Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014081.1 Corchorus capsularis cultivar CVL-1 contig14102, 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: 24685
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:50 original size:2 final size:2
Alignment explanation
Indices: 43--82 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
33 TGACAACACA
43 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
83 AAAGTACGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3030 original size:19 final size:20
Alignment explanation
Indices: 2985--3031 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
2975 GTGGCACGCT
*
2985 ACATGTACCAAAAAGTCGTGCC
1 ACATGTACCAAAAA--CGTGAC
3007 ACATGTACCAAAAA-GTGAC
1 ACATGTACCAAAAACGTGAC
3026 ACATGT
1 ACATGT
3032 CACGCCACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
22 14 0.58
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (20 bp):
ACATGTACCAAAAACGTGAC
Found at i:3036 original size:53 final size:53
Alignment explanation
Indices: 2951--3053 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
2941 GACGTGGCAC
* ** *
2951 GCCACGTGTACCAAAAAGTGACATGTGGCACGCTACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* * *
3004 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAGAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
3054 GACACGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:3070 original size:31 final size:31
Alignment explanation
Indices: 3003--3083 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
2993 CAAAAAGTCG
*
3003 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
* * * *
3034 CGCCACGTGTACCAGAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
**
3065 TGCCACATGTTTCAAAAAG
1 TGCCACATGTACCAAAAAG
3084 CACAAAAGGA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACATGGCA
Found at i:7961 original size:24 final size:26
Alignment explanation
Indices: 7934--7986 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
7924 AAGAATAGTA
7934 TATTATAGGTAGTATATAT-A-ATCT
1 TATTATAGGTAGTATATATCATATCT
*
7958 TATTATAGGTAGTGTATATCATATCT
1 TATTATAGGTAGTATATATCATATCT
7984 TAT
1 TAT
7987 GTTTACAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 18 0.69
25 1 0.04
26 7 0.27
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (26 bp):
TATTATAGGTAGTATATATCATATCT
Found at i:8675 original size:22 final size:22
Alignment explanation
Indices: 8650--8904 Score: 133
Period size: 22 Copynumber: 11.8 Consensus size: 22
8640 AGTAATCACA
*
8650 CTATGAAATTGTGAT-AACCTC
1 CTATGAAATTTTGATAAACCTC
*
8671 GCTATGAAATTTTGATAAATCTTC
1 -CTATGAAATTTTGATAAA-CCTC
*
8695 CTATGAAACTTTGATAAACCTCC
1 CTATGAAATTTTGATAAACCT-C
* *
8718 CTATAAAATTTTGAT-AACTTTC
1 CTATGAAATTTTGATAAAC-CTC
* *
8740 TTATGAAATCTTGAT-AA----
1 CTATGAAATTTTGATAAACCTC
*
8757 CTA-CAAATTTTGAT-AACCTCC
1 CTATGAAATTTTGATAAACCT-C
**
8778 CTATGATTTTTTTGAT-AACCTC
1 CTATGA-AATTTTGATAAACCTC
* * *
8800 ATTATGAAATTTTG-TTAATCTCC
1 -CTATGAAATTTTGATAAACCT-C
** * *
8823 CTATGAAATTTTGATCTACATA
1 CTATGAAATTTTGATAAACCTC
*
8845 CTATGAAATTTTGATAACCCTC
1 CTATGAAATTTTGATAAACCTC
* * *
8867 TTGTGAAATTTTG--AAA-CTAAA
1 CTATGAAATTTTGATAAACCT--C
8888 CTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
8905 TCTTATCCTC
Statistics
Matches: 177, Mismatches: 37, Indels: 37
0.71 0.15 0.15
