Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 11 of 175
Found at i:3215678 original size:19 final size:19
Alignment explanation
Indices: 3215642--3215696 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3215632 TTGCCCTTCC
3215642 CTTTTATT-TATTTATTTAT
1 CTTTTATTAT-TTTATTTAT
*
3215661 CTTTTATTATTTTGTTTAT
1 CTTTTATTATTTTATTTAT
*
3215680 -TTGTTTTTATTTTATTT
1 CTT-TTATTATTTTATTT
3215697 TATTTTGGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 2 0.06
19 28 0.90
20 1 0.03
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (19 bp):
CTTTTATTATTTTATTTAT
Found at i:3215681 original size:27 final size:27
Alignment explanation
Indices: 3215643--3215695 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3215633 TGCCCTTCCC
*
3215643 TTTTATTTATTTATTTATCTTTTATTA
1 TTTTATTTATTTATTTATATTTTATTA
* * *
3215670 TTTTGTTTATTTGTTTTTATTTTATT
1 TTTTATTTATTTATTTATATTTTATT
3215696 TTATTTTGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (27 bp):
TTTTATTTATTTATTTATATTTTATTA
Found at i:3217301 original size:5 final size:5
Alignment explanation
Indices: 3217283--3217360 Score: 52
Period size: 5 Copynumber: 15.0 Consensus size: 5
3217273 AGGATCATTG
* *
3217283 ATTTT A-TTT GTTTT ATTTTT AATTTT ATTTA ATTTT ATGTTT -TTTCT
1 ATTTT ATTTT ATTTT A-TTTT -ATTTT ATTTT ATTTT AT-TTT ATTT-T
* * *
3217330 ATTTT ATGTT GTTTT GTTTT ATTTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT A-TTTT ATTTT
3217361 CTTGTACTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
4 5 0.09
5 33 0.57
6 19 0.33
7 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.06, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:3225805 original size:30 final size:31
Alignment explanation
Indices: 3225771--3225872 Score: 111
Period size: 30 Copynumber: 3.4 Consensus size: 31
3225761 TAAAAAATAA
*
3225771 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
3225801 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* * * *
3225831 AAATTTCACTTAGACCCCTAAATTTTTAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
*
3225861 AAACTTCATTTT
1 AAATTTCATTTT
3225873 AATCCTAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
29 4 0.07
30 51 0.86
31 4 0.07
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:3226187 original size:17 final size:19
Alignment explanation
Indices: 3226140--3226182 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
3226130 ATTCGAAGGA
3226140 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
3226158 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
3226177 AAAAGA
1 AAAAGA
3226183 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:3226248 original size:3 final size:3
Alignment explanation
Indices: 3226242--3226313 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
3226232 GCTAGACTTT
*
3226242 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
*
3226289 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
3226314 ATAATAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3226260 original size:10 final size:10
Alignment explanation
Indices: 3226245--3226273 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3226235 AGACTTTGAA
3226245 GAAGAAGAAG
1 GAAGAAGAAG
3226255 GAAGAAGAAG
1 GAAGAAGAAG
3226265 GAAGAAGAA
1 GAAGAAGAA
3226274 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:3226260 original size:13 final size:13
Alignment explanation
Indices: 3226242--3226287 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
3226232 GCTAGACTTT
3226242 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
3226255 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
3226268 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
3226279 GAAGAAGAA
1 GAAGAAGAA
3226288 AGAAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:3226470 original size:23 final size:23
Alignment explanation
