Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014046.1 Corchorus capsularis cultivar CVL-1 contig14067, 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: 36924
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3583 original size:15 final size:15
Alignment explanation
Indices: 3554--3612 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
3544 CATCATCCTC
*
3554 AACTTCTTCACCATT
1 AACTTCTGCACCATT
* *
3569 AAATTCTGCAGCATT
1 AACTTCTGCACCATT
*
3584 AACTTCTGGACCATT
1 AACTTCTGCACCATT
3599 AACTTCTGCACCAT
1 AACTTCTGCACCAT
3613 CACCATTACT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (15 bp):
AACTTCTGCACCATT
Found at i:5557 original size:22 final size:22
Alignment explanation
Indices: 5532--5576 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5522 AAAAAATTTC
5532 AACCCCACGTGTGAAACACCTG
1 AACCCCACGTGTGAAACACCTG
5554 AACCCCACGTGTGAAACACCTG
1 AACCCCACGTGTGAAACACCTG
5576 A
1 A
5577 CAAAGTACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.36, G:0.18, T:0.13
Consensus pattern (22 bp):
AACCCCACGTGTGAAACACCTG
Found at i:8354 original size:24 final size:24
Alignment explanation
Indices: 8308--8359 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
8298 TTCACCAACT
* *
8308 TGATTGTTCTGTGTCTCTTGAACC
1 TGATTGTTCTGTGTCCCTCGAACC
* *
8332 TGATTGTTTTGTGTCCCTCGAACT
1 TGATTGTTCTGTGTCCCTCGAACC
8356 TGAT
1 TGAT
8360 ATTTCTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.46
Consensus pattern (24 bp):
TGATTGTTCTGTGTCCCTCGAACC
Found at i:8556 original size:60 final size:61
Alignment explanation
Indices: 8406--8561 Score: 172
Period size: 63 Copynumber: 2.5 Consensus size: 61
8396 CGTTGTGTGC
* * * * * * * *
8406 CTTGCTTTTTGTCTCCTTAACTCCATCGTTTTGTGTCTCTTGAACTCGTTTGTTCTGTGCCTT
1 CTTGCTTTGTCTCTCCTGAACTCCATTGTTTTGTGTCCCTCGAACTCGATTGTTCCGT--CTT
* * *
8469 CTTGCTTTGTCTCTCCTGCA-TCTCATTGTTTTGTGTCCCTCGATCTTGATTGTTCCGT-TT
1 CTTGCTTTGTCTCTCCTGAACTC-CATTGTTTTGTGTCCCTCGAACTCGATTGTTCCGTCTT
8529 CTTGCTTTGTCTCTCCTGAACTCCATTGTTTTG
1 CTTGCTTTGTCTCTCCTGAACTCCATTGTTTTG
8562 CGTCTTTTGA
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
60 31 0.39
61 2 0.03
62 2 0.03
63 44 0.56
ACGTcount: A:0.08, C:0.26, G:0.16, T:0.50
Consensus pattern (61 bp):
CTTGCTTTGTCTCTCCTGAACTCCATTGTTTTGTGTCCCTCGAACTCGATTGTTCCGTCTT
Found at i:13567 original size:18 final size:18
Alignment explanation
Indices: 13540--13583 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
13530 TCGGATAGAT
* *
13540 CTTCGGGTCTGGACGGAC
1 CTTCGAGTCTAGACGGAC
13558 CTTCGAGTCTAGACGGAC
1 CTTCGAGTCTAGACGGAC
*
13576 CTTTGAGT
1 CTTCGAGT
13584 TAGGGCATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.25, G:0.32, T:0.27
Consensus pattern (18 bp):
CTTCGAGTCTAGACGGAC
Found at i:16998 original size:31 final size:31
Alignment explanation
Indices: 16896--16990 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 31
16886 GCACGCCTCG
*
16896 TGTACC-AAAAGTGACATGTGACATGCCACA
1 TGTACCAAAAAGTGACACGTGACATGCCACA
* * * *
16926 TGTACCAAAAAGTGACACATGTCACGCCACG
1 TGTACCAAAAAGTGACACGTGACATGCCACA
*
16957 TGTACCAAAAAGTGACACGTGGCATGCCACA
1 TGTACCAAAAAGTGACACGTGACATGCCACA
16988 TGT
1 TGT
16991 TTCAAAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
30 6 0.11
31 49 0.89
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (31 bp):
TGTACCAAAAAGTGACACGTGACATGCCACA
Found at i:24023 original size:30 final size:29
Alignment explanation
Indices: 23956--24027 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
23946 ACACCGAACC
****
23956 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
23985 GCCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATT-AAAAAA
24015 GTCAAATAAGCCC
1 GTCAAATAAGCCC
24028 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:24740 original size:17 final size:17
Alignment explanation
Indices: 24718--24750 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
24708 AAAGCTTGGC
24718 TTATAGATTCTCATGTA
