Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 84 of 210
Found at i:29159818 original size:45 final size:44
Alignment explanation
Indices: 29159709--29159869 Score: 162
Period size: 45 Copynumber: 3.6 Consensus size: 44
29159699 GATCGCATCT
* * ** *
29159709 AGTCTTATCTCCTTGAAGTTGCAGAGGAGTAGA-CTGAGTAAGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAG-A
* *
29159753 GGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAG-A
** * *
29159798 AGTCTTATCTCCCTGAAGTTGCAGTGGACCAAACTCAAGAAAGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAG-A
* * *
29159843 AGTCTTATCCCCCTGAAATTGAAGTGG
1 AGTCTTATCTCCCTGAAGTTGCAGTGG
29159870 GGCAAACTAA
Statistics
Matches: 98, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
44 30 0.31
45 68 0.69
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGA
Found at i:29159876 original size:45 final size:45
Alignment explanation
Indices: 29159583--29159877 Score: 180
Period size: 44 Copynumber: 6.7 Consensus size: 45
29159573 AGATGGCGAA
* * * * *
29159583 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAA-TAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAG-AAAGTAAG
* ** * *
29159627 TCTTATCTCCCAGAAGTTGCAGTGGAGCTGA-TTAA-AATG-ACAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGTA-AG
* * * * * **
29159670 ATCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-TC--GCATCT-AG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGTAAG
* * * * * * *
29159711 TCTTATCTCCTTGAAGTTGCAGAGGAGTAGACT-GAGTAAGTAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGTAAG
* * * **
29159755 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGCGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGTAAG
*
29159800 TCTTATCTCCCTGAAGTTGCAGTGGACCAAACTCAAGAAAGTAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGTAAG
* * * *
29159845 TCTTATCCCCCTGAAATTGAAGTGGGGCAAACT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACT
29159878 AAGTAAGCAA
Statistics
Matches: 199, Mismatches: 40, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
40 20 0.10
41 11 0.06
42 4 0.02
43 12 0.06
44 79 0.40
45 73 0.37
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGTAAG
Found at i:29160723 original size:13 final size:13
Alignment explanation
Indices: 29160707--29160731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29160697 TTTCTTTCAT
29160707 TTTTTATTTTTTA
1 TTTTTATTTTTTA
29160720 TTTTTATTTTTT
1 TTTTTATTTTTT
29160732 TACATGCAAA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:29161562 original size:37 final size:38
Alignment explanation
Indices: 29161477--29161571 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 38
29161467 CTACAGTTCA
29161477 ATATAGTTTTTTTTCATTATTTTTTAATTAATTAATAATGT
1 ATATA-TTTTTTTT-ATTATTTTTTAA-TAATTAATAATGT
29161518 A-ATTATTTTTTTTATT-TTTTTTAA-AATCT-ATATATGT
1 ATA-TATTTTTTTTATTATTTTTTAATAAT-TAATA-ATGT
29161555 ATATATTTATTATTTAT
1 ATATATTT-TT-TTTAT
29161572 ATATGTGCAC
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
36 6 0.12
37 11 0.23
38 11 0.23
39 8 0.17
40 9 0.19
41 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (38 bp):
ATATATTTTTTTTATTATTTTTTAATAATTAATAATGT
Found at i:29161747 original size:14 final size:13
Alignment explanation
Indices: 29161720--29161754 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
29161710 TATTTCTTTT
*
29161720 TATAAATGTGTTA
1 TATAAATTTGTTA
29161733 TATATAATTTGTTA
1 TATA-AATTTGTTA
29161747 TATAAATT
1 TATAAATT
29161755 CTATAATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
TATAAATTTGTTA
Found at i:29163231 original size:29 final size:29
Alignment explanation
Indices: 29163169--29163309 Score: 131
Period size: 29 Copynumber: 4.9 Consensus size: 29
29163159 ATGTTATTTT
* ** *
29163169 GATTTTGGCTTAGGG-TTTTGAAGTTTGG
1 GATTTTGGTTTAGGGTTTTTGATTTTTGA
* * * *
29163197 GAATTTTGCTTTAGGATTTTTTACTTTTGA
1 G-ATTTTGGTTTAGGGTTTTTGATTTTTGA
*
29163227 GATTTTGGTTTAGGGCTTTTGATTTTTGA
1 GATTTTGGTTTAGGGTTTTTGATTTTTGA
* ** *
29163256 TATTTTTATTAAGGGTTTTTGATTTTTGA
1 GATTTTGGTTTAGGGTTTTTGATTTTTGA
* *
29163285 GATATTGGTTTAGGGTTTTTTATTT
1 GATTTTGGTTTAGGGTTTTTGATTT
29163310 GACTACCTAC
Statistics
Matches: 88, Mismatches: 23, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
28 1 0.01
29 77 0.88
30 10 0.11
ACGTcount: A:0.17, C:0.03, G:0.24, T:0.56
Consensus pattern (29 bp):
GATTTTGGTTTAGGGTTTTTGATTTTTGA
Found at i:29165597 original size:29 final size:30
Alignment explanation
Indices: 29165547--29165640 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 30
29165537 GTTAAATGAC
29165547 TTTTTAT-AG-TTTTA--AATTTTTAATAA
1 TTTTTATAAGTTTTTAGGAATTTTTAATAA
*
29165573 TTTTTATAA-TTTATT-GGAATTTTTAATAC
1 TTTTTATAAGTTT-TTAGGAATTTTTAATAA
* * *
29165602 TATTTATAAGTTTTTATGAATTTTT-ATATG
1 TTTTTATAAGTTTTTAGGAATTTTTAATA-A
29165632 TTTTTATAA
1 TTTTTATAA
29165641 AATTTTAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
26 7 0.13
27 3 0.05
28 2 0.04
29 24 0.44
30 19 0.35
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (30 bp):
TTTTTATAAGTTTTTAGGAATTTTTAATAA
Found at i:29165733 original size:36 final size:33
Alignment explanation
Indices: 29165654--29165736 Score: 87
Period size: 36 Copynumber: 2.4 Consensus size: 33
29165644 TTTAAATATA
*
29165654 TTTTATTAATTTATAATTTTTTAATATTTATAAGT
1 TTTTA-TAATTT-TAATTTTTTAATATTAATAAGT
*
29165689 TTCTATAATTTTAATATATTTTAAATACTTAATAA-T
1 TTTTATAATTTTAAT-T-TTTT-AATA-TTAATAAGT
29165725 TTTTATAATTTT
1 TTTTATAATTTT
29165737 TTTATTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 8 0.20
36 16 0.39
37 6 0.15
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (33 bp):
TTTTATAATTTTAATTTTTTAATATTAATAAGT
Found at i:29165734 original size:9 final size:9
Alignment explanation
Indices: 29165547--29165769 Score: 113
Period size: 10 Copynumber: 24.0 Consensus size: 9
29165537 GTTAAATGAC
29165547 TTTTTAT-A
1 TTTTTATAA
*
29165555 GTTTTA-AA
1 TTTTTATAA
29165563 TTTTTAATAA
1 TTTTT-ATAA
29165573 TTTTTATAA
1 TTTTTATAA
**
29165582 TTTATTGGAA
1 TTT-TTATAA
*
29165592 TTTTTAATAC
1 TTTTT-ATAA
*
29165602 TATTTATAA
1 TTTTTATAA
29165611 GTTTTTATGAA
1 -TTTTTAT-AA
*
29165622 TTTTTATATG
1 TTTTTATA-A
29165632 TTTTTATAAA
1 TTTTTAT-AA
* *
29165642 ATTTTAAATA
1 TTTTTATA-A
29165652 TATTTTATTAA
1 T-TTTTA-TAA
29165663 --TTTATAA
1 TTTTTATAA
29165670 TTTTT-TAA
1 TTTTTATAA
*
29165678 TATTTATAA
1 TTTTTATAA
*
29165687 GTTTCTATAA
1 -TTTTTATAA
*
29165697 TTTTAAT-A
1 TTTTTATAA
29165705 TATTTTA-AA
1 T-TTTTATAA
* *
29165714 TACTTAATAA
1 T-TTTTATAA
29165724 TTTTTATAA
1 TTTTTATAA
*
29165733 TTTTT-TTA
1 TTTTTATAA
29165741 TTTTTA-ACGA
1 TTTTTATA--A
29165751 TTTTTATAA
1 TTTTTATAA
29165760 CTTTTTATAA
1 -TTTTTATAA
29165770 CCATAAGCTA
Statistics
Matches: 163, Mismatches: 28, Indels: 46
0.69 0.12 0.19
Matches are distributed among these distances:
7 3 0.02
8 30 0.18
9 48 0.29
10 71 0.44
11 10 0.06
12 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29168107 original size:10 final size:9
Alignment explanation
Indices: 29168078--29168357 Score: 139
Period size: 9 Copynumber: 30.3 Consensus size: 9
29168068 GTTAAATGAC
29168078 TTTTTAT-A
1 TTTTTATAA
*
29168086 GTTTTA-AA
1 TTTTTATAA
29168094 TTTTTAATAA
1 TTTTT-ATAA
29168104 TTTTTATAA
1 TTTTTATAA
**
29168113 TTTATTGGAA
1 TTT-TTATAA
*
29168123 TTTTTAATAC
1 TTTTT-ATAA
*
29168133 TATTTATAA
1 TTTTTATAA
29168142 GTTTTTATGAA
1 -TTTTTAT-AA
*
29168153 TTTTTATATG
1 TTTTTATA-A
29168163 TTTTTATAA
1 TTTTTATAA
**
29168172 AATTT-TAA
1 TTTTTATAA
* *
29168180 TTATTATAT
1 TTTTTATAA
29168189 TTTTTATAA
1 TTTTTATAA
*
29168198 TATTTATAA
1 TTTTTATAA
*
29168207 GTTTTTATAT
1 -TTTTTATAA
29168217 TTTTTACTAA
1 TTTTTA-TAA
*
29168227 TTTATAT-A
1 TTTTTATAA
29168235 -TTTT-TAA
1 TTTTTATAA
*
29168242 TATTTTATGA
1 T-TTTTATAA
*
29168252 TTTTCATAAAA
1 TTTT--TATAA
** *
29168263 TTGTAAATATT
1 TT-TTTATA-A
29168274 TTTTTATTAA
1 TTTTTA-TAA
29168284 -TTTTATAAA
1 TTTTTAT-AA
* *
29168293 ATTTTATGA
1 TTTTTATAA
*
29168302 TTTGT-TAA
1 TTTTTATAA
29168310 TTTTT-TATA
1 TTTTTATA-A
29168319 TTTTTATAA
1 TTTTTATAA
*
29168328 TATTTATAA
1 TTTTTATAA
29168337 GTTTTTATAA
1 -TTTTTATAA
29168347 TTTTTA-AA
1 TTTTTATAA
29168355 TTT
1 TTT
29168358 GTGTCCATTT
Statistics
Matches: 204, Mismatches: 43, Indels: 50
0.69 0.14 0.17
Matches are distributed among these distances:
6 1 0.00
7 4 0.02
8 30 0.15
9 80 0.39
10 77 0.38
11 11 0.05
12 1 0.00
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29168128 original size:29 final size:30
Alignment explanation
Indices: 29168078--29168171 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 30
29168068 GTTAAATGAC
29168078 TTTTTAT-AG-TTTTA--AATTTTTAATAA
1 TTTTTATAAGTTTTTAGGAATTTTTAATAA
*
29168104 TTTTTATAA-TTTATT-GGAATTTTTAATAC
1 TTTTTATAAGTTT-TTAGGAATTTTTAATAA
* * *
29168133 TATTTATAAGTTTTTATGAATTTTT-ATATG
1 TTTTTATAAGTTTTTAGGAATTTTTAATA-A
29168163 TTTTTATAA
1 TTTTTATAA
29168172 AATTTTAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
26 7 0.13
27 3 0.05
28 2 0.04
29 24 0.44
30 19 0.35
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (30 bp):
TTTTTATAAGTTTTTAGGAATTTTTAATAA
Found at i:29168158 original size:20 final size:19
Alignment explanation
Indices: 29168078--29168352 Score: 96
Period size: 19 Copynumber: 14.3 Consensus size: 19
29168068 GTTAAATGAC
29168078 TTTTTAT-AG-TTTTA-AA
1 TTTTTATAAGTTTTTATAA
29168094 TTTTTAATAA-TTTTTATAA
1 TTTTT-ATAAGTTTTTATAA
** *
29168113 TTTATTGGAA-TTTTTAATAC
1 TTT-TTATAAGTTTTT-ATAA
*
29168133 TATTTATAAGTTTTTATGAA
1 TTTTTATAAGTTTTTAT-AA
*
29168153 TTTTTATATGTTTTTATAAAA
1 TTTTTATAAGTTTTTAT--AA
*
29168174 TTTTAATTATTATATTTTTTATAA
1 -TTT--TTA-TA-AGTTTTTATAA
* *
29168198 TATTTATAAGTTTTTATAT
1 TTTTTATAAGTTTTTATAA
*
29168217 TTTTTACTAA-TTTATAT-A
1 TTTTTA-TAAGTTTTTATAA
*
