Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 172 of 250
Found at i:55069241 original size:29 final size:30
Alignment explanation
Indices: 55069180--55069239 Score: 90
Period size: 27 Copynumber: 2.1 Consensus size: 30
55069170 CATTTTCTGT
55069180 TATTTATTATTATTAATTATAATCTTTATA
1 TATTTATTATTATTAATTATAATCTTTATA
*
55069210 TATTTATTA-TATTTATTAT-AT-TTTATA
1 TATTTATTATTATTAATTATAATCTTTATA
55069237 TAT
1 TAT
55069240 ATAGTAGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 9 0.31
28 2 0.07
29 9 0.31
30 9 0.31
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (30 bp):
TATTTATTATTATTAATTATAATCTTTATA
Found at i:55073498 original size:6 final size:6
Alignment explanation
Indices: 55073483--55073512 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
55073473 GAAAATTTAT
55073483 ATAA-A ATAACA ATAACA ATAACA ATAACA A
1 ATAACA ATAACA ATAACA ATAACA ATAACA A
55073513 AGTTCTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAACA
Found at i:55082092 original size:11 final size:11
Alignment explanation
Indices: 55082078--55082115 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55082068 AGAAGAGAAT
55082078 GAAAAATAAAA
1 GAAAAATAAAA
*
55082089 GAAAATTAAAA
1 GAAAAATAAAA
*
55082100 G-AACATAAAA
1 GAAAAATAAAA
55082110 GAAAAA
1 GAAAAA
55082116 AAACTCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.76, C:0.03, G:0.11, T:0.11
Consensus pattern (11 bp):
GAAAAATAAAA
Found at i:55082108 original size:10 final size:10
Alignment explanation
Indices: 55082080--55082118 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
55082070 AAGAGAATGA
55082080 AAAATAAAAG
1 AAAATAAAAG
55082090 AAAATTAAAAG
1 AAAA-TAAAAG
*
55082101 AACATAAAAG
1 AAAATAAAAG
55082111 AAAA-AAAA
1 AAAATAAAA
55082119 CTCAAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 4 0.15
10 13 0.50
11 9 0.35
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (10 bp):
AAAATAAAAG
Found at i:55085435 original size:13 final size:13
Alignment explanation
Indices: 55085417--55085441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55085407 GAATTAGTAT
55085417 GTGTGAAAATTTC
1 GTGTGAAAATTTC
55085430 GTGTGAAAATTT
1 GTGTGAAAATTT
55085442 AATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:55086659 original size:43 final size:44
Alignment explanation
Indices: 55086536--55086694 Score: 186
Period size: 43 Copynumber: 3.7 Consensus size: 44
55086526 TATGTGTTTT
* *
55086536 CATGTAAGACCACGTCTGGGACATTGGCATCGACT-TATGATTTA
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGATTTA
* * * *
55086580 CGTTTAAGATCACGTCTGGGACGTTAGCATCG-TATTTGATTT-
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTA
*
55086622 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTG-TTTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTTA
55086665 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACGTTGGCAT
55086695 TTTACGAGCA
Statistics
Matches: 98, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 30 0.31
43 39 0.40
44 28 0.29
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (44 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTA
Found at i:55086708 original size:86 final size:86
Alignment explanation
Indices: 55086533--55086709 Score: 198
Period size: 86 Copynumber: 2.1 Consensus size: 86
55086523 CACTATGTGT
* * * * *
55086533 TTTCATGTAAGACCACGTCTGGGACATTGGCATCGACTTATGATTTACGTTTAAGATCACGTCTG
1 TTTCGTGTAAGACCACGTCTGGGACAGTGGCATCGACTTATGATTTACATGTAAGACCACGTCTG
***
55086598 GGACGTTAGCATCGTATTTGA
66 GGACGTTAGCATCGTACGAGA
*
55086619 TTTCGTGTAAGACC-CTGTCTGGGACAGTGGCATCGA-TATTTG-TTTACATGTAAGACCACGTC
1 TTTCGTGTAAGACCAC-GTCTGGGACAGTGGCATCGACT-TATGATTTACATGTAAGACCACGTC
* **
55086681 TGGGACGTTGGCATTTTACGAGCA
64 TGGGACGTTAGCATCGTACGAG-A
55086705 TTTCG
1 TTTCG
55086710 AGCTATCTAC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
85 35 0.46
86 41 0.54
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (86 bp):
TTTCGTGTAAGACCACGTCTGGGACAGTGGCATCGACTTATGATTTACATGTAAGACCACGTCTG
GGACGTTAGCATCGTACGAGA
Found at i:55087607 original size:43 final size:43
Alignment explanation
Indices: 55087546--55087634 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 43
55087536 GGTGGCAAAT
* * * *
55087546 TGGCTTTTCAAATGGCTTATTTTTGTTCATACGGGCAGAGACA
1 TGGCTTCTCAAATGGCTTATTTTTGTCCATACGGGCAAAAACA
55087589 TGGCTTCTCAAATGGCTTATTTTTGTCCATACGGGCAAAAACA
1 TGGCTTCTCAAATGGCTTATTTTTGTCCATACGGGCAAAAACA
55087632 TGG
1 TGG
55087635 GCATGTGTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (43 bp):
TGGCTTCTCAAATGGCTTATTTTTGTCCATACGGGCAAAAACA
Found at i:55089047 original size:11 final size:11
Alignment explanation
Indices: 55089031--55089056 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55089021 GTTCATAGTC
55089031 TTTTTTTTTGT
1 TTTTTTTTTGT
55089042 TTTTTTTTTGT
1 TTTTTTTTTGT
55089053 TTTT
1 TTTT
55089057 GTGAAGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:55091810 original size:21 final size:22
Alignment explanation
Indices: 55091786--55091832 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
55091776 TACCCTTAAA
**
55091786 TAAATTTTAA-ATTATTGTTAT
1 TAAATTTTAATAGGATTGTTAT
55091807 TAAATTTTAATAGGATTGTTAT
1 TAAATTTTAATAGGATTGTTAT
55091829 TAAA
1 TAAA
55091833 AATAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TAAATTTTAATAGGATTGTTAT
Found at i:55091851 original size:16 final size:16
Alignment explanation
Indices: 55091830--55091861 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55091820 GATTGTTATT
55091830 AAAAATAAATTAATAA
1 AAAAATAAATTAATAA
*
55091846 AAAAATAATTTAATAA
1 AAAAATAAATTAATAA
55091862 TATTTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATAAATTAATAA
Found at i:55092047 original size:17 final size:16
Alignment explanation
Indices: 55092018--55092061 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
55092008 TATTCATTAG
* *
55092018 TATTACCAAAAAATAAC
1 TATTA-CAAAAAAAAAA
55092035 TATTACAAAAAAAAAA
1 TATTACAAAAAAAAAA
*
55092051 TAATACAAAAA
1 TATTACAAAAA
55092062 TAATGATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.20
Consensus pattern (16 bp):
TATTACAAAAAAAAAA
Found at i:55094868 original size:7 final size:6
Alignment explanation
Indices: 55094827--55094867 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
55094817 ATAATTTAAT
*
55094827 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
55094868 AATATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:55094868 original size:20 final size:20
Alignment explanation
Indices: 55094830--55094868 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55094820 ATTTAATAAA
**
55094830 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
55094850 TAAAAATAAAAATAAAAAA
1 TAAAAATAAAAATAAAAAA
55094869 ATATAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:55094916 original size:9 final size:9
Alignment explanation
Indices: 55094886--55094944 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
55094876 TTTATACAAA
55094886 TAATTCGGT
1 TAATTCGGT
*
55094895 TAATTTAGG-
1 TAA-TTCGGT
55094904 TAATTCGGT
1 TAATTCGGT
*
55094913 TAATTCGAT
1 TAATTCGGT
* *
55094922 TAATTTGTT
1 TAATTCGGT
55094931 TAATTCGGT
1 TAATTCGGT
55094940 TAATT
1 TAATT
55094945 TTATACTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
8 4 0.10
9 33 0.80
10 4 0.10
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (9 bp):
TAATTCGGT
Found at i:55094924 original size:27 final size:27
Alignment explanation
Indices: 55094886--55094944 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
55094876 TTTATACAAA
*
55094886 TAATTCGGTTAATTTAG-GTAATTCGGT
1 TAATTCGATTAATTT-GTGTAATTCGGT
*
55094913 TAATTCGATTAATTTGTTTAATTCGGT
1 TAATTCGATTAATTTGTGTAATTCGGT
55094940 TAATT
1 TAATT
55094945 TTATACTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (27 bp):
TAATTCGATTAATTTGTGTAATTCGGT
Found at i:55098000 original size:35 final size:35
Alignment explanation
Indices: 55097960--55098031 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
55097950 ACAAGCATCA
* *
55097960 AAATCATGAGTCAAAAACTCATAATAAAATAAATT
1 AAATCATGAATCAAAAACTAATAATAAAATAAATT
*** *
55097995 AAATCATGAATCATGTACTAATAATAAAATAATTT
1 AAATCATGAATCAAAAACTAATAATAAAATAAATT
55098030 AA
1 AA
55098032 TGTTAAAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.29
Consensus pattern (35 bp):
AAATCATGAATCAAAAACTAATAATAAAATAAATT
Found at i:55098074 original size:31 final size:31
Alignment explanation
Indices: 55098036--55098099 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
55098026 ATTTAATGTT
*
55098036 AAAAAGAATCTATGCTTACTTGTGGAAATGG
1 AAAAAGAATCCATGCTTACTTGTGGAAATGG
*
55098067 AAAAAGAATCCATGTTTACTTGTGGAAATGG
1 AAAAAGAATCCATGCTTACTTGTGGAAATGG
55098098 AA
1 AA
55098100 TAGAAATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (31 bp):
AAAAAGAATCCATGCTTACTTGTGGAAATGG
Found at i:55100426 original size:102 final size:102
Alignment explanation
Indices: 55100309--55100505 Score: 349
Period size: 102 Copynumber: 1.9 Consensus size: 102
55100299 CTGACATCTA
55100309 TCTCATTATGAAATATCATATATCTCAGGAAATATTATATTGGTGATTGTATTGATTTGAAATTA
1 TCTCATTATGAAATATCATATATCTCAGGAAATATTATATTGGTGATTGTATTGATTTGAAATTA
