Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 49 of 199
Found at i:19403759 original size:10 final size:10
Alignment explanation
Indices: 19403744--19403772 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19403734 CCAACCAATC
19403744 TTCGGTGCCT
1 TTCGGTGCCT
19403754 TTCGGTGCCT
1 TTCGGTGCCT
19403764 TTCGGTGCC
1 TTCGGTGCC
19403773 AACTTTCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.31, T:0.38
Consensus pattern (10 bp):
TTCGGTGCCT
Found at i:19411734 original size:18 final size:18
Alignment explanation
Indices: 19411711--19411747 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19411701 GCTGGGCAGT
* *
19411711 AGAAGAAGGAGAAGAGAA
1 AGAAGAAGAAAAAGAGAA
19411729 AGAAGAAGAAAAAGAGAA
1 AGAAGAAGAAAAAGAGAA
19411747 A
1 A
19411748 AAAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAAAAAGAGAA
Found at i:19414490 original size:25 final size:23
Alignment explanation
Indices: 19414437--19414491 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
19414427 TAAAAATAAA
* *
19414437 AAATACTATTAAAATAATTTAAT
1 AAATAATATTAAAATAATTCAAT
19414460 ATAATAATATATAAAATAATTCATAT
1 A-AATAATAT-TAAAATAATTCA-AT
19414486 AAATAA
1 AAATAA
19414492 AAATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 7 0.26
25 16 0.59
26 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATAATATTAAAATAATTCAAT
Found at i:19414505 original size:18 final size:20
Alignment explanation
Indices: 19414456--19414506 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
19414446 TAAAATAATT
*
19414456 TAATATAATAATATATAAAA
1 TAATTTAATAATATATAAAA
*
19414476 TAATTCATATAA-ATA-AAAA
1 TAATTTA-ATAATATATAAAA
*
19414495 TATTTTAATAAT
1 TAATTTAATAAT
19414507 TTTTAAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 8 0.32
21 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTTAATAATATATAAAA
Found at i:19415035 original size:5 final size:6
Alignment explanation
Indices: 19415009--19415033 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19414999 AATCAGATCG
19415009 TTGTTT TTGTTT TTGTTT TTGTTT T
1 TTGTTT TTGTTT TTGTTT TTGTTT T
19415034 GTGGTTGCAT
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:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTGTTT
Found at i:19422492 original size:88 final size:90
Alignment explanation
Indices: 19422364--19422538 Score: 255
Period size: 88 Copynumber: 2.0 Consensus size: 90
19422354 TATATCACTG
*
19422364 GTAAAAAGTTTTAAGGCATATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGAT
1 GTAAAAAGTTTAAAGGCA-ATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGAT
19422429 GAGTCTCTGGA-TTGATCTAGAAGCA
65 GAGTCTCTGGATTTGATCTAGAAGCA
* * * * ** *
19422454 GTAAAATGTTTAAAGGC-ATAAACGAGATGGAGATATGAATGTGAAAGTAGATAGATCATGGATG
1 GTAAAAAGTTTAAAGGCAATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGATG
19422518 AGTCTCTGGATTTGATCTAGA
66 AGTCTCTGGATTTGATCTAGA
19422539 TTCAAGAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
88 51 0.67
89 10 0.13
90 15 0.20
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.26
Consensus pattern (90 bp):
GTAAAAAGTTTAAAGGCAATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGATG
AGTCTCTGGATTTGATCTAGAAGCA
Found at i:19427451 original size:37 final size:37
Alignment explanation
Indices: 19427410--19427483 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
19427400 TTGTTGAAAC
19427410 TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
1 TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
19427447 TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
1 TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
19427484 CTCAAATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (37 bp):
TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
Found at i:19430423 original size:18 final size:18
Alignment explanation
Indices: 19430402--19430438 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
19430392 TGTTATATAC
19430402 GAGTACCAACTTATTTCG
1 GAGTACCAACTTATTTCG
*
19430420 GAGTACTAACTTATTTCG
1 GAGTACCAACTTATTTCG
19430438 G
1 G
19430439 CGTTCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (18 bp):
GAGTACCAACTTATTTCG
Found at i:19438795 original size:103 final size:104
Alignment explanation
Indices: 19438581--19438789 Score: 381
Period size: 103 Copynumber: 2.0 Consensus size: 104
19438571 GAATATATAC
19438581 TCAAAAATGTAATAAGTATAAATTCACAAAAATATACCCTAAATACACATATAATATCAACTATT
1 TCAAAAATGTAATAAGTATAAATTCACAAAAATATACCCTAAATACACATATAATATCAACTATT
19438646 GATTAATATATATATATGCAGGTATATTTAATCATTTTA
66 GATTAATATATATATATGCAGGTATATTTAATCATTTTA
19438685 TCAAAAATGTAATAA-TATAAATTCACAAAAATATACCCTAAATACACATATAATATCAACTATT
1 TCAAAAATGTAATAAGTATAAATTCACAAAAATATACCCTAAATACACATATAATATCAACTATT
19438749 GATT-A-ATATATATATGCAGGTATA-TTAATCATTTTAA
66 GATTAATATATATATATGCAGGTATATTTAATCATTTT-A
19438786 TCAA
1 TCAA
19438790 TAAAATCTAT
Statistics
Matches: 104, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
100 11 0.11
101 24 0.23
102 1 0.01
103 53 0.51
104 15 0.14
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (104 bp):
TCAAAAATGTAATAAGTATAAATTCACAAAAATATACCCTAAATACACATATAATATCAACTATT
GATTAATATATATATATGCAGGTATATTTAATCATTTTA
Found at i:19438934 original size:22 final size:23
Alignment explanation
Indices: 19438906--19438956 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
19438896 ACAATAAAGA
*
19438906 TAAATAATATTTGTATT-AACAT
1 TAAATAATATTTATATTAAACAT
*
19438928 TAAATAATATTTATATTAAATAT
1 TAAATAATATTTATATTAAACAT
19438951 TAAATA
1 TAAATA
19438957 TTATCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATAATATTTATATTAAACAT
Found at i:19441000 original size:27 final size:27
Alignment explanation
Indices: 19440947--19440999 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
19440937 TATAACTTTT
19440947 TTTATTTACCAAAATATTATAAAAAAA
1 TTTATTTACCAAAATATTATAAAAAAA
*
19440974 TTTATTTACTAAAATA-TATAAAAAAA
1 TTTATTTACCAAAATATTATAAAAAAA
19441000 AACAAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (27 bp):
TTTATTTACCAAAATATTATAAAAAAA
Found at i:19441668 original size:19 final size:18
Alignment explanation
Indices: 19441644--19441731 Score: 81
Period size: 18 Copynumber: 4.7 Consensus size: 18
19441634 TCTAATTAAG
19441644 TAATAATTCTATTTCAATT
1 TAATAA-TCTATTTCAATT
*
19441663 TAATAAACTATTCTCAA-T
1 TAATAATCTATT-TCAATT
* *
19441681 TAACAACTCTATTTTAATT
1 TAATAA-TCTATTTCAATT
*
19441700 TAATAAACTATTCTC-ATT
1 TAATAATCTATT-TCAATT
19441718 TAATAACTCTATTT
1 TAATAA-TCTATTT
19441732 TCATTTAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
18 29 0.52
19 27 0.48
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATAATCTATTTCAATT
Found at i:19441693 original size:37 final size:37
Alignment explanation
Indices: 19441651--19441739 Score: 135
Period size: 37 Copynumber: 2.4 Consensus size: 37
19441641 AAGTAATAAT
19441651 TCTATTTCAATTTAATAAACTATTCTCAATTAACAAC
1 TCTATTTCAATTTAATAAACTATTCTCAATTAACAAC
* * *
19441688 TCTATTTTAATTTAATAAACTATTCTCATTTAATAAC
1 TCTATTTCAATTTAATAAACTATTCTCAATTAACAAC
19441725 TCTATTTTC-ATTTAA
1 TCTA-TTTCAATTTAA
19441740 AATATAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
37 44 0.94
38 3 0.06
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (37 bp):
TCTATTTCAATTTAATAAACTATTCTCAATTAACAAC
Found at i:19441735 original size:19 final size:18
Alignment explanation
Indices: 19441644--19441739 Score: 86
Period size: 19 Copynumber: 5.2 Consensus size: 18
19441634 TCTAATTAAG
19441644 TAATAATTCTA-TTTCAATT
1 TAATAA-TCTATTTTC-ATT
* * *
19441663 TAATAAACTATTCTCAAT
1 TAATAATCTATTTTCATT
* *
19441681 TAACAACTCTATTTTAATT
1 TAATAA-TCTATTTTCATT
* *
19441700 TAATAAACTATTCTCATT
1 TAATAATCTATTTTCATT
19441718 TAATAACTCTATTTTCATT
1 TAATAA-TCTATTTTCATT
19441737 TAA
1 TAA
19441740 AATATAAAAT
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
18 25 0.42
19 35 0.58
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATAATCTATTTTCATT
Found at i:19441907 original size:82 final size:82
Alignment explanation
Indices: 19441808--19441972 Score: 303
Period size: 82 Copynumber: 2.0 Consensus size: 82
19441798 TTAATTAAAA
19441808 TAGTCTAACATGTTTATGTTAGAAATCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
1 TAGTCTAACATGTTTATGTTAGAAATCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
19441873 TTTATGTTTCCATTATT
66 TTTATGTTTCCATTATT
* *
19441890 TAGTCTAACATGTTTATGTTATAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
1 TAGTCTAACATGTTTATGTTAGAAATCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
*
19441955 TTTATGTTTCCGTTATT
66 TTTATGTTTCCATTATT
19441972 T
1 T
19441973 TTTTCTTTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (82 bp):
TAGTCTAACATGTTTATGTTAGAAATCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
TTTATGTTTCCATTATT
Found at i:19442517 original size:27 final size:25
Alignment explanation
Indices: 19442487--19442545 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 25
19442477 ATTTTTTGTT
