Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024114.1 Corchorus olitorius cultivar O-4 contig24147, 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: 60333
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1070 original size:15 final size:15
Alignment explanation
Indices: 1050--1079 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1040 ATCAGGCTGC
*
1050 CACGATACACGATAT
1 CACGATACACAATAT
1065 CACGATACACAATAT
1 CACGATACACAATAT
1080 TTCAACCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:3227 original size:75 final size:75
Alignment explanation
Indices: 3141--3303 Score: 186
Period size: 75 Copynumber: 2.2 Consensus size: 75
3131 ATGATGATTT
* * * *
3141 GCAACAACTTGAAGCTGATTCACTTTATCAGG-TTTCTGATTCGAATT-TAAATTTTGAGCATCA
1 GCAACATCTTGAAGCTGATTCACCTAATCAGGATGT-TGATTCGAATTCT-AATTTTGAGCATCA
* *
3204 TAATGATGATAG
64 CAATGACGATAG
* * * * *
3216 GCAGCATCTTGAAGCTGATTCTCCTAATCAGGATGTTGTTTCGAATTCTAATTTTGAGCTTCCCA
1 GCAACATCTTGAAGCTGATTCACCTAATCAGGATGTTGATTCGAATTCTAATTTTGAGCATCACA
3281 ATGACGATAG
66 ATGACGATAG
*
3291 GCAACATTTTGAA
1 GCAACATCTTGAA
3304 AATGTTATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
75 70 0.96
76 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (75 bp):
GCAACATCTTGAAGCTGATTCACCTAATCAGGATGTTGATTCGAATTCTAATTTTGAGCATCACA
ATGACGATAG
Found at i:3821 original size:23 final size:23
Alignment explanation
Indices: 3795--3838 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3785 TGGAGGAAGA
3795 GGGTTAGTGGTGACTGTTTTGAT
1 GGGTTAGTGGTGACTGTTTTGAT
3818 GGGTTAGTGGTGACTGTTTTG
1 GGGTTAGTGGTGACTGTTTTG
3839 GTGCATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.05, G:0.41, T:0.43
Consensus pattern (23 bp):
GGGTTAGTGGTGACTGTTTTGAT
Found at i:16227 original size:17 final size:16
Alignment explanation
Indices: 16205--16256 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 16
16195 TTTCTTGCCC
16205 TTATTTTTTTATTTTT
1 TTATTTTTTTATTTTT
16221 GTTATTTTTCTT-TTTCTT
1 -TTATTTTT-TTATTT-TT
16239 TTATTTCTGTTTATTTTT
1 TTATTT-T-TTTATTTTT
16257 CTTAGTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
17 17 0.57
18 9 0.30
19 4 0.13
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.81
Consensus pattern (16 bp):
TTATTTTTTTATTTTT
Found at i:17424 original size:21 final size:21
Alignment explanation
Indices: 17385--17433 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
17375 TCAATGCTTT
**
17385 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
17407 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
17428 A-GAAGC
1 AGGAAGC
17434 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:17908 original size:16 final size:17
Alignment explanation
Indices: 17877--17910 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17867 ACCTTTTCCA
*
17877 TCAAATTCATCAAGTTT
1 TCAAATTCAGCAAGTTT
17894 TCAAATT-AGCAAGTTT
1 TCAAATTCAGCAAGTTT
17910 T
1 T
17911 GGAGAAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (17 bp):
TCAAATTCAGCAAGTTT
