Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022083.1 Corchorus olitorius cultivar O-4 contig22116, 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: 8349
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:974 original size:30 final size:30
Alignment explanation
Indices: 933--1598 Score: 892
Period size: 30 Copynumber: 22.1 Consensus size: 30
923 TTAACTGATG
* *
933 AAGCAATGATCCTAAACCAGGATTAAAACA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* **
963 AAGCCATGATCCT-AGACCAAAATTAAAATA
1 AAGCAATGATCCTCA-ACCAGGATTAAAATA
* *
993 AAGCAACGATCCTCAACTAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
1023 AAGCAACGATCCTCAACCAGGATAAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
1053 AATCAATGATCCTAAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1083 AAGCAATGATCCTCGACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1113 ATGCAAAT-ATCCTCAACCAGGATTAAAATA
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
*
1143 ATGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1173 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1203 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1233 AAGCAATGATCCTCAACCAGGAATAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1263 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1293 AAGCAATGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
** *
1323 AAGCAGCGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * *
1353 AAGCTGACGATCCTCAAACAGGATTGAAATTA
1 AAGC-AATGATCCTCAACCAGGATT-AAAATA
1385 AA-CAAAT-ATCCTCAACCAGGATTAAAATA
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
1414 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1444 AAGCAATGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
** * *
1474 AAGCAGCGATCCTCAAACAGGAGTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * * *
1504 AAGCTGACGATCCTCAAACAGGATTGAAATA
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
**
1535 AAGCAAAT-ATTTTCAACCAGGATTAAAATA
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
* * *
1565 AAGCAGTGATCCTAAAACAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1595 AAGC
1 AAGC
1599 TGATAAAGCA
Statistics
Matches: 566, Mismatches: 60, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.03
30 492 0.87
31 51 0.09
32 7 0.01
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (30 bp):
AAGCAATGATCCTCAACCAGGATTAAAATA
Found at i:1616 original size:39 final size:39
Alignment explanation
Indices: 1562--1683 Score: 149
Period size: 39 Copynumber: 3.2 Consensus size: 39
1552 CAGGATTAAA
* *
1562 ATAAAGCAGTGATCCTAAAACAGGATTAAAATAAAGCTG
1 ATAAAGCAATGATCCTAAACCAGGATTAAAATAAAGCTG
*
1601 ATAAAGCAATGATCCTAAACCAGGATTAAAAATAAAGC-A
1 ATAAAGCAATGATCCTAAACCAGGATT-AAAATAAAGCTG
* * ** *
1640 ATCACGCAATGATCCTAAACCAGGATCGAGATAAA-CTG
1 ATAAAGCAATGATCCTAAACCAGGATTAAAATAAAGCTG
1678 ATAAAG
1 ATAAAG
1684 TGGAATAGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
37 1 0.01
38 10 0.14
39 49 0.70
40 10 0.14
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (39 bp):
ATAAAGCAATGATCCTAAACCAGGATTAAAATAAAGCTG
Found at i:2362 original size:37 final size:36
Alignment explanation
Indices: 2287--2379 Score: 116
Period size: 37 Copynumber: 2.6 Consensus size: 36
2277 GAAGACCTCT
* *
2287 CTGGATCAACTGAAACAAACTGAAGAACAAATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAACAAATCACC
* * *
2323 CTGGATCAACATGAAATGAACTGATGGAA-AGATCACC
1 CTGGATCAAC-TGAAATAAACTGA-AGAACAAATCACC
2360 CTGGATCAACTGAAATAAAC
1 CTGGATCAACTGAAATAAAC
2380 CTGGATCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 19 0.39
37 27 0.55
38 3 0.06
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (36 bp):
CTGGATCAACTGAAATAAACTGAAGAACAAATCACC
Found at i:2384 original size:20 final size:20
Alignment explanation
