Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015907.1 Corchorus olitorius cultivar O-4 contig15940, 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: 5142
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:436 original size:29 final size:26
Alignment explanation
Indices: 379--451 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 26
369 AAGTGAACCT
*
379 AAAATTACCAAAATG-CCCTTCGTGC
1 AAAATTACCAAAATGCCCCTACGTGC
404 AAAATTACCAAAAATGCCCCTAGACGTGC
1 AAAATTACC-AAAATGCCCCT--ACGTGC
*
433 AAAATGACCAAAATGCCCC
1 AAAATTACCAAAATGCCCC
452 CCTGGATGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
25 9 0.21
26 6 0.14
27 4 0.10
28 10 0.24
29 13 0.31
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.18
Consensus pattern (26 bp):
AAAATTACCAAAATGCCCCTACGTGC
Found at i:1057 original size:30 final size:30
Alignment explanation
Indices: 971--1423 Score: 622
Period size: 30 Copynumber: 15.1 Consensus size: 30
961 TTAACTGAAG
*
971 AAGCAATGATCCTAAACCAGGATTAAAA-A
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
1000 AAACAATGATCCTAAACCAGGATTTAAAATA
1 AAGCAATGATCCTCAACCAGGA-TTAAAATA
***
1031 AAATGATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1061 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1091 AAGCAATGATCCTCAACTAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
1121 AAG-AATGATCCTCAAACAGAATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1150 AAGCAACGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
1180 AAGCAGTGATCCTCAATCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
1210 CAGCAATGATTCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
1240 AAGCAATGATCCTAAATCAGGACTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1270 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
1300 AAGCAATGACCCTAAACCAGGGTTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* **
1330 AAGCAATGATCCTAAAAAAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
** *
1360 AAGCAATGATCCTCAAATAGGATTAACATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
1390 AAGCGACGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1420 AAGC
1 AAGC
1424 TGATAAAGCA
Statistics
Matches: 375, Mismatches: 46, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
29 47 0.13
30 308 0.82
31 20 0.05
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (30 bp):
AAGCAATGATCCTCAACCAGGATTAAAATA
Found at i:1945 original size:169 final size:169
Alignment explanation
Indices: 1514--2130 Score: 1022
Period size: 169 Copynumber: 3.7 Consensus size: 169
1504 TGCTCAGAGA
* * * * *
1514 ACTTACCAATACAAACTCTGGATAGAGACCTTGACCAAGGATTTTAGACATAAACATGAACTTTT
1 ACTTACCAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTT
1579 GATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
66 GATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
* *
1644 TAATTAATACCCGGAGGGTTTCTGAATTTGTGCCAGGAGG
131 GAATTAATACCCGGA-GGTTTCTGAATTTGTGCCCGGAGG
* * *
1684 ATTTACCAATGCAAACTCTGAATAAAGACCTTAAACAAGGATTTTAAACTTAAACATGAACTTTT
1 ACTTACCAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTT
1749 GATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
66 GATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
1814 GAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGG
131 GAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGG
* *
1853 ACTTACCAATGTAAACTCTGAATAGAGACCTTGAACAAGAATTTTAAACTTAAACATGAACTTTT
1 ACTTACCAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTT
* * * *
1918 GATGAAAAACTTAATGAAATGAAATGGTACCCGGAGGTTTTACCGATTGCCCGGAGGACTTATCA
66 GATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
*
1983 GAATTAATACCCGGAGGTTTCTGAATTCGTGCCCGGAGG
131 GAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGG
* *
2022 ACTTACCAACGCAAACTCTGAATAGAGACCTTGACCAAGGATTTT-AACTTAAACATGAA-TTTT
1 ACTTACCAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTT
* *
2085 GATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAA
66 GATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAA
2131 ATGGAAATAA
Statistics
Matches: 419, Mismatches: 28, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
167 46 0.11
168 14 0.03
169 223 0.53
170 136 0.32
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (169 bp):
ACTTACCAATGCAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTT
GATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
GAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGG
Found at i:2241 original size:339 final size:333
Alignment explanation
Indices: 1514--2140 Score: 859
Period size: 339 Copynumber: 1.9 Consensus size: 333
1504 TGCTCAGAGA
** * * * * * *
1514 ACTTACCAATACAAACTCTGGATAGAGACCTTGACCAAGGATTTTAGACATAAACATGAACTTTT
1 ACTTACCAATGTAAACTCTGAATAGAGACCTTGAACAAGAATCTTAAACTTAAACATGAACTTTT
* *
1579 GATGAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
66 GATGAAAAACTTAATGAAATCAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCA
* * * *
1644 TAATTAATACCCGGAGGGTTTCTGAATTTGTGCCAGGAGGATTTACCAATGCAAACTCTGAATAA
131 GAATTAATACCCGGAGGGTTTCTGAATTCGTGCCAGGAGGACTTACCAACGCAAACTCTGAATAA
1709 AGACCTTAAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAAACTTGATGAAATCAAAT
196 AGACCTTAAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAAACTTGATGAAATCAAAT
* * * * * * **
1774 GGTACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAA
261 GATACCCGGAGGTTTTATCAAAT---CGGA-GAATAACCAGAATTAATACCCGGAAGTGGCTGAA
* * * *
1839 TTTGTGCCCGGAGG
322 TGTATG--CGAACG
*
1853 ACTTACCAATGTAAACTCTGAATAGAGACCTTGAACAAGAATTTTAAACTTAAACATGAACTTTT
1 ACTTACCAATGTAAACTCTGAATAGAGACCTTGAACAAGAATCTTAAACTTAAACATGAACTTTT
* *
1918 GATGAAAAACTTAATGAAATGAAATGGTACCCGGAGGTTTTACCGATTGCCCGGAGGACTTATCA
66 GATGAAAAACTTAATGAAATCAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCA
* *
1983 GAATTAATACCCGGA-GGTTTCTGAATTCGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAG
131 GAATTAATACCCGGAGGGTTTCTGAATTCGTGCCAGGAGGACTTACCAACGCAAACTCTGAATAA
* * *
2047 AGACCTTGACCAAGGATTTT-AACTTAAACATGAA-TTTTGATGAAAAACTTGATGAAATGAAAT
196 AGACCTTAAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAAACTTGATGAAATCAAAT
2110 GATACCCGGAGGTTTTATCAAAT-GGA-AATAA
261 GATACCCGGAGGTTTTATCAAATCGGAGAATAA
2141 GCCTAAATTG
Statistics
Matches: 264, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
330 3 0.01
332 3 0.01
336 49 0.19
337 14 0.05
338 62 0.23
339 133 0.50
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (333 bp):
ACTTACCAATGTAAACTCTGAATAGAGACCTTGAACAAGAATCTTAAACTTAAACATGAACTTTT
GATGAAAAACTTAATGAAATCAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCA
GAATTAATACCCGGAGGGTTTCTGAATTCGTGCCAGGAGGACTTACCAACGCAAACTCTGAATAA
AGACCTTAAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAAACTTGATGAAATCAAAT
GATACCCGGAGGTTTTATCAAATCGGAGAATAACCAGAATTAATACCCGGAAGTGGCTGAATGTA
TGCGAACG
Found at i:3588 original size:7 final size:8
Alignment explanation
Indices: 3569--3613 Score: 74
Period size: 8 Copynumber: 5.8 Consensus size: 8
3559 CTCTTTCCTT
3569 TTTTTTCA
1 TTTTTTCA
3577 TTTTTTCA
1 TTTTTTCA
3585 TTTTTTCA
1 TTTTTTCA
3593 TTTTTTCA
1 TTTTTTCA
*
3601 -TTTTCCA
1 TTTTTTCA
3608 TTTTTT
1 TTTTTT
3614 TGTGCACTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 6 0.18
8 28 0.82
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3927 original size:9 final size:9
Alignment explanation
Indices: 3915--4006 Score: 60
Period size: 9 Copynumber: 9.4 Consensus size: 9
3905 TTTATTTTGG
3915 TTTTTTTAT
1 TTTTTTTAT
3924 TTTTTTTATT
1 TTTTTTTA-T
3934 GATTTTTTTGATTT
1 --TTTTTTT-A--T
3948 TTTTTTTACT
1 TTTTTTTA-T
*
3958 TTTTTGTAT
1 TTTTTTTAT
*
3967 TTTTTTTGT
1 TTTTTTTAT
3976 TTTTTTT-T
1 TTTTTTTAT
* *
3984 ATATTTTGAT
1 -TTTTTTTAT
*
3994 TTTTTTTGT
1 TTTTTTTAT
4003 TTTT
1 TTTT
4007 GTTTGAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
8 1 0.01
9 38 0.57
10 10 0.15
11 1 0.01
12 14 0.21
13 1 0.01
14 2 0.03
ACGTcount: A:0.10, C:0.01, G:0.07, T:0.83
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:3928 original size:21 final size:19
