Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 2 of 50
Found at i:724228 original size:2 final size:2
Alignment explanation
Indices: 724223--724256 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
724213 ACACACACAA
724223 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
724257 CACTAGGTAC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:724575 original size:13 final size:13
Alignment explanation
Indices: 724551--724585 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
724541 GGGGTTAGAG
724551 AAAGAA-AGAACA
1 AAAGAAGAGAACA
*
724563 AGAGAAGAGAACA
1 AAAGAAGAGAACA
724576 AAAGAAGAGA
1 AAAGAAGAGA
724586 TTAAGACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.69, C:0.06, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAAGAGAACA
Found at i:741563 original size:6 final size:6
Alignment explanation
Indices: 741552--741581 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
741542 TGCAATATAA
741552 ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG
1 ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG
741582 GAGGAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (6 bp):
ACAGAG
Found at i:745208 original size:18 final size:17
Alignment explanation
Indices: 745179--745223 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
745169 CTTTTTTTTG
745179 AAATGTTCTCAATCTTC
1 AAATGTTCTCAATCTTC
*
745196 GAATGTCTCTCAATCTTC
1 AAATGT-TCTCAATCTTC
745214 AAATGCTTCT
1 AAATG-TTCT
745224 AAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 18 0.75
19 1 0.04
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (17 bp):
AAATGTTCTCAATCTTC
Found at i:745487 original size:56 final size:56
Alignment explanation
Indices: 745378--745487 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 56
745368 AAGTTATTAG
* * * **
745378 CTCTAAATTATCTTAATTTAGTTAGAGATAAATTAAATAATTAAATTTGATTTTAT
1 CTCTAAATTAACATAATTTAGTTAGAGATAAATTAAATAATAAAATTAAATTTTAT
*
745434 CTCTAAATTAACATAA-TTA-TTAGAGATAAATTAAATGATCAATAATTAAATTTT
1 CTCTAAATTAACATAATTTAGTTAGAGATAAATTAAATAAT-AA-AATTAAATTTT
745488 GATTGGTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 19 0.41
55 4 0.09
56 23 0.50
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (56 bp):
CTCTAAATTAACATAATTTAGTTAGAGATAAATTAAATAATAAAATTAAATTTTAT
Found at i:746754 original size:18 final size:18
Alignment explanation
Indices: 746731--746766 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
746721 ATTATTAATT
746731 ATTTTTATATACTTTTAA
1 ATTTTTATATACTTTTAA
*
746749 ATTTTTATATATTTTTAA
1 ATTTTTATATACTTTTAA
746767 TATAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTATATACTTTTAA
Found at i:747050 original size:9 final size:9
Alignment explanation
Indices: 747036--747061 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
747026 ATACTCTTTC
747036 AATAATTTT
1 AATAATTTT
747045 AATAATTTT
1 AATAATTTT
747054 AATAATTT
1 AATAATTT
747062 AATTTTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AATAATTTT
Found at i:748223 original size:23 final size:24
Alignment explanation
Indices: 748175--748223 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
748165 AAATTTCAAA
*
748175 ATTTATAAAAATTTATTTTTAATT
1 ATTTATAAAAATTTATTTTGAATT
*
748199 ATTT-TAAAAA-TTATTCTTGACTT
1 ATTTATAAAAATTTATT-TTGAATT
748222 AT
1 AT
748224 ATTCAACCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTATAAAAATTTATTTTGAATT
Found at i:755798 original size:35 final size:35
Alignment explanation
Indices: 755759--755832 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
755749 ATTATGAGAC
*
755759 AAATAT-AAATATTTGACATGAGTGATATTATCTGA
1 AAATATAAAAT-TTTGACATGAGTGATAATATCTGA
**
755794 AAATATAAAATTTTGATGTGAGTGATAATATCTGA
1 AAATATAAAATTTTGACATGAGTGATAATATCTGA
755829 AAAT
1 AAAT
755833 TCTTTTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 31 0.89
36 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (35 bp):
AAATATAAAATTTTGACATGAGTGATAATATCTGA
Found at i:756073 original size:44 final size:44
Alignment explanation
Indices: 756022--756129 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 44
756012 TTCATTGCCG
756022 CTTGATCTTGATCACGAACTTCGTCGCTTCAAGGGT-TTAGGCGA
1 CTTGATCTTGATCACGAACTTCGTCGCTTCAAGGGTCTT-GGCGA
*
756066 CTTGATCTTGAT--C-AACTTCGTTGCTTCAAGGGTCTTGGCGA
1 CTTGATCTTGATCACGAACTTCGTCGCTTCAAGGGTCTTGGCGA
* *
756107 CTTGATCTTAATCATGAACTTCG
1 CTTGATCTTGATCACGAACTTCG
756130 CTTGATATCT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
41 35 0.61
42 3 0.05
44 19 0.33
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (44 bp):
CTTGATCTTGATCACGAACTTCGTCGCTTCAAGGGTCTTGGCGA
Found at i:756235 original size:18 final size:18
Alignment explanation
Indices: 756214--756261 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
756204 AAATGTTCTC
756214 AATCTTCGAATGTCTCCT
1 AATCTTCGAATGTCTCCT
* *
756232 AATCTTTGAATGTCTCTT
1 AATCTTCGAATGTCTCCT
756250 AATCTTCGAATG
1 AATCTTCGAATG
756262 CTTCCAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (18 bp):
AATCTTCGAATGTCTCCT
Found at i:762644 original size:57 final size:57
Alignment explanation
Indices: 762530--762644 Score: 137
Period size: 57 Copynumber: 2.0 Consensus size: 57
762520 GACAAAGTTA
* * * **
762530 TTATCTCTAAATTATCTTAATTTAGTTAGAGATAAATTAAATAATTAAATTTGATTT
1 TTATCTCTAAATTAGCATAATTTAGTTAGAGATAAATTAAATAAATAAATTAAATTT
762587 TTATCTCTAAATTAGCATAA-TTA-TTAGAGATAAATTAAATGACCAAT-AATTAAATTT
1 TTATCTCTAAATTAGCATAATTTAGTTAGAGATAAATTAAAT-A--AATAAATTAAATTT
762644 T
1 T
762645 GATTGGTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
55 17 0.34
56 4 0.08
57 27 0.54
58 2 0.04
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (57 bp):
TTATCTCTAAATTAGCATAATTTAGTTAGAGATAAATTAAATAAATAAATTAAATTT
Found at i:765070 original size:5 final size:6
Alignment explanation
Indices: 765053--765077 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
765043 TTTTATACAC
765053 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
765078 CTGCTGCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:767727 original size:9 final size:9
Alignment explanation
Indices: 767715--767756 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
767705 TTATTTAATC
767715 GTGTTAAAT
1 GTGTTAAAT
*
767724 GTGTTAAAC
1 GTGTTAAAT
767733 GTGTT-AAT
1 GTGTTAAAT
767741 CGTGTTAAAT
1 -GTGTTAAAT
767751 GTGTTA
1 GTGTTA
767757 TTAATCGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.83
10 3 0.10
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.43
Consensus pattern (9 bp):
GTGTTAAAT
Found at i:767735 original size:18 final size:19
Alignment explanation
Indices: 767709--767766 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
767699 ATATTTTTAT
*
767709 TTAATCGTGTTAAAT-GTG
1 TTAAACGTGTTAAATCGTG
767727 TTAAACGTGTT-AATCGTG
1 TTAAACGTGTTAAATCGTG
*
767745 TTAAATGTGTTATTAATCGTG
1 TTAAACGTGTTA--AATCGTG
767766 T
1 T
767767 CGTGTCATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 3 0.09
18 23 0.68
21 8 0.24
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (19 bp):
TTAAACGTGTTAAATCGTG
Found at i:768739 original size:14 final size:14
Alignment explanation
Indices: 768715--768748 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
768705 TTTAAATCAA
*
768715 AATTGAAAATTTTT
1 AATTAAAAATTTTT
*
768729 GATTAAAAATTTTT
1 AATTAAAAATTTTT
768743 AATTAA
1 AATTAA
768749 TATAGTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
AATTAAAAATTTTT
Found at i:773330 original size:44 final size:44
Alignment explanation
Indices: 773245--773360 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 44
