Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012972.1 Corchorus olitorius cultivar O-4 contig13005, 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: 31784
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:4175 original size:25 final size:25
Alignment explanation
Indices: 4147--4215 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
4137 TGTCTATGAA
*
4147 TTTGGATGATATGATTCCTTTTTCT
1 TTTGGATGATATGGTTCCTTTTTCT
* *
4172 TTTGGATGATATGGTTACTTTTTTT
1 TTTGGATGATATGGTTCCTTTTTCT
4197 TTTGGATGATATGGTTCCT
1 TTTGGATGATATGGTTCCT
4216 ATAGCTTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (25 bp):
TTTGGATGATATGGTTCCTTTTTCT
Found at i:5299 original size:19 final size:19
Alignment explanation
Indices: 5275--5320 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5265 CAGATTGATC
5275 AGAGAGGAA-GAATAGAGAA
1 AGAGAGGAAGGAA-AGAGAA
* *
5294 AGAGA-GAAGGAACGGGAA
1 AGAGAGGAAGGAAAGAGAA
5312 AGAGAGGAA
1 AGAGAGGAA
5321 CTGGGATCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.54, C:0.02, G:0.41, T:0.02
Consensus pattern (19 bp):
AGAGAGGAAGGAAAGAGAA
Found at i:10075 original size:74 final size:73
Alignment explanation
Indices: 9946--10089 Score: 166
Period size: 74 Copynumber: 2.0 Consensus size: 73
9936 ATCTAGACTA
* * * **
9946 TGAGCAAAAGAATGATGAGTTTTAATCAAAATCTTCAAAAATCAGTTTTATTCAAAGCTTTGATT
1 TGAGCAAAAGAATGACGAGTTTTAATCAAAATCTTCAAAAATCAGTTTTAGTCAAAACAATGATT
10011 TCGAGTTG
66 TCGAGTTG
* * * *
10019 TGAGTAAAAGAATGACG-GTTTTAATCAAAAGGTGTTTC-ATAATCAGTTTTGGTCAAAACAATG
1 TGAGCAAAAGAATGACGAGTTTTAATCAAAA--T-CTTCAAAAATCAGTTTTAGTCAAAACAATG
10082 ATTTCGAG
63 ATTTCGAG
10090 GTGACTGAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
72 13 0.22
73 15 0.25
74 28 0.47
75 3 0.05
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (73 bp):
TGAGCAAAAGAATGACGAGTTTTAATCAAAATCTTCAAAAATCAGTTTTAGTCAAAACAATGATT
TCGAGTTG
Found at i:10509 original size:15 final size:15
Alignment explanation
Indices: 10489--10552 Score: 67
Period size: 15 Copynumber: 4.2 Consensus size: 15
10479 TCCCAATATA
*
10489 AAAAAAAATCAAAAT
1 AAAAAAAATGAAAAT
10504 AAAAAAAGAATGAAAAT
1 -AAAAAA-AATGAAAAT
**
10521 TGAAAAAATGAAAAT
1 AAAAAAAATGAAAAT
*
10536 GAAAAAAA-GAAAAT
1 AAAAAAAATGAAAAT
10550 AAA
1 AAA
10553 GGCACTTGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 8 0.20
15 15 0.37
16 10 0.24
17 8 0.20
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAAAAATGAAAAT
Found at i:10510 original size:17 final size:18
Alignment explanation
Indices: 10483--10520 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
10473 ATGATTTCCC
10483 AATATAAAAAAAAATCAA
1 AATATAAAAAAAAATCAA
* *
10501 AATA-AAAAAAGAATGAA
1 AATATAAAAAAAAATCAA
10518 AAT
1 AAT
10521 TGAAAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (18 bp):
AATATAAAAAAAAATCAA
Found at i:10540 original size:14 final size:14
Alignment explanation
Indices: 10507--10549 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
10497 TCAAAATAAA
10507 AAAAGAATGAAAATTG
1 AAAA-AATGAAAA-TG
10523 AAAAAATGAAAATG
1 AAAAAATGAAAATG
*
10537 AAAAAAAGAAAAT
1 AAAAAATGAAAAT
10550 AAAGGCACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.54
15 8 0.31
16 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAAATGAAAATG
Found at i:11019 original size:29 final size:28
Alignment explanation
Indices: 10930--11021 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
10920 AGAAATTCCA
10930 AAAAAAAAAG-AAAATCAAAAATC-AAAC
1 AAAAAAAAAGTAAAATC-AAAATCAAAAC
** *
10957 AAACGAAAAAAGTAAAAAAAAAATCAATCAC
1 AAA--AAAAAAGTAAAATCAAAATCAA-AAC
*
10988 AAAAAAAAAGTCAAATCAAAATCAAAATC
1 AAAAAAAAAGTAAAATCAAAATCAAAA-C
11017 AAAAA
1 AAAAA
11022 GGGAATTGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
27 3 0.06
28 1 0.02
29 38 0.73
30 5 0.10
31 5 0.10
ACGTcount: A:0.74, C:0.12, G:0.04, T:0.10
Consensus pattern (28 bp):
AAAAAAAAAGTAAAATCAAAATCAAAAC
Found at i:11706 original size:50 final size:50
Alignment explanation
Indices: 11631--11826 Score: 304
Period size: 50 Copynumber: 3.9 Consensus size: 50
11621 TTACAATAAG
*
11631 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
1 ATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
*
