Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 62 of 125
Found at i:12347129 original size:9 final size:9
Alignment explanation
Indices: 12347090--12347173 Score: 73
Period size: 9 Copynumber: 9.1 Consensus size: 9
12347080 TTTCTTTTTC
12347090 TTTTTTCAT
1 TTTTTTCAT
*
12347099 CTTTTTCAT
1 TTTTTTCAT
12347108 CTTTTTTCAT
1 -TTTTTTCAT
*
12347118 TTTTTTCTTT
1 TTTTTTC-AT
*
12347128 TTTCTTTCCT
1 TTT-TTTCAT
12347138 TTTTCTTCAT
1 TTTT-TTCAT
*
12347148 TTGTTT--T
1 TTTTTTCAT
12347155 TTTTTTCAT
1 TTTTTTCAT
*
12347164 TTTCTTCAT
1 TTTTTTCAT
12347173 T
1 T
12347174 CTTTCACCTA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
7 6 0.10
9 28 0.46
10 23 0.38
11 4 0.07
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:12347154 original size:26 final size:25
Alignment explanation
Indices: 12347125--12347173 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
12347115 CATTTTTTTC
*
12347125 TTTTTTCTTTCCTTTTTCTTCATTTG
1 TTTTTT-TTTCCATTTTCTTCATTTG
*
12347151 TTTTTTTTTTCATTTTCTTCATT
1 TTTTTTTTTCCATTTTCTTCATT
12347174 CTTTCACCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTTTTTTTCCATTTTCTTCATTTG
Found at i:12351415 original size:54 final size:55
Alignment explanation
Indices: 12351278--12351488 Score: 264
Period size: 55 Copynumber: 3.8 Consensus size: 55
12351268 TATATATATT
* * *
12351278 TTTTGAAAATGTTATTTTCAATG-GAAATTGATACTTTCAACTTTCCCTAAAATGT
1 TTTTGAAAATTTTATTTTCAA-GAAAAATTGATACTTTCAACTTTCCCTAAAATGC
* * * ** *
12351333 TTTTGGAAATTTTATTTTTAAAAAAAATTGATACTTTCAACTTTTTCTTAAA-GC
1 TTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTCCCTAAAATGC
* * * *
12351387 ATTTGGAAATTTTATTTTCAAGAGAAATTGATACTTTCAACTTTCCCTAAAATAC
1 TTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTCCCTAAAATGC
*
12351442 TTTTGAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACATTTCC
1 TTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAAC-TTTCC
12351489 TCAAAAAAAA
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
54 46 0.35
55 81 0.61
56 5 0.04
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (55 bp):
TTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTCCCTAAAATGC
Found at i:12351430 original size:109 final size:109
Alignment explanation
Indices: 12351279--12351482 Score: 338
Period size: 109 Copynumber: 1.9 Consensus size: 109
12351269 ATATATATTT
** *
12351279 TTTGAAAATGTTATTTTCAATGGAAATTGATACTTTCAACTTTCCCTAAAATGTTTTTGGAAATT
1 TTTGAAAATGTTATTTTCAATGGAAATTGATACTTTCAACTTTCCCTAAAATACTTTTGAAAATT
12351344 TTATTTTTAAAAAAAATTGATACTTTCAACTTTTTCTTAAAGCA
66 TTATTTTTAAAAAAAATTGATACTTTCAACTTTTTCTTAAAGCA
* *
12351388 TTTGGAAATTTTATTTTCAA-GAGAAATTGATACTTTCAACTTTCCCTAAAATACTTTTGAAAAT
1 TTTGAAAATGTTATTTTCAATG-GAAATTGATACTTTCAACTTTCCCTAAAATACTTTTGAAAAT
*
12351452 TTTATTTTTAAGAAAAATTGATACTTTCAAC
65 TTTATTTTTAAAAAAAATTGATACTTTCAAC
12351483 ATTTCCTCAA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 1 0.01
109 87 0.99
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (109 bp):
TTTGAAAATGTTATTTTCAATGGAAATTGATACTTTCAACTTTCCCTAAAATACTTTTGAAAATT
TTATTTTTAAAAAAAATTGATACTTTCAACTTTTTCTTAAAGCA
Found at i:12353135 original size:12 final size:13
Alignment explanation
Indices: 12353101--12353134 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12353091 ATAAAAATAA
**
12353101 AAATAAAAAAATG
1 AAATAAAAATCTG
12353114 AAATAAAAATCTG
1 AAATAAAAATCTG
12353127 AAATAAAA
1 AAATAAAA
12353135 TGAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (13 bp):
AAATAAAAATCTG
Found at i:12359672 original size:16 final size:17
Alignment explanation
Indices: 12359645--12359679 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12359635 ATCAAGACGC
12359645 ATTAATTATTATACTTT
1 ATTAATTATTATACTTT
*
12359662 ATTAA-TATTATATTTT
1 ATTAATTATTATACTTT
12359678 AT
1 AT
12359680 ATTCTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTAATTATTATACTTT
Found at i:12360074 original size:16 final size:17
Alignment explanation
Indices: 12360053--12360094 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
12360043 TAAATTTAAT
12360053 TATTCATGAACCT-AAC
1 TATTCATGAACCTAAAC
*
12360069 TATTCATGAACTTAAAC
1 TATTCATGAACCTAAAC
12360086 -ATTCATGAA
1 TATTCATGAA
12360095 TTCATTGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (17 bp):
TATTCATGAACCTAAAC
Found at i:12360204 original size:17 final size:17
Alignment explanation
Indices: 12360182--12360218 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12360172 GTCTAGATTT
12360182 ATATAAAA-AATTCATTA
1 ATATAAAATAATT-ATTA
12360199 ATATAAAATAATTATTA
1 ATATAAAATAATTATTA
12360216 ATA
1 ATA
12360219 AAATCCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAAAATAATTATTA
Found at i:12361335 original size:222 final size:216
Alignment explanation
Indices: 12360952--12361378 Score: 504
Period size: 222 Copynumber: 1.9 Consensus size: 216
12360942 CAAAGATCAT
* *
12360952 AATTAAAATAATTCTGAATAACTAAATTATAACAAATACCTAAATCAAAAATTAAAAAGGAAACC
1 AATTAAAACAATTCTGAATAACTAAATCATAACAAATACCTAAATCAAAAATTAAAAAGGAAACC
* * *
12361017 TAGAAATCAAGTGAAACCATATATGGGAGTAGCTACAAATATATAAAAGGTAAAGAAATAAATAA
66 TAGAAATCAAGTGAAACCACATATGGGAGTAACTACAAATAAATAAAAGGTAAAGAAATAAATAA
* * * *
12361082 AATATTTTGGGTAAGTGAAATACATGAGATGATAAACTAAACA-ATGTTTC-ACCATGGCATGTT
131 AATATTTTAGGTAAGCGAAAGACAAGAGATGATAAACTAAACAGA-GTTTCGACCA-GGCATGTT
*
12361145 GGATGTTGTTTATAGAGTACCAA
194 GCATGTTGTTTATAGAGTACCAA
* * * *
12361168 AATTAAAACAA-TCTCGAATAACTAAATCATACCAAAATAAACCTAAATCAAGCAA-TAAAGATG
1 AATTAAAACAATTCT-GAATAACTAAATCATAAC-AAAT--ACCTAAATCAA-AAATTAAAAAGG
* ** * * *
12361231 AATCCTAGAAATCAAGTGAAAGTACATGTGGGAGCATTAACTACAAATAAATTAGAGGTAAAGAT
61 AAACCTAGAAATCAAGTGAAACCACATATGGGAG---TAACTACAAATAAATAAAAGGTAAAGA-
* ** *
12361296 AA-AAGTAAAATATTTTAGGTAAGCGAAAGACAAGAGATGATAAACTAATTAGAGTTTCGACGAG
122 AATAAATAAAATATTTTAGGTAAGCGAAAGACAAGAGATGATAAACTAAACAGAGTTTCGACCAG
12361360 GCATGTTGCATGTTGTTTA
187 GCATGTTGCATGTTGTTTA
12361379 CGCATTTAGT
Statistics
Matches: 176, Mismatches: 24, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
215 3 0.02
216 26 0.15
217 4 0.02
219 46 0.26
220 2 0.01
222 89 0.51
223 6 0.03
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (216 bp):
AATTAAAACAATTCTGAATAACTAAATCATAACAAATACCTAAATCAAAAATTAAAAAGGAAACC
TAGAAATCAAGTGAAACCACATATGGGAGTAACTACAAATAAATAAAAGGTAAAGAAATAAATAA
AATATTTTAGGTAAGCGAAAGACAAGAGATGATAAACTAAACAGAGTTTCGACCAGGCATGTTGC
ATGTTGTTTATAGAGTACCAA
Found at i:12362161 original size:23 final size:23
Alignment explanation
Indices: 12362135--12362185 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
12362125 GAAACTGTTC
* *
12362135 ATTTTGAATAAACTTATCTATCT
1 ATTTTGAACAAACTTAACTATCT
*
12362158 ATTTTGTACAAACTTAACTATCT
1 ATTTTGAACAAACTTAACTATCT
12362181 ATTTT
1 ATTTT
12362186 TATTTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTTTGAACAAACTTAACTATCT
Found at i:12363309 original size:21 final size:21
Alignment explanation
Indices: 12363284--12363347 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
12363274 TTTATATATA
*
12363284 TGATTTTTATTTCTTTATCTT
1 TGATTTTTATTTATTTATCTT
* *
12363305 TGATTTTTATTAATTTATTTT
1 TGATTTTTATTTATTTATCTT
* *
12363326 TAACTTTTATTTATTTATCTT
1 TGATTTTTATTTATTTATCTT
12363347 T
1 T
12363348 AAATATTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.70
Consensus pattern (21 bp):
TGATTTTTATTTATTTATCTT
Found at i:12363359 original size:21 final size:21
Alignment explanation
Indices: 12363288--12363361 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
12363278 TATATATGAT
* * *
12363288 TTTTATTTCTTTATCTTTGAT
1 TTTTATTTATTTATCTTTAAA
* * *
12363309 TTTTATTAATTTATTTTTAAC
1 TTTTATTTATTTATCTTTAAA
12363330 TTTTATTTATTTATCTTTAAA
1 TTTTATTTATTTATCTTTAAA
12363351 TATTT-TTTATT
1 T-TTTATTTATT
12363362 AGGTGTTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 41 0.93
22 3 0.07
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.70
Consensus pattern (21 bp):
TTTTATTTATTTATCTTTAAA
Found at i:12364325 original size:15 final size:15
Alignment explanation
Indices: 12364280--12364391 Score: 70
Period size: 15 Copynumber: 7.5 Consensus size: 15
12364270 TTGATATATT
12364280 TTTATTTATTTATTTA
1 TTTATTT-TTTATTTA
* *
12364296 TTT-TTATTTAGTTA
1 TTTATTTTTTATTTA
12364310 TTTATTTTTTATTTA
1 TTTATTTTTTATTTA
* **
12364325 TTTGTTTTCAATTT-
1 TTTATTTTTTATTTA
* *
12364339 TTGTGTTTATTTTTTTA
1 TT-TATTT-TTTATTTA
12364356 -TTATTTGTTTA-TTA
1 TTTATTT-TTTATTTA
* **
12364370 TTTATTTGTTATCCA
1 TTTATTTTTTATTTA
12364385 TTTATTT
1 TTTATTT
12364392 GTAAATATTA
Statistics
Matches: 74, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
14 18 0.24
15 48 0.65
16 8 0.11
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.73
Consensus pattern (15 bp):
TTTATTTTTTATTTA
Found at i:12364381 original size:11 final size:11
Alignment explanation
Indices: 12364285--12364381 Score: 63
Period size: 11 Copynumber: 8.4 Consensus size: 11
12364275 ATATTTTTAT
*
12364285 TTATTTATTTA
1 TTATTTATTTG
12364296 TT-TTTATTTAG
1 TTATTTATTT-G
*
12364307 TTATTTATTTT
1 TTATTTATTTG
12364318 TTATTTATTTG
1 TTATTTATTTG
12364329 TTTTCAATTT-TTGTG
1 --TT--ATTTATT-TG
* *
12364344 TTTATTTTTTTA
1 -TTATTTATTTG
* *
12364356 TTATTTGTTTA
1 TTATTTATTTG
12364367 TTATTTATTTG
1 TTATTTATTTG
12364378 TTAT
1 TTAT
12364382 CCATTTATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
10 7 0.10
11 37 0.52
12 12 0.17
13 4 0.06
14 5 0.07
15 6 0.08
ACGTcount: A:0.19, C:0.01, G:0.06, T:0.74
Consensus pattern (11 bp):
TTATTTATTTG
Found at i:12364391 original size:4 final size:4
Alignment explanation
Indices: 12364280--12364376 Score: 73
Period size: 4 Copynumber: 25.8 Consensus size: 4
12364270 TTGATATATT
*
12364280 TTTA TTTA TTTA TTTA -TT- TTTA TTTA GTTA TTTA TTT- TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* ** * * *
12364325 TTTG TTT- TCAA TTT- TTGTG TTTA TTTT TTTA -TTA TTTG TTTA -TTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
12364370 TTTA TTT
1 TTTA TTT
12364377 GTTATCCATT
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
3 16 0.22
4 55 0.75
5 2 0.03
ACGTcount: A:0.19, C:0.01, G:0.05, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:12364421 original size:16 final size:16
Alignment explanation
Indices: 12364402--12364432 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12364392 GTAAATATTA
*
12364402 TTTTAAATAAAAATAT
1 TTTTAAACAAAAATAT
12364418 TTTTAAACAAAAATA
1 TTTTAAACAAAAATA
12364433 AAAAAAAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTTAAACAAAAATAT
Found at i:12364506 original size:57 final size:58
Alignment explanation
Indices: 12364434--12364545 Score: 181
Period size: 57 Copynumber: 1.9 Consensus size: 58
12364424 ACAAAAATAA
* *
12364434 AAAAAAATCTTACCAACATATTAGAGAGCTCAAGTTTCTAAAAAATAATTTTTAAAAT
1 AAAAAAATCGTACCAACATATTAGAGAGCTCAAGTTTCTAAAAAAGAATTTTTAAAAT
* *
12364492 AAAAAAAT-GTACCAACATATTGGAGAGTTCAAGTTTCTAAAAAAGAATTTTTAA
1 AAAAAAATCGTACCAACATATTAGAGAGCTCAAGTTTCTAAAAAAGAATTTTTAA
12364546 TAAAAATTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 42 0.84
58 8 0.16
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (58 bp):
AAAAAAATCGTACCAACATATTAGAGAGCTCAAGTTTCTAAAAAAGAATTTTTAAAAT
Found at i:12372745 original size:17 final size:17
Alignment explanation
Indices: 12372725--12372772 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
12372715 CCAATAACTC
12372725 AACTAAAGAAATAAGAG
1 AACTAAAGAAATAAGAG
*
12372742 AACT--A-AACT-A-AG
1 AACTAAAGAAATAAGAG
12372754 AACTAAAGAAATAAGAG
1 AACTAAAGAAATAAGAG
12372771 AA
1 AA
12372773 GTGAGGAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
12 6 0.25
13 1 0.04
14 4 0.17
15 4 0.17
16 1 0.04
17 8 0.33
ACGTcount: A:0.65, C:0.08, G:0.15, T:0.12
Consensus pattern (17 bp):
AACTAAAGAAATAAGAG
Found at i:12378728 original size:17 final size:17
Alignment explanation
Indices: 12378706--12378742 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12378696 ATACTCTTGG
* *
12378706 TATATTTTTTTTTTGTT
1 TATATTTTTTATCTGTT
12378723 TATATTTTTTATCTGTT
1 TATATTTTTTATCTGTT
12378740 TAT
1 TAT
12378743 TTATTTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (17 bp):
