Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009267.1 Hibiscus syriacus cultivar Beakdansim tig00112925_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1725308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:829830 original size:14 final size:14
Alignment explanation
Indices: 829813--829849 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
829803 AAAAAATGAA
829813 AAAATAAAAAAAAG
1 AAAATAAAAAAAAG
829827 AAAA-AAGAAAAAAG
1 AAAATAA-AAAAAAG
829841 -AAATAAAAA
1 AAAATAAAAA
829850 TGAAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.86, C:0.00, G:0.08, T:0.05
Consensus pattern (14 bp):
AAAATAAAAAAAAG
Found at i:829838 original size:55 final size:55
Alignment explanation
Indices: 829735--829838 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
829725 AAGAAGAAAG
* * * *
829735 AATGAATGAATGAAAAAAATGAAAAAGTGAAAAAGAAAAATAACAAAAATGACTA
1 AATGAATAAATGAAAAAAATGAAAAAATGAAAAAAAAAAAAAACAAAAATGACTA
*
829790 AATGAATAAATGAAAAAAATGAAAAAAT-AAAAAAAAGAAAAAAGAAAAA
1 AATGAATAAATGAAAAAAATGAAAAAATGAAAAAAAA-AAAAAACAAAAA
829839 AGAAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 7 0.16
55 36 0.84
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (55 bp):
AATGAATAAATGAAAAAAATGAAAAAATGAAAAAAAAAAAAAACAAAAATGACTA
Found at i:829848 original size:16 final size:15
Alignment explanation
Indices: 829764--829867 Score: 61
Period size: 16 Copynumber: 6.7 Consensus size: 15
829754 TGAAAAAGTG
*
829764 AAAAAGAAAAATAACA
1 AAAAAGAAAAA-AAGA
* ** *
829780 AAAATGACTAAATGA
1 AAAAAGAAAAAAAGA
*
829795 ATAAATGAAAAAAATGA
1 A-AAAAGAAAAAAA-GA
*
829812 AAAAATAAAAAAAAGA
1 AAAAA-GAAAAAAAGA
829828 AAAAAG-AAAAAAGA
1 AAAAAGAAAAAAAGA
*
829842 AATAAA-AATGAAAAG-
1 AA-AAAGAA-AAAAAGA
829857 AAAAAGAAAAA
1 AAAAAGAAAAA
829868 GGAGGGTTCG
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
14 15 0.22
15 11 0.16
16 32 0.47
17 10 0.15
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.10
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:830930 original size:105 final size:105
Alignment explanation
Indices: 830797--831098 Score: 478
Period size: 105 Copynumber: 2.9 Consensus size: 105
830787 AACAACTATG
*
830797 ATCCACCGCAGAATGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTA
1 ATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTA
*
830862 AAGGAGAAAGTTCATAATGAGAAGAACATGTTCCTTTCAA
66 AAGGAGAAAGTTCATAATGAGAAGAACATGCTCCTTTCAA
* *
830902 ATCCACCGCAGAAGGAGGTGAACTAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTTA
1 ATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTA
* * *
830967 AAGGAGAAATTTCTTAATGAGAAGAACTTGCTCCTTTCAA
66 AAGGAGAAAGTTCATAATGAGAAGAACATGCTCCTTTCAA
* * * * *
831007 ATCCATCGCATAAGGACGTGAACCAACATTTCTAGAAGAGTTCATAATGAGAAGAACTCGCCTTA
1 ATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTA
* *
831072 GAGGAGGAAGTTCATAATGAGAAGAAC
66 AAGGAGAAAGTTCATAATGAGAAGAAC
831099 TTACTCAATT
Statistics
Matches: 179, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 179 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (105 bp):
ATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTA
AAGGAGAAAGTTCATAATGAGAAGAACATGCTCCTTTCAA
Found at i:835356 original size:19 final size:20
Alignment explanation
Indices: 835328--835367 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
835318 TTAATAATAA
**
835328 TTTTAGAACAAGTTTAATCT
1 TTTTAGAACAAACTTAATCT
835348 TTTTA-AACAAACTTAATCT
1 TTTTAGAACAAACTTAATCT
835367 T
1 T
835368 CAACATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTAGAACAAACTTAATCT
Found at i:842405 original size:21 final size:22
Alignment explanation
Indices: 842379--842423 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
842369 GAATGCAAAT
842379 AGGGAATC-AGTACCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
* *
842400 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
842422 AG
1 AG
842424 TACTGCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAATCGAGTACCCTGCTAC
Found at i:843046 original size:23 final size:23
Alignment explanation
Indices: 842980--843065 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 23
842970 TCATATAAAT
842980 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
843003 TTTGTC-CCGAA-TGGCCGCGTAGAGA
1 -TTG-CACCGAAGT-GCCACGTAGA-A
843028 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
843050 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
843066 TATAATATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
22 2 0.04
23 31 0.58
24 18 0.34
25 2 0.04
ACGTcount: A:0.26, C:0.27, G:0.28, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:850096 original size:56 final size:55
Alignment explanation
Indices: 850010--850158 Score: 192
Period size: 56 Copynumber: 2.7 Consensus size: 55
850000 TGCCTTCAAA
*
850010 TGTGATGACAATAAACTTTGGTTGAAATAATAACCAAATTTTTATTTAGCTGTATG
1 TGTGATGACAATAAA-TTTGGTTGAAATAATAACCAAATTTTTATTTAACTGTATG
* * * *
850066 TGTGATGACAATAAATTATGGTT-AAGATAATAATCAGATTTTTATTTAATTGTGTG
1 TGTGATGACAATAAATT-TGGTTGAA-ATAATAACCAAATTTTTATTTAACTGTATG
* *
850122 TGTGATGGCAATAAACTGTGGTTGAAATAATAACCAA
1 TGTGATGACAATAAA-TTTGGTTGAAATAATAACCAA
850159 CAACAAACAT
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
55 4 0.05
56 73 0.91
57 3 0.04
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (55 bp):
TGTGATGACAATAAATTTGGTTGAAATAATAACCAAATTTTTATTTAACTGTATG
Found at i:853593 original size:34 final size:32
Alignment explanation
Indices: 853540--853609 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
853530 CCTTACAAAC
*
853540 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
853572 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
853606 TCCC
1 TCCC
853610 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:853991 original size:19 final size:20
Alignment explanation
Indices: 853956--854015 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
853946 TCGTTAGACA
853956 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
* *
853976 GGGGGAATC-GTTCCCCCTA
1 GGGGGAATCGGTACCCCCTG
*
853995 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
854015 G
1 G
854016 ACAATCTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.15, C:0.30, G:0.37, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:856064 original size:15 final size:15
Alignment explanation
Indices: 856036--856069 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
856026 CCGTAGGACC
856036 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
* *
856051 ACTACGTCCTGAAGG
1 ACTACATCCCGAAGG
856066 ACTA
1 ACTA
856070 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:856660 original size:64 final size:64
Alignment explanation
Indices: 856591--856747 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
856581 TAATGAAGGT
* **
856591 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAG
856654 A
64 A
* * * * * *
856655 ATGCATCGATGCA-TGCCTTATGGATCAATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
* *
856719 GTGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
856748 ACACCTTCAA
Statistics
Matches: 74, Mismatches: 15, Indels: 8
0.76 0.15 0.08
Matches are distributed among these distances:
63 1 0.01
64 64 0.86
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:856815 original size:21 final size:21
Alignment explanation
Indices: 856789--856858 Score: 140
Period size: 21 Copynumber: 3.3 Consensus size: 21
856779 TGATGAATCA
856789 ATGCACTATGAATATGCATCG
1 ATGCACTATGAATATGCATCG
856810 ATGCACTATGAATATGCATCG
1 ATGCACTATGAATATGCATCG
856831 ATGCACTATGAATATGCATCG
1 ATGCACTATGAATATGCATCG
856852 ATGCACT
1 ATGCACT
856859 CTGCCCAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (21 bp):
ATGCACTATGAATATGCATCG
Found at i:857682 original size:19 final size:20
Alignment explanation
Indices: 857639--857686 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
857629 TCTACATCCT
*
857639 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
857659 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
857678 TTTTCAAAA
1 TTTTCAAAA
857687 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:858987 original size:20 final size:20
Alignment explanation
Indices: 858962--859018 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
858952 CCGTTAGACA
858962 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
* *
858982 GGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCGGTACCCCCT
859002 GGGGGGAATCGGTACCC
1 GGGGGGAATCGGTACCC
859019 GGGGTGAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.28, G:0.40, T:0.18
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:859039 original size:37 final size:39
Alignment explanation
Indices: 858962--859040 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 39
858952 CCGTTAGACA
*
858962 GGGGGGAATCGGTACCCCCTGGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCGGTA-CCCCTGGGGGGAATCTGTACCCCCT
* *
859002 GGGGGGAATCGGTA-CCC-GGGGTGAATCTGTACGCCCT
1 GGGGGGAATCGGTACCCCTGGGGGGAATCTGTACCCCCT
859039 GG
1 GG
859041 ACAATCTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 19 0.53
38 3 0.08
40 14 0.39
ACGTcount: A:0.14, C:0.27, G:0.41, T:0.19
Consensus pattern (39 bp):
GGGGGGAATCGGTACCCCTGGGGGGAATCTGTACCCCCT
Found at i:862328 original size:47 final size:47
Alignment explanation
Indices: 862235--862375 Score: 160
Period size: 47 Copynumber: 3.0 Consensus size: 47
862225 TTTCAAAATC
* * * *
862235 ATGCATACTTCATAGATACATCATCTAC-ATAGAGGCGTATGCAAAAA
