Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2375
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: 210449
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
File 1 of 2
Found at i:808 original size:319 final size:324
Alignment explanation
Indices: 370--979 Score: 1060
Period size: 319 Copynumber: 1.9 Consensus size: 324
360 AGTGGGCCTT
*
370 TTTTTTTTCTTTCCTGGCCTAATTTTTTTGGATGGAAAACTCTTAATTATAATTTTCTCGGCCTT
1 TTTTTTTTCTTTCCTGGCCTAATTTTTTTGGATGGAAAACTCTTAATTATAATTTTCTCGACCTT
435 TACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCTAC
66 TACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCTAC
* *
500 TAACTTTTCATG-TAGGAGGAT-AAGGGTATTCATGAATAGCATTAAGGTTTCTTTCTTAATCAA
131 T-ACTTTTCATGATAGGAGGATAAAGGGTATTCACGAAAAGCATTAAGGTTTCTTTCTTAATCAA
563 AAGA-GGTCGGACCTGAGAGGCC-TTTTCTCTA-TTTTGTGT-TAATTCCTTAAAAGATTTCATG
195 AAGATGGTCGGACCTGAGAGGCCATTTTCTCTATTTTTGTGTAT-ATTCCTTAAAAGA-TTCATG
624 GACTTCTTTTCCATGCTCTGAAGGGTTAGTTTACAGTCATTTTAAAGAGGTCGGACCTGAGAGGC
258 GACTTCTTTTCCATGCTCTGAAGGGTTAGTTTACAGTCATTTTAAAGAGGTCGGACCTGAGAGGC
689 CA
323 CA
*
691 TTTTTTTTCTTTCCTGGCCCTAA-TTTTTTGGATGGAAAAACTTTTAATTATAA-TTTCTCGACC
1 TTTTTTTTCTTTCCTGG-CCTAATTTTTTTGGATGG-AAAACTCTTAATTATAATTTTCTCGACC
754 -TTACAGTCATTTT-ATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
64 TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
817 ACTACTTTTCATGATAGGAGGATAAAGGGTATTCACGAAAAGCATTAAGGTTTCTTTCTTAATCA
129 ACTACTTTTCATGATAGGAGGATAAAGGGTATTCACGAAAAGCATTAAGGTTTCTTTCTTAATCA
882 AAAGATGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTCATG
194 AAAGATGGTCGGACCTGAGAGGCCA-TTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTCATG
947 GACTTCTTTTCCATGCTCTGAAGGGTTAGTTTA
258 GACTTCTTTTCCATGCTCTGAAGGGTTAGTTTA
980 TCAGGCAACC
Statistics
Matches: 276, Mismatches: 4, Indels: 16
0.93 0.01 0.05
Matches are distributed among these distances:
318 10 0.04
319 62 0.22
320 57 0.21
321 56 0.20
322 21 0.08
323 48 0.17
324 21 0.08
325 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (324 bp):
TTTTTTTTCTTTCCTGGCCTAATTTTTTTGGATGGAAAACTCTTAATTATAATTTTCTCGACCTT
TACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCTAC
TACTTTTCATGATAGGAGGATAAAGGGTATTCACGAAAAGCATTAAGGTTTCTTTCTTAATCAAA
AGATGGTCGGACCTGAGAGGCCATTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTCATGGAC
TTCTTTTCCATGCTCTGAAGGGTTAGTTTACAGTCATTTTAAAGAGGTCGGACCTGAGAGGCCA
Found at i:2154 original size:52 final size:52
Alignment explanation
Indices: 2091--2217 Score: 186
Period size: 52 Copynumber: 2.4 Consensus size: 52
2081 CTGATCTTTG
2091 TATCGATACATGCAGGCAAATTT-GCCCAGATATATCGATTACACTA-TAAATA
1 TATCGATACATGCAGGCAAATTTGGCCCAGATAT-TCGA-TACACTATTAAATA
* * *
2143 TATCGATACATGCAGGCCAATTTGGCCCAGATGTTCGATACACTATTAAATG
1 TATCGATACATGCAGGCAAATTTGGCCCAGATATTCGATACACTATTAAATA
*
2195 TATTGATACATGCAGGCAAATTT
1 TATCGATACATGCAGGCAAATTT
2218 TTCATATTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
51 7 0.10
52 52 0.76
53 9 0.13
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGGCCCAGATATTCGATACACTATTAAATA
Found at i:5126 original size:21 final size:21
Alignment explanation
Indices: 5100--5140 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5090 CTAATTTGCC
*
5100 AAGAATAATTAACTGAGAGAT
1 AAGAATAATTAACTAAGAGAT
5121 AAGAATAATTAACTAAGAGA
1 AAGAATAATTAACTAAGAGA
5141 GTGAATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (21 bp):
AAGAATAATTAACTAAGAGAT
Found at i:6573 original size:13 final size:13
Alignment explanation
Indices: 6555--6613 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
6545 AGATTTCATC
6555 ATGTATCGATACA
1 ATGTATCGATACA
*
6568 ATGTATTGATAC-
1 ATGTATCGATACA
6580 AT-T-TC-AT-C-
1 ATGTATCGATACA
6588 ATGTATCGATACA
1 ATGTATCGATACA
6601 ATGTATCGATACA
1 ATGTATCGATACA
6614 TTATACCATG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 3 0.08
11 3 0.08
12 3 0.08
13 24 0.62
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:6573 original size:33 final size:33
Alignment explanation
Indices: 6532--6634 Score: 163
Period size: 33 Copynumber: 3.1 Consensus size: 33
6522 GCTGTTACAA
*
6532 ACAATGTATCGATAGATTTCATCATGTATCGAT
1 ACAATGTATCGATACATTTCATCATGTATCGAT
*
6565 ACAATGTATTGATACATTTCATCATGTATCGAT
1 ACAATGTATCGATACATTTCATCATGTATCGAT
*
6598 ACAATGTATCGATACATTAT-ACCATGTATCGAT
1 ACAATGTATCGATACATT-TCATCATGTATCGAT
6631 ACAA
1 ACAA
6635 ATAGTGATAG
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
33 64 0.98
34 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (33 bp):
ACAATGTATCGATACATTTCATCATGTATCGAT
Found at i:6619 original size:20 final size:20
Alignment explanation
Indices: 6596--6633 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6586 TCATGTATCG
6596 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
*
6616 ATACCATGTATCGATACA
1 ATACAATGTATCGATACA
6634 AATAGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:6721 original size:13 final size:13
Alignment explanation
Indices: 6703--6729 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6693 TACAATAAAT
6703 ATGTATCGATACA
1 ATGTATCGATACA
6716 ATGTATCGATACA
1 ATGTATCGATACA
6729 A
1 A
6730 AGAAAGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:6745 original size:33 final size:32
Alignment explanation
Indices: 6684--6748 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
6674 ACAATTGTCC
* *
6684 ATGTATCGATACAATAAATATGTATCGATACA
1 ATGTATCGATACAAGAAAGATGTATCGATACA
6716 ATGTATCGATACAAAGAAAGATGTATCGATACA
1 ATGTATCGATAC-AAGAAAGATGTATCGATACA
6749 TCTAGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAGAAAGATGTATCGATACA
Found at i:15414 original size:19 final size:19
Alignment explanation
Indices: 15370--15425 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
15360 CTGCCAGTTT
**
15370 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
15390 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
15409 CATGTATCGATACAATG
1 CATGTATCGATACAATG
15426 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:15428 original size:13 final size:13
Alignment explanation
Indices: 15410--15436 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15400 TACAATGAAC
15410 ATGTATCGATACA
1 ATGTATCGATACA
15423 ATGTATCGATACA
1 ATGTATCGATACA
15436 A
1 A
15437 AGCAAGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:15452 original size:33 final size:32
Alignment explanation
Indices: 15391--15455 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
15381 ACAATTGTCC
* *
15391 ATGTATTGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
15423 ATGTATCGATACAAAGCAAGATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
15456 TTTGGCTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:22664 original size:13 final size:13
Alignment explanation
Indices: 22646--22673 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22636 ATTACTCAAA
22646 TGTATCGATACAT
1 TGTATCGATACAT
22659 TGTATCGATACAT
1 TGTATCGATACAT
22672 TG
1 TG
22674 ATCTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:38053 original size:28 final size:28
Alignment explanation
Indices: 37978--38706 Score: 721
Period size: 28 Copynumber: 25.4 Consensus size: 28
37968 ACCTTTTTCC
* * *
37978 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
*
38007 AAAGCCCACAAATCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
38035 AAAGCCCACAAGTCTGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
