Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023086.1 Corchorus olitorius cultivar O-4 contig23119, 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: 20592
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1821 original size:22 final size:22
Alignment explanation
Indices: 1793--1873 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
1783 TGTCTATGTG
1793 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
1815 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
1838 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
1859 TGGTTACCAAAATTT
1 TGGTTATCAAAATTT
1874 AATAGGATCA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
22 42 0.91
23 3 0.07
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:2018 original size:22 final size:22
Alignment explanation
Indices: 1993--2107 Score: 73
Period size: 21 Copynumber: 5.4 Consensus size: 22
1983 AGGTTATAAG
1993 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTGTGGTTAACAA
*
2015 AATTT--TA-TGAGGTT-ACTAA
1 AATTTCATAGTGTGGTTAAC-AA
* * * *
2034 TATTTCAT-GGGAGGTTATCAA
1 AATTTCATAGTGTGGTTAACAA
* *
2055 AATTTTATAGTGTGGTTATCCAA
1 AATTTCATAGTGTGGTTA-ACAA
* *
2078 AATTT-TTAGTGTCGG-TATCAA
1 AATTTCATAGTGT-GGTTAACAA
2099 AATTTCATA
1 AATTTCATA
2108 CAAAGGTTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
18 2 0.03
19 12 0.17
20 2 0.03
21 23 0.32
22 23 0.32
23 10 0.14
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTAACAA
Found at i:2028 original size:41 final size:40
Alignment explanation
Indices: 1982--2062 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
1972 ATATCATAGC
* *
1982 GAGGTTA-TAAGAATTTCATAGTGTGGTTAACAAAATTTTAT
1 GAGGTTACTAA-AATTTCAT-GGGAGGTTAACAAAATTTTAT
* *
2023 GAGGTTACTAATATTTCATGGGAGGTTATCAAAATTTTAT
1 GAGGTTACTAAAATTTCATGGGAGGTTAACAAAATTTTAT
2063 AGTGTGGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 18 0.51
41 14 0.40
42 3 0.09
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.40
Consensus pattern (40 bp):
GAGGTTACTAAAATTTCATGGGAGGTTAACAAAATTTTAT
Found at i:2081 original size:23 final size:22
Alignment explanation
Indices: 2046--2103 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 22
2036 TTTCATGGGA
2046 GGTTATCAAAATTTTATAGTGT-
1 GGTTATCAAAATTTT-TAGTGTC
2068 GGTTATCCAAAATTTTTAGTGTC
1 GGTTAT-CAAAATTTTTAGTGTC
2091 GG-TATCAAAATTT
1 GGTTATCAAAATTT
2104 CATACAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.24
22 15 0.44
23 11 0.32
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (22 bp):
GGTTATCAAAATTTTTAGTGTC
Found at i:2197 original size:22 final size:22
Alignment explanation
Indices: 2146--2377 Score: 127
Period size: 22 Copynumber: 10.5 Consensus size: 22
2136 AGGAGTGCCA
*
2146 AAAATTTGATAGAAG-G-TTATC
1 AAAATTTCATAG-AGTGATTATC
*
2167 -AAATCTCATAGAGTGATTATC
1 AAAATTTCATAGAGTGATTATC
*
2188 GAAATTTCATAGAGATCGGATTATC
1 AAAATTTCATAGAG-T--GATTATC
*
2213 AAAATTT-ATAG-GAAGATTATC
1 AAAATTTCATAGAG-TGATTATC
* * * *
2234 AAAATTTCAAAGCGAGGTTATC
1 AAAATTTCATAGAGTGATTATC
* *
2256 AAAATTACTTA-ATGTGATTATC
1 AAAATTTCATAGA-GTGATTATC
* * * *
2278 AAAATTTCATAGAGGGGTCAAC
1 AAAATTTCATAGAGTGATTATC
* * * *
2300 AAAATTTTATAGGGAGGTTATC
1 AAAATTTCATAGAGTGATTATC
