Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014641.1 Corchorus capsularis cultivar CVL-1 contig14662, 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: 4740
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Found at i:58 original size:2 final size:2
Alignment explanation
Indices: 5--47 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 AGCC
5 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47 T
1 T
48 TATGAATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2274 original size:2 final size:2
Alignment explanation
Indices: 2267--2299 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2257 TTTTTAATGG
*
2267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2300 AAGTACGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3375 original size:19 final size:19
Alignment explanation
Indices: 3336--3385 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
3326 GTAAATTTCC
3336 TTTAATATTATT-TTTTGAA
1 TTTAATATT-TTATTTTGAA
3355 TTTAATATTTTACTTTT-AA
1 TTTAATATTTTA-TTTTGAA
3374 TTTCAAT-TTTTA
1 TTT-AATATTTTA
3386 AATGTCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 19 0.68
20 7 0.25
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTAATATTTTATTTTGAA
Found at i:3715 original size:22 final size:22
Alignment explanation
Indices: 3553--3717 Score: 100
Period size: 22 Copynumber: 7.3 Consensus size: 22
3543 TTGTCTCTAT
* *
3553 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATTAAAATTTCATAGG
* * *
3575 ATGATTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * *
3597 GAGGTTATCAAAA-TTCATAGT
1 GTGGTTATTAAAATTTCATAGG
** * *
3618 GTGGTTACCAAAAGTTCATATAGT
1 GTGGTTATTAAAATTTC--ATAGG
**
3642 GTGGTTACCAAAATTTTCATAGG
1 GTGGTTATTAAAA-TTTCATAGG
* *
3665 ATCAGGTTATTAAAATTTCTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
3689 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
3711 GTGGTTA
1 GTGGTTA
3718 ATTATCACAA
Statistics
Matches: 112, Mismatches: 23, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
21 16 0.14
22 52 0.46
23 5 0.04
24 27 0.24
25 12 0.11
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:3959 original size:22 final size:23
Alignment explanation
Indices: 3748--4054 Score: 134
Period size: 22 Copynumber: 13.8 Consensus size: 23
3738 AGGTTATTAA
* *
3748 AGAGATTATCAAAATGTCATAA-
1 AGAGGTTATCAAAATTTCATAAG
*
3770 CGAGGTTAT-AAGAATTTCAT-AG
1 AGAGGTTATCAA-AATTTCATAAG
* * * *
3792 TGTGGTTA-AAAAATTTCATTAG
1 AGAGGTTATCAAAATTTCATAAG
* *
3814 -GAGGTTA-CTAATATTTCAT-GG
1 AGAGGTTATC-AAAATTTCATAAG
* *
3835 GGAGGTTATCAAAATTTTAT-AG
1 AGAGGTTATCAAAATTTCATAAG
* * * *
3857 TGTGGTTATCAAAATTTCAGATG
1 AGAGGTTATCAAAATTTCATAAG
*
3880 A-AGGTTATAAAAATCTCAATTTCATAAG
1 AGAGGTTAT--CAA----AATTTCATAAG
* *
3908 -GA-G-TACCAAAATTT-ATAGG
1 AGAGGTTATCAAAATTTCATAAG
*
3927 A-AGATTATCAAAATTTCA-AAG
1 AGAGGTTATCAAAATTTCATAAG
* *
3948 CGAGGTTATCAAAATTACATAATG
1 AGAGGTTATCAAAATTTCATAA-G
*
3972 TA-A--TTATCAGAATTTCAT-AG
1 -AGAGGTTATCAAAATTTCATAAG
* * * *
3992 AGGGGTCAACAAAATTTTATAA-
1 AGAGGTTATCAAAATTTCATAAG
4014 AGAGGTTATCAAAATTTCATAA-
1 AGAGGTTATCAAAATTTCATAAG
*
4036 AGAGGTTATCAAATTTTCA
1 AGAGGTTATCAAAATTTCA
4055 AAATGTGATT
Statistics
Matches: 214, Mismatches: 44, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
19 6 0.03
20 6 0.03
21 31 0.14
22 147 0.69
23 5 0.02
24 6 0.03
26 2 0.01
27 1 0.00
28 10 0.05
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (23 bp):
AGAGGTTATCAAAATTTCATAAG
Found at i:3980 original size:44 final size:44
