **
495 TATGATTTTTTGATAACTTTAT
1 TATGAAATTTTGATAACCTTCC
* * *
517 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
*** * *
539 TATGAAATTTTGATCTTCATAC
1 TATGAAATTTTGATAACCTTCC
* *
561 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * **
583 TGTGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
605 TATGAAATTTTCATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
627 TATGAAATTTTGATA
1 TATGAAATTTTGATA
642 TCCTCCCTGA
Statistics
Matches: 392, Mismatches: 125, Indels: 44
0.70 0.22 0.08
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
21 29 0.07
22 284 0.72
23 64 0.16
24 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:419 original size:23 final size:23
Alignment explanation
Indices: 388--472 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
378 GATAACCTCG
*
388 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
411 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
434 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
456 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
473 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:471 original size:45 final size:45
Alignment explanation
Indices: 349--472 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 45
339 TCACAATCTG
* * *
349 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
393 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* *
439 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
473 CTACAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
44 11 0.16
45 31 0.46
46 26 0.38
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:818 original size:22 final size:22
Alignment explanation
Indices: 791--836 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
781 ATTTTGCAAA
791 TTTGATAACCCCTTTATAAAAT
1 TTTGATAACCCCTTTATAAAAT
*
813 TTTGATAACCTCTTTATAAAAT
1 TTTGATAACCCCTTTATAAAAT
835 TT
1 TT
837 CGTTGACCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTGATAACCCCTTTATAAAAT
Found at i:939 original size:22 final size:23
Alignment explanation
Indices: 847--1014 Score: 101
Period size: 22 Copynumber: 7.6 Consensus size: 23
837 CGTTGACCCC
**
847 TCTATGAAATTCTT-ATAATCAGA
1 TCTATGAAATT-TTGATAATCACT
*
870 T-TATGTAATTTTGATAA-C-CT
1 TCTATGAAATTTTGATAATCACT
* *
890 CGCTTTGAAATTTTGATAA-CAAC-
1 -TCTATGAAATTTTGATAATC-ACT
* *
913 ACTATGAAATTTTGATAATC-TT
1 TCTATGAAATTTTGATAATCACT
935 TCTAT-AAATTTTGATAATACGATCT
1 TCTATGAAATTTTGATAAT-C-A-CT
*
960 T-TATGAAATTTCGATAATCACT
1 TCTATGAAATTTTGATAATCACT
*
982 T-TATGAGA-TTTGATAA-C-CT
1 TCTATGAAATTTTGATAATCACT
*
1001 TCTATCAAATTTTG
1 TCTATGAAATTTTG
1015 GTACTCCTTA
Statistics
Matches: 115, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
19 3 0.03
20 6 0.05
21 27 0.23
22 57 0.50
23 3 0.03
24 5 0.04
25 14 0.12
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (23 bp):
TCTATGAAATTTTGATAATCACT
Found at i:1067 original size:22 final size:22
Alignment explanation
Indices: 1037--1092 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
1027 AAATTGAGAC
* * *
1037 TTTT-ATAACCTTAATGTGAAA
1 TTTTGATAACCTCAATATAAAA
* *
1058 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCAATATAAAA
1080 TTTTGATAACCTC
1 TTTTGATAACCTC
1093 CCCATGAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTCAATATAAAA
Found at i:1102 original size:22 final size:22
Alignment explanation
Indices: 1053--1102 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1043 AACCTTAATG
*
1053 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCACACCA
* * *
1075 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCACACCA
1097 TGAAAT
1 TGAAAT
1103 ATTTAATGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (22 bp):
TGAAATTTTGATAACCACACCA
Found at i:1166 original size:22 final size:22
Alignment explanation
