Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007365.1 Corchorus capsularis cultivar CVL-1 contig07386, 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: 66843
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:3153 original size:10 final size:10
Alignment explanation
Indices: 3140--3165 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3130 ATCCGTCGAT
3140 ATATCCGTAA
1 ATATCCGTAA
3150 ATATCCGTAA
1 ATATCCGTAA
3160 ATATCC
1 ATATCC
3166 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:3389 original size:22 final size:22
Alignment explanation
Indices: 3345--3390 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3335 GACCCGGGTG
*
3345 TTGCTAAACACCGCCCCCGTTT
1 TTGCTAAACACCGCCCCAGTTT
* *
3367 TTGCTAAATACCGCCCCATTTT
1 TTGCTAAACACCGCCCCAGTTT
3389 TT
1 TT
3391 ACACTTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.35
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCAGTTT
Found at i:3603 original size:38 final size:33
Alignment explanation
Indices: 3512--3584 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
3502 TCGTAGTGCT
* *
3512 GCCCCA-GAGGGGCGGCCTGA-CCACGGTATGCC
1 GCCCCAGGA-GGGCGGCATGAGCCACGGCATGCC
3544 GCCCCAGGAGGGCGGCATGAGCCACGGCATGCC
1 GCCCCAGGAGGGCGGCATGAGCCACGGCATGCC
3577 GCCCCAGG
1 GCCCCAGG
3585 GCCATAGGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 16 0.43
33 21 0.57
ACGTcount: A:0.16, C:0.38, G:0.38, T:0.07
Consensus pattern (33 bp):
GCCCCAGGAGGGCGGCATGAGCCACGGCATGCC
Found at i:4760 original size:12 final size:12
Alignment explanation
Indices: 4743--4797 Score: 83
Period size: 12 Copynumber: 4.5 Consensus size: 12
4733 CATCGATACC
*
4743 TCGATATATCCA
1 TCGATATATCCG
4755 TCGATATATCCG
1 TCGATATATCCG
4767 TCGATATATCCG
1 TCGATATATCCG
*
4779 TCCGATATATCTG
1 T-CGATATATCCG
4792 TCGATA
1 TCGATA
4798 CCTGTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
12 29 0.73
13 11 0.28
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:4794 original size:25 final size:24
Alignment explanation
Indices: 4743--4797 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
4733 CATCGATACC
4743 TCGATATATCCATCGATATATCCG
1 TCGATATATCCATCGATATATCCG
* *
4767 TCGATATATCCGTCCGATATATCTG
1 TCGATATATCCAT-CGATATATCCG
4792 TCGATA
1 TCGATA
4798 CCTGTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (24 bp):
TCGATATATCCATCGATATATCCG
Found at i:4868 original size:29 final size:29
Alignment explanation
Indices: 4824--4881 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
4814 TGCATACAAC
4824 TTCCACTTGTTCCAGTAAAAAAAAAAAAA
1 TTCCACTTGTTCCAGTAAAAAAAAAAAAA
*
4853 TTCCACTTGTTTCAGTAAAAAAAAAAAAA
1 TTCCACTTGTTCCAGTAAAAAAAAAAAAA
4882 AAAGACTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.26
Consensus pattern (29 bp):
TTCCACTTGTTCCAGTAAAAAAAAAAAAA
Found at i:4889 original size:29 final size:29
Alignment explanation
Indices: 4827--4889 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
4817 ATACAACTTC
***
4827 CACTTGTTCCAGTAAAAAAAAAAAAATTC
1 CACTTGTTCCAGTAAAAAAAAAAAAAAAA
*
4856 CACTTGTTTCAGTAAAAAAAAAAAAAAAA
1 CACTTGTTCCAGTAAAAAAAAAAAAAAAA
*
4885 GACTT
1 CACTT
4890 CTACTTGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (29 bp):
CACTTGTTCCAGTAAAAAAAAAAAAAAAA
Found at i:5856 original size:13 final size:13
Alignment explanation
Indices: 5838--5864 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5828 CCCATTAATA
5838 TCACGAGAAAATG
1 TCACGAGAAAATG
5851 TCACGAGAAAATG
1 TCACGAGAAAATG
5864 T
1 T
5865 TTTTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (13 bp):
TCACGAGAAAATG
Found at i:13408 original size:2 final size:2
Alignment explanation
