Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011889.1 Corchorus olitorius cultivar O-4 contig11922, 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: 23007
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:2176 original size:16 final size:16
Alignment explanation
Indices: 2152--2218 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
2142 TAGTGTTGAA
2152 TTCGGGTATTTTCGGG
1 TTCGGGTATTTTCGGG
*
2168 TTCGAGTATTTTCGGG
1 TTCGGGTATTTTCGGG
* *
2184 ATCGGGTATTTTCAGG
1 TTCGGGTATTTTCGGG
2200 TTCGGGT-TTTTCGGG
1 TTCGGGTATTTTCGGG
2215 TTCG
1 TTCG
2219 AGTTTCTTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
15 11 0.24
16 34 0.76
ACGTcount: A:0.09, C:0.13, G:0.34, T:0.43
Consensus pattern (16 bp):
TTCGGGTATTTTCGGG
Found at i:3485 original size:16 final size:16
Alignment explanation
Indices: 3424--3487 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
3414 TAAATTCAGG
*
3424 TTTTTTCAGG-TTCAAG
1 TTTTTTC-GGATTCAAA
*
3440 TTTTTTCGGA-TAAGAA
1 TTTTTTCGGATTCA-AA
* *
3456 TTTTTTCAGTTTCAAA
1 TTTTTTCGGATTCAAA
3472 TTTTTTCGGATTCAAA
1 TTTTTTCGGATTCAAA
3488 CTCAAGCGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
15 4 0.11
16 32 0.84
17 2 0.05
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (16 bp):
TTTTTTCGGATTCAAA
Found at i:5115 original size:2 final size:2
Alignment explanation
Indices: 5108--5133 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5098 GTTATTTTAT
5108 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5134 AATGTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6834 original size:10 final size:10
Alignment explanation
Indices: 6818--6852 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
6808 GTTGCCCAAA
6818 AAAAAAAAAGG
1 AAAAAAAAA-G
6829 AAAAAAAAAG
1 AAAAAAAAAG
6839 AAAAGAAAAAG
1 AAAA-AAAAAG
6850 AAA
1 AAA
6853 TAGAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:6835 original size:15 final size:15
Alignment explanation
Indices: 6815--6848 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6805 CTGGTTGCCC
*
6815 AAAAAAAAA-AAAGG
1 AAAAAAAAAGAAAAG
6829 AAAAAAAAAGAAAAG
1 AAAAAAAAAGAAAAG
6844 AAAAA
1 AAAAA
6849 GAAATAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:6836 original size:16 final size:15
Alignment explanation
Indices: 6815--6848 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6805 CTGGTTGCCC
*
6815 AAAAAAAAAAAAGGA
1 AAAAAAAAAAAAAGA
*
6830 AAAAAAAAGAAAAGA
1 AAAAAAAAAAAAAGA
6845 AAAA
1 AAAA
6849 GAAATAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:12368 original size:21 final size:21
Alignment explanation
Indices: 12344--12383 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12334 TTTCTCCGTT
12344 TTTCT-TTTGATTTTATTTTTC
1 TTTCTATTT-ATTTTATTTTTC
*
12365 TTTCTATTTCTTTTATTTT
1 TTTCTATTTATTTTATTTT
12384 CTCCAGCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTCTATTTATTTTATTTTTC
Found at i:13492 original size:314 final size:315
Alignment explanation
Indices: 12901--13536 Score: 1055
Period size: 314 Copynumber: 2.0 Consensus size: 315
12891 ATGGATGTTG
*
12901 GTCCAAATAGTGCTTTGAAACCAACTTTGGTTGCAATGTTTGGATGGAAACAGACATGTCATCTG
1 GTCCAAATAGTGCTTTGAAACCAACTTTGGTCGCAATGTTTGGATGGAAACAGACATGTCATCTG
*
12966 ATATCATCATACCAGATGGTGGTTAGGATCTCTCAAAGGCTGAAGGGTGATTTTGTTATTCTCAA
66 ATA-CATCATACCAGATGGTGGTTAGGATCTCTCAAAGGCTGAAGGGTGATTTTGTGATTCTCAA
*
13031 AATTGTGTAAGGGTCGCTATTCCTAGTGACACCGAATAATCATTTCTGAGGTGGGGGTTCAAAAT
130 AATTGTGTAAGGGTCGCTATTCCTAGTGACACCGAATAATCATTTCAGAGGTGGGGGTTCAAAAT
* * * *
13096 GACCATCCAATCGTTTTAATAAATACACCTCGAACAGCTATTACAAGTTACGGCGGTTCTTGAAC
195 GACCATCCAATCCTTTTAATAAATACACCTCGAACAGCTATTACAAGTAACAGCGGATCTTGAAC
* *
13161 CACATGCATGGACAGAGCATGGGCATGAAATTCAGGACAAAAGGATTAGCCATTTA
260 CACATGCATGGACAGAGCATGGGCATGAAATACAGGAAAAAAGGATTAGCCATTTA
* *
13217 GTCCAAATCAGTGTTTTGAGACCAACTTTGGTCGCAATGTTTGGATGGAAACAGACATGTCATCT
1 GTCCAAAT-AGTGCTTTGAAACCAACTTTGGTCGCAATGTTTGGATGGAAACAGACATGTCATCT
*
13282 GA-A-ATCATACCAGATGGTGGTTAGGATTTCTCAAAGGCTGAAGGGTGATTTTGTGATTCTCAA
65 GATACATCATACCAGATGGTGGTTAGGATCTCTCAAAGGCTGAAGGGTGATTTTGTGATTCTCAA
* *
13345 AATTGTGTAAGGGTCGCTATTCCTTGTGGCACCGAATAATCATTAT-AGAGGTGGGGGTTTC-AA
130 AATTGTGTAAGGGTCGCTATTCCTAGTGACACCGAATAATCATT-TCAGAGGTGGGGG-TTCAAA
* *
13408 ATGACCATCCAATCCTTTTAATGAATACACCTCGAACAGCTATTACATGTAACAGCGGATCTTGA
193 ATGACCATCCAATCCTTTTAATAAATACACCTCGAACAGCTATTACAAGTAACAGCGGATCTTGA
*
13473 ACCACGTGCATGGACAGAGCATGGGCATGAAATACAGGAAAAAAGGATTAGCCATTTA
258 ACCACATGCATGGACAGAGCATGGGCATGAAATACAGGAAAAAAGGATTAGCCATTTA
13531 GTCCAA
1 GTCCAA
13537 CTAAACATAG
Statistics
Matches: 300, Mismatches: 17, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
314 232 0.77
315 4 0.01
316 9 0.03
317 55 0.18
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (315 bp):
GTCCAAATAGTGCTTTGAAACCAACTTTGGTCGCAATGTTTGGATGGAAACAGACATGTCATCTG
ATACATCATACCAGATGGTGGTTAGGATCTCTCAAAGGCTGAAGGGTGATTTTGTGATTCTCAAA
ATTGTGTAAGGGTCGCTATTCCTAGTGACACCGAATAATCATTTCAGAGGTGGGGGTTCAAAATG
ACCATCCAATCCTTTTAATAAATACACCTCGAACAGCTATTACAAGTAACAGCGGATCTTGAACC
ACATGCATGGACAGAGCATGGGCATGAAATACAGGAAAAAAGGATTAGCCATTTA
Found at i:18448 original size:22 final size:23
Alignment explanation
Indices: 18409--18451 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
18399 AATCCTAATC
18409 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
18432 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
18452 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Done.