Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 17 of 402
Found at i:3978200 original size:18 final size:19
Alignment explanation
Indices: 3978177--3978215 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3978167 TTTTTTACTG
3978177 ATTAATAAATT-ATTTTTT
1 ATTAATAAATTAATTTTTT
*
3978195 ATTAATCAATTAATTTTTT
1 ATTAATAAATTAATTTTTT
3978214 AT
1 AT
3978216 CAAATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTAATAAATTAATTTTTT
Found at i:3978209 original size:22 final size:22
Alignment explanation
Indices: 3978166--3978213 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
3978156 TAGTAACTTC
* *
3978166 ATTTTTTACTGATTAATAAATT
1 ATTTTTTACTAATCAATAAATT
* *
3978188 ATTTTTTATTAATCAATTAATT
1 ATTTTTTACTAATCAATAAATT
3978210 -TTTT
1 ATTTT
3978214 ATCAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTTTTACTAATCAATAAATT
Found at i:3981329 original size:17 final size:18
Alignment explanation
Indices: 3981297--3981335 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3981287 TTATATATTA
3981297 ATAAATTTTATATAAAT-
1 ATAAATTTTATATAAATG
* *
3981314 ATAAATTTTTTTTAAATG
1 ATAAATTTTATATAAATG
3981332 ATAA
1 ATAA
3981336 TATAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATAAATTTTATATAAATG
Found at i:3983021 original size:31 final size:31
Alignment explanation
Indices: 3982985--3983057 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
3982975 TAAAATATTA
***
3982985 CAAATGAAATCCGTGTGCATTAATATTTTAT
1 CAAATGAAATCCACATGCATTAATATTTTAT
* *
3983016 CAAATGAAATCTACATGCATTTATATTTTAT
1 CAAATGAAATCCACATGCATTAATATTTTAT
3983047 CAAATGAAATC
1 CAAATGAAATC
3983058 AAATTAACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (31 bp):
CAAATGAAATCCACATGCATTAATATTTTAT
Found at i:3985136 original size:13 final size:13
Alignment explanation
Indices: 3985116--3985167 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
3985106 ATAATATTTT
3985116 TATTAAATTAATA
1 TATTAAATTAATA
* *
3985129 TCTTAAATTAAAA
1 TATTAAATTAATA
3985142 TATTAAA-TAATA
1 TATTAAATTAATA
*
3985154 -ATTATATTAATA
1 TATTAAATTAATA
3985166 TA
1 TA
3985168 ATATATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 5 0.16
12 9 0.28
13 18 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
TATTAAATTAATA
Found at i:3985176 original size:17 final size:16
Alignment explanation
Indices: 3985141--3985190 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 16
3985131 TTAAATTAAA
3985141 ATATTAAATAATAATT
1 ATATTAAATAATAATT
3985157 ATATTAATATAAT-ATAT
1 ATATTAA-ATAATAAT-T
3985174 ATAATTAAATAAATAAT
1 AT-ATTAAAT-AATAAT
3985191 AAAAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.31
17 10 0.34
18 8 0.28
19 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTAAATAATAATT
Found at i:3985188 original size:23 final size:22
Alignment explanation
Indices: 3985116--3985193 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
3985106 ATAATATTTT
*
3985116 TATTAAATTAATATCTTAAATTAAAA
1 TATTAAA-TAATA-ATTAAA-T-AAA
* *
3985142 TATTAAATAATAATTATATTAA
1 TATTAAATAATAATTAAATAAA
3985164 TA-TAATATATATAATTAAATAAA
1 TATTAA-ATA-ATAATTAAATAAA
*
3985187 TAATAAA
1 TATTAAA
3985194 AAAATTTACA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
21 3 0.07
22 7 0.16
23 15 0.34
24 7 0.16
25 5 0.11
26 7 0.16
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTAAATAATAATTAAATAAA
Found at i:3985843 original size:92 final size:92
Alignment explanation
Indices: 3985686--3985866 Score: 283
Period size: 92 Copynumber: 2.0 Consensus size: 92
3985676 TAAGGCACTG
* *
3985686 AACCCCTACAGACAAGCCAAGCATCAATAATCCCTCTGCTTCTTTCTAGAGTTAACCCTGAAGCC
1 AACCCCTACAGACAAGCCAAGCATCAATAATCCCTCTGCTCCTTACTAGAGTTAACCCTGAAGCC
3985751 AAAACAAACAAAAAGACTGAAAAGCTA
66 AAAACAAACAAAAAGACTGAAAAGCTA
** *
3985778 AACCCCTACAGACAAGCCAAGCATCAATAATCCCTCTGCTCCTTACTCTATTTAACCCAT-AAGC
1 AACCCCTACAGACAAGCCAAGCATCAATAATCCCTCTGCTCCTTACTAGAGTTAACCC-TGAAGC
* *
3985842 CAAAACAAGCGAAAAGACTGAAAAG
65 CAAAACAAACAAAAAGACTGAAAAG
3985867 AAAGGAACAA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 80 0.99
93 1 0.01
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.18
Consensus pattern (92 bp):
AACCCCTACAGACAAGCCAAGCATCAATAATCCCTCTGCTCCTTACTAGAGTTAACCCTGAAGCC
AAAACAAACAAAAAGACTGAAAAGCTA
Found at i:3993123 original size:64 final size:65
Alignment explanation
Indices: 3993008--3993129 Score: 178
Period size: 64 Copynumber: 1.9 Consensus size: 65
3992998 GAAACAAAAC
*
3993008 TTCTCCAAAAGCTTGGAAAGAGAAGCTTCTCTAAAAATCCAAAGTCTTATC-TTGTTTCATAAAT
1 TTCTCCAAAAGCTTGGAAAGAGAAGCTTCTCCAAAAATCCAAAGTCTTATCTTTGTTTCATAAAT
* *
3993072 TTCTCCAAAAGCTT-GAAGGGAGAAGCTTCTCCAAAAATCCAAGGT-TCTATCTTTGTTT
1 TTCTCCAAAAGCTTGGAA-AGAGAAGCTTCTCCAAAAATCCAAAGTCT-TATCTTTGTTT
3993130 TTTAACAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
63 4 0.08
64 42 0.81
65 6 0.12
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (65 bp):
TTCTCCAAAAGCTTGGAAAGAGAAGCTTCTCCAAAAATCCAAAGTCTTATCTTTGTTTCATAAAT
Found at i:3994645 original size:10 final size:10
Alignment explanation
Indices: 3994625--3994657 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
3994615 AGTTCCTTAG
3994625 TTTGA-GATA
1 TTTGAGGATA
3994634 TTTGAGGATA
1 TTTGAGGATA
3994644 TTTGAGGATA
1 TTTGAGGATA
3994654 TTTG
1 TTTG
3994658 GTATTAGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (10 bp):
TTTGAGGATA
Found at i:3995855 original size:16 final size:16
Alignment explanation
Indices: 3995834--3995867 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3995824 AATGACTGGA
3995834 GGTTATTTTCAA-TTTG
1 GGTTATTTT-AACTTTG
3995850 GGTTATTTTAACTTTG
1 GGTTATTTTAACTTTG
3995866 GG
1 GG
3995868 ATTTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.18, C:0.06, G:0.24, T:0.53
Consensus pattern (16 bp):
GGTTATTTTAACTTTG
Found at i:3997747 original size:63 final size:63
Alignment explanation
Indices: 3997672--3997844 Score: 213
Period size: 63 Copynumber: 2.7 Consensus size: 63
3997662 AATCAATTTT
* * *
3997672 TGGTAGACTCTTTCTTTTGATCAGATCTATAAGTTTGTTGTGGAGAAAATAGACCATGTGAAA
1 TGGTAAACTCTTTCTTTTGATCAGATCTATGAGTTTATTGTGGAGAAAATAGACCATGTGAAA
* * * * * * *
3997735 TGGTAAACTCTTTCTTCTGATCAGATCCATGAGTTTATTGTGGAAAAAATGGATCATTTGGAA
1 TGGTAAACTCTTTCTTTTGATCAGATCTATGAGTTTATTGTGGAGAAAATAGACCATGTGAAA
* * *
3997798 TGATAAATTCTTT-TTTCTGATCAGATCTATGAGATTATTGTGGAGAA
1 TGGTAAACTCTTTCTTT-TGATCAGATCTATGAGTTTATTGTGGAGAA
3997845 GATTGATTGT
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
62 2 0.02
63 91 0.98
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (63 bp):
TGGTAAACTCTTTCTTTTGATCAGATCTATGAGTTTATTGTGGAGAAAATAGACCATGTGAAA
Found at i:4001970 original size:2 final size:2
Alignment explanation
Indices: 4001963--4001994 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4001953 ATTAAGAAGC
4001963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4001995 CAGTTAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4002955 original size:2 final size:2
Alignment explanation
Indices: 4002948--4002984 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4002938 TCCATCTTTT
4002948 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4002985 GGTGATCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4004771 original size:2 final size:2
Alignment explanation
Indices: 4004764--4004791 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4004754 AATATTATTC
4004764 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4004792 GGTTCAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4005335 original size:19 final size:18
Alignment explanation
Indices: 4005311--4005347 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
4005301 AAAAAAATTT
4005311 ATTATAATATATTTTTTTA
1 ATTATAATAT-TTTTTTTA
*
4005330 ATTATAATCTTTTTTTTA
1 ATTATAATATTTTTTTTA
4005348 TAAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATAATATTTTTTTTA
Found at i:4007385 original size:3 final size:3
Alignment explanation
Indices: 4007377--4007413 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
4007367 GTAATTTTGT
*
4007377 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4007414 TCTTCTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4008071 original size:14 final size:14
Alignment explanation
Indices: 4008052--4008118 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 14
4008042 TAAATTTATT
4008052 TTTATTTTTATTTA
1 TTTATTTTTATTTA
* *
4008066 TTTATTTATATATA
1 TTTATTTTTATTTA
4008080 TTT-TTTATTATTTA
1 TTTATTT-TTATTTA
4008094 TCTAATAATATTTTATTTA
1 T-T--T-AT-TTTTATTTA
4008113 TTTATT
1 TTTATT
4008119 AATTATCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
13 3 0.07
14 22 0.52
15 3 0.07
16 1 0.02
17 1 0.02
18 1 0.02
19 9 0.21
20 2 0.05
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:4008081 original size:24 final size:24
Alignment explanation
Indices: 4008045--4008118 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
