Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 7 of 135
Found at i:3092898 original size:21 final size:21
Alignment explanation
Indices: 3092861--3092904 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3092851 AGTTTTTTAG
3092861 TTTAGTGCTTAAGGTTTATGAT
1 TTTAGTGCTTAAGGTTTA-GAT
*
3092883 TTTAGTG-TTTAGGTTTAGAT
1 TTTAGTGCTTAAGGTTTAGAT
3092903 TT
1 TT
3092905 AAAATTAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.20, C:0.02, G:0.23, T:0.55
Consensus pattern (21 bp):
TTTAGTGCTTAAGGTTTAGAT
Found at i:3093119 original size:32 final size:31
Alignment explanation
Indices: 3093074--3093135 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 31
3093064 GTTTAAAATG
*
3093074 AGTATGTTACTAATCTGAGCTCTCTCTTTTTA
1 AGTATGTTACTAATCTAAGCTCTCT-TTTTTA
*
3093106 AGTATGTTTCTAATCTAAGCTCTCTTTTTT
1 AGTATGTTACTAATCTAAGCTCTCTTTTTT
3093136 CTTAAATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50
Consensus pattern (31 bp):
AGTATGTTACTAATCTAAGCTCTCTTTTTTA
Found at i:3105328 original size:24 final size:24
Alignment explanation
Indices: 3105284--3105335 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3105274 AATCAATGTG
* * *
3105284 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAACAAATACT
*
3105308 AAATATATTATACTCACAAATACT
1 AAATATATTATACTAACAAATACT
3105332 AAAT
1 AAAT
3105336 CTTCTAGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATATATTATACTAACAAATACT
Found at i:3120287 original size:20 final size:19
Alignment explanation
Indices: 3120245--3120288 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
3120235 TGGTAGGGTT
* *
3120245 TAATTTTTTTTTTCTGGTT
1 TAATTTTTTTTTTCTAGTA
*
3120264 TAATTTTTATTTTTTTAGTA
1 TAATTTTT-TTTTTCTAGTA
3120284 TAATT
1 TAATT
3120289 ATGCTTTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.70
Consensus pattern (19 bp):
TAATTTTTTTTTTCTAGTA
Found at i:3121107 original size:21 final size:20
Alignment explanation
Indices: 3121063--3121108 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
3121053 ATATGTAAGT
*
3121063 AATTTTTTTAATGTGACATG
1 AATTTTTTTAATGTGACATC
3121083 AATTTTTTTAATG-GCACTATC
1 AATTTTTTTAATGTG-AC-ATC
3121104 AATTT
1 AATTT
3121109 ATCCTGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 15 0.65
21 7 0.30
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (20 bp):
AATTTTTTTAATGTGACATC
Found at i:3126928 original size:1 final size:1
Alignment explanation
Indices: 3126913--3126946 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
3126903 TTAGCCTCTC
* *
3126913 TTTTCTTTTTCTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3126947 GGGGGGGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:3131014 original size:17 final size:18
Alignment explanation
Indices: 3130984--3131032 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
3130974 TCAGAAAAAA
3130984 ATAATAAAGATTTTT-GCC
1 ATAA-AAAGATTTTTGGCC
*
3131002 ATAAAAAGGTTTTTGGCC
1 ATAAAAAGATTTTTGGCC
*
3131020 CTAAAAAAGATTT
1 AT-AAAAAGATTT
3131033 AAGTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 9 0.35
18 8 0.31
19 9 0.35
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (18 bp):
ATAAAAAGATTTTTGGCC
Found at i:3132568 original size:22 final size:22
Alignment explanation
Indices: 3132539--3132606 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
3132529 TGCACTAATG
3132539 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
3132561 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
3132583 AACAGAGAGCACTAACGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
3132605 AA
1 AA
3132607 TATCAGAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:3132636 original size:25 final size:25
Alignment explanation
Indices: 3132541--3132630 Score: 77
Period size: 22 Copynumber: 3.8 Consensus size: 25
3132531 CACTAATGAA
* *
3132541 CAGAGAGCACTAAAGTGCT--ATA-
1 CAGAGAGCACCAACGTGCTAAATAT
*
3132563 CAGAGAGCA-CAGATGTGCT-AA-A-
1 CAGAGAGCACCA-ACGTGCTAAATAT
*
3132585 CAGAGAGCACTAACGTGCTAAATAT
1 CAGAGAGCACCAACGTGCTAAATAT
*
3132610 CAGAGTGCACCAACGTGCTAA
1 CAGAGAGCACCAACGTGCTAA
3132631 TAATCAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.02
22 31 0.55
23 4 0.07
24 1 0.02
25 19 0.34
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAAATAT
Found at i:3134065 original size:37 final size:38
Alignment explanation
Indices: 3134004--3134136 Score: 119
Period size: 37 Copynumber: 3.5 Consensus size: 38
3133994 ACTAATATTA
* * *
3134004 TTATTATGGTTAGTTATTAGGATTAGTAAAACCCTAAT
1 TTATTATTGTTAGTTAGTATGATTAGTAAAACCCTAAT
* *****
3134042 TTATTATT-TTAGTTAGTATGATTA-TTAGTTTTTACAT
1 TTATTATTGTTAGTTAGTATGATTAGTAAAACCCTA-AT
* **
3134079 TATATTATTGTTAGTTATTATTTTTAGTAAAACCCTAA-
1 T-TATTATTGTTAGTTAGTATGATTAGTAAAACCCTAAT
3134117 TTATTATTGTTAGTTAGTAT
1 TTATTATTGTTAGTTAGTAT
3134137 TATTTTTAGT
Statistics
Matches: 72, Mismatches: 19, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
36 4 0.06
37 35 0.49
38 15 0.21
39 14 0.19
40 4 0.06
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (38 bp):
TTATTATTGTTAGTTAGTATGATTAGTAAAACCCTAAT
Found at i:3134098 original size:76 final size:77
Alignment explanation
Indices: 3134000--3134146 Score: 217
Period size: 76 Copynumber: 1.9 Consensus size: 77
3133990 AAAAACTAAT
3134000 ATTATTATTATGGTTAGTTATTAGGATTAGTAAAACCCTAATTTATTATT-TTAGTTAGTATGAT
1 ATTATTATTATGGTTAGTTATTAGGATTAGTAAAACCCTAA-TTATTATTGTTAGTTAGTATGAT
3134064 TATTAGTTTTTAC
65 TATTAGTTTTTAC
* *** *
3134077 ATTA-TATTATTGTTAGTTATTATTTTTAGTAAAACCCTAATTATTATTGTTAGTTAGTATTATT
1 ATTATTATTATGGTTAGTTATTAGGATTAGTAAAACCCTAATTATTATTGTTAGTTAGTATGATT
*
3134141 TTTAGT
66 ATTAGT
3134147 AAAAAACTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 8 0.13
76 51 0.81
77 4 0.06
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.53
Consensus pattern (77 bp):
ATTATTATTATGGTTAGTTATTAGGATTAGTAAAACCCTAATTATTATTGTTAGTTAGTATGATT
ATTAGTTTTTAC
Found at i:3134161 original size:76 final size:77
Alignment explanation
Indices: 3134002--3134179 Score: 211
Period size: 76 Copynumber: 2.4 Consensus size: 77
3133992 AAACTAATAT
* **
3134002 TATTATTATGGTTAGTTATTAGGATTAGTAAAACCCTAATTTATTATTTTAGTTAGTATGATTAT
1 TATTATTATTGTTAGTTATTATTATTAGTAAAACCCTAATTTATTATTTTAGTTAGTATGATTAT
*** * *
3134067 TAGTTTTTACAT
66 TAGTTAAAAAAC
* * *
3134079 TA-TATTATTGTTAGTTATTATTTTTAGTAAAACCCTAA-TTATTATTGTTAGTTAGTATTATTT
1 TATTATTATTGTTAGTTATTATTATTAGTAAAACCCTAATTTATTATT-TTAGTTAGTATGATTA
3134142 TTAG-TAAAAAAC
65 TTAGTTAAAAAAC
*
3134154 TATTATTATTATTA-TTATTATTATTA
1 TATTATTATTGTTAGTTATTATTATTA
3134180 TTATTATTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
75 24 0.28
76 60 0.70
77 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (77 bp):
TATTATTATTGTTAGTTATTATTATTAGTAAAACCCTAATTTATTATTTTAGTTAGTATGATTAT
TAGTTAAAAAAC
Found at i:3134162 original size:3 final size:3
Alignment explanation
Indices: 3134154--3134196 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3134144 AGTAAAAAAC
3134154 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3134197 GTGTTAGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3135790 original size:12 final size:12
Alignment explanation
Indices: 3135773--3135830 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
3135763 GAATGTGATT
3135773 GCTCGGGATCTG
1 GCTCGGGATCTG
*
3135785 GCTCGGGCTCTG
1 GCTCGGGATCTG
* * *
3135797 GCTTGGGCTCCG
1 GCTCGGGATCTG
* * *
3135809 GTTCGAGATCAG
1 GCTCGGGATCTG
3135821 GCTCGGGATC
1 GCTCGGGATC
3135831 AGGATCTGTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.09, C:0.28, G:0.40, T:0.24
Consensus pattern (12 bp):
GCTCGGGATCTG
Found at i:3138016 original size:155 final size:156
Alignment explanation
Indices: 3137451--3138159 Score: 1037
Period size: 148 Copynumber: 4.6 Consensus size: 156
3137441 ACTTCAAAAC
* * *
3137451 AAATTTAGTAAAAAAACCCTTATTTTGG-CATTTGTTCGTATTTTTCTTTTTTCCCGAATTTTAT
1 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTA----T-TTTTTTCTCGGATTTTAT
3137515 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
61 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTG
*
3137580 AAATGTATCAATTTAGTGTGTTTTTTTATAT
126 AAATGTATCAATTTAATGTGTTTTTTTATAT
*
3137611 AAATTTAGT-AAAAAACCCTTA------CCCTTTGTTAGTA-TTTTTTCTCGGATTTTATTACTT
1 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTT
3137668 TCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
66 TCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
*
3137733 TATCAATTTAGTGTGTTTTTTTATAT
131 TATCAATTTAATGTGTTTTTTTATAT
*
3137759 AAATTTAGT-AAAAAACCCTTA------CCCTTTGTTAGTA-TTTTTTCTCGGATTTTATTACTT
1 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTT
3137816 TCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACAT-ATCGTTTGAAAT
66 TCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAAT-GTTTGAAAT
* *
3137880 GTATTAATTTAATGTG-TTTTTTATGT
130 GTATCAATTTAATGTGTTTTTTTATAT
3137906 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTT
1 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTT
*
3137971 TCAAAAAATATAATATTTTCGTATTTTATTATTTTATATTATTTTAGTACAT-ATCGTTTGAAAT
66 TCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAAT-GTTTGAAAT
* *
3138035 GTATTAATTTAATGTG-TTTTTTATGT
130 GTATCAATTTAATGTGTTTTTTTATAT
*
3138061 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTCTCGAATTTTATT
1 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTA---TT-TTTTTCTCGGATTTTATT
* *
3138126 ACTTTAAAAAAATATACTATTTTCGTTTTTTATT
62 ACTTTCAAAAAATATACTATTTTCGTATTTTATT
3138160 TCTTTTCGTA
Statistics
Matches: 522, Mismatches: 13, Indels: 29
0.93 0.02 0.05
Matches are distributed among these distances:
