Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 150 of 187
Found at i:44671768 original size:11 final size:11
Alignment explanation
Indices: 44671720--44671770 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
44671710 AGAATAAAAA
44671720 TTAAATTTATT
1 TTAAATTTATT
*
44671731 TTAAAATTATT
1 TTAAATTTATT
*
44671742 ATTTAA-TTA-T
1 -TTAAATTTATT
44671752 TTAAATTTATT
1 TTAAATTTATT
44671763 TTAAATTT
1 TTAAATTT
44671771 GGAATTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 22 0.65
12 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:44671786 original size:31 final size:32
Alignment explanation
Indices: 44671720--44671795 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
44671710 AGAATAAAAA
**
44671720 TTAAATTTATTTTAAAATTATTATTTAATTAT
1 TTAAATTTATTTTAAAATTAGAATTTAATTAT
* * *
44671752 TTAAATTTATTTTAAATTTGGAATTT-ATTTT
1 TTAAATTTATTTTAAAATTAGAATTTAATTAT
*
44671783 TTAAA-ATATTTTA
1 TTAAATTTATTTTA
44671796 TATTATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 7 0.18
31 9 0.24
32 22 0.58
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (32 bp):
TTAAATTTATTTTAAAATTAGAATTTAATTAT
Found at i:44674606 original size:25 final size:26
Alignment explanation
Indices: 44674568--44674636 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
44674558 AAGTTCAAGC
*
44674568 GAGCCA-T-ATCAGGAAGCTC-CAGA
1 GAGCCATTAATCAGGAAGCTCACAAA
*
44674591 GAGCCATTAATCAGGAAACTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
*
44674617 GAGCCTTTAATCAGGAAGCT
1 GAGCCATTAATCAGGAAGCT
44674637 TATGAAGAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
23 6 0.15
24 1 0.03
25 11 0.28
26 21 0.54
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACAAA
Found at i:44674791 original size:25 final size:25
Alignment explanation
Indices: 44674737--44674793 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
44674727 CTATTATCGG
*
44674737 GAAGCT-AGCAAGAACCATATAATA
1 GAAGCTCAGCAAGAACCATATAAGA
44674761 GAAAGCTCA-CAAGAACCATATAACGA
1 G-AAGCTCAGCAAGAACCATATAA-GA
44674787 GAAGCTC
1 GAAGCTC
44674794 GAGTGGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.03
25 25 0.86
26 3 0.10
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (25 bp):
GAAGCTCAGCAAGAACCATATAAGA
Found at i:44675118 original size:5 final size:5
Alignment explanation
Indices: 44675089--44675127 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
44675079 TAAATTTAGC
* *
44675089 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
44675128 CATCTTAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:44678356 original size:18 final size:18
Alignment explanation
Indices: 44678333--44678369 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
44678323 AATTTTTTAT
44678333 TATCAAATTCTCTATTGA
1 TATCAAATTCTCTATTGA
44678351 TATCAAATTCTCTATTGA
1 TATCAAATTCTCTATTGA
44678369 T
1 T
44678370 CCACATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (18 bp):
TATCAAATTCTCTATTGA
Found at i:44683507 original size:18 final size:17
Alignment explanation
Indices: 44683477--44683511 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44683467 AAGAAATTTT
44683477 TAAAAATTCTAAAAATA
1 TAAAAATTCTAAAAATA
*
44683494 TAAAAATATTTAAAAATA
1 TAAAAAT-TCTAAAAATA
44683512 CATAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAATTCTAAAAATA
Found at i:44691105 original size:42 final size:43
Alignment explanation
Indices: 44691037--44691119 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
44691027 TTTTACATGT
*
44691037 AATCAAATAACGATGACACTGTCCCAAACAAGGTCTTACACGA
1 AATCAAATAACGATGACAATGTCCCAAACAAGGTCTTACACGA
* * *
44691080 AATCATAT-ACGATGCCAATGTCCCAAACATGGTCTTACAC
1 AATCAAATAACGATGACAATGTCCCAAACAAGGTCTTACAC
44691120 ATAAATCTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 29 0.81
43 7 0.19
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.22
Consensus pattern (43 bp):
AATCAAATAACGATGACAATGTCCCAAACAAGGTCTTACACGA
Found at i:44705608 original size:13 final size:13
Alignment explanation
Indices: 44705590--44705651 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
44705580 AACATGGAGT
44705590 TAAGTGGTACCGC
1 TAAGTGGTACCGC
* *
44705603 TAAGTGTTACCTC
1 TAAGTGGTACCGC
* **
44705616 TAAGTGATACCAT
1 TAAGTGGTACCGC
*
44705629 TAAGTGGTATCG-
1 TAAGTGGTACCGC
44705641 TAAGGTGGTAC
1 TAA-GTGGTAC
44705652 TGCGAACTGA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
12 3 0.08
13 36 0.92
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (13 bp):
TAAGTGGTACCGC
Found at i:44718545 original size:20 final size:20
Alignment explanation
Indices: 44718517--44718555 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44718507 TTAAATTCAA
*
44718517 TAATGTTAAATTTAATTTTTT
1 TAATGTTAAAATT-ATTTTTT
44718538 TAAT-TTAAAATTATTTTT
1 TAATGTTAAAATTATTTTT
44718556 ATTGTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TAATGTTAAAATTATTTTTT
Found at i:44719310 original size:19 final size:19
Alignment explanation
Indices: 44719286--44719341 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
44719276 CATAATGCAA
44719286 ATTTAATATATATTTTATT
1 ATTTAATATATATTTTATT
* * *
44719305 ATTTAATATAAAATATATT
1 ATTTAATATATATTTTATT
* *
44719324 ATTTATTATTTATTTTAT
1 ATTTAATATATATTTTAT
44719342 GTATATAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTAATATATATTTTATT
Found at i:44725260 original size:16 final size:16
Alignment explanation
Indices: 44725229--44725265 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
44725219 ATGTGAAGAA
44725229 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
44725245 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
44725261 TATTA
1 TATTA
44725266 AAATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:44725320 original size:28 final size:29
Alignment explanation
Indices: 44725279--44725338 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
44725269 TAAATTTAGA
44725279 ATATTAAATAATTTATTAAATAAAAAATT
1 ATATTAAATAATTTATTAAATAAAAAATT
* * *
44725308 ATATT-AATAATTTATTATATGAATAATT
1 ATATTAAATAATTTATTAAATAAAAAATT
44725336 ATA
1 ATA
44725339 ATATTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
ATATTAAATAATTTATTAAATAAAAAATT
Found at i:44725324 original size:16 final size:16
Alignment explanation
Indices: 44725305--44725335 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44725295 TAAATAAAAA
*
44725305 ATTATATTAATAATTT
1 ATTATATGAATAATTT
44725321 ATTATATGAATAATT
1 ATTATATGAATAATT
44725336 ATAATATTTT
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATTATATGAATAATTT
Found at i:44725362 original size:22 final size:22
Alignment explanation
Indices: 44725314--44725367 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
44725304 AATTATATTA
44725314 ATAAT-TTATTATATGAATAATT
1 ATAATATT-TTATATGAATAATT
* *
44725336 ATAATATTTTATATTAATATTT
1 ATAATATTTTATATGAATAATT
*
44725358 TTAATATTTT
1 ATAATATTTT
44725368 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATAATATTTTATATGAATAATT
Found at i:44741196 original size:60 final size:60
Alignment explanation
Indices: 44741072--44741273 Score: 189
Period size: 60 Copynumber: 3.4 Consensus size: 60
44741062 TAGGCCATCT
* * *
44741072 TAAATCTTATTTGAAACAC-CCAGCAGATA-CCA-AGGTCAGCCAAACC-AATAAGCAGTCC
1 TAAATCTTACTTGAAACTCTCAAGCAGATAGCCACA--TCAGCCAAACCTAATAAGCAGTCC
* * * * *
44741130 TAAATCTTACTTGAAACTCTCAAGCATATATCCACATCAGCCAAGCCTAATAAGCACTCG
1 TAAATCTTACTTGAAACTCTCAAGCAGATAGCCACATCAGCCAAACCTAATAAGCAGTCC
* * * * *
44741190 TAAATCTTCCTTGAGA-TGGTCATGCAGATAGCCACATCAGCCAAACATAATAAGCAGTCC
1 TAAATCTTACTTGAAACT-CTCAAGCAGATAGCCACATCAGCCAAACCTAATAAGCAGTCC
* ** *
44741250 TAAAACAAACTTGTAACTCTCAAG
1 TAAATCTTACTTGAAACTCTCAAG
44741274 TAGACATGAA
Statistics
Matches: 113, Mismatches: 25, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
58 17 0.15
59 19 0.17
60 75 0.66
61 2 0.02
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (60 bp):
TAAATCTTACTTGAAACTCTCAAGCAGATAGCCACATCAGCCAAACCTAATAAGCAGTCC
Found at i:44755658 original size:31 final size:31
Alignment explanation
Indices: 44755623--44755690 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
44755613 AAAAATACTC
44755623 AATAGCTC-AATAACTTAAATAAAAACTTTTG
1 AATAG-TCAAATAACTTAAATAAAAACTTTTG
* * *
44755654 AATAGTCAAATGAGTTAAATGAAAACTTTTG
1 AATAGTCAAATAACTTAAATAAAAACTTTTG
44755685 AATAGT
1 AATAGT
44755691 TCAGTAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (31 bp):
AATAGTCAAATAACTTAAATAAAAACTTTTG
Found at i:44760864 original size:27 final size:27
Alignment explanation
Indices: 44760789--44760867 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
44760779 GGGGCTGAAG
* *
44760789 GTGGTGCCAATGAGAATGGTGACACCA
1 GTGGTGCCAATGAGAATGGCGGCACCA
44760816 GTGGTGCCAATGAGAATGGCGGCACCA
1 GTGGTGCCAATGAGAATGGCGGCACCA
44760843 GTGGTGCCAATGAGAATGGCGGCAC
1 GTGGTGCCAATGAGAATGGCGGCAC
44760868 AGGACTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.27, C:0.20, G:0.37, T:0.16
Consensus pattern (27 bp):
GTGGTGCCAATGAGAATGGCGGCACCA
Found at i:44764194 original size:20 final size:21
Alignment explanation
Indices: 44764171--44764210 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44764161 GGGTTCATCA
44764171 AATATA-TACTTTAAATATAT
1 AATATATTACTTTAAATATAT
*
44764191 AATATATTATTTTAAATATA
1 AATATATTACTTTAAATATA
44764211 ATATAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATATTACTTTAAATATAT
Found at i:44764213 original size:5 final size:5
Alignment explanation
Indices: 44764187--44764254 Score: 102
Period size: 5 Copynumber: 13.8 Consensus size: 5
44764177 TACTTTAAAT
* * *
44764187 ATATA ATATA TTATT TTA-A ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
44764236 ATATA ATATA ATATA ATAT
1 ATATA ATATA ATATA ATAT
44764255 TTTATTTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
4 2 0.03
5 56 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
ATATA
Found at i:44766333 original size:3 final size:3
Alignment explanation
Indices: 44766327--44766379 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
44766317 TTTTTTAATG
* * *
44766327 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTG CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44766375 -TA TTA