* * *
2322 AAAATTTCATAAAGAGGTTATC
1 AAAATTTCATAGAGTGATTATC
* * *
2344 AAATTTTCA-AAATGTGATTACC
1 AAAATTTCATAGA-GTGATTATC
*
2366 AAAATTTTATAG
1 AAAATTTCATAG
2378 TGGTATTTCT
Statistics
Matches: 165, Mismatches: 34, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.01
20 10 0.06
21 22 0.13
22 108 0.65
23 6 0.04
24 4 0.02
25 13 0.08
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.33
Consensus pattern (22 bp):
AAAATTTCATAGAGTGATTATC
Found at i:2240 original size:88 final size:86
Alignment explanation
Indices: 2146--2377 Score: 227
Period size: 88 Copynumber: 2.6 Consensus size: 86
2136 AGGAGTGCCA
* *
2146 AAAATTTGATAGAAGGTTATCAAATCT-CATAGA-GTGATTATCGAAATTTCATAGAGATCGGAT
1 AAAATTTCATAGAAGGTTATCAAAT-TACATA-ATGTGATTATCAAAATTTCATAGAG---GGAT
* *
2209 TATCAAAA-TTTATAGGAAGATTATC
61 CAACAAAATTTTATAGGAAGATTATC
* * * *
2234 AAAATTTCAAAGCGAGGTTATCAAAATTACTTAATGTGATTATCAAAATTTCATAGAGGGGTCAA
1 AAAATTTCATAG-AAGGTTATC-AAATTACATAATGTGATTATCAAAATTTCATAGAGGGATCAA
* *
2299 CAAAATTTTATAGGGAGGTTATC
64 CAAAATTTTATAGGAAGATTATC
* * * * *
2322 AAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTACCAAAATTTTATAG
1 AAAATTTCATAGA-AGGTTATCAAA-TTACATAATGTGATTATCAAAATTTCATAG
2378 TGGTATTTCT
Statistics
Matches: 119, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
87 12 0.10
88 68 0.57
89 10 0.08
90 29 0.24
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.33
Consensus pattern (86 bp):
AAAATTTCATAGAAGGTTATCAAATTACATAATGTGATTATCAAAATTTCATAGAGGGATCAACA
AAATTTTATAGGAAGATTATC
Found at i:2720 original size:23 final size:21
Alignment explanation
Indices: 2477--3037 Score: 199
Period size: 22 Copynumber: 25.7 Consensus size: 21
2467 TAAGGAAGAA
* *
2477 TATCAAAATTTCATATGAAGAT
1 TATCAAAATTTCATA-GGAGGT
* *
2499 TATTAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAG--GAGGT
* *
2521 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAGGA-GGT
* **
2543 TATCAAAATTTCATAGTATGCA
1 TATCAAAATTTCATAGGA-GGT
* * *
2565 GATCAAAATTTCGTAGGAAGAT
1 TATCAAAATTTCATAGG-AGGT
* **
2587 TAACAAAATTTCATAATTAGGT
1 TATCAAAATTTCAT-AGGAGGT
* **
2609 CATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATA-GGAGGT
*
2631 TATCAAAA-TT--T-GTA-GT
1 TATCAAAATTTCATAGGAGGT
*
2647 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCAT-AGGAGGT
* * * *
2669 TGTCAAAATTTTATAAGAGATT
1 TATCAAAATTTCATAGGAG-GT
* *
2691 TAACAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATAGG-AGG-T
2714 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAG-GAGGT
* * *
2736 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAG-GAGGT
* * *
2758 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAG-GAGGT
*
2780 TA-CTAACAA-TTCATATGAAGGT
1 TATC-AA-AATTTCATA-GGAGGT
* * * * *
2802 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCAT-AGGAGGT
* * *
2824 AATCAATATATCATATGGAGGT
1 TATCAAAATTTCATA-GGAGGT
** *
2846 TATCAACGTCTT-ATAGTGTTGGT
1 TATCAAAAT-TTCATAG-G-AGGT
* *
2869 TATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCA-TAGGAGGT
*
2891 TATCAAAATTTCATAATGAGGT
1 TATCAAAATTTCAT-AGGAGGT
* *
2913 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATA-GGAGGT
* *
