Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 170 of 199
Found at i:49678393 original size:20 final size:20
Alignment explanation
Indices: 49678368--49678405 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
49678358 ATTCGCTCTA
49678368 ATTTTTCCAACCTTTGTTCC
1 ATTTTTCCAACCTTTGTTCC
*
49678388 ATTTTTCTAACCTTTGTT
1 ATTTTTCCAACCTTTGTT
49678406 TGGATACCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTTTCCAACCTTTGTTCC
Found at i:49680803 original size:15 final size:15
Alignment explanation
Indices: 49680785--49680831 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
49680775 AAAATAAAAC
49680785 TAATAACAATAATAA
1 TAATAACAATAATAA
*
49680800 TAATAACATTAA-AA
1 TAATAACAATAATAA
*
49680814 TAATTAACTA-AATAA
1 TAA-TAACAATAATAA
49680829 TAA
1 TAA
49680832 AATTGCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATAACAATAATAA
Found at i:49701037 original size:18 final size:20
Alignment explanation
Indices: 49701011--49701047 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49701001 CAGACACTCC
49701011 ATGTGC-TTTCT-TCTTTTT
1 ATGTGCTTTTCTCTCTTTTT
*
49701029 ATGTTCTTTTCTCTCTTTT
1 ATGTGCTTTTCTCTCTTTT
49701048 ATAACGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 5 0.31
20 6 0.38
ACGTcount: A:0.05, C:0.19, G:0.08, T:0.68
Consensus pattern (20 bp):
ATGTGCTTTTCTCTCTTTTT
Found at i:49702907 original size:3 final size:3
Alignment explanation
Indices: 49702899--49702944 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
49702889 ATTATATATT
49702899 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
49702945 AAGAAAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:49703972 original size:40 final size:39
Alignment explanation
Indices: 49703851--49703985 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 39
49703841 GACTTCGAGT
*
49703851 CAATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CAATGAGACACTGGGTGTCAATTTA-TACTTCGGATT-ATC
* * * * *
49703892 CGATGAGGCACTGGGTGCCAA--TATACTTCGGTTTAGC
1 CAATGAGACACTGGGTGTCAATTTATACTTCGGATTATC
*
49703929 CAATGAGACACTGGGTGTCAATTTATTACTTCGAATTATC
1 CAATGAGACACTGGGTGTCAATTTA-TACTTCGGATTATC
*
49703969 CAATGAGGCACTGGGTG
1 CAATGAGACACTGGGTG
49703986 CCAAACTGCT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.24
38 10 0.13
39 4 0.05
40 27 0.35
41 18 0.23
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (39 bp):
CAATGAGACACTGGGTGTCAATTTATACTTCGGATTATC
Found at i:49707115 original size:11 final size:11
Alignment explanation
Indices: 49707099--49707129 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
49707089 ATATTTTTCC
*
49707099 TAAATACTAAA
1 TAAATACCAAA
49707110 TAAATACCAAA
1 TAAATACCAAA
49707121 TAAATACCA
1 TAAATACCA
49707130 TATGAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (11 bp):
TAAATACCAAA
Found at i:49708418 original size:15 final size:15
Alignment explanation
Indices: 49708398--49708429 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49708388 CATTTCACTA
*
49708398 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
49708413 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
49708428 TT
1 TT
49708430 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:49710041 original size:37 final size:37
Alignment explanation
Indices: 49709987--49710078 Score: 89
Period size: 37 Copynumber: 2.4 Consensus size: 37
49709977 GTTCCAAAAA
* *
49709987 TAATATTATTTTGATAGT-TTAATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTATT-ATATTAAATTAATATT
* *
49710023 TAATACTTATCTTAATAGTATTTTATTAATTTAATATT
1 TAATA-TTATCTTAATAGTATTATATTAAATTAATATT
*
49710061 AAAGTAGTTATCTTAATA
1 TAA-TA-TTATCTTAATA
49710079 TTAAATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
36 5 0.11
37 21 0.46
38 7 0.15
39 13 0.28
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.51
Consensus pattern (37 bp):
TAATATTATCTTAATAGTATTATATTAAATTAATATT
Found at i:49713709 original size:3 final size:3
Alignment explanation
Indices: 49713701--49713799 Score: 180
Period size: 3 Copynumber: 33.0 Consensus size: 3
49713691 TATCTGGTAC
49713701 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
49713749 GAA GAA GAA GAA GAA GAA GAA TAA GAA GAA GAA GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
49713797 GAA
1 GAA
49713800 ATAAAGATGA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:49716566 original size:3 final size:3
Alignment explanation
Indices: 49716560--49716607 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
49716550 TTTTTCTCTT
* * *
49716560 CTC CTC CTC CTC CTT CTC TTC CTC CTC CTC CTC CTC CCC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
49716608 ATCATCATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:49716629 original size:3 final size:3
Alignment explanation
Indices: 49716623--49716689 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
49716613 CATCATCATT
49716623 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
** *
49716670 TTC CGC TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TT
49716690 TTATTTCCCA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:49730993 original size:23 final size:23
Alignment explanation
Indices: 49730967--49731012 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
49730957 TGGTATTCAC
49730967 CTTTTACAAGAAAAAAATATTAA
1 CTTTTACAAGAAAAAAATATTAA
49730990 CTTTTACAAGAAAAAAATATTAA
1 CTTTTACAAGAAAAAAATATTAA
49731013 ATTAATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (23 bp):
CTTTTACAAGAAAAAAATATTAA
Found at i:49737926 original size:22 final size:23
Alignment explanation
Indices: 49737883--49737926 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
49737873 AAACACGCAA
*
49737883 AGTAGAAGAAAATAATGCAAAAC
1 AGTAGAAGAAAATAATGAAAAAC
49737906 AGTAGAA-AAAATAGAT-AAAAA
1 AGTAGAAGAAAATA-ATGAAAAA
49737927 TATATTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.14
Consensus pattern (23 bp):
AGTAGAAGAAAATAATGAAAAAC
Found at i:49739015 original size:62 final size:59
Alignment explanation
Indices: 49738943--49739067 Score: 169
Period size: 62 Copynumber: 2.1 Consensus size: 59
49738933 TCTATACATA
* * *
49738943 TTTTTAATTTTCATATATACATACTTTATATCTTACATCATTATATATCTTTATATACGCAT
1 TTTTTAATTTTCATATATACATACCTTACATCTT--AT-ATTATATATCTTTATACACGCAT
* * *
49739005 TTTTTAATTTTCATATATATATACCTTGCATCTTATATTATATATCTTTATACACGTAT
1 TTTTTAATTTTCATATATACATACCTTACATCTTATATTATATATCTTTATACACGCAT
49739064 TTTT
1 TTTT
49739068 AAACTCATGT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 25 0.44
60 2 0.04
62 30 0.53
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.54
Consensus pattern (59 bp):
TTTTTAATTTTCATATATACATACCTTACATCTTATATTATATATCTTTATACACGCAT
Found at i:49740113 original size:106 final size:106
Alignment explanation
Indices: 49739928--49740119 Score: 269
Period size: 106 Copynumber: 1.8 Consensus size: 106
49739918 TAATAAATGC
* * * *
49739928 AATATTTTGCATTTGGAAATTCGAGAAAGCGTATCCTAATGTGTTGGGTTTCAATTTTTTCGTTC
1 AATATTTTGCATTTAGAAATTCGAGAAAGCGTACCCTAATGTGCTAGGTTTCAATTTTTTCGTTC
*
49739993 GACCGAATAGCCAAATATCCTTTAAAATTTCAAAGTAAGGT
66 GACCAAATAGCCAAATATCCTTTAAAATTTCAAAGTAAGGT
* * * * *
49740034 AATATTTTGCGTTTAGAAATTCGAGGAAA-TGTGCCCTAATGTGCTAGGTTTCGATTTTTTTGTT
1 AATATTTTGCATTTAGAAATTCGA-GAAAGCGTACCCTAATGTGCTAGGTTTCAATTTTTTCGTT
*
49740098 TGACCAAATAGCCAAATATCCT
65 CGACCAAATAGCCAAATATCCT
49740120 CTTATATCTT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
106 70 0.95
107 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (106 bp):
AATATTTTGCATTTAGAAATTCGAGAAAGCGTACCCTAATGTGCTAGGTTTCAATTTTTTCGTTC
GACCAAATAGCCAAATATCCTTTAAAATTTCAAAGTAAGGT
Found at i:49750549 original size:17 final size:18
Alignment explanation
Indices: 49750522--49750555 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
49750512 TTATGTTTTC
*
49750522 TTTTTACTCTATAACAAT
1 TTTTTACTCTACAACAAT
49750540 TTTTTA-TCTACAACAA
1 TTTTTACTCTACAACAA
49750556 CAACCATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTTACTCTACAACAAT
Found at i:49752651 original size:3 final size:3
Alignment explanation
Indices: 49752643--49752669 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
49752633 ACAAAATTGC
49752643 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
49752670 TGTGTGTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:49760105 original size:67 final size:71
Alignment explanation
Indices: 49759984--49760122 Score: 232
Period size: 67 Copynumber: 2.0 Consensus size: 71
49759974 AAAAACAAAG
49759984 CTGACATTATTTCCAATTTAATAAATAAATAAAAATATTTTCACTTTTGTTCCATATGAGGTACT
1 CTGACATTATTTCCAATTT-ATAAATAAATAAAAATATTTTCACTTTTGTTCCATATGAGGTACT
49760049 ATTCTTT
65 ATTCTTT
*
49760056 CTGACATTATTTCCAA-TT-T-AATAAA-AAAAATATTTTCACTTTTGTTCCATATGAGGTACTC
1 CTGACATTATTTCCAATTTATAAATAAATAAAAATATTTTCACTTTTGTTCCATATGAGGTACTA
49760117 TTCTTT
66 TTCTTT
49760123 ATTACAAATT
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
67 41 0.62
68 6 0.09
69 1 0.02
71 2 0.03
72 16 0.24
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (71 bp):
CTGACATTATTTCCAATTTATAAATAAATAAAAATATTTTCACTTTTGTTCCATATGAGGTACTA
TTCTTT
Found at i:49763090 original size:151 final size:151
Alignment explanation
Indices: 49762808--49763114 Score: 535
Period size: 151 Copynumber: 2.0 Consensus size: 151
49762798 TAAATTCCAC
*
49762808 TTTCAAACTCTGAAATCCAAGTTGAATCCAGGCATGGGAACTCAGTTAATAAGTTTGAAACTCTT
1 TTTCAAACTCTGAAATCCAAGTTGAATCCAGACATGGGAACTCAGTTAATAAGTTTGAAACTCTT
49762873 CAACACCCAGCTACATTGCGGGGTGACATTTATATTACCGGGTTTTTTACTGGAATAATT-AAAA
66 CAACACCCAGCTACATTGCGGGGTGACATTTATATTACCGGGTTTTTTACTGGAATAATTAAAAA
*
49762937 AAAATTATATACTGAAATAGG
131 AAAATTATATACGGAAATAGG
* *
49762958 TTTCAAACTCTGAAATCCAAGTTGAATCCAGACAATGGGAACTGAGTTAATAGGTTTGAAACTCT
1 TTTCAAACTCTGAAATCCAAGTTGAATCCAGAC-ATGGGAACTCAGTTAATAAGTTTGAAACTCT
49763023 TCAACACCCAGCTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAATTTAA
65 TCAACACCCAGCTACATTGCGGGGT-GACATTTATATTACCGGGTTTTTTACTGGAATAA-TT-A
49763088 AAAAAAAATTATATACGGAAATAGG
127 AAAAAAAATTATATACGGAAATAGG
49763113 TT
1 TT