4008035 AAATGGATAA
* *
4008045 ATTTATTTTTATTTTTATTTATTT
1 ATTTATATATATTTTTATTTATTT
4008069 ATTTATATATATTTTT-TATTATTT
1 ATTTATATATATTTTTAT-TTATTT
*
4008093 ATCTA-ATA-ATATTTTATTTATTT
1 ATTTATATATAT-TTTTATTTATTT
4008116 ATT
1 ATT
4008119 AATTATCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
22 2 0.05
23 16 0.37
24 25 0.58
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (24 bp):
ATTTATATATATTTTTATTTATTT
Found at i:4008084 original size:30 final size:30
Alignment explanation
Indices: 4008048--4008144 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 30
4008038 TGGATAAATT
*
4008048 TATTTTTATTTTTATTTATTTATTTATATA
1 TATTTTTATTTTTATTTATCTATTTATATA
* *
4008078 TA-TTTT-TTATTATTTATCTA-ATA-ATA
1 TATTTTTATTTTTATTTATCTATTTATATA
* * *
4008104 TTTTATTTATTTATTAATTATCTATTAATATA
1 TATT-TTTATTT-TTATTTATCTATTTATATA
*
4008136 TATATTTAT
1 TATTTTTAT
4008145 CTATTATTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
26 4 0.08
27 3 0.06
28 15 0.29
29 6 0.12
30 12 0.24
31 6 0.12
32 5 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (30 bp):
TATTTTTATTTTTATTTATCTATTTATATA
Found at i:4008154 original size:3 final size:3
Alignment explanation
Indices: 4008114--4008182 Score: 77
Period size: 3 Copynumber: 21.7 Consensus size: 3
4008104 TTTTATTTAT
*
4008114 TTA TTAA TTA TCTA TTA ATA -TA TATA TTTA TCTA TTA TTA TTA TTA
1 TTA TT-A TTA T-TA TTA TTA TTA T-TA -TTA T-TA TTA TTA TTA TTA
4008160 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
4008183 TTACTTTATC
Statistics
Matches: 59, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
2 2 0.03
3 43 0.73
4 13 0.22
5 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:4008492 original size:11 final size:11
Alignment explanation
Indices: 4008478--4008504 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4008468 TAGAGTTTTT
4008478 TTTTTGAAAAA
1 TTTTTGAAAAA
4008489 TTTTTGAAAAA
1 TTTTTGAAAAA
4008500 TTTTT
1 TTTTT
4008505 AGAATCCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (11 bp):
TTTTTGAAAAA
Found at i:4008907 original size:3 final size:3
Alignment explanation
Indices: 4008899--4008959 Score: 88
Period size: 3 Copynumber: 20.0 Consensus size: 3
4008889 TGATTGATTG
*
4008899 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT CCTT AATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT -ATT ATT
4008946 ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT
4008960 TTAATATTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.89
4 4 0.08
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4009159 original size:74 final size:76
Alignment explanation
Indices: 4008991--4009177 Score: 222
Period size: 75 Copynumber: 2.5 Consensus size: 76
4008981 AATGATTTTC
** * * *
4008991 CTAAAATAAAAAATTC-AAAAATATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTGA
1 CTAAAATAAAATTTTCAAAAAAAATATATTTTGAGGAAAAAGTTGAAAGTATCAATTTTCCTTGA
4009055 AAATAAAATTA
66 AAATAAAATTA
* * *
4009066 CTAAAATAAAATTTCCAAAAAAAATGTATTTTGA-GAAAAAGTTGAAAGTATTAATTTTCCTT-A
1 CTAAAATAAAATTTTCAAAAAAAATATATTTTGAGGAAAAAGTTGAAAGTATCAATTTTCCTTGA
** *
4009129 AAATGCAATTT
66 AAATAAAATTA
* *
4009140 CTAAAATAAAATTTTC--AAAAAATACATTTTGGGGAAAA
1 CTAAAATAAAATTTTCAAAAAAAATATATTTTGAGGAAAA
4009178 GTTAGAAGTA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
72 13 0.14
73 5 0.05
74 24 0.25
75 39 0.41
76 14 0.15
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (76 bp):
CTAAAATAAAATTTTCAAAAAAAATATATTTTGAGGAAAAAGTTGAAAGTATCAATTTTCCTTGA
AAATAAAATTA
Found at i:4013389 original size:19 final size:18
Alignment explanation
Indices: 4013367--4013427 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 18
4013357 AAACAAAATG
4013367 GAAAAGAAAAAAAAAGTAA
1 GAAAAG-AAAAAAAAGTAA
*
4013386 GAAAAG-AAAAAAA-T-G
1 GAAAAGAAAAAAAAGTAA
4013401 GAAAAGAAAAAAAAG-AA
1 GAAAAGAAAAAAAAGTAA
4013418 GAAAA-AAAAA
1 GAAAAGAAAAA
4013428 TAAAAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 6 0.16
16 13 0.35
17 12 0.32
19 6 0.16
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
GAAAAGAAAAAAAAGTAA
Found at i:4013399 original size:34 final size:31
Alignment explanation
Indices: 4013356--4013427 Score: 108
Period size: 34 Copynumber: 2.2 Consensus size: 31
4013346 ACGAATGAAG
*
4013356 AAAACAAAATGGAAAAGAAAAAAAAAGTAAGAA
1 AAAAAAAAATGGAAAAG-AAAAAAAAG-AAGAA
4013389 AAGAAAAAAATGGAAAAGAAAAAAAAGAAGAA
1 AA-AAAAAAATGGAAAAGAAAAAAAAGAAGAA
4013421 AAAAAAA
1 AAAAAAA
4013428 TAAAAAAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 5 0.14
32 7 0.19
33 11 0.30
34 14 0.38
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.04
Consensus pattern (31 bp):
AAAAAAAAATGGAAAAGAAAAAAAAGAAGAA
Found at i:4014505 original size:20 final size:20
Alignment explanation
Indices: 4014480--4014531 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4014470 TTGGATCATT
4014480 GCATTTGCATCATTAAAGAA
1 GCATTTGCATCATTAAAGAA
*
4014500 GCATTTGCATCATTAAGGAA
1 GCATTTGCATCATTAAAGAA
4014520 GCATTTGCATCA
1 GCATTTGCATCA
4014532 ATGATCATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (20 bp):
GCATTTGCATCATTAAAGAA
Found at i:4014652 original size:21 final size:21
Alignment explanation
Indices: 4014626--4014706 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
4014616 CTTTATTTTC
*
4014626 AAATGAAAATATTTGAGTCTT
1 AAATGAAAATCTTTGAGTCTT
* * *
4014647 AAATGAGAATCTTTAAGACATTTT
1 AAATGAAAATCTTT--GA-GTCTT
* *
4014671 CAAATGAGAATCTTTCAGTCTT
1 -AAATGAAAATCTTTGAGTCTT
4014693 AAATGAAAATCTTT
1 AAATGAAAATCTTT
4014707 AAGAATCTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
21 25 0.52
22 3 0.06
23 3 0.06
24 3 0.06
25 14 0.29
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATGAAAATCTTTGAGTCTT
Found at i:4014670 original size:46 final size:46
Alignment explanation
Indices: 4014620--4014710 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
4014610 TAGGATCTTT
* *
4014620 ATTTTCAAATGAAAATATTTGAGTCTTAAATGAGAATCTTTAAGAC
1 ATTTTCAAATGAAAATATTTCAGTCTTAAATGAAAATCTTTAAGAC
* *
4014666 ATTTTCAAATGAGAATCTTTCAGTCTTAAATGAAAATCTTTAAGA
1 ATTTTCAAATGAAAATATTTCAGTCTTAAATGAAAATCTTTAAGA
4014711 ATCTTTGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (46 bp):
ATTTTCAAATGAAAATATTTCAGTCTTAAATGAAAATCTTTAAGAC
Found at i:4014941 original size:92 final size:92
Alignment explanation
Indices: 4014790--4014983 Score: 273
Period size: 92 Copynumber: 2.1 Consensus size: 92
4014780 TAATGAAAAG
* ** * *
4014790 TTTGAAACTTTTGGATGTGAATCTCTAAAATTCAAATGAAAAGTTTTAAACTCAACTTTTGGATG
1 TTTG-AACTTTTGGATGTGAATCTCCAAAATTCAAACAAAAAGCTTTAAACTCAACTTTTGGATA
4014855 CAAATATCTAAATTTTTGAGCGAAAA-T
65 CAAATATCTAAATTTTTGAGCGAAAACT
*
4014882 CTTTGAACTTTTGGATGTGAATCTCCAAAATTCAAACAAAAAGCTTTGAACTCAACTTTTGGATA
1 -TTTGAACTTTTGGATGTGAATCTCCAAAATTCAAACAAAAAGCTTTAAACTCAACTTTTGGATA
* * * *
4014947 CGAATCTCTAAATTTTTGAGTGAGAACT
65 CAAATATCTAAATTTTTGAGCGAAAACT
4014975 TTTGAACTT
1 TTTGAACTT
4014984 AAATGTGAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
92 85 0.94
93 5 0.06
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (92 bp):
TTTGAACTTTTGGATGTGAATCTCCAAAATTCAAACAAAAAGCTTTAAACTCAACTTTTGGATAC
AAATATCTAAATTTTTGAGCGAAAACT
Found at i:4014943 original size:48 final size:48
Alignment explanation
Indices: 4014795--4014958 Score: 149
Period size: 48 Copynumber: 3.5 Consensus size: 48
4014785 AAAAGTTTGA
* * * *
4014795 AACTTTTGGATGTGAATCTCTAAAATTCAAATGAAAAGTTTTAAACTC
1 AACTTTTGGATGCGAATCTCTAAAATTCAAACGAAAAGCTTTGAACTC
* * * ** * *
4014843 AACTTTTGGATGCAAATATCTAAATTTTTGAGCGAAAATCTTTG-----
1 AACTTTTGGATGCGAATCTCTAAA-ATTCAAACGAAAAGCTTTGAACTC
* * *
4014887 AACTTTTGGATGTGAATCTCCAAAATTCAAACAAAAAGCTTTGAACTC
1 AACTTTTGGATGCGAATCTCTAAAATTCAAACGAAAAGCTTTGAACTC
*
4014935 AACTTTTGGATACGAATCTCTAAA
1 AACTTTTGGATGCGAATCTCTAAA
4014959 TTTTTGAGTG
Statistics
Matches: 86, Mismatches: 24, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
43 13 0.15
44 20 0.23
48 42 0.49
49 11 0.13
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (48 bp):
AACTTTTGGATGCGAATCTCTAAAATTCAAACGAAAAGCTTTGAACTC
Found at i:4015379 original size:42 final size:42
Alignment explanation
Indices: 4015320--4015695 Score: 248
Period size: 42 Copynumber: 8.9 Consensus size: 42
4015310 TTAAGAAGCA
* *
4015320 ATTTATTTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGC-
1 ATTTA-TTTTTTCAAAGTTATGGAGCCTCTGTTTAGAGGAGCT
* *
4015362 ATTTATTTCTTTAAAAGTTATGGAACCTCTGTTTAGAGGAGCTTT
1 ATTTATTT-TTTCAAAGTTATGGAGCCTCTGTTTAGAGGAGC--T
* * * * * *
4015407 GTTTATTTTTTCAAAGTCATTGAGTCTCTGTTTATAGGAGCA
1 ATTTATTTTTTCAAAGTTATGGAGCCTCTGTTTAGAGGAGCT
* *
4015449 ATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTAGAGAAGCT
1 ATTTATTTTTTCAAAGTTATGGAGCCTCTGTTTAGAGGAGCT
** * * * *
4015491 -TTGT-TTATTTCTCAAAGTCGTTGAGCCTCTATTTGGAAGAGCTTT
1 ATT-TATT-TTT-TCAAAGTTATGGAGCCTCTGTTTAGAGGAGC--T
* * ** * *
