Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015029.1 Corchorus capsularis cultivar CVL-1 contig15050, 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: 72243
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:161 original size:27 final size:26
Alignment explanation
Indices: 126--178 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
116 AAATAAAATC
126 ACTAAATCACTAATCAAACTATAAGTA
1 ACTAAATCACTAATCAAAC-ATAAGTA
* *
153 ACTACATCACTAATCACACATAAGTA
1 ACTAAATCACTAATCAAACATAAGTA
179 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.49, C:0.23, G:0.04, T:0.25
Consensus pattern (26 bp):
ACTAAATCACTAATCAAACATAAGTA
Found at i:182 original size:2 final size:2
Alignment explanation
Indices: 177--201 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
167 CACACATAAG
177 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
202 GTTAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1013 original size:24 final size:26
Alignment explanation
Indices: 986--1039 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
976 ATTTTAATGT
986 TTAAATT-TTATTTT-TATTAAAAAA
1 TTAAATTATTATTTTATATTAAAAAA
*
1010 TT-AATTATTATTTTATTTTAAAAAA
1 TTAAATTATTATTTTATATTAAAAAA
1035 -TAAAT
1 TTAAAT
1040 ATGGACGGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 4 0.15
24 10 0.38
25 12 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTAAATTATTATTTTATATTAAAAAA
Found at i:4724 original size:13 final size:14
Alignment explanation
Indices: 4706--4735 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4696 AATAATTTTT
4706 AAATTT-ATTAAAA
1 AAATTTAATTAAAA
4719 AAATTTAATTAAAA
1 AAATTTAATTAAAA
4733 AAA
1 AAA
4736 AAAAACTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTTAATTAAAA
Found at i:5975 original size:33 final size:33
Alignment explanation
Indices: 5955--6101 Score: 249
Period size: 33 Copynumber: 4.5 Consensus size: 33
5945 ATGGGATTGT
*
5955 TGGCGGCAGAAATGGTGGAGTTTGAGGAGTTGC
1 TGGCGGCAGCAATGGTGGAGTTTGAGGAGTTGC
*
5988 TGGCGGCAGCAATGGTGGGGTTTGAGGAGTTGC
1 TGGCGGCAGCAATGGTGGAGTTTGAGGAGTTGC
6021 TGGCGGCAGCAATGGTGGAGTTTGAGGAGTTGC
1 TGGCGGCAGCAATGGTGGAGTTTGAGGAGTTGC
* *
6054 TGGCGGCAGCAATGGTGGGGTTTGAGGAGTTGA
1 TGGCGGCAGCAATGGTGGAGTTTGAGGAGTTGC
*
6087 TGGGGGCAGCAATGG
1 TGGCGGCAGCAATGG
6102 GGTTTCCGGC
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 108 1.00
ACGTcount: A:0.18, C:0.11, G:0.48, T:0.23
Consensus pattern (33 bp):
TGGCGGCAGCAATGGTGGAGTTTGAGGAGTTGC
Found at i:10791 original size:22 final size:21
Alignment explanation
Indices: 10757--10803 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
10747 TTTCAAAAAT
10757 CTTT-TTATAAATTTT-TTAAA
1 CTTTCTTATAAATTTTGTT-AA
10777 CTTTCTTATGAAATTTTGTTAA
1 CTTTCTTAT-AAATTTTGTTAA
10799 CTTTC
1 CTTTC
10804 CTAAGGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 14 0.58
23 2 0.08
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (21 bp):
CTTTCTTATAAATTTTGTTAA
Found at i:10813 original size:22 final size:23
Alignment explanation
Indices: 10765--10816 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
10755 ATCTTTTTAT
* *
10765 AAATTTT-TTAAACTTTCTTATG
1 AAATTTTGTTAAACTTTCCTAAG
10787 AAATTTTGTT-AACTTTCCTAAG
1 AAATTTTGTTAAACTTTCCTAAG
*
10809 GAATTTTG
1 AAATTTTG
10817 AAGACCTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (23 bp):
AAATTTTGTTAAACTTTCCTAAG
Found at i:10906 original size:22 final size:22
Alignment explanation
Indices: 10783--11088 Score: 130
Period size: 22 Copynumber: 13.8 Consensus size: 22
10773 TAAACTTTCT
* *
10783 TATGAAATTTTGTTAACTTTCC-
1 TATGAAATTTTGATAAC-CTCCA
* * *
10805 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCCA
*
10827 TATGAAATTTTGATAACTTCCCA
1 TATGAAATTTTGATAACCT-CCA
**
10850 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
10871 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * **
10894 TATGATATATTGATAACCACTT
1 TATGAAATTTTGATAACCTCCA
* *
10916 TATAAAATTTT-TTAAACCTCCA
1 TATGAAATTTTGAT-AACCTCCA
*
10938 TATG-AATTGTTGGTAA--TCACA
1 TATGAAATT-TTGATAACCTC-CA
* *
10959 CTTTAAAATTTTGATAA--TCACA
1 -TATGAAATTTTGATAACCTC-CA
*
10981 CTATGAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCTC-CA
*
11004 TATGAAATTTTGATAAATCTTCC-
1 TATGAAATTTTGAT-AA-CCTCCA
* * *