2935 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCAT-AGGAGGT
** **
2957 TAAAAAAAATTT-ATAAAAAGGT
1 T-ATCAAAATTTCAT-AGGAGGT
* * * * *
2979 TCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGA-GGT
* *
3001 TATTAAAATATCATAGGAAGGT
1 TATCAAAATTTCATAGG-AGGT
3023 TATCAAAATTTCATA
1 TATCAAAATTTCATA
3038 AGGAAGTCAT
Statistics
Matches: 392, Mismatches: 109, Indels: 76
0.68 0.19 0.13
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
19 2 0.01
20 1 0.00
21 23 0.06
22 298 0.76
23 52 0.13
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
TATCAAAATTTCATAGGAGGT
Found at i:3052 original size:22 final size:22
Alignment explanation
Indices: 3005--3054 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2995 TATCGTTATT
* *
3005 AAAATATCATAGGAAGGTTATC
1 AAAATATCATAGGAAGGTCATA
*
3027 AAAATTTCATAAGGAA-GTCATA
1 AAAATATCAT-AGGAAGGTCATA
3049 AAAATA
1 AAAATA
3055 GTGTAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAATATCATAGGAAGGTCATA
Found at i:4121 original size:24 final size:25
Alignment explanation
Indices: 4066--4122 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
4056 TATCAAACTC
*
4066 TCTCTTC-CTTTCTTCATGACTCTT
1 TCTCTTCTCTTTCTTCATCACTCTT
*
4090 TC-CTTTCTCTTTCTTC-TCTCTCTT
1 TCTC-TTCTCTTTCTTCATCACTCTT
4114 TCTCTTCTC
1 TCTCTTCTC
4123 ATCCTTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 1 0.04
24 18 0.64
25 9 0.32
ACGTcount: A:0.04, C:0.37, G:0.02, T:0.58
Consensus pattern (25 bp):
TCTCTTCTCTTTCTTCATCACTCTT
Found at i:5675 original size:10 final size:10
Alignment explanation
Indices: 5660--5691 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
5650 ATATAAGCCA
5660 TTCTCTCTCT
1 TTCTCTCTCT
5670 TTCTCTCTCT
1 TTCTCTCTCT
*
5680 CTCTCTCTCT
1 TTCTCTCTCT
5690 TT
1 TT
5692 TTCTGCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (10 bp):
TTCTCTCTCT
Found at i:9160 original size:97 final size:97
Alignment explanation
Indices: 8992--9189 Score: 333
Period size: 97 Copynumber: 2.0 Consensus size: 97
8982 AGGATGATGT
* *
8992 CACTGCGTGAGAAATTAACTGCTCCTAAGGTTAGCAGGACTATTTCTGAGTTCTTTCAAAATCTC
1 CACTGCGTGAAAAATTAACTGCTCCTAAGGGTAGCAGGACTATTTCTGAGTTCTTTCAAAATCTC
9057 AAAAGCACAGCTGATGAATTAGCCCTCATTGA
66 AAAAGCACAGCTGATGAATTAGCCCTCATTGA
* * *
9089 CACTGTGTGAAAAATTAACTGCTCCTTAGGGTAGCAGGACTATTTTTGAGTTCTTTCAAAATCTC
1 CACTGCGTGAAAAATTAACTGCTCCTAAGGGTAGCAGGACTATTTCTGAGTTCTTTCAAAATCTC
* *
9154 AGAAGCATAGCTGATGAATTAGCCCTCATTGA
66 AAAAGCACAGCTGATGAATTAGCCCTCATTGA
9186 CACT
1 CACT
9190 ATGATCCCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (97 bp):
CACTGCGTGAAAAATTAACTGCTCCTAAGGGTAGCAGGACTATTTCTGAGTTCTTTCAAAATCTC
AAAAGCACAGCTGATGAATTAGCCCTCATTGA
Found at i:14328 original size:10 final size:10
Alignment explanation
Indices: 14313--14337 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
14303 GAATTGATCT
14313 AATTTGGTAC
1 AATTTGGTAC
14323 AATTTGGTAC
1 AATTTGGTAC
14333 AATTT
1 AATTT
14338 TTGGCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (10 bp):
AATTTGGTAC
Found at i:15358 original size:28 final size:28
Alignment explanation
Indices: 15318--15500 Score: 217
Period size: 28 Copynumber: 6.5 Consensus size: 28
15308 CTTTGCTTCT
