Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013275.1 Corchorus olitorius cultivar O-4 contig13308, 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: 12990
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Found at i:2712 original size:30 final size:31
Alignment explanation
Indices: 2678--2754 Score: 115
Period size: 30 Copynumber: 2.5 Consensus size: 31
2668 TAATGACAAA
2678 ATCAGAATTC-TCTCCTTCACAAACAAAGAG
1 ATCAGAATTCTTCTCCTTCACAAACAAAGAG
2708 ATCAGAA-TCTTCTCCTTCACAAACAAAGAG
1 ATCAGAATTCTTCTCCTTCACAAACAAAGAG
*
2738 ATCGGAA-TCTTCCTCCT
1 ATCAGAATTCTT-CTCCT
2755 CGTCATACTC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 2 0.05
30 37 0.84
31 5 0.11
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.26
Consensus pattern (31 bp):
ATCAGAATTCTTCTCCTTCACAAACAAAGAG
Found at i:3492 original size:22 final size:23
Alignment explanation
Indices: 3453--3495 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
3443 AATCCTAATC
3453 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
3476 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
3496 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:7357 original size:49 final size:49
Alignment explanation
Indices: 7285--7384 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
7275 AATCACCACT
* *
7285 ATTCCTCATAATCCCAAACACCTAATCAAGCATACCCATGATCAAAACA
1 ATTCCTCATAATCCCAAACACCTAATCAAACATACCCAAGATCAAAACA
*
7334 ATTCCTCATAATGCCAAACACCTAATCAAACATACCCAAGATCAAAACA
1 ATTCCTCATAATCCCAAACACCTAATCAAACATACCCAAGATCAAAACA
7383 AT
1 AT
7385 CCAGAAAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.45, C:0.31, G:0.04, T:0.20
Consensus pattern (49 bp):
ATTCCTCATAATCCCAAACACCTAATCAAACATACCCAAGATCAAAACA
Found at i:8393 original size:49 final size:49
Alignment explanation
Indices: 8321--8420 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
8311 AATCACCACT
*
8321 ATTCCTCATAATCCCAAACACCTAATCAAGCATACCCATGATCAAAACA
1 ATTCCTCATAATCCCAAACACCTAATCAAGCATACCCAAGATCAAAACA
*
8370 ATTCCTCATAATGCCAAACACCTAATCAAGCATACCCAAGATCAAAACA
1 ATTCCTCATAATCCCAAACACCTAATCAAGCATACCCAAGATCAAAACA
8419 AT
1 AT
8421 CCAGAAAATC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.44, C:0.31, G:0.05, T:0.20
Consensus pattern (49 bp):
ATTCCTCATAATCCCAAACACCTAATCAAGCATACCCAAGATCAAAACA
Found at i:11681 original size:19 final size:20
Alignment explanation
Indices: 11648--11693 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
11638 GGGGAAGGGC
* *
11648 AAAACGAGAATAAAAGGTTG
1 AAAACAAGAATAAAAGATTG
*
11668 AGAACAAGAA-AAAAGATTG
1 AAAACAAGAATAAAAGATTG
11687 AAAACAA
1 AAAACAA
11694 CACATTCCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.63, C:0.07, G:0.20, T:0.11
Consensus pattern (20 bp):
AAAACAAGAATAAAAGATTG
Found at i:11753 original size:20 final size:20
Alignment explanation
Indices: 11715--11780 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
11705 CGGGAAGGGC
*
11715 AAACAAGAATAAAACATTGA
1 AAACAAGAACAAAACATTGA
* * *
11735 AGACAGGAACAAGACATTGA
1 AAACAAGAACAAAACATTGA
*
11755 AAACAAGAATAAAACATTGA
1 AAACAAGAACAAAACATTGA
11775 AAACAA
1 AAACAA
11781 CACCTCCCGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.62, C:0.12, G:0.14, T:0.12
Consensus pattern (20 bp):
AAACAAGAACAAAACATTGA
Found at i:11831 original size:20 final size:20
Alignment explanation
Indices: 11808--11849 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