11027 TATAAAATTTTAATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * * * *
11050 TATAAAATTTCGATAACTTTCT
1 TATGAAATTTTGATAACCTCCA
*
11072 TATGAAATCTTGATAAC
1 TATGAAATTTTGATAAC
11089 TACAAATTTT
Statistics
Matches: 217, Mismatches: 50, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
20 2 0.01
21 12 0.06
22 142 0.65
23 55 0.25
24 6 0.03
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:10907 original size:45 final size:45
Alignment explanation
Indices: 10827--10912 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
10817 AAGACCTCAA
* * *
10827 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
* *
10872 TATGAGATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCCA-ATGAAATATTGATAACCA
10913 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
Found at i:11294 original size:20 final size:20
Alignment explanation
Indices: 11229--11298 Score: 90
Period size: 19 Copynumber: 3.6 Consensus size: 20
11219 AACCTTTATA
* *
11229 TGAAGTTTTGATATCCTCAC
1 TGAAATTTTGATATCCTCCC
11249 TG-AATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* *
11268 T-AAATTTTGGTATCATCCC
1 TGAAATTTTGATATCCTCCC
11287 TGAAATTTTGAT
1 TGAAATTTTGAT
11299 TACTCCATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
19 32 0.74
20 11 0.26
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:11564 original size:21 final size:23
Alignment explanation
Indices: 11514--11591 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 23
11504 AACCTCGCAT
11514 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAATCAACACTA
**
11536 TGAAATTTTGATAATCTTCA-TA
1 TGAAATTTTGATAATCAACACTA
*
11558 T-AAATTTTGATAATC-ACTCTA
1 TGAAATTTTGATAATCAACACTA
*
11579 TGAGA-TTTGATAA
1 TGAAATTTTGATAA
11592 CCTTCTATCA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.02
21 25 0.52
22 19 0.40
23 3 0.06
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (23 bp):
TGAAATTTTGATAATCAACACTA
Found at i:11606 original size:20 final size:19
Alignment explanation
Indices: 11542--11606 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 19
11532 ACTATGAAAT
*
11542 TTTGATAATCTTCATATAAA
1 TTTGATAACCTTC-TATAAA
*
11562 TTTTGATAATCAC-TCTATGAGA
1 -TTTGATAA-C-CTTCTAT-AAA
11584 TTTGATAACCTTCTATCAAA
1 TTTGATAACCTTCTAT-AAA
11604 TTT
1 TTT
11607 TGGTACTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 19 0.53
22 4 0.11
23 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (19 bp):
TTTGATAACCTTCTATAAA
Found at i:11608 original size:21 final size:21
Alignment explanation
Indices: 11404--11683 Score: 110
Period size: 22 Copynumber: 12.7 Consensus size: 21
11394 AATCAGATTT
*
11404 TGAAAATTTGATAAC-CTCTTTA
1 TGAAATTTTGATAACACTC--TA
*
11426 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACA-CTCTA
* * * *
11448 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGAT-AACACTCTA
* * *
11470 TGAAACTTTGAAAATCA-TATTA
1 TGAAATTTTGATAA-CACT-CTA
* *
11492 TGTAATTTTGATAAC-CTCGCA
1 TGAAATTTTGATAACACTC-TA
*
11513 TTGAAATTTTGATAACAACACTA
1 -TGAAATTTTGATAAC-ACTCTA
*
11536 TGAAATTTTGATAATC-TTCATA
1 TGAAATTTTGATAA-CACTC-TA
11558 T-AAATTTTGATAATCACTCTA
1 TGAAATTTTGATAA-CACTCTA
*
11579 TGAGA-TTTGATAAC-CTTCTA
1 TGAAATTTTGATAACAC-TCTA
* * *
11599 TCAAATTTTGGT-ACTC-CTTA
1 TGAAATTTTGATAACACTC-TA
* *
11619 TGAAATTGAGACTTTTATAACATTCATA
1 TGAAA-T-----TTTGATAACACTC-TA
*
11647 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAA-CACTCTA
*
11669 TAAAATTTTGATAAC
1 TGAAATTTTGATAAC
11684 CTCCCGATGA
Statistics
Matches: 192, Mismatches: 39, Indels: 55
0.67 0.14 0.19
Matches are distributed among these distances:
19 2 0.01
20 16 0.08
21 39 0.20
22 109 0.57
23 7 0.04
24 4 0.02
26 4 0.02
27 3 0.02
28 8 0.04
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
TGAAATTTTGATAACACTCTA
Found at i:11866 original size:24 final size:22
Alignment explanation
Indices: 11815--11869 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
11805 TAACTACCCC
11815 ATGAAATTTCAATAACCAACCT
1 ATGAAATTTCAATAACCAACCT
* *
11837 AAGAAATTTCAATAACCTGATCCT
1 ATGAAATTTCAATAACC--AACCT
11861 ATGAAATTT
1 ATGAAATTT
11870 TGGTAACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 16 0.57
24 12 0.43
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (22 bp):