29168235 -TTTT-TAA-TATTTTATGA
1 TTTTTATAAGT-TTTTATAA
* * ** *
29168252 TTTTCATAAAATTGTAAATATT
1 TTTTTAT-AAGTT-TTTATA-A
29168274 TTTTTATTAA--TTTTATAAA
1 TTTTTA-TAAGTTTTTAT-AA
* * *
29168293 ATTTTATGA-TTTGT-TAA
1 TTTTTATAAGTTTTTATAA
29168310 TTTTT-TATA-TTTTTATAA
1 TTTTTATA-AGTTTTTATAA
*
29168328 TATTTATAAGTTTTTATAA
1 TTTTTATAAGTTTTTATAA
29168347 TTTTTA
1 TTTTTA
29168353 AATTTGTGTC
Statistics
Matches: 193, Mismatches: 36, Indels: 57
0.67 0.13 0.20
Matches are distributed among these distances:
15 4 0.02
16 11 0.06
17 18 0.09
18 20 0.10
19 66 0.34
20 38 0.20
21 9 0.05
22 10 0.05
23 3 0.02
24 5 0.03
25 2 0.01
26 7 0.04
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTATAAGTTTTTATAA
Found at i:29168239 original size:28 final size:28
Alignment explanation
Indices: 29168157--29168247 Score: 93
Period size: 28 Copynumber: 3.3 Consensus size: 28
29168147 TATGAATTTT
* *
29168157 TATATGTTTTTATAAAATTT-TAA-TTAT
1 TATAT-TTTTTATAATATTTATAAGTTTT
29168184 TATATTTTTTATAATATTTATAAGTTTT
1 TATATTTTTTATAATATTTATAAGTTTT
29168212 TATATTTTTTACT-A-ATTTATATA-TTTT
1 TATATTTTTTA-TAATATTTATA-AGTTTT
29168239 TAATATTTT
1 T-ATATTTT
29168248 ATGATTTTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
26 13 0.23
27 20 0.35
28 23 0.40
29 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (28 bp):
TATATTTTTTATAATATTTATAAGTTTT
Found at i:29168247 original size:9 final size:10
Alignment explanation
Indices: 29168093--29168352 Score: 68
Period size: 10 Copynumber: 27.7 Consensus size: 10
29168083 ATAGTTTTAA
29168093 ATTTTTA-AT
1 ATTTTTATAT
29168102 AATTTTTATA-
1 -ATTTTTATAT
**
29168112 ATTTATTGGA-
1 ATTT-TTATAT
29168122 ATTTTTA-AT
1 ATTTTTATAT
*
29168131 ACTATTTATA-
1 A-TTTTTATAT
29168141 AGTTTTTATGA-
1 A-TTTTTAT-AT
29168152 ATTTTTATAT
1 ATTTTTATAT
*
29168162 GTTTTTATA-
1 ATTTTTATAT
**
29168171 AAATTT-TA-
1 ATTTTTATAT
*
29168179 ATTATTATAT
1 ATTTTTATAT
29168189 -TTTTTATA-
1 ATTTTTATAT
*
29168197 ATATTTATA-
1 ATTTTTATAT
29168206 AGTTTTTATAT
1 A-TTTTTATAT
29168217 -TTTTTACTA-
1 ATTTTTA-TAT
29168226 A--TTTATAT
1 ATTTTTATAT
29168234 ATTTTTA-AT
1 ATTTTTATAT
*
29168243 A-TTTTAT-G
1 ATTTTTATAT
* *
29168251 ATTTTCATAA
1 ATTTTTATAT
* * *
29168261 AATTGTAAAT
1 ATTTTTATAT
*
29168271 ATTTTTTTATT
1 ATTTTTATA-T
* *
29168282 AATTTTATAA
1 ATTTTTATAT
* *
29168292 AATTTTAT-G
1 ATTTTTATAT
*
29168301 ATTTGT-TA-
1 ATTTTTATAT
29168309 ATTTTT-TAT
1 ATTTTTATAT
29168318 ATTTTTATA-
1 ATTTTTATAT
*
29168327 ATATTTATA-
1 ATTTTTATAT
29168336 AGTTTTTATA-
1 A-TTTTTATAT
29168346 ATTTTTA
1 ATTTTTA
29168353 AATTTGTGTC
Statistics
Matches: 188, Mismatches: 37, Indels: 51
0.68 0.13 0.18
Matches are distributed among these distances:
7 2 0.01
8 25 0.13
9 67 0.36
10 82 0.44
11 12 0.06
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:29169047 original size:2 final size:2
Alignment explanation
Indices: 29169040--29169074 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29169030 TAAGCTGATA
29169040 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
29169075 GTAGTAGCAA
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:29177162 original size:19 final size:22
Alignment explanation
Indices: 29177117--29177159 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
29177107 AGAAAAAAAA
29177117 TTAAATTTCTTTATATATTTTT
1 TTAAATTTCTTTATATATTTTT
29177139 TTAAATTT-TTTATA-ATTTTT
1 TTAAATTTCTTTATATATTTTT
29177159 T
1 T
29177160 AAAAAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTAAATTTCTTTATATATTTTT
Found at i:29177166 original size:22 final size:22
Alignment explanation
Indices: 29177119--29177163 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
29177109 AAAAAAAATT
*
29177119 AAATTTCTTTATATATTTTTTT
1 AAATTTCTTTATATATTTTTTA
29177141 AAATTT-TTTATA-ATTTTTTA
1 AAATTTCTTTATATATTTTTTA
29177161 AAA
1 AAA
29177164 AATGAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 6 0.27
22 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
AAATTTCTTTATATATTTTTTA
Found at i:29189304 original size:3 final size:3
Alignment explanation
Indices: 29189296--29189321 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29189286 TATGGAGATG
29189296 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
29189322 ATCCAATATG
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:29192810 original size:19 final size:20
Alignment explanation
Indices: 29192774--29192811 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
29192764 TAAAAACATT
*
29192774 ATACACCTAACTAAATAAAA
1 ATACACCTAAATAAATAAAA
*
29192794 ATACA-CTAAATATATAAA
1 ATACACCTAAATAAATAAA
29192812 GTGAAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.24
Consensus pattern (20 bp):
ATACACCTAAATAAATAAAA
Found at i:29194149 original size:5 final size:5
Alignment explanation
Indices: 29194141--29194172 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
29194131 AAGGAAACAA
*
29194141 AAATC AAATC AAACC AAATC AAATC AAATC AA
1 AAATC AAATC AAATC AAATC AAATC AAATC AA
29194173 GAAGATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (5 bp):
AAATC
Found at i:29195745 original size:99 final size:99
Alignment explanation
Indices: 29195629--29195825 Score: 331
Period size: 99 Copynumber: 2.0 Consensus size: 99
29195619 AAAAATCATG
* *
29195629 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTCTT
29195694 AAATCTTGGATAAGTGGATGTTCTTTTAAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAAGTA
* **
29195728 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGGTCGTGCCCTAACGTATTGGGTGTAATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTCTT
* *
29195793 AAATCTTGGATGAGTGGATGTTCTTTTACAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAAGT
29195826 TTTATTGCAT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 91 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (99 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAAGTA
Found at i:29206985 original size:132 final size:132
Alignment explanation
Indices: 29206748--29207052 Score: 529
Period size: 132 Copynumber: 2.3 Consensus size: 132
29206738 NNNNNNNNNN
*
29206748 TAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAATGGGAAGCAGATT
1 TAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAAATAATGGGAAGCAGATT
* *
29206813 TAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGAAGAAAATTGAAGATTGTAGATCTTATCTC
66 TAAGCCACCAAGCCCTGTCTCCCTGAGTAACAGCGAAGAAAATTGAAGATTGTAGATCTTATCTC
29206878 CC
131 CC
* *
29206880 TAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATCTTATCTTTCCAAAATAGTGGGAAGCAGATT
1 TAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAAATAATGGGAAGCAGATT
* *
29206945 TGAGCCACCAAGCCCTGTCTCCCTGAGTAACAGCGGAGAAAATTGAAGATTGTAGATCTTATCTC
66 TAAGCCACCAAGCCCTGTCTCCCTGAGTAACAGCGAAGAAAATTGAAGATTGTAGATCTTATCTC
*
29207010 CT
131 CC
*
29207012 TAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCT
1 TAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCT
29207053 CCCTGAAGTT
Statistics
Matches: 163, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 163 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (132 bp):
TAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAAATAATGGGAAGCAGATT
TAAGCCACCAAGCCCTGTCTCCCTGAGTAACAGCGAAGAAAATTGAAGATTGTAGATCTTATCTC
CC
Found at i:29207096 original size:44 final size:43
Alignment explanation
Indices: 29207043--29207164 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
29207033 GAAGATGGCA
*
29207043 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-AC
* * * * *
29207087 AATCCTATCTCCCTAAAGTTACAGTGG-GATAGATTAAAATCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAAACCAC
* *
29207130 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
29207165 CATCTAGTCT
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
43 10 0.16
44 53 0.84
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAC
Found at i:29208435 original size:19 final size:19
Alignment explanation
Indices: 29208411--29208447 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29208401 GTTGAGAGGT
29208411 TTTTTTTTAAAAAAAAGGA
1 TTTTTTTTAAAAAAAAGGA
*
29208430 TTTTTTTTAAAAGAAAGG
1 TTTTTTTTAAAAAAAAGG
29208448 TTGGAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
TTTTTTTTAAAAAAAAGGA
Found at i:29209461 original size:99 final size:99
Alignment explanation
Indices: 29209336--29209532 Score: 315
Period size: 99 Copynumber: 2.0 Consensus size: 99
29209326 AAAAATCATG
* * *
29209336 AAGGAAATATTCTGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTCTT
29209401 AAATCTTGGATAAGTGGATGTTCTTTTAAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAAGTA
**
29209435 AAGGAAATATTCCGAGTTTG-GTATTCTAAAGGGGTCGTGCCCTAACGTATTGGGTGTAATTTCT
1 AAGGAAATATTCCGAGTTTGAG-ATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTCT
* *
29209499 TAAATCTTGGATGAGTGGATGTTCTTTTACAAGT
65 TAAATCTTGGATAAGTGGATGTTCTTTTAAAAGT
29209533 TTTATTGCAT
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
98 1 0.01
99 89 0.99
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (99 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAAGTA
Found at i:29211904 original size:73 final size:73
Alignment explanation
Indices: 29211783--29211929 Score: 213
Period size: 73 Copynumber: 2.0 Consensus size: 73
29211773 TTTTATCATC
* * * * * *
29211783 TTAATTCGATTTAAATTTTTTTTCAGTTGAGTCAAGCGAGATAGAATTTAAATTGAAGCGAATTG
1 TTAATTCGATTTAAACTTTTTTTCAATTCAGTCAAGCGAGATAAAATTTAAATCGAAGCAAATTG
29211848 AATATATT
66 AATATATT
* * *
29211856 TTAATTCGATTTAAACTTTTTTTGAATTCAGTCGAGTGAGATAAAATTTAAATCGAAGCAAATTG
1 TTAATTCGATTTAAACTTTTTTTCAATTCAGTCAAGCGAGATAAAATTTAAATCGAAGCAAATTG
29211921 AATATATT
66 AATATATT
29211929 T
1 T
29211930 GTTTGAACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (73 bp):