38064 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
38092 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACC--TTCA
38122 AAAGCCCACAAG-CTAGTGGCAACCTTCA
1 AAAGCCCACAAGTC-AGTGGCAACCTTCA
* * * *
38150 AAAGCCCACAAGTCCGTGGCATCTTTTCCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTT-CA
38180 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
38208 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACC--TTCA
* * *
38238 AAAGCCCACAAGTCTGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACC--TTCA
* * * *
38268 AAAGCCCACAAGTCTGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
38297 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
38325 AAAGCCCACAAGTCCGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
*
38354 AAAGCCCACAAGTCAGTGGCAACCTTTA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
38382 AAAGCCCACAAGTCCGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
38411 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
38439 AAAGCCCATAAGTCAGTGACACCCTTTTCT
1 AAAGCCCACAAGTCAGTGGCAACC--TTCA
* * *
38469 AAAGCCCACAAGTCCA-TGGCATCTTTTCC
1 AAAGCCCACAAGT-CAGTGGCAAC-CTTCA
38498 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
38526 AAAGCCCACAAGTCCGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
38555 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
38583 AAAGCCCACAAGTCATTGACACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACC--TTCA
* * *
38613 AAAGCCCAC-AGTCAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
*
38641 AAACCCCACAAGTCAGTGGCAA-CTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* **
38668 AAAGCACACAAGTTGGT-GCAACCCTTTCA
1 AAAGCCCACAAGTCAGTGGCAA-CC-TTCA
38697 AAAGCCCACA
1 AAAGCCCACA
38707 CAAGTTGGTG
Statistics
Matches: 584, Mismatches: 91, Indels: 50
0.81 0.13 0.07
Matches are distributed among these distances:
26 4 0.01
27 17 0.03
28 228 0.39
29 201 0.34
30 132 0.23
31 2 0.00
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:38066 original size:57 final size:57
Alignment explanation
Indices: 37978--38680 Score: 923
Period size: 57 Copynumber: 12.2 Consensus size: 57
37968 ACCTTTTTCC
*
37978 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAATCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
*
38035 AAAGCCCACAAGTCTGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
*
38092 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAG-CTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTC-AGTGGCAACCTTCA
*
38150 AAAGCCCACAAGTCCGTGGCATCTTTTCCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTT-CCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
38208 AAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCTGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCAACC--TTCA
*
38268 AAAGCCCACAAGTCTGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* *
38325 AAAGCCCACAAGTCCGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTTA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
*
38382 AAAGCCCACAAGTCCGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * * * * *
38439 AAAGCCCATAAGTCAGTGACACCCTTTTCTAAAGCCCACAAGTCCA-TGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGT-CAGTGGCAAC-CTTCA
* * * * * * *
38498 AAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTCCGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAAC-CTTCA
* * * * * * *
38555 AAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTCATTGACACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACC--TTCA
* * *
38613 AAAGCCCAC-AGTCAGTGGTATCTTTTCAAAACCCCACAAGTCAGTGGCAA-CTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
*
38668 AAAGCACACAAGT
1 AAAGCCCACAAGT
38681 TGGTGCAACC
Statistics
Matches: 584, Mismatches: 47, Indels: 31
0.88 0.07 0.05
Matches are distributed among these distances:
55 11 0.02
56 4 0.01
57 301 0.52
58 186 0.32
59 59 0.10
60 23 0.04
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.20
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:38475 original size:144 final size:145
Alignment explanation
Indices: 37967--38706 Score: 959
Period size: 144 Copynumber: 5.1 Consensus size: 145
37957 AGACATTCCT
* * * * *
37967 CACCTTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAATCAGTGGCAACC-
1 CACCCTTTTCCAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTCAGTGGCAACCT
*
38031 -TTCAAAAGCCCACAAGTCTGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAA
65 TTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAA
*
38095 GCCCACAAGTCAGTGG
130 GCCCACAAGTCCGTGG
* *
38111 CACCCTTTTCCAAAGCCCACAAG-CTAGTGGCAACCTTCAAAAGCCCACAAGTCCGTGGC-ATCT
1 CACCCTTTTCCAAAGCCCACAAGTC-AGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCT
* * * * * *
38174 TTTCCCAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCC
65 TTT-CAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACC--TTCA
*
38238 AAAGCCCACAAGTCTGTGG
127 AAAGCCCACAAGTCCGTGG
* * * *
38257 CACCCTTTTCCAAAGCCCACAAGTCTGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACC-
1 CACCCTTTTCCAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTCAGTGGCAACCT
* *
38321 -TTCAAAAGCCCACAAGTCCGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTTAAAA
65 TTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAA
38385 GCCCACAAGTCCGTGG
130 GCCCACAAGTCCGTGG
* * * *
38401 CA-TCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCATAAGTCAGTGACACCCTT
1 CACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTT
*
38465 TTCTAAAGCCCACAAGTCCA-TGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAA
66 TTCAAAAGCCCACAAGT-CAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAA
38529 GCCCACAAGTCCGTGG
130 GCCCACAAGTCCGTGG
* * * *
38545 CA-TCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCATTGACACCCTT
1 CACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTT
* * * *
38609 TTCCAAAGCCCAC-AGTCAGTGGTATCTTTTCAAAACCCCACAAGTCAGTGGCAA-CTTCAAAAG
66 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAG
* **
38672 CACACAAGTTGGT-G
131 CCCACAAGTCCGTGG
*
38686 CAACCC-TTTCAAAAGCCCACA
1 C-ACCCTTTTCCAAAGCCCACA
38707 CAAGTTGGTG
Statistics
Matches: 528, Mismatches: 52, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
141 2 0.00
142 62 0.12
143 86 0.16
144 229 0.43
145 45 0.09
146 79 0.15
147 23 0.04
148 2 0.00
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (145 bp):
CACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTT
TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAG
CCCACAAGTCCGTGG
Found at i:38848 original size:50 final size:49
Alignment explanation
Indices: 38769--39063 Score: 299
Period size: 50 Copynumber: 6.0 Consensus size: 49
38759 ATATTGGCAC
* * *
38769 CTTTAAAT-CAATGTCGCTAGCCTTGAATCAGCACATTGGCATCTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTC-AT
*
38818 CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCACATTGGCATCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* * *
38867 CTTTAAGTCCAATATCGCCGGCCTTAAATCAAGCACATTGGTATCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATC-AGCACATTGGCATCTTCAT
** * * * *
38917 CTTTAAGTCTGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* * * ** *
38966 CATTCCTAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGGCA--TTCTT
1 C-TT--TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
* * * * *
39016 CTTCAAGTCTAATGTCGCTGGCCATGAATCAGCACATTGTCATTCTTC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-TCTTC
