Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, 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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 91
Found at i:220182 original size:23 final size:23
Alignment explanation
Indices: 220152--220207 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
220142 TATGGCATTA
220152 CGGTGCAATTCTACGCGACACTC
1 CGGTGCAATTCTACGCGACACTC
* * *
220175 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGACACTC
*
220198 AGGTGCAATT
1 CGGTGCAATT
220208 ATGACCTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGACACTC
Found at i:224189 original size:23 final size:21
Alignment explanation
Indices: 224146--224186 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
224136 TAATAATTAT
224146 TTAAAAAATTAAATAAAAATA
1 TTAAAAAATTAAATAAAAATA
*
224167 TTAAAAATATTTAATAAAAA
1 TTAAAAA-ATTAAATAAAAA
224187 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAAAAATTAAATAAAAATA
Found at i:224867 original size:18 final size:17
Alignment explanation
Indices: 224835--224868 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
224825 TCAGCCGGTC
224835 CGGTTTGAACGGTTCAG
1 CGGTTTGAACGGTTCAG
*
224852 CGGTTCTGACCGGTTCA
1 CGGTT-TGAACGGTTCA
224869 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAG
Found at i:226321 original size:29 final size:29
Alignment explanation
Indices: 226279--226337 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
226269 TTTTTTTTCT
226279 ACATTTTAAATATTGATGAATATGAACTA
1 ACATTTTAAATATTGATGAATATGAACTA
226308 ACATTTTAAATATTGATGAATATGAACTA
1 ACATTTTAAATATTGATGAATATGAACTA
226337 A
1 A
226338 AATGACACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (29 bp):
ACATTTTAAATATTGATGAATATGAACTA
Found at i:226477 original size:23 final size:23
Alignment explanation
Indices: 226457--226558 Score: 93
Period size: 23 Copynumber: 4.4 Consensus size: 23
226447 TAAACGAACA
226457 ATAAACGAACATGTTCTCGAAAG
1 ATAAACGAACATGTTCTCGAAAG
*
226480 TTAAACGAACATGTTCGT-GAAAG
1 ATAAACGAACATGTTC-TCGAAAG
* *
226503 CTACACGAACATGTTCGT-GAAAG
1 ATAAACGAACATGTTC-TCGAAAG
* *
226526 CTACACGAACATGTTCGT-GAAAG
1 ATAAACGAACATGTTC-TCGAAAG
* *
226549 CTACACGAAC
1 ATAAACGAAC
226559 GAACACGAAC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
23 74 0.99
24 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (23 bp):
ATAAACGAACATGTTCTCGAAAG
Found at i:226534 original size:46 final size:46
Alignment explanation
Indices: 226461--226558 Score: 162
Period size: 46 Copynumber: 2.1 Consensus size: 46
226451 CGAACAATAA
*
226461 ACGAACATGTTCTCGAAAGTTAAACGAACATGTTCGTGAAAGCTAC
1 ACGAACATGTTCTCGAAAGCTAAACGAACATGTTCGTGAAAGCTAC
*
226507 ACGAACATGTTCGT-GAAAGCTACACGAACATGTTCGTGAAAGCTAC
1 ACGAACATGTTC-TCGAAAGCTAAACGAACATGTTCGTGAAAGCTAC
226553 ACGAAC
1 ACGAAC
226559 GAACACGAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 48 0.98
47 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (46 bp):
ACGAACATGTTCTCGAAAGCTAAACGAACATGTTCGTGAAAGCTAC
Found at i:231328 original size:19 final size:19
Alignment explanation
Indices: 231296--231383 Score: 117
Period size: 19 Copynumber: 4.6 Consensus size: 19
231286 AAACCGGTTC
231296 TGACCGGTCTGAACCGGCT
1 TGACCGGTCTGAACCGGCT
* *
231315 TGATCGGT-TCGAACCGGTT
1 TGACCGGTCT-GAACCGGCT
231334 TGACCGGTCTGAACCGGCT
1 TGACCGGTCTGAACCGGCT
231353 TGACCGGTCTGAACCGG-T
1 TGACCGGTCTGAACCGGCT
*
231371 CTGACCAGTCTGA
1 -TGACCGGTCTGA
231384 CCCGACCCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
18 2 0.03
19 58 0.95
20 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.31, T:0.24
Consensus pattern (19 bp):
TGACCGGTCTGAACCGGCT
Found at i:231341 original size:38 final size:38
Alignment explanation
Indices: 231287--231383 Score: 142
Period size: 38 Copynumber: 2.5 Consensus size: 38
231277 GGCTGCTGGA
*
231287 AACCGGTTCTGACCGGTCTGAACCGGCTTGATCGGT-TCG
1 AACCGGTT-TGACCGGTCTGAACCGGCTTGACCGGTCT-G
231326 AACCGGTTTGACCGGTCTGAACCGGCTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTGAACCGGCTTGACCGGTCTG
* *
231364 AACCGGTCTGACCAGTCTGA
1 AACCGGTTTGACCGGTCTGA
231384 CCCGACCCGA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
38 45 0.83
39 9 0.17
ACGTcount: A:0.18, C:0.29, G:0.30, T:0.24
Consensus pattern (38 bp):
AACCGGTTTGACCGGTCTGAACCGGCTTGACCGGTCTG
Found at i:231383 original size:9 final size:9
Alignment explanation
Indices: 231288--231385 Score: 76
Period size: 9 Copynumber: 10.3 Consensus size: 9
231278 GCTGCTGGAA
231288 ACCGGTTCTG
1 ACCGG-TCTG
231298 ACCGGTCTG
1 ACCGGTCTG
231307 AACCGG-CTTG
1 -ACCGGTC-TG
*
231317 ATCGGT-TCG
1 ACCGGTCT-G
*
231326 AACCGGTTTG
1 -ACCGGTCTG
231336 ACCGGTCTG
1 ACCGGTCTG
231345 AACCGG-CTTG
1 -ACCGGTC-TG
231355 ACCGGTCTG
1 ACCGGTCTG
231364 AACCGGTCTG
1 -ACCGGTCTG
*
231374 ACCAGTCTG
1 ACCGGTCTG
231383 ACC
1 ACC
231386 CGACCCGACC
Statistics
Matches: 74, Mismatches: 4, Indels: 21
0.75 0.04 0.21
Matches are distributed among these distances:
8 1 0.01
9 37 0.50
10 35 0.47
11 1 0.01
ACGTcount: A:0.16, C:0.31, G:0.30, T:0.23
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:231392 original size:5 final size:5
Alignment explanation
Indices: 231382--231439 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
231372 TGACCAGTCT
* *
231382 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
231431 GACCC GACC
1 GACCC GACC
231440 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:231407 original size:22 final size:22
Alignment explanation
Indices: 231382--231446 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
231372 TGACCAGTCT
231382 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
231404 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
231426 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
231447 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:231448 original size:7 final size:7
Alignment explanation
Indices: 231436--231462 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
231426 GACCCGACCC
231436 GACCGTT
1 GACCGTT
231443 GACCGTT
1 GACCGTT
231450 GACCGTT
1 GACCGTT
231457 GACCGT
1 GACCGT
231463 CGACTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:247210 original size:23 final size:23
Alignment explanation
Indices: 247184--247227 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
247174 TTACATATTA
247184 AATACAATAAATA-TATTATTTAT
1 AATA-AATAAATATTATTATTTAT
*
247207 AATAAATTAATATTATTATTT
1 AATAAATAAATATTATTATTT
247228 TTTAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AATAAATAAATATTATTATTTAT
Found at i:247472 original size:48 final size:49
Alignment explanation
Indices: 247412--247521 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 49
247402 AATAATATAA
* * * *
247412 ATTTTATTAATATTTATTATATCTTATTAA-ATTAAAAATATAA-TATCTT
1 ATTTTA-TAATATTGATTATATATTA-TAATATTAAAAAAATAATTATATT
*
247461 ATTTTATAATATTGATTATTTATTATAATATTAAAAAAATAATTATATT
1 ATTTTATAATATTGATTATATATTATAATATTAAAAAAATAATTATATT
*
247510 ATTATA-AATATT
1 ATTTTATAATATT
247522 AATAAATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
47 3 0.06
48 34 0.64
49 16 0.30
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (49 bp):
ATTTTATAATATTGATTATATATTATAATATTAAAAAAATAATTATATT
Found at i:247539 original size:48 final size:48
Alignment explanation
Indices: 247442--247540 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 48
247432 ATCTTATTAA
* * * * *
247442 ATTAAAAATATAATATCTTATTTTATAATATTGATTATTTATTATAAT
1 ATTAAAAAAATAATATATTATTATATAATATTAATAATTTATTATAAT
*
247490 ATTAAAAAAATAATTATATTATTATA-AATATTAATAAATTTTTTA-AAT
1 ATTAAAAAAATAA-TATATTATTATATAATATTAAT-AATTTATTATAAT
247538 ATT
1 ATT
247541 TTAATAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
48 26 0.60
49 17 0.40
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (48 bp):
ATTAAAAAAATAATATATTATTATATAATATTAATAATTTATTATAAT
Found at i:252316 original size:21 final size:21
Alignment explanation
Indices: 252290--252329 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
252280 AAGAGGAGAT
252290 GAGGTCCACGAGAGTAGAGGA
1 GAGGTCCACGAGAGTAGAGGA
252311 GAGGTCCACGAGAGTAGAG
1 GAGGTCCACGAGAGTAGAG
252330 AAAGAGTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.42, T:0.10
Consensus pattern (21 bp):
GAGGTCCACGAGAGTAGAGGA
Found at i:254976 original size:20 final size:19
Alignment explanation
Indices: 254924--254986 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
254914 AAATCAATCG
254924 CTTTTAAAAGGATCGATCC
1 CTTTTAAAAGGATCGATCC
* **
254943 ATTGGGAGAAAGGATCGATCC
1 CTT-TTA-AAAGGATCGATCC
*
254964 CTTTTCAAAAGGATCGATTC
1 CTTTT-AAAAGGATCGATCC
254984 CTT
1 CTT
254987 GGAGAAAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.06
20 16 0.47
21 16 0.47
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (19 bp):
CTTTTAAAAGGATCGATCC
Found at i:255006 original size:41 final size:40
Alignment explanation
Indices: 254916--254993 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
254906 ATCTAGAAAA
*
254916 ATCAATCGCTTTTAAAAGGATCGATCCATTGGGAGAAAGG
1 ATCAATCCCTTTTAAAAGGATCGATCCATTGGGAGAAAGG
*
254956 ATCGATCCCTTTTCAAAAGGATCGATTCC-TT-GGAGAAA
1 ATCAATCCCTTTT-AAAAGGATCGA-TCCATTGGGAGAAA
254994 ATGATTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 18 0.53
41 13 0.38
42 3 0.09
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (40 bp):
ATCAATCCCTTTTAAAAGGATCGATCCATTGGGAGAAAGG
Found at i:262129 original size:324 final size:316
Alignment explanation
Indices: 261515--262159 Score: 1069
Period size: 324 Copynumber: 2.0 Consensus size: 316
261505 TGCGCCTAAA
*
261515 ATGTTATCAGAAGTTTAGTTGATGGAGCCTTAATTTTCCATGATAGGAAAATAAGTTAAGAGTTG
1 ATGTTATCAGAAGTTTAGTTGATGGAGCCTTAATTTTCCATGATAGGAAAATAAGTTAAAAGTTG
* *
261580 AAAATGTTATGACTATTATAAAATGGGTTGCGCCGAAGAATGTCATGGCTCACTAAGAATAGGTT
66 AAAATGTTATGACGATTATAAAATGGGTTGCGCCCAAGAATGTCATGGCTCACTAAGAATAGGTT
261645 GAGATATTTAATATTAATATTTTTTAATAAAATAGGTTAAACCTATGTAGTAACGAAATTAGACG