1 TTA TTA
44766380 ATATAATTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:44772172 original size:2 final size:2
Alignment explanation
Indices: 44772165--44772192 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44772155 GGCCAAGTGA
44772165 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
44772193 TTACAAAAAG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44776465 original size:99 final size:97
Alignment explanation
Indices: 44776294--44776523 Score: 293
Period size: 99 Copynumber: 2.4 Consensus size: 97
44776284 TCAGCTGACC
* * * * * *
44776294 TGGGAACAGATCCATCTTCTT-TAGGGAAAACCTCTATTTTGGGTGCAAACATATCATTCGTACT
1 TGGGAACAGATCCATCTTCTTCAATGAAAAACCTCTATTTCGGGTGCAAACATATCAATCGTACA
* * *
44776358 GCAGTCAGCTGAGCCAGAGGTTGACGACGACT
66 GCAATCAGCTGAGCCAGAAGTTGAAGACGACT
* * *
44776390 TGGGAACAGATCCATCTTCTTCAATGAAAAACTCCTCTATTTCGGTTGGAACCATATCAATCGTA
1 TGGGAACAGATCCATCTTCTTCAATGAAAAA--CCTCTATTTCGGGTGCAAACATATCAATCGTA
* *
44776455 CAGCAATCAGCTGAGCCAGAATTTGAAGACGATT
64 CAGCAATCAGCTGAGCCAGAAGTTGAAGACGACT
*
44776489 TGGGAACAGATCCATCTTCTTCAATG-GAAACCTCT
1 TGGGAACAGATCCATCTTCTTCAATGAAAAACCTCT
44776524 TCCCTTTCGG
Statistics
Matches: 116, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
96 26 0.22
97 6 0.05
98 3 0.03
99 81 0.70
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (97 bp):
TGGGAACAGATCCATCTTCTTCAATGAAAAACCTCTATTTCGGGTGCAAACATATCAATCGTACA
GCAATCAGCTGAGCCAGAAGTTGAAGACGACT
Found at i:44784046 original size:23 final size:26
Alignment explanation
Indices: 44784018--44784078 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
44784008 ATCAGCTCTT
44784018 ATGAGCTTACCG-T-TTCAGCTC-G-
1 ATGAGCTTACCGTTCTTCAGCTCGGA
*
44784040 ATAGAGCTTATCGTTCTTCAGCTCGGA
1 AT-GAGCTTACCGTTCTTCAGCTCGGA
44784067 ATGAGCTTACCG
1 ATGAGCTTACCG
44784079 ATCATGGCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 2 0.06
23 9 0.28
24 1 0.03
25 8 0.25
26 10 0.31
27 2 0.06
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (26 bp):
ATGAGCTTACCGTTCTTCAGCTCGGA
Found at i:44796714 original size:19 final size:20
Alignment explanation
Indices: 44796690--44796738 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
44796680 GTGAACTGTT
*
44796690 GTATCAGTACC-A-AAGTAA
1 GTATCAGTACCTATAAGGAA
*
44796708 GGTATCAATACCTATAAGGAA
1 -GTATCAGTACCTATAAGGAA
44796729 GTATCAGTAC
1 GTATCAGTAC
44796739 ATTGATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 10 0.40
20 10 0.40
21 5 0.20
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (20 bp):
GTATCAGTACCTATAAGGAA
Found at i:44799023 original size:9 final size:9
Alignment explanation
Indices: 44799005--44799053 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
44798995 TTTGGTTAAA
44799005 AATTAACCG
1 AATTAACCG
*
44799014 AATTACCCG
1 AATTAACCG
44799023 AATTAACCG
1 AATTAACCG
*
44799032 AATTACCCG
1 AATTAACCG
*
44799041 AATTAACCA
1 AATTAACCG
44799050 AATT
1 AATT
44799054 GAATCACTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:44799028 original size:18 final size:18
Alignment explanation
Indices: 44799005--44799053 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
44798995 TTTGGTTAAA
44799005 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
44799023 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
44799041 AATTAACCAAATT
1 AATTAACCGAATT
44799054 GAATCACTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:44801941 original size:112 final size:113
Alignment explanation
Indices: 44801755--44802040 Score: 326
Period size: 112 Copynumber: 2.5 Consensus size: 113
44801745 ATTTTTCAAT
* * * * * * * *
44801755 AGCATAATAATGCTTACTTTGAGACACTGAAGCAACACTTTAATTTAATTTAGGACAGCAT-AAT
1 AGCATAAAAATGCTCAATTTGAAACACTAAAACAACACTTTAATTCAATTTATGACAGCATGAAT
* * * *
44801819 AATACCCAATTTAAAACA-TTAAACAGGAGCTTAATTTAATTTAAGAT
66 AATACCCAATTTAAAACACTAAAACAGCAGCTTAATTCAATTTAAGAC
* * *
44801866 AGCATAAAAATGCTCAATTTGATAGACTAAAACACCAACTTTAATTCAATTTATGACAGCATGAA
1 AGCATAAAAATGCTCAATTTGAAACACTAAAACAAC-ACTTTAATTCAATTTATGACAGCATGAA
* * * * *
44801931 -AATGCTCAATTTGAAACACTAAAATAGCAGCTTGATTCAATTTAAGAC
65 TAATACCCAATTTAAAACACTAAAACAGCAGCTTAATTCAATTTAAGAC
* * * *
44801979 AGTATGAAAATGCTCAATTTGAAACACTCAAACAACAGTTTAATTCAATTTATGACAGCATG
1 AGCATAAAAATGCTCAATTTGAAACACTAAAACAACACTTTAATTCAATTTATGACAGCATG
44802041 CAAACAGTAA
Statistics
Matches: 146, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
111 28 0.19
112 63 0.43
113 55 0.38
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.30
Consensus pattern (113 bp):
AGCATAAAAATGCTCAATTTGAAACACTAAAACAACACTTTAATTCAATTTATGACAGCATGAAT
AATACCCAATTTAAAACACTAAAACAGCAGCTTAATTCAATTTAAGAC
Found at i:44801989 original size:56 final size:56
Alignment explanation
Indices: 44801755--44802040 Score: 256
Period size: 56 Copynumber: 5.1 Consensus size: 56
44801745 ATTTTTCAAT
* * * * * * *
44801755 AGCAT-AATAATGCTTACTTTGAGACACTGAAGCAACA-CTTTAATTTAATTTAGGAC
1 AGCATGAA-AATGCTCAATTTGAAACACTAAAACAACAGC-TTAATTCAATTTAAGAC
* * * * ** * *
44801811 AGCAT-AATAATACCCAATTTAAAACA-TTAAACAGGAGCTTAATTTAATTTAAGAT
1 AGCATGAA-AATGCTCAATTTGAAACACTAAAACAACAGCTTAATTCAATTTAAGAC
* * * * * *
44801866 AGCATAAAAATGCTCAATTTGATAGACTAAAACACCAACTTTAATTCAATTTATGAC
1 AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAGC-TTAATTCAATTTAAGAC
* * *
44801923 AGCATGAAAATGCTCAATTTGAAACACTAAAATAGCAGCTTGATTCAATTTAAGAC
1 AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAGCTTAATTCAATTTAAGAC
* * * *
44801979 AGTATGAAAATGCTCAATTTGAAACACTCAAACAACAGTTTAATTCAATTTATGAC
1 AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAGCTTAATTCAATTTAAGAC
44802035 AGCATG
1 AGCATG
44802041 CAAACAGTAA
Statistics
Matches: 186, Mismatches: 40, Indels: 8
0.79 0.17 0.03
Matches are distributed among these distances:
55 39 0.21
56 100 0.54
57 47 0.25
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.30
Consensus pattern (56 bp):
AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAGCTTAATTCAATTTAAGAC
Found at i:44802788 original size:6 final size:6
Alignment explanation
Indices: 44802777--44802805 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
44802767 ACTTTTAGAC
44802777 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
44802806 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:44802829 original size:20 final size:20
Alignment explanation
Indices: 44802762--44802818 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
44802752 CACTGTTGAG
* *
44802762 TTTAGACTTTTAGACTTTAGT
1 TTTAGAATTTTAG-TTTTAGT
44802783 TTTAG--TTTTAGTTTTAGT
1 TTTAGAATTTTAGTTTTAGT
*
44802801 TTTAGAATTTTATTTTTA
1 TTTAGAATTTTAGTTTTA
44802819 TTTATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 11 0.34
19 6 0.19
20 10 0.31
21 5 0.16
ACGTcount: A:0.23, C:0.04, G:0.12, T:0.61
Consensus pattern (20 bp):
TTTAGAATTTTAGTTTTAGT
Found at i:44805031 original size:21 final size:21
Alignment explanation
Indices: 44804989--44805033 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
44804979 ATTAATCACT
* *
44804989 TTTTTATTTTGTTTTTGGATA
1 TTTTTATTTTGTCTGTGGATA
44805010 TTTTTATTTT-TCTGTGGCATA
1 TTTTTATTTTGTCTGTGG-ATA
44805031 TTT
1 TTT
44805034 GTTTTCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.13, C:0.04, G:0.13, T:0.69
Consensus pattern (21 bp):
TTTTTATTTTGTCTGTGGATA
Found at i:44805273 original size:18 final size:17
Alignment explanation
Indices: 44805239--44805284 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
44805229 AGGTTTTATG
44805239 TGTGTTTA-TTT-TTCT
1 TGTGTTTATTTTATTCT
*
44805254 TGTTTTTATGTTTATTCT
1 TGTGTTTAT-TTTATTCT
44805272 TGTGTTTATTTTA
1 TGTGTTTATTTTA
44805285 GTTTTTATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 7 0.27
17 7 0.27
18 12 0.46
ACGTcount: A:0.11, C:0.04, G:0.13, T:0.72
Consensus pattern (17 bp):
TGTGTTTATTTTATTCT
Found at i:44825826 original size:17 final size:18
Alignment explanation
Indices: 44825794--44825827 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44825784 TAAAAAAGAA
*
44825794 TTCTATCCTCATTTTTTT
1 TTCTATACTCATTTTTTT
44825812 TTCTATACT-ATTTTTT
1 TTCTATACTCATTTTTT
44825828 GGTAGAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (18 bp):
TTCTATACTCATTTTTTT
Found at i:44826226 original size:18 final size:17
Alignment explanation
Indices: 44826195--44826229 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
44826185 GGTTTAGGGT
44826195 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
44826212 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
44826230 AAATCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:44826379 original size:31 final size:29
Alignment explanation
Indices: 44826344--44826403 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
44826334 TGATCACTTC
44826344 GTAACAAAATGATAACATAAGTGACTAAAAT
1 GTAACAAAATG--AACATAAGTGACTAAAAT
***
44826375 GTAACATTTTGAACATAAGTGACTAAAAT
1 GTAACAAAATGAACATAAGTGACTAAAAT
44826404 ATAATTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 18 0.69
31 8 0.31
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (29 bp):
GTAACAAAATGAACATAAGTGACTAAAAT
Found at i:44827946 original size:17 final size:18
Alignment explanation
Indices: 44827913--44827949 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
44827903 ATATGGCATA
*
44827913 CCTGTGTGGGCCTACACG
1 CCTGTGTGGGCCCACACG
44827931 CCTGTGT-GGCCCACACG
1 CCTGTGTGGGCCCACACG
44827948 CC
1 CC
44827950 CTACTTAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.11, C:0.41, G:0.30, T:0.19
Consensus pattern (18 bp):
CCTGTGTGGGCCCACACG
Found at i:44828618 original size:6 final size:6
Alignment explanation
Indices: 44828607--44828646 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
44828597 AAATTTTGGG
44828607 AAAAAT AAAAAT AAAAAT AAAAAT AGAAAAT -AAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAA
44828647 TCTATTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.16
6 22 0.69
7 5 0.16
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:44832701 original size:43 final size:44
Alignment explanation
Indices: 44832653--44832744 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 44
44832643 GTGTTTTCCC
* * *
