Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold27
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: 2789374
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 115785 characters in sequence are not A, C, G, or T
File 14 of 16
Found at i:2313972 original size:19 final size:21
Alignment explanation
Indices: 2313948--2313999 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2313938 AGCGATACAC
*
2313948 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
2313967 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
2313988 TGTATCGATACA
1 TGTATCGATACA
2314000 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:2317183 original size:22 final size:22
Alignment explanation
Indices: 2317158--2317216 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
2317148 AGTTTTTCAA
2317158 TTTTCTCTCTATTTT-TTTCTCT
1 TTTTCTCTCTATTTTCTTTC-CT
* * *
2317180 TTTTATGTCTTTTTTCTTTCCT
1 TTTTCTCTCTATTTTCTTTCCT
2317202 TTTTCTC-CTTATTTT
1 TTTTCTCTC-TATTTT
2317217 GCACCTGATC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 24 0.83
23 4 0.14
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTCTCTCTATTTTCTTTCCT
Found at i:2317550 original size:10 final size:9
Alignment explanation
Indices: 2317535--2317559 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2317525 ATAAATAAAA
2317535 TTAAAAAGT
1 TTAAAAAGT
2317544 TTAAAAAGT
1 TTAAAAAGT
2317553 TTAAAAA
1 TTAAAAA
2317560 TCAGACCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (9 bp):
TTAAAAAGT
Found at i:2318433 original size:164 final size:163
Alignment explanation
Indices: 2317696--2318564 Score: 757
Period size: 164 Copynumber: 5.4 Consensus size: 163
2317686 ATGAAACAAT
* * * * * *
2317696 ATGAATTTTCT-AAAACTGATTT-A-AT-AATTTAATAACAATATTAGATGAATTTTAAAAATTT
1 ATGAATTTT-TGAAAATTGATTTAATATGAATTAAATAATAATATTTGATAAATTTTAAAAATTA
* ** * * * * * *
2317757 TAAACTAAG-AAAATCCTTTCGAAAACATTTACGGAGTAG-AAACTCGGTTTTTCGAAAATAGAA
65 AAAACTAAGAAAAATCCCCT-AAAAATATTTACGGAGTAGAAAATTCAGTATTTCGAAAATAAAA
*
2317820 AAATTTCAAGAAAAAATGAAAAACTCATGAAAATGA
129 AAATTTCAAGAAAAAAAGAAAAA-TCATGAAAATGA
* * * * * * **
2317856 AAGAATTTTTGAAAACTGATTCAATAT-AAATAAATAATAATATTTTATGAATTTTAAAAACCAA
1 ATGAATTTTTGAAAATTGATTTAATATGAATTAAATAATAATATTTGATAAATTTTAAAAATTAA
* * *
2317920 AAACCAAGAAAAATCCCCTCGAAAAA-ATTTATGAAGTAGAAAACTTC-GTATTTC-AGAAATAG
66 AAACTAAGAAAAATCCCCT--AAAAATATTTACGGAGTAGAAAA-TTCAGTATTTCGA-AAATA-
** *
2317982 AGGAAATTT-------TAAAGAAAAA--A-GAAAAATGA
126 AAAAAATTTCAAGAAAAAAAGAAAAATCATG-AAAATGA
* * *
2318011 ATGAATTTTTGAAAATTGATTTAATATGGATTAAATAATAAAATTTGATGAATTTTAAAAAAATT
1 ATGAATTTTTGAAAATTGATTTAATATGAATTAAATAATAATATTTGATAAATTTT--AAAAATT
* * * ** *
2318076 AAAAACTGAGAAAAATACCCCCAAAAATATTTGAAGG-GTAGAAAACACTA-TATTTTGAAAATA
64 AAAAACTAAGAAAAAT-CCCCTAAAAATATTT-ACGGAGTAGAAAATTC-AGTATTTCGAAAATA
*
2318139 AGAAAAATTTCAAGAAAAAAAAGAAAAATGAATGAAAATGA
126 A-AAAAATTTCAAG-AAAAAAAGAAAAAT-CATGAAAATGA
* * * *
2318180 ATGAATTTTT-AAAAATAATTTAATATGAATTAAATAATAATATTTTATGAA-TTTAAAAATTAA
1 ATGAATTTTTGAAAATTGATTTAATATGAATTAAATAATAATATTTGATAAATTTTAAAAATTAA
* *
2318243 AAACCAAGAAAAATCCCCTCAAAAATATTTACGGAGTAGAAAATTCAGTATTTCAAAAATAAAAA
66 AAACTAAGAAAAATCCCCT-AAAAATATTTACGGAGTAGAAAATTCAGTATTTCGAAAATAAAAA
** * *
2318308 AAAATCAAGAAAAAAAGACGAACTCATGAAAATGA
130 AATTTCAAGAAAAAAAGA-AAAATCATGAAAATGA
*
2318343 ATGAATTTTTGAAAATTTATTTAATATGAATTAAATAATAATATTTGATAAATTTTAAAAATTAA
1 ATGAATTTTTGAAAATTGATTTAATATGAATTAAATAATAATATTTGATAAATTTTAAAAATTAA
** * * * * *
2318408 AAACTAAGAAATCTCCCCTAAAAATATTTACAGAGTAAAAAACTT-TGTATTTCGAAAAGAGGAA
66 AAACTAAGAAAAATCCCCTAAAAATATTTACGGAGTAGAAAA-TTCAGTATTTCGAAAATA-AAA
*
2318472 AAATTTCAAGAAAAAAAGAAAAATTCATAAAAATGA
129 AAATTTCAAGAAAAAAAGAAAAA-TCATGAAAATGA
* ** * * *
2318508 ATGAATTTTTAAAAATTGA-TTAATGGGAGTTAAATGACAATATTTGA-AGAATTTTAA
1 ATGAATTTTTGAAAATTGATTTAATATGAATTAAATAATAATATTTGATA-AATTTTAA
2318565 TGATTGAAAC
Statistics
Matches: 579, Mismatches: 88, Indels: 80
0.78 0.12 0.11
Matches are distributed among these distances:
154 1 0.00
155 32 0.06
156 24 0.04
157 7 0.01
158 55 0.09
159 8 0.01
160 18 0.03
161 1 0.00
162 37 0.06
163 50 0.09
164 142 0.25
165 137 0.24
166 9 0.02
167 3 0.01
168 36 0.06
169 18 0.03
170 1 0.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (163 bp):
ATGAATTTTTGAAAATTGATTTAATATGAATTAAATAATAATATTTGATAAATTTTAAAAATTAA
AAACTAAGAAAAATCCCCTAAAAATATTTACGGAGTAGAAAATTCAGTATTTCGAAAATAAAAAA
ATTTCAAGAAAAAAAGAAAAATCATGAAAATGA
Found at i:2323144 original size:2 final size:2
Alignment explanation
Indices: 2323137--2323199 Score: 83
Period size: 2 Copynumber: 30.5 Consensus size: 2
2323127 TGTACAACAG
*
2323137 AT AT AT AT AT AT AT AT AT GAGT -T GAG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -A-T AT -AT AT AT AT AT AT AT AT AT
2323179 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
2323200 ATCTCTATCC
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 1 0.02
2 52 0.95
3 1 0.02
4 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2324124 original size:6 final size:6
Alignment explanation
Indices: 2324115--2324143 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2324105 AAGATAAGGT
2324115 TTCAGG TTCAGG TTCAGG TTCAGG TTCAG
1 TTCAGG TTCAGG TTCAGG TTCAGG TTCAG
2324144 AGTCAGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.34
Consensus pattern (6 bp):
TTCAGG
Found at i:2326849 original size:20 final size:20
Alignment explanation
Indices: 2326824--2326862 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2326814 TATATCATAC
2326824 ATTTTTAAAATAATTATATA
1 ATTTTTAAAATAATTATATA
* *
2326844 ATTTTTAATATATTTATAT
1 ATTTTTAAAATAATTATAT
2326863 TAAAAAAAGG
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTAAAATAATTATATA
Found at i:2326976 original size:15 final size:16
Alignment explanation
Indices: 2326956--2326989 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2326946 TAATGAATAG
2326956 TAGGTTAAA-TTTAAA
1 TAGGTTAAACTTTAAA
2326971 TAGGTTAAACCTTTAAA
1 TAGGTTAAA-CTTTAAA
2326988 TA
1 TA
2326990 TCTTATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
TAGGTTAAACTTTAAA
Found at i:2328085 original size:2 final size:2
Alignment explanation
Indices: 2328078--2328120 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2328068 ACTGTGATTT
2328078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2328120 T
1 T
2328121 CTTTATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2330524 original size:18 final size:18
Alignment explanation
Indices: 2330498--2330552 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
2330488 TTATTAATAT
2330498 AAATATTATTTTTAAATTA
1 AAAT-TTATTTTTAAATTA
*
2330517 AAATTTATTTACTAAA-TA
1 AAATTTATTT-TTAAATTA
2330535 ATAATTT-TTATTTAAATT
1 A-AATTTATT-TTTAAATT
2330553 TTAGATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTTATTTTTAAATTA
Found at i:2331601 original size:20 final size:21
Alignment explanation
Indices: 2331555--2331603 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
2331545 CTTTATGAAA
2331555 TGTATTGTTTGCTGATGTGATT
1 TGTATT-TTTGCTGATGTGATT
*
2331577 T-TATTTTTG-TGATGTGTTT
1 TGTATTTTTGCTGATGTGATT
2331596 TGTATTTT
1 TGTATTTT
2331604 GGTCATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 10 0.40
20 10 0.40
21 4 0.16
22 1 0.04
ACGTcount: A:0.12, C:0.02, G:0.22, T:0.63
Consensus pattern (21 bp):
TGTATTTTTGCTGATGTGATT
Found at i:2332648 original size:32 final size:32
Alignment explanation
Indices: 2332605--2332675 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
2332595 TTCAACGATT
2332605 TGTATCAATACAAAAGTGTTGAATCGATACAA
1 TGTATCAATACAAAAGTGTTGAATCGATACAA
* * * *
2332637 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACAAAAGTGTTGAATCGATACAA
2332669 TGTATCA
1 TGTATCA
2332676 CTACGAAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (32 bp):
TGTATCAATACAAAAGTGTTGAATCGATACAA
Found at i:2332856 original size:51 final size:52
Alignment explanation
Indices: 2332753--2332880 Score: 240
Period size: 51 Copynumber: 2.5 Consensus size: 52
2332743 CACTGATCTT
2332753 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
2332805 TGTATCGATACATACAGGCAAATTTG-CCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
2332856 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2332881 TCATATTTCG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
51 49 0.66
52 25 0.34
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:2335842 original size:13 final size:13
Alignment explanation
Indices: 2335824--2335848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2335814 CATAAAGTGT
2335824 TGTATCGATACAA
1 TGTATCGATACAA
2335837 TGTATCGATACA
1 TGTATCGATACA
2335849 TATTTTTTTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2335929 original size:13 final size:13
Alignment explanation
Indices: 2335911--2335935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2335901 ATCACTTAAA
2335911 TGTATCGATACAT
1 TGTATCGATACAT
2335924 TGTATCGATACA
1 TGTATCGATACA
2335936 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2336000 original size:52 final size:52
Alignment explanation
Indices: 2335944--2336072 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2335934 CACTGATCTT
*
2335944 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
2335996 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2336048 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2336073 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2349921 original size:1 final size:1
Alignment explanation
Indices: 2349915--2350001 Score: 84
Period size: 1 Copynumber: 87.0 Consensus size: 1
2349905 CGTCCTCCAC
* * * * * * * *
2349915 AAAAAAAAAAAAAACAAAACAAAAAGAAAACAAAACAAAACAAAAAAAAACAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2349980 AAAAACAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
2350002 GGGGTTCGGA
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.89, C:0.10, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:2349933 original size:10 final size:10
Alignment explanation
Indices: 2349913--2350001 Score: 121
Period size: 10 Copynumber: 9.0 Consensus size: 10
2349903 GGCGTCCTCC
2349913 ACAAAAAAAA
1 ACAAAAAAAA
2349923 A-AAAAACAAA
1 ACAAAAA-AAA
2349933 ACAAAAAGAAA
1 ACAAAAA-AAA
*
2349944 ACAAAACAAA
1 ACAAAAAAAA
2349954 ACAAAAAAAA
1 ACAAAAAAAA
2349964 AC-AAAAAAA
1 ACAAAAAAAA
2349973 ACAAAAAAAA
1 ACAAAAAAAA
*
2349983 A-ACAAAAAA
1 ACAAAAAAAA
2349992 ACAAAAAAAA
1 ACAAAAAAAA
2350002 GGGGTTCGGA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
9 22 0.31
10 34 0.49
11 14 0.20
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:2349936 original size:20 final size:19
Alignment explanation
Indices: 2349913--2350001 Score: 124
Period size: 19 Copynumber: 4.5 Consensus size: 19
2349903 GGCGTCCTCC
2349913 ACAAAAAAAAAAAAAACAAA
1 ACAAAAAAAAAAAAAA-AAA
*
2349933 ACAAAAAGAAAACAAAACAAA
1 ACAAAAA-AAAA-AAAAAAAA