39064 GCATCTTCGA
Statistics
Matches: 205, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
47 31 0.15
49 56 0.27
50 86 0.42
52 32 0.16
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (49 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
Found at i:39024 original size:99 final size:97
Alignment explanation
Indices: 38777--39063 Score: 306
Period size: 99 Copynumber: 2.9 Consensus size: 97
38767 ACCTTTAAAT
* *
38777 CAATGTCGCTAGCCTTGAATCAGCACATTGGCATCTTCAATCTTTAAGTCCAATATCGCTGGCCT
1 CAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTC-ATCTTTAAGTCTAATATCGCTGGCCT
* * *
38842 TAAATCAGCACATTGGCATCTTCATCTTTAAGTC
64 TGAATCAGCACATTGGCATCTTCAACTTTAAGCC
* * * * * *
38876 CAATATCGCCGGCCTTAAATCAAGCACATTGGTATCTTCATCTTTAAGTCTGATATCGTTGGCCT
1 CAATGTCGCTGGCCTTGAATC-AGCACATTGGCA-CTTCATCTTTAAGTCTAATATCGCTGGCCT
* *
38941 TGAATCAGCATATTGGCATCTTTAACATTCCTAAGCC
64 TGAATCAGCACATTGGCATCTTCAAC-TT--TAAGCC
* ** * * * *
38978 CAATGTCGTTGGCCTTGTCTCAGCACATTGGCA-TTCTTCTTCAAGTCTAATGTCGCTGGCCATG
1 CAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCTAATATCGCTGGCCTTG
*
39042 AATCAGCACATTGTCATTCTTC
66 AATCAGCACATTGGCA-TCTTC
39064 GCATCTTCGA
Statistics
Matches: 154, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
99 101 0.66
100 22 0.14
101 11 0.07
102 20 0.13
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.33
Consensus pattern (97 bp):
CAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCTAATATCGCTGGCCTTG
AATCAGCACATTGGCATCTTCAACTTTAAGCC
Found at i:39837 original size:19 final size:19
Alignment explanation
Indices: 39813--39869 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
39803 AAACGGTAAC
39813 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
39832 TGTATCGATAC---A---T
1 TGTATCGATACATAAGTGT
39845 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
39864 TGTATC
1 TGTATC
39870 AATATAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 12 0.38
16 2 0.06
19 18 0.56
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:39849 original size:13 final size:13
Alignment explanation
Indices: 39831--39857 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39821 TACATAAGTG
39831 TTGTATCGATACA
1 TTGTATCGATACA
39844 TTGTATCGATACA
1 TTGTATCGATACA
39857 T
1 T
39858 AAGTGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:39854 original size:32 final size:32
Alignment explanation
Indices: 39813--39888 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
39803 AAACGGTAAC
* *
39813 TGTATCGATACATAAGTGTTGTATCGATACAT
1 TGTATCGATACATAAGTGTTGTATCAATACAA
*
39845 TGTATCGATACATAAGTGTTGTATCAATATAA
1 TGTATCGATACATAAGTGTTGTATCAATACAA
*
39877 TGTATCGCTACA
1 TGTATCGATACA
39889 AAGCTACTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCAATACAA
Found at i:39946 original size:13 final size:13
Alignment explanation
Indices: 39928--39955 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39918 ATTACTCAAA
39928 TGTATCGATACAT
1 TGTATCGATACAT
39941 TGTATCGATACAT
1 TGTATCGATACAT
39954 TG
1 TG
39956 ATCTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:45494 original size:29 final size:29
Alignment explanation
Indices: 45378--45548 Score: 127
Period size: 29 Copynumber: 6.0 Consensus size: 29
45368 GCCATTTTAA
* * *
45378 GGTCAAAATGTAATTTTAAAAAGTTTAAG
1 GGTCAAAGTGTAATTTTGAAAAGTTTAGG
* * *
45407 GGAC-AA-TGTAATTTTGAAAATTTTAGA
1 GGTCAAAGTGTAATTTTGAAAAGTTTAGG
* * * * * **
45434 AGTCAATGTGCAA-TATAAAAAGTTTACA
1 GGTCAAAGTGTAATTTTGAAAAGTTTAGG
45462 GGTCAAAGTGCT-ATTTTGAAAAGTGTT-GG
1 GGTCAAAGTG-TAATTTTGAAAAGT-TTAGG
*
45491 GGTCAAAGTGTAATTTTGGAAAGTTTAGG
1 GGTCAAAGTGTAATTTTGAAAAGTTTAGG
** * *
45520 GGTCAAAGCATAACTTTGAAAAGTCTAGG
1 GGTCAAAGTGTAATTTTGAAAAGTTTAGG
45549 AACTTAATAG
Statistics
Matches: 109, Mismatches: 26, Indels: 14
0.73 0.17 0.09
Matches are distributed among these distances:
27 19 0.17
28 26 0.24
29 62 0.57
30 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (29 bp):
GGTCAAAGTGTAATTTTGAAAAGTTTAGG
Found at i:51907 original size:13 final size:13
Alignment explanation
Indices: 51889--51914 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51879 TACAGCAAGT
51889 ATGTATCGATACA
1 ATGTATCGATACA
51902 ATGTATCGATACA
1 ATGTATCGATACA
51915 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:54168 original size:21 final size:21
Alignment explanation
Indices: 54135--54179 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
54125 TTGCAAGTTG
*
54135 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
54157 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
54177 AAA
1 AAA
54180 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:56002 original size:15 final size:15
Alignment explanation
Indices: 55982--56012 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55972 TAAAAATGTC
*
55982 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
55997 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
56012 C
1 C
56013 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:58096 original size:20 final size:20
Alignment explanation
Indices: 58017--58096 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
58007 AATGTCCAAA
*
58017 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
58037 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
58062 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
58082 TTGTATCGATACATT
1 ATGTATCGATACATT
58097 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:58121 original size:13 final size:13
Alignment explanation
Indices: 58083--58121 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
58073 CATTTTTCTT
*
58083 TGTATCGATACAT
1 TGTATCGATACAG
58096 TGTATCGATACAG
1 TGTATCGATACAG
58109 TGTATCGATACAG
1 TGTATCGATACAG
58122 GGTGATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:58268 original size:21 final size:21
Alignment explanation
Indices: 58244--58290 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
58234 AAATCTTTTG
58244 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
58265 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
58285 CAAAAT
1 CAAAAT
58291 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:58287 original size:20 final size:19
Alignment explanation
Indices: 58246--58288 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
58236 ATCTTTTGCA
58246 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
58266 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
58286 AAA
1 AAA
58289 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:60685 original size:13 final size:13
Alignment explanation
Indices: 60667--60692 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60657 TACAGCAAGT
60667 ATGTATCGATACA
1 ATGTATCGATACA
60680 ATGTATCGATACA
1 ATGTATCGATACA
60693 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:62327 original size:36 final size:35
Alignment explanation
Indices: 62242--62340 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 35
62232 AACCTTACAA
62242 CCCTATC-TTTC-AAGGCTAAGATAGAAA---C-CT
1 CCCTATCTTTTCAAAGGCTAAGATA-AAACCTCTCT
**
62272 CCCTATCTTTTCACGGGCTAAGATAAAACCTCTCT
1 CCCTATCTTTTCAAAGGCTAAGATAAAACCTCTCT
*
62307 CCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 CCCTATC-TTTTCAAAGGCTAAGATAAAACCTCT
62341 TAATCACTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
30 7 0.12
31 7 0.12
32 10 0.18
