Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012874.1 Corchorus capsularis cultivar CVL-1 contig12895, 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: 10556
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Found at i:505 original size:13 final size:13
Alignment explanation
Indices: 487--534 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
477 GTAGTAATTC
487 TTAATTTAATTTG
1 TTAATTTAATTTG
** *
500 TTAATTTTTAAACTA
1 TTAA--TTTAATTTG
515 TTAATTTAATTTG
1 TTAATTTAATTTG
528 TTAATTT
1 TTAATTT
535 CTTTAAACTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 17 0.63
15 10 0.37
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (13 bp):
TTAATTTAATTTG
Found at i:519 original size:28 final size:30
Alignment explanation
Indices: 487--545 Score: 104
Period size: 28 Copynumber: 2.0 Consensus size: 30
477 GTAGTAATTC
487 TTAATTTAATTTGTTAA-TT-TTTAAACTA
1 TTAATTTAATTTGTTAATTTCTTTAAACTA
515 TTAATTTAATTTGTTAATTTCTTTAAACTA
1 TTAATTTAATTTGTTAATTTCTTTAAACTA
545 T
1 T
546 ATATAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 17 0.59
29 2 0.07
30 10 0.34
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (30 bp):
TTAATTTAATTTGTTAATTTCTTTAAACTA
Found at i:1151 original size:2 final size:2
Alignment explanation
Indices: 1144--1180 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1134 ATTAATATTT
1144 TA TA TA TA 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 TA TA TA TA T
1181 TCATGATCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1348 original size:18 final size:18
Alignment explanation
Indices: 1325--1366 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1315 TTTTATCCAT
1325 GTGATAGGCTTAAG-ATAA
1 GTGATAGGC-TAAGTATAA
1343 GTGATAGGCTAAGTATAA
1 GTGATAGGCTAAGTATAA
*
1361 GAGATA
1 GTGATA
1367 TACATGTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.40, C:0.05, G:0.29, T:0.26
Consensus pattern (18 bp):
GTGATAGGCTAAGTATAA
Found at i:1819 original size:2 final size:2
Alignment explanation
Indices: 1812--1840 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1802 CGGTAACCTC
1812 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
1841 GCACCAAAAC
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:2393 original size:2 final size:2
Alignment explanation
Indices: 2386--2410 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2376 AAATTAAAAC
2386 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2411 ATTATCATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2518 original size:3 final size:3
Alignment explanation
Indices: 2510--2535 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2500 AATGACTAAG
2510 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2536 GAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4971 original size:15 final size:15
Alignment explanation
Indices: 4922--4979 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 15
4912 AAATAATATT
*
4922 TTAATTATTCCATTA
1 TTAATTATTCAATTA
* *
4937 TT--TT-TTTAATCA
1 TTAATTATTCAATTA
*
4949 TAAATTATTCAATTA
1 TTAATTATTCAATTA
*
4964 TTAATTATTAAATTA
1 TTAATTATTCAATTA
4979 T
1 T
4980 ATATAATACG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
12 6 0.19
13 2 0.06
14 2 0.06
15 22 0.69
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTATTCAATTA
Found at i:5117 original size:37 final size:37
Alignment explanation
Indices: 5022--5117 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 37
5012 AATTTGGCTT
* *
5022 TTTGTTTCTAACGTCCTATTTAATTTTGTCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATCTTGTCTTTTGTC
* **
5059 TTTGTTTCCAATCATTGTATTTAATCTTG-CTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATCTTGTC-TTTTGTC
5097 TTTGTTTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
5118 GGACTTAGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 18 0.37
38 31 0.63
ACGTcount: A:0.15, C:0.18, G:0.10, T:0.57
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATCTTGTCTTTTGTC
Found at i:5253 original size:22 final size:22
Alignment explanation
Indices: 5176--5280 Score: 75
Period size: 22 Copynumber: 4.7 Consensus size: 22
5166 AATAACGTGA
* * *
5176 TTATCAATATATCATATGGAGG
1 TTATCAAAATTTCATATTGAGG
* * * *
5198 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATATTG-AGG
5221 TTATCAAAATTTCATATTGAGG
1 TTATCAAAATTTCATATTGAGG
* * * ***
5243 TTTTCAAAATTCCTTGGGGAGG
1 TTATCAAAATTTCATATTGAGG
*
5265 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
5281 AGAAGGCTAA
Statistics
Matches: 62, Mismatches: 20, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
22 44 0.71
23 18 0.29
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATATTGAGG
Found at i:9182 original size:25 final size:27
Alignment explanation
Indices: 9130--9182 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
9120 TTACTCAACT
**
9130 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
9157 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
9182 A
1 A
9183 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Done.