131 GAGATATTTAATATTAATATTTTTTAATAAAATAGGTTAAACCTATGTAGTAACGAAATTAGACG
* *
261710 GTAAATAAAACAACTAATCGTTAGCTAATCAGCTAAGGAAAGGGAAAACACGAAGTTTAATATGA
196 GTAAATAAAACAACCAATCCTTAGCTAATCAGCTAAGGAAAGGGAAAACACGAAGTTTAATATGA
*
261775 TCTTTGGATACTTCCTCTAATTTTATGCTTGAACAAACCATGTGAAATTCTGTGTG
261 TCTTTGGATACTCCCTCTAATTTTATGCTTGAACAAACCATGTGAAATTCTGTGTG
*
261831 ATGTTATCAGAATTTTAGTTGATGGAGCCTTAAATTTTCCATGATAGGAAAATAAGTTAAAAGTT
1 ATGTTATCAGAAGTTTAGTTGATGGAGCCTT-AATTTTCCATGATAGGAAAATAAGTTAAAAGTT
*
261896 GAAAATGTTATGAACGATTATAAGAAATATGGTTGCGCCCAAGAATGTCATGGCTCACTAAGAAA
65 GAAAATGTTATG-ACGATTAT-A-AAAT-GGGTTGCGCCCAAGAATGTCATGGCTCACTAAG-AA
*
261961 TAGGTTGCGATATTTAATATTAATATTTTTTTAATAAAATAGGTTAAACCTATGTAGTAACGAAA
125 TAGGTTGAGATATTTAATATTAATA-TTTTTTAATAAAATAGGTTAAACCTATGTAGTAACGAAA
* *
262026 TTAGGC-GTAAATAAAA-AACCAATCCTTAGCTAAATCATCTAAGGAAAAAGGGAAAACACGAAG
189 TTAGACGGTAAATAAAACAACCAATCCTTAGCT-AATCAGCTAAGG--AAAGGGAAAACACGAAG
* *
262089 TTTAATATGATCTTTGGATACTCCCTCTGATTTTATGCTTGAACAAACCATGTGAAATTCTTTGT
251 TTTAATATGATCTTTGGATACTCCCTCTAATTTTATGCTTGAACAAACCATGTGAAATTCTGTGT
262154 G
316 G
262155 ATGTT
1 ATGTT
262160 TGTACAGGTT
Statistics
Matches: 306, Mismatches: 13, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
316 30 0.10
317 44 0.14
318 7 0.02
319 1 0.00
320 4 0.01
321 44 0.14
322 47 0.15
323 44 0.14
324 85 0.28
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (316 bp):
ATGTTATCAGAAGTTTAGTTGATGGAGCCTTAATTTTCCATGATAGGAAAATAAGTTAAAAGTTG
AAAATGTTATGACGATTATAAAATGGGTTGCGCCCAAGAATGTCATGGCTCACTAAGAATAGGTT
GAGATATTTAATATTAATATTTTTTAATAAAATAGGTTAAACCTATGTAGTAACGAAATTAGACG
GTAAATAAAACAACCAATCCTTAGCTAATCAGCTAAGGAAAGGGAAAACACGAAGTTTAATATGA
TCTTTGGATACTCCCTCTAATTTTATGCTTGAACAAACCATGTGAAATTCTGTGTG
Found at i:270653 original size:19 final size:19
Alignment explanation
Indices: 270617--270676 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
270607 GAGTTTCAAA
* * *
270617 ACCTTAAGGCTTTTAAACT
1 ACCTTAGGGGTTTGAAACT
*
270636 ACCTTAGGGGTTTGAAACC
1 ACCTTAGGGGTTTGAAACT
*
270655 ACCTAATGGGGTTTCGAAACT
1 ACCTTA-GGGGTTT-GAAACT
270676 A
1 A
270677 GGCAAACTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 20 0.61
20 7 0.21
21 6 0.18
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (19 bp):
ACCTTAGGGGTTTGAAACT
Found at i:276406 original size:21 final size:21
Alignment explanation
Indices: 276366--276406 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
276356 TCACAAATGT
*
276366 ATAACTTTTATATTAGATATG
1 ATAACTTTTAAATTAGATATG
276387 ATAACATTTTAAATTA-ATAT
1 ATAAC-TTTTAAATTAGATAT
276407 CCGTTACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (21 bp):
ATAACTTTTAAATTAGATATG
Found at i:279678 original size:14 final size:16
Alignment explanation
Indices: 279655--279695 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
279645 CTAGTGTGAT
279655 TAGA-GAAGAAA-A-A
1 TAGACGAAGAAAGAGA
279668 TAGACGAAGAAAAGAGA
1 TAGACGAAG-AAAGAGA
279685 TAGACGAAGAA
1 TAGACGAAGAA
279696 TAAAGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 3 0.12
16 3 0.12
17 10 0.42
ACGTcount: A:0.61, C:0.05, G:0.27, T:0.07
Consensus pattern (16 bp):
TAGACGAAGAAAGAGA
Found at i:284043 original size:20 final size:20
Alignment explanation
Indices: 284018--284071 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
284008 AATAGGCATT
284018 TAGCGGCGTTTTTAGCTCTA
1 TAGCGGCGTTTTTAGCTCTA
*
284038 TAGCGGCATTTTTAGCTCTA
1 TAGCGGCGTTTTTAGCTCTA
284058 TAGCGGCGTTTTTA
1 TAGCGGCGTTTTTA
284072 AGCGCCTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.41
Consensus pattern (20 bp):
TAGCGGCGTTTTTAGCTCTA
Found at i:284196 original size:42 final size:43
Alignment explanation
Indices: 284149--284258 Score: 152
Period size: 42 Copynumber: 2.6 Consensus size: 43
284139 TTTGTGAACA
* *
284149 AAAAACGCCGCAAAAAGTCTAGCTCTATAGC-G-GTGTTTTCTG
1 AAAAACGCCGCAAAAGGTCAAGCTCTATAGCAGCGT-TTTTCTG
*
284191 AAAAACGCCGCAAAAGGTCAAGCTCTATAGCAGCGTTTTTCTT
1 AAAAACGCCGCAAAAGGTCAAGCTCTATAGCAGCGTTTTTCTG
*
284234 AAAACACCCCGCAAAAGGTCAAGCT
1 AAAA-ACGCCGCAAAAGGTCAAGCT
284259 TTGTCAAGCT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
42 29 0.48
43 11 0.18
44 21 0.34
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCAAAAGGTCAAGCTCTATAGCAGCGTTTTTCTG
Found at i:286208 original size:43 final size:43
Alignment explanation
Indices: 286125--286386 Score: 250
Period size: 42 Copynumber: 6.2 Consensus size: 43
286115 GTTTGTGAAC
* * * * *
286125 AAAAACCGCCGCAAAAAGTCTAGCTCTATAGCGGTG-TTTTCTG
1 AAAAA-CGCAGCAAAAGGTCAAGCTCTATAGCGGCGTTTTTCTT
* * *
286168 AAAAACACAGCAAAAGGTCAAGATCTACAGCGGCGTTTTTCTT
1 AAAAACGCAGCAAAAGGTCAAGCTCTATAGCGGCGTTTTTCTT
* *
286211 -AAAACGCCA-CAAAAGGCCAAGCTCTATAGCGGCATTTTTCTT
1 AAAAACG-CAGCAAAAGGTCAAGCTCTATAGCGGCGTTTTTCTT
* * * *
286253 TAAAATGCCGCAAAAGGTCAAGCTCTATAGCAGCGTTTTTCTT
1 AAAAACGCAGCAAAAGGTCAAGCTCTATAGCGGCGTTTTTCTT
* *
286296 AAAACACGCCGCAAAAGGTCAAGCTTTATAGCGGCG---TT-TT
1 AAAA-ACGCAGCAAAAGGTCAAGCTCTATAGCGGCGTTTTTCTT
* * * * **
286336 AAAAACGCCGCAAAAGATCAAGCTCTATAGTGGCATTTTTGAT
1 AAAAACGCAGCAAAAGGTCAAGCTCTATAGCGGCGTTTTTCTT
286379 AAAAACGC
1 AAAAACGC
286387 CGCTAATTAC
Statistics
Matches: 183, Mismatches: 27, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
39 27 0.15
40 6 0.03
41 2 0.01
42 60 0.33
43 60 0.33
44 28 0.15
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (43 bp):
AAAAACGCAGCAAAAGGTCAAGCTCTATAGCGGCGTTTTTCTT
Found at i:286268 original size:85 final size:87
Alignment explanation
Indices: 286177--286335 Score: 241
Period size: 85 Copynumber: 1.9 Consensus size: 87
286167 GAAAAACACA
*
286177 GCAAAAGGTCAAGATCTACAGCGGCGTTTTTCTT-AAA-ACGCCACAAAAGGCCAAGCTCTATAG
1 GCAAAAGGTCAAGATCTACAGCAGCGTTTTTCTTAAAACACGCCACAAAAGGCCAAGCTCTATAG
286240 CGGCATTTTTCTTTAAAATGCC
66 CGGCATTTTTCTTTAAAATGCC
* * * * *
286262 GCAAAAGGTCAAGCTCTATAGCAGCGTTTTTCTTAAAACACGCCGCAAAAGGTCAAGCTTTATAG
1 GCAAAAGGTCAAGATCTACAGCAGCGTTTTTCTTAAAACACGCCACAAAAGGCCAAGCTCTATAG
*
286327 CGGCGTTTT
66 CGGCATTTT
286336 AAAAACGCCG
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 31 0.48
86 3 0.05
87 31 0.48
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (87 bp):
GCAAAAGGTCAAGATCTACAGCAGCGTTTTTCTTAAAACACGCCACAAAAGGCCAAGCTCTATAG
CGGCATTTTTCTTTAAAATGCC
Found at i:290257 original size:41 final size:41
Alignment explanation
Indices: 290212--290763 Score: 291
Period size: 41 Copynumber: 13.5 Consensus size: 41
290202 AAAAAACATA
* * * *
290212 ACTAAAGTACGAGTCTTTGGCGGGGTTTGTATGAAAACGAC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGAC
* * * * * *
290253 ACTAAAGTATGGGTTTTTAGCGACGTTTG-A-AAAAATTGCC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAA-CGAC
*
290293 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAGAAAC-ACC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGA-C
* * * * * * *
290334 TCTAAAGTACGAATCTTTGGCAGCGTTTGTGCTTAAAAC-ACC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGT-ATAAAAACGA-C
* * *
290376 ACTAAAGTAC-AGTATTTAGCGGCGTTTATACAAAAACGCC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGAC
* * * * * * *
290416 ACTAAAATACAAGCATTTAGCGGCATTTGTTCTTAAAACGCC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTG-TATAAAAACGAC
* * * * * *
290458 ACTAAAGTA-TAATATTTAGCGGCGTTTATACAAAAATGCC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGAC
* * * * * *
290498 ACTAAAGTACGAGCACTTAGTGGCGTTTGTGCTTAAAACGCC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGT-ATAAAAACGAC
* * * * *
290540 ACTAAAGTAC-AGTATTTAGCGTCATTTATACAAAAACGCC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGAC
* ** * * * * *
290580 ACTAAAGAATAAGCATTTAGCGGCGTTTGTGTGCTTAAAATGCC
1 ACTAAAGTACGAGTATTTAGCGGCG-TT-TGT-ATAAAAACGAC
* * * **
290624 ACTAAAGTA-TAGTATTTAGCGGTGTTTGTGCTTGAAACG-C
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGT-ATAAAAACGAC
* * * * * *
290664 TACTAAAGTA-TATTATTTAGCGGCGTTTATACAAAAATGCC
1 -ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGAC
* * *
290705 ACTAAAGTAC-ATTATTTAGTGGCGTTTATATAAAAAC-ACC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGA-C
* *
290745 ACTAAAGAACAAGTATTTA
1 ACTAAAGTACGAGTATTTA
290764 CTGGTGTTTG
Statistics
Matches: 392, Mismatches: 100, Indels: 38
0.74 0.19 0.07
Matches are distributed among these distances:
39 4 0.01
40 124 0.32
41 176 0.45
42 59 0.15
43 14 0.04
44 15 0.04
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (41 bp):
ACTAAAGTACGAGTATTTAGCGGCGTTTGTATAAAAACGAC
Found at i:290421 original size:82 final size:82
Alignment explanation
Indices: 290290--290751 Score: 457
Period size: 82 Copynumber: 5.6 Consensus size: 82
290280 TGAAAAAATT
* * * * * * *
290290 GCCACTAAAGTACGAGTATTTAGCGGCGTTTGTATAGAAACACCTCTAAAGTACGAATCTTTGGC
1 GCCACTAAAGTAC-AGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAAGCTTTAGC
*
290355 AGCGTTTGTGCTTAAAAC
65 GGCGTTTGTGCTTAAAAC
* *
290373 ACCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAATAC-AAGCATTTAGC
1 GCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAAGC-TTTAGC
* *
290437 GGCATTTGTTCTTAAAAC
65 GGCGTTTGTGCTTAAAAC
* * * * *
290455 GCCACTAAAGTATAATATTTAGCGGCGTTTATACAAAAATGCCACTAAAGTACG-AGCACTTAGT
1 GCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAAGC-TTTAGC
290519 GGCGTTTGTGCTTAAAAC
65 GGCGTTTGTGCTTAAAAC
* * **
290537 GCCACTAAAGTACAGTATTTAGCGTCATTTATACAAAAACGCCACTAAAG-AATAAGCATTTAGC
1 GCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAAGC-TTTAGC
*
290601 GGCGTTTGTGTGCTTAAAAT
65 GGCG-TT-TGTGCTTAAAAC
* * * * ** * * ***
290621 GCCACTAAAGTATAGTATTTAGCGGTGTTTGTGCTTGAAACGCTACTAAAGTA-TATTATTTAGC
1 GCCACTAAAGTACAGTATTTAGCGGCGTTTATAC-AAAAACGCCACTAAAGTACGAAGCTTTAGC
* * * *
290685 GGCGTTTATAC-AAAAAT
65 GGCGTTTGTGCTTAAAAC
* * * *
290702 GCCACTAAAGTACATTATTTAGTGGCGTTTATATAAAAACACCACTAAAG
1 GCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAG
290752 AACAAGTATT
Statistics
Matches: 315, Mismatches: 57, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