ATGAAATTTCAATAACCAACCT
Found at i:11890 original size:22 final size:22
Alignment explanation
Indices: 11859--11942 Score: 132
Period size: 22 Copynumber: 3.8 Consensus size: 22
11849 TAACCTGATC
*
11859 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
*
11881 CTGTGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
11903 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
11925 CTATGGAATTTTGATAAC
1 CTATGAAATTTTGGTAAC
11943 ATCCTCATGG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:11987 original size:22 final size:22
Alignment explanation
Indices: 11859--11990 Score: 126
Period size: 22 Copynumber: 6.0 Consensus size: 22
11849 TAACCTGATC
* *
11859 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGATAACCACA
* *
11881 CTGTGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
11903 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
11925 CTATGGAATTTTGATAA-CATC-
1 CTATGAAATTTTGATAACCA-CA
* * *
11946 CTCATGGAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
11969 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
11991 TAGAGACAAG
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.05
22 85 0.89
23 5 0.05
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:16222 original size:12 final size:12
Alignment explanation
Indices: 16205--16229 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16195 AAAACAGCAC
16205 CTTTATTGGTTA
1 CTTTATTGGTTA
16217 CTTTATTGGTTA
1 CTTTATTGGTTA
16229 C
1 C
16230 ATGTAACCAA
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:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (12 bp):
CTTTATTGGTTA
Found at i:16393 original size:78 final size:78
Alignment explanation
Indices: 16264--16421 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
16254 AGGTTTAGGG
16264 TTTAGGTAGGTTACTGGGCCTCAAGTTTTTGCCTAGAAATGGTAAGCATCAAGGACTAGTTATAG
1 TTTAGGTAGGTTACTGGGCCTCAAGTTTTTGCCTAGAAATGGTAAGCATCAAGGACTAGTTATAG
16329 AAAGAATCCAAAT
66 AAAGAATCCAAAT
16342 TTTAGGTAGGTTACTGGGCCTCAAGTTTTTGCCTAGAAATGGTAAGCATCAAGGACTAGTTATAG
1 TTTAGGTAGGTTACTGGGCCTCAAGTTTTTGCCTAGAAATGGTAAGCATCAAGGACTAGTTATAG
16407 AAAGAATCCAAAT
66 AAAGAATCCAAAT
16420 TT
1 TT
16422 CCCATTTCTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (78 bp):
TTTAGGTAGGTTACTGGGCCTCAAGTTTTTGCCTAGAAATGGTAAGCATCAAGGACTAGTTATAG
AAAGAATCCAAAT
Found at i:17118 original size:12 final size:12
Alignment explanation
Indices: 17101--17125 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17091 TGTCAGCCAA
17101 TATATAATGAAG
1 TATATAATGAAG
17113 TATATAATGAAG
1 TATATAATGAAG
17125 T
1 T
17126 TTTCGGACCT
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:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TATATAATGAAG
Found at i:19018 original size:30 final size:30
Alignment explanation
Indices: 18982--19038 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
18972 TTGCGTCGAA
18982 ATTAAAACCAACGGTAGAATTATGGAGAGC
1 ATTAAAACCAACGGTAGAATTATGGAGAGC
*
19012 ATTAAAACCAACGGTAGTATTATGGAG
1 ATTAAAACCAACGGTAGAATTATGGAG
19039 TGTAGTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (30 bp):
ATTAAAACCAACGGTAGAATTATGGAGAGC
Found at i:20218 original size:38 final size:38
Alignment explanation
Indices: 20169--20249 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
20159 AAAAGAACTT
*
20169 GCATCATTTGAAAATAGATAGAACAAAATCAAGACAAG
1 GCATAATTTGAAAATAGATAGAACAAAATCAAGACAAG
20207 GCATAATTTGAAAATAGATAGAACAAAATCAAGACAAG
1 GCATAATTTGAAAATAGATAGAACAAAATCAAGACAAG
20245 GCATA
1 GCATA
20250 GCTGCCATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (38 bp):
GCATAATTTGAAAATAGATAGAACAAAATCAAGACAAG
Found at i:20580 original size:50 final size:50
Alignment explanation
Indices: 20521--20621 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
20511 TAAATGGATG
* *
20521 CACCATTATACCTTAATGTATAATAGGAATGCCATCTTTTTTGCTGCAAA
1 CACCATTATACCTTAATGTATAATAGGAATGCCATCTCTTTCGCTGCAAA
20571 CACCATTATACCTTAATGTATAATAGGAATGCCATCTCTTTCGCTGCAAA
1 CACCATTATACCTTAATGTATAATAGGAATGCCATCTCTTTCGCTGCAAA
20621 C
1 C
20622 CGAAATTCCC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.34
Consensus pattern (50 bp):
CACCATTATACCTTAATGTATAATAGGAATGCCATCTCTTTCGCTGCAAA
Found at i:22128 original size:375 final size:379