Indices: 3226440--3226485 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3226430 AAAAAGTAGC
3226440 AAAAAAGAAGAAGAAAGAAGCAG
1 AAAAAAGAAGAAGAAAGAAGCAG
3226463 AAAAAAGAAGAAGAAAGAAGCAG
1 AAAAAAGAAGAAGAAAGAAGCAG
3226486 CCCAAATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.70, C:0.04, G:0.26, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAGAAGAAAGAAGCAG
Found at i:3226636 original size:17 final size:16
Alignment explanation
Indices: 3226606--3226664 Score: 75
Period size: 17 Copynumber: 3.6 Consensus size: 16
3226596 GCCCAGCAAA
3226606 AAAAAAGAGAAAAAA-
1 AAAAAAGAGAAAAAAG
3226621 AGAAAAAGAGAGAAAAAG
1 A-AAAAAGAGA-AAAAAG
*
3226639 AAAAAAGAAAAAACAAG
1 AAAAAAGAGAAAA-AAG
3226656 AAAAAAGAG
1 AAAAAAGAG
3226665 GTTCAATTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
15 1 0.03
16 12 0.32
17 24 0.63
18 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAAGAGAAAAAAG
Found at i:3226657 original size:23 final size:23
Alignment explanation
Indices: 3226616--3226660 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3226606 AAAAAAGAGA
*
3226616 AAAAAAGAAAAAGAGAGAAAAAG
1 AAAAAAGAAAAAGAAAGAAAAAG
3226639 AAAAAAGAAAAA-ACAAGAAAAA
1 AAAAAAGAAAAAGA-AAGAAAAA
3226661 AGAGGTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAAGAAAGAAAAAG
Found at i:3226660 original size:16 final size:16
Alignment explanation
Indices: 3226603--3226651 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
3226593 CCAGCCCAGC
3226603 AAAA-AAAAAGAGAAA
1 AAAAGAAAAAGAGAAA
*
3226618 AAAAGAAAAAGAGAGA
1 AAAAGAAAAAGAGAAA
3226634 AAAAGAAAAA-AGAAA
1 AAAAGAAAAAGAGAAA
3226649 AAA
1 AAA
3226652 CAAGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAGAAA
Found at i:3227044 original size:16 final size:16
Alignment explanation
Indices: 3227018--3227060 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
3227008 AAAATTCCCA
* *
3227018 TGTTTCAAAAATCTTCG
1 TGTTTCAAAATTC-TAG
3227035 TGTTTCAAAATTCTAG
1 TGTTTCAAAATTCTAG
3227051 TGTTTCAAAA
1 TGTTTCAAAA
3227061 ATTTTCTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (16 bp):
TGTTTCAAAATTCTAG
Found at i:3227045 original size:33 final size:33
Alignment explanation
Indices: 3226985--3227072 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
3226975 AAAATTGTAA
* *
3226985 TTTCAATAATCCTCGTGCTTTTAAAAATTCCCA-TG
1 TTTCAAAAATCTTCGTG--TTTAAAAATT-CCAGTG
* *
3227020 TTTCAAAAATCTTCGTGTTTCAAAATTCTAGTG
1 TTTCAAAAATCTTCGTGTTTAAAAATTCCAGTG
* *
3227053 TTTCAAAAATTTTCTTGTTT
1 TTTCAAAAATCTTCGTGTTT
3227073 TCAGAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 2 0.04
33 29 0.63
35 15 0.33
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.45
Consensus pattern (33 bp):
TTTCAAAAATCTTCGTGTTTAAAAATTCCAGTG
Found at i:3227071 original size:17 final size:17
Alignment explanation
Indices: 3227018--3227506 Score: 205
Period size: 17 Copynumber: 28.3 Consensus size: 17
3227008 AAAATTCCCA
*
3227018 TGTTTCAAAAATCTTCG
1 TGTTTCAAAAATTTTCG
* *
3227035 TGTTTC-AAAATTCTAG
1 TGTTTCAAAAATTTTCG
*
3227051 TGTTTCAAAAATTTTCT
1 TGTTTCAAAAATTTTCG
*
3227068 TGTTTTCAGAAAAAAATTTCG
1 TG-TTTC---AAAAATTTTCG
* * *
3227089 TGTTTTATAAATTTCCG
1 TGTTTCAAAAATTTTCG
* **
3227106 TATTTTCAAAAA-AATCATG
1 T-GTTTCAAAAATTTTC--G
*
3227125 TCTTTCAAAAATTTTCG
1 TGTTTCAAAAATTTTCG
*** *
3227142 TGTTTTCAAAAAAAATGACCT
1 TG-TTTC---AAAAATTTTCG
*
3227163 TGTTTCAAAAATTTCCG
1 TGTTTCAAAAATTTTCG
** *
3227180 TGTTAAAAAAAATCTTCG
1 TGTT-TCAAAAATTTTCG
* *
3227198 TATTTTCAAAAAAATTTCG
1 T-GTTTC-AAAAATTTTCG
*
3227217 TGTTTC-AAAATCTTCG
1 TGTTTCAAAAATTTTCG
3227233 TGTTTTCAAAAA-TTTCGG
1 TG-TTTCAAAAATTTTC-G
* *
3227251 TGTTTTAAAGATTTTCG
1 TGTTTCAAAAATTTTCG
* *
3227268 TGTTTTCAAAAA-CTCCGG
1 TG-TTTCAAAAATTTTC-G
* ***
3227286 TGATTTTAAAAAAAATCG
1 TG-TTTCAAAAATTTTCG
*
3227304 T-TTTCTAAAAAATTTCCG
1 TGTTTC--AAAAATTTTCG
3227322 TGTTTCAAAAATTTTCG