55100374 CCCAAGATAATCCCTTCGATCATGATTATGCTAGATG
66 CCCAAGATAATCCCTTCGATCATGATTATGCTAGATG
* * *
55100411 TCTCATTATGGAATATCATATATCTTAGGGAATATTATATTGGTGATTGTATTGATTTGAAATTA
1 TCTCATTATGAAATATCATATATCTCAGGAAATATTATATTGGTGATTGTATTGATTTGAAATTA
* *
55100476 CCTAAGATAATCCCTTCGCTCATGATTATG
66 CCCAAGATAATCCCTTCGATCATGATTATG
55100506 TTGGATGAGC
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (102 bp):
TCTCATTATGAAATATCATATATCTCAGGAAATATTATATTGGTGATTGTATTGATTTGAAATTA
CCCAAGATAATCCCTTCGATCATGATTATGCTAGATG
Found at i:55101553 original size:28 final size:28
Alignment explanation
Indices: 55101522--55101576 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
55101512 GGGATTGGGA
55101522 AGATAGTTAAGGGATTTAGTGTACCATG
1 AGATAGTTAAGGGATTTAGTGTACCATG
55101550 AGATAGTTAAGGGATTTAGTGTACCAT
1 AGATAGTTAAGGGATTTAGTGTACCAT
55101577 TAGTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (28 bp):
AGATAGTTAAGGGATTTAGTGTACCATG
Found at i:55115294 original size:19 final size:19
Alignment explanation
Indices: 55115257--55115305 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
55115247 ATTATCATCA
*
55115257 TCATTTTTT-TACTTTATT
1 TCATTTTTTATACTTAATT
55115275 T-ATTTTTTATATCTTAATT
1 TCATTTTTTATA-CTTAATT
55115294 TCATTTTCTTAT
1 TCATTTT-TTAT
55115306 TTGATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.27
18 3 0.12
19 7 0.27
20 5 0.19
21 4 0.15
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.69
Consensus pattern (19 bp):
TCATTTTTTATACTTAATT
Found at i:55117759 original size:28 final size:29
Alignment explanation
Indices: 55117713--55117778 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
55117703 TTTTATGTAC
*
55117713 TTAATTTTTCCAATAAATTTTTAATTTT-A
1 TTAA-TTTTCCAATAAATTTCTAATTTTAA
* *
55117742 TTGAATTTTCCACT-AATTTCTATTTTTAA
1 TT-AATTTTCCAATAAATTTCTAATTTTAA
55117771 TTAATTTT
1 TTAATTTT
55117779 AACTATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 17 0.53
29 13 0.41
30 2 0.06
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (29 bp):
TTAATTTTCCAATAAATTTCTAATTTTAA
Found at i:55121018 original size:30 final size:30
Alignment explanation
Indices: 55120963--55121026 Score: 71
Period size: 30 Copynumber: 2.1 Consensus size: 30
55120953 TATTAACTTA
55120963 ATTTAATTAATTATATTATAGATATAGT-TT
1 ATTTAATTAATTATATTATAGATATA-TCTT
*
55120993 ATTTAATTTAATTATCA-TAT-TATATATCTT
1 ATTTAA-TTAATTAT-ATTATAGATATATCTT
55121023 ATTT
1 ATTT
55121027 TTAATCGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
29 1 0.03
30 17 0.57
31 11 0.37
32 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (30 bp):
ATTTAATTAATTATATTATAGATATATCTT
Found at i:55123893 original size:20 final size:21
Alignment explanation
Indices: 55123868--55123907 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
55123858 GTGAGTTGCA
55123868 ACTGAT-TATACAATGATAGC
1 ACTGATATATACAATGATAGC
*
55123888 ACTGATAATATTCAATGATA
1 ACTGAT-ATATACAATGATA
55123908 AAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
ACTGATATATACAATGATAGC
Found at i:55126368 original size:28 final size:28
Alignment explanation
Indices: 55126328--55126386 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
55126318 TTATAAAAAC
*
55126328 TTTATCTATTTTTGAAAATTTTATCTAT
1 TTTATCTAATTTTGAAAATTTTATCTAT
* * * * *
55126356 TTTATTTAATTTTTAGATTTTTATGTAT
1 TTTATCTAATTTTGAAAATTTTATCTAT
55126384 TTT
1 TTT
55126387 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.66
Consensus pattern (28 bp):
TTTATCTAATTTTGAAAATTTTATCTAT
Found at i:55127610 original size:22 final size:22
Alignment explanation
Indices: 55127585--55127640 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
55127575 AAAAAACTTC
55127585 AATATATAATTAATCATGAGTG
1 AATATATAATTAATCATGAGTG
55127607 AATATATAATTAATCATGAGTG
1 AATATATAATTAATCATGAGTG
*
55127629 AACATAATAATT
1 AATAT-ATAATT
55127641 TAATTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (22 bp):
AATATATAATTAATCATGAGTG
Found at i:55128180 original size:46 final size:46
Alignment explanation
Indices: 55128130--55128222 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 46
55128120 TTATTTATTT
* * *
55128130 TATTTATTATTA-TTAATTTTTAAATTTTTGAAATATATA-TTTAAAA
1 TATTTATTAATACATAATTTTTAAA-TATT-AAATATATATTTTAAAA
* *
55128176 TATTTTTTAATACATATTTTTTAAATATTAAATATATATTTTAAAA
1 TATTTATTAATACATAATTTTTAAATATTAAATATATATTTTAAAA
55128222 T
1 T
55128223 TACATTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 9 0.22
46 21 0.52
47 10 0.25
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (46 bp):
TATTTATTAATACATAATTTTTAAATATTAAATATATATTTTAAAA
Found at i:55128217 original size:20 final size:20
Alignment explanation
Indices: 55128189--55128265 Score: 60
Period size: 20 Copynumber: 4.1 Consensus size: 20
55128179 TTTTTAATAC
*
55128189 ATATTTTTTAAATATTAAAT
1 ATATATTTTAAATATTAAAT
55128209 ATATATTTTAAA-A-T---T
1 ATATATTTTAAATATTAAAT
* *
55128224 ACAT-TTTTAAATTTTAAAT
1 ATATATTTTAAATATTAAAT
55128243 AT-TATTTTTAAATATTTAAAT
1 ATATA-TTTTAAATA-TTAAAT
55128264 AT
1 AT
55128266 TTTAAACTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
14 7 0.16
15 4 0.09
16 1 0.02
18 2 0.05
19 3 0.07
20 19 0.43
21 8 0.18
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTTTAAATATTAAAT
Found at i:55128237 original size:21 final size:20
Alignment explanation
Indices: 55128194--55128266 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
55128184 AATACATATT
** * *
55128194 TTTTAAATATTAAATATATA
1 TTTTAAATATTATTTTTAAA
55128214 TTTTAAA-ATTACATTTTTAAA
1 TTTTAAATATT--ATTTTTAAA
55128235 TTTTAAATATTATTTTTAAA
1 TTTTAAATATTATTTTTAAA
55128255 TATTTAAATATT
1 T-TTTAAATATT
55128267 TTAAACTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
19 3 0.07
20 17 0.38
21 22 0.49
22 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAATATTATTTTTAAA
Found at i:55128352 original size:14 final size:15
Alignment explanation
Indices: 55128324--55128356 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
55128314 TTAATTTGTT
*
55128324 TTATAATATTTTAAA
1 TTATAATATTATAAA
55128339 TTATAA-ATTATAAA
1 TTATAATATTATAAA
55128353 TTAT
1 TTAT
55128357 TTTTAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATAATATTATAAA
Found at i:55128674 original size:15 final size:15
Alignment explanation
Indices: 55128633--55128674 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
55128623 AATTAAAAAA
*
55128633 TAAAAAAT-ATTTGT
1 TAAAAAATAATTTAT
55128647 TAAAAAATGAATTTAT
1 TAAAAAAT-AATTTAT
*
55128663 TTAAAAATAATT
1 TAAAAAATAATT
55128675 AAATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
16 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
TAAAAAATAATTTAT
Found at i:55134944 original size:42 final size:42
Alignment explanation
Indices: 55134885--55134965 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
55134875 AAGTAAGAGA
55134885 ATTAAAAAGGTCAAATATTCTGGACCAGATTTCATTGTGAGG
1 ATTAAAAAGGTCAAATATTCTGGACCAGATTTCATTGTGAGG
*
55134927 ATTAAAAAGGTCAAATATTTTGGACCAGATTTCATTGTG
1 ATTAAAAAGGTCAAATATTCTGGACCAGATTTCATTGTG
55134966 TTTCTTGTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (42 bp):
ATTAAAAAGGTCAAATATTCTGGACCAGATTTCATTGTGAGG
Found at i:55137676 original size:29 final size:28
Alignment explanation
Indices: 55137634--55137725 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
55137624 ACATGGCTTG
* *
55137634 GAAT-TGATTCGGGCCGGATGGGCCATAT
1 GAATGTGATTTGGGCC-AATGGGCCATAT
*
55137662 GAATGTGATTTGGGCCTAATGGACCATAT
1 GAATGTGATTTGGGCC-AATGGGCCATAT
*
55137691 GAATGTGATTTGGGCCTAGTGGGCCATAT
1 GAATGTGATTTGGGCC-AATGGGCCATAT
*
55137720 GCATGT
1 GAATGT
55137726 ATGTAAACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 4 0.07
29 52 0.93
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (28 bp):
GAATGTGATTTGGGCCAATGGGCCATAT
Found at i:55139025 original size:16 final size:17
Alignment explanation
Indices: 55138993--55139025 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55138983 TTTAAAGAAG
55138993 GGTTTTCAATGAAAACAA
1 GGTTTTCAA-GAAAACAA
55139011 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
55139026 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAA
Found at i:55143989 original size:22 final size:22
Alignment explanation
Indices: 55143959--55144010 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
55143949 TAGGATTTTC
*
55143959 TTTG-TATTTTGGG-CTTGTATT
1 TTTGTTATTTTGGGTC-TGTAAT
55143980 TTTGTTA-TTTGGGTCTGTAAT
1 TTTGTTATTTTGGGTCTGTAAT
55144001 TTTGTTATTT
1 TTTGTTATTT
55144011 ATTAAGGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.12, C:0.04, G:0.21, T:0.63
Consensus pattern (22 bp):
TTTGTTATTTTGGGTCTGTAAT
Found at i:55144229 original size:45 final size:45
Alignment explanation
Indices: 55144165--55144296 Score: 160
Period size: 45 Copynumber: 3.0 Consensus size: 45
55144155 GCAGCCATGT
* * *
55144165 TCTTCAATCTGCCCTACTGCAACTTTAGGGAGATAAGATTTGTTA
1 TCTTCAATCTGCTCTACTGCAACTTTAAGGAGATAAGATTTGTCA
55144210 TCTTCAATCTGCTCTACTGCAA-TTTCAAGGAGATAAGATTTG-CA
1 TCTTCAATCTGCTCTACTGCAACTTT-AAGGAGATAAGATTTGTCA
* * * * * *
55144254 TATTCAATTTTCTCCACTGCAACTTCAAGGAGATAAGGTTTGT
1 TCTTCAATCTGCTCTACTGCAACTTTAAGGAGATAAGATTTGT