Alignment explanation
Indices: 21372--22897 Score: 2129
Period size: 387 Copynumber: 4.0 Consensus size: 379
21362 AGTACAAACA
* * *
21372 GAATACCACCACCACAAAGAATTCTTATCTTACCAACCTTAACTCGATGCACCATTATACCTTCA
1 GAATGCCACCAACACAAAGAATTCTTATCTTACCAACCTTAACTCGATGCACCATTATACCTTGA
* * * *
21437 TGTATAATAGAAATACAACAGTTGTGCATTTTAGTATTAAAAAAATGCCATGTAACAAAAGAACT
66 TGTATAATAGGAATGCAACAGTTGTGCCTTTTAGCATTAAAAAAATGCCATGTAACAAAAGAACT
21502 TGCATCGTTTGAAAATAGATAGAACAAAATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGC
131 TGCATCGTTTGAAAATAGATAGAACAAAATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGC
* * * * *
21567 AGTGAATACTAAACAGTCAAATAACAACTTTAAGTGTAAAACTTAAATTGCTCATGGTGCTGTAT
196 AGTGAATACTAAACAGTCAAAAAACAACTTTGAGTATAAAACTTAAATTGCTCATGGTGGTGAAT
* * *
21632 CAAAAGAAATGGAGTGGGCGAGGGAGCATGAGCCTTCAAGATTGTTCATATTTCATTGCACAGTA
261 CAGAAGAAATGGAGTGGGCGAAGGAGCATGAGCCTTCAAGATTGTTCATATTTCATTGCACAATA
* * ** *
21697 AGATTTCCAGGTATATTACATTAACTGGCACCACTATACCTTTATGTATTGTAG
326 AGAGTTCCAGGAATATTACACGAACTGGCACCACTATACCTTTATGTATAGTAG
21751 GAATGCCACCAACACAAAGAATTCTTATCTTACCAACCTTAACTCGATGCACCATTATACCTTGA
1 GAATGCCACCAACACAAAGAATTCTTATCTTACCAACCTTAACTCGATGCACCATTATACCTTGA
* *
21816 TGTATAATAGGAATGCAACAGTTGTGCCTTTTAGCATTAAAAAGATGCCATGTAACAAAACAACT
66 TGTATAATAGGAATGCAACAGTTGTGCCTTTTAGCATTAAAAAAATGCCATGTAACAAAAGAACT
**
21881 TGCATCGTTTG-AAATAGATAGAACAAAATCAAAACAAGGC-GCGCTGCCATTTCATGGGTGTGC
131 TGCATCGTTTGAAAATAGATAGAACAAAATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGC
**
21944 AGTGAATACTAAACAGTC-AAAAACAACTTT-AGTATAAAACTTAAATTGCTCATGGTGGTTTAT
196 AGTGAATACTAAACAGTCAAAAAACAACTTTGAGTATAAAACTTAAATTGCTCATGGTGGTGAAT
* * * *
22007 CAGAAGAAATGGAGTGGACGAAGGAGCATGAGCTTTCAAGATTGTTCATTTTTCATTCCACAATA
261 CAGAAGAAATGGAGTGGGCGAAGGAGCATGAGCCTTCAAGATTGTTCATATTTCATTGCACAATA
22072 AGAGTTCCAGGAATATTACACGAACTGGCACCACTATACCTTTATGTATAGTAG
326 AGAGTTCCAGGAATATTACACGAACTGGCACCACTATACCTTTATGTATAGTAG
* * *
22126 GAATGCCACC-ACATCAAAGAA----TA-CTTACCAACCTTTATTCGATG-A--ATTATACTTTG
1 GAATGCCACCAACA-CAAAGAATTCTTATCTTACCAACCTTAACTCGATGCACCATTATACCTTG
* * *
22182 ATGTATAACAGGAATGCCACTGTTGTGCCTTTTAGCATTAAAAAAAAATGCCATGTAACAAAAGA
65 ATGTATAATAGGAATGCAACAGTTGTGCCTTTTAGCATT--AAAAAAATGCCATGTAACAAAAGA
*
22247 ACTTGCATCGTTTGAAAATAGATAGAACAAAATCAAAACAAGGCATAGCTGCCATTTCATGTGTG
128 ACTTGCATCGTTTGAAAATAGATAGAACAAAATCAAAACAAGGCATAGCTGCCATTTCATGGGTG
* * *
22312 TGCATTGAATACTAAATAGTCAAAAAACAACTTTGAGTATAAATCTTAAATTGCTCATGGTGGTG
193 TGCAGTGAATACTAAACAGTCAAAAAACAACTTTGAGTATAAAACTTAAATTGCTCATGGTGGTG
*
22377 AATCAGAA-AGCAT-GAGTGGGCG-AGAGAGCATGAGCCTTCAAGATTGTTCATATTTCATTGCA
258 AATCAGAAGA-AATGGAGTGGGCGAAG-GAGCATGAGCCTTCAAGATTGTTCATATTTCATTGCA
* * * *
22439 CTATAACAGTTCCA-GATATATTACACGAACTTGCACCACTATACCTTTATGTATACTAG
321 CAATAAGAGTTCCAGGA-ATATTACACGAACTGGCACCACTATACCTTTATGTATAGTAG
* ** * * * * * * *
22498 GAATGTCATCTCTTTTGCTGCAAATAGAAATTCCTGTC--ACCAACTTTTATTCAGAGGCACCAT
1 GAATGCCA-C-C---AAC-AC-AA-AG-AATTCTTATCTTACCAACCTTAACTC-GATGCACCAT
** * **
22561 TATACCTTGATGTATAATAGGAGCGCCACTTTTGTGCCTTTTAGCATTTAAAAAAATGCCATGTA
56 TATACCTTGATGTATAATAGGAATGCAACAGTTGTGCCTTTTAGCA-TTAAAAAAATGCCATGTA
* * *
22626 ACAAAAGAACTTGCATCTTTTAAAAATAGATAGAACAAAATCAAAACAAGGCATAGCTGCAATTT
120 ACAAAAGAACTTGCATCGTTTGAAAATAGATAGAACAAAATCAAAACAAGGCATAGCTGCCATTT
*
22691 CATTGGTGTGCAGTGAATACTAAACAGTCAAAAAACAACTTTGAGTATAAAACTTAAATTGCTCA
185 CATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAACTTTGAGTATAAAACTTAAATTGCTCA
*
22756 TGGTGGTGAATCAGAAAAAATGGAGTGGGC-AAGGGAGCATGAGCCTTCAAGATTGTTCATATTT
250 TGGTGGTGAATCAGAAGAAATGGAGTGGGCGAA-GGAGCATGAGCCTTCAAGATTGTTCATATTT
* * *
22820 CATTGCACTATAAGAGTTCCAGGTATCTTACACGAAACTGGCACCACTATACCTTTATGTATAGT
314 CATTGCACAATAAGAGTTCCAGGAATATTACACG-AACTGGCACCACTATACCTTTATGTATAGT
22885 AG
378 AG
22887 GAATGCCACCA
1 GAATGCCACCA
22898 GATTGTGCCT
Statistics
Matches: 1032, Mismatches: 79, Indels: 67
0.88 0.07 0.06
Matches are distributed among these distances:
367 46 0.04
369 37 0.04
370 48 0.05
371 42 0.04
372 114 0.11
373 38 0.04
374 4 0.00
375 154 0.15
376 11 0.01
377 39 0.04
378 31 0.03
379 134 0.13
380 2 0.00
381 2 0.00
384 13 0.01
385 4 0.00
386 2 0.00
387 157 0.15
388 113 0.11
389 41 0.04
