Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 50 of 427
Found at i:12060523 original size:254 final size:248
Alignment explanation
Indices: 12060012--12060590 Score: 762
Period size: 254 Copynumber: 2.3 Consensus size: 248
12060002 TTCAATTTCT
* * *
12060012 GTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
*
12060077 TTCAATTTC----TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
66 TTCAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
* *
12060138 CACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGA
131 CACACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTGA
* ** * * * **
12060203 GTTGAGCCTCGGGTTACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATTCT
195 GTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA
* *
12060257 GTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
* *
12060321 TTCAATTTCTGTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA
66 TTCAATTTCTGTTTTTCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCA
* * * * * * *
12060386 -ATTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGC
128 GA--TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGC
*
12060448 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAA
186 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA
12060511 G-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
12060575 TTCAATTTCTGTTTTT
66 TTCAATTTCTGTTTTT
12060591 AATGTCTGTT
Statistics
Matches: 291, Mismatches: 28, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
244 62 0.21
245 6 0.02
248 13 0.04
249 30 0.10
250 1 0.00
251 3 0.01
252 2 0.01
253 5 0.02
254 146 0.50
255 5 0.02
256 13 0.04
257 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (248 bp):
GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
TTCAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
CACACACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTGAG
TTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA
Found at i:12061271 original size:30 final size:30
Alignment explanation
Indices: 12061235--12061326 Score: 123
Period size: 34 Copynumber: 3.0 Consensus size: 30
12061225 AGCCCCCCAA
12061235 AAAAACCTAACCCAAAAAAAAAGAAAAAAG
1 AAAAACCTAACCCAAAAAAAAAGAAAAAAG
12061265 AAAAACCTAACCCAAAAAAAAAAGAAAAAAAAAG
1 AAAAACCTAACCC-AAAAAAAAAG---AAAAAAG
* *
12061299 AAAAACCTAA-CAAAAAAAAAATAAAAAA
1 AAAAACCTAACCCAAAAAAAAAGAAAAAA
12061327 ACCTAGCCAC
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.11
30 13 0.23
31 10 0.18
32 9 0.16
33 1 0.02
34 17 0.30
ACGTcount: A:0.77, C:0.14, G:0.04, T:0.04
Consensus pattern (30 bp):
AAAAACCTAACCCAAAAAAAAAGAAAAAAG
Found at i:12061294 original size:10 final size:10
Alignment explanation
Indices: 12061279--12061303 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12061269 ACCTAACCCA
12061279 AAAAAAAAAG
1 AAAAAAAAAG
12061289 AAAAAAAAAG
1 AAAAAAAAAG
12061299 AAAAA
1 AAAAA
12061304 CCTAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:12061327 original size:30 final size:30
Alignment explanation
Indices: 12061235--12061327 Score: 116
Period size: 30 Copynumber: 3.0 Consensus size: 30
12061225 AGCCCCCCAA
* *
12061235 AAAAACCTAACCCAAAAAAAAAGAAAAAAG
1 AAAAACCTAACCAAAAAAAAAAAAAAAAAG
12061265 AAAAACCTAACCCAAAAAAAAAAGAAAAAAAAAG
1 AAAAACCTAA-CC--AAAAAAAA-AAAAAAAAAG
12061299 AAAAACCTAA-CAAAAAAAAAATAAAAAAA
1 AAAAACCTAACCAAAAAAAAAA-AAAAAAA
12061328 CCTAGCCACC
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
29 2 0.04
30 25 0.45
31 2 0.04
32 1 0.02
33 7 0.12
34 19 0.34
ACGTcount: A:0.77, C:0.14, G:0.04, T:0.04
Consensus pattern (30 bp):
AAAAACCTAACCAAAAAAAAAAAAAAAAAG
Found at i:12061894 original size:24 final size:24
Alignment explanation
Indices: 12061817--12061904 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 24
12061807 ATTTTATATA
* * *
12061817 TATTATGTATATATTTTTTAATGC
1 TATTATGTATATATTCTTAAATAC
* ** *
12061841 CATTA-GTTATATATTTCTTATGTATT
1 TATTATG-TATATA-TTCTTAAATA-C
12061867 TATTATGTATATATTCTTAAATAC
1 TATTATGTATATATTCTTAAATAC
*
12061891 TATTATATATATAT
1 TATTATGTATATAT
12061905 ATATATTTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
23 1 0.02
24 23 0.48
25 13 0.27
26 10 0.21
27 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (24 bp):
TATTATGTATATATTCTTAAATAC
Found at i:12062021 original size:10 final size:10
Alignment explanation
Indices: 12062006--12062057 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 10
12061996 TTTTATGTAC
12062006 ATATGTATAT
1 ATATGTATAT
12062016 ATATGTATAT
1 ATATGTATAT
12062026 ATA--TATAT
1 ATATGTATAT
*
12062034 ATATATATAT
1 ATATGTATAT
* *
12062044 ATTTGTACAT
1 ATATGTATAT
12062054 ATAT
1 ATAT
12062058 TATTTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
8 8 0.22
10 28 0.78
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATGTATAT
Found at i:12062057 original size:2 final size:2
Alignment explanation
Indices: 12062006--12062045 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
12061996 TTTTATGTAC
* *
12062006 AT AT GT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12062046 TTGTACATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12062095 original size:14 final size:14
Alignment explanation
Indices: 12062076--12062103 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12062066 ATTATTGTTG
12062076 TATATTTTTATGTA
1 TATATTTTTATGTA
12062090 TATATTTTTATGTA
1 TATATTTTTATGTA
12062104 CGTTTCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TATATTTTTATGTA
Found at i:12062162 original size:37 final size:37
Alignment explanation
Indices: 12062120--12062221 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 37
12062110 CTAATATTTT
12062120 CTTTTATTGTAGATATTATTATTATTATTAT-TACATA
1 CTTTTATT-TAGATATTATTATTATTATTATGTACATA
*
12062157 CTTTTATTATATGCATATATATATATGTATTTTTATGTACATA
1 CTTTTATT-TA-G-ATAT-TAT-TAT-TATTATTATGTACATA
*
12062200 -TTATTATTT-TATATTATTATTA
1 CTT-TTATTTAGATATTATTATTA
12062222 CCAAATATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 8 0.15
40 3 0.05
41 3 0.05
42 11 0.20
43 11 0.20
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (37 bp):
CTTTTATTTAGATATTATTATTATTATTATGTACATA
Found at i:12062918 original size:3 final size:3
Alignment explanation
Indices: 12062912--12062983 Score: 117
Period size: 3 Copynumber: 24.0 Consensus size: 3
12062902 AAGTCGCTAC
12062912 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
12062960 AAT AAT AGT AAT AGC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
12062984 GTAAATATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12063120 original size:26 final size:24
Alignment explanation
Indices: 12063067--12063143 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
12063057 ATAGCAATAG
*
12063067 TAATAATA-TAATAATAAAGTAAAA
1 TAATAATAGTAATAATTAA-TAAAA
12063091 -AATAATAGTAATACATTAATAAGAA
1 TAATAATAGTAATA-ATTAATAA-AA
12063116 TAATAATAGT-AT-ATTAATAACAA
1 TAATAATAGTAATAATTAATAA-AA
12063139 TAATA
1 TAATA
12063144 GAAAATAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
23 22 0.47
24 8 0.17
25 8 0.17
26 9 0.19
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (24 bp):
TAATAATAGTAATAATTAATAAAA
Found at i:12063242 original size:3 final size:3
Alignment explanation
Indices: 12063236--12063308 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
12063226 CAACAAGAGA
* * * *
12063236 AAT AAT AAC AAT AAC AGAAT AAA AAT AAT GAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
12063283 AAT AGC AAT AAT AAT AA- AATT AAT AA
1 AAT AAT AAT AAT AAT AAT AA-T AAT AA
12063309 ATAAATATAA
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
2 2 0.04
3 47 0.87
4 4 0.07
5 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:12063313 original size:13 final size:12
Alignment explanation
Indices: 12063267--12063341 Score: 57
Period size: 12 Copynumber: 6.0 Consensus size: 12
12063257 AAAATAATGA
12063267 TAATAATAATAA-
1 TAATAATAA-AAT
*
12063279 TAATAATAGCAA-
1 TAATAATA-AAAT
12063291 TAATAATAAAAT
1 TAATAATAAAAT
12063303 TAATAA-ATAAAT
1 TAATAATA-AAAT
*
12063315 ATAATTAATAAATTT
1 -TAA-TAATAAA-AT
12063330 TAATAATAAAAT
1 TAATAATAAAAT
12063342 GGCAAATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
11 3 0.06
12 29 0.56
13 10 0.19
14 8 0.15
15 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (12 bp):
TAATAATAAAAT
Found at i:12063320 original size:17 final size:17
Alignment explanation
Indices: 12063295--12063327 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12063285 TAGCAATAAT
12063295 AATAAAATTAATAAATA
1 AATAAAATTAATAAATA
*
12063312 AATATAATTAATAAAT
1 AATAAAATTAATAAAT
12063328 TTTAATAATA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAAATTAATAAATA
Found at i:12065405 original size:87 final size:86
Alignment explanation
Indices: 12065231--12065465 Score: 294
Period size: 87 Copynumber: 2.7 Consensus size: 86
12065221 CCTGTTACCT
* * * * * * *
12065231 TACTGCTTAAGGCGATAATATCTATAAACTTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAAAC
1 TACTGCTTAGGGAGATAAGATCTGTAAATTTAACCTTGTTACCCTACTGCTTAGGGGGTTAAAAC
12065296 TTCGTCTTCGATCTGCTCCAC
66 TTCGTCTTCGATCTGCTCCAC
* * *
12065317 TACTGCTTAGGGAGATAAGATCT-TCAATTTAACCTTGTTACCCTACTGCTTAGGGGTTTAAGGT
1 TACTGCTTAGGGAGATAAGATCTGTAAATTTAACCTTGTTACCCTACTGCTTAGGGGGTTAA--A
* *
12065381 TCTTCGTCTTCGATCTGTTCCAC
64 ACTTCGTCTTCGATCTGCTCCAC
* * **
12065404 TACTGCTTAGGGGGTTAAGATCTGTAAATTTAGTC-TGTTACCCTACTGCTTAGGGGGTTAAA
