Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007951.1 Corchorus capsularis cultivar CVL-1 contig07972, 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: 6551
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:2560 original size:18 final size:19
Alignment explanation
Indices: 2537--2573 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2527 AGAGTCATGA
2537 TTTTC-AAAAATGTTTTTT
1 TTTTCAAAAAATGTTTTTT
2555 TTTTCAAAAAATGTTTTTT
1 TTTTCAAAAAATGTTTTTT
2574 CCAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTCAAAAAATGTTTTTT
Found at i:2571 original size:16 final size:16
Alignment explanation
Indices: 2552--2582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2542 AAAAATGTTT
*
2552 TTTTTTTCAAAAAATG
1 TTTTTTCCAAAAAATG
2568 TTTTTTCCAAAAAAT
1 TTTTTTCCAAAAAAT
2583 AACTTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (16 bp):
TTTTTTCCAAAAAATG
Found at i:3246 original size:16 final size:17
Alignment explanation
Indices: 3220--3262 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
3210 TTCCAAGTGC
*
3220 AATGAAGAAAAAAAA-G
1 AATGAAAAAAAAAAATG
*
3236 GATGAAAAAAAAAAATG
1 AATGAAAAAAAAAAATG
3253 AATGAAAAAA
1 AATGAAAAAA
3263 TGAATGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (17 bp):
AATGAAAAAAAAAAATG
Found at i:3249 original size:17 final size:17
Alignment explanation
Indices: 3227--3262 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3217 TGCAATGAAG
*
3227 AAAAAAAAGGATGAAAA
1 AAAAAAAAGAATGAAAA
*
3244 AAAAAAATGAATGAAAA
1 AAAAAAAAGAATGAAAA
3261 AA
1 AA
3263 TGAATGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (17 bp):
AAAAAAAAGAATGAAAA
Found at i:3253 original size:13 final size:14
Alignment explanation
Indices: 3220--3262 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
3210 TTCCAAGTGC
3220 AATGAAGAAAAAAA
1 AATGAAGAAAAAAA
3234 AGGATGAA-AAAAAAA
1 A--ATGAAGAAAAAAA
3249 AATGAATGAAAAAA
1 AATGAA-GAAAAAA
3263 TGAATGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 5 0.20
14 1 0.04
15 14 0.56
16 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (14 bp):
AATGAAGAAAAAAA
Found at i:4364 original size:45 final size:44
Alignment explanation
Indices: 4271--4388 Score: 125
Period size: 45 Copynumber: 2.6 Consensus size: 44
4261 CAAATCTTCC
* *
4271 ATTATTCAGTTCTTCAATACTTCAAATTATCTCTTCGACTCTTTA
1 ATTATTCAATTCTTCAATACTTC-AATTATCTCTTCCACTCTTTA
* *
4316 ATTATTCAATTCTTCAATACTTCAATCTATTTCTTCCA-TTTTTCA
1 ATTATTCAATTCTTCAATACTTCAAT-TATCTCTTCCACTCTTT-A
*
4361 ATTACTT--ATTGCTTCAATTCTTCAATTA
1 ATTA-TTCAATT-CTTCAATACTTCAATTA
4389 CTCAATGCTT
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
44 12 0.19
45 50 0.78
46 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.03, T:0.49
Consensus pattern (44 bp):
ATTATTCAATTCTTCAATACTTCAATTATCTCTTCCACTCTTTA
Found at i:4375 original size:24 final size:24
