Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, whole genome shotgun sequence
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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 13 of 18
Found at i:5386700 original size:15 final size:16
Alignment explanation
Indices: 5386676--5386708 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5386666 ACATATGAAC
*
5386676 AAATAGAATAAA-AAT
1 AAATAAAATAAATAAT
5386691 AAATAAAATAAATAAT
1 AAATAAAATAAATAAT
5386707 AA
1 AA
5386709 TAAGAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATAAAATAAATAAT
Found at i:5387083 original size:22 final size:23
Alignment explanation
Indices: 5387055--5387097 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
5387045 TAAAGCCGAA
5387055 AGACTACAAAGCTGGG-TGTGTC
1 AGACTACAAAGCTGGGCTGTGTC
5387077 AGACTACAAAGCTGGGCTGTG
1 AGACTACAAAGCTGGGCTGTG
5387098 AAGACACACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.21
Consensus pattern (23 bp):
AGACTACAAAGCTGGGCTGTGTC
Found at i:5387102 original size:22 final size:22
Alignment explanation
Indices: 5387054--5387102 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
5387044 ATAAAGCCGA
5387054 AAGACTACAAAGCTGGGTGTGT
1 AAGACTACAAAGCTGGGTGTGT
*
5387076 CAGACTACAAAGCTGGGCTGTG-
1 AAGACTACAAAGCTGGG-TGTGT
5387098 AAGAC
1 AAGAC
5387103 ACACGCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (22 bp):
AAGACTACAAAGCTGGGTGTGT
Found at i:5388165 original size:20 final size:20
Alignment explanation
Indices: 5388140--5388180 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5388130 GATTATGCCT
5388140 TGCTTGTTGCTTTCCATAGG
1 TGCTTGTTGCTTTCCATAGG
5388160 TGCTTGTTGCTTTCCATAGG
1 TGCTTGTTGCTTTCCATAGG
5388180 T
1 T
5388181 ACATCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (20 bp):
TGCTTGTTGCTTTCCATAGG
Found at i:5394117 original size:49 final size:49
Alignment explanation
Indices: 5394037--5394178 Score: 196
Period size: 49 Copynumber: 2.9 Consensus size: 49
5394027 ACAAAGTTCG
* * *
5394037 TGATCAAGATCAAGT-TTGAAGACCTTTGAAGCCAAGATCAAGTGCTCA
1 TGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTGCTCA
* **
5394085 TGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTGTTTG
1 TGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTGCTCA
* * *
5394134 TTATTAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATTAAGTG
1 TGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTG
5394179 ATGTTCGTGA
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
48 15 0.18
49 69 0.82
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
TGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATCAAGTGCTCA
Found at i:5398653 original size:30 final size:30
Alignment explanation
Indices: 5398592--5398666 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
5398582 ATTTCTTGAT
* * *
5398592 TGAAGATGAAGTAGATGACATGCAAAAAGA
1 TGAAGATAAAGAAGATAACATGCAAAAAGA
* * *
5398622 TGCAGATAAAGAAGATAACATGGAAAGAGA
1 TGAAGATAAAGAAGATAACATGCAAAAAGA
5398652 TGAAGATGAAA-AAGA
1 TGAAGAT-AAAGAAGA
5398667 AGAAGTTGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 34 0.92
31 3 0.08
ACGTcount: A:0.53, C:0.05, G:0.27, T:0.15
Consensus pattern (30 bp):
TGAAGATAAAGAAGATAACATGCAAAAAGA
Found at i:5398662 original size:15 final size:16
Alignment explanation
Indices: 5398592--5398690 Score: 59
Period size: 15 Copynumber: 6.4 Consensus size: 16
5398582 ATTTCTTGAT
*
5398592 TGAAGATG-AAGTAGA
1 TGAAGATGAAAGAAGA
*
5398607 TG-ACATGCAAA-AAGA
1 TGAAGATG-AAAGAAGA
*
5398622 TGCAGAT-AAAGAAGA
1 TGAAGATGAAAGAAGA
*
5398637 T-AACATGGAAAG-AGA
1 TGAAGAT-GAAAGAAGA
5398652 TGAAGATGAAA-AAGA
1 TGAAGATGAAAGAAGA
* *
5398667 AGAAGTTGAAGACGAAGA
1 TGAAGATGAA-A-GAAGA
5398685 TGAAGA
1 TGAAGA
5398691 AACTTTTAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
14 10 0.16
15 31 0.49
16 14 0.22
18 8 0.13
ACGTcount: A:0.53, C:0.05, G:0.28, T:0.14
Consensus pattern (16 bp):
TGAAGATGAAAGAAGA
Found at i:5417456 original size:6 final size:6
Alignment explanation
Indices: 5417440--5417492 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
5417430 TCTGCACCGA
* * *
5417440 CAAATT GAAATT CAAATT GAAATT CAAATGT -AAATT CAAATT GAAATT
1 CAAATT CAAATT CAAATT CAAATT CAAAT-T CAAATT CAAATT CAAATT
*
5417488 TAAAT
1 CAAAT
5417493 GTAAAAGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 1 0.03
6 37 0.95
7 1 0.03
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (6 bp):
CAAATT
Found at i:5417457 original size:12 final size:12
Alignment explanation
Indices: 5417440--5417492 Score: 81
Period size: 12 Copynumber: 4.4 Consensus size: 12
5417430 TCTGCACCGA
5417440 CAAATTGAAATT
1 CAAATTGAAATT
5417452 CAAATTGAAATT
1 CAAATTGAAATT
5417464 CAAA-TGTAAATT
1 CAAATTG-AAATT
5417476 CAAATTGAAATT
1 CAAATTGAAATT
*
5417488 TAAAT
1 CAAAT
5417493 GTAAAAGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (12 bp):
CAAATTGAAATT
Found at i:5422673 original size:15 final size:16
Alignment explanation
Indices: 5422636--5422681 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5422626 AATTTTATGC
5422636 ATGTTATT-TATGTTAA
1 ATGTTATTATAT-TTAA
*
5422652 ATTTTATTATATTT-A
1 ATGTTATTATATTTAA
5422667 ATGTTATTATTATTT
1 ATGTTATTA-TATTT
5422682 TATTATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 9 0.35
16 14 0.54
17 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
ATGTTATTATATTTAA
Found at i:5422683 original size:26 final size:28
Alignment explanation
Indices: 5422652--5422711 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
5422642 TTTATGTTAA
*
5422652 ATTTTATTATATTTAATGTT-ATTATT-
1 ATTTTATTATAATTAATGTTAATTATTG
* *
5422678 ATTTTATTATAATTATTTTTAATTATTG
1 ATTTTATTATAATTAATGTTAATTATTG
5422706 ATTTTA
1 ATTTTA
5422712 AATTTTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 17 0.59
27 6 0.21
28 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (28 bp):
ATTTTATTATAATTAATGTTAATTATTG
Found at i:5424765 original size:18 final size:18
Alignment explanation
Indices: 5424742--5424780 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5424732 TTAAGGTTTA
*
5424742 ATATTACGTGACTGGTTG
1 ATATTACGTGACTGATTG
5424760 ATATTACGTGACTGATTG
1 ATATTACGTGACTGATTG
5424778 ATA
1 ATA
5424781 GGTCATTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.38
Consensus pattern (18 bp):
ATATTACGTGACTGATTG
Found at i:5425012 original size:113 final size:113
Alignment explanation
Indices: 5424766--5425026 Score: 335
Period size: 113 Copynumber: 2.3 Consensus size: 113
5424756 GTTGATATTA
* * * *
5424766 CGTGACTGATTGATAGGTCATTGCATGACAGCATGACTGGATTTTGGCTTGGGGTTAGAGTGTGT
1 CGTGACTGATTGATAGGTCATTGCGTGACAGCATGACTGGATTTAGGCATGGGGTTAGAGTGTGC
* *
5424831 ATGATTGCATTAGAGTTTAACATTGCATGACTAATTAATAGGTCTTTG
66 ATGATTGCATTAGAGTTTAACATTGCATGACTAATTAATAGATCATTG
* * *
5424879 CGTGACTTG-TTGATAAGTCATTGCGTGACAACATGACTGGATTTAGGCATGGGGTTAGGGTGTG
1 CGTGAC-TGATTGATAGGTCATTGCGTGACAGCATGACTGGATTTAGGCATGGGGTTAGAGTGTG
* * * ** *
5424943 CGTGATTGCATTAGGGTTTAACATTGCATGATTGGTTGATAGATCATTG
65 CATGATTGCATTAGAGTTTAACATTGCATGACTAATTAATAGATCATTG
* * * *
5424992 TGTGGCTGATTGACAGGTCATTGTGTGACAGCATG
1 CGTGACTGATTGATAGGTCATTGCGTGACAGCATG
5425027 GCGTCACTTA
Statistics
Matches: 125, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
112 2 0.02
113 121 0.97
114 2 0.02
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (113 bp):
CGTGACTGATTGATAGGTCATTGCGTGACAGCATGACTGGATTTAGGCATGGGGTTAGAGTGTGC
ATGATTGCATTAGAGTTTAACATTGCATGACTAATTAATAGATCATTG
Found at i:5425211 original size:191 final size:200
Alignment explanation
Indices: 5424887--5425365 Score: 573
Period size: 191 Copynumber: 2.4 Consensus size: 200
5424877 TGCGTGACTT
* * * *
5424887 GTTGATAAGTCATTGCGTGACAACATGACTGGATTTAGGCATGGGGTTAGGGTGTGCGTGATTGC
1 GTTGATAGGTCATTGCGTGACAGCATGAATGGATTTAGGCATGGGGTTAAGGTGTGCGTGATTGC
* ** *
5424952 ATTAGGGTTTAACATTGCATGATTGGTTGATAGATCATTGTGTGGCTGATTGACAGGTCATTGTG
66 ATTAGGATTTAACATTGCATGATTGGTTGATAGATCATTACGTAGCTGATTGACAGGTCATTGTG
* * * **
5425017 TG-A-CA-G-C-A-T-GGC-G-TCACTTATGCTGTGCGTGATTGCATTAGGGTTTAACATTGTGT
131 TGAAGCATGACGATTAGGCAGATCACTTATGCTGTGCATGATTGCATTAAGGTTTAACAGTGCAT
**
5425073 GATTG
196 GACAG
* * *
5425078 GTTGATAGGTCATTGCATGACAGCATGATTGGATTTAGGAATGGGGTTAAGGTGTGCGTGATTGC
1 GTTGATAGGTCATTGCGTGACAGCATGAATGGATTTAGGCATGGGGTTAAGGTGTGCGTGATTGC
* * * *
5425143 ATTAAGATTTAACATTGCATGTTTGGTTGATA-AGTCATTACGTAGCTTATTGAGAGGTCATTGT
66 ATTAGGATTTAACATTGCATGATTGGTTGATAGA-TCATTACGTAGCTGATTGACAGGTCATTGT
5425207 GTGACAGCATGACTGGATTTAGGCATGGCATCACTTATGCTGTGCATGATTGCATTAAGGTTTAA
130 GTGA-AGCATGAC--GA-TTAGGCA--G-ATCACTTATGCTGTGCATGATTGCATTAAGGTTTAA
5425272 CAGTGCATGACAG
188 CAGTGCATGACAG
** * * *
5425285 GTTGATAGGTTTTTGCGTGACAGCATGAATGGATTTAGGCATGGGGTTATGGTGTGCATGATTGT
1 GTTGATAGGTCATTGCGTGACAGCATGAATGGATTTAGGCATGGGGTTAAGGTGTGCGTGATTGC
5425350 ATTAGGATTTAACATT
66 ATTAGGATTTAACATT
5425366 ACGTGATTAA
Statistics
Matches: 241, Mismatches: 30, Indels: 18
0.83 0.10 0.06
Matches are distributed among these distances:
190 1 0.00
191 116 0.48
193 1 0.00
194 2 0.01
195 1 0.00
196 1 0.00
199 1 0.00
201 1 0.00
202 3 0.01
205 1 0.00
207 113 0.47
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.35
Consensus pattern (200 bp):
GTTGATAGGTCATTGCGTGACAGCATGAATGGATTTAGGCATGGGGTTAAGGTGTGCGTGATTGC
ATTAGGATTTAACATTGCATGATTGGTTGATAGATCATTACGTAGCTGATTGACAGGTCATTGTG
TGAAGCATGACGATTAGGCAGATCACTTATGCTGTGCATGATTGCATTAAGGTTTAACAGTGCAT
GACAG
Found at i:5425475 original size:94 final size:94
Alignment explanation
Indices: 5425192--5425478 Score: 343
Period size: 94 Copynumber: 3.1 Consensus size: 94
5425182 ACGTAGCTTA
* * * *
5425192 TTGAGAGGTCATTGTGTGACAGCATGACTGGATTTAGGCATGGCATCACTTATGCTGTGCATGAT
1 TTGATAGGTTATTGTGTGACAGCATGAATGGATTTAGGCATGGCGTCACTTATGCTGTGCATGAT
* * * *
5425257 TGCATTAAGGTTTAACAGTGCATGACAGG
66 TGTATTAAGGTTTAACATTACATGACTGG
* * * *
5425286 TTGATAGGTTTTTGCGTGACAGCATGAATGGATTTAGGCATGG-G---GTTATGGTGTGCATGAT
1 TTGATAGGTTATTGTGTGACAGCATGAATGGATTTAGGCATGGCGTCACTTATGCTGTGCATGAT
* * **
5425347 TGTATT-AGGATTTAACATTACGTGATTAA
66 TGTATTAAGG-TTTAACATTACATGACTGG
* **
5425376 TTGATAGGTTATTGTGTGACTA-CATGATTGGATTTAGGCATGGCGTCACTTATGCTGTGTGTGA
1 TTGATAGGTTATTGTGTGAC-AGCATGAATGGATTTAGGCATGGCGTCACTTATGCTGTGCATGA
5425440 TTGTATTAAGGTTTAACATTACATGACTGG
65 TTGTATTAAGGTTTAACATTACATGACTGG
5425470 TTGATAGGT
1 TTGATAGGT
