Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 43 of 345
Found at i:12391652 original size:12 final size:12
Alignment explanation
Indices: 12391637--12391661 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12391627 AATAAATTAC
12391637 TAACAAAATATT
1 TAACAAAATATT
12391649 TAACAAAATATT
1 TAACAAAATATT
12391661 T
1 T
12391662 TTACATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TAACAAAATATT
Found at i:12391671 original size:34 final size:33
Alignment explanation
Indices: 12391560--12391748 Score: 119
Period size: 34 Copynumber: 5.3 Consensus size: 33
12391550 TTTATAATAA
*
12391560 ATTACTAACAAAATATTTAACAAAATAATTTTAC
1 ATTACTAA-AAAATATTTAACAAAATATTTTTAC
* * *** *
12391594 ATTACCAAAAACTCACAAAACTCAAAA-ATTTATAATAA
1 ATTACTAAAAAAT-ATTTAA--CAAAATATTT-T--TAC
12391632 ATTACTAACAAAATATTTAACAAAATATTTTTAC
1 ATTACTAA-AAAATATTTAACAAAATATTTTTAC
* *** * *
12391666 ATTACTAAAAACTCACAAAACAGAAAAATTTATAATAA
1 ATTACTAAAAAAT-ATTTAACA-AAATATTT-T--TAC
*
12391704 ATTACTAGAAAAATATTTAACAAAATAATTTTAC
1 ATTACTA-AAAAATATTTAACAAAATATTTTTAC
12391738 ATTACTAAAAA
1 ATTACTAAAAA
12391749 CTCACCAAAT
Statistics
Matches: 115, Mismatches: 26, Indels: 29
0.68 0.15 0.17
Matches are distributed among these distances:
33 12 0.10
34 34 0.30
35 10 0.09
36 14 0.12
37 10 0.09
38 26 0.23
39 9 0.08
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.31
Consensus pattern (33 bp):
ATTACTAAAAAATATTTAACAAAATATTTTTAC
Found at i:12391833 original size:59 final size:60
Alignment explanation
Indices: 12391767--12391884 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 60
12391757 ATACTAAACT
12391767 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTT-AAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
12391826 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA
12391885 TAAAAAATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 49 0.84
60 9 0.16
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
Found at i:12393618 original size:27 final size:28
Alignment explanation
Indices: 12393586--12393641 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
12393576 TTAATTAACT
*
12393586 AATTAA-TTATTTAATAATATAAAATTA
1 AATTAATTTATTTAATAATAAAAAATTA
12393613 AATTAATTTATTTAATAATAAAAAATTA
1 AATTAATTTATTTAATAATAAAAAATTA
12393641 A
1 A
12393642 TATAATAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTAATTTATTTAATAATAAAAAATTA
Found at i:12393647 original size:28 final size:28
Alignment explanation
Indices: 12393585--12393647 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
12393575 TTTAATTAAC
*
12393585 TAAT-TAA-TTATTTAATAATATAAAAT
1 TAATATAATTTATTTAATAATAAAAAAT
12393611 TAA-ATTAATTTATTTAATAATAAAAAAT
1 TAATA-TAATTTATTTAATAATAAAAAAT
12393639 TAATATAAT
1 TAATATAAT
12393648 AAGAGATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
27 3 0.09
28 25 0.78
29 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATATAATTTATTTAATAATAAAAAAT
Found at i:12396121 original size:27 final size:27
Alignment explanation
Indices: 12396084--12396198 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
12396074 AGCATGGCTG
* *
12396084 CCAGAACAGATA-ATGTGACAGAGTCA
1 CCAGAACAGATATATGTGGCAGAGCCA
*
12396110 CCAGATACAGATA-ATCGTGGCAAAGCCA
1 CCAGA-ACAGATATAT-GTGGCAGAGCCA
12396138 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* *
12396165 CCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
12396192 CCAGAAC
1 CCAGAAC
12396199 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 16 0.20
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATATATGTGGCAGAGCCA
Found at i:12396143 original size:54 final size:54
Alignment explanation
Indices: 12396084--12396198 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
12396074 AGCATGGCTG
*
12396084 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAAAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAAAGCCA
* * * *
12396138 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAAAGCCA
12396192 CCAGAAC
1 CCAGAAC
12396199 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAAAGCCA
Found at i:12397849 original size:26 final size:26
Alignment explanation
Indices: 12397813--12397948 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
12397803 CATGAAAGTC
12397813 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
12397839 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
* *
12397865 TTATTATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
12397891 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
12397917 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
12397943 TTATCA
1 TTATCA
12397949 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:12398543 original size:64 final size:64
Alignment explanation
Indices: 12398470--12398680 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
12398460 CTGGGCCAGA
*
12398470 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
12398534 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
12398596 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
12398607 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
12398671 GCCCATTTCA
1 GCCCATTTCA
12398681 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:12398608 original size:137 final size:137
Alignment explanation
Indices: 12398436--12398722 Score: 556
Period size: 137 Copynumber: 2.1 Consensus size: 137
12398426 CATTGGGCCT
**
12398436 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
12398501 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
12398566 CATATGC
131 CATATGC
12398573 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
12398638 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
12398703 CATATGC
131 CATATGC
12398710 AAGCCCATTTGGG
1 AAGCCCATTTGGG
12398723 GAGACTACTC
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:12400537 original size:26 final size:26
Alignment explanation
Indices: 12400499--12400556 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
12400489 CATAAAATTC
12400499 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
12400525 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12400551 TTATCA
1 TTATCA
12400557 ATTTGTATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:12402341 original size:25 final size:25
Alignment explanation
Indices: 12402301--12402358 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
12402291 GTGATAAACT
* *
12402301 GTAAGCTCATCTGAGTTGAATATCA
1 GTAAGCTCATCCGAGTTGAATAACA
* *
12402326 GTAAGCTCCTCCGAGTTGAATAACG
1 GTAAGCTCATCCGAGTTGAATAACA
12402351 GTAAGCTC
1 GTAAGCTC
12402359 TTAAGAGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (25 bp):
GTAAGCTCATCCGAGTTGAATAACA
Found at i:12404066 original size:15 final size:14
Alignment explanation
Indices: 12404036--12404081 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
12404026 TTATTATTAC
*
12404036 TATTACTTTTATTAT
1 TATTACTTTT-CTAT
12404051 TATTACTGTTTCTAT
1 TATTACT-TTTCTAT
*
12404066 TATTGCTTTTCTAT
1 TATTACTTTTCTAT
12404080 TA
1 TA
12404082 CCATTTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.32
15 16 0.57
16 3 0.11
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (14 bp):
TATTACTTTTCTAT
Found at i:12404078 original size:14 final size:15
Alignment explanation
Indices: 12404048--12404081 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12404038 TTACTTTTAT
12404048 TATTATTACTGTTTC
1 TATTATTACTGTTTC
*
12404063 TATTATTGCT-TTTC
1 TATTATTACTGTTTC
12404077 TATTA
1 TATTA
12404082 CCATTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (15 bp):
TATTATTACTGTTTC
Found at i:12404185 original size:23 final size:23
Alignment explanation
Indices: 12404155--12404218 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
12404145 TCATTACTTT
* *
12404155 CTATTATTGTTATTATTAATATA
1 CTATTATTATTATTATTAACATA
* *
12404178 CTATTATTATTCTTATTAACGTA
1 CTATTATTATTATTATTAACATA
*
12404201 TTATTATTATTATTATTA
1 CTATTATTATTATTATTA
12404219 TTATTATTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (23 bp):
CTATTATTATTATTATTAACATA
Found at i:12404274 original size:3 final size:3
Alignment explanation
Indices: 12404110--12404258 Score: 125
Period size: 3 Copynumber: 50.7 Consensus size: 3
12404100 GCACTATTCT
*
12404110 TTA TT- TTA TTA TTA TTA TTA TT- TT- TTA TTA TT- TTA TCA TTA CTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * *
12404154 TCTA TTA TTG TTA TTA TTA ATA -TA CTA TTA TTA TTC TTA TTAA CGTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A -TTA
*
12404201 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA CT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
