Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 124 of 172
Found at i:35086936 original size:19 final size:19
Alignment explanation
Indices: 35086912--35086948 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35086902 TTATTAATAA
*
35086912 ATTTATAATTATAATAAAT
1 ATTTATAATTAAAATAAAT
*
35086931 ATTTATTATTAAAATAAA
1 ATTTATAATTAAAATAAA
35086949 ATTGAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTATAATTAAAATAAAT
Found at i:35087267 original size:19 final size:18
Alignment explanation
Indices: 35087224--35087267 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
35087214 ACGTTGACTA
**
35087224 ATAAATCATTTTCTATTG
1 ATAAATCATTTTCTATAC
35087242 ATCAAATCATTTTCTATAC
1 AT-AAATCATTTTCTATAC
35087261 AGTAAAT
1 A-TAAAT
35087268 ACAGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 19 0.86
20 1 0.05
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.43
Consensus pattern (18 bp):
ATAAATCATTTTCTATAC
Found at i:35089082 original size:27 final size:27
Alignment explanation
Indices: 35089052--35089122 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 27
35089042 GCATTATGCC
* *
35089052 TTAAGTTGAAAATTTAGTCATTATATT
1 TTAAATTGAAAATTTAGTCAATATATT
* *
35089079 TTAATTTGATTAATTTTAGTCAATATATT
1 TTAAATTGA--AAATTTAGTCAATATATT
* *
35089108 TGAAATTTAAAATTT
1 TTAAATTGAAAATTT
35089123 CACTCCTACC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
27 13 0.37
29 22 0.63
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (27 bp):
TTAAATTGAAAATTTAGTCAATATATT
Found at i:35095246 original size:33 final size:33
Alignment explanation
Indices: 35095204--35095267 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
35095194 ATATTTGTGT
35095204 TAGGTTATCAGCCTATGCTAAACCTTTATAATG
1 TAGGTTATCAGCCTATGCTAAACCTTTATAATG
35095237 TAGGTTATCAGCCTATGCTAAACCTTTATAA
1 TAGGTTATCAGCCTATGCTAAACCTTTATAA
35095268 AAACACATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (33 bp):
TAGGTTATCAGCCTATGCTAAACCTTTATAATG
Found at i:35105130 original size:31 final size:31
Alignment explanation
Indices: 35105095--35105162 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
35105085 TTTAGCTAAT
*
35105095 TTTGACCCTCAACATTTT-AAAAAGAGACGAA
1 TTTGACCATCAAC-TTTTCAAAAAGAGACGAA
* **
35105126 TTTGATCATCAACTTTTCAAAAAGAGTTGAA
1 TTTGACCATCAACTTTTCAAAAAGAGACGAA
35105157 TTTGAC
1 TTTGAC
35105163 TAACAACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (31 bp):
TTTGACCATCAACTTTTCAAAAAGAGACGAA
Found at i:35106138 original size:9 final size:9
Alignment explanation
Indices: 35106126--35106215 Score: 60
Period size: 9 Copynumber: 9.8 Consensus size: 9
35106116 ATTTTTCCAT
35106126 TTTTTATAA
1 TTTTTATAA
*
35106135 TTTTTAAAAA
1 TTTTT-ATAA
*
35106145 TCCTATTTTTAA
1 T--T-TTTATAA
*
35106157 TTTTTTTAA
1 TTTTTATAA
35106166 TATTTTATAA
1 T-TTTTATAA
35106176 TTTTTA-AA
1 TTTTTATAA
** *
35106184 -AATTCTAA
1 TTTTTATAA
35106192 TTTTTATAA
1 TTTTTATAA
35106201 -TTTTATAA
1 TTTTTATAA
35106209 TTTTTAT
1 TTTTTAT
35106216 GATATTTAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
7 2 0.03
8 12 0.19
9 29 0.46
10 13 0.21
12 4 0.06
13 3 0.05
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:35106151 original size:42 final size:41
Alignment explanation
Indices: 35106105--35106186 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
35106095 TAAATATATG
* *
35106105 CTATTCTTAATATTTTTCCATTTTTTATAATTTTTAAAAATC
1 CTATTCTTAAT-TTTTTCAATATTTTATAATTTTTAAAAATC
* *
35106147 CTATTTTTAATTTTTTTAATATTTTATAATTTTTAAAAAT
1 CTATTCTTAATTTTTTCAATATTTTATAATTTTTAAAAAT
35106187 TCTAATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 26 0.72
42 10 0.28
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (41 bp):
CTATTCTTAATTTTTTCAATATTTTATAATTTTTAAAAATC
Found at i:35106174 original size:41 final size:42
Alignment explanation
Indices: 35106126--35106227 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 42
35106116 ATTTTTCCAT
* *
35106126 TTTTTATAATTTTTAAAAATCCT-ATTTTTA-ATTTTTTTAA
1 TTTTTATAATTTTTAAAAATCCTAATTTTTATAATTTTATAA
*
35106166 TATTTTATAATTTTTAAAAATTCTAATTTTTATAATTTTATAA
1 T-TTTTATAATTTTTAAAAATCCTAATTTTTATAATTTTATAA
* *
35106209 TTTTTATGATATTTAAAAA
1 TTTTTATAATTTTTAAAAA
35106228 AAAATGATAG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 1 0.02
41 21 0.39
42 23 0.43
43 9 0.17
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (42 bp):
TTTTTATAATTTTTAAAAATCCTAATTTTTATAATTTTATAA
Found at i:35106215 original size:17 final size:17
Alignment explanation
Indices: 35106149--35106215 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
35106139 TAAAAATCCT
*
35106149 ATTTT-TAATTTTTTTAA
1 ATTTTATAATTTTTAT-A
35106166 TATTTTATAATTTTTA-A
1 -ATTTTATAATTTTTATA
** *
35106183 AAATTCTAATTTTTATA
1 ATTTTATAATTTTTATA
35106200 ATTTTATAATTTTTAT
1 ATTTTATAATTTTTAT
35106216 GATATTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
16 12 0.30
17 15 0.38
18 5 0.12
19 8 0.20
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTATAATTTTTATA
Found at i:35106856 original size:29 final size:27
Alignment explanation
Indices: 35106816--35106882 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
35106806 AAAAAAATAG
* *
35106816 AAATTATTAAAAACTAA-AAATACTTAT
1 AAATTATAAAAAACTAATAAAT-CTAAT
*
35106843 AAATATTATAAAAATCTAATAAATCTAAT
1 -AA-ATTATAAAAAACTAATAAATCTAAT
35106872 AAATTATAAAA
1 AAATTATAAAA
35106883 TTAATAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
28 4 0.12
29 17 0.50
30 4 0.12
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATTATAAAAAACTAATAAATCTAAT
Found at i:35106873 original size:20 final size:21
Alignment explanation
Indices: 35106830--35106874 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
35106820 TATTAAAAAC
* *
35106830 TAAAAATACTTATAAATATTA
1 TAAAAATACTAATAAATATAA
*
35106851 TAAAAAT-CTAATAAATCTAA
1 TAAAAATACTAATAAATATAA
35106871 TAAA
1 TAAA
35106875 TTATAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAATACTAATAAATATAA
Found at i:35108860 original size:18 final size:17
Alignment explanation
Indices: 35108837--35108871 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
35108827 TTAAAAATTC
35108837 TTTATATATAAAGTTTAT
1 TTTATATA-AAAGTTTAT
*
35108855 TTTATATAAAATTTTAT
1 TTTATATAAAAGTTTAT
35108872 ATACAAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTATATAAAAGTTTAT
Found at i:35109331 original size:23 final size:22
Alignment explanation
Indices: 35109299--35109345 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
35109289 AATAATATTT
*
35109299 GTTTTTTTTTTCTCTTGTCATGA
1 GTTTTCTTTTTCTCTTG-CATGA
35109322 GTTTTCTTTTTCTCTTGCATGA
1 GTTTTCTTTTTCTCTTGCATGA
35109344 GT
1 GT
35109346 AAATAGTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.62
Consensus pattern (22 bp):
GTTTTCTTTTTCTCTTGCATGA
Found at i:35111324 original size:26 final size:26
Alignment explanation
Indices: 35111288--35111350 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
35111278 ACATATTTTC
* *
35111288 TCAAAATTTTACTAGGGGAAAAATCA
1 TCAAAATTTTACCAAGGGAAAAATCA
*
35111314 TCAAAATTTTACCAAGGGTAAAATCA
1 TCAAAATTTTACCAAGGGAAAAATCA
*
35111340 TCAAAAGTTTA
1 TCAAAATTTTA
35111351 TTGGGATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.29
Consensus pattern (26 bp):
TCAAAATTTTACCAAGGGAAAAATCA
Found at i:35116623 original size:82 final size:82
Alignment explanation
Indices: 35116480--35116728 Score: 446
Period size: 82 Copynumber: 3.0 Consensus size: 82
35116470 ATATCTCTCC
* *
35116480 CACA-TGTGATTCATCCTAACAACTATATATTAGGTTTTTCTACTTAATTAAGTTGGTTATGCAA
1 CACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGTTATGCAA
35116544 AGTTTTTTTAATTTGTT
66 AGTTTTTTTAATTTGTT
* *
35116561 CATAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGCTATGCAA
1 CACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGTTATGCAA
35116626 AGTTTTTTTAATTTGTT
66 AGTTTTTTTAATTTGTT
*
35116643 CACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTAGTTATGCAA
1 CACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGTTATGCAA
35116708 AGTTTTTTTAATTTGTT
66 AGTTTTTTTAATTTGTT
35116725 CACA
1 CACA
35116729 TAGGCATCGT
Statistics
Matches: 160, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 3 0.02
82 157 0.98
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (82 bp):
CACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGTTATGCAA
AGTTTTTTTAATTTGTT
Found at i:35117344 original size:15 final size:15
Alignment explanation
Indices: 35117324--35117362 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
35117314 ATTTAGAAGA
35117324 AATTTTGAATTAGTG
1 AATTTTGAATTAGTG
*
35117339 AATTTTGTGATTTAGTG
1 AA-TTT-TGAATTAGTG
35117356 AATTTTG
1 AATTTTG
35117363 CGATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 11 0.52
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (15 bp):
AATTTTGAATTAGTG
Found at i:35117353 original size:17 final size:17
Alignment explanation
Indices: 35117333--35117369 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
35117323 AAATTTTGAA
*
35117333 TTAGTGAATTTTGTGAT
1 TTAGTGAATTTTGCGAT
35117350 TTAGTGAATTTTGCGAT
1 TTAGTGAATTTTGCGAT
35117367 TTA
1 TTA
35117370 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTTTGCGAT
Found at i:35118662 original size:46 final size:46
Alignment explanation
Indices: 35118595--35118733 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 46