1 ATGCATACTTCATAGGTGCATCATCT-CTGTAGAGGCATATGCAAAAA
* * *
862282 ATGCATACTTCATAGGTGCATTATCTCTGTAAAGGCATATGTAAAAAA
1 ATGCATACTTCATAGGTGCATCATCTCTGTAGAGGCATATG-CAAAAA
* *
862330 ATGCATACCTCAT-GGATGAATCATCTCTGTAGAGGCATATGCAAAA
1 ATGCATACTTCATAGG-TGCATCATCTCTGTAGAGGCATATGCAAAA
862376 TGCATGCTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
46 1 0.01
47 39 0.49
48 39 0.49
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (47 bp):
ATGCATACTTCATAGGTGCATCATCTCTGTAGAGGCATATGCAAAAA
Found at i:862356 original size:48 final size:48
Alignment explanation
Indices: 862267--862375 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
862257 ATCTACATAG
* * * *
862267 AGGCGTATGC-AAAAAATGCATACTTCATAGGTGCATTATCTCTGTAA
1 AGGCATATGCAAAAAAATGCATACCTCATAGGTGAATCATCTCTGTAA
* *
862314 AGGCATATGTAAAAAAATGCATACCTCAT-GGATGAATCATCTCTGTAG
1 AGGCATATGCAAAAAAATGCATACCTCATAGG-TGAATCATCTCTGTAA
862362 AGGCATATGCAAAA
1 AGGCATATGCAAAA
862376 TGCATGCTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 10 0.19
48 43 0.81
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (48 bp):
AGGCATATGCAAAAAAATGCATACCTCATAGGTGAATCATCTCTGTAA
Found at i:867139 original size:29 final size:29
Alignment explanation
Indices: 867078--867133 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
867068 TATTTATTTC
*
867078 TAACTACTAACTTTTATTTTATTGCATAT
1 TAACTACTAACTTTTATTTTATTACATAT
*
867107 TAACTACTGACTTTTATTTTATTACAT
1 TAACTACTAACTTTTATTTTATTACAT
867134 TATAACCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (29 bp):
TAACTACTAACTTTTATTTTATTACATAT
Found at i:867259 original size:127 final size:127
Alignment explanation
Indices: 867106--867345 Score: 399
Period size: 127 Copynumber: 1.9 Consensus size: 127
867096 TTATTGCATA
* * *
867106 TTAACTACTGACTTTTATTTTATTACATTATAACCATTATTTATTTATTTATTGTTTCTATTATT
1 TTAACTACTAAATTTTATTTTATTACATTATAACAATTATTTATTTATTTATTGTTTCTATTATT
* *
867171 CGATTTGACCTTGTGGTGACCAGATCTGGGGTATAATCTGCATTATTATAGTTTGAACTATG
66 CGATTCGACCTTGTGGTGACCAGATCTGGGGTATAATCCGCATTATTATAGTTTGAACTATG
* *
867233 TTAACTACTAAATTTTATTTTATTACATTCTAACAATTGTTTATTTATTTATTGTTTCTATTATT
1 TTAACTACTAAATTTTATTTTATTACATTATAACAATTATTTATTTATTTATTGTTTCTATTATT
* *
867298 CGATTCGACCTTGTGGTGACCAGATCTGTGGTATGATCCGCATTATTA
66 CGATTCGACCTTGTGGTGACCAGATCTGGGGTATAATCCGCATTATTA
867346 ACCATTTTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
127 104 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (127 bp):
TTAACTACTAAATTTTATTTTATTACATTATAACAATTATTTATTTATTTATTGTTTCTATTATT
CGATTCGACCTTGTGGTGACCAGATCTGGGGTATAATCCGCATTATTATAGTTTGAACTATG
Found at i:867375 original size:84 final size:84
Alignment explanation
Indices: 867272--867429 Score: 248
Period size: 84 Copynumber: 1.9 Consensus size: 84
867262 CTAACAATTG
* *
867272 TTTATTTATTTATTGTTTCTATTATTCGATTCGACCTTGTGGTGAC-CAGA-TCTGTGGTATGAT
1 TTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACTC-GATTCAG-GGTATGAT
867335 CCGCATTATTAACCATTTTTA
64 CCGCATTATTAACCATTTTTA
*
867356 TTTATTTATTTATTGTTTCTAATATTCGATTCGGCCTTGTGGTGACTCGATTCAGGGTATGATCC
1 TTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACTCGATTCAGGGTATGATCC
*
867421 GTATTATTA
66 GCATTATTA
867430 TGGTTCAGAC
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
84 64 0.94
85 4 0.06
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (84 bp):
TTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACTCGATTCAGGGTATGATCC
GCATTATTAACCATTTTTA
Found at i:867396 original size:211 final size:213
Alignment explanation
Indices: 867142--867532 Score: 497
Period size: 211 Copynumber: 1.8 Consensus size: 213
867132 ATTATAACCA
* * *
867142 TTATTTATTTATTTATTGTTTCTATTATTCGATTTGACCTTGTGGTGAC-CAGA-TCTGGGGTAT
1 TTATTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACTC-GATTC-AGGGTAT
* * * **
867205 AATCTGCATTATTATAGTT-TGAACTATGTTAACTACTAAATTTTATTTTATTAC-ATTCTAA-C
64 AATCCGCATTATTATGGTTCAG-ACTATACTAACTACTAAATTTTATTTTATTACGATT-TAATC
* * *
867267 A-ATTGTTTATTTATTTATTGTTTCTATTATTCGATTCGACCTTGTGGTGACCAGATCTGTGGTA
127 AGATTATTTATTTATTTATTATTTCTAATATTCGATTCGACCTTGTGGTGACCAGATCTGTGGTA
867331 TGATCCGCATTATTAACCATTT
192 TGATCCGCATTATTAACCATTT
* *
867353 TTATTTATTTATTTATTGTTTCTAATATTCGATTCGGCCTTGTGGTGACTCGATTCAGGGTATGA
1 TTATTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACTCGATTCAGGGTATAA
* * * * * * *
867418 TCCGTATTATTATGGTTCAGACTATACTAATTACTGATTTTTATTTTATTGCGCTTTAATCAGTG
66 TCCGCATTATTATGGTTCAGACTATACTAACTACTAAATTTTATTTTATTACGATTTAATCAG-A
* *
867483 TTATTTATTTATTTATTATTTCTAATATTTGATTCGGCCTTGTGGTGACC
130 TTATTTATTTATTTATTATTTCTAATATTCGATTCGACCTTGTGGTGACC
867533 TAATTCGGGG
Statistics
Matches: 151, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
211 98 0.65
212 8 0.05
214 45 0.30
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (213 bp):
TTATTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACTCGATTCAGGGTATAA
TCCGCATTATTATGGTTCAGACTATACTAACTACTAAATTTTATTTTATTACGATTTAATCAGAT
TATTTATTTATTTATTATTTCTAATATTCGATTCGACCTTGTGGTGACCAGATCTGTGGTATGAT
CCGCATTATTAACCATTT
Found at i:867593 original size:16 final size:17
Alignment explanation
Indices: 867574--867616 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
867564 TTGAACTCTG
867574 CTAACCGCTAA-CTTTT
1 CTAACCGCTAACCTTTT
**
867590 CTAACAACTAACCTTTT
1 CTAACCGCTAACCTTTT
867607 -TAACCGCTAA
1 CTAACCGCTAA
867617 TTACTAATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (17 bp):
CTAACCGCTAACCTTTT
Found at i:874608 original size:19 final size:19
Alignment explanation
Indices: 874571--874622 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
874561 TCTAAATCAT
874571 TTTTCAAAATTTC-ATTTTGA
1 TTTTCAAAA--TCAATTTTGA
*
874591 TTTTCAAAATCAATTTTGG
1 TTTTCAAAATCAATTTTGA
*
874610 CTTTCAAAATCAA
1 TTTTCAAAATCAA
874623 ATCATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 18 0.62
20 9 0.31
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (19 bp):
TTTTCAAAATCAATTTTGA
Found at i:877930 original size:12 final size:12
Alignment explanation
Indices: 877906--877973 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 12
877896 ACATCAAAGC
877906 AAAGAAAGAAAA
1 AAAGAAAGAAAA
877918 AAAGCAAAGAAAA
1 AAAG-AAAGAAAA
* *
877931 AAATAAGCAAAAGAA
1 AAAGAA--AGAA-AA
877946 AAAGTAAAGAAAA
1 AAAG-AAAGAAAA
877959 AAA-AAAGACAAA
1 AAAGAAAGA-AAA
877971 AAA
1 AAA
877974 CACATGCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
11 5 0.11
12 12 0.26
13 16 0.35
14 6 0.13
15 5 0.11
16 2 0.04
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.03
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:877938 original size:16 final size:16
Alignment explanation
Indices: 877901--877948 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
877891 AGATTACATC
877901 AAAGCAAAGAAAGAAAA
1 AAAGCAAAGAAA-AAAA
877918 AAAGCAAAGAAAAAAA
1 AAAGCAAAGAAAAAAA
*
877934 TAAGCAAAAGAAAAA
1 AAAGC-AAAGAAAAA
877949 GTAAAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAGCAAAGAAAAAAA
Found at i:877954 original size:28 final size:29
Alignment explanation
Indices: 877916--877971 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
877906 AAAGAAAGAA
*
877916 AAAAAGCAAAGAAAAAAATAAG-CAAAAG
1 AAAAAGCAAAGAAAAAAAAAAGACAAAAG
*
877944 AAAAAGTAAAGAAAAAAAAAAGACAAAA
1 AAAAAGCAAAGAAAAAAAAAAGACAAAA
877972 AACACATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.79, C:0.05, G:0.12, T:0.04
Consensus pattern (29 bp):
AAAAAGCAAAGAAAAAAAAAAGACAAAAG
Found at i:879210 original size:37 final size:36
Alignment explanation
Indices: 879111--879224 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 36
879101 TTTGAGACGC
* * * *
879111 TTTCTCTCATAACAAAGTGTTGTCTCGCTAGAGACAAT
1 TTTCTCTCAAAACAAA-T-TTGTCTCACTTGAGACATT
** *
879149 TTTCT-GAAAAATAAATTTTGTCTCACTTGAGACATT
1 TTTCTCTCAAAACAAA-TTTGTCTCACTTGAGACATT
879185 TTTCTCTCAAAACAAATTTCGTCTCACTTGAGACATT
1 TTTCTCTCAAAACAAATTT-GTCTCACTTGAGACATT
879222 TTT
1 TTT
879225 ACTTTAGGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
36 24 0.38
37 34 0.54
38 5 0.08
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTCTCTCAAAACAAATTTGTCTCACTTGAGACATT
Found at i:879393 original size:65 final size:65
Alignment explanation
Indices: 879286--879530 Score: 391
Period size: 65 Copynumber: 3.8 Consensus size: 65
879276 CTTTAACTAT
*
879286 GTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAAAT
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGAT
879351 C
65 C
* *
879352 GTTTCCCTTGAAACAAAGTTTGTCTCTCTTAAGACAATTTCTCTTGAAACATCATCTTTGAGATC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATC
* ** *
879417 GTTTCACTTGAAACGGATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATC
* * *
879482 GTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAA
879531 TAAATCCCTA
Statistics
Matches: 166, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 152 0.92
66 14 0.08
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (65 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATC
Found at i:879426 original size:29 final size:29
Alignment explanation
Indices: 879389--879495 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 29
879379 CTTAAGACAA
879389 TTTCTCTTGAAACATCATCTTTGAGATCG
1 TTTCTCTTGAAACATCATCTTTGAGATCG
*
879418 TTTCACTTGAAACGGATTTTGTC-TCTCTTGAGA-CAG
1 TTTCTCTTGAAAC--A-----TCATCT-TTGAGATC-G
879454 TTTCTCTTGAAACATCATCTTTGAGATCG
1 TTTCTCTTGAAACATCATCTTTGAGATCG
*
879483 TTTCCCTTGAAAC
1 TTTCTCTTGAAAC
879496 GAATTTTGTC
Statistics
Matches: 64, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