147 20 0.04
148 256 0.49
154 22 0.04
155 153 0.29
158 2 0.00
159 60 0.11
160 9 0.02
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (156 bp):
AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTT
TCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
TATCAATTTAATGTGTTTTTTTATAT
Found at i:3138167 original size:17 final size:17
Alignment explanation
Indices: 3138145--3138177 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3138135 AAATATACTA
*
3138145 TTTTCGTTTTTTATTTC
1 TTTTCGTATTTTATTTC
3138162 TTTTCGTATTTTATTT
1 TTTTCGTATTTTATTT
3138178 TTTCATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTCGTATTTTATTTC
Found at i:3138389 original size:19 final size:20
Alignment explanation
Indices: 3138365--3138403 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3138355 TTTTTTACAT
3138365 AAATAATA-CAAAAAAATTA
1 AAATAATACCAAAAAAATTA
3138384 AAATAATACCAAAAAAATTA
1 AAATAATACCAAAAAAATTA
3138404 TCTTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAATACCAAAAAAATTA
Found at i:3138526 original size:6 final size:6
Alignment explanation
Indices: 3138477--3138523 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
3138467 TTTCCCGCGC
* *
3138477 CTCCTT CTCCTT CTCCTT CTCCTT CTTCTT CTTCTT CTCCTT -TCCTT
1 CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT
3138524 TTCTTTCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (6 bp):
CTCCTT
Found at i:3138554 original size:30 final size:29
Alignment explanation
Indices: 3138480--3138568 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
3138470 CCCGCGCCTC
* *
3138480 CTTCTCCTTCTCCTTCTCCTTCTTCTTCTT
1 CTTCTCCTT-TCCTTTTCTTTCTTCTTCTT
*
3138510 CTTCTCCTTTCCTTTTCTTTCTTTTTCTTT
1 CTTCTCCTTTCCTTTTCTTTCTTCTTC-TT
*
3138540 CTTCTCCTTTCCTTTT-TTTCTTCTCCTT
1 CTTCTCCTTTCCTTTTCTTTCTTCTTCTT
3138568 C
1 C
3138569 AGTCGAATCT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
28 3 0.06
29 23 0.43
30 27 0.51
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (29 bp):
CTTCTCCTTTCCTTTTCTTTCTTCTTCTT
Found at i:3138561 original size:19 final size:20
Alignment explanation
Indices: 3138526--3138567 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
3138516 CTTTCCTTTT
*
3138526 CTTTCTTTTTCTTTCTTCTC
1 CTTTCCTTTTCTTTCTTCTC
3138546 CTTTCCTTTT-TTTCTTCTC
1 CTTTCCTTTTCTTTCTTCTC
3138565 CTT
1 CTT
3138568 CAGTCGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
CTTTCCTTTTCTTTCTTCTC
Found at i:3150159 original size:71 final size:71
Alignment explanation
Indices: 3150043--3150188 Score: 292
Period size: 71 Copynumber: 2.1 Consensus size: 71
3150033 AAGGTAAGTA
3150043 AACATGATTTACTACTAGTTCATTTGGCTTAAATATTTATTTTTGAAAAAAAGCCACACTCTGAA
1 AACATGATTTACTACTAGTTCATTTGGCTTAAATATTTATTTTTGAAAAAAAGCCACACTCTGAA
3150108 GCCTCT
66 GCCTCT
3150114 AACATGATTTACTACTAGTTCATTTGGCTTAAATATTTATTTTTGAAAAAAAGCCACACTCTGAA
1 AACATGATTTACTACTAGTTCATTTGGCTTAAATATTTATTTTTGAAAAAAAGCCACACTCTGAA
3150179 GCCTCT
66 GCCTCT
3150185 AACA
1 AACA
3150189 AAATAGGGTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (71 bp):
AACATGATTTACTACTAGTTCATTTGGCTTAAATATTTATTTTTGAAAAAAAGCCACACTCTGAA
GCCTCT
Found at i:3151161 original size:27 final size:23
Alignment explanation
Indices: 3151112--3151162 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 23
3151102 AGAACCCATC
3151112 TAACAATAATTTTTTTATTTTAT
1 TAACAATAATTTTTTTATTTTAT
3151135 TAACAATAAATATTGTTTTATTATTAT
1 TAACAAT-AAT-TT-TTTTATT-TTAT
3151162 T
1 T
3151163 TAATCACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 7 0.29
24 3 0.12
25 2 0.08
26 7 0.29
27 5 0.21
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
TAACAATAATTTTTTTATTTTAT
Found at i:3155402 original size:31 final size:31
Alignment explanation
Indices: 3155367--3155498 Score: 138
Period size: 31 Copynumber: 4.1 Consensus size: 31
3155357 TGGTAGTTAA
3155367 ATTTCATACGTATTTTTAATGTAGTATTTAT
1 ATTTCATACGTATTTTTAATGTAGTATTTAT
*
3155398 ATTTCATACGTATTTTTAATGTAGTATTTACG
1 ATTTCATACGTATTTTTAATGTAGTATTTA-T
* * * * * * * * *
3155430 ATTTTTAAAGCTTAATATATAATTTGGTAGTTAA
1 A-TTTCATA-CGT-ATTTTTAATGTAGTATTTAT
3155464 ATTTCATACGTATTTTTAATGTAGTATTTAT
1 ATTTCATACGTATTTTTAATGTAGTATTTAT
3155495 ATTT
1 ATTT
3155499 TTTTTATTAA
Statistics
Matches: 78, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
31 48 0.62
32 3 0.04
33 10 0.13
34 3 0.04
35 14 0.18
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (31 bp):
ATTTCATACGTATTTTTAATGTAGTATTTAT
Found at i:3162783 original size:31 final size:31
Alignment explanation
Indices: 3162733--3162817 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
3162723 CCTTTTTACA
*
3162733 AATTTAAATATAATAATAAATAAGAATTAAAT
1 AATTT-AATATAATGATAAATAAGAATTAAAT
* * * *
3162765 AATTTAATATTATGATAAATTATATTTAAAT
1 AATTTAATATAATGATAAATAAGAATTAAAT
* *
3162796 AATTTATTATAATGATACATAA
1 AATTTAATATAATGATAAATAA
3162818 AATATTAGTC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 39 0.89
32 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (31 bp):
AATTTAATATAATGATAAATAAGAATTAAAT
Found at i:3163911 original size:126 final size:125
Alignment explanation
Indices: 3163677--3164151 Score: 632
Period size: 126 Copynumber: 3.8 Consensus size: 125
3163667 AGTCACGCCT
* * * * *
3163677 ACGTTTCTAAGCAAATAGTTTAAAAAACGCTTCAAACAGGATGCTTTGTGAGAAGAATTTGTGAA
1 ACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATGAGAAGAATTTGTGAA
* * * * * * *
3163742 ATCGGGCCCTCATGAACGCGCTTTTACTACAGTTGGTCTTGAAAGAAATAATTTCGAGTTG
66 ATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAA-AAATAATTTCGAGTTG
* * *
3163803 ACGTTTTTGAGCAAATAGTTTAAAAAACGCTTCAAGCAAGATGCTTTATAAGAAGAATTTGTGAA
1 ACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATGAGAAGAATTTGTGAA
* * *
3163868 GTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTT
66 ATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTG
* *
3163928 ATGTTTCTGAGCAAATAGTATAAAACAACGCTGCAAGC-AGCATGCTATT-TGAGAAGAATTTGT
1 ACGTTTCTGAGCAAATAGTATAAAA-AACGCTTCAAGCAAG-ATGCT-TTATGAGAAGAATTTGT
* * * * *
3163991 GAAATCGCGCCCTCGTGGACGCACTTTTGCTACAGTTGGTCCTGGAAAAATAATTTCGACTTG
63 GAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTG
** * *
3164054 ACGTTTCTGAGCAAATAGTAT-AAAATTGCTTCTAGCAAAATGCTTTATGAGAAGAATTTGTGAA
1 ACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATGAGAAGAATTTGTGAA
3164118 ATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
66 ATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
3164152 ACATGTTTGG
Statistics
Matches: 306, Mismatches: 38, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
123 2 0.01
124 61 0.20
125 42 0.14
126 199 0.65
127 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (125 bp):
ACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATGAGAAGAATTTGTGAA
ATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTG
Found at i:3164137 original size:250 final size:251
Alignment explanation
Indices: 3163679--3164151 Score: 718
Period size: 250 Copynumber: 1.9 Consensus size: 251
3163669 TCACGCCTAC
* * *
3163679 GTTTCTAAGCAAATAGTTTAAAAAACGCTTCAAACAGGATGCTTTGTGAGAAGAATTTGTGAAAT
1 GTTTCTAAGCAAATAGTATAAAAAACGCTGCAAACAGCATGCTTTGTGAGAAGAATTTGTGAAAT
* * * *
3163744 CGGGCCCTCATGAACGCGCTTTTACTACAGTTGGTCTTGAAAGAAATAATTTCGAGTTGACGTTT
66 CGCGCCCTCATGAACGCACTTTTACTACAGTTGGTCCTGAAAGAAATAATTTCGACTTGACGTTT
* * * *
3163809 TTGAGCAAATAGTTTAAAAAACGCTTCAAGCAAGATGCTTTATAAGAAGAATTTGTGAAGTCGCG
131 CTGAGCAAATAGTATAAAAAACGCTTCAAGCAAAATGCTTTATAAGAAGAATTTGTGAAATCGCG
3163874 CCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTTAT
196 CCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTTAT
* *
3163930 GTTTCTGAGCAAATAGTATAAAACAACGCTGCAAGCAGCATGCTATT-TGAGAAGAATTTGTGAA
1 GTTTCTAAGCAAATAGTATAAAA-AACGCTGCAAACAGCATGCT-TTGTGAGAAGAATTTGTGAA
* * * *
3163994 ATCGCGCCCTCGTGGACGCACTTTTGCTACAGTTGGTCCTGGAA-AAATAATTTCGACTTGACGT
64 ATCGCGCCCTCATGAACGCACTTTTACTACAGTTGGTCCTGAAAGAAATAATTTCGACTTGACGT
** * *
3164058 TTCTGAGCAAATAGTAT-AAAATTGCTTCTAGCAAAATGCTTTATGAGAAGAATTTGTGAAATCG
129 TTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAAATGCTTTATAAGAAGAATTTGTGAAATCG
3164122 CGCCCACGTGGACGCGCTTTTGCTACAGTA
194 CGCCCACGTGGACGCGCTTTTGCTACAGTA
3164152 ACATGTTTGG
Statistics
Matches: 199, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
250 71 0.36
251 55 0.28
252 71 0.36
253 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (251 bp):
GTTTCTAAGCAAATAGTATAAAAAACGCTGCAAACAGCATGCTTTGTGAGAAGAATTTGTGAAAT
CGCGCCCTCATGAACGCACTTTTACTACAGTTGGTCCTGAAAGAAATAATTTCGACTTGACGTTT
CTGAGCAAATAGTATAAAAAACGCTTCAAGCAAAATGCTTTATAAGAAGAATTTGTGAAATCGCG
CCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTTAT
Found at i:3165950 original size:27 final size:27
Alignment explanation
Indices: 3165912--3165966 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3165902 ACTCATCAGC
*
3165912 ATCATCTGAAAAGGA-GGTTGCGTGGGT
1 ATCATCT-AAAAAGACGGTTGCGTGGGT
*
3165939 ATCATCTAAAAAGACGGTTGCGTTGGT
1 ATCATCTAAAAAGACGGTTGCGTGGGT
3165966 A
1 A
3165967 ACACAGGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (27 bp):
ATCATCTAAAAAGACGGTTGCGTGGGT
Found at i:3166757 original size:20 final size:20
Alignment explanation
Indices: 3166720--3166757 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3166710 TTTATTTTTA
*
3166720 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
3166740 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
3166758 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:3167785 original size:22 final size:21
Alignment explanation
Indices: 3167760--3167814 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
