Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014874.1 Corchorus olitorius cultivar O-4 contig14907, 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: 67776
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2760 original size:36 final size:36
Alignment explanation
Indices: 2720--2789 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2710 AGATGGAGAT
2720 TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA
1 TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA
* **
2756 TTAGCCAATGTCTTTAGATGTTGATGAAATAAAT
1 TTAGCCAATGTCTTGAGACATTGATGAAATAAAT
2790 TAGAGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (36 bp):
TTAGCCAATGTCTTGAGACATTGATGAAATAAATGA
Found at i:5914 original size:21 final size:19
Alignment explanation
Indices: 5889--5946 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
5879 GCTGCTCTAA
5889 TAATCTCATATGTACAGTACC
1 TAATCTCATATGTACAGT--C
* * *
5910 TAATCTAATCTGTACAGTG
1 TAATCTCATATGTACAGTC
5929 TAATCTCATATGTACAGT
1 TAATCTCATATGTACAGT
5947 TTCTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATATGTACAGTC
Found at i:8081 original size:26 final size:26
Alignment explanation
Indices: 8031--8081 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
8021 TAAAACCCTA
* **
8031 AACATAACACCCTATTTTTTTTTAAG
1 AACATAACACCCTATTTATACTTAAG
8057 AACATAACACCCTATTTATACTTAA
1 AACATAACACCCTATTTATACTTAA
8082 AAATACTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (26 bp):
AACATAACACCCTATTTATACTTAAG
Found at i:8612 original size:9 final size:9
Alignment explanation
Indices: 8598--8624 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
8588 CAAATGGGAA
8598 TGGGCTGAT
1 TGGGCTGAT
8607 TGGGCTGAT
1 TGGGCTGAT
8616 TGGGCTGAT
1 TGGGCTGAT
8625 GAGGATCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.44, T:0.33
Consensus pattern (9 bp):
TGGGCTGAT
Found at i:20746 original size:6 final size:6
Alignment explanation
Indices: 20735--20760 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20725 TAATAATATA
20735 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
20761 TGGGTACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:22164 original size:25 final size:25
Alignment explanation
Indices: 22136--22217 Score: 82
Period size: 25 Copynumber: 3.2 Consensus size: 25
22126 GCCAAATGCC
22136 AATTATGTAATTTTTGAACAAAATA
1 AATTATGTAATTTTTGAACAAAATA
*
22161 AATTATGTAATTTTTTTTG-AC-CAA-A
1 AATTATGTAA---TTTTTGAACAAAATA
22186 AATTATGTAATTTTTGAA-AAACATGA
1 AATTATGTAATTTTTGAACAAA-AT-A
22212 AATTAT
1 AATTAT
22218 CAAAATATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
22 6 0.13
23 2 0.04
24 1 0.02
25 21 0.45
26 9 0.19
27 2 0.04
28 6 0.13
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.43
Consensus pattern (25 bp):
AATTATGTAATTTTTGAACAAAATA
Found at i:28897 original size:13 final size:14
Alignment explanation
Indices: 28879--28907 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28869 CAGACTGATC
28879 AAAGAAAA-AAAAA
1 AAAGAAAAGAAAAA
28892 AAAGAAAAGAAAAA
1 AAAGAAAAGAAAAA
28906 AA
1 AA
28908 CAAACAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAA
Found at i:47237 original size:179 final size:180
Alignment explanation
Indices: 46791--47311 Score: 836
Period size: 186 Copynumber: 2.9 Consensus size: 180
46781 TATCCTTTTA
46791 TCTTATGACTTTACACAAGTCTTGTGTTGTCTTGTTATCTATTGCTTTTGCTTATGCTTATATAT
1 TCTTATGACTTTACACAAGTCTTGTGTTGTCTTGTTATCTATTGCTTTTGCTTATGCTTATATAT
**
46856 GTACTAACCAGTTTCTATTAATAAAATCTTTGTCTTGGTACAAAAAAAAAAAAGAGTAAGCATTT
66 GTACTAACCAGTTTCTATTAATAAAAAATTTGTCTTGGTAC---AAAAAAAAA-AGTAAGCATTT
*
46921 CATCTCAAATATTTCTATATCATGGTTTTTTCTTCTTTTTTTTCTCTTACACTTGT
127 CATCTCAAATATTTCTATATCATGGTTTTTTCTTC--TTTTCTCTCTTACACTTGT
* *
46977 TCTTATGACTTTACACAAGTCTTGTGTTGTCTTTTTATCTATTGCTTTTGCTTATGCTTATATTT
