Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000114.1 Corchorus capsularis cultivar CVL-1 contig00114, 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: 8906
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:3467 original size:23 final size:21
Alignment explanation
Indices: 3436--4101 Score: 111
Period size: 22 Copynumber: 30.4 Consensus size: 21
3426 AGGTTATCAG
3436 ATTTCATAGAGAGTTTACCAAA
1 ATTTCATAGAGAG-TTACCAAA
*
3458 TTTTCAATAGTAGA-TTACCAAA
1 ATTTC-ATAG-AGAGTTACCAAA
*
3480 ATTTCATAGTGAGGTTACCAAA
1 ATTTCATAGAGA-GTTACCAAA
* * * *
3502 ATTTCAATTGCGAGGTAACCATA
1 ATTTC-ATAGAGA-GTTACCAAA
* *
3525 ATTTCATAG-GCAGGTTATCAGA
1 ATTTCATAGAG-A-GTTACCAAA
*** *
3547 ATTTCATTTTGAGTTTACAAAAA
1 ATTTCATAGAGAG-TTAC-CAAA
* ***
3570 ATTT-ATAG-GCGTTACTGGA
1 ATTTCATAGAGAGTTACCAAA
3589 ATTTCATAG-GTAAGTTACCAAAA
1 ATTTCATAGAG--AGTTACC-AAA
* *
3612 ATATCACT-GAGAGGTTATCAAA
1 ATTTCA-TAGAGA-GTTACCAAA
* * *
3634 ATTTTATACG-GAGGTTACTAAT
1 ATTTCATA-GAGA-GTTACCAAA
*
3656 ATTTCACATGA-AGGTTACCAAA
1 ATTTCATA-GAGA-GTTACCAAA
*
3678 ATTTCATAGAAAAGTTA-CAAGA
1 ATTTCATAG-AGAGTTACCAA-A
*
3700 ATTTCATAG-GTAAGTTATCAAA
1 ATTTCATAGAG--AGTTACCAAA
** **
3722 ATTTCATA-AGGAGGTTGTCGGA
1 ATTTCATAGA-GA-GTTACCAAA
* *
3744 ATTTCATAGGGAGGTTATCAAA
1 ATTTCATAGAGA-GTTACCAAA
* * *
3766 TTTTCA-CGAG-GTTACAAAA
1 ATTTCATAGAGAGTTACCAAA
* **
3785 ATTTCATAGGGAGGTT-TGAATA
1 ATTTCATAGAGA-GTTACCAA-A
* *
3807 ATTTTATACG-GAGTTTACTAGAA
1 ATTTCATA-GAGAG-TTACCA-AA
* *
3830 A-TTCATACG-GAAGTTGCAAAA
1 ATTTCATA-GAG-AGTTACCAAA
*
3851 ATTTCATAGCGATGTTACCAAA
1 ATTTCATAGAGA-GTTACCAAA
** * *
3873 ATTTCATACTGGGTTACTAAA
1 ATTTCATAGAGAGTTACCAAA
*
3894 ATTTAATATGA-AGATTACCAAA
1 ATTTCATA-GAGAG-TTACCAAA
* * *
3916 ATTCCGCTATGA-TGTTACCAAA
1 ATTTC-ATA-GAGAGTTACCAAA
* **
3938 ATTTTATA-AGAGGTTACCGGA
1 ATTTCATAGAGA-GTTACCAAA
* *
3959 ATTTCGTAG-GTAAGGTACCAAA
1 ATTTCATAGAG--AGTTACCAAA
*
3981 ATTTCATA-ATGAGGTTACAAAA
1 ATTTCATAGA-GA-GTTACCAAA
* * * *
4003 ATATCGTAG-GAGGATTGCCAGA
1 ATTTCATAGAGA-G-TTACCAAA
* *
4025 ATTTCAAAG-GTAAGTTTCCAAA
1 ATTTCATAGAG--AGTTACCAAA
* * *
4047 ATTTTATAGTGAGATTATCCATAT
1 ATTTCATAGAGAG-TTA-CCA-AA
* *
4071 ATTTCATAGTGAGCTTACCCAA
1 ATTTCATAGAGAG-TTACCAAA
4093 ATTTCATAG
1 ATTTCATAG
4102 GAATGATACA
Statistics
Matches: 474, Mismatches: 110, Indels: 120
0.67 0.16 0.17
Matches are distributed among these distances:
19 18 0.04
20 13 0.03
21 63 0.13
22 289 0.61
23 68 0.14
24 23 0.05
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (21 bp):
ATTTCATAGAGAGTTACCAAA
Found at i:3529 original size:45 final size:43
Alignment explanation
Indices: 3436--3552 Score: 117
Period size: 45 Copynumber: 2.6 Consensus size: 43
3426 AGGTTATCAG
* * * *
3436 ATTTCATAGAGAGTTTACCAAATTTTCAATAGTAGATTACCAAA
1 ATTTCATAG-GAGGTTACCAAAATTTCAATAGGAGATAACCAAA
* * *
