Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008226.1 Hibiscus syriacus cultivar Beakdansim tig00110860_pilon, 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: 835745
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:7255 original size:21 final size:21
Alignment explanation
Indices: 7229--7360 Score: 122
Period size: 21 Copynumber: 6.3 Consensus size: 21
7219 AGCGGAAAAT
* *
7229 GAAGCAAGGGAAGCAGAGAGA
1 GAAGCAACGGAAGCACAGAGA
* * *
7250 GCAGCAACAGAAGCA-ACCAGA
1 GAAGCAACGGAAGCACA-GAGA
* * * *
7271 GCAGCAGCGGAAGCAGAGAAA
1 GAAGCAACGGAAGCACAGAGA
* * *
7292 GAAGCAGCGGCATCACAGAGA
1 GAAGCAACGGAAGCACAGAGA
*
7313 GAAGCAACGGCAGCACAGAGA
1 GAAGCAACGGAAGCACAGAGA
*
7334 GAAGCAACGGCAGCACAGAGA
1 GAAGCAACGGAAGCACAGAGA
7355 GAAGCA
1 GAAGCA
7361 GCATATCAGC
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
20 1 0.01
21 92 0.98
22 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.34, T:0.01
Consensus pattern (21 bp):
GAAGCAACGGAAGCACAGAGA
Found at i:7334 original size:23 final size:21
Alignment explanation
Indices: 7268--7360 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
7258 AGAAGCAACC
* * * *
7268 AGAGCAGCAGCGGAAGCAGAG
1 AGAGAAGCAACGGCAGCACAG
* * *
7289 AAAGAAGCAGCGGCATCACAG
1 AGAGAAGCAACGGCAGCACAG
7310 AGAGAAGCAACGGCAGCACAG
1 AGAGAAGCAACGGCAGCACAG
7331 AGAGAAGCAACGGCAGCACAG
1 AGAGAAGCAACGGCAGCACAG
7352 AGAGAAGCA
1 AGAGAAGCA
7361 GCATATCAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.43, C:0.22, G:0.34, T:0.01
Consensus pattern (21 bp):
AGAGAAGCAACGGCAGCACAG
Found at i:7804 original size:43 final size:42
Alignment explanation
Indices: 7757--8110 Score: 347
Period size: 43 Copynumber: 8.2 Consensus size: 42
7747 AGGCCTGTAC
* * * *
7757 CGGCGTTTTTAGCAGAAACGCCGCAAAACATCAACACCTACTG
1 CGGCGTTTTTAG-ACAAACGCCGCTAAATATCAACACCTATTG
* * *
7800 CGGCGTTTTTTGTTA-AAACGCCGCTAAACATCATA-ACATATTG
1 CGGCGTTTTTAG--ACAAACGCCGCTAAATATCA-ACACCTATTG
* * * * *
7843 CGGCGTTTGTCT-GAGAAACACTGCTAAATATTAACACCTATTA
1 CGGCGTTT-T-TAGACAAACGCCGCTAAATATCAACACCTATTG
*
7886 CGGCGTTTTTATGACAAACGTCGCTAAATATCAACACCTATTG
1 CGGCGTTTTTA-GACAAACGCCGCTAAATATCAACACCTATTG
* * * * *
7929 CGGCGTTTTTATAAAAAAACACCACTAAATATCAACACCTATTA
1 CGGCG-TTTT-TAGACAAACGCCGCTAAATATCAACACCTATTG
* *
7973 CGGCGTTTGTT-GAAAAACGCTGCTAAATATCAACACCTATTG
1 CGGCGTTT-TTAGACAAACGCCGCTAAATATCAACACCTATTG
* *
8015 CGGCGTTTTTATGACAAATGCCGCTAAATATCAACACTTATTG
1 CGGCGTTTTTA-GACAAACGCCGCTAAATATCAACACCTATTG
* * *
8058 CGACGTTTTTCACACAAACGCCGCTAAATATCAATACCTATTG
1 CGGCGTTTTT-AGACAAACGCCGCTAAATATCAACACCTATTG
8101 CGGCGTTTTT
1 CGGCGTTTTT
8111 TGTGAAAAAA
Statistics
Matches: 259, Mismatches: 38, Indels: 28
0.80 0.12 0.09
Matches are distributed among these distances:
41 3 0.01
42 37 0.14
43 176 0.68
44 40 0.15
45 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (42 bp):
CGGCGTTTTTAGACAAACGCCGCTAAATATCAACACCTATTG
Found at i:7996 original size:129 final size:128
Alignment explanation
Indices: 7757--8108 Score: 438
Period size: 129 Copynumber: 2.7 Consensus size: 128
7747 AGGCCTGTAC
* * * * ***
7757 CGGCGTTTTTA-GCAGAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTTTTGTTAAAACGC
1 CGGCGTTTTTATG-ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAAAAAACGC
* * * *
7821 CGCTAAACATCATAACATATTGCGGCGTTTGTCTGAGAAACACTGCTAAATATTAACACCTATTA
65 CGCTAAATATCA-AACCTATTGCGGCGTTTGTCTGAAAAACACTGCTAAATATCAACACCTATTA
* *
7886 CGGCGTTTTTATGACAAACGTCGCTAAATATCAACACCTATTGCGGCGTTTTTATAAAAAAACAC
1 CGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT-TAAAAAAACGC
* * * *
7951 CACTAAATATCAACACCTATTACGGCGTTTGT-TGAAAAACGCTGCTAAATATCAACACCTATTG
65 CGCTAAATATCAA-ACCTATTGCGGCGTTTGTCTGAAAAACACTGCTAAATATCAACACCTATTA
* * * * * *
8015 CGGCGTTTTTATGACAAATGCCGCTAAATATCAACACTTATTGCGACGTTTTTCACACAAACGCC
1 CGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAAAAAACGCC
8080 GCTAAATATCAATACCTATTGCGGCGTTT
66 GCTAAATATCAA-ACCTATTGCGGCGTTT
8109 TTTGTGAAAA
Statistics
Matches: 192, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
128 34 0.18
129 124 0.65
130 34 0.18
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (128 bp):
CGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAAAAAACGCC
GCTAAATATCAAACCTATTGCGGCGTTTGTCTGAAAAACACTGCTAAATATCAACACCTATTA
Found at i:9929 original size:12 final size:12
Alignment explanation
Indices: 9914--9939 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9904 CGTTCTTATT
9914 AACGAGTTGATA
1 AACGAGTTGATA
9926 AACGAGTTGATA
1 AACGAGTTGATA
9938 AA
1 AA
9940 TGAGCCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (12 bp):
AACGAGTTGATA
Found at i:11074 original size:20 final size:19
Alignment explanation
Indices: 11029--11078 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
11019 ATACCACGTG
*
11029 AACAGTATCGATACTGTTT
1 AACAGTATCGATACTGTAT
* *
11048 ATGCAGTATTGATACTGTAAT
1 A-ACAGTATCGATACTGT-AT
11069 AACAGTATCG
1 AACAGTATCG
11079 GTATTATGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.04
20 21 0.88
21 2 0.08
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (19 bp):
AACAGTATCGATACTGTAT
Found at i:12141 original size:77 final size:79
Alignment explanation
Indices: 12060--12230 Score: 190
Period size: 80 Copynumber: 2.2 Consensus size: 79
12050 ATTAATAATT
* * *
12060 TATTATATTGTTAAAATAAAAATAT-AATATCATATATTATT-ATAA-TAT-AATTAAGTATATT
1 TATTATATTGTTAAAATAAAAATATCAATA-AAGATATTATTAAAAAGTATCAA-TAAGTATATT
12121 ATTATAATATTAAAAA
64 ATTATAATATTAAAAA
* * * *
12137 TATTATATT-ATATTATTAAAAATATCAATAAAGATATTTTTCAAAAAGTATCAATAAGTATATT
1 TATTATATTGTTA-AAATAAAAATATCAATAAAGATATTATT-AAAAAGTATCAATAAGTATATT
12201 ATTATAATATTAAAAA
64 ATTATAATATTAAAAA
* *
12217 TATAATATAGTTAA
1 TATTATATTGTTAA
12231 GTATTTATGT
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
76 2 0.03
77 27 0.36
78 4 0.05
79 3 0.04
80 36 0.47
81 4 0.05
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (79 bp):
TATTATATTGTTAAAATAAAAATATCAATAAAGATATTATTAAAAAGTATCAATAAGTATATTAT
TATAATATTAAAAA
Found at i:12148 original size:22 final size:22
Alignment explanation
Indices: 12120--12161 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12110 TTAAGTATAT
12120 TATTATAATATTAAAAATATTA
1 TATTATAATATTAAAAATATTA
*
12142 TATTATATTATTAAAAATAT
1 TATTATAATATTAAAAATAT
12162 CAATAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTATAATATTAAAAATATTA
Found at i:12189 original size:26 final size:24
Alignment explanation
Indices: 12146--12204 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
12136 ATATTATATT
12146 ATATTATTAAAAATATCAATAAAG
1 ATATTATTAAAAATATCAATAAAG
*
12170 ATATTTTTCAAAAAGTATCAAT-AAG
1 ATATTATT-AAAAA-TATCAATAAAG
12195 TATATTATTA
1 -ATATTATTA
12205 TAATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 7 0.23
25 9 0.30
26 14 0.47
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (24 bp):
ATATTATTAAAAATATCAATAAAG
Found at i:17204 original size:14 final size:14
Alignment explanation
Indices: 17185--17214 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17175 GCTGCTAATC
*
17185 TATACACTGTAAAT
1 TATACACTGCAAAT
17199 TATACACTGCAAAT
1 TATACACTGCAAAT
17213 TA
1 TA
17215 GATTATGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
TATACACTGCAAAT
Found at i:18827 original size:60 final size:60
Alignment explanation
Indices: 18719--18852 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
18709 TATTGAATTT
* * *
18719 CATAGTTTTGAGATGAAATTAGAATATTAAAAAGTTCGATGACCAATTTAGAATGAGAGT
1 CATAGTTTGGAGATGAAATTAGAATATTAAAAAGTTCGATGACCAATTTAAAATGAGAGC
* * * * * * *
18779 TATAGTTTGGATATGAAATTAGAATGTTTAAAAGTTTG-TGAACTAATTTAAAATGATAGC
1 CATAGTTTGGAGATGAAATTAGAATATTAAAAAGTTCGATG-ACCAATTTAAAATGAGAGC
18839 CATAGTTTGG-GATG
1 CATAGTTTGGAGATG
18853 TGCGGTGAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
59 5 0.08
60 56 0.92
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (60 bp):
CATAGTTTGGAGATGAAATTAGAATATTAAAAAGTTCGATGACCAATTTAAAATGAGAGC
Found at i:20971 original size:21 final size:21
Alignment explanation
Indices: 20942--20983 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20932 TCACGCCTCT
* *
20942 GGCGTGGACTGGCACTCCTGC
1 GGCGAGGACTGCCACTCCTGC
*
20963 GGCGAGGACTGCCGCTCCTGC
1 GGCGAGGACTGCCACTCCTGC
20984 TCCTACTCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.36, G:0.38, T:0.17
Consensus pattern (21 bp):
GGCGAGGACTGCCACTCCTGC
Found at i:31076 original size:428 final size:428
Alignment explanation
Indices: 30279--31135 Score: 1642
Period size: 428 Copynumber: 2.0 Consensus size: 428
30269 CTCATTAAAG
30279 GTACTTAGATGATAAATTATGAGAATATTTCGATTAGGTAAAATTACGAAATTACCCTTATGTTG
1 GTACTTAGATGATAAATTATGAGAATATTTCGATTAGGTAAAATTACGAAATTACCCTTATGTTG
*
30344 GAAAATGACAAGAATTATCCTTGGAAGTTGATTAATAAATCTGAAAAGAATTATTGATCTTCTAA
66 GAAAATGACAAGAATTATCCCTGGAAGTTGATTAATAAATCTGAAAAGAATTATTGATCTTCTAA
30409 AACTATTGATGTGCATAAGAAATGTTAGTTTTACTTGGAAATTATAGATAATCGATTTTTAACCC
131 AACTATTGATGTGCATAAGAAATGTTAGTTTTACTTGGAAATTATAGATAATCGATTTTTAACCC
30474 CAAGAATGTTTATGCTAGATACTAGAAGTCTTTTAATGAATCATTTCAAGATCAAAGAATGTTCG
196 CAAGAATGTTTATGCTAGATACTAGAAGTCTTTTAATGAATCATTTCAAGATCAAAGAATGTTCG
* *
30539 AGGAAGCAATTAATCACAGGATCTCTATATTATATTATTTTTGTTAAGAGCTCATATAGAAATTA
261 AGGAAGCAATTAATCACAGGATCTCTATATTATATTATTTTCGTTAAGAGCTAATATAGAAATTA
*
30604 TCTGGTTAAGAAATTACGAAAATGCCCTTGAGAGGTAAAATAGTCAGAGTTGACCCTGAAGGAGA
326 TCTGGTTAAGAAATTACGAAAATACCCTTGAGAGGTAAAATAGTCAGAGTTGACCCTGAAGGAGA
*
30669 AAATACTTTGAGGATTTGTACTTAACTCGATTAAGTAC
391 AAATACTTTGAGAATTTGTACTTAACTCGATTAAGTAC
30707 GTACTTAGATGATAAATTATGAGAATATTTCGATTAGGTAAAATTACGAAATTACCCTTATGTTG
1 GTACTTAGATGATAAATTATGAGAATATTTCGATTAGGTAAAATTACGAAATTACCCTTATGTTG
*
30772 GAAAATGACAAGAATTGTCCCTGGAAGTTGATTAATAAATCTGAAAAGAATTATTGATCTTCTAA
66 GAAAATGACAAGAATTATCCCTGGAAGTTGATTAATAAATCTGAAAAGAATTATTGATCTTCTAA
* *
30837 AACTATTGATGTGCATAAGAAATGTTAGTTTTACTTGGAAATTATGGATAATCGGTTTTTAACCC
131 AACTATTGATGTGCATAAGAAATGTTAGTTTTACTTGGAAATTATAGATAATCGATTTTTAACCC
30902 CAAGAATGTTTATGCTAGATACTAGAAGTCTTTTAATGAATCATTTCAAGATCAAAGAATGTTCG
196 CAAGAATGTTTATGCTAGATACTAGAAGTCTTTTAATGAATCATTTCAAGATCAAAGAATGTTCG