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (379 bp):
GAATGCCACCAACACAAAGAATTCTTATCTTACCAACCTTAACTCGATGCACCATTATACCTTGA
TGTATAATAGGAATGCAACAGTTGTGCCTTTTAGCATTAAAAAAATGCCATGTAACAAAAGAACT
TGCATCGTTTGAAAATAGATAGAACAAAATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGC
AGTGAATACTAAACAGTCAAAAAACAACTTTGAGTATAAAACTTAAATTGCTCATGGTGGTGAAT
CAGAAGAAATGGAGTGGGCGAAGGAGCATGAGCCTTCAAGATTGTTCATATTTCATTGCACAATA
AGAGTTCCAGGAATATTACACGAACTGGCACCACTATACCTTTATGTATAGTAG
Found at i:22324 original size:748 final size:759
Alignment explanation
Indices: 21400--22897 Score: 2197
Period size: 748 Copynumber: 2.0 Consensus size: 759
21390 GAATTCTTAT
*
21400 CTTACCAACCTTAACTCGATGCACCATTATACCTTCATGTATAATAGAAATACAACAGTTGTGCA
1 CTTACCAACCTTAACTCGATGCA-CATTATACCTTCATGTATAACAGAAATACAACAGTTGTGCA
*
21465 TTTTAGTATTAAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATAGAACAAA
65 TTTTAGCATTAAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATAGAACAAA
*
21530 ATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAATAACAAC
130 ATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAAC
* * *
21595 TTTAAGTGTAAAACTTAAATTGCTCATGGTGCTGTATCA-AAAGAAATGGAGTGGGCGAGGGAGC
195 TTTAAGTATAAAACTTAAATTGCTCATGGTGCTGAATCAGAAAG-AAT-GAGTGGGCGAGAGAGC
* * * **
21659 ATGAGCCTTCAAGATTGTTCATATTTCATTGCAC-AGTAAGATTTCCAGGTATATTACATTAACT
258 ATGAGCCTTCAAGATTGTTCATATTTCATTGCACTA-TAACAGTTCCAGATATATTACACGAACT
** *
21723 GGCACCACTATACCTTTATGTATTGTAGGAATGCCA-C-C-AAC-AC-AA-AG-AATTCTTATCT
322 GGCACCACTATACCTTTATGTATACTAGGAATGCCATCTCTAACTACAAATAGAAATTCCTATC-
* *
21781 TACCAACCTTAACTC-GATGCACCATTATACCTTGATGTATAATAGGAATGCAACAGTTGTGCCT
386 -ACCAACCTTAACTCAGAGGCACCATTATACCTTGATGTATAATAGGAACGCAACAGTTGTGCCT
* *
21845 TTTAGCA-TTAAAAAGATGCCATGTAACAAAACAACTTGCATCGTTT-GAAATAGATAGAACAAA
450 TTTAGCATTTAAAAAAATGCCATGTAACAAAACAACTTGCATCGTTTAAAAATAGATAGAACAAA
* *
21908 ATCAAAACAAGGC-GCGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTC-AAAAACAAC
515 ATCAAAACAAGGCAGAGCTGCAATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAAC
** *
21971 TTT-AGTATAAAACTTAAATTGCTCATGGTGGTTTATCAGAAGAAATGGAGTGGACGAA-GGAGC
580 TTTGAGTATAAAACTTAAATTGCTCATGGTGGTGAATCAGAAAAAATGGAGTGGAC-AAGGGAGC
* *
22034 ATGAGCTTTCAAGATTGTTCATTTTTCATTCCACAATAAGAGTTCCAGGAATATTACACG-AACT
644 ATGAGCCTTCAAGATTGTTCATATTTCATTCCACAATAAGAGTTCCAGGAATATTACACGAAACT
22098 GGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACATCAAAGAATA
709 GGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACATCAAAGAATA
* * * * * * * * *
22149 CTTACCAACCTTTATTCGATG-A-ATTATACTTTGATGTATAACAGGAATGCCACTGTTGTGCCT
1 CTTACCAACCTTAACTCGATGCACATTATACCTTCATGTATAACAGAAATACAACAGTTGTGCAT
22212 TTTAGCATTAAAAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATAGAACAA
66 TTTAGCATT--AAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATAGAACAA
* * *
22277 AATCAAAACAAGGCATAGCTGCCATTTCATGTGTGTGCATTGAATACTAAATAGTCAAAAAACAA
129 AATCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAA
* * * *
22342 CTTTGAGTATAAATCTTAAATTGCTCATGGTGGTGAATCAGAAAGCATGAGTGGGCGAGAGAGCA
194 CTTTAAGTATAAAACTTAAATTGCTCATGGTGCTGAATCAGAAAGAATGAGTGGGCGAGAGAGCA
*
22407 TGAGCCTTCAAGATTGTTCATATTTCATTGCACTATAACAGTTCCAGATATATTACACGAACTTG
259 TGAGCCTTCAAGATTGTTCATATTTCATTGCACTATAACAGTTCCAGATATATTACACGAACTGG
* ** * *
22472 CACCACTATACCTTTATGTATACTAGGAATGTCATCTCTTTTGCTGCAAATAGAAATTCCTGTCA
324 CACCACTATACCTTTATGTATACTAGGAATGCCATCTC--TAACTACAAATAGAAATTCCTATCA
* * * * * **
22537 CCAACTTTTATTCAGAGGCACCATTATACCTTGATGTATAATAGGAGCGCCACTTTTGTGCCTTT
387 CCAACCTTAACTCAGAGGCACCATTATACCTTGATGTATAATAGGAACGCAACAGTTGTGCCTTT
* *
22602 TAGCATTTAAAAAAATGCCATGTAACAAAAGAACTTGCATCTTTTAAAAATAGATAGAACAAAAT
452 TAGCATTTAAAAAAATGCCATGTAACAAAACAACTTGCATCGTTTAAAAATAGATAGAACAAAAT
* *
22667 CAAAACAAGGCATAGCTGCAATTTCATTGGTGTGCAGTGAATACTAAACAGTCAAAAAACAACTT
517 CAAAACAAGGCAGAGCTGCAATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAACTT
*
22732 TGAGTATAAAACTTAAATTGCTCATGGTGGTGAATCAGAAAAAATGGAGTGGGCAAGGGAGCATG
582 TGAGTATAAAACTTAAATTGCTCATGGTGGTGAATCAGAAAAAATGGAGTGGACAAGGGAGCATG
* * * *
22797 AGCCTTCAAGATTGTTCATATTTCATTGCACTATAAGAGTTCCAGGTATCTTACACGAAACTGGC
647 AGCCTTCAAGATTGTTCATATTTCATTCCACAATAAGAGTTCCAGGAATATTACACGAAACTGGC
22862 ACCACTATACCTTTATGTATAGTAGGAATGCCACCA