19442487 TTTTAGTATATTTTGGTAAATAAAAAA
1 TTTTA-TATATTTT-GTAAATAAAAAA
19442514 TTTTATAATATTTTGTAAATAAAAAA
1 TTTTAT-ATATTTTGTAAATAAAAAA
*
19442540 ATTTAT
1 TTTTAT
19442546 TTTATTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (25 bp):
TTTTATATATTTTGTAAATAAAAAA
Found at i:19442553 original size:26 final size:27
Alignment explanation
Indices: 19442494--19442545 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
19442484 GTTTTTTAGT
*
19442494 ATATTTTGGTAAATAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAATTTATA
19442521 ATATTTT-GTAAATAAAAAAATTTAT
1 ATATTTTGGTAAATAAAAAAATTTAT
19442546 TTTATTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAATTTATA
Found at i:19442554 original size:27 final size:27
Alignment explanation
Indices: 19442494--19442556 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 27
19442484 GTTTTTTAGT
* *
19442494 ATATTTTGGTAAATAAAAAATTTTATA
1 ATATTTTTGTAAATAAAAAAATTTATA
*
19442521 ATA-TTTTGTAAATAAAAAAATTTATT
1 ATATTTTTGTAAATAAAAAAATTTATA
*
19442547 TTATTTTTGT
1 ATATTTTTGT
19442557 TATTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.71
27 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (27 bp):
ATATTTTTGTAAATAAAAAAATTTATA
Found at i:19442561 original size:14 final size:13
Alignment explanation
Indices: 19442541--19442572 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
19442531 AATAAAAAAA
19442541 TTTATTTTATTTT
1 TTTATTTTATTTT
19442554 TGTTATTTTATTTT
1 T-TTATTTTATTTT
19442568 TTTAT
1 TTTAT
19442573 AATAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:19447578 original size:19 final size:19
Alignment explanation
Indices: 19447540--19447593 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
19447530 ATACTCATTT
*
19447540 AAAATAGT-GTAACAAAAA
1 AAAATAGTAATAACAAAAA
* *
19447558 AAACGTTGTAATAACAAAAA
1 AAA-ATAGTAATAACAAAAA
19447578 AAAATAGTAATAACAA
1 AAAATAGTAATAACAA
19447594 TCGATCTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 3 0.10
19 14 0.48
20 12 0.41
ACGTcount: A:0.65, C:0.07, G:0.09, T:0.19
Consensus pattern (19 bp):
AAAATAGTAATAACAAAAA
Found at i:19450780 original size:18 final size:17
Alignment explanation
Indices: 19450752--19450795 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
19450742 ATAATTTATT
19450752 TTTAAAAATACAATTAA
1 TTTAAAAATACAATTAA
* *
19450769 TTTAATAAATACTATTAT
1 TTTAA-AAATACAATTAA
19450787 TTTGAAAAA
1 TTT-AAAAA
19450796 AAAAATTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 16 0.70
19 2 0.09
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTAAAAATACAATTAA
Found at i:19453238 original size:30 final size:30
Alignment explanation
Indices: 19453204--19453262 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
19453194 TACTATTAAC
* *
19453204 ATTTAATGTCTGATTCAGTGATCGTTAAAT
1 ATTTAATGTCTGATTCAATGATCATTAAAT
*
19453234 ATTTAATGTTTGATTCAATGATCATTAAA
1 ATTTAATGTCTGATTCAATGATCATTAAA
19453263 GTTAGTTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (30 bp):
ATTTAATGTCTGATTCAATGATCATTAAAT
Found at i:19453335 original size:21 final size:21
Alignment explanation
Indices: 19453306--19453347 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19453296 GATACCTGGT
*
19453306 AAAAAGTATCGATACTTTTTG
1 AAAAAGTATCGACACTTTTTG
*
19453327 AAAATGTATCGACACTTTTTG
1 AAAAAGTATCGACACTTTTTG
19453348 TAATTGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (21 bp):
AAAAAGTATCGACACTTTTTG
Found at i:19475986 original size:21 final size:21
Alignment explanation
Indices: 19475960--19476000 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19475950 ATCTGCTCAA
* *
19475960 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
19475981 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
19476001 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:19481257 original size:119 final size:116
Alignment explanation
Indices: 19481061--19481403 Score: 546
Period size: 119 Copynumber: 3.0 Consensus size: 116
19481051 TTTTATATTT
19481061 TTCTCTCAGCACTCTACAATTTTTATTTTTA--TTACTTATTATTAATAATTATTATTTTAAAAA
1 TTCTCTCAGCACTCTACAATTTTTATTTTTATTTTACTTATTATTAATAATTATTA-TTTAAAAA
*
19481124 ATTAAAATT-TTCTTTTTGGTGTTTCATAAGACTACTTTATAATAATAATAAAAA
65 ATT-AAATTGTTCTTTTTGGTGTTTCATAAGACTACTTTCTAATAA-AA-AAAAA
19481178 TTCTCTCAGCACTCTACAATTTTTATTTTTATTTTACTTATTATTAATAATTATTATTTAAAAAA
1 TTCTCTCAGCACTCTACAATTTTTATTTTTATTTTACTTATTATTAATAATTATTATTT-AAAAA
*
19481243 ATTAAATTGTTCTTTTTGGTGTTTCATAAGACTACTTTCTAAT-AAAAAATA
65 ATTAAATTGTTCTTTTTGGTGTTTCATAAGACTACTTTCTAATAAAAAAAAA
19481294 TTCTCTCAGCACTCTACAA-----A-TTTT-TTTTACTTATTATTAATAATTATTATTTAAAAAA
1 TTCTCTCAGCACTCTACAATTTTTATTTTTATTTTACTTATTATTAATAATTATTATTTAAAAAA
19481352 TTAAATTGTTCTTTTTGGTGTTTCATAAGACTACTTTCTAATAAAAAAAAA
66 TTAAATTGTTCTTTTTGGTGTTTCATAAGACTACTTTCTAATAAAAAAAAA
19481403 T
1 T
19481404 AACAATTTAT
Statistics
Matches: 218, Mismatches: 3, Indels: 18
0.91 0.01 0.08
Matches are distributed among these distances:
108 48 0.22
109 36 0.17
110 4 0.02
111 1 0.00
116 23 0.11
117 33 0.15
118 9 0.04
119 64 0.29
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (116 bp):
TTCTCTCAGCACTCTACAATTTTTATTTTTATTTTACTTATTATTAATAATTATTATTTAAAAAA
TTAAATTGTTCTTTTTGGTGTTTCATAAGACTACTTTCTAATAAAAAAAAA
Found at i:19495862 original size:12 final size:12
Alignment explanation
Indices: 19495845--19495869 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19495835 AAAAATTAAT
19495845 TTTAATTATTCA
1 TTTAATTATTCA
19495857 TTTAATTATTCA
1 TTTAATTATTCA
19495869 T
1 T
19495870 CTTTTTTAAT
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:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAATTATTCA
Found at i:19496793 original size:22 final size:22
Alignment explanation
Indices: 19496766--19496833 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
19496756 ATTTTGAAAA
*
19496766 ATTATTTATTTATAATTTTAAT
1 ATTATTTATTAATAATTTTAAT
* * *
19496788 ATTATTAATATGAT-ATTTTTAT
1 ATTATTTAT-TAATAATTTTAAT
* *
19496810 TTTATTTCTTAATAATTTTAAT
1 ATTATTTATTAATAATTTTAAT
19496832 AT
1 AT
19496834 GTTAATTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 3 0.09
22 29 0.83
23 3 0.09
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (22 bp):
ATTATTTATTAATAATTTTAAT
Found at i:19496822 original size:35 final size:36
Alignment explanation
Indices: 19496765--19496844 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 36
19496755 AATTTTGAAA
19496765 AATTATTTATTTATAATTTTAAT-ATTATTAATATGAT
1 AATT-TTTATTTATAATTTTAATAATT-TTAATATGAT
* *
19496802 -ATTTTTATTT-TATTTCTTAATAATTTTAATATGTT
1 AATTTTTATTTATAATT-TTAATAATTTTAATATGAT
19496837 AATTTTTA
1 AATTTTTA
19496845 ATAAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
34 4 0.11
35 21 0.55
36 13 0.34
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (36 bp):
AATTTTTATTTATAATTTTAATAATTTTAATATGAT
Found at i:19501528 original size:21 final size:22
Alignment explanation
Indices: 19501468--19501531 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
19501458 CAGAAGCAGT
* *
19501468 ATACAACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
19501490 A-ACGACACACT-T-GATGCCT-A
1 ATACGACACA-TATAG-TGCCTGA
19501510 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
19501532 TCGGCAAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
20 4 0.12
21 26 0.76
22 4 0.12
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:19503834 original size:47 final size:47
Alignment explanation
Indices: 19503783--19503878 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
19503773 TTTTGTAGTG
* *
19503783 TTAATTATATTTTTTAATCAAACAATATAAGTAATATAAAATATTGT
1 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAAAATTGT
19503830 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAAAATTGT
1 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAAAATTGT
19503877 TT
1 TT
19503879 GAAGACCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (47 bp):
TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAAAATTGT
Found at i:19509868 original size:137 final size:137
Alignment explanation
Indices: 19509706--19509980 Score: 514
Period size: 137 Copynumber: 2.0 Consensus size: 137
19509696 TGGCATTCTC
19509706 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
1 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
* * **
19509771 TTTGTGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTTTAGTTCTCTTC
66 CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
19509836 TATTTTA
131 TATTTTA
19509843 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
1 TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
19509908 CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
66 CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
19509973 TATTTTA
131 TATTTTA
19509980 T
1 T
19509981 GTGTGAAATT
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (137 bp):
TACTCTCAATTAATTGTTGCTTGGTATGACTTTTAGACCTTTAGCAAAGTGCTTATATGAATATC
CTTGAGAGCATCTATTTTATCTTTCTACATTGTGGAAGTATTAGAAGAATTTTACAGTTCTCTTC
