Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 411 of 438
Found at i:127749646 original size:3 final size:3
Alignment explanation
Indices: 127749640--127749856 Score: 74
Period size: 3 Copynumber: 72.3 Consensus size: 3
127749630 AAAATACAAC
* * *
127749640 AAT AAT AAT AGT AA- AAG ATAT AAT AACCT AAT AAT -AT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AA--T AAT AAT AAT AAT AAT AAT
* * * * * * * *
127749686 AGT AAC AAT -AT GAC GAT AAT AGT AAA AAT AAT -AT ATT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
* * *
127749730 AGT AAT AAT AAT AAT AAT ATAT AAT AAT AAT AAT AAT -CT ATT AAGT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA-T
* * * * * *
127749776 TAT AAT GAA- AAT AAT GAT AAT GAT GAT -AT ATT AGAT AAT AAT AGT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * * *
127749821 AA- AAT AAT -AT AGT AAC AAT GAT AAAT TAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A
127749857 GTGATGAGAA
Statistics
Matches: 156, Mismatches: 40, Indels: 36
0.67 0.17 0.16
Matches are distributed among these distances:
2 17 0.11
3 121 0.78
4 15 0.10
5 3 0.02
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:127749646 original size:22 final size:22
Alignment explanation
Indices: 127749595--127749655 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
127749585 ATAAGTAAAT
* *
127749595 ACAAAAATAA-AGGAAAATATA
1 ACAAAAATAATAGAAAAATACA
* *
127749616 ATAACAATAATAGAAAAATACA
1 ACAAAAATAATAGAAAAATACA
* *
127749638 ACAATAATAATAGTAAAA
1 ACAAAAATAATAGAAAAA
127749656 GATATAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (22 bp):
ACAAAAATAATAGAAAAATACA
Found at i:127749877 original size:16 final size:16
Alignment explanation
Indices: 127749856--127749887 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
127749846 TTATAATAAT
127749856 AGTGATGAGAATAACA
1 AGTGATGAGAATAACA
*
127749872 AGTGATGATAATAACA
1 AGTGATGAGAATAACA
127749888 GTAACAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (16 bp):
AGTGATGAGAATAACA
Found at i:127750019 original size:16 final size:16
Alignment explanation
Indices: 127749990--127750027 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
127749980 TATACGTATG
*
127749990 AAAA-ATAATGATAGT
1 AAAATATAATAATAGT
127750005 AAAATATAATAATAGT
1 AAAATATAATAATAGT
127750021 AATAATA
1 AA-AATA
127750028 ACAATGGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 12 0.60
17 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (16 bp):
AAAATATAATAATAGT
Found at i:127750137 original size:3 final size:3
Alignment explanation
Indices: 127750129--127750165 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
127750119 ACACTACCAT
127750129 ATA ATA ATA ATA ATA AT- ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
127750166 TAGAAATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:127750255 original size:14 final size:14
Alignment explanation
Indices: 127750208--127750259 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
127750198 TTTAAAAAAC
*
127750208 AATACTATATATAAA
1 AATA-TATACATAAA
* *
127750223 AGTATATACATACA
1 AATATATACATAAA
* *
127750237 TATATGTACATAAA
1 AATATATACATAAA
127750251 AATATATAC
1 AATATATAC
127750260 TAATATATAA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
14 25 0.89
15 3 0.11
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (14 bp):
AATATATACATAAA
Found at i:127750274 original size:3 final size:3
Alignment explanation
Indices: 127750246--127750304 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
127750236 ATATATGTAC
* *
127750246 ATA AAA ATA TATA CTA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
127750293 ATA ATA ATA ATA
1 ATA ATA ATA ATA
127750305 TTAAAATGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:127750829 original size:24 final size:25
Alignment explanation
Indices: 127750775--127750842 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 25
127750765 AATCTCAAAA
* *
127750775 AAAAAAAAAATCCCCTCTTGAATCT
1 AAAAAAAAAATCTCTTCTTGAATCT
127750800 CAAAAAAAAAATCTCTTCTTGAATCT
1 -AAAAAAAAAATCTCTTCTTGAATCT
127750826 -AAAAAAAAATCTCTTCT
1 AAAAAAAAAATCTCTTCT
127750843 CTCCAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 17 0.43
26 23 0.57
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.28
Consensus pattern (25 bp):
AAAAAAAAAATCTCTTCTTGAATCT
Found at i:127751117 original size:20 final size:20
Alignment explanation
Indices: 127751090--127751130 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
127751080 TTTTCTTTTT
127751090 TTTGTTTTTTG-TTTGGGTA
1 TTTGTTTTTTGTTTTGGGTA
127751109 TTTGTTTTTTGTTTTGGGTA
1 TTTGTTTTTTGTTTTGGGTA
127751129 TT
1 TT
127751131 GGGCTAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.05, C:0.00, G:0.24, T:0.71
Consensus pattern (20 bp):
TTTGTTTTTTGTTTTGGGTA
Found at i:127752739 original size:19 final size:18
Alignment explanation
Indices: 127752715--127752750 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
127752705 ACTTGAAGGT
127752715 TTTTTTTAAGTAATTCATA
1 TTTTTTTAA-TAATTCATA
127752734 TTTTTTTAATAATTCAT
1 TTTTTTTAATAATTCAT
127752751 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTTTTAATAATTCATA
Found at i:127753503 original size:10 final size:9
Alignment explanation
Indices: 127753485--127753514 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
127753475 AACTCTTCTT
127753485 AATAAAAAA
1 AATAAAAAA
127753494 AATAAAAAA
1 AATAAAAAA
127753503 AATAAAACAA
1 AATAAAA-AA
127753513 AA
1 AA
127753515 GTATGATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (9 bp):
AATAAAAAA
Found at i:127755939 original size:15 final size:15
Alignment explanation
Indices: 127755919--127755948 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
127755909 TTTGGCTTGC
127755919 ATGCAAGTATTATTT
1 ATGCAAGTATTATTT
*
127755934 ATGCAATTATTATTT
1 ATGCAAGTATTATTT
127755949 TTTAATGATG
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:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (15 bp):
ATGCAAGTATTATTT
Found at i:127759753 original size:42 final size:42
Alignment explanation
Indices: 127759689--127759774 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
127759679 TGTTATTATT
127759689 TTTACCATTTCAGTCAAAATGTGCTGCTAAACTCTAGCATAC
1 TTTACCATTTCAGTCAAAATGTGCTGCTAAACTCTAGCATAC
* *
127759731 TTTATCATTTCAGTCAACATGTGCTGCTAAACTCTAGCATAC
1 TTTACCATTTCAGTCAAAATGTGCTGCTAAACTCTAGCATAC
127759773 TT
1 TT
127759775 CGGTTGAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (42 bp):
TTTACCATTTCAGTCAAAATGTGCTGCTAAACTCTAGCATAC
Found at i:127759905 original size:23 final size:23
Alignment explanation
Indices: 127759875--127759920 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
127759865 AAGCGTAGCA
127759875 GAAGCAGATATTGTTAAATCTAT
1 GAAGCAGATATTGTTAAATCTAT
127759898 GAAGCAGATATTGTTAAATCTAT
1 GAAGCAGATATTGTTAAATCTAT
127759921 CATCACGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (23 bp):
GAAGCAGATATTGTTAAATCTAT
Found at i:127774821 original size:21 final size:21
Alignment explanation
Indices: 127774779--127774823 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
127774769 TTTTTTTAAT
*
127774779 ATTTTTAACAATTGAAACTAA
1 ATTTTTAACAATTGAAAATAA
*
127774800 ATTTTTAA-ATTTGAAAAATAA
1 ATTTTTAACAATTG-AAAATAA
127774821 ATT
1 ATT
127774824 ATGACATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (21 bp):
ATTTTTAACAATTGAAAATAA
Found at i:127775413 original size:52 final size:52
Alignment explanation
Indices: 127775339--127775588 Score: 164
Period size: 53 Copynumber: 4.7 Consensus size: 52
127775329 AATTTATAAT
* * *
127775339 AAAAAATTAGGTGCTGTGACACTGATGACCTGCACCCTTGTACTAGA-TTAA
1 AAAAAATTGGGTGCTGAGACACTGATGACCTGCACCCTTGTACCAGATTTAA
* * *
127775390 AAAAAATTGGGTTGCTGAGACACTGATGATCGGCA-CCTTAGTACCAAATTTTAAAA
1 AAAAAATTGGG-TGCTGAGACACTGATGACCTGCACCCTT-GTACCAGA-TTT--AA
* * * * *
127775446 AAAAAATTGAGTGCTGAAATACTGATG-GCTGACACCGTTGTACCAGATTTAA
1 AAAAAATTGGGTGCTGAGACACTGATGACCTG-CACCCTTGTACCAGATTTAA
* * * * * * * * * * *
127775498 AAAAAATTTAGTTGTTGGGGCACTAATGGCCAGCACTCTTCTACGAGATTTAA
1 AAAAAA-TTGGGTGCTGAGACACTGATGACCTGCACCCTTGTACCAGATTTAA
* * * * *
127775551 AAAAATTTTAGGTGCTGAAACATTGATGGCCTGCACCC
1 AAAAA-ATTGGGTGCTGAGACACTGATGACCTGCACCC
127775589 CAATGTTAGG
Statistics
Matches: 150, Mismatches: 38, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
51 14 0.09
52 34 0.23
53 55 0.37
54 9 0.06
55 23 0.15
56 15 0.10
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (52 bp):
AAAAAATTGGGTGCTGAGACACTGATGACCTGCACCCTTGTACCAGATTTAA
Found at i:127776117 original size:49 final size:49
Alignment explanation
Indices: 127776041--127776134 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 49
127776031 CAGCACCCAA
* *
127776041 ACTTTTTTTTTAAATTTGCTATAAGGGTGTTGGTC-ATTAGTGTCCTAAC
1 ACTTTTTTTTTAAATCTGCTATAAGGGTGCTGG-CAATTAGTGTCCTAAC
*
127776090 ACTTTTTTTTTAAATCTGGTACT-AGGGTGCTGGCAATTAGTGTCC
1 ACTTTTTTTTTAAATCTGCTA-TAAGGGTGCTGGCAATTAGTGTCC
127776135 CATCACCCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
48 1 0.03
49 38 0.95
50 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (49 bp):
ACTTTTTTTTTAAATCTGCTATAAGGGTGCTGGCAATTAGTGTCCTAAC
Found at i:127785454 original size:21 final size:21
Alignment explanation
Indices: 127785404--127785454 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
127785394 GATAATATTT
* *
127785404 TATAATAAATAGTAAGTTATA
1 TATAATTAATAATAAGTTATA
127785425 TA-AATTTAATAATAA-TTAATA
1 TATAA-TTAATAATAAGTT-ATA
127785446 TATAATTAA
1 TATAATTAA
127785455 ATTTTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 4 0.16
21 19 0.76
22 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TATAATTAATAATAAGTTATA
Found at i:127785573 original size:23 final size:24
Alignment explanation
Indices: 127785546--127785601 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