TATATTTTTTATCTGTT
Found at i:12378757 original size:23 final size:22
Alignment explanation
Indices: 12378730--12378808 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
12378720 GTTTATATTT
* *
12378730 TTTATCTGTTTATTTATTTTCTA
1 TTTATTTGTTTATTT-TTTTTTA
*
12378753 TTTATGTGTTTATTTTCTTTTTA
1 TTTATTTGTTTATTTT-TTTTTA
*
12378776 -TTATTTGCTTATTTGTTTTTTA
1 TTTATTTGTTTATTT-TTTTTTA
12378798 TTTATTTGTTT
1 TTTATTTGTTT
12378809 TCCATTTACT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
22 19 0.40
23 29 0.60
ACGTcount: A:0.14, C:0.05, G:0.08, T:0.73
Consensus pattern (22 bp):
TTTATTTGTTTATTTTTTTTTA
Found at i:12378848 original size:17 final size:18
Alignment explanation
Indices: 12378822--12378858 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
12378812 ATTTACTTGT
*
12378822 AAATATTTTTTAAATAAA
1 AAATATTTTTTAAACAAA
12378840 AAATA-TTTTTAAACAAA
1 AAATATTTTTTAAACAAA
12378857 AA
1 AA
12378859 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTTTTTAAACAAA
Found at i:12378946 original size:61 final size:61
Alignment explanation
Indices: 12378856--12379066 Score: 211
Period size: 61 Copynumber: 3.5 Consensus size: 61
12378846 TTTTAAACAA
* * * * *
12378856 AAAT-AAAAAA-AATCTAACCAATATTTTGGAAGATTCAAGTTTCTAAAAAATAATTTTTT
1 AAATAAAAAAAGAATCTTACCAACATATTGGAAGGTTCAAGTTTCTAAAAAATAAATTTTT
* * *
12378915 AATTAAAAAAAGAATCTTACTACCATATTGGAAGGTTCAAGTTTCTAAAAAATAAATTTTT
1 AAATAAAAAAAGAATCTTACCAACATATTGGAAGGTTCAAGTTTCTAAAAAATAAATTTTT
** * * *
12378976 AAATAAAAACTGAATCTTACCAACATATTAGAAGGTTC-AGATTT-T-TAAAATAAATTCTT
1 AAATAAAAAAAGAATCTTACCAACATATTGGAAGGTTCAAG-TTTCTAAAAAATAAATTTTT
* * *
12379035 CAATAAAATAAAG--CCTTACCAATATATTGGAA
1 AAATAAAA-AAAGAATCTTACCAACATATTGGAA
12379067 AGCAATTTTA
Statistics
Matches: 126, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
58 16 0.13
59 22 0.17
60 11 0.09
61 77 0.61
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (61 bp):
AAATAAAAAAAGAATCTTACCAACATATTGGAAGGTTCAAGTTTCTAAAAAATAAATTTTT
Found at i:12379223 original size:17 final size:18
Alignment explanation
Indices: 12379196--12379229 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12379186 ATTGGAGGGT
12379196 TTGTGATTTTAAATAAGC
1 TTGTGATTTTAAATAAGC
12379214 TTGT-ATTTTAAATAAG
1 TTGTGATTTTAAATAAG
12379230 ATTTTACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (18 bp):
TTGTGATTTTAAATAAGC
Found at i:12387136 original size:3 final size:3
Alignment explanation
Indices: 12387128--12387165 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12387118 TAAACGTACC
12387128 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12387166 ATGACAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12394747 original size:35 final size:35
Alignment explanation
Indices: 12394704--12394776 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
12394694 TTAATCAAAT
12394704 AATCATCCCTATTTGATAGGTGCATGTAAAACTCA
1 AATCATCCCTATTTGATAGGTGCATGTAAAACTCA
12394739 AATCATCCCTATTTGATAGGTGCATGTAAAACTCA
1 AATCATCCCTATTTGATAGGTGCATGTAAAACTCA
12394774 AAT
1 AAT
12394777 TGTAAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (35 bp):
AATCATCCCTATTTGATAGGTGCATGTAAAACTCA
Found at i:12405660 original size:6 final size:6
Alignment explanation
Indices: 12405649--12405679 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12405639 TGTATATGAC
12405649 TAATAT TAATAT TAATAT T-ATAT TAATAT TA
1 TAATAT TAATAT TAATAT TAATAT TAATAT TA
12405680 TTAATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:12405673 original size:11 final size:11
Alignment explanation
Indices: 12405649--12405680 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
12405639 TGTATATGAC
12405649 TAATATTAATAT
1 TAATATT-ATAT
12405661 TAATATTATAT
1 TAATATTATAT
12405672 TAATATTAT
1 TAATATTAT
12405681 TAATATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAATATTATAT
Found at i:12405687 original size:17 final size:17
Alignment explanation
Indices: 12405651--12405687 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12405641 TATATGACTA
*
12405651 ATATTAATATTAATATT
1 ATATTAATATTAATAAT
*
12405668 ATATTAATATTATTAAT
1 ATATTAATATTAATAAT
12405685 ATA
1 ATA
12405688 AAAAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTAATATTAATAAT
Found at i:12408126 original size:18 final size:19
Alignment explanation
Indices: 12408091--12408128 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12408081 AAGAATTATT
12408091 ATTCTAAACCTAAAAAATA
1 ATTCTAAACCTAAAAAATA
*
12408110 ATTCTAAA-CTAATAAATA
1 ATTCTAAACCTAAAAAATA
12408128 A
1 A
12408129 GTGTTAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (19 bp):
ATTCTAAACCTAAAAAATA
Found at i:12408604 original size:19 final size:18
Alignment explanation
Indices: 12408580--12408625 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
12408570 GGTAACATAA
12408580 AAAAAATAGTATTATAAA-T
1 AAAAAATA--ATTATAAACT
*
12408599 AAAAAATAATTTTAAACT
1 AAAAAATAATTATAAACT
12408617 AAAAAATAA
1 AAAAAATAA
12408626 GTGTTAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 10 0.40
19 8 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAAAATAATTATAAACT
Found at i:12408632 original size:19 final size:19
Alignment explanation
Indices: 12408580--12408632 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
12408570 GGTAACATAA
12408580 AAAAAAT-AGTATTATAAAT
1 AAAAAATAAGTATTA-AAAT
* *
12408599 AAAAAATAA-TTTTAAACT
1 AAAAAATAAGTATTAAAAT
*
12408617 AAAAAATAAGTGTTAA
1 AAAAAATAAGTATTAA
12408633 TGTAAAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 12 0.41
19 16 0.55
20 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (19 bp):
AAAAAATAAGTATTAAAAT
Found at i:12408640 original size:19 final size:18
Alignment explanation
Indices: 12408594--12408632 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12408584 AATAGTATTA
*
12408594 TAAA-TAAAAAATAATTT
1 TAAACTAAAAAATAATGT
12408611 TAAACTAAAAAATAAGTGT
1 TAAACTAAAAAATAA-TGT
12408630 TAA
1 TAA
12408633 TGTAAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 10 0.53
19 5 0.26
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (18 bp):
TAAACTAAAAAATAATGT
Found at i:12408830 original size:17 final size:18
Alignment explanation
Indices: 12408796--12408837 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
12408786 TTGATAATAA
*
12408796 AAAAAATATTATTATAAAT
1 AAAAAATA-TATTATAAAC
*
12408815 AAAAAATA-ATTCTAAAC
1 AAAAAATATATTATAAAC
12408832 AAAAAA
1 AAAAAA
12408838 GATGTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.62
19 8 0.38
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAATATATTATAAAC
Found at i:12409020 original size:712 final size:719
Alignment explanation
Indices: 12407887--12409389 Score: 1626
Period size: 717 Copynumber: 2.1 Consensus size: 719
12407877 AATAATATTT
* ** * **
12407887 AAAAA-AATTTT-AACTAAAAAAT-TGT-TTAGCGTAAAAAAGTGAGAATTATCCCAAAATTGAT
1 AAAAATAATTTTAAACTAAAAAATAAGTGTTAATGT-AAAAAGTGAGAATAATCATAAAATTGAT
* * * * * * *
12407948 ATCATTTGTTATAAAATGTGTTAGAAATGTCGTAATATCTTAAGAGAGAGTTGTAATAATTTAAA
65 ATCATTTGGTATAAAATATATTAGAAATATCGTAATACCTTAAGAAAAAGTTGTAATAATTTAAA
* * *
12408013 CATAATAAATGTTAAAACAAGCATAAAAAGATATTATTATAATGTAAAAAATTAAGTTGACAATG
130 CATAATAAAAGGTAAAACAAACATAAAAAGATATTATTATAATGTAAAAAATTAAGTTGACAA-G
* * * * * *
12408078 TAAAAGAATTATTATTCTAAACCTAAAAAATAATTCTAAACTAATAAATAAGTGTTAACATAAAA
194 TAAAAAAAATATTATTATAAA-CTAAAAAATAATTCTAAACTAAAAAAGAAGTATTAACATAAAA
* * ** ** *
12408143 AGATGAGAATAATTATAAAATTGGGATCATTTAATGTAAAATGTGTTAGAAGTATTACAATGTAA
258 AGATGAGAATAATTATAAAATTGGAATAATTTAACATAAAACATGTTAGAAGTATTACAAGGTAA
* ** * *
12408208 AAAGGTAAGAATAACTTTAAAGTTGGTGTTACTTGATGTAAAATGAGTTAGAAAGATCGTAACAC
323 AAAGGTAAGAATAACTTTAAAATTAATGTTACTTGATGTAAAATGAGTTAAAAAGATCATAACAC
* * * * *
12408273 CCTTATAAAGAGTTTTGATAATTCTAAACATAAT-AAAAGATAATAACAAG-TATAAAAAATATT
388 CCTTACAAAGAGTTGTGATAATTCTAAACATAATAAAAAG-CAAGAACAAGATAAAAAAAATATT
* * * * *
12408336 ATTTTAATATAAACAATTA-AGTTCGCAAAATAAAAGAATTATTATTACAAATAAAAAATAATTT
452 ATTATAACATAAACAA-TACAGTTAGCAAAATAAAAGAACTATTATTACAAATAAAAAATAATTC
12408400 TAAATAGAAAATAAGAGTTAACATA-AAATA-ATAAAAATAATCATAAAACTGATATTATTTAAC
516 T--A-A-AAAA-AAGAGTTAACATATAAA-AGATAAAAATAATCATAAAACTGATATTATTTAAC
* * *
12408463 ATAAAATAGTTAGAAGTATTGTTATA-CCTT-A-AAAAAATTGTAACAATTCT-AAACATAATGA
575 ATAAAATAGTTAGAAGTATTGTAATATCCTTAAGAAAAAATTATAACAATTCTAAAAC-TAA-CA
* * *
12408524 ACA-GTAATAACAAATGTAAAAAAATATT-TT-TGA-A-ACGTAA-TAAATTGGTAACATAAAAA
638 AAAGGTAATAACAAATGTAAAAAAATATTATTATAATATAAGTAATTAAATTGGTAACATAAAAA
*
12408583 AAATAGTATTATAAATA
703 AAATAGTATTACAAATA
** *
12408600 AAAAATAATTTTAAACTAAAAAATAAGTGTTAATGTAAAAAGGTGAGAATAATTGTAAAATTAAT
1 AAAAATAATTTTAAACTAAAAAATAAGTGTTAATGTAAAAA-GTGAGAATAATCATAAAATTGAT
* * * * *
12408665 ATCATTTGGTGTAAAATATATTAGAAGTATCTTAATACCTTAA-AAAAAGTTTTGATAATTTTAA
65 ATCATTTGGTATAAAATATATTAGAAATATCGTAATACCTTAAGAAAAAGTTGTAATAA-TTTAA
* * * * * *
12408729 ATATAATAAAAGGTAAGAACAAACAT-GAAAGATTTTATTATAATTTAAATAATTAAGTTGATAA
129 ACATAATAAAAGGTAA-AACAAACATAAAAAGATATTATTATAATGTAAAAAATTAAGTTGACAA
* *
12408793 -TAAAAAAAATATTATTATAAA-TAAAAAATAATTCTAAAC-AAAAAAGATGTATTAACGTAAAA
193 GTAAAAAAAATATTATTATAAACTAAAAAATAATTCTAAACTAAAAAAGAAGTATTAACATAAAA
* * * *
12408855 ATG-TGAGAATAATTGTAAAATTGGAATAATTTAGCATAAAGCATGTTAGAAGTATTGCAAGGTA
258 A-GATGAGAATAATTATAAAATTGGAATAATTTAACATAAAACATGTTAGAAGTATTACAAGGTA
* * * * *
12408919 AAAATGTAAGAAT-AGTTGTAAAATTAATGTTATTTGATGTAAATTG-GATTAAAAATG-TTATA
322 AAAAGGTAAGAATAACTT-TAAAATTAATGTTACTTGATGTAAAATGAG-TTAAAAA-GATCATA
* * *
12408981 ACA-CTTTAACAAAGAGTTGTGATAATTTTAAATATAATAAAAAGCAAGAACAAGAATAAAAAAA
384 ACACCCTT-ACAAAGAGTTGTGATAATTCTAAACATAATAAAAAGCAAGAACAAG-ATAAAAAAA
* ** * *
12409045 ATATTATTATAACATAAATAATACTTTTAGCAACATAAAAGAACTATTATTACAAATAAATAATA
447 ATATTATTATAACATAAACAATACAGTTAGCAAAATAAAAGAACTATTATTACAAATAAAAAATA
* * * * * * * * **
12409110 ATTCTAAAAAAAAGTGTTAATATATAAAAGATGAGAGTAATCGTAAAATTGGTATTATTTGGCAT
512 ATTCTAAAAAAAAGAGTTAACATATAAAAGATAAAAATAATCATAAAACTGATATTATTTAACAT
* * * *
12409175 AAAATTGTTAGAAGTATTGTAATATCTTTAAGAAAAAATTATAATAATTTTAAAACTAACAAAAG
577 AAAATAGTTAGAAGTATTGTAATATCCTTAAGAAAAAATTATAACAATTCTAAAACTAACAAAAG
* * ** *
12409240 GTAATAACAAATGTAAAAAGATATTATTATAATATAAGTAATTAAGTTGGTAATGTAAAAAAATT
642 GTAATAACAAATGTAAAAAAATATTATTATAATATAAGTAATTAAATTGGTAACATAAAAAAAAT
*
12409305 ATTATTACAAATA
707 AGTATTACAAATA
* *
12409318 AAAAATAATTTTAAAC-AAAAAATAAGAGTTAATATAAAACAGTGAGAATAATCATAAAATTGAT
1 AAAAATAATTTTAAACTAAAAAATAAGTGTTAATGTAAAA-AGTGAGAATAATCATAAAATTGAT
*
12409382 ATTATTTG
65 ATCATTTG
12409390 ATTAATAAAA
Statistics
Matches: 652, Mismatches: 109, Indels: 54
0.80 0.13 0.07
Matches are distributed among these distances:
709 12 0.02
710 56 0.09
711 11 0.02
712 155 0.24
713 75 0.12
714 76 0.12
715 31 0.05
716 19 0.03
717 162 0.25
718 55 0.08
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (719 bp):
AAAAATAATTTTAAACTAAAAAATAAGTGTTAATGTAAAAAGTGAGAATAATCATAAAATTGATA
TCATTTGGTATAAAATATATTAGAAATATCGTAATACCTTAAGAAAAAGTTGTAATAATTTAAAC
ATAATAAAAGGTAAAACAAACATAAAAAGATATTATTATAATGTAAAAAATTAAGTTGACAAGTA
AAAAAAATATTATTATAAACTAAAAAATAATTCTAAACTAAAAAAGAAGTATTAACATAAAAAGA
TGAGAATAATTATAAAATTGGAATAATTTAACATAAAACATGTTAGAAGTATTACAAGGTAAAAA
GGTAAGAATAACTTTAAAATTAATGTTACTTGATGTAAAATGAGTTAAAAAGATCATAACACCCT
TACAAAGAGTTGTGATAATTCTAAACATAATAAAAAGCAAGAACAAGATAAAAAAAATATTATTA
TAACATAAACAATACAGTTAGCAAAATAAAAGAACTATTATTACAAATAAAAAATAATTCTAAAA
AAAAGAGTTAACATATAAAAGATAAAAATAATCATAAAACTGATATTATTTAACATAAAATAGTT
AGAAGTATTGTAATATCCTTAAGAAAAAATTATAACAATTCTAAAACTAACAAAAGGTAATAACA
AATGTAAAAAAATATTATTATAATATAAGTAATTAAATTGGTAACATAAAAAAAATAGTATTACA
AATA
Found at i:12410101 original size:190 final size:190
Alignment explanation
Indices: 12409772--12410153 Score: 584
Period size: 190 Copynumber: 2.0 Consensus size: 190
12409762 AATAATCATA
*
12409772 AAATTGATAAAATTTAACATAAAATATTTTAAAAGTGTCATAATTTAAAAATATAAAAATAGTCG
1 AAATTGATAAAATTTAACATAAAATATTTTAAAAGTGTCATAATTTAAAAATATAAAAATAGTCA
* * * *
12409837 TAAAATTGGTATCCTTTGGTATAAAATTAGTTAAAAGTGTTGTAACACCCTAAGAAAAAATTGTG
66 TAAAATTGATATCCTTTGGTATAAAATTAGTTAAAAGTATTATAACACCCTAAGAAAAAACTGTG
