Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018111.1 Corchorus olitorius cultivar O-4 contig18144, 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: 7886
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:788 original size:28 final size:27
Alignment explanation
Indices: 732--836 Score: 167
Period size: 27 Copynumber: 3.9 Consensus size: 27
722 AGTGAACTTG
* *
732 AAATGACCAAAATGCCCCT-GAATGCGC
1 AAATGACTAAAATGCCCCTAG-ATGTGC
759 AAATGACTAAAATGCCCCCTAGATGTGC
1 AAATGACTAAAATG-CCCCTAGATGTGC
787 AAATGACTAAAATGCCCCTAGATGTGC
1 AAATGACTAAAATGCCCCTAGATGTGC
814 AAATGACTAAAATGCCCCTAGAT
1 AAATGACTAAAATGCCCCTAGAT
837 TTGTTTTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
27 49 0.66
28 24 0.32
29 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTAGATGTGC
Found at i:799 original size:55 final size:54
Alignment explanation
Indices: 732--836 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 54
722 AGTGAACTTG
732 AAATGACCAAAATGCCCCT-GAATGCGCAAATGACTAAAATGCCCCCTAGATGTGC
1 AAATGACCAAAATGCCCCTAG-ATGCGCAAATGACTAAAATG-CCCCTAGATGTGC
* *
787 AAATGACTAAAATGCCCCTAGATGTGCAAATGACTAAAATGCCCCTAGAT
1 AAATGACCAAAATGCCCCTAGATGCGCAAATGACTAAAATGCCCCTAGAT
837 TTGTTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
54 9 0.19
55 37 0.79
56 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (54 bp):
AAATGACCAAAATGCCCCTAGATGCGCAAATGACTAAAATGCCCCTAGATGTGC
Found at i:1258 original size:35 final size:35
Alignment explanation
Indices: 1212--1603 Score: 535
Period size: 35 Copynumber: 11.2 Consensus size: 35
1202 CGAATCCCAC
*
1212 TTGAAGATGCTTCACCGAGTCATCTGATT-TCATCT
1 TTGAAGATGCTACACCGAGTCATCTGATTCT-ATCT
*
1247 TTGAAGATGCTTCACCGAGTCATCTGGATTC-ATCT
1 TTGAAGATGCTACACCGAGTCATCT-GATTCTATCT
1282 TTGAAGATGCTACACCGAGTCATCTGAGTTC-ATCT
1 TTGAAGATGCTACACCGAGTCATCTGA-TTCTATCT
*
1317 TTGAAGATGCTACACCGAGTCATCTAAGTTC-ATCT
1 TTGAAGATGCTACACCGAGTCATCTGA-TTCTATCT
* *
1352 TTGAAGATGCTACACTGAGTCATCTGGATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCT-GATTCTATCT
* *
1387 TTGAAGATGCTGCACCGAGTCATCTGAAGTC-ATCT
1 TTGAAGATGCTACACCGAGTCATCTG-ATTCTATCT
*
1422 TTGAAGATGCTACACCGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTATCT
* * *
1457 TTGAAGATGCTACACTGAGTCATCCGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTATCT
*
1492 TTGAAGATGCTACACCGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTATCT
* *
1527 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTATCT
* *
1562 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTATCT
*
1597 TCGAAGA
1 TTGAAGA
1604 AATTTCATTT
Statistics
Matches: 333, Mismatches: 16, Indels: 16
0.91 0.04 0.04
Matches are distributed among these distances:
34 8 0.02
35 318 0.95
36 7 0.02
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGATTCTATCT
Found at i:1867 original size:64 final size:64
Alignment explanation
Indices: 1785--2138 Score: 516
Period size: 64 Copynumber: 5.5 Consensus size: 64
1775 TCCGGTGTAT
* * *
1785 CAAGATCGTCCTCTGATCAACTTCTGAAAACTCTCGAGAAACCATCTTCTGGTGTACTTCTTGA
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
* *
1849 TAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAAAAACCATCTTCTGGTGTACTTCTTGA
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
* * *
1913 CAAGATCGTCTTCCGATCAATTTCTGAAAATTCTTGAAAAACCATCTTCTGGTGTACTTCTTGA
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
* * *
1977 CCAGATCGTCTTCCGATCAATTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACCTT-TTAA
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTA-CTTCTTGA
* * * *
2041 TAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCT-G-GTACTTCTTTGA
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTC-TTGA
* *
2104 CAAGATCGTCTTCCGATCAATTTCTAAAAACTCTT
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTT
2139 TCTAGCAAAC
Statistics
Matches: 262, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
61 3 0.01
62 3 0.01
63 33 0.13
64 220 0.84
65 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (64 bp):
CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
Found at i:2323 original size:66 final size:66
Alignment explanation
Indices: 2106--2361 Score: 334
Period size: 67 Copynumber: 3.8 Consensus size: 66