1 TGTTTCAAAAATTTTCG
*
3227339 TGTTTTAAAAATTTTCG
1 TGTTTCAAAAATTTTCG
* *
3227356 TGTTTTAAAAATTCTCG
1 TGTTTCAAAAATTTTCG
* *
3227373 TATTT--TAAA-TTT--
1 TGTTTCAAAAATTTTCG
* **
3227385 T-TTTAAGAAAAAATT-G
1 TGTTTCA-AAAATTTTCG
* * *
3227401 TGTTTCAAAAAATGTCT
1 TGTTTCAAAAATTTTCG
*
3227418 TGTTTTAAAAATTTTCG
1 TGTTTCAAAAATTTTCG
* *
3227435 TGTTTCAAAAAATGTCG
1 TGTTTCAAAAATTTTCG
* *
3227452 TGTTTTAAAAACTTTCG
1 TGTTTCAAAAATTTTCG
*** *
3227469 TGTTTTTGAAATTTCCG
1 TGTTTCAAAAATTTTCG
*
3227486 TGTTT-AAAAATTCTCG
1 TGTTTCAAAAATTTTCG
3227502 TGTTT
1 TGTTT
3227507 TTAAAAAAAA
Statistics
Matches: 351, Mismatches: 88, Indels: 67
0.69 0.17 0.13
Matches are distributed among these distances:
11 3 0.01
12 1 0.00
14 5 0.01
15 5 0.01
16 45 0.13
17 167 0.48
18 77 0.22
19 21 0.06
20 7 0.02
21 20 0.06
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (17 bp):
TGTTTCAAAAATTTTCG
Found at i:3227093 original size:38 final size:38
Alignment explanation
Indices: 3227018--3227226 Score: 154
Period size: 38 Copynumber: 5.7 Consensus size: 38
3227008 AAAATTCCCA
* * *
3227018 TGTTTCAAAAATCTTCGTG-TTTC---AAAATTC-TAG
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATCATCG
* *
3227051 TGTTTCAAAAATTTTCTTGTTTTCAGAAAAAAAT-TTCG
1 TGTTTCAAAAATTTTCGTGTTTTCA-AAAAAAATCATCG
* * * *
3227089 TGTTTTATAAATTTCCGTATTTTC-AAAAAAATCAT-G
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATCATCG
* * * *
3227125 TCTTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCT
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATCATCG
* *
3227163 TGTTTCAAAAATTTCCGTG--TT-AAAAAAAATCTTCG
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATCATCG
* *
3227198 TATTTTCAAAAAAATTTCGTG-TTTCAAAA
1 T-GTTTC-AAAAATTTTCGTGTTTTCAAAA
3227227 TCTTCGTGTT
Statistics
Matches: 136, Mismatches: 27, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
33 17 0.12
34 4 0.03
35 11 0.08
36 34 0.25
37 21 0.15
38 45 0.33
39 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.42
Consensus pattern (38 bp):
TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATCATCG
Found at i:3227205 original size:74 final size:72
Alignment explanation
Indices: 3227053--3227226 Score: 181
Period size: 74 Copynumber: 2.4 Consensus size: 72
3227043 AATTCTAGTG
* ** * * * *
3227053 TTTCAAAAATTTTCTTGTTTTCAGAAAAAAATTTCGTGTTTTATAAATTTCCGTATTTTCAAAAA
1 TTTCAAAAATTTTCGTGTTTTCA-AAAAAAATACCGTGTTTCAAAAATTTCCG-ATGTTAAAAAA
3227118 AATCATGTC
64 AATCATGTC
*
3227127 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCTTGTTTCAAAAATTTCCG-TGTTAAAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAAT-ACCGTGTTTCAAAAATTTCCGATGTTAAAAAAA
* *
3227191 ATCTTCGTAT
65 ATCAT-GT-C
*
3227201 TTTCAAAAAAATTTCGTG-TTTCAAAA
1 TTTC-AAAAATTTTCGTGTTTTCAAAA
3227227 TCTTCGTGTT
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
72 13 0.15
73 10 0.12
74 50 0.59
75 12 0.14
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (72 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAATACCGTGTTTCAAAAATTTCCGATGTTAAAAAAAA
TCATGTC
Found at i:3227332 original size:35 final size:35
Alignment explanation
Indices: 3227020--3227366 Score: 171
Period size: 35 Copynumber: 9.7 Consensus size: 35
3227010 AATTCCCATG
*** *
3227020 TTTCAAAAATCTT-CGTGTTTC-AAAATTCTAGTG-
1 TTTCAAAAAT-TTCCGTGTTTCAAAAAAAATCGTGT
* *
3227053 TTTCAAAAATTTTCTTGTTTTCAGAAAAAAATTTCGTGT
1 TTTCAAAAATTTCCGTG-TTTCA-AAAAAAA--TCGTGT
* * *
3227092 TTT-ATAAATTTCCGTATTTTC-AAAAAAATCATGT
1 TTTCAAAAATTTCCGT-GTTTCAAAAAAAATCGTGT
* *
3227126 CTTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCT-T
1 -TTTCAAAAATTTCCGTG-TTTCAAAAAAAAT--CGTGT
*
3227164 GTTTCAAAAATTTCCGTG-TT-AAAAAAAATCTTCGTAT
1 -TTTCAAAAATTTCCGTGTTTCAAAAAAAA---TCGTGT
***
3227201 TTTCAAAAAAATTT-CGTGTTTC-AAAATCTTCGTGT
1 TTTC--AAAAATTTCCGTGTTTCAAAAAAAATCGTGT
* * * ***
3227236 TTTCAAAAATTTCGGTGTTTTAAAGATTTTCGTGT