*
2349954 ACAAAAAAAAACAAAAAAA
1 ACAAAAAAAAAAAAAAAAA
*
2349973 ACAAAAAAAAAACAAAAAA
1 ACAAAAAAAAAAAAAAAAA
2349992 ACAAAAAAAA
1 ACAAAAAAAA
2350002 GGGGTTCGGA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
19 33 0.53
20 11 0.18
21 14 0.23
22 4 0.06
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (19 bp):
ACAAAAAAAAAAAAAAAAA
Found at i:2351465 original size:29 final size:30
Alignment explanation
Indices: 2351426--2351601 Score: 175
Period size: 29 Copynumber: 6.0 Consensus size: 30
2351416 TCACCCTTCA
*
2351426 AAAGTCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* *
2351455 AAAGCCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
2351485 AAAAGCCCACAAGTCAGTGGCAAC-C---TTC
1 -AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
* * * *
2351513 AAAGCCTACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
2351543 GAAGCCCACAAGTCGGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
2351572 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
2351602 TTTTGTAAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.02
27 19 0.16
28 3 0.02
29 44 0.36
30 33 0.27
31 20 0.16
32 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTTC
Found at i:2351493 original size:31 final size:30
Alignment explanation
Indices: 2351422--2351715 Score: 172
Period size: 29 Copynumber: 9.7 Consensus size: 30
2351412 TTCCTCACCC
*
2351422 TTCAAAAGTCCACAAGTCAGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
*
2351452 TTC-AAAGCCCACAAGTCAGTGGCATTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TCTTT
* *
2351482 TTCAAAAGCCCACAAGTCAGTGGCAAC--C
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
* * * *
2351510 TTC-AAAGCCTACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
** *
2351539 TTCCGAAGCCCACAAGTCGGTGGCATC-TT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
* * * *
2351568 TTCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TCTTT
** * * *
2351599 TTCTTTTGTAAGCTCACAACTCTA-TAGCACTCTTT
1 TTC----AAAAGCCCACAAGTC-AGTGGCA-TCTTT
** * * *
2351634 TTCTTTTTAAGCCCACAAGTTAGTGGCACCCTT
1 TTC---AAAAGCCCACAAGTCAGTGGCATCTTT
* * *
2351667 TTCAAAAGCCCACAAGTCCGTGGCAAC-CT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
*
2351696 TT-AAAAGCCCACAGGTCAGT
1 TTCAAAAGCCCACAAGTCAGT
2351716 AGCAACCTTC
Statistics
Matches: 212, Mismatches: 39, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
27 20 0.09
28 19 0.09
29 49 0.23
30 49 0.23
31 26 0.12
33 7 0.03
34 18 0.08
35 24 0.11
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTTT
Found at i:2351523 original size:27 final size:27
Alignment explanation
Indices: 2351486--2351538 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2351476 TTTTTTTTCA
*
2351486 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
* *
2351513 AAAGCCTACAAATCAGTGGCACCCTT
1 AAAGCCCACAAATCAGTGGCAACCTT
2351539 TTCCGAAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:2351668 original size:34 final size:36
Alignment explanation
Indices: 2351577--2351668 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 36
2351567 TTTCCAAAGT
*
2351577 CCACAACTC-CGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAGC
* *
2351612 TCACAACTCTA-TAGCACTCTTTTTCTTTT-TAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAGC
* *
2351646 CCACAAGT-TAGTGGCACCCTTTT
1 CCACAACTCTAGTGGCACTCTTTT
2351669 CAAAAGCCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.04
34 21 0.44
35 25 0.52
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (36 bp):
CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAGC
Found at i:2351676 original size:30 final size:29
Alignment explanation
Indices: 2351642--2351765 Score: 121
Period size: 28 Copynumber: 4.3 Consensus size: 29
2351632 TTTTCTTTTT
* *
2351642 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAA
*
2351672 AAGCCCACAAGTCCGTGGCAACCTTT-AA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* *
2351700 AAGCCCACAGGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* * *
2351728 AAGCACACAAGT-TGAT-GCAAACCTCTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTTCAA
2351757 AAGCCCACA
1 AAGCCCACA
2351766 CAAGTTGGTG
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
27 5 0.06
28 39 0.49
29 15 0.19
30 20 0.25
ACGTcount: A:0.35, C:0.31, G:0.16, T:0.17
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:2351911 original size:49 final size:48
Alignment explanation
Indices: 2351785--2352014 Score: 272
Period size: 48 Copynumber: 4.8 Consensus size: 48
2351775 GGCGTCTCCT
* *
2351785 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCC
* * *
2351833 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC-CC
* * *
2351882 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCA-----CC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCC
*
2351925 TTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TTCC--C
* * *
2351977 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
2352015 ACATCCTTTT
Statistics
Matches: 153, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
43 38 0.25
48 42 0.27
49 37 0.24
50 1 0.01
52 35 0.23
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (48 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCC
Found at i:2351949 original size:43 final size:43
Alignment explanation
Indices: 2351881--2351970 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
2351871 GCACCTTCAT
*
2351881 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
* * *
2351924 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
2351967 CTTT
1 CTTT
2351971 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
Found at i:2351967 original size:92 final size:95
Alignment explanation
Indices: 2351785--2352023 Score: 313
Period size: 92 Copynumber: 2.5 Consensus size: 95
2351775 GGCGTCTCCT
* * * * * *
2351785 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGTCCAATATCGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATT-G-A-CAT-CCTTTAAGTCCAATATAGC
2351850 TGGCCTTAAATCAGCATATTGGCACC-TT-CATC
62 TGGCCTTAAATCAGCATATTGGCACCTTTCCATC
* *
2351882 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCA-CCTTTAAGTCCAATATAGTTGGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
*
2351946 CTTGAATCAGCATATTGGCACCTTTTCCATC
66 CTTAAATCAGCATATTGGCACC-TTTCCATC
* *
2351977 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTT
2352024 TTCTCATCTT
Statistics
Matches: 126, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
92 42 0.33
94 3 0.02
95 42 0.33
96 6 0.05
97 33 0.26
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (95 bp):
TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
CTTAAATCAGCATATTGGCACCTTTCCATC
Found at i:2352002 original size:52 final size:55
Alignment explanation
Indices: 2351924--2352073 Score: 198
Period size: 52 Copynumber: 2.8 Consensus size: 55
2351914 ACATTGGCAC
2351924 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCCTTTTTCTCAT
* * * * *
2351976 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCCTTTTTCTCAT
* * * *
2352031 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCAT
2352074 TTTTATCACT
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 37 0.46
53 2 0.02
54 5 0.06
55 37 0.46
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCCTTTTTCTCAT
Found at i:2352884 original size:13 final size:13
Alignment explanation
Indices: 2352866--2352890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2352856 CATAAAGTGT
2352866 TGTATCGATACAA
1 TGTATCGATACAA
2352879 TGTATCGATACA
1 TGTATCGATACA
2352891 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2352888 original size:33 final size:33
Alignment explanation
Indices: 2352846--2352912 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2352836 TTCAACGATT
2352846 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
2352879 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2352912 T
1 T
2352913 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2352971 original size:13 final size:13
Alignment explanation
Indices: 2352953--2352977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2352943 ATCACTTAAA
2352953 TGTATCGATACAT
1 TGTATCGATACAT
2352966 TGTATCGATACA
1 TGTATCGATACA
2352978 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2353042 original size:52 final size:52
Alignment explanation
Indices: 2352986--2353115 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
2352976 CACTGATCTT
*
2352986 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATAAAA
* **
2353038 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATAAAA
2353090 TGTATCGATACATGCAGGCAAATTTT
1 TGTATCGATACATGCAGGC-AATTTT
2353116 CATATTTCGG
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
52 67 0.93
53 5 0.07
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAATTTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2356538 original size:401 final size:401
Alignment explanation
Indices: 2355790--2356574 Score: 1381
Period size: 401 Copynumber: 2.0 Consensus size: 401
2355780 ACCAATATCG
* *
2355790 AGTCAAAACGTTGCTAGTAAGGTACCAATTTCGGGCGTCGCGAGGAGGTTCGTACCTCTTTGCGC
1 AGTCAAAACATTGCTAGTAAGGTACCAATTTCGGGCGTCACGAGGAGGTTCGTACCTCTTTGCGC
* * *
2355855 GTAACCAACTCCCGAACCCAACCGGCGAATCTCTAAAGTACGCAGACCATGGGATCGATGTTTTG
66 GTAACCAACTCCCGAACCCAACCGGCAAATCTCTAAAGTACACAGACCACGGGATCGATGTTTTG
* * *
2355920 AGTTTTGTAACTCAAGACATAGGTTTCAATAGGCATCCGATTATGCCTAGCCCGAAATGATCGGT
131 AGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGATCGAT
* *
2355985 GGCGACTCCAAAATTTTGGTCACTTCATAGTGACCATTGAAGATCAATTAGATGGGCGATTCATC
196 GGCGACTCCAAAATTTCGGTCACTTCATAGTGACCATTGAAGATCAATTAGATAGGCGATTCATC
*
2356050 TACTGATCTTCCCCCTTTAATCAGCACACTTCCCATCATGCCATAGAAATCCCCAATCGCGAGGG
261 TACTGATCTTCCCCCTTTAATCAACACACTTCCCATCATGCCATAGAAATCCCCAATCGCGAGGG
* **
2356115 ATATTAAGTCGAGCGTGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCTTGTTACGACACAATGT
326 ATATTAAGTCGAGCGCGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACACAATGT
2356180 AATCAACTTCA
391 AATCAACTTCA
* * *
2356191 AGTCAAAACATTGCTAGTAAGGTACCGATTTCGGGTGTCACGAGGAGGTTCGTATCTCTTTGCGC
1 AGTCAAAACATTGCTAGTAAGGTACCAATTTCGGGCGTCACGAGGAGGTTCGTACCTCTTTGCGC
* *
2356256 GTAACCAACTCCCGAACCCAACCGGCAAATCTTTAAAGTACATAGACCACGGGATCGATGTTTTG
66 GTAACCAACTCCCGAACCCAACCGGCAAATCTCTAAAGTACACAGACCACGGGATCGATGTTTTG
*
2356321 AGTTTCGTAACTCAAGACATAGGTTTCAATGGGCATCCGATCATGCCTAGCCCGAAATGATCGAT
131 AGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGATCGAT
*
2356386 GGCGACTCCAAAATTTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATAGGCGATTCATC
196 GGCGACTCCAAAATTTCGGTCACTTCATAGTGACCATTGAAGATCAATTAGATAGGCGATTCATC
2356451 TACTGATCTTCCCCCTTTAATCAACACACTTCCCATCATGCCATAGAAATCCCCAATCGCGAGGG
261 TACTGATCTTCCCCCTTTAATCAACACACTTCCCATCATGCCATAGAAATCCCCAATCGCGAGGG
2356516 ATATTAAGTCGAGCGCGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACA
326 ATATTAAGTCGAGCGCGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACA
2356575 GTTTGGCGAC
Statistics
Matches: 363, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
401 363 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (401 bp):
AGTCAAAACATTGCTAGTAAGGTACCAATTTCGGGCGTCACGAGGAGGTTCGTACCTCTTTGCGC
GTAACCAACTCCCGAACCCAACCGGCAAATCTCTAAAGTACACAGACCACGGGATCGATGTTTTG
AGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGATCGAT
GGCGACTCCAAAATTTCGGTCACTTCATAGTGACCATTGAAGATCAATTAGATAGGCGATTCATC
TACTGATCTTCCCCCTTTAATCAACACACTTCCCATCATGCCATAGAAATCCCCAATCGCGAGGG
ATATTAAGTCGAGCGCGCCTCATTTGCCCTATCGCCGGGGTCGAGCGCACGTTACGACACAATGT
AATCAACTTCA
Found at i:2367351 original size:1 final size:1
Alignment explanation
Indices: 2367345--2367435 Score: 56
Period size: 1 Copynumber: 91.0 Consensus size: 1
2367335 CGTCATCCGC
* * * * * * * * * *
2367345 AAAAAAAAAAACAAAAAACAAAACAAAACAAAAAAAAGAGACAAAAAAAACAAAAAACAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * **
2367410 AAACAACAAAAAAAAACGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2367436 CAAACAAACA
Statistics
Matches: 63, Mismatches: 27, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:2367362 original size:11 final size:11
Alignment explanation
Indices: 2367345--2367456 Score: 90
Period size: 10 Copynumber: 10.5 Consensus size: 11
2367335 CGTCATCCGC
2367345 AAAAAAAA-AA
1 AAAAAAAACAA
*
2367355 ACAAAAAAC-A
1 AAAAAAAACAA
*
2367365 AAACAAAACAA
1 AAAAAAAACAA
* * *
2367376 AAAAAAGAGAC
1 AAAAAAAACAA
2367387 AAAAAAAAC-A
1 AAAAAAAACAA
*
2367397 AAAAACAACAA
1 AAAAAAAACAA
*
2367408 AAAAACAAC-A
1 AAAAAAAACAA
*
2367418 AAAAAAAAC-G
1 AAAAAAAACAA
2367428 AAAAAAAACAA
1 AAAAAAAACAA
*
2367439 ACAAACAAACAA
1 A-AAAAAAACAA
2367451 CAAAAA
1 -AAAAA
2367457 GGGTCCGGAT
Statistics
Matches: 80, Mismatches: 16, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
10 41 0.51
11 26 0.32
12 12 0.15
13 1 0.01
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:2367380 original size:31 final size:29
Alignment explanation
Indices: 2367345--2367439 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 29
2367335 CGTCATCCGC
*
2367345 AAAAAAAAAAACAAAAAACAAAACAAAACA
1 AAAAAAAAAAAAAAAAAACAAAA-AAAACA
*
2367375 AAAAAAAGAGACAAAAAAAACAAAAAACAACA
1 AAAAAAA-A-AAAAAAAAAACAAAAAA-AACA
*
2367407 AAAAAACAACAAAAAAAAACGAAAAAAAACA
1 AAAAAA-AAAAAAAAAAAAC-AAAAAAAACA
2367438 AA
1 AA
2367440 CAAACAAACA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
30 7 0.12
31 18 0.32
32 30 0.54
33 1 0.02
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAAAAAAAAACAAAAAAAACA
Found at i:2367393 original size:32 final size:31
Alignment explanation
Indices: 2367345--2367456 Score: 115
Period size: 31 Copynumber: 3.5 Consensus size: 31
2367335 CGTCATCCGC
*
2367345 AAAAAAA-AA-AACAAAAAACAAAACAAAACA
1 AAAAAAACAACAAAAAAAAACAAAA-AAAACA
*
2367375 AAAAAAAGAGAC-AAAAAAAACAAAAAACAAC-
1 AAAAAAACA-ACAAAAAAAAACAAAAAA-AACA
2367406 AAAAAAACAACAAAAAAAAACGAAAAAAAACAA
1 AAAAAAACAACAAAAAAAAAC-AAAAAAAAC-A
2367439 ACAAACAAACAACAAAAA
1 A-AAA-AAACAACAAAAA
2367457 GGGTCCGGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
30 9 0.13
31 23 0.33
32 22 0.31
33 1 0.01
34 3 0.04
35 12 0.17
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (31 bp):
AAAAAAACAACAAAAAAAAACAAAAAAAACA
Found at i:2367398 original size:39 final size:40
Alignment explanation
Indices: 2367348--2367447 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 40
2367338 CATCCGCAAA
* *
2367348 AAAAAAAACAAAAAACAAAACAAAACAA-AAAAAAGAGAC-
1 AAAAAAAACAAAAAACAAAAAAAAACAACAAAAAA-AAACG
2367387 AAAAAAAACAAAAAACAACAAAAAAACAACAAAAAAAAACG
1 AAAAAAAACAAAAAACAA-AAAAAAACAACAAAAAAAAACG
2367428 AAAAAAAACAAACAAACAAA
1 AAAAAAAACAAA-AAACAAA
2367448 CAACAAAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
39 18 0.33
40 12 0.22
41 19 0.35
42 6 0.11
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (40 bp):
AAAAAAAACAAAAAACAAAAAAAAACAACAAAAAAAAACG
Found at i:2368931 original size:30 final size:28
Alignment explanation
Indices: 2368885--2369101 Score: 230
Period size: 30 Copynumber: 7.5 Consensus size: 28
2368875 CATTCCTCAC
* *
2368885 CCTTTTCAAAAGCCCACAAGTCAATGGCA
1 CCTTTTC-AAAGCCCACAAATCAGTGGCA
*
2368914 CCATTTTCTAAACCCCACAAATCAGTGGCAA
1 CC-TTTTC-AAAGCCCACAAATCAGTGGC-A
* *
2368945 CC--TTCAAAGCCCACAAATTAATGGCA
1 CCTTTTCAAAGCCCACAAATCAGTGGCA
*
2368971 CTCTTTTCCGAAGCCCACAAATCAGTGGCAA
1 C-CTTTT-CAAAGCCCACAAATCAGTGGC-A
2369002 CC--TTCAAAGCCCACAAATCAGTGGCA
1 CCTTTTCAAAGCCCACAAATCAGTGGCA
2369028 CCCTTTTCCAAAGCCCACAAATCAGTGGCAA
1 -CCTTTT-CAAAGCCCACAAATCAGTGGC-A
2369059 CC--TTCAAAGCCCACAAATCAGTGGCA
1 CCTTTTCAAAGCCCACAAATCAGTGGCA
2369085 CCATTTTCCAAAGCCCA
1 CC-TTTT-CAAAGCCCA
2369102 TAAGCCAGCG
Statistics
Matches: 161, Mismatches: 11, Indels: 31
0.79 0.05 0.15
Matches are distributed among these distances:
26 6 0.04
27 61 0.38
28 7 0.04
29 8 0.05
30 73 0.45
31 6 0.04
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.20
Consensus pattern (28 bp):
CCTTTTCAAAGCCCACAAATCAGTGGCA
Found at i:2368969 original size:27 final size:27
Alignment explanation
Indices: 2368927--2369084 Score: 210
Period size: 27 Copynumber: 5.6 Consensus size: 27
2368917 TTTTCTAAAC
2368927 CCCACAAATCAGTGGCAACCTTCAAAG
1 CCCACAAATCAGTGGCAACCTTCAAAG
* * *
2368954 CCCACAAATTAATGGC-ACTCTTTTCCGAAG
1 CCCACAAATCAGTGGCAAC-C--TT-CAAAG
2368984 CCCACAAATCAGTGGCAACCTTCAAAG
1 CCCACAAATCAGTGGCAACCTTCAAAG
*
2369011 CCCACAAATCAGTGGCACCCTTTTCCAAAG
1 CCCACAAATCAGTGGCAACC--TT-CAAAG
2369041 CCCACAAATCAGTGGCAACCTTCAAAG
1 CCCACAAATCAGTGGCAACCTTCAAAG
2369068 CCCACAAATCAGTGGCA
1 CCCACAAATCAGTGGCA
2369085 CCATTTTCCA
Statistics
Matches: 115, Mismatches: 8, Indels: 16
0.83 0.06 0.12
Matches are distributed among these distances:
26 2 0.02
27 60 0.52
28 4 0.03
29 4 0.03
30 43 0.37
31 2 0.02
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.18
Consensus pattern (27 bp):
CCCACAAATCAGTGGCAACCTTCAAAG
Found at i:2368978 original size:57 final size:57
Alignment explanation
Indices: 2368893--2369125 Score: 333
Period size: 57 Copynumber: 4.1 Consensus size: 57
2368883 ACCCTTTTCA
* * *
2368893 AAAGCCCACAAGTCAATGGCACCATTTTCTAAACCCCACAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAATGGCACCATTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
* *
2368950 AAAGCCCACAAATTAATGGCACTC-TTTTCCGAAGCCCACAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAATGGCAC-CATTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
* *
2369007 AAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
1 AAAGCCCACAAATCAATGGCACCATTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
* * ** *
2369064 AAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCATAAGCCAGCGGCAACCTTC
1 AAAGCCCACAAATCAATGGCACCATTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
2369121 TAAAG
1 -AAAG
2369126 TCTACAACTC
Statistics
Matches: 160, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
56 1 0.01
57 154 0.96
58 5 0.03
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.18
Consensus pattern (57 bp):
AAAGCCCACAAATCAATGGCACCATTTTCCAAAGCCCACAAATCAGTGGCAACCTTC
Found at i:2369246 original size:34 final size:35
Alignment explanation
Indices: 2369129--2369282 Score: 197
Period size: 34 Copynumber: 4.4 Consensus size: 35
2369119 TCTAAAGTCT
* *
2369129 ACAACTCCGTGGCAC-CTTTCTTCTTTTTAAAGCCC
1 ACAACTCTGTGGCACTCTTT-TTCCTTTTAAAGCCC
* *
2369164 ACAACTCTGCGGCGCTCTTTTTCCTTTTTAAAGCCC
1 ACAACTCTGTGGCACTCTTTTTCC-TTTTAAAGCCC
*
2369200 ACAACTCTGTGGCACTCTTTTTCCTTTT-AAGCTC
1 ACAACTCTGTGGCACTCTTTTTCCTTTTAAAGCCC
* *
2369234 ACAACTCCGTGGCACTCTTTTTCCTTTT-AAGTCC
1 ACAACTCTGTGGCACTCTTTTTCCTTTTAAAGCCC
*
2369268 ATAACTCTGTGGCAC
1 ACAACTCTGTGGCAC
2369283 CCTTCTCAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
34 49 0.47
35 19 0.18
36 37 0.35
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (35 bp):
ACAACTCTGTGGCACTCTTTTTCCTTTTAAAGCCC
Found at i:2369328 original size:33 final size:33
Alignment explanation
Indices: 2369276--2369426 Score: 179
Period size: 33 Copynumber: 4.7 Consensus size: 33
2369266 CCATAACTCT
*
2369276 GTGGCACCCTTC-TC-AAAGCCCACACAAGTCG
1 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCG
* *
2369307 GTGGCAACCTTTTTCTAAAGCCCACACAAGTTG
1 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCG
*
2369340 GTGGCAATCC--CCTCTAAAGCCCACACAAGTCG
1 GTGGCAA-CCTTCTTCTAAAGCCCACACAAGTCG
* *
2369372 GTGGCAACCTTCTTCAAAAGCCCACACAAGTTG
1 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCG
* *
2369405 GTGGC-ATCTTCTT-TTAAGCCCA
1 GTGGCAACCTTCTTCTAAAGCCCA
2369427 ATATTGCTGG
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
31 19 0.18
32 35 0.34
33 47 0.46
34 2 0.02
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (33 bp):
GTGGCAACCTTCTTCTAAAGCCCACACAAGTCG
Found at i:2369576 original size:49 final size:49
Alignment explanation
Indices: 2369417--2370215 Score: 877
Period size: 49 Copynumber: 16.9 Consensus size: 49
2369407 GGCATCTTCT
* * *
2369417 TTTAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * *
2369466 TTTAAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG------TACC
1 TTT-AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
*
2369510 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
2369559 TTTCAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
*
2369602 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
2369651 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
** *
2369700 TTTGGGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
2369749 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
2369792 TTTAAGTCTAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
2369841 TTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACC--T-TC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * * * *
2369887 ---AAGCCCAATATCGTTGGCCGTGAATCAGCATATTGGCATCTTCACC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
*
2369933 TTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
2369982 TTTATGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
2370031 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--T-TC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * * * *
2370077 ---AAGCCCAATATCGTTGGCCGTGAATCAGCATATTGGCATCTTCACC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * **
2370123 TCTAAGTCTAATAGCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT-C
* * * * *
2370172 GTCTTGAGTCCAATGTAGCTTGCCTTGAATCAGCACATTAGCAC
1 -T-TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
2370216 AAGCCCAATA
Statistics
Matches: 627, Mismatches: 89, Indels: 66
0.80 0.11 0.08
Matches are distributed among these distances:
43 173 0.28
44 6 0.01
46 6 0.01
47 2 0.00
48 2 0.00
49 373 0.59
50 33 0.05
51 32 0.05
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (49 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
