Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009780.1 Corchorus capsularis cultivar CVL-1 contig09801, 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: 29198
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--58 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
59 ATAACGGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1623 original size:25 final size:24
Alignment explanation
Indices: 1595--1652 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
1585 ATCCTAAATC
1595 AGGATTGAAATTAACTCTTAAAGCA
1 AGGATTGAAATTAACTCTTAAAG-A
* *
1620 AGGATAG-AA-TAATTCTTAAAGA
1 AGGATTGAAATTAACTCTTAAAGA
1642 A-GATATGAAAT
1 AGGAT-TGAAAT
1653 GCCCGGAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
21 3 0.11
22 3 0.11
23 13 0.48
24 2 0.07
25 6 0.22
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (24 bp):
AGGATTGAAATTAACTCTTAAAGA
Found at i:8294 original size:2 final size:2
Alignment explanation
Indices: 8281--8310 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8271 TATTCTGTTG
*
8281 AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8311 GTAAAAGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9514 original size:22 final size:22
Alignment explanation
Indices: 9487--9543 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
9477 GATTGATAAT
9487 TTTTGAAAGAATAACCAAACTA
1 TTTTGAAAGAATAACCAAACTA
9509 TTTTGAAAGAATAACCAAACTA
1 TTTTGAAAGAATAACCAAACTA
9531 TTTTGAAAGAATA
1 TTTTGAAAGAATA
9544 TCGCTTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (22 bp):
TTTTGAAAGAATAACCAAACTA
Found at i:11043 original size:34 final size:34
Alignment explanation
Indices: 11004--11070 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
10994 TGATATCCAT
*
11004 AAAAAA-ACATCTTTTCTCCATTAATAATTTGCAG
1 AAAAAATA-ATCTTTTCTCCAATAATAATTTGCAG
*
11038 AAAAAATAATTTTTTCTCCAATAATAATTTGCA
1 AAAAAATAATCTTTTCTCCAATAATAATTTGCA
11071 AAACAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAAAATAATCTTTTCTCCAATAATAATTTGCAG
Found at i:11194 original size:9 final size:8
Alignment explanation
Indices: 11180--11232 Score: 51
Period size: 6 Copynumber: 6.9 Consensus size: 8
11170 TCGGGGTAGC
11180 TTATAATA
1 TTATAATA
11188 GTTATAATTA
1 -TTATAA-TA
*
11198 TAATAATA
1 TTATAATA
11206 TTAT-A-A
1 TTATAATA
11212 TTATAATA
1 TTATAATA
11220 --ATAATA
1 TTATAATA
11226 TTATAAT
1 TTATAAT
11233 TATTGATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
6 11 0.30
7 2 0.05
8 11 0.30
9 11 0.30
10 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
TTATAATA
Found at i:11211 original size:17 final size:18
Alignment explanation
Indices: 11182--11222 Score: 75
Period size: 17 Copynumber: 2.3 Consensus size: 18
11172 GGGGTAGCTT
11182 ATAATAGTTATAATTATA
1 ATAATAGTTATAATTATA
11200 ATAATA-TTATAATTATA
1 ATAATAGTTATAATTATA
11217 ATAATA
1 ATAATA
11223 ATATTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
ATAATAGTTATAATTATA
Found at i:11222 original size:20 final size:20
Alignment explanation
Indices: 11197--11235 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
11187 AGTTATAATT
11197 ATAATAATATTATAATTATA
1 ATAATAATATTATAATTATA
11217 ATAATAATATTATAATTAT
1 ATAATAATATTATAATTAT
11236 TGATTAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAATATTATAATTATA
Found at i:12332 original size:18 final size:18
Alignment explanation
Indices: 12309--12344 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12299 TTAGTGTGGT
12309 TCGAACTTTGTATCTTAA
1 TCGAACTTTGTATCTTAA
12327 TCGAACTTTGTATCTTAA
1 TCGAACTTTGTATCTTAA
12345 AAAGATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
TCGAACTTTGTATCTTAA
Found at i:15264 original size:2 final size:2
Alignment explanation
Indices: 15257--15294 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
15247 ATACAATCTT
*
15257 TA TA TA TA -A TA TA TA TA TA TA TA TA TA T- TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15295 ATTGCATTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:15281 original size:19 final size:19
Alignment explanation
Indices: 15243--15294 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
15233 GGATATATTT
* *
15243 TATAATACA-ATCTTTATA
1 TATAATACATATATATATA
*
15261 TATAATATATATATATATA
1 TATAATACATATATATATA
*
15280 TATATTACATATATA
1 TATAATACATATATA
15295 ATTGCATTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAATACATATATATATA
Found at i:21197 original size:24 final size:24
Alignment explanation
Indices: 21170--21224 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
21160 AAATTCTCAA
21170 TGACTTAGAGTCTAACAAAACTTT
1 TGACTTAGAGTCTAACAAAACTTT
*
21194 TGACTCAGAGTCTAACAAAACTTT
1 TGACTTAGAGTCTAACAAAACTTT
21218 TGCACTT
1 TG-ACTT
21225 CTTTTCTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (24 bp):
TGACTTAGAGTCTAACAAAACTTT
Found at i:25033 original size:21 final size:20
Alignment explanation
Indices: 24991--25033 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
24981 CAGAGGGAGT
* *
24991 AAAAGAAAGCAATTAAACTA
1 AAAACAAAGCAAGTAAACTA
*
25011 AAAACAAAGCAAAGTAAATTA
1 AAAACAAAGC-AAGTAAACTA
25032 AA
1 AA
25034 TCTAAATCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAACAAAGCAAGTAAACTA
Found at i:25780 original size:16 final size:15
Alignment explanation
Indices: 25759--25788 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25749 ACCCTAGCCC
25759 TAAAACTAAAGAAAAA
1 TAAAACTAAA-AAAAA
25775 TAAAACTAAAAAAA
1 TAAAACTAAAAAAA
25789 GGTAGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (15 bp):
TAAAACTAAAAAAAA
Found at i:26421 original size:19 final size:18
Alignment explanation
Indices: 26384--26423 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
26374 TTCTTGAAAT
*
26384 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
26402 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
26421 AAT
1 AAT
26424 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Done.