35118585 CATGGCCAAG
*
35118595 TGTGAAACA-TAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
1 TGTGAAA-AGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
35118641 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
35118687 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTAAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
35118733 T
1 T
35118734 ATAGCCTTGT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 83 0.99
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:35126132 original size:145 final size:145
Alignment explanation
Indices: 35125869--35126157 Score: 517
Period size: 145 Copynumber: 2.0 Consensus size: 145
35125859 ATTTGGGGGC
* *
35125869 ACTATTTATATGGTGAGAAATGCTATGTGTATACAGATCATAAAAGTCTAACGTATTTAATGACT
1 ACTATTTATACGGTGAGAAAGGCTATGTGTATACAGATCATAAAAGTCTAACGTATTTAATGACT
*
35125934 TAGAAGGAGTTGAATTTAAGACAGAGACAGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTAT
66 TAGAAGAAGTTGAATTTAAGACAGAGACAGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTAT
35125999 TGATTAACACCCGGG
131 TGATTAACACCCGGG
35126014 ACTATTTATACGGTGAGAAAGGCTATGTGTATACAGATCATAAAAGTCTGAA-GTATTTAATGAC
1 ACTATTTATACGGTGAGAAAGGCTATGTGTATACAGATCATAAAAGTCT-AACGTATTTAATGAC
*
35126078 TTAGAAGAAGTTGAATTTAAGACAGAGACGGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTA
65 TTAGAAGAAGTTGAATTTAAGACAGAGACAGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTA
*
35126143 TTGATTACCACCCGG
130 TTGATTAACACCCGG
35126158 AGAAAGCTAA
Statistics
Matches: 138, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
145 136 0.99
146 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (145 bp):
ACTATTTATACGGTGAGAAAGGCTATGTGTATACAGATCATAAAAGTCTAACGTATTTAATGACT
TAGAAGAAGTTGAATTTAAGACAGAGACAGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTAT
TGATTAACACCCGGG
Found at i:35127905 original size:17 final size:17
Alignment explanation
Indices: 35127868--35127916 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
35127858 GAATTTAGAA
*
35127868 GAATTTT-TGAATTAAT
1 GAATTTTGTGATTTAAT
*
35127884 GAATTTTGTGATTTAGT
1 GAATTTTGTGATTTAAT
*
35127901 GAATTTTGCGATTTAA
1 GAATTTTGTGATTTAA
35127917 AAAGAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (17 bp):
GAATTTTGTGATTTAAT
Found at i:35129169 original size:46 final size:46
Alignment explanation
Indices: 35129102--35129240 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
35129092 CATGGCCAAG
* *
35129102 TGTGAAACGTAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
35129148 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
35129194 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
35129240 T
1 T
35129241 ATAGCCTTGT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:35155045 original size:18 final size:18
Alignment explanation
Indices: 35155011--35155043 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
35155001 AAAAATCACT
35155011 TTTATCTTTTTTATTTTC
1 TTTATCTTTTTTATTTTC
35155029 TTTA--TTTTTTATTTT
1 TTTATCTTTTTTATTTT
35155044 TTAAAATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTATCTTTTTTATTTTC
Found at i:35155439 original size:30 final size:30
Alignment explanation
Indices: 35155403--35155465 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
35155393 ACTTAACAAG
35155403 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
35155433 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
35155463 CAA
1 CAA
35155466 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:35156449 original size:12 final size:13
Alignment explanation
Indices: 35156420--35156446 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35156410 CTTGATTAGT
35156420 AATAAAAAAATTG
1 AATAAAAAAATTG
35156433 AATAAAAAAATTG
1 AATAAAAAAATTG
35156446 A
1 A
35156447 TAATATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
AATAAAAAAATTG
Found at i:35160631 original size:31 final size:31
Alignment explanation
Indices: 35160574--35160633 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
35160564 GGAGGTGGGA
*
35160574 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* * *
35160605 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
35160634 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:35160779 original size:30 final size:31
Alignment explanation
Indices: 35160734--35160798 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
35160724 TGGGGGGTTG
35160734 AAAG-GGGAGAGGAGTAAAAGTTTTGGGGGA
1 AAAGTGGGAGAGGAGTAAAAGTTTTGGGGGA
35160764 AAAGTGGGA-AGGAGTAAAAGTTTTGGGGGA
1 AAAGTGGGAGAGGAGTAAAAGTTTTGGGGGA
35160794 AAAGT
1 AAAGT
35160799 AAAAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.18
Consensus pattern (31 bp):
AAAGTGGGAGAGGAGTAAAAGTTTTGGGGGA
Found at i:35160861 original size:9 final size:9
Alignment explanation
Indices: 35160847--35160883 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
35160837 TATAGTTTGA
35160847 TATTCGAAT
1 TATTCGAAT
35160856 TATTCGAAT
1 TATTCGAAT
*
35160865 TATTCGAGT
1 TATTCGAAT
35160874 TATTCGAAT
1 TATTCGAAT
35160883 T
1 T
35160884 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:35167172 original size:7 final size:6
Alignment explanation
Indices: 35167155--35167184 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
35167145 AGATATATTT
35167155 TAAAAA TAAAAA TAAAAA TAAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA T-AAAAA TAAAA
35167185 CAAAACCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:35167172 original size:12 final size:13
Alignment explanation
Indices: 35167155--35167184 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35167145 AGATATATTT
35167155 TAAAAAT-AAAAA
1 TAAAAATAAAAAA
35167167 TAAAAATAAAAAA
1 TAAAAATAAAAAA
35167180 TAAAA
1 TAAAA
35167185 CAAAACCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:35168970 original size:41 final size:42
Alignment explanation
Indices: 35168913--35169025 Score: 138
Period size: 41 Copynumber: 2.7 Consensus size: 42
35168903 ACTTCCGAGG
* **
35168913 TATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCG-TA
1 TATGA-TTCATGTAAGACCATGTCTGGGACAGGGGCATCGATA
*
35168955 TATGATTCATGTAAGACCCTGTCTGGGACAGGGGCATCGATA
1 TATGATTCATGTAAGACCATGTCTGGGACAGGGGCATCGATA
* * *
35168997 TGTGATAACATGTAAGACCATATCTGGGA
1 TATGAT-TCATGTAAGACCATGTCTGGGA
35169026 TATGACATTG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 30 0.49
42 12 0.20
43 19 0.31
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (42 bp):
TATGATTCATGTAAGACCATGTCTGGGACAGGGGCATCGATA
Found at i:35185284 original size:27 final size:27
Alignment explanation
Indices: 35185253--35185322 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
35185243 CATTTACGAA
35185253 AAATAAATTATATTAAATACAGTAGTT
1 AAATAAATTATATTAAATACAGTAGTT
*
35185280 AAATAAATTATATTAAATATAGTAGTT
1 AAATAAATTATATTAAATACAGTAGTT
35185307 AACAGTAAA-TATATTA
1 AA-A-TAAATTATATTA
35185323 TAATGATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 28 0.70
28 8 0.20
29 4 0.10
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (27 bp):
AAATAAATTATATTAAATACAGTAGTT
Found at i:35185297 original size:14 final size:14
Alignment explanation
Indices: 35185253--35185298 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
35185243 CATTTACGAA
35185253 AAATAAATTATATT
1 AAATAAATTATATT
* * *
35185267 AAATACAGTA-GTT
1 AAATAAATTATATT
35185280 AAATAAATTATATT
1 AAATAAATTATATT
35185294 AAATA
1 AAATA
35185299 TAGTAGTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (14 bp):
AAATAAATTATATT
Found at i:35189471 original size:24 final size:24
Alignment explanation
Indices: 35189444--35189492 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
35189434 ATAATAAGTG
*
35189444 TGTGACTAGCTTTGGCTAAAAAAA
1 TGTGACTAACTTTGGCTAAAAAAA
35189468 TGTGACTAACTTTGGCTAAAAAAA
1 TGTGACTAACTTTGGCTAAAAAAA
35189492 T
1 T
35189493 ACTTTTGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (24 bp):
TGTGACTAACTTTGGCTAAAAAAA
Found at i:35193915 original size:14 final size:16
Alignment explanation
Indices: 35193880--35193917 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35193870 GCTTGCTCAA
35193880 ATATATGTGTTACATG
1 ATATATGTGTTACATG
*
35193896 ATATATGT-TTGCATG
1 ATATATGTGTTACATG
35193911 A-ATATGT
1 ATATATGT
35193918 AAATGCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (16 bp):
ATATATGTGTTACATG
Found at i:35196597 original size:91 final size:88
Alignment explanation
Indices: 35196438--35196626 Score: 263
Period size: 91 Copynumber: 2.1 Consensus size: 88
35196428 AACCATTTTA
* * * *
35196438 TGGATAAACCACCAGTGTTGCAGGTTAATATGTTGTCAGTAGTTGTGAATACACAACGGGTTTAT
1 TGGATAAACCACAAGTGTTGCAGGTTAATATGCTGCCAGTAGCTGTGAATACACAACGGGTTTAT
35196503 AGA-TAATAGTTGCCAGTATAAGTTG
66 AGATTAA-AGTTGCCAG--TAAGTTG
* *
35196528 TGGATAAACCACAAGTGCTTGCAGGTTAATATGCTGCCAGTAGCTGTGAATACACAATGGGTTTG
1 TGGATAAACCACAAGTG-TTGCAGGTTAATATGCTGCCAGTAGCTGTGAATACACAACGGGTTTA
* *
35196593 TAGATTAAAGTTGCTAGTAATTTG
65 TAGATTAAAGTTGCCAGTAAGTTG
35196617 TGGATAAACC
1 TGGATAAACC
35196627 TCCAGTATTT
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
89 16 0.18
90 16 0.18
91 54 0.61
92 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (88 bp):
TGGATAAACCACAAGTGTTGCAGGTTAATATGCTGCCAGTAGCTGTGAATACACAACGGGTTTAT
AGATTAAAGTTGCCAGTAAGTTG
Found at i:35199344 original size:13 final size:13
