Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 10 of 32
Found at i:5144411 original size:28 final size:28
Alignment explanation
Indices: 5144379--5144435 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
5144369 AAAACAATTT
5144379 ATTTAAATTTCAATTATAAGA-AATTTTC
1 ATTTAAATTTCAATTATAA-ATAATTTTC
* * *
5144407 ATTTAAGTTTTAATTGTAAATAATTTTC
1 ATTTAAATTTCAATTATAAATAATTTTC
5144435 A
1 A
5144436 GTCCAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (28 bp):
ATTTAAATTTCAATTATAAATAATTTTC
Found at i:5148459 original size:24 final size:24
Alignment explanation
Indices: 5148430--5148566 Score: 175
Period size: 24 Copynumber: 5.7 Consensus size: 24
5148420 TTCCAGTACT
*
5148430 CCTGCCTTTGGTGCAACGAGCACC
1 CCTGCCTTCGGTGCAACGAGCACC
* *
5148454 CCTGCCTTTGGAGCAACGAGCACC
1 CCTGCCTTCGGTGCAACGAGCACC
5148478 CCTGCCTTCGGTGCAACGAGCACC
1 CCTGCCTTCGGTGCAACGAGCACC
* *
5148502 CCTGCCTTCGGTGCCACAAGCACC
1 CCTGCCTTCGGTGCAACGAGCACC
**** *
5148526 CCTGCCTTCGGTATTTCAAGCACC
1 CCTGCCTTCGGTGCAACGAGCACC
*
5148550 CCTGCCTTCGGTTCAAC
1 CCTGCCTTCGGTGCAAC
5148567 TGGAAGTCCA
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 100 1.00
ACGTcount: A:0.17, C:0.40, G:0.22, T:0.21
Consensus pattern (24 bp):
CCTGCCTTCGGTGCAACGAGCACC
Found at i:5148670 original size:24 final size:24
Alignment explanation
Indices: 5148643--5148725 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 24
5148633 AGGAGGCACA
5148643 TTTGGAGCATCAAGCACTCCTGCT
1 TTTGGAGCATCAAGCACTCCTGCT
* * *
5148667 TTTGGCA-CTTCCAGTACTCCTGCT
1 TTTGG-AGCATCAAGCACTCCTGCT
* *
5148691 TTTGGTGCTTCAAGCACTCCTGCT
1 TTTGGAGCATCAAGCACTCCTGCT
5148715 TTTGGAGCATC
1 TTTGGAGCATC
5148726 TTCTACTCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 48 0.98
25 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.35
Consensus pattern (24 bp):
TTTGGAGCATCAAGCACTCCTGCT
Found at i:5156656 original size:15 final size:14
Alignment explanation
Indices: 5156629--5156670 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5156619 AAATAAGTTC
5156629 TTTAAAAAATAAAT
1 TTTAAAAAATAAAT
5156643 TTTAAAACAATAAA-
1 TTTAAAA-AATAAAT
* *
5156657 ATTAAAAAAAAAAT
1 TTTAAAAAATAAAT
5156671 GCTTAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.21
14 13 0.54
15 6 0.25
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
TTTAAAAAATAAAT
Found at i:5158582 original size:17 final size:16
Alignment explanation
Indices: 5158557--5158588 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5158547 TTATAAATTC
5158557 AATATTTATAAAAATA
1 AATATTTATAAAAATA
5158573 AATATATTATAAAAAT
1 AATAT-TTATAAAAAT
5158589 TTAAAAGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATTTATAAAAATA
Found at i:5164922 original size:4 final size:4
Alignment explanation
Indices: 5164915--5164940 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5164905 GTGTTTGTGT
5164915 GTGA GTGA GTGA GTGA GTGA GTGA GT
1 GTGA GTGA GTGA GTGA GTGA GTGA GT
5164941 TACTGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.50, T:0.27
Consensus pattern (4 bp):
GTGA
Found at i:5164952 original size:2 final size:2
Alignment explanation
Indices: 5164945--5164972 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5164935 GTGAGTTACT
5164945 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5164973 TCTTTGCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5178239 original size:6 final size:6
Alignment explanation
Indices: 5178230--5178254 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5178220 TTTGGTTTCT
5178230 GAGAGG GAGAGG GAGAGG GAGAGG G
1 GAGAGG GAGAGG GAGAGG GAGAGG G
5178255 GGATTGCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:5197943 original size:28 final size:28
Alignment explanation
Indices: 5197903--5197960 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
5197893 CATATGAGAA
*
5197903 AGTCTTTTGAAATGATAGAACACATCTT
1 AGTCTTTTGAAATGATAGAACACAGCTT
*
5197931 AGTCTTTTGAAATGATAGAACTCAGCTT
1 AGTCTTTTGAAATGATAGAACACAGCTT
5197959 AG
1 AG
5197961 AGTTTTCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (28 bp):
AGTCTTTTGAAATGATAGAACACAGCTT
Found at i:5215363 original size:21 final size:21
Alignment explanation
Indices: 5215318--5215363 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5215308 TTCTTCCAAT
*
5215318 TCGTCATCATCTTCATCATCT
1 TCGTCATCATCTTCATCATCC
* *
5215339 TCGTCTTCATCTTCATCTTCC
1 TCGTCATCATCTTCATCATCC
5215360 TCGT
1 TCGT
5215364 GATCCATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.35, G:0.07, T:0.46
Consensus pattern (21 bp):
TCGTCATCATCTTCATCATCC
Found at i:5218086 original size:5 final size:5
Alignment explanation
Indices: 5218076--5218104 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5218066 GAGAAAAAAG
5218076 CCCAT CCCAT CCCAT CCCAT CCCAT CCCA
1 CCCAT CCCAT CCCAT CCCAT CCCAT CCCA
5218105 CCAGTATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.62, G:0.00, T:0.17
Consensus pattern (5 bp):
CCCAT
Found at i:5230629 original size:88 final size:90
Alignment explanation
Indices: 5230536--5230706 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 90
5230526 TTCTTGGCAG
*
5230536 AAAGAAATATGGTCTCAG-AAAAAAAAA-TGCAGAATATTGCCACGTGGTTGGAATGTCTCTGAT
1 AAAGAAATATGGTCTCAGAAAAAAAAAAGAGCAGAATATTGCCACGTGGTTGGAATGTCTCTGAT
5230599 CGAAAGTAAAAGCAATGACGACCCT
66 CGAAAGTAAAAGCAATGACGACCCT
* *
5230624 AAAGAAATATGGTCTCAGAAAAAAAAAAGAGCAGAATATTGCCACGTGGTTGGAATGTTTCTGGT
1 AAAGAAATATGGTCTCAGAAAAAAAAAAGAGCAGAATATTGCCACGTGGTTGGAATGTCTCTGAT
5230689 CGAAAGTAAAAGCAATGA
66 CGAAAGTAAAAGCAATGA
5230707 AGAGCTTCTT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
88 18 0.23
89 9 0.12
90 51 0.65
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (90 bp):
AAAGAAATATGGTCTCAGAAAAAAAAAAGAGCAGAATATTGCCACGTGGTTGGAATGTCTCTGAT
CGAAAGTAAAAGCAATGACGACCCT
Found at i:5231806 original size:26 final size:26
Alignment explanation
Indices: 5231745--5231806 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
5231735 CTAATGGTTT
5231745 GACTAGAGTCGTTACAATGACATCAAA
1 GACT-GAGTCGTTACAATGACATCAAA
* ** * * *
5231772 GCCCAAGTCGTTACAATGATATTAGA
1 GACTGAGTCGTTACAATGACATCAAA
5231798 GACTGAGTC
1 GACTGAGTC
5231807 AGTTCGATGT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (26 bp):
GACTGAGTCGTTACAATGACATCAAA
Found at i:5232313 original size:15 final size:14
Alignment explanation
Indices: 5232292--5232328 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
5232282 ACTTTTAACA
*
5232292 TAAAAAATATTAAT
1 TAAAAAATAATAAT
5232306 TAATAAAATAATAAT
1 TAA-AAAATAATAAT
5232321 TAAAAAAT
1 TAAAAAAT
5232329 TAAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAAAATAATAAT
Found at i:5235523 original size:2 final size:2
Alignment explanation
Indices: 5235516--5235542 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5235506 GCTTCTCCGC
5235516 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
5235543 GCACTCTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5256425 original size:2 final size:2
Alignment explanation
Indices: 5256420--5256464 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5256410 AAAATCTTCA
5256420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5256462 AT A
1 AT A
5256465 ACACTAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5258191 original size:23 final size:23
Alignment explanation
Indices: 5258165--5258218 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
5258155 AAATAATATT
*
5258165 ATAATATTTAATATATAAATAAA
1 ATAATATTTAAAATATAAATAAA
* *