* *
12409902 ATGATTTTAAACAAAATGCAAGGTAAGAATAAGTACAAAAAATATTATTATAACATAAAT
131 ATAATTTTAAACAAAATGCAAGGTAAGAATAAATACAAAAAATATTATTATAACATAAAT
* *
12409962 AAATTGATAAAATTTAACATAAAATGTTTTAAAAGTGTCGTAATTTAAAAATATAAAAATAGTCA
1 AAATTGATAAAATTTAACATAAAATATTTTAAAAGTGTCATAATTTAAAAATATAAAAATAGTCA
* * ** *
12410027 TAAAATTGATATCGTTTGGTATAAAATTAGTTAAAAGTATTATAATACTTTAAGAAAGAACTGTG
66 TAAAATTGATATCCTTTGGTATAAAATTAGTTAAAAGTATTATAACACCCTAAGAAAAAACTGTG
* * ** * *
12410092 ATAATTTTAAACATAATGTAAGGTAAGAATAAATGTAAAAAATATTATTGTAATATAAAT
131 ATAATTTTAAACAAAATGCAAGGTAAGAATAAATACAAAAAATATTATTATAACATAAAT
12410152 AA
1 AA
12410154 GTAACTTAAC
Statistics
Matches: 172, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
190 172 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.34
Consensus pattern (190 bp):
AAATTGATAAAATTTAACATAAAATATTTTAAAAGTGTCATAATTTAAAAATATAAAAATAGTCA
TAAAATTGATATCCTTTGGTATAAAATTAGTTAAAAGTATTATAACACCCTAAGAAAAAACTGTG
ATAATTTTAAACAAAATGCAAGGTAAGAATAAATACAAAAAATATTATTATAACATAAAT
Found at i:12410401 original size:219 final size:213
Alignment explanation
Indices: 12410088--12410866 Score: 600
Period size: 214 Copynumber: 3.6 Consensus size: 213
12410078 AAGAAAGAAC
** ** * ** *
12410088 TGTGATAATTTTAAACATAATGTAAGGTAAGAATAAATGTAAAAAATATTATTGTAATATAAATA
1 TGTGATAATTTTAAACATAATAAAATATAA-AAAAAACATAAAAAATA-TATTATAA-ATAAATA
* * * *
12410153 AGTAACTT-AACAGTGTAAAAGAATTATTATTATAAATAAAAAATAATTCTAAACCAAAAAAATA
63 ATTAAGTTGAA-A-AGTAAAAAAATTATTATTATAAATAAAAAATAATTCTAAACCAAAAAAATA
** *
12410217 AGTGTTTATGT-AAAAGATAAAAATAATAGTAAAATTAGTATAATTTCTCTTAAAATAGATTAGA
126 AGTGTTTATGTAAAAAG-TAAAAATAATA-TAAAATTAGTATAATTTGACATAAAATAGATTAGA
* **
12410281 AGTACCATAATATCCTAAAAAGAGT
189 AATATTATAATATCCTAAAAAGAGT
* *
12410306 TGTGATAATTTTAAACGTAATAAAATATAAAAATAAACATAAAAAAGTACTATTATAAAGTCAAT
1 TGTGATAATTTTAAACATAATAAAATATAAAAA-AAACATAAAAAA-TA-TATTATAAA-TAAAT
* ** *
12410371 AATTAAGTTGACAAAGTAAAAAAATTATTATTATAAAT-AAAAATAATTTTGGA-CAAAAAAA-G
62 AATTAAGTTGA-AAAGTAAAAAAATTATTATTATAAATAAAAAATAATTCTAAACCAAAAAAATA
* * * *
12410433 AGTGTTAATGTTAAAAAGTGAAAATAATAATAAAATTAGTATCATTTGACATAAAATATG-TTAT
126 AGTGTTTATG-TAAAAAGTAAAAATAAT-ATAAAATTAGTATAATTTGACATAAAATA-GATTAG
* * * *
12410497 AACTATTGTAACATCTTAAGAAAGAGT
188 AAATATTATAATATCCTAA-AAAGAGT
** * * * * * *
12410524 TGTGATAATTTTAAATTTAATGAAATGT-GAAAACACGTATAAAAA-ATATTCTAATATAAATAA
1 TGTGATAATTTTAAACATAATAAAATATAAAAAAAACATA-AAAAATATATTATAA-ATAAATAA
* * * *
12410587 TTAAGTTAGTAACA-TAAAAGAATTATTATTATAAATAAAAAATAATTC--AATC-AAAGAATAA
64 TTAAGTT-G-AAAAGTAAAAAAATTATTATTATAAATAAAAAATAATTCTAAACCAAAAAAATAA
* * * * *
12410648 ATGTTTATGTAAAAAAGTAAAAATAATCATAAAATTTA-CATGATTTGACATAAAGTATATTAGA
127 GTGTTTATGT-AAAAAGTAAAAATAAT-ATAAAA-TTAGTATAATTTGACATAAAATAGATTAGA
* * *
12410712 AATGTTATTATA-CCTTAAGAAAAAAGT
189 AATATTATAATATCC-T-A-AAAAGAGT
* * ** *
12410739 TGTGATAATTTTAAACATAATAAACTATAAGAACAAGTATAAATATATATTATTATAAAATAAAT
1 TGTGATAATTTTAAACATAATAAAATATAA-AAAAAACATAAA-AAATA-TATTAT-AAATAAAT
* * * *
12410804 AATTAAATTGGTAATGT-AAAAAATTATTATTTATAAATAAAAAGTAATT-TCAAACCAAAAAAA
62 AATTAAGTT-GAAAAGTAAAAAAATTATTA-TTATAAATAAAAAATAATTCT-AAACCAAAAAAA
12410867 AGTGTTACCG
Statistics
Matches: 441, Mismatches: 85, Indels: 66
0.74 0.14 0.11
Matches are distributed among these distances:
213 8 0.02
214 99 0.22
215 48 0.11
216 18 0.04
217 75 0.17
218 99 0.22
219 81 0.18
220 4 0.01
221 4 0.01
222 5 0.01
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (213 bp):
TGTGATAATTTTAAACATAATAAAATATAAAAAAAACATAAAAAATATATTATAAATAAATAATT
AAGTTGAAAAGTAAAAAAATTATTATTATAAATAAAAAATAATTCTAAACCAAAAAAATAAGTGT
TTATGTAAAAAGTAAAAATAATATAAAATTAGTATAATTTGACATAAAATAGATTAGAAATATTA
TAATATCCTAAAAAGAGT
Found at i:12410665 original size:214 final size:212
Alignment explanation
Indices: 12410168--12410912 Score: 620
Period size: 214 Copynumber: 3.4 Consensus size: 212
12410158 CTTAACAGTG
12410168 TAAAAGAATTATTATTATAAATAAAAAATAA-TTCTAAACCAAAAAAATAAGTGTTTATGTAAAA
1 TAAAAGAATTATTATTATAAATAAAAAATAATTTC-AAACC-AAAAAA-AA-TGTTTATGTAAAA
* * * ** * * **
12410232 GA-TAAAAATAATAGTAAAATTAGTATAATTTCTCTTAAAATA-GATTAGAAGTACCATAATATC
62 AAGTAAAAATAATAATAAAATTAGTATCATTTGACATAAAATATG-TTAGAAATATTATAATATC
* * * *
12410295 CTAA-AAAGAGTTGTGATAATTTTAAACGTAATAAAATATAAAAATAAACATA-AAAAAGTACTA
126 TTAAGAAAGAGTTGTGATAATTTTAAACATAAT-AAATAT--AAA-ACACGTATAAAAA-TACTA
*
12410358 TTATAAAGTCAATAATTAAGTTG-ACAAA
186 TTATAAA-TAAATAATTAAGTTGTA-AAA
* *** * *
12410386 GTAAAAAAATTATTATTATAAAT-AAAAATAATTTTGGA-CAAAAAAAGAGTGTTAATGTTAAAA
1 -TAAAAGAATTATTATTATAAATAAAAAATAATTTCAAACCAAAAAAA-A-TGTTTATGTAAAAA
* * * * *
12410449 AGTGAAAATAATAATAAAATTAGTATCATTTGACATAAAATATGTTATAACTATTGTAACATCTT
63 AGTAAAAATAATAATAAAATTAGTATCATTTGACATAAAATATGTTAGAAATATTATAATATCTT
** * *
12410514 AAGAAAGAGTTGTGATAATTTTAAATTTAATGAAATGTGAAAACACGTATAAAAA-A-TATTCTA
128 AAGAAAGAGTTGTGATAATTTTAAACATAAT-AAATAT-AAAACACGTATAAAAATACTATTATA
*
12410577 ATATAAATAATTAAGTTAGTAACA
191 A-ATAAATAATTAAGTT-GTAAAA
*
12410601 TAAAAGAATTATTATTATAAATAAAAAATAA-TTC-AATCAAAGAATAAATGTTTATGTAAAAAA
1 TAAAAGAATTATTATTATAAATAAAAAATAATTTCAAACCAAA-AA-AAATGTTTATGTAAAAAA
* * * * * * * *
12410664 GTAAAAATAATCATAAAATTTA-CATGATTTGACATAAAGTATATTAGAAATGTTATTATACCTT
64 GTAAAAATAATAATAAAA-TTAGTATCATTTGACATAAAATATGTTAGAAATATTATAATATCTT
* * *
12410728 AAGAAAAAAGTTGTGATAATTTTAAACATAATAAACTATAAGAACAAGTATAAATATATATTATT
128 AAG-AAAGAGTTGTGATAATTTTAAACATAATAAA-TATAA-AACACGTATAAA-A-ATACTATT
* **
12410793 ATAAAATAAATAATTAAATTGGTAATG
188 AT-AAATAAATAATTAAGTT-GTAAAA
* *
12410820 TAAAA-AATTATTATTTATAAATAAAAAGTAATTTCAAACCAAAAAAAA-GTGTTACCGTAAAAA
1 TAAAAGAATTATTA-TTATAAATAAAAAATAATTTCAAACCAAAAAAAATGT-TTA-TGTAAAAA
* * * ** *
12410883 AATGAATATAATCGTAAAATTAATATCATT
63 AGTAAAAATAATAATAAAATTAGTATCATT
12410913 ATCGTAACAC
Statistics
Matches: 431, Mismatches: 67, Indels: 55
0.78 0.12 0.10
Matches are distributed among these distances:
213 1 0.00
214 115 0.27
215 58 0.13
216 29 0.07
217 60 0.14
218 52 0.12
219 76 0.18
220 34 0.08
221 6 0.01
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (212 bp):
TAAAAGAATTATTATTATAAATAAAAAATAATTTCAAACCAAAAAAAATGTTTATGTAAAAAAGT
AAAAATAATAATAAAATTAGTATCATTTGACATAAAATATGTTAGAAATATTATAATATCTTAAG
AAAGAGTTGTGATAATTTTAAACATAATAAATATAAAACACGTATAAAAATACTATTATAAATAA
ATAATTAAGTTGTAAAA
Found at i:12421369 original size:2 final size:2
Alignment explanation
Indices: 12421362--12421391 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12421352 ATGTTTTCAT
12421362 TA 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 TA
12421392 CACATCTTGC
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):
TA
Found at i:12425500 original size:139 final size:139
Alignment explanation
Indices: 12425250--12425531 Score: 564
Period size: 139 Copynumber: 2.0 Consensus size: 139
12425240 ACATTTTGAG
12425250 GAGTGGTAGCATTATATTTCAACAACAAGCTTTGAATTCTAAATTCATTTGTGTGAGAGAACCTT
1 GAGTGGTAGCATTATATTTCAACAACAAGCTTTGAATTCTAAATTCATTTGTGTGAGAGAACCTT
12425315 GGATAGGAATAAGTAATTAATTGCTGATTTAAATTGATTTACAGGACATGAAAATTGAAGATTTG
66 GGATAGGAATAAGTAATTAATTGCTGATTTAAATTGATTTACAGGACATGAAAATTGAAGATTTG
12425380 GAAATTGTT
131 GAAATTGTT
12425389 GAGTGGTAGCATTATATTTCAACAACAAGCTTTGAATTCTAAATTCATTTGTGTGAGAGAACCTT
1 GAGTGGTAGCATTATATTTCAACAACAAGCTTTGAATTCTAAATTCATTTGTGTGAGAGAACCTT
12425454 GGATAGGAATAAGTAATTAATTGCTGATTTAAATTGATTTACAGGACATGAAAATTGAAGATTTG
66 GGATAGGAATAAGTAATTAATTGCTGATTTAAATTGATTTACAGGACATGAAAATTGAAGATTTG
12425519 GAAATTGTT
131 GAAATTGTT
12425528 GAGT
1 GAGT
12425532 TGGTGAAACA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 143 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.35
Consensus pattern (139 bp):
GAGTGGTAGCATTATATTTCAACAACAAGCTTTGAATTCTAAATTCATTTGTGTGAGAGAACCTT
GGATAGGAATAAGTAATTAATTGCTGATTTAAATTGATTTACAGGACATGAAAATTGAAGATTTG
GAAATTGTT
Found at i:12436667 original size:2 final size:2
Alignment explanation
Indices: 12436660--12436692 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12436650 TAGTTACAAT
12436660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12436693 GTTTCATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12441330 original size:21 final size:21
Alignment explanation
Indices: 12441306--12441369 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
12441296 TGCTTTAAAG
12441306 TTAAGATAGTATTATGGTATA
1 TTAAGATAGTATTATGGTATA
* * * *
12441327 TTAATATA-TA-CAT-TTTTA
1 TTAAGATAGTATTATGGTATA
*
12441345 TTAAGATAGTATTACGGTATA
1 TTAAGATAGTATTATGGTATA
12441366 TTAA
1 TTAA
12441370 TATATAAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
18 10 0.32
19 4 0.13
20 3 0.10
21 14 0.45
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.45
Consensus pattern (21 bp):
TTAAGATAGTATTATGGTATA
Found at i:12441364 original size:39 final size:39
Alignment explanation
Indices: 12441306--12441384 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
12441296 TGCTTTAAAG
* *
12441306 TTAAGATAGTATTATGGTATATTAATATATACATTTTTA
1 TTAAGATAGTATTACGGTATATTAATATATAAATTTTTA
12441345 TTAAGATAGTATTACGGTATATTAATATATAAATTTTTA
1 TTAAGATAGTATTACGGTATATTAATATATAAATTTTTA
12441384 T
1 T
12441385 ATTCTTCATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (39 bp):
TTAAGATAGTATTACGGTATATTAATATATAAATTTTTA
Found at i:12459985 original size:21 final size:21
Alignment explanation
Indices: 12459931--12459986 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
12459921 TCGATTGCTT
*
12459931 TCATG-AGGGGATTGATCCTG
1 TCATGTAGGGGATTGATCCTC
*
12459951 TCAT-TGGGGAGATTGATCC-C
1 TCATGTAGGG-GATTGATCCTC
12459971 TCATGTAGGGTGATTG
1 TCATGTAGGG-GATTG
12459987 TTCTCTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.32
Consensus pattern (21 bp):
TCATGTAGGGGATTGATCCTC
Found at i:12465272 original size:240 final size:238
Alignment explanation
Indices: 12464761--12465221 Score: 599
Period size: 239 Copynumber: 1.9 Consensus size: 238
12464751 TTATTAACAA
* *
12464761 TAAACTTAGTAATAAAATTTTTGTTGCTAATTCTCTTATCATTTTTATTTAAAGAAAAATAAAAT
1 TAAA-TTAGCAATAGAA-TTTTGTTGCTAATTCTCTTATCATTTTTATTTAAAGAAAAATAAAAT
* * *
12464826 TATTTTTGAAATTTTTATTTTTTTATTAGTGACCAAATTAACAACCTAAATTCCATCGTTAATTC
64 TATTTTTCAAATTTTTATTTTTTTATTAGTGACCAAATTAACAACCTAAACTCCATCGCTAATTC
** *
12464891 CTTCAAAAAATAAATTTTACTTAAAAAACATTTTTTAAGATCTTTTTGTTTTTCCATTAGTGATG
129 CTTCAAAAAATAAATTTTACTTAAAAAACATTTTTTAAGATCTTTTTGTTTTTCCATTAAAGATA
* * * * * *
12464956 GAATTTTGTCGCTAGTTAGCCATGAAAATTTCGCAGCTAACAGCTT
194 GAATTTCGTCACTAGATAG-CATCAAAATTTAGCAGCTAACAGCTC
* * *
12465002 TAAATTAGCAATAGAATTTT-TATCGCTAATTCTTTTATCGTTTTTATTTTAAGAAAAATAAAAT
1 TAAATTAGCAATAGAATTTTGT-T-GCTAATTCTCTTATCATTTTTATTTAAAGAAAAATAAAAT
* * * * *
12465066 TATTTTTCAAATTTTTA-TTTTTTATTAGTGACGAAATTAGCGACTTAAACTCCATTGCTAATTC
64 TATTTTTCAAATTTTTATTTTTTTATTAGTGACCAAATTAACAACCTAAACTCCATCGCTAATTC
* * *
12465130 CTTTAAAAAATAAATTTTAGTTAAAAAAACA-TTTTTAAGATCTTTTTGTTTTTTCATTAAAGAT
129 CTTCAAAAAATAAATTTTACTT-AAAAAACATTTTTTAAGATCTTTTTGTTTTTCCATTAAAGAT
*
12465194 AGAATTTCGTCACTA-ATAG-GTCAAAATT
193 AGAATTTCGTCACTAGATAGCATCAAAATT
12465222 CTATCACTAA
Statistics
Matches: 193, Mismatches: 24, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
236 7 0.04
238 4 0.02
239 107 0.55
240 71 0.37
241 4 0.02
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (238 bp):
TAAATTAGCAATAGAATTTTGTTGCTAATTCTCTTATCATTTTTATTTAAAGAAAAATAAAATTA
TTTTTCAAATTTTTATTTTTTTATTAGTGACCAAATTAACAACCTAAACTCCATCGCTAATTCCT
TCAAAAAATAAATTTTACTTAAAAAACATTTTTTAAGATCTTTTTGTTTTTCCATTAAAGATAGA
ATTTCGTCACTAGATAGCATCAAAATTTAGCAGCTAACAGCTC
Found at i:12468989 original size:36 final size:36
Alignment explanation
Indices: 12468937--12469006 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
12468927 CTTATCTCTT
**
12468937 TTTGAAACTTAACTTTAATTTTTTTTGTTATGTTCA
1 TTTGAAACTTAACTTTAAACTTTTTTGTTATGTTCA
*
12468973 TTTGAAACTTAGCTTTAAACTTTTTTGTTATGTT
1 TTTGAAACTTAACTTTAAACTTTTTTGTTATGTT
12469007 TGAACATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.24, C:0.09, G:0.10, T:0.57
Consensus pattern (36 bp):
TTTGAAACTTAACTTTAAACTTTTTTGTTATGTTCA
Found at i:12472667 original size:14 final size:14