1 TACTGCTTAGGGAGATAAGATCTGTAAATTTAACCTTGTTACCCTACTGCTTAGGGGGTTAAA
12065466 GCTTGGTGGT
Statistics
Matches: 128, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
85 33 0.26
86 20 0.16
87 67 0.52
88 8 0.06
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (86 bp):
TACTGCTTAGGGAGATAAGATCTGTAAATTTAACCTTGTTACCCTACTGCTTAGGGGGTTAAAAC
TTCGTCTTCGATCTGCTCCAC
Found at i:12065409 original size:44 final size:43
Alignment explanation
Indices: 12065274--12065464 Score: 162
Period size: 43 Copynumber: 4.4 Consensus size: 43
12065264 GCTTGTTACC
* *
12065274 CTACTGCTTAGGGGGTTAA-AACTTCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGATCTTCGTCTTCGATCTGTTCCA
* * * * *
12065316 CTACTGCTTAGGGAGATAAGATCTTCAAT-TT-AACCTTGTTACC-
1 CTACTGCTTAGGGGGTTAAGATCTTC-GTCTTCGATC-TGTT-CCA
* *
12065359 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGTTCCA
1 CTACTGCTTAGGGGGTTAA-GATCTTCGTCTTCGATCTGTTCCA
** *
12065403 CTACTGCTTAGGGGGTTAAGATCTGTAAAT-TTAG-TCTGTTACC-
1 CTACTGCTTAGGGGGTTAAGATCT-T-CGTCTTCGATCTGTT-CCA
12065446 CTACTGCTTAGGGGGTTAA
1 CTACTGCTTAGGGGGTTAA
12065465 AGCTTGGTGG
Statistics
Matches: 119, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
42 19 0.16
43 58 0.49
44 39 0.33
45 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (43 bp):
CTACTGCTTAGGGGGTTAAGATCTTCGTCTTCGATCTGTTCCA
Found at i:12065631 original size:43 final size:44
Alignment explanation
Indices: 12065553--12065639 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
12065543 AGGGAGGTAC
*
12065553 GGTCTGTGATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAA
1 GGTCTGTGAATTTCAGCCTATTACCCTACTACTTAGGGGGTTAA
* * * *
12065597 GGTCTGTGAATTT-AGCTTGTTACCCTATTGCTTAGGGGGTTAA
1 GGTCTGTGAATTTCAGCCTATTACCCTACTACTTAGGGGGTTAA
12065640 AGCTCAGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 26 0.68
44 12 0.32
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (44 bp):
GGTCTGTGAATTTCAGCCTATTACCCTACTACTTAGGGGGTTAA
Found at i:12066051 original size:66 final size:65
Alignment explanation
Indices: 12065946--12066111 Score: 192
Period size: 66 Copynumber: 2.5 Consensus size: 65
12065936 TGCTATGGTC
* * * ** * * *
12065946 GAATCAAATGCTCCTAACTAGA-TGTGATGAATGTGTCAAATAATTAGGATGGTATGATCGAAAT
1 GAATCAAATGCTCTTAATTAGAGTGTTATGAATGAATCAAATAACTAGGATGCTATGATCAAAAT
* * *
12066010 TAATCAAATGCTCTTAATTAAACGTGTTATGAATGAATCAAATAACTAGGATGCTATGATTAAAA
1 GAATCAAATGCTCTTAATTAGA-GTGTTATGAATGAATCAAATAACTAGGATGCTATGATCAAAA
12066075 T
65 T
12066076 GAATCAAATGCT-TCTAATTAGATGTGTTATGAATGA
1 GAATCAAATGCTCT-TAATTAGA-GTGTTATGAATGA
12066112 TGTATGAATG
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
64 18 0.21
65 1 0.01
66 66 0.78
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (65 bp):
GAATCAAATGCTCTTAATTAGAGTGTTATGAATGAATCAAATAACTAGGATGCTATGATCAAAAT
Found at i:12074072 original size:19 final size:20
Alignment explanation
Indices: 12074045--12074085 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12074035 TCTTTTCACA
* *
12074045 AAATTTAATGCACATG-ATG
1 AAATGTAATGCAAATGAATG
12074064 AAATGTAATGCAAATGAATG
1 AAATGTAATGCAAATGAATG
12074084 AA
1 AA
12074086 TGCAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGAATG
Found at i:12080891 original size:31 final size:30
Alignment explanation
Indices: 12080819--12080891 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 30
12080809 TACTAAGAAA
*
12080819 AAAATATATATATATATAAATAATAGTATT
1 AAAATATATATATATATAAATAATAATATT
* *
12080849 AGAAATCATATAGTATATATAACTGATAATATT
1 A-AAAT-ATATA-TATATATAAATAATAATATT
12080882 AAAATATATA
1 AAAATATATA
12080892 CATAATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 9 0.24
32 9 0.24
33 18 0.49
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAATATATATATATATAAATAATAATATT
Found at i:12081067 original size:14 final size:16
Alignment explanation
Indices: 12081038--12081069 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
12081028 AGGTAAATAT
12081038 AATAAAATGATATTAA
1 AATAAAATGATATTAA
12081054 AATAAAA-G-TATTAA
1 AATAAAATGATATTAA
12081068 AA
1 AA
12081070 ACAGTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AATAAAATGATATTAA
Found at i:12081115 original size:3 final size:3
Alignment explanation
Indices: 12081107--12081154 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
12081097 ACAAGGATAT
12081107 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12081155 TTGAAACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12081272 original size:3 final size:3
Alignment explanation
Indices: 12081258--12081312 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
12081248 AATGTATTTC
*
12081258 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12081306 AAT AAT A
1 AAT AAT A
12081313 TTGAAATGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12081806 original size:11 final size:12
Alignment explanation
Indices: 12081790--12081836 Score: 73
Period size: 11 Copynumber: 4.2 Consensus size: 12
12081780 AGGAAAAAAA
12081790 GAAGAGAG-AGG
1 GAAGAGAGAAGG
12081801 GAAGAGAGAA-G
1 GAAGAGAGAAGG
12081812 GAAGAGAGAAGG
1 GAAGAGAGAAGG
12081824 G-AGAGAGAAGG
1 GAAGAGAGAAGG
12081835 GA
1 GA
12081837 GGGGAATCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 30 0.91
12 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:12082387 original size:34 final size:35
Alignment explanation
Indices: 12082343--12082410 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
12082333 GAGTGTGTGA
*
12082343 TGGTGTTGGT-GCAGACAGCATGGGAGAATGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAATGGGAG
*
12082377 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAATGGGA
12082411 AGAGGCAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.22, C:0.10, G:0.49, T:0.19
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAATGGGAG
Found at i:12083218 original size:53 final size:53
Alignment explanation
Indices: 12083138--12083334 Score: 184
Period size: 53 Copynumber: 3.5 Consensus size: 53
12083128 GCGTGCCCCG
* *
12083138 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAACAACAGAAATAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAA
* * * **
12083191 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AA-AACTAAAAATACCTCAGCGTGCCCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAACAAC-AAAAATA----A-------AA
*
12083253 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAA
*
12083306 AGGCTTAACTCACCTCTCGCAATATGAGT
1 AGGCTCAACTCACCTCTCGCAATATGAGT
12083335 CAATTTAAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
50 3 0.03
51 8 0.07
52 5 0.04
53 53 0.46
55 1 0.01
60 1 0.01
62 26 0.23
63 5 0.04
64 9 0.08
65 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.26
Consensus pattern (53 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAA
Found at i:12083311 original size:115 final size:116
Alignment explanation
Indices: 12083024--12083405 Score: 687
Period size: 115 Copynumber: 3.3 Consensus size: 116
12083014 GTGTCCTGAA
*
12083024 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAAAGGCTGAACTCACC
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAAAGGCTTAACTCACC
*
12083089 TTTCGCAATATGAGTCAATTTAAAACTAAAAATACCTCAGCGTGCCCCGAG
66 TCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTCAGCGTGCCCCGAG
*
12083140 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAACAACAGAAATAAAAAGGCTTAACTCACC
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAAAGGCTTAACTCACC
12083205 TCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTCAGCGTG-CCCGAG
66 TCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTCAGCGTGCCCCGAG
12083255 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAAAGGCTTAACTCACC
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAAAGGCTTAACTCACC
* **
12083320 TCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTCAGCGTGTCTTGAG
66 TCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTCAGCGTGCCCCGAG
*
12083371 GCTCAACTCACCTCT-GCAATATGAGTTGATTTTGA
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTGA
12083406 CGAACAGAAA
Statistics
Matches: 258, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
115 134 0.52
116 124 0.48
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.27
Consensus pattern (116 bp):
GCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAACAACAAAAATAAAAAGGCTTAACTCACC
TCTCGCAATATGAGTCAATTTAAAACTAAAAATACCTCAGCGTGCCCCGAG
Found at i:12083425 original size:14 final size:14
Alignment explanation
Indices: 12083408--12083436 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12083398 GATTTTGACG
12083408 AACAGAAATTGAAA
1 AACAGAAATTGAAA
12083422 AACAGAAATTGAAA
1 AACAGAAATTGAAA
12083436 A
1 A
12083437 TACCTCAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AACAGAAATTGAAA
Found at i:12083595 original size:14 final size:14
Alignment explanation
Indices: 12083578--12083606 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12083568 GATTTTGACG
12083578 AACAGAAATTGAAA
1 AACAGAAATTGAAA
12083592 AACAGAAATTGAAA
1 AACAGAAATTGAAA
12083606 A
1 A
12083607 TACCTCAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AACAGAAATTGAAA
Found at i:12083633 original size:170 final size:169
Alignment explanation
Indices: 12083346--12083655 Score: 584
Period size: 170 Copynumber: 1.8 Consensus size: 169
12083336 AATTTAAAAC
*
12083346 TAAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTGCAATATGAGTTGATTTTGACGAAC
1 TAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTGCAATATGAGTTGATTTTGACGAAC
