Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024225.1 Corchorus olitorius cultivar O-4 contig24258, 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: 27276
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:2591 original size:15 final size:16
Alignment explanation
Indices: 2562--2591 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2552 GTGTGAATTC
2562 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
2578 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
2592 TAAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:18697 original size:21 final size:23
Alignment explanation
Indices: 18658--18699 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
18648 ACATATGATG
18658 TTGATATCTTCGACAATTGAATC
1 TTGATATCTTCGACAATTGAATC
*
18681 TTGAT-TCTTC-ATAATTGAA
1 TTGATATCTTCGACAATTGAA
18700 AGATTGGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 5 0.28
23 5 0.28
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (23 bp):
TTGATATCTTCGACAATTGAATC
Found at i:22370 original size:22 final size:22
Alignment explanation
Indices: 22259--22379 Score: 90
Period size: 22 Copynumber: 5.6 Consensus size: 22
22249 TAATTACACT
* * *
22259 AATTTCGATGACCTCCTTATGA
1 AATTTTGATAACCTTCTTATGA
*
22281 AATTTTGATAACCTTCCTATGA
1 AATTTTGATAACCTTCTTATGA
* * *
22303 AATTTTAATAACGATAC-TATGA
1 AATTTTGATAAC-CTTCTTATGA
*
22325 AATTTTGAGAACCTT-TTA--A
1 AATTTTGATAACCTTCTTATGA
**
22344 TAATTTTTTTAACCTTCTTATGA
1 -AATTTTGATAACCTTCTTATGA
*
22367 AA-TTTGTTAACCT
1 AATTTTGATAACCT
22380 CCCTAAGGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.01
20 12 0.15
21 16 0.21
22 46 0.59
23 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (22 bp):
AATTTTGATAACCTTCTTATGA
Found at i:24554 original size:22 final size:22
Alignment explanation
Indices: 24497--24578 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
24487 AAAACCTCCA
*
24497 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* *
24519 TCTAAAACTT-TGATAATCACAC
1 TATGAAA-TTGTGATAATCACAC
* * *
24541 TATGAAATTGTGATAACCTCGC
1 TATGAAATTGTGATAATCACAC
*
24563 TATGAAATTTTGATAA
1 TATGAAATTGTGATAA
24579 ACCTTCCTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.04
22 40 0.83
23 4 0.08
24 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:24615 original size:22 final size:21
Alignment explanation
Indices: 24540--24811 Score: 164
Period size: 22 Copynumber: 12.7 Consensus size: 21
24530 GATAATCACA
*
24540 CTATGAAATTGTGATAACCTC
1 CTATGAAATTTTGATAACCTC
24561 GCTATGAAATTTTGATAAACCTTC
1 -CTATGAAATTTTGAT-AACC-TC
*
24585 CTATAAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACCTC
* *
24606 CTTATGAAATCTTGATGA----
1 C-TATGAAATTTTGATAACCTC
24624 CTA--AATATTTTGATAACTCTC
1 CTATGAA-ATTTTGATAAC-CTC
* *
24645 CTATGAATTTTTGATAACCTTA
1 CTATGAAATTTTGATAACC-TC
* * *
24667 TTATGAAATTTTGTTAATCTCC
1 CTATGAAATTTTGATAACCT-C
* * * *
24689 CTATGTAATTTTGATCTACATA
1 CTATGAAATTTTGAT-AACCTC
*
24711 TTATGAAATTTTGATAACCCTC
1 CTATGAAATTTTGATAA-CCTC
* * *
24733 TTATGAAATTTTGA-AAACTAAA
1 CTATGAAATTTTGATAACCT--C
*
24755 CTATGAAATTTTGATACACTTC
1 CTATGAAATTTTGATA-ACCTC
* * *
24777 ATATGAAATTTTAATATCCTC