34 1 0.02
35 9 0.16
36 23 0.40
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.30
Consensus pattern (35 bp):
CCCTATCTTTTCAAAGGCTAAGATAAAACCTCTCT
Found at i:62826 original size:20 final size:20
Alignment explanation
Indices: 62771--62817 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
62761 ATTGGGCTCA
*
62771 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATGCACC
*
62791 ATGTATCGATACAATGCATC
1 ATGTATCGATACAATGCACC
62811 ATGTATC
1 ATGTATC
62818 TATATAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATGCACC
Found at i:62902 original size:13 final size:13
Alignment explanation
Indices: 62884--62909 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62874 ATATTTTAAT
62884 ATGTATCGATACA
1 ATGTATCGATACA
62897 ATGTATCGATACA
1 ATGTATCGATACA
62910 TCTAGGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:63030 original size:20 final size:21
Alignment explanation
Indices: 63005--63048 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
62995 GATACTTTGA
63005 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTGAAAAAC
63025 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTA-GCTTGAAAAAC
63047 AT
1 AT
63049 CTATACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAC
Found at i:64689 original size:13 final size:13
Alignment explanation
Indices: 64671--64695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64661 ATGTTGCACA
64671 GTATCGATACATT
1 GTATCGATACATT
64684 GTATCGATACAT
1 GTATCGATACAT
64696 GACTAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:64708 original size:20 final size:21
Alignment explanation
Indices: 64683--64735 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
64673 ATCGATACAT
**
64683 TGTATCGATACATGACTAA-A
1 TGTATCGATACATGAAAAAGA
*
64703 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
64724 TGTATCGATACA
1 TGTATCGATACA
64736 GATCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:64828 original size:33 final size:32
Alignment explanation
Indices: 64767--64834 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
64757 GTAGCCAAAC
* ** *
64767 TTGTATCGATACACACAGTATGTATCGATGCA
1 TTGTATCGATACACAAAAAATGTATCGATACA
64799 TTGTATCGATACACAAAAAAATGTATCGATACA
1 TTGTATCGATACAC-AAAAAATGTATCGATACA
64832 TTG
1 TTG
64835 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (32 bp):
TTGTATCGATACACAAAAAATGTATCGATACA
Found at i:66429 original size:9 final size:9
Alignment explanation
Indices: 66415--66450 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
66405 TCAACCATCA
66415 AAGATGATG
1 AAGATGATG
66424 AAGATGATG
1 AAGATGATG
*
66433 AAGTTGATG
1 AAGATGATG
*
66442 ATGATGATG
1 AAGATGATG
66451 GTGACTTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.28
Consensus pattern (9 bp):
AAGATGATG
Found at i:66462 original size:21 final size:22
Alignment explanation
Indices: 66416--66463 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
66406 CAACCATCAA
*
66416 AGATGATGAAGATGATGAAGTT
1 AGATGATGAAGATGATGAACTT
* *
66438 -GATGATGATGATGGTG-ACTT
1 AGATGATGAAGATGATGAACTT
66458 AGATGA
1 AGATGA
66464 AGAAATAGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.35, C:0.02, G:0.33, T:0.29
Consensus pattern (22 bp):
AGATGATGAAGATGATGAACTT
Found at i:73481 original size:13 final size:13
Alignment explanation
Indices: 73463--73487 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73453 ATGTTGCACA
73463 GTATCGATACATT
1 GTATCGATACATT
73476 GTATCGATACAT
1 GTATCGATACAT
73488 GACTAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:73500 original size:20 final size:21
Alignment explanation
Indices: 73475--73527 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
73465 ATCGATACAT
**
73475 TGTATCGATACATGACTAA-A
1 TGTATCGATACATGAAAAAGA
*
73495 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
73516 TGTATCGATACA
1 TGTATCGATACA
73528 GATCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:73603 original size:20 final size:19
Alignment explanation
Indices: 73560--73610 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
73550 TAGCCAAACT
* **
73560 TGTATCGATACACACAGTA
1 TGTATCGATACACAAAAAA
73579 TGTATCGATACACAAAAAAA
1 TGTATCGATACAC-AAAAAA
*
73599 TGTATCAATACA
1 TGTATCGATACA
73611 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (19 bp):
TGTATCGATACACAAAAAA
Found at i:76190 original size:7 final size:7
Alignment explanation
Indices: 76177--76210 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
76167 TTGTCCGTAT
76177 TATTATA
1 TATTATA
*
76184 GATTATA
1 TATTATA
*
76191 TATTTTA
1 TATTATA
76198 TATTATA
1 TATTATA
76205 TATTAT
1 TATTAT
76211 CCAATGTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (7 bp):
TATTATA
Found at i:77017 original size:33 final size:32
Alignment explanation
Indices: 76975--77039 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
76965 TACACCCAGA
* *
76975 TGTATCGATACATTATGCTTTATATCGATACAT
1 TGTATCGATACATGAT-CATTATATCGATACAT
*
77008 TGTATCGATACATGATCATTGTATCGATACAT
1 TGTATCGATACATGATCATTATATCGATACAT
77040 GATGAATGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTATATCGATACAT
Found at i:77029 original size:19 final size:20
Alignment explanation
Indices: 77005--77059 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
76995 TATATCGATA
77005 CATTGTATCGATACATGAT-
1 CATTGTATCGATACATGATG
77024 CATTGTATCGATACATGATG
1 CATTGTATCGATACATGATG
* *
77044 AATGGTATCGATACAT
1 CATTGTATCGATACAT
77060 TGCTTCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (20 bp):
CATTGTATCGATACATGATG
Found at i:83091 original size:13 final size:13
Alignment explanation
Indices: 83073--83098 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
83063 TTTTCCAGAA
83073 TGTATCGATACAT
1 TGTATCGATACAT
83086 TGTATCGATACAT
1 TGTATCGATACAT
83099 GGGTTACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:85614 original size:19 final size:18
Alignment explanation
Indices: 85586--85643 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
85576 TTGTATCGAT
*
85586 ACATTATATCGATACATG
1 ACATTGTATCGATACATG
85604 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
85624 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
85643 A
1 A
85644 AACCGGCAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.50
20 17 0.47
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:85617 original size:32 final size:33
Alignment explanation
Indices: 85559--85621 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
85549 CACCCAAATG
* *
85559 TATCGATACATTATGCTTTGTATCGATACATTA
1 TATCGATACATGATGCATTGTATCGATACATTA
85592 TATCGATACATGAT-CATTGTATCGATACAT
1 TATCGATACATGATGCATTGTATCGATACAT
85622 GGACAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (33 bp):
TATCGATACATGATGCATTGTATCGATACATTA
Found at i:85632 original size:20 final size:20
Alignment explanation
Indices: 85587--85642 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
85577 TGTATCGATA
*
85587 CATTATATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
85606 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
85625 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
85643 AAACCGGCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:87537 original size:13 final size:13
Alignment explanation
Indices: 87519--87543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87509 TACCAAGAAC
87519 ATGTATCGATACA
1 ATGTATCGATACA
87532 ATGTATCGATAC
1 ATGTATCGATAC
