Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024811.1 Corchorus olitorius cultivar O-4 contig24844, 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: 5597
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Found at i:225 original size:28 final size:27
Alignment explanation
Indices: 150--223 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 27
140 ATGTGAACTT
150 AAAATGACCAAAATGCCCCTGAACATGC
1 AAAATGACCAAAATGCCCCTG-ACATGC
178 AAAATGACCAAAATGCCCCTG-CATGC
1 AAAATGACCAAAATGCCCCTGACATGC
204 AAAAATGACCAAAATGCCCC
1 -AAAATGACCAAAATGCCCC
224 CTAAATGACC
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
26 5 0.11
27 19 0.42
28 21 0.47
ACGTcount: A:0.43, C:0.30, G:0.14, T:0.14
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGACATGC
Found at i:2041 original size:27 final size:27
Alignment explanation
Indices: 2000--2098 Score: 135
Period size: 27 Copynumber: 3.7 Consensus size: 27
1990 AGTGAGCTTA
*
2000 AAATGACCAAAATGCCCCTGAATGTGT
1 AAATGACCAAAATGCCCCTGAATGTGC
*
2027 AAATGACCAAGATGCCCCTGAATGTGC
1 AAATGACCAAAATGCCCCTGAATGTGC
* * *
2054 AAATGACAAAAATGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGAATGTGC
* *
2081 AAATGACAAAAACGCCCC
1 AAATGACCAAAATGCCCC
2099 ACAGATGACC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGTGC
Found at i:2529 original size:50 final size:50
Alignment explanation
Indices: 2399--2793 Score: 547
Period size: 50 Copynumber: 7.8 Consensus size: 50
2389 GAAGTAAGGC
* * * * * *
2399 TTGACTCATATGGAAACGTGTTTGACTTATGGAAAAGTCTATATGGCTTGGATAG
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-C-CTAT-G-TT-GATAA
*
2454 TTGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* * *
2504 TTGACTCGTATAGAAACGAGCTTGGCTTGTGGAAAAAGCCTGTGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGG-AAAAGCCTATGTTGATAA
*
2555 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* *
2605 TTGACTCGTATGGAAACAAGTTAGGCTTGTGGAAAAGCCTATGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
*
2655 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAA
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* * * * *
2705 TTGACTCATATGGAAACGAGTTTGGCTTGTAGAAGAGCCTGTGTTGATAT
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
* *
2755 TTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
1 TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
2794 AAAGCATTCG
Statistics
Matches: 309, Mismatches: 30, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
50 223 0.72
51 49 0.16
52 1 0.00
53 3 0.01
54 1 0.00
55 32 0.10
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (50 bp):
TTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAA
Found at i:3473 original size:50 final size:50
Alignment explanation
Indices: 3407--3544 Score: 204
Period size: 51 Copynumber: 2.7 Consensus size: 50
3397 AAAATCGACC
* * *
3407 TTTGGTCTTGGTCTCACAAATGGAGTGCAATTTTATTTTGAAAAGCGAAT
1 TTTGATCTTGGACTCACAAATGGAATGCAATTTTATTTTGAAAAGCGAAT
**
3457 TTTGATCTTGGACTCACAAATGGAATGCAAATTTCGTTTTGAAAAGCGAAT
1 TTTGATCTTGGACTCACAAATGGAATGC-AATTTTATTTTGAAAAGCGAAT
* *
3508 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATT
1 TTTGATCTTGGACTCACAAATGGAATGCAATTTTATT
3545 GTAAATCTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 31 0.40
51 47 0.60
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (50 bp):
TTTGATCTTGGACTCACAAATGGAATGCAATTTTATTTTGAAAAGCGAAT
Found at i:4146 original size:22 final size:22
Alignment explanation