44832653 ACAAACACCGCTATAGAACATGATATTTAGCGGTGCTTTTA-CT
1 ACAAACACCGCTAAAGAACATGATATTTAGCAGCGCTTTTAGCT
* * * *
44832696 ACAAACGCCGCTAAAGAACATGGTCTTTTGCAGCGCTTTTAGCT
1 ACAAACACCGCTAAAGAACATGATATTTAGCAGCGCTTTTAGCT
44832740 ACAAA
1 ACAAA
44832745 TGCCACAACA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 34 0.83
44 7 0.17
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (44 bp):
ACAAACACCGCTAAAGAACATGATATTTAGCAGCGCTTTTAGCT
Found at i:44836277 original size:2 final size:2
Alignment explanation
Indices: 44836270--44836297 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44836260 TGGGGTTAAC
44836270 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
44836298 CAGAATCGAA
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:44838194 original size:18 final size:17
Alignment explanation
Indices: 44838167--44838200 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
44838157 CTTATTCAAC
*
44838167 TAAAATTTTATTTTTGG
1 TAAAATTTTATATTTGG
44838184 TAAATATTTTATATTTG
1 TAAA-ATTTTATATTTG
44838201 AAATTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
TAAAATTTTATATTTGG
Found at i:44845193 original size:16 final size:17
Alignment explanation
Indices: 44845160--44845193 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44845150 TGAAAATCTC
* *
44845160 AGTGGTTTTTGGGAAAA
1 AGTGATTTTTGAGAAAA
44845177 AGTGATTTTTGAGAAAA
1 AGTGATTTTTGAGAAAA
44845194 TTAATTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (17 bp):
AGTGATTTTTGAGAAAA
Found at i:44852629 original size:98 final size:98
Alignment explanation
Indices: 44852476--44852679 Score: 338
Period size: 98 Copynumber: 2.1 Consensus size: 98
44852466 ATTCAACACT
* * * *
44852476 ATATTATATATTTAACGCAAGTAGATATTCAAGTCTAAAAAAAATCATTTTTTAATGTATATCCA
1 ATATTATATATTTAACGCAAATAGATATCCAACTCTAAAAAAAATCAATTTTTAATGTATATCCA
44852541 ATACTACTATAAAAATATAAATGTCATAAACTA
66 ATACTACTATAAAAATATAAATGTCATAAACTA
* **
44852574 ATATTATATATTTAACGCAAATAGATATCCAACTCTAATAAATCTCAATTTTTAATGTATATCCA
1 ATATTATATATTTAACGCAAATAGATATCCAACTCTAAAAAAAATCAATTTTTAATGTATATCCA
44852639 ATACTACTATAAAAATATAAATGTCATAAACTA
66 ATACTACTATAAAAATATAAATGTCATAAACTA
44852672 ATA-TATAT
1 ATATTATAT
44852680 TCAATAATAA
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
97 5 0.05
98 94 0.95
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (98 bp):
ATATTATATATTTAACGCAAATAGATATCCAACTCTAAAAAAAATCAATTTTTAATGTATATCCA
ATACTACTATAAAAATATAAATGTCATAAACTA
Found at i:44855867 original size:15 final size:16
Alignment explanation
Indices: 44855831--44855867 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
44855821 GAATTTTAAA
*
44855831 TTTTTTGGGTTTGTAT
1 TTTTTTAGGTTTGTAT
44855847 TTTTTTAGGTTTG-AT
1 TTTTTTAGGTTTGTAT
44855862 TTTTTT
1 TTTTTT
44855868 CAGGCTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.08, C:0.00, G:0.19, T:0.73
Consensus pattern (16 bp):
TTTTTTAGGTTTGTAT
Found at i:44857208 original size:5 final size:5
Alignment explanation
Indices: 44857198--44857223 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44857188 TGAGCATTCG
44857198 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
44857224 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:44858253 original size:9 final size:9
Alignment explanation
Indices: 44858239--44858275 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44858229 TATAGTTTGA
44858239 TATTCGAAT
1 TATTCGAAT
44858248 TATTCGAAT
1 TATTCGAAT
*
44858257 TATTCGAGT
1 TATTCGAAT
44858266 TATTCGAAT
1 TATTCGAAT
44858275 T
1 T
44858276 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:44858319 original size:11 final size:11
Alignment explanation
Indices: 44858305--44858337 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
44858295 GAACTCGAAA
44858305 TTCGATTTTTT
1 TTCGATTTTTT
44858316 TTCGATTTTTT
1 TTCGATTTTTT
44858327 TTCGATTTTTT
1 TTCGATTTTTT
44858338 CGAGTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.73
Consensus pattern (11 bp):
TTCGATTTTTT
Found at i:44861581 original size:62 final size:62
Alignment explanation
Indices: 44861484--44861608 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
44861474 TTGGCATTAA
* * * *
44861484 TAGGTCACCAACCACATCTGTGGCCTCTCGTTGCTAGGTAAAAATAAAATACAATTTTAGCT
1 TAGGTCACCAACCACATCTATGGCCACTCGTTGCTAAGAAAAAATAAAATACAATTTTAGCT
44861546 TAGGTCACCAACCACATCTATGGCCACTCGTTGCTAAGAAAAAATAAAATACAATTTTAGCT
1 TAGGTCACCAACCACATCTATGGCCACTCGTTGCTAAGAAAAAATAAAATACAATTTTAGCT
44861608 T
1 T
44861609 GCCACACTGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (62 bp):
TAGGTCACCAACCACATCTATGGCCACTCGTTGCTAAGAAAAAATAAAATACAATTTTAGCT
Found at i:44862682 original size:19 final size:19
Alignment explanation
Indices: 44862658--44862707 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
44862648 CGATTGCTGA
*
44862658 AGTCCCACGTTGTCGGGGG
1 AGTCCCACGTTGTCAGGGG
*
44862677 AGTCCCAAGTTGTCAGGGG
1 AGTCCCACGTTGTCAGGGG
44862696 AGTCCCAACGTT
1 AGTCCC-ACGTT
44862708 ACACCCCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.22
Consensus pattern (19 bp):
AGTCCCACGTTGTCAGGGG
Found at i:44867452 original size:370 final size:371
Alignment explanation
Indices: 44866731--44867828 Score: 2048
Period size: 370 Copynumber: 3.0 Consensus size: 371
44866721 CATGTGATGG
* *
44866731 TCATCAACGAGCTAACAAATGTCACAATATATTCTGATTTTTTTTTTGAACTCATGCACTTTGTA
1 TCATCAACGAGCCAACAAATGTCACAATATATTCT-AATTTTTTTTT-AACTCATGCACTTTGTA
44866796 ACTATACACTTGCTTATCTATATTGACCTTTTCTACAATATACTGTTTGAAATGAATTAACTCAT
64 ACTATACACTTGCTTATCTATATTGACCTTTTCTACAATATACTGTTTGAAATGAATTAACTCAT
*
44866861 CTTGAAATTTTTTGAAGATTTTTCTTGTGTAAACATTTGATGCTTTTTTCTCCATTGGGTATAAT
129 CTTGAAATTTTTTGAAGATTTTTCTTGTGTAAACATCTGATGCTTTTTTCTCCATTGGGTATAAT
44866926 GAGTTAAAAATTATCTTTGAATTCATTGTTTTGAAATTCTTCCCTCTTTCTTTGTTGTATCTTAC
194 GAGTTAAAAATTATCTTTGAATTCATTGTTTTGAAATTCTTCCCTCTTTCTTTGTTGTATCTTAC
* *
44866991 GTCAAAGGACTTGTCATATTGAATTACAAACTTACTCATTGATGTGCTCGAGTTGAGAAAATCCT
259 GTCAAGGGCCTTGTCATATTGAATTACAAACTTACTCATTGATGTGCTCGAGTTGAGAAAATCCT
*
44867056 TGAAATATTTGTTCATCCTTTCACTTCTTTAAGTAGTGAAATATTTGT
324 TGAAATATTTGTTCATCCTTTCACTTCTTTAAGTAGTGAAACATTTGT
*
44867104 TTATCAACGAGCCAACAAATGTCACAATATATTCTAATTTTTTTTTAACTCATGCACTTTGTAAC
1 TCATCAACGAGCCAACAAATGTCACAATATATTCTAATTTTTTTTTAACTCATGCACTTTGTAAC
44867169 TATACACTTGCTTATCTATATTGACCTTTTCTACAATATACTGTTTGAAATGAATTAACTCATCT
66 TATACACTTGCTTATCTATATTGACCTTTTCTACAATATACTGTTTGAAATGAATTAACTCATCT
44867234 T-AAATTTTTTGAAGATTTTTCTTGTGTAAACATCTGATGCTTTTTTCTCCATTGGGTATAATGA
131 TGAAATTTTTTGAAGATTTTTCTTGTGTAAACATCTGATGCTTTTTTCTCCATTGGGTATAATGA
44867298 GTTAAAAATTATCTTTGAATTCATTGTTTTGAAATTCTTCCCTCTTTCTTTGTTGTATCTTACGT
196 GTTAAAAATTATCTTTGAATTCATTGTTTTGAAATTCTTCCCTCTTTCTTTGTTGTATCTTACGT
*
44867363 CAAGGGCCTTGTCATATTGAAATACAAACTTACTCATTGATGTGCTCGAGTTGAGAAAATCCTTG
261 CAAGGGCCTTGTCATATTGAATTACAAACTTACTCATTGATGTGCTCGAGTTGAGAAAATCCTTG
44867428 AAATATTTGTTCATCCTTTCACTTCTTTAAGTAGTGAAACATTTGT
326 AAATATTTGTTCATCCTTTCACTTCTTTAAGTAGTGAAACATTTGT
*
44867474 TCATCAACGAGCCAACAAATGTCACAATATATTCTAA--TTTTTTTAACTCACGCACTTTGTAAC
1 TCATCAACGAGCCAACAAATGTCACAATATATTCTAATTTTTTTTTAACTCATGCACTTTGTAAC
44867537 TATACACTTGCTTATCTATATTGACCTTTTCTACAATATACTGTTTGAAATGAATTAACTCATCT
66 TATACACTTGCTTATCTATATTGACCTTTTCTACAATATACTGTTTGAAATGAATTAACTCATCT
44867602 TGAAATTTTTTGAAGATTTTTCTTGTGTAAACATCTGATGCTTTTTTCTCCATTGGGTATAATGA
131 TGAAATTTTTTGAAGATTTTTCTTGTGTAAACATCTGATGCTTTTTTCTCCATTGGGTATAATGA
44867667 GTTAAAAATTATCTTTGAATTCATTGTTTTGAAATTC-T---TCTTTCTTTGTTGTATCTTACGT
196 GTTAAAAATTATCTTTGAATTCATTGTTTTGAAATTCTTCCCTCTTTCTTTGTTGTATCTTACGT
44867728 CAAGGGCCTTGTCATATTGAATTACAAACTTACTCATTGATGTGCTCGAGTTGAGAAAATCCTTG
261 CAAGGGCCTTGTCATATTGAATTACAAACTTACTCATTGATGTGCTCGAGTTGAGAAAATCCTTG
44867793 AAATATTTGTTCATCCTTTCACTTCTTTAAGTAGTG
326 AAATATTTGTTCATCCTTTCACTTCTTTAAGTAGTG
44867829 GACATTCCAG
Statistics
Matches: 713, Mismatches: 11, Indels: 10
0.97 0.01 0.01
Matches are distributed among these distances:
365 123 0.17
368 92 0.13
369 100 0.14
370 270 0.38
371 85 0.12
372 10 0.01
373 33 0.05
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (371 bp):
TCATCAACGAGCCAACAAATGTCACAATATATTCTAATTTTTTTTTAACTCATGCACTTTGTAAC
TATACACTTGCTTATCTATATTGACCTTTTCTACAATATACTGTTTGAAATGAATTAACTCATCT
TGAAATTTTTTGAAGATTTTTCTTGTGTAAACATCTGATGCTTTTTTCTCCATTGGGTATAATGA
GTTAAAAATTATCTTTGAATTCATTGTTTTGAAATTCTTCCCTCTTTCTTTGTTGTATCTTACGT
CAAGGGCCTTGTCATATTGAATTACAAACTTACTCATTGATGTGCTCGAGTTGAGAAAATCCTTG
AAATATTTGTTCATCCTTTCACTTCTTTAAGTAGTGAAACATTTGT
Found at i:44869915 original size:6 final size:6
Alignment explanation
Indices: 44869906--44869934 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
44869896 AAATAAAATT
44869906 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
44869935 GTCTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:44872589 original size:9 final size:9
Alignment explanation
Indices: 44872575--44872659 Score: 61
Period size: 9 Copynumber: 9.4 Consensus size: 9
44872565 TTTTTTCATA
44872575 AAAAATATT
1 AAAAATATT
44872584 AAAAATCA-T
1 AAAAAT-ATT
*
44872593 AAATATATAT
1 AAAAATAT-T
*
44872603 AAAATTATT
1 AAAAATATT
44872612 AAAAATATTT
1 AAAAATA-TT
44872622 AAAAA-ATT
1 AAAAATATT
*
44872630 AAAGAT-TAT
1 AAAAATAT-T
*
44872639 AAAAA-AAT
1 AAAAATATT
*
44872647 AAAACTATT
1 AAAAATATT
44872656 AAAA
1 AAAA
44872660 TTTATACAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
8 13 0.22
9 31 0.53
10 15 0.25
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATATT
Found at i:44872632 original size:18 final size:18
Alignment explanation
Indices: 44872609--44872659 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
44872599 ATATAAAATT
44872609 ATTAAAAATATTTAAAAA
1 ATTAAAAATATTTAAAAA
* *
44872627 ATTAAAGAT-TATAAAAA
1 ATTAAAAATATTTAAAAA
* *
44872644 AATAAAACTA-TTAAAA
1 ATTAAAAATATTTAAAA
44872660 TTTATACAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
ATTAAAAATATTTAAAAA
Found at i:44872694 original size:8 final size:9
Alignment explanation
Indices: 44872572--44872993 Score: 82
Period size: 10 Copynumber: 44.8 Consensus size: 9
44872562 ATATTTTTTC
*
44872572 ATAAAAAAT
1 ATAAAAATT
*
44872581 ATTAAAAATC