1 CTATGAAATTTTGATAACCTC
* *
24798 C-CTGAAGTTTTGAT
1 CTATGAAATTTTGAT
24812 TACACTATAT
Statistics
Matches: 191, Mismatches: 40, Indels: 40
0.70 0.15 0.15
Matches are distributed among these distances:
15 2 0.01
16 8 0.04
17 2 0.01
18 1 0.01
20 12 0.06
21 14 0.07
22 125 0.65
23 23 0.12
24 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:24703 original size:82 final size:83
Alignment explanation
Indices: 24551--24703 Score: 202
Period size: 82 Copynumber: 1.9 Consensus size: 83
24541 TATGAAATTG
* *
24551 TGATAACCTCGCTATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAACCTCCTTATGAAAT
1 TGATAACCTCGCTATGAAATTTTGATAAACCTTACTATAAAATTTTGATAACCTCCCTATGAAAT
24616 CTTGATGACTAAATATTT
66 CTTGATGACTAAATATTT
* * * * * *
24634 TGATAACTCTC-CTATGAATTTTTGAT-AACCTTATTATGAAATTTTGTTAATCTCCCTATGTAA
1 TGATAAC-CTCGCTATGAAATTTTGATAAACCTTACTATAAAATTTTGATAACCTCCCTATGAAA
*
24697 TTTTGAT
65 TCTTGAT
24704 CTACATATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
82 36 0.60
83 21 0.35
84 3 0.05
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (83 bp):
TGATAACCTCGCTATGAAATTTTGATAAACCTTACTATAAAATTTTGATAACCTCCCTATGAAAT
CTTGATGACTAAATATTT
Found at i:24782 original size:66 final size:65
Alignment explanation
Indices: 24562--24788 Score: 184
Period size: 66 Copynumber: 3.5 Consensus size: 65
24552 GATAACCTCG
* * * * **
24562 CTATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAA-CCTCCTTATGAAATCTTGATGACT
1 CTATGAAATTTTGATACA-CTTCATATGAAATTTTGATAACCCT-CTTATGAAATTTTGAAAACT
24626 AA
64 AA
* * * * * *
24628 --AT---ATTTTGATA-ACTCTCCTATGAATTTTTGATAACCTTATTATGAAATTTTGTTAATCT
1 CTATGAAATTTTGATACACT-TCATATGAAATTTTGATAACCCTCTTATGAAATTTTG-AAAACT
**
24687 CC
64 AA
* *
24689 CTATGTAATTTTGAT-CTACAT-ATTATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACT
1 CTATGAAATTTTGATAC-ACTTCA-TATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACT
24752 AAA
64 -AA
24755 CTATGAAATTTTGATACACTTCATATGAAATTTT
1 CTATGAAATTTTGATACACTTCATATGAAATTTT
24789 AATATCCTCC
Statistics
Matches: 125, Mismatches: 22, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
59 2 0.02
60 30 0.24
61 13 0.10
63 2 0.02
64 2 0.02
65 4 0.03
66 68 0.54
67 4 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (65 bp):
CTATGAAATTTTGATACACTTCATATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAA
Found at i:25091 original size:22 final size:23
Alignment explanation
Indices: 25062--25188 Score: 94
Period size: 22 Copynumber: 5.8 Consensus size: 23
25052 AAATTGAGAC
* *
25062 TTTT-ATAACCTTCA-TGTGAAA
1 TTTTGATAACCTACACTATGAAA
25083 TTTTGATAACC-ACACTATGAAA
1 TTTTGATAACCTACACTATGAAA
* *
25105 TTTTGATAACCT-CCCCATGAAA
1 TTTTGATAACCTACACTATGAAA
*
25127 TATT-AGTAACCT-C-CTTATGAAA
1 TTTTGA-TAACCTACAC-TATGAAA
*
25149 TTTTGTTAACC-ACACTATGAAA
1 TTTTGATAACCTACACTATGAAA
*
25171 TTCTT-ATAAGCT-CACTAT
1 TT-TTGATAACCTACACTAT
25189 CACATTTTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
21 8 0.09
22 75 0.87
23 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.37
Consensus pattern (23 bp):
TTTTGATAACCTACACTATGAAA
Found at i:25138 original size:66 final size:66