29 33 0.52
30 4 0.06
31 1 0.02
34 1 0.02
35 4 0.06
36 21 0.33
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (29 bp):
TTTCTCTTGAAACATCATCTTTGAGATCG
Found at i:879457 original size:36 final size:35
Alignment explanation
Indices: 879409--879530 Score: 100
Period size: 36 Copynumber: 3.6 Consensus size: 35
879399 AACATCATCT
*
879409 TTGAGATCGTTTCACTTGAAACGGATTTTGTCTCTC
1 TTGAGATCGTTTCTCTTGAAAC-GATTTTGTCTCTC
879445 TTGAGA-CAGTTTCTCTTGAAAC-A-----TCATCT-
1 TTGAGATC-GTTTCTCTTGAAACGATTTTGTC-TCTC
* *
879474 TTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCCC
1 TTGAGATCGTTTCTCTTGAAACG-ATTTTGTCTCTC
*
879510 TTGAGA-CATTTTCTCTTGAAA
1 TTGAGATC-GTTTCTCTTGAAA
879531 TAAATCCCTA
Statistics
Matches: 69, Mismatches: 5, Indels: 24
0.70 0.05 0.24
Matches are distributed among these distances:
29 21 0.30
30 4 0.06
31 1 0.01
34 1 0.01
35 4 0.06
36 38 0.55
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.40
Consensus pattern (35 bp):
TTGAGATCGTTTCTCTTGAAACGATTTTGTCTCTC
Found at i:879777 original size:131 final size:131
Alignment explanation
Indices: 879534--879795 Score: 345
Period size: 131 Copynumber: 2.0 Consensus size: 131
879524 CTTGAAATAA
* *
879534 ATCCCTAAAAATGGCATATCATCCTCATCGCGTAGGAACCGTGTCATCCACCAACCATATCTCCT
1 ATCCCTAAAAATGGCATATCATCCTCATCACGTAGGAACCATGTCATCCACCAACCATATCTCCT
* ** * *
879599 CATCACATAGGAGCCGCGTCAACCTTAGATAACCAGTTGTCCTCATCACGTAGGAACCATGTTAT
66 CATAACATAGGAGAAGCGTCAACCTTAGATAACCAATTGTCCGCATCACGTAGGAACCATGTTAT
879664 C
131 C
*
879665 ATCCCTAAAGATGGTCA-ATCATCCTCATCACGTAGGAACCATGTCATCC-CTCAACCATATCTC
1 ATCCCTAAAAATGG-CATATCATCCTCATCACGTAGGAACCATGTCATCCAC-CAACCATATCTC
* * *
879728 CTCATAACGTAGGAGAAGCGT-TACCTTTAGATAA-CAATAAT-TCCGCATCACGTAGGAGCCAT
64 CTCATAACATAGGAGAAGCGTCAACC-TTAGATAACCAAT--TGTCCGCATCACGTAGGAACCAT
879790 GTTATC
126 GTTATC
879796 TCTAAATTTA
Statistics
Matches: 115, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
130 7 0.06
131 105 0.91
132 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.25
Consensus pattern (131 bp):
ATCCCTAAAAATGGCATATCATCCTCATCACGTAGGAACCATGTCATCCACCAACCATATCTCCT
CATAACATAGGAGAAGCGTCAACCTTAGATAACCAATTGTCCGCATCACGTAGGAACCATGTTAT
C
Found at i:882132 original size:14 final size:14
Alignment explanation
Indices: 882115--882166 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 14
882105 ACGGTCAACG
882115 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
882129 GTCGGGTCTGATCGGGTCA
1 GTC-GG---G-TCGGGTCA
882148 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
882162 TGTCG
1 -GTCG
882167 ACCCAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 11 0.34
15 7 0.22
18 3 0.09
19 11 0.34
ACGTcount: A:0.08, C:0.21, G:0.46, T:0.25
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:882136 original size:19 final size:19
Alignment explanation
Indices: 882114--882160 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
882104 AACGGTCAAC
882114 GGTCGGGTCGGGTCAGTCG
1 GGTCGGGTCGGGTCAGTCG
* *
882133 GGTCTGATCGGGTCAGTCG
1 GGTCGGGTCGGGTCAGTCG
882152 GGTCGGGTC
1 GGTCGGGTC
882161 ATGTCGACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.06, C:0.21, G:0.49, T:0.23
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAGTCG
Found at i:882143 original size:10 final size:9
Alignment explanation
Indices: 882120--882155 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
882110 CAACGGTCGG
882120 GTCGGGTCA
1 GTCGGGTCA
*
882129 GTCGGGTCT
1 GTCGGGTCA
882138 GATCGGGTCA
1 G-TCGGGTCA
882148 GTCGGGTC
1 GTCGGGTC
882156 GGGTCATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.08, C:0.22, G:0.44, T:0.25
Consensus pattern (9 bp):
GTCGGGTCA
Found at i:887363 original size:14 final size:14
Alignment explanation
Indices: 887328--887354 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
887318 ACGGTCAACG
887328 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
887342 GTCGGGTCGGGTC
1 GTCGGGTCGGGTC
887355 GGATCGGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:887371 original size:9 final size:9
Alignment explanation
Indices: 887359--887439 Score: 63
Period size: 9 Copynumber: 8.4 Consensus size: 9
887349 CGGGTCGGAT
887359 CGGTCAAAC
1 CGGTCAAAC
*
887368 CGGTTCAGAC
1 CGG-TCAAAC
887378 CGGTCAAAC
1 CGGTCAAAC
* *
887387 CGGTTCGAAT
1 CGG-TCAAAC
887397 CGGTCAAAC
1 CGGTCAAAC
* *
887406 AGATCAGAAC
1 CGGTCA-AAC
*
887416 CGGTTGAAAAC
1 CGG-T-CAAAC
887427 CGGTCAAAC
1 CGGTCAAAC
887436 CGGT
1 CGGT
887440 TTCCAGCCCT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
9 27 0.49
10 20 0.36
11 7 0.13
12 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.26, T:0.16
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:887383 original size:19 final size:19
Alignment explanation
Indices: 887359--887405 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
887349 CGGGTCGGAT
887359 CGGTCAAACCGGTTC-AGAC
1 CGGTCAAACCGGTTCGA-AC
*
887378 CGGTCAAACCGGTTCGAAT
1 CGGTCAAACCGGTTCGAAC
887397 CGGTCAAAC
1 CGGTCAAAC
887406 AGATCAGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 25 0.96
20 1 0.04
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.17
Consensus pattern (19 bp):
CGGTCAAACCGGTTCGAAC
Found at i:888680 original size:24 final size:27
Alignment explanation
Indices: 888651--888710 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
888641 TGCTATGTTA
888651 TTTATT-T-TTAACTACTAAC-TTTAT
1 TTTATTATATTAACTACTAACTTTTAT
*
888675 TTTATTGCATATTAACTACTGACTTTTAT
1 TTTATT--ATATTAACTACTAACTTTTAT
888704 TTTATTA
1 TTTATTA
888711 CATTCTAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 6 0.20
27 2 0.07
28 11 0.37
29 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTATTATATTAACTACTAACTTTTAT
Found at i:888719 original size:29 final size:28
Alignment explanation
Indices: 888658--888713 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
888648 TTATTTATTT
*
888658 TTAACTACTAACTTTATTTTATTGCATA
1 TTAACTACTAACTTTATTTTATTACATA
*
888686 TTAACTACTGACTTTTATTTTATTACAT
1 TTAACTACTAAC-TTTATTTTATTACAT
888714 TCTAACCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (28 bp):
TTAACTACTAACTTTATTTTATTACATA
Found at i:889089 original size:134 final size:127
Alignment explanation
Indices: 888687--889078 Score: 543
Period size: 127 Copynumber: 3.0 Consensus size: 127
888677 TATTGCATAT
*
888687 TAACTACTGACTTTTATTTTATTACATTCTAACCATTGTTTATTTATTTATTGTTTCTATTATTC
1 TAACTACTAACTTTTATTTTATTACATTCTAACCATTGTTTATTTATTTATTGTTTCTATTATTC
* * ** * ** * *
888752 GATTTGACCTTGTGGTGACCATATTTGAGGTATGATCCACATTATTATGGTTCGGACTTTGC
66 GATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCGTATTATTATGGTTCAGACTCTGC
888814 TAACTACTAACTTTTATTTTATTACATTCTAACCATTGTTTATTTATTTATTGTTTCTATTATTC
1 TAACTACTAACTTTTATTTTATTACATTCTAACCATTGTTTATTTATTTATTGTTTCTATTATTC
* *
888879 TATTCGACCTTGTGGTGACCAGATCCGGGGTATAATCCGTATTATTATGGTTCAGACTCTGC
66 GATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCGTATTATTATGGTTCAGACTCTGC
* *
888941 TAATTACTAACTTTTATTTTATTGCACTT-TAACCATTGTTATTTATTTATTTATTTATTGTTTC
1 TAACTACTAACTTTTATTTTATTACA-TTCTAACCATTG-------TTTATTTATTTATTGTTTC
* * * *
889005 TAATATTCGATTCGTCCTTGTGGAGACCCGATCCGGGGTATGATCCGTATTATTATGGTTCAGAC
58 TATTATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCGTATTATTATGGTTCAGAC
889070 TCTGC
123 TCTGC
889075 TAAC
1 TAAC
889079 CGATAACTTT
Statistics
Matches: 236, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
127 148 0.63
128 2 0.01
134 86 0.36
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.46
Consensus pattern (127 bp):
TAACTACTAACTTTTATTTTATTACATTCTAACCATTGTTTATTTATTTATTGTTTCTATTATTC
GATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCGTATTATTATGGTTCAGACTCTGC
Found at i:889755 original size:18 final size:19
Alignment explanation
Indices: 889730--889773 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
889720 TTGAAATAAA
889730 TCAAATTTATT-TTACTAAT
1 TCAAATTT-TTATTACTAAT
*
889749 T-AAATTTTTATTTCTAAT
1 TCAAATTTTTATTACTAAT
889767 TCAAATT
1 TCAAATT
889774 ACGCAATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (19 bp):
TCAAATTTTTATTACTAAT
Found at i:890307 original size:20 final size:20
Alignment explanation
Indices: 890290--890328 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
890280 AAATAAAAGT
890290 CATAATT-TTTTTTAAAAAA
1 CATAATTGTTTTTTAAAAAA
*
890309 CTTAATTGTTTTTTAAAAAA
1 CATAATTGTTTTTTAAAAAA
890329 AATGGTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (20 bp):
CATAATTGTTTTTTAAAAAA
Found at i:890484 original size:18 final size:18
Alignment explanation
Indices: 890461--890497 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
890451 CTTATTAAAG
890461 AAAATGAAATAAAATGGA
1 AAAATGAAATAAAATGGA
890479 AAAATGAAATAAAATGGA
1 AAAATGAAATAAAATGGA
890497 A
1 A
890498 TGATAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (18 bp):
AAAATGAAATAAAATGGA
Found at i:891650 original size:4 final size:4
Alignment explanation
Indices: 891641--891668 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
891631 ATTATACACC
891641 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
891669 CTTCTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:904353 original size:31 final size:31
Alignment explanation
Indices: 904307--904369 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
904297 GACAATTATA
* *
904307 GATTACCTATGTTCTTC-GGAACATATGGACT
1 GATTACATATATTCTTCGGGAAC-TATGGACT
*
904338 GATTACATATATTCTTCGGGATCTATGGACT
1 GATTACATATATTCTTCGGGAACTATGGACT