Alignment explanation
Indices: 12472643--12472677 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
12472633 ACCCAAATTT
*
12472643 AATATAAAATAAATA
1 AATA-AAAATAAAAA
12472658 AATAAAAATAAAAA
1 AATAAAAATAAAAA
12472672 AATAAA
1 AATAAA
12472678 TAAACCAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:12472676 original size:18 final size:19
Alignment explanation
Indices: 12472646--12472681 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
12472636 CAAATTTAAT
12472646 ATAAAATAAATAAATAAAA
1 ATAAAATAAATAAATAAAA
12472665 ATAAAA-AAATAAATAAA
1 ATAAAATAAATAAATAAA
12472682 CCAAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (19 bp):
ATAAAATAAATAAATAAAA
Found at i:12478848 original size:30 final size:30
Alignment explanation
Indices: 12478803--12478873 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
12478793 ATACATGCAT
* * *
12478803 TGCATCTCATCCATATCAATGGATGGTATA
1 TGCATCCCATTCATATCAATGGATAGTATA
12478833 TGCATCCCATTCATATCAATGGATAGTATA
1 TGCATCCCATTCATATCAATGGATAGTATA
12478863 TGCATCCCATT
1 TGCATCCCATT
12478874 TTATGCACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (30 bp):
TGCATCCCATTCATATCAATGGATAGTATA
Found at i:12482425 original size:16 final size:17
Alignment explanation
Indices: 12482399--12482431 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12482389 TCCACTAAAT
12482399 GAAAGAAAAAAGACAAA
1 GAAAGAAAAAAGACAAA
*
12482416 GAAA-AAAAAATACAAA
1 GAAAGAAAAAAGACAAA
12482432 AAATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.03
Consensus pattern (17 bp):
GAAAGAAAAAAGACAAA
Found at i:12484605 original size:33 final size:33
Alignment explanation
Indices: 12484565--12484634 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
12484555 TAATTTTTTA
* *
12484565 AAAGTTTCATGGCCTCTGATTGGAGGAGCACTT
1 AAAGTTTCATGGCCTCTAATTGGAGGAGCAATT
12484598 AAAGTTTCATGGCCTCTAATTGGAGGAGCAATT
1 AAAGTTTCATGGCCTCTAATTGGAGGAGCAATT
12484631 AAAG
1 AAAG
12484635 ATTTTGATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (33 bp):
AAAGTTTCATGGCCTCTAATTGGAGGAGCAATT
Found at i:12484751 original size:88 final size:88
Alignment explanation
Indices: 12484598--12484897 Score: 379
Period size: 88 Copynumber: 3.4 Consensus size: 88
12484588 AGGAGCACTT
* * * *
12484598 AAAGTTTCATGGCCTCTAATTGGAGGAGCAATTAAAGATTTTGATATTTGTAAGACCTTCAGGCA
1 AAAGTTTCATGGCCTCTAATTGGAGGAGCATTTAAAGATTTTGAGATTTGTAAGACTTTAAGGCA
*
12484663 TAATCTCTAAACATTTTAAATTC
66 TAATCTCTAAACATTTTAAACTC
* * * **
12484686 AAAGTTTCATGGCCTTTCATTGGATGAGCATTTAAAGATTTTGAGATTTGTAAGACTTTTGGGCA
1 AAAGTTTCATGGCCTCTAATTGGAGGAGCATTTAAAGATTTTGAGATTTGTAAGACTTTAAGGCA
* *
12484751 TTATCT-TCAAACCTTTTAAACTC
66 TAATCTCT-AAACATTTTAAACTC
* * * * * *
12484774 AAAGTTTCATAGCCTTTGATTGGAGGAGCATTTAAAGATTTTAAGATTTGTAAGA-TCTCAAAGC
1 AAAGTTTCATGGCCTCTAATTGGAGGAGCATTTAAAGATTTTGAGATTTGTAAGACT-TTAAGGC
*
12484838 ATAATCTCCAAACATTTTAAACTC
65 ATAATCTCTAAACATTTTAAACTC
* *
12484862 AAATTTTCATGGCCTCTAATTGGAAGAGCATTTAAA
1 AAAGTTTCATGGCCTCTAATTGGAGGAGCATTTAAA
12484898 AGTTTTGTGA
Statistics
Matches: 182, Mismatches: 27, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
87 2 0.01
88 180 0.99
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (88 bp):
AAAGTTTCATGGCCTCTAATTGGAGGAGCATTTAAAGATTTTGAGATTTGTAAGACTTTAAGGCA
TAATCTCTAAACATTTTAAACTC
Found at i:12487896 original size:17 final size:17
Alignment explanation
Indices: 12487875--12487906 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12487865 TTGGAATAGT
12487875 TTTTTTAA-AAATAAAA
1 TTTTTTAAGAAATAAAA
12487891 TTTTTTAAGAAATAAA
1 TTTTTTAAGAAATAAA
12487907 TGAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTTTTAAGAAATAAAA
Found at i:12490028 original size:51 final size:51
Alignment explanation
Indices: 12489963--12490062 Score: 157
Period size: 51 Copynumber: 1.9 Consensus size: 51
12489953 TTCTCTTTTG
*
12489963 AATTTCTAAATTTTCCACCATTTGGTCCTATTTAGAAATT-TTTTTTTCAA
1 AATTTCTAAATTTTCCACCATTTGGGCCTATTTAGAAATTATTTTTTTCAA
*
12490013 AATTTCTAACTTTTTCCACCATTTGGGCCTATTTAGAAATTCATTTTTTT
1 AATTTCTAA-ATTTTCCACCATTTGGGCCTATTTAGAAATT-ATTTTTTT
12490063 TATTTTTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 9 0.20
51 29 0.64
53 7 0.16
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (51 bp):
AATTTCTAAATTTTCCACCATTTGGGCCTATTTAGAAATTATTTTTTTCAA
Found at i:12490676 original size:12 final size:11
Alignment explanation
Indices: 12490651--12490702 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
12490641 ATAATCATGC
* *
12490651 AAAAAAATACT
1 AAAAAAAAAAT
12490662 AAAAAAACAAAT
1 AAAAAAA-AAAT
*
12490674 AAATAAATAAAT
1 AAA-AAAAAAAT
*
12490686 AAAATAAAAAT
1 AAAAAAAAAAT
12490697 AAAAAA
1 AAAAAA
12490703 TACCAAAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 18 0.55
12 12 0.36
13 3 0.09
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:12490681 original size:23 final size:21
Alignment explanation
Indices: 12490652--12490705 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
12490642 TAATCATGCA
12490652 AAAAAATACTAAAAAAACAAAT
1 AAAAAATACTAAAAAAA-AAAT
* *
12490674 AAATAAATAAATAAAATAAAAAT
1 AAA-AAAT-ACTAAAAAAAAAAT
12490697 AAAAAATAC
1 AAAAAATAC
12490706 CAAAGAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 1 0.04
22 7 0.26
23 11 0.41
24 8 0.30
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAAAATACTAAAAAAAAAAT
Found at i:12491068 original size:20 final size:20
Alignment explanation
Indices: 12491043--12491089 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
12491033 GAATGTTTTA
*
12491043 CCAAAAACTGGAAAAATATG
1 CCAAAAACTGAAAAAATATG
*
12491063 CCAAAAATTGAAAAAATATG
1 CCAAAAACTGAAAAAATATG
*
12491083 TCAAAAA
1 CCAAAAA
12491090 ATTTAAACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.17
Consensus pattern (20 bp):
CCAAAAACTGAAAAAATATG
Found at i:12491664 original size:140 final size:141
Alignment explanation
Indices: 12491505--12491798 Score: 378
Period size: 148 Copynumber: 2.0 Consensus size: 141
12491495 ATTTTCTGTG
* * ** *
12491505 AAATAGGAATTGTGCAAAGACGTAAACAA-CCTAATCAACTCAATGCATTTTTGTGTTTTTTTTT
1 AAATAAGAATTGTGCAAAGACGTAAACAATCC-AATCAACTAAACACATTTTTGTG-TATTTTTT
* *
12491569 TTGTTCAAAAAGT-A-CCTCTAAATAGAGGCTTAATGATAATAAATGCTCCTCTAAATAGAGACA
64 TTGTTCAAAAAGTAACCCTCTAAACAGAGGCTCAATGATAATAAATGCTCCTCTAAATAGAGACA
* *
12491632 CCACAATTTTGTA
129 CCACAACTTTGAA
*
12491645 AAATAAGAATTGTGCAAAGACGTAGACAATCCAATCAACTAAACACATTTTTGTGTATTTTTTTT
1 AAATAAGAATTGTGCAAAGACGTAAACAATCCAATCAACTAAACACATTTTTGTGTATTTTTTTT
*
12491710 GTTGAAAAAGTGAACAAAGCTCCTCTAAACAGAGGCTCAATGATAATAAATGCTCCTCTAAATAG
66 GTTCAAAAAGT-----AA-C-CCTCTAAACAGAGGCTCAATGATAATAAATGCTCCTCTAAATAG
*
12491775 AGGCACCACAACTTTGAA
124 AGACACCACAACTTTGAA
12491793 AAATAA
1 AAATAA
12491799 AATACTTCTC
Statistics
Matches: 132, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
139 19 0.14
140 47 0.36
141 2 0.02
145 1 0.01
148 63 0.48
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (141 bp):
AAATAAGAATTGTGCAAAGACGTAAACAATCCAATCAACTAAACACATTTTTGTGTATTTTTTTT
GTTCAAAAAGTAACCCTCTAAACAGAGGCTCAATGATAATAAATGCTCCTCTAAATAGAGACACC
ACAACTTTGAA
Found at i:12491919 original size:42 final size:41
Alignment explanation
Indices: 12491754--12492220 Score: 542
Period size: 41 Copynumber: 11.3 Consensus size: 41
12491744 GCTCAATGAT
*
12491754 AATAAA-TGCTCCTCTAAATAGAGGCACCACAACTTTGAAA
1 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAA
* * * * *
12491794 AATAAAATACTTCTCTAAACAGAGGTACCACAACTATGAAA
1 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAA
* * * * *
12491835 AATAAAATGCTCTTTTAAATAGAGACACCACAACTTTGAAA
1 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAA
* * * * * *
12491876 AATAAAATGCTTCTTTAAATAAAGGTACCACAACTTTGGAAA
1 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTT-GAAA
* * * *
12491918 AATAAATTGCACCTCTAAATAGAGGAACCACCACTTTGAAAA
1 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTG-AAA
* ** *
12491960 AATAAATTGCTCCTCTAAACAAAGGCACCATGACTTTGGAA
1 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAA
*
12492001 AATAAATTGCTCCTCTAAACAGAGGCACCACCACTTTGAAAA
1 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTG-AAA
* *** *
12492043 AATAAATTGTTCCTCTAAACAGAGGCACCGTGACTTTGGAA
1 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAA
* *
12492084 AATAAATTGCTCTTCTAAATAGAGGCACCACAACTTTGAAA
1 AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAA
12492125 AATAAATTGCTCCTCTAAACAGAGGCAACCACAACTTTGAAA
1 AATAAATTGCTCCTCTAAACAGAGGC-ACCACAACTTTGAAA
* *
12492167 AATAAATTGCTCCTTTAAACATAGGCAACCACAACTTTTG-AA
1 AATAAATTGCTCCTCTAAACAGAGGC-ACCACAAC-TTTGAAA
*
12492209 AATAAAATGCTC
1 AATAAATTGCTC
12492221 ATTGACAATC
Statistics
Matches: 368, Mismatches: 53, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
40 6 0.02
41 192 0.52
42 166 0.45
43 4 0.01
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.25
Consensus pattern (41 bp):
AATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAA
Found at i:12492003 original size:83 final size:82
Alignment explanation
Indices: 12491754--12492220 Score: 535
Period size: 83 Copynumber: 5.6 Consensus size: 82
12491744 GCTCAATGAT
* * * *
12491754 AATAAA-TGCTCCTCTAAATAGAGGCACCACAACTTTGAAAAATAAAATACTTCTCTAAACAGAG
1 AATAAATTGCTCCTCTAAATAGAGGAACCACAACTTTGAAAAATAAATTGCTCCTCTAAACAGAG
* * *
12491818 GTACCACAACTATGAAA
66 GCACCACAACTTTGGAA
* * * * * * * *
12491835 AATAAAATGCTCTTTTAAATAGA-GACACCACAACTTTGAAAAATAAAATGCTTCTTTAAATAAA
1 AATAAATTGCTCCTCTAAATAGAGGA-ACCACAACTTTGAAAAATAAATTGCTCCTCTAAACAGA
*
12491899 GGTACCACAACTTTGGAAA
65 GGCACCACAACTTTGG-AA
* * *
12491918 AATAAATTGCACCTCTAAATAGAGGAACCACCACTTTGAAAAAATAAATTGCTCCTCTAAACAAA
1 AATAAATTGCTCCTCTAAATAGAGGAACCACAACTTTG-AAAAATAAATTGCTCCTCTAAACAGA
**
12491983 GGCACCATGACTTTGGAA
65 GGCACCACAACTTTGGAA
* * * *
12492001 AATAAATTGCTCCTCTAAACAGAGGCACCACCACTTTGAAAAAATAAATTGTTCCTCTAAACAGA
1 AATAAATTGCTCCTCTAAATAGAGGAACCACAACTTTG-AAAAATAAATTGCTCCTCTAAACAGA
***
12492066 GGCACCGTGACTTTGGAA
65 GGCACCACAACTTTGGAA
* *
12492084 AATAAATTGCTCTTCTAAATAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTCTAAACAGAG
1 AATAAATTGCTCCTCTAAATAGAGGAACCACAACTTTGAAAAATAAATTGCTCCTCTAAACAGAG
*
12492149 GCAACCACAACTTTGAAA
66 GC-ACCACAACTTTGGAA
* * * *
12492167 AATAAATTGCTCCTTTAAACATAGGCAACCACAACTTTTG-AAAATAAAATGCTC
1 AATAAATTGCTCCTCTAAATAGAGG-AACCACAAC-TTTGAAAAATAAATTGCTC
12492221 ATTGACAATC
Statistics
Matches: 337, Mismatches: 41, Indels: 13
0.86 0.10 0.03
Matches are distributed among these distances:
81 7 0.02
82 90 0.27
83 178 0.53
84 58 0.17
85 4 0.01
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.25
Consensus pattern (82 bp):
AATAAATTGCTCCTCTAAATAGAGGAACCACAACTTTGAAAAATAAATTGCTCCTCTAAACAGAG
GCACCACAACTTTGGAA
Found at i:12493239 original size:10 final size:10
Alignment explanation
Indices: 12493226--12493271 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
12493216 GTCTTTCTTT
12493226 TTTTTTCTCC
1 TTTTTTCTCC
*
12493236 TTTTTTTTCC
1 TTTTTTCTCC
*
12493246 TTTTTTTTCC
1 TTTTTTCTCC
12493256 -TTTTTCTCTC
1 TTTTTTCTC-C
12493266 TTTTTT
1 TTTTTT
12493272 TTTTTTAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
9 7 0.22
10 20 0.62
11 5 0.16
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTCTCC
Found at i:12493251 original size:20 final size:20
Alignment explanation
Indices: 12493225--12493273 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
12493215 AGTCTTTCTT
*
12493225 TTTTTTTCTCCTTTTT-TTTCC
1 TTTTTTT-TCCTTTTTCTCT-C
12493246 TTTTTTTTCCTTTTTCTCTC
1 TTTTTTTTCCTTTTTCTCTC
12493266 TTTTTTTT
1 TTTTTTTT
12493274 TTTTAAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTTCCTTTTTCTCTC
Found at i:12496780 original size:17 final size:18
Alignment explanation
Indices: 12496758--12496800 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
12496748 AATGTATAGG
*
12496758 AAAAATGGAAAAA-TAAA
1 AAAAATGAAAAAACTAAA
*
12496775 AAAAAT-AAAAAACTAGA
1 AAAAATGAAAAAACTAAA
12496792 AAAAATGAA
1 AAAAATGAA
12496801 TGAAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 15 0.68
18 2 0.09
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (18 bp):
AAAAATGAAAAAACTAAA