49763115 GTCAGATAGA
Statistics
Matches: 148, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
150 32 0.22
151 54 0.36
152 34 0.23
153 2 0.01
155 26 0.18
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (151 bp):
TTTCAAACTCTGAAATCCAAGTTGAATCCAGACATGGGAACTCAGTTAATAAGTTTGAAACTCTT
CAACACCCAGCTACATTGCGGGGTGACATTTATATTACCGGGTTTTTTACTGGAATAATTAAAAA
AAAATTATATACGGAAATAGG
Found at i:49764297 original size:19 final size:17
Alignment explanation
Indices: 49764273--49764313 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
49764263 TTTTCTTTGT
49764273 TCTTTTTCTTCTCTTCTTC
1 TCTTTTTC-TCTCTT-TTC
49764292 TC-TTTTCTCTCTTTTC
1 TCTTTTTCTCTCTTTTC
49764308 T-TTTTT
1 TCTTTTT
49764314 TGCCATGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.38
17 6 0.29
18 5 0.24
19 2 0.10
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
TCTTTTTCTCTCTTTTC
Found at i:49764314 original size:17 final size:16
Alignment explanation
Indices: 49764257--49764314 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
49764247 AATACATTAC
*
49764257 CTTTTTTTTTCTTTGTT
1 CTTTTTTTCTCTTT-TT
*
49764274 CTTTTTCTTCTCTTCTT
1 CTTTTT-TTCTCTTTTT
*
49764291 C-TCTTTTCTCTCTTTT
1 CTTTTTTTCTCT-TTTT
49764307 CTTTTTTT
1 CTTTTTTT
49764315 GCCATGGTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 6 0.18
16 7 0.21
17 14 0.42
18 6 0.18
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (16 bp):
CTTTTTTTCTCTTTTT
Found at i:49764487 original size:24 final size:25
Alignment explanation
Indices: 49764442--49764489 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
49764432 TTTATATTTA
*
49764442 AATATTTTTAATAAAAATAAAAAAT
1 AATATTTTTAATAAAAACAAAAAAT
* *
49764467 AATA-TTTTAATCAAACCAAAAAA
1 AATATTTTTAATAAAAACAAAAAA
49764490 AATTAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (25 bp):
AATATTTTTAATAAAAACAAAAAAT
Found at i:49765127 original size:24 final size:24
Alignment explanation
Indices: 49765082--49765173 Score: 115
Period size: 21 Copynumber: 4.1 Consensus size: 24
49765072 CGGAGGGAAA
*
49765082 GGAGGGTATGGAGGT-G-GG-CAC
1 GGAGGGTATGGTGGTGGTGGCCAC
49765103 GGAGGGTATGGTGGTGGTGGCCAC
1 GGAGGGTATGGTGGTGGTGGCCAC
49765127 GGAGGGTA---TGGTGGTGGCCAC
1 GGAGGGTATGGTGGTGGTGGCCAC
* *
49765148 GGAGGATACGGTGGTGGTGGCCAC
1 GGAGGGTATGGTGGTGGTGGCCAC
49765172 GG
1 GG
49765174 CGGTCACGGT
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
21 34 0.54
22 1 0.02
23 2 0.03
24 26 0.41
ACGTcount: A:0.15, C:0.13, G:0.54, T:0.17
Consensus pattern (24 bp):
GGAGGGTATGGTGGTGGTGGCCAC
Found at i:49765132 original size:45 final size:45
Alignment explanation
Indices: 49765082--49765173 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
49765072 CGGAGGGAAA
* * *
49765082 GGAGGGTATGGAGGTGGGCACGGAGGGTATGGTGGTGGTGGCCAC
1 GGAGGGTATGGAGGTGGCCACGGAGGATACGGTGGTGGTGGCCAC
*
49765127 GGAGGGTATGGTGGTGGCCACGGAGGATACGGTGGTGGTGGCCAC
1 GGAGGGTATGGAGGTGGCCACGGAGGATACGGTGGTGGTGGCCAC
49765172 GG
1 GG
49765174 CGGTCACGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.15, C:0.13, G:0.54, T:0.17
Consensus pattern (45 bp):
GGAGGGTATGGAGGTGGCCACGGAGGATACGGTGGTGGTGGCCAC
Found at i:49765182 original size:24 final size:23
Alignment explanation
Indices: 49765094--49765185 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 23
49765084 AGGGTATGGA
* *
49765094 GGTGGGCACGGAGGGTATGGTGGT
1 GGTGGCCACGGA-GGTACGGTGGT
49765118 GGTGGCCACGGAGGGTA---TGGT
1 GGTGGCCACGGA-GGTACGGTGGT
49765139 GGTGGCCACGGAGGATACGGTGGT
1 GGTGGCCACGGAGG-TACGGTGGT
*
49765163 GGTGGCCACGGCGGTCACGGTGG
1 GGTGGCCACGGAGGT-ACGGTGG
49765186 ACATGGAGGA
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
20 2 0.03
21 18 0.30
23 1 0.02
24 40 0.66
ACGTcount: A:0.13, C:0.16, G:0.53, T:0.17
Consensus pattern (23 bp):
GGTGGCCACGGAGGTACGGTGGT
Found at i:49765185 original size:45 final size:45
Alignment explanation
Indices: 49765094--49765185 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
49765084 AGGGTATGGA
* * * * *
49765094 GGTGGGCACGGAGGGTATGGTGGTGGTGGCCACGGAGGGTATGGT
1 GGTGGCCACGGAGGATACGGTGGTGGTGGCCACGGACGGTACGGT
49765139 GGTGGCCACGGAGGATACGGTGGTGGTGGCCACGG-CGGTCACGGT
1 GGTGGCCACGGAGGATACGGTGGTGGTGGCCACGGACGGT-ACGGT
49765184 GG
1 GG
49765186 ACATGGAGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 3 0.07
45 38 0.93
ACGTcount: A:0.13, C:0.16, G:0.53, T:0.17
Consensus pattern (45 bp):
GGTGGCCACGGAGGATACGGTGGTGGTGGCCACGGACGGTACGGT
Found at i:49765944 original size:17 final size:18
Alignment explanation
Indices: 49765922--49765956 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
49765912 AAAAAAAATC
*
49765922 TAATTTT-ATTTTTTATT
1 TAATTTTAATTATTTATT
49765939 TAATTTTAATTATTTATT
1 TAATTTTAATTATTTATT
49765957 GAAGTGGTTA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TAATTTTAATTATTTATT
Found at i:49770116 original size:16 final size:16
Alignment explanation
Indices: 49770095--49770128 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
49770085 CAAAATCTGA
49770095 ATTTAATT-TTTGATTT
1 ATTTAATTATTT-ATTT
49770111 ATTTAATTATTTATTT
1 ATTTAATTATTTATTT
49770127 AT
1 AT
49770129 GATGTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTAATTATTTATTT
Found at i:49771493 original size:5 final size:5
Alignment explanation
Indices: 49771483--49771577 Score: 190
Period size: 5 Copynumber: 19.0 Consensus size: 5
49771473 TTAAATATAT
49771483 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
49771533 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
49771578 ATAGATGAGA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 90 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:49771820 original size:12 final size:12
Alignment explanation
Indices: 49771798--49771827 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
49771788 GAAAGAGACC
49771798 AAAACAGGGAAAG
1 AAAA-AGGGAAAG
49771811 AAAAAGGGAAAG
1 AAAAAGGGAAAG
49771823 AAAAA
1 AAAAA
49771828 AAAGGGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.70, C:0.03, G:0.27, T:0.00
Consensus pattern (12 bp):
AAAAAGGGAAAG
Found at i:49777641 original size:41 final size:40
Alignment explanation
Indices: 49777576--49777654 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
49777566 TAAAAGGTAT
*
49777576 TTAAATATTTAGATTAATTTATATTTTATGTATCATTATA
1 TTAAATATTTAAATTAATTTATATTTTATGTATCATTATA
*
49777616 TTAAATTATTTAAATT-ATTTAATATTTTATTTATCATTA
1 TTAAA-TATTTAAATTAATTT-ATATTTTATGTATCATTA
49777655 ATTTTACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 9 0.26
41 26 0.74
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (40 bp):
TTAAATATTTAAATTAATTTATATTTTATGTATCATTATA
Found at i:49777693 original size:23 final size:22
Alignment explanation
Indices: 49777643--49777694 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
49777633 TTTAATATTT
*
49777643 TATTTATCATTAATTTTACAAA
1 TATTTATCATTAATTTTAAAAA
49777665 TAATTTAT-ATTAATTTTTTAAAAA
1 T-ATTTATCATTAA--TTTTAAAAA
49777689 TATTTA
1 TATTTA
49777695 AAATTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.23
23 11 0.42
24 9 0.35
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTATCATTAATTTTAAAAA
Found at i:49787001 original size:50 final size:50
Alignment explanation
Indices: 49786935--49787064 Score: 224
Period size: 50 Copynumber: 2.6 Consensus size: 50
49786925 CAGTGCCCAT
*
49786935 GCCATGTCCCAGACATGGTCTTACAGGGGACCCATTGTCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCCATTGTCTCGGTGCCAAC
* *
49786985 GCCATGTCCCAAACATGGTCTTACATGGGACCCCTTGTCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCCATTGTCTCGGTGCCAAC
*
49787035 TCCATGTCCCAGACATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
49787065 TCTCTTTACC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.24
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCCATTGTCTCGGTGCCAAC
Found at i:49788506 original size:18 final size:18
Alignment explanation
Indices: 49788485--49788612 Score: 70
Period size: 18 Copynumber: 7.3 Consensus size: 18
49788475 TGATATATAT
*
49788485 TTATGTAAATTATGTAAA
1 TTATGTAAGTTATGTAAA
*
49788503 TTATGTAAGTTATG-ATA
1 TTATGTAAGTTATGTAAA
* ***
49788520 TGATGTTTTTTTTATGT--A
1 TTATG--TAAGTTATGTAAA
49788538 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATGTAAA
* *
49788556 TTATGTAATTTATG-ATA
1 TTATGTAAGTTATGTAAA
* * *
49788573 TGATATATATTTATGT--A
1 TTATGTA-AGTTATGTAAA
* *
49788590 TTATGCAAGTTATGTAAG
1 TTATGTAAGTTATGTAAA
49788608 TTATG
1 TTATG
49788613 ATCCAAAGTT
Statistics
Matches: 82, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
16 14 0.17
17 18 0.22
18 44 0.54
19 6 0.07
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATGTAAGTTATGTAAA
Found at i:49788543 original size:53 final size:52
Alignment explanation
Indices: 49788485--49788612 Score: 184
Period size: 53 Copynumber: 2.4 Consensus size: 52
49788475 TGATATATAT
* * * *
49788485 TTATGTAAATTATGTAAATTATGTAAGTTATGATATGATGTTTTTTTTATGTA
1 TTATGTAAGTTATGTAAATTATGTAAGTTATGATATGAT-ATATATTTATGTA
*
49788538 TTATGTAAGTTATGTAAATTATGTAATTTATGATATGATATATATTTATGTA
1 TTATGTAAGTTATGTAAATTATGTAAGTTATGATATGATATATATTTATGTA
* *
49788590 TTATGCAAGTTATGTAAGTTATG
1 TTATGTAAGTTATGTAAATTATG
49788613 ATCCAAAGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
52 31 0.46
53 37 0.54
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.50
Consensus pattern (52 bp):
TTATGTAAGTTATGTAAATTATGTAAGTTATGATATGATATATATTTATGTA
Found at i:49788608 original size:9 final size:9
Alignment explanation
Indices: 49788458--49788612 Score: 61
Period size: 9 Copynumber: 17.6 Consensus size: 9
49788448 ATCCAAAGTT
49788458 TTATGTAAG
1 TTATGTAAG
*
49788467 TTATGATATG
1 TTATG-TAAG
* * *
49788477 ATATAT-AT
1 TTATGTAAG
*
49788485 TTATGTAAA
1 TTATGTAAG
*
49788494 TTATGTAAA
1 TTATGTAAG
49788503 TTATGTAAG
1 TTATGTAAG
*
49788512 TTATGATATG
1 TTATG-TAAG
* * * ***
49788522 ATGTTTTTT
1 TTATGTAAG
49788531 TTATGT-A-
1 TTATGTAAG
49788538 TTATGTAAG
1 TTATGTAAG
*
49788547 TTATGTAAA
1 TTATGTAAG
*
49788556 TTATGTAAT
1 TTATGTAAG
*
49788565 TTATGATATG
1 TTATG-TAAG
* * *
49788575 ATATAT-AT
1 TTATGTAAG