4015536 GTTTATGTTTCTCAAAGTCGTTGAGCCTCTGTTTAGATGAGCT
1 ATTTAT-TTTTTCAAAGTTATGGAGCCTCTGTTTAGAGGAGCT
* * * * *
4015579 TTTTATTTTTT-TAAGTTGTTGAGCCTTTGTTTAGAGGAGCCT
1 ATTTATTTTTTCAAAGTTATGGAGCCTCTGTTTAGAGGAG-CT
* * * *
4015621 -TTTA-TTTTTCTAAGTTGTTGAGCCTCTGCTTAGA-GAGC-
1 ATTTATTTTTTCAAAGTTATGGAGCCTCTGTTTAGAGGAGCT
* * * *
4015659 CTTTATTTTTTCAAAAGTTGT-CAGCCTCTGCTTAGAG
1 ATTTATTTTTTC-AAAGTTATGGAGCCTCTGTTTAGAG
4015696 ATGCCTTTAT
Statistics
Matches: 274, Mismatches: 42, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
39 5 0.02
40 28 0.10
41 64 0.23
42 78 0.28
43 29 0.11
44 27 0.10
45 37 0.14
46 5 0.02
47 1 0.00
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (42 bp):
ATTTATTTTTTCAAAGTTATGGAGCCTCTGTTTAGAGGAGCT
Found at i:4015467 original size:86 final size:85
Alignment explanation
Indices: 4015344--4015520 Score: 257
Period size: 86 Copynumber: 2.1 Consensus size: 85
4015334 AAGTTGTGGT
*
4015344 GCCTCTGTTTAGAGGAGCATTTATTTCTTTAAAAGTTATGGAACCTCTGTTTAGAGGAGCTTTGT
1 GCCTCTGTTTAGAGGAGCATTTATTTCTTTAAAAGTTATGGAACCTCTGTTTAGAGAAGCTTTGT
*
4015409 TTATTTTTTCAAAGTCATTGA
66 TTA-TTTCTCAAAGTCATTGA
* * * **
4015430 GTCTCTGTTTATAGGAGCAATTTATTT-TTTCAAAGTTATGGTGCCTCTGTTTAGAGAAGCTTTG
1 GCCTCTGTTTAGAGGAGC-ATTTATTTCTTTAAAAGTTATGGAACCTCTGTTTAGAGAAGCTTTG
*
4015494 TTTATTTCTCAAAGTCGTTGA
65 TTTATTTCTCAAAGTCATTGA
4015515 GCCTCT
1 GCCTCT
4015521 ATTTGGAAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
85 20 0.25
86 53 0.65
87 8 0.10
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.44
Consensus pattern (85 bp):
GCCTCTGTTTAGAGGAGCATTTATTTCTTTAAAAGTTATGGAACCTCTGTTTAGAGAAGCTTTGT
TTATTTCTCAAAGTCATTGA
Found at i:4015610 original size:41 final size:39
Alignment explanation
Indices: 4015321--4015711 Score: 203
Period size: 41 Copynumber: 9.3 Consensus size: 39
4015311 TAAGAAGCAA
* * *
4015321 TTTATTTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCA
1 TTTATTTTTTT--AAGTTGTTGAGCCTCTGTTTAGA-GAGCT
* * * *
4015363 TTTATTTCTTTAAAAGTTATGGAACCTCTGTTTAGAGGAGCTTT
1 TTTATTT-TTT-TAAGTTGTTGAGCCTCTGTTTAGA-GAGC--T
* ** * * *
4015407 GTTTATTTTTTCAAAGTCATTGAGTCTCTGTTTATAGGAGCAA
1 -TTTATTTTTT-TAAGTTGTTGAGCCTCTGTTTAGA-GAGC-T
* * * *
4015450 TTTATTTTTTCAAAGTTATGGTGCCTCTGTTTAGAGAAGCT
1 TTTATTTTTT-TAAGTTGTTGAGCCTCTGTTTAGAG-AGCT
* * * *
4015491 TTGT-TTATTTCTCAAAGTCGTTGAGCCTCTATTTGGAAGAGCT
1 TT-TATT-TTT-T-TAAGTTGTTGAGCCTCTGTTTAG-AGAGCT
*
4015534 TTGT-TTATGTTTCTCAAAGTCGTTGAGCCTCTGTTTAGATGAGCTT
1 TT-TATT-T-TTT-T--AAGTTGTTGAGCCTCTGTTTAGA-GAGC-T
*
4015580 TTTATTTTTTTAAGTTGTTGAGCCTTTGTTTAGAGGAGCCT
1 TTTATTTTTTTAAGTTGTTGAGCCTCTGTTTAGA-GAG-CT
* * *
4015621 TTTATTTTTCTAAGTTGTTGAGCCTCTGCTTAGAGAGCC
1 TTTATTTTTTTAAGTTGTTGAGCCTCTGTTTAGAGAGCT
* * * *
4015660 TTTATTTTTTCAAAAGTTG-TCAGCCTCTGCTTAGAGATGCC
1 TTTATTTTTT--TAAGTTGTTGAGCCTCTGTTTAGAGA-GCT
4015701 TTTATTTTTTT
1 TTTATTTTTTT
4015712 TTCTTTCAAA
Statistics
Matches: 290, Mismatches: 39, Indels: 43
0.78 0.10 0.12
Matches are distributed among these distances:
39 10 0.03
40 20 0.07
41 80 0.28
42 70 0.24
43 37 0.13
44 35 0.12
45 33 0.11
46 5 0.02
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (39 bp):
TTTATTTTTTTAAGTTGTTGAGCCTCTGTTTAGAGAGCT
Found at i:4015996 original size:20 final size:18
Alignment explanation
Indices: 4015966--4016023 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 18
4015956 TGTAGGAATT
4015966 TTTATTCATTTTTATTTCGTA
1 TTTA-TCATTTTTATTT--TA
4015987 TTTATCATTTATTTATTTTA
1 TTTATCA-TT-TTTATTTTA
4016007 TTT-T-ATTTTTATTTTA
1 TTTATCATTTTTATTTTA
4016023 T
1 T
4016024 GGTCAATCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 10 0.29
17 2 0.06
18 1 0.03
19 1 0.03
20 8 0.23
21 6 0.17
22 7 0.20
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTATCATTTTTATTTTA
Found at i:4018290 original size:61 final size:61
Alignment explanation
Indices: 4018225--4018390 Score: 196
Period size: 61 Copynumber: 2.8 Consensus size: 61
4018215 CATTTTGGAG
* * *
4018225 AAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAGTCTTTTTAAAAAAATATTTTT-A-GAA
1 AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAGT-GTTCT-AAAAAATATTTTTGAGGAA
* * *
4018286 AAAGTTGAAAATATCAATTTCCCTTGAAAATAAAAGTGTTCTAAAAAATATTTTTGAGGAA
1 AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAGTGTTCTAAAAAATATTTTTGAGGAA
* * * *
4018347 AAAATTGAAAGTATCAATTTTCTTTGAAAACAAAA-T-TTCTAAAA
1 AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAGTGTTCTAAAA
4018391 TAAAAATTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
59 21 0.23
60 5 0.05
61 66 0.72
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (61 bp):
AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAGTGTTCTAAAAAATATTTTTGAGGAA
Found at i:4018361 original size:192 final size:193
Alignment explanation
Indices: 4018145--4018496 Score: 514
Period size: 192 Copynumber: 1.8 Consensus size: 193
4018135 AAAATATATT
* *
4018145 TTTTTGAGAAAAAATTGAAAGTATCAATTTTCTTTAAAAATAAAGTTTCTAAAATAAAAATTGC-
1 TTTTTGAGAAAAAATTGAAAGTATCAATTTTCTTTAAAAACAAAATTTCTAAAATAAAAATTGCT
* * * ***
4018209 CAGAAGCATTTTG-GAGAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAGTCTTTTTAAAAA
66 AAAAAGCATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAA-T-TTCAGAAAAA
4018273 AATAT-TTTT-AGAAAAAGTTGAAAATATCAATTTCCCTTGAAAATAAAAGTGTTCTAAAAAATA
129 AATATATTTTGAGAAAAAGTTGAAAATATCAATTTCCCTTGAAAATAAAAGTGTTCTAAAAAATA
* *
4018336 TTTTTGAGGAAAAAATTGAAAGTATCAATTTTCTTTGAAAACAAAATTTCTAAAATAAAAATTTC
1 TTTTTGA-GAAAAAATTGAAAGTATCAATTTTCTTTAAAAACAAAATTTCTAAAATAAAAATTGC
* * *
4018401 TAAAAAGTATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTTCAGAAAAAA
65 TAAAAAGCATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAGAAAAAA
* *
4018466 ATATATTTTGAGGAAAAGTTGAAAGTATCAA
130 ATATATTTTGAGAAAAAGTTGAAAATATCAA
4018497 ATTTTCTTGT
Statistics
Matches: 141, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
191 7 0.05
192 65 0.46
193 15 0.11
194 54 0.38
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (193 bp):
TTTTTGAGAAAAAATTGAAAGTATCAATTTTCTTTAAAAACAAAATTTCTAAAATAAAAATTGCT
AAAAAGCATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAGAAAAAAA
TATATTTTGAGAAAAAGTTGAAAATATCAATTTCCCTTGAAAATAAAAGTGTTCTAAAAAATA
Found at i:4018395 original size:14 final size:15
Alignment explanation
Indices: 4018373--4018405 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4018363 ATTTTCTTTG
4018373 AAAAC-AAAATTTCT
1 AAAACAAAAATTTCT
*
4018387 AAAATAAAAATTTCT
1 AAAACAAAAATTTCT
4018402 AAAA
1 AAAA
4018406 AGTATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAACAAAAATTTCT
Found at i:4018431 original size:72 final size:75
Alignment explanation
Indices: 4018312--4018457 Score: 210
Period size: 72 Copynumber: 2.0 Consensus size: 75
4018302 ATTTCCCTTG
*
4018312 AAAATAAAAGTGTTCTAAAAAATATTTTTGAGGAAAAAATTGAAAGTATCAA-TTTTCTTTGAAA
1 AAAATAAAAATGTTCTAAAAAATATTTTTGAGGAAAAAATTGAAAGTATCAATTTTTC-TTGAAA
4018376 ACAAAATTTCT
65 ACAAAATTTCT
* * *
4018387 AAAATAAAAAT-TTCTAAAAAGTA-TTTTGA-GAAAAAGTTGAAAGTATCAATTTTTCTTGAAAT
1 AAAATAAAAATGTTCTAAAAAATATTTTTGAGGAAAAAATTGAAAGTATCAATTTTTCTTGAAAA
*
4018449 TAAAATTTC
66 CAAAATTTC
4018458 AGAAAAAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
72 33 0.51
73 11 0.17
74 11 0.17
75 10 0.15
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (75 bp):
AAAATAAAAATGTTCTAAAAAATATTTTTGAGGAAAAAATTGAAAGTATCAATTTTTCTTGAAAA
CAAAATTTCT
Found at i:4020051 original size:14 final size:14
Alignment explanation
Indices: 4020034--4020075 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
4020024 TTTAACTTTT
4020034 TTAAACAAATAAAA
1 TTAAACAAATAAAA
*
4020048 TTAAAAAAAT-AAA
1 TTAAACAAATAAAA
*
4020061 TAAAACAAATTAAAA
1 TTAAACAAA-TAAAA
4020076 AACTTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 10 0.43
14 10 0.43
15 3 0.13
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (14 bp):
TTAAACAAATAAAA
Found at i:4020060 original size:22 final size:22
Alignment explanation
Indices: 4020035--4020077 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4020025 TTAACTTTTT
4020035 TAAACAAATA-AAATTAAAAAAA
1 TAAACAAA-ACAAATTAAAAAAA
*
4020057 TAAATAAAACAAATTAAAAAA
1 TAAACAAAACAAATTAAAAAA
4020078 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAACAAAACAAATTAAAAAAA
Found at i:4021820 original size:19 final size:19
Alignment explanation
Indices: 4021796--4021839 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4021786 AATTCGTGAA
*
4021796 TTTAATCAAATTTTTA-TAT
1 TTTAAT-AAATTTTAATTAT
*
4021815 TTTAATATATTTTAATTAT
1 TTTAATAAATTTTAATTAT
4021834 TTTAAT
1 TTTAAT
4021840 TTATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATAAATTTTAATTAT
Found at i:4021823 original size:10 final size:10
Alignment explanation
Indices: 4021810--4021839 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4021800 ATCAAATTTT
4021810 TATATTTTAA
1 TATATTTTAA
4021820 TATATTTTAA
1 TATATTTTAA