12404246 -TA TTA TTA CTA TT
1 TTA TTA TTA TTA TT
12404259 GCTATCATCA
Statistics
Matches: 120, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
2 14 0.12
3 98 0.82
4 7 0.06
5 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:12404355 original size:15 final size:15
Alignment explanation
Indices: 12404335--12404364 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12404325 ATTTATTTAC
12404335 ATTATTATTACTATT
1 ATTATTATTACTATT
*
12404350 ATTATTATTTCTATT
1 ATTATTATTACTATT
12404365 TTTTTGAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTACTATT
Found at i:12404698 original size:23 final size:23
Alignment explanation
Indices: 12404666--12404717 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
12404656 TAGGTTTTCA
* * *
12404666 CTTATAATATTATTATTGTCATT
1 CTTATTATATGATTATTATCATT
*
12404689 CTTATTATATGGTTATTATCATT
1 CTTATTATATGATTATTATCATT
*
12404712 ATTATT
1 CTTATT
12404718 CTCACCATCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.58
Consensus pattern (23 bp):
CTTATTATATGATTATTATCATT
Found at i:12406736 original size:38 final size:37
Alignment explanation
Indices: 12406689--12406883 Score: 133
Period size: 38 Copynumber: 5.4 Consensus size: 37
12406679 AAACTCACAA
*
12406689 AACACAATAATTTATAATAAATTACTAACAAAATATTT
1 AACAAAATAATTTATAATAAATTACTAA-AAAATATTT
* * ***
12406727 AACAAAATAATTT-TACAT---TT-CCAAAAACTCACAA
1 AACAAAATAATTTATA-ATAAATTACTAAAAAAT-ATTT
*
12406761 AACTCAAA-AATTTATAATAAATTACTAACAAAATATTT
1 AAC-AAAATAATTTATAATAAATTACTAA-AAAATATTT
* * ***
12406799 AACAAAAT-ATTT-T--TACATTACTAAAAACTCACAA
1 AACAAAATAATTTATAATAAATTACTAAAAAAT-ATTT
12406833 AACAGAAA-AATTTATAATAAATTACTAGAAAAATATTT
1 AACA-AAATAATTTATAATAAATTACTA-AAAAATATTT
12406871 AACAAAATAATTT
1 AACAAAATAATTT
12406884 TACATTACTA
Statistics
Matches: 116, Mismatches: 23, Indels: 36
0.66 0.13 0.21
Matches are distributed among these distances:
33 8 0.07
34 29 0.25
35 14 0.12
36 2 0.02
37 14 0.12
38 40 0.34
39 9 0.08
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.31
Consensus pattern (37 bp):
AACAAAATAATTTATAATAAATTACTAAAAAATATTT
Found at i:12406773 original size:72 final size:72
Alignment explanation
Indices: 12406666--12406902 Score: 404
Period size: 72 Copynumber: 3.3 Consensus size: 72
12406656 TTTAAAAAAA
*
12406666 TTTACATTACTAAAAACTCACAAAACACAATAATTTATAATAAATTACTAACAAAATATTTAACA
1 TTTACATTACTAAAAACTCACAAAACACAAAAATTTATAATAAATTACTAACAAAATATTTAACA
12406731 AAATAAT
66 AAATAAT
* * *
12406738 TTTACATTTCCAAAAACTCACAAAACTCAAAAATTTATAATAAATTACTAACAAAATATTTAACA
1 TTTACATTACTAAAAACTCACAAAACACAAAAATTTATAATAAATTACTAACAAAATATTTAACA
*
12406803 AAATATT
66 AAATAAT
*
12406810 TTTACATTACTAAAAACTCACAAAACAGAAAAATTTATAATAAATTACTAGA-AAAATATTTAAC
1 TTTACATTACTAAAAACTCACAAAACACAAAAATTTATAATAAATTACTA-ACAAAATATTTAAC
12406874 AAAATAAT
65 AAAATAAT
12406882 TTTACATTACTAAAAACTCAC
1 TTTACATTACTAAAAACTCAC
12406903 CAAATACTAA
Statistics
Matches: 154, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
72 153 0.99
73 1 0.01
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (72 bp):
TTTACATTACTAAAAACTCACAAAACACAAAAATTTATAATAAATTACTAACAAAATATTTAACA
AAATAAT
Found at i:12406801 original size:12 final size:12
Alignment explanation
Indices: 12406786--12406810 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12406776 AATAAATTAC
12406786 TAACAAAATATT
1 TAACAAAATATT
12406798 TAACAAAATATT
1 TAACAAAATATT
12406810 T
1 T
12406811 TTACATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TAACAAAATATT
Found at i:12406982 original size:59 final size:60
Alignment explanation
Indices: 12406916--12407033 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 60
12406906 ATACTAAACT
12406916 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTT-AAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
12406975 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA
12407034 TAAAAAATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 49 0.84
60 9 0.16
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
Found at i:12408766 original size:27 final size:27
Alignment explanation
Indices: 12408734--12408788 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
12408724 TTAATTAACT
12408734 AATTAATT-ATTTAATAATATAAAATTA
1 AATTAATTCATTTAATAATA-AAAATTA
12408761 AATTAATTCATTTAATAATAAAAATTA
1 AATTAATTCATTTAATAATAAAAATTA
12408788 A
1 A
12408789 TATAATAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTAATTCATTTAATAATAAAAATTA
Found at i:12408794 original size:27 final size:27
Alignment explanation
Indices: 12408733--12408794 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
12408723 TTTAATTAAC
12408733 TAAT-TAATTATTTAATAATATAAAAT
1 TAATATAATTATTTAATAATATAAAAT
12408759 TAA-ATTAATTCATTTAATAATA-AAAAT
1 TAATA-TAATT-ATTTAATAATATAAAAT
12408786 TAATATAAT
1 TAATATAAT
12408795 AAGAGATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
26 3 0.09
27 17 0.53
28 12 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TAATATAATTATTTAATAATATAAAAT
Found at i:12410847 original size:47 final size:47
Alignment explanation
Indices: 12410776--12411096 Score: 253
Period size: 47 Copynumber: 6.7 Consensus size: 47
12410766 GTATAATGCT
* * *
12410776 GATGCCATGTCCCAAACATAGTCTTACACTGGCTCATCTATCAAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTATCAAGCC
* * * *
12410823 GATGCCATGTCCCAAACATGGTCTTACACTGACT-ATCGAAATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC--TATC-AAGCC
* * * *
12410872 GACGTCATGTCCCAGACATGGTCTTACACTAGCTC-TCACATATCCATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT--C-TAT-CAAGCC
* * * * *
12410922 GATGCCATGTCTCAGACATGGTCTTACACTGAC-AACTGTATACATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCA-TCTAT-CAAGCC
* * * * *
12410970 GATG-CATGTCCCGGACAT-TTCTTACACTGGCTTACATCT-TGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCTATCAAGCC
* * * *
12411016 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTTGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTATCAA-GCC
12411062 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC
12411097 TCATAATGTG
Statistics
Matches: 220, Mismatches: 38, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
44 3 0.01
45 3 0.01
46 51 0.23
47 59 0.27
48 32 0.15
49 34 0.15
50 35 0.16
51 3 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTATCAAGCC
Found at i:12411118 original size:47 final size:47
Alignment explanation
Indices: 12410776--12411137 Score: 225
Period size: 47 Copynumber: 7.6 Consensus size: 47
12410766 GTATAATGCT
* *
12410776 GATGCCATGTCCCAAACATAGTCTTACACTGGCTCATCTATCAA-GT--C
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TC-AT-AATGTGCC
* * * *
12410823 GATGCCATGTCCCAAACATGGTCTTACACTGACTATCGA-AATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-ATAAT-G-TGCC
* * * * *
12410872 GACGTCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT--GTGCC
* * * *
12410922 GATGCCATGTCTCAGACATGGTCTTACACTGACAACTGTATACA--TGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TCT-CATA-ATGTGCC
* * ** * *
12410970 GATG-CATGTCCCGGACAT-TTCTTACACTGGCT-TACATCTTGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATG-TGCC
*
12411016 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTTGTC-TCAA--TGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC---TCAT-AATGTGCC
*
12411062 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT-GCC
*
12411110 GATG-CATGTCCCAGACA-CGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
12411138 AGCACACAAA
Statistics
Matches: 248, Mismatches: 43, Indels: 49
0.73 0.13 0.14
Matches are distributed among these distances:
44 5 0.02
45 4 0.02
46 63 0.25
47 72 0.29
48 30 0.12
49 34 0.14
50 34 0.14
51 3 0.01
52 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGCC
Found at i:12411140 original size:94 final size:96
Alignment explanation
Indices: 12410766--12411137 Score: 322
Period size: 94 Copynumber: 3.9 Consensus size: 96
12410756 CAAACACAGG
* * * * *
12410766 GTAT-AATGCTGATGCCATGTCCCAAACATAGTCTTACACTGGCTCATC-T-ATCAAGTCGATGC
1 GTATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATGAGGTCGATGC
* * *
12410828 CATGTCCCAAACATGGTCTTACACTGACTATC
65 CATGTCCCAGACATGGTCTTACACTGACTCTT
* * * * * * * * * *
12410860 GAAATCGAGGCCGACGTCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCATGCCGAT
1 G-TATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT-GAGGTCGAT
* *
12410925 GCCATGTCTCAGACATGGTCTTACACTGACAAC-T
63 GCCATGTCCCAGACATGGTCTTACACTGAC-TCTT
* * **
12410959 GTAT-ACATGCCGATG-CATGTCCCGGACAT-TTCTTACACTGGCT-TACATCTTGAGG-CTGAT