12083411 AGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGGCTCAACTCACCTCTCGC
66 AGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGGCTCAACTCACCTCTCGC
12083476 AATATGAGTTAATTAATTTTTTTGTTGATGAACAGAAAT
131 AATATGAGTTAATTAATTTTTTTGTTGATGAACAGAAAT
*
12083515 TAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGACGAA
1 TAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT-GCAATATGAGTTGATTTTGACGAA
*
12083580 CAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGGCTCAACTCACTTCTCG
65 CAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGGCTCAACTCACCTCTCG
12083645 CAATATGAGTT
130 CAATATGAGTT
12083656 GATTCTTTGG
Statistics
Matches: 137, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
169 38 0.28
170 99 0.72
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (169 bp):
TAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTGCAATATGAGTTGATTTTGACGAAC
AGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGGCTCAACTCACCTCTCGC
AATATGAGTTAATTAATTTTTTTGTTGATGAACAGAAAT
Found at i:12090514 original size:43 final size:44
Alignment explanation
Indices: 12090444--12090596 Score: 201
Period size: 43 Copynumber: 3.6 Consensus size: 44
12090434 TTGGGCGGGN
* *
12090444 CGCTACAGAGACGCCAAATCTGTTATCTTCGATCCGATCTCCGC
1 CGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
12090488 CGCTACAGAGACG-CAAATCTGTTATCTTCGATCTGCTCTCCG-
1 CGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
* * *
12090530 CTCTACAGAGATGCCAAATC----ATCTTCGATCTGCTCTTCGC
1 CGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
* *
12090570 CGCTACGGAGACGCCAAATCTATTATC
1 CGCTACAGAGACGCCAAATCTGTTATC
12090597 CGCCGAGAGA
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
39 18 0.19
40 17 0.18
42 11 0.12
43 33 0.35
44 16 0.17
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.27
Consensus pattern (44 bp):
CGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
Found at i:12090563 original size:39 final size:40
Alignment explanation
Indices: 12090444--12091139 Score: 532
Period size: 44 Copynumber: 16.9 Consensus size: 40
12090434 TTGGGCGGGN
* *
12090444 CGCTACAGAGACGCCAAATCTGTTATCTTCGATCCGATCTCCGC
1 CGCTACAGAGACGCCAAATC----ATCTTCGATCTGCTCTCCGC
12090488 CGCTACAGAGACG-CAAATCTGTTATCTTCGATCTGCTCTCCG-
1 CGCTACAGAGACGCCAAATC----ATCTTCGATCTGCTCTCCGC
* * *
12090530 CTCTACAGAGATGCCAAATCATCTTCGATCTGCTCTTCGC
1 CGCTACAGAGACGCCAAATCATCTTCGATCTGCTCTCCGC
* * * **
12090570 CGCTACGGAGACGCCAAATC-TATT--ATCCGC-C-GAG-
1 CGCTACAGAGACGCCAAATCATCTTCGATCTGCTCTCCGC
* * ** *
12090604 AGACT-CA-A-A---TATGTTAT-TTCGATCTGCTCTCCGC
1 CG-CTACAGAGACGCCAAATCATCTTCGATCTGCTCTCCGC
** *
12090638 CGCTATGGAGACACCAAAATCTGTTATCTTCGATCTGCTCTCCGC
1 CGCTACAGAGACGCC-AAATC----ATCTTCGATCTGCTCTCCGC
*
12090683 CGCT-CAGAGATGCCAAATCATCTTCGATCTGCTCTCCGC
1 CGCTACAGAGACGCCAAATCATCTTCGATCTGCTCTCCGC
*
12090722 CGCTACAG-GATGCCAAATCTATTATCTTCGATCTGCTCTCCGC
1 CGCTACAGAGACGCCAAATC----ATCTTCGATCTGCTCTCCGC
*
12090765 CG-TACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCCGC
1 CGCTACAGAGACGCCAAATC----ATCTTCGATCTGCTCTCCGC
* *
12090808 CGCTACAGAGACGCCAAATCTGCTACCTTCGATCTGCTCTCCAC
1 CGCTACAGAGACGCCAAA--T-C-ATCTTCGATCTGCTCTCCGC
* * *
12090852 CGCTACAAACACGCCAAATCTTTTATCTTCGATCTGCTTTCCGC
1 CGCTACAGAGACGCCAAATC----ATCTTCGATCTGCTCTCCGC
*
12090896 CGCTACAGAGACGCCAAATCTGTTATC-TCGATTTGCTCTCCGC
1 CGCTACAGAGACGCCAAATC----ATCTTCGATCTGCTCTCCGC
* *
12090939 CGCTACATAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
1 CGCTACAGAGACGCCAAATC----ATCTTCGATCTGCTCTCCGC
* *
12090983 TGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCCGC
1 CGCTACAGAGACGCCAAATCATCTTCGATCTGCTCTCCGC
* * *
12091023 CACTACAGAGATGCCAAATCATCTTCGATCTGCTCTCTGC
1 CGCTACAGAGACGCCAAATCATCTTCGATCTGCTCTCCGC
* *
12091063 CGCTATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTG-
1 CGCTACAGAGACGCCAAATC----ATCTTCGATCTGCTCTCCGC
* *
12091106 CGCTACAGAGACGCCAAATCATCTTGGATTTGCT
1 CGCTACAGAGACGCCAAATCATCTTCGATCTGCT
12091140 TCAACGTAAA
Statistics
Matches: 551, Mismatches: 62, Indels: 83
0.79 0.09 0.12
Matches are distributed among these distances:
29 4 0.01
30 1 0.00
31 5 0.01
32 2 0.00
33 4 0.01
34 3 0.01
35 4 0.01
36 2 0.00
37 5 0.01
39 68 0.12
40 96 0.17
41 1 0.00
42 17 0.03
43 152 0.28
44 164 0.30
45 21 0.04
46 1 0.00
47 1 0.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (40 bp):
CGCTACAGAGACGCCAAATCATCTTCGATCTGCTCTCCGC
Found at i:12090726 original size:152 final size:150
Alignment explanation
Indices: 12090458--12090747 Score: 440
Period size: 152 Copynumber: 1.9 Consensus size: 150
12090448 ACAGAGACGC
* *
12090458 CAAATCTGTTATCTTCGATCCGATCTCCGCCGCTACAGAGACGCAAATCTGTTATCTTCGATCTG
1 CAAATATGTTATCTTCGATCCGATCTCCGCCGCTACAGAGACCCAAATCTGTTATCTTCGATCTG
* * *
12090523 CTCTCCGCTCTACAGAGATGCCAAATCATCTTCGATCTGCTCTTCGCCGCTACGGAGACGCCAAA
66 CTCTCCGCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCCGCCGCTACAG-GACGCCAAA
12090588 TCTATTATCCGCCGAGAGACT
130 TCTATTATCCGCCGAGAGACT
* * **
12090609 CAAATATGTTAT-TTCGATCTGCTCTCCGCCGCTATGGAGACACCAAAATCTGTTATCTTCGATC
1 CAAATATGTTATCTTCGATCCGATCTCCGCCGCTACAGAGAC-CC-AAATCTGTTATCTTCGATC
*
12090673 TGCTCTCCGCCGCT-CAGAGATGCCAAATCATCTTCGATCTGCTCTCCGCCGCTACAGGATGCCA
64 TGCTCTCCG-CGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCCGCCGCTACAGGACGCCA
12090737 AATCTATTATC
128 AATCTATTATC
12090748 TTCGATCTGC
Statistics
Matches: 126, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
150 25 0.20
151 29 0.23
152 69 0.55
153 3 0.02
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.28
Consensus pattern (150 bp):
CAAATATGTTATCTTCGATCCGATCTCCGCCGCTACAGAGACCCAAATCTGTTATCTTCGATCTG
CTCTCCGCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCCGCCGCTACAGGACGCCAAAT
CTATTATCCGCCGAGAGACT
Found at i:12090838 original size:44 final size:44
Alignment explanation
Indices: 12090609--12091125 Score: 674
Period size: 44 Copynumber: 12.1 Consensus size: 44
12090599 CCGAGAGACT
* ** *
12090609 CAAATATGTTAT-TTCGATCTGCTCTCCGCCGCTATGGAGACAC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
*
12090652 CAAAATCTGTTATCTTCGATCTGCTCTCCGCCGCT-CAGAGATGC
1 C-AAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
*
12090696 CAAATC----ATCTTCGATCTGCTCTCCGCCGCTACAG-GATGC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
* *
12090735 CAAATCTATTATCTTCGATCTGCTCTCCGCCG-TACAGAGACAC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
12090778 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
* * * * *
12090822 CAAATCTGCTACCTTCGATCTGCTCTCCACCGCTACAAACACGC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
* *
12090866 CAAATCTTTTATCTTCGATCTGCTTTCCGCCGCTACAGAGACGC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
* * *
12090910 CAAATCTGTTATC-TCGATTTGCTCTCCGCCGCTACATAGATGC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
* *
12090953 CAAATCTGTTATCTTCGATCTGCTCTCCGCTGCTACAGAGATGC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
* *
12090997 CAAATC----ATCTTCGATCTGCTCTCCGCCACTACAGAGATGC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
* *
12091037 CAAATC----ATCTTCGATCTGCTCTCTGCCGCTATAGAGACGC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
*
12091077 CAAATCTGTTATCTTCGATCTGCTCTCTG-CGCTACAGAGACGC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
12091120 CAAATC
1 CAAATC
12091126 ATCTTGGATT
Statistics
Matches: 424, Mismatches: 36, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
39 35 0.08
40 77 0.18
42 5 0.01
43 120 0.28
44 166 0.39
45 21 0.05
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.28
Consensus pattern (44 bp):
CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGC
Found at i:12090973 original size:87 final size:88
Alignment explanation
Indices: 12090609--12091125 Score: 674
Period size: 87 Copynumber: 6.1 Consensus size: 88
12090599 CCGAGAGACT
* ** *
12090609 CAAATATGTTAT-TTCGATCTGCTCTCCGCCGCTATGGAGACACCAAAATCTGTTATCTTCGATC
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCC-AAATCTGTTATCTTCGATC
*
12090673 TGCTCTCCGCCGCT-CAGAGATGC
65 TGCTCTCCGCCGCTACAGAGACGC
* *
12090696 CAAATC----ATCTTCGATCTGCTCTCCGCCGCTACAG-GATGCCAAATCTATTATCTTCGATCT
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCT
*
12090756 GCTCTCCGCCG-TACAGAGACAC
66 GCTCTCCGCCGCTACAGAGACGC
* *
12090778 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTACCTTCGATCT
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCT
* * *
12090843 GCTCTCCACCGCTACAAACACGC
66 GCTCTCCGCCGCTACAGAGACGC
* * *
12090866 CAAATCTTTTATCTTCGATCTGCTTTCCGCCGCTACAGAGACGCCAAATCTGTTATC-TCGATTT
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCT
* *
12090930 GCTCTCCGCCGCTACATAGATGC
66 GCTCTCCGCCGCTACAGAGACGC
* *
12090953 CAAATCTGTTATCTTCGATCTGCTCTCCGCTGCTACAGAGATGCCAAATC----ATCTTCGATCT
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCT
* *
12091014 GCTCTCCGCCACTACAGAGATGC
66 GCTCTCCGCCGCTACAGAGACGC
* *
12091037 CAAATC----ATCTTCGATCTGCTCTCTGCCGCTATAGAGACGCCAAATCTGTTATCTTCGATCT
1 CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCT
*
12091098 GCTCTCTG-CGCTACAGAGACGC
66 GCTCTCCGCCGCTACAGAGACGC
12091120 CAAATC
1 CAAATC
12091126 ATCTTGGATT
Statistics
Matches: 378, Mismatches: 39, Indels: 30
0.85 0.09 0.07
Matches are distributed among these distances:
80 36 0.10
81 1 0.00
82 43 0.11
83 27 0.07
84 74 0.20
86 28 0.07
87 108 0.29
88 61 0.16
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.28