5425479 CTTTACGTGA
Statistics
Matches: 159, Mismatches: 27, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
89 3 0.02
90 70 0.44
91 2 0.01
94 81 0.51
95 3 0.02
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.36
Consensus pattern (94 bp):
TTGATAGGTTATTGTGTGACAGCATGAATGGATTTAGGCATGGCGTCACTTATGCTGTGCATGAT
TGTATTAAGGTTTAACATTACATGACTGG
Found at i:5425489 original size:23 final size:23
Alignment explanation
Indices: 5425458--5425501 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5425448 AGGTTTAACA
5425458 TTACATGACTGGTTGATAGGTCT
1 TTACATGACTGGTTGATAGGTCT
* *
5425481 TTACGTGACTTGTTGATAGGT
1 TTACATGACTGGTTGATAGGT
5425502 GAGTGAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.41
Consensus pattern (23 bp):
TTACATGACTGGTTGATAGGTCT
Found at i:5427651 original size:24 final size:25
Alignment explanation
Indices: 5427619--5427665 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
5427609 TGCAATGTAG
* * *
5427619 TTGGAGATCTAGCGGGCAATGCAAT
1 TTGGAGATCCAACGAGCAATGCAAT
5427644 TTGG-GATCCAACGAGCAATGCA
1 TTGGAGATCCAACGAGCAATGCA
5427666 GTTGCAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (25 bp):
TTGGAGATCCAACGAGCAATGCAAT
Found at i:5429369 original size:26 final size:26
Alignment explanation
Indices: 5429354--5429405 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5429344 ATCTTTAAAT
5429354 TATTCTTTGGTGTATCATTTACAAAA
1 TATTCTTTGGTGTATCATTTACAAAA
**
5429380 TATTCTTTTTTGTATCATTTAACAAA
1 TATTCTTTGGTGTATCATTT-ACAAA
5429406 GAGAAAAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (26 bp):
TATTCTTTGGTGTATCATTTACAAAA
Found at i:5429972 original size:72 final size:72
Alignment explanation
Indices: 5429852--5429993 Score: 169
Period size: 72 Copynumber: 2.0 Consensus size: 72
5429842 CGTTACTAGT
* * * * *
5429852 TATTATGGAATCACGTGAGTAATAAATATAGAAATGTATTACTTGTTATTATGAAATCGCGTGAC
1 TATTATAGAATCACATGAGTAATAAATATAGAAATGCATCACTTGTTATTATGAAATCACGTGAC
5429917 TAGTTGA
66 TAGTTGA
* * ** *
5429924 TATTATAGAATCACATGAGTAGTAAATATGGAGTTGCATCA-TTAGTTATTATGGAATCACGTGA
1 TATTATAGAATCACATGAGTAATAAATATAGAAATGCATCACTT-GTTATTATGAAATCACGTGA
*
5429988 GTAGTT
65 CTAGTT
5429994 ATTATGGAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
71 2 0.03
72 56 0.97
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (72 bp):
TATTATAGAATCACATGAGTAATAAATATAGAAATGCATCACTTGTTATTATGAAATCACGTGAC
TAGTTGA
Found at i:5429992 original size:23 final size:23
Alignment explanation
Indices: 5429966--5430010 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5429956 GTTGCATCAT
5429966 TAGTTATTATGGAATCACGTGAG
1 TAGTTATTATGGAATCACGTGAG
*
5429989 TAGTTATTATGGAATCGCGTGA
1 TAGTTATTATGGAATCACGTGA
5430011 CTCTTTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.36
Consensus pattern (23 bp):
TAGTTATTATGGAATCACGTGAG
Found at i:5433894 original size:22 final size:22
Alignment explanation
Indices: 5433857--5433919 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
5433847 CTGGCCTAAT
* *
5433857 GTCAGGCAATACATAACAA-CA
1 GTCACGCAATACATAAAAATCA
*
5433878 GATCACGCAATATATAAAAATCA
1 G-TCACGCAATACATAAAAATCA
* *
5433901 GTCACACAATACTTAAAAA
1 GTCACGCAATACATAAAAA
5433920 CTAGTGAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.03
22 30 0.88
23 3 0.09
ACGTcount: A:0.51, C:0.21, G:0.10, T:0.19
Consensus pattern (22 bp):
GTCACGCAATACATAAAAATCA
Found at i:5434107 original size:22 final size:22
Alignment explanation
Indices: 5434060--5434109 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5434050 CTAGCCCAGT
* *
5434060 GTCACGTAATACATAATAATAG
1 GTCACGCAATACATAAAAATAG
*
5434082 GTCACGCAATATATAAAAATCA-
1 GTCACGCAATACATAAAAAT-AG
5434104 GTCACG
1 GTCACG
5434110 TAATGCCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (22 bp):
GTCACGCAATACATAAAAATAG
Found at i:5434275 original size:202 final size:202
Alignment explanation
Indices: 5433705--5434316 Score: 789
Period size: 203 Copynumber: 3.0 Consensus size: 202
5433695 ATATTTATGC
* *
5433705 AATGCTTAAAAACTAGAGAACAAAAGCCTCAAAACAAGAGATGAATTACACAAGTCATGCACCAC
1 AATGCTTAAAAACTAGTGAACAAAAACCTC-AAACAAGAGATGAATTACACAAGTCATGCACCAC
* * * *
5433770 CAGTCTCGCAATACCTAATAATAAGTCACTCAATACTTAATATCCACTTACATTATGCCAACATA
65 CAGTCTTGCAATACCTAATAATAAGTCACTTAATGCTTAATATCCACTCACATTATGCCAACATA
* * * *
5433835 ACTAGTCACGTACT-GGCCTAATGTCAGGCAATACATAACAACAGATCACGCAATATATAAAAAT
130 ACCAGTCACGTACTAGACC-AATGTCACGCAATACATAACAACAGGTCACGCAATATATAAAAAT
**
5433899 CAGTCACAC
194 CAGTCACGT
* * * * *
5433908 AATACTTAAAAACTAGTGAACAAAAACCTCAAAGTAAGAGATGAATGACACAAGTCATACACCCC
1 AATGCTTAAAAACTAGTGAACAAAAACCTCAAA-CAAGAGATGAATTACACAAGTCATGCACCAC
* *
5433973 CAGTTTTGCAATACCTAATAATAAGTCACTTAATGCTTAATATCCACTCACATTATGCCAATATA
65 CAGTCTTGCAATACCTAATAATAAGTCACTTAATGCTTAATATCCACTCACATTATGCCAACATA
* * * * *
5434038 ACCAGTCACGTACTAGCCCAGTGTCACGTAATACATAATAATAGGTCACGCAATATATAAAAATC
130 ACCAGTCACGTACTAGACCAATGTCACGCAATACATAACAACAGGTCACGCAATATATAAAAATC
5434103 AGTCACGT
195 AGTCACGT
* * *
5434111 AATGCCTAAAAACTAGTGAACAAAAACCTCAAACAAGAGATGAATTACAAAAGTCACGCACCACC
1 AATGCTTAAAAACTAGTGAACAAAAACCTCAAACAAGAGATGAATTACACAAGTCATGCACCACC
* * * * * * *
5434176 AGCCTTACAATATCTAATAATAAGTCACTTGATGCCTAATATCAACTCACATTATGCTAACATAA
66 AGTCTTGCAATACCTAATAATAAGTCACTTAATGCTTAATATCCACTCACATTATGCCAACATAA
* * * * * * *
5434241 CCGGTTACGTACTAGACCAACGTTACGCAATACATAACAACAAGTCACG-ATATACATACAAA-C
131 CCAGTCACGTACTAGACCAATGTCACGCAATACATAACAACAGGTCACGCA-ATATATAAAAATC
5434304 TAGTCACGT
195 -AGTCACGT
5434313 AATG
1 AATG
5434317 TTTCAACAGA
Statistics
Matches: 353, Mismatches: 52, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
201 2 0.01
202 145 0.41
203 203 0.58
204 3 0.01
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (202 bp):
AATGCTTAAAAACTAGTGAACAAAAACCTCAAACAAGAGATGAATTACACAAGTCATGCACCACC
AGTCTTGCAATACCTAATAATAAGTCACTTAATGCTTAATATCCACTCACATTATGCCAACATAA
CCAGTCACGTACTAGACCAATGTCACGCAATACATAACAACAGGTCACGCAATATATAAAAATCA
GTCACGT
Found at i:5434295 original size:22 final size:22
Alignment explanation
Indices: 5434270--5434311 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5434260 ACGTTACGCA
5434270 ATACATA-ACAACAAGTCACGAT
1 ATACATACA-AACAAGTCACGAT
*
5434292 ATACATACAAACTAGTCACG
1 ATACATACAAACAAGTCACG
5434312 TAATGTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.48, C:0.24, G:0.10, T:0.19
Consensus pattern (22 bp):
ATACATACAAACAAGTCACGAT
Found at i:5437404 original size:2 final size:2
Alignment explanation
Indices: 5437397--5437429 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5437387 CTAAAGGAAT
5437397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5437430 TCAAGATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5446305 original size:3 final size:3
Alignment explanation
Indices: 5446297--5446354 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
5446287 GCATTTACAT
5446297 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5446345 TAA TAA TAA T
1 TAA TAA TAA T
5446355 TGTTATGAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5452442 original size:17 final size:17
Alignment explanation
Indices: 5452422--5452458 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5452412 TAAGAACAAA
5452422 AAATAATAA-AATAAAAT
1 AAATAATAATAAT-AAAT
5452439 AAATAATAATAATAAAT
1 AAATAATAATAATAAAT
5452456 AAA
1 AAA
5452459 AAGGTGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAATAATAATAAAT
Found at i:5454544 original size:19 final size:18
Alignment explanation
Indices: 5454522--5454577 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
5454512 AATATTTTAT
5454522 AATATTAAATATTAAAATA
1 AATATTAAATA-TAAAATA
5454541 AATA-TATAATATAAGAATA
1 AATATTA-AATATAA-AATA
5454560 AA-ATTAAA-ATAAAATA
1 AATATTAAATATAAAATA
5454576 AA
1 AA
5454578 ATATAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.18
17 4 0.12
18 8 0.24
19 16 0.47
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AATATTAAATATAAAATA
Found at i:5454560 original size:11 final size:10
Alignment explanation
Indices: 5454520--5454593 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 10
5454510 AAAATATTTT
*
5454520 ATAATATTAA
1 ATAATATAAA
5454530 AT-AT-TAAA
1 ATAATATAAA
*
5454538 ATAA-AT-AT
1 ATAATATAAA
5454546 ATAATATAAGA
1 ATAATATAA-A
*
5454557 ATAAAATTAAA
1 ATAATA-TAAA
*
5454568 ATAAAATAAA
1 ATAATATAAA
*
5454578 AT-ATAAAAA
1 ATAATATAAA
5454587 ATAATAT
1 ATAATAT
5454594 TTATATAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
8 10 0.20
9 13 0.26
10 12 0.24
11 12 0.24
12 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (10 bp):
ATAATATAAA
Found at i:5454572 original size:5 final size:5
Alignment explanation
Indices: 5454534--5454590 Score: 53
Period size: 5 Copynumber: 10.6 Consensus size: 5
5454524 TATTAAATAT
*
5454534 TAAAA TAAATA TATAATA TAAGAA TAAAA TTAAAA TAAAA TAAAA TATAA
1 TAAAA TAAA-A TA-AA-A TAA-AA TAAAA -TAAAA TAAAA TAAAA TAAAA
5454584 -AAAA TAA
1 TAAAA TAA
5454591 TATTTATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 3 0.07
5 22 0.49
6 13 0.29
7 7 0.16
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (5 bp):
TAAAA
Found at i:5454749 original size:14 final size:14
Alignment explanation
Indices: 5454730--5454797 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
5454720 GAATGATATT
5454730 ATATAAAATTAATA
1 ATATAAAATTAATA
*
5454744 ATATAAATATAAAT-
1 ATATAAA-ATTAATA
*
5454758 ATATTAAAAATAA-A
1 ATA-TAAAATTAATA
5454772 ATAATAAATATATAATA
1 AT-ATAAA-AT-TAATA
5454789 ATAATAAAA
1 AT-ATAAAA
5454798 ATAAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 19 0.44
15 11 0.26
16 4 0.09
17 9 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATAAAATTAATA
Found at i:5454768 original size:11 final size:10
Alignment explanation
Indices: 5454729--5455028 Score: 66
Period size: 10 Copynumber: 30.2 Consensus size: 10
5454719 AGAATGATAT
*
5454729 TATATAAAAT
1 TATATAAAAA
5454739 TA-ATAATATAA
1 TATATAA-A-AA
*
5454750 -ATATAAATA
1 TATATAAAAA
5454759 TAT-TAAAAA
1 TATATAAAAA
*
5454768 TAAAATAATAAA
1 T-ATATAA-AAA
*
5454780 TATATAATAA
1 TATATAAAAA
5454790 TA-ATAAAAA
1 TATATAAAAA
*
5454799 TA-AAAAAAA
1 TATATAAAAA
* *
5454808 TATATGAACA
1 TATATAAAAA
*
5454818 T-TA-AAATA
1 TATATAAAAA
*
5454826 TATTTAAGAAA
1 TATATAA-AAA
5454837 TGATAT-----
1 T-ATATAAAAA
5454843 TATATAAAAA
1 TATATAAAAA
*
5454853 T-TAATAAATA
1 TAT-ATAAAAA
* *