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
19 2 0.01
20 2 0.01
21 15 0.08
22 85 0.48
23 57 0.32
24 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
CTATGAAATTTTGATAAACCTC
Found at i:8702 original size:23 final size:23
Alignment explanation
Indices: 8650--8756 Score: 103
Period size: 23 Copynumber: 4.7 Consensus size: 23
8640 AGTAATCACA
* *
8650 CTATGAAATTGTGAT-AA-CCTC
1 CTATGAAATTTTGATAAATCTTC
8671 GCTATGAAATTTTGATAAATCTTC
1 -CTATGAAATTTTGATAAATCTTC
* * *
8695 CTATGAAACTTTGATAAACCTCC
1 CTATGAAATTTTGATAAATCTTC
* *
8718 CTATAAAATTTTGATAACT-TTC
1 CTATGAAATTTTGATAAATCTTC
* *
8740 TTATGAAATCTTGATAA
1 CTATGAAATTTTGATAA
8757 CTACAAATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
22 30 0.43
23 37 0.53
24 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
CTATGAAATTTTGATAAATCTTC
Found at i:8710 original size:45 final size:44
Alignment explanation
Indices: 8650--8904 Score: 158
Period size: 45 Copynumber: 5.9 Consensus size: 44
8640 AGTAATCACA
* *
8650 CTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTC
1 CTATGAAATT-TGATAACCTCACTATGAAATTTTGATAAATCTCC
* * * *
8695 CTATGAAACTTTGATAAACCTCCCTATAAAATTTTGATAACT-TTC
1 CTATGAAA-TTTGAT-AACCTCACTATGAAATTTTGATAAATCTCC
* *
8740 TTATGAAATCTTGATAA-CT-AC----AAATTTTGAT-AACCTCC
1 CTATGAAAT-TTGATAACCTCACTATGAAATTTTGATAAATCTCC
** * *
8778 CTATGATTTTTTTGATAACCTCATTATGAAATTTTG-TTAATCTCC
1 CTATGA--AATTTGATAACCTCACTATGAAATTTTGATAAATCTCC
* * **
8823 CTATGAAATTTTGATCTACAT-ACTATGAAATTTTGATAACCCT-C
1 CTATGAAA-TTTGAT-AACCTCACTATGAAATTTTGATAAATCTCC
* * *
8867 TTGTGAAATTTTGA-AA-CTAAACTATGAAATTTTGATAA
1 CTATGAAA-TTTGATAACCT-CACTATGAAATTTTGATAA
8905 TCTTATCCTC
Statistics
Matches: 167, Mismatches: 25, Indels: 38
0.73 0.11 0.17
Matches are distributed among these distances:
37 1 0.01
38 17 0.10
39 7 0.04
40 3 0.02
41 2 0.01
42 2 0.01
43 20 0.12
44 36 0.22
45 54 0.32
46 25 0.15
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (44 bp):
CTATGAAATTTGATAACCTCACTATGAAATTTTGATAAATCTCC
Found at i:8932 original size:19 final size:20
Alignment explanation
Indices: 8908--8947 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
8898 TTGATAATCT
*
8908 TATCCTCCCTG-AATTTTGA
1 TATCCTCACTGAAATTTTGA
*
8927 TATCCTCATTGAAATTTTGA
1 TATCCTCACTGAAATTTTGA
8947 T
1 T
8948 TACTTCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (20 bp):
TATCCTCACTGAAATTTTGA
Found at i:9082 original size:22 final size:22
Alignment explanation
Indices: 9057--9181 Score: 94
Period size: 22 Copynumber: 5.7 Consensus size: 22
9047 AATCACATTT
9057 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
9079 TGAAAATTTGATGACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * *
9101 T-AAAATTTTGTTGACCCCTTTA
1 TGAAAA-TTTGATAACCTCTTTA
* * * *
9123 TG-AAATTCTTATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * *
9145 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
*
9167 TGAAATTTTGATAAC
1 TGAAAATTTGATAAC
9182 AATGCTATGA
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
21 6 0.07
22 71 0.86
23 6 0.07
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:9192 original size:22 final size:21
Alignment explanation
Indices: 9143--9224 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 21
9133 ATAATCACAT
* *
9143 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACAT-GC