1 GTATCA-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATGAGGTC-GAT
12411019 G-CATGTCCCAGACAT-GTCTTACACT-AGCTCTT
63 GCCATGTCCCAGACATGGTCTTACACTGA-CTCTT
* *
12411051 GTCTCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATG-C
1 GTATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGAGGTCGATGCC
*
12411115 ATGTCCCAGACA-CGTCTTACACT
66 ATGTCCCAGACATGGTCTTACACT
12411138 AGCACACAAA
Statistics
Matches: 223, Mismatches: 37, Indels: 36
0.75 0.12 0.12
Matches are distributed among these distances:
91 2 0.01
92 24 0.11
93 28 0.13
94 54 0.24
95 8 0.04
96 47 0.21
97 13 0.06
98 11 0.05
99 36 0.16
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (96 bp):
GTATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGAGGTCGATGCC
ATGTCCCAGACATGGTCTTACACTGACTCTT
Found at i:12416190 original size:120 final size:120
Alignment explanation
Indices: 12415976--12416213 Score: 424
Period size: 120 Copynumber: 2.0 Consensus size: 120
12415966 TTCCAACCTT
*
12415976 AACGAGCTTCCGAGTTACTATAAAATAGGGGAAATAAAATAGAGTAAGCATTTAATGCTTAGTAA
1 AACGAGCTTCCGAGTTACTATAAAATAGGGGAAATAAAACAGAGTAAGCATTTAATGCTTAGTAA
** *
12416041 GTTTGTATAACATGAAATTTAACTTACCATTTAATGACATTTAAGGTAAGCATTTA
66 GTTCATATAACATGAAATTTAACTTACCATTTAATCA-ATTTAAGGTAAGCATTTA
12416097 AACGAGCTTCCGAGTTACTATAAAATAGGGG-AATAAAACAGAGTAAGCATTTAATGCTTAGTAA
1 AACGAGCTTCCGAGTTACTATAAAATAGGGGAAATAAAACAGAGTAAGCATTTAATGCTTAGTAA
12416161 GTTCATATAACATGAAATTTAACTTACCATTTAATCAATTTAAGGTAAGCATT
66 GTTCATATAACATGAAATTTAACTTACCATTTAATCAATTTAAGGTAAGCATT
12416214 CTAGGCATAT
Statistics
Matches: 113, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
119 16 0.14
120 66 0.58
121 31 0.27
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (120 bp):
AACGAGCTTCCGAGTTACTATAAAATAGGGGAAATAAAACAGAGTAAGCATTTAATGCTTAGTAA
GTTCATATAACATGAAATTTAACTTACCATTTAATCAATTTAAGGTAAGCATTTA
Found at i:12416615 original size:25 final size:25
Alignment explanation
Indices: 12416587--12416656 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
12416577 AGCTGTATAA
*
12416587 CGGGAAGCTCTTGCGAGCCAATTAT
1 CGGGAAGCTCTTGCAAGCCAATTAT
12416612 CGGGAAGCTCTTGCAAGCCAATTAT
1 CGGGAAGCTCTTGCAAGCCAATTAT
* *
12416637 CGGGAAGCTCATACAAGCCA
1 CGGGAAGCTCTTGCAAGCCA
12416657 TAAACGAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (25 bp):
CGGGAAGCTCTTGCAAGCCAATTAT
Found at i:12416701 original size:25 final size:24
Alignment explanation
Indices: 12416587--12416704 Score: 98
Period size: 25 Copynumber: 4.8 Consensus size: 24
12416577 AGCTGTATAA
* *
12416587 CGGGAAGCTCTTGCGAGCCAATTAT
1 CGGGAAGCTCATGAGAGCC-ATTAT
*
12416612 CGGGAAGCTCTTGCA-AGCCAATTAT
1 CGGGAAGCTCATG-AGAGCC-ATTAT
* * *
12416637 CGGGAAGCTCAT-ACAAGCCATAAA
1 CGGGAAGCTCATGA-GAGCCATTAT
*
12416661 CGAGAAG-TCATGAGAGCCATTAAT
1 CGGGAAGCTCATGAGAGCCATT-AT
*
12416685 CGGGAAGCTCGTGAGAGCCA
1 CGGGAAGCTCATGAGAGCCA
12416705 AATTGTAGCA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
23 11 0.14
24 17 0.22
25 49 0.64
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (24 bp):
CGGGAAGCTCATGAGAGCCATTAT
Found at i:12419396 original size:26 final size:26
Alignment explanation
Indices: 12419360--12419470 Score: 168
Period size: 26 Copynumber: 4.3 Consensus size: 26
12419350 ACATGTAATT
*
12419360 ATTATCATGAAATATTTACCTAACCC
1 ATTATCATGAAACATTTACCTAACCC
12419386 ATTATCATGAAACATTTACCTAACCC
1 ATTATCATGAAACATTTACCTAACCC
* * *
12419412 ATTATCATGGAATATTTACCTAATCC
1 ATTATCATGAAACATTTACCTAACCC
* *
12419438 ATTGTCATGGAACATTTACCTAACCC
1 ATTATCATGAAACATTTACCTAACCC
12419464 ATTATCA
1 ATTATCA
12419471 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.34
Consensus pattern (26 bp):
ATTATCATGAAACATTTACCTAACCC
Found at i:12419417 original size:52 final size:52
Alignment explanation
Indices: 12419360--12419470 Score: 186
Period size: 52 Copynumber: 2.1 Consensus size: 52
12419350 ACATGTAATT
12419360 ATTATCATGAAATATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
1 ATTATCATGAAATATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
* * * *
12419412 ATTATCATGGAATATTTACCTAATCCATTGTCATGGAACATTTACCTAACCC
1 ATTATCATGAAATATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
12419464 ATTATCA
1 ATTATCA
12419471 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.34
Consensus pattern (52 bp):
ATTATCATGAAATATTTACCTAACCCATTATCATGAAACATTTACCTAACCC
Found at i:12421737 original size:10 final size:9
Alignment explanation
Indices: 12421704--12421746 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
12421694 TGACACGTGG
*
12421704 TAAAAATGA
1 TAAAAATAA
*
12421713 TAAAAACTAT
1 TAAAAA-TAA
*
12421723 TAAAATTAA
1 TAAAAATAA
12421732 TAAAAATAA
1 TAAAAATAA
12421741 TAAAAA
1 TAAAAA
12421747 ATATAGAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 22 0.79
10 6 0.21
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (9 bp):
TAAAAATAA
Found at i:12431084 original size:22 final size:21
Alignment explanation
Indices: 12431049--12431106 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
12431039 AAAAGGTATC
* * *
12431049 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAAAT
12431070 TACAAAATCATATCTTCTAAAAT
1 TAC-AAATCATATC-TCTAAAAT
* *
12431093 TGCATATCATATCT
1 TACAAATCATATCT
12431107 AAGATTGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAAAT
Found at i:12431113 original size:19 final size:19
Alignment explanation
Indices: 12431085--12431138 Score: 85
Period size: 17 Copynumber: 2.9 Consensus size: 19
12431075 AATCATATCT
*
12431085 TCTAAAATTGCATATCATA
1 TCTAAGATTGCATATCATA
12431104 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
12431121 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
12431139 TGAAGATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 17 0.53
19 15 0.47
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12435367 original size:6 final size:7
Alignment explanation
Indices: 12435356--12435380 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12435346 TTTAATTTTT
12435356 TAAAAAA
1 TAAAAAA
12435363 TAAAAAA
1 TAAAAAA
12435370 TAAAAAA
1 TAAAAAA
12435377 TAAA
1 TAAA
12435381 TTTATTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:12437192 original size:15 final size:16
Alignment explanation
Indices: 12437168--12437201 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12437158 TTTTAATTAA
12437168 TAAATATA-TTATTTT
1 TAAATATATTTATTTT
*
12437183 TAAATTTATTTATTTT
1 TAAATATATTTATTTT
12437199 TAA
1 TAA
12437202 TTCATCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAAATATATTTATTTT
Found at i:12437203 original size:15 final size:15
Alignment explanation
Indices: 12437176--12437217 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
12437166 AATAAATATA
*
12437176 TTATTTTTAAATTTAT
1 TTATTTTT-AATTCAT
12437192 TTATTTTTAATTCAT
1 TTATTTTTAATTCAT
*
12437207 CT-TTTTTAATT
1 TTATTTTTAATT
12437218 AATAGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 8 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTTTTAATTCAT
Found at i:12438280 original size:18 final size:18
Alignment explanation
Indices: 12438253--12438292 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12438243 AATTATATTA
12438253 TTAAAATTTTACTATAAT
1 TTAAAATTTTACTATAAT
* *
12438271 TTAAACTTTTATTATAAT
1 TTAAAATTTTACTATAAT
12438289 TTAA
1 TTAA
12438293 TATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAAATTTTACTATAAT
Found at i:12438305 original size:17 final size:18
Alignment explanation
Indices: 12438280--12438323 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
12438270 TTTAAACTTT
*
12438280 TATTATAATTTAA-TATA
1 TATTATAATTCAACTATA
*
12438297 TATTTTAATTCAACTATA
1 TATTATAATTCAACTATA
12438315 TA-TATAATT
1 TATTATAATT
12438324 AAATACATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTATAATTCAACTATA
Found at i:12455955 original size:44 final size:45
Alignment explanation
Indices: 12455865--12455993 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
12455855 GACAGAACGA
*
12455865 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
12455911 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
12455955 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
12455994 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:12462091 original size:44 final size:45
Alignment explanation
Indices: 12462001--12462129 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
12461991 GACAGAACGA
*
12462001 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
12462047 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
12462091 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