Found at i:20241 original size:26 final size:25
Alignment explanation
Indices: 20199--20247 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
20189 TGTCCCTCTG
*
20199 AAAAAAAAAGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGAGTTAGTAACCTC
*
20224 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAA-AAAAAGAGAGTTAGTAACC
20248 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.53, C:0.10, G:0.20, T:0.16
Consensus pattern (25 bp):
AAAAAAAAAGAGAGTTAGTAACCTC
Found at i:23038 original size:65 final size:65
Alignment explanation
Indices: 22934--23065 Score: 230
Period size: 65 Copynumber: 2.0 Consensus size: 65
22924 CATATTTTCT
22934 TTTTTTAATGTTTAGTAACAAGGAAGAAAATTAGAAGAAA-TGAAAAAACTAATAATTTAATTCC
1 TTTTTTAATGTTTAGTAACAAGGAAGAAAATTAGAAGAAAGT-AAAAAACTAATAATTTAATTCC
22998 A
65 A
* *
22999 TTTTTTAATGTTTAGTAACAAGGAAGGAAATTAGAAGAAAGTAAAAAACTAATACTTTAATTCCA
1 TTTTTTAATGTTTAGTAACAAGGAAGAAAATTAGAAGAAAGTAAAAAACTAATAATTTAATTCCA
23064 TT
1 TT
23066 GTTTGGTAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 63 0.98
66 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (65 bp):
TTTTTTAATGTTTAGTAACAAGGAAGAAAATTAGAAGAAAGTAAAAAACTAATAATTTAATTCCA
Found at i:25926 original size:11 final size:11
Alignment explanation
Indices: 25912--25965 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
25902 TTCGTTATTA
25912 TTCGTTTATAG
1 TTCGTTTATAG
25923 TTCGTTTAATAG
1 TTCGTTT-ATAG
* *
25935 ATCGTTTATAA
1 TTCGTTTATAG
*
25946 CTCGTTTAT-G
1 TTCGTTTATAG
*
25956 TTCTTTTATA
1 TTCGTTTATA
25966 TTATATATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 7 0.20
11 18 0.51
12 10 0.29
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (11 bp):
TTCGTTTATAG
Found at i:25974 original size:7 final size:7
Alignment explanation
Indices: 25962--26004 Score: 56
Period size: 6 Copynumber: 6.6 Consensus size: 7
25952 TATGTTCTTT
25962 TATATTA
1 TATATTA
25969 TATATTA
1 TATATTA
25976 TATATTA
1 TATATTA
25983 TA-ATTA
1 TATATTA
*
25989 TAT-TTT
1 TATATTA
25995 TAT-TTA
1 TATATTA
26001 TATA
1 TATA
26005 AATATTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 16 0.50
7 16 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATATTA
Found at i:33913 original size:28 final size:28
Alignment explanation
Indices: 33842--33909 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
33832 ACAATGGGCC
33842 TTAGTAATTAATTATTGGTTTATTATTCA
1 TTAGTAA-TAATTATTGGTTTATTATTCA
* * *
33871 CATA-AAAAAATTATTGGTTTATTA-TCA
1 -TTAGTAATAATTATTGGTTTATTATTCA
33898 TTAGTAATAATT
1 TTAGTAATAATT
33910 TATTACAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 2 0.06
27 9 0.29
28 16 0.52
29 2 0.06
30 2 0.06
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (28 bp):
TTAGTAATAATTATTGGTTTATTATTCA
Found at i:35665 original size:2 final size:2
Alignment explanation
Indices: 35660--35690 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35650 TATGTTATTG
35660 AT 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 A