87544 TAAGTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:87541 original size:32 final size:33
Alignment explanation
Indices: 87500--87561 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
87490 ACAATTCACT
87500 ATGTATCGATACCAAG-AACATGTATCGATACA
1 ATGTATCGATACCAAGTAACATGTATCGATACA
* *
87532 ATGTATCGATACTAAGTAATATGTATCGAT
1 ATGTATCGATACCAAGTAACATGTATCGAT
87562 GCATCTGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACCAAGTAACATGTATCGATACA
Found at i:88230 original size:20 final size:22
Alignment explanation
Indices: 88205--88244 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
88195 ATTTATAACT
88205 TCCCC-TTAATAAAA-ATTTTC
1 TCCCCTTTAATAAAATATTTTC
88225 TCCCCTTTAATAAAATATTT
1 TCCCCTTTAATAAAATATTT
88245 AATGCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (22 bp):
TCCCCTTTAATAAAATATTTTC
Found at i:90604 original size:13 final size:14
Alignment explanation
Indices: 90580--90608 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
90570 TATTAGAGAT
90580 ATCATAAAGGGTAC
1 ATCATAAAGGGTAC
90594 ATCAT-AAGGGTAC
1 ATCATAAAGGGTAC
90607 AT
1 AT
90609 AAACTTGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (14 bp):
ATCATAAAGGGTAC
Found at i:94533 original size:21 final size:21
Alignment explanation
Indices: 94500--94540 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
94490 CCAAGTAAAA
94500 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
94521 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
94541 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:94605 original size:20 final size:19
Alignment explanation
Indices: 94580--94650 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
94570 ACCCTGAAAA
94580 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
94600 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
94619 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
94640 GTATCGATACA
1 GTATCGATACA
94651 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:94703 original size:53 final size:53
Alignment explanation
Indices: 94620--94756 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
94610 AGATTGCATA
94620 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
94674 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
94727 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
94757 TTGGCAGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:94865 original size:13 final size:13
Alignment explanation
Indices: 94847--94897 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
94837 TCACTATTCA
*
94847 TGTATCGATACAT
1 TGTATCGATACAG
94860 TGTATCGATACAG
1 TGTATCGATACAG
94873 TGTATCGATACAG
1 TGTATCGATACAG
94886 TGTATCGATACA
1 TGTATCGATACA
94898 TCATAAATAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:100113 original size:13 final size:13
Alignment explanation
Indices: 100095--100120 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
100085 TACAGCAAGT
100095 ATGTATCGATACA
1 ATGTATCGATACA
100108 ATGTATCGATACA
1 ATGTATCGATACA
100121 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:102372 original size:21 final size:21
Alignment explanation
Indices: 102339--102383 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
102329 TTGCAAGTTG
*
102339 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
102361 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
102381 AAA
1 AAA
102384 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:104206 original size:15 final size:15
Alignment explanation
Indices: 104186--104216 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
104176 TAAAAATGTC
*
104186 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
104201 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
104216 C
1 C
104217 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:106311 original size:13 final size:13
Alignment explanation
Indices: 106293--106331 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
106283 ATACATTTTC
106293 TTGTATCGATACA
1 TTGTATCGATACA
106306 TTGTATCGATACA
1 TTGTATCGATACA
106319 TTGTATCGATACA
1 TTGTATCGATACA
106332 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:106495 original size:20 final size:20
Alignment explanation
Indices: 106452--106498 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
106442 AAATCTTTTG
106452 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
106473 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
106493 CAAAAT
1 CAAAAT
106499 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:108900 original size:13 final size:13
Alignment explanation
Indices: 108882--108907 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
108872 TACAGCAAGT
108882 ATGTATCGATACA
1 ATGTATCGATACA
108895 ATGTATCGATACA
1 ATGTATCGATACA
108908 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:110212 original size:21 final size:21
Alignment explanation
Indices: 110179--110219 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
110169 CTAAGTAAAA
110179 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
110200 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
110220 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:110284 original size:20 final size:19
Alignment explanation
Indices: 110259--110329 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
110249 ACCCTAAAAA
110259 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
110279 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
110298 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
110319 GTATCGATACA
1 GTATCGATACA
110330 GGACATTGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:110382 original size:53 final size:53
Alignment explanation
Indices: 110299--110435 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
110289 AGATTGCATA
*
110299 GTATCGATACACACAAATATGTATCGATACAGGACATTGGTAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
110353 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
110406 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
110436 TTGGCAGTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:114707 original size:21 final size:20
Alignment explanation
Indices: 114683--114733 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
114673 TTGCATGTTG
114683 AAATAAAAATTTAGCTAATG-A
1 AAATAAAAA-TTAGCTAA-GAA
*
114704 AAATAATGAATTAGCTAAGAA
1 AAATAA-AAATTAGCTAAGAA
114725 AAATAAAAA
1 AAATAAAAA
114734 CTTGCATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.12
21 21 0.81
22 2 0.08
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.24
Consensus pattern (20 bp):
AAATAAAAATTAGCTAAGAA
Found at i:118650 original size:13 final size:13
Alignment explanation
Indices: 118632--118670 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
118622 ACATCTTTCT
118632 TTGTATCGATACA
1 TTGTATCGATACA
118645 TTGTATCGATACA
1 TTGTATCGATACA
*
118658 CTGTATCGATACA
1 TTGTATCGATACA
118671 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:120386 original size:11 final size:11
Alignment explanation
Indices: 120370--120394 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
120360 ATTATTATCT
120370 TTTATCGCATA
1 TTTATCGCATA
120381 TTTATCGCATA
1 TTTATCGCATA
120392 TTT
1 TTT
120395 CCATCTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (11 bp):
TTTATCGCATA
Found at i:120805 original size:13 final size:13
Alignment explanation
