Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 6 of 18
Found at i:814593 original size:45 final size:44
Alignment explanation
Indices: 814483--814604 Score: 163
Period size: 45 Copynumber: 2.7 Consensus size: 44
814473 TATTTAATAA
* *
814483 AAACCCAAACTCAATTAAAACTCAACTAAAAATCTATATAAACTT
1 AAACCCAAAC-CAATTAAAATTTAACTAAAAATCTATATAAACTT
**
814528 AAATTCAAACCCAATTAAAATTTAACTAAAAATCTATATAAACTT
1 AAACCCAAA-CCAATTAAAATTTAACTAAAAATCTATATAAACTT
* *
814573 AAGCCCAAATCCAATTAAAATTTAATTAAAAA
1 AAACCCAAA-CCAATTAAAATTTAACTAAAAA
814605 AATAATAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 66 0.99
46 1 0.01
ACGTcount: A:0.54, C:0.18, G:0.01, T:0.27
Consensus pattern (44 bp):
AAACCCAAACCAATTAAAATTTAACTAAAAATCTATATAAACTT
Found at i:815407 original size:234 final size:234
Alignment explanation
Indices: 814993--815459 Score: 871
Period size: 234 Copynumber: 2.0 Consensus size: 234
814983 AGAACCCAGA
* *
814993 ACAAGAGCAACATATGAATTAGAACCCATAAAATAAAAGTTTCTAGGTTTTCGGCATTACATGTC
1 ACAAGAGCAACATATGAACTAGAACCCATAAAATAAAAGTTTCTAGGCTTTCGGCATTACATGTC
815058 TCTTGCTTGTCCTAAATTTCGTATGCCATCATCATGGACTGTTGTTAGGGATTGCTATGAAATTT
66 TCTTGCTTGTCCTAAATTTCGTATGCCATCATCATGGACTGTTGTTAGGGATTGCTATGAAATTT
*
815123 ATTGTAATAAAAAGAATAGCCTAAGGCAATTTATGAAATCATCTTCTGTAAGAATATCATTTACA
131 ATTGTAATAAAAAGAATAGCCTAAGGCAATTTATGAAATCATCTTCTGTAAGAATATCACTTACA
815188 ATCGACACATAAATCTCAATACAAAGATAAAATTATATT
196 ATCGACACATAAATCTCAATACAAAGATAAAATTATATT
* *
815227 ACAATAGCAACATATGAACTAGAACCCATAAAATAAAAGTTTCTTGGCTTTCGGCATTACATGTC
1 ACAAGAGCAACATATGAACTAGAACCCATAAAATAAAAGTTTCTAGGCTTTCGGCATTACATGTC
* *
815292 TCTTGCTTGTCCTAGATTTCGTATGCCATCATCATGGACTGTTGTTAGGGATTGTTATGAAATTT
66 TCTTGCTTGTCCTAAATTTCGTATGCCATCATCATGGACTGTTGTTAGGGATTGCTATGAAATTT
815357 ATTGTAATAAAAAGAATAGCCTAAGGCAATTTATGAAATCATCTTCTGTAAGAATATCACTTACA
131 ATTGTAATAAAAAGAATAGCCTAAGGCAATTTATGAAATCATCTTCTGTAAGAATATCACTTACA
815422 ATCGACACATAAATCTCAATACAAAGATAAAATTATAT
196 ATCGACACATAAATCTCAATACAAAGATAAAATTATAT
815460 GTGTTTTACG
Statistics
Matches: 226, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
234 226 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (234 bp):
ACAAGAGCAACATATGAACTAGAACCCATAAAATAAAAGTTTCTAGGCTTTCGGCATTACATGTC
TCTTGCTTGTCCTAAATTTCGTATGCCATCATCATGGACTGTTGTTAGGGATTGCTATGAAATTT
ATTGTAATAAAAAGAATAGCCTAAGGCAATTTATGAAATCATCTTCTGTAAGAATATCACTTACA
ATCGACACATAAATCTCAATACAAAGATAAAATTATATT
Found at i:817845 original size:2 final size:2
Alignment explanation
Indices: 817838--817887 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
817828 TTTAAGTGAA
817838 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
817880 AT AT AT AT
1 AT AT AT AT
817888 TCTCTAATAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:822260 original size:65 final size:65
Alignment explanation
Indices: 822179--822301 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 65
822169 TCCTCCCCAT
** * *
822179 ATCAAAATCCCCATGCAAGGGGGAAAACTCTAAATATAATTATCATAAAGCTCACTGCTTCCTAA
1 ATCAAAATCCCCATGCAAAAGAGAAAACTCTAAATATAATTATCAGAAAGCTCACTGCTTCCTAA
* * * *
822244 ATCAAAATCCCCATGCAAAAGAGAATATTCTAAGTATAATTATCGGAAAGCTCACTGC
1 ATCAAAATCCCCATGCAAAAGAGAAAACTCTAAATATAATTATCAGAAAGCTCACTGC
822302 CTCGTCCTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 50 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (65 bp):
ATCAAAATCCCCATGCAAAAGAGAAAACTCTAAATATAATTATCAGAAAGCTCACTGCTTCCTAA
Found at i:827760 original size:31 final size:31
Alignment explanation
Indices: 827710--827775 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
827700 TTTTTTATTA
827710 AATATTTATATTATAATTTTATCAAATAATAT
1 AATATTTATATTATAATTTTATCAAATAA-AT
* *
827742 AATATTT-TATTTTAATTTTATTAAATAAAT
1 AATATTTATATTATAATTTTATCAAATAAAT
827772 AATA
1 AATA
827776 ATATAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 6 0.19
31 19 0.59
32 7 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
AATATTTATATTATAATTTTATCAAATAAAT
Found at i:828403 original size:19 final size:20
Alignment explanation
Indices: 828371--828410 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
828361 TTATACTTAC
*
828371 ATATAAATATAAATAAATTT
1 ATATAAATAAAAATAAATTT
*
828391 ATAT-AATAAAAATATATTT
1 ATATAAATAAAAATAAATTT
828410 A
1 A
828411 AATGATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAATAAAAATAAATTT
Found at i:828412 original size:25 final size:25
Alignment explanation
Indices: 828355--828425 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 25
828345 TTAAATATTC
*
828355 ATAAATTTATACTTACATATAAATATAA
1 ATAAATTTATA--TA-ATAAAAATATAA
*
828383 ATAAATTTATATAATAAAAATATAT
1 ATAAATTTATATAATAAAAATATAA
*
828408 TTAAATGATTATATAATA
1 ATAAAT--TTATATAATA
828426 TATATTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 15 0.39
26 2 0.05
27 10 0.26
28 11 0.29
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (25 bp):
ATAAATTTATATAATAAAAATATAA
Found at i:829693 original size:21 final size:21
Alignment explanation
Indices: 829633--829694 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
829623 ATAATGTAAC
*
829633 AAAAAAAT-TTTAACTTTTTT
1 AAAAAAATATTTATCTTTTTT
** * * *
829653 AGCTAAAATAATAATATTTTTT
1 A-AAAAAATATTTATCTTTTTT
829675 AAAAAAATATTTATCTTTTT
1 AAAAAAATATTTATCTTTTT
829695 ATTTAAATAA
Statistics
Matches: 29, Mismatches: 11, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
20 1 0.03
21 19 0.66
22 9 0.31
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAAAAATATTTATCTTTTTT
Found at i:830039 original size:19 final size:19
Alignment explanation
Indices: 830008--830154 Score: 84
Period size: 19 Copynumber: 7.2 Consensus size: 19
829998 TATTTTTTAA
830008 ATATAATTATTTATATATTT
1 ATATAA-TATTTATATATTT
830028 ATATAATATTTATATATTAT
1 ATATAATATTTATATATT-T
*
830048 AATTATTTTAAAATATTATATATTT
1 -A-TA---TAATAT-TTATATATTT
* *
830073 ATATAAAATTTATTATTATTA
1 ATATAATATTTA-TA-TATTT
*
830094 ATAATCTATATTATATATATTT
1 AT-AT-AATATT-TATATATTT
**
830116 -TATAATAAATATATATTT
1 ATATAATATTTATATATTT
* *
830134 TTATTATATTT-TATA-TT
1 ATATAATATTTATATATTT
830151 ATAT
1 ATAT
830155 TTTAATAAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 29
0.71 0.08 0.20
Matches are distributed among these distances:
17 5 0.05
18 13 0.13
19 25 0.25
20 17 0.17
21 8 0.08
22 8 0.08
23 8 0.08
24 3 0.03
25 6 0.06
26 9 0.09
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATAATATTTATATATTT
Found at i:830063 original size:21 final size:20
Alignment explanation
Indices: 830039--830108 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
830029 TATAATATTT
*
830039 ATATATTATAATTATTTTAAA
1 ATATATTATAATTA-TATAAA
*
830060 ATAT-TATATATTTATATAAA
1 ATATAT-TATAATTATATAAA
* * *
830080 ATTTATTATTATTA-ATAAT
1 ATATATTATAATTATATAAA
*
830099 CTATATTATA
1 ATATATTATA
830109 TATATTTTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 11 0.29
20 15 0.39
21 12 0.32
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATAATTATATAAA
Found at i:830067 original size:45 final size:44
Alignment explanation
Indices: 830018--830175 Score: 134
Period size: 45 Copynumber: 3.7 Consensus size: 44
830008 ATATAATTAT
830018 TTATATATTTATATAATATTTATATATTATAATTATTTTAAAATA
1 TTATATATTTATATAATATTTATATATTATAATTATTTT-AAATA
* * *
830063 TTATATATTTATATAAAATTTAT-TATTATTAA-TAATCT--ATA
1 TTATATATTTATATAATATTTATATATTA-TAATTATTTTAAATA
* ** * * *
830104 TTATATATATTTTATAATAAATATATATTTTTATTATATTT-TATA
1 TTATATAT-TTATATAATATTTATATATTATAATTAT-TTTAAATA
830149 TTATAT-TTTA-ATAA-ATTTTATATATTA
1 TTATATATTTATATAATA-TTTATATATTA
830176 CATCGTATAA
Statistics
Matches: 91, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
41 12 0.13
42 25 0.27
43 8 0.09
44 12 0.13
45 34 0.37
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (44 bp):
TTATATATTTATATAATATTTATATATTATAATTATTTTAAATA
Found at i:830107 original size:22 final size:21
Alignment explanation
Indices: 830038--830162 Score: 52
Period size: 22 Copynumber: 6.0 Consensus size: 21
830028 ATATAATATT
*
830038 TATATATTATAATTATT-TTAA
1 TATATATTAT-ATTATTAATAA
830059 -A-ATATTATA-TATTTATATAA
1 TATATATTATATTA-TTA-ATAA
830079 -A-AT-TTATTATTATTAATAA
1 TATATATTA-TATTATTAATAA
* *
830098 TCTATATTATATATATTTTATAA
1 TATATATTATAT-TA-TTAATAA
* * *
830121 TAAATA-TATATTTTTATTATAT