*
9165 TTTGAAATTTTGATAACAATGC
1 TATGAAATTTTGATAAC-ATGC
* * *
9187 TATGAAATTTTGACAATCTTCC
1 TATGAAATTTTGATAA-CATGC
9209 TAT-AAATTTTGATAAC
1 TATGAAATTTTGATAAC
9225 CCGATCTCTA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.02
21 11 0.22
22 36 0.72
23 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGATAACATGC
Found at i:9338 original size:22 final size:23
Alignment explanation
Indices: 9309--9363 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
9299 AAATTGAGAC
* *
9309 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
9330 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
9352 TTTTGATAACCT
1 TTTTGATAACCT
9364 CCCCATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:9374 original size:22 final size:22
Alignment explanation
Indices: 9324--9374 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
9314 TAACCTTCAT
*
9324 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
9346 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
9368 ATGAAAT
1 ATGAAAT
9375 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:9438 original size:22 final size:22
Alignment explanation
Indices: 9380--9438 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
9370 GAAATATTTA
*
9380 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCACACT
* *
9402 ATGAAATTCTT-ATAACCTCGCT
1 ATGAAATT-TTGATAACCACACT
*
9424 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
9439 TCTCTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:9613 original size:22 final size:22
Alignment explanation
Indices: 9511--9613 Score: 84
Period size: 22 Copynumber: 4.6 Consensus size: 22
9501 GACATAAGAG
*
9511 ATTTTAATAACCCGATCTTATGAA
1 ATTTTGATAA-CC-ATCTTATGAA
* * *
9535 ATTTTGGTAACCA-CACTATGTA
1 ATTTTGATAACCATC-TTATGAA
*
9557 ATTTTGATAACC-TCCTCATGAA
1 ATTTTGATAACCAT-CTTATGAA
* * *
9579 ATTGTAATAACCATCTTATTAA
1 ATTTTGATAACCATCTTATGAA
9601 ATTTTGATAACCA
1 ATTTTGATAACCA
9614 CATAGAGACA
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
21 1 0.02
22 48 0.79
23 4 0.07
24 8 0.13
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
ATTTTGATAACCATCTTATGAA
Found at i:9810 original size:19 final size:20
Alignment explanation
Indices: 9779--9816 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
9769 TATTGACATT
9779 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
9798 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
9817 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:10010 original size:38 final size:35
Alignment explanation
Indices: 9955--10030 Score: 107
Period size: 38 Copynumber: 2.1 Consensus size: 35
9945 TTAAGACAAA
9955 AAAGACAAAGCAAAATTAAATACAACGATTGGAAAC
1 AAAGACAAAGCAAAATTAAATACAACG-TTGGAAAC
**
9991 AAAGACAAAAGGCAAAATTAAATAGGACGTTGGAAAC
1 AAAGAC-AAA-GCAAAATTAAATACAACGTTGGAAAC
10028 AAA
1 AAA
10031 AAGTCAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 6 0.17
37 14 0.39
38 16 0.44
ACGTcount: A:0.58, C:0.12, G:0.17, T:0.13
Consensus pattern (35 bp):
AAAGACAAAGCAAAATTAAATACAACGTTGGAAAC
Found at i:11740 original size:120 final size:120
Alignment explanation
Indices: 11527--11770 Score: 488
Period size: 120 Copynumber: 2.0 Consensus size: 120
11517 GTTCAAGCTT
11527 TGTTAGAAACTACATTTTAAATGCTGACATGATTAGATAAATGTGTTAGGACCAGAGTGTTGAAT
