Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007169.1 Corchorus capsularis cultivar CVL-1 contig07190, 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: 39499
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1509 original size:13 final size:13
Alignment explanation
Indices: 1491--1535 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1481 AATTATTGTT
1491 TGCTTTATTAATC
1 TGCTTTATTAATC
* *
1504 TGCTTTTTTAATT
1 TGCTTTATTAATC
1517 TGCTTTA-TAATC
1 TGCTTTATTAATC
1529 TGCTTTA
1 TGCTTTA
1536 GATTTAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.58
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:1532 original size:12 final size:12
Alignment explanation
Indices: 1491--1535 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1481 AATTATTGTT
1491 TGCTTTATTAATC
1 TGCTTTA-TAATC
* *
1504 TGCTTTTTTAATT
1 TGC-TTTATAATC
1517 TGCTTTATAATC
1 TGCTTTATAATC
1529 TGCTTTA
1 TGCTTTA
1536 GATTTAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 14 0.52
13 10 0.37
14 3 0.11
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.58
Consensus pattern (12 bp):
TGCTTTATAATC
Found at i:1543 original size:6 final size:6
Alignment explanation
Indices: 1532--1563 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1522 TATAATCTGC
1532 TTTAGA TTTAGA TTTAGA TTTAGA TTT-GA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1564 CCTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:2302 original size:10 final size:9
Alignment explanation
Indices: 2279--2303 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2269 GAAAAATATC
2279 AAAAAAATA
1 AAAAAAATA
2288 AAAAAAATA
1 AAAAAAATA
2297 AAAAAAA
1 AAAAAAA
2304 GATTCGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:9018 original size:12 final size:12
Alignment explanation
Indices: 9001--9025 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8991 CCTGGCAATC
9001 CGTGTTTCGTGT
1 CGTGTTTCGTGT
9013 CGTGTTTCGTGT
1 CGTGTTTCGTGT
9025 C
1 C
9026 ATATTAACGT
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:0.00, C:0.20, G:0.32, T:0.48
Consensus pattern (12 bp):
CGTGTTTCGTGT
Found at i:13988 original size:18 final size:18
Alignment explanation
Indices: 13965--14000 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13955 TTAACAATAT
13965 TTATTGAAAACCAATTTA
1 TTATTGAAAACCAATTTA
13983 TTATTGAAAACCAATTTA
1 TTATTGAAAACCAATTTA
14001 CCCTCAATTG
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:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
TTATTGAAAACCAATTTA
Found at i:14197 original size:3 final size:3
Alignment explanation
Indices: 14189--14235 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
14179 TCTAATCTTA
14189 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
14236 AACCTACTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:18502 original size:32 final size:32
Alignment explanation
Indices: 18463--18617 Score: 202
Period size: 32 Copynumber: 4.8 Consensus size: 32
18453 TCTGAACCTG
18463 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
* * *** *