49788583 TTATGT-A-
1 TTATGTAAG
*
49788590 TTATGCAAG
1 TTATGTAAG
49788599 TTATGTAAG
1 TTATGTAAG
49788608 TTATG
1 TTATG
49788613 ATCCAAAGTT
Statistics
Matches: 107, Mismatches: 31, Indels: 16
0.69 0.20 0.10
Matches are distributed among these distances:
7 11 0.10
8 11 0.10
9 69 0.64
10 16 0.15
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.50
Consensus pattern (9 bp):
TTATGTAAG
Found at i:49788624 original size:96 final size:96
Alignment explanation
Indices: 49788458--49788634 Score: 266
Period size: 96 Copynumber: 1.8 Consensus size: 96
49788448 ATCCAAAGTT
* **
49788458 TTATGTAAGTTATGATATGATATATATTTATGTAAATTATGTAAATTATGTAAGTTATGATATGA
1 TTATGTAAGTTATGATATGATATATATTTATGT-AATTATGCAAATTATGTAAGTTATGATACAA
*
49788523 TGTTTTTTTTATGTATTATGTAAGTTATGTAAA
65 AGTTTTTTTTAT-TATTATGTAAGTTATGTAAA
* * *
49788556 TTATGTAATTTATGATATGATATATATTTATGT-ATTATGCAAGTTATGTAAGTTATGATCCAAA
1 TTATGTAAGTTATGATATGATATATATTTATGTAATTATGCAAATTATGTAAGTTATGATACAAA
49788620 GTTTTTTTTATTATT
66 GTTTTTTTTATTATT
49788635 TAAATGTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
95 4 0.06
96 36 0.50
98 32 0.44
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (96 bp):
TTATGTAAGTTATGATATGATATATATTTATGTAATTATGCAAATTATGTAAGTTATGATACAAA
GTTTTTTTTATTATTATGTAAGTTATGTAAA
Found at i:49789290 original size:13 final size:13
Alignment explanation
Indices: 49789252--49789298 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
49789242 TTAAGTCCTT
49789252 TACAGATACAGATA
1 TACAGA-ACAGATA
*
49789266 -ACAGAATTAGATA
1 TACAGAA-CAGATA
*
49789279 TGCAGAACAGATA
1 TACAGAACAGATA
49789292 TACAGAA
1 TACAGAA
49789299 TCCTACCCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
12 1 0.04
13 21 0.78
14 5 0.19
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.19
Consensus pattern (13 bp):
TACAGAACAGATA
Found at i:49792454 original size:12 final size:12
Alignment explanation
Indices: 49792437--49792467 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
49792427 CAAAAGCATG
49792437 CTCCATTCTCAA
1 CTCCATTCTCAA
*
49792449 CTCCATTCTCGA
1 CTCCATTCTCAA
49792461 CTCCATT
1 CTCCATT
49792468 TACAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.42, G:0.03, T:0.35
Consensus pattern (12 bp):
CTCCATTCTCAA
Found at i:49794027 original size:22 final size:22
Alignment explanation
Indices: 49793984--49794027 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
49793974 AATATATAAT
*
49793984 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
49794006 TAAA-TAATCCAAAAATTGCAAA
1 TAAATTAAT-CAAAAATTACAAA
49794028 CAGCAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:49794871 original size:25 final size:26
Alignment explanation
Indices: 49794833--49794881 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
49794823 GGACAGAATT
49794833 TTGTTAAAATGAAATAATAAAAATAA
1 TTGTTAAAATGAAATAATAAAAATAA
49794859 TTGTT-AAATGAAATAATAAAAAT
1 TTGTTAAAATGAAATAATAAAAAT
49794882 TGAGCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (26 bp):
TTGTTAAAATGAAATAATAAAAATAA
Found at i:49798904 original size:27 final size:27
Alignment explanation
Indices: 49798874--49798926 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
49798864 TGGAGGTTAT
49798874 GGAGGATACGGAGGGCGCGGTGGGTAC
1 GGAGGATACGGAGGGCGCGGTGGGTAC
*
49798901 GGAGGATACGGAGGGCGTGGTGGGTA
1 GGAGGATACGGAGGGCGCGGTGGGTA
49798927 TGGTGGTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.11, G:0.57, T:0.13
Consensus pattern (27 bp):
GGAGGATACGGAGGGCGCGGTGGGTAC
Found at i:49800112 original size:30 final size:29
Alignment explanation
Indices: 49800044--49800112 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
49800034 ACAGAACTAC
** *
49800044 AATTTAGTCTTTGTACTTTTATTTTTAAG
1 AATTTAGTCTTTGTACTTTTAAATTTAAA
*
49800073 AATTTAGTCTTTTTACTTTTCAAATTTAAA
1 AATTTAGTCTTTGTACTTTT-AAATTTAAA
*
49800103 AATTAAGTCT
1 AATTTAGTCT
49800113 AACTGTTGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (29 bp):
AATTTAGTCTTTGTACTTTTAAATTTAAA
Found at i:49800864 original size:32 final size:32
Alignment explanation
Indices: 49800819--49800883 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
49800809 AATATATATA
* *
49800819 ATTTTTTAGATAAATTCAAG-TACCAATTAAAT
1 ATTTTCTAAATAAATT-AAGATACCAATTAAAT
*
49800851 ATTTTCTAAATAAATTATGATACCAATTAAAT
1 ATTTTCTAAATAAATTAAGATACCAATTAAAT
49800883 A
1 A
49800884 CTTATAGGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 27 0.93
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (32 bp):
ATTTTCTAAATAAATTAAGATACCAATTAAAT
Found at i:49801170 original size:27 final size:27
Alignment explanation
Indices: 49801131--49801191 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
49801121 GCCTGATCAG
* *
49801131 GCCAATCACATTGGAGGCACCAAAGGT
1 GCCAATGACATTGGAGGCACCAAAGGA
* * *
49801158 GCCAATGAGATTGGCGGCACCAATGGA
1 GCCAATGACATTGGAGGCACCAAAGGA
49801185 GCCAATG
1 GCCAATG
49801192 GACTAAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.30, T:0.15
Consensus pattern (27 bp):
GCCAATGACATTGGAGGCACCAAAGGA
Found at i:49802211 original size:16 final size:16
Alignment explanation
Indices: 49802179--49802218 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
49802169 GTGTTCATCG
*
49802179 TTTCTTTT-TTTTTAT
1 TTTCTTTTATTTTCAT
49802194 TTTCTTTTATTTTCAT
1 TTTCTTTTATTTTCAT
*
49802210 TTTATTTTA
1 TTTCTTTTA
49802219 CCTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTCTTTTATTTTCAT
Found at i:49802212 original size:11 final size:10
Alignment explanation
Indices: 49802183--49802217 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
49802173 TCATCGTTTC
*
49802183 TTTTTTTTTA
1 TTTTCTTTTA
49802193 TTTTCTTTTA
1 TTTTCTTTTA
49802203 TTTTCATTTTA
1 TTTTC-TTTTA
49802214 TTTT
1 TTTT
49802218 ACCTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:49802977 original size:16 final size:16
Alignment explanation
Indices: 49802935--49802978 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
49802925 TTTTCATATA
49802935 TATATACATTATTATTT
1 TATATACA-TATTATTT
* * *
49802952 TATTTTCATATTTTTT
1 TATATACATATTATTT
49802968 TATATACATAT
1 TATATACATAT
49802979 ATATACTCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATACATATTATTT
Found at i:49804825 original size:19 final size:19
Alignment explanation
Indices: 49804785--49804826 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
49804775 GTCTCTTTTC
* *
49804785 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
49804804 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
49804823 GCAT
1 GCAT
49804827 CAAAGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:49807661 original size:21 final size:21
Alignment explanation
Indices: 49807622--49807670 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
49807612 AGTGATGTGA
*
49807622 AAAAATGAAAAGATGAAAA-T
1 AAAAATGAAAAGATAAAAAGT
49807642 GAAAAATGAACAAG-TAAAAAGT
1 -AAAAATGAA-AAGATAAAAAGT
49807664 AAAAATG
1 AAAAATG
49807671 GAGAGGCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.67, C:0.02, G:0.16, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAAGT
Found at i:49809059 original size:132 final size:132
Alignment explanation
Indices: 49808813--49809590 Score: 1252
Period size: 132 Copynumber: 5.9 Consensus size: 132
49808803 TTGACAGCGA
* ***
49808813 AGCAGATCGAAGATGGAAAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
49808878 TTTATCTCCCT-AGACAGTAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
66 TCTATCTCCCTGAG-CAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
49808942 TGG
130 TGG
* * * *
49808945 AGTAGATTAAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTAGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
49809010 TCTATCTCCCTAAGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
66 TCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
49809075 GG
131 GG
* *
49809077 AGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGTCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
49809142 TCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCACTAAGCAGTAGT
66 TCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
49809207 GG
131 GG
* * *
49809209 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
49809274 TCTATCTCCCTGGGCAACAGTGGAATATATTGAAGATTACAGATCTTATCTCCCTAAACAGTAGT
66 TCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
49809339 GG
131 GG
* * *
49809341 AGCAGATCAAGGATGGCGGGTTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
49809406 TCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
66 TCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
49809471 GG
131 GG
* ** *
49809473 AGCAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
49809538 TCTATCTCCCTGGGCAGCAGTCGAATAGATTGAAGATTACAGATCTTATCTCC
66 TCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCC
49809591 TTAGGCAGCG
Statistics
Matches: 599, Mismatches: 46, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
132 597 1.00
133 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
AGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:49811162 original size:18 final size:18
Alignment explanation
Indices: 49811120--49811165 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
49811110 TATTGTATCC
* *
49811120 TTATTATTATATTATTCG
1 TTATTTTTATATTATTCA
49811138 TTA-TTTTATCATTATT-A
1 TTATTTTTAT-ATTATTCA
49811155 TTATTTTTATA
1 TTATTTTTATA
49811166 CACTTACATG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (18 bp):
TTATTTTTATATTATTCA
Found at i:49811279 original size:16 final size:16
Alignment explanation
Indices: 49811237--49811280 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
49811227 TTTACATATA
49811237 TATATACATTATTATTT
1 TATATACA-TATTATTT
* * *
49811254 TATTTTCATATTTTTT
1 TATATACATATTATTT
49811270 TATATACATAT
1 TATATACATAT
49811281 ATATACTCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATACATATTATTT
Found at i:49812196 original size:19 final size:19
Alignment explanation
Indices: 49812140--49812196 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 19