1 TTATAGATTCTCATGTA
*
24735 TTATAGATTTTCATGT
1 TTATAGATTCTCATGT
24751 TATGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (17 bp):
TTATAGATTCTCATGTA
Found at i:35643 original size:41 final size:40
Alignment explanation
Indices: 35598--35706 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
35588 TACGAAATTA
* *
35598 TGATAACCTTTTTTATTAAATTATGATAATTACACTATTTT
1 TGATAACC-TTCTTATGAAATTATGATAATTACACTATTTT
*
35639 TGATAACCTTCTTATGAAATTATGATAATTACATTATTTT
1 TGATAACCTTCTTATGAAATTATGATAATTACACTATTTT
* * * *
35679 TTATGACGCCT-TTATGAAATTTTGATAA
1 TGATAAC-CTTCTTATGAAATTATGATAA
35707 CCTTCCTATG
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 50 0.83
41 10 0.17
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (40 bp):
TGATAACCTTCTTATGAAATTATGATAATTACACTATTTT
Found at i:35716 original size:22 final size:22
Alignment explanation
Indices: 35691--35861 Score: 66
Period size: 22 Copynumber: 7.8 Consensus size: 22
35681 ATGACGCCTT
35691 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** ** *
35713 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
35735 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** * *
35757 TAT-AATTTTTTTTAACCATCT
1 TATGAAATTTTGATAACCTTCC
35778 TATGAAATTTT-ATTAACC-TCC
1 TATGAAATTTTGA-TAACCTTCC
* * *
35799 TTAAGGAATTTTGA-AGATC-TCAC
1 -TATGAAATTTTGATA-ACCTTC-C
* * *
35822 TATCAAGTTTTAATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
*
35843 AAATGAAATTTTGATAACC
1 -TATGAAATTTTGATAACC
35862 AACACTATAA
Statistics
Matches: 106, Mismatches: 33, Indels: 19
0.67 0.21 0.12
Matches are distributed among these distances:
21 19 0.18
22 83 0.78
23 4 0.04
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:35972 original size:22 final size:22
Alignment explanation
Indices: 35946--36248 Score: 94
Period size: 22 Copynumber: 14.1 Consensus size: 22
35936 AAATTGTCAG
*
35946 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
35968 TAATCATACAATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
35990 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
36012 TAAAC-CTTCCAATAAAATTTTGA
1 TAATCAC--ACTATGAAATTTTGA
* * * * *
36035 TAAAACTCCCTGTAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
* * *
36058 TAA--GCTC-ATGAAATCTTGA
1 TAATCACACTATGAAATTTTGA
*
36077 TAA-C-TAC-A---AATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
36093 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
36115 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
36137 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
36159 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
**
36181 TAA-CATTCTTATGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
36203 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
36225 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
36247 TA
1 TA
36249 TCCTCCCTGA
Statistics
Matches: 216, Mismatches: 48, Indels: 34
0.72 0.16 0.11
Matches are distributed among these distances:
16 10 0.05
17 1 0.00
18 1 0.00
19 15 0.07
20 2 0.01
21 8 0.04
22 140 0.65
23 34 0.16
24 4 0.02
25 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:36029 original size:23 final size:23
Alignment explanation
Indices: 36003--36060 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
35993 CCTCGCTATG
* *
36003 AAATTTTGATAAACCTTCCAATA
1 AAATTTTGATAAAACTCCCAATA
**
36026 AAATTTTGATAAAACTCCCTGTA
1 AAATTTTGATAAAACTCCCAATA
36049 AAATTTTGATAA
1 AAATTTTGATAA
36061 GCTCATGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAAACTCCCAATA
Found at i:36030 original size:45 final size:46
Alignment explanation
Indices: 35957--36060 Score: 113
Period size: 46 Copynumber: 2.3 Consensus size: 46
35947 AATCACACTC
* * * *
35957 TGAAATTTTGAT-AATCATACAATGAAATTGTGAT-AACCTCGCTA
1 TGAAATTTTGATAAACCATACAATAAAATTGTGATAAAACTCCCTA
* * * *
36001 TGAAATTTTGATAAACCTTCCAATAAAATTTTGATAAAACTCCCTG
1 TGAAATTTTGATAAACCATACAATAAAATTGTGATAAAACTCCCTA