1 A-TAAAAATT
*
44872591 ATAAATA-T
1 ATAAAAATT
44872599 ATATAAAATT
1 ATA-AAAATT
44872609 ATTAAAAATAT
1 A-TAAAAAT-T
* *
44872620 TTAAAAAAT
1 ATAAAAATT
*
44872629 -TAAAGATT
1 ATAAAAATT
*
44872637 ATAAAAA-A
1 ATAAAAATT
*
44872645 AT-AAAACT
1 ATAAAAATT
*
44872653 ATTAAAATTT
1 A-TAAAAATT
*
44872663 ATACAAACTT
1 ATA-AAAATT
**
44872673 ATAAGTATT
1 ATAAAAATT
44872682 ATAAAAA-T
1 ATAAAAATT
44872690 ATAAAAATT
1 ATAAAAATT
*
44872699 ATAATGAATT
1 ATAA-AAATT
44872709 ATAATAAATT
1 ATAA-AAATT
**
44872719 AT-AATTTT
1 ATAAAAATT
* *
44872727 TTATCAAATT
1 ATA-AAAATT
*
44872737 AATTAAACATGT
1 -A-TAAAAAT-T
*
44872749 TTAAAAATTT
1 ATAAAAA-TT
44872759 ATGAAAACA-T
1 AT-AAAA-ATT
44872769 ATAAAAATT
1 ATAAAAATT
* *
44872778 CTTAAAAACAT
1 -ATAAAAA-TT
*
44872789 ATGAAAAA-C
1 AT-AAAAATT
*
44872798 ATAAAAA-A
1 ATAAAAATT
*
44872806 ATATTAAA-T
1 ATA-AAAATT
*
44872815 ATTAAAATT
1 ATAAAAATT
*
44872824 ATTAAAATT
1 ATAAAAATT
*
44872833 ATATAAACTT
1 ATA-AAAATT
44872843 A-AAAAAGTT
1 ATAAAAA-TT
* *
44872852 ATAGGAAATC
1 ATA-AAAATT
*
44872862 ATAAAAATC
1 ATAAAAATT
44872871 AT-AAAA-T
1 ATAAAAATT
*
44872878 ATAATAACTT
1 ATAA-AAATT
*
44872888 ATAAAAAAT
1 ATAAAAATT
44872897 AT-AAAATT
1 ATAAAAATT
44872905 AATAAAATATAT
1 -ATAAAA-AT-T
* *
44872917 TTAAAATTTT
1 ATAAAA-ATT
* *
44872927 ATGGAAACTT
1 AT-AAAAATT
*
44872937 ATGAAAATT
1 ATAAAAATT
44872946 CATAAAAAGCTT
1 -ATAAAAA--TT
44872958 ATAAATAA-T
1 ATAAA-AATT
44872967 ATAATAAATT
1 ATAA-AAATT
* *
44872977 CTTATAAATT
1 -ATAAAAATT
44872987 ATAAAAA
1 ATAAAAA
44872994 AATCATTTAA
Statistics
Matches: 303, Mismatches: 65, Indels: 90
0.66 0.14 0.20
Matches are distributed among these distances:
7 6 0.02
8 49 0.16
9 94 0.31
10 106 0.35
11 39 0.13
12 9 0.03
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:44872694 original size:45 final size:44
Alignment explanation
Indices: 44872575--44872695 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 44
44872565 TTTTTTCATA
* * *
44872575 AAAAATATTAAAAATCATAAATATATATAAAATTATTAAAAATATTT
1 AAAAA-ATTAAAGATTATAAA-A-ATATAAAACTATTAAAAATATTT
*
44872622 AAAAAATTAAAGATTATAAAAAAATAAAACTATT-AAAAT-TTAT
1 AAAAAATTAAAGATTATAAAAATATAAAACTATTAAAAATATT-T
* *
44872665 ACAAACTTATAAGTATTATAAAAATATAAAA
1 AAAAAATTA-AAG-ATTATAAAAATATAAAA
44872696 ATTATAATGA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.03
43 13 0.20
44 14 0.22
45 17 0.27
46 13 0.20
47 5 0.08
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (44 bp):
AAAAAATTAAAGATTATAAAAATATAAAACTATTAAAAATATTT
Found at i:44872783 original size:30 final size:31
Alignment explanation
Indices: 44872749--44872807 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
44872739 TTAAACATGT
** *
44872749 TTAAAAATTTATG-AAAACATATAAAAATTC
1 TTAAAAACATATGAAAAACATAAAAAAATTC
44872779 TTAAAAACATATGAAAAACATAAAAAAAT
1 TTAAAAACATATGAAAAACATAAAAAAAT
44872808 ATTAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (31 bp):
TTAAAAACATATGAAAAACATAAAAAAATTC
Found at i:44872911 original size:16 final size:16
Alignment explanation
Indices: 44872857--44872915 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
44872847 AAGTTATAGG
* *
44872857 AAATCATAAAAATCATA
1 AAAT-ATAAAATTAATA
*
44872874 AAATATAATAACTTATAAA
1 AAATATAA-AA-TTA-ATA
44872893 AAATATAAAATTAATA
1 AAATATAAAATTAATA
44872909 AAATATA
1 AAATATA
44872916 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 13 0.37
17 9 0.26
18 3 0.09
19 10 0.29
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATAAAATTAATA
Found at i:44872915 original size:25 final size:27
Alignment explanation
Indices: 44872864--44872915 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
44872854 AGGAAATCAT
**
44872864 AAAAATCATAAAATATAATAACTTATA
1 AAAAATCATAAAATATAATAAAATATA
44872891 AAAAAT-ATAAAAT-TAATAAAATATA
1 AAAAATCATAAAATATAATAAAATATA
44872916 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 10 0.43
26 7 0.30
27 6 0.26
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAAATCATAAAATATAATAAAATATA
Found at i:44880973 original size:46 final size:46
Alignment explanation
Indices: 44880923--44881217 Score: 313
Period size: 46 Copynumber: 6.2 Consensus size: 46
44880913 TGTGATTTAT
* * *
44880923 AGCTTTAATCTACTGCGATGCCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTC
*
44880969 AGCTTTAATCTGTCCCACTACAACGCCAAGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATC--T---ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* * * *
44881020 AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTTGTTGCCTTC
1 AGCTTTAATCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* *
44881066 AGCTTTAATCTGTTCCATTGCAACGCCAAGGAAATGAGATTCGCTGCCTTC
1 AGCTTTAATC---T--ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* * * *
44881117 ATCTTTAATCTACTGCGACGGC-AGAGAAATAAGATTCGTTGCCTTC
1 AGCTTTAATCTACTGCAACGCCAAG-GAAATAAGATTCGCTGCCTTC
* * * * *
44881163 AGCTTTAATCTATTGCAATGCCAAGGAAACAAGATCCGTTGCCTTC
1 AGCTTTAATCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTC
44881209 AGCTTTAAT
1 AGCTTTAAT
44881218 TTGTTCCACT
Statistics
Matches: 209, Mismatches: 28, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
45 2 0.01
46 122 0.58
47 2 0.01
48 2 0.01
49 2 0.01
51 79 0.38
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (46 bp):
AGCTTTAATCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTC
Found at i:44881024 original size:97 final size:97
Alignment explanation
Indices: 44880923--44881173 Score: 412
Period size: 97 Copynumber: 2.6 Consensus size: 97
44880913 TGTGATTTAT
* *
44880923 AGCTTTAATCTACTGCGATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTCCCACT
1 AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCTGTCCCACT
44880988 ACAACGCCAAGGAAATAAGATTCGCTGCCTTC
66 ACAACGCCAAGGAAATAAGATTCGCTGCCTTC
* * *
44881020 AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTTGTTGCCTTCAGCTTTAATCTGTTCCATT
1 AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCTGTCCCACT
* *
44881085 GCAACGCCAAGGAAATGAGATTCGCTGCCTTC
66 ACAACGCCAAGGAAATAAGATTCGCTGCCTTC
* * *
44881117 ATCTTTAATCTACTGCGACGGCAGAGAAATAAGATTCGTTGCCTTCAGCTTTAATCT
1 AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCT
44881174 ATTGCAATGC
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 143 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (97 bp):
AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCTGTCCCACT
ACAACGCCAAGGAAATAAGATTCGCTGCCTTC
Found at i:44881229 original size:97 final size:94
Alignment explanation
Indices: 44880923--44881217 Score: 405
Period size: 97 Copynumber: 3.1 Consensus size: 94
44880913 TGTGATTTAT
* * *
44880923 AGCTTTAATCTACTGCGATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTCCCACT
1 AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCT-T--CATT
*
44880988 ACAACGCCAAGGAAATAAGATTCGCTGCCTTC
63 GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
*
44881020 AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTTGTTGCCTTCAGCTTTAATCTGTTCCATT
1 AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATC--TT-CATT
*
44881085 GCAACGCCAAGGAAATGAGATTCGCTGCCTTC
63 GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* * *
44881117 ATCTTTAATCTACTGCGACGGCAGAGAAATAAGATTCGTTGCCTTCAGCTTTAATC-T-ATTGCA
1 AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCTTCATTGCA
* * * *
44881180 ATGCCAAGGAAACAAGATCCGTTGCCTTC
66 ACGCCAAGGAAATAAGATTCGCTGCCTTC
44881209 AGCTTTAAT
1 AGCTTTAAT
44881218 TTGTTCCACT
Statistics
Matches: 180, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
92 38 0.21
94 1 0.01
97 139 0.77
98 1 0.01
99 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (94 bp):
AGCTTTAATCTACTGCGACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCTTCATTGCA
ACGCCAAGGAAATAAGATTCGCTGCCTTC
Found at i:44882476 original size:13 final size:13
Alignment explanation
Indices: 44882460--44882486 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44882450 AAAGGCCATG
44882460 GAGAAGTCATAAC
1 GAGAAGTCATAAC
44882473 GAGAAGTCATAAC
1 GAGAAGTCATAAC
44882486 G
1 G
44882487 TCCTTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (13 bp):
GAGAAGTCATAAC
Found at i:44888103 original size:22 final size:22
Alignment explanation
Indices: 44888078--44888119 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
44888068 AGGCAAATAA
*
44888078 ATTAATAATGGAATAAAACAAT
1 ATTAATAATGGAAAAAAACAAT
44888100 ATTAATAATGGAAAAAAACA
1 ATTAATAATGGAAAAAAACA
44888120 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (22 bp):
ATTAATAATGGAAAAAAACAAT
Found at i:44888125 original size:19 final size:21
Alignment explanation
Indices: 44888080--44888126 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
44888070 GCAAATAAAT
*
44888080 TAATAATGGAATAAAACAATA
1 TAATAATGGAAAAAAACAATA
44888101 TTAATAATGGAAAAAAAC-ATA
1 -TAATAATGGAAAAAAACAATA
44888122 -AATAA
1 TAATAA
44888127 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
21 3 0.12
22 16 0.67
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.23
Consensus pattern (21 bp):
TAATAATGGAAAAAAACAATA
Found at i:44888931 original size:22 final size:22
Alignment explanation
Indices: 44888896--44888953 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
44888886 TTGTTATTGT
* *
44888896 TATTTTTTTTATTTTTGGACTG
1 TATTATTTGTATTTTTGGACTG
44888918 ATATTATTTG-A--TTTGGACTG
1 -TATTATTTGTATTTTTGGACTG
44888938 TATTATTTGTATTTTT
1 TATTATTTGTATTTTT
44888954 ATATTGTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 9 0.30
20 10 0.33
22 4 0.13
23 7 0.23
ACGTcount: A:0.19, C:0.03, G:0.14, T:0.64
Consensus pattern (22 bp):
TATTATTTGTATTTTTGGACTG
Found at i:44888943 original size:19 final size:21
Alignment explanation
Indices: 44888909--44888951 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
44888899 TTTTTTTATT
44888909 TTTGGACTGATATTATTTG-A
1 TTTGGACTGATATTATTTGTA
44888929 TTTGGACTG-TATTATTTGTA
1 TTTGGACTGATATTATTTGTA
44888949 TTT
1 TTT
44888952 TTATATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.21, C:0.05, G:0.19, T:0.56
Consensus pattern (21 bp):
TTTGGACTGATATTATTTGTA
Found at i:44891120 original size:20 final size:20
Alignment explanation
Indices: 44891065--44891114 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