49812130 TCTAATGAAG
*
49812140 TAATAGCTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
49812159 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
49812177 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
49812196 T
1 T
49812197 TAAAAAAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:49812283 original size:124 final size:129
Alignment explanation
Indices: 49812125--49812383 Score: 395
Period size: 124 Copynumber: 2.0 Consensus size: 129
49812115 TTCGACACTT
49812125 AGAATTCTAATGAAGTAATAGCTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATT
1 AGAATTCTAATGAAGTAATAGCTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATT
*
49812190 TTAATTT-TAAAA-AAATT-A-AG-T-TTAATTTTTTTAAAATTAAAATAGAGTTATTAAATGAG
66 TTAATTTAAAAAATAAATTAATAGTTATTAATTTTTTT-AAATTAAAATAGAGTTATTAAATGAG
* *
49812249 AGAATTCTAATTAAGTAATATCTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATT
1 AGAATTCTAATGAAGTAATAGCTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATT
49812314 TTAATTTAAAAAATTAAATTAAAATAGTTTACTTAATTTTTTTAAATTAAAATAGAGTTATTAAA
66 TTAATTTAAAAAA-TAAATT--AATAG-TTA-TTAATTTTTTTAAATTAAAATAGAGTTATTAAA
49812379 TGAG
126 TGAG
49812383 A
1 A
49812384 ATAGTTTATT
Statistics
Matches: 121, Mismatches: 3, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
124 70 0.58
125 4 0.03
127 5 0.04
130 1 0.01
131 2 0.02
133 1 0.01
134 27 0.22
135 11 0.09
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (129 bp):
AGAATTCTAATGAAGTAATAGCTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATT
TTAATTTAAAAAATAAATTAATAGTTATTAATTTTTTTAAATTAAAATAGAGTTATTAAATGAG
Found at i:49812293 original size:18 final size:19
Alignment explanation
Indices: 49812272--49812322 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
49812262 AGTAATATCT
49812272 CTATTTTAATTTAATAA-A
1 CTATTTTAATTTAATAACA
* * *
49812290 CTATTCTCATTTAATAACT
1 CTATTTTAATTTAATAACA
49812309 CTATTTTAATTTAA
1 CTATTTTAATTTAA
49812323 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (19 bp):
CTATTTTAATTTAATAACA
Found at i:49812320 original size:19 final size:19
Alignment explanation
Indices: 49812264--49812322 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
49812254 TCTAATTAAG
*
49812264 TAATATCTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
49812283 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
49812301 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
49812320 TAA
1 TAA
49812323 AAAATTAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:49812399 original size:37 final size:37
Alignment explanation
Indices: 49812355--49812484 Score: 251
Period size: 37 Copynumber: 3.5 Consensus size: 37
49812345 CTTAATTTTT
49812355 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
49812392 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
*
49812429 TTAAATTAAAATAGAGTTATTAAATGGGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
49812466 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
49812485 CTACTTAATT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 92 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:49812478 original size:18 final size:19
Alignment explanation
Indices: 49812355--49812484 Score: 149
Period size: 18 Copynumber: 7.0 Consensus size: 19
49812345 CTTAATTTTT
49812355 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
49812374 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
49812392 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
49812411 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
49812429 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
*** *
49812448 TTAAATGGGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
49812466 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
49812485 CTACTTAATT
Statistics
Matches: 88, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
18 44 0.50
19 44 0.50
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:49813077 original size:27 final size:27
Alignment explanation
Indices: 49813039--49813107 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
49813029 CATTTTAGTC
49813039 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
49813066 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
* *
49813093 CATTGGCACCTTTGG
1 CTTTGGCACCATTGG
49813108 CAGCAATTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.14, C:0.32, G:0.23, T:0.30
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:49813226 original size:27 final size:27
Alignment explanation
Indices: 49813188--49813254 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
49813178 TTTTAGTCCT
49813188 TTGGCACCATTGGTGCCGCCAATCTAA
1 TTGGCACCATTGGTGCCGCCAATCTAA
* *
49813215 TTGGCACCATTGGTGTCGCCAATCTCA
1 TTGGCACCATTGGTGCCGCCAATCTAA
49813242 TTGGCACCATTGG
1 TTGGCACCATTGG
49813255 CAGCAATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.28
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTAA
Found at i:49813235 original size:147 final size:147
Alignment explanation
Indices: 49812964--49813401 Score: 786
Period size: 147 Copynumber: 3.0 Consensus size: 147
49812954 CGCATAGTAA
49812964 CAATTCACTTTCAAAATTTAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAGTTA
1 CAATTCACTTTCAAAATTTAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAGTTA
49813029 CATTTTAGTCCTTTGGCACCATTGGTGCCGCCAATCTCTTTGGCACCATTGGTGCCGCCAATCTC
66 CATTTTAGTCCTTTGGCACCATTGGTGCCGCCAATCTCTTTGGCACCATTGGTGCCGCCAATCTC
49813094 ATTGGCACCTTTGGCAG
131 ATTGGCACCTTTGGCAG
* *
49813111 CAATTCACTTTCAAAATTTAAAATGGTAAATTTGCATGTCAGATCCTTAAAACTGTAGAAAGTTA
1 CAATTCACTTTCAAAATTTAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAGTTA
** *
49813176 CATTTTAGTCCTTTGGCACCATTGGTGCCGCCAATCTAATTGGCACCATTGGTGTCGCCAATCTC
66 CATTTTAGTCCTTTGGCACCATTGGTGCCGCCAATCTCTTTGGCACCATTGGTGCCGCCAATCTC
*
49813241 ATTGGCACCATTGGCAG
131 ATTGGCACCTTTGGCAG
*
49813258 CAATTCACTTTCAAAATTTAAAATGGTAAATTTACATGTCAGGTCCTTAAAACTGCAGAAAGTTA
1 CAATTCACTTTCAAAATTTAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAGTTA
* *
49813323 CATTTTAGTCCTTTAGCACCATTGGTACCGCCAATCTCTTTGGCACCATTGGTGCCGCCAATCTC
66 CATTTTAGTCCTTTGGCACCATTGGTGCCGCCAATCTCTTTGGCACCATTGGTGCCGCCAATCTC
*
49813388 ATTGGCACTTTTGG
131 ATTGGCACCTTTGG
49813402 TGCCTCCAAT
Statistics
Matches: 275, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 275 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (147 bp):
CAATTCACTTTCAAAATTTAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAGTTA
CATTTTAGTCCTTTGGCACCATTGGTGCCGCCAATCTCTTTGGCACCATTGGTGCCGCCAATCTC
ATTGGCACCTTTGGCAG
Found at i:49813401 original size:27 final size:27
Alignment explanation
Indices: 49813338--49813420 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 27
49813328 TAGTCCTTTA
* *
49813338 GCACCATTGGTACCGCCAATCTCTTTG
1 GCACCATTGGTGCCGCCAATCTCATTG
49813365 GCACCATTGGTGCCGCCAATCTCATTG
1 GCACCATTGGTGCCGCCAATCTCATTG
** * * *
49813392 GCACTTTTGGTGCCTCCAATGTGATTG
1 GCACCATTGGTGCCGCCAATCTCATTG
49813419 GC
1 GC
49813421 CTAATCAGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.30
Consensus pattern (27 bp):
GCACCATTGGTGCCGCCAATCTCATTG
Found at i:49813484 original size:27 final size:28
Alignment explanation
Indices: 49813454--49813508 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
49813444 TTTTCCGTTT
*
49813454 TTTTTTTGGT-ATATTTTGATAAATAAA
1 TTTTTTTGATAATATTTTGATAAATAAA
*
49813481 TTTTTTTTATAATATTTTGATAAATAAA
1 TTTTTTTGATAATATTTTGATAAATAAA
49813509 AAAAAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (28 bp):
TTTTTTTGATAATATTTTGATAAATAAA
Found at i:49820021 original size:21 final size:21
Alignment explanation
Indices: 49819992--49820041 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
49819982 AGTTAAACTA
* *
49819992 AGAAGTAGGTGTTGTAGGTTG
1 AGAATTAGGTGTTGTAGGGTG
49820013 AGAATTAGGTGTTGTAGGGTG
1 AGAATTAGGTGTTGTAGGGTG
*
49820034 AGTATTAG
1 AGAATTAG
49820042 TAATAGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.40, T:0.34
Consensus pattern (21 bp):
AGAATTAGGTGTTGTAGGGTG
Found at i:49824399 original size:18 final size:19
Alignment explanation
Indices: 49824357--49824399 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
49824347 TCAAGATCTT
*
49824357 AAATTAATATGGTCCAAAC
1 AAATTAATACGGTCCAAAC
*
49824376 AAATTAATGCGGTCCAAA-
1 AAATTAATACGGTCCAAAC
49824394 AAATTA
1 AAATTA
49824400 GTTAGTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (19 bp):
AAATTAATACGGTCCAAAC
Found at i:49827840 original size:27 final size:28
Alignment explanation
Indices: 49827809--49827870 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
49827799 AAATATGTTG
*
49827809 AATAATAATAATACTTAT-ATCTTTAAT
1 AATAATAATAATACTTATAATATTTAAT
*
49827836 GATAATAATAATACTTATAATATTTAAT
1 AATAATAATAATACTTATAATATTTAAT
49827864 AATAATA
1 AATAATA
49827871 CAATAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (28 bp):
AATAATAATAATACTTATAATATTTAAT
Found at i:49827875 original size:27 final size:26
Alignment explanation
Indices: 49827800--49827875 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
49827790 TAATAATAAA
49827800 AATATGTTGAATAATAAT-AATACTTAT
1 AATAT-TT-AATAATAATAAATACTTAT
* *
49827827 -ATCTTTAATGATAATAATAATACTTAT
1 AATATTTAATAATAAT-A-AATACTTAT
49827854 AATATTTAATAATAATACAATA
1 AATATTTAATAATAATA-AATA
49827876 ATAAAAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
24 8 0.20
25 2 0.05
26 3 0.08
27 14 0.35
28 13 0.32
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (26 bp):
AATATTTAATAATAATAAATACTTAT
Found at i:49834982 original size:57 final size:53
Alignment explanation
Indices: 49834932--49835090 Score: 154
Period size: 54 Copynumber: 3.1 Consensus size: 53
49834922 TATTTTCAAT
*
49834932 AATTTTATGAAATTATATATTATTATTAAATTATATGTAATAATAATTATTTTA
1 AATTTTATCAAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTTA
* * * *
49834986 AATTATA-CAAATTCATATA--A-GA--AAATT-TATTAGTTATAATTATTTTA
1 AATTTTATCAAATT-ATATATTATTATTAAATTATATTAATAATAATTATTTTA
* * *
49835033 AATTTTATTAAATTATATATT-TTAATTAAAATATATTTAATAATAATTATGTTA
