Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016239.1 Corchorus olitorius cultivar O-4 contig16272, 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: 15289
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:854 original size:22 final size:22
Alignment explanation
Indices: 829--897 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
819 AAATATAAAT
* *
829 ATTTTATAGTGTGGTTACCAAA
1 ATTTCATAGTGTGGTTATCAAA
*
851 ATTTCATA-TGAAGGTTATC-AA
1 ATTTCATAGTG-TGGTTATCAAA
* *
872 ACTTCATAGTGTAGTTATCAAA
1 ATTTCATAGTGTGGTTATCAAA
894 ATTT
1 ATTT
898 TATATAGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
21 17 0.46
22 20 0.54
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (22 bp):
ATTTCATAGTGTGGTTATCAAA
Found at i:879 original size:21 final size:21
Alignment explanation
Indices: 853--893 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
843 TTACCAAAAT
853 TTCATA-TGAAGGTTATCAAAC
1 TTCATAGTGAA-GTTATCAAAC
*
874 TTCATAGTGTAGTTATCAAA
1 TTCATAGTGAAGTTATCAAA
894 ATTTTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TTCATAGTGAAGTTATCAAAC
Found at i:939 original size:22 final size:22
Alignment explanation
Indices: 886--941 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
876 CATAGTGTAG
* *
886 TTATCAAAATTTTATATAGAAA
1 TTATCAAAATTTCATATAAAAA
908 TTA-CAAAAATTTCATA-AAAAGA
1 TTATC-AAAATTTCATATAAAA-A
930 TTATCAAAATTT
1 TTATCAAAATTT
942 TTTAGAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 4 0.14
22 24 0.83
23 1 0.03
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATATAAAAA
Found at i:961 original size:44 final size:44
Alignment explanation
Indices: 886--1012 Score: 114
Period size: 44 Copynumber: 2.9 Consensus size: 44
876 CATAGTGTAG
* **
886 TTATCAAAATTTTATATAGAAATT-ACAAAAATTTCATAAAAAGA
1 TTATCAAAATTTTATAGAGATGTTAAC-AAAATTTCATAAAAAGA
* * ** *
930 TTATCAAAATTTTTTAGAGATGTTAACAAAATTCCATACGAAGG
1 TTATCAAAATTTTATAGAGATGTTAACAAAATTTCATAAAAAGA
* * * *
974 TTATCGAAATTTTATAGTG-TGGTTATCAAAATTTTATAA
1 TTATCAAAATTTTATAGAGAT-GTTAACAAAATTTCATAA
1013 GGATGTTAAC
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
43 1 0.02
44 63 0.95
45 2 0.03
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTTATAGAGATGTTAACAAAATTTCATAAAAAGA
Found at i:1020 original size:22 final size:22
Alignment explanation
Indices: 930--1055 Score: 78
Period size: 22 Copynumber: 5.5 Consensus size: 22
920 CATAAAAAGA
*
930 TTATCAAAATTTT-TTAGAGATG
1 TTATCAAAATTTTATAAG-GATG
* ** * * *
952 TTAACAAAATTCCATACGAAGG
1 TTATCAAAATTTTATAAGGATG
*
974 TTATCGAAATTTTAT-AGTG-TGG
1 TTATCAAAATTTTATAAG-GAT-G
996 TTATCAAAATTTTATAAGGATG
1 TTATCAAAATTTTATAAGGATG
* *
1018 TTAACAAAATTTCATAGGGAGGGATG
1 TTATCAAAATTTTATA---A-GGATG
1044 TTATCAAAATTT
1 TTATCAAAATTT
1056 GTGCTTATCA
Statistics
Matches: 77, Mismatches: 18, Indels: 14
0.71 0.17 0.13
Matches are distributed among these distances:
21 1 0.01
22 54 0.70
23 5 0.06
25 1 0.01
26 16 0.21
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTTATAAGGATG
Found at i:1273 original size:22 final size:22
Alignment explanation
Indices: 1177--1423 Score: 146
Period size: 22 Copynumber: 11.3 Consensus size: 22
1167 CATATGGAGG
* * *
1177 TTATCGAAATTTCATGGTGTAA
1 TTATCAAAATTTCATAGTGTGA
* * * *
1199 TTA-CATAATTTTATGAG-GAGG
1 TTATCAAAATTTCAT-AGTGTGA
*
1220 TTATCAAAATTTTCATAGTGTGG
1 TTATCAAAA-TTTCATAGTGTGA
* * **
1243 CTA-C-CAATTTTTTAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
* * *
1263 TTATCAAAATTTGATAGGGAGA
1 TTATCAAAATTTCATAGTGTGA
* * *
1285 TTATCACAATTTCACACTGATG-
1 TTATCAAAATTTCATAGTG-TGA
*
1307 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGA
* *
1329 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCATAGTGTGA
* *
1351 TTATCAAATTTTCATAAG-GTGG
1 TTATCAAAATTTCAT-AGTGTGA
* * * * *
1373 TTATCCAGATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGTGA
* *
1395 TTATCAAATTTTCACAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
1417 TTATCAA
1 TTATCAA
1424 TGTTTCTACG
Statistics
Matches: 170, Mismatches: 45, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
20 12 0.07
21 18 0.11
22 127 0.75
23 13 0.08
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:1355 original size:66 final size:66
Alignment explanation
Indices: 1255--1423 Score: 180
Period size: 66 Copynumber: 2.6 Consensus size: 66
1245 ACCAATTTTT
* * * * * *
1255 TAGTGTGATTATCAAAATTTGATAGGGAGATTATCACAA-TTTCACACTGAT-GTTATCAAAATT
1 TAGTGTGGTTATCAAAATTTCACAGTGTGATTATCA-AATTTTCACA-AGATGGTTATCAAAATT
1318 TCA
64 TCA
* * * * *
1321 TAGTGTGGTTATCAAAATTTCACAGTGTGGTTATCAAATTTTCATAAGGTGGTTATCCAGATTTC
1 TAGTGTGGTTATCAAAATTTCACAGTGTGATTATCAAATTTTCACAAGATGGTTATCAAAATTTC
1386 A
66 A
* * *
1387 TAATGAGGTTATCAAATTTTCACAGTGTGATTATCAA
1 TAGTGTGGTTATCAAAATTTCACAGTGTGATTATCAA
1424 TGTTTCTACG
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
65 4 0.05
66 82 0.95
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (66 bp):
TAGTGTGGTTATCAAAATTTCACAGTGTGATTATCAAATTTTCACAAGATGGTTATCAAAATTTC
A
Found at i:3709 original size:18 final size:19
Alignment explanation
Indices: 3678--3715 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3668 GAGCCAATCC
3678 AATTTTTCACTATA-TATT
1 AATTTTTCACTATATTATT
3696 AATTTTTC-CGTATATTATT
1 AATTTTTCAC-TATATTATT
3715 A
1 A
3716 TATTCCTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 12 0.67
19 5 0.28
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (19 bp):
AATTTTTCACTATATTATT
Found at i:12565 original size:23 final size:24
Alignment explanation
Indices: 12530--12576 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
12520 TTATGTTTTT
12530 TGTTGTTTTGATCTTCTT-TTCTC
1 TGTTGTTTTGATCTTCTTCTTCTC
12553 TGTT-TTTTCGATCTTCTTCTTCTC
1 TGTTGTTTT-GATCTTCTTCTTCTC
12577 ATTCAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.04, C:0.21, G:0.11, T:0.64
Consensus pattern (24 bp):
TGTTGTTTTGATCTTCTTCTTCTC
Done.