Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold377
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: 400731
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.31
Warning! 22032 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:7942 original size:37 final size:36
Alignment explanation
Indices: 7901--8009 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 36
7891 ATTAATCATC
* *
7901 AATAGAATGAGAAAACAAGCAAGAAAGGTATGTTCAA
1 AATAGAATGAGAATACAA-CAAGAAAGGTATATTCAA
*
7938 AATAGAATGAGAATACTAACAAGAAAGGTATATTCAT
1 AATAGAATGAGAATAC-AACAAGAAAGGTATATTCAA
* *
7975 AATCGAATGAGAATACAAACAAGAAAGCTATATTC
1 AATAGAATGAGAATAC-AACAAGAAAGGTATATTC
8010 CTATGAATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 63 0.97
38 2 0.03
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.20
Consensus pattern (36 bp):
AATAGAATGAGAATACAACAAGAAAGGTATATTCAA
Found at i:8401 original size:14 final size:14
Alignment explanation
Indices: 8384--8412 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8374 ATTATAGAAC
8384 TCAATATTTTTATT
1 TCAATATTTTTATT
8398 TCAATATTTTTATT
1 TCAATATTTTTATT
8412 T
1 T
8413 TTAACCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
TCAATATTTTTATT
Found at i:10455 original size:2 final size:2
Alignment explanation
Indices: 10450--10485 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10440 CTCTCTCTTA
10450 AT AT AT 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
10486 TTAGTAGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10991 original size:153 final size:151
Alignment explanation
Indices: 10686--11216 Score: 613
Period size: 159 Copynumber: 3.5 Consensus size: 151
10676 CAACGGTAAG
* * * *
10686 AAAGGA-AAACAAGTATGCCTTTGTTTATGGTTTCAGCTTACTTATGTAGC-AAGAAAAGTGAAT
1 AAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAGTGAAT
* * * *** **
10749 ATAAACACATATATTTAGTATGGATTCTTGAACTTGAATTGAGCAAAGAATTAAAAACAACAACA
66 ATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTTAAA-AACAACA
*
10814 AAGAAACAAGAAAGCCATTTAAA
130 AAGAAACAAGAAAACCA-TTAAA
*
10837 AAAGGAGAAAAATGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAGTGAAT
1 AAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAGTGAAT
* *
10902 ATAAATATATATATTTAATATGGTTTATTGAACTTGAATTGAATGAAGAATTTTAAAAACAACAA
66 ATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTTAAAAACAACAA
* *
10967 AGAATCAAGAAAATCATTAAAA
131 AGAAACAAGAAAACCATT-AAA
* ** * **
10989 AAAGGGAAAAAAAAAGCGTGCCTTTGTTTATGATTTTGGCTTGCTTGTGTAGCAAGAAAAGTGAA
1 AAA-GG-AGAAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAA-AAAA---AA
* *
11054 TATAAATATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAA-TTTAAAA
60 -GTGAATATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTTAAAA
*
11118 AGCGAA-AAAGAAACAAGAAAACCATTTAA
124 A-C-AACAAAGAAACAAGAAAACCATTAAA
* * ** * *
11147 AAAGGCGAAAAAAAGTATTCCTTTGTTTATGGTTTTGGATTGCTTGTGGAGCAAAAAAAA-TGAA
1 AAAGGAG-AAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAGTGAA
11211 TATAAA
65 TATAAA
11217 CAATGAACGT
Statistics
Matches: 326, Mismatches: 41, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
151 17 0.05
152 67 0.21
153 63 0.19
154 41 0.13
155 4 0.01
156 4 0.01
157 42 0.13
158 15 0.05
159 71 0.22
160 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (151 bp):
AAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAGTGAAT
ATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTTAAAAACAACAA
AGAAACAAGAAAACCATTAAA
Found at i:13322 original size:19 final size:21
Alignment explanation
Indices: 13274--13332 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
13264 TTTTTTAATC
* *
13274 AAGTTGAGTAAAATAAAATTT
1 AAGTCGAGTTAAATAAAATTT
13295 AAGTCGAGTTAAAT-AAATTT
1 AAGTCGAGTTAAATAAAATTT
*
13315 -ATTCGAGTTAAATTAAAA
1 AAGTCGAGTTAAA-TAAAA
13333 AAATTAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 11 0.33
20 7 0.21
21 15 0.45
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (21 bp):
AAGTCGAGTTAAATAAAATTT
Found at i:21108 original size:64 final size:63
Alignment explanation
Indices: 21034--21152 Score: 202
Period size: 64 Copynumber: 1.9 Consensus size: 63
21024 TGTCATCAAG
* * *
21034 CTGCATGCACTTCAACCAAAAAATGTAACAGCAGCATGGTTGGCAAATTTCTAACATTTTTTTT
1 CTGCATGCACTTCAACCAAAAAATGTAACAGCAGAATGATTGGC-AATTTCCAACATTTTTTTT
21098 CTGCATGCACTTCAACCAAAAAATGTAACAGCAGAATGATTGGCAATTTCCAACA
1 CTGCATGCACTTCAACCAAAAAATGTAACAGCAGAATGATTGGCAATTTCCAACA
21153 GTTCCCGTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 10 0.19
64 42 0.81
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (63 bp):
CTGCATGCACTTCAACCAAAAAATGTAACAGCAGAATGATTGGCAATTTCCAACATTTTTTTT
Found at i:23021 original size:17 final size:18
Alignment explanation
Indices: 22999--23032 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22989 TTGTCTATAA
22999 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
23016 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
23033 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:24773 original size:37 final size:37
Alignment explanation
Indices: 24708--24813 Score: 124
Period size: 37 Copynumber: 2.8 Consensus size: 37
24698 GCAACATTAA
*
24708 TCATCAATAGAACGAGAATACGAACAAGAAAGGTATAT
1 TCAT-AATAGAATGAGAATACGAACAAGAAAGGTATAT
* *
24746 TCATAATAGAATGAGAACAC-AAGCAAGAAAGGTATGT
1 TCATAATAGAATGAGAATACGAA-CAAGAAAGGTATAT
* * * *
24783 TAAAAAAAGAATGAGAATACTAACAAGAAAG
1 TCATAATAGAATGAGAATACGAACAAGAAAG
24814 CCATGTTCCT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
36 2 0.03
37 51 0.86
38 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (37 bp):
TCATAATAGAATGAGAATACGAACAAGAAAGGTATAT
Found at i:24959 original size:27 final size:27
Alignment explanation
Indices: 24909--24960 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
24899 TATAAATTTG
*
24909 TATATATAATTTCATTTGTTATTTATA
1 TATATATAATTTCATTTGTGATTTATA
24936 TATATATAATTTCATCTT-TGATTTA
1 TATATATAATTTCAT-TTGTGATTTA
24961 AAAGAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.58
Consensus pattern (27 bp):
TATATATAATTTCATTTGTGATTTATA
Found at i:25983 original size:20 final size:21
Alignment explanation
Indices: 25958--26000 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
25948 GTATCAGATG
*
25958 ATATAATTA-AAAATAATATT
1 ATATAATTATAAAATAAAATT
25978 ATATAATTATTAAAATAAAATT
1 ATATAATTA-TAAAATAAAATT
26000 A
1 A
26001 AGTTTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAATTATAAAATAAAATT
Found at i:27498 original size:16 final size:16
Alignment explanation
Indices: 27479--27509 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27469 TAAACATATA
27479 TATATATATAGTATGG
1 TATATATATAGTATGG
27495 TATATATATAGTATG
1 TATATATATAGTATG
27510 ATTTCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (16 bp):
TATATATATAGTATGG
Found at i:27764 original size:155 final size:151
Alignment explanation
Indices: 27563--28089 Score: 679
Period size: 155 Copynumber: 3.5 Consensus size: 151
27553 GATAAAAAGG
* * * * *
27563 GGAAAAAAAGGTATGCCTTTGTTTATAGTTTCGGCTTGCTTATGTAGCAAGAAAAGTGAATATAA
1 GGAAAAAAATGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAAAAAAGCGAATATAA
* *
27628 ACATATATAATTAGTATGATTTCTTGAACTTGAATTGAATGAAGAATCTAAAAAACAACAAAGAA
66 ACATATATAATTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTAAAAAACAACAAAGAA
* *
27693 ACAAAAAAAAAAATGCATTTAAAAAA
131 AC----AAGAAAA-CCATTTAAAAAA
*
27719 GG-AAAAAATGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAGCGAATATAA
1 GGAAAAAAATGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAAAAAAGCGAATATAA
* * *
27783 ATATATAT-TTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTTAAAAACAACAAAGAA
66 ACATATATAATTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTAAAAAACAACAAAGAA
*
27847 TCAAGAAAACCA-TTAAAAAA
131 ACAAGAAAACCATTTAAAAAA
* * *
27867 GGAAATAAAATGCATGCCTTTGTTTATGGTTTTGGCTTGCTTGTGTAGCAAGAAAAGCGAATATA
1 GGAAA-AAAATGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAAAAAAGCGAATATA
* * *
27932 AACATATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTGAAAAGCGGA-
65 AAC--ATATATA-A-TTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTAAAAAAC-AAC
27996 AAAGAAACAAGAAAACCATTTAAAAAA
125 AAAGAAACAAGAAAACCATTTAAAAAA
* * * **
28023 GGCAAAAAA-GTACT-CCTTTGTTTATGGTTTCGGATTGCTTGTGGAGCAAAAAAAATGAATATA
1 GGAAAAAAATGTA-TGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAAAAAAGCGAATATA
28086 AACA
65 AACA
28090 GCGTATGCGA
Statistics
Matches: 329, Mismatches: 32, Indels: 24
0.85 0.08 0.06
Matches are distributed among these distances:
148 10 0.03
149 4 0.01
150 63 0.19
152 7 0.02
154 101 0.31
155 129 0.39
156 15 0.05
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (151 bp):
GGAAAAAAATGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAAAAAAGCGAATATAA
ACATATATAATTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTAAAAAACAACAAAGAA
ACAAGAAAACCATTTAAAAAA
Found at i:32263 original size:21 final size:19
Alignment explanation
Indices: 32229--32267 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
32219 ATAATCCTCC
32229 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
32248 GGAAACATGGTCTTAGATAG
1 GGAAA-ATGG-CTTAGATAG
32268 GGAGGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:40042 original size:21 final size:19
Alignment explanation
Indices: 40008--40046 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
39998 ATAATCCTCT
40008 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