1 TGTTAGAAACTACATTTTAAATGCTGACATGATTAGATAAATGTGTTAGGACCAGAGTGTTGAAT
11592 GAATGACTGAGTTAATACCTTGCTGTTTCTTCTGCCCTTGATGATGTTATTACTA
66 GAATGACTGAGTTAATACCTTGCTGTTTCTTCTGCCCTTGATGATGTTATTACTA
11647 TGTTAGAAACTACATTTTAAATGCTGACATGATTAGATAAATGTGTTAGGACCAGAGTGTTGAAT
1 TGTTAGAAACTACATTTTAAATGCTGACATGATTAGATAAATGTGTTAGGACCAGAGTGTTGAAT
11712 GAATGACTGAGTTAATACCTTGCTGTTTCTTCTGCCCTTGATGATGTTATTACTA
66 GAATGACTGAGTTAATACCTTGCTGTTTCTTCTGCCCTTGATGATGTTATTACTA
11767 TGTT
1 TGTT
11771 TTCTGAAATT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 124 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (120 bp):
TGTTAGAAACTACATTTTAAATGCTGACATGATTAGATAAATGTGTTAGGACCAGAGTGTTGAAT
GAATGACTGAGTTAATACCTTGCTGTTTCTTCTGCCCTTGATGATGTTATTACTA
Found at i:17779 original size:31 final size:30
Alignment explanation
Indices: 17744--17854 Score: 87
Period size: 31 Copynumber: 3.9 Consensus size: 30
17734 AGCATGCCAC
17744 GTGTCACTTTTTGGTACACGTGGCGTGACA
1 GTGTCACTTTTTGGTACACGTGGCGTGACA
** *
17774 TGTGTCACTTTTTTATACATGTGGC---AC-
1 -GTGTCACTTTTTGGTACACGTGGCGTGACA
*
17801 --G--ACTTTTTGGTACATGTGGCGTGCCACA
1 GTGTCACTTTTTGGTACACGTGGCGTG--ACA
*
17829 -TGTCACTTTTTGGTACACGTGACGTG
1 GTGTCACTTTTTGGTACACGTGGCGTG
17855 CCACGTCGGA
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
22 17 0.27
24 1 0.02
27 2 0.03
28 2 0.03
29 1 0.02
31 41 0.64
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (30 bp):
GTGTCACTTTTTGGTACACGTGGCGTGACA
Found at i:18846 original size:29 final size:29
Alignment explanation
Indices: 18800--18855 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
18790 ACATGGAATA
* *
18800 AAAATAAAACATTAGGGTGCAAAGTGATC
1 AAAATAAAAAATTAGGGTACAAAGTGATC
18829 AAAATAAAAAA-TATGGGTACAAAGTGA
1 AAAATAAAAAATTA-GGGTACAAAGTGA
18856 CAGTCCGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.20
Consensus pattern (29 bp):
AAAATAAAAAATTAGGGTACAAAGTGATC
Found at i:21804 original size:199 final size:199
Alignment explanation
Indices: 21100--22396 Score: 1754
Period size: 199 Copynumber: 6.5 Consensus size: 199
21090 GCACTATTAA
*
21100 TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCTGCTTATGGAGTCCAAAATTTACA
1 TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACA
* * * *
21165 CTGAAAATGTATTGTATAATAATCCTATAAGAAAAGTTATACTATACACCGTAAGTGGAGTTTAG
66 CTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGGAGTTTAG
* * * *
21230 CAGACTGCACGTGCATGGTTTAAGGGTTG-CATGTGTCCCGTTAGGGAATTTGTATTAATATTAT
131 CAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAA
*
21294 ATTT
196 ATAT
* * * ** * *
21298 TTAATTGATGATGAAAT-GAGGTATGTGTCAACTTTTTAACTTGCTTATAGAGTCTAAAATTTAC
1 TTAATTAATTATGAAATAG-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTAC
* * ** * *
21362 ACTGACAATATGCTGTATAATAATCTTATAAGAAAAATTATA-TAATACACCGTCAGTGGATTTT
65 ACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACT-ATACACCGTCAGTGGAGTTT
21426 AGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATT
129 AGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATT
21491 ATTATATAT
194 A--A-ATAT
* * *
21500 TTAATTAATGATGAAAT-GAGGTATATGTCAACTTCTTAACCCGCTTATGGAGTCTAAAATTTAC
1 TTAATTAATTATGAAATAG-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTAC
* * * * * *
21564 ATTGACATTGTATTATATAATAATCCTATAAGAAAAATTATACTATACACTGTCAATGGATTTTA