35691 AGCAATTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36739 original size:34 final size:34
Alignment explanation
Indices: 36696--36760 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
36686 TTTTCAACTT
36696 ATATATAACATATATTAAAGTTGAAAATGTAGTA
1 ATATATAACATATATTAAAGTTGAAAATGTAGTA
36730 ATATATAACATATATTAAAGTTGAAAATGTA
1 ATATATAACATATATTAAAGTTGAAAATGTA
36761 ATTACCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (34 bp):
ATATATAACATATATTAAAGTTGAAAATGTAGTA
Found at i:43784 original size:35 final size:34
Alignment explanation
Indices: 43738--43808 Score: 133
Period size: 35 Copynumber: 2.1 Consensus size: 34
43728 TCCTCGGATT
43738 AATTTTGACAAACCTATTCATCAGAAAGAAAAAAA
1 AATTTTGACAAACCTATTCATCAGAAA-AAAAAAA
43773 AATTTTGACAAACCTATTCATCAGAAAAAAAAAA
1 AATTTTGACAAACCTATTCATCAGAAAAAAAAAA
43807 AA
1 AA
43809 GAAAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 9 0.25
35 27 0.75
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.23
Consensus pattern (34 bp):
AATTTTGACAAACCTATTCATCAGAAAAAAAAAA
Found at i:44557 original size:15 final size:15
Alignment explanation
Indices: 44537--44568 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
44527 CATATGGCCC
44537 ATGTGGCTTTAATGA
1 ATGTGGCTTTAATGA
44552 ATGTGGCTTTAATGA
1 ATGTGGCTTTAATGA
44567 AT
1 AT
44569 TTAATGGCCA
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:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (15 bp):
ATGTGGCTTTAATGA
Found at i:45024 original size:71 final size:72
Alignment explanation
Indices: 44944--45076 Score: 250
Period size: 72 Copynumber: 1.9 Consensus size: 72
44934 TGAGAAATAA
44944 GGGCAACAAATTGGGTTTCTTT-GGGTTTGATTTCTTGGTGATCCAAAGAGGTAAATCCTTGAGA
1 GGGCAACAAATTGGGTTTCTTTGGGGTTTGATTTCTTGGTGATCCAAAGAGGTAAATCCTTGAGA
45008 GATAAGT
66 GATAAGT
*
45015 GGGCAACAAATTGGGTTTCTTTGGGGTTTGATTTCTTGGTGATGCAAAGAGGTAAATCCTTG
1 GGGCAACAAATTGGGTTTCTTTGGGGTTTGATTTCTTGGTGATCCAAAGAGGTAAATCCTTG
45077 TATTTTAGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
71 22 0.37
72 38 0.63
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (72 bp):
GGGCAACAAATTGGGTTTCTTTGGGGTTTGATTTCTTGGTGATCCAAAGAGGTAAATCCTTGAGA
GATAAGT
Found at i:48532 original size:19 final size:19
Alignment explanation
Indices: 48508--48544 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
48498 TTCTCTTGCT
48508 CTATGTTGATGATATGTTA
1 CTATGTTGATGATATGTTA
48527 CTATGTTGATGATATGTT
1 CTATGTTGATGATATGTT
48545 GATTGTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (19 bp):
CTATGTTGATGATATGTTA
Found at i:52362 original size:28 final size:29
Alignment explanation
Indices: 52298--52368 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
52288 GCCATGTCGT
* *
52298 CCTGCCACGCCATTCGTTGACCGAGTCAA
1 CCTGCCACGTCATTCCTTGACCGAGTCAA
52327 CCTGCCACGTCATTCCTTGACCG-GTCAA
1 CCTGCCACGTCATTCCTTGACCGAGTCAA
52355 CCTGCCACGTCATT
1 CCTGCCACGTCATT
52369 TTGCCACATC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 19 0.47
29 21 0.52
ACGTcount: A:0.18, C:0.39, G:0.18, T:0.24
Consensus pattern (29 bp):