904369 G
1 G
904370 GTCCTTTAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (31 bp):
GATTACATATATTCTTCGGGAACTATGGACT
Found at i:906993 original size:479 final size:479
Alignment explanation
Indices: 906096--907061 Score: 1914
Period size: 479 Copynumber: 2.0 Consensus size: 479
906086 GTTGTGGAGC
906096 GAAGGAGAGACAAAAATGTTCCAGCTCAACTCCAAAGCCATCCATATCATTTTTTGTGCTCTTGG
1 GAAGGAGAGACAAAAATGTTCCAGCTCAACTCCAAAGCCATCCATATCATTTTTTGTGCTCTTGG
906161 ACCAGATGAATACGGAAGAGTTTCATCGTGTACAACCGCCAAAGAAATATGGGACAAACTTCAAG
66 ACCAGATGAATACGGAAGAGTTTCATCGTGTACAACCGCCAAAGAAATATGGGACAAACTTCAAG
906226 TCACTCATGAAGGTACCGATGAGGTAAAGAAATCTAAAATTAGTATTCTAACGCATAGCTATGAA
131 TCACTCATGAAGGTACCGATGAGGTAAAGAAATCTAAAATTAGTATTCTAACGCATAGCTATGAA
906291 AATTTCAGGATAAAACCAAATGAAGATATCAAAGCTATAACGGATAGATTTTCAACGATTGTCAA
196 AATTTCAGGATAAAACCAAATGAAGATATCAAAGCTATAACGGATAGATTTTCAACGATTGTCAA
906356 TGGTCTCAAATCATATGGAGAGATCATTTCAAATGAAAAGCTTGTGAGGAAGTTAGTCTACTCCA
261 TGGTCTCAAATCATATGGAGAGATCATTTCAAATGAAAAGCTTGTGAGGAAGTTAGTCTACTCCA
906421 TCCCAAAATCGTGGCAATCAAAGAAGACGGCAATCATCGAGTCTAAGGACTTAACGTCCTTAACT
326 TCCCAAAATCGTGGCAATCAAAGAAGACGGCAATCATCGAGTCTAAGGACTTAACGTCCTTAACT
906486 CTTGAAGAGCTAATTGGGTCACTCCTCACTCATGAAATGATGCTCGAAGATGAGGTGGACCTCGA
391 CTTGAAGAGCTAATTGGGTCACTCCTCACTCATGAAATGATGCTCGAAGATGAGGTGGACCTCGA
906551 CAAAATTGACGAGACACCAAAGGA
456 CAAAATTGACGAGACACCAAAGGA
906575 GAAGGAGAGACAAAAATGTTCCAGCTCAACTCCAAAGCCATCCATATCATTTTTTGTGCTCTTGG
1 GAAGGAGAGACAAAAATGTTCCAGCTCAACTCCAAAGCCATCCATATCATTTTTTGTGCTCTTGG
906640 ACCAGATGAATACGGAAGAGTTTCATCGTGTACAACCGCCAAAGAAATATGGGACAAACTTCAAG
66 ACCAGATGAATACGGAAGAGTTTCATCGTGTACAACCGCCAAAGAAATATGGGACAAACTTCAAG
*
906705 TCACTCATGAAGGTACCGATGAGGTAAATAAATCTAAAATTAGTATTCTAACGCATAGCTATGAA
131 TCACTCATGAAGGTACCGATGAGGTAAAGAAATCTAAAATTAGTATTCTAACGCATAGCTATGAA
906770 AATTTCAGGATAAAACCAAATGAAGATATCAAAGCTATAACGGATAGATTTTCAACGATTGTCAA
196 AATTTCAGGATAAAACCAAATGAAGATATCAAAGCTATAACGGATAGATTTTCAACGATTGTCAA
*
906835 TGGTCTCAAATCATATGGAGAGATCATTTCAAATGAAAAGCTTGTGAGGAAGTTAGTCTACTCCC
261 TGGTCTCAAATCATATGGAGAGATCATTTCAAATGAAAAGCTTGTGAGGAAGTTAGTCTACTCCA
906900 TCCCAAAATCGTGGCAATCAAAGAAGACGGCAATCATCGAGTCTAAGGACTTAACGTCCTTAACT
326 TCCCAAAATCGTGGCAATCAAAGAAGACGGCAATCATCGAGTCTAAGGACTTAACGTCCTTAACT
906965 CTTGAAGAGCTAATTGGGTCACTCCTCACTCATGAAATGATGCTCGAAGATGAGGTGGACCTCGA
391 CTTGAAGAGCTAATTGGGTCACTCCTCACTCATGAAATGATGCTCGAAGATGAGGTGGACCTCGA
907030 CAAAATTGACGAGACACCAAAGGA
456 CAAAATTGACGAGACACCAAAGGA
907054 GAAGGAGA
1 GAAGGAGA
907062 AGAAGAAAAA
Statistics
Matches: 485, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
479 485 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (479 bp):
GAAGGAGAGACAAAAATGTTCCAGCTCAACTCCAAAGCCATCCATATCATTTTTTGTGCTCTTGG
ACCAGATGAATACGGAAGAGTTTCATCGTGTACAACCGCCAAAGAAATATGGGACAAACTTCAAG
TCACTCATGAAGGTACCGATGAGGTAAAGAAATCTAAAATTAGTATTCTAACGCATAGCTATGAA
AATTTCAGGATAAAACCAAATGAAGATATCAAAGCTATAACGGATAGATTTTCAACGATTGTCAA
TGGTCTCAAATCATATGGAGAGATCATTTCAAATGAAAAGCTTGTGAGGAAGTTAGTCTACTCCA
TCCCAAAATCGTGGCAATCAAAGAAGACGGCAATCATCGAGTCTAAGGACTTAACGTCCTTAACT
CTTGAAGAGCTAATTGGGTCACTCCTCACTCATGAAATGATGCTCGAAGATGAGGTGGACCTCGA
CAAAATTGACGAGACACCAAAGGA
Found at i:911449 original size:20 final size:20
Alignment explanation
Indices: 911406--911443 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
911396 CCCCCTTTGA
*
911406 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
911426 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
911444 CTAGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:913615 original size:16 final size:16
Alignment explanation
Indices: 913594--913626 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
913584 GAAGTGGTTT
913594 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
913610 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
913626 T
1 T
913627 GATAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TAAGTGTGTTTTAAAA
Found at i:915107 original size:21 final size:21
Alignment explanation
Indices: 915083--915134 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
915073 TTCGAAGTTA
* *
915083 CTGTAGTAATGTATCGATACC
1 CTGTAGCAAGGTATCGATACC
*
915104 CTGTAGCAGGGTATCGATACCC
1 CTGTAGCAAGGTATCGATA-CC
*
915126 CTGAAGCAA
1 CTGTAGCAA
915135 TCAGGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
CTGTAGCAAGGTATCGATACC
Found at i:915133 original size:22 final size:21
Alignment explanation
Indices: 915093--915133 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
915083 CTGTAGTAAT
*
915093 GTATCGATACCCTGTAGCAGG
1 GTATCGATACCCTGAAGCAGG
915114 GTATCGATACCCCTGAAGCA
1 GTATCGATA-CCCTGAAGCA
915134 ATCAGGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (21 bp):
GTATCGATACCCTGAAGCAGG
Found at i:915517 original size:30 final size:30
Alignment explanation
Indices: 915379--915558 Score: 141
Period size: 30 Copynumber: 6.1 Consensus size: 30
915369 AAATGTCTGC
* * *
915379 TTTTACTATTTTAGTCTTTTAAATTTCTGT
1 TTTTACTATTTTAGTCCTTTAACTTTCTAT
* * *
915409 ATTTGCTATTGTAGTCCTTTAACTTTCTAT
1 TTTTACTATTTTAGTCCTTTAACTTTCTAT
* * * **
915439 ATTTAC-GTTTCAACCCTTTAACTTTCTAT
1 TTTTACTATTTTAGTCCTTTAACTTTCTAT
*
915468 TTTT-CTA-TTTAGTTCTTTAACTTTCTAT
1 TTTTACTATTTTAGTCCTTTAACTTTCTAT
* * * * *
915496 TTTTATTATTTTAGTCATTTAAGTTTATGT
1 TTTTACTATTTTAGTCCTTTAACTTTCTAT
* * * * *
915526 TTTTATTGTTTCAGTCCCTTAAATTTCTAT
1 TTTTACTATTTTAGTCCTTTAACTTTCTAT
915556 TTT
1 TTT
915559 AAGAGGAAGT
Statistics
Matches: 116, Mismatches: 31, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
28 22 0.19
29 23 0.20
30 71 0.61
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (30 bp):
TTTTACTATTTTAGTCCTTTAACTTTCTAT
Found at i:923504 original size:23 final size:23
Alignment explanation
Indices: 923473--923551 Score: 58
Period size: 23 Copynumber: 3.6 Consensus size: 23
923463 CAAAAAAAAT
923473 TGTCA-AAAGACAGAAGAAAACG
1 TGTCATAAAGACAGAAGAAAACG
** *
923495 TGTCATAAAGGTA-AA-AAAAAG
1 TGTCATAAAGACAGAAGAAAACG
* * *
923516 TGTTATAAA-AGTAGAGGAAAACG
1 TGTCATAAAGA-CAGAAGAAAACG
*
923539 TGTCATACAGACA
1 TGTCATAAAGACA
923552 AACTTACTGA
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
21 15 0.36
22 8 0.19
23 18 0.43
24 1 0.02
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.18
Consensus pattern (23 bp):
TGTCATAAAGACAGAAGAAAACG
Found at i:925302 original size:2 final size:2
Alignment explanation
Indices: 925295--925342 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
925285 TATTTTAATA
925295 AT AT AT 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 AT AT AT
925337 AT AT AT
1 AT AT AT
925343 GGTTCATGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:925995 original size:20 final size:20
Alignment explanation
Indices: 925970--926021 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 20
925960 AACCATCTCG
925970 TTGACTTTGAC-TGTTGACCA
1 TTGACTTTGACATGTTGA-CA
925990 TTGACTTTGACATGTTGACA
1 TTGACTTTGACATGTTGACA
926010 TTGACTATTGAC
1 TTGACT-TTGAC
926022 CGTCGACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGACTTTGACATGTTGACA
Found at i:926014 original size:34 final size:34
Alignment explanation
Indices: 925969--926033 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
925959 GAACCATCTC
* * *
925969 GTTGACTTTGACTGTTGACCATTGACTTTGACAT
1 GTTGACATTGACTATTGACCATCGACTTTGACAT
*
926003 GTTGACATTGACTATTGACCGTCGACTTTGA
1 GTTGACATTGACTATTGACCATCGACTTTGA
926034 TCTAAAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (34 bp):
GTTGACATTGACTATTGACCATCGACTTTGACAT
Found at i:939288 original size:92 final size:93
Alignment explanation
Indices: 939141--939314 Score: 264
Period size: 92 Copynumber: 1.9 Consensus size: 93
939131 TTTTTGGAGC
* * * *
939141 ATTTTGGCCTTAATGTTTCATTTTAGGGTAAAAAAGTCTATAATGTTTGAACAAATAATCACTTT
1 ATTTTGGCCCTAACGTTTCATTTTAGCGTAAAAAAGTCCATAATGTTTGAACAAATAATCACTTT
939206 GGC-CGTTATTCTTTTTTTTTTATAGAAT
66 GGCTC-TTATTCTTTTTTTTTTATAGAAT
*
939234 ATTTTGGCCCTAACGTTTCATTTTA-CG-ACAAAAAGTCCATAATGTTTGACCAAATAATCACTT
1 ATTTTGGCCCTAACGTTTCATTTTAGCGTA-AAAAAGTCCATAATGTTTGAACAAATAATCACTT
939297 TGGCTCTTATTCTTTTTT
65 TGGCTCTTATTCTTTTTT
939315 CTAGAGTATT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
91 1 0.01
92 49 0.66
93 24 0.32
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (93 bp):
ATTTTGGCCCTAACGTTTCATTTTAGCGTAAAAAAGTCCATAATGTTTGAACAAATAATCACTTT
GGCTCTTATTCTTTTTTTTTTATAGAAT
Found at i:939972 original size:16 final size:16
Alignment explanation
Indices: 939951--939983 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
939941 TAATAAATAG
939951 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
939967 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
939983 A
1 A
939984 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:940065 original size:10 final size:10
Alignment explanation
Indices: 940050--940124 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
940040 CATTTAATAA
940050 ATAAACGAAC
1 ATAAACGAAC
940060 ATAAACGAAC
1 ATAAACGAAC
940070 ----ACGAAC
1 ATAAACGAAC
940076 ATAAACGAAC
1 ATAAACGAAC
** *
940086 ACGAAC-ATAA
1 ATAAACGA-AC
940096 ATGAACACGAAC
1 AT-AA-ACGAAC
940108 ATAAACGAAC
1 ATAAACGAAC
940118 ATAAACG
1 ATAAACG
940125 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:940075 original size:16 final size:16
Alignment explanation
Indices: 940054--940118 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
940044 TAATAAATAA
940054 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