712 ACCACTATACCTTTATGTATAGTAGGAATGCCACCA
22898 GATTGTGCCT
Statistics
Matches: 665, Mismatches: 63, Indels: 30
0.88 0.08 0.04
Matches are distributed among these distances:
746 41 0.06
747 104 0.16
748 155 0.23
749 24 0.04
752 1 0.00
753 1 0.00
754 13 0.02
755 52 0.08
756 44 0.07
757 29 0.04
758 37 0.06
759 14 0.02
760 107 0.16
761 43 0.06
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (759 bp):
CTTACCAACCTTAACTCGATGCACATTATACCTTCATGTATAACAGAAATACAACAGTTGTGCAT
TTTAGCATTAAAAAAATGCCATGTAACAAAAGAACTTGCATCGTTTGAAAATAGATAGAACAAAA
TCAAAACAAGGCATAGCTGCCATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAACT
TTAAGTATAAAACTTAAATTGCTCATGGTGCTGAATCAGAAAGAATGAGTGGGCGAGAGAGCATG
AGCCTTCAAGATTGTTCATATTTCATTGCACTATAACAGTTCCAGATATATTACACGAACTGGCA
CCACTATACCTTTATGTATACTAGGAATGCCATCTCTAACTACAAATAGAAATTCCTATCACCAA
CCTTAACTCAGAGGCACCATTATACCTTGATGTATAATAGGAACGCAACAGTTGTGCCTTTTAGC
ATTTAAAAAAATGCCATGTAACAAAACAACTTGCATCGTTTAAAAATAGATAGAACAAAATCAAA
ACAAGGCAGAGCTGCAATTTCATGGGTGTGCAGTGAATACTAAACAGTCAAAAAACAACTTTGAG
TATAAAACTTAAATTGCTCATGGTGGTGAATCAGAAAAAATGGAGTGGACAAGGGAGCATGAGCC
TTCAAGATTGTTCATATTTCATTCCACAATAAGAGTTCCAGGAATATTACACGAAACTGGCACCA
CTATACCTTTATGTATAGTAGGAATGCCACCACATCAAAGAATA
Found at i:25057 original size:36 final size:35
Alignment explanation
Indices: 25009--25149 Score: 169
Period size: 36 Copynumber: 4.0 Consensus size: 35
24999 TGTGATTATT
* *
25009 AAACTACGTAACAATACC-TTAACCGTTTGTAGAGTC
1 AAACTACATAACAATACCGTAAACC--TTGTAGAGTC
* * *
25045 AAACTACATAACAACACCGTAAACCTTGTATA-TT
1 AAACTACATAACAATACCGTAAACCTTGTAGAGTC
* * *
25079 AAACTACGTAACAATACCTTAACCGCTTGTAGAGTC
1 AAACTACATAACAATACCGTAAAC-CTTGTAGAGTC
25115 AAACTACATAACAATACCGTAAACCTTGTAGAGTC
1 AAACTACATAACAATACCGTAAACCTTGTAGAGTC
25150 CAAATTTTAC
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
34 21 0.24
35 24 0.27
36 38 0.43
37 5 0.06
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (35 bp):
AAACTACATAACAATACCGTAAACCTTGTAGAGTC
Found at i:25087 original size:70 final size:71
Alignment explanation
Indices: 24996--25144 Score: 264
Period size: 70 Copynumber: 2.1 Consensus size: 71
24986 AAGAAAAGAC
*
24996 CCTTGTGATTATTAAACTACGTAACAATACCTTAACCGTTTGTAGAGTCAAACTACATAACAACA
1 CCTTGT-ATTATTAAACTACGTAACAATACCTTAACCGCTTGTAGAGTCAAACTACATAACAACA
25061 CCGTAAA
65 CCGTAAA
*
25068 CCTTGTA-TATTAAACTACGTAACAATACCTTAACCGCTTGTAGAGTCAAACTACATAACAATAC
1 CCTTGTATTATTAAACTACGTAACAATACCTTAACCGCTTGTAGAGTCAAACTACATAACAACAC
25132 CGTAAA
66 CGTAAA
25138 CCTTGTA
1 CCTTGTA
25145 GAGTCCAAAT
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
70 68 0.91
71 1 0.01
72 6 0.08
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (71 bp):
CCTTGTATTATTAAACTACGTAACAATACCTTAACCGCTTGTAGAGTCAAACTACATAACAACAC
CGTAAA
Found at i:27706 original size:6 final size:6
Alignment explanation
Indices: 27695--27719 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27685 TTTCTTTGCA
27695 TTGTTC TTGTTC TTGTTC TTGTTC T
1 TTGTTC TTGTTC TTGTTC TTGTTC T
27720 GCTTAGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TTGTTC
Found at i:39850 original size:49 final size:49
Alignment explanation
Indices: 39778--39878 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
39768 AAGCAACAAT
39778 AAATCCTTAATACAATCAGGGGGACTGAACAAAATAGAAAAGGAGTCGG
1 AAATCCTTAATACAATCAGGGGGACTGAACAAAATAGAAAAGGAGTCGG
39827 AAATCCTTAATACAATCAGGGGGACTGAACAAAATAGAAAAGGAGTCGG
1 AAATCCTTAATACAATCAGGGGGACTGAACAAAATAGAAAAGGAGTCGG
39876 AAA
1 AAA
39879 GTGAACTACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.47, C:0.14, G:0.24, T:0.16
Consensus pattern (49 bp):
AAATCCTTAATACAATCAGGGGGACTGAACAAAATAGAAAAGGAGTCGG
Found at i:45166 original size:11 final size:11
Alignment explanation
Indices: 45150--45180 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
45140 TCTGTTTTTT
45150 GTTTTTGTTTC
1 GTTTTTGTTTC
*
45161 GTTTTTGTTTT
1 GTTTTTGTTTC
45172 GTTTTTGTT
1 GTTTTTGTT
45181 GCGCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:45989 original size:18 final size:21
Alignment explanation
Indices: 45978--46093 Score: 61
Period size: 21 Copynumber: 5.6 Consensus size: 21
45968 ATATATATTT
45978 ATTATAATATATATAATTATA
1 ATTATAATATATATAATTATA
*
45999 ATTATAAT-T-TATAA-AATA
