Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014375.1 Corchorus capsularis cultivar CVL-1 contig14396, 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: 37861
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:12248 original size:20 final size:20
Alignment explanation
Indices: 12202--12249 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
12192 TAAACCAATT
* *
12202 TAGATTTAGATTTAGGGTTT
1 TAGATTTAAATTTAGGGTTC
* **
12222 TAAATTTAAATTTATTGTTC
1 TAGATTTAAATTTAGGGTTC
12242 TAGATTTA
1 TAGATTTA
12250 GGGTTTTATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (20 bp):
TAGATTTAAATTTAGGGTTC
Found at i:13591 original size:14 final size:15
Alignment explanation
Indices: 13563--13591 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13553 GTGTGGCTTC
13563 AAATTGATCTTTTGA
1 AAATTGATCTTTTGA
13578 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
13592 TTAACTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (15 bp):
AAATTGATCTTTTGA
Found at i:13914 original size:19 final size:18
Alignment explanation
Indices: 13890--13926 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
13880 AAGACTTATC
13890 GAAGATAATTTGAAGAATT
1 GAAGATAA-TTGAAGAATT
*
13909 GAAGATCATTGAAGAATT
1 GAAGATAATTGAAGAATT
13927 ATTTCAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.30
Consensus pattern (18 bp):
GAAGATAATTGAAGAATT
Found at i:17590 original size:36 final size:35
Alignment explanation
Indices: 17542--17723 Score: 173
Period size: 36 Copynumber: 5.3 Consensus size: 35
17532 CTCTTTTTAG
* *
17542 ATTAAGTCTTTATTAACTCCACTTAATTACCCTGA
1 ATTAAGCCTTTATTGACTCCACTTAATTACCCTGA
*
17577 ATTAAGCCTTTTATTGACTCCACTTAATTACCTTGA
1 ATTAAGCC-TTTATTGACTCCACTTAATTACCCTGA
* *
17613 ATTAATCCTTTTATTGA-TGCTACTTAATTACCCTGA
1 ATTAAGCC-TTTATTGACT-CCACTTAATTACCCTGA
**
17649 ATTAAGTCC---A-TGACTTGACTTAATTACCCTGA
1 ATTAAG-CCTTTATTGACTCCACTTAATTACCCTGA
* **
17681 ATTAAGCCCTTA---ACTTGACTTAATTACCCTGA
1 ATTAAGCCTTTATTGACTCCACTTAATTACCCTGA
17713 ATTAAGTCCTT
1 ATTAAG-CCTT
17724 GACTCTACTT
Statistics
Matches: 129, Mismatches: 10, Indels: 18
0.82 0.06 0.11
Matches are distributed among these distances:
31 2 0.02
32 50 0.39
33 5 0.04
34 1 0.01
35 8 0.06
36 61 0.47
37 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.40
Consensus pattern (35 bp):
ATTAAGCCTTTATTGACTCCACTTAATTACCCTGA
Found at i:17675 original size:32 final size:32
Alignment explanation
Indices: 17634--17774 Score: 169
Period size: 32 Copynumber: 4.2 Consensus size: 32
17624 TATTGATGCT
*
17634 ACTTAATTACCCTGAATTAAGTCCATGACTTG
1 ACTTAATTACCCTGAATTAAGTCCTTGACTTG
* *
17666 ACTTAATTACCCTGAATTAAGCCCTTAACTTG
1 ACTTAATTACCCTGAATTAAGTCCTTGACTTG
17698 ACTTAATTACCCTGAATTAAGTCCTTGACTCT-
1 ACTTAATTACCCTGAATTAAGTCCTTGACT-TG
*
17730 ACTTAATTTCCTTCCCTGAAATTAAGTCCTTGACTCT-
1 ACTTAA--T--TACCCTG-AATTAAGTCCTTGACT-TG
17767 ACTTAATT
1 ACTTAATT
17775 TCCTTCCCTG
Statistics
Matches: 97, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
32 63 0.65
33 2 0.02
34 1 0.01
35 1 0.01
36 6 0.06
37 24 0.25
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTCCTTGACTTG
Found at i:17772 original size:18 final size:18
Alignment explanation
Indices: 17714--17772 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
17704 TTACCCTGAA
17714 TTAAGTCCTTGACTCTAC
1 TTAAGTCCTTGACTCTAC
* ** ** *
17732 TTAATTTCCTTCCCTGAAA
1 TTAA-GTCCTTGACTCTAC
17751 TTAAGTCCTTGACTCTAC
1 TTAAGTCCTTGACTCTAC
17769 TTAA
1 TTAA
17773 TTTCCTTCCC
Statistics
Matches: 28, Mismatches: 12, Indels: 2
0.67 0.29 0.05
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.41
Consensus pattern (18 bp):
TTAAGTCCTTGACTCTAC
Found at i:17810 original size:37 final size:37
Alignment explanation
Indices: 17707--17797 Score: 175
Period size: 37 Copynumber: 2.5 Consensus size: 37
17697 GACTTAATTA
17707 CCCTG-AATTAAGTCCTTGACTCTACTTAATTTCCTT
1 CCCTGAAATTAAGTCCTTGACTCTACTTAATTTCCTT
17743 CCCTGAAATTAAGTCCTTGACTCTACTTAATTTCCTT
1 CCCTGAAATTAAGTCCTTGACTCTACTTAATTTCCTT
17780 CCCTGAAATTAAGTCCTT
1 CCCTGAAATTAAGTCCTT
17798 TTCTTTACTT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 5 0.09
37 49 0.91
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (37 bp):
CCCTGAAATTAAGTCCTTGACTCTACTTAATTTCCTT
Found at i:17872 original size:36 final size:35
Alignment explanation
Indices: 17815--17917 Score: 102
Period size: 36 Copynumber: 2.9 Consensus size: 35
17805 CTTAATCCCC
* *
17815 TTGGGTTAAGTCTTAAT-CTGATCTTGCTTAATCATCT
1 TTGGATTAAGTCTT--TGCTGATCTTACTTAAT-ATCT
* *
17852 TTGGATTAAGTCTTTGCTGATTTTACTTAATTTCT
1 TTGGATTAAGTCTTTGCTGATCTTACTTAATATCT
* *
17887 TTGAAATTAAGTCTTTGCTGAT-ATACTTAAT
1 TTG-GATTAAGTCTTTGCTGATCTTACTTAAT
17918 TACCCTAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
35 15 0.26
36 30 0.52
37 13 0.22
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.49
Consensus pattern (35 bp):
TTGGATTAAGTCTTTGCTGATCTTACTTAATATCT
Found at i:19111 original size:23 final size:21
Alignment explanation
Indices: 19073--19114 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
19063 ACATGAGGAG
19073 TTCAATAGTTTACTTTCATGT
1 TTCAATAGTTTACTTTCATGT
*
19094 TTCAATTATGTTTGCTTTCAT
1 TTCAA-TA-GTTTACTTTCAT
19115 ATATATAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (21 bp):
TTCAATAGTTTACTTTCATGT
Found at i:20012 original size:11 final size:10
Alignment explanation
Indices: 20000--20045 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
19990 TTTTTTAAAT
20000 TATTTTTTTA
1 TATTTTTTTA
*
20010 T-TATTTTTA
1 TATTTTTTTA
*
20019 -ATTTTTTAAA
1 TATTTTTT-TA
20029 TATTTTTTTA
1 TATTTTTTTA
20039 TATTTTT
1 TATTTTT
20046 ATTTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 12 0.41
10 10 0.34
11 7 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TATTTTTTTA
Found at i:20035 original size:28 final size:28
Alignment explanation
Indices: 19990--20063 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
19980 CCTACGTGGC
19990 TTTTTTAAATTATTTTTTTATTATTTTTAA
1 TTTTTTAAA-TATTTTTTTA-TATTTTTAA
*
20020 TTTTTTAAATATTTTTTTATATTTTTAT
1 TTTTTTAAATATTTTTTTATATTTTTAA
20048 TTTTTTAAATATTTTT
1 TTTTTTAAATATTTTT
20064 AAACCAGCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 24 0.56
29 10 0.23
30 9 0.21
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTTTTAAATATTTTTTTATATTTTTAA