30967 AGGAAGCAATTAATCACAGGATCTCTATATTATATTATTTTCGTTAAGAGCTAATATAGAAATTA
261 AGGAAGCAATTAATCACAGGATCTCTATATTATATTATTTTCGTTAAGAGCTAATATAGAAATTA
31032 TCTGGTTAAGAAATTACGAAAATACCCTTGAGAGGTAAAATAGTCAGAGTTGACCCTGAAGGAGA
326 TCTGGTTAAGAAATTACGAAAATACCCTTGAGAGGTAAAATAGTCAGAGTTGACCCTGAAGGAGA
31097 AAATACTTTGAGAATTTGTACTTAACTCGATTAAGTAC
391 AAATACTTTGAGAATTTGTACTTAACTCGATTAAGTAC
31135 G
1 G
31136 AATTTAATTA
Statistics
Matches: 421, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
428 421 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (428 bp):
GTACTTAGATGATAAATTATGAGAATATTTCGATTAGGTAAAATTACGAAATTACCCTTATGTTG
GAAAATGACAAGAATTATCCCTGGAAGTTGATTAATAAATCTGAAAAGAATTATTGATCTTCTAA
AACTATTGATGTGCATAAGAAATGTTAGTTTTACTTGGAAATTATAGATAATCGATTTTTAACCC
CAAGAATGTTTATGCTAGATACTAGAAGTCTTTTAATGAATCATTTCAAGATCAAAGAATGTTCG
AGGAAGCAATTAATCACAGGATCTCTATATTATATTATTTTCGTTAAGAGCTAATATAGAAATTA
TCTGGTTAAGAAATTACGAAAATACCCTTGAGAGGTAAAATAGTCAGAGTTGACCCTGAAGGAGA
AAATACTTTGAGAATTTGTACTTAACTCGATTAAGTAC
Found at i:32514 original size:12 final size:12
Alignment explanation
Indices: 32476--32568 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
32466 ATTTCCGACT
32476 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
32488 TG-ATATATGACC
1 TGAAT-TCTGTTC
32500 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
32512 TGATTTCTGATC
1 TGAATTCTGTTC
*
32524 TGGATTCTGTTC
1 TGAATTCTGTTC
*
32536 TG-ATATCTGTTT
1 TGAAT-TCTGTTC
*
32548 TGAATTCTGTTT
1 TGAATTCTGTTC
*
32560 TGATTTCTG
1 TGAATTCTG
32569 ATATCTCTGT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
11 4 0.06
12 56 0.88
13 4 0.06
ACGTcount: A:0.17, C:0.14, G:0.18, T:0.51
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:32544 original size:24 final size:24
Alignment explanation
Indices: 32476--32570 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
32466 ATTTCCGACT
* *
32476 TGAATTCTGTTCTGATATATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
32500 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* * *
32524 TGGATTCTGTTCTGATATCTGTTT
1 TGAATTCTGTTCTGATATCTGATC
* *
32548 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
32571 ATCTCTGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:32567 original size:48 final size:48
Alignment explanation
Indices: 32462--32570 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
32452 AAATATTTTA
* *
32462 TCTGATTTCCGA-CTTGAATTCTGTTCTGATATATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATATATGACCTGAATTCTGT
* ***
32510 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTTTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATATATGACCTGAATTCTGT
*
32558 TTTGATTTCTGAT
1 TCTGATTTCTGAT
32571 ATCTCTGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATATATGACCTGAATTCTGT
Found at i:34657 original size:2 final size:2
Alignment explanation
Indices: 34652--34678 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34642 CCCCCAAAAA
34652 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
34679 AAAGGATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41671 original size:3 final size:3
Alignment explanation
Indices: 41609--41660 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
41599 TCATTCCATT
41609 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
41655 TTA TTA
1 TTA TTA
41661 AAATATTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41676 original size:22 final size:21
Alignment explanation
Indices: 41609--41676 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 21
41599 TCATTCCATT
*
41609 TTATT-ATTATTATT--ATTA
1 TTATTAATTATTATTAAAATA
**
41627 TTATT-ATTATTATTATTAT-
1 TTATTAATTATTATTAAAATA
41646 TTATT-ATTATTATTAAAATA
1 TTATTAATTATTATTAAAATA
41666 TTATTACATTA
1 TTATTA-ATTA
41677 CAGGCCATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 14 0.34
19 17 0.41
20 6 0.15
22 4 0.10
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTAATTATTATTAAAATA
Found at i:42980 original size:14 final size:12
Alignment explanation
Indices: 42946--43006 Score: 72
Period size: 11 Copynumber: 5.1 Consensus size: 12
42936 TTAATTACAA
42946 TTTTATT-TTAT
1 TTTTATTATTAT
42957 TTTTATTATTAT
1 TTTTATTATTAT
42969 TTTTGATATATTAT
1 TTTT-AT-TATTAT
* *
42983 TTTCATGATTA-
1 TTTTATTATTAT
42994 TTTTATTATTAT
1 TTTTATTATTAT
43006 T
1 T
43007 ATCTTAAGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
11 16 0.38
12 13 0.31
13 4 0.10
14 9 0.21
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:42999 original size:17 final size:16
Alignment explanation
Indices: 42945--43005 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
42935 TTTAATTACA
**
42945 ATTTTATTTTATTTTT
1 ATTTTATTTTATGATT
42961 ATTATTATTTT-TGA-T
1 ATT-TTATTTTATGATT
*
42976 ATATTATTTTCATGATT
1 ATTTTATTTT-ATGATT
42993 ATTTTATTATTAT
1 ATTTTATT-TTAT
43006 TATCTTAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 7 0.19
15 3 0.08
16 7 0.19
17 17 0.47
18 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (16 bp):
ATTTTATTTTATGATT
Found at i:43098 original size:13 final size:12
Alignment explanation
Indices: 43080--43133 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 12
43070 TAAAATCCTA
43080 TTTATAATTTAAT
1 TTTATAATTT-AT
*
43093 TTTATAAATTAT
1 TTTATAATTTAT
43105 TTT-TAATTATAT
1 TTTATAATT-TAT
43117 TTTAATATATTTAT
1 TTT-ATA-ATTTAT
43131 TTT
1 TTT
43134 TCAATATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 4 0.11
12 11 0.31
13 9 0.26
14 8 0.23
15 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATAATTTAT
Found at i:43111 original size:24 final size:26
Alignment explanation
Indices: 43078--43143 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 26
43068 ATTAAAATCC
*
43078 TATTTATAATTTAATTTT-ATA-AAT
1 TATTTTTAATTTAATTTTAATATAAT
*
43102 TATTTTTAA-TTATATTTTAATATATT
1 TATTTTTAATTTA-ATTTTAATATAAT
43128 TATTTTTCAATATTAA
1 TATTTTT-AAT-TTAA
43144 GAAAGTGACA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 3 0.09
24 13 0.38
25 3 0.09
26 9 0.26
27 2 0.06
28 1 0.03
29 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTTTTAATTTAATTTTAATATAAT
Found at i:43353 original size:2 final size:2
Alignment explanation
Indices: 43346--43384 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
43336 TTATAAATAA
*
43346 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43385 TTTTTCTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46428 original size:8 final size:8
Alignment explanation
Indices: 46411--46447 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
46401 TTTACATTTA
*
46411 CATTTTTG
1 CATTTATG
46419 CATTTATG
1 CATTTATG
46427 CATTTATG
1 CATTTATG
46435 CATTT-TG
1 CATTTATG
46442 CATTTA
1 CATTTA
46448 CATTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.22, C:0.14, G:0.11, T:0.54
Consensus pattern (8 bp):
CATTTATG
Found at i:53319 original size:22 final size:22
Alignment explanation
Indices: 53294--53370 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
53284 ATCTACACTT
53294 TTCAAAGATGATAGACTCTTTC
1 TTCAAAGATGATAGACTCTTTC
* * *
53316 TTCAAAGATGATAGCCTATCTC
1 TTCAAAGATGATAGACTCTTTC
* *
53338 TTTAAAGATGATAGATTCTCTT-
1 TTCAAAGATGATAGACTCT-TTC
53360 TTCAAAGATGA
1 TTCAAAGATGA
53371 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGACTCTTTC
Found at i:54190 original size:91 final size:92
Alignment explanation
Indices: 54034--54271 Score: 433
Period size: 91 Copynumber: 2.6 Consensus size: 92
54024 CTATTTCCCA
54034 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
54099 GCTTGATGTTTTCAAAAACCTTCAGGT
66 GCTTGATGTTTTCAAAAACCTTCAGGT
* *
54126 CATCTGTAAGCCCTTCAATGCTTGATGTTTT-TAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
54190 GCTTGATGTTTTCAAAAACCTTCGGGT
66 GCTTGATGTTTTCAAAAACCTTCAGGT
*
54217 CATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTGTAA
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAA
54272 AACCTTCGGG
Statistics
Matches: 139, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
91 87 0.63
92 52 0.37
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (92 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
GCTTGATGTTTTCAAAAACCTTCAGGT
Found at i:54278 original size:46 final size:46
Alignment explanation
Indices: 54034--54271 Score: 433
Period size: 46 Copynumber: 5.2 Consensus size: 46
54024 CTATTTCCCA
54034 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
54080 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
54126 CATCTGTAAGCCCTTCAATGCTTGATGTTTT-TAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
54171 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
54217 CATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
54263 CATCTGTAA
1 CATCTGTAA
54272 AACCTTCGGG
Statistics
Matches: 184, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 42 0.23
46 142 0.77
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (46 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
Found at i:54291 original size:112 final size:112
Alignment explanation
Indices: 54157--54383 Score: 454
Period size: 112 Copynumber: 2.0 Consensus size: 112
54147 TTGATGTTTT
54157 TAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCT
1 TAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCT
54222 GTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTG
66 GTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTG
54269 TAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCT
1 TAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCT
54334 GTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTG
66 GTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTG
54381 TAA
1 TAA
54384 GTCATTCAAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 115 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (112 bp):
TAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCT
GTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTG
Found at i:54298 original size:20 final size:20
Alignment explanation
Indices: 54250--54291 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
54240 GAAGTTTTCA
54250 AAAACCTTCGGGTCATCTGT