Alignment explanation
Indices: 3930--4076 Score: 129
Period size: 44 Copynumber: 3.3 Consensus size: 44
3920 TTATAGGAAG
* *
3930 ATTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTA
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTA
* * * * * * *
3974 ATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAG-A
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTA
* * * *
4017 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTG
1 -ATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGTA
4062 ATTA-CAAAAATTTCA
1 ATTATC-AAAATTTCA
4077 TAGTGGTATT
Statistics
Matches: 78, Mismatches: 21, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
43 2 0.03
44 75 0.96
45 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (44 bp):
ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTA
Found at i:4273 original size:22 final size:22
Alignment explanation
Indices: 4179--4563 Score: 136
Period size: 22 Copynumber: 17.5 Consensus size: 22
4169 TCAGGGAAGA
* *
4179 TATCAAAATTTCATGGTTTA-GT
1 TATCAAAATTTCATAG-TGAGGT
* *
4201 TTTCAAAATTTCATAGT-ATGT
1 TATCAAAATTTCATAGTGAGGT
* * *
4222 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTGAGGT
* *
4245 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTGAGGT
*** *
4267 TATCAAAAAAACATAGGGAGGT
1 TATCAAAATTTCATAGTGAGGT
4289 TATC-AAA-TT--T-GT-A-GT
1 TATCAAAATTTCATAGTGAGGT
* * *
4304 TATCAAAATTTTATTGGGAGGTT
1 TATCAAAATTTCATAGTGAGG-T
*
4327 TATCAAAA-TTCTATAG-GAAGATT
1 TATCAAAATTTC-ATAGTG-AG-GT
*
4350 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGTGAGGT
* * * **
4372 TATCACAATTTCATAATGTGAC
1 TATCAAAATTTCATAGTGAGGT
* *
4394 TATCAACATTTCAGAGTGTGATGTGAT
1 TATCAAAATTTCATA--GTGA-G-G-T
4421 TA-CTAACAA-TTCATA-TGTAGGT
1 TATC-AA-AATTTCATAGTG-AGGT
* * ** *
4443 TTTTAAAATTTCATAACGTGGT
1 TATCAAAATTTCATAGTGAGGT
* * *
4465 TATCAATATATCATA-TGGAGTT
1 TATCAAAATTTCATAGT-GAGGT
* * * *
4487 TATTAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTG-AGGT
* * *
4510 TATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCATAGTGAGGT
*
4532 TATCAAAATTTCATATTGAGGT
1 TATCAAAATTTCATAGTGAGGT
4554 CT-TCAAAATT
1 -TATCAAAATT
4564 CCTCAGGAAA
Statistics
Matches: 264, Mismatches: 68, Indels: 62
0.67 0.17 0.16
Matches are distributed among these distances:
15 6 0.02
16 4 0.02
17 3 0.01
18 1 0.00
19 1 0.00
20 2 0.01
21 9 0.03
22 166 0.63
23 50 0.19
24 9 0.03
25 2 0.01
26 1 0.00
27 9 0.03
28 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGAGGT
Found at i:4329 original size:23 final size:23
Alignment explanation
Indices: 4303--4382 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
4293 AAATTTGTAG
*
4303 TTATCAAAATTTTATTGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
4326 TTATCAAAATTCTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
4349 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
4371 TTATCACAATTT
1 TTATCAAAATTT
4383 CATAATGTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 11 0.23
23 36 0.77
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:4611 original size:20 final size:22
Alignment explanation
Indices: 4574--4618 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
4564 CCTCAGGAAA
* *
4574 GTTAACAAAATTTCATAAGAAG
1 GTTAACAAAAATTCATAAAAAG
4596 GTTAA-AAAAATT-ATAAAAAG
1 GTTAACAAAAATTCATAAAAAG
4616 GTT
1 GTT
4619 CTTGAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 6 0.29
22 5 0.24
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.29
Consensus pattern (22 bp):
GTTAACAAAAATTCATAAAAAG
Done.