Consensus pattern (88 bp):
CAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCT
GCTCTCCGCCGCTACAGAGACGC
Found at i:12091211 original size:88 final size:88
Alignment explanation
Indices: 12091088--12091310 Score: 360
Period size: 88 Copynumber: 2.6 Consensus size: 88
12091078 AAATCTGTTA
* * * *
12091088 TCTTCGATCTGCTCTCTG-C-GCTACAGAGACGCCAAATCATCTTGGATTTGCTTCAACGTAAAC
1 TCTTCGATCTGCTCCCTGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAAC
12091151 ACGTGAAAGCCAAATCAGCTATG
66 ACGTGAAAGCCAAATCAGCTATG
*
12091174 TCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAAC
1 TCTTCGATCTGCTCCCTGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAAC
12091239 ACGTGAAAGCCAAATCAGCTATG
66 ACGTGAAAGCCAAATCAGCTATG
* * *
12091262 TCTTTGATCTGCTCCCTGCCTGATACAAAAATGCCAAATCATCTTGGAT
1 TCTTCGATCTGCTCCCTGCCTGATACAGAGATGCCAAATCATCTTGGAT
12091311 ATCTTCAGCT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
86 16 0.13
87 1 0.01
88 109 0.87
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (88 bp):
TCTTCGATCTGCTCCCTGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAAC
ACGTGAAAGCCAAATCAGCTATG
Found at i:12091251 original size:41 final size:41
Alignment explanation
Indices: 12091118--12091255 Score: 111
Period size: 41 Copynumber: 3.2 Consensus size: 41
12091108 CTACAGAGAC
*
12091118 GCCAAATCATCTTGGATTTGCTTCAACGTAAACACGTGAAA
1 GCCAAATCATCTTGGATCTGCTTCAACGTAAACACGTGAAA
* ** * * *
12091159 GCCAAATCAGCTATGTCTTCGATCTGC-TCCCCGCCTGATACA-GAG-AT
1 GCCAAAT---C-A--TCTTGGATCTGCTTCAACG--T-AAACACGTGAAA
12091206 GCCAAATCATCTTGGATCTGCTTCAACGTAAACACGTGAAA
1 GCCAAATCATCTTGGATCTGCTTCAACGTAAACACGTGAAA
12091247 GCCAAATCA
1 GCCAAATCA
12091256 GCTATGTCTT
Statistics
Matches: 72, Mismatches: 13, Indels: 24
0.66 0.12 0.22
Matches are distributed among these distances:
39 4 0.06
40 3 0.04
41 28 0.39
42 4 0.06
43 1 0.01
44 2 0.03
45 1 0.01
46 4 0.06
47 18 0.25
48 3 0.04
49 4 0.06
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (41 bp):
GCCAAATCATCTTGGATCTGCTTCAACGTAAACACGTGAAA
Found at i:12102120 original size:19 final size:19
Alignment explanation
Indices: 12102096--12102133 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12102086 GAAATGAATA
*
12102096 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
12102115 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
12102134 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:12102409 original size:2 final size:2
Alignment explanation
Indices: 12102402--12102429 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12102392 GTAGCTAAAT
12102402 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12102430 CATAAACAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12103323 original size:7 final size:7
Alignment explanation
Indices: 12103313--12103337 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12103303 TTTTCTTCAT
12103313 TTTTTTA
1 TTTTTTA
12103320 TTTTTTA
1 TTTTTTA
12103327 TTTTTTA
1 TTTTTTA
12103334 TTTT
1 TTTT
12103338 GGGTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:12103524 original size:43 final size:45
Alignment explanation
Indices: 12103454--12103558 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 45
12103444 CCCAAACAGG
* * * *
12103454 GTCTTACACGAAATC-GAATAACGATGCCAAAGTCTCAGACA-TA
1 GTCTTACACGTAATCACAATAACAATGCCAAAGTCCCAGACATTA
* * *
12103497 GTCTTACACGTAATCACAAT-ACAATGCCAATGTCCCATACATTT
1 GTCTTACACGTAATCACAATAACAATGCCAAAGTCCCAGACATTA
*
12103541 GTCTTACATGTAATCACA
1 GTCTTACACGTAATCACA
12103559 TCTCGGTAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
43 31 0.60
44 21 0.40
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (45 bp):
GTCTTACACGTAATCACAATAACAATGCCAAAGTCCCAGACATTA
Found at i:12105303 original size:2 final size:2
Alignment explanation
Indices: 12105296--12105326 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
12105286 CAATTCATGC
12105296 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
12105327 TAAATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12106184 original size:16 final size:15
Alignment explanation
Indices: 12106165--12106207 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
12106155 AAATTTCAAT
12106165 GAAAAGAAAAGGAAA
1 GAAAAGAAAAGGAAA
* *
12106180 GGAAAGAAAGAGGGAA
1 GAAAAGAAA-AGGAAA
12106196 GAAATAGAAAAG
1 GAAA-AGAAAAG
12106208 ATGGATGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 8 0.35
16 10 0.43
17 5 0.22
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (15 bp):
GAAAAGAAAAGGAAA
Found at i:12107030 original size:34 final size:34
Alignment explanation
Indices: 12106960--12107055 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 34
12106950 CATGCATATA
*
12106960 TAGTAATAATCATGC-TATAACAAATCAGTACGG
1 TAGTAATAATCATGCTTATAACAAATCAGTACAG
*
12106993 TAGTAATAATCATGCTTATAACAAAT-A-TATTTAG
1 TAGTAATAATCATGCTTATAACAAATCAGTA--CAG
**
12107027 TAGTAATTGTCATGCTTTATAACAAATCA
1 TAGTAATAATCATGC-TTATAACAAATCA
12107056 TAACAATAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
32 2 0.04
33 16 0.30
34 24 0.44
35 11 0.20
36 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (34 bp):
TAGTAATAATCATGCTTATAACAAATCAGTACAG
Found at i:12107954 original size:12 final size:13
Alignment explanation
Indices: 12107937--12107968 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12107927 AGAGGGAAAT
12107937 GAAGAAA-AGAGA
1 GAAGAAATAGAGA
12107949 GAAGAAATAGAGA
1 GAAGAAATAGAGA
12107962 GAAGAAA
1 GAAGAAA
12107969 GAAAATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (13 bp):
GAAGAAATAGAGA
Found at i:12109258 original size:137 final size:137
Alignment explanation
Indices: 12109012--12109298 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
12109002 TATTGGGCCT
**
12109012 AAGCCCATTAAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
12109077 AGCCCCTTATTCAGATAACAGTATGGCTCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
12109142 CATATGC
131 CATATGC
12109149 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
12109214 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCTATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
12109279 CATATGC
131 CATATGC
12109286 AAGCCCATTTGGG
1 AAGCCCATTTGGG
12109299 GAGACTACTC
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:12111122 original size:26 final size:26
Alignment explanation
Indices: 12111086--12111195 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
12111076 CATGATATTC
12111086 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
12111112 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
12111138 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
12111164 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
12111190 TTATCA
1 TTATCA
12111196 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:12111206 original size:10 final size:10
Alignment explanation
Indices: 12111191--12111215 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12111181 CCTAACCTAT
12111191 TATCAATTTG
1 TATCAATTTG
12111201 TATCAATTTG
1 TATCAATTTG
12111211 TATCA
1 TATCA
12111216 TAAATTATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (10 bp):
TATCAATTTG
Found at i:12111368 original size:10 final size:10
Alignment explanation
Indices: 12111353--12111380 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
12111343 TAGCCTATAG
12111353 CATTTTCAAA
1 CATTTTCAAA
12111363 CATTTTCAAA
1 CATTTTCAAA
12111373 CATTTTCA
1 CATTTTCA
12111381 CATAGGTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (10 bp):
CATTTTCAAA
Found at i:12113671 original size:21 final size:22
Alignment explanation
Indices: 12113631--12113674 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
12113621 ATATTCCTAC
12113631 ATTACATGTGTTTATAGTATTT
1 ATTACATGTGTTTATAGTATTT
* *
12113653 ATTACAT-TGTTTTTTGTATTT
1 ATTACATGTGTTTATAGTATTT
12113674 A
1 A
12113675 ATAACTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (22 bp):
ATTACATGTGTTTATAGTATTT
Found at i:12114696 original size:50 final size:50
Alignment explanation
Indices: 12114642--12114737 Score: 192
Period size: 50 Copynumber: 1.9 Consensus size: 50
12114632 ACTTATCTAT
12114642 TTTTACTGTTAAAAACTGTCGGAGTTGACGAAACAACCAAACACGTGGCA
1 TTTTACTGTTAAAAACTGTCGGAGTTGACGAAACAACCAAACACGTGGCA
12114692 TTTTACTGTTAAAAACTGTCGGAGTTGACGAAACAACCAAACACGT
1 TTTTACTGTTAAAAACTGTCGGAGTTGACGAAACAACCAAACACGT
12114738 ATGCCACATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (50 bp):
TTTTACTGTTAAAAACTGTCGGAGTTGACGAAACAACCAAACACGTGGCA
Found at i:12116780 original size:43 final size:43
Alignment explanation
Indices: 12116732--12116923 Score: 187
Period size: 43 Copynumber: 4.5 Consensus size: 43
12116722 GCCACTAAAA
* *
12116732 AAACGCCGCTAAAAGTCAT-GATCTTTAGCGGCACTTTCCCCAC
1 AAACGCCGCTAAAAGTCATAG-TCTTTAGCGGCGCTTTTCCCAC
* *
12116775 AAACGCCGCTAAAGGTCAT-GATCTTTAGCGCCGCTTTAT-CCAC
1 AAACGCCGCTAAAAGTCATAG-TCTTTAGCGGCGCTTT-TCCCAC
* * *
12116818 AAACGCCGCT-AAAGACCATAGTCTTTAGCGGCGCTTTTTCTAC
1 AAACGCCGCTAAAAG-TCATAGTCTTTAGCGGCGCTTTTCCCAC
* * * *
12116861 AAACGCCG-TTAAAGACCATAGCCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTAAAAG-TCATAGTCTTTAGCGGCGCTTTTCCCAC
* *
12116904 AAACGCCACTAAAGGTCATA
1 AAACGCCGCTAAAAGTCATA
12116924 AAATTTTAAA
Statistics
Matches: 127, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
42 5 0.04
43 117 0.92
44 5 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAAGTCATAGTCTTTAGCGGCGCTTTTCCCAC
Found at i:12116887 original size:86 final size:87