3480 ATTTCATAGTGAGGTTACCAAAATTTCAATTGCGAGGTAACCATA
1 ATTTCATAG-GAGGTTACCAAAATTTCAATAG-GAGATAACCAAA
* *
3525 ATTTCATAGGCAGGTTATCAGAATTTCA
1 ATTTCATAGG-AGGTTACCAAAATTTCA
3553 TTTTGAGTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 29 0.48
45 32 0.52
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (43 bp):
ATTTCATAGGAGGTTACCAAAATTTCAATAGGAGATAACCAAA
Found at i:3955 original size:21 final size:21
Alignment explanation
Indices: 3436--4004 Score: 134
Period size: 22 Copynumber: 26.1 Consensus size: 21
3426 AGGTTATCAG
*
3436 ATTTCATAGAGAGTTTACCAAA
1 ATTTCATA-AGAGGTTACCAAA
* *
3458 TTTTCA-ATAGTAGATTACCAAA
1 ATTTCATA-AG-AGGTTACCAAA
*
3480 ATTTCATAGTGAGGTTACCAAA
1 ATTTCATA-AGAGGTTACCAAA
** * *
3502 ATTTCAATTGCGAGGTAACCATA
1 ATTTC-A-TAAGAGGTTACCAAA
* * *
3525 ATTTCATAGGCAGGTTATCAGA
1 ATTTCATAAG-AGGTTACCAAA
** * *
3547 ATTTCATTTTGAGTTTACAAAAA
1 ATTTCA-TAAGAGGTTAC-CAAA
***
3570 ATTT-AT-AG-GCGTTACTGGA
1 ATTTCATAAGAG-GTTACCAAA
* *
3589 ATTTCATAGGTAAGTTACCAAAA
1 ATTTCATAAG-AGGTTACC-AAA
* * *
3612 ATATCACTGAGAGGTTATCAAA
1 ATTTCA-TAAGAGGTTACCAAA
* * * *
3634 ATTTTATACGGAGGTTACTAAT
1 ATTTCATA-AGAGGTTACCAAA
* *
3656 ATTTCACATGAAGGTTACCAAA
1 ATTTCATAAG-AGGTTACCAAA
* *
3678 ATTTCATAGAAAAGTTA-CAAGA
1 ATTTCATA-AGAGGTTACCAA-A
* * *
3700 ATTTCATAGGTAAGTTATCAAA
1 ATTTCATAAG-AGGTTACCAAA
** **
3722 ATTTCATAAGGAGGTTGTCGGA
1 ATTTCATAA-GAGGTTACCAAA
* *
3744 ATTTCATAGGGAGGTTATCAAA
1 ATTTCATA-AGAGGTTACCAAA
* * *
3766 TTTTC--ACGAGGTTACAAAA
1 ATTTCATAAGAGGTTACCAAA
* **
3785 ATTTCATAGGGAGGTT-TGAATA
1 ATTTCATA-AGAGGTTACCAA-A
* * * *
3807 ATTTTATACGGAGTTTACTAGAA
1 ATTTCATA-AGAGGTTACCA-AA
* * * *
3830 A-TTCATACGGAAGTTGCAAAA
1 ATTTCATA-AGAGGTTACCAAA
* *
3851 ATTTCATAGCGATGTTACCAAA
1 ATTTCATA-AGAGGTTACCAAA
* *
3873 ATTTCATACTG-GGTTACTAAA
1 ATTTCATA-AGAGGTTACCAAA
* * *
3894 ATTTAATATGAAGATTACCAAA
1 ATTTCATAAG-AGGTTACCAAA
* * * *
3916 ATTCCGCTATGATGTTACCAAA
1 ATTTC-ATAAGAGGTTACCAAA
* **
3938 ATTTTATAAGAGGTTACCGGA
1 ATTTCATAAGAGGTTACCAAA
* *
3959 ATTTCGTAGGTAAGG-TACCAAA
1 ATTTCATAAG--AGGTTACCAAA
*
3981 ATTTCATAATGAGGTTACAAAA
1 ATTTCATAA-GAGGTTACCAAA
4003 AT
1 AT
4005 ATCGTAGGAG
Statistics
Matches: 397, Mismatches: 114, Indels: 72
0.68 0.20 0.12
Matches are distributed among these distances:
19 20 0.05
20 10 0.03
21 54 0.14
22 256 0.64
23 53 0.13
24 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (21 bp):
ATTTCATAAGAGGTTACCAAA
Found at i:4079 original size:24 final size:22
Alignment explanation
Indices: 4045--4101 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
4035 TAAGTTTCCA
* *
4045 AAATTTTATAGTGAGATTATCC
1 AAATTTCATAGTGAGATTACCC
*
4067 ATATATTTCATAGTGAGCTTACCC
1 A-A-ATTTCATAGTGAGATTACCC
4091 AAATTTCATAG
1 AAATTTCATAG
4102 GAATGATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.33
23 2 0.07