773235 TTCATTTAAA
773245 AATAAATA-AAT--AAATA-TATTTAA-A-TATTATTTAACTAT
1 AATAAATATAATAAAAATATTATTTAATATTATTATTTAACTAT
*
773283 AATAAATATTATAAAAATATTATTTAATATTATTATTTGAA-TAT
1 AATAAATATAATAAAAATATTATTTAATATTATTATTT-AACTAT
* *
773327 AATAAATATAATAAAGATATTATTTAGTATTATT
1 AATAAATATAATAAAAATATTATTTAATATTATT
773361 TAAATTTAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
38 8 0.12
39 2 0.03
41 5 0.07
42 7 0.10
43 1 0.01
44 42 0.63
45 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.45
Consensus pattern (44 bp):
AATAAATATAATAAAAATATTATTTAATATTATTATTTAACTAT
Found at i:773470 original size:22 final size:22
Alignment explanation
Indices: 773443--773510 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
773433 CTTTTAAGAC
773443 AAAATATTATTGAATTATAATA
1 AAAATATTATTGAATTATAATA
** * * *
773465 AAAATA-TATTGTTTTTTGATG
1 AAAATATTATTGAATTATAATA
* *
773486 AAAATATTATTTAATTATAGTA
1 AAAATATTATTGAATTATAATA
773508 AAA
1 AAA
773511 GTTATTTTGA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
AAAATATTATTGAATTATAATA
Found at i:773804 original size:33 final size:33
Alignment explanation
Indices: 773767--773832 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
773757 CAATCTATAT
* *
773767 AATAATTATTCTTCTCTT-ATTTTATTTTTTTAA
1 AATAATTATT-TTATCTTCATTTTATTTCTTTAA
*
773800 AATAATTATTTTATTTTCATTTTATTTCTTTAA
1 AATAATTATTTTATCTTCATTTTATTTCTTTAA
773833 GTAAACCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.64
Consensus pattern (33 bp):
AATAATTATTTTATCTTCATTTTATTTCTTTAA
Found at i:777009 original size:35 final size:35
Alignment explanation
Indices: 776963--777031 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
776953 ATCCTCCACC
*
776963 GCCCTATCCTAAGCTAATCCTAGTTTCAACCATCA
1 GCCCTATCCTAAGCTAATCATAGTTTCAACCATCA
*
776998 GCCCTGTCCTAAGCTAATCATAGTTTCAACCATC
1 GCCCTATCCTAAGCTAATCATAGTTTCAACCATC
777032 CTCTCAGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.33, G:0.10, T:0.29
Consensus pattern (35 bp):
GCCCTATCCTAAGCTAATCATAGTTTCAACCATCA
Found at i:781182 original size:20 final size:21
Alignment explanation
Indices: 781137--781185 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
781127 CAATTACTCT
781137 ATTTTCAAAACCAGTATTCAA
1 ATTTTCAAAACCAGTATTCAA
781158 ATTTTCAAAACCAGTATTCAA
1 ATTTTCAAAACCAGTATTCAA
*
781179 TTTTTCA
1 ATTTTCA
781186 GAAAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTTTCAAAACCAGTATTCAA
Found at i:781209 original size:13 final size:13
Alignment explanation
Indices: 781191--781216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
781181 TTTCAGAAAA
781191 TTTATAAAATCAT
1 TTTATAAAATCAT
781204 TTTATAAAATCAT
1 TTTATAAAATCAT
781217 AATTTCTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:787927 original size:19 final size:21
Alignment explanation
Indices: 787897--787945 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
787887 ATGTAGTTAA
787897 ATTAA-AATAAATTTA-A-TTT
1 ATTAATAA-AAATTTATATTTT
787916 ATTAATAAAAATTTATTATTTT
1 ATTAATAAAAATTTA-TATTTT
787938 ATTAATAA
1 ATTAATAA
787946 TTATATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 12 0.46
20 2 0.08
21 1 0.04
22 11 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATAAAAATTTATATTTT
Found at i:787984 original size:17 final size:18
Alignment explanation
Indices: 787959--788000 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
787949 TATATCAATT
787959 AATAAATTAAAT-ATTTA
1 AATAAATTAAATAATTTA
* *
787976 AATACATTACATAATTTA
1 AATAAATTAAATAATTTA
*
787994 ACTAAAT
1 AATAAAT
788001 GAATAGAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAAATTAAATAATTTA
Found at i:788079 original size:41 final size:41
Alignment explanation
Indices: 788019--788097 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
788009 TTTAGGCATC
*
788019 TTGATTTGACCCAATCAATT-AGTACAATTGATTAAGATATT
1 TTGATTTGACCCAACCAATTGA-TACAATTGATTAAGATATT
* *
788060 TTGATTTGACCCAACCAATTGATACGATTTATTAAGAT
1 TTGATTTGACCCAACCAATTGATACAATTGATTAAGAT
788098 CCAACCAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 33 0.97
42 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (41 bp):
TTGATTTGACCCAACCAATTGATACAATTGATTAAGATATT
Found at i:792198 original size:33 final size:33
Alignment explanation
Indices: 792154--792218 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
792144 AGGTTTTGTC
* *
792154 ATCTTCGTTCCAAGACCTCAAATTACAGAAGTT
1 ATCTTCATTCCAAGACCTCAAAGTACAGAAGTT
792187 ATCTTCATTCCAAGACCTCAAAGTACAGAAGT
1 ATCTTCATTCCAAGACCTCAAAGTACAGAAGT
792219 AAGAGCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (33 bp):
ATCTTCATTCCAAGACCTCAAAGTACAGAAGTT
Found at i:793366 original size:13 final size:13
Alignment explanation
Indices: 793348--793373 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
793338 GTTTTGCATT
793348 AAAATATTTTTAA
1 AAAATATTTTTAA
793361 AAAATATTTTTAA
1 AAAATATTTTTAA
793374 GACTTATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATATTTTTAA
Found at i:793776 original size:241 final size:239
Alignment explanation
Indices: 793349--793799 Score: 701
Period size: 241 Copynumber: 1.9 Consensus size: 239
793339 TTTTGCATTA
793349 AAATATTTTTAAAAAATATTTTTAAGACTTATATTTGTTTAGCAGACGAAAAATTAATTTTAGAT
1 AAATATTTTTAAAAAATATTTTTAAGACTTATATTTGTTTAGCAGACGAAAAATTAATTTTAGAT
* * * * *
793414 GTAAAAGATTTTACGAATCAATAAAGTTAATCATAAAAAATATCTTACGCTATTGAAAGACGTAA
66 GCAAAAGATTTTACGAATCAACAAAGTTAATCATAAAAAATATCTTACACCATGGAAAGACGTAA
* * *
793479 AACATTTTTTATAAAACAATAAAAACACTTTTATATTAAGTTTATGAGTATAAGTTTGATAAATA
131 AACATTTTTCAGAAAACAACAAAAACACTTTTATATTAAGTTTATGAGTATAAGTTTGATAAATA
793544 TTAATATTTAAATTATACAAAATAATTAAAATTAAAANTGATGTT
196 TTAATATTTAAATTATACAAAATAATTAAAATTAAAA-TGATGTT
793589 AAATATTTTTAAAAAA-ATATTTTAAGACTTATATTTGTTTAGCAGACGAAAAATTAATTTTAGA
1 AAATATTTTTAAAAAATAT-TTTTAAGACTTATATTTGTTTAGCAGACGAAAAATTAATTTTAGA
* * * * * *
793653 TGCAAAATATTTTAC-AAGTCAACAAGAGTTAATTATAGAAAATGTCTTACACCCTGG-AAGAGT
65 TGCAAAAGATTTTACGAA-TCAACAA-AGTTAATCATAAAAAATATCTTACACCATGGAAAGA-C
*
793716 GTAAAACATTTTTCAGAAAACAACAAAAATACTTTTATATTAAGTTTATGAGTATAAGTTTGATA
127 GTAAAACATTTTTCAGAAAACAACAAAAACACTTTTATATTAAGTTTATGAGTATAAGTTTGATA
793781 AATATTAATATTTAAATTA
192 AATATTAATATTTAAATTA
793800 AAATATCTAA
Statistics
Matches: 192, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
239 4 0.02
240 84 0.44
241 104 0.54
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (239 bp):
AAATATTTTTAAAAAATATTTTTAAGACTTATATTTGTTTAGCAGACGAAAAATTAATTTTAGAT
GCAAAAGATTTTACGAATCAACAAAGTTAATCATAAAAAATATCTTACACCATGGAAAGACGTAA
AACATTTTTCAGAAAACAACAAAAACACTTTTATATTAAGTTTATGAGTATAAGTTTGATAAATA
TTAATATTTAAATTATACAAAATAATTAAAATTAAAATGATGTT
Found at i:794019 original size:74 final size:74
Alignment explanation
Indices: 793874--794027 Score: 170
Period size: 74 Copynumber: 2.1 Consensus size: 74
793864 ATAAATAGAA
* *
793874 TAAATCTAACTAATAATTACAATAAAAAAAATTTCAATGATCATCATTTGATGAATACACATTTA
1 TAAATCTAACTAATAATTACAAT-AAAAAAATTTCAATAATCATCATTTAATGAATACACATTTA
793939 TAATAAA-TT
65 TAATAAATTT
* * * * ** *
793948 TAAATCTTACTAATAATTATAAT-AAAATATTT-AATAATTATTTTTTAATGAATACATATTTAT
1 TAAATCTAACTAATAATTACAATAAAAAAATTTCAATAATCATCATTTAATGAATACACATTTAT
794011 AAGTATAAATTT
66 -A--ATAAATTT
794023 TAAAT
1 TAAAT
794028 ATCTTACACA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
71 25 0.37
72 9 0.13
74 26 0.39
75 7 0.10
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (74 bp):
TAAATCTAACTAATAATTACAATAAAAAAATTTCAATAATCATCATTTAATGAATACACATTTAT
AATAAATTT
Found at i:794320 original size:33 final size:33
Alignment explanation