3167750 TATGGATTTT
*
3167760 AGAGAAATTTTGAAGGAAATTG
1 AGAGAAATTTAGAA-GAAATTG
3167782 AGAGCAAATTTAGAAGAAATTG
1 AGAG-AAATTTAGAAGAAATTG
3167804 AGAGGAAATTT
1 AGA-GAAATTT
3167815 GAGATAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.47, C:0.02, G:0.25, T:0.25
Consensus pattern (21 bp):
AGAGAAATTTAGAAGAAATTG
Found at i:3167818 original size:12 final size:12
Alignment explanation
Indices: 3167763--3167818 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
3167753 GGATTTTAGA
3167763 GAAATTTTGA-AG
1 GAAA-TTTGAGAG
3167775 GAAA-TTGAGAG
1 GAAATTTGAGAG
* *
3167786 CAAATTT-AGAA
1 GAAATTTGAGAG
3167797 GAAA-TTGAGAG
1 GAAATTTGAGAG
3167808 GAAATTTGAGA
1 GAAATTTGAGA
3167819 TAGGATTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 6 0.17
11 18 0.50
12 12 0.33
ACGTcount: A:0.46, C:0.02, G:0.27, T:0.25
Consensus pattern (12 bp):
GAAATTTGAGAG
Found at i:3171027 original size:22 final size:23
Alignment explanation
Indices: 3170963--3171027 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
3170953 AATAATTAAA
* *
3170963 TAAATAATTATTTTTAAAGTGCG
1 TAAATAAATATTTTTAAATTGCG
*
3170986 TAAATAAATATTTTTCAATTGTCG
1 TAAATAAATATTTTTAAATTG-CG
*
3171010 TATATAAA-A-TTTTAAATT
1 TAAATAAATATTTTTAAATT
3171028 ATGTTTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.22
23 19 0.53
24 9 0.25
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.46
Consensus pattern (23 bp):
TAAATAAATATTTTTAAATTGCG
Found at i:3175618 original size:5 final size:5
Alignment explanation
Indices: 3175608--3175645 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
3175598 AAAGGAAATA
*
3175608 AAAAG AAAAG AAAAG AAAAG AAAAG AAGAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
3175646 GAGATATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3180723 original size:14 final size:14
Alignment explanation
Indices: 3180706--3180740 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3180696 TTTTTAAGAT
*
3180706 AAATTTTCATATAA
1 AAATTTTAATATAA
3180720 AAATTTTAATATAA
1 AAATTTTAATATAA
3180734 ATAATTT
1 A-AATTT
3180741 ATCTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATTTTAATATAA
Found at i:3181248 original size:295 final size:295
Alignment explanation
Indices: 3180718--3181302 Score: 1170
Period size: 295 Copynumber: 2.0 Consensus size: 295
3180708 ATTTTCATAT
3180718 AAAAATTTTAATATAAATAATTTATCTTTATATCATTAATAAGTTCAAATTAATTTAAAATAAAT
1 AAAAATTTTAATATAAATAATTTATCTTTATATCATTAATAAGTTCAAATTAATTTAAAATAAAT
3180783 AAAATTTCTAAAAACCGTTCAAACATTTCCAATTTTATTACACCGATTCACGTATTTCGTATAGG
66 AAAATTTCTAAAAACCGTTCAAACATTTCCAATTTTATTACACCGATTCACGTATTTCGTATAGG
3180848 GTTCTTTTCTTTTCCCTGGATGAAACATCGTCTTTTCGTTAACGCCAGTTTTTCATGTTATAAAA
131 GTTCTTTTCTTTTCCCTGGATGAAACATCGTCTTTTCGTTAACGCCAGTTTTTCATGTTATAAAA
3180913 CAAGGCCACCATTTCATCGCTTTTTCCAGAATAAGGAATCATTTGAATTGAATCCCCCACCAAAT
196 CAAGGCCACCATTTCATCGCTTTTTCCAGAATAAGGAATCATTTGAATTGAATCCCCCACCAAAT
3180978 CATAGAAACAATATGTTTTCAGCAATCAGAATTAA
261 CATAGAAACAATATGTTTTCAGCAATCAGAATTAA
3181013 AAAAATTTTAATATAAATAATTTATCTTTATATCATTAATAAGTTCAAATTAATTTAAAATAAAT
1 AAAAATTTTAATATAAATAATTTATCTTTATATCATTAATAAGTTCAAATTAATTTAAAATAAAT
3181078 AAAATTTCTAAAAACCGTTCAAACATTTCCAATTTTATTACACCGATTCACGTATTTCGTATAGG
66 AAAATTTCTAAAAACCGTTCAAACATTTCCAATTTTATTACACCGATTCACGTATTTCGTATAGG
3181143 GTTCTTTTCTTTTCCCTGGATGAAACATCGTCTTTTCGTTAACGCCAGTTTTTCATGTTATAAAA
131 GTTCTTTTCTTTTCCCTGGATGAAACATCGTCTTTTCGTTAACGCCAGTTTTTCATGTTATAAAA
3181208 CAAGGCCACCATTTCATCGCTTTTTCCAGAATAAGGAATCATTTGAATTGAATCCCCCACCAAAT
196 CAAGGCCACCATTTCATCGCTTTTTCCAGAATAAGGAATCATTTGAATTGAATCCCCCACCAAAT
3181273 CATAGAAACAATATGTTTTCAGCAATCAGA
261 CATAGAAACAATATGTTTTCAGCAATCAGA
3181303 TCAAAGCAGT
Statistics
Matches: 290, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
295 290 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (295 bp):
AAAAATTTTAATATAAATAATTTATCTTTATATCATTAATAAGTTCAAATTAATTTAAAATAAAT
AAAATTTCTAAAAACCGTTCAAACATTTCCAATTTTATTACACCGATTCACGTATTTCGTATAGG
GTTCTTTTCTTTTCCCTGGATGAAACATCGTCTTTTCGTTAACGCCAGTTTTTCATGTTATAAAA
CAAGGCCACCATTTCATCGCTTTTTCCAGAATAAGGAATCATTTGAATTGAATCCCCCACCAAAT
CATAGAAACAATATGTTTTCAGCAATCAGAATTAA
Found at i:3189242 original size:17 final size:16
Alignment explanation
Indices: 3189207--3189236 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3189197 TTTAATCGTA
3189207 TCTTTTTTTTCTTTTT
1 TCTTTTTTTTCTTTTT
3189223 TCTTTTTTTT-TTTT
1 TCTTTTTTTTCTTTT
3189237 AATTCTCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TCTTTTTTTTCTTTTT
Found at i:3191253 original size:3 final size:3
Alignment explanation
Indices: 3191245--3191274 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3191235 ATGATCGGTT
3191245 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3191275 ACATTTTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3191267 original size:14 final size:14
Alignment explanation
Indices: 3191248--3191274 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3191238 ATCGGTTATA
3191248 ATAATAATAATAAT
1 ATAATAATAATAAT
3191262 ATAATAATAATAA
1 ATAATAATAATAA
3191275 ACATTTTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:3209053 original size:17 final size:17
Alignment explanation
Indices: 3209033--3209066 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3209023 TATATTTATT
*
3209033 TTTTAAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
3209050 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
3209067 AATACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:3209204 original size:11 final size:11
Alignment explanation
Indices: 3209157--3209215 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
3209147 GCTTATGAAT
3209157 TTTTTCAAAATA
1 TTTTT-AAAATA
3209169 CTTTTTAAAATA
1 -TTTTTAAAATA
*
3209181 TTTTT---TTA
1 TTTTTAAAATA
*
3209189 ATTTTAAAATA
1 TTTTTAAAATA
3209200 TTTTTAAAATA
1 TTTTTAAAATA
3209211 TTTTT
1 TTTTT
3209216 TTTATTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 6 0.15
11 22 0.56
12 6 0.15
13 5 0.13
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:3209205 original size:30 final size:32
Alignment explanation
Indices: 3209158--3209230 Score: 114
Period size: 31 Copynumber: 2.3 Consensus size: 32
3209148 CTTATGAATT
3209158 TTTTCAAAATACTTTTTAAAATA-TTTTTTTAA
1 TTTT-AAAATACTTTTTAAAATATTTTTTTTAA
*
3209190 TTTTAAAATA-TTTTTAAAATATTTTTTTTAT
1 TTTTAAAATACTTTTTAAAATATTTTTTTTAA
3209221 TTTTAAAATA
1 TTTTAAAATA
3209231 AATTTTTGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 11 0.28
31 24 0.62
32 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (32 bp):
TTTTAAAATACTTTTTAAAATATTTTTTTTAA
Found at i:3209236 original size:20 final size:21
Alignment explanation
Indices: 3209198--3209251 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
3209188 AATTTTAAAA
* *
3209198 TATTTTTAAAAT-ATTTTTTT
1 TATTTTTAAAATAAATTTTTG
3209218 TATTTTTAAAATAAATTTTTGG
1 TATTTTTAAAATAAATTTTT-G
3209240 TATTTATTAAAA
1 TATTT-TTAAAA
3209252 ATAGGCCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.41
21 6 0.21
22 5 0.17
23 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:3223162 original size:20 final size:20
Alignment explanation
Indices: 3223137--3223176 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3223127 AATATTTTCC
*
3223137 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3223157 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3223177 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3223182 original size:34 final size:35
Alignment explanation
Indices: 3223125--3223191 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3223115 CAAACACCGG
*
3223125 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3223160 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3223192 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3225397 original size:67 final size:67
Alignment explanation
Indices: 3225289--3225420 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
3225279 TTTCCAATTC
3225289 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
3225354 CA
66 CA
* * * *
3225356 AGAGAGCACACTCCTGCGTACCTTATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
3225421 TAATATAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.22
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:3225637 original size:57 final size:59
Alignment explanation
Indices: 3225549--3225688 Score: 187
Period size: 57 Copynumber: 2.4 Consensus size: 59
3225539 TTCGGATTAT
*
3225549 CCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A-GATCAC
1 CCGTCCGGGCTAGATCC-TTTTCCACATATTCTTCGGGAGGGCTATATCGATAGGATCAC
* * *
3225606 CCGTCTGGGCTAGATTCTTTTCACATATATTCTTCGGGAGGGCTATATCAGGATAGGATCAC
1 CCGTCCGGGCTAGATCCTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATAGGATCAC
3225668 CCGTCCGGGCTAGATCCTTTT
1 CCGTCCGGGCTAGATCCTTTT
3225689 TACCGTCAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
56 5 0.07
57 39 0.55
60 1 0.01
61 1 0.01
62 25 0.35
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (59 bp):
CCGTCCGGGCTAGATCCTTTTCCACATATTCTTCGGGAGGGCTATATCGATAGGATCAC
Found at i:3229559 original size:2 final size:2
Alignment explanation
Indices: 3229552--3229586 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3229542 AATAATACTA
*
3229552 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3229587 GGATTTGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3233784 original size:42 final size:42
Alignment explanation
Indices: 3233727--3233807 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
3233717 GGAAGCTCGT
3233727 AAGAGCTGAACGAAAACCCATAAGGGTTAAACAAAAGCTTAA