11798 GGACAAAATT
11808 GGAATAAAACAATGAAAACA
1 GGAATAAAACAATGAAAACA
*
11828 GGAATAAAACATTGAAAACA
1 GGAATAAAACAATGAAAACA
11848 GG
1 GG
11850 GACAAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.10, G:0.19, T:0.12
Consensus pattern (20 bp):
GGAATAAAACAATGAAAACA
Found at i:11842 original size:88 final size:87
Alignment explanation
Indices: 11655--11904 Score: 306
Period size: 88 Copynumber: 2.9 Consensus size: 87
11645 GGCAAAACGA
** * * * *
11655 GAATAAAAGGTTGAGAACAAGAAAAAAGATTGAAAACAACACATTCCTACCGGGAAGGGCAAACA
1 GAATAAAACATTGAAAACAAGAAAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAA-A
* * *
11720 --AGAATAAAACATTGAAGACAG
65 TTGGAATAAAACAATGAAAACAG
* * * *
11741 GAACAAGACATTGAAAACAAGAATAAAACATTGAAAACAACACCTCCCGACCGGGAAGGACAAAA
1 GAATAAAACATTGAAAACAAGAA-AAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAA
11806 TTGGAATAAAACAATGAAAACAG
65 TTGGAATAAAACAATGAAAACAG
* * **
11829 GAATAAAACATTGAAAACAGGGACAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAA
1 GAATAAAACATTGAAAACA-AGAAAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAA
11894 TTGGAATAAAA
65 TTGGAATAAAA
11905 TATTGAAGAC
Statistics
Matches: 139, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
86 19 0.14
87 35 0.25
88 83 0.60
89 2 0.01
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.13
Consensus pattern (87 bp):
GAATAAAACATTGAAAACAAGAAAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAT
TGGAATAAAACAATGAAAACAG
Found at i:11856 original size:20 final size:20
Alignment explanation
Indices: 11808--11867 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
11798 GGACAAAATT
* *
11808 GGAATAAAACAATGAAAACA
1 GGAACAAAACATTGAAAACA
*
11828 GGAATAAAACATTGAAAACA
1 GGAACAAAACATTGAAAACA
* **
11848 GGGACAAAATGTTGAAAACA
1 GGAACAAAACATTGAAAACA
11868 ACACCTTCCG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.58, C:0.10, G:0.18, T:0.13
Consensus pattern (20 bp):
GGAACAAAACATTGAAAACA
Found at i:11911 original size:48 final size:48
Alignment explanation
Indices: 11842--12337 Score: 733
Period size: 48 Copynumber: 10.4 Consensus size: 48
11832 TAAAACATTG
* *
11842 AAAACAGGGACAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
** * * *
11890 AAAATTGGAATAAAATATTGAAGACAACACCTTCCGACCGGAAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
* *
11938 AAAACAGGAATGAAATATTGAAAACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
* * *
11986 AAAACATGAATAAAATGTTGAAAACAACGCCTTCCGACCAGGAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
* *
12034 AAAACGGGAATACAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
*
12082 AAAATAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
*
12130 AAAACAGGAATATAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
* * *
12178 AAAACGGGAATATAATGTTGAAAACAACACCTTCCGAACGGGAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
* * **
12226 AAAACGGGAATACAATGTTGAAAACAACACCTTCCGACTAGGAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
** * * *
12274 AAAATTGGAATACACTGTTGAAAACAACACCTTCCGACTGGGAAGGGC
1 AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
12322 AAAACA-GAATAAAATG
1 AAAACAGGAATAAAATG
12338 GGATTGAAAT
Statistics
Matches: 407, Mismatches: 41, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
47 8 0.02
48 399 0.98
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (48 bp):
AAAACAGGAATAAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGC
Done.