Found at i:12502659 original size:50 final size:50
Alignment explanation
Indices: 12502602--12502696 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 50
12502592 TGCAAATGAT
* *
12502602 AATGTTAAAACATGATCATGAAAATGATGCATAGAATGAAATGATATGGA
1 AATGTTAAAACATAAGCATGAAAATGATGCATAGAATGAAATGATATGGA
* * * *
12502652 AATGTTAAAACATAAGGATGGAAATGATGTATAGAATGGAATGAT
1 AATGTTAAAACATAAGCATGAAAATGATGCATAGAATGAAATGAT
12502697 GTTGTGATGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.26
Consensus pattern (50 bp):
AATGTTAAAACATAAGCATGAAAATGATGCATAGAATGAAATGATATGGA
Found at i:12504424 original size:4 final size:4
Alignment explanation
Indices: 12504415--12504459 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
12504405 AAAAATACTA
* *
12504415 AAAT AAAT AAAC ACAT AAAAT AAAT AAAT AAAT AAAT AAAAT AAA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT -AAAT AAA
12504460 AATACCAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 28 0.80
5 7 0.20
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:12504440 original size:21 final size:21
Alignment explanation
Indices: 12504415--12504459 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
12504405 AAAAATACTA
*
12504415 AAATAAATAAACACATAAAAT
1 AAATAAATAAACAAATAAAAT
*
12504436 AAATAAATAAATAAATAAAAT
1 AAATAAATAAACAAATAAAAT
12504457 AAA
1 AAA
12504460 AATACCAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATAAATAAACAAATAAAAT
Found at i:12504449 original size:17 final size:17
Alignment explanation
Indices: 12504413--12504459 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
12504403 CAAAAAATAC
*
12504413 TAAAATAAATAAACACA
1 TAAAATAAATAAACAAA
*
12504430 TAAAATAAATAAATAAA
1 TAAAATAAATAAACAAA
12504447 T-AAATAAAATAAA
1 TAAAAT-AAATAAA
12504460 AATACCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAATAAATAAACAAA
Found at i:12512190 original size:11 final size:11
Alignment explanation
Indices: 12512176--12512219 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
12512166 TATTTGAAAA
12512176 TTTTAAAAATT
1 TTTTAAAAATT
12512187 TTTTAAAAATAT
1 TTTTAAAAAT-T
*
12512199 ATATTTAAAAATG
1 -T-TTTAAAAATT
12512212 TTTTAAAA
1 TTTTAAAA
12512220 TAACTAGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 17 0.59
12 2 0.07
13 1 0.03
14 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
TTTTAAAAATT
Found at i:12522714 original size:13 final size:13
Alignment explanation
Indices: 12522696--12522727 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
12522686 GTTTAACATA
12522696 TTTTTGTTTTTGT
1 TTTTTGTTTTTGT
12522709 TTTTTGTTTTTGT
1 TTTTTGTTTTTGT
12522722 TTTTTG
1 TTTTTG
12522728 CCTACTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
TTTTTGTTTTTGT
Found at i:12522727 original size:7 final size:6
Alignment explanation
Indices: 12522696--12522725 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
12522686 GTTTAACATA
12522696 TTTTTG TTTTTG TTTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG -TTTTTG TTTTTG TTTTT
12522726 TGCCTACTAT
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:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTTG
Found at i:12533886 original size:63 final size:63
Alignment explanation
Indices: 12533768--12533887 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 63
12533758 AAATTGACAA
* * * ** * *
12533768 TGAAAAAAATTACAAATATCAATTATTGTGTTTTAAAACAAAGCAATGCAATAATTGATTATT
1 TGAAAAAAAGTACAAAGATCAATTACTACGTTATAAAACAAAACAATGCAATAATTGATTATT
* * *
12533831 TGAAAAAAAGTACAAAGATCAATTACTACGTTATAAAACAAAATAATGTAGTAATTG
1 TGAAAAAAAGTACAAAGATCAATTACTACGTTATAAAACAAAACAATGCAATAATTG
12533888 TACATTTGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 47 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (63 bp):
TGAAAAAAAGTACAAAGATCAATTACTACGTTATAAAACAAAACAATGCAATAATTGATTATT
Found at i:12534124 original size:63 final size:63
Alignment explanation
Indices: 12534056--12534422 Score: 231
Period size: 63 Copynumber: 5.8 Consensus size: 63
12534046 GAACCAAGCG
* * *
12534056 ACGTAGTAATTGATTGTTTTAAAACAATTACATTTATCAATTATTGCGTTTTAAAACAAAGAA
1 ACGTAATAATTGATTATTTTAAAACAATTACATTTATCAATTATTGCGTTATAAAACAAAGAA
* * * * * * * *
12534119 ACGTAGTAATTAATCATTTGAATAA-AATTACCA-TTACCAATTATTGTGTTATGATACAAA-AC
1 ACGTAATAATTGATTATTTTAA-AACAATTA-CATTTATCAATTATTGCGTTATAAAACAAAGA-
12534181 A
63 A
* * * * * * * *
12534182 ATGCAACATTTGATTGTTTTAAAACAATTAAATTTATCAATTATTACGTTTTAAAACAAAGAA
1 ACGTAATAATTGATTATTTTAAAACAATTACATTTATCAATTATTGCGTTATAAAACAAAGAA
* * * * * * * * * * * * *
12534245 ATGCAATAATTAATCATCTGATTAA-AATTAAAATTATCAATTACTGTGTTATAAAACTAAGCA
1 ACGTAATAATTGATTATTTTA-AAACAATTACATTTATCAATTATTGCGTTATAAAACAAAGAA
* * * **
12534308 ACATAATAATTGATTATTTTAAAACAATTATATTTATCAATTACTGCAATATAAAACAAA-AGA
1 ACGTAATAATTGATTATTTTAAAACAATTACATTTATCAATTATTGCGTTATAAAACAAAGA-A
* * * * * * * *
12534371 GCGTAGTAATTGATGGATCCTTAAAAAAATTACAATTACCAATTATTACGTT
1 ACGTAATAATTGAT-TAT-TTTAAAACAATTACATTTATCAATTATTGCGTT
12534423 TCAAAGCATA
Statistics
Matches: 225, Mismatches: 68, Indels: 20
0.72 0.22 0.06
Matches are distributed among these distances:
62 6 0.03
63 186 0.83
64 9 0.04
65 24 0.11
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (63 bp):
ACGTAATAATTGATTATTTTAAAACAATTACATTTATCAATTATTGCGTTATAAAACAAAGAA
Found at i:12534217 original size:126 final size:126
Alignment explanation
Indices: 12534063--12534417 Score: 390
Period size: 126 Copynumber: 2.8 Consensus size: 126
12534053 GCGACGTAGT
*
12534063 AATTGATTGTTTTAAAACAATTACATTTATCAATTATTGCGTTTTAAAACAAAGAAACGTAGTAA
1 AATTGATTGTTTTAAAACAATTAAATTTATCAATTATTGCGTTTTAAAACAAAGAAACGTAGTAA
* * * **
12534128 TTAATCATTTGAATAAAATTACCATTACCAATTATTGTGTTATGATACAAAACAATGCAAC
66 TTAATCATTTGAATAAAATTACAATTACCAATTATTGTGTTATAAAACAAAACAACACAAC
* * * * *
12534189 ATTTGATTGTTTTAAAACAATTAAATTTATCAATTATTACGTTTTAAAACAAAGAAATGCAATAA
1 AATTGATTGTTTTAAAACAATTAAATTTATCAATTATTGCGTTTTAAAACAAAGAAACGTAGTAA
* * * * * * * * *
12534254 TTAATCATCTGATTAAAATTAAAATTATCAATTACTGTGTTATAAAACTAAGCAACATAAT
66 TTAATCATTTGAATAAAATTACAATTACCAATTATTGTGTTATAAAACAAAACAACACAAC
* * * ** * *
12534315 AATTGATTATTTTAAAACAATTATATTTATCAATTACTGCAATATAAAACAAA-AGAGCGTAGTA
1 AATTGATTGTTTTAAAACAATTAAATTTATCAATTATTGCGTTTTAAAACAAAGA-AACGTAGTA
* * *
12534379 ATTGATGGATCCTT-AAAAAAATTACAATTACCAATTATT
65 ATTAAT-CAT--TTGAATAAAATTACAATTACCAATTATT
12534418 ACGTTTCAAA
Statistics
Matches: 185, Mismatches: 40, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
125 1 0.01
126 161 0.87
127 2 0.01
128 20 0.11
129 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (126 bp):
AATTGATTGTTTTAAAACAATTAAATTTATCAATTATTGCGTTTTAAAACAAAGAAACGTAGTAA
TTAATCATTTGAATAAAATTACAATTACCAATTATTGTGTTATAAAACAAAACAACACAAC
Found at i:12536473 original size:15 final size:16
Alignment explanation
Indices: 12536453--12536483 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
12536443 ATTTAAGAAG
12536453 ATTTTTCTATT-TTTT
1 ATTTTTCTATTGTTTT
12536468 ATTTTTCTATTGTTTT
1 ATTTTTCTATTGTTTT
12536484 TTGAAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
ATTTTTCTATTGTTTT
Found at i:12536600 original size:31 final size:32
Alignment explanation
Indices: 12536563--12536632 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
12536553 TACAATGAGT
**
12536563 AATAAAAAAACTGAAAATA-AAAAT-AAAATCA
1 AATAAAAAAA-TGAAAATATAAAATGAAAAAAA
*
12536594 AATAAAAAAATTAAAATATAAAATGAAAAAAA
1 AATAAAAAAATGAAAATATAAAATGAAAAAAA
12536626 AATAAAA
1 AATAAAA
12536633 GTCATGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 7 0.21
31 15 0.44
32 12 0.35
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (32 bp):
AATAAAAAAATGAAAATATAAAATGAAAAAAA
Found at i:12536624 original size:24 final size:24
Alignment explanation
Indices: 12536576--12536632 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
12536566 AAAAAAACTG
12536576 AAAATAAAAATAAAATCAAATAAA
1 AAAATAAAAATAAAATCAAATAAA
*
12536600 AAAATTAAAATATAAAAT-GAA-AAA
1 AAAA-TAAAA-ATAAAATCAAATAAA
12536624 AAAATAAAA
1 AAAATAAAA
12536633 GTCATGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.17
24 11 0.37
25 7 0.23
26 7 0.23
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (24 bp):
AAAATAAAAATAAAATCAAATAAA
Found at i:12538170 original size:120 final size:119
Alignment explanation
Indices: 12537957--12538464 Score: 497
Period size: 120 Copynumber: 4.2 Consensus size: 119
12537947 TGACTAGGAA
* * * *
12537957 AAACCACGAGACAGAAGAAATAATTTGGACTGAGCCAAGATC-AGGTGACCAGGATGAAAA-CAT
1 AAACCACGAGTCATAAGAAATAATTTGGACTGAGCCAAGATCGA-GTGATCA-GAT-AAAACCAC
* * * * * * *
12538020 AAGTAAAAAATGAAGCCACCAGGGCTGAGTCAAGGTC-AAGAATAAATGATCGGGATG
63 GAGTCAAAGATGAAGCGACCAGGACCGAGTCAAGGTCGAA-AATAAATGATCGAGATG
* *
12538077 AAACCACGAGTCATAAGAAATTATTTGGACTGAGCCAAGATCGAGTGATTGAGATAAAACCACGA
1 AAACCACGAGTCATAAGAAATAATTTGGACTGAGCCAAGATCGAGTGA-TCAGATAAAACCACGA
* * * * * *
12538142 GTGAAAGATAAAGCGAGCAGGACCGAGTCGAGGTCGAAAATAAATGA-CTAAGACG
65 GTCAAAGATGAAGCGACCAGGACCGAGTCAAGGTCGAAAATAAATGATC-GAGATG
* * * * * ** * * *
12538197 AAACCACAAGTCATAAGAAATGATCTAGACTGAGCCAAGATCGGGTGATTGGGACAAAACCATGG
1 AAACCACGAGTCATAAGAAATAATTTGGACTGAGCCAAGATCGAGTGA-TCAGATAAAACCACGA
* *
12538262 GTCAAAGATGAAGCGACCAAGACCGAGTCAAAGTCGAAAATAAATGATCGAGATG
65 GTCAAAGATGAAGCGACCAGGACCGAGTCAAGGTCGAAAATAAATGATCGAGATG
* * * * * * *
12538317 AAACCACAAGTCATAATAAATGATCTGGATTAAGCCAAGAT-GGGTGATCAGA-ACGAAACCACG
1 AAACCACGAGTCATAAGAAATAATTTGGACTGAGCCAAGATCGAGTGATCAGATA--AAACCACG
* * ** *
12538380 AGTCAAAGATGAAGCGATCAGGACCGAGTCGAGGTAAAAAATAAATGACCGAGATG
64 AGTCAAAGATGAAGCGACCAGGACCGAGTCAAGGTCGAAAATAAATGATCGAGATG
*
12538436 AAATCACGAGTCATAAGAAATAATTTGGA
1 AAACCACGAGTCATAAGAAATAATTTGGA
12538465 TGAAACTGAG
Statistics
Matches: 325, Mismatches: 55, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
117 1 0.00
118 3 0.01
119 90 0.28
120 226 0.70
121 5 0.02
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (119 bp):
AAACCACGAGTCATAAGAAATAATTTGGACTGAGCCAAGATCGAGTGATCAGATAAAACCACGAG
TCAAAGATGAAGCGACCAGGACCGAGTCAAGGTCGAAAATAAATGATCGAGATG
Found at i:12538930 original size:155 final size:154
Alignment explanation
Indices: 12538744--12539124 Score: 436
Period size: 155 Copynumber: 2.5 Consensus size: 154
12538734 AAGGATTTTT
**
12538744 CAAGAAAAAAATG-TTCGCAAGATTTCAAGTTTCGCAAAGGTTCTAGATTTGCAAAGATGCAAGG
1 CAAGAAAAAAA-GATTCGCAAGATTTCAAGTTTCATAAAGGTTCTAGATTTGCAAAGATGCAAGG
* * *
12538808 TTCACAAGGA-TTTTGAGATTCACAAGAAAGAAAGATTCACAAGATTCCAAGTTTCT-CAAAGGT
65 TTCGCAAGGACTTTT-AGATTCACAAAAAAGAAAGATTCACAAGACTCCAAGTTT-TGCAAAGGT
* * *
12538871 GCAAGATTTGCAAGGACTTTC-AGATTCC
128 GCAAGATTTGCAAAGA--TGCAAGATTCA
* * *
12538899 CAAGAAAGAAAA-ATTCACAAGATTTCAAGTTTCATAAAGGTTTTAGATTCT-CAAAGATTGTAA
1 CAAGAAA-AAAAGATTCGCAAGATTTCAAGTTTCATAAAGGTTCTAGATT-TGCAAAGA-TGCAA
**
12538962 -GTTCGCAAGGACTTTTAGATTCACAAAAAAGAAAGATTCACAAGACTCTGAGTTTTGCAAAGGT
63 GGTTCGCAAGGACTTTTAGATTCACAAAAAAGAAAGATTCACAAGACTCCAAGTTTTGCAAAGGT
***
12539026 TTTAGATTTGCAAAGATGCAAGATTCA
128 GCAAGATTTGCAAAGATGCAAGATTCA
* * * * *
12539053 CAAGAAAAAAAGATTCGCAAGA-CTCTAAGATTCATAAATGTTCTAGATTCGCAAAGATGCAAGA
1 CAAGAAAAAAAGATTCGCAAGATTTC-AAGTTTCATAAAGGTTCTAGATTTGCAAAGATGCAAGG
12539117 TTCGCAAG
65 TTCGCAAG
12539125 AAAGAAAGAT
Statistics
Matches: 191, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
153 12 0.06
154 57 0.30
155 109 0.57
156 13 0.07
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (154 bp):
CAAGAAAAAAAGATTCGCAAGATTTCAAGTTTCATAAAGGTTCTAGATTTGCAAAGATGCAAGGT
TCGCAAGGACTTTTAGATTCACAAAAAAGAAAGATTCACAAGACTCCAAGTTTTGCAAAGGTGCA
AGATTTGCAAAGATGCAAGATTCA
Found at i:12538950 original size:86 final size:86
Alignment explanation
Indices: 12538860--12539056 Score: 229
Period size: 86 Copynumber: 2.3 Consensus size: 86
12538850 GATTCCAAGT
* * * * *
12538860 TTCTCAAAGGTGCAAGATTTGCAAGGACTTTCAGATTCCCAAGAAAGAAAAATTCACAAGA-TTT
1 TTCTCAAAGATGCAAGATTCGCAAGGACTTTCAGATTCACAAAAAAGAAAAATTCACAAGACTCT
*
12538924 CAAGTTTCATAAAGGTTTTAGA
66 -AAGTTTCACAAAGGTTTTAGA
* * *
12538946 TTCTCAAAGATTGTAAG-TTCGCAAGGACTTTTAGATTCACAAAAAAGAAAGATTCACAAGACTC
1 TTCTCAAAGA-TGCAAGATTCGCAAGGACTTTCAGATTCACAAAAAAGAAAAATTCACAAGACTC
* **