4021830 T-TATTTTAA
1 TATATTTTAA
4021839 T
1 T
4021840 TTATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:4043861 original size:171 final size:172
Alignment explanation
Indices: 4043554--4043864 Score: 446
Period size: 171 Copynumber: 1.8 Consensus size: 172
4043544 CACATGAGAA
* * * *
4043554 GGGCCTGTTAAAGTGAGTTATCCCACATTTAATAAATTTTTAATTTTTTATAGACTTATATTCAG
1 GGGCCTATTAAAGTGAGTTATCCCACATCTAATAAATTTTTAATATCTTATAGACTTATATTCAG
* * * * * *
4043619 GTTTGGCCCTTCTATTTATAGCTAATTGGCTTTAAGTTGGATGCTTAACATGGTATTAGAGCTAG
66 GTTGGGCCCTTCCACTTATAGCTAATTGACTTTAAGTTGGATGCTTAACATGGTATCAAAGCTAG
4043684 GACTTTCTTTCCATTGCTTCCATCTTCCCTTACATATGATGG
131 GACTTTCTTTCCATTGCTTCCATCTTCCCTTACATATGATGG
* *
4043726 GGGCCTATTAAAGTG-GTTATCCCACATCTAATAAATTTTTAATATCTTGTAGTCTTATATTCAG
1 GGGCCTATTAAAGTGAGTTATCCCACATCTAATAAATTTTTAATATCTTATAGACTTATATTCAG
* * * *
4043790 GTTGGGTCCTTCCACTTATTGCTAATTGATTTTAAGTTGGATGCTTAACATGTTATCAAAGGC-A
66 GTTGGGCCCTTCCACTTATAGCTAATTGACTTTAAGTTGGATGCTTAACATGGTATCAAA-GCTA
*
4043854 TGACTTTCTTT
130 GGACTTTCTTT
4043865 TCGTTACCTT
Statistics
Matches: 121, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
171 105 0.87
172 16 0.13
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (172 bp):
GGGCCTATTAAAGTGAGTTATCCCACATCTAATAAATTTTTAATATCTTATAGACTTATATTCAG
GTTGGGCCCTTCCACTTATAGCTAATTGACTTTAAGTTGGATGCTTAACATGGTATCAAAGCTAG
GACTTTCTTTCCATTGCTTCCATCTTCCCTTACATATGATGG
Found at i:4051858 original size:25 final size:26
Alignment explanation
Indices: 4051798--4051858 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
4051788 ATCAAAGATC
* *
4051798 ACAGAAACCCCTTTGGTGTAATGGGAAG
1 ACAGAAACCCCTTTAGTGCAAT--GAAG
*
4051826 ACAAAAACCCCTTTAGTGCAAT-AAG
1 ACAGAAACCCCTTTAGTGCAATGAAG
4051851 ACAGAAAC
1 ACAGAAAC
4051859 ATATCACGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 10 0.34
28 19 0.66
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (26 bp):
ACAGAAACCCCTTTAGTGCAATGAAG
Found at i:4053905 original size:23 final size:24
Alignment explanation
Indices: 4053879--4053938 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
4053869 TTCTCAAAAT
4053879 ATAATCCATACAAAGT-AAATTCC
1 ATAATCCATACAAAGTAAAATTCC
* *
4053902 ATAAT-CATTCCAAAGTAAAATTTC
1 ATAATCCA-TACAAAGTAAAATTCC
*
4053926 ATATTCCA-ACAAA
1 ATAATCCATACAAA
4053939 CGATGGATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 2 0.07
23 16 0.53
24 10 0.33
25 2 0.07
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.28
Consensus pattern (24 bp):
ATAATCCATACAAAGTAAAATTCC
Found at i:4054259 original size:19 final size:19
Alignment explanation
Indices: 4054235--4054271 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
4054225 AAGAAATATT
4054235 CAAAAATCA-AAATTTAACC
1 CAAAAA-CATAAATTTAACC
4054254 CAAAAACATAAATTTAAC
1 CAAAAACATAAATTTAAC
4054272 AAGGAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (19 bp):
CAAAAACATAAATTTAACC
Found at i:4054592 original size:20 final size:20
Alignment explanation
Indices: 4054567--4054604 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4054557 GAATTAACAT
4054567 AGTAAAAATAT-ATTAAAATA
1 AGTAAAAAT-TCATTAAAATA
4054587 AGTAAAAATTCATTAAAA
1 AGTAAAAATTCATTAAAA
4054605 ATAATATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
AGTAAAAATTCATTAAAATA
Found at i:4066823 original size:14 final size:14
Alignment explanation
Indices: 4066799--4066889 Score: 78
Period size: 14 Copynumber: 6.3 Consensus size: 14
4066789 TCTTTAGCCT
*
4066799 TAAAATCCAAACCC
1 TAAAATTCAAACCC
*
4066813 TAAATTTCAAAACCC
1 TAAAATTC-AAACCC
*
4066828 TAAAATTAAAACCC
1 TAAAATTCAAACCC
*
4066842 TAAAA-TCTAATCCC
1 TAAAATTC-AAACCC
*
4066856 TAAACCTTTCAAACCC
1 TAAA--ATTCAAACCC
4066872 TAAAAATT-AAACCC
1 T-AAAATTCAAACCC
4066886 TAAA
1 TAAA
4066890 CCCTCTAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.06
14 33 0.53
15 14 0.23
16 6 0.10
17 5 0.08
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAATTCAAACCC
Found at i:4066872 original size:30 final size:29
Alignment explanation
Indices: 4066836--4066937 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 29
4066826 CCTAAAATTA
4066836 AAACCCTAAAATCTAATCCCTAAACCTTTC
1 AAACCCTAAAATCTAATCCCTAAACC-TTC
* *
4066866 AAACCCTAAAAAT-TAAACCCTAAACCCTC
1 AAACCCT-AAAATCTAATCCCTAAACCTTC
* * * *
4066895 TAAATCCTAAAATCAAAATCCC-AAATCTCC
1 -AAACCCTAAAATC-TAATCCCTAAACCTTC
4066925 AAACCCTAAAATC
1 AAACCCTAAAATC
4066938 AAAACCCCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
29 19 0.32
30 30 0.51
31 10 0.17
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (29 bp):
AAACCCTAAAATCTAATCCCTAAACCTTC
Found at i:4066884 original size:44 final size:43
Alignment explanation
Indices: 4066799--4066889 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 43
4066789 TCTTTAGCCT
4066799 TAAAATCCAAACCCTAAATTTCAAAACCCTAAAATTAAAACCC
1 TAAAATCCAAACCCTAAATTTCAAAACCCTAAAATTAAAACCC
* *
4066842 TAAAATCTAATCCCTAAACCTTTC-AAACCCTAAAAATT-AAACCC
1 TAAAATCCAAACCCTAAA--TTTCAAAACCCT-AAAATTAAAACCC
4066886 TAAA
1 TAAA
4066890 CCCTCTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 16 0.37
44 17 0.40
45 10 0.23
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.23
Consensus pattern (43 bp):
TAAAATCCAAACCCTAAATTTCAAAACCCTAAAATTAAAACCC
Found at i:4066932 original size:29 final size:29
Alignment explanation
Indices: 4066803--4066985 Score: 113
Period size: 29 Copynumber: 6.2 Consensus size: 29
4066793 TAGCCTTAAA
* *
4066803 ATCCAAACCCTAAATTTCAAAACCCTAAA-
1 ATCCAAACCCTAAA-ATCAAAACCCCAAAC
** * * *
4066832 ATTAAAACCCTAAAATCTAATCCCTAAACC
1 ATCCAAACCCTAAAATCAAAACCCCAAA-C
* * * *
4066862 TTTCAAACCCTAAAAAT-TAAACCCTAAACC
1 ATCCAAACCCT-AAAATCAAAACCCCAAA-C
* * * *
4066892 CTCTAAATCCTAAAATCAAAATCCCAAATC
1 ATCCAAACCCTAAAATCAAAACCCCAAA-C
4066922 -TCCAAACCCTAAAATCAAAACCCCAAAC
1 ATCCAAACCCTAAAATCAAAACCCCAAAC
* * * *
4066950 ATCCAAGCTCTAAAATCCAAAACACTAAA-
1 ATCCAAACCCTAAAAT-CAAAACCCCAAAC
4066979 ATCCAAA
1 ATCCAAA
4066986 ATCCCAAGCC
Statistics
Matches: 124, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
28 12 0.10
29 60 0.48
30 47 0.38
31 5 0.04
ACGTcount: A:0.49, C:0.31, G:0.01, T:0.20
Consensus pattern (29 bp):
ATCCAAACCCTAAAATCAAAACCCCAAAC
Found at i:4071079 original size:34 final size:34
Alignment explanation
Indices: 4071031--4071103 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
4071021 GGAATGGAGC
*
4071031 CAGAAAGTTTATTTTCATAGAGCTGGAGAATTGT
1 CAGACAGTTTATTTTCATAGAGCTGGAGAATTGT
*
4071065 CAGACAGTTTATTTTCATAGAGTTGGAGAATTGT
1 CAGACAGTTTATTTTCATAGAGCTGGAGAATTGT
4071099 CAGAC
1 CAGAC
4071104 CTGTCAAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (34 bp):
CAGACAGTTTATTTTCATAGAGCTGGAGAATTGT
Found at i:4085660 original size:16 final size:16
Alignment explanation
Indices: 4085639--4085676 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
4085629 CTTTAAAAAA
*
4085639 CATCATAAATCATCAT
1 CATCATAAATAATCAT
4085655 CATCATAAATAATCAT
1 CATCATAAATAATCAT
*
4085671 TATCAT
1 CATCAT
4085677 TTGTTTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (16 bp):
CATCATAAATAATCAT
Found at i:4094978 original size:13 final size:12
Alignment explanation
Indices: 4094936--4095035 Score: 59
Period size: 12 Copynumber: 8.3 Consensus size: 12
4094926 ATTTTTTATA
4094936 TTTTTATTAAA-
1 TTTTTATTAAAT
4094947 -TTTTATT-AAT
1 TTTTTATTAAAT
*
4094957 TTATCTATTTAAAT
1 TT-TTTA-TTAAAT
4094971 TTTTTATT-AAT
1 TTTTTATTAAAT
4094982 ATTTTTATTAAATT
1 -TTTTTATTAAA-T
*
4094996 ATTTTTAATAAAT
1 -TTTTTATTAAAT
*
4095009 AATTTTA-TAAAT
1 -TTTTTATTAAAT
**
4095021 TTCATA-TAAAT
1 TTTTTATTAAAT
4095032 TTTT
1 TTTT
4095036 GTTTGAAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
9 2 0.03
10 7 0.10
11 14 0.19
12 18 0.25
13 14 0.19
14 17 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTTTATTAAAT
Found at i:4094998 original size:14 final size:14
Alignment explanation
Indices: 4094971--4095014 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
4094961 CTATTTAAAT
4094971 TTTTTATT-AA-TA
1 TTTTTATTAAATTA
4094983 TTTTTATTAAATTA
1 TTTTTATTAAATTA
* *
4094997 TTTTTAATAAATAA
1 TTTTTATTAAATTA
4095011 TTTT
1 TTTT
4095015 ATAAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 8 0.29
13 2 0.07
14 18 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTATTAAATTA
Found at i:4094999 original size:27 final size:26
Alignment explanation
Indices: 4094969--4095021 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
4094959 ATCTATTTAA
* * *
4094969 ATTTTTTATTAATATTTTTATTAAATT
1 ATTTTTAATAAATAATTTTA-TAAATT
4094996 ATTTTTAATAAATAATTTTATAAATT
1 ATTTTTAATAAATAATTTTATAAATT
4095022 TCATATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTAATAAATAATTTTATAAATT
Found at i:4095000 original size:25 final size:25
Alignment explanation
Indices: 4094925--4095000 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
4094915 GATTTTTACA
4094925 TATTTT-TT-ATATTTTTATT-AA-