127785536 CGATTTAAAC
*
127785546 AAATATTTATA-TTTATATTATTA
1 AAATATTTATATTTTATATTATAA
*
127785569 AAATATTAATATTTTATATTATAA
1 AAATATTTATATTTTATATTATAA
*
127785593 AAATGTTTA
1 AAATATTTA
127785602 ATATGAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATATTTATATTTTATATTATAA
Found at i:127788671 original size:15 final size:17
Alignment explanation
Indices: 127788650--127788690 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
127788640 TAATATTTTA
127788650 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
127788666 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
127788682 AAAATTATA
1 AAAATTATA
127788691 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:127791368 original size:9 final size:9
Alignment explanation
Indices: 127791354--127791390 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
127791344 TATAGTTTGA
127791354 TATTCGAAT
1 TATTCGAAT
127791363 TATTCGAAT
1 TATTCGAAT
*
127791372 TATTCGAGT
1 TATTCGAAT
127791381 TATTCGAAT
1 TATTCGAAT
127791390 T
1 T
127791391 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:127794111 original size:30 final size:30
Alignment explanation
Indices: 127794072--127794133 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
127794062 TACATGAAAT
127794072 ACATGGAAAT-GAT-ATTACATGATATATTGAA
1 ACATGGAAATGGATGA-TACATG-TATA-TGAA
127794103 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATGGAAATGGATGATACATGTATATGAA
127794132 AC
1 AC
127794134 TTGCTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.21
30 9 0.31
31 13 0.45
32 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (30 bp):
ACATGGAAATGGATGATACATGTATATGAA
Found at i:127801737 original size:38 final size:38
Alignment explanation
Indices: 127801688--127801762 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
127801678 TGATATGAAA
127801688 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
127801726 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCT
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCT
127801763 AATATGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (38 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:127801793 original size:46 final size:46
Alignment explanation
Indices: 127801729--127801896 Score: 203
Period size: 46 Copynumber: 3.7 Consensus size: 46
127801719 CAACCTGTGT
* * * *
127801729 GTAAGACCATGGTTGAAAGATACCATGGCAACCTAATATGAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGA
* * * *
127801775 GTAAGACCATGGTTGAAAGATACTATGACAACGTGACATGAAAAGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGA
* *
127801821 ATAAGACCATGGTTGAAAGATACCATGGCAATATGACA-GAAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGA
* * *
127801867 GTAAGACCATAGTTGAAAGACACTATGGCA
1 GTAAGACCATGGTTGAAAGATACCATGGCA
127801897 TCACGTCAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
45 1 0.01
46 103 0.99
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
GTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGA
Found at i:127802201 original size:23 final size:25
Alignment explanation
Indices: 127802156--127802202 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
127802146 AATAAATATA
*
127802156 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
127802181 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
127802203 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:127813207 original size:12 final size:12
Alignment explanation
Indices: 127813190--127813214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
127813180 TCCAAATACT
127813190 AAATATATAATA
1 AAATATATAATA
127813202 AAATATATAATA
1 AAATATATAATA
127813214 A
1 A
127813215 TTTTTTTTCA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATATATAATA
Found at i:127813400 original size:19 final size:20
Alignment explanation
Indices: 127813376--127813422 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
127813366 TTAAAAATAT
*
127813376 TTTTAAATATTTTTA-T-AA
1 TTTTAAATAATTTTAGTAAA
127813394 TTGTTAAATAATTTTAGTAAA
1 TT-TTAAATAATTTTAGTAAA
127813415 TTTTAAAT
1 TTTTAAAT
127813423 TTTAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 12 0.48
20 7 0.28
21 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTAAATAATTTTAGTAAA
Found at i:127818834 original size:3 final size:3
Alignment explanation
Indices: 127818826--127819178 Score: 127
Period size: 3 Copynumber: 116.0 Consensus size: 3
127818816 TAATTTAATA
* * * *
127818826 TAT TAT TAT TAT TATT TCT TCT TAT TAT TAT TAT T-T TAC TGT TACT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * * *
127818872 TA- TATT TAT TAT CAT TAC TAT TAT TAC TAT TA- TAT TAC TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
127818916 TAT T-T TCAC TAT CT-T CAT TAT TAT TAT TAC TAT TAT TAT T-T TCAT
1 TAT TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
* * ** * * * * *
127818961 TAT CTAC TAC TAT TATT TAT TAT CGT TAT TAC CAT TAT CAT TAC TGT
1 TAT -TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
127819008 TACT TA- TAT T-T TAT TAT TAT GAT TAT TGT TTT TATT TAT TATT TAT
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT
* * * * * *
127819054 AAT GTGGT TGT TAT TAT TAT TAT TAT TAT TAT TAAT TAC TGT TAC TAT
1 TAT -T-AT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
* * **
127819102 TAT T-T CTTT TAT TAT T-T AAT ATAT TAT TAT TAT CCT GT-T TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT
* * * * *
127819147 TGT TAT TAC TAT T-G TAC TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
127819179 ACTTTCACCT
Statistics
Matches: 255, Mismatches: 66, Indels: 58
0.67 0.17 0.15
Matches are distributed among these distances:
2 18 0.07
3 204 0.80
4 32 0.13
5 1 0.00
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:127818839 original size:22 final size:21
Alignment explanation
Indices: 127818814--127818863 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 21
127818804 AATTAAATTA
127818814 ATTAATTTAATATATTATTATT
1 ATTAATTTAAT-TATTATTATT
* *
127818836 ATT-ATTT-CTTCTTATTATT
1 ATTAATTTAATTATTATTATT
*
127818855 ATTATTTTA
1 ATTAATTTA
127818864 CTGTTACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
19 12 0.52
20 4 0.17
21 4 0.17
22 3 0.13
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTAATTTAATTATTATTATT
Found at i:127818969 original size:22 final size:21
Alignment explanation
Indices: 127818938--127818978 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
127818928 CTTCATTATT
*
127818938 ATTATTACTATTATTATTTTC
1 ATTATTACTACTATTATTTTC
127818959 ATTATCTACTACTATTATTT
1 ATTAT-TACTACTATTATTT
127818979 ATTATCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTACTACTATTATTTTC
Found at i:127819229 original size:19 final size:16
Alignment explanation
Indices: 127819190--127819237 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
127819180 CTTTCACCTA
127819190 TATTT-GTTTTCTTAT
1 TATTTAGTTTTCTTAT
127819205 TATTTAGTTTTCATTTAT
1 TATTTAGTTTTC--TTAT
*
127819223 CTATTTATTTTTCTT
1 -TATTTAGTTTTCTT
127819238 GCCTACTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 5 0.18
16 6 0.21
17 2 0.07
18 4 0.14
19 11 0.39
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.71
Consensus pattern (16 bp):
TATTTAGTTTTCTTAT
Found at i:127823186 original size:31 final size:31
Alignment explanation
Indices: 127823148--127823209 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
127823138 GAACAGTTCA
*
127823148 AAACACCACAATCAGATGAATTTTTTATTTT
1 AAACACCACAATCAGATGAATTTTTGATTTT
127823179 AAACACCACAATCAGATGAATTTTTGATTTT
1 AAACACCACAATCAGATGAATTTTTGATTTT
127823210 TTCTTTATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (31 bp):
AAACACCACAATCAGATGAATTTTTGATTTT
Found at i:127824130 original size:2 final size:2
Alignment explanation
Indices: 127824117--127824154 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
127824107 AGGTTTGAGT
*
127824117 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
127824155 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:127826682 original size:3 final size:3
Alignment explanation
Indices: 127826674--127827055 Score: 156
Period size: 3 Copynumber: 125.7 Consensus size: 3
127826664 CGTAAAAAAT
*
127826674 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GCTAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA TAA
* * * * * *
127826721 CAA TAA T-A TGAA GAAA TAA TAA TAA GAA TAA TGA TAA TTA TAA GACA
1 TAA TAA TAA T-AA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * * * *
127826768 AAA T-A TAA TTA TAG T-A TAA -AA GTAA AAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * * * * * * * *
127826811 TAA TAT TAA TAA AAA GAA TAA AAA AAA CAA TGAA T-G TGA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * * * *
127826856 CATA TAA TAA TAA TGA -AA TAA CAC TAG TAA TAGA -AA TATA TAA -AA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA
* * ** * * *
127826901 TAA CAA TAA TAA TAA TGA T-A TGT TAA CAA TAA TGA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
127826948 TAA CATA TGAA TAA TAA TAGA CTAA TAA TAA CAA TAG TAA AAA TAA -AA
1 TAA TA-A T-AA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
127826996 -AA TAA TAT TAA TGGAA TAA AAA TAA TAT TAA TAA TCA TAC TAA TAA
1 TAA TAA TAA TAA T--AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
127827042 TAA CAA TAA TAA TA
1 TAA TAA TAA TAA TA
127827056 TTAAAATTAA
Statistics
Matches: 276, Mismatches: 77, Indels: 52
0.68 0.19 0.13
Matches are distributed among these distances:
2 18 0.07
3 228 0.83
4 21 0.08
5 9 0.03
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:127826977 original size:17 final size:17
Alignment explanation
Indices: 127826928--127826984 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
127826918 ATATGTTAAC
*
127826928 AATAAT-GA-TAAAAAT
1 AATAATAGACTAATAAT
127826943 AATAATA-AC-ATATGAAT
1 AATAATAGACTA-AT-AAT