TTAATTCGATTTAAACTTTTTTTCAATTCAGTCAAGCGAGATAAAATTTAAATCGAAGCAAATTG
AATATATT
Found at i:29214923 original size:25 final size:25
Alignment explanation
Indices: 29214852--29214937 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
29214842 ACAACTCTTT
** *
29214852 TGAGCTTTTCGATACTTGGCTCTCA
1 TGAGCTTCCCGATATTTGGCTCTCA
** *
29214877 TGAGCTTCCC-A-ATTAACAGCTCTCT
1 TGAGCTTCCCGATATT--TGGCTCTCA
*
29214902 TGAGCTTCCCGATATTTGGCTCGCA
1 TGAGCTTCCCGATATTTGGCTCTCA
*
29214927 AGAGCTTCCCG
1 TGAGCTTCCCG
29214938 TTAAATGGCT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
23 2 0.04
24 1 0.02
25 39 0.85
26 1 0.02
27 3 0.07
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.33
Consensus pattern (25 bp):
TGAGCTTCCCGATATTTGGCTCTCA
Found at i:29214946 original size:25 final size:25
Alignment explanation
Indices: 29214903--29214964 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
29214893 CAGCTCTCTT
* **
29214903 GAGCTTCCCGATATTTGGCTCGCAA
1 GAGCTTCCCGTTAAATGGCTCGCAA
*
29214928 GAGCTTCCCGTTAAATGGCTCGGAA
1 GAGCTTCCCGTTAAATGGCTCGCAA
29214953 GAGCTTCCCGTT
1 GAGCTTCCCGTT
29214965 TACATGCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.27
Consensus pattern (25 bp):
GAGCTTCCCGTTAAATGGCTCGCAA
Found at i:29217137 original size:42 final size:42
Alignment explanation
Indices: 29217078--29217238 Score: 200
Period size: 42 Copynumber: 3.8 Consensus size: 42
29217068 TTAGGGTTAC
*
29217078 TGAGATTACGTGTAAGACCATATTTGGGATATGGCATCGATA
1 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
* *
29217120 TGAGAATT-CGTGTAAGACCATATTTGGGATATGACATCGATA
1 TGAG-ATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
** * *
29217162 TGAGAATT-CGTGTAAGACCATGGCTGGGTTATTGGCATCAATA
1 TGAG-ATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* *
29217205 CGAGATTACATGTAAGACCATATCTGGGATATGG
1 TGAGATTACGTGTAAGACCATATCTGGGATATGG
29217239 AATTGTTACG
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
42 70 0.67
43 34 0.33
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:29217225 original size:85 final size:84
Alignment explanation
Indices: 29217078--29217237 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 84
29217068 TTAGGGTTAC
** * * *
29217078 TGAGATTACGTGTAAGACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAAGACCATAT
1 TGAGATTACGTGTAAGACCATAGCTGGGATATGGCATCAATACGAGAATTCATGTAAGACCATAT
*
29217143 TTGGGATATGACATCGATA
66 CTGGGATATGACATCGATA
* *
29217162 TGAGAATT-CGTGTAAGACCATGGCTGGGTTATTGGCATCAATACGAG-ATTACATGTAAGACCA
1 TGAG-ATTACGTGTAAGACCATAGCTGGGATA-TGGCATCAATACGAGAATT-CATGTAAGACCA
29217225 TATCTGGGATATG
63 TATCTGGGATATG
29217238 GAATTGTTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
84 26 0.40
85 39 0.60
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (84 bp):
TGAGATTACGTGTAAGACCATAGCTGGGATATGGCATCAATACGAGAATTCATGTAAGACCATAT
CTGGGATATGACATCGATA
Found at i:29225122 original size:20 final size:20
Alignment explanation
Indices: 29225099--29225151 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
29225089 GAAAAGATGA
*
29225099 AAATTTTATTAAAAAATTCT
1 AAATTTTATGAAAAAATTCT
*
29225119 AAATTTTGTGAAAAAATTCT
1 AAATTTTATGAAAAAATTCT
*
29225139 AAATTTTGTGAAA
1 AAATTTTATGAAA
29225152 TACATGGGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (20 bp):
AAATTTTATGAAAAAATTCT
Found at i:29228470 original size:21 final size:21
Alignment explanation
Indices: 29228444--29228483 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29228434 CTATTTAGTT
29228444 ACTATCTCTGACAGCATGGTA
1 ACTATCTCTGACAGCATGGTA
29228465 ACTATCTCTGACAGCATGG
1 ACTATCTCTGACAGCATGG
29228484 GCGGCGCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (21 bp):
ACTATCTCTGACAGCATGGTA
Found at i:29229073 original size:19 final size:19
Alignment explanation
Indices: 29229033--29229074 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29229023 GGGGTTTGGA
* *
29229033 GGAAGTAAAAATTTTGAGG
1 GGAAGTAAAAATTTTAAAG
*
29229052 GGAAGTAAAAGTTTTAAAG
1 GGAAGTAAAAATTTTAAAG
29229071 GGAA
1 GGAA
29229075 AATAAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (19 bp):
GGAAGTAAAAATTTTAAAG
Found at i:29235497 original size:16 final size:16
Alignment explanation
Indices: 29235476--29235540 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
29235466 TTCGCTGTAT
29235476 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
29235492 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
29235508 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
29235524 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
29235540 T
1 T
29235541 AGCAATTCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.37, C:0.05, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:29235581 original size:45 final size:44
Alignment explanation
Indices: 29235520--29235614 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 44
29235510 GAATAGAGGC
29235520 GTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* *
29235565 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
*
29235609 GGAATG
1 GTAATG
29235615 ATGTTGTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:29240607 original size:40 final size:40
Alignment explanation
Indices: 29240563--29240654 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
29240553 ATCTAATGTT
* *
29240563 CCATTTCATATACCTATTTCCATATAACTGATTCATATCA
1 CCATTTCATATACCTATTTCCATATAACCGATTCATATAA
* ** *
29240603 CCATTTCGTATATTTATTTCTATATAACCGATTCATATAA
1 CCATTTCATATACCTATTTCCATATAACCGATTCATATAA
*
29240643 CTATTTCATATA
1 CCATTTCATATA
29240655 AACACTTCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (40 bp):
CCATTTCATATACCTATTTCCATATAACCGATTCATATAA
Found at i:29240640 original size:13 final size:13
Alignment explanation
Indices: 29240624--29240671 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
29240614 ATTTATTTCT
29240624 ATATAACCGA-TTC
1 ATATAACC-ACTTC
* *
29240637 ATATAACTATTTC
1 ATATAACCACTTC
*
29240650 ATATAAACACTTC
1 ATATAACCACTTC
29240663 ATATAACCA
1 ATATAACCA
29240672 TTTCTATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 1 0.03
13 28 0.97
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (13 bp):
ATATAACCACTTC
Found at i:29240663 original size:26 final size:27
Alignment explanation
Indices: 29240617--29240678 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
29240607 TTCGTATATT
*
29240617 TATTTCTATATAACCGATTCATATAAC
1 TATTTCTATATAAACGATTCATATAAC
29240644 TATTTC-ATATAAAC-ACTTCATATAAC
1 TATTTCTATATAAACGA-TTCATATAAC
*
29240670 CATTTCTAT
1 TATTTCTAT
29240679 TTACTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 1 0.03
26 22 0.71
27 8 0.26
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (27 bp):
TATTTCTATATAAACGATTCATATAAC
Found at i:29242050 original size:18 final size:18
Alignment explanation
Indices: 29242017--29242069 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
29242007 ATTCACCTAA
*
29242017 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
29242036 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
29242054 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
29242070 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:29242187 original size:9 final size:9
Alignment explanation
Indices: 29242173--29242257 Score: 116
Period size: 9 Copynumber: 9.4 Consensus size: 9
29242163 GTAGTGATTC
29242173 AATTCGGTT
1 AATTCGGTT
29242182 AATTCGGTT
1 AATTCGGTT
*
29242191 AATTCGGGT
1 AATTCGGTT
29242200 AATTCGGTT
1 AATTCGGTT
* *
29242209 AATTTGGGT
1 AATTCGGTT
* *
29242218 AATCCAGTT
1 AATTCGGTT
29242227 AATTCGGTT
1 AATTCGGTT
*
29242236 AATTCGGGT
1 AATTCGGTT
29242245 AATTCGGTT
1 AATTCGGTT
29242254 AATT
1 AATT
29242258 TTTAACCAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 64 1.00
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:29257016 original size:32 final size:32
Alignment explanation
Indices: 29256964--29257042 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
29256954 ATTTTCCATT
*
29256964 TGAACTTGTTC-AAAAGTACCTAGTTGGTGCC
1 TGAACTTGTCCAAAAAGTACCTAGTTGGTGCC
*
29256995 T-ACACTTGTCCAAAAAGTACCTAGTTGGTGCT
1 TGA-ACTTGTCCAAAAAGTACCTAGTTGGTGCC
*
29257027 TGAACTTATCCAAAAA
1 TGAACTTGTCCAAAAA
29257043 ATTATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.02
31 8 0.19
32 32 0.76
33 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
TGAACTTGTCCAAAAAGTACCTAGTTGGTGCC
Found at i:29259069 original size:20 final size:19
Alignment explanation
Indices: 29259016--29259067 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
29259006 AAAAAAAGAA
*
29259016 TCAAAATAATTTTTAAAAAT
1 TCAAAAT-ATTTATAAAAAT
29259036 TCAAAATATTTATAAAAAT
1 TCAAAATATTTATAAAAAT
*
29259055 TCTAAA-ATTTATA
1 TCAAAATATTTATA
29259068 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 7 0.23
19 16 0.53
20 7 0.23
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (19 bp):
TCAAAATATTTATAAAAAT
Found at i:29259160 original size:8 final size:8
Alignment explanation
Indices: 29259147--29259171 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29259137 TTGGGGCTTA
29259147 AATAAATT
1 AATAAATT
29259155 AATAAATT
1 AATAAATT
29259163 AATAAATT
1 AATAAATT
29259171 A
1 A
29259172 TTCAAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AATAAATT
Found at i:29265852 original size:2 final size:2
Alignment explanation
Indices: 29265847--29265878 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29265837 ATATATATAT
29265847 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29265879 GAGGGCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29268835 original size:18 final size:19
Alignment explanation
Indices: 29268794--29268835 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
29268784 CCTATGTTGT
* *
29268794 CGGCCCGTGTGGGCCTACA
1 CGGCTCGTGTGGGCCCACA
