Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021561.1 Corchorus olitorius cultivar O-4 contig21594, 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: 19994
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40 CTAGTTAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1627 original size:58 final size:58
Alignment explanation
Indices: 1531--1643 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
1521 ATTAATCAAA
*
1531 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACATTTTCGGAACGAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACATTTTAGGAACGAGGCT
* * * * *
1589 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACATTTTAGGAACGAG
1644 ACATGATGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 33 0.69
59 15 0.31
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACATTTTAGGAACGAGGCT
Found at i:2336 original size:36 final size:36
Alignment explanation
Indices: 2289--2358 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
2279 TTCAATAAGC
* * *
2289 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATAATCATATTTCTTA
*
2325 TTACATTTTTTGTAATTTTGATAATCATATTTCT
1 TTACATCTTTTGTAATTTTGATAATCATATTTCT
2359 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.09, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATAATCATATTTCTTA
Found at i:3185 original size:25 final size:24
Alignment explanation
Indices: 3151--3197 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
3141 ACGTTTGCAC
3151 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
3176 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
3198 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:3831 original size:21 final size:20
Alignment explanation
Indices: 3779--3831 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
3769 AAAAAGGTGT
* *
3779 TAAAAATTTTATAAGATTAT
1 TAAAAATCTTATAAGATTAC
* *
3799 TAAAAAAACTTATAAGGTTAC
1 T-AAAAATCTTATAAGATTAC
3820 TAAAAATGCTTA
1 TAAAAAT-CTTA
3832 AAAACTTCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.36
Consensus pattern (20 bp):
TAAAAATCTTATAAGATTAC
Found at i:4325 original size:12 final size:12
Alignment explanation
Indices: 4308--4332 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4298 TTTATCAATC
4308 TATATTTAATTT
1 TATATTTAATTT
4320 TATATTTAATTT
1 TATATTTAATTT
4332 T
1 T
4333 TATCATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTAATTT
Found at i:5191 original size:142 final size:136
Alignment explanation
Indices: 5021--5300 Score: 461
Period size: 142 Copynumber: 2.0 Consensus size: 136
5011 TATGTTATAT
5021 TATATATGTTCTTGATAATTTTTAGCAACACATAGTTTACAAATCTAATAATTAGTTGCTTATGA
1 TATATATGTTCTTGATAATTTTTAGCAACACATAGTTTACAAATCTAATAATTAGTTGCTTATGA
*
5086 GGGTTTTGAACTTACAAAAACAAATGATCAAAATTATAAATATAGATGCTAATATATATTGTGAC
66 GGGTTTTGAACTTACAAAAACAAATGATC-AAA--AT---TATAGATGCTAACATATATTGTGAC
5151 TTGGCTAAAAAA
125 TTGGCTAAAAAA
*
5163 TATATATGTTCTTGATAATTTTTAGCAACACATAGTTTACAAATCTAATAATTAGTTGCTTATGC
1 TATATATGTTCTTGATAATTTTTAGCAACACATAGTTTACAAATCTAATAATTAGTTGCTTATGA
* * *
5228 TGGTTTTGAACTTACAAAAACAAATGATCGAAATTATAGATGCTAACATATGTTGTGACTTGGCT
66 GGGTTTTGAACTTACAAAAACAAATGATCAAAATTATAGATGCTAACATATATTGTGACTTGGCT
5293 AAAAAA
131 AAAAAA
5299 TA
1 TA
5301 CATGAAGAGT
Statistics
Matches: 133, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
136 37 0.28
139 2 0.02
141 2 0.02
142 92 0.69
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (136 bp):
TATATATGTTCTTGATAATTTTTAGCAACACATAGTTTACAAATCTAATAATTAGTTGCTTATGA
GGGTTTTGAACTTACAAAAACAAATGATCAAAATTATAGATGCTAACATATATTGTGACTTGGCT
AAAAAA
Found at i:11549 original size:11 final size:11
Alignment explanation
Indices: 11529--11563 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
11519 TTGACAGCGC
11529 AACAAAAACAA
1 AACAAAAACAA
*
11540 AACGAAAACAA
1 AACAAAAACAA
11551 AACAAAAACAA
1 AACAAAAACAA
11562 AA
1 AA
11564 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:16774 original size:21 final size:19
Alignment explanation
Indices: 16729--16786 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
16719 CTATTTAGCA
16729 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
16748 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
16769 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
16787 TTAGAGCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:17129 original size:7 final size:7
Alignment explanation
Indices: 17117--17150 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
17107 GACCAAAGCA
17117 TATGCAT
1 TATGCAT
17124 TATGCAT
1 TATGCAT
17131 TATGCAT
1 TATGCAT
17138 TATGCAT
1 TATGCAT
17145 TATGCA
1 TATGCA
17151 ACGTGGATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (7 bp):
TATGCAT
Found at i:17639 original size:33 final size:32
Alignment explanation
Indices: 17602--17755 Score: 98
Period size: 33 Copynumber: 4.7 Consensus size: 32
17592 TATAGAAAAA
17602 ATGGCAGTGGCGCCCCAGGGGGGCGCCGTCGGC
1 ATGGC-GTGGCGCCCCAGGGGGGCGCCGTCGGC
* * *
17635 ATGGCGATGGCG-CCCTGTTGGGGCGTCGTCGGC
1 ATGGCG-TGGCGCCCCAG-GGGGGCGCCGTCGGC
* * * **
17668 ATGGCGATGGCG-CCCTGCCGGGGCGGCGTCACC
1 ATGGCG-TGGCGCCCCAG-GGGGGCGCCGTCGGC
** ** *
17701 ATATCGGTGGCGCCCC-CTGGAGCGCCGTCGGC
1 ATGGC-GTGGCGCCCCAGGGGGGCGCCGTCGGC
*
17733 ATGGTGGTGGCGCCCCAGGGGGG
1 ATGG-CGTGGCGCCCCAGGGGGG
17756 TGCCACCGCC
Statistics
Matches: 93, Mismatches: 22, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
32 27 0.29
33 62 0.67
34 4 0.04
ACGTcount: A:0.08, C:0.32, G:0.45, T:0.14
Consensus pattern (32 bp):
ATGGCGTGGCGCCCCAGGGGGGCGCCGTCGGC
Found at i:18209 original size:27 final size:27
Alignment explanation
Indices: 18171--18226 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
18161 AAGGGAGAAA
18171 GAGGCTGAGGCTACTCGGATGTATAGG
1 GAGGCTGAGGCTACTCGGATGTATAGG
*
18198 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTACTCGGATGTATAGG
18225 GA
1 GA
18227 TAGGGAGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.14, G:0.43, T:0.21
Consensus pattern (27 bp):
GAGGCTGAGGCTACTCGGATGTATAGG
Found at i:18535 original size:20 final size:20
Alignment explanation
Indices: 18510--18551 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
18500 TATTATGTGA
*
18510 TATTATAAATTGAAATTAAT
1 TATTATAAATTGAAATAAAT
18530 TATTATAAATTGAAATAAAT
1 TATTATAAATTGAAATAAAT
18550 TA
1 TA
18552 AATAAATTAT
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:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
TATTATAAATTGAAATAAAT
Done.