12539010 TGAGTTTTGCAAAGGTTTTAGA
65 TAAGTTTCACAAAGGTTTTAGA
*
12539032 TT-TGCAAAGATGCAAGATTCACAAG
1 TTCT-CAAAGATGCAAGATTCGCAAG
12539057 AAAAAAAGAT
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
85 6 0.06
86 80 0.86
87 7 0.08
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (86 bp):
TTCTCAAAGATGCAAGATTCGCAAGGACTTTCAGATTCACAAAAAAGAAAAATTCACAAGACTCT
AAGTTTCACAAAGGTTTTAGA
Found at i:12539065 original size:68 final size:68
Alignment explanation
Indices: 12538978--12539178 Score: 260
Period size: 68 Copynumber: 3.0 Consensus size: 68
12538968 AAGGACTTTT
* * * *
12538978 AGATTCACAA-AAAAGAAAGATTCACAAGACTCTGAGTTTTGCAAAGGTTTTAGATTTGCAAAGA
1 AGATTCACAAGAAAA-AAAGATTCGCAAGACTCTAAGTTTCGCAAAGGTTCTAGATTTGCAAAGA
12539042 TGCA
65 TGCA
* ** * *
12539046 AGATTCACAAGAAAAAAAGATTCGCAAGACTCTAAGATTCATAAATGTTCTAGATTCGCAAAGAT
1 AGATTCACAAGAAAAAAAGATTCGCAAGACTCTAAGTTTCGCAAAGGTTCTAGATTTGCAAAGAT
12539111 GCA
66 GCA
* * * * *
12539114 AGATTCGCAAGAAAGAAAGATTCGTAAGACTCCAAGTTTCGCAGAGGTTCTAGATTTGCAAAGAT
1 AGATTCACAAGAAAAAAAGATTCGCAAGACTCTAAGTTTCGCAAAGGTTCTAGATTTGCAAAGAT
12539179 TTCATAACAA
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
68 109 0.96
69 4 0.04
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (68 bp):
AGATTCACAAGAAAAAAAGATTCGCAAGACTCTAAGTTTCGCAAAGGTTCTAGATTTGCAAAGAT
GCA
Found at i:12539135 original size:34 final size:33
Alignment explanation
Indices: 12539029--12539137 Score: 82
Period size: 34 Copynumber: 3.2 Consensus size: 33
12539019 CAAAGGTTTT
* *
12539029 AGATTTGCAAAGATGCAAGATTCACAAGAAAAAA
1 AGATTCGCAAAGATGCAAGATTC-CAAGAAAGAA
* **
12539063 AGATTCGC-AAGACT-CTAAGATT-CATA-AATGTTCT
1 AGATTCGCAAAGA-TGC-AAGATTCCA-AGAAAG--AA
12539097 AGATTCGCAAAGATGCAAGATTCGCAAGAAAGAA
1 AGATTCGCAAAGATGCAAGATTC-CAAGAAAGAA
12539131 AGATTCG
1 AGATTCG
12539138 TAAGACTCCA
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
32 4 0.07
33 6 0.11
34 36 0.63
35 6 0.11
36 5 0.09
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (33 bp):
AGATTCGCAAAGATGCAAGATTCCAAGAAAGAA
Found at i:12539774 original size:26 final size:26
Alignment explanation
Indices: 12539738--12539789 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12539728 TAGACACACA
*
12539738 TTTGGTTTGGGCCTAATTAGGCCCAT
1 TTTGGTCTGGGCCTAATTAGGCCCAT
*
12539764 TTTGGTCTGGGCCTGATTAGGCCCAT
1 TTTGGTCTGGGCCTAATTAGGCCCAT
12539790 CTTAATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.21, G:0.29, T:0.37
Consensus pattern (26 bp):
TTTGGTCTGGGCCTAATTAGGCCCAT
Found at i:12539966 original size:3 final size:3
Alignment explanation
Indices: 12539958--12540018 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
12539948 GGTGTTTTAC
* * * *
12539958 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAG TAT TAT TAC TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12540006 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
12540019 TTTTTCGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:12552190 original size:120 final size:119
Alignment explanation
Indices: 12551823--12552300 Score: 489
Period size: 120 Copynumber: 4.0 Consensus size: 119
12551813 ATTATCTCAC
* * * * *
12551823 TCACTTAATCTTGGCTCAGCCTAGATCACTTCTT-ATGATTTATGGTTTCGTCCCGATCATTTAT
1 TCACTTGATCTTGGCTCAGTCTAAATCA-TTCTTCATGATTCATGGTTTCGTCCCAATCATTTAT
* ** * * * * *
12551887 TTTTTACCTTAACTTAATCCTAGTCATTTTATTTTGGCTTGTGGTTTCATCTC-A
65 TTTTGACCTCGACTTAGTCCTAGTCACTTTATTTTGACTTGTGGTTTCACCCCGA
* * * **
12551941 GTCACTTGGTCTTGGCTTAGTCTAGATCATTCTTCATGATTCATGGTTTCG-CCTGATCATTTA-
1 -TCACTTGATCTTGGCTCAGTCTAAATCATTCTTCATGATTCATGGTTTCGTCCCAATCATTTAT
* * * * * * *
12552004 TTTTGATCTTGACTCAGTCCTAGTTACTTTATTTTGGCTTGTGGTTTCATCTCGA
65 TTTTGACCTCGACTTAGTCCTAGTCACTTTATTTTGACTTGTGGTTTCACCCCGA
* * * *
12552059 TCACTTGATCTTGGCTCAGTCTAAATCATTCTTCATGATTCGTGGCTTCATCCCAATCATTTCTT
1 TCACTTGATCTTGGCTCAGTCTAAATCATTCTTCATGATTCATGGTTTCGTCCCAATCATTTATT
* * * *
12552124 TTTGACCTCGACTTGGTCTTGGTCACTTCATTTTTGACTTGTGGTTTCACCCCGA
66 TTTGACCTCGACTTAGTCCTAGTCACTTTA-TTTTGACTTGTGGTTTCACCCCGA
* * * * *
12552179 TCACCTGATCTTGGCTTAGTCCAAATAATTCTTCATGATTCATGGTTTCGTCCTAATCATTTATT
1 TCACTTGATCTTGGCTCAGTCTAAATCATTCTTCATGATTCATGGTTTCGTCCCAATCATTTATT
* * * * * *
12552244 TTTTAGCTCGATTTGGTCCTAATCACTTTATTTTAGA-TTGTGGTTTCTCCCCGA
66 TTTGACCTCGACTTAGTCCTAGTCACTTTATTTT-GACTTGTGGTTTCACCCCGA
12552298 TCA
1 TCA
12552301 TTATTTTTGA
Statistics
Matches: 303, Mismatches: 50, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
117 90 0.30
118 26 0.09
119 85 0.28
120 102 0.34
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (119 bp):
TCACTTGATCTTGGCTCAGTCTAAATCATTCTTCATGATTCATGGTTTCGTCCCAATCATTTATT
TTTGACCTCGACTTAGTCCTAGTCACTTTATTTTGACTTGTGGTTTCACCCCGA
Found at i:12552332 original size:62 final size:62
Alignment explanation
Indices: 12552234--12552350 Score: 139
Period size: 62 Copynumber: 1.9 Consensus size: 62
12552224 TTTCGTCCTA
* * * *
12552234 ATCATTTATTTTTTAGCTCGATTTGGTCCTAATCACTTTATTTTAGA-TTGTGGTTTCTCCCCG
1 ATCATTTATTTTTGACCTCGACTTGGTCCTAATCACTTCA--TTAGACTTGTGGTTTCTCCCCG
* **
12552297 ATCA-TTATTTTTGACCTCGACTTGGTCTTGGTCACTTCATTAGACTTGTGGTTT
1 ATCATTTATTTTTGACCTCGACTTGGTCCTAATCACTTCATTAGACTTGTGGTTT
12552351 AATCTTGGTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 5 0.11
61 9 0.20
62 28 0.61
63 4 0.09
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (62 bp):
ATCATTTATTTTTGACCTCGACTTGGTCCTAATCACTTCATTAGACTTGTGGTTTCTCCCCG
Found at i:12552511 original size:26 final size:26
Alignment explanation
Indices: 12552475--12552548 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
12552465 GTTGTAGACA
*
12552475 CCCATTTTGGTCCGGACCCGATTAGG
1 CCCATTTTGGTCCGGACCCAATTAGG
*
12552501 CCCATTTTGGTCCGGACCTAATTAGG
1 CCCATTTTGGTCCGGACCCAATTAGG
*
12552527 CCCATCTTGGTCTC-GACCCAAT
1 CCCATTTTGGTC-CGGACCCAAT
12552549 ATGGTTCGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 42 0.98
27 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.22, T:0.28
Consensus pattern (26 bp):
CCCATTTTGGTCCGGACCCAATTAGG
Found at i:12552692 original size:3 final size:3
Alignment explanation
Indices: 12552686--12552744 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
12552676 ATTTTTGTTG
12552686 TTA TTA TTA TTA 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 TTA TTA TTA TTA
12552734 TTA TTA TTA TT
1 TTA TTA TTA TT
12552745 TATTTCCTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12553184 original size:9 final size:9
Alignment explanation
Indices: 12553170--12553213 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
12553160 ATTTGGAATT
12553170 TTTTTTGGA
1 TTTTTTGGA
12553179 TTTTTTGGA
1 TTTTTTGGA
*
12553188 TCTTTTTGGG
1 T-TTTTTGGA
*
12553198 TTTTTCTGGG
1 TTTTT-TGGA
12553208 TTTTTT
1 TTTTTT
12553214 AAAGAACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 15 0.47
10 17 0.53
ACGTcount: A:0.05, C:0.05, G:0.23, T:0.68
Consensus pattern (9 bp):
TTTTTTGGA
Found at i:12553697 original size:9 final size:9
Alignment explanation
Indices: 12553664--12553698 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
12553654 CTAATTTAAA
12553664 AAAAAAAAG
1 AAAAAAAAG
*
12553673 AAAAAGAAG
1 AAAAAAAAG
12553682 AGAAAAAAAG
1 A-AAAAAAAG
12553692 AAAAAAA
1 AAAAAAA
12553699 TTATTCTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:12554443 original size:7 final size:7
Alignment explanation
Indices: 12554426--12554456 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
12554416 TTTTTTCTTC
12554426 TTTTG-T
1 TTTTGCT
12554432 TTTTGCT
1 TTTTGCT
12554439 TTTTGCT
1 TTTTGCT
12554446 TTTTGCT
1 TTTTGCT
12554453 TTTT
1 TTTT
12554457 TCTTCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.00, C:0.10, G:0.13, T:0.77
Consensus pattern (7 bp):
TTTTGCT
Found at i:12554448 original size:14 final size:13
Alignment explanation
Indices: 12554382--12554456 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 13
12554372 CTTTCGTCTA
12554382 TTTTT-TTTTT-C
1 TTTTTGTTTTTGC
*
12554393 TTTTTGTTTTATTTGG
1 TTTTTG--TT-TTTGC
*
12554409 TTTGTTGTTTTTTC
1 TTT-TTGTTTTTGC
12554423 TTCTTTTGTTTTTGC
1 -T-TTTTGTTTTTGC
12554438 TTTTTGCTTTTTGC
1 TTTTTG-TTTTTGC
12554452 TTTTT
1 TTTTT
12554457 TCTTCTTCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
11 5 0.10
13 5 0.10
14 18 0.35
15 15 0.29
16 5 0.10
17 3 0.06
ACGTcount: A:0.01, C:0.08, G:0.12, T:0.79
Consensus pattern (13 bp):
TTTTTGTTTTTGC
Found at i:12554758 original size:6 final size:6
Alignment explanation
Indices: 12554747--12554788 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
12554737 ACCCCATCAA
*
12554747 TTTTCT TTTTCT TATTCT TTTTC- TTTT-T TTTTCT TTTT-T TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTT
12554789 GGTGGAGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 12 0.38
6 20 0.62
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:12554766 original size:12 final size:11
Alignment explanation
Indices: 12554747--12554788 Score: 61
Period size: 10 Copynumber: 3.9 Consensus size: 11
12554737 ACCCCATCAA
12554747 TTTTCTTTTTC
1 TTTTCTTTTTC
12554758 TTATTCTTTTTC
1 TT-TTCTTTTTC
12554770 TTTT-TTTTTC
1 TTTTCTTTTTC
12554780 TTTT-TTTTT
1 TTTTCTTTTT
12554789 GGTGGAGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 15 0.50
11 4 0.13
12 11 0.37
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:12554880 original size:52 final size:51
Alignment explanation
Indices: 12554772--12554880 Score: 134
Period size: 52 Copynumber: 2.1 Consensus size: 51
12554762 TCTTTTTCTT
*
12554772 TTTTTTTCTTTTTTTTTGGTGGAGCACATTAGCTTTTGCCCTATCAATTTC
1 TTTTTTTCTTTTTTTTTGGTGGAGCACATTAGCTTTTGCCCTATCAATTTA
* *
12554823 GTTTTTTCTTTTTCTTTTGGAT-GAGCACATTGGCATTTTG-CCTCATC-ATTTA
1 TTTTTTTCTTTTT-TTTTGG-TGGAGCACATTAGC-TTTTGCCCT-ATCAATTTA
12554875 TTTTTT
1 TTTTTT
12554881 ATTTGTTAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
51 12 0.24
52 29 0.58
53 9 0.18
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.56
Consensus pattern (51 bp):
TTTTTTTCTTTTTTTTTGGTGGAGCACATTAGCTTTTGCCCTATCAATTTA
Found at i:12557722 original size:44 final size:42
Alignment explanation
Indices: 12557668--12557787 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 42
12557658 TATATACACT
*
12557668 AAATAAATAATCAAGCAAATATAAGCAATGAATAAAAAAAAGA
1 AAATAAATAATCAAGCAAGTATAAGCAATGAA-AAAAAAAAGA
* * ** *
12557711 CAAATGAATAATTAAGCAAGTATACA-CAATGAAAAGGAAAATA
1 -AAATAAATAATCAAGCAAGTATA-AGCAATGAAAAAAAAAAGA
12557754 AAATAAATAA-CAAAGCAAGTATAAGCAAT-AAAAA
1 AAATAAATAATC-AAGCAAGTATAAGCAATGAAAAA
12557788 GGAATAAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
41 5 0.08
42 24 0.38
43 7 0.11
44 27 0.42
45 1 0.02
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17
Consensus pattern (42 bp):
AAATAAATAATCAAGCAAGTATAAGCAATGAAAAAAAAAAGA
Found at i:12562774 original size:16 final size:17
Alignment explanation
Indices: 12562746--12562783 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
12562736 ATAACTCAAT
12562746 CTATAAATAAAAAAAAA
1 CTATAAATAAAAAAAAA
*
12562763 CTATAAAT-AAAAGAAA
1 CTATAAATAAAAAAAAA
12562779 CTATA
1 CTATA
12562784 TCCAAATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.21
Consensus pattern (17 bp):
CTATAAATAAAAAAAAA
Found at i:12567429 original size:60 final size:59
Alignment explanation
Indices: 12567297--12567537 Score: 169
Period size: 60 Copynumber: 3.9 Consensus size: 59
12567287 ATACCTTAAC
* * * *
12567297 AAATGCCTAAAATAATTTCCTTTAAAAAATATTAGAGATCATTTAAGGTGTTTTTGGTCA
1 AAATGCCTTAAATAA-TCCCTTTAAAAAATATTAGAGATCATTTAAAGCGTTTTTGGTCA
* * * * **
12567357 AAACGTCATAAATAATCCCTTTTTAAAAATATTAGAGATCATTTAAAGCGTTTTTGGTTT
1 AAATGCCTTAAATAATCCC-TTTAAAAAATATTAGAGATCATTTAAAGCGTTTTTGGTCA
** * * * * *
12567417 AAATGCCTTAAATAATATCTTTCAAAAAAT-TGAAGAATATTATTTAAAGTGTTTTTAGTCAAA
1 AAATGCCTTAAATAATCCCTTT-AAAAAATAT-TAG-AGATCATTTAAAGCGTTTTTGGTC--A
* ** * * *
12567480 AAAAGCCTTAAGCAATCCTCTTTAAAAAAAAAAATTAGAGATTATTTCAAGCGTTTTT
1 AAATGCCTTAAATAATCC-CTTT---AAAAAATATTAGAGATCATTTAAAGCGTTTTT
12567538 TAATTCCCTC
Statistics
Matches: 137, Mismatches: 34, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
59 7 0.05
60 68 0.50
61 19 0.14
63 13 0.09