1 TATATATTATATTATTA--ATAA
*
830143 TTTATATTATATT-TTAATAA
1 TATATATTATATTATTAATAA
830163 ATTTTATATA
Statistics
Matches: 80, Mismatches: 11, Indels: 27
0.68 0.09 0.23
Matches are distributed among these distances:
17 2 0.03
18 3 0.04
19 14 0.17
20 17 0.21
21 8 0.10
22 20 0.25
23 16 0.20
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATATTATATTATTAATAA
Found at i:830152 original size:12 final size:12
Alignment explanation
Indices: 830127--830171 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
830117 ATAATAAATA
830127 TATATTTT-TAT
1 TATATTTTATAT
830138 TATATTTTATAT
1 TATATTTTATAT
830150 TATATTTTA-A-
1 TATATTTTATAT
*
830160 TAAATTTTATAT
1 TATATTTTATAT
830172 ATTACATCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 8 0.27
11 10 0.33
12 12 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:830166 original size:22 final size:23
Alignment explanation
Indices: 830127--830171 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
830117 ATAATAAATA
* *
830127 TATATTTTTATTATATTTTATAT
1 TATATTTTTAATAAATTTTATAT
830150 TATA-TTTTAATAAATTTTATAT
1 TATATTTTTAATAAATTTTATAT
830172 ATTACATCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATATTTTTAATAAATTTTATAT
Found at i:830348 original size:3 final size:3
Alignment explanation
Indices: 830340--830364 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
830330 GTCTTCCCCT
830340 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
830365 GAAGCCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:830596 original size:33 final size:36
Alignment explanation
Indices: 830527--830608 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 36
830517 ATTTAGTTTT
** *
830527 AATATATATTTAAATATAAATATAATTTTTTTTTAAA
1 AATATATAAATAAATATAAATATAA-TTTTTATTAAA
830564 AATATATAAATAAAT-TAAATA-AA-TTTTATTAAA
1 AATATATAAATAAATATAAATATAATTTTTATTAAA
*
830597 AATATATCAATA
1 AATATATAAATA
830609 TTTGATAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 20 0.49
35 2 0.05
36 6 0.15
37 13 0.32
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (36 bp):
AATATATAAATAAATATAAATATAATTTTTATTAAA
Found at i:835736 original size:33 final size:32
Alignment explanation
Indices: 835693--835763 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 32
835683 TAATAAATAT
*
835693 AAAAT-TAATTTAATTATTTTTTAATTAGTAA
1 AAAATATAATTTAATTATTTTTTAATGAGTAA
835724 AAAGATATAATTTAATTATTTTTTAATGAGTAA
1 AAA-ATATAATTTAATTATTTTTTAATGAGTAA
835757 AAAATAT
1 AAAATAT
835764 TTAATGTACA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 3 0.08
32 6 0.16
33 28 0.76
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (32 bp):
AAAATATAATTTAATTATTTTTTAATGAGTAA
Found at i:839235 original size:3 final size:3
Alignment explanation
Indices: 839227--839252 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
839217 GATAGGCTGC
839227 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
839253 CATTTCTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:840939 original size:50 final size:50
Alignment explanation
Indices: 840885--841144 Score: 317
Period size: 50 Copynumber: 5.2 Consensus size: 50
840875 AGTTACTTAG
* ** * * *
840885 AGTCAACAATTACGACCACCTCTCTTTATTATCAAAGGTTGGTAAAAAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * *
840935 AGTCAACAATTATGGCCACCTTTCTCAATTGTCAAAGGTTGATGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
840985 CA-TTAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 -AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * *
841035 AGTCAACAATTACGGTCACCTCTATCGATTGTCAAAGATTGGTAAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * *
841085 AGTCAAC-GTTACAGCCACCTCTCTCGATTGTTAAAAGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
841134 AATCAACAATT
1 AGTCAACAATT
841145 CTCTCACTTA
Statistics
Matches: 178, Mismatches: 29, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
49 41 0.23
50 136 0.76
51 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:845175 original size:19 final size:19
Alignment explanation
Indices: 845137--845186 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
845127 CTCACTGTTT
* *
845137 TATGTGCACAGTAACTGTA
1 TATGTGAACAGTAACCGTA
* *
845156 TGTGTGAACAGTACCCGTA
1 TATGTGAACAGTAACCGTA
*
845175 TACGTGAACAGT
1 TATGTGAACAGT
845187 GTCTCGACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (19 bp):
TATGTGAACAGTAACCGTA
Found at i:845498 original size:50 final size:50
Alignment explanation
Indices: 845438--845647 Score: 258
Period size: 50 Copynumber: 4.2 Consensus size: 50
845428 AGTTGCTTAG
* *
845438 AGTCAATAATTACGACCACCTCTCTCTATTATCAAAGATTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTATCAAAGATTGGTGAAGAAT
* * *
845488 CGTCAATAATTACGACCACCTCTCTCGATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTATCAAAGATTGGTGAAGAAT
** * * * * *
845538 AGTCAACAATTACGGTCACCTCTCTTGATTGTCAAAGGTTGTTAAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTATCAAAGATTGGTGAAGAAT
** * * *
845588 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAATATTGATGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTATCAAAGATTGGTGAAGAAT
*
845638 AGTGAACAAT
1 AGTCAACAAT
845648 GACAATACCT
Statistics
Matches: 143, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 143 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTACGACCACCTCTCTCGATTATCAAAGATTGGTGAAGAAT
Found at i:848993 original size:2 final size:2
Alignment explanation
Indices: 848986--849017 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
848976 TGAGTATTAG
848986 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
849018 CAGACACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:850264 original size:29 final size:29
Alignment explanation
Indices: 850222--850282 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
850212 TGAAAATCAA
850222 AGTAAGATACATAAATTCATGGTATAGAC
1 AGTAAGATACATAAATTCATGGTATAGAC
*
850251 AGTAAGATATATAAATTCATGGTATAGAC
1 AGTAAGATACATAAATTCATGGTATAGAC
850280 AGT
1 AGT
850283 TTTTTTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (29 bp):
AGTAAGATACATAAATTCATGGTATAGAC
Found at i:851745 original size:13 final size:13
Alignment explanation
Indices: 851724--851762 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
851714 TTTGAATTTT
*
851724 TTATTTTATTAAA
1 TTATATTATTAAA
851737 TTATATTATTAAAA
1 TTATATTATT-AAA
*
851751 TTTTATTATTAA
1 TTATATTATTAA
851763 TTTTATTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATATTATTAAA
Found at i:851757 original size:14 final size:13
Alignment explanation
Indices: 851729--851770 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
851719 ATTTTTTATT
*
851729 TTATTAAATTATA
1 TTATTAAATTTTA
851742 TTATTAAAATTTTA
1 TTATT-AAATTTTA
851756 TTATT-AATTTTA
1 TTATTAAATTTTA
851768 TTA
1 TTA
851771 AGTAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 10 0.37
13 5 0.19
14 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTAAATTTTA
Found at i:851778 original size:13 final size:12
Alignment explanation
Indices: 851726--851780 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
851716 TGAATTTTTT
*
851726 ATTTTATTAAATT
1 ATTTTATT-AATA
*
851739 ATATTATTAA-A
1 ATTTTATTAATA
*
851750 ATTTTATTATTA
1 ATTTTATTAATA
851762 ATTTTATTAAGTA
1 ATTTTATTAA-TA
851775 ATTTTA
1 ATTTTA
851781 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 8 0.23
12 12 0.34
13 15 0.43
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
ATTTTATTAATA
Found at i:851949 original size:13 final size:14
Alignment explanation
Indices: 851923--851953 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
851913 AACTAAATAA
851923 TAATAATAATAATT
1 TAATAATAATAATT
851937 TAATAAT-ATAATT
1 TAATAATAATAATT
851950 TAAT
1 TAAT
851954 TAATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATAATAATAATT
Found at i:851957 original size:25 final size:25
Alignment explanation
Indices: 851873--851957 Score: 61
Period size: 25 Copynumber: 3.4 Consensus size: 25
851863 TTAAGTCAAT
* *
851873 TTTAATTAAAAATTT-TTAATA-AA
1 TTTAATTAATAATTTAATAATATAA
* *
851896 ATTAATTTAAATGATTTAACTAA-ATAA
1 TTTAA-TT-AATAATTTAA-TAATATAA
*
851923 TAATAA-TAATAATTTAATAATATAA
1 T-TTAATTAATAATTTAATAATATAA
851948 TTTAATTAAT
1 TTTAATTAAT
851958 TTAAAATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
23 4 0.09