1 AAAACCTTCGGGTCATCTGT
54270 AAAACCTTCGGGTCATCTGT
1 AAAACCTTCGGGTCATCTGT
54290 AA
1 AA
54292 GCCCTTCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (20 bp):
AAAACCTTCGGGTCATCTGT
Found at i:54323 original size:46 final size:46
Alignment explanation
Indices: 54270--54873 Score: 927
Period size: 46 Copynumber: 13.3 Consensus size: 46
54260 GGTCATCTGT
54270 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
*
54316 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
* * *
54362 AAAACCTTCGGGTCATCTGTAAGTCATTCA--ACTTGATGTTTTC-
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
*
54405 AAAACCTTCGGGTCATCTGTAAGCCCTTAAGTGCTTGATGTTTTCA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
* *
54451 AAAACCTTTGGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTCA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
* *
54497 AAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCTTGATATTTTC-
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
54542 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
*
54587 AAAACCTTCGGGCCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
* *
54633 AAAACGTTCGAGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
* *
54679 AAAACCTTTGGGTCATCTGTAAGCCCTTAAGTGCTTGATGTTTTC-
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
* * * * *
54724 AAAACTTTTGGGTCATCTGTAAGTCTTTTAGTGCTTGATGTTTTCA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
* *
54770 AAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
* *
54815 AAAACCTTAGGGTCATCAT-TAAGCCCTTCAGTGCATGATGTTTTCA
1 AAAACCTTCGGGTCATC-TGTAAGCCCTTCAGTGCTTGATGTTTTCA
54861 AAAAGCCTTCGGG
1 AAAA-CCTTCGGG
54874 AGCTTTTTGG
Statistics
Matches: 513, Mismatches: 37, Indels: 15
0.91 0.07 0.03
Matches are distributed among these distances:
43 27 0.05
44 11 0.02
45 182 0.35
46 286 0.56
47 7 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (46 bp):
AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCA
Found at i:54344 original size:66 final size:66
Alignment explanation
Indices: 54204--54337 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
54194 GATGTTTTCA
54204 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTG
54269 T
66 T
*
54270 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTG
54335 T
66 T
54336 AA
1 AA
54338 GCCCTTCAGT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (66 bp):
AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTG
T
Found at i:54363 original size:158 final size:154
Alignment explanation
Indices: 54113--54426 Score: 520
Period size: 158 Copynumber: 2.0 Consensus size: 154
54103 GATGTTTTCA
*
54113 AAAACCTTCAGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTTAAAACCTTCGGGTCATCTGT
1 AAAACCTTCAGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTAAAAACCTTCGGGTCATCTGT
* * *
54178 AAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGAA
66 AAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCATTCA--ACTTGAA
54243 GTTTTCAAAAACCTTCGGGTCATCTGT
129 GTTTTC-AAAACCTTCGGGTCATCTGT
* *
54270 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
1 AAAACCTTCAGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTT-AAAAACCTTCGGGTCATCTG
* *
54335 TAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCATTCAACTTGATG
65 TAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCATTCAACTTGAAG
54400 TTTTCAAAACCTTCGGGTCATCTGT
130 TTTTCAAAACCTTCGGGTCATCTGT
54425 AA
1 AA
54427 GCCCTTAAGT
Statistics
Matches: 148, Mismatches: 8, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
155 22 0.15
156 11 0.07
157 42 0.28
158 73 0.49
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (154 bp):
AAAACCTTCAGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTAAAAACCTTCGGGTCATCTGT
AAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCATTCAACTTGAAGT
TTTCAAAACCTTCGGGTCATCTGT
Found at i:54560 original size:91 final size:92
Alignment explanation
Indices: 54270--54873 Score: 927
Period size: 91 Copynumber: 6.6 Consensus size: 92
54260 GGTCATCTGT
54270 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
*
54335 TAAGCCCTTCAGTGCTTGAAGTTTTCA
66 TAAGCCCTTCAGTGCTTGATGTTTTCA
* * *
54362 AAAACCTTCGGGTCATCTGTAAGTCATTCA--ACTTGATGTTTTC-AAAACCTTCGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
*
54424 TAAGCCCTTAAGTGCTTGATGTTTTCA
66 TAAGCCCTTCAGTGCTTGATGTTTTCA
* *
54451 AAAACCTTTGGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
* *
54516 TAAGACCTTCAGTGCTTGATATTTTC-
66 TAAGCCCTTCAGTGCTTGATGTTTTCA
*
54542 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGCCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
54606 TAAGCCCTTCAGTGCTTGATGTTTTCA
66 TAAGCCCTTCAGTGCTTGATGTTTTCA
* * *
54633 AAAACGTTCGAGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTTGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
*
54698 TAAGCCCTTAAGTGCTTGATGTTTTC-
66 TAAGCCCTTCAGTGCTTGATGTTTTCA
* * * * * *
54724 AAAACTTTTGGGTCATCTGTAAGTCTTTTAGTGCTTGATGTTTTCAAAAACCTTTGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
*
54789 TAAGCCCTTCAGTGCATGATGTTTTC-
66 TAAGCCCTTCAGTGCTTGATGTTTTCA
* *
54815 AAAACCTTAGGGTCATCAT-TAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGG
1 AAAACCTTCGGGTCATC-TGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAA-CCTTCGGG
54874 AGCTTTTTGG
Statistics
Matches: 468, Mismatches: 37, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
89 71 0.15
90 54 0.12
91 223 0.48
92 120 0.26
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (92 bp):
AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTG
TAAGCCCTTCAGTGCTTGATGTTTTCA
Found at i:55109 original size:3 final size:3
Alignment explanation
Indices: 55101--55163 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
55091 TCATTACGTT
*
55101 TTA TTA TTA TTA TTA TTA ATA 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
*
55149 TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA
55164 CGGCCATTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:56542 original size:12 final size:13
Alignment explanation
Indices: 56493--56546 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 13
56483 TTTTATTTTG
56493 TTTTTATTATTAT
1 TTTTTATTATTAT
*
56506 TTTTGATATATTAT
1 TTTTTAT-TATTAT
*
56520 TTTCATGATTATT-T
1 TTT--TTATTATTAT
56534 TTTTTATTATTAT
1 TTTTTATTATTAT
56547 CTTAAGTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
12 7 0.20
13 7 0.20
14 13 0.37
15 4 0.11
16 4 0.11
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (13 bp):
TTTTTATTATTAT
Found at i:56883 original size:2 final size:2
Alignment explanation
Indices: 56871--56921 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
56861 ATATCTTATT
* *
56871 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56913 T- TA -A TA TA T
1 TA TA TA TA TA T
56922 TTTTTCTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:58702 original size:12 final size:12
Alignment explanation
Indices: 58685--58737 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
58675 ACTATAGCAT
58685 TGTTCATGGTAC
1 TGTTCATGGTAC
*
58697 TGTTCATGATAC
1 TGTTCATGGTAC
*
58709 TGTTTAT--TAC
1 TGTTCATGGTAC
**
58719 TGTTCACAGTAC
1 TGTTCATGGTAC
58731 TGTTCAT
1 TGTTCAT
58738 ACCGTATAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.24
12 26 0.76
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (12 bp):
TGTTCATGGTAC
Found at i:59819 original size:30 final size:31
Alignment explanation
Indices: 59785--59852 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
59775 AAACATAATT
59785 AAAATAATAAAAACAACA-AATAA-AAAAATA
1 AAAATAATAAAAACAACATAA-AATAAAAATA
* * *
59815 AAAATAGTAAAAACAATATAAAATAAAGATA
1 AAAATAATAAAAACAACATAAAATAAAAATA
59846 AAAATAA
1 AAAATAA
59853 AATATGAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.16
Consensus pattern (31 bp):
AAAATAATAAAAACAACATAAAATAAAAATA
Found at i:59832 original size:18 final size:18
Alignment explanation
Indices: 59805--59839 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
59795 AAACAACAAA
59805 TAAAAAAATA-AAAATAG
1 TAAAAAAATATAAAATAG
59822 TAAAAACAATATAAAATA
1 TAAAAA-AATATAAAATA
59840 AAGATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
TAAAAAAATATAAAATAG
Found at i:67013 original size:55 final size:55
Alignment explanation
Indices: 66954--67157 Score: 218
Period size: 55 Copynumber: 3.7 Consensus size: 55
66944 TCTTCAAGTG
* * * * *
66954 ACGGGTCTGCTCCCTATTCTTTCAGGAAGTATA-AGACTTGAATAATCTTCATA-AA
1 ACGGGTCCGCTCTCTATTCCTTCAGGAAGTATAGA-ACTCGAACAATCTTCA-ACAA
*
67009 ACGGGTCCGCTCTCTATTCCTTCAGAAAGTATAGAACTCGAACAATCTTCAACAA
1 ACGGGTCCGCTCTCTATTCCTTCAGGAAGTATAGAACTCGAACAATCTTCAACAA
* *
67064 ACGGGTCCGATCTCTATTCCTTCA-GAGAGTATAGAACTCGAACAATCTTCAACGA
1 ACGGGTCCGCTCTCTATTCCTTCAGGA-AGTATAGAACTCGAACAATCTTCAACAA
*** * * *
67119 ATTTGTCCGCTCCCTATTCCCTCA-GAGAGTATAGGACTC
1 ACGGGTCCGCTCTCTATTCCTTCAGGA-AGTATAGAACTC
67158 AATCTTCAAC
Statistics
Matches: 130, Mismatches: 16, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
54 2 0.02
55 127 0.98
56 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (55 bp):
ACGGGTCCGCTCTCTATTCCTTCAGGAAGTATAGAACTCGAACAATCTTCAACAA
Found at i:68313 original size:23 final size:22
Alignment explanation
Indices: 68287--68406 Score: 117
Period size: 21 Copynumber: 5.5 Consensus size: 22
68277 TTGAACCCCC
68287 TTTTTTTCTTTTCTTTTCATCTT
1 TTTTTTTCTTTTCTTTTCAT-TT
*
68310 TTTTTTTCTTTTTTTTTCATCATTT
1 TTTTTTTC-TTTTCTTT--TCATTT
*
68335 TTTTTTTCTTTTTTTTTCATTT
1 TTTTTTTCTTTTCTTTTCATTT
*
68357 TTTTTTT-TCTTC--TT--TTT
1 TTTTTTTCTTTTCTTTTCATTT
*
68374 ATTTTTTCTTTT-TTTTCATTT
1 TTTTTTTCTTTTCTTTTCATTT
*
68395 TTTATTTCTTTT
1 TTTTTTTCTTTT
68407 TCAAGCGAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
17 9 0.11
18 3 0.04
19 4 0.05
21 16 0.20
22 13 0.16
23 8 0.10
24 15 0.18
25 10 0.12
26 4 0.05
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTTCTTTTCTTTTCATTT
Found at i:68323 original size:25 final size:24
Alignment explanation
Indices: 68287--68402 Score: 114
Period size: 25 Copynumber: 4.8 Consensus size: 24
68277 TTGAACCCCC
*
68287 TTTTTTTC-TTTTCTTTTCATCTT
