Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012302.1 Corchorus olitorius cultivar O-4 contig12335, 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: 16517
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:631 original size:17 final size:17
Alignment explanation
Indices: 609--650 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
599 GAGCCTGAAC
*
609 CCGAACCCTACCCGAGA
1 CCGAACCCTACCCAAGA
626 CCGAACCCTACCCAAGA
1 CCGAACCCTACCCAAGA
643 CCGAACCC
1 CCGAACCC
651 GAAAATACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.50, G:0.14, T:0.05
Consensus pattern (17 bp):
CCGAACCCTACCCAAGA
Found at i:664 original size:16 final size:16
Alignment explanation
Indices: 643--731 Score: 92
Period size: 16 Copynumber: 5.6 Consensus size: 16
633 CTACCCAAGA
643 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
659 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
*
675 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
**
691 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
*
707 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
*
723 CCAAACCCG
1 CCGAACCCG
732 CCCGAAACTC
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
15 5 0.09
16 48 0.83
17 5 0.09
ACGTcount: A:0.37, C:0.42, G:0.15, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:687 original size:32 final size:32
Alignment explanation
Indices: 643--731 Score: 151
Period size: 32 Copynumber: 2.8 Consensus size: 32
633 CTACCCAAGA
*
643 CCGAACCCGAAAATACCCGAACCCGACATAAC
1 CCGAGCCCGAAAATACCCGAACCCGACATAAC
*
675 CCGAGCCCGAAAATACCCGAACCCGACTTAAC
1 CCGAGCCCGAAAATACCCGAACCCGACATAAC
*
707 CCGAGCCCGAAAATACCCAAACCCG
1 CCGAGCCCGAAAATACCCGAACCCG
732 CCCGAAACTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.37, C:0.42, G:0.15, T:0.07
Consensus pattern (32 bp):
CCGAGCCCGAAAATACCCGAACCCGACATAAC
Found at i:877 original size:62 final size:62
Alignment explanation
Indices: 771--892 Score: 181
Period size: 62 Copynumber: 2.0 Consensus size: 62
761 ACACTAAAAA
* * * **
771 TGGATCTCACTGACTTGACCATCGGAGAAGGTCCCCCCTTAAACACCACAGGGGAACCTCAG
1 TGGACCTCACTAACTTGACCATCGGAGAAGGTCCCCCCTCAAACACCACAGAAGAACCTCAG
* *
833 TGGACCTCACTAACTTGACCGTCGGAGGAGGTCCCCCCTCAAACACCACAGAAGAACCTC
1 TGGACCTCACTAACTTGACCATCGGAGAAGGTCCCCCCTCAAACACCACAGAAGAACCTC
893 TCTAACGATT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.16
Consensus pattern (62 bp):
TGGACCTCACTAACTTGACCATCGGAGAAGGTCCCCCCTCAAACACCACAGAAGAACCTCAG
Found at i:1164 original size:53 final size:57
Alignment explanation
Indices: 1091--1247 Score: 178
Period size: 61 Copynumber: 2.7 Consensus size: 57
1081 AACTACGTCG
* * * *
1091 TTTGATGATCTTTCAATCATT-GTT-CC-CGTT-TCTTCCCCTCGTTAAAATATGGT
1 TTTGATTATCTTTCATTCATTCGTTCCCTCGTTATCATCCACTCGTTAAAATATGGT
*
1144 TTTGATTATCTTTCATTCATTCTTTCCCTCGTTAATCATCCACTCGTTAAAATATGGT
1 TTTGATTATCTTTCATTCATTCGTTCCCTCGTT-ATCATCCACTCGTTAAAATATGGT
* *
1202 TTTAATTACTATCTTTCATTCATTCTTTCCCTCGTTAATCATCCAC
1 TTTGA-T--TATCTTTCATTCATTCGTTCCCTCGTT-ATCATCCAC
1248 CAAACCTCGA
Statistics
Matches: 90, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
53 19 0.21
54 2 0.02
55 2 0.02
56 4 0.04
58 25 0.28
59 1 0.01
61 37 0.41
ACGTcount: A:0.21, C:0.24, G:0.08, T:0.46
Consensus pattern (57 bp):
TTTGATTATCTTTCATTCATTCGTTCCCTCGTTATCATCCACTCGTTAAAATATGGT
Found at i:1202 original size:58 final size:60
Alignment explanation