55144297 GGCTTCAATA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
44 37 0.49
45 38 0.51
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (45 bp):
TCTTCAATCTGCTCTACTGCAACTTTAAGGAGATAAGATTTGTCA
Found at i:55144304 original size:44 final size:44
Alignment explanation
Indices: 55144180--55144339 Score: 160
Period size: 44 Copynumber: 3.6 Consensus size: 44
55144170 AATCTGCCCT
* * * * *
55144180 ACTGCAACTTTAGGGAGATAAGATTTGTTATCTTCAATCTGCTCT
1 ACTGCAACTTCAAGGAGATAAGATTTG-TATCTTCAATATACTCC
* * * * *
55144225 ACTGCAATTTCAAGGAGATAAGATTTGCATATTCAATTTTCTCC
1 ACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAATATACTCC
* **
55144269 ACTGCAACTTCAAGGAGATAAGGTTTGTGGCTTCAATATACTCC
1 ACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAATATACTCC
* *
55144313 ACTGCAACTAC-AGAGAAATAAGATTTG
1 ACTGCAACTTCAAG-GAGATAAGATTTG
55144340 CCATGGTAAA
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 2 0.02
44 69 0.73
45 24 0.25
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (44 bp):
ACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAATATACTCC
Found at i:55144352 original size:89 final size:89
Alignment explanation
Indices: 55144180--55144390 Score: 194
Period size: 88 Copynumber: 2.3 Consensus size: 89
55144170 AATCTGCCCT
* * * * * * * * *
55144180 ACTGCAACTTTAGGGAGATAAGATTTGTTATCTTCAATCTGCTCTACTGCAATTTCAAGGAGATA
1 ACTGCAACTTCAAGGAGATAAGATTTGTTAGCTTCAATATACTCCACTGCAACTACAAGGAAATA
* *
55144245 AGATTTGCATATTCAATTTTCTCC
66 AGATTTGCATAGTAAATTTTCTCC
* *
55144269 ACTGCAACTTCAAGGAGATAAGGTTTG-TGGCTTCAATATACTCCACTGCAACTAC-AGAGAAAT
1 ACTGCAACTTCAAGGAGATAAGATTTGTTAGCTTCAATATACTCCACTGCAACTACAAG-GAAAT
*
55144332 AAGATTTGCCATGGTAAATTTGATCTAACC
65 AAGATTTG-CATAGTAAATTT--TCT--CC
*
55144362 TACTGCAACTTCAGAGG-TATAAGATTTGT
1 -ACTGCAACTTCA-AGGAGATAAGATTTGT
55144391 AACTTGTAGC
Statistics
Matches: 97, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
87 2 0.02
88 33 0.34
89 33 0.34
91 3 0.03
93 2 0.02
94 21 0.22
95 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (89 bp):
ACTGCAACTTCAAGGAGATAAGATTTGTTAGCTTCAATATACTCCACTGCAACTACAAGGAAATA
AGATTTGCATAGTAAATTTTCTCC
Found at i:55145388 original size:30 final size:30
Alignment explanation
Indices: 55145348--55145409 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
55145338 ACTTCTAGAG
55145348 GACCCTTTTGGACTTGATATGAATTTCGGA
1 GACCCTTTTGGACTTGATATGAATTTCGGA
*
55145378 GACCTTTTTGGACTTGATATGAATTTCGGA
1 GACCCTTTTGGACTTGATATGAATTTCGGA
55145408 GA
1 GA
55145410 TTTAGAGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (30 bp):
GACCCTTTTGGACTTGATATGAATTTCGGA
Found at i:55150260 original size:4 final size:4
Alignment explanation
Indices: 55150251--55150279 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
55150241 TGAAATAAGC
55150251 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
55150280 TAAAACATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:55150385 original size:3 final size:3
Alignment explanation
Indices: 55150377--55150511 Score: 73
Period size: 3 Copynumber: 45.3 Consensus size: 3
55150367 ATAAAAGACC
** * *
55150377 ATA ATA ATA ATA ACG ATA ATA ATA ATA ATA AT- ATA ATA CCT- ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * ** * * *
55150421 ATA CTA ATA ATA GTA ATA ATA GGA A-A ATTA ATA TTA GTA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
* * *
55150466 ATA ATGGA A-A ATA ATA ATA ACA ATG ATA AT- ATA GTA ATA ATA ATA
1 ATA AT--A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55150511 A
1 A
55150512 ACGTGAAATT
Statistics
Matches: 99, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
2 9 0.09
3 85 0.86
4 3 0.03
5 2 0.02
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55150701 original size:12 final size:12
Alignment explanation
Indices: 55150684--55150710 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55150674 ATGTACATAA
55150684 TATATATATATG
1 TATATATATATG
55150696 TATATATATATG
1 TATATATATATG
55150708 TAT
1 TAT
55150711 TAGAAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:55151118 original size:81 final size:81
Alignment explanation
Indices: 55151022--55151185 Score: 292
Period size: 81 Copynumber: 2.0 Consensus size: 81
55151012 AGAAAAGAGT
* * *
55151022 AAAAAAAAGGACGAAATTGGGTTGAAAATGGAATTTTAGGGGCAAATTTTAGAATAAATAAAGGA
1 AAAAAAAAGGACGAAATTAGGTTGAAAACGGAATTTTAGAGGCAAATTTTAGAATAAATAAAGGA
55151087 GGAGGGGACTGATTTG
66 GGAGGGGACTGATTTG
*
55151103 AAAAAAAAGGACGAAATTAGGTTGAAAACGGAATTTTAGAGGCGAATTTTAGAATAAATAAAGGA
1 AAAAAAAAGGACGAAATTAGGTTGAAAACGGAATTTTAGAGGCAAATTTTAGAATAAATAAAGGA
55151168 GGAGGGGACTGATTTG
66 GGAGGGGACTGATTTG
55151184 AA
1 AA
55151186 CACACGAGCA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.45, C:0.04, G:0.29, T:0.23
Consensus pattern (81 bp):
AAAAAAAAGGACGAAATTAGGTTGAAAACGGAATTTTAGAGGCAAATTTTAGAATAAATAAAGGA
GGAGGGGACTGATTTG
Found at i:55151704 original size:17 final size:18
Alignment explanation
Indices: 55151684--55151721 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
55151674 CTCATTTTTT
*
55151684 TTTAATTTATGTAT-TTA
1 TTTAATATATGTATGTTA
55151701 TTTAATATATGTATGTTA
1 TTTAATATATGTATGTTA
55151719 TTT
1 TTT
55151722 TTAATAAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (18 bp):
TTTAATATATGTATGTTA
Found at i:55152695 original size:43 final size:43
Alignment explanation
Indices: 55152648--55152931 Score: 174
Period size: 43 Copynumber: 6.5 Consensus size: 43
55152638 CGATCTATTT
*
55152648 CCCTACTACTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* * * * *
55152691 CCCTACTGCTTAGGGGTTTAAG----GCCCATGCATCGTTGATCAA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGC-CTG-T-TA
* ** * * *
55152733 CTCCACTACTGCTTAGGGAG-ATAAGATCT-ATAATCTTCAACCTGCTG
1 --CC-CTACTGCTTAGGG-GTTTAAGATCTGCCAA--TTCAGCCTGTTA
* **
55152780 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* *
55152823 CCCTACTGCTTAGGGGTTTAAGGCCCATC-GCC--TTC-GATCTGTTT
1 CCCTACTGCTTAGGGGTTTAA-G---ATCTGCCAATTCAG-CCTGTTA
* * **
55152867 CCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
*
55152910 CCCTACTACTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGTTTAAG
55152932 GCCCATCGTC
Statistics
Matches: 182, Mismatches: 35, Indels: 48
0.69 0.13 0.18
Matches are distributed among these distances:
39 8 0.04
40 4 0.02
41 2 0.01
42 1 0.01
43 81 0.45
44 53 0.29
45 21 0.12
46 2 0.01
47 3 0.02
48 1 0.01
49 2 0.01
50 4 0.02
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (43 bp):
CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
Found at i:55152794 original size:44 final size:43
Alignment explanation
Indices: 55152738--55152837 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 43
55152728 ATCAACTCCA
* *
55152738 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTGCTGCC
1 CTACTGCTTAGGGAGATAAGATCTATAA-ATTCAACCTGCTACC
* * * * *
55152782 CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTATAAATTCAACCTGCTACC
55152825 CTACTGCTTAGGG
1 CTACTGCTTAGGG
55152838 GTTTAAGGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 24 0.49
44 25 0.51
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (43 bp):
CTACTGCTTAGGGAGATAAGATCTATAAATTCAACCTGCTACC
Found at i:55152871 original size:44 final size:44
Alignment explanation
Indices: 55152817--55152968 Score: 137
Period size: 44 Copynumber: 3.5 Consensus size: 44
55152807 TAAATTCAGC
* *
55152817 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGAT
1 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCGACTTCGAT
* * * ***** * * *
55152861 CTGTTTCCCTACTGCTTAGGGGGTTAAGATTTGT-AAATTC-AGC
1 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCGACTTCGA-T
* *
55152904 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCGTCTTTGAT
1 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCGACTTCGAT
*
55152948 CTGTTTCCCTACTACTTAGGG
1 CTGTTACCCTACTACTTAGGG
55152969 TGATAAGATC
Statistics
Matches: 80, Mismatches: 25, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
42 1 0.01
43 29 0.36
44 49 0.61
45 1 0.01
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.36
Consensus pattern (44 bp):
CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCGACTTCGAT
Found at i:55153020 original size:87 final size:87
Alignment explanation
Indices: 55152780--55153011 Score: 392
Period size: 87 Copynumber: 2.7 Consensus size: 87
55152770 CAACCTGCTG
55152780 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
55152845 GCCCATCGCCTTCGATCTGTTT
66 GCCCATCGCCTTCGATCTGTTT
* *
55152867 CCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTACTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
* *
55152932 GCCCATCGTCTTTGATCTGTTT
66 GCCCATCGCCTTCGATCTGTTT
* * * *
55152954 CCCTACTACTTAGGGTGATAAGATCTGTAAACTCAGCCTGTTACCCTACTGCTTAGGG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGG
55153012 AGATAAGGCT
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 135 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (87 bp):
CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
GCCCATCGCCTTCGATCTGTTT
Found at i:55155871 original size:17 final size:18
Alignment explanation
Indices: 55155838--55155873 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55155828 TCGAAACAGG