1 ATTATAATATATATAATTATA
* *
46017 AATAT-ATATAAAGTAAATATATA
1 ATTATAATATATA-T-AAT-TATA
*
46040 ATTACT-TTATATAT-ATTAT-
1 ATTA-TAATATATATAATTATA
*
46059 ATATATAA-AGTAAATACA-TATA
1 AT-TATAATA-TATATA-ATTATA
46081 ATTATAATATATA
1 ATTATAATATATA
46094 ATTTATATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 28
0.65 0.09 0.26
Matches are distributed among these distances:
17 2 0.03
18 8 0.11
19 10 0.14
20 11 0.15
21 23 0.32
22 4 0.06
23 7 0.10
24 6 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTATAATATATATAATTATA
Found at i:45998 original size:15 final size:15
Alignment explanation
Indices: 45967--46093 Score: 74
Period size: 15 Copynumber: 8.5 Consensus size: 15
45957 TATAAAAGTA
*
45967 AATATATATTTATTAT
1 AATATATA-TAATTAT
45983 AATATATATAATTAT
1 AATATATATAATTAT
*
45998 AATTATAATTTATAA-AAT
1 AA-TAT-A--TATAATTAT
46016 AAATATATATAA--AGT
1 -AATATATATAATTA-T
46031 AA-ATATATAATTACT
1 AATATATATAATTA-T
*
46046 -TTATATAT-ATTAT
1 AATATATATAATTAT
*
46059 -ATATATA-AAGTA-
1 AATATATATAATTAT
*
46071 AATACATATAATTAT
1 AATATATATAATTAT
46086 AATATATA
1 AATATATA
46094 ATTTATATTT
Statistics
Matches: 89, Mismatches: 9, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
13 24 0.27
14 11 0.12
15 29 0.33
16 11 0.12
17 2 0.02
18 5 0.06
19 7 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
AATATATATAATTAT
Found at i:46100 original size:41 final size:39
Alignment explanation
Indices: 45935--46101 Score: 123
Period size: 39 Copynumber: 4.2 Consensus size: 39
45925 CGGGTTATTT
* * *
45935 ATTTATATATATAAAATAAAGTTATAAAAGTA-AATATAT-
1 ATTTATATATATAAAGTAAA--TATATAATTATAATATATA
* *
45974 ATTTAT-TATAATATA-TATAAT-TATAATTATAATTTATAAA
1 ATTTATATAT-ATAAAGTA-AATATATAATTATAA--TATATA
** *
46014 ATAAATATATATAAAGTAAATATATAATTACT-TTATAT-
1 ATTTATATATATAAAGTAAATATATAATTA-TAATATATA
46052 ATATTATATATATAAAGTAAATACATATAATTATAATATATA
1 AT-TTATATATATAAAGTAAAT--ATATAATTATAATATATA
46094 ATTTATAT
1 ATTTATAT
46102 TTATTATTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 28
0.72 0.09 0.20
Matches are distributed among these distances:
36 6 0.06
37 3 0.03
38 7 0.07
39 37 0.37
40 12 0.12
41 33 0.33
42 3 0.03
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (39 bp):
ATTTATATATATAAAGTAAATATATAATTATAATATATA
Found at i:46101 original size:11 final size:13
Alignment explanation
Indices: 45986--46096 Score: 69
Period size: 13 Copynumber: 8.8 Consensus size: 13
45976 TTATTATAAT
45986 ATATATAATTATA
1 ATATATAATTATA
45999 AT-TATAATTTATA
1 ATATATAA-TTATA
*
46012 A-A-ATAAATAT-
1 ATATATAATTATA
*
46022 ATATA-AAGTA-A
1 ATATATAATTATA
46033 ATATATAATTACT-
1 ATATATAATTA-TA
*
46046 TTATATATATTAT-
1 ATATATA-ATTATA
*
46059 ATATATAAAGTA-A
1 ATATAT-AATTATA
46072 ATACATATAATTATA
1 AT--ATATAATTATA
46087 ATATATAATT
1 ATATATAATT
46097 TATATTTATT
Statistics
Matches: 77, Mismatches: 7, Indels: 28
0.69 0.06 0.25
Matches are distributed among these distances:
10 1 0.01
11 13 0.17
12 14 0.18
13 33 0.43
14 9 0.12
15 7 0.09
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATATAATTATA
Found at i:49895 original size:41 final size:41
Alignment explanation
Indices: 49838--49915 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
49828 GCTATATGTT
*
49838 TTTTTGAAGGATATTTAAGAAAATATTTTTTAAAGGACTTA
1 TTTTTAAAGGATATTTAAGAAAATATTTTTTAAAGGACTTA
**
49879 TTTTTAAAGGATATTTAAGAATGTATTTTTTAAAGGA
1 TTTTTAAAGGATATTTAAGAAAATATTTTTTAAAGGA
49916 TATATACTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.45
Consensus pattern (41 bp):
TTTTTAAAGGATATTTAAGAAAATATTTTTTAAAGGACTTA
Found at i:51078 original size:72 final size:72
Alignment explanation
Indices: 50961--51104 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 72
50951 ATCAAATTTA
* *
50961 GCTAAACTATGAGTACAAATATTAGCTTTCCTTTTCGTTGAAATTTTTGGTTAATTCTCGGATCT
1 GCTAAACTATGAGCACAAATATTAGCTTTCCTTTTCGTTGAAATTTTTGGTTAATTCTCGAATCT
51026 CCATAAT
66 CCATAAT
* * * *
51033 GCTAAACTATGAGCACGAATGTTAGCTTTTCTTTTTGTTGAAATTTTTGGTTAATTCTCGAATCT
1 GCTAAACTATGAGCACAAATATTAGCTTTCCTTTTCGTTGAAATTTTTGGTTAATTCTCGAATCT
51098 CCATAAT
66 CCATAAT
51105 TTAGGTAAGC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (72 bp):
GCTAAACTATGAGCACAAATATTAGCTTTCCTTTTCGTTGAAATTTTTGGTTAATTCTCGAATCT