Indices: 1128--1247 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 60
1118 GTTTCTTCCC
*
1128 CTCGTTAAAATATGGTTTTGA-T-TATCTTTCATTCATTCTTTCCCTCGTTAATCATCCA
1 CTCGTTAAAATATGGTTTTAATTATATCTTTCATTCATTCTTTCCCTCGTTAATCATCCA
1186 CTCGTTAAAATATGGTTTTAATTACTATCTTTCATTCATTCTTTCCCTCGTTAATCATCCA
1 CTCGTTAAAATATGGTTTTAATTA-TATCTTTCATTCATTCTTTCCCTCGTTAATCATCCA
1247 C
1 C
1248 CAAACCTCGA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
58 20 0.34
59 1 0.02
61 37 0.64
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.46
Consensus pattern (60 bp):
CTCGTTAAAATATGGTTTTAATTATATCTTTCATTCATTCTTTCCCTCGTTAATCATCCA
Found at i:1420 original size:17 final size:17
Alignment explanation
Indices: 1398--1430 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1388 CATATTTCCC
1398 AAGTCCAATTTTTCATG
1 AAGTCCAATTTTTCATG
1415 AAGTCCAATTTTTCAT
1 AAGTCCAATTTTTCAT
1431 TCATTCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (17 bp):
AAGTCCAATTTTTCATG
Found at i:11468 original size:178 final size:177
Alignment explanation
Indices: 11130--11576 Score: 510
Period size: 178 Copynumber: 2.5 Consensus size: 177
11120 AACTTTTCAA
* * * * * * *
11130 AAGCATTTTTGGTATTTGAAAAATAAAATTTAGCTTTCAAGTCCTACATGAAAGTTGAAGATCAC
1 AAGCTTTTTTGATACTTGAAACATAAAATTTAGCTTTC-AGTCCTGCATGAAAGTTGTAGATCAT
* * * ** *
11195 GAAACAGCCTTTTAATAGACACTTAAATCATCTCAATTGGACATCTGGAGCAAAAATTATGTATT
65 GAAACAACCTTTTAATAGACACTTGAATCAGCTCAATAAGACATCTGGAGCAAAAATAATGTATT
* * * * * * * *
11260 ATTAAGTGGACCGTTCATTCTCGCTAACCGAAAAAATTATTTTTTTGG
130 ACTAAATGGACCGTCCATTCCCGCTAACCGAAAAAACTAATTATTCGG
* *
11308 AAG-TATTTTTTATACTTGAAACATAAAATTTAGCTTTCGAGTCCTGCATAAAAGTTGTAGATCA
1 AAGCT-TTTTTGATACTTGAAACATAAAATTTAGCTTTC-AGTCCTGCATGAAAGTTGTAGATCA
* * * *
11372 TAAAATAACCTTTT-ATGAGACACTTGAGTCAGCTCAATAAGACATCTGGAGCAAAAGTAATGT-
64 TGAAACAACCTTTTAAT-AGACACTTGAATCAGCTCAATAAGACATCTGGAGCAAAAATAATGTA
* * *
11435 TATACTAAATGGATCGTCCATTCCCGTTAACCGAAACAACTAATTATTCGG
128 T-TACTAAATGGACCGTCCATTCCCGCTAACCGAAAAAACTAATTATTCGG
* *
11486 AAGCTTTTTTGATACTTGAAACATTAAATTTAGTTTTC-GT--TGCATGAAAGTTGTAGATCATG
1 AAGCTTTTTTGATACTTGAAACATAAAATTTAGCTTTCAGTCCTGCATGAAAGTTGTAGATCATG
*
11548 GAACAACCTTTTAATAGACACTTGAATCA
66 AAACAACCTTTTAATAGACACTTGAATCA
11577 CCTTAATCGG
Statistics
Matches: 225, Mismatches: 39, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
174 43 0.19
175 2 0.01
176 2 0.01
177 3 0.01
178 174 0.77
179 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (177 bp):
AAGCTTTTTTGATACTTGAAACATAAAATTTAGCTTTCAGTCCTGCATGAAAGTTGTAGATCATG
AAACAACCTTTTAATAGACACTTGAATCAGCTCAATAAGACATCTGGAGCAAAAATAATGTATTA
CTAAATGGACCGTCCATTCCCGCTAACCGAAAAAACTAATTATTCGG
Found at i:12567 original size:20 final size:21
Alignment explanation
Indices: 12542--12580 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12532 CTACCGCATA
12542 CTCCA-TTCCCCACTTTTGTT
1 CTCCATTTCCCCACTTTTGTT
*
12562 CTCCATTTCTCCACTTTTG
1 CTCCATTTCCCCACTTTTG
12581 CTTTCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.38, G:0.05, T:0.46
Consensus pattern (21 bp):
CTCCATTTCCCCACTTTTGTT
Found at i:14406 original size:25 final size:25
Alignment explanation
Indices: 14372--14420 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
14362 CCAAACAATC
14372 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
14397 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
14421 CAAATCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Done.