11681 ATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAA
1 ATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
* * **
11731 ATTGCTTTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAGG
1 ATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
* *
11781 ATTGCATTT-CATTTGTGAGTCCAAGATTAAAATTTGCTTTTCAAAG
1 ATTGC-TTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
11827 GGCATTTAAG
Statistics
Matches: 136, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
50 133 0.98
51 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (50 bp):
ATTGCTTTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
Found at i:12632 original size:69 final size:68
Alignment explanation
Indices: 12556--12972 Score: 559
Period size: 69 Copynumber: 6.0 Consensus size: 68
12546 TCTTCTAAGA
**
12556 CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCACGGGCTTTTCCA
1 CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-CATAGGCTTTTCCA
*
12621 CAAA
65 CAAG
* * * *
12625 CCAAACTCATTTCCATACAAGTGAGTTTAAGCCTTGGTTCCATCCAAGGCACATAGGCTTTTCCA
1 CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAA-GCACATAGGCTTTTCCA
12690 CAAG
65 CAAG
*
12694 CCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCGACATAGGCTTTTCCA
1 CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC-ACATAGGCTTTTCCA
12759 CAAG
65 CAAG
* *
12763 CCAAACTCGTTTCCATACGAGTCAATTTAAGCCTTGGTTCCATCCAAGTCACATAGGCTTTTCCA
1 CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG-CACATAGGCTTTTCCA
12828 CAAG
65 CAAG
* * * *
12832 CCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTTCATCCAAGCCATATAGACTTTTCCA
1 CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG-CACATAGGCTTTTCCA
*
12897 TAAG
65 CAAG
* * * * *
12901 TCAAACTCGTTTCCATGCGAGTCAGTTTCAA-CATTGGGTCCATCCATA-CAGCAGAGGCTTTTC
1 CCAAACTCGTTTCCATACGAGTCAG-TTCAAGCCTTGGTTCCATCCA-AGCA-CATAGGCTTTTC
*
12964 CATAAG
63 CACAAG
12970 CCA
1 CCA
12973 TGTTTAATGA
Statistics
Matches: 315, Mismatches: 27, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
68 4 0.01
69 301 0.96
70 10 0.03
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (68 bp):
CCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCACATAGGCTTTTCCAC
AAG
Found at i:12640 original size:105 final size:104
Alignment explanation
Indices: 12453--12641 Score: 297
Period size: 105 Copynumber: 1.8 Consensus size: 104
12443 TTCCATAAGT
* * *
12453 CAAACTCATTTCCATACGGGTCAGTTAAGCCTTGGTTCCATCCAAGCAGCAAGTGCTTTTCCATA
1 CAAACTCATTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACA
* *
12518 AGCCAAATTCATCTCCATATAAATTCAGTCTTCTAAGAC
66 AACCAAACTCATCTCCATATAAATTCAGTCTTCTAAGAC
* *
12557 CAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCACGGGCTTTTCCAC
1 CAAACTCATTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCAC
*
12622 AAACCAAACTCATTTCCATA
65 AAACCAAACTCATCTCCATA
12642 CAAGTGAGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
104 24 0.32
105 52 0.68
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (104 bp):
CAAACTCATTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACA
AACCAAACTCATCTCCATATAAATTCAGTCTTCTAAGAC
Found at i:15845 original size:7 final size:7
Alignment explanation
Indices: 15833--15874 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
15823 CACACACAAA
15833 AAAAAAG
1 AAAAAAG
15840 AAAAAAG
1 AAAAAAG
15847 AAAAAAG
1 AAAAAAG
15854 AAAAAAG
1 AAAAAAG
*
15861 AAGAAAG
1 AAAAAAG
15868 CAAAAAA
1 -AAAAAA
15875 AGATTTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:23405 original size:14 final size:15
Alignment explanation
Indices: 23386--23414 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23376 CAATTAGGAA
23386 AAATAAAT-AACAAG
1 AAATAAATAAACAAG
23400 AAATAAATAAACAAG
1 AAATAAATAAACAAG
23415 GATTGGACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATAAATAAACAAG
Found at i:25032 original size:16 final size:15
Alignment explanation
Indices: 24994--25035 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
24984 ACAGAGATTG
*
24994 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
25009 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
25024 ACTAGAAAACAA
1 AC-AGAAAACAA
25036 AGCAAAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.