Indices: 120787--120812 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
120777 TACACCAAGT
120787 ATGTATCGATACA
1 ATGTATCGATACA
120800 ATGTATCGATACA
1 ATGTATCGATACA
120813 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:120810 original size:32 final size:33
Alignment explanation
Indices: 120769--120832 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
120759 TAGCCAAACT
* **
120769 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
120801 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
120833 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:123043 original size:21 final size:21
Alignment explanation
Indices: 123010--123054 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
123000 TTGCAAGATG
*
123010 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
123032 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
123052 AAA
1 AAA
123055 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:126933 original size:20 final size:20
Alignment explanation
Indices: 126854--126933 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
126844 AATGTCCAAA
*
126854 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
126874 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
126899 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
126919 TTGTATCGATACATT
1 ATGTATCGATACATT
126934 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:126937 original size:13 final size:13
Alignment explanation
Indices: 126919--126957 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
126909 ACATTTTTCT
126919 TTGTATCGATACA
1 TTGTATCGATACA
126932 TTGTATCGATACA
1 TTGTATCGATACA
* *
126945 CTGAATCGATACA
1 TTGTATCGATACA
126958 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:129512 original size:13 final size:13
Alignment explanation
Indices: 129494--129519 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
129484 TACAGCAAGT
129494 ATGTATCGATACA
1 ATGTATCGATACA
129507 ATGTATCGATACA
1 ATGTATCGATACA
129520 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:131702 original size:15 final size:15
Alignment explanation
Indices: 131682--131712 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
131672 TAAAAATGTC
*
131682 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
131697 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
131712 C
1 C
131713 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:136392 original size:13 final size:13
Alignment explanation
Indices: 136374--136399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
136364 TACAGCAAGT
136374 ATGTATCGATACA
1 ATGTATCGATACA
136387 ATGTATCGATACA
1 ATGTATCGATACA
136400 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:138024 original size:13 final size:13
Alignment explanation
Indices: 138006--138031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
137996 TACACCAAGT
138006 ATGTATCGATACA
1 ATGTATCGATACA
138019 ATGTATCGATACA
1 ATGTATCGATACA
138032 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:138050 original size:34 final size:32
Alignment explanation
Indices: 137988--138052 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
137978 TAGCCAAACT
**
137988 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
138020 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
138053 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:140150 original size:17 final size:17
Alignment explanation
Indices: 140128--140162 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
140118 TACTGTCAAT
140128 TTCATGTATCGATACAA
1 TTCATGTATCGATACAA
140145 TTCATGTATCGATACAA
1 TTCATGTATCGATACAA
140162 T
1 T
140163 GTATCGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (17 bp):
TTCATGTATCGATACAA
Found at i:140166 original size:13 final size:13
Alignment explanation
Indices: 140148--140172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
140138 GATACAATTC
140148 ATGTATCGATACA
1 ATGTATCGATACA
140161 ATGTATCGATAC
1 ATGTATCGATAC
140173 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:142199 original size:12 final size:12
Alignment explanation
Indices: 142184--142213 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
142174 TAAAATTTAT
142184 CAATTAATTAAC
1 CAATTAATTAAC
142196 CAATTAATTAAC
1 CAATTAATTAAC
*
142208 AAATTA
1 CAATTA
142214 CTAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (12 bp):
CAATTAATTAAC
Found at i:144656 original size:3 final size:3
Alignment explanation
Indices: 144648--144706 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
144638 AAGGAAGGAT
*
144648 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
144696 TAA TAA TAA TA
1 TAA TAA TAA TA
144707 GTAAAAAACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:146527 original size:2 final size:2
Alignment explanation
Indices: 146522--146551 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
146512 GGATATATTT
146522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
146552 ATCAAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:154040 original size:19 final size:20
Alignment explanation
Indices: 154012--154064 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
154002 AGCGATACAT
*
154012 TGTATTGATACAACACT-TA
1 TGTATCGATACAACACTGTA
* *
154031 TGTATCGATACATTCACTGTT
1 TGTATCGATACA-ACACTGTA
154052 TGTATCGATACAA
1 TGTATCGATACAA
154065 ATTGTTGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 11 0.39
20 4 0.14
21 13 0.46
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTATCGATACAACACTGTA
Found at i:155633 original size:2 final size:2
Alignment explanation
Indices: 155626--155665 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
155616 ATCATTAAAA
*
155626 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155666 CTAACTCCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:155841 original size:31 final size:31
Alignment explanation
Indices: 155799--155891 Score: 141
Period size: 31 Copynumber: 3.0 Consensus size: 31
155789 TGGCATGATT
*
155799 ACAAAAACCACTATTCTTATCCGATGGCACG
1 ACAAAAACCACTATTCTTATCCGGTGGCACG
*
155830 ACAAAAGCCACTATTCTTATCCGGTGGCACG
1 ACAAAAACCACTATTCTTATCCGGTGGCACG
* * *
155861 ATAAAAACCATTATTCTTAACCGGTGGCACG
1 ACAAAAACCACTATTCTTATCCGGTGGCACG
155892 GTTTGAAACC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (31 bp):
ACAAAAACCACTATTCTTATCCGGTGGCACG
Found at i:155908 original size:31 final size:31
Alignment explanation
Indices: 155777--155891 Score: 99
Period size: 31 Copynumber: 3.6 Consensus size: 31
155767 AAAAATCGTT
* *
155777 ATTCTAAACCGGTGGCATGATTACAAAAACCACT-
1 ATTCTTAACCGGTGGCACGA-T--AAAAACCA-TG
* * * *
155811 ATTCTTATCCGATGGCACGACAAAAGCCACT-
1 ATTCTTAACCGGTGGCACGATAAAAACCA-TG
* *
155842 ATTCTTATCCGGTGGCACGATAAAAACCATT
1 ATTCTTAACCGGTGGCACGATAAAAACCATG
155873 ATTCTTAACCGGTGGCACG
1 ATTCTTAACCGGTGGCACG
155892 GTTTGAAACC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.01
31 53 0.76
34 16 0.23
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (31 bp):
ATTCTTAACCGGTGGCACGATAAAAACCATG
Found at i:156766 original size:21 final size:22
Alignment explanation
Indices: 156737--156786 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
156727 AAATTAATAA
*
156737 AACTGAAATTTATATTATTTTT
1 AACTGAAATATATATTATTTTT
*
156759 AACT-AAATATATTTTA-TTTT
1 AACTGAAATATATATTATTTTT
*
156779 ATCTGAAA
1 AACTGAAA
156787 ATAACTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.29