44891055 AAACAGGGTC
* *
44891065 AATGTCACAACATTGGCTTTG
1 AATGTCACGACATTGAC-TTG
*
44891086 AATGTCATGACATTGACTTG
1 AATGTCACGACATTGACTTG
44891106 AATGTCACG
1 AATGTCACG
44891115 TTATTGGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (20 bp):
AATGTCACGACATTGACTTG
Found at i:44894591 original size:58 final size:58
Alignment explanation
Indices: 44894501--44894617 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
44894491 TTTCGCATGG
44894501 CTACATATATAAAGATTAAAATGAACCATATCGAAACAAGCCTATACATGCCATATGT
1 CTACATATATAAAGATTAAAATGAACCATATCGAAACAAGCCTATACATGCCATATGT
*
44894559 CTACATATATAAAGATTAAAATGAACCATATCGAAACTAGCCTATACATGCCATATGT
1 CTACATATATAAAGATTAAAATGAACCATATCGAAACAAGCCTATACATGCCATATGT
44894617 C
1 C
44894618 AATAGTACAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (58 bp):
CTACATATATAAAGATTAAAATGAACCATATCGAAACAAGCCTATACATGCCATATGT
Found at i:44895088 original size:43 final size:43
Alignment explanation
Indices: 44895040--44895193 Score: 190
Period size: 43 Copynumber: 3.6 Consensus size: 43
44895030 CAATGTCATA
* * * **
44895040 TCCCAGATATGGTCTTACATGTTATCATATATCGATGCCTCTG
1 TCCCAGACATGGTCTTACACGTAATCATATATCGATGCCAATG
*
44895083 TCCCAGACAGGGTCTTACACG-AATCATATA-C-AGTGCCAATG
1 TCCCAGACATGGTCTTACACGTAATCATATATCGA-TGCCAATG
*
44895124 TCCCAGACATGGTCTTACACGTAATC-TCATATTGATGCCAATG
1 TCCCAGACATGGTCTTACACGTAATCAT-ATATCGATGCCAATG
*
44895167 TCCCAGACATGGTCTTACACGAAATCA
1 TCCCAGACATGGTCTTACACGTAATCA
44895194 CAACTCGAAA
Statistics
Matches: 96, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
40 1 0.01
41 28 0.29
42 15 0.16
43 51 0.53
44 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATCATATATCGATGCCAATG
Found at i:44895886 original size:68 final size:68
Alignment explanation
Indices: 44895538--44895886 Score: 518
Period size: 68 Copynumber: 5.1 Consensus size: 68
44895528 AAATCAATAG
* * * * * * * * *
44895538 ATTCGAACAGCTACATTTATTAAATAAAACAGCATAAATGGTAGTGCATTGAACAGTGAATTTAA
1 ATTCGGACAACTACATTTACTAAATAAAATAGCATAAATGATGGTGCTTTGATCAGTGAATCTAA
44895603 CAC
66 CAC
* * * * * *
44895606 ATTCAGACAACTATATTTACTAAATAAAATAGCATAAATGATAGTGCATTGAACAGTGAATTTAA
1 ATTCGGACAACTACATTTACTAAATAAAATAGCATAAATGATGGTGCTTTGATCAGTGAATCTAA
44895671 CAC
66 CAC
* * *
44895674 ATTCGGACAGCTACATTTACTAAATAAAACACCATAAATGATGGTGCTTTGATCAGTGAATCTAA
1 ATTCGGACAACTACATTTACTAAATAAAATAGCATAAATGATGGTGCTTTGATCAGTGAATCTAA
44895739 CAC
66 CAC
*
44895742 ATTCGGAAAACTACATTTACTAAATAAAATAGCATAAATGATGGTGCTTTGATCAGTGAATCTAA
1 ATTCGGACAACTACATTTACTAAATAAAATAGCATAAATGATGGTGCTTTGATCAGTGAATCTAA
44895807 CAC
66 CAC
*
44895810 ATTTGGACAACTACATTTACTAAATAAAATAGCATAAATGATGGTGCTTTGATCAGTGAATCTAA
1 ATTCGGACAACTACATTTACTAAATAAAATAGCATAAATGATGGTGCTTTGATCAGTGAATCTAA
44895875 CAC
66 CAC
44895878 ATTCGGACA
1 ATTCGGACA
44895887 GCTTAATTTT
Statistics
Matches: 258, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 258 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.29
Consensus pattern (68 bp):
ATTCGGACAACTACATTTACTAAATAAAATAGCATAAATGATGGTGCTTTGATCAGTGAATCTAA
CAC
Found at i:44900597 original size:25 final size:26
Alignment explanation
Indices: 44900560--44900610 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
44900550 GTTGTAAATC
*
44900560 AGAAAAATATCTTTAGA-AATTTTCT
1 AGAAAAATATCTTAAGAGAATTTTCT
* *
44900585 AGAATAATCTCTTAAGAGAATTTTCT
1 AGAAAAATATCTTAAGAGAATTTTCT
44900611 CTCTACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (26 bp):
AGAAAAATATCTTAAGAGAATTTTCT
Found at i:44909059 original size:25 final size:25
Alignment explanation
Indices: 44909031--44909081 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
44909021 TGACTTGACT
44909031 AGTTCAAAGCAAAT-AAATTATAAAA
1 AGTTCAAAG-AAATAAAATTATAAAA
**
44909056 AGTTCAAAGTTATAAAATTATAAAA
1 AGTTCAAAGAAATAAAATTATAAAA
44909081 A
1 A
44909082 TCAATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.59, C:0.06, G:0.08, T:0.27
Consensus pattern (25 bp):
AGTTCAAAGAAATAAAATTATAAAA
Found at i:44913202 original size:50 final size:50
Alignment explanation
Indices: 44913127--44913335 Score: 265
Period size: 50 Copynumber: 4.1 Consensus size: 50
44913117 CATGGGATGT
* * *
44913127 TCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACC
1 TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACC
* *
44913177 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
1 TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACC
* *
44913227 TCTCGTCTCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACC
1 TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACC
* * * *
44913277 TCTTATGATCTTAAGGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
1 TC---TCATC-T-CGG-TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACC
44913333 TCT
1 TCT
44913336 TTACCCAAAT
Statistics
Matches: 138, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
50 93 0.67
53 4 0.03
54 1 0.01
55 2 0.01
56 38 0.28
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACC
Found at i:44913247 original size:100 final size:104
Alignment explanation
Indices: 44913134--44913335 Score: 313
Period size: 100 Copynumber: 2.0 Consensus size: 104
44913124 TGTTCTCATA
* *
44913134 TCGGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTC-TCATC-T-CGG-TGCCAAC
1 TCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGGATGCCAAC
44913195 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTC
66 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTC
*
44913234 TCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGGATGCCA
1 TCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGGATGCCA
* *
44913299 ATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
64 ACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
44913336 TTACCCAAAT
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
100 44 0.48
103 4 0.04
104 1 0.01
105 2 0.02
106 40 0.44
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.26
Consensus pattern (104 bp):
TCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGGATGCCAAC
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTC
Found at i:44913451 original size:13 final size:13
Alignment explanation
Indices: 44913430--44913461 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
44913420 GCTTGGATCA
*
44913430 TCATCAAATAAAT
1 TCATAAAATAAAT
44913443 TCATAAAATAAAT
1 TCATAAAATAAAT
44913456 TCATAA
1 TCATAA
44913462 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:44913708 original size:30 final size:30
Alignment explanation
Indices: 44913673--44913730 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
44913663 CCTCGACTCT
*
44913673 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
44913703 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
44913731 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:44915462 original size:14 final size:16
Alignment explanation
Indices: 44915442--44915476 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
44915432 TCCTAGTTGC
44915442 TGAAAAAT-AAAAGAG
1 TGAAAAATGAAAAGAG
44915457 -GAAAAATGAAAAGAG
1 TGAAAAATGAAAAGAG
44915472 TGAAA
1 TGAAA
44915477 CTTGAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.39
15 7 0.39
16 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (16 bp):
TGAAAAATGAAAAGAG
Found at i:44920114 original size:86 final size:85
Alignment explanation
Indices: 44919968--44920693 Score: 568
Period size: 89 Copynumber: 8.6 Consensus size: 85
44919958 ATTCAAAAAT
* * * *
44919968 AAATATTAAAATTAAATAAAATCTGTTTCAGGATTTCTCCCCGCCGTTCAACAGATTTTATTCTC
1 AAATATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGAATTTATTC-C
* *
44920033 TATTTTGTTTTTATTTCCAAA
65 AATTTTGATTTTATTTCCAAA
* * * * * *
44920054 AAATATTAAAATTAAATAAAATCTATTTCGGGTTTTGTTCTCACCGTTTAACAGAA--T-TT---
1 AAATATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGAATTTATTCCA
*
44920113 A-TTTGATTTTGTTT-C---
66 ATTTTGATTTTATTTCCAAA
*
44920128 -AA-ATTAAAAGTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAAC-GAATTTTATT-C
1 AAATATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGAA-TTTATTCC
*
44920189 AATTTTTATTTTATTTCCAAA
65 AATTTTGATTTTATTTCCAAA
* *
44920210 AGGGAA-ATTAAAGTTAAATAAATTCTGTTTCGGGATTTATTCCCGCCGTTCAACA-AATTTTAT
1 A---AATATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGAA-TTTAT
44920273 TCCAATTTTGATTTTATTTCCAAA
62 TCCAATTTTGATTTTATTTCCAAA
** * * * *
44920297 ACGAGCATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCACCGTTCAACGGATTTTATT
1 A--AATATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGAATTTATT
* *
44920362 CCAATTTTAATTTTATATCCAAA
63 CCAATTTTGATTTTATTTCCAAA
* * * * *
44920385 AACGAGTATTAAAATTAAAATAAAACCTGTTTTGAGATTTATTCCCGCTGTTCAACAGATTTTAT
1 AA--A-TATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGAATTTAT
*
44920450 TCCAATTTTGATTTTATTTCTAAAA
62 TCCAATTTTGATTTTATTTC-CAAA
* * * * *
44920475 ACAAGTATTAAAATTAAAATAAAATCTATTTTGGAATTTATTCCCGCCGTTTAATA-AGATCTTA
1 A-AA-TATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGA-AT-TTA
** * *
44920539 TT-TGA-TTTGATTTTGTTTCCAATTT
61 TTCCAATTTTGATTTTATTTCCAA--A
* * * * * * * *
44920564 AGA-ATT-AAATTAAATTAAATCTGTTCCGGGATCTATTCCCGCCATTTAACAAGATTTTATT-T
1 AAATATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAAC-AGAATTTATTCC
* *
44920626 GATTTTG-TTTTGTTTCCAAA
65 AATTTTGATTTTATTTCCAAA
* * * *
44920646 TTAGA-ATT-AAATTACATTAAATCTGTTTCGGGATTTATTCCCACCGTT
1 --AAATATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTT
44920694 TAAAAAATTT
Statistics
Matches: 533, Mismatches: 73, Indels: 70
0.79 0.11 0.10
Matches are distributed among these distances:
71 3 0.01
72 41 0.08
73 2 0.00
74 1 0.00
75 2 0.00
77 2 0.00
78 22 0.04
79 2 0.00
83 2 0.00
84 93 0.17
85 11 0.02
86 110 0.21
87 32 0.06
88 79 0.15
89 121 0.23
90 9 0.02
91 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (85 bp):
AAATATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAGAATTTATTCCA
ATTTTGATTTTATTTCCAAA
Found at i:44920194 original size:72 final size:72
Alignment explanation
Indices: 44920058--44920194 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 72
44920048 TCCAAAAAAT
