Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 12 of 226
Found at i:4214662 original size:8 final size:8
Alignment explanation
Indices: 4214639--4214663 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4214629 TTTTTTATGA
4214639 TATTTTAT
1 TATTTTAT
4214647 TATTTTAT
1 TATTTTAT
4214655 TATTTTAT
1 TATTTTAT
4214663 T
1 T
4214664 TAGTGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:4221152 original size:30 final size:31
Alignment explanation
Indices: 4221108--4221170 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
4221098 TAGTAAAAAT
4221108 AAAATTATACTTTAACCCCTTAAAAATGATA
1 AAAATTATACTTTAACCCCTTAAAAATGATA
* * * *
4221139 AAAATT-TATTTTAATCCTTTAAAAATTATA
1 AAAATTATACTTTAACCCCTTAAAAATGATA
4221169 AA
1 AA
4221171 TATATAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (31 bp):
AAAATTATACTTTAACCCCTTAAAAATGATA
Found at i:4221436 original size:17 final size:16
Alignment explanation
Indices: 4221400--4221438 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
4221390 TTATTTTATG
*
4221400 TTAATTTAAATATATT
1 TTAATTTAAATATATC
*
4221416 TTAATTGTAAGTATATC
1 TTAATT-TAAATATATC
4221433 TTAATT
1 TTAATT
4221439 ATTAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (16 bp):
TTAATTTAAATATATC
Found at i:4253161 original size:10 final size:10
Alignment explanation
Indices: 4253125--4253173 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
4253115 TTTTATATTT
*
4253125 AAAATTATTA
1 AAAATTATAA
4253135 AAAATTAT-A
1 AAAATTATAA
**
4253144 AGGA-TATAA
1 AAAATTATAA
4253153 AAAATTATAA
1 AAAATTATAA
4253163 AAAA-TATAA
1 AAAATTATAA
4253172 AA
1 AA
4253174 GTGAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
8 3 0.09
9 13 0.39
10 17 0.52
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:4253173 original size:18 final size:18
Alignment explanation
Indices: 4253133--4253210 Score: 52
Period size: 18 Copynumber: 4.3 Consensus size: 18
4253123 TTAAAATTAT
**
4253133 TAAAAATTAT-AAGGATA
1 TAAAAATTATAAAAAATA
4253150 TAAAAAATTATAAAAAATA
1 T-AAAAATTATAAAAAATA
* * * *
4253169 TAAAAGTGAAAAAAAAAA
1 TAAAAATTATAAAAAATA
* *
4253187 TTAAAA-TATAGAAAATTA
1 TAAAAATTATA-AAAAATA
4253205 TAAAAA
1 TAAAAA
4253211 ATGGTTTTTT
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
17 3 0.07
18 36 0.80
19 6 0.13
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (18 bp):
TAAAAATTATAAAAAATA
Found at i:4253182 original size:28 final size:28
Alignment explanation
Indices: 4253125--4253189 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
4253115 TTTTATATTT
* *
4253125 AAAATTATTAAAAATTATAAGGATATAA
1 AAAATTATAAAAAATTAAAAGGATATAA
* *
4253153 AAAATTATAAAAAATATAAAAGTGAAAAAA
1 AAAATTATAAAAAAT-TAAAAG-GATATAA
4253183 AAAATTA
1 AAAATTA
4253190 AAATATAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 14 0.45
29 5 0.16
30 12 0.39
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (28 bp):
AAAATTATAAAAAATTAAAAGGATATAA
Found at i:4253272 original size:20 final size:22
Alignment explanation
Indices: 4253247--4253291 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
4253237 AAAAAAATTT
*
4253247 AAATGTATTGAAAT-TT-TAAA
1 AAATGTATTAAAATATTATAAA
*
4253267 AAATGTTTTAAAATATTATAAA
1 AAATGTATTAAAATATTATAAA
4253289 AAA
1 AAA
4253292 ATAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 2 0.10
22 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
AAATGTATTAAAATATTATAAA
Found at i:4253454 original size:28 final size:27
Alignment explanation
Indices: 4253407--4253505 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 27
4253397 TTTTCTTATG
*
4253407 ATAATAAGTTTTA-ATTTTTTGAAATTTT
1 ATAATAA-TTTTATATATTTTGAAA-TTT
* **
4253435 ATTATAATTATTATA-ATTTTGTCATTT
1 ATAATAATT-TTATATATTTTGAAATTT
* * *
4253462 ATAATAATTTTATATATTTTTATACTT
1 ATAATAATTTTATATATTTTGAAATTT
4253489 -TAAT-ATTTTATA-ATTTT
1 ATAATAATTTTATATATTTT
4253506 CTATTTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
24 5 0.08
25 8 0.14
26 9 0.15
27 21 0.36
28 15 0.25
29 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (27 bp):
ATAATAATTTTATATATTTTGAAATTT
Found at i:4253504 original size:8 final size:8
Alignment explanation
Indices: 4253436--4253505 Score: 52
Period size: 8 Copynumber: 8.2 Consensus size: 8
4253426 TGAAATTTTA
4253436 TTATAATT
1 TTATAATT
4253444 ATTATAATT
1 -TTATAATT
* *
4253453 TTGTCATT
1 TTATAATT
4253461 TATAATAATT
1 T-T-ATAATT
4253471 TTATATATTT
1 TTATA-A-TT
*
4253481 TTATACTT
1 TTATAATT
*
4253489 TAAT-ATT
1 TTATAATT
4253496 TTATAATT
1 TTATAATT
4253504 TT
1 TT
4253506 CTATTTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
7 5 0.10
8 20 0.42
9 11 0.23
10 12 0.25
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (8 bp):
TTATAATT
Found at i:4255165 original size:20 final size:20
Alignment explanation
Indices: 4255130--4255171 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4255120 CACAAAACAA
*
4255130 TACTTAAATTATACTTA-AT
1 TACTTAAATGATACTTAGAT
4255149 TACTTAAAGTGATACTTAGAT
1 TACTTAAA-TGATACTTAGAT
4255170 TA
1 TA
4255172 TATAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 8 0.40
21 4 0.20
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (20 bp):
TACTTAAATGATACTTAGAT
Found at i:4262399 original size:13 final size:13
Alignment explanation
Indices: 4262381--4262408 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4262371 GAGGTTAGAC
4262381 AAAGGAAAGAATA
1 AAAGGAAAGAATA
4262394 AAAGGAAAGAATA
1 AAAGGAAAGAATA
4262407 AA
1 AA
4262409 GTTGAAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (13 bp):
AAAGGAAAGAATA
Found at i:4262718 original size:50 final size:50
Alignment explanation
Indices: 4262642--4262934 Score: 415
Period size: 50 Copynumber: 5.8 Consensus size: 50
4262632 ATTTGGGTAA
*
4262642 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
4262692 TGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
4262742 ATAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
4262792 AGAGGTCCCATATAAAACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
4262842 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
4262892 AGTACATCCCATGTAAGACCACGTCTGAGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
4262935 TGTTATGATC
Statistics
Matches: 213, Mismatches: 29, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
50 181 0.85
51 32 0.15
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:4274069 original size:127 final size:126
Alignment explanation
Indices: 4273843--4274100 Score: 507
Period size: 127 Copynumber: 2.0 Consensus size: 126
4273833 AACTCTTTCA
4273843 ACTAGGCGGAATAACTGAAATCAACTCGGAATTTCTGGAAACTGATTAAACAAACTAGTATCATC
1 ACTAGGCGGAATAACTGAAATCAACTCGGAATTTCTGGAAACTGATTAAACAAACTAGTATCATC
4273908 TGTTTTGAACTTCTTGAGCTTAGGGGAATAACTGCATGCAGGCCCTGCAGTCTTGATCCTTG
66 TGTTTTGAACTTCTTGAGCTTAGGGGAATAACTGCATGCAGG-CCTGCAGTCTTGATCCTTG
4273970 ACTAGGCGGAATAACTGAAATCAACTCGGAATTTCTGGAAACTGATTAAACAAACTAGTATCATC
1 ACTAGGCGGAATAACTGAAATCAACTCGGAATTTCTGGAAACTGATTAAACAAACTAGTATCATC
4274035 TGTTTTGAACTTCTTGAGCTTAGGGGAATAACTGCATGCAGGCCTGCAGTCTTGATCCTTG
66 TGTTTTGAACTTCTTGAGCTTAGGGGAATAACTGCATGCAGGCCTGCAGTCTTGATCCTTG
4274096 ACTAG
1 ACTAG
4274101 ACATTTTCTT
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 24 0.18
127 107 0.82
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (126 bp):
ACTAGGCGGAATAACTGAAATCAACTCGGAATTTCTGGAAACTGATTAAACAAACTAGTATCATC
TGTTTTGAACTTCTTGAGCTTAGGGGAATAACTGCATGCAGGCCTGCAGTCTTGATCCTTG
Found at i:4285068 original size:19 final size:20
Alignment explanation
Indices: 4285027--4285070 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
4285017 ATTTTACAAG
* *
4285027 TATAATTATTAATATTAGGA
1 TATAATTATTAATATAAAGA
*
4285047 TATAA-TATTAATATAAATA
1 TATAATTATTAATATAAAGA
4285066 TATAA
1 TATAA
4285071 ATACATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
TATAATTATTAATATAAAGA
Found at i:4296893 original size:31 final size:31
Alignment explanation
Indices: 4296833--4296894 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
4296823 ATAGTCGAAC
**
4296833 GACTTAAATAAAAACATTTAAATTGTTCAGT
1 GACTTAAATAAAAACATTTAAATAATTCAGT
* *
4296864 GACTTAAATAAAAACTTTTGAATAATTCAGT
1 GACTTAAATAAAAACATTTAAATAATTCAGT
4296895 AATCAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (31 bp):
GACTTAAATAAAAACATTTAAATAATTCAGT
Found at i:4300730 original size:2 final size:2
Alignment explanation
Indices: 4300723--4300757 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4300713 GTCTTTCAAG
4300723 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4300758 TATATATGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4307492 original size:14 final size:15
Alignment explanation
Indices: 4307461--4307510 Score: 66
Period size: 14 Copynumber: 3.3 Consensus size: 15
4307451 TATGTTAATA
4307461 AAAAAATTTAAAAAT
1 AAAAAATTTAAAAAT
* *
4307476 AAAAAA-TTCAAATT
1 AAAAAATTTAAAAAT
4307490 AAAAATATTTAAAAAT
1 AAAAA-ATTTAAAAAT
4307506 AAAAA
1 AAAAA
4307511 TATTACCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 11 0.38
15 7 0.24
16 11 0.38
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAATTTAAAAAT
Found at i:4307511 original size:16 final size:16
Alignment explanation
Indices: 4307457--4307514 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
4307447 ATATTATGTT
*
4307457 AATAAAAAAATTTAAA
1 AATAAAAATATTTAAA
*
4307473 AATAAAAA-A-TTCAA
1 AATAAAAATATTTAAA
*
4307487 ATTAAAAATATTTAAA
1 AATAAAAATATTTAAA
4307503 AATAAAAATATT
1 AATAAAAATATT
4307515 ACCTACCATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.31
15 2 0.06
16 23 0.64
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAAATATTTAAA
Found at i:4309665 original size:24 final size:26
Alignment explanation
Indices: 4309638--4309685 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
4309628 CCAATAAATT
*
4309638 TAAAATCGAA-ATAATTA-CACATAA
1 TAAAATCGAACATAAATATCACATAA