127826960 AATAATAGACTAATAAT
1 AATAATAGACTAATAAT
*
127826977 AACAATAG
1 AATAATAG
127826985 TAAAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
15 8 0.24
16 1 0.03
17 20 0.59
18 4 0.12
19 1 0.03
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.26
Consensus pattern (17 bp):
AATAATAGACTAATAAT
Found at i:127829312 original size:14 final size:15
Alignment explanation
Indices: 127829291--127829332 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
127829281 TTTTTCCTAC
*
127829291 TATTTATTATGCTAT
1 TATTTATTATACTAT
127829306 T-TTTATTATACTAT
1 TATTTATTATACTAT
127829320 TATTTATTATACT
1 TATTTATTATACT
127829333 TATCATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTTATTATACTAT
Found at i:127833639 original size:24 final size:24
Alignment explanation
Indices: 127833612--127833664 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
127833602 TCAGAGGTTT
*
127833612 GAGCAAATGCAAAAGGAGATGCAA
1 GAGCAAATGCAAAAGCAGATGCAA
** *
127833636 GAGCAAATGCAGGATCAGATGCAA
1 GAGCAAATGCAAAAGCAGATGCAA
127833660 GAGCA
1 GAGCA
127833665 GCTAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.15, G:0.30, T:0.09
Consensus pattern (24 bp):
GAGCAAATGCAAAAGCAGATGCAA
Found at i:127833645 original size:12 final size:12
Alignment explanation
Indices: 127833612--127833664 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
127833602 TCAGAGGTTT
127833612 GAGCAAATGCAA
1 GAGCAAATGCAA
* * *
127833624 AAGGAGATGCAA
1 GAGCAAATGCAA
*
127833636 GAGCAAATGCAG
1 GAGCAAATGCAA
* *
127833648 GATCAGATGCAA
1 GAGCAAATGCAA
127833660 GAGCA
1 GAGCA
127833665 GCTAGCTAAG
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.45, C:0.15, G:0.30, T:0.09
Consensus pattern (12 bp):
GAGCAAATGCAA
Found at i:127841323 original size:35 final size:35
Alignment explanation
Indices: 127841256--127841423 Score: 185
Period size: 35 Copynumber: 4.6 Consensus size: 35
127841246 TCCTCATTGA
*** *
127841256 AATACCATACCTACATTTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACA-TTTCACAACTCAGTAT-GGAT
* **
127841292 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
127841332 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
127841367 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
127841402 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
127841424 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
35 74 0.63
36 14 0.12
39 3 0.03
40 27 0.23
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:127841382 original size:75 final size:73
Alignment explanation
Indices: 127841251--127841423 Score: 210
Period size: 75 Copynumber: 2.4 Consensus size: 73
127841241 GGTTTTCCTC
*** * * **
127841251 ATTGAAATACCATACCTACATTTTTTTAACTCGGTATGGGAAATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACA-TTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAAC
127841316 TCAGTATGG
65 TCAGTATGG
*
127841325 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-GGATAATACCATACCTACATTTCACA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGGA-AATACCATACCTACATTTCACA
127841389 ACTCAGTATGG
63 ACTCAGTATGG
127841400 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
127841424 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 2 0.02
74 4 0.05
75 46 0.52
76 15 0.17
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:127848818 original size:35 final size:35
Alignment explanation
Indices: 127848753--127848918 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
127848743 TCCTCATTGA
** *
127848753 AATACCATACCTACATTT-TTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
127848787 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
127848827 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
127848862 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
127848897 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
127848919 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
34 17 0.14
35 71 0.60
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:127848877 original size:75 final size:72
Alignment explanation
Indices: 127848748--127848920 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 72
127848738 GGTTTTCCTC
* * * **
127848748 ATTGAAATACCATACCTACATTTTTA-ACTCGGTATGGGAAATGCCATACCTACATTTCTTAACT
1 ATTGAAATACCATACCTACA-TTTCACACTCAGTATGGGAAATACCATACCTACATTTCACAACT
127848812 CAGTATGG
65 CAGTATGG
127848820 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-GGATAATACCATACCTACATTTCACA
1 A-TTGA-AATACCATACCTACATTTCACA-CTCAGTATGGGA-AATACCATACCTACATTTCACA
127848884 ACTCAGTATGG
62 ACTCAGTATGG
127848895 A-TG--ATACCATACCTACATTTCACACT
1 ATTGAAATACCATACCTACATTTCACACT
127848921 TTGCCATGGA
Statistics
Matches: 91, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
69 2 0.02
70 21 0.23
72 1 0.01
73 10 0.11
74 19 0.21
75 38 0.42
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (72 bp):
ATTGAAATACCATACCTACATTTCACACTCAGTATGGGAAATACCATACCTACATTTCACAACTC
AGTATGG
Found at i:127850350 original size:44 final size:44
Alignment explanation
Indices: 127850296--127850564 Score: 170
Period size: 44 Copynumber: 6.0 Consensus size: 44
127850286 CATTCCAACC
*
127850296 ATCAACCTTATCTTCACTGAGCAGGAGTGAAGCAGGTTAAACAT
1 ATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGTTAAACAT
* * * * * *
127850340 ATTAGCCTTATCTTCACTGAGCAGGGGTGGAGCAAGCTAAGCAT
1 ATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGTTAAACAT
* * * * * *
127850384 AGCAGATCTTATCTTCGCTGAGCAGGAGCGAAGCA-GAT-CACATT
1 ATCAG-CCTTATCTTCACTGAGCAGGAGTGAAGCAGGTTAAACA-T
* * * * * * * * *
127850428 TTCAACAAATCTTATCTCCA-TGTATC-GGTAATGGAGCAGATTCCAAC-C
1 ATCAGC----CTTATCTTCACTG-AGCAGG-AGTGAAGCAGGTT-AAACAT
* * *
127850476 ATCAACCTTATCTTCACTAAGCAGGAGTGAAGCGGGTTAAACAT
1 ATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGTTAAACAT
* * *
127850520 ATCAGCCTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAACAT
1 ATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGTTAAACAT
127850564 A
1 A
127850565 CCAGATTTTA
Statistics
Matches: 164, Mismatches: 47, Indels: 28
0.69 0.20 0.12
Matches are distributed among these distances:
43 5 0.03
44 104 0.63
45 27 0.16
46 4 0.02
47 16 0.10
48 6 0.04
50 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (44 bp):
ATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGTTAAACAT
Found at i:127851939 original size:14 final size:15
Alignment explanation
Indices: 127851918--127851959 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
127851908 TTTTTCCTAC
*
127851918 TATTTATTATGCTAT
1 TATTTATTATACTAT
127851933 T-TTTATTATACTAT
1 TATTTATTATACTAT
127851947 TATTTATTATACT
1 TATTTATTATACT
127851960 TATCATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTTATTATACTAT
Found at i:127852046 original size:28 final size:26
Alignment explanation
Indices: 127851996--127852049 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
127851986 TTTTTCTAAT
* *
127851996 AATTTTTTTTTGTATTATTTATTTTA
1 AATTTTTTTTTCTATTATATATTTTA
127852022 AATTATTTTTTTCTATATATATATTTTA
1 AATT-TTTTTTTCTAT-TATATATTTTA
127852050 TTAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 10 0.42
28 10 0.42
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (26 bp):
AATTTTTTTTTCTATTATATATTTTA
Found at i:127864973 original size:20 final size:19
Alignment explanation
Indices: 127864928--127864976 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
127864918 ATTATATTTT
*
127864928 ATAATTTTTAATACTTATA
1 ATAATTTTTAATACTTAAA
* **
127864947 ATTATTTTTAATTTTCTAAA
1 ATAATTTTTAATACT-TAAA
127864967 ATAATTTTTA
1 ATAATTTTTA
127864977 TATATTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
ATAATTTTTAATACTTAAA
Found at i:127864983 original size:23 final size:22
Alignment explanation
Indices: 127864925--127864988 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 22
127864915 AAAATTATAT
127864925 TTTATAATTTTTAATACTTATAATTA
1 TTTATAATTTTTAA-A---ATAATTA
*
127864951 TTTTTAATTTTCTAAAATAATT-
1 TTTATAATTTT-TAAAATAATTA
127864973 TTTATATATTTTTAAA
1 TTTATA-ATTTTTAAA
127864989 GTTTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 9 0.26
23 11 0.32
26 11 0.32
27 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATAATTTTTAAAATAATTA
Found at i:127868332 original size:18 final size:20
Alignment explanation
Indices: 127868309--127868355 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
127868299 AAGGAGAATG
127868309 ATTAAATTATATAAA-AAA-
1 ATTAAATTATATAAATAAAT
*
127868327 ATTAAAATATATAAATTAAAT
1 ATTAAATTATATAAA-TAAAT
127868348 ATTAAATT
1 ATTAAATT
127868356 TTAACATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.58
20 3 0.12
21 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTAAATTATATAAATAAAT
Found at i:127871643 original size:39 final size:38
Alignment explanation
Indices: 127871597--127871697 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 38
127871587 GCTCTGATGA
*
127871597 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAGCACTTGCGT
1 GCTTCAGTTAGCCTTC-GGCTTCCGTTTAGCACTTACGT
*
127871636 GCTTCAGTTAGCCTTCGGACTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGG-CTTCCGTTTAGCACTTACGT
* *
127871675 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTC-GGCTTC
127871698 AAATCACGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 2 0.04
39 52 0.93
40 2 0.04
ACGTcount: A:0.14, C:0.28, G:0.23, T:0.36
Consensus pattern (38 bp):
GCTTCAGTTAGCCTTCGGCTTCCGTTTAGCACTTACGT
Found at i:127874513 original size:40 final size:40
Alignment explanation
Indices: 127874477--127874699 Score: 246
Period size: 40 Copynumber: 5.6 Consensus size: 40
127874467 CTACTCGTTT
*
127874477 AAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
*
127874517 AAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCAC
* *
127874557 CAATGCCTTCGGG-CTTAGCCCGG-GATTAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCAC
* *