Indices: 794282--794355 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 33
794272 CACCATGATG
*
794282 AAAAATATTTTTC-ACAAAATGATCTAAACAATA
1 AAAAATATTTTTCGAC-AAATGATCTAAACAACA
* * **
794315 GAAAAT-GTTTTCGACAGTTGATCTAAACAACA
1 AAAAATATTTTTCGACAAATGATCTAAACAACA
794347 AAAAATATT
1 AAAAATATT
794356 AAATTTCTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
32 24 0.75
33 8 0.25
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (33 bp):
AAAAATATTTTTCGACAAATGATCTAAACAACA
Found at i:797880 original size:55 final size:58
Alignment explanation
Indices: 797798--797918 Score: 169
Period size: 55 Copynumber: 2.1 Consensus size: 58
797788 AATTTCAACA
797798 AAAATTTTCCAACGAAAATTTCTGTTGGAAAGCCTATTTCCAACAG-AAAATCCATTG
1 AAAATTTTCCAACGAAAATTTCTGTTGGAAAGCCTATTTCCAACAGAAAAATCCATTG
* * *
797855 AAAATTTT-CAAC-AGAATTT-TCGTTGGAAATCCTATTTCCAACAGAAAAATCTATTG
1 AAAATTTTCCAACGAAAATTTCT-GTTGGAAAGCCTATTTCCAACAGAAAAATCCATTG
*
797911 AAATTTTT
1 AAAATTTT
797919 TTCATTGGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
54 1 0.02
55 28 0.48
56 21 0.36
57 8 0.14
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (58 bp):
AAAATTTTCCAACGAAAATTTCTGTTGGAAAGCCTATTTCCAACAGAAAAATCCATTG
Found at i:798026 original size:31 final size:30
Alignment explanation
Indices: 797991--798084 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 30
797981 CATTTTGGCA
797991 TTTCCAACGAAAATTTCCGTGGGAAATAATT
1 TTTCCAACGAAAATTTCCGT-GGAAATAATT
* *
798022 TTTCCAAC-AGAAATTTCCGCTGAAAATAACT
1 TTTCCAACGA-AAATTTCCG-TGGAAATAATT
* * *
798053 TTTCCAACGGAATTTTTCGTTGGAAAT-ATT
1 TTTCCAACGAAAATTTCCG-TGGAAATAATT
798083 TT
1 TT
798085 AACCTATTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (30 bp):
TTTCCAACGAAAATTTCCGTGGAAATAATT
Found at i:798483 original size:12 final size:12
Alignment explanation
Indices: 798463--798496 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
798453 CACATTTCTC
798463 ATTTCTTCACGT
1 ATTTCTTCACGT
*
798475 ATTTTTTCACGT
1 ATTTCTTCACGT
*
798487 ATTTCCTCAC
1 ATTTCTTCAC
798497 ATATCTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.26, G:0.06, T:0.50
Consensus pattern (12 bp):
ATTTCTTCACGT
Found at i:801547 original size:2 final size:2
Alignment explanation
Indices: 801540--801569 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
801530 NNNNNNNNNN
*
801540 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
801570 TTTCTATAGC
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:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:805036 original size:19 final size:20
Alignment explanation
Indices: 804994--805037 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
804984 AATTTAAATA
804994 ATTAAAAAATAAAAAATCTC
1 ATTAAAAAATAAAAAATCTC
805014 -TTAAAAAATAAAAAATC-C
1 ATTAAAAAATAAAAAATCTC
805032 ATTAAA
1 ATTAAA
805038 TTCCTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (20 bp):
ATTAAAAAATAAAAAATCTC
Found at i:805381 original size:34 final size:33
Alignment explanation
Indices: 805343--805406 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
805333 TAATATGATA
805343 TAAT-ATTTATATTATTTAAATATAATTAATAATC
1 TAATAATTT-TATTATTTAAATAT-ATTAATAATC
* *
805377 TAATAATTTTTTTATTTATATATATTAATA
1 TAATAATTTTATTATTTAAATATATTAATA
805407 TCATGACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 7 0.26
34 16 0.59
35 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (33 bp):
TAATAATTTTATTATTTAAATATATTAATAATC
Found at i:811464 original size:45 final size:45
Alignment explanation
Indices: 811404--811497 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
811394 ATTATATTAA
** *
811404 TATTATTTAACTATAATAAATATTATAAAGAATATTATTTAATAT
1 TATTATTTAACTATAATAAATACAATAAAGAATAATATTTAATAT
* *
811449 TATTATTTGAA-TATAATAAATGCAATAAAGAATAATATTTAGTAT
1 TATTATTT-AACTATAATAAATACAATAAAGAATAATATTTAATAT
811494 TATT
1 TATT
811498 TAAATTTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 41 0.95
46 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (45 bp):
TATTATTTAACTATAATAAATACAATAAAGAATAATATTTAATAT
Found at i:814873 original size:33 final size:33
Alignment explanation
Indices: 814829--814893 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
814819 AGGTTTTGTC
* *
814829 ATCTTCGTTCCAAGACCTCAAATTACAGAAGTT
1 ATCTTCATTCCAAGACCTCAAAGTACAGAAGTT
814862 ATCTTCATTCCAAGACCTCAAAGTACAGAAGT
1 ATCTTCATTCCAAGACCTCAAAGTACAGAAGT
814894 AAGAGCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (33 bp):
ATCTTCATTCCAAGACCTCAAAGTACAGAAGTT
Found at i:828907 original size:2 final size:2
Alignment explanation
Indices: 828900--828930 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
828890 AGTTTAAAAG
828900 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
828931 CGTATAGAAT
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:830923 original size:52 final size:52
Alignment explanation
Indices: 830861--830972 Score: 188
Period size: 52 Copynumber: 2.2 Consensus size: 52
830851 ACATGGAGCA
*
830861 ATTGGGCCTTGGCTGATGAACTGCAATGTCTATTTGCCAAAGAGCCACAGTT
1 ATTGGGCCTTGGCTGATGAACTGCAATGTCTATTTGCAAAAGAGCCACAGTT
* *
830913 ATTGGGCCTTGGCTGATGAACTGCAATGTCTATTTGCAAAAGAGCCCCTGTT
1 ATTGGGCCTTGGCTGATGAACTGCAATGTCTATTTGCAAAAGAGCCACAGTT
*
830965 TTTGGGCC
1 ATTGGGCC
830973 AAGCCTGTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (52 bp):
ATTGGGCCTTGGCTGATGAACTGCAATGTCTATTTGCAAAAGAGCCACAGTT
Found at i:852995 original size:26 final size:26
Alignment explanation
Indices: 852886--853003 Score: 98
Period size: 26 Copynumber: 4.5 Consensus size: 26
852876 ACTGACTTTG
852886 GGCATTGCGTGACTAGTTTTTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* * * *
852912 AGTATTGCGTAACTAGTTTCTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* * * * *
852938 GACATTGCATGA-TTGACTTTGGACATAA
1 GGCATTGCGTGACTAG-TTTTTG--ATAA
*
852966 --CATTGCATGACTAGTTTTTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
852990 GGCATTGCGTGACT
1 GGCATTGCGTGACT
853004 TGTTAGTAAT
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
24 4 0.06
25 2 0.03
26 57 0.83
27 2 0.03
28 4 0.06
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (26 bp):
GGCATTGCGTGACTAGTTTTTGATAA
Found at i:853073 original size:22 final size:22
Alignment explanation
Indices: 853038--853088 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
853028 AGGCATTGCT
* * **
853038 TAAAAATCAGTCACGCAATGTC
1 TAAAAACCAATCACGCAATACC
*
853060 TAAAAACCAATCACGTAATACC
1 TAAAAACCAATCACGCAATACC
853082 TAAAAAC
1 TAAAAAC
853089 TAGTCACACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.24, G:0.08, T:0.20
Consensus pattern (22 bp):
TAAAAACCAATCACGCAATACC
Found at i:860939 original size:50 final size:50
Alignment explanation
Indices: 860864--860963 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
860854 CCAGCATAAA
*
860864 GCTCAAATGAGAAGCATTTCTTTTCTAGATAATTAAATGTTTTGTTTTAC
1 GCTCAAACGAGAAGCATTTCTTTTCTAGATAATTAAATGTTTTGTTTTAC
860914 GCTCAAACGAGAAGCATTTCTTTTCTAGATAATTAAATGTTTTGTTTTAC
1 GCTCAAACGAGAAGCATTTCTTTTCTAGATAATTAAATGTTTTGTTTTAC
860964 ATTCCCCAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (50 bp):
GCTCAAACGAGAAGCATTTCTTTTCTAGATAATTAAATGTTTTGTTTTAC
Found at i:863339 original size:17 final size:17
Alignment explanation
Indices: 863314--863347 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
863304 GATAAGAACT
* *
863314 CCCCCCCCCCCACCCCA
1 CCCCACCCCCAACCCCA
863331 CCCCACCCCCAACCCCA
1 CCCCACCCCCAACCCCA
863348 AAAAAAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (17 bp):
CCCCACCCCCAACCCCA
Found at i:874407 original size:25 final size:25