TATTTTA
Found at i:19517267 original size:18 final size:18
Alignment explanation
Indices: 19517246--19517285 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
19517236 CGAAGTGTTG
* *
19517246 GAGGATGATGGTGATGAT
1 GAGGACGATGGCGATGAT
19517264 GAGGACGATGGCGATGAT
1 GAGGACGATGGCGATGAT
19517282 GAGG
1 GAGG
19517286 GTGGTGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.47, T:0.20
Consensus pattern (18 bp):
GAGGACGATGGCGATGAT
Found at i:19524622 original size:32 final size:33
Alignment explanation
Indices: 19524581--19524648 Score: 120
Period size: 32 Copynumber: 2.1 Consensus size: 33
19524571 TTTAAATTTG
19524581 ATAAATCTACTTTTTTATAC-TTTTCTAATGTT
1 ATAAATCTACTTTTTTATACTTTTTCTAATGTT
*
19524613 ATAAATCTACTTTTTTATACTTTTTTTAATGTT
1 ATAAATCTACTTTTTTATACTTTTTCTAATGTT
19524646 ATA
1 ATA
19524649 TTAAACCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 20 0.59
33 14 0.41
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.57
Consensus pattern (33 bp):
ATAAATCTACTTTTTTATACTTTTTCTAATGTT
Found at i:19526263 original size:14 final size:14
Alignment explanation
Indices: 19526243--19526280 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
19526233 GTTTAGGATC
19526243 ATTATAATTTTAAA
1 ATTATAATTTTAAA
* *
19526257 TTTATAATTATAAA
1 ATTATAATTTTAAA
19526271 ATTAT-ATTTT
1 ATTATAATTTT
19526281 GATCCCTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATAATTTTAAA
Found at i:19526465 original size:19 final size:20
Alignment explanation
Indices: 19526427--19526472 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
19526417 GACAAATTAT
* *
19526427 ATATTATAATATATATTTTA
1 ATATTATAATATAGACTTTA
19526447 ATATTA-AATATAGACTTTA
1 ATATTATAATATAGACTTTA
*
19526466 ATGTTAT
1 ATATTAT
19526473 TTAAATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (20 bp):
ATATTATAATATAGACTTTA
Found at i:19527118 original size:20 final size:20
Alignment explanation
Indices: 19527093--19527173 Score: 85
Period size: 20 Copynumber: 4.0 Consensus size: 20
19527083 ATTTAATTAT
19527093 AAAAATTAT-AAAAAGTCATA
1 AAAAATTATCAAAAA-TCATA
*
19527113 AAAAATTATCAAAAACCATA
1 AAAAATTATCAAAAATCATA
* *
19527133 TAAAATTAT-AAATAATCAGA
1 AAAAATTATCAAA-AATCATA
* *
19527153 TAAAATTATCAAAAATAATA
1 AAAAATTATCAAAAATCATA
19527173 A
1 A
19527174 TAATTACTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.06
20 40 0.78
21 8 0.16
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAATTATCAAAAATCATA
Found at i:19527223 original size:10 final size:10
Alignment explanation
Indices: 19527204--19527240 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
19527194 TGATATAAAC
19527204 TTAT-AAATA
1 TTATAAAATA
19527213 TTATAAAATA
1 TTATAAAATA
19527223 TTATAAAATA
1 TTATAAAATA
19527233 TTATAAAA
1 TTATAAAA
19527241 GATATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.15
10 23 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TTATAAAATA
Found at i:19527233 original size:20 final size:19
Alignment explanation
Indices: 19527204--19527250 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
19527194 TGATATAAAC
19527204 TTATAAATATTATAAAATA
1 TTATAAATATTATAAAATA
*
19527223 TTATAAAATATTATAAAAGA
1 TTAT-AAATATTATAAAATA
19527243 -TATAAATA
1 TTATAAATA
19527251 AATCTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 7 0.27
20 14 0.54
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TTATAAATATTATAAAATA
Found at i:19527268 original size:10 final size:10
Alignment explanation
Indices: 19527208--19527268 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
19527198 ATAAACTTAT
*
19527208 AAATATTATA
1 AAATATAATA
*
19527218 AAATATTATA
1 AAATATAATA
*
19527228 AAATATTATAA
1 AAATATAAT-A
19527239 AAGATATAA-A
1 AA-ATATAATA
*
19527249 TAAATCTAATA
1 -AAATATAATA
19527260 AAATATAAT
1 AAATATAAT
19527269 TGTAAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
10 33 0.75
11 6 0.14
12 5 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (10 bp):
AAATATAATA
Found at i:19527809 original size:9 final size:9
Alignment explanation
Indices: 19527795--19527941 Score: 56
Period size: 9 Copynumber: 16.0 Consensus size: 9
19527785 TATATCGATG
19527795 TTAATATTT
1 TTAATATTT
19527804 TTAATATTT
1 TTAATATTT
* *
19527813 TTCAAGAATT
1 TT-AATATTT
*
19527823 CTAATATGTT
1 TTAATAT-TT
19527833 TT--T-TTT
1 TTAATATTT
19527839 TTAATATTT
1 TTAATATTT
* *
19527848 TAAATAGGTT
1 TTAATA-TTT
19527858 TTATATAGTTT
1 TTA-ATA-TTT
19527869 ATTAGAT-TTT
1 -TTA-ATATTT
19527879 TT-ATATTT
1 TTAATATTT
*
19527887 TT-ATAATAT
1 TTAAT-ATTT
**
19527896 TT-ATAAGT
1 TTAATATTT
*
19527904 TTAATAATT
1 TTAATATTT
**
19527913 TTATATAAAAT
1 TTA-AT-ATTT
19527924 TTAATATTT
1 TTAATATTT
19527933 TTAATATTT
1 TTAATATTT
19527942 ATTTATTATA
Statistics
Matches: 107, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
6 4 0.04
7 3 0.03
8 13 0.12
9 50 0.47
10 20 0.19
11 12 0.11
12 5 0.05
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (9 bp):
TTAATATTT
Found at i:19527941 original size:28 final size:26
Alignment explanation
Indices: 19527874--19527941 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
19527864 AGTTTATTAG
* *
19527874 ATTTTTTATATTTTTATAATATTTAT
1 ATTTTTAATATTTTTATAAAATTTAT
**
19527900 AAGTTTAATAATTTTATATAAAATTTAAT
1 ATTTTTAAT-ATTTT-TATAAAATTT-AT
19527929 ATTTTTAATATTT
1 ATTTTTAATATTT
19527942 ATTTATTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 6 0.18
27 5 0.15
28 13 0.39
29 9 0.27
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (26 bp):
ATTTTTAATATTTTTATAAAATTTAT
Found at i:19528444 original size:5 final size:5
Alignment explanation
Indices: 19528392--19528437 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
19528382 ATGTGTTAAA
* *
19528392 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATT ATAT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATATT ATAT
19528438 ATTATATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 27 0.77
6 8 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (5 bp):
ATATT
Found at i:19529783 original size:18 final size:19
Alignment explanation
Indices: 19529760--19529798 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19529750 ATATATAGAT
19529760 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
19529778 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
19529797 AT
1 AT
19529799 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:19530315 original size:18 final size:19
Alignment explanation
Indices: 19530294--19530334 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
19530284 AATGAAATGA
19530294 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
19530312 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
19530331 GAAA
1 GAAA
19530335 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:19534862 original size:5 final size:5
Alignment explanation
Indices: 19534836--19534890 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
19534826 ATGTGTTAAA
* *
19534836 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATT ATA-T ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATATT ATATT ATATT
19534887 ATAT
1 ATAT
19534891 AAATAAGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
4 4 0.09
5 31 0.72
6 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:19534891 original size:26 final size:24
Alignment explanation
Indices: 19534836--19534891 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
19534826 ATGTGTTAAA
19534836 ATATATATATTAAATTATTATTAT
1 ATATATATATTAAATTATTATTAT
*
19534860 ATTATAGTATATTATATTA-TA-TAT
1 A-TATA-TATATTAAATTATTATTAT
19534884 AT-TATATA
1 ATATATATA
19534892 AATAAGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 4 0.14
22 2 0.07
23 1 0.03
24 5 0.17
25 6 0.21
26 11 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATATATATTAAATTATTATTAT
Found at i:19536222 original size:18 final size:19
Alignment explanation
Indices: 19536199--19536237 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19536189 ATATATAGAT
19536199 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
19536217 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
19536236 AT
1 AT
19536238 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:19536754 original size:18 final size:19
Alignment explanation
Indices: 19536733--19536773 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
19536723 AATGAAATGA
19536733 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
19536751 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
19536770 GAAA
1 GAAA
19536774 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:19558267 original size:55 final size:56
Alignment explanation
Indices: 19558183--19558406 Score: 156
Period size: 58 Copynumber: 3.9 Consensus size: 56
19558173 CATTTTGGGA
* * * * *
19558183 CTTGAACTTGACAAATTTTTTCATATTGGGG-TCT-AATTTTTTGTCCAAGTTAGGT
1 CTTGAACTTGACAAATTTCTTCACATTGGGGCT-TAAATTTTTTATCCAAGTCAGGC
*
19558238 CTTGAACTTGATAAATATTCTT-ACATTGGGGCTTGAAAATTTTTTATCCAAGTCAGGC