CCATAAT
Found at i:53307 original size:109 final size:109
Alignment explanation
Indices: 53116--53409 Score: 450
Period size: 109 Copynumber: 2.7 Consensus size: 109
53106 TAAATTAAAA
*
53116 TGGTAAAAATAAA-AAATATATATAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAATAAAGTAAT-TATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
53178 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
*
53225 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATTGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
53290 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
53334 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
53399 GTAGAATAAAA
61 GTAGAATAAAA
53410 CTATAATAGT
Statistics
Matches: 171, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
108 2 0.01
109 135 0.79
110 6 0.04
111 1 0.01
114 27 0.16
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:53759 original size:67 final size:63
Alignment explanation
Indices: 53692--53821 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 63
53682 TTAAACTAAA
* *
53692 TTAAATGGTAAAAATAAAATAGGTATTAGGACATTAG-ATTTAATTAAATAAAAATAGAGTTT
1 TTAAATGGTAAAAATAAAATAGGTATAAGGAAATTAGTATTTAATTAAATAAAAATAGAGTTT
53754 TTAAATGGTAAAAATAAAATAGGTATAAGGAAATTAGATTTAATTTAATTAAATAAAAATAGAGT
1 TTAAATGGTAAAAATAAAATAGGTATAAGGAAATTAG---T-ATTTAATTAAATAAAAATAGAGT
53819 TT
62 TT
53821 T
1 T
53822 AGTTTAGTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
62 35 0.57
67 26 0.43
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.35
Consensus pattern (63 bp):
TTAAATGGTAAAAATAAAATAGGTATAAGGAAATTAGTATTTAATTAAATAAAAATAGAGTTT
Found at i:59343 original size:15 final size:15
Alignment explanation
Indices: 59272--59343 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
59262 TAGTGCTTTT
*
59272 CAAGGAGAGTGATTC
1 CAAGGAGAGTAATTC
* * **
59287 CCAGAAGAGTGCTCTC
1 CAAGGAGAGTAAT-TC
* *
59303 CATGGAGAGTCATTC
1 CAAGGAGAGTAATTC
59318 CAAGGAGAGTAATTCC
1 CAAGGAGAGTAATT-C
59334 CAA-GAGAGTA
1 CAAGGAGAGTA
59344 CTTTCCATAC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
15 31 0.69
16 14 0.31
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.19
Consensus pattern (15 bp):
CAAGGAGAGTAATTC
Found at i:59514 original size:53 final size:53
Alignment explanation
Indices: 59399--59514 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 53
59389 GAAAGTTGGG
**
59399 TTACTTTCCCACCTTTATTTAATTAAACCAAACCATAGAAAGTGTTTCCACCTT
1 TTACTTTCCCACCTTTA-TTAATTAAACCAAACCATAGAAAGTGTTTCCACCCA
* * *
59453 TTATTTTCCCACCTATTA-TAACTT-AACCAAACCATGGAGAGTGTTTCCACCCA
1 TTACTTTCCCACCT-TTATTAA-TTAAACCAAACCATAGAAAGTGTTTCCACCCA
59506 TTACTTTCC
1 TTACTTTCC
59515 TAGGAAAGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
53 36 0.67
54 15 0.28
55 3 0.06
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (53 bp):
TTACTTTCCCACCTTTATTAATTAAACCAAACCATAGAAAGTGTTTCCACCCA
Found at i:69978 original size:6 final size:6
Alignment explanation
Indices: 69967--69991 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
69957 ATTTTCACTC
69967 CATTTT CATTTT CATTTT CATTTT C
1 CATTTT CATTTT CATTTT CATTTT C
69992 TAAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (6 bp):
CATTTT
Found at i:70313 original size:15 final size:15
Alignment explanation
Indices: 70271--70320 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
70261 GGTTGGATTT
70271 GGGTCAGGTTAATTC
1 GGGTCAGGTTAATTC
* *
70286 GGGTTCGGGTTAATTT
1 GGG-TCAGGTTAATTC
70302 GGGTCAGGTTAATTC
1 GGGTCAGGTTAATTC
70317 GGGT
1 GGGT
70321 TCGGGTTCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.16, C:0.10, G:0.38, T:0.36
Consensus pattern (15 bp):
GGGTCAGGTTAATTC
Found at i:70325 original size:31 final size:32
Alignment explanation
Indices: 70253--70327 Score: 127
Period size: 31 Copynumber: 2.4 Consensus size: 32
70243 CGGGTTTGAA
*
70253 TCGGGTTC-GGTTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
70284 TCGGGTTCGGGTT-AATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
70315 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
70328 CTGTTTGGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 38 0.90
32 4 0.10
ACGTcount: A:0.12, C:0.11, G:0.39, T:0.39
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
Done.