Alignment explanation
Indices: 874369--874419 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
874359 AAGCATAAAG
874369 GGAAACTACAACTGTGAAAATTCAT
1 GGAAACTACAACTGTGAAAATTCAT
** *
874394 GGAAACTATGACTGTGACAATTCAT
1 GGAAACTACAACTGTGAAAATTCAT
874419 G
1 G
874420 AATTTTCCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (25 bp):
GGAAACTACAACTGTGAAAATTCAT
Found at i:878897 original size:14 final size:15
Alignment explanation
Indices: 878874--878902 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
878864 TTGAAATAAG
878874 AAAAGAATAAAAATA
1 AAAAGAATAAAAATA
878889 AAAAG-ATAAAAATA
1 AAAAGAATAAAAATA
878903 CCCTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAGAATAAAAATA
Found at i:879208 original size:22 final size:21
Alignment explanation
Indices: 879183--879255 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 21
879173 TTTATTTTAT
879183 TTTATCTTTTAAATATTAATAA
1 TTTAT-TTTTAAATATTAATAA
*
879205 TTTATTTTTTAAATATTAATAG
1 TTTA-TTTTTAAATATTAATAA
* * *
879227 TTGATTATTTAACTATTAATAT
1 TTTATT-TTTAAATATTAATAA
879249 TTTATTT
1 TTTATTT
879256 GTAATTTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.07
22 40 0.91
23 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (21 bp):
TTTATTTTTAAATATTAATAA
Found at i:879244 original size:125 final size:127
Alignment explanation
Indices: 879025--879276 Score: 329
Period size: 125 Copynumber: 2.0 Consensus size: 127
879015 TTTATAATTT
879025 AATGTTATAATGATTATTTATTTTTAATTATTTATTTTAAACATTAATAATGTATAATTTATTTA
1 AATGTTATAATGATTATTTATTTTTAATTATTTATTTTAAACATTAATAATGTATAATTTATTTA
*
879090 AAATATTAAAAATTGATAGTTTAAATATTAATATTTTATTTATATTTTAATCATTAATATTA
66 AAATATTAAAAATTGATAGTTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTA
** * *
879152 AATGTTATTGTGATTA-TTATTTTTATTTTATTTTATCTTTTAAATATTAATAAT-T-T-ATTT-
1 AATGTTATAATGATTATTTATTTTTA-ATTA-TTTA--TTTTAAACATTAATAATGTATAATTTA
* * * *
879212 TTT-AAATATTAATAGTTGATTA-TTTAACTATTAATATTTTATTTGTAATTTAATCATTAATAT
62 TTTAAAATATTAAAAATTGA-TAGTTTAAATATTAATATTTTATTTATAATTTAATCATTAATAT
879275 TA
126 TA
879277 TAAAATACTA
Statistics
Matches: 111, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
125 54 0.49
126 14 0.13
127 21 0.19
128 5 0.05
129 1 0.01
130 16 0.14
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (127 bp):
AATGTTATAATGATTATTTATTTTTAATTATTTATTTTAAACATTAATAATGTATAATTTATTTA
AAATATTAAAAATTGATAGTTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTA
Found at i:879459 original size:51 final size:51
Alignment explanation
Indices: 879363--879465 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
879353 AATTTATAAT
*
879363 TGATTGAAAATATTAATAATTGGTAATTTAATTTATAATTTAAATATTATTA
1 TGATTGAAAATATTAATAATTGGTAATTTAATTTATAATTAAAATATT-TTA
* * *
879415 TGATT-AAAATATTAATACTT-TTAA-TTAATTTTTAAATTCAAAATATTTTA
1 TGATTGAAAATATTAATAATTGGTAATTTAATTTAT-AATT-AAAATATTTTA
879465 T
1 T
879466 AATATATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
49 8 0.18
50 11 0.24
51 21 0.47
52 5 0.11
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (51 bp):
TGATTGAAAATATTAATAATTGGTAATTTAATTTATAATTAAAATATTTTA
Found at i:879551 original size:16 final size:16
Alignment explanation
Indices: 879530--879560 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
879520 ACAATTTTAT
*
879530 TTATAATTTAAATATG
1 TTATAATTAAAATATG
879546 TTATAATTAAAATAT
1 TTATAATTAAAATAT
879561 AAAAATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATAATTAAAATATG
Found at i:879612 original size:28 final size:29
Alignment explanation
Indices: 879562--879619 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
879552 TTAAAATATA
* *
879562 AAAATAATTAATATTTTATATTTTAATTT
1 AAAATAATTAATATTTTAAATTTAAATTT
879591 AAAAT-ATTAAT-TTTATAAATTTAAATTT
1 AAAATAATTAATATTT-TAAATTTAAATTT
879619 A
1 A
879620 TAATTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.12
28 18 0.69
29 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
AAAATAATTAATATTTTAAATTTAAATTT
Found at i:879614 original size:14 final size:14
Alignment explanation
Indices: 879574--879622 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
879564 AATAATTAAT
*
879574 ATTTTAT-ATTTTA
1 ATTTTATAAATTTA
879587 A-TTTA-AAATATTA
1 ATTTTATAAAT-TTA
879600 ATTTTATAAATTTA
1 ATTTTATAAATTTA
*
879614 AATTTATAA
1 ATTTTATAA
879623 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 6 0.20
13 5 0.17
14 15 0.50
15 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTATAAATTTA
Found at i:887827 original size:33 final size:32
Alignment explanation
Indices: 887786--887859 Score: 121
Period size: 33 Copynumber: 2.3 Consensus size: 32
887776 GTAGGAGGAG
*
887786 AAAGGAAGGATTAGAATAACAATGCAAGAAGA
1 AAAGGAAGGATTAGAATAAAAATGCAAGAAGA
*
887818 AAAGGGAAGGATTAGAATAAAAATGGAAGAAGA
1 AAA-GGAAGGATTAGAATAAAAATGCAAGAAGA
887851 AAAGGAAGG
1 AAAGGAAGG
887860 TCGTTACCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
32 9 0.23
33 30 0.77
ACGTcount: A:0.57, C:0.03, G:0.30, T:0.11
Consensus pattern (32 bp):
AAAGGAAGGATTAGAATAAAAATGCAAGAAGA
Found at i:917178 original size:15 final size:15
Alignment explanation
Indices: 917154--917183 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
917144 TCACTCACAA
917154 AAAAGAAAAGAAAAT
1 AAAAGAAAAGAAAAT
*
917169 AAAAGGAAAGAAAAT
1 AAAAGAAAAGAAAAT
917184 GCATTGTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAGAAAAT
Found at i:917361 original size:3 final size:3
Alignment explanation
Indices: 917353--917382 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
917343 TGAGCAGTAC
*
917353 GAT GAT GAT GAT GAT GAT GGT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
917383 ATCCATGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:920306 original size:2 final size:2
Alignment explanation
Indices: 920299--920335 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
920289 CTATATTTAA
920299 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
920336 AGTGACAACG
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:938521 original size:16 final size:16
Alignment explanation
Indices: 938487--938519 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
938477 TGTTTCTGGG
938487 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTTCT
938503 TTTCTTTTT-TTTT-T
1 TTTCTTTTTCTTTTCT
938517 TTT
1 TTT
938520 TTTGGGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 4 0.24
16 9 0.53
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTCTTTTTCTTTTCT
Found at i:950503 original size:19 final size:19
Alignment explanation
Indices: 950471--950512 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
950461 TCACAAGATA
950471 ATTTAAGTCAAGATAATAT
1 ATTTAAGTCAAGATAATAT
950490 ANTTTAAG-CAAGATAATAT
1 A-TTTAAGTCAAGATAATAT
950509 ATTT
1 ATTT
950513 TTTTAATGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 13 0.59
20 6 0.27
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.38
Consensus pattern (19 bp):
ATTTAAGTCAAGATAATAT
Found at i:951719 original size:149 final size:147
Alignment explanation
Indices: 951406--951684 Score: 423
Period size: 149 Copynumber: 1.9 Consensus size: 147
951396 TTTGATGAAG
** * *
951406 AGACACATTGAATCTGAACAAAAGCAATTGACCTTAGTAAGCTGTGTCTTTTCAATCAGAATAAT
1 AGACACACCGAATCTGAACAAAAGCAATTGACCTTAGTAAGCTCTGTCTTTTCAATCACAATAAT
951471 CAACTCCTTTATCAAGGTTAATTGCCCTTTAATCACTGTAATTATTACCAAATACTAATCCATTA
66 CAACTCCTTTATCAAGGTTAATTGCCCTTTAATCACTGTAATTATTACCAAATACTAATCCATTA
** * *
951536 ATCAATGGATTTGATCAAG
131 ATCAA--GATCCGATAAAC
** *
951555 AGACACATTGAATCTGAACAAAAGCAATTGACCTTATTAAGCTCTGTCTTTTCAATCACAATAAT
