Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005191.1 Corchorus capsularis cultivar CVL-1 contig05209, 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: 40062
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:136 original size:20 final size:18
Alignment explanation
Indices: 111--155 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
101 ACACATGTTT
111 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
131 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
149 TACTAAT
1 TACTAAT
156 TTTGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:548 original size:14 final size:14
Alignment explanation
Indices: 514--548 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
504 GCACAAATCT
514 TTTTCTTTAGTTAA
1 TTTTCTTTAGTTAA
* *
528 ATCTCTTTAGTTAA
1 TTTTCTTTAGTTAA
542 TTTTCTT
1 TTTTCTT
549 ATGGAAGGCT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (14 bp):
TTTTCTTTAGTTAA
Found at i:4325 original size:17 final size:17
Alignment explanation
Indices: 4303--4335 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4293 ACAATCAAAC
*
4303 AATTCAAGTATAAGAAA
1 AATTCAAGTACAAGAAA
4320 AATTCAAGTACAAGAA
1 AATTCAAGTACAAGAA
4336 TGAAGGAGAC
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:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AATTCAAGTACAAGAAA
Found at i:6827 original size:14 final size:14
Alignment explanation
Indices: 6808--6834 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6798 GTAAATATAT
6808 ATAAATTCTTTTTG
1 ATAAATTCTTTTTG
6822 ATAAATTCTTTTT
1 ATAAATTCTTTTT
6835 TATCTTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (14 bp):
ATAAATTCTTTTTG
Found at i:11590 original size:17 final size:16
Alignment explanation
Indices: 11547--11600 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
11537 CCATTTGATA
11547 TCGTTTTCGTTTTTCTGT
1 TCGTTTTCGTTTTT-T-T
11565 T--TTTT-GTTTTTGTT
1 TCGTTTTCGTTTTT-TT
11579 TCGTTTTCGTTTTATTT
1 TCGTTTTCGTTTT-TTT
11596 TCGTT
1 TCGTT
11601 GCGTTGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 2 0.06
15 7 0.23
16 8 0.26
17 12 0.39
18 2 0.06
ACGTcount: A:0.02, C:0.11, G:0.15, T:0.72
Consensus pattern (16 bp):
TCGTTTTCGTTTTTTT
Found at i:22478 original size:22 final size:20
Alignment explanation
Indices: 22453--22495 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
22443 AATAAATTAC
22453 AAAGAAAACTCACAATTCCGTG
1 AAAG-AAACTCAC-ATTCCGTG
*
22475 AAAGCAACTCACATTCCGTG
1 AAAGAAACTCACATTCCGTG
22495 A
1 A
22496 GAGTAGAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 7 0.35
22 4 0.20
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.19
Consensus pattern (20 bp):
AAAGAAACTCACATTCCGTG
Found at i:22818 original size:10 final size:10
Alignment explanation
Indices: 22777--22844 Score: 75
Period size: 10 Copynumber: 6.7 Consensus size: 10
22767 ATGCTTATCA
22777 GAATTATTGT
1 GAATTATTGT
* *
22787 G-CTAATTGT
1 GAATTATTGT
*
22796 TAATTATTTGT
1 GAATTA-TTGT
22807 GAATTATTGT
1 GAATTATTGT
22817 GAATTATTGT
1 GAATTATTGT
*
22827 GAATTATTTGC
1 GAATTA-TTGT
22838 GAATTAT
1 GAATTAT
22845 ATTTGTTAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 6 0.12
10 24 0.50
11 18 0.38