Alignment explanation
Indices: 25066--25406 Score: 242
Period size: 66 Copynumber: 5.0 Consensus size: 66
25056 TGAGACTTTT
*
25066 ATAACCTTCATGTGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATT
1 ATAACCTTCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAAT-TT
25131 AG
65 AG
* * * *
25133 -TAACCTCCTTATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAAGCTCACTATCACATTT
1 ATAACCTTCATATGAAATTTTGATAACCACACTATGAAATT-TTGATAACCTC-C---C-CA---
* *
25196 TTATAATCTCTTTG
57 TGA-AA--T-TTAG
** * * * * * **
25210 ATAACCTTTCTATAAAATTGTGATAACCACACTATG-AATTTTCAATAACCTTCCTAAAAAATTT
1 ATAACCTTCATATGAAATTTTGATAACCACACTATGAAATTTT-GATAACCTCCCCATGAAA-TT
25274 TA-
64 TAG
* * * * *
25276 ATAATCTGATCCTATCAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
1 ATAACCT--TCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATT
*
25341 TTG
64 TAG
* * * *
25344 ATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTTATAACCTCCTCATGAAATT
1 ATAACCTT-CATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATT
25407 AAATAAACTG
Statistics
Matches: 217, Mismatches: 37, Indels: 41
0.74 0.13 0.14
Matches are distributed among these distances:
65 1 0.00
66 98 0.45
67 10 0.05
68 44 0.20
69 8 0.04
70 2 0.01
71 2 0.01
73 1 0.00
74 3 0.01
75 2 0.01
76 2 0.01
77 9 0.04
78 35 0.16
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.37
Consensus pattern (66 bp):
ATAACCTTCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATTTA
G
Found at i:25317 original size:22 final size:22
Alignment explanation
Indices: 25287--25406 Score: 104
Period size: 22 Copynumber: 5.5 Consensus size: 22
25277 TAATCTGATC
* *
25287 CTATCAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
25309 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
25331 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
25354 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* * *
25375 CTATGGAATTTTTATAACCTC-
1 CTATGAAATTTTGATAACCACA
25396 CTCATGAAATT
1 CT-ATGAAATT
25407 AAATAAACTG
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
20 1 0.01
21 4 0.05
22 73 0.91
23 1 0.01
24 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:25385 original size:44 final size:43
Alignment explanation
Indices: 25206--25406 Score: 120
Period size: 44 Copynumber: 4.5 Consensus size: 43
25196 TTATAATCTC
* * * *
25206 TTTGATAACCTTTCTATAAAATTGTGATAACC-ACACTATG-AAT
1 TTTGATAACC-TCCTATGAAATTTTGATAACCTAC-CCATGAAAT
* ** * * * *
25249 TTTCAATAACCTTCCTAAAAAATTTTAATAATCTGATCCTATCAAAT
1 TTT-GATAACC-TCCTATGAAATTTTGATAACCT-A-CCCATGAAAT
* * *
25296 TTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTC-CTATGAAATTTTGATAACCTACCCATGAAAT
* * * *
25340 TTTGATAACTTCCATATGAAATTTTGGTAACC-ACACTATGGAAT
1 TTTGATAACCTCC-TATGAAATTTTGATAACCTAC-CCATGAAAT
*
25384 TTTTATAACCTCCTCATGAAATT
1 TTTGATAACCTCCT-ATGAAATT
25407 AAATAAACTG
Statistics
Matches: 123, Mismatches: 26, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
43 6 0.05
44 83 0.67
45 1 0.01
46 26 0.21
47 7 0.06
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.37
Consensus pattern (43 bp):
TTTGATAACCTCCTATGAAATTTTGATAACCTACCCATGAAAT
Done.