Alignment explanation
Indices: 35199326--35199353 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35199316 TAATAGAACT
35199326 TAAACTTACCATA
1 TAAACTTACCATA
35199339 TAAACTTACCATA
1 TAAACTTACCATA
35199352 TA
1 TA
35199354 CATTAGATAA
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:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTTACCATA
Found at i:35200151 original size:76 final size:76
Alignment explanation
Indices: 35200031--35200342 Score: 302
Period size: 76 Copynumber: 4.1 Consensus size: 76
35200021 GGTGTACCCT
* * * * * *
35200031 GCACTAGTCGGATAAACCGACAACGTCTTGCGCCTAGCGCTAGTTGGATAAACTGACGATGTCAA
1 GCACTAGTCGAATAAACCAACAACGTCTTGCACCCAGCGCTAATCGGATAAACTGACGATGTCAA
35200096 ATATGTGCCCA
66 ATATGTGCCCA
* * * * * * *
35200107 GCACTAGTCGAATAACCCAACAATGTTTTGCACCCAGCGCTAGTTGGATAAATTGACGATATCAA
1 GCACTAGTCGAATAAACCAACAACGTCTTGCACCCAGCGCTAATCGGATAAACTGACGATGTCAA
* *
35200172 ATGTGTGCCTA
66 ATATGTGCCCA
* * ** ** **
35200183 GCACTAGCCGAATAAACCAACAGCGTCTTGTGCCCAATGCTAATCGGATAAA-TCGAAAATGTCA
1 GCACTAGTCGAATAAACCAACAACGTCTTGCACCCAGCGCTAATCGGATAAACT-GACGATGTCA
35200247 AATATGTGCCCA
65 AATATGTGCCCA
* * * * ** * * *
35200259 GCACTACTCGGATAACCCGACAATATTTTTCACCCAGCGCTAATCGGATAAACTAACGATGTCAA
1 GCACTAGTCGAATAAACCAACAACGTCTTGCACCCAGCGCTAATCGGATAAACTGACGATGTCAA
*
35200324 ATGTGTGCCCA
66 ATATGTGCCCA
*
35200335 ACACTAGT
1 GCACTAGT
35200343 TGGTTATACT
Statistics
Matches: 187, Mismatches: 47, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
75 1 0.01
76 185 0.99
77 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (76 bp):
GCACTAGTCGAATAAACCAACAACGTCTTGCACCCAGCGCTAATCGGATAAACTGACGATGTCAA
ATATGTGCCCA
Found at i:35202909 original size:61 final size:61
Alignment explanation
Indices: 35202825--35202952 Score: 166
Period size: 61 Copynumber: 2.1 Consensus size: 61
35202815 ATGAAGGTTT
* ** * * *
35202825 TCCTTTACATTCAGTACTCGCCACAAAGGCTTTATTGTCTAGAGTTCTGCCACAAAGGCTA
1 TCCTTTACATTCAATACTCGCCACAAAGGCAATAGTGTCCAGAATTCTGCCACAAAGGCTA
* * * *
35202886 TCCTTTACATTCAATACTTGCCACAAAGGCAATCGTGTCCAGAATTGTGCCACAAAGGCTT
1 TCCTTTACATTCAATACTCGCCACAAAGGCAATAGTGTCCAGAATTCTGCCACAAAGGCTA
35202947 TCCTTT
1 TCCTTT
35202953 CCAGATTTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (61 bp):
TCCTTTACATTCAATACTCGCCACAAAGGCAATAGTGTCCAGAATTCTGCCACAAAGGCTA
Found at i:35202974 original size:29 final size:29
Alignment explanation
Indices: 35202904--35202976 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
35202894 ATTCAATACT
* *
35202904 TGCCACAAAGGCAATCGTGTCCAGAATTG
1 TGCCACAAAGGCTATCCTGTCCAGAATTG
* * *
35202933 TGCCACAAAGGCTTTCCTTTCCAGATTTG
1 TGCCACAAAGGCTATCCTGTCCAGAATTG
35202962 TGCCACAAAGGCTAT
1 TGCCACAAAGGCTAT
35202977 TCTTTACTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (29 bp):
TGCCACAAAGGCTATCCTGTCCAGAATTG
Found at i:35205826 original size:26 final size:27
Alignment explanation
Indices: 35205796--35205853 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
35205786 ATTCAGATGC
* * *
35205796 AAATAAAAATTTATTATTAT-TTTAAA
1 AAATAAAAAATAATAATTATGTTTAAA
35205822 AAATAAAAAATAATAATTATGTTTAAA
1 AAATAAAAAATAATAATTATGTTTAAA
35205849 AAATA
1 AAATA
35205854 TGTCATTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
AAATAAAAAATAATAATTATGTTTAAA
Found at i:35205924 original size:184 final size:184
Alignment explanation
Indices: 35205611--35206036 Score: 609
Period size: 184 Copynumber: 2.3 Consensus size: 184
35205601 TTATAATATT
* * *
35205611 AAATAAAATTTTATTATTATTTTGAAAATTAAAAAATAATATTTATATTTTAAAAAACATGTCAC
1 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAATAATTATA-TTTAAAAAACATGTCAC
* * *
35205676 TTAGTACATAATTTGTGGCATAAATTACGCTTTTCTATAACATTACAACTTTCAGCTGTGTTTAT
65 TTAGTACATAACTTGTGGCACAAATTACGCTTTTCTATAACATTACAACTTTCAGCTATGTTTAT
* * * *
35205741 TCATTACGAATCTTTTCTAAAAGCTATGTTTATTTGAATAAATTTATTCAGATGC
130 TCATTACGAATCTTTTCTAAAAGCTACGCTTATTTGAATAAATCTATTCAGATGA
* * * *
35205796 AAATAAAAATTTATTATTATTTTAAAAAATAAAAAATAATAATTATGTTTAAAAAATATGTCATT
1 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAATAATTATATTTAAAAAACATGTCACT
** * * * *
35205861 TAGTATGTAACTTGTGGCACAAGTTATGCTTTTTTATAACATTATAACTTTCAGCTATGTTTATT
66 TAGTACATAACTTGTGGCACAAATTACGCTTTTCTATAACATTACAACTTTCAGCTATGTTTATT
* * * *
35205926 CATTGCGAATCTTTTTTTAAAGTTACGCTTATTTGAATAAATCTATTCAGATGA
131 CATTACGAATCTTTTCTAAAAGCTACGCTTATTTGAATAAATCTATTCAGATGA
* *
35205980 AAATAAAAATTTATTTTTATTTTGAAAAATAAAAAATAATTATTATATTTAAAAAAC
1 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAATAATTATATTTAAAAAAC
35206037 TTATTTGCAC
Statistics
Matches: 212, Mismatches: 29, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
184 170 0.80
185 42 0.20
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (184 bp):
AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAATAATTATATTTAAAAAACATGTCACT
TAGTACATAACTTGTGGCACAAATTACGCTTTTCTATAACATTACAACTTTCAGCTATGTTTATT
CATTACGAATCTTTTCTAAAAGCTACGCTTATTTGAATAAATCTATTCAGATGA
Found at i:35206025 original size:26 final size:27
Alignment explanation
Indices: 35205979--35206035 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
35205969 TATTCAGATG
* * * *
35205979 AAAATAAAAATTTATTTTTAT-TTTGA
1 AAAATAAAAAATAATTATTATATTTAA
35206005 AAAATAAAAAATAATTATTATATTTAA
1 AAAATAAAAAATAATTATTATATTTAA
35206032 AAAA
1 AAAA
35206036 CTTATTTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AAAATAAAAAATAATTATTATATTTAA
Found at i:35206218 original size:19 final size:21
Alignment explanation
Indices: 35206177--35206218 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
35206167 ACTAACAATT
* *
35206177 TAAATATATAAAACTAGAGTA
1 TAAATATATAAAAATACAGTA
35206198 TAAATATA-AAAAATACA-TA
1 TAAATATATAAAAATACAGTA
35206217 TA
1 TA
35206219 TGTGTTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
TAAATATATAAAAATACAGTA
Found at i:35221305 original size:16 final size:16
Alignment explanation
Indices: 35221284--35221317 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
35221274 ACCATTGAAA
35221284 AAAAATTAA-ATTTATT
1 AAAAATTAATATTT-TT
35221300 AAAAATTAATATTTTT
1 AAAAATTAATATTTTT
35221316 AA
1 AA
35221318 TGATTTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAAATTAATATTTTT
Found at i:35227466 original size:27 final size:27
Alignment explanation
Indices: 35227414--35227468 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
35227404 AATATATTGG
* *
35227414 TTTTATTTAATATTCAATAATTATATT
1 TTTTATTAAATATTCAATAATAATATT
*
35227441 TTTTATTAAATATTTAA-ACATAATATT
1 TTTTATTAAATATTCAATA-ATAATATT
35227468 T
1 T
35227469 ACATTGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTATTAAATATTCAATAATAATATT
Found at i:35230581 original size:3 final size:3
Alignment explanation
Indices: 35230575--35230615 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
35230565 CTTCATGTGC
* *
35230575 ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT ATT AGT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
35230616 GACAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:35236697 original size:26 final size:26
Alignment explanation
Indices: 35236668--35236718 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
35236658 TTTGAAATGG
*
35236668 AAAAAT-AATATGAATTTTACATTCAT
1 AAAAATGAATA-GAATTTTAAATTCAT
*
35236694 AAAAATGCATAGAATTTTAAATTCA
1 AAAAATGAATAGAATTTTAAATTCA
35236719 AAGTTGACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (26 bp):
AAAAATGAATAGAATTTTAAATTCAT
Found at i:35237493 original size:14 final size:15
Alignment explanation
Indices: 35237469--35237499 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
35237459 ACTTCGCAGT
35237469 TATATATATATATAA
1 TATATATATATATAA
35237484 TATA-ATATATATAA
1 TATATATATATATAA
35237498 TA
1 TA
35237500 ATGTTATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:35238339 original size:21 final size:21
Alignment explanation
Indices: 35238323--35238366 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35238313 AATAATTGAG
35238323 AATATATAATTATTAATTAAA
1 AATATATAATTATTAATTAAA
*
35238344 AATAATATAAATATT-ATTAAA
1 AAT-ATATAATTATTAATTAAA
35238365 AA
1 AA
35238367 ATAATATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATATAATTATTAATTAAA
Found at i:35238358 original size:22 final size:22
Alignment explanation
Indices: 35238326--35238373 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35238316 AATTGAGAAT
*
35238326 ATATAATTATTAATT-AAAAATA
1 ATATAAATATT-ATTAAAAAATA
35238348 ATATAAATATTATTAAAAAATA
1 ATATAAATATTATTAAAAAATA
35238370 ATAT
1 ATAT
35238374 GGGTGATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAAATATTATTAAAAAATA
Found at i:35239072 original size:6 final size:6
Alignment explanation
Indices: 35239061--35239089 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
35239051 CCAACAGTTT
35239061 TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
35239090 TTTCCCAGCA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCC
Found at i:35242804 original size:20 final size:20
Alignment explanation
Indices: 35242779--35242819 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35242769 GTCTCTTGTC
35242779 TACTAAATAATCAGTTCATG
1 TACTAAATAATCAGTTCATG
35242799 TACTAAATAATCAGTTCATG
1 TACTAAATAATCAGTTCATG
35242819 T
1 T
35242820 GAATGTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (20 bp):