55155838 TCGGTTAACCAAAAAAAT
1 TCGGTTAACCAAAAAAAT
55155856 TCGGTTAACCAAAAAAAT
1 TCGGTTAACCAAAAAAAT
55155874 AATATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (18 bp):
TCGGTTAACCAAAAAAAT
Found at i:55164439 original size:3 final size:3
Alignment explanation
Indices: 55164431--55164574 Score: 91
Period size: 3 Copynumber: 48.3 Consensus size: 3
55164421 ATAAAAGACC
**
55164431 ATA ATA ATA ATA ATA ACG ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * ** * *
55164478 CCT- ATG ATA CTA ATA ATA GTA ATA ATA GGA A-A ATTA ATA TTA GTA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* * * *
55164523 TTA ATA ATA ATGGA A-A ATA ATA ATA ACA ATG ATA AT- ATA GTA ATA
1 ATA ATA ATA AT--A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55164568 ATA ATA A
1 ATA ATA A
55164575 ACGTGAAATT
Statistics
Matches: 108, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
2 9 0.08
3 94 0.87
4 3 0.03
5 2 0.02
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55164764 original size:12 final size:12
Alignment explanation
Indices: 55164747--55164773 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55164737 ATGTACATAA
55164747 TATATATATATG
1 TATATATATATG
55164759 TATATATATATG
1 TATATATATATG
55164771 TAT
1 TAT
55164774 TAGAAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:55165181 original size:80 final size:80
Alignment explanation
Indices: 55165086--55165247 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
55165076 GAAAAGAGTA
*
55165086 AAAAAAAGGACGAAATTGGGTTGAAAATGGAATTTTAGAGGCGAATTTTAGAATAAATAAAGGAG
1 AAAAAAAGGACGAAATTGGGTTGAAAACGGAATTTTAGAGGCGAATTTTAGAATAAATAAAGGAG
55165151 GAGGGGACTGATTTG
66 GAGGGGACTGATTTG
55165166 AAAAAAAGGACGAAATTGGGTTGAAAACGGAATTTTAGAGGCGAATTTTAGAATAAATAAAGGAG
1 AAAAAAAGGACGAAATTGGGTTGAAAACGGAATTTTAGAGGCGAATTTTAGAATAAATAAAGGAG
55165231 GAGGGGACTGATTTG
66 GAGGGGACTGATTTG
55165246 AA
1 AA
55165248 CACACGAGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.43, C:0.04, G:0.30, T:0.23
Consensus pattern (80 bp):
AAAAAAAGGACGAAATTGGGTTGAAAACGGAATTTTAGAGGCGAATTTTAGAATAAATAAAGGAG
GAGGGGACTGATTTG
Found at i:55165765 original size:17 final size:17
Alignment explanation
Indices: 55165740--55165782 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
55165730 TTTTTCTCTC
* *
55165740 ATTTTTTTAATTTATGT
1 ATTTATTTAATATATGT
55165757 ATTTATTTAATATATGT
1 ATTTATTTAATATATGT
55165774 ATGTTATTT
1 AT-TTATTT
55165783 TTAATAAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (17 bp):
ATTTATTTAATATATGT
Found at i:55166758 original size:43 final size:43
Alignment explanation
Indices: 55166711--55167212 Score: 236
Period size: 43 Copynumber: 11.5 Consensus size: 43
55166701 CGATCTATTT
*
55166711 CCCTACTACTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* * * * *
55166754 CCCTACTGCTTAGGGGTTTAAG----GCCCATGCATCGTTGATCAA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGC-CTG-T-TA
* ** * * *
55166796 CTCTACTACTGCTTAGGGAG-ATAAGATCT-ATAATCTTCAACCTGCTG
1 C-C--CTACTGCTTAGGG-GTTTAAGATCTGCCAA--TTCAGCCTGTTA
* **
55166843 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* *
55166886 CCCTACTGCTTA-GGGTTTAAGGCCCATC-GCC--TTC-GATCTGTTT
1 CCCTACTGCTTAGGGGTTTAA-G---ATCTGCCAATTCAG-CCTGTTA
* * **
55166929 CCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* * * * *
55166972 CCCTACTGCTTAGGGGTTTAAG----GCCCATGCATCGTTGATCAA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGC-CTG-T-TA
* ** * * *
55167014 CTCCACTACTGCTTAGGGAG-ATAAGATCT-ATAATCTTCAACCTGCTG
1 --CC-CTACTGCTTAGGG-GTTTAAGATCTGCCAA--TTCAGCCTGTTA
* **
55167061 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
* *
55167104 CCCTACTGCTTAGGGGTTTAAGGCCCATC-GCC--TTC-GATCTGTTT
1 CCCTACTGCTTAGGGGTTTAA-G---ATCTGCCAATTCAG-CCTGTTA
* * **
55167148 CCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
55167191 CCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGTTTAAG
55167213 GCCCATCGTC
Statistics
Matches: 341, Mismatches: 69, Indels: 98
0.67 0.14 0.19
Matches are distributed among these distances:
39 14 0.04
40 8 0.02
41 4 0.01
42 11 0.03
43 156 0.46
44 82 0.24
45 41 0.12
46 7 0.02
47 4 0.01
48 2 0.01
49 4 0.01
50 8 0.02
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (43 bp):
CCCTACTGCTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTA
Found at i:55167062 original size:218 final size:218
Alignment explanation
Indices: 55166643--55167292 Score: 1027
Period size: 218 Copynumber: 3.0 Consensus size: 218
55166633 CAAAGAGAAG
* * * ** *
55166643 AGATTTGTAATTTCCAGCCTGTTACCCTACTGCTTGAGGGGTTAAGGCCCATCATCTTCGATCTA
1 AGATCTGTAAATT-CAGCCTGTTACCCTACTGCTT-AGGGTTTAAGGCCCATCGCCTTCGATCTG
* * * **
55166708 TTTCCCTACTACTTAGGGGTTTAAGATCTGCCAATTCAGCCTGTTACCCTACTGCTTAGGGGTTT
64 TTTCCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTT
*
55166773 AAGGCCCATGCATCGTTGATCAACTCTACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACC
129 AAGGCCCATGCATCGTTGATCAACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACC
55166838 TGCTGCCCTACTGCTTAGGGGGTTA
194 TGCTGCCCTACTGCTTAGGGGGTTA
55166863 AGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGTTTAAGGCCCATCGCCTTCGATCTGTT
1 AGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGTTTAAGGCCCATCGCCTTCGATCTGTT
55166928 TCCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAA
66 TCCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAA
55166993 GGCCCATGCATCGTTGATCAACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTG
131 GGCCCATGCATCGTTGATCAACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTG
55167058 CTGCCCTACTGCTTAGGGGGTTA
196 CTGCCCTACTGCTTAGGGGGTTA
55167081 AGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTGT
1 AGATCTGTAAATTCAGCCTGTTACCCTACTGCTTA-GGGTTTAAGGCCCATCGCCTTCGATCTGT
55167146 TTCCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTA
65 TTCCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTA
* * *** * * * * *
55167211 AGGCCCAT-CGTCTTTGATCTGTTTCC-CTACTACTTAGGGTGATAAGATCTGTAAAC-TCAGCC
130 AGGCCCATGCATCGTTGATC-AACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACC
* *
55167273 TGTTACCCTACTGCTTAGGG
194 TGCTGCCCTACTGCTTAGGG
55167293 AGATAAGGCT
Statistics
Matches: 404, Mismatches: 24, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
217 23 0.06
218 244 0.60
219 126 0.31
220 11 0.03
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (218 bp):
AGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGTTTAAGGCCCATCGCCTTCGATCTGTT
TCCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAA
GGCCCATGCATCGTTGATCAACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTG
CTGCCCTACTGCTTAGGGGGTTA
Found at i:55167290 original size:43 final size:43
Alignment explanation
Indices: 55166801--55167292 Score: 267
Period size: 43 Copynumber: 11.3 Consensus size: 43
55166791 ATCAACTCTA
* * * * * *
55166801 CTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTGCTGCC
1 CTACTGCTTAGGGGGTTAAGATCTATAAAC-TCAGCCTGTTACC
* *
55166845 CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
1 CTACTGCTTAGGGGGTTAAGATCTATAAACTCAGCCTGTTACC
* ** * *** * *
55166888 CTACTGCTTA-GGGTTTAAGGCCCATCGCCTTC-GATCTGTTTCC
1 CTACTGCTTAGGGGGTTAAGATCTATAAAC-TCAG-CCTGTTACC
* * *
55166931 CTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACC
1 CTACTGCTTAGGGGGTTAAGATCTATAAACTCAGCCTGTTACC
* ** * ** * *
55166974 CTACTGCTTAGGGGTTTAAGGCCCATGCA-TC-G-TTGATCAACTCC
1 CTACTGCTTAGGGGGTTAAGATCTATAAACTCAGCCTG-T-TA--CC
* * * * * *
55167018 ACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTGCTGCC
1 -CTACTGCTTAGGGGGTTAAGATCTATAAAC-TCAGCCTGTTACC
* *
55167063 CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
1 CTACTGCTTAGGGGGTTAAGATCTATAAACTCAGCCTGTTACC
* ** * *** * *
55167106 CTACTGCTTAGGGGTTTAAGGCCCATCGCCTTC-GATCTGTTTCC
1 CTACTGCTTAGGGGGTTAAGATCTATAAAC-TCAG-CCTGTTACC
* * *
55167150 CTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACC
1 CTACTGCTTAGGGGGTTAAGATCTATAAACTCAGCCTGTTACC
* ** * *** ** * *
55167193 CTACTGCTTAGGGGTTTAAGGCCCATCGTCTTTGATCTGTTTCC
1 CTACTGCTTAGGGGGTTAAGATCTATAAACTCAG-CCTGTTACC
* * * *
55167237 CTACTACTTAGGGTGATAAGATCTGTAAACTCAGCCTGTTACC
1 CTACTGCTTAGGGGGTTAAGATCTATAAACTCAGCCTGTTACC
55167280 CTACTGCTTAGGG
1 CTACTGCTTAGGG
55167293 AGATAAGGCT
Statistics
Matches: 315, Mismatches: 116, Indels: 35
0.68 0.25 0.08
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 14 0.04
43 151 0.48
44 120 0.38
45 22 0.07
47 2 0.01
49 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (43 bp):
CTACTGCTTAGGGGGTTAAGATCTATAAACTCAGCCTGTTACC
Found at i:55167301 original size:87 final size:87
Alignment explanation
Indices: 55167061--55167292 Score: 401
Period size: 87 Copynumber: 2.7 Consensus size: 87
55167051 CAACCTGCTG
55167061 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
55167126 GCCCATCGCCTTCGATCTGTTT
66 GCCCATCGCCTTCGATCTGTTT
*
55167148 CCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
* *
55167213 GCCCATCGTCTTTGATCTGTTT
66 GCCCATCGCCTTCGATCTGTTT
* * * *
55167235 CCCTACTACTTAGGGTGATAAGATCTGTAAACTCAGCCTGTTACCCTACTGCTTAGGG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGG
55167293 AGATAAGGCT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 137 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (87 bp):
CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
GCCCATCGCCTTCGATCTGTTT
Found at i:55171747 original size:17 final size:18
Alignment explanation
Indices: 55171720--55171754 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
55171710 AATAAATATT
55171720 TTTATTTGCTGTAATTTA
1 TTTATTTGCTGTAATTTA
55171738 TTTA-TTGCTGTAATTTA
1 TTTATTTGCTGTAATTTA
55171755 CAAATTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (18 bp):
TTTATTTGCTGTAATTTA
Found at i:55174476 original size:9 final size:9
Alignment explanation
Indices: 55174464--55174524 Score: 68
Period size: 9 Copynumber: 6.8 Consensus size: 9
55174454 GCTTTTTTTT
55174464 GTTAATTCG
1 GTTAATTCG
*
55174473 GTTAATTCA
1 GTTAATTCG
*
55174482 GTTAAATCG
1 GTTAATTCG
* * *
55174491 TTTAAATAG
1 GTTAATTCG
*
55174500 GTTAAATCG
1 GTTAATTCG
55174509 GTTAATTCG
1 GTTAATTCG
55174518 GTTAATT
1 GTTAATT
55174525 TTTATACTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (9 bp):
GTTAATTCG
Found at i:55178527 original size:47 final size:49
Alignment explanation
Indices: 55178451--55178583 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 49
55178441 TGTAACCCGC
55178451 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
55178501 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
55178544 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
55178584 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
44 2 0.03
45 2 0.03
46 29 0.40
47 30 0.42
48 2 0.03
49 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:55178599 original size:46 final size:44
Alignment explanation
Indices: 55178459--55178599 Score: 135
Period size: 46 Copynumber: 3.0 Consensus size: 44
55178449 GCCCATAAGC
*
55178459 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-AGT
* * *
55178506 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTAGT
55178552 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTAGT
55178598 GA
1 GA
55178600 CATGTCACTT
Statistics
Matches: 79, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.42
47 31 0.39
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (44 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTAGT
Found at i:55186025 original size:47 final size:47
Alignment explanation
Indices: 55185956--55186128 Score: 239
Period size: 47 Copynumber: 3.7 Consensus size: 47
55185946 CGCCCATAAG
55185956 CGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCA
55186003 CGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCA
* * *
55186050 CAAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCATAA
1 CGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-TCA
*
55186095 GTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 -CGAACTCGGACTCAACTCAACGAGTTCGGATGC
55186129 TCAACCATCC
Statistics
Matches: 114, Mismatches: 5, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 28 0.25
47 76 0.67
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (47 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:55194092 original size:4 final size:4
Alignment explanation
Indices: 55194083--55194111 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
55194073 TGAAATAAGC
55194083 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
55194112 TAAAACATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:55194217 original size:3 final size:3
Alignment explanation
Indices: 55194209--55194343 Score: 73
Period size: 3 Copynumber: 45.3 Consensus size: 3
55194199 ATAAAAGACC
** * *
55194209 ATA ATA ATA ATA ACG ATA ATA ATA ATA ATA AT- ATA ATA CCT- ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * ** * * *
55194253 ATA CTA ATA ATA GTA ATA ATA GGA A-A ATTA ATA TTA GTA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
* * *
55194298 ATA ATGGA A-A ATA ATA ATA ACA ATG ATA AT- ATA CTA ATA ATA ATA
1 ATA AT--A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55194343 A
1 A
55194344 ACGTGAAATT
Statistics
Matches: 99, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
2 9 0.09
3 85 0.86
4 3 0.03
5 2 0.02
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55194533 original size:12 final size:12
Alignment explanation
Indices: 55194516--55194542 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55194506 ATGTACATAA
55194516 TATATATATATG
1 TATATATATATG
55194528 TATATATATATG
1 TATATATATATG
55194540 TAT
1 TAT
55194543 TAGAAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:55204391 original size:21 final size:21
Alignment explanation
Indices: 55204341--55204393 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
55204331 CTAGGGTTTT
* *
55204341 CTTTG-TATTTTGGGCTTGTAT
1 CTTTGTTA-TTTGGGCTTATAA
* *
55204362 TTTTATTATTTGGGCTTATAA
1 CTTTGTTATTTGGGCTTATAA
55204383 CTTTGTTATTT
1 CTTTGTTATTT
55204394 ATTAAGGCCT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.15, C:0.08, G:0.17, T:0.60
Consensus pattern (21 bp):
CTTTGTTATTTGGGCTTATAA
Found at i:55206328 original size:63 final size:63
Alignment explanation
Indices: 55206233--55206358 Score: 166
Period size: 63 Copynumber: 2.0 Consensus size: 63
55206223 TCGGATTTGA
* * * *
55206233 GTGTGAGTGTCGCCTATAGATATATGGAGTTGATACATCTATGTTCTTTTTGCTTATTTGAGT
1 GTGTGAGTGTCGCCTATAGATAAATGGAGTTGATACATCTATGTTCTCTTCGCGTATTTGAGT
* *
55206296 GTGTGCGTGTCGCCTATAGGTATAAAT-G-GTTGATACATTTATGTTCTCTTCGCGTATTTGAGT
1 GTGTGAGTGTCGCCTATA-G-ATAAATGGAGTTGATACATCTATGTTCTCTTCGCGTATTTGAGT
55206359 CTAAGTGTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 48 0.87
64 2 0.04
65 5 0.09
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.43
Consensus pattern (63 bp):
GTGTGAGTGTCGCCTATAGATAAATGGAGTTGATACATCTATGTTCTCTTCGCGTATTTGAGT
Found at i:55206901 original size:235 final size:232
Alignment explanation
Indices: 55206422--55207125 Score: 868
Period size: 235 Copynumber: 2.9 Consensus size: 232
55206412 ATGTGGAAGG
*
55206422 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGTATAAGGGTACTTAAAAAGAAAAAAAATG
1 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGAT-AGGGTACTTAAAAAG---AAAAATG
* * * *
55206487 AATAGTCCGAACAACATAGGAAAAATATTTATATCTTCTCATTTATTTGATTGTGAAAGTTAATG
62 AATAGT-CGAACAACATAGGAAAAA-ATTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGG
* * * * *
55206552 AACAATAGGATATGATCTGTTAAGGCGTTGAAGTTACTGAATGTCTTTCTGGATATTTGATGTTT
125 AACAATGGGATATGATCTATTAAGGTGTTGAAGTTACTGAAT-TCTTTCTGAATATTT-ATGTCT
** * *
55206617 GGTAATAATTTTTTTATTTATTTATGATCTACCGATAGGTGCCCT
188 GGTAATAAGCTATTCATTTATTTATGATCTACCGATAGGTGCCCT
* *
55206662 TTGTTAGAGGATCTTATCTCCTTTGGAAATGTGTTGGATAGGGATACTTAAAAAGAAAAATGAAT
1 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAGGG-TACTTAAAAAGAAAAATGAAT
* *
55206727 AGTCGAAACAACAGAGGAAAAAAGTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGGAACA
65 AGTCG-AACAACATAGGAAAAAATTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGGAACA
* *
55206792 ATGGGATATGATCTATTAAGGTGTTGAAGTTATTGAATTCTTTCTGAATATTTAATGGCTGGTAA
129 ATGGGATATGATCTATTAAGGTGTTGAAGTTACTGAATTCTTTCTGAATATTT-ATGTCTGGTAA
* *
55206857 TAAGCTATTCATTTATTTATGATCTACCGGTAGGTGCTCT
193 TAAGCTATTCATTTATTTATGATCTACCGATAGGTGCCCT
* *
55206897 TTGTTAGAGGATCATATCTCCTTCGAAAATGTGTTGGATAGGGTTACTTAAAAAGAAAAACGAAT
1 TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAGGG-TACTTAAAAAGAAAAATGAAT
*
55206962 AGTCGGAAGAACATAGGAAAAAAATTTACATCTTTCCCATTTATTTGATTGTGAAAGTGAATGAA
65 AGTC-GAACAACATAGG-AAAAAATTTACATC-TTCCCATTTATTTGATTGTGAAAGT--A--AA
** * * * * * * * *
55207027 GTTGAACAATGAAATATAATATTTTGAGGTGTTCAAGTTACTGAACGTCTTTCTGCATATTTTTG
123 G--GAACAATGGGATATGATCTATTAAGGTGTTGAAGTTACTGAA-TTCTTTCTGAATATTTATG
** *
55207092 TCTGGTAATAAGCTATTGGTTTATTTCTGATCTA
185 TCTGGTAATAAGCTATTCATTTATTTATGATCTA
55207126 TCAATTGGTG
Statistics
Matches: 406, Mismatches: 46, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
235 130 0.32
236 88 0.22
237 53 0.13
239 5 0.01
240 47 0.12
241 3 0.01
243 66 0.16
244 14 0.03
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.37
Consensus pattern (232 bp):
TTGTTAGAGGATCATATCTCCTTTGAAAATGTGTTGGATAGGGTACTTAAAAAGAAAAATGAATA
GTCGAACAACATAGGAAAAAATTTACATCTTCCCATTTATTTGATTGTGAAAGTAAAGGAACAAT
GGGATATGATCTATTAAGGTGTTGAAGTTACTGAATTCTTTCTGAATATTTATGTCTGGTAATAA
GCTATTCATTTATTTATGATCTACCGATAGGTGCCCT
Found at i:55208738 original size:96 final size:96
Alignment explanation
Indices: 55208574--55208822 Score: 306
Period size: 96 Copynumber: 2.6 Consensus size: 96
55208564 GTTCCCGTAG
* * *
55208574 TTCTGTGAACAATACTGGGAATCCTCCTGCATCCCTACCAAACAGCGAACTGAACTCCTTTGCCA
1 TTCTGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTGAACTCCTTTGCCA
* ***
55208639 GTTTTAACAGCCTGAGTGCA-ATCACT-TCTAA
66 GTTTTAACAGCC-CAACCCAGATCACTAT-TAA
* *
55208670 TTCTGTGAACAATTCTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTAAACTCCTCTT-CC
1 TTCTGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTGAACTCCT-TTGCC
* * *
55208734 AGTTTTAACAGCCCAACCCAGTTCAGTATTAG
65 AGTTTTAACAGCCCAACCCAGATCACTATTAA
* * * *
55208766 TTCCGTGAACAATAGTGGGAACTCTCCTGCATCCCTACCGAACAACCAACTGAACTC