80 12 0.04
81 36 0.11
82 186 0.59
83 16 0.05
84 49 0.16
85 15 0.05
86 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (82 bp):
GCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAAGCTTTAGCG
GCGTTTGTGCTTAAAAC
Found at i:290476 original size:164 final size:162
Alignment explanation
Indices: 290290--290794 Score: 527
Period size: 164 Copynumber: 3.1 Consensus size: 162
290280 TGAAAAAATT
*
290290 GCCACTAAAGTACGAGTATTTAGCGGCGTTTGTATAGAAACACCTCTAAAGTACGAATCTTTGGC
1 GCCACTAAAGTA-TAGTATTTAGCGGCGTTTGTATAGAAAC-CCTCTAAAGTACGAATCTTTGGC
*
290355 AGCGTTTGTGCTTAAAACACCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTA
64 -GCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTA
*
290420 AA-ATACAAGCATTTAGCGGCATTTGTTCTTAAAAC
128 AAGA-ACAAGCATTTAGCGGCGTTTGTTCTTAAAAC
* * * * * * *
290455 GCCACTAAAGTATAATATTTAGCGGCGTTTATACAAAAATGCCACTAAAGTACGAGCA-CTTAGT
1 GCCACTAAAGTATAGTATTTAGCGGCGTTTGTATAGAAA-CCCTCTAAAGTACGA--ATCTTTG-
* *
290519 G-GCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGTCATTTATACAAAAACGCCACT
62 GCGCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACT
* *
290583 AAAGAATAAGCATTTAGCGGCGTTTGTGTGCTTAAAAT
127 AAAGAACAAGCATTTAGCGGCGTTTGT-T-CTTAAAAC
* * * * * * * *
290621 GCCACTAAAGTATAGTATTTAGCGGTGTTTGTGCTTGAAACGCTACTAAAGTA-TATTATTTAGC
1 GCCACTAAAGTATAGTATTTAGCGGCGTTTGT-ATAGAAACCCT-CTAAAGTACGAATCTTTGGC
* * * * * * * *
290685 GGCGTTTATAC-AAAAATGCCACTAAAGTACATTATTTAGTGGCGTTTATATAAAAACACCACTA
64 -GCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTA
* * **
290749 AAGAACAAGTATTTA-CTGGTGTTTGTTCAAAAAAC
128 AAGAACAAGCATTTAGC-GGCGTTTGTTCTTAAAAC
*
290784 GCCGCTAAAGT
1 GCCACTAAAGT
290795 GTCGCTAAAA
Statistics
Matches: 281, Mismatches: 46, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
163 15 0.05
164 121 0.43
165 86 0.31
166 48 0.17
167 11 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (162 bp):
GCCACTAAAGTATAGTATTTAGCGGCGTTTGTATAGAAACCCTCTAAAGTACGAATCTTTGGCGC
GTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAG
AACAAGCATTTAGCGGCGTTTGTTCTTAAAAC
Found at i:292190 original size:17 final size:16
Alignment explanation
Indices: 292160--292193 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
292150 TTAAAAAAAG
*
292160 GTAAACACCGGTCAAC
1 GTAAACACCAGTCAAC
292176 GTAAGACACCAGTCAAC
1 GTAA-ACACCAGTCAAC
292193 G
1 G
292194 ATGACAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.29, G:0.21, T:0.12
Consensus pattern (16 bp):
GTAAACACCAGTCAAC
Found at i:292965 original size:30 final size:30
Alignment explanation
Indices: 292929--293002 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
292919 TTTTAATTAT
* * *
292929 AATTTCATTTTAGTCCATAAATTTCACTAA
1 AATTTCATTTTAGTCCACAAACTTAACTAA
** * *
292959 AATTTCAACTTAGTCCCCAAACTTAATTAA
1 AATTTCATTTTAGTCCACAAACTTAACTAA
292989 AA-TTCATTTTAGTC
1 AATTTCATTTTAGTC
293003 ATTAGAATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 10 0.29
30 25 0.71
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.41
Consensus pattern (30 bp):
AATTTCATTTTAGTCCACAAACTTAACTAA
Found at i:294806 original size:29 final size:29
Alignment explanation
Indices: 294729--294808 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
294719 GCTAGTGACT
* **
294729 AAAATATAAGTTTTGAAAGTTTGGTGGTA
1 AAAATATAACTTTTGAAAGTTTGGTGCCA
* *
294758 AAAGTATAAACTTTTAAAAGTTTAGG-GACCA
1 AAAATAT-AACTTTTGAAAGTTT-GGTG-CCA
294789 AAAATATAA-TTTTGAAAGTT
1 AAAATATAACTTTTGAAAGTT
294809 ACATATTCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 16 0.39
30 16 0.39
31 9 0.22
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (29 bp):
AAAATATAACTTTTGAAAGTTTGGTGCCA
Found at i:296842 original size:15 final size:15
Alignment explanation
Indices: 296779--296844 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
296769 AATGTTATAA
296779 TGAAAATGTGATCTACG
1 TGAAAATGT-A-CTACG
* * *
296796 TG-AACTGTTCTATG
1 TGAAAATGTACTACG
* *
296810 TGAAAATGTATTAAG
1 TGAAAATGTACTACG
*
296825 TGAAAATGTCCTACG
1 TGAAAATGTACTACG
296840 TGAAA
1 TGAAA
296845 GTAGACTACG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
14 6 0.16
15 25 0.66
16 5 0.13
17 2 0.05
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (15 bp):
TGAAAATGTACTACG
Found at i:297057 original size:23 final size:23
Alignment explanation
Indices: 296977--297037 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
296967 GAGTTGAGGG
296977 TTCTACGCGGTCCTTCAGGACAA
1 TTCTACGCGGTCCTTCAGGACAA
297000 TTCTACGCGGTCCTTCAGGACAA
1 TTCTACGCGGTCCTTCAGGACAA
*
297023 TTCTATGCGGTCCTT
1 TTCTACGCGGTCCTT
297038 TGGGATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.31
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCAGGACAA
Found at i:297065 original size:23 final size:23
Alignment explanation
Indices: 296977--297086 Score: 98
Period size: 23 Copynumber: 4.8 Consensus size: 23
296967 GAGTTGAGGG
* * *
296977 TTCTACGCGGTCCTTCAGGACAA
1 TTCTATGCGGTCTTTCGGGACAA
* * *
297000 TTCTACGCGGTCCTTCAGGACAA
1 TTCTATGCGGTCTTTCGGGACAA
* *
297023 TTCTATGCGGTCCTTT-GGGATAT
1 TTCTATGCGGT-CTTTCGGGACAA
297046 TTCTATGCGGTCTTTCGGGAC-A
1 TTCTATGCGGTCTTTCGGGACAA
* *
297068 TATATATGTGGTCTTTCGG
1 T-TCTATGCGGTCTTTCGG
297087 TGCATATTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.07
23 67 0.89
24 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (23 bp):
TTCTATGCGGTCTTTCGGGACAA
Found at i:303307 original size:18 final size:18
Alignment explanation
Indices: 303263--303312 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
303253 GCACATATAC
*
303263 TATCATTATCATCATCAA
1 TATCATTATCATTATCAA
*
303281 CATTC-TTATCATTATCAA
1 TA-TCATTATCATTATCAA
303299 TATCATTATCATTA
1 TATCATTATCATTA
303313 ATCGTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (18 bp):
TATCATTATCATTATCAA
Found at i:303555 original size:21 final size:22
Alignment explanation
Indices: 303520--303589 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
303510 CACCGAAGTG
303520 CCACATAGAATGTCCCAAAAGA
1 CCACATAGAATGTCCCAAAAGA
* *
303542 CCACATAG-ATGTCCCGAAGGA
1 CCACATAGAATGTCCCAAAAGA
* * *
303563 CCGCGTAGAAATGTCCCAAATGA
1 CCACATAG-AATGTCCCAAAAGA
303586 CCAC
1 CCAC
303590 GTAGGATTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 17 0.44
22 8 0.21
23 14 0.36
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.14
Consensus pattern (22 bp):
CCACATAGAATGTCCCAAAAGA
Found at i:303582 original size:44 final size:46
Alignment explanation
Indices: 303528--303618 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
303518 TGCCACATAG
303528 AATGTCCCAAAAGACCACATA-GA-TGTCCCGAAGGACCGCGTAGA
1 AATGTCCCAAAAGACCACATAGGATTGTCCCGAAGGACCGCGTAGA
* * *
303572 AATGTCCCAAATGACCACGTAGGATTGTCTCGAAGGACCGCGTAGA
1 AATGTCCCAAAAGACCACATAGGATTGTCCCGAAGGACCGCGTAGA
303618 A
1 A
303619 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 19 0.45
45 2 0.05
46 21 0.50
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.16
Consensus pattern (46 bp):
AATGTCCCAAAAGACCACATAGGATTGTCCCGAAGGACCGCGTAGA
Found at i:303587 original size:23 final size:23
Alignment explanation
Indices: 303520--303618 Score: 78
Period size: 23 Copynumber: 4.4 Consensus size: 23
303510 CACCGAAGTG
* *
303520 CCACATAG-AATGTCCCAAAAGA
1 CCACGTAGAAATGTCCCAAAGGA
* *
303542 CCACATAG--ATGTCCCGAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
* *
303563 CCGCGTAGAAATGTCCCAAATGA
1 CCACGTAGAAATGTCCCAAAGGA
* * * *
303586 CCACGTAGGATTGTCTCGAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
*
303609 CCGCGTAGAA
1 CCACGTAGAA
303619 CCCTCGACTC
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
21 17 0.28
22 8 0.13
23 36 0.59
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.16
Consensus pattern (23 bp):
CCACGTAGAAATGTCCCAAAGGA
Found at i:305317 original size:15 final size:15
Alignment explanation
Indices: 305263--305321 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
305253 TGTTATATGA
305263 TAAGTGAAAATG--T
1 TAAGTGAAAATGTAT
305276 TATAGTGAAAATGTAAT
1 TA-AGTGAAAATGT-AT
*
305293 CTACGTGAAAATGTAT
1 -TAAGTGAAAATGTAT
305309 TAAGTGAAAATGT
1 TAAGTGAAAATGT
305322 CCTATGTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 2 0.05
14 10 0.26
15 12 0.31
16 2 0.05
17 11 0.28
18 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.32
Consensus pattern (15 bp):
TAAGTGAAAATGTAT
Found at i:305384 original size:23 final size:22
Alignment explanation
Indices: 305352--305435 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 22
305342 GAGAATGAAC
305352 TTCGGAACATTTCTATGTGGTCA
1 TTCGGAACATTTCTATGTGGT-A
* * * *
305375 TTCGGGACATTTCTACGCGGTTT
1 TTCGGAACATTTCTATGTGG-TA
*
305398 TTCAGG-ACATGTCTATGTGGTA
1 TTC-GGAACATTTCTATGTGGTA
305420 CTTCGGAACATTTCTA
1 -TTCGGAACATTTCTA
305436 CATGGCACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
22 3 0.06
23 42 0.88
24 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (22 bp):
TTCGGAACATTTCTATGTGGTA
Found at i:305445 original size:23 final size:24
Alignment explanation
Indices: 305419--305472 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
305409 TCTATGTGGT
*
305419 ACTTCGGAACAT-TTCTACATGGC
1 ACTTCGGAACATATTCTACACGGC
** *
305442 ACTTCGGTGCATATTCTACGCGGC
1 ACTTCGGAACATATTCTACACGGC
305466 ACTTCGG
1 ACTTCGG
305473 TGCAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (24 bp):
ACTTCGGAACATATTCTACACGGC
Found at i:307664 original size:21 final size:21
Alignment explanation
Indices: 307638--307712 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
307628 CGTTATACCA
*
307638 AAGGGATCAATCCTTTT-TGGG
1 AAGGGATCAATCCTTTTCT-CG
*
307659 AAGGGATCGATCCTTTTCCTCG
1 AAGGGATCAATCCTTTT-CTCG
*
307681 -AGGGATCAATCCTTTTGTC-
1 AAGGGATCAATCCTTTTCTCG
*
307700 AAGGGATCGATCC
1 AAGGGATCAATCC
307713 CAAACTCACT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 13 0.28
21 31 0.67
22 1 0.02
23 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
