Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009376.1 Corchorus capsularis cultivar CVL-1 contig09397, 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: 41867
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4347 original size:31 final size:32
Alignment explanation
Indices: 4300--4363 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
4290 GTAAAAGAAA
* *
4300 ATTGGAATGCGCAAATTATCCTCAAGACTTAT
1 ATTGGAATGCCCAAATTACCCTCAAGACTTAT
* *
4332 ATTGG-ATGCCCAAATTACCCTCGAGGCTTAT
1 ATTGGAATGCCCAAATTACCCTCAAGACTTAT
4363 A
1 A
4364 CGAAATAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (32 bp):
ATTGGAATGCCCAAATTACCCTCAAGACTTAT
Found at i:9540 original size:31 final size:31
Alignment explanation
Indices: 9505--9581 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
9495 TTTTTCTGTT
* *
9505 TTTAGCCTCAAATTGAACAACTTTTGAAATG
1 TTTAGACTCAAATTGAACAACTTTTGAAAGG
9536 TTTAGACTCAAATTGAACAACTTTTGAAAGG
1 TTTAGACTCAAATTGAACAACTTTTGAAAGG
9567 TTTAGACTCAAATTG
1 TTTAGACTCAAATTG
9582 GTAATTTGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (31 bp):
TTTAGACTCAAATTGAACAACTTTTGAAAGG
Found at i:15110 original size:51 final size:51
Alignment explanation
Indices: 15046--15145 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
15036 CAGAGGTTCC
15046 TCAATCTATGAAAACGAATTTGAATGAAC-TCCCTCATCTTAACATTGACCT
1 TCAATCTATGAAAACGAATTTGAAT-AACATCCCTCATCTTAACATTGACCT
*
15097 TCAATCTATGAAAATGAATTTGAATAACATCCCTCATCTTAACATTGAC
1 TCAATCTATGAAAACGAATTTGAATAACATCCCTCATCTTAACATTGAC
15146 ATGCTTTTGC
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 3 0.06
51 44 0.94
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (51 bp):
TCAATCTATGAAAACGAATTTGAATAACATCCCTCATCTTAACATTGACCT
Found at i:15328 original size:13 final size:13
Alignment explanation
Indices: 15310--15336 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15300 TTGTGACTGA
15310 TGGATTTTATTTT
1 TGGATTTTATTTT
15323 TGGATTTTATTTT
1 TGGATTTTATTTT
15336 T
1 T
15337 AACACGTGTT
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:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (13 bp):
TGGATTTTATTTT
Found at i:18904 original size:11 final size:11
Alignment explanation
Indices: 18880--18914 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
18870 TTGACAGCGC
18880 AACAAAAACAA
1 AACAAAAACAA
* *
18891 AACGAAAACGA
1 AACAAAAACAA
18902 AACAAAAACAA
1 AACAAAAACAA
18913 AA
1 AA
18915 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:18906 original size:16 final size:16
Alignment explanation
Indices: 18885--18943 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
18875 AGCGCAACAA
18885 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
18901 AAACAAAAACAAAAAAC-
1 AAAC-AAAAC-GAAAACG
*
18918 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
* *
18933 ATACCAAACGA
1 AAACAAAACGA
18944 CCCCTAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 10 0.29
17 7 0.21
18 5 0.15
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:20020 original size:2 final size:2
Alignment explanation
Indices: 20013--20048 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20003 TGACATAATC
20013 AT AT AT AT AT AT AT 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 AT AT AT
20049 TAAAACCGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20998 original size:25 final size:25
Alignment explanation
Indices: 20942--20998 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
20932 TATCAACTAC
*
20942 ATTTTTTATTATTTTTTTTCTCTAA
1 ATTTTTTATTATTTTTTTTATCTAA
*
20967 CTTTTTTATT-TATTTTTTTATC-AA
1 ATTTTTTATTAT-TTTTTTTATCTAA
20991 ATTCTTTT
1 ATT-TTTT
20999 CTTCCCCGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (25 bp):
ATTTTTTATTATTTTTTTTATCTAA
Found at i:22361 original size:15 final size:15
Alignment explanation
Indices: 22341--22385 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
22331 TTTTAGTTTG
22341 TATATTATTCAATTA
1 TATATTATTCAATTA