TACTAAATAATCAGTTCATG
Found at i:35242841 original size:21 final size:21
Alignment explanation
Indices: 35242817--35242857 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
35242807 AATCAGTTCA
35242817 TGTGAATGTAATATTGACTAT
1 TGTGAATGTAATATTGACTAT
35242838 TGTGAATGTAATATTGACTA
1 TGTGAATGTAATATTGACTA
35242858 CAAATAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (21 bp):
TGTGAATGTAATATTGACTAT
Found at i:35242907 original size:20 final size:21
Alignment explanation
Indices: 35242882--35242920 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
35242872 CGTTAACTCG
35242882 ATTTGACTCG-AAATTTTTTT
1 ATTTGACTCGAAAATTTTTTT
*
35242902 ATTTGATTCGAAAATTTTT
1 ATTTGACTCGAAAATTTTT
35242921 AAATGAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (21 bp):
ATTTGACTCGAAAATTTTTTT
Found at i:35243051 original size:21 final size:21
Alignment explanation
Indices: 35243025--35243071 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
35243015 TGCTTCAACG
35243025 TCAAATTAGCAGTTACTCGTA
1 TCAAATTAGCAGTTACTCGTA
35243046 TCAAATTAGCAGTTACTCGTA
1 TCAAATTAGCAGTTACTCGTA
35243067 T-AAAT
1 TCAAAT
35243072 GAATAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (21 bp):
TCAAATTAGCAGTTACTCGTA
Found at i:35244410 original size:236 final size:237
Alignment explanation
Indices: 35243951--35244427 Score: 573
Period size: 236 Copynumber: 2.0 Consensus size: 237
35243941 AACAAATCAA
* * * * * * *
35243951 ATGCCCTTGTATCAACAAAAGCACTTATTCTTCAGCCTACTAAGTTGATGTTTATGAACATCAAT
1 ATGCCCATGTATCAACAAAAGCACTTATTCTTCAACCTACTAAGTTAATGTCTACGAACATAAAC
* * * *
35244016 CATTTCTGCTTGTGATTCCTCTTCACTTTAGTAGAATTGAATATCGTTGGACCAAGCTTTAAAGC
66 CATTTCTGCTTGTGATCCCTCTTCACTTTAGCAGAATCGAATATC--TGAACCAAGCTTTAAAGC
* * *** * * *
35244081 CTCTGTAACACCCCTTGCCTGACCTGTTCGTCAGGTTTGAGCTACGGAATGCTACATTCATTATC
129 CTCTATAACACCCCTTGCCTAACCCAATCGTCAGGTATGAGCTACAGAATGCTACATTCATTACC
* *
35244146 GGAGCAACTACAACCAATTAGACATCATACAATCATTTATACAT
194 AGAACAACTACAACCAATTAGACATCATACAATCATTTATACAT
* *
35244190 ATGCCCATGTATCAACAAAATCACTTATTCTTCAACCTGCTATA-TTAATGTCTACGAACATAAA
1 ATGCCCATGTATCAACAAAAGCACTTATTCTTCAACCTACTA-AGTTAATGTCTACGAACATAAA
* * *
35244254 CCATTTCTGCTTGTGATCCCTCTTCGCTTTAGCAGAATCGAGTATC-GAACCAAGCTTTAAAGCT
65 CCATTTCTGCTTGTGATCCCTCTTCACTTTAGCAGAATCGAATATCTGAACCAAGCTTTAAAGCC
* * * * * * *
35244318 TTTATAACATCTCTTGTCC-AACCCAATCGTTAGGTATGAGCTACAGAATGCTATATTCGTTGCC
130 TCTATAACACCCCTTG-CCTAACCCAATCGTCAGGTATGAGCTACAGAATGCTACATTCATTACC
* * *
35244382 AGAACAACTATAACCAATTAGACATCATACAATTATTTATATAT
194 AGAACAACTACAACCAATTAGACATCATACAATCATTTATACAT
35244426 AT
1 AT
35244428 AATCTAATAC
Statistics
Matches: 200, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
236 103 0.51
237 2 0.01
239 94 0.47
240 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (237 bp):
ATGCCCATGTATCAACAAAAGCACTTATTCTTCAACCTACTAAGTTAATGTCTACGAACATAAAC
CATTTCTGCTTGTGATCCCTCTTCACTTTAGCAGAATCGAATATCTGAACCAAGCTTTAAAGCCT
CTATAACACCCCTTGCCTAACCCAATCGTCAGGTATGAGCTACAGAATGCTACATTCATTACCAG
AACAACTACAACCAATTAGACATCATACAATCATTTATACAT
Found at i:35271050 original size:2 final size:2
Alignment explanation
Indices: 35271043--35271080 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
35271033 CCCCTCGTTC
35271043 CT CT CT CT 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 CT
35271081 TTGAGCTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:35271944 original size:5 final size:5
Alignment explanation
Indices: 35271934--35271962 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
35271924 TTTCAAACAA
35271934 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
35271963 ACAATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:35276993 original size:12 final size:12
Alignment explanation
Indices: 35276976--35277015 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
35276966 ATTGATTTTT
35276976 AAAATATTTTAA
1 AAAATATTTTAA
*
35276988 AAAATATTTTTA
1 AAAATATTTTAA
* *
35277000 AATATTTTTTAA
1 AAAATATTTTAA
35277012 AAAA
1 AAAA
35277016 AGCTTTTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:35277009 original size:24 final size:23
Alignment explanation
Indices: 35276970--35277036 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
35276960 ATTATAATTG
*
35276970 ATTTTTAAA-ATATTTTAAAAAA
1 ATTTTTAAATATTTTTTAAAAAA
35276992 TATTTTTAAATATTTTTTAAAAAA
1 -ATTTTTAAATATTTTTTAAAAAA
*
35277016 AGCTTTTATAAT-TTTTTTAAA
1 A-TTTTTA-AATATTTTTTAAA
35277037 TTTTAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.26
24 26 0.67
25 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (23 bp):
ATTTTTAAATATTTTTTAAAAAA
Found at i:35288631 original size:128 final size:127
Alignment explanation
Indices: 35288362--35288592 Score: 293
Period size: 128 Copynumber: 1.8 Consensus size: 127
35288352 AGTGAATATT
* * * * *
35288362 ATAGACCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCAAATCTTATCTTCAAGTGT
1 ATAGATCTTATCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGACAAATCTTATCTTCAAGTGT
* * * * * *
35288427 AAGAAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATT
66 AAGAAAGCAGATTGAAGCCACAAGTCCTATCTCCCTGATCAGCAGTGGAAGAGATT-GAAATA
* * *
35288490 ACAGATCTTATCTCCCTAAGCAATAGCAGAGCAGATCGAAGACGACGAATCTTATCTTCAAGTGT
1 ATAGATCTTATCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGACAAATCTTATCTTCAAGTGT
* *
35288555 AAGGAAGCAGATTGAAGCCGATAA-TCCTATCTCCCTGA
66 AAGAAAGCAGATTGAAGCC-ACAAGTCCTATCTCCCTGA
35288593 AATTGTAGTG
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
128 86 0.97
129 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (127 bp):
ATAGATCTTATCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGACAAATCTTATCTTCAAGTGT
AAGAAAGCAGATTGAAGCCACAAGTCCTATCTCCCTGATCAGCAGTGGAAGAGATTGAAATA
Found at i:35288714 original size:44 final size:44
Alignment explanation
Indices: 35288660--35289304 Score: 203
Period size: 44 Copynumber: 14.8 Consensus size: 44
35288650 TGGATCTCAT
* *
35288660 CAGGTCTTATCTCCTTGAAGTTGCAGCGGAGCAGACTGAGTAAG
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAAG
* * *
35288704 CAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGA-TCGAAG-ATG
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-G-AGTAAG
** * * * * *
35288748 ACAAATCTTATCTCCTTGAAGTTACAATGGAGCAGATTGAAGCCAA-
1 -CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AG-TAAG
* ** * * * *
35288794 TAATTC-TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAA-
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAGTAAG
* * * * * * * * * *
35288837 TAGATCTTATTTCCCTGAAGTTGTAGTAGAG-TGAAT-CG-CAT
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAAG
* * ** *
35288878 CAGGTTTTATCTCCTTGAAGTTATAGCGGAGCAGACTGAGTAAG
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAAG
* * * *
35288922 CAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATTGAAG-ATGG
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AGTA-AG
* ** ** * **
35288967 TAAATCTTATCTCCCTGAAGTTATAGTGGAGCAGATTGAAGCCA-
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AGTAAG
* * * * * * *
35289011 CTA-ATCCTATCTCCCTGAAATTACAGAGGAGCAGATTAAAGTAA-
1 C-AGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAGTAAG
* * * * * * * * *
35289055 TAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGA-T-CG-CAT
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAAG
* * * * *
35289096 CAGGTCTTATCTCCATGAGGTTACAGTGGAGCAGACTGAGAAAA
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAAG
* * * ** * *
35289140 CAAGTCTTATCCCCCTAAAGTCACAGTGGGGTAGACTGAAG-AAG
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AGTAAG
** * * * *
35289184 CAAATCTTATCTCCCTGAGGTTGCAGTGAAGCAGATTGA--AAT
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAAG
** * * * * *
35289226 CGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAA-
1 C-A-GGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAGTAAG
* * * *
35289272 TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
1 CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
35289305 CATCGCATCA
Statistics
Matches: 448, Mismatches: 125, Indels: 56
0.71 0.20 0.09
Matches are distributed among these distances:
40 2 0.00
41 51 0.11
42 7 0.02
43 16 0.04
44 288 0.64
45 80 0.18
46 1 0.00
47 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGTAAG
Found at i:35288810 original size:218 final size:217
Alignment explanation
Indices: 35288560--35289302 Score: 1058
Period size: 218 Copynumber: 3.4 Consensus size: 217
35288550 AGTGTAAGGA
*
35288560 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAATTGTAGTGGAGCGAATTAAAGTAATAGATC
1 AGCAGATTGAAGCCAATAATCCTATCTCCCTGAAATTGTAGTGGAGCGAATTAAAGTAATAGATC
* *
35288625 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCTCATCAGGTCTTATCTCCTTGAAGTTGCAGCGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCTTGAAGTTACAGCGGA
35288690 GCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATGACAAATC
131 GCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATG-CAAATC
* *
35288755 TTATCTCCTTGAAGTTACAATGG
195 TTATCTCCCTGAAGTTACAGTGG
* * *
35288778 AGCAGATTGAAGCCAATAATTCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCAATAATCCTATCTCCCTGAAATTGTAGTGGAGCGAATTAAAGTAATAGATC
* * * * * *
35288843 TTATTTCCCTGAAGTTGTAGTAGAGTGAATCGCATCAGGTTTTATCTCCTTGAAGTTATAGCGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCTTGAAGTTACAGCGGA
* *
35288908 GCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATTGAAGATGGTAAATC
131 GCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGAT-GCAAATC
*
35288973 TTATCTCCCTGAAGTTATAGTGG
195 TTATCTCCCTGAAGTTACAGTGG
* ** *
35288996 AGCAGATTGAAGCCACTAATCCTATCTCCCTGAAATTACAGAGGAGC-AGATTAAAGTAATAGAT
1 AGCAGATTGAAGCCAATAATCCTATCTCCCTGAAATTGTAGTGGAGCGA-ATTAAAGTAATAGAT
* * * * *
35289060 CTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGCATCAGGTCTTATCTCCATGAGGTTACAGTGG
65 CTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCTTGAAGTTACAGCGG
* * * * ** * *
35289125 AGCAGACTGAGAAAACAAGTCTTATCCCCCTAAAGTCACAGTGGGGTAGA-CTGAAGAAGCAAAT
130 AGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATC-GAAGATGCAAAT
* * *
35289189 CTTATCTCCCTGAGGTTGCAGTGA
194 CTTATCTCCCTGAAGTTACAGTGG
** * * *
35289213 AGCAGATTGAAATCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCAATAATCCTATCTCCCTGAAATTGTAGTGGAGCGAATTAAAGTAATAGATC
35289278 TTATCTCTCTGAAGTTGCAGTAGAG
66 TTATCTCTCTGAAGTTGCAGTAGAG
35289303 CACATCGCAT
Statistics
Matches: 464, Mismatches: 57, Indels: 9
0.88 0.11 0.02
Matches are distributed among these distances:
217 104 0.22
218 359 0.77
219 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (217 bp):
AGCAGATTGAAGCCAATAATCCTATCTCCCTGAAATTGTAGTGGAGCGAATTAAAGTAATAGATC
TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCTTGAAGTTACAGCGGA
GCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATGCAAATCT
TATCTCCCTGAAGTTACAGTGG
Found at i:35297342 original size:62 final size:62
Alignment explanation
Indices: 35297245--35297368 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
35297235 AAGATTGAAC
35297245 ACTGCTGGTAATTGGTTCAACCAGAAGCAAAGTCATAAATGACAACGAAATAAATGTGCAAA
1 ACTGCTGGTAATTGGTTCAACCAGAAGCAAAGTCATAAATGACAACGAAATAAATGTGCAAA
35297307 ACTGCTGGTAATTGGTTCAACCAGAAGCAAAGTCATAAATGACAACGAAATAAATGTGCAAA
1 ACTGCTGGTAATTGGTTCAACCAGAAGCAAAGTCATAAATGACAACGAAATAAATGTGCAAA
35297369 TTGTACAAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (62 bp):
ACTGCTGGTAATTGGTTCAACCAGAAGCAAAGTCATAAATGACAACGAAATAAATGTGCAAA
Found at i:35301167 original size:15 final size:16
Alignment explanation
Indices: 35301136--35301169 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35301126 TAATATTAAT
35301136 AAACTAAAAAAATTGA
1 AAACTAAAAAAATTGA
*
35301152 AAACTCAAAAAA-TGA
1 AAACTAAAAAAATTGA
35301167 AAA
1 AAA
35301170 AACTCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (16 bp):
AAACTAAAAAAATTGA
Found at i:35301222 original size:12 final size:12
Alignment explanation
Indices: 35301207--35301234 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
35301197 TCCTCCTCCC
35301207 TCTCCATGTCCA
1 TCTCCATGTCCA
35301219 TCTCCATGTCCA
1 TCTCCATGTCCA
35301231 TCTC
1 TCTC
35301235 TAATCAGATT
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:0.14, C:0.43, G:0.07, T:0.36
Consensus pattern (12 bp):
TCTCCATGTCCA
Found at i:35302173 original size:4 final size:4
Alignment explanation
Indices: 35302164--35302258 Score: 75
Period size: 4 Copynumber: 24.0 Consensus size: 4
35302154 CCCGAGAGAA
* * * * **
35302164 TATG TATG TATG TATG TACG TA-G TATG TACG CACG TATG TCCG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
** ** * *
35302211 TACA TATG CGTG TATA TATG TATG TATG TATG TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
35302259 CGGAAAAACC
Statistics
Matches: 69, Mismatches: 21, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
3 3 0.04
4 66 0.96
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.42
Consensus pattern (4 bp):
TATG
Found at i:35304961 original size:18 final size:18
Alignment explanation
Indices: 35304940--35304995 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
35304930 GTCTATTTTC
*
35304940 TTTTCTTTTATTATTATT
1 TTTTCTTTTATTTTTATT
*
35304958 TTTTCTTTTATTTTTA-A
1 TTTTCTTTTATTTTTATT
35304975 TTTTCTGTTTATTTTTATT
1 TTTTCT-TTTATTTTTATT
35304994 TT
1 TT
35304996 CTTAGACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.18
18 25 0.76
19 2 0.06
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTCTTTTATTTTTATT
Found at i:35304977 original size:7 final size:6
Alignment explanation
Indices: 35304945--35304995 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
35304935 TTTTCTTTTC
* * * *
35304945 TTTTAT TATTAT TTTT-T CTTTTAT TTTTAA TTTTCT GTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
35304993 TTT
1 TTT
35304996 CTTAGACTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
5 1 0.03
6 33 0.94
7 1 0.03
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:35309955 original size:27 final size:27
Alignment explanation
Indices: 35309916--35310189 Score: 225
Period size: 27 Copynumber: 10.3 Consensus size: 27
35309906 AGAGGTTAAT
*
35309916 AAATGATCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* ** * *
35309943 AAATGACCAAATTACCTTCAAAAGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * *
35309970 AAATAATCGAATTA---CCACATGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
35309994 AAATGACCGAATTACCCTCACAAGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * *
35310021 ACATGACCGAATTACCCTCACAAGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * *
35310048 AAATAACCGAATTATCCCCACAAGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
35310075 AAATAACCGAATTACCCCTACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* ***
35310102 AAAT-AGCTGAATTATCCCCTGTAGGGTA
1 AAATGA-CCGAATTA-CCCCCACAGGGTA
*
35310130 AAATGACCGAATTACCCCCA-TGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * * ** *
35310156 AAATGAACAAAATACCCTTATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
35310183 AAATGAC
1 AAATGAC
35310190 TGTTATACCC
Statistics
Matches: 202, Mismatches: 38, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
24 19 0.09
26 21 0.10
27 139 0.69
28 22 0.11
29 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCACAGGGTA
Found at i:35310046 original size:78 final size:79
Alignment explanation
Indices: 35309916--35310105 Score: 247
Period size: 78 Copynumber: 2.4 Consensus size: 79
35309906 AGAGGTTAAT
* * * *
35309916 AAATGATCGAATTACCCCCACAGGGTAAAATGACCAAATTACCTTCAAAAGGTAAAATAATCGAA
1 AAATGACCGAATTACCCCCACAAGGTAAAATGACCAAATTACCCTCAAAAGGTAAAATAACCGAA
*
35309981 TTA-CCACATGGTA
66 TTACCCACAAGGTA
* * * *
35309994 AAATGACCGAATTACCCTCACAAGGTAACATGACCGAATTACCCTCACAAGGTAAAATAACCGAA
1 AAATGACCGAATTACCCCCACAAGGTAAAATGACCAAATTACCCTCAAAAGGTAAAATAACCGAA
35310059 TTATCCCCACAAGGTA
66 TTA--CCCACAAGGTA
* * *
35310075 AAATAACCGAATTACCCCTACAGGGTAAAAT
1 AAATGACCGAATTACCCCCACAAGGTAAAAT
35310106 AGCTGAATTA
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
78 60 0.63
81 35 0.37
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.20
Consensus pattern (79 bp):
AAATGACCGAATTACCCCCACAAGGTAAAATGACCAAATTACCCTCAAAAGGTAAAATAACCGAA
TTACCCACAAGGTA
Found at i:35310681 original size:33 final size:33
Alignment explanation
Indices: 35310634--35310699 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
35310624 ATGATATTAC
* *
35310634 TTACTGTATTGGGCTAAGGCCCACACTGTACTG
1 TTACTGAATAGGGCTAAGGCCCACACTGTACTG
* * *
35310667 TTACTGAATAGGGCTCAGGCCTAGACTGTACTG
1 TTACTGAATAGGGCTAAGGCCCACACTGTACTG
35310700 CTTGTTGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (33 bp):
TTACTGAATAGGGCTAAGGCCCACACTGTACTG
Found at i:35313761 original size:17 final size:18
Alignment explanation
Indices: 35313736--35313770 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35313726 AATATACAAA
*
35313736 GTAACAATC-TCAAAAAC
1 GTAAAAATCATCAAAAAC
35313753 GTAAAAATCATCAAAAAC
1 GTAAAAATCATCAAAAAC
35313771 TGAGCTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.57, C:0.20, G:0.06, T:0.17
Consensus pattern (18 bp):
GTAAAAATCATCAAAAAC
Found at i:35321946 original size:26 final size:27
Alignment explanation
Indices: 35321905--35321959 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
35321895 TGAACATTGA
*
35321905 AAAAAAAGAAACTCAGGTACCTAGTTG
1 AAAAAAAGAAACTCAGGTACCAAGTTG
*
35321932 AAAAAAA-AAATTCAGGTACCAAGTTG
1 AAAAAAAGAAACTCAGGTACCAAGTTG
35321958 AA
1 AA
35321960 CATTGAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (27 bp):
AAAAAAAGAAACTCAGGTACCAAGTTG
Found at i:35333900 original size:44 final size:43
Alignment explanation
Indices: 35333759--35333958 Score: 162
Period size: 44 Copynumber: 4.7 Consensus size: 43
35333749 TGTGGTTTTC
* ** * *
35333759 ATCTGCACCACTACAACTTCAGGGAGATAGGA-TTGATTTATTTTG
1 ATCTGCTCCACTACTGCTT-AGGGAGATAGGACTTGA-TT-CTTCG
* * **
35333804 -TCTGCTCCACTACTGCTTAGGGAGATA-AAATCTGCAAGCTTCG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGACT-TG-ATTCTTCG
* * *
35333847 ACCTACTCCACTACTGCTTAGGAAGATAGGACTTGATTTCTTCTG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGACTTGA-TTCTTC-G
* *
35333892 -TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGA--C-GCG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGACTTGATTCTTCG
35333931 ATCTGCTCCACTACTGCTTAGGGAGATA
1 ATCTGCTCCACTACTGCTTAGGGAGATA
35333959 AGATTTGTGG
Statistics
Matches: 127, Mismatches: 20, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
39 1 0.01
40 28 0.22
41 1 0.01
42 1 0.01
43 14 0.11
44 78 0.61
45 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAGGACTTGATTCTTCG
Found at i:35333947 original size:40 final size:42
Alignment explanation
Indices: 35333804--35333961 Score: 171
Period size: 44 Copynumber: 3.7 Consensus size: 42
35333794 ATTTATTTTG
* *
35333804 TCTGCTCCACTACTGCTTAGGGAGATAA-AATCTGCAAGCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACT-TG--ATCTTCGA
* * * *
35333848 CCTACTCCACTACTGCTTAGGAAGATAGGACTTGATTTCTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGA--TCTTC-GA
*
35333892 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGA-C-GCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATCTTCGA
35333932 TCTGCTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
35333962 TTTGTGGTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
39 1 0.01
40 31 0.32
41 1 0.01
42 1 0.01
44 61 0.62
45 3 0.03
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (42 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATCTTCGA
Found at i:35334333 original size:87 final size:87
Alignment explanation
Indices: 35334185--35334859 Score: 1158
Period size: 87 Copynumber: 7.8 Consensus size: 87
35334175 GCTAGTACTT
*
35334185 AGGAAGGCAAGATCTGCTATCTTTAACCAGC-CCACTGCAACTGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
35334249 TGATCTGCTTCGCTATTAACGC
66 CGATCTGCTTCGCTGTTAACGC
*
35334271 AGGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
35334336 CGATCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
*
35334358 AGGAAGGCAAAATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
35334423 CGATCTGCTTTGCTGTTGACGC
66 CGATCTGCTTCGCTGTTAACGC
* *
35334445 AGGAAGGCAAGATCTGATGTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
35334510 CGATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAACGC
* * *
35334532 AGGAAGGCAAGATCTGATGTCTTTAACCAGCTCCACTGCAACCAATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
35334597 CGATCTGCTTCGCTGGTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* * *
35334619 AAGAAGGCAAGATCTGCTATCTTTAACCAGCTCCATTGCAACCGATTGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
35334684 CGATCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
*
35334706 AGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGTAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
35334770 CGATCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
*
35334792 AGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAAACGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
35334856 CGAT
66 CGAT
35334860 ATTCATTTAT
Statistics
Matches: 558, Mismatches: 30, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
86 161 0.29
87 397 0.71
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTGCTTCGCTGTTAACGC
Found at i:35336507 original size:13 final size:13
Alignment explanation
Indices: 35336489--35336536 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
35336479 TGGCCTCTCC
*
35336489 TTTTCTTTTTCCT
1 TTTTCTTTTTCAT
*
35336502 TTTTCTTTTTCTT
1 TTTTCTTTTTCAT
*
35336515 TTTTCCTTTTCAT
1 TTTTCTTTTTCAT
*
35336528 TTTTATTTT
1 TTTTCTTTT
35336537 GACTTTGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTTCAT
Found at i:35336536 original size:20 final size:20
Alignment explanation
Indices: 35336494--35336536 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
35336484 TCTCCTTTTC
*
35336494 TTTTTCCTTTTTCTTTTTCT
1 TTTTTCCTTTTTCTTTTTAT
35336514 TTTTTCC-TTTTCATTTTTAT
1 TTTTTCCTTTTTC-TTTTTAT
35336534 TTT
1 TTT
35336537 GACTTTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCCTTTTTCTTTTTAT
Found at i:35347085 original size:29 final size:29
Alignment explanation
Indices: 35347052--35347144 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
35347042 TTTCACTTTT
35347052 AAGCTTAAATTCTAACAATTTAACACCAA
1 AAGCTTAAATTCTAACAATTTAACACCAA
* * ** *
35347081 AAGCTTCAAGCATTC-ATC-ATTTCACTTC-T
1 AAGCTT-AA--ATTCTAACAATTTAACACCAA
35347110 AAGCTTAAATTCTAACAATTTAACACCAA
1 AAGCTTAAATTCTAACAATTTAACACCAA
35347139 AAGCTT
1 AAGCTT
35347145 CAAGCAGTCA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
28 9 0.19
29 18 0.38
30 9 0.19
31 2 0.04
32 4 0.08
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (29 bp):
AAGCTTAAATTCTAACAATTTAACACCAA
Found at i:35347132 original size:58 final size:58
Alignment explanation
Indices: 35347042--35347157 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
35347032 ACTAGTGCTT
* *
35347042 TTTCACTTTTAAGCTTAAATTCTAACAATTTAACACCAAAAGCTTCAAGCATTCATCA
1 TTTCACTTCTAAGCTTAAATTCTAACAATTTAACACCAAAAGCTTCAAGCAGTCATCA
35347100 TTTCACTTCTAAGCTTAAATTCTAACAATTTAACACCAAAAGCTTCAAGCAGTCATCA
1 TTTCACTTCTAAGCTTAAATTCTAACAATTTAACACCAAAAGCTTCAAGCAGTCATCA
35347158 ATGACATCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (58 bp):
TTTCACTTCTAAGCTTAAATTCTAACAATTTAACACCAAAAGCTTCAAGCAGTCATCA
Found at i:35349442 original size:25 final size:25
Alignment explanation
Indices: 35349390--35349471 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
35349380 GAAGCTTCGG
*
35349390 AGAGCCATTAATCGAGAAGCTCATA
1 AGAGCCATTAATCGAGAAGCTCACA
*
35349415 AGAGCCAATT-ATCGAGAAGCTCGCA
1 AGAGCC-ATTAATCGAGAAGCTCACA
* * *
35349440 AGAACCATATAA-CGGGAAGCTCA-G
1 AGAGCCAT-TAATCGAGAAGCTCACA
35349464 AGAGCCAT
1 AGAGCCAT
35349472 ATATTGGGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
24 9 0.19
25 34 0.72
26 4 0.09
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (25 bp):
AGAGCCATTAATCGAGAAGCTCACA
Found at i:35349474 original size:24 final size:24
Alignment explanation
Indices: 35349298--35349474 Score: 69
Period size: 25 Copynumber: 7.2 Consensus size: 24
35349288 CATATAAGCA
**
35349298 CATA-AACGGGAAGCTCTATCGAGC
1 CATATAACGGGAAGCTC-AGAGAGC
* * *
35349322 CATATAATGGGAAGCTCATGTGAGT
1 CATATAACGGGAAGCTCA-GAGAGC
* * * * * *
35349347 CA-ATATCAGAAAGTTCAAGTGAGT
1 CATATAACGGGAAGCTC-AGAGAGC
* *
35349371 CA-ATATCGGGAAGCTTCGGAGAGC
1 CATATAACGGGAAGC-TCAGAGAGC
* *
35349395 CAT-TAATCGAGAAGCTCATAAGAGC
1 CATATAA-CGGGAAGCTCA-GAGAGC
* * *
35349420 CA-ATTATCGAGAAGCTC-GCAAGAAC
1 CATA-TAACGGGAAGCTCAG--AGAGC
35349445 CATATAACGGGAAGCTCAGAGAGC
1 CATATAACGGGAAGCTCAGAGAGC
35349469 CATATA
1 CATATA
35349475 TTGGGATGCT
Statistics
Matches: 115, Mismatches: 25, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
24 51 0.44
25 60 0.52
26 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (24 bp):
CATATAACGGGAAGCTCAGAGAGC
Found at i:35351759 original size:17 final size:16
Alignment explanation
Indices: 35351723--35351761 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
35351713 GAACGCAAGC
*
35351723 TATTCTTAAATAGAGT
1 TATTCTTAAAAAGAGT
*
35351739 TATTCTTAAACAAGGGT
1 TATTCTTAAA-AAGAGT
35351756 TATTCT
1 TATTCT
35351762 GACATGTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (16 bp):
TATTCTTAAAAAGAGT
Found at i:35352889 original size:21 final size:23
Alignment explanation
Indices: 35352858--35352902 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
35352848 CAATAGCTTA
35352858 AATAATAACTTTT-AAATAATTC
1 AATAATAACTTTTGAAATAATTC
*
35352880 AATAA-AACTTTTGAAATAGTTC
1 AATAATAACTTTTGAAATAATTC
35352902 A
1 A
35352903 GTGACCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (23 bp):
AATAATAACTTTTGAAATAATTC
Found at i:35366060 original size:25 final size:25
Alignment explanation
Indices: 35365971--35366060 Score: 101
Period size: 25 Copynumber: 3.6 Consensus size: 25
35365961 ATTCATGTAT
* * * *
35365971 GCTCATACGAGCTATGAATCAGTAT
1 GCTCATACGAGCTGTAAATCAGGAA
*
35365996 GCTC-TCACGAGCTGCAAATCAGGAA
1 GCTCAT-ACGAGCTGTAAATCAGGAA
* *
35366021 GCTCATACAAGCTGTAAATCGGGAA
1 GCTCATACGAGCTGTAAATCAGGAA
35366046 GCTCATACGAGCTGT
1 GCTCATACGAGCTGT
35366061 GGTATGTCCG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 1 0.02
25 52 0.96
26 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (25 bp):
GCTCATACGAGCTGTAAATCAGGAA
Found at i:35367878 original size:28 final size:28
Alignment explanation
Indices: 35367777--35367878 Score: 64
Period size: 27 Copynumber: 3.4 Consensus size: 28
35367767 AAATTTGTTT
*
35367777 ATATTTGTAAATAATTATTTACTTTTTTTTAG
1 ATATTT-TAAATAATT-TTTA-TTTTTATT-G
* * * *
35367809 ATTTTTTTAATTTAATTTTTTATTTTAATTTC
1 A-TATTTTAA-ATAA-TTTTTATTTTTA-TTG
*
35367841 ATA-TCT-AATAATTTTTATTTTTATTG
1 ATATTTTAAATAATTTTTATTTTTATTG
35367867 ATATTTTAAATA
1 ATATTTTAAATA
35367879 CAGATAACAT
Statistics
Matches: 53, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
26 5 0.09
27 13 0.25
28 7 0.13
29 1 0.02
30 2 0.04
31 1 0.02
32 9 0.17
33 13 0.25
34 2 0.04
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (28 bp):
ATATTTTAAATAATTTTTATTTTTATTG
Found at i:35385139 original size:20 final size:20
Alignment explanation
Indices: 35385103--35385140 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35385093 ATGGATAGAT
35385103 TTTTATATTATTTTTTAATA
1 TTTTATATTATTTTTTAATA
35385123 TTTTA-ATTATTTATTTAA
1 TTTTATATTATTT-TTTAA
35385141 GTAGATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATATTATTTTTTAATA
Found at i:35388064 original size:29 final size:28
Alignment explanation
Indices: 35388000--35388066 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 28
35387990 ATTAAAAAGA
35388000 GACTAAAATTGATCAATTCAAAAAGTATAG
1 GACTAAAATTGATCAATT--AAAAGTATAG
*
35388030 GAACTAAAATTGATCAAATT-AAAGTATAAT
1 G-ACTAAAATTGATC-AATTAAAAGTAT-AG
35388060 GACTAAA
1 GACTAAA
35388067 TCCACAACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