*
4309662 TAAAATTGAACATAAATATCACAT
1 TAAAATCGAACATAAATATCACAT
4309686 CACTTAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 6 0.30
26 5 0.25
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.27
Consensus pattern (26 bp):
TAAAATCGAACATAAATATCACATAA
Found at i:4313024 original size:22 final size:23
Alignment explanation
Indices: 4312981--4313030 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
4312971 AGTCCGGGTT
* *
4312981 ATTAAAATTATATTTTTATTAAA
1 ATTAAAACTATATTGTTATTAAA
4313004 ATTAAAACTA-ATTGTTATTAAA
1 ATTAAAACTATATTGTTATTAAA
4313026 ATTAA
1 ATTAA
4313031 TTGTTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAAAACTATATTGTTATTAAA
Found at i:4313043 original size:16 final size:16
Alignment explanation
Indices: 4313004--4313045 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
4312994 TTTTATTAAA
*
4313004 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
4313020 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
4313036 ATTAAAATTA
1 ATTAAAATTA
4313046 TATCAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:4313144 original size:35 final size:35
Alignment explanation
Indices: 4313098--4313266 Score: 115
Period size: 35 Copynumber: 4.6 Consensus size: 35
4313088 ATCTAACATT
* *
4313098 TTGTTAGTAAAATTATTAATTGTTAATTGTATTAA
1 TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
*
4313133 TTGTTAGTAAAATTATCAAATTATATCAAAT-TATTAA
1 TTGTTAGTAAAATTAT-AAATTGT-T-AAATGTATTAA
* * * * * * ** *
4313170 TTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATT
1 TTGTTAGTA-AAATTATAA-A--TTGTTAAATGTATTA-A
* * *
4313210 TTGTTAGTCAAATTATTAATTGTTAATTGTATTAA
1 TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
4313245 TTGTTAGTAAAATTATCAAATT
1 TTGTTAGTAAAATTAT-AAATT
4313267 ATATCAAATT
Statistics
Matches: 98, Mismatches: 26, Indels: 19
0.69 0.18 0.13
Matches are distributed among these distances:
35 31 0.32
36 19 0.19
37 18 0.18
38 12 0.12
39 7 0.07
40 11 0.11
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (35 bp):
TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
Found at i:4313193 original size:112 final size:110
Alignment explanation
Indices: 4313040--4313277 Score: 422
Period size: 112 Copynumber: 2.1 Consensus size: 110
4313030 ATTGTTATTA
* *
4313040 AAATTATATCAAATTATATTTTTTGTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTAG
1 AAATTATATCAAATTATATTGTTAGTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTAG
4313105 TAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
66 TAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
*
4313150 AAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTT
1 AAATTATATCAAATTA-T-ATTGTTAGTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTT
*
4313215 AGTCAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
64 AGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
4313262 AAATTATATCAAATTA
1 AAATTATATCAAATTA
4313278 GGGTTAGGGT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
110 16 0.13
111 1 0.01
112 105 0.86
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (110 bp):
AAATTATATCAAATTATATTGTTAGTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTAG
TAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
Found at i:4313286 original size:6 final size:6
Alignment explanation
Indices: 4313275--4313303 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4313265 TTATATCAAA
4313275 TTAGGG TTAGGG TTAGGG TTAGGG TTAGG
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGG
4313304 ATTTTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.34
Consensus pattern (6 bp):
TTAGGG
Found at i:4313378 original size:53 final size:53
Alignment explanation
Indices: 4313283--4313697 Score: 327
Period size: 53 Copynumber: 7.7 Consensus size: 53
4313273 AATTAGGGTT
*
4313283 AGGGTTAGGGTTAGGGTTAGGATTTTTGTTAGCATTAAGGTTTTGGTGTTTTTAAGTTA
1 AGGGTTAGGGTTAGGGTTAGGGTTTTTGTTAG------GGTTTTGGTGTTTTTAAGTTA
* * *
4313342 AAGGTTAGGGTTAGGGCTAGAGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
1 AGGGTTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
* * *
4313395 AGGGTTAGGGTTATGGTTAGGGTTTTTAAGTTAAGGG-TTAGG-G---TTAGGGTT-
1 AGGGTTAGGGTTAGGGTTAGGGTTTTT--GTT-AGGGTTTTGGTGTTTTTA-AGTTA
*** *
4313446 AGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTGGGGTTAGG-GTTTTTAAGTTA
1 AGGGTTAGGGTTAGGG-TTAGG-GTTTTT--GTT-AGGGTT----TT-GGTGTTTTTAAGTTA
*
4313508 AGGGTTAGGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
1 AGGGTTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
* * *** * * **
4313561 AGGGTT----TTA-AGTTAAGAGTTAGAGTTA-TGATTAAG-GTTTTTAAGTTA
1 AGGGTTAGGGTTAGGGTT-AGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
* *
4313608 AGGGTTAAGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
1 AGGGTTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
*
4313661 AGGGTTAGGGTTATGGTTAGGGTTTTTGTTAGGGTTT
1 AGGGTTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTT
4313698 GTCAATTAAA
Statistics
Matches: 286, Mismatches: 45, Indels: 56
0.74 0.12 0.14
Matches are distributed among these distances:
47 18 0.06
48 6 0.02
49 12 0.04
51 27 0.09
52 15 0.05
53 126 0.44
54 2 0.01
55 7 0.02
56 4 0.01
57 6 0.02
58 4 0.01
59 31 0.11
60 6 0.02
61 6 0.02
62 16 0.06
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.45
Consensus pattern (53 bp):
AGGGTTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
Found at i:4313406 original size:6 final size:6
Alignment explanation
Indices: 4313395--4313451 Score: 53
Period size: 6 Copynumber: 9.0 Consensus size: 6
4313385 TTTTAAGTTA
* *
4313395 AGGGTT AGGGTT ATGGTT AGGGTTTTT A-AGTT AAGGGTT AGGGTT AGGGTT
1 AGGGTT AGGGTT AGGGTT AGGG---TT AGGGTT -AGGGTT AGGGTT AGGGTT
4313446 AGGGTT
1 AGGGTT
4313452 TTTGTTAGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 2 0.05
6 33 0.79
7 3 0.07
8 1 0.02
9 3 0.07
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.39
Consensus pattern (6 bp):
AGGGTT
Found at i:4313414 original size:12 final size:12
Alignment explanation
Indices: 4313397--4313468 Score: 53
Period size: 12 Copynumber: 6.2 Consensus size: 12
4313387 TTAAGTTAAG
4313397 GGTTAGGGTTAT
1 GGTTAGGGTTAT
4313409 GGTTAGGGTT-T
1 GGTTAGGGTTAT
* *
4313420 --TTA-AGTTAAG
1 GGTTAGGGTT-AT
*
4313430 GGTTAGGGTTAG
1 GGTTAGGGTTAT
*
4313442 GGTTAGGGTTTT
1 GGTTAGGGTTAT
* *
4313454 TGTTAGGGTTTT
1 GGTTAGGGTTAT
4313466 GGT
1 GGT
4313469 GTTTTTAAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
11 1 0.02
12 38 0.79
13 3 0.06
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.44
Consensus pattern (12 bp):
GGTTAGGGTTAT
Found at i:4313425 original size:33 final size:33
Alignment explanation
Indices: 4313369--4313534 Score: 154
Period size: 33 Copynumber: 5.5 Consensus size: 33
4313359 TAGAGTTTTT
*
4313369 GTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTAGG
1 GTTAGGG-TTAGG-GTTTTTAAGTTAAGGGTTAGG
*
4313404 GTTATGGTTAGGGTTTTTAAGTTAAGGGTTAGG
1 GTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGG
4313437 GTTAGGGTTAGGGTTTTT--GTT-AGGGTT---
1 GTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGG
4313464 -TT--GG-T---GTTTTTAAGTTAAGGGTT---
1 GTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGG
4313487 G---GGGTTAGGGTTTTTAAGTTAAGGGTTAGG
1 GTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGG
*
4313517 GTTAGGGCTAGGGTTTTT
1 GTTAGGGTTAGGGTTTTT
4313535 GTTAGGGTTT
Statistics
Matches: 112, Mismatches: 4, Indels: 32
0.76 0.03 0.22
Matches are distributed among these distances:
20 6 0.05
22 3 0.03
23 9 0.08
24 3 0.03
26 2 0.02
27 18 0.16
30 7 0.06
31 3 0.03
33 51 0.46
34 4 0.04
35 6 0.05
ACGTcount: A:0.17, C:0.01, G:0.38, T:0.45
Consensus pattern (33 bp):
GTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGG
Found at i:4313428 original size:86 final size:85
Alignment explanation
Indices: 4313330--4313687 Score: 492
Period size: 80 Copynumber: 4.1 Consensus size: 85
4313320 AGGTTTTGGT
* *
4313330 GTTTTTAAGTTAAAGGTTAGGGTTAGGGCTAGAGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
1 GTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
4313395 AGGGTTAGGGTTATGGTTAGG
66 AGGGTTAGGGTTA-GGTTAGG
*
4313416 GTTTTTAAGTTAAGGGTTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
1 GTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
4313481 AGGGTT--GG---GGTTAGG
66 AGGGTTAGGGTTAGGTTAGG
4313496 GTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
1 GTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
4313561 AGGGTTTTAAGTTAAGAGTTAGAGTTATGATTAAG
66 AGGG--TT-AG----G-GTTAG-GTTA-G-----G
*
4313596 GTTTTTAAGTTAAGGGTTAAGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
1 GTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
4313661 AGGGTTAGGGTTATGGTTAGG
66 AGGGTTAGGGTTA-GGTTAGG
4313682 GTTTTT
1 GTTTTT
4313688 GTTAGGGTTT
Statistics
Matches: 246, Mismatches: 5, Indels: 42
0.84 0.02 0.14
Matches are distributed among these distances:
80 75 0.30
82 2 0.01
84 2 0.01
86 75 0.30
89 1 0.00
90 1 0.00
91 1 0.00
92 8 0.03
93 3 0.01
94 4 0.02
95 1 0.00
97 2 0.01
98 2 0.01
100 69 0.28
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.45
Consensus pattern (85 bp):
GTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTA
AGGGTTAGGGTTAGGTTAGG
Found at i:4313439 original size:27 final size:27
Alignment explanation
Indices: 4313401--4313523 Score: 128
Period size: 27 Copynumber: 4.6 Consensus size: 27
4313391 GTTAAGGGTT
*
4313401 AGGGTTATGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTAGGGTTTTTAAGTTA
*
4313428 AGGGTTAGGGTTAGGG---TTAGGGTT-
1 AGGGTTAGGGTTAGGGTTTTTA-AGTTA
*** *
4313452 TTTGTTAGGGTTTTGGTGTTTTTAAGTTA
1 AGGGTTAGGG-TTAGG-GTTTTTAAGTTA
*
4313481 AGGGTTGGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTAGGGTTTTTAAGTTA
4313508 AGGGTTAGGGTTAGGG
1 AGGGTTAGGGTTAGGG