1 TTTTTTTCTTTTTTTTTTCATCTT
68310 TTTTTTTC-TTTTTTTTTCATCATT
1 TTTTTTTCTTTTTTTTTTCATC-TT
*
68334 TTTTTTT-TCTTTTTTTTTCATTTT
1 TTTTTTTCT-TTTTTTTTTCATCTT
**
68358 TTTTTTTCTTCTTTTTATTTTTTC-T
1 TTTTTTTCTT-TTTTT-TTTCATCTT
*
68383 TTTTTTTCATTTTTTATTTC
1 TTTTTTTC-TTTTTTTTTTC
68403 TTTTTCAAGC
Statistics
Matches: 79, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
23 20 0.25
24 22 0.28
25 31 0.39
26 6 0.08
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTTTCTTTTTTTTTTCATCTT
Found at i:68386 original size:48 final size:47
Alignment explanation
Indices: 68287--68407 Score: 140
Period size: 48 Copynumber: 2.5 Consensus size: 47
68277 TTGAACCCCC
* *
68287 TTTTTTTCTTTTCTTTTCATCTTTTTTTTTCTTTTTTTTTCATCATTT
1 TTTTTTTCTTTTTTTTTCATTTTTTTTTTTCTTTTTTTTT-ATCATTT
*
68335 TTTTTTTCTTTTTTTTTCATTTTTTTTTTTCTTCTTTTTATT-T-TTTCT
1 TTTTTTTCTTTTTTTTTCATTTTTTTTTTTCTT-TTTTT-TTATCATT-T
68383 TTTTTTTCATTTTTTATTTC-TTTTT
1 TTTTTTTC-TTTTTT-TTTCATTTTT
68408 CAAGCGAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
47 2 0.03
48 41 0.63
49 16 0.25
50 6 0.09
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.83
Consensus pattern (47 bp):
TTTTTTTCTTTTTTTTTCATTTTTTTTTTTCTTTTTTTTTATCATTT
Found at i:68407 original size:1 final size:1
Alignment explanation
Indices: 68308--68389 Score: 56
Period size: 1 Copynumber: 82.0 Consensus size: 1
68298 TCTTTTCATC
* ** ** * ** * *
68308 TTTTTTTTTCTTTTTTTTTCATCATTTTTTTTTTCTTTTTTTTTCATTTTTTTTTTTCTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
68373 TATTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTT
68390 CATTTTTTAT
Statistics
Matches: 60, Mismatches: 21, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:68407 original size:22 final size:21
Alignment explanation
Indices: 68287--68407 Score: 115
Period size: 24 Copynumber: 5.6 Consensus size: 21
68277 TTGAACCCCC
*
68287 TTTTTTTCTTTTCTTTTCATCTT
1 TTTTTTTCTTTTTTTTTCA--TT
68310 TTTTTTTCTTTTTTTTTCATCATTT
1 TTTTTTTC-TTTTTTTT--TCA-TT
68335 TTTTTTTCTTTTTTTTTCATT
1 TTTTTTTCTTTTTTTTTCATT
* *
68356 TTTTTTT-TTCTTCTTT--TT
1 TTTTTTTCTTTTTTTTTCATT
*
68374 ATTTTTTC-TTTTTTTTCATT
1 TTTTTTTCTTTTTTTTTCATT
68394 TTTTATTTCTTTTT
1 TTTT-TTTCTTTTT
68408 CAAGCGAAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
18 14 0.17
20 12 0.15
21 13 0.16
22 7 0.09
23 8 0.10
24 15 0.18
25 10 0.12
26 3 0.04
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTTCTTTTTTTTTCATT
Found at i:78066 original size:45 final size:45
Alignment explanation
Indices: 77995--78123 Score: 177
Period size: 45 Copynumber: 2.8 Consensus size: 45
77985 TGTTATTCAC
* *
77995 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTGGTCG
1 AAAAATAAA-CCTAACCACATGATATCTAATTCGCATGCTTGGTCG
* * * *
78041 AAAAATAAACCTAACCTCATTATATCTAATTCACATGCTTGTTCG
1 AAAAATAAACCTAACCACATGATATCTAATTCGCATGCTTGGTCG
* *
78086 AAAAATAAACCTAACCACATGATATCTAGTTCGTATGC
1 AAAAATAAACCTAACCACATGATATCTAATTCGCATGC
78124 ATTTATTTGA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
45 65 0.89
46 8 0.11
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (45 bp):
AAAAATAAACCTAACCACATGATATCTAATTCGCATGCTTGGTCG
Found at i:80616 original size:2 final size:2
Alignment explanation
Indices: 80609--80643 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
80599 TTTTGGATTG
80609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
80644 AAAAAAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:80780 original size:2 final size:2
Alignment explanation
Indices: 80773--80799 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
80763 TATATTACCC
80773 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
80800 GTAATTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:91601 original size:13 final size:13
Alignment explanation
Indices: 91566--91604 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
91556 CATCATCCGG
91566 TCTTTAATTTTTT
1 TCTTTAATTTTTT
* *
91579 TCCTT-CTTTTTT
1 TCTTTAATTTTTT
91591 TCTTTAATTTTTT
1 TCTTTAATTTTTT
91604 T
1 T
91605 AGCTTTTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTAATTTTTT
Found at i:92658 original size:74 final size:75
Alignment explanation
Indices: 92530--92675 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 75
92520 AATTACTATT
92530 ATTGCAAATGATTTAACGTTAATAATTGTTTTTGTTACTCTTGAAACTTAAAAGAAAACTTTTCA
1 ATTGCAAATGATTTAACGTTAATAATTGTTTTTGTTACTCTTGAAACTTAAAAG-AAACTTTTCA
92595 TATTTCAAGCC
65 TATTTCAAGCC
92606 ATTGCAAATGATTTAACGTTAATAA-TG-TTTTGTTACTCTTGAAACTTAAAAGAAACTTTTCAT
1 ATTGCAAATGATTTAACGTTAATAATTGTTTTTGTTACTCTTGAAACTTAAAAGAAACTTTTCAT
92669 ATTTCAA
66 ATTTCAA
92676 TACCATTTAG
Statistics
Matches: 70, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
73 18 0.26
74 25 0.36
75 2 0.03
76 25 0.36
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (75 bp):
ATTGCAAATGATTTAACGTTAATAATTGTTTTTGTTACTCTTGAAACTTAAAAGAAACTTTTCAT
ATTTCAAGCC
Found at i:96667 original size:21 final size:22
Alignment explanation
Indices: 96632--96673 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
96622 CTCGAATTTA
*
96632 AAAATTTATATATCAAAATTAT
1 AAAATTTATAAATCAAAATTAT
96654 AAAA-TTATAAATCAAAATTA
1 AAAATTTATAAATCAAAATTA
96674 ACTCGAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATTTATAAATCAAAATTAT
Found at i:97910 original size:29 final size:29
Alignment explanation
Indices: 97864--98083 Score: 185
Period size: 28 Copynumber: 7.6 Consensus size: 29
97854 CCCGTTGAAC
**
97864 TGGTGATATTTTAATAATTATTTTTAAAA
1 TGGTGATATTTTTGTAATTATTTTTAAAA
* *
97893 TGGTGATATTTTGGTAATTA-TTTTCAAA
1 TGGTGATATTTTTGTAATTATTTTTAAAA
* * **
97921 TTGTGCTATTTTCATAATTA-TTTTAAAA
1 TGGTGATATTTTTGTAATTATTTTTAAAA
*
97949 TGGTGATATTTTTGTAATTA-TTTAAAAA
1 TGGTGATATTTTTGTAATTATTTTTAAAA
* *
97977 AGATGATATTTTTGTAATTATTTTTAAAAAA
1 TGGTGATATTTTTGTAATTATTTTT--AAAA
* * * * **
98008 AGGTGACAGTTTCGTAATTATTTAAAAAA
1 TGGTGATATTTTTGTAATTATTTTTAAAA
* * *
98037 GGGTGATATTTTTGTAAATATTTCTTCAAA
1 TGGTGATATTTTTGTAATTATTT-TTAAAA
* * *
98067 GGGTGATAATTGTGTAA
1 TGGTGATATTTTTGTAA
98084 AATGGTTGAT
Statistics
Matches: 155, Mismatches: 32, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
28 71 0.46
29 43 0.28
30 18 0.12
31 23 0.15
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (29 bp):
TGGTGATATTTTTGTAATTATTTTTAAAA
Found at i:99222 original size:117 final size:117
Alignment explanation
Indices: 99011--99347 Score: 512
Period size: 117 Copynumber: 2.9 Consensus size: 117
99001 GAAAATATTT
* *
99011 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGAGTGCATGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTGTGCAGGTGGGTGTATGGTTCTGG
*
99076 GGAACCTACACATTTTAGTAATCGGAGTGATTGGATGGGGAATTTATTACCG
66 GGAACCTACACATTTTAGTAATCGGAGTGATTGGATGGGGAAGTTATTACCG
*
99128 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTGTGCAGGTGAGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTGTGCAGGTGGGTGTATGGTTCTGG
* *
99193 GGAACCTGCACATTTTAGTAATCGAAGTGATTGGATGGGGAAGTTATTACCG
66 GGAACCTACACATTTTAGTAATCGGAGTGATTGGATGGGGAAGTTATTACCG
* ** * * * *
99245 TAGGCTCCTCGGCTTTGTGCTTAGAGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTGTGCAGGTGGGTGTATGGTTCTGG
* * * * *
99310 AGAACATACAAATTCTAGTAATCGGAGTGATTAGATGG
66 GGAACCTACACATTTTAGTAATCGGAGTGATTGGATGG
99348 AAATAGTGTT
Statistics
Matches: 199, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 199 1.00
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.33
Consensus pattern (117 bp):
CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTGTGCAGGTGGGTGTATGGTTCTGG
GGAACCTACACATTTTAGTAATCGGAGTGATTGGATGGGGAAGTTATTACCG
Found at i:106115 original size:32 final size:32
Alignment explanation
Indices: 106079--106157 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 32
106069 ATCATCCAAT
* *
106079 GTGATGACGTGGTGTATCTCACATCACCTAAG
1 GTGATGACGTGATATATCTCACATCACCTAAG
* * * * * *
106111 GTGATGTCGTAATATATGTCTCATCTCCTAAT
1 GTGATGACGTGATATATCTCACATCACCTAAG
106143 GTGATGACGTGATAT
1 GTGATGACGTGATAT
106158 GTATCACGTC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (32 bp):
GTGATGACGTGATATATCTCACATCACCTAAG
Found at i:107294 original size:26 final size:27
Alignment explanation
Indices: 107264--107326 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 27
107254 TTTTTTTCCT
* *
107264 TAAAATCTTATAAATTTATT-CTCATC
1 TAAAATCTTATAAATTCATTCCTAATC
* *
107290 TAAAATTTTATAAATTCGTTCCTAATC
1 TAAAATCTTATAAATTCATTCCTAATC
107317 TAAAATCTTA
1 TAAAATCTTA
107327 CTTCTACCCC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (27 bp):
TAAAATCTTATAAATTCATTCCTAATC
Found at i:109088 original size:112 final size:112
Alignment explanation
Indices: 108888--109353 Score: 671
Period size: 112 Copynumber: 4.1 Consensus size: 112
108878 TTGTCGGTTT
* * * * *
108888 GTGTCGATATTTTATAAAAATATATTGATCCATAATAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
108953 GGTCTATAAATGATAAACCAGGTAAAACGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * * **
109000 ATATCGATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATAACAAAATT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
109065 AGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
**
109112 GTGTCGATACTTTATAAAAATGTATCGATCCACCATATTAATATAACAGGTAAAAAAATGACAAA
1 GTGTCGATACTTTATAAAAATGTATCGAT---CCATAACAATATAACAGGTAAAAAAATGACAAA
**
109177 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACTAGATATATTGAAA
63 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
109227 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * * *
109292 GGTCTATAAATAACAAAACAGATAAAGTGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
109339 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
109354 TATAAGTATC
Statistics
Matches: 313, Mismatches: 38, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
112 211 0.67
115 102 0.33
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:109326 original size:227 final size:224
Alignment explanation
Indices: 108888--109353 Score: 689
Period size: 227 Copynumber: 2.1 Consensus size: 224
108878 TTGTCGGTTT
* * *