1 AGACACACCGAATCTGAACAAAAGCAATTGACCTTAGTAAGCTCTGTCTTTTCAATCACAATAAT
*
951620 CAACCTCCTTTATCAAGTTTAATTGCCCTTTAATCACTGTAATTATTACCAAATACTAATCCATT
66 CAA-CTCCTTTATCAAGGTTAATTGCCCTTTAATCACTGTAATTATTACCAAATACTAATCCATT
951685 TAAATACGAA
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
149 65 0.52
150 60 0.48
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (147 bp):
AGACACACCGAATCTGAACAAAAGCAATTGACCTTAGTAAGCTCTGTCTTTTCAATCACAATAAT
CAACTCCTTTATCAAGGTTAATTGCCCTTTAATCACTGTAATTATTACCAAATACTAATCCATTA
ATCAAGATCCGATAAAC
Found at i:952868 original size:3 final size:3
Alignment explanation
Indices: 952860--952889 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
952850 AGTGCTCATA
*
952860 TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
952890 CTGTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:968732 original size:2 final size:2
Alignment explanation
Indices: 968725--968752 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
968715 CAAATATGTA
968725 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
968753 CTTAATTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:975076 original size:18 final size:18
Alignment explanation
Indices: 975040--975078 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
975030 AAATAAAATC
*
975040 ATATTTTATTTAATTTTA
1 ATATTTTATTTAATATTA
975058 ATATTTTAATTT-ATATTA
1 ATATTTT-ATTTAATATTA
975076 ATA
1 ATA
975079 AATAGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTTATTTAATATTA
Found at i:979953 original size:21 final size:20
Alignment explanation
Indices: 979919--979958 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
979909 AGAGAGTAGT
979919 TTTCTTTTTATTTTCTTTTTC
1 TTTCTTTTTATTTT-TTTTTC
979940 TTTC-TTTTAGTTTTTTTTT
1 TTTCTTTTTA-TTTTTTTTT
979959 GGTTTGGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTCTTTTTATTTTTTTTTC
Found at i:980018 original size:50 final size:50
Alignment explanation
Indices: 979922--980021 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 50
979912 GAGTAGTTTT
**
979922 CTTTTTATTTTCTTTTTCTTTCTTTTAGTTTTTTTTTGGTTTGGTCTCAC
1 CTTTTTATTTTCTTTTTCTTTCTTCCAGTTTTTTTTTGGTTTGGTCTCAC
*
979972 NCTTTTTA-TTTCTTTTTC-TT-TTCCATTTTTTTTTTGGTTTTGGGTCTCAC
1 -CTTTTTATTTTCTTTTTCTTTCTTCCAGTTTTTTTTTGG-TTT-GGTCTCAC
980022 ACAGAGAGCG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
48 14 0.32
49 5 0.11
50 18 0.41
51 7 0.16
ACGTcount: A:0.06, C:0.15, G:0.10, T:0.68
Consensus pattern (50 bp):
CTTTTTATTTTCTTTTTCTTTCTTCCAGTTTTTTTTTGGTTTGGTCTCAC
Found at i:980643 original size:14 final size:16
Alignment explanation
Indices: 980613--980645 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
980603 TCTGCTCAGT
980613 TTCTGTTTGATTTTGC
1 TTCTGTTTGATTTTGC
980629 TTCTGTTT-A-TTTGC
1 TTCTGTTTGATTTTGC
980643 TTC
1 TTC
980646 GAAATATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.06, C:0.15, G:0.15, T:0.64
Consensus pattern (16 bp):
TTCTGTTTGATTTTGC
Found at i:1010925 original size:29 final size:29
Alignment explanation
Indices: 1010883--1010942 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1010873 CCTTGAAGCC
*
1010883 TAGATTAATGTTCAAGAAGTGAGGCTGGT
1 TAGATTAATGTTCAAGAACTGAGGCTGGT
1010912 TAGATTAATGTTCAAGAACTGAGGCTGGT
1 TAGATTAATGTTCAAGAACTGAGGCTGGT
1010941 TA
1 TA
1010943 AGTAAAGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (29 bp):
TAGATTAATGTTCAAGAACTGAGGCTGGT
Found at i:1018559 original size:39 final size:39
Alignment explanation
Indices: 1018516--1018591 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
1018506 AACATCAACA
1018516 GGGAGGATAAGGTCTAAGCGTTTCATTGACAATCAGACC
1 GGGAGGATAAGGTCTAAGCGTTTCATTGACAATCAGACC
1018555 GGGAGGATAAGGTCTAAGCGTTTCATTGACAATCAGA
1 GGGAGGATAAGGTCTAAGCGTTTCATTGACAATCAGA
1018592 GTCACCTGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (39 bp):
GGGAGGATAAGGTCTAAGCGTTTCATTGACAATCAGACC
Found at i:1022579 original size:2 final size:2
Alignment explanation
Indices: 1022572--1022643 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1022562 CTCCTGAACT
1022572 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
1022614 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
1022644 CCCTCACCAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1038191 original size:18 final size:18
Alignment explanation
Indices: 1038155--1038195 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1038145 TAGATACCTG
1038155 CAAAAATAATCAGAGTCA
1 CAAAAATAATCAGAGTCA
*
1038173 CCAAAAATAATCA-ATTCA
1 -CAAAAATAATCAGAGTCA
1038191 CAAAA
1 CAAAA
1038196 CAAATCCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 4 0.19
19 12 0.57
ACGTcount: A:0.59, C:0.20, G:0.05, T:0.17
Consensus pattern (18 bp):
CAAAAATAATCAGAGTCA
Found at i:1051943 original size:5 final size:5
Alignment explanation
Indices: 1051919--1051959 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
1051909 ATATTTTAAA
*
1051919 AAAAT AATAAT AATAAT AAAAT AAAAT AAAAT AAAAC AAAA
1 AAAAT AA-AAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAA
1051960 AAGGAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 23 0.68
6 11 0.32
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1073391 original size:24 final size:24
Alignment explanation
Indices: 1073325--1073392 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
1073315 ATAGTATAAC
* *
1073325 TCTAATTAACTAATAATATTGTAT
1 TCTAATTAACTAATAATATTATAG
*
1073349 TATAACCTTAACT-AT-ATATTATAG
1 TCTAA--TTAACTAATAATATTATAG
*
1073373 TCTAATTAAATAATAATATT
1 TCTAATTAACTAATAATATT
1073393 GTATTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
22 5 0.14
23 2 0.06
24 20 0.57
25 2 0.06
26 6 0.17
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (24 bp):
TCTAATTAACTAATAATATTATAG
Found at i:1074672 original size:2 final size:2
Alignment explanation
Indices: 1074665--1074689 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1074655 AATTCCTGGA
1074665 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 A
1074690 CACACGCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1108718 original size:2 final size:2
Alignment explanation
Indices: 1108711--1108755 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1108701 CTACAATTTC
1108711 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1108753 GA G
1 GA G
1108756 CTGAATTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1119364 original size:2 final size:2
Alignment explanation
Indices: 1119359--1119383 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1119349 TTAAAATTTT
1119359 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1119384 TGAGTTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1132030 original size:2 final size:2
Alignment explanation
Indices: 1132017--1132058 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1132007 ATGCATCCAC
*
1132017 AT AT AC 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
1132059 TATTTATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1132136 original size:62 final size:63
Alignment explanation
Indices: 1132031--1132159 Score: 226
Period size: 62 Copynumber: 2.1 Consensus size: 63
1132021 ACATATATAT
*
1132031 ATATATATATATATATATATATATATATTATTTATTTGTTTTATTGATCAATATTAGAATCCC
1 ATATATATATATATATATATATATATATTATTTATTTGGTTTATTGATCAATATTAGAATCCC
1132094 ATANTATATATA-ATATATAT-TATATATTATTTATTTGGTTTATTGATCAATATTAGAATCCC
1 ATA-TATATATATATATATATATATATATTATTTATTTGGTTTATTGATCAATATTAGAATCCC
1132156 ATAT
1 ATAT
1132160 CTTGATGTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
61 1 0.02
62 44 0.69
63 11 0.17
64 8 0.12
