Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011993.1 Corchorus olitorius cultivar O-4 contig12026, 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: 57435
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2250 original size:15 final size:15
Alignment explanation
Indices: 2230--2269 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
2220 TTACATATTG
*
2230 AATGAACACAAACAT
1 AATGAACAAAAACAT
*
2245 AATGAATAAAAACAT
1 AATGAACAAAAACAT
2260 AATGAACAAA
1 AATGAACAAA
2270 GCATTAGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (15 bp):
AATGAACAAAAACAT
Found at i:6016 original size:25 final size:26
Alignment explanation
Indices: 5981--6038 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
5971 CTTTTTTGTC
**
5981 TTTTTTATTTC-TTACTCTATTGTAA
1 TTTTTTATTTCACAACTCTATTGTAA
*
6006 TTTTTTTTTTCACAACTCTATTGTAA
1 TTTTTTATTTCACAACTCTATTGTAA
*
6032 TTCTTTA
1 TTTTTTA
6039 GTCTTTCTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.21, C:0.14, G:0.03, T:0.62
Consensus pattern (26 bp):
TTTTTTATTTCACAACTCTATTGTAA
Found at i:6516 original size:2 final size:2
Alignment explanation
Indices: 6509--6542 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6499 TACTGTCTTT
6509 TA TA TA TA 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 TA TA TA TA
6543 ACGGTTGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15555 original size:75 final size:75
Alignment explanation
Indices: 15465--15613 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 75
15455 AAGCCTCCAT
15465 ACCTTACCAGCTTTGAATGTAATCAAATTCAACTACAAAGAACCAGTCCACACTCTTTATCTACA
1 ACCTTACCAGCTTTGAATGTAATCAAATTCAACTACAAAGAACCAGTCCACACTCTTTATCTACA
15530 GTATTCTCTC
66 GTATTCTCTC
* *
15540 ACCTTACCAGCTTTGAATGTAATCAAATTCAACTACAAAGAACCAGTTCACACTTTTTATCTACA
1 ACCTTACCAGCTTTGAATGTAATCAAATTCAACTACAAAGAACCAGTCCACACTCTTTATCTACA
15605 GTATTCTCT
66 GTATTCTCT
15614 TATGACAACA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (75 bp):
ACCTTACCAGCTTTGAATGTAATCAAATTCAACTACAAAGAACCAGTCCACACTCTTTATCTACA
GTATTCTCTC
Found at i:32359 original size:15 final size:15
Alignment explanation
Indices: 32339--32369 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32329 GCAGAGGTTG
32339 AAAGAAAACAATTAA
1 AAAGAAAACAATTAA
*
32354 AAAGAAAGCAATTAA
1 AAAGAAAACAATTAA
32369 A
1 A
32370 CTAGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAGAAAACAATTAA
Found at i:38840 original size:22 final size:24
Alignment explanation
Indices: 38798--38850 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
38788 ATATGACGCA
*
38798 AAAACTTTTTTTTATCGCAAAACCG
1 AAAACTTTTTTTTATC-CAAAAACG
38823 AAAACTTTTTTTT-T-CAAAAACG
1 AAAACTTTTTTTTATCCAAAAACG
*
38845 CAAACT
1 AAAACT
38851 CAAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 12 0.46
24 1 0.04
25 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.36
Consensus pattern (24 bp):
AAAACTTTTTTTTATCCAAAAACG
Found at i:39191 original size:15 final size:15
Alignment explanation
Indices: 39171--39201 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39161 GCAGAGGTTG
39171 AAAGAAAACAATTAA
1 AAAGAAAACAATTAA
*
39186 AAAGAAAGCAATTAA
1 AAAGAAAACAATTAA
39201 A
1 A
39202 CTAGAACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAGAAAACAATTAA
Found at i:39222 original size:24 final size:24
Alignment explanation
Indices: 39186--39231 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39176 AAACAATTAA
39186 AAAGAAAGCAATTAAA-CTAGAAC
1 AAAGAAAGCAATTAAATCTAGAAC
*
39209 AAAGCAAAGTAATTAAATCTAGA
1 AAAG-AAAGCAATTAAATCTAGA
39232 TCCATGGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (24 bp):
AAAGAAAGCAATTAAATCTAGAAC
Found at i:41682 original size:3 final size:3
Alignment explanation
Indices: 41674--41713 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
41664 CTCCCTTTGA
41674 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
41714 ATTGAGCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:42826 original size:17 final size:17
Alignment explanation
Indices: 42794--42827 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42784 TAATTTATAT
* *
42794 TATTAATAATTTAGAAA
1 TATTAATAAATAAGAAA
42811 TATTAATAAATAAGAAA
1 TATTAATAAATAAGAAA
42828 GTATAAAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
TATTAATAAATAAGAAA
Found at i:44816 original size:29 final size:30
Alignment explanation
Indices: 44783--44839 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
44773 AGTTTAGAGT
*
44783 AATTTCTGA-TTTAATTTCTATGTATTGTA
1 AATTTCTGATTTTAATTTCTAAGTATTGTA
*
44812 AATTTTTGATTTTAATTTCTAAGTATTG
1 AATTTCTGATTTTAATTTCTAAGTATTG
44840 AAAACCGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.56
Consensus pattern (30 bp):
AATTTCTGATTTTAATTTCTAAGTATTGTA
Found at i:52247 original size:2 final size:2
Alignment explanation
Indices: 52236--52269 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
52226 ATAATATTTG
52236 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52270 TTGACTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52951 original size:30 final size:30
Alignment explanation
Indices: 52915--52975 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
52905 ATTTTTATCT
52915 TGACTTTCCTCTTATACCCTT-AAACTTTAA
1 TGACTTTCCTCTTATA-CCTTCAAACTTTAA
*
52945 TGACTTTCCTCTTATACCTTCAAATTTTAA
1 TGACTTTCCTCTTATACCTTCAAACTTTAA
52975 T
1 T
52976 ATCATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.26, C:0.25, G:0.03, T:0.46
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCTTCAAACTTTAA
Found at i:54739 original size:16 final size:16
Alignment explanation
Indices: 54718--54758 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
54708 CACACCGGTA
54718 ATTACTTCTTAAATTG
1 ATTACTTCTTAAATTG
54734 ATTACTTCTTAAATTG
1 ATTACTTCTTAAATTG
*
54750 ATTTCTTCT
1 ATTACTTCT
54759 CTCATACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.27, C:0.15, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTACTTCTTAAATTG
Done.