Alignment explanation
Indices: 4327--4416 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
4317 TTATTCAATT
* *
4327 CTTCAATACTTCAA-T-C-TATTT
1 CTTCAATTCTTCAATTACTTATTG
* *
4348 CTTCCATTTTTCAATTACTTATTG
1 CTTCAATTCTTCAATTACTTATTG
* *
4372 CTTCAATTCTTCAATTACTCAATG
1 CTTCAATTCTTCAATTACTTATTG
4396 CTTCAATTCTTCAATTCACTT
1 CTTCAATTCTTCAATT-ACTT
4417 TCAATGACCC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 11 0.20
22 1 0.02
23 1 0.02
24 40 0.71
25 3 0.05
ACGTcount: A:0.26, C:0.24, G:0.02, T:0.48
Consensus pattern (24 bp):
CTTCAATTCTTCAATTACTTATTG
Found at i:4385 original size:8 final size:8
Alignment explanation
Indices: 4217--4412 Score: 82
Period size: 8 Copynumber: 24.0 Consensus size: 8
4207 GCTTCGATTT
*
4217 TTCAATCC
1 TTCAATTC
*
4225 TTCAATGC
1 TTCAATTC
4233 TTCAATTTTC
1 TTCAA--TTC
* *
4243 TTCAACTA
1 TTCAATTC
4251 TTCAATGT-
1 TTCAAT-TC
*
4259 TTCAAATC
1 TTCAATTC
* *
4267 TTCCATTA
1 TTCAATTC
*
4275 TTCAGTTC
1 TTCAATTC
*
4283 TTCAATAC
1 TTCAATTC
4291 TTCAAATTATCTC
1 TTC--A--AT-TC
* *
4304 TTCGACTC
1 TTCAATTC
* *
4312 TTTAATTA
1 TTCAATTC
4320 TTCAATTC
1 TTCAATTC
*
4328 TTCAATAC
1 TTCAATTC
4336 TTCAA-TC
1 TTCAATTC
*
4343 -T-ATTTC
1 TTCAATTC
* *
4349 TTCCATTT
1 TTCAATTC
4357 TTCAATTAC
1 TTCAATT-C
4366 TT--ATTGC
1 TTCAATT-C
4373 TTCAATTC
1 TTCAATTC
4381 TTCAATTAC
1 TTCAATT-C
*
4390 -TCAATGC
1 TTCAATTC
4397 TTCAATTC
1 TTCAATTC
4405 TTCAATTC
1 TTCAATTC
4413 ACTTTCAATG
Statistics
Matches: 137, Mismatches: 34, Indels: 34
0.67 0.17 0.17
Matches are distributed among these distances:
5 1 0.01
6 3 0.02
7 10 0.07
8 101 0.74
9 8 0.06
10 8 0.06
12 2 0.01
13 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (8 bp):
TTCAATTC
Found at i:4453 original size:59 final size:58
Alignment explanation
Indices: 4390--4528 Score: 154
Period size: 58 Copynumber: 2.4 Consensus size: 58
4380 CTTCAATTAC
* * * *
4390 TCAATGCTTCAATTCTTCAATTCACTTTCAATGACCCATGGTGGTCTTTCTTCGTTTCT
1 TCAATGATTCAATGCTTCAATTCAC-TTCAATAACACATGGTGGTCTTTCTTCGTTTCT
* ** * *
4449 TCAATTATTCAATGCTTCAATTGGCTTCAATAATACATGGTGGTCTTTCTTCCG-TTCC
1 TCAATGATTCAATGCTTCAATTCACTTCAATAACACATGGTGGTCTTTCTT-CGTTTCT
* *
4507 TCAATTATTCAATGCCTCAATT
1 TCAATGATTCAATGCTTCAATT
4529 TCAATTTTCA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 47 0.68
59 22 0.32
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (58 bp):
TCAATGATTCAATGCTTCAATTCACTTCAATAACACATGGTGGTCTTTCTTCGTTTCT
Found at i:4540 original size:21 final size:21
Alignment explanation
Indices: 4507--4562 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
4497 CTTCCGTTCC
4507 TCAATTATTCAATGCCTCAATT
1 TCAATT-TTCAATGCCTCAATT
* *
4529 TCAATTTTCAATGCTTTAATT
1 TCAATTTTCAATGCCTCAATT
4550 TCAATGTTTCAAT
1 TCAAT-TTTCAAT
4563 TCCAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.46
Consensus pattern (21 bp):
TCAATTTTCAATGCCTCAATT