1 CTTGAACTTGACAAAT-TTCTTCACATTGGGGCTT--AAATTTTTTATCCAAGTCAGGC
* ** * * *
19558296 CTTGAACTT-AGCAAATATCCCCACATTGAGGCTTGAAATTTTTT-TGCCCAAGTTAGGG
1 CTTGAACTTGA-CAAATTTCTTCACATTGGGGCTT-AAATTTTTTAT--CCAAGTCAGGC
* * *
19558354 CTTGAACTT-AGCAAATATTC-CCACATTGTGGCTTCAACTTTTTTTATCCAAGT
1 CTTGAACTTGA-CAAAT-TTCTTCACATTGGGGCTT-AA-ATTTTTTATCCAAGT
19558407 TAGTCCTTAA
Statistics
Matches: 139, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
55 24 0.17
56 6 0.04
57 12 0.09
58 88 0.63
59 8 0.06
60 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (56 bp):
CTTGAACTTGACAAATTTCTTCACATTGGGGCTTAAATTTTTTATCCAAGTCAGGC
Found at i:19558300 original size:58 final size:58
Alignment explanation
Indices: 19558217--19558414 Score: 227
Period size: 58 Copynumber: 3.4 Consensus size: 58
19558207 ATTGGGGTCT
* * * ** *
19558217 AATTTTTTGTCCAAGTTAGGTCTTGAACTT-GATAAATATTCTTACATTGGGGCTTGAA
1 AATTTTTTATCCAAGTTAGGCCTTGAACTTAG-CAAATATTCCCACATTGAGGCTTGAA
* *
19558275 AATTTTTTATCCAAGTCAGGCCTTGAACTTAGCAAATATCCCCACATTGAGGCTTGAA
1 AATTTTTTATCCAAGTTAGGCCTTGAACTTAGCAAATATTCCCACATTGAGGCTTGAA
* ** * * *
19558333 ATTTTTTTGCCCAAGTTAGGGCTTGAACTTAGCAAATATTCCCACATTGTGGCTTCAA
1 AATTTTTTATCCAAGTTAGGCCTTGAACTTAGCAAATATTCCCACATTGAGGCTTGAA
** *
19558391 CTTTTTTTATCCAAGTTAGTCCTT
1 AATTTTTTATCCAAGTTAGGCCTT
19558415 AAAAATCCTA
Statistics
Matches: 118, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
58 117 0.99
59 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (58 bp):
AATTTTTTATCCAAGTTAGGCCTTGAACTTAGCAAATATTCCCACATTGAGGCTTGAA
Found at i:19578637 original size:32 final size:31
Alignment explanation
Indices: 19578575--19578668 Score: 152
Period size: 31 Copynumber: 3.0 Consensus size: 31
19578565 AGGCAAATTA
*
19578575 CAAGAGTAATTGAATCTTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
19578606 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
* *
19578638 AAAGAGTAATTGAATTCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
19578669 AAAATTATCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 30 0.51
32 29 0.49
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:19581820 original size:14 final size:14
Alignment explanation
Indices: 19581801--19581849 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
19581791 AGGTAGGCAA
19581801 CTTTTTTTTTTGCG
1 CTTTTTTTTTTGCG
*
19581815 CTTTTTTGCTTTT-TG
1 CTTTTTT--TTTTGCG
19581830 CTTTTTTTTTTGCG
1 CTTTTTTTTTTGCG
19581844 CTTTTT
1 CTTTTT
19581850 ACTCTCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 4 0.13
14 14 0.47
15 8 0.27
16 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.12, T:0.73
Consensus pattern (14 bp):
CTTTTTTTTTTGCG
Found at i:19581869 original size:43 final size:44
Alignment explanation
Indices: 19581815--19581925 Score: 167
Period size: 43 Copynumber: 2.6 Consensus size: 44
19581805 TTTTTTTGCG
19581815 CTTTTTT--GCTTTTTGCTTTTTTTTTTGCGCTTTTTACTCTCT
1 CTTTTTTGCGCTTTTTGCTTTTTTTTTTGCGCTTTTTACTCTCT
*
19581857 -TTTTTTGCGCTTTTT-TTGTTTTTTTTTGCGCTTTTTACTCTCT
1 CTTTTTTGCGCTTTTTGCT-TTTTTTTTTGCGCTTTTTACTCTCT
19581900 CTTTTTTGCGCTTTTTTGCTTTTTTT
1 CTTTTTTGCGC-TTTTTGCTTTTTTT
19581926 GCTTTTTTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
41 6 0.10
42 1 0.02
43 32 0.52
44 10 0.16
45 11 0.18
46 1 0.02
ACGTcount: A:0.02, C:0.17, G:0.11, T:0.70
Consensus pattern (44 bp):
CTTTTTTGCGCTTTTTGCTTTTTTTTTTGCGCTTTTTACTCTCT
Found at i:19581871 original size:23 final size:22
Alignment explanation
Indices: 19581834--19581915 Score: 121
Period size: 22 Copynumber: 3.7 Consensus size: 22
19581824 TTTTTGCTTT
19581834 TTTTTTTGCGCTTTTTACTCTC
1 TTTTTTTGCGCTTTTTACTCTC
* * *
19581856 TTTTTTTGCGCTTTTT-TTGTT
1 TTTTTTTGCGCTTTTTACTCTC
19581877 TTTTTTTGCGCTTTTTACTCTC
1 TTTTTTTGCGCTTTTTACTCTC
19581899 TCTTTTTTGCGCTTTTT
1 T-TTTTTTGCGCTTTTT
19581916 TGCTTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.35
22 19 0.37
23 15 0.29
ACGTcount: A:0.02, C:0.18, G:0.11, T:0.68
Consensus pattern (22 bp):
TTTTTTTGCGCTTTTTACTCTC
Found at i:19581923 original size:9 final size:9
Alignment explanation
Indices: 19581901--19581954 Score: 63
Period size: 10 Copynumber: 5.7 Consensus size: 9
19581891 TTACTCTCTC
*
19581901 TTTTTTGCGC
1 TTTTTTGC-T
19581911 TTTTTTGCT
1 TTTTTTGCT
19581920 TTTTTTGCTT
1 TTTTTTGC-T
19581930 TTTTTTGCT
1 TTTTTTGCT
*
19581939 GTTTTTGCT
1 TTTTTTGCT
19581948 GTTTTTT
1 -TTTTTT
19581955 TTACTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
9 17 0.44
10 22 0.56
ACGTcount: A:0.00, C:0.11, G:0.15, T:0.74
Consensus pattern (9 bp):
TTTTTTGCT
Found at i:19582570 original size:32 final size:31
Alignment explanation
Indices: 19582508--19582601 Score: 152
Period size: 31 Copynumber: 3.0 Consensus size: 31
19582498 AGGCAAATTA
*
19582508 CAAGAGTAATTGAATCTTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
19582539 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
* *
19582571 AAAGAGTAATTGAATTCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
19582602 AAAACTATCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 30 0.51
32 29 0.49
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:19588111 original size:23 final size:24
Alignment explanation
Indices: 19588085--19588129 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
19588075 TTTTTTTAAA
*
19588085 AAAAATTTGATGATA-TAATTTTT
1 AAAAATTTGATGAGATTAATTTTT
* *
19588108 AAAATTTTTATGAGATTAATTT
1 AAAAATTTGATGAGATTAATTT
19588130 ACCAATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
AAAAATTTGATGAGATTAATTTTT
Found at i:19590741 original size:17 final size:18
Alignment explanation
Indices: 19590719--19590753 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
19590709 GGTGGATAAG
19590719 AAATAATGCCTA-TTTTT
1 AAATAATGCCTAGTTTTT
19590736 AAATAATGCCTAGTTTTT
1 AAATAATGCCTAGTTTTT
19590754 TTAGTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (18 bp):
AAATAATGCCTAGTTTTT
Found at i:19611506 original size:80 final size:80
Alignment explanation
Indices: 19611410--19611569 Score: 286
Period size: 80 Copynumber: 2.0 Consensus size: 80
19611400 GTCCGGCTCG
19611410 ACGGCCTGCCCAAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGGCTTTG-GCA
1 ACGGCCTGCCCAAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGG-TTTGAGCA
19611474 AAAAAACGAGGCCCGT
65 AAAAAACGAGGCCCGT
**
19611490 ACGGCCTGCCTGAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGGTTTGAGCAA
1 ACGGCCTGCCCAAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGGTTTGAGCAA
19611555 AAAAACGAGGCCCGT
66 AAAAACGAGGCCCGT
19611570 TTAAAAAACG
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
79 4 0.05
80 73 0.95
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (80 bp):
ACGGCCTGCCCAAAATATGGGAGGGTTCAGGTAAAAATATAGGCCCGAAATATGGGTTTGAGCAA
AAAAACGAGGCCCGT
Found at i:19611697 original size:6 final size:7
Alignment explanation
Indices: 19611649--19611695 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
19611639 ATAAATATAT
19611649 ATTTTTA
1 ATTTTTA
*
19611656 TTTTTTA
1 ATTTTTA
*
19611663 TTTTTTA
1 ATTTTTA
19611670 ATTTTTA
1 ATTTTTA
19611677 ATTTTTA
1 ATTTTTA
19611684 ATTTTTA
1 ATTTTTA
19611691 ATTTT
1 ATTTT
19611696 AAAATACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
ATTTTTA
Found at i:19616571 original size:5 final size:5
Alignment explanation
Indices: 19616563--19616588 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19616553 ATAAATAAGT
19616563 TATTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA T
19616589 TATATAAACA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:19616672 original size:16 final size:19
Alignment explanation
Indices: 19616629--19616679 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
19616619 ATGGAAATTG
19616629 AAACGAAAACAGAGAAGCAA
1 AAACGAAAA-AGAGAAGCAA
19616649 AAACGAAAAAGA-AAG-AA
1 AAACGAAAAAGAGAAGCAA
19616666 AAA-GAAAAAGAGAA
1 AAACGAAAAAGAGAA
19616680 AGAAGGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.27
17 7 0.23
18 3 0.10
19 3 0.10
20 9 0.30
ACGTcount: A:0.73, C:0.08, G:0.20, T:0.00
Consensus pattern (19 bp):
AAACGAAAAAGAGAAGCAA
Found at i:19616679 original size:18 final size:19
Alignment explanation
Indices: 19616629--19616683 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
19616619 ATGGAAATTG
19616629 AAACGAAAACAGAG-AAGCAA
1 AAACGAAAA-AGAGAAAG-AA
19616649 AAACG-AAAA-AGAAAGAA
1 AAACGAAAAAGAGAAAGAA
19616666 AAA-GAAAAAGAGAAAGAA
1 AAACGAAAAAGAGAAAGAA
19616684 GGAAGCCCCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.03
17 11 0.34
18 12 0.38
19 3 0.09
20 5 0.16
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (19 bp):
AAACGAAAAAGAGAAAGAA
Found at i:19617611 original size:27 final size:25
Alignment explanation
Indices: 19617555--19617612 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
19617545 ACTTTAGTGC
* * *
19617555 GCTCTCTGATTATTAGCATGCTGGT
1 GCTCTCTGATTACTAGCACGCAGGT
19617580 GCTCTCTGATTACTAGCACGTCA-GT