1 AAGAGCTGAACGAAAACCCATAAGGGTTAAACAAAAGCTTAA
* * *
3233769 AAGAGTTGAATGAAAACCCATAAGGGTTAAACAGAAGCT
1 AAGAGCTGAACGAAAACCCATAAGGGTTAAACAAAAGCT
3233808 CGTGAGAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.16
Consensus pattern (42 bp):
AAGAGCTGAACGAAAACCCATAAGGGTTAAACAAAAGCTTAA
Found at i:3235552 original size:26 final size:26
Alignment explanation
Indices: 3235516--3235567 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
3235506 CAAGGTTCTC
3235516 TATGTATATGTTGAAATAAACTGTGA
1 TATGTATATGTTGAAATAAACTGTGA
*
3235542 TATGTATATGTTGGAATAAACTGTGA
1 TATGTATATGTTGAAATAAACTGTGA
3235568 AGATTCTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (26 bp):
TATGTATATGTTGAAATAAACTGTGA
Found at i:3236956 original size:21 final size:21
Alignment explanation
Indices: 3236932--3236975 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3236922 TTACAAACAC
*
3236932 AAAATTACAATATTCATATAA
1 AAAATTACAATATTCATACAA
3236953 AAAATTACAATATTCATACAA
1 AAAATTACAATATTCATACAA
3236974 AA
1 AA
3236976 TACTAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATTACAATATTCATACAA
Found at i:3237028 original size:19 final size:19
Alignment explanation
Indices: 3237009--3237046 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3236999 AAATTTAATT
3237009 ATAAAATAATTACAATATTA
1 ATAAAA-AATTACAATATTA
*
3237029 ATACAAAATTACAATATT
1 ATAAAAAATTACAATATT
3237047 CATTGGCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAAATTACAATATTA
Found at i:3237083 original size:27 final size:27
Alignment explanation
Indices: 3237045--3237111 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
3237035 AATTACAATA
3237045 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
3237072 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
3237099 TTCATTGGCGCCT
1 TTCATTGGCGCCT
3237112 ACCTGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:3237218 original size:17 final size:17
Alignment explanation
Indices: 3237196--3237228 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3237186 AAAAAAATAT
3237196 AAAAAAATATT-TTATTC
1 AAAAAAA-ATTATTATTC
3237213 AAAAAAAATTATTATT
1 AAAAAAAATTATTATT
3237229 TTTTTATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAAAAATTATTATTC
Found at i:3250991 original size:38 final size:38
Alignment explanation
Indices: 3250940--3251017 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
3250930 TTTTGAGATT
3250940 TTATTTTCATTCACTTTTGGTCTTTCATAATTTCCATG
1 TTATTTTCATTCACTTTTGGTCTTTCATAATTTCCATG
3250978 TTATTTTCATTCACTTTTGGTCTTTCATAATTTCCATG
1 TTATTTTCATTCACTTTTGGTCTTTCATAATTTCCATG
3251016 TT
1 TT
3251018 CAAAGAGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.56
Consensus pattern (38 bp):
TTATTTTCATTCACTTTTGGTCTTTCATAATTTCCATG
Found at i:3260631 original size:2 final size:2
Alignment explanation
Indices: 3260624--3260679 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
3260614 GATCCAACAG
* * *
3260624 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TG TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3260666 TA TC TA TA TA TA TA
1 TA TA TA TA TA TA TA
3260680 GCTTCGTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3266723 original size:20 final size:20
Alignment explanation
Indices: 3266695--3266732 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3266685 AAATGTTAGC
*
3266695 TTAATTTAATTAAACTAAGT
1 TTAAGTTAATTAAACTAAGT
*
3266715 TTAAGTTAATTAAGCTAA
1 TTAAGTTAATTAAACTAA
3266733 ATTAATTAAA
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:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (20 bp):
TTAAGTTAATTAAACTAAGT
Found at i:3293729 original size:22 final size:21
Alignment explanation
Indices: 3293700--3293747 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
3293690 CCTTTCTCTT
*
3293700 TTTCTTTCCTTTTCT-CTTCTG
1 TTTCTTT-CTATTCTCCTTCTG
*
3293721 TTTCGTTTCTATTCTCCTTCTT
1 TTTC-TTTCTATTCTCCTTCTG
3293743 TTTCT
1 TTTCT
3293748 CTTATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.02, C:0.27, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTCTTTCTATTCTCCTTCTG
Found at i:3293768 original size:5 final size:5
Alignment explanation
Indices: 3293754--3293788 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
3293744 TTCTCTTATT
3293754 TAAT- TAATA TAATA TAATA TAATA T-ATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
3293789 TAAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:3293782 original size:14 final size:15
Alignment explanation
Indices: 3293754--3293788 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
3293744 TTCTCTTATT
3293754 TAAT-TAATATAATA
1 TAATATAATATAATA
3293768 TAATATAATAT-ATA
1 TAATATAATATAATA
3293782 TAATATA
1 TAATATA
3293789 TAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATATAATATAATA
Found at i:3293796 original size:19 final size:19
Alignment explanation
Indices: 3293760--3293798 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3293750 TATTTAATTA
*
3293760 ATATAATATAATATAATAT
1 ATATAATATAATAAAATAT
3293779 ATATAATAT-ATAAAA-AT
1 ATATAATATAATAAAATAT
3293796 ATA
1 ATA
3293799 CGATTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAATATAATAAAATAT
Found at i:3294713 original size:16 final size:16
Alignment explanation
Indices: 3294692--3294730 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
3294682 TTCACAATAA
3294692 AGCAGTCCACCTGCGC
1 AGCAGTCCACCTGCGC
3294708 AGCAGTCCACCTGCGC
1 AGCAGTCCACCTGCGC
3294724 AGCAGTC
1 AGCAGTC
3294731 ACTAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.21, C:0.41, G:0.26, T:0.13
Consensus pattern (16 bp):
AGCAGTCCACCTGCGC
Found at i:3296179 original size:17 final size:19
Alignment explanation
Indices: 3296142--3296186 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3296132 TTTTATTCTC
3296142 ATTTCATCAATAAATATAT
1 ATTTCATCAATAAATATAT
3296161 ATTTCATC-ATACAATATAT
1 ATTTCATCAATA-AATATAT
*
3296180 AATTCAT
1 ATTTCAT
3296187 GAATTTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTCATCAATAAATATAT
Found at i:3297847 original size:18 final size:17
Alignment explanation
Indices: 3297824--3297860 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3297814 TTACGACTAT
3297824 TAAATATAAATGAAAAAA
1 TAAATATAAAT-AAAAAA
*
3297842 TAAATATGAATAAAAAA
1 TAAATATAAATAAAAAA
3297859 TA
1 TA
3297861 TCGCAGCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (17 bp):
TAAATATAAATAAAAAA
Found at i:3299558 original size:64 final size:65
Alignment explanation
Indices: 3299463--3299593 Score: 221
Period size: 64 Copynumber: 2.0 Consensus size: 65
3299453 AATTTCCTCC
3299463 TTGTTTGTCGAATTATCCCTAAAAGAACATTGCAATCAAGAATGGGTGTCAAT-CATTTTTTCCT
1 TTGTTTGTCGAATTATCCCTAAAAGAACATTGCAATCAAGAATGGGTGTC-ATCCATTTTTTCCT
3299527 G
65 G
* *
3299528 TTGTTTGTCGAATTAT-CCTTAAAGAACATTGTAATCAAGAATGGGTGTCATCCATTTTTTCCTG
1 TTGTTTGTCGAATTATCCCTAAAAGAACATTGCAATCAAGAATGGGTGTCATCCATTTTTTCCTG
3299592 TT
1 TT
3299594 CCATCGTGGA
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
63 2 0.03
64 45 0.71
65 16 0.25
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (65 bp):
TTGTTTGTCGAATTATCCCTAAAAGAACATTGCAATCAAGAATGGGTGTCATCCATTTTTTCCTG
Found at i:3300324 original size:236 final size:239
Alignment explanation
Indices: 3299896--3300385 Score: 815
Period size: 236 Copynumber: 2.0 Consensus size: 239
3299886 GAATCCATGC
* *
3299896 TTACTATTCAAAATTTAGCTTCCGACAGAGCTGTGGTTACTCAACAAGGCAGCTTCTTGGTCTCA
1 TTACCATTCAAAATTTAGCTTCAGACAGAGCTGTGGTTACTCAACAAGGCAGCTTCTTGGTCTCA
*
3299961 AATCATAGAAATAGGCAATAATGTCCTTTTTGAATGAAGATAAAATAGTAGAAGATTAAACTATA
66 AATCAT--AAAT----AAT-ATCTCCTTTTTGAATGAAGATAAAATAGTAGAAGATTAAACTATA
*
3300026 GAAACTCCACTGGCAAAATGTTGAAATAAAACTGGAAAGATCTATAGCTATTTGTCATCACTCGA
124 GAAACTCCAATGGCAAAATGTTGAAATAAAACTGGAAAGATCTATAGCTATTTGTCATCACTCGA
* * *
3300091 GGAACAACTTCTTGTCAGTATGATAATTATTTGGTCTGCTTTTGTCATTAA
189 GGAACAACTTCTTGACAATATGATAATTATTTGGTCTGCTTTTATCATTAA
3300142 TTACCATTCAAAATTTAGCTTCAGACAGAGCTGTGGTTACTCAACAAGGCAGCTTCTTGGTCTCA
1 TTACCATTCAAAATTTAGCTTCAGACAGAGCTGTGGTTACTCAACAAGGCAGCTTCTTGGTCTCA
*
3300207 AATCAT-AAT-AT-TCTCCTTTTTGAATGAAGATAAAATAGTAGAAGATTAAACTATTGAAACTC
66 AATCATAAATAATATCTCCTTTTTGAATGAAGATAAAATAGTAGAAGATTAAACTATAGAAACTC
3300269 CAATGGCAAAATGTTGAAATAAAACTGGAAAGATCTATAGCTATTTGTCATCACTCGAGGAACAA
131 CAATGGCAAAATGTTGAAATAAAACTGGAAAGATCTATAGCTATTTGTCATCACTCGAGGAACAA
*
3300334 CTTCTTGACAATATGATAGTTATTTGGTCTGCTTTTATCATTAA
196 CTTCTTGACAATATGATAATTATTTGGTCTGCTTTTATCATTAA
3300378 TTACCATT
1 TTACCATT
3300386 GTGATCTTTA
Statistics
Matches: 235, Mismatches: 9, Indels: 10
0.93 0.04 0.04
Matches are distributed among these distances:
236 161 0.69
238 2 0.01
243 3 0.01
246 69 0.29
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (239 bp):
TTACCATTCAAAATTTAGCTTCAGACAGAGCTGTGGTTACTCAACAAGGCAGCTTCTTGGTCTCA
AATCATAAATAATATCTCCTTTTTGAATGAAGATAAAATAGTAGAAGATTAAACTATAGAAACTC
CAATGGCAAAATGTTGAAATAAAACTGGAAAGATCTATAGCTATTTGTCATCACTCGAGGAACAA
CTTCTTGACAATATGATAATTATTTGGTCTGCTTTTATCATTAA
Found at i:3305659 original size:12 final size:12
Alignment explanation
Indices: 3305629--3305661 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3305619 ATGAATATAC
3305629 ATTTAAATT-TT
1 ATTTAAATTATT
*
3305640 ATTAAAATTATT
1 ATTTAAATTATT
3305652 ATTTAAATTA
1 ATTTAAATTA
3305662 AATTAATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTAAATTATT
Found at i:3311213 original size:9 final size:9
Alignment explanation
Indices: 3311199--3311254 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
3311189 TTTAAATTTT
3311199 AAATTTTAA
1 AAATTTTAA
3311208 AAATTTTAA
1 AAATTTTAA