Found at i:4551 original size:14 final size:14
Alignment explanation
Indices: 4527--4575 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
4517 AATGCCTCAA
4527 TTTCAATTTTCAATG
1 TTTCAA-TTTCAATG
4542 CTTT-AATTTCAATG
1 -TTTCAATTTCAATG
* *
4556 TTTCAATTCCAATT
1 TTTCAATTTCAATG
4570 TTTCAA
1 TTTCAA
4576 ATGCAATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 3 0.10
14 22 0.73
15 2 0.07
16 3 0.10
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (14 bp):
TTTCAATTTCAATG
Found at i:4604 original size:16 final size:16
Alignment explanation
Indices: 4579--4615 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4569 TTTTCAAATG
*
4579 CAATTCTTCAATCCTT
1 CAATTATTCAATCCTT
*
4595 CAATTATTCAATGCTT
1 CAATTATTCAATCCTT
4611 CAATT
1 CAATT
4616 TACTTGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (16 bp):
CAATTATTCAATCCTT
Found at i:4701 original size:22 final size:22
Alignment explanation
Indices: 4676--4724 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
4666 ACGCTTCAAT
*
4676 TTCAATTCTCCAAATT-CAATCC
1 TTCAATGCTCC-AATTCCAATCC
*
4698 TTCAATGCTCCAATTCCAATTC
1 TTCAATGCTCCAATTCCAATCC
4720 TTCAA
1 TTCAA
4725 ATTCAATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.31, C:0.31, G:0.02, T:0.37
Consensus pattern (22 bp):
TTCAATGCTCCAATTCCAATCC
Found at i:4757 original size:36 final size:36
Alignment explanation
Indices: 4668--4760 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
4658 ATTCAATGAC
* *
4668 GCTTCAATTTCAATTCTCCAAATTCAATCCTTCAAT
1 GCTTCAATTCCAATTCTTCAAATTCAATCCTTCAAT
* *
4704 GCTCCAATTCCAATTCTTCAAATTCAATCCTTCGAT
1 GCTTCAATTCCAATTCTTCAAATTCAATCCTTCAAT
* *
4740 GTTTCAATTGCAATTCTTCAA
1 GCTTCAATTCCAATTCTTCAA
4761 TGTTTCAGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (36 bp):
GCTTCAATTCCAATTCTTCAAATTCAATCCTTCAAT
Found at i:4775 original size:22 final size:22
Alignment explanation
Indices: 4724--4808 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 22
4714 CAATTCTTCA
* *
4724 AATT-CAATCCTTCGATGTTTC
1 AATTCCAATTCTTCAATGTTTC
*
4745 AATTGCAATTCTTCAATGTTTC
1 AATTCCAATTCTTCAATGTTTC
* *
4767 AGTTCCAATTTCATTTCCAATGCTTC
1 AATTCCAA-TTC--TT-CAATGTTTC
*
4793 AATTTCAATTCTTCAA
1 AATTCCAATTCTTCAA
4809 ATTCAGTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
21 4 0.08
22 24 0.46
23 5 0.10
25 5 0.10
26 14 0.27
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (22 bp):
AATTCCAATTCTTCAATGTTTC
Found at i:5102 original size:22 final size:22
Alignment explanation
Indices: 5074--5123 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5064 CAATTTCATT
*
5074 TTCAATGTTTCAATTTCAACGC
1 TTCAATGGTTCAATTTCAACGC
* **
5096 TTCAATGGTTCACTTTCAATTC
1 TTCAATGGTTCAATTTCAACGC
5118 TTCAAT
1 TTCAAT
5124 TCCTCAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Consensus pattern (22 bp):
TTCAATGGTTCAATTTCAACGC
Done.