1 GCTCTCTGATTACTAGCACG-CAGGT
*
19617605 GTTCTCTG
1 GCTCTCTG
19617613 TTTAGCACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGCAGGT
Found at i:19617627 original size:22 final size:22
Alignment explanation
Indices: 19617593--19617636 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19617583 CTCTGATTAC
19617593 TAGCACGTCAGTGTTCTCTGTT
1 TAGCACGTCAGTGTTCTCTGTT
* *
19617615 TAGCACTTTAGTGTTCTCTGTT
1 TAGCACGTCAGTGTTCTCTGTT
19617637 CATTAGTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (22 bp):
TAGCACGTCAGTGTTCTCTGTT
Found at i:19618728 original size:17 final size:17
Alignment explanation
Indices: 19618706--19618744 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
19618696 TGCGGATGAA
*
19618706 AAATGCCCTTGGCTGAT
1 AAATGCCCTTGACTGAT
* *
19618723 AAATGCTCTTGACTGGT
1 AAATGCCCTTGACTGAT
19618740 AAATG
1 AAATG
19618745 GACCTCGTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (17 bp):
AAATGCCCTTGACTGAT
Found at i:19620439 original size:22 final size:22
Alignment explanation
Indices: 19620411--19620456 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
19620401 CACCAAAGCT
19620411 TGGGTTTCGTGATATCGCTACC
1 TGGGTTTCGTGATATCGCTACC
19620433 TGGGTTTCGTGATATCGCTACC
1 TGGGTTTCGTGATATCGCTACC
19620455 TG
1 TG
19620457 ACAGGGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (22 bp):
TGGGTTTCGTGATATCGCTACC
Found at i:19623982 original size:37 final size:36
Alignment explanation
Indices: 19623906--19623979 Score: 87
Period size: 39 Copynumber: 2.0 Consensus size: 36
19623896 TTAGTTCAGT
*
19623906 TTCACTTTTTCACTTTCAATCACAATTCAATTCAAAA
1 TTCACTTTTCCACTTTCAATCACAATTCAATT-AAAA
*
19623943 TTCACTTTTCCATTTTTCAAATCA-ATATTCAATTAAA
1 TTCACTTTTCCA-CTTTC-AATCACA-ATTCAATTAAA
19623980 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 11 0.34
38 8 0.25
39 13 0.41
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (36 bp):
TTCACTTTTCCACTTTCAATCACAATTCAATTAAAA
Found at i:19628729 original size:40 final size:40
Alignment explanation
Indices: 19628651--19628761 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 40
19628641 ATAAGAATAT
* *
19628651 GTATGTGTATATAAATTATATGAAAATATAAAACATATAA
1 GTATGTGTATATAAATTATAAGAAAATAAAAAACATATAA
* **
19628691 GTATGTGTATAT-ATTTATAAG-AAATAAAAAATGTATATA
1 GTATGTGTATATAAATTATAAGAAAATAAAAAACATATA-A
*
19628730 GATATATAG-ATATAAATTATAA-AAAATAAAAA
1 G-TATGT-GTATATAAATTATAAGAAAATAAAAA
19628762 TATAACAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
38 13 0.22
39 9 0.15
40 20 0.34
41 17 0.29
ACGTcount: A:0.55, C:0.01, G:0.10, T:0.34
Consensus pattern (40 bp):
GTATGTGTATATAAATTATAAGAAAATAAAAAACATATAA
Found at i:19628858 original size:21 final size:22
Alignment explanation
Indices: 19628822--19628864 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
19628812 TAAATGAGCA
19628822 AATAACAGTAATAATAATTAAT
1 AATAACAGTAATAATAATTAAT
*
19628844 AATAACAGT-ATAATATTTAAT
1 AATAACAGTAATAATAATTAAT
19628865 TTATTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (22 bp):
AATAACAGTAATAATAATTAAT
Found at i:19632188 original size:67 final size:67
Alignment explanation
Indices: 19632077--19632208 Score: 221
Period size: 67 Copynumber: 2.0 Consensus size: 67
19632067 TTTTCAATTC
* *
19632077 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACGGGCTTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACAGGATTACCAGTCCAGGCTAAATCCCCTG
19632142 CA
66 CA
*
19632144 AGAGAGCAGC-CTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
1 AGAGAGCA-CACTCCCGCGAACCTCATTTCTTACAACAGGATTACCAGTCCAGGCTAAATCCCCT
19632208 G
65 G
19632209 TAATATAAAC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 60 0.98
68 1 0.02
ACGTcount: A:0.27, C:0.35, G:0.19, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACAGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:19641333 original size:6 final size:6
Alignment explanation
Indices: 19641322--19641358 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
19641312 AAAAATATAA
19641322 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T
19641359 TATATTAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:19648004 original size:22 final size:24
Alignment explanation
Indices: 19647954--19648004 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
19647944 TTGCAATGCT
19647954 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
19647979 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
19648000 TTTAT
1 TTTAT
19648005 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:19648220 original size:34 final size:35
Alignment explanation
Indices: 19648162--19648228 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
19648152 CAAATACCAG
19648162 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
19648197 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
19648229 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:19654701 original size:16 final size:16
Alignment explanation
Indices: 19654680--19654720 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
19654670 CATCTATAAT
*
19654680 ACACACACA-GACACAG
1 ACACACACATG-CACAC
19654696 ACACACACATGCACAC
1 ACACACACATGCACAC
19654712 ACACACACA
1 ACACACACA
19654721 CGGAGAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.49, C:0.41, G:0.07, T:0.02
Consensus pattern (16 bp):
ACACACACATGCACAC
Found at i:19657149 original size:21 final size:21
Alignment explanation
Indices: 19657123--19657188 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
19657113 GATCTGATAG
19657123 GAGATTATACGAAGAATATAA
1 GAGATTATACGAAGAATATAA
* * * *
19657144 GAGATTATATGAAG-CT-GAG
1 GAGATTATACGAAGAATATAA
19657163 GAGATTATACGAAGAATATAA
1 GAGATTATACGAAGAATATAA
19657184 GAGAT
1 GAGAT
19657189 ACGAACAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 14 0.40
20 2 0.06
21 19 0.54
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (21 bp):
GAGATTATACGAAGAATATAA
Found at i:19663233 original size:99 final size:99
Alignment explanation
Indices: 19662903--19663198 Score: 511
Period size: 99 Copynumber: 3.0 Consensus size: 99
19662893 GGCGAAAGCC
* * *
19662903 GCATCCTCTTTGCTGCTGGTTGCTCGGATAAATCTGCCAGAGAATCATTGACAATGATGGCCTCC
1 GCATCCTCTTTGCTGCCGGTTGCTCAGATAAATCTGCAAGAGAATCATTGACAAT-A--GCCTCC
19662968 TTGTTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
63 TTGTTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
* *
19663005 GCATCCTCTTTGCTGCCGGTTGCTCAGATAATTCTGCAAGAGAATCATTGACGATAGCCTCCTTG
1 GCATCCTCTTTGCTGCCGGTTGCTCAGATAAATCTGCAAGAGAATCATTGACAATAGCCTCCTTG
19663070 TTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
66 TTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
*
19663104 GCATCCTCTTTGCTGCCGGTTGCTCAGATAACTCTGCAAGAGAATCATTGACAATAGCCTCCTTG
1 GCATCCTCTTTGCTGCCGGTTGCTCAGATAAATCTGCAAGAGAATCATTGACAATAGCCTCCTTG
19663169 TTTTCAGCCACTTCAGAATCTTGATTCAAT
66 TTTTCAGCCACTTCAGAATCTTGATTCAAT
19663199 GCTTCAGCCA
Statistics
Matches: 187, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
99 136 0.73
101 1 0.01
102 50 0.27
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (99 bp):
GCATCCTCTTTGCTGCCGGTTGCTCAGATAAATCTGCAAGAGAATCATTGACAATAGCCTCCTTG
TTTTCAGCCACTTCAGAATCTTGATTCAATTGTT
Found at i:19677076 original size:20 final size:20
Alignment explanation
Indices: 19677048--19677085 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19677038 TATTTTCCAA
*
19677048 TAAATTATTTTACAGAAAAG
1 TAAAATATTTTACAGAAAAG
*
19677068 TAAAATATTTTCCAGAAA
1 TAAAATATTTTACAGAAA
19677086 TCATTTTACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (20 bp):
TAAAATATTTTACAGAAAAG
Found at i:19677100 original size:34 final size:35
Alignment explanation
Indices: 19677034--19677100 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
19677024 CAAATACCTG
* *
19677034 AAAATATTTTCCAATAAATTATTTTACAGAAAAGT
1 AAAATATTTTCCAAGAAATCATTTTACAGAAAAGT
*
19677069 AAAATATTTTCC-AGAAATCATTTTACGGAAAA
1 AAAATATTTTCCAAGAAATCATTTTACAGAAAA
19677101 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAAGAAATCATTTTACAGAAAAGT
Found at i:19677377 original size:18 final size:18
Alignment explanation
Indices: 19677354--19677389 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
19677344 CTAAATTTTG
19677354 AAATC-TAAAAAGTAAAAA
1 AAATCTTAAAAA-TAAAAA
19677372 AAATCTTAAAAATAAAAA
1 AAATCTTAAAAATAAAAA
19677390 TATAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCTTAAAAATAAAAA
Found at i:19680384 original size:21 final size:22
Alignment explanation
Indices: 19680359--19680400 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
19680349 TCATTGGCTC
19680359 ATAC-TCTCTTAAGCAAATTGG
1 ATACTTCTCTTAAGCAAATTGG
*
19680380 ATACTTTCTCTTAAGCGAATT
1 ATAC-TTCTCTTAAGCAAATT
19680401 TTGATATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (22 bp):
ATACTTCTCTTAAGCAAATTGG
Found at i:19690941 original size:15 final size:15
Alignment explanation
Indices: 19690923--19690952 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19690913 ATATTATAAT