40027 GGAAACATGGTCTTAGATAG
1 GGAAA-ATGG-CTTAGATAG
40047 GGAGGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:44606 original size:43 final size:43
Alignment explanation
Indices: 44559--44901 Score: 123
Period size: 42 Copynumber: 8.1 Consensus size: 43
44549 TATAGTGGCA
* *
44559 TTTGT-GAAGAAAGTGCTGCTAAAGAACACT-A-CTTTTAGCGGTG
1 TTTGTAGAAG-AAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGTG
*
44602 TTTGTAGATGAAGCGCCGCTAAAGAACATGATCTTTAGCGGTG
1 TTTGTAGAAGAAGCGCCGCTAAAGAACATGATCTTTAGCGGTG
* ** * * * *
44645 TTTTTTACCA-AA-CGCTGCTATAGAACATTAGT-TTTAGCGGCG
1 -TTTGTAGAAGAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGTG
* * * *
44687 TTTTTTTGTA-AA-CGCCGCTAAAGAACATGATCTTTAGCGGCG
1 -TTTGTAGAAGAAGCGCCGCTAAAGAACATGATCTTTAGCGGTG
* ***** * * *
44729 TTTTTTTCCTAAGTGCCGCTAAAGATCATG-TCCTTTAGCGGCG
1 TTTGTAGAAGAAGCGCCGCTAAAGAACATGAT-CTTTAGCGGTG
***** * * **
44772 TTT-TTTCCCAAGCGCCGCTAAAGAACATGATCATCAGCGACG
1 TTTGTAGAAGAAGCGCCGCTAAAGAACATGATCTTTAGCGGTG
***** *
44814 TTT-TTTCCCAAGCGCCGCTAAAGAACATGATCATTAGCGGTG
1 TTTGTAGAAGAAGCGCCGCTAAAGAACATGATCTTTAGCGGTG
* ***** * * *
44856 TTTTTTTCCTAAGCGCCGCTAAAGGACATGACCTTTAGCGGCG
1 TTTGTAGAAGAAGCGCCGCTAAAGAACATGATCTTTAGCGGTG
44899 TTT
1 TTT
44902 TTTTCTGTAA
Statistics
Matches: 253, Mismatches: 36, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
41 7 0.03
42 135 0.53
43 102 0.40
44 9 0.04
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (43 bp):
TTTGTAGAAGAAGCGCCGCTAAAGAACATGATCTTTAGCGGTG
Found at i:44682 original size:42 final size:42
Alignment explanation
Indices: 44615--44904 Score: 314
Period size: 42 Copynumber: 6.9 Consensus size: 42
44605 GTAGATGAAG
*
44615 CGCCGCTAAAGAACATGATCTTTAGCGGTGTTTTTTACCAAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACCAAA
* * * ***
44657 CGCTGCTATAGAACATTAGT-TTTAGCGGCGTTTTTTTGTAAA
1 CGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTTACCAAA
* *
44699 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACC-AAA
* * * *
44742 TGCCGCTAAAGATCATG-TCCTTTAGCGGCGTTTTTTCCCAAG
1 CGCCGCTAAAGAACATGAT-CTTTAGCGGCGTTTTTTACCAAA
* * * * *
44784 CGCCGCTAAAGAACATGATCATCAGCGACGTTTTTTCCCAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACCAAA
* * * *
44826 CGCCGCTAAAGAACATGATCATTAGCGGTGTTTTTTTCCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACC-AAA
* *
44869 CGCCGCTAAAGGACATGACCTTTAGCGGCGTTTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
44905 TCTGTAAACG
Statistics
Matches: 213, Mismatches: 29, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
41 1 0.00
42 139 0.65
43 73 0.34
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACCAAA
Found at i:44792 original size:85 final size:83
Alignment explanation
Indices: 44612--44906 Score: 358
Period size: 85 Copynumber: 3.5 Consensus size: 83
44602 TTTGTAGATG
* * * * *
44612 AAGCGCCGCTAAAGAACATGATCTTTAGCGGTGTTTTTTACCAAACGCTGCTATAGAACATTAGT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCAAGCGCCGCTAAAGAACA-T-GT
**
44677 -TTTAGCGGCGTTTTTTTGT
64 CTTTAGCGGCGTTTTTTCCT
* * *
44696 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCTAAGTGCCGCTAAAGATCATGTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCC-AAGCGCCGCTAAAGAACATGT-
*
44761 CTTTAGCGGCGTTTTTTCCC
64 CTTTAGCGGCGTTTTTTCCT
* * * *
44781 AAGCGCCGCTAAAGAACATGATCATCAGCGACGTTTTTTCCCAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCAAGCGCCGCTAAAGAACATG-TC
* *
44846 ATTAGCGGTGTTTTTTTCCT
65 TTTAGCGGCG-TTTTTTCCT
* *
44866 AAGCGCCGCTAAAGGACATGACCTTTAGCGGCGTTTTTTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
44907 TGTAAACGCT
Statistics
Matches: 179, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
83 2 0.01
84 67 0.37
85 110 0.61
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (83 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCAAGCGCCGCTAAAGAACATGTCT
TTAGCGGCGTTTTTTCCT
Found at i:44816 original size:127 final size:126
Alignment explanation
Indices: 44612--44904 Score: 374
Period size: 127 Copynumber: 2.3 Consensus size: 126
44602 TTTGTAGATG
* * * *
44612 AAGCGCCGCTAAAGAACATGAT-CTTTAGCGGTGTTTTTTACCAAACGCTGCTATAGAACATTAG
1 AAGCGCCGCTAAAG-ACATG-TCCTTTAGCGGCGTTTTTTACCAAACGCCGCTAAAGAACATGAG
* * * *** *
44676 TTTTAGCGGCGTTTTTTTGTAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCT
64 TATCAGCGACGTTTTTTCCCAAACGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
* * *
44739 AAGTGCCGCTAAAGATCATGTCCTTTAGCGGCGTTTTTTCCCAAGCGCCGCTAAAGAACATGA-T
1 AAGCGCCGCTAAAGA-CATGTCCTTTAGCGGCGTTTTTTACCAAACGCCGCTAAAGAACATGAGT
* *
44803 CATCAGCGACGTTTTTTCCCAAGCGCCGCTAAAGAACATGATCATTAGCGGTGTTTTTTTCCT
65 -ATCAGCGACGTTTTTTCCCAAACGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
*
44866 AAGCGCCGCTAAAGGACATGACCTTTAGCGGCGTTTTTT
1 AAGCGCCGCTAAA-GACATGTCCTTTAGCGGCGTTTTTT
44905 TCTGTAAACG
Statistics
Matches: 144, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
126 3 0.02
127 139 0.97
128 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (126 bp):
AAGCGCCGCTAAAGACATGTCCTTTAGCGGCGTTTTTTACCAAACGCCGCTAAAGAACATGAGTA
TCAGCGACGTTTTTTCCCAAACGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
Found at i:49448 original size:21 final size:20
Alignment explanation
Indices: 49422--49463 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
49412 TTTTTTAATC
49422 AAGTTGAGTGAAATAAAATTT
1 AAGTTGAGTGAAAT-AAATTT
*
49443 AAGTTGAGTTAAATAAATTT
1 AAGTTGAGTGAAATAAATTT
49463 A
1 A
49464 TTCGAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.36
Consensus pattern (20 bp):
AAGTTGAGTGAAATAAATTT
Found at i:50889 original size:42 final size:42
Alignment explanation
Indices: 50837--51118 Score: 377
Period size: 42 Copynumber: 6.7 Consensus size: 42
50827 TTAAAAAAAA
* * * *
50837 CGCCTCTAAAGAACATGGTCTTTGGCGGCATTCCTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
* *
50879 CGCCGCTAAAGAACATGCTCTTTAGCGGCGTTTATTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT-CTTTCTAAG
* *
50922 CGCTGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
50964 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
* * *
51006 TGCCTCTAAAGAACATTGTCTTTAGCGGCGTTTCTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
* * * * *
51048 CGCCGCTGAAGAACATGGTCTTTAACGGTGTTTTTTTGTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
**
51090 CGCCG-TAAAAGAACATTATCTTTAGCGGC
1 CGCCGCT-AAAGAACATGGTCTTTAGCGGC
51119 ACTTTTATAC
Statistics
Matches: 212, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
41 1 0.00
42 172 0.81
43 39 0.18
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAG
Found at i:55957 original size:9 final size:9
Alignment explanation
Indices: 55943--56181 Score: 175
Period size: 9 Copynumber: 27.9 Consensus size: 9
55933 TTTTTATTTA
55943 TTATGTAAG
1 TTATGTAAG
55952 TTATGTAAG
1 TTATGTAAG
55961 TTATGT-A-
1 TTATGTAAG
55968 TTATGT-A-
1 TTATGTAAG
55975 TTATGTAAG
1 TTATGTAAG
55984 -TACTGTAAG
1 TTA-TGTAAG
* *
55993 TAATGTACG
1 TTATGTAAG
56002 TTATGTAAG
1 TTATGTAAG
*
56011 TAATGT-A-
1 TTATGTAAG
*
56018 TTATGAAAG
1 TTATGTAAG
*
56027 TTGTGTATA-
1 TTATGTA-AG
*
56036 ATAT-TAA-
1 TTATGTAAG
*
56043 TTATGTGAG
1 TTATGTAAG
**
56052 TCGTGT-A-
1 TTATGTAAG
*
56059 TAATGTAAG
1 TTATGTAAG
*
56068 TTAAG-AAGG
1 TTATGTAA-G
56077 TTATGT-A-
1 TTATGTAAG
*
56084 TAATGTAAG
1 TTATGTAAG
*
56093 TTATGAAAG
1 TTATGTAAG
* *
56102 TTATTTAAT
1 TTATGTAAG
56111 TTATGTAAG
1 TTATGTAAG
56120 TTATGTAAG
1 TTATGTAAG
* *
56129 TTATTTAAT
1 TTATGTAAG
56138 TTATGTAAG
1 TTATGTAAG
56147 TTATGTAAG
1 TTATGTAAG
* *
56156 TTATTTAAT
1 TTATGTAAG
56165 TTATGTAAG
1 TTATGTAAG
56174 TTATGTAA
1 TTATGTAA
56182 TTAGAAATTT
Statistics
Matches: 179, Mismatches: 36, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
7 30 0.17
8 15 0.08
9 132 0.74
10 2 0.01
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:55980 original size:32 final size:33
Alignment explanation
Indices: 55936--56008 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
55926 TGATATATTT
* *
55936 TTATTTATTATGTAAGTTA-TGTAAGTTATGTA-
1 TTATGTATTATGTAAG-TACTGTAAGTAATGTAC
55968 TTATGTATTATGTAAGTACTGTAAGTAATGTAC
1 TTATGTATTATGTAAGTACTGTAAGTAATGTAC
56001 GTTATGTA
1 -TTATGTA
56009 AGTAATGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 2 0.06
32 27 0.75
34 7 0.19
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.48
Consensus pattern (33 bp):
TTATGTATTATGTAAGTACTGTAAGTAATGTAC
Found at i:56219 original size:20 final size:20
Alignment explanation
Indices: 56194--56231 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
56184 AGAAATTTTG
56194 TCTTAATACTATATAAGTAA
1 TCTTAATACTATATAAGTAA
*
56214 TCTTAATATTATATAAGT
1 TCTTAATACTATATAAGT
56232 TATATTAATT
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:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
TCTTAATACTATATAAGTAA
Found at i:56239 original size:20 final size:20
Alignment explanation
Indices: 56196--56245 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
56186 AAATTTTGTC
* *
56196 TTAATACTATATAAGTAATC
1 TTAATATTATATAAGTAATA
*
56216 TTAATATTATATAAGTTATA
1 TTAATATTATATAAGTAATA
*
56236 TTAATTTTAT
1 TTAATATTAT
56246 TTTATTTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (20 bp):
TTAATATTATATAAGTAATA
Found at i:56624 original size:144 final size:144
Alignment explanation
Indices: 56364--56723 Score: 720
Period size: 144 Copynumber: 2.5 Consensus size: 144
56354 TTACTTAAGC
56364 TATATGCATGTTATATATTATGTAAGTTACATAAAATACATAAATTATGAAATCTGATCCAAAGA