1 AATTTTATCAAATTATATATTATT-ATTAAATTATA-TTAATAATAATTATTTTA
49835087 AATT
1 AATT
49835091 ATCTTTTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
47 26 0.31
48 8 0.10
49 5 0.06
50 1 0.01
51 1 0.01
52 5 0.06
53 7 0.08
54 30 0.36
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (53 bp):
AATTTTATCAAATTATATATTATTATTAAATTATATTAATAATAATTATTTTA
Found at i:49834986 original size:26 final size:28
Alignment explanation
Indices: 49834932--49834992 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
49834922 TATTTTCAAT
* *
49834932 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
49834960 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
49834986 AATTATA
1 AATTATA
49834993 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:49835005 original size:101 final size:96
Alignment explanation
Indices: 49834894--49835092 Score: 215
Period size: 101 Copynumber: 2.0 Consensus size: 96
49834884 TAATTATTTT
49834894 AAATTATAT-AAATTCATATAAG-AAAATTTATTTTCAATAATTTTATGAAATTATATATTATT-
1 AAATTATATAAAATT--TATAAGTAAAA-TTATTTT--A-AATTTTATGAAATTATATATT-TTA
* *
49834956 ATTAAATTATATGTAATAATAATTATTTTAAATTATAC
59 ATTAAAATATATGTAATAATAATTATGTTAAATTATAC
* * *
49834994 AAATTCATATAAGAAAATTTATTAGTTATAATTATTTTAAATTTTATTAAATTATATATTTTAAT
1 AAATT-ATAT---AAAATTTATAAG-TAAAATTATTTTAAATTTTATGAAATTATATATTTTAAT
*
49835059 TAAAATATATTTAATAATAATTATGTTAAATTAT
61 TAAAATATATGTAATAATAATTATGTTAAATTAT
49835093 CTTTTATAGT
Statistics
Matches: 85, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
100 7 0.08
101 57 0.67
102 1 0.01
103 5 0.06
104 7 0.08
105 8 0.09
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (96 bp):
AAATTATATAAAATTTATAAGTAAAATTATTTTAAATTTTATGAAATTATATATTTTAATTAAAA
TATATGTAATAATAATTATGTTAAATTATAC
Found at i:49835062 original size:18 final size:17
Alignment explanation
Indices: 49835034--49835068 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49835024 ATTATTTTAA
*
49835034 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
49835051 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
49835069 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:49835088 original size:54 final size:54
Alignment explanation
Indices: 49835021--49835215 Score: 167
Period size: 54 Copynumber: 3.4 Consensus size: 54
49835011 TTTATTAGTT
*
49835021 ATAATTATTTTAAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
1 ATAATTATGTTAAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
* * * * *
49835075 ATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATTAGAAT
1 ATAATTATGTTAAATT-T-TATTA-A--AT--TATA-TAT--TTTAATTAAAAT-ATATT-TAAT
49835140 A
54 A
* * * *
49835141 TTAATTAT-TAAGAATTTTATTAAATTATATATTTTAATTATAATATTTTTAATA
1 ATAATTATGTTA-AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
*
49835195 ATAATTATGTTAAATTATATT
1 ATAATTATGTTAAATTTTATT
49835216 TTATAGTATC
Statistics
Matches: 109, Mismatches: 18, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
54 34 0.31
55 7 0.06
56 12 0.11
57 1 0.01
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 1 0.01
64 13 0.12
65 8 0.07
66 15 0.14
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (54 bp):
ATAATTATGTTAAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
Found at i:49835146 original size:66 final size:65
Alignment explanation
Indices: 49835071--49835260 Score: 181
Period size: 66 Copynumber: 3.1 Consensus size: 65
49835061 AAATATATTT
49835071 AATAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATTA
1 AATAATAATTATGTTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATTA
49835136 G
65 G
* * * * * *
49835137 AATATTAATTAT-TAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-TAATATT--T-TT
1 AATAATAATTATGTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAA-ATTCATATT
49835191 --
64 AG
* *
49835191 AATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGCTTTGAGTAAATTCATATAA
1 AATAATAATTATGTTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATTA
49835256 G
65 G
49835257 AATA
1 AATA
49835261 TTGATTATTA
Statistics
Matches: 94, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
54 15 0.16
55 3 0.03
56 6 0.06
57 2 0.02
58 3 0.03
59 13 0.14
60 7 0.07
61 13 0.14
62 3 0.03
63 2 0.02
64 5 0.05
65 3 0.03
66 19 0.20
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (65 bp):
AATAATAATTATGTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATTAG
Found at i:49835157 original size:120 final size:120
Alignment explanation
Indices: 49835033--49835281 Score: 444
Period size: 120 Copynumber: 2.1 Consensus size: 120
49835023 AATTATTTTA
*
49835033 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
49835098 ATAGTATCATATATTATGATTTGAGTAAATTCATATTAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
49835153 AATTTTATTAAATTATATATTTTAATTATAATATTTTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
49835218 ATAGTATCATATATTATGCTTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
49835273 AATTTTATT
1 AATTTTATT
49835282 CCATTCAACC
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:49835192 original size:15 final size:15
Alignment explanation
Indices: 49835163--49835213 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
49835153 AATTTTATTA
49835163 AATTAT-ATA-TTTT
1 AATTATAATATTTTT
49835176 AATTATAATATTTTT
1 AATTATAATATTTTT
* * *
49835191 AATAATAATTATGTTA
1 AATTATAA-TATTTTT
49835207 AATTATA
1 AATTATA
49835214 TTTTATAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 6 0.19
14 3 0.10
15 11 0.35
16 11 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
AATTATAATATTTTT
Found at i:49835331 original size:44 final size:45
Alignment explanation
Indices: 49835283--49835373 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 45
49835273 AATTTTATTC
**
49835283 CATTCAACCAAACACA-AGA-TTACTATTATGCCTCTATTCCATTA
1 CATTCAACCAAACA-ATAGATTTACTATTACACCTCTATTCCATTA
*
49835327 CATTCAACCAAACAATTGATTTACTATTACACCTCTATTCCATTA
1 CATTCAACCAAACAATAGATTTACTATTACACCTCTATTCCATTA
49835372 CA
1 CA
49835374 CCTCTAATCC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.38
45 25 0.60
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (45 bp):
CATTCAACCAAACAATAGATTTACTATTACACCTCTATTCCATTA
Found at i:49835406 original size:16 final size:16
Alignment explanation
Indices: 49835352--49835404 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
49835342 TTGATTTACT
*
49835352 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
49835368 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
49835384 ATTACGCCTCTAATCC
1 ATTACACCTCTAATCC
49835400 ATTAC
1 ATTAC
49835405 GCATCTATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.28, C:0.36, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:49835411 original size:16 final size:16
Alignment explanation
Indices: 49835352--49835411 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
49835342 TTGATTTACT
* *
49835352 ATTACACCTCTATTCC
1 ATTACGCCTCTAATCC
*
49835368 ATTACACCTCTAATCC
1 ATTACGCCTCTAATCC
49835384 ATTACGCCTCTAATCC
1 ATTACGCCTCTAATCC
*
49835400 ATTACGCATCTA
1 ATTACGCCTCTA
49835412 TTCTAATACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.33
Consensus pattern (16 bp):
ATTACGCCTCTAATCC
Found at i:49852753 original size:28 final size:29
Alignment explanation
Indices: 49852712--49853010 Score: 199
Period size: 28 Copynumber: 10.5 Consensus size: 29
49852702 GAAACACACT
* * * * *
49852712 TCGCATACACAGTGCTC-ACTGACTGATT
1 TCGCACACATAGTGCTCGACTTACAGATC
* *
49852740 TCGCACACATAGTGCTCGA-TTAAAGAAC
1 TCGCACACATAGTGCTCGACTTACAGATC
** *
49852768 TCGCACACATAGTGCTTAAATTACCA-ATC
1 TCGCACACATAGTGCTCGACTTA-CAGATC
* *
49852797 TCGTACACATAGTGCTCGA-TTGA-AGAAC
1 TCGCACACATAGTGCTCGACTT-ACAGATC
* *
49852825 TCGCACACATAGTGCCTCAAC-TACTGATC
1 TCGCACACATAGTG-CTCGACTTACAGATC
* * *
49852854 TGGCACACATAGTGCTCGA-TTAAAGAAC
1 TCGCACACATAGTGCTCGACTTACAGATC
** * *
49852882 TCGCACACATAGTGCTTAAATTACAAATC
1 TCGCACACATAGTGCTCGACTTACAGATC
* *
49852911 TCGTACACATAGTGCTCGA-TTGA-AGAAC
1 TCGCACACATAGTGCTCGACTT-ACAGATC
* *
49852939 TCGCACACATAGTGCCTCAAC-TACTGATC
1 TCGCACACATAGTG-CTCGACTTACAGATC
* * *
49852968 TGGCACACATAGTGCTCG-GTTGA-AGAGC
1 TCGCACACATAGTGCTCGACTT-ACAGATC
*
49852996 TTGCACACATAGTGC
1 TCGCACACATAGTGC
49853011 CTCATAATTC
Statistics
Matches: 210, Mismatches: 45, Indels: 32
0.73 0.16 0.11
Matches are distributed among these distances:
27 1 0.00
28 119 0.57
29 89 0.42
30 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (29 bp):
TCGCACACATAGTGCTCGACTTACAGATC
Found at i:49852804 original size:29 final size:29
Alignment explanation
Indices: 49852740--49852983 Score: 175
Period size: 29 Copynumber: 8.6 Consensus size: 29
49852730 CTGACTGATT
* *
49852740 TCGCACACATAGTGC-TCGATTA-AAGAAC
1 TCGCACACATAGTGCTTCAATTACAA-ATC
* *
49852768 TCGCACACATAGTGCTTAAATTACCAATC
1 TCGCACACATAGTGCTTCAATTACAAATC
* *
49852797 TCGTACACATAGTGC-TCGATTGA-AGAA-C
1 TCGCACACATAGTGCTTCAATT-ACA-AATC
* * **
49852825 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCTTCAATTACAAATC
* * *
49852854 TGGCACACATAGTGC-TCGATTA-AAGAAC
1 TCGCACACATAGTGCTTCAATTACAA-ATC
*
49852882 TCGCACACATAGTGCTTAAATTACAAATC
1 TCGCACACATAGTGCTTCAATTACAAATC
* *
49852911 TCGTACACATAGTGC-TCGATTGA-AGAA-C
1 TCGCACACATAGTGCTTCAATT-ACA-AATC
* * **
49852939 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCTTCAATTACAAATC
*
49852968 TGGCACACATAGTGCT
1 TCGCACACATAGTGCT
49852984 CGGTTGAAGA
Statistics
Matches: 168, Mismatches: 33, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
28 79 0.47
29 86 0.51
30 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (29 bp):
TCGCACACATAGTGCTTCAATTACAAATC
Found at i:49852933 original size:114 final size:114
Alignment explanation
Indices: 49852712--49853010 Score: 494
Period size: 114 Copynumber: 2.6 Consensus size: 114
49852702 GAAACACACT
* * * *
49852712 TCGCATACACAGTG-CTC-ACTGACTGATTTCGCACACATAGTGCTCGATTAAAGAACTCGCACA
1 TCGCACACATAGTGCCTCAACT-ACTGATCTGGCACACATAGTGCTCGATTAAAGAACTCGCACA
*
49852775 CATAGTGCTTAAATTACCAATCTCGTACACATAGTGCTCGATTGAAGAAC
