Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005644.1 Corchorus capsularis cultivar CVL-1 contig05662, 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: 13292
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Found at i:968 original size:15 final size:16
Alignment explanation
Indices: 931--969 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
921 GAACCTGAAC
*
931 CCGAAAAAACTCAAAT
1 CCGAAAAAACCCAAAT
*
947 CCGAAAAAACCCGAAT
1 CCGAAAAAACCCAAAT
963 CC-AAAAA
1 CCGAAAAA
970 TTTATGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.56, C:0.28, G:0.08, T:0.08
Consensus pattern (16 bp):
CCGAAAAAACCCAAAT
Found at i:1159 original size:32 final size:32
Alignment explanation
Indices: 1123--1193 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
1113 ACAGAATCCG
*
1123 AACCCGAATTGACCTGACCCAAATTCAACCCA
1 AACCCGAATTAACCTGACCCAAATTCAACCCA
* *
1155 AACCCGAATTAATCTGACCCAAATTCAACCCG
1 AACCCGAATTAACCTGACCCAAATTCAACCCA
1187 AACCCGA
1 AACCCGA
1194 CTCAAGTCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.38, C:0.37, G:0.10, T:0.15
Consensus pattern (32 bp):
AACCCGAATTAACCTGACCCAAATTCAACCCA
Found at i:1336 original size:7 final size:7
Alignment explanation
Indices: 1326--1353 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1316 AAAAAATACT
1326 TGGCTAC
1 TGGCTAC
1333 TGGCTAC
1 TGGCTAC
1340 TGGCTAC
1 TGGCTAC
1347 TGGCTAC
1 TGGCTAC
1354 GATCAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
TGGCTAC
Found at i:3499 original size:4 final size:4
Alignment explanation
Indices: 3500--3544 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
3490 TGTTTTTTTT
*
3500 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT- TTT- TTTT TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
3545 TTCTTTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
3 6 0.15
4 33 0.85
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:3545 original size:12 final size:12
Alignment explanation
Indices: 3492--3554 Score: 65
Period size: 12 Copynumber: 5.0 Consensus size: 12
3482 TGTGTGCATG
3492 TTTTTTTTTTTC
1 TTTTTTTTTTTC
* *
3504 TTTCTTTCTTTC
1 TTTTTTTTTTTC
3516 TTTCTTTCTTTCTT-
1 TTT-TTT-TTT-TTC
3530 TTTTTTTTTTTC
1 TTTTTTTTTTTC
3542 TTTTTCTTTTTTC
1 TTTTT-TTTTTTC
3555 CATGATAGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
11 2 0.05
12 21 0.50
13 12 0.29
14 5 0.12
15 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:3553 original size:8 final size:8
Alignment explanation
Indices: 3492--3546 Score: 62
Period size: 8 Copynumber: 7.2 Consensus size: 8
3482 TGTGTGCATG
3492 TTTT-TTT
1 TTTTCTTT
3499 TTTTCTTT
1 TTTTCTTT
*
3507 CTTTCTTT
1 TTTTCTTT
*
3515 CTTTCTTT
1 TTTTCTTT
*
3523 CTTTC-TT
1 TTTTCTTT
3530 TTTT-TTT
1 TTTTCTTT
3537 TTTTCTTT
1 TTTTCTTT
3545 TT
1 TT
3547 CTTTTTTCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
7 15 0.35
8 28 0.65
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTCTTT
Found at i:7296 original size:15 final size:15
Alignment explanation
Indices: 7276--7307 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
7266 TGCTAATCAG
7276 GTTGTTTCGAAATAT
1 GTTGTTTCGAAATAT
7291 GTTGTTTCGAAATAT
1 GTTGTTTCGAAATAT
7306 GT
1 GT
7308 GAGAGGAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (15 bp):
GTTGTTTCGAAATAT
Found at i:10128 original size:58 final size:58
Alignment explanation
Indices: 10038--10460 Score: 515
Period size: 58 Copynumber: 7.0 Consensus size: 58
10028 CACTTTTGAG
* *
10038 TACGATTCAGGGATCGTTTAATCTTGATAAAACGATCTCGAAGGAGACGTTCGTCTTT
1 TACGATTCAAGGATCGTTCAATCTTGATAAAACGATCTCGAAGGAGACGTTCGTCTTT
*
10096 TACGATTCAAGGATCGTTTAATCTTGATAAAACGATCTCGAAGGAGACGTTCGTCTTT
1 TACGATTCAAGGATCGTTCAATCTTGATAAAACGATCTCGAAGGAGACGTTCGTCTTT