CCTGCCACGTCATTCCTTGACCGAGTCAA
Found at i:52666 original size:18 final size:18
Alignment explanation
Indices: 52641--52684 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
52631 CCTGCTTTCT
52641 TCCTGTTTGACCTCTT-GG
1 TCCTGTTTGACCT-TTCGG
*
52659 TTCTGTTTGACCTTTCGG
1 TCCTGTTTGACCTTTCGG
52677 TCCTGTTT
1 TCCTGTTT
52685 CTGCATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.05, C:0.25, G:0.20, T:0.50
Consensus pattern (18 bp):
TCCTGTTTGACCTTTCGG
Found at i:52713 original size:18 final size:18
Alignment explanation
Indices: 52690--52777 Score: 77
Period size: 18 Copynumber: 5.3 Consensus size: 18
52680 TGTTTCTGCA
52690 TGTTTGACCTCTTGGTCC
1 TGTTTGACCTCTTGGTCC
52708 TGTTTGACC-CTTTGGTCC
1 TGTTTGACCTC-TTGGTCC
*
52726 TGTTT----TC-T-G-CT
1 TGTTTGACCTCTTGGTCC
52737 TGTTTGACCTCTTGGTCC
1 TGTTTGACCTCTTGGTCC
*
52755 TGTTTGACAT-TTCGGTCC
1 TGTTTGACCTCTT-GGTCC
52773 TGTTT
1 TGTTT
52778 TCTGCCTGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
11 6 0.11
12 1 0.02
13 1 0.02
15 3 0.05
16 1 0.02
17 4 0.07
18 41 0.72
ACGTcount: A:0.06, C:0.24, G:0.22, T:0.49
Consensus pattern (18 bp):
TGTTTGACCTCTTGGTCC
Found at i:52720 original size:47 final size:47
Alignment explanation
Indices: 52617--52806 Score: 251
Period size: 47 Copynumber: 4.1 Consensus size: 47
52607 ATTCCGTTTT
* * * * *
52617 TTTGACATTTCGATCCTGCTTTCTTCCTGTTTGACCTCTTGGTTCTG
1 TTTGACCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCTG
*
52664 TTTGACCTTTCGGTCCTG-TTTCTGCATGTTTGACCTCTTGGTCCTG
1 TTTGACCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCTG
*
52710 TTTGACCCTTT-GGTCCTGTTTTCTGCTTGTTTGACCTCTTGGTCCTG
1 TTTGA-CCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCTG
* * *
52757 TTTGACATTTCGGTCCTGTTTTCTGCCTGATTGACCT-TCCGGTCCTG
1 TTTGACCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTCT-TGGTCCTG
52804 TTT
1 TTT
52807 TTAGCCCTTG
Statistics
Matches: 129, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
46 42 0.33
47 87 0.67
ACGTcount: A:0.07, C:0.26, G:0.20, T:0.47
Consensus pattern (47 bp):
TTTGACCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTCTTGGTCCTG
Found at i:52776 original size:93 final size:94
Alignment explanation
Indices: 52630--52806 Score: 259
Period size: 93 Copynumber: 1.9 Consensus size: 94
52620 GACATTTCGA
* * * *
52630 TCCTGCTTTCTTCCTGTTTGACCTCTTGGTTCTGTTTGACCTTTCGGTCCTG-TTTCTGCATGTT
1 TCCTGCTTTCTGCCTGTTTGACCTCTTGGTCCTGTTTGACATTTCGGTCCTGTTTTCTGCATGAT
*
52694 TGACC-TCTTGGTCCTGTTTGACCCTTTGG
66 TGACCTTC-CGGTCCTGTTTGACCCTTTGG
* * *
52723 TCCTGTTTTCTGCTTGTTTGACCTCTTGGTCCTGTTTGACATTTCGGTCCTGTTTTCTGCCTGAT
1 TCCTGCTTTCTGCCTGTTTGACCTCTTGGTCCTGTTTGACATTTCGGTCCTGTTTTCTGCATGAT
52788 TGACCTTCCGGTCCTGTTT
66 TGACCTTCCGGTCCTGTTT
52807 TTAGCCCTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
93 47 0.64
94 25 0.34
95 2 0.03
ACGTcount: A:0.06, C:0.27, G:0.20, T:0.47
Consensus pattern (94 bp):
TCCTGCTTTCTGCCTGTTTGACCTCTTGGTCCTGTTTGACATTTCGGTCCTGTTTTCTGCATGAT
TGACCTTCCGGTCCTGTTTGACCCTTTGG
Done.