12462130 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:12467455 original size:31 final size:30
Alignment explanation
Indices: 12467420--12467488 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
12467410 TATTTAAATT
12467420 TTAAAATTA-TTATTAAAATAAAAATGTAATA
1 TTAAAATTATTTATTAAAATAAAAAT-T-ATA
* * *
12467451 TT-AAATAATTTATTAAGATAATAATTATA
1 TTAAAATTATTTATTAAAATAAAAATTATA
12467480 TTAATAATT
1 TTAA-AATT
12467489 TATCATATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
29 5 0.16
30 7 0.23
31 19 0.61
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
TTAAAATTATTTATTAAAATAAAAATTATA
Found at i:12470872 original size:17 final size:17
Alignment explanation
Indices: 12470850--12470884 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12470840 CTCCTACCTA
12470850 AGTTTGAGTTTATCTAG
1 AGTTTGAGTTTATCTAG
12470867 AGTTTGAGTTTATCTAG
1 AGTTTGAGTTTATCTAG
12470884 A
1 A
12470885 TTTCAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (17 bp):
AGTTTGAGTTTATCTAG
Found at i:12476254 original size:2 final size:2
Alignment explanation
Indices: 12476247--12476278 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12476237 GCTTTTGGCC
12476247 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
12476279 TAATCAAGTT
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:12484485 original size:20 final size:21
Alignment explanation
Indices: 12484446--12484484 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12484436 TAAAACTTAC
12484446 AAAATATAAAAATCATTTTTA
1 AAAATATAAAAATCATTTTTA
12484467 AAAAT-TAAAAAT-ATTTTT
1 AAAATATAAAAATCATTTTT
12484485 TTATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATATAAAAATCATTTTTA
Found at i:12485349 original size:22 final size:24
Alignment explanation
Indices: 12485309--12485362 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
12485299 TAATTTAATA
12485309 AAAACATAAAATATATATAATTGTT
1 AAAA-ATAAAATATATATAATTGTT
*
12485334 AAAAATAAAA-AT-TATAATTTTT
1 AAAAATAAAATATATATAATTGTT
12485356 AAAAATA
1 AAAAATA
12485363 TATATATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 16 0.57
23 2 0.07
24 6 0.21
25 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAATAAAATATATATAATTGTT
Found at i:12485371 original size:24 final size:23
Alignment explanation
Indices: 12485318--12485386 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
12485308 AAAAACATAA
*
12485318 AATATA-TATAATTGTTAAAAAT
1 AATATATTATAATTTTTAAAAAT
*
12485340 AA-AAATTATAATTTTTAAAAAT
1 AATATATTATAATTTTTAAAAAT
* *
12485362 ATATATATTAAAATTTATTTAAAAT
1 A-ATATATTATAATTT-TTAAAAAT
12485387 TCAAAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.05
22 18 0.47
23 1 0.03
24 10 0.26
25 7 0.18
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (23 bp):
AATATATTATAATTTTTAAAAAT
Found at i:12486560 original size:16 final size:17
Alignment explanation
Indices: 12486552--12486586 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
12486542 TAAAAATAAA
12486552 AATAAATAACTAAAAACAC
1 AATAAATAA--AAAAACAC
12486571 AATAAATAAAAAAACA
1 AATAAATAAAAAAACA
12486587 TGACATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.14
Consensus pattern (17 bp):
AATAAATAAAAAAACAC
Found at i:12487694 original size:16 final size:16
Alignment explanation
Indices: 12487675--12487709 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12487665 CATATAATAA
*
12487675 ATTATATTAATAATTT
1 ATTATATTAATAAATT
*
12487691 ATTATTTTAATAAATT
1 ATTATATTAATAAATT
12487707 ATT
1 ATT
12487710 TAATATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATATTAATAAATT
Found at i:12487741 original size:13 final size:14
Alignment explanation
Indices: 12487725--12487766 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
12487715 TTTCAATTTT
12487725 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
12487738 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
12487753 ATTTTAAATAATAT
1 ATTTT-AATAATAT
12487767 TCTTCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:12487751 original size:16 final size:16
Alignment explanation
Indices: 12487729--12487765 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
12487719 AATTTTATTT
12487729 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
12487746 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
12487761 TAATA
1 TAATA
12487766 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:12487809 original size:14 final size:15
Alignment explanation
Indices: 12487785--12487820 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12487775 TATTATTGAA
12487785 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
12487798 AAATATTTTAATAAT
1 AAATATTTTAATAAT
12487813 AAATATTT
1 AAATATTT
12487821 ATTACATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 6 0.29
15 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:12487821 original size:14 final size:13
Alignment explanation
Indices: 12487785--12487821 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
12487775 TATTATTGAA
12487785 AAATATTTAATAT
1 AAATATTTAATAT
12487798 AAATATTTTAATAAT
1 AAATA-TTTAAT-AT
12487813 AAATATTTA
1 AAATATTTA
12487822 TTACATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 10 0.45
15 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATATTTAATAT
Found at i:12487916 original size:21 final size:22
Alignment explanation
Indices: 12487878--12487926 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
12487868 TTATTTAAAC
* *
12487878 AATACTCATATATATAATTA-A
1 AATATTCATATATATAATAATA
* *
12487899 AATATTCATATTTTTAATAATA
1 AATATTCATATATATAATAATA
12487921 AATATT
1 AATATT
12487927 TATAACAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATTCATATATATAATAATA
Found at i:12496932 original size:28 final size:30
Alignment explanation
Indices: 12496872--12496944 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 30
12496862 AAATTTAATT
* *
12496872 TTTTTAAAATTTTATTTAATTATAATTTCTA
1 TTTTTAAATTTTTATTTAATTATAA-TACTA
*
12496903 TTTTTAAATTTTTATTTTATTA-AA-ACTA
1 TTTTTAAATTTTTATTTAATTATAATACTA
*
12496931 TTTATAAATTTTTA
1 TTTTTAAATTTTTA
12496945 CAAATATAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 16 0.42
30 2 0.05
31 20 0.53
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTAAATTTTTATTTAATTATAATACTA
Found at i:12497866 original size:2 final size:2
Alignment explanation
Indices: 12497859--12497884 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12497849 TCAATTTGCA
12497859 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
12497885 GTTGAGAGAG
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:12499801 original size:22 final size:22
Alignment explanation
Indices: 12499775--12499838 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
12499765 CGGGTGAGAA
12499775 AGAAAGGAGAGAAAGGAGAAGG
1 AGAAAGGAGAGAAAGGAGAAGG
* * *
12499797 AGAAAAGA-AGGAAGGTGAAGG
1 AGAAAGGAGAGAAAGGAGAAGG
* *
12499818 AG-AAGAAGAAGAAAGAAGAAG
1 AGAAAGGAG-AGAAAGGAGAAG
12499839 AAGGAAGAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 3 0.09
21 13 0.41
22 16 0.50
ACGTcount: A:0.58, C:0.00, G:0.41, T:0.02
Consensus pattern (22 bp):
AGAAAGGAGAGAAAGGAGAAGG
Found at i:12499810 original size:15 final size:15
Alignment explanation
Indices: 12499770--12499853 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 15
12499760 ATTTACGGGT
12499770 GAGAAAG-A-AAGGA
1 GAGAAAGAAGAAGGA
*
12499783 GAGAAAGGAGAAGGA
1 GAGAAAGAAGAAGGA
*
12499798 GA-AAAGAAGGAAGGT
1 GAGAAAGAA-GAAGGA
12499813 GAAGGAGAAGAAGAA-GA
1 G-A-GA-AAGAAGAAGGA
*
12499830 AAG-AAGAAGAAGGA
1 GAGAAAGAAGAAGGA
12499844 -AG-AAGAAGAA
1 GAGAAAGAAGAA
12499854 AAAAAAGGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
13 25 0.42
14 8 0.14
15 14 0.24
16 2 0.03
17 1 0.02
18 4 0.07
19 5 0.08
ACGTcount: A:0.60, C:0.00, G:0.39, T:0.01
Consensus pattern (15 bp):
GAGAAAGAAGAAGGA
Found at i:12499816 original size:21 final size:22
Alignment explanation
Indices: 12499787--12499851 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
12499777 AAAGGAGAGA
12499787 AAGGAGAAGGAGAA-AAGAAGG
1 AAGGAGAAGGAGAAGAAGAAGG
* *
12499808 AAGGTGAAGGAGAAGAAGAAGA
1 AAGGAGAAGGAGAAGAAGAAGG
* *
12499830 AAGAAGAAGAAGGAAGAAGAAG
1 AAGGAGAAGGA-GAAGAAGAAG
12499852 AAAAAAAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.35
22 14 0.38
23 10 0.27
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (22 bp):
AAGGAGAAGGAGAAGAAGAAGG
Found at i:12499826 original size:3 final size:3
Alignment explanation
Indices: 12499791--12499853 Score: 56
Period size: 3 Copynumber: 20.3 Consensus size: 3
12499781 GAGAGAAAGG
* * * *
12499791 AGA AGG AGA A-A AGA AGGA AGG TGA AGG AGA AGA AGA AGAA AGA AGA