24 8 0.17
25 24 0.52
26 2 0.04
27 5 0.11
28 3 0.07
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (25 bp):
TTTAATTAATAATTTAATAATATAA
Found at i:852144 original size:18 final size:18
Alignment explanation
Indices: 852110--852172 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
852100 GTATATTTAT
*
852110 TATATTAT-TTTTA-AAA
1 TATATTATATTTAATAAA
852126 TATATTATATTTAATAAA
1 TATATTATATTTAATAAA
*
852144 T-T-TTAATATATTAATAATT
1 TATATT-ATAT-TTAATAA-A
852163 TATATTATAT
1 TATATTATAT
852173 AAATTTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 10 0.26
17 9 0.24
18 11 0.29
19 1 0.03
20 5 0.13
21 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATTATATTTAATAAA
Found at i:852191 original size:21 final size:21
Alignment explanation
Indices: 852125--852200 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
852115 TATTTTTAAA
852125 ATATATTATATTTAATAAATTTT
1 ATATA-TAT-TTTAATAAATTTT
* ** *
852148 A-ATATATTAATAATTTATATT
1 ATATATATT-TTAATAAATTTT
*
852169 ATATAAATTTTAATAAATTTT
1 ATATATATTTTAATAAATTTT
*
852190 ATTTATATTTT
1 ATATATATTTT
852201 TATACCAGTA
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.73
22 9 0.22
23 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATATTTTAATAAATTTT
Found at i:852995 original size:21 final size:23
Alignment explanation
Indices: 852952--852997 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
852942 AGAGTTTAGA
* *
852952 TTAAAAATATTTAAATTTTATTT
1 TTAAAAATATTTAAAATTAATTT
852975 TTAAAAA-A-TTAAAATTAATTT
1 TTAAAAATATTTAAAATTAATTT
852996 TT
1 TT
852998 TTAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 1 0.05
23 7 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAAAAATATTTAAAATTAATTT
Found at i:853004 original size:10 final size:10
Alignment explanation
Indices: 852991--853018 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
852981 AATTAAAATT
852991 AATTTTTTTA
1 AATTTTTTTA
853001 AATTTTTTTA
1 AATTTTTTTA
853011 AATTTTTT
1 AATTTTTT
853019 ATTAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:853572 original size:29 final size:29
Alignment explanation
Indices: 853527--853654 Score: 150
Period size: 30 Copynumber: 4.3 Consensus size: 29
853517 AATTGAAAAG
* *
853527 ATTTTTAATTTTGTTATTTTATTTAAATAA
1 ATTTTTAATTTT-TAATTATATTTAAATAA
853557 ATTTTTATATTTTT-ATTATATTTAAATAA
1 ATTTTTA-ATTTTTAATTATATTTAAATAA
* *
853586 TTTTTTTATTTTTAATTTATATTTAAATAA
1 ATTTTTAATTTTTAA-TTATATTTAAATAA
* * *
853616 TTTTTTAATTTTTAATTAATATCTAAGTAA
1 ATTTTTAATTTTTAATT-ATATTTAAATAA
853646 ATTTTTAAT
1 ATTTTTAAT
853655 AGAAATATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
28 6 0.07
29 22 0.25
30 54 0.62
31 5 0.06
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (29 bp):
ATTTTTAATTTTTAATTATATTTAAATAA
Found at i:853651 original size:59 final size:59
Alignment explanation
Indices: 853527--853652 Score: 150
Period size: 59 Copynumber: 2.1 Consensus size: 59
853517 AATTGAAAAG
* *
853527 ATTTTTAATTTTGTTATTTTATTTAAATAAATTTTTATATTTTTATTATATTTAAATAAT
1 ATTTTT-ATTTTGTAATTTTATTTAAATAAATTTTTATATTTTTATTATATCTAAATAAT
* * *
853587 TTTTTTATTTT-TAATTTATATTTAAATAATTTTTTA-ATTTTTAATTAATATCTAAGTAA-
1 ATTTTTATTTTGTAATTT-TATTTAAATAAATTTTTATATTTTT-ATT-ATATCTAAATAAT
853646 ATTTTTA
1 ATTTTTA
853653 ATAGAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
58 11 0.19
59 31 0.54
60 15 0.26
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.63
Consensus pattern (59 bp):
ATTTTTATTTTGTAATTTTATTTAAATAAATTTTTATATTTTTATTATATCTAAATAAT
Found at i:855849 original size:13 final size:13
Alignment explanation
Indices: 855831--855855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
855821 ATTTTTATGT
855831 TAAATATAAATAA
1 TAAATATAAATAA
855844 TAAATATAAATA
1 TAAATATAAATA
855856 TTTTTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATATAAATAA
Found at i:856894 original size:2 final size:2
Alignment explanation
Indices: 856887--856975 Score: 56
Period size: 2 Copynumber: 44.0 Consensus size: 2
856877 TAAAAATGAA
* * *
856887 AT AT AT AT AT AT AT AT AT AT AT GA- ACT AGG AT TT A- AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT -AT A-T A-T AT AT AT AT AT AT
* * * * * *
856928 AT AT GT AT AC AT GT AC AT GT GT 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
856970 AT AT AT
1 AT AT AT
856976 GGATGTAGAT
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
1 2 0.03
2 61 0.92
3 3 0.05
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (2 bp):
AT
Found at i:857117 original size:6 final size:6
Alignment explanation
Indices: 857106--857141 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
857096 GTATTAATAG
857106 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA
857142 CGCAGGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:857797 original size:17 final size:17
Alignment explanation
Indices: 857763--857797 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
857753 TTATCAAAAT
* *
857763 TTTAAATATTTAATAGA
1 TTTAAATATCTAACAGA
857780 TTTAAATATCTAACAGA
1 TTTAAATATCTAACAGA
857797 T
1 T
857798 ATTATCATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (17 bp):
TTTAAATATCTAACAGA
Found at i:858075 original size:6 final size:6
Alignment explanation
Indices: 858064--858090 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
858054 TTTGACTTTC
858064 TCTTCA TCTTCA TCTTCA TCTTCA TCT
1 TCTTCA TCTTCA TCTTCA TCTTCA TCT
858091 CTTTGACGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:859866 original size:19 final size:20
Alignment explanation
Indices: 859826--859869 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
859816 GCATGTCATA
859826 ATTTTTTAAATATTAAATAT
1 ATTTTTTAAATATTAAATAT
859846 ATTTTTTCAAAT-TTAAA-AT
1 ATTTTTT-AAATATTAAATAT
859865 ATTTT
1 ATTTT
859870 CCTTAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTTAAATATTAAATAT
Found at i:860054 original size:16 final size:18
Alignment explanation
Indices: 860033--860069 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
860023 TTATGTCATC
860033 ATTAAAA-ATT-AATAAT
1 ATTAAAAGATTGAATAAT
*
860049 ATTAAAAGATTGAATTAT
1 ATTAAAAGATTGAATAAT
860067 ATT
1 ATT
860070 GACAGACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTAAAAGATTGAATAAT
Found at i:862408 original size:2 final size:2
Alignment explanation
Indices: 862401--862427 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
862391 TATGTGTATG
862401 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 T
862428 GCTTTCACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:867163 original size:26 final size:25
Alignment explanation
Indices: 867132--867203 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 25
867122 TTTAAATTAC
*
867132 TATTTAATAATAAAAATAATATATTT
1 TATTTAATAATAAAAATAATATA-TA
* * **
867158 TGTTTAA-ATTTAATTATAATATATA
1 TATTTAATA-ATAAAAATAATATATA
867183 TATTTAAT-ATAAAAATAATAT
1 TATTTAATAATAAAAATAATAT
867204 TTAAAAAATA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
24 10 0.29
25 8 0.23
26 17 0.49
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (25 bp):
TATTTAATAATAAAAATAATATATA
Found at i:871764 original size:2 final size:2
Alignment explanation
Indices: 871757--871794 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
871747 AAAACCATTG
871757 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
871795 GATTGTAATT
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):
AT
Found at i:871872 original size:2 final size:2
Alignment explanation
Indices: 871865--871890 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
871855 GTATAATTTC
871865 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
871891 TTGTGTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:876389 original size:50 final size:50
Alignment explanation
Indices: 876323--876528 Score: 227
Period size: 50 Copynumber: 4.1 Consensus size: 50
876313 GCTTAGAGTC
* *
876323 AACAATTACGATCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATCGTA
1 AACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTA
* * * * * *
876373 AATAATTACGACCACCTCTCTCGATTATCAAATGTTGGTAAAGAATAATT
1 AACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTA
* * * *
876423 AACAATTACTG-TCACCTCTCTCGATTGTCAAAGGTCGGTGAAGAATAGTC
1 AACAATTAC-GACCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTA
* * * * *
876473 AACAATTAC-AGCCGCCTCTTTCGATTGTCAAAAGTTGGTGAAAAATATTC
1 AACAATTACGA-CCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTA
876523 AACAAT
1 AACAAT
876529 GGCAACACTT
Statistics
Matches: 130, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 129 0.99
51 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (50 bp):
AACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTA
Found at i:876497 original size:100 final size:100
Alignment explanation
Indices: 876321--876528 Score: 271
Period size: 100 Copynumber: 2.1 Consensus size: 100
876311 TTGCTTAGAG
* * *
876321 TCAACAATTACGATCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATCGTAAATAATTACGACC
1 TCAACAATTACGATCACCTCTCTCGATTGTCAAAAGTCGGTGAAGAATAGTAAACAATTACGACC
*
876386 ACCTCTCTCGATTATCAAATGTTGGT-AAAGAATAAT
66 ACCTCTCTCGATTATCAAAAGTTGGTGAAA-AAT-AT
* *
876422 T-AACAATTACTG-TCACCTCTCTCGATTGTCAAAGGTCGGTGAAGAATAGTCAACAATTAC-AG
1 TCAACAATTAC-GATCACCTCTCTCGATTGTCAAAAGTCGGTGAAGAATAGTAAACAATTACGA-
* * *
876484 CCGCCTCTTTCGATTGTCAAAAGTTGGTGAAAAATAT
64 CCACCTCTCTCGATTATCAAAAGTTGGTGAAAAATAT
876521 TCAACAAT
1 TCAACAAT
876529 GGCAACACTT
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
99 4 0.04
100 85 0.90
101 5 0.05
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (100 bp):
TCAACAATTACGATCACCTCTCTCGATTGTCAAAAGTCGGTGAAGAATAGTAAACAATTACGACC
ACCTCTCTCGATTATCAAAAGTTGGTGAAAAATAT
Found at i:880444 original size:50 final size:50
Alignment explanation
Indices: 880367--880626 Score: 369
Period size: 50 Copynumber: 5.2 Consensus size: 50
880357 AGTTGCTTAG
* *
880367 AGTCAACAATTACGGTCACCTCTCTCGATTGTTAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAAAAT
* * **
880417 ATTCAACAATTACGGCCACCTCTCTCGATTGTCAAAAATTGGTGAAAAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAAAAT
*
880467 CGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGT-AAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAA-AAT
* **
880517 AATCAACAATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAAAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAAAAT
* ** *
880567 AGTCAACAATTACGGTCTCCTCTCTCGATTGTCAAAGGTCAGTAAAAAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAAAAT
*
880617 AATCAACAAT
1 AGTCAACAAT
880627 GACAACACTT
Statistics
Matches: 185, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
49 3 0.02
50 179 0.97
51 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAAAAT
Found at i:880493 original size:100 final size:100
Alignment explanation
Indices: 880367--880626 Score: 421
Period size: 100 Copynumber: 2.6 Consensus size: 100
880357 AGTTGCTTAG
* * * *
880367 AGTCAACAATTACGGTCACCTCTCTCGATTGTTAAAGGTTGGTGAAGAATATTCAACAATTACGG
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTAAAGAATAATCAACAATTACGA
880432 CCACCTCTCTCGATTGTCAAAAATTGGTGAAAAAT
66 CCACCTCTCTCGATTGTCAAAAATTGGTGAAAAAT
*
880467 CGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTAAAGAATAATCAACAATTACGA
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTAAAGAATAATCAACAATTACGA
**
880532 CCACCTCTCTCGATTGTCAAAGGTTGGTGAAAAAT
66 CCACCTCTCTCGATTGTCAAAAATTGGTGAAAAAT
* ** *
880567 AGTCAACAATTACGGTCTCCTCTCTCGATTGTCAAAGGTCAGTAAAAAATAATCAACAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTAAAGAATAATCAACAAT
880627 GACAACACTT
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
100 148 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (100 bp):
AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTAAAGAATAATCAACAATTACGA
CCACCTCTCTCGATTGTCAAAAATTGGTGAAAAAT
Found at i:882862 original size:19 final size:19
Alignment explanation
Indices: 882838--882876 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
882828 AATAAAAAAA
882838 TTTTATAATTA-TTTTAAAT
1 TTTTAT-ATTATTTTTAAAT
*
882857 TTTTATTTTATTTTTAAAT
1 TTTTATATTATTTTTAAAT
882876 T
1 T
882877 ATTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATATTATTTTTAAAT
Found at i:883013 original size:15 final size:15
Alignment explanation
Indices: 882958--883015 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 15
882948 ATTTAAAAAC
882958 TTTATTTTATTAATTATT
1 TTTATTTTATT-A-TA-T
882976 TTTATTTT-TTATAT
1 TTTATTTTATTATAT
882990 TTAAATATTTTATTATAT
1 TT---TATTTTATTATAT
883008 TTTATTTT
1 TTTATTTT
883016 TGAATAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
14 3 0.08
15 8 0.22
16 1 0.03
17 8 0.22
18 16 0.44
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTTATTATAT
Found at i:883961 original size:22 final size:19
Alignment explanation
Indices: 883931--883983 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
883921 TAATTTTATT
883931 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
883952 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
* *
883972 TTATTTTAATAT
1 TAAATTTAATAT
883984 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.24
20 6 0.21
21 12 0.41
22 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:885857 original size:28 final size:28
Alignment explanation
Indices: 885810--885896 Score: 147
Period size: 28 Copynumber: 3.1 Consensus size: 28
885800 ACCATGACAA
* *
885810 TTTTTCAATTGCCATATAGGGATCAAAG
1 TTTTTCAATTGCTATCTAGGGATCAAAG
*
885838 TTTTTCAATTGCTATCTAGGGGTCAAAG
1 TTTTTCAATTGCTATCTAGGGATCAAAG
885866 TTTTTCAATTGCTATCTAGGGATCAAAG
1 TTTTTCAATTGCTATCTAGGGATCAAAG
885894 TTT
1 TTT
885897 CAAATTGCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (28 bp):
TTTTTCAATTGCTATCTAGGGATCAAAG
Found at i:892255 original size:22 final size:23
Alignment explanation
Indices: 892219--892264 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
892209 ATTGAATTTG
892219 AATTATTATTTAA-TTAATAAAA
1 AATTATTATTTAATTTAATAAAA
*
892241 AATT-TTATTTAAATTTAATTAAA
1 AATTATTATTT-AATTTAATAAAA
892264 A
1 A
892265 TATATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATTATTATTTAATTTAATAAAA
Found at i:892309 original size:29 final size:29
Alignment explanation
Indices: 892279--892345 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
892269 TAAAAATATT
* *
892279 AATATAAAAATAAATTTATTAATATTTTTA
1 AATATAAAAA-AAATCTATAAATATTTTTA
* *
892309 AATAATAAAAAAGATCTATAAATTTTTTTA
1 AAT-ATAAAAAAAATCTATAAATATTTTTA
892339 AATATAA
1 AATATAA
892346 TTCGAATCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 4 0.12
30 21 0.66
31 7 0.22
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (29 bp):
AATATAAAAAAAATCTATAAATATTTTTA
Found at i:892850 original size:13 final size:13
Alignment explanation
Indices: 892834--892876 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
892824 ATTGAAAACC
892834 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
**
892847 AAAAGAAGCAAAA
1 AAAAGAAAAAAAA
**
892860 AATTGAAAAAAAA
1 AAAAGAAAAAAAA
892873 AAAA
1 AAAA
892877 AGCATTTTGA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:896168 original size:2 final size:2
Alignment explanation
Indices: 896161--896194 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
896151 CTCTGTCAAC
896161 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
896195 TAAAAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:898249 original size:19 final size:19
Alignment explanation
Indices: 898213--898252 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
898203 GTTAATACAT
*
898213 ATTTTATTTAATTCAAAAA
1 ATTTTATTTAATTAAAAAA
* *
898232 ATTTTCTTTTATTAAAAAA
1 ATTTTATTTAATTAAAAAA
898251 AT
1 AT
898253 AACTCTTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTATTTAATTAAAAAA
Found at i:898675 original size:20 final size:20
Alignment explanation
Indices: 898650--898758 Score: 67
Period size: 20 Copynumber: 5.0 Consensus size: 20
898640 TTTTATACTT
* *
898650 TTTAATATTTTAAATTTTAA
1 TTTAATATTTAAAATATTAA
898670 TTTAATATTTAAAATATTAA
1 TTTAATATTTAAAATATTAA
**
898690 -AAAATAATTTAAAATATTCACA
1 TTTAAT-ATTTAAAATATT-A-A
* * *
898712 TTATAAAAATTTTTAATTATATTTA
1 TT-T---AATATTTAA-AATATTAA
898737 TATTAATATTTAAAATATTAA
1 T-TTAATATTTAAAATATTAA
898758 T
1 T
898759 ACAAAATTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 19
0.68 0.12 0.19
Matches are distributed among these distances:
19 3 0.04
20 30 0.45
21 8 0.12
22 9 0.13
25 3 0.04
26 6 0.09
27 8 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATATTTAAAATATTAA
Found at i:898802 original size:30 final size:29
Alignment explanation
Indices: 898744--898803 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 29
898734 TTATATTAAT
* *
898744 ATTTAAAATATTAATACAAAATTTTATTA
1 ATTTAAAATATTAAAAAAAAATTTTATTA
898773 ATTT-AAATATTAAAAAAATAATATTTATTA
1 ATTTAAAATATTAAAAAAA-AAT-TTTATTA
898803 A
1 A
898804 AAAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 12 0.44
29 7 0.26
30 8 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTTAAAATATTAAAAAAAAATTTTATTA
Found at i:899054 original size:14 final size:14
Alignment explanation
Indices: 899035--899069 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
899025 AATCAAAAGT
899035 AAATTTTTTTTTTA
1 AAATTTTTTTTTTA
*
899049 AAATTTATTTTTTA
1 AAATTTTTTTTTTA
*
899063 GAATTTT
1 AAATTTT
899070 AAGAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
AAATTTTTTTTTTA
Found at i:899088 original size:70 final size:71
Alignment explanation
Indices: 899009--899151 Score: 243
Period size: 71 Copynumber: 2.0 Consensus size: 71
898999 TTATAGAAGC
* * * *
899009 ATAAATATTATTTATCAATCAAAAGT-AAATTTTTTTTTTAAAATTTATTTTTTAGAATTTTAAG
1 ATAAATATTATTTATCAATCAAAAGTAAAATCTTTTTTCTAAAATTTATTTTTCAGAATTTCAAG
899073 AAAAAA
66 AAAAAA
899079 ATAAATATTATTTATCAATCAAAAGTAAAATCTTTTTTCTAAAATTTATTTTTCAGAATTTCAAG
1 ATAAATATTATTTATCAATCAAAAGTAAAATCTTTTTTCTAAAATTTATTTTTCAGAATTTCAAG
899144 AAAAAA
66 AAAAAA
899150 AT
1 AT
899152 CTATTAGTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
70 26 0.38
71 42 0.62
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (71 bp):
ATAAATATTATTTATCAATCAAAAGTAAAATCTTTTTTCTAAAATTTATTTTTCAGAATTTCAAG
AAAAAA
Found at i:899770 original size:27 final size:27
Alignment explanation
Indices: 899740--899796 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
899730 AATTGAATCG
899740 AAATTT-T-AAAATATATAATAAAAAATT
1 AAATTTATAAAAAT-TATAA-AAAAAATT
899767 AAATTTATAAAAATTATAAAAAAAATT
1 AAATTTATAAAAATTATAAAAAAAATT
899794 AAA
1 AAA
899797 AATCAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 17 0.61
28 6 0.21
29 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATTTATAAAAATTATAAAAAAAATT
Found at i:900028 original size:22 final size:21
Alignment explanation
Indices: 899984--900045 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
899974 AAATATTTAA
*
899984 ATTTAAATTTGAATATTTTTTAT
1 ATTT-AATTT-AATATTTATTAT
900007 ATTTAATTTAATTATTTATTAT
1 ATTTAATTTAA-TATTTATTAT
*
900029 -TTATTATTTAAATATTT
1 ATT-TAATTT-AATATTT
900046 TTTAAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.12
22 24 0.71
23 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTAATTTAATATTTATTAT
Found at i:900029 original size:29 final size:29
Alignment explanation
Indices: 899976--900035 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
899966 AAATTTTAAA
*
899976 ATATTTAAATTTAAATTTGAATATTTTTT
1 ATATTTAAATTTAAATTTGAATATTTATT
*
900005 ATATTT-AATTTAATTATTT-ATTATTTATT
1 ATATTTAAATTTAA--ATTTGAATATTTATT
900034 AT
1 AT
900036 TTAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.26
29 16 0.59
30 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
ATATTTAAATTTAAATTTGAATATTTATT
Found at i:900098 original size:21 final size:21
Alignment explanation
Indices: 900050--900116 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
900040 ATATTTTTTA
* **
900050 AATACATTAAATATTTAAATTT
1 AATAAATT-AATATTTAAAAAT
*
900072 ATTAAATTAATATTTAAAAAT
1 AATAAATTAATATTTAAAAAT
*
900093 AATAAATATTAA-ATATAAAAAT
1 AAT-AA-ATTAATATTTAAAAAT
900115 AA
1 AA
900117 ATAACAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 13 0.35
22 19 0.51
23 5 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAAATTAATATTTAAAAAT
Found at i:900127 original size:24 final size:22
Alignment explanation
Indices: 900075--900132 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
900065 TAAATTTATT
*
900075 AAATTAATATTTAAAAATAATAA
1 AAATTAA-ATATAAAAATAATAA
*
900098 ATATTAAATATAAAAATAAATAA
1 AAATTAAATATAAAAAT-AATAA
900121 CAAATTAAATAT
1 -AAATTAAATAT
900133 TTAGATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.30
23 11 0.37
24 10 0.33
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATTAAATATAAAAATAATAA
Found at i:900140 original size:24 final size:24
Alignment explanation
Indices: 900075--900156 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
900065 TAAATTTATT
900075 AAATT-AATATTTAA-AAATAATA
1 AAATTAAATATTTAATAAATAATA
** *
900097 AATATTAAATATAAAAATAAATAA-C
1 AA-ATTAAATAT-TTAATAAATAATA
*
900122 AAATTAAATATTTAGATAAATAAAA
1 AAATTAAATATTTA-ATAAATAATA
*
900147 AAATTGAATA
1 AAATTAAATA
900157 CGTGTTGACA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
22 2 0.04
23 4 0.09
24 22 0.47
25 13 0.28
26 6 0.13
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTAAATATTTAATAAATAATA
Found at i:900463 original size:29 final size:30
Alignment explanation
Indices: 900411--900469 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
900401 AGTCAAATTA
900411 AAAATAAATTATCAAAATAATATT-TTTTT
1 AAAATAAATTATCAAAATAATATTATTTTT
*
900440 AAAATAAATTAT-AAAATTATTATTATTTTT
1 AAAATAAATTATCAAAA-TAATATTATTTTT
900470 TCGTTGACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 18 0.67
30 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
AAAATAAATTATCAAAATAATATTATTTTT
Found at i:900958 original size:30 final size:35
Alignment explanation
Indices: 900923--900988 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 35
900913 AGTAATTTAG
900923 TATTTTA-AAGTT-TTAAAAT-TTG-TT-TTATTT
1 TATTTTATAAGTTATTAAAATATTGATTATTATTT
*
900953 TATTTTATAATTTATTAAAATATTGATTATTATTT
1 TATTTTATAAGTTATTAAAATATTGATTATTATTT
900988 T
1 T
900989 TTGTAACACT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 7 0.23
31 4 0.13
32 7 0.23
33 3 0.10
34 2 0.07
35 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (35 bp):
TATTTTATAAGTTATTAAAATATTGATTATTATTT
Found at i:901398 original size:25 final size:25
Alignment explanation
Indices: 901370--901421 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
901360 AATGGAAAGC
901370 TATGTGAAAGATTGAATAGTGTTAG
1 TATGTGAAAGATTGAATAGTGTTAG
901395 TATGTGAAAGATTGAATAGTGTTAG
1 TATGTGAAAGATTGAATAGTGTTAG
901420 TA
1 TA
901422 CTAAAGGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (25 bp):
TATGTGAAAGATTGAATAGTGTTAG
Found at i:906860 original size:14 final size:14
Alignment explanation
Indices: 906841--906875 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
906831 CATATATTTT
*
906841 TAAAAATATAATAAC
1 TAAAAAT-TAATAAA
906856 TAAAAATTAATAAA
1 TAAAAATTAATAAA
906870 TAAAAA
1 TAAAAA
906876 ATATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAAATTAATAAA
Found at i:906861 original size:15 final size:15
Alignment explanation
Indices: 906841--906882 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
906831 CATATATTTT
*
906841 TAAAAATATAATAAC
1 TAAAAATATAATAAA
906856 TAAAAAT-TAATAAA
1 TAAAAATATAATAAA
906870 TAAAAAATATAAT
1 T-AAAAATATAAT
906883 TTTATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 13 0.54
16 4 0.17
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAATATAATAAA
Found at i:907075 original size:23 final size:22
Alignment explanation
Indices: 907049--907152 Score: 76
Period size: 23 Copynumber: 4.7 Consensus size: 22
907039 TGTAACAAAA
907049 ATTTATTATCATAATTAATTAAT
1 ATTTATTAT-ATAATTAATTAAT
*
907072 ATTTGATTA-A-AA-AAATT-AT
1 ATTT-ATTATATAATTAATTAAT
* *
907091 AGTTT-TTATCTAATTAA-TATTT
1 A-TTTATTATATAATTAATTA-AT
*
907113 ATTTATTAATATAATTATTTAAT
1 ATTTATT-ATATAATTAATTAAT
907136 ATTTATTAATATAATTA
1 ATTTATT-ATATAATTA
907153 TTTATTAATA
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
18 3 0.05
19 3 0.05
20 10 0.16
21 7 0.11
22 5 0.08
23 30 0.47
24 6 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTATTATATAATTAATTAAT
Found at i:907132 original size:16 final size:16
Alignment explanation
Indices: 907132--907168 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
907122 TATAATTATT
907132 TAAT-ATTTATTAATA
1 TAATTATTTATTAATA
907147 TAATTATTTATTAATA
1 TAATTATTTATTAATA
907163 TAATTA
1 TAATTA
907169 ATTAAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATTATTTATTAATA
Found at i:907136 original size:13 final size:13
Alignment explanation
Indices: 907118--907156 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
907108 TATTTATTTA
907118 TTAATATAATTAT
1 TTAATATAATTAT
907131 TTAATAT--TTA-
1 TTAATATAATTAT
907141 TTAATATAATTAT
1 TTAATATAATTAT
907154 TTA
1 TTA
907157 TTAATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 7 0.30
11 3 0.13
12 3 0.13
13 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATATAATTAT
Found at i:907153 original size:23 final size:23
Alignment explanation
Indices: 907112--907156 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
907102 AATTAATATT
907112 TATTTATTAATATAATTATTTAA
1 TATTTATTAATATAATTATTTAA
907135 TATTTATTAATATAATTATTTA
1 TATTTATTAATATAATTATTTA
907157 TTAATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTTATTAATATAATTATTTAA
Found at i:907297 original size:13 final size:14
Alignment explanation
Indices: 907273--907310 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
907263 TTCATAACAA
907273 AATAACAATATTTT
1 AATAACAATATTTT
907287 AATAA-AATATTTT
1 AATAACAATATTTT
*
907300 AA-AATAATATT
1 AATAACAATATT
907311 ATTTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 16 0.70
14 5 0.22
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AATAACAATATTTT
Found at i:907331 original size:28 final size:29
Alignment explanation
Indices: 907271--907331 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
907261 TCTTCATAAC
*
907271 AAAATAACAATATTTTAATAAAATATTTT
1 AAAATAACAATATTTTAATAAAATATTTA
* * **
907300 AAAATAATATTATTTT-ATAATTTATTTA
1 AAAATAACAATATTTTAATAAAATATTTA
907328 AAAA
1 AAAA
907332 ATAAAGGTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATAACAATATTTTAATAAAATATTTA
Found at i:914696 original size:3 final size:3
Alignment explanation
Indices: 914688--914729 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
914678 TGATGAGGTC
*
914688 GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
914730 AATGAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:922430 original size:25 final size:26
Alignment explanation
Indices: 922358--922447 Score: 69
Period size: 25 Copynumber: 3.5 Consensus size: 26
922348 GAAAATATTT
* *
922358 TATTTTTAATATATTCAACAATTAAA
1 TATTTTTAATTTATTTAACAATTAAA
* ** *
922384 -ATTTTT-ATATCAAATAATAATTAAA
1 TATTTTTAAT-TTATTTAACAATTAAA
*
922409 TATTTTTAATTTATTTAA-AATTTAA
1 TATTTTTAATTTATTTAACAATTAAA
* *
922434 TATGTATAATTTAT
1 TATTTTTAATTTAT
922448 GCATAATTAA
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
24 2 0.04
25 34 0.69
26 11 0.22
27 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (26 bp):
TATTTTTAATTTATTTAACAATTAAA
Found at i:922455 original size:25 final size:25
Alignment explanation
Indices: 922400--922457 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
922390 ATATCAAATA
* * **
922400 ATAATTAAATATTTTTAATTTATTT
1 ATAATTAAATATGTATAATTTATGC
* *
922425 AAAATTTAATATGTATAATTTATGC
1 ATAATTAAATATGTATAATTTATGC
922450 ATAATTAA
1 ATAATTAA
922458 TTTAACTTTA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (25 bp):
ATAATTAAATATGTATAATTTATGC
Found at i:925870 original size:33 final size:34
Alignment explanation
Indices: 925739--925869 Score: 153
Period size: 34 Copynumber: 3.9 Consensus size: 34
925729 CTAAAACCAA
* * *
925739 ATGAACAGAATTTCTGAATATCATTGGAAGCTA-
1 ATGAACAGAATTTCAGAATATCATTGAAAACTAC
* *
925772 AGTGAACAAAATCTCAGAATATCATTGAAAACTAC
1 A-TGAACAGAATTTCAGAATATCATTGAAAACTAC
*
925807 AAT-AACATG-ATTTCAGAATATCATTGAAAATTAC
1 -ATGAACA-GAATTTCAGAATATCATTGAAAACTAC
925841 ATGAA-AGAATTTCAGAATATCATTGAAAA
1 ATGAACAGAATTTCAGAATATCATTGAAAA
925870 TCTTTAAGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
32 1 0.01
33 25 0.30
34 56 0.67
35 1 0.01
36 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (34 bp):
ATGAACAGAATTTCAGAATATCATTGAAAACTAC
Found at i:927076 original size:454 final size:449
Alignment explanation
Indices: 926229--927135 Score: 1329
Period size: 454 Copynumber: 2.0 Consensus size: 449
926219 CAAAAAAATC
* * *
926229 ATCATCATTCAAGTAAGCAATCCAACAAATTTTACCAGTTAGATTAAGGATTAAATATTAGCTAA
1 ATCATCATTCAAGTAAGCAATCCAACAAATATTACCAGTTAGATTAAGGATTAAATAATAGATAA
* *
926294 GAAAGAAAAAAAAAGACCGCTTTCAATGTGAATAACAGCAGCATGAAGACGGTGCCCATTTGGCA
66 GAAAGAAAAAAAAAGACCGCTTTCAATGTGAATAACAGCAGCATGAAGACAGTGCACATTTGGCA
* * *
926359 AGTTCACCTCCTCACAATAATATCATAAGAATATAATAGCCGCCAAGAGCAAGAAGGGGAAAGGG
131 AGTTCACCTCCTCACAATAATATCACAAGAATATAATAGCCGCCAAGAGCAAAAAGGGGAAAGAG
* * * *
926424 GGAGATATATGGCAAAACAGGAGGTACCAAGCAACAAGGAAGAGCATGACAGTTAAATTGAGGAT
196 GGAGATAAATGGCAAAACAGGAGGTAACAAGCAACAAGGAAGAGCATGACAGTTAAATTCAGAAT
* * * *
926489 AAATATACAAATTTGTATCCAAAGGTAGTTACAAAAGCATTGAAAACACAGAGTTCAAACTTTCA
261 AAATATACAAATTTG--TCCAAAGCTAGCTACAAAAGCACTGAAAACACA-AGTTCAAACTTTAA
*
926554 AAGCTCAGAAGCCAAGCGTAACAAGTATATTTCATAGAAGAACCCAACAAATAGATCCTTCTTAC
323 AAGCTCAGAAGCCAAGCGTAACAAGTACATTTCATAGAAGAACCCAACAAATAGATCCTTCTTAC
*
926619 ATGTTATTGCTTCATCACTGCAAGATAAAGCTTCCAAGAAAAATTTATATTTGAATGCAAACAA
388 ATGTTATTGCTTCATCACTGCAAGACAAA-CTTCCAAG-AAAATTTATATTTGAATGCAAACAA
* *
926683 ATCATCATTCAAGTAAGCAATCTAACAAATATTACCAGTTAGTTTAAGGATTAAATAATAGATAA
1 ATCATCATTCAAGTAAGCAATCCAACAAATATTACCAGTTAGATTAAGGATTAAATAATAGATAA
* * * *
926748 GAAAAGAAATAAAAGGACCGC-TTCAATGTTAATAACCGCAGCATGAAGACAGTGCACATTTGGC
66 G-AAAGAAAAAAAAAGACCGCTTTCAATGTGAATAACAGCAGCATGAAGACAGTGCACATTTGGC
* * * *
926812 AAGTTCACTTGCTTACAA-ATATATCACAAGAATATAATAGCTGCCAAGAGCAAAAAGGGGAAAA
130 AAGTTCACCTCCTCACAATA-ATATCACAAGAATATAATAGCCGCCAAGAGCAAAAAGGGG-AAA
* * *
926876 GAGGGAGA-AGAATGGCAAAACAGGAGGTAAGAAGCAACATGGGAGAGCATGACAGTTAAATTCA
193 GAGGGAGATA-AATGGCAAAACAGGAGGTAACAAGCAACAAGGAAGAGCATGACAGTTAAATTCA
* * *
926940 GAATTAATATACACAATTATG-CCAAAATCTAGCTACATAAAGCACTGAAAACAC-AGTTTAAAC
257 GAATAAATATACA-AATT-TGTCC-AAAGCTAGCTACA-AAAGCACTGAAAACACAAGTTCAAAC
*
927003 TTTAAAAGCTCAGAAGCCAAGCGTAACAAGTACATTTCATAGAAGAACCCAACAAATAGATTCTT
318 TTTAAAAGCTCAGAAGCCAAGCGTAACAAGTACATTTCATAGAAGAACCCAACAAATAGATCCTT
* *
927068 CTTACATGTTATTGCTTCATCACTGCAAGACAAATTTCCAAGAAAATTTATATTTGAATGCAAGC
383 CTTACATGTTATTGCTTCATCACTGCAAGACAAACTTCCAAGAAAATTTATATTTGAATGCAAAC
927133 AA
448 AA
927135 A
1 A
927136 CTACACCTTT
Statistics
Matches: 408, Mismatches: 37, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
452 25 0.06
453 8 0.02
454 258 0.63
455 96 0.24
456 19 0.05
457 2 0.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (449 bp):
ATCATCATTCAAGTAAGCAATCCAACAAATATTACCAGTTAGATTAAGGATTAAATAATAGATAA
GAAAGAAAAAAAAAGACCGCTTTCAATGTGAATAACAGCAGCATGAAGACAGTGCACATTTGGCA
AGTTCACCTCCTCACAATAATATCACAAGAATATAATAGCCGCCAAGAGCAAAAAGGGGAAAGAG
GGAGATAAATGGCAAAACAGGAGGTAACAAGCAACAAGGAAGAGCATGACAGTTAAATTCAGAAT
AAATATACAAATTTGTCCAAAGCTAGCTACAAAAGCACTGAAAACACAAGTTCAAACTTTAAAAG
CTCAGAAGCCAAGCGTAACAAGTACATTTCATAGAAGAACCCAACAAATAGATCCTTCTTACATG
TTATTGCTTCATCACTGCAAGACAAACTTCCAAGAAAATTTATATTTGAATGCAAACAA
Found at i:928782 original size:2 final size:2
Alignment explanation
Indices: 928775--928805 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
928765 TAACAAATGC
928775 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 A
928806 CAAAAGAAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:929138 original size:2 final size:2
Alignment explanation
Indices: 929131--929167 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
929121 AGTATATTCA
*
929131 AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
929168 TGAGTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:936680 original size:84 final size:84
Alignment explanation
Indices: 936539--936706 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 84
936529 AAGCATCCTT
936539 CACAGTTTCACAGAGTAAAAATTGCCAGAACTGGAATGACATGTGAAATGATATTTCAAATTAAA
1 CACAGTTTCACAGAGTAAAAATTGCCAGAACTGGAATGACATGTGAAATGATATTTCAAATTAAA
*
936604 AGGAAAGGAATATAAGAAA
66 ACGAAAGGAATATAAGAAA
*
936623 CACAGTTTCAGAGAGTAAAAATTGCCAGAACTGGAATGACATGTGAAATGATATTTCAAATTAAA
1 CACAGTTTCACAGAGTAAAAATTGCCAGAACTGGAATGACATGTGAAATGATATTTCAAATTAAA
936688 ACGAAAGGAATATAAGAAA
66 ACGAAAGGAATATAAGAAA
936707 GTGTTCCTTC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.23
Consensus pattern (84 bp):
CACAGTTTCACAGAGTAAAAATTGCCAGAACTGGAATGACATGTGAAATGATATTTCAAATTAAA
ACGAAAGGAATATAAGAAA
Found at i:936898 original size:24 final size:25
Alignment explanation
Indices: 936864--936911 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
936854 CTTAAGGAGT
*
936864 TATCTGAAGCATCTCGTACAAGTAC
1 TATCTGAAGCATCTAGTACAAGTAC
936889 TATCT-AAGCATCTAGTACAAGTA
1 TATCTGAAGCATCTAGTACAAGTA
936912 TGGCTGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (25 bp):
TATCTGAAGCATCTAGTACAAGTAC
Found at i:937402 original size:153 final size:153
Alignment explanation
Indices: 937124--937432 Score: 546
Period size: 153 Copynumber: 2.0 Consensus size: 153
937114 AGGGTCAAAC
* *
937124 AAGAATTTTCAGTTTGTCCCATCTATGACATGTTAATCAGGGCGATTCTCAGTGATGGTACCGTA
1 AAGAATTTTCAGTTTGTCCCACCTATGACATGTTAATCAGGGCGATTCTCAGTGATGGTACCATA
937189 TGAAATCTTCCAAGAACATGTTGCTTTTCAGATGGGTGACCCAGTTGAGCCAATGCTGGCAGCAA
66 TGAAATCTTCCAAGAACATGTTGCTTTTCAGATGGGTGACCCAGTTGAGCCAATGCTGGCAGCAA
*
937254 AACCTATTGAAGCTGTATCTGAG
131 AACCTATTGAAGCTGTACCTGAG
** *
937277 AAGAATTTTCAGTTTGTCCTGCCTATGACATGTTAATCAGGGCGATTCTCAGTGATGGTACTATA
1 AAGAATTTTCAGTTTGTCCCACCTATGACATGTTAATCAGGGCGATTCTCAGTGATGGTACCATA
* *
937342 TGGAATCTTCCAAGAACATGTTGCTTTTCAGATGGGTGACCCAGTTGAGCCACTGCTGGCAGCAA
66 TGAAATCTTCCAAGAACATGTTGCTTTTCAGATGGGTGACCCAGTTGAGCCAATGCTGGCAGCAA
937407 AACCTATTGAAGCTGTACCTGAG
131 AACCTATTGAAGCTGTACCTGAG
937430 AAG
1 AAG
937433 TTTTGAAAGA
Statistics
Matches: 148, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
153 148 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (153 bp):
AAGAATTTTCAGTTTGTCCCACCTATGACATGTTAATCAGGGCGATTCTCAGTGATGGTACCATA
TGAAATCTTCCAAGAACATGTTGCTTTTCAGATGGGTGACCCAGTTGAGCCAATGCTGGCAGCAA
AACCTATTGAAGCTGTACCTGAG
Found at i:941140 original size:27 final size:25
Alignment explanation
Indices: 941095--941157 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
941085 GCTGTGGCTT
941095 CCACTGTCACT-TCCACTATCACTGCTG
1 CCACTGTCACTATCCACTATCA--G-TG
* *
941122 TCACTGTCACTAT-CGCTATCAGTG
1 CCACTGTCACTATCCACTATCAGTG
941146 CCACTGTCACTA
1 CCACTGTCACTA
941158 GCACTATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 13 0.41
25 1 0.03
27 17 0.53
28 1 0.03
ACGTcount: A:0.21, C:0.37, G:0.13, T:0.30
Consensus pattern (25 bp):
CCACTGTCACTATCCACTATCAGTG
Found at i:951050 original size:34 final size:34
Alignment explanation
Indices: 950979--951163 Score: 255
Period size: 34 Copynumber: 5.5 Consensus size: 34
950969 GAATCTGAAA
* *
950979 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
951012 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACA
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
951046 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
951080 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
951114 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
951148 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
951164 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 13 0.10
34 119 0.90
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:951524 original size:19 final size:19
Alignment explanation
Indices: 951468--951530 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
951458 TGGTTGTCGA
**
951468 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
951487 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
951506 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
951525 GTTACT
1 GGTACT
951531 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:955667 original size:34 final size:34
Alignment explanation
Indices: 955596--955780 Score: 255
Period size: 34 Copynumber: 5.5 Consensus size: 34
955586 AAGTGGGAGA
* *
955596 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
955629 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACA
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
955663 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
955697 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
955731 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
955765 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
955781 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 13 0.10
34 119 0.90
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:961768 original size:15 final size:17
Alignment explanation
Indices: 961734--961772 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
961724 ATTAATAAAA
961734 AAATTAATAACAATATT
1 AAATTAATAACAATATT
*
961751 AAATTATTAA-AA-ATT
1 AAATTAATAACAATATT
961766 AAATTAA
1 AAATTAA
961773 AAATAACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.45
16 2 0.10
17 9 0.45
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTAATAACAATATT
Found at i:963429 original size:2 final size:2
Alignment explanation
Indices: 963422--963451 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
963412 TCCTTTATTT
*
963422 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
963452 ATGTGTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:967217 original size:13 final size:13
Alignment explanation
Indices: 967201--967244 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
967191 TCTATCTATT
967201 TTTTTAAATATAA
1 TTTTTAAATATAA
* *
967214 -TTTTAATTATCA
1 TTTTTAAATATAA
*
967226 TTTATAAATATAA
1 TTTTTAAATATAA
967239 TTTTTA
1 TTTTTA
967245 CAATTTATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAATATAA
Found at i:967233 original size:25 final size:24
Alignment explanation
Indices: 967205--967265 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 24
967195 TCTATTTTTT
967205 TAAATATAATTTTAATTATC-ATTTA
1 TAAATATAATTTT-ATTA-CAATTTA
967230 TAAATATAA-TTT-TTACAATTTA
1 TAAATATAATTTTATTACAATTTA
967252 TAAATA-AATTTTAT
1 TAAATATAATTTTAT
967266 ATATATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 3 0.09
22 17 0.52
23 1 0.03
24 3 0.09
25 9 0.27
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (24 bp):
TAAATATAATTTTATTACAATTTA
Found at i:967310 original size:7 final size:7
Alignment explanation
Indices: 967298--967328 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
967288 TGTATTAAAA
967298 AAATAAT
1 AAATAAT
967305 AAATAAT
1 AAATAAT
967312 AAATAAT
1 AAATAAT
967319 AAATAAT
1 AAATAAT
967326 AAA
1 AAA
967329 GGAAATCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:969542 original size:54 final size:52
Alignment explanation
Indices: 969474--969582 Score: 173
Period size: 54 Copynumber: 2.1 Consensus size: 52
969464 ACAATTCAAT
* * *
969474 TAAATTAAGGTTTTATAATAAGTACATATACAAATATAATATATTTATATATA
1 TAAATTAAGCTTTTATAATAAGTACATATACAAATACAATATA-TAATATATA
969527 TAAATTAAAGCTTTTATAATAAGTACATATACAAATACAATATATAATATATA
1 TAAATT-AAGCTTTTATAATAAGTACATATACAAATACAATATATAATATATA
969580 TAA
1 TAA
969583 TTGTTCAACT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 17 0.33
54 35 0.67
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.39
Consensus pattern (52 bp):
TAAATTAAGCTTTTATAATAAGTACATATACAAATACAATATATAATATATA
Found at i:969948 original size:6 final size:7
Alignment explanation
Indices: 969932--969957 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
969922 TTCAAATAAT
969932 AAAATTA
1 AAAATTA
969939 AAAATTA
1 AAAATTA
969946 AAAATTA
1 AAAATTA
969953 AAAAT
1 AAAAT
969958 ATATCCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:970641 original size:21 final size:20
Alignment explanation
Indices: 970609--970662 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 20
970599 TTAAATATAT
970609 TATAATTATAAAATACATAAAA
1 TATAA-TATAAAATA-ATAAAA
970631 TATAATATAAAATAATATAAA
1 TATAATATAAAATAATA-AAA
*
970652 CATAATATAAA
1 TATAATATAAA
970663 TATATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 3 0.10
21 22 0.73
22 5 0.17
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TATAATATAAAATAATAAAA
Found at i:970658 original size:11 final size:10
Alignment explanation
Indices: 970610--970670 Score: 65
Period size: 10 Copynumber: 6.0 Consensus size: 10
970600 TAAATATATT
970610 ATAATTATAAA
1 ATAA-TATAAA
970621 ATACATA-AAA
1 ATA-ATATAAA
970631 TATAATATAAA
1 -ATAATATAAA
970642 ATAATATAAA
1 ATAATATAAA
970652 CATAATAT-AA
1 -ATAATATAAA
970662 AT-ATATAAA
1 ATAATATAAA
970671 TATTTTAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.09
9 4 0.09
10 18 0.40
11 18 0.40
12 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAATATAAA
Found at i:970703 original size:17 final size:16
Alignment explanation
Indices: 970681--970747 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 16
970671 TATTTTAAAA
970681 ATTATATAATATAAATT
1 ATTATA-AATATAAATT
970698 ATTATAACAT-TAACATT
1 ATTATAA-ATATAA-ATT
* *
970715 TTTATAAATATAAAAT
1 ATTATAAATATAAATT
*
970731 ATTTTAAATAT-AATT
1 ATTATAAATATAAATT
970746 AT
1 AT
970748 AAAAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 5 0.12
16 17 0.40
17 20 0.48
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTATAAATATAAATT
Found at i:970709 original size:25 final size:26
Alignment explanation
Indices: 970630--970709 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 26
970620 AATACATAAA
* *
970630 ATATAATATAAAATAATATAAACATA
1 ATATAATATAAAATATTATAAACATT
* *
970656 ATATAAATATATAAATATTTTAAAAATT
1 ATAT-AATATA-AAATATTATAAACATT
*
970684 ATATAATATAAATTATTAT-AACATT
1 ATATAATATAAAATATTATAAACATT
970709 A
1 A
970710 ACATTTTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
25 6 0.13
26 11 0.24
27 12 0.27
28 16 0.36
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (26 bp):
ATATAATATAAAATATTATAAACATT
Found at i:971001 original size:12 final size:12
Alignment explanation
Indices: 970984--971015 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
970974 ACTTGTATCT
970984 CCATCACCACCA
1 CCATCACCACCA
970996 CCATCACCACCA
1 CCATCACCACCA
*
971008 CCACCACC
1 CCATCACC
971016 CTGCACTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.62, G:0.00, T:0.06
Consensus pattern (12 bp):
CCATCACCACCA
Found at i:973804 original size:29 final size:27
Alignment explanation
Indices: 973767--973836 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 27
973757 TATTTTATTT
973767 AAAATAAAAATTATTTAAATATAAATAA
1 AAAATAAAAATTATTTAAATAT-AATAA
* *
973795 AAAATAAAAAATTACTTAATTATAATAA
1 AAAAT-AAAAATTATTTAAATATAATAA
973823 AAAATAAAAATTAT
1 AAAATAAAAATTAT
973837 AAAATAATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.21
28 15 0.39
29 15 0.39
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAATAAAAATTATTTAAATATAATAA
Found at i:975048 original size:35 final size:34
Alignment explanation
Indices: 975009--975074 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
974999 TTTATGATAT
*
975009 ATTTAATTTATTAAAATAAAATAATTATAAAAGTA
1 ATTTAATTTAATAAAATAAAAT-ATTATAAAAGTA
*
975044 ATTTAATTTAATATAATAAAATATTATAAAA
1 ATTTAATTTAATAAAATAAAATATTATAAAA
975075 TTTAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (34 bp):
ATTTAATTTAATAAAATAAAATATTATAAAAGTA
Found at i:975118 original size:20 final size:21
Alignment explanation
Indices: 975071--975120 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
975061 AAAATATTAT
*
975071 AAAATTTAAATTTTTGATAAA
1 AAAATTTAAATTTTTCATAAA
975092 AAGAATTTAAATTTTTCA-AAA
1 AA-AATTTAAATTTTTCATAAA
*
975113 TAAATTTA
1 AAAATTTA
975121 TATATTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 6 0.23
22 14 0.54
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (21 bp):
AAAATTTAAATTTTTCATAAA
Found at i:976582 original size:3 final size:3
Alignment explanation
Indices: 976574--976605 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
976564 TGGAGTTTCC
976574 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
976606 ACTGAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:977764 original size:17 final size:17
Alignment explanation
Indices: 977742--977776 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
977732 AACATCAGAC
*
977742 AACATTTAAATCCATTT
1 AACATTTAAATCAATTT
977759 AACATTTAAATCAATTT
1 AACATTTAAATCAATTT
977776 A
1 A
977777 TTCATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (17 bp):
AACATTTAAATCAATTT
Found at i:977912 original size:56 final size:56
Alignment explanation
Indices: 977806--977919 Score: 140
Period size: 56 Copynumber: 2.0 Consensus size: 56
977796 ATAATATGCG
** *
977806 TTTTATTTAAGTATCAAAACGGTAGTTAGGTCATCTTGCAGATCAAATATTAGGCT
1 TTTTATTTAAGTATCAAAACGGTAACTAGGCCATCTTGCAGATCAAATATTAGGCT
* * * **
977862 TTTTATTTAAGTATCAAAATGGTAACTATGCCATTTTGTGGAT-AAGATATTAGGCT
1 TTTTATTTAAGTATCAAAACGGTAACTAGGCCATCTTGCAGATCAA-ATATTAGGCT
977918 TT
1 TT
977920 GCATATTTGG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 2 0.04
56 47 0.96
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (56 bp):
TTTTATTTAAGTATCAAAACGGTAACTAGGCCATCTTGCAGATCAAATATTAGGCT
Found at i:979907 original size:28 final size:29
Alignment explanation
Indices: 979867--979925 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 29
979857 AGTTGAAAGG
979867 AAGTAGAAACTGTGGTG-AAATTTTAACA
1 AAGTAGAAACTGTGGTGAAAATTTTAACA
*
979895 AAGTAGGAACTGTGGTGAAAATTTTAACA
1 AAGTAGAAACTGTGGTGAAAATTTTAACA
979924 AA
1 AA
979926 ACGCAGTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (29 bp):
AAGTAGAAACTGTGGTGAAAATTTTAACA
Found at i:981671 original size:16 final size:17
Alignment explanation
Indices: 981627--981674 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
981617 AGAAAAAAAA
* *
981627 AAAAGAAAGGAACGAGG
1 AAAAGAAAGGAAAGAAG
981644 AAAAGAAA-GAAAGAAG
1 AAAAGAAAGGAAAGAAG
981660 AAAA-AAAGGAAAGAA
1 AAAAGAAAGGAAAGAA
981675 AAATTTGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 3 0.11
16 17 0.61
17 8 0.29
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGGAAAGAAG
Found at i:981675 original size:13 final size:13
Alignment explanation
Indices: 981596--981677 Score: 53
Period size: 13 Copynumber: 6.1 Consensus size: 13
981586 TAGGTGGGGC
981596 AAAGGAGAAGAAATA
1 AAAGGA-AAGAAA-A
981611 AAAGG-AAGAAAA
1 AAAGGAAAGAAAA
**
981623 AAAAAAAAGAAAGGA
1 AAAGGAAAGAAA--A
* *
981638 ACGAGGAAAAGAAAG
1 A-AAGG-AAAGAAAA
981653 AAA-G-AAGAAAA
1 AAAGGAAAGAAAA
981664 AAAGGAAAGAAAA
1 AAAGGAAAGAAAA
981677 A
1 A
981678 TTTGTCTGGC
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
11 9 0.17
12 5 0.10
13 21 0.40
14 1 0.02
15 8 0.15
16 1 0.02
17 7 0.13
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (13 bp):
AAAGGAAAGAAAA
Found at i:982705 original size:7 final size:7
Alignment explanation
Indices: 982695--982731 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
982685 CCCCAGGGGC
982695 AAAAAA-
1 AAAAAAG
*
982701 AAAAAGG
1 AAAAAAG
982708 AAAAAAG
1 AAAAAAG
982715 -AAAAAG
1 AAAAAAG
982721 AAAAAAG
1 AAAAAAG
982728 AAAA
1 AAAA
982732 GGAGACAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 11 0.41
7 16 0.59
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:982713 original size:13 final size:13
Alignment explanation
Indices: 982695--982734 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
982685 CCCCAGGGGC
982695 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
982708 AAAAAAGAAAAA-G
1 AAAAAA-AAAAAGG
*
982721 AAAAAAGAAAAGG
1 AAAAAAAAAAAGG
982734 A
1 A
982735 GACAGAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 15 0.62
14 5 0.21
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:986616 original size:2 final size:2
Alignment explanation
Indices: 986609--986660 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
986599 CTCCGTGCAT
986609 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
986651 TC TC TC TC TC
1 TC TC TC TC TC
986661 ACGGATTGCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:986940 original size:2 final size:2
Alignment explanation
Indices: 986930--986962 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
986920 TAAAAAAATA
986930 AT AT A- 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
986963 TTCTCTCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:987130 original size:20 final size:20
Alignment explanation
Indices: 987107--987147 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
987097 TATAAAAAAT
*
987107 AAAAAATAATTAAAATTTTA
1 AAAAAATAATTAAAATATTA
* *
987127 AAAAAATTATTTAAATATTA
1 AAAAAATAATTAAAATATTA
987147 A
1 A
987148 TATCATATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAAATAATTAAAATATTA
Found at i:987305 original size:15 final size:15
Alignment explanation
Indices: 987285--987335 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
987275 TTTTTTAGTT
987285 ATTAAAAATATAAAA
1 ATTAAAAATATAAAA
*
987300 ATT-AAAATATTAAA
1 ATTAAAAATATAAAA
* * * *
987314 CTTAATAATACAATA
1 ATTAAAAATATAAAA
987329 ATTAAAA
1 ATTAAAA
987336 TATTTTATTG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAAATATAAAA
Done.