127874596 AAATGCCTT-TGGATCTTAGTCCGGATT-TAGTAACTCGCAC
1 AAATGCCTTCGGGA-CTTAGCCCGG-TTATAGTAACTCGCAC
* * *
127874636 AAATGCCTTC-GGATCTTAGTCCGAATT-TAGTAACTTAGCAC
1 AAATGCCTTCGGGA-CTTAGCCCG-GTTATAGTAAC-TCGCAC
127874677 AAA-GCCTTCGGGACTTAGCCCGG
1 AAATGCCTTCGGGACTTAGCCCGG
127874700 ACATTATTCG
Statistics
Matches: 159, Mismatches: 13, Indels: 23
0.82 0.07 0.12
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 114 0.72
41 13 0.08
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
Found at i:127874587 original size:79 final size:78
Alignment explanation
Indices: 127874477--127874700 Score: 281
Period size: 79 Copynumber: 2.8 Consensus size: 78
127874467 CTACTCGTTT
* * *
127874477 AAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AAATGCCTTCGGG-CTTAGCCCGGAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
127874542 TTTAGTAACTCGCAC
64 TTTAGTAACTCGCAC
* * *
127874557 CAATGCCTTCGGGCTTAGCCCGGGATTAGTAACTCGCACAAATGCCTT-TGGATCTTAGTCCGGA
1 AAATGCCTTCGGGCTTAGCCC-GGATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGA
127874621 TTTAGTAACTCGCAC
64 TTTAGTAACTCGCAC
* * * *
127874636 AAATGCCTTCGGATCTTAGTCCGAATTTAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGG
1 AAATGCCTTCGG-GCTTAGCCCGGA-TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGG
127874700 A
63 A
127874701 CATTATTCGA
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 3 0.02
79 66 0.53
80 45 0.36
81 11 0.09
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (78 bp):
AAATGCCTTCGGGCTTAGCCCGGATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT
TAGTAACTCGCAC
Found at i:127877561 original size:43 final size:41
Alignment explanation
Indices: 127877433--127877566 Score: 198
Period size: 42 Copynumber: 3.2 Consensus size: 41
127877423 TAGATGGCGT
*
127877433 CGCTAAAGGTC-TGGCCTTTAGCGCTCTTTTACCACAAACGC
1 CGCTAAAGGTCATGGCCTTTAGCGC-CTTTTCCCACAAACGC
*
127877474 CGCTAAAGGTAATGGCCTTTAGCGTCCTTTTCCCACAAACGC
1 CGCTAAAGGTCATGGCCTTTAGCG-CCTTTTCCCACAAACGC
*
127877516 CGCTAAAGGTCATGGCCATTAGCGACACTTTTCCCACAAACGC
1 CGCTAAAGGTCATGGCCTTTAGCG-C-CTTTTCCCACAAACGC
127877559 CGCTAAAG
1 CGCTAAAG
127877567 AGGTCATGAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
41 10 0.12
42 50 0.59
43 25 0.29
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (41 bp):
CGCTAAAGGTCATGGCCTTTAGCGCCTTTTCCCACAAACGC
Found at i:127877730 original size:19 final size:19
Alignment explanation
Indices: 127877685--127877731 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
127877675 ATCAAATTAA
*
127877685 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
127877704 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
127877723 AATAAAAAT
1 AATAAAAAT
127877732 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:127879679 original size:46 final size:46
Alignment explanation
Indices: 127879626--127880062 Score: 524
Period size: 46 Copynumber: 9.5 Consensus size: 46
127879616 ATAATCCACA
*
127879626 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
*
127879672 ACTTCAATTTACAGCATTAAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* * ** * *
127879718 ATTTCAATTAACAATATTTATAGCACTTCAATTTGCAACA-TTTAAGC
1 ACTTCAATTTACAGCATTTA-AACACTTCAATTTGCAGCACTTTAA-C
*
127879765 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* * *
127879811 ATTTCAATTAACAACATTTAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
*
127879857 ACTTCAATTTACAGCATTAAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* * * * *
127879903 ATTTCAATTAACAACATTTAAACA-TCTCAATTTCCAGCAAC-TAAAC
1 ACTTCAATTTACAGCATTTAAACACT-TCAATTTGCAGC-ACTTTAAC
* * * * * *
127879949 ACTTCAATTTGCAGTACTTAAACACTCCAATTTACAGCACTCTAAC
1 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
* * *
127879995 ACTTCAATTTGCAGCACTTT-AACAGTTCAATTTACAGCA-TTTAAAC
1 ACTTCAATTTACAGCA-TTTAAACACTTCAATTTGCAGCACTTT-AAC
*
127880041 ACTTCAATTTGCAGCACTTTAA
1 ACTTCAATTTACAGCA-TTTAA
127880063 CATCTCAATT
Statistics
Matches: 337, Mismatches: 44, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
45 5 0.01
46 288 0.85
47 44 0.13
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (46 bp):
ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAAC
Found at i:127880064 original size:23 final size:23
Alignment explanation
Indices: 127879626--127880072 Score: 414
Period size: 23 Copynumber: 19.4 Consensus size: 23
127879616 ATAATCCACA
*
127879626 ACTTCAATTTACAGCA-TTCAAAC
1 ACTTCAATTTACAGCACTT-TAAC
*
127879649 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
*
127879672 ACTTCAATTTACAGCA-TTAAAAC
1 ACTTCAATTTACAGCACTT-TAAC
*
127879695 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
* * **
127879718 ATTTCAATTAACAATA-TTTATAGC
1 ACTTCAATTTACAGCACTTTA-A-C
* *
127879742 ACTTCAATTTGCAACA-TTTAAGC
1 ACTTCAATTTACAGCACTTTAA-C
*
127879765 ACTTCAATTTACAGCA-TTCAAAC
1 ACTTCAATTTACAGCACTT-TAAC
*
127879788 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
* * *
127879811 ATTTCAATTAACAACA-TTTAAAC
1 ACTTCAATTTACAGCACTTT-AAC
*
127879834 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
*
127879857 ACTTCAATTTACAGCA-TTAAAAC
1 ACTTCAATTTACAGCACTT-TAAC
*
127879880 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
* * *
127879903 ATTTCAATTAACAACA-TTTAA-
1 ACTTCAATTTACAGCACTTTAAC
* *
127879924 ACATCTCAATTTCCAGCAAC-TAAAC
1 AC-T-TCAATTTACAGC-ACTTTAAC
* * *
127879949 ACTTCAATTTGCAGTACTTAAAC
1 ACTTCAATTTACAGCACTTTAAC
* *
127879972 ACTCCAATTTACAGCACTCTAAC
1 ACTTCAATTTACAGCACTTTAAC
*
127879995 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
*
127880018 AGTTCAATTTACAGCA-TTTAAAC
1 ACTTCAATTTACAGCACTTT-AAC
*
127880041 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAAC
127880064 A-TCTCAATT
1 ACT-TCAATT
127880073 AACAACTTTT
Statistics
Matches: 349, Mismatches: 55, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.00
22 23 0.07
23 285 0.82
24 38 0.11
25 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (23 bp):
ACTTCAATTTACAGCACTTTAAC
Found at i:127880465 original size:12 final size:12
Alignment explanation
Indices: 127880448--127880497 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
127880438 ACACACACAT
127880448 ATTAACATCTCA
1 ATTAACATCTCA
*
127880460 ATTAACA--ACA
1 ATTAACATCTCA
* *
127880470 TTTATACACCTCA
1 ATTA-ACATCTCA
127880483 ATTAACATCTCA
1 ATTAACATCTCA
127880495 ATT
1 ATT
127880498 TCCAGCAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
10 5 0.17
11 3 0.10
12 17 0.57
13 5 0.17
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (12 bp):
ATTAACATCTCA
Found at i:127881727 original size:15 final size:15
Alignment explanation
Indices: 127881707--127881737 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
127881697 CCTTGAATTA
127881707 GAAGAAAACCAGTAG
1 GAAGAAAACCAGTAG
127881722 GAAGAAAACCAGTAG
1 GAAGAAAACCAGTAG
127881737 G
1 G
127881738 TTACCTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.13, G:0.29, T:0.06
Consensus pattern (15 bp):
GAAGAAAACCAGTAG
Found at i:127883176 original size:7 final size:7
Alignment explanation
Indices: 127883162--127883222 Score: 59
Period size: 7 Copynumber: 8.7 Consensus size: 7
127883152 ATAGTTAACT
127883162 CATAAAC
1 CATAAAC
*
127883169 CTTAAAC
1 CATAAAC
*
127883176 CTTAAAC
1 CATAAAC
*
127883183 CCTAAAC
1 CATAAAC
* *
127883190 CATATAT
1 CATAAAC
*
127883197 CTTAAAC
1 CATAAAC
127883204 CATAAAC
1 CATAAAC
127883211 CATAAAC
1 CATAAAC
*
127883218 TATAA
1 CATAA
127883223 TGATAATTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (7 bp):
CATAAAC
Found at i:127883181 original size:14 final size:14
Alignment explanation
Indices: 127883162--127883222 Score: 68
Period size: 14 Copynumber: 4.4 Consensus size: 14
127883152 ATAGTTAACT
127883162 CATAAACCTTAAAC
1 CATAAACCTTAAAC
* *
127883176 CTTAAACCCTAAAC
1 CATAAACCTTAAAC
* *
127883190 CATATATCTTAAAC
1 CATAAACCTTAAAC
*
127883204 CATAAACCATAAAC
1 CATAAACCTTAAAC
*
127883218 TATAA
1 CATAA
127883223 TGATAATTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (14 bp):
CATAAACCTTAAAC
Found at i:127883188 original size:21 final size:21
Alignment explanation
Indices: 127883162--127883217 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
127883152 ATAGTTAACT
*
127883162 CATAAACCTTAAACCTTAAAC
1 CATAAACCATAAACCTTAAAC
* * *
127883183 CCTAAACCATATATCTTAAAC
1 CATAAACCATAAACCTTAAAC
127883204 CATAAACCATAAAC
1 CATAAACCATAAAC
127883218 TATAATGATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (21 bp):
CATAAACCATAAACCTTAAAC
Found at i:127883535 original size:40 final size:40
Alignment explanation
Indices: 127883379--127883515 Score: 170
Period size: 41 Copynumber: 3.4 Consensus size: 40
127883369 GTTATATGAC
*
127883379 TTTTAGTGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCT-GT
*
127883420 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGTTCT-T
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGT
* * * *
127883459 TTTTTGCGGCATTTTTTACTAAAA-CGCCGCTATTGCTCTGT
1 TTTTAGCGGC-GTTTTT-CCAAAAGCGCCGCTAATGCTCTGT
*
127883500 TTTTAGTGGCGTTTTT
1 TTTTAGCGGCGTTTTT
127883516 GGTAAAACGC
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
39 10 0.12
40 23 0.28
41 50 0.60
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGT
Found at i:127892895 original size:17 final size:17
Alignment explanation
Indices: 127892873--127892908 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
127892863 ATTATTTAAT
127892873 AATATTTTTATT-TCTAA
1 AATATTTTT-TTATCTAA
127892890 AATATTTTTTTATCTAA
1 AATATTTTTTTATCTAA
127892907 AA
1 AA
127892909 AAATGATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
AATATTTTTTTATCTAA
Found at i:127897543 original size:2 final size:2
Alignment explanation
Indices: 127897536--127897567 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
127897526 GTGAATTGGT
127897536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