1 TATATGCATGTTATATATTATGTAAGTTACATAAAATACATAAATTATGAAATCTGATCCAAAGA
56429 TTTTGCAAGTCTTGAAATTTGATCTTAATATTATATAAGTTTAATTTATATTAAGCAAGTTAATA
66 TTTTGCAAGTCTTGAAATTTGATCTTAATATTATATAAGTTTAATTTATATTAAGCAAGTTAATA
56494 CCATTTACAAAAGT
131 CCATTTACAAAAGT
56508 TATATGCATGTTATATATTATGTAAGTTACATAAAATACATAAATTATGAAATCTGATCCAAAGA
1 TATATGCATGTTATATATTATGTAAGTTACATAAAATACATAAATTATGAAATCTGATCCAAAGA
56573 TTTTGCAAGTCTTGAAATTTGATCTTAATATTATATAAGTTTAATTTATATTAAGCAAGTTAATA
66 TTTTGCAAGTCTTGAAATTTGATCTTAATATTATATAAGTTTAATTTATATTAAGCAAGTTAATA
56638 CCATTTACAAAAGT
131 CCATTTACAAAAGT
56652 TATATGCATGTTATATATTATGTAAGTTACATAAAATACATAAATTATGAAATCTGATCCAAAGA
1 TATATGCATGTTATATATTATGTAAGTTACATAAAATACATAAATTATGAAATCTGATCCAAAGA
56717 TTTTGCA
66 TTTTGCA
56724 TTTAAATAAA
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 216 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (144 bp):
TATATGCATGTTATATATTATGTAAGTTACATAAAATACATAAATTATGAAATCTGATCCAAAGA
TTTTGCAAGTCTTGAAATTTGATCTTAATATTATATAAGTTTAATTTATATTAAGCAAGTTAATA
CCATTTACAAAAGT
Found at i:57912 original size:18 final size:18
Alignment explanation
Indices: 57871--57912 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
57861 ATATAGTTAC
57871 TGAAAAATTTAAATACTT
1 TGAAAAATTTAAATACTT
*
57889 AG-AAAATATTAAA-ACTT
1 TGAAAAAT-TTAAATACTT
57906 TGAAAAA
1 TGAAAAA
57913 GTAATAACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (18 bp):
TGAAAAATTTAAATACTT
Found at i:60170 original size:14 final size:13
Alignment explanation
Indices: 60153--60220 Score: 64
Period size: 14 Copynumber: 4.9 Consensus size: 13
60143 TCATAAATCC
60153 TAAACCCTAAACT
1 TAAACCCTAAACT
*
60166 ATAAACCCTTAACCT
1 -TAAACCC-TAAACT
60181 TAAACCCTAAATCT
1 TAAACCCTAAA-CT
* * *
60195 CAAAACATCAAACT
1 TAAACCCT-AAACT
60209 TAAACCCTAAAC
1 TAAACCCTAAAC
60221 CCGTCAATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 7 0.16
14 28 0.65
15 8 0.19
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAACCCTAAACT
Found at i:60179 original size:21 final size:21
Alignment explanation
Indices: 60145--60185 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
60135 TTAATTAATC
*
60145 ATAAATCCTAAACCCTAAACT
1 ATAAACCCTAAACCCTAAACT
* *
60166 ATAAACCCTTAACCTTAAAC
1 ATAAACCCTAAACCCTAAAC
60186 CCTAAATCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
ATAAACCCTAAACCCTAAACT
Found at i:67390 original size:15 final size:15
Alignment explanation
Indices: 67370--67399 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
67360 GTAGAAAATC
67370 CTTAATTTAATTTCT
1 CTTAATTTAATTTCT
67385 CTTAATTTAATTTCT
1 CTTAATTTAATTTCT
67400 TATCATACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (15 bp):
CTTAATTTAATTTCT
Found at i:71002 original size:21 final size:19
Alignment explanation
Indices: 70968--71006 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
70958 ATAATCCTCC
70968 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
70987 GGAAACATGGTCTTAGATAG
1 GGAAA-ATGG-CTTAGATAG
71007 GGAGGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:72602 original size:17 final size:18
Alignment explanation
Indices: 72580--72613 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
72570 TTGTTTATAA
72580 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
72597 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
72614 AAGTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:74039 original size:37 final size:36
Alignment explanation
Indices: 73998--74106 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 36
73988 ATTAATCATC
*
73998 AATAGAATGAGAAAACAAGCAAGAAAGGTATGTTCAA
1 AATAGAATGAGAAAACAA-CAAGAAAGGTATATTCAA
*
74035 AATAGAATGAGAAAACTAACAAGAAAGGTATATTCAT
1 AATAGAATGAGAAAAC-AACAAGAAAGGTATATTCAA
* * *
74072 AATCGAATGAGAATACAAACAAGAAAGCTATATTC
1 AATAGAATGAGAAAAC-AACAAGAAAGGTATATTC
74107 CTATGAACTA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 63 0.97
38 2 0.03
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.19
Consensus pattern (36 bp):
AATAGAATGAGAAAACAACAAGAAAGGTATATTCAA
Found at i:78163 original size:2 final size:2
Alignment explanation
Indices: 78158--78183 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78148 ATATCCATCC
78158 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
78184 CAATACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78218 original size:7 final size:7
Alignment explanation
Indices: 78206--78251 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
78196 TAACTTATTT
78206 ATTTGGA
1 ATTTGGA
78213 ATTTGGA
1 ATTTGGA
78220 ATTTGGA
1 ATTTGGA
78227 ATTTGGA
1 ATTTGGA
**
78234 ATTTCTA
1 ATTTGGA
78241 ATTTGGA
1 ATTTGGA
78248 ATTT
1 ATTT
78252 CTAGATTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (7 bp):
ATTTGGA
Found at i:79024 original size:124 final size:124
Alignment explanation
Indices: 78798--79142 Score: 561
Period size: 124 Copynumber: 2.8 Consensus size: 124
78788 TTATTTCGAG
78798 TTGAC-TTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAA-AAGAAATTG
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTT-AAGAAGAAATTG
* * *
78860 TGAAATCGCGCCCTCGTGGACGCGATTCTGCTACAGTAGGTTATGTAAGAAATAATTTTTT
64 TGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAATAGGTCATGTAAGAAATAATTTTTT
* * *
78921 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTGTACCAAGATGCTATTTAAGAAGAAATTATG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGTG
* *
78986 AAATCGGGCCCTCGTGGACGGGATTTTGCTACAATAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAATAGGTCATGTAAGAAATAATTTTTT
*
79045 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGTG
*
79110 AAATCGCACCCTCGTGGACGCGATTTTGCTACA
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACA
79143 GTAACAAGTT
Statistics
Matches: 204, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
123 7 0.03
124 196 0.96
125 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTAAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAATAGGTCATGTAAGAAATAATTTTTT
Found at i:82149 original size:10 final size:10
Alignment explanation
Indices: 82134--82160 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
82124 TAAAATTATC
82134 AAATTATGTA
1 AAATTATGTA
82144 AAATTATGTA
1 AAATTATGTA
82154 AAATTAT
1 AAATTAT
82161 TAAGCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
AAATTATGTA
Found at i:82310 original size:55 final size:55
Alignment explanation
Indices: 82144--82548 Score: 641
Period size: 55 Copynumber: 7.3 Consensus size: 55
82134 AAATTATGTA
82144 AAATTATGTAAAATTATTAAG-CCAAAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCC--AAAAATTGTGTTAATGGTTAGTAAAATTATC
* ** *
82200 AAATTATGTAAAATTATTATGGTATAAAAAATTTTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTA-AGT-CCAAAAATTGTGTTAATGGTTAGTAAAATTATC
82257 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
82312 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGCTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
* * *
82367 AAATTATGTAAAATTATTAAGTCTAAGAATTGTATTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
* * *
82422 AAATTATGTAAAATTATTAAGTCTAAGAATTGTATTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
* * *
82477 AAATTATGTAAAATTATTAAGTCTAAGAATTGTATTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
82532 AAATTATGTAAAATTAT
1 AAATTATGTAAAATTAT
82549 NNNNNNNNNN
Statistics
Matches: 333, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
55 262 0.79
56 21 0.06
57 50 0.15
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.39
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:82644 original size:29 final size:29
Alignment explanation
Indices: 82595--83001 Score: 575
Period size: 29 Copynumber: 14.1 Consensus size: 29
82585 NNNNNNNNNN
**
82595 GTTAGGGTTTTTAATTAAATTAGGTTTTG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
82624 GTTAGGGTTTTTATTTGAATTAGGTTA-G
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
82652 GTTAGGGTTTTTAATTAAGTTAGGTTAGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
82681 GTTTGGGTTTTTAATTAAGTTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
82710 GTTAGGGCTTTTAATTAAATTAGGTTATG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
82739 GTTAGGGTTTTTATTTGAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* **
82768 GTTAGGGTTTTTAATTAAATTAAGTTTTG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
82797 GTTAGGGTTTTTATTTGAATTAGGTTA-G
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
82825 GTTAGGGTTTTTAATTAAGTTAGGTTAGA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
82854 GTTAGGGTTTTTAATTAAATTAGGTTATG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
82883 GTTAGGGTTTTTATTTGAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
82912 GTTAGGGTTTTTAATTAAAGTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
82941 GTTAGGGTTTTTATTTGAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
82970 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
82999 GTT
1 GTT
83002 TTTAATTAAA
Statistics
Matches: 332, Mismatches: 44, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
28 50 0.15
29 282 0.85
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (29 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGG
Found at i:82799 original size:173 final size:173
Alignment explanation
Indices: 82595--83016 Score: 647
Period size: 173 Copynumber: 2.5 Consensus size: 173
82585 NNNNNNNNNN