18495 AATCCGAAAAGATATGAACCCGAAAAAGCTTA
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
* * *
18527 AATCCGAAAAGACACGAACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
* *
18559 AACCCGAAAAAAACCCGAATCCGAAAAACCTCA
1 AACCCG-AAAAAACCCGAACCCGAAAAAGCTCA
18592 AACCCGAAAAAACCCGAACCCGAAAA
1 AACCCGAAAAAACCCGAACCCGAAAA
18618 TTTATGAAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
32 79 0.74
33 28 0.26
ACGTcount: A:0.51, C:0.30, G:0.13, T:0.06
Consensus pattern (32 bp):
AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
Found at i:18585 original size:15 final size:15
Alignment explanation
Indices: 18457--18617 Score: 88
Period size: 16 Copynumber: 10.1 Consensus size: 15
18447 AACCCGTCTG
*
18457 AACCTGAACCCGAAAA
1 AACCCGAACCCG-AAA
18473 AACCCGAACCCGAAA
1 AACCCGAACCCGAAA
* * *
18488 AAGCTCAAATCCGAAA
1 AA-CCCGAACCCGAAA
***
18504 AGATATGAACCCGAAA
1 A-ACCCGAACCCGAAA
*** *
18520 AAGCTTAAATCCGAAA
1 AA-CCCGAACCCGAAA
*
18536 AGACACGAACCCGAAA
1 A-ACCCGAACCCGAAA
* *
18552 AAGCTCAAACCCGAAAAA
1 AA-CCCGAACCCG--AAA
*
18570 AACCCGAATCCGAAA
1 AACCCGAACCCGAAA
*
18585 AACCTCAAACCCGAAAA
1 AACC-CGAACCCG-AAA
18602 AACCCGAACCCGAAA
1 AACCCGAACCCGAAA
18617 A
1 A
18618 TTTATGAAAA
Statistics
Matches: 111, Mismatches: 25, Indels: 19
0.72 0.16 0.12
Matches are distributed among these distances:
15 18 0.16
16 72 0.65
17 16 0.14
18 5 0.05
ACGTcount: A:0.50, C:0.30, G:0.13, T:0.07
Consensus pattern (15 bp):
AACCCGAACCCGAAA
Found at i:18790 original size:32 final size:32
Alignment explanation
Indices: 18754--18841 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
18744 ATCTGGCCAA
* *
18754 AACCCAAACAGAATCCGAACCCGAATTAACCT
1 AACCCAAACACAACCCGAACCCGAATTAACCT
**
18786 AACCCAAATTCAACCCGAACCCGAATTAACCT
1 AACCCAAACACAACCCGAACCCGAATTAACCT
*
18818 GACCCAAATC-CAACCCGAACCCGA
1 AACCCAAA-CACAACCCGAACCCGA
18842 CTCAAGCCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.41, C:0.39, G:0.09, T:0.11
Consensus pattern (32 bp):
AACCCAAACACAACCCGAACCCGAATTAACCT
Found at i:18795 original size:15 final size:15
Alignment explanation
Indices: 18771--18826 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
18761 ACAGAATCCG
*
18771 AACCCGAATTAACCT
1 AACCCAAATTAACCT
*
18786 AACCCAAATTCAACCCG
1 AACCCAAATT-AA-CCT
*
18803 AACCCGAATTAACCT
1 AACCCAAATTAACCT
*
18818 GACCCAAAT
1 AACCCAAAT
18827 CCAACCCGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 18 0.55
16 4 0.12
17 11 0.33
ACGTcount: A:0.41, C:0.36, G:0.07, T:0.16
Consensus pattern (15 bp):
AACCCAAATTAACCT
Found at i:18812 original size:17 final size:17
Alignment explanation
Indices: 18768--18859 Score: 86
Period size: 17 Copynumber: 5.6 Consensus size: 17
18758 CAAACAGAAT
18768 CCGAACCCGAATT-AA-
1 CCGAACCCGAATTCAAC
* *
18783 CCTAACCCAAATTCAAC
1 CCGAACCCGAATTCAAC
18800 CCGAACCCGAATT-AAC
1 CCGAACCCGAATTCAAC
* * *
18816 CTG-ACCCAAATCCAAC
1 CCGAACCCGAATTCAAC
*
18832 CCGAACCCG-ACTCAAGC
1 CCGAACCCGAATTCAA-C
18849 CCGAACCCGAA
1 CCGAACCCGAA
18860 AATGGTCCTA
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
15 18 0.30
16 16 0.27
17 25 0.42
18 1 0.02
