Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021744.1 Corchorus olitorius cultivar O-4 contig21777, 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: 6994
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Found at i:596 original size:16 final size:15
Alignment explanation
Indices: 558--599 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
548 ACAGAGATTG
* *
558 ACAGAAAGCAATTAA
1 ACAGAAAACAATGAA
573 ACAGAAAACAATGAA
1 ACAGAAAACAATGAA
588 ACTAGAAAACAA
1 AC-AGAAAACAA
600 AGCAAAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAATGAA
Found at i:1369 original size:11 final size:11
Alignment explanation
Indices: 1353--1378 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1343 CCTTTGCCTA
1353 AAAACTAGAAG
1 AAAACTAGAAG
1364 AAAACTAGAAG
1 AAAACTAGAAG
1375 AAAA
1 AAAA
1379 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:2521 original size:16 final size:16
Alignment explanation
Indices: 2480--2525 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2470 TTTGCAAGAT
2480 AATT-GTTTTCAAGAAA
1 AATTAGTTTTCAA-AAA
* *
2496 AA-AAGCTTTCAAAAA
1 AATTAGTTTTCAAAAA
2511 AATTAGTTTTCAAAA
1 AATTAGTTTTCAAAA
2526 GGTTTTAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (16 bp):
AATTAGTTTTCAAAAA
Found at i:2836 original size:12 final size:12
Alignment explanation
Indices: 2819--2843 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2809 CGTTAAGTAA
2819 TTCAAATCAAAG
1 TTCAAATCAAAG
2831 TTCAAATCAAAG
1 TTCAAATCAAAG
2843 T
1 T
2844 GAATCAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (12 bp):
TTCAAATCAAAG
Found at i:4939 original size:64 final size:64
Alignment explanation
Indices: 4854--5014 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 64
4844 AAGACAATCT
* * *
4854 TTTCTCAACAA-TTCTCTGAAGTTGATCGGAAGACGATCTT-GTCAAA-AAGTACACCAGAAGAT
1 TTTCTCAAAAATTTC-CAGAAGTTGATCGGAAGACGAT-TTAATCAAAGAAGTACACCAGAA-AT
4916 GG
63 GG
* *
4918 TTTCTCAAAAATTTCCAGAAGTTGATCGGAAGATGATTTAATCAAAGAAGTATACCAGAAATGG
1 TTTCTCAAAAATTTCCAGAAGTTGATCGGAAGACGATTTAATCAAAGAAGTACACCAGAAATGG
* * *
4982 TTTCTCAAGAGTTTTCAGAAGTTGAT-GGAAGAC
1 TTTCTCAAAAATTTCCAGAAGTTGATCGGAAGAC
5015 AACCTCATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 8 0.09
64 62 0.73
65 15 0.18
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (64 bp):
TTTCTCAAAAATTTCCAGAAGTTGATCGGAAGACGATTTAATCAAAGAAGTACACCAGAAATGG
Found at i:5305 original size:41 final size:41
Alignment explanation
Indices: 5223--5305 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
5213 AGATAGTTAT
* *
5223 TTAGAAATAGATTTTCAGAATTGGTTCGGAAGGCGACCTCA
1 TTAGAAATAGATTTTCAGAATTGGTTCGGAAGACAACCTCA
*
5264 TTAGAAATAGATTTTCAGAATTGGTTCGGAAGACAATCTCA
1 TTAGAAATAGATTTTCAGAATTGGTTCGGAAGACAACCTCA
5305 T
1 T
5306 CAATTCATCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (41 bp):
TTAGAAATAGATTTTCAGAATTGGTTCGGAAGACAACCTCA
Found at i:5377 original size:64 final size:65
Alignment explanation
Indices: 5309--5570 Score: 241
Period size: 64 Copynumber: 4.0 Consensus size: 65
5299 ATCTCATCAA
*
5309 TTCATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTTCAAAA-ATTTTTAGAAG
1 TTCATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTTCAAAAGATTTTCAGAAG
* * * * * *
5373 TTCATCGAAAGACGATCTTGTCAAGAAGTACATCGGAAGA-CGATTTGCTAGAAAGAGTTTTCAG
1 TTCATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTTC-A-AAAGA-TTTTCAG
*
5437 AAA
63 AAG
* * * *
5440 TTGATCGGAAGACGATCTCGTCAAAGAAGTACACCAGAAGATGGTTTCTCAACA-ATTTTCAG-A
1 TTCATCGGAAGACGATCTTGTC-AAGAAGTACACCAGAAGATGGTTTTTCAAAAGATTTTCAGAA
5503 -
65 G
* * * * * *
5503 -TGATCGGAAGACGATCTTGTTAAG-AGATGCACCAGAAGACGGTTATTTAGAAATAGATTTTTA
1 TTCATCGGAAGACGATCTTGTCAAGAAG-TACACCAGAAGATGGTT-TTT-CAAA-AGATTTTCA
5566 GAAG
62 GAAG
5570 T
1 T
5571 CAATCAGAAG
Statistics
Matches: 158, Mismatches: 26, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
60 2 0.01
61 18 0.11
62 21 0.13
63 7 0.04
64 40 0.25
65 17 0.11
66 3 0.02
67 29 0.18
68 17 0.11
69 4 0.03
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (65 bp):
TTCATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTTTCAAAAGATTTTCAGAAG
Found at i:5860 original size:51 final size:51
Alignment explanation
Indices: 5796--6156 Score: 580
Period size: 51 Copynumber: 7.1 Consensus size: 51
5786 AAACACGATT
** * *
5796 GGAAGACAATCCTTTTTAAGAATAAATTGGAAGACAGTTCAAAGGATAAGC
1 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
*
5847 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAATTCAAAGGATAAGC
1 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
*
5898 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAAC
1 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
*
5949 GGAAGACGGTCCTTCTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
1 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
6000 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
1 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
* * *
6051 GGAAGACGGTCCTTTTTAAGATCGAATTGGAGGACAGTTCAAAGGATGAGC
1 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
* * * *
6102 GGGAGATGGTCC-TTTTAAGATTGAATTGGAAGACAATTCAAGGGATAAGC
1 GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
6152 AGGAA
1 -GGAA
6157 ACGATCCATT
Statistics
Matches: 288, Mismatches: 21, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
50 33 0.11
51 255 0.89
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (51 bp):
GGAAGACGGTCCTTTTTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGC
Found at i:6441 original size:26 final size:27
Alignment explanation
Indices: 6385--6456 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
6375 AGGGTCACCC
**
6385 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCATTTTGGTCATTTGCACACTA
* * *
6412 A-GGGCATTTTGGTCATTTGCATATTT
1 AGGGGCATTTTGGTCATTTGCACACTA
**
6438 AGGGGCACATTGGTCATTT
1 AGGGGCATTTTGGTCATTT
6457 TAAGTACACT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.40
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACACTA
Done.