Found at i:20059 original size:18 final size:16
Alignment explanation
Indices: 19999--20064 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 16
19989 CTTTTTTAAA
19999 TTATTTTTTTATTATTT
1 TTATTTTTTTA-TATTT
*
20016 TTAATTTTTTA-A---
1 TTATTTTTTTATATTT
*
20028 ATATTTTTTTATATTT
1 TTATTTTTTTATATTT
20044 TTATTTTTTTAAATATTT
1 TTATTTTTTT--ATATTT
20062 TTA
1 TTA
20065 AACCAGCTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
12 9 0.23
13 1 0.03
15 1 0.03
16 9 0.23
17 10 0.26
18 9 0.23
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTTTTATATTT
Found at i:20064 original size:10 final size:10
Alignment explanation
Indices: 19991--20066 Score: 61
Period size: 10 Copynumber: 7.8 Consensus size: 10
19981 CTACGTGGCT
19991 TTTTTAAATTA
1 TTTTTAAA-TA
* *
20002 TTTTTTTATTA
1 -TTTTTAAATA
20013 TTTTT-AAT-
1 TTTTTAAATA
20021 TTTTTAAATA
1 TTTTTAAATA
**
20031 TTTTTTTATA
1 TTTTTAAATA
*
20041 TTTTT--ATT
1 TTTTTAAATA
20049 TTTTTAAATA
1 TTTTTAAATA
20059 TTTTTAAA
1 TTTTTAAA
20067 CCAGCTCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
8 12 0.23
9 5 0.09
10 28 0.53
11 2 0.04
12 6 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:26118 original size:14 final size:14
Alignment explanation
Indices: 26096--26133 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
26086 AGAAGGATTT
*
26096 GAAGAATTGAAATC
1 GAAGCATTGAAATC
*
26110 GAAGCATTGAAATT
1 GAAGCATTGAAATC
26124 GAAGCATTGA
1 GAAGCATTGA
26134 CATATTGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (14 bp):
GAAGCATTGAAATC
Found at i:26165 original size:36 final size:36
Alignment explanation
Indices: 26119--26224 Score: 117
Period size: 36 Copynumber: 2.9 Consensus size: 36
26109 CGAAGCATTG
26119 AAATTGAAGCATTGACATATTGGAATTGAAACATCA
1 AAATTGAAGCATTGACATATTGGAATTGAAACATCA
* **
26155 AAATTAAAGCATTGACAT-TTGGAATTTGAAGA-ATTG
1 AAATTGAAGCATTGACATATTGGAA-TTGAA-ACATCA
* * * *
26191 GATTTGAAGCATTGAAATATTGAAATTGAAACAT
1 AAATTGAAGCATTGACATATTGGAATTGAAACAT
26225 TGAAAAATTG
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
35 7 0.12
36 45 0.78
37 6 0.10
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (36 bp):
AAATTGAAGCATTGACATATTGGAATTGAAACATCA
Found at i:26195 original size:14 final size:15
Alignment explanation
Indices: 26173--26214 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
26163 GCATTGACAT
26173 TTGGAATTTGAAGAA
1 TTGGAATTTGAAGAA
*
26188 TTGG-ATTTGAAGCA
1 TTGGAATTTGAAGAA
*
26202 TTGAAATATTGAA
1 TTGGAAT-TTGAA
26215 ATTGAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.52
15 6 0.26
16 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (15 bp):
TTGGAATTTGAAGAA
Found at i:26205 original size:22 final size:22
Alignment explanation
Indices: 26180--26286 Score: 130
Period size: 22 Copynumber: 5.0 Consensus size: 22
26170 CATTTGGAAT
* * *
26180 TTGAAGAATTGGATTTGAAGCA
1 TTGAAGAATTGAAATTGAAACA
26202 TTGAA-ATATTGAAATTGAAACA
1 TTGAAGA-ATTGAAATTGAAACA
*
26224 TTGAAAAATTGAAATTGAAACA
1 TTGAAGAATTGAAATTGAAACA
* *
26246 TTGAAGGATTGAAATTG-AA-G
1 TTGAAGAATTGAAATTGAAACA
26266 TTGAAGAATTGAAATTGAAAC
1 TTGAAGAATTGAAATTGAAAC