29268813 C-GCTCGTGT-GGCCCACA
1 CGGCTCGTGTGGGCCCACA
29268830 CGGCTC
1 CGGCTC
29268836 AGAATGGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 8 0.40
18 11 0.55
19 1 0.05
ACGTcount: A:0.10, C:0.40, G:0.33, T:0.17
Consensus pattern (19 bp):
CGGCTCGTGTGGGCCCACA
Found at i:29275636 original size:9 final size:10
Alignment explanation
Indices: 29275610--29275635 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29275600 AATTGATCTC
29275610 TTTTTTTAAA
1 TTTTTTTAAA
29275620 TTTTTTTAAA
1 TTTTTTTAAA
29275630 TTTTTT
1 TTTTTT
29275636 ACTATACTCA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:29300382 original size:30 final size:31
Alignment explanation
Indices: 29300313--29300383 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
29300303 GGTGCAAAGC
* * *
29300313 TTTGATTTTGGTTCAATTCTATAAATGGAAT
1 TTTGATTTTGGTTCAATTATACAAATGAAAT
* *
29300344 TTTAATTTTGGTTCAATTATACACAT-AAAT
1 TTTGATTTTGGTTCAATTATACAAATGAAAT
29300374 TTTGATTTTG
1 TTTGATTTTG
29300384 ATCTAATTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.51
Consensus pattern (31 bp):
TTTGATTTTGGTTCAATTATACAAATGAAAT
Found at i:29301846 original size:12 final size:12
Alignment explanation
Indices: 29301829--29301854 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29301819 CTTGACTGTA
29301829 AGACCTATTTGT
1 AGACCTATTTGT
29301841 AGACCTATTTGT
1 AGACCTATTTGT
29301853 AG
1 AG
29301855 TTTCATTTGA
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:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (12 bp):
AGACCTATTTGT
Found at i:29309981 original size:5 final size:5
Alignment explanation
Indices: 29309973--29309998 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29309963 TACCCGTACC
29309973 GTGCT GTGCT GTGCT GTGCT GTGCT G
1 GTGCT GTGCT GTGCT GTGCT GTGCT G
29309999 GTGACTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.42, T:0.38
Consensus pattern (5 bp):
GTGCT
Found at i:29312707 original size:12 final size:12
Alignment explanation
Indices: 29312690--29312723 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29312680 AACTCAAAGT
29312690 TTTCATATATGC
1 TTTCATATATGC
*
29312702 TTTCATATATTC
1 TTTCATATATGC
*
29312714 TTTTATATAT
1 TTTCATATAT
29312724 TATATACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.03, T:0.59
Consensus pattern (12 bp):
TTTCATATATGC
Found at i:29313134 original size:3 final size:3
Alignment explanation
Indices: 29313126--29313152 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29313116 ACAACAGTTG
29313126 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
29313153 GGCAAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29314544 original size:44 final size:44
Alignment explanation
Indices: 29314495--29314626 Score: 264
Period size: 44 Copynumber: 3.0 Consensus size: 44
29314485 CCTTTGCCTT
29314495 ATAATCGGGTTCACATTGTTCTCCTCTCGTGTTCGGGTCATGGG
1 ATAATCGGGTTCACATTGTTCTCCTCTCGTGTTCGGGTCATGGG
29314539 ATAATCGGGTTCACATTGTTCTCCTCTCGTGTTCGGGTCATGGG
1 ATAATCGGGTTCACATTGTTCTCCTCTCGTGTTCGGGTCATGGG
29314583 ATAATCGGGTTCACATTGTTCTCCTCTCGTGTTCGGGTCATGGG
1 ATAATCGGGTTCACATTGTTCTCCTCTCGTGTTCGGGTCATGGG
29314627 TCAGATGTTC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 88 1.00
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (44 bp):
ATAATCGGGTTCACATTGTTCTCCTCTCGTGTTCGGGTCATGGG
Found at i:29316642 original size:41 final size:41
Alignment explanation
Indices: 29316587--29316695 Score: 173
Period size: 41 Copynumber: 2.6 Consensus size: 41
29316577 CTTAATTTAA
* *
29316587 CAGATTCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
29316629 TAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
29316670 CAGATCACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
29316696 ACGTGTAGTC
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
41 59 0.95
42 3 0.05
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:29320415 original size:57 final size:58
Alignment explanation
Indices: 29320323--29320434 Score: 165
Period size: 57 Copynumber: 1.9 Consensus size: 58
29320313 AATATAGATT
* * *
29320323 CGCGAGCTGTTTTGTACTTGGGAAAATTTTGTAAAGTAATAAGCTT-GGAATGTGACTC
1 CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAATAAG-TTGGGAATGTGACTC
*
29320381 CGCGAACTTTTTTATACTT-GGAAAATTTTCTAAAGTAATAAGTTGGGAATGTGA
1 CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAATAAGTTGGGAATGTGA
29320435 AGTTGCGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.04
57 31 0.63
58 16 0.33
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (58 bp):
CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAATAAGTTGGGAATGTGACTC
Found at i:29320443 original size:57 final size:57
Alignment explanation
Indices: 29320323--29320454 Score: 162
Period size: 57 Copynumber: 2.3 Consensus size: 57
29320313 AATATAGATT
* * *
29320323 CGCGAGCTGTTTTGTACTTGGGAAAATTTTGTAAAGTAATAAGCTTGGAATGTGACTC
1 CGCGAACT-TTTTATACTTGGGAAAATTTTCTAAAGTAATAAGCTTGGAATGTGACTC
*
29320381 CGCGAACTTTTTTATACTT-GGAAAATTTTCTAAAGTAATAAG-TTGGGAATGTGAAGT-
1 CGCGAAC-TTTTTATACTTGGGAAAATTTTCTAAAGTAATAAGCTT-GGAATGTG-ACTC
*
29320438 TGCGAACTTTTTATACT
1 CGCGAACTTTTTATACT
29320455 AGTAGAATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
56 12 0.18
57 36 0.55
58 17 0.26
59 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (57 bp):
CGCGAACTTTTTATACTTGGGAAAATTTTCTAAAGTAATAAGCTTGGAATGTGACTC
Found at i:29320888 original size:138 final size:138
Alignment explanation
Indices: 29320663--29321016 Score: 404
Period size: 138 Copynumber: 2.6 Consensus size: 138
29320653 TTTGCATACG
* * * * * * * * *
29320663 AGCCTTAGTATGACAGTTGGAAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGTGACTTTTCGCT
1 AGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGTAACTCTTCGCC
* * *
29320728 TGTGAGCCTTAGTGTGATAGCTG-GAAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCT
66 TGTGAGCCTTAGTGTGACAGCTGAGAA-CTTTGCTCTCGCTAACTGTGCTGAAAGTTGCAGCTCT
29320792 TCACCTGCA
130 TCACCTGCA
* * **
29320801 AGCCATAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACAACTCTTCGCC
1 AGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGTAACTCTTCGCC
* * * ** * *
29320866 TGTAAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGTTAATTGTTTTGAAAGTTGCAGTTTTT
66 TGTGAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGCTAACTGTGCTGAAAGTTGCAGCTCTT
* *
29320931 CGCCTGCG
131 CACCTGCA
* ** * * * *
29320939 AGCTTTAGTGTGACAGTTAAGAGCTTTGCTCTCGTTAATTGTGTTGGAGGTTGTAGCTCTTCACC
1 AGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGTAACTCTTCGCC
29321004 TGTGAGCCTTAGT
66 TGTGAGCCTTAGT
29321017 TTAATAGTTG
Statistics
Matches: 178, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
138 175 0.98
139 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (138 bp):
AGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGTAACTCTTCGCC
TGTGAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGCTAACTGTGCTGAAAGTTGCAGCTCTT
CACCTGCA
Found at i:29321032 original size:69 final size:69
Alignment explanation
Indices: 29320662--29321065 Score: 353
Period size: 69 Copynumber: 5.9 Consensus size: 69
29320652 CTTTGCATAC
* * * * * * *
29320662 GAGCCTTAGTATGACAGTTGGAAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGTG-A-CTTTTC
1 GAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGG-T-TGCAGCTCTTC
* *
29320725 GCTTGT
64 ACCTGT
* * * * *
29320731 GAGCCTTAGTGTGATAGCTGGAAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTCAC
1 GAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGTTGCAGCTCTTCAC
*
29320796 CTGC
66 CTGT
* * * * * * *
29320800 AAGCCATAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACAACTCTTCGC
1 GAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGTTGCAGCTCTTCAC
29320865 CTGT
66 CTGT
* * * * * * * * * * *
29320869 AAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGTTAATTGTTTTGAAAGTTGCAGTTTTTCGC
1 GAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGTTGCAGCTCTTCAC
*
29320934 CTGC
66 CTGT
* ** * *
29320938 GAGCTTTAGTGTGACAGTTAAGAGCTTTGCTCTCGTTAATTGTGTTGGAGGTTGTAGCTCTTCAC
1 GAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGTTGCAGCTCTTCAC
29321003 CTGT
66 CTGT
* * * * * * * *
29321007 GAGCCTTAGTTTAATAGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTACAGCT
1 GAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGTTGCAGCT
29321066 TTTCGCTTGC
Statistics
Matches: 270, Mismatches: 63, Indels: 4
0.80 0.19 0.01
Matches are distributed among these distances:
67 2 0.01
68 2 0.01
69 266 0.99
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (69 bp):
GAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGTTGCAGCTCTTCAC
CTGT
Found at i:29321047 original size:138 final size:138
Alignment explanation
Indices: 29320728--29321085 Score: 419
Period size: 138 Copynumber: 2.6 Consensus size: 138
29320718 ACTTTTCGCT
* * ** * *
29320728 TGTGAGCCTTAGTGTGATAGCTGGAAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTT
1 TGTGAGCCTTAGTGTGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGCAGCTTTT
* * ** **
29320793 CACCTGCAAGCCATAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACAAC
66 CGCCTGCGAGCTTTAGTGTGACAGTTAAGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACAAC
*
29320858 TCTTCGCC
131 TCTTCACC
* * * * * * *
29320866 TGTAAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGTTAATTGTTTTGAAAGTTGCAGTTTTT
1 TGTGAGCCTTAGTGTGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGCAGCTTTT
* * * ** *
29320931 CGCCTGCGAGCTTTAGTGTGACAGTTAAGAGCTTTGCTCTCGTTAATTGTGTTGGAGGTTGTAGC
66 CGCCTGCGAGCTTTAGTGTGACAGTTAAGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACAAC
29320996 TCTTCACC
131 TCTTCACC
* * * * * *
29321004 TGTGAGCCTTAGTTTAATAGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTACAGCTTTT
1 TGTGAGCCTTAGTGTGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGCAGCTTTT
*
29321069 CGCTTGCGAGCTTTAGT
66 CGCCTGCGAGCTTTAGT
29321086 ATGGCAGAAA
Statistics
Matches: 180, Mismatches: 40, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
138 180 1.00
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (138 bp):
TGTGAGCCTTAGTGTGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGCAGCTTTT
CGCCTGCGAGCTTTAGTGTGACAGTTAAGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACAAC
TCTTCACC
Found at i:29322993 original size:5 final size:5
Alignment explanation
Indices: 29322956--29322992 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
29322946 TGAATCACAT
* *
29322956 ATATG GTATG ATATG ATATG ATATG ATATG ATTTG AT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG AT
29322993 TAAATATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (5 bp):
ATATG
Found at i:29324587 original size:21 final size:21
Alignment explanation
Indices: 29324550--29324589 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29324540 CCTTTTCCAT
*
29324550 TTTCTTTTCTTCTTTTCTTTC
1 TTTCTTTTCTTCGTTTCTTTC
29324571 TTTCTCTTT-TTCGTTTCTT
1 TTTCT-TTTCTTCGTTTCTT
29324590 ATTTCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTCTTTTCTTCGTTTCTTTC
Found at i:29338225 original size:1 final size:1
Alignment explanation
Indices: 29338219--29338258 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
29338209 CTCTCTATTC
29338219 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29338259 TGCATTGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29338387 original size:126 final size:126
Alignment explanation
Indices: 29338171--29338418 Score: 408
Period size: 126 Copynumber: 2.0 Consensus size: 126
29338161 TTCGAAGCCA
29338171 CAATTTTGAGTGAATGAAATTGAATAGAAAAACACAAGCTCTCTATTCAAAAAAAAAAAAAAAAA
1 CAATTTTGAGTGAATGAAATTGAATAGAAAAACACAAGCTCTCTATTCAAAAAAAAAAAAAAAAA
*
29338236 AAAAAAAAAAAAAAAAAAAAAAATGCATTGATTTTTCACTAAAATTAAAAAAAAAATTTTT
66 AAAAAAAAAAAAAAAAAAAAAAATGCATTGATATTTCACTAAAATTAAAAAAAAAATTTTT
29338297 CAATTTTGAGTGAATGAAAATTGAATAGAAAAAC-CAAGCTCTCTATTCAAAAAAAAAAAAAAAA
1 CAATTTTGAGTGAATG-AAATTGAATAGAAAAACACAAGCTCTCTATTCAAAAAAAAAAAAAAAA
* * * * * * *
29338361 AGAAGAAAAAAGATAATAAGATAATGCATTGATATTTCACTAAAATTAAAAAAAAAAT
65 AAAAAAAAAAAAAAAAAAAAAAAATGCATTGATATTTCACTAAAATTAAAAAAAAAAT
29338419 CTCTTAATTA
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
126 96 0.85
127 17 0.15
ACGTcount: A:0.60, C:0.08, G:0.09, T:0.23
Consensus pattern (126 bp):
CAATTTTGAGTGAATGAAATTGAATAGAAAAACACAAGCTCTCTATTCAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAATGCATTGATATTTCACTAAAATTAAAAAAAAAATTTTT
Found at i:29339023 original size:42 final size:42
Alignment explanation
Indices: 29338954--29339079 Score: 189
Period size: 42 Copynumber: 3.0 Consensus size: 42
29338944 AAATATATAC
* *
29338954 TCTCAATGTGGATTAAAATTTAGTTTAGTTAGCACGGTTGTT
1 TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
* *
29338996 TCTTAACGTGGATTAAATTTTACTTTAGTTAGCACGGTTGTT
1 TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
* * *
29339038 TCTCAATGTGGATTAAATTTTAGTTTAGTTAACACGTTTGTT
1 TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
29339080 ATTAACTGAC
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.45
Consensus pattern (42 bp):
TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
Found at i:29339870 original size:27 final size:23
Alignment explanation
Indices: 29339804--29339858 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
29339794 TCTTCAATCA
*
29339804 CTAGTATGTTAGTAGGCCAAAAC
1 CTAGTATATTAGTAGGCCAAAAC
29339827 CTAGTATATTAGTAGGCCAAAAC
1 CTAGTATATTAGTAGGCCAAAAC
29339850 CTAGTATAT
1 CTAGTATAT
29339859 ATATTTCGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (23 bp):
CTAGTATATTAGTAGGCCAAAAC
Found at i:29341613 original size:22 final size:24
Alignment explanation
Indices: 29341588--29341631 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
29341578 CATAAAACTG
29341588 TTAAAG-ATTTTA-TGATTTTTCA
1 TTAAAGAATTTTAGTGATTTTTCA
* *
29341610 TTAATGAATTTTAGTTATTTTT
1 TTAAAGAATTTTAGTGATTTTT
29341632 TATGTTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 6 0.33
24 7 0.39
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (24 bp):
TTAAAGAATTTTAGTGATTTTTCA
Found at i:29342150 original size:25 final size:26
Alignment explanation
Indices: 29342117--29342165 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
29342107 TATGTTGTTT
29342117 TGAATTATTTTGA-ATTGAAATGTTGC
1 TGAATTA-TTTGACATTGAAATGTTGC
*
29342143 TGAA-TATTTGACATTGGAATGTT
1 TGAATTATTTGACATTGAAATGTT
29342166 AATTATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (26 bp):
TGAATTATTTGACATTGAAATGTTGC
Found at i:29343672 original size:58 final size:58
Alignment explanation
Indices: 29343582--29343697 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
29343572 TTTTTCAGTG
29343582 GTGTCGGAAACAGTAGTTTTAGGTCACCAAATCCAGCGAGTAAGCTCGTAAATTTTAT
1 GTGTCGGAAACAGTAGTTTTAGGTCACCAAATCCAGCGAGTAAGCTCGTAAATTTTAT
* * ** *
29343640 GTGTCGGAAATAGTGGTTTTAGGTCACCAAATCTGGTGAGTAAGCTCGTAAATTTTAT
1 GTGTCGGAAACAGTAGTTTTAGGTCACCAAATCCAGCGAGTAAGCTCGTAAATTTTAT
29343698 TAATTAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (58 bp):
GTGTCGGAAACAGTAGTTTTAGGTCACCAAATCCAGCGAGTAAGCTCGTAAATTTTAT
Found at i:29345002 original size:24 final size:24
Alignment explanation
Indices: 29344955--29345002 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
29344945 TCGTTCTGTG
**
29344955 GCAAAGGATGAATTGACAGTAAAT
1 GCAAAGGATGAATTGACAACAAAT
29344979 GCAAAGGATGAATTGACAACAAAT
1 GCAAAGGATGAATTGACAACAAAT
29345003 TACCCAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (24 bp):
GCAAAGGATGAATTGACAACAAAT
Found at i:29345157 original size:42 final size:41
Alignment explanation
Indices: 29345087--29345222 Score: 164
Period size: 42 Copynumber: 3.2 Consensus size: 41
29345077 TGTTAACTCA
* *
29345087 TATGAGTTTCTGTTTAACCCTAATGGGTTTTCGTTCAGCTCT
1 TATGAGCTTC-GTTTAACCCTTATGGGTTTTCGTTCAGCTCT
* *
29345129 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTC-GTTTAACCCTTATGGGTTTTCGTTCAGCTCT
* * * *
29345171 TATGAGCTTTCGTTCAACCCTTATGGGTTTTTGTTTAGCACT
1 TATGAGC-TTCGTTTAACCCTTATGGGTTTTCGTTCAGCTCT
*
29345213 TATGTGCTTC
1 TATGAGCTTC
29345223 TATTCAGCCT
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
41 3 0.04
42 75 0.93
43 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (41 bp):
TATGAGCTTCGTTTAACCCTTATGGGTTTTCGTTCAGCTCT
Found at i:29345174 original size:21 final size:21
Alignment explanation
Indices: 29345087--29345200 Score: 77
Period size: 21 Copynumber: 5.4 Consensus size: 21
29345077 TGTTAACTCA
* * *
29345087 TATGAGTTTCTGTTTAACCCT
1 TATGGGTTTCCGTTCAACCCT
* * * *
29345108 AATGGGTTTTCGTTCAGCTCT
1 TATGGGTTTCCGTTCAACCCT
* * * * *
29345129 TTTGAGCTTCAGTTTAACCCT
1 TATGGGTTTCCGTTCAACCCT
* *
29345150 TATGGGTTTCCGTTCAGCTCT
1 TATGGGTTTCCGTTCAACCCT
*
29345171 TATGAGCTTT-CGTTCAACCCT
1 TATG-GGTTTCCGTTCAACCCT
29345192 TATGGGTTT
1 TATGGGTTT
29345201 TTGTTTAGCA
Statistics
Matches: 65, Mismatches: 27, Indels: 3
0.68 0.28 0.03
Matches are distributed among these distances:
20 4 0.06
21 57 0.88
22 4 0.06
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (21 bp):
TATGGGTTTCCGTTCAACCCT
Found at i:29348496 original size:3 final size:3
Alignment explanation
Indices: 29348490--29348555 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
29348480 TTTTCTTTTT
29348490 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29348538 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
29348556 AGCTTAACTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29352715 original size:7 final size:7
Alignment explanation
Indices: 29352703--29352729 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29352693 AGTATGTATA
29352703 TATAAAT
1 TATAAAT
29352710 TATAAAT
1 TATAAAT
29352717 TATAAAT
1 TATAAAT
29352724 TATAAA
1 TATAAA
29352730 ATATGGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TATAAAT
Found at i:29352958 original size:21 final size:20
Alignment explanation
Indices: 29352930--29352981 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
29352920 AATGTACGTA
29352930 TATATATATTAGCAAAATATGTG
1 TATATATATTAGCAAAA-A--TG
*
29352953 TATATATATT-GTAAAAATG
1 TATATATATTAGCAAAAATG
29352972 TATATATATT
1 TATATATATT
29352982 TAATGTGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.43
21 1 0.04
22 5 0.18
23 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (20 bp):
TATATATATTAGCAAAAATG
Found at i:29352960 original size:23 final size:21
Alignment explanation
Indices: 29352927--29352980 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 21
29352917 TAAAATGTAC
29352927 GTATATATATATTAGCAAAATAT
1 GTATATATATATT-GCAAAA-AT
* *
29352950 GTGTATATATATTGTAAAAAT
1 GTATATATATATTGCAAAAAT
29352971 GTATATATAT
1 GTATATATAT
29352981 TTAATGTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.39
22 5 0.18
23 12 0.43
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (21 bp):
GTATATATATATTGCAAAAAT
Found at i:29353040 original size:3 final size:3
Alignment explanation
Indices: 29353032--29353065 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
29353022 GTGAATAATG
29353032 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
29353066 TAATAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:29353070 original size:3 final size:3
Alignment explanation
Indices: 29353064--29353097 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
29353054 CAACAACAAC
29353064 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29353098 GTATTAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29354081 original size:490 final size:489
Alignment explanation
