Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018530.1 Corchorus olitorius cultivar O-4 contig18563, 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: 16264
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:1561 original size:21 final size:23
Alignment explanation
Indices: 1532--1573 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1522 TTTTTTAAAA
1532 CGCAGAAA-CAAATTTTTTTTAT
1 CGCAGAAACCAAATTTTTTTTAT
*
1554 CGCA-AAACCGAATTTTTTTT
1 CGCAGAAACCAAATTTTTTTT
1574 CTAAAAACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (23 bp):
CGCAGAAACCAAATTTTTTTTAT
Found at i:1723 original size:39 final size:37
Alignment explanation
Indices: 1617--1711 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 37
1607 AATAACGCAA
*
1617 ATTAAAAACGCAAAAACAAAAAAAAAATCTTTTTTTTTTAG
1 ATTAAAAACGCAGAAAC--AAAAAAAA--TTTTTTTTTTAG
* * *
1658 -TAAAAAACGCAGAAAACGAAACAAATTTTTTTTTTAG
1 ATTAAAAACGCAG-AAACAAAAAAAATTTTTTTTTTAG
1695 ATTAAAAACGCAGAAAC
1 ATTAAAAACGCAGAAAC
1712 TAAGAGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
37 16 0.34
38 11 0.23
39 6 0.13
40 10 0.21
41 4 0.09
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (37 bp):
ATTAAAAACGCAGAAACAAAAAAAATTTTTTTTTTAG
Found at i:1801 original size:31 final size:31
Alignment explanation
Indices: 1764--1832 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
1754 CCTTACTTCC
1764 CCGGCAAAAACCAGGAGAAAGTTTTCCTTAA
1 CCGGCAAAAACCAGGAGAAAGTTTTCCTTAA
**
1795 CCGGCAAAAACCAGGAGAAAGTTTTCCTTCC
1 CCGGCAAAAACCAGGAGAAAGTTTTCCTTAA
1826 CCGGCAA
1 CCGGCAA
1833 CGGTGCCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (31 bp):
CCGGCAAAAACCAGGAGAAAGTTTTCCTTAA
Found at i:5268 original size:2 final size:2
Alignment explanation
Indices: 5261--5293 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5251 ATTATTTTTC
5261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5294 CTTGCTATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9829 original size:39 final size:38
Alignment explanation
Indices: 9765--9877 Score: 129
Period size: 38 Copynumber: 2.9 Consensus size: 38
9755 TCTCTATCTT
*** *
9765 AGTAAACCTGCTTAGGTCCCCATTTAGAGT-TGCCATTTA
1 AGTAAACCTGCTTAGGTCTATATTTAGAATCT--CATTTA
9804 AGTAAACCTGCTTAGGTCTATATTTAGAATCTCATTTA
1 AGTAAACCTGCTTAGGTCTATATTTAGAATCTCATTTA
* * **
9842 AGGAAACCTGTTTAGGTCTATGCTTAGAATCTCATT
1 AGTAAACCTGCTTAGGTCTATATTTAGAATCTCATT
9878 AGAATTTCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
38 38 0.58
39 26 0.40
40 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (38 bp):
AGTAAACCTGCTTAGGTCTATATTTAGAATCTCATTTA
Found at i:9979 original size:39 final size:39
Alignment explanation
Indices: 9886--10021 Score: 168
Period size: 39 Copynumber: 3.5 Consensus size: 39
9876 TTAGAATTTC
* * * *
9886 TAAGAAAACCTGTTTAGGTCCTCGCTTAGAA--TCGCGTT
1 TAAGCAAACCTGCTTAGGTCCTTGTTTAGAATTTC-CGTT
* **
9924 TGATTAAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTT
1 TAAGCAAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTT
*
9963 TAAGCAAACCTACTTAGGTCCTTGTTTAGAATTTCCGTT
1 TAAGCAAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTT
*
10002 TAGGCAAACCTGCTTAGGTC
1 TAAGCAAACCTGCTTAGGTC
10022 TCTGTTCCGT
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
38 25 0.30
39 57 0.68
40 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (39 bp):
TAAGCAAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTT
Found at i:10123 original size:39 final size:38
Alignment explanation
Indices: 10080--10206 Score: 134
Period size: 39 Copynumber: 3.3 Consensus size: 38
10070 TCGAGTAAAA
10080 CTGCTTAGGTCTTCGTTTAGAAGTTTCGTTTAATCAAAC
1 CTGCTTAGGTCTT-GTTTAGAAGTTTCGTTTAATCAAAC
** * *
10119 CTGCTTAGGTTCTTGTTTAGAA-TCCCCGCTTAAGT-GAAC
1 CTGCTTAGG-TCTTGTTTAGAAGT-TTCGTTTAA-TCAAAC
* *
10158 CTGCTTAGGTCTATGCTTAG-AGTTTCGTTCAATCAAAC
1 CTGCTTAGGTCT-TGTTTAGAAGTTTCGTTTAATCAAAC
10196 CTGCTTAGGTC
1 CTGCTTAGGTC
10207 CCTCTTTATA
Statistics
Matches: 72, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
37 1 0.01
38 24 0.33
39 42 0.58
40 5 0.07
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (38 bp):
CTGCTTAGGTCTTGTTTAGAAGTTTCGTTTAATCAAAC
Found at i:11878 original size:11 final size:11
Alignment explanation
Indices: 11854--11905 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
11844 TTGACAGCGC
11854 AACAAAAACAA
1 AACAAAAACAA
* *
11865 AACGAAAACGA
1 AACAAAAACAA
11876 AACAAAAACAA
1 AACAAAAACAA
11887 AA-AAACAA-AA
1 AACAAA-AACAA
*
11897 AACGAAAAC
1 AACAAAAAC
11906 GATGCCAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:11880 original size:16 final size:17
Alignment explanation
Indices: 11859--11907 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
11849 AGCGCAACAA
11859 AAAC-AAAACGAAAACG
1 AAACAAAAACGAAAACG
11875 AAACAAAAAC-AAAA--
1 AAACAAAAACGAAAACG
11889 AAACAAAAAACGAAAACG
1 AAAC-AAAAACGAAAACG
11907 A
1 A
11908 TGCCAAACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 12 0.43
17 5 0.18
18 1 0.04
ACGTcount: A:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (17 bp):
AAACAAAAACGAAAACG
Found at i:16226 original size:68 final size:68
Alignment explanation
Indices: 16117--16247 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 68
16107 CAACCAAGGA
* * * * *
16117 AAAAAATGGTGGGAACACCATTAATTATATTTCAATGCTAAAATTACATATGAAGACAATGCACT
1 AAAAAATGATAGGAACACCATTAATTACATTCCAATGCTAAAATTACATATAAAGACAATGCACT
16182 GAG
66 GAG
16185 AAAAAATGATAGGAACACCATTAATTACA-TCCAAATGCTAAAATTACATATAAAGACAATGCA
1 AAAAAATGATAGGAACACCATTAATTACATTCC-AATGCTAAAATTACATATAAAGACAATGCA
16248 TTTCAAGTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 2 0.04
68 55 0.96
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (68 bp):
AAAAAATGATAGGAACACCATTAATTACATTCCAATGCTAAAATTACATATAAAGACAATGCACT
GAG
Done.