*
19690923 TATAATAAAATAAAG
1 TATAATAAAAGAAAG
19690938 TATAATAAAAGAAAG
1 TATAATAAAAGAAAG
19690953 AGAACATGCA
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:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (15 bp):
TATAATAAAAGAAAG
Found at i:19695697 original size:50 final size:50
Alignment explanation
Indices: 19695575--19695823 Score: 293
Period size: 50 Copynumber: 4.8 Consensus size: 50
19695565 GATAATAACA
* * ** * *
19695575 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
19695626 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
19695676 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
19695726 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
19695781 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
19695824 TTACCCAAAT
Statistics
Matches: 172, Mismatches: 19, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 94 0.55
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:19695753 original size:100 final size:104
Alignment explanation
Indices: 19695574--19695823 Score: 366
Period size: 100 Copynumber: 2.4 Consensus size: 104
19695564 TGATAATAAC
* **
19695574 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
19695639 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
*
19695676 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
19695739 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
19695781 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
19695824 TTACCCAAAT
Statistics
Matches: 134, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.01
106 41 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:19695939 original size:13 final size:13
Alignment explanation
Indices: 19695918--19695949 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19695908 GCTTGGATCA
*
19695918 TCATCAAATAAAT
1 TCATAAAATAAAT
19695931 TCATAAAATAAAT
1 TCATAAAATAAAT
19695944 TCATAA
1 TCATAA
19695950 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:19728048 original size:20 final size:20
Alignment explanation
Indices: 19728023--19728075 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
19728013 TTAATAATGA
*
19728023 TAAAAAAATAAGTTAATCTT
1 TAAAAAAATAAGTTAATATT
*
19728043 TAAAAAAATTAATTTAATATT
1 TAAAAAAA-TAAGTTAATATT
19728064 TAAAAAATATAA
1 TAAAAAA-ATAA
19728076 ATATATAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.28
21 20 0.69
22 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAAAAATAAGTTAATATT
Found at i:19729100 original size:103 final size:104
Alignment explanation
Indices: 19728934--19729205 Score: 379
Period size: 103 Copynumber: 2.6 Consensus size: 104
19728924 CGGGGCCAAA
* *
19728934 ATACGAAAAAAGTAAAAACAAAATTTTGGGTGGCCTGGCAATGGCCAACACCCCTTTTCTACAAT
1 ATACGAAAAAAGTAAAAA-AAAA-TTTGGGTGGCCTGGCAATGGCCGACACCCCCTTTCTACAA-
* * ***
19728999 AAT-TTTTTTTTACTTTTGGTGTGTCAATGGTCGGCACCAGT
63 AATATTTTTTTTACTTTTGGTCTGTCAATGGCCAAAACCAGT
* * *
19729040 ATACGAAAAAAGTAAAAAAAAAATT-GATGGCCTGGCAATGGCCGACACCCCCTTTATACAAAAT
1 ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGCCGACACCCCCTTTCTACAAAAT
* *
19729104 ATTTTTTTTCCTTTTGGTCTTTCAATGGCCAAAACCAGT
66 ATTTTTTTTACTTTTGGTCTGTCAATGGCCAAAACCAGT
*
19729143 ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGTCGACA-CCCCTTTCTACAAAA
1 ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGCCGACACCCCCTTTCTACAAAA
19729206 AAAAATTTAC
Statistics
Matches: 148, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
102 3 0.02
103 101 0.68
104 22 0.15
105 4 0.03
106 18 0.12
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (104 bp):
ATACGAAAAAAGTAAAAAAAAATTTGGGTGGCCTGGCAATGGCCGACACCCCCTTTCTACAAAAT
ATTTTTTTTACTTTTGGTCTGTCAATGGCCAAAACCAGT
Found at i:19735182 original size:21 final size:21
Alignment explanation
Indices: 19735158--19735198 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19735148 AGTAAATTTA
*
19735158 ACTCAATTTAATACAATTCAT
1 ACTCAATTCAATACAATTCAT
*
19735179 ACTCAATTCAATCCAATTCA
1 ACTCAATTCAATACAATTCA
19735199 CATCATAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (21 bp):
ACTCAATTCAATACAATTCAT
Found at i:19738206 original size:41 final size:41
Alignment explanation
Indices: 19738161--19738344 Score: 325
Period size: 41 Copynumber: 4.5 Consensus size: 41
19738151 TACGCGCCTT
*
19738161 GCAGGCTATGTGCCGGTGATTTGAATCGGGTTATAAACCTA
1 GCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAACCTA
19738202 GCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAACCTA
1 GCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAACCTA
19738243 GCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAACCTA
1 GCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAACCTA
* *
19738284 GCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAACCTA
1 GCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAACCTA
*
19738325 GCA-GCTACGTGCTGGTGATT
1 GCAGGCTACGTGCCGGTGATT
19738345 GATCTGATAT
Statistics
Matches: 138, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
40 15 0.11
41 123 0.89
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (41 bp):
GCAGGCTACGTGCCGGTGATTTGAATCGGGTTATAAACCTA
Found at i:19741029 original size:22 final size:22
Alignment explanation
Indices: 19740935--19741029 Score: 70
Period size: 22 Copynumber: 4.3 Consensus size: 22
19740925 TAGTATACTT
*
19740935 TTATTTTAAA-TTATCATAAATA
1 TTATTTTAAACTTATCAT-ATTA
19740957 TTA-TTTAAACTTATCATA-TA
1 TTATTTTAAACTTATCATATTA
* * * **
19740977 TCCTAATTTAAAATTTATCATGTGC
1 T--T-ATTTTAAACTTATCATATTA
*
19741002 TAATTTTAAACTTATCATATTA
1 TTATTTTAAACTTATCATATTA
19741024 TTATTT
1 TTATTT
19741030 AGATTTATTA
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.05
21 7 0.13
22 31 0.56
23 1 0.02
24 12 0.22
25 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATTTTAAACTTATCATATTA
Found at i:19746154 original size:19 final size:19
Alignment explanation
Indices: 19746099--19746135 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19746089 TAATAAACAT
*
19746099 TAAAAAATTATTTTAAAAA
1 TAAAAAAATATTTTAAAAA
19746118 TAAAAAAATATTTTAAAA
1 TAAAAAAATATTTTAAAA
19746136 GTATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAAATATTTTAAAAA
Found at i:19748144 original size:16 final size:17
Alignment explanation
Indices: 19748125--19748166 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
19748115 TCAATTAATT
19748125 AATTAATTAA-TTTCTC
1 AATTAATTAATTTTCTC
*
19748141 AATTAAATAATTTTCTC
1 AATTAATTAATTTTCTC
19748158 AACTTAATT
1 AA-TTAATT
19748167 CTAATTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 8 0.36
18 5 0.23
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTAATTAATTTTCTC
Found at i:19750598 original size:9 final size:9
Alignment explanation
Indices: 19750584--19750608 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19750574 CTCAAAGCTC
19750584 CACCACCAG
1 CACCACCAG
19750593 CACCACCAG
1 CACCACCAG
19750602 CACCACC
1 CACCACC
19750609 CTCGTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.60, G:0.08, T:0.00
Consensus pattern (9 bp):
CACCACCAG
Found at i:19754128 original size:18 final size:19
Alignment explanation
Indices: 19754107--19754146 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
19754097 TAATTTTTTC
19754107 TTTTTTAACTT-AAGCTTT
1 TTTTTTAACTTGAAGCTTT
* *
19754125 TTTTTTAATTTGAATCTTT
1 TTTTTTAACTTGAAGCTTT
19754144 TTT
1 TTT
19754147 AATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTTAACTTGAAGCTTT
Found at i:19763527 original size:85 final size:84
Alignment explanation
Indices: 19763384--19763693 Score: 245
Period size: 85 Copynumber: 3.6 Consensus size: 84
19763374 CCGAAAATCC
* * * *
19763384 TATCTCCCTGAAGTTGTAGTGGAGC-GAATTAA-AACCACAAATCTTATCTCTTTGAAGTTGTAG
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAATAA--ACCAATCTTATCTC-CTGAAGTTGTAG
*
19763447 TAGAGCAGATCGTGTCCAGTCT
63 TAGAGCAGATCGAGTCCAGTCT
* * *
19763469 TATCTCCCTGAAATTGTAGTGGGGCAGACTGAATAAACCAATCTTATCTCCATGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAATAAACCAATCTTATCTCC-TGAAGTTGTAGTA
** ** * *
19763534 GAATAGATTAAAG-CCAATAATCC
65 GAGCAGA-TCGAGTCC---AGTCT
* * * * * *
19763557 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTAAA--GATCTGATCTCTCTGAAGTTGTAG
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACT-GAA-TAAACCAATCTTATCTC-CTGAAGTTGTAG
19763620 TAGAGCAGATCGCA-TCCAGTCT
63 TAGAGCAGATCG-AGTCCAGTCT
* * * * *
19763642 CATCTCCATGAAGTTGTAGTGGAGCAGACAGAAGAAACCAATCATATCTCCT
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAATAAACCAATCTTATCTCCT
19763694 TAAATTTGCA
Statistics
Matches: 171, Mismatches: 40, Indels: 29
0.71 0.17 0.12
Matches are distributed among these distances:
83 3 0.02
84 4 0.02
85 90 0.53
86 7 0.04
87 3 0.02
88 57 0.33
89 3 0.02
90 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAATAAACCAATCTTATCTCCTGAAGTTGTAGTAG
AGCAGATCGAGTCCAGTCT
Found at i:19763647 original size:129 final size:129
Alignment explanation
Indices: 19763514--19763844 Score: 353
