Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009586.1 Corchorus capsularis cultivar CVL-1 contig09607, 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: 43414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1213 original size:18 final size:18
Alignment explanation
Indices: 1147--1218 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
1137 ACCGACCGAA
1147 TTATATATATATATTAT-T
1 TTATATATATA-ATTATAT
*
1165 TATATGAAATATAA-TATAGT
1 T-TAT-ATATATAATTATA-T
*
1185 TT-TAGTTTATAATTATAT
1 TTATA-TATATAATTATAT
1203 TTATATATATAATTAT
1 TTATATATATAATTAT
1219 TACTTTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
17 1 0.02
18 23 0.53
19 11 0.26
20 8 0.19
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TTATATATATAATTATAT
Found at i:1234 original size:21 final size:19
Alignment explanation
Indices: 1174--1236 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 19
1164 TTATATGAAA
*
1174 TATAA-TATAGTT-TTAGTT
1 TATAATTATATTTATTAG-T
1192 TATAATTATATTTA-TA-T
1 TATAATTATATTTATTAGT
1209 ATATAATTATTACTTTATTAGT
1 -TATAATTA-TA-TTTATTAGT
1231 TATAAT
1 TATAAT
1237 ATACTAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 1 0.03
18 13 0.35
19 10 0.27
20 4 0.11
21 8 0.22
22 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (19 bp):
TATAATTATATTTATTAGT
Found at i:1257 original size:30 final size:27
Alignment explanation
Indices: 1203--1258 Score: 67
Period size: 30 Copynumber: 2.0 Consensus size: 27
1193 ATAATTATAT
* *
1203 TTATATATATAATTATTACTTTATTAG
1 TTATATATATAATAATTACCTTATTAG
1230 TTATAATATACTAATAATCTACCTTATTA
1 TTAT-ATATA-TAATAAT-TACCTTATTA
1259 TAACTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.17
28 5 0.21
29 6 0.25
30 9 0.38
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (27 bp):
TTATATATATAATAATTACCTTATTAG
Found at i:2767 original size:47 final size:47
Alignment explanation
Indices: 2694--2910 Score: 192
Period size: 47 Copynumber: 4.6 Consensus size: 47
2684 TTGGCCATGT
* * * * *
2694 TTTTGACCAGCAATGGTCGTGGTGGTTAACCTTTAGT-GTTTTGCCCAA
1 TTTTG-CCACCAAGGGTCGTGATGGTTAACCTTT-GTCATTTTGACCAA
* * * *
2742 -TTTGACCATCAAGGGTCGTGATGGTTAGCCCTTG-CACTTTG-CCTAA
1 TTTTG-CCACCAAGGGTCGTGATGGTTAACCTTTGTCATTTTGACC-AA
* * * *
2788 TTTTGGCCATCGAGGGTCGTGATGGTT-ACGTTTGTCATTTTGACAAA
1 TTTT-GCCACCAAGGGTCGTGATGGTTAACCTTTGTCATTTTGACCAA
* * * *
2835 TTTTGGCACCGATGGTCGTGATGGTTAGCCTTTGTCATTTTGACCAA
1 TTTTGCCACCAAGGGTCGTGATGGTTAACCTTTGTCATTTTGACCAA
*
2882 TTTTGGCACCAAGGGTCGTGATGGTTAAC
1 TTTTGCCACCAAGGGTCGTGATGGTTAAC
2911 TTGGTAATTT
Statistics
Matches: 140, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
45 2 0.01
46 30 0.21
47 106 0.76
48 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (47 bp):
TTTTGCCACCAAGGGTCGTGATGGTTAACCTTTGTCATTTTGACCAA
Found at i:3314 original size:25 final size:25
Alignment explanation
Indices: 3245--3316 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 25
3235 TCGGTCCAAT
*
3245 TTTGACCACCTTCGATCGTGATGGA
1 TTTGACCACCATCGATCGTGATGGA
** * *
3270 --TGGTCACCATCCATTGTGATGGA
1 TTTGACCACCATCGATCGTGATGGA
*
3293 TTTGACCACCATCGATCATGATGG
1 TTTGACCACCATCGATCGTGATGG
3317 TTAGCGTTGA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
23 18 0.51
25 17 0.49
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (25 bp):
TTTGACCACCATCGATCGTGATGGA