* ** *
3311217 AGGATTACATT
1 A-AATTTTA-A
3311228 AAATTTT-A
1 AAATTTTAA
3311236 AAATTTTAA
1 AAATTTTAA
3311245 AAATTTTAA
1 AAATTTTAA
3311254 A
1 A
3311255 TTACCTAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
8 7 0.19
9 21 0.58
10 7 0.19
11 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (9 bp):
AAATTTTAA
Found at i:3322619 original size:14 final size:15
Alignment explanation
Indices: 3322598--3322627 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3322588 CTTACTTTTA
3322598 CTTTTTTTTCCCCAG
1 CTTTTTTTTCCCCAG
3322613 CTTTTTTTTCCCCAG
1 CTTTTTTTTCCCCAG
3322628 AAAACTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.33, G:0.07, T:0.53
Consensus pattern (15 bp):
CTTTTTTTTCCCCAG
Found at i:3327319 original size:33 final size:33
Alignment explanation
Indices: 3327249--3327322 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
3327239 GTTGTCACTC
* ** **
3327249 AAGACCATAGCTGGGCTATGGCATTTTAATGAA
1 AAGACCATAACTGGGCTATGGCACATTAAACAA
* *
3327282 AAGACCATAACTGGGTTATGGCACATTAAACAT
1 AAGACCATAACTGGGCTATGGCACATTAAACAA
3327315 AAGACCAT
1 AAGACCAT
3327323 GGTTGGACCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (33 bp):
AAGACCATAACTGGGCTATGGCACATTAAACAA
Found at i:3331144 original size:594 final size:594
Alignment explanation
Indices: 3330010--3331200 Score: 1870
Period size: 594 Copynumber: 2.0 Consensus size: 594
3330000 AAGTAATATC
* *
3330010 CGGCATGATATACAACATCCACACAAACTACACAATTAAACATATGATTAAAATACTAATTACAA
1 CGGCATGATATACAACATCCACACAAACTACACAATTAAAAACATGATTAAAATACTAATTACAA
* * *
3330075 CGTAATTTAATAAATAAATTGATTACATGACATTAATATAATTTAATTTTTTGATAATAAATTAC
66 CGTAATTTAATAAATAAACTAATTACATGACATTAATATAATTTAATTTTTTGAAAATAAATTAC
*
3330140 CCTATCCCGACGTATGCCTCGATCATCTGTTGGTATACAATTAGATTTTCTGACTTCCCAATGTT
131 CCTATCCCGACGTATGCCTCGATCATCTGTCGGTATACAATTAGATTTTCTGACTTCCCAATGTT
*
3330205 CGGACAAGTATTCCATCTAAAATATAAACTAAACTCTTTAGAAAATATTTTCGTGAAAAAAATAT
196 CGGACAAATATTCCATCTAAAATATAAACTAAACTCTTTAGAAAATATTTTCGTGAAAAAAATAT
* * * *
3330270 TGATCCAAGTTTTTTTTTTTTTTCACATATTCGCAAGTGGGAACACATGTACTTGATGACCCACT
261 TGATCAAAGTTTATTTTTTTTTTCACATATTCACAAGTGGGAACACATGTACTTGATAACCCACT
* *
3330335 GATGCTAGAAAAGGCATCCTGTATAGCGCTCAAGATTGTAGTAGTATCAGAAAACCACCTATATC
326 GATGCTAGAAAAGGCATCCTGTATAGCACTCAAGATTGTAGTAATATCAGAAAACCACCTATATC
* * * * *
3330400 GACAATTCTATGCTTTGTCCCCCGACAAAGTTCACGATATAGCATCGCTAGTACTGTTAAACCCC
391 GACAATTCTACGCCTTGTCCCCCGACAAAGCTCACGATATAGCATCGCTAGTACTATCAAACCCC
* * *
3330465 AGCTATAAGAACGGGCACATTGCAAATCACTTAGTAAAGGCAGGTATATAAAGTGGACTCTATTA
456 AGCTATAAGAACAGGCACATTGCAAATCACTCAATAAAGGCAGGTATATAAAGTGGACTCTATTA
*
3330530 TTATTGGAATCCAACATAAGTACCCCCTATAAGTTGTAGTATATAGGCTCGAGTAGCCTGTATCT
521 TTATTGGAATCCAACATAAGTACCCCCTATAAGTTGTAGTATATAGGCTCGAGCAGCCTGTATCT
*
3330595 TCTCCATGT
586 TCTCCATCT
* * *
3330604 CGGCGTGATATACAACATCCACACGAACTACATAATTAAAAACATGATTAAAATACTAATTACAA
1 CGGCATGATATACAACATCCACACAAACTACACAATTAAAAACATGATTAAAATACTAATTACAA
*
3330669 TGTAATTTAATAAATAAACTAATTACATGACATTAATATAATTTAATTTTTTGAAAATAAATTAC
66 CGTAATTTAATAAATAAACTAATTACATGACATTAATATAATTTAATTTTTTGAAAATAAATTAC
3330734 CCTATCCCCGACGTATGCCTCGATCATCTGTCGGTATACAATTAGAGTTTT-TGACTTCCCAATG
131 CCTAT-CCCGACGTATGCCTCGATCATCTGTCGGTATACAATTAGA-TTTTCTGACTTCCCAATG
* *
3330798 TTCGGACAAATATTCCATCTAAAATATAAACTAAGCTCTTTAGAAAATATTTTCGTGAAAGAAAT
194 TTCGGACAAATATTCCATCTAAAATATAAACTAAACTCTTTAGAAAATATTTTCGTGAAAAAAAT
3330863 ATTGATCAAAGTTTAATTTTTTTTTT-ACATATTCACAAGTGGGAACACATGTACTTGATAACCC
259 ATTGATCAAAGTTT-ATTTTTTTTTTCACATATTCACAAGTGGGAACACATGTACTTGATAACCC
* * * *
3330927 ACTGATGCTAGAAATGGCTTCCTGTATAGTACTCAAGATTGTA-TCAATATCA-AACAACCATCT
323 ACTGATGCTAGAAAAGGCATCCTGTATAGCACTCAAGATTGTAGT-AATATCAGAA-AACCACCT
* * **
3330990 ATATCGACAATTCTACGCCTT-TCCCCTGACAAAGCTCACGATATAGCGTCGCTAGTACTATCGG
386 ATATCGACAATTCTACGCCTTGTCCCCCGACAAAGCTCACGATATAGCATCGCTAGTACTATCAA
** * * *
3331054 ACCCTTGCTATAGGAACAGGCACATTGCAAATCACTCAATTAGGGCAGGTATATAAAGTGGACTC
451 ACCCCAGCTATAAGAACAGGCACATTGCAAATCACTCAATAAAGGCAGGTATATAAAGTGGACTC
* * * * *
3331119 TATTATTATTGGAATCCAGCATAAGTACTCCTTATAAGTTGTAGTTTATAGGCTTGAGCAGCCTG
516 TATTATTATTGGAATCCAACATAAGTACCCCCTATAAGTTGTAGTATATAGGCTCGAGCAGCCTG
*
3331184 TATCTTTTCCATCT
581 TATCTTCTCCATCT
3331198 CGG
1 CGG
3331201 TTGCATAATC
Statistics
Matches: 544, Mismatches: 48, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
594 296 0.54
595 234 0.43
596 14 0.03
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (594 bp):
CGGCATGATATACAACATCCACACAAACTACACAATTAAAAACATGATTAAAATACTAATTACAA
CGTAATTTAATAAATAAACTAATTACATGACATTAATATAATTTAATTTTTTGAAAATAAATTAC
CCTATCCCGACGTATGCCTCGATCATCTGTCGGTATACAATTAGATTTTCTGACTTCCCAATGTT
CGGACAAATATTCCATCTAAAATATAAACTAAACTCTTTAGAAAATATTTTCGTGAAAAAAATAT
TGATCAAAGTTTATTTTTTTTTTCACATATTCACAAGTGGGAACACATGTACTTGATAACCCACT
GATGCTAGAAAAGGCATCCTGTATAGCACTCAAGATTGTAGTAATATCAGAAAACCACCTATATC
GACAATTCTACGCCTTGTCCCCCGACAAAGCTCACGATATAGCATCGCTAGTACTATCAAACCCC
AGCTATAAGAACAGGCACATTGCAAATCACTCAATAAAGGCAGGTATATAAAGTGGACTCTATTA
TTATTGGAATCCAACATAAGTACCCCCTATAAGTTGTAGTATATAGGCTCGAGCAGCCTGTATCT
TCTCCATCT
Found at i:3332417 original size:312 final size:313
Alignment explanation
Indices: 3332076--3332701 Score: 1236
Period size: 312 Copynumber: 2.0 Consensus size: 313
3332066 GCTGTGGGAA
3332076 GGGACCATCCAAGTGTTTGTAATATAAAAAAAATAAAAAATCAAAGATACAAATTATTTAATACT
1 GGGACCATCCAAGTGTTTGTAATATAAAAAAAATAAAAAATCAAAGATACAAATTATTTAATACT
3332141 AACCTTTTAACACAAATATCACACCTTAATATTAAACATCTACTAATATAACTAATTATACTAAA
66 AACCTTTTAACACAAATATCACACCTTAATATTAAACATCTACTAATATAACTAATTATACTAAA
3332206 AAAATTTAAAACATACTTTTATTTTGATTTTCAAGGATAATAAGTACTAACCTCTTAACAAAATA
131 AAAATTTAAAACATACTTTTATTTTGATTTTCAAGGATAATAAGTACTAACCTCTTAACAAAATA
3332271 ACATACTTCAATAATACTAACCTACTATTAAAATAACTAATTACACAGAAATAAATAAATAAATA
196 ACATACTTCAATAATACTAACCTACTATTAAAATAACTAATTACACAGAAATAAATAAATAAATA
3332336 AATAAAGTAAAAAAAAAAAAAAACATAATAAAACAAAGGAA-GGAAGCTTACC
261 AATAAAGTAAAAAAAAAAAAAAACATAATAAAACAAAGGAAGGGAAGCTTACC
3332388 GGGACCATCCAAGTGTTTGTAATATAAAAAAAATAAAAAATCAAAGATACAAATTATTTAATACT
1 GGGACCATCCAAGTGTTTGTAATATAAAAAAAATAAAAAATCAAAGATACAAATTATTTAATACT
3332453 AACCTTTTAACACAAATATCACACCTTAATATTAAACATCTACTAATATAACTAATTATACTAAA
66 AACCTTTTAACACAAATATCACACCTTAATATTAAACATCTACTAATATAACTAATTATACTAAA
3332518 AAAATTTAAAACATACTTTTATTTTGATTTTCAAGGATAATAAGTACTAACCTCTTAACAAAATA
131 AAAATTTAAAACATACTTTTATTTTGATTTTCAAGGATAATAAGTACTAACCTCTTAACAAAATA
3332583 ACATACTTCAATAATACTAACCTACTATTAAAATAACTAATTACACAGAAATAAATAAATAAATA
196 ACATACTTCAATAATACTAACCTACTATTAAAATAACTAATTACACAGAAATAAATAAATAAATA
3332648 AATAAAGTAAAAAAAAAAAAAAACATAATAAAACAAAGGAAGGGGAAGCTTACC
261 AATAAAGTAAAAAAAAAAAAAAACATAATAAAACAAAGGAA-GGGAAGCTTACC
3332702 TTCGGTGGTG
Statistics
Matches: 312, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
312 301 0.96
314 11 0.04
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (313 bp):
GGGACCATCCAAGTGTTTGTAATATAAAAAAAATAAAAAATCAAAGATACAAATTATTTAATACT
AACCTTTTAACACAAATATCACACCTTAATATTAAACATCTACTAATATAACTAATTATACTAAA
AAAATTTAAAACATACTTTTATTTTGATTTTCAAGGATAATAAGTACTAACCTCTTAACAAAATA
ACATACTTCAATAATACTAACCTACTATTAAAATAACTAATTACACAGAAATAAATAAATAAATA
AATAAAGTAAAAAAAAAAAAAAACATAATAAAACAAAGGAAGGGAAGCTTACC
Found at i:3333767 original size:24 final size:24
Alignment explanation
Indices: 3333722--3333786 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
3333712 TGGTTTTACC
*
3333722 TGACTCATCAAAC-TTAAAGGACA
1 TGACTCAACAAACTTTAAAGGACA
* *
3333745 TTACTCAGCAAACTTTAAAGGACA
1 TGACTCAACAAACTTTAAAGGACA
3333769 TGACTCAACAAACTTTAA
1 TGACTCAACAAACTTTAA
3333787 CAAAAGATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 11 0.30
24 26 0.70
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.25
Consensus pattern (24 bp):
TGACTCAACAAACTTTAAAGGACA
Found at i:3333875 original size:24 final size:24
Alignment explanation
Indices: 3333846--3333898 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
3333836 AGATAAAGGA
3333846 CAACAAACTTTAAAGGACATGACT
1 CAACAAACTTTAAAGGACATGACT
3333870 CAACAAACTTTAAAGGACATGACT
1 CAACAAACTTTAAAGGACATGACT
3333894 CAACA
1 CAACA
3333899 GCTTTTCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (24 bp):
CAACAAACTTTAAAGGACATGACT
Found at i:3345428 original size:33 final size:34
Alignment explanation
Indices: 3345381--3345447 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
3345371 GCCAGACACG
*
3345381 ATAACAATGAATAAGATTAATTGGGTGA-TACGA
1 ATAAAAATGAATAAGATTAATTGGGTGATTACGA
3345414 ATAAAAATGAATAAGATTAATTGGGTGATTACGA
1 ATAAAAATGAATAAGATTAATTGGGTGATTACGA
3345448 GGCCTTACCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.28
Consensus pattern (34 bp):
ATAAAAATGAATAAGATTAATTGGGTGATTACGA
Found at i:3352995 original size:340 final size:342
Alignment explanation
Indices: 3352370--3353055 Score: 1358
Period size: 340 Copynumber: 2.0 Consensus size: 342
3352360 CCGATGTCCA
3352370 AATACAGTAGAATTATCTAAGCCTATAGTACTCGAACACGTGCCTGGTTAAGACGTTTTAATGAA
1 AATACAGTAGAATTATCTAAGCCTATAGTACTCGAACACGTGCCTGGTTAAGACGTTTTAATGAA
3352435 TTAATTACTGCTACATCTGTACATGAGTTAGAACTATCCCTTTAAACTCAACGTTAGCTCAAAAT
66 TTAATTACTGCTACATCTGTACATGAGTTAGAACTATCCCTTTAAACTCAACGTTAGCTCAAAAT
3352500 TTGAAATAGTTTTAGTAAAACTATTAAACCTGTAAAAAGTTAGACTCATTTAAAATATGGACTTA
131 TTGAAATAGTTTTAGTAAAACTATTAAACCTGTAAAAAGTTAGACTCATTTAAAATATGGACTTA
3352565 GTTTAGGCTTAAACATTTAAGACCAAGCTCGATCTTTTTTAAATTTATAATATTTTATATTATTT
196 GTTTAGGCTTAAACATTTAAGACCAAGCTCGATCTTTTTTAAATTTATAATATTTTATATTATTT
3352630 TTGTATACTATGTAATTTATAATGAATTAAAAAATAAATGTATGATAAATATATAATACTACTAT