24 18 0.60
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (22 bp):
AAATTTCATAGTGAGATTACCC
Found at i:4207 original size:22 final size:22
Alignment explanation
Indices: 4126--4236 Score: 75
Period size: 22 Copynumber: 5.0 Consensus size: 22
4116 TTTGTAAAGG
*
4126 GGTTACCAAAATCTT-ATATGGA
1 GGTTATCAAAAT-TTCATATGGA
* * * * *
4148 GGATAGCATAATTTCATCTTGA
1 GGTTATCAAAATTTCATATGGA
** *
4170 AATTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATATGGA
4192 GGTTAT-AAAATATTCATA-GTGA
1 GGTTATCAAAAT-TTCATATG-GA
* *
4214 AGTTATCAAAATTTTATATGGA
1 GGTTATCAAAATTTCATATGGA
4236 G
1 G
4237 TTCTCCTTAT
Statistics
Matches: 66, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
21 8 0.12
22 52 0.79
23 6 0.09
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATATGGA
Found at i:4208 original size:44 final size:43
Alignment explanation
Indices: 4128--4236 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 43
4118 TGTAAAGGGG
* **
4128 TTACCAAAATCTTATATGGAGGATAGCATAATTTCATCTTGAAA
1 TTACCAAAAT-TTATATGGAGGATAGCAAAATTTCATAGTGAAA
* * *
4172 TTACCAAAATTTCATATGGAGGTTA-TAAAATATTCATAGTGAAG
1 TTACCAAAATTT-ATATGGAGGATAGCAAAAT-TTCATAGTGAAA
*
4216 TTATCAAAATTTTATATGGAG
1 TTACCAAAA-TTTATATGGAG
4237 TTCTCCTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
43 6 0.11
44 46 0.84
45 3 0.05
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (43 bp):
TTACCAAAATTTATATGGAGGATAGCAAAATTTCATAGTGAAA
Found at i:4317 original size:22 final size:22
Alignment explanation
Indices: 4287--4422 Score: 118
Period size: 22 Copynumber: 6.2 Consensus size: 22
4277 AAAATTATAT
* *
4287 GGAGTTTATCCAAATTGCATAA
1 GGAGGTTATCCAAATTTCATAA
* **
4309 GGAGGTTATCAAAATTAAATAA
1 GGAGGTTATCCAAATTTCATAA
*
4331 CGAGGTTAT-CAGAATTTCA-AA
1 GGAGGTTATCCA-AATTTCATAA
4352 TGGAGGTTATCCAAATTTCAT-A
1 -GGAGGTTATCCAAATTTCATAA
** *
4374 GTGATATTAT-CAGAATCTCATAA
1 G-GAGGTTATCCA-AATTTCATAA
*
4397 GGAGGTTATCCAAATTTCATAG
1 GGAGGTTATCCAAATTTCATAA
4419 GGAG
1 GGAG
4423 ATTAACAAAT
Statistics
Matches: 90, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
21 6 0.07
22 78 0.87
23 6 0.07
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (22 bp):
GGAGGTTATCCAAATTTCATAA
Found at i:4384 original size:66 final size:66
Alignment explanation
Indices: 4285--4415 Score: 151
Period size: 66 Copynumber: 2.0 Consensus size: 66
4275 AAAAAATTAT
* *
4285 ATGGAGTTTATCCAAATTGCATAAGGAGGTTATCAAAAT-TAAATAACGAGGTTAT-CAGAATTT
1 ATGGAGGTTATCCAAATTGCATAAGGAGATTATCAAAATCT-AATAACGAGGTTATCCA-AATTT
4348 CAA
64 CAA
* * * * *
4351 ATGGAGGTTATCCAAATTTCAT-AGTGATATTATCAGAATCTCATAAGGAGGTTATCCAAATTTC
1 ATGGAGGTTATCCAAATTGCATAAG-GAGATTATCAAAATCTAATAACGAGGTTATCCAAATTTC
4415 A
65 A
4416 TAGGGAGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
65 2 0.04
66 50 0.91