Alignment explanation
Indices: 12116730--12116917 Score: 206
Period size: 86 Copynumber: 2.2 Consensus size: 87
12116720 ATGCCACTAA
* **
12116730 AAAAACGCCGCTAAA-AGTCATGATCTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGGTCAT
1 AAAAACGCCGCTAAAGAGCCATGATCTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGACCAT
*
12116794 GATCTTTAGCGCCGCTTTAT-CC
66 GACCTTTAGCGCCGCTTT-TCCC
* * ** * *
12116816 ACAAACGCCGCTAAAGA-CCAT-AGTCTTTAGCGGCGCTTTTTCTACAAACGCCGTTAAAGACCA
1 AAAAACGCCGCTAAAGAGCCATGA-TCTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGACCA
*
12116879 T-AGCCTTTAGCGGCGCTTTTCCC
65 TGA-CCTTTAGCGCCGCTTTTCCC
*
12116902 AAAAACGCCACTAAAG
1 AAAAACGCCGCTAAAG
12116918 GTCATAAAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
85 3 0.04
86 81 0.95
87 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (87 bp):
AAAAACGCCGCTAAAGAGCCATGATCTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGACCAT
GACCTTTAGCGCCGCTTTTCCC
Found at i:12116946 original size:6 final size:6
Alignment explanation
Indices: 12116930--12116986 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
12116920 CATAAAATTT
* * *
12116930 TAAAAA AAAAAA TAAAAA TAAAAA TATAGAA TCAAAAC T-AAAA TAAATAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA-AAAA T-AAAAA TAAAAA TAAA-AA
12116980 TAAAAA T
1 TAAAAA T
12116987 TAGATTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
5 4 0.10
6 23 0.56
7 13 0.32
8 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:12118876 original size:22 final size:21
Alignment explanation
Indices: 12118836--12118877 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12118826 ATTCAAATAT
*
12118836 ATATATAAATCATAAAAATTA
1 ATATAAAAATCATAAAAATTA
*
12118857 ATATAAAAATACATATAAATT
1 ATATAAAAAT-CATAAAAATT
12118878 GTTATGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATAAAAATCATAAAAATTA
Found at i:12118933 original size:12 final size:12
Alignment explanation
Indices: 12118916--12118940 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12118906 TAAAAATAAC
12118916 AATTTAACACTA
1 AATTTAACACTA
12118928 AATTTAACACTA
1 AATTTAACACTA
12118940 A
1 A
12118941 TTTGAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
AATTTAACACTA
Found at i:12121817 original size:17 final size:17
Alignment explanation
Indices: 12121797--12121829 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12121787 AACGAAGGAT
12121797 CGAGAGAAAAACAGTAA
1 CGAGAGAAAAACAGTAA
*
12121814 CGAGAGAAAAAGAGTA
1 CGAGAGAAAAACAGTA
12121830 GCTAAATTTT
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:0.58, C:0.09, G:0.27, T:0.06
Consensus pattern (17 bp):
CGAGAGAAAAACAGTAA
Found at i:12122204 original size:7 final size:7
Alignment explanation
Indices: 12122191--12122241 Score: 84
Period size: 7 Copynumber: 7.0 Consensus size: 7
12122181 TTAAATATTA
12122191 AATTTTT
1 AATTTTT
12122198 AAGTTTTTT
1 AA--TTTTT
12122207 AATTTTT
1 AATTTTT
12122214 AATTTTT
1 AATTTTT
12122221 AATTTTT
1 AATTTTT
12122228 AATTTTT
1 AATTTTT
12122235 AATTTTT
1 AATTTTT
12122242 TTTGAAGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
7 35 0.83
9 7 0.17
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (7 bp):
AATTTTT
Found at i:12122613 original size:28 final size:28
Alignment explanation
Indices: 12122581--12122638 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
12122571 CGATGGAGGA
12122581 GATGGGTTGCGACGCACGGGGCGAAGGC
1 GATGGGTTGCGACGCACGGGGCGAAGGC
*
12122609 GATGGGTTGCGATGCACGGGGCGAAGGC
1 GATGGGTTGCGACGCACGGGGCGAAGGC
12122637 GA
1 GA
12122639 CAAACAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.50, T:0.12
Consensus pattern (28 bp):
GATGGGTTGCGACGCACGGGGCGAAGGC
Found at i:12122979 original size:16 final size:17
Alignment explanation
Indices: 12122952--12122986 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
12122942 GTTTAGTGTT
12122952 TTTTAGGGGGTTAGGGA
1 TTTTAGGGGGTTAGGGA
12122969 TTTTA-GGGGTTAGGGA
1 TTTTAGGGGGTTAGGGA
12122985 TT
1 TT
12122987 AGTGTTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (17 bp):
TTTTAGGGGGTTAGGGA
Found at i:12123023 original size:46 final size:46
Alignment explanation
Indices: 12122897--12123026 Score: 127
Period size: 48 Copynumber: 2.7 Consensus size: 46
12122887 TCAACATCCA
* *** *
12122897 TATGATGTTTTTTGAGGTTTAGGGTTTTAAAAGTTATAGATTAATGTT
1 TATGAT-TTTTTTG-GGTTTAGGATTTTAGGGGTTAGAGATTAATGTT
* * * *
12122945 TAGTG-TTTTTTAGGGGGTTAGGGATTTTAGGGGTTAGGGATTAGTGTT
1 TA-TGATTTTTT-TGGGTTTA-GGATTTTAGGGGTTAGAGATTAATGTT
12122993 TATGATTTTTTTGGGTTTAGGATTTTAGGGGTTA
1 TATGATTTTTTTGGGTTTAGGATTTTAGGGGTTA
12123027 TATGACTTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
46 15 0.22
47 18 0.27
48 32 0.48
49 2 0.03
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (46 bp):
TATGATTTTTTTGGGTTTAGGATTTTAGGGGTTAGAGATTAATGTT
Found at i:12123127 original size:81 final size:81
Alignment explanation
Indices: 12123033--12123347 Score: 399
Period size: 81 Copynumber: 3.9 Consensus size: 81
12123023 GTTATATGAC
* * *
12123033 TTTTT-GCGGCGTTTTGAGCAAAAACGCCGCTACTGCT-TAGTTTTTTAGCGGCGTTTGACCAAA
1 TTTTTAGCGGCG-TTTGACCAAAAACACCGCTATTGCTCT-GTTTTTTAGCGGCGTTTGACCAAA
* * *
12123096 AATGCAGCTATTGCT-TT
64 AACGCCGCTATTGCTCTG
* * * **
12123113 TTTTTAGCGGCGTTTTGAGCAAAAACACCGCTATTACTCTGTTTTTTAGTGGCGTTTTTGGTC--
1 TTTTTAGCGGCG-TTTGACCAAAAACACCGCTATTGCTCTGTTTTTTAGCGGCG--TTTGACCAA
12123176 AAACGCCGCTATTGCTCTG
63 AAACGCCGCTATTGCTCTG
* *
12123195 TTTTTAGCGGCGTTTGACCAAAAACACCGCTATTGCTCTATTTTTTAGCGGTGTTTGACCAAAAA
1 TTTTTAGCGGCGTTTGACCAAAAACACCGCTATTGCTCTGTTTTTTAGCGGCGTTTGACCAAAAA
12123260 CGCCGCTATTGCTCTG
66 CGCCGCTATTGCTCTG
* * *
12123276 TTTTTAGCGGTGTTTGACCAAAAACGCCGCTATTGCTCTG-TTTTTAGCGGCGTTTGACCACAAA
1 TTTTTAGCGGCGTTTGACCAAAAACACCGCTATTGCTCTGTTTTTTAGCGGCGTTTGACCAAAAA
12123340 CGCCGCTA
66 CGCCGCTA
12123348 ATGTATAATT
Statistics
Matches: 207, Mismatches: 21, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
79 5 0.02
80 35 0.17
81 148 0.71
82 14 0.07
83 5 0.02
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (81 bp):
TTTTTAGCGGCGTTTGACCAAAAACACCGCTATTGCTCTGTTTTTTAGCGGCGTTTGACCAAAAA
CGCCGCTATTGCTCTG
Found at i:12123360 original size:40 final size:40
Alignment explanation
Indices: 12123033--12123347 Score: 379
Period size: 40 Copynumber: 7.8 Consensus size: 40
12123023 GTTATATGAC
* *
12123033 TTTTT-GCGGCGTTTTGAGCAAAAACGCCGCTACTGCT-TAG
1 TTTTTAGCGGCG-TTTGACCAAAAACGCCGCTATTGCTCT-G
* * *
12123073 TTTTTTAGCGGCGTTTGACCAAAAATGCAGCTATTGCT-TT
1 -TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTG
* * *
12123113 TTTTTAGCGGCGTTTTGAGCAAAAACACCGCTATTACTCTG
1 TTTTTAGCGGCG-TTTGACCAAAAACGCCGCTATTGCTCTG
* **
12123154 TTTTTTAGTGGCGTTTTTGGTC--AAACGCCGCTATTGCTCTG
1 -TTTTTAGCGGCG--TTTGACCAAAAACGCCGCTATTGCTCTG
* *
12123195 TTTTTAGCGGCGTTTGACCAAAAACACCGCTATTGCTCTAT
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCT-G
*
12123236 TTTTTAGCGGTGTTTGACCAAAAACGCCGCTATTGCTCTG
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTG
*
12123276 TTTTTAGCGGTGTTTGACCAAAAACGCCGCTATTGCTCTG
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTG
*
12123316 TTTTTAGCGGCGTTTGACCACAAACGCCGCTA
1 TTTTTAGCGGCGTTTGACCAAAAACGCCGCTA
12123348 ATGTATAATT
Statistics
Matches: 240, Mismatches: 26, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
38 5 0.02
39 12 0.05
40 118 0.49
41 82 0.34
42 17 0.07
43 6 0.03
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTGACCAAAAACGCCGCTATTGCTCTG
Found at i:12123360 original size:121 final size:124
Alignment explanation
Indices: 12123041--12123347 Score: 398
Period size: 121 Copynumber: 2.5 Consensus size: 124
12123031 ACTTTTTGCG
* * * *
12123041 GCGT-TTTGAGCAAAAACGCCGCTACTGCT-TAGTTTTTTAGCGGCGTTTGACCAAAAATGCAGC
1 GCGTGTTTGACCAAAAACGCCGCTATTGCTCT-G-TTTTTAGCGGCGTTTGACCAAAAACGCCGC
* *
12123104 TATTGCTT-TTTTTTAGCGGCGTTTTGAGCAAAAACACCGCTATTACTCTGTTTTTTAGTG
64 TATTGCTTATTTTTTAGCGGCGTTTTGACCAAAAACACCGCTATTACTCTGTTTTTTAGTC
* ** *
12123164 GCGTTTTTGGTC--AAACGCCGCTATTGCTCTGTTTTTAGCGGCGTTTGACCAAAAACACCGCTA
1 GCGTGTTTGACCAAAAACGCCGCTATTGCTCTGTTTTTAGCGGCGTTTGACCAAAAACGCCGCTA
* * *
12123227 TTGCTCTATTTTTTAGCGGTG-TTTGACCAAAAACGCCGCTATTGCTCTG-TTTTTAG-C
66 TTGCT-TATTTTTTAGCGGCGTTTTGACCAAAAACACCGCTATTACTCTGTTTTTTAGTC
*
12123284 G-GTGTTTGACCAAAAACGCCGCTATTGCTCTGTTTTTAGCGGCGTTTGACCACAAACGCCGCTA
1 GCGTGTTTGACCAAAAACGCCGCTATTGCTCTGTTTTTAGCGGCGTTTGACCAAAAACGCCGCTA
12123348 ATGTATAATT
Statistics
Matches: 162, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
119 7 0.04
120 1 0.01
121 90 0.56
122 42 0.26
123 17 0.10
124 5 0.03
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (124 bp):
GCGTGTTTGACCAAAAACGCCGCTATTGCTCTGTTTTTAGCGGCGTTTGACCAAAAACGCCGCTA
TTGCTTATTTTTTAGCGGCGTTTTGACCAAAAACACCGCTATTACTCTGTTTTTTAGTC
Found at i:12124640 original size:21 final size:21
Alignment explanation
Indices: 12124614--12124654 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12124604 ATTTCTACCT
12124614 AGCTAACAACCAACTGACTTC
1 AGCTAACAACCAACTGACTTC
* *
12124635 AGCTAACTACTAACTGACTT
1 AGCTAACAACCAACTGACTT
12124655 GACAAACTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.24
Consensus pattern (21 bp):
AGCTAACAACCAACTGACTTC
Found at i:12129230 original size:51 final size:49
Alignment explanation
Indices: 12129141--12129279 Score: 170
Period size: 51 Copynumber: 2.8 Consensus size: 49
12129131 TATTGTGAGG
* *