AAGGGATCAATCCTTTTCTCG
Found at i:307755 original size:20 final size:20
Alignment explanation
Indices: 307730--307785 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
307720 ACTGTTGTCC
*
307730 AAGGGATCGATATTTTTACA
1 AAGGGATCGATACTTTTACA
* * *
307750 AAGGGATCGATCCTTTTGCT
1 AAGGGATCGATACTTTTACA
*
307770 AAGGGATCGATTCTTT
1 AAGGGATCGATACTTT
307786 GAGCCAGAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (20 bp):
AAGGGATCGATACTTTTACA
Found at i:317328 original size:20 final size:20
Alignment explanation
Indices: 317305--317353 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
317295 TGGGGTATGG
*
317305 GTATCGATATTGGTTGTACA
1 GTATCGATAATGGTTGTACA
*
317325 GTATCGATAATGGTTGTATA
1 GTATCGATAATGGTTGTACA
317345 GTATCGATA
1 GTATCGATA
317354 CCATAAGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (20 bp):
GTATCGATAATGGTTGTACA
Found at i:317404 original size:17 final size:16
Alignment explanation
Indices: 317381--317433 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 16
317371 ATAAATTATT
317381 CAAGGAGTATCGATAC
1 CAAGGAGTATCGATAC
317397 CGAAGGAGTAGTGTCGATAC
1 C-AAGGAGTA---TCGATAC
*
317417 CAAGG-GTACCGATAC
1 CAAGGAGTATCGATAC
317432 CA
1 CA
317434 TTATGCAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 8 0.25
16 1 0.03
17 8 0.25
18 3 0.09
19 4 0.12
20 8 0.25
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (16 bp):
CAAGGAGTATCGATAC
Found at i:318167 original size:21 final size:21
Alignment explanation
Indices: 318109--318170 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
318099 GTCGAGGGTT
*
318109 CTATGCGGTCCTTCGGGACAA
1 CTATGTGGTCCTTCGGGACAA
* *
318130 CGTTATGTAGTCATTCGGGACATA
1 C--TATGTGGTCCTTCGGGACA-A
318154 -TATGTGGTCCTTCGGGA
1 CTATGTGGTCCTTCGGGA
318171 TATTCTATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
21 16 0.48
23 16 0.48
24 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (21 bp):
CTATGTGGTCCTTCGGGACAA
Found at i:318182 original size:22 final size:23
Alignment explanation
Indices: 318154--318220 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
318144 TCGGGACATA
318154 TATGTGGTCCTTCGG-G-ATATTC
1 TATGTGGTCCTTCGGTGCAT-TTC
318176 TATGTGG-CACTTCGGTGCATTTC
1 TATGTGGTC-CTTCGGTGCATTTC
* *
318199 TACGTGGTACTTCGGTGCATTT
1 TATGTGGTCCTTCGGTGCATTT
318221 TATACGAGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.03
22 13 0.33
23 23 0.59
24 2 0.05
ACGTcount: A:0.13, C:0.19, G:0.27, T:0.40
Consensus pattern (23 bp):
TATGTGGTCCTTCGGTGCATTTC
Found at i:318205 original size:23 final size:23
Alignment explanation
Indices: 318173--318220 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
318163 CTTCGGGATA
*
318173 TTCTATGTGGCACTTCGGTGCAT
1 TTCTACGTGGCACTTCGGTGCAT
*
318196 TTCTACGTGGTACTTCGGTGCAT
1 TTCTACGTGGCACTTCGGTGCAT
318219 TT
1 TT
318221 TATACGAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.12, C:0.21, G:0.25, T:0.42
Consensus pattern (23 bp):
TTCTACGTGGCACTTCGGTGCAT
Found at i:321987 original size:85 final size:85
Alignment explanation
Indices: 321824--321987 Score: 260
Period size: 85 Copynumber: 1.9 Consensus size: 85
321814 AAATACAATC
*
321824 ATGACACACGAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCA
1 ATGACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCA
* *
321889 TACATGCATGTCATTAATTT
66 TAAATGCACGTCATTAATTT
*
321909 ATGACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACTCAATG-AATGTC
1 ATGACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAA-GTC
321973 ATAAATG-AGCGTCAT
65 ATAAATGCA-CGTCAT
321988 AAATGCGCTT
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
84 3 0.04
85 70 0.96
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (85 bp):
ATGACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCA
TAAATGCACGTCATTAATTT
Found at i:326068 original size:18 final size:18
Alignment explanation
Indices: 326037--326071 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
326027 AGTTAGAATA
*
326037 TTTAATATAATTCATAAT
1 TTTAAAATAATTCATAAT
*
326055 TTTAAAATAGTTCATAA
1 TTTAAAATAATTCATAA
326072 AGATAGTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTAAAATAATTCATAAT
Found at i:326626 original size:19 final size:19
Alignment explanation
Indices: 326602--326671 Score: 104
Period size: 19 Copynumber: 3.7 Consensus size: 19
326592 GCTCAACTCG
*
326602 GTTCGGTTTGGTTCGACCA
1 GTTCGGTTCGGTTCGACCA
*
326621 GTTCGGTTCAGTTCGACCA
1 GTTCGGTTCGGTTCGACCA
*
326640 GTTCGGTTCGGTTCGACTA
1 GTTCGGTTCGGTTCGACCA
*
326659 GTTCGATTCGGTT
1 GTTCGGTTCGGTT
326672 GGGATAGTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.11, C:0.21, G:0.30, T:0.37
Consensus pattern (19 bp):
GTTCGGTTCGGTTCGACCA
Found at i:335033 original size:57 final size:57
Alignment explanation
Indices: 334915--335034 Score: 138
Period size: 57 Copynumber: 2.1 Consensus size: 57
334905 ATCTAAGTTT
* * **
334915 AAGATTGTCTACTCGCCAAGGATCCTCCATATTATTTTTTTGTCTCATATTATTTTT
1 AAGATTGTATACTCGCCAAGGATCCTCCATATTATTTTTATGTCTCATATTATTTAA
* *
334972 AAGATTGTATACTCGCCAATGATTCTCCATATTATTTTTGCAT-TC-CATACTT-TTTAA
1 AAGATTGTATACTCGCCAAGGATCCTCCATATTATTTTT--ATGTCTCATA-TTATTTAA
335029 AAGATT
1 AAGATT
335035 TAGAAGTATC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
57 49 0.91
58 4 0.07
59 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (57 bp):
AAGATTGTATACTCGCCAAGGATCCTCCATATTATTTTTATGTCTCATATTATTTAA
Found at i:335923 original size:16 final size:16
Alignment explanation
Indices: 335875--335915 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
335865 AGTTAGTGAC
335875 GGTGATTGTATCGTTG
1 GGTGATTGTATCGTTG
335891 GGTGATTGTATCGTTG
1 GGTGATTGTATCGTTG
335907 GGTGATTGT
1 GGTGATTGT
335916 GTTGTTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.05, G:0.39, T:0.44
Consensus pattern (16 bp):
GGTGATTGTATCGTTG
Found at i:343479 original size:12 final size:12
Alignment explanation
Indices: 343462--343486 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
343452 AATAAAGTAA
343462 CAAGAACTTTAT
1 CAAGAACTTTAT
343474 CAAGAACTTTAT
1 CAAGAACTTTAT
343486 C
1 C
343487 TAAGGAAAAT
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:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (12 bp):
CAAGAACTTTAT
Found at i:362262 original size:21 final size:20
Alignment explanation
Indices: 362236--362290 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
362226 TCACTTACCA
* *
362236 AAAATTTATTTTATTATTATC
1 AAAATTAATTTTAATATT-TC
*
362257 AAAATTAATATTAATATTTC
1 AAAATTAATTTTAATATTTC
* *
362277 AAAAATCATTTTAA
1 AAAATTAATTTTAA
362291 CAATTAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATTAATTTTAATATTTC
Found at i:364697 original size:36 final size:36
Alignment explanation
Indices: 364522--364720 Score: 188
Period size: 36 Copynumber: 5.5 Consensus size: 36
364512 TTTTATAGCA
* * *
364522 ATATAATATA-ATTTTTGAAAAT-GTTTTTAAAATAT
1 ATATAATATATAGTTTTG-AAATCATTTTGAAAATAT
* * ** * **
364557 ATGTACTATATAGTTTCAAAAACATTCCGAAAATAT
1 ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
* * ** *
364593 ATATAGTATATAGTTTTAAAAAAAATTTTGAAAACAT
1 ATATAATATATAGTTTT-GAAATCATTTTGAAAATAT
*
364630 ATATAATGTATAGTTTTTGAAAATGCA-TTTGAAAATAT
1 ATATAATATATAG-TTTTG-AAAT-CATTTTGAAAATAT
364668 ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
1 ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
364704 ATATAATATATAGTTTT
1 ATATAATATATAGTTTT
364721 TTTTAAAAAA
Statistics
Matches: 133, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
35 13 0.10
36 59 0.44
37 31 0.23
38 29 0.22
39 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
Found at i:366074 original size:11 final size:11
Alignment explanation
Indices: 366058--366102 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
366048 ATATTTTTCT
366058 TATTTATTTAA
1 TATTTATTTAA
*
366069 TATTTATTTAT
1 TATTTATTTAA
366080 TATTTATTTAA
1 TATTTATTTAA
366091 T-TTTAATTTAA
1 TATTT-ATTTAA
366102 T
1 T
366103 TTCTTTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 3 0.10
11 28 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:366085 original size:22 final size:22
Alignment explanation
Indices: 366057--366100 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
366047 AATATTTTTC
366057 TTATTTATTTAATATTT-ATTTA
1 TTATTTATTTAAT-TTTAATTTA
366079 TTATTTATTTAATTTTAATTTA
1 TTATTTATTTAATTTTAATTTA
366101 ATTTCTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTTATTTAATTTTAATTTA
Found at i:367258 original size:16 final size:17
Alignment explanation
Indices: 367237--367268 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
367227 CTCACTAACC
367237 CTTTTATTTT-TGTTCT
1 CTTTTATTTTGTGTTCT
367253 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
367269 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.72
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:367922 original size:19 final size:19
Alignment explanation
Indices: 367888--367932 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
367878 ATTTAGACAT
367888 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
367906 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
367925 TTTGCATT
1 TTTGCATT
367933 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:371523 original size:162 final size:163
Alignment explanation
Indices: 371256--371982 Score: 875
Period size: 162 Copynumber: 4.4 Consensus size: 163
371246 GCAGCTTAGT
* * **
371256 TCAAGGCCAGAAGGGCTATCTGCCCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 TCAAGGCTAGAAGGGTTATCTG-TTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * *
371320 ACATCATTTGCAGTATAGCTTAAGTTGAGAAGAGCTATCTG-C-CAAAGACCCTTAAGTTCGATT
65 ACATCATTTGCAG-ATAGCTTAAGTCGAGAAGGGTTATCTGCCACAAAGACCCTTAAGTTCGATT
371383 ACACTCAGCTTCAAGGGCATAACATTTACAGCAAC
129 ACACTCAGCTTCAAGGGCATAACATTTACAGCAAC
* *
371418 TCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
1 TCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