*
10154 TACGATTCAAGGATCGTTCAATTTTGATAAAACGATCTCGAAGGAGACGTTCGTCTTT
1 TACGATTCAAGGATCGTTCAATCTTGATAAAACGATCTCGAAGGAGACGTTCGTCTTT
* *
10212 TACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTAAGT
1 TACGATTCAAGGATCGTTCAATCTTGATAAAACGATCTCGAAGGAGACGTTCG---T-C-T---T
10277 T
58 T
* * *
10278 TACGATTCAAGGATCGTTCAATTCTTTG-TAAAACGGTCTCGAGGGAGACGTTCCTCTTACT
1 TACGATTCAAGGATCGTTCAA-TC-TTGATAAAACGATCTCGAAGGAGACGTTCGTCTT--T
* * * *
10339 TAAGTTTTCGGTTCAAGGATCGTTCAATTTTGATAAAACAACCTCGAAGGAGACGTTCGTCTTT
1 T-A-----CGATTCAAGGATCGTTCAATCTTGATAAAACGATCTCGAAGGAGACGTTCGTCTTT
* * * *
10403 TACGATTCAAGGATCGTTCAATTCTTGGTAAAACGGTCTCGAGGGAGATGTTCGTCTT
1 TACGATTCAAGGATCGTTCAA-TCTTGATAAAACGATCTCGAAGGAGACGTTCGTCTT
10461 ACTTAAGTTT
Statistics
Matches: 323, Mismatches: 22, Indels: 39
0.84 0.06 0.10
Matches are distributed among these distances:
58 183 0.57
59 30 0.09
61 3 0.01
62 3 0.01
63 3 0.01
64 3 0.01
65 3 0.01
66 49 0.15
67 43 0.13
68 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (58 bp):
TACGATTCAAGGATCGTTCAATCTTGATAAAACGATCTCGAAGGAGACGTTCGTCTTT
Found at i:10336 original size:67 final size:67
Alignment explanation
Indices: 10210--10495 Score: 378
Period size: 67 Copynumber: 4.4 Consensus size: 67
10200 ACGTTCGTCT
10210 TTTACGATTCAAGGATCGTTCAA-TTTTGATAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTA
1 TTTACGATTCAAGGATCGTTCAATTTTTGATAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTA
10274 AG
66 AG
* *
10276 TTTACGATTCAAGGATCGTTCAATTCTTTG-TAAAACGGTCTCGAGGGAGACGTTCCTCTTACTT
1 TTTACGATTCAAGGATCGTTCAATT-TTTGATAAAACGGTCTCGAAGGAGACGTTCGTCTTACTT
10340 AAG
65 AAG
* * ***
10343 TTTTCGGTTCAAGGATCGTTCAA-TTTTGATAAAACAACCTCGAAGGAGACGTTCG---T-C-T-
1 TTTACGATTCAAGGATCGTTCAATTTTTGATAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTA
10401 --
66 AG
* * * *
10401 TTTACGATTCAAGGATCGTTCAATTCTTGGTAAAACGGTCTCGAGGGAGATGTTCGTCTTACTTA
1 TTTACGATTCAAGGATCGTTCAATTTTTGATAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTA
10466 AG
66 AG
*
10468 TTTTCGATTCAAGGATCGTTCAATTTTT
1 TTTACGATTCAAGGATCGTTCAATTTTT
10496 TGGTCTTCAA
Statistics
Matches: 188, Mismatches: 20, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
58 21 0.11
59 25 0.13
61 1 0.01
62 2 0.01
63 2 0.01
64 1 0.01
65 4 0.02
66 45 0.24
67 83 0.44
68 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (67 bp):
TTTACGATTCAAGGATCGTTCAATTTTTGATAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTA
AG
Found at i:10426 original size:125 final size:129
Alignment explanation
Indices: 10209--10494 Score: 436
Period size: 125 Copynumber: 2.2 Consensus size: 129
10199 GACGTTCGTC
***
10209 TTTTACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAAGGAGACGTTCGTCTTACTTA
1 TTTT-CGATTCAAGGATCGTTCAATTTTGATAAAACAACCTCGAAGGAGACGTTCG--TTACTT-
*
10274 AGTTTACGATTCAAGGATCGTTCAATTCTTTGTAAAACGGTCTCGAGGGAGACGTTCCTCTTACT
62 A-TTTACGATTCAAGGATCGTTCAATTCTTGGTAAAACGGTCTCGAGGGAGACGTTCCTCTTACT
10339 TAAG
126 TAAG
*
10343 TTTTCGGTTCAAGGATCGTTCAATTTTGATAAAACAACCTCGAAGGAGACGTTCG-T-C-T-TTT
1 TTTTCGATTCAAGGATCGTTCAATTTTGATAAAACAACCTCGAAGGAGACGTTCGTTACTTATTT
* *
10404 ACGATTCAAGGATCGTTCAATTCTTGGTAAAACGGTCTCGAGGGAGATGTTCGTCTTACTTAAG
66 ACGATTCAAGGATCGTTCAATTCTTGGTAAAACGGTCTCGAGGGAGACGTTCCTCTTACTTAAG
10468 TTTTCGATTCAAGGATCGTTCAATTTT
1 TTTTCGATTCAAGGATCGTTCAATTTT
10495 TTGGTCTTCA
Statistics
Matches: 144, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
125 90 0.62
128 1 0.01
129 1 0.01
130 1 0.01
133 47 0.33
134 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (129 bp):
TTTTCGATTCAAGGATCGTTCAATTTTGATAAAACAACCTCGAAGGAGACGTTCGTTACTTATTT
ACGATTCAAGGATCGTTCAATTCTTGGTAAAACGGTCTCGAGGGAGACGTTCCTCTTACTTAAG
Done.