64 4 0.03
65 17 0.12
66 8 0.06
67 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (59 bp):
AAATGCCTTAAATAATCCCTTTAAAAAATATTAGAGATCATTTAAAGCGTTTTTGGTCA
Found at i:12568012 original size:22 final size:22
Alignment explanation
Indices: 12567991--12568036 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
12567981 CATAAGTTCA
12567991 AATTTT-TACTAAATTTGATTC
1 AATTTTATACTAAATTTGATTC
* *
12568012 AATTTTATATTAAATTT-ATTT
1 AATTTTATACTAAATTTGATTC
12568033 AATT
1 AATT
12568037 ATATTTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
AATTTTATACTAAATTTGATTC
Found at i:12573207 original size:2 final size:2
Alignment explanation
Indices: 12573200--12573236 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
12573190 ACTTGACCAG
*
12573200 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
12573237 CCACATAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12574124 original size:2 final size:2
Alignment explanation
Indices: 12574117--12574150 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
12574107 AAAGCTTTGG
* *
12574117 AT AT AT AT AT AT AT AT AT AA AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12574151 CTGAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12580571 original size:23 final size:23
Alignment explanation
Indices: 12580545--12580596 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
12580535 CTCGAAATTA
12580545 ATAAAATATTATTTTTTTAAAAT
1 ATAAAATATTATTTTTTTAAAAT
12580568 ATAAAATATTATTTTTTTAAAAT
1 ATAAAATATTATTTTTTTAAAAT
12580591 ATAAAA
1 ATAAAA
12580597 ATATAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAAATATTATTTTTTTAAAAT
Found at i:12580599 original size:8 final size:8
Alignment explanation
Indices: 12580586--12580639 Score: 60
Period size: 8 Copynumber: 7.1 Consensus size: 8
12580576 TTATTTTTTT
12580586 AAAATATA
1 AAAATATA
12580594 AAAATATA
1 AAAATATA
12580602 AAAATAT-
1 AAAATATA
*
12580609 AATATATA
1 AAAATATA
*
12580617 TAAATA-A
1 AAAATATA
12580624 AAAAT-TA
1 AAAATATA
*
12580631 AAAAAATA
1 AAAATATA
12580639 A
1 A
12580640 TTTTTTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
7 16 0.42
8 22 0.58
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAATATA
Found at i:12589070 original size:33 final size:33
Alignment explanation
Indices: 12588978--12589075 Score: 99
Period size: 33 Copynumber: 3.0 Consensus size: 33
12588968 TTAAGGAAAA
* *
12588978 TAGCGGCGTTTTAGGA-AAAAATGCCACTAAAT
1 TAGCGGCATTTTAAGACAAAAATGCCACTAAAT
* * * * * * *
12589010 TAGTGGTATTTGAAGTCACAAACGCCACTAACT
1 TAGCGGCATTTTAAGACAAAAATGCCACTAAAT
*
12589043 TAGCGGCATTTTAAGACATAAATGCCACTAAAT
1 TAGCGGCATTTTAAGACAAAAATGCCACTAAAT
12589076 CAACAGCGTT
Statistics
Matches: 49, Mismatches: 16, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
32 10 0.20
33 39 0.80
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (33 bp):
TAGCGGCATTTTAAGACAAAAATGCCACTAAAT
Found at i:12589731 original size:127 final size:127
Alignment explanation
Indices: 12589505--12589763 Score: 385
Period size: 127 Copynumber: 2.0 Consensus size: 127
12589495 ATTTGATGAA
* * **
12589505 GAGTTTTTTCTACCACAATCACTAGCTTGCTGAAGGACCTACTAAAATAGGTAAAACAAGTTTTT
1 GAGTTTGTTCTACCACAATCACTAGCTTGCTCAAGGACCTACTAAAATAAATAAAACAAGTTTTT
* * *
12589570 ATACTTGATAATAAACTATTTCCAATATTAAAAAATATAAATAGTTATTAAGTATAATACCT
66 ATACTTAATAATAAACTATTTCCAATATTAAAAAATATAAATAGTTACTAAATATAATACCT
* *
12589632 GAGTTTGTTCTACCACAATCATTAGCTTGTTCAAGGACCTACTGAAAA-AAATAAAACAAGTTTT
1 GAGTTTGTTCTACCACAATCACTAGCTTGCTCAAGGACCTACT-AAAATAAATAAAACAAGTTTT
* * *
12589696 TATACTTAATAATGAATTATTTCTAATATTAAAAAATATAAATAGTTACTAAATATAATACCT
65 TATACTTAATAATAAACTATTTCCAATATTAAAAAATATAAATAGTTACTAAATATAATACCT
*
12589759 AAGTT
1 GAGTT
12589764 GGTGGACCAT
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
127 114 0.97
128 4 0.03
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (127 bp):
GAGTTTGTTCTACCACAATCACTAGCTTGCTCAAGGACCTACTAAAATAAATAAAACAAGTTTTT
ATACTTAATAATAAACTATTTCCAATATTAAAAAATATAAATAGTTACTAAATATAATACCT
Found at i:12590746 original size:161 final size:157
Alignment explanation
Indices: 12590445--12591689 Score: 861
Period size: 161 Copynumber: 7.7 Consensus size: 157
12590435 ATTGGACATA
* * * * * * *
12590445 TTTAATAAAATGTAATAAGAGCTATCTAAACTGTTAAAATAAAATAATTGTAAAATTGCAATTTT
1 TTTAATATAATGTATTGA-AGCTATCTAAACTGTTAAAACAAAATAAATGTAAAATTACATTTTT
* * *
12590510 GCCTTTTAA---CATTACAAAAAGTTCTAAACAGACATAAATC-ATAACTTATTCATACATATCA
65 GCCTTTTAACGGCA-TA-AAAAAGTCCTAAACAGATATAAA-CGATAACTT-TTCACACATATC-
* * * **
12590571 AATCGTGAAAACCAAATTCAATCATTTGGACAAG
125 ACT-ATGAAAACCAAGTTCAATCATTCAGACAAG
* * *
12590605 TTTAATATCATGTATTGAAGTTATCTAAACTGTTAAAACATAAATACAATGTAAAATTATATTTT
1 TTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACA-AAATA-AATGTAAAATTACATTTT
* ** * * *
12590670 TGCCATTTAACGGTGTAACAAAGTCCTAAACAGATATAAATGGTAACATTTTCACACATATCAGC
64 TGCCTTTTAACGGCATAAAAAAGTCCTAAACAGATATAAACGATAAC-TTTTCACACATATCA-C
* * *
12590735 TATGGAAACCAAGTTCAATCAATCATTCAGATAAA
127 TATGAAAACCAAG-T---TCAATCATTCAGACAAG
* *** *
12590770 TTTAATATAATGTATTGAAGCTATCTAAA-TGTCAAAACAAAATAATAAACACAAATTTGCATTT
1 TTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACAAAATAA-ATGTA-AAA-TTACATTT
* * * * * * *
12590834 TAGCCTTTTAACGGCACAAAAAAGTGCTAAACAAATATAAACGGTAACTTTATCACATATATCAT
63 TTGCCTTTTAACGGCATAAAAAAGTCCTAAACAGATATAAACGATAACTTT-TCACACATATCAC
* *
12590899 TCATAAAAACCAAGTTCAATCATTCAGAAAAG
127 T-ATGAAAACCAAGTTCAATCATTCAGACAAG
* * *
12590931 TTTAATATAATGTATTTAAGCTATCTAAACTGTTAAAACATAAAAATAAATGCAAAATGACATTT
1 TTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAAC---AAAATAAATGTAAAATTACATTT
* * * *
12590996 TTACC-TTTAACAGCATAACAAAA-TCCTAAAAAGACATAAAC-AGTAACTTTTTCACACATATC
63 TTGCCTTTTAACGGCATAA-AAAAGTCCTAAACAGATATAAACGA-TAAC-TTTTCACACATATC
* * * * *
12591058 AATCATGGAAACCAAGTTTAATTATCCAGACAAG
125 ACT-ATGAAAACCAAGTTCAATCATTCAGACAAG
* * * * * * *
12591092 TTTAATATTATGTATTGAAACTATCTAAATTGTTAAAATAGAATAATAAATGCAAATTTGCATTT
1 TTTAATATAATGTATTGAAGCTATCTAAACTGTT-AAA-ACAA-AATAAATGTAAAATTACATTT
* * * * * *
12591157 TGGCCTTTTAACAGCATAAAAAA-TCTTAAATAGATATAAACGACAACCTTTTCACATATATCAA
63 TTGCCTTTTAACGGCATAAAAAAGTCCTAAACAGATATAAACGATAA-CTTTTCACACATATC-A
* * ** *
12591221 CTGTGCAAAGTAAGTTCAATCATTCAAACAAG
126 CTATGAAAACCAAGTTCAATCATTCAGACAAG
* * * * ** * *
12591253 TTTAATATCATTTATTGAAGCTATCTAAACTGCTAAAATGGAATAATAAAAATAAATTTTCA-TT
1 TTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAA--CAA-AATAAATGTAAAATTACATTT
* * * ** *
12591317 TTGACCTTTTAACGGCATAAAAAAAATGCTAAACAGACATAAATAATAACATTTTCTCACATCAA
63 TTG-CCTTTTAACGGCAT-AAAAAAGTCCTAAACAGATATAAACGATAAC-TTTTCACACAT--A
* *
12591382 TCA-TA-G--AACCAAATTCAATCATTCGGACAAG
123 TCACTATGAAAACCAAGTTCAATCATTCAGACAAG
* * * * *
12591413 TTTAATATTATGTATTTAAGCTATCCAAACTGTTAAAACATAAATATAA-CTACATATTTACATT
1 TTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACA-AAATA-AATGTA-A-AATTACATT
* * * * * *
12591477 TTTGCCCTTTAATGGCACAACAAAGTCCTAAAAAGATATAAACGATAACTTTTTC-CGCATATCA
62 TTTGCCTTTTAACGGCATAAAAAAGTCCTAAACAGATATAAACGATAAC-TTTTCACACATATC-
** * * *
12591541 ACCGTGAAAATCAAGTTCAATCATTCGGGCAAG
125 ACTATGAAAACCAAGTTCAATCATTCAGACAAG
* * * * * *
12591574 TTTCATATAATGTATT-AGAGCTATCCAAACTGTTAAAACAAAAAAAAAATTGTATATTTATATT
1 TTTAATATAATGTATTGA-AGCTATCTAAACTGTTAAAAC--AAAATAAA-TGTAAAATTACATT
* * * * * ** *
12591638 TTTGCCCTTTAATGACACAAAAAA-TTCTAAATGGATATAAACGACAACTTTT
62 TTTGCCTTTTAACGGCATAAAAAAGTCCTAAACAGATATAAACGATAACTTTT
12591690 TTATTTGATG
Statistics
Matches: 871, Mismatches: 160, Indels: 109
0.76 0.14 0.10
Matches are distributed among these distances:
156 3 0.00
157 1 0.00
158 11 0.01
159 59 0.07
160 119 0.14
161 403 0.46
162 94 0.11
163 44 0.05
164 21 0.02
165 116 0.13
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (157 bp):
TTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACAAAATAAATGTAAAATTACATTTTTG
CCTTTTAACGGCATAAAAAAGTCCTAAACAGATATAAACGATAACTTTTCACACATATCACTATG
AAAACCAAGTTCAATCATTCAGACAAG
Found at i:12591276 original size:322 final size:319
Alignment explanation
Indices: 12590464--12591623 Score: 1021
Period size: 322 Copynumber: 3.6 Consensus size: 319
12590454 ATGTAATAAG
** ***
12590464 AGCTATCTAAACTGTTAAAATAAAATAAT-TGTA-AAA-TTGCAATTTT-GCCTTTTAACATTAC
1 AGCTATCTAAA-TGTTAAAAT-AAATAATAAATACAAATTTGC-ATTTTAGCCTTTTAACGGCAC
* * * * * * * *
12590525 AAAAAGTTCTAAACAGACATAAATC-ATAA-CTTATTCATACATATCAAATCGTGAAAACCAAAT
63 AAAAA-ATCTAAAAAGATATAAA-CGATAACCTT-TTCACATATATCAACT-GTGAAAA-TAAGT
*** * *
12590588 TCAATCATTTGGACAAGTTTAATATCATGTATTGAAGTTATCTAAACTGTTAAAACAT--AAATA
123 TCAATCATTCAAACAAGTTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACATAAAAATA
* * ** * * *
12590651 CAATGTAAAATTATATTTTTGCCATTTAACGGTGTAACAAAGTCCTAAACAGATATAAATGGTAA
188 -AATGTAAAATTACATTTTTACCATTTAACGGCATAACAAAATCCTAAACAGACATAAATAGTAA
* * * *
12590716 CATTTTCACACATATC-AGCTATGGAAACCAAGTTCAATCAATCATTCAGATAAATTTAATATAA
252 CATTTTCACACATATCAATC-ATGGAAACCAAGTT---T-AATCATTCAGACAAGTTTAATATTA
12590780 TGTATTGA
312 TGTATTGA
* * *
12590788 AGCTATCTAAATGTCAAAACAAAATAATAAACACAAATTTGCATTTTAGCCTTTTAACGGCACAA
1 AGCTATCTAAATGTTAAAA-TAAATAATAAATACAAATTTGCATTTTAGCCTTTTAACGGCACAA
* * * * *
12590853 AAAAGTGCTAAACAA-ATATAAACGGTAA-CTTTATCACATATATC-ATTCATAAAAACCAAGTT
65 AAAA-T-CTAAA-AAGATATAAACGATAACCTTT-TCACATATATCAACT-GTGAAAA-TAAGTT
*
12590915 CAATCATTCAGAA-AAGTTTAATATAATGTATTTAAGCTATCTAAACTGTTAAAACATAAAAATA
124 CAATCATTCA-AACAAGTTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACATAAAAATA
* * * * *
12590979 AATGCAAAATGACATTTTTACC-TTTAACAGCATAACAAAATCCTAAAAAGACATAAACAGTAAC
188 AATGTAAAATTACATTTTTACCATTTAACGGCATAACAAAATCCTAAACAGACATAAATAGTAAC
* * *
12591043 TTTTTCACACATATCAATCATGGAAACCAAGTTTAATTATCCAGACAAGTTTAATATTATGTATT
253 ATTTTCACACATATCAATCATGGAAACCAAGTTTAATCATTCAGACAAGTTTAATATTATGTATT
12591108 GA
318 GA
* * * * *
12591110 AACTATCTAAATTGTTAAAATAGAATAATAAATGCAAATTTGCATTTTGGCCTTTTAACAGCATA
1 AGCTATCTAAA-TGTTAAAATA-AATAATAAATACAAATTTGCATTTTAGCCTTTTAACGGCACA
* * *
12591175 AAAAATCTTAAATAGATATAAACGACAACCTTTTCACATATATCAACTGTGCAAAGTAAGTTCAA
64 AAAAATC-TAAAAAGATATAAACGATAACCTTTTCACATATATCAACTGTG-AAAATAAGTTCAA
* * * *** * **
12591240 TCATTCAAACAAGTTTAATATCATTTATTGAAGCTATCTAAACTGCTAAAATGGAATAATAAAAA
127 TCATTCAAACAAGTTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACATAAAAATAAATG
* * * * * * *
12591305 TAAATTTTCATTTTGACCTTTTAACGGCATAAAAAAAATGCTAAACAGACATAAATAATAACATT
192 TAAAATTACATTTTTACCATTTAACGGCAT-AACAAAATCCTAAACAGACATAAATAGTAACATT
* * * * * *
12591370 TTCTCAC--ATCAATCATAG-AACCAAATTCAATCATTCGGACAAGTTTAATATTATGTATTTA
256 TTCACACATATCAATCATGGAAACCAAGTTTAATCATTCAGACAAGTTTAATATTATGTATTGA
* * * * * * *
12591431 AGCTATCCAAACTGTTAAAACATAAAT-ATAACTACATATTTACATTTTTGCCCTTTAATGGCAC
1 AGCTATCTAAA-TGTT-AAA-ATAAATAATAAATACAAATTTGCATTTTAGCCTTTTAACGGCAC
* * ** *
12591495 AACAAAGTCCTAAAAAGATATAAACGATAACTTTTTC-CGCATATCAACCGTGAAAATCAAGTTC
63 AA-AAAAT-CTAAAAAGATATAAACGATAACCTTTTCACATATATCAACTGTGAAAAT-AAGTTC
*** * * *
12591559 AATCATTCGGGCAAGTTTCATATAATGTATT-AGAGCTATCCAAACTGTTAAAACA-AAAAAAAA
125 AATCATTCAAACAAGTTTAATATAATGTATTGA-AGCTATCTAAACTGTTAAAACATAAAAATAA
12591622 AT
189 AT
12591624 TGTATATTTA
Statistics
Matches: 684, Mismatches: 122, Indels: 64
0.79 0.14 0.07
Matches are distributed among these distances:
320 12 0.02
321 145 0.21
322 184 0.27
323 87 0.13
324 46 0.07
325 8 0.01
326 149 0.22
327 47 0.07
328 6 0.01
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.31
Consensus pattern (319 bp):
AGCTATCTAAATGTTAAAATAAATAATAAATACAAATTTGCATTTTAGCCTTTTAACGGCACAAA
AAATCTAAAAAGATATAAACGATAACCTTTTCACATATATCAACTGTGAAAATAAGTTCAATCAT
TCAAACAAGTTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACATAAAAATAAATGTAAA
ATTACATTTTTACCATTTAACGGCATAACAAAATCCTAAACAGACATAAATAGTAACATTTTCAC
ACATATCAATCATGGAAACCAAGTTTAATCATTCAGACAAGTTTAATATTATGTATTGA
Found at i:12591662 original size:482 final size:482
Alignment explanation
Indices: 12590533--12591690 Score: 1197
Period size: 482 Copynumber: 2.4 Consensus size: 482
12590523 ACAAAAAGTT
* * * *
12590533 CTAAACAGACATAAATCA-TAACTTATTCATACATATCAAATCGTGAAAACCAAATTCAATCATT