* * ** *
371483 CATCATCTGCAGAATAGCTTAAGTCGAGAAGGGATATCTG-C-CAAAGACCCTCGAGTTCGACTA
66 CATCATTTGCAG-ATAGCTTAAGTCGAGAAGGGTTATCTGCCACAAAGACCCTTAAGTTCGATTA
** * * * *
371546 CGTTCAGCTTCGAA-GGCACATCATTTGCAGTAAC
130 CACTCAGCTTC-AAGGGCATAACATTTACAGCAAC
* * * * * * *
371580 TTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGC
1 TCAAGGCTAGAAGGGTTATCTG-TTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
*
371645 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGA
65 ACATCATTTGCAG-ATAGCTTAAGTCGAGAAGGGTTATCTGCC-AC-AAAGACCCTTAAGTTCGA
371710 TTACACTCAGCTTCAAGGGCATATATCATTTACAGCATAAC
127 TTACACTCAGCTTCAAGGGCATA-A-CATTTACAGC--AAC
* *
371751 TCAAGGCTAGAAGGGTTAACTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
1 TCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
* * * * * *
371816 TATCA-TTGC-GGTAGCTTAAGTCTAGAAGGGTTGTCTGCCAACAAAGA-CCTTCGAGTTTGATT
66 CATCATTTGCAGATAGCTTAAGTCGAGAAGGGTTATCTGCC-ACAAAGACCCTT-AAGTTCGATT
** *
371878 ACACTCAGCTTCGGGGGCAT--CATTTACA-TAAC
129 ACACTCAGCTTCAAGGGCATAACATTTACAGCAAC
* *
371910 TCAAGGCTAGGAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
1 TCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
371975 CATCATTT
66 CATCATTT
371983 ACAACATAGC
Statistics
Matches: 489, Mismatches: 62, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
159 69 0.14
160 2 0.00
161 2 0.00
162 163 0.33
163 77 0.16
164 1 0.00
165 4 0.01
166 34 0.07
167 60 0.12
168 1 0.00
169 12 0.02
170 43 0.09
171 21 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (163 bp):
TCAAGGCTAGAAGGGTTATCTGTTACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
CATCATTTGCAGATAGCTTAAGTCGAGAAGGGTTATCTGCCACAAAGACCCTTAAGTTCGATTAC
ACTCAGCTTCAAGGGCATAACATTTACAGCAAC
Found at i:371866 original size:80 final size:83
Alignment explanation
Indices: 371264--371982 Score: 659
Period size: 80 Copynumber: 8.8 Consensus size: 83
371254 GTTCAAGGCC
* * *
371264 AGAAGGGCTATCTGCCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* *
371329 GCAGTATAGCTTAAGT-T
66 GCAGCATAACTTAAGTCT
* * * * * * * *
371346 GAGAAGAGCTATCTG-C--CAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACA
1 -AGAAGGGTTATCTGCCAACAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCA
* * *
371407 TTTACAGC--AACTCAAGGCT
63 TTTGCAGCATAACTTAAGTCT
** * * *
371426 AGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATCT
1 AGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
371491 GCAGAATAGCTTAAGTCG
66 GCAGCATAACTTAAGTCT
* * * *
371509 AGAAGGGATATCTG-C--CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
*
371571 TGCAG--TAACTTAAGTCA
65 TGCAGCATAACTTAAGTCT
* * *
371588 AGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
371653 TGCAGCATAACTTAAGTCG
65 TGCAGCATAACTTAAGTCT
* * * * *
371672 AGAAGGGTTATCTGCCAACTAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATATAT
1 AGAAGGGTTATCTGCCAAC-AAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGC--ACAT
* * *
371736 CATTTACAGCATAACTCAAGGCT
61 CATTTGCAGCATAACTTAAGTCT
* * * *
371759 AGAAGGGTTAACTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCA-TT
1 AGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* *
371823 GC-G-GTAGCTTAAGTCT
66 GCAGCATAACTTAAGTCT
* * * * * * **
371839 AGAAGGGTTGTCTGCCAACAAAGACCTTCGAGTTTGATTACACTCAGCTTC-GGGGGCATCATTT
1 AGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* *
371903 --A-CATAACTCAAGGCT
66 GCAGCATAACTTAAGTCT
* ** *
371918 AGGAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
371983 ACAACATAGC
Statistics
Matches: 515, Mismatches: 96, Indels: 53
0.78 0.14 0.08
Matches are distributed among these distances:
79 98 0.19
80 117 0.23
81 53 0.10
82 51 0.10
83 64 0.12
84 55 0.11
85 14 0.03
86 25 0.05
87 38 0.07
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (83 bp):
AGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTCT
Found at i:372624 original size:38 final size:34
Alignment explanation
Indices: 372582--372679 Score: 121
Period size: 38 Copynumber: 2.8 Consensus size: 34
372572 TAAAATTTTT
372582 TTTGAAAACATATATAATGTATAGTTTTTGAAAATGCA
1 TTTGAAAA-ATATATAAT-TATAGTTTTTG-AAAT-CA
372620 TTTGAAAATATATATAA-TATAG-TTTTGAAATCA
1 TTTGAAAA-ATATATAATTATAGTTTTTGAAATCA
372653 TTTG-AAAATATATAATATATAGTTTTT
1 TTTGAAAAATATATAAT-TATAGTTTTT
372680 TTAAAAAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
31 8 0.14
32 3 0.05
33 11 0.20
34 8 0.14
35 5 0.09
36 5 0.09
38 16 0.29
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (34 bp):
TTTGAAAAATATATAATTATAGTTTTTGAAATCA
Found at i:372660 original size:33 final size:35
Alignment explanation
Indices: 372582--372678 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 35
372572 TAAAATTTTT
*
372582 TTTGAAAACATATATAATGTATAGTTTTTGAAAATGCA
1 TTTGAAAATATATATAA--TATAG-TTTTGAAAATGCA
372620 TTTGAAAATATATATAATATAGTTTTG-AAAT-CA
1 TTTGAAAATATATATAATATAGTTTTGAAAATGCA
372653 TTTGAAAATATATA-ATATATAGTTTT
1 TTTGAAAATATATATA-ATATAGTTTT
372679 TTTAAAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
32 1 0.02
33 26 0.46
34 4 0.07
35 5 0.09
36 5 0.09
38 16 0.28
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (35 bp):
TTTGAAAATATATATAATATAGTTTTGAAAATGCA
Found at i:372748 original size:40 final size:39
Alignment explanation
Indices: 372653--372737 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 39
372643 TTTGAAATCA
* **
372653 TTTGAAAATATATAATATATAGTTTTTTTAAAAAAAACAT
1 TTTGGAAA-ATATAATATATAGTAGTTTTAAAAAAAACAT
*
372693 TTTGGAAAAT-TAATATATA-TAGTTTTAAAAAAACATAT
1 TTTGGAAAATATAATATATAGTAGTTTTAAAAAAA-ACAT
372731 TTTGGAA
1 TTTGGAA
372738 TCTTATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
37 12 0.30
38 19 0.47
39 2 0.05
40 7 0.17
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.41
Consensus pattern (39 bp):
TTTGGAAAATATAATATATAGTAGTTTTAAAAAAAACAT
Found at i:372859 original size:3 final size:3
Alignment explanation
Indices: 372846--372889 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
372836 ATATAGTTTA
* *
372846 TAT TA- TAT TAT TAT TAG TA- TGT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
372890 TGCATTTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 3 0.08
3 33 0.92
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:374009 original size:20 final size:20
Alignment explanation
Indices: 373986--374029 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
373976 TTACTTTTAA
*
373986 TAATATTTTTCTTATTTATT
1 TAATATTTTTATTATTTATT
374006 TAATATTTTTATTATTTATT
1 TAATATTTTTATTATTTATT
374026 TAAT
1 TAAT
374030 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TAATATTTTTATTATTTATT
Found at i:374024 original size:24 final size:22
Alignment explanation
Indices: 373989--374130 Score: 77
Period size: 20 Copynumber: 6.5 Consensus size: 22
373979 CTTTTAATAA
* *
373989 TATTTTTCTTATTTATTTA--A
1 TATTTTTATTATTTATTTATTT
374009 TATTTTTATTATTTATTTAATTT
1 TATTTTTATTATTTATTT-ATTT
* * * *
374032 TAATTTAATTTCTTTGATTTATTG
1 TATTTTTA-TTATTT-ATTTATTT
*
374056 T-TTTTTA-TA-TTATTTACTT
1 TATTTTTATTATTTATTTATTT
374075 TATTTATTATTA-TTA-TTATTAT
1 TATTT-TTATTATTTATTTATT-T
* *
374097 TA-TTATATTATTTGATTTATTA
1 TATTTTTATTATTT-ATTTATTT
374119 TATCTTTT-TTAT
1 TAT-TTTTATTAT
374131 CATCTAACAT
Statistics
Matches: 93, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
19 7 0.08
20 27 0.29
21 13 0.14
22 11 0.12
23 19 0.20
24 12 0.13
25 4 0.04
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTTTTATTATTTATTTATTT
Found at i:374076 original size:5 final size:4
Alignment explanation
Indices: 373997--374117 Score: 50
Period size: 4 Copynumber: 31.2 Consensus size: 4
373987 AATATTTTTC
* * *
373997 TTAT TTAT TTAAT ATT-T TTA- TTAT TTAT TTAA TT-T TAAT TTAAT TTCT
1 TTAT TTAT TT-AT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TTAT
*
374045 TTGAT TTA- TTGT TT-T TTAT ATTAT TTACT TTAT TTA- TTA- TTA- TTA-
1 TT-AT TTAT TTAT TTAT TTAT -TTAT TTA-T TTAT TTAT TTAT TTAT TTAT
374090 TTA- TTA- TTA- TTAT ATTAT TTGAT TTAT T
1 TTAT TTAT TTAT TTAT -TTAT TT-AT TTAT T
374118 ATATCTTTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 28
0.73 0.05 0.21
Matches are distributed among these distances:
3 32 0.33
4 37 0.39
5 25 0.26
6 2 0.02
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:374117 original size:12 final size:11
Alignment explanation
Indices: 373997--374119 Score: 68
Period size: 9 Copynumber: 11.4 Consensus size: 11
373987 AATATTTTTC
373997 TTATTTATTTA
1 TTATTTATTTA
*
374008 ATA-TT-TTTA
1 TTATTTATTTA
374017 TTATTTATTTAA
1 TTATTTATTT-A
*
374029 TT-TTAATTTAA
1 TTATTTATTT-A
*
374040 TTTCTTTGATTTA
1 -TTATTT-ATTTA
*
374053 TTGTTT-TTTA
1 TTATTTATTTA
374063 -TA-TTATTTA
1 TTATTTATTTA
374072 CTTTATTTA-TTA
1 --TTATTTATTTA
374084 TTA-TTA-TTA
1 TTATTTATTTA
374093 TTA-TTATTATA
1 TTATTTATT-TA
374104 TTATTTGATTTA
1 TTATTT-ATTTA
374116 TTAT
1 TTAT
374120 ATCTTTTTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
8 2 0.02
9 23 0.25
10 12 0.13
11 18 0.20
12 23 0.25
13 9 0.10
14 4 0.04
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:374119 original size:3 final size:3
Alignment explanation
Indices: 374078--374108 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
374068 TTTACTTTAT
374078 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
374109 TGATTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:377436 original size:22 final size:22
Alignment explanation
Indices: 377411--377677 Score: 143
Period size: 22 Copynumber: 12.1 Consensus size: 22
377401 AAATAAAATA
*
377411 ATATATATATGTTTTCAAAAC-
1 ATATATATATATTTTCAAAACT
* *
377432 -TATATA-A-ACTTTCAAAATT
1 ATATATATATATTTTCAAAACT
377451 ATATTATATATATGTTTTCAAAACT
1 ATA-TATATATA--TTTTCAAAACT
*
377476 ATATACTATA-A-TTTCAAAATT
1 ATATA-TATATATTTTCAAAACT
* *
377497 AT-TATATTATAATTTCAAAATT
1 ATATATA-TATATTTTCAAAACT
*
377519 AT-TATATTATAATTTCAAAACT
1 ATATATA-TATATTTTCAAAACT
* *
377541 ATATATACTCTATATGTTTTTAAAA-A
