Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022757.1 Corchorus olitorius cultivar O-4 contig22790, 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: 33224
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1422 original size:22 final size:23
Alignment explanation
Indices: 1396--1453 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
1386 GTCGATTTCA
*
1396 AGAAGAAAATTTGTCGACTAAAG
1 AGAAGAAAATTTGTCAACTAAAG
* **
1419 -GAAGCAAA-CAGTCAACTAAAG
1 AGAAGAAAATTTGTCAACTAAAG
1440 AGAAGAACAATTTG
1 AGAAGAA-AATTTG
1454 ACTAAGGAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 5
0.68 0.19 0.14
Matches are distributed among these distances:
21 10 0.40
22 12 0.48
23 2 0.08
24 1 0.04
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (23 bp):
AGAAGAAAATTTGTCAACTAAAG
Found at i:7256 original size:20 final size:22
Alignment explanation
Indices: 7211--7257 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
7201 CAAAAGGTTT
*
7211 GAAAATATTGAAATTTATCATC
1 GAAAATATTAAAATTTATCATC
*
7233 -AAAA-ATTAAAATTTAT-GTC
1 GAAAATATTAAAATTTATCATC
7252 GAAAAT
1 GAAAAT
7258 CAATTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.10
20 15 0.71
21 4 0.19
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (22 bp):
GAAAATATTAAAATTTATCATC
Found at i:7700 original size:21 final size:21
Alignment explanation
Indices: 7676--7721 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
7666 CTAAGATGCA
*
7676 TAAAAA-AATAAATCTTAAATC
1 TAAAAACAAGAAAT-TTAAATC
7697 TAAAAACAAGAAATTTAAATC
1 TAAAAACAAGAAATTTAAATC
7718 TAAA
1 TAAA
7722 CCTAGATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAACAAGAAATTTAAATC
Found at i:18273 original size:30 final size:30
Alignment explanation
Indices: 18237--18294 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
18227 ATTCTTGCTC
*
18237 CTTGAAATAATTCTTCAATGA-TCTTCAAGT
1 CTTGAAATAA-TCTTCAAAGAGTCTTCAAGT
*
18267 CTTGAAATTATCTTCAAAGAGTCTTCAA
1 CTTGAAATAATCTTCAAAGAGTCTTCAA
18295 ACACGAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (30 bp):
CTTGAAATAATCTTCAAAGAGTCTTCAAGT
Found at i:18732 original size:15 final size:15
Alignment explanation
Indices: 18712--18741 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18702 CATCATTCTT
18712 AAGTAGCCATAATCA
1 AAGTAGCCATAATCA
*
18727 AAGTAGCCTTAATCA
1 AAGTAGCCATAATCA
18742 CTTACCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (15 bp):
AAGTAGCCATAATCA
Found at i:23346 original size:9 final size:9
Alignment explanation
Indices: 23332--23357 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
23322 CTGTTCGTGA
23332 TTGAAGAGC
1 TTGAAGAGC
23341 TTGAAGAGC
1 TTGAAGAGC
23350 TTGAAGAG
1 TTGAAGAG
23358 TCAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.23
Consensus pattern (9 bp):
TTGAAGAGC
Found at i:23557 original size:76 final size:76
Alignment explanation
Indices: 23463--23614 Score: 182
Period size: 76 Copynumber: 2.0 Consensus size: 76
23453 TGATGAGCTA
* * *
23463 TGACACAGCCCATCTGGGTGATCAGGCGAAAC-ACATGAGTCTTC-AGACAAACCATGTGGGCAC
1 TGACACAGCCCACCTGGGTCATCAAGC-AAACTACATGAGTCTTCAAGAC-AACCATGTGGGCAC
*
23526 CCAGTTGGAGTCG