5454863 TAAAATATAAA
1 T-ATATAAAAA
5454874 TAT-TAAAAA
1 TATATAAAAA
*
5454883 TAAAATATAAAA
1 T-ATATA-AAAA
*
5454895 TATATAAATA
1 TATATAAAAA
5454905 TATAATAAAAA
1 TAT-ATAAAAA
*
5454916 TA-A-AATATA
1 TATATAA-AAA
5454925 TGATATTAAAATA
1 T-ATA-TAAAA-A
* *
5454938 TATTTAAGAA
1 TATATAAAAA
* * *
5454948 -A-ATGATAT
1 TATATAAAAA
5454956 TATATAAAAA
1 TATATAAAAA
5454966 T-TAATAAAAA
1 TAT-ATAAAAA
*
5454976 -ATATAAATA
1 TATATAAAAA
5454985 TAT-TAAAAAA
1 TATAT-AAAAA
*
5454995 TATATATATAA
1 TATATA-AAAA
*
5455006 TATTATAATAA
1 TA-TATAAAAA
*
5455017 TAAATAAAAA
1 TATATAAAAA
5455027 TA
1 TA
5455029 AAATATATGA
Statistics
Matches: 209, Mismatches: 42, Indels: 78
0.64 0.13 0.24
Matches are distributed among these distances:
5 4 0.02
6 1 0.00
8 9 0.04
9 51 0.24
10 68 0.33
11 53 0.25
12 19 0.09
13 4 0.02
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
TATATAAAAA
Found at i:5454785 original size:31 final size:31
Alignment explanation
Indices: 5454740--5454803 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
5454730 ATATAAAATT
*
5454740 AATAATATAAATATAA-ATATATTAAAAATAA
1 AATAATATAAATATAATA-ATAATAAAAATAA
5454771 AATAATA-AATATATAATAATAATAAAAATAA
1 AATAATATAA-ATATAATAATAATAAAAATAA
5454802 AA
1 AA
5454804 AAAATATATG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 2 0.07
31 27 0.90
32 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (31 bp):
AATAATATAAATATAATAATAATAAAAATAA
Found at i:5454800 original size:23 final size:23
Alignment explanation
Indices: 5454621--5454802 Score: 80
Period size: 23 Copynumber: 8.0 Consensus size: 23
5454611 ACAAATTGAA
*
5454621 ATATAATATATAATATAAA-AAAT
1 ATATAATA-ATAATAAAAATAAAT
5454644 ATATTAA-AGA-AATGAAAAA-AAAT
1 ATA-TAATA-ATAAT-AAAAATAAAT
* *
5454667 ATAAAATTATAATAATAAATAAA-
1 ATATAATAATAATAA-AAATAAAT
* *
5454690 ATAAAATATATGACATTAAAAT--AT
1 ATATAATA-AT-A-ATAAAAATAAAT
* * * * *
5454714 ATTTAAGAATGATATTATATAAA-
1 ATATAATAATAATA-AAAATAAAT
*
5454737 AT-TAATAAT-ATAAATATAAAT
1 ATATAATAATAATAAAAATAAAT
* *
5454758 ATATTAAAAATAA-AATAATAAAT
1 ATA-TAATAATAATAAAAATAAAT
5454781 ATATAATAATAATAAAAATAAA
1 ATATAATAATAATAAAAATAAA
5454803 AAAAATATAT
Statistics
Matches: 121, Mismatches: 20, Indels: 36
0.68 0.11 0.20
Matches are distributed among these distances:
20 7 0.06
21 7 0.06
22 25 0.21
23 59 0.49
24 15 0.12
25 5 0.04
26 3 0.02
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (23 bp):
ATATAATAATAATAAAAATAAAT
Found at i:5454823 original size:51 final size:51
Alignment explanation
Indices: 5454729--5454825 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 51
5454719 AGAATGATAT
* * *
5454729 TATATAAAATTAATAATATAAATATAAATATATTAAAAATAAAATAATAAA
1 TATATAAAATTAATAAAATAAATAAAAATATATGAAAAATAAAATAATAAA
* *
5454780 TATATAATAA-TAATAAAAATAAA-AAAAATATATGAACATTAAAATA
1 TATATAA-AATTAAT-AAAATAAATAAAAATATATGAAAAATAAAATA
5454826 TATTTAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
51 30 0.77
52 9 0.23
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (51 bp):
TATATAAAATTAATAAAATAAATAAAAATATATGAAAAATAAAATAATAAA
Found at i:5454870 original size:7 final size:7
Alignment explanation
Indices: 5454858--5454939 Score: 75
Period size: 7 Copynumber: 12.0 Consensus size: 7
5454848 AAAAATTAAT
5454858 AAATATA
1 AAATATA
5454865 AAATAT-
1 AAATATA
5454871 AAATATTA
1 AAATA-TA
5454879 AAA-ATA
1 AAATATA
5454885 AAATATA
1 AAATATA
5454892 AAATATA
1 AAATATA
5454899 TAAATAT-
1 -AAATATA
*
5454906 ATA-ATA
1 AAATATA
5454912 AAA-ATA
1 AAATATA
5454918 AAATATA
1 AAATATA
**
5454925 TGATATTA
1 AAATA-TA
5454933 AAATATA
1 AAATATA
5454940 TTTAAGAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
5 2 0.03
6 20 0.32
7 26 0.42
8 14 0.23
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (7 bp):
AAATATA
Found at i:5454925 original size:20 final size:20
Alignment explanation
Indices: 5454854--5455049 Score: 65
Period size: 20 Copynumber: 10.6 Consensus size: 20
5454844 ATATAAAAAT
* *
5454854 TAATAAATATAAAATATAAA
1 TAATAAAAATAAAATATATA
*
5454874 TATTAAAAATAAAATATA-A
1 TAATAAAAATAAAATATATA
*
5454893 -AAT----ATATAA-ATATA
1 TAATAAAAATAAAATATATA
5454907 TAATAAAAATAAAATATATGA
1 TAATAAAAATAAAATATAT-A
*
5454928 T-AT-----TAAAATATATT
1 TAATAAAAATAAAATATATA
* * *
5454942 TAA-GAAAATGATAT-TATA
1 TAATAAAAATAAAATATATA
*
5454960 TAA-AAATTAATAAAAAATATA
1 TAATAAA--AATAAAATATATA
*
5454981 -AATATATTAA-AAAATATATA
1 TAATA-A-AAATAAAATATATA
* * *
5455001 T-ATAATATTATAATA-ATA
1 TAATAAAAATAAAATATATA
5455019 -AATAAAAATAAAATATATGA
1 TAATAAAAATAAAATATAT-A
*
5455039 TATTAAAAATA
1 TAATAAAAATA
5455050 TATTTAAAAA
Statistics
Matches: 129, Mismatches: 21, Indels: 51
0.64 0.10 0.25
Matches are distributed among these distances:
13 3 0.02
14 7 0.05
15 14 0.11
18 26 0.20
19 18 0.14
20 42 0.33
21 18 0.14
22 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TAATAAAAATAAAATATATA
Found at i:5454993 original size:18 final size:18
Alignment explanation
Indices: 5454970--5455004 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5454960 TAAAAATTAA
5454970 TAAAAAATATAAATATAT
1 TAAAAAATATAAATATAT
*
5454988 TAAAAAATATATATATA
1 TAAAAAATATAAATATA
5455005 ATATTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAAATATAAATATAT
Found at i:5455001 original size:16 final size:17
Alignment explanation
Indices: 5454822--5455003 Score: 53
Period size: 16 Copynumber: 11.4 Consensus size: 17
5454812 TGAACATTAA
*
5454822 AATATATTTAAGAAATGAT
1 AATATA-TTAAAAAAT-AT
*
5454841 ATTATA-T-AAAAAT-T
1 AATATATTAAAAAATAT
* *
5454855 AATA-AATATAAAATAT
1 AATATATTAAAAAATAT
5454871 AA-ATATT-AAAAATA-
1 AATATATTAAAAAATAT
*
5454885 AA-ATA-TAAAATATAT
1 AATATATTAAAAAATAT
* *
5454900 AAATATATAATAAAAATAA
1 -AATATATTA-AAAAATAT
**
5454919 AATATATGATATTAAA-AT
1 AATATAT--TAAAAAATAT
5454937 -ATAT-TTAAGAAAATGAT
1 AATATATTAA-AAAAT-AT
*
5454954 ATTATA-T-AAAAAT-T
1 AATATATTAAAAAATAT
*
5454968 AATA-A--AAAATATA-
1 AATATATTAAAAAATAT
5454981 AATATATTAAAAAATAT
1 AATATATTAAAAAATAT
5454998 -ATATAT
1 AATATAT
5455004 AATATTATAA
Statistics
Matches: 120, Mismatches: 20, Indels: 49
0.63 0.11 0.26
Matches are distributed among these distances:
13 12 0.10
14 23 0.19
15 15 0.12
16 31 0.26
17 11 0.09
18 13 0.11
19 14 0.12
20 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AATATATTAAAAAATAT
Found at i:5455040 original size:111 final size:110
Alignment explanation
Indices: 5454658--5455102 Score: 617
Period size: 111 Copynumber: 4.0 Consensus size: 110
5454648 TAAAGAAATG
5454658 AAAA-AAAATATAAAAT-TATAATAATAAAT-AAAATAAAATATATGACATTAAAATATATTTAA
1 AAAATAAAATATAAAATATATAATAATAAATAAAAATAAAATATATGACATTAAAATATATTTAA
5454720 G-AATGATATTATAT-AAAATTAATAATATAAATATAAATATATTA
66 GAAATGATATTATATAAAAATTAATAA-ATAAATATAAATATATTA
*
5454764 AAAATAAAATAATAAATATATAATAATAATAAA-AATAAAAAAAATATATGAACATTAAAATATA
1 AAAATAAAAT-ATAAA-ATAT-ATAATAATAAATAA-AAATAAAATATATG-ACATTAAAATATA
*
5454828 TTTAAGAAATGATATTATATAAAAATTAATAAATATAAAATATAA-ATATTA
61 TTTAAGAAATGATATTATATAAAAATTAATAAATA-AATATA-AATATATTA
*
5454879 AAAATAAAATATAAAATATATAA-ATATATAATAAAAATAAAATATATGATATTAAAATATATTT
1 AAAATAAAATATAAAATATATAATA-ATA-AATAAAAATAAAATATATGACATTAAAATATATTT
5454943 AAGAAAATGATATTATATAAAAATTAATAAA-AAATATAAATATATTA
64 AAG-AAATGATATTATATAAAAATTAATAAATAAATATAAATATATTA
* * *
5454990 AAAA-ATATATATATAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATT
1 AAAATA-AAATATAAAATA-TATAATAATAAATAAAAATAAAATATATGACATT-AAAATATATT
5455054 TAA-AAATGATATTATATAAAAATTAATTAAA-AAATATAAATATATTA
63 TAAGAAATGATATTATATAAAAATTAA-TAAATAAATATAAATATATTA
5455101 AA
1 AA
5455103 CTTATATTTT
Statistics
Matches: 310, Mismatches: 7, Indels: 39
0.87 0.02 0.11
Matches are distributed among these distances:
106 4 0.01
107 5 0.02
108 5 0.02
109 2 0.01
110 27 0.09
111 84 0.27
112 60 0.19
113 66 0.21
114 23 0.07
115 32 0.10
116 2 0.01
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (110 bp):
AAAATAAAATATAAAATATATAATAATAAATAAAAATAAAATATATGACATTAAAATATATTTAA
GAAATGATATTATATAAAAATTAATAAATAAATATAAATATATTA
Found at i:5455052 original size:18 final size:17
Alignment explanation
Indices: 5454972--5455052 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 17
5454962 AAAATTAATA
*
5454972 AAAAATATAAATATATT
1 AAAAATATATATATATT
5454989 AAAAA-ATATATATA-T
1 AAAAATATATATATATT
* * *
5455004 AATATTATA-ATAATAAAT
1 AAAAATATATAT-AT-ATT
5455022 AAAAATAAAATATATGATATT
1 AAAAAT---ATATAT-ATATT
5455043 AAAAATATAT
1 AAAAATATAT
5455053 TTAAAAATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
15 6 0.12
16 13 0.27
17 6 0.12
18 9 0.18
21 11 0.22
22 4 0.08
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (17 bp):
AAAAATATATATATATT
Found at i:5455058 original size:33 final size:33
Alignment explanation
Indices: 5454980--5455060 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
5454970 TAAAAAATAT
* *
5454980 AAATATATTAAAAAATATATATATAATATTATA
1 AAATATATTTAAAAATAAATATATAATATTATA
* *
5455013 ATAATA-A-ATAAAAATAAAATATATGATATTA-A
1 A-AATATATTTAAAAAT-AAATATATAATATTATA
5455045 AAATATATTTAAAAAT
1 AAATATATTTAAAAAT
5455061 GATATTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
31 4 0.10
32 9 0.23
33 22 0.56
34 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (33 bp):
AAATATATTTAAAAATAAATATATAATATTATA
Found at i:5455065 original size:13 final size:13
Alignment explanation
Indices: 5455035--5455066 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5455025 AATAAAATAT
5455035 ATGATA-TTAAAA
1 ATGATATTTAAAA
5455047 AT-ATATTTAAAA
1 ATGATATTTAAAA
5455059 ATGATATT
1 ATGATATT
5455067 ATATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 10 0.56
13 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (13 bp):
ATGATATTTAAAA
Found at i:5455072 original size:171 final size:170
Alignment explanation
Indices: 5454665--5455102 Score: 415
Period size: 169 Copynumber: 2.6 Consensus size: 170
5454655 ATGAAAAAAA
* * *
5454665 ATATAAAATTATAATAATAAAT-AAAATAAAATATATGACATTAAAATATATTTAAGAATGATAT
1 ATATAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAATATATTTAAAAATGATAT
* * *
5454729 TATATAAAATTAAT-AATATAAATATAAATATATTAAAAATAAAATAATAAATATATAATAATAA
66 TATATAAAATTAATAAAAATAAA-ATATATATATTAAAAATAAAATAAGAAATATATAATAATAA
* *
5454793 TAAAAATAAAAAAAATATATGAACATTAAAATATATTTAAG
130 TAAAAATAAAAAAAATATATAAACATTAAAATATATATAAG
* * * * * * * *
5454834 AAATGATATTATATAAAAATTAATAAATATAAAATATA-AATATTAAAA-ATA---AAATAT-AA