Found at i:2369609 original size:92 final size:92
Alignment explanation
Indices: 2369417--2370168 Score: 1002
Period size: 92 Copynumber: 8.0 Consensus size: 92
2369407 GGCATCTTCT
* * * * *
2369417 TTTAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAAGACCAATGTC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT-AAGTCCAATGTA
*
2369482 GCTGGCCTTGAATCAGCACATTGGTACC
65 GCTGGCCTTGAATCAGCACATTGGCACC
* *
2369510 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTTATCTTTCAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
2369575 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
2369602 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATATAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
*
2369667 CTGGCCTTGAATCAGCATATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
2369694 TTTATCTTTGGGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCA
1 TTTA------AGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCA
2369759 ATGTAGCTGGCCTTGAATCAGCACATTGGCACC
60 ATGTAGCTGGCCTTGAATCAGCACATTGGCACC
* *
2369792 TTTAAGTCTAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
*
2369857 CTAGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * * * * * * * *
2369884 TTCAAGCCCAATATCGTTGGCCGTGAATCAGCATATTGGCATCTTCACCTTTAAGTCCAATATAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
* *
2369949 CTAGCCTTGAATCAGCATATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
2369976 TTTATCTTTATGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGTCCA
1 TTTA-----A-GTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCA
2370041 ATGTAGCTGGCCTTGAATCAGCACATTGGCACC
60 ATGTAGCTGGCCTTGAATCAGCACATTGGCACC
* * * * * * * * * * *
2370074 TTCAAGCCCAATATCGTTGGCCGTGAATCAGCATATTGGCATCTTCACCTCTAAGTCTAATAG-C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT-GTA
*
2370138 GCTGGCCTTGAATCAGCATATTGGCACC
65 GCTGGCCTTGAATCAGCACATTGGCACC
2370166 TTT
1 TTT
2370169 TCCGTCTTGA
Statistics
Matches: 593, Mismatches: 53, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
92 373 0.63
93 50 0.08
97 1 0.00
98 169 0.28
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (92 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:2369684 original size:141 final size:135
Alignment explanation
Indices: 2369417--2370349 Score: 841
Period size: 141 Copynumber: 6.6 Consensus size: 135
2369407 GGCATCTTCT
* * * * * *
2369417 TTTAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAAGACCAATGTC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCA-C-----CTTT-AAGTCCAATATA
*
2369482 GCTGGCCTTGAATCAGCACATTGGTACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
59 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
*
2369547 AGCACCTTTATC
124 GGCACCTTTATC
* *
2369559 TTTCAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATAGCTGGCC
*
2369624 TTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
66 TTGAATCAGCACATTGGCAC------CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
2369689 GCACCTTTATC
125 GCACCTTTATC
** * * *
2369700 TTTGGGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCA-C-----CTTTAAGTCCAATATAG
* *
2369765 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCTAATATAGCTAGCCTTGAATCAGCATATTG
60 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
2369830 GCACCTTTATC
125 GCACCTTTATC
* * * * * *
2369841 TTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTTCAAGCCCAATATCGTTGGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATAGCTGGCC
* * *
2369906 GTGAATCAGCATATTGGCATCTTCACCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTG
66 TTGAATCAGCACATTGG------CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
2369971 GCACCTTTATC
125 GCACCTTTATC
* * * *
2369982 TTTATGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCA-C-----CTTTAAGTCCAATATAG
* * * * *
2370047 CTGGCCTTGAATCAGCACATTGGCACCTTCAAGCCCAATATCGTTGGCCGTGAATCAGCATATTG
60 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
* * *
2370112 GCATCTTCACC
125 GCACCTTTATC
* * * * *
2370123 TCTAAGTCTAATAG-CGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCGTCTTGAGTCCAATG
1 TTTAAGTCCAAT-GTAGCTGGCCTTGAATCAGCATATTGGCA------CC-T-TTAAGTCCAATA
* * * * * *
2370187 TAGCTTGCCTTGAATCAGCACATTAGCA-C---AAGCCCAATATCGTTGGCCGTGAATCAGCATA
57 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
* *
2370248 TTGGCATCTTTAAC
122 TTGGCACCTTTATC
* * * * ** * * * * *
2370262 ATTCCTAAGCCCAAAGTCGCTGACCTTGTCTCAACACATTGGCATTCTTCTTCAAGTCCAATGTC
1 -TT--TAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCA--C--CTTTAAGTCCAATATA
2370327 GCTGGCCTTGAATCAGCACATTG
59 GCTGGCCTTGAATCAGCACATTG
2370350 TCATTCTTCC
Statistics
Matches: 675, Mismatches: 78, Indels: 80
0.81 0.09 0.10
Matches are distributed among these distances:
135 67 0.10
136 4 0.01
138 35 0.05
139 45 0.07
140 3 0.00
141 339 0.50
142 69 0.10
143 37 0.05
146 2 0.00
147 74 0.11
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (135 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATAGCTGGCC
TTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
TTATC
Found at i:2370076 original size:190 final size:184
Alignment explanation
Indices: 2369417--2370168 Score: 1000
Period size: 190 Copynumber: 4.0 Consensus size: 184
2369407 GGCATCTTCT
* * * * *
2369417 TTTAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAAGACCAATGTC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT-AAGTCCAATGTA
* * * *
2369482 GCTGGCCTTGAATCAGCACATTGGTACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT
65 GCTGGCCTTGAATCAGCACATTGGCACCTTCAAGCCCAATATAGCTGGCCGTGAATCAGCATATT
* * * * *
2369547 AGCACCTTTATCTTTCAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
130 GGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC
* *
2369602 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATATAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
* ** * * *
2369667 CTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTGGGTCCAATATAGCTAGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCACC--T-TC---AAGCCCAATATAGCTGGCCGTGAATCAGC
* * *
2369732 ATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
125 ATATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC
* *
2369792 TTTAAGTCTAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
* * *
2369857 CTAGCCTTGAATCAGCACATTGGCACCTTCAAGCCCAATATCGTTGGCCGTGAATCAGCATATTG
66 CTGGCCTTGAATCAGCACATTGGCACCTTCAAGCCCAATATAGCTGGCCGTGAATCAGCATATTG
* * *
2369922 GCATCTTCACCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACC
131 GCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC
* *
2369976 TTTATCTTTATGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGTCCA
1 TTTA-----A-GTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCA
* *
2370041 ATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAAGCCCAATATCGTTGGCCGTGAATCAGC
60 ATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAAGCCCAATATAGCTGGCCGTGAATCAGC
* * * ** *
2370106 ATATTGGCATCTTCACCTCTAAGTCTAATAGCGCTGGCCTTGAATCAGCATATTGGCACC
125 ATATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC
2370166 TTT
1 TTT
2370169 TCCGTCTTGA
Statistics
Matches: 511, Mismatches: 44, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
184 115 0.23
185 48 0.09
186 1 0.00
187 3 0.01
188 1 0.00
189 1 0.00
190 342 0.67
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (184 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACCTTCAAGCCCAATATAGCTGGCCGTGAATCAGCATATTG
GCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC
Found at i:2374523 original size:29 final size:29
Alignment explanation
Indices: 2374491--2374569 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
2374481 TTAGGCTCAG
*
2374491 AGTGTGATTTTGAAAAGTTTAGGAGTCAA
1 AGTGTAATTTTGAAAAGTTTAGGAGTCAA
*
2374520 AGTGTAATTTTGAAAAGTTTAGGGGTCAA
1 AGTGTAATTTTGAAAAGTTTAGGAGTCAA
* *
2374549 AGAGTAATTTTAAAAAGTTTA
1 AGTGTAATTTTGAAAAGTTTA
2374570 AGGACTTAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
AGTGTAATTTTGAAAAGTTTAGGAGTCAA
Found at i:2375035 original size:157 final size:157
Alignment explanation
Indices: 2374678--2375064 Score: 394
Period size: 157 Copynumber: 2.5 Consensus size: 157
2374668 AGGTTATCGG
* * * * * * * * ** *
2374678 GATACTTTCATGTCAAAAGTATATCCCACGGGCACTTTCATAGTTTT-CTTAAAACCGAGTCTTA
1 GATACTTTAATGTTAAAGGTATATACCAAGAGCACTTTTATAATTTTCCTTAAAATTGAATCTTA
* * * * * * *
2374742 TGTAGTCA-TCAGGTCGATTTTATACCAAA-GACGTGCATTTAGGATAAGTTTGTCCTTTTACTT
66 AGTAGTCACT-AGGTTGTTTTTATGCCAAACG-TGTGCATTTAGGATAAGTTTATCATTTTACTT
*
2374805 ATCATTTTTGTGTCATTTAGGGTTACTAA
129 ATCATTTTCGTGTCATTTAGGGTTACTAA
* * **
2374834 GATACTTTAATGTTAAAGGTATATACCAAGAGTACTTTTGTAATTTTTTTTAAAATTGAATCTTA
1 GATACTTTAATGTTAAAGGTATATACCAAGAGCACTTTTATAATTTTCCTTAAAATTGAATCTTA
*
2374899 AGTAGTCACTAGGTTGTTTTTATGCCAAACGTGTGCATTTATGAT-AGATTTATCATTTTACTTA
66 AGTAGTCACTAGGTTGTTTTTATGCCAAACGTGTGCATTTAGGATAAG-TTTATCATTTTACTTA
* *
2374963 TTATTTTCGTGTCCTTTAGGGTTACTAA
130 TCATTTTCGTGTCATTTAGGGTTACTAA
* * *
2374991 GATACTTTCATGTTGAAA-GTATATTTA-GAAG-GCA-TTTTCATAATTTTCCTTAAAATTGAGT
1 GATACTTTAATGTT-AAAGGTATA--TACCAAGAGCACTTTT-ATAATTTTCCTTAAAATTGAAT
2375052 CTTAAGTAGTCAC
62 CTTAAGTAGTCAC
2375065 CAAGCTGTTT
Statistics
Matches: 191, Mismatches: 32, Indels: 15
0.80 0.13 0.06
Matches are distributed among these distances:
156 43 0.23
157 138 0.72
158 8 0.04
159 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (157 bp):
GATACTTTAATGTTAAAGGTATATACCAAGAGCACTTTTATAATTTTCCTTAAAATTGAATCTTA
AGTAGTCACTAGGTTGTTTTTATGCCAAACGTGTGCATTTAGGATAAGTTTATCATTTTACTTAT
CATTTTCGTGTCATTTAGGGTTACTAA
Found at i:2376667 original size:16 final size:17
Alignment explanation
Indices: 2376634--2376667 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2376624 AATAAAAATT
2376634 TTAAAATATTACATAAAA
1 TTAAAATATTA-ATAAAA
2376652 TTAAAATATT-ATAAAA
1 TTAAAATATTAATAAAA
2376668 ATACATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAATATTAATAAAA
Found at i:2377727 original size:71 final size:71
Alignment explanation
Indices: 2377603--2377748 Score: 184
Period size: 71 Copynumber: 2.1 Consensus size: 71
2377593 CTCAAGTACA
* *
2377603 AGTCTAAAAAGTCCAACTCTAAAAAGAAATCCAAGATCATAGTCCTACTAAAACTCTGGTTAAAG
1 AGTCTAAAAAGTCCAACTCTAAAAAGAAATCCAAGATCATAGTCCTACCAAAACTCTAGTTAAAG
2377668 AGTCTT
66 AGTCTT
* ** * * * * * * *
2377674 AGTCTAAAGAGTCCAGGTCTAAGAAGAAATCCATGATGATGGTTCTACCAAAACTCTATTTAAGG
1 AGTCTAAAAAGTCCAACTCTAAAAAGAAATCCAAGATCATAGTCCTACCAAAACTCTAGTTAAAG
2377739 AGTCTT
66 AGTCTT
2377745 AGTC
1 AGTC
2377749 ACACTAAAGC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (71 bp):
AGTCTAAAAAGTCCAACTCTAAAAAGAAATCCAAGATCATAGTCCTACCAAAACTCTAGTTAAAG
AGTCTT
Found at i:2382588 original size:32 final size:32
Alignment explanation
Indices: 2382551--2382616 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
2382541 TTGAAATCCA