Indices: 1108--1166 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1098 GAAATATTTA
*
1108 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCACACT
* *
1130 ATGAAATTCTT-ATAACCTCGCT
1 ATGAAATT-TTGATAACCACACT
*
1152 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
1167 TCTCTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:1234 original size:22 final size:22
Alignment explanation
Indices: 1202--1341 Score: 122
Period size: 22 Copynumber: 6.3 Consensus size: 22
1192 TTGTGATAAT
* *
1202 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTAA
* * *
1224 TAACCAACCTAAGAGATTTTAA
1 TAACCATCCTATGAAATTTTAA
**
1246 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTAA
* *
1270 TAACCA-CACTATGGAATTTTGA
1 TAACCATC-CTATGAAATTTTAA
*
1292 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTAA
* *
1314 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTAA
1336 TAACCA
1 TAACCA
1342 CATAGAGCCA
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
21 3 0.03
22 72 0.76
23 3 0.03
24 17 0.18
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTAA
Found at i:1288 original size:68 final size:66
Alignment explanation
Indices: 1202--1343 Score: 160
Period size: 68 Copynumber: 2.1 Consensus size: 66
1192 TTGTGATAAT
* * *
1202 TAACCACCCTATGAAATTTCAATAACCAACCT-AAGAGATTTTAATAACCTGATCCTATGAAATT
1 TAACCACACTATGAAATTTCAATAACC-ACCTCAAGAAATTATAATAACC--ATCCTATGAAATT
*
1266 TTGG
63 TTGA
* ** * * *
1270 TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTG
1 TAACCACACTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTG
1335 A
66 A
1336 TAACCACA
1 TAACCACA
1344 TAGAGCCAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
66 23 0.37
67 3 0.05
68 37 0.59
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (66 bp):
TAACCACACTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTG
A
Found at i:1739 original size:38 final size:35
Alignment explanation
Indices: 1681--1757 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 35
1671 AATTTAAGAC
1681 CAAAGACAAAGCAAAATTAAATAGAACGATTGGAAA
1 CAAAGACAAAGCAAAATTAAATAGAACG-TTGGAAA
*
1717 CAAAGACAAAAGACAAAATTAAATAGGACGTTGGAAA
1 CAAAGAC-AAAG-CAAAATTAAATAGAACGTTGGAAA
1754 CAAA
1 CAAA
1758 AAGTCAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 7 0.18
37 15 0.39
38 16 0.42
ACGTcount: A:0.58, C:0.12, G:0.17, T:0.13
Consensus pattern (35 bp):
CAAAGACAAAGCAAAATTAAATAGAACGTTGGAAA
Found at i:2068 original size:3 final size:3
Alignment explanation
Indices: 2060--2093 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2050 GAGGGAGTAT
*
2060 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2094 GACTTTGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:8591 original size:17 final size:18
Alignment explanation
Indices: 8569--8604 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
8559 CGGCATGATT
8569 ACAAGAAAAAAACA-AAC
1 ACAAGAAAAAAACAGAAC
*
8586 ACAAGAAAGAAACAGAAC
1 ACAAGAAAAAAACAGAAC
8604 A
1 A
8605 AAAACCCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.72, C:0.17, G:0.11, T:0.00
Consensus pattern (18 bp):
ACAAGAAAAAAACAGAAC
Found at i:8779 original size:2 final size:2
Alignment explanation
Indices: 8774--8821 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
8764 TGTTTAATGT
* *
8774 TA TA TA TG TA TA TA TA TA T- TCA GA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
8816 -A TA TA T
1 TA TA TA T
8822 TTACCAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:8864 original size:26 final size:27
Alignment explanation
Indices: 8800--8866 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
8790 TATTCAGATA
8800 TATA-TATATATATATAATATATTTACC
1 TATACTATATATA-ATAATATATTTACC
* * * *
8827 AAAACTAAATATAAT-ATATATTTATC
1 TATACTATATATAATAATATATTTACC
8853 TATACTATATATAA
1 TATACTATATATAA
