Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023247.1 Corchorus olitorius cultivar O-4 contig23280, 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: 10162
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:99 original size:25 final size:24
Alignment explanation
Indices: 71--122 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
61 GTGGATTGTA
*
71 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
96 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
120 AAA
1 AAA
123 AATTCAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:131 original size:22 final size:25
Alignment explanation
Indices: 71--131 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
61 GTGGATTGTA
* *
71 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTCAAGAATTAAGACATT
*
96 AAATAAATTTAAGAATTAA-ACATT
1 AAATAAATTCAAGAATTAAGACATT
120 -AA-AAATTCAAGA
1 AAATAAATTCAAGA
132 CTGACCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.27
23 2 0.06
24 5 0.15
25 17 0.52
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (25 bp):
AAATAAATTCAAGAATTAAGACATT
Found at i:973 original size:26 final size:27
Alignment explanation
Indices: 943--995 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
933 TGAGTAAAAC
*
943 TATAAAAGTATATTTAAA-AATTATAA
1 TATAAAAGTATAATTAAATAATTATAA
*
969 TATAAAAGTATAATTAAATAGTTATAA
1 TATAAAAGTATAATTAAATAATTATAA
996 GGATATTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (27 bp):
TATAAAAGTATAATTAAATAATTATAA
Found at i:1188 original size:15 final size:15
Alignment explanation
Indices: 1168--1198 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1158 TCGTACTTTT
1168 TATATATAGTATAGA
1 TATATATAGTATAGA
1183 TATATATAGTATAGA
1 TATATATAGTATAGA
1198 T
1 T
1199 GATGTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (15 bp):
TATATATAGTATAGA
Found at i:2190 original size:48 final size:48
Alignment explanation
Indices: 2116--2212 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
2106 CACTTTGAAC
*
2116 AATGAGATAACCGTTTCCATTCGTTAACTATTTAGTTTAACAAAAGCT
1 AATGAGATAACCGATTCCATTCGTTAACTATTTAGTTTAACAAAAGCT
* *
2164 AATGAGATAACTGATTCCATTTGTTAACTATTTAGTTTAACAAAAGCT
1 AATGAGATAACCGATTCCATTCGTTAACTATTTAGTTTAACAAAAGCT
2212 A
1 A
2213 CTTCCTCTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (48 bp):
AATGAGATAACCGATTCCATTCGTTAACTATTTAGTTTAACAAAAGCT
Found at i:4123 original size:19 final size:19
Alignment explanation
Indices: 4099--4149 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
4089 CAAAATGAAA
*
4099 AAAATAGCCACGTGGTATT
1 AAAATAGCCACGTGGCATT
4118 AAAATAGCCACGTGGCATT
1 AAAATAGCCACGTGGCATT
*
4137 AAAATAGTCACGT
1 AAAATAGCCACGT
4150 CGAATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (19 bp):
AAAATAGCCACGTGGCATT
Found at i:8866 original size:19 final size:20
Alignment explanation
Indices: 8836--8899 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
8826 TTGACACTGT
8836 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
8857 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
* *
8876 TTAGGTACTGTACAGAGGAGA
1 TTA-GCACTGTACAGATGAGA
8897 TTA
1 TTA
8900 TTAATTAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:8897 original size:21 final size:19
Alignment explanation
Indices: 8842--8899 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
8832 CTGTTTAGCA
8842 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
8861 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
8882 ACTGTACAGAGGAGATTA
1 ACTGTACAGATGAGATTA
8900 TTAATTAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Done.