940070 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
940086 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
940102 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
940118 A
1 A
940119 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:940886 original size:14 final size:14
Alignment explanation
Indices: 940869--940924 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
940859 AATGAACATA
940869 AACGAACATAATCG
1 AACGAACATAATCG
940883 AACGAACAT-A---
1 AACGAACATAATCG
* * *
940893 AACAAACATAACCA
1 AACGAACATAATCG
940907 AACGAACATAATCG
1 AACGAACATAATCG
940921 AACG
1 AACG
940925 TTCACGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 24 0.71
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:940889 original size:24 final size:24
Alignment explanation
Indices: 940849--940923 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
940839 GATTGAGTTA
*
940849 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
940873 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* * *
940897 AACATAACCAAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
940921 AAC
1 AAC
940924 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:941635 original size:23 final size:23
Alignment explanation
Indices: 941609--941679 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 23
941599 ACATTACAAT
941609 TAAAAATCAAATTGAACAAAATA
1 TAAAAATCAAATTGAACAAAATA
* ** *
941632 T-AAAGTTGAA--GGACTAAAAT-
1 TAAAAATCAAATTGAAC-AAAATA
941652 TAAAAAATCAAATTGAACAAAATA
1 T-AAAAATCAAATTGAACAAAATA
941676 TAAA
1 TAAA
941680 GTTGAAGGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
20 4 0.12
21 5 0.15
22 12 0.35
23 9 0.26
24 4 0.12
ACGTcount: A:0.62, C:0.07, G:0.08, T:0.23
Consensus pattern (23 bp):
TAAAAATCAAATTGAACAAAATA
Found at i:941668 original size:44 final size:43
Alignment explanation
Indices: 941606--941688 Score: 157
Period size: 44 Copynumber: 1.9 Consensus size: 43
941596 ATAACATTAC
941606 AATTAAAAATCAAATTGAACAAAATATAAAGTTGAAGGACTAA
1 AATTAAAAATCAAATTGAACAAAATATAAAGTTGAAGGACTAA
941649 AATTAAAAAATCAAATTGAACAAAATATAAAGTTGAAGGA
1 AATT-AAAAATCAAATTGAACAAAATATAAAGTTGAAGGA
941689 ATTTATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
43 4 0.10
44 35 0.90
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.23
Consensus pattern (43 bp):
AATTAAAAATCAAATTGAACAAAATATAAAGTTGAAGGACTAA
Found at i:942465 original size:23 final size:24
Alignment explanation
Indices: 942420--942465 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
942410 TTATTATATG
* *
942420 TTTAAAAATGTTTAAAATTATAAT
1 TTTAAAAATGATTAAAATAATAAT
*
942444 TTTAAAAAT-ATTATAATAATAA
1 TTTAAAAATGATTAAAATAATAA
942466 ACATATCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTTAAAAATGATTAAAATAATAAT
Found at i:958617 original size:13 final size:14
Alignment explanation
Indices: 958599--958627 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
958589 TTTGGAAAAT
958599 ATATAAATT-TAAA
1 ATATAAATTCTAAA
958612 ATATAAATTCTAAA
1 ATATAAATTCTAAA
958626 AT
1 AT
958628 TTTGAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATAAATTCTAAA
Found at i:960936 original size:14 final size:14
Alignment explanation
Indices: 960896--960954 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
960886 CAAGGTAAAG
*
960896 AAAACAAATAAGAT
1 AAAACAAATAAAAT
*
960910 AAAGA-GAATAAAAT
1 AAA-ACAAATAAAAT
960924 AAAAGCAAA-AAAAT
1 AAAA-CAAATAAAAT
*
960938 AAAATAAATAAAAT
1 AAAACAAATAAAAT
960952 AAA
1 AAA
960955 TAAATAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 4 0.11
14 30 0.81
15 3 0.08
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAACAAATAAAAT
Found at i:960966 original size:9 final size:9
Alignment explanation
Indices: 960916--960958 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
960906 AGATAAAGAG
960916 AATAAAATA
1 AATAAAATA
*
960925 AA-AGCAAAAA
1 AATA--AAATA
960935 AATAAAATA
1 AATAAAATA
960944 AATAAAATA
1 AATAAAATA
960953 AATAAA
1 AATAAA
960959 TAAGATAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 1 0.03
9 21 0.72
10 6 0.21
11 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (9 bp):
AATAAAATA
Found at i:961024 original size:2 final size:2
Alignment explanation
Indices: 961017--961061 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
961007 TGAAAAAGGA
961017 AT AT AT 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 AT AT AT
961059 AT A
1 AT A
961062 CACACATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:961214 original size:41 final size:39
Alignment explanation
Indices: 961149--961225 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
961139 TCACTTCACC
* *
961149 GAAAGTGGGGGGCTTTAGTCAGAAATAAGACAAAAAGAG
1 GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
*
961188 GAAAGTGGGAGAGACTTTAGTTAGAAATAAAACAAAAA
1 GAAAGTGGG-G-GACTTTAGTCAGAAATAAAACAAAAA
961226 AAATGAGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 9 0.27
40 1 0.03
41 23 0.70
ACGTcount: A:0.48, C:0.06, G:0.29, T:0.17
Consensus pattern (39 bp):
GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
Found at i:961646 original size:17 final size:18
Alignment explanation
Indices: 961613--961648 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
961603 ATATATACAT
*
961613 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
961631 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
961648 A
1 A
961649 AATATCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:964072 original size:106 final size:106
Alignment explanation
Indices: 963798--964425 Score: 764
Period size: 106 Copynumber: 6.0 Consensus size: 106
963788 TGTATTGTTC
* * * * * * * *
963798 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTGTATGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* * * * *
963863 GCCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTG-CTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTC-GTCT
* *
963904 TGAGTCTAATATCCTTCG-TGTGAAGTTGAAATTGAC-CTTGAAATTGGGAAATTATTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC-TGAAATTGGGAAATTATTTGTTGAC
963967 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
* * *
964009 AGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* * * * *
964074 ACCAGCCGTTCCTTCATTATGAAGTTAAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
* * * * * *
964115 CTAGTCCAATATCCTTCGATGTGAAGTTAAAATTGACCCTGAAATTGGAAAATTATTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* *
964180 ACTAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
* * * *
964221 CGAGTCCAATATCCTTC-C-CT--A--TG-----G-CTCTAAAATTGGGAGATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* *
964274 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
*
964315 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTATGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* *
964380 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
*
964421 TGAGT
1 CGAGT
964426 GACGTGATAT
Statistics
Matches: 444, Mismatches: 62, Indels: 32
0.83 0.12 0.06
Matches are distributed among these distances:
94 77 0.17
95 2 0.00
96 1 0.00
98 1 0.00
100 3 0.01
102 1 0.00
104 2 0.00
105 88 0.20
106 268 0.60
107 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
Found at i:964393 original size:200 final size:200
Alignment explanation
Indices: 964042--964425 Score: 617
Period size: 200 Copynumber: 1.9 Consensus size: 200
964032 AAGTTGAAAT
* *
964042 TGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTTCCTTCATTATGAAGTTAAACTTG
1 TGGCTCTAAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCATTATGAAGTTAAACTTG
* *
964107 TGTTGTCTCTAGTCCAATATCCTTCGATGTGAAGTTAAAATTGACCCTGAAATTGGAAAATTATT
66 TGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTAAAATTGACCATGAAATTGGAAAATTATT
*
964172 TATTGACAACTAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTT
131 TATTGACAACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTT
964237 CCCTA
196 CCCTA
* * *
964242 TGGCTCTAAAATTGGGAGATTGTTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTG
1 TGGCTCTAAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCATTATGAAGTTAAACTTG
* * * *
964307 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTATGAAATTGGGAAATTATT
66 TGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTAAAATTGACCATGAAATTGGAAAATTATT
* * *
964372 TGTTGACAACCAG-TCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
131 TATTGACAACCAGCT-GTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGT
964426 GACGTGATAT
Statistics
Matches: 168, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
199 1 0.01
200 167 0.99
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (200 bp):
TGGCTCTAAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCATTATGAAGTTAAACTTG
TGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTAAAATTGACCATGAAATTGGAAAATTATT
TATTGACAACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTT
CCCTA
Found at i:972793 original size:5 final size:5
Alignment explanation
Indices: 972729--972804 Score: 50
Period size: 5 Copynumber: 15.0 Consensus size: 5
972719 ATAATGAGGA
* * * * *
972729 AAAAT ACAAAG AAAAT AGAAA- ATAAAT GAAA- AAAAT ACAAT CACAT
1 AAAAT A-AAAT AAAAT A-AAAT A-AAAT AAAAT AAAAT AAAAT AAAAT
972775 AAAAT AAAGA- AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT
972805 GTAAGTTAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
4 4 0.07
5 42 0.78
6 8 0.15
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:972901 original size:2 final size:2