26287 TGGGGCCTTG
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
20 16 0.22
21 5 0.07
22 52 0.70
23 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.30
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAACA
Found at i:26212 original size:8 final size:7
Alignment explanation
Indices: 26201--26285 Score: 63
Period size: 8 Copynumber: 12.0 Consensus size: 7
26191 GATTTGAAGC
26201 ATTGAAA
1 ATTGAAA
26208 TATTG-AA
1 -ATTGAAA
26215 ATTGAAA
1 ATTGAAA
26222 CATTGAAAA
1 -ATTG-AAA
26231 ATTG-AA
1 ATTGAAA
26237 ATTGAAA
1 ATTGAAA
*
26244 CATTGAAGG
1 -ATTGAA-A
26253 ATTG-AA
1 ATTGAAA
26259 ATTG-AA
1 ATTGAAA
*
26265 GTTGAAGA
1 ATTGAA-A
26273 ATTG-AA
1 ATTGAAA
26279 ATTGAAA
1 ATTGAAA
26286 CTGGGGCCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
6 24 0.38
7 11 0.17
8 26 0.41
9 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.29
Consensus pattern (7 bp):
ATTGAAA
Found at i:26218 original size:14 final size:13
Alignment explanation
Indices: 26209--26285 Score: 68
Period size: 14 Copynumber: 5.5 Consensus size: 13
26199 GCATTGAAAT
26209 ATTG-AAATTGAAA
1 ATTGAAAATTG-AA
26222 CATTGAAAAATTGAA
1 -ATTG-AAAATTGAA
26237 ATTGAAACATTGAA
1 ATTGAAA-ATTGAA
26251 GGATTG-AAATTGAA
1 --ATTGAAAATTGAA
*
26265 GTTGAAGAATTGAA
1 ATTGAA-AATTGAA
26279 ATTGAAA
1 ATTGAAA
26286 CTGGGGCCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
12 3 0.06
13 5 0.09
14 32 0.59
15 4 0.07
16 10 0.19
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (13 bp):
ATTGAAAATTGAA
Found at i:26220 original size:6 final size:6
Alignment explanation
Indices: 26209--26285 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
26199 GCATTGAAAT
26209 ATTGAA ATTGAAA CATTGAAAA ATTGAA ATTGAAA CATTGAA GGATTGAA
1 ATTGAA ATTG-AA -ATTG--AA ATTGAA ATTG-AA -ATTGAA --ATTGAA
*
26259 ATTGAA GTTGAAGA ATTGAA ATTGAA A
1 ATTGAA ATTG-A-A ATTGAA ATTGAA A
26286 CTGGGGCCTT
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
6 27 0.45
7 8 0.13
8 22 0.37
9 3 0.05
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (6 bp):
ATTGAA
Found at i:26387 original size:8 final size:8
Alignment explanation
Indices: 26376--26643 Score: 67
Period size: 8 Copynumber: 36.8 Consensus size: 8
26366 GCATTGAATT
26376 ATTGAAGA
1 ATTGAAGA
*
26384 ATTGAAGC
1 ATTGAAGA
*
26392 ATTGGATG-
1 ATT-GAAGA
26400 ATTGAAGA
1 ATTGAAGA
26408 ATTGAAGA
1 ATTGAAGA
*
26416 A-AGATA-A
1 ATTGA-AGA
*
26423 ATTGAAGC
1 ATTGAAGA
26431 ATT---GA
1 ATTGAAGA
*
26436 ATTGAAGG
1 ATTGAAGA
26444 ATTG-A-A
1 ATTGAAGA
* *
26450 CTTGAAGC
1 ATTGAAGA
26458 ATTG-A-A
1 ATTGAAGA
26464 ATTG-A-A
1 ATTGAAGA
* *
26470 ACTGAAGC
1 ATTGAAGA
*
26478 ATTTAA-A
1 ATTGAAGA
26485 TATTG-A-A
1 -ATTGAAGA
26492 ATTGAAGA
1 ATTGAAGA
26500 ATTGAA-A
1 ATTGAAGA
* *
26507 AATGGA-A
1 ATTGAAGA
*
26514 ATTGAAGT
1 ATTGAAGA
26522 ATTGAAGA
1 ATTGAAGA
**
26530 AGCG-A-A
1 ATTGAAGA
*
26536 ATTGAAGC
1 ATTGAAGA
26544 ATTG--GCA
1 ATTGAAG-A
*
26551 TTTG--GA
1 ATTGAAGA
26557 ATTTG-A-A
1 A-TTGAAGA
*
26564 ATTGAAGC
1 ATTGAAGA
*
26572 ATTGAAGG
1 ATTGAAGA
26580 ATTG-A-A
1 ATTGAAGA
*
26586 TTTGAAGA
1 ATTGAAGA
*
26594 ATTG-A-T
1 ATTGAAGA
*