108888 GTGTCGATATTTTATAAAAATATATTGATCCATAATAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACC
* * *
108953 GGTCTATAAATGATAAACCAGGTAAAACGCTACCGGATATATTGAAAATATCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAATATCGATACTTTATAAA
* ** * *
109018 AATGTATCGATCTATAACAATATAACAGGTAAAAAAATAACAAAATTAGTTTATAAATGACAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCAGTCTATAAATAACAAAA
*
109083 CAGGTAAAGCGCTACCGGATATATTGAAA
196 CAGATAAAGCGCTACCGGATATATTGAAA
* *
109112 GTGTCGATACTTTATAAAAATGTATCGATCCACCATATTAATATAACAGGTAAAAAAATGACAAA
1 GTGTCGATACTTTATAAAAATATATCGAT---CCATAATAATATAACAGGTAAAAAAATGACAAA
* * * *
109177 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACTAGATATATTGAAAGTGTCGATACTTTAT
63 ACCGGTCTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAATATCGATACTTTAT
* * *
109242 AAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACCGGTCTATAAATAACA
128 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCAGTCTATAAATAACA
* * *
109307 AAACAGATAAAGTGCTACCGGATATGTTGATA
193 AAACAGATAAAGCGCTACCGGATATATTGAAA
109339 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
109354 TATAAGTATC
Statistics
Matches: 215, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
224 26 0.12
227 189 0.88
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAATATCGATACTTTATAAA
AATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCAGTCTATAAATAACAAAA
CAGATAAAGCGCTACCGGATATATTGAAA
Found at i:109531 original size:182 final size:182
Alignment explanation
Indices: 109224--109679 Score: 736
Period size: 182 Copynumber: 2.5 Consensus size: 182
109214 AGATATATTG
* *
109224 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** * * * *
109289 ACCGGTCTATAAATAACAAAACAGATAAAGTGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
** * * * *
109354 TATAAGTATCGACACTTTTGGAATTTAAAATAGAAGAAGTTGTAGCACTAAT
131 TATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
109406 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
109471 ACCGGTCTCGAAATGACAAAACCGGTAAAG-GACTACCGGATATGTTGAAAGTGTCGATACTTTA
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGTG-CTACCGGATATGTTGAAAGTGTCGATACTTTA
*
109535 TTATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
130 TTATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
*
109588 AAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
109653 ATCGGT-TCGAAATGACAAAACCGGTAA
66 ACCGGTCTCGAAATGACAAAACCGGTAA
109680 TAAAAAAGTG
Statistics
Matches: 256, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
181 22 0.09
182 234 0.91
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
TATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
Found at i:113032 original size:2 final size:2
Alignment explanation
Indices: 113025--113087 Score: 76
Period size: 2 Copynumber: 32.5 Consensus size: 2
113015 ACCACAATAA
* * * *
113025 AT AT AT AT AT TT AT AT GT -T GT AT -T AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113065 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
113088 AGTATTATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:117500 original size:98 final size:91
Alignment explanation
Indices: 117261--117520 Score: 254
Period size: 93 Copynumber: 2.7 Consensus size: 91
117251 GCATTATAAT
* * * *
117261 ATTAT-ATATACAATAAAACTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCTCGGCTTTAT
1 ATTATAATATACAAT-GAACTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCC-CGGCTTTAT
* **
117325 GGATAGATTTAACCAACCAGATAAGGTG
64 GGATAAATTTAACCAACCAGATAAGGCA
* * * *
117353 ATTATAATATGCAATGAAGCTTGAGTTGTCCTTCTAGAGAAATTGGTTAAACGCCACGGCTTTAT
1 ATTATAATATACAATGAA-CTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCC-CGGCTTTAT
* * * *
117418 GGATAAAATTTAGCTAGCCTGATAAAGGCA
64 GGAT-AAATTTAACCAACCAGAT-AAGGCA
117448 ATTATAATATCTATACAATGATA-TTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTTGGC
1 ATTAT-A-A--TATACAATGA-ACTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCC--GGC
117512 TTTATGGAT
59 TTTATGGAT
117521 TCAGCTAGCC
Statistics
Matches: 139, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
92 7 0.05
93 53 0.38
94 13 0.09
95 9 0.06
96 1 0.01
97 2 0.01
98 32 0.23
99 21 0.15
100 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (91 bp):
ATTATAATATACAATGAACTTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCGGCTTTATGG
ATAAATTTAACCAACCAGATAAGGCA
Found at i:119065 original size:19 final size:19
Alignment explanation
Indices: 119041--119089 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
119031 ACCATGAACA
119041 TAGGGGAATCGATTCCTTG
1 TAGGGGAATCGATTCCTTG
119060 TAGGGGAATCGATTCCTTG
1 TAGGGGAATCGATTCCTTG
119079 TAGGGGAATCG
1 TAGGGGAATCG
119090 TACCCCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.14, G:0.35, T:0.29
Consensus pattern (19 bp):
TAGGGGAATCGATTCCTTG
Found at i:119730 original size:162 final size:161
Alignment explanation
Indices: 119447--119772 Score: 557
Period size: 162 Copynumber: 2.0 Consensus size: 161
119437 AATACAATTC
* *
119447 ATGCATGATTTTCAATGTCAAATTCAAAAATGACATAAATCATTTTACCGTGATCAAAATAATAA
1 ATGCATGATTTTCAATGTCAAATTCAAAAATGACATAAATAATTTTACCATGATCAAAATAATAA
119512 AATCTCTTACTATGTGTCTTCTCTAGACACTCTAGTACTACCTAATATTGCAGTTGCTAGACTCT
66 AATCTCTTACTATGTGTCTTCTCTAGACACTCTAG-A-TACCTAATATTGCAGTTGCTAGACTCT
*
119577 ATGGCTTGCCATTAATACCACTGATCCTCAATA
129 ATGGCATGCCATTAATACCACTGATCCTCAATA
*
119610 ATGCATGA-TTTCAATGTCAAATTCAAAAATGCCATAAAATAATTTTACCATGATCAAAATAATA
1 ATGCATGATTTTCAATGTCAAATTCAAAAATGACAT-AAATAATTTTACCATGATCAAAAT-A-A
119674 TAAAATCTCTTACTATGTGTCTTCTCTAGACACTCTAG-TACCTAATATTGCAGTTGCTAGACTC
63 TAAAATCTCTTACTATGTGTCTTCTCTAGACACTCTAGATACCTAATATTGCAGTTGCTAGACTC
119738 TATGGCATGCCATTAATACCACTGATCCTCAATA
128 TATGGCATGCCATTAATACCACTGATCCTCAATA
119772 A
1 A
119773 CATACTTGGG
Statistics
Matches: 156, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
162 86 0.55
163 30 0.19
164 1 0.01
165 39 0.25
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.34
Consensus pattern (161 bp):
ATGCATGATTTTCAATGTCAAATTCAAAAATGACATAAATAATTTTACCATGATCAAAATAATAA
AATCTCTTACTATGTGTCTTCTCTAGACACTCTAGATACCTAATATTGCAGTTGCTAGACTCTAT
GGCATGCCATTAATACCACTGATCCTCAATA
Found at i:121892 original size:34 final size:35
Alignment explanation
Indices: 121780--121894 Score: 160
Period size: 36 Copynumber: 3.2 Consensus size: 35
121770 TAATTTACTC
121780 AAAACAAAGTTTTTTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA--TTTTTCTCTCTTGAGACAGTTTCTCTT
*
121817 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGT
1 AAAACAAATTTT-TCTCTCTTGAGACAGTTTCTCTT
* *
121853 AAAACAAA-TTTTCTCTCTTGAGATAGTTTCCCTT
1 AAAACAAATTTTTCTCTCTTGAGACAGTTTCTCTT
*
121887 GAAACAAA
1 AAAACAAA
121895 AACTTTGAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.38
35 7 0.10
36 30 0.42
37 8 0.11
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (35 bp):
AAAACAAATTTTTCTCTCTTGAGACAGTTTCTCTT
Found at i:121954 original size:17 final size:17
Alignment explanation
Indices: 121929--121964 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
121919 ACAAATTTCG
121929 TCTCCCTTGAGATAGTT
1 TCTCCCTTGAGATAGTT
*
121946 TCTCTCTTGAGATAGTT
1 TCTCCCTTGAGATAGTT
121963 TC
1 TC
121965 CCTTGAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (17 bp):
TCTCCCTTGAGATAGTT
Found at i:122045 original size:82 final size:82
Alignment explanation
Indices: 121862--122030 Score: 338
Period size: 82 Copynumber: 2.1 Consensus size: 82
121852 TAAAACAAAT
121862 TTTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAATTT
1 TTTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAATTT
121927 CGTCTCCCTTGAGATAG
66 CGTCTCCCTTGAGATAG
121944 TTTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAATTT
1 TTTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAATTT
122009 CGTCTCCCTTGAGATAG
66 CGTCTCCCTTGAGATAG
122026 TTTCT
1 TTTCT
122031 TTTGGAACTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 87 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (82 bp):
TTTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAATTT
CGTCTCCCTTGAGATAG
Found at i:122089 original size:36 final size:36
Alignment explanation
Indices: 121994--122286 Score: 183
Period size: 36 Copynumber: 8.3 Consensus size: 36
121984 AATCTGTTTT
* * *
121994 CCTTGAAAC-AAATTTCGTCTCCCTTGAGATAGTTTC
1 CCTTGAAACAAAATTT-GTCTCTCTTGAGACAATTTC
** * ** * *
122030 TTTTGGAACTAAGTTTTGGCTCTCTTTAGACAATTTC
1 CCTTGAAAC-AAAATTTGTCTCTCTTGAGACAATTTC
* *
122067 TCTTGAAACAAAATTTGTCTCTCTTGAGATAATTTC
1 CCTTGAAACAAAATTTGTCTCTCTTGAGACAATTTC
* * *
122103 CCTTGAATCAAATTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAAATTTGTCTCTCTTGAGACAATTTC
* * *
122139 CCTTGAAACAAAA------TCT-TTGA-ATATGTTTT
1 CCTTGAAACAAAATTTGTCTCTCTTGAGACA-ATTTC
* * **
122168 CCTTTAAAC-AAATTTCGTCTCTCTCGAGACTGTTTC
1 CCTTGAAACAAAATTT-GTCTCTCTTGAGACAATTTC
** * ** * *
122204 TTTTGGAACTAAGTTTTATCTCTCTTGAGACAGTTTC
1 CCTTGAAAC-AAAATTTGTCTCTCTTGAGACAATTTC
**
122241 CCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTC
1 CCTTGAAACAAAATTTGTCTCTCTTGAGACAATTTC
*
122277 TCTTGAAACA
1 CCTTGAAACA
122287 CCAACCTTTG
Statistics
Matches: 197, Mismatches: 46, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
28 5 0.03
29 16 0.08
30 3 0.02
35 3 0.02
36 116 0.59
37 46 0.23
38 8 0.04
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
CCTTGAAACAAAATTTGTCTCTCTTGAGACAATTTC
Found at i:122144 original size:174 final size:174
Alignment explanation
Indices: 121946--122283 Score: 525
Period size: 174 Copynumber: 1.9 Consensus size: 174
121936 TGAGATAGTT
* *
121946 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCTTGAAACAAATTTCG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATATGTTTTCCTTGAAACAAATTTCG
* * * *
122011 TCTCCCTTGAGA-TAGTTTCTTTTGGAACTAAGTTTTGGCTCTCTTTAGACAATTTCTCTTGAAA
66 TCTCCCTCGAGACT-GTTTCTTTTGGAACTAAGTTTTAGCTCTCTTGAGACAATTTCCCTTGAAA
*
122075 CAAAATTTGTCTCTCTTGAGATAATTTCCCTTGAATCAAATTTTG
130 CAAAATTTGTCTCTCTTGAGACAATTTCCCTTGAATCAAATTTTG
* *
122120 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTTAAACAAATTTCG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATATGTTTTCCTTGAAACAAATTTCG