1 ATATAATA-T-TATAATAATAAATAAAAATAAAATATATGATATTAAAATATATTTAAAAATGAT
* **
5454893 AATATATAAATATATAATAAAAATAAAATATATGATATT-AAAATATATTTAAGAAA-ATGAT-A
64 ATTATATAAA-AT-TAATAAAAATAAAATATAT-ATATTAAAAATA-AAATAAGAAATAT-ATAA
* * *
5454955 TTAT-ATAAAAATTAATAAAAAATATA-AATATATTAAAA-A-ATAT-AT
124 TAATAATAAAAA-TAA-AAAAAATATATAA-ACATTAAAATATATATAAG
5455000 ATATAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAAATGATA
1 ATATAATATTATAATAATAAATAAAAATAAAATATATGATATT-AAAATATATTTAAAAATGATA
* * *
5455065 TTATATAAAAATTAATTAAAA-AATATAAATATATTAAA
65 TTATAT-AAAATTAATAAAAATAAAATATATATATTAAA
5455103 CTTATATTTT
Statistics
Matches: 214, Mismatches: 34, Indels: 42
0.74 0.12 0.14
Matches are distributed among these distances:
164 24 0.11
165 6 0.03
166 21 0.10
167 19 0.09
168 31 0.14
169 53 0.25
170 17 0.08
171 28 0.13
172 15 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (170 bp):
ATATAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAATATATTTAAAAATGATAT
TATATAAAATTAATAAAAATAAAATATATATATTAAAAATAAAATAAGAAATATATAATAATAAT
AAAAATAAAAAAAATATATAAACATTAAAATATATATAAG
Found at i:5455097 original size:28 final size:28
Alignment explanation
Indices: 5455028--5455098 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 28
5455018 AAATAAAAAT
* *
5455028 AAAATATATGATAT-TAAAAATATATTTA
1 AAAATATA-AATATATAAAAATATATTAA
*
5455056 AAAATGAT-ATTATATAAAAAT-TAATTAA
1 AAAAT-ATAAATATATAAAAATAT-ATTAA
5455084 AAAATATAAATATAT
1 AAAATATAAATATAT
5455099 TAAACTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
27 6 0.17
28 27 0.77
29 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
AAAATATAAATATATAAAAATATATTAA
Found at i:5455272 original size:15 final size:15
Alignment explanation
Indices: 5455247--5455292 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
5455237 TATTATTTTC
*
5455247 CCTGTAATCACATTG
1 CCTGCAATCACATTG
* *
5455262 CTTGCAATCACATTA
1 CCTGCAATCACATTG
*
5455277 CCTGTAATCACATTG
1 CCTGCAATCACATTG
5455292 C
1 C
5455293 ATTGTAATGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (15 bp):
CCTGCAATCACATTG
Found at i:5456981 original size:21 final size:21
Alignment explanation
Indices: 5456935--5456981 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5456925 TTTGATTGGC
*
5456935 TATCTATTGATAGATGTTGTG
1 TATCTATTGATAGATGTTATG
*
5456956 CATCTATTGATAGATGTTCAT-
1 TATCTATTGATAGATGTT-ATG
5456977 TATCT
1 TATCT
5456982 TCAAAGTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.47
Consensus pattern (21 bp):
TATCTATTGATAGATGTTATG
Found at i:5458669 original size:34 final size:34
Alignment explanation
Indices: 5458650--5458718 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5458640 TAATGAGTCC
5458650 ACCCTAAAAACTCAAAATTTGCAAGATATGGAAA
1 ACCCTAAAAACTCAAAATTTGCAAGATATGGAAA
5458684 ACCCTAAAAACTCAAAATTTGCAAGATATGGAAA
1 ACCCTAAAAACTCAAAATTTGCAAGATATGGAAA
5458718 A
1 A
5458719 TGAATGGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (34 bp):
ACCCTAAAAACTCAAAATTTGCAAGATATGGAAA
Found at i:5459417 original size:50 final size:50
Alignment explanation
Indices: 5459354--5459458 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 50
5459344 ATAGTGCAAC
* * *
5459354 CTATCAATTGATGCTTCTT-AGTTTAGTTTAGGGTAATTTTGTTTGTTTAT
1 CTATCAATAGATGCTT-TTCAGTTTAATTTAGGGTAATTTTGTTTGGTTAT
5459404 CTATCAATAGATGCTTTTCAGTTTAATTTAGGGTAATTTTGTTTGGTTAT
1 CTATCAATAGATGCTTTTCAGTTTAATTTAGGGTAATTTTGTTTGGTTAT
5459454 CTATC
1 CTATC
5459459 TCAATTTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
49 2 0.04
50 49 0.96
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (50 bp):
CTATCAATAGATGCTTTTCAGTTTAATTTAGGGTAATTTTGTTTGGTTAT
Found at i:5462463 original size:2 final size:2
Alignment explanation
Indices: 5462456--5462487 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5462446 TTTTTCTAGA
5462456 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
5462488 GTGTGTGTGT
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:5473868 original size:21 final size:21
Alignment explanation
Indices: 5473837--5473900 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
5473827 CTCCAAATAC
*
5473837 ACATT-TTAAAACCTTTAGGT
1 ACATTCTTAAAACCTCTAGGT
5473857 ACATTCTTAAAACCTCTAGGT
1 ACATTCTTAAAACCTCTAGGT
*
5473878 ACATTCTTAAAACCTCTAAGT
1 ACATTCTTAAAACCTCTAGGT
5473899 AC
1 AC
5473901 CTATCATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 5 0.12
21 36 0.88
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (21 bp):
ACATTCTTAAAACCTCTAGGT
Found at i:5474011 original size:144 final size:145
Alignment explanation
Indices: 5473763--5474037 Score: 337
Period size: 144 Copynumber: 1.9 Consensus size: 145
5473753 GTAATTAGTG
*
5473763 TCAATATTTCTTTAAAGTTAAGTAACCTCATTTAGAGATGAAGAGTAACCTTTTTTTATGAAACC
1 TCAATATTTCTTTAAAGTTAAGTAACCTCATTTAGAGATGAAGAGCAACCTTTTTTTATGAAACC
* * *
5473828 TCCAAATACACATTTTAAAACCTTTAGGTACATTCTTAAAACCTCTAGG-TACATTCT-TAAAAC
66 TCCAAATACACATTCTAAAACCTTGAGGTACATTCTTAAAACCTCT-GGATACATTCTCCAAAAC
5473891 CTCTAAGTACCTATCA
130 CTCTAAGTACCTATCA
* * * *
5473907 TCAATATTTCTTTAAAGTTATGTAGCCTTATTTAGAGATGAGGAGCAA-CTTTTTCTTATGAAAC
1 TCAATATTTCTTTAAAGTTAAGTAACCTCATTTAGAGATGAAGAGCAACCTTTTT-TTATGAAAC
* * * * * *
5473971 CTTCGAGTATA-ATATCT-AAACCTTCGGGTGTAC-TTTTTAAAACCTCTGGATACATTCTCCAA
65 CTCCAAATACACAT-TCTAAAACCTT-GAG-GTACATTCTTAAAACCTCTGGATACATTCTCCAA
5474033 AACCT
127 AACCT
5474038 TCGGGTAATC
Statistics
Matches: 111, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
143 17 0.15
144 83 0.75
145 11 0.10
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (145 bp):
TCAATATTTCTTTAAAGTTAAGTAACCTCATTTAGAGATGAAGAGCAACCTTTTTTTATGAAACC
TCCAAATACACATTCTAAAACCTTGAGGTACATTCTTAAAACCTCTGGATACATTCTCCAAAACC
TCTAAGTACCTATCA
Found at i:5477425 original size:14 final size:15
Alignment explanation
Indices: 5477406--5477435 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5477396 ATAAGCCTAA
5477406 TTGCTAA-CACTTTT
1 TTGCTAACCACTTTT
5477420 TTGCTAACCACTTTT
1 TTGCTAACCACTTTT
5477435 T
1 T
5477436 GTATAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.23, G:0.07, T:0.50
Consensus pattern (15 bp):
TTGCTAACCACTTTT
Found at i:5494748 original size:21 final size:21
Alignment explanation
Indices: 5494719--5494758 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5494709 GTGATTTGGC
*
5494719 TAGTATATTAGTTTTAATTGT
1 TAGTATATTAGTTTCAATTGT
*
5494740 TAGTTTATTAGTTTCAATT
1 TAGTATATTAGTTTCAATT
5494759 TTTCTTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (21 bp):
TAGTATATTAGTTTCAATTGT
Found at i:5497777 original size:79 final size:79
Alignment explanation
Indices: 5497646--5497806 Score: 304
Period size: 79 Copynumber: 2.0 Consensus size: 79
5497636 GTTTTGGTAT
*
5497646 TTTGGCCATAACTCTCTCTAAAGAGTACCAAATGAAGTGACTCTTGGACTATTGGAAAGATAAGA
1 TTTGGCCATAACTCTCTCTAAAGAGTACCAAATGAAGCGACTCTTGGACTATTGGAAAGATAAGA
5497711 GAAAAAGATACAAC
66 GAAAAAGATACAAC
5497725 TTTGGCCATAACTCTCTCTAAAGAGTACCAAATGAAGCGACTCTTGGACTATTGGAAAGATAAGA
1 TTTGGCCATAACTCTCTCTAAAGAGTACCAAATGAAGCGACTCTTGGACTATTGGAAAGATAAGA
*
5497790 GAAAAATATACAAC
66 GAAAAAGATACAAC
5497804 TTT
1 TTT
5497807 CATGTTCACA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (79 bp):
TTTGGCCATAACTCTCTCTAAAGAGTACCAAATGAAGCGACTCTTGGACTATTGGAAAGATAAGA
GAAAAAGATACAAC
Found at i:5501405 original size:41 final size:41
Alignment explanation
Indices: 5501348--5501432 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
5501338 AAATCTAAGT
*
5501348 CTATCATAATATATTATATCTTAACAGTCCAACCCAATAAC
1 CTATCATAATATATTATATCTAAACAGTCCAACCCAATAAC
* * * *
5501389 CTATCATGATATATTATATCTAAATAGTTCAACCCAATAGC
1 CTATCATAATATATTATATCTAAACAGTCCAACCCAATAAC
5501430 CTA
1 CTA
5501433 ATATATTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (41 bp):
CTATCATAATATATTATATCTAAACAGTCCAACCCAATAAC
Found at i:5511695 original size:15 final size:14
Alignment explanation
Indices: 5511672--5511719 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
5511662 TCCTTGTCTT
5511672 TTTCTTCTTTCTCC
1 TTTCTTCTTTCTCC
*
5511686 TTTCTGTCTTTCTCT
1 TTTCT-TCTTTCTCC
5511701 TTTCTTCCTTTCTCTC
1 TTTCTT-CTTTCTC-C
5511717 TTT
1 TTT
5511720 GTTTCCAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.21
15 20 0.69
16 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTCTTCTTTCTCC
Found at i:5512871 original size:11 final size:11
Alignment explanation
Indices: 5512855--5512881 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5512845 GTTAGAATAT
5512855 TAATATTTTAA
1 TAATATTTTAA
5512866 TAATATTTTAA
1 TAATATTTTAA
5512877 TAATA
1 TAATA
5512882 AAATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAATATTTTAA
Found at i:5516836 original size:23 final size:23
Alignment explanation
Indices: 5516806--5517001 Score: 94
Period size: 23 Copynumber: 8.4 Consensus size: 23
5516796 GAATTTAGAG
5516806 TTTGTGACACGGCATGGAGGGAA
1 TTTGTGACACGGCATGGAGGGAA
* *
5516829 TTTGTGACACGGCCTAGAGGGAA
1 TTTGTGACACGGCATGGAGGGAA
* ** **
5516852 TCTGTGACACATCA--GAGTTCAGA
1 TTTGTGACACGGCATGGAG-GGA-A
* * *
5516875 GTT-TGACACGACATGGATGGAA
1 TTTGTGACACGGCATGGAGGGAA
* ** *
5516897 TTTGTGACACGGCA-GTATTCAGAG
1 TTTGTGACACGGCATGGA--GGGAA
* * *
5516921 TTTGTGACAAGCCATGTAGGGAA
1 TTTGTGACACGGCATGGAGGGAA
* * * *** *
5516944 TTTATGACATGGCAGGGTTCAGAG
1 TTTGTGACACGGCATGG-AGGGAA
5516968 TTTGGTGACACGGCATGGAGGGAA
1 TTT-GTGACACGGCATGGAGGGAA
5516992 TTTGTGACAC
1 TTTGTGACAC
5517002 TCCAAAGTTC
Statistics
Matches: 121, Mismatches: 42, Indels: 20
0.66 0.23 0.11
Matches are distributed among these distances:
21 3 0.02
22 14 0.12
23 64 0.53
24 26 0.21
25 14 0.12
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (23 bp):
TTTGTGACACGGCATGGAGGGAA
Found at i:5516952 original size:47 final size:47
Alignment explanation
Indices: 5516829--5517391 Score: 465
Period size: 47 Copynumber: 12.1 Consensus size: 47
5516819 ATGGAGGGAA
* **
5516829 TTTGTGACACGGCC-TAGAGGGAATCTGTGACACATCAG-AGTTCAGAG
1 TTTGTGACAC-GCCATGGAGGGAATCTGTGACACGGCAGTA-TTCAGAG
* * *
5516876 -TT-TGACACGACATGGATGGAATTTGTGACACGGCAGTATTCAGAG
1 TTTGTGACACGCCATGGAGGGAATCTGTGACACGGCAGTATTCAGAG
* * * * * **
5516921 TTTGTGACAAGCCATGTAGGGAATTTATGACATGGCAGGGTTCAGAG
1 TTTGTGACACGCCATGGAGGGAATCTGTGACACGGCAGTATTCAGAG
* * ** *
5516968 TTTGGTGACACGGCATGGAGGGAATTTGTGACACTCCA-AAGTTCAGAG
1 TTT-GTGACACGCCATGGAGGGAATCTGTGACACGGCAGTA-TTCAGAG