Indices: 29353162--29354136 Score: 1860
Period size: 490 Copynumber: 2.0 Consensus size: 489
29353152 CTAAATCGGA
29353162 GAAAAAATTAAAATTTGGACTTGAATCGCAAATAAAATCAAAGGGAAGGGACTATGCTGAACGCG
1 GAAAAAATTAAAATTTGGACTTGAATCGCAAATAAAATCAAAGGGAAGGGACTATGCTGAACGCG
29353227 CGTATAACATAGAGGGGCTAGAAGGGAAATTTTCCCCTCTCCTCTAAAACAACGTCGTTCCAATG
66 CGTATAACATAGAGGGGCTAGAAGGGAAATTTTCCCCTCTCCTCTAAAACAACGTCGTTCCAATG
29353292 GGACCAAATTGAAAACGGTAATAAAATAAAAGGGAAATTTAAGAATGTAAAAAAACCTGATTGAA
131 GGACCAAATTGAAAACGGTAATAAAATAAAAGGGAAATTTAAGAATGTAAAAAAACCTGATTGAA
29353357 AAACATTAAAAAAGAGGAAGGGCTAAAAGTGCAATTAGCCCTTCCATTGAAAACACGCGGATCCC
196 AAACATTAAAAAAGAGGAAGGGCTAAAAGTGCAATTAGCCCTTCCATTGAAAACACGCGGATCCC
* *
29353422 CCTGGAGCGGGTCAGATTTTCGGGCCAGGAGCTAAACGACGCCGTTTTGGCGTTTTAAAGGGGTG
261 CCTAGAGCGGGTCAGATTTTCAGGCCAGGAGCTAAACGACGCCGTTTTGGCGTTTTAAAGGGGTG
29353487 AGCAAAACGACGCCGTTTTGCTTCCCTATTTAAACCAGTTTTTTCCAAAAACTTTCATTTTTCTT
326 AGCAAAACGACGCCGTTTTGCTTCCCTATTTAAACCAGTTTTTTCCAAAAACTTTCATTTTTCTT
*
29353552 TCTTCTTAAAAAAAAATCCCCAAAAATCCTCTCAACTCTCCCCTTTTCTCTCCGAGCACCGGTCA
391 TCTTCTTAAAAAAAAATCCCCAAAAATCCTCTCAACTCTCCACTTTTCTCTCCGAGCACCGGTCA
29353617 AGGGTCCGGCCGAGAGCCACCGTACCGGCCACCC
456 AGGGTCCGGCCGAGAGCCACCGTACCGGCCACCC
29353651 GAAAAAATTAAAATTTGGACTTGAATCGCAAATAAAATCAAAGGGAAGGGACTATGCTGAACGCG
1 GAAAAAATTAAAATTTGGACTTGAATCGCAAATAAAATCAAAGGGAAGGGACTATGCTGAACGCG
29353716 CGTATAACATAGAGGGGCTAGAAGGGAAATTTTCCCCTCTCCTCTAAAACAACGTCGTTCCAATG
66 CGTATAACATAGAGGGGCTAGAAGGGAAATTTTCCCCTCTCCTCTAAAACAACGTCGTTCCAATG
*
29353781 GGACCAAATTGAAAACGGTAATAAAATAAAGGGGAAATTTAAGAATGTAAAAAAAACCTGATTGA
131 GGACCAAATTGAAAACGGTAATAAAATAAAAGGGAAATTTAAGAATGT-AAAAAAACCTGATTGA
29353846 AAAACATTAAAAAAGAGGAAGGGCTAAAAGTGCAATTAGCCCTTCCATTGAAAACACGCGGATCC
195 AAAACATTAAAAAAGAGGAAGGGCTAAAAGTGCAATTAGCCCTTCCATTGAAAACACGCGGATCC
*
29353911 CCCTAGAGCGGGTCGGATTTTCAGGCCAGGAGCTAAACGACGCCGTTTTGGCGTTTTAAAGGGGT
260 CCCTAGAGCGGGTCAGATTTTCAGGCCAGGAGCTAAACGACGCCGTTTTGGCGTTTTAAAGGGGT
29353976 GAGCAAAACGACGCCGTTTTGCTTCCCTATTTAAACCAGTTTTTTCCAAAAACTTTCATTTTTCT
325 GAGCAAAACGACGCCGTTTTGCTTCCCTATTTAAACCAGTTTTTTCCAAAAACTTTCATTTTTCT
* * *
29354041 TTCTTCTTCAAAAAAAATCCCCAAAAATCCTCTCAACTCTCCACTTTTCTCTCCGAGCGCCGGTT
390 TTCTTCTTAAAAAAAAATCCCCAAAAATCCTCTCAACTCTCCACTTTTCTCTCCGAGCACCGGTC
*
29354106 AAGGGTCCGGCTGAGAGCCACCGTACCGGCC
455 AAGGGTCCGGCCGAGAGCCACCGTACCGGCC
29354137 GCCGTCCTCC
Statistics
Matches: 476, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
489 177 0.37
490 299 0.63
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (489 bp):
GAAAAAATTAAAATTTGGACTTGAATCGCAAATAAAATCAAAGGGAAGGGACTATGCTGAACGCG
CGTATAACATAGAGGGGCTAGAAGGGAAATTTTCCCCTCTCCTCTAAAACAACGTCGTTCCAATG
GGACCAAATTGAAAACGGTAATAAAATAAAAGGGAAATTTAAGAATGTAAAAAAACCTGATTGAA
AAACATTAAAAAAGAGGAAGGGCTAAAAGTGCAATTAGCCCTTCCATTGAAAACACGCGGATCCC
CCTAGAGCGGGTCAGATTTTCAGGCCAGGAGCTAAACGACGCCGTTTTGGCGTTTTAAAGGGGTG
AGCAAAACGACGCCGTTTTGCTTCCCTATTTAAACCAGTTTTTTCCAAAAACTTTCATTTTTCTT
TCTTCTTAAAAAAAAATCCCCAAAAATCCTCTCAACTCTCCACTTTTCTCTCCGAGCACCGGTCA
AGGGTCCGGCCGAGAGCCACCGTACCGGCCACCC
Found at i:29355068 original size:50 final size:49
Alignment explanation
Indices: 29355009--29355272 Score: 247
Period size: 50 Copynumber: 5.4 Consensus size: 49
29354999 TTTATTCTGT
29355009 TCCGCTGTTGTAGCTTCAATCTTTTTAATGGCAATGTCAGGGAAGTAAGA
1 TCCGCTGTTGTAGCTTCAATCTTTTTAAT-GCAATGTCAGGGAAGTAAGA
** * ** *
29355059 TCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAA-CACTAGGAAAGTAAGA
1 TCCGCTGTTGTAGCTTCAATCT-TTTTAATGCAATGTC-AGGGAAGTAAGA
* * * *
29355109 TCCGTTGTTATAGCTTCAATCTTTTTAA--C--TGTCGGGGAAGCAAGA
1 TCCGCTGTTGTAGCTTCAATCTTTTTAATGCAATGTCAGGGAAGTAAGA
** * *
29355154 TCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAA--TC-TGGAAGTAAGA
1 TCCGCTGTTGTAGCTTCAATCT-TTTTAATGCAATGTCAGGGAAGTAAGA
* * * * *
29355201 TTCACTGTTGTGGCTTCAATTTTTTTAATTGCAATGTCAAGGAAGTAAGA
1 TCCGCTGTTGTAGCTTCAATCTTTTTAA-TGCAATGTCAGGGAAGTAAGA
*
29355251 TCCGCTGCTGTAGCTTCAATCT
1 TCCGCTGTTGTAGCTTCAATCT
29355273 ATTCCACTGC
Statistics
Matches: 166, Mismatches: 36, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
45 29 0.17
46 7 0.04
47 33 0.20
48 3 0.02
49 6 0.04
50 84 0.51
51 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (49 bp):
TCCGCTGTTGTAGCTTCAATCTTTTTAATGCAATGTCAGGGAAGTAAGA
Found at i:29355209 original size:47 final size:47
Alignment explanation
Indices: 29355049--29355689 Score: 306
Period size: 47 Copynumber: 13.3 Consensus size: 47
29355039 GCAATGTCAG
* * *
29355049 GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAA-TCT
* ** * * ** *
29355097 AGGAAAGTAAGATCCGTTGTTATAGCTTCAATCTTTTTAACTG---TCGG
1 -GG-AAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAATC-T
* * *
29355144 GGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAATCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAATCT
* * * * * ** * *
29355191 GGAAGTAAGATTCACTGTTGTGGCTTCAATTTTTTTAATTGCAATGTCAA
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAA--TC-T
* * * * *
29355241 GGAAGTAAGATCCGCTGCTGTAGCTTCAATCTATTCCACTGCAACGCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAA-TCT
* ** * * ** * **
29355289 AGGAAAGTAAGATTCGCCGTTGTGGCTTTGATTTTTTAAATTGCAATGG
1 -GG-AAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAATCT
* * *
29355338 GGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAAT---CT
* * * * * ** * **
29355387 GGAAATAAGATTCGCCGTTGTGGCTTCGATATTTTAAATTGCAATGG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAATCT
* *
29355434 GGAAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAAT---CT
* * * * ** * **
29355483 GGAAATAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAATCT
* * * **
29355530 GGAAGTCAGACTCGCTGTTGTAGCTTCAATCTGTTCCGTTGC-ATCGCCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAAT---CT
* * * * * ** * **
29355579 GGAAGTAAAATTCACCGTTGTGGCTTCGATCTTTTAAATTGCAATGG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAATCT
* * * *
29355626 GGAAGTGAGACTCACCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAAT---CT
29355675 GGAAGTAAGATTCGC
1 GGAAGTAAGATTCGC
29355690 TATTGTGGCT
Statistics
Matches: 428, Mismatches: 139, Indels: 50
0.69 0.23 0.08
Matches are distributed among these distances:
45 33 0.08
46 11 0.03
47 160 0.37
48 4 0.01
49 114 0.27
50 106 0.25
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (47 bp):
GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAATCT
Found at i:29355284 original size:50 final size:49
Alignment explanation
Indices: 29355009--29355316 Score: 231
Period size: 50 Copynumber: 6.3 Consensus size: 49
29354999 TTTATTCTGT
** * *
29355009 TCCGCTGTTGTAGCTTCAATCTTTTTAATGGCAATGTCAGGGAAGTAAGA
1 TCCGCTGTTGTAGCTTCAATCTTTCCACT-GCAATGTCAAGGAAGTAAGA
** *
29355059 TCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAA-CACTAGGAAAGTAAGA
1 TCCGCTGTTGTAGCTTCAATCT-TTCCACTGCAATGTCAAGG-AAGTAAGA
* * * ** *
29355109 TCCGTTGTTATAGCTTCAATCTTT----T-TAACTGTCGGGGAAGCAAGA
1 TCCGCTGTTGTAGCTTCAATCTTTCCACTGCAA-TGTCAAGGAAGTAAGA
*
29355154 TCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAA--TC-TGGAAGTAAGA
1 TCCGCTGTTGTAGCTTCAATCT-TTCCACTGCAATGTCAAGGAAGTAAGA
* * * * ** *
29355201 TTCACTGTTGTGGCTTCAATTTTTTTAATTGCAATGTCAAGGAAGTAAGA
1 TCCGCTGTTGTAGCTTCAA-TCTTTCCACTGCAATGTCAAGGAAGTAAGA
* * *
29355251 TCCGCTGCTGTAGCTTCAATCTATTCCACTGCAACG-CTAGGAAAGTAAGA
1 TCCGCTGTTGTAGCTTCAATCT-TTCCACTGCAATGTCAAGG-AAGTAAGA
* * *
29355301 TTCGCCGTTGTGGCTT
1 TCCGCTGTTGTAGCTT
29355317 TGATTTTTTA
Statistics
Matches: 200, Mismatches: 42, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
44 2 0.01
45 28 0.14
46 5 0.03
47 33 0.17
48 4 0.02
49 13 0.06
50 109 0.55
51 6 0.03
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (49 bp):
TCCGCTGTTGTAGCTTCAATCTTTCCACTGCAATGTCAAGGAAGTAAGA
Found at i:29355426 original size:96 final size:96
Alignment explanation
Indices: 29355015--29355705 Score: 747
Period size: 96 Copynumber: 7.2 Consensus size: 96
29355005 CTGTTCCGCT
* * * * *
29355015 GTTGTAGCTTCAATCTTTTTAATGGCAATGTCAGGGAAGTAAGA-TCCGCTGTTGTAGCTTCAAT
1 GTTGTGGCTTCGATCTTTTAAATTGCAATG---GGGAAGTAAGACT-CGCCGTTGTAGCTTCAAT
* * * * **
29355079 CTGTTCCACTGCAAC-ACTAGGAAAGTAAGATCCGTT
62 CTGTTCCGCTGCATCGCCT-GGAAA-TAAGATTCGCC
* * * * * * *
29355115 GTTATAGCTTCAATCTTTTTAACTG---TCGGGGAAGCAAGA-TCCGCTGTTGTAGCTTCAATCT
1 GTTGTGGCTTCGATCTTTTAAATTGCAAT-GGGGAAGTAAGACT-CGCCGTTGTAGCTTCAATCT
* * * *
29355176 GTTCCACTGCAAT---CTGGAAGTAAGATTCACT
64 GTTCCGCTGC-ATCGCCTGGAAATAAGATTCGCC
* * * * * *
29355207 GTTGTGGCTTCAATTTTTTTAATTGCAATGTCAAGGAAGTAAGA-TCCGCTGCTGTAGCTTCAAT
1 GTTGTGGCTTCGATCTTTTAAATTGCAATG---GGGAAGTAAGACT-CGCCGTTGTAGCTTCAAT
* * *
29355271 CTATTCCACTGCAACG-CTAGGAAAGTAAGATTCGCC
62 CTGTTCCGCTGCATCGCCT-GGAAA-TAAGATTCGCC
* * *
29355307 GTTGTGGCTTTGATTTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGT
1 GTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTAAGACTCGCCGTTGTAGCTTCAATCTGT
29355372 TCCGCTGCATCGCCTGGAAATAAGATTCGCC
66 TCCGCTGCATCGCCTGGAAATAAGATTCGCC
*
29355403 GTTGTGGCTTCGATATTTTAAATTGCAATGGGGAAGTAAGACTCGCCGTTGTAGCTTCAATCTGT
1 GTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTAAGACTCGCCGTTGTAGCTTCAATCTGT
29355468 TCCGCTGCATCGCCTGGAAATAAGATTCGCC
66 TCCGCTGCATCGCCTGGAAATAAGATTCGCC
* *
29355499 GTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTCAGACTCGCTGTTGTAGCTTCAATCTGT
1 GTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTAAGACTCGCCGTTGTAGCTTCAATCTGT
* * * *
29355564 TCCGTTGCATCGCCTGGAAGTAAAATTCACC
66 TCCGCTGCATCGCCTGGAAATAAGATTCGCC
* *
29355595 GTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCACCGTTGTAGCTTCAATCTGT
1 GTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTAAGACTCGCCGTTGTAGCTTCAATCTGT
* *
29355660 TCCGCTGCATCGCCTGGAAGTAAGATTCGCT