4313524 CTAGGGTTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
24 10 0.13
25 7 0.09
26 1 0.01
27 42 0.55
28 7 0.09
29 9 0.12
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.42
Consensus pattern (27 bp):
AGGGTTAGGGTTAGGGTTTTTAAGTTA
Found at i:4313568 original size:14 final size:14
Alignment explanation
Indices: 4313551--4313613 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 14
4313541 GTTTTGGTGT
4313551 TTTTAAGTTAAGGG
1 TTTTAAGTTAAGGG
*
4313565 TTTTAAGTTAAGAG
1 TTTTAAGTTAAGGG
* *
4313579 TTAGAGTTATGATTAAGGT
1 TT----TTAAG-TTAAGGG
4313598 TTTTAAGTTAAGGG
1 TTTTAAGTTAAGGG
4313612 TT
1 TT
4313614 AAGGTTAGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
14 23 0.61
15 4 0.11
18 4 0.11
19 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTTTAAGTTAAGGG
Found at i:4313697 original size:12 final size:12
Alignment explanation
Indices: 4313663--4313697 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4313653 TTAAGTTAAG
*
4313663 GGTTAGGGTTAT
1 GGTTAGGGTTTT
4313675 GGTTAGGGTTTT
1 GGTTAGGGTTTT
*
4313687 TGTTAGGGTTT
1 GGTTAGGGTTT
4313698 GTCAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.11, C:0.00, G:0.40, T:0.49
Consensus pattern (12 bp):
GGTTAGGGTTTT
Found at i:4313716 original size:7 final size:7
Alignment explanation
Indices: 4313704--4313743 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
4313694 GTTTGTCAAT
4313704 TAAATTA
1 TAAATTA
4313711 TAAATT-
1 TAAATTA
4313717 T-AATTA
1 TAAATTA
4313723 TAAATTA
1 TAAATTA
4313730 TAAATTTA
1 TAAA-TTA
4313738 TAAATT
1 TAAATT
4313744 TTTAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 17 0.57
8 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATTA
Found at i:4313716 original size:12 final size:12
Alignment explanation
Indices: 4313701--4313743 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
4313691 AGGGTTTGTC
4313701 AATTAAATTATA
1 AATTAAATTATA
*
4313713 AATTTAATTATA
1 AATTAAATTATA
4313725 AATTATAAATTTATA
1 AA-T-TAAA-TTATA
4313740 AATT
1 AATT
4313744 TTTAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 13 0.50
13 2 0.08
14 4 0.15
15 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATTAAATTATA
Found at i:4315461 original size:12 final size:12
Alignment explanation
Indices: 4315444--4315471 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4315434 GGAGCAACGC
4315444 CGGCACGACGGA
1 CGGCACGACGGA
4315456 CGGCACGACGGA
1 CGGCACGACGGA
4315468 CGGC
1 CGGC
4315472 GACTGAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.36, G:0.43, T:0.00
Consensus pattern (12 bp):
CGGCACGACGGA
Found at i:4316019 original size:3 final size:3
Alignment explanation
Indices: 4315945--4316010 Score: 73
Period size: 3 Copynumber: 22.7 Consensus size: 3
4315935 TTTGCTTTAT
* * *
4315945 TTA TTA TT- TTG TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
4315992 TT- TTA CTA TTA TTA GTA TT
1 TTA TTA TTA TTA TTA TTA TT
4316011 GGTATTATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4316209 original size:18 final size:18
Alignment explanation
Indices: 4316194--4316245 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
4316184 TACATATACA
*
4316194 TATTTTTATTTTTATAAG
1 TATTTATATTTTTATAAG
* *
4316212 TATTTATATTTATATGTATG
1 TATTTATATTT-T-TATAAG
4316232 TATTTATATATTTT
1 TATTTATAT-TTTT
4316246 TGTATATCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 10 0.36
19 2 0.07
20 14 0.50
21 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
TATTTATATTTTTATAAG
Found at i:4328776 original size:46 final size:44
Alignment explanation
Indices: 4328709--4329076 Score: 203
Period size: 44 Copynumber: 8.5 Consensus size: 44
4328699 ATTATACAGG
*
4328709 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* *
4328755 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAG--A
* * * * * *
4328799 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * *
4328838 TCTTATCT-CCTGA-AGTTACAGTAGAGA-AGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGATTCAGA
* * *
4328878 TCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCGGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* * ** ****
4328924 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * *
4328968 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCA-GA
* * * * **
4329011 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA-ATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGATTCA-GA
* *
4329055 TCTTATCTCTCTGAGGTTACAG
1 TCTTATCTCCCTGAGATTACAG
4329077 CAGAGTGGAT
Statistics
Matches: 250, Mismatches: 51, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
36 1 0.00
37 1 0.00
38 15 0.06
39 8 0.03
40 10 0.04
41 19 0.08
42 6 0.02
43 32 0.13
44 89 0.36
45 1 0.00
46 68 0.27
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
Found at i:4328826 original size:44 final size:46
Alignment explanation
Indices: 4328712--4329038 Score: 173
Period size: 46 Copynumber: 7.5 Consensus size: 46
4328702 ATACAGGTCT
* * * *
4328712 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGTCAGATCC
*
4328758 TATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-ATAGT-A-ATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAAT-GTCAGATCC
* * * * *
4328802 TATCTCCTTGAGATTACAATGGAGCGGAT--TA-AA-G---GATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGTCAGATCC
* * * * *
4328841 TATCT-CCTGA-AGTTACAGTAGAGAAGATC--A-CA--TCAGGTCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGAATGTCAGATCC
** * * * *
4328881 TATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCGGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGTCAGATCC
* ** * *
4328927 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-G--AGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-AATGTCAGATCC
* * *
4328971 TATCTCCCTGAGATTACAGCGGAGCAGATC---GAA-GACACTATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGTCA-GATCC
4329014 TATCTCCCTGA-AGTTACAGTGGAGC
1 TATCTCCCTGAGA-TTACAGTGGAGC
4329039 GGATTAAAAT
Statistics
Matches: 220, Mismatches: 41, Indels: 43
0.72 0.13 0.14
Matches are distributed among these distances:
37 1 0.00
38 18 0.08
39 8 0.04
40 12 0.05
41 19 0.09
42 5 0.02
43 26 0.12
44 61 0.28
45 3 0.01
46 66 0.30
47 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (46 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGTCAGATCC
Found at i:4329936 original size:12 final size:12
Alignment explanation
Indices: 4329919--4329946 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4329909 GGAGCAACGC
4329919 CGGCACGACGGA
1 CGGCACGACGGA
4329931 CGGCACGACGGA
1 CGGCACGACGGA
4329943 CGGC
1 CGGC
4329947 GACTGAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.36, G:0.43, T:0.00
Consensus pattern (12 bp):
CGGCACGACGGA
Found at i:4330501 original size:3 final size:3
Alignment explanation
Indices: 4330423--4330492 Score: 95
Period size: 3 Copynumber: 23.3 Consensus size: 3
4330413 GTACTTTTGC
*
4330423 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
4330471 CAT TTT TAC TAT TAT TAG TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
4330493 GGTATTATTG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:4330692 original size:18 final size:18
Alignment explanation
Indices: 4330677--4330728 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
4330667 TACATATACA
*
4330677 TATTTTTATTTTTATAAG
1 TATTTATATTTTTATAAG
* *
4330695 TATTTATATTTATATGTATG
1 TATTTATATTT-T-TATAAG
4330715 TATTTATATATTTT
1 TATTTATAT-TTTT
4330729 TGTATATCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 10 0.36
19 2 0.07
20 14 0.50
21 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
TATTTATATTTTTATAAG
Found at i:4333145 original size:21 final size:22
Alignment explanation
Indices: 4333120--4333168 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
4333110 TTTTTACGAT
4333120 TTAAAAAACATTTTAAAAA-AA
1 TTAAAAAACATTTTAAAAATAA
***
4333141 TT-AAAATTTTTTTAAAAATAA
1 TTAAAAAACATTTTAAAAATAA
4333162 TTAAAAA
1 TTAAAAA
4333169 TAGGGATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 13 0.57
21 6 0.26
22 4 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAAAAACATTTTAAAAATAA
Found at i:4333204 original size:11 final size:11
Alignment explanation
Indices: 4333190--4333276 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
4333180 GAGAAATTTA
4333190 AGAGGAAATTG
1 AGAGGAAATTG
*
4333201 AGAGCAAATTG
1 AGAGGAAATTG
**
4333212 AGATTAAA-T-
1 AGAGGAAATTG
* *
4333221 A-TGG-ATTTG
1 AGAGGAAATTG
4333230 AGA-GAAATTTG
1 AGAGGAAA-TTG
4333241 -GAAGGAAATTG
1 AG-AGGAAATTG
* *
4333252 AGAGCAATTTG
1 AGAGGAAATTG
4333263 AGAGGAAATTG
1 AGAGGAAATTG
4333274 AGA
1 AGA
4333277 AATGATTAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 3 0.05
11 42 0.76
12 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:4333221 original size:51 final size:51
Alignment explanation
Indices: 4333166--4333265 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
4333156 AAATAATTAA
4333166 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * *
4333217 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAATTTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
4333266 GGAAATTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:4333252 original size:22 final size:22
Alignment explanation
Indices: 4333227--4333276 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
4333217 AAATATGGAT
4333227 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
*
4333249 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGAAATTTGAGAGGAAA
4333271 TTGAGA
1 TTGAGA
4333277 AATGATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.32, T:0.24
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:4336201 original size:84 final size:84
Alignment explanation
Indices: 4336044--4336202 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
4336034 AACCAACCCT
* * *
4336044 AAATTCAAACCCCTTTGTCTCCATGGTCAAAGGCATTGGTTTGAAGTTGTCTATCATGCTAATAT