Indices: 13401--13430 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13391 TAAAGACATA
*
13401 AT AT AT AT AT AA 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
13431 TGTGTCTTAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13988 original size:21 final size:21
Alignment explanation
Indices: 13950--13990 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13940 TATCCTATAT
*
13950 TATGTAAAAATAAATTTATTG
1 TATGTAAAAAGAAATTTATTG
* *
13971 TATGTAAAGAGAATTTTATT
1 TATGTAAAAAGAAATTTATT
13991 ATTGGTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (21 bp):
TATGTAAAAAGAAATTTATTG
Found at i:21408 original size:15 final size:15
Alignment explanation
Indices: 21388--21419 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21378 TGCGTGTACC
21388 AAGAAACTTCCTTGT
1 AAGAAACTTCCTTGT
21403 AAGAAACTTCCTTGT
1 AAGAAACTTCCTTGT
21418 AA
1 AA
21420 TGAGCATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (15 bp):
AAGAAACTTCCTTGT
Found at i:42201 original size:29 final size:29
Alignment explanation
Indices: 42169--42244 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
42159 CAAAAAAGTG
*
42169 AAGAAAATAATCAATACAAC-AGCA-AAT
1 AAGAAAATAATCAATACAACTACCATAAT
*
42196 CCAAGAAAATAATCAA-ATCGACTACCATAAT
1 --AAGAAAATAATCAATA-CAACTACCATAAT
42227 AAGAAAATAATCAATACA
1 AAGAAAATAATCAATACA
42245 TGAGAAAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 1 0.03
29 32 0.80
30 4 0.10
31 3 0.08
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (29 bp):
AAGAAAATAATCAATACAACTACCATAAT
Found at i:42274 original size:25 final size:24
Alignment explanation
Indices: 42246--42328 Score: 73
Period size: 25 Copynumber: 3.5 Consensus size: 24
42236 ATCAATACAT
42246 GAGAAAACAAAAAATACCCAATTCA
1 GAGAAAACAAAAAA-ACCCAATTCA
* * * *
42271 GAGAAAGCAAAGCAAACCTAATCCA
1 GAGAAAACAAA-AAAACCCAATTCA
*
42296 -AGAAAAGC--AGAAACCCAATTCA
1 GAGAAAA-CAAAAAAACCCAATTCA
42318 GAGAAAACAAA
1 GAGAAAACAAA
42329 TCAAGGCCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
22 11 0.24
23 7 0.16
24 6 0.13
25 19 0.42
26 2 0.04
ACGTcount: A:0.58, C:0.20, G:0.13, T:0.08
Consensus pattern (24 bp):
GAGAAAACAAAAAAACCCAATTCA
Found at i:42315 original size:47 final size:49
Alignment explanation
Indices: 42261--42365 Score: 142
Period size: 50 Copynumber: 2.2 Consensus size: 49
42251 AACAAAAAAT
* *
42261 ACCCAATTCAGAGAAAGCAAAGCAA-ACC-TAATCCAAGAAAAGCAGAA
1 ACCCAATTCAGAGAAAACAAAGCAAGACCATAATCCAAGAAAAACAGAA
* * *
42308 ACCCAATTCAGAGAAAACAAATCAAGGCCAATATTCCAAGAAAAACAGAA
1 ACCCAATTCAGAGAAAACAAAGCAAGACC-ATAATCCAAGAAAAACAGAA
42358 ACCCAATT
1 ACCCAATT
42366 AACGCCCAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
47 23 0.46
48 2 0.04
50 25 0.50
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.11
Consensus pattern (49 bp):
ACCCAATTCAGAGAAAACAAAGCAAGACCATAATCCAAGAAAAACAGAA
Found at i:43316 original size:15 final size:15
Alignment explanation
Indices: 43296--43329 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43286 CTTGGATTTA
43296 AATTTTTT-ATAATT
1 AATTTTTTAATAATT
43310 AATTTTTTAATAATT
1 AATTTTTTAATAATT
*
43325 TATTT
1 AATTT
43330 AATTCAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTTTTTAATAATT
Found at i:47155 original size:2 final size:2
Alignment explanation
Indices: 47150--47197 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
47140 AAATACATAC
* * *
47150 AT AT AT AT AG AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47192 AT AT AT
1 AT AT AT
47198 GTATTTTTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:47224 original size:42 final size:42
Alignment explanation