261 TTGTATACTATGTAATTTATAATGAATTAAAAAATAAATGTATGATAAATATATAATACTACTAT
3352695 AATGTAAACA-TAAAAT
326 AATGTAAACATTAAAAT
3352711 AATA-AGTAGAATTATCTAAGCCTATAGTACTCGAACACGTGCCTGGTTAAGACGTTTTAATGAA
1 AATACAGTAGAATTATCTAAGCCTATAGTACTCGAACACGTGCCTGGTTAAGACGTTTTAATGAA
3352775 TTAATTACTGCTACATCTGTACATGAGTTAGAACTATCCCTTTAAACTCAACGTTAGCTCAAAAT
66 TTAATTACTGCTACATCTGTACATGAGTTAGAACTATCCCTTTAAACTCAACGTTAGCTCAAAAT
3352840 TTGAAATAGTTTTAGTAAAACTATTAAACCTGTAAAAAGTTAGACTCATTTAAAATATGGACTTA
131 TTGAAATAGTTTTAGTAAAACTATTAAACCTGTAAAAAGTTAGACTCATTTAAAATATGGACTTA
3352905 GTTTAGGCTTAAACATTTAAGACCAAGCTCGATCTTTTTTAAATTTATAATATTTTATATTATTT
196 GTTTAGGCTTAAACATTTAAGACCAAGCTCGATCTTTTTTAAATTTATAATATTTTATATTATTT
3352970 TTGTATACTATGTAATTTATAATGAATTAAAAAATAAATGTATGATAAATATATAATACTACTAT
261 TTGTATACTATGTAATTTATAATGAATTAAAAAATAAATGTATGATAAATATATAATACTACTAT
3353035 AATGTAAACATTAAAAT
326 AATGTAAACATTAAAAT
3353052 AATA
1 AATA
3353056 TTAAGATGAC
Statistics
Matches: 344, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
340 330 0.96
341 14 0.04
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (342 bp):
AATACAGTAGAATTATCTAAGCCTATAGTACTCGAACACGTGCCTGGTTAAGACGTTTTAATGAA
TTAATTACTGCTACATCTGTACATGAGTTAGAACTATCCCTTTAAACTCAACGTTAGCTCAAAAT
TTGAAATAGTTTTAGTAAAACTATTAAACCTGTAAAAAGTTAGACTCATTTAAAATATGGACTTA
GTTTAGGCTTAAACATTTAAGACCAAGCTCGATCTTTTTTAAATTTATAATATTTTATATTATTT
TTGTATACTATGTAATTTATAATGAATTAAAAAATAAATGTATGATAAATATATAATACTACTAT
AATGTAAACATTAAAAT
Found at i:3353103 original size:15 final size:16
Alignment explanation
Indices: 3353083--3353112 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3353073 AAAAGGTTAA
3353083 TAAATTAAAA-AATAT
1 TAAATTAAAATAATAT
3353098 TAAATTAAAATAATA
1 TAAATTAAAATAATA
3353113 GAAACGGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATTAAAATAATAT
Found at i:3362781 original size:24 final size:24
Alignment explanation
Indices: 3362729--3362774 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3362719 TAATCAAAGT
* *
3362729 TAAATATATTGTGCTAATAAATGA
1 TAAATATATTATACTAATAAATGA
*
3362753 TAAATATATTATACTCATAAAT
1 TAAATATATTATACTAATAAAT
3362775 ACTAAATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (24 bp):
TAAATATATTATACTAATAAATGA
Found at i:3380933 original size:3 final size:3
Alignment explanation
Indices: 3380927--3380957 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3380917 AATCTTGATG
3380927 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3380958 AGGGTGGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3383151 original size:125 final size:125
Alignment explanation
Indices: 3382930--3383222 Score: 417
Period size: 125 Copynumber: 2.4 Consensus size: 125
3382920 AACAAATAAG
* ** * * * *
3382930 TCGCGCCCACGTTTACGTGCTTTTACTACAGTAGGTCCT-GAAAAAATAATTTCGAGTTGATGTT
1 TCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTT
* * * * *
3382994 TCTAAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTGTTTGATAATAATTTGTGAAA
66 TCTAAGCAAATAGTATAAAATCACTTATAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
* *
3383054 TCGCGGCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGGAATAAATAATTTCGAGTTGACGTT
1 TCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTT
* *
3383119 TCTGAGCAAATAGTATAAAATCACTTATAGCAGGATGTTATTTGAGAAGAATTTGTGAAA
66 TCTAAGCAAATAGTATAAAATCACTTATAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
* *
3383179 TCGTGCCCTCGTGGACGCGCTTTTGCTATAGTGGGTCCTGGAAA
1 TCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGGAAA
3383223 TTGAGAGGAA
Statistics
Matches: 148, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
124 32 0.22
125 116 0.78
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (125 bp):
TCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTT
TCTAAGCAAATAGTATAAAATCACTTATAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
Found at i:3390842 original size:21 final size:21
Alignment explanation
Indices: 3390818--3390863 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3390808 ATCTATAAAA
3390818 AAATTAAT-TTTGTTAAACATT
1 AAATTAATATTT-TTAAACATT
3390839 AAA-TAATAATTTTTAAACATT
1 AAATTAAT-ATTTTTAAACATT
3390860 AAAT
1 AAAT
3390864 GACAACTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATTAATATTTTTAAACATT
Found at i:3391444 original size:17 final size:17
Alignment explanation
Indices: 3391422--3391455 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3391412 TATATACTTT
*
3391422 TTTTAAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
3391439 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
3391456 AATACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:3391486 original size:21 final size:21
Alignment explanation
Indices: 3391448--3391487 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3391438 ATTTTAAAAT
**
3391448 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
3391469 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
3391488 AGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:3391494 original size:22 final size:21
Alignment explanation
Indices: 3391447--3391505 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
3391437 AATTTTAAAA
* *
3391447 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
3391467 TAATTTTTAAAATAAATTTTTAG
1 T-ATTTTTAAAATAAATTTTT-G
3391490 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
3391506 GGGCCGGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:3395580 original size:101 final size:101
Alignment explanation
Indices: 3395399--3395596 Score: 360
Period size: 101 Copynumber: 2.0 Consensus size: 101
3395389 CCGTTGGAGT
* *
3395399 GTGACAAAAGAACCTCACATAAAAATATTTGGGAAAAATGAAGCATAATACAGTAGCTACCTTTT
1 GTGACAAAAGAACCTCACATAAAAATATTGGGGAAAAATCAAGCATAATACAGTAGCTACCTTTT
*
3395464 CTATTCGTAACATCAATAAACCCATTCTGCTTGAGG
66 CTATTCGTAAAATCAATAAACCCATTCTGCTTGAGG
3395500 GTGACAAAAGAACCTCACATAAAAATATTGGGGAAAAATCAAGCATAATACAGTAGCTACCTTTT
1 GTGACAAAAGAACCTCACATAAAAATATTGGGGAAAAATCAAGCATAATACAGTAGCTACCTTTT
*
3395565 CTATTCTTAAAATCAATAAACCCATTCTGCTT
66 CTATTCGTAAAATCAATAAACCCATTCTGCTT
3395597 AATTCTTTGT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 93 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (101 bp):
GTGACAAAAGAACCTCACATAAAAATATTGGGGAAAAATCAAGCATAATACAGTAGCTACCTTTT
CTATTCGTAAAATCAATAAACCCATTCTGCTTGAGG
Found at i:3396884 original size:6 final size:6
Alignment explanation
Indices: 3396873--3396898 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3396863 GAAGGTAAAT
3396873 CTGAGA CTGAGA CTGAGA CTGAGA CT
1 CTGAGA CTGAGA CTGAGA CTGAGA CT
3396899 CAAGGAGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (6 bp):
CTGAGA
Found at i:3399075 original size:1 final size:1
Alignment explanation
Indices: 3399071--3399123 Score: 97
Period size: 1 Copynumber: 53.0 Consensus size: 1
3399061 CAAGCAGAAC
*
3399071 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3399124 CCAAAGAGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.98, C:0.02, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3403657 original size:22 final size:22
Alignment explanation
Indices: 3403626--3403675 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
3403616 AAATAAATCC
3403626 TTTCTC-TAATTTCCCCTC-AA
1 TTTCTCTTAATTTCCCCTCAAA
*
3403646 TTTGCTCTTAATTTCCTCTCAAA
1 TTT-CTCTTAATTTCCCCTCAAA
3403669 TTTCTCT
1 TTTCTCT
3403676 CAAATCCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 3 0.12
22 15 0.58
23 5 0.19
ACGTcount: A:0.18, C:0.30, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTCTCTTAATTTCCCCTCAAA
Found at i:3406108 original size:13 final size:14
Alignment explanation
Indices: 3406090--3406123 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3406080 AGGTAATATG
3406090 TTGAATAT-TTATT
1 TTGAATATGTTATT
*
3406103 TTGAATATGTTTTT
1 TTGAATATGTTATT
3406117 TTGAATA
1 TTGAATA
3406124 AAGTAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (14 bp):
TTGAATATGTTATT
Found at i:3444854 original size:17 final size:17
Alignment explanation
Indices: 3444832--3444864 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3444822 CCAACAGTTG
3444832 GTAAAAAAAATGCGATA
1 GTAAAAAAAATGCGATA
3444849 GTAAAAAAAATGCGAT
1 GTAAAAAAAATGCGAT
3444865 GATTGCTTAC
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:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
GTAAAAAAAATGCGATA
Found at i:3457937 original size:26 final size:27
Alignment explanation
Indices: 3457870--3457937 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 27
3457860 AAATGATAAG
3457870 TACATAAAATCATGAAATTAAATTTGAAA
1 TACATAAAAT-ATGAAATT-AATTTGAAA
* *
3457899 TACATAGAA-ATGATAATT-ATTTGATA
1 TACATAAAATATGA-AATTAATTTGAAA
3457925 TAC-TAAAATATGA
1 TACATAAAATATGA
3457938 CATGGAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 4 0.12
26 14 0.41
27 4 0.12
28 4 0.12
29 8 0.24
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (27 bp):
TACATAAAATATGAAATTAATTTGAAA
Found at i:3458587 original size:46 final size:46
Alignment explanation
Indices: 3458520--3458781 Score: 470
Period size: 46 Copynumber: 5.7 Consensus size: 46
3458510 NNNNNNNNNN
3458520 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
1 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
3458566 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
1 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
3458612 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
1 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
*
3458658 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGA
1 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