21 13 0.54
22 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (22 bp):
AACTGAAATATATATTATTTTT
Found at i:162976 original size:2 final size:2
Alignment explanation
Indices: 162969--163002 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
162959 ATCATCAAAA
*
162969 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
163003 CTAACTCCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:163438 original size:13 final size:13
Alignment explanation
Indices: 163420--163445 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
163410 TACAGCAAGT
163420 ATGTATCGATACA
1 ATGTATCGATACA
163433 ATGTATCGATACA
1 ATGTATCGATACA
163446 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:164232 original size:38 final size:38
Alignment explanation
Indices: 164187--164291 Score: 147
Period size: 38 Copynumber: 2.8 Consensus size: 38
164177 GTAAGCTTTC
* *
164187 ACCACTATTTTAAACCGGTGGCACGGTTAGAAATGAAA
1 ACCACTATTCTAAACCGGTAGCACGGTTAGAAATGAAA
* * * *
164225 ATCACTATTCTAAGCCGGTAGTACGGTTCGAAATGAAA
1 ACCACTATTCTAAACCGGTAGCACGGTTAGAAATGAAA
*
164263 ACCACTATTCTAAACCAGTAGCACGGTTA
1 ACCACTATTCTAAACCGGTAGCACGGTTA
164292 AATACAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (38 bp):
ACCACTATTCTAAACCGGTAGCACGGTTAGAAATGAAA
Found at i:164302 original size:38 final size:37
Alignment explanation
Indices: 164187--164325 Score: 120
Period size: 38 Copynumber: 3.7 Consensus size: 37
164177 GTAAGCTTTC
* *
164187 ACCACTATTTTAAACCGGTGGCACGGTTAGAA-ATGAAA
1 ACCACTATTCTAAACCGGTAGCACGGTTA-AATA-GAAA
* * *
164225 ATCACTATTCTAAGCCGGTAGTACGGTTCGAAAT-GAAA
1 ACCACTATTCTAAACCGGTAGCACGGTT--AAATAGAAA
* *
164263 ACCACTATTCTAAACCAGTAGCACGGTTAAATACAAAA
1 ACCACTATTCTAAACCGGTAGCACGGTTAAATA-GAAA
* * * *
164301 ACCATTATTCTTATCCGGTGGCACG
1 ACCACTATTCTAAACCGGTAGCACG
164326 ACAAAAGCCA
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
36 4 0.05
38 74 0.91
39 2 0.02
40 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (37 bp):
ACCACTATTCTAAACCGGTAGCACGGTTAAATAGAAA
Found at i:164341 original size:31 final size:31
Alignment explanation
Indices: 164295--164414 Score: 152
Period size: 31 Copynumber: 3.9 Consensus size: 31
164285 ACGGTTAAAT
*
164295 ACAAAAACCATTATTCTTATCCGGTGGCACG
1 ACAAAAACCACTATTCTTATCCGGTGGCACG
*
164326 ACAAAAGCCACTATTCTTATCCGGTGGCACG
1 ACAAAAACCACTATTCTTATCCGGTGGCACG
* * *
164357 GCAAAAACTACTATTCTTATCCGATGGCAC-
1 ACAAAAACCACTATTCTTATCCGGTGGCACG
* * *
164387 AGCACAAATCACTATTCTTAACCGGTGG
1 A-CAAAAACCACTATTCTTATCCGGTGG
164415 TACGGTTTGA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (31 bp):
ACAAAAACCACTATTCTTATCCGGTGGCACG
Found at i:164969 original size:21 final size:23
Alignment explanation
Indices: 164928--164969 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
164918 ATATATATCT
*
164928 AAAAATTAGAATTTAACTAACTA
1 AAAAAATAGAATTTAACTAACTA
164951 AAAAAATA-AATTTAA-TAAC
1 AAAAAATAGAATTTAACTAAC
164970 GTACAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAAATAGAATTTAACTAACTA
Found at i:167645 original size:48 final size:49
Alignment explanation
Indices: 167562--167659 Score: 121
Period size: 48 Copynumber: 2.0 Consensus size: 49
167552 TTTGAGCCAA
*
167562 ATTTAAATAATAAATTTTTTTAAATTAAATTAATTTAATT-TGAATTATT
1 ATTTAAATAATAAATTATTTTAAATTAAATTAATTTAATTAT-AATTATT
* * *
167611 ATTTAAATAATAAA-TATTTT-ATTTTATTTAAATTTAATTATAATTATT
1 ATTTAAATAATAAATTATTTTAAATTAAATT-AATTTAATTATAATTATT
167659 A
1 A
167660 ATATAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
47 6 0.14
48 22 0.51
49 15 0.35
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (49 bp):
ATTTAAATAATAAATTATTTTAAATTAAATTAATTTAATTATAATTATT
Found at i:168935 original size:18 final size:17
Alignment explanation
Indices: 168898--168945 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
168888 CTATTATATG
*
168898 ATAAAA-AAATAATTAAA
1 ATAAAATAAAT-ATAAAA
*
168915 ATATAATATAATATAAAA
1 ATAAAATA-AATATAAAA
168933 ATAAAATAAATAT
1 ATAAAATAAATAT
168946 GATACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 10 0.38
18 13 0.50
19 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATAAATATAAAA
Found at i:168936 original size:16 final size:16
Alignment explanation
Indices: 168903--168941 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
168893 ATATGATAAA
168903 AAAATAATTAAAATAT
1 AAAATAATTAAAATAT
*
168919 AATATAATATAAAA-AT
1 AAAATAAT-TAAAATAT
168935 AAAATAA
1 AAAATAA
168942 ATATGATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATAATTAAAATAT
Found at i:168954 original size:22 final size:23
Alignment explanation
Indices: 168911--168957 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
168901 AAAAAATAAT
*
168911 TAAAATATAATATAATATAAAAA
1 TAAAATATAATATAATACAAAAA
*
168934 TAAAATA-AATATGATACAAAAA
1 TAAAATATAATATAATACAAAAA
168956 TA
1 TA
168958 TTATGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
TAAAATATAATATAATACAAAAA
Found at i:169014 original size:20 final size:22
Alignment explanation
Indices: 168989--169039 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
168979 AACATGATCG
* *
168989 AAAATACAACACG-ATG-CATA
1 AAAATAAAACAAGCATGACATA
169009 AAAATAAAACAAGCATGACATA
1 AAAATAAAACAAGCATGACATA
169031 AAACATAAA
1 AAA-ATAAA
169040 TGAATATACC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 11 0.42
21 3 0.12
22 7 0.27
23 5 0.19
ACGTcount: A:0.63, C:0.16, G:0.08, T:0.14
Consensus pattern (22 bp):
AAAATAAAACAAGCATGACATA
Found at i:169562 original size:18 final size:18
Alignment explanation
Indices: 169539--169582 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
169529 ATTTGTGTTA
169539 TTTTTATATCATGTTAAT
1 TTTTTATATCATGTTAAT
* * *
169557 TTTTTATGTTATGTTTAT
1 TTTTTATATCATGTTAAT
169575 TTTTTATA
1 TTTTTATA
169583 GTATTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (18 bp):
TTTTTATATCATGTTAAT
Found at i:172775 original size:20 final size:21
Alignment explanation
Indices: 172752--172802 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
172742 TATTATTAAA
172752 ATATATTAAAAAT-TATTTTT
1 ATATATTAAAAATATATTTTT
* **
172772 ATATTAGTAATTATATATTTTT
1 ATA-TATTAAAAATATATTTTT
172794 ATA-ATTAAA
1 ATATATTAAA
172803 TTAAAATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATATATTAAAAATATATTTTT
Found at i:172811 original size:22 final size:22
Alignment explanation
Indices: 172760--172811 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
172750 AAATATATTA
172760 AAAATTATTTTTATATTAGTAATT
1 AAAA-TATTTTTATATTAG-AATT
*
172784 -ATATATTTTTATAATTA-AATT
1 AAAATATTTTTAT-ATTAGAATT
172805 AAAATAT
1 AAAATAT
172812 AAATTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AAAATATTTTTATATTAGAATT
Found at i:173250 original size:2 final size:2
Alignment explanation
Indices: 173243--173274 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
173233 ATGATTTAAG
*
173243 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173275 CCAATTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:174008 original size:21 final size:21
Alignment explanation
Indices: 173974--174013 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
173964 AATTATTATT
173974 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
173995 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
174014 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:174502 original size:26 final size:26
Alignment explanation