1 AAATTCAAACCCCTATGTCTCCATGGTCAAAGGCATTGGTTTGAAGTTCTCTATCATGCTAATAA
*
4336109 TTTTTTTTTTAATTTTCAA
66 TTTATTTTTTAATTTTCAA
* * * * * *
4336128 AAATTCTAACCCCTATGTCTCTATGGTCAAATGCATT-GTTTGAAGTTCTGTATTATGCTTATAA
1 AAATTCAAACCCCTATGTCTCCATGGTCAAAGGCATTGGTTTGAAGTTCTCTATCATGCTAAT-A
4336192 ATTTATTTTTT
65 ATTTATTTTTT
4336203 TCAAAGTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
83 21 0.33
84 43 0.67
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (84 bp):
AAATTCAAACCCCTATGTCTCCATGGTCAAAGGCATTGGTTTGAAGTTCTCTATCATGCTAATAA
TTTATTTTTTAATTTTCAA
Found at i:4353721 original size:79 final size:76
Alignment explanation
Indices: 4353574--4353730 Score: 215
Period size: 79 Copynumber: 2.0 Consensus size: 76
4353564 GACTTCAATG
* * * * *
4353574 CTCATAGACTTGATCTCACTATTCATAGGACTGATATTCTGAGCAGGCATCGAGCATGTTAAACA
1 CTCATAGACTTGACCCCACTATTCATAGAACTGATATTCTAAACAGGCATCGAGCATGTTAAACA
*
4353639 TGTGTATTATT
66 TGTGTATCATT
* *
4353650 CTCATGGACTTGACCCCACTATTCATAGAACTGATGACATTCTAAACAGGCCTCGAGCATGTTAA
1 CTCATAGACTTGACCCCACTATTCATAGAACTGAT---ATTCTAAACAGGCATCGAGCATGTTAA
4353715 ACATGTGTATCATT
63 ACATGTGTATCATT
4353729 CT
1 CT
4353731 AGGTCGCCTC
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
76 31 0.44
79 39 0.56
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (76 bp):
CTCATAGACTTGACCCCACTATTCATAGAACTGATATTCTAAACAGGCATCGAGCATGTTAAACA
TGTGTATCATT
Found at i:4355875 original size:6 final size:6
Alignment explanation
Indices: 4355864--4355899 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
4355854 ATCCTTTCTT
4355864 TCTTTC TCTTTC TCTTTC TCTTTC TCCTTT- TCTTTC
1 TCTTTC TCTTTC TCTTTC TCTTTC T-CTTTC TCTTTC
4355900 ATTTCTGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 4 0.14
6 20 0.71
7 4 0.14
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TCTTTC
Found at i:4357103 original size:19 final size:18
Alignment explanation
Indices: 4357076--4357116 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
4357066 CATAATTTTC
*
4357076 AAAATAATTAAACAGCCCA
1 AAAAAAATTAAA-AGCCCA
*
4357095 AAAAAAATTACAAGCCCA
1 AAAAAAATTAAAAGCCCA
4357113 AAAA
1 AAAA
4357117 TAAAAAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.63, C:0.20, G:0.05, T:0.12
Consensus pattern (18 bp):
AAAAAAATTAAAAGCCCA
Found at i:4358532 original size:21 final size:21
Alignment explanation
Indices: 4358508--4358557 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
4358498 GATTCATTAG
*
4358508 TATTATAT-TTATTCTTGTTGT
1 TATTAT-TGTTATTCTTATTGT
*
4358529 TATTATTGTTATTGTTATTGT
1 TATTATTGTTATTCTTATTGT
4358550 TA-TATTGT
1 TATTATTGT
4358558 CATTTGCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.66
Consensus pattern (21 bp):
TATTATTGTTATTCTTATTGT
Found at i:4360266 original size:88 final size:87
Alignment explanation
Indices: 4359886--4360496 Score: 753
Period size: 88 Copynumber: 7.1 Consensus size: 87
4359876 AGATCAGTGA
* * * *
4359886 AGATCGAAAA-CAAAACTTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATTTTTC
1 AGATCGAAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGC
* *
4359950 CTTCTTGCATTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
*
4359972 AGATCGAAAA-CAAAGCCTTGCCTCCATCGGTTGCAGTGTAGCTGGTTAAAGAAGCAGATCTTGC
1 AGATCGAAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGC
* *
4360036 CTT-CTGC--AAATCAGCAAAGC
66 CTTCCTGCGTTAA-CAGCGAAGC
* * *
4360056 AGATC-AAAAGCAAAGCTTTGCCTCCATCGGTTGCAGTGGAGTTGGTTAAAGAAGCAGATCTTGA
1 AGATCGAAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGC
* *
4360120 CTTCCT--G-TAGATTATCGAAGC
66 CTTCCTGCGTTA-A-CAGCGAAGC
*
4360141 AGATCG-AAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTG
1 AGATCGAAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTG
4360205 CCTTCCTGCGTTAACAGCGAAGC
65 CCTTCCTGCGTTAACAGCGAAGC
* * * *
4360228 AGGTCGAAAACCCAAGCCTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 AGATCGAAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTG
* ** ** *
4360293 CCCTCCTATGTCGACAGTGAAGC
65 CCTTCCTGCGTTAACAGCGAAGC
* * * * *
4360316 AGATCGAAGACCCAAGCCTTGTCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATATTGC
1 AGATCGAAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGC
* *
4360381 CTTCCTGCAG--ATCAGCAAAGC
66 CTTCCTGC-GTTAACAGCGAAGC
4360402 AGATCG-AAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 AGATCGAAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTG
* *
4360466 CATTCCTGCGTTAACAGTGAAGC
65 CCTTCCTGCGTTAACAGCGAAGC
*
4360489 AAATCGAA
1 AGATCGAA
4360497 GATTACAAGC
Statistics
Matches: 454, Mismatches: 55, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
83 6 0.01
84 67 0.15
85 105 0.23
86 109 0.24
87 41 0.09
88 124 0.27
89 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (87 bp):
AGATCGAAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:4360293 original size:44 final size:44
Alignment explanation
Indices: 4360157--4360294 Score: 113
Period size: 44 Copynumber: 3.1 Consensus size: 44
4360147 AAAGCAAAGC
*
4360157 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGAT
1 CTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAACAGAT
** * * * * ** *
4360201 CTTGCCTTCC-TGCGTTAACAGCGAAGCAGGTCGAAA-A-CCCA-AGC
1 CTTGCC-TCCAT-CGTTTGCAGTGGAGCTGGT-TAAAGATAACAGA-T
*
4360245 CTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
1 CTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAACAGAT
4360289 CTTGCC
1 CTTGCC
4360295 CTCCTATGTC
Statistics
Matches: 67, Mismatches: 19, Indels: 16
0.66 0.19 0.16
Matches are distributed among these distances:
42 3 0.04
43 19 0.28
44 24 0.36
45 18 0.27
46 3 0.04
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (44 bp):
CTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAACAGAT
Found at i:4360387 original size:261 final size:256
Alignment explanation
Indices: 4359886--4360496 Score: 859
Period size: 261 Copynumber: 2.4 Consensus size: 256
4359876 AGATCAGTGA
* * * * *
4359886 AGATCGAAAACAAAACTTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATTTTTC
1 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * *
4359950 CTTCTTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGTAGCT
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
* * *
4360015 GGTTAAAGAAGCAGATCTTGCCTTCTGCAAATCAGCAAAGCAGATCAAAAGCAAAGCTTTGCCTC
131 GGTTAAAGAAGCAGATCTTGCCTTATGCAAATCAGCAAAGCAGATCAAAACCAAAGCCTTGCCTC
* * * * * *
4360080 CATCGGTTGCAGTGGAGTTGGTTAAAGAAGCAGATCTTGACTTCCTGTAGATTATCGAAGC
196 CATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATATTGACTTCCTGCAGATCAGCAAAGC
*
4360141 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGC
1 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * *
4360206 CTTCCTGCGTTAACAGCGAAGCAGGTCGAAAACCCAAGCCTTGCCTCCATCGTTTGCAGTGGAGC
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAA-CAAAGCCTTGCCTCCATCGGTTGCAGTGGAGC
* ** * *
4360271 TGGTTAAAGATAGCAGATCTTGCCCTCCTATGTC-GA-CAGTGAAGCAGATCGAAGACCCAAGCC
130 TGGTTAAAGA-AGCAGATCTTG-CCT--TATG-CAAATCAGCAAAGCAGATC-AAAACCAAAGCC
* *
4360334 TTGTCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATATTGCCTTCCTGCAGATCAGCAA
189 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATATTGACTTCCTGCAGATCAGCAA
4360399 AGC
254 AGC
4360402 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * *
4360467 ATTCCTGCGTTAACAGTGAAGCAAATCGAA
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAA
4360497 GATTACAAGC
Statistics
Matches: 315, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
255 49 0.16
256 38 0.12
257 39 0.12
258 11 0.03
259 3 0.01
260 12 0.04
261 162 0.51
262 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (256 bp):
AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
GGTTAAAGAAGCAGATCTTGCCTTATGCAAATCAGCAAAGCAGATCAAAACCAAAGCCTTGCCTC
CATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATATTGACTTCCTGCAGATCAGCAAAGC
Found at i:4360498 original size:173 final size:171
Alignment explanation
Indices: 4359886--4360496 Score: 775
Period size: 173 Copynumber: 3.5 Consensus size: 171
4359876 AGATCAGTGA
* * * * * *
4359886 AGATCGAAAACAAAACTTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATTTTTCC
1 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCA
* * * *
4359951 TTCTTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGTAGCTG
66 TTCCTGCGTTAACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTG
*
4360016 GTTAAAGAAGCAGATCTTGCCTT-CTGCAAATCAGCAAAGC
131 GTTAAAGAAGCAGATCTTGCCTTCCTGCAGATCAGCAAAGC
* * *
4360056 AGATCAAAAGCAAAGCTTTGCCTCCATCGGTTGCAGTGGAGTTGGTTAAAGAAGCAGATCTTG-A
1 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCA
* * *
4360120 CTTCCTGTAGATTATC---GAAGCAGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAG
66 -TTCCTG-CG-TTAACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAG
* * *
4360182 CTGGTTAAAGATAACAGATCTTGCCTTCCTGC-GTTAACAGCGAAGC
128 CTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCAG--ATCAGCAAAGC
* * * *
4360228 AGGTCGAAAACCCAAGCCTTGCCTCCATCGTTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 AGATCG-AAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTG
** ** ** * * *
4360293 CCCTCCTATGTCGACAGTGAAGCAGATCGAAGACCCAAGCCTTGTCTCCATCGGTTGCAGTGGAG
64 CATTCCTGCGTTAACAGTGAAGCAGATCGAA-AACAAAGCCTTGCCTCCATCGGTTGCAGTGGAG
*
4360358 CTGGTTAAAGAAGCAGATATTGCCTTCCTGCAGATCAGCAAAGC
128 CTGGTTAAAGAAGCAGATCTTGCCTTCCTGCAGATCAGCAAAGC
4360402 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGC
*
4360467 ATTCCTGCGTTAACAGTGAAGCAAATCGAA
65 ATTCCTGCGTTAACAGTGAAGCAGATCGAA
4360497 GATTACAAGC
Statistics
Matches: 377, Mismatches: 49, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
169 55 0.15
170 76 0.20
171 4 0.01
172 19 0.05
173 121 0.32
174 29 0.08
175 31 0.08
176 42 0.11
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (171 bp):
AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCA
TTCCTGCGTTAACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTG
GTTAAAGAAGCAGATCTTGCCTTCCTGCAGATCAGCAAAGC
Found at i:4360726 original size:44 final size:44
Alignment explanation
Indices: 4360677--4360794 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 44
4360667 ATCGCATCGG
*
4360677 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGA-AAACAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCGA-ACAAACAA
* * ** * *
4360721 GTCTTATCCCCCTAAAGTCACAGTGGGGCAGACCGAACAAGCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCGAACAAACAA
* *
4360765 ATCTTATCTCCCTGAGGTTGCAGTGGAGCA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCA
4360795 ACTTGAAGTC
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
43 1 0.02
44 58 0.98
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (44 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCGAACAAACAA
Found at i:4364151 original size:29 final size:30
Alignment explanation
Indices: 4364098--4364174 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
4364088 TGATAAAAAA
* **
4364098 AATTAATTAAATTTTTAATTCAAAATT-GC
1 AATTAATTAAACTTTTAATAAAAAATTAGC
*
4364127 AATTAATTAAA-TTTTAATAAAAAAATTAGT
1 AATTAATTAAACTTTTAAT-AAAAAATTAGC
*
4364157 AATAAATTAAACTTTTAA
1 AATTAATTAAACTTTTAA
4364175 AATATAATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.17
29 17 0.41
30 11 0.27
31 6 0.15
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.42
Consensus pattern (30 bp):
AATTAATTAAACTTTTAATAAAAAATTAGC
Found at i:4364538 original size:28 final size:28
Alignment explanation
Indices: 4364498--4364566 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
4364488 AAACTCTTAG
**
4364498 AAATTATTGAAAATTATAAAAAAAT-ATAA
1 AAATTATT-AAAACCAT-AAAAAATCATAA
*
4364527 AAATTATTAAAACCATAAAAAATCATCA
1 AAATTATTAAAACCATAAAAAATCATAA
*
4364555 AATTTATTAAAA
1 AAATTATTAAAA
4364567 GTTTTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.20
28 20 0.57
29 8 0.23
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (28 bp):
AAATTATTAAAACCATAAAAAATCATAA
Found at i:4365035 original size:33 final size:31
Alignment explanation
Indices: 4364990--4365066 Score: 75
Period size: 33 Copynumber: 2.4 Consensus size: 31
4364980 TTTATTTTTA
4364990 TTTTTTAATTTTAAAATACTTTTAAAATAAAT
1 TTTTTTAATTTTAAAATACTTTTAAAAT-AAT
* *** *
4365022 TTTTTTATTTTTTATTTTATTTTTAAAATAA-
1 TTTTTTA-ATTTTAAAATACTTTTAAAATAAT
4365053 TTTTTTAATGTTTA
1 TTTTTTAAT-TTTA
4365067 TTTTAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
30 1 0.03
31 11 0.30
32 9 0.24
33 16 0.43
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (31 bp):
TTTTTTAATTTTAAAATACTTTTAAAATAAT
Found at i:4365040 original size:44 final size:46
Alignment explanation
Indices: 4364968--4365056 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 46
4364958 CGAATATAAT
* * *
4364968 AAATATATATTTTTTATTTTTATTTTTTAATTTTAAAATACTTTTA
1 AAATAAATATTTTTTATTTTTATATTTTAATTTTAAAATAATTTTA
*
4365014 AAATAAAT-TTTTTTATTTTT-TATTTTATTTTTAAAATAATTTT
1 AAATAAATATTTTTTATTTTTATATTTTAATTTTAAAATAATTTT
4365057 TTAATGTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 20 0.51
45 12 0.31
46 7 0.18
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (46 bp):
AAATAAATATTTTTTATTTTTATATTTTAATTTTAAAATAATTTTA
Found at i:4365070 original size:25 final size:24
Alignment explanation
Indices: 4365028--4365076 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
4365018 AAATTTTTTT
4365028 ATTTTTTATTTTATTTTTAAAATA
1 ATTTTTTATTTTATTTTTAAAATA
*
4365052 ATTTTTTAATGTTTATTTTAAAAAT
1 ATTTTTT-AT-TTTATTTTTAAAAT
4365077 GGGCCGGGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 2 0.09
26 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTTTTATTTTATTTTTAAAATA
Found at i:4365515 original size:16 final size:20
Alignment explanation
Indices: 4365482--4365521 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
4365472 TTTTTACCAT
4365482 TTTTATTATTTGTATAAT-A
1 TTTTATTATTTGTATAATAA
4365501 TTTTATT-TTT-T-TAATAA
1 TTTTATTATTTGTATAATAA
4365518 TTTT
1 TTTT
4365522 GTATAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.20
17 6 0.30
18 3 0.15
19 7 0.35
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTATTATTTGTATAATAA
Found at i:4374132 original size:23 final size:23
Alignment explanation
Indices: 4374103--4374175 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
4374093 GTTTGGATTT
4374103 TTTTATTATTGGATTTTCTAGTA
1 TTTTATTATTGGATTTTCTAGTA
* **
4374126 TTTTATTCAGTGTG-TGAT-T--T-
1 TTTTATT-ATTG-GATTTTCTAGTA
4374146 TTTTATTATTGGATTTTCTAGTA
1 TTTTATTATTGGATTTTCTAGTA
4374169 TTTTATT
1 TTTTATT
4374176 CAGTGTGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 8 0.22
21 1 0.03
22 1 0.03
23 15 0.41
24 5 0.14
25 1 0.03
ACGTcount: A:0.19, C:0.04, G:0.14, T:0.63
Consensus pattern (23 bp):
TTTTATTATTGGATTTTCTAGTA
Found at i:4374147 original size:43 final size:43
Alignment explanation
Indices: 4374098--4374188 Score: 182
Period size: 43 Copynumber: 2.1 Consensus size: 43
4374088 AAAGTGTTTG
4374098 GATTTTTTTATTATTGGATTTTCTAGTATTTTATTCAGTGTGT
1 GATTTTTTTATTATTGGATTTTCTAGTATTTTATTCAGTGTGT
4374141 GATTTTTTTATTATTGGATTTTCTAGTATTTTATTCAGTGTGT
1 GATTTTTTTATTATTGGATTTTCTAGTATTTTATTCAGTGTGT
4374184 GATTT
1 GATTT
4374189 ATTTGATGAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.19, C:0.04, G:0.16, T:0.60
Consensus pattern (43 bp):
GATTTTTTTATTATTGGATTTTCTAGTATTTTATTCAGTGTGT
Found at i:4379962 original size:13 final size:14
Alignment explanation
Indices: 4379946--4379974 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4379936 TTTGACTTAA
4379946 TTTTAATTA-TATT
1 TTTTAATTATTATT
4379959 TTTTAATTATTATT
1 TTTTAATTATTATT
4379973 TT
1 TT
4379975 ATTTAGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTAATTATTATT
Found at i:4380594 original size:18 final size:18
Alignment explanation
Indices: 4380571--4380611 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
4380561 TTTTACATAG
*
4380571 AAGAAACCGTGTAAGCGA
1 AAGAAACCGTGTAAGCAA
*
4380589 AAGAAACGGTGTAAGCAA
1 AAGAAACCGTGTAAGCAA
4380607 AAGAA
1 AAGAA
4380612 TTTCATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.12, G:0.27, T:0.10
Consensus pattern (18 bp):
AAGAAACCGTGTAAGCAA
Found at i:4382116 original size:42 final size:42
Alignment explanation
Indices: 4382057--4382160 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 42
4382047 ATGAGTTTTG
* ** *
4382057 GTTTAACCCTTATGGGTTTCCGTTCAGCTCTTTTGAGCTTCA
1 GTTTAACCCTTATGGGTTTCCGTTCAACTCTTACGAACTTCA
*
4382099 GTTTAACCCTTATGGGTTTCCGTTCAACTCTTACGAACTTCC
1 GTTTAACCCTTATGGGTTTCCGTTCAACTCTTACGAACTTCA
*
4382141 GTTCAACCCTTATGGGTTTC
1 GTTTAACCCTTATGGGTTTC
4382161 TATTTAGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.16, C:0.26, G:0.17, T:0.40
Consensus pattern (42 bp):
GTTTAACCCTTATGGGTTTCCGTTCAACTCTTACGAACTTCA
Found at i:4384603 original size:9 final size:9
Alignment explanation
Indices: 4384589--4384619 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4384579 GTTAAACGAA
4384589 TCGAGTTAT
1 TCGAGTTAT
*
4384598 TCGAGTTAA
1 TCGAGTTAT
4384607 TCGAGTTAT
1 TCGAGTTAT
4384616 TCGA
1 TCGA
4384620 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:4409170 original size:16 final size:16
Alignment explanation
Indices: 4409136--4409171 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4409126 GTATCACGAG
*
4409136 TTAATTAGATATTAAT
1 TTAATTAGATAGTAAT
*
4409152 TTAATTAGATAGTAGT
1 TTAATTAGATAGTAAT
4409168 TTAA
1 TTAA
4409172 ATATTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (16 bp):
TTAATTAGATAGTAAT
Found at i:4409783 original size:28 final size:28
Alignment explanation
Indices: 4409729--4409791 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
4409719 GTTAAATAAG
* *
4409729 TTTTATAAATTTTTAAAATATTTTTTAA
1 TTTTATAAAATTTTAAAATATTATTTAA
*
4409757 TTTTATAAAATTTT-AATTCATTATTTAA
1 TTTTATAAAATTTTAAAAT-ATTATTTAA
4409785 TTATTAT
1 TT-TTAT
4409792 TAGACCGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 3 0.10
28 23 0.77
29 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTATAAAATTTTAAAATATTATTTAA
Found at i:4412956 original size:103 final size:103
Alignment explanation
Indices: 4412827--4413039 Score: 318
Period size: 103 Copynumber: 2.1 Consensus size: 103
4412817 CACTAACTTT
* * * * *
4412827 TTATCTTATTGATTTGTTAGATTTTTATTTACGATATTTCTTTCAATAGTTTTAGTTTTAATTTA
1 TTATTTTATTGATTTGTTAAAATTTTATATACGATATTTATTTCAATAGTTTTAGTTTTAATTTA
* *
4412892 AATTTTTAATTTTCAAATCCCTTTTATTTTTATTTTAC
66 AATTTTAAATTTTAAAATCCCTTTTATTTTTATTTTAC
* * *
4412930 TTATTTTATTGATTTTTTAAAATTTTATATATGGTATTTATTTCAATAGTTTTAGTTTTAATTTA
1 TTATTTTATTGATTTGTTAAAATTTTATATACGATATTTATTTCAATAGTTTTAGTTTTAATTTA
*
4412995 ACTTTTAAATTTTAAAATCCCTTTTATTTTTATTTTAC
66 AATTTTAAATTTTAAAATCCCTTTTATTTTTATTTTAC
*
4413033 TGATTTT
1 TTATTTT
4413040 TTACTAATCA
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.27, C:0.07, G:0.06, T:0.61
Consensus pattern (103 bp):
TTATTTTATTGATTTGTTAAAATTTTATATACGATATTTATTTCAATAGTTTTAGTTTTAATTTA
AATTTTAAATTTTAAAATCCCTTTTATTTTTATTTTAC
Found at i:4419227 original size:17 final size:19
Alignment explanation
Indices: 4419185--4419228 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
4419175 AGAATACTAA
4419185 AATAATAA-ATAAATGAAT
1 AATAATAATATAAATGAAT
*
4419203 GAT-ATAATA-AAAT-AAT
1 AATAATAATATAAATGAAT
4419219 AATAATAATA
1 AATAATAATA
4419229 CACCAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AATAATAATATAAATGAAT
Found at i:4420706 original size:18 final size:18
Alignment explanation
Indices: 4420683--4420717 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4420673 GTAATTAGAC
*
4420683 TTTATTATTTGGTCTTGT
1 TTTATTATTGGGTCTTGT
4420701 TTTATTATTGGGTCTTG
1 TTTATTATTGGGTCTTG
4420718 GGCCGGACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.06, G:0.20, T:0.63
Consensus pattern (18 bp):