1 AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AG-A AGA AGA
12499837 AGA AGGA AGA AGA AGA A
1 AGA A-GA AGA AGA AGA A
12499854 AAAAAAGGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 37 0.77
4 9 0.19
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:12499836 original size:13 final size:13
Alignment explanation
Indices: 12499818--12499853 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
12499808 AAGGTGAAGG
12499818 AGAAGAAGAAGAA
1 AGAAGAAGAAGAA
*
12499831 AGAAGAAGAAGGA
1 AGAAGAAGAAGAA
12499844 AGAAGAAGAA
1 AGAAGAAGAA
12499854 AAAAAAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAAGAA
Found at i:12499851 original size:10 final size:10
Alignment explanation
Indices: 12499813--12499851 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
12499803 GAAGGAAGGT
*
12499813 GAAGGAGAA-
1 GAAGAAGAAG
*
12499822 GAAGAAGAAA
1 GAAGAAGAAG
12499832 GAAGAAGAAG
1 GAAGAAGAAG
12499842 GAAGAAGAAG
1 GAAGAAGAAG
12499852 AAAAAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:12500262 original size:114 final size:115
Alignment explanation
Indices: 12500119--12500446 Score: 483
Period size: 113 Copynumber: 2.9 Consensus size: 115
12500109 AATTATAGTT
* * *
12500119 GATTTGGTTATATAAATTGTTAGTCTTTAGTAGTTTAGTGTATTAGTGTATTGTGA-TTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
12500183 TAATATATTTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
* * *
12500233 GATTAGGTTATATAAATTATTAGTGTTTAGTGGTTTA--GTATTAGCGTATTGTAATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
12500296 TAATATATTTTTAAAAAAAT-ATGTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTTAAAAAAATAAT-TTTATAGCTATTTTATTAGTAATTTAA
*
12500346 GATTAGGTTATAT--ATTGTTAGTGTTTAGTGGTTTAGTGTGTATTAATGTATTGTGATTTTTTT
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTA--GTGTATTAGTGTATTGTGA-TTTTTT
* *
12500409 TAGTAATGTA--TTTAAAAAAATAATTTTATAGTTATTTT
63 TAGTAATATATTTTTAAAAAAATAATTTTATAGCTATTTT
12500447 GTGTTAGTAT
Statistics
Matches: 194, Mismatches: 12, Indels: 16
0.87 0.05 0.07
Matches are distributed among these distances:
111 21 0.11
112 17 0.09
113 68 0.35
114 57 0.29
115 16 0.08
116 15 0.08
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (115 bp):
GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
TAATATATTTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
Found at i:12500533 original size:15 final size:16
Alignment explanation
Indices: 12500504--12500535 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12500494 TGTGATTTTT
12500504 TAATGTAATTTTTATA
1 TAATGTAATTTTTATA
12500520 TAATGTAA-TTTTATA
1 TAATGTAATTTTTATA
12500535 T
1 T
12500536 TATTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATGTAATTTTTATA
Found at i:12502358 original size:33 final size:32
Alignment explanation
Indices: 12502321--12502433 Score: 109
Period size: 33 Copynumber: 3.4 Consensus size: 32
12502311 ACTTATCTCA
*
12502321 GTACTCTACTCCTTCCGGACCGTATCCACCTAT
1 GTACTCTACTCC-TCCGGACCGTATCCACCTAC
* * **
12502354 GTACTCAACTCCTCCAGAGCCGTATCCACCGCC
1 GTACTCTACTCCTCCGGA-CCGTATCCACCTAC
* * *
12502387 GTACTCTACTCCTCCTGGCCCATATCCACCTCC
1 GTACTCTACTCCTCC-GGACCGTATCCACCTAC
* *
12502420 ATATTCTACTCCTC
1 GTACTCTACTCCTC
12502434 TCGGCTCAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 5 0.08
33 60 0.91
34 1 0.02
ACGTcount: A:0.19, C:0.43, G:0.11, T:0.27
Consensus pattern (32 bp):
GTACTCTACTCCTCCGGACCGTATCCACCTAC
Found at i:12505015 original size:13 final size:13
Alignment explanation
Indices: 12504997--12505024 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12504987 TATATATATA
12504997 AAAGAAACAAAAG
1 AAAGAAACAAAAG
12505010 AAAGAAACAAAAG
1 AAAGAAACAAAAG
12505023 AA
1 AA
12505025 TAAAAAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAGAAACAAAAG
Found at i:12506025 original size:15 final size:15
Alignment explanation
Indices: 12506007--12506063 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
12505997 TATCTGTTTT
12506007 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
12506022 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
12506037 ATTGAATTTATATTG
1 ATTGAATTTATATTG
12506052 ATTGAA-TTATAT
1 ATTGAATTTATAT
12506064 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:12506042 original size:30 final size:28
Alignment explanation
Indices: 12506003--12506061 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
12505993 TGAATATCTG
12506003 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
12506032 TTTTGATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
12506061 T
1 T
12506062 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:12506482 original size:21 final size:21
Alignment explanation
Indices: 12506447--12506542 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
12506437 AGGCACTTTA
*
12506447 TGTGTCGTATTTCAGGTACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
12506470 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
12506491 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* * * **
12506512 TGTGTCGTTTTAGGCACTTTA
1 TGTGTCGTATCAGGCACCTCG
12506533 TGTGTCGTAT
1 TGTGTCGTAT
12506543 ACTGATCAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 57 0.86
23 9 0.14
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:12506723 original size:18 final size:19
Alignment explanation
Indices: 12506702--12506742 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
12506692 AATGAAATGA
12506702 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
12506720 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
12506739 GAAA
1 GAAA
12506743 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:12510094 original size:18 final size:19
Alignment explanation
Indices: 12510062--12510102 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
12510052 TTTTCATGTA
*
12510062 TTATCTATTTAAAATTGTT
1 TTATCTATTTAAAATTATT
*
12510081 TTAT-TATTTTAAATTATT
1 TTATCTATTTAAAATTATT
12510099 TTAT
1 TTAT
12510103 ATACCTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATCTATTTAAAATTATT
Found at i:12510221 original size:13 final size:15
Alignment explanation
Indices: 12510192--12510233 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12510182 CATTTTACCC
*
12510192 TTTTATGTA-TATAT
1 TTTTATATATTATAT
12510206 ATTTTA-ATATTATAT
1 -TTTTATATATTATAT
12510221 TTTTATATATTAT
1 TTTTATATATTAT
12510234 GTATATAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTATATATTATAT
Found at i:12511265 original size:11 final size:11
Alignment explanation
Indices: 12511251--12511290 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
12511241 GTTTTCTCTC
*
12511251 TATTTTGCTAT
1 TATTTTACTAT
12511262 TATTTTACTAT
1 TATTTTACTAT
* *
12511273 TATATTACTAC
1 TATTTTACTAT
12511284 TATTTTA
1 TATTTTA
12511291 TTTTTATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60
Consensus pattern (11 bp):
TATTTTACTAT
Found at i:12514524 original size:28 final size:27
Alignment explanation
Indices: 12514483--12514541 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
12514473 GCGACTCTTT
* * *
12514483 TTTTTTATATTAAAATATATTTTTTTTG
1 TTTTTTAAAATAAAATAT-TATTTTTTG
12514511 TTTTTTAAAATAAAATATTATTTTTTG
1 TTTTTTAAAATAAAATATTATTTTTTG
12514538 TTTT
1 TTTT
12514542 CAGATTATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (27 bp):
TTTTTTAAAATAAAATATTATTTTTTG
Found at i:12514610 original size:27 final size:27
Alignment explanation
Indices: 12514569--12514637 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
12514559 TACAAGTTGT
*
12514569 GCCTATCTCTA-AGGCGCGACTAATTGA
1 GCCTATCTC-AGAGGCGCGACTAATCGA
* *
12514596 GCCTTTCTCAGAGGCGCGACTAATCGT
1 GCCTATCTCAGAGGCGCGACTAATCGA
12514623 GCCTATCTCAGAGGC
1 GCCTATCTCAGAGGC
12514638 ACAAATGGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.25
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCGACTAATCGA
Found at i:12515005 original size:60 final size:61
Alignment explanation
Indices: 12514921--12515054 Score: 200
Period size: 60 Copynumber: 2.2 Consensus size: 61
12514911 ATATTAAACT
* * *
12514921 AAACAC-AACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
*
12514981 AAACACAAAAAATTT-TAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAT
1 AAACACAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
* *
12515041 AAAAAAAAAAAATT
1 AAACACAAAAAATT
12515055 ACATTCATAC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 60 0.90
61 7 0.10
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (61 bp):
AAACACAAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:12515120 original size:7 final size:7
Alignment explanation