65 ACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGGAGTTTA
* *
21629 GCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGAAATATGTATTAATATTA
130 GCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTA
21694 AATAT
195 AATAT
* *
21699 TTAATTAATTATGAAATAGGGTATATGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATCTACA
1 TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACA
* * * * *
21764 TTGATAGTCTATTGTATAATAATTCTATAAGAACAATTATAC---A-ACCGTCAGTGGAGTTTAG
66 CTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGGAGTTTAG
* * * * * *
21825 CGGACTGCATGAGC-GGCTTTAAGGGTTAACATGTGTCCCTTTAGGGAATATGTATTAATATTAA
131 CAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAA
21889 ATAT
196 ATAT
* * *
21893 TTTATTAATTATGAAGTAGGGTATGTGTCAACTTCTTAACCTGCTTATGGAGTCCAAAATTTACA
1 TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACA
* * * *
21958 CTGACAGTGTATCGCATAATAATCCTATAAAAAAAAATTATACTATACACCGTCAGTCGAGTTTA
66 CTGACAGTGTATTGTATAATAATCCTAT-AAGAAAAATTATACTATACACCGTCAGTGGAGTTTA
* *
22023 GCAGACTGCATGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTA
130 GCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTA
22088 AATAT
195 AATAT
* *
22093 TTAATTAATTATGAAAT-GTGGTATATGTCAACTTCTTAACTCGCTTATGGAGTCCAAAATTTAC
1 TTAATTAATTATGAAATAG-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTAC
* * * * *
22157 ACTGACAGTGGATTATATAATAATCTTATAAGAAAAATTATACTATACACCGTCAGTCGAATTTA
65 ACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGGAGTTTA
* * * * *
22222 GCAGACTGCACGTGCAGAGTTTATGGGTTGACATATGTCCCCTTAAGGAATATGCATTAATATTA
130 GCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTA
22287 AATAT
195 AATAT
* * * * **
22292 TTGATTGATTATGAAATAGGGTATGTGTCAACTTCTTAACACGCTTAGGGAGTGTAAAATTTACA
1 TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACA
*
22357 CTGAAAAGTGTATTGTATAATAATCCTAT-A-AAAAATTATA
66 CTG-ACAGTGTATTGTATAATAATCCTATAAGAAAAATTATA
22397 TAAAGTGATT
Statistics
Matches: 978, Mismatches: 104, Indels: 34
0.88 0.09 0.03
Matches are distributed among these distances:
194 132 0.13
195 38 0.04
196 1 0.00
197 2 0.00
198 151 0.15
199 319 0.33
200 156 0.16
202 178 0.18
203 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (199 bp):
TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACA
CTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGGAGTTTAG
CAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAA
ATAT
Found at i:22233 original size:593 final size:594
Alignment explanation
Indices: 21100--22396 Score: 1880
Period size: 593 Copynumber: 2.2 Consensus size: 594
21090 GCACTATTAA
*
21100 TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCTGCTTATGGAGTCCAAAATTTACA
1 TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACA
*
21165 CTGAAAATGTATTGTATAATAATCCTATAAGAAAAGTTATACTATACACCGTAAGTGGAGTTTAG
66 CTGAAAGTGTATTGTATAATAATCCTATAAGAAAA-TTATAC--TACACCGTAAGTGGAGTTTAG
* * * *
21230 CAGACTGCACGTGCATGGTTTAAGGGTTGCATGTGTCCCGTTAGGGAATTTGTATTAATATTATA
128 CAGACTGCACGAGCA-GGTTTAAGGGTTACATGTGTCCCGTTAGGGAATATGTATTAATATTAAA
* * * *
21295 TTTTTAATTGATGATGAAATGAGGTATGTGTCAACTTTTTAACTTGCTTATAGAGTCTAAAATTT
192 TTTTTAATTAATGATGAAATGAGGTATGTGTCAACTTCTTAACCTGCTTATAGAGTCCAAAATTT
* * * * *
21360 ACACTGACAATATGCTGTATAATAATCTTATAAGAAAAATTATATAATACACCGTCAGTGGATTT
257 ACACTGACAATATGCTGCATAATAATCCTATAAAAAAAATTATATAATACACCGTCAGTCGAGTT