TTTATTATTGGGTCTTGT
Found at i:4421476 original size:25 final size:26
Alignment explanation
Indices: 4421423--4421491 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
4421413 CTTCTAAAAG
*
4421423 AAACTCAAGAGAAATTCTTGAAAGAA
1 AAACTCAAGAGAATTTCTTGAAAGAA
* *
4421449 AAACTCAATAGAATTTTTTGAAAGAA
1 AAACTCAAGAGAATTTCTTGAAAGAA
4421475 AAACTCAAAGAGAATTT
1 AAACTC-AAGAGAATTT
4421492 ATTAACTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
26 29 0.76
27 9 0.24
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (26 bp):
AAACTCAAGAGAATTTCTTGAAAGAA
Found at i:4425840 original size:8 final size:8
Alignment explanation
Indices: 4425827--4425854 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4425817 ACACACTTTA
4425827 AAAGCAAT
1 AAAGCAAT
4425835 AAAGCAAT
1 AAAGCAAT
4425843 AAAGCAAT
1 AAAGCAAT
4425851 AAAG
1 AAAG
4425855 GGCAACTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.11, G:0.14, T:0.11
Consensus pattern (8 bp):
AAAGCAAT
Found at i:4430517 original size:17 final size:17
Alignment explanation
Indices: 4430495--4430527 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4430485 TACTAAAAAT
4430495 ATAATTT-TATTATTTAA
1 ATAATTTATATT-TTTAA
4430512 ATAATTTATATTTTTA
1 ATAATTTATATTTTTA
4430528 TGATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTATATTTTTAA
Found at i:4437690 original size:14 final size:14
Alignment explanation
Indices: 4437671--4437701 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4437661 ATCACACAAT
4437671 ACTCAATTTTCATC
1 ACTCAATTTTCATC
4437685 ACTCAATTTTCATC
1 ACTCAATTTTCATC
4437699 ACT
1 ACT
4437702 TGCTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (14 bp):
ACTCAATTTTCATC
Found at i:4437995 original size:22 final size:23
Alignment explanation
Indices: 4437934--4438033 Score: 71
Period size: 25 Copynumber: 4.3 Consensus size: 23
4437924 TAATGAACAA
* *
4437934 AGAGCACTAAAGTGCTAAA-CAG
1 AGAGCACCAACGTGCTAAATCAG
* * * *
4437956 ATAGCA-CAGATGTACTAAA-CGG
1 AGAGCACCA-ACGTGCTAAATCAG
*
4437978 AGAGCACCATCGTGCTAATAATCAG
1 AGAGCACCAACGTGCT-A-AATCAG
4438003 AGAGCACCAACGTGCTAATAATCAG
1 AGAGCACCAACGTGCT-A-AATCAG
4438028 AGAGCA
1 AGAGCA
4438034 TTGGCGTACT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.02
22 24 0.39
23 3 0.05
24 2 0.03
25 32 0.52
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (23 bp):
AGAGCACCAACGTGCTAAATCAG
Found at i:4438006 original size:25 final size:25
Alignment explanation
Indices: 4437977--4438059 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 25
4437967 GTACTAAACG
*
4437977 GAGAGCACCATCGTGCTAATAATCA
1 GAGAGCACCAACGTGCTAATAATCA
4438002 GAGAGCACCAACGTGCTAATAATCA
1 GAGAGCACCAACGTGCTAATAATCA
**** *
4438027 GAGAGCATTGGCGTACTAATAATCA
1 GAGAGCACCAACGTGCTAATAATCA
4438052 GAGAGCAC
1 GAGAGCAC
4438060 TGACATGGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (25 bp):
GAGAGCACCAACGTGCTAATAATCA
Found at i:4438074 original size:25 final size:25
Alignment explanation
Indices: 4437988--4438078 Score: 110
Period size: 25 Copynumber: 3.6 Consensus size: 25
4437978 AGAGCACCAT
**
4437988 CGTGCTAATAATCAGAGAGCACCAA
1 CGTGCTAATAATCAGAGAGCACTGA
* *
4438013 CGTGCTAATAATCAGAGAGCATTGG
1 CGTGCTAATAATCAGAGAGCACTGA
*
4438038 CGTACTAATAATCAGAGAGCACTGA
1 CGTGCTAATAATCAGAGAGCACTGA
* * *
4438063 CATGGTACTAATCAGA
1 CGTGCTAATAATCAGA
4438079 AAGCGCGCTA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (25 bp):
CGTGCTAATAATCAGAGAGCACTGA
Found at i:4438967 original size:26 final size:26
Alignment explanation
Indices: 4438938--4438995 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
4438928 GAAATCCCAA
4438938 GTTTTCTTT-CTTTCCTTCCCC-TTTTC
1 GTTTTCTTTCCTTT-C-TCCCCGTTTTC
4438964 GTTTTCTTTCCTTTCTCCCCTGTTTTC
1 GTTTTCTTTCCTTTCTCCCC-GTTTTC
4438991 GTTTT
1 GTTTT
4438996 GCTTCTCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.17
26 10 0.34
27 14 0.48
ACGTcount: A:0.00, C:0.31, G:0.07, T:0.62
Consensus pattern (26 bp):
GTTTTCTTTCCTTTCTCCCCGTTTTC
Found at i:4446655 original size:6 final size:6
Alignment explanation
Indices: 4446644--4446668 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4446634 TGGTGAATGA
4446644 GAGAGG GAGAGG GAGAGG GAGAGG G
1 GAGAGG GAGAGG GAGAGG GAGAGG G
4446669 GCTTATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:4447570 original size:10 final size:9
Alignment explanation
Indices: 4447553--4447578 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4447543 TCTATCAAAC
4447553 TCTTTTTTT
1 TCTTTTTTT
4447562 TCTTTTTTT
1 TCTTTTTTT
4447571 TCTTTTTT
1 TCTTTTTT
4447579 CTTAATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:4449611 original size:6 final size:6
Alignment explanation
Indices: 4449600--4449639 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
4449590 ATACAGATTT
*
4449600 ATGAAA ATGAAA ATG-AA ATCGAAA ACGAAA ATGAAA ATGA
1 ATGAAA ATGAAA ATGAAA AT-GAAA ATGAAA ATGAAA ATGA
4449640 GAAGTTTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.13
6 23 0.77
7 3 0.10
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.15
Consensus pattern (6 bp):
ATGAAA
Found at i:4449785 original size:6 final size:6
Alignment explanation
Indices: 4449762--4449796 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
4449752 AAACTGAAAC
*
4449762 TAGGGT TAGTGTT TAGGGT TAGGGT TAGGGT TAGG
1 TAGGGT TAG-GGT TAGGGT TAGGGT TAGGGT TAGG
4449797 CAGTCATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (6 bp):
TAGGGT
Found at i:4460470 original size:13 final size:13
Alignment explanation
Indices: 4460452--4460488 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
4460442 AATAAGAAAA
*
4460452 AAAAAGTGAAAGT
1 AAAAAGTAAAAGT
4460465 AAAAAGTAAAAGT
1 AAAAAGTAAAAGT
4460478 -AAAAGTAAAAG
1 AAAAAGTAAAAG
4460489 AAGAAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.14
Consensus pattern (13 bp):
AAAAAGTAAAAGT
Found at i:4460502 original size:21 final size:19
Alignment explanation
Indices: 4460478--4460516 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
4460468 AAGTAAAAGT
4460478 AAAAGTAAAAGAAGAAAAAAC
1 AAAAGTAAAA-AA-AAAAAAC
4460499 AAAAGTAAAAAAAAAAAA
1 AAAAGTAAAAAAAAAAAA
4460517 TTGATGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (19 bp):
AAAAGTAAAAAAAAAAAAC
Found at i:4460508 original size:6 final size:6
Alignment explanation
Indices: 4460453--4460488 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
4460443 ATAAGAAAAA
*
4460453 AAAAGT GAAAGT AAAAAGT AAAAGT AAAAGT AAAAG
1 AAAAGT AAAAGT -AAAAGT AAAAGT AAAAGT AAAAG
4460489 AAGAAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (6 bp):
AAAAGT
Found at i:4475379 original size:13 final size:13
Alignment explanation
Indices: 4475357--4475390 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
4475347 TCTTCATACT
*
4475357 TTTTAAATATGTA
1 TTTTATATATGTA
4475370 TTTTATATATGTA
1 TTTTATATATGTA
4475383 TTTTATAT
1 TTTTATAT
4475391 GTATATGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
TTTTATATATGTA
Found at i:4476775 original size:7 final size:7
Alignment explanation
Indices: 4476763--4476789 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4476753 CAGAAAAAAA
4476763 TCAAACT
1 TCAAACT
4476770 TCAAACT
1 TCAAACT
4476777 TCAAACT
1 TCAAACT
4476784 TCAAAC
1 TCAAAC
4476790 CCCAACATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (7 bp):
TCAAACT
Found at i:4490200 original size:28 final size:29
Alignment explanation
Indices: 4490140--4490219 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 29
4490130 CTACACCATA
*
4490140 GGTCACTCAACTATTGATTTTTTTAATTT
1 GGTCACCCAACTATTGATTTTTTTAATTT
*
4490169 GGTCACCCAACTATTGGTCTTTTTT-A-TT
1 GGTCACCCAACTATTGAT-TTTTTTAATTT
**
4490197 GGTCACCCAACTATCAATTTTTT
1 GGTCACCCAACTATTGATTTTTT
4490220 AGTTTGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
27 5 0.11
28 17 0.38
29 17 0.38
30 6 0.13
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (29 bp):
GGTCACCCAACTATTGATTTTTTTAATTT
Found at i:4493108 original size:40 final size:40
Alignment explanation
Indices: 4493057--4493173 Score: 189
Period size: 40 Copynumber: 2.9 Consensus size: 40
4493047 CGTTTGGAGC
* * * **
4493057 AAAAGTGCCGCTAAAGAGTGAGCAATAGCGGCGTTTAATT
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
4493097 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
4493137 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
4493174 TAGATAACGC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.21
Consensus pattern (40 bp):
AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
Found at i:4493422 original size:112 final size:112
Alignment explanation
Indices: 4493121--4493709 Score: 968
Period size: 112 Copynumber: 5.3 Consensus size: 112
4493111 AGAGTGAGCA
** *
4493121 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
4493186 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGGGGGAC
4493234 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
4493299 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
* * *
4493346 TTAGTGGCATTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTATAAATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
4493411 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
**
4493457 TTAGTGGCGTTTATTGCGAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
4493522 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
* ** * * * *
4493568 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGCTTATAAAAAAATGCC
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAT-AGATAACGCC
* * *
4493633 GCAAATAATACTCCCAGACGGTGCCGTTTTGTGTCCTTTGGGGGGCA-
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
*
4493680 TTAGTGGCGTTTTTTGTAAAGCGCCGCTAA
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAA
4493710 TCTAGGTGTT
Statistics
Matches: 450, Mismatches: 24, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
111 162 0.36