* * *
5517016 TTTGTGACACGACATGGAGGGAATCTGTGACAC-ACTAG-AGTTTAGAG
1 TTTGTGACACGCCATGGAGGGAATCTGTGACACGGC-AGTA-TTCAGAG
* * * *
5517063 -TT-TGACACAG-CATAGATGGAATCTGTGACATGACAGTATTCAGAG
1 TTTGTGACAC-GCCATGGAGGGAATCTGTGACACGGCAGTATTCAGAG
* *** **
5517108 TTTGTGACACGCCATGGAGGAAATCTGTGACACAATAGGGTTCA-AGG
1 TTTGTGACACGCCATGGAGGGAATCTGTGACACGGCAGTATTCAGA-G
* *
5517155 TTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGTGTTCAGAG
1 TTTGTGACACGCCATGGAGGGAATCTGTGACACGGCAGTATTCAGAG
* * * * * ** *
5517202 TTTATGACACGGCATGGAAGGAATCTTTAACACACCAG-AGTTTAGAG
1 TTTGTGACACGCCATGGAGGGAATCTGTGACACGGCAGTA-TTCAGAG
* * *
5517249 -TT-TGACACAG-CATGGATGGAATCTGTGACACGGTAGTATTCAAAG
1 TTTGTGACAC-GCCATGGAGGGAATCTGTGACACGGCAGTATTCAGAG
* * ** *
5517294 TTTGTGACACGCCATGGAGGGAATCTGGGACACAGCAGGGTTCAGGG
1 TTTGTGACACGCCATGGAGGGAATCTGTGACACGGCAGTATTCAGAG
*
5517341 TTTGTGACACGCCATGGAGGGAATCTGTGACAC-GCTAGTGTTCAGAG
1 TTTGTGACACGCCATGGAGGGAATCTGTGACACGGC-AGTATTCAGAG
5517388 TTTG
1 TTTG
5517392 ACATGCCAGC
Statistics
Matches: 422, Mismatches: 71, Indels: 46
0.78 0.13 0.09
Matches are distributed among these distances:
44 2 0.00
45 95 0.23
46 25 0.06
47 262 0.62
48 38 0.09
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (47 bp):
TTTGTGACACGCCATGGAGGGAATCTGTGACACGGCAGTATTCAGAG
Found at i:5517139 original size:23 final size:23
Alignment explanation
Indices: 5517110--5517191 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
5517100 ATTCAGAGTT
5517110 TGTGACACGCCATGGAGGAAATC
1 TGTGACACGCCATGGAGGAAATC
*** * *** * *
5517133 TGTGACACAATAGGGTTCAAGGTT
1 TGTGACACGCCATGGAGGAA-ATC
*
5517157 TGTGACACGCCATGGAGGGAATC
1 TGTGACACGCCATGGAGGAAATC
5517180 TGTGACACGCCA
1 TGTGACACGCCA
5517192 GTGTTCAGAG
Statistics
Matches: 39, Mismatches: 19, Indels: 2
0.65 0.32 0.03
Matches are distributed among these distances:
23 26 0.67
24 13 0.33
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (23 bp):
TGTGACACGCCATGGAGGAAATC
Found at i:5517244 original size:186 final size:186
Alignment explanation
Indices: 5516833--5517390 Score: 778
Period size: 186 Copynumber: 3.0 Consensus size: 186
5516823 AGGGAATTTG
* * * *
5516833 TGACACGGCCTAGAGGGAATCTGTGACACATCAGAGTTCAGAGTTTGACAC-GACATGGATGGAA
1 TGACACGGCATGGAGGGAATCTGTGACACACCAGAGTTTAGAGTTTGACACAG-CATGGATGGAA
* * * * * **
5516897 TTTGTGACACGGCAGTATTCAGAGTTTGTGACAAGCCATGTAGGGAATTTATGACATGGCAGGGT
65 TCTGTGACACGGCAGTATTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACAGCAGGGT
* * * ** *
5516962 TC-AGAGTTTGGTGACACGGCATGGAGGGAATTTGTGACACTCCAAAGTTCAGAGTTTG
130 TCAAG-GTTT-GTGACACGCCATGGAGGGAATCTGTGACACGCCAGTGTTCAGAGTTTA
* * *
5517020 TGACACGACATGGAGGGAATCTGTGACACACTAGAGTTTAGAGTTTGACACAGCATAGATGGAAT
1 TGACACGGCATGGAGGGAATCTGTGACACACCAGAGTTTAGAGTTTGACACAGCATGGATGGAAT
* * * **
5517085 CTGTGACATGACAGTATTCAGAGTTTGTGACACGCCATGGAGGAAATCTGTGACACAATAGGGTT
66 CTGTGACACGGCAGTATTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACAGCAGGGTT
5517150 CAAGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGTGTTCAGAGTTTA
131 CAAGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGTGTTCAGAGTTTA
* * *
5517206 TGACACGGCATGGAAGGAATCTTTAACACACCAGAGTTTAGAGTTTGACACAGCATGGATGGAAT
1 TGACACGGCATGGAGGGAATCTGTGACACACCAGAGTTTAGAGTTTGACACAGCATGGATGGAAT
* * *
5517271 CTGTGACACGGTAGTATTCAAAGTTTGTGACACGCCATGGAGGGAATCTGGGACACAGCAGGGTT
66 CTGTGACACGGCAGTATTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACAGCAGGGTT
* *
5517336 CAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCTAGTGTTCAGAGTTT
131 CAAGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGTGTTCAGAGTTT
5517391 GACATGCCAG
Statistics
Matches: 328, Mismatches: 41, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
186 211 0.64
187 114 0.35
188 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (186 bp):
TGACACGGCATGGAGGGAATCTGTGACACACCAGAGTTTAGAGTTTGACACAGCATGGATGGAAT
CTGTGACACGGCAGTATTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACAGCAGGGTT
CAAGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGTGTTCAGAGTTTA
Found at i:5517337 original size:139 final size:138
Alignment explanation
Indices: 5516845--5517399 Score: 429
Period size: 139 Copynumber: 4.0 Consensus size: 138
5516835 ACACGGCCTA
* * * * *
5516845 GAGGGAATCTGTGACAC-ATCA-GAGTTCAGAG-TT-TGACACGACATGGATGGAATTTGTGACA
1 GAGGAAATCTGTGACACAAT-AGGA-TTCAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACA
* * * * * * * *** *
5516906 CGGCAGTA-TTCAGAGTTTGTGACAAGCCATGTAGGGAATTTATGACATGGCAGGGTTCAGAGTT
64 CAGCAG-AGTTCAGAGTTT-TGACACGGCATGGAAGGAATCTGTGACACACCAGAGTTCAGAG-T
*
5516970 TGGTGACACGGCATG
126 T--TGACACGCCATG
* * * *
5516985 GAGGGAATTTGTGACACTCCAA-A-G-TTCAGAGTTTGTGACACGACATGGAGGGAATCTGTGAC
1 GAGGAAATCTGTGACA---CAATAGGATTCAAAGTTTGTGACACGCCATGGAGGGAATCTGTGAC
* * * * *
5517047 ACA-CTAGAGTTTAGAG-TTTGACACAGCATAGATGGAATCTGTGACATGA-CAGTA-TTCAGAG
63 ACAGC-AGAGTTCAGAGTTTTGACACGGCATGGAAGGAATCTGTGACA-CACCAG-AGTTCAGAG
5517108 TTTGTGACACGCCATG
125 -TT-TGACACGCCATG
* *
5517124 GAGGAAATCTGTGACACAATAGGGTTCAAGGTTTGTGACACGCCATGGAGGGAATCTGTGACAC-
1 GAGGAAATCTGTGACACAATAGGATTCAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACACA
* * * *
5517188 GCCAGTGTTCAGAGTTTATGACACGGCATGGAAGGAATCTTTAACACACCAGAGTTTAGAGTTTG
66 G-CAGAGTTCAGAGTTT-TGACACGGCATGGAAGGAATCTGTGACACACCAGAGTTCAGAGTTTG
5517253 ACACAG-CATG
129 ACAC-GCCATG
** * *
5517263 GATGG-AATCTGTGACACGGTAGTATTCAAAGTTTGTGACACGCCATGGAGGGAATCTGGGACAC
1 GA-GGAAATCTGTGACACAATAGGATTCAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACAC
* * * * * * *
5517327 AGCAGGGTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCTAGTGTTCAGAGTTTG
65 AGCAGAGTTCAGAGTTT-TGACACGGCATGGAAGGAATCTGTGACACACCAGAGTTCAGAGTTTG
*
5517392 ACATGCCA
129 ACACGCCA
5517400 GCATTTAGGG
Statistics
Matches: 343, Mismatches: 49, Indels: 47
0.78 0.11 0.11
Matches are distributed among these distances:
136 3 0.01
137 1 0.00
138 2 0.01
139 194 0.57
140 66 0.19
141 38 0.11
142 37 0.11
143 1 0.00
144 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (138 bp):
GAGGAAATCTGTGACACAATAGGATTCAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACACA
GCAGAGTTCAGAGTTTTGACACGGCATGGAAGGAATCTGTGACACACCAGAGTTCAGAGTTTGAC
ACGCCATG
Found at i:5517370 original size:23 final size:23
Alignment explanation
Indices: 5517296--5517375 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 23
5517286 ATTCAAAGTT
5517296 TGTGACACGCCATGGAGGGAATC
1 TGTGACACGCCATGGAGGGAATC
* * *
5517319 TGGGACACAG-CAGGGTTCAGGG--TT
1 TGTGACAC-GCCATGG---AGGGAATC
5517343 TGTGACACGCCATGGAGGGAATC
1 TGTGACACGCCATGGAGGGAATC
5517366 TGTGACACGC
1 TGTGACACGC
5517376 TAGTGTTCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
21 4 0.09
23 23 0.52
24 13 0.30
26 4 0.09
ACGTcount: A:0.24, C:0.21, G:0.36, T:0.19
Consensus pattern (23 bp):
TGTGACACGCCATGGAGGGAATC
Found at i:5517447 original size:23 final size:24
Alignment explanation
Indices: 5517406--5517453 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
5517396 GCCAGCATTT
*
5517406 AGGGTTTGTGACACGACAGGGTTC
1 AGGGTTTGTGACACGACAGCGTTC
5517430 AGGG-TTGTGACA-GAACAGCGTTC
1 AGGGTTTGTGACACG-ACAGCGTTC
5517453 A
1 A
5517454 AGGTATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 17 0.77
24 4 0.18
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (24 bp):
AGGGTTTGTGACACGACAGCGTTC
Found at i:5518035 original size:31 final size:31
Alignment explanation
Indices: 5518009--5518362 Score: 446
Period size: 31 Copynumber: 11.4 Consensus size: 31
5517999 TCATGTCATG
* * *
5518009 ACATTTGACTTGATATGCATGGCATGTGATC
1 ACATTTTACTTGTTATGCATGGCGTGTGATC
* *
5518040 ACATTTTACTTGTTATGCATGGCGTGTCACC
1 ACATTTTACTTGTTATGCATGGCGTGTGATC
* * *
5518071 ATATTTTACTTGTTATGCATGGCGTGTCACC
1 ACATTTTACTTGTTATGCATGGCGTGTGATC
*
5518102 ACATTTTACTTGTTATGCATGGCGTGTGATG
1 ACATTTTACTTGTTATGCATGGCGTGTGATC
*
5518133 ACCTTTTACTTGTTATGCATGGCGTGTGA-C
1 ACATTTTACTTGTTATGCATGGCGTGTGATC
* *
5518163 TACATTTTACTAGTTATACATGGCGTGTGA-C
1 -ACATTTTACTTGTTATGCATGGCGTGTGATC
* *
5518194 GACCTTTTACTTGTTATGCATGGTGTGTGATC
1 -ACATTTTACTTGTTATGCATGGCGTGTGATC
* * *
5518226 ACATTTTACTTATTATGCATGACGTGTGATG
1 ACATTTTACTTGTTATGCATGGCGTGTGATC
*
5518257 ACCTTTTACTTGTTATGCATGGCGTGTGA-C
1 ACATTTTACTTGTTATGCATGGCGTGTGATC
* * *
5518287 TACATTTTACTTGTTATGAATGGCATGTGACC
1 -ACATTTTACTTGTTATGCATGGCGTGTGATC
5518319 ACATTTTACTTGTTATGCATGGCGTGTGA-C
1 ACATTTTACTTGTTATGCATGGCGTGTGATC
*
5518349 GACCTTTTACTTGT
1 -ACATTTTACTTGT
5518363 NNNNNNNNNN
Statistics
Matches: 283, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
30 1 0.00
31 280 0.99
32 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (31 bp):
ACATTTTACTTGTTATGCATGGCGTGTGATC
Found at i:5518789 original size:31 final size:31
Alignment explanation
Indices: 5518751--5518887 Score: 220
Period size: 31 Copynumber: 4.4 Consensus size: 31
5518741 NNNNNNNNNN
* * *
5518751 TTTACTTGTTATGCATGGCGTGTGACGACCT
1 TTTACTTGTTATGCATGGCGTGTCACCACAT
5518782 TTTACTTGTTATGCATGGCGTGTCACCACAT
1 TTTACTTGTTATGCATGGCGTGTCACCACAT
* * *
5518813 TTTACTTGTTATGCATGGCTTGTGACCATAT
1 TTTACTTGTTATGCATGGCGTGTCACCACAT
5518844 TTTACTTGTTATGCATGGCGTGTCACCACAT
1 TTTACTTGTTATGCATGGCGTGTCACCACAT
5518875 TTTACTTGTTATG
1 TTTACTTGTTATG
5518888 TGATAACTCT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 97 1.00
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (31 bp):
TTTACTTGTTATGCATGGCGTGTCACCACAT
Found at i:5519802 original size:63 final size:63
Alignment explanation
Indices: 5519695--5519813 Score: 175
Period size: 63 Copynumber: 1.9 Consensus size: 63
5519685 CCATAGCACC
* *
5519695 ATGACGATGGTGCTCAACAGAGAGTTGACAAAGCTCATACAGTTCAGAAAGTTGAGCGACCTG
1 ATGACAATGGTGCTCAACAGAGAGTTAACAAAGCTCATACAGTTCAGAAAGTTGAGCGACCTG
* * * * *
5519758 ATGACAATGGTGCTTAACAGAGAGTTAACAGAGTTGATATAGTTCAGAAAGTTGAG
1 ATGACAATGGTGCTCAACAGAGAGTTAACAAAGCTCATACAGTTCAGAAAGTTGAG
5519814 AGAGAAAGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (63 bp):
ATGACAATGGTGCTCAACAGAGAGTTAACAAAGCTCATACAGTTCAGAAAGTTGAGCGACCTG
Found at i:5523474 original size:19 final size:19
Alignment explanation
Indices: 5523450--5523499 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
5523440 TACAGGATAG
5523450 TGATATATCCACTAAGAAA
1 TGATATATCCACTAAGAAA
5523469 TGATATATCCACTAAGAAA
1 TGATATATCCACTAAGAAA
5523488 TGATATATCCAC
1 TGATATATCCAC