Indices: 174466--174518 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
174456 AATTAACATC
174466 ATTCATCCGCAACAACAAGTTTGACA
1 ATTCATCCGCAACAACAAGTTTGACA
*
174492 ATTCATCCGCAACAAGAAGTTTGACA
1 ATTCATCCGCAACAACAAGTTTGACA
174518 A
1 A
174519 GACGCAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.23
Consensus pattern (26 bp):
ATTCATCCGCAACAACAAGTTTGACA
Found at i:175733 original size:3 final size:3
Alignment explanation
Indices: 175727--175756 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
175717 AAAAGGTGTT
175727 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
175757 TATTTTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:176957 original size:19 final size:20
Alignment explanation
Indices: 176921--176958 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
176911 ATCCACAAGG
* *
176921 AAAATCGAATTATTAAGAAA
1 AAAATCCAATTATGAAGAAA
176941 AAAATCCAATTA-GAAGAA
1 AAAATCCAATTATGAAGAA
176959 TTTGGATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.21
Consensus pattern (20 bp):
AAAATCCAATTATGAAGAAA
Found at i:178611 original size:34 final size:33
Alignment explanation
Indices: 178566--178651 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
178556 CTCATTTAGT
* *
178566 AGGACACAAGTTTGACTCTATTAACTTGTTTAGAA
1 AGGACATAAGTTTGACTCT-TTAACCTGTTTA-AA
**
178601 A-GACATAAGTTCAACTC-TTAACCTGTTTAAA
1 AGGACATAAGTTTGACTCTTTAACCTGTTTAAA
*
178632 AGGAAATAAGTTTGACTCTT
1 AGGACATAAGTTTGACTCTT
178652 GACCTATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
31 3 0.07
32 24 0.57
33 1 0.02
34 13 0.31
35 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (33 bp):
AGGACATAAGTTTGACTCTTTAACCTGTTTAAA
Found at i:178628 original size:32 final size:33
Alignment explanation
Indices: 178586--178662 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 33
178576 TTTGACTCTA
* *
178586 TTAACTTGTTTAGAAA-GACATAAGTTCAACTC
1 TTAACCTGTTTAGAAAGGAAATAAGTTCAACTC
**
178618 TTAACCTGTTTA-AAAGGAAATAAGTTTGACTC
1 TTAACCTGTTTAGAAAGGAAATAAGTTCAACTC
* *
178650 TTGACCTATTTAG
1 TTAACCTGTTTAG
178663 GAGGATATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 3 0.08
32 34 0.92
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (33 bp):
TTAACCTGTTTAGAAAGGAAATAAGTTCAACTC
Found at i:178779 original size:33 final size:34
Alignment explanation
Indices: 178706--178860 Score: 131
Period size: 34 Copynumber: 4.6 Consensus size: 34
178696 ATAGGATAAG
* * * *
178706 AGTTTGATTCTTTTAATTTG-TTGAAAAAGACACA
1 AGTTTGACTCTTTTAACTTGCTTG-GAAAGACATA
*
178740 TG-TTGACTC-TTTAACTTGCTTGGAAAGACATA
1 AGTTTGACTCTTTTAACTTGCTTGGAAAGACATA
* * * *
178772 AGTTTGACACTTTTAACTTG-TTCGAAAGGAAACA
1 AGTTTGACTCTTTTAACTTGCTTGGAAA-GACATA
* * *
178806 AGCTTGACTCTTTTAATTTGCTTGGAAGGACATA
1 AGTTTGACTCTTTTAACTTGCTTGGAAAGACATA
178840 AGTTTGA-TACTTTTTAACTTG
1 AGTTTGACT-C-TTTTAACTTG
178861 TTCAAAAAAA
Statistics
Matches: 95, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
32 17 0.18
33 22 0.23
34 42 0.44
35 14 0.15
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (34 bp):
AGTTTGACTCTTTTAACTTGCTTGGAAAGACATA
Found at i:178874 original size:35 final size:35
Alignment explanation
Indices: 178835--178925 Score: 116
Period size: 33 Copynumber: 2.7 Consensus size: 35
178825 GCTTGGAAGG
* *
178835 ACATAAGTTTGATACTTTTTAACTTGTTCAAAAAA
1 ACATAAGTTTGATACTTTTTAACTTATTAAAAAAA
178870 ACATAAG-TT-AT-CTCTTTTAACTTATTAAAAAAA
1 ACATAAGTTTGATACT-TTTTAACTTATTAAAAAAA
* *
178903 ACAGAAGTTTGACACTTTTTAAC
1 ACATAAGTTTGATACTTTTTAAC
178926 CTGAAAGCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
32 2 0.04
33 25 0.52
34 4 0.08
35 15 0.31
36 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (35 bp):
ACATAAGTTTGATACTTTTTAACTTATTAAAAAAA
Found at i:178885 original size:68 final size:66
Alignment explanation
Indices: 178706--178892 Score: 209
Period size: 68 Copynumber: 2.8 Consensus size: 66
178696 ATAGGATAAG
* * * * *
178706 AGTTTGATTCTTTTAATTTGTTGAAAAAGACACATGTTGACTC-TTTAACTTGCTTGGAAAGACA
1 AGTTTGATACTTTTAACTTGTTCAAAAAAACA-AAGTTGACTCTTTTAACTTGCTTGGAAAGACA
178770 TA
65 TA
* * * *
178772 AGTTTGACACTTTTAACTTGTTCGAAAGGAAAC-AAGCTTGACTCTTTTAATTTGCTTGGAAGGA
1 AGTTTGATACTTTTAACTTGTTC-AAA-AAAACAAAG-TTGACTCTTTTAACTTGCTTGGAAAGA
178836 CATA
63 CATA
178840 AGTTTGATACTTTTTAACTTGTTCAAAAAAACATAAGTT-ATCTCTTTTAACTT
1 AGTTTGATAC-TTTTAACTTGTTCAAAAAAACA-AAGTTGA-CTCTTTTAACTT
178893 ATTAAAAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
66 21 0.21
67 15 0.15
68 49 0.49
69 16 0.16
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (66 bp):
AGTTTGATACTTTTAACTTGTTCAAAAAAACAAAGTTGACTCTTTTAACTTGCTTGGAAAGACAT
A
Found at i:179714 original size:33 final size:32
Alignment explanation
Indices: 179670--179733 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
179660 TACAAGCCAA
* *
179670 TGTATCGATACATTTTGGGATGCATCGATACAT
1 TGTATCAATACATCTTGGG-TGCATCGATACAT
* *
179703 TGTATCAATACATCTTGTGTGTATCGATACA
1 TGTATCAATACATCTTGGGTGCATCGATACA
179734 AACAGTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (32 bp):
TGTATCAATACATCTTGGGTGCATCGATACAT
Found at i:179822 original size:20 final size:21
Alignment explanation
Indices: 179775--179826 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
179765 GCCAATGACC
*
179775 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
179796 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
179816 TGTATCGATAC
1 TGTATCGATAC
179827 TGTGCAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:182504 original size:8 final size:8
Alignment explanation
Indices: 182491--182516 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
182481 AACATCATTC
182491 ATCACAAA
1 ATCACAAA
182499 ATCACAAA
1 ATCACAAA
182507 ATCACAAA
1 ATCACAAA
182515 AT
1 AT
182517 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:188476 original size:13 final size:13
Alignment explanation
Indices: 188458--188483 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
188448 CATTTTGGGA
188458 TGTATCGATACAT
1 TGTATCGATACAT
188471 TGTATCGATACAT
1 TGTATCGATACAT
188484 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:188480 original size:33 final size:32
Alignment explanation
Indices: 188438--188501 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
188428 TACAAGCCAA
*
188438 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
188471 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
188502 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:190353 original size:17 final size:18
Alignment explanation
Indices: 190327--190360 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
190317 ATTCTTCCTT
*
190327 TTTTTTTTCT-TTTTTTA
1 TTTTTATTCTATTTTTTA
190344 TTTTTATTCTATTTTTT
1 TTTTTATTCTATTTTTT
190361 CAACGATTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTATTCTATTTTTTA
Found at i:190719 original size:17 final size:16
Alignment explanation
Indices: 190699--190777 Score: 70
Period size: 16 Copynumber: 4.8 Consensus size: 16
190689 TTGTATTATA
*
190699 TTTTTTTC-TTTTTGT
1 TTTTTTTCTTTTTTTT
* *
190714 TTTTTTTCTTTATTTC
1 TTTTTTTCTTTTTTTT
*
190730 TTTATTTCTTTCTTTTCT
1 TTTTTTTCTTT-TTTT-T
190748 TTTTTCTTCTTTTTTCTT
1 TTTTT-TTCTTTTTT-TT
*
190766 TCTTTTTCTTTT
1 TTTTTTTCTTTT
190778 GATCGGAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
15 8 0.16
16 14 0.27
17 10 0.20
18 12 0.24
19 7 0.14
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (16 bp):
TTTTTTTCTTTTTTTT
Done.