8867 AAGTACGAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 21 0.66
27 4 0.12
28 7 0.22
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.43
Consensus pattern (27 bp):
TATACTATATATAATAATATATTTACC
Found at i:8929 original size:31 final size:31
Alignment explanation
Indices: 8894--8954 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
8884 AACTTTATGT
*
8894 TTTCCGATTGTACCATTATTTTTAAA-ATATA
1 TTTCCAATTGTACCATT-TTTTTAAACATATA
*
8925 TTTCCAATTGTACCCTTTTTTTAAACATAT
1 TTTCCAATTGTACCATTTTTTTAAACATAT
8955 TTCTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCATTTTTTTAAACATATA
Found at i:8964 original size:30 final size:31
Alignment explanation
Indices: 8900--8972 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
8890 ATGTTTTCCG
* *
8900 ATTGTACCATTATTTTTAAAATATATTTCCA
1 ATTGTACCATTATTTTTAAAACATATTTCAA
*
8931 ATTGTACCCTT-TTTTT-AAACATATTTCTAA
1 ATTGTACCATTATTTTTAAAACATATTTC-AA
8961 ATTG--CCATTATT
1 ATTGTACCATTATT
8973 AAATAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 4 0.11
29 12 0.33
30 10 0.28
31 10 0.28
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (31 bp):
ATTGTACCATTATTTTTAAAACATATTTCAA
Found at i:13359 original size:25 final size:27
Alignment explanation
Indices: 13307--13359 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
13297 TTACTCAACT
**
13307 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
13334 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
13359 A
1 A
13360 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:22519 original size:13 final size:13
Alignment explanation
Indices: 22482--22522 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
22472 TGTAAGGCCC
*
22482 TCTTCTTTCTTCTT
1 TCTT-TTTCTTTTT
*
22496 TCATTTTCTTTTT
1 TCTTTTTCTTTTT
22509 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
22522 T
1 T
22523 ATTAATTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 21 0.88
14 3 0.12
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTTTTTCTTTTT
Found at i:24389 original size:2 final size:2
Alignment explanation
Indices: 24378--24412 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
24368 GATATGATTC
24378 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24413 GTACTTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27367 original size:27 final size:26
Alignment explanation
Indices: 27298--27367 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 26
27288 AAAAAAAAAG
***
27298 AGGATATTCCTTTTTTTTTTGTTTTT
1 AGGATATTCCTTTTTTTTTTGTAAAT
27324 AGGGATATTCCCTTTTTTTTTTTGGTAAAT
1 A-GGATATT-CC-TTTTTTTTTT-GTAAAT
27354 AGGATATTCCTTTT
1 AGGATATTCCTTTT
27368 ACTAGTTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 1 0.03
27 11 0.30
28 4 0.11
29 17 0.46
30 4 0.11
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.59
Consensus pattern (26 bp):
AGGATATTCCTTTTTTTTTTGTAAAT
Found at i:30411 original size:36 final size:36
Alignment explanation
Indices: 30357--30440 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
30347 CTGTGTTCAT
* * * *
30357 TGCTGGGACTATGTTCAGTACTGAGACTGTATTTGG
1 TGCTGGGACTGTGCTCAGTACTGAGACTGTATTCGA
* * * *
30393 TGTTGGGACTGTGCTCAGTGCTGGGATTGTATTCGA
1 TGCTGGGACTGTGCTCAGTACTGAGACTGTATTCGA
30429 TGCTGGGACTGT
1 TGCTGGGACTGT
30441 ATTAGCAGGT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.15, C:0.14, G:0.35, T:0.36
Consensus pattern (36 bp):
TGCTGGGACTGTGCTCAGTACTGAGACTGTATTCGA
Found at i:35420 original size:17 final size:17
Alignment explanation
Indices: 35400--35438 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
35390 CTTAATGAAA
35400 TTCTATACTAACTAAAC
1 TTCTATACTAACTAAAC
*
35417 TTCTATACTAACTTAAC
1 TTCTATACTAACTAAAC
35434 TTCTA
1 TTCTA
35439 ACACCAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (17 bp):
TTCTATACTAACTAAAC
Done.