Period size: 129 Copynumber: 2.6 Consensus size: 129
19763504 AACCAATCTT
* * * * * *
19763514 ATCTCCATGAAGTTGCAGTAGAATAGATTA-AAGCCAA-TAATCCTATCTCCCTGAAGTTGCAGT
1 ATCTCCATGAAGTTGCAGTAGAACAGA-CAGAAG-AAACCAATCATATCTCCCTAAAGTTGCAGT
* *
19763577 GGAGCGGATTAAAACTAAAGATCTGATCTCTCTGAAGTTGTAGTAGAGCAGATCGCATCCAGTCT
64 GGAGCGGATTAAAACCAAAGATCTGATCTCTCTGAAGTTATAGTAGAGCAGATCGCATCCAGTCT
19763642 C
129 C
* * * * *
19763643 ATCTCCATGAAGTTGTAGTGGAGCAGACAGAAGAAACCAATCATATCTCCTTAAATTTGCAGTGG
1 ATCTCCATGAAGTTGCAGTAGAACAGACAGAAGAAACCAATCATATCTCCCTAAAGTTGCAGTGG
* * * ** *
19763708 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTATAGTAGAGCGGATCGTGTCCAGTCTT
66 AGCGGATTAAAACCAAAGATCTGATCTCTCTGAAGTTATAGTAGAGCAGATCGCATCCAGTCTC
* * * ** * * * *
19763772 GTCTCCCTGAAGTTGCAGTGGGGCAGACTA-AATAAACCAATCTTATCTCTCTGAAGTTGCAGTG
1 ATCTCCATGAAGTTGCAGTAGAACAGAC-AGAAGAAACCAATCATATCTCCCTAAAGTTGCAGTG
*
19763836 GAGCAGATT
65 GAGCGGATT
19763845 GAAGAAACCA
Statistics
Matches: 169, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
128 3 0.02
129 165 0.98
130 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (129 bp):
ATCTCCATGAAGTTGCAGTAGAACAGACAGAAGAAACCAATCATATCTCCCTAAAGTTGCAGTGG
AGCGGATTAAAACCAAAGATCTGATCTCTCTGAAGTTATAGTAGAGCAGATCGCATCCAGTCTC
Found at i:19763718 original size:173 final size:173
Alignment explanation
Indices: 19763378--19763758 Score: 487
Period size: 173 Copynumber: 2.2 Consensus size: 173
19763368 GTGAAACCGA
* * *
19763378 AAATCCTATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAACCACAAATCTTATCTCTTTGAAGTT
1 AAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACCACAAATCTGATCTCTCTGAAGTT
** * * * * *
19763443 GTAGTAGAGCAGATCGTGTCCAGTCTTATCTCCCTGAAATTGTAGTGGGGCAGACTGAATAAACC
66 GTAGTAGAGCAGATCGCATCCAGTCTCATCTCCATGAAATTGTAGTGGAGCAGACAGAAGAAACC
* * * *
19763508 AATCTTATCTCCATGAAGTTGCAGTAGAATAGATTAAAGCCA-
131 AATCATATCTCCATAAAGTTGCAGTAGAACAGATTAAAACCAC
* *
19763550 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTA-AAGATCTGATCTCTCTGAAG
1 A-AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACCACAA-ATCTGATCTCTCTGAAG
*
19763614 TTGTAGTAGAGCAGATCGCATCCAGTCTCATCTCCATGAAGTTGTAGTGGAGCAGACAGAAGAAA
64 TTGTAGTAGAGCAGATCGCATCCAGTCTCATCTCCATGAAATTGTAGTGGAGCAGACAGAAGAAA
* * * * *
19763679 CCAATCATATCTCCTTAAATTTGCAGTGGAGCGGATTAAAACCAC
129 CCAATCATATCTCCATAAAGTTGCAGTAGAACAGATTAAAACCAC
* * * * *
19763724 AGATCTTATCTCTCTGAAGTTATAGTAGAGCGGAT
1 AAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGAT
19763759 CGTGTCCAGT
Statistics
Matches: 178, Mismatches: 28, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
172 3 0.02
173 174 0.98
174 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (173 bp):
AAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACCACAAATCTGATCTCTCTGAAGTT
GTAGTAGAGCAGATCGCATCCAGTCTCATCTCCATGAAATTGTAGTGGAGCAGACAGAAGAAACC
AATCATATCTCCATAAAGTTGCAGTAGAACAGATTAAAACCAC
Found at i:19763842 original size:44 final size:43
Alignment explanation
Indices: 19763379--19763882 Score: 215
Period size: 44 Copynumber: 11.7 Consensus size: 43
19763369 TGAAACCGAA
* * * *
19763379 AATCCTATCTCCCTGAAGTTGTAGTGGAGC-GAATTAAA-ACCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-A-TAAATA-AACC
** * * ** **
19763423 AATCTTATCTCTTTGAAGTTGTAGTAGAGCAGAT-CGT-GTCC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAATAAACC
* * * * *
19763464 AGTCTTATCTCCCTGAAATTGTAGTGGGGCAGACTGAATAAACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAATAAACC
* * ** ** *
19763508 AATCTTATCTCCATGAAGTTGCAGTAGAATAGATTAAAGCCAA-T
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAA-TAAACC
* *
19763552 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTAAA--
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-AAA-TAAACC
* * * * * **
19763596 GATCTGATCTCTCTGAAGTTGTAGTAGAGCAGATCGCAT---CC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-AAATAAACC
* * * * * *
19763637 AGTCTCATCTCCATGAAGTTGTAGTGGAGCAGACAGAAGAAACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATA-AATAAACC
* * * * * * *
19763681 AATCATATCTCCTTAAATTTGCAGTGGAGCGGATTAA-AACCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAATAAAC-C
* ** * * ** **
19763724 AGATCTTATCTCTCTGAAGTTATAGTAGAGCGGAT-CGT-GTCC
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAATAAACC
* * *
19763766 AGTCTTGTCTCCCTGAAGTTGCAGTGGGGCAGACTAAATAAACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAATAAACC
* * *
19763810 AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGAAACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAATAAACC
* *
19763854 AATCCTATCGCCCTGAAGTTGCAGTGGAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG
19763883 TGGATCAAAA
Statistics
Matches: 335, Mismatches: 106, Indels: 38
0.70 0.22 0.08
Matches are distributed among these distances:
41 80 0.24
42 8 0.02
43 10 0.03
44 229 0.68
45 8 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAATAAACC
Found at i:19763888 original size:129 final size:129
Alignment explanation
Indices: 19763552--19763888 Score: 308
Period size: 129 Copynumber: 2.6 Consensus size: 129
19763542 TAAAGCCAAT
* * * * * * *
19763552 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAACTAAAGAT-CTGATCTCTCTGAAGT
1 AATCATATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAAAC-ACAGATCCT-ATCGCCCTGAAGT
** * ** *
19763615 TGTAGTAGAGCAGATCGCATCCAGTCTCATCTCCATGAAGTTGTAGTGGAGCAGACAGAAGAAAC
64 TACAGTAGAGCGGATCGTGTCCAGTCTCATCTCCATGAAGTTGCAGTGGAGCAGACAGAAGAAAC
19763680 C
129 C
* * * * * *
19763681 AATCATATCTCCTTAAATTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
1 AATCATATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAAACACAGATCCTATCGCCCTGAAGTTA
* ** * * *
19763746 TAGTAGAGCGGATCGTGTCCAGTCTTGTCTCCCTGAAGTTGCAGTGGGGCAGACTA-AATAAACC
66 CAGTAGAGCGGATCGTGTCCAGTCTCATCTCCATGAAGTTGCAGTGGAGCAGAC-AGAAGAAACC
* *
19763810 AATCTTATCT-CTCTGAAGTTGCAGTGGAGCAGATTGAAGAAAC-CA-ATCCTATCGCCCTGAAG
1 AATCATATCTCCT-TAAAGTTGCAGTGGAGCAGATT-AA-AAACACAGATCCTATCGCCCTGAAG
* * *
19763872 TTGCAGTGGAGTGGATC
63 TTACAGTAGAGCGGATC
19763889 AAAATGATGG
Statistics
Matches: 173, Mismatches: 29, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
128 2 0.01
129 158 0.91
130 10 0.06
131 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (129 bp):
AATCATATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAAACACAGATCCTATCGCCCTGAAGTTA
CAGTAGAGCGGATCGTGTCCAGTCTCATCTCCATGAAGTTGCAGTGGAGCAGACAGAAGAAACC
Found at i:19765894 original size:18 final size:19
Alignment explanation
Indices: 19765857--19765897 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
19765847 TTATTTCAAC
19765857 TTATTTCAAAATTGTTAAT
1 TTATTTCAAAATTGTTAAT
* *
19765876 TTATTTTAATATT-TTAAT
1 TTATTTCAAAATTGTTAAT
19765894 TTAT
1 TTAT
19765898 ATATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATTTCAAAATTGTTAAT
Found at i:19766669 original size:23 final size:23
Alignment explanation
Indices: 19766643--19766686 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
19766633 TTATACCTTT
*
19766643 TTTTATTTACCAATATATATATA
1 TTTTATTTACCAAAATATATATA
19766666 TTTTATTTACCAAAATATATA
1 TTTTATTTACCAAAATATATA
19766687 AAAAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTATTTACCAAAATATATATA
Found at i:19766886 original size:10 final size:10
Alignment explanation
Indices: 19766871--19766911 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
19766861 GAGGTGCTAC
19766871 AGAAAAGAAG
1 AGAAAAGAAG
*
19766881 AGAAAAAAAG
1 AGAAAAGAAG
19766891 AGAAAAGAAG
1 AGAAAAGAAG
19766901 AGAAAAAGAAG
1 AG-AAAAGAAG
19766912 GTATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AGAAAAGAAG
Found at i:19768806 original size:5 final size:5
Alignment explanation
Indices: 19768798--19768911 Score: 79
Period size: 5 Copynumber: 24.6 Consensus size: 5
19768788 TTTTCTCTTC
* *
19768798 TCCTT TCCTT TCCTT TCCTT TTCTT TCC-T T-CTT T-CTT T-CTT T-TTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
* * * *
19768843 TCTCTT CTCCTT TCCTT TTCTT TCC-T TCTTT TTCTT T-CTT TCCTC TCC-T
1 TC-CTT -TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
19768892 TCCTT T-CTT T-CTT T-CTT TCC
1 TCCTT TCCTT TCCTT TCCTT TCC
19768912 CTCTCCTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
3 1 0.01
4 37 0.41
5 45 0.50
6 5 0.06
7 2 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (5 bp):
TCCTT
Found at i:19768833 original size:4 final size:4
Alignment explanation
Indices: 19768817--19768910 Score: 68
Period size: 4 Copynumber: 23.0 Consensus size: 4
19768807 TTCCTTTCCT
* * *
19768817 TTTC TTTC CTTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC
* * *
19768867 CTTC -TT- TTTC TTTC TTTCC TCTCC TTCC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC
19768911 CCTCTCCTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
3 6 0.08
4 54 0.74
5 9 0.12
6 4 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:19768834 original size:52 final size:52
Alignment explanation