Alignment explanation
Indices: 972894--972950 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
972884 AATTATAATA
972894 AT AT AT 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 AT AT AT
972936 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
972951 ACTTATAAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:973007 original size:26 final size:24
Alignment explanation
Indices: 972978--973028 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 24
972968 AAAAAATAAT
*
972978 AGTAATAATAAGTATTAAAATAAAAA
1 AGTAATAAT-AGTAAT-AAATAAAAA
973004 AGTAATAATAGTAATAAATAAAAA
1 AGTAATAATAGTAATAAATAAAAA
973028 A
1 A
973029 ACAGAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 5 0.21
26 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (24 bp):
AGTAATAATAGTAATAAATAAAAA
Found at i:973106 original size:23 final size:23
Alignment explanation
Indices: 973080--973123 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
973070 AATATATATA
*
973080 TATATATAAAAAAAAAAATAAAG
1 TATAAATAAAAAAAAAAATAAAG
* *
973103 TATAAATGAAATAAAAAATAA
1 TATAAATAAAAAAAAAAATAA
973124 TAATAATGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (23 bp):
TATAAATAAAAAAAAAAATAAAG
Found at i:973649 original size:35 final size:35
Alignment explanation
Indices: 973603--973674 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
973593 CTAAAAAACC
973603 CTATTTTAGACTAGTACTTGAGTCGTAATCCAACT
1 CTATTTTAGACTAGTACTTGAGTCGTAATCCAACT
* *
973638 CTATTTTAGACTAGTATTTGAGTCTTAATCCAACT
1 CTATTTTAGACTAGTACTTGAGTCGTAATCCAACT
973673 CT
1 CT
973675 TCTTTGTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTACTTGAGTCGTAATCCAACT
Found at i:974123 original size:3 final size:3
Alignment explanation
Indices: 974110--974156 Score: 60
Period size: 3 Copynumber: 15.0 Consensus size: 3
974100 TTTTCAACTC
974110 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTTA TTTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA
974157 CAAAATACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.73
4 9 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:977829 original size:96 final size:96
Alignment explanation
Indices: 977714--977910 Score: 261
Period size: 96 Copynumber: 2.1 Consensus size: 96
977704 ATCACTGATT
** * *
977714 TACTGGCTTATGAACTATGGCTACATGGTATATGTTCTCTGGTTACATGTTTTCATTGGAAGATA
1 TACTGGCTTATGAACTATGGCTACATGAAATATGTTATCTGGTTACATGTTTTCATTGGAAAATA
*
977779 TAATAGTTCCTGAA-TTATGGATGATGGAATC
66 TAATAGTTCCT-AATTTATGGATCATGGAATC
* * * * * *
977810 TACTGGTTTATGAACTATGGTTACCTGAAATGTGTTATCTGGTTTCTTGTTTTCATTGGAAAATA
1 TACTGGCTTATGAACTATGGCTACATGAAATATGTTATCTGGTTACATGTTTTCATTGGAAAATA
* *
977875 TGATTGTTCCTAATTTATGGATCATGGAATC
66 TAATAGTTCCTAATTTATGGATCATGGAATC
977906 TACTG
1 TACTG
977911 ATTCACTGGA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
95 2 0.02
96 85 0.98
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (96 bp):
TACTGGCTTATGAACTATGGCTACATGAAATATGTTATCTGGTTACATGTTTTCATTGGAAAATA
TAATAGTTCCTAATTTATGGATCATGGAATC
Found at i:994985 original size:114 final size:114
Alignment explanation
Indices: 994743--995075 Score: 405
Period size: 114 Copynumber: 2.9 Consensus size: 114
994733 GGATAAACCA
* * * * *
994743 ATCAACATTTCCAATGGATGGGTTCTTAATGAGAAGAACTCGTTCGACGAGGGAGAATAAGTTCA
1 ATCAACATTTCCAATGGA-GAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
* * *
994808 TAATTAGAAGAACTTGTTCAACCTTTGTTCGATTCCATCACAGAAAGAGGTGT
65 TAA-T-G-AGAACTTGTTCAACCTTGGTTCGATTCCAACACAGAAAGAGGTGG
* * *
994861 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGACAAGAAGTTTAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCAT
* * *
994926 AATGAGAACTTGTTCAACCTTGGTTTGATTTCAACACAGAAGGAGGTGG
66 AATGAGAACTTGTTCAACCTTGGTTCGATTCCAACACAGAAAGAGGTGG
* * * * * *
994975 ATTAATATTTCCAGTGGAGAGTTTATAATGAGAAAAACTCATCCGACGAGGTAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCAT
* *
995040 AATGAGAATAACTTGTTCAAACTTAGTTCGATTCCA
66 AATGAG---AACTTGTTCAACCTTGGTTCGATTCCA
995076 TCATATAAGG
Statistics
Matches: 185, Mismatches: 27, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
114 101 0.55
115 1 0.01
116 1 0.01
117 64 0.35
118 18 0.10
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (114 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCAT
AATGAGAACTTGTTCAACCTTGGTTCGATTCCAACACAGAAAGAGGTGG
Found at i:995444 original size:27 final size:25
Alignment explanation
Indices: 995392--995446 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
995382 TTCAACTCTT
*
995392 ATATTATTATTATTATTATTATAAA
1 ATATTATTATTATTATTATTACAAA
995417 ATATTATTATTTATTTATTATTACAAA
1 ATATTATTA-TTA-TTATTATTACAAA
995444 ATA
1 ATA
995447 CCCAAACTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 9 0.33
26 3 0.11
27 15 0.56
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTATTATTATTATTATTACAAA
Found at i:996637 original size:22 final size:22
Alignment explanation
Indices: 996612--996654 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
996602 TCCTGGCATA
996612 TTTATTTTCTT-ATTTTAATTTT
1 TTTA-TTTCTTAATTTTAATTTT
996634 TTTATTTCTTAATTTTAATTT
1 TTTATTTCTTAATTTTAATTT
996655 AATTTGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTCTTAATTTTAATTTT
Found at i:997520 original size:2 final size:2
Alignment explanation
Indices: 997513--997570 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
997503 TATGTTCTTT
997513 TA TA TA TA TA TA 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 TA TA TA TA TA TA
997555 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
997571 GGGGGTATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:997851 original size:13 final size:13
Alignment explanation
Indices: 997833--997858 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
997823 GGATTTTTTT
997833 AAAATATTGTTTC
1 AAAATATTGTTTC
997846 AAAATATTGTTTC
1 AAAATATTGTTTC
997859 GATTTTTTTT
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:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
AAAATATTGTTTC
Found at i:998739 original size:23 final size:23
Alignment explanation
Indices: 998673--998743 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
998663 ACCAAAATAT
* * **
998673 GTGCCA-AAAGGTAGAAGAAAAT
1 GTGCCATAAAGGCAGAGGAAAGC
*
998695 GTGTCATAAAGGCAGAGGAAAGC
1 GTGCCATAAAGGCAGAGGAAAGC
*
998718 GTGCCATACAGGCAGAGGAAAGC
1 GTGCCATAAAGGCAGAGGAAAGC
998741 GTG
1 GTG
998744 TCATGCATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 5 0.12
23 36 0.88
ACGTcount: A:0.39, C:0.14, G:0.34, T:0.13
Consensus pattern (23 bp):
GTGCCATAAAGGCAGAGGAAAGC
Found at i:999322 original size:26 final size:26
Alignment explanation
Indices: 999272--999323 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
999262 TAAAATTTAT
*
999272 AAAATTTTAGATAAAATAAACATAAA
1 AAAATTTTAGATAAAAGAAACATAAA
999298 AAAATTTTATAGA-AAAAGAAA-ATAAA
1 AAAA-TTT-TAGATAAAAGAAACATAAA
999324 TTATCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.39
27 10 0.43
28 4 0.17
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (26 bp):
AAAATTTTAGATAAAAGAAACATAAA
Found at i:1003207 original size:3 final size:3
Alignment explanation
Indices: 1003199--1003233 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1003189 CTGAAAACAA
1003199 AAT AAT AAT AAT AA- AAT AAAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
1003234 CCCCGACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1003725 original size:42 final size:41
Alignment explanation
Indices: 1003626--1003732 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
1003616 GGTCGAAGGT
* * *
1003626 CTTACGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGG
1 CTTACTGATAGCCCGAAGGACTTATCATCATGATCGAAAGA
* * *
1003667 CTTA-TAGAT-GATCCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACT-GATAG-CCCGAAGGACTT-ATCATCATGATCGAAAGA
*
1003709 CTTACTGATAGCCCGAATGACTTA
1 CTTACTGATAGCCCGAAGGACTTA
1003733 CCAATTTGGG
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
40 1 0.02
41 18 0.35
42 31 0.60
43 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (41 bp):
CTTACTGATAGCCCGAAGGACTTATCATCATGATCGAAAGA
Found at i:1003988 original size:255 final size:253
Alignment explanation
Indices: 1003532--1004050 Score: 756
Period size: 255 Copynumber: 2.0 Consensus size: 253
1003522 GATGACCTTC
* * * *
1003532 CTTTTCTAAAATTTCAATTTTCATATTTAAATGAGAAACTTTGGAAATCATTCTCATTTTTTAAA
1 CTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACTTTGGAAATCATTATCATTTTTCAAA
**
1003597 AAACACGTGAAAACATCCTGGTCGAAGGTCTTACGGATAGCCCGAAGGACTTATCATCTTGATCG
66 AAACACGTGAAAACATCCTGCCCGAAGGTCTTACGGATAGCCCGAAGGACTTATCATCTTGATCG
* * * *
1003662 AAAGGCTTATAGATGATCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAT
131 AAAGGCTTATAGATGACCCAAAGGATTTAATCATAATGCTCGAAAGACTTACTGATAGCCCGAAG
1003727 GACTTACCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAAT-AGTTTTATT-A
196 GACTTACCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCA-TTTT-TTCA
* * * *
1003785 CTTTTCAAAAATTTCAATTTTTAAATTTAAATGAGAAACTTTGGGAATCGTTTTATCATTTTTCG
1 CTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACTTTGGAAATC--ATTATCATTTTTCA
* * * *
1003850 AAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGAT-GACCTGAAGGACTTATCATCTTGC
64 AAAAACACGTGAAAACATCCTGCCCGAAGGTCTTACGGATAG-CCCGAAGGACTTATCATCTTGA
* * * *
1003914 TCGAAAGGCTTGTAGATGACCCAAATGATTTAATCATAATGCTTGAAAGACTTACTGATGGCCCG
128 TCGAAAGGCTTATAGATGACCCAAAGGATTTAATCATAATGCTCGAAAGACTTACTGATAGCCCG