64 CCAGGTGGAGTCG
* * * * * *
23539 TGACACCGCCCACCTGGGTCCTCAAGCAAACTACATGGGTGTTCAAGGCAACCATGTGGGCGCCC
1 TGACACAGCCCACCTGGGTCATCAAGCAAACTACATGAGTCTTCAAGACAACCATGTGGGCACCC
23604 AGGTGGAGTCG
66 AGGTGGAGTCG
23615 GGGCCCTTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
75 4 0.06
76 57 0.89
77 3 0.05
ACGTcount: A:0.25, C:0.28, G:0.29, T:0.18
Consensus pattern (76 bp):
TGACACAGCCCACCTGGGTCATCAAGCAAACTACATGAGTCTTCAAGACAACCATGTGGGCACCC
AGGTGGAGTCG
Found at i:31119 original size:17 final size:17
Alignment explanation
Indices: 31097--31130 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31087 TAAAGGTAAT
31097 CTACTAAAACTAAATGC
1 CTACTAAAACTAAATGC
31114 CTACTAAAACTAAATGC
1 CTACTAAAACTAAATGC
31131 TAACATGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (17 bp):
CTACTAAAACTAAATGC
Found at i:32188 original size:3 final size:3
Alignment explanation
Indices: 32180--32215 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
32170 GTTTGAAGGT
32180 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32216 CTAGATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:32852 original size:77 final size:77
Alignment explanation
Indices: 32763--32931 Score: 329
Period size: 77 Copynumber: 2.2 Consensus size: 77
32753 AAGGATGAGA
32763 ACCCCCGGCACACCCGTCTAGAGACGGTACCTCTAAGTCTAATGTGTTCTAAAATAAAAAGGTTG
1 ACCCCCGGCACACCCGTCTAGAGACGGTACCTCTAAGTCTAATGTGTTCTAAAATAAAAAGGTTG
32828 CTTTTAGACGGT
66 CTTTTAGACGGT
*
32840 ACCCCCGGCACACCCGTCTAGAGACGGTACCTCTAAGTCTAATGTGTTTTAAAATAAAAAGGTTG
1 ACCCCCGGCACACCCGTCTAGAGACGGTACCTCTAAGTCTAATGTGTTCTAAAATAAAAAGGTTG
32905 CTTTTAGACGGT
66 CTTTTAGACGGT
32917 ACCCCCGGCACACCC
1 ACCCCCGGCACACCC
32932 TTTCTTTCTT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 91 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (77 bp):
ACCCCCGGCACACCCGTCTAGAGACGGTACCTCTAAGTCTAATGTGTTCTAAAATAAAAAGGTTG
CTTTTAGACGGT
Found at i:33082 original size:20 final size:20
Alignment explanation
Indices: 33044--33082 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33034 GGCAAAACGG
*
33044 GAATAAAACATTGAAAACAA
1 GAATAAAACAATGAAAACAA
* *
33064 GAATAAAATAATGAGAACA
1 GAATAAAACAATGAAAACA
33083 TCACCTTCCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (20 bp):
GAATAAAACAATGAAAACAA
Found at i:33103 original size:68 final size:68
Alignment explanation
Indices: 33018--33199 Score: 222
Period size: 68 Copynumber: 2.7 Consensus size: 68
33008 AGGAATGACC
* *
33018 CCTTCCGATGGGGAAGGGCAAAACGGGAATAAAACATTGAAAACAAGAATAAAATA-ATGAGAAC
1 CCTTCCGACGGGGAAGGGCAAAACGTGAATAAAACATTGAAAACAAGAATAAAATATA-GAGAAC
*
33082 ATCA
65 AACA
* * * * * * *
33086 CCTTCCGACCGGGAAGGGCAAAACGTGAATAAAACATCGAAAACAGGGATCAAGTCTAGAGAACA
1 CCTTCCGACGGGGAAGGGCAAAACGTGAATAAAACATTGAAAACAAGAATAAAATATAGAGAACA
33151 ACA
66 ACA
* * **
33154 CCCTCCGACGGGGAAGGGCAAAACATGAATAAAATGTTGAAAACAA
1 CCTTCCGACGGGGAAGGGCAAAACGTGAATAAAACATTGAAAACAA
33200 CACCTTCCGA
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
68 95 0.99
69 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (68 bp):
CCTTCCGACGGGGAAGGGCAAAACGTGAATAAAACATTGAAAACAAGAATAAAATATAGAGAACA
ACA
Done.