Found at i:3494 original size:31 final size:30
Alignment explanation
Indices: 3456--3621 Score: 137
Period size: 31 Copynumber: 5.5 Consensus size: 30
3446 GGTTAATTGT
3456 TCAAATAAGGGCCTAACGTTTGACAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
* * * **
3487 TCAAATAAGGGTCTGATC-TTT-TAATTTGGC
1 TCAAATAAGGGCCT-AACGTTTGCAAAAT-GC
3517 T-AAATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
*** **
3547 TCAAATAAGGGTCCGGTC-TTTG-AATTTGGC
1 TCAAATAAGGG-CCTAACGTTTGCAAAAT-GC
3577 -CAAATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-CAAAATGC
3607 TCAAATAAGGGCCTA
1 TCAAATAAGGGCCTA
3622 TCTCATGCGT
Statistics
Matches: 103, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 5 0.05
29 34 0.33
30 10 0.10
31 49 0.48
32 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (30 bp):
TCAAATAAGGGCCTAACGTTTGCAAAATGC
Found at i:3543 original size:60 final size:60
Alignment explanation
Indices: 3457--3617 Score: 277
Period size: 60 Copynumber: 2.7 Consensus size: 60
3447 GTTAATTGTT
* * *
3457 CAAATAAGGGCCTAACGTTTGACAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTGAATTTGGC
* *
3517 TAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGGTCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTGAATTTGGC
3577 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
3618 CCTATCTCAT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTGAATTTGGC
Found at i:3689 original size:31 final size:30
Alignment explanation
Indices: 3651--3751 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 30
3641 TGACATCAGA
3651 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTC-ATAACGTTAGG
* * * *
3682 CCCTTATTTG-GCCATATT-A-AAAGATCGAG
1 CCCTTATTTGAG-CATTTTCATAACGTTAG-G
*
3711 CCCTTATTTGAGCATTTTCAATAACATTAGG
1 CCCTTATTTGAGCATTTTC-ATAACGTTAGG
3742 CCCTTATTTG
1 CCCTTATTTG
3752 GCCAAATTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 5 0.09
29 17 0.31
30 2 0.04
31 27 0.49
32 4 0.07
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTCATAACGTTAGG
Found at i:3719 original size:29 final size:28
Alignment explanation
Indices: 3681--3780 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 28
3671 ATAACGTTAG
3681 GCCCTTATTTGGCCATATTAAAAGATCGA
1 GCCCTTATTTGGCCATATTAAAAGATC-A
* * *
3710 GCCCTTATTTGAG-CATTTTCAATAACATTA
1 GCCCTTATTTG-GCCATATT-AA-AAGATCA
*
3740 GGCCCTTATTTGGCCAAATTAAAAGATCA
1 -GCCCTTATTTGGCCATATTAAAAGATCA
*
3769 GACTCTTATTTG
1 G-CCCTTATTTG
3781 AGCATTTTGG
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
28 1 0.02
29 30 0.53
30 7 0.12
31 19 0.33
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (28 bp):
GCCCTTATTTGGCCATATTAAAAGATCA
Found at i:3744 original size:60 final size:60
Alignment explanation
Indices: 3645--3788 Score: 236
Period size: 60 Copynumber: 2.4 Consensus size: 60
3635 CCAAACTGAC
* * *
3645 ATCAGACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCATATTAAAAG
1 ATCAGACCCTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGGCCAAATTAAAAG
3705 ATC-GAGCCCTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGGCCAAATTAAAAG
1 ATCAGA-CCCTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGGCCAAATTAAAAG
*
3765 ATCAGACTCTTATTTGAGCATTTT
1 ATCAGACCCTTATTTGAGCATTTT
3789 GGCAAATGTT
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
59 2 0.03
60 74 0.95