5523500 AGTGATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (19 bp):
TGATATATCCACTAAGAAA
Found at i:5525317 original size:4 final size:4
Alignment explanation
Indices: 5525310--5525336 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5525300 AGAAAGCATG
5525310 GTGC GTGC GTGC GTGC GTGC GTGC GTG
1 GTGC GTGC GTGC GTGC GTGC GTGC GTG
5525337 TATATATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.52, T:0.26
Consensus pattern (4 bp):
GTGC
Found at i:5526423 original size:2 final size:2
Alignment explanation
Indices: 5526416--5526448 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5526406 GTGGGGCTTT
5526416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5526449 TTCAAAAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5529820 original size:18 final size:18
Alignment explanation
Indices: 5529784--5529821 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5529774 TTCTCCACAC
*
5529784 TTCTCTTTCTTTTTCTCT
1 TTCTCTTTCTTTTTATCT
5529802 TTCTC-TTCTCTTTTATCT
1 TTCTCTTTCT-TTTTATCT
5529820 TT
1 TT
5529822 TTATTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (18 bp):
TTCTCTTTCTTTTTATCT
Found at i:5530493 original size:53 final size:53
Alignment explanation
Indices: 5530436--5530544 Score: 121
Period size: 53 Copynumber: 2.1 Consensus size: 53
5530426 TTAACAATTT
* * *
5530436 AAATTTATATAAG-TTTTCATATTTACCAATATAAATAAACATAAAGTAGAAAA
1 AAATTAATATAAGATTTTCACATTAACCAATAT-AATAAACATAAAGTAGAAAA
* ** * * *
5530489 AAATTAATATTAGATTTTCACATTAAGTATTGTAATAGACATAAAGTAGAAAA
1 AAATTAATATAAGATTTTCACATTAACCAATATAATAAACATAAAGTAGAAAA
5530542 AAA
1 AAA
5530545 AATTTACATT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
53 33 0.72
54 13 0.28
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (53 bp):
AAATTAATATAAGATTTTCACATTAACCAATATAATAAACATAAAGTAGAAAA
Found at i:5530565 original size:55 final size:53
Alignment explanation
Indices: 5530469--5530578 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 53
5530459 TACCAATATA
* * *
5530469 AATAAACATAAAGTAGAAAAAAATTAATATTAGATTTTCACATTAAGTATTGT
1 AATAAACATAAAGTAGAAAAAAATTAACATTAAATTTTCACATTAAGTATCGT
* * *
5530522 AATAGACATAAAGTAGAAAAAAAAATTTACATTAAATTTTCACATTAGGTATCGT
1 AATAAACATAAAGTAG--AAAAAAATTAACATTAAATTTTCACATTAAGTATCGT
5530577 AA
1 AA
5530579 GTTGTGCTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
53 15 0.31
55 34 0.69
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (53 bp):
AATAAACATAAAGTAGAAAAAAATTAACATTAAATTTTCACATTAAGTATCGT
Found at i:5534709 original size:28 final size:28
Alignment explanation
Indices: 5534606--5534710 Score: 90
Period size: 28 Copynumber: 3.7 Consensus size: 28
5534596 CAATAATAAA
*
5534606 AATACTTTTAAACTCAC-TAGAAGTGGATG
1 AATACTTTT-AAC-CACTTGGAAGTGGATG
* * *
5534635 AATACTTTTAAACCACCT-GAAATTGATG
1 AATACTTTT-AACCACTTGGAAGTGGATG
* * *
5534663 AATATTTTTAATCTA-TTGGGAGTGGATG
1 AATACTTTTAA-CCACTTGGAAGTGGATG
5534691 AATACTTTTAACCACTTGGA
1 AATACTTTTAACCACTTGGA
5534711 GTAGATCTAG
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
27 5 0.08
28 42 0.69
29 14 0.23
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (28 bp):
AATACTTTTAACCACTTGGAAGTGGATG
Found at i:5541927 original size:35 final size:35
Alignment explanation
Indices: 5541804--5541929 Score: 125
Period size: 35 Copynumber: 3.7 Consensus size: 35
5541794 AAGCTTTTAG
* * *
5541804 AATGGCTTTTCGCAAGCTCAGCCACAACCTTTAAT
1 AATGGCTTTTCACAAGATCAACCACAACCTTTAAT
* * * *
5541839 AATGGTTTTTCACCAGATCAATCAAAACC--T-AT
1 AATGGCTTTTCACAAGATCAACCACAACCTTTAAT
* *
5541871 AATGGTTTTTCA-AAGGCTCAACCACAACCTTTAAT
1 AATGGCTTTTCACAA-GATCAACCACAACCTTTAAT
*
5541906 AATGGCTTTTCACAAAATCAACCA
1 AATGGCTTTTCACAAGATCAACCA
5541930 AAACTCAAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
31 1 0.01
32 25 0.35
33 1 0.01
34 1 0.01
35 42 0.58
36 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (35 bp):
AATGGCTTTTCACAAGATCAACCACAACCTTTAAT
Found at i:5545412 original size:20 final size:22
Alignment explanation
Indices: 5545383--5545426 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5545373 ATTTGATTTT
5545383 AATTTCAAAATAT-ATATTTAA
1 AATTTCAAAATATAATATTTAA
5545404 AATTT-AAAATATAAATATTTAA
1 AATTTCAAAATAT-AATATTTAA
5545426 A
1 A
5545427 TATTAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTTCAAAATATAATATTTAA
Found at i:5545936 original size:54 final size:54
Alignment explanation
Indices: 5545869--5546123 Score: 280
Period size: 54 Copynumber: 4.7 Consensus size: 54
5545859 AATTAACATT
* *
5545869 ACACTTTCTTTAATATACCAAACACTACAATGTTATCTTTCTAGCATTTTAATC
1 ACACTTTCCTTAATATACCAAACACTGCAATGTTATCTTTCTAGCATTTTAATC
** * * *
5545923 ACACTTTCCTTAATATACCAGGCATTGCAATGTTATCTTTTTAACATTTTAATC
1 ACACTTTCCTTAATATACCAAACACTGCAATGTTATCTTTCTAGCATTTTAATC
** * ** *
5545977 ACACCCTCCTTAATATACTAAATGCTGCAATGTTAT-TTTCTCAGTATTTTAATC
1 ACACTTTCCTTAATATACCAAACACTGCAATGTTATCTTTCT-AGCATTTTAATC
* * * **
5546031 ATAATTTTCTTAATATATTAAACACTGCAATGTTATC-TTCTTAGCATTTTAATC
1 ACACTTTCCTTAATATACCAAACACTGCAATGTTATCTTTC-TAGCATTTTAATC
* * **
5546085 ACATTTTCCTTAATATACCAAACATTATAATGTTATCTT
1 ACACTTTCCTTAATATACCAAACACTGCAATGTTATCTT
5546124 ATTTGCAGTC
Statistics
Matches: 162, Mismatches: 35, Indels: 7
0.79 0.17 0.03
Matches are distributed among these distances:
53 4 0.02
54 156 0.96
55 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (54 bp):
ACACTTTCCTTAATATACCAAACACTGCAATGTTATCTTTCTAGCATTTTAATC
Found at i:5551310 original size:19 final size:20
Alignment explanation
Indices: 5551276--5551315 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5551266 CTTACCGCAT
*
5551276 TTCTTAACTCATCCATCTTG
1 TTCTTAAATCATCCATCTTG
*
5551296 TTCTTAAAT-ATCCATTTTG
1 TTCTTAAATCATCCATCTTG
5551315 T
1 T
5551316 ACCAACAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.50
Consensus pattern (20 bp):
TTCTTAAATCATCCATCTTG
Found at i:5556491 original size:2 final size:2
Alignment explanation
Indices: 5556484--5556526 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
5556474 CATTTTCTTA
* * *
5556484 AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AC AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5556525 AT
1 AT
5556527 TACTAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5556767 original size:17 final size:17
Alignment explanation
Indices: 5556747--5556792 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
5556737 TATGGTTAAA
5556747 TAAAAAATAGATATATG
1 TAAAAAATAGATATATG
* *
5556764 T-AAAAATA-AAATATT
1 TAAAAAATAGATATATG
5556779 TAAAAAAATAGATA
1 T-AAAAAATAGATA
5556793 AATATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
15 6 0.26
16 7 0.30
17 8 0.35
18 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (17 bp):
TAAAAAATAGATATATG
Found at i:5557082 original size:3 final size:3
Alignment explanation
Indices: 5557064--5557109 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
5557054 AATAAGGAAG
* *
5557064 TAA TGA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5557110 CAAAAAGGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:5557389 original size:20 final size:24
Alignment explanation
Indices: 5557351--5557403 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 24
5557341 GGTAATTTAA
5557351 AAAAAT-AAAAAATTGAATTA-T-
1 AAAAATGAAAAAATTGAATTAGTG
5557372 AAAAATGAAAAAA-T-AATTAGTG
1 AAAAATGAAAAAATTGAATTAGTG
5557394 AAAAA-GAAAA
1 AAAAATGAAAA
5557404 TAGGTTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.17
21 13 0.45
22 11 0.38
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (24 bp):
AAAAATGAAAAAATTGAATTAGTG
Found at i:5562373 original size:2 final size:2
Alignment explanation
Indices: 5562368--5562406 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5562358 CTCTCTCTCT
*
5562368 CA CA CA CA CA CA CA CA CA CG CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
5562407 TCTTACACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.51, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5570151 original size:41 final size:41
Alignment explanation
Indices: 5570094--5570174 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
5570084 CGTGGTTTGT
* * * *
5570094 TAACATGTTATAATTGATAATGATGTGACATGCTAATATGC
1 TAACATATTATAATTGATAATGACGTAACATGATAATATGC
*
5570135 TAACATATTATAATTGATGATGACGTAACATGATAATATG
1 TAACATATTATAATTGATAATGACGTAACATGATAATATG
5570175 AATATGTAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (41 bp):
TAACATATTATAATTGATAATGACGTAACATGATAATATGC
Found at i:5574880 original size:15 final size:15
Alignment explanation
Indices: 5574860--5574895 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5574850 ATGCAATGTA
*
5574860 ATTGCAAGTAATATG
1 ATTGCAAGCAATATG
*
5574875 ATTGCAAGCAATGTG
1 ATTGCAAGCAATATG
5574890 ATTGCA
1 ATTGCA
5574896 GAGAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (15 bp):
ATTGCAAGCAATATG
Found at i:5575164 original size:16 final size:17
Alignment explanation
Indices: 5575145--5575176 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5575135 AATAATCTTT
5575145 TATATTT-TATTTTTAA
1 TATATTTATATTTTTAA
5575161 TATATTTATATTTTTA
1 TATATTTATATTTTTA
5575177 TTATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTTATATTTTTAA
Found at i:5575175 original size:23 final size:23
Alignment explanation
Indices: 5575111--5575192 Score: 73
Period size: 23 Copynumber: 3.5 Consensus size: 23
5575101 TTTTAATGTC
5575111 ATATATTT-TATTTTTATTTATT-
1 ATATATTTATATTTTTATTT-TTA
*
5575133 ATAATAATCTTTTATATTTTATTTTTA
1 AT-AT-AT-TTATAT-TTTTATTTTTA
*
5575160 ATATATTTATATTTTTATTATTA
1 ATATATTTATATTTTTATTTTTA
5575183 AT-T-TTTATAT
1 ATATATTTATAT
5575193 AATATCATCT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
21 7 0.13
22 3 0.06
23 14 0.27
24 7 0.13
25 4 0.08
26 7 0.13
27 10 0.19
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATATTTATATTTTTATTTTTA
Found at i:5575190 original size:113 final size:114
Alignment explanation
Indices: 5575042--5575270 Score: 424
Period size: 113 Copynumber: 2.0 Consensus size: 114
5575032 AAAATACAAG
5575042 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
* *
5575107 TGTCATATATTTTATTTTTATTTATTATAATAATCTTTTATATTTTATT
66 TGTCATATATTTTATTTTCATTTATTATAATAATCTTATATATTTTATT
5575156 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
*
5575220 TGTCATATATTTTATTTTCATTTATTATTATAATCTTATATATTTTATT