2096 TTCTTTGACA
* * * * * *
2106 AGATCGTCTTCCGATCAATTTCTAAAAACTCTTTCTAGCAAACCGTCTTCCGATGTATTCTTTAA
1 AGATTGTCTTCCAATCAATTTTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGTATAC-TTAA
2171 TG
65 TG
**** * *
2173 AGATTGTCTTCCAATCAGCACTTGAAAACTCTTTCTAGCAAACCGTCCTCCAGTGTGT-TCCTTA
1 AGATTGTCTTCCAATCAATTTTTGAAAACTCTTTCTAGCAAACCGTCTTCC-G-GTGTATACTTA
2237 ATG
64 ATG
* * *
2240 AGATTGTCTTCCAATCAATTTTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGCGTAAACTTAAT
1 AGATTGTCTTCCAATCAATTTTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGTATACTTAAT
2305 G
66 G
*
2306 AGATTGTCTTCCAATCAATTTTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGT
1 AGATTGTCTTCCAATCAATTTTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGT
2362 TCTTCTAAAA
Statistics
Matches: 163, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
65 3 0.02
66 61 0.37
67 93 0.57
68 3 0.02
69 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (66 bp):
AGATTGTCTTCCAATCAATTTTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGTATACTTAAT
G
Found at i:2341 original size:133 final size:134
Alignment explanation
Indices: 2106--2361 Score: 361
Period size: 133 Copynumber: 1.9 Consensus size: 134
2096 TTCTTTGACA
* * **
2106 AGATCGTCTTCCGATCAATTTCTAAAAACTCTTTCTAGCAAACCGTCTTCCGATGTATTCTTTAA
1 AGATCGTCTTCCAATCAATTTCTAAAAACTCTTTCTAGCAAACCGTCTTCCGACGTAAACTTTAA
*
2171 TGAGATTGTCTTCCAATCAGCACTTGAAAACTCTTTCTAGCAAACCGTCCTCCAGTGTGTTCCTT
66 TGAGATTGTCTTCCAATCAACACTTGAAAACTCTTTCTAGCAAACCGTCCTCCAGTGTGTTCCTT
2236 AATG
131 AATG
* * * * *
2240 AGATTGTCTTCCAATCAATTTTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGCGTAAAC-TTAA
1 AGATCGTCTTCCAATCAATTTCTAAAAACTCTTTCTAGCAAACCGTCTTCCGACGTAAACTTTAA
*** * * *
2304 TGAGATTGTCTTCCAATCAATTTTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGT
66 TGAGATTGTCTTCCAATCAACACTTGAAAACTCTTTCTAGCAAACCGTCCTCCAGTGT
2362 TCTTCTAAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
133 55 0.52
134 51 0.48
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (134 bp):
AGATCGTCTTCCAATCAATTTCTAAAAACTCTTTCTAGCAAACCGTCTTCCGACGTAAACTTTAA
TGAGATTGTCTTCCAATCAACACTTGAAAACTCTTTCTAGCAAACCGTCCTCCAGTGTGTTCCTT
AATG
Found at i:3825 original size:12 final size:12
Alignment explanation
Indices: 3779--3825 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
3769 GCTCGTTCTT
3779 ATTTCTCTTTTTC
1 ATTTCT-TTTTTC
3792 A--TCATTTTTTC
1 ATTTC-TTTTTTC
*
3803 ATTTCATTTTTC
1 ATTTCTTTTTTC
3815 ATTTCTTTTTT
1 ATTTCTTTTTT
3826 TGGTTAGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 9 0.31
12 17 0.59
13 3 0.10
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTCTTTTTTC
Found at i:3906 original size:20 final size:19
Alignment explanation
Indices: 3864--3906 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
3854 TTTGAAAAAC
* * *
3864 TTTTGAAAAACACTTTTTC
1 TTTTGAAAAACAATTTCTA
3883 TTTTGCAAAAACAATTTCTA
1 TTTTG-AAAAACAATTTCTA
3903 TTTT
1 TTTT
3907 AGGAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTTGAAAAACAATTTCTA
Found at i:4485 original size:12 final size:12
Alignment explanation
Indices: 4468--4504 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 12
4458 TAAAAGACTC
4468 AAAACCTTTTTG
1 AAAACCTTTTTG
4480 AAAACCTATTTTTG
1 AAAACC--TTTTTG
4494 AAAACCTTTTT
1 AAAACCTTTTT
4505 CTTGAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 11 0.48
14 12 0.52
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (12 bp):
AAAACCTTTTTG
Found at i:4493 original size:14 final size:14
Alignment explanation
Indices: 4474--4513 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
4464 ACTCAAAACC
4474 TTTTTGAAAACCTA
1 TTTTTGAAAACCTA
*
4488 TTTTTGAAAACCTT
1 TTTTTGAAAACCTA
4502 TTTCTTGAAAAC
1 TTT-TTGAAAAC
4514 AATTTCCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACCTA
Found at i:4509 original size:15 final size:15
Alignment explanation
Indices: 4477--4527 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
4467 CAAAACCTTT
*
4477 TTGAAAACCTATTT-
1 TTGAAAACCTTTTTC
4491 TTGAAAACCTTTTTC
1 TTGAAAACCTTTTTC
** *
4506 TTGAAAACAATTTCC
1 TTGAAAACCTTTTTC
4521 TTGAAAA
1 TTGAAAA
4528 ACATGTCTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (15 bp):
TTGAAAACCTTTTTC
Done.