Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020517.1 Corchorus olitorius cultivar O-4 contig20550, 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: 7947
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1734 original size:28 final size:28
Alignment explanation
Indices: 1690--1758 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
1680 GAAATCAAAC
**
1690 ATGGAATATGCGCATGTAACTTCTTAAA
1 ATGGAATATGCAAATGTAACTTCTTAAA
*
1718 ATGGGATATGCAAATGTAACTTCTTAAA
1 ATGGAATATGCAAATGTAACTTCTTAAA
1746 ATGGAATATGCAA
1 ATGGAATATGCAA
1759 CTTAAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (28 bp):
ATGGAATATGCAAATGTAACTTCTTAAA
Found at i:1922 original size:27 final size:27
Alignment explanation
Indices: 1889--1964 Score: 136
Period size: 26 Copynumber: 2.9 Consensus size: 27
1879 ATGCCTCCTA
1889 TGCAAATGACTAAAATGCCCCTGAAGG
1 TGCAAATGACTAAAATGCCCCTGAAGG
*
1916 TGCAAATGACTAAAATG-CCCTGAATG
1 TGCAAATGACTAAAATGCCCCTGAAGG
1942 TGCAAATGACTAAAATGCCCCTG
1 TGCAAATGACTAAAATGCCCCTG
1965 GTTGATTCTA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 25 0.53
27 22 0.47
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (27 bp):
TGCAAATGACTAAAATGCCCCTGAAGG
Found at i:2267 original size:50 final size:50
Alignment explanation
Indices: 2205--2480 Score: 396
Period size: 50 Copynumber: 5.5 Consensus size: 50
2195 CGATCAAATT
* * * **
2205 CTTTGAATTGTCTTCCAA-TCTAATAT-TAAAAGTACCGTCTTCTACTTATC
1 CTTTGAACTGTCTACCAATTC-AAT-TCTAAAAGGACCGTCTTCCGCTTATC
*
2255 CTTTGAACTGTCTACCAATTCAA-TCTTAAAAGGATCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATTC-TAAAAGGACCGTCTTCCGCTTATC
* *
2305 CTTTGAATTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCTGCTTATC
1 CTTTGAACTGTCTACCAATTCAATTCT-AAAAGGACCGTCTTCCGCTTATC
*
2356 GTTTGAACTGTCTACCAATTCAATTCTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATTCTAAAAGGACCGTCTTCCGCTTATC
2406 CTTTGAACTGTCTACCAATTCAATTCTATAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATTC--TAAAAGGACCGTCTTCCGCTTATC
2458 CTTTGAACTGTCTACCAATTCAA
1 CTTTGAACTGTCTACCAATTCAA
2481 AAAACGGTAA
Statistics
Matches: 206, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
48 1 0.00
50 108 0.52
51 50 0.24
52 47 0.23
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (50 bp):
CTTTGAACTGTCTACCAATTCAATTCTAAAAGGACCGTCTTCCGCTTATC
Found at i:2379 original size:101 final size:101
Alignment explanation
Indices: 2205--2480 Score: 425
Period size: 101 Copynumber: 2.7 Consensus size: 101
2195 CGATCAAATT
* * *
2205 CTTTGAATTGTCTTCCAA-TCTAATAT-T-AAAAGTACCGTCTTCTACTTATCCTTTGAACTGTC
1 CTTTGAATTGTCTACCAATTC-AAT-TCTAAAAAGGACCGTCTTCTGCTTATCCTTTGAACTGTC
*
2267 TACCAATTCAA-TCTTAAAAGGATCGTCTTCCGCTTATC
64 TACCAATTCAATTC-TAAAAGGACCGTCTTCCGCTTATC
*
2305 CTTTGAATTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCTGCTTATCGTTTGAACTGTCTA
1 CTTTGAATTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCTGCTTATCCTTTGAACTGTCTA
2370 CCAATTCAATTCTAAAAGGACCGTCTTCCGCTTATC
66 CCAATTCAATTCTAAAAGGACCGTCTTCCGCTTATC
* *
2406 CTTTGAACTGTCTACCAATTCAATTCTATAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCT
1 CTTTGAATTGTCTACCAATTCAATTCTA-AAAAGGACCGTCTTCTGCTTATCCTTTGAACTGTCT
2471 ACCAATTCAA
65 ACCAATTCAA
2481 AAAACGGTAA
Statistics
Matches: 163, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
99 1 0.01
100 21 0.13
101 95 0.58
102 46 0.28
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (101 bp):
CTTTGAATTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCTGCTTATCCTTTGAACTGTCTA
CCAATTCAATTCTAAAAGGACCGTCTTCCGCTTATC
Found at i:2567 original size:48 final size:48
Alignment explanation
Indices: 2496--2601 Score: 212
Period size: 48 Copynumber: 2.2 Consensus size: 48
2486 GGTAATGCAC
2496 CGTATGGAAACGGATGTGGCTTGGATGAAACCAAGGTTTGAAATGACT
1 CGTATGGAAACGGATGTGGCTTGGATGAAACCAAGGTTTGAAATGACT
2544 CGTATGGAAACGGATGTGGCTTGGATGAAACCAAGGTTTGAAATGACT
1 CGTATGGAAACGGATGTGGCTTGGATGAAACCAAGGTTTGAAATGACT
2592 CGTATGGAAA
1 CGTATGGAAA
2602 TGAGTTCAGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.25
Consensus pattern (48 bp):
CGTATGGAAACGGATGTGGCTTGGATGAAACCAAGGTTTGAAATGACT
Found at i:2649 original size:50 final size:50
Alignment explanation
Indices: 2587--2724 Score: 231
Period size: 50 Copynumber: 2.8 Consensus size: 50
2577 AGGTTTGAAA
* **
2587 TGACTCGTATGGAAATGAGTTCAGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
2637 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
2687 CGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
2725 AAAACATTCG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:2663 original size:98 final size:100
Alignment explanation
Indices: 2539--2724 Score: 231
Period size: 100 Copynumber: 1.9 Consensus size: 100
2529 AGGTTTGAAA
2539 TGACTCGTATGGAAACGGATGTGGC-T-TGGATGAAA-CCAAGGTTTGA-AAT-GACTCGTATGG
1 TGACTCGTATGGAAACGGATGTGGCTTGTGGA--AAAGCCAAGG-TTGATAATCGACTCGTATGG
* *
2599 AAATGAGTTCAGCTTGTGGAAAAGCCTATGTTGATAAT
63 AAACGAGTTCAGCTTATGGAAAAGCCTATGTTGATAAT
* * *
2637 TGACTCGTATGGAAAC-GAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATCGACTCGTATGGAA
1 TGACTCGTATGGAAACGGA-TGTGGCTTGTGGAAAAGCCAAGGTTGATAATCGACTCGTATGGAA
**
2701 ACGAGTTTGGCTTATGGAAAAGCC
65 ACGAGTTCAGCTTATGGAAAAGCC
2725 AAAACATTCG
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
97 2 0.03
98 28 0.37
99 8 0.11
100 37 0.49
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (100 bp):
TGACTCGTATGGAAACGGATGTGGCTTGTGGAAAAGCCAAGGTTGATAATCGACTCGTATGGAAA
CGAGTTCAGCTTATGGAAAAGCCTATGTTGATAAT
Found at i:3416 original size:50 final size:50
Alignment explanation
Indices: 3327--3525 Score: 274
Period size: 50 Copynumber: 4.0 Consensus size: 50
3317 CTTAAATGCC
* * * * *
3327 CTTTGAAAAGCAAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATCTTA
* *
3377 CTTTGAAAAGCGAATTTTAATCTTGAACTCTCAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATCTTA
* *
3427 TTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATCTTA
* * *
3477 TTTTGAACAGCGAATTTTGATCTTGAACTCAT-AAATGGAAAGAAATCTT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTC-TCAAATGGAAAGCAATCTT
3526 GTTATAGAAC
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 135 0.99
51 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATCTTA
Found at i:4146 original size:10 final size:10
Alignment explanation
Indices: 4133--4171 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
4123 TGATTTTTTC
4133 TTTTTTTTAT
1 TTTTTTTTAT
4143 TTTTTTTTAT
1 TTTTTTTTAT
4153 TTTTTATTT-T
1 TTTTT-TTTAT
4163 TATTTTTTT
1 T-TTTTTTT
4172 GATTGATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:4146 original size:17 final size:17
Alignment explanation
Indices: 4120--4168 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
4110 TTGATTTTGA
* *
4120 TTTTGATTTTTTCTT-T
1 TTTTTATTTTTTTTTAT
4136 TTTTTATTTTTTTTTAT
1 TTTTTATTTTTTTTTAT
4153 TTTTTATTTTTATTTT
1 TTTTTATTTTT-TTTT
4169 TTTGATTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 13 0.45
17 12 0.41
18 4 0.14
ACGTcount: A:0.10, C:0.02, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTTATTTTTTTTTAT
Found at i:4162 original size:6 final size:6
Alignment explanation
Indices: 4108--4169 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
4098 ATCAATTCTC
* * * *
4108 TTTTGA TTTTGA TTTTGA TTTTT- TCTTT- TTTTTA -TTTT- TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
4152 TTTTTTA TTTTTA TTTTT
1 -TTTTTA TTTTTA TTTTT
4170 TTGATTGATT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
5 16 0.33
6 27 0.55
7 6 0.12
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:4184 original size:23 final size:23
Alignment explanation
Indices: 4136--4186 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
4126 TTTTTTCTTT
* * *
4136 TTTTTATTTTTTTTTATTTTTTA
1 TTTTTATTTTTTTTGATTATTGA
4159 TTTTTA-TTTTTTTGATTGATTGA
1 TTTTTATTTTTTTTGATT-ATTGA
4182 TTTTT
1 TTTTT
4187 TGAATTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (23 bp):
TTTTTATTTTTTTTGATTATTGA
Found at i:4602 original size:24 final size:22
Alignment explanation
Indices: 4564--4627 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 22
4554 TCCAAGTGCC
*
4564 TTTATTTTCCTTTTTTCATTTTCAT
1 TTTATTTT-CATTTTTCA--TTCAT
4589 TTT-TTTTCAATTTTTCATTCAT
1 TTTATTTTC-ATTTTTCATTCAT
4611 TTTGATTTTCATTTTTC
1 TTT-ATTTTCATTTTTC
4628 TGGGAAATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 8 0.23
23 8 0.23
24 16 0.46
25 3 0.09
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTATTTTCATTTTTCATTCAT
Found at i:4603 original size:18 final size:16
Alignment explanation
Indices: 4574--4626 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
4564 TTTATTTTCC
4574 TTTTTTCATTTTCATT
1 TTTTTTCATTTTCATT
4590 TTTTTTCAATTTTTCATT
1 TTTTTTC-A-TTTTCATT
** *
4608 CATTTTGATTTTCATT
1 TTTTTTCATTTTCATT
4624 TTT
1 TTT
4627 CTGGGAAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 16 0.53
17 2 0.07
18 12 0.40
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTTTCATTTTCATT
Found at i:7255 original size:16 final size:16
Alignment explanation
Indices: 7226--7258 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7216 AATCTTGTTT
7226 ATTATCAAAAAAAATG
1 ATTATCAAAAAAAATG
7242 ATTAT-AAAAGAAAATG
1 ATTATCAAAA-AAAATG
7258 A
1 A
7259 AATCATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (16 bp):
ATTATCAAAAAAAATG
Done.