Indices: 12515108--12515132 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12515098 TAAATATTTT
12515108 ATAATTA
1 ATAATTA
12515115 ATAATTA
1 ATAATTA
12515122 ATAATTA
1 ATAATTA
12515129 ATAA
1 ATAA
12515133 CAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAATTA
Found at i:12517492 original size:2 final size:2
Alignment explanation
Indices: 12517487--12517515 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12517477 TCAAAAAATC
12517487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12517516 TTCAATCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12518599 original size:2 final size:2
Alignment explanation
Indices: 12518592--12518631 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12518582 CTTTAGCTTC
12518592 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
12518632 GAAAATTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12522786 original size:75 final size:75
Alignment explanation
Indices: 12522667--12522837 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
12522657 CATGGCAAAG
** *
12522667 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
12522726 CCATACTGAGC
65 CCATACCGAGC
12522737 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
12522802 CATACCGAGT
66 CATACCGAGC
***
12522812 TAAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
12522838 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:12522805 original size:35 final size:35
Alignment explanation
Indices: 12522670--12522835 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 35
12522660 GGCAAAGTGT
* **
12522670 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
12522705 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
12522740 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
12522780 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
*
12522815 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
12522836 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
35 85 0.73
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:12530255 original size:75 final size:75
Alignment explanation
Indices: 12530136--12530307 Score: 205
Period size: 75 Copynumber: 2.4 Consensus size: 75
12530126 CATGGCAAAG
** *
12530136 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
12530195 CCATACTGAGC
65 CCATACCGAGC
12530206 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
12530271 CATACCGAGT
66 CATACCGAGC
***
12530281 TAAAAAAATGTAGGTATGGTATT-TCAA
1 T-GTGAAATGTAGGTATGGTATTATCAA
12530308 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 1 0.01
75 46 0.53
76 18 0.21
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:12530274 original size:35 final size:35
Alignment explanation
Indices: 12530139--12530305 Score: 167
Period size: 35 Copynumber: 4.6 Consensus size: 35
12530129 GGCAAAGTGT
* **
12530139 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
12530174 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
12530209 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
12530249 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
*
12530285 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
12530306 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
35 64 0.55
36 21 0.18
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:12530297 original size:36 final size:35
Alignment explanation
Indices: 12530235--12530305 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
12530225 ATTATCAAAT
* *
12530235 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
*
12530270 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTT-AAAAAATGTAGGTATGGCATTTC
12530306 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (35 bp):
CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
Found at i:12531725 original size:30 final size:30
Alignment explanation
Indices: 12531689--12531745 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12531679 GGCTGGCACA
*
12531689 TGGGCATGTGGC-CTGCCCGTGTGGATCACT
1 TGGGCATGT-GCTCAGCCCGTGTGGATCACT
*
12531719 TGGGCATGTGCTCAGTCCGTGTGGATC
1 TGGGCATGTGCTCAGCCCGTGTGGATC
12531746 CTGAAAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.11, C:0.25, G:0.37, T:0.28
Consensus pattern (30 bp):
TGGGCATGTGCTCAGCCCGTGTGGATCACT
Found at i:12535746 original size:25 final size:25
Alignment explanation
Indices: 12535718--12535766 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12535708 GAATTTTATA
*
12535718 TTTACATATTAAATACATAAATAAT
1 TTTACATATTAAATACAAAAATAAT
** *
12535743 TTTATTTATTAAATATAAAAATAA
1 TTTACATATTAAATACAAAAATAA
12535767 ACTAAAGCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTACATATTAAATACAAAAATAAT
Found at i:12540858 original size:53 final size:53
Alignment explanation
Indices: 12540717--12540867 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
12540707 ACAAGTGTGC
* **
12540717 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
12540770 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* * *
12540823 CTGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
12540868 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:12545915 original size:25 final size:24
Alignment explanation
Indices: 12545853--12545915 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 24
12545843 CAAGTGGTCC
*
12545853 AACATTGAAAAACTCTTAGGAAAA
1 AACATTGAAAAACACTTAGGAAAA
*
12545877 AGTAGC-TT-ACAAACACTTAGGAAAGA
1 A--A-CATTGAAAAACACTTAGGAAA-A
12545903 AACATTGAAAAAC
1 AACATTGAAAAAC
12545916 TCTTGAAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 11
0.68 0.07 0.25
Matches are distributed among these distances:
23 1 0.03
24 4 0.13
25 19 0.63
26 5 0.17
27 1 0.03
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (24 bp):
AACATTGAAAAACACTTAGGAAAA
Found at i:12547245 original size:16 final size:15
Alignment explanation
Indices: 12547221--12547270 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
12547211 TAAAGCTTTA
*
12547221 ATTTCATTAAATGATG
1 ATTTTATTAAA-GATG
12547237 ATTTTATT-AAG-TG
1 ATTTTATTAAAGATG
* *
12547250 ATTTTAATAAAAATG
1 ATTTTATTAAAGATG
12547265 ATTTTA
1 ATTTTA
12547271 GGACCTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 9 0.31
14 3 0.10
15 10 0.34
16 7 0.24
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (15 bp):
ATTTTATTAAAGATG
Found at i:12547892 original size:47 final size:47
Alignment explanation
Indices: 12547830--12548063 Score: 245
Period size: 47 Copynumber: 4.9 Consensus size: 47
12547820 TTGCAACATA
*
12547830 TGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG
1 TGATATGTG-CTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG
* *
12547878 TGATATGTGCTTCCGTATAAGACCATAACTGGACTATGGCATCAGTGTGATG
1 TGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCA----G-TG
* * * * *
12547930 TGATTATGTGCTTCCGTATAATACCATATCTGGGATATAGCATCAATG
1 TGA-TATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG
** * ** *
12547978 TGATATGTGCTTCTATGTAAGACCATATTTGGGATATGGCATCAGTG
1 TGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG
* * *
12548025 TGATATGTG-ATCCGTGTAAGACCATGGCTGGGCTATGGC
1 TGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGC
12548064 TTCGGTGTAT
Statistics
Matches: 157, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
46 23 0.15
47 78 0.50
48 14 0.09
51 1 0.01
52 5 0.03
53 36 0.23
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (47 bp):
TGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG
Found at i:12547956 original size:100 final size:100
Alignment explanation
Indices: 12547841--12548028 Score: 270
Period size: 100 Copynumber: 1.9 Consensus size: 100
12547831 GATATGTGAT
* * * *
12547841 TTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTGTGATATGTGCTTCCGTATAAGACCATAA
1 TTCCGTATAAGACCATAGCTGGGATATAGCATCAATGTGATATGTGCTTCCATATAAGACCATAA
12547906 CT-GGACTATGGCATCAGTGTGATGTGATTATGTGC
66 CTGGGA-TATGGCATCAGTGTGATGTGATTATGTGC
* * * * *
12547941 TTCCGTATAATACCATATCTGGGATATAGCATCAATGTGATATGTGCTTCTATGTAAGACCATAT
1 TTCCGTATAAGACCATAGCTGGGATATAGCATCAATGTGATATGTGCTTCCATATAAGACCATAA
*
12548006 TTGGGATATGGCATCAGTGTGAT
66 CTGGGATATGGCATCAGTGTGAT
12548029 ATGTGATCCG
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 74 0.96
101 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (100 bp):
TTCCGTATAAGACCATAGCTGGGATATAGCATCAATGTGATATGTGCTTCCATATAAGACCATAA
CTGGGATATGGCATCAGTGTGATGTGATTATGTGC
Found at i:12565869 original size:53 final size:53
Alignment explanation
Indices: 12565788--12565888 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
12565778 GCTCCCAATC
** *
12565788 AATTTCCTTCTTATTGTATTTGCAATCTTTAATTAACTTGTTCATTTCGAGTT