1 TATTTTATTAATATTTTTATTAAAT
*
4094946 -ATTTTATTAAT-TTATCTATTTAAAT
1 TATTTTATTAATATT-TTTA-TTAAAT
4094971 T-TTTTATTAATATTTTTATTAAAT
1 TATTTTATTAATATTTTTATTAAAT
4094995 TATTTT
1 TATTTT
4095001 TAATAAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
20 5 0.11
21 4 0.09
22 5 0.11
23 2 0.05
24 9 0.20
25 17 0.39
26 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTTTATTAATATTTTTATTAAAT
Found at i:4095003 original size:35 final size:32
Alignment explanation
Indices: 4094928--4095003 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 32
4094918 TTTTACATAT
* *
4094928 TTTTTATATTTTTATTAAATTTTATTAATTTA
1 TTTTTAAATTTTTATTAAATTTTATTAAATTA
4094960 TCTATTTAAATTTTTTATTAATATTTTTATTAAATTA
1 T-T-TTTAAA-TTTTTATTAA-A-TTTTATTAAATTA
4094997 TTTTTAA
1 TTTTTAA
4095004 TAAATAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
32 1 0.03
33 1 0.03
34 5 0.14
35 15 0.41
36 2 0.05
37 13 0.35
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (32 bp):
TTTTTAAATTTTTATTAAATTTTATTAAATTA
Found at i:4097170 original size:412 final size:413
Alignment explanation
Indices: 4096405--4097242 Score: 1552
Period size: 412 Copynumber: 2.0 Consensus size: 413
4096395 AACAAATGGA
*
4096405 TAAAATAATATATATTATATGTTTCAACTCTAAATATATTGAGATTGATTTTTAAGGATATAAAA
1 TAAAATAATATATATTATATGTTTCAACTCTAAATATATTGAAATTGATTTTTAAGGATATAAAA
4096470 ACTAAAAGGATGTCAAGTCACTTATCTAATGTGCTAAAACGAAACTTAAACAGAAAATTACTCAA
66 ACTAAAAGGATGTCAAGTCACTTATCTAATGTGCTAAAACGAAACTTAAACAGAAAATTACTCAA
*
4096535 TTATCTTAATATCCTAATAATTCAAGAAATATTAAAAAATCAAAATTTATCCTAATAACATAAAT
131 TTATCTTAATATCCTAATAATTCAAGAAATATTAAAAAATCAAAATTTATCCCAATAACATAAAT
4096600 TTAATAAGGCAAATTGCCTAAAATTAAGCATAAAAATGAAATCAAGAAAGCAAAACATAAAAATC
196 TTAATAAGGCAAATTGCCTAAAATTAAGCATAAAAATGAAATCAAGAAAGCAAAACATAAAAATC
*
4096665 AATATCAATATACATTTTTACAAATATTTAATTTTTTTACATTTAATTGTAATCATCTTCCGTAA
261 AATATCAATATAAATTTTTACAAATATTTAATTTTTTTACATTTAATTGTAATCATCTTCCGTAA
4096730 ATCTAGATATAATTTAATAGCCATTTAATAATATTAATAACATAAAATTAACACAATAAAACTAT
326 ATCTAGATATAATTTAATAGCCATTTAATAATATTAATAACATAAAATTAACACAATAAAACTAT
4096795 ATTTTAAAAAAATAAAAATTTAT
391 ATTTTAAAAAAATAAAAATTTAT
*
4096818 TAAAATAATATATCTTATATGTTTCAACTCTAAATATATTGAAATTGATTTTTAAGGATATAAAA
1 TAAAATAATATATATTATATGTTTCAACTCTAAATATATTGAAATTGATTTTTAAGGATATAAAA
* *
4096883 ACT-AAAGGATGTCAAGTCACTTATCTGATGTGCTAAAATGAAACTTAAACAGAAAATTACTCAA
66 ACTAAAAGGATGTCAAGTCACTTATCTAATGTGCTAAAACGAAACTTAAACAGAAAATTACTCAA
* *
4096947 TTCTCTTAATATCCTAATAATTCAAGAAATATTAAAAAATCAAAATTTATCCCAATAACATAGAT
131 TTATCTTAATATCCTAATAATTCAAGAAATATTAAAAAATCAAAATTTATCCCAATAACATAAAT
4097012 TTAATAAGGCAAATTGCCTAAAATTAAGCATAAAAATGAAATCAAGAAAGCAAAACATAAAAATC
196 TTAATAAGGCAAATTGCCTAAAATTAAGCATAAAAATGAAATCAAGAAAGCAAAACATAAAAATC
* * *
4097077 AATATCAATATAAATTTTTACAAATATTTAATTTTTTTACGTTTAATTGTAATCATTTTCTGTAA
261 AATATCAATATAAATTTTTACAAATATTTAATTTTTTTACATTTAATTGTAATCATCTTCCGTAA
*
4097142 ATCTAGATATAATTTAATAGCCATTTAATAATATTAATAACATGAAATTAACACAATAAAACTAT
326 ATCTAGATATAATTTAATAGCCATTTAATAATATTAATAACATAAAATTAACACAATAAAACTAT
4097207 ATTTTAAAAAAATAAAAATTTAT
391 ATTTTAAAAAAATAAAAATTTAT
4097230 TAAAACTAATATA
1 TAAAA-TAATATA
4097243 ACTAAAATTT
Statistics
Matches: 412, Mismatches: 12, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
412 339 0.82
413 73 0.18
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (413 bp):
TAAAATAATATATATTATATGTTTCAACTCTAAATATATTGAAATTGATTTTTAAGGATATAAAA
ACTAAAAGGATGTCAAGTCACTTATCTAATGTGCTAAAACGAAACTTAAACAGAAAATTACTCAA
TTATCTTAATATCCTAATAATTCAAGAAATATTAAAAAATCAAAATTTATCCCAATAACATAAAT
TTAATAAGGCAAATTGCCTAAAATTAAGCATAAAAATGAAATCAAGAAAGCAAAACATAAAAATC
AATATCAATATAAATTTTTACAAATATTTAATTTTTTTACATTTAATTGTAATCATCTTCCGTAA
ATCTAGATATAATTTAATAGCCATTTAATAATATTAATAACATAAAATTAACACAATAAAACTAT
ATTTTAAAAAAATAAAAATTTAT
Found at i:4103530 original size:26 final size:23
Alignment explanation
Indices: 4103481--4103533 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
4103471 CTTAGAAAGA
* *
4103481 AAATTTTTTTAGCCTTTATTGCT
1 AAATTTTTTTAGCCTTCATAGCT
4103504 AAATTTTATTTCAGGCCTTCATAGCT
1 AAATTTT-TTT-A-GCCTTCATAGCT
4103530 AAAT
1 AAAT
4103534 ATTGTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
24 3 0.12
25 1 0.04
26 14 0.56
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (23 bp):
AAATTTTTTTAGCCTTCATAGCT
Found at i:4107311 original size:22 final size:22
Alignment explanation
Indices: 4107283--4107325 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4107273 TGTATATTTA
* *
4107283 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
4107305 TATTTGTATCCCTAAAATTAA
1 TATTTGTATCCCTAAAATTAA
4107326 AGATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:4109316 original size:22 final size:20
Alignment explanation
Indices: 4109288--4109335 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 20
4109278 TAAAATTAAC
*
4109288 ATAATAAAAATATTTTTAAAAA
1 ATAATAAAAA-ATTATT-AAAA
4109310 ATAATAAAAAATTATTAAAA
1 ATAATAAAAAATTATTAAAA
4109330 ATAATA
1 ATAATA
4109336 TAACTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.40
21 5 0.20
22 10 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATAAAAAATTATTAAAA
Found at i:4109338 original size:22 final size:22
Alignment explanation
Indices: 4109288--4109335 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
4109278 TAAAATTAAC
*
4109288 ATAATAAAAATATTTTTAAAAA
1 ATAATAAAAATATTTTAAAAAA
4109310 ATAATAAAAA-ATTATTAAAAATA
1 ATAATAAAAATATT-TTAAAAA-A
4109333 ATA
1 ATA
4109336 TAACTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 3 0.13
22 16 0.70
23 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATAAAAATATTTTAAAAAA
Found at i:4110946 original size:27 final size:27
Alignment explanation
Indices: 4110902--4110959 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
4110892 ATTTTTAATT
* **
4110902 TTTTCTTTTTTTTGGAAATAGAAATGG
1 TTTTCTTTTATTCAGAAATAGAAATGG
4110929 TTTTCTTTTATTCAGAAATAGAAATGG
1 TTTTCTTTTATTCAGAAATAGAAATGG
4110956 TTTT
1 TTTT
4110960 TATTAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.52
Consensus pattern (27 bp):
TTTTCTTTTATTCAGAAATAGAAATGG
Found at i:4122376 original size:14 final size:15
Alignment explanation
Indices: 4122211--4122390 Score: 63
Period size: 14 Copynumber: 12.2 Consensus size: 15
4122201 AGGCTTGGGA
*
4122211 TTTTGGATTTTAGGG
1 TTTTGAATTTTAGGG
*
4122226 TTTTGAATTTTAGAG
1 TTTTGAATTTTAGGG
* * *
4122241 CTTAG-ATGTTTGGGG
1 TTTTGAAT-TTTAGGG
*
4122256 TTTT-TATTTTAGGG
1 TTTTGAATTTTAGGG
* * *
4122270 TTTGGAGATTTGA-GA
1 TTTTGA-ATTTTAGGG
*
4122285 TTTT-TATTTTAGGG
1 TTTTGAATTTTAGGG
* ** **
4122299 TTTAGAGGGTTTAAAG
1 TTTTGA-ATTTTAGGG
4122315 -TTT-AATTTTTAGGG
1 TTTTGAA-TTTTAGGG
*
4122329 -TTTGAAAGGTTTAGGG
1 TTTTG-AA-TTTTAGGG
* *
4122345 ATTAG-ATTTTAGGG
1 TTTTGAATTTTAGGG
4122359 TTTT-AATTTTAGGG
1 TTTTGAATTTTAGGG
* *
4122373 TTTTGAAATTTAAGG
1 TTTTGAATTTTAGGG
4122388 TTT
1 TTT
4122391 GGATTTTAAG
Statistics
Matches: 116, Mismatches: 36, Indels: 26
0.65 0.20 0.15
Matches are distributed among these distances:
13 5 0.04
14 46 0.40
15 43 0.37
16 19 0.16
17 3 0.03
ACGTcount: A:0.22, C:0.01, G:0.27, T:0.50
Consensus pattern (15 bp):
TTTTGAATTTTAGGG
Found at i:4124005 original size:15 final size:15
Alignment explanation
Indices: 4123985--4124018 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
4123975 AACCAATATT
4123985 ATTATTATTATTAAA
1 ATTATTATTATTAAA
*
4124000 ATTATTATTATTAAT
1 ATTATTATTATTAAA
4124015 ATTA
1 ATTA
4124019 AACAAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATTATTATTAAA
Found at i:4124563 original size:19 final size:19
Alignment explanation
Indices: 4124541--4124577 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4124531 TTAACACAGT
4124541 TAAAATATATTAAAATAAG
1 TAAAATATATTAAAATAAG
*
4124560 TAAAATTTATTAAAATAA
1 TAAAATATATTAAAATAA
4124578 TATAACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAAATATATTAAAATAAG
Found at i:4141647 original size:16 final size:17
Alignment explanation
Indices: 4141626--4141659 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4141616 TGTTAATATA
*
4141626 TATTTTTATAT-TATTT
1 TATTTTTAAATATATTT
4141642 TATTTTTAAATATATTT
1 TATTTTTAAATATATTT
4141659 T
1 T
4141660 TAAAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTAAATATATTT
Found at i:4148456 original size:56 final size:56
Alignment explanation
Indices: 4148310--4148625 Score: 247
Period size: 55 Copynumber: 5.6 Consensus size: 56
4148300 TAATTTCAAA
* * * ** *
4148310 TTTTGAA-AAAGGTTAAAGAATCAATTTTCTTTTAAAATAAAATTTTTAAAAAATA-
1 TTTTGAAGAAAAGTTGAAGTATCAATTTTCTTAAAAAATAAAA-TTTTAAAAAAAAG
* * *
4148365 TTTT-AAGAAAAATTGAAGTATCAATTTTTTTAAAAAATAAAATTTAAAAAAAAAAG
1 TTTTGAAGAAAAGTTGAAGTATCAATTTTCTTAAAAAATAAAATTT-TAAAAAAAAG
* * *
4148421 TTTTGAGGAAAAGTTGAAGTATCAATTTT-TT-AAAAATAAAAATTTTCAAAAAATG
1 TTTTGAAGAAAAGTTGAAGTATCAATTTTCTTAAAAAAT-AAAATTTTAAAAAAAAG