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.50
Consensus pattern (63 bp):
ATATATATATATATATATATATATATATTATTTATTTGGTTTATTGATCAATATTAGAATCCC
Found at i:1135022 original size:131 final size:132
Alignment explanation
Indices: 1134821--1135077 Score: 480
Period size: 131 Copynumber: 2.0 Consensus size: 132
1134811 TTAAGAAGTC
1134821 CATGTAAATCTTAAGTAACAGACCATACCCCATTTTTCTGCAATACATATTTATTTACAGGAAAG
1 CATGTAAATCTTAAGTAACAGACCATACCCCATTTTTCTGCAATACATATTTATTTACAGGAAAG
1134886 TACAAGTCATACAGATTTCCAACATATATAGCCTCACAATCATTTACCTTCCCAATAGCAGGAAA
66 TACAAGTCATACAGATTTCCAACATATATAGCCTCACAATCATTTACCTTCCCAATAGCAGGAAA
1134951 TA
131 TA
*
1134953 CATGTAAATCTT-AGTAACAGACCATACCCCATTTTTCTGCAATACATATTTATTTACAGGGAAG
1 CATGTAAATCTTAAGTAACAGACCATACCCCATTTTTCTGCAATACATATTTATTTACAGGAAAG
* *
1135017 TACAAGTCATACAGATTTCCAACATATATAGCCTCACGATCATTTACTTTCCCAATAGCAG
66 TACAAGTCATACAGATTTCCAACATATATAGCCTCACAATCATTTACCTTCCCAATAGCAG
1135078 CTAATAAACT
Statistics
Matches: 122, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
131 110 0.90
132 12 0.10
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (132 bp):
CATGTAAATCTTAAGTAACAGACCATACCCCATTTTTCTGCAATACATATTTATTTACAGGAAAG
TACAAGTCATACAGATTTCCAACATATATAGCCTCACAATCATTTACCTTCCCAATAGCAGGAAA
TA
Found at i:1138445 original size:21 final size:21
Alignment explanation
Indices: 1138420--1138459 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1138410 CAAATTGAAG
1138420 AACTTATTGACTCTTGAACAA
1 AACTTATTGACTCTTGAACAA
1138441 AACTTATTGACTCTTGAAC
1 AACTTATTGACTCTTGAAC
1138460 TACCTTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (21 bp):
AACTTATTGACTCTTGAACAA
Found at i:1143340 original size:2 final size:2
Alignment explanation
Indices: 1143333--1143362 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1143323 TTATTTTCAT
1143333 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1143363 GTTTAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1144208 original size:3 final size:3
Alignment explanation
Indices: 1144202--1144252 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1144192 CAACAACAGA
1144202 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1144250 AAG
1 AAG
1144253 GGCAACATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1156605 original size:99 final size:97
Alignment explanation
Indices: 1156461--1156638 Score: 270
Period size: 99 Copynumber: 1.8 Consensus size: 97
1156451 CTCATTAAGG
* *
1156461 GATACTAGTATAGTAGGATCATAGCAGGAAGGAGTTAAGATCGAGGAACTATGGGAA-TTTTAT-
1 GATACTAGCATAGTAGGATCATAGCAGGAAGGAGTTAAGATCGAGGAACTATGAGAACTTTT-TG
*
1156524 TAGCCATTTTTACCTCTTTAAATGGGCAATTAT
65 TAACCATTTTTACCTCTTTAAATGGGCAATTAT
*
1156557 GATACTAGCATAGTAGGATCATAGCACGAGGAAGGGGTTAAGATCGAGGAACTATGAGAACTTTT
1 GATACTAGCATAGTAGGATCATAG--C-AGGAAGGAGTTAAGATCGAGGAACTATGAGAACTTTT
1156622 TGTAACCATTTTTACCT
63 TGTAACCATTTTTACCT
1156639 GGTTAAAGGA
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
96 23 0.32
98 1 0.01
99 31 0.42
100 18 0.25
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (97 bp):
GATACTAGCATAGTAGGATCATAGCAGGAAGGAGTTAAGATCGAGGAACTATGAGAACTTTTTGT
AACCATTTTTACCTCTTTAAATGGGCAATTAT
Found at i:1157171 original size:54 final size:54
Alignment explanation
Indices: 1157107--1157214 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
1157097 ACAGGCAGTA
1157107 TGCCTGAAATTTAAGTAGGGTCCGCCACTGATTCTTACCAAGTAACTAATCCTC
1 TGCCTGAAATTTAAGTAGGGTCCGCCACTGATTCTTACCAAGTAACTAATCCTC
1157161 TGCCTGAAATTTAAGTAGGGTCCGCCACTGATTCTTACCAAGTAACTAATCCTC
1 TGCCTGAAATTTAAGTAGGGTCCGCCACTGATTCTTACCAAGTAACTAATCCTC
1157215 AGCTTGTATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (54 bp):
TGCCTGAAATTTAAGTAGGGTCCGCCACTGATTCTTACCAAGTAACTAATCCTC
Found at i:1181882 original size:18 final size:18
Alignment explanation
Indices: 1181859--1181894 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1181849 TAAATCTATT
1181859 AAGTTATACCCGGATTAA
1 AAGTTATACCCGGATTAA
*
1181877 AAGTTATACCTGGATTAA
1 AAGTTATACCCGGATTAA
1181895 TTCAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (18 bp):
AAGTTATACCCGGATTAA
Found at i:1207792 original size:2 final size:2
Alignment explanation
Indices: 1207785--1207862 Score: 104
Period size: 2 Copynumber: 37.0 Consensus size: 2
1207775 CATCTGTCCC
1207785 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT ACT ACT ACT ACT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT -CT -CT -CT
1207829 NCT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1207863 ATACCAACAG
Statistics
Matches: 73, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
1 1 0.01
2 59 0.81
3 13 0.18
ACGTcount: A:0.05, C:0.47, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:1221846 original size:5 final size:5
Alignment explanation
Indices: 1221836--1221860 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1221826 CAGAAATGGG
1221836 GATTT GATTT GATTT GATTT GATTT
1 GATTT GATTT GATTT GATTT GATTT
1221861 TGACCTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
GATTT
Found at i:1230753 original size:60 final size:60
Alignment explanation
Indices: 1230625--1230753 Score: 195
Period size: 60 Copynumber: 2.1 Consensus size: 60
1230615 CAGCCAGAGA
* * * * *
1230625 AGGGCCATGATATGTCGGGGTAAATTCGACGCCAGAATACTCTTATAACTCTTTTGGAGG
1 AGGGCCATGATATGACCGGGTAAATTCGACGCAAAAATACTCTTATAACTCTTTAGGAGG
**
1230685 AGAACCATGATATGACCGGGTAAATTCGACGCAAAAATACTCTTATAACTCTTTAGGAGG
1 AGGGCCATGATATGACCGGGTAAATTCGACGCAAAAATACTCTTATAACTCTTTAGGAGG
1230745 AGGGCCATG
1 AGGGCCATG
1230754 CTATAATGTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (60 bp):
AGGGCCATGATATGACCGGGTAAATTCGACGCAAAAATACTCTTATAACTCTTTAGGAGG
Found at i:1249231 original size:2 final size:2
Alignment explanation
Indices: 1249218--1249257 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1249208 CTCCAACGAA
*
1249218 AG AG AG -G A- AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1249258 GATCTAATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1253394 original size:14 final size:14
Alignment explanation
Indices: 1253375--1253402 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1253365 CTTAACCACT
1253375 GGCTTGAGACAAAA
1 GGCTTGAGACAAAA
1253389 GGCTTGAGACAAAA
1 GGCTTGAGACAAAA
1253403 ATAGGAAAAT
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:0.14, G:0.29, T:0.14
Consensus pattern (14 bp):
GGCTTGAGACAAAA
Found at i:1280002 original size:32 final size:32
Alignment explanation
Indices: 1279965--1280025 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1279955 CCCGACAAGT
* **
1279965 AAATGGGCCAACTGGCCTGTCTTTTTTGGTAC
1 AAATGGGCCAACAGGCCTGTAGTTTTTGGTAC
*
1279997 AAATGGGCCTACAGGCCTGTAGTTTTTGG
1 AAATGGGCCAACAGGCCTGTAGTTTTTGG
1280026 ATCACTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (32 bp):
AAATGGGCCAACAGGCCTGTAGTTTTTGGTAC
Found at i:1282267 original size:2 final size:2
Alignment explanation
Indices: 1282260--1282285 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1282250 CATATAACCA
1282260 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
1282286 TTTGTATTTG
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:1284543 original size:15 final size:16
Alignment explanation
Indices: 1284523--1284555 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1284513 TAGGCATGAA
1284523 GAAGCAG-AAAAAAGG
1 GAAGCAGCAAAAAAGG
*
1284538 GAAGCAGCAAAACAGG
1 GAAGCAGCAAAAAAGG
1284554 GA
1 GA
1284556 GAAAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.55, C:0.12, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAGCAGCAAAAAAGG
Found at i:1301214 original size:25 final size:24
Alignment explanation
Indices: 1301186--1301233 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1301176 CATGCGTATA
1301186 TATAA-TAAAAATTATATTTATAAAT
1 TATAATTAAAAA-TATA-TTATAAAT
1301211 TATAATTAAAAATATATTATAAA
1 TATAATTAAAAATATATTATAAA
1301234 GTAATCGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 9 0.41
26 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TATAATTAAAAATATATTATAAAT
Found at i:1303917 original size:2 final size:2
Alignment explanation
Indices: 1303910--1303937 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1303900 GCTCATTTTG
1303910 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1303938 TGAAGCAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1304959 original size:2 final size:2
Alignment explanation
Indices: 1304952--1304994 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1304942 ATTCTGATAA
* * *
1304952 TC TC TC TC TC CC TC TC AC TC TC TC TC TC TT 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
1304994 T
1 T
1304995 TTTGTGTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1311204 original size:21 final size:22
Alignment explanation
Indices: 1311180--1311240 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
1311170 GCATAATATT
1311180 TTAAAAATTAAATT-ATT-TTAA
1 TTAAAAATT-AATTAATTATTAA
*
1311201 TTAATAATT-ATTAATTATTAA
1 TTAAAAATTAATTAATTATTAA
* *
1311222 TTAAATATT-ATTTATTATT
1 TTAAAAATTAATTAATTATT
1311241 CTCTACGTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 28 0.82
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAAAATTAATTAATTATTAA
Found at i:1311298 original size:18 final size:18
Alignment explanation
Indices: 1311275--1311317 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1311265 GTGGATAGCA
1311275 TCATGACACAATAATTTG
1 TCATGACACAATAATTTG
1311293 TCATGACACAATAATTTG
1 TCATGACACAATAATTTG
1311311 TCATGAC
1 TCATGAC
1311318 TACATGATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (18 bp):
TCATGACACAATAATTTG
Found at i:1336379 original size:22 final size:22
Alignment explanation
Indices: 1336298--1336378 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 22
1336288 AAACTTAAGC
*
1336298 ATTATGTAACTGATTTTGAG-T
1 ATTACGTAACTGATTTTGAGAT
* *
1336319 ATTACGTTATTGATTTTGA-AT
1 ATTACGTAACTGATTTTGAGAT
* *
1336340 ATTACGTGACTGATTTTTAGAT
1 ATTACGTAACTGATTTTGAGAT
* *
1336362 ATAACGTAATTGATTTT
1 ATTACGTAACTGATTTT
1336379 TGACATTGCA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 33 0.67
22 16 0.33
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (22 bp):
ATTACGTAACTGATTTTGAGAT
Found at i:1338565 original size:80 final size:81
Alignment explanation
Indices: 1338444--1338733 Score: 286
Period size: 80 Copynumber: 3.6 Consensus size: 81
1338434 CATCATAATG
* * *** * *
1338444 TTACATGTCATGTTG--AAAAAATATTATTGTTACATACCATATACAAAAACATGTTATACGTTA
1 TTACATGTCATATTGAAAAAAAATATTATTATTACACGTCATATACAAAAATATGTTATACGTCA
*
1338507 TGGTTAAAAAAAGTTT
66 TGGTTAAAAAAAGTTA
* * *
1338523 TTACATGTCATATT-AAAAAAAATATTATTATTGCACGTCATATACAAAAATATATTACACGTCA
1 TTACATGTCATATTGAAAAAAAATATTATTATTACACGTCATATACAAAAATATGTTATACGTCA
*
1338587 TGTTTAAAAAAAGTTA
66 TGGTTAAAAAAAGTTA
** * * *
1338603 TTACA-CACAAAATTGAAAAAAAA-ATTATGATTACACGTCATGTACAAAAATATGTTATAC-TC
1 TTACATGTC-ATATTGAAAAAAAATATTATTATTACACGTCATATACAAAAATATGTTATACGT-
*
1338665 CATGGTTAAAAAAAGTTG
64 CATGGTTAAAAAAAGTTA
* * * * * * *
1338683 TTATATGTCATGTTGAAAAAAAAAAATTATTGTTACAAGTTATGTACAAAA
1 TTACATGTCATATTG-AAAAAAAATATTATTATTACACGTCATATACAAAA
1338734 TCATTTTACA
Statistics
Matches: 172, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
79 15 0.09
80 118 0.69
81 17 0.10
82 22 0.13
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (81 bp):
TTACATGTCATATTGAAAAAAAATATTATTATTACACGTCATATACAAAAATATGTTATACGTCA
TGGTTAAAAAAAGTTA
Found at i:1338604 original size:26 final size:26
Alignment explanation
Indices: 1338501--1338608 Score: 69
Period size: 26 Copynumber: 4.1 Consensus size: 26
1338491 AACATGTTAT
* * *
1338501 ACGTTATGGTTAAAAAAAGTTTTTAC
1 ACGTCATGTTTAAAAAAAGTTATTAC
* * * *
1338527 ATGTCATATTAAAAAAAATATTATTATTGC
1 ACGTCATGTTTAAAAAAA-GTTATTA---C
* *
1338557 ACGTCA--TATACAAAAA-TATATTAC
1 ACGTCATGTTTAAAAAAAGT-TATTAC
1338581 ACGTCATGTTTAAAAAAAGTTATTAC
1 ACGTCATGTTTAAAAAAAGTTATTAC
1338607 AC
1 AC
1338609 ACAAAATTGA
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
24 7 0.11
26 30 0.49
27 11 0.18
28 7 0.11
30 6 0.10
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (26 bp):
ACGTCATGTTTAAAAAAAGTTATTAC
Found at i:1338773 original size:160 final size:159
Alignment explanation
Indices: 1338485--1338774 Score: 363
Period size: 160 Copynumber: 1.8 Consensus size: 159
1338475 ACATACCATA
* * *
1338485 TACAAAAACATGTTATACGTTATGGTTAAAAAAAGTTTTTACATGTCATATTAAAAAAAATATTA
1 TACAAAAACATGTTATACGTCATGGTTAAAAAAAGTTGTTACATGTCATATTAAAAAAAAAATTA
* * * *
1338550 TTATTGCACGTCATATACAAAAATATATTACACGTCATGTTTAAAAAAAGTTATTACACACAAAA
66 TTATTACAAGTCATATACAAAAATATATTACACATCATGATTAAAAAAAGTTATTA-ACACAAAA
1338615 TTGAAAAAAAAATTATGATTACACGTCATG
130 TTGAAAAAAAAATTATGATTACACGTCATG
* * *
1338645 TACAAAAATATGTTATAC-TCCATGGTTAAAAAAAGTTGTTATATGTCATGTTGAAAAAAAAAAA
1 TACAAAAACATGTTATACGT-CATGGTTAAAAAAAGTTGTTACATGTCATATT--AAAAAAAAAA
* * * * *
1338709 TTATTGTTACAAGTTATGTAC-AAAATCATTTTACACATCATGATT-AAAAACGATTATT-ACAC
63 TTATTATTACAAGTCATATACAAAAAT-ATATTACACATCATGATTAAAAAAAG-TTATTAACAC
1338771 AAAA
126 AAAA
1338775 GCGGTTGTTA
Statistics
Matches: 110, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
159 1 0.01
160 53 0.48
161 11 0.10
162 45 0.41
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.33
Consensus pattern (159 bp):
TACAAAAACATGTTATACGTCATGGTTAAAAAAAGTTGTTACATGTCATATTAAAAAAAAAATTA
TTATTACAAGTCATATACAAAAATATATTACACATCATGATTAAAAAAAGTTATTAACACAAAAT
TGAAAAAAAAATTATGATTACACGTCATG
Found at i:1341439 original size:2 final size:2
Alignment explanation
Indices: 1341432--1341539 Score: 99
Period size: 2 Copynumber: 54.0 Consensus size: 2
1341422 GAATTTCATT
* ** *
1341432 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA CG TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
1341474 CA TA TA TA CA TA TA TA TA TA CA TA CA CA CA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1341516 TA TA TA TA TA CA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1341540 AGACAATATG
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (2 bp):
TA
Found at i:1346654 original size:16 final size:18
Alignment explanation
Indices: 1346626--1346662 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1346616 TAATTTTTAA
1346626 TTATAATTTAA-TTATTT
1 TTATAATTTAATTTATTT
1346643 TTATAA-TTAATTTATTT
1 TTATAATTTAATTTATTT
1346660 TTA
1 TTA
1346663 AGTGAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATAATTTAATTTATTT
Found at i:1357556 original size:26 final size:26
Alignment explanation
Indices: 1357509--1357565 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
1357499 ATTTTAAGTT
* *
1357509 TTTTTTTTTTTACTATTGGATTTTAGC
1 TTTTTGTTTTTACTATTGGATTAT-GC
* *
1357536 TTTTTGTTTTTA-TTTTTGATTATGC
1 TTTTTGTTTTTACTATTGGATTATGC
1357561 TTTTT
1 TTTTT
1357566 ATTGGTGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 7 0.27
26 8 0.31
27 11 0.42
ACGTcount: A:0.12, C:0.05, G:0.11, T:0.72
Consensus pattern (26 bp):
TTTTTGTTTTTACTATTGGATTATGC
Found at i:1363847 original size:12 final size:12
Alignment explanation
Indices: 1363830--1363873 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
1363820 AGCAGCTGCA