15318 CATTTTGGTCATTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
15346 CATTTTGGTCATTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* * * *
15374 TATTTTGGTCATTCTACAGGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* *
15402 CATTTTGGTCATTCTTTCAGGACCAGGGGG
1 CATTTTGGTCATT-TTTCATGTCCA-GGGG
* *
15432 CATTGTGGTCATTATTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* * *
15460 TATTTTGGTCA-TTTGCACGTCC-GGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
15486 ACATTTTAGTCATTT
1 -CATTTTGGTCATTT
15501 CATGCACATT
Statistics
Matches: 132, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 4 0.03
27 17 0.13
28 79 0.60
29 16 0.12
30 16 0.12
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (28 bp):
CATTTTGGTCATTTTTCATGTCCAGGGG
Found at i:15405 original size:56 final size:57
Alignment explanation
Indices: 15318--15473 Score: 215
Period size: 58 Copynumber: 2.7 Consensus size: 57
15308 CTTTGCTTCT
* * *
15318 CATTTTGGTCATTTTTCATGTCCAGGGGCATTTTGGTCATTTTTCATGTCCA-GGGG
1 CATTTTGGTCATTATTCATGTCCAGGGGCATTTTGGTCATTTTTCAGGACCAGGGGG
* * * *
15374 TATTTTGGTCATTCTACAGGTCCAGGGGCATTTTGGTCATTCTTTCAGGACCAGGGGG
1 CATTTTGGTCATTATTCATGTCCAGGGGCATTTTGGTCATT-TTTCAGGACCAGGGGG
* *
15432 CATTGTGGTCATTATTCATGTCCAGGGGTATTTTGGTCATTT
1 CATTTTGGTCATTATTCATGTCCAGGGGCATTTTGGTCATTT
15474 GCACGTCCGG
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
56 37 0.43
57 10 0.12
58 39 0.45
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.40
Consensus pattern (57 bp):
CATTTTGGTCATTATTCATGTCCAGGGGCATTTTGGTCATTTTTCAGGACCAGGGGG
Found at i:15450 original size:86 final size:83
Alignment explanation
Indices: 15318--15500 Score: 260
Period size: 86 Copynumber: 2.2 Consensus size: 83
15308 CTTTGCTTCT
* * * *
15318 CATTTTGGTCATTTTTCATGTCCAGGGGCATTTTGGTCATTTTTCATGTCCAGGGGTATTTTGGT
1 CATTTTGGTCATTTTTCAGGACCAGGGGCATTGTGGTCATTATTCATGTCCAGGGGTATTTTGGT
*
15383 CATTCTACAGGTCCAGGGG-
66 CATT-TACACGTCC-GGGGA
15402 CATTTTGGTCATTCTTTCAGGACCAGGGGGCATTGTGGTCATTATTCATGTCCAGGGGTATTTTG
1 CATTTTGGTCATT-TTTCAGGACCA-GGGGCATTGTGGTCATTATTCATGTCCAGGGGTATTTTG
*
15467 GTCATTTGCACGTCCGGGGA
64 GTCATTTACACGTCCGGGGA
*
15487 CATTTTAGTCATTT
1 CATTTTGGTCATTT
15501 CATGCACATT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
84 18 0.20
85 28 0.31
86 43 0.48
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (83 bp):
CATTTTGGTCATTTTTCAGGACCAGGGGCATTGTGGTCATTATTCATGTCCAGGGGTATTTTGGT
CATTTACACGTCCGGGGA
Found at i:16841 original size:16 final size:16
Alignment explanation
Indices: 16820--16852 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16810 AGAAGAACCG
16820 CATTCTAAGGCCAGGA
1 CATTCTAAGGCCAGGA
*
16836 CATTCTAAGGTCAGGA
1 CATTCTAAGGCCAGGA
16852 C
1 C
16853 TATCATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (16 bp):
CATTCTAAGGCCAGGA
Found at i:18287 original size:9 final size:9
Alignment explanation
Indices: 18273--18297 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18263 TCCATTTTTA
18273 TGATAAAGT
1 TGATAAAGT
18282 TGATAAAGT
1 TGATAAAGT
18291 TGATAAA
1 TGATAAA
18298 TTTAGTTCAT
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:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (9 bp):
TGATAAAGT
Done.