61 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (60 bp):
ATCAGACCCTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGGCCAAATTAAAAG
Found at i:3801 original size:60 final size:60
Alignment explanation
Indices: 3645--3811 Score: 234
Period size: 60 Copynumber: 2.8 Consensus size: 60
3635 CCAAACTGAC
*
3645 ATCAGACCCTTATTTGAGCATTTT-CGATAACGTTAGGCCCTTATTTGGCCATATTAAAAG
1 ATCAGACCCTTATTTGAGCATTTTGC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAG
*
3705 ATC-GAGCCCTTATTTGAGCATTTT-CAATAACATTAGGCCCTTATTTGGCCAAATTAAAAG
1 ATCAGA-CCCTTATTTGAGCATTTTGC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAG
* *
3765 ATCAGACTCTTATTTGAGCATTTTGGCA-AATGTTAGGCCCTTATTTG
1 ATCAGACCCTTATTTGAGCATTTT-GCATAACGTTAGGCCCTTATTTG
3812 AACAATTAGC
Statistics
Matches: 97, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
59 2 0.02
60 91 0.94
61 3 0.03
62 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (60 bp):
ATCAGACCCTTATTTGAGCATTTTGCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAG
Found at i:6418 original size:16 final size:15
Alignment explanation
Indices: 6389--6422 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
6379 ATAATTTTTT
6389 TTAATTAAAAAAAAA
1 TTAATTAAAAAAAAA
*
6404 TTAATGTAAAGAAAAA
1 TTAAT-TAAAAAAAAA
6420 TTA
1 TTA
6423 CTTTGAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
TTAATTAAAAAAAAA
Found at i:7556 original size:2 final size:2
Alignment explanation
Indices: 7545--7580 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
7535 CCATCAAGCG
7545 AT AT AT -T AT AT 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 AT AT AT AT AT AT A
7581 CTTATTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11523 original size:25 final size:25
Alignment explanation
Indices: 11495--11547 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
11485 TTTCTATTCC
11495 ATTCCGCAAACCAAACCTACCCCTA
1 ATTCCGCAAACCAAACCTACCCCTA
* * * *
11520 ATTCTGCATACCAAACGTGCCCCTA
1 ATTCCGCAAACCAAACCTACCCCTA
11545 ATT
1 ATT
11548 TGGTCAATCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.38, G:0.08, T:0.23
Consensus pattern (25 bp):
ATTCCGCAAACCAAACCTACCCCTA
Found at i:12322 original size:27 final size:27
Alignment explanation
Indices: 12280--12338 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
12270 AAACAATGGC
*
12280 TTCCACCGTCCACGTCAATATGAAAAG
1 TTCCACCATCCACGTCAATATGAAAAG
*
12307 TTCCACCATCCTCGTCAATATGAAAAG
1 TTCCACCATCCACGTCAATATGAAAAG
12334 TTCCA
1 TTCCA
12339 AGGACCTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.31, G:0.12, T:0.25
Consensus pattern (27 bp):
TTCCACCATCCACGTCAATATGAAAAG
Found at i:14559 original size:29 final size:29
Alignment explanation
Indices: 14523--14591 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
14513 CTTGGCAACA
****
14523 GGGCTTATTTGGCCTTTTTAAGAGTTCAG
1 GGGCTTATTTGGCCGAAATAAGAGTTCAG
*
14552 GGGCTTATTTGGCCGAAATAATAGTTCAG
1 GGGCTTATTTGGCCGAAATAAGAGTTCAG
14581 GGGCTTATTTG
1 GGGCTTATTTG
14592 ACGGTTCAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.20, C:0.13, G:0.29, T:0.38
Consensus pattern (29 bp):
GGGCTTATTTGGCCGAAATAAGAGTTCAG
Found at i:29424 original size:32 final size:33
Alignment explanation
Indices: 29383--29455 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
29373 ACAAAGTTTA
*