65 CATAGTGCTTAAATTACAAATCTCGTACACATAGTGCTCGATTGAAGAAC
49852825 TCGCACACATAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCGATTAAAGAACTCGCACAC
1 TCGCACACATAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCGATTAAAGAACTCGCACAC
49852890 ATAGTGCTTAAATTACAAATCTCGTACACATAGTGCTCGATTGAAGAAC
66 ATAGTGCTTAAATTACAAATCTCGTACACATAGTGCTCGATTGAAGAAC
* * * *
49852939 TCGCACACATAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCGGTTGAAGAGCTTGCACAC
1 TCGCACACATAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCGATTAAAGAACTCGCACAC
49853004 ATAGTGC
66 ATAGTGC
49853011 CTCATAATTC
Statistics
Matches: 175, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
113 12 0.07
114 160 0.91
115 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (114 bp):
TCGCACACATAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCGATTAAAGAACTCGCACAC
ATAGTGCTTAAATTACAAATCTCGTACACATAGTGCTCGATTGAAGAAC
Found at i:49853013 original size:57 final size:57
Alignment explanation
Indices: 49852712--49853014 Score: 385
Period size: 57 Copynumber: 5.3 Consensus size: 57
49852702 GAAACACACT
* * * *
49852712 TCGCATACACAGTG-CTC-ACTGACTGATTTCGCACACATAGTGCTCGATTAAAGAAC
1 TCGCACACATAGTGCCTCAACT-ACTGATCTCGCACACATAGTGCTCGATTGAAGAAC
* * * ** *
49852768 TCGCACACATAGTGCTTAAATTACCAATCTCGTACACATAGTGCTCGATTGAAGAAC
1 TCGCACACATAGTGCCTCAACTACTGATCTCGCACACATAGTGCTCGATTGAAGAAC
* *
49852825 TCGCACACATAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCGATTAAAGAAC
1 TCGCACACATAGTGCCTCAACTACTGATCTCGCACACATAGTGCTCGATTGAAGAAC
* * * ** *
49852882 TCGCACACATAGTGCTTAAATTACAAATCTCGTACACATAGTGCTCGATTGAAGAAC
1 TCGCACACATAGTGCCTCAACTACTGATCTCGCACACATAGTGCTCGATTGAAGAAC
* * *
49852939 TCGCACACATAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCGGTTGAAGAGC
1 TCGCACACATAGTGCCTCAACTACTGATCTCGCACACATAGTGCTCGATTGAAGAAC
*
49852996 TTGCACACATAGTGCCTCA
1 TCGCACACATAGTGCCTCA
49853015 TAATTCCAGC
Statistics
Matches: 209, Mismatches: 36, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
56 12 0.06
57 195 0.93
58 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (57 bp):
TCGCACACATAGTGCCTCAACTACTGATCTCGCACACATAGTGCTCGATTGAAGAAC
Found at i:49853076 original size:39 final size:39
Alignment explanation
Indices: 49853020--49853173 Score: 188
Period size: 39 Copynumber: 4.0 Consensus size: 39
49853010 CCTCATAATT
* * *
49853020 CCAGCACGAATGC-CTTCGAGGTTTAGCCCAGATATATCA
1 CCAGCACGAATGCTCTTCG-GGCTTAGCCCGGATATAACA
*
49853059 CTAGCAC-AATGCTCTTCGGGACTTAGCCCGGATATAACA
1 CCAGCACGAATGCTCTTCGGG-CTTAGCCCGGATATAACA
*
49853098 CCAGCACGAATGCTCTTCGGACTTAGCCCGGATATAACA
1 CCAGCACGAATGCTCTTCGGGCTTAGCCCGGATATAACA
* * * *
49853137 CCAGCATGAATGCTCTTCGGAC-TAGCCAGAATATAAC
1 CCAGCACGAATGCTCTTCGGGCTTAGCCCGGATATAAC
49853174 TCTCATTCTC
Statistics
Matches: 103, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
38 20 0.19
39 71 0.69
40 12 0.12
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (39 bp):
CCAGCACGAATGCTCTTCGGGCTTAGCCCGGATATAACA
Found at i:49861008 original size:8 final size:8
Alignment explanation
Indices: 49860992--49861042 Score: 93
Period size: 8 Copynumber: 6.2 Consensus size: 8
49860982 CTATTTATTT
49860992 TTTTAAAAA
1 TTTT-AAAA
49861001 TTTTAAAA
1 TTTTAAAA
49861009 TTTTAAAA
1 TTTTAAAA
49861017 TTTTAAAA
1 TTTTAAAA
49861025 TTTTAAAA
1 TTTTAAAA
49861033 TTTTAAAA
1 TTTTAAAA
49861041 TT
1 TT
49861043 AAAATATAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
8 38 0.90
9 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TTTTAAAA
Found at i:49861959 original size:22 final size:24
Alignment explanation
Indices: 49861916--49861963 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
49861906 TATTAAAATA
49861916 AAATATCATCATAATCAATTTCATT
1 AAATATCAT-ATAATCAATTTCATT
*
49861941 AAATATCAT-TAA-CATTTTCATT
1 AAATATCATATAATCAATTTCATT
49861963 A
1 A
49861964 CAAAATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 3 0.14
25 9 0.41
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATCATATAATCAATTTCATT
Found at i:49869656 original size:47 final size:47
Alignment explanation
Indices: 49869590--49870208 Score: 995
Period size: 47 Copynumber: 13.1 Consensus size: 47
49869580 GAAATGATAG
*
49869590 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGGATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
49869637 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
49869686 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
49869733 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
49869780 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
49869827 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
49869876 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
49869923 TAAGGCCTAATAGCCGATGTGGTGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
49869970 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
49870017 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
49870064 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
49870111 TAAGGCCTAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
49870158 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
49870205 TAAG
1 TAAG
49870209 TCCCGAAGGG
Statistics
Matches: 538, Mismatches: 30, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
47 446 0.83
49 92 0.17
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:49869913 original size:190 final size:190
Alignment explanation
Indices: 49869590--49870208 Score: 1037
Period size: 190 Copynumber: 3.3 Consensus size: 190
49869580 GAAATGATAG
* *
49869590 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGGATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
49869655 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
49869720 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
131 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
49869780 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
49869845 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
49869910 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGGTGAATGTGAAAGTGTATATATGTGA
131 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
49869970 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* *
49870035 GTGATGAATGTGAAAGTG--TATATGTGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
49870098 TGTATATATGTGATAAGGCCTAAT-GACCGATGTGATGAATGTGAAAGTGTATATATGTGA
131 TGTATATGTGTGATAAGGCCTAATAG-CCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * * *
49870158 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGATAAG
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
49870209 TCCCGAAGGG
Statistics
Matches: 407, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
187 1 0.00
188 139 0.34
190 267 0.66
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (190 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:49870383 original size:37 final size:37
Alignment explanation
Indices: 49870327--49870405 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
49870317 CCGAGCTCTA
* * *
49870327 AAGACCCGATGACTACGTGTGG-GAATTTTGTTCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
49870364 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
49870401 AAGAC
1 AAGAC
49870406 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:49877275 original size:12 final size:12
Alignment explanation
Indices: 49877258--49877282 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49877248 TAATTAAATG
49877258 AATTAAAAGCCA
1 AATTAAAAGCCA
49877270 AATTAAAAGCCA
1 AATTAAAAGCCA
49877282 A
1 A
49877283 TTTTTTTTCC
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:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AATTAAAAGCCA
Found at i:49894462 original size:93 final size:93
Alignment explanation
Indices: 49894355--49894525 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
49894345 GCGCCTAAGT
* *
49894355 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
49894420 TGAGTTCGGATGCCTAGTTACATTTCAC
66 TGAGTTCGGATGCCTAGTTACATTTCAC
*
49894448 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
49894513 TGAGTTCGGATGC
66 TGAGTTCGGATGC
49894526 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
TGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:49894522 original size:46 final size:46
Alignment explanation
Indices: 49894350--49894522 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
49894340 AACTCGCGCC
* * *
49894350 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
49894396 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
49894444 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
49894489 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
49894523 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 59 0.57
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:49902508 original size:30 final size:30
Alignment explanation
Indices: 49902474--49902533 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
49902464 ATTTAATACG
49902474 AACTTTGAAAAAATTACACTTTTGCCCCTA
1 AACTTTGAAAAAATTACACTTTTGCCCCTA
* * * *
49902504 AACTTTTACATAATTATACTTTTGCCCCTA
1 AACTTTGAAAAAATTACACTTTTGCCCCTA
49902534 GTTTTGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTGAAAAAATTACACTTTTGCCCCTA
Found at i:49926345 original size:31 final size:32
Alignment explanation
Indices: 49926296--49926355 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
49926286 TTGGTACTTG
*
49926296 AATTTGACATGTTTTTCTTAA-TTTAGTATCTC
1 AATTTGACATCTTTTTCTTAAGTTT-GTATCTC
49926328 AATTTGACA-CTTTTTCTTAAGTTTGTAT
1 AATTTGACATCTTTTTCTTAAGTTTGTAT
49926356 TTAAACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (32 bp):
AATTTGACATCTTTTTCTTAAGTTTGTATCTC
Found at i:49926601 original size:18 final size:18
Alignment explanation
Indices: 49926580--49926615 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
49926570 TCAATTGCTT
49926580 TTAATTTTATTTAATTAA
1 TTAATTTTATTTAATTAA
*
49926598 TTAATTTTTTTTAATTAA
1 TTAATTTTATTTAATTAA
49926616 AAATAACGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAATTTTATTTAATTAA
Found at i:49927849 original size:27 final size:26
Alignment explanation
Indices: 49927775--49927845 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 26
49927765 ATTAATTTTT
* *
49927775 TTAAAATT-TTTAAAAATTTAAAAATA
1 TTAAAATTATTTAAAAAGTGAAAAA-A
* *
49927801 ATAAAAGTTATTTTTAAAAGTGAAAAAA
1 TTAAAA-TTA-TTTAAAAAGTGAAAAAA
49927829 TTAAAATTATTTAAAAA
1 TTAAAATTATTTAAAAA
49927846 AGTGTCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
26 12 0.33
27 5 0.14
28 6 0.17
29 13 0.36
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (26 bp):
TTAAAATTATTTAAAAAGTGAAAAAA
Found at i:49927855 original size:27 final size:28
Alignment explanation
Indices: 49927802--49927858 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
49927792 TTAAAAATAA
**
49927802 TAAAAGTTATTTTTAAAAGTGAAAAAAT
1 TAAAAGTTATTTAAAAAAGTGAAAAAAT
**
49927830 TAAAA-TTATTTAAAAAAGTGTCAAAAT
1 TAAAAGTTATTTAAAAAAGTGAAAAAAT
49927857 TA
1 TA
49927859 CAAAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (28 bp):
TAAAAGTTATTTAAAAAAGTGAAAAAAT
Found at i:49933956 original size:34 final size:33
Alignment explanation
Indices: 49933885--49933962 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 33
49933875 CAATAACATT
* * *
49933885 TCAGT-TCAGTTGGGCCTTTGCCTATTGCAGTA
1 TCAGTATCAGTTGGGCCTTAGCCCATTACAGTA
49933917 TCAGTATCAGTGTGGGCCTTAGCCCATTACAGTGA
1 TCAGTATCAGT-TGGGCCTTAGCCCATTACAGT-A
*
49933952 -CAGTAACAGTT
1 TCAGTATCAGTT
49933963 CAGATATGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 5 0.13
33 6 0.15
34 27 0.69
35 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (33 bp):
TCAGTATCAGTTGGGCCTTAGCCCATTACAGTA
Found at i:49934268 original size:27 final size:27
Alignment explanation
Indices: 49934228--49934299 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
49934218 ATAACATAAA
*
49934228 GCAT-ACAGTTATTTTATAACATAGGG
1 GCATAACAGTCATTTTATAACATAGGG
** *
49934254 GCATAACAGTCATTTTACCACGTAGGG
1 GCATAACAGTCATTTTATAACATAGGG
*
49934281 GCATAACAATCATTTTATA
1 GCATAACAGTCATTTTATA
49934300 TCAGTTTGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 4 0.11
27 34 0.89
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (27 bp):
GCATAACAGTCATTTTATAACATAGGG
Found at i:49935980 original size:23 final size:23
Alignment explanation
Indices: 49935954--49936001 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
49935944 GGAGTTGTCT
49935954 TTGATGACCAATGTTCGAATCCC
1 TTGATGACCAATGTTCGAATCCC
*
49935977 TTGATGACCAGTGTTCGAATCCC
1 TTGATGACCAATGTTCGAATCCC
49936000 TT
1 TT
49936002 CCTTCTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (23 bp):
TTGATGACCAATGTTCGAATCCC
Found at i:49941315 original size:257 final size:257
Alignment explanation
Indices: 49940859--49941371 Score: 972
Period size: 257 Copynumber: 2.0 Consensus size: 257
49940849 AGTTCCTTTG
49940859 GAGATTGGAAAACATCTTCAAATTCTGCCAATACCAATTGCAAATCCCTACTATCAACCAGACCT
1 GAGATTGGAAAACATCTTCAAATTCTGCCAATACCAATTGCAAATCCCTACTATCAACCAGACCT
49940924 GACATATGTAGAAGGGTGTGCTTGCTCAGGGTGATGAGCAATGGCCAAGTACTCTGATCAGACAG
66 GACATATGTAGAAGGGTGTGCTTGCTCAGGGTGATGAGCAATGGCCAAGTACTCTGATCAGACAG
*
49940989 ATGCACCAACTTAGTGCTTTGAGTCCCTATCATAATCTGAATAGCTCCTAAAAGTATTCATTGTA
131 ATGCACCAACTTAGTGCTTTGAGTACCTATCATAATCTGAATAGCTCCTAAAAGTATTCATTGTA
*
49941054 AAGTACAATAGTGATCATTGTATACAAACTGCATAGTAAGAGAACTGAAATTCTAGACTATT
196 AAGTACAATAGTGATCATTGTATACAAACTGCATAGTAAGAGAACTGAAATTCCAGACTATT
49941116 GAGATTGGAAAACATCTTCAAATTCTGCCAATACCAATTGCAAATCCCTACTATCAACCAGACCT
1 GAGATTGGAAAACATCTTCAAATTCTGCCAATACCAATTGCAAATCCCTACTATCAACCAGACCT
49941181 GACATATGTAGAAGGGTGTGCTTGCTCAGGGTGATGAGCAATGGCCAAGTACTCTGATCAGACAG
66 GACATATGTAGAAGGGTGTGCTTGCTCAGGGTGATGAGCAATGGCCAAGTACTCTGATCAGACAG
* *
49941246 ATGCACCAACTTAGTTCTTTGAGTACCTATCATAATCTGAATAGCTCCTAGAAGTATTCATTGTA
131 ATGCACCAACTTAGTGCTTTGAGTACCTATCATAATCTGAATAGCTCCTAAAAGTATTCATTGTA
**
49941311 AAGTACAATAGTGATTGTTGTATACAAACTGCATAGTAAGAGAACTGAAATTCCAGACTAT
196 AAGTACAATAGTGATCATTGTATACAAACTGCATAGTAAGAGAACTGAAATTCCAGACTAT
49941372 GGACCCTAAG
Statistics
Matches: 250, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
257 250 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (257 bp):
GAGATTGGAAAACATCTTCAAATTCTGCCAATACCAATTGCAAATCCCTACTATCAACCAGACCT
GACATATGTAGAAGGGTGTGCTTGCTCAGGGTGATGAGCAATGGCCAAGTACTCTGATCAGACAG
ATGCACCAACTTAGTGCTTTGAGTACCTATCATAATCTGAATAGCTCCTAAAAGTATTCATTGTA
AAGTACAATAGTGATCATTGTATACAAACTGCATAGTAAGAGAACTGAAATTCCAGACTATT
Found at i:49943724 original size:29 final size:28
Alignment explanation
Indices: 49943692--49943752 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
49943682 AAAAGCCTTT
49943692 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** *
49943721 TTTTTTGATTATTTACCGGAATGGGCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
49943749 TTTT
1 TTTT
49943753 CCGCGAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:49944021 original size:7 final size:7
Alignment explanation
Indices: 49944009--49944038 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
49943999 GCCAAAGGCA
49944009 GTTTAGG
1 GTTTAGG
*
49944016 GTTTAGA
1 GTTTAGG
49944023 GTTTAGG
1 GTTTAGG
49944030 GTTTAGG
1 GTTTAGG
49944037 GT
1 GT
49944039 GGTTTGCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:49944769 original size:29 final size:29
Alignment explanation
Indices: 49944712--49944776 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
49944702 GATTTCGCGG
49944712 AAATGGCCCATTCCAGTAAATAATTAAAA
1 AAATGGCCCATTCCAGTAAATAATTAAAA
* * * *
49944741 ATATGGCCCATTTCGGTAAAT-TTTGAAAA
1 AAATGGCCCATTCCAGTAAATAATT-AAAA
49944770 AAATGGC
1 AAATGGC
49944777 TTTTTTTGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (29 bp):
AAATGGCCCATTCCAGTAAATAATTAAAA
Found at i:49945964 original size:11 final size:11
Alignment explanation
Indices: 49945950--49945974 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
49945940 GAGAAGGACG
49945950 GGAGTGGGGGA
1 GGAGTGGGGGA
49945961 GGAGTGGGGGA
1 GGAGTGGGGGA
49945972 GGA
1 GGA
49945975 CGATGGGGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.72, T:0.08
Consensus pattern (11 bp):
GGAGTGGGGGA
Found at i:49946040 original size:12 final size:12
Alignment explanation
Indices: 49946009--49946034 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49945999 AATTTCATTT
49946009 AATATTAATATA
1 AATATTAATATA
49946021 AATATTAATATA
1 AATATTAATATA
49946033 AA
1 AA
49946035 ATTTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATTAATATA
Found at i:49948314 original size:2 final size:2
Alignment explanation
Indices: 49948307--49948331 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49948297 AAAAGACAGA
49948307 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
49948332 AAGGAAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49952317 original size:6 final size:6
Alignment explanation
Indices: 49952306--49952389 Score: 107
Period size: 6 Copynumber: 13.8 Consensus size: 6
49952296 GGTTTTCTCA
* *
49952306 AAATGG AAATGG AAATGG AAATTG AAATGG AAATGG AAATGG AAATAG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
* *
49952354 AAATGG AAATAG AAA-GAG AAATGA AAATGAG AAATG
1 AAATGG AAATGG AAATG-G AAATGG AAATG-G AAATG
49952390 ATTCATTTGC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
6 61 0.91
7 6 0.09
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:49956734 original size:22 final size:22
Alignment explanation
Indices: 49956709--49956787 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
49956699 TGTTGTTTTC
49956709 TTAGCACTTCGGTACTCTTTGT
1 TTAGCACTTCGGTACTCTTTGT
* * *
49956731 TTAGCACTTTGGTACTCTCTAT
1 TTAGCACTTCGGTACTCTTTGT
* * *
49956753 TTAGCACTTTGATGCTCTTTGT
1 TTAGCACTTCGGTACTCTTTGT
* *
49956775 TCAACACTTCGGT
1 TTAGCACTTCGGT
49956788 GTTCTCCGTT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.44
Consensus pattern (22 bp):
TTAGCACTTCGGTACTCTTTGT
Found at i:49960497 original size:29 final size:29
Alignment explanation
Indices: 49960449--49960527 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
49960439 AAAATAATAT
* **
49960449 ATAAATTTAAA-AT-TTAAAATAAATTTGA
1 ATAAA-TTAAAGATGTTAAAATAAACTAAA
* * *
49960477 ATAAATTAACGATGTTGAAATAAGCTAAA
1 ATAAATTAAAGATGTTAAAATAAACTAAA
49960506 ATAAATTAAAGATGTTAAAATA
1 ATAAATTAAAGATGTTAAAATA
49960528 TTTGAAAGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 4 0.10
28 7 0.17
29 30 0.73
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.33
Consensus pattern (29 bp):
ATAAATTAAAGATGTTAAAATAAACTAAA
Found at i:49962434 original size:50 final size:50
Alignment explanation
Indices: 49962312--49962558 Score: 196
Period size: 50 Copynumber: 4.9 Consensus size: 50
49962302 TGTGATGTCG
** * * ** **
49962312 GGGAAGCAAGATTCGCCATTGTAGCTTCAATCTATTTC-ACTGCACCGCCAA
1 GGGAAGCAAGATTCGCTGTTGTGGCTTTAATCT-TTTCAACTGCAATG-TTA
* * * *
49962363 GGAAAGTAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTACAATGTTA
1 GGGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTCAACTGCAATGTTA
* * *
49962413 GGGAAGCAAGATTCG-TCGTTGTGGCTTTAATCTGTTCCACTGC-ATCGCCTA
1 GGGAAGCAAGATTCGCT-GTTGTGGCTTTAATCTTTTCAACTGCAAT-G-TTA
* * * **
49962464 -GGAAGTAAGATTCGCTATTGTAGCTTTAATCTTTTCAACTGCAATGTCG
1 GGGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTCAACTGCAATGTTA
* * * * *
49962513 GGGAAGCGAGATTCGCAGTTGTGGCTTTAATATGTTCCACTGCAAT
1 GGGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTCAACTGCAAT
49962559 CTCAGGAAGA
Statistics
Matches: 154, Mismatches: 35, Indels: 15
0.75 0.17 0.07
Matches are distributed among these distances:
49 3 0.02
50 113 0.73
51 38 0.25
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (50 bp):
GGGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTCAACTGCAATGTTA
Found at i:49962509 original size:100 final size:100
Alignment explanation
Indices: 49962306--49962556 Score: 324
Period size: 100 Copynumber: 2.5 Consensus size: 100
49962296 CTTAACTGTG
* * * * * *
49962306 ATGTCGGGGAAGCAAGATTCGCCATTGTAGCTTCAATCTATTTCACTGCACCGCCAAGGAAAGTA