12129141 TCACATGTGTAGTACTAAGTGCAGGCAACTATGCGTACCCAATAATTTCGA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCAATAA-TT-GA
* ** ** *
12129192 TCACGTGTGTAGTACTAAGTGCAGGCTACTGCGTGTACCGGATAATTGG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCAATAATTGA
* *
12129241 TCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTACC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACC
12129280 AGATAGCTTT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
49 35 0.47
50 2 0.03
51 38 0.51
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (49 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCAATAATTGA
Found at i:12129254 original size:49 final size:51
Alignment explanation
Indices: 12129139--12129284 Score: 181
Period size: 49 Copynumber: 2.9 Consensus size: 51
12129129 TTTATTGTGA
* *
12129139 GGTCACATGTGTAGTACTAAGTGCAGGCAACTATGCGTACCCA-ATAATTTC
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTA-CCAGATAATTTC
* * ** *
12129190 GATCACGTGTGTAGTACTAAGTGCAGGCTACTGCGTGTACCGGATAA-TT-
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTTC
* *
12129239 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
12129285 GCTTTGGCTA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 39 0.49
50 4 0.05
51 37 0.46
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTTC
Found at i:12142754 original size:40 final size:39
Alignment explanation
Indices: 12142686--12142767 Score: 110
Period size: 40 Copynumber: 2.1 Consensus size: 39
12142676 AAATCTCTCA
* *
12142686 TTTATCTTTCAAGTTTACTATCTCTTTGTATTGATTTTT
1 TTTATCTTTCAAGTGTACTATCTCTTTGTATTGATATTT
* * *
12142725 TTTATCTTTTCTAGTGTATTATCTTTTTGTATTGATATTT
1 TTTATC-TTTCAAGTGTACTATCTCTTTGTATTGATATTT
12142765 TTT
1 TTT
12142768 CATAAGTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 6 0.16
40 31 0.84
ACGTcount: A:0.17, C:0.10, G:0.09, T:0.65
Consensus pattern (39 bp):
TTTATCTTTCAAGTGTACTATCTCTTTGTATTGATATTT
Found at i:12144380 original size:22 final size:22
Alignment explanation
Indices: 12144355--12144401 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
12144345 AAATGTTCCA
12144355 TCCACATTGATAATTACATCAT
1 TCCACATTGATAATTACATCAT
12144377 TCCACATTGATAATTACATCAT
1 TCCACATTGATAATTACATCAT
12144399 TCC
1 TCC
12144402 TTTTAAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (22 bp):
TCCACATTGATAATTACATCAT
Found at i:12146322 original size:12 final size:12
Alignment explanation
Indices: 12146302--12146336 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12146292 TCACAATTTG
*
12146302 AAAACATAAAAT
1 AAAAAATAAAAT
12146314 AAAAAATAAAAT
1 AAAAAATAAAAT
*
12146326 AGAAAATAAAA
1 AAAAAATAAAA
12146337 GACAGAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:12148797 original size:27 final size:27
Alignment explanation
Indices: 12148729--12148784 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
12148719 AAAAGATTAA
**
12148729 ATAAAATTGGTATATCATGAAACTTGT
1 ATAAAATTAATATATCATGAAACTTGT
12148756 ATAAAATTAATATATCATGAAACTTGT
1 ATAAAATTAATATATCATGAAACTTGT
12148783 AT
1 AT
12148785 CTTATTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (27 bp):
ATAAAATTAATATATCATGAAACTTGT
Found at i:12153222 original size:16 final size:18
Alignment explanation
Indices: 12153188--12153224 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12153178 AGAGTTTGTA
*
12153188 ATATATTATGTTATTTTT
1 ATATATTATGTTATATTT
12153206 ATATATTATG-TA-ATTT
1 ATATATTATGTTATATTT
12153222 ATA
1 ATA
12153225 ATACATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
ATATATTATGTTATATTT
Found at i:12153338 original size:15 final size:15
Alignment explanation
Indices: 12153317--12153363 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
12153307 ATTTTAATAA
12153317 ATAAAATATATAAAT
1 ATAAAATATATAAAT
*
12153332 ATTAAATAT-TAAAT
1 ATAAAATATATAAAT
12153346 -TAAAATAATATAAAT
1 ATAAAAT-ATATAAAT
12153361 ATA
1 ATA
12153364 TTTTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
15 13 0.48
16 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAAATATATAAAT
Found at i:12153679 original size:18 final size:19
Alignment explanation
Indices: 12153658--12153705 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
12153648 TTTCTATAGT
12153658 TTTAAATTTTTTTA-AAAA
1 TTTAAATTTTTTTATAAAA
* * **
12153676 TTTATATATTTTTATAATC
1 TTTAAATTTTTTTATAAAA
12153695 TTTAAATTTTT
1 TTTAAATTTTT
12153706 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAAATTTTTTTATAAAA
Found at i:12156170 original size:18 final size:18
Alignment explanation
Indices: 12156140--12156174 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12156130 ATAAAATATA
12156140 TATAATAAAATTAAAATG
1 TATAATAAAATTAAAATG
12156158 TATAA-AAATATTAAAAT
1 TATAATAAA-ATTAAAAT
12156175 AAAACTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TATAATAAAATTAAAATG
Found at i:12166090 original size:18 final size:17
Alignment explanation
Indices: 12166046--12166086 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
12166036 ACTATTCTTG
12166046 TATTATTATT-TTTAACA
1 TATT-TTATTATTTAACA
12166063 TATTTTATTATTTAGACA
1 TATTTTATTATTTA-ACA
12166081 T-TTTTA
1 TATTTTA
12166087 ATTAATACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 13 0.59
18 4 0.18
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTTTATTATTTAACA
Found at i:12166136 original size:23 final size:23
Alignment explanation
Indices: 12166110--12166156 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12166100 ATATATATAC
*
12166110 TTTATATATATTCTTATAGTTGT
1 TTTATATATATTATTATAGTTGT
*
12166133 TTTATATATATTATTATTGTTGT
1 TTTATATATATTATTATAGTTGT
12166156 T
1 T
12166157 CCTAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTATATATATTATTATAGTTGT
Found at i:12166164 original size:23 final size:23
Alignment explanation
Indices: 12166112--12166166 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
12166102 ATATATACTT
* *
12166112 TATATATATTCTTATAGTTGTTT
1 TATATATATTATTATAGTTGTTC
*
12166135 TATATATATTATTATTGTTGTTCC
1 TATATATATTATTATAGTTGTT-C
12166159 TA-ATATAT
1 TATATATAT
12166167 GTTTTATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.58
Consensus pattern (23 bp):
TATATATATTATTATAGTTGTTC
Found at i:12166487 original size:19 final size:18
Alignment explanation
Indices: 12166463--12166503 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12166453 TGTAAATATC
*
12166463 ATATTATGTTTTATCATGT
1 ATATTATG-TATATCATGT
*
12166482 ATATTATGTATGTCATGT
1 ATATTATGTATATCATGT
12166500 ATAT
1 ATAT
12166504 GTTTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (18 bp):
ATATTATGTATATCATGT
Found at i:12166600 original size:24 final size:25
Alignment explanation
Indices: 12166545--12166600 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
12166535 GTATGTTATG
* *
12166545 TATATATTATGTATATGCTTTTAAA
1 TATATATTATATATATGATTTTAAA
* *
12166570 TAT-TATTATATATCT-ATTTTCAA
1 TATATATTATATATATGATTTTAAA
12166593 TATATATT
1 TATATATT
12166601 TATGTAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.35
24 14 0.54
25 3 0.12
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (25 bp):
TATATATTATATATATGATTTTAAA
Found at i:12166778 original size:2 final size:2
Alignment explanation
Indices: 12166735--12166764 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12166725 TATTATTATC
12166735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12166765 TTTCTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12178235 original size:55 final size:55
Alignment explanation
Indices: 12178147--12178266 Score: 222
Period size: 55 Copynumber: 2.2 Consensus size: 55
12178137 TCTGGGGCAC
12178147 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
* *
12178202 CTATTCCCTTTTTATTCATTTTGTATTCTAGCAATGTTTGTTGATTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
12178257 CTATTCCCTT
1 CTATTCCCTT
12178267 CAAATTTTGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.53
Consensus pattern (55 bp):
CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
Found at i:12178830 original size:43 final size:43
Alignment explanation
Indices: 12178761--12179016 Score: 148
Period size: 44 Copynumber: 5.8 Consensus size: 43
12178751 CTAAAATTAG
* * *
12178761 TGAATTCACCAGAACTTAACCACCTAAGCAGTAGGGTAACAGGT
1 TGAATTCA-TAGATCTTAACCTCCTAAGCAGTAGGGTAACAGGT
* * *
12178805 TGAATTCATAGATCATAACCTCCTAAGCAGTAGGGAAACAGAT
1 TGAATTCATAGATCTTAACCTCCTAAGCAGTAGGGTAACAGGT
** * * *
12178848 TGAAAGCGACA-AGCTTTAA-CTCCCTAAGCAGTAGGGTAACAAGT
1 TGAATTC-ATAGATC-TTAACCT-CCTAAGCAGTAGGGTAACAGGT
*
12178892 TGAAGTTCATAAGATCTTATCAC-CCTAAGCAGTAGGG-AA-ATGGAT
1 TGAA-TTCAT-AGATCTTAAC-CTCCTAAGCAGTAGGGTAACA-GG-T
* ** * * * * *
12178937 CGAAGGCA-ACGAGCTTTAACCCCCTAAGCAGTAAGGTAACAAGC
1 TGAATTCATA-GATC-TTAACCTCCTAAGCAGTAGGGTAACAGGT
* *
12178981 TAAAGTTCATAGATCTTATCAC-CCTAAGCAGTAGGG
1 TGAA-TTCATAGATCTTAAC-CTCCTAAGCAGTAGGG
12179017 AAGCAGATCA
Statistics
Matches: 159, Mismatches: 35, Indels: 36
0.69 0.15 0.16
Matches are distributed among these distances:
42 1 0.01
43 43 0.27
44 78 0.49
45 32 0.20
46 4 0.03
47 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (43 bp):
TGAATTCATAGATCTTAACCTCCTAAGCAGTAGGGTAACAGGT
Found at i:12178954 original size:89 final size:88
Alignment explanation
Indices: 12178776--12179030 Score: 334
Period size: 89 Copynumber: 2.9 Consensus size: 88
12178766 TCACCAGAAC
* * * *
12178776 TTAACCACCTAAGCAGTAGGGTAACAGGTTGAA-TTCATAGATCATAAC-CTCCTAAGCAGTAGG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGTTGAAGTTCATAGATCTTATCAC-CCTAAGCAGTAGG