1 ATATATA---TATA--TTTTCAAAACT
* *
377567 AT-TAATATATGTTTTCAAAATT
1 ATAT-ATATATATTTTCAAAACT
*
377589 ATATATATATATATTC-AAA--
1 ATATATATATATTTTCAAAACT
* *
377608 A-ATACATATGTTTTCAAAACT
1 ATATATATATATTTTCAAAACT
*
377629 ATATATTATGCATATGTTTCAAAAGT
1 ATATA-TAT--ATAT-TTTCAAAACT
377655 ATAT-TATATATTTTCAAAA-T
1 ATATATATATATTTTCAAAACT
377675 ATA
1 ATA
377678 CTAGGATCAG
Statistics
Matches: 197, Mismatches: 22, Indels: 55
0.72 0.08 0.20
Matches are distributed among these distances:
18 19 0.10
19 7 0.04
20 16 0.08
21 36 0.18
22 53 0.27
23 11 0.06
24 6 0.03
25 24 0.12
26 18 0.09
27 7 0.04
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (22 bp):
ATATATATATATTTTCAAAACT
Found at i:377459 original size:43 final size:45
Alignment explanation
Indices: 377412--377602 Score: 160
Period size: 43 Copynumber: 4.2 Consensus size: 45
377402 AATAAAATAA
*
377412 TATATATATGTTTTCAAAACTATATA-A-ACTTTCAAAATTATAT
1 TATATATATGTTTTCAAAACTATATACATAATTTCAAAATTATAT
377455 TATATATATGTTTTCAAAACTATATACTATAATTTCAAAA-T-TAT
1 TATATATATGTTTTCAAAACTATATAC-ATAATTTCAAAATTATAT
** * * *
377499 TATAT-TATAATTTCAAAATTATTATATTATAATTTCAAAACTATAT
1 TATATATATGTTTTCAAAACTA-TATA-CATAATTTCAAAATTATAT
* * * * **
377545 ATACTCTATATGTTTTTAAAA-AATTAATATATGTTTTCAAAATTATAT
1 -TA-TATATATGTTTTCAAAACTA-T-ATACATAATTTCAAAATTATAT
377593 ATATATATAT
1 -TATATATAT
377603 TCAAAAATAC
Statistics
Matches: 123, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
43 39 0.32
44 24 0.20
45 3 0.02
46 12 0.10
47 8 0.07
48 24 0.20
49 13 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (45 bp):
TATATATATGTTTTCAAAACTATATACATAATTTCAAAATTATAT
Found at i:377594 original size:18 final size:18
Alignment explanation
Indices: 377564--377634 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 18
377554 ATGTTTTTAA
377564 AAAATTAATATATGTTTTC
1 AAAATT-ATATATGTTTTC
*
377583 AAAATTATATATATATATATTC
1 AAAA-T-TATATATGT-T-TTC
* *
377605 AAAAATACATATGTTTTC
1 AAAATTATATATGTTTTC
*
377623 AAAACTATATAT
1 AAAATTATATAT
377635 TATGCATATG
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
18 13 0.31
19 5 0.12
20 15 0.36
21 2 0.05
22 7 0.17
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (18 bp):
AAAATTATATATGTTTTC
Found at i:380268 original size:3 final size:3
Alignment explanation
Indices: 380262--380309 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
380252 TTCATTTAAA
*
380262 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAAA TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
380308 TA
1 TA
380310 CAGGCCCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 1 0.03
3 36 0.90
4 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:380778 original size:17 final size:17
Alignment explanation
Indices: 380752--380786 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
380742 GACAACCAGC
*
380752 AAAAACAGAGAACAAAA
1 AAAAAAAGAGAACAAAA
*
380769 AAAAAAAGAGGACAAAA
1 AAAAAAAGAGAACAAAA
380786 A
1 A
380787 GCAATTCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.09, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAGAACAAAA
Found at i:381596 original size:28 final size:26
Alignment explanation
Indices: 381551--381606 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 26
381541 TAATTTTAAA
*
381551 TATTAATTAAATTAAGTATTTAATTT
1 TATTAATTAAATTAAGTAATTAATTT
*
381577 TATTAGATTATAATTTAGTAATTAATTT
1 TATTA-ATTA-AATTAAGTAATTAATTT
381605 TA
1 TA
381607 AATATTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
28 17 0.65
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (26 bp):
TATTAATTAAATTAAGTAATTAATTT
Found at i:381680 original size:20 final size:20
Alignment explanation
Indices: 381643--381687 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
381633 GTTCTAATCG
* *
381643 TATTTTTATTATTGTTTATT
1 TATTTTTATTATTATTTATA
381663 TATTTTTAATT-TTATTTATA
1 TATTTTT-ATTATTATTTATA
381683 TATTT
1 TATTT
381688 AAATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TATTTTTATTATTATTTATA
Found at i:381698 original size:19 final size:16
Alignment explanation
Indices: 381658--381756 Score: 55
Period size: 16 Copynumber: 6.1 Consensus size: 16
381648 TTATTATTGT
*
381658 TTATTTATTTTTAATT
1 TTATTTATTTTTAATA
381674 TTATTTATATATTTAA-A
1 TTATTTAT-T-TTTAATA
*
381691 -TA-TTATTTTTATTA
1 TTATTTATTTTTAATA
* **
381705 TTATATATAGTCATAATTA
1 TTAT-T-TATTTTTAA-TA
381724 TT-TTTA-TTTTAATA
1 TTATTTATTTTTAATA
381738 TTTATTTATTTTTCAATA
1 -TTATTTATTTTT-AATA
381756 T
1 T
381757 CAAAGAAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 23
0.67 0.09 0.24
Matches are distributed among these distances:
13 4 0.06
14 4 0.06
15 12 0.19
16 16 0.25
17 8 0.13
18 15 0.24
19 4 0.06
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (16 bp):
TTATTTATTTTTAATA
Found at i:381705 original size:28 final size:28
Alignment explanation
Indices: 381674--381738 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
381664 ATTTTTAATT
* *
381674 TTATT-TATATATTTAAATATTATTTTTA
1 TTATTATATATAGTCAAA-ATTATTTTTA
*
381702 TTATTATATATAGTCATAATTATTTTTA
1 TTATTATATATAGTCAAAATTATTTTTA
381730 TT-TTA-ATAT
1 TTATTATATAT
381739 TTATTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 4 0.12
27 3 0.09
28 17 0.52
29 9 0.27
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TTATTATATATAGTCAAAATTATTTTTA
Found at i:381706 original size:20 final size:20
Alignment explanation
Indices: 381649--381706 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
381639 ATCGTATTTT
*
381649 TATTATTGTTTATTTATTTTTAA
1 TATTATT-TTTA-TTA-TTTAAA
* *
381672 TTTTATTTATA-TATTTAAA
1 TATTATTTTTATTATTTAAA
381691 TATTATTTTTATTATT
1 TATTATTTTTATTATT
381707 ATATATAGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 14 0.48
20 6 0.21
22 3 0.10
23 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTATTTTTATTATTTAAA
Found at i:392896 original size:8 final size:8
Alignment explanation
Indices: 392883--392917 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
392873 CTTGAAGAAC
392883 AAAAAAGA
1 AAAAAAGA
392891 AAAAAAGA
1 AAAAAAGA
392899 AAAAAAGGA
1 AAAAAA-GA
392908 AAAAAA-A
1 AAAAAAGA
392915 AAA
1 AAA
392918 GGGGTCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.15
8 14 0.54
9 8 0.31
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:392896 original size:10 final size:9
Alignment explanation
Indices: 392877--392914 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
392867 ATTATGCTTG
392877 AAGAACAAAA
1 AAGAA-AAAA
392887 AAG-AAAAA
1 AAGAAAAAA
392895 AAGAAAAAA
1 AAGAAAAAA
*
392904 AGGAAAAAA
1 AAGAAAAAA
392913 AA
1 AA
392915 AAAGGGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 15 0.60
10 3 0.12
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:392904 original size:18 final size:18
Alignment explanation
Indices: 392877--392917 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
392867 ATTATGCTTG
*
392877 AAGAACAAAAAAGAAAAA
1 AAGAAAAAAAAAGAAAAA
*
392895 AAG-AAAAAAAGGAAAAA
1 AAGAAAAAAAAAGAAAAA
392912 AA-AAAA
1 AAGAAAA
392918 GGGGTCAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAAAGAAAAA
Found at i:394510 original size:114 final size:114
Alignment explanation
Indices: 394305--394528 Score: 333
Period size: 114 Copynumber: 2.0 Consensus size: 114
394295 GTGCCATGTA
*
394305 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTCATTTGAGTTATCTGATCTG
1 CTCATAGTACAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTCATTTGAGTTATCTGATCTG
* * * ** * *
394370 ATTTGGTATGAACCCCAAAATTAATCATTGGATTTGAAAGATGAATTTG
66 ATTCGGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTG
*
394419 CTCATAGTACAAATAA-AGAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCT
1 CTCATAGTACAAATAAGA-AGACCCAATAGCATCTTCTGGAAGTGTCATTTGAGTTATCTGATCT
* *
394483 GGTTCGGTAGGAACCACAGAACCAATCATTGGAATTAAAAGATGAA
65 GATTCGGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAA
394529 CTGCATGATC
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
113 1 0.01
114 97 0.99
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
CTCATAGTACAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTCATTTGAGTTATCTGATCTG
ATTCGGTAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTG
Found at i:395534 original size:113 final size:111
Alignment explanation
Indices: 395251--395899 Score: 804
Period size: 110 Copynumber: 5.8 Consensus size: 111
395241 CACCAGTCGG
395251 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* *
395316 CATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATACATCATTCGG
66 CATAAT--GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGA
395364 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* *
395429 CATAAT-AAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGG
66 CATAATGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGA
*
395474 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
1 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
** * * *
395539 CATAATGAGAAGAACTTACTCAACTTTTTGCTTGAATTCATGATTCAA
66 CATAAT--GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGA
* * *
395587 TGGATCAACATTACCAGTTCGAGTTTATAAT--G-AGAACTCGTCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
*
395649 CATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGA
66 CATAAT--GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGA
* * * *
395697 TGGATCAACATTGCCAGATAGAGTTCATAATAAGAAGAACTCGTCATCTGAAGAA-GAA-AA-AA
1 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAA
* * *
395759 -TTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TAAATCCATCACTT-GA
63 GTTCATAAT--GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCA-TTCGA
* * ****
395808 TGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAGAAGTT
1 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * *
395869 CACAATGAGAAGAGCTTGTTCAACCTTTTGC
66 CATAAT--GAAGAACTTGTTCAACTTTTTGC
395900 ATAATTCTAT
Statistics
Matches: 486, Mismatches: 37, Indels: 31
0.88 0.07 0.06
Matches are distributed among these distances:
105 6 0.01
106 2 0.00
107 2 0.00
108 36 0.07
109 1 0.00
110 204 0.42
111 46 0.09
112 34 0.07
113 138 0.28
114 2 0.00
115 4 0.01
116 11 0.02
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (111 bp):
TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGA
Found at i:395646 original size:223 final size:223
Alignment explanation
Indices: 395247--396022 Score: 853
Period size: 223 Copynumber: 3.4 Consensus size: 223
395237 AATCCACCAG
*
395247 TCGGTGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TCGGTGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
** *
395312 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATACATCATTCGGTGGATCAACATTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATACATCATTCAATGGATCAACATTA
395377 CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT-AAGAAC
131 CCAGTTCGAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAAC
395441 TTGTTCAACTTTTTGCTTAAATTCATCAC
195 TTGTTCAACTTTTTGCTTAAATTCATCAC
395470 TCGGTGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
1 TCGGTGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
** * * *
395535 AGTTCATAATGAGAAGAACTTACTCAACTTTTTGCTTGAATTCATGATTCAATGGATCAACATTA
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATACATCATTCAATGGATCAACATTA
* *
395600 CCAGTTCGAGTTTATAAT-G-AGAACTCGTCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
131 CCAGTTCGAGTTCATAATAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT--GAAGAA
*
395663 CTTGTTCAACTTTTTGCTTAAATTCATCAT
194 CTTGTTCAACTTTTTGCTTAAATTCATCAC
* * * * * *
395693 TTGATGGATCAACATTGCCAGATAGAGTTCATAATAAGAAGAACTCGTCATCTGAAG-AAGAA-A
1 TCGGTGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAAGAAGA
* * * * *
395756 A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TAAATCCATCACTT-GATGGATCAGC
63 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATACATCA-TTCAATGGATCAAC
* * **** *
395817 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAGAAGTTCACAATGAG
127 ATTACCAGTTCGAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT--G
* * *
395878 AAGAGCTTGTTCAACCTTTTGCAT-AATTCTATCAC
189 AAGAACTTGTTCAACTTTTTGCTTAAATTC-ATCAC
* * * ****
395913 AGAAGCAGATAGATTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-
1 ----TC-G---G--T-GGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
395977 AAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
55 AAAG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
396023 AATGACTCTA
Statistics
Matches: 474, Mismatches: 52, Indels: 45
0.83 0.09 0.08
Matches are distributed among these distances:
219 5 0.01
220 80 0.17
221 36 0.08
222 31 0.07
223 212 0.45
224 12 0.03
225 7 0.01
226 10 0.02
228 12 0.03
229 3 0.01
230 3 0.01
231 34 0.07
232 29 0.06
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (223 bp):
TCGGTGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATACATCATTCAATGGATCAACATTA
CCAGTTCGAGTTCATAATAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAACT
TGTTCAACTTTTTGCTTAAATTCATCAC
Found at i:396034 original size:124 final size:124
Alignment explanation
Indices: 395818--396110 Score: 395
Period size: 124 Copynumber: 2.4 Consensus size: 124
395808 TGGATCAGCT
395818 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG---AAG-AAGAAGAAGTTCACAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCACAATGAGA
* * * * * *
395879 AGAGCTTGTTCAACCTTTTGCATAATTCTATCACAG-AAGCAGATAGATTAGCATCAACC
66 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAAG-AAATAGATCAACATCAACC
*
395938 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCACAATGAGA
* * *
396003 AGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAAGAAATAGGTCAACATCATCC
66 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACC
*
396062 ---CCAGTGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAA-AAAGA-AAGAA
396111 TTTATTCAAC
Statistics
Matches: 154, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
120 37 0.24
121 4 0.03
122 31 0.20
123 8 0.05
124 71 0.46
125 3 0.02
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (124 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCACAATGAGA
AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACC
Found at i:396321 original size:27 final size:31
Alignment explanation
Indices: 396252--396325 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 31
396242 TAAATATTAT
*
396252 TTATATTATTATTATTATTATTATTATAATAA
1 TTATAATATTATTATTATTATTATTAT-ATAA
*
396284 TTATTATTATTATTATTATT-TTATTAT-TAA
1 TTA-TAATATTATTATTATTATTATTATATAA
396314 -TA-AATATTATTA
1 TTATAATATTATTA
396326 CAGGCCCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 9 0.22
29 2 0.05
30 3 0.08
32 10 0.25
33 16 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TTATAATATTATTATTATTATTATTATATAA
Found at i:396325 original size:3 final size:3
Alignment explanation
Indices: 396246--396312 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
396236 TTCATTTAAA
* *
396246 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
396291 TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
396313 ATAAATATTA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 3 0.05
3 55 0.93
4 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:397590 original size:28 final size:26
Alignment explanation
Indices: 397546--397600 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
397536 ATTTTAAATA
*
397546 ATTAATTAAATTAAGTATTTAATTTT
1 ATTAATTAAATTAAGTAATTAATTTT
*
397572 ATTAGATTATAATTTAGTAATTAATTTT
1 ATTA-ATTA-AATTAAGTAATTAATTTT
397600 A
1 A
397601 AATATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 17 0.68
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (26 bp):
ATTAATTAAATTAAGTAATTAATTTT
Found at i:397694 original size:19 final size:17
Alignment explanation
Indices: 397653--397754 Score: 70
Period size: 18 Copynumber: 6.1 Consensus size: 17
397643 TTATTATTGT
* *
397653 TTATTTATGTTTTAATT
1 TTATTTATATTTTAATA
397670 TTATTTATATATTTAA-A
1 TTATTTATAT-TTTAATA
*
397687 -TA-TTAT-TTTTATTA
1 TTATTTATATTTTAATA
**
397701 TTATTATATAGTCATAA-A
1 TTATT-TATA-TTTTAATA
*
397719 TTATTTTTATTTTAATA
1 TTATTTATATTTTAATA
*
397736 TTTATTTATTTTTTAATA
1 -TTATTTATATTTTAATA
397754 T
1 T
397755 CAAAGAAAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
13 4 0.06
14 2 0.03
15 6 0.09
16 7 0.11
17 17 0.26
18 26 0.40
19 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (17 bp):
TTATTTATATTTTAATA
Found at i:397710 original size:30 final size:29
Alignment explanation
Indices: 397657--397744 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
397647 TATTGTTTAT
397657 TTATGTTTTAATTTTATTTATATATTTA-AATA
1 TTAT-TTTT-ATTTTA-TTATATATTTATAA-A
* *
397689 TTATTTTTATTATTATTATATAGTCATAAA
1 TTATTTTTATT-TTATTATATATTTATAAA
* *
397719 TTATTTTTATTTTAATATTTATTTAT
1 TTATTTTTATTTTATTATATATTTAT
397745 TTTTTAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 11 0.23
30 24 0.50
31 9 0.19
32 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (29 bp):
TTATTTTTATTTTATTATATATTTATAAA
Found at i:405031 original size:3 final size:3
Alignment explanation
Indices: 405025--405085 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
405015 TTTAAACTCT
405025 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
405072 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
405086 TATTTATTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:409867 original size:20 final size:20
Alignment explanation
Indices: 409838--409910 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
409828 GCAGCCTTCG
* *
409838 TGCATGGATGCATAGCAGGA
1 TGCATCGATGCACAGCAGGA
**
409858 TGCATCGATGCACAGCTTGA
1 TGCATCGATGCACAGCAGGA
*
409878 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
409898 TGCATCGATGCAC
1 TGCATCGATGCAC
409911 TAATTGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:410109 original size:29 final size:29
Alignment explanation
Indices: 410088--410145 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
410078 AAACTTTGAA
410088 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
410117 TAAATTCAATTCAAGTCCAAAAATCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
410146 TTCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:410135 original size:30 final size:30
Alignment explanation
Indices: 410088--410146 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
410078 AAACTTTGAA
410088 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
410117 TAAATTCAATTCAAGTCCAAAAATCATTTT
1 TAAATTCAATT-AAGTCCAAAAATCATTTT
410147 TCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:412353 original size:32 final size:34
Alignment explanation
Indices: 412316--412385 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
412306 ACCTTACAAC
* *
412316 TCCCTAG-TTTTTC-CGGGCTAACCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAACCTAGAACCTT
*
412348 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAACCTAGAACCTT
412382 TCCC
1 TCCC
412386 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAACCTAGAACCTT
Found at i:412781 original size:20 final size:21
Alignment explanation
Indices: 412752--412825 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 21
412742 GCAGCCTTCG
*
412752 TGCATGGATGCACA-ACAGGA
1 TGCATCGATGCACAGACAGGA
* **
412772 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAGACAGGA
*
412793 TGCATCGATGAACAGA-AGGA
1 TGCATCGATGCACAGACAGGA
412813 TGCATCGATGCAC
1 TGCATCGATGCAC
412826 TAATTGCATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.61
21 17 0.39
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (21 bp):
TGCATCGATGCACAGACAGGA
Found at i:412788 original size:41 final size:41
Alignment explanation
Indices: 412743--412825 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
412733 CTAGCCGTTG
* *
412743 CAGCCTTCG-TGCATGGATGCACA-ACAGGATGCATCGATGCA