* * *
3458704 GCTACCACTTATCATTTTGTCACTTGATCAGGTAAGTGTAGCTAGA
1 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
* *
3458750 GCTACCACTTATCACTTTATCTCTTGATCAGA
1 GCTACCACTTATCACTTTGTCACTTGATCAGA
3458782 AGTACTCAAA
Statistics
Matches: 209, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 209 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (46 bp):
GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
Found at i:3465835 original size:22 final size:21
Alignment explanation
Indices: 3465779--3465819 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3465769 AAATGTTTAT
3465779 ATTATAAA--AAATAAAAATA
1 ATTATAAATTAAATAAAAATA
3465798 ATTATAAATTAAATAAAAATA
1 ATTATAAATTAAATAAAAATA
3465819 A
1 A
3465820 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
ATTATAAATTAAATAAAAATA
Found at i:3466319 original size:11 final size:11
Alignment explanation
Indices: 3466290--3466319 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3466280 TAAAAGGTAA
3466290 AAAAAAAATTG
1 AAAAAAAATTG
*
3466301 AAACAAAATTG
1 AAAAAAAATTG
3466312 AAAAAAAA
1 AAAAAAAA
3466320 GAGGAGACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:3474103 original size:75 final size:75
Alignment explanation
Indices: 3474010--3474156 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 75
3474000 TTACAAACAA
*
3474010 CTAAGATAAAAAACCGAGTGGTTAAAAGGAAAAGAATTTTTAAATGATGAGCTACCTAGGATACT
1 CTAAGATAAAAAACCGAGTGGTTAAAAGGAAAACAATTTTTAAATGATGAGCTACCTAGGATACT
3474075 TCCCCAACCT
66 TCCCCAACCT
* * * *
3474085 CTAAGATAAAAAATCGAGTGGTTAAACGTAAAACAATTTTTAAATGATGCGCTACCTAGGATACT
1 CTAAGATAAAAAACCGAGTGGTTAAAAGGAAAACAATTTTTAAATGATGAGCTACCTAGGATACT
3474150 TCCCCAA
66 TCCCCAA
3474157 GCTTTTCATC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (75 bp):
CTAAGATAAAAAACCGAGTGGTTAAAAGGAAAACAATTTTTAAATGATGAGCTACCTAGGATACT
TCCCCAACCT
Found at i:3485288 original size:95 final size:96
Alignment explanation
Indices: 3485181--3485372 Score: 377
Period size: 95 Copynumber: 2.0 Consensus size: 96
3485171 TATAAATGGC
3485181 TGGATAGTTTTTTTTTTTTTAAATCAAAGTGGATCTTTTCTTGAGAGAAATATGCATCCCTCTGG
1 TGGATAGTTTTTTTTTTTTTAAATCAAAGTGGATCTTTTCTTGAGAGAAATATGCATCCCTCTGG
3485246 ATTGTTTTTTTAATATAATAA-AAAATTTTT
66 ATTGTTTTTTTAATATAATAATAAAATTTTT
3485276 TGGATAGTTTTTTTTTTTTTAAATCAAAGTGGATCTTTTCTTGAGAGAAATATGCATCCCTCTGG
1 TGGATAGTTTTTTTTTTTTTAAATCAAAGTGGATCTTTTCTTGAGAGAAATATGCATCCCTCTGG
3485341 ATTGTTTTTTTAATATAATAATAAAATTTTT
66 ATTGTTTTTTTAATATAATAATAAAATTTTT
3485372 T
1 T
3485373 TATAAAATTT
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 86 0.90
96 10 0.10
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (96 bp):
TGGATAGTTTTTTTTTTTTTAAATCAAAGTGGATCTTTTCTTGAGAGAAATATGCATCCCTCTGG
ATTGTTTTTTTAATATAATAATAAAATTTTT
Found at i:3486616 original size:13 final size:15
Alignment explanation
Indices: 3486586--3486618 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3486576 TTTAGTGACA
3486586 AAATAAAACAGAAAC
1 AAATAAAACAGAAAC
3486601 AAATAAAA-AG-AAC
1 AAATAAAACAGAAAC
3486614 AAATA
1 AAATA
3486619 CAAGAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 2 0.11
15 8 0.44
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (15 bp):
AAATAAAACAGAAAC
Found at i:3489026 original size:22 final size:23
Alignment explanation
Indices: 3488983--3489026 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3488973 ATATGACTTG
* *
3488983 TAATCTTAGAAGATATGATTTTA
1 TAATCTTAAAAAATATGATTTTA
3489006 TAATCTTAAAAAAT-TGATTTT
1 TAATCTTAAAAAATATGATTTT
3489027 GTAGATAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (23 bp):
TAATCTTAAAAAATATGATTTTA
Found at i:3491369 original size:2 final size:2
Alignment explanation
Indices: 3491357--3491392 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3491347 AATCTCCTCA
*
3491357 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3491393 ATAATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:3492467 original size:137 final size:137
Alignment explanation
Indices: 3492244--3492517 Score: 505
Period size: 137 Copynumber: 2.0 Consensus size: 137
3492234 CTCTGTTTTT
*
3492244 CTACCTTCTTTATCTCTTTTAATATACCAGAAAGTCGAATTGGAGTGAAAAAAAGAAGCATGGTA
1 CTACCTTCTTTATCTCTTTTAACATACCAGAAAGTCGAATTGGAGTGAAAAAAAGAAGCATGGTA
3492309 TGAGTTTATGGGTTTTGGTTATAGGCAAATGATGACAGTCGACTTCTTACTTCTTTTTTCATTGC
66 TGAGTTTATGGGTTTTGGTTATAGGCAAATGATGACAGTCGACTTCTTACTTCTTTTTTCATTGC
3492374 CAATTCA
131 CAATTCA
* *
3492381 CTACCTTCTTTATTTCTTTTAACATACCAGGAAGTCGAATTGGTAGTG-AAAAAAGAAGCATGGT
1 CTACCTTCTTTATCTCTTTTAACATACCAGAAAGTCGAATTGG-AGTGAAAAAAAGAAGCATGGT
3492445 ATGAGTTTATGGGTTTTGGTTATAGGCAAATGATGACAGTCGACTTCTTACTTCTTTTTTCATTG
65 ATGAGTTTATGGGTTTTGGTTATAGGCAAATGATGACAGTCGACTTCTTACTTCTTTTTTCATTG
3492510 CCAATTCA
130 CCAATTCA
3492518 ACTTCCTAAT
Statistics
Matches: 133, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
137 129 0.97
138 4 0.03
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (137 bp):
CTACCTTCTTTATCTCTTTTAACATACCAGAAAGTCGAATTGGAGTGAAAAAAAGAAGCATGGTA
TGAGTTTATGGGTTTTGGTTATAGGCAAATGATGACAGTCGACTTCTTACTTCTTTTTTCATTGC
CAATTCA
Found at i:3508108 original size:12 final size:12
Alignment explanation
Indices: 3508093--3508118 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3508083 TATAAGCTTG
3508093 ATATTCTTATTC
1 ATATTCTTATTC
3508105 ATATTCTTATTC
1 ATATTCTTATTC
3508117 AT
1 AT
3508119 CTCATATGGA
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:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATTCTTATTC
Found at i:3510446 original size:26 final size:25
Alignment explanation
Indices: 3510402--3510467 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 25
3510392 GAATATATAA
3510402 TAAATATATATTTTTATTTTTTAATTT
1 TAAA-ATAT-TTTTTATTTTTTAATTT
3510429 TAAAATATTTTTTAATTTTTTAATTT
1 TAAAATATTTTTT-ATTTTTTAATTT
3510455 TAAAATATTTTTT
1 TAAAATATTTTTT
3510468 GGTGTTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 5 0.13
26 29 0.76
27 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TAAAATATTTTTTATTTTTTAATTT
Found at i:3521128 original size:5 final size:5
Alignment explanation
Indices: 3521118--3521149 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
3521108 TTGGACACAG
3521118 TCAAA TCAAA TCAAA TCAAA TCAAA TCAAA TC
1 TCAAA TCAAA TCAAA TCAAA TCAAA TCAAA TC
3521150 CAAGAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (5 bp):
TCAAA
Found at i:3522765 original size:47 final size:47
Alignment explanation
Indices: 3522712--3522851 Score: 148
Period size: 47 Copynumber: 3.0 Consensus size: 47
3522702 TTAATAATGA
*
3522712 TATATAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
** * * *
3522759 TATATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATGA
1 TATATAATTTCATAAAATTCTTAATAATAAAT-T-TTCTTATATGAAT-T
*
3522803 TATATAATTTCATAAAATTCTTAATAATAAATATTCTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
3522850 TA
1 TA
3522852 CTAAAATCAT
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
43 3 0.04
44 25 0.35
45 7 0.10
46 6 0.08
47 28 0.39
48 3 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (47 bp):
TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
Found at i:3522807 original size:44 final size:44
Alignment explanation
Indices: 3522689--3522812 Score: 119
Period size: 44 Copynumber: 2.8 Consensus size: 44
3522679 NNNNNNNNNN
** *
3522689 TATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTGA
1 TATTAAATATAATTTAATAATGATATATAA-TT--TAAAATAATTAA
* * *
3522736 TAATAAAT-T-TTCTTATATGAAT-TTATATAATTTAAAATAATTAA
1 TATTAAATATAAT-TTA-AT-AATGATATATAATTTAAAATAATTAA
3522780 TATTAAATATAATTTAATAATGATATATAATTT
1 TATTAAATATAATTTAATAATGATATATAATTT
3522813 CATAAAATTC
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
43 3 0.05
44 28 0.45
45 5 0.08
46 7 0.11
47 16 0.26
48 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (44 bp):
TATTAAATATAATTTAATAATGATATATAATTTAAAATAATTAA
Found at i:3523086 original size:24 final size:24
Alignment explanation
Indices: 3523051--3523100 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
3523041 GATAAAGTAT
*
3523051 TTATCACCTCAAATGTGATTTGGG
1 TTATCACATCAAATGTGATTTGGG
3523075 TTATCACATCAAATGTGATTTGGG
1 TTATCACATCAAATGTGATTTGGG
3523099 TT
1 TT
3523101 CAAATTATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
TTATCACATCAAATGTGATTTGGG
Found at i:3527132 original size:20 final size:20
Alignment explanation
Indices: 3527103--3527148 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3527093 TCAAATTAGC
*
3527103 AAAAAA-AAATT-GAATTTT
1 AAAAAATAAATTAAAATTTT
3527121 ATAAAAATAAATTAAAATTTT
1 A-AAAAATAAATTAAAATTTT
3527142 AAAAAAT
1 AAAAAAT
3527149 GTTAAGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.04
19 5 0.21
20 11 0.46
21 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAAATAAATTAAAATTTT
Found at i:3529837 original size:25 final size:25
Alignment explanation
Indices: 3529807--3529856 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3529797 TAAATAAATT
*
3529807 TTATTATTTTAAAAT-TTAATTTTAA
1 TTATTAATTTAAAATATT-ATTTTAA
*
3529832 TTATTAATTTATAATATTATTTTAA
1 TTATTAATTTAAAATATTATTTTAA
3529857 AGCAATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATTAATTTAAAATATTATTTTAA
Found at i:3551956 original size:23 final size:23
Alignment explanation
Indices: 3551925--3551980 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3551915 CATCAATAAG
* * *
3551925 ACTAATGTAATATCCCGAAAATT
1 ACTACTGTAATACCCCAAAAATT
3551948 ACTACTGTAATACCCCAAAAATT
1 ACTACTGTAATACCCCAAAAATT
*
3551971 ACTACAGTAA
1 ACTACTGTAA