2382551 TTATCGAAGGAGTTGTAGTGTCTTGGAAATCT
1 TTATCGAAGGAGTTGTAGTGTCTTGGAAATCT
2382583 TTATCGAAGGAGTTGTAGTGTCTTGGAAATCT
1 TTATCGAAGGAGTTGTAGTGTCTTGGAAATCT
2382615 TT
1 TT
2382617 TAAACAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.39
Consensus pattern (32 bp):
TTATCGAAGGAGTTGTAGTGTCTTGGAAATCT
Found at i:2385238 original size:31 final size:32
Alignment explanation
Indices: 2385185--2385272 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 32
2385175 AATTTGATGA
* * *
2385185 ATTAAATATAATTACTCTTAAATTTCATAAAT
1 ATTAAACATAATTACTCATAAATTTAATAAAT
*
2385217 ATTAAACA-AATTATTCATAAATTTAATAAAT
1 ATTAAACATAATTACTCATAAATTTAATAAAT
* *
2385248 ATT-AGCTATAATTACTTATAAATTT
1 ATTAAAC-ATAATTACTCATAAATTT
2385273 GACAATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.04
31 24 0.51
32 21 0.45
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (32 bp):
ATTAAACATAATTACTCATAAATTTAATAAAT
Found at i:2388486 original size:2 final size:2
Alignment explanation
Indices: 2388425--2388473 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
2388415 TGTTCTTGCT
* * * *
2388425 TA TA TA TA TA TA TA TA TA TA TA TA AA AA TA GA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2388467 TA T- TA TA
1 TA TA TA TA
2388474 GATGGATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2388709 original size:30 final size:30
Alignment explanation
Indices: 2388673--2388735 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
2388663 AACCGCGATG
2388673 TTATTTCATTTACCTACATTGATTGCTCTT
1 TTATTTCATTTACCTACATTGATTGCTCTT
2388703 TTATTTCATTTACCTACATTGATTGCTCTT
1 TTATTTCATTTACCTACATTGATTGCTCTT
2388733 TTA
1 TTA
2388736 GAAGGTTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (30 bp):
TTATTTCATTTACCTACATTGATTGCTCTT
Found at i:2389365 original size:17 final size:17
Alignment explanation
Indices: 2389311--2389365 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
2389301 GATATTACAA
2389311 TTATTATTTTA-TAAT-T
1 TTATT-TTTTATTAATAT
*
2389327 TTATTTTTTTATT-ATAA
1 TTA-TTTTTTATTAATAT
*
2389344 ATATTTTTTATTAATAT
1 TTATTTTTTATTAATAT
2389361 TTATT
1 TTATT
2389366 ATAATTAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTTTTATTAATAT
Found at i:2391299 original size:35 final size:35
Alignment explanation
Indices: 2391252--2391322 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
2391242 CTCCAAAATC
*
2391252 TTAAGAACAAAAATATTTTTCACAAATCATGGTCA
1 TTAAGAACAAAAATATTCTTCACAAATCATGGTCA
*
2391287 TTAAGAATAAAAATATTCTTCACAAATCATGGTCA
1 TTAAGAACAAAAATATTCTTCACAAATCATGGTCA
2391322 T
1 T
2391323 ATCAAACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.32
Consensus pattern (35 bp):
TTAAGAACAAAAATATTCTTCACAAATCATGGTCA
Found at i:2391807 original size:3 final size:3
Alignment explanation
Indices: 2391801--2391834 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
2391791 AAAAAAATCA
*
2391801 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
2391835 AAAATTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2393662 original size:19 final size:20
Alignment explanation
Indices: 2393640--2393677 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2393630 ATTTTTTATT
*
2393640 GTGTTTTTACTTT-TATTTA
1 GTGTATTTACTTTGTATTTA
*
2393659 GTGTATTTATTTTGTATTT
1 GTGTATTTACTTTGTATTT
2393678 CTATTATTTT
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:0.16, C:0.03, G:0.13, T:0.68
Consensus pattern (20 bp):
GTGTATTTACTTTGTATTTA
Found at i:2395740 original size:2 final size:2
Alignment explanation
Indices: 2395735--2395771 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2395725 TTTCTAACTC
2395735 AT 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 AT A
2395772 AAACTTACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2397065 original size:13 final size:13
Alignment explanation
Indices: 2397047--2397076 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2397037 ACAATTCTTC
2397047 ATGTATCGATACA
1 ATGTATCGATACA
2397060 ATGTATCGATACA
1 ATGTATCGATACA
2397073 ATGT
1 ATGT
2397077 GCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2397070 original size:33 final size:33
Alignment explanation
Indices: 2397026--2397093 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
2397016 CGTTTGAGAT
2397026 AATGTAACGATACAAT-T-CTTCATGTATCGATAC
1 AATGTAACGATACAATGTGC--CATGTATCGATAC
*
2397059 AATGTATCGATACAATGTGCCATGTATCGATAC
1 AATGTAACGATACAATGTGCCATGTATCGATAC
2397092 AA
1 AA
2397094 ACTGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
AATGTAACGATACAATGTGCCATGTATCGATAC
Found at i:2397166 original size:19 final size:19
Alignment explanation
Indices: 2397123--2397177 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
2397113 TGCCAGTTTT
**
2397123 ATGTATCGATACAATTGTGC
1 ATGTATCGATACAA-TGAAC
*
2397143 ATGTATTGATACAATGAAC
1 ATGTATCGATACAATGAAC
2397162 ATGTATCGATACAATG
1 ATGTATCGATACAATG
2397178 TATCGATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:2397180 original size:13 final size:13
Alignment explanation
Indices: 2397162--2397188 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2397152 TACAATGAAC
2397162 ATGTATCGATACA
1 ATGTATCGATACA
2397175 ATGTATCGATACA
1 ATGTATCGATACA
2397188 A
1 A
2397189 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2405532 original size:33 final size:33
Alignment explanation
Indices: 2405476--2405540 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2405466 TTTGGGATAA
*
2405476 TGTATCGATACAATTCTTCATGTATTGATACAT
1 TGTATCGATACAATTCTTCATGTATCGATACAT
2405509 TGTATCGATACAATGTGC-T-ATGTATCGATACA
1 TGTATCGATACAAT-T-CTTCATGTATCGATACA
2405541 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.90
34 2 0.07
35 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAATTCTTCATGTATCGATACAT
Found at i:2410548 original size:8 final size:8
Alignment explanation
Indices: 2410537--2410577 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
2410527 TTAATTGATA
2410537 AATTTGAC
1 AATTTGAC
*
2410545 AATTTAAC
1 AATTTGAC
2410553 AATTTGAC
1 AATTTGAC
*
2410561 AATTTAAC
1 AATTTGAC
2410569 AATTTGAC
1 AATTTGAC
2410577 A
1 A
2410578 CCTCATAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (8 bp):
AATTTGAC
Found at i:2410556 original size:16 final size:16
Alignment explanation
Indices: 2410537--2410577 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
2410527 TTAATTGATA
2410537 AATTTGACAATTTAAC
1 AATTTGACAATTTAAC
2410553 AATTTGACAATTTAAC
1 AATTTGACAATTTAAC
2410569 AATTTGACA
1 AATTTGACA
2410578 CCTCATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (16 bp):
AATTTGACAATTTAAC
Found at i:2412062 original size:166 final size:164
Alignment explanation
Indices: 2411873--2412295 Score: 468
Period size: 165 Copynumber: 2.6 Consensus size: 164
2411863 TTTTAATTTC
* * * * * *
2411873 AAAATTCTTTAAATATCATCATTTAATTCACATTAAATCAAGTTTTTAAAAAAATTTCTTTTA-T
1 AAAATTCATCAAATATCATCATTTGATTCAAAGTAAATCAA--TTTT-AAAAAA-TTCATTTACT
* * *
2411937 TTCATGAA--TTTT-ATATTTTTC-TTGAAATTTCTC-TATTTTCGAGATAC-AGTTTTATACTC
62 TTCAT-AAGTTTTTCAT-TTTTTCTTTGAAATTTCCCTTATTTTCGAAATACAAATTTTATACTC
* * * * * *
2411996 TGTAAACGCTTTT-GGCGGAGATTTTTCTTGATTTACATTTTTT
125 CGTAAA-GATTTTAGG-AG-GATTTTTATAG-TTTACAATTTTT
* * * *
2412039 AAAATTCATCAAATATCATCATTTGATTCATAGCAAATCAATTTTGAAAAGTTCATTTACTTTCA
1 AAAATTCATCAAATATCATCATTTGATTCAAAGTAAATCAATTTTAAAAAATTCATTTACTTTCA
* *
2412104 TAAGTTTTTTCATTTTTTCTTTGAAA-TTCCCTTGTTTTCGAAATACTAAATTTTTTACTCCGTA
66 TAAG-TTTTTCATTTTTTCTTTGAAATTTCCCTTATTTTCGAAATAC-AAATTTTATACTCCGTA
* *
2412168 AATATTTTAGGAGGATTTTTATAGTTTATAATTTTT
129 AAGATTTTAGGAGGATTTTTATAGTTTACAATTTTT
2412204 AAAATTCATCAAATATCATCATTTGATTCAAAGTAAATCAATTTTAAAAAATTCATTTACTTTCA
1 AAAATTCATCAAATATCATCATTTGATTCAAAGTAAATCAATTTTAAAAAATTCATTTACTTTCA
2412269 TAAGTTTTTCATTTTTTCTTTGAAATT
66 TAAGTTTTTCATTTTTTCTTTGAAATT
2412296 CTCCTCTTTT
Statistics
Matches: 220, Mismatches: 26, Indels: 23
0.82 0.10 0.09
Matches are distributed among these distances:
162 9 0.04
163 10 0.05
164 25 0.11
165 90 0.41
166 64 0.29
167 5 0.02
168 17 0.08
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (164 bp):
AAAATTCATCAAATATCATCATTTGATTCAAAGTAAATCAATTTTAAAAAATTCATTTACTTTCA
TAAGTTTTTCATTTTTTCTTTGAAATTTCCCTTATTTTCGAAATACAAATTTTATACTCCGTAAA
GATTTTAGGAGGATTTTTATAGTTTACAATTTTT
Found at i:2412928 original size:11 final size:11
Alignment explanation
Indices: 2412912--2412965 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
2412902 TAAGTGTAGA
2412912 AAAAAAAAGAG
1 AAAAAAAAGAG
2412923 AAAAAAAAG-G
1 AAAAAAAAGAG
*
2412933 AAAAAAGTA-AG
1 AAAAAA-AAGAG
*
2412944 AAAAAAGAGAG
1 AAAAAAAAGAG
2412955 AAAATAAAAGA
1 AAAA-AAAAGA
2412966 AAAGCTAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.22
11 23 0.64
12 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:2412937 original size:21 final size:22
Alignment explanation
Indices: 2412912--2412965 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
2412902 TAAGTGTAGA
2412912 AAAAAAAAGAGAAAAAAAAG-G
1 AAAAAAAAGAGAAAAAAAAGAG
* *
2412933 AAAAAAGTA-AGAAAAAAGAGAG
1 AAAAAA-AAGAGAAAAAAAAGAG
2412955 AAAATAAAAGA
1 AAAA-AAAAGA
2412966 AAAGCTAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
21 16 0.62
22 7 0.27
23 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (22 bp):
AAAAAAAAGAGAAAAAAAAGAG
Found at i:2413751 original size:19 final size:20
Alignment explanation
Indices: 2413723--2413776 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
2413713 ACATTATGCT
*
2413723 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGCTCAA
* * *
2413742 TTGTACCGATGCATACTCAA
1 TTGTATCGATACATGCTCAA
2413762 TTGTATCGATACATG
1 TTGTATCGATACATG
2413777 AAACTGGCAG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCTCAA
Found at i:2414236 original size:13 final size:13
Alignment explanation
Indices: 2414197--2414241 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
2414187 ACAAACAGTA
2414197 AATGTATCGATAC
1 AATGTATCGATAC
2414210 ATAAGTGTTATCGATAC
1 --AA-TG-TATCGATAC
2414227 AATGTATCGATAC
1 AATGTATCGATAC
2414240 AA
1 AA
2414242 GCTACCCTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 4 0.14
16 2 0.07
17 9 0.32
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2422794 original size:52 final size:52
Alignment explanation
Indices: 2422716--2422819 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
2422706 CGAAATATGA
2422716 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
2422768 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
2422820 TGGCAAAGGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2422927 original size:135 final size:135
Alignment explanation
Indices: 2422685--2422954 Score: 540
Period size: 135 Copynumber: 2.0 Consensus size: 135
2422675 AAAACTAGTT
2422685 TGGCAAAGGAAGAAAAAGTCCCGAAATATGAAAATTTGCCTGCATGTATCGATACATTTCATAGT
1 TGGCAAAGGAAGAAAAAGTCCCGAAATATGAAAATTTGCCTGCATGTATCGATACATTTCATAGT