Alignment explanation
Indices: 3903--3990 Score: 79
Period size: 21 Copynumber: 4.3 Consensus size: 19
3893 ATCAATTCTC
*
3903 TTTTTATTTTGGTTTTTTTA
1 TTTTT-TTTTTGTTTTTTTA
3923 TTTTTTTTATTGATTTTTTTGA
1 TTTTTTTT-TTG-TTTTTTT-A
*
3945 TTTTTTTTTTACTTTTTTGTA
1 TTTTTTTTTT-GTTTTTT-TA
3966 TTTTTTTTGTT-TTTTTTTA
1 TTTTTTTT-TTGTTTTTTTA
3985 TATTTT
1 T-TTTT
3991 GATTTTTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
19 6 0.10
20 17 0.29
21 24 0.41
22 12 0.20
ACGTcount: A:0.10, C:0.01, G:0.07, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTTGTTTTTTTA
Found at i:3938 original size:13 final size:12
Alignment explanation
Indices: 3915--3955 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
3905 TTTATTTTGG
3915 TTTTT-TTATTT
1 TTTTTATTATTT
3926 TTTTTATTGATTT
1 TTTTTATT-ATTT
*
3939 TTTTGATT-TTT
1 TTTTTATTATTT
3950 TTTTTA
1 TTTTTA
3956 CTTTTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 13 0.50
12 2 0.08
13 11 0.42
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (12 bp):
TTTTTATTATTT
Found at i:3999 original size:21 final size:21
Alignment explanation
Indices: 3915--4006 Score: 55
Period size: 21 Copynumber: 4.3 Consensus size: 21
3905 TTTATTTTGG
* * *
3915 TTTTTTTATTTTTTTTATTGAT
1 TTTTTTTATATTTTAT-TTGTT
*
3937 TTTTTTGAT-TTTT-TTT-TT
1 TTTTTTTATATTTTATTTGTT
* * *
3955 ACTTTTTTGTATTTTTTTTGTT
1 -TTTTTTTATATTTTATTTGTT
*
3977 TTTTTTTATATTTTGATTTTTT
1 TTTTTTTATATTTT-ATTTGTT
3999 TTGTTTTT
1 TT-TTTTT
4007 GTTTGAATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
18 1 0.02
19 8 0.15
20 5 0.09
21 19 0.35
22 17 0.31
23 5 0.09
ACGTcount: A:0.10, C:0.01, G:0.07, T:0.83
Consensus pattern (21 bp):
TTTTTTTATATTTTATTTGTT
Found at i:4016 original size:27 final size:28
Alignment explanation
Indices: 3936--4016 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 28
3926 TTTTTATTGA
* *
3936 TTTTTTTGATTTTTTTTTTACTTTTTTGTAT
1 TTTTTTTG--TTTTTTTTGA-TATTTTGTAT
*
3967 TTTTTTTGTTTTTTTTTATATTTTG-AT
1 TTTTTTTGTTTTTTTTGATATTTTGTAT
3994 TTTTTTTGTTTTTGTTTGA-ATTT
1 TTTTTTTGTTTTT-TTTGATATTT
4017 CTTGATGGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 19 0.40
28 10 0.21
29 10 0.21
31 8 0.17
ACGTcount: A:0.10, C:0.01, G:0.09, T:0.80
Consensus pattern (28 bp):
TTTTTTTGTTTTTTTTGATATTTTGTAT
Found at i:4021 original size:29 final size:26
Alignment explanation
Indices: 3932--4022 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 26
3922 ATTTTTTTTA
* *
3932 TTGATTTTTTTGATTTTTTTTTTACTTTT
1 TTGATTTTTTT--TGTTTTTTTTA-ATTT
*
3961 TTGTATTTTTTTTGTTTTTTTTTATATT
1 TTG-ATTTTTTTTGTTTTTTTTAAT-TT
3989 TTGATTTTTTTTGTTTTTGTTTGAATTT
1 TTGATTTTTTTTGTTTTT-TTT-AATTT
4017 CTTGAT
1 -TTGAT
4023 GGAGTGGACT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 16 0.30
28 19 0.36
29 10 0.19
30 8 0.15
ACGTcount: A:0.11, C:0.02, G:0.10, T:0.77
Consensus pattern (26 bp):
TTGATTTTTTTTGTTTTTTTTAATTT
Found at i:4404 original size:15 final size:16
Alignment explanation
Indices: 4386--4427 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
4376 AGTGCCTTTA
*
4386 TTTTAATTTTTAAATT
1 TTTTCATTTTTAAATT
**
4402 TTTTCATTTTTTCA-T
1 TTTTCATTTTTAAATT
4417 TTTTCATTTTT
1 TTTTCATTTTT
4428 CATTTCATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTCATTTTTAAATT
Found at i:4411 original size:6 final size:7
Alignment explanation
Indices: 4401--4432 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
4391 ATTTTTAAAT
4401 TTTTTCA
1 TTTTTCA
4408 TTTTTTCA
1 -TTTTTCA
4416 TTTTTCA
1 TTTTTCA
4423 TTTTTCA
1 TTTTTCA
4430 TTT
1 TTT
4433 CATCATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:4426 original size:22 final size:23
Alignment explanation
Indices: 4401--4450 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
4391 ATTTTTAAAT
** *
4401 TTTTTCATTTTTTCATT-TTTCA
1 TTTTTCATTTCATCATTCATTCA
4423 TTTTTCATTTCATCATTCATTCA
1 TTTTTCATTTCATCATTCATTCA
4446 TTTTT
1 TTTTT
4451 TTATGGGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTCATTTCATCATTCATTCA
Done.