Indices: 2359--2399 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2349 GAAAGATCAC
2359 CCTGGATCAACTGAAATAAA
1 CCTGGATCAACTGAAATAAA
*
2379 CCTGGATCAACTGAGATAAA
1 CCTGGATCAACTGAAATAAA
2399 C
1 C
2400 TGAAGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (20 bp):
CCTGGATCAACTGAAATAAA
Found at i:2405 original size:93 final size:92
Alignment explanation
Indices: 2287--2471 Score: 273
Period size: 92 Copynumber: 2.0 Consensus size: 92
2277 GAAGACCTCT
* *
2287 CTGGATCAACTGAAACAAACTGAAGAACAA-ATCGCCCTGGATCAACATGAAATGAACTGATGGA
1 CTGGATCAACTGAAACAAACTGAAGAA-AAGATCGCCCTGGATCAAC-TGAAATAAACTGAAGGA
2351 AAGATCACCCTGGATCAACTGAAATAAAC
64 AAGATCACCCTGGATCAACTGAAATAAAC
* * *
2380 CTGGATCAACTGAGATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAGATAAACTGAAGGAAA
1 CTGGATCAACTGAAACAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGGAAA
* * *
2445 GATCGCCTTGGATCAATTGAAATAAAC
66 GATCACCCTGGATCAACTGAAATAAAC
2472 TGAAGAAAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
92 42 0.51
93 41 0.49
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.18
Consensus pattern (92 bp):
CTGGATCAACTGAAACAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGGAAA
GATCACCCTGGATCAACTGAAATAAAC
Found at i:2410 original size:56 final size:57
Alignment explanation
Indices: 2322--2435 Score: 167
Period size: 56 Copynumber: 2.0 Consensus size: 57
2312 AACAAATCGC
* * *
2322 CCTGGATCAACATGAAATGAACTGATGGAAAGATCACCCTGGATCAACTGAAATAAA
1 CCTGGATCAACATGAAATAAACTGAAGAAAAGATCACCCTGGATCAACTGAAATAAA
* * *
2379 CCTGGATCAAC-TGAGATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAGATAAA
1 CCTGGATCAACATGAAATAAACTGAAGAAAAGATCACCCTGGATCAACTGAAATAAA
2435 C
1 C
2436 TGAAGGAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 40 0.78
57 11 0.22
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (57 bp):
CCTGGATCAACATGAAATAAACTGAAGAAAAGATCACCCTGGATCAACTGAAATAAA
Found at i:2426 original size:36 final size:35
Alignment explanation
Indices: 2379--2511 Score: 185
Period size: 36 Copynumber: 3.7 Consensus size: 35
2369 CTGAAATAAA
*
2379 CCTGGATCAACTGAGATAAACTGAAGAAAAGATCGC
1 CCTGGATCAACTGAAATAAACTGAAG-AAAGATCGC
*
2415 CCTGGATCAACTGAGATAAACTGAAGGAAAGATCGC
1 CCTGGATCAACTGAAATAAACTGAA-GAAAGATCGC
* * *
2451 CTTGGATCAATTGAAATAAACTGAAGAAAGACCGC
1 CCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
* *
2486 CCTGGGTCAACTGAAATGAACTGAAG
1 CCTGGATCAACTGAAATAAACTGAAG
2512 CATCTGAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
35 31 0.35
36 56 0.64
37 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (35 bp):
CCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
Found at i:4051 original size:14 final size:13
Alignment explanation
Indices: 4017--4057 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
4007 AGCATCCTCG
* *
4017 TGAAAACAAATTT
1 TGAAAACCATTTT
4030 TGAAAACCATTTT
1 TGAAAACCATTTT
4043 TGAAAAACCATTTT
1 TG-AAAACCATTTT
4057 T
1 T
4058 TTGAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (13 bp):
TGAAAACCATTTT
Found at i:4072 original size:16 final size:16
Alignment explanation
Indices: 4027--4065 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4017 TGAAAACAAA
4027 TTTTG-AAAACCA--T
1 TTTTGAAAAACCATTT
4040 TTTTGAAAAACCATTT
1 TTTTGAAAAACCATTT
4056 TTTTGAAAAA
1 TTTTGAAAAA
4066 ATCTTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
16 11 0.48
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (16 bp):
TTTTGAAAAACCATTT
Found at i:6768 original size:16 final size:16
Alignment explanation
Indices: 6743--6773 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6733 CAGATACTTA
6743 TGATGATTTGCATGAC
1 TGATGATTTGCATGAC
*
6759 TGATGCTTTGCATGA
1 TGATGATTTGCATGA
6774 ATGCATTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (16 bp):
TGATGATTTGCATGAC
Done.