* * * **
4148476 TTTTG-AGAAAAAGTTAAAAG-ATCAATTTTCCTAAAATAA-AAGAA-TTTCAAAAAGTG
1 TTTTGAAG-AAAAGTT-GAAGTATCAATTTTCTTAAAA-AATAA-AATTTTAAAAAAAAG
* * * * *
4148532 TTTTAAATAAAAGTTGAAATATCAATTTTTCTTAAATAAA-AAATATTTCAAAAAAAAT
1 TTTTGAAGAAAAGTTGAAGTATCAA-TTTTCTTAAA-AAATAAA-ATTTTAAAAAAAAG
* *
4148590 TTTTGAAGAAAAGTTGAAATATCAAATTTTTTTAAA
1 TTTTGAAGAAAAGTTGAAGTATC-AATTTTCTTAAA
4148626 TAAAGCATTA
Statistics
Matches: 212, Mismatches: 31, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
54 6 0.03
55 75 0.35
56 47 0.22
57 42 0.20
58 40 0.19
59 2 0.01
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (56 bp):
TTTTGAAGAAAAGTTGAAGTATCAATTTTCTTAAAAAATAAAATTTTAAAAAAAAG
Found at i:4151680 original size:26 final size:27
Alignment explanation
Indices: 4151641--4151700 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
4151631 CCATAAATAG
* *
4151641 TGTTAATATATATTTTTATATTATTTA
1 TGTTAATATATATTTTTAAAATATTTA
*
4151668 TTTTAA-ATATATTTTTAAAATATTTA
1 TGTTAATATATATTTTTAAAATATTTA
4151694 TGTTAAT
1 TGTTAAT
4151701 TCTTTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (27 bp):
TGTTAATATATATTTTTAAAATATTTA
Found at i:4158569 original size:57 final size:57
Alignment explanation
Indices: 4158485--4158634 Score: 148
Period size: 57 Copynumber: 2.7 Consensus size: 57
4158475 ATAAATTTTT
* * *
4158485 AAAAAATA-TTTTAAGGAAAA-ATGAAGTAT-AATTTTTTAAAAACAT-AAAATTTGAA
1 AAAAAAAAGTTTTGAGGAAAAGTTGAAGTATCAATTTTTTAAAAA-ATAAAAATTT-AA
* * **
4158540 AAAAAAAAGTTTTGAGGAAAAGTTGAAGTATCAATTTTTTTAAAATTAAAAATTTTC
1 AAAAAAAAGTTTTGAGGAAAAGTTGAAGTATCAATTTTTTAAAAAATAAAAATTTAA
* * *
4158597 AAAAAAATGTTTTGAGAAAAAGTTAAAAG-ATCAATTTT
1 AAAAAAAAGTTTTGAGGAAAAGTT-GAAGTATCAATTTT
4158635 CCTAAAATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
55 7 0.09
56 11 0.14
57 40 0.50
58 22 0.28
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.34
Consensus pattern (57 bp):
AAAAAAAAGTTTTGAGGAAAAGTTGAAGTATCAATTTTTTAAAAAATAAAAATTTAA
Found at i:4158641 original size:57 final size:58
Alignment explanation
Indices: 4158540--4158758 Score: 191
Period size: 57 Copynumber: 3.8 Consensus size: 58
4158530 AAAATTTGAA
* * * *
4158540 AAAAAAAAGTTTTGAGGAAAAGTT-GAAGTATCAATTTTTTTAAAATTAAAAATTTTC
1 AAAAAAATGTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTAAAATTAAAAATTTTC
* *
4158597 AAAAAAATGTTTTGAGAAAAAGTTAAAAG-ATCAATTTTCCTAAAA-TAAAAGAATTTC
1 AAAAAAATGTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTAAAATTAAAA-ATTTTC
* * * * * *
4158654 --AAAAGTGTTTTTAAATAAAAGTTGAAAA-TATTAATTTTTCTTAAATAAAAAAATATTT-
1 AAAAAAATGTTTTGAGA-AAAAGTT-AAAAGTATCAATTTTTCTAAAAT-TAAAAAT-TTTC
* * *
4158712 AAAAAAATATTTTAAGAAAAAAGTTAAAAGTATCAAATTTTTTTAAA
1 AAAAAAATGTTTTGAG-AAAAAGTTAAAAGTATC-AATTTTTCTAAA
4158759 TAAAGCATTA
Statistics
Matches: 128, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
55 12 0.09
56 12 0.09
57 58 0.45
58 4 0.03
59 11 0.09
60 20 0.16
61 11 0.09
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.36
Consensus pattern (58 bp):
AAAAAAATGTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTAAAATTAAAAATTTTC
Found at i:4158718 original size:13 final size:13
Alignment explanation
Indices: 4158699--4158732 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
4158689 TTTTCTTAAA
4158699 TAAAAAAATA-TT
1 TAAAAAAATATTT
4158711 TAAAAAAATATTT
1 TAAAAAAATATTT
4158724 TAAGAAAAA
1 TAA-AAAAA
4158733 AGTTAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 5 0.25
14 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
TAAAAAAATATTT
Found at i:4158772 original size:48 final size:47
Alignment explanation
Indices: 4158719--4158809 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
4158709 TTTAAAAAAA
* *
4158719 TATTTTAAGAAA-AAAGTTAAAAGTATCAAATTTTTTTAAATAAAGCAT
1 TATTTTAAGAAATAAA-ATAAAA-TAACAAATTTTTTTAAATAAAGCAT
***
4158767 TATTTTTTTAAATAAAATAAAATAACAAATTTTTTTAAATAAA
1 TATTTTAAGAAATAAAATAAAATAACAAATTTTTTTAAATAAA
4158810 AGTTGAAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
47 20 0.54
48 14 0.38
49 3 0.08
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (47 bp):
TATTTTAAGAAATAAAATAAAATAACAAATTTTTTTAAATAAAGCAT
Found at i:4164107 original size:30 final size:29
Alignment explanation
Indices: 4164067--4164128 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 29
4164057 ATCGAATTCA
4164067 TTTTTTAAAAAT-AAAAAATAAAAAATAAT
1 TTTTTTAAAAATAAAAAAATAAAAAAT-AT
4164096 TTTTTTAAAAAATAAAAAAATAAAAAATAT
1 TTTTTT-AAAAATAAAAAAATAAAAAATAT
4164126 TTT
1 TTT
4164129 CTCCCACCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 6 0.19
30 11 0.35
31 14 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
TTTTTTAAAAATAAAAAAATAAAAAATAT
Found at i:4173783 original size:18 final size:20
Alignment explanation
Indices: 4173762--4173800 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
4173752 TTATCTCTTT
4173762 TATTTTA-TTTGT-TTTATC
1 TATTTTAGTTTGTATTTATC
*
4173780 TATTTTAGTTTTTATTTATC
1 TATTTTAGTTTGTATTTATC
4173800 T
1 T
4173801 TTAATTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (20 bp):
TATTTTAGTTTGTATTTATC
Found at i:4173785 original size:23 final size:25
Alignment explanation
Indices: 4173745--4173796 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 25
4173735 TTATTGCTCT
*
4173745 TTTGTATTTATCTCTTTTA-TTTTA
1 TTTGTATTTATCTATTTTAGTTTTA
4173769 TTTGT-TTTATCTATTTTAGTTTTTA
1 TTTGTATTTATCTATTTTAG-TTTTA
4173794 TTT
1 TTT
4173797 ATCTTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 12 0.48
24 5 0.20
25 8 0.32
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (25 bp):
TTTGTATTTATCTATTTTAGTTTTA
Found at i:4174514 original size:2 final size:2
Alignment explanation
Indices: 4174504--4174555 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
4174494 GAGAATCAGA
*
4174504 AG AG CAG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
4174547 AG AA AG AG A
1 AG AG AG AG A
4174556 CAGACAGACA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4186216 original size:21 final size:21
Alignment explanation
Indices: 4186190--4186242 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
4186180 CAATAATAGA
* *
4186190 GGTAATATTAATTATTATAAT
1 GGTAATATTAATTACTACAAT
4186211 GGTAATATTAATTACTACAAT
1 GGTAATATTAATTACTACAAT
* *
4186232 GATAAAATTAA
1 GGTAATATTAA
4186243 AATCAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (21 bp):
GGTAATATTAATTACTACAAT
Found at i:4189078 original size:23 final size:23
Alignment explanation
Indices: 4189052--4189100 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
4189042 TAAAAAGTAA
*
4189052 AAAAAATGATA-AAAAGTAATTTT
1 AAAAAATGAAACAAAAG-AATTTT
* *
4189075 AAAATATTAAACAAAAGAATTTT
1 AAAAAATGAAACAAAAGAATTTT
4189098 AAA
1 AAA
4189101 TATTAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (23 bp):
AAAAAATGAAACAAAAGAATTTT
Found at i:4189104 original size:22 final size:23
Alignment explanation
Indices: 4189062--4189120 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
4189052 AAAAAATGAT
4189062 AAAAAGTAATTTTAAAATATTAA
1 AAAAAGTAATTTTAAAATATTAA
4189085 ACAAAAG-AATTTT-AAATATTAA
1 A-AAAAGTAATTTTAAAATATTAA
*
4189107 AAAAATATAATTTT
1 AAAAA-GTAATTTT
4189121 GAGACATCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.12
22 10 0.31
23 13 0.41
24 5 0.16
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (23 bp):
AAAAAGTAATTTTAAAATATTAA
Found at i:4189118 original size:23 final size:24
Alignment explanation
Indices: 4189068--4189138 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 24
4189058 TGATAAAAAG
*
4189068 TAATTTTAAAATATTAAACAAA-A
1 TAATTTTAAAATATTAAAAAAATA
*
4189091 GAATTTT-AAATATTAAAAAAATA
1 TAATTTTAAAATATTAAAAAAATA
* * *
4189114 TAATTTTGAGACATCTAAAAAAATA
1 TAATTTTAAAATAT-TAAAAAAATA
4189139 AAAATGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 13 0.32
23 13 0.32
24 4 0.10
25 10 0.25
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (24 bp):
TAATTTTAAAATATTAAAAAAATA
Found at i:4189367 original size:17 final size:17
Alignment explanation
Indices: 4189342--4189375 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4189332 GATTCCAGAG
* *
4189342 AAAAGTGTGATCCTCGA
1 AAAAATGTGATACTCGA
4189359 AAAAATGTGATACTCGA
1 AAAAATGTGATACTCGA
4189376 GATTTTCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (17 bp):
AAAAATGTGATACTCGA
Found at i:4189892 original size:149 final size:150
Alignment explanation
Indices: 4189691--4189980 Score: 415
Period size: 149 Copynumber: 1.9 Consensus size: 150
4189681 TGAATAATTT
* * *
4189691 CTAAACCTTAAACTCTAAACTCATAAAAATTTAATGGGATTATTCAAGGCATTTTTGCCCTGAAA
1 CTAAACCTTAAACTCTAAACTCATAAAAATTTAAAGAGATTATTCAAGGCATTTTTGCCCAGAAA
* * * *
4189756 A-TACCTTGAATAATCCTTTACAAAAAATTTAAT-GGAGTTATTGAAGGCATTTTTGA-CAAAAA
66 ACT-CCTTGAATAATCCTTTACAAAAAATTAAATAGG-GTTATTGAAGGCATTTCTAATAAAAAA
4189818 CACCTTGAATAATTCTTAAATC
129 CACCTTGAATAATTCTTAAATC
* * *