* * *
122185 TCTCTCTCGAGACTGTTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGACAGTTTCCCTTGAAAC
66 TCTCCCTCGAGACTGTTTCTTTTGGAACTAAGTTTTAGCTCTCTTGAGACAATTTCCCTTGAAAC
** *
122250 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAA
131 AAAATTTGTCTCTCTTGAGACAATTTCCCTTGAA
122284 ACACCAACCT
Statistics
Matches: 148, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
174 147 0.99
175 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (174 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATATGTTTTCCTTGAAACAAATTTCG
TCTCCCTCGAGACTGTTTCTTTTGGAACTAAGTTTTAGCTCTCTTGAGACAATTTCCCTTGAAAC
AAAATTTGTCTCTCTTGAGACAATTTCCCTTGAATCAAATTTTG
Found at i:122272 original size:21 final size:20
Alignment explanation
Indices: 122214--122272 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
122204 TTTTGGAACT
122214 AAGTTTTATCTCTCTTGAGAC
1 AAGTTTT-TCTCTCTTGAGAC
*
122235 -AG--TTTC-C-CTTGAAAC
1 AAGTTTTTCTCTCTTGAGAC
122250 AAGTTTTGTCTCTCTTGAGAC
1 AAGTTTT-TCTCTCTTGAGAC
122271 AA
1 AA
122273 TTTCTCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.23
16 3 0.10
17 2 0.07
18 4 0.13
19 2 0.07
20 3 0.10
21 9 0.30
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (20 bp):
AAGTTTTTCTCTCTTGAGAC
Found at i:124019 original size:16 final size:15
Alignment explanation
Indices: 123977--124026 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
123967 TATTTAAATA
123977 TATATATTATATATTG
1 TATAT-TTATATATTG
123993 TATATTT-TATACTT-
1 TATATTTATATA-TTG
124007 TATCATTTATATA-TG
1 TAT-ATTTATATATTG
124022 TATAT
1 TATAT
124027 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 10 0.33
15 11 0.37
16 9 0.30
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (15 bp):
TATATTTATATATTG
Found at i:124209 original size:31 final size:31
Alignment explanation
Indices: 124155--124214 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
124145 TTTATTTATT
* *
124155 TATTTCTAATTTCTTTTTCTTTTT-CTTTTC
1 TATTTCTAATTTCTCTTTATTTTTACTTTTC
*
124185 TATTTTTAATATTCTCTTTATTTTTACTTT
1 TATTTCTAAT-TTCTCTTTATTTTTACTTT
124215 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.36
31 12 0.48
32 4 0.16
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (31 bp):
TATTTCTAATTTCTCTTTATTTTTACTTTTC
Found at i:124269 original size:19 final size:19
Alignment explanation
Indices: 124230--124268 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
124220 TATTTCCTTG
124230 TTGTTCATTTTATTGTATT
1 TTGTTCATTTTATTGTATT
*
124249 TTGTT-ATTTTATTTTATT
1 TTGTTCATTTTATTGTATT
124267 TT
1 TT
124269 TATTTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (19 bp):
TTGTTCATTTTATTGTATT
Found at i:124435 original size:9 final size:9
Alignment explanation
Indices: 124302--124427 Score: 64
Period size: 9 Copynumber: 13.7 Consensus size: 9
124292 GATTGTCCTC
124302 ATTTTCTTT
1 ATTTTCTTT
*
124311 A-TTTATTT
1 ATTTTCTTT
124319 ATTTTCTTT
1 ATTTTCTTT
*
124328 ATTTGT-ATT
1 ATTT-TCTTT
*
124337 -TTTACTTTT
1 ATTTTC-TTT
* *
124346 GTTCTTTTTT
1 ATT-TTCTTT
124356 ATTTTTCTTT
1 A-TTTTCTTT
*
124366 ATCTTT-TTC
1 AT-TTTCTTT
*
124375 ATCTTCATGTT
1 ATTTTC-T-TT
124386 ATTTTCTTT
1 ATTTTCTTT
124395 A-TTTCTTTT
1 ATTTTC-TTT
* *
124404 GTTTTTTTT
1 ATTTTCTTT
124413 ATTTTCTTT
1 ATTTTCTTT
124422 ATTTTC
1 ATTTTC
124428 ATTTTTTTAT
Statistics
Matches: 87, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
8 16 0.18
9 42 0.48
10 20 0.23
11 9 0.10
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (9 bp):
ATTTTCTTT
Found at i:124435 original size:18 final size:17
Alignment explanation
Indices: 124384--124435 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
124374 CATCTTCATG
*
124384 TTATTTTCTTTATTTCTT
1 TTATTTTCTTTTTTTC-T
* *
124402 TTGTTTTTTTTATTTTCT
1 TTATTTTCTTT-TTTTCT
124420 TTATTTTCATTTTTTT
1 TTATTTTC-TTTTTTT
124436 ATCTGACACT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.81
Consensus pattern (17 bp):
TTATTTTCTTTTTTTCT
Found at i:124435 original size:27 final size:27
Alignment explanation
Indices: 124302--124435 Score: 80
Period size: 27 Copynumber: 4.9 Consensus size: 27
124292 GATTGTCCTC
* *
124302 ATTTTCTTTATTT-ATTTATTTTCTTT
1 ATTTTCTTTATTTCATTTGTTTTTTTT
* * *
124328 ATTTGTATTT-TTACTTTTGTTCTTTTTT
1 ATTT-TCTTTATTTCATTTGTT-TTTTTT
* * *
124356 ATTTTTCTTTATCTT--TTTCATCTTCATGTT
1 A-TTTTCTTTAT-TTCATTT-GT-TT-TTTTT
*
124386 ATTTTCTTTATTTCTTTTGTTTTTTTT
1 ATTTTCTTTATTTCATTTGTTTTTTTT
124413 ATTTTCTTTATTTTCATTT-TTTT
1 ATTTTCTTTA-TTTCATTTGTTTT
124436 ATCTGACACT
Statistics
Matches: 82, Mismatches: 14, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
26 6 0.07
27 26 0.32
28 24 0.29
29 17 0.21
30 9 0.11
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (27 bp):
ATTTTCTTTATTTCATTTGTTTTTTTT
Found at i:130508 original size:21 final size:21
Alignment explanation
Indices: 130482--130522 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
130472 GATTTTTATA
130482 TTATTTT-TAATAAATTTATTT
1 TTATTTTCTAA-AAATTTATTT
*
130503 TTATTTTCTAAAATTTTATT
1 TTATTTTCTAAAAATTTATT
130523 AATGCACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTTTCTAAAAATTTATTT
Found at i:135017 original size:14 final size:16
Alignment explanation
Indices: 134986--135017 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
134976 ATGTTATATG
134986 TATATATTATTTATAA
1 TATATATTATTTATAA
135002 TATATATT-TTTA-AA
1 TATATATTATTTATAA
135016 TA
1 TA
135018 CTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 4 0.25
16 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATATTATTTATAA
Found at i:135182 original size:19 final size:19
Alignment explanation
Indices: 135158--135195 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
135148 TTAATATTTA
135158 AATTTTTAAATTTTAAAAT
1 AATTTTTAAATTTTAAAAT
**
135177 AATTTTTATTTTTTAAAAT
1 AATTTTTAAATTTTAAAAT
135196 TAAATAAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTTTAAATTTTAAAAT
Found at i:135516 original size:13 final size:13
Alignment explanation
Indices: 135498--135550 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
135488 AACCTAATTT
135498 TTTATAAAATATA
1 TTTATAAAATATA
* * * *
135511 TTTATATACTGTTT
1 TTTATAAAAT-ATA
135525 TTTATAAAATATA
1 TTTATAAAATATA
*
135538 TTTATAGAATATA
1 TTTATAAAATATA
135551 GAACATAAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
13 21 0.70
14 9 0.30
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (13 bp):
TTTATAAAATATA
Found at i:139116 original size:23 final size:23
Alignment explanation
Indices: 139090--139137 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
139080 ATAAAGTACA
*
139090 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
139113 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
139136 AT
1 AT
139138 TTAACTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:139842 original size:333 final size:335
Alignment explanation
Indices: 139177--139845 Score: 1279
Period size: 333 Copynumber: 2.0 Consensus size: 335
139167 TTATACCGAT
139177 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
*
139242 TCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
139307 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
131 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
*
139372 TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCATAACGTAAAAAATAAATCATT
196 TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCATAACGAAAAAAATAAATCATT
*
139437 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACTTTAAATTAATGTT
261 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
139502 TTCCACAGTG
326 TTCCACAGTG
*
139512 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAATGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
139577 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
139641 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
131 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
*
139706 TAAAATATTATTTAGAA-TTTTAATTTAATAATAATATATATCGTAACGAAAAAAATAAATCATT
196 TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCATAACGAAAAAAATAAATCATT
139770 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
261 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
139835 TTCCACAGTG
326 TTCCACAGTG
139845 A
1 A
139846 AAAAAGTATG
Statistics
Matches: 329, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
333 120 0.36
334 108 0.33
335 101 0.31
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (335 bp):
AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCATAACGAAAAAAATAAATCATT
AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
TTCCACAGTG
Found at i:139924 original size:23 final size:23
Alignment explanation
Indices: 139898--139960 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
139888 ATATAACCAC
139898 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
139921 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
139944 TACCTATTACATCATAT
1 TACCTATTACATTATAT
139961 GTTACCTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:140415 original size:39 final size:39
Alignment explanation
Indices: 140361--140447 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
140351 TCAAGTTGTA
*
140361 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
140400 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
140439 GATTTTGAT
1 GATTTTGAT
140448 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:140727 original size:18 final size:18
Alignment explanation
Indices: 140704--140740 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
140694 CGAAATATAT
140704 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
140722 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
140740 A
1 A
140741 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:141511 original size:23 final size:23
Alignment explanation
Indices: 141448--141520 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
141438 ACACTTTACA
* *
141448 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
141471 ATATAAACGATACATATTACATT
1 ATATAAACGCTACCTATTACATT
** *
141494 ATATAAGGGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