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
GAATTATTGT
Found at i:22821 original size:21 final size:21
Alignment explanation
Indices: 22791--22844 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
22781 TATTGTGCTA
*
22791 ATTGTTAATTATTTGTGAATT
1 ATTGTGAATTATTTGTGAATT
22812 ATTGTGAATTA-TTGTGAATT
1 ATTGTGAATTATTTGTGAATT
*
22832 ATTTGCGAATTAT
1 A-TTGTGAATTAT
22845 ATTTGTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (21 bp):
ATTGTGAATTATTTGTGAATT
Found at i:22832 original size:31 final size:30
Alignment explanation
Indices: 22777--22844 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
22767 ATGCTTATCA
* * *
22777 GAATTATTGTGCTAATTGTTAATTATTTGT
1 GAATTATTGTGATAATTGTGAATTATTTGC
*
22807 GAATTATTGTGAATTATTGTGAATTATTTGC
1 GAATTATTGTG-ATAATTGTGAATTATTTGC
22838 GAATTAT
1 GAATTAT
22845 ATTTGTTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (30 bp):
GAATTATTGTGATAATTGTGAATTATTTGC
Found at i:23207 original size:9 final size:9
Alignment explanation
Indices: 23193--23317 Score: 57
Period size: 9 Copynumber: 15.6 Consensus size: 9
23183 AGTCAGTTTT
23193 TTCGGGTCA
1 TTCGGGTCA
23202 TTCGGGT--
1 TTCGGGTCA
23209 TTCGGGTCA
1 TTCGGGTCA
*
23218 TTTGGG---
1 TTCGGGTCA
23224 TTCGGGTCA
1 TTCGGGTCA
* *
23233 ATCAGGT--
1 TTCGGGTCA
23240 TTCGGGTCA
1 TTCGGGTCA
* *
23249 ATCGGTTC-
1 TTCGGGTCA
*
23257 -TCGGGTTA
1 TTCGGGTCA
23265 TTCGGGTC-
1 TTCGGGTCA
* *
23273 -TCAGGTTA
1 TTCGGGTCA
23281 TTCGGGTC-
1 TTCGGGTCA
23289 -TCGGG-CTA
1 TTCGGGTC-A
23297 TTCGGGT--
1 TTCGGGTCA
23304 TTCGGGTCA
1 TTCGGGTCA
23313 TTCGG
1 TTCGG
23318 TTCTCAGGTT
Statistics
Matches: 84, Mismatches: 15, Indels: 34
0.63 0.11 0.26
Matches are distributed among these distances:
6 6 0.07
7 34 0.40
9 44 0.52
ACGTcount: A:0.10, C:0.19, G:0.35, T:0.36
Consensus pattern (9 bp):
TTCGGGTCA
Found at i:23229 original size:15 final size:16
Alignment explanation
Indices: 23192--23388 Score: 140
Period size: 16 Copynumber: 12.6 Consensus size: 16
23182 CAGTCAGTTT
23192 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
23208 TTTCGGGTCATTTGGG
1 TTTCGGGTCATTCGGG
* *
23224 -TTCGGGTCAATCAGG
1 TTTCGGGTCATTCGGG
*
23239 TTTCGGGTCAATC-GG
1 TTTCGGGTCATTCGGG
*
23254 TTCTCGGGTTATTCGGG
1 TT-TCGGGTCATTCGGG
* * *
23271 TCTCAGGTTATTCGGG
1 TTTCGGGTCATTCGGG
*
23287 TCTCGGG-CTATTCGGG
1 TTTCGGGTC-ATTCGGG
23303 TTTCGGGTCATTC-GG
1 TTTCGGGTCATTCGGG
* * *
23318 TTCTCAGGTTAATCGGG
1 TT-TCGGGTCATTCGGG
* *
23335 TCTCGGGTTATTC-GG
1 TTTCGGGTCATTCGGG
* * *
23350 ATTCGGGT--TT-AGA
1 TTTCGGGTCATTCGGG
*
23363 CTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
23379 TCTCGGGTCA
1 TTTCGGGTCA
23389 AATGGGTCAG
Statistics
Matches: 145, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
13 10 0.07
15 30 0.21
16 98 0.68
17 7 0.05
ACGTcount: A:0.11, C:0.19, G:0.34, T:0.36
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:23316 original size:48 final size:46
Alignment explanation
Indices: 23194--23357 Score: 168
Period size: 48 Copynumber: 3.4 Consensus size: 46
23184 GTCAGTTTTT
* * * * *
23194 TCGGGTCATTCGGGTTTCGGGTCATTTGGGT-TCGGGTCAATCAGGTT
1 TCGGGT-ATTC-GGTTTCGGGTCATTCGGGTCTCAGGTTAATCGGGTC
* * *
23241 TCGGGTCAATCGGTTCTCGGGTTATTCGGGTCTCAGGTTATTCGGGTC