82595 GTTAGGGTTTTTAATTAAATTAGGTTTTGGTTAGGGTTTTTATTTGAATTAGGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTTTGGTTAGGGTTTTTATTTGAATTAGGTTAGGTTAGGGT
* * *
82660 TTTTAATTAAGTTAGGTTAGTGTTTGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGCTTTTAAT
66 TTTTAATTAAGTTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGCTTTTAAT
* * * *
82725 TAAATTAGGTTATGGTTAGGGTTTTTATTTGAATTAGGTTAGG
131 TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAGTAGGTTAGG
*
82768 GTTAGGGTTTTTAATTAAATTAAGTTTTGGTTAGGGTTTTTATTTGAATTAGGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTTTGGTTAGGGTTTTTATTTGAATTAGGTTAGGTTAGGGT
* * *
82833 TTTTAATTAAGTTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTATGGTTAGGGTTTTTATT
66 TTTTAATTAAGTTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGCTTTTAAT
*
82898 TGAATTAGGTTAGGGTTAGGGTTTTTAATTAAAGTAGGTTAGG
131 TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAGTAGGTTAGG
* * ** *
82941 GTTAGGGTTTTTATTTGAATTAGGTTAGGGTTAGGGTTTTTAATT-AA--A--TTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTTTGGTTAGGGTTTTTATTTGAATTAGGTTAGGTTAGGGT
*
83001 TTTTAATTAAATTAGG
66 TTTTAATTAAGTTAGG
83017 GTTTTTATTA
Statistics
Matches: 230, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
168 27 0.12
170 1 0.00
172 2 0.01
173 200 0.87
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (173 bp):
GTTAGGGTTTTTAATTAAATTAGGTTTTGGTTAGGGTTTTTATTTGAATTAGGTTAGGTTAGGGT
TTTTAATTAAGTTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGCTTTTAAT
TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAGTAGGTTAGG
Found at i:83008 original size:18 final size:18
Alignment explanation
Indices: 82971--83023 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 18
82961 TAGGTTAGGG
82971 TTAGGGTTTTTAATTAAATTA
1 TTAGGGTTTTTAATT-AA--A
82992 GGTTAGGGTTTTTAATTAAA
1 --TTAGGGTTTTTAATTAAA
83012 TTAGGGTTTTTA
1 TTAGGGTTTTTA
83024 TTACATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.40
20 1 0.03
22 2 0.07
23 15 0.50
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (18 bp):
TTAGGGTTTTTAATTAAA
Found at i:83010 original size:23 final size:23
Alignment explanation
Indices: 82969--83016 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
82959 ATTAGGTTAG
82969 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
82992 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
83015 GG
1 GG
83017 GTTTTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:83128 original size:25 final size:25
Alignment explanation
Indices: 83094--83204 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
83084 TTTCTATGCC
*
83094 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
*
83119 TATTACATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * * **
83140 AATAAC-TCGAAA-AAATTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
83165 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
83190 TATTACATCAAATAA
1 TATTACATCAAATAA
83205 TAAATTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.03
21 11 0.17
22 2 0.03
23 2 0.03
24 4 0.06
25 34 0.52
26 11 0.17
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:83129 original size:71 final size:71
Alignment explanation
Indices: 83022--83206 Score: 316
Period size: 71 Copynumber: 2.6 Consensus size: 71
83012 TTAGGGTTTT
* *
83022 TATTACATCAAATAGAACTTCTATTTTATTATATCAAATAATATCAAAATAGCTAGAAAAAATTT
1 TATTACATCAAATA-AACTTCTATTTTATTACATCAAATAATATCAAAATAACTAGAAAAAATTT
83087 CTATGCC
65 CTATGCC
* *
83094 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTAGAAAAAATTTC
*
83159 TATGCG
66 TATGCC
83165 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
83207 AATTTAAATA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 94 0.88
72 13 0.12
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTAGAAAAAATTTC
TATGCC
Found at i:84302 original size:7 final size:7
Alignment explanation
Indices: 84292--84316 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
84282 TTATATACAT
84292 AATACTA
1 AATACTA
84299 AATACTA
1 AATACTA
84306 AATACTA
1 AATACTA
84313 AATA
1 AATA
84317 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:85236 original size:31 final size:31
Alignment explanation
Indices: 85201--85265 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
85191 GCCATTGATG
*
85201 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
*
85232 AAAATATAAAAAAAATTATAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
85263 AAA
1 AAA
85266 TAGATTTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAAATTAAAATTATTTTAAA
Found at i:85347 original size:22 final size:22
Alignment explanation
Indices: 85322--85372 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
85312 AGATATGGGT
85322 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
85344 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
85366 TTGAGAG
1 TTGAGAG
85373 GATTAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:92875 original size:21 final size:19
Alignment explanation
Indices: 92841--92879 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
92831 ATAATCCTCT
92841 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
92860 GGAAACATGGTCTTAGATAG
1 GGAAA-ATGG-CTTAGATAG
92880 GGAGGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:102819 original size:143 final size:143
Alignment explanation
Indices: 102561--102976 Score: 744
Period size: 143 Copynumber: 2.9 Consensus size: 143
102551 ATAAAATTGG
* * *
102561 AAAAAAGGAAGA-CTACGAAAGTATTCTATTTAAAAGTATATAGTCAGTCTTACTTAATTAGAAA
1 AAAAAAGGAAGACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTATTTAATTAG--A
* *
102625 AAAAAGGAAGAGTAGGAAAATGAGTGGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTA
64 AAAAAGGAAGAGTAGGTAAATGAATGGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTA
102690 AATAAAAGTGGGAAA
129 AATAAAAGTGGGAAA
102705 AAAAAAGGAAGACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTATTTAATTAGAAA
1 AAAAAAGGAAGACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTATTTAATTAGAAA
102770 AAAGGAAGAGTAGGTAAATGAATGGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAA
66 AAAGGAAGAGTAGGTAAATGAATGGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAA
102835 TAAAAGTGGGAAA
131 TAAAAGTGGGAAA
*
102848 AAAAAAGGAAGACCTAGGAAAGTATTTTATTTAAAAGTATATAGTGAGTCTTATTTAATTAGAAA
1 AAAAAAGGAAGACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTATTTAATTAGAAA
*
102913 AAAGGAAGAGTAGGTAAATGAATGGAGGACTTAATCAACTCACTTCCACTTTATCTAATACTAA
66 AAAGGAAGAGTAGGTAAATGAATGGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAA
102977 TCTTTATACT
Statistics
Matches: 264, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
143 206 0.78
144 12 0.05
145 46 0.17
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (143 bp):
AAAAAAGGAAGACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTATTTAATTAGAAA
AAAGGAAGAGTAGGTAAATGAATGGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAA
TAAAAGTGGGAAA
Found at i:103165 original size:22 final size:23
Alignment explanation
Indices: 103140--103182 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
103130 TCATCATATT
*
103140 ATTA-AATTGATATTTTAAAATA
1 ATTATAATTAATATTTTAAAATA
*
103162 ATTATAATTAATTTTTTAAAA
1 ATTATAATTAATATTTTAAAA
103183 ATTTTGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTATAATTAATATTTTAAAATA
Found at i:103596 original size:19 final size:20
Alignment explanation
Indices: 103574--103615 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
103564 CCCAGTACAC
103574 TTAAACAAACCCAAA-CCAA
1 TTAAACAAACCCAAACCCAA
**
103593 TTAAACCTACCCAAACCCAA
1 TTAAACAAACCCAAACCCAA
103613 TTA
1 TTA
103616 CAGACCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (20 bp):
TTAAACAAACCCAAACCCAA
Found at i:112198 original size:18 final size:18
Alignment explanation
Indices: 112168--112240 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 18
112158 CACAACTACT
*
112168 GTATATGTGAATAGTATC
1 GTATATGTAAATAGTATC
* *
112186 GTCTATGTAAATAGTGTC
1 GTATATGTAAATAGTATC
**
112204 GTGGATG-AACA-A-TATC
1 GTATATGTAA-ATAGTATC
*
112220 GTATACGTAAATAGTATC
1 GTATATGTAAATAGTATC
112238 GTA
1 GTA
112241 AACGGTCGTA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
16 8 0.19
17 6 0.14
18 28 0.67
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (18 bp):
GTATATGTAAATAGTATC
Found at i:113075 original size:15 final size:15
Alignment explanation
Indices: 113055--113084 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
113045 AAAAGTAATG
*
113055 TTTTTTTGTTTAAAA
1 TTTTTTTATTTAAAA
113070 TTTTTTTATTTAAAA
1 TTTTTTTATTTAAAA
113085 GTAAACTGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTTTATTTAAAA
Found at i:113446 original size:23 final size:23
Alignment explanation
Indices: 113418--113464 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
113408 CCCAAATTTC
*
113418 CTTAGTTTTCCCCAAGTCAGAAT
1 CTTAGTTTTCCCCAAGTCAAAAT
113441 CTTAGTTTTCCCCAAGTCAAAAT
1 CTTAGTTTTCCCCAAGTCAAAAT
113464 C
1 C
113465 AGATTTCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.34
Consensus pattern (23 bp):
CTTAGTTTTCCCCAAGTCAAAAT
Found at i:115902 original size:22 final size:22
Alignment explanation
Indices: 115877--115925 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
115867 CAGATGTGAA
*
115877 GAAAACGGCGGAAA-GAAATTGG
1 GAAAACGG-GGAAATGAAATCGG
**
115899 GAAATTGGGGAAATGAAATCGG
1 GAAAACGGGGAAATGAAATCGG
115921 GAAAA
1 GAAAA