112 182 0.40
113 106 0.24
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (112 bp):
TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
Found at i:4493731 original size:223 final size:223
Alignment explanation
Indices: 4493121--4493709 Score: 984
Period size: 223 Copynumber: 2.6 Consensus size: 223
4493111 AGAGTGAGCA
** * * *
4493121 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTATAAATAACGCCG
4493186 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGACTTAGTGGCGTTTATTGT
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT--GGGGGGACTTAGTGGCGTTTATTGT
4493251 AAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCGCAAATAATACACCCAGA
129 AAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCGCAAATAATACACCCAGA
4493316 CGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
194 CGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
*
4493346 TTAGTGGCATTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTATAAATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTATAAATAACGCCG
**
4493411 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATTGCGA
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATTGTAA
4493476 AGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCGCAAATAATACACCCAGACG
131 AGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCGCAAATAATACACCCAGACG
4493541 GTGCCGTTTTGTGGCCTTT-GGGGGGAC
196 GTGCCGTTTTGTGGCCTTTGGGGGGGAC
* * * * *
4493568 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGCTTATAAAAAAATGCC
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTAT-AAATAACGCC
* * *
4493633 GCAAATAATACTCCCAGACGGTGCCGTTTTGTGTCCTTTGGGGGG-CATTAGTGGCGTTTTTTGT
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGAC-TTAGTGGCGTTTATTGT
4493697 AAAGCGCCGCTAA
129 AAAGCGCCGCTAA
4493710 TCTAGGTGTT
Statistics
Matches: 343, Mismatches: 19, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
222 59 0.17
223 187 0.55
225 97 0.28
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (223 bp):
TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTATAAATAACGCCG
CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGACTTAGTGGCGTTTATTGTAA
AGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCGCAAATAATACACCCAGACG
GTGCCGTTTTGTGGCCTTTGGGGGGGAC
Found at i:4494339 original size:12 final size:12
Alignment explanation
Indices: 4494322--4494347 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4494312 ATATATAACT
4494322 GTAAAAGAGGTC
1 GTAAAAGAGGTC
4494334 GTAAAAGAGGTC
1 GTAAAAGAGGTC
4494346 GT
1 GT
4494348 GCTATTTTAA
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:0.38, C:0.08, G:0.35, T:0.19
Consensus pattern (12 bp):
GTAAAAGAGGTC
Found at i:4494861 original size:82 final size:83
Alignment explanation
Indices: 4494733--4494931 Score: 303
Period size: 82 Copynumber: 2.4 Consensus size: 83
4494723 TAGTTAAACT
* *
4494733 TTTAGTGGCGTTTTT-AAGAAAATGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGT
1 TTTAGTGGCGTTTTTCAA-AAAACG-CACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGT
4494797 TTCTGTTCACAGCTGTAATA
64 TTCTGTTCACAGCTGTAATA
* *
4494817 TTTAGTGGCGTTTTTCTAAAAACGCA-AAAAAATGCAATTCCAGACCACGAAAACGGTGTTGTTT
1 TTTAGTGGCGTTTTTCAAAAAACGCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTTT
4494881 CTGTTCACAGCTGTAATA
66 CTGTTCACAGCTGTAATA
*
4494899 TTTAGTGGCGTTTTTACCAAAAACGCCACAAAA
1 TTTAGTGGCGTTTTT-CAAAAAACG-CACAAAA
4494932 CGGTGTTAAT
Statistics
Matches: 106, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
82 69 0.65
83 10 0.09
84 22 0.21
85 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (83 bp):
TTTAGTGGCGTTTTTCAAAAAACGCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTTT
CTGTTCACAGCTGTAATA
Found at i:4495952 original size:11 final size:11
Alignment explanation
Indices: 4495915--4495954 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
4495905 GAATATCTCA
4495915 AACT-ATGGGT
1 AACTAATGGGT
*
4495925 AACTAGTGGGT
1 AACTAATGGGT
4495936 AACTAATGGGT
1 AACTAATGGGT
4495947 AACTAATG
1 AACTAATG
4495955 TATTATCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:4497319 original size:17 final size:17
Alignment explanation
Indices: 4497297--4497397 Score: 114
Period size: 17 Copynumber: 5.6 Consensus size: 17
4497287 GTTAAATTTA
4497297 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
4497314 TTACTAAAATAAATTAC
1 TTACTAAAATACATTAC
*
4497331 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
4497354 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
4497371 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
4497388 TTACTAAAAT
1 TTACTAAAAT
4497398 TTGTTTAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 16
0.80 0.02 0.17
Matches are distributed among these distances:
16 3 0.04
17 55 0.74
23 13 0.18
24 3 0.04
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.40
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:4497376 original size:57 final size:57
Alignment explanation
Indices: 4497288--4497430 Score: 250
Period size: 57 Copynumber: 2.5 Consensus size: 57
4497278 CGATTGAATG
4497288 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
*
4497345 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACTAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
* **
4497402 TTAAATTTATTACTTAAATATGTTACTTA
1 TTAAATTTATTACTAAAATACATTACTTA
4497431 AATTTATTAC
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 82 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (57 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
Found at i:4497420 original size:13 final size:13
Alignment explanation
Indices: 4497402--4497472 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
4497392 TAAAATTTGT
4497402 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
4497415 TTAAATATGTTAC
1 TTAAATTTATTAC
4497428 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
4497441 TTAAATATGTTAC
1 TTAAATTTATTAC
4497454 TTAAATTTATTAC
1 TTAAATTTATTAC
4497467 TTAAAT
1 TTAAAT
4497473 AATTATAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (13 bp):
TTAAATTTATTAC
Found at i:4497438 original size:26 final size:26
Alignment explanation
Indices: 4497402--4497473 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
4497392 TAAAATTTGT
4497402 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
4497428 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
4497454 TTAAATTTATTACTTAAATA
1 TTAAATTTATTACTTAAATA
4497474 ATTATAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (26 bp):
TTAAATTTATTACTTAAATATGTTAC
Found at i:4497697 original size:35 final size:34
Alignment explanation
Indices: 4497658--4497771 Score: 86
Period size: 35 Copynumber: 3.2 Consensus size: 34
4497648 GACTATTAAA
4497658 ATAAAATGTTATTTTATTGAATATTATTAATAATT
1 ATAAAATGTTATTTTATT-AATATTATTAATAATT
*** * * * * *
4497693 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAA-A
1 ATAAAATGTTAT-T---TTATTAATATT-ATTAATAATT
4497731 ATAAAATGTTATTTTATTAAATATTATTAATAATT
1 ATAAAATGTTATTTTATT-AATATTATTAATAATT
4497766 ATAAAA
1 ATAAAA
4497772 AAATATGTGG
Statistics
Matches: 56, Mismatches: 16, Indels: 14
0.65 0.19 0.16
Matches are distributed among these distances:
34 10 0.18
35 20 0.36
36 1 0.02
37 1 0.02
38 14 0.25
39 10 0.18
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (34 bp):
ATAAAATGTTATTTTATTAATATTATTAATAATT
Found at i:4497702 original size:73 final size:73
Alignment explanation
Indices: 4497619--4497806 Score: 358
Period size: 73 Copynumber: 2.6 Consensus size: 73
4497609 TAAAATAAAA
* *
4497619 TATAAAAAAATATGTGGAATACTAAAATTGACTATTAAAATAAAATGTTATTTTATTGAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
4497684 TTAATAAT
66 TTAATAAT
4497692 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
4497757 TTAATAAT
66 TTAATAAT
4497765 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATA
4497807 TGTGGAATAA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 113 1.00
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (73 bp):
TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
TTAATAAT
Found at i:4497735 original size:38 final size:38
Alignment explanation
Indices: 4497620--4497806 Score: 124
Period size: 38 Copynumber: 5.1 Consensus size: 38
4497610 AAAATAAAAT
*
4497620 ATAAAAAAATATGTGGAATACTAAAATTGACTATTAAA
1 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
*** * * * * *
4497658 ATAAAATGTTAT-T---TTATTGAATATT-ATTAATAATT
1 ATAAAAAAATATGTGGAATATT-AAAATTGACTATTAA-A
4497693 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
1 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
*** * * * *
4497731 ATAAAATGTTAT-T---TTATTAAATATT-ATTAATAATT
1 ATAAAAAAATATGTGGAATATTAAA-ATTGACTATTAA-A
4497766 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
1 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
4497804 ATA
1 ATA
4497807 TGTGGAATAA
Statistics
Matches: 104, Mismatches: 31, Indels: 28
0.64 0.19 0.17
Matches are distributed among these distances:
34 22 0.21
35 26 0.25
36 2 0.02
37 2 0.02
38 29 0.28
39 23 0.22
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (38 bp):
ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
Found at i:4498067 original size:21 final size:21
Alignment explanation
Indices: 4498041--4498111 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
4498031 CTACAACTTA
* *
4498041 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
4498062 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
4498083 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
4498104 AAGCAGAG
1 AAGCAGAG
4498112 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:4498487 original size:41 final size:42
Alignment explanation
Indices: 4498434--4498723 Score: 186
Period size: 42 Copynumber: 6.9 Consensus size: 42
4498424 GTTTTTGTAT
* * *
