Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021376.1 Corchorus olitorius cultivar O-4 contig21409, 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: 9115
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:748 original size:109 final size:109
Alignment explanation
Indices: 624--841 Score: 391
Period size: 109 Copynumber: 2.0 Consensus size: 109
614 CGATCAAAAA
* * * *
624 CGAATCACGGCAACATTTTCTTCGAAGGTAAGAATTGATCAAGAGCAATTAGAGATTTAATTTGA
1 CGAATCACGGAAACATTTTCTTCGAAGGTAAGAATTGATCAAGAGCAATTACAGATTAAATTCGA
689 AGGAAAAAAAAAGGAAAGTTGGTTTAGCAGGAAAAAAAAAGAAC
66 AGGAAAAAAAAAGGAAAGTTGGTTTAGCAGGAAAAAAAAAGAAC
733 CGAATCACGGAAACATTTTCTTCGAAGGTAAGAATTGATCAAGAGCAATTACAGATTAAATTCGA
1 CGAATCACGGAAACATTTTCTTCGAAGGTAAGAATTGATCAAGAGCAATTACAGATTAAATTCGA
*
798 AGGGAAAAAAAAGGAAAGTTGGTTTAGCAGGAAAAAAAAAGAAC
66 AGGAAAAAAAAAGGAAAGTTGGTTTAGCAGGAAAAAAAAAGAAC
842 TGCTAATTTT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (109 bp):
CGAATCACGGAAACATTTTCTTCGAAGGTAAGAATTGATCAAGAGCAATTACAGATTAAATTCGA
AGGAAAAAAAAAGGAAAGTTGGTTTAGCAGGAAAAAAAAAGAAC
Found at i:1153 original size:7 final size:8
Alignment explanation
Indices: 1136--1182 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
1126 CCTACCATTG
1136 TATATTATC
1 TATA-TATC
1145 TA-ATATC
1 TATATATC
*
1152 TATATATA
1 TATATATC
*
1160 TATATATA
1 TATATATC
*
1168 TATATATA
1 TATATATC
1176 TATATAT
1 TATATAT
1183 TCTTGGCTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
7 6 0.17
8 28 0.78
9 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (8 bp):
TATATATC
Found at i:1159 original size:2 final size:2
Alignment explanation
Indices: 1147--1182 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1137 ATATTATCTA
*
1147 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1183 TCTTGGCTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1332 original size:13 final size:12
Alignment explanation
Indices: 1311--1345 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
1301 AATAAAGTAA
1311 TAATACTATTAT
1 TAATACTATTAT
1323 TAATTACTATTAT
1 TAA-TACTATTAT
1336 TAATACTATT
1 TAATACTATT
1346 TCAATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Found at i:2836 original size:2 final size:2
Alignment explanation
Indices: 2829--2858 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2819 ATTGCTAGTA
2829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2859 GAGGGATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8446 original size:21 final size:21
Alignment explanation
Indices: 8422--8489 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
8412 CTCCTTTTTT
8422 TCCTCCTTCTTCCTCTCCTTC
1 TCCTCCTTCTTCCTCTCCTTC
*
8443 TCCTCC-TCCTCTCTCTCCTTC
1 TCCTCCTTCTTC-CTCTCCTTC
* *
8464 TCCTCCTTCTTTCTCTTCTTC
1 TCCTCCTTCTTCCTCTCCTTC
8485 TCCTC
1 TCCTC
8490 ATCATCGTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.10
21 34 0.83
22 3 0.07
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (21 bp):
TCCTCCTTCTTCCTCTCCTTC
Found at i:8471 original size:9 final size:9
Alignment explanation
Indices: 8403--8473 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 9
8393 TTCTTCTTTC
*
8403 CTCCTCCTC
1 CTCCTCCTT
**
8412 CTCCTTTTT
1 CTCCTCCTT
*
8421 TTCCTCCTT
1 CTCCTCCTT
8430 CTTCCTCTCCTT
1 C-T-C-CTCCTT
8442 CTCCTCCTCCT
1 CTCCTCCT--T
8453 CTCTCTCCTT
1 CTC-CTCCTT
8463 CTCCTCCTT
1 CTCCTCCTT
8472 CT
1 CT
8474 TTCTCTTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
9 25 0.51
10 6 0.12
11 6 0.12
12 12 0.24
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (9 bp):
CTCCTCCTT
Found at i:8823 original size:37 final size:38
Alignment explanation
Indices: 8764--8843 Score: 128
Period size: 37 Copynumber: 2.1 Consensus size: 38
8754 GAATATTGCT
*
8764 CTTTGCTTGGGCACTTCGGAAGA-ATACTATGACCTTGG
1 CTTTGCTTGGGCACTTCGGAAGAGAT-CTAGGACCTTGG
8802 CTTTGCTTGGG-ACTTCGGAAGAGATCTAGGACCTTGG
1 CTTTGCTTGGGCACTTCGGAAGAGATCTAGGACCTTGG
8839 CTTTG
1 CTTTG
8844 GTGTTGGATG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
37 27 0.68
38 13 0.32
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.33
Consensus pattern (38 bp):
CTTTGCTTGGGCACTTCGGAAGAGATCTAGGACCTTGG
Done.