67 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (66 bp):
ATGGAGGTTATCCAAATTGCATAAGGAGATTATCAAAATCTAATAACGAGGTTATCCAAATTTCA
A
Found at i:4413 original size:44 final size:44
Alignment explanation
Indices: 4304--4426 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 44
4294 ATCCAAATTG
* ** * * *
4304 CATAAGGAGGTTATCAAAATTAAATAACGAGGTTATCAGAATTT
1 CATAAGGAGGTTATCCAAATTTCATAGCGAGATTATCAGAATCT
* *
4348 CA-AATGGAGGTTATCCAAATTTCATAGTGATATTATCAGAATCT
1 CATAA-GGAGGTTATCCAAATTTCATAGCGAGATTATCAGAATCT
*
4392 CATAAGGAGGTTATCCAAATTTCATAGGGAGATTA
1 CATAAGGAGGTTATCCAAATTTCATAGCGAGATTA
4427 ACAAATTTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.03
44 63 0.94
45 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (44 bp):
CATAAGGAGGTTATCCAAATTTCATAGCGAGATTATCAGAATCT
Found at i:4433 original size:21 final size:21
Alignment explanation
Indices: 4363--4434 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
4353 GGAGGTTATC
* * *
4363 CAAATTTCATAGTGATATTAT
1 CAAATTTCATAGGGAGATTAA
* * * *
4384 CAGAATCTCATAAGGAGGTTATC
1 CA-AATTTCATAGGGAGATTA-A
4407 CAAATTTCATAGGGAGATTAA
1 CAAATTTCATAGGGAGATTAA
4428 CAAATTT
1 CAAATTT
4435 TCAAAAATTG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
21 9 0.23
22 28 0.72
23 2 0.05
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (21 bp):
CAAATTTCATAGGGAGATTAA
Found at i:4448 original size:44 final size:44
Alignment explanation
Indices: 4340--4460 Score: 118
Period size: 44 Copynumber: 2.8 Consensus size: 44
4330 ACGAGGTTAT
* ** * * *
4340 CAGAATTTCAAATGGAGGTTATCCAAATTTCATAGTGATATTAT
1 CAGAATCTCAAAAAGAGGTTATCCAAATTTCATAGGGAGATTAA
* *
4384 CAGAATCTCATAAGGAGGTTATCCAAATTTCATAGGGAGATTAA
1 CAGAATCTCAAAAAGAGGTTATCCAAATTTCATAGGGAGATTAA
* ** *
4428 CA-AATTTTCAAAAATTGGTTATCAAAATTTCAT
1 CAGAA-TCTCAAAAAGAGGTTATCCAAATTTCAT
4461 TGAGGTTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 2 0.03
44 62 0.97
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (44 bp):
CAGAATCTCAAAAAGAGGTTATCCAAATTTCATAGGGAGATTAA
Found at i:4916 original size:76 final size:77
Alignment explanation
Indices: 4829--4983 Score: 294
Period size: 76 Copynumber: 2.0 Consensus size: 77
4819 ACTATATGTT
*
4829 ATATACGCTATTACTGAATCCTTTTTTATTATTAATAGTAACTTTTGCCCATAAAATTGTTAA-A
1 ATATACGCTATTACTGAATCCTTTTTTATTATTAATAGTAACTTTTGCCCATAAAATTGTAAAGA
4893 AAAAATAGACAA
66 AAAAATAGACAA
4905 ATATACGCTATTACTGAATCCTTTTTTATTATTAATAGTAACTTTTGCCCATAAAATTGTAAAGA
1 ATATACGCTATTACTGAATCCTTTTTTATTATTAATAGTAACTTTTGCCCATAAAATTGTAAAGA
4970 AAAAATAGACAA
66 AAAAATAGACAA
4982 AT
1 AT
4984 TGATTTTGAA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
76 62 0.81
77 15 0.19
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.37
Consensus pattern (77 bp):
ATATACGCTATTACTGAATCCTTTTTTATTATTAATAGTAACTTTTGCCCATAAAATTGTAAAGA
AAAAATAGACAA
Done.