127897568 AGACTTTAGA
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):
TA
Found at i:127903960 original size:3 final size:3
Alignment explanation
Indices: 127903949--127904203 Score: 74
Period size: 3 Copynumber: 83.7 Consensus size: 3
127903939 AAAAAAGAAG
* * * * * *
127903949 TAA TGA TAA TAA TAA TAG GAG TAA TAA TAA TAA T-A TAA TGA TGA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* * * * * *
127903997 CAA TAA TAA -AA GGAA CAA AAA TAA TAG TAA TAA TAA -AGA TATT TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TAA
* ** * *
127904043 TAA TAG TAA TAA TAA CGA TGA T-A TAAA TAA TAA TATA TACA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA-A TA-A TAA TAA
* * * * * *
127904090 TAA TAGT TAGA -AA TAA AAA TAA TGGA -AA TAG TAA TAA CAA TAG TAA
1 TAA TA-A TA-A TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * * *
127904136 TAG TAA TAA -AGA TAA CAA CAA CAA CAA CAA CAA CAA CAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
127904181 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
127904204 TATTTAATTC
Statistics
Matches: 195, Mismatches: 42, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
2 10 0.05
3 166 0.85
4 19 0.10
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:127905719 original size:44 final size:44
Alignment explanation
Indices: 127905659--127906166 Score: 296
Period size: 44 Copynumber: 11.6 Consensus size: 44
127905649 AATTTTCAGC
* * *
127905659 CTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATTACCTTCGAT
* * ** ** * ** *
127905703 ATATTTCCCTACTGCTTAGGGGGATAA-GATCTTGTAAATTC-AGC
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCAT-TACCTTCGA-T
* * * *
127905747 CTGTTACCCCACTACTTAGGGGTTTAAGGCCCATCACCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATTACCTTCGAT
** ** * ** * *
127905791 CTGTTTCCCTACTGCTTAGGGG-TTAAGATCTGTAAATTTAG-C
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATTACCTTCGAT
* * * *
127905833 CCGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTTGAT
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATTACCTTCGAT
* * * ** * ** *
127905877 CTATTTCCCTACTACTTAGGGGGTTAA-GATCTTGTAAATTC-AA
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCAT-TACCTTCGAT
* * *
127905920 CATGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCTTCGAT
1 C-TGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATTACCTTCGAT
* ** ** * ** * *
127905965 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAG-C
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATTACCTTCGAT
* * *
127906008 CTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATTACCTTCGAT
* * ** * ** * *
127906052 CTATTTCCCTATTGCTTAGGGG-TTAA-GATCTTGTAAATTCAAC
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCAT-TACCTTCGAT
* * *
127906095 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATTACCTTCGAT
*
127906139 CTGTTTCCCTACTGCTTAGGGGGTTAAG
1 CTGTTTCCCTACTGCTTAGGGGTTTAAG
127906167 ATATTGTAAA
Statistics
Matches: 330, Mismatches: 120, Indels: 28
0.69 0.25 0.06
Matches are distributed among these distances:
42 23 0.07
43 90 0.27
44 205 0.62
45 12 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (44 bp):
CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATTACCTTCGAT
Found at i:127905963 original size:174 final size:175
Alignment explanation
Indices: 127905656--127906185 Score: 902
Period size: 174 Copynumber: 3.0 Consensus size: 175
127905646 TATAATTTTC
*
127905656 AGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGATATATTTCCCTACTGCTTA
1 AGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGCTTA
* * * * * **
127905721 GGGGGATAAGATCTTGTAAATTCAGCCTGTTACCCCACTACTTAGGGGTTTAAGGCCCATCACCT
66 GGGGGTTAAGATCTTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCT
127905786 TCGATCTGTTTCCCTACTGCTTA-GGGGTTAAGATCTGTAAATTT
131 TCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
* * * *
127905830 AGCCCGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTTGATCTATTTCCCTACTACTTA
1 AGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGCTTA
*
127905895 GGGGGTTAAGATCTTGTAAATTCAACATGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCT
66 GGGGGTTAAGATCTTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCT
127905960 TCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
131 TCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
*
127906005 AGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTATTGCTTA
1 AGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGCTTA
127906070 -GGGGTTAAGATCTTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCT
66 GGGGGTTAAGATCTTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCT
*
127906134 TCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATATTGTAAATTT
131 TCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGAT-CTGTAAATTT
127906180 AGCCTG
1 AGCCTG
127906186 CTCTACTGCA
Statistics
Matches: 334, Mismatches: 20, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
174 238 0.71
175 96 0.29
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (175 bp):
AGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGCTTA
GGGGGTTAAGATCTTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCT
TCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
Found at i:127906048 original size:87 final size:88
Alignment explanation
Indices: 127905653--127906185 Score: 804
Period size: 88 Copynumber: 6.1 Consensus size: 88
127905643 ATCTATAATT
* *
127905653 TTCAGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGATATATTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGC
*
127905718 TTAGGGGGATAAGATCTTGTAAA
66 TTAGGGGGTTAAGATCTTGTAAA
* * *
127905741 TTCAGCCTGTTACCCCACTACTTAGGGGTTTAAGGCCCATCACCTTCGATCTGTTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGC
127905806 TTA-GGGGTTAAGATC-TGTAAA
66 TTAGGGGGTTAAGATCTTGTAAA
* * * *
127905827 TTTAGCCCGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTTGATCTATTTCCCTACTAC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGC
127905892 TTAGGGGGTTAAGATCTTGTAAA
66 TTAGGGGGTTAAGATCTTGTAAA
* * * ** *
127905915 TTCAACATGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCTTCGATCTGTTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGC
127905980 TTAGGGGGTTAAGATC-TGTAAA
66 TTAGGGGGTTAAGATCTTGTAAA
* * *
127906002 TTTAGCCTGTTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTATTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGC
127906067 TTA-GGGGTTAAGATCTTGTAAA
66 TTAGGGGGTTAAGATCTTGTAAA
* * ** *
127906089 TTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATTGCCTTCGATCTGTTTCCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGC
*
127906154 TTAGGGGGTTAAGATATTGTAAA
66 TTAGGGGGTTAAGATCTTGTAAA
*
127906177 TTTAGCCTG
1 TTCAGCCTG
127906186 CTCTACTGCA
Statistics
Matches: 398, Mismatches: 43, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
86 79 0.20
87 154 0.39
88 165 0.41
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (88 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCACCTTCGATCTATTTCCCTACTGC
TTAGGGGGTTAAGATCTTGTAAA
Found at i:127906280 original size:43 final size:44
Alignment explanation
Indices: 127906190--127906280 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 44
127906180 AGCCTGCTCT
* * * *
127906190 ACTGCAACTTCAAGGAGATGAGACTTGTAACTTCAGTCTTCTAC
1 ACTGCAACTTCAAGGAGATAAGACTAGTAACTTCACTCTGCTAC
* * * *
127906234 ACTGC-ACTTCAGGGAGATAAGGCTAGTGACTTCACTCTGCTTC
1 ACTGCAACTTCAAGGAGATAAGACTAGTAACTTCACTCTGCTAC
127906277 ACTG
1 ACTG
127906281 AGGCTTCAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 34 0.87
44 5 0.13
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
ACTGCAACTTCAAGGAGATAAGACTAGTAACTTCACTCTGCTAC
Found at i:127912744 original size:22 final size:22
Alignment explanation
Indices: 127912701--127912744 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
127912691 CCGGAGCTCC
* *
127912701 CTCTCCCTCTCCCCTTTCTTTT
1 CTCTCCCTCTCCCCTCTATTTT
* *
127912723 CTCTCCCTCTTCTCTCTATTTT
1 CTCTCCCTCTCCCCTCTATTTT
127912745 TTTTTCCTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.52
Consensus pattern (22 bp):
CTCTCCCTCTCCCCTCTATTTT
Found at i:127913315 original size:13 final size:14
Alignment explanation
Indices: 127913291--127913321 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
127913281 ATCATTATTA
127913291 ATATTAATATATGT
1 ATATTAATATATGT
127913305 ATATT-ATATATGT
1 ATATTAATATATGT
127913318 ATAT
1 ATAT
127913322 ATTCGTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
ATATTAATATATGT
Found at i:127913541 original size:12 final size:11
Alignment explanation
Indices: 127913520--127913549 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
127913510 TTCTTAATAT
127913520 TATATTTTATA
1 TATATTTTATA
127913531 TATATTATTATA
1 TATATT-TTATA
127913543 TATATTT
1 TATATTT
127913550 AAATATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTTATA
Found at i:127916009 original size:24 final size:24
Alignment explanation
Indices: 127915963--127916009 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
127915953 AGGACCGTAA
**
127915963 AGGAGTTCCAAGATATTTTTCCGG
1 AGGAGTTCCAAGATATTCCTCCGG
127915987 AGGAGCTTCCAAGAT-TTCCTCCG
1 AGGAG-TTCCAAGATATTCCTCCG
127916010 AACCGAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (24 bp):
AGGAGTTCCAAGATATTCCTCCGG
Found at i:127917931 original size:26 final size:26
Alignment explanation
Indices: 127917892--127917975 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
127917882 TGATACAAAT
* *
127917892 TGATAATAGATTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
127917918 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
127917944 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
127917970 TGATAA
1 TGATAA
127917976 GAATATCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:127920006 original size:137 final size:137