1 CAGCCTT-GATGCATCGATGAACAGA-AGGATGCATCGATGCA
412784 CAGCCTTGATGCATCGATGAACAGAAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGAACAGAAGGATGCATCGATGCA
412825 C
1 C
412826 TAATTGCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 1 0.03
41 36 0.95
42 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (41 bp):
CAGCCTTGATGCATCGATGAACAGAAGGATGCATCGATGCA
Found at i:413032 original size:29 final size:31
Alignment explanation
Indices: 413000--413058 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 31
412990 AAACTTTGAA
413000 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
413029 TAAATTCAATTCAAGTCCAAAAATCATTTT
1 TAAATTCAATTCAAGTCCAAAAATCATTTT
413059 TCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAATCATTTTG
Found at i:415279 original size:32 final size:34
Alignment explanation
Indices: 415242--415311 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
415232 ACCTTACAAC
* *
415242 TCCCTAG-TTTTTC-CGGGCTAACCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAACCTAGAACCTT
*
415274 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAACCTAGAACCTT
415308 TCCC
1 TCCC
415312 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAACCTAGAACCTT
Found at i:415551 original size:20 final size:22
Alignment explanation
Indices: 415526--415565 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
415516 TGTTGTATAT
415526 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
415546 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
415566 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:415709 original size:20 final size:21
Alignment explanation
Indices: 415684--415751 Score: 86
Period size: 20 Copynumber: 3.3 Consensus size: 21
415674 TTCGTGTATG
415684 GATGCACA-ACAGGATGCATC
1 GATGCACAGACAGGATGCATC
* **
415704 GATGCACAGCCTTGATGCATC
1 GATGCACAGACAGGATGCATC
*
415725 GATGAACAGA-AGGATGCATC
1 GATGCACAGACAGGATGCATC
415745 GATGCAC
1 GATGCAC
415752 TAATTGCATT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (21 bp):
GATGCACAGACAGGATGCATC
Found at i:415841 original size:21 final size:20
Alignment explanation
Indices: 415773--415870 Score: 99
Period size: 21 Copynumber: 4.7 Consensus size: 20
415763 GGTGTTTGAG
*
415773 TGCATGGATGCACTGCATGA
1 TGCATGGATGCACTGCAGGA
**
415793 TGCATCAATGCACTAGTACAGG-
1 TGCATGGATGCACT-G--CAGGA
415815 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
415836 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCA-GGA
*
415857 TGCATGAATGCACT
1 TGCATGGATGCACT
415871 TTGACACCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.03
20 14 0.21
21 35 0.53
22 12 0.18
23 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:415859 original size:42 final size:42
Alignment explanation
Indices: 415772--415870 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
415762 CGGTGTTTGA
* *
415772 GTGCATGGATGCACTGCATGATGCATCAATGCACTAGTACAG
1 GTGCATGGATGCACTGCAGGATGCATCAATGCACTAGCACAG
** **
415814 GTGCATGGATGCACTGCAGGGATGCATGGATGCACT-GCAGGG
1 GTGCATGGATGCACTGCA-GGATGCATCAATGCACTAGCACAG
*
415856 GTGCATGAATGCACT
1 GTGCATGGATGCACT
415871 TTGACACCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 35 0.71
43 14 0.29
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.22
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAGGATGCATCAATGCACTAGCACAG
Found at i:415971 original size:29 final size:29
Alignment explanation
Indices: 415950--416007 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
415940 AAACTTTGAA
415950 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
415979 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
416008 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:415997 original size:30 final size:30
Alignment explanation
Indices: 415950--416009 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
415940 AAACTTTGAA
415950 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
415979 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
416010 CCTTAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:430695 original size:31 final size:31
Alignment explanation
Indices: 430653--430729 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
430643 ACAAGGAATT
* * *
430653 AGGGATTAAATTACAATTACAAATAAATTCC
1 AGGGATCAAATTACAATTAAAAAGAAATTCC
* * *
430684 AGGGATCAAATTGCATTTAAAAAGAAATTCT
1 AGGGATCAAATTACAATTAAAAAGAAATTCC
430715 A-GGATCAAATTACAA
1 AGGGATCAAATTACAA
430730 GTTCAGTGAC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (31 bp):
AGGGATCAAATTACAATTAAAAAGAAATTCC
Found at i:432887 original size:20 final size:20
Alignment explanation
Indices: 432862--432968 Score: 62
Period size: 20 Copynumber: 5.3 Consensus size: 20
432852 TATGCCTATA
432862 TATATATATGTATTCAAAAC
1 TATATATATGTATTCAAAAC
* *
432882 TATATAATAT-AATTTCATAA-
1 TATAT-ATATGTA-TTCAAAAC
*
432902 TATATATAAT-AATTTCAAAAC
1 TATATAT-ATGTA-TTCAAAAC
* * *
432923 TATATAT-TGTTTTAAAAAT
1 TATATATATGTATTCAAAAC
* *
432942 TA-ATATAATGTTTTCAAAAT
1 TATATAT-ATGTATTCAAAAC
432962 TATATAT
1 TATATAT
432969 TATAAAGTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
18 4 0.06
19 11 0.15
20 35 0.49
21 21 0.30
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (20 bp):
TATATATATGTATTCAAAAC
Found at i:436960 original size:15 final size:15
Alignment explanation
Indices: 436940--436971 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
436930 ATCTCATCTT
*
436940 CGGCTTGCTTCTCGC
1 CGGCTTGCTGCTCGC
436955 CGGCTTGCTGCTCGC
1 CGGCTTGCTGCTCGC
436970 CG
1 CG
436972 TGCTGTGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (15 bp):
CGGCTTGCTGCTCGC
Found at i:442742 original size:25 final size:25
Alignment explanation
Indices: 442711--442793 Score: 76
Period size: 25 Copynumber: 3.1 Consensus size: 25
442701 TTTCGAGAGT
442711 TTATAATTTTGAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
* *
442736 TTTTAATTTTGGAAATATTTTTTTATTTAA
1 TTATAATTTT-G-AA-A--TTTTAATTTAA
* * *
442766 TCAAAATTTTAAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
442791 TTA
1 TTA
442794 GTATTACTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
25 21 0.47
26 1 0.02
27 3 0.07
28 3 0.07
30 17 0.38
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (25 bp):
TTATAATTTTGAAATTTTAATTTAA
Found at i:443437 original size:50 final size:51
Alignment explanation
Indices: 443378--443479 Score: 163
Period size: 50 Copynumber: 2.0 Consensus size: 51
443368 ATTTTCTGCT
*
443378 GTTTCTAGTAGGAATGTGTTTCCTTGACCTTT-ATCA-CGAACTCTGATTTG
1 GTTTCTAGTAGGAATGAGTTTCCTTGACCTTTCAT-AGCGAACTCTGATTTG
*
443428 GTTTCTAGTAGGATTGAGTTTCCTTGACCTTTCATAGCGAACTCTGATTTG
1 GTTTCTAGTAGGAATGAGTTTCCTTGACCTTTCATAGCGAACTCTGATTTG
443479 G
1 G
443480 ACCAAGACTT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
50 31 0.65
51 17 0.35
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (51 bp):
GTTTCTAGTAGGAATGAGTTTCCTTGACCTTTCATAGCGAACTCTGATTTG
Found at i:443772 original size:14 final size:14
Alignment explanation
Indices: 443753--443795 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
443743 ATTAAATCAA
443753 ATTAGAATATAAAT
1 ATTAGAATATAAAT
* *
443767 ATTAGATTTTAAAT
1 ATTAGAATATAAAT
*
443781 TTTA-AATATAAAT
1 ATTAGAATATAAAT
443794 AT
1 AT
443796 AATTATGTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
ATTAGAATATAAAT
Found at i:445661 original size:19 final size:16
Alignment explanation
Indices: 445620--445658 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
445610 TTTTTCTTCA
445620 TGTTGTTCGTCTTGCT
1 TGTTGTTCGTCTTGCT
445636 TGTTGTTCGTCTTGCT
1 TGTTGTTCGTCTTGCT
445652 TGTTGTT
1 TGTTGTT
445659 GTTGCTCCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.00, C:0.15, G:0.26, T:0.59
Consensus pattern (16 bp):
TGTTGTTCGTCTTGCT
Found at i:450643 original size:64 final size:65
Alignment explanation
Indices: 450530--450674 Score: 197
Period size: 64 Copynumber: 2.2 Consensus size: 65
450520 TGCACTAGGA
* *
450530 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCTAGAGTGCATCGATGCATGG-CTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAACTAGAGTGCATCGATGCATGGACTG
** * *
450594 GTGCATCGATGCATCAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAACT-A-GAGTGCATCGATGCATGGAC
450657 TG
64 TG
450659 GTGCATCGATGCATCA
1 GTGCATCGATGCATCA
450675 CTTTGATAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
63 8 0.11
64 45 0.62
65 19 0.26
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAACTAGAGTGCATCGATGCATGGACTG
Found at i:451352 original size:14 final size:15
Alignment explanation
Indices: 451333--451361 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
451323 TCAAGCATTT
451333 AACAATCCA-AAACA
1 AACAATCCAGAAACA
451347 AACAATCCAGAAACA
1 AACAATCCAGAAACA
451362 TCAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:453141 original size:23 final size:22
Alignment explanation
Indices: 453111--453190 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
453101 GCATAGCCTT
453111 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
453133 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
453155 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
453177 ATGCATCGATGCAC
1 GTGCATCGATGCAC
453191 TGTTAAGTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.32
22 16 0.34
23 16 0.34
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:453167 original size:21 final size:21
Alignment explanation
Indices: 453111--453190 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
453101 GCATAGCCTT
453111 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAA-G
* * *
453133 CGTGCATCGGTGCACCTTCATG
1 -GTGCATCGATGCACATTCAAG
*
453155 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
453176 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
453191 TGTTAAGTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.38
22 13 0.27
23 17 0.35
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCACATTCAAG
Done.