1 TTCTGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTGAACTC
55208823 TACTGCTTTT
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
95 3 0.02
96 126 0.95
97 3 0.02
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (96 bp):
TTCTGTGAACAATACTGGGAACCCTCCTGCATCCCTACCGAACAGCCAACTGAACTCCTTTGCCA
GTTTTAACAGCCCAACCCAGATCACTATTAA
Found at i:55210554 original size:29 final size:29
Alignment explanation
Indices: 55210512--55210573 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
55210502 ATATTTCACG
55210512 AATTAAACAAATAACTCGATCCGTAAACA
1 AATTAAACAAATAACTCGATCCGTAAACA
55210541 AATTAAACAAATAACTCGATCCGTAAACA
1 AATTAAACAAATAACTCGATCCGTAAACA
55210570 AATT
1 AATT
55210574 TACATTGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (29 bp):
AATTAAACAAATAACTCGATCCGTAAACA
Found at i:55212402 original size:31 final size:31
Alignment explanation
Indices: 55212364--55212424 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
55212354 AACAGTTCAA
*
55212364 TGACTTAAATAAAAACTTTTGAATAATTTAG
1 TGACTTAAATAAAAACTTTCGAATAATTTAG
*
55212395 TGACTTAAATGAAAACTTTCGAATAATTTA
1 TGACTTAAATAAAAACTTTCGAATAATTTA
55212425 ATGATCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCGAATAATTTAG
Found at i:55215839 original size:29 final size:29
Alignment explanation
Indices: 55215766--55215824 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
55215756 TTTGACTCAA
* *
55215766 TGTATAATGTCATACATAAATTTTAATTT
1 TGTATAATTTTATACATAAATTTTAATTT
*
55215795 TGTATGATTTTATACATAAAATTTTAATTT
1 TGTATAATTTTATACAT-AAATTTTAATTT
55215825 GATTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (29 bp):
TGTATAATTTTATACATAAATTTTAATTT
Found at i:55228383 original size:15 final size:15
Alignment explanation
Indices: 55228363--55228394 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55228353 GTGGCTATGC
55228363 GTAGTTCTAAGTATT
1 GTAGTTCTAAGTATT
55228378 GTAGTTCTAAGTATT
1 GTAGTTCTAAGTATT
55228393 GT
1 GT
55228395 GTAAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (15 bp):
GTAGTTCTAAGTATT
Found at i:55229438 original size:14 final size:14
Alignment explanation
Indices: 55229419--55229445 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55229409 ATAATTTTAA
55229419 TAAATTAAAAATAT
1 TAAATTAAAAATAT
55229433 TAAATTAAAAATA
1 TAAATTAAAAATA
55229446 ATATAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTAAAAATAT
Found at i:55230521 original size:16 final size:17
Alignment explanation
Indices: 55230500--55230535 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
55230490 ATTTATAAAA
55230500 ATAAAAAT-AACTTAAT
1 ATAAAAATAAACTTAAT
*
55230516 ATAAAAATAAATTTAAT
1 ATAAAAATAAACTTAAT
55230533 ATA
1 ATA
55230536 TTTTACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAAATAAACTTAAT
Found at i:55231494 original size:20 final size:21
Alignment explanation
Indices: 55231455--55231494 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55231445 AACATGCAAG
*
55231455 AAATTATTAATAATATTATTT
1 AAATTATTAATAATAATATTT
*
55231476 AAATTA-TAATAGTAATATT
1 AAATTATTAATAATAATATT
55231495 CAAACCATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AAATTATTAATAATAATATTT
Found at i:55231902 original size:23 final size:23
Alignment explanation
Indices: 55231876--55231941 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
55231866 ATTATTACAC
55231876 ATTAAGATATTTTTATGTAACAA
1 ATTAAGATATTTTTATGTAACAA
*
55231899 ATTAA-A-A-TTTCAT-T-ACAA
1 ATTAAGATATTTTTATGTAACAA
55231917 ATTAAGATATTTTTATG-ATACAA
1 ATTAAGATATTTTTATGTA-ACAA
55231940 AT
1 AT
55231942 ACATACTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
18 9 0.26
19 2 0.06
20 6 0.17
21 6 0.17
22 1 0.03
23 11 0.31
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (23 bp):
ATTAAGATATTTTTATGTAACAA
Found at i:55237431 original size:38 final size:38
Alignment explanation
Indices: 55237375--55237471 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 38
55237365 TTATCAATTG
* * * *
55237375 CATGTTCAGCATGCCTACTGTTACTGTTGAACTGATTA
1 CATGTTAAGCATGTCTACTGTTACTATTGAACTGAATA
* *
55237413 CATGTTAAGCATGTCTACTGCTACTATTGAATTGAATA
1 CATGTTAAGCATGTCTACTGTTACTATTGAACTGAATA
*
55237451 CAT-TTAAGCATGTCTATTGTT
1 CATGTTAAGCATGTCTACTGTT
55237472 TTTAGATGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 16 0.31
38 35 0.69
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (38 bp):
CATGTTAAGCATGTCTACTGTTACTATTGAACTGAATA
Found at i:55241130 original size:13 final size:13
Alignment explanation
Indices: 55241114--55241141 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55241104 CCGGTAAATT
55241114 TACTTTTAATTTA
1 TACTTTTAATTTA
55241127 TACTTTTAATTTA
1 TACTTTTAATTTA
55241140 TA
1 TA
55241142 GGCACAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (13 bp):
TACTTTTAATTTA
Found at i:55249010 original size:15 final size:15
Alignment explanation
Indices: 55248992--55249021 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55248982 TATTTTTTCC
55248992 TTTACCTTTTTATAT
1 TTTACCTTTTTATAT
55249007 TTTACCTTTTTATAT
1 TTTACCTTTTTATAT
55249022 ATTATATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTACCTTTTTATAT
Found at i:55250318 original size:14 final size:15
Alignment explanation
Indices: 55250277--55250322 Score: 58
Period size: 14 Copynumber: 3.0 Consensus size: 15
55250267 AAAAAATATT
*
55250277 TTTTTACAATTTTGTA
1 TTTTTATAATTTT-TA
55250293 TTTTTAATAATTTTTA
1 TTTTT-ATAATTTTTA
55250309 -TTTTATAATTTTTA
1 TTTTTATAATTTTTA
55250323 AAAAAAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.36
15 4 0.14
16 7 0.25
17 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTTATAATTTTTA
Found at i:55250791 original size:24 final size:24
Alignment explanation
Indices: 55250744--55250791 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55250734 TTAGTATGAC
*
55250744 AAAATAAAATCTAAATAATTATAA
1 AAAATAAAATCTAAATAATCATAA
*
55250768 AAAATTAAAATC-AAATTATCATAA
1 AAAA-TAAAATCTAAATAATCATAA
55250792 CTATATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAATAAAATCTAAATAATCATAA
Found at i:55251464 original size:44 final size:43
Alignment explanation
Indices: 55251405--55251506 Score: 177
Period size: 44 Copynumber: 2.3 Consensus size: 43
55251395 CTTTGATAAC
*
55251405 ATTTCTTATAAATAATATAACTTTTTCATAACTTTATAAAGTT
1 ATTTTTTATAAATAATATAACTTTTTCATAACTTTATAAAGTT
*
55251448 ATTTTTTTATAAATAATATAACTTTTTCATAATTTTATAAAGTT
1 A-TTTTTTATAAATAATATAACTTTTTCATAACTTTATAAAGTT
55251492 ATTTTTTATAAATAA
1 ATTTTTTATAAATAA
55251507 GTTATGATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
43 15 0.27
44 41 0.73
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (43 bp):
ATTTTTTATAAATAATATAACTTTTTCATAACTTTATAAAGTT
Found at i:55251659 original size:13 final size:13
Alignment explanation
Indices: 55251641--55251669 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
55251631 AATATATTAT
55251641 AATACTTATAATA
1 AATACTTATAATA
55251654 AATACTTATAATA
1 AATACTTATAATA
55251667 AAT
1 AAT
55251670 TTTTTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (13 bp):
AATACTTATAATA
Found at i:55251731 original size:24 final size:23
Alignment explanation
Indices: 55251704--55251778 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 23
55251694 TTTAGGATTC
55251704 AAATAATATTTTTATTACTTTATA
1 AAATAATATTTTTATTA-TTTATA
* * *
55251728 AAATACACA-ATTTATTTTTTATA
1 AAATA-ATATTTTTATTATTTATA
* *
55251751 ATATAAT-TTTTTAGTATTTATA
1 AAATAATATTTTTATTATTTATA
*
55251773 ATATAA
1 AAATAA
55251779 GAAGTTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
22 18 0.44
23 10 0.24
24 11 0.27
25 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (23 bp):
AAATAATATTTTTATTATTTATA
Found at i:55254114 original size:14 final size:14
Alignment explanation
Indices: 55254095--55254123 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55254085 TGAAAGATAA
55254095 ATTTTATTAAAACT
1 ATTTTATTAAAACT
55254109 ATTTTATTAAAACT
1 ATTTTATTAAAACT
55254123 A
1 A
55254124 AGTAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTTATTAAAACT
Found at i:55254842 original size:13 final size:15
Alignment explanation
Indices: 55254814--55254845 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
55254804 TATTAAATAT
55254814 TTTTTTATTATGTAA
1 TTTTTTATTATGTAA
55254829 TTTTTT-TTAT-TAA
1 TTTTTTATTATGTAA
55254842 TTTT
1 TTTT
55254846 GCATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 4 0.24
15 6 0.35
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTTTATTATGTAA
Found at i:55260193 original size:59 final size:60
Alignment explanation
Indices: 55260041--55260182 Score: 180
Period size: 61 Copynumber: 2.4 Consensus size: 60
55260031 TTTTCAGAAA
*
55260041 ATAAAGGATATATTGATCATTTAAGCGTTTTAATATATTTGGATATTTTTATAAAAAAAATT
1 ATAAAGG-TATATTGATCATTTAA-CCTTTTAATATATTTGGATATTTTTATAAAAAAAATT
** ** **
55260103 ATTTATTTATATTGATCATTTAAGCCTTTTAATATATTTGGATATTTTTAT-AAAAAGTTT
1 ATAAAGGTATATTGATCATTTAA-CCTTTTAATATATTTGGATATTTTTATAAAAAAAATT
55260163 A-AAAGGTATATTGATCATTT
1 ATAAAGGTATATTGATCATTT
55260183 CATTCTTTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 15 0.22
60 8 0.12
61 43 0.62
62 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (60 bp):