Alignment explanation
Indices: 127919760--127920046 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
127919750 GAGTAGTCTC
127919760 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
127919825 TATTATCTGAATAAGGGGCTAAAGCCCAGTTTATTGTAATCTGAAAAGGGCTCTTGCCCAGTACC
66 TATTATCTGAATAAGGGGCTAAAGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
127919890 ACTGTTA
131 ACTGTTA
127919897 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
127919962 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TATTATCTGAATAAGGGGCTAAAGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
127920027 ACTGTTA
131 ACTGTTA
**
127920034 CCTGAATGGGCTT
1 CCCAAATGGGCTT
127920047 AGGCCCAATG
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TATTATCTGAATAAGGGGCTAAAGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:127921272 original size:30 final size:29
Alignment explanation
Indices: 127921238--127921302 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
127921228 AACGAGGAAA
127921238 TAGAAACCCCATAAGTTAGGGTACGATTTC
1 TAGAAACCCCA-AAGTTAGGGTACGATTTC
**** *
127921268 TAGAAATTTTAAATTTAGGGTACGATTTC
1 TAGAAACCCCAAAGTTAGGGTACGATTTC
127921297 TAGAAA
1 TAGAAA
127921303 TTTGAAATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (29 bp):
TAGAAACCCCAAAGTTAGGGTACGATTTC
Found at i:127921287 original size:29 final size:29
Alignment explanation
Indices: 127921253--127921310 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
127921243 ACCCCATAAG
*
127921253 TTAGGGTACGATTTCTAGAAATTTTAAAT
1 TTAGGGTACGATTTCTAGAAATTTGAAAT
127921282 TTAGGGTACGATTTCTAGAAATTTGAAAT
1 TTAGGGTACGATTTCTAGAAATTTGAAAT
127921311 ACAAAATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (29 bp):
TTAGGGTACGATTTCTAGAAATTTGAAAT
Found at i:127921587 original size:15 final size:14
Alignment explanation
Indices: 127921566--127921602 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
127921556 AAAGGCCAAG
127921566 AATAAAATAAAGTAA
1 AATAAAATAAA-TAA
*
127921581 GATAAAATAAATAA
1 AATAAAATAAATAA
127921595 AATAAAAT
1 AATAAAAT
127921603 GAAGGTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (14 bp):
AATAAAATAAATAA
Found at i:127923567 original size:45 final size:44
Alignment explanation
Indices: 127923515--127923996 Score: 216
Period size: 44 Copynumber: 10.6 Consensus size: 44
127923505 TTTAATTTAT
* * *
127923515 TCCACTGCAACTTTAGGGAAATAAGATTCACTATCTTCAGTCTAT
1 TCCACTGCAACTTTAGGGAGATAAGATT-ACTATCTTCAATCTAC
* * * * *
127923560 TTCACTGCAACTTTAGGGAGATGAGGTTA--ATGGTTACAATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTACTAT-CTT-CAATCTAC
* **
127923604 TCCACTGCAACTTTAGGGAGATGAGATTTGTATCTTCAATCTAC
1 TCCACTGCAACTTTAGGGAGATAAGATTACTATCTTCAATCTAC
* * * * * *
127923648 TCCACTGTAACTTCAGGGAGATAATACTCACTATCTTCAGTCTGC
1 TCCACTGCAACTTTAGGGAGATAAGA-TTACTATCTTCAATCTAC
* * ** ** ** * *
127923693 TCTACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAGTCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTACTATCTTCAATCTAC
* * * * *
127923737 TCCACTGCAACTTCAGGAAGATAAGATTCGTCATAATTTGTAGCTTTAATCTAT
1 TCCACTGCAACTTTAGGGAGATAAGATT--AC-T-A----T--CTTCAATCTAC
* * * * * * *
127923791 TCCACTACAACTTCAAGGAAATGAGATTCGCTATCTTCAGTCTAC
1 TCCACTGCAACTTTAGGGAGATAAGATT-ACTATCTTCAATCTAC
* * * ** * **
127923836 TCCGCTGTAACTTTAAGGAGATAAGGCTAGTGGCTTCAATCTAC
1 TCCACTGCAACTTTAGGGAGATAAGATTACTATCTTCAATCTAC
* * * * * *
127923880 TCCATTGTAACTTTAAGAAGATAAGATT-CGTCATCTTCGATCTTC
1 TCCACTGCAACTTTAGGGAGATAAGATTAC-T-ATCTTCAATCTAC
* * * * *
127923925 TCCACTACAACTTCAAGGAGATAAGATCTAC-AACTTCAATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGAT-TACTATCTTCAATCTAC
* * * *
127923969 TCTACTGCTACTTCAGGGAGATGAGATT
1 TCCACTGCAACTTTAGGGAGATAAGATT
127923997 TGTGGATTCA
Statistics
Matches: 328, Mismatches: 90, Indels: 40
0.72 0.20 0.09
Matches are distributed among these distances:
42 2 0.01
43 3 0.01
44 164 0.50
45 120 0.37
46 3 0.01
47 3 0.01
51 1 0.00
52 1 0.00
53 1 0.00
54 30 0.09
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTTAGGGAGATAAGATTACTATCTTCAATCTAC
Found at i:127923684 original size:133 final size:133
Alignment explanation
Indices: 127923515--127923990 Score: 393
Period size: 133 Copynumber: 3.5 Consensus size: 133
127923505 TTTAATTTAT
* * * * *
127923515 TCCACTGCAACTTTAGGGAAATAAGATTCACTATCTTCAGTCT-ATTTCACTGCAACTTTAGGGA
1 TCCACTGCAACTTCAGGGAAATAAGACTCACTATCTTCAGTCTGCTCT-ACTGCAACTTCAGGGA
* * * * *
127923579 GATGAGGTTAATGG-TTACAATCTGCTCCACTGCAACTTTAGGGAGATGAGATTTGTATCTTCAA
65 GATAAGGCTAATGGCTT-CAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGTATCTTCAA
127923643 TCTAC
129 TCTAC
* * *
127923648 TCCACTGTAACTTCAGGGAGATAATACTCACTATCTTCAGTCTGCTCTACTGCAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGAAATAAGACTCACTATCTTCAGTCTGCTCTACTGCAACTTCAGGGAG
** *
127923713 ATAAGGCTGGTGGCTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGTCATAATTTGT
66 ATAAGGCTAATGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGAT-A-A---G-----ATTTGT
* * *
127923778 AGCTTTAATCTAT
121 ATCTTCAATCTAC
* * * * * * ** * * *
127923791 TCCACTACAACTTCAAGGAAATGAGATTCGCTATCTTCAGTCTACTCCGCTGTAACTTTAAGGAG
1 TCCACTGCAACTTCAGGGAAATAAGACTCACTATCTTCAGTCTGCTCTACTGCAACTTCAGGGAG
* * * * * * * *
127923856 ATAAGGCTAGTGGCTTCAATCTACTCCATTGTAACTTTAAGAAGATAAGATTCGTCATCTTCGAT
66 ATAAGGCTAATGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGT-ATCTTCAAT
*
127923921 CTTC
130 CTAC
* * * * * *
127923925 TCCACTACAACTTCAAGGAGATAAGA-TCTAC-AACTTCAATCTGCTCTACTGCTACTTCAGGGA
1 TCCACTGCAACTTCAGGGAAATAAGACTC-ACTATCTTCAGTCTGCTCTACTGCAACTTCAGGGA
127923988 GAT
65 GAT
127923991 GAGATTTGTG
Statistics
Matches: 271, Mismatches: 58, Indels: 28
0.76 0.16 0.08
Matches are distributed among these distances:
133 123 0.45
134 37 0.14
135 1 0.00
138 2 0.01
141 1 0.00
142 1 0.00
143 106 0.39
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (133 bp):
TCCACTGCAACTTCAGGGAAATAAGACTCACTATCTTCAGTCTGCTCTACTGCAACTTCAGGGAG
ATAAGGCTAATGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGTATCTTCAATC
TAC
Found at i:127933158 original size:22 final size:23
Alignment explanation
Indices: 127933132--127933176 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
127933122 ACCTGATCAG
127933132 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
127933154 AATACGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
127933177 TCAGTAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:127933436 original size:28 final size:26
Alignment explanation
Indices: 127933367--127933484 Score: 131
Period size: 23 Copynumber: 4.6 Consensus size: 26
127933357 AAATGTCCAA
127933367 CCAAAACACACCAG---TATAATCCT
1 CCAAAACACACCAGATATATAATCCT
127933390 CCAAAACACACCAG---TATAATCCT
1 CCAAAACACACCAGATATATAATCCT
*
127933413 CCAAAATACACCAGTATCATATAATCCT
1 CCAAAACACACCAG-AT-ATATAATCCT
*
127933441 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG-AT-ATATAATCC-T
127933470 CCAAAACACACCAGA
1 CCAAAACACACCAGA
127933485 ATAGCACAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
23 36 0.43
28 33 0.40
29 14 0.17
ACGTcount: A:0.46, C:0.33, G:0.04, T:0.17
Consensus pattern (26 bp):
CCAAAACACACCAGATATATAATCCT
Found at i:127939778 original size:19 final size:19
Alignment explanation
Indices: 127939754--127939797 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
127939744 TGTGACATTT
*
127939754 AATGCATATG-ATGCGATG
1 AATGCAAATGCATGCGATG
*
127939772 AAATGCAAATGCATGGGATG
1 -AATGCAAATGCATGCGATG
127939792 AATGCA
1 AATGCA
127939798 GAAAAAGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (19 bp):
AATGCAAATGCATGCGATG
Found at i:127943743 original size:3 final size:3
Alignment explanation
Indices: 127943735--127943781 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
127943725 TATGTAAATA
* *
127943735 AAT AAT AAT AGAT AA- AAT AAT AAT AAT GAT AGT AAT AAT AAAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
127943781 A
1 A
127943782 TATATAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:127943756 original size:18 final size:19
Alignment explanation
Indices: 127943730--127943781 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
127943720 AAACCTATGT
127943730 AAATAAATAATAATAGATA-
1 AAAT-AATAATAATAGATAG
127943749 AAATAATAATAAT-GATAG
1 AAATAATAATAATAGATAG
*
127943767 TAATAATAAATAATA
1 AAATAAT-AATAATA
127943782 TATATAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.14
18 15 0.52
19 10 0.34
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (19 bp):
AAATAATAATAATAGATAG
Found at i:127943899 original size:18 final size:17
Alignment explanation
Indices: 127943878--127943916 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
127943868 GACTTTAGGT
127943878 ATATAAAAA-AAATAATA
1 ATATAAAAATAAA-AATA
127943895 GATATAAAAATAAAAATA
1 -ATATAAAAATAAAAATA
127943913 ATAT
1 ATAT
127943917 TAACTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 13 0.65
19 3 0.15
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATATAAAAATAAAAATA
Found at i:127943911 original size:21 final size:20
Alignment explanation
Indices: 127943877--127943915 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
127943867 TGACTTTAGG
*
127943877 TATATAAAAAAAATAATAGA
1 TATAAAAAAAAAATAATAGA
127943897 TATAAAAATAAAAATAATA
1 TATAAAAA-AAAAATAATA
127943916 TTAACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
TATAAAAAAAAAATAATAGA
Found at i:127945008 original size:20 final size:22
Alignment explanation
Indices: 127944974--127945023 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
127944964 TTCGCAGGTA
127944974 TGGAG-GTACGAAGGC-G-ACG
1 TGGAGTGTACGAAGGCTGTACG
*
127944993 TGGAGTGTACGGAGGCTGTACG
1 TGGAGTGTACGAAGGCTGTACG
127945015 TGTGAGTGT
1 TG-GAGTGT
127945024 CAACGTGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 5 0.19
20 9 0.35
21 1 0.04