115926 TCTGATTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.47, C:0.06, G:0.35, T:0.12
Consensus pattern (22 bp):
GAAAACGGGGAAATGAAATCGG
Found at i:115950 original size:36 final size:36
Alignment explanation
Indices: 115909--115983 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
115899 GAAATTGGGG
*
115909 AAATGAAATCG-GGAAAATCTGATTTTGACTTAGGGA
1 AAATGAAATCGAGG-AAATCTGATTCTGACTTAGGGA
*
115945 AAATGAAATCGAGGAAATCTGATTCTGACTTGGGGA
1 AAATGAAATCGAGGAAATCTGATTCTGACTTAGGGA
115981 AAA
1 AAA
115984 CTAAGGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.25
Consensus pattern (36 bp):
AAATGAAATCGAGGAAATCTGATTCTGACTTAGGGA
Found at i:116421 original size:22 final size:22
Alignment explanation
Indices: 116375--116421 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
116365 TTGTCATATT
116375 ATTAAATTAATATTTAAAAATA
1 ATTAAATTAATATTTAAAAATA
*
116397 ATTATAATTAATTTTTAAAAA-A
1 ATTA-AATTAATATTTAAAAATA
116419 ATT
1 ATT
116422 GGAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAAATTAATATTTAAAAATA
Found at i:116835 original size:19 final size:20
Alignment explanation
Indices: 116813--116854 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
116803 CCCAGTACAC
116813 TTAAACAAACCCAAA-CCAA
1 TTAAACAAACCCAAACCCAA
**
116832 TTAAACCTACCCAAACCCAA
1 TTAAACAAACCCAAACCCAA
116852 TTA
1 TTA
116855 CAGACCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (20 bp):
TTAAACAAACCCAAACCCAA
Found at i:117920 original size:3 final size:3
Alignment explanation
Indices: 117912--117991 Score: 114
Period size: 3 Copynumber: 27.7 Consensus size: 3
117902 CCTTTTTAGC
*
117912 ATT ATT ATT ATT ATT ATT ATT -TT -TT CTT CATT ATT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
117955 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
117992 AACATACATG
Statistics
Matches: 72, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
2 8 0.11
3 62 0.86
4 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:118834 original size:109 final size:109
Alignment explanation
Indices: 118638--118962 Score: 451
Period size: 109 Copynumber: 3.0 Consensus size: 109
118628 TCAAAAAAGG
* * *
118638 AAAATTTTTAAAATAAGGTAATATTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAATTTTTAAAATAAGGCAATATTTTGCGTTT-GGAAATTCGAGAAAACGTGCCCTAAGGTGTT
*
118703 AGGTGTCGATTTTTCTCGTTCAATCAAATGGCTAAATATCCTTTT
65 GGGTGTCGATTTTTCTCGTTCAATCAAATGGCTAAATATCCTTTT
118748 AAAATTTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGTTG
1 AAAATTTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGTTG
* *
118813 GGTGTCGATTTTTCTCATTCAATCAAATGACTAAATA-CCTTTTT
66 GGTGTCGATTTTTCTCGTTCAATCAAATGGCTAAATATCC-TTTT
* * * * * *
118857 AAAAATTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAACGTGTTG
1 AAAATTTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGTTG
* * * * *
118921 GGTTTCGA--TTTCTCGTTTAACCAAATTGCCAAATATCCTTTT
66 GGTGTCGATTTTTCTCGTTCAATCAAATGGCTAAATATCCTTTT
118963 GAATTTCAAT
Statistics
Matches: 194, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
106 25 0.13
107 2 0.01
108 27 0.14
109 108 0.56
110 32 0.16
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (109 bp):
AAAATTTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGTTG
GGTGTCGATTTTTCTCGTTCAATCAAATGGCTAAATATCCTTTT
Found at i:128537 original size:30 final size:31
Alignment explanation
Indices: 128503--128568 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
128493 CTGAGTTTAT
128503 TTGAATTTTTAGTTTAAT-T-CAAGGATTAAA
1 TTGAATTTTTA-TTTAATATACAAGGATTAAA
* *
128533 TTGAATTTTTATTTAATATATAAGGATTAAT
1 TTGAATTTTTATTTAATATACAAGGATTAAA
128564 TTGAA
1 TTGAA
128569 CAATAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 6 0.19
30 12 0.38
31 14 0.44
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (31 bp):
TTGAATTTTTATTTAATATACAAGGATTAAA
Found at i:128646 original size:39 final size:39
Alignment explanation
Indices: 128592--128667 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
128582 CTGTGTTAGC
128592 TTTTCCTCACTTATCTAATGACAATTAATGAGAAAGTAA
1 TTTTCCTCACTTATCTAATGACAATTAATGAGAAAGTAA
*
128631 TTTTCCTCACTTATCTAATGACAATTAATGGGAAAGT
1 TTTTCCTCACTTATCTAATGACAATTAATGAGAAAGT
128668 GATCAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (39 bp):
TTTTCCTCACTTATCTAATGACAATTAATGAGAAAGTAA
Found at i:136260 original size:13 final size:13
Alignment explanation
Indices: 136211--136269 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
136201 TATTTCAGAA
136211 GATG-AAAG-CTT
1 GATGAAAAGACTT
136222 GATTG-AAA-ACTT
1 GA-TGAAAAGACTT
* *
136234 GATTAAAAACACTT
1 GA-TGAAAAGACTT
136248 GATGAAAAGACTT
1 GATGAAAAGACTT
136261 GATGAAAAG
1 GATGAAAAG
136270 CTTAAAAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 2 0.05
12 12 0.29
13 21 0.51
14 6 0.15
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.25
Consensus pattern (13 bp):
GATGAAAAGACTT
Found at i:136279 original size:22 final size:23
Alignment explanation
Indices: 136252--136297 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
136242 ACACTTGATG
136252 AAAAG-ACTTGATG-AAAAGCTTA
1 AAAAGAACTTGATGCAAAA-CTTA
136274 AAAAGAACTTGATGCAAAACTTA
1 AAAAGAACTTGATGCAAAACTTA
136297 A
1 A
136298 TAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (23 bp):
AAAAGAACTTGATGCAAAACTTA
Found at i:145226 original size:33 final size:33
Alignment explanation
Indices: 145189--145254 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
145179 AAAGAAAGAG
*
145189 AAAGCAAAGCTAACAAATAAATATAGGAATGGT
1 AAAGCAAAGCTAACAAATAAATATAAGAATGGT
145222 AAAGCAAAGCTAACAAATAAATATAAGAATGGT
1 AAAGCAAAGCTAACAAATAAATATAAGAATGGT
145255 CACCGCAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.56, C:0.09, G:0.17, T:0.18
Consensus pattern (33 bp):
AAAGCAAAGCTAACAAATAAATATAAGAATGGT
Found at i:147362 original size:20 final size:19
Alignment explanation
Indices: 147321--147362 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
147311 GTAATCCTCC
147321 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
147340 GGAAACATGGTCTTAGATA-A
1 GGAAA-ATGG-CTTAGATAGA
147360 GGA
1 GGA
147363 GGCAAATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.40, C:0.07, G:0.31, T:0.21
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:150999 original size:17 final size:17
Alignment explanation
Indices: 150977--151011 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
150967 TATGTAATAA
150977 CATTTCAACAATTTTTT
1 CATTTCAACAATTTTTT
150994 CATTTCAACAATTTTTT
1 CATTTCAACAATTTTTT
151011 C
1 C
151012 CATGTCATTG
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:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (17 bp):
CATTTCAACAATTTTTT
Found at i:152198 original size:33 final size:33
Alignment explanation
Indices: 152156--152223 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
152146 TACACAACTT
*
152156 CTCTGCTAATTCTTGATCTCTTTTCTTCCTATC
1 CTCTGCTAATTCTTCATCTCTTTTCTTCCTATC
152189 CTCTGCTAATTCTTCATCTCTTTTCTTCCTATC
1 CTCTGCTAATTCTTCATCTCTTTTCTTCCTATC
152222 CT
1 CT
152224 TGACATTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.12, C:0.32, G:0.04, T:0.51
Consensus pattern (33 bp):
CTCTGCTAATTCTTCATCTCTTTTCTTCCTATC
Found at i:153206 original size:37 final size:37
Alignment explanation
Indices: 153141--153291 Score: 187
Period size: 37 Copynumber: 4.1 Consensus size: 37
153131 GCAACATTAA
* *
153141 TCATCAATAGAACGAGAATACGAACAAGAAAGGTATAT
1 TCAT-AATAGAATGAGAATACGAACAAGAAAGCTATAT
* * *
153179 TCATAATAGAATGAGAAAAC-AAGCAAGAAAGGTATGT
1 TCATAATAGAATGAGAATACGAA-CAAGAAAGCTATAT
* *
153216 TCAAAATAGAATGAGAATACTAACAAGAAAGCTATAT
1 TCATAATAGAATGAGAATACGAACAAGAAAGCTATAT
** *
153253 TCATAACCGAATGAGAATACAAACAAGAAAGCTATAT
1 TCATAATAGAATGAGAATACGAACAAGAAAGCTATAT
153290 TC
1 TC
153292 CTATGAATTA
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
36 2 0.02
37 92 0.92
38 6 0.06
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.20
Consensus pattern (37 bp):
TCATAATAGAATGAGAATACGAACAAGAAAGCTATAT
Found at i:153235 original size:74 final size:74
Alignment explanation
Indices: 153146--153283 Score: 213
Period size: 74 Copynumber: 1.9 Consensus size: 74
153136 ATTAATCATC
* * *
153146 AATAGAACGAGAATACGAACAAGAAAGGTATATTCATAATAGAATGAGAAAACAAGCAAGAAAGG
1 AATAGAACGAGAATACGAACAAGAAAGCTATATTCATAACAGAATGAGAAAACAAACAAGAAAGG
153211 TATGTTCAA
66 TATGTTCAA
* * * *
153220 AATAGAATGAGAATACTAACAAGAAAGCTATATTCATAACCGAATGAGAATACAAACAAGAAAG
1 AATAGAACGAGAATACGAACAAGAAAGCTATATTCATAACAGAATGAGAAAACAAACAAGAAAG
153284 CTATATTCCT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 57 1.00
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.17
Consensus pattern (74 bp):
AATAGAACGAGAATACGAACAAGAAAGCTATATTCATAACAGAATGAGAAAACAAACAAGAAAGG
TATGTTCAA
Found at i:153971 original size:18 final size:19
Alignment explanation
Indices: 153950--153993 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
153940 AATTCTATTA
*
153950 AAATTTGACAATGAC-GAG
1 AAATTTGACAAAGACAGAG
* *
153968 AAATTAGGCAAAGACAGAG
1 AAATTTGACAAAGACAGAG
153987 AAATTTG
1 AAATTTG
153994 GTTGTGAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.20
Consensus pattern (19 bp):
AAATTTGACAAAGACAGAG
Found at i:168332 original size:21 final size:19
Alignment explanation
Indices: 168298--168336 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
168288 ATAATCCTCC
168298 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
168317 GGAAACATGGTCTTAGATAG
1 GGAAA-ATGG-CTTAGATAG