* *
12178839 GAAACAGATTGAAAGCGACAAGCT
65 GAAACAGATCGAAAGCAACAAGCT
*
12178863 TTAACTCCCTAAGCAGTAGGGTAACAAGTTGAAGTTCATAAGATCTTATCACCCTAAGCAGTAGG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGTTGAAGTTCAT-AGATCTTATCACCCTAAGCAGTAGG
** * *
12178928 GAAATGGATCGAAGGCAACGAGCT
65 GAAACAGATCGAAAGCAACAAGCT
* * *
12178952 TTAACCCCCTAAGCAGTAAGGTAACAAGCTAAAGTTCATAGATCTTATCACCCTAAGCAGTAGGG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGTTGAAGTTCATAGATCTTATCACCCTAAGCAGTAGGG
* *
12179017 AAGCAGATCAAAAG
66 AAACAGATCGAAAG
12179031 ACGGCGAATC
Statistics
Matches: 145, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
87 30 0.21
88 40 0.28
89 74 0.51
90 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (88 bp):
TTAACCCCCTAAGCAGTAGGGTAACAAGTTGAAGTTCATAGATCTTATCACCCTAAGCAGTAGGG
AAACAGATCGAAAGCAACAAGCT
Found at i:12179219 original size:43 final size:44
Alignment explanation
Indices: 12179172--12179278 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
12179162 AGATGATGGG
12179172 CTTAACCCCCTAAGCAA-TAGGGTAACAAGCTAAATTTACAGAC
1 CTTAACCCCCTAAGCAAGTAGGGTAACAAGCTAAATTTACAGAC
* ** * * * *
12179215 CTTAAACCCCTAAATAAGTAGGGTGACAGGCTGAATTTACAGAT
1 CTTAACCCCCTAAGCAAGTAGGGTAACAAGCTAAATTTACAGAC
* *
12179259 CTTATCTCCCTAAGC-AGTAG
1 CTTAACCCCCTAAGCAAGTAG
12179279 TGGAGCAGAT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
43 19 0.37
44 32 0.63
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (44 bp):
CTTAACCCCCTAAGCAAGTAGGGTAACAAGCTAAATTTACAGAC
Found at i:12180960 original size:23 final size:23
Alignment explanation
Indices: 12180916--12180962 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12180906 ATATATATAC
*
12180916 TTTATATATATTCTTATAGTTGT
1 TTTATATATATTATTATAGTTGT
*
12180939 TTTATATATATTATTATTGTTGT
1 TTTATATATATTATTATAGTTGT
12180962 T
1 T
12180963 CCTAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTATATATATTATTATAGTTGT
Found at i:12180970 original size:23 final size:23
Alignment explanation
Indices: 12180918--12180972 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
12180908 ATATATACTT
* *
12180918 TATATATATTCTTATAGTTGTTT
1 TATATATATTATTATAGTTGTTC
*
12180941 TATATATATTATTATTGTTGTTCC
1 TATATATATTATTATAGTTGTT-C
12180965 TA-ATATAT
1 TATATATAT
12180973 GTTTTATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.58
Consensus pattern (23 bp):
TATATATATTATTATAGTTGTTC
Found at i:12181293 original size:19 final size:18
Alignment explanation
Indices: 12181269--12181309 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12181259 TGTAAATATC
*
12181269 ATATTATGTTTTATCATGT
1 ATATTATG-TATATCATGT
*
12181288 ATATTATGTATGTCATGT
1 ATATTATGTATATCATGT
12181306 ATAT
1 ATAT
12181310 GTTTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (18 bp):
ATATTATGTATATCATGT
Found at i:12181406 original size:24 final size:25
Alignment explanation
Indices: 12181351--12181406 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
12181341 GTATGTTATG
* *
12181351 TATATATTATGTATATGCTTTTAAA
1 TATATATTATATATATGATTTTAAA
* *
12181376 TAT-TATTATATATCT-ATTTTCAA
1 TATATATTATATATATGATTTTAAA
12181399 TATATATT
1 TATATATT
12181407 TATGTAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.35
24 14 0.54
25 3 0.12
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (25 bp):
TATATATTATATATATGATTTTAAA
Found at i:12181548 original size:2 final size:2
Alignment explanation
Indices: 12181541--12181576 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12181531 TATTATTATC
12181541 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12181577 CTTATAACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12187810 original size:34 final size:35
Alignment explanation
Indices: 12187767--12187836 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
12187757 AAGAAAAAAT
12187767 TCAT-AAAAAAAATTAAAAGAAAACTCCTATTTTC
1 TCATAAAAAAAAATTAAAAGAAAACTCCTATTTTC
12187801 TCATAAAAAAAAATTAAAAGAAAACTCCTATTTTC
1 TCATAAAAAAAAATTAAAAGAAAACTCCTATTTTC
12187836 T
1 T
12187837 TACTTATTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 4 0.11
35 31 0.89
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.30
Consensus pattern (35 bp):
TCATAAAAAAAAATTAAAAGAAAACTCCTATTTTC
Found at i:12191051 original size:36 final size:36
Alignment explanation
Indices: 12190955--12191052 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 36
12190945 AATAATAAGT
*
12190955 TGTGTCCAACGCTAGTCGGTAA-AACCGAAAAATAGA
1 TGTGTCCAACACTAGTC-GTAATAACCGAAAAATAGA
* * * * *
12190991 TGTGTCCAGCACTGGTCGTTATAACCGAAAAATGGG
1 TGTGTCCAACACTAGTCGTAATAACCGAAAAATAGA
12191027 TGTGTCCAACACGTAGTCG-AATAACC
1 TGTGTCCAACAC-TAGTCGTAATAACC
12191053 CTTAACTCTT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
35 3 0.06
36 43 0.84
37 5 0.10
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (36 bp):
TGTGTCCAACACTAGTCGTAATAACCGAAAAATAGA
Found at i:12198585 original size:19 final size:19
Alignment explanation
Indices: 12198561--12198597 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
12198551 CTACGTTTGA
12198561 TAGCTGAAAATCCTACCTG
1 TAGCTGAAAATCCTACCTG
12198580 TAGCTGAAAATCCTACCT
1 TAGCTGAAAATCCTACCT
12198598 ACTGATGAAC
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:0.27, G:0.14, T:0.27
Consensus pattern (19 bp):
TAGCTGAAAATCCTACCTG
Found at i:12198606 original size:19 final size:19
Alignment explanation
Indices: 12198565--12198606 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12198555 GTTTGATAGC
* *
12198565 TGAAAATCCTACCTGTAGC
1 TGAAAATCCTACCTCTAGA
12198584 TGAAAATCCTACCTACT-GA
1 TGAAAATCCTACCT-CTAGA
12198603 TGAA
1 TGAA
12198607 CTTATTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (19 bp):
TGAAAATCCTACCTCTAGA
Found at i:12199041 original size:19 final size:20
Alignment explanation
Indices: 12199014--12199067 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
12199004 TAAAAATTAC
12199014 AAAATAATTTAAAATCATTT-T
1 AAAA-AATTTAAAAT-ATTTAT
* *
12199035 -TAAAATTCAAAATATTTAT
1 AAAAAATTTAAAATATTTAT
12199054 AAAAAATTTAAAAT
1 AAAAAATTTAAAAT
12199068 TCAAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 4 0.15
19 10 0.37
20 13 0.48
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATTTAAAATATTTAT
Found at i:12199056 original size:18 final size:19
Alignment explanation
Indices: 12199019--12199057 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
12199009 ATTACAAAAT
* *
12199019 AATTTAAAATCATTTTTAA
1 AATTCAAAATCATTTATAA
12199038 AATTCAAAAT-ATTTATAA
1 AATTCAAAATCATTTATAA
12199056 AA
1 AA
12199058 AATTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATCATTTATAA
Found at i:12199070 original size:27 final size:25
Alignment explanation
Indices: 12199033--12199091 Score: 91
Period size: 27 Copynumber: 2.3 Consensus size: 25
12199023 TAAAATCATT
12199033 TTTAAAATTCAAAATATTTATAAAAAA
1 TTTAAAATTCAAAAT-TTT-TAAAAAA
12199060 TTTAAAATTCAAAATTTTTAAAAAA
1 TTTAAAATTCAAAATTTTTAAAAAA
*
12199085 TTCAAAA
1 TTTAAAA
12199092 AGATATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 13 0.42
26 3 0.10
27 15 0.48
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
TTTAAAATTCAAAATTTTTAAAAAA
Found at i:12203965 original size:17 final size:16
Alignment explanation
Indices: 12203947--12203987 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
12203937 TAAATTAATA
12203947 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
*
12203963 AAATAAATAATAAAACT
1 AAATAAA-AATAAAAAT
12203980 AAATAAAA
1 AAATAAAA
12203988 TAATAACTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:12203967 original size:21 final size:20
Alignment explanation
Indices: 12203938--12203990 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 20
12203928 AGCCTATTCT
*
12203938 AAATTAATAAAATAAAAATAA
1 AAATAAATAAAAT-AAAATAA
12203959 AAATAAAT-AAAT--AATAA
1 AAATAAATAAAATAAAATAA
*
12203976 AACTAAATAAAATAA
1 AAATAAATAAAATAA
12203991 TAACTTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 12 0.44
18 4 0.15
20 4 0.15
21 7 0.26
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAATAAATAAAATAAAATAA
Found at i:12203992 original size:21 final size:22
Alignment explanation
Indices: 12203943--12203993 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
12203933 ATTCTAAATT
12203943 AATAA-AATAAAAATAAAAATA
1 AATAATAATAAAAATAAAAATA
* *
12203964 AATAAATAATAAAACTAAATA-A
1 AAT-AATAATAAAAATAAAAATA
12203986 AATAATAA
1 AATAATAA
12203994 CTTCTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 6 0.23
23 12 0.46
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
AATAATAATAAAAATAAAAATA
Found at i:12206987 original size:17 final size:16
Alignment explanation
Indices: 12206965--12206999 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
12206955 GTGTTTAAAA
*
12206965 TTTTATTTTTGTTTATT
1 TTTTATTTGTG-TTATT
12206982 TTTTATTTGTGTTATT
1 TTTTATTTGTGTTATT
12206998 TT
1 TT
12207000 AGGTTGGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.80
Consensus pattern (16 bp):
TTTTATTTGTGTTATT
Found at i:12214131 original size:17 final size:16
Alignment explanation
Indices: 12214113--12214153 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
12214103 TAAGTTAATA
12214113 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
*
12214129 AAATAAATAATAAAACT
1 AAATAAA-AATAAAAAT
12214146 AAATAAAA
1 AAATAAAA
12214154 TAATATCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:12214158 original size:21 final size:22
