Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 100 of 325
Found at i:29470756 original size:2 final size:2
Alignment explanation
Indices: 29470749--29470793 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
29470739 TTGTTATCTT
29470749 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
29470791 TA T
1 TA T
29470794 TCAATTTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29472030 original size:19 final size:19
Alignment explanation
Indices: 29472006--29472070 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
29471996 GCTAGCATGT
*
29472006 AAGTGCATACTAGTACACA
1 AAGTGCATACTAGCACACA
* *
29472025 AAGTGCATCCTAGCGCACA
1 AAGTGCATACTAGCACACA
* * * *
29472044 AAGCGCATACTGGCTCACG
1 AAGTGCATACTAGCACACA
29472063 AAGTGCAT
1 AAGTGCAT
29472071 CCTGGCGCGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (19 bp):
AAGTGCATACTAGCACACA
Found at i:29472075 original size:19 final size:19
Alignment explanation
Indices: 29472021--29472078 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
29472011 CATACTAGTA
*
29472021 CACAAAGTGCATCCTAGCG
1 CACAAAGTGCATCCTGGCG
* * *
29472040 CACAAAGCGCATACTGGCT
1 CACAAAGTGCATCCTGGCG
*
29472059 CACGAAGTGCATCCTGGCG
1 CACAAAGTGCATCCTGGCG
29472078 C
1 C
29472079 GTAGGTGCAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.24, T:0.16
Consensus pattern (19 bp):
CACAAAGTGCATCCTGGCG
Found at i:29475035 original size:46 final size:46
Alignment explanation
Indices: 29474976--29475149 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 46
29474966 TATTTTGGCA
*
29474976 TCCGAGCTCGTTGAGTTGAGTCCGTGTTCACTTATGGATGCGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * *
29475022 TCCTAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
29475067 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
29475115 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTAT
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT
29475150 AGGCGGGTTA
Statistics
Matches: 106, Mismatches: 13, Indels: 18
0.77 0.09 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 59 0.56
47 27 0.25
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:29475082 original size:93 final size:93
Alignment explanation
Indices: 29474972--29475144 Score: 310
Period size: 93 Copynumber: 1.9 Consensus size: 93
29474962 CGGATATTTT
* * *
29474972 GGCATCCGAGCTCGTTGAGTTGAGTCCGTGTTCACTTATGGATGCGAACGTCCTAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29475037 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
29475065 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29475130 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
29475145 CTTATAGGCG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:29477757 original size:36 final size:36
Alignment explanation
Indices: 29477717--29477790 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
29477707 GGAAAGATGT
29477717 TAGCCAATGATCGATAAGGATGTCTTGAAAGTCAGA
1 TAGCCAATGATCGATAAGGATGTCTTGAAAGTCAGA
* *
29477753 TAGCCAATGCTTGATAAGGATGTCTTGAAAGTCAGA
1 TAGCCAATGATCGATAAGGATGTCTTGAAAGTCAGA
29477789 TA
1 TA
29477791 CATCTCATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (36 bp):
TAGCCAATGATCGATAAGGATGTCTTGAAAGTCAGA
Found at i:29482456 original size:41 final size:42
Alignment explanation
Indices: 29482399--29482483 Score: 154
Period size: 41 Copynumber: 2.0 Consensus size: 42
29482389 GTCTTCCAAT
29482399 TGGGATAAGAGTAATGGCTTTACTATCAT-CTCATTAAAAAA
1 TGGGATAAGAGTAATGGCTTTACTATCATCCTCATTAAAAAA
*
29482440 TGGGATAAGAGTAATGGCTTTACTATCATCCTCATTAAACAA
1 TGGGATAAGAGTAATGGCTTTACTATCATCCTCATTAAAAAA
29482482 TG
1 TG
29482484 ATCTTAAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 29 0.69
42 13 0.31
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (42 bp):
TGGGATAAGAGTAATGGCTTTACTATCATCCTCATTAAAAAA
Found at i:29485445 original size:18 final size:18
Alignment explanation
Indices: 29485422--29485458 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29485412 GCTTTCCTGA
*
29485422 TTATGGTCGAGAAATTAT
1 TTATGGTCGAGAAACTAT
*
29485440 TTATGGTTGAGAAACTAT
1 TTATGGTCGAGAAACTAT
29485458 T
1 T
29485459 ACCAATCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (18 bp):
TTATGGTCGAGAAACTAT
Found at i:29486856 original size:32 final size:31
Alignment explanation
Indices: 29486819--29486890 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 31
29486809 ATATTACAAA
29486819 AAACAAATTAAAATGAATTAATTAAACTAAC
1 AAACAAATTAAAATGAATTAATTAAACTAAC
29486850 ATAACAAATTAAAATGAATTAATTAAACTAAC
1 A-AACAAATTAAAATGAATTAATTAAACTAAC
29486882 AAA-AAATTA
1 AAACAAATTA
29486891 TCTAACATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
30 6 0.15
31 3 0.08
32 31 0.77
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.26
Consensus pattern (31 bp):
AAACAAATTAAAATGAATTAATTAAACTAAC
Found at i:29490968 original size:45 final size:44
Alignment explanation
Indices: 29490842--29490970 Score: 129
Period size: 45 Copynumber: 2.9 Consensus size: 44
29490832 ATGTCATACA
* * * * *
29490842 ATGCCAACGTCCTAGACGCGGTCTTACATGCTATCAC--ATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-AAACACATATATCG
* * *
29490885 ATGCC-ACTGTCCCAGACATGGTCTTACACGTAACCACATATATTG
1 ATGCCAAC-GTCCCAGACGTGGTCTTACACG-AAACACATATATCG
29490930 ATGCCAACGTCCCAGACGTGGTCTTACACGAGAACACATAT
1 ATGCCAACGTCCCAGACGTGGTCTTACACGA-AACACATAT
29490971 CGAAAATCCT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 2 0.03
43 27 0.38
44 1 0.01
45 39 0.55
46 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAACACATATATCG
Found at i:29492843 original size:39 final size:38
Alignment explanation
Indices: 29492734--29492858 Score: 169
Period size: 38 Copynumber: 3.3 Consensus size: 38
29492724 AGTTAACATA
* *
29492734 CTTAACATGTTTTCAGTTCAATAGTAGCATTAGGCATG
1 CTTAACATGTATTCAGTTCAATAGTAGCAGTAGGCATG
* **
29492772 CTTAACATGTATTCAGTTCAATAGTAACAGTAGATATG
1 CTTAACATGTATTCAGTTCAATAGTAGCAGTAGGCATG
** *
29492810 CTTAACATGTATTGGGGTTCAATAGTAGTAGTAGGCATG
1 CTTAACATGTATT-CAGTTCAATAGTAGCAGTAGGCATG
29492849 CTTAACATGT
1 CTTAACATGT
29492859 GTTTCGTAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 46 0.61
39 29 0.39
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (38 bp):
CTTAACATGTATTCAGTTCAATAGTAGCAGTAGGCATG
Found at i:29493763 original size:16 final size:16
Alignment explanation
Indices: 29493741--29493788 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
29493731 GAATTATGAT
29493741 GAAAAGAATAGAAAAA
1 GAAAAGAATAGAAAAA
* * *
29493757 TAAAAGAAAATAAAAA
1 GAAAAGAATAGAAAAA
*
29493773 GAGAAGAAATAGAAAA
1 GAAAAG-AATAGAAAA
29493789 GATGGAAACT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (16 bp):
GAAAAGAATAGAAAAA
Found at i:29497319 original size:123 final size:123
Alignment explanation
Indices: 29497095--29497556 Score: 825
Period size: 123 Copynumber: 3.8 Consensus size: 123
29497085 GAATTATGTG
*
29497095 AAATAAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
*
29497160 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
*
29497218 AAATGAAATATGGATGTGTAATTATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
29497283 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
*
29497341 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCCG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
29497406 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
* * * * *
29497464 AAATGAAATATGGATGTGTAATGATTATTGATTTATGTGTGCATGAGCAATTGAATGATACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
* *
29497529 GCTAAGTCCCGAAGACATTTATGCTAGT
66 GCTAAGTCCCGAAGGCAATTATGCTAGT
29497557 AATTATATCC
Statistics
Matches: 326, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 326 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (123 bp):
AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
Found at i:29497580 original size:40 final size:40
Alignment explanation
Indices: 29497525--29497768 Score: 292
Period size: 40 Copynumber: 6.1 Consensus size: 40
29497515 TGAATGATAC
* * * * **
29497525 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * * *
29497565 CCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT
*
29497605 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
*
29497645 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* *
29497685 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * * ** *
29497725 CCGGGCGAAGACCCGAGGGCATTCGTGCGTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
29497765 CCGG
1 CCGG
29497769 TTGTATTCCA
Statistics
Matches: 181, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
40 179 0.99
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
Found at i:29503657 original size:41 final size:40
Alignment explanation
Indices: 29503612--29503861 Score: 209
Period size: 41 Copynumber: 6.1 Consensus size: 40
29503602 GCAAAAATTT
**
29503612 TAAAATACAGAGCAATAGCAACGTTTTACAAAAAACGCCGC
1 TAAAA-ACAGAGCAATAGCGGCGTTTTACAAAAAACGCCGC
* * * *
29503653 TAAAAATAGAGCAACAACGGCGTTTTAGTAAAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGTTTTA-CAAAAAACGCCGC
* * ***
29503694 TAAAAACAGAGCATTAGCGGCGCTTTAGGTAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGTTTTACAAAAAACGCCGC
* ***
29503734 TAAAAACCAGAGCATTAGCGGCGCTTTT-GGTAAAACGCCGC
1 TAAAAA-CAGAGCAATAGCGGCG-TTTTACAAAAAACGCCGC
* ***
29503775 TAAAAACCAGAGCATTAGCGGCGCTTTT-GGTAAAACGCCGC
1 TAAAAA-CAGAGCAATAGCGGCG-TTTTACAAAAAACGCCGC
* **
29503816 TAAAAACTAGAGCATTAGCGGCGCTTTTA-GTAAAACGCCGC
1 TAAAAAC-AGAGCAATAGCGGCG-TTTTACAAAAAACGCCGC
29503857 TAAAA
1 TAAAA
29503862 GTCATATAAC
Statistics
Matches: 189, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
40 34 0.18
41 152 0.80
42 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGTTTTACAAAAAACGCCGC
Found at i:29503800 original size:82 final size:81
Alignment explanation
Indices: 29503643--29503861 Score: 343
Period size: 82 Copynumber: 2.7 Consensus size: 81
29503633 CGTTTTACAA
** *
29503643 AAAACGCCGCTAAAAA-TAGAGCAACAACGGCG-TTTTAGTAAAAAACGCCGCTAAAAACAGAGC
1 AAAACGCCGCTAAAAACTAGAGCATTAGCGGCGCTTTTAGT--AAAACGCCGCTAAAAACAGAGC
29503706 ATTAGCGGCGCTTTAGGT
64 ATTAGCGGCGCTTTAGGT
* *
29503724 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCA
1 AAAACGCCGCTAAAAACTAGAGCATTAGCGGCGCTTTTAGTAAAACGCCGCTAAAAA-CAGAGCA
*
29503789 TTAGCGGCGCTTTTGGT
65 TTAGCGGCGCTTTAGGT
29503806 AAAACGCCGCTAAAAACTAGAGCATTAGCGGCGCTTTTAGTAAAACGCCGCTAAAA
1 AAAACGCCGCTAAAAACTAGAGCATTAGCGGCGCTTTTAGTAAAACGCCGCTAAAA
29503862 GTCATATAAC
Statistics
Matches: 127, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
81 32 0.25
82 89 0.70
83 6 0.05
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (81 bp):
AAAACGCCGCTAAAAACTAGAGCATTAGCGGCGCTTTTAGTAAAACGCCGCTAAAAACAGAGCAT
TAGCGGCGCTTTAGGT
Found at i:29504653 original size:14 final size:14
Alignment explanation
Indices: 29504634--29504678 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
29504624 TTAATTATCA
29504634 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
29504648 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
* * *
29504662 GTATGGTTTAAGGT
1 TTATAGTTTAGGGT
29504676 TTA
1 TTA
29504679 ATTTTTAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:29507865 original size:26 final size:26
Alignment explanation
Indices: 29507829--29507938 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
29507819 CATGAAATTC
29507829 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29507855 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
29507881 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
29507907 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
29507933 TTATCA
1 TTATCA
29507939 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29513479 original size:30 final size:30
Alignment explanation
Indices: 29513445--29513501 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
29513435 TTCCCGAGCC
29513445 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
29513475 TAGGGGCAAAATTGTAATTTTGCAAAA
1 TAGGGGCAAAAGTGTAAATATGCAAAA
29513502 TTTTGAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.26
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:29514298 original size:64 final size:64
Alignment explanation
Indices: 29514217--29514388 Score: 177
Period size: 67 Copynumber: 2.7 Consensus size: 64
29514207 AGACATTATG
* *
29514217 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * ** * *
29514281 ATGTAGCTAGGTCGCATGCGTGGTTCCGGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATAC-TATG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
29514346 AA
63 AA
* * * *
29514348 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGT
29514389 GTACAACAGA
Statistics
Matches: 85, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
63 9 0.11
64 21 0.25
65 6 0.07
66 17 0.20
67 32 0.38
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:29519371 original size:29 final size:29
Alignment explanation
Indices: 29519338--29519439 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
29519328 TGACGAGATC
29519338 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
29519367 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
** * *
29519396 GGCACTAAGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
**
29519425 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
29519440 AGCTCGGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAATATAT
Found at i:29526621 original size:29 final size:29
Alignment explanation
Indices: 29526588--29526689 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
29526578 TGACGAGATC
29526588 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
29526617 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
** * *
29526646 GGCACTAAGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
**
29526675 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
29526690 AGCTCGGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAATATAT
Found at i:29529493 original size:42 final size:42
Alignment explanation
Indices: 29529443--29529618 Score: 187
Period size: 42 Copynumber: 4.0 Consensus size: 42
29529433 CTTCATTTTC
** * *
29529443 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
29529486 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
29529527 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT---AT-TCACATA
* *
29529576 TCAATGCCATAACCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
29529617 TC
1 TC
29529619 TCACTGATGT
Statistics
Matches: 116, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
41 11 0.09
42 63 0.54
43 2 0.02
45 2 0.02
47 1 0.01
48 2 0.02
49 35 0.30
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:29529586 original size:49 final size:48
Alignment explanation
Indices: 29529513--29529618 Score: 167
Period size: 49 Copynumber: 2.2 Consensus size: 48
29529503 TATGGTCTTA
* * *
29529513 CACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATA-TCACATATCAATGCCATAACCCAGCTATGGTCTTACACG-AAT
29529563 CACATATCACATATCAATGCCATAACCCAGCTATGGTCTTACACGAAT
1 CACATATCACATATCAATGCCATAACCCAGCTATGGTCTTACACGAAT
29529611 CACATATC
1 CACATATC
29529619 TCACTGATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
48 11 0.21
49 36 0.68
50 6 0.11
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.27
Consensus pattern (48 bp):
CACATATCACATATCAATGCCATAACCCAGCTATGGTCTTACACGAAT
Found at i:29529680 original size:47 final size:46
Alignment explanation
Indices: 29529528--29529698 Score: 162
Period size: 47 Copynumber: 3.6 Consensus size: 46
29529518 ATTCATATAT
* * * * *
29529528 CGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATAT
1 CGATGCCATATCCCAGATATGGTCTTATACG-AAGCACATATCAC--AC
* * * * * *
29529577 CAATGCCATAACCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * * * *
29529623 TGATGTCATATCTCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
29529670 CGATGCCATATCCCAGATATGGTCTTATA
1 CGATGCCATATCCCAGATATGGTCTTATA
29529699 TGGAAATCAC
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
46 24 0.23
47 38 0.37
48 12 0.12
49 29 0.28
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:29529753 original size:31 final size:31
Alignment explanation
Indices: 29529718--29529826 Score: 155
Period size: 31 Copynumber: 3.5 Consensus size: 31
29529708 CTTGTCACTT
* *
29529718 GTAGCCGAAGCTACTACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
29529749 GTAGCCGGAGCTACCATTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
29529780 GTAGCCGAAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
29529811 GTAGCAGAAGCTACCA
1 GTAGCCGAAGCTACCA
29529827 TGGCCTTACA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:29529944 original size:47 final size:46
Alignment explanation
Indices: 29529851--29529968 Score: 155
Period size: 47 Copynumber: 2.5 Consensus size: 46
29529841 TTCATATATC
* * * *
29529851 GATGCCATAGCCCAGCTATGGTCTTACACGAATCATATATCTCACT
1 GATGCCATATCCCAGATATGGTCTTACACGAAGCATATATCACACT
* * * *
29529897 GATGTCATATCTCAGATATGGTCTTATACAGTAGCATATATCACACT
1 GATGCCATATCCCAGATATGGTCTTACAC-GAAGCATATATCACACT
29529944 GATGCCATATCCCAGATATGGTCTT
1 GATGCCATATCCCAGATATGGTCTT
29529969 TTACGGAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
46 24 0.39
47 37 0.61
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (46 bp):
GATGCCATATCCCAGATATGGTCTTACACGAAGCATATATCACACT
Found at i:29530034 original size:31 final size:31
Alignment explanation
Indices: 29529991--29530139 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
29529981 CTTGTCACTT
* *
29529991 GTAGCCGAAGCTACCACTATTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
29530022 GTAGCCGGAGCTACCATTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
29530053 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
** *
29530084 GTAGTAGAAGCTATCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
29530115 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
29530140 TGTCATTTGT
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:29530067 original size:273 final size:272
Alignment explanation
Indices: 29529563--29530096 Score: 951
Period size: 273 Copynumber: 2.0 Consensus size: 272
29529553 TACACGTAAT
29529563 CACATATCACATATCAATGCCATAACCCAGCTATGGTCTTACACGAATCACATATCTCACTGATG
1 CACATATCACATATCAATGCCATAACCCAGCTATGGTCTTACACGAATCACATATCTCACTGATG
29529628 TCATATCTCAGATATGGTCTTATACAGTAGCATATATCACACCGATGCCATATCCCAGATATGGT
66 TCATATCTCAGATATGGTCTTATACAGTAGCATATATCACACCGATGCCATATCCCAGATATGGT
* *
29529693 CTTATATGGAAATCACTTGTCACTTGTAGCCGAAGCTACTACTATTCACTGATCAGGTAGCCGGA
131 CTTATACGGAAATCACTTGTCACTTGTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCGGA
29529758 GCTACCATTTTTCACTGATTAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAGCAGAAGCT
196 GCTACCATTTTTCACTGATTAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAGCAGAAGCT
29529823 ACCATGGCCTTA
261 ACCATGGCCTTA
* * * *
29529835 CACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCATATATCTCACTGAT
1 CACATA-TCACATATCAATGCCATAACCCAGCTATGGTCTTACACGAATCACATATCTCACTGAT
*
29529900 GTCATATCTCAGATATGGTCTTATACAGTAGCATATATCACACTGATGCCATATCCCAGATATGG
65 GTCATATCTCAGATATGGTCTTATACAGTAGCATATATCACACCGATGCCATATCCCAGATATGG
* *
29529965 TCTTTTACGGAAATCACTTGTCACTTGTAGCCGAAGCTACCACTATTCATTGATCAGGTAGCCGG
130 TCTTATACGGAAATCACTTGTCACTTGTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCGG
* * *
29530030 AGCTACCATTTTTCACTGATTAGGTAGCCGGAGCTACCACTTTTCACTGATCAGGTAGTAGAAGC
195 AGCTACCATTTTTCACTGATTAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAGCAGAAGC
29530095 TA
260 TA
29530097 TCACTTTTCA
Statistics
Matches: 249, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
272 6 0.02
273 243 0.98
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (272 bp):
CACATATCACATATCAATGCCATAACCCAGCTATGGTCTTACACGAATCACATATCTCACTGATG
TCATATCTCAGATATGGTCTTATACAGTAGCATATATCACACCGATGCCATATCCCAGATATGGT
CTTATACGGAAATCACTTGTCACTTGTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCGGA
GCTACCATTTTTCACTGATTAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAGCAGAAGCT
ACCATGGCCTTA
Found at i:29530226 original size:50 final size:50
Alignment explanation
Indices: 29530115--29530291 Score: 264
Period size: 50 Copynumber: 3.5 Consensus size: 50
29530105 CACTGATCAG
* * *
29530115 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTACTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* *
29530166 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATATGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* * *
29530216 GTAGTCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGA
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
29530266 GTAGCCGAAGCTATCATTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
29530292 GTTGCCATGG
Statistics
Matches: 113, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 89 0.79
51 24 0.21
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:29531105 original size:25 final size:25
Alignment explanation
Indices: 29531071--29531118 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
29531061 TACAAAGTCA
29531071 GAACAGGGGAACCCGAAATCATTTT
1 GAACAGGGGAACCCGAAATCATTTT
29531096 GAACAGGGGAACCCGAAATCATT
1 GAACAGGGGAACCCGAAATCATT
29531119 CTGACCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.17
Consensus pattern (25 bp):
GAACAGGGGAACCCGAAATCATTTT
Found at i:29534014 original size:2 final size:2
Alignment explanation
Indices: 29534007--29534039 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29533997 CATGTTGAAG
29534007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29534040 TAGAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29535033 original size:7 final size:7
Alignment explanation
Indices: 29535021--29535045 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29535011 ATTATGTGGG
29535021 AAAAGAA
1 AAAAGAA
29535028 AAAAGAA
1 AAAAGAA
29535035 AAAAGAA
1 AAAAGAA
29535042 AAAA
1 AAAA
29535046 ACACAGCCCT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:29538371 original size:46 final size:44
Alignment explanation
Indices: 29538267--29538374 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
29538257 TGTCTTTGAC
** * * *
29538267 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
29538311 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
29538357 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
29538375 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:29549828 original size:29 final size:29
Alignment explanation
Indices: 29549782--29549838 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
29549772 AGTTGACGGA
*
29549782 AAAAAAAAGCTAAGGTACCAATCTGGGAC
1 AAAAAAAACCTAAGGTACCAATCTGGGAC
* *
29549811 AAAAAAAACCATAA-GTACTAATTTGGGA
1 AAAAAAAACC-TAAGGTACCAATCTGGGA
29549839 GAAGCGGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.18
Consensus pattern (29 bp):
AAAAAAAACCTAAGGTACCAATCTGGGAC
Found at i:29551399 original size:20 final size:20
Alignment explanation
Indices: 29551374--29551423 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
29551364 TACGACCCCC
29551374 TAGCTCGCAGTACACTTGGT
1 TAGCTCGCAGTACACTTGGT
*
29551394 TAGCTCGAAGTACACTTGGT
1 TAGCTCGCAGTACACTTGGT
*
29551414 TAGTTCGCAG
1 TAGCTCGCAG
29551424 GTTTTATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (20 bp):
TAGCTCGCAGTACACTTGGT
Found at i:29552509 original size:18 final size:19
Alignment explanation
Indices: 29552468--29552511 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
29552458 CATACTTCAA
*
29552468 ATAGGTTCACATATAGCAT
1 ATAGGTTCACACATAGCAT
*
29552487 ATAGGTTCGCACAT-GCAT
1 ATAGGTTCACACATAGCAT
*
29552505 CTAGGTT
1 ATAGGTT
29552512 TGCATAAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (19 bp):
ATAGGTTCACACATAGCAT
Found at i:29552727 original size:18 final size:18
Alignment explanation
Indices: 29552668--29552727 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
29552658 CATGTGTTAG
*
29552668 GGTTCGCATAT-CATAGA
1 GGTTCGCATATACATATA
*
29552685 -GTTCGCACATACATATA
1 GGTTCGCATATACATATA
**
29552702 GGCCCGCATATACATATA
1 GGTTCGCATATACATATA
29552720 GGTTCGCA
1 GGTTCGCA
29552728 CATGTATATG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 9 0.26
17 5 0.15
18 20 0.59
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (18 bp):
GGTTCGCATATACATATA
Found at i:29555471 original size:46 final size:46
Alignment explanation
Indices: 29555404--29555571 Score: 178
Period size: 46 Copynumber: 3.6 Consensus size: 46
29555394 TGTAACCCGC
* *
29555404 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
* * * *
29555450 CCATAAGTGAACTCGGACTCAATTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG-TTCGCAT
* * * * * **
29555496 ACATTTCA-CGAACTCGGACTCAACTCGACGAGTTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
29555543 CCATAAGTGAACTCGGACTCAACTCAACG
1 CCATAAGTGAACTCGGACTCAACTCAACG
29555572 TGTGACAGCC
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
45 2 0.02
46 61 0.64
47 31 0.32
48 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTCGCAT
Found at i:29557343 original size:40 final size:40
Alignment explanation
Indices: 29557258--29557408 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
29557248 AATTGAATGA
* * *
29557258 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
29557298 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
29557339 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
29557378 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
29557409 ACGTGATTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:29557422 original size:40 final size:40
Alignment explanation
Indices: 29557294--29557424 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
29557284 TATGCTGGAA
* * *
29557294 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
** * * **
29557334 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGAC
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
*
29557374 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTG
29557414 ATTATATCCGG
1 ATTATATCCGG
29557425 TTATATTCCG
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 72 0.99
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
Found at i:29559257 original size:30 final size:30
Alignment explanation
Indices: 29559223--29559282 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
29559213 ATTTAATACG
29559223 AACTTTGGA-AAAATTACACTTTTGCCCCTA
1 AACTTT-GACAAAATTACACTTTTGCCCCTA
* *
29559253 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
29559283 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:29561280 original size:13 final size:12
Alignment explanation
Indices: 29561250--29561283 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
29561240 AAGAAGATGA
29561250 AAAAGAAAAGGG
1 AAAAGAAAAGGG
*
29561262 AGAAGAAATAGGG
1 AAAAGAAA-AGGG
29561275 AAAAGAAAA
1 AAAAGAAAA
29561284 CAAAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAGGG
Found at i:29561856 original size:22 final size:22
Alignment explanation
Indices: 29561828--29561871 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
29561818 CAAATATAAA
*
29561828 TGCATTCATAAAGTTTTTGAGT
1 TGCATTCATAAAGCTTTTGAGT
29561850 TGCATTCATAAAGCTTTTGAGT
1 TGCATTCATAAAGCTTTTGAGT
29561872 GATCCATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.43
Consensus pattern (22 bp):
TGCATTCATAAAGCTTTTGAGT
Found at i:29563280 original size:2 final size:2
Alignment explanation
Indices: 29563275--29563311 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29563265 TTTTTTAATA
29563275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29563312 AGTATTTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29563410 original size:14 final size:14
Alignment explanation
Indices: 29563391--29563418 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29563381 TGTGTGTGTG
29563391 TGTATATATATATA
1 TGTATATATATATA
29563405 TGTATATATATATA
1 TGTATATATATATA
29563419 ATATAAGATT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TGTATATATATATA
Found at i:29563607 original size:13 final size:13
Alignment explanation
Indices: 29563574--29563605 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
29563564 ATTTGTTTTA
29563574 TTAAAAATAACTT
1 TTAAAAATAACTT
29563587 TTAAAAATAA-TT
1 TTAAAAATAACTT
29563599 TTAAAAA
1 TTAAAAA
29563606 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAAATAACTT
Found at i:29564614 original size:2 final size:2
Alignment explanation
Indices: 29564609--29564646 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
29564599 TATAGTAATT
29564609 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
29564647 AAAGGTATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29582009 original size:24 final size:25
Alignment explanation
Indices: 29581982--29582048 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 25
29581972 TTAATTTTTT
*
29581982 TTAA-ATTTTAAGTTTGAAT-CGAAA
1 TTAATATTTTAA-TTTGAATACAAAA
*
29582006 TTAATTTTTTAATTTGAATACAAAA
1 TTAATATTTTAATTTGAATACAAAA
29582031 TTATAATATTTTATATTT
1 -T-TAATATTTTA-ATTT
29582049 TTACATCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 11 0.31
25 10 0.29
26 1 0.03
27 9 0.26
28 4 0.11
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (25 bp):
TTAATATTTTAATTTGAATACAAAA
Found at i:29582377 original size:21 final size:20
Alignment explanation
Indices: 29582342--29582387 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
29582332 AGGGTCAGAG
*
29582342 GAAAAGAAGAAGGAGAAGAA
1 GAAAAGAAAAAGGAGAAGAA
29582362 GAAAAGAAAAAAGGAGAAGAA
1 GAAAAG-AAAAAGGAGAAGAA
29582383 GAAAA
1 GAAAA
29582388 ATGGAGATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
GAAAAGAAAAAGGAGAAGAA
Found at i:29582381 original size:18 final size:16
Alignment explanation
Indices: 29582361--29582394 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29582351 AAGGAGAAGA
29582361 AGAA-AAGAAAAAAGG
1 AGAAGAAGAAAAAAGG
*
29582376 AGAAGAAGAAAAATGG
1 AGAAGAAGAAAAAAGG
29582392 AGA
1 AGA
29582395 TGCTTGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (16 bp):
AGAAGAAGAAAAAAGG
Found at i:29591655 original size:6 final size:6
Alignment explanation
Indices: 29591644--29591690 Score: 76
Period size: 6 Copynumber: 7.5 Consensus size: 6
29591634 ATAATTTAAT
29591644 AAATAA AAATAA AAATAA AAATAAA AAACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAAT-AA AAA-TAA AAATAA AAATAA AAA
29591691 ACATATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 28 0.72
7 10 0.26
8 1 0.03
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:29591676 original size:20 final size:20
Alignment explanation
Indices: 29591644--29591692 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
29591634 ATAATTTAAT
29591644 AAAT-AAAAA-TAAAAATAA
1 AAATAAAAAACTAAAAATAA
29591662 AAATAAAAAACTAAAAATAA
1 AAATAAAAAACTAAAAATAA
29591682 AAATAAAAAAC
1 AAATAAAAAAC
29591693 ATATAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 20 0.69
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.14
Consensus pattern (20 bp):
AAATAAAAAACTAAAAATAA
Found at i:29591730 original size:9 final size:9
Alignment explanation
Indices: 29591718--29591795 Score: 52
Period size: 9 Copynumber: 8.7 Consensus size: 9
29591708 AATAATTTAG
29591718 TTAATTCGA
1 TTAATTCGA
*
29591727 TTAATTCGG
1 TTAATTCGA
*
29591736 TTAATTTGGA
1 TTAA-TTCGA
*
29591746 -TAATTCGG
1 TTAATTCGA
* *
29591754 GTAACTCCG-
1 TTAA-TTCGA
*
29591763 GTAATTCGA
1 TTAATTCGA
29591772 TTAATTCGA
1 TTAATTCGA
* *
29591781 TCAATTCGG
1 TTAATTCGA
29591790 TTAATT
1 TTAATT
29591796 TTATACTTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
8 6 0.11
9 42 0.78
10 6 0.11
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (9 bp):
TTAATTCGA
Found at i:29591738 original size:18 final size:18
Alignment explanation
Indices: 29591717--29591795 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
29591707 AAATAATTTA
29591717 GTTAATTCGATTAATTCG
1 GTTAATTCGATTAATTCG
*
29591735 GTTAATTTGGA-TAATTCG
1 GTTAA-TTCGATTAATTCG
* * *
29591753 GGTAACTCCG-GTAATTCG
1 GTTAA-TTCGATTAATTCG
* *
29591771 ATTAATTCGATCAATTCG
1 GTTAATTCGATTAATTCG
29591789 GTTAATT
1 GTTAATT
29591796 TTATACTTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
17 3 0.06
18 40 0.85
19 4 0.09
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (18 bp):
GTTAATTCGATTAATTCG
Found at i:29591749 original size:27 final size:27
Alignment explanation
Indices: 29591710--29591796 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
29591700 TTTATACAAA
*
29591710 TAATTTAGTTAATTCGATTAATTCGGT
1 TAATTTAGATAATTCGATTAATTCGGT
* ** *
29591737 TAATTTGGATAATTCGGGTAACTCCGG-
1 TAATTTAGATAATTCGATTAA-TTCGGT
* *
29591764 TAA-TTCGATTAATTCGATCAATTCGGT
1 TAATTTAGA-TAATTCGATTAATTCGGT
29591791 TAATTT
1 TAATTT
29591797 TATACTTATT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
26 8 0.17
27 32 0.70
28 6 0.13
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (27 bp):
TAATTTAGATAATTCGATTAATTCGGT
Found at i:29599293 original size:9 final size:9
Alignment explanation
Indices: 29599279--29599364 Score: 109
Period size: 9 Copynumber: 9.6 Consensus size: 9
29599269 ATAAGTATAA
29599279 AATTAACCG
1 AATTAACCG
29599288 AATTAACCG
1 AATTAACCG
* *
29599297 AGTTAATCG
1 AATTAACCG
*
29599306 AATTAACTG
1 AATTAACCG
*
29599315 AATTAACTG
1 AATTAACCG
*
29599324 AATTATCCG
1 AATTAACCG
* *
29599333 AATTACCCA
1 AATTAACCG
29599342 AATTAACCG
1 AATTAACCG
29599351 AATTAACCG
1 AATTAACCG
29599360 AATTA
1 AATTA
29599365 TTTGTATAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:29599395 original size:6 final size:6
Alignment explanation
Indices: 29599384--29599430 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
29599374 AATTATATGT
* *
29599384 TTTTTA TTTTTA TTTTTA GTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
29599431 ATTAAATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
6 27 0.77
7 7 0.20
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:29606268 original size:58 final size:58
Alignment explanation
Indices: 29606198--29606323 Score: 243
Period size: 58 Copynumber: 2.2 Consensus size: 58
29606188 ATAATGGGTT
29606198 AAGGGTTAATATTGAGGGTAATACAAGGAATGACTTGTTAGGCTCAAAGGGGTATACA
1 AAGGGTTAATATTGAGGGTAATACAAGGAATGACTTGTTAGGCTCAAAGGGGTATACA
*
29606256 AAGGGTTAATATTGAGGGTAATACAAGGAATGACTTGTTAGGCTCAAAGGGGTTTACA
1 AAGGGTTAATATTGAGGGTAATACAAGGAATGACTTGTTAGGCTCAAAGGGGTATACA
29606314 AAGGGTTAAT
1 AAGGGTTAAT
29606324 CGTGGAGGTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 67 1.00
ACGTcount: A:0.36, C:0.08, G:0.29, T:0.27
Consensus pattern (58 bp):
AAGGGTTAATATTGAGGGTAATACAAGGAATGACTTGTTAGGCTCAAAGGGGTATACA
Found at i:29611650 original size:31 final size:31
Alignment explanation
Indices: 29611612--29611729 Score: 175
Period size: 31 Copynumber: 3.8 Consensus size: 31
29611602 ACAAATGACA
* *
29611612 AGTGAAAAGTGGTAGTTCCGGTTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
29611643 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
29611674 AATGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
29611705 AGTGAATAGTGGTAGCGT-CGGCTAC
1 AGTGAAAAGTGGTAGC-TCCGGCTAC
29611730 AAGTGACAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 78 0.99
32 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:29611824 original size:47 final size:46
Alignment explanation
Indices: 29611754--29611918 Score: 160
Period size: 47 Copynumber: 3.7 Consensus size: 46
29611744 AAGTGATTTC
* *
29611754 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * *
29611800 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * * *
29611847 CGTGTAAGACCATAGCTAGGCTATGGCATC-----GATATATGAATA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATG-ATA
* * * *
29611889 TGTGTAAGACCATAGCTGGGCTATGGCATC
1 CGTATAAGACCATATCTGGGATATGGCATC
29611919 ATTATGTGAA
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
41 7 0.07
42 30 0.29
46 26 0.25
47 41 0.39
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
Found at i:29611911 original size:42 final size:43
Alignment explanation
Indices: 29611848--29611962 Score: 162
Period size: 42 Copynumber: 2.7 Consensus size: 43
29611838 TATGTGATTC
* *
29611848 GTGTAAGACCATAGCTAGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
29611890 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
29611932 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
29611963 GAAAATGAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 63 0.97
43 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:29616377 original size:50 final size:51
Alignment explanation
Indices: 29616300--29616428 Score: 192
Period size: 50 Copynumber: 2.5 Consensus size: 51
29616290 GACCATGGCA
29616300 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
29616351 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* *
29616401 ACAAGTGAAAAGTGGTAG-TTCCGGCTAC
1 ACAAGTGATAAGTGATAGCTT-CGGCTAC
29616429 CTGACCAGTG
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
50 47 0.65
51 25 0.35
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:29616442 original size:31 final size:31
Alignment explanation
Indices: 29616399--29616521 Score: 183
Period size: 31 Copynumber: 4.0 Consensus size: 31
29616389 CAATGACAAA
* *
29616399 TGACAAGTGAAAAGTGGTAGTTCCGGCTACC
1 TGACCAGTGAAAAGTGGTAGCTCCGGCTACC
29616430 TGACCAGTGAAAAGTGGTAGCTCCGGCTACC
1 TGACCAGTGAAAAGTGGTAGCTCCGGCTACC
* *
29616461 TGATCAGTGAAAAATGGTAGCTCCGGCTACC
1 TGACCAGTGAAAAGTGGTAGCTCCGGCTACC
* * *
29616492 TGATCAGTGAATAGTGGTAGCTTCGGCTAC
1 TGACCAGTGAAAAGTGGTAGCTCCGGCTAC
29616522 AAGTGACAAG
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (31 bp):
TGACCAGTGAAAAGTGGTAGCTCCGGCTACC
Found at i:29616616 original size:47 final size:46
Alignment explanation
Indices: 29616546--29616669 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
29616536 AAGTGATTTC
* *
29616546 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * *
29616592 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * * *
29616639 CGTGTAAGACCATAGCTAGGCTATGGCATCG
1 CGTATAAGACCATATCTGGGATATGGCATCG
29616670 ATATATGAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 26 0.39
47 41 0.61
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
Found at i:29616733 original size:42 final size:39
Alignment explanation
Indices: 29616640--29616752 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 39
29616630 TATGTGATTC
*
29616640 GTGTAAGACCATAGCTAGGCTATGGCATCGATATATGAAT
1 GTGTAAGACCATAG-TTGGCTATGGCATCGATATATGAAT
*
29616680 GTGTAAGACCATAGTTGGTCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGTTGG-CTATGGCATCGA-TATATG-A-AT
* *
29616722 GTGTAAGACCATGGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGTTG-GCTATGGCATCGA
29616753 GAAAATGAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
39 4 0.06
40 29 0.46
41 1 0.02
42 28 0.44
43 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (39 bp):
GTGTAAGACCATAGTTGGCTATGGCATCGATATATGAAT
Found at i:29620445 original size:38 final size:35
Alignment explanation
Indices: 29620386--29620486 Score: 129
Period size: 31 Copynumber: 2.9 Consensus size: 35
29620376 TCAATCATGC
*
29620386 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
29620425 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
29620456 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATT
29620487 ACTGGGCCGG
Statistics
Matches: 57, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
31 27 0.47
33 3 0.05
34 1 0.02
36 1 0.02
38 14 0.25
39 11 0.19
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:29620447 original size:31 final size:31
Alignment explanation
Indices: 29620409--29620503 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
29620399 CCTTTTCATA
*
29620409 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
29620440 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
*
29620471 TTTCATATTTCATATTACTGGGCCGGAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
29620502 TT
1 TT
29620504 ACTGTAAACG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:29620746 original size:24 final size:24
Alignment explanation
Indices: 29620695--29620908 Score: 344
Period size: 24 Copynumber: 9.0 Consensus size: 24
29620685 GCTTTATCAT
* *
29620695 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* **
29620720 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTG
29620744 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
29620767 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
29620791 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
29620815 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
29620838 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
29620862 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
29620886 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
29620909 TCACTTCCTC
Statistics
Matches: 181, Mismatches: 5, Indels: 7
0.94 0.03 0.04
Matches are distributed among these distances:
23 46 0.25
24 123 0.68
25 12 0.07
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:29620774 original size:47 final size:48
Alignment explanation
Indices: 29620695--29620908 Score: 344
Period size: 47 Copynumber: 4.5 Consensus size: 48
29620685 GCTTTATCAT
* * * **
29620695 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTG
29620744 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
29620791 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
29620838 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
29620886 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
29620909 TCACTTCCTC
Statistics
Matches: 158, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
47 91 0.58
48 55 0.35
49 12 0.08
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
Found at i:29620795 original size:71 final size:71
Alignment explanation
Indices: 29620694--29620908 Score: 360
Period size: 71 Copynumber: 3.0 Consensus size: 71
29620684 TGCTTTATCA
* * * **
29620694 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
1 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
29620758 AGCCCTTT
64 AGCCCTTT
29620766 TATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG
1 TATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG
29620831 CCCTTT
66 CCCTTT
29620837 TATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG
1 TATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG
29620902 CCCTTT
66 CCCTTT
29620908 T
1 T
29620909 TCACTTCCTC
Statistics
Matches: 137, Mismatches: 5, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
71 124 0.91
72 13 0.09
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (71 bp):
TATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG
CCCTTT
Found at i:29620984 original size:20 final size:20
Alignment explanation
Indices: 29620959--29621038 Score: 133
Period size: 20 Copynumber: 4.0 Consensus size: 20
29620949 TATGATTACC
29620959 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
29620979 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATA
*
29620999 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATA
*
29621019 TCATGTGCATCTCATACATA
1 TCATGTGCATATCATACATA
29621039 CCATATTTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:29620989 original size:11 final size:11
Alignment explanation
Indices: 29620959--29621013 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
29620949 TATGATTACC
29620959 TCATGTGCATA
1 TCATGTGCATA
*
29620970 TCA--TACATA
1 TCATGTGCATA
29620979 TCATGTGCATA
1 TCATGTGCATA
* *
29620990 TCA--TACATG
1 TCATGTGCATA
29620999 TCATGTGCATA
1 TCATGTGCATA
29621010 TCAT
1 TCAT
29621014 ACATGTCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:29621113 original size:25 final size:25
Alignment explanation
Indices: 29621081--29621128 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29621071 ATACATAAAC
* * *
29621081 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29621106 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29621129 CATGGTATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29625234 original size:11 final size:11
Alignment explanation
Indices: 29625218--29625242 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29625208 TCATAACACC
29625218 AAAACATGGTT
1 AAAACATGGTT
29625229 AAAACATGGTT
1 AAAACATGGTT
29625240 AAA
1 AAA
29625243 TTAAAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (11 bp):
AAAACATGGTT
Found at i:29628704 original size:21 final size:20
Alignment explanation
Indices: 29628667--29628708 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
29628657 GAACACAAAT
*
29628667 TTAACTTGCCATATTAGCTGG
1 TTAACTTGCCACATTAG-TGG
*
29628688 TTAACTTGCCACGTTAGTGG
1 TTAACTTGCCACATTAGTGG
29628708 T
1 T
29628709 CCTATTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TTAACTTGCCACATTAGTGG
Found at i:29630914 original size:39 final size:38
Alignment explanation
Indices: 29630871--29630968 Score: 115
Period size: 39 Copynumber: 2.6 Consensus size: 38
29630861 AACATGTTTT
** *
29630871 TGAGTATTGTGATATATGCTTGAATGTTATGCGATTATA
1 TGAGTATTGTGATATATGCTTGAACATTATG-GAATATA
* * *
29630910 TGAGTATTGCGATATGTGCTTGAACATTATGTAATATA
1 TGAGTATTGTGATATATGCTTGAACATTATGGAATATA
* *
29630948 TGTGTAATGTGATATATGCTT
1 TGAGTATTGTGATATATGCTT
29630969 AAAAGTGAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (38 bp):
TGAGTATTGTGATATATGCTTGAACATTATGGAATATA
Found at i:29645760 original size:24 final size:24
Alignment explanation
Indices: 29645733--29645782 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
29645723 GTACTGATTC
*
29645733 TAAAAAATTCAAAAAATATAATTT
1 TAAAAAATTCAAAAAATATAAATT
* * *
29645757 TAAAAACTTGAAAATATATAAATT
1 TAAAAAATTCAAAAAATATAAATT
29645781 TA
1 TA
29645783 TTAGAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (24 bp):
TAAAAAATTCAAAAAATATAAATT
Found at i:29645921 original size:23 final size:23
Alignment explanation
Indices: 29645895--29645940 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29645885 ATTTTAACAA
29645895 AATTTTTTAGAGATTCAACCAAT
1 AATTTTTTAGAGATTCAACCAAT
29645918 AATTTTTTAGAGATTCAACCAAT
1 AATTTTTTAGAGATTCAACCAAT
29645941 TTTAACCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (23 bp):
AATTTTTTAGAGATTCAACCAAT
Found at i:29646400 original size:10 final size:10
Alignment explanation
Indices: 29646385--29646409 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29646375 AGATTGTGAG
29646385 GTTTGGGTGT
1 GTTTGGGTGT
29646395 GTTTGGGTGT
1 GTTTGGGTGT
29646405 GTTTG
1 GTTTG
29646410 TAATTTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (10 bp):
GTTTGGGTGT
Found at i:29647342 original size:5 final size:5
Alignment explanation
Indices: 29647305--29647360 Score: 60
Period size: 5 Copynumber: 11.2 Consensus size: 5
29647295 TATTTACGTG
* * * *
29647305 TTTA- TTTAT TTTAA TTTAA TTTAA TATATT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT
29647355 TTTAT T
1 TTTAT T
29647361 AATATAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
4 4 0.09
5 39 0.85
6 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:29647343 original size:21 final size:21
Alignment explanation
Indices: 29647313--29647357 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29647303 TGTTTATTTA
29647313 TTTTAATTTAATTTAATATAT
1 TTTTAATTTAATTTAATATAT
* * * *
29647334 TTTTATTTTATTTTATTTTAT
1 TTTTAATTTAATTTAATATAT
29647355 TTT
1 TTT
29647358 ATTAATATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTAATTTAATTTAATATAT
Found at i:29649313 original size:32 final size:32
Alignment explanation
Indices: 29649277--29649340 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
29649267 CGGAAGAAGA
29649277 TGTGCCACCTATGGCTACGCAATATCTATGTC
1 TGTGCCACCTATGGCTACGCAATATCTATGTC
29649309 TGTGCCACCTATGGCTACGCAATATCTATGTC
1 TGTGCCACCTATGGCTACGCAATATCTATGTC
29649341 ACTTCCCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (32 bp):
TGTGCCACCTATGGCTACGCAATATCTATGTC
Found at i:29651421 original size:46 final size:45
Alignment explanation
Indices: 29651369--29651544 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
29651359 TGGTTGAGCA
29651369 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
29651415 TTCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
29651462 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
29651508 CCCGAGCTCATTGAGTTGAGTTCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29651545 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.62
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:29651525 original size:93 final size:93
Alignment explanation
Indices: 29651366--29651536 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
29651356 GGATGGTTGA
* ** *
29651366 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
29651431 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
29651459 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
*
29651524 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
29651537 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:29656780 original size:17 final size:17
Alignment explanation
Indices: 29656758--29656794 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
29656748 TGAAAAGGAG
29656758 AACAAATGAATCTTAAA
1 AACAAATGAATCTTAAA
29656775 AACAAATGAATCTTAAA
1 AACAAATGAATCTTAAA
29656792 AAC
1 AAC
29656795 TTAATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.22
Consensus pattern (17 bp):
AACAAATGAATCTTAAA
Found at i:29660566 original size:29 final size:29
Alignment explanation
Indices: 29660533--29660693 Score: 223
Period size: 29 Copynumber: 5.6 Consensus size: 29
29660523 GTGACGAGAT
29660533 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
29660562 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
29660591 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * *
29660620 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ** *
29660649 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
29660678 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
29660694 AGCTCGAAGG
Statistics
Matches: 120, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 120 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:29660721 original size:87 final size:87
Alignment explanation
Indices: 29660529--29660713 Score: 219
Period size: 87 Copynumber: 2.1 Consensus size: 87
29660519 TATGGTGACG
* * * ** * *
29660529 AGAT-TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCGTGCTGGAAATATATG
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATATGACACTAAGTGTGCAAGCTGGAAAAATACG
* *
29660593 GCACTAAGTGTGCGTGCTGGAA
66 GCACTAAGTGTGCGAGCTCGAA
* * *
29660615 ATATAAGGCACTAAGTGTGCATGCTGGAAAAATATGACACTATGTGTGCAAGCTGGAAAAATACG
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATATGACACTAAGTGTGCAAGCTGGAAAAATACG
**
29660680 GCACTGGGTGTGCGAGCTCGAA
66 GCACTAAGTGTGCGAGCTCGAA
* *
29660702 GGGTATGGCACT
1 AGATATGGCACT
29660714 GTGTGTGCGG
Statistics
Matches: 80, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
86 3 0.04
87 77 0.96
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.24
Consensus pattern (87 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAAAATATGACACTAAGTGTGCAAGCTGGAAAAATACG
GCACTAAGTGTGCGAGCTCGAA
Found at i:29668696 original size:57 final size:57
Alignment explanation
Indices: 29668625--29668774 Score: 203
Period size: 57 Copynumber: 2.6 Consensus size: 57
29668615 GTGACGAGAT
* *
29668625 TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATAAGGCACTAAGTGTGCATGCTGGAAA-ATA
29668683 TGGCACTAA-TGTGCGTGCTGGAAATATAAGGCACTAAGTGTGCATGCTGGAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATAAGGCACTAAGTGTGCATGCTGGAAAATA
* ** ** * *
29668739 TGACACTCTGTGTGCAAGCTGGAAAAATACGGCACT
1 TGGCACTAAGTGTGCGTGCTGGAAATATAAGGCACT
29668775 GGGTGTGCGA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
56 9 0.11
57 64 0.78
58 9 0.11
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (57 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATAAGGCACTAAGTGTGCATGCTGGAAAATA
Found at i:29668704 original size:28 final size:29
Alignment explanation
Indices: 29668625--29668783 Score: 205
Period size: 29 Copynumber: 5.6 Consensus size: 29
29668615 GTGACGAGAT
29668625 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
29668654 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
29668683 TGGCACTAA-TGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* *
29668711 AGGCACTAAGTGTGCATGCTGGAAA-ATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** ** *
29668739 TGACACTCTGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
29668768 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
29668784 AGCTCGAAGG
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
28 50 0.43
29 66 0.57
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:29677756 original size:2 final size:2
Alignment explanation
Indices: 29677749--29677780 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
29677739 TTGATATGAC
*
29677749 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29677781 TGTTGAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29681463 original size:35 final size:35
Alignment explanation
Indices: 29681416--29681485 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
29681406 TCCTTAGTGA
*
29681416 GAAGTATGTTATAGCCCAATTTTGCCCTATGACCC
1 GAAGTATATTATAGCCCAATTTTGCCCTATGACCC
*
29681451 GAAGTATATTATAGCCCAATTTTGTCCTATGACCC
1 GAAGTATATTATAGCCCAATTTTGCCCTATGACCC
29681486 ATTTACAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (35 bp):
GAAGTATATTATAGCCCAATTTTGCCCTATGACCC
Found at i:29681640 original size:13 final size:13
Alignment explanation
Indices: 29681622--29681674 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
29681612 TGCCCTATGG
29681622 TCTGCCACCACCT
1 TCTGCCACCACCT
*
29681635 TCTGCCACCACCG
1 TCTGCCACCACCT
* *
29681648 TCGGCCACCTACCC
1 TCTGCCACC-ACCT
29681662 TCTGCCACCACCT
1 TCTGCCACCACCT
29681675 GCTCCTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.15, C:0.55, G:0.11, T:0.19
Consensus pattern (13 bp):
TCTGCCACCACCT
Found at i:29682583 original size:3 final size:3
Alignment explanation
Indices: 29682575--29682729 Score: 118
Period size: 3 Copynumber: 51.0 Consensus size: 3
29682565 CTTTATTAAA
* * * *
29682575 TAT TAT TAT TAT CAT T-T CTAA TAT TAT TAA TAT TAT TAT T-T AGAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * * * * * * *
29682620 TAT TGT TAT TAT TAC TAT TAT TAA TAT TCT TGT TAT TAA CAT TGT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
29682668 TAT TCCT T-T TAT TAAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT T-AT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
29682715 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
29682730 CATCAATATG
Statistics
Matches: 119, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
2 4 0.03
3 106 0.89
4 9 0.08
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:29683148 original size:19 final size:19
Alignment explanation
Indices: 29683124--29683162 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
29683114 TACTATTTTA
*
29683124 TGTATATTTCTAATATCAT
1 TGTATATTTCTAACATCAT
29683143 TGTATATTTCTAACATCAT
1 TGTATATTTCTAACATCAT
29683162 T
1 T
29683163 ATTATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (19 bp):
TGTATATTTCTAACATCAT
Found at i:29683240 original size:24 final size:22
Alignment explanation
Indices: 29683210--29683256 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
29683200 AATAGTTTTT
29683210 TATATTAT-TATCATTTCTAATATA
1 TATATTATATAT-ATTT-T-ATATA
29683234 TATATTATATATATTTTATATA
1 TATATTATATATATTTTATATA
29683256 T
1 T
29683257 TATGTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 1 0.05
24 12 0.55
25 3 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATTATATATATTTTATATA
Found at i:29683244 original size:9 final size:9
Alignment explanation
Indices: 29683230--29683259 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
29683220 TCATTTCTAA
29683230 TATATATAT
1 TATATATAT
29683239 TATATATAT
1 TATATATAT
*
29683248 TTTATATAT
1 TATATATAT
29683257 TAT
1 TAT
29683260 GTATGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATATATAT
Found at i:29683524 original size:22 final size:21
Alignment explanation
Indices: 29683499--29683567 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
29683489 ATATATAGTA
29683499 TTATT-TTCATACATCATTATAT
1 TTATTATT-ATACAT-ATTATAT
29683521 TTATTATTATACATATTAT-T
1 TTATTATTATACATATTATAT
* *
29683541 TTCACTATTATCACTTATTAT-T
1 TT-ATTATTAT-ACATATTATAT
29683563 TTATT
1 TTATT
29683568 TTAATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 3 0.07
21 14 0.34
22 22 0.54
23 2 0.05
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATTATTATACATATTATAT
Found at i:29683750 original size:2 final size:2
Alignment explanation
Indices: 29683743--29683773 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29683733 TATTACTATT
29683743 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29683774 TCTACGTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29694952 original size:44 final size:44
Alignment explanation
Indices: 29694889--29694973 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
29694879 TGCCTAAAAA
* * *
29694889 AAAAAAGAATCAAGGTGAAAATCCGAAAAGGGCGTCTTGATAAT
1 AAAAAAGAATCAAGGTGAAAACCCAAAAAGAGCGTCTTGATAAT
*
29694933 AAAAAAGGATCAAGGTGAAAACCCAAAAAGAGCGTCTTGAT
1 AAAAAAGAATCAAGGTGAAAACCCAAAAAGAGCGTCTTGAT
29694974 TAACACAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.16
Consensus pattern (44 bp):
AAAAAAGAATCAAGGTGAAAACCCAAAAAGAGCGTCTTGATAAT
Found at i:29694984 original size:44 final size:43
Alignment explanation
Indices: 29694889--29695000 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 43
29694879 TGCCTAAAAA
* * * *
29694889 AAAAAAGAATCAAGGTGAAAATCCGAAAAGGGCGTCTTGATAAT
1 AAAAAAGGATCAAGGTGAAAACCCAAAAAGAGCGTCTTGAT-AT
29694933 AAAAAAGGATCAAGGTGAAAACCCAAAAAGAGCGTCTTGAT-T
1 AAAAAAGGATCAAGGTGAAAACCCAAAAAGAGCGTCTTGATAT
*
29694975 AACACAAAGGAT-TAGGATGAAAACCC
1 AA-A-AAAGGATCAAGG-TGAAAACCC
29695001 GAAAGGGAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
42 3 0.05
43 4 0.07
44 53 0.88
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.16
Consensus pattern (43 bp):
AAAAAAGGATCAAGGTGAAAACCCAAAAAGAGCGTCTTGATAT
Found at i:29696060 original size:73 final size:72
Alignment explanation
Indices: 29695790--29696093 Score: 430
Period size: 74 Copynumber: 4.2 Consensus size: 72
29695780 TGATGTTTTT
* * * *
29695790 ATTTTTGTTGTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG-TACGCTGAGG
1 ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGG
29695854 TATTTTCA
65 TATTTTCA
* ** * * *
29695862 ATTTCTGCTTTTCAAAAATTCAACTCATATTGTGAGAAATGACTTGAGCCTCAGGGCATGCTGAG
1 ATTTCTG-TTTTCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
29695927 GTATTTTCA
64 GTATTTTCA
*
29695936 ATTTCTGTCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGGGCCTCAGGACACGCTGAG
1 ATTTCTGT-TTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
29696001 GTAATTTCA
64 GTATTTTCA
*
29696010 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
1 ATTTCTGTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
29696075 TATTTTCA
65 TATTTTCA
29696083 ATTTCTGTTTT
1 ATTTCTGTTTT
29696094 TTTTTCAATT
Statistics
Matches: 206, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
72 7 0.03
73 82 0.40
74 112 0.54
75 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (72 bp):
ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
ATTTTCA
Found at i:29696111 original size:18 final size:18
Alignment explanation
Indices: 29696077--29696112 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29696067 CGCTGAGGTA
**
29696077 TTTTCAATTTCTGTTTTT
1 TTTTCAATTTCAATTTTT
29696095 TTTTCAATTTCAATTTTT
1 TTTTCAATTTCAATTTTT
29696113 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTCAATTTCAATTTTT
Found at i:29696236 original size:88 final size:87
Alignment explanation
Indices: 29696005--29696265 Score: 262
Period size: 91 Copynumber: 2.9 Consensus size: 87
29695995 GCTGAGGTAA
*
29696005 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
1 TTTCAATTTATGTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
** * *
29696070 TGAGGTATTTTCAATTTCTGTTTTTT
65 CAAGGTATTTTCAATTTCCG---TCT
* * **
29696096 TTTCAATTTCAAT-TTTTCAAAAATCAACTCATATTACGAGAGATGAGTTGAGCCTCGGGCCACA
1 TTTCAATTT--ATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACA
*
29696160 TGCCAAGGTATTTTCAATTTCCG-CT
62 CGCCAAGGTATTTTCAATTTCCGTCT
* *
29696185 TTTCAATTTATGTTTT-AAAATATCGACTCCTATTGCGAGAGGTGAGTTGAGCCTC-AGATCACG
1 TTTCAATTTATGTTTTCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA-CACG
* *
29696248 CTGAA-GTGTTTTCAATTT
64 C-CAAGGTATTTTCAATTT
29696266 ATGTTTCAAA
Statistics
Matches: 144, Mismatches: 18, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
85 1 0.01
86 16 0.11
87 9 0.06
88 34 0.24
89 10 0.07
91 48 0.33
92 3 0.02
93 23 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (87 bp):
TTTCAATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCC
AAGGTATTTTCAATTTCCGTCT
Found at i:29696305 original size:160 final size:160
Alignment explanation
Indices: 29696095--29696558 Score: 601
Period size: 160 Copynumber: 2.9 Consensus size: 160
29696085 TTCTGTTTTT
* * * * *
29696095 TTTTCAATTTCAATTTTTC-AAAAATCAACTCATATTACGAGAGATGAGTTGAGCCTCGGGCCAC
1 TTTTCAATTT--ATGTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCAC
* *
29696159 ATGCCAAGGTATTTTCAATTTCCGCTTTTCAATTTATGTTTTAAAATATCGACTCCTATTGCGAG
64 ATGACAAGGTATTTTCAATTTCCGCTTTTCAATTTATGTTTTAAAATATCGACTCATATTGCGAG
29696224 AGGTGAGTTGAGCCTCAGATCACGCTGAA-GTG
129 AGGTGAGTTGAGCCTCAGATCACG-TGAAGGTG
* *
29696256 TTTTCAATTTATGTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGTTCACAT
1 TTTTCAATTTATGTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACAT
*
29696321 GACAAGGTATTTTCAATTTCCGCTTTTCAATTCATGTTTTAAAATATCGACTCATATTGCGAGAG
66 GACAAGGTATTTTCAATTTCCGCTTTTCAATTTATGTTTTAAAATATCGACTCATATTGCGAGAG
* * * * *
29696386 ATGAGTTGAGCGTCAGGTCATGTTAAGGTG
131 GTGAGTTGAGCCTCAGATCACGTGAAGGTG
* * * *
29696416 TTTTCAATTTATGTTTCATAAAATTAACTCATATTGTAAGAGGTGTGTTGAGCCTCGGGTCACAT
1 TTTTCAATTTATGTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACAT
* * ** * * * * * * *
29696481 GGCGAGGTATTTTCAAAATCTGCCTTTCAAATTAAGTTTCAAAA-AACTAACTCATATTGCGAGA
66 GACAAGGTATTTTCAATTTCCGCTTTTCAATTTATGTTTTAAAATATC-GACTCATATTGCGAGA
29696545 GGTGAGTTGAGCCT
130 GGTGAGTTGAGCCT
29696559 TGGCTTACGT
Statistics
Matches: 265, Mismatches: 35, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
159 11 0.04
160 244 0.92
161 10 0.04
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (160 bp):
TTTTCAATTTATGTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACAT
GACAAGGTATTTTCAATTTCCGCTTTTCAATTTATGTTTTAAAATATCGACTCATATTGCGAGAG
GTGAGTTGAGCCTCAGATCACGTGAAGGTG
Found at i:29696466 original size:72 final size:72
Alignment explanation
Indices: 29696344--29696477 Score: 164
Period size: 72 Copynumber: 1.9 Consensus size: 72
29696334 CAATTTCCGC
* * *
29696344 TTTTCAATTCATGTTTTAAAATATCGACTCATATTGCGAGAGATGAGTTGAGCGTCAGGTCATGT
1 TTTTCAATTCATGTTTTAAAATATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGTCATGT
29696409 TAAGGTG
66 TAAGGTG
* * * * *
29696416 TTTTCAATTTATGTTTCATAAAAT-T-AACTCATATTGTAAGAGGTGTGTTGAGCCTCGGGTCA
1 TTTTCAATTCATGTTT--TAAAATATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGTCA
29696478 CATGGCGAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
72 45 0.87
73 1 0.02
74 6 0.12
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (72 bp):
TTTTCAATTCATGTTTTAAAATATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGTCATGT
TAAGGTG
Found at i:29696580 original size:88 final size:88
Alignment explanation
Indices: 29696417--29696584 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
29696407 GTTAAGGTGT
* * * * * * *
29696417 TTTCAATTTATGTTTCATAAAATTAACTCATATTGTAAGAGGTGTGTTGAGCCTCGGGTCACATG
1 TTTCAAATTAAGTTTCAAAAAACTAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACATG
*
29696482 GCGAGGTATTTTCAAAATCTGCC
66 GCGAGCTATTTTCAAAATCTGCC
* * * *
29696505 TTTCAAATTAAGTTTCAAAAAACTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTTACGT-
1 TTTCAAATTAAGTTTCAAAAAACTAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACATG
29696569 GCTGAGCTATTTTCAA
66 GC-GAGCTATTTTCAA
29696585 TTTCTGTTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
87 2 0.03
88 65 0.97
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (88 bp):
TTTCAAATTAAGTTTCAAAAAACTAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACATG
GCGAGCTATTTTCAAAATCTGCC
Found at i:29697083 original size:25 final size:25
Alignment explanation
Indices: 29697046--29697093 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29697036 AAAAGTCTTT
*
29697046 ACTCTATTCTCGTTACACGACAACA
1 ACTCTATTATCGTTACACGACAACA
* *
29697071 ACTCTGTTATCGTTATACGACAA
1 ACTCTATTATCGTTACACGACAA
29697094 TGAGTAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (25 bp):
ACTCTATTATCGTTACACGACAACA
Found at i:29697315 original size:13 final size:13
Alignment explanation
Indices: 29697276--29697315 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
29697266 TGCCCTATGG
*
29697276 TCTGCCACCACCG
1 TCTGCCACCACCT
*
29697289 TCGGCCACCTACCT
1 TCTGCCACC-ACCT
29697303 TCTGCCACCACCT
1 TCTGCCACCACCT
29697316 GCTCCTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.15, C:0.53, G:0.12, T:0.20
Consensus pattern (13 bp):
TCTGCCACCACCT
Found at i:29698205 original size:3 final size:3
Alignment explanation
Indices: 29698197--29698363 Score: 112
Period size: 3 Copynumber: 56.0 Consensus size: 3
29698187 CTTTATTAAA
* * * *
29698197 TAT TAT TAT TAT CAT T-T CTAA TAT TAT TAA TAT TAT TAT T-T AGAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * * * * * * *
29698242 TAT TGT TAT TAT TAC TAT TAT TAA TAT TCT TGT TAT TAA CAT TGT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
29698290 TAT TCCT T-T TAT TAAT T-T T-T TATT TAT TAA TA- TAT TAT TAT TAT
1 TAT T-AT TAT TAT T-AT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
29698334 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29698364 GTAATAATGT
Statistics
Matches: 128, Mismatches: 26, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
2 10 0.08
3 109 0.85
4 9 0.07
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:29698640 original size:12 final size:11
Alignment explanation
Indices: 29698594--29698667 Score: 55
Period size: 11 Copynumber: 6.6 Consensus size: 11
29698584 TCCTAATATT
*
29698594 TATATATTATG
1 TATATATTATA
* *
29698605 TAAATATTTTAA
1 TATATATTAT-A
29698617 TATTATATTATA
1 TA-TATATTATA
29698629 TATATATCTATA
1 TATATAT-TATA
29698641 TAT-T-TT-TA
1 TATATATTATA
*
29698649 GTATATATTATG
1 -TATATATTATA
29698661 TATATAT
1 TATATAT
29698668 GTTTTCAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
8 2 0.04
9 4 0.08
10 2 0.04
11 23 0.46
12 13 0.26
13 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (11 bp):
TATATATTATA
Found at i:29698644 original size:32 final size:32
Alignment explanation
Indices: 29698589--29698667 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
29698579 TTTATTCCTA
*
29698589 ATAT-TTATATAT-TATGTAAATA-TTTTAAT
1 ATATATTATATATATATCTAAATATTTTTAAT
* *
29698618 ATTATATTATATATATATCTATATATTTTTAGT
1 A-TATATTATATATATATCTAAATATTTTTAAT
*
29698651 ATATATTATGTATATAT
1 ATATATTATATATATAT
29698668 GTTTTCAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.02
30 3 0.07
31 8 0.19
32 23 0.55
33 7 0.17
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (32 bp):
ATATATTATATATATATCTAAATATTTTTAAT
Found at i:29698678 original size:24 final size:24
Alignment explanation
Indices: 29698626--29698672 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
29698616 ATATTATATT
29698626 ATATATATATCTATATATTTTTAG
1 ATATATATATCTATATATTTTTAG
*
29698650 -TATATATTATGTATATATGTTTT
1 ATATATA-TATCTATATAT-TTTT
29698673 CAATATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (24 bp):
ATATATATATCTATATATTTTTAG
Found at i:29698771 original size:19 final size:19
Alignment explanation
Indices: 29698747--29698785 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
29698737 TACTATTTTA
*
29698747 TGTATATTTCTAATATCAT
1 TGTATATTTCTAACATCAT
29698766 TGTATATTTCTAACATCAT
1 TGTATATTTCTAACATCAT
29698785 T
1 T
29698786 ATTATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (19 bp):
TGTATATTTCTAACATCAT
Found at i:29699149 original size:22 final size:21
Alignment explanation
Indices: 29699124--29699192 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
29699114 ATATATAGTA
29699124 TTATT-TTCATACATCATTATAT
1 TTATTATT-ATACAT-ATTATAT
29699146 TTATTATTATACATATTAT-T
1 TTATTATTATACATATTATAT
* *
29699166 TTCACTATTATCACTTATTAT-T
1 TT-ATTATTAT-ACATATTATAT
29699188 TTATT
1 TTATT
29699193 TTAATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 3 0.07
21 14 0.34
22 22 0.54
23 2 0.05
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATTATTATACATATTATAT
Found at i:29699363 original size:2 final size:2
Alignment explanation
Indices: 29699356--29699392 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29699346 ATTACTATTT
29699356 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29699393 TACGTACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29706248 original size:403 final size:406
Alignment explanation
Indices: 29705494--29706306 Score: 1213
Period size: 403 Copynumber: 2.0 Consensus size: 406
29705484 ATAAGAAAGA
* * *
29705494 AACAAATCAAATTTTTTAAAATTTGGTGTGATTTTTATTTTATCTTTTTTTTAAAAAAAAAAGAA
1 AACAAATCAAATTTGTTAAAATTTAGTATGATTTTTATTTTATCTTTTTTTTAAAAAAAAAAGAA
* * *
29705559 AAATCCCTAAAATTCCTCTCTTGTTTACCATCCAACTACCCTACTACCCCATCTTCTCTATTTTT
66 AAATCCCTAAAATTCCTCTCCTGTTTACCATCCAACTACCCCACTACCCCATCTTCTCCATTTTT
***
29705624 TTTGCCATTTTCCTCTCAATTGGCTATTGGGATTTTTCTCTCTGTCATTTGTTCTCTAATGATTA
131 TTTGCCATTTTCCTCTCAATTGGC--TT--GATTTTTCTCTCTGTCATTCCCTCTCTAATGATTA
* * *
29705689 TCCTTCATCTTCTTTTCATTTTATTTGTTCCTTAATTTCGTGGGCGATTCCTTGTTCGGTTTTTT
192 TCCTTCATCTTCTTTTCATTTTATTTATTCCTTAATTTCATGGGCGATTCCTTGTTCAGTTTTTT
* * * * *
29705754 TAGTGCCCTTCAAAATTTGATTTCTTATGGTGACATTGGTAATTTTTACTCCATTACTGGTTGTG
257 TAGTACCCTCCAAAATTTGATTTCTTAAGGTGACATTGGTAATTCTTACTCCATTACTAGTTGTG
* *
29705819 GGTGCTTCAAAACTTCAATATAGTTGTATAACTATTGGTGGTTGTATTTTGTGGTCATAATTCAT
322 GGTACTTCAAAACTTCAATATAGTTGTATAACTATCGGTGGTTGTATTTTGTGGTCATAATTCAT
29705884 TTGTTATTGAAGGTTGTTTT
387 TTGTTATTGAAGGTTGTTTT
** *
29705904 AACAAATCAAATTTGTTAAAATTTAGTATGATTTTTATTTTATCTTTTCTTTT-TTAAAAAAGGA
1 AACAAATCAAATTTGTTAAAATTTAGTATGATTTTTATTTTATCTTTT-TTTTAAAAAAAAAAGA
29705968 AAAATCCCTAAAATTCCTCTCCTGTTTACCATCCAACTACCCCACTACCCCATCTTCTCCATTTT
65 AAAATCCCTAAAATTCCTCTCCTGTTTACCATCCAACTACCCCACTACCCCATCTTCTCCATTTT
** * ** *
29706033 TTTT-CCATTTTCCTCTCAATTGGC-T-ATTTTTCTCTCTGTTGTTCCCTCTTTGCTGATTCTCC
130 TTTTGCCATTTTCCTCTCAATTGGCTTGATTTTTCTCTCTGTCATTCCCTCTCTAATGATTATCC
* *
29706095 TTCATCTTCTTTTCATTTTGTTTATTCCTTAATTTCATGGGTGATTCCTTGTT-AGTTTGTTTTA
195 TTCATCTTCTTTTCATTTTATTTATTCCTTAATTTCATGGGCGATTCCTTGTTCAGTTT-TTTTA
* * * *
29706159 GTACCGTCCAGATTTTGATTTCTTAAGGTGACATTGGTAATTCTTACTCCATTGCTAGTTGTGGG
259 GTACCCTCCAAAATTTGATTTCTTAAGGTGACATTGGTAATTCTTACTCCATTACTAGTTGTGGG
*
29706224 TACTTCAAAACTTCAATTTAGTTGTATAACTATCGGTGGTTGTATTTTGTGGTCATAATTCATTT
324 TACTTCAAAACTTCAATATAGTTGTATAACTATCGGTGGTTGTATTTTGTGGTCATAATTCATTT
*
29706289 TTTATTGAAGGTTGTTTT
389 GTTATTGAAGGTTGTTTT
29706307 GATTTTGGGT
Statistics
Matches: 365, Mismatches: 36, Indels: 11
0.89 0.09 0.03
Matches are distributed among these distances:
402 4 0.01
403 217 0.59
406 1 0.00
409 20 0.05
410 119 0.33
411 4 0.01
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (406 bp):
AACAAATCAAATTTGTTAAAATTTAGTATGATTTTTATTTTATCTTTTTTTTAAAAAAAAAAGAA
AAATCCCTAAAATTCCTCTCCTGTTTACCATCCAACTACCCCACTACCCCATCTTCTCCATTTTT
TTTGCCATTTTCCTCTCAATTGGCTTGATTTTTCTCTCTGTCATTCCCTCTCTAATGATTATCCT
TCATCTTCTTTTCATTTTATTTATTCCTTAATTTCATGGGCGATTCCTTGTTCAGTTTTTTTAGT
ACCCTCCAAAATTTGATTTCTTAAGGTGACATTGGTAATTCTTACTCCATTACTAGTTGTGGGTA
CTTCAAAACTTCAATATAGTTGTATAACTATCGGTGGTTGTATTTTGTGGTCATAATTCATTTGT
TATTGAAGGTTGTTTT
Found at i:29719603 original size:15 final size:15
Alignment explanation
Indices: 29719583--29719611 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29719573 CTACTTGCAT
29719583 TATTATCTGTATATC
1 TATTATCTGTATATC
29719598 TATTATCTGTATAT
1 TATTATCTGTATAT
29719612 GCTTATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (15 bp):
TATTATCTGTATATC
Found at i:29723531 original size:39 final size:39
Alignment explanation
Indices: 29723483--29723680 Score: 236
Period size: 39 Copynumber: 5.1 Consensus size: 39
29723473 GCTACTCGTT
* * * * *
29723483 CAAACGCCTTCGGGACATAGCCCGGTTAT-GTAACCCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
* *
29723522 CAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
* *
29723562 CAATTGCCTTCGGGCTTAGCCCGGATATCATATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
* * *
29723601 CAATTGCCTTCGGGCTTAGCCCGGATATCACAATTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
* * *
29723640 CAATTGCCTTCGGGCTTAGCCCGGATATCACAATTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
29723679 CA
1 CA
29723681 TTCATACACA
Statistics
Matches: 144, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 124 0.86
40 20 0.14
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
Found at i:29723639 original size:78 final size:79
Alignment explanation
Indices: 29723518--29723669 Score: 270
Period size: 78 Copynumber: 1.9 Consensus size: 79
29723508 TTATGTAACC
29723518 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
29723583 CGGATATCATATCT
66 CGGATATCATATCT
* * *
29723597 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
29723661 CGGATATCA
66 CGGATATCA
29723670 CAATTCGCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 53 0.76
79 17 0.24
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (79 bp):
CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
CGGATATCATATCT
Done.