66 TGTCATATATTTTATTTTCATTTATTATAATAATCTTATATATTTTATT
5575269 TT
1 TT
5575271 CATTTCTTTA
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
113 97 0.87
114 15 0.13
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (114 bp):
TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
TGTCATATATTTTATTTTCATTTATTATAATAATCTTATATATTTTATT
Found at i:5575240 original size:15 final size:15
Alignment explanation
Indices: 5575208--5575273 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 15
5575198 CATCTCTTAA
* *
5575208 ATATATTTTTAATGTC
1 ATATA-TTTTATTTTC
5575224 ATATATTTTATTTTC
1 ATATATTTTATTTTC
*
5575239 ATTTATTATTATAATCTT-
1 ATATATT-TTAT--T-TTC
5575257 ATATATTTTATTTTC
1 ATATATTTTATTTTC
5575272 AT
1 AT
5575274 TTCTTTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
14 2 0.05
15 17 0.41
16 9 0.22
17 4 0.10
18 7 0.17
19 2 0.05
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (15 bp):
ATATATTTTATTTTC
Found at i:5575360 original size:5 final size:5
Alignment explanation
Indices: 5575336--5575414 Score: 56
Period size: 5 Copynumber: 15.2 Consensus size: 5
5575326 TACTATATAA
* *
5575336 ATTTT AATTTT -TTAT ATTTT ATTTT ATTTT AATTTCTT ATTCTT ATATT
1 ATTTT -ATTTT ATTTT ATTTT ATTTT ATTTT -A-TT-TT ATT-TT ATTTT
*
5575385 A-TAT ATTTT ATTTT AATTTT -TTTT ATTTT A
1 ATTTT ATTTT ATTTT -ATTTT ATTTT ATTTT A
5575415 ATTATAACAT
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
4 9 0.15
5 28 0.47
6 18 0.30
7 3 0.05
8 2 0.03
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:5575363 original size:55 final size:52
Alignment explanation
Indices: 5575284--5575417 Score: 152
Period size: 55 Copynumber: 2.6 Consensus size: 52
5575274 TTCTTTAATA
*
5575284 TATTTTTTATATTATATATTTTATTTTAATTTGTT-TTACCTATACTATATAAATTT
1 TATTTTTTATATT-T-TATTTTATTTTAATTTCTTATT-CCTATA-T-TATAAATTT
* *
5575340 TAATTTTTTATATTTTATTTTATTTTAATTTCTTATTCTTATATTATATATTT
1 T-ATTTTTTATATTTTATTTTATTTTAATTTCTTATTCCTATATTATAAATTT
5575393 TA--TTTTA-ATTTT-TTTTATTTTAATT
1 TATTTTTTATATTTTATTTTATTTTAATT
5575418 ATAACATTAT
Statistics
Matches: 73, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
48 13 0.18
49 5 0.07
50 5 0.07
52 1 0.01
53 9 0.12
54 1 0.01
55 23 0.32
56 4 0.05
57 12 0.16
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.68
Consensus pattern (52 bp):
TATTTTTTATATTTTATTTTATTTTAATTTCTTATTCCTATATTATAAATTT
Found at i:5575419 original size:33 final size:37
Alignment explanation
Indices: 5575348--5575420 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 37
5575338 TTTAATTTTT
*
5575348 TATATTTTATTTTATTTTAATTTCTTATTCTTATATTA
1 TATATTTTATTTTAATTT-ATTTCTTATTCTTATATTA
5575386 TATATTTTATTTTAATTT-TTT-TTATT-TTA-ATTA
1 TATATTTTATTTTAATTTATTTCTTATTCTTATATTA
5575419 TA
1 TA
5575421 ACATTATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
33 6 0.18
34 3 0.09
35 5 0.15
36 3 0.09
38 17 0.50
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (37 bp):
TATATTTTATTTTAATTTATTTCTTATTCTTATATTA
Found at i:5575420 original size:38 final size:37
Alignment explanation
Indices: 5575336--5575420 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 37
5575326 TACTATATAA
5575336 ATTTTAATT-T-TTTATATTTTATTTTATTTTAATTT
1 ATTTTAATTATATTTATATTTTATTTTATTTTAATTT
* * *
5575371 CTTATT-CTTATATTATATATTTTATTTTAATTTT-TTTT
1 ATT-TTAATTATATT-TATATTTTATTTT-ATTTTAATTT
5575409 ATTTTAATTATA
1 ATTTTAATTATA
5575421 ACATTATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
35 4 0.10
36 3 0.08
37 4 0.10
38 23 0.59
39 5 0.13
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (37 bp):
ATTTTAATTATATTTATATTTTATTTTATTTTAATTT
Found at i:5580455 original size:2 final size:2
Alignment explanation
Indices: 5580448--5580482 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5580438 TATCTCCTTT
5580448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5580483 TGCAAACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5589593 original size:21 final size:21
Alignment explanation
Indices: 5589569--5589617 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5589559 TTTTTAAGTG
*
5589569 ATTTATTTTAATTTTATGT-TT
1 ATTTATTTTAATTTGAT-TATT
5589590 ATTT-TCTTTAATTTGATTATT
1 ATTTAT-TTTAATTTGATTATT
5589611 ATTTATT
1 ATTTATT
5589618 AGTTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (21 bp):
ATTTATTTTAATTTGATTATT
Found at i:5605922 original size:26 final size:27
Alignment explanation
Indices: 5605838--5605994 Score: 97
Period size: 26 Copynumber: 5.7 Consensus size: 27
5605828 CCTTTCAACT
* * *
5605838 TTAATATATATATAAA-AAATAAATAT
1 TTAAAATATATATAAATAAATAAAAAA
* * *
5605864 TTATAATGT-TATAATTAAAATAAAAATA
1 TTAAAATATATATAAAT-AAATAAAAA-A
* *
5605892 TTTAAAATATATATTAGT-AATAAAAAA
1 -TTAAAATATATATAAATAAATAAAAAA
*
5605919 TTAAAATA-AAATAAATAAATAAAAAA
1 TTAAAATATATATAAATAAATAAAAAA
* * **
5605945 TTAACATTTATATAATATAGGTAAAACAA
1 TTAAAATATATATAA-ATAAATAAAA-AA
* *
5605974 ATAAAATAATATATATATAAA
1 TTAAAAT-ATATATAAATAAA
5605995 AAATATATTA
Statistics
Matches: 97, Mismatches: 24, Indels: 17
0.70 0.17 0.12
Matches are distributed among these distances:
25 10 0.10
26 29 0.30
27 14 0.14
28 16 0.16
29 17 0.18
30 11 0.11
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
TTAAAATATATATAAATAAATAAAAAA
Found at i:5606117 original size:23 final size:22
Alignment explanation
Indices: 5606091--5606156 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
5606081 ATTATATTAA
*
5606091 ATTAATAATTATAATATAAATAT
1 ATTAATAATTAAAATATAAA-AT
* *
5606114 ATTAAAAAATAAAATATAAAAT
1 ATTAATAATTAAAATATAAAAT
5606136 ATTATATAA-T-AAATA-AAAAT
1 ATTA-ATAATTAAAATATAAAAT
5606156 A
1 A
5606157 AATATTGACA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 6 0.16
21 5 0.13
22 7 0.18
23 20 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTAATAATTAAAATATAAAAT
Found at i:5606131 original size:28 final size:27
Alignment explanation
Indices: 5606083--5606158 Score: 68
Period size: 28 Copynumber: 2.9 Consensus size: 27
5606073 AATATGTAAT
* * *
5606083 TATATTAAATTAAT-AATTATAATATAAA
1 TATATTAAA-AAATAAAATATAAAAT-AA
*
5606111 TATATTAAAAAATAAAATATAAAATAT
1 TATATTAAAAAATAAAATATAAAATAA
*
5606138 TATA-TAATAAATAAAA-ATAAA
1 TATATTAAAAAATAAAATATAAA
5606159 TATTGACATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
25 5 0.12
26 11 0.26
27 8 0.19
28 18 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TATATTAAAAAATAAAATATAAAATAA
Found at i:5606159 original size:24 final size:24
Alignment explanation
Indices: 5606103--5606162 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
5606093 TAATAATTAT
5606103 AATATAAATA-TATTAAAAAATAA
1 AATATAAATATTATTAAAAAATAA
*
5606126 AATATAAAATATTATATAATAAATAA
1 AATAT-AAATATTAT-TAAAAAATAA
5606152 AA-ATAAATATT
1 AATATAAATATT
5606163 GACATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 5 0.15
24 12 0.36
25 5 0.15
26 11 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATATAAATATTATTAAAAAATAA
Found at i:5606174 original size:25 final size:25
Alignment explanation
Indices: 5606103--5606175 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
5606093 TAATAATTAT
5606103 AATATAAATATATT--A-AAAAATAA
1 AATATAAA-ATATTACATAAAAATAA
*
5606126 AATATAAAATATTATATAATAAATAA
1 AATATAAAATATTACATAA-AAATAA
5606152 AA-AT-AAATATTGACATTAAAAATA
1 AATATAAAATATT-ACA-TAAAAATA
5606176 TATTTAAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
22 5 0.12
23 8 0.19
24 8 0.19
25 11 0.26
26 11 0.26
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (25 bp):
AATATAAAATATTACATAAAAATAA
Found at i:5606196 original size:110 final size:115
Alignment explanation
Indices: 5605995--5606230 Score: 276
Period size: 110 Copynumber: 2.1 Consensus size: 115
5605985 TATATATAAA
* * *
5605995 AAATATATTAAAGAAATGAAAATAATTATAGATTATAATACAAATGAAAATAAAATATATGACAT
1 AAATATATTAAAGAAATGAAAATAATAAAAGATTATAATACAAATAAAAATAAAATATATGACAT
* * * * *
5606060 TGAAAATATATTTAATATGTAATTATAT-TAAATTAATAAT-TATAATAT
66 TAAAAATATATTTAAAATGTAATTATATAAAAATTAATAATAAAAAATAT
* *
5606108 AAATATATTAAA-AAAT-AAAAT-ATAAAATATTAT-ATAATAAATAAAAAT-AAATAT-TGACA
1 AAATATATTAAAGAAATGAAAATAATAAAAGATTATAAT-ACAAATAAAAATAAAATATATGACA
5606167 TTAAAAATATATTTAAGAAATG-ATATTATATAAAAATTAATAATAAAAAATAT
65 TTAAAAATATATTT-A-AAATGTA-ATTATATAAAAATTAATAATAAAAAATAT
5606220 AAATA-ATTAAA
1 AAATATATTAAA
5606231 CTTGTATTTT
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
108 18 0.17
109 10 0.09
110 30 0.28
111 22 0.21
112 15 0.14
113 12 0.11
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (115 bp):
AAATATATTAAAGAAATGAAAATAATAAAAGATTATAATACAAATAAAAATAAAATATATGACAT
TAAAAATATATTTAAAATGTAATTATATAAAAATTAATAATAAAAAATAT
Found at i:5606568 original size:12 final size:11
Alignment explanation
Indices: 5606529--5606581 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
5606519 ATGTTATAAT
5606529 TAAAATAAAAA
1 TAAAATAAAAA
*
5606540 TATAATATAAGAA
1 TA-AA-ATAAAAA
*
5606553 TAAAAATTAAAA
1 T-AAAATAAAAA
5606565 TAAAATAAAATA
1 TAAAATAAAA-A
5606577 TAAAA
1 TAAAA
5606582 AATCAACATT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
11 10 0.29
12 14 0.41
13 9 0.26
14 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:5607814 original size:33 final size:33
Alignment explanation
Indices: 5607767--5607839 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
5607757 TAAGACATAT
* * *
5607767 AATATATAAAATTATATTAAGAAATAAAAGGAA
1 AATATATAAAATTATAATAAAAAATAAAAAGAA
* * *
5607800 AATATTTAAGATTATAATAAAAAATAAAAATAA
1 AATATATAAAATTATAATAAAAAATAAAAAGAA
5607833 AATATAT
1 AATATAT
5607840 GATTTTAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (33 bp):
AATATATAAAATTATAATAAAAAATAAAAAGAA
Found at i:5608721 original size:15 final size:16
Alignment explanation
Indices: 5608671--5608721 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5608661 AGATGATTGA
* * *
5608671 AATTCAAATTGATCTG
1 AATTCAAAATAATTTG
* *
5608687 AATTTAAAATAATTTA
1 AATTCAAAATAATTTG
5608703 AATTCAAAAT-ATTTG
1 AATTCAAAATAATTTG
5608718 AATT
1 AATT
5608722 TCTTTTAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
AATTCAAAATAATTTG
Found at i:5609952 original size:18 final size:18
Alignment explanation
Indices: 5609916--5609966 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
5609906 TTAACTTATC
5609916 TTTTTTAA-TATATATTTA
1 TTTTTTAATTAT-TATTTA
5609934 TATTTTTAATTATTA-TTA
1 T-TTTTTAATTATTATTTA
5609952 TTATTTTAATTATTA