1 ATGTCAGGGAAGCAAGATTCG-CGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAAGGAAAGTA
* * *
49962371 AGATTCGCTGTTGTGGCTTTAATCTTTTTAACTACA
65 AGATTCGCTATTGTAGCTTTAATCTTTTCAACTACA
* * *
49962407 ATGTTAGGGAAGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCACTGCATCGCCTAGG-AAGTA
1 ATGTCAGGGAAGCAAGATTCG-CGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAAGGAAAGTA
*
49962471 AGATTCGCTATTGTAGCTTTAATCTTTTCAACTGCA
65 AGATTCGCTATTGTAGCTTTAATCTTTTCAACTACA
* * *
49962507 ATGTCGGGGAAGCGAGATTCGCAGTTGTGGCTTTAATATGTTCCACTGCA
1 ATGTCAGGGAAGCAAGATTCGC-GTTGTGGCTTTAATCTGTTCCACTGCA
49962557 ATCTCAGGAA
Statistics
Matches: 131, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
99 1 0.01
100 81 0.62
101 49 0.37
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (100 bp):
ATGTCAGGGAAGCAAGATTCGCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCAAGGAAAGTAA
GATTCGCTATTGTAGCTTTAATCTTTTCAACTACA
Found at i:49962614 original size:44 final size:44
Alignment explanation
Indices: 49962548--49962839 Score: 177
Period size: 44 Copynumber: 6.7 Consensus size: 44
49962538 TTTAATATGT
* *
49962548 TCCACTGCAATCTCAGGAAGATAAGATTTCTGGCCTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGC
* * * * ** **
49962592 TCCACTGTAACCTCAGGGAGATAAGATTTGAAAT-TCTTCGGTCTAT
1 TCCACTGTAATCTCAGGGAGATAAGATTT---CTGGCCTCAATCTGC
* * * *
49962638 TCCACTGTAATCCCAGGGAGATAAGA--CCTGATG-C-GAA-CTAC
1 TCCACTGTAATCTCAGGGAGATAAGATTTCTG--GCCTCAATCTGC
* * * * *** * *
49962679 TCTACTGTAATTTTAGAGAGATAAGATCCTT-T-ATTTTAATCCGC
1 TCCACTGTAATCTCAGGGAGATAAGAT--TTCTGGCCTCAATCTGC
* * * *
49962723 TCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGC
* *
49962767 TCTACTGTAATCTCAGGGACATAAGATTTCTGGCCTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGC
* * *
49962811 TCCACCGTAACCTCAGAGAGATAAGATTT
1 TCCACTGTAATCTCAGGGAGATAAGATTT
49962840 GAAATTCTTC
Statistics
Matches: 181, Mismatches: 52, Indels: 30
0.69 0.20 0.11
Matches are distributed among these distances:
41 25 0.14
42 1 0.01
43 3 0.02
44 121 0.67
46 30 0.17
47 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
TCCACTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGC
Found at i:49962944 original size:219 final size:219
Alignment explanation
Indices: 49962551--49962947 Score: 679
Period size: 219 Copynumber: 1.8 Consensus size: 219
49962541 AATATGTTCC
* * *
49962551 ACTGCAATCTCAGGAAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGATAA
1 ACTGCAATCTCAGGAACATAAGATTTCTGGCCTCAATCTGCTCCACCGTAACCTCAGAGAGATAA
49962616 GATTTGAAATTCTTCGGTCTATTCCACTGTAATCCCAGGGAGATAAGACCTGATGCGAACTACTC
66 GATTTGAAATTCTTCGGTCTATTCCACTGTAATCCCAGGGAGATAAGACCTGATGCGAACTACTC
* * * * *
49962681 TACTGTAATTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATA
131 TACTATAACTTCAGAGAGATAAGATCCTTTACTTTAACCCGCTCCACTGTAATCTCAGGGAAATA
49962746 GGATTACTGGCTTCAATCTGCTCT
196 GGATTACTGGCTTCAATCTGCTCT
* *
49962770 ACTGTAATCTCAGGGACATAAGATTTCTGGCCTCAATCTGCTCCACCGTAACCTCAGAGAGATAA
1 ACTGCAATCTCAGGAACATAAGATTTCTGGCCTCAATCTGCTCCACCGTAACCTCAGAGAGATAA
*
49962835 GATTTGAAATTCTTCGGTCTATTCCACTGTAATCCCAGGGAGATAAGACCTGATGCGATCTACTC
66 GATTTGAAATTCTTCGGTCTATTCCACTGTAATCCCAGGGAGATAAGACCTGATGCGAACTACTC
49962900 TACTATAACTTCAGAGAGATAAGAT-CTATTACTTTAACCCGCTCCACT
131 TACTATAACTTCAGAGAGATAAGATCCT-TTACTTTAACCCGCTCCACT
49962948 ACAACTTCAG
Statistics
Matches: 166, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
218 2 0.01
219 164 0.99
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (219 bp):
ACTGCAATCTCAGGAACATAAGATTTCTGGCCTCAATCTGCTCCACCGTAACCTCAGAGAGATAA
GATTTGAAATTCTTCGGTCTATTCCACTGTAATCCCAGGGAGATAAGACCTGATGCGAACTACTC
TACTATAACTTCAGAGAGATAAGATCCTTTACTTTAACCCGCTCCACTGTAATCTCAGGGAAATA
GGATTACTGGCTTCAATCTGCTCT
Found at i:49963676 original size:129 final size:127
Alignment explanation
Indices: 49962956--49963639 Score: 1064
Period size: 128 Copynumber: 5.3 Consensus size: 127
49962946 CTACAACTTC
* *
49962956 AGGGAGATAGGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGC
1 AGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGC
* * ** *
49963021 TTAAATATGCTTCCTTACACTTGAAGATAAGATTCACCATCTTTGATCTGCTCCGCTATTGCTT
65 TTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCC-GCTTTGATCTGCTCCGCTATTGCTT
*
49963085 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGATATAGGACTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
*
49963150 TAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTT
66 TAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGCTTT-GATCTGCTCCGCTATTGCTT
* * * *
49963213 AGGGAGACAAGATCTGTAATTTCCAAACTATTCCACTACTGACCAGGGATATAAGACTTGTAGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
* *
49963278 TAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGCTTTTGACCTGCTCCGCTACTGCTT
66 TAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGC-TTTGATCTGCTCCGCTATTGCTT
* *
49963341 AGGGAGACAAGATCTGTAATTTCCAAACTATTCTACTGCTGACCAGGGATATAGGACTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
49963406 TAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGCTTTTGATCTGCTCCGCTACTT-CTT
66 TAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGC-TTTGATCTGCTCCGCTA-TTGCTT
*
49963469 AGAGAGACAAGATCTGTAATTTCCAAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGC
1 AGGGAGACAAGATCTGTAATTTCC-AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGC
* * * * *
49963534 TTAAATTTGATTCCTTACACTTGAAGATAAGATTCGTCGTCTTTGATCTGCTCCGCTATTGCTT
65 TTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCG-CTTTGATCTGCTCCGCTATTGCTT
*
49963598 AGGGAGATAAGATCTGTAATTTCCCAACCTATTCCACTGCTG
1 AGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTG
49963640 GTCAGGGAGC
Statistics
Matches: 517, Mismatches: 31, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
127 4 0.01
128 357 0.69
129 153 0.30
130 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (127 bp):
AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
TAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGCTTTGATCTGCTCCGCTATTGCTT
Found at i:49965841 original size:6 final size:6
Alignment explanation
Indices: 49965832--49965924 Score: 118
Period size: 6 Copynumber: 15.7 Consensus size: 6
49965822 CTTCTCTCTT
* * * **
49965832 TTTTCA TTTTCA TTTTGA CTTTGA TTTTGA TTTTGA TTTTTC TTCTT--
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TT-TTGA
49965879 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
49965925 TTTTGAATTG
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
6 73 0.92
7 2 0.03
ACGTcount: A:0.14, C:0.05, G:0.12, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:49965894 original size:47 final size:48
Alignment explanation
Indices: 49965823--49965918 Score: 158
Period size: 47 Copynumber: 2.0 Consensus size: 48
49965813 TTTCTTTTTC
49965823 TTCTCTCTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTTGATTT
1 TTCTCTCTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTTGATTT
* * *
49965871 TTCT-TCTTTTTTGATTTTGATTTTGATTTTGATTTTGATTTTGATTT
1 TTCTCTCTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTTGATTT
49965918 T
1 T
49965919 GATTTTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 41 0.91
48 4 0.09
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.69
Consensus pattern (48 bp):
TTCTCTCTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTTGATTT
Found at i:49970207 original size:29 final size:30
Alignment explanation
Indices: 49970159--49970237 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
49970149 AAAATAATAT
**
49970159 ATAAATTTAAA-AT-TTAAAATAAATTTG-A
1 ATAAA-TTAAAGATGTTAAAATAAAGCTGAA
* *
49970187 ATAAATTAACGATGTTGAAAT-AAGCTGAA
1 ATAAATTAAAGATGTTAAAATAAAGCTGAA
49970216 ATAAATTAAAGATGTTAAAATA
1 ATAAATTAAAGATGTTAAAATA
49970238 TTTGAAAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
27 4 0.10
28 11 0.27
29 26 0.63
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (30 bp):
ATAAATTAAAGATGTTAAAATAAAGCTGAA
Found at i:49982220 original size:30 final size:30
Alignment explanation
Indices: 49982184--49982246 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
49982174 ACTTATTTTA
49982184 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
49982214 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
49982244 TTG
1 TTG
49982247 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:49992410 original size:40 final size:40
Alignment explanation
Indices: 49992351--49992766 Score: 523
Period size: 40 Copynumber: 10.4 Consensus size: 40
49992341 TCGTCAGATT
* * * *
49992351 AACCG-AACACACCAGACAGAAGCTCACAAGAGCTAATCC
1 AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTGATCC
* *
49992390 AACCGAAATACACCAAACAGAAGCTCATAAGAGCTGATCC
1 AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTGATCC
* *
49992430 AACCGAAACACGCCAAACA-AATACTCATAAAAGCTGATCC
1 AACCGAAACACGCCAAACAGAA-GCTCATAAGAGCTGATCC
* * * *
49992470 AATCGAAACACACCAAACATAAGCTCATAAGGGCTGATCC
1 AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTGATCC
*
49992510 AACCGAAACACGCCAAACAGAAGCTTATAAGAGCTGATCC
1 AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTGATCC
** *
49992550 AACC-AAATCATACCAAACAGAAGCTTATAAGAGCTGATCC
1 AACCGAAA-CACGCCAAACAGAAGCTCATAAGAGCTGATCC
*
49992590 AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTAATCC
1 AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTGATCC
* * * *
49992630 AACCAAAACACGCCAAACAAAAGGTCATAAGAGCTAATCC
1 AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTGATCC
* * * *
49992670 AACCAAAACACGCCAAACAGAAGCTCAAAAAAGCTGGTCC
1 AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTGATCC
* * *
49992710 AATCGAAACACGCCAAACAGAAGTTCATAAGAGCTAATCC
1 AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTGATCC
* *
49992750 AACCAAAACATGCCAAA
1 AACCGAAACACGCCAAA
49992767 TAGAGAGTAT
Statistics
Matches: 329, Mismatches: 43, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
39 10 0.03
40 314 0.95
41 5 0.02
ACGTcount: A:0.46, C:0.28, G:0.14, T:0.12
Consensus pattern (40 bp):
AACCGAAACACGCCAAACAGAAGCTCATAAGAGCTGATCC
Done.