4498434 AAAAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTG-TA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
* *
4498475 AAAAATGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTGAAA
* * ****
4498518 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCC
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
** * * ****
4498560 TTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTC
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
** * * * * * ****
4498602 CTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
* * * ****
4498644 ACAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
** * * *
4498686 CTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTT
4498724 TTTTCTAAGC
Statistics
Matches: 214, Mismatches: 33, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
41 32 0.15
42 149 0.70
43 33 0.15
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (42 bp):
AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
Found at i:4498661 original size:126 final size:126
Alignment explanation
Indices: 4498520--4498756 Score: 422
Period size: 126 Copynumber: 1.9 Consensus size: 126
4498510 ATTAGAAAAA
*
4498520 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCC-CTTAAGCGCCGCTAAAGAACATGTT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCTC-TAAGCGCCGCTAAAGAACATGAT
4498584 CTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC
65 CTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC
**
4498646 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCTCTAAGCGCCGCTAAAGAACATGATC
*
4498711 TTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTA
66 TTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTTA
4498757 ACGGCGTTTT
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
126 105 0.99
127 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (126 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCTCTAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC
Found at i:4498767 original size:42 final size:42
Alignment explanation
Indices: 4498523--4498767 Score: 368
Period size: 42 Copynumber: 5.8 Consensus size: 42
4498513 AGAAAAAAAA
**
4498523 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCTTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-TAAG
* *
4498565 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * * *
4498607 CGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC-AAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-CTAAG
4498649 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
4498691 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* *
4498733 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
4498768 GTTTGTAAAC
Statistics
Matches: 187, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
41 1 0.01
42 179 0.96
43 7 0.04
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:4499984 original size:3 final size:3
Alignment explanation
Indices: 4499976--4500021 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
4499966 GCAATGCCTC
4499976 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4500022 ATCATCTTTG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4506828 original size:15 final size:15
Alignment explanation
Indices: 4506808--4506838 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4506798 TGTATTAAAA
4506808 ATTATTTTTTAAATT
1 ATTATTTTTTAAATT
*
4506823 ATTATTTTTTATATT
1 ATTATTTTTTAAATT
4506838 A
1 A
4506839 ATCAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTATTTTTTAAATT
Found at i:4507402 original size:20 final size:19
Alignment explanation
Indices: 4507377--4507420 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
4507367 AGAATTTTTG
4507377 TTATGAATATTTTATAATAT
1 TTATGAAT-TTTTATAATAT
*
4507397 TTATG-ATTTTTTTAATAT
1 TTATGAATTTTTATAATAT
4507415 TT-TGAA
1 TTATGAA
4507421 AAAATTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 2 0.09
20 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
TTATGAATTTTTATAATAT
Found at i:4512656 original size:18 final size:18
Alignment explanation
Indices: 4512611--4512659 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
4512601 ATGTCACGTC
*
4512611 AATAAATAATT-TTAAAA
1 AATAAAAAATTATTAAAA
*
4512628 ATATAAAAAAATTATTCAAA
1 A-AT-AAAAAATTATTAAAA
4512648 AATAAAAAATTA
1 AATAAAAAATTA
4512660 ACATAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 11 0.41
19 9 0.33
20 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAAAATTATTAAAA
Found at i:4515349 original size:17 final size:17
Alignment explanation
Indices: 4515329--4515361 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4515319 TATAATTTTA
4515329 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
4515346 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
4515362 TATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:4517491 original size:52 final size:52
Alignment explanation
Indices: 4517420--4517669 Score: 368
Period size: 52 Copynumber: 4.9 Consensus size: 52
4517410 ATCAAGTGAC
*
4517420 AAAGTGATAGGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
4517472 AAAGTGATAAGTGATAGCTTCGACTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* * *
4517524 AAAGTGATAAGTGATAGCTTCTGCTATACTTATCTGATCAAGAGACAA-T--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
4517573 ---GTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
** *
4517622 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
4517670 AGTGATAAGT
Statistics
Matches: 178, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
46 41 0.23
47 1 0.01
51 1 0.01
52 135 0.76
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:4517601 original size:46 final size:46
Alignment explanation
Indices: 4517527--4517680 Score: 184
Period size: 46 Copynumber: 3.2 Consensus size: 46
4517517 CAAGTGGAAA
* * *
4517527 GTGATAAGTGATAGCTTCTGCTATACTTATCTGATCAAGAGACAAT
1 GTGATAAGTGATAGTTTCAGCTACACTTATCTGATCAAGAGACAAT
* *
4517573 GTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGTGACAAGT
1 GTGATAAGTGATAGTTTCAGCTACACTTATCTGATCAAGAGACAA-T
*
4517620 GAAAAGTGATAAGTGATAGCTTT-AGCTACACTTATCTGATCAAGAGACAAA
1 -----GTGATAAGTGATAG-TTTCAGCTACACTTATCTGATCAAGAGACAAT
4517671 GTGATAAGTG
1 GTGATAAGTG
4517681 GCTACACTTA
Statistics
Matches: 94, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
46 51 0.54
47 1 0.01
52 39 0.41
53 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (46 bp):
GTGATAAGTGATAGTTTCAGCTACACTTATCTGATCAAGAGACAAT
Found at i:4517602 original size:98 final size:98
Alignment explanation
Indices: 4517412--4517680 Score: 387
Period size: 98 Copynumber: 2.7 Consensus size: 98
4517402 TACTTATGAT
* * *
4517412 CAAGTGACAAAGTGATAGGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGGAAAGT
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCTGCTACACTTATCTGATCAAGAGACAA-T-----GT
4517477 GATAAGTGATAGCTTCGACTACACTTATCTGATCAAGTGA
59 GATAAGTGATAGCTTCGACTACACTTATCTGATCAAGTGA
* *
4517517 CAAGTGGAAAGTGATAAGTGATAGCTTCTGCTATACTTATCTGATCAAGAGACAATGTGATAAGT
1 CAAGTGAAAAGTGATAAGTGATAGCTTCTGCTACACTTATCTGATCAAGAGACAATGTGATAAGT
* *
4517582 GATAGTTTCGGCTACACTTATCTGATCAAGTGA
66 GATAGCTTCGACTACACTTATCTGATCAAGTGA
*
4517615 CAAGTGAAAAGTGATAAGTGATAGCTT-TAGCTACACTTATCTGATCAAGAGACAAAGTGATAAG
1 CAAGTGAAAAGTGATAAGTGATAGCTTCT-GCTACACTTATCTGATCAAGAGACAATGTGATAAG
4517679 TG
65 TG
4517681 GCTACACTTA
Statistics
Matches: 153, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
97 1 0.01
98 101 0.66
103 1 0.01
104 44 0.29
105 6 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (98 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCTGCTACACTTATCTGATCAAGAGACAATGTGATAAGT
GATAGCTTCGACTACACTTATCTGATCAAGTGA
Found at i:4517688 original size:37 final size:37
Alignment explanation
Indices: 4517644--4517752 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
4517634 GATAGCTTTA
4517644 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
4517681 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
4517718 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
4517753 ATCATACGTA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 12 0.17
36 4 0.06
37 53 0.77
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:4518330 original size:16 final size:16
Alignment explanation
Indices: 4518309--4518340 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4518299 TTGGTAATGC
4518309 CTCGTACCCTATTCCG
1 CTCGTACCCTATTCCG
4518325 CTCGTACCCTATTCCG
1 CTCGTACCCTATTCCG
4518341 GTGTTGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.44, G:0.12, T:0.31
Consensus pattern (16 bp):
CTCGTACCCTATTCCG
Found at i:4523581 original size:29 final size:30
Alignment explanation
Indices: 4523535--4523623 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 30
4523525 AAATATATAT
*
4523535 TTTTTATACTTTT-TAAATAATTTTAATG-A
1 TTTTTA-ACTTTTAAAAATAATTTTAATGAA
*
4523564 TTTTTAACTTTTAAAAATAACTTTT-TTGAA
1 TTTTTAACTTTTAAAAATAA-TTTTAATGAA
* * *
4523594 TTTTTAAAATTTGTAAAAATCATTTAAATG
1 TTTTT-AACTTT-TAAAAATAATTTTAATG
4523624 CTGATGTGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
28 6 0.12
29 14 0.29
30 10 0.21
31 8 0.17
32 10 0.21
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (30 bp):
TTTTTAACTTTTAAAAATAATTTTAATGAA
Found at i:4527365 original size:27 final size:29
Alignment explanation
Indices: 4527287--4527365 Score: 74
Period size: 33 Copynumber: 2.6 Consensus size: 29
4527277 CTGCAACGAT
*
4527287 ACCACTACCATCATCATCTGCACCAGTACCA
1 ACCA-TACCATCATCATCAGCACCA-TACCA
4527318 ACACAATCACCATCA-CGATCAGCACC-TA-CA
1 AC-C-AT-ACCATCATC-ATCAGCACCATACCA
4527348 ACCATACCATCATCATCA
1 ACCATACCATCATCATCA
4527366 TCTGCAACAA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
27 11 0.26
28 3 0.07
29 1 0.02
30 4 0.10
31 4 0.10
32 3 0.07
33 16 0.38
ACGTcount: A:0.37, C:0.41, G:0.05, T:0.18
Consensus pattern (29 bp):
ACCATACCATCATCATCAGCACCATACCA
Done.