5258188 ATAATAATTAAAATGTAAATAAA
1 ATAATATTTAAAATATAAATAAA
5258211 ATAATATT
1 ATAATATT
5258219 ATAGTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATAATATTTAAAATATAAATAAA
Found at i:5258212 original size:11 final size:12
Alignment explanation
Indices: 5258174--5258216 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5258164 TATAATATTT
5258174 AATATATAAATAA
1 AATA-ATAAATAA
*
5258187 AATAATAATTAA
1 AATAATAAATAA
*
5258199 AAT-GTAAATAA
1 AATAATAAATAA
5258210 AATAATA
1 AATAATA
5258217 TTATAGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 9 0.36
12 12 0.48
13 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
AATAATAAATAA
Found at i:5258411 original size:37 final size:36
Alignment explanation
Indices: 5258332--5258420 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 36
5258322 TATTATTTTA
* *
5258332 AATATATTTTTATTATTTTATTTTATTTTCATACTT
1 AATATAATTTTATTATTTTATTTTATTTTCATACAT
* **
5258368 ATTATAATTTTATATATTTTATTTTTATTTTTTTA-AT
1 AATATAATTTTAT-TATTTTA-TTTTATTTTCATACAT
5258405 AATATAAATTTTATTA
1 AATAT-AATTTTATTA
5258421 ATAGTTATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 11 0.25
37 14 0.32
38 19 0.43
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (36 bp):
AATATAATTTTATTATTTTATTTTATTTTCATACAT
Found at i:5265421 original size:20 final size:20
Alignment explanation
Indices: 5265361--5265422 Score: 72
Period size: 21 Copynumber: 3.1 Consensus size: 20
5265351 TTTGTCATGC
*
5265361 TTATATTTTTA-ATATAAAA
1 TTATATTTATATATATAAAA
* *
5265380 ATATATTTATTATATAAAAAA
1 TTATATTTA-TATATATAAAA
*
5265401 TTATATTTATATATTTAAAA
1 TTATATTTATATATATAAAA
5265421 TT
1 TT
5265423 CATCTTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
19 7 0.20
20 13 0.37
21 15 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATATTTATATATATAAAA
Found at i:5278996 original size:19 final size:19
Alignment explanation
Indices: 5278974--5279017 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5278964 AAATATTATG
5278974 AATAATATATGAT-TGTATA
1 AATAATATAT-ATATGTATA
*
5278993 AATATTATATATATGTATA
1 AATAATATATATATGTATA
*
5279012 TATAAT
1 AATAAT
5279018 TATTTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (19 bp):
AATAATATATATATGTATA
Found at i:5279291 original size:242 final size:244
Alignment explanation
Indices: 5279000--5279481 Score: 603
Period size: 242 Copynumber: 2.0 Consensus size: 244
5278990 ATAAATATTA
* * * *
5279000 TATATATGTATATATAATTATTTTATATATAAACATTACTATAACTTATAATAAAATTTATTTAT
1 TATATATATACATATAATTAATTTATACATAAACATTACTATAACTTATAATAAAATTTATTTAT
* * * *
5279065 ATGATTATATTTAGTAACCTTATTAA-TTATCACTATAATTTTTATAACATATTGTTTATAATTA
66 ATGATTATACTTAATAACCTTA-TAAGCTATCACTATAATTTTTATAACATATTATTTATAATTA
* * *
5279129 GTTATTATTTATACAAATTTTGATAT-AAC-ACATTATAACATATAAGTTATATCATTAATTTCA
130 GTTATTATTTATACAAAGTTTGATATAAACAACATTATAACATATAAATTATATCATTAATCTCA
*
5279192 TATATACATAATAA-AATAATATATTATACATTAAATTTATAAAAAAAAAT
195 TATATACATAATAATAA-AAAATATTATACATTAAATTTATAAAAAAAAAT
* * * * * *
5279242 TATATATATACATATATTTAATTTATACATGAATATTACTGTAACTTATAATAGATTTTATTTAT
1 TATATATATACATATAATTAATTTATACATAAACATTACTATAACTTATAATAAAATTTATTTAT
* ** * * *
5279307 ATGATTTTACTTAATAATTTTATAAGCTATTATTTTAATTTTTATAACATATTATTTATAATTAG
66 ATGATTATACTTAATAACCTTATAAGCTATCACTATAATTTTTATAACATATTATTTATAATTAG
* * *
5279372 TTATTATTTATACAAAGTTTGATATAAAACTTAAAATATTATAACGTATAAATTATGTCATTAAT
131 TTATTATTTATACAAAGTTTGATAT-AAAC----AACATTATAACATATAAATTATATCATTAAT
* * *
5279437 CTCATATATATATAATAATAAAAAATATTATATATTTAATTTATA
191 CTCATATATACATAATAATAAAAAATATTATACATTAAATTTATA
5279482 TATAATATAT
Statistics
Matches: 201, Mismatches: 30, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
241 3 0.01
242 130 0.65
244 3 0.01
249 63 0.31
250 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.47
Consensus pattern (244 bp):
TATATATATACATATAATTAATTTATACATAAACATTACTATAACTTATAATAAAATTTATTTAT
ATGATTATACTTAATAACCTTATAAGCTATCACTATAATTTTTATAACATATTATTTATAATTAG
TTATTATTTATACAAAGTTTGATATAAACAACATTATAACATATAAATTATATCATTAATCTCAT
ATATACATAATAATAAAAAATATTATACATTAAATTTATAAAAAAAAAT
Found at i:5279352 original size:22 final size:23
Alignment explanation
Indices: 5279320--5279369 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
5279310 ATTTTACTTA
5279320 ATAA-TTTTATAAGC-TATTATTT
1 ATAATTTTTATAA-CATATTATTT
5279342 -TAATTTTTATAACATATTATTT
1 ATAATTTTTATAACATATTATTT
5279364 ATAATT
1 ATAATT
5279370 AGTTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.16
22 16 0.64
23 5 0.20
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
ATAATTTTTATAACATATTATTT
Found at i:5291093 original size:19 final size:21
Alignment explanation
Indices: 5291066--5291105 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
5291056 AAATGCATTC
*
5291066 TTTTTTTATTA-A-TTTAAAA
1 TTTTATTATTATATTTTAAAA
5291085 TTTTATTATTATATTTTAAAA
1 TTTTATTATTATATTTTAAAA
5291106 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTATTATTATATTTTAAAA
Found at i:5302105 original size:21 final size:19
Alignment explanation
Indices: 5302079--5302118 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
5302069 TATGAAATAA
5302079 TATTTTAAAAAGTATTTAAAT
1 TATTTTAAAAA--ATTTAAAT
5302100 TATTTTAAAAAATTTAAAT
1 TATTTTAAAAAATTTAAAT
5302119 AACTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TATTTTAAAAAATTTAAAT
Found at i:5302126 original size:21 final size:21
Alignment explanation
Indices: 5302073--5302127 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
5302063 TATTTGTATG
5302073 AAATAATATTTTAAAAAGTATTT
1 AAATAAT-TTTTAAAAAG-ATTT
*
5302096 AAATTA-TTTTAAAAA-ATTT
1 AAATAATTTTTAAAAAGATTT
5302115 AAATAACTTTTTA
1 AAATAA-TTTTTA
5302128 TTCATCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 9 0.32
21 14 0.50
23 5 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AAATAATTTTTAAAAAGATTT
Found at i:5309143 original size:17 final size:18
Alignment explanation
Indices: 5309109--5309143 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5309099 TATTTTAAAA
5309109 AAATTTTAAAATTATATT
1 AAATTTTAAAATTATATT
*
5309127 AAATTTTTAAA-TATATT
1 AAATTTTAAAATTATATT
5309144 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATTTTAAAATTATATT
Found at i:5309155 original size:29 final size:28
Alignment explanation
Indices: 5309123--5309203 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
5309113 TTTAAAATTA
5309123 TATTAAATTTTTAAATATATTTTTATTTT
1 TATT-AATTTTTAAATATATTTTTATTTT
* *
5309152 TATTATATTTAATTAAGT-TA-TTGTATTTT
1 TATTA-ATTT--TTAAATATATTTTTATTTT
*
5309181 TATT--TTTTTAAATAAATTTTTAT
1 TATTAATTTTTAAATATATTTTTAT
5309204 GATTAACACT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
24 5 0.12
25 1 0.02
26 8 0.19
28 1 0.02
29 20 0.48
30 2 0.05
31 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TATTAATTTTTAAATATATTTTTATTTT
Found at i:5311389 original size:10 final size:10
Alignment explanation
Indices: 5311371--5311410 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
5311361 TTTAATGTCA
5311371 TATATTTTAT
1 TATATTTTAT
5311381 T-TCATTTTAT
1 TAT-ATTTTAT
5311391 TATATTTTAT
1 TATATTTTAT
5311401 ATATATTTTA
1 -TATATTTTA
5311411 ATTTTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.04
10 16 0.59
11 10 0.37
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (10 bp):
TATATTTTAT
Found at i:5311486 original size:32 final size:32
Alignment explanation
Indices: 5311450--5311517 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
5311440 TTTTAATGTC
*