*
1003979 AAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCATTTTTTCA
193 AAGGACTTACCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCATTTTTTCA
*
1004040 TTTTTCAAAAA
1 CTTTTCAAAAA
1004051 ACATGTGAAA
Statistics
Matches: 237, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
253 45 0.19
254 3 0.01
255 188 0.79
256 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (253 bp):
CTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACTTTGGAAATCATTATCATTTTTCAAA
AAACACGTGAAAACATCCTGCCCGAAGGTCTTACGGATAGCCCGAAGGACTTATCATCTTGATCG
AAAGGCTTATAGATGACCCAAAGGATTTAATCATAATGCTCGAAAGACTTACTGATAGCCCGAAG
GACTTACCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCATTTTTTCA
Found at i:1004123 original size:41 final size:42
Alignment explanation
Indices: 1004078--1004180 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
1004068 GTCCGAAATT
* ** *
1004078 CTTATGGATGGCCCGAAGGATTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGATTTAATCATCAAGCTCAAAAGA
** *
1004119 CTTATAGATGAACCGAAGAATTTAATCATCAAGCTCAAAAGA
1 CTTATAGATGGCCCGAAGGATTTAATCATCAAGCTCAAAAGA
* *
1004161 CTTATTGATGGCACGAAGGA
1 CTTATAGATGGCCCGAAGGA
1004181 CTTACCAATT
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 19 0.39
42 30 0.61
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (42 bp):
CTTATAGATGGCCCGAAGGATTTAATCATCAAGCTCAAAAGA
Found at i:1004162 original size:197 final size:197
Alignment explanation
Indices: 1003818--1004246 Score: 621
Period size: 197 Copynumber: 2.2 Consensus size: 197
1003808 AATTTAAATG
* * * * * *
1003818 AGAAACTTTGGGAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCT
1 AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCATGCCCGAAAGTCT
* * * *
1003883 TATGGATGACCTGAAGGACTTATCATCTTGCTCGAAAGGCTTGTAGATGACCCAAATGATTTAAT
66 TATGGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGAACCAAATGATTTAAT
** *
1003948 CATAATGCTTGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
131 CATAATGCTCAAAAGACTTACTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
1004013 TA
196 TA
* *
1004015 AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCATGTCCGAAATTCT
1 AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCATGCCCGAAAGTCT
* * *
1004080 TATGGATGGCCCGAAGGATTTATCATCTTGCTCGAAAGACTTATAGATGAACCGAA-GAATTTAA
66 TATGGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGAACCAAATG-ATTTAA
*
1004144 TCATCAA-GCTCAAAAGACTTATTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTA
130 TCAT-AATGCTCAAAAGACTTACTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTA
1004208 GGTA
194 GGTA
* *
1004212 AGAAACTTTGGAAGTCATTTTCTT-ACTTTTCAAAA
1 AGAAACTTTGGAAATCATTTT-TTCATTTTTCAAAA
1004247 TTTCAATTTT
Statistics
Matches: 208, Mismatches: 21, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
196 1 0.00
197 203 0.98
198 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (197 bp):
AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCATGCCCGAAAGTCT
TATGGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGAACCAAATGATTTAAT
CATAATGCTCAAAAGACTTACTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTAGG
TA
Found at i:1004438 original size:451 final size:450
Alignment explanation
Indices: 1003565--1004439 Score: 1344
Period size: 451 Copynumber: 1.9 Consensus size: 450
1003555 TATTTAAATG
* * *
1003565 AGAAACTTTGGAAATCATTCTCATTTTTTAAAAAACACGTGAAAACATCCTGGTCGAAGGTCTTA
1 AGAAACTTTGGAAATCATTCTCATTTTTCAAAAAACACGTGAAAACATCATGGTCGAAAGTCTTA
* * *
1003630 CGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGGCTTATAGATGATCCGAAGGATTTAATCA
66 CGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGACTTATAGATGAACCGAAGAATTTAATCA
* * * *
1003695 TCATGCTCGAAAGACTTACTGATAGCCCGAATGACTTACCAATTTGGGAAATAGTTTACTAGGTA
131 TCAAGCTCAAAAGACTTACTGATAGCACGAAGGACTTACCAATTTGGGAAATAGTTTACTAGGTA
*
1003760 AGAAACTTTGGAAATAGTTTTATTACTTTTCAAAAATTTCAATTTTTAAATTTAAATGAGAAACT
196 AGAAACTTTGGAAATAGTTTTATTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACT
*
1003825 TTGGGAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGAT
261 TTGGAAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGAT
* *
1003890 GACCTGAAGGACTTATCATCTTGCTCGAAAGGCTTGTAGATGACCCAAATGATTTAATCATAATG
326 GACCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCAAATGATTTAATCATAATG
* *
1003955 CTTGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTA
391 CTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTA
* * *
1004015 AGAAACTTTGGAAATCATTTTTTCATTTTTCAAAAAACATGTGAAAACATCAT-GTCCGAAATTC
1 AGAAACTTTGGAAATCA--TTCTCATTTTTCAAAAAACACGTGAAAACATCATGGT-CGAAAGTC
* * * *
1004079 TTATGGATGGCCCGAAGGATTTATCATCTTGCTCGAAAGACTTATAGATGAACCGAAGAATTTAA
63 TTACGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGACTTATAGATGAACCGAAGAATTTAA
* * *
1004144 TCATCAAGCTCAAAAGACTTATTGATGGCACGAAGGACTTACCAATTTTGGAAATAGTTTACTAG
128 TCATCAAGCTCAAAAGACTTACTGATAGCACGAAGGACTTACCAATTTGGGAAATAGTTTACTAG
* * *
1004209 GTAAGAAACTTTGGAAGTCA-TTTTCTTACTTTTC-AAAATTTCAATTTTCAGATTTAAATGAGA
193 GTAAGAAACTTTGGAAAT-AGTTTTATTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGA
* * * *
1004272 AACTTTGGAAATTGTTTTCTTATTTTTTGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTAT
257 AACTTTGGAAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTAT
* * *
1004337 GGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGGCCTAAA-GTATTTAATCA
322 GGATGACCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCAAATG-ATTTAATCA
*
1004401 TCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTAC
386 TAATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTAC
1004440 TAATGGCCCG
Statistics
Matches: 383, Mismatches: 37, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
450 18 0.05
451 182 0.48
452 182 0.48
453 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (450 bp):
AGAAACTTTGGAAATCATTCTCATTTTTCAAAAAACACGTGAAAACATCATGGTCGAAAGTCTTA
CGGATAGCCCGAAGGACTTATCATCTTGATCGAAAGACTTATAGATGAACCGAAGAATTTAATCA
TCAAGCTCAAAAGACTTACTGATAGCACGAAGGACTTACCAATTTGGGAAATAGTTTACTAGGTA
AGAAACTTTGGAAATAGTTTTATTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACT
TTGGAAATCGTTTTATCATTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGAT
GACCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCAAATGATTTAATCATAATG
CTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTA
Found at i:1004457 original size:19 final size:19
Alignment explanation
Indices: 1004410--1004461 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
1004400 ATCATGCTCG
*
1004410 AAAGACTTACTGATGGCCC
1 AAAGACTTACTAATGGCCC
1004429 AAAGGACTTACTAATGGCCC
1 AAA-GACTTACTAATGGCCC
*
1004449 GAAGACTTACTAA
1 AAAGACTTACTAA
1004462 GTAAGAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (19 bp):
AAAGACTTACTAATGGCCC
Found at i:1005637 original size:12 final size:12
Alignment explanation
Indices: 1005620--1005647 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1005610 GAATGACAGA
1005620 ATTTTGTAAAGT
1 ATTTTGTAAAGT
1005632 ATTTTGTAAAGT
1 ATTTTGTAAAGT
1005644 ATTT
1 ATTT
1005648 CCCCTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (12 bp):
ATTTTGTAAAGT
Found at i:1006176 original size:2 final size:2
Alignment explanation
Indices: 1006169--1006221 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1006159 AGTTTTATTG
1006169 TA TA TA TA TA TA 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 TA TA TA TA TA TA
*
1006211 TA TA TA CA TA T
1 TA TA TA TA TA T
1006222 TCTACCGCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1016240 original size:21 final size:19
Alignment explanation
Indices: 1016202--1016247 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1016192 AATTAATCCT
1016202 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
1016222 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
1016243 A-TAAT
1 ACTAAT
1016248 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:1031658 original size:17 final size:18
Alignment explanation
Indices: 1031636--1031676 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1031626 GAATTCCAGA
1031636 ATACCAAAAT-GGTATCG
1 ATACCAAAATGGGTATCG
1031653 ATACCAAAATGGGTATCG
1 ATACCAAAATGGGTATCG
*
1031671 GTACCA
1 ATACCA
1031677 TAGAAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (18 bp):
ATACCAAAATGGGTATCG
Found at i:1032021 original size:12 final size:12
Alignment explanation
Indices: 1032004--1032043 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1031994 ATTACTTATT
*
1032004 TATTTTATGTAA
1 TATTTTATGCAA
1032016 TATTTTATGCAA
1 TATTTTATGCAA
1032028 TATTTTA--CAA
1 TATTTTATGCAA
1032038 TATTTT
1 TATTTT
1032044 GTTATACTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (12 bp):
TATTTTATGCAA
Found at i:1035881 original size:32 final size:32
Alignment explanation
Indices: 1035840--1035905 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1035830 ATACTATATA
1035840 GACAGAGTTTGTATTCCAAATGATGAGGAATT
1 GACAGAGTTTGTATTCCAAATGATGAGGAATT
1035872 GACAGAGTTTGTATTCCAAATGATGAGGAATT
1 GACAGAGTTTGTATTCCAAATGATGAGGAATT
1035904 GA
1 GA
1035906 AAAGAGATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (32 bp):
GACAGAGTTTGTATTCCAAATGATGAGGAATT
Found at i:1038139 original size:17 final size:18
Alignment explanation
Indices: 1038117--1038154 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1038107 ATTCATAATG
1038117 CCAAAAT-GGTATCGATA
1 CCAAAATGGGTATCGATA
*
1038134 CCAAAATGGGTATCGGTA
1 CCAAAATGGGTATCGATA
1038152 CCA
1 CCA
1038155 TAGAATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (18 bp):
CCAAAATGGGTATCGATA
Found at i:1038796 original size:23 final size:24
Alignment explanation
Indices: 1038752--1038828 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
1038742 GAGTTGAGGG
* **
1038752 TTCTACACGGTCCTTCAAGAC-AA
1 TTCTACATGGTCCTTCGGGACAAA
1038775 TTCTACATGGTCCTTCGGGACAAA
1 TTCTACATGGTCCTTCGGGACAAA
*
1038799 TTCT--ATGCAGTCATTCGGGACAAA
1 TTCTACATG--GTCCTTCGGGACAAA
1038823 TTCTAC
1 TTCTAC
1038829 GTGGCACTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
22 3 0.07
23 18 0.40
24 24 0.53
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (24 bp):
TTCTACATGGTCCTTCGGGACAAA
Found at i:1038839 original size:24 final size:24
Alignment explanation
Indices: 1038773--1038840 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
1038763 CCTTCAAGAC
*
1038773 AATTCTACATGGTC-CTTCGGGACA
1 AATTCTACGTGG-CACTTCGGGACA
* * *
1038797 AATTCTATGCAGTCA-TTCGGGACA
1 AATTCTACG-TGGCACTTCGGGACA
1038821 AATTCTACGTGGCACTTCGG
1 AATTCTACGTGGCACTTCGG
1038841 TGCAATTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
23 3 0.09
24 30 0.88
25 1 0.03
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGGACA
Found at i:1040376 original size:20 final size:21
Alignment explanation
Indices: 1040331--1040380 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1040321 AGATGAACAA
*
1040331 TATCGATACTTATTAAAGAAG
1 TATCGATACTGATTAAAGAAG
* *
1040352 TATCGATACTGA-TATAGAGG
1 TATCGATACTGATTAAAGAAG
1040372 TATCGATAC
1 TATCGATAC
1040381 CAAGAGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (21 bp):
TATCGATACTGATTAAAGAAG
Found at i:1042025 original size:15 final size:16
Alignment explanation
Indices: 1042002--1042034 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1041992 TCAAACCTTA
1042002 AAAACTCAAAACCCTC
1 AAAACTCAAAACCCTC
*
1042018 AAAA-TCAAAGCCCTC
1 AAAACTCAAAACCCTC
1042033 AA
1 AA
1042035 CTCCCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.52, C:0.33, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAACTCAAAACCCTC
Found at i:1044567 original size:16 final size:17
Alignment explanation
Indices: 1044526--1044560 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1044516 ATATGATTTA
1044526 TAAC-TTAAAAGCTTTG
1 TAACTTTAAAAGCTTTG
1044542 TAACTTTAAAAGC-TTG
1 TAACTTTAAAAGCTTTG
1044558 TAA
1 TAA
1044561 TATTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
TAACTTTAAAAGCTTTG
Found at i:1046857 original size:34 final size:34
Alignment explanation
Indices: 1046819--1046904 Score: 163
Period size: 34 Copynumber: 2.5 Consensus size: 34
1046809 TATATATATA
1046819 TATATATATAATATTTTTTATTTTTTATATTAAT
1 TATATATATAATATTTTTTATTTTTTATATTAAT
*
1046853 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTTTATTTTTTATATTAAT
1046887 TATATATATAATATTTTT
1 TATATATATAATATTTTT
1046905 GGGTTCGGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (34 bp):
TATATATATAATATTTTTTATTTTTTATATTAAT
Found at i:1046891 original size:25 final size:25
Alignment explanation
Indices: 1046803--1046891 Score: 62
Period size: 25 Copynumber: 3.6 Consensus size: 25
1046793 CCCCGCCCCG
*
1046803 ATTATATATA-TATATATATATATATA
1 ATTATATATATTATAT-TTTATAT-TA
* *
1046829 A-TAT-T-TTTTATTTTTTATATTA
1 ATTATATATATTATATTTTATATTA
* *
1046851 ATTATATATATAATATTTTATATTT
1 ATTATATATATTATATTTTATATTA
*
1046876 TTTATAT-TAATTATAT
1 ATTATATAT-ATTATAT
1046892 ATATAATATT
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
22 3 0.06
23 10 0.20
24 7 0.14
25 28 0.57
26 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTATATATATTATATTTTATATTA
Found at i:1059161 original size:16 final size:19
Alignment explanation
Indices: 1059123--1059161 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1059113 ACGAGAGAAA
1059123 AAGATATTCCTTTAGGATT
1 AAGATATTCCTTTAGGATT
1059142 AAGATATT-CTTT-GG-TT
1 AAGATATTCCTTTAGGATT
1059158 AAGA
1 AAGA
1059162 GTAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 4 0.20
19 8 0.40
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (19 bp):
AAGATATTCCTTTAGGATT
Found at i:1064138 original size:24 final size:24
Alignment explanation
Indices: 1064111--1064185 Score: 100
Period size: 23 Copynumber: 3.2 Consensus size: 24
1064101 AAACAAACAC
*
1064111 TAAATGAACACGTTCATGAATATA
1 TAAATGAACACGTTCGTGAATATA
*
1064135 TAAATGAACACGTTCGTGAACAT-
1 TAAATGAACACGTTCGTGAATATA
* *
1064158 TAAACGAACATGTTCGTGAATA-A
1 TAAATGAACACGTTCGTGAATATA
1064181 TAAAT
1 TAAAT
1064186 AAACGAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 23 0.52
24 21 0.48
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (24 bp):
TAAATGAACACGTTCGTGAATATA
Found at i:1064575 original size:2 final size:2
Alignment explanation
Indices: 1064568--1064596 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1064558 CCCCATACAT
1064568 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1064597 AATAAACCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1068341 original size:3 final size:3
Alignment explanation
Indices: 1068327--1068382 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
1068317 TCATTTCATT
* **
1068327 TTA TTA TAA TTA TTA TTA TTA AAA TTA TTA TTA TTA TATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
1068372 TT- TTT TTA TTA
1 TTA TTA TTA TTA
1068383 ATAAATTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1068373 original size:15 final size:15
Alignment explanation
Indices: 1068327--1068370 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1068317 TCATTTCATT
1068327 TTATTATAATTATTA
1 TTATTATAATTATTA
*
1068342 TTATTAAAATTATTA
1 TTATTATAATTATTA
1068357 TTATTATATATTAT
1 TTATTATA-ATTAT
1068371 ATTTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATAATTATTA
Found at i:1069737 original size:22 final size:23
Alignment explanation
Indices: 1069683--1069780 Score: 82
Period size: 22 Copynumber: 4.4 Consensus size: 23
1069673 TTTTCTAATA
* * *
1069683 TTTTTAAATGAATAAATATTTTAC
1 TTTTTAAAT-TATATATATATTAC
1069707 TTTTATAAATTATATATATATTA-
1 TTTT-TAAATTATATATATATTAC
*
1069730 TTTTTAAA-TA-A-ATATTTTAC
1 TTTTTAAATTATATATATATTAC
*
1069750 TTTTATAAA-T-TATATATATTAT
1 TTTT-TAAATTATATATATATTAC
1069772 TTTTTAAAT
1 TTTTTAAAT
1069781 GTTATATTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
19 7 0.11
20 5 0.08
21 12 0.19
22 15 0.24
23 4 0.06
24 14 0.23
25 5 0.08
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (23 bp):
TTTTTAAATTATATATATATTAC
Found at i:1069786 original size:21 final size:20
Alignment explanation
Indices: 1069721--1069798 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 20
1069711 ATAAATTATA
*
1069721 TATATATTA-TTTTTAAATA
1 TATATATTATTTTTTAAATT
* * *
1069740 AATATTTTACTTTTATAAATT
1 TATATATTA-TTTTTTAAATT
1069761 ATATATATTATTTTTTAAATGT
1 -TATATATTATTTTTTAAAT-T
*
1069783 TATATTAATATTTTTT
1 TATA-TATTATTTTTT
1069799 TTACTTTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
19 7 0.15
21 21 0.46
22 18 0.39
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (20 bp):
TATATATTATTTTTTAAATT
Found at i:1069788 original size:43 final size:43
Alignment explanation
Indices: 1069693--1069780 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
1069683 TTTTTAAATG
1069693 AATAAATATTTTACTTTTATAAATTATATATATATTATTTTTA
1 AATAAATATTTTACTTTTATAAATTATATATATATTATTTTTA
1069736 AATAAATATTTTACTTTTATAAA-T-TATATATATTATTTTTTA
1 AATAAATATTTTACTTTTATAAATTATATATATATTA-TTTTTA
1069778 AAT
1 AAT
1069781 GTTATATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
41 11 0.25
42 10 0.23
43 23 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (43 bp):
AATAAATATTTTACTTTTATAAATTATATATATATTATTTTTA
Found at i:1069895 original size:2 final size:2
Alignment explanation
Indices: 1069883--1069921 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1069873 ATATCTTATT
*
1069883 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1069922 TTTTCTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1071741 original size:14 final size:14
Alignment explanation
Indices: 1071717--1071751 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1071707 AAATTAGTAC
*
1071717 TTTATTTATTTATTT
1 TTTA-TTATTTATAT
1071732 TTTATTATTTATAT
1 TTTATTATTTATAT
1071746 TTTATT
1 TTTATT
1071752 CACTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTATTTATAT
Found at i:1071888 original size:17 final size:17
Alignment explanation
Indices: 1071868--1071931 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
1071858 TTTTAAATGA
1071868 ATAAATATTTTACTTTT
1 ATAAATATTTTACTTTT
*
1071885 ATAAATTATATATATTATTTTT
1 AT-AA--ATAT-T-TTACTTTT
1071907 AAATAAATATTTTACTTTT
1 --ATAAATATTTTACTTTT
1071926 ATAAAT
1 ATAAAT
1071932 TATATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 7 0.18
20 5 0.13
21 5 0.13
22 7 0.18
23 2 0.05
24 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAAATATTTTACTTTT
Found at i:1071899 original size:24 final size:24
Alignment explanation
Indices: 1071872--1071941 Score: 91
Period size: 20 Copynumber: 3.2 Consensus size: 24
1071862 AAATGAATAA
1071872 ATATTTTACTTTTATAAATTATAT
1 ATATTTTACTTTTATAAATTATAT
1071896 ATA--TTA-TTTT-TAAA-TA-A-
1 ATATTTTACTTTTATAAATTATAT
1071913 ATATTTTACTTTTATAAATTATAT
1 ATATTTTACTTTTATAAATTATAT
1071937 ATATT
1 ATATT
1071942 ATTTTTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
17 3 0.08
18 1 0.03
19 5 0.13
20 8 0.21
21 8 0.21
22 5 0.13
23 1 0.03
24 8 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTTTACTTTTATAAATTATAT
Done.