1363830 AAGGATGAGAAG
1 AAGGATGAGAAG
1363842 AAGGATGAGAAG
1 AAGGATGAGAAG
1363854 AAGG-TCGAGAAG
1 AAGGAT-GAGAAG
1363866 AAGGATGA
1 AAGGATGA
1363874 CCGGAGAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.03
12 28 0.93
13 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.41, T:0.09
Consensus pattern (12 bp):
AAGGATGAGAAG
Found at i:1369881 original size:2 final size:2
Alignment explanation
Indices: 1369874--1369903 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1369864 CAACAAGCTC
1369874 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
1369904 AAGGTAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1383824 original size:27 final size:27
Alignment explanation
Indices: 1383786--1383840 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1383776 GGAAAAATCC
1383786 TAGTGGAAATTGCCTGAGTATCTAGGG
1 TAGTGGAAATTGCCTGAGTATCTAGGG
1383813 TAGTGGAAATTGCCTGAGTATCTAGGG
1 TAGTGGAAATTGCCTGAGTATCTAGGG
1383840 T
1 T
1383841 TTAACTTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.33, T:0.31
Consensus pattern (27 bp):
TAGTGGAAATTGCCTGAGTATCTAGGG
Found at i:1386314 original size:2 final size:2
Alignment explanation
Indices: 1386307--1386334 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1386297 TGTACAAAGC
1386307 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1386335 GTGACTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1388259 original size:2 final size:2
Alignment explanation
Indices: 1388252--1388290 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1388242 AGAAGGAGAA
1388252 AT AT AT AT AT -T 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
1388291 TGTGGGAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1394073 original size:3 final size:3
Alignment explanation
Indices: 1394060--1394091 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1394050 GAAAGAACAG
*
1394060 AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1394092 GGATACATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1394927 original size:162 final size:163
Alignment explanation
Indices: 1394660--1394975 Score: 526
Period size: 162 Copynumber: 1.9 Consensus size: 163
1394650 CTCTATCCAG
* ** * *
1394660 GCTTCACTGTCTGCCTCGTCATCTGTGCCTCTGACATACTTCCGATTTGCAGCTCTATCACATCT
1 GCTTCACTGTCTGCCTCGTCATCTATGCCTCCAACATACTTCCGATTGGCAGCCCTATCACATCT
* * *
1394725 TCTCCTCTTCAGGGTCTCTCTAATCCGGTTAGCATCACTCTTACTAAAGGTATTATGAACTGAAA
66 CCTCCTCTTCAAGGTCTCTCTAATCCGGTCAGCATCACTCTTACTAAAGGTATTATGAACTGAAA
1394790 CAATCTTAAAGCTTGGG-TCAGATTCCTCAGTT
131 CAATCTTAAAGCTTGGGTTCAGATTCCTCAGTT
*
1394822 GCTTCACTGTCTGCCTCGTCTTCTATGCCTCCAACATACTTCCGATTGGCAGCCCTATCACATCT
1 GCTTCACTGTCTGCCTCGTCATCTATGCCTCCAACATACTTCCGATTGGCAGCCCTATCACATCT
* *
1394887 CCTCCTCTTCAAGTTCTCTCTAATCCGGTCAGCATCACTCTTGCTAAAGGTATTATGAACTGAAA
66 CCTCCTCTTCAAGGTCTCTCTAATCCGGTCAGCATCACTCTTACTAAAGGTATTATGAACTGAAA
1394952 CAATCTTAAAGCTTGGGTTCAGAT
131 CAATCTTAAAGCTTGGGTTCAGAT
1394976 CAGATTCTTC
Statistics
Matches: 142, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
162 136 0.96
163 6 0.04
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.34
Consensus pattern (163 bp):
GCTTCACTGTCTGCCTCGTCATCTATGCCTCCAACATACTTCCGATTGGCAGCCCTATCACATCT
CCTCCTCTTCAAGGTCTCTCTAATCCGGTCAGCATCACTCTTACTAAAGGTATTATGAACTGAAA
CAATCTTAAAGCTTGGGTTCAGATTCCTCAGTT
Found at i:1425124 original size:6 final size:6
Alignment explanation
Indices: 1425113--1425151 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
1425103 TAAGGGTAAA
*
1425113 AAACCC AAACCC AAACCC AAACCC AAATCC AAACTCC AA
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAAC-CC AA
1425152 CCAACTTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.51, C:0.44, G:0.00, T:0.05
Consensus pattern (6 bp):
AAACCC
Found at i:1428416 original size:26 final size:26
Alignment explanation
Indices: 1428366--1428417 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1428356 TTATAAACTT
*
1428366 TTTATTATAAATAAAAATAATAATAA
1 TTTATTATAAATAAAAATAAGAATAA
1428392 TTTATT-TAAATATAATAA-AAGAATAA
1 TTTATTATAAATA-AA-AATAAGAATAA
1428418 AAACTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 6 0.26
26 15 0.65
27 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
TTTATTATAAATAAAAATAAGAATAA
Found at i:1436211 original size:7 final size:7
Alignment explanation
Indices: 1436201--1436226 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1436191 CAAAAACTTA
1436201 AAAAAAT
1 AAAAAAT
1436208 AAAAAAT
1 AAAAAAT
1436215 AAAAAAT
1 AAAAAAT
1436222 AAAAA
1 AAAAA
1436227 GAAGAAAAGG
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1446996 original size:45 final size:45
Alignment explanation
Indices: 1446923--1447039 Score: 171
Period size: 45 Copynumber: 2.6 Consensus size: 45
1446913 ATAAAATTAT
* * *
1446923 ACGTCATGTACAAAAACATGTTATACGTCATGGTTAGGTTGTTAC
1 ACGTTATGTACAAAAACATGTGACACGTCATGGTTAGGTTGTTAC
* *
1446968 ATGTTATGTACAAAAACATGTGACACGTCATGGTTAGGTTTTTAC
1 ACGTTATGTACAAAAACATGTGACACGTCATGGTTAGGTTGTTAC
* *
1447013 ACGTTATGTGCAAAAATATGTGACACG
1 ACGTTATGTACAAAAACATGTGACACG
1447040 CCATAATTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (45 bp):
ACGTTATGTACAAAAACATGTGACACGTCATGGTTAGGTTGTTAC
Found at i:1454568 original size:2 final size:2
Alignment explanation
Indices: 1454561--1454645 Score: 98
Period size: 2 Copynumber: 42.0 Consensus size: 2
1454551 ATTTCATTTC
* *
1454561 AT AT AT AT AT AT AT AT AT AC AT TT CAT 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
* * * * *
1454604 GT AT AT AT AT AT AT GT AT AT AT GT AT AT GT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1454646 TTAATGTACC
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
2 67 0.99
3 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1458365 original size:19 final size:18
Alignment explanation
Indices: 1458332--1458372 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1458322 TAATAATAAT
*
1458332 AATTTAATTTTAAAATTG
1 AATTTAATTTTAAAATTA
*
1458350 AATTTTATTTTAAAAATTA
1 AATTTAATTTT-AAAATTA
1458369 AATT
1 AATT
1458373 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATTTAATTTTAAAATTA
Found at i:1476775 original size:18 final size:19
Alignment explanation
Indices: 1476752--1476792 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1476742 GTCTGGCAGA
*
1476752 TTTTCT-TTTCTTTGTTGT
1 TTTTCTATTTCTTTGATGT
*
1476770 TTTTCTATTTGTTTGATGT
1 TTTTCTATTTCTTTGATGT
1476789 TTTT
1 TTTT
1476793 GACTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.05, C:0.07, G:0.12, T:0.76
Consensus pattern (19 bp):
TTTTCTATTTCTTTGATGT
Found at i:1490466 original size:1 final size:1
Alignment explanation
Indices: 1490462--1490495 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
1490452 GCCGGGGGCC
*
1490462 GGGGGGGGGGGGGGGNGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1490496 TTTACTATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:1494464 original size:2 final size:2
Alignment explanation
Indices: 1494459--1494486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1494449 GTGTGTGTGT
1494459 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1494487 ATTCATCCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1510508 original size:6 final size:6
Alignment explanation
Indices: 1510474--1510506 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1510464 TTTTATTTTT
*
1510474 CTTCTC CTTCTC CTTCTC CTTCTC CTTGTC CTT
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTT
1510507 GTTGTCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (6 bp):
CTTCTC
Done.