141517 ATAT
1 ATAT
141521 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:141922 original size:25 final size:25
Alignment explanation
Indices: 141865--141930 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
141855 CACTCAAAAG
*
141865 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
141890 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
141915 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
141931 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:144706 original size:183 final size:183
Alignment explanation
Indices: 144394--145651 Score: 2282
Period size: 183 Copynumber: 6.9 Consensus size: 183
144384 TTAAAATTAC
* *
144394 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
144459 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
144524 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
144577 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
144642 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
144707 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
144760 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* * *
144825 ATTATAAAGTGTCGATATAAGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
144890 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
144943 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
145008 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAATCAGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
145073 ATATTACAAAATTATTTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
145126 CAACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
145191 ATTAAAAAATGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
145256 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
145309 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
145374 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
145439 ATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
145492 CGACACTTTTGTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
145557 ATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * * **
145622 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTATCTATTACATTATAAT
145652 ATGTTGAAAG
Statistics
Matches: 1035, Mismatches: 40, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 1035 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:147075 original size:3 final size:3
Alignment explanation
Indices: 147067--147120 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
147057 ACTTGTTTGG
* * *
147067 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
147115 TTC ATC
1 ATC ATC
147121 GTCAGCTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:147084 original size:12 final size:12
Alignment explanation
Indices: 147067--147124 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
147057 ACTTGTTTGG
* *
147067 ATCATCATCTTC
1 ATCATCGTCATC
*
147079 ATCATCATCATC
1 ATCATCGTCATC
147091 ATCATCGTCATC
1 ATCATCGTCATC
147103 ATCATCGTCATC
1 ATCATCGTCATC
*
147115 TTCATCGTCA
1 ATCATCGTCA
147125 GCTTCATCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (12 bp):
ATCATCGTCATC
Found at i:147090 original size:18 final size:18
Alignment explanation
Indices: 147067--147135 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
147057 ACTTGTTTGG
* *
147067 ATCATCATCTTCATCATC
1 ATCATCATCATCTTCATC
*
147085 ATCATCATCATCGTCATC
1 ATCATCATCATCTTCATC
*
147103 ATCATCGTCATCTTCATC
1 ATCATCATCATCTTCATC
* * *
147121 GTCAGCTTCATCTTC
1 ATCATCATCATCTTC
147136 TGCGACCGCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (18 bp):
ATCATCATCATCTTCATC
Found at i:147129 original size:12 final size:12
Alignment explanation
Indices: 147080--147132 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
147070 ATCATCTTCA
* *
147080 TCATCATCATCA
1 TCATCGTCATCT
*
147092 TCATCGTCATCA
1 TCATCGTCATCT
147104 TCATCGTCATCT
1 TCATCGTCATCT
*
147116 TCATCGTCAGCT
1 TCATCGTCATCT
147128 TCATC
1 TCATC
147133 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:148989 original size:197 final size:198
Alignment explanation
Indices: 148593--150149 Score: 2991
Period size: 197 Copynumber: 7.9 Consensus size: 198
148583 TTTAAATTAG
148593 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
148658 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
148722 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
148787 AAA
196 AAA
148790 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
148855 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
148920 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
148984 AAA
196 AAA
148987 TATCGAC-C-AACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
149050 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
149115 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
149180 AAA
196 AAA
*
149183 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCGCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
149248 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
149313 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
149377 AAA
196 AAA
149380 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
149445 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
149510 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
149575 AAA
196 AAA
149578 TATCGACAC-AACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
149642 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
149707 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
149772 AAA
196 AAA
149775 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
*
149840 ATTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
149905 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
149970 AAAA
195 AAAA
*
149974 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
150039 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
150104 CGACACTTTTTATATATGGATCGATACTTTATGGGTGCACCCTGTT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
150150 GGCCATATTG
Statistics
Matches: 1342, Mismatches: 11, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
195 181 0.13
196 14 0.01
197 488 0.36
198 479 0.36
199 180 0.13
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:149775 original size:395 final size:395
Alignment explanation
Indices: 148593--150149 Score: 2996
Period size: 395 Copynumber: 3.9 Consensus size: 395
148583 TTTAAATTAG
148593 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
148658 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
148722 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
148787 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGT
148852 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
148917 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
148982 AAAAA
391 AAAAA
148987 TATCGAC-C-AACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
149050 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
149115 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
149180 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCGCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGT
149245 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
149310 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
149375 AAAAA
391 AAAAA
149380 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
149445 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
149510 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
149575 AAATATCGACAC-AACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGT
149639 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
*
149704 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-
149769 AAAAAA
390 AAAAAA
149775 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
*
149840 ATTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
149905 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
*
149970 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGG
150035 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
150100 GGATCGACACTTTTTATATATGGATCGATACTTTATGGGTGCACCCTGTT
325 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
150150 GGCCATATTG
Statistics
Matches: 1147, Mismatches: 10, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
392 73 0.06
393 317 0.28
394 187 0.16
395 391 0.34
396 16 0.01
397 163 0.14
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (395 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
AAAAA
Found at i:150314 original size:19 final size:19
Alignment explanation
Indices: 150268--150316 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
150258 TTATATTCAC
*
150268 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
150287 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
150306 ATACAAAATTA
1 ATACAAAATTA
150317 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:152153 original size:32 final size:32
Alignment explanation
Indices: 152111--152171 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
152101 TTAATATCAC
*
152111 CCCTTAACACCCCAACTTCTTTCACCACTTCA
1 CCCTCAACACCCCAACTTCTTTCACCACTTCA
* *
152143 CCCTCAACACCTCTACTTCTTTCACCACT
1 CCCTCAACACCCCAACTTCTTTCACCACT
152172 CCATCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.30
Consensus pattern (32 bp):
CCCTCAACACCCCAACTTCTTTCACCACTTCA
Found at i:152245 original size:21 final size:21
Alignment explanation
Indices: 152205--152269 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
152195 CCCCTTATGC
* *
152205 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
152226 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
152247 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
152268 CT
1 CT
152270 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:154521 original size:17 final size:18
Alignment explanation
Indices: 154499--154541 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
154489 ATATATCCGG
154499 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
154516 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
154536 TATCAT
1 TATCAT