ACGTcount: A:0.37, C:0.41, G:0.11, T:0.11
Consensus pattern (17 bp):
CCGAACCCGAATTCAAC
Found at i:19365 original size:15 final size:15
Alignment explanation
Indices: 19345--19375 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19335 CAATAAAGCT
19345 ATAAAACGTTTCTGC
1 ATAAAACGTTTCTGC
19360 ATAAAACGTTTCTGC
1 ATAAAACGTTTCTGC
19375 A
1 A
19376 AGTTTCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (15 bp):
ATAAAACGTTTCTGC
Found at i:20690 original size:22 final size:22
Alignment explanation
Indices: 20664--20710 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
20654 TGGAAGAAAG
20664 TCAATATGAACCACTATCAGAA
1 TCAATATGAACCACTATCAGAA
20686 TCAATATGAACCACTATCAGAA
1 TCAATATGAACCACTATCAGAA
20708 TCA
1 TCA
20711 TTGCAGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (22 bp):
TCAATATGAACCACTATCAGAA
Found at i:21833 original size:57 final size:58
Alignment explanation
Indices: 21772--21897 Score: 202
Period size: 57 Copynumber: 2.2 Consensus size: 58
21762 TAATATATAG
*
21772 AAGTATAGTAATTAGTAACTTTAATCAAAT-TCGAAGTC-TTTTTTTTAATCAAATCAA
1 AAGTATAGTAATTAGTAACTTTAATCAAATCT-AAAGTCTTTTTTTTTAATCAAATCAA
*
21829 AAGTATAGTAATTAGTAACTTTAATCAAATCTAAAGTCTTTTTTTTTAATCAAATCCA
1 AAGTATAGTAATTAGTAACTTTAATCAAATCTAAAGTCTTTTTTTTTAATCAAATCAA
*
21887 AAGTCTAGTAA
1 AAGTATAGTAA
21898 ATTTAATCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
57 35 0.55
58 29 0.45
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (58 bp):
AAGTATAGTAATTAGTAACTTTAATCAAATCTAAAGTCTTTTTTTTTAATCAAATCAA
Found at i:21909 original size:26 final size:26
Alignment explanation
Indices: 21841--21914 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 26
21831 GTATAGTAAT
* *
21841 TAGTAACTTTAATCAAATCTAAAGTC
1 TAGTAAATTTAATCAAATCCAAAGTC
* ***
21867 T-TTTTTTTTAATCAAATCCAAAGTC
1 TAGTAAATTTAATCAAATCCAAAGTC
*
21892 TAGTAAATTTAATCAAATTCAAA
1 TAGTAAATTTAATCAAATCCAAA
21915 TTCCAAATTA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 20 0.54
26 17 0.46
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (26 bp):
TAGTAAATTTAATCAAATCCAAAGTC
Found at i:21914 original size:57 final size:56
Alignment explanation
Indices: 21772--21915 Score: 150
Period size: 57 Copynumber: 2.5 Consensus size: 56
21762 TAATATATAG
** *
21772 AAGTATAGTAATTAGTAACTTTAATCAAAT-TCGAAGTCTTTTTTTTAATCAAATCAA
1 AAGTATAGTAATTA-TAACTCAAATCAAATCT-AAAGTCTTTTTTTTAATCAAATCAA
** *
21829 AAGTATAGTAATTAGTAACTTTAATCAAATCTAAAGTCTTTTTTTTTAATCAAATCCA
1 AAGTATAGTAATTA-TAACTCAAATCAAATCTAAAGTC-TTTTTTTTAATCAAATCAA
*
21887 AAGTCTAGTAAATT-TAA-TCAAATTCAAAT
1 AAGTATAGT-AATTATAACTCAAA-TCAAAT
21916 TCCAAATTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
56 3 0.04
57 44 0.56
58 27 0.35
59 4 0.05
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (56 bp):
AAGTATAGTAATTATAACTCAAATCAAATCTAAAGTCTTTTTTTTAATCAAATCAA
Found at i:22063 original size:6 final size:6
Alignment explanation
Indices: 22046--22084 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
22036 GTACTTTTTA
22046 ATATAG -TATAG ATATAG --ATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