ATAAAGGTATATTGATCATTTAACCTTTTAATATATTTGGATATTTTTATAAAAAAAATT
Found at i:55266776 original size:21 final size:20
Alignment explanation
Indices: 55266746--55266803 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
55266736 TGACAGACAT
55266746 AAAT-TAAATTTTTTTAAAA
1 AAATATAAATTTTTTTAAAA
* *
55266765 AAAGTATAAATTAATATTAAAA
1 AAA-TATAAATT-TTTTTAAAA
*
55266787 AGATATAACATTTTTTT
1 AAATATAA-ATTTTTTT
55266804 GGAGAAGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.10
20 1 0.03
21 14 0.47
22 12 0.40
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (20 bp):
AAATATAAATTTTTTTAAAA
Found at i:55266977 original size:23 final size:24
Alignment explanation
Indices: 55266951--55266995 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
55266941 CACAAAAATA
55266951 CAAACTAATAT-TATTTTAATATC
1 CAAACTAATATATATTTTAATATC
* * *
55266974 CAAATTTATCTATATTTTAATA
1 CAAACTAATATATATTTTAATA
55266996 AAATATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (24 bp):
CAAACTAATATATATTTTAATATC
Found at i:55267008 original size:24 final size:23
Alignment explanation
Indices: 55266977--55267022 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
55266967 TAATATCCAA
55266977 ATTTATCTATAT-TTTAATAAAAT
1 ATTTATCTATATATTTAA-AAAAT
*
55267000 ATTTAATCTTTATATTTAAAAAA
1 ATTT-ATCTATATATTTAAAAAA
55267023 GTTAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTATCTATATATTTAAAAAAT
Found at i:55273005 original size:19 final size:19
Alignment explanation
Indices: 55272976--55273040 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
55272966 TAATAAACTA
55272976 TTAAT-ATAAATTATTATT
1 TTAATAATAAATTATTATT
55272994 TTAATAATAAATTATTATT
1 TTAATAATAAATTATTATT
** *
55273013 AAAATAAT-AA-T-TTATA
1 TTAATAATAAATTATTATT
55273029 TTAATAATAAAT
1 TTAATAATAAAT
55273041 ATTTTGTAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 10 0.26
17 3 0.08
18 7 0.18
19 19 0.49
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATAATAAATTATTATT
Found at i:55273044 original size:19 final size:18
Alignment explanation
Indices: 55272974--55273040 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
55272964 TATAATAAAC
55272974 TATTAAT-ATAAATTATTA
1 TATTAATAATAAATT-TTA
* *
55272992 TTTTAATAATAAATTAT-
1 TATTAATAATAAATTTTA
*
55273009 TATTAA-AATAATAATTTA
1 TATTAATAATAA-ATTTTA
55273027 TATTAATAATAAAT
1 TATTAATAATAAAT
55273041 ATTTTGTAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 5 0.13
17 8 0.21
18 14 0.36
19 12 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAATAATAAATTTTA
Found at i:55273657 original size:10 final size:10
Alignment explanation
Indices: 55273642--55273667 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
55273632 GTAAATTGCA
55273642 TTATAATATT
1 TTATAATATT
55273652 TTATAATATT
1 TTATAATATT
55273662 TTATAA
1 TTATAA
55273668 CAAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATAATATT
Found at i:55273873 original size:33 final size:32
Alignment explanation
Indices: 55273805--55273877 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
55273795 CAAGTTTTAT
* *
55273805 AAAATATTTTTAGAAAATTTATCAAACAATAA
1 AAAATATTTTCAGAAAATTCATCAAACAATAA
* *
55273837 AAAATATTTTACATAAAATTCATTCAAAC-ATTA
1 AAAATATTTT-CAGAAAATTCA-TCAAACAATAA
55273870 AAAATATT
1 AAAATATT
55273878 AATTCTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 10 0.29
33 19 0.54
34 6 0.17
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.36
Consensus pattern (32 bp):
AAAATATTTTCAGAAAATTCATCAAACAATAA
Found at i:55278922 original size:22 final size:22
Alignment explanation
Indices: 55278892--55278947 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
55278882 AATTATTCTG
55278892 TAATATTTAAATTTAGAA-AAATT
1 TAAT-TTTAAATTTA-AATAAATT
*
55278915 TAATTTTAATTTTAAATAAATT
1 TAATTTTAAATTTAAATAAATT
* *
55278937 AAATTTAAAAT
1 TAATTTTAAAT
55278948 GATACGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.79
23 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAATTTTAAATTTAAATAAATT
Found at i:55279245 original size:24 final size:29
Alignment explanation
Indices: 55279190--55279252 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
55279180 AAAATTTACA
*
55279190 TAAATAAATAAATTTTATTATTAATGTAT
1 TAAATAAATAAATGTTATTATTAATGTAT
55279219 TAAAT-AAT-AATGTTATT-TTAA-GT-T
1 TAAATAAATAAATGTTATTATTAATGTAT
55279243 TAAAATAAAT
1 T-AAATAAAT
55279253 TATTTGTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 2 0.06
25 6 0.19
26 7 0.23
27 8 0.26
28 3 0.10
29 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
TAAATAAATAAATGTTATTATTAATGTAT
Found at i:55283606 original size:22 final size:22
Alignment explanation
Indices: 55283581--55283622 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
55283571 ATAAGCTCAT
*
55283581 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
55283603 TTACATTCAATCAATAAATG
1 TTACATTCAATCAATAAATG
55283623 AGAAATTAAG
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:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:55284066 original size:11 final size:11
Alignment explanation
Indices: 55284050--55284074 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55284040 TGTTGAACTT
55284050 CTAAATTATCA
1 CTAAATTATCA
55284061 CTAAATTATCA
1 CTAAATTATCA
55284072 CTA
1 CTA
55284075 GAATGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (11 bp):
CTAAATTATCA
Found at i:55287366 original size:24 final size:24
Alignment explanation
Indices: 55287334--55287389 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
55287324 TAATTAGATA
55287334 AATATTATTTTATTAATATTTTAAT
1 AATA-TATTTTATTAATATTTTAAT
* *
55287359 AATATATTTTATTATTATTTTATT
1 AATATATTTTATTAATATTTTAAT
*
55287383 ATTATAT
1 AATATAT
55287390 AAAGAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
AATATATTTTATTAATATTTTAAT
Found at i:55287384 original size:11 final size:11
Alignment explanation
Indices: 55287336--55287387 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
55287326 ATTAGATAAA
55287336 TATTATTTTAT
1 TATTATTTTAT
*
55287347 TAATATTTTAAT
1 TATTATTTT-AT
*
55287359 AATATATTTTAT
1 TAT-TATTTTAT
55287371 TATTATTTTAT
1 TATTATTTTAT
55287382 TATTAT
1 TATTAT
55287388 ATAAAGAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 22 0.63
12 7 0.20
13 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:55289564 original size:46 final size:46
Alignment explanation
Indices: 55289512--55289739 Score: 277
Period size: 46 Copynumber: 5.0 Consensus size: 46
55289502 AGTGTGCTCT
*
55289512 CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATATATAAGACCATGGTTGAAAGATACCATGGCAAC
55289558 CTGATATGAAATGA-ATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAAT-ATATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
55289604 GTGATATGAAATGA-ATAAGACCATGGTTGAAAAATACCATGGCAAC
1 CTGATATGAAAT-ATATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
55289650 GTGACATGAAA-ATAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATAT-ATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
55289696 ATGACA-GAAA-ATGAGTAAGACAATAGTTGAAAGACACTATGGCA
1 CTGATATGAAATAT-A-TAAGACCATGGTTGAAAGATACCATGGCA
55289740 TTATGTCAAA
Statistics
Matches: 167, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.01
45 7 0.04
46 158 0.95
47 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATATATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:55289670 original size:92 final size:92
Alignment explanation
Indices: 55289513--55289727 Score: 310
Period size: 92 Copynumber: 2.3 Consensus size: 92
55289503 GTGTGCTCTC
* *
55289513 TGATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAATAAG
1 TGATATGAAATGA-GTAAGACCATGGTTGAAAAATACCATGGCAACCTGACATGAAATGAATAAG
*
55289577 ACCATGGTTGAAAGATACCATGGCAACG
65 ACCATGGTTGAAAGATACCATGGCAACA
* *
55289605 TGATATGAAATGAATAAGACCATGGTTGAAAAATACCATGGCAACGTGACATGAAAAT-AATAAG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAAATACCATGGCAACCTGACATG-AAATGAATAAG
55289669 ACCATGGTTGAAAGATACCATGGCAACA
65 ACCATGGTTGAAAGATACCATGGCAACA
* * *
55289697 TGACA-GAAAATGAGTAAGACAATAGTTGAAA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAA
55289728 GACACTATGG
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
91 1 0.01
92 105 0.95
93 5 0.05
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (92 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAAATACCATGGCAACCTGACATGAAATGAATAAGA
CCATGGTTGAAAGATACCATGGCAACA
Found at i:55291145 original size:13 final size:13
Alignment explanation
Indices: 55291127--55291154 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55291117 TAAATGTATG
55291127 AATTATGTATGTT
1 AATTATGTATGTT
55291140 AATTATGTATGTT
1 AATTATGTATGTT
55291153 AA
1 AA
55291155 ATGATGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
AATTATGTATGTT
Found at i:55293345 original size:53 final size:53
Alignment explanation
Indices: 55293149--55293352 Score: 133
Period size: 53 Copynumber: 3.8 Consensus size: 53
55293139 AGGGTTTAAG
* * * * * * * *
55293149 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGCAAG
1 GATACCATGTAAGACCATTCCAAGACATGACAATGGTAAG-TTCATAAGGCAAA
* * * * * * * * *