1 AATTTCCTTCTTATTACATTTGCAATCTTTAATTAACTTATTCATTTCGAGTT
* * *
12565841 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAATTTATTCATTTC
1 AATTTCCTTCTTATTACATTTGCAATCTTTAATTAACTTATTCATTTC
12565889 AAGCTATGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (53 bp):
AATTTCCTTCTTATTACATTTGCAATCTTTAATTAACTTATTCATTTCGAGTT
Found at i:12566600 original size:87 final size:86
Alignment explanation
Indices: 12566448--12566609 Score: 188
Period size: 87 Copynumber: 1.9 Consensus size: 86
12566438 GTTATAATGA
* * * * *
12566448 TGAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGCCACTAAACTTTATCTCCCTGAAG
1 TGAATCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAGACACGAAACTTTATCTCCCTGAAG
12566513 -TAGCAGTGGAGCAGGTTGAAT
66 TTA-CAGTGGAGCAGGTTGAAT
* *
12566534 TGAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAGATAGCGAATCTCATT-T-TCCC-
1 TGAA-TCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAGACA-CGAAACT--TTATCTCCCT
12566596 GAAGTTACAGTGGA
62 GAAGTTACAGTGGA
12566610 ATAGATTGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
86 4 0.06
87 46 0.72
88 11 0.17
89 1 0.02
90 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (86 bp):
TGAATCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAGACACGAAACTTTATCTCCCTGAAG
TTACAGTGGAGCAGGTTGAAT
Found at i:12566843 original size:164 final size:169
Alignment explanation
Indices: 12566567--12567056 Score: 641
Period size: 164 Copynumber: 2.9 Consensus size: 169
12566557 GCAGTGGAGC
* *
12566567 AGACTGAAGATAGCGAATCTCATTTTCCC-GAAGTTACAGTGGAATAGATTGAAGCTATAAATAA
1 AGACTGAAGATAGCGAATCTCA-TTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATAA
* * * * * * **
12566631 ACAGATCTTATCTCTCTGAAGTTACAGTTGAGCAGATCATAGCAAACCTCATCTGCTTTTAGTAG
65 ATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTAAAGTAG
*
12566696 CAGTGGAGCAGGTTGAAATTAAATTCTTATCT-C-T-C-T
130 CAGTGGAGCAGGTTGAAATTAAAGTCTTATCTCCGTCCGT
* *
12566732 A-ACTGAAGATAGCGAATCTCATTTCCCTGAAGCTGCAGTGGAACAAATTGAAGCTATAAATAAA
1 AGACTGAAGATAGCGAATCTCATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATAAA
* * *
12566796 TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAACAAACCTTATCTCCCTGAACTAGC
66 TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTAAAGTAGC
*
12566861 AATGGAGCAGGTTGAAATTAAAGTCTTATCTCCCGGAAGTTGCCGTGGAAT
131 AGTGGAGCAGGTTGAAATTAAAGTCTTATCT-CC----G-T-CC---G--T
*
12566912 AGACTGAAGATAGCGAATCTCATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAGTAAA
1 AGACTGAAGATAGCGAATCTCATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATAAA
* *
12566977 TAGATCTTATATCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTAAAGTTGC
66 TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTAAAGTAGC
12567042 AGTGGAGCAGGTTGA
131 AGTGGAGCAGGTTGA
12567057 TGTCACAAAT
Statistics
Matches: 282, Mismatches: 25, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
163 6 0.02
164 136 0.48
165 1 0.00
166 1 0.00
172 1 0.00
174 1 0.00
180 2 0.01
181 134 0.48
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (169 bp):
AGACTGAAGATAGCGAATCTCATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATAAA
TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACCTTATCTCCCTAAAGTAGC
AGTGGAGCAGGTTGAAATTAAAGTCTTATCTCCGTCCGT
Found at i:12567179 original size:44 final size:44
Alignment explanation
Indices: 12567113--12567207 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 44
12567103 TACCATGGCG
*
12567113 AATCTTGTCTCCCTAAAAGTGCAGTGGAGCAGATTGAAGCCACA
1 AATCTTATCTCCCTAAAAGTGCAGTGGAGCAGATTGAAGCCACA
* * * *
12567157 AATCTTATCTCCTTGAAGGTGCAGTGGAGTAGATTGAAGCCACA
1 AATCTTATCTCCCTAAAAGTGCAGTGGAGCAGATTGAAGCCACA
12567201 AATCTTA
1 AATCTTA
12567208 AATTGCAGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAAGTGCAGTGGAGCAGATTGAAGCCACA
Found at i:12567225 original size:35 final size:35
Alignment explanation
Indices: 12567176--12567242 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
12567166 TCCTTGAAGG
* *
12567176 TGCAGTGGAGTAGATTGAAGCCACAAATCTTAAAT
1 TGCAGTAGAATAGATTGAAGCCACAAATCTTAAAT
* * *
12567211 TGCAGTAGAATAGATTGGAGTCACTAATCTTA
1 TGCAGTAGAATAGATTGAAGCCACAAATCTTA
12567243 TCCCCTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (35 bp):
TGCAGTAGAATAGATTGAAGCCACAAATCTTAAAT
Found at i:12575915 original size:15 final size:16
Alignment explanation
Indices: 12575897--12575929 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12575887 TTTACTATTC
*
12575897 TTTC-ATTTTTTTTAT
1 TTTCAATTTTTTTCAT
12575912 TTTCAATTTTTTTCAT
1 TTTCAATTTTTTTCAT
12575928 TT
1 TT
12575930 ATCTAGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCAATTTTTTTCAT
Found at i:12576060 original size:3 final size:3
Alignment explanation
Indices: 12576052--12576095 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
12576042 CATTGTTCTC
12576052 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12576096 ATCTATTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12576182 original size:3 final size:3
Alignment explanation
Indices: 12576174--12576200 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12576164 TACTCACACA
12576174 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
12576201 GTGTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12578750 original size:50 final size:50
Alignment explanation
Indices: 12578693--12578794 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
12578683 TCAATTGAGT
12578693 TAATTTTTTATTGACTCTTAATTCTAATTTAATCAGATTTAAATATAGTA
1 TAATTTTTTATTGACTCTTAATTCTAATTTAATCAGATTTAAATATAGTA
12578743 TAATTTTTTATTGACTCTTAATTCTAATTTAATCAGATTTAAATATAGTA
1 TAATTTTTTATTGACTCTTAATTCTAATTTAATCAGATTTAAATATAGTA
12578793 TA
1 TA
12578795 GATAGAGATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (50 bp):
TAATTTTTTATTGACTCTTAATTCTAATTTAATCAGATTTAAATATAGTA
Found at i:12584778 original size:27 final size:27
Alignment explanation
Indices: 12584759--12584813 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
12584749 AAAAGAGTCA
12584759 AATTCTATGAAGATATAAAAAACACAT
1 AATTCTATGAAGATATAAAAAACACAT
12584786 AATTCTATGAAGATATAAAAAACACAT
1 AATTCTATGAAGATATAAAAAACACAT
12584813 A
1 A
12584814 CACCCCACAA
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:0.56, C:0.11, G:0.07, T:0.25
Consensus pattern (27 bp):
AATTCTATGAAGATATAAAAAACACAT
Found at i:12596445 original size:309 final size:305
Alignment explanation
Indices: 12595887--12596506 Score: 915
Period size: 309 Copynumber: 2.0 Consensus size: 305
12595877 GGAAAGGACC
* *
12595887 CCAAAAAATTATTTCTTCAAAAGTGAAGAAAACTCTTCATCTTCTAAGCTTTTTGATACATTACA
1 CCAAAAAAATATTTCTTCAAAAGTGAAAAAAACTCTTCATCTTCTAAGCTTTTTGATACATTACA
** *
12595952 GGCAGGAAAAAAAAAACAGAGGAGTTCATTGCAGTAGGAAAAAAAAAGGAAAAAAATAAAATAGA
66 AACAGGAAAAAAAAAACAGAGGAGTTCATTGCAGTAGGAAAAAAAAAGGAAAAAAATAAAAGAGA
* * *
12596017 CTTTCAATTCTTCCCCTTCATCTCCAACTCTTTGACTTCTCAAACCTCTTTTGGTTACTAAATTT
131 CTTTCAATTCTTCCCCTTCATCTCCAACTCCTTGACTTCTCAAACCACTTCTGGTTACTAAATTT
12596082 CAACTCCTACCATTAAAGCTAAAAACAATTTCATCCCCCTCCACCCCAAAAA-AAATCAACCATT
196 CAACTCCTACCATTAAAGCTAAAAACAATTTCATCCCCCTCCACCCCAAAAAGAAATCAACCATT
*
12596146 ACTAGCATTGTTGCAGGTATAATTCATTAATTCCCCCTCCTTCCT
261 ACTAGCACTGTTGCAGGTATAATTCATTAATTCCCCCTCCTTCCT
*
12596191 CCAAAAAAATATTTCTTCAAAAGTGAAAAAAACTCTTCATCTTCTAGGCTTTTTGATACATTACA
1 CCAAAAAAATATTTCTTCAAAAGTGAAAAAAACTCTTCATCTTCTAAGCTTTTTGATACATTACA
* ** *
12596256 AATAGGAAAAAAAAAAACAGAGGAGTTCATTTTAGTA-G-AAAAGAAAGGAAAAAAATAAAAGAG
66 AACAGG-AAAAAAAAAACAGAGGAGTTCATTGCAGTAGGAAAAAAAAAGGAAAAAAATAAAAGAG
* *
12596319 ACTTTCAATTATTCCCCTTCCCCTTCATCTCTAACTCCTTGACTTCTCAAATCACTTCTGGTTAC
130 ACTTTC-A--ATT---CTTCCCCTTCATCTCCAACTCCTTGACTTCTCAAACCACTTCTGGTTAC
* * *
12596384 TAAATTTCAACTCCTATCATTAAAGTTAAAAACAATTTCATTCCCCTCC-CTCCTCAAAAAAAAA
189 TAAATTTCAACTCCTACCATTAAAGCTAAAAACAATTTCATCCCCCTCCAC-CC-C----AAAAA
*
12596448 GAAATCAACCATTACTAGCACTGTTGTAGGTATAATTCATTAATTCCCCCTCCTTCCT
248 GAAATCAACCATTACTAGCACTGTTGCAGGTATAATTCATTAATTCCCCCTCCTTCCT
12596506 C
1 C
12596507 TTTGTAACTT
Statistics
Matches: 282, Mismatches: 20, Indels: 17
0.88 0.06 0.05
Matches are distributed among these distances:
303 29 0.10
304 67 0.24
305 28 0.10
306 3 0.01
308 1 0.00
309 92 0.33
310 1 0.00
314 5 0.02
315 56 0.20
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (305 bp):
CCAAAAAAATATTTCTTCAAAAGTGAAAAAAACTCTTCATCTTCTAAGCTTTTTGATACATTACA
AACAGGAAAAAAAAAACAGAGGAGTTCATTGCAGTAGGAAAAAAAAAGGAAAAAAATAAAAGAGA
CTTTCAATTCTTCCCCTTCATCTCCAACTCCTTGACTTCTCAAACCACTTCTGGTTACTAAATTT
CAACTCCTACCATTAAAGCTAAAAACAATTTCATCCCCCTCCACCCCAAAAAGAAATCAACCATT