154542 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:154559 original size:20 final size:19
Alignment explanation
Indices: 154504--154550 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
154494 TCCGGTATCA
154504 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
154523 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
154544 TTTTACC
1 TTTTACC
154551 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:157270 original size:3 final size:3
Alignment explanation
Indices: 157262--157287 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
157252 ACGAGGTAAA
157262 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
157288 AAACAACGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:158562 original size:14 final size:14
Alignment explanation
Indices: 158543--158584 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
158533 AATCATTGTT
158543 ATAAATTTAATTTA
1 ATAAATTTAATTTA
158557 ATAAATTTAATTTA
1 ATAAATTTAATTTA
158571 ATAAATTTAATTTA
1 ATAAATTTAATTTA
158585 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAAATTTAATTTA
Found at i:179522 original size:31 final size:31
Alignment explanation
Indices: 179483--179554 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
179473 AATATTACAA
179483 AGACTTAACTTTAATTCCAACAATCCCCATC
1 AGACTTAACTTTAATTCCAACAATCCCCATC
*
179514 AGATTTAACTTTAATTCCAACAATCCCCATC
1 AGACTTAACTTTAATTCCAACAATCCCCATC
179545 AGACTTAACT
1 AGACTTAACT
179555 AAACAAAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (31 bp):
AGACTTAACTTTAATTCCAACAATCCCCATC
Found at i:180216 original size:26 final size:26
Alignment explanation
Indices: 180187--180236 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
180177 TTAGAACATA
*
180187 GATGAGAAGGAAC-CTTCTCAGAATTG
1 GATGAG-AGGAACTCTTCCCAGAATTG
*
180213 GATGAGCGGAACTCTTCCCAGAAT
1 GATGAGAGGAACTCTTCCCAGAAT
180237 CTCTTGAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (26 bp):
GATGAGAGGAACTCTTCCCAGAATTG
Found at i:184780 original size:22 final size:22
Alignment explanation
Indices: 184739--184796 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
184729 TAATATCAAT
184739 TAAAATATATT-AC--T-TTTA
1 TAAAATATATTGACTATATTTA
184757 TAAAA-ATAATTGACTATATTTA
1 TAAAATAT-ATTGACTATATTTA
*
184779 TAAAATATATTGATTATA
1 TAAAATATATTGACTATA
184797 ACATAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 2 0.06
18 8 0.24
19 2 0.06
21 1 0.03
22 18 0.55
23 2 0.06
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (22 bp):
TAAAATATATTGACTATATTTA
Found at i:185117 original size:2 final size:2
Alignment explanation
Indices: 185110--185134 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
185100 CAAATAAAAT
185110 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 T
185135 TTGAGTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:186583 original size:21 final size:22
Alignment explanation
Indices: 186546--186590 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
186536 TAAATAGAAT
186546 TAGTGATTTCTTTTAAAAAAAA
1 TAGTGATTTCTTTTAAAAAAAA
186568 TAGTGATTTC-TTTAAAAAAAA
1 TAGTGATTTCTTTTAAAAAAAA
186589 TA
1 TA
186591 ATACCTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (22 bp):
TAGTGATTTCTTTTAAAAAAAA
Found at i:186599 original size:20 final size:21
Alignment explanation
Indices: 186557--186599 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
186547 AGTGATTTCT
* **
186557 TTTAAAAAAAATAGTGATTTC
1 TTTAAAAAAAATAATGACCTC
186578 TTTAAAAAAAATAAT-ACCTC
1 TTTAAAAAAAATAATGACCTC
186598 TT
1 TT
186600 ATATCAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (21 bp):
TTTAAAAAAAATAATGACCTC
Found at i:189630 original size:2 final size:2
Alignment explanation
Indices: 189623--189650 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
189613 GATAATTTTA
189623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
189651 TAAAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:190360 original size:2 final size:2
Alignment explanation
Indices: 190353--190411 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
190343 ATTTACGAAT
190353 TA TA TA TA TA TA 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 TA TA TA TA TA TA
190395 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
190412 CATTTTGCCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:195312 original size:24 final size:23
Alignment explanation
Indices: 195283--195376 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 23
195273 ATCGAGGTGT
*
195283 CACGTAGAATTTGTCCCGAAGGAC
1 CACGTAGAA-TTATCCCGAAGGAC
* * *
195307 CGCGTAGAATTTGTCCCTAAGGAC
1 CACGTAGAA-TTATCCCGAAGGAC
* *
195331 CACGTAGAAGTATCCCGAAGGAT
1 CACGTAGAATTATCCCGAAGGAC
*
195354 CACATA-AATTATCCCGAAGGAC
1 CACGTAGAATTATCCCGAAGGAC
195376 C
1 C
195377 GCATAGAACC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 15 0.25
23 15 0.25
24 30 0.50
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (23 bp):
CACGTAGAATTATCCCGAAGGAC
Found at i:205856 original size:21 final size:21
Alignment explanation
Indices: 205805--205867 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 21
205795 GATTCTCCTG
205805 TGGGGGGAATCGGTTCTCCTTCA
1 TGGGGGGAATCGGTTC-CC-TCA
**
205828 AAGGGGGAATCGGTTCCCTCA
1 TGGGGGGAATCGGTTCCCTCA
*
205849 TGGGGGG-ATCGATTCCCTC
1 TGGGGGGAATCGGTTCCCTC
205868 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 11 0.31
21 8 0.23
22 2 0.06
23 14 0.40
ACGTcount: A:0.16, C:0.24, G:0.35, T:0.25
Consensus pattern (21 bp):
TGGGGGGAATCGGTTCCCTCA
Found at i:205859 original size:20 final size:21
Alignment explanation
Indices: 205805--205867 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
205795 GATTCTCCTG
205805 TGGGGGGAATCGGTTCTCCTTCAA
1 TGGGGGG-ATCGGTTC-CC-TCAA
* *
205829 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
205849 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
205868 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 2 0.06
23 8 0.24
24 5 0.15
ACGTcount: A:0.16, C:0.24, G:0.35, T:0.25
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:223345 original size:21 final size:20
Alignment explanation
Indices: 223279--223358 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 20
223269 TTGGTGCAGA
* *
223279 GGGAATCGA-TCCCCCCATG
1 GGGAACCGATTCCCCCCAAG
*
223298 AGGGAACCGATTCCCCTTCGAAG
1 -GGGAACCGATTCCCC--CCAAG
223321 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCA-AG
* *
223342 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
223359 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 10 0.20
21 22 0.44
22 15 0.30
23 3 0.06
ACGTcount: A:0.24, C:0.38, G:0.25, T:0.14
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCAAG
Found at i:229966 original size:2 final size:2
Alignment explanation
Indices: 229955--230004 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
229945 AATTTATAAA
229955 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
229996 AT AT AT AT A
1 AT AT AT AT A
230005 CATTAAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:236714 original size:37 final size:37
Alignment explanation
Indices: 236641--236715 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
236631 GTTGAAAAAT
* *
236641 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
236678 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
236715 A
1 A
236716 AATATTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:248216 original size:24 final size:23
Alignment explanation
Indices: 248182--248226 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
248172 TGTTTGGTGA
248182 TAATATATAATAGTCTGACAGTCG
1 TAATATATAATA-TCTGACAGTCG
* *
248206 TAATATCTAATATTTGACAGT
1 TAATATATAATATCTGACAGT
248227 GGAGATGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (23 bp):
TAATATATAATATCTGACAGTCG
Found at i:259557 original size:24 final size:23
Alignment explanation
Indices: 259513--259559 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
259503 ATACTGATAG
*
259513 ATTTTTAAAGTCATTTCATAAAT
1 ATTTTTAAAATCATTTCATAAAT
*
259536 ATTTTTAAAATGATTT-ATATAAT
1 ATTTTTAAAATCATTTCATA-AAT
259559 A
1 A
259560 AAAATGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTTTTAAAATCATTTCATAAAT
Found at i:264247 original size:9 final size:9
Alignment explanation
Indices: 264233--264283 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
264223 TTTTTTCTTC
264233 TATTTTTTT
1 TATTTTTTT
*
264242 TATTTTTGT
1 TATTTTTTT
264251 TATTTTTTT
1 TATTTTTTT
* *
264260 AATTTCTTT
1 TATTTTTTT
*
264269 TATTATTTT
1 TATTTTTTT
*
264278 TCTTTT
1 TATTTT
264284 CTTTGTTATA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (9 bp):
TATTTTTTT
Found at i:264256 original size:18 final size:18
Alignment explanation
Indices: 264233--264302 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
264223 TTTTTTCTTC
264233 TATTTTTTTTATTTTTGT
1 TATTTTTTTTATTTTTGT
*
264251 TATTTTTTTAATTTCTT-T
1 TATTTTTTTTATTT-TTGT
*
264269 TATTATTTTTCTTTTCTTTGT
1 TATT-TTTTT-TATT-TTTGT
*
264290 TATATTATTTTAT
1 TAT-TTTTTTTAT
264303 CTTATTCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 18 0.44
19 7 0.17
20 6 0.15
21 9 0.22
22 1 0.02
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.77
Consensus pattern (18 bp):
TATTTTTTTTATTTTTGT
Found at i:264267 original size:36 final size:41
Alignment explanation
Indices: 264226--264301 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 41
264216 ACATAATTTT
264226 TTTCTTCTATT-TTTTT-TATT-TTTGTTAT-TT-TTTTAA
1 TTTCTTCTATTATTTTTCTATTCTTTGTTATATTATTTTAA
* *
264262 TTTCTTTTATTATTTTTCTTTTCTTTGTTATATTATTTTA
1 TTTCTTCTATTATTTTTCTATTCTTTGTTATATTATTTTA
264302 TCTTATTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 10 0.30
37 5 0.15
38 3 0.09
39 8 0.24
40 2 0.06
41 5 0.15
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (41 bp):
TTTCTTCTATTATTTTTCTATTCTTTGTTATATTATTTTAA
Found at i:265585 original size:3 final size:3
Alignment explanation
Indices: 265577--265623 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
265567 TTTCATTGTT
265577 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
265624 TCCAACTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Done.