55293203 GAAATCATATAAGACTATGT-CAAGACATGGCATTGATAAACTACGATAAGGCAAA
1 GATACCATGTAAGACCAT-TCCAAGACATGACAATGGT-AAGTTC-ATAAGGCAAA
* * * * *
55293258 GATCCCATGTAAGACTATTCCAAGGCATGACAATGGTGAGTTCATAAGGCAAG
1 GATACCATGTAAGACCATTCCAAGACATGACAATGGTAAGTTCATAAGGCAAA
* *
55293311 GATACCATGTAAGACCATGT-TAAGACATGTCAATGGTAAGTT
1 GATACCATGTAAGACCAT-TCCAAGACATGACAATGGTAAGTT
55293353 TAAAAAGGAT
Statistics
Matches: 114, Mismatches: 31, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
53 43 0.38
54 34 0.30
55 37 0.32
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (53 bp):
GATACCATGTAAGACCATTCCAAGACATGACAATGGTAAGTTCATAAGGCAAA
Found at i:55299180 original size:13 final size:14
Alignment explanation
Indices: 55299155--55299218 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 14
55299145 TTCTCCATAG
55299155 TTTTTTCTCTTCTC
1 TTTTTTCTCTTCTC
55299169 TTTTTTCTTTCTTTCTC
1 TTTTTTC--TC-TTCTC
* *
55299186 TCTCTCTCTCTCTCTC
1 T-TTTTTCTCT-TCTC
55299202 TTTTTTCT-TT-TC
1 TTTTTTCTCTTCTC
55299214 TTTTT
1 TTTTT
55299219 GGCTTTCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 7 0.17
13 1 0.02
14 8 0.20
15 6 0.15
16 9 0.22
17 6 0.15
18 4 0.10
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTCTCTTCTC
Found at i:55300446 original size:87 final size:87
Alignment explanation
Indices: 55300298--55300499 Score: 233
Period size: 87 Copynumber: 2.3 Consensus size: 87
55300288 ATTTGATCTC
* ** * * *
55300298 AACTTATCGGTACAGTGGTTTACCGCATTGTACCACTTGTACGTCAGCTTTGCTGCATACTATTA
1 AACTTATAGGTACAGCAGTTTACCGCACTATACCACATGTACGTCAGCTTTGCTGCATACTATTA
*
55300363 TCTGATCTAGTAGTTTAACTGT
66 TCTGATCTAGCAGTTTAACTGT
* * * * *
55300385 AACTTATAGGTACAGCAGTTTATCGCACTATACCGCATGTATGTCAGTTTTGCTGCGTACTATTA
1 AACTTATAGGTACAGCAGTTTACCGCACTATACCACATGTACGTCAGCTTTGCTGCATACTATTA
*
55300450 TCTGATCTAGCAGTTTAAACTGC
66 TCTGATCTAGCAGTTT-AACTGT
* ** * *
55300473 AACATATCTGTGCAGTAGTTTACCGCA
1 AACTTATAGGTACAGCAGTTTACCGCA
55300500 ATGCACTGTA
Statistics
Matches: 95, Mismatches: 19, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
87 69 0.73
88 26 0.27
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (87 bp):
AACTTATAGGTACAGCAGTTTACCGCACTATACCACATGTACGTCAGCTTTGCTGCATACTATTA
TCTGATCTAGCAGTTTAACTGT
Found at i:55302201 original size:25 final size:25
Alignment explanation
Indices: 55302173--55302221 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
55302163 ATTTTATAAT
55302173 CAGAATAACATTTCATTATCAGAAC
1 CAGAATAACATTTCATTATCAGAAC
* * *
55302198 CAGAATGACATTTGATTATTAGAA
1 CAGAATAACATTTCATTATCAGAA
55302222 TTAAAGTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (25 bp):
CAGAATAACATTTCATTATCAGAAC
Found at i:55302269 original size:74 final size:74
Alignment explanation
Indices: 55302191--55302337 Score: 183
Period size: 74 Copynumber: 2.0 Consensus size: 74
55302181 CATTTCATTA
* * *
55302191 TCAGAACCAGA-ATGACATTTGA-TTATTAGAATTAA-AGTGACATTTTATTATCAAATCAAAAT
1 TCAGAACCA-ATATGACATTT-ATTTATTAGAA-TAAGAATAACATTTCATTATCAAATCAAAAT
55302253 GACATATCATAT
63 GACATATCATAT
* * * *
55302265 TCAGAATCAATATGATATTTATTTATTAGAATAAGAATAACATTTCATTATCAAATCAGAATGTC
1 TCAGAACCAATATGACATTTATTTATTAGAATAAGAATAACATTTCATTATCAAATCAAAATGAC
55302330 ATATCATA
66 ATATCATA
55302338 ATTTACTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
73 5 0.08
74 58 0.92
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (74 bp):
TCAGAACCAATATGACATTTATTTATTAGAATAAGAATAACATTTCATTATCAAATCAAAATGAC
ATATCATAT
Found at i:55302315 original size:25 final size:24
Alignment explanation
Indices: 55302180--55302315 Score: 89
Period size: 25 Copynumber: 5.5 Consensus size: 24
55302170 AATCAGAATA
* * *
55302180 ACATTTCATTATCAGAACCAGAATG
1 ACATTTCATTATTAGAA-TAAAATG
* *
55302205 ACATTTGATTATTAGAATTAAAGTG
1 ACATTTCATTATTAGAA-TAAAATG
* *
55302230 ACATTTTATTATCA-AATCAAAATG
1 ACATTTCATTATTAGAAT-AAAATG
* *
55302254 ACATATCA-TATTCAGAATCAATATG
1 ACATTTCATTATT-AGAAT-AAAATG
* *
55302279 ATATTT-ATTTATTAGAATAAGAATA
1 ACATTTCA-TTATTAGAATAA-AATG
55302304 ACATTTCATTAT
1 ACATTTCATTAT
55302316 CAAATCAGAA
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
23 4 0.05
24 17 0.20
25 60 0.70
26 5 0.06
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (24 bp):
ACATTTCATTATTAGAATAAAATG
Found at i:55309192 original size:17 final size:17
Alignment explanation
Indices: 55309172--55309204 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55309162 GATATCAGGA
*
55309172 TAAAATTTTAATATTAT
1 TAAAATTTAAATATTAT
55309189 TAAAATTTAAATATTA
1 TAAAATTTAAATATTA
55309205 AAAACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAATTTAAATATTAT
Found at i:55312464 original size:3 final size:3
Alignment explanation
Indices: 55312456--55312506 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
55312446 TTATCATATT
55312456 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55312504 TAA
1 TAA
55312507 AGAATTACAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55315853 original size:51 final size:51
Alignment explanation
Indices: 55315793--55315891 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
55315783 ACCAAGGTTA
55315793 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCGAT
1 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCGAT
*
55315844 GTTGAGGACTTAAATGTAATATTTTCAAAATTGTCGGGTTGGTGTTGC
1 GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGC
55315892 AACGTTAAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (51 bp):
GTTGAGGACTTAAATGTAATATTTTCAAAATTATCGGGTTGGTGTTGCGAT
Found at i:55321154 original size:39 final size:39
Alignment explanation
Indices: 55321097--55321223 Score: 182
Period size: 39 Copynumber: 3.2 Consensus size: 39
55321087 GGACTTTAGC
* * * * *
55321097 CCGGACATATTTCTAGCACGTAGCCTACGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
55321136 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
* *
55321175 CCGGATATAATTCCAGCACATAGCCTGCGAACCTTTAAGC
1 CCGGATATAATTCCAGCACATAGCCTGCGGACC-TTAAGT
55321215 CCGGATATA
1 CCGGATATA
55321224 TGTCAAATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 66 0.82
40 14 0.17
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
Found at i:55333907 original size:13 final size:13
Alignment explanation
Indices: 55333889--55333920 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
55333879 ATTTAGTCCA
55333889 TATACTAAATCCC
1 TATACTAAATCCC
55333902 TATACTAAATCCC
1 TATACTAAATCCC
55333915 TATACT
1 TATACT
55333921 TTAAAAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (13 bp):
TATACTAAATCCC
Found at i:55337940 original size:24 final size:24
Alignment explanation
Indices: 55337913--55337964 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
55337903 ACTAATCCGG
55337913 CTCCCACCGGCCCTACCACGACTC
1 CTCCCACCGGCCCTACCACGACTC
* * *
55337937 CTCCGACTGGCCCTACCATGACTC
1 CTCCCACCGGCCCTACCACGACTC
55337961 CTCC
1 CTCC
55337965 GACTGGGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.15, C:0.54, G:0.13, T:0.17
Consensus pattern (24 bp):
CTCCCACCGGCCCTACCACGACTC
Found at i:55337965 original size:24 final size:24
Alignment explanation
Indices: 55337921--55338012 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
55337911 GGCTCCCACC
55337921 GGCCCTACCACGACTCCTCCGACT
1 GGCCCTACCACGACTCCTCCGACT
*
55337945 GGCCCTACCATGACTCCTCCGACT
1 GGCCCTACCACGACTCCTCCGACT
** * * *
55337969 GGGACAACCACAACTCCTCCAACT
1 GGCCCTACCACGACTCCTCCGACT
** * *
55337993 GGGACAACCACAACTCCTCC
1 GGCCCTACCACGACTCCTCC
55338013 AACAGGGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.24, C:0.46, G:0.15, T:0.15
Consensus pattern (24 bp):
GGCCCTACCACGACTCCTCCGACT
Found at i:55338013 original size:24 final size:24
Alignment explanation
Indices: 55337957--55338051 Score: 163
Period size: 24 Copynumber: 4.0 Consensus size: 24
55337947 CCCTACCATG
* *
55337957 ACTCCTCCGACTGGGACAACCACA
1 ACTCCTCCAACAGGGACAACCACA
*
55337981 ACTCCTCCAACTGGGACAACCACA
1 ACTCCTCCAACAGGGACAACCACA
55338005 ACTCCTCCAACAGGGACAACCACA
1 ACTCCTCCAACAGGGACAACCACA
55338029 ACTCCTCCAACAGGGACAACCAC
1 ACTCCTCCAACAGGGACAACCAC
55338052 GAGTCCAGGA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.34, C:0.42, G:0.14, T:0.11
Consensus pattern (24 bp):
ACTCCTCCAACAGGGACAACCACA
Found at i:55341242 original size:22 final size:21
Alignment explanation
Indices: 55341200--55341242 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
55341190 CTCAAAATAT
* *
55341200 ATGAAAAAATCTTTTTAAAAA
1 ATGAAAAAATCATGTTAAAAA
*
55341221 ATGAAAATAATCATGTTGAAAA
1 ATGAAAA-AATCATGTTAAAAA
55341243 CATTCCCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (21 bp):
ATGAAAAAATCATGTTAAAAA
Found at i:55343525 original size:20 final size:20
Alignment explanation
Indices: 55343468--55343530 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
55343458 TTTATTCATA
*
55343468 TAATAAATTA-TTAATATAAT
1 TAATAAATTATTTAATAT-TT
*
55343488 TAATATAA--ATTTATTATTT
1 TAATA-AATTATTTAATATTT
55343507 TAATAAATTATTTAATATTT
1 TAATAAATTATTTAATATTT
55343527 TAAT
1 TAAT
55343531 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.06
19 7 0.19
20 25 0.69
21 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATAAATTATTTAATATTT
Done.