4189840 CTAAACCTTAAACTTTAAGCTCATAAAAATTTAAAGAGATTATTCAATGCATTTTTGCCCAGAAA
1 CTAAACCTTAAACTCTAAACTCATAAAAATTTAAAGAGATTATTCAAGGCATTTTTGCCCAGAAA
* * * *
4189905 ACTTCTTGAATAATCTTTTACAAAAAATTAAATAGGGTTATTGAAGGCGTTTCTAATAAAAAATA
66 ACTCCTTGAATAATCCTTTACAAAAAATTAAATAGGGTTATTGAAGGCATTTCTAATAAAAAACA
4189970 CCTTGAATAAT
131 CCTTGAATAAT
4189981 CCTTTTAAAT
Statistics
Matches: 124, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
149 104 0.84
150 20 0.16
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.34
Consensus pattern (150 bp):
CTAAACCTTAAACTCTAAACTCATAAAAATTTAAAGAGATTATTCAAGGCATTTTTGCCCAGAAA
ACTCCTTGAATAATCCTTTACAAAAAATTAAATAGGGTTATTGAAGGCATTTCTAATAAAAAACA
CCTTGAATAATTCTTAAATC
Found at i:4196321 original size:16 final size:16
Alignment explanation
Indices: 4196289--4196322 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4196279 AAATATGAAC
* *
4196289 ATATAATATGAATATA
1 ATATAATATAAACATA
4196305 ATATAATATAAACATA
1 ATATAATATAAACATA
4196321 AT
1 AT
4196323 GATATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (16 bp):
ATATAATATAAACATA
Found at i:4198000 original size:2 final size:2
Alignment explanation
Indices: 4197993--4198020 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4197983 GTGTAGGTTT
4197993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4198021 GAACTACTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4198395 original size:2 final size:2
Alignment explanation
Indices: 4198388--4198412 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4198378 AAAACAAGAT
4198388 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
4198413 CATTTCTAAT
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:4199947 original size:5 final size:5
Alignment explanation
Indices: 4199937--4199973 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
4199927 ATTATAATAG
*
4199937 ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAGT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
4199974 TGCTAAAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:4205211 original size:18 final size:18
Alignment explanation
Indices: 4205185--4205220 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4205175 GATTGATTGG
*
4205185 TAATTTATAATATTTATA
1 TAATGTATAATATTTATA
4205203 TAATGTATAATATTTATA
1 TAATGTATAATATTTATA
4205221 CATTATCAAT
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TAATGTATAATATTTATA
Found at i:4205274 original size:16 final size:17
Alignment explanation
Indices: 4205231--4205282 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
4205221 CATTATCAAT
*
4205231 TTATCAAAT-ATTAATTTT
1 TTAT-AAATAATTAA-TTA
*
4205249 TTATATATAATT-ATTA
1 TTATAAATAATTAATTA
4205265 TTATAAATAATTAATTA
1 TTATAAATAATTAATTA
4205282 T
1 T
4205283 AATTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 13 0.45
17 9 0.31
18 7 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATAAATAATTAATTA
Found at i:4206428 original size:12 final size:13
Alignment explanation
Indices: 4206406--4206469 Score: 64
Period size: 12 Copynumber: 5.1 Consensus size: 13
4206396 ATATATAAAA
4206406 ATTAT-TTTAATT
1 ATTATATTTAATT
4206418 ATT-TATTTAATT
1 ATTATATTTAATT
*
4206430 -TTATATTTATTT
1 ATTATATTTAATT
4206442 ATATATATTTAATT
1 AT-TATATTTAATT
*
4206456 -TTATTTTTATATT
1 ATTATATTTA-ATT
4206469 A
1 A
4206470 AAAATAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
11 3 0.07
12 25 0.58
13 5 0.12
14 10 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTATATTTAATT
Found at i:4206441 original size:20 final size:20
Alignment explanation
Indices: 4206416--4206467 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
4206406 ATTATTTTAA
* *
4206416 TTATTTATTTA-ATTTTATAT
1 TTATTTATATATATTTAAT-T
4206436 TTATTTATATATATTTAATT
1 TTATTTATATATATTTAATT
*
4206456 TTATTTTTATAT
1 TTATTTATATAT
4206468 TAAAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTTATATATATTTAATT
Found at i:4206526 original size:28 final size:26
Alignment explanation
Indices: 4206478--4206532 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
4206468 TAAAAATAAT
* *
4206478 ATTTTATTAATTTCGAATCGAATATA
1 ATTTTATTAATATCAAATCGAATATA
4206504 ATTTTATATAATATCAAATTCGAATATA
1 ATTTTAT-TAATATCAAA-TCGAATATA
4206532 A
1 A
4206533 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 8 0.32
28 10 0.40
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (26 bp):
ATTTTATTAATATCAAATCGAATATA
Found at i:4209760 original size:2 final size:2
Alignment explanation
Indices: 4209751--4209817 Score: 55
Period size: 2 Copynumber: 33.5 Consensus size: 2
4209741 TATGTTGTAG
** *
4209751 TA TA -A TA TA TA TGA TA TA TA TA TA TA TA TA CG TA TA TA TA TG
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
4209793 TA TG TA TA CA TA TG TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4209818 GATTGAGTCA
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4213499 original size:4 final size:4
Alignment explanation
Indices: 4213490--4213523 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
4213480 CCCCAAAACA
4213490 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
4213524 TAATGCTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:4216477 original size:2 final size:2
Alignment explanation
Indices: 4216472--4216499 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4216462 ATAGTGTGTG
4216472 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4216500 GTAACCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4217340 original size:2 final size:2
Alignment explanation
Indices: 4217333--4217382 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
4217323 TATGGAAATA
4217333 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4217375 AG AG AG AG
1 AG AG AG AG
4217383 TTCAAAGAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4218949 original size:19 final size:19
Alignment explanation
Indices: 4218920--4218957 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
4218910 AGGCAAGCAG
4218920 CAAAGGAAAGAAAAACAAAA
1 CAAAGGAAAGAAAAA-AAAA
4218940 CAAA-GAAAGAAAAAAAAA
1 CAAAGGAAAGAAAAAAAAA
4218958 GGAGGGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (19 bp):
CAAAGGAAAGAAAAAAAAA
Found at i:4220452 original size:20 final size:20
Alignment explanation
Indices: 4220423--4220460 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4220413 TTTTTTATCA
4220423 AAAATAAATAAATCAAAATT
1 AAAATAAATAAATCAAAATT
* *
4220443 AAAATTAATAAATTAAAA
1 AAAATAAATAAATCAAAA
4220461 GATCTCATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAAATAAATCAAAATT
Found at i:4221694 original size:23 final size:23
Alignment explanation
Indices: 4221668--4221724 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
4221658 GTCCTTTTGT
*
4221668 TTTATTTTT-TTTAATGATTTTTA
1 TTTATTTTTATTTAATG-TTATTA
*
4221691 TTTATTTTTATTTTATGTTATTA
1 TTTATTTTTATTTAATGTTATTA
*
4221714 TTT-TCTTTATT
1 TTTATTTTTATT
4221725 CATTTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.23
23 17 0.57
24 6 0.20
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTATTTTTATTTAATGTTATTA
Found at i:4221701 original size:10 final size:10
Alignment explanation
Indices: 4221667--4221731 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
4221657 GGTCCTTTTG
4221667 TTTTATTT-T
1 TTTTATTTAT
* *
4221676 TTTTAATGAT
1 TTTTATTTAT
4221686 TTTTATTTAT
1 TTTTATTTAT
4221696 TTTTATTTTAT
1 TTTTA-TTTAT
4221707 GTTATTATTT-T
1 -TT-TTATTTAT
* *
4221718 CTTTATTCAT
1 TTTTATTTAT
4221728 TTTT
1 TTTT
4221732 TTGGAATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
9 11 0.25
10 19 0.43
11 6 0.14
12 5 0.11
13 3 0.07
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:4227419 original size:21 final size:21
Alignment explanation
Indices: 4227363--4227475 Score: 136
Period size: 21 Copynumber: 5.2 Consensus size: 21
4227353 AGAATATTTG
4227363 TCTTTGAGTTTTAAATGAAAA
1 TCTTTGAGTTTTAAATGAAAA
* *
4227384 TTTTTAAGAAGTTTTAAATGAGAA
1 TCTTT--G-AGTTTTAAATGAAAA
* *
4227408 TATTTGAGTTTTAAATAAAAA
1 TCTTTGAGTTTTAAATGAAAA
* *
4227429 TCTTTTAATTTTAAATGAAAA
1 TCTTTGAGTTTTAAATGAAAA
*
4227450 TCTTTGAGTTTTAAATGAAGA
1 TCTTTGAGTTTTAAATGAAAA
4227471 TCTTT
1 TCTTT
4227476 AAAAAGTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
21 57 0.74
22 1 0.01
23 1 0.01
24 18 0.23
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (21 bp):
TCTTTGAGTTTTAAATGAAAA
Found at i:4227456 original size:42 final size:44
Alignment explanation
Indices: 4227363--4227494 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 44
4227353 AGAATATTTG
*
4227363 TCTTTGAGTTTTAAATGAAAAT-TTTTAAGAAGTTTTAAATGAGAA
1 TCTTTGAGTTTTAAATGAAAATCTTTT-A-AAGTTTTAAATGAAAA
* *
4227408 TATTTGAGTTTTAAATAAAAATCTTTT-AA-TTTTAAATGAAAA
1 TCTTTGAGTTTTAAATGAAAATCTTTTAAAGTTTTAAATGAAAA
* * *
4227450 TCTTTGAGTTTTAAATGAAGATCTTTAAAAAGTTTTAAATAAAAA
1 TCTTTGAGTTTTAAATGAAAATCTTT-TAAAGTTTTAAATGAAAA