* *
22356 TATATT-TTTAATTTG
1 TATATTATTCAA-TTA
22371 TATATTATTCAATTA
1 TATATTATTCAATTA
22386 GACAAAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (15 bp):
TATATTATTCAATTA
Found at i:22558 original size:23 final size:22
Alignment explanation
Indices: 22519--22563 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
22509 AATGAGTTCC
* *
22519 TTTATTTTTTTGTTTTTCTAAA
1 TTTATTTGTTTGATTTTCTAAA
*
22541 TTTATTCTGTTTGATTTTTTAAA
1 TTTATT-TGTTTGATTTTCTAAA
22564 AAAGCTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTATTTGTTTGATTTTCTAAA
Found at i:23991 original size:26 final size:26
Alignment explanation
Indices: 23925--23992 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
23915 TACTTAGTTT
*
23925 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGATTAATTAGTATCTA
* *
23951 ATTAGTTTATTATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATCTA
*
23977 ATTAGTTTACGATTAA
1 ATTAGTTTATGATTAA
23993 AATGAAGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATCTA
Found at i:24040 original size:24 final size:25
Alignment explanation
Indices: 24001--24060 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
23991 AAAATGAAGG
*
24001 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
24024 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
24049 GAAATTAAGTTT
1 AAAATGAAGTTT
24061 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:26121 original size:20 final size:17
Alignment explanation
Indices: 26098--26140 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
26088 AACTTAACAA
26098 TTAACTAACTAGGTTTAAC
1 TTAACTAA--AGGTTTAAC
26117 TTTAACT-AAGGTTTAAC
1 -TTAACTAAAGGTTTAAC
26134 TTAACTA
1 TTAACTA
26141 CTAACTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
19 1 0.05
20 6 0.27
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (17 bp):
TTAACTAAAGGTTTAAC
Found at i:26130 original size:17 final size:16
Alignment explanation
Indices: 26098--26140 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
26088 AACTTAACAA
26098 TTAAC-TAACT-AGGT
1 TTAACTTAACTAAGGT
26112 TTAACTTTAACTAAGGT
1 TTAAC-TTAACTAAGGT
26129 TTAACTTAACTA
1 TTAACTTAACTA
26141 CTAACTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.19
16 12 0.46
17 9 0.35
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (16 bp):
TTAACTTAACTAAGGT
Found at i:31033 original size:21 final size:20
Alignment explanation
Indices: 30993--31042 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
30983 TTATATACAG
*
30993 AACTAACTAACTCTATAATT
1 AACTAACTAACTCTACAATT
*
31013 GACTTAACTAACT-TAACAATT
1 AAC-TAACTAACTCT-ACAATT
31034 AACTAACTA
1 AACTAACTA
31043 GGTTTAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (20 bp):
AACTAACTAACTCTACAATT
Found at i:31055 original size:20 final size:17
Alignment explanation
Indices: 31032--31074 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
31022 AACTTAACAA
31032 TTAACTAACTAGGTTTAAC
1 TTAACTAA--AGGTTTAAC
31051 TTTAACT-AAGGTTTAAC
1 -TTAACTAAAGGTTTAAC
31068 TTAACTA
1 TTAACTA
31075 CTAACTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
19 1 0.05
20 6 0.27
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (17 bp):
TTAACTAAAGGTTTAAC
Found at i:31064 original size:17 final size:16
Alignment explanation
Indices: 31032--31074 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
31022 AACTTAACAA
31032 TTAAC-TAACT-AGGT
1 TTAACTTAACTAAGGT
31046 TTAACTTTAACTAAGGT
1 TTAAC-TTAACTAAGGT
31063 TTAACTTAACTA
1 TTAACTTAACTA
31075 CTAACTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.19
16 12 0.46
17 9 0.35
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (16 bp):
TTAACTTAACTAAGGT
Found at i:36935 original size:2 final size:2
Alignment explanation
Indices: 36928--36953 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36918 TGAAAACAAA
36928 AT AT 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
36954 TAAAGCACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.