Alignment explanation
Indices: 12214109--12214158 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
12214099 ATTCTAAGTT
12214109 AATAA-AATAAAAATAAAAATA
1 AATAATAATAAAAATAAAAATA
* *
12214130 AATAAATAATAAAACTAAATA-A
1 AAT-AATAATAAAAATAAAAATA
12214152 AATAATA
1 AATAATA
12214159 TCTTCTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 6 0.24
23 12 0.48
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
AATAATAATAAAAATAAAAATA
Found at i:12222085 original size:8 final size:8
Alignment explanation
Indices: 12222072--12222098 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12222062 CTGCACAATT
12222072 TGTGTAAA
1 TGTGTAAA
12222080 TGTGTAAA
1 TGTGTAAA
12222088 TGTGTAAA
1 TGTGTAAA
12222096 TGT
1 TGT
12222099 TGAGGTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (8 bp):
TGTGTAAA
Found at i:12222961 original size:17 final size:19
Alignment explanation
Indices: 12222883--12222954 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
12222873 ATAATCTTCA
12222883 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
12222902 ATGATAT--AGTCTTAGAT
1 ATGATATGCAATCTTAGAT
12222919 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
12222937 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
12222955 AGATATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.02
17 14 0.29
18 14 0.29
19 19 0.40
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:12222964 original size:40 final size:35
Alignment explanation
Indices: 12222871--12222954 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 35
12222861 TCATATGGAA
*
12222871 ATATAATCTT-CA-ATGATATGCAATCTTAGATATG
1 ATATAATCTTAGATATGAT-TGCAATCTTAGATATG
*
12222905 ATATAGTCTTAGATATGATTGCAATCTTAGATATG
1 ATATAATCTTAGATATGATTGCAATCTTAGATATG
12222940 ATATGCAATCTTAGA
1 ATAT--AATCTTAGA
12222955 AGATATGATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 9 0.21
35 21 0.49
36 5 0.12
37 8 0.19
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (35 bp):
ATATAATCTTAGATATGATTGCAATCTTAGATATG
Found at i:12222980 original size:22 final size:22
Alignment explanation
Indices: 12222915--12222977 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
12222905 ATATAGTCTT
12222915 AGATATGAT-TGCAATCTT---
1 AGATATGATATGCAATCTTAGA
12222933 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATCTTAGA
* *
12222955 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGCAATCTTAGA
12222978 GATTTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 9 0.24
19 9 0.24
22 8 0.21
23 12 0.32
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATCTTAGA
Found at i:12226331 original size:12 final size:11
Alignment explanation
Indices: 12226302--12226360 Score: 59
Period size: 12 Copynumber: 5.3 Consensus size: 11
12226292 TTTGGTAGCA
12226302 AAAAC-AAAGC
1 AAAACAAAAGC
12226312 AAAACAAAAGC
1 AAAACAAAAGC
12226323 AAGAACAAAATG-
1 AA-AACAAAA-GC
*
12226335 AAAACAGAAGC
1 AAAACAAAAGC
*
12226346 AAAAACGAAAGC
1 -AAAACAAAAGC
12226358 AAA
1 AAA
12226361 GTGTTTGAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 6 0.15
11 16 0.39
12 18 0.44
13 1 0.02
ACGTcount: A:0.69, C:0.15, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAACAAAAGC
Found at i:12242009 original size:22 final size:22
Alignment explanation
Indices: 12241950--12242011 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
12241940 AATATTAATT
*
12241950 TAAAAAATTGTGT-AAATAATAA
1 TAAAAAAATG-GTAAAATAATAA
* *
12241972 T-AAAATATGCTAAAAATAATAA
1 TAAAAAAATGGT-AAAATAATAA
12241994 TAAAAAAATGGTAAAATA
1 TAAAAAAATGGTAAAATA
12242012 GAATCATGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.03
21 6 0.19
22 17 0.53
23 8 0.25
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (22 bp):
TAAAAAAATGGTAAAATAATAA
Found at i:12242642 original size:13 final size:12
Alignment explanation
Indices: 12242623--12242654 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
12242613 TTTTTTATTT
12242623 TATATGTATCTA
1 TATATGTATCTA
12242635 TAATATGTATCTA
1 T-ATATGTATCTA
12242648 TATATGT
1 TATATGT
12242655 TAATAGGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (12 bp):
TATATGTATCTA
Found at i:12243440 original size:42 final size:42
Alignment explanation
Indices: 12243392--12243473 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
12243382 CATGATTTCA
12243392 ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAGCTTCG
1 ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAGCTTCG
*
12243434 ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTGGCTT
1 ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAGCTT
12243474 TTAGCTGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (42 bp):
ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAGCTTCG
Found at i:12244083 original size:43 final size:44
Alignment explanation
Indices: 12243997--12244106 Score: 116
Period size: 43 Copynumber: 2.5 Consensus size: 44
12243987 CTGTACATTT
* * *
12243997 AGTCTGCTCCACTGCGACTTCAAGGAGATGAGACTTGTAACTTC
1 AGTCTGCTTCACTGCGACTTCAAGGAGATAAGACTAGTAACTTC
* * *
12244041 AGTCTGCTTCACTGC-ACTTCAGGGAGATAAGGCTAGTGACTTC
1 AGTCTGCTTCACTGCGACTTCAAGGAGATAAGACTAGTAACTTC
* * * *
12244084 AATC-GCTTCGCTGAGGCTTCAAG
1 AGTCTGCTTCACTGCGACTTCAAG
12244107 AAGACAGGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
42 8 0.15
43 32 0.59
44 14 0.26
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (44 bp):
AGTCTGCTTCACTGCGACTTCAAGGAGATAAGACTAGTAACTTC
Found at i:12256162 original size:2 final size:2
Alignment explanation
Indices: 12256157--12256183 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12256147 TATAAAGGAA
12256157 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12256184 ATAGTACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12257136 original size:22 final size:22
Alignment explanation
Indices: 12257077--12257138 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
12257067 AATATTAATT
*
12257077 TAAAAAATTGTGT-AAATAATAA
1 TAAAAAAATG-GTAAAATAATAA
* * *
12257099 T-GAAATATGCTAAAAATAATAA
1 TAAAAAAATGGT-AAAATAATAA
12257121 TAAAAAAATGGTAAAATA
1 TAAAAAAATGGTAAAATA
12257139 GAATCATGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.03
21 5 0.17
22 17 0.57
23 7 0.23
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (22 bp):
TAAAAAAATGGTAAAATAATAA
Found at i:12257767 original size:13 final size:12
Alignment explanation
Indices: 12257748--12257779 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
12257738 TTTTTTATTT
12257748 TATATGTATCTA
1 TATATGTATCTA
12257760 TAATATGTATCTA
1 T-ATATGTATCTA
12257773 TATATGT
1 TATATGT
12257780 TAATAGGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (12 bp):
TATATGTATCTA
Found at i:12258564 original size:42 final size:42
Alignment explanation
Indices: 12258516--12258597 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
12258506 CATGATTTCA
12258516 ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAGCTTCG
1 ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAGCTTCG
*
12258558 ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTGGCTT
1 ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAGCTT
12258598 TTAACTGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (42 bp):
ATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAGCTTCG
Found at i:12259206 original size:43 final size:44
Alignment explanation
Indices: 12259120--12259207 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 44
12259110 CTGTACATTT
* *
12259120 AGTCTGCTCCACTGCGACTTCAAAGAGATGAGACTTGTAACTTC
1 AGTCTGCTCCACTGCGACTTCAAAGAGATAAGACTAGTAACTTC
** * *
12259164 AGTCTGCTCCACTGC-ACTTCAGGGAGATAAGGCTAGTGACTTC
1 AGTCTGCTCCACTGCGACTTCAAAGAGATAAGACTAGTAACTTC
12259207 A
1 A
12259208 ATCGCTTCGC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
43 23 0.61
44 15 0.39
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (44 bp):
AGTCTGCTCCACTGCGACTTCAAAGAGATAAGACTAGTAACTTC
Found at i:12272154 original size:22 final size:22
Alignment explanation
Indices: 12272120--12272178 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
12272110 ATATGTATAC
* **
12272120 ATAAAACATATAT-TAGGAACA
1 ATAAAATATATATATAACAACA
*
12272141 ATAATAATATATATATAACAACT
1 ATAA-AATATATATATAACAACA
12272164 ATAAAATATATATAT
1 ATAAAATATATATAT
12272179 GTAATATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 4 0.12
22 19 0.59
23 9 0.28
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (22 bp):
ATAAAATATATATATAACAACA
Found at i:12277531 original size:39 final size:39
Alignment explanation
Indices: 12277482--12277557 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
12277472 ATAGCGGTGT
*
12277482 TTTTTCATAAACGCTACTAAAGATAAAACAATGGCGGCA
1 TTTTTCATAAACGCTACTAAAGATAAAACAATAGCGGCA
* * *
12277521 TTTTTCATAAACGCTGCTAAAGGTAAAGCAATAGCGG
1 TTTTTCATAAACGCTACTAAAGATAAAACAATAGCGG
12277558 TGTTTATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (39 bp):
TTTTTCATAAACGCTACTAAAGATAAAACAATAGCGGCA
Found at i:12277681 original size:20 final size:20
Alignment explanation
Indices: 12277645--12277696 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
12277635 CCTAAATCAG
* *
12277645 TTTCCCGAAACCCCTTATTTT
1 TTTCCC-AAATCCCTTAGTTT
12277666 TTTCCCAAATCCCTTAGTTT
1 TTTCCCAAATCCCTTAGTTT
*
12277686 TTCCCCAAATC
1 TTTCCCAAATC
12277697 AAATTCCCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.21, C:0.35, G:0.04, T:0.40
Consensus pattern (20 bp):
TTTCCCAAATCCCTTAGTTT
Done.