26600 ATTGAAGG
1 ATTGAAGA
26608 ATTGAAGA
1 ATTGAAGA
26616 ATTG-A-A
1 ATTGAAGA
*
26622 ATTGAAGT
1 ATTGAAGA
26630 ATTGAAGA
1 ATTGAAGA
26638 ATTGAA
1 ATTGAA
26644 ATTGACCAAC
Statistics
Matches: 188, Mismatches: 43, Indels: 58
0.65 0.15 0.20
Matches are distributed among these distances:
5 4 0.02
6 36 0.19
7 43 0.23
8 102 0.54
9 3 0.02
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.29
Consensus pattern (8 bp):
ATTGAAGA
Found at i:26391 original size:24 final size:24
Alignment explanation
Indices: 26359--26414 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
26349 CACTGAAGCA
* *
26359 AATTAAAGCATTGAATTATTGAAG
1 AATTGAAGCATTGAATGATTGAAG
*
26383 AATTGAAGCATTGGATGATTGAAG
1 AATTGAAGCATTGAATGATTGAAG
26407 AATTGAAG
1 AATTGAAG
26415 AAAGATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (24 bp):
AATTGAAGCATTGAATGATTGAAG
Found at i:26463 original size:22 final size:22
Alignment explanation
Indices: 26436--26598 Score: 116
Period size: 22 Copynumber: 7.2 Consensus size: 22
26426 GAAGCATTGA
* *
26436 ATTGAAGGATTGAACTTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
*
26458 ATTG-A-AATTGAAACTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
* *
26478 ATTTAA-ATATTGAAATTGAAGA
1 ATTGAAGA-ATTGAAATTGAAGC
* * *
26500 ATTGAAAAATGGAAATTGAAGT
1 ATTGAAGAATTGAAATTGAAGC
**
26522 ATTGAAGAAGCGAAATTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
*
26544 ATTGGCATTTGGAATTTGAAATTGAAGC
1 ATT-G-A---AGAA-TTGAAATTGAAGC
* * *
26572 ATTGAAGGATTGAATTTGAAGA
1 ATTGAAGAATTGAAATTGAAGC
26594 ATTGA
1 ATTGA
26599 TATTGAAGGA
Statistics
Matches: 112, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
20 15 0.13
21 3 0.03
22 70 0.62
23 4 0.04
24 1 0.01
26 1 0.01
27 4 0.04
28 14 0.12
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.29
Consensus pattern (22 bp):
ATTGAAGAATTGAAATTGAAGC
Found at i:26505 original size:14 final size:14
Alignment explanation
Indices: 26421--26648 Score: 92
Period size: 14 Copynumber: 15.5 Consensus size: 14
26411 GAAGAAAGAT
*
26421 AAATTGAAGCATTG
1 AAATTGAAGAATTG
*
26435 -AATTGAAGGATTG
1 AAATTGAAGAATTG
* *
26448 AACTTGAAGCATTG
1 AAATTGAAGAATTG
*
26462 AAATTG-A-AACTG
1 AAATTGAAGAATTG
*
26474 AAGCATTTAA-ATATTG
1 AA--ATTGAAGA-ATTG
26490 AAATTGAAGAATTG
1 AAATTGAAGAATTG
* *
26504 AAAAATGGA-AATTG
1 -AAATTGAAGAATTG
**
26518 AAGTATTGAAGAAGCG
1 AA--ATTGAAGAATTG
*
26534 AAATTGAAGCATTGG
1 AAATTGAAGAATT-G
* *
26549 CATTTGGAATTTGAAATTG
1 AAATT-GAA---G-AATTG
*
26568 AAGCATTGAAGGATTG
1 AA--ATTGAAGAATTG
*
26584 AATTTGAAGAATTG
1 AAATTGAAGAATTG
* *
26598 ATATTGAAGGATTG
1 AAATTGAAGAATTG
26612 AAGAATTG-A-AATTG
1 -A-AATTGAAGAATTG
26626 AAGTATTGAAGAATTG
1 AA--ATTGAAGAATTG
26642 AAATTGA
1 AAATTGA
26649 CCAACTGTCA
Statistics
Matches: 159, Mismatches: 31, Indels: 48
0.67 0.13 0.20
Matches are distributed among these distances:
12 6 0.04
13 16 0.10
14 75 0.47
15 20 0.13
16 30 0.19
17 1 0.01
19 3 0.02
20 6 0.04
21 2 0.01
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (14 bp):
AAATTGAAGAATTG
Found at i:26525 original size:36 final size:36
Alignment explanation
Indices: 26485--26635 Score: 114
