Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017904.1 Corchorus olitorius cultivar O-4 contig17937, 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: 7150
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Found at i:1089 original size:29 final size:30
Alignment explanation
Indices: 1029--1103 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
1019 GCTAAATATC
* * *
1029 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATATTTT-CTTTCGGGA
1060 CAAAATAATCCCTTATATTTT-TTTCGGGA
1 CAAAATAATCCCTTATATTTTCTTTCGGGA
*
1089 CAAATTAATCCCTTA
1 CAAAATAATCCCTTA
1104 CGTTTCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 21 0.52
31 19 0.47
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (30 bp):
CAAAATAATCCCTTATATTTTCTTTCGGGA
Found at i:1254 original size:31 final size:31
Alignment explanation
Indices: 1208--1344 Score: 186
Period size: 31 Copynumber: 4.4 Consensus size: 31
1198 CCACGTCAGC
**
1208 AAGGGATTGATTTGTCCCAAAAGAAAAACAT
1 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
* *
1239 AAGTGATTTTTTTGTCCCAAAAGAACAACAT
1 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
* *
1270 AAGGGATTTTTTTGTCCTAAAAGAACAACAT
1 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
*
1301 AAGGGA-TTTTTTGTCCCAAAAGAAAAATAT
1 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
*
1331 AAGAGAATTTTTTT
1 AAG-GGATTTTTTT
1345 TAGTATTTAG
Statistics
Matches: 94, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.26
31 64 0.68
32 6 0.06
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (31 bp):
AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
Found at i:2152 original size:126 final size:125
Alignment explanation
Indices: 1977--2204 Score: 316
Period size: 126 Copynumber: 1.8 Consensus size: 125
1967 TATTTCTTAA
* **
1977 TTAAATGCTATTTTTAAACTTTTACATTTTTACTCAATTAAAAACTCTATTTTTATTTAATC-AA
1 TTAAATGCTATTTTTAAACTTTTACAGTTTTACTCAACCAAAAACTCTATTTTTATTTAATCAAA
* *
2041 GTCTAATATATTTATAACTATTTTATTTTTACCATTTTACTAATTTAATTAAATATATTTC
66 TTC-AATATATTTATAACTATTTTATCTTTACCATTTTACTAATTTAATTAAATATATTTC
* ** * *
2102 TTAAATGAC-ATTATTTAAACTTTTACAGTTTTATTTTACCAAAAATTCTATTTTTATTTAATTA
1 TTAAATG-CTATT-TTTAAACTTTTACAGTTTTACTCAACCAAAAACTCTATTTTTATTTAATCA
*
2166 AATTCAATATTTTTATAACTATTTTATCTTTACCATTTT
64 AATTCAATATATTTATAACTATTTTATCTTTACCATTTT
2205 TTTAGGGAAT
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
125 10 0.11
126 75 0.84
127 4 0.04
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.53
Consensus pattern (125 bp):
TTAAATGCTATTTTTAAACTTTTACAGTTTTACTCAACCAAAAACTCTATTTTTATTTAATCAAA
TTCAATATATTTATAACTATTTTATCTTTACCATTTTACTAATTTAATTAAATATATTTC
Found at i:2606 original size:29 final size:31
Alignment explanation
Indices: 2563--2631 Score: 106
Period size: 29 Copynumber: 2.3 Consensus size: 31
2553 TTTTGTAACG
*
2563 TAAGGGATTAATTTGTCCC-GAAA-AAAACA
1 TAAGGGATTAATTTGTCCCAAAAACAAAACA
*
2592 TAAGGGATTATTTTGTCCCAAAAACAAAACA
1 TAAGGGATTAATTTGTCCCAAAAACAAAACA
2623 TAAGGGATT
1 TAAGGGATT
2632 TTTCTGGGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 18 0.50
30 3 0.08
31 15 0.42
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (31 bp):
TAAGGGATTAATTTGTCCCAAAAACAAAACA
Found at i:3355 original size:21 final size:20
Alignment explanation
Indices: 3327--3369 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
3317 TCCAATTCTG
*
3327 TGATTCCGATGTCCGTTGTC
1 TGATTCCGATGTCCGCTGTC
3347 TGATGTCCGATGTCCGCTGTC
1 TGAT-TCCGATGTCCGCTGTC
3368 TG
1 TG
3370 TTTCTGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.09, C:0.26, G:0.28, T:0.37
Consensus pattern (20 bp):
TGATTCCGATGTCCGCTGTC
Found at i:3726 original size:44 final size:44
Alignment explanation
Indices: 3677--3765 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
3667 TATCATATAT
3677 TACTTTATAATATATAATATATATAATTTAAATAAAAATAAAAA
1 TACTTTATAATATATAATATATATAATTTAAATAAAAATAAAAA
* *
3721 TACTTTATAATATATAATATGTATAATTTAAATAAAAATCAAAA
1 TACTTTATAATATATAATATATATAATTTAAATAAAAATAAAAA
3765 T
1 T
3766 CAAAATCCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (44 bp):
TACTTTATAATATATAATATATATAATTTAAATAAAAATAAAAA
Found at i:3928 original size:22 final size:23
Alignment explanation
Indices: 3889--3931 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
3879 AATCCTAATC
3889 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
3912 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
3932 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
Found at i:6876 original size:29 final size:30
Alignment explanation
Indices: 6810--6885 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 30
6800 TAATGACAAA
6810 ATCAGAAT-TCTCTCCTTCACAAACAAAGAG
1 ATCAGAATCT-TCTCCTTCACAAACAAAGAG
6840 ATCAGAATCTTCTCCTTCAC-AACAAAGAG
1 ATCAGAATCTTCTCCTTCACAAACAAAGAG
*
6869 ATCGGAATCTTCCTCCT
1 ATCAGAATCTT-CTCCT
6886 CGTCATACTC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 19 0.44
30 23 0.53
31 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (30 bp):
ATCAGAATCTTCTCCTTCACAAACAAAGAG
Done.