29 13 0.39
30 3 0.09
31 13 0.39
32 4 0.12
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (28 bp):
GACTAAAATTGATCAATTAAAAGTATAG
Found at i:35390362 original size:17 final size:15
Alignment explanation
Indices: 35390342--35390379 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
35390332 CATGGTCTTT
*
35390342 TTCTTCCTC-TTCTC
1 TTCTTCTTCTTTCTC
35390356 TTCTTCTT-TTTCTC
1 TTCTTCTTCTTTCTC
35390370 TTCTTCTTCT
1 TTCTTCTTCT
35390380 ACTGCCCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 20 0.95
15 1 0.05
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
TTCTTCTTCTTTCTC
Found at i:35390376 original size:14 final size:14
Alignment explanation
Indices: 35390351--35390377 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35390341 TTTCTTCCTC
35390351 TTCTCTTCTTCTTT
1 TTCTCTTCTTCTTT
35390365 TTCTCTTCTTCTT
1 TTCTCTTCTTCTT
35390378 CTACTGCCCA
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:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTCTTCTTCTTT
Found at i:35390453 original size:32 final size:32
Alignment explanation
Indices: 35390417--35390486 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
35390407 GCCATTTAAC
35390417 ATGACAACTAGGATGCCAACGAGGCCAGTTGA
1 ATGACAACTAGGATGCCAACGAGGCCAGTTGA
*
35390449 ATGACAACTAGGATGCCAACGTGGCCAGTTGA
1 ATGACAACTAGGATGCCAACGAGGCCAGTTGA
35390481 ATGACA
1 ATGACA
35390487 GGTCTGCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.17
Consensus pattern (32 bp):
ATGACAACTAGGATGCCAACGAGGCCAGTTGA
Found at i:35393114 original size:15 final size:15
Alignment explanation
Indices: 35393094--35393124 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35393084 TTGATCTTTC
35393094 TAGTATTATATATTA
1 TAGTATTATATATTA
35393109 TAGTATTATATATTA
1 TAGTATTATATATTA
35393124 T
1 T
35393125 GATTTTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TAGTATTATATATTA
Found at i:35393185 original size:17 final size:17
Alignment explanation
Indices: 35393165--35393199 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
35393155 ATATTAAGAA
35393165 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
35393182 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
35393199 T
1 T
35393200 AAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:35393250 original size:113 final size:114
Alignment explanation
Indices: 35393105--35393465 Score: 466
Period size: 122 Copynumber: 3.1 Consensus size: 114
35393095 AGTATTATAT
* *
35393105 ATTATAGTATTATA-TA-TTATGATTTTAGTAAATTCATATAAAAATATTTAATATTAAGAATTT
1 ATTATAGTTTTATAGTATTTATGATTTTAGTAAATTCAT-TAAGAATATTTAATATTAAGAATTT
* *
35393168 TATTAAATTATAT-TTTTTATTAAATTATATTTAAAAATAATTAATTTAA
65 TATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
35393217 ATTATA-TTTTATAGTATTTATGATTTTAGTAAATTC--TAAGAATATTTAATATTAAGAATTTT
1 ATTATAGTTTTATAGTATTTATGATTTTAGTAAATTCATTAAGAATATTTAATATTAAGAATTTT
* ** *
35393279 ATTAAATAATATATTTTTACCAAATTATATTTTTAATAATTATTATTTTAA
66 ATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTTTAA
* * * *
35393330 ATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCATTTAAGAATATTTAATATTAAA
1 ATTATAGTTT-T-ATA--GTAT-TTATGATTTTAGTAAATTCA-TTAAGAATATTTAATATTAAG
*
35393395 AATTTTATTAAATTATATGTTTTTATTAAATTATATTTAATAATAATTATTTTAA
60 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
*
35393450 ATTATA-TTATATAGTA
1 ATTATAGTTTTATAGTA
35393466 AGTATGACTC
Statistics
Matches: 217, Mismatches: 18, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
110 36 0.17
111 20 0.09
112 8 0.04
113 42 0.19
114 3 0.01
115 3 0.01
116 3 0.01
117 3 0.01
118 4 0.02
119 20 0.09
120 25 0.12
122 50 0.23
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (114 bp):
ATTATAGTTTTATAGTATTTATGATTTTAGTAAATTCATTAAGAATATTTAATATTAAGAATTTT
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
Found at i:35393319 original size:15 final size:15
Alignment explanation
Indices: 35393283--35393351 Score: 60
Period size: 15 Copynumber: 4.7 Consensus size: 15
35393273 AATTTTATTA
35393283 AATAA-TATATTTTT
1 AATAATTATATTTTT
35393297 ACCA-AATTATATTTTT
1 A--ATAATTATATTTTT
35393313 AATAATTAT-TATTTT
1 AATAATTATAT-TTTT
35393328 -A-AATTATATTTTAT
1 AATAATTATATTTT-T
35393342 AAT-ATTATAT
1 AATAATTATAT
35393352 ATTATAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.20
14 6 0.13
15 20 0.43
16 11 0.24
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
AATAATTATATTTTT
Found at i:35393331 original size:28 final size:29
Alignment explanation
Indices: 35393300--35393354 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
35393290 TATTTTTACC
35393300 AAATTATATTTT-TAATAATTAT-TATTTT
1 AAATTATATTTTATAAT-ATTATATATTTT
35393328 AAATTATATTTTATAATATTATATATT
1 AAATTATATTTTATAATATTATATATT
35393355 ATAATTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
AAATTATATTTTATAATATTATATATTTT
Found at i:35393332 original size:13 final size:14
Alignment explanation
Indices: 35393309--35393360 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 14
35393299 CAAATTATAT
35393309 TTTTAATAATTATTA
1 TTTT-ATAATTATTA
35393324 TTTTA-AATTA-TA
1 TTTTATAATTATTA
35393336 TTTTATAA-TATTA
1 TTTTATAATTATTA
35393349 TATATTATAATT
1 T-T-TTATAATT
35393361 TTAGTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 9 0.28
13 10 0.31
14 2 0.06
15 10 0.31
16 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTATAATTATTA
Found at i:35393356 original size:15 final size:15
Alignment explanation
Indices: 35393302--35393359 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
35393292 TTTTTACCAA
*
35393302 ATTATAT-TTTTAAT
1 ATTATATATTATAAT
*
35393316 AATTAT-TATTTTAA-
1 -ATTATATATTATAAT
*
35393330 ATTATATTTTATAAT
1 ATTATATATTATAAT
35393345 ATTATATATTATAAT
1 ATTATATATTATAAT
35393360 TTTAGTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.14
14 7 0.19
15 25 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATATATTATAAT
Found at i:35393369 original size:38 final size:39
Alignment explanation
Indices: 35393327--35393412 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 39
35393317 ATTATTATTT
* * *
35393327 TAAATTATATTTTATAATA-TTATATATT-ATAATTTTAG
1 TAAATTATATTTAAGAATATTTA-ATATTAAAAATTTTAG
* *
35393365 TAAATT-CATTTAAGAATATTTAATATTAAAAATTTTAT
1 TAAATTATATTTAAGAATATTTAATATTAAAAATTTTAG
35393403 TAAATTATAT
1 TAAATTATAT
35393413 GTTTTTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
37 14 0.36
38 23 0.59
39 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (39 bp):
TAAATTATATTTAAGAATATTTAATATTAAAAATTTTAG
Found at i:35398034 original size:48 final size:48
Alignment explanation
Indices: 35397955--35398048 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
35397945 AGGGAATTCT
* *
35397955 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
35398003 GTTGAATCCATTATTGGTG-GAAGTT-AGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCATTATTGGTGCG-AGTTGA-GCTGACTTAGGCGTTTTTA
35398049 AGCCAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 2 0.05
48 40 0.95
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:35400546 original size:48 final size:48
Alignment explanation
Indices: 35400467--35400560 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
35400457 AGGAAATTCT
* *
35400467 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
35400515 GTTGAATCCATTATTGGTG-GAAGTT-AGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCATTATTGGTGCG-AGTTGA-GCTGACTTAGGCGTTTTTA
35400561 AGCCAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 2 0.05
48 40 0.95
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:35402474 original size:17 final size:17
Alignment explanation
Indices: 35402454--35402487 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35402444 AATATTAAAA
35402454 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
35402471 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
35402488 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:35402719 original size:45 final size:44
Alignment explanation
Indices: 35402641--35402736 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
35402631 ATTACAACAT
* *
35402641 CATTCCATTTAACCAAACATAAGAATACTATTACGCCTCTATTC
1 CATTACATTCAACCAAACATAAGAATACTATTACGCCTCTATTC
* *
35402685 CATTACATTCAACCAAACAATTAA-ATTACTATTACGCCTCTATTT
1 CATTACATTCAACCAAAC-A-TAAGAATACTATTACGCCTCTATTC
35402730 CATTACA
1 CATTACA
35402737 GCTCTATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
44 16 0.35
45 27 0.59
46 3 0.07
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (44 bp):
CATTACATTCAACCAAACATAAGAATACTATTACGCCTCTATTC
Found at i:35402741 original size:16 final size:16
Alignment explanation
Indices: 35402722--35402770 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
35402712 ACTATTACGC
*
35402722 CTCTATTTCATTACAG
1 CTCTATTCCATTACAG
**
35402738 CTCTATTCCATTACTC
1 CTCTATTCCATTACAG
35402754 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
35402770 C
1 C
35402771 GACCCAAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.22, C:0.33, G:0.04, T:0.41
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:35411713 original size:19 final size:19
Alignment explanation
Indices: 35411691--35411727 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35411681 AATTAAAAAT
35411691 ATTTTAAAAATATAAATTA