Indices: 19768785--19768884 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
19768775 TTCTTCTTCT
19768785 TTTTTTTCTCTTCTCCTTTCCTTTCCTTTCCTT-TTCTTTCCTTCTTTCTTTC
1 TTTTTTTCTCTTCTCCTTTCCTTTCCTTTCCTTCTT-TTTCCTTCTTTCTTTC
* *
19768837 TTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTC
1 TTTTTTTCTCTTCTCCTTTCCTTTCCTTTCCTTCTTTTTCCTTCTTTC
19768885 CTCTCCTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 43 0.96
53 2 0.04
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (52 bp):
TTTTTTTCTCTTCTCCTTTCCTTTCCTTTCCTTCTTTTTCCTTCTTTCTTTC
Found at i:19768860 original size:42 final size:41
Alignment explanation
Indices: 19768800--19768910 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 41
19768790 TTCTCTTCTC
19768800 CTTTCCTT-TCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTT
1 CTTTCCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTT
*
19768840 TTTTCTCTTCTCCTTTCCTTTTCTTTCCTTC-TT-TTTCTTT
1 CTTTC-CTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTT
*
19768880 CTTTCC-TCTCC-TTCC-TTTCTTTCTTTCTTTC
1 CTTTCCTTCTCCTTTCCTTTTCTTTCCTTCTTTC
19768911 CCTCTCCTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
36 11 0.17
37 6 0.09
38 5 0.08
39 1 0.02
40 15 0.23
41 5 0.08
42 21 0.33
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (41 bp):
CTTTCCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTT
Found at i:19768916 original size:27 final size:27
Alignment explanation
Indices: 19768864--19768919 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
19768854 TTCCTTTTCT
*
19768864 TTCCTTCTTTTTCTTTCTTTCCTCTCC
1 TTCCTTCTCTTTCTTTCTTTCCTCTCC
19768891 TTCCTT-TCTTTCTTTCTTTCCCTCTCC
1 TTCCTTCTCTTTCTTTCTTT-CCTCTCC
19768918 TT
1 TT
19768920 TTGCCCGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (27 bp):
TTCCTTCTCTTTCTTTCTTTCCTCTCC
Found at i:19768993 original size:27 final size:27
Alignment explanation
Indices: 19768953--19769032 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
19768943 CCTTTTTATG
* *
19768953 CATTGGTGCTGCCAATGGTATTGGCAC
1 CATTGGTGCCGCCAATGCTATTGGCAC
19768980 CATTGGTGCCGCCAATAGCT-TTGGCAC
1 CATTGGTGCCGCCAAT-GCTATTGGCAC
* *
19769007 CTTTGGTGCCGCCAATGCCATTGGCA
1 CATTGGTGCCGCCAATGCTATTGGCA
19769033 TGATCAATGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.04
27 43 0.91
28 2 0.04
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGCTATTGGCAC
Found at i:19774368 original size:20 final size:21
Alignment explanation
Indices: 19774332--19774371 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19774322 AAAAAATATT
*
19774332 AATAATATTTTATTAAATAAA
1 AATAATATTTTAATAAATAAA
19774353 AATAATA-TTTAATAAATAA
1 AATAATATTTTAATAAATAA
19774372 GATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAATATTTTAATAAATAAA
Found at i:19774424 original size:3 final size:3
Alignment explanation
Indices: 19774416--19774452 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
19774406 TAAATCTCAC
*
19774416 TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19774453 ACTTTTCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:19776840 original size:7 final size:7
Alignment explanation
Indices: 19776828--19776856 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
19776818 TGTTCAAAAT
19776828 AGAAAGA
1 AGAAAGA
19776835 AGAAAGA
1 AGAAAGA
19776842 AGAAAGA
1 AGAAAGA
19776849 AG-AAGA
1 AGAAAGA
19776855 AG
1 AG
19776857 CAAATTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (7 bp):
AGAAAGA
Found at i:19783959 original size:87 final size:87
Alignment explanation
Indices: 19783812--19784159 Score: 455
Period size: 87 Copynumber: 4.0 Consensus size: 87
19783802 TTTGAGGTGA
* *
19783812 ATGTTTATTTGTCGTAAATGATTCTTGCTTCTTCCCTTTCTCAGGTTCTA-CTTTGTCCACATTC
1 ATGTTTATTTGCCGTAAATGATTCTTGCTTCTTCCCTTTCTCAGATTC-AGCTTTGTCCACATTC
* *
19783876 GTTTCCTGCTGAAGCAGATTCTT
65 ATTTCCTGCTGAACCAGATTCTT
* * * *
19783899 TTGTTTATTTTCCGTAAATGATTCTTGCTTCTTCCCTTTCTCTGATTCAGCTTTGTCCACATTCG
1 ATGTTTATTTGCCGTAAATGATTCTTGCTTCTTCCCTTTCTCAGATTCAGCTTTGTCCACATTCA
*
19783964 TTTCCTGCTGAACCGGATTCTT
66 TTTCCTGCTGAACCAGATTCTT
* * * *
19783986 ATGTTTATTTGCTGTAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCGCTTTGTCCACATCCA
1 ATGTTTATTTGCCGTAAATGATTCTTGCTTCTTCCCTTTCTCAGATTCAGCTTTGTCCACATTCA
* *
19784051 TTTCCTGCTGAACCGGATTCCT
66 TTTCCTGCTGAACCAGATTCTT
* * * ** * *
19784073 ATGTCTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCACCTTCCGCTTTGTCCACTTTCA
1 ATGTTTATTTGCCGTAAATGATTCTTGCTTCTTCCCTTTCTCAGATTCAGCTTTGTCCACATTCA
* * *
19784138 TTTCCTTCTGCAGCAGATTCTT
66 TTTCCTGCTGAACCAGATTCTT
19784160 GGTTCAGAGA
Statistics
Matches: 232, Mismatches: 28, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
86 1 0.00
87 231 1.00
ACGTcount: A:0.15, C:0.26, G:0.14, T:0.45
Consensus pattern (87 bp):
ATGTTTATTTGCCGTAAATGATTCTTGCTTCTTCCCTTTCTCAGATTCAGCTTTGTCCACATTCA
TTTCCTGCTGAACCAGATTCTT
Found at i:19787544 original size:9 final size:9
Alignment explanation
Indices: 19787532--19787565 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
19787522 CGTCATCACA
*
19787532 TTCATCGTC
1 TTCATCATC
*
19787541 TTCATAATC
1 TTCATCATC
19787550 TTCATCATC
1 TTCATCATC
19787559 TTCATCA
1 TTCATCA
19787566 GACTCATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.44
Consensus pattern (9 bp):
TTCATCATC
Found at i:19798952 original size:19 final size:20
Alignment explanation
Indices: 19798914--19798953 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
19798904 TTTTGACTAT
19798914 TTATTTTTTACTCTTAAATTTC
1 TTATTTTTTACTC-T-AATTTC
19798936 TTATTTTTTACTC-AATTT
1 TTATTTTTTACTCTAATTT
19798954 TGTAGGTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
22 13 0.72
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTTTTACTCTAATTTC
Found at i:19802722 original size:46 final size:45
Alignment explanation
Indices: 19802655--19802894 Score: 304
Period size: 46 Copynumber: 5.5 Consensus size: 45
19802645 TTTGAGTACT
* *
19802655 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
19802701 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
19802737 TCTGATCAAGAGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
19802783 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
19802829 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
19802874 TCTGATC-AGGGAC-AAGTGATA
1 TCTGATCAAGTGACAAAGTGATA
19802895 GGTGATCATA
Statistics
Matches: 174, Mismatches: 10, Indels: 23
0.84 0.05 0.11
Matches are distributed among these distances:
36 30 0.17
37 2 0.01
40 2 0.01
42 2 0.01
43 8 0.05
44 5 0.03
45 22 0.13
46 103 0.59
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:19802732 original size:36 final size:36
Alignment explanation
Indices: 19802691--19802763 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
19802681 GGTAGCTTTA
*
19802691 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGT
*
19802727 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGT
19802763 G
1 G
19802764 TTAGCCTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGT
Found at i:19802792 original size:82 final size:86
Alignment explanation
Indices: 19802655--19802881 Score: 320
Period size: 82 Copynumber: 2.6 Consensus size: 86
19802645 TTTGAGTACT
* *
19802655 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
19802720 GAT-A-AG-T-GCTACACTTA
66 GATAAGAGCTAGCTACACTTA
* *
19802737 TCTGATCAAGAGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
19802802 GATAAGTGGTAGCCTTAGCTACACTTA
66 GATAA---G-AG-C-TAGCTACACTTA
*
19802829 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TAGCTACACTTATCTGATCA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCA
19802882 GGGACAAGTG
Statistics
Matches: 129, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
82 64 0.50
83 1 0.01
88 2 0.02
91 21 0.16
92 41 0.32
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (86 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGAGCTAGCTACACTTA
Found at i:19814073 original size:12 final size:12
Alignment explanation
Indices: 19814056--19814082 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19814046 GATAGGGGAA
19814056 TTTCTTTTCTTT
1 TTTCTTTTCTTT
19814068 TTTCTTTTCTTT
1 TTTCTTTTCTTT
19814080 TTT
1 TTT
19814083 AGATTCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTCTTT
Found at i:19834331 original size:13 final size:13
Alignment explanation
Indices: 19834313--19834338 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19834303 GTTTAAGTTT
19834313 TATTAGATAAATA
1 TATTAGATAAATA
19834326 TATTAGATAAATA
1 TATTAGATAAATA
19834339 CAAACTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
TATTAGATAAATA
Found at i:19845558 original size:18 final size:20
Alignment explanation
Indices: 19845532--19845569 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
19845522 GATTTAAAAT
19845532 TTTAATTTTT-TT-ATTAAA
1 TTTAATTTTTATTCATTAAA
*
19845550 TTTAGTTTTTATTCATTAAA
1 TTTAATTTTTATTCATTAAA
19845570 ATAATATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTAATTTTTATTCATTAAA
Done.