1 TCTTATGACTTTACACAAGTCTTGTGTTGTCTTGTTATCTATTGCTTTTGCTTATGCTTATATAT
* *
47042 GTACTAACTAGTTTCTATTAATAAAAAATCTGTCTTGGTACCAAAAAAAAAAGTAAGCATTTCAT
66 GTACTAACCAGTTTCTATTAATAAAAAATTTGTCTTGGTA-CAAAAAAAAAAGTAAGCATTTCAT
47107 CTCAAATATTTCTATATCATGGTTTTTT-TTC-TTTCTCTCTTACACTTGT
130 CTCAAATATTTCTATATCATGGTTTTTTCTTCTTTTCTCTCTTACACTTGT
*
47156 TCTTATGACTTTACACAAGTCTTGTGTTGTCTTGTTATCTATTGCTTTTGCTTATGCTCATATAT
1 TCTTATGACTTTACACAAGTCTTGTGTTGTCTTGTTATCTATTGCTTTTGCTTATGCTTATATAT
* * *
47221 GTACCAACCGGTTTCTATTAAT-AAAATTTTGTCTTGGT--AAAAAAAAAAGTAAGCATTTCATC
66 GTACTAACCAGTTTCTATTAATAAAAAATTTGTCTTGGTACAAAAAAAAAAGTAAGCATTTCATC
*
47283 TCAAATATTTCTATATCATGATTTTTTCT
131 TCAAATATTTCTATATCATGGTTTTTTCT
47312 GTTTTCTTTT
Statistics
Matches: 317, Mismatches: 16, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
175 50 0.16
176 1 0.00
178 14 0.04
179 98 0.31
182 3 0.01
183 42 0.13
184 9 0.03
186 99 0.31
187 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (180 bp):
TCTTATGACTTTACACAAGTCTTGTGTTGTCTTGTTATCTATTGCTTTTGCTTATGCTTATATAT
GTACTAACCAGTTTCTATTAATAAAAAATTTGTCTTGGTACAAAAAAAAAAGTAAGCATTTCATC
TCAAATATTTCTATATCATGGTTTTTTCTTCTTTTCTCTCTTACACTTGT
Found at i:47664 original size:17 final size:17
Alignment explanation
Indices: 47642--47675 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
47632 TAAACTTCAT
*
47642 TATATGAATAATTATTA
1 TATATGAATAAATATTA
47659 TATATGAATAAATATTA
1 TATATGAATAAATATTA
47676 AATAAGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TATATGAATAAATATTA
Found at i:47958 original size:25 final size:24
Alignment explanation
Indices: 47930--47986 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
47920 GTGGATTGTA
*
47930 AAATAAATTGAATAATAAAGACATT
1 AAATAAATTGAAGAATAAA-ACATT
* *
47955 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATAAAACATT
47979 AAA-AAATT
1 AAATAAATT
47987 CAAGGCTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 16 0.55
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (24 bp):
AAATAAATTGAAGAATAAAACATT
Found at i:51973 original size:14 final size:14
Alignment explanation
Indices: 51946--51992 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
51936 TTTTAGAGGG
51946 AAAA-AAAAGAAGAA
1 AAAAGAAAAG-AGAA
*
51960 AAAAGAAAATAGAA
1 AAAAGAAAAGAGAA
* *
51974 AATAGAAAAGAGTA
1 AAAAGAAAAGAGAA
51988 AAAAG
1 AAAAG
51993 TATAAAAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (14 bp):
AAAAGAAAAGAGAA
Found at i:52420 original size:5 final size:5
Alignment explanation
Indices: 52410--52435 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52400 TTACTTATAG
52410 AGAGA AGAGA AGAGA AGAGA AGAGA A
1 AGAGA AGAGA AGAGA AGAGA AGAGA A
52436 ATTACGTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AGAGA
Found at i:56547 original size:2 final size:2
Alignment explanation
Indices: 56542--56571 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
56532 CTCTCCATTG
*
56542 CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
56572 GAGCAGAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:57626 original size:29 final size:29
Alignment explanation
Indices: 57594--57664 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
57584 ATGAATTTAA
*
57594 AAGACTATAATCAATTTTTTTTAAAAAAT
1 AAGACTATAATCAATTTTTTTAAAAAAAT
57623 AAGACTATAATCAATTTTTTTAAAAAAAT
1 AAGACTATAATCAATTTTTTTAAAAAAAT
57652 AAGACTATAATCA
1 AAGACTATAATCA
57665 TTCTATTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (29 bp):
AAGACTATAATCAATTTTTTTAAAAAAAT
Found at i:60210 original size:13 final size:13
Alignment explanation
Indices: 60194--60218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60184 TTATTCAAGC
60194 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
60207 TTTTTCTTTTTT
1 TTTTTCTTTTTT
60219 CAATCTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Done.