*
36047 TAAAATTTTGATAA
1 TGAAATTTTGATAA
36061 GCTCATGAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 12 0.24
45 17 0.35
46 20 0.41
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (46 bp):
TGAAATTTTGATAAACCATACAATAAAATTGTGATAAAACTCCCTA
Found at i:36092 original size:16 final size:18
Alignment explanation
Indices: 36049--36096 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
36039 ACTCCCTGTA
*
36049 AAATTTTGATAAGCTCATG
1 AAATTTTGATAA-CTCATC
*
36068 AAATCTTGATAACT-A-C
1 AAATTTTGATAACTCATC
36084 AAATTTTGATAAC
1 AAATTTTGATAAC
36097 CTCCCTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 2 0.08
19 11 0.42
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (18 bp):
AAATTTTGATAACTCATC
Found at i:36172 original size:44 final size:44
Alignment explanation
Indices: 36084--36247 Score: 163
Period size: 44 Copynumber: 3.7 Consensus size: 44
36074 TGATAACTAC
** * * *
36084 AAATTTTGATAACCTCCCTATGATTTTTTGAT-AACCTCATTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATCTACAT-ACTATG
* *
36128 AAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATCTACATACTATG
* * * *
36172 AAATTTTGATAACATTCTTATGAAATTTTGAAAACTA-A-ACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTG--ATCTACATACTATG
* *
36216 AAATTTTGATAACCTTCATATGAAATTTTGAT
1 AAATTTTGATAACCTCCCTATGAAATTTTGAT
36248 ATCCTCCCTG
Statistics
Matches: 101, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.01
44 92 0.91
45 4 0.04
46 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (44 bp):
AAATTTTGATAACCTCCCTATGAAATTTTGATCTACATACTATG
Found at i:36273 original size:19 final size:20
Alignment explanation
Indices: 36236--36273 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36226 AACCTTCATA
* *
36236 TGAAATTTTGATATCCTCCC
1 TGAAATTTGGATATACTCCC
36256 TGAAATTTGGAT-TACTCC
1 TGAAATTTGGATATACTCC
36274 ATAATAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (20 bp):
TGAAATTTGGATATACTCCC
Found at i:36398 original size:22 final size:22
Alignment explanation
Indices: 36373--36493 Score: 127
Period size: 22 Copynumber: 5.5 Consensus size: 22
36363 AATCATATTT
* *
36373 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
36395 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
36417 TAAAATTTTGTTAACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
36439 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * * *
36461 TGTAATTTTGATAACCGCACTT
1 TGAAATTTTGATAACCTCTCTA
36483 TGAAATTTTGA
1 TGAAATTTTGA
36494 AATTGGATCA
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 81 0.99
23 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:36399 original size:44 final size:44
Alignment explanation
Indices: 36348--36493 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 44
36338 AGAAATACCA
* * *
36348 CTATGAAATTTTGGTAATCATATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCATATTATGAAAATTTGATAACCCCT
* * * *
36392 TTATGAAATTTTGATAA-CCTCTCTAT-AAAATTTTGTTAACCCCT
1 CTATGAAATTTTGATAATCATAT-TATGAAAA-TTTGATAACCCCT
* * * * *
36436 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCGCA
1 CTATGAAATTTTGATAATCATATTATGAAAATTTGATAACCCCT
*
36480 CTTTGAAATTTTGA
1 CTATGAAATTTTGA
36494 AATTGGATCA
Statistics
Matches: 81, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
43 7 0.09
44 70 0.86
45 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCATATTATGAAAATTTGATAACCCCT
Found at i:36829 original size:31 final size:30
Alignment explanation
Indices: 36781--36841 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
36771 GAAATATGTT
*
36781 TTTTAAAAAAAGATACAATTGG-AAATATA
1 TTTTAAAAAAAGATACAATCGGAAAATATA
*
36810 TTTTAAAAATAAGGGTACAATCGGAAAATATA
1 TTTTAAAAA-AA-GATACAATCGGAAAATATA
36842 AAGTTTTCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 9 0.33
30 2 0.07
31 9 0.33
32 7 0.26
ACGTcount: A:0.52, C:0.05, G:0.13, T:0.30
Consensus pattern (30 bp):
TTTTAAAAAAAGATACAATCGGAAAATATA
Done.