22085 CTACGTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.13
5 5 0.17
6 21 0.70
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:22068 original size:10 final size:10
Alignment explanation
Indices: 22046--22075 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
22036 GTACTTTTTA
22046 ATATAGTATAG
1 ATATAG-ATAG
22057 ATATAGATAG
1 ATATAGATAG
22067 ATATAGATA
1 ATATAGATA
22076 TAGATATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (10 bp):
ATATAGATAG
Found at i:22073 original size:16 final size:15
Alignment explanation
Indices: 22048--22081 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
22038 ACTTTTTAAT
22048 ATAGTATAGATATAG
1 ATAGTATAGATATAG
22063 ATAGATATAGATATAG
1 ATAG-TATAGATATAG
22079 ATA
1 ATA
22082 TAGCTACGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (15 bp):
ATAGTATAGATATAG
Found at i:27456 original size:63 final size:63
Alignment explanation
Indices: 27355--27481 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
27345 AGCCTTAGTC
27355 TGTATGGTCTAAAGATTAACAAAGGTTGCTTTCAGTTTCTAGCATTCTTTGATCACATTAAAA
1 TGTATGGTCTAAAGATTAACAAAGGTTGCTTTCAGTTTCTAGCATTCTTTGATCACATTAAAA
*
27418 TGTATGGTCTAAAGATTAACAAAGGTTGCTTTCGGTTTCTAGCATTCTTTGATCACATTAAAA
1 TGTATGGTCTAAAGATTAACAAAGGTTGCTTTCAGTTTCTAGCATTCTTTGATCACATTAAAA
27481 T
1 T
27482 TTATTCCAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (63 bp):
TGTATGGTCTAAAGATTAACAAAGGTTGCTTTCAGTTTCTAGCATTCTTTGATCACATTAAAA
Found at i:29511 original size:42 final size:42
Alignment explanation
Indices: 29452--29546 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
29442 ATCATGCCCC
* * *
29452 TATACTGACGGTTACTAGCACATGGTCAGGATAGTATTAGTA
1 TATACTGACGGATACTAGCACATGGTCAGAATAGTATCAGTA
*
29494 TATACTGACGGATACTAGCACATGGTCAGAATAGTATCAGTG
1 TATACTGACGGATACTAGCACATGGTCAGAATAGTATCAGTA
29536 TATACTGACGG
1 TATACTGACGG
29547 GTATAAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (42 bp):
TATACTGACGGATACTAGCACATGGTCAGAATAGTATCAGTA
Found at i:30122 original size:54 final size:54
Alignment explanation
Indices: 30032--30165 Score: 214
Period size: 54 Copynumber: 2.5 Consensus size: 54
30022 AACCACTCCA
* * *
30032 AACAGTGCCAACATTAAATGAAGGAGCGCACGTGATGGTGATAAGGACGATGTG
1 AACAGTGCCAACATTAAATGAAGGAGCGCACATGATGATGATAAAGACGATGTG
*
30086 AACAATGCCAACATTAAATGAAGGAGCGCACATGATGATGATAAAGACGATGTG
1 AACAGTGCCAACATTAAATGAAGGAGCGCACATGATGATGATAAAGACGATGTG
* *
30140 AATAGTGTCAACATTAAATGAAGGAG
1 AACAGTGCCAACATTAAATGAAGGAG
30166 TGCGTGAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 73 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.19
Consensus pattern (54 bp):
AACAGTGCCAACATTAAATGAAGGAGCGCACATGATGATGATAAAGACGATGTG
Found at i:36467 original size:17 final size:17
Alignment explanation
Indices: 36445--36479 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
36435 AAAGACTAAG
36445 CTGAAAATCTGAGAAAC
1 CTGAAAATCTGAGAAAC
36462 CTGAAAATCTGAGAAAC
1 CTGAAAATCTGAGAAAC
36479 C
1 C
36480 AAAACATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (17 bp):
CTGAAAATCTGAGAAAC
Done.