2422750 GTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATC
66 GTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATC
2422815 TGGGC
131 TGGGC
2422820 TGGCAAAGGAAGAAAAAGTCCCGAAATATGAAAATTTGCCTGCATGTATCGATACATTTCATAGT
1 TGGCAAAGGAAGAAAAAGTCCCGAAATATGAAAATTTGCCTGCATGTATCGATACATTTCATAGT
2422885 GTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATC
66 GTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATC
2422950 TGGGC
131 TGGGC
2422955 AAATTTGCCT
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 135 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (135 bp):
TGGCAAAGGAAGAAAAAGTCCCGAAATATGAAAATTTGCCTGCATGTATCGATACATTTCATAGT
GTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATC
TGGGC
Found at i:2422999 original size:52 final size:52
Alignment explanation
Indices: 2422851--2422979 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
2422841 CGAAATATGA
2422851 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
2422903 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
2422955 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2422980 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2423006 original size:13 final size:13
Alignment explanation
Indices: 2422988--2423012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2422978 CAAAGATCAG
2422988 TGTATCGATACAA
1 TGTATCGATACAA
2423001 TGTATCGATACA
1 TGTATCGATACA
2423013 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2423092 original size:13 final size:13
Alignment explanation
Indices: 2423074--2423098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2423064 ACAAAACTTA
2423074 TGTATCGATACAT
1 TGTATCGATACAT
2423087 TGTATCGATACA
1 TGTATCGATACA
2423099 ACACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2423094 original size:32 final size:32
Alignment explanation
Indices: 2423053--2423117 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
2423043 AGTAGCTTAT
2423053 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
2423085 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
2423117 A
1 A
2423118 ACACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:2423128 original size:20 final size:19
Alignment explanation
Indices: 2423055--2423138 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
2423045 TAGCTTATAT
*
2423055 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
2423074 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
2423087 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
2423106 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
2423126 TGTATCGATACAA
1 TGTATCGATACAA
2423139 ATCGTTGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 5 0.09
18 1 0.02
19 25 0.44
20 16 0.28
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:2431980 original size:11 final size:11
Alignment explanation
Indices: 2431966--2431992 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2431956 AAAAAGAGAA
2431966 AAAAAAACAAC
1 AAAAAAACAAC
2431977 AAAAAAACAAC
1 AAAAAAACAAC
2431988 AAAAA
1 AAAAA
2431993 GGGTCCAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:2433038 original size:37 final size:37
Alignment explanation
Indices: 2432997--2433077 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
2432987 ACAATCATGC
2432997 ATTTGTGACATTCATAACATTTCATTTTGCATGATGA
1 ATTTGTGACATTCATAACATTTCATTTTGCATGATGA
*
2433034 ATTTGTGACATTCATAACATTTCATTTTGCATGATGC
1 ATTTGTGACATTCATAACATTTCATTTTGCATGATGA
2433071 ATTTGTG
1 ATTTGTG
2433078 TTTCATCTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (37 bp):
ATTTGTGACATTCATAACATTTCATTTTGCATGATGA
Found at i:2433480 original size:32 final size:32
Alignment explanation
Indices: 2433439--2433670 Score: 292
Period size: 32 Copynumber: 7.4 Consensus size: 32
2433429 ATTCCTCACC
* * * *
2433439 TTTCAAAGCCCACACGAGTCAGTGGCAACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
2433471 TTTCAAAGCCTACACAAGTTGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
2433503 TTTCAAAGCCCACACAAGTCGGTGGCGACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
** *
2433535 TTTCAAAG-CC-CACAAGTTAGTGGC-A-TCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
2433563 TTTCAGAGCCCACACAAATCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
2433595 TTTGAAAGCCCACACAAGTTGGTGACAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
2433627 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
2433659 TTTCAAAGCCCA
1 TTTCAAAGCCCA
2433671 TAAATCAGTG
Statistics
Matches: 171, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
28 9 0.05
29 3 0.02
30 23 0.13
31 3 0.02
32 133 0.78
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.20
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:2433603 original size:92 final size:95
Alignment explanation
Indices: 2433439--2433670 Score: 308
Period size: 92 Copynumber: 2.5 Consensus size: 95
2433429 ATTCCTCACC
* * * *
2433439 TTTCAAAGCCCACACGAGTCAGTGGCAACTCTTTTCAAAGCCTACACAAGTTGGTGGCAACCCAT
1 TTTCAAAGCCCACAC-AGTCAGTGGCAACTCATTTCAAAGCCCACACAAATCGGTGGCAACCCAT
* *
2433504 TTCAAAGCCCACACAAGTCGGTGGCGACCCA
65 TTCAAAGCCCACACAAGTCGGTGACAACCCA
* * *
2433535 TTTCAAAGCCCACA-AGTTAGTGGC-A-TCATTTCAGAGCCCACACAAATCGGTGGCAACTCATT
1 TTTCAAAGCCCACACAGTCAGTGGCAACTCATTTCAAAGCCCACACAAATCGGTGGCAACCCATT
* *
2433597 TGAAAGCCCACACAAGTTGGTGACAACCCA
66 TCAAAGCCCACACAAGTCGGTGACAACCCA
* *
2433627 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 TTTCAAAGCCCACAC-AGTCAGTGGCAACTCATTTCAAAGCCCA
2433671 TAAATCAGTG
Statistics
Matches: 117, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
92 71 0.61
93 1 0.01
94 17 0.15
95 1 0.01
96 27 0.23
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.20
Consensus pattern (95 bp):
TTTCAAAGCCCACACAGTCAGTGGCAACTCATTTCAAAGCCCACACAAATCGGTGGCAACCCATT
TCAAAGCCCACACAAGTCGGTGACAACCCA
Found at i:2433659 original size:124 final size:124
Alignment explanation
Indices: 2433439--2433670 Score: 383
Period size: 124 Copynumber: 1.9 Consensus size: 124
2433429 ATTCCTCACC
* * * * *
2433439 TTTCAAAGCCCACACGAGTCAGTGGCAACTCTTTTCAAAGCCTACACAAGTTGGTGGCAACCCAT
1 TTTCAAAGCCCACACAAATCAGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGACAACCCAT
*
2433504 TTCAAAGCCCACACAAGTCGGTGGCGACCCATTTCAAAGCCCACAAGTTAGTGGCATCA
66 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTTAGTGGCATCA
* * *
2433563 TTTCAGAGCCCACACAAATCGGTGGCAACTCATTTGAAAGCCCACACAAGTTGGTGACAACCCAT
1 TTTCAAAGCCCACACAAATCAGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGACAACCCAT
2433628 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
66 TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2433671 TAAATCAGTG
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 99 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.20
Consensus pattern (124 bp):
TTTCAAAGCCCACACAAATCAGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGACAACCCAT
TTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTTAGTGGCATCA
Found at i:2433687 original size:20 final size:20
Alignment explanation
Indices: 2433662--2433703 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2433652 CAACCCATTT
*
2433662 CAAAGCCCATAAATCAGTGG
1 CAAAGCCCACAAATCAGTGG
*
2433682 CAAAGCCCACAAGTCAGTGG
1 CAAAGCCCACAAATCAGTGG
2433702 CA
1 CA
2433704 CCCTTTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.29, G:0.21, T:0.12
Consensus pattern (20 bp):
CAAAGCCCACAAATCAGTGG
Found at i:2433722 original size:28 final size:28
Alignment explanation
Indices: 2433682--2434001 Score: 375
Period size: 28 Copynumber: 11.3 Consensus size: 28
2433672 AAATCAGTGG
*
2433682 CAAAGCCCACAAGTCAGTGGCACCCTTT
1 CAAAGCCCACAAGTCAGTGGCAACCTTT
2433710 CAAAGCCCACAAGTCAGTGGCAACC-TT
1 CAAAGCCCACAAGTCAGTGGCAACCTTT
*
2433737 CAGAAGCCCATAAGTCAGTGGC-ACCTTTT
1 CA-AAGCCCACAAGTCAGTGGCAACC-TTT
2433766 CAAAGCCCACAAGTCAGTGGCAACC-TT
1 CAAAGCCCACAAGTCAGTGGCAACCTTT
* *
2433793 CAGAAGCCCACAAGTCGGTGGCACCCCTTT
1 CA-AAGCCCACAAGTCAGTGGCA-ACCTTT
*
2433823 CAAAGCCCACAAGTTAGTGGCAACC-TT
1 CAAAGCCCACAAGTCAGTGGCAACCTTT
* * * *
2433850 CAAAAGCCTACAAGTCAGTGGTATCTTTT
1 C-AAAGCCCACAAGTCAGTGGCAACCTTT
* *
2433879 CAAAAGCCCACAAGTTAGAGGC-ACCTTTT
1 C-AAAGCCCACAAGTCAGTGGCAACC-TTT
2433908 CAAAGCCCACAAGTCAGTGGCAACC-TT
1 CAAAGCCCACAAGTCAGTGGCAACCTTT
* *
2433935 CAGAAGCCCACAAGTCGGTGGCACTCCTTT
1 CA-AAGCCCACAAGTCAGTGGCA-ACCTTT
*
2433965 CAAAGCTCACAAGTCAGTGGCAACC-TT
1 CAAAGCCCACAAGTCAGTGGCAACCTTT
2433992 CAAAAGCCCA
1 C-AAAGCCCA
2434002 TACAAGTTGG
Statistics
Matches: 250, Mismatches: 27, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
27 21 0.08
28 147 0.59
29 74 0.30
30 8 0.03
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (28 bp):
CAAAGCCCACAAGTCAGTGGCAACCTTT
Found at i:2433851 original size:57 final size:55
Alignment explanation
Indices: 2433682--2434001 Score: 385
Period size: 57 Copynumber: 5.7 Consensus size: 55
2433672 AAATCAGTGG
2433682 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTT
1 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTT
* *
2433737 CAGAAGCCCATAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTT
1 CA-AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTT
* *
2433793 CAGAAGCCCACAAGTCGGTGGCACCCCTTTCAAAGCCCACAAGTTAGTGGCAACCTT
1 CA-AAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCAACCTT
* * * * * *
2433850 CAAAAGCCTACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTTAGAGGC-ACCTTTT
1 C-AAAGCCCACAAGTCAGTGGCACCCTTTC-AAAGCCCACAAGTCAGTGGCAACC--TT
* * *
2433908 CAAAGCCCACAAGTCAGTGGCAACC-TTCAGAAGCCCACAAGTCGGTGGCACTCCTTT
1 CAAAGCCCACAAGTCAGTGGCACCCTTTCA-AAGCCCACAAGTCAGTGGCA-ACC-TT
* *
2433965 CAAAGCTCACAAGTCAGTGGCAACC-TTCAAAAGCCCA
1 CAAAGCCCACAAGTCAGTGGCACCCTTTC-AAAGCCCA
2434002 TACAAGTTGG
Statistics
Matches: 234, Mismatches: 21, Indels: 18
0.86 0.08 0.07
Matches are distributed among these distances:
55 3 0.01
56 99 0.42
57 125 0.53
58 7 0.03
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (55 bp):
CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTT
Found at i:2433937 original size:142 final size:141
Alignment explanation
Indices: 2433682--2434008 Score: 503
Period size: 142 Copynumber: 2.3 Consensus size: 141
2433672 AAATCAGTGG
* * *
2433682 CAAAGCCCACAAGTCAGTGGCACCCTTTC-AAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCC
1 CAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCTACAAGTCAGTGGCAACCTTCAAAAGCCC
* *
2433746 ATAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGG
65 ACAAGTCAGAGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGG
2433811 TGGCACCCCTTT
130 TGGCACCCCTTT
* * * *
2433823 CAAAGCCCACAAGTTAGTGGCAACCTTCAAAAGCCTACAAGTCAGTGGTATCTTTTCAAAAGCCC
1 CAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCTACAAGTCAGTGGCAAC-CTTCAAAAGCCC
*
2433888 ACAAGTTAGAGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGG
65 ACAAGTCAGAGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGG
*
2433953 TGGCACTCCTTT
130 TGGCACCCCTTT
*
2433965 CAAAGCTCACAAGTCAGTGGCAACCTTCAAAAGCCCATACAAGT
1 CAAAGCCCACAAGTCAGTGGCAACCTTCAAAAG-CC-TACAAGT
2434009 TGGTGGCATC
Statistics
Matches: 169, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
140 3 0.02
141 43 0.25
142 114 0.67
143 2 0.01
144 7 0.04
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (141 bp):
CAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCTACAAGTCAGTGGCAACCTTCAAAAGCCCA
CAAGTCAGAGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTCGGT
GGCACCCCTTT
Found at i:2434148 original size:49 final size:49
Alignment explanation
Indices: 2434075--2434429 Score: 239
Period size: 52 Copynumber: 7.0 Consensus size: 49
2434065 CTCATCTTCA
* * * *
2434075 TCATCTTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATGGGCACCT
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT
*
2434124 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATT
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T
* * *
2434175 GTCATCTTTAAGT-AAATATCGCTGGCCTTGAATCAGTACATTAGCACCT
1 -TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT
* * * ** * * * *
2434224 TCACCTTTAAGTCCAAAATCACTAACCTTAAATAAGCATATTGGCATCT
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT
* ** * *
2434273 GTAACAT-TCCTAAACCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTT
1 -T--CATCT-TTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--CCT
* * * * ** * * *
2434327 CTCATCTTCAAGTCTAATGTTGCTAACCGTGAATCAGCACATTGACATTCTT
1 -TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--CCT
* * ** *
2434379 TACATCTATAAGCCCAATATCATTGGTCC-TGAATCAGCATATTGGCACCT
1 T-CATCTTTAAGTCCAATATCGCTGG-CCTTGAATCAGCACATTGGCACCT
2434429 T
1 T
2434430 TATCACTCTT
Statistics
Matches: 234, Mismatches: 59, Indels: 25
0.74 0.19 0.08
Matches are distributed among these distances:
48 11 0.05
49 69 0.29
50 4 0.02
51 34 0.15
52 111 0.47
53 3 0.01
54 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (49 bp):
TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT
Found at i:2434202 original size:51 final size:49
Alignment explanation
Indices: 2434075--2434239 Score: 206
Period size: 49 Copynumber: 3.3 Consensus size: 49
2434065 CTCATCTTCA
* * *
2434075 TCATCTTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATGGGCACCT
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATGGGCACCT
* *
2434124 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATT
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATGGGCACC--T
* * **
2434175 GTCATCTTTAAGT-AAATATCGCTGGCCTTGAATCAGTACATTAGCACCT
1 -TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATGGGCACCT
*
2434224 TCACCTTTAAGTCCAA
1 TCATCTTTAAGTCCAA
2434240 AATCACTAAC
Statistics
Matches: 101, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
48 11 0.11
49 46 0.46
51 32 0.32
52 12 0.12
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (49 bp):
TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATGGGCACCT
Found at i:2434209 original size:100 final size:101
Alignment explanation
Indices: 2434075--2434269 Score: 257
Period size: 100 Copynumber: 1.9 Consensus size: 101
2434065 CTCATCTTCA
* * * * *
2434075 TCATCTTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATGGGCACCTTCATCTTTAAGTCCAA
1 TCATCTTTAAGTCAAATATCGCTGGCCTTAAATCAGCACATGAGCACCTTCACCTTTAAGTCCAA
* * ** * *
2434140 TATCGCTGGCCTTGAATCAGCATATTGGCACCATTG
66 AATCACTAACCTTAAATAAGCATATTGGCACCATTG
* * *
2434176 TCATCTTTAAGT-AAATATCGCTGGCCTTGAATCAGTACATTAGCACCTTCACCTTTAAGTCCAA
1 TCATCTTTAAGTCAAATATCGCTGGCCTTAAATCAGCACATGAGCACCTTCACCTTTAAGTCCAA
2434240 AATCACTAACCTTAAATAAGCATATTGGCA
66 AATCACTAACCTTAAATAAGCATATTGGCA
2434270 TCTGTAACAT
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
100 68 0.85
101 12 0.15
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (101 bp):
TCATCTTTAAGTCAAATATCGCTGGCCTTAAATCAGCACATGAGCACCTTCACCTTTAAGTCCAA
AATCACTAACCTTAAATAAGCATATTGGCACCATTG
Found at i:2434930 original size:13 final size:13
Alignment explanation
Indices: 2434912--2434938 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2434902 CATTATTCAA
2434912 TGTATCAATACAT
1 TGTATCAATACAT
2434925 TGTATCAATACAT
1 TGTATCAATACAT
2434938 T
1 T
2434939 AATCTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:2434936 original size:33 final size:33
Alignment explanation
Indices: 2434892--2434957 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2434882 GCCAAGGAAA
* *
2434892 TGTATCGATACATTATTCAATGTATCAATACAT
1 TGTATCAATACATTAATCAATGTATCAATACAT
** *
2434925 TGTATCAATACATTAATCTTTGTATCGATACAT
1 TGTATCAATACATTAATCAATGTATCAATACAT
2434958 ATGAGAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (33 bp):
TGTATCAATACATTAATCAATGTATCAATACAT
Found at i:2435000 original size:20 final size:20
Alignment explanation
Indices: 2434975--2435028 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2434965 TTTTACCCAG
2434975 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
2434995 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
*
2435015 ACGTATCGATACAT
1 ATGTATCGATACAT
2435029 GCAGGTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTATTCA
Found at i:2448365 original size:19 final size:20
Alignment explanation
Indices: 2448335--2448389 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
2448325 GTATCGATAC
* *
2448335 ATTATATTGATACATATTC-
1 ATTATATCGATACATACTCA
*
2448354 ATTGTATCGATACATACTCA
1 ATTATATCGATACATACTCA
2448374 ATTATATCGATACATA
1 ATTATATCGATACATA
2448390 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (20 bp):
ATTATATCGATACATACTCA
Found at i:2448448 original size:20 final size:20
Alignment explanation
Indices: 2448415--2448470 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2448405 ACCCTAAGTA
2448415 AAAAGTATCGATACATGG-G
1 AAAAGTATCGATACATGGTG
* *
2448434 ACAATGTATCAATACATGGTG
1 A-AAAGTATCGATACATGGTG
2448455 AAAAGTATCGATACAT
1 AAAAGTATCGATACAT
2448471 CGTGCCCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.90
21 2 0.06
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (20 bp):
AAAAGTATCGATACATGGTG
Found at i:2458228 original size:3 final size:3
Alignment explanation
Indices: 2458214--2458260 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
2458204 GGCCTATTTC
*
2458214 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2458261 AGATCATAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2461853 original size:29 final size:30
Alignment explanation
Indices: 2461821--2461898 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
2461811 TTTTAATTTT
* *
2461821 TTAAATGAATTTTTATATTTTT-A-TTGTAC
1 TTAAATAAATTTTTAT-TTTTTAATTTATAC
*
2461850 TTAAATAAATTTTTATTTTTTAATTTATAT
1 TTAAATAAATTTTTATTTTTTAATTTATAC
2461880 TTAAATAAATTTTTATTTT
1 TTAAATAAATTTTTATTTT
2461899 AAATTAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 5 0.11
29 16 0.36
30 23 0.52
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.62
Consensus pattern (30 bp):
TTAAATAAATTTTTATTTTTTAATTTATAC
Found at i:2461903 original size:29 final size:30
Alignment explanation
Indices: 2461850--2461912 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
2461840 TTTATTGTAC
* * *
2461850 TTAAATAAATTTTTATTTTTTAATTTATAT
1 TTAAATAAATTTTTATTTTTAAATTAAAAT
2461880 TTAAATAAATTTTTA-TTTTAAATTAAAAT
1 TTAAATAAATTTTTATTTTTAAATTAAAAT
2461909 TTAA
1 TTAA
2461913 TGGTATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTAAATAAATTTTTATTTTTAAATTAAAAT
Found at i:2461906 original size:18 final size:17
Alignment explanation
Indices: 2461850--2461902 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
2461840 TTTATTGTAC
2461850 TTAAATAAATTTTTATT
1 TTAAATAAATTTTTATT
* *
2461867 TT---TTAATTTATA-T
1 TTAAATAAATTTTTATT
2461880 TTAAATAAATTTTTATT
1 TTAAATAAATTTTTATT
2461897 TTAAAT
1 TTAAAT
2461903 TAAAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
13 3 0.11
14 8 0.29
16 8 0.29
17 9 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAAATAAATTTTTATT
Found at i:2461951 original size:30 final size:28
Alignment explanation
Indices: 2461917--2462029 Score: 93
Period size: 30 Copynumber: 3.9 Consensus size: 28
2461907 ATTTAATGGT
*
2461917 ATATAAATTAAATGATACAAATTTATTTAA
1 ATATAATTTAAAT-ATA-AAATTTATTTAA
* *
2461947 ATATATTTTAAAAATTAAAAATTTATTTAA
1 ATATAATTTAAATA-T-AAAATTTATTTAA
* *
2461977 TTATACATTTAAAT-TAAAATTTTATTTTA
1 ATATA-ATTTAAATATAAAA-TTTATTTAA
** *
2462006 ATATAATAAAAATATAAAAATTAT
1 ATATAATTTAAATATAAAATTTAT
2462030 CAAAAAATTA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
28 14 0.21
29 19 0.28
30 27 0.40
31 7 0.10
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (28 bp):
ATATAATTTAAATATAAAATTTATTTAA
Found at i:2462023 original size:29 final size:29
Alignment explanation
Indices: 2461935--2462027 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
2461925 TAAATGATAC
* **
2461935 AAATTTATTTAAATATATTTTAAAAATTAA
1 AAATTTATTTAATTATA-CATAAAAATTAA
**
2461965 AAATTTATTTAATTATACATTTAAATTAA
1 AAATTTATTTAATTATACATAAAAATTAA
*
2461994 AATTTTATTTTAA-TATA-ATAAAAATATAA
1 AAATTTA-TTTAATTATACATAAAAAT-TAA
2462023 AAATT
1 AAATT
2462028 ATCAAAAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
28 6 0.12
29 25 0.48
30 21 0.40
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
AAATTTATTTAATTATACATAAAAATTAA
Found at i:2462229 original size:24 final size:24
Alignment explanation
Indices: 2462202--2462255 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
2462192 CATGGGATTT
*
2462202 TCTTTTTCTTT-TTTCTTCTTTTTA
1 TCTTTTTCTTTATTT-TTATTTTTA
*
2462226 TCTTTATCTTTATTTTTATTTTTA
1 TCTTTTTCTTTATTTTTATTTTTA
2462250 TCTTTT
1 TCTTTT
2462256 CATGTTCACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (24 bp):
TCTTTTTCTTTATTTTTATTTTTA
Found at i:2462241 original size:18 final size:18
Alignment explanation
Indices: 2462220--2462254 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2462210 TTTTTTCTTC
2462220 TTTTTATCTTTATCTTTA
1 TTTTTATCTTTATCTTTA
*
2462238 TTTTTATTTTTATCTTT
1 TTTTTATCTTTATCTTT
2462255 TCATGTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTATCTTTATCTTTA
Found at i:2462243 original size:12 final size:12
Alignment explanation
Indices: 2462220--2462254 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2462210 TTTTTTCTTC
2462220 TTTTTATCTTTA
1 TTTTTATCTTTA
* *
2462232 TCTTTATTTTTA
1 TTTTTATCTTTA
2462244 TTTTTATCTTT
1 TTTTTATCTTT
2462255 TCATGTTCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATCTTTA
Found at i:2462331 original size:18 final size:19
Alignment explanation
Indices: 2462294--2462332 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2462284 GGGATAATTT
*
2462294 ATTTTATTTTATTTTAATA
1 ATTTTATTTAATTTTAATA
*
2462313 ATTTT-TTTAATTTTTATA
1 ATTTTATTTAATTTTAATA
2462331 AT
1 AT
2462333 ACATTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTATTTAATTTTAATA
Found at i:2462332 original size:21 final size:21