22 5 0.19
23 6 0.23
ACGTcount: A:0.20, C:0.12, G:0.46, T:0.22
Consensus pattern (22 bp):
TGGAGTGTACGAAGGCTGTACG
Found at i:127947378 original size:21 final size:19
Alignment explanation
Indices: 127947348--127947393 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
127947338 ATCGAGAATT
*
127947348 GTTTTAATTTAGTAATTTATG
1 GTTTTTATTTA-TAA-TTATG
*
127947369 GTTTTTATTTATAATTCTG
1 GTTTTTATTTATAATTATG
127947388 GTTTTT
1 GTTTTT
127947394 GAGAGTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 10 0.43
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.63
Consensus pattern (19 bp):
GTTTTTATTTATAATTATG
Found at i:127949161 original size:25 final size:25
Alignment explanation
Indices: 127949132--127949181 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
127949122 TGTTGATTTG
127949132 ATTCTCACTTTCCTTT-TTTAATATA
1 ATTCTCAC-TTCCTTTATTTAATATA
*
127949157 ATTCTCACTTCCTTTATTTGATATA
1 ATTCTCACTTCCTTTATTTAATATA
127949182 TGAATTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.24, C:0.20, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTCTCACTTCCTTTATTTAATATA
Found at i:127949384 original size:54 final size:54
Alignment explanation
Indices: 127949302--127949408 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
127949292 TGTTATAGAG
*
127949302 AAGGTTTACTATAGTATAGATATCGATATGTTTGGTTCAAACTGATGTTTAAAT
1 AAGGTTTACTATAATATAGATATCGATATGTTTGGTTCAAACTGATGTTTAAAT
127949356 AAGGTTTACTATAATATAGATATCGATATGTTTGGTTCAAACTGATGTTTAAA
1 AAGGTTTACTATAATATAGATATCGATATGTTTGGTTCAAACTGATGTTTAAA
127949409 CTAATTAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (54 bp):
AAGGTTTACTATAATATAGATATCGATATGTTTGGTTCAAACTGATGTTTAAAT
Found at i:127949721 original size:26 final size:24
Alignment explanation
Indices: 127949689--127949738 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
127949679 AAATAAAAAA
*
127949689 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
127949715 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
127949739 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:127949758 original size:21 final size:21
Alignment explanation
Indices: 127949709--127949767 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
127949699 ATAATAAATC
*
127949709 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
127949729 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
127949751 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
127949768 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:127952691 original size:6 final size:6
Alignment explanation
Indices: 127952682--127952706 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
127952672 AATAAATCAT
127952682 TTAAAA TTAAAA TTAAAA TTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA T
127952707 AATTAATTAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAA
Found at i:127953867 original size:31 final size:32
Alignment explanation
Indices: 127953824--127953892 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
127953814 TTTTTTTCTC
127953824 TTTACTCACAAAATGAGT-AATTAGTTGGTTAT
1 TTTA-TCACAAAATGAGTAAATTAGTTGGTTAT
127953856 TTTATCACAAAATGAGTAAATTAGTTGGTTAT
1 TTTATCACAAAATGAGTAAATTAGTTGGTTAT
127953888 TTTAT
1 TTTAT
127953893 TAAAGTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 13 0.36
32 23 0.64
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (32 bp):
TTTATCACAAAATGAGTAAATTAGTTGGTTAT
Found at i:127963014 original size:4 final size:4
Alignment explanation
Indices: 127963005--127963153 Score: 298
Period size: 4 Copynumber: 37.2 Consensus size: 4
127962995 CTAGCTAACT
127963005 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
127963053 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
127963101 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
127963149 CATA C
1 CATA C
127963154 TATTTTTTCC
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 145 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:127969121 original size:24 final size:24
Alignment explanation
Indices: 127969094--127969139 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
127969084 GTGAAACTAT
* *
127969094 AAAGGCTGAAAAGCCGAAAAGTCA
1 AAAGGCTGAAAAACCAAAAAGTCA
127969118 AAAGGCTGAAAAACCAAAAAGT
1 AAAGGCTGAAAAACCAAAAAGT
127969140 AGGTTGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.22, T:0.09
Consensus pattern (24 bp):
AAAGGCTGAAAAACCAAAAAGTCA
Found at i:127969543 original size:27 final size:27
Alignment explanation
Indices: 127969513--127969630 Score: 89
Period size: 27 Copynumber: 4.4 Consensus size: 27
127969503 TTATTTACTT
127969513 GTAAAATGACT-GAAATACCCCTATAAG
1 GTAAAATGA-TAGAAATACCCCTATAAG
* * *
127969540 GTAAAATGACCA-AAATATCGCC-ATAGG
1 GTAAAATGA-TAGAAATA-CCCCTATAAG
* * *
127969567 GTAAAATGATAGAAATACACCTGTAGG
1 GTAAAATGATAGAAATACCCCTATAAG
* * * *
127969594 GTAAAATGATCGTAGTACCCCTGTAAG
1 GTAAAATGATAGAAATACCCCTATAAG
*
127969621 ATAAAATGAT
1 GTAAAATGAT
127969631 TGTTTTACCT
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
26 4 0.05
27 68 0.91
28 3 0.04
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (27 bp):
GTAAAATGATAGAAATACCCCTATAAG
Found at i:127969652 original size:27 final size:27
Alignment explanation
Indices: 127969622--127969832 Score: 224
Period size: 27 Copynumber: 7.8 Consensus size: 27
127969612 CCCTGTAAGA
* * * *
127969622 TAAAATGATTGTTTTACCTTTATGTGT
1 TAAAATGACTATTTTGCCCTTATGTGT
* * *
127969649 TAAAATGACTATTTTGTCCTCATGTGA
1 TAAAATGACTATTTTGCCCTTATGTGT
*
127969676 TAAAATGACAATTTTGCCCTTATGTGT
1 TAAAATGACTATTTTGCCCTTATGTGT
*
127969703 TAAAATAACTATTTTGCCCTTATGTGT
1 TAAAATGACTATTTTGCCCTTATGTGT
* * *
127969730 TAAAATAACTGTTTTGCCTTTATGTGT
1 TAAAATGACTATTTTGCCCTTATGTGT
** * *
127969757 TAAAATGACGGTTTTGCCCTTATATGG
1 TAAAATGACTATTTTGCCCTTATGTGT
** * * *
127969784 TAAAATGACGGTTTTGCTCTTATGAGG
1 TAAAATGACTATTTTGCCCTTATGTGT
*
127969811 TAAAATGACTATTTTGCTCTTA
1 TAAAATGACTATTTTGCCCTTA
127969833 CGTGGTAGGA
Statistics
Matches: 159, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 159 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGTGT
Found at i:127969678 original size:54 final size:54
Alignment explanation
Indices: 127969620--127969855 Score: 249
Period size: 54 Copynumber: 4.4 Consensus size: 54
127969610 ACCCCTGTAA
* * * *
127969620 GATAAAATGATTGTTTTACCTTTATGTGTTAAAATGACTATTTTGTCCTCATGT
1 GATAAAATGACTGTTTTGCCTTTATGTGTTAAAATGACTATTTTGCCCTTATGT
** * *
127969674 GATAAAATGACAATTTTGCCCTTATGTGTTAAAATAACTATTTTGCCCTTATGT
1 GATAAAATGACTGTTTTGCCTTTATGTGTTAAAATGACTATTTTGCCCTTATGT
* * ** *
127969728 GTTAAAATAACTGTTTTGCCTTTATGTGTTAAAATGACGGTTTTGCCCTTATAT
1 GATAAAATGACTGTTTTGCCTTTATGTGTTAAAATGACTATTTTGCCCTTATGT
* * * * * *
127969782 GGTAAAATGACGGTTTTG-CTCTTATGAGGTAAAATGACTATTTTGCTCTTACGT
1 GATAAAATGACTGTTTTGCCT-TTATGTGTTAAAATGACTATTTTGCCCTTATGT
* ** *
127969836 GGTAGGATGATTGTTTTGCC
1 GATAAAATGACTGTTTTGCC
127969856 CCTATATGAT
Statistics
Matches: 149, Mismatches: 31, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
53 2 0.01
54 146 0.98
55 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (54 bp):
GATAAAATGACTGTTTTGCCTTTATGTGTTAAAATGACTATTTTGCCCTTATGT
Found at i:127969852 original size:27 final size:27
Alignment explanation
Indices: 127969676--127969854 Score: 92
Period size: 27 Copynumber: 6.6 Consensus size: 27
127969666 CCTCATGTGA
** * * * *
127969676 TAAAATGACAATTTTGCCCTTATGTGT
1 TAAAATGACTGTTTTGCTCTTACGAGG
* * * * * *
127969703 TAAAATAACTATTTTGCCCTTATGTGT
1 TAAAATGACTGTTTTGCTCTTACGAGG
* * * *
127969730 TAAAATAACTGTTTTGC-CTTTATGTGT
1 TAAAATGACTGTTTTGCTC-TTACGAGG
* * *
127969757 TAAAATGACGGTTTTGCCCTTA-TATGG
1 TAAAATGACTGTTTTGCTCTTACGA-GG
* *
127969784 TAAAATGACGGTTTTGCTCTTATGAGG
1 TAAAATGACTGTTTTGCTCTTACGAGG
* *
127969811 TAAAATGACTATTTTGCTCTTACGTGG
1 TAAAATGACTGTTTTGCTCTTACGAGG
** *
127969838 TAGGATGATTGTTTTGC
1 TAAAATGACTGTTTTGC
127969855 CCCTATATGA
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.01
27 127 0.98
28 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCTCTTACGAGG
Found at i:127969852 original size:81 final size:81
Alignment explanation
Indices: 127969649--127969863 Score: 191
Period size: 81 Copynumber: 2.7 Consensus size: 81
127969639 CTTTATGTGT
* * * * ** * * *
127969649 TAAAATGACTATTTTGTCC-TCATGTGATAAAATGACAATTTTGCCCTTATGTGTTAAAATAACT
1 TAAAATAACTATTTTG-CCTTTACGTGGTAAAATGACGGTTTTGCCCTTATATGGTAAAATAACG
* *
127969713 ATTTTGCCCTTATGTGT
65 ATTTTGCCCTTATGAGG
* * * * *
127969730 TAAAATAACTGTTTTGCCTTTATGTGTTAAAATGACGGTTTTGCCCTTATATGGTAAAATGACGG
1 TAAAATAACTATTTTGCCTTTACGTGGTAAAATGACGGTTTTGCCCTTATATGGTAAAATAACGA
*
127969795 TTTTGCTCTTATGAGG
66 TTTTGCCCTTATGAGG
* ** ** *
127969811 TAAAATGACTATTTTG-CTCTTACGTGGTAGGATGATTGTTTTGCCCCTATATG
1 TAAAATAACTATTTTGCCT-TTACGTGGTAAAATGACGGTTTTGCCCTTATATG
127969864 ATTTATGTTT
Statistics
Matches: 109, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
80 4 0.04
81 105 0.96
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (81 bp):
TAAAATAACTATTTTGCCTTTACGTGGTAAAATGACGGTTTTGCCCTTATATGGTAAAATAACGA
TTTTGCCCTTATGAGG
Found at i:127970196 original size:18 final size:18
Alignment explanation
Indices: 127970169--127970214 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
127970159 TACTGCTTAT
127970169 TGTTACTGCACTAATTAC
1 TGTTACTGCACTAATTAC
* *
127970187 TGTTATTGCACTATTTAC
1 TGTTACTGCACTAATTAC
*
127970205 TATTACTGCA
1 TGTTACTGCA
127970215 ATGGGTTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (18 bp):
TGTTACTGCACTAATTAC
Found at i:127972941 original size:3 final size:3
Alignment explanation
Indices: 127972933--127972993 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
127972923 TGTAATGAAC
127972933 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
127972981 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