1 ATTTTAAAAATATAAATTA
**
35411710 ATTTTGTAAATATAAATT
1 ATTTTAAAAATATAAATT
35411728 TGTGGATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTTAAAAATATAAATTA
Found at i:35412301 original size:22 final size:22
Alignment explanation
Indices: 35412270--35412318 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
35412260 TATAAAAGTA
*
35412270 AAAAAGATTA-AATATATATTTT
1 AAAAAGATTACAATAAAT-TTTT
35412292 AGAAAA-ATTACAATAAATTTTT
1 A-AAAAGATTACAATAAATTTTT
35412314 AAAAA
1 AAAAA
35412319 TATTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 10 0.42
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAAAGATTACAATAAATTTTT
Found at i:35434456 original size:5 final size:5
Alignment explanation
Indices: 35434446--35434473 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
35434436 ATTTCTCTTG
35434446 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
35434474 ATTGGCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:35438139 original size:3 final size:3
Alignment explanation
Indices: 35438131--35438166 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35438121 ATATTATGCT
35438131 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35438167 CTTGATAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35438312 original size:8 final size:8
Alignment explanation
Indices: 35438299--35438385 Score: 50
Period size: 8 Copynumber: 11.9 Consensus size: 8
35438289 TCAGTAATTA
35438299 TATATATT
1 TATATATT
35438307 TATATA--
1 TATATATT
35438313 TA-A-ATT
1 TATATATT
35438319 TATGAT-TT
1 TAT-ATATT
35438327 TATA-ATT
1 TATATATT
*
35438334 TTTATATT
1 TATATATT
*
35438342 TAAATATT
1 TATATATT
* *
35438350 TTTATAAAT
1 TATAT-ATT
35438359 T-TATA-T
1 TATATATT
35438365 TATAT-TT
1 TATATATT
35438372 T-TATATT
1 TATATATT
35438379 TATATAT
1 TATATAT
35438386 ATTTCAAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
4 1 0.02
5 1 0.02
6 9 0.15
7 15 0.25
8 32 0.52
9 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (8 bp):
TATATATT
Found at i:35438371 original size:21 final size:18
Alignment explanation
Indices: 35438301--35438389 Score: 96
Period size: 18 Copynumber: 4.9 Consensus size: 18
35438291 AGTAATTATA
**
35438301 TATATTTATATATAAATT
1 TATATTTATATATATTTT
35438319 TATGATTT-TATA-ATTTT
1 TAT-ATTTATATATATTTT
35438336 TATATTTA-A-ATATTTT
1 TATATTTATATATATTTT
35438352 TATAAATTTATATTATATTTT
1 TAT--ATTTATA-TATATTTT
35438373 TATATTTATATATATTT
1 TATATTTATATATATTT
35438390 CAAAATAACA
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
15 1 0.02
16 13 0.21
17 6 0.10
18 19 0.31
19 12 0.20
21 10 0.16
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (18 bp):
TATATTTATATATATTTT
Found at i:35447857 original size:8 final size:8
Alignment explanation
Indices: 35447837--35447893 Score: 59
Period size: 8 Copynumber: 7.5 Consensus size: 8
35447827 AGAAAAAAAA
35447837 AAGA-GAG
1 AAGAGGAG
35447844 AA-AGGAG
1 AAGAGGAG
35447851 AAGAGGAG
1 AAGAGGAG
35447859 -A-AGGAG
1 AAGAGGAG
*
35447865 AAGAAGAAG
1 AAG-AGGAG
*
35447874 AAGAGAAG
1 AAGAGGAG
35447882 AAGAGGAG
1 AAGAGGAG
35447890 AAGA
1 AAGA
35447894 AGAAGAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
6 6 0.14
7 9 0.21
8 21 0.49
9 7 0.16
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (8 bp):
AAGAGGAG
Found at i:35447862 original size:14 final size:14
Alignment explanation
Indices: 35447845--35447899 Score: 65
Period size: 14 Copynumber: 3.7 Consensus size: 14
35447835 AAAAGAGAGA
35447845 AAGGAGAAGAGGAG
1 AAGGAGAAGAGGAG
*
35447859 AAGGAGAAGAAGAAG
1 AAGGAGAAG-AGGAG
35447874 AAGAGAAGAAGAGGAG
1 AAG-G-AGAAGAGGAG
*
35447890 AAGAAGAAGA
1 AAGGAGAAGA
35447900 AGAAAGTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 15 0.43
15 7 0.20
16 8 0.23
17 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (14 bp):
AAGGAGAAGAGGAG
Found at i:35447871 original size:3 final size:3
Alignment explanation
Indices: 35447857--35447903 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
35447847 GGAGAAGAGG
* *
35447857 AGA AGG AGA AGA AGA AGA AG- AGA AGA AG- AGG AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
35447903 A
1 A
35447904 AGTTTATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:35448100 original size:22 final size:21
Alignment explanation
Indices: 35448073--35448287 Score: 156
Period size: 22 Copynumber: 10.0 Consensus size: 21
35448063 TAGATTAGAA
*
35448073 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGT-AATT
35448095 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
35448114 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
35448135 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
35448157 TATAGATTTGGAT-TAGTAATT
1 TTTTG-TATGAATATTGTAATT
35448178 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
35448197 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGT-AATT
35448219 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
35448244 AATTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAA-TT
*
35448268 TTTTATATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
35448288 ATTGTAATTT
Statistics
Matches: 154, Mismatches: 22, Indels: 35
0.73 0.10 0.17
Matches are distributed among these distances:
19 34 0.22
20 10 0.06
21 18 0.12
22 60 0.39
23 9 0.06
24 2 0.01
25 4 0.03
26 1 0.01
27 16 0.10
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:35448121 original size:19 final size:19
Alignment explanation
Indices: 35448097--35448133 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
35448087 TTTAAATTTT
35448097 TTGTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
35448116 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
35448134 TATTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:35448141 original size:83 final size:83
Alignment explanation
Indices: 35448054--35448293 Score: 216
Period size: 83 Copynumber: 2.8 Consensus size: 83
35448044 ATATTTAGTG
* * *
35448054 TTTATAGTTTAGATTAGAATTTTGTATGAATATTTTAAATTTTTTGTATGAATATTGTAATGTTG
1 TTTATA-TTTAAATTAGAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGTAATATTG
*
35448119 TATGAATATTGT-AATTAT
65 TATGAATATTATAAATTAT
* * * * * * *
35448137 TTTATAATTAAATTTGTATTTATAGATTTGGAT-TAGT-AATTTTTTGTATGAATATTGTAATTT
1 TTTATATTTAAATTAGAATTT-T-G-TATGAATATTGTAAATTTTTTGTATGAATATTGTAATAT
*
35448200 TGTATGAATATTATAAATTTTT
63 TGTATGAATATTATAAA-TTAT
* * * *
35448222 TGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTATATGAATATTGTAA
1 T-T-T--ATATT-TAA-ATTAGAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGTAA
35448287 TATTGTA
60 TATTGTA
35448294 ATTTTGCATG
Statistics
Matches: 122, Mismatches: 22, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
82 11 0.09
83 45 0.37
84 5 0.04
85 9 0.07
86 1 0.01
87 1 0.01
88 5 0.04
89 7 0.06
90 31 0.25
91 7 0.06
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (83 bp):
TTTATATTTAAATTAGAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGTAATATTGT
ATGAATATTATAAATTAT
Found at i:35448202 original size:19 final size:19
Alignment explanation
Indices: 35448178--35448320 Score: 95
Period size: 19 Copynumber: 8.4 Consensus size: 19
35448168 ATTAGTAATT
35448178 TTTTGTATGAATATTGTAA
1 TTTTGTATGAATATTGTAA
*
35448197 TTTTGTATGAATATTATAAA
1 TTTTGTATGAATATTGT-AA
35448217 TTTT-T-TG--TA-TG-AA
1 TTTTGTATGAATATTGTAA
* *
35448230 TATTG--T-AATATTATAA
1 TTTTGTATGAATATTGTAA
*
35448246 TTTTGTATGAATATTGCAA
1 TTTTGTATGAATATTGTAA
*
35448265 TTTT-T-T-TATA-TG-AA
1 TTTTGTATGAATATTGTAA
*
35448279 TATTG--T-AATATTGTAA
1 TTTTGTATGAATATTGTAA
*
35448295 TTTTGCATGAATATTGTAA
1 TTTTGTATGAATATTGTAA
35448314 TTTTGTA
1 TTTTGTA
35448321 AGTTAGCCGG
Statistics
Matches: 97, Mismatches: 12, Indels: 30
0.70 0.09 0.22
Matches are distributed among these distances:
13 6 0.06
14 11 0.11
15 6 0.06
16 17 0.18
17 1 0.01
18 5 0.05
19 45 0.46
20 6 0.06
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (19 bp):
TTTTGTATGAATATTGTAA
Found at i:35448240 original size:30 final size:27
Alignment explanation
Indices: 35448219--35448314 Score: 121
Period size: 27 Copynumber: 3.7 Consensus size: 27
35448209 ATTATAAATT
35448219 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTATAA
*
35448246 TTTTGTATGAATATTG-CA-ATT-T--
1 TTTTGTATGAATATTGTAATATTATAA
* *
35448268 TTTTATATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATATTATAA
*
35448295 TTTTGCATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
35448315 TTTGTAAGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
22 15 0.25
23 1 0.02
24 4 0.07
25 4 0.07
26 1 0.02
27 34 0.58
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (27 bp):
TTTTGTATGAATATTGTAATATTATAA
Found at i:35448240 original size:49 final size:49
Alignment explanation
Indices: 35448187--35448317 Score: 201
Period size: 49 Copynumber: 2.7 Consensus size: 49
35448177 TTTTTGTATG
* *
35448187 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTATATGAATATTGT
* * *
35448236 AATATTATAATTTTGTATGAATATTGCAATTTTTTTATATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTATATGAATATTGT
*
35448285 AATATTGTAATTTTGCATGAATATTGT-AATTTT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTT
35448318 GTAAGTTAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
48 5 0.07
49 68 0.93
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGTAAATTTTTTATATGAATATTGT
Done.