1 TCGGGT-ATTCGGTT-TCGGGTCATTCGGGTCTCAGGTTAATCGGGTC
*
23289 TCGGGCTATTCGGGTTTCGGGTCATTCGGTTCTCAGGTTAATCGGGTC
1 TCGGG-TATTC-GGTTTCGGGTCATTCGGGTCTCAGGTTAATCGGGTC
*
23337 TCGGGTTATTCGGATTCGGGT
1 TCGGG-TATTCGGTTTCGGGT
23358 TTAGACTTCG
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
46 4 0.04
47 32 0.32
48 58 0.59
49 5 0.05
ACGTcount: A:0.10, C:0.19, G:0.35, T:0.36
Consensus pattern (46 bp):
TCGGGTATTCGGTTTCGGGTCATTCGGGTCTCAGGTTAATCGGGTC
Found at i:28545 original size:13 final size:13
Alignment explanation
Indices: 28527--28555 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28517 TACATACTAC
28527 ATAAATTTGTCCT
1 ATAAATTTGTCCT
28540 ATAAATTTGTCCT
1 ATAAATTTGTCCT
28553 ATA
1 ATA
28556 CTACATCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (13 bp):
ATAAATTTGTCCT
Found at i:37935 original size:23 final size:22
Alignment explanation
Indices: 37887--37937 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
37877 ATTAGCCTTA
37887 TTCTTTCCCTTCTCTATATTTT
1 TTCTTTCCCTTCTCTATATTTT
* * *
37909 TTCTTTCCGCTTTTCTTTCTTTT
1 TTCTTTCC-CTTCTCTATATTTT
37932 TTCTTT
1 TTCTTT
37938 TTTTTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.04, C:0.25, G:0.02, T:0.69
Consensus pattern (22 bp):
TTCTTTCCCTTCTCTATATTTT
Found at i:37943 original size:12 final size:12
Alignment explanation
Indices: 37919--37952 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
37909 TTCTTTCCGC
*
37919 TTTTC-TTTCTT
1 TTTTCTTTTTTT
37930 TTTTCTTTTTTT
1 TTTTCTTTTTTT
37942 TTTTCTTTTTT
1 TTTTCTTTTTT
37953 GTTAAACGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:39242 original size:214 final size:214
Alignment explanation
Indices: 38873--39305 Score: 857
Period size: 214 Copynumber: 2.0 Consensus size: 214
38863 TCTAGCATGG
*
38873 AACAAGTCAAGATTGATGCACGAACAACAATGATTAAAAGGAGAGAAGCCGAACTTCAAGCTAGA
1 AACAAGTCAAGATTGATGCACGAACAACAATGATTAAAAAGAGAGAAGCCGAACTTCAAGCTAGA
38938 TCTGATGCTTTGGCTAACATGGTGATTGCTTTAAGTGAAGCTCAAAATGAGTTTCTTGGACTTTC
66 TCTGATGCTTTGGCTAACATGGTGATTGCTTTAAGTGAAGCTCAAAATGAGTTTCTTGGACTTTC
39003 TAACCAAGAAAAGGCCAAGATTGGTGATGACACAAATGATGGCTTAAGCATCAATGATGATGTTG
131 TAACCAAGAAAAGGCCAAGATTGGTGATGACACAAATGATGGCTTAAGCATCAATGATGATGTTG
39068 ATACCATAAGTGAAAACAA
196 ATACCATAAGTGAAAACAA
39087 AACAAGTCAAGATTGATGCACGAACAACAATGATTAAAAAGAGAGAAGCCGAACTTCAAGCTAGA
1 AACAAGTCAAGATTGATGCACGAACAACAATGATTAAAAAGAGAGAAGCCGAACTTCAAGCTAGA
39152 TCTGATGCTTTGGCTAACATGGTGATTGCTTTAAGTGAAGCTCAAAATGAGTTTCTTGGACTTTC
66 TCTGATGCTTTGGCTAACATGGTGATTGCTTTAAGTGAAGCTCAAAATGAGTTTCTTGGACTTTC
39217 TAACCAAGAAAAGGCCAAGATTGGTGATGACACAAATGATGGCTTAAGCATCAATGATGATGTTG
131 TAACCAAGAAAAGGCCAAGATTGGTGATGACACAAATGATGGCTTAAGCATCAATGATGATGTTG
39282 ATACCATAAGTGAAAACAA
196 ATACCATAAGTGAAAACAA
39301 AACAA
1 AACAA
39306 TGCAAGTGGA
Statistics
Matches: 218, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 218 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (214 bp):
AACAAGTCAAGATTGATGCACGAACAACAATGATTAAAAAGAGAGAAGCCGAACTTCAAGCTAGA
TCTGATGCTTTGGCTAACATGGTGATTGCTTTAAGTGAAGCTCAAAATGAGTTTCTTGGACTTTC
TAACCAAGAAAAGGCCAAGATTGGTGATGACACAAATGATGGCTTAAGCATCAATGATGATGTTG
ATACCATAAGTGAAAACAA
Done.