4227495 ATTTTGAATG
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
42 35 0.47
43 2 0.03
44 2 0.03
45 32 0.43
46 4 0.05
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.42
Consensus pattern (44 bp):
TCTTTGAGTTTTAAATGAAAATCTTTTAAAGTTTTAAATGAAAA
Found at i:4227667 original size:45 final size:45
Alignment explanation
Indices: 4227616--4227721 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 45
4227606 AAAAGTGTTC
* * * *
4227616 GAATGAGAAGCTTTGAAATTTTGAATATAAACCCCTA-AATTTTTT
1 GAATGAGAACCTTTGAAATTTAG-ATATAAAACCCTAGAATTTATT
* *
4227661 GAATGAGAACCTTTG-AATTTAGATGTAAAACTCTAGAATTTATT
1 GAATGAGAACCTTTGAAATTTAGATATAAAACCCTAGAATTTATT
*
4227705 GAATGAGAATCTTTGAA
1 GAATGAGAACCTTTGAA
4227722 CATGAATGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 10 0.19
44 27 0.52
45 15 0.29
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (45 bp):
GAATGAGAACCTTTGAAATTTAGATATAAAACCCTAGAATTTATT
Found at i:4227729 original size:20 final size:20
Alignment explanation
Indices: 4227704--4227741 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4227694 TAGAATTTAT
*
4227704 TGAATGAGAATCTTTGAACA
1 TGAATGAGAAACTTTGAACA
4227724 TGAATGAGAAACTTTGAA
1 TGAATGAGAAACTTTGAA
4227742 ATTTTGGATG
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:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (20 bp):
TGAATGAGAAACTTTGAACA
Found at i:4228001 original size:16 final size:16
Alignment explanation
Indices: 4227980--4228013 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4227970 ATATTTCAAA
4227980 TGTGAAATCGAGTTCT
1 TGTGAAATCGAGTTCT
* *
4227996 TGTGAATTTGAGTTCT
1 TGTGAAATCGAGTTCT
4228012 TG
1 TG
4228014 CGAATCCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (16 bp):
TGTGAAATCGAGTTCT
Found at i:4228067 original size:73 final size:73
Alignment explanation
Indices: 4227943--4228087 Score: 175
Period size: 73 Copynumber: 2.0 Consensus size: 73
4227933 TTTTGATGCA
* * ** *** *
4227943 AATCTTTGAATTAAACTATAGATGTGAATATTTCAAATGTGAAATCGAGTTCTTGTGAATTTGAG
1 AATCCTTGAATTAAACTATAGATGTGAATATCTCAAATGAAAAATCGAGTTCTTACAAATCTGAG
4228008 TTCTTGCG
66 TTCTTGCG
* * *
4228016 AATCCTTGAATTAAACTTTGGATGTGAATCTCTCAAATGCAAAAAT-GAGTTCTTACAAATCTGA
1 AATCCTTGAATTAAACTATAGATGTGAATATCTCAAATG-AAAAATCGAGTTCTTACAAATCTGA
4228080 GTTCTTGC
65 GTTCTTGC
4228088 AAATATGAGT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 56 0.93
74 4 0.07
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.37
Consensus pattern (73 bp):
AATCCTTGAATTAAACTATAGATGTGAATATCTCAAATGAAAAATCGAGTTCTTACAAATCTGAG
TTCTTGCG
Found at i:4228080 original size:16 final size:16
Alignment explanation
Indices: 4228061--4228108 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
4228051 AATGCAAAAA
4228061 TGAGTTCTTACAAATC
1 TGAGTTCTTACAAATC
* *
4228077 TGAGTTCTTGCAAATA
1 TGAGTTCTTACAAATC
* *
4228093 TGAGTTTTTACGAATC
1 TGAGTTCTTACAAATC
4228109 CTTGAATTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (16 bp):
TGAGTTCTTACAAATC
Found at i:4228140 original size:89 final size:90
Alignment explanation
Indices: 4227984--4228176 Score: 264
Period size: 89 Copynumber: 2.2 Consensus size: 90
4227974 TTCAAATGTG
** * *
4227984 AAATC-GAGTTCTTGTGAATTTGAGTTCTTGCGAATCCTTGAATTAAACTTTGGATGTGAATCTC
1 AAATCTGAGTTCTTGCAAATATGAGTTCTTACGAATCCTTGAATTAAACTTTGGATGTGAATCTC
** *
4228048 TCAAATGCAAAAATG-AGTTCTTAC
66 TCAAATGCAAAAATGAAAATATTAC
* *
4228072 AAATCTGAGTTCTTGCAAATATGAGTTTTTACGAATCCTTGAATTAAATTTTGGATGTGAATCTC
1 AAATCTGAGTTCTTGCAAATATGAGTTCTTACGAATCCTTGAATTAAACTTTGGATGTGAATCTC
** *
4228137 TCAAATGTGAAACTGAAAATATTAC
66 TCAAATGCAAAAATGAAAATATTAC
4228162 AAATCTGAGTTCTTG
1 AAATCTGAGTTCTTG
4228177 TGAATATAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 5 0.05
89 65 0.71
90 21 0.23
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (90 bp):
AAATCTGAGTTCTTGCAAATATGAGTTCTTACGAATCCTTGAATTAAACTTTGGATGTGAATCTC
TCAAATGCAAAAATGAAAATATTAC
Found at i:4228238 original size:27 final size:27
Alignment explanation
Indices: 4228199--4228250 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
4228189 TTTAAGAATC
4228199 AAATACTTGTGAAGCTAAAATTCTTGA
1 AAATACTTGTGAAGCTAAAATTCTTGA
* * *
4228226 AAATTCTTTTGAAGCTGAAATTCTT
1 AAATACTTGTGAAGCTAAAATTCTT
4228251 TCGAATCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (27 bp):
AAATACTTGTGAAGCTAAAATTCTTGA
Found at i:4228248 original size:17 final size:17
Alignment explanation
Indices: 4228226--4228262 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4228216 AAATTCTTGA
*
4228226 AAATTCTTTTGAAGCTG
1 AAATTCTTTCGAAGCTG
*
4228243 AAATTCTTTCGAATCTG
1 AAATTCTTTCGAAGCTG
4228260 AAA
1 AAA
4228263 CTTTTGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (17 bp):
AAATTCTTTCGAAGCTG
Found at i:4234951 original size:19 final size:19
Alignment explanation
Indices: 4234929--4234965 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4234919 TTTTCACCTA
4234929 AATTTTTAATTTATATTTT
1 AATTTTTAATTTATATTTT
4234948 AATTTTTAATTTATATTT
1 AATTTTTAATTTATATTT
4234966 GAGAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
AATTTTTAATTTATATTTT
Found at i:4235436 original size:32 final size:32
Alignment explanation
Indices: 4235372--4235436 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
4235362 CATGCATAAT
**
4235372 ATAAATAAATAAAATAATAATATGAAACAAAA
1 ATAAATAAATAAAATAATAATACAAAACAAAA
*
4235404 ATAAATAAATAAAATAA-AATACCAAAATAAAA
1 ATAAATAAATAAAATAATAATA-CAAAACAAAA
4235436 A
1 A
4235437 AATAGCTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.20
Consensus pattern (32 bp):
ATAAATAAATAAAATAATAATACAAAACAAAA
Found at i:4236577 original size:32 final size:32
Alignment explanation
Indices: 4236521--4236593 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
4236511 CATATTCGTA
*
4236521 AAGATTTT-GGACTTACAAGGATTTGATTCTC
1 AAGATTTTAGGACTTACAAGAATTTGATTCTC
*
4236552 AAGGATTTTAGG-CTTGCAAGAATTTGATTCTC
1 AA-GATTTTAGGACTTACAAGAATTTGATTCTC
*
4236584 AAAATTTTAG
1 AAGATTTTAG
4236594 ATTCACAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 9 0.24
32 26 0.70
33 2 0.05
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (32 bp):
AAGATTTTAGGACTTACAAGAATTTGATTCTC
Found at i:4236603 original size:31 final size:32
Alignment explanation
Indices: 4236524--4236604 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
4236514 ATTCGTAAAG
* *
4236524 ATTTT-GGACTTACAAGGATTTGATTCTCAAGG
1 ATTTTAGGA-TTACAAGAATTTGATTCTCAAGA
* *
4236556 ATTTTAGGCTTGCAAGAATTTGATTCTCAA-A
1 ATTTTAGGATTACAAGAATTTGATTCTCAAGA
4236587 ATTTTA-GATTCACAAGAA
1 ATTTTAGGATT-ACAAGAA
4236605 CTTCGATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
30 3 0.07
31 12 0.29
32 24 0.59
33 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (32 bp):
ATTTTAGGATTACAAGAATTTGATTCTCAAGA
Found at i:4236793 original size:21 final size:21
Alignment explanation
Indices: 4236769--4236829 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
4236759 ATTGCAAAGC
*
4236769 TCACATCCAAAATTTAAATAT
1 TCACATTCAAAATTTAAATAT
* ** *
4236790 TCACATTCAAATTTTGGAGAT
1 TCACATTCAAAATTTAAATAT
*
4236811 TCACATTCAAAAGTTAAAT
1 TCACATTCAAAATTTAAAT
4236830 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (21 bp):
TCACATTCAAAATTTAAATAT
Found at i:4237169 original size:22 final size:21
Alignment explanation
Indices: 4237150--4237211 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 21
4237140 ACAAATTCTC
4237150 AAGATT-TCCATTTAAAATTCA
1 AAGATTCT-CATTTAAAATTCA
*
4237171 AAGATTCTCATTTAAAACTTTTTA
1 AAGATTCTCATTTAAAA---TTCA
4237195 AAGATTCTCATTTAAAA
1 AAGATTCTCATTTAAAA
4237212 GACAAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 15 0.42
22 1 0.03
24 20 0.56
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (21 bp):
AAGATTCTCATTTAAAATTCA
Found at i:4237223 original size:45 final size:45
Alignment explanation
Indices: 4237150--4237250 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
4237140 ACAAATTCTC
** * * *
4237150 AAGATT-TCCATTTAAAATTCAAAGATTCTCATTTAAAACTTTTTA
1 AAGATTCT-CATTTAAAAGACAAAGATTCTAATTCAAAACTCTTTA
*
4237195 AAGATTCTCATTTAAAAGACAAATATTCTAATTCAAAACTCTTTA
1 AAGATTCTCATTTAAAAGACAAAGATTCTAATTCAAAACTCTTTA
*
4237240 AAAATTCTCAT
1 AAGATTCTCAT
4237251 AAAAAACTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 47 0.98
46 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.39
Consensus pattern (45 bp):
AAGATTCTCATTTAAAAGACAAAGATTCTAATTCAAAACTCTTTA
Found at i:4238504 original size:14 final size:17
Alignment explanation
Indices: 4238471--4238506 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
4238461 TTTTTTCTTT
4238471 TTTTTACACATTTCTCA
1 TTTTTACACATTTCTCA
4238488 TTTTT-CAC-TTT-TCA
1 TTTTTACACATTTCTCA
4238502 TTTTT
1 TTTTT
4238507 TTCACTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.42
15 3 0.16
16 3 0.16
17 5 0.26
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTACACATTTCTCA
Done.