168337 GGAGTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:172098 original size:20 final size:21
Alignment explanation
Indices: 172053--172100 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
172043 CCTTTAACTG
*
172053 CAAGATTCAGGGTTCAAGATT
1 CAAGGTTCAGGGTTCAAGATT
* *
172074 -TAGGTTCAGGGTTCGAG-TT
1 CAAGGTTCAGGGTTCAAGATT
172093 CAAGGTTC
1 CAAGGTTC
172101 GGAGTTTTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (21 bp):
CAAGGTTCAGGGTTCAAGATT
Found at i:173101 original size:17 final size:18
Alignment explanation
Indices: 173079--173112 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
173069 TTGTTTGTAA
173079 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
173096 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
173113 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:175658 original size:146 final size:145
Alignment explanation
Indices: 175390--175864 Score: 857
Period size: 145 Copynumber: 3.3 Consensus size: 145
175380 NNNNNNNNNN
*
175390 GGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAATAAAAGTGGAAAAAAAAAAAAGG
1 GGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAATAAAAGTGG--GAAAAAAAAAGG
175455 AAGA-CTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTACTTAATTAGAAAAAAAAGGA
64 AAGACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTACTTAATTAGAAAAAAAAGGA
175519 AGAGTAGGAAAATGAGT
129 AGAGTAGGAAAATGAGT
175536 GGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAATAAAAGTGGGAAAAAAAAAGGAA
1 GGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAATAAAAGTGGGAAAAAAAAAGGAA
175601 GACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTACTTAATTAGAAAAAAAAGGAAG
66 GACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTACTTAATTAGAAAAAAAAGGAAG
175666 AGTAGGAAAATGAGT
131 AGTAGGAAAATGAGT
175681 GGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAATAAAAGTGGGAAAAAAAAAGGAA
1 GGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAATAAAAGTGGGAAAAAAAAAGGAA
*
175746 GACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTATTTAATTAG--AAAAAAGGAAG
66 GACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTACTTAATTAGAAAAAAAAGGAAG
* *
175809 AGTAGGTAAATGAAT
131 AGTAGGAAAATGAGT
* *
175824 GGAGGACTTAATCAACTCACTTCCACTTTATCCAATACTAA
1 GGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAA
175865 TCTTTATACT
Statistics
Matches: 322, Mismatches: 6, Indels: 5
0.97 0.02 0.02
Matches are distributed among these distances:
143 63 0.20
144 15 0.05
145 193 0.60
146 51 0.16
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (145 bp):
GGAGGACTTAATCAACTCACTTCCACTTTATCTAACACTAAATAAAAGTGGGAAAAAAAAAGGAA
GACCTAGGAAAGTATTTTATTTAAAAGTATATAGTCAGTCTTACTTAATTAGAAAAAAAAGGAAG
AGTAGGAAAATGAGT
Found at i:180592 original size:39 final size:39
Alignment explanation
Indices: 180538--180616 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
180528 CTGTGTTAGC
*
180538 TTTTCCTCACTTATCTAATGACAATTAATGAGAAAGTGA
1 TTTTCCTAACTTATCTAATGACAATTAATGAGAAAGTGA
180577 TTTTCCTAACTTATCTAATGACAATTAATGAGAAAGTGA
1 TTTTCCTAACTTATCTAATGACAATTAATGAGAAAGTGA
180616 T
1 T
180617 AAAAATAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (39 bp):
TTTTCCTAACTTATCTAATGACAATTAATGAGAAAGTGA
Found at i:181614 original size:29 final size:29
Alignment explanation
Indices: 181582--181642 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
181572 TCATTATAAA
181582 TCTAGACTATATTAGTATACTCACTTAAT
1 TCTAGACTATATTAGTATACTCACTTAAT
181611 TCTAGACTATATTAGTATACTCACTTAAT
1 TCTAGACTATATTAGTATACTCACTTAAT
181640 TCT
1 TCT
181643 GTTACTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.43
Consensus pattern (29 bp):
TCTAGACTATATTAGTATACTCACTTAAT
Found at i:184644 original size:3 final size:3
Alignment explanation
Indices: 184636--184707 Score: 99
Period size: 3 Copynumber: 23.3 Consensus size: 3
184626 TTAAAAGAGT
* *
184636 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
184684 ATTA ATAA ATA ACA ATA ATA ATA A
1 A-TA AT-A ATA ATA ATA ATA ATA A
184708 CATATCATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:213495 original size:20 final size:21
Alignment explanation
Indices: 213472--213514 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
213462 TTCAAGATTT
213472 AGGTTCAGGG-TTTGAGTTCA
1 AGGTTCAGGGTTTTGAGTTCA
* *
213492 AGGTTCGGGGTTTTGGGTTCA
1 AGGTTCAGGGTTTTGAGTTCA
213513 AG
1 AG
213515 ATAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.35
Consensus pattern (21 bp):
AGGTTCAGGGTTTTGAGTTCA
Found at i:229908 original size:23 final size:23
Alignment explanation
Indices: 229882--229976 Score: 118
Period size: 23 Copynumber: 4.1 Consensus size: 23
229872 AAGTTAGAAG
229882 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
229905 AGTGAAAAAAACTTGAATATGAAT
1 AGTG-AAGAGACTTGAATATGAAA
* *
229929 AGTGAAGAGACTTGGAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
229952 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
229975 AG
1 AG
229977 ATACACACAT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 39 0.66
24 20 0.34
ACGTcount: A:0.47, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:234165 original size:23 final size:23
Alignment explanation
Indices: 234139--234233 Score: 136
Period size: 23 Copynumber: 4.1 Consensus size: 23
234129 TGAAAAGTTA
234139 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
*
234162 GAAGAGTGAAAAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
* *
234185 GAATAGTGAAGAGACTTGAAGAT
1 GAAGAGTGAAGAGACTTGAATAT
* * *
234208 GAAAAGTTAAGAGGCTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
234231 GAA
1 GAA
234234 AGGATACACA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.45, C:0.04, G:0.28, T:0.22
Consensus pattern (23 bp):
GAAGAGTGAAGAGACTTGAATAT
Found at i:238578 original size:190 final size:190
Alignment explanation
Indices: 238249--238622 Score: 581
Period size: 190 Copynumber: 2.0 Consensus size: 190
238239 AGCCACAGTA
*
238249 TTGGAGTATGATAGAAGGAACATCTTTGACTATGTAGAAATCTTCTCCTCATTTCTCCAATCTTT
1 TTGGAATATGATAGAAGGAACATCTTTGACTATGTAGAAATCTTCTCCTCATTTCTCCAATCTTT
* * * *
238314 CTTTGAATGCCTTTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGGAGCTCAATCCC
66 CTTTGAATGCATCTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGAACCTCAATCCC
* * *
238379 TCTGGAAGCATCTTCAAGCTTGGGCAATGCC-TGATATCCAATCGCTGAAGAGAACATGCG
131 TCTGGAAGCATCTTCAAGCCTAGGCAA-CCCTTGATATCCAATCGCTGAAGAGAACATGCG
* * *
238439 TTGGAATATGATAGAAGGAACATGTTTGACTTTGTAGAAATCTTCTCCTC-CTTCTTCCAATCTT
1 TTGGAATATGATAGAAGGAACATCTTTGACTATGTAGAAATCTTCTCCTCATTTC-TCCAATCTT
* *
238503 TTTTTGAATTCATCTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGAACCTCAATCC
65 TCTTTGAATGCATCTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGAACCTCAATCC
* *
238568 CTCTGGAAGCATCTTCAATCCTAGGCAACCCTTGATCTCCAATCGCTGAAGAGAA
130 CTCTGGAAGCATCTTCAAGCCTAGGCAACCCTTGATATCCAATCGCTGAAGAGAA
238623 GGCATGGCTC
Statistics
Matches: 167, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
189 5 0.03
190 162 0.97
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (190 bp):
TTGGAATATGATAGAAGGAACATCTTTGACTATGTAGAAATCTTCTCCTCATTTCTCCAATCTTT
CTTTGAATGCATCTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGAACCTCAATCCC
TCTGGAAGCATCTTCAAGCCTAGGCAACCCTTGATATCCAATCGCTGAAGAGAACATGCG
Found at i:240046 original size:21 final size:19
Alignment explanation
Indices: 240012--240052 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
240002 ATAATCCTCT
240012 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
240031 GGAAACATGGTCTTAGATAGA
1 GGAAA-ATGG-CTTAGATAGA
240052 G
1 G
240053 AGGCAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.39, C:0.07, G:0.32, T:0.22
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:252425 original size:7 final size:7
Alignment explanation
Indices: 252413--252439 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
252403 AATGTATCAT
252413 CCTAAAC
1 CCTAAAC
252420 CCTAAAC
1 CCTAAAC
252427 CCTAAAC
1 CCTAAAC
252434 CCTAAA
1 CCTAAA
252440 TGTATCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Found at i:252491 original size:6 final size:7
Alignment explanation
Indices: 252474--252502 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
252464 TATTTTTTTG
252474 AAAAATT
1 AAAAATT
252481 AAAAATT
1 AAAAATT
252488 AAAAATT
1 AAAAATT
252495 AAAAATT
1 AAAAATT
252502 A
1 A
252503 TTTTTAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAAATT
Found at i:252566 original size:19 final size:19
Alignment explanation
Indices: 252525--252560 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
252515 TCTTACTAAC
*
252525 ATTT-AGTTTTAAGTTTTA
1 ATTTAAGTTTTAACTTTTA
252543 ATTTAAGTTTTAACTTTT
1 ATTTAAGTTTTAACTTTT
252561 TTTTTACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (19 bp):
ATTTAAGTTTTAACTTTTA
Found at i:253432 original size:2 final size:2
Alignment explanation
Indices: 253427--253462 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
253417 CTCTCTCTTA
253427 AT AT AT 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
253463 TTAGTAGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:254244 original size:156 final size:154
Alignment explanation
Indices: 253682--254223 Score: 611
Period size: 156 Copynumber: 3.5 Consensus size: 154
253672 CAGCAACGGT
* * * *
253682 AAAAAAGGA-ATAAAATGTAAGTCTTTGTTTATGGTTTCGGCTTGCTTATGTAGCAAGAAAAGTG
1 AAAAAAGGAGA-AAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAGAAAAGTG
* *
253746 AATATAAACACATATAT-T-TAGT-AT-GGTTTCTTGAACTTGAATTGAACGAAGAATTTAAAAA
65 AATATAAACACATATATATATA-TAATAGGTTTCTTGAAATTGAATTGAATGAAGAATTT-AAAA
*
253807 ACAACAAAGAAACAAGAAAGCCATTT-
128 ACAACAAAGAAACAAGAAAACCATTTA
* * * * **
253833 AAAAAAGGAG-AAAATGTATGCCTTTATTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAACG
1 AAAAAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGC-AAGAAAAGTG
* *
253897 AATATAAATATATATATATATATAATATGGTTTCTT-AAACTTGAATTGAATGAAGAATTTTAAA
65 AATATAAACACATATATATATATAATA-GGTTTCTTGAAA-TTGAATTGAATGAAGAA-TTTAAA
* *
253961 AACAATAAAGAATCAAGAAAACCA-TTA
127 AACAACAAAGAAACAAGAAAACCATTTA
* * ** * * * *
253988 AAAAAAAGAAAAAAAAACATGCTTTTGTTTATGGTTTTGGCTTGCTTGTGTAGTAAGAAAAGTAA
1 AAAAAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAGAAAAGTGA
* *
254053 ATATAAACATATATATATATTTAAATATGGTTTCTTGAAATTGAATTGAATGAAGAATTTAAAAA
66 ATATAAACACATATATATATAT-AATA-GGTTTCTTGAAATTGAATTGAATGAAGAATTTAAAAA
*
254118 GCGGA-AAAGAAACAAGAAAACCATTTA
129 -C-AACAAAGAAACAAGAAAACCATTTA
* * * *
254145 AAAAAAGGCGAAAAAAGTATTCCTTTGTTTATGGTTTCGGATTGCTTGTGGAGCAA-AAAAGTGA
1 AAAAAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAGAAAAGTGA
254209 ATATAAACAGCATAT
66 ATATAAACA-CATAT
254224 GTGATTCCTC
Statistics
Matches: 328, Mismatches: 46, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
150 38 0.12
151 31 0.09
152 2 0.01
153 4 0.01
154 4 0.01
155 91 0.28
156 102 0.31
157 56 0.17
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.31
Consensus pattern (154 bp):
AAAAAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAGAAAAGTGA
ATATAAACACATATATATATATAATAGGTTTCTTGAAATTGAATTGAATGAAGAATTTAAAAACA
ACAAAGAAACAAGAAAACCATTTA
Found at i:265986 original size:21 final size:21
Alignment explanation
Indices: 265943--265988 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
265933 TAATTTTTTT
* *
265943 ACCCTGAATCCAGAATCTTAA
1 ACCCTGAATCCAGAAACTAAA
265964 ACCCTGAATCCA-AAACATAAA
1 ACCCTGAATCCAGAAAC-TAAA
265985 ACCC
1 ACCC
265989 CAAACTCGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.33, G:0.07, T:0.17
Consensus pattern (21 bp):
ACCCTGAATCCAGAAACTAAA
Found at i:266090 original size:20 final size:19
Alignment explanation
Indices: 266052--266090 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
266042 ACCCTTGAAC
*
266052 TTTAAACTTGAACCTCGAA
1 TTTAAACTTAAACCTCGAA
*
266071 TTTAAACTTTAAATCTCGAA
1 TTTAAAC-TTAAACCTCGAA
266091 ACCAAACCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (19 bp):
TTTAAACTTAAACCTCGAA
Found at i:266351 original size:17 final size:18
Alignment explanation
Indices: 266329--266362 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
266319 TTGTTTGTAA
266329 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
266346 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
266363 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:268877 original size:21 final size:21
Alignment explanation
Indices: 268853--268905 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
268843 CAGTAAATTA
268853 CGTCCACGTCAGCACTATTTG
1 CGTCCACGTCAGCACTATTTG
268874 CGTCCACGTCAGCACTATTTG
1 CGTCCACGTCAGCACTATTTG
*
268895 TGTCCACGTCA
1 CGTCCACGTCA
268906 ACATAGCGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.34, G:0.19, T:0.28
Consensus pattern (21 bp):
CGTCCACGTCAGCACTATTTG
Found at i:269451 original size:58 final size:58
Alignment explanation
Indices: 269361--269473 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 58
269351 GTTCCTTGAG
*
269361 GGAATTCTATTGAATCTTTTATCGTCGCAAGTTAAGCTGACTTAGGCGTTTTTGGAGT
1 GGAATTCTATTGAATCCTTTATCGTCGCAAGTTAAGCTGACTTAGGCGTTTTTGGAGT
* *
269419 GGAATTCTGTTGAATCCTTTATCGTCGCAAGTTAGGCTGACTTAGGCGTTTTTGG
1 GGAATTCTATTGAATCCTTTATCGTCGCAAGTTAAGCTGACTTAGGCGTTTTTGG
269474 GAGCAAAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (58 bp):
GGAATTCTATTGAATCCTTTATCGTCGCAAGTTAAGCTGACTTAGGCGTTTTTGGAGT
Found at i:275214 original size:14 final size:14
Alignment explanation
Indices: 275195--275222 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
275185 ATGATAGAAA
275195 ATCCTGTTAAAATC
1 ATCCTGTTAAAATC
275209 ATCCTGTTAAAATC
1 ATCCTGTTAAAATC
275223 GTCGATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
ATCCTGTTAAAATC
Found at i:278346 original size:31 final size:31
Alignment explanation
Indices: 278276--278352 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
278266 AGCAGGCAAT
278276 TTACA-GGGATCAAAATGAGATTTTCACTATA
1 TTACAGGGGA-CAAAATGAGATTTTCACTATA
*
278307 TTACAGGGGCCAAAATGAGATTTTTC-CTATA
1 TTACAGGGGACAAAATGAGA-TTTTCACTATA
278338 TTACAGGGGACAAAA
1 TTACAGGGGACAAAA
278353 CAAGTATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 34 0.81
32 8 0.19
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (31 bp):
TTACAGGGGACAAAATGAGATTTTCACTATA
Found at i:285431 original size:21 final size:19
Alignment explanation
Indices: 285397--285435 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
285387 ATAATCCTCC
285397 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
285416 GGAAACATGGTCTTAGATAG
1 GGAAA-ATGG-CTTAGATAG
285436 GGAGGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:289276 original size:17 final size:18
Alignment explanation
Indices: 289254--289287 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
289244 TTGTTTATAA
289254 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
289271 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
289288 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:293320 original size:20 final size:22
Alignment explanation
Indices: 293270--293320 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
293260 TAGCTAGACC
*
293270 AAGTCAATTTTTTATTTAAAAA
1 AAGTCAATTTTTTATATAAAAA
*
293292 AAGTC-ATTTTTTA-ATAATAA
1 AAGTCAATTTTTTATATAAAAA
293312 AAG-CAATTT
1 AAGTCAATTT
293321 CTATGAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 12 0.46
21 8 0.31
22 5 0.19
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (22 bp):
AAGTCAATTTTTTATATAAAAA
Found at i:296243 original size:3 final size:3
Alignment explanation
Indices: 296237--296288 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
296227 TATCATCATC
296237 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
296285 ATT A
1 ATT A
296289 CTATACATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:308344 original size:44 final size:44
Alignment explanation
Indices: 308286--308440 Score: 168
Period size: 44 Copynumber: 3.5 Consensus size: 44
308276 GAGTAGGTTG
* *
308286 AAAGATAACGGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
1 AAAGATAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * * * * * *
308330 AGAGATATCAGATCTTGCCTTC-TCATACTGGTGGCGAAGCAGATC
1 AAAGATAGCAGATCTTGTCTTCAT-GTACTGG-CGTGAAGTAGATC
*
308375 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
1 AAAGATAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * *
308419 AAAGATAGTAGGTCCTGTCTTC
1 AAAGATAGCAGATCTTGTCTTC
308441 CTATATCGGT
Statistics
Matches: 88, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
43 1 0.01
44 52 0.59
45 34 0.39
46 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
AAAGATAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
Found at i:308404 original size:45 final size:44
Alignment explanation
Indices: 308296--308423 Score: 159
Period size: 45 Copynumber: 2.9 Consensus size: 44
308286 AAAGATAACG
* * *
308296 GATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATATCA
1 GATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCA
* * * * *
308340 GATCTTGCCTTC-TCATACTGGTGGCGAAGCAGATCAAAGAAAGCA
1 GATCTTGTCTTCAT-GTACTGG-CGTGAAGTAGATCAAAGAAAGCA
308385 GATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
1 GATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA
308424 TAGTAGGTCC
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
43 1 0.01
44 32 0.47
45 34 0.50
46 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
GATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCA
Found at i:308654 original size:89 final size:88
Alignment explanation
Indices: 308503--308686 Score: 228
Period size: 89 Copynumber: 2.1 Consensus size: 88
308493 GTGGTGGAGT
* * *
308503 AGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGACAACAGATCTTATCTTCCCATACTG
*
308568 ATGGCAAAGTAGA-TCGAAGAAAAC
66 ACGGC-AAGTAGAGT-GAAGAAAAC
* * * *
308592 AGATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATCAAATACAACATATTTTATCTTCCCATACT
1 AGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATCAAAGACAACAGATCTTATCTTCCCATACT
* **
308656 GGCGGCAAGTAGAGTGAAGATTAC
65 GACGGCAAGTAGAGTGAAGAAAAC
308680 AGATCTT
1 AGATCTT
308687 ATCTCCCTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
88 22 0.27
89 60 0.73
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (88 bp):
AGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGACAACAGATCTTATCTTCCCATACTG
ACGGCAAGTAGAGTGAAGAAAAC
Found at i:308688 original size:208 final size:208
Alignment explanation
Indices: 308296--308693 Score: 507
Period size: 208 Copynumber: 1.9 Consensus size: 208
308286 AAAGATAACG
* * * * *
308296 GATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATATCAGATCTTGCCTTCTCATACTGG
1 GATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGA
* * *
308361 TGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
66 TGGCAAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGACA
** * * * * * * *
308426 GTAGGTCCTGTCTTCCTATATCGGTAGCGAAGTGGATCGAATATACATATCTTATCTCCCCATAC
131 ACAGATCCTATCTTCCCATATCGGCAGCGAAGTAGATCGAAGATACAGATCTTATCTCCCCATAC
308491 TGGTGGTGGAGTA
196 TGGTGGTGGAGTA
*
308504 GATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGA
1 GATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGA
* * *
308569 TGGCAAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATCAAATAC
66 TGGCAAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAAGAC
* ** *
308633 AACATATTTTATCTTCCCATA-CTGGCGGC-AAGTAGAGT-GAAGATTACAGATCTTATCTCCC
130 AACAGATCCTATCTTCCCATATC-GGCAGCGAAGTAGA-TCGAAGA-TACAGATCTTATCTCCC
308694 TAAGCAGTAG
Statistics
Matches: 161, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
207 12 0.07
208 149 0.93
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (208 bp):
GATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGA
TGGCAAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGACA
ACAGATCCTATCTTCCCATATCGGCAGCGAAGTAGATCGAAGATACAGATCTTATCTCCCCATAC
TGGTGGTGGAGTA
Found at i:309630 original size:77 final size:77
Alignment explanation
Indices: 309523--309674 Score: 263
Period size: 77 Copynumber: 2.0 Consensus size: 77
309513 AACCCTAGCT
309523 GCATCTGCCCCAGCGCCACAACAGCACCCACGCCGCGCCCAACGCCCGATCGCCGCACGTTTCGG
1 GCATCTGCCCCAGCGCCACAACAGCACCCACGCCGCGCCCAACGCCCGATCGCCGCACGTTTCGG
309588 CCTCCACGCGTC
66 CCTCCACGCGTC
*
309600 GCATCTGCCTCACAGCGCCAC-A-AGCCCCCACGCCGCGCCCAACGCCCGATCGCCGCACGTTTC
1 GCATCTGCC-C-CAGCGCCACAACAGCACCCACGCCGCGCCCAACGCCCGATCGCCGCACGTTTC
309663 GGCCTCCACGCG
64 GGCCTCCACGCG
309675 CGCCAAACTC
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
77 61 0.85
78 2 0.03
79 9 0.12
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (77 bp):
GCATCTGCCCCAGCGCCACAACAGCACCCACGCCGCGCCCAACGCCCGATCGCCGCACGTTTCGG
CCTCCACGCGTC
Found at i:310548 original size:3 final size:3
Alignment explanation
Indices: 310537--310575 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
310527 TTTTAAATAT
*
310537 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
310576 CTATACATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:316126 original size:7 final size:7
Alignment explanation
Indices: 316114--316143 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
316104 TTCATATTGC
316114 AGCTTAG
1 AGCTTAG
316121 AGCTTAG
1 AGCTTAG
316128 AGCTTAG
1 AGCTTAG
316135 AGCTTAG
1 AGCTTAG
316142 AG
1 AG
316144 GGATAATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (7 bp):
AGCTTAG
Found at i:316537 original size:18 final size:18
Alignment explanation
Indices: 316516--316566 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
316506 ATGCCTCTAA
316516 AATAATAACAAAATTA-AC
1 AATAA-AACAAAATTAGAC
316534 AATAAAACAAAATTAGAC
1 AATAAAACAAAATTAGAC
*
316552 AATAACAACATAATT
1 AATAA-AACAAAATT
316567 GTGATAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 10 0.33
18 12 0.40
19 8 0.27
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAAAACAAAATTAGAC
Found at i:329160 original size:11 final size:11
Alignment explanation
Indices: 329140--329169 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
329130 TTTAAGTTTG
329140 ATTAAGGGTTA
1 ATTAAGGGTTA
*
329151 ATTTAGGGTTA
1 ATTAAGGGTTA
329162 ATTAAGGG
1 ATTAAGGG
329170 AAAAACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (11 bp):
ATTAAGGGTTA
Found at i:329558 original size:73 final size:74
Alignment explanation
Indices: 329469--329617 Score: 291
Period size: 73 Copynumber: 2.0 Consensus size: 74
329459 TAAAAAATTT
329469 AAAACTTTAATTAATTTAATTAATGATAATACAATTCAAATAATAATCGAATTTTTGTTTCAAAA
1 AAAACTTTAATTAATTTAATTAATGATAATACAATTCAAATAATAATCGAATTTTTGTTTCAAAA
329534 TCACTCTAA
66 TCACTCTAA
329543 AAAACTTTAA-TAATTTAATTAATGATAATACAATTCAAATAATAATCGAATTTTTGTTTCAAAA
1 AAAACTTTAATTAATTTAATTAATGATAATACAATTCAAATAATAATCGAATTTTTGTTTCAAAA
329607 TCACTCTAA
66 TCACTCTAA
329616 AA
1 AA
329618 CATTTTCAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 65 0.87
74 10 0.13
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (74 bp):
AAAACTTTAATTAATTTAATTAATGATAATACAATTCAAATAATAATCGAATTTTTGTTTCAAAA
TCACTCTAA
Found at i:329907 original size:31 final size:30
Alignment explanation
Indices: 329872--329946 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
329862 ATTTTTCTTT
*
329872 AAATTTTAATTAGATTCTC-TCAAAATTTTGA
1 AAATTTTAATTAGA-TCTCATAAAAATTTT-A
*
329903 AAATTTTCATTA-ATCTCATAAAAATTTTA
1 AAATTTTAATTAGATCTCATAAAAATTTTA
329932 AAATTTTTAATTAGA
1 AAA-TTTTAATTAGA
329947 CTCCAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 8 0.21
30 18 0.47
31 12 0.32
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (30 bp):
AAATTTTAATTAGATCTCATAAAAATTTTA
Found at i:339293 original size:19 final size:19
Alignment explanation
Indices: 339269--339319 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
339259 AGACATTTAT
339269 ATTAAAAAAATAATGAAAA
1 ATTAAAAAAATAATGAAAA
339288 ATT--AAAAATAA--AAAA
1 ATTAAAAAAATAATGAAAA
*
339303 AATAAAAAAA-AATGAAA
1 ATTAAAAAAATAATGAAA
339320 CGACTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
15 6 0.22
16 2 0.07
17 13 0.48
18 3 0.11
19 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (19 bp):
ATTAAAAAAATAATGAAAA
Found at i:341469 original size:20 final size:21
Alignment explanation
Indices: 341423--341466 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
341413 TTAAAGGGTC
*
341423 TTTTA-TAAAATTTTATAATT
1 TTTTATTAAAATTTAATAATT
341443 TTTTATTAAAATTTAATAATT
1 TTTTATTAAAATTTAATAATT
341464 TTT
1 TTT
341467 ATTGATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATTAAAATTTAATAATT
Found at i:342215 original size:31 final size:31
Alignment explanation
Indices: 342179--342240 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
342169 AGCCCTAGTA
*
342179 TTTCGA-AACAAAAATAAAAATCGAAAAATAG
1 TTTCGATAA-AAAAAGAAAAATCGAAAAATAG
* *
342210 TTTCGATAAAAAAAGAAAATTGGAAAAATAG
1 TTTCGATAAAAAAAGAAAAATCGAAAAATAG
342241 AAAATCCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.21
Consensus pattern (31 bp):
TTTCGATAAAAAAAGAAAAATCGAAAAATAG
Found at i:348352 original size:34 final size:34
Alignment explanation
Indices: 348309--348379 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
348299 TATTAATGTG
348309 ATTGAATTTCTTTAAAAAAAAAACGAAACACGTA
1 ATTGAATTTCTTTAAAAAAAAAACGAAACACGTA
348343 ATTGAATTTCTTTAAAAAAAAAACGAAACACGTA
1 ATTGAATTTCTTTAAAAAAAAAACGAAACACGTA
348377 ATT
1 ATT
348380 AAATATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.28
Consensus pattern (34 bp):
ATTGAATTTCTTTAAAAAAAAAACGAAACACGTA
Found at i:360752 original size:5 final size:5
Alignment explanation
Indices: 360742--360766 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
360732 TTCGTAAAGG
360742 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
360767 TGCTCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:363289 original size:15 final size:15
Alignment explanation
Indices: 363269--363298 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
363259 AAAATTCAAC
363269 TCTTTTTAAAAAAAT
1 TCTTTTTAAAAAAAT
*
363284 TCTTTTTTAAAAAAT
1 TCTTTTTAAAAAAAT
363299 AATTACCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TCTTTTTAAAAAAAT
Found at i:363347 original size:26 final size:27
Alignment explanation
Indices: 363292--363353 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
363282 ATTCTTTTTT
**
363292 AAAAA-ATAATTACCAAATTTAAC-TT
1 AAAAATATAATTACCAAATTTAACAAA
*
363317 TAAAATATAATTACCAAA-TTAACAAAA
1 AAAAATATAATTACCAAATTTAAC-AAA
363344 AAAAATATAA
1 AAAAATATAA
363354 ATATTCATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 9 0.30
26 12 0.40
27 9 0.30
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAATATAATTACCAAATTTAACAAA
Found at i:368188 original size:21 final size:20
Alignment explanation
Indices: 368142--368196 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
368132 AAAATTTAAA
* *
368142 AATA-TTTTTTTATAATTTT
1 AATACTTTTTTAATAATGTT
*
368161 TATACTTTTTTAATAATGTT
1 AATACTTTTTTAATAATGTT
*
368181 AATAACTTATTTAATA
1 AAT-ACTTTTTTAATA
368197 TTTTTTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 3 0.10
20 15 0.52
21 11 0.38
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
AATACTTTTTTAATAATGTT
Found at i:368627 original size:31 final size:31
Alignment explanation
Indices: 368592--368650 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
368582 CAAAACAGTT
368592 ACTGAACTA-TTCAAAATTTTTCATTTAAGTC
1 ACTGAACTATTTCAAAATTTTT-ATTTAAGTC
* *
368623 ACTGAACTATTTGAAAGTTTTTATTTAA
1 ACTGAACTATTTCAAAATTTTTATTTAA
368651 ATCATTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (31 bp):
ACTGAACTATTTCAAAATTTTTATTTAAGTC
Found at i:373502 original size:17 final size:16
Alignment explanation
Indices: 373466--373499 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
373456 AATATTCATC
*
373466 TTATAAAAAATAAATA
1 TTATAAAAAATAAAAA
*
373482 TTATTAAAAATAAAAA
1 TTATAAAAAATAAAAA
373498 TT
1 TT
373500 TATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTATAAAAAATAAAAA
Found at i:377243 original size:19 final size:19
Alignment explanation
Indices: 377201--377244 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
377191 TTAAATTTTT
377201 CAAAAATTATTAAAAAATA
1 CAAAAATTATTAAAAAATA
* *
377220 GAAAAA-TATTATAAAATTA
1 CAAAAATTATTA-AAAAATA
377239 CAAAAA
1 CAAAAA
377245 CAATATAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (19 bp):
CAAAAATTATTAAAAAATA
Done.