1 TTTCAAAAATTTCCGTGTTTCAAAAAAAATCGTGT
* *
3227271 TTTCAAAAA-CTCCGGTGATTTTAAAAAAAATCGT-T
1 TTTCAAAAATTTCC-GTG-TTTCAAAAAAAATCGTGT
* ***
3227306 TTCTAAAAAATTTCCGTGTTTCAAAAATTTTCGTGT
1 TT-TCAAAAATTTCCGTGTTTCAAAAAAAATCGTGT
* *
3227342 TTT-AAAAATTTTCGTGTTTTAAAAA
1 TTTCAAAAATTTCCGTGTTTCAAAAA
3227367 TTCTCGTATT
Statistics
Matches: 246, Mismatches: 39, Indels: 57
0.72 0.11 0.17
Matches are distributed among these distances:
32 2 0.01
33 21 0.09
34 37 0.15
35 59 0.24
36 57 0.23
37 16 0.07
38 49 0.20
39 5 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (35 bp):
TTTCAAAAATTTCCGTGTTTCAAAAAAAATCGTGT
Found at i:3227527 original size:20 final size:20
Alignment explanation
Indices: 3227504--3227542 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3227494 AATTCTCGTG
3227504 TTTTTAAAAAAAAACTTTCA
1 TTTTTAAAAAAAAACTTTCA
* *
3227524 TTTTTTAAAAAAAATTTTC
1 TTTTTAAAAAAAAACTTTC
3227543 GTGCTTCAAA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTTAAAAAAAAACTTTCA
Found at i:3227553 original size:17 final size:17
Alignment explanation
Indices: 3227533--3227570 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3227523 ATTTTTTAAA
*
3227533 AAAAATTTTCGTG-CTT
1 AAAAATTCTCGTGTCTT
*
3227549 CAAAATTCTCGTGTCTT
1 AAAAATTCTCGTGTCTT
3227566 AAAAA
1 AAAAA
3227571 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (17 bp):
AAAAATTCTCGTGTCTT
Found at i:3235272 original size:19 final size:20
Alignment explanation
Indices: 3235258--3235301 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3235248 CAAACATGTG
3235258 CATAT-CATGATAACATATA
1 CATATACATGATAACATATA
*
3235277 CATATATATGATAACATCATA
1 CATATACATGATAACAT-ATA
3235298 CATA
1 CATA
3235302 GCATATACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (20 bp):
CATATACATGATAACATATA
Found at i:3235289 original size:20 final size:22
Alignment explanation
Indices: 3235259--3235301 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3235249 AAACATGTGC
3235259 ATATCATGATAACAT-ATACAT
1 ATATCATGATAACATCATACAT
3235280 ATAT-ATGATAACATCATACAT
1 ATATCATGATAACATCATACAT
3235301 A
1 A
3235302 GCATATACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (22 bp):
ATATCATGATAACATCATACAT
Found at i:3235599 original size:69 final size:67
Alignment explanation
Indices: 3235428--3235599 Score: 220
Period size: 67 Copynumber: 2.5 Consensus size: 67
3235418 GCTTTCAAGG
* *
3235428 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTAATTTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTAATTTTTT
3235493 TT
66 TT
* ** * *
3235495 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTA-TTTTAATTT-T
3235560 GTTTT
64 -TTTT
** *
3235565 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
3235600 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
67 47 0.52
68 8 0.09
69 32 0.35
70 4 0.04
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (67 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTAATTTTTT
TT
Found at i:3235824 original size:52 final size:51
Alignment explanation
Indices: 3235747--3235844 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 51
3235737 GAGGTATTTT
**
3235747 TTTTTGTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAAGCCTTTTAA
1 TTTTTGTTTTAAAATCAACTCATATTGCGAGAAATGAGTTG-AGCCTTTTAA
3235799 TTTTTGTTTTCAAAAT-AACTCATATTGCGAGAAATGAGTTGAGCCT
1 TTTTTGTTTT-AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
3235845 CAAGACACGT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 5 0.12
52 33 0.77
53 5 0.12
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (51 bp):
TTTTTGTTTTAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTTTAA
Found at i:3236237 original size:121 final size:116
Alignment explanation
Indices: 3236069--3236314 Score: 352
Period size: 121 Copynumber: 2.1 Consensus size: 116
3236059 AACTACAGAT
3236069 TTGAGC-CGGGCAGCCGAGTATTTTAