Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015764.1 Corchorus capsularis cultivar CVL-1 contig15785, 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: 29421
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3195 original size:141 final size:139
Alignment explanation
Indices: 3032--3311 Score: 515
Period size: 141 Copynumber: 2.0 Consensus size: 139
3022 TTGAACGGAT
* *
3032 ATATCGACGGATATGTCGAGGTATCGATGAAATTCAAAAATAAGTGGTTCAAAATGCACTAAAAC
1 ATATCGACGGATATATCGAGGTATCGATGAAATTCAAAAATAAGTGGTTAAAAATGCACTAAAAC
*
3097 GACGTATATTTATAGTAAACGTTTGAATTTTGCCTTGAAATTTTGACCAATTCTTATTTACATAT
66 GACATATATTTATAGTAAACGTTTGAATTTTGCCTTGAAATTTTGACCAATTCTTATTTAC--AT
3162 ATTTCCACATA
129 ATTTCCACATA
3173 ATATCGACGGATATATCGAGGTATCGATGAAATTCAAAAATAAGTGGTTAAAAATGCACTAAAAC
1 ATATCGACGGATATATCGAGGTATCGATGAAATTCAAAAATAAGTGGTTAAAAATGCACTAAAAC
3238 GACATATATTTATAGTAAACGTTTGAATTTTGCCTTGAAATTTTGACCAATTCTTATTTACATAT
66 GACATATATTTATAGTAAACGTTTGAATTTTGCCTTGAAATTTTGACCAATTCTTATTTACATAT
3303 TTCCACATA
131 TTCCACATA
3312 TTTTAGAATC
Statistics
Matches: 136, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
139 13 0.10
141 123 0.90
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (139 bp):
ATATCGACGGATATATCGAGGTATCGATGAAATTCAAAAATAAGTGGTTAAAAATGCACTAAAAC
GACATATATTTATAGTAAACGTTTGAATTTTGCCTTGAAATTTTGACCAATTCTTATTTACATAT
TTCCACATA
Found at i:4274 original size:3 final size:3
Alignment explanation
Indices: 4266--4298 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4256 TCATTTCACC
4266 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA- CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
4299 TTCCGTGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:14249 original size:19 final size:17
Alignment explanation
Indices: 14222--14260 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
14212 ACCCTCTTCT
*
14222 AAAATTAGAGAGAAAACTA
1 AAAACTAGA-AGAAAA-TA
14241 AAAACTAGAAGAAAATA
1 AAAACTAGAAGAAAATA
14258 AAA
1 AAA
14261 TAATAGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.69, C:0.05, G:0.13, T:0.13
Consensus pattern (17 bp):
AAAACTAGAAGAAAATA
Found at i:14267 original size:18 final size:17
Alignment explanation
Indices: 14222--14278 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
14212 ACCCTCTTCT
*
14222 AAAATTAGAGAGAAAACTA
1 AAAAATAGA-AGAAAA-TA
*
14241 AAAACTAGAAGAAAATA
1 AAAAATAGAAGAAAATA
* *
14258 AAATAATAGATGAAAAGA
1 AAA-AATAGAAGAAAATA
14276 AAA
1 AAA
14279 GATGTAGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 5 0.15
18 20 0.61
19 8 0.24
ACGTcount: A:0.68, C:0.04, G:0.14, T:0.14
Consensus pattern (17 bp):
AAAAATAGAAGAAAATA
Found at i:14848 original size:30 final size:30
Alignment explanation
Indices: 14814--14870 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
14804 GCTCTTTCTC
* *
14814 CTTGAAAACTTTCTTCAAT-GATCTTCATGA
1 CTTG-AAACTATCTTCAATAAATCTTCATGA
14844 CTTGAAACTATCTTCAATAAATCTTCA
1 CTTGAAACTATCTTCAATAAATCTTCA
14871 ATCACGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (30 bp):
CTTGAAACTATCTTCAATAAATCTTCATGA
Found at i:18184 original size:2 final size:2
Alignment explanation
Indices: 18177--18205 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18167 TTGTTTTCCT
18177 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18206 TATTTGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18575 original size:13 final size:14
Alignment explanation
Indices: 18553--18586 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
18543 GGCCCTAATT
*
18553 TTTGTTTTTTTC-C
1 TTTGTATTTTTCAC
18566 TTTGTATTTTTCAC
1 TTTGTATTTTTCAC
18580 TTTGTAT
1 TTTGTAT
18587 ATGGTAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.09, C:0.12, G:0.09, T:0.71
Consensus pattern (14 bp):
TTTGTATTTTTCAC
Found at i:23415 original size:10 final size:10
Alignment explanation
Indices: 23400--23479 Score: 60
Period size: 10 Copynumber: 8.2 Consensus size: 10
23390 AGATATGTTT
*
23400 TAATAATAAA
1 TAATAATATA
23410 TAATAATATA
1 TAATAATATA
*
23420 TACTAATATA
1 TAATAATATA
*
23430 T-A-AATATT
1 TAATAATATA
* *
23438 TACTAATTTA
1 TAATAATATA
23448 CTAATAATATA
1 -TAATAATATA
23459 -AAT-ATATA
1 TAATAATATA
*
23467 TTAAAAATATA
1 -TAATAATATA
23478 TA
1 TA
23480 TTGTTAAGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
8 11 0.20
9 3 0.06
10 27 0.50
11 13 0.24
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (10 bp):
TAATAATATA
Found at i:23453 original size:18 final size:17
Alignment explanation
Indices: 23408--23466 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
23398 TTTAATAATA
23408 AATA-ATAATATATACT
1 AATATATAATATATACT
*
23424 AATATATAAATATTTACT
1 AATATAT-AATATATACT
*
23442 AATTTACTAATA-ATA-T
1 AATATA-TAATATATACT
23458 AAATATATA
1 -AATATATA
23467 TTAAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 7 0.20
17 9 0.26
18 18 0.51
19 1 0.03
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATATAATATATACT
Done.