* * * * * **
44920058 ATTAAAATTAAATAAAATCTATTTCGGGTTTTGTTCTCACCGTTTAACAGAATTTATTTGATTTT
1 ATTAAAAGTAAATAAAATCTATTTCGGGATTTATTCCCACCGTTCAACAGAATTTATTCAATTTT
44920123 GTTTCAA
66 GTTTCAA
* *
44920130 ATTAAAAGTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAAC-GAATTTTATTCAATTT
1 ATTAAAAGTAAATAAAATCTATTTCGGGATTTATTCCCACCGTTCAACAGAA-TTTATTCAATTT
44920194 T
65 T
44920195 TATTTTATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 3 0.05
72 52 0.95
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (72 bp):
ATTAAAAGTAAATAAAATCTATTTCGGGATTTATTCCCACCGTTCAACAGAATTTATTCAATTTT
GTTTCAA
Found at i:44920272 original size:158 final size:160
Alignment explanation
Indices: 44919972--44920631 Score: 469
Period size: 158 Copynumber: 3.9 Consensus size: 160
44919962 AAAAATAAAT
* * * *
44919972 ATTAAAATTAAATAAAATCTGTTTCAGGATTTCTCCCCGCCGTTCAAC-AGATTTTATTCTCTAT
1 ATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGA-ATTTTA-T-TCAAT
* * * * *
44920036 TTTGT-TTTTATTTCCAAAA-AATATTAAAATTAAATAAAATCTATTTCGGGTTTTGTTCTCACC
63 TTT-TATTTTATTTCCAAAAGAA-ATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCC
* *
44920099 GTTTAACAGAA-TTTATTTGATTTTGTTT-C-A-A-
126 GTTCAACA-AATTTTATTTGATTTTATTTCCAACAC
*
44920130 ATTAAAAGTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATTCAATTTT
1 ATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATTCAATTTT
* *
44920195 TATTTTATTTCCAAAAGGGAAATTAAAGTTAAATAAATTCTGTTTCGGGATTTATTCCCGCCGTT
66 TATTTTATTTCCAAAA--GAAATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTT
44920260 CAACAAATTTTATTCCAATTTTGATTTTATTTCCAAAACGAGC
129 CAACAAA--TT-TT---A-TTTGATTTTATTTCC--AAC-A-C
* * *
44920303 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCACCGTTCAACGGATTTTATTCCAATT
1 ATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATT-CAATT
* * * * * *
44920368 TTAATTTTATATCCAAAAACGAGTATTAAAATTAAAATAAAACCTGTTTTGAGATTTATTCCCGC
64 TTTATTTTATTTCC-AAAA-GA-AATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGC
* * * *
44920433 TGTTCAACAGATTTTATTCCAATTTTGATTTTATTTCTAAAAACAAGT
125 CGTTCAACA-A-ATT-TT---A-TTTGATTTTATTTC---CAAC-A-C
* * * * ** * **
44920481 ATTAAAATTAAAATAAAATCTATTTTGGAATTTATTCCCGCCGTTTAATAAGATCTTATTTGA-T
1 ATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGA-ATTTTATTCAATT
* * * * * * *
44920545 TTGATTTTGTTTCCAATTTAG-AATT-AAATTAAATTAAATCTGTTCCGGGATCTATTCCCGCCA
64 TTTATTTTATTTCCAA--AAGAAATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCG
*
44920608 TTTAACAAGATTTTATTTGATTTT
127 TTCAACAA-ATTTTATTTGATTTT
44920632 GTTTTGTTTC
Statistics
Matches: 410, Mismatches: 58, Indels: 59
0.78 0.11 0.11
Matches are distributed among these distances:
155 1 0.00
156 21 0.05
157 3 0.01
158 91 0.22
159 3 0.01
160 1 0.00
161 2 0.00
164 1 0.00
165 12 0.03
166 1 0.00
167 9 0.02
168 1 0.00
169 1 0.00
171 3 0.01
172 3 0.01
173 39 0.10
174 51 0.12
175 22 0.05
176 14 0.03
177 72 0.18
178 52 0.13
179 7 0.02
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (160 bp):
ATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATTCAATTTT
TATTTTATTTCCAAAAGAAATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCA
ACAAATTTTATTTGATTTTATTTCCAACAC
Found at i:44920348 original size:88 final size:86
Alignment explanation
Indices: 44920129--44920707 Score: 569
Period size: 89 Copynumber: 6.7 Consensus size: 86
44920119 TTTTGTTTCA
* *
44920129 AATTAAAAGTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATTCAATTT
1 AATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATTCAATTT
* *
44920194 TTATTTTATTTCCAAAA-GGG
66 TGATTTTATTTCCAAAACGAG
* *
44920214 AAATTAAAGTTAAATAAATTCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATTCCAAT
1 -AATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATT-CAAT
44920279 TTTGATTTTATTTCCAAAACGAG
64 TTTGATTTTATTTCCAAAACGAG
* * * **
44920302 CATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCACCGTTCAACGGATTTTATTCCAAT
1 AATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATT-CAAT
* *
44920367 TTTAATTTTATATCCAAAAACGAG
64 TTTGATTTTATTTCC-AAAACGAG
* * * * * *
44920391 TATTAAAATTAAAATAAAACCTGTTTTGAGATTTATTCCCGCTGTTCAACAGATTTTATTCCAAT
1 AATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATT-CAAT
* *
44920456 TTTGATTTTATTTCTAAAAACAAG
64 TTTGATTTTATTTC-CAAAACGAG
* * * * * * * **
44920480 TATTAAAATTAAAATAAAATCTATTTTGGAATTTATTCCCGCCGTTTAATAAGATCTTATTTGA-
1 AATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAA-ATTTTATTCAAT
* ***
44920544 TTTGATTTTGTTTCC-AATTTAG
64 TTTGATTTTATTTCCAAAACGAG
* * * * * **
44920566 AATT-AAATTAAATTAAATCTGTTCCGGGATCTATTCCCGCCATTTAACAAGATTTTATTTGATT
1 AATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAA-ATTTTATTCAATT
* **
44920630 TTG-TTTTGTTTCC-AAATTAG
65 TTGATTTTATTTCCAAAACGAG
* * * * *
44920650 AATT-AAATTACATTAAATCTGTTTCGGGATTTATTCCCACCGTTTAAAAAATTTTATT
1 AATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATT
44920708 TTGATTTAAT
Statistics
Matches: 428, Mismatches: 58, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
83 8 0.02
84 104 0.24
85 9 0.02
86 62 0.14
87 30 0.07
88 77 0.18
89 131 0.31
90 7 0.02
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (86 bp):
AATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACAAATTTTATTCAATTT
TGATTTTATTTCCAAAACGAG
Found at i:44920461 original size:177 final size:175
Alignment explanation
Indices: 44920130--44920525 Score: 562
Period size: 177 Copynumber: 2.3 Consensus size: 175
44920120 TTTGTTTCAA
* *
44920130 ATTAAAAGT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATTCAATTT
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACGAATTTTATTCAATTT
* * ** * ** *
44920194 TTATTTTATTTCCAAAAGGGAAATTAAAGTTAAATAAATTCTGTTTCGGGATTTATTCCCGCCGT
66 TAATTTTATATCCAAAAACGAAATTAAAATTAAATAAAACCTGTTTCGAGATTTATTCCCGCCGT
* *
44920259 TCAACAAATTTTATTCCAATTTTGATTTTATTTC-CAAAACGAGC
131 TCAACAAATTTTATTCCAATTTTGATTTTATTTCTAAAAACAAGC
* *
44920303 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCACCGTTCAACGGATTTTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACGAATTTTATT-CAATT
* *
44920368 TTAATTTTATATCCAAAAACGAGTATTAAAATTAAAATAAAACCTGTTTTGAGATTTATTCCCGC
65 TTAATTTTATATCCAAAAACGA-AATTAAAATT-AAATAAAACCTGTTTCGAGATTTATTCCCGC
* * *
44920433 TGTTCAACAGATTTTATTCCAATTTTGATTTTATTTCTAAAAACAAGT
128 CGTTCAACAAATTTTATTCCAATTTTGATTTTATTTCTAAAAACAAGC
* *
44920481 ATTAAAATTAAAATAAAATCTATTTTGGAATTTATTCCCGCCGTT
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTT
44920526 TAATAAGATC
Statistics
Matches: 196, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
173 8 0.04
174 46 0.23
175 23 0.12
176 8 0.04
177 62 0.32
178 49 0.25
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (175 bp):
ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACGAATTTTATTCAATTT
TAATTTTATATCCAAAAACGAAATTAAAATTAAATAAAACCTGTTTCGAGATTTATTCCCGCCGT
TCAACAAATTTTATTCCAATTTTGATTTTATTTCTAAAAACAAGC
Found at i:44920603 original size:84 final size:82
Alignment explanation
Indices: 44920513--44920714 Score: 287
Period size: 84 Copynumber: 2.4 Consensus size: 82
44920503 TTTTGGAATT
* *
44920513 TATTCCCGCCGTTTAATAAGATCTTATTTGATTTGATTTTGTTTCCAATTTAGAATTAAATTAAA
1 TATTCCCGCCGTTTAA-AAGATTTTATTTGATTTG-TTTTGTTTCCAAATTAGAATTAAATTAAA
44920578 TTAAATCTGTTCCGGGATC
64 TTAAATCTGTTCCGGGATC
* *
44920597 TATTCCCGCCATTTAACAAGATTTTATTTGATTTTGTTTTGTTTCCAAATTAGAATTAAATTACA
1 TATTCCCGCCGTTTAA-AAGATTTTATTTGA-TTTGTTTTGTTTCCAAATTAGAATTAAATTAAA
* *
44920662 TTAAATCTGTTTCGGGATT
64 TTAAATCTGTTCCGGGATC
* *
44920681 TATTCCCACCGTTTAAAAAATTTTATTTTGATTT
1 TATTCCCGCCGTTTAAAAGATTTTA-TTTGATTT
44920715 AATTACATAA
Statistics
Matches: 106, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
83 11 0.10
84 91 0.86
85 4 0.04
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (82 bp):
TATTCCCGCCGTTTAAAAGATTTTATTTGATTTGTTTTGTTTCCAAATTAGAATTAAATTAAATT
AAATCTGTTCCGGGATC
Found at i:44933306 original size:52 final size:52
Alignment explanation
Indices: 44933228--44933331 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
44933218 TTATCTTTAG
44933228 CTATAGTTTAATTTCTGGAATAAATAGTTAATACTGTTTTAGTTAAATTAAT
1 CTATAGTTTAATTTCTGGAATAAATAGTTAATACTGTTTTAGTTAAATTAAT
* * *
44933280 CTATAGTTTTATTGT-TGGAATAAATAGTTAATTCTGTTTTTGTTAAATTAAT
1 CTATAGTTTAATT-TCTGGAATAAATAGTTAATACTGTTTTAGTTAAATTAAT
44933332 TTAATTATGT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (52 bp):
CTATAGTTTAATTTCTGGAATAAATAGTTAATACTGTTTTAGTTAAATTAAT
Found at i:44934763 original size:15 final size:16
Alignment explanation
Indices: 44934737--44934780 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
44934727 TATACTTTCA
44934737 GAATTAAAAAAAATTC
1 GAATTAAAAAAAATTC
44934753 GAATT-AAAAAAATTC
1 GAATTAAAAAAAATTC
44934768 G--TGTAAAAAAAAT
1 GAAT-TAAAAAAAAT
44934781 ATGTTCATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.04
14 1 0.04
15 19 0.73
16 5 0.19
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (16 bp):
GAATTAAAAAAAATTC
Found at i:44935364 original size:21 final size:21
Alignment explanation
Indices: 44935338--44935392 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
44935328 AACAAAGTCG
**
44935338 TCAAGGATTCCATCATCATTT
1 TCAAGGATTCCATCATCATCA
* *
44935359 TCAAGGAGTCCATCGTCATCA
1 TCAAGGATTCCATCATCATCA
*
44935380 TCAACGATTCCAT
1 TCAAGGATTCCAT
44935393 TGTCCTCGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (21 bp):
TCAAGGATTCCATCATCATCA
Found at i:44935973 original size:18 final size:18
Alignment explanation
Indices: 44935920--44935978 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
44935910 AATGATTGTT
44935920 GAAAAAGAAATG-GTG--
1 GAAAAAGAAATGAGTGAA
*
44935935 GAAAAAGAAA-GAGAGATA
1 GAAAAAGAAATGAGTGA-A
44935953 GAAAAAGAAATGAGTGAA
1 GAAAAAGAAATGAGTGAA
*
44935971 GAACAAGA
1 GAAAAAGA
44935979 GAGCGTTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 1 0.03
15 12 0.33
18 18 0.50
19 5 0.14
ACGTcount: A:0.61, C:0.02, G:0.29, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAATGAGTGAA
Found at i:44938569 original size:27 final size:27
Alignment explanation
Indices: 44938539--44938816 Score: 221
Period size: 27 Copynumber: 10.3 Consensus size: 27
44938529 GTATTGGGCC