127972994 TTAAGAACAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:127989760 original size:20 final size:19
Alignment explanation
Indices: 127989722--127989760 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
127989712 ACCTTTCAGA
* *
127989722 AGAAAATAAATGAAGAATT
1 AGAAAATAAATAAAAAATT
127989741 AGAAAATAAAATAAAAAATT
1 AGAAAAT-AAATAAAAAATT
127989761 TAAATTGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATAAAAAATT
Found at i:127993696 original size:27 final size:27
Alignment explanation
Indices: 127993666--127993739 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
127993656 TTATTTACTT
* *
127993666 GTAAAACGACCGAAATACCCCCATAGG
1 GTAAAATGACTGAAATACCCCCATAGG
*
127993693 GTAAAATAACTGAAATACCCCCATAGG
1 GTAAAATGACTGAAATACCCCCATAGG
127993720 GTAAAATGACTGAAATACCC
1 GTAAAATGACTGAAATACCC
127993740 TTGTAAGGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.16
Consensus pattern (27 bp):
GTAAAATGACTGAAATACCCCCATAGG
Found at i:127993749 original size:27 final size:27
Alignment explanation
Indices: 127993677--127993755 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
127993667 TAAAACGACC
*
127993677 GAAATACCCCCATAGGGTAAAATAACT
1 GAAATACCCCCATAAGGTAAAATAACT
* *
127993704 GAAATACCCCCATAGGGTAAAATGACT
1 GAAATACCCCCATAAGGTAAAATAACT
***
127993731 GAAATACCCTTGTAAGGTAAAATAA
1 GAAATACCCCCATAAGGTAAAATAA
127993756 TTGTTTTGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.20
Consensus pattern (27 bp):
GAAATACCCCCATAAGGTAAAATAACT
Found at i:127993943 original size:27 final size:27
Alignment explanation
Indices: 127993719--127993954 Score: 174
Period size: 27 Copynumber: 8.8 Consensus size: 27
127993709 ACCCCCATAG
*** * * *
127993719 GGTAAAATGACTGAAATACCCTTGTAA
1 GGTAAAATGACTGTTTTGCCCTTATAT
* * * *
127993746 GGTAAAATAATTGTTTTGCCTTTATGT
1 GGTAAAATGACTGTTTTGCCCTTATAT
* *
127993773 GTTAAAATGA-TGATTTTGCCCTTATGT
1 GGTAAAATGACTG-TTTTGCCCTTATAT
* * * *
127993800 GATAAAATGA-TGATTTAGCCCTTGTGT
1 GGTAAAATGACTG-TTTTGCCCTTATAT
* *
127993827 GGCAAAATAAC-GTTTTTG-CCTTATAT
1 GGTAAAATGACTG-TTTTGCCCTTATAT
* * * *
127993853 GTTAAAATAACAGTTTTGCCCTTATGT
1 GGTAAAATGACTGTTTTGCCCTTATAT
* *
127993880 GGTAAAATGACGGTTTTGCCCTTATAA
1 GGTAAAATGACTGTTTTGCCCTTATAT
*
127993907 GGTAAAATGACTATTTTGCCCTTATAT
1 GGTAAAATGACTGTTTTGCCCTTATAT
**
127993934 GGTAGGATGACTGTTTTGCCC
1 GGTAAAATGACTGTTTTGCCC
127993955 CTATGTGATG
Statistics
Matches: 168, Mismatches: 37, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
26 22 0.13
27 146 0.87
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (27 bp):
GGTAAAATGACTGTTTTGCCCTTATAT
Found at i:127996322 original size:20 final size:20
Alignment explanation
Indices: 127996285--127996333 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
127996275 TTAAATTCAA
*
127996285 AAAGATAAATAGAAATAATT
1 AAAGATAAATAGAAATAAAT
*
127996305 AAAGATAATTA-AATATAAAT
1 AAAGATAAATAGAA-ATAAAT
*
127996325 AAACATAAA
1 AAAGATAAA
127996334 AGCTAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.24
Consensus pattern (20 bp):
AAAGATAAATAGAAATAAAT
Found at i:128011778 original size:26 final size:26
Alignment explanation
Indices: 128011749--128011814 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
128011739 TCAAACATGC
128011749 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGT-AATTTAACACCTAGGGGT
* **
128011775 ATTTCGGTAATTTTCCACCTAGGGGT
1 ATTTAGGTAATTTAACACCTAGGGGT
128011801 ATTATA-GTAATTTA
1 ATT-TAGGTAATTTA
128011815 GCTGCTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 6 0.18
26 26 0.79
27 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (26 bp):
ATTTAGGTAATTTAACACCTAGGGGT
Found at i:128013294 original size:26 final size:26
Alignment explanation
Indices: 128013258--128013393 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
128013248 CATGATATTC
128013258 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
128013284 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
128013310 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
128013336 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
128013362 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
128013388 TTATCA
1 TTATCA
128013394 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:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:128014436 original size:5 final size:5
Alignment explanation
Indices: 128014418--128014472 Score: 83
Period size: 5 Copynumber: 10.6 Consensus size: 5
128014408 ATAACTCATA
*
128014418 AATTCC AATTC AATAC AATTC AATTC AATTC AATTC AATTC AATTC AATTTC
1 AATT-C AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC AA-TTC
128014470 AAT
1 AAT
128014473 ACTACAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
5 37 0.80
6 9 0.20
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTC
Found at i:128020932 original size:16 final size:18
Alignment explanation
Indices: 128020889--128020925 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
128020879 AATTAAAAAG
128020889 AAAA-ATATATAATATTT
1 AAAATATATATAATATTT
128020906 AAAATATATATAAT-TTT
1 AAAATATATATAATATTT
128020923 AAA
1 AAA
128020926 CTAATATCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATATATAATATTT
Found at i:128020932 original size:18 final size:19
Alignment explanation
Indices: 128020892--128020932 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
128020882 TAAAAAGAAA
128020892 AATATATAATATTTAAAAT
1 AATATATAATATTTAAAAT
*
128020911 -ATATATAAT-TTTAAACT
1 AATATATAATATTTAAAAT
128020928 AATAT
1 AATAT
128020933 CCTCCTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATATAATATTTAAAAT
Found at i:128022413 original size:20 final size:22
Alignment explanation
Indices: 128022357--128022413 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
128022347 ATTAGATTGG
128022357 TTTTTTTTAAAT--GATTTTGA
1 TTTTTTTTAAATAGGATTTTGA
*
128022377 TTTTTTTTAGAGTTAGGATTTT-A
1 TTTTTTTTA-A-ATAGGATTTTGA
128022400 -TTTTTTTAAATAGG
1 TTTTTTTTAAATAGG
128022414 GTTAGGGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 13 0.42
21 2 0.06
22 9 0.29
23 1 0.03
24 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (22 bp):
TTTTTTTTAAATAGGATTTTGA
Found at i:128022495 original size:19 final size:20
Alignment explanation
Indices: 128022471--128022518 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
128022461 TTTTAAGTTT
128022471 TTTTTTTA-ATATT-TTTAAG
1 TTTTTTTATATATTCTTT-AG
128022490 -TTTTTTATATATTCTTTAG
1 TTTTTTTATATATTCTTTAG
128022509 TTTTTTTATA
1 TTTTTTTATA
128022519 ATTTTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.27
19 7 0.27
20 12 0.46
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTTTTTATATATTCTTTAG
Found at i:128022495 original size:20 final size:19
Alignment explanation
Indices: 128022470--128022525 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
128022460 GTTTTAAGTT
128022470 TTTTTTTTAATATTTTTAAG
1 TTTTTTTTAATATTTTT-AG
*
128022490 TTTTTTAT-ATATTCTTTAG
1 TTTTTTTTAATATT-TTTAG
128022509 TTTTTTTATAAT-TTTTT
1 TTTTTTT-TAATATTTTT
128022526 TGAGATGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 16 0.52
20 13 0.42
21 2 0.06
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTTTTTAATATTTTTAG
Found at i:128029425 original size:86 final size:85
Alignment explanation
Indices: 128029276--128029433 Score: 219
Period size: 86 Copynumber: 1.8 Consensus size: 85
128029266 TCGTAAACTT
* * * * *
128029276 CCAACGTCCCAGACATGGTCTTATATGTAATCACATATCGATACCACTGTCCTAGACAGGGTCTT
1 CCAACGTCCCAGACATGGTCTTACACGAAATCACAAATCGATACCACTGTCCCAGACAGGGTCTT
128029341 ACATGAACTCATATACGATG
66 ACATGAACTCATATACGATG
* * *
128029361 CCAATGTCCCAGACATGGTCTTACACGCAAATCACAAATCGATGCCAAC-GTCCCAGACATGGTC
1 CCAACGTCCCAGACATGGTCTTACACG-AAATCACAAATCGATACC-ACTGTCCCAGACAGGGTC
128029425 TTACATGAA
64 TTACATGAA
128029434 ATCACATATC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
85 24 0.38
86 37 0.59
87 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (85 bp):
CCAACGTCCCAGACATGGTCTTACACGAAATCACAAATCGATACCACTGTCCCAGACAGGGTCTT
ACATGAACTCATATACGATG
Found at i:128029463 original size:43 final size:42
Alignment explanation
Indices: 128029284--128029445 Score: 182
Period size: 43 Copynumber: 3.8 Consensus size: 42
128029274 TTCCAACGTC
* * *
128029284 CCAGACATGGTCTTATATGTAATCACATATCGATACCACTGT
1 CCAGACATGGTCTTACATGAAATCACATATCGATACCAATGT
* * * *
128029326 CCTAGACAGGGTCTTACATGAACTCATATA-CGATGCCAATGT
1 CC-AGACATGGTCTTACATGAAATCACATATCGATACCAATGT
* * * *
128029368 CCCAGACATGGTCTTACACGCAAATCACAAATCGATGCCAACGT
1 -CCAGACATGGTCTTACATG-AAATCACATATCGATACCAATGT
128029412 CCCAGACATGGTCTTACATGAAATCACATATCGA
1 -CCAGACATGGTCTTACATGAAATCACATATCGA
128029446 AATCATATGT
Statistics
Matches: 101, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
42 27 0.27
43 44 0.44
44 30 0.30
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (42 bp):
CCAGACATGGTCTTACATGAAATCACATATCGATACCAATGT
Found at i:128035525 original size:4 final size:4
Alignment explanation
Indices: 128035516--128035567 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
128035506 TTTTCCGCCG
* * * * * *
128035516 TATT TATT TATT TATT TATT TATT CATA TACT TACT CATT TATT TACT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
128035564 TATT
1 TATT
128035568 ACCCTTTTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (4 bp):
TATT
Found at i:128035604 original size:3 final size:3
Alignment explanation
Indices: 128035598--128035702 Score: 192
Period size: 3 Copynumber: 34.7 Consensus size: 3
128035588 TTTCTTTTTC
*
128035598 TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
128035646 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
128035694 TTA TCTA TT
1 TTA T-TA TT
128035703 CATGCATTTT
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
3 96 0.97
4 3 0.03
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Done.