Period size: 36 Copynumber: 4.2 Consensus size: 36
26475 AGCATTTAAA
*
26485 TATTGAAATTGAAGAATTGAAAAATGGAAATTGAAG
1 TATTGAAATTGAAGAATTGAAGAATGGAAATTGAAG
* * *
26521 TATTG-AA--GAAGCGAAATTGAAGCATTGGCATTTGGAA-
1 TATTGAAATTGAA--G-AATTGAAG-AATGGAAATT-GAAG
* * * *
26558 T-TTGAAATTGAAGCATTGAAGGATTGAATTTGAAG
1 TATTGAAATTGAAGAATTGAAGAATGGAAATTGAAG
* * * *
26593 AATTGATATTGAAGGATTGAAGAATTGAAATTGAAG
1 TATTGAAATTGAAGAATTGAAGAATGGAAATTGAAG
26629 TATTGAA
1 TATTGAA
26636 GAATTGAAAT
Statistics
Matches: 89, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
33 3 0.03
34 3 0.03
35 9 0.10
36 57 0.64
37 11 0.12
38 3 0.03
39 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (36 bp):
TATTGAAATTGAAGAATTGAAGAATGGAAATTGAAG
Found at i:26947 original size:69 final size:70
Alignment explanation
Indices: 26836--26966 Score: 219
Period size: 69 Copynumber: 1.9 Consensus size: 70
26826 AACTCCATGT
* *
26836 TGCTTGGATGGAACCAATGCTTGAACTGACTTGTAGGGAAACGAGTTTG-CTTGTGGAAAAGCCC
1 TGCTTGAATGGAACCAATGCTTGAACTGACTCGTAGGGAAACGAGTTTGACTTGTGGAAAAGCCC
26900 CTGAA
66 CTGAA
* *
26905 TGCTTGAATGGAACCAATGTTTGAACTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAG
1 TGCTTGAATGGAACCAATGCTTGAACTGACTCGTAGGGAAACGAGTTTGACTTGTGGAAAAG
26967 TCAAAGTGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 45 0.79
70 12 0.21
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.27
Consensus pattern (70 bp):
TGCTTGAATGGAACCAATGCTTGAACTGACTCGTAGGGAAACGAGTTTGACTTGTGGAAAAGCCC
CTGAA
Found at i:27580 original size:16 final size:17
Alignment explanation
Indices: 27561--27593 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
27551 TATTTTGAAA
27561 TCTTGTCTTT-TTTTTT
1 TCTTGTCTTTCTTTTTT
*
27577 TCTTTTCTTTCTTTTTT
1 TCTTGTCTTTCTTTTTT
27594 GAGACGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TCTTGTCTTTCTTTTTT
Found at i:27874 original size:22 final size:23
Alignment explanation
Indices: 27849--27891 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
27839 TTTCTTTTGT
*
27849 TTTTTTTTC-TTCTTTTTTTTCA
1 TTTTCTTTCTTTCTTTTTTTTCA
27871 TTTTCTTTCTTTCTTTTTTTT
1 TTTTCTTTCTTTCTTTTTTTT
27892 TTTCATGCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTCTTTCTTTCTTTTTTTTCA
Found at i:27908 original size:26 final size:26
Alignment explanation
Indices: 27854--27908 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
27844 TTTGTTTTTT
*** *
27854 TTTCTTCTTTTTTTTCATTTTCTTTC
1 TTTCTTCTTTTTTTTCATGCGCTTGC
*
27880 TTTCTTTTTTTTTTTCATGCGCTTGC
1 TTTCTTCTTTTTTTTCATGCGCTTGC
27906 TTT
1 TTT
27909 TGAAAAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.73
Consensus pattern (26 bp):
TTTCTTCTTTTTTTTCATGCGCTTGC
Found at i:28347 original size:12 final size:12
Alignment explanation
Indices: 28330--28376 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
28320 TTGTTTCACT
28330 TTTGATTTGAAC
1 TTTGATTTGAAC
*
28342 TTTGATTTAAAC
1 TTTGATTTGAAC
28354 TTTGATTTGAAC
1 TTTGATTTGAAC
28366 TTTGATTTGAA
1 TTTGATTTGAA
28377 TTATTTGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (12 bp):
TTTGATTTGAAC
Found at i:28705 original size:15 final size:16
Alignment explanation
