Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021459.1 Corchorus olitorius cultivar O-4 contig21492, 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: 16003
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:844 original size:163 final size:161
Alignment explanation
Indices: 507--803 Score: 407
Period size: 161 Copynumber: 1.8 Consensus size: 161
497 TCTGTTGAGA
*
507 AAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGGAGAGGGAATTT
1 AAAACGCCGCTATATATTACAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGGAGAGGGAATTT
* * *
572 TTCCCTCCAAACAAAGAAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGGCGTTTACTGTTC
66 TTCCCTCCAAAAAAAGAAAAAAAAATCTCTCCCTCCATATATTAAAACAGCGGCGTTTACTGATC
* * *
637 TAGACGCCACAAATTAACGGCGTCTTGTTTT
131 AAAACGCCACAAATTAACGGCGTCTTGATTT
** ** *
668 AAAACGCCGCTATATATTACAGGTTTAGAGTTGGAAGCTTTCTTTGTTTTAGTGGGGAGGGAATT
1 AAAACGCCGCTATATATTACAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAG-GGAGAGGGAATT
* * * * *
733 TTTCCCTCCAAAAAAAGGAGAAAAAAATCTCTCCCTCCATGTATTAATACGGCGGCGTCTTTCT-
65 TTTCCCTCCAAAAAAA-GAAAAAAAAATCTCTCCCTCCATATATTAAAACAGCGGCGT-TTACTG
797 ATCAAAA
128 ATCAAAA
804 GGCCGCTAGA
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
161 47 0.40
162 26 0.22
163 40 0.34
164 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (161 bp):
AAAACGCCGCTATATATTACAGGCGTAGAGTTGGAAAATTTCTTTGTTTTAGGGAGAGGGAATTT
TTCCCTCCAAAAAAAGAAAAAAAAATCTCTCCCTCCATATATTAAAACAGCGGCGTTTACTGATC
AAAACGCCACAAATTAACGGCGTCTTGATTT
Found at i:4135 original size:2 final size:2
Alignment explanation
Indices: 4128--4152 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4118 AGGATACATT
4128 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 T
4153 TTGGTAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4189 original size:16 final size:16
Alignment explanation
Indices: 4157--4220 Score: 76
Period size: 16 Copynumber: 4.0 Consensus size: 16
4147 ATATATTTGG
*
4157 TAGGGAGGAAA-GAAA
1 TAGGAAGGAAAGGAAA
4172 TAGGAAGGAAAGGAAA
1 TAGGAAGGAAAGGAAA
*
4188 TAGCAATGGAAAGGAAA
1 TAGGAA-GGAAAGGAAA
* *
4205 TAGGGAGGAAGGGAAA
1 TAGGAAGGAAAGGAAA
4221 GGAAGTCACC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
15 10 0.24
16 18 0.43
17 14 0.33
ACGTcount: A:0.52, C:0.02, G:0.39, T:0.08
Consensus pattern (16 bp):
TAGGAAGGAAAGGAAA
Found at i:4200 original size:17 final size:16
Alignment explanation
Indices: 4162--4207 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 16
4152 TTTGGTAGGG
*
4162 AGGAAA-GAAATAGGA
1 AGGAAAGGAAATAGCA
4177 AGGAAAGGAAATAGCA
1 AGGAAAGGAAATAGCA
4193 ATGGAAAGGAAATAG
1 A-GGAAAGGAAATAG
4208 GGAGGAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.57, C:0.02, G:0.33, T:0.09
Consensus pattern (16 bp):
AGGAAAGGAAATAGCA
Found at i:5691 original size:42 final size:43
Alignment explanation
Indices: 5644--5731 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 43
5634 AACTAATATT
*
5644 GTTTCTTAACTGA-TTTTAACTTCT-AATTTCTAAACAGTTATA
1 GTTTCTGAACT-ATTTTTAACTTCTGAATTTCTAAACAGTTATA
* *
5686 GTTTCTGAACTATTTTTAACTTCTGATTTTCTAAATAGTTATA
1 GTTTCTGAACTATTTTTAACTTCTGAATTTCTAAACAGTTATA
5729 GTT
1 GTT
5732 GTTCAGAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
41 1 0.02
42 21 0.51
43 19 0.46
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.50
Consensus pattern (43 bp):
GTTTCTGAACTATTTTTAACTTCTGAATTTCTAAACAGTTATA
Found at i:14091 original size:161 final size:161
Alignment explanation
Indices: 13769--14096 Score: 513
Period size: 160 Copynumber: 2.0 Consensus size: 161
13759 ATATTCCAAT
13769 ATATAGTCAACAATTTTTTTTTTGGTAAAAATGTCAATAAATCATTGAATTTGCAAACGTATTAT
1 ATATAGTCAACAATTTTTTTTTTGGTAAAAATGTCAATAAATCATTGAATTTGC-AAC-TATTAT
* * *
13834 ATAATATATATATATGGCTGGCCCACGTTAATTGCTTTGCAATAATCGAAACGAATTAATAAGAA
64 ACAATACATATATATGGCTGACCCACGTTAATTGCTTTGCAATAATCGAAACGAATTAATAAGAA
13899 TCCAAAAATGAAGTACTAGCTAAATATATGTTC
129 TCCAAAAATGAAGTACTAGCTAAATATATGTTC
13932 ATATAGTCAACAAATTTTTTTTTTTTGGTAAAAATGTCAATAAATCATTGAATTTGC-A-T-TT-
1 ATATAGTCAAC-AA--TTTTTTTTTTGGTAAAAATGTCAATAAATCATTGAATTTGCAACTATTA
* *
13993 TGCAA-ACGTATATATGGCTGACCCACGTTAAATTGCTTTGCAATAATCGAAACGAATTAATAAG
63 TACAATACATATATATGGCTGACCCACGTT-AATTGCTTTGCAATAATCGAAACGAATTAATAAG
14057 AATCCAGAAAATGAAGTACTAGCTAAATATATGTTC
127 AATCCA-AAAATGAAGTACTAGCTAAATATATGTTC
14093 ATAT
1 ATAT
14097 TATATATTTT
Statistics
Matches: 155, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
159 21 0.14
160 43 0.28
161 35 0.23
162 1 0.01
163 11 0.07
164 3 0.02
166 41 0.26
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (161 bp):
ATATAGTCAACAATTTTTTTTTTGGTAAAAATGTCAATAAATCATTGAATTTGCAACTATTATAC
AATACATATATATGGCTGACCCACGTTAATTGCTTTGCAATAATCGAAACGAATTAATAAGAATC
CAAAAATGAAGTACTAGCTAAATATATGTTC
Found at i:15974 original size:1 final size:1
Alignment explanation
Indices: 15968--16003 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
15958 TGAATTTGAG
*
15968 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Done.