66 TCCGCTGCATCGCCTGGAAATAAGATTCGCC
* *
29355691 ATTGTGGCTTAGATC
1 GTTGTGGCTTCGATC
29355706 GCATGGGAAG
Statistics
Matches: 527, Mismatches: 50, Indels: 32
0.87 0.08 0.05
Matches are distributed among these distances:
92 29 0.06
93 4 0.01
94 3 0.01
95 43 0.08
96 297 0.56
97 83 0.16
98 6 0.01
99 4 0.01
100 58 0.11
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (96 bp):
GTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTAAGACTCGCCGTTGTAGCTTCAATCTGT
TCCGCTGCATCGCCTGGAAATAAGATTCGCC
Found at i:29356173 original size:44 final size:44
Alignment explanation
Indices: 29356110--29356196 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
29356100 GCCCCCACTA
29356110 TAAACCTCCAAGTTCAATCCACTGGATACAAAATTTAAACCATG
1 TAAACCTCCAAGTTCAATCCACTGGATACAAAATTTAAACCATG
* * *
29356154 TAAACCTTCAAGTTCAATCCACTGGATGCAAAATTTGAACCAT
1 TAAACCTCCAAGTTCAATCCACTGGATACAAAATTTAAACCAT
29356197 CTTTCTCCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.26
Consensus pattern (44 bp):
TAAACCTCCAAGTTCAATCCACTGGATACAAAATTTAAACCATG
Found at i:29357141 original size:12 final size:11
Alignment explanation
Indices: 29357119--29357153 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
29357109 CTGGCCTCTC
29357119 CTTTTTTTTTT
1 CTTTTTTTTTT
29357130 CTTTTCTTTTTT
1 CTTTT-TTTTTT
29357142 CTTTTTGTTTTT
1 CTTTTT-TTTTT
29357154 TGATCTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:29358321 original size:5 final size:6
Alignment explanation
Indices: 29358305--29358344 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
29358295 TTGACCTCTC
*
29358305 CTTTTT CTTTTT CTTTTT CTTATTT CTTATTT CTCTTT CT
1 CTTTTT CTTTTT CTTTTT CTT-TTT CTT-TTT CTTTTT CT
29358345 CCTATTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 20 0.62
7 12 0.38
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (6 bp):
CTTTTT
Found at i:29358350 original size:22 final size:20
Alignment explanation
Indices: 29358301--29358351 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
29358291 TGCCTTGACC
*
29358301 TCTCCTTTTTCTTTTTCTTT
1 TCTCCTATTTCTTTTTCTTT
*
29358321 T-TCTTATTTCTTATTTCTCTT
1 TCTCCTATTTCTT-TTTCT-TT
29358342 TCTCCTATTT
1 TCTCCTATTT
29358352 TTGACTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 9 0.36
20 6 0.24
21 3 0.12
22 7 0.28
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTCCTATTTCTTTTTCTTT
Found at i:29358386 original size:6 final size:6
Alignment explanation
Indices: 29358371--29358415 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
29358361 AGTTTTTCAA
*
29358371 TTTT-T TTTTGT TTTTGT TTTTGT GTTTGT TTTTGT TTTT-T TTTTG
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTG
29358416 AATCTGAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 9 0.25
6 27 0.75
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTGT
Found at i:29358389 original size:24 final size:24
Alignment explanation
Indices: 29358362--29358414 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
29358352 TTGACTTTGA
*
29358362 GTTTTTCAATTTTTTTTTGTTTTT
1 GTTTTTCAATTTGTTTTTGTTTTT
***
29358386 GTTTTTGTGTTTGTTTTTGTTTTT
1 GTTTTTCAATTTGTTTTTGTTTTT
29358410 -TTTTT
1 GTTTTT
29358415 GAATCTGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.81
Consensus pattern (24 bp):
GTTTTTCAATTTGTTTTTGTTTTT
Found at i:29369479 original size:4 final size:4
Alignment explanation
Indices: 29369470--29369497 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
29369460 TCAATCGGAA
29369470 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
29369498 ATGCAGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:29374096 original size:101 final size:101
Alignment explanation
Indices: 29373971--29374176 Score: 376
Period size: 101 Copynumber: 2.0 Consensus size: 101
29373961 ATCTTCTAAC
*
29373971 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGGGGTGGAAAAGCACTTTTTGACAGCACA
1 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
*
29374036 AGCAATGCCAAACAATCAGCTTTAACATCAAATTAA
66 AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
*
29374072 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCATA
1 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
*
29374137 AACAATGCCAAACAATCAGCTTTAACATCAAATTAG
66 AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
29374173 TTTT
1 TTTT
29374177 TCAACCCAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (101 bp):
TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
Found at i:29379692 original size:13 final size:15
Alignment explanation
Indices: 29379661--29379690 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29379651 ATTTTTTTTC
*
29379661 ATTTTTTATTAAAAT
1 ATTTTTTAATAAAAT
29379676 ATTTTTTAATAAAAT
1 ATTTTTTAATAAAAT
29379691 TTGATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTTTAATAAAAT
Found at i:29379886 original size:12 final size:12
Alignment explanation
Indices: 29379869--29379893 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29379859 ATAGTTTATA
29379869 TATTTATATTTT
1 TATTTATATTTT
29379881 TATTTATATTTT
1 TATTTATATTTT
29379893 T
1 T
29379894 TTCTGTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:29389590 original size:14 final size:14
Alignment explanation
Indices: 29389571--29389598 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29389561 AAAAAAAGAA
29389571 AGGAAATAAAGTTT
1 AGGAAATAAAGTTT
29389585 AGGAAATAAAGTTT
1 AGGAAATAAAGTTT
29389599 CAAGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
AGGAAATAAAGTTT
Found at i:29391590 original size:13 final size:12
Alignment explanation
Indices: 29391568--29391604 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
29391558 TATCAAATCC
29391568 AATGAAAAAAAA
1 AATGAAAAAAAA
29391580 AATGTAAAAAAAA
1 AATG-AAAAAAAA
29391593 AA--AAAAAAAA
1 AATGAAAAAAAA
29391603 AA
1 AA
29391605 AAACTACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
12 4 0.17
13 10 0.42
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.08
Consensus pattern (12 bp):
AATGAAAAAAAA
Found at i:29394622 original size:3 final size:3
Alignment explanation
Indices: 29394614--29394638 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29394604 ACACAATCAA
29394614 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
29394639 GCAACCTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:29397037 original size:20 final size:21
Alignment explanation
Indices: 29397009--29397056 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
29396999 AATGGTTATA
* *
29397009 GAAAATAATTTTTA-AAAAAT
1 GAAATTAATTTTAATAAAAAT
29397029 GAAATTAATTTTAATAAAAAT
1 GAAATTAATTTTAATAAAAAT
29397050 GATAATT
1 GA-AATT
29397057 CCGGGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 8 0.33
22 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (21 bp):
GAAATTAATTTTAATAAAAAT
Found at i:29399088 original size:20 final size:20
Alignment explanation
Indices: 29399063--29399101 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29399053 CGCCTATGTG
* *
29399063 AAGGAGGCATACGCCCGTGA
1 AAGGAGGCACACGACCGTGA
29399083 AAGGAGGCACACGACCGTG
1 AAGGAGGCACACGACCGTG
29399102 TGTCGATAAC
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:0.31, C:0.26, G:0.36, T:0.08
Consensus pattern (20 bp):
AAGGAGGCACACGACCGTGA
Found at i:29400805 original size:6 final size:6
Alignment explanation
Indices: 29400794--29400833 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
29400784 TTCCACATTT
*
29400794 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTT CCTCTTC CCT
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTC-TC CCT
29400834 TTCTTTCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CCTCTC
Found at i:29407723 original size:14 final size:14
Alignment explanation
Indices: 29407702--29407735 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
29407692 TGGTATGGGT
29407702 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
29407715 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
29407729 TTATAGG
1 TTATAGG
29407736 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:29407891 original size:24 final size:25
Alignment explanation
Indices: 29407864--29407910 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
29407854 AGAGGAAAGT
29407864 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
29407888 TTAAATTACTTAAAACGAAAAAA
1 TTAAAGAACATAAAACGAAAAAA
29407911 TATGGGGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:29409906 original size:27 final size:27
Alignment explanation
Indices: 29409842--29409906 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
29409832 TATTTTATTA
29409842 TTATTATTTATTTCTTTTTGGTCATTTT
1 TTATTATTT-TTTCTTTTTGGTCATTTT
* *
29409870 CTATCT-TTTTTTCTTCTTT-TTCATTTT
1 TTAT-TATTTTTTCTT-TTTGGTCATTTT
29409897 TTATTATTTT
1 TTATTATTTT
29409907 ATTAATCGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 1 0.03
27 20 0.65
28 9 0.29
29 1 0.03
ACGTcount: A:0.12, C:0.11, G:0.03, T:0.74
Consensus pattern (27 bp):
TTATTATTTTTTCTTTTTGGTCATTTT
Found at i:29416544 original size:22 final size:21
Alignment explanation
Indices: 29416506--29416549 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
29416496 ACAAATTATA
29416506 ATTTAAAAATCTCAATTAAAT
1 ATTTAAAAATCTCAATTAAAT
29416527 ATTTAACAAATCAT-AATTAAAT
1 ATTTAA-AAATC-TCAATTAAAT
29416549 A
1 A
29416550 AATTAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 14 0.67
23 1 0.05
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTAAAAATCTCAATTAAAT
Found at i:29417423 original size:2 final size:2
Alignment explanation
Indices: 29417416--29417485 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
29417406 AAATACCATT
* *
29417416 CA CA CA CA CA CA CC CA CA CA CA CA CA CA CA CA CA CA CA CC CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