Indices: 28687--28725 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
28677 AAACTCATTT
28687 TTGAAAAACC-TTTTC
1 TTGAAAAACCATTTTC
*
28702 TTG-AAGACCATTTTC
1 TTGAAAAACCATTTTC
28717 TTGAAAAAC
1 TTGAAAAAC
28726 GTCTCTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 4 0.20
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (16 bp):
TTGAAAAACCATTTTC
Found at i:28847 original size:46 final size:50
Alignment explanation
Indices: 28782--28874 Score: 131
Period size: 48 Copynumber: 1.9 Consensus size: 50
28772 TTGCAATTCT
*
28782 TTTTATTTTCTTTTTGCGACCAC-TTC-TTTTTTAGGCCTAGTTTTTTTC
1 TTTTATTTTCTTTTTGCGACCACTTTCTTTTTTTAGGCCCAGTTTTTTTC
* *
28830 TTTT-TTTT-TTTTTGCGACCTCTTTCTTTTTTTAGTCCCAGTTTTT
1 TTTTATTTTCTTTTTGCGACCACTTTCTTTTTTTAGGCCCAGTTTTT
28875 CTTTTTCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 12 0.30
47 7 0.17
48 21 0.52
ACGTcount: A:0.09, C:0.18, G:0.10, T:0.63
Consensus pattern (50 bp):
TTTTATTTTCTTTTTGCGACCACTTTCTTTTTTTAGGCCCAGTTTTTTTC
Found at i:28875 original size:46 final size:46
Alignment explanation
Indices: 28782--28880 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 46
28772 TTGCAATTCT
*
28782 TTTTATTTTCTTTTTGCGACCACTTCTTTTTTAGGCCTAGTTTTTTTC
1 TTTT-TTTTCTTTTTGCGACCACTTCTTTTTTAGGCCCAG-TTTTTTC
* *
28830 TTTTTTTT-TTTTTGCGACCTCTTTCTTTTTTTAGTCCCAG-TTTTTC
1 TTTTTTTTCTTTTTGCGACCAC-TTC-TTTTTTAGGCCCAGTTTTTTC
28876 TTTTT
1 TTTTT
28881 CTTTGATGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
46 23 0.50
47 7 0.15
48 16 0.35
ACGTcount: A:0.08, C:0.18, G:0.09, T:0.65
Consensus pattern (46 bp):
TTTTTTTTCTTTTTGCGACCACTTCTTTTTTAGGCCCAGTTTTTTC
Found at i:36584 original size:13 final size:12
Alignment explanation
Indices: 36561--36603 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
36551 TAAATACAGG
36561 TATCGACGGATA
1 TATCGACGGATA
36573 TATCGAACGGATA
1 TATCG-ACGGATA
36586 TATCGACGGATA
1 TATCGACGGATA
36598 TATCGA
1 TATCGA
36604 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:37631 original size:10 final size:10
Alignment explanation
Indices: 37616--37651 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
37606 AATTTAATAT
37616 GGATATTTAC
1 GGATATTTAC
*
37626 GGATATTTAT
1 GGATATTTAC
37636 GGATATTTAC
1 GGATATTTAC
37646 GGATAT
1 GGATAT
37652 ATCGAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:37638 original size:20 final size:20
Alignment explanation
Indices: 37613--37651 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
37603 TTTAATTTAA
37613 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
37633 TATGGATATTTACGGATAT
1 TATGGATATTTACGGATAT
37652 ATCGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
TATGGATATTTACGGATATT
Found at i:37779 original size:12 final size:12
Alignment explanation
Indices: 37762--37800 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
37752 GTATAGATAT
37762 CGGATATATCGA
1 CGGATATATCGA
37774 CGGATATATCGA
1 CGGATATATCGA
37786 ---A-ATATCGA
1 CGGATATATCGA
37794 CGGATAT
1 CGGATAT
37801 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
11 1 0.04
12 14 0.61
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Done.