Indices: 4123--4204 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 22
4113 CCATTCTCTT
*
4123 TTGATTTTGGTTTGATTTGATTT
1 TTGA-TTTGATTTGATTTGATTT
**
4146 TTGATTTGATTTGATTTTTTTCT
1 TTGATTTGATTTGATTTGATT-T
*
4169 TTTA-TTGACTTTGATTTGATTTT
1 TTGATTTGA-TTTGATTTGA-TTT
4192 TTGATTTTGATTT
1 TTGA-TTTGATTT
4205 TTTTTTAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
22 18 0.38
23 20 0.43
24 5 0.11
25 4 0.09
ACGTcount: A:0.15, C:0.02, G:0.16, T:0.67
Consensus pattern (22 bp):
TTGATTTGATTTGATTTGATTT
Found at i:4147 original size:23 final size:23
Alignment explanation
Indices: 4121--4204 Score: 86
Period size: 22 Copynumber: 3.7 Consensus size: 23
4111 ATCCATTCTC
*
4121 TTTTGATTTTGGTTTGATTTGAT
1 TTTTGATTTTGATTTGATTTGAT
4144 TTTTGA-TTTGATTTGATTT--T
1 TTTTGATTTTGATTTGATTTGAT
*
4164 TTTCT-TTTATTGACTTTGATTTGATT
1 TTT-TGATT-TTGA-TTTGATTTGA-T
4190 TTTTGATTTTGATTT
1 TTTTGATTTTGATTT
4205 TTTTTTAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
20 4 0.08
21 2 0.04
22 16 0.32
23 14 0.28
24 3 0.06
25 5 0.10
26 6 0.12
ACGTcount: A:0.14, C:0.02, G:0.15, T:0.68
Consensus pattern (23 bp):
TTTTGATTTTGATTTGATTTGAT
Found at i:4153 original size:17 final size:17
Alignment explanation
Indices: 4122--4164 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
4112 TCCATTCTCT
*
4122 TTTGA-TTTTGGTTTGA
1 TTTGATTTTTGATTTGA
4138 TTTGATTTTTGATTTGA
1 TTTGATTTTTGATTTGA
4155 TTTGATTTTT
1 TTTGATTTTT
4165 TTCTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.14, C:0.00, G:0.19, T:0.67
Consensus pattern (17 bp):
TTTGATTTTTGATTTGA
Found at i:4182 original size:6 final size:5
Alignment explanation
Indices: 4122--4204 Score: 50
Period size: 5 Copynumber: 16.6 Consensus size: 5
4112 TCCATTCTCT
* **
4122 TTTGA TTTTGG TTTGA TTTGA TTTTTGA TTTGA TTTGA TTT-- TTTTC
1 TTTGA -TTTGA TTTGA TTTGA --TTTGA TTTGA TTTGA TTTGA TTTGA
*
4168 TTTTA -TTGA CTTTGA TTTGA TTT-- TTTGA TTTTGA TTT
1 TTTGA TTTGA -TTTGA TTTGA TTTGA TTTGA -TTTGA TTT
4205 TTTTTTAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
3 6 0.09
4 3 0.05
5 37 0.58
6 13 0.20
7 5 0.08
ACGTcount: A:0.14, C:0.02, G:0.16, T:0.67
Consensus pattern (5 bp):
TTTGA
Found at i:4202 original size:14 final size:13
Alignment explanation
Indices: 4150--4207 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
4140 TGATTTTTGA
4150 TTTGATTTGATTT
1 TTTGATTTGATTT
** * *
4163 TTTTCTTTTATTGAC
1 TTTGATTTGATT--T
4178 TTTGATTTGATTT
1 TTTGATTTGATTT
4191 TTTGATTTTGATTT
1 TTTGA-TTTGATTT
4205 TTT
1 TTT
4208 TTTAAATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
13 14 0.41
14 11 0.32
15 9 0.26
ACGTcount: A:0.14, C:0.03, G:0.12, T:0.71
Consensus pattern (13 bp):
TTTGATTTGATTT
Found at i:4638 original size:15 final size:15
Alignment explanation
Indices: 4610--4658 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
4600 TTATTTTCCT
*
4610 TTTTTTTCATTTTTTA
1 TTTTCTTCA-TTTTTA
* *
4626 TTTTCTTTATTTTCA
1 TTTTCTTCATTTTTA
4641 TTTTCTTCATTTTT-
1 TTTTCTTCATTTTTA
4655 TTTT
1 TTTT
4659 GGTAAATCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 4 0.14
15 17 0.61
16 7 0.25
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTCATTTTTA
Found at i:5151 original size:9 final size:9
Alignment explanation
Indices: 5137--5162 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5127 GATTACAACT
5137 GATTTTGAA
1 GATTTTGAA
5146 GATTTTGAA
1 GATTTTGAA
5155 GATTTTGA
1 GATTTTGA
5163 TTAAAACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (9 bp):
GATTTTGAA
Done.