*
44938539 TAAAATGATCGAATTACCCCTGAAGGG
1 TAAAATGATCGAAATACCCCTGAAGGG
* *
44938566 TAAAATGACCGAACTACCTCC-GAAGGG
1 TAAAATGATCGAAATACC-CCTGAAGGG
*
44938593 TAAAATGATCGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCCTGAAGGG
*
44938620 TAAAATGA-CTGAAATA-CCCTCGAAAGG
1 TAAAATGATC-GAAATACCCCT-GAAGGG
* * * *
44938647 TAAAAAGACCGAAATA-CCCTCGAAAGA
1 TAAAATGATCGAAATACCCCT-GAAGGG
** *
44938674 TAAAATGATCGAAATACCCCCAAAAGG
1 TAAAATGATCGAAATACCCCTGAAGGG
* * * *
44938701 TAAAATGA-CTGAATTACCCTTGAATGA
1 TAAAATGATC-GAAATACCCCTGAAGGG
* * *
44938728 TAAAATGATCGAATTACCCCCGAAGGA
1 TAAAATGATCGAAATACCCCTGAAGGG
* * * * *
44938755 TAAAATGACCAAAATA-TCCTCAAATGG
1 TAAAATGATCGAAATACCCCT-GAAGGG
44938782 TAAAATGA-CTGAAATACCCC-GAAGGG
1 TAAAATGATC-GAAATACCCCTGAAGGG
44938808 TAAAATGAT
1 TAAAATGAT
44938817 TGTTATACCC
Statistics
Matches: 205, Mismatches: 34, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
26 22 0.11
27 174 0.85
28 9 0.04
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.19
Consensus pattern (27 bp):
TAAAATGATCGAAATACCCCTGAAGGG
Found at i:44938621 original size:54 final size:53
Alignment explanation
Indices: 44938539--44938816 Score: 263
Period size: 54 Copynumber: 5.2 Consensus size: 53
44938529 GTATTGGGCC
* *
44938539 TAAAATGATCGAATTACCC-CTGAAGGGTAAAATGACCGAACTACCTCCGAAGGG
1 TAAAATGATCGAAATACCCTC-GAAGGGTAAAATGACCGAAATACC-CCGAAGGG
* * *
44938593 TAAAATGATCGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAAGG
1 TAAAATGATCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCC-CGAAGGG
* * * * * * *
44938647 TAAAAAGACCGAAATACCCTCGAAAGATAAAATGATCGAAATACCCCCAAAAGG
1 TAAAATGATCGAAATACCCTCGAAGGGTAAAATGACCGAAATA-CCCCGAAGGG
* * * * * * *
44938701 TAAAATGA-CTGAATTACCCTTGAATGATAAAATGATCGAATTACCCCCGAAGGA
1 TAAAATGATC-GAAATACCCTCGAAGGGTAAAATGACCGAAATA-CCCCGAAGGG
* * * * * *
44938755 TAAAATGACCAAAATATCCTCAAATGGTAAAATGACTGAAATACCCCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCGAAGGG
44938808 TAAAATGAT
1 TAAAATGAT
44938817 TGTTATACCC
Statistics
Matches: 188, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
53 19 0.10
54 164 0.87
55 5 0.03
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.19
Consensus pattern (53 bp):
TAAAATGATCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCGAAGGG
Found at i:44938678 original size:81 final size:80
Alignment explanation
Indices: 44938539--44938815 Score: 315
Period size: 81 Copynumber: 3.4 Consensus size: 80
44938529 GTATTGGGCC
* * *
44938539 TAAAATGA-TCGAATTACCCCTGAAGGGTAAAATGACCGAACTA-CCTCCGAAGGGTAAAATGAT
1 TAAAATGACT-GAAATACCCC-GAAGGGTAAAATGACCGAAATACCCT-CGAAGGATAAAATGAT
* *
44938602 CGAAATACCCCCGAAGGG
63 CGAAATACCCCCAAAAGG
* * *
44938620 TAAAATGACTGAAATACCCTCGAAAGGTAAAAAGACCGAAATACCCTCGAAAGATAAAATGATCG
1 TAAAATGACTGAAATACCC-CGAAGGGTAAAATGACCGAAATACCCTCGAAGGATAAAATGATCG
44938685 AAATACCCCCAAAAGG
65 AAATACCCCCAAAAGG
* * * * * * * * *
44938701 TAAAATGACTGAATTACCCTTGAATGATAAAATGATCGAATTACCCCCGAAGGATAAAATGACCA
1 TAAAATGACTGAAATACCC-CGAAGGGTAAAATGACCGAAATACCCTCGAAGGATAAAATGATCG
* * *
44938766 AAATATCCTCAAATGG
65 AAATACCCCCAAAAGG
44938782 TAAAATGACTGAAATACCCCGAAGGGTAAAATGA
1 TAAAATGACTGAAATACCCCGAAGGGTAAAATGA
44938816 TTGTTATACC
Statistics
Matches: 167, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
80 12 0.07
81 150 0.90
82 5 0.03
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (80 bp):
TAAAATGACTGAAATACCCCGAAGGGTAAAATGACCGAAATACCCTCGAAGGATAAAATGATCGA
AATACCCCCAAAAGG
Found at i:44939020 original size:26 final size:26
Alignment explanation
Indices: 44938991--44939067 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
44938981 TTGCTACATA
*
44938991 TACTGTTACCGGCAGCTTTGTTGCGT
1 TACTGTTACTGGCAGCTTTGTTGCGT
*
44939017 TACTGTTACTGGCAGCTTTGTTGCAT
1 TACTGTTACTGGCAGCTTTGTTGCGT
* * *
44939043 CACTATTACTGGCAGCTTTGCTGCG
1 TACTGTTACTGGCAGCTTTGTTGCG
44939068 ATATTGGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGTTGCGT
Found at i:44940244 original size:4 final size:4
Alignment explanation
Indices: 44940223--44940262 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
44940213 GAAGATAAGG
*
44940223 AAGA AGAGA GAGA GAAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA A-AGA AAGA -AAGA AAGA AAGA AAGA AAGA AAGA AA
44940263 AGATATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 26 0.81
5 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:44944292 original size:48 final size:48
Alignment explanation
Indices: 44944237--44944434 Score: 256
Period size: 48 Copynumber: 4.1 Consensus size: 48
44944227 TCCAAGGTAC
* * *
44944237 CTAATTTATATTACAAAGTATGTTTCTTGTTTTAATGTTGCAATATAT
1 CTAATTTATATTACAAAGTTTGTTTCTCGTTTTAATGTTGCAATGTAT
* *
44944285 CTAATTTATATTACAAAGTTTG-TTCATCGTTTAAATGTTGTAATGTAT
1 CTAATTTATATTACAAAGTTTGTTTC-TCGTTTTAATGTTGCAATGTAT
* *
44944333 CTAATTTATATTACAAAGTTTGTTCCTCGTTTTAATGTTGTAATGTAT
1 CTAATTTATATTACAAAGTTTGTTTCTCGTTTTAATGTTGCAATGTAT
* * ** *
44944381 CTAATTTATGTTACAAAGTTTATTTCAAGTTTTAATGTTACAAT-TAAT
1 CTAATTTATATTACAAAGTTTGTTTCTCGTTTTAATGTTGCAATGT-AT
44944429 CTAATT
1 CTAATT
44944435 AAACAAATAC
Statistics
Matches: 133, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
47 4 0.03
48 127 0.95
49 2 0.02
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (48 bp):
CTAATTTATATTACAAAGTTTGTTTCTCGTTTTAATGTTGCAATGTAT
Found at i:44946523 original size:12 final size:12
Alignment explanation
Indices: 44946506--44946530 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44946496 CTAAATGTGA
44946506 TACAATAAATTT
1 TACAATAAATTT
44946518 TACAATAAATTT
1 TACAATAAATTT
44946530 T
1 T
44946531 CATTACAAAA
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TACAATAAATTT
Found at i:44947153 original size:31 final size:31
Alignment explanation
Indices: 44947093--44947171 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
44947083 TCCTTCTAAC
*
44947093 CCCAAATACAACCTCTTAATTTTTTTCAAA-
1 CCCAAACACAACCTCTTAATTTTTTTCAAAT
*
44947123 CACTAAACACAACC-C-TAATTCTTTTCTCAAAT
1 C-CCAAACACAACCTCTTAATT-TTTT-TCAAAT
44947155 CCCAAACACAACCTCTT
1 CCCAAACACAACCTCTT
44947172 CTCCTTCCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
29 5 0.12
30 6 0.15
31 26 0.65
32 2 0.05
33 1 0.03
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (31 bp):
CCCAAACACAACCTCTTAATTTTTTTCAAAT
Found at i:44947187 original size:12 final size:13
Alignment explanation
Indices: 44947170--44947198 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
44947160 ACACAACCTC
44947170 TTCTCC-TTCCTT
1 TTCTCCTTTCCTT
44947182 TTCTCCTTTCCTT
1 TTCTCCTTTCCTT
44947195 TTCT
1 TTCT
44947199 TCTCTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTCCTTTCCTT
Found at i:44950231 original size:6 final size:6
Alignment explanation
Indices: 44950222--44950260 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
44950212 GAGAGAGACT
44950222 AGGCAC AGGCAC AGGCAC AGGCAC AGGCAC AGGCAC AGG
1 AGGCAC AGGCAC AGGCAC AGGCAC AGGCAC AGGCAC AGG
44950261 AACTATAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.31, G:0.36, T:0.00
Consensus pattern (6 bp):
AGGCAC
Found at i:44954037 original size:29 final size:27
Alignment explanation
Indices: 44954000--44954067 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 27
44953990 TAAATCTTAA
* *
44954000 AATTATATATGAACTTTAGTTTAATATGT
1 AATTTTATATGAACTTTAATTT--TATGT
*
44954029 AATTTTATACATGAATTTTAATTTTATGT
1 AATTTTAT--ATGAACTTTAATTTTATGT
*
44954058 AAATTTATAT
1 AATTTTATAT
44954068 ATATGAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 2 0.06
29 19 0.58
31 12 0.36
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.51
Consensus pattern (27 bp):
AATTTTATATGAACTTTAATTTTATGT
Found at i:44954077 original size:31 final size:30
Alignment explanation
Indices: 44954002--44954084 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 30
44953992 AATCTTAAAA
* *
44954002 TTATATATGAACTTTAGTTTAATATGTAATT
1 TTATATATGAATTTTAATTT-ATATGTAATT
*
44954033 TTATACATGAATTTTAATTT-TATGTAAATT
1 TTATATATGAATTTTAATTTATATGT-AATT
44954063 TATATATATGAATTTTTAATTT
1 T-TATATATGAA-TTTTAATTT
44954085 GATTCAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
29 5 0.11
30 5 0.11
31 26 0.58
32 9 0.20
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.54
Consensus pattern (30 bp):
TTATATATGAATTTTAATTTATATGTAATT
Found at i:44957667 original size:21 final size:21
Alignment explanation
Indices: 44957643--44957704 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
44957633 ATAAACATTC
*
44957643 TATTACTTTAATAAGATTTAA
1 TATTAATTTAATAAGATTTAA
* *
44957664 TATTAAATTAATATA-ATATTTA
1 TATTAATTTAATA-AGAT-TTAA
44957686 TATTAAATTTAATAAGATT
1 TATT-AATTTAATAAGATT
44957705 AGATTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 13 0.39
22 10 0.30
23 10 0.30
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (21 bp):
TATTAATTTAATAAGATTTAA
Found at i:44957712 original size:21 final size:21
Alignment explanation
Indices: 44957649--44957705 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
44957639 ATTCTATTAC
44957649 TTTAATAAGATTTAATATTAAA
1 TTTAATAAGA-TTAATATTAAA
* * *
44957671 TTAATATAATATTTATATTAAA
1 TTTA-ATAAGATTAATATTAAA
44957693 TTTAATAAGATTA
1 TTTAATAAGATTA
44957706 GATTTAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 7 0.25
22 16 0.57
23 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTAATAAGATTAATATTAAA
Found at i:44957719 original size:27 final size:25
Alignment explanation
Indices: 44957651--44957719 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 25
44957641 TCTATTACTT
44957651 TAATAAGATTTAATATTAAATTAATA
1 TAAT-AGATTTAATATTAAATTAATA
44957677 TAAT--ATTT-ATATTAAATTTAATA
1 TAATAGATTTAATATTAAA-TTAATA
44957700 -AGATTAGATTTAATATTAAA
1 TA-A-TAGATTTAATATTAAA
44957720 GTGATTAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
22 9 0.24
23 11 0.30
24 1 0.03
26 8 0.22
27 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (25 bp):
TAATAGATTTAATATTAAATTAATA
Found at i:44957861 original size:25 final size:25
Alignment explanation
Indices: 44957824--44957873 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
44957814 AGTTGTAGAG