Alignment explanation
Indices: 2462269--2462338 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
2462259 GTTCACCTTT
**
2462269 ATTTTTTT-ATTTTTAGGGATA
1 ATTTTTTTAATTTTTA-TAATA
* *
2462290 ATTTATTTTATTTTATTTTAATA
1 ATTT-TTTTAATTT-TTATAATA
2462313 ATTTTTTTAATTTTTATAATA
1 ATTTTTTTAATTTTTATAATA
2462334 CATTT
1 -ATTT
2462339 GATTAATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
21 11 0.28
22 16 0.41
23 10 0.26
24 2 0.05
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (21 bp):
ATTTTTTTAATTTTTATAATA
Found at i:2462508 original size:18 final size:20
Alignment explanation
Indices: 2462471--2462510 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2462461 AAATTCTCAA
2462471 TAAAATAAGTTTAAATATTT
1 TAAAATAAGTTTAAATATTT
*
2462491 TAAAATAA-TTT-CATATTT
1 TAAAATAAGTTTAAATATTT
2462509 TA
1 TA
2462511 TCTAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TAAAATAAGTTTAAATATTT
Found at i:2467141 original size:20 final size:20
Alignment explanation
Indices: 2467099--2467149 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2467089 GTTTGGGACA
**
2467099 ATGTATCGATACAATTATTC
1 ATGTATCGATACAATTAGCC
2467119 ATGTATCGATACAATGT-GCC
1 ATGTATCGATACAAT-TAGCC
2467139 ATGTATCGATA
1 ATGTATCGATA
2467150 TAAATAGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTAGCC
Found at i:2467210 original size:20 final size:20
Alignment explanation
Indices: 2467185--2467235 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2467175 CAGTTTCATT
***
2467185 TATCGATACAATTGTGTATG
1 TATCGATACAATTGAACATG
2467205 TATCGATACAA-TGAACATG
1 TATCGATACAATTGAACATG
2467224 TATCGATACAAT
1 TATCGATACAAT
2467236 GTATCGATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
TATCGATACAATTGAACATG
Found at i:2467239 original size:13 final size:13
Alignment explanation
Indices: 2467221--2467247 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2467211 TACAATGAAC
2467221 ATGTATCGATACA
1 ATGTATCGATACA
2467234 ATGTATCGATACA
1 ATGTATCGATACA
2467247 A
1 A
2467248 AGCATGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2482473 original size:20 final size:20
Alignment explanation
Indices: 2482448--2482495 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2482438 CGATACAATA
*
2482448 TATCGATACATTGAATAATG
1 TATCGATAAATTGAATAATG
2482468 TATCGATAAATTGAATAATG
1 TATCGATAAATTGAATAATG
*
2482488 TATTGATA
1 TATCGATA
2482496 TATTTCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (20 bp):
TATCGATAAATTGAATAATG
Found at i:2483503 original size:49 final size:49
Alignment explanation
Indices: 2483344--2483986 Score: 471
Period size: 49 Copynumber: 13.1 Consensus size: 49
2483334 GAAGAATGAT
* * ** *
2483344 AATGTGCTGATTCATGGCCAGCGACATTAGACTTGAAGA-AGAA--TGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATA-AAGGTGCC
** * * * * * *
2483391 AATGTGCTGAGACAAGGCCAGCGACGTTGGGCTTAGGAATGTTAAAGATGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTA--AA-GATAAAGGTGCC
* * *
2483443 AATATGTTGATTCAAGGCCAACGATATCGGACTTAAAGATAAAGGTGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAAAGGTGCC
* ** *
2483492 AATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAGA-AGAA--TGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATA-AAGGTGCC
** * * * * *
2483539 AATGTGCTGAGACAAGACCAGCGACATTAGG-CTTAGGAATGTTAAAGATGCC
1 AATGTGCTGATTCAAGGCCAACGACA-TCGGACTTA--AA-GATAAAGGTGCC
* * * * * *
2483591 AATATGCTGATTTAAGGCCAACAATATCGAACTTAAAGATGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAAAGGTGCC
* * ** *
2483640 AATGTGCTGATTCAAGGCCAGCGAAATTAGACTTGAAGA-AGAA--TGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATA-AAGGTGCC
* * ** * * * *
2483687 ACTGTGTTGAGACAAGGCCAGCGACATTAGG-CTTAGGAATGTTAAAGATGCC
1 AATGTGCTGATTCAAGGCCAACGACA-TCGGACTTA--AA-GATAAAGGTGCC
* * * * *
2483739 AATATGCTGATTTAAGGCCAACAATATCGGACTTAAAGATGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAAAGGTGCC
* * *
2483788 AATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGCGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAAAGGTGCC
* ** *
2483837 AATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATAAAGGTGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAAAGGTGCC
* * * * *
2483886 AATATGCTGATTCAAGGCCAATGATATCGGACTTAAAGATGAAGGTGTC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAAAGGTGCC
* * * * *
2483935 AATGTGCTGATTTAAGGCCAACGACATCAGTCTTAAAGATGAAGGCGCC
1 AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAAAGGTGCC
2483984 AAT
1 AAT
2483987 CCTCCACATA
Statistics
Matches: 466, Mismatches: 106, Indels: 46
0.75 0.17 0.07
Matches are distributed among these distances:
47 86 0.18
48 5 0.01
49 271 0.58
50 15 0.03
51 8 0.02
52 81 0.17
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (49 bp):
AATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATAAAGGTGCC
Found at i:2483530 original size:148 final size:148
Alignment explanation
Indices: 2483344--2483961 Score: 927
Period size: 148 Copynumber: 4.2 Consensus size: 148
2483334 GAAGAATGAT
*
2483344 AATGTGCTGATTCATGGCCAGCGACATTAGACTTGAAGAAGAATGCCAATGTGCTGAGACAAGGC
1 AATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAGAAGAATGCCAATGTGCTGAGACAAGGC
* * * *
2483409 CAGCGACGTTGGGCTTAGGAATGTTAAAGATGCCAATATGTTGATTCAAGGCCAACGATATCGGA
66 CAGCGACATTAGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACAATATCGGA
*
2483474 CTTAAAGATAAAGGTGCC
131 CTTAAAGATGAAGGTGCC
*
2483492 AATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAGAAGAATGCCAATGTGCTGAGACAAGAC
1 AATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAGAAGAATGCCAATGTGCTGAGACAAGGC
* *
2483557 CAGCGACATTAGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTTAAGGCCAACAATATCGAA
66 CAGCGACATTAGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACAATATCGGA
2483622 CTTAAAGATGAAGGTGCC
131 CTTAAAGATGAAGGTGCC
* * *
2483640 AATGTGCTGATTCAAGGCCAGCGAAATTAGACTTGAAGAAGAATGCCACTGTGTTGAGACAAGGC
1 AATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAGAAGAATGCCAATGTGCTGAGACAAGGC
*
2483705 CAGCGACATTAGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTTAAGGCCAACAATATCGGA
66 CAGCGACATTAGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACAATATCGGA
2483770 CTTAAAGATGAAGGTGCC
131 CTTAAAGATGAAGGTGCC
* ** * * * * **
2483788 AATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGCGCCAATGTGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAGAAGAA--TGCCAATGTGCTGAGACAAG
* * * **
2483853 GCCAGCGACATTAGTCTTA--AA-GATAAAGGTGCCAATATGCTGATTCAAGGCCAATGATATCG
64 GCCAGCGACATTAGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACAATATCG
*
2483915 GACTTAAAGATGAAGGTGTC
129 GACTTAAAGATGAAGGTGCC
* *
2483935 AATGTGCTGATTTAAGGCCAACGACAT
1 AATGTGCTGATTCAAGGCCAGCGACAT
2483962 CAGTCTTAAA
Statistics
Matches: 434, Mismatches: 34, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
147 81 0.19
148 320 0.74
150 33 0.08
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (148 bp):
AATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAGAAGAATGCCAATGTGCTGAGACAAGGC
CAGCGACATTAGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACAATATCGGA
CTTAAAGATGAAGGTGCC
Found at i:2497355 original size:13 final size:13
Alignment explanation
Indices: 2497337--2497393 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
2497327 TTCAACAATT
2497337 TGTATCGATACAA
1 TGTATCGATACAA
2497350 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
2497365 GTGTTGTATAGATACAA
1 ----TGTATCGATACAA
2497382 TGTATCGATACA
1 TGTATCGATACA
2497394 CAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2497379 original size:32 final size:32
Alignment explanation
Indices: 2497336--2497425 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
2497326 TTTCAACAAT
*
2497336 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACACAAGTG
* *
2497368 TTGTATAGATACAATGTATCGATACACAAGTT
1 TTGTATCGATACAATGTATCGATACACAAGTG
* *
2497400 TTGTATCGATACAATGCATCGCTACA
1 TTGTATCGATACAATGTATCGATACA
2497426 AAGCTACTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACACAAGTG
Found at i:2499313 original size:11 final size:11
Alignment explanation
Indices: 2499297--2499323 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2499287 CATCCTCCAC
2499297 AAAAAAAGAAG
1 AAAAAAAGAAG
2499308 AAAAAAAGAAG
1 AAAAAAAGAAG
2499319 AAAAA
1 AAAAA
2499324 GAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:2499324 original size:20 final size:20
Alignment explanation
Indices: 2499295--2499344 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2499285 GGCATCCTCC
*
2499295 ACAA-AAAAAGAAGAAAAAA
1 ACAACAAAAAGAAAAAAAAA
* *
2499314 AGAAGAAAAAGAAAAAAAAA
1 ACAACAAAAAGAAAAAAAAA
2499334 ACAACAAAAAG
1 ACAACAAAAAG
2499345 GGTCTGGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (20 bp):
ACAACAAAAAGAAAAAAAAA
Found at i:2500770 original size:28 final size:28
Alignment explanation
Indices: 2500738--2501011 Score: 297
Period size: 28 Copynumber: 9.7 Consensus size: 28
2500728 ACATCCTCAC
*
2500738 CTTTTCAAAGCCCACAAGTCATTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
2500766 CTTTTCCAAAGCCCACAAGTCAGTGGCAA
1 CTTTT-CAAAGCCCACAAGTCAGTGGCAT
*
2500795 C-CTTCAAAAGCCCACAAGTCAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
*
2500823 CTTTTCCAAAGCCCACAAGTCAGTGGCAA
1 CTTTT-CAAAGCCCACAAGTCAGTGGCAT
*
2500852 C-CTTCAAAAGCCCACAAGTCAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
2500880 CTTTTCCAAAGCCCACAAGTCAGTGGCAAT
1 CTTTT-CAAAGCCCACAAGTCAGTGGC-AT
* * * *
2500910 C--TTCAAAAGCGCACAAGTTAGTGACACC
1 CTTTTC-AAAGCCCACAAGTCAGTGGCA-T
* *
2500938 CCTTTC-AAGCCCACAAGTCAGTGGTAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
2500965 CCTTTCAAAGCCCACAAGTCAGTGGCAA
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
2500993 CCTTTAAAAGCACACAAGT
1 CTTTTCAAAGCCCACAAGT
2501012 TGATGCAACC
Statistics
Matches: 211, Mismatches: 22, Indels: 26
0.81 0.08 0.10
Matches are distributed among these distances:
27 10 0.05
28 125 0.59
29 68 0.32
30 8 0.04
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:2500828 original size:57 final size:57
Alignment explanation
Indices: 2500744--2500991 Score: 376
Period size: 57 Copynumber: 4.4 Consensus size: 57
2500734 TCACCTTTTC
*
2500744 AAAGCCCACAAGTCATTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
2500801 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
*
2500858 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAATCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * * * * *
2500915 AAAGCGCACAAGTTAGTGACACCCCTTT-C-AAGCCCACAAGTCAGTGGTATCCTTTC-
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCAACC-TTCA
2500971 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
2500992 ACCTTTAAAA
Statistics
Matches: 176, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
56 38 0.22
57 134 0.76
58 4 0.02
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
Done.