1 CTAAAAAGACATAAA-CAGTAACTTTTTCACACATATC-AATCGTGAAAACCAAGTTCAATCATT
* * * * * * *
12590597 TGGACAAGTTTAATATCATGTATTGAAGTTATCTAAACTGTTAAAACATAAATACAATGTAAAAT
64 CGGACAAGTTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACAAAAAAAAAATGTAAATT
*** * * * * **
12590662 TATATTTTTGCCATTTAACGGTGTAACAAAGTCCTAAACAGATATAAATGGTAACATTTTCACAC
129 TATATTTTTGCCATTTAA-GACATAA-AAAATCTTAAATAGATATAAACGACAACATTTTCACAC
* * * *
12590727 ATATCAGCTATGGAAACCAAGTTCAATCAATCATTCAGATAAATTTAATATAATGTATTGAAGCT
192 ATATCAACTATGCAAACCAAGTT--ATCAATCATTCAAACAAATTTAATATAATGTATTGAAGCT
* *
12590792 ATCTAAATGTCAAAACAAAATAATAAACACAAATTTGCATTTTAGCCTTTTAACGGCACAAAAAA
255 ATCTAAATGTCAAAACAAAATAATAAAAACAAATTTGCATTTTAGCCTTTTAACGGCAAAAAAAA
* * ** * * *
12590857 GTGCTAAACAAATATAAACGGTAACTTTATCACATATATCATTCATAAAAACCAAGTTCAATCAT
320 ATGCTAAACAAACATAAACAATAACTTTATCACA-ACATCAATCATAAAAACCAAATTCAATCAT
* *
12590922 TCAGAAAAGTTTAATATAATGTATTTAAGCTATCTAAACTGTTAAAACATAAAAATAAATGCAAA
384 TCAGAAAAGTTTAATATAATGTATTTAAGCTATCCAAACTGTTAAAACATAAAAATAAATACAAA
*
12590987 ATGACATTTTTACCTTTAACAGCATAACAAAATC
449 ATGACATTTTTACCTTTAACAGCACAACAAAATC
* * * * * *
12591021 CTAAAAAGACATAAACAGTAACTTTTTCACACATATCAATCATGGAAACCAAGTTTAATTATCCA
1 CTAAAAAGACATAAACAGTAACTTTTTCACACATATCAATCGTGAAAACCAAGTTCAATCATTCG
* * * * * * *
12591086 GACAAGTTTAATATTATGTATTGAAACTATCTAAATTGTTAAAATAGAATAATAAATGCAAATTT
66 GACAAGTTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACA-AAAAAAAAATGTAAATTT
** * * * * *
12591151 GCATTTTGGCCTTTTAACAGCATAAAAAATCTTAAATAGATATAAACGACAACCTTTTCACATAT
130 ATATTTTTGCCATTTAAGA-CATAAAAAATCTTAAATAGATATAAACGACAACATTTTCACACAT
* ** * * *
12591216 ATCAACTGTGCAAAGTAAG-T-TCAATCATTCAAACAAGTTTAATATCATTTATTGAAGCTATCT
194 ATCAACTATGCAAACCAAGTTATCAATCATTCAAACAAATTTAATATAATGTATTGAAGCTATCT
*** * *
12591279 AAACTG-CTAAAATGGAATAATAAAAATAAATTTTCATTTT-GACCTTTTAACGGCATAAAAAAA
259 AAA-TGTC-AAAACAAAATAATAAAAACAAATTTGCATTTTAG-CCTTTTAACGGCA-AAAAAAA
* * * *
12591342 ATGCTAAACAGACATAAATAATAACATTT-TCTC-ACATCAATCAT-AGAACCAAATTCAATCAT
320 ATGCTAAACAAACATAAACAATAAC-TTTATCACAACATCAATCATAAAAACCAAATTCAATCAT
* * * * * *
12591404 TCGGACAAGTTTAATATTATGTATTTAAGCTATCCAAACTGTTAAAACATAAATATAACTACATA
384 TCAGAAAAGTTTAATATAATGTATTTAAGCTATCCAAACTGTTAAAACATAAAAATAAATACAAA
* * * ** *
12591469 TTTACATTTTTGCCCTTTAATGGCACAACAAAGTC
449 ATGACATTTTT-ACCTTTAACAGCACAACAAAATC
* * * *
12591504 CTAAAAAGATATAAAC-GATAACTTTTTC-CGCATATCAACCGTGAAAATCAAGTTCAATCATTC
1 CTAAAAAGACATAAACAG-TAACTTTTTCACACATATCAATCGTGAAAACCAAGTTCAATCATTC
* * * *
12591567 GGGCAAGTTTCATATAATGTATT-AGAGCTATCCAAACTGTTAAAACAAAAAAAAAATTGTATAT
65 GGACAAGTTTAATATAATGTATTGA-AGCTATCTAAACTGTTAAAACAAAAAAAAAA-TGTAAAT
* * * *
12591631 TTATATTTTTGCCCTTTAATGACACAAAAAAT-TCTAAATGGATATAAACGACAACTTTTT
128 TTATATTTTTGCCATTTAA-GACATAAAAAATCT-TAAATAGATATAAACGACAACATTTT
12591691 TATTTGATGC
Statistics
Matches: 545, Mismatches: 111, Indels: 34
0.79 0.16 0.05
Matches are distributed among these distances:
481 9 0.02
482 200 0.37
483 96 0.18
484 41 0.08
485 28 0.05
486 4 0.01
487 109 0.20
488 58 0.11
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (482 bp):
CTAAAAAGACATAAACAGTAACTTTTTCACACATATCAATCGTGAAAACCAAGTTCAATCATTCG
GACAAGTTTAATATAATGTATTGAAGCTATCTAAACTGTTAAAACAAAAAAAAAATGTAAATTTA
TATTTTTGCCATTTAAGACATAAAAAATCTTAAATAGATATAAACGACAACATTTTCACACATAT
CAACTATGCAAACCAAGTTATCAATCATTCAAACAAATTTAATATAATGTATTGAAGCTATCTAA
ATGTCAAAACAAAATAATAAAAACAAATTTGCATTTTAGCCTTTTAACGGCAAAAAAAAATGCTA
AACAAACATAAACAATAACTTTATCACAACATCAATCATAAAAACCAAATTCAATCATTCAGAAA
AGTTTAATATAATGTATTTAAGCTATCCAAACTGTTAAAACATAAAAATAAATACAAAATGACAT
TTTTACCTTTAACAGCACAACAAAATC
Found at i:12597090 original size:16 final size:16
Alignment explanation
Indices: 12597069--12597102 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12597059 AAATAAAAGT
* *
12597069 AAAAAAATATTTGACA
1 AAAAAAACATTCGACA
12597085 AAAAAAACATTCGACA
1 AAAAAAACATTCGACA
12597101 AA
1 AA
12597103 TAGCTATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAAAAACATTCGACA
Found at i:12599674 original size:19 final size:19
Alignment explanation
Indices: 12599650--12599708 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
12599640 AATATAGAAG
12599650 ATATTACAATCATAATTAA
1 ATATTACAATCATAATTAA
* *
12599669 ATATTATATTCAT-A-T--
1 ATATTACAATCATAATTAA
*
12599684 ATAATACAATCATAATTAA
1 ATATTACAATCATAATTAA
*
12599703 GTATTA
1 ATATTA
12599709 AATTCATATA
Statistics
Matches: 29, Mismatches: 7, Indels: 8
0.66 0.16 0.18
Matches are distributed among these distances:
15 10 0.34
16 1 0.03
17 2 0.07
18 1 0.03
19 15 0.52
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATTACAATCATAATTAA
Found at i:12599692 original size:34 final size:34
Alignment explanation
Indices: 12599654--12599721 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
12599644 TAGAAGATAT
*
12599654 TACAATCATAATTAAATATTATATTCATATATAA
1 TACAATCATAATTAAATATTAAATTCATATATAA
*
12599688 TACAATCATAATTAAGTATTAAATTCATATATAA
1 TACAATCATAATTAAATATTAAATTCATATATAA
12599722 AAGATCATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (34 bp):
TACAATCATAATTAAATATTAAATTCATATATAA
Found at i:12601895 original size:2 final size:2
Alignment explanation
Indices: 12601890--12601917 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12601880 TGTATATATA
12601890 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
12601918 AAAATTCATG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12605031 original size:20 final size:21
Alignment explanation
Indices: 12604996--12605037 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
12604986 ATGCATCTCA
12604996 TATTGGATAAACAAATTTAAT
1 TATTGGATAAACAAATTTAAT
*
12605017 TATTGG-TAAATAAATTTAAT
1 TATTGGATAAACAAATTTAAT
12605037 T
1 T
12605038 TTTGTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (21 bp):
TATTGGATAAACAAATTTAAT
Found at i:12605355 original size:21 final size:20
Alignment explanation
Indices: 12605322--12605360 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12605312 TTTAAAGCCA
*
12605322 ATTTTTTTTTTATTGTTTCT
1 ATTTTTTATTTATTGTTTCT
12605342 ATTTTCTTATTTATTGTTT
1 ATTTT-TTATTTATTGTTT
12605361 TAACAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (20 bp):
ATTTTTTATTTATTGTTTCT
Found at i:12610161 original size:15 final size:14
Alignment explanation
Indices: 12610115--12610161 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
12610105 AAATTCTAAG
12610115 AAAAATGTATATTTT
1 AAAAAT-TATATTTT
*
12610130 -AAAATTATTATTAT
1 AAAAATTA-TATTTT
12610144 AAAAATTATATTCTT
1 AAAAATTATATT-TT
12610159 AAA
1 AAA
12610162 TATAAATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 14 0.52
15 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (14 bp):
AAAAATTATATTTT
Found at i:12613372 original size:24 final size:23
Alignment explanation
Indices: 12613310--12613360 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
12613300 ATTTTTTTAA
*
12613310 AAATTAAACTATAAAATAAATTTC
1 AAATTAAA-AATAAAATAAATTTC
* *
12613334 AAATTAAAAACAAAATAACCTTTC
1 AAATTAAAAATAAAATAA-ATTTC
12613358 AAA
1 AAA
12613361 ATTCAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATTAAAAATAAAATAAATTTC
Found at i:12613389 original size:30 final size:31
Alignment explanation
Indices: 12613331--12613392 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
12613321 TAAAATAAAT
* *
12613331 TTCAAATTAAAAACAAAATAACCTTTCAAAA
1 TTCAAATAAAAAACAAAATAACCCTTCAAAA
12613362 TTCAAATAAAAAACAAAAT-ACCCTTCAAAA
1 TTCAAATAAAAAACAAAATAACCCTTCAAAA
12613392 T
1 T
12613393 GCTAAAATCC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (31 bp):
TTCAAATAAAAAACAAAATAACCCTTCAAAA
Found at i:12613597 original size:22 final size:22
Alignment explanation
Indices: 12613568--12613625 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
12613558 GTGGCAAAAC
12613568 ATATTATTTTGAAATAATAATAT
1 ATATTATTTTGAAATAA-AATAT
*
12613591 -TTTTATTTT-ACAA-AAAATAT
1 ATATTATTTTGA-AATAAAATAT
12613611 ATATTATTTTGAAAT
1 ATATTATTTTGAAAT
12613626 TTCACGTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.17
21 13 0.45
22 11 0.38
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (22 bp):
ATATTATTTTGAAATAAAATAT
Found at i:12615223 original size:20 final size:19
Alignment explanation
Indices: 12615200--12615575 Score: 104
Period size: 20 Copynumber: 18.7 Consensus size: 19
12615190 TTTACATAAC
12615200 TAATATTATATTTGCATGAT
1 TAATATT-TATTTGCATGAT
12615220 TAATATTATATTTGCATGA-
1 TAATATT-TATTTGCATGAT
* *
12615239 T-A-ATTTATTTGCCT-AA
1 TAATATTTATTTGCATGAT
*
12615255 T-AT-TTTATTTACATGAT
1 TAATATTTATTTGCATGAT
*
12615272 T-A-ATTTATTTGCATGAC
1 TAATATTTATTTGCATGAT
* * *
12615289 TATTAATATGTTTGCATGAT
1 TAAT-ATTTATTTGCATGAT
*
12615309 TATTAATTTATTTGCATGATT
1 TAAT-ATTTATTTGCATGA-T
**
12615330 ATCAATTTATTTATTTGTGTGAT
1 -T-AA--TATTTATTTGCATGAT
* ** *
12615353 CACATGATTATTATTATATATTTAAT
1 TA-AT-A-T-TTATT-TGCA--TGAT
* *
12615379 TGCATGTTTATTTGCATGAT
1 T-AATATTTATTTGCATGAT
* * *
12615399 TTATATTATTATTTGTATTAT
1 TAATA-T-TTATTTGCATGAT
**
12615420 TATATATTTAACTGCATGAT
1 TA-ATATTTATTTGCATGAT
* *
12615440 AAAATATTTATTTGCATGTT
1 -TAATATTTATTTGCATGAT
* *
12615460 TTATATTGTTAATTGCATGAT
1 TAATA-T-TTATTTGCATGAT
* *
12615481 AAAATATTTATTTGCATGTT
1 -TAATATTTATTTGCATGAT
* *
12615501 TTATATTGTTAATTGCATGA-
1 TAATA-T-TTATTTGCATGAT
* * *
12615521 TAATATATATTTGCGTGTTT
1 TAATATTTATTTGCATG-AT
* * *
12615541 TATTTTGTTAATTGCATGAT
1 TAATAT-TTATTTGCATGAT
*
12615561 AATATATTTATTTGC
1 TA-ATATTTATTTGC
12615576 TTGTTTTATA
Statistics
Matches: 258, Mismatches: 65, Indels: 66
0.66 0.17 0.17
Matches are distributed among these distances:
15 1 0.00
16 19 0.07
17 19 0.07
18 9 0.03
19 10 0.04
20 107 0.41
21 49 0.19
22 11 0.04
23 12 0.05
24 15 0.06
25 1 0.00
26 5 0.02
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (19 bp):
TAATATTTATTTGCATGAT
Found at i:12615258 original size:32 final size:33
Alignment explanation
Indices: 12615220--12615283 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
12615210 TTTGCATGAT
*
12615220 TAATATTATATTTGCATGA-TAATTTATTTGCC
1 TAATATTATATTTACATGATTAATTTATTTGCC
*
12615252 TAATATTTTATTTACATGATTAATTTATTTGC
1 TAATATTATATTTACATGATTAATTTATTTGC
12615284 ATGACTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (33 bp):
TAATATTATATTTACATGATTAATTTATTTGCC
Found at i:12615464 original size:41 final size:41
Alignment explanation
Indices: 12615419--12615599 Score: 269
Period size: 41 Copynumber: 4.5 Consensus size: 41
12615409 ATTTGTATTA
*
12615419 TTATATAT-TTAACTGCATGATAAAATATTTATTTGCATGTT
1 TTATAT-TGTTAATTGCATGATAAAATATTTATTTGCATGTT
12615460 TTATATTGTTAATTGCATGATAAAATATTTATTTGCATGTT
1 TTATATTGTTAATTGCATGATAAAATATTTATTTGCATGTT
* *
12615501 TTATATTGTTAATTGCATGAT--AATATATATTTGCGTGTT
1 TTATATTGTTAATTGCATGATAAAATATTTATTTGCATGTT
* * *
12615540 TTATTTTGTTAATTGCATGATAATATATTTATTTGCTTGTT
1 TTATATTGTTAATTGCATGATAAAATATTTATTTGCATGTT
*
12615581 TTATATTGTTAATTACATG
1 TTATATTGTTAATTGCATG
12615600 TGTTAATTCC
Statistics
Matches: 128, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
39 36 0.28
40 1 0.01
41 91 0.71
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (41 bp):
TTATATTGTTAATTGCATGATAAAATATTTATTTGCATGTT
Found at i:12615542 original size:80 final size:81
Alignment explanation
Indices: 12615419--12615599 Score: 267
Period size: 80 Copynumber: 2.2 Consensus size: 81
12615409 ATTTGTATTA
* *
12615419 TTATATAT-TTAACTGCATGATAAAATATTTATTTGCATGTTTTATATTGTTAATTGCATGATAA
1 TTATAT-TGTTAATTGCATGAT-AAATATATATTTGCATGTTTTATATTGTTAATTGCATGATAA
12615483 AATATTTATTTGCATGTT
64 AATATTTATTTGCATGTT
* * *
12615501 TTATATTGTTAATTGCATGAT-AATATATATTTGCGTGTTTTATTTTGTTAATTGCATGATAATA
1 TTATATTGTTAATTGCATGATAAATATATATTTGCATGTTTTATATTGTTAATTGCATGATAAAA
*
12615565 TATTTATTTGCTTGTT
66 TATTTATTTGCATGTT
*
12615581 TTATATTGTTAATTACATG
1 TTATATTGTTAATTGCATG
12615600 TGTTAATTCC
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
80 72 0.79
81 1 0.01
82 18 0.20
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (81 bp):
TTATATTGTTAATTGCATGATAAATATATATTTGCATGTTTTATATTGTTAATTGCATGATAAAA
TATTTATTTGCATGTT
Done.