29383 TTTAACATGCATAATCT-CTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTTCTTCTACCTTTC
29415 TTTATCATGCATAATCTCCTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTTCTTCTACCTTTC
29448 TTTATCAT
1 TTTATCAT
29456 TAAAAATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 16 0.41
33 23 0.59
ACGTcount: A:0.21, C:0.27, G:0.03, T:0.49
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTTCTTCTACCTTTC
Found at i:29535 original size:36 final size:35
Alignment explanation
Indices: 29488--29653 Score: 225
Period size: 33 Copynumber: 4.8 Consensus size: 35
29478 ACTACCTAGT
29488 ATATTAGTGGCACCTGAAGTTGTCACATAATCAAGA
1 ATATTAGTGGCACCTGAAGTTGTCACAT-ATCAAGA
*
29524 ATATTAGTGGCACCTGAAGTTGTCAC--ATCAAGT
1 ATATTAGTGGCACCTGAAGTTGTCACATATCAAGA
*
29557 ATATTAGTGACACCTGAAGTTGTCACATGATCAAGA
1 ATATTAGTGGCACCTGAAGTTGTCACAT-ATCAAGA
*
29593 ATGTTAGTGGCACCTGAAGTTGTCAC--ATCAA-A
1 ATATTAGTGGCACCTGAAGTTGTCACATATCAAGA
* *
29625 CATATTAGTGACACCTAAAGTTGTCACAT
1 -ATATTAGTGGCACCTGAAGTTGTCACAT
29654 CAAAGAAATA
Statistics
Matches: 116, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
32 1 0.01
33 59 0.51
36 56 0.48
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (35 bp):
ATATTAGTGGCACCTGAAGTTGTCACATATCAAGA
Found at i:29600 original size:69 final size:69
Alignment explanation
Indices: 29485--29653 Score: 284
Period size: 69 Copynumber: 2.4 Consensus size: 69
29475 AATACTACCT
*
29485 AGTATATTAGTGGCACCTGAAGTTGTCACATAATCAAGAATATTAGTGGCACCTGAAGTTGTCAC
1 AGTATATTAGTGACACCTGAAGTTGTCACATAATCAAGAATATTAGTGGCACCTGAAGTTGTCAC
29550 ATCA
66 ATCA
* *
29554 AGTATATTAGTGACACCTGAAGTTGTCACATGATCAAGAATGTTAGTGGCACCTGAAGTTGTCAC
1 AGTATATTAGTGACACCTGAAGTTGTCACATAATCAAGAATATTAGTGGCACCTGAAGTTGTCAC
29619 ATCA
66 ATCA
** *
29623 AACATATTAGTGACACCTAAAGTTGTCACAT
1 AGTATATTAGTGACACCTGAAGTTGTCACAT
29654 CAAAGAAATA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 94 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (69 bp):
AGTATATTAGTGACACCTGAAGTTGTCACATAATCAAGAATATTAGTGGCACCTGAAGTTGTCAC
ATCA
Found at i:31136 original size:38 final size:38
Alignment explanation
Indices: 31076--31149 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
31066 CTATATTGGG
* *
31076 TGTGCAAATTTGATTGATGGCTCTAG-AAGAGCTAGTAT
1 TGTGCAAATTTGATTAAAGGCTC-AGAAAGAGCTAGTAT
*
31114 TGTGCAAATTTGATTAAAGGCTCCGAAAGAGCTAGT
1 TGTGCAAATTTGATTAAAGGCTCAGAAAGAGCTAGT
31150 GTTCTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (38 bp):
TGTGCAAATTTGATTAAAGGCTCAGAAAGAGCTAGTAT
Found at i:31540 original size:83 final size:82
Alignment explanation
Indices: 31384--31541 Score: 246
Period size: 83 Copynumber: 1.9 Consensus size: 82
31374 AGTAAGAATG
*
31384 AAACATATGCTTTGTTAAACAGAAGTTTATTGATTGCATTATATTTATTGTTTGGCATGACCGCT
1 AAACAAATGCTTTGTTAAACAGAAGTTTATTGATTGCATTATATTTATTGTTTGGCATGACCGCT
*
31449 TAGGCCATCCTGATAAT
66 TAGACCATCCTGATAAT
*
31466 AAACAAATGCTTT-TGTAAACCAGAAGTTTATTGATTGCATTATGTTTATTGTTTGGCATGACCG
1 AAACAAATGCTTTGT-TAAA-CAGAAGTTTATTGATTGCATTATATTTATTGTTTGGCATGACCG
* *
31530 GTTTGACCATCC
64 CTTAGACCATCC
31542 CGGTTCAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
81 1 0.01
82 16 0.23
83 52 0.75
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (82 bp):
AAACAAATGCTTTGTTAAACAGAAGTTTATTGATTGCATTATATTTATTGTTTGGCATGACCGCT
TAGACCATCCTGATAAT
Done.