29417458 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
29417486 TATATATACA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:29428692 original size:26 final size:26
Alignment explanation
Indices: 29428625--29428686 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
29428615 CTTGTAAGTG
*
29428625 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATATATGCTATGATA
* *
29428651 TTCTAAAACTGATATATGTTATGATA
1 TTCTGAAACTGATATATGCTATGATA
29428677 TTCTGAAACT
1 TTCTGAAACT
29428687 ACTATAGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (26 bp):
TTCTGAAACTGATATATGCTATGATA
Found at i:29428916 original size:73 final size:74
Alignment explanation
Indices: 29428797--29428943 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 74
29428787 ATGGGTTTGG
*
29428797 GCAAAAAACGAGGCCCGTTTTCCTCGGGTAAAACATTTTTGGCCCGGACTCGGCCTGGCCTAG-C
1 GCAAAAAACGAGGCCCGTTTGCCTCGGGTAAAACATTTTTGGCCCGGACTCGGCCTGGCCTAGCC
29428861 CGACCCGAA
66 CGACCCGAA
29428870 GCAAAAAACGAGGCCCGTTTGCCTCGGGTAAAACATTTTTGGCCCGGACTCGGCCTGGCCTAGCC
1 GCAAAAAACGAGGCCCGTTTGCCTCGGGTAAAACATTTTTGGCCCGGACTCGGCCTGGCCTAGCC
29428935 CGACCCGAA
66 CGACCCGAA
29428944 TTATATATTA
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 62 0.86
74 10 0.14
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (74 bp):
GCAAAAAACGAGGCCCGTTTGCCTCGGGTAAAACATTTTTGGCCCGGACTCGGCCTGGCCTAGCC
CGACCCGAA
Found at i:29428988 original size:17 final size:17
Alignment explanation
Indices: 29428968--29429000 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29428958 TATATTTTTA
29428968 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
29428985 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
29429001 TATATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:29437641 original size:13 final size:13
Alignment explanation
Indices: 29437619--29437648 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29437609 TCTTTAGGTA
*
29437619 TTTAATTGACTTG
1 TTTAACTGACTTG
29437632 TTTAACTGACTTG
1 TTTAACTGACTTG
29437645 TTTA
1 TTTA
29437649 GTTTGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.53
Consensus pattern (13 bp):
TTTAACTGACTTG
Found at i:29438145 original size:22 final size:21
Alignment explanation
Indices: 29438097--29438142 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29438087 TAATATTTTA
*
29438097 ATTTAAATTTAATCATAAAAT
1 ATTTAAATTTAATAATAAAAT
*
29438118 ACTTAAATATTAA-AATAAAAT
1 ATTTAAAT-TTAATAATAAAAT
29438139 ATTT
1 ATTT
29438143 TAATACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAAATTTAATAATAAAAT
Found at i:29441332 original size:9 final size:9
Alignment explanation
Indices: 29441318--29441366 Score: 89
Period size: 9 Copynumber: 5.4 Consensus size: 9
29441308 TTTGGTTAAA
29441318 AATTAACCG
1 AATTAACCG
29441327 AATTAACCG
1 AATTAACCG
*
29441336 AATTACCCG
1 AATTAACCG
29441345 AATTAACCG
1 AATTAACCG
29441354 AATTAACCG
1 AATTAACCG
29441363 AATT
1 AATT
29441367 GAATCATTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:29442097 original size:77 final size:78
Alignment explanation
Indices: 29441994--29442148 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
29441984 ATGTGTTAAG
29441994 AATAAAGCAAATATCACGTCTCCATCACTTACATGAAATCTTTGCTAAAATTGTTTTAAAATAG-
1 AATAAAGCAAATATCACGTCTCCATCACTTACATGAAATCTTTGCTAAAATTGTTTTAAAATAGT
29442058 TTTAATATATAAA
66 TTTAATATATAAA
29442071 AATAAAGCAAATATCACGTCTCCATCACTTACATGAAATCTTTGCTAAAATTGTTTTAAAATAGT
1 AATAAAGCAAATATCACGTCTCCATCACTTACATGAAATCTTTGCTAAAATTGTTTTAAAATAGT
29442136 TTTAATATATAAA
66 TTTAATATATAAA
29442149 TTATAATAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 64 0.83
78 13 0.17
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (78 bp):
AATAAAGCAAATATCACGTCTCCATCACTTACATGAAATCTTTGCTAAAATTGTTTTAAAATAGT
TTTAATATATAAA
Found at i:29448564 original size:2 final size:2
Alignment explanation
Indices: 29448557--29448581 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29448547 CTCTTCCTGG
29448557 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 A
29448582 AAAATCCCTT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29452306 original size:20 final size:21
Alignment explanation
Indices: 29452274--29452317 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
29452264 CAATCACTTT
29452274 ATAATATAATTAAAAAATAAA
1 ATAATATAATTAAAAAATAAA
**
29452295 ATAATA-AATTAAGTAATAAA
1 ATAATATAATTAAAAAATAAA
29452315 ATA
1 ATA
29452318 TATTTATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
ATAATATAATTAAAAAATAAA
Found at i:29454376 original size:29 final size:30
Alignment explanation
Indices: 29454315--29454377 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
29454305 AATAAAGATA
* *
29454315 AAAAATGTATATGGGTATATATTTACAAAAT
1 AAAAATGTATA-GAGTATATATATACAAAAT
* *
29454346 AAAAATGTATA-AGTATATATATAGAATAT
1 AAAAATGTATAGAGTATATATATACAAAAT
29454375 AAA
1 AAA
29454378 GTATATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 17 0.61
31 11 0.39
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (30 bp):
AAAAATGTATAGAGTATATATATACAAAAT
Found at i:29456327 original size:21 final size:21
Alignment explanation
Indices: 29456303--29456342 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
29456293 TTTTAAATTT
29456303 TAAAAATTATTAAA-AAAATCA
1 TAAAAATTA-TAAACAAAATCA
29456324 TAAAAATTATAAACAAAAT
1 TAAAAATTATAAACAAAAT
29456343 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAATTATAAACAAAATCA
Found at i:29456490 original size:13 final size:12
Alignment explanation
Indices: 29456464--29456496 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29456454 AATATAATTT
29456464 TAAATTTTTTTA
1 TAAATTTTTTTA
29456476 TAAATTTTGTTTA
1 TAAATTTT-TTTA
29456489 T-AATTTTT
1 TAAATTTTT
29456497 ATGGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 14 0.70
13 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (12 bp):
TAAATTTTTTTA
Found at i:29458447 original size:23 final size:23
Alignment explanation
Indices: 29458376--29458448 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
29458366 ACATGCCAGC
*
29458376 TCTCATTGTCATGA-GTC-GGGA
1 TCTCCTTGTCATGACGTCGGGGA
* *
29458397 TCTCCTTGTCATGACGTTGGAGA
1 TCTCCTTGTCATGACGTCGGGGA
*
29458420 TCTCCTTGTCCTGACGTCGGGGA
1 TCTCCTTGTCATGACGTCGGGGA
*
29458443 CCTCCT
1 TCTCCT
29458449 CTTCCTGACG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.30
22 2 0.05
23 28 0.65
ACGTcount: A:0.14, C:0.27, G:0.26, T:0.33
Consensus pattern (23 bp):
TCTCCTTGTCATGACGTCGGGGA
Found at i:29460361 original size:41 final size:42
Alignment explanation
Indices: 29460271--29460371 Score: 118
Period size: 41 Copynumber: 2.4 Consensus size: 42
29460261 ACTCAATGTT
* *
29460271 TCACACACTAAATGCCATCGCATAGCCGAAGCTATTAGAATC
1 TCACACACTAAGTGCCATCACATAGCCGAAGCTATTAGAATC
* * *
29460313 CCGCACACTAAGTGCC-TTACATAGCCGAAGCTATCTCAG-A-C
1 TCACACACTAAGTGCCATCACATAGCCGAAGCTAT-T-AGAATC
29460354 TCACACACTAAGTGCCAT
1 TCACACACTAAGTGCCAT
29460372 TATTATCAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
41 31 0.63
42 16 0.33
43 2 0.04
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.21
Consensus pattern (42 bp):
TCACACACTAAGTGCCATCACATAGCCGAAGCTATTAGAATC
Found at i:29471488 original size:41 final size:42
Alignment explanation
Indices: 29471395--29471555 Score: 152
Period size: 41 Copynumber: 3.9 Consensus size: 42
29471385 CTCAATGTTG
* * * * *
29471395 CGCACACTAAATGCCATTGCATAGCGGAAGCTAT-TATAATCC
1 CGCACACTAAGTGCCATTACATAGCCGAAGCTATCT-CAATCT
*
29471437 CGCACTCTAAGTGCC-TTACATAGCCGAAGCTATCTCAATCT
1 CGCACACTAAGTGCCATTACATAGCCGAAGCTATCTCAATCT
* * * *
29471478 CGGACACTAAGTGCCATATATATAGTCGAAGCTATTCTCAGT-T
1 CGCACACTAAGTGCCAT-TACATAGCCGAAGCTA-TCTCAATCT
* *
29471521 -GCACACTAAGTGCCA-TAAATAGTCGAAGCTATCTC
1 CGCACACTAAGTGCCATTACATAGCCGAAGCTATCTC
29471556 GAGTCGAATA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
39 4 0.04
40 15 0.15
41 33 0.32
42 29 0.28
43 15 0.15
44 6 0.06
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
CGCACACTAAGTGCCATTACATAGCCGAAGCTATCTCAATCT
Found at i:29471583 original size:39 final size:40
Alignment explanation
Indices: 29471443--29471585 Score: 123
Period size: 40 Copynumber: 3.5 Consensus size: 40
29471433 ATCCCGCACT
* * * * *
29471443 CTAAGTGCCTTACATAGCCGAAGCTA-TCTCAATCTCGGACA
1 CTAAGTGCCATAAATAGTCGAAGCTATTCTC-A-GTCGAACA
* *
29471484 CTAAGTGCCATATATATAGTCGAAGCTATTCTCAGTTGCACA
1 CTAAGTGCCATA-A-ATAGTCGAAGCTATTCTCAGTCGAACA
*
29471526 CTAAGTGCCATAAATAGTCGAAGCTA-TCTCGAGTCGAATA
1 CTAAGTGCCATAAATAGTCGAAGCTATTCTC-AGTCGAACA
*
29471566 CT-AGTGCTA-AACATAGTCGA
1 CTAAGTGCCATAA-ATAGTCGA
29471586 TTCATCGTCG
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
38 2 0.02
39 18 0.21
40 21 0.24
41 12 0.14
42 17 0.20
43 13 0.15
44 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (40 bp):
CTAAGTGCCATAAATAGTCGAAGCTATTCTCAGTCGAACA
Found at i:29471605 original size:21 final size:21
Alignment explanation
Indices: 29471575--29471614 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29471565 ACTAGTGCTA
29471575 AACATAGTCG-ATTCATCGTCG
1 AACATAGTCGTATTC-TCGTCG
*
29471596 AACATGGTCGTATTCTCGT
1 AACATAGTCGTATTCTCGT
29471615 GCATACAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (21 bp):
AACATAGTCGTATTCTCGTCG
Found at i:29473509 original size:25 final size:27
Alignment explanation
Indices: 29473481--29473530 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
29473471 ATTTGTAAAT
29473481 TAGAAAAATATC-TCA-AGAATTTTTC
1 TAGAAAAATATCTTCAGAGAATTTTTC
* *
29473506 TAGAATAATCTCTTCAGAGAATTTT
1 TAGAAAAATATCTTCAGAGAATTTT
29473531 CTCTCTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 3 0.14
27 8 0.38
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (27 bp):
TAGAAAAATATCTTCAGAGAATTTTTC
Done.