Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015805.1 Corchorus olitorius cultivar O-4 contig15838, 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: 24885
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Found at i:1209 original size:136 final size:135
Alignment explanation
Indices: 966--1236 Score: 524
Period size: 136 Copynumber: 2.0 Consensus size: 135
956 TTAATTTCTC
*
966 TAGTCAAATCGGGTTGGACGGGTTATCTAGGTTTATCAGATTTTGATAGTTTTACTTATAATTAA
1 TAGTCAAATCGGGTTGGACGGGTTATCTAGGTTGATCAGATTTTGATAGTTTTACTTATAATTAA
1031 TTTCAATTATTATTTTAATTTTCTTTTAATTTAAATACGATGGGTCACGTGCACCGCACGTGAAA
66 TTTCAATTATTATTTTAATTTTCTTTTAATTTAAATACGATGGGTCACGTGCACCGCACGTGAAA
1096 GTGAA
131 GTGAA
1101 TAGTCAAATCGGGTTGGACGGGTTATCTAGGTTGGATCAGATTTTGATAGTTTTACTTATAATTA
1 TAGTCAAATCGGGTTGGACGGGTTATCTAGGTT-GATCAGATTTTGATAGTTTTACTTATAATTA
1166 ATTTCAATTATTATTTTAATTTTCTTTTAATTTAAATACGATGGGTCACGTGCACCGCACGTGAA
65 ATTTCAATTATTATTTTAATTTTCTTTTAATTTAAATACGATGGGTCACGTGCACCGCACGTGAA
1231 AGTGAA
130 AGTGAA
1237 AACTAGTTAA
Statistics
Matches: 134, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
135 33 0.25
136 101 0.75
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (135 bp):
TAGTCAAATCGGGTTGGACGGGTTATCTAGGTTGATCAGATTTTGATAGTTTTACTTATAATTAA
TTTCAATTATTATTTTAATTTTCTTTTAATTTAAATACGATGGGTCACGTGCACCGCACGTGAAA
GTGAA
Found at i:1500 original size:21 final size:22
Alignment explanation
Indices: 1462--1506 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1452 TTCATATTTT
*
1462 TATAAATTCAAAAGCCTCTCCC
1 TATAAATTCAAAACCCTCTCCC
*
1484 TATAATTTC-AAACCCTCTCCC
1 TATAAATTCAAAACCCTCTCCC
1505 TA
1 TA
1507 ATAAGTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.31
Consensus pattern (22 bp):
TATAAATTCAAAACCCTCTCCC
Found at i:3190 original size:53 final size:53
Alignment explanation
Indices: 3132--3400 Score: 466
Period size: 53 Copynumber: 5.1 Consensus size: 53
3122 TCTTTAAATC
3132 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
* *
3185 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAGTAGATT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
*
3238 CAATAGTTCATTACATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
* * * *
3291 TAATAGTTCATTGTATTTTGTATTATTTGATATGTGTGCTTATTTAATATGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
*
3344 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTTTTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
3397 CAAT
1 CAAT
3401 TGAATAAAGA
Statistics
Matches: 201, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 201 1.00
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.52
Consensus pattern (53 bp):
CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
Found at i:4017 original size:27 final size:27
Alignment explanation
Indices: 3987--4042 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
3977 CCATATTACT
*
3987 CCCTCTGTTCCTTATTACTTGTCATTA
1 CCCTCTATTCCTTATTACTTGTCATTA
* * *
4014 CCCTCTATTCCTTCTTATTTGTCGTTA
1 CCCTCTATTCCTTATTACTTGTCATTA
4041 CC
1 CC
4043 ATTTACAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.12, C:0.32, G:0.07, T:0.48
Consensus pattern (27 bp):
CCCTCTATTCCTTATTACTTGTCATTA
Found at i:17880 original size:15 final size:14
Alignment explanation
Indices: 17860--17904 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
17850 GTCTATTATG
17860 GCTTTCTTCTTCTCT
1 GCTTTCTTCTTCT-T
*
17875 GCTTTCTTTCTGCTT
1 GCTTTC-TTCTTCTT
17890 GCTTTCTTGCTTCTT
1 GCTTTCTT-CTTCTT
17905 CAGTGCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 2 0.08
15 18 0.69
16 6 0.23
ACGTcount: A:0.00, C:0.29, G:0.11, T:0.60
Consensus pattern (14 bp):
GCTTTCTTCTTCTT
Found at i:22123 original size:15 final size:16
Alignment explanation
Indices: 22090--22129 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
22080 TTACTTTGCT
22090 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
22106 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
22121 TTGCTTTCT
1 TTGTTTTCT
22130 TTCAACTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Done.