3551981 GAAAGTAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.27
Consensus pattern (23 bp):
ACTACTGTAATACCCCAAAAATT
Found at i:3553084 original size:274 final size:257
Alignment explanation
Indices: 3552584--3553114 Score: 670
Period size: 274 Copynumber: 2.0 Consensus size: 257
3552574 TCTTTACAAA
* * *
3552584 TTGGTCCTTTCACCAAAAATTCCCTATTTTCACCTAGAAATCAAAAGAATTTCCATAGCTTCCAA
1 TTGGTCCTTCCACCAAAAATTCCCTATTTTCACCTAGAAATCAAAAGAATTTCCATACCATCCAA
* * * * * * * * *
3552649 GAGAGAAAAATGATAAGGAGACAATGGGGAGCTATAATGTGAAGTTAGATTTAATAAATTGAAGT
66 GAGAGAAAAATAACAAGGAGACAATAGGGAGCTAGAATATCAAGTTAGATTTAAGAAATAGAAGC
*
3552714 TGTAGGAGAGAGAAAATCAAGTTAAAGATTGAAATCAATAGCACAAGGTAAGAACATCAAAATTT
131 TGGAGGAGAGAGAAAATCAAGTTAAAGATTGAAATCAATAGCACAAGGTAAGAACATCAAAATTT
* * *
3552779 CAATATATTTTTAAGTTTGTTATTGTTGAAAAAGCATGGAAATGATGTTATAGTAGAGTTTT
196 CAATATATTTTTAAGTTTGATATTATTGAAAAAACATGGAAATGATGTTATAGTAGAGTTTT
3552841 NNNNNNNNNNNNNNNNNTTGGTCCTTCCACCAAAAATTCACC-ATTTTCACCTAGAAATCAAAAG
1 -----------------TTGGTCCTTCCACCAAAAATTC-CCTATTTTCACCTAGAAATCAAAAG
* * *
3552905 AATTTCCATATCCAT-CAAGAGAGAAAGATAACAATGAGACTATAGGGAGCTAGAATATCAAGTT
48 AATTTCCATA-CCATCCAAGAGAGAAAAATAACAAGGAGACAATAGGGAGCTAGAATATCAAGTT
* * *
3552969 AGATTTAAGAAATAGAAGCTGGAGGAGAGAGAAAATCAAGTTAAAGTTTGAAATTAATAGGACAA
112 AGATTTAAGAAATAGAAGCTGGAGGAGAGAGAAAATCAAGTTAAAGATTGAAATCAATAGCACAA
*
3553034 GGTAAGAACATCAAGATTTCAATATATTTTTAAGTTTGATATTATTGAAAAAACATGGAAATGAT
177 GGTAAGAACATCAAAATTTCAATATATTTTTAAGTTTGATATTATTGAAAAAACATGGAAATGAT
3553099 GTTATAGTAGAGTTTT
242 GTTATAGTAGAGTTTT
3553115 ATTAAATAAG
Statistics
Matches: 232, Mismatches: 23, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
274 228 0.98
275 4 0.02
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.28
Consensus pattern (257 bp):
TTGGTCCTTCCACCAAAAATTCCCTATTTTCACCTAGAAATCAAAAGAATTTCCATACCATCCAA
GAGAGAAAAATAACAAGGAGACAATAGGGAGCTAGAATATCAAGTTAGATTTAAGAAATAGAAGC
TGGAGGAGAGAGAAAATCAAGTTAAAGATTGAAATCAATAGCACAAGGTAAGAACATCAAAATTT
CAATATATTTTTAAGTTTGATATTATTGAAAAAACATGGAAATGATGTTATAGTAGAGTTTT
Found at i:3555696 original size:45 final size:45
Alignment explanation
Indices: 3555610--3555697 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
3555600 TGTGAACCGA
* * * * *
3555610 ACATGATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCAG
1 ACATCATTAATTAATAAGGTGGTTACTATGTGCTGAATCCACCAG
*
3555655 ACATCATTAATTAATAATGTGGTTACTATGTGCTGAATCCACC
1 ACATCATTAATTAATAAGGTGGTTACTATGTGCTGAATCCACC
3555698 GAGTATCTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (45 bp):
ACATCATTAATTAATAAGGTGGTTACTATGTGCTGAATCCACCAG
Found at i:3555769 original size:23 final size:22
Alignment explanation
Indices: 3555743--3555786 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
3555733 AATTGACTAA
3555743 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
3555766 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
3555787 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:3559056 original size:41 final size:41
Alignment explanation
Indices: 3559028--3559170 Score: 232
Period size: 41 Copynumber: 3.5 Consensus size: 41
3559018 TGATTCAGAA
*
3559028 CACTGGCATTAAGCCTGCTAGATGTAAAGTCTGAAATATTT
1 CACTGGCATTAAGCCTGCTAGATGTAAAGTCTGAATTATTT
* * *
3559069 CACCGGCATTAAGCCTGCTAGACGTAAAGTTTGAATTATTT
1 CACTGGCATTAAGCCTGCTAGATGTAAAGTCTGAATTATTT
*
3559110 CACTGGCATTAAGGCTGCTAGATGTAAAGTCTGAATTATTT
1 CACTGGCATTAAGCCTGCTAGATGTAAAGTCTGAATTATTT
*
3559151 CACTAGCATTAAGCCTGCTA
1 CACTGGCATTAAGCCTGCTA
3559171 AGCACAGAGC
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (41 bp):
CACTGGCATTAAGCCTGCTAGATGTAAAGTCTGAATTATTT
Found at i:3559185 original size:41 final size:41
Alignment explanation
Indices: 3559028--3559186 Score: 160
Period size: 41 Copynumber: 3.9 Consensus size: 41
3559018 TGATTCAGAA
* * * *
3559028 CACTGGCATTAAGCCTGCTAGATGTAAAGTCTGAAATATTT
1 CACTAGCATTAAGCCTGCTAGATGCAAAGCCTGAATTATTT
** * * **
3559069 CACCGGCATTAAGCCTGCTAGACGTAAAGTTTGAATTATTT
1 CACTAGCATTAAGCCTGCTAGATGCAAAGCCTGAATTATTT
* * * *
3559110 CACTGGCATTAAGGCTGCTAGATGTAAAGTCTGAATTATTT
1 CACTAGCATTAAGCCTGCTAGATGCAAAGCCTGAATTATTT
3559151 CACTAGCATTAAGCCTGCTA-A-GCACAGAGCCTGAAT
1 CACTAGCATTAAGCCTGCTAGATGCA-A-AGCCTGAAT
3559187 AACTCAGATA
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 100 0.96
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (41 bp):
CACTAGCATTAAGCCTGCTAGATGCAAAGCCTGAATTATTT
Found at i:3561255 original size:21 final size:21
Alignment explanation
Indices: 3561218--3561300 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 21
3561208 CGAAAACGCT
*
3561218 AACAGAAGCTTATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * *
3561239 AAAAAAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
3561260 AACAGAAGCTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
*
3561281 AACAGAAGCTCGTAAGAGCT
1 AACAGAAGCTCATAAGAGCT
3561301 TATCCACCCG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:3562783 original size:165 final size:167
Alignment explanation
Indices: 3562511--3562842 Score: 650
Period size: 165 Copynumber: 2.0 Consensus size: 167
3562501 TTTTTTAACA
3562511 AAATTTTAATACCACTTTAACAACACTCCGTAAATATTTATAAAAATATTTACGGCTCGGTTTAT
1 AAATTTTAATACCACTTTAACAACACTCCGTAAATATTTATAAAAATATTTACGGCTCGGTTTAT
3562576 AGATATGAGGTCCCGATACCTTATTTTCTAAAATCACTTGAACTTAATAATTCGCTTATATAACA
66 AGATATGAGGTCCCGATACCTTATTTTCTAAAATCACTTGAACTTAATAATTCGCTTATATAACA
3562641 AAAATCACTATATCAAAAAC-TTTTT-AAACCATATT
131 AAAATCACTATATCAAAAACTTTTTTAAAACCATATT
3562676 AAATTTTAATACCACTTTAACAACACTCCGTAAATATTTATAAAAATATTTACGGCTCGGTTTAT
1 AAATTTTAATACCACTTTAACAACACTCCGTAAATATTTATAAAAATATTTACGGCTCGGTTTAT
3562741 AGATATGAGGTCCCGATACCTTATTTTCTAAAATCACTTGAACTTAATAATTCGCTTATATAACA
66 AGATATGAGGTCCCGATACCTTATTTTCTAAAATCACTTGAACTTAATAATTCGCTTATATAACA
3562806 AAAATCACTATATCAAAAACTTTTTTAAAACCATATT
131 AAAATCACTATATCAAAAACTTTTTTAAAACCATATT
3562843 TAACTCGTAA
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
165 150 0.91
166 5 0.03
167 10 0.06
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.36
Consensus pattern (167 bp):
AAATTTTAATACCACTTTAACAACACTCCGTAAATATTTATAAAAATATTTACGGCTCGGTTTAT
AGATATGAGGTCCCGATACCTTATTTTCTAAAATCACTTGAACTTAATAATTCGCTTATATAACA
AAAATCACTATATCAAAAACTTTTTTAAAACCATATT
Found at i:3572249 original size:17 final size:18
Alignment explanation
Indices: 3572227--3572260 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3572217 TTAAATTACC
*
3572227 TTAGTTTATTTT-CTCTA
1 TTAGTTAATTTTGCTCTA
3572244 TTAGTTAATTTTGCTCT
1 TTAGTTAATTTTGCTCT
3572261 TAAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.62
Consensus pattern (18 bp):
TTAGTTAATTTTGCTCTA
Found at i:3588627 original size:163 final size:165
Alignment explanation
Indices: 3588434--3588780 Score: 545
Period size: 176 Copynumber: 2.0 Consensus size: 165
3588424 CACGGTCCAG
*
3588434 AAAGAACAAAAAACCCTACTTAGACTTTTGTTTGTTTTTC-A-AATGCAGGCATTCATTTCATTT
1 AAAGAAAAAAAAACCCTACTTAGACTTTTGTTTGTTTTTCAAGAATGCAGGCATTCATTTCATTT
*
3588497 AGAAAAACAAAGACTTAAAATACTAGCATGAGAACATCCTTAAGAGTTAGGTAAACAAAAATACT
66 AGAAAAACAAAGACTTAAAATACTAGCATGAGAACATCCTTAAGAGTTAAGTAAACAAAAATACT
3588562 AAAATTAACTTCTCTACATCTAGATGAGGAAAAAT
131 AAAATTAACTTCTCTACATCTAGATGAGGAAAAAT
3588597 AAAGAAAAAAAAACCCTACTTAGACTTTTGTTTGTTTTTCAAGGGGTATAAATGAATGCAGGCAT
1 AAAGAAAAAAAAACCCTACTTAGACTTTTGTTTGTTTTTC----------AA-GAATGCAGGCAT
*
3588662 TCATTTCATTTAGAAAAACAAAGACTTAAAATGCTAGCATGAGAACATCCTTAAGAGTTAAGTAA
55 TCATTTCATTTAGAAAAACAAAGACTTAAAATACTAGCATGAGAACATCCTTAAGAGTTAAGTAA
*
3588727 ACAAAAATATTAAAATTAACTTCTCTACATCTAGATGAGGAAAAAT
120 ACAAAAATACTAAAATTAACTTCTCTACATCTAGATGAGGAAAAAT
3588773 AAAGAAAA
1 AAAGAAAA
3588781 GACAATTAGC
Statistics
Matches: 167, Mismatches: 4, Indels: 13
0.91 0.02 0.07
Matches are distributed among these distances:
163 39 0.23
174 1 0.01
176 127 0.76
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (165 bp):
AAAGAAAAAAAAACCCTACTTAGACTTTTGTTTGTTTTTCAAGAATGCAGGCATTCATTTCATTT
AGAAAAACAAAGACTTAAAATACTAGCATGAGAACATCCTTAAGAGTTAAGTAAACAAAAATACT
AAAATTAACTTCTCTACATCTAGATGAGGAAAAAT
Found at i:3599506 original size:19 final size:21
Alignment explanation
Indices: 3599484--3599529 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
3599474 TTATTTAATA
*
3599484 AAAATTATTATTT-T-TAAAT
1 AAAATTAATATTTGTATAAAT
* *
3599503 AAAAATAATATTTGTATATAT
1 AAAATTAATATTTGTATAAAT
3599524 AAAATT
1 AAAATT
3599530 CATCTTTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
19 11 0.52
20 1 0.05
21 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AAAATTAATATTTGTATAAAT
Found at i:3601248 original size:2 final size:2
Alignment explanation
Indices: 3601241--3601273 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3601231 TAACCACGAC
3601241 AT AT AT AT AT AT A- AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3601274 AACTAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3601261 original size:15 final size:15
Alignment explanation
Indices: 3601241--3601273 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3601231 TAACCACGAC
3601241 ATATATATATATAAT
1 ATATATATATATAAT
3601256 ATATATATATATAAT
1 ATATATATATATAAT
3601271 ATA
1 ATA
3601274 AACTAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATATATATAAT
Found at i:3601273 original size:13 final size:13
Alignment explanation
Indices: 3601241--3601266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3601231 TAACCACGAC
3601241 ATATATATATATA
1 ATATATATATATA
3601254 ATATATATATATA
1 ATATATATATATA
3601267 TAATATAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Done.