Indices: 47178--47258 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
47168 ATATATATAC
47178 ATATATATATATAGATATATGTATTTTTGGCACCTTTGGCAT
1 ATATATATATATAGATATATGTATTTTTGGCACCTTTGGCAT
*
47220 ATATATATATATATATATATGTATTTTTGGCACCTTTGG
1 ATATATATATATAGATATATGTATTTTTGGCACCTTTGG
47259 GGAGTTAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.47
Consensus pattern (42 bp):
ATATATATATATAGATATATGTATTTTTGGCACCTTTGGCAT
Found at i:48126 original size:12 final size:12
Alignment explanation
Indices: 48109--48133 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48099 ATTTTCCTAT
48109 GGAAATATGTCC
1 GGAAATATGTCC
48121 GGAAATATGTCC
1 GGAAATATGTCC
48133 G
1 G
48134 ACTTATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (12 bp):
GGAAATATGTCC
Found at i:52487 original size:23 final size:23
Alignment explanation
Indices: 52460--52516 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
52450 TAAAGTAATT
*
52460 ATAAAGATATTAGATT-TAATTGA
1 ATAAAAATA-TAGATTCTAATTGA
* *
52483 ATAAAAATATAGTTTCTAGTTGA
1 ATAAAAATATAGATTCTAATTGA
*
52506 ATAAAACTATA
1 ATAAAAATATA
52517 ATAGTTAAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.37
Consensus pattern (23 bp):
ATAAAAATATAGATTCTAATTGA
Found at i:52685 original size:36 final size:36
Alignment explanation
Indices: 52638--52709 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
52628 ACGTGCCTTG
*
52638 CACGTGACCTAATATGTTTAAATTAAATTAAAATTA
1 CACGTGACCTAATATATTTAAATTAAATTAAAATTA
*
52674 CACGTGACCTAATATATTTAAATTAAATTAATATTA
1 CACGTGACCTAATATATTTAAATTAAATTAAAATTA
52710 AAATCTTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (36 bp):
CACGTGACCTAATATATTTAAATTAAATTAAAATTA
Found at i:53367 original size:18 final size:18
Alignment explanation
Indices: 53330--53368 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53320 GTACTTTGAC
* **
53330 ATATAGTATATATTTTAT
1 ATATAGTATAGATTAGAT
53348 ATATAGTATAGATTAGAT
1 ATATAGTATAGATTAGAT
53366 ATA
1 ATA
53369 GATAGATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (18 bp):
ATATAGTATAGATTAGAT
Found at i:53383 original size:16 final size:16
Alignment explanation
Indices: 53328--53384 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
53318 TCGTACTTTG
*
53328 ACATATAGTATATATTTT
1 ACATATAGTATAGA--TT
*
53346 ATATATAGTATAGATT
1 ACATATAGTATAGATT
*
53362 AGATATAG-ATAGATAT
1 ACATATAGTATAGAT-T
53378 ACATATA
1 ACATATA
53385 TGTTAGAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.18
16 16 0.47
18 12 0.35
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.40
Consensus pattern (16 bp):
ACATATAGTATAGATT
Found at i:57288 original size:19 final size:18
Alignment explanation
Indices: 57247--57288 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
57237 TTAGATATGA
*
57247 AAATTGATAATCCTAATT
1 AAATTGATAATCCTAACT
57265 AAATTGATGAAATCCT-ACT
1 AAATTGAT--AATCCTAACT
57284 AAATT
1 AAATT
57289 TATTAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (18 bp):
AAATTGATAATCCTAACT
Found at i:57682 original size:12 final size:12
Alignment explanation
Indices: 57644--57683 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
57634 ATACTACAAA
57644 TTAATATATGAT
1 TTAATATATGAT
* *
57656 TTATTATATTTAT
1 TTAATATA-TGAT
57669 TTAATATATGAT
1 TTAATATATGAT
57681 TTA
1 TTA
57684 TAAATTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (12 bp):
TTAATATATGAT
Found at i:59386 original size:2 final size:2
Alignment explanation
Indices: 59379--59407 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59369 AAATTTAACT
59379 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
59408 TTCACCCGTA
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
Done.