1 TT-TTTTAATTATTA
5609967 CTTCACTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.03
18 17 0.57
19 9 0.30
20 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTAATTATTATTTA
Found at i:5611021 original size:15 final size:14
Alignment explanation
Indices: 5610988--5611018 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5610978 ATTATAATTT
5610988 ATTAATATTAAAAA
1 ATTAATATTAAAAA
*
5611002 ATTAATTTTAAAAA
1 ATTAATATTAAAAA
5611016 ATT
1 ATT
5611019 TAAAAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTAATATTAAAAA
Found at i:5613756 original size:21 final size:21
Alignment explanation
Indices: 5613730--5613808 Score: 95
Period size: 21 Copynumber: 3.8 Consensus size: 21
5613720 ACATTCTGTC
*
5613730 AGGTATCAAGACTTTGAAATT
1 AGGTATCAAGACTTTGAAACT
*
5613751 AGGTATCAAGATTTTGAAACT
1 AGGTATCAAGACTTTGAAACT
* * *
5613772 AGGTATCAAGACGTTGAATCC
1 AGGTATCAAGACTTTGAAACT
* *
5613793 AAGTATTAAGACTTTG
1 AGGTATCAAGACTTTG
5613809 TGAAATGTCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (21 bp):
AGGTATCAAGACTTTGAAACT
Found at i:5616722 original size:19 final size:18
Alignment explanation
Indices: 5616684--5616722 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5616674 ATTAATTGAG
*
5616684 TATTTAGTATTACAAGAT
1 TATTTAGTATTACAAAAT
*
5616702 TATTTAAGTATTAGAAAAT
1 TATTT-AGTATTACAAAAT
5616721 TA
1 TA
5616723 ATAATATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (18 bp):
TATTTAGTATTACAAAAT
Found at i:5636869 original size:172 final size:175
Alignment explanation
Indices: 5636543--5636871 Score: 389
Period size: 172 Copynumber: 1.9 Consensus size: 175
5636533 GATAGGAATG
* * * *
5636543 GTTCAAGATTTTCCATTCATCTTGAAATAAGCAAAACGTTTCATTTTTTTTCAAATTCGGTGCAA
1 GTTCAAGATTTTCCATCCATCTTGAAATAAGAAAAACGTTTCA-TATTTTTCAAATTCGATGCAA
* * * *
5636608 ATTTAAAACAAAGAGAAAATGGGAAAAAAAAAGAAAGAACAAAAAGGTTAAAAAGAATTATATGG
65 AATTAAAACAAAGAGAAAATGGG-AAAAAAAAGAAAGAACAAAAAGGTGAAAAAGAATTACAGGG
*
5636673 AAGAAAACAGTTTTTGCATTTTGGTTGTAAAGAAAAGGAAATGAAGA
129 AAGAAAACAGCTTTTGCATTTTGGTTGTAAAGAAAAGGAAATGAAGA
* * * * *
5636720 GTTCAAGATTTTCCATCCATCTTGGAATAATAAAAATGTTTCA-ATTTTTCAAATTTGATGTAAA
1 GTTCAAGATTTTCCATCCATCTTGAAATAAGAAAAACGTTTCATATTTTTCAAATTCGATGCAAA
* * * * * *
5636784 ATTGAAATAAATAGAAAGT-GG-AAAAAAAGAACGAA-AGAGAAGGTGAAAAAGAATTACAGGGA
66 ATTAAAACAAAGAGAAAATGGGAAAAAAAAGAAAGAACA-AAAAGGTGAAAAAGAATTACAGGGA
* *
5636846 AGAAAA-TGACTTTTGCGTTTTGGTTG
130 AGAAAACAG-CTTTTGCATTTTGGTTG
5636872 CTTCCGTCCA
Statistics
Matches: 128, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
171 2 0.02
172 55 0.43
174 2 0.02
175 31 0.24
177 38 0.30
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.29
Consensus pattern (175 bp):
GTTCAAGATTTTCCATCCATCTTGAAATAAGAAAAACGTTTCATATTTTTCAAATTCGATGCAAA
ATTAAAACAAAGAGAAAATGGGAAAAAAAAGAAAGAACAAAAAGGTGAAAAAGAATTACAGGGAA
GAAAACAGCTTTTGCATTTTGGTTGTAAAGAAAAGGAAATGAAGA
Found at i:5637099 original size:27 final size:27
Alignment explanation
Indices: 5637069--5637429 Score: 107
Period size: 27 Copynumber: 13.3 Consensus size: 27
5637059 TATATAAGAT
5637069 TTTTTTTTTCAATATGACATGTAACAA
1 TTTTTTTTTCAATATGACATGTAACAA
* * *
5637096 TTTTTTTTTTAATATGATATATAACAA
1 TTTTTTTTTCAATATGACATGTAACAA
** * * *
5637123 ---CATTTTGAACATGACGCGTGTCAA-AA
1 TTTTTTTTTCAATATGA--CATGT-AACAA
*** * * *
5637149 ACATTTTTTCAAGA-AAGCGTGTAACAA
1 TTTTTTTTTCAATATGA-CATGTAACAA
*
5637176 CTTTTTTTTT-AATAT-A-ATGTTGAATAA
1 -TTTTTTTTTCAATATGACATG-T-AACAA
* * * **
5637203 CTTTTTTATCAACATGATGTGTAACAA
1 TTTTTTTTTCAATATGACATGTAACAA
*
5637230 TTTTTTTTTTAAATATGACATGTAACAA
1 -TTTTTTTTTCAATATGACATGTAACAA
* * *
5637258 TTTTTTTTTCAACAT-AGCATGCAATAA
1 TTTTTTTTTCAATATGA-CATGTAACAA
** * * *
5637285 TAACATTTTTCCAACATGGCATGTAACAA
1 T--TTTTTTTTCAATATGACATGTAACAA
* * * *
5637314 TAATATTTTTTCAATAT-AGTATGAAATAA
1 T--TTTTTTTTCAATATGA-CATGTAACAA
* * *
5637343 CTTTTTTTT-AATATAACATGTAATAA
1 TTTTTTTTTCAATATGACATGTAACAA
* * * *
5637369 CTTTTTTTT-AACATGATATGTAATAA
1 TTTTTTTTTCAATATGACATGTAACAA
***
5637395 TTTTTTTTTTCAATATGGTTTGTAACAA
1 -TTTTTTTTTCAATATGACATGTAACAA
*
5637423 TATTTTT
1 TTTTTTT
5637430 CATATGTGTT
Statistics
Matches: 249, Mismatches: 62, Indels: 46
0.70 0.17 0.13
Matches are distributed among these distances:
24 10 0.04
25 2 0.01
26 51 0.20
27 94 0.38
28 43 0.17
29 49 0.20
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (27 bp):
TTTTTTTTTCAATATGACATGTAACAA
Found at i:5637128 original size:29 final size:28
Alignment explanation
Indices: 5637045--5637122 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 28
5637035 AATTGTAATA
* ** *
5637045 TTTTTTCAACATGGTATATAA-GATTTT
1 TTTTTTCAATATGACATATAACAATTTT
*
5637072 TTTTTTCAATATGACATGTAACAATTTT
1 TTTTTTCAATATGACATATAACAATTTT
*
5637100 TTTTTT-AATATGATATATAACAA
1 TTTTTTCAATATGACATATAACAA
5637123 CATTTTGAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 32 0.74
28 11 0.26
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (28 bp):
TTTTTTCAATATGACATATAACAATTTT
Found at i:5637235 original size:28 final size:27
Alignment explanation
Indices: 5637204--5637403 Score: 102
Period size: 26 Copynumber: 7.3 Consensus size: 27
5637194 GTTGAATAAC
* **
5637204 TTTTTTATCAACATGATGTGTAACAATT
1 TTTTTTTTCAACATGACATGTAACAA-T
* *
5637232 TTTTTTTTAAATATGACATGTAACAAT
1 TTTTTTTTCAACATGACATGTAACAAT
* *
5637259 TTTTTTTTCAACAT-AGCATGCAATAAT
1 TTTTTTTTCAACATGA-CATGTAACAAT
** * *
5637286 AACATTTTTCCAACATGGCATGTAACAAT
1 --TTTTTTTTCAACATGACATGTAACAAT
* * * * * *
5637315 AATATTTTTTCAATAT-AGTATGAAATAAC
1 --TTTTTTTTCAACATGA-CATGTAACAAT
* * * *
5637344 TTTTTTTT-AATATAACATGTAATAAC
1 TTTTTTTTCAACATGACATGTAACAAT
* *
5637370 TTTTTTTT-AACATGATATGTAATAAT
1 TTTTTTTTCAACATGACATGTAACAAT
5637396 TTTTTTTT
1 TTTTTTTT
5637404 TCAATATGGT
Statistics
Matches: 136, Mismatches: 30, Indels: 14
0.76 0.17 0.08
Matches are distributed among these distances:
26 45 0.33
27 30 0.22
28 21 0.15
29 40 0.29
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (27 bp):
TTTTTTTTCAACATGACATGTAACAAT
Found at i:5637263 original size:55 final size:54
Alignment explanation
Indices: 5637167--5637272 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 54
5637157 TCAAGAAAGC
*
5637167 GTGTAACAACTTTTTTTTTAATATAATGTTGAATAACTTTTTTATCAACATGAT
1 GTGTAACAACTTTTTTTTTAATATAATGTTGAACAACTTTTTTATCAACATGAT
* * *
5637221 GTGTAACAATTTTTTTTTTAAATATGACATG-T-AACAATTTTTTTTTCAACAT
1 GTGTAACAACTTTTTTTTT-AATAT-A-ATGTTGAACAACTTTTTTATCAACAT
5637273 AGCATGCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 18 0.40
55 22 0.49
56 2 0.04
57 3 0.07
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.49
Consensus pattern (54 bp):
GTGTAACAACTTTTTTTTTAATATAATGTTGAACAACTTTTTTATCAACATGAT
Found at i:5637293 original size:29 final size:29
Alignment explanation
Indices: 5637261--5637342 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
5637251 GTAACAATTT
*
5637261 TTTTTTCAACATAGCATGCAATAATAACA
1 TTTTTTCAACATAGCATGAAATAATAACA
* * * * *
5637290 TTTTTCCAACATGGCATGTAACAATAATA
1 TTTTTTCAACATAGCATGAAATAATAACA
* *
5637319 TTTTTTCAATATAGTATGAAATAA
1 TTTTTTCAACATAGCATGAAATAA
5637343 CTTTTTTTTA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTTTTCAACATAGCATGAAATAATAACA
Found at i:5637418 original size:28 final size:27
Alignment explanation
Indices: 5637204--5637429 Score: 75
Period size: 26 Copynumber: 8.2 Consensus size: 27
5637194 GTTGAATAAC
* * * *
5637204 TTTTTTATCAACATGATGTGTAACAATT
1 TTTTTT-TTAACATGATATGTAATAATA
* * *
5637232 TTTTTTTTAAATATGACATGTAACAAT-
1 TTTTTTTT-AACATGATATGTAATAATA
* *
5637259 TTTTTTTTCAACAT-AGCATGCAATAATAA
1 TTTTTTTT-AACATGA-TATGTAATAAT-A
* ** ** *
5637288 CATTTTTCCAACATGGCATGTAACAATAA
1 -TTTTTTTTAACATGATATGTAATAAT-A
* * * *
5637317 TATTTTTTCAATAT-AGTATGAAATAA-C
1 T-TTTTTTTAACATGA-TATGTAATAATA
* * * *
5637344 TTTTTTTTAATATAACATGTAATAA-C
1 TTTTTTTTAACATGATATGTAATAATA
*
5637370 TTTTTTTTAACATGATATGTAATAATT
1 TTTTTTTTAACATGATATGTAATAATA
* * * *
5637397 TTTTTTTTCAATATGGTTTGTAACAATA
1 TTTTTTTT-AACATGATATGTAATAATA
5637425 TTTTT
1 TTTTT
5637430 CATATGTGTT
Statistics
Matches: 153, Mismatches: 34, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
26 43 0.28
27 32 0.21
28 40 0.26
29 33 0.22
30 5 0.03
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTTTTTTAACATGATATGTAATAATA
Found at i:5638466 original size:17 final size:17
Alignment explanation
Indices: 5638440--5638485 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
5638430 TTTATATAAC
**
5638440 ATAAATTTATAATTAATA
1 ATAAA-TTATAAAAAATA
5638458 ATAAATTATAAAAAATA
1 ATAAATTATAAAAAATA
*
5638475 ATAATTTATAA
1 ATAAATTATAA
5638486 GTAACACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAATTATAAAAAATA
Found at i:5646144 original size:34 final size:34
Alignment explanation
Indices: 5646106--5646171 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
5646096 AAGGGAAGCT
* * * *
5646106 TTGGCGTGTAATATATGGTGTTGAAGCTTTGAAC
1 TTGGCATGTAACATATAGTGTTAAAGCTTTGAAC
*
5646140 TTGGCATGTAACATTTAGTGTTAAAGCTTTGA
1 TTGGCATGTAACATATAGTGTTAAAGCTTTGA
5646172 CCTTTTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (34 bp):
TTGGCATGTAACATATAGTGTTAAAGCTTTGAAC
Found at i:5652344 original size:73 final size:74
Alignment explanation
Indices: 5652220--5652393 Score: 185
Period size: 73 Copynumber: 2.4 Consensus size: 74
5652210 AGATAGAGAA
* * ** * * * *
5652220 GACTTAGTCGACTAAAAAATATTGTTAGTCGACTAAGAACTTATTGCCAAAAACT-AGATTTAG-
1 GACTTAATCGACTAAGAAGCATTGTTAGTCGACCAAGAACTCACTGCCAAAAACTAAGA-TCAGA
*
5652283 AGACA-AAGAT
65 AGACATAA-AC
* * *
5652293 GACTTAATCGACTAAGAAGCATTGTTAGTCGACCAAGACCTCACTGTCAAAAGCTAAGATCAGAA
1 GACTTAATCGACTAAGAAGCATTGTTAGTCGACCAAGAACTCACTGCCAAAAACTAAGATCAGAA
5652358 GACATAAAC
66 GACATAAAC
*
5652367 GACTTAATGGACTAAGAAGCA-TGTTAG
1 GACTTAATCGACTAAGAAGCATTGTTAG
5652394 CCAACTAAGA
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
73 54 0.64
74 29 0.34
75 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (74 bp):
GACTTAATCGACTAAGAAGCATTGTTAGTCGACCAAGAACTCACTGCCAAAAACTAAGATCAGAA
GACATAAAC
Found at i:5658792 original size:2 final size:2
Alignment explanation
Indices: 5658785--5658814 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5658775 GGTATATCTC
5658785 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
5658815 GTATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.