ACTAGCACTGTTGCAGGTATAATTCATTAATTCCCCCTCCTTCCT
Found at i:12596806 original size:6 final size:6
Alignment explanation
Indices: 12596795--12596819 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12596785 CCTCATTTTC
12596795 CCTCTA CCTCTA CCTCTA CCTCTA C
1 CCTCTA CCTCTA CCTCTA CCTCTA C
12596820 AGCTTTTTAT
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:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTCTA
Found at i:12604883 original size:17 final size:16
Alignment explanation
Indices: 12604845--12604887 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
12604835 ATATAGTGTT
*
12604845 TCAATAGTTATAAATA
1 TCAAAAGTTATAAATA
12604861 --AAAAGTTATAAATAA
1 TCAAAAGTTATAAAT-A
12604876 TCAAAAGTTATA
1 TCAAAAGTTATA
12604888 TCAATTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 12 0.52
15 1 0.04
17 10 0.43
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
TCAAAAGTTATAAATA
Found at i:12611484 original size:20 final size:20
Alignment explanation
Indices: 12611447--12611484 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12611437 AAATCACATT
*
12611447 AATTAAAAAATTTCAAATCA
1 AATTAAAAAAATTCAAATCA
12611467 AATTAAAATAAATT-AAAT
1 AATTAAAA-AAATTCAAAT
12611485 ATTAACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTAAAAAAATTCAAATCA
Found at i:12613776 original size:6 final size:6
Alignment explanation
Indices: 12613760--12613799 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
12613750 ATTGGAGTCC
*
12613760 AAAGTA AAA-AA AAA-AA AAAGAA AAAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
12613800 GAGAGGCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:12613789 original size:21 final size:22
Alignment explanation
Indices: 12613760--12613801 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
12613750 ATTGGAGTCC
12613760 AAAGTAAAAAAAAAAAAAAGAA
1 AAAGTAAAAAAAAAAAAAAGAA
* *
12613782 AAAG-AAAAAGAAAAAGAAGA
1 AAAGTAAAAAAAAAAAAAAGA
12613802 GAGGCTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAGTAAAAAAAAAAAAAAGAA
Found at i:12614525 original size:16 final size:16
Alignment explanation
Indices: 12614489--12614523 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12614479 AGTCATTATA
12614489 TTTTATTTTTGATGAT
1 TTTTATTTTTGATGAT
*
12614505 TTTTATTTTTTAT-AT
1 TTTTATTTTTGATGAT
12614520 TTTT
1 TTTT
12614524 TAAAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTATTTTTGATGAT
Found at i:12614960 original size:19 final size:18
Alignment explanation
Indices: 12614920--12614962 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12614910 GTTGGAATTA
*
12614920 ATAATAAAAATAAAATAT
1 ATAATAAAAATAAAATAC
* *
12614938 ATAATTAAACTAAAAGTAC
1 ATAATAAAAATAAAA-TAC
12614957 ATAATA
1 ATAATA
12614963 TTAAAACTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (18 bp):
ATAATAAAAATAAAATAC
Found at i:12616361 original size:39 final size:39
Alignment explanation
Indices: 12616302--12616385 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
12616292 ATAGATTAGT
*
12616302 GCTAAGTGTTTCTGAACATGGTAGAGTAATAGGTGGATA
1 GCTATGTGTTTCTGAACATGGTAGAGTAATAGGTGGATA
*
12616341 GTTATGTGTTTCTGAACATGGTAGAGTAATAGGTGGATA
1 GCTATGTGTTTCTGAACATGGTAGAGTAATAGGTGGATA
12616380 GCTATG
1 GCTATG
12616386 GAATCTACTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (39 bp):
GCTATGTGTTTCTGAACATGGTAGAGTAATAGGTGGATA
Found at i:12621424 original size:56 final size:57
Alignment explanation
Indices: 12621319--12621426 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 57
12621309 GCTTGTTAGT
* * *
12621319 GTTCAGATTCTGGGTAAATGCTTTTATCTGAATTGATATAATTTCTTATAATTGTGC
1 GTTCAGATTCTGGATAAATGCTTTTATCTGAACTGACATAATTTCTTATAATTGTGC
* * *
12621376 GTTCAGATT-TTGATAAATGCTTTTATCT-AAGCTGACATATTTTGTTATAAT
1 GTTCAGATTCTGGATAAATGCTTTTATCTGAA-CTGACATAATTTCTTATAAT
12621427 CTTGCAGATG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 2 0.05
56 33 0.75
57 9 0.20
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (57 bp):
GTTCAGATTCTGGATAAATGCTTTTATCTGAACTGACATAATTTCTTATAATTGTGC
Found at i:12634387 original size:21 final size:21
Alignment explanation
Indices: 12634361--12634401 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12634351 AGACGAGCAA
* *
12634361 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
12634382 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
12634402 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:12658620 original size:3 final size:3
Alignment explanation
Indices: 12658612--12658647 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
12658602 GCCTCAATGG
12658612 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12658648 TGTTAATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12664245 original size:25 final size:25
Alignment explanation
Indices: 12664211--12664261 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12664201 ATGCATATAA
12664211 ACAAATCATTTCAAATTGGATTGAT
1 ACAAATCATTTCAAATTGGATTGAT
12664236 ACAAATCATTTCAAATTGGATTGAT
1 ACAAATCATTTCAAATTGGATTGAT
12664261 A
1 A
12664262 AGAAGAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (25 bp):
ACAAATCATTTCAAATTGGATTGAT
Found at i:12664457 original size:16 final size:17
Alignment explanation
Indices: 12664436--12664476 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
12664426 AATTGTAAAG
12664436 AAAATTAGAA-AGATGA
1 AAAATTAGAAGAGATGA
*
12664452 AAAATTA-AAGGGATGA
1 AAAATTAGAAGAGATGA
*
12664468 AAAAATAGA
1 AAAATTAGA
12664477 TAAATGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 18 0.86
17 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (17 bp):
AAAATTAGAAGAGATGA
Found at i:12664928 original size:29 final size:29
Alignment explanation
Indices: 12664895--12664960 Score: 109
Period size: 27 Copynumber: 2.3 Consensus size: 29
12664885 ATTCATTTTT
*
12664895 ATTACAATGTAAATTTTTTTAGTTATATG
1 ATTACCATGTAAATTTTTTTAGTTATATG
12664924 ATTACCA--TAAATTTTTTTAGTTATATG
1 ATTACCATGTAAATTTTTTTAGTTATATG
12664951 ATTACCATGT
1 ATTACCATGT
12664961 GAGCTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 27 0.79
29 7 0.21
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (29 bp):
ATTACCATGTAAATTTTTTTAGTTATATG
Found at i:12664935 original size:27 final size:27
Alignment explanation
Indices: 12664904--12664958 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
12664894 TATTACAATG
12664904 TAAATTTTTTTAGTTATATGATTACCA
1 TAAATTTTTTTAGTTATATGATTACCA
12664931 TAAATTTTTTTAGTTATATGATTACCA
1 TAAATTTTTTTAGTTATATGATTACCA
12664958 T
1 T
12664959 GTGAGCTTTT
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:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (27 bp):
TAAATTTTTTTAGTTATATGATTACCA
Found at i:12677023 original size:46 final size:46
Alignment explanation
Indices: 12676973--12677239 Score: 235
Period size: 46 Copynumber: 5.8 Consensus size: 46
12676963 TTTGGGCATT
*
12676973 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
* * *
12677019 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--TC
* * *
12677066 CGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGGC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
* * * *
12677112 CGAACTCATTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--TC
* * * *
12677159 CGAGCTCGTTGAGTTGAGTCTGAGTTTACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
* *
12677205 CGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12677240 GCGGGTTACA
Statistics
Matches: 175, Mismatches: 28, Indels: 36
0.73 0.12 0.15
Matches are distributed among these distances:
42 6 0.03
43 8 0.05
45 6 0.03
46 85 0.49
47 50 0.29
48 6 0.03
50 8 0.05
51 6 0.03
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
Found at i:12677078 original size:93 final size:93
Alignment explanation
Indices: 12676967--12677232 Score: 451
Period size: 93 Copynumber: 2.9 Consensus size: 93
12676957 CGGATATTTG
* * * **
12676967 GGCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTTCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12677032 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
12677060 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGGCCGAACTCATTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12677125 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
12677153 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTTACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12677218 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
12677233 CTTATGGGCG
Statistics
Matches: 163, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 163 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Done.