21425 TAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATAT
322 TAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATAT
*
21490 TATTATATATTTAATTAATGATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATGGAGTCT
387 TA-TATATATTTAATTAATGATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATGGAGTCC
* * * *
21555 AAAATTTACATTGACATTGTATTATATAATAATCCTATAAGAAAAATTATACTATACACTGTCAA
451 AAAATTTACACTGACAGTGGATTATATAATAATCCTATAAGAAAAATTATACTATACACCGTCAA
* * * * * *
21620 TGGATTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTT-AGGAAATATGT
516 TCGAATTTAGCAGACTGCACGTGCAGAGTTTAAGGGTTGACATATGTCCCCTTAAGG-AATATGC
21684 ATTAATATTAAATAT
580 ATTAATATTAAATAT
* *
21699 TTAATTAATTATGAAATAGGGTATATGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATCTACA
1 TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACA
* * * * * *
21764 TTGATAGTCTATTGTATAATAATTCTATAAGAACAATTATAC-A-ACCGTCAGTGGAGTTTAGCG
66 CTGAAAGTGTATTGTATAATAATCCTATAAGAA-AATTATACTACACCGTAAGTGGAGTTTAGCA
* *
21827 GACTGCATGAGC-GGCTTTAAGGGTTAACATGTGTCCCTTTAGGGAATATGTATTAATATTAAAT
130 GACTGCACGAGCAGG-TTTAAGGGTT-ACATGTGTCCCGTTAGGGAATATGTATTAATATTAAAT
* * *
21891 ATTTT-ATTAATTATGAAGT-AGGGTATGTGTCAACTTCTTAACCTGCTTATGGAGTCCAAAATT
193 -TTTTAATTAATGATGAAATGA-GGTATGTGTCAACTTCTTAACCTGCTTATAGAGTCCAAAATT
*
21954 TACACTGACAGTGTAT-C-GCATAATAATCCTATAAAAAAAAATTATACT-ATACACCGTCAGTC
256 TACACTGACA--ATATGCTGCATAATAATCCTAT-AAAAAAAATTATA-TAATACACCGTCAGTC
* *
22016 GAGTTTAGCAGACTGCATGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATT
317 GAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATT
* * *
22081 AATATTA-A-ATATTTAATTAATTATGAAATGTGGTATATGTCAACTTCTTAACTCGCTTATGGA
382 AATATTATATATATTTAATTAATGATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATGGA
*
22144 GTCCAAAATTTACACTGACAGTGGATTATATAATAATCTTATAAGAAAAATTATACTATACACCG
447 GTCCAAAATTTACACTGACAGTGGATTATATAATAATCCTATAAGAAAAATTATACTATACACCG
* *
22209 TCAGTCGAATTTAGCAGACTGCACGTGCAGAGTTTATGGGTTGACATATGTCCCCTTAAGGAATA
512 TCAATCGAATTTAGCAGACTGCACGTGCAGAGTTTAAGGGTTGACATATGTCCCCTTAAGGAATA
22274 TGCATTAATATTAAATAT
577 TGCATTAATATTAAATAT
* * * * **
22292 TTGATTGATTATGAAATAGGGTATGTGTCAACTTCTTAACACGCTTAGGGAGTGTAAAATTTACA
1 TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACA
22357 CTGAAAAGTGTATTGTATAATAATCCTATAA-AAAATTATA
66 CTG-AAAGTGTATTGTATAATAATCCTATAAGAAAATTATA
22397 TAAAGTGATT
Statistics
Matches: 627, Mismatches: 60, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
592 7 0.01
593 245 0.39
594 39 0.06
595 134 0.21
596 100 0.16
597 4 0.01
599 96 0.15
600 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (594 bp):
TTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACA
CTGAAAGTGTATTGTATAATAATCCTATAAGAAAATTATACTACACCGTAAGTGGAGTTTAGCAG
ACTGCACGAGCAGGTTTAAGGGTTACATGTGTCCCGTTAGGGAATATGTATTAATATTAAATTTT
TAATTAATGATGAAATGAGGTATGTGTCAACTTCTTAACCTGCTTATAGAGTCCAAAATTTACAC
TGACAATATGCTGCATAATAATCCTATAAAAAAAATTATATAATACACCGTCAGTCGAGTTTAGC
AGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTATA
TATATTTAATTAATGATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATGGAGTCCAAAAT
TTACACTGACAGTGGATTATATAATAATCCTATAAGAAAAATTATACTATACACCGTCAATCGAA
TTTAGCAGACTGCACGTGCAGAGTTTAAGGGTTGACATATGTCCCCTTAAGGAATATGCATTAAT
ATTAAATAT
Done.