44957824 AAAAAATTCTCTAAAGAGAT-TTTTTC
1 AAAAAATTCTCT--AGAGATCTTTTTC
44957850 AAAAAATT-TCTAGAGATCTTTTTC
1 AAAAAATTCTCTAGAGATCTTTTTC
44957874 TAATTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.26
24 6 0.26
25 3 0.13
26 8 0.35
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (25 bp):
AAAAAATTCTCTAGAGATCTTTTTC
Found at i:44958303 original size:18 final size:18
Alignment explanation
Indices: 44958280--44958319 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
44958270 TATAAGAGAA
44958280 AAAAGAGAAATCAAAGAG
1 AAAAGAGAAATCAAAGAG
*
44958298 AAAAGAGAAATCAGAGAG
1 AAAAGAGAAATCAAAGAG
44958316 AAAA
1 AAAA
44958320 TGATGTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.68, C:0.05, G:0.23, T:0.05
Consensus pattern (18 bp):
AAAAGAGAAATCAAAGAG
Found at i:44966488 original size:25 final size:25
Alignment explanation
Indices: 44966450--44966499 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
44966440 TTCATCTTGC
*
44966450 CTCTGCTTCGCTATAACAGAATTTA
1 CTCTGCTTCACTATAACAGAATTTA
44966475 CTCTGCTTCACTATAACAGAATTTA
1 CTCTGCTTCACTATAACAGAATTTA
44966500 TTCTTGGAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (25 bp):
CTCTGCTTCACTATAACAGAATTTA
Found at i:44966773 original size:28 final size:28
Alignment explanation
Indices: 44966739--44966806 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
44966729 AAATCCAACT
* * * *
44966739 TATAAGATAATCCTAATAGATTTCCATA
1 TATAAGATAATCCTAACAAACTTCCACA
* *
44966767 TATAAGATAATCTTGACAAACTTCCACA
1 TATAAGATAATCCTAACAAACTTCCACA
44966795 TATAAGATAATC
1 TATAAGATAATC
44966807 TTGGCAGACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.32
Consensus pattern (28 bp):
TATAAGATAATCCTAACAAACTTCCACA
Found at i:44966825 original size:28 final size:28
Alignment explanation
Indices: 44966760--44966825 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
44966750 CCTAATAGAT
44966760 TTCCATATATAAGATAATCTTGACAAAC
1 TTCCATATATAAGATAATCTTGACAAAC
* * *
44966788 TTCCACATATAAGATAATCTTGGCAGAC
1 TTCCATATATAAGATAATCTTGACAAAC
*
44966816 TTTCATATAT
1 TTCCATATAT
44966826 CTTTCATAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (28 bp):
TTCCATATATAAGATAATCTTGACAAAC
Found at i:44976500 original size:95 final size:95
Alignment explanation
Indices: 44976399--44976616 Score: 269
Period size: 95 Copynumber: 2.3 Consensus size: 95
44976389 TGTTTATTGT
* * * *
44976399 TTTTTAAGAAAAAATCAATTAAATTAAGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTT
1 TTTTTAAGAAAAAATCAAATAAATTAAGGTTCAAGGTTACTTGAGTAAATTAATTAAAAAAATTT
44976464 AA-AAATCAGATTAGGGTTTAGAGTTAAAGG-
66 AATAAATCAGATTAGGGTTTAGAGTT--AGGA
* * * **
44976494 TTTTTAAGGAAAAATCAAATAAATTAGGGTTCAAGGTTACTTGAGTAAATTAATTATAAATTTTT
1 TTTTTAAGAAAAAATCAAATAAATTAAGGTTCAAGGTTACTTGAGTAAATTAATTAAAAAAATTT
* * *
44976559 AATAAATTAGTTTAGGGTTTAGTGTTAGGA
66 AATAAATCAGATTAGGGTTTAGAGTTAGGA
44976589 TTTTTAAGAAAAAAAACTCAAATAAATT
1 TTTTTAAG--AAAAAA-TCAAATAAATT
44976617 TGGGTTTGGG
Statistics
Matches: 105, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
94 3 0.03
95 66 0.63
96 20 0.19
97 5 0.05
98 11 0.10
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.37
Consensus pattern (95 bp):
TTTTTAAGAAAAAATCAAATAAATTAAGGTTCAAGGTTACTTGAGTAAATTAATTAAAAAAATTT
AATAAATCAGATTAGGGTTTAGAGTTAGGA
Found at i:44976908 original size:126 final size:125
Alignment explanation
Indices: 44976663--44976963 Score: 460
Period size: 126 Copynumber: 2.4 Consensus size: 125
44976653 TTGTTAATTT
* * * * *
44976663 AAAGAAGCT-CCACGTGGATGCGCTTTTGCTATAGTATGTCTTGAGAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTA-GCCCTGAAAAAATAATTTCGAGTAGAC
* * * *
44976727 GTTTCTGAGCAAACAGTGTCAAAAATGCTTTAAGAAGGATGTTTTCTCAGTAGAAGTACTG
65 GTTTCTGAGAAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTCTCAGCAGAAGTACTG
*
44976788 AAAGAAGCTCCCACATGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAG-CCCTGAAAAAATAATTTCGAGTAGAC
* *
44976853 GTTTCTGAGAAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
65 GTTTCTGAGAAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTCTCAGCAGAAGTACTG
44976914 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAAGCCCTGAAAAAA
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGT-AGCCCTGAAAAAA
44976964 GCTCCCACGT
Statistics
Matches: 160, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
125 10 0.06
126 148 0.93
127 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (125 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCTGAAAAAATAATTTCGAGTAGACG
TTTCTGAGAAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTCTCAGCAGAAGTACTG
Found at i:44976966 original size:44 final size:44
Alignment explanation
Indices: 44976911--44976994 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
44976901 AGCAGAAGTA
* *
44976911 CTGAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAAGCC
1 CTGAAAAAAGCTCCCACGTGGACGCACTTTTGCTACAGTAAGCC
44976955 CTGAAAAAAGCTCCCACGTGGACGCACTTTTGCTACAGTA
1 CTGAAAAAAGCTCCCACGTGGACGCACTTTTGCTACAGTA
44976995 GCGCATGGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (44 bp):
CTGAAAAAAGCTCCCACGTGGACGCACTTTTGCTACAGTAAGCC
Found at i:44982531 original size:11 final size:11
Alignment explanation
Indices: 44982517--44982573 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
44982507 TTTAAATAGG
44982517 AATTTGAGAGA
1 AATTTGAGAGA
*
44982528 AATTTGAGAGG
1 AATTTGAGAGA
* * * *
44982539 GAGTTAAGAGG
1 AATTTGAGAGA
44982550 AATTTGAGAGA
1 AATTTGAGAGA
*
44982561 ATATTAGAGAGA
1 A-ATTTGAGAGA
44982573 A
1 A
44982574 TATTAGAGAA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
11 26 0.72
12 10 0.28
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.25
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:44982572 original size:12 final size:12
Alignment explanation
Indices: 44982555--44982582 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
44982545 AGAGGAATTT
44982555 GAGAGAATATTA
1 GAGAGAATATTA
44982567 GAGAGAATATTA
1 GAGAGAATATTA
44982579 GAGA
1 GAGA
44982583 AAGGATTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (12 bp):
GAGAGAATATTA
Found at i:44985882 original size:38 final size:38
Alignment explanation
Indices: 44985839--44985914 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
44985829 TAAGGAAAAG
44985839 ATTGCTTGAGCTTTCGACTAAAGCGAAAACATGATCGC
1 ATTGCTTGAGCTTTCGACTAAAGCGAAAACATGATCGC
44985877 ATTGCTTGAGCTTTCGACTAAAGCGAAAACATGATCGC
1 ATTGCTTGAGCTTTCGACTAAAGCGAAAACATGATCGC
44985915 TGAGGGCACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (38 bp):
ATTGCTTGAGCTTTCGACTAAAGCGAAAACATGATCGC
Found at i:44985956 original size:16 final size:15
Alignment explanation
Indices: 44985935--44986002 Score: 82
Period size: 16 Copynumber: 4.3 Consensus size: 15
44985925 TTTGGTTCGC
*
44985935 TGTATTGAATTAGAGG
1 TGTATGGAA-TAGAGG
*
44985951 TGTATTGAATTAGAGG
1 TGTATGGAA-TAGAGG
44985967 TGTAATGGAATAGAGG
1 TGT-ATGGAATAGAGG
44985983 TGTAATGGAATAGAGG
1 TGT-ATGGAATAGAGG
44985999 TGTA
1 TGTA
44986003 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
15 1 0.02
16 44 0.88
17 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (15 bp):
TGTATGGAATAGAGG
Found at i:44986003 original size:16 final size:16
Alignment explanation
Indices: 44985945--44986004 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
44985935 TGTATTGAAT
*
44985945 TAGAGGTGT-ATTGAA
1 TAGAGGTGTAATGGAA
44985960 TTAGAGGTGTAATGGAA
1 -TAGAGGTGTAATGGAA
44985977 TAGAGGTGTAATGGAA
1 TAGAGGTGTAATGGAA
44985993 TAGAGGTGTAAT
1 TAGAGGTGTAAT
44986005 AGCAAATCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
16 37 0.88
17 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (16 bp):
TAGAGGTGTAATGGAA
Found at i:44986088 original size:39 final size:43
Alignment explanation
Indices: 44985983--44986092 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
44985973 GGAATAGAGG
44985983 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
44986028 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
44986068 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
44986093 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:44986291 original size:16 final size:15
Alignment explanation
Indices: 44986266--44986312 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
44986256 TATAATTTAG
44986266 TAAAATTCTTAACAT
1 TAAAATTCTTAACAT
*
44986281 TAAATATTCTT-ATA-
1 TAAA-ATTCTTAACAT
44986295 T-AAATTCTTAACAT
1 TAAAATTCTTAACAT
44986309 TAAA
1 TAAA
44986313 TATAATTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 2 0.08
15 8 0.31
16 6 0.23
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATTCTTAACAT
Found at i:44986312 original size:14 final size:14
Alignment explanation
Indices: 44986268--44986313 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 14
44986258 TAATTTAGTA
44986268 AAATTCTTAACATT
1 AAATTCTTAACATT
*
44986282 AAATATTCTT-ATA-T
1 -AA-ATTCTTAACATT
44986296 AAATTCTTAACATT
1 AAATTCTTAACATT
44986310 AAAT
1 AAAT
44986314 ATAATTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 6 0.23
15 4 0.15
16 6 0.23
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTCTTAACATT
Found at i:44994145 original size:19 final size:20
Alignment explanation
Indices: 44994096--44994146 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
44994086 TTAAATACAT
44994096 TTTTAAATTTT-TATAACAC
1 TTTTAAATTTTATATAACAC
* **
44994115 TTTTCAATTTTTATATATTA-
1 TTTT-AAATTTTATATAACAC
44994135 TTTTAAATTTTA
1 TTTTAAATTTTA
44994147 AAAAATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 11 0.42
20 10 0.38
21 5 0.19
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTAAATTTTATATAACAC
Found at i:44994163 original size:31 final size:33
Alignment explanation
Indices: 44994128--44994188 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
44994118 TCAATTTTTA
44994128 TATATTATTTTA-AA-TTT-TAAAAAATTATAAT
1 TATA-TATTTTAGAATTTTATAAAAAATTATAAT
44994159 TATATATTTTAGAATTTTATAAAAAATTAT
1 TATATATTTTAGAATTTTATAAAAAATTAT
44994189 TTTTAAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 7 0.26
31 6 0.22
32 3 0.11
33 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (33 bp):
TATATATTTTAGAATTTTATAAAAAATTATAAT
Done.