5311450 ATATATTTTATTTTCATTATT-ATTATAATTTT
1 ATATATTTTATTTTAATTATTAATTAT-ATTTT
* * *
5311482 ATATATTTTTTTTTAATTTTTAATTATTTTTT
1 ATATATTTTATTTTAATTATTAATTATATTTT
5311514 ATAT
1 ATAT
5311518 TATATATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (32 bp):
ATATATTTTATTTTAATTATTAATTATATTTT
Found at i:5311500 original size:20 final size:20
Alignment explanation
Indices: 5311475--5311538 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 20
5311465 ATTATTATTA
5311475 TAATTTTATATATTTTTTTT
1 TAATTTTATATATTTTTTTT
*
5311495 TAATTTT-TA-ATTATTTTT
1 TAATTTTATATATTTTTTTT
* * *
5311513 T-ATATTATATATTTATATT
1 TAATTTTATATATTTTTTTT
5311532 TAATTTT
1 TAATTTT
5311539 GTTTTACCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 4 0.11
18 11 0.31
19 9 0.26
20 11 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TAATTTTATATATTTTTTTT
Found at i:5311511 original size:30 final size:32
Alignment explanation
Indices: 5311450--5311527 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 32
5311440 TTTTAATGTC
* *
5311450 ATATATTTTATTTTCATTATTATTATAATTTT
1 ATATATTTTATTTTAATTATTATAATAATTTT
* *
5311482 ATATATTTTTTTTTAATT-TT-TAATTATTTT
1 ATATATTTTATTTTAATTATTATAATAATTTT
* *
5311512 TTATATTATATATTTA
1 ATATATTTTAT-TTTA
5311528 TATTTAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 16 0.42
31 6 0.16
32 16 0.42
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (32 bp):
ATATATTTTATTTTAATTATTATAATAATTTT
Found at i:5311513 original size:18 final size:18
Alignment explanation
Indices: 5311460--5311514 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
5311450 ATATATTTTA
* *
5311460 TTTTCATTATTATTATAAT
1 TTTTAATTATT-TTTTAAT
*
5311479 TTTATATATTTTTTTTTAAT
1 TTT-TA-ATTATTTTTTAAT
5311499 TTTTAATTATTTTTTA
1 TTTTAATTATTTTTTA
5311515 TATTATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 10 0.33
19 5 0.17
20 10 0.33
21 5 0.17
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTAATTATTTTTTAAT
Found at i:5311642 original size:38 final size:40
Alignment explanation
Indices: 5311567--5311644 Score: 99
Period size: 38 Copynumber: 2.0 Consensus size: 40
5311557 AAATTTAATT
* * *
5311567 TTTTATTTTTATTTTGTTTTAATTTTTATTAATTATTATA
1 TTTTATTTTAATATTGTTTTAATTTTAATTAATTATTATA
5311607 TTTTATTTTAATATT-TTTT-ATTTTAATT-ATATATTATA
1 TTTTATTTTAATATTGTTTTAATTTTAATTAAT-TATTATA
5311645 AACTATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 2 0.06
38 15 0.44
39 4 0.12
40 13 0.38
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (40 bp):
TTTTATTTTAATATTGTTTTAATTTTAATTAATTATTATA
Found at i:5312115 original size:22 final size:22
Alignment explanation
Indices: 5312087--5312142 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
5312077 GGAATGATGC
5312087 AATAAAAATATATTTAATTTAA
1 AATAAAAATATATTTAATTTAA
5312109 AATAAAAATATATTTAATTTAA
1 AATAAAAATATATTTAATTTAA
5312131 AATAAAAATATA
1 AATAAAAATATA
5312143 AAAATTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAAAATATATTTAATTTAA
Found at i:5317741 original size:24 final size:24
Alignment explanation
Indices: 5317709--5317754 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5317699 GTCAAAAACC
5317709 TAATCTGTGGGATGTTGTGTCACT
1 TAATCTGTGGGATGTTGTGTCACT
5317733 TAATCTGTGGGATGTTGTGTCA
1 TAATCTGTGGGATGTTGTGTCA
5317755 AAGCAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.11, G:0.30, T:0.41
Consensus pattern (24 bp):
TAATCTGTGGGATGTTGTGTCACT
Found at i:5326339 original size:3 final size:3
Alignment explanation
Indices: 5326331--5326365 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5326321 GGACTCTGTT
5326331 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5326366 TTTATTGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:5335218 original size:2 final size:2
Alignment explanation
Indices: 5335211--5335237 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5335201 AGCATCTGTC
5335211 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 T
5335238 GATTCCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5341858 original size:22 final size:23
Alignment explanation
Indices: 5341828--5341874 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
5341818 ATATAGAGTT
5341828 ATTTGAGCTTAATT-TTGATAATA
1 ATTTGAGCTTAATTCTT-ATAATA
*
5341851 ATTT-AGCTTAGTTCTTATAATA
1 ATTTGAGCTTAATTCTTATAATA
5341873 AT
1 AT
5341875 GCATATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (23 bp):
ATTTGAGCTTAATTCTTATAATA
Found at i:5348964 original size:16 final size:16
Alignment explanation
Indices: 5348943--5348976 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5348933 CCTTATCATG
5348943 ATCAAATCAAATAAGC
1 ATCAAATCAAATAAGC
5348959 ATCAAATCAAATAAGC
1 ATCAAATCAAATAAGC
5348975 AT
1 AT
5348977 TAAAAGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.18, G:0.06, T:0.21
Consensus pattern (16 bp):
ATCAAATCAAATAAGC
Found at i:5349281 original size:16 final size:16
Alignment explanation
Indices: 5349256--5349300 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
5349246 TTATAGTACC
*
5349256 AGTGTGTTTACTTTAG
1 AGTGTCTTTACTTTAG
5349272 AGTGTCTTTACTTTAG
1 AGTGTCTTTACTTTAG
* *
5349288 TGTG-CTTTGCTTT
1 AGTGTCTTTACTTT
5349301 TGAACAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.13, C:0.11, G:0.22, T:0.53
Consensus pattern (16 bp):
AGTGTCTTTACTTTAG
Found at i:5361773 original size:2 final size:2
Alignment explanation
Indices: 5361766--5361857 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
5361756 TGACTAACTA
5361766 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5361808 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5361850 CT CT CT CT
1 CT CT CT CT
5361858 GTCGGCTAAG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5370968 original size:60 final size:60
Alignment explanation
Indices: 5370875--5370994 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
5370865 TCGATACATG
* *
5370875 CATGTCAAAAAATATCGGACAAGAGACATTATTGAGTGAGCTACATAAGGTATGGTTCCC
1 CATGTCAAAAAAAATCGGACAAGAGACATTATTGAGTGAGCTACATAAGCTATGGTTCCC
* *
5370935 CATGTCAAAAAAAATTGGACAAGAGTCATTATTGAGTGAGCTACATAAGCTATGGTTCCC
1 CATGTCAAAAAAAATCGGACAAGAGACATTATTGAGTGAGCTACATAAGCTATGGTTCCC
5370995 TGTTTTTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (60 bp):
CATGTCAAAAAAAATCGGACAAGAGACATTATTGAGTGAGCTACATAAGCTATGGTTCCC
Found at i:5371342 original size:7 final size:8
Alignment explanation
Indices: 5371320--5371353 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
5371310 CCCAGGTATA
5371320 TGATTTTT
1 TGATTTTT
5371328 TGATTTTT
1 TGATTTTT
5371336 TGATTTTT
1 TGATTTTT
*
5371344 TGATTCTT
1 TGATTTTT
5371352 TG
1 TG
5371354 CTCTTTACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.71
Consensus pattern (8 bp):
TGATTTTT
Found at i:5378813 original size:12 final size:12
Alignment explanation
Indices: 5378798--5378834 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5378788 ATCGTCCTCG
*
5378798 TCATCCTCATCC
1 TCATCATCATCC
5378810 TCATCATCATCC
1 TCATCATCATCC
*
5378822 TCATCATCTTCC
1 TCATCATCATCC
5378834 T
1 T
5378835 TGACGTCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.19, C:0.43, G:0.00, T:0.38
Consensus pattern (12 bp):
TCATCATCATCC
Found at i:5378816 original size:9 final size:9
Alignment explanation
Indices: 5378786--5378829 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
5378776 ATCCTCCTTG
*
5378786 TCATCGTCC
1 TCATCATCC
*
5378795 TCGTCATCC
1 TCATCATCC
* *
5378804 TCATCCTCA
1 TCATCATCC
5378813 TCATCATCC
1 TCATCATCC
5378822 TCATCATC
1 TCATCATC
5378830 TTCCTTGACG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.18, C:0.43, G:0.05, T:0.34
Consensus pattern (9 bp):
TCATCATCC
Found at i:5378949 original size:21 final size:22
Alignment explanation
Indices: 5378907--5378952 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5378897 AAACATAAAA
5378907 AAAAAAAGGGAAATGAAAGGAT
1 AAAAAAAGGGAAATGAAAGGAT
* * *
5378929 AAAATAAGTGAAATG-ATGGAT
1 AAAAAAAGGGAAATGAAAGGAT
5378950 AAA
1 AAA
5378953 CCTGGGGCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (22 bp):
AAAAAAAGGGAAATGAAAGGAT
Found at i:5383737 original size:55 final size:55
Alignment explanation
Indices: 5383647--5383750 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 55
5383637 AGAAGTTGCA
* * *
5383647 CTCCGTTTATTCGTTGCGTGTCCTGAAAAGCGTTTTGCAATATAATTGGTTTACT
1 CTCCGTTTACTCATTGCGTGTCCAGAAAAGCGTTTTGCAATATAATTGGTTTACT
*
5383702 CTCCGTTTACTCATTGCGTGTCCAGATAATG-GTTTTGCAATATAATTGG
1 CTCCGTTTACTCATTGCGTGTCCAGA-AAAGCGTTTTGCAATATAATTGG
5383751 ACGTCGTTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 41 0.93
56 3 0.07
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.40
Consensus pattern (55 bp):
CTCCGTTTACTCATTGCGTGTCCAGAAAAGCGTTTTGCAATATAATTGGTTTACT
Found at i:5384142 original size:30 final size:30
Alignment explanation
Indices: 5384098--5384165 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
5384088 TTTAATTAAA
*
5384098 TTTTTATATTTTTATTTTGAATCAAATAAG
1 TTTTTATATGTTTATTTTGAATCAAATAAG
* * *
5384128 TTTTTGTATGTTTATTTTTAATCAAATAAA
1 TTTTTATATGTTTATTTTGAATCAAATAAG
*
5384158 TTCTTATA
1 TTTTTATA
5384166 ATTAATTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.57
Consensus pattern (30 bp):
TTTTTATATGTTTATTTTGAATCAAATAAG
Found at i:5385897 original size:114 final size:114
Alignment explanation
Indices: 5385766--5385996 Score: 435
Period size: 114 Copynumber: 2.0 Consensus size: 114
5385756 GATAACTCAC
* *
5385766 TTACTATTATATTACTTGTTAATTATGTGCACTTGCATGATGTTTTGCTAAAATTGATAAAAATC
1 TTACTACTATATTACTTGTTAATCATGTGCACTTGCATGATGTTTTGCTAAAATTGATAAAAATC
*
5385831 TTAAAGTAATTTATCTTGATAAATTAGCAAGCAATAATATTATGTAATG
66 TTAAAGTAATTTATCTTGATAAATAAGCAAGCAATAATATTATGTAATG
5385880 TTACTACTATATTACTTGTTAATCATGTGCACTTGCATGATGTTTTGCTAAAATTGATAAAAATC
1 TTACTACTATATTACTTGTTAATCATGTGCACTTGCATGATGTTTTGCTAAAATTGATAAAAATC
5385945 TTAAAGTAATTTATCTTGATAAATAAGCAAGCAATAATATTATGTAATG
66 TTAAAGTAATTTATCTTGATAAATAAGCAAGCAATAATATTATGTAATG
5385994 TTA
1 TTA
5385997 ATGTAACATG
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (114 bp):
TTACTACTATATTACTTGTTAATCATGTGCACTTGCATGATGTTTTGCTAAAATTGATAAAAATC
TTAAAGTAATTTATCTTGATAAATAAGCAAGCAATAATATTATGTAATG
Found at i:5405145 original size:29 final size:30
Alignment explanation
Indices: 5405111--5405168 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
5405101 TAAATTTGAA
* * *
5405111 TAAGTATTTATTTTTTTA-TTATATTCAAT
1 TAAGTATTCATATTTTTATTTATAATCAAT
5405140 TAAGTATTCATATTTTTATTTATAATCAA
1 TAAGTATTCATATTTTTATTTATAATCAA
5405169 ATAAATCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (30 bp):
TAAGTATTCATATTTTTATTTATAATCAAT
Found at i:5405924 original size:29 final size:28
Alignment explanation
Indices: 5405887--5405946 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
5405877 CATTAATCAT
* *
5405887 AAATATTTATTTAATTTAAAATAAAATATA
1 AAATATTTAATTAA-ATAAAATAAAA-ATA
*
5405917 AAAT-TTTAATTAAATATAATAAAAATA
1 AAATATTTAATTAAATAAAATAAAAATA
5405944 AAA
1 AAA
5405947 AATCATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.22
28 9 0.33
29 8 0.30
30 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATATTTAATTAAATAAAATAAAAATA
Found at i:5405931 original size:23 final size:24
Alignment explanation
Indices: 5405896--5405942 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
5405886 TAAATATTTA
5405896 TTTAATTTAAAATAAAATATAAAAT
1 TTTAATTTAAAATAAAATA-AAAAT
*
5405921 TTTAA-TT-AAATATAATAAAAAT
1 TTTAATTTAAAATAAAATAAAAAT
5405943 AAAAAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 2 0.10
25 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTTAATTTAAAATAAAATAAAAAT
Found at i:5415634 original size:31 final size:31
Alignment explanation
Indices: 5415588--5415647 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5415578 GTAAAAAAGA
* *
5415588 TAGTTTTCAACTAAGTGACTAATAATTAACT
1 TAGTTTTCAACTAAGTAACTAACAATTAACT
* *
5415619 TAGTTTTTAATTAAGTAACTAACAATTAA
1 TAGTTTTCAACTAAGTAACTAACAATTAA
5415648 TTTGAAGACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (31 bp):
TAGTTTTCAACTAAGTAACTAACAATTAACT
Found at i:5418017 original size:109 final size:109
Alignment explanation
Indices: 5417869--5418087 Score: 429
Period size: 109 Copynumber: 2.0 Consensus size: 109
5417859 TCTGCTTTAA
5417869 AGAATGAAATGGAAAGACATGTTCATGAAAAATCACATTGCTTGATATGAAAACTTTGTTAGCAA
1 AGAATGAAATGGAAAGACATGTTCATGAAAAATCACATTGCTTGATATGAAAACTTTGTTAGCAA
*
5417934 GAAGATCATAAACCTTATAACATTTGACACTATTAGGATAACCT
66 GAAGATCATAAACCTTATAACATTTGACACAATTAGGATAACCT
5417978 AGAATGAAATGGAAAGACATGTTCATGAAAAATCACATTGCTTGATATGAAAACTTTGTTAGCAA
1 AGAATGAAATGGAAAGACATGTTCATGAAAAATCACATTGCTTGATATGAAAACTTTGTTAGCAA
5418043 GAAGATCATAAACCTTATAACATTTGACACAATTAGGATAACCT
66 GAAGATCATAAACCTTATAACATTTGACACAATTAGGATAACCT
5418087 A
1 A
5418088 AAAATATGCA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (109 bp):
AGAATGAAATGGAAAGACATGTTCATGAAAAATCACATTGCTTGATATGAAAACTTTGTTAGCAA
GAAGATCATAAACCTTATAACATTTGACACAATTAGGATAACCT
Found at i:5421351 original size:18 final size:19
Alignment explanation
Indices: 5421295--5421353 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
5421285 ATGAATATTT
*
5421295 TTAAGTATATTTTAAATATA
1 TTAA-TATATTTTAAAAATA
* *
5421315 TTAATAATTTTTTATAAATA
1 TTAAT-ATATTTTAAAAATA
5421335 TT-ATATATTTTAAAAATA
1 TTAATATATTTTAAAAATA
5421353 T
1 T
5421354 ATTATTCATG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 13 0.39
19 3 0.09
20 17 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAATATATTTTAAAAATA
Found at i:5421359 original size:16 final size:18
Alignment explanation
Indices: 5421300--5421353 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
5421290 TATTTTTAAG
*
5421300 TATATTTTAAATATATTAA
1 TATATTTTAAAAATATT-A
* *
5421319 TAATTTTTTATAAATATTA
1 T-ATATTTTAAAAATATTA
5421338 TATATTTTAAAAATAT
1 TATATTTTAAAAATAT
5421354 ATTATTCATG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 13 0.45
19 3 0.10
20 13 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATTTTAAAAATATTA
Found at i:5428144 original size:2 final size:2
Alignment explanation
Indices: 5428125--5428172 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
5428115 AGGGAGAACT
* *
5428125 GA GA -A GA GA GA CA CA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5428166 GA GA GA G
1 GA GA GA G
5428173 GGGAAGAGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.04, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5453142 original size:15 final size:15
Alignment explanation
Indices: 5453119--5453148 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5453109 CTTAGGGTTT
5453119 GTTTGTTTCCTGGAA
1 GTTTGTTTCCTGGAA
*
5453134 GTTTTTTTCCTGGAA
1 GTTTGTTTCCTGGAA
5453149 AATCTGGAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.50
Consensus pattern (15 bp):
GTTTGTTTCCTGGAA
Found at i:5463921 original size:16 final size:16
Alignment explanation
Indices: 5463900--5463930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5463890 ATTTTAAAAT
5463900 TTTTTTAAAAAAATAA
1 TTTTTTAAAAAAATAA
*
5463916 TTTTTTTAAAAAATA
1 TTTTTTAAAAAAATA
5463931 GTTTAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTTTAAAAAAATAA
Found at i:5465419 original size:32 final size:32
Alignment explanation
Indices: 5465370--5465433 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
5465360 TTAATTTACT
*
5465370 TTACTTATACTTCAAGTTGAAGTTAAGTAGTA
1 TTACTTATACTTCAAGTTGAAGTTAAGGAGTA
* *
5465402 TTACTTGTAC-TCAAAGTTTAAGTTAAGGAGTA
1 TTACTTATACTTC-AAGTTGAAGTTAAGGAGTA
5465434 GTAAACTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.39
Consensus pattern (32 bp):
TTACTTATACTTCAAGTTGAAGTTAAGGAGTA
Found at i:5468974 original size:12 final size:12
Alignment explanation
Indices: 5468959--5468992 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
5468949 TAGATATAGA
5468959 GAGAGAGAGAGG
1 GAGAGAGAGAGG
5468971 GAGAGAGAGAGG
1 GAGAGAGAGAGG
*
5468983 GAGGGAGAGA
1 GAGAGAGAGA
5468993 CAGATAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (12 bp):
GAGAGAGAGAGG
Found at i:5468975 original size:16 final size:16
Alignment explanation
Indices: 5468956--5468992 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
5468946 ATATAGATAT
5468956 AGAGAGAGAGAGAGGG
1 AGAGAGAGAGAGAGGG
*
5468972 AGAGAGAGAGGGAGGG
1 AGAGAGAGAGAGAGGG
5468988 AGAGA
1 AGAGA
5468993 CAGATAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (16 bp):
AGAGAGAGAGAGAGGG
Found at i:5473988 original size:2 final size:2
Alignment explanation
Indices: 5473981--5474014 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5473971 GATCCCGGGA
5473981 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5474015 ATCCTTAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5483150 original size:29 final size:29
Alignment explanation
Indices: 5483088--5483161 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
5483078 AGGCATTAAA
*
5483088 GTGTAATAA-AATA-TTTTTAAATATGAC
1 GTGTAATAACAATATTTTTTAAACATGAC
* * **
5483115 GTATAATAACAATATTTTTTCAACATGGT
1 GTGTAATAACAATATTTTTTAAACATGAC
*
5483144 GTGTAATAACAGTATTTT
1 GTGTAATAACAATATTTT
5483162 CTTTTTCAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 8 0.21
28 4 0.11
29 26 0.68
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (29 bp):
GTGTAATAACAATATTTTTTAAACATGAC
Found at i:5502089 original size:6 final size:6
Alignment explanation
Indices: 5502074--5502104 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
5502064 GTCTGCCTGA
5502074 TTTT-C TTTTGC TTTTGC TTTTGC TTTTGC TT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TT
5502105 CCGTTAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.00, C:0.16, G:0.13, T:0.71
Consensus pattern (6 bp):
TTTTGC
Found at i:5511775 original size:23 final size:23
Alignment explanation
Indices: 5511731--5511786 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5511721 TAAATTTTTA
* * *
5511731 TTTTTATATTATATTTACTAATT
1 TTTTTATATTAAATTAAATAATT
*
5511754 TTTTTATTTTAAATTAAATAATT
1 TTTTTATATTAAATTAAATAATT
5511777 TTTTATATAT
1 TTTT-TATAT
5511787 AATTAGTACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTTATATTAAATTAAATAATT
Found at i:5540301 original size:6 final size:6
Alignment explanation
Indices: 5540291--5540336 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
5540281 ACACCAGATG
* * *
5540291 TGGTGG TGGTGA TGGTGA TGGTGA TGGTGA TGGTGC TGGTGC TGGT
1 TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA TGGT
5540337 CTTTATCGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.09, C:0.04, G:0.52, T:0.35
Consensus pattern (6 bp):
TGGTGA
Found at i:5564733 original size:55 final size:57
Alignment explanation
Indices: 5564645--5564758 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 57
5564635 ACGAATCTTA
* *
5564645 AAAAAAAAGTAAAATTTCAATTTATAACATAAATAATTTAATATGTTACAG-ATGCAT
1 AAAAAAAAGTAAAATTTCAACTAATAACATAAATAATTTAATATGTTA-AGCATGCAT
5564702 AAAAAAAA-TAAAATTT-AACTAATAACATAAATAATTTAATATGTTAAGCATGCAT
1 AAAAAAAAGTAAAATTTCAACTAATAACATAAATAATTTAATATGTTAAGCATGCAT
5564757 AA
1 AA
5564759 TATTAATATG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
54 2 0.04
55 36 0.67
56 8 0.15
57 8 0.15
ACGTcount: A:0.55, C:0.07, G:0.06, T:0.32
Consensus pattern (57 bp):
AAAAAAAAGTAAAATTTCAACTAATAACATAAATAATTTAATATGTTAAGCATGCAT
Found at i:5564759 original size:135 final size:135
Alignment explanation
Indices: 5564569--5564819 Score: 314
Period size: 135 Copynumber: 1.9 Consensus size: 135
5564559 TAATGTTTAG
* * *
5564569 AAAAATAAAATTTTAACTAATAATATAAATAATTTAATAAATTACAAATATATAATA-TGATATG
1 AAAAATAAAATTTTAACTAATAACATAAATAATTTAATAAATTACAAATACATAATATTAATATG
* *
5564633 TTACGAAT-CTTAAAAAAAAAGTAAAAT-TTCAATTTATAACATAAATAATTTAATATGTTACAG
66 TTACGAATGCTT--AAAAAAA-TAAAATCTT-AACTAATAACATAAATAATTTAATATGTTACAG
5564696 ATGCATAAA
127 ATGCATAAA
** * *
5564705 AAAAATAAAA-TTTAACTAATAACATAAATAATTTAATATGTTA-AGCATGCATAATATTAATAT
1 AAAAATAAAATTTTAACTAATAACATAAATAATTTAATAAATTACA-AATACATAATATTAATAT
* * *
5564768 GTTAGGGATGCTTAGAAAAATAAAATCTTAACTAATAACATAAATAATTTAA
65 GTTACGAATGCTTAAAAAAATAAAATCTTAACTAATAACATAAATAATTTAA
5564820 AAGCAATCCG
Statistics
Matches: 99, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
134 28 0.28
135 46 0.46
136 22 0.22
137 3 0.03
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (135 bp):
AAAAATAAAATTTTAACTAATAACATAAATAATTTAATAAATTACAAATACATAATATTAATATG
TTACGAATGCTTAAAAAAATAAAATCTTAACTAATAACATAAATAATTTAATATGTTACAGATGC
ATAAA
Found at i:5575230 original size:5 final size:5
Alignment explanation
Indices: 5575220--5575244 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5575210 AAGGGAATGG
5575220 TACCC TACCC TACCC TACCC TACCC
1 TACCC TACCC TACCC TACCC TACCC
5575245 ATGCAAACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
TACCC
Found at i:5575752 original size:23 final size:23
Alignment explanation
Indices: 5575726--5575785 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
5575716 TTTCATAACT
5575726 TGCAGCCAGGTTGCAATAAGCAG
1 TGCAGCCAGGTTGCAATAAGCAG
5575749 TGCAGCCAGGTTGCAATAAGCAG
1 TGCAGCCAGGTTGCAATAAGCAG
5575772 TGCAGCCAGGTTGC
1 TGCAGCCAGGTTGC
5575786 TTTGACATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.32, T:0.18
Consensus pattern (23 bp):
TGCAGCCAGGTTGCAATAAGCAG
Found at i:5577178 original size:5 final size:5
Alignment explanation
Indices: 5577168--5577192 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5577158 ACGAGCTCAA
5577168 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
5577193 GGACAGCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5591275 original size:6 final size:6
Alignment explanation
Indices: 5591266--5591290 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5591256 GAGTGGGATA
5591266 GAAATG GAAATG GAAATG GAAATG G
1 GAAATG GAAATG GAAATG GAAATG G
5591291 GAGTCATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GAAATG
Found at i:5597983 original size:21 final size:20
Alignment explanation
Indices: 5597959--5598015 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
5597949 TTTTATTAAT
5597959 AATATTATAATTAAAATAAAA
1 AATATTA-AATTAAAATAAAA
* * *
5597980 AATATTAAAATAAAATATAT
1 AATATTAAATTAAAATAAAA
*
5598000 AATATAAAAATTAAAA
1 AATAT-TAAATTAAAA
5598016 ATTAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATTAAATTAAAATAAAA
Found at i:5597986 original size:15 final size:15
Alignment explanation
Indices: 5597968--5598048 Score: 64
Period size: 15 Copynumber: 5.5 Consensus size: 15
5597958 TAATATTATA
5597968 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
5597983 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
*
5597998 A-TAATAT-AAAAAT
1 ATTAAAATAAAAAAT
*
5598011 -TAAAAATTAAAATAA-
1 ATTAAAA-TAAAA-AAT
*
5598026 AATAAAATATAAAAA-
1 ATTAAAATA-AAAAAT
5598041 ATTAAAAT
1 ATTAAAAT
5598049 TTATATAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
13 8 0.15
14 6 0.12
15 29 0.56
16 9 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:5598002 original size:33 final size:34
Alignment explanation
Indices: 5597959--5598144 Score: 100
Period size: 33 Copynumber: 5.5 Consensus size: 34
5597949 TTTTATTAAT
5597959 AATATTATAAT-T-AAAATAAAAAATATTAAAATAA
1 AATATTATAATATAAAAAT-AAAAA-ATTAAAATAA
*
5597993 AATA-TATAATATAAAAATTAAAAATTAAAATAA
1 AATATTATAATATAAAAATAAAAAATTAAAATAA
* * *
5598026 AATA--A-AATATAAAAA-ATTAAAATTTATATAA
1 AATATTATAATATAAAAATA-AAAAATTAAAATAA
* * * * * *
5598057 TATAGGTAAAATAAATTAAAATAAAATATATAATATAA
1 AATA-TTATAAT--ATAAAAATAAAAAAT-TAAAATAA
* * * * *
5598095 AACATTATATTAAAAAAAT-AAAAATAAAAATAT
1 AATATTATAATATAAAAATAAAAAATTAAAATAA
*
5598128 AAGATTATAATAATAAA
1 AATATTATAAT-ATAAA
5598145 TGAAAATAAA
Statistics
Matches: 116, Mismatches: 24, Indels: 24
0.71 0.15 0.15
Matches are distributed among these distances:
31 24 0.21
32 1 0.01
33 34 0.29
34 19 0.16
35 14 0.12
37 14 0.12
38 10 0.09
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (34 bp):
AATATTATAATATAAAAATAAAAAATTAAAATAA
Found at i:5598006 original size:38 final size:39
Alignment explanation
Indices: 5597956--5598048 Score: 92
Period size: 38 Copynumber: 2.5 Consensus size: 39
5597946 TTATTTTATT
* * *
5597956 AATA-ATATTATAATTAAAATAAAAA-ATATTAAAATAA
1 AATATATAATATAATTAAAATAAAAATAAAATAAAATAA
*
5597993 AATATATAATATAA--AAATTAAAAATTAAAATAAAATAA
1 AATATATAATATAATTAAAATAAAAA-TAAAATAAAATAA
5598031 AATATA-AA-A-AATTAAAAT
1 AATATATAATATAATTAAAAT
5598049 TTATATAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
35 2 0.04
36 10 0.22
37 10 0.22
38 24 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (39 bp):
AATATATAATATAATTAAAATAAAAATAAAATAAAATAA
Found at i:5598058 original size:24 final size:25
Alignment explanation
Indices: 5598012--5598124 Score: 84
Period size: 30 Copynumber: 4.2 Consensus size: 25
5598002 TATAAAAATT
5598012 AAAAATTAAAATAAAATAAAATATA
1 AAAAATTAAAATAAAATAAAATATA
* * *
5598037 AAAAATTAAAATTTATATAATATAGGTAA
1 AAAAATTAAAA-TAAAATAAAATA--T-A
5598066 AATAAATTAAAATAAAATATATAATATA
1 AA-AAATTAAAATAAAATA-A-AATATA
* *
5598094 AAACATTATATTAAAAAAATAAAA-ATA
1 AAAAATTA-A--AATAAAATAAAATATA
5598121 AAAA
1 AAAA
5598125 TATAAGATTA
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
25 11 0.16
26 9 0.13
27 11 0.16
28 7 0.10
29 10 0.14
30 18 0.26
31 3 0.04
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAAATTAAAATAAAATAAAATATA
Found at i:5598083 original size:15 final size:15
Alignment explanation
Indices: 5597967--5598084 Score: 63
Period size: 15 Copynumber: 8.0 Consensus size: 15
5597957 ATAATATTAT
5597967 AATTAAAATAAAA-A
1 AATTAAAATAAAATA
5597981 ATATTAAAATAAAAT-
1 A-ATTAAAATAAAATA
* *
5597996 -A-TATAATATAA-A
1 AATTAAAATAAAATA
5598008 AATTAAAAATTAAAATA
1 AATT-AAAA-TAAAATA
*
5598025 AAATAAAATATAAA-A
1 AATTAAAATA-AAATA
**
5598040 AATTAAAAT-TTATA
1 AATTAAAATAAAATA
**
5598054 TAA-TATAGGTAAAATA
1 -AATTA-AAATAAAATA
5598070 AATTAAAATAAAATA
1 AATTAAAATAAAATA
5598085 TATAATATAA
Statistics
Matches: 76, Mismatches: 14, Indels: 27
0.65 0.12 0.23
Matches are distributed among these distances:
12 8 0.11
13 3 0.04
14 5 0.07
15 40 0.53
16 16 0.21
17 4 0.05
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
AATTAAAATAAAATA
Found at i:5598156 original size:88 final size:91
Alignment explanation
Indices: 5597965--5598156 Score: 217
Period size: 88 Copynumber: 2.2 Consensus size: 91
5597955 TAATAATATT
*
5597965 ATAATTAAAATAAAA-AATATTAAAATAAAATATATAATATAAAAATTAAAAATTAAAATAAAAT
1 ATAAATAAAATAAAATAATATTAAAATAAAATATATAATATAAAAATT-AAAATTAAAATAAAAT
5598029 AAAATATAAAAAATTAAAATT-T-AT-
65 AAAATATAAAAAATTAAAATTATAATA
** *
5598053 AT-AATATAGGTAAAATAA-ATTAAAATAAAATATATAATATAAAACATT-ATATT-AAA-AAAA
1 ATAAATA-AAATAAAATAATATTAAAATAAAATATATAATATAAAA-ATTAAAATTAAAATAAAA
*
5598113 TAAAA-AT-AAAAATATAAGATTATAATA
64 TAAAATATAAAAAAT-TAAAATTATAATA
5598140 ATAAATGAAAATAAAAT
1 ATAAAT-AAAATAAAAT
5598157 TTATGATATT
Statistics
Matches: 88, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
83 6 0.07
84 8 0.09
85 10 0.11
86 5 0.06
87 9 0.10
88 44 0.50
89 6 0.07
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.30
Consensus pattern (91 bp):
ATAAATAAAATAAAATAATATTAAAATAAAATATATAATATAAAAATTAAAATTAAAATAAAATA
AAATATAAAAAATTAAAATTATAATA
Found at i:5600177 original size:18 final size:18
Alignment explanation
Indices: 5600137--5600179 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5600127 ATGGTAAACA
5600137 TGATCCTGATATTGTTTG
1 TGATCCTGATATTGTTTG
* * * *
5600155 CGATCCTGGTCTTGTTTT
1 TGATCCTGATATTGTTTG
5600173 TGATCCT
1 TGATCCT
5600180 CCGTTTTTTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.49
Consensus pattern (18 bp):
TGATCCTGATATTGTTTG
Found at i:5628168 original size:46 final size:46
Alignment explanation
Indices: 5628101--5628193 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
5628091 CTATAAAGAA
* *
5628101 TGGATTCTATGAGCAATTTACAGATTTAACTTTAACCAGTAACTCT
1 TGGATTCTATAAGCAATTTACAAATTTAACTTTAACCAGTAACTCT
* *
5628147 TGGATTCTATAAGGAATTTACAAATTTAACTTTAACCAGTTACTCT
1 TGGATTCTATAAGCAATTTACAAATTTAACTTTAACCAGTAACTCT
5628193 T
1 T
5628194 TTCTTCAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (46 bp):
TGGATTCTATAAGCAATTTACAAATTTAACTTTAACCAGTAACTCT
Found at i:5631700 original size:7 final size:7
Alignment explanation
Indices: 5631690--5631730 Score: 52
Period size: 6 Copynumber: 6.3 Consensus size: 7
5631680 TGCCAAGACT
5631690 AAAGAAA
1 AAAGAAA
5631697 AAAGAAA
1 AAAGAAA
*
5631704 AATG-AA
1 AAAGAAA
5631710 AAA-AAA
1 AAAGAAA
5631716 AAAG-AA
1 AAAGAAA
5631722 AAAGAAA
1 AAAGAAA
5631729 AA
1 AA
5631731 TCCTCCACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 15 0.52
7 14 0.48
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:5631718 original size:19 final size:18
Alignment explanation
Indices: 5631694--5631730 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
5631684 AAGACTAAAG
5631694 AAAAAAGAAAAATGAAAAA
1 AAAAAAGAAAAA-GAAAAA
5631713 AAAAAAGAAAAAGAAAAA
1 AAAAAAGAAAAAGAAAAA
5631731 TCCTCCACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAAAGAAAAAGAAAAA
Found at i:5635527 original size:2 final size:2
Alignment explanation
Indices: 5635520--5635552 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5635510 CATAAGTAAT
5635520 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
5635553 TCTATTCCTT
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:5636025 original size:22 final size:24
Alignment explanation
Indices: 5635984--5636030 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
5635974 CTATTGTCTT
5635984 AATTATATTATTTAATTTATAATAA
1 AATTATATTATTTAATTTAT-ATAA
5636009 AATT-TATT-TTT-ATTTATATAA
1 AATTATATTATTTAATTTATATAA
5636030 A
1 A
5636031 TAATCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 3 0.14
24 4 0.18
25 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTATATTATTTAATTTATATAA
Found at i:5652380 original size:44 final size:44
Alignment explanation
Indices: 5652323--5652408 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
5652313 ATTTATTCTG
* *
5652323 ACTCCTCTTCTGTTTTTTTCCCCCCTAAGAAATCAGGTATTTAA
1 ACTCCTCTTCTGTTGTTTTCCCCCCTAAGAAATCAGGAATTTAA
*
5652367 ACTCCTCTTCTGTTGTTTTCCCCCCTTAGAAATCAGGAATTT
1 ACTCCTCTTCTGTTGTTTTCCCCCCTAAGAAATCAGGAATTT
5652409 CATCCTTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (44 bp):
ACTCCTCTTCTGTTGTTTTCCCCCCTAAGAAATCAGGAATTTAA
Found at i:5668652 original size:21 final size:20
Alignment explanation
Indices: 5668614--5668654 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
5668604 TATCATATTA
*
5668614 AATAAATTTTTATAATTAAT
1 AATAAATTATTATAATTAAT
*
5668634 AATAAATTAATTATTATTAAT
1 AATAAATT-ATTATAATTAAT
5668655 TAAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAAATTATTATAATTAAT
Found at i:5668821 original size:24 final size:23
Alignment explanation
Indices: 5668780--5668847 Score: 55
Period size: 24 Copynumber: 2.8 Consensus size: 23
5668770 ACAAATATTA
*
5668780 TTTTAATAACAAATAATTAATCAAT
1 TTTTAATTA-AAA-AATTAATCAAT
* **
5668805 TTTTAATTATAAAAATTTATTTAT
1 TTTTAATTA-AAAAATTAATCAAT
* *
5668829 TTTAAAATAAAAAATTAAT
1 TTTTAATTAAAAAATTAAT
5668848 TTAACATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 9 0.26
24 15 0.43
25 11 0.31
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTTAATTAAAAAATTAATCAAT
Found at i:5673720 original size:15 final size:16
Alignment explanation
Indices: 5673679--5673732 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
5673669 GATTTAGTCC
*
5673679 ATAAATTAAATAATAAA
1 ATAAATTACATAA-AAA
* * *
5673696 ACATATTACA-AACAA
1 ATAAATTACATAAAAA
5673711 ATAAATTACATAAAAA
1 ATAAATTACATAAAAA
5673727 ATAAAT
1 ATAAAT
5673733 AGCAAATACA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 10 0.34
16 12 0.41
17 7 0.24
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAATTACATAAAAA
Found at i:5673738 original size:27 final size:26
Alignment explanation
Indices: 5673708--5673759 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5673698 ATATTACAAA
5673708 CAAATAAATTACATAAAAAATAAATAG
1 CAAATAAATTAC-TAAAAAATAAATAG
* * *
5673735 CAAATACATTACTCAAATATAAATA
1 CAAATAAATTACTAAAAAATAAATA
5673760 AAATTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.25
Consensus pattern (26 bp):
CAAATAAATTACTAAAAAATAAATAG
Found at i:5680930 original size:63 final size:63
Alignment explanation
Indices: 5680847--5680967 Score: 242
Period size: 63 Copynumber: 1.9 Consensus size: 63
5680837 ACATACATGC
5680847 ATATATATATATATTTGTCTTTTTTAAAGCTATGTTATGTCTCACTAATTCAGTTTAATATGT
1 ATATATATATATATTTGTCTTTTTTAAAGCTATGTTATGTCTCACTAATTCAGTTTAATATGT
5680910 ATATATATATATATTTGTCTTTTTTAAAGCTATGTTATGTCTCACTAATTCAGTTTAA
1 ATATATATATATATTTGTCTTTTTTAAAGCTATGTTATGTCTCACTAATTCAGTTTAA
5680968 CTTAAAAAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (63 bp):
ATATATATATATATTTGTCTTTTTTAAAGCTATGTTATGTCTCACTAATTCAGTTTAATATGT
Found at i:5680967 original size:31 final size:31
Alignment explanation
Indices: 5680869--5680967 Score: 73
Period size: 31 Copynumber: 3.2 Consensus size: 31
5680859 ATTTGTCTTT
5680869 TTTAAAGCTATGTTATGTCTCACTAATTCAG
1 TTTAAAGCTATGTTATGTCTCACTAATTCAG
* * **
5680900 TTT-AA--TATGTATATATAT-A-TATATTTGTCTTT
1 TTTAAAGCTATGT-TATGTCTCACTA-A--T-TC-AG
5680932 TTTAAAGCTATGTTATGTCTCACTAATTCAG
1 TTTAAAGCTATGTTATGTCTCACTAATTCAG
5680963 TTTAA
1 TTTAA
5680968 CTTAAAAAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 22
0.62 0.10 0.28
Matches are distributed among these distances:
27 2 0.04
28 7 0.14
29 5 0.10
30 3 0.06
31 10 0.20
32 5 0.10
33 3 0.06
34 5 0.10
35 7 0.14
36 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.48
Consensus pattern (31 bp):
TTTAAAGCTATGTTATGTCTCACTAATTCAG
Found at i:5684705 original size:2 final size:2
Alignment explanation
Indices: 5684698--5684729 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5684688 TGAGAAATAC
5684698 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
5684730 TCGTTTGCTC
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:5697636 original size:3 final size:3
Alignment explanation
Indices: 5697628--5697654 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5697618 GAGACTAGCT
5697628 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
5697655 GACTGTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:5698239 original size:2 final size:2
Alignment explanation
Indices: 5698232--5698267 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5698222 GATCAACAAT
5698232 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5698268 ACAGCATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5698624 original size:20 final size:20
Alignment explanation
Indices: 5698578--5698631 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
5698568 TATTAACTAT
* *
5698578 AATTAATTTAT-AAACAAAA
1 AATTAATATATAAAACTAAA
5698597 AATT-ATATATAAAACTAAA
1 AATTAATATATAAAACTAAA
*
5698616 ATTTAATAT-TAAAACT
1 AATTAATATATAAAACT
5698632 TATTACTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 5 0.17
19 21 0.70
20 4 0.13
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTAATATATAAAACTAAA
Found at i:5710399 original size:53 final size:53
Alignment explanation
Indices: 5710332--5710437 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
5710322 TCCCATGTAA
* *
5710332 ATCAGAATATATGCTGTGGCATTCATTGTACAAAGAAGCAAGAAGCTTTTGTG
1 ATCAGAATATATGCTGTGGCATTCATTCTACAAAGAAGCAAGAAGCCTTTGTG
* *
5710385 ATCAGTATTTATGCTGTGGCATTCATTCTACAAAGAAGCAAGAAGCCTTTGTG
1 ATCAGAATATATGCTGTGGCATTCATTCTACAAAGAAGCAAGAAGCCTTTGTG
5710438 GTGCCAGCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (53 bp):
ATCAGAATATATGCTGTGGCATTCATTCTACAAAGAAGCAAGAAGCCTTTGTG
Found at i:5731373 original size:30 final size:32
Alignment explanation
Indices: 5731320--5731380 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
5731310 TTTATAATTT
5731320 ATATATGTATTTAAAAATTAAAATAAATTAAA
1 ATATATGTATTTAAAAATTAAAATAAATTAAA
** *
5731352 ATATAT-TATTTATTAA-TAAAATAATTTAA
1 ATATATGTATTTAAAAATTAAAATAAATTAA
5731381 TTTGAGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 12 0.46
31 8 0.31
32 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (32 bp):
ATATATGTATTTAAAAATTAAAATAAATTAAA
Found at i:5740634 original size:3 final size:3
Alignment explanation
Indices: 5740626--5740677 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
5740616 CTAACTCTTG
5740626 CAT CAT CAT CAAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT C-AT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
5740672 CAT CAT
1 CAT CAT
5740678 TATCCGGGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:5750972 original size:2 final size:2
Alignment explanation
Indices: 5750965--5750993 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5750955 AGTATTGGTA
5750965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5750994 AATAGAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5768586 original size:6 final size:6
Alignment explanation
Indices: 5768575--5768602 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5768565 TTTGTGCATT
5768575 AAATCC AAATCC AAATCC AAATCC AAAT
1 AAATCC AAATCC AAATCC AAATCC AAAT
5768603 GCAATTTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATCC
Found at i:5771861 original size:3 final size:3
Alignment explanation
Indices: 5771853--5771893 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
5771843 GTTAATTACA
*
5771853 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5771894 AGAACAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5781467 original size:22 final size:21
Alignment explanation
Indices: 5781430--5781480 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
5781420 TCTTCCTTCT
*
5781430 TTTTTTAAATATATAATAATAA
1 TTTTTTAAATATATAA-AAAAA
5781452 TTTTTTAAAT-TAATAAAAAAA
1 TTTTTTAAATAT-ATAAAAAAA
*
5781473 TATTTTAA
1 TTTTTTAA
5781481 TCTTTTCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTTTAAATATATAAAAAAA
Found at i:5781480 original size:21 final size:22
Alignment explanation
Indices: 5781432--5781480 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5781422 TTCCTTCTTT
* *
5781432 TTTTAAATATATAATAATAATT
1 TTTTAAATATATAATAAAAATA
5781454 TTTTAAAT-TAATAA-AAAAATA
1 TTTTAAATAT-ATAATAAAAATA
5781475 TTTTAA
1 TTTTAA
5781481 TCTTTTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTAAATATATAATAAAAATA
Found at i:5784152 original size:23 final size:23
Alignment explanation
Indices: 5784122--5784167 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5784112 AAGATGCCCT
5784122 GTTTCTCAAATGTTGACAGCAGC
1 GTTTCTCAAATGTTGACAGCAGC
5784145 GTTTCTCAAATGTTGACAGCAGC
1 GTTTCTCAAATGTTGACAGCAGC
5784168 TCCTACTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (23 bp):
GTTTCTCAAATGTTGACAGCAGC
Found at i:5790882 original size:30 final size:29
Alignment explanation
Indices: 5790841--5790911 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
5790831 CATAATACTC
*
5790841 AAATAAGTTTTTAAATTATT-TAAAATATTT
1 AAATAAATTTTT--ATTATTGTAAAATATTT
* *
5790871 AAATAAATTTTTATTTTTGTAATATATTT
1 AAATAAATTTTTATTATTGTAAAATATTT
*
5790900 AATTAAATTTTT
1 AAATAAATTTTT
5790912 TATATTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 5 0.14
29 20 0.56
30 11 0.31
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
AAATAAATTTTTATTATTGTAAAATATTT
Found at i:5791215 original size:22 final size:23
Alignment explanation
Indices: 5791175--5791218 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
5791165 TCTTAAGAGT
5791175 TTATTTGATATAAAAATAAAAAC
1 TTATTTGATATAAAAATAAAAAC
*
5791198 TTATTTGAT-TCAAAATAAAAA
1 TTATTTGATATAAAAATAAAAA
5791219 TATAAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (23 bp):
TTATTTGATATAAAAATAAAAAC
Found at i:5793038 original size:9 final size:9
Alignment explanation
Indices: 5793024--5793051 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5793014 AATGGTATGA
5793024 AAGTAGGCT
1 AAGTAGGCT
5793033 AAGTAGGCT
1 AAGTAGGCT
5793042 AAGTAGGCT
1 AAGTAGGCT
5793051 A
1 A
5793052 CAGCCTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (9 bp):
AAGTAGGCT
Found at i:5794284 original size:2 final size:2
Alignment explanation
Indices: 5794277--5794310 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5794267 CAGTTATGTA
5794277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5794311 GTTGAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5808007 original size:18 final size:18
Alignment explanation
Indices: 5807984--5808021 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
5807974 TATTTTATAA
5807984 TTGATTA-TCTTGTATTAT
1 TTGATTACT-TTGTATTAT
5808002 TTGATTACTTTGTATTAT
1 TTGATTACTTTGTATTAT
5808020 TT
1 TT
5808022 TATCTGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (18 bp):
TTGATTACTTTGTATTAT
Found at i:5809258 original size:16 final size:17
Alignment explanation
Indices: 5809237--5809270 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5809227 CTAATAAGTG
5809237 ATTAATGTAT-ATTAAA
1 ATTAATGTATAATTAAA
*
5809253 ATTAATTTATAATTAAA
1 ATTAATGTATAATTAAA
5809270 A
1 A
5809271 GTTTTATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTAATGTATAATTAAA
Found at i:5811406 original size:15 final size:16
Alignment explanation
Indices: 5811379--5811415 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5811369 TTAAGAAGGT
*
5811379 TTCTT-TTGAATTTGC
1 TTCTTGTTGAATTTAC
5811394 TTCTTGTTG-ATTTAC
1 TTCTTGTTGAATTTAC
5811409 TTCTTGT
1 TTCTTGT
5811416 GCTTGTGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.62
Consensus pattern (16 bp):
TTCTTGTTGAATTTAC
Found at i:5814573 original size:5 final size:5
Alignment explanation
Indices: 5814563--5814589 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5814553 ATTCTTTCTC
5814563 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
5814590 TTGACTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:5817524 original size:6 final size:6
Alignment explanation
Indices: 5817513--5817543 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5817503 AGATGGCAAC
5817513 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT T
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT T
5817544 GGATTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTGAT
Found at i:5828994 original size:8 final size:8
Alignment explanation
Indices: 5828968--5829006 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
5828958 TTGATCTTTC
5828968 AACAAAAA
1 AACAAAAA
*
5828976 AAAAAAAA
1 AACAAAAA
5828984 AACAAAAA
1 AACAAAAA
5828992 AACAAGAAA
1 AACAA-AAA
*
5829001 ATCAAA
1 AACAAA
5829007 GCAATCCACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.03
Consensus pattern (8 bp):
AACAAAAA
Found at i:5875123 original size:230 final size:230
Alignment explanation
Indices: 5874718--5875182 Score: 788
Period size: 230 Copynumber: 2.0 Consensus size: 230
5874708 AATTGATTTA
*
5874718 TGCTTGATATGGCCTGTTTTTAATAGGACTCTATCTGCAGCCCAAGAATGCCTGAATGCATAAAT
1 TGCTTGATATGGCCTGTTTTTAATAGGACTCTATATGCAGCCCAAGAATGCCTGAATGCATAAAT
*
5874783 CTGTTGCTTAACCCAAGCAGAAAAAATTAGGAAATTTTGGTAGCTATCAGAACAGTGGTCATGAT
66 CTGTTGCTTAACCCAAGCAGAAAAAATAAGGAAATTTTGGTAGCTATCAGAACAGTGGTCATGAT
* * *
5874848 TAGAATTATATCTTAAACTTCTCTTATTGGATCTAGGAGGGCCTTTCTCAATGGGACTTCTCTGT
131 TAGAATTATATCTTAAACTTCTCTTATTGGATCTAAGAAGGCCTTTCTCAATGGGAATTCTCTGT
*
5874913 TTCTGTCGCTGTAGT-CCCTGCCATCTAGAGCAATG
196 TTCTGTCGCTCTA-TACCCTGCCATCTAGAGCAATG
* *
5874948 TGCTTGATATGGCCTGTTTTTAATAGGACTCTATATGCTGTCCAAGAATGCCTGAATGCATAAAT
1 TGCTTGATATGGCCTGTTTTTAATAGGACTCTATATGCAGCCCAAGAATGCCTGAATGCATAAAT
* * * * *
5875013 CTGTTGCTTTACTCGAGCAGAAGAAATAAGGAAATTTTGGTAGCTATCAGAGCAGTGGTCATGAT
66 CTGTTGCTTAACCCAAGCAGAAAAAATAAGGAAATTTTGGTAGCTATCAGAACAGTGGTCATGAT
5875078 TAGAATTATATCTTAAACTTCTCTTATTGGATCTAAGAAGGCCTTTCTCAATGGGAATTCTCTGT
131 TAGAATTATATCTTAAACTTCTCTTATTGGATCTAAGAAGGCCTTTCTCAATGGGAATTCTCTGT
*
5875143 TTCTGTCGCTCTATATCCTGCCATCTAGAGCAATG
196 TTCTGTCGCTCTATACCCTGCCATCTAGAGCAATG
5875178 TGCTT
1 TGCTT
5875183 TGGATAGTTA
Statistics
Matches: 220, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
229 1 0.00
230 219 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (230 bp):
TGCTTGATATGGCCTGTTTTTAATAGGACTCTATATGCAGCCCAAGAATGCCTGAATGCATAAAT
CTGTTGCTTAACCCAAGCAGAAAAAATAAGGAAATTTTGGTAGCTATCAGAACAGTGGTCATGAT
TAGAATTATATCTTAAACTTCTCTTATTGGATCTAAGAAGGCCTTTCTCAATGGGAATTCTCTGT
TTCTGTCGCTCTATACCCTGCCATCTAGAGCAATG
Found at i:5876690 original size:4 final size:4
Alignment explanation
Indices: 5876681--5876705 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5876671 CTTGTTTTCT
5876681 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
5876706 CTGTATAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5876955 original size:15 final size:15
Alignment explanation
Indices: 5876932--5876970 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5876922 AAAAAAACAA
*
5876932 AAAACAAAAATTAAAG
1 AAAA-AAAAATGAAAG
5876948 AAAAAAAAATGAAAG
1 AAAAAAAAATGAAAG
5876963 AGAAAAAA
1 A-AAAAAA
5876971 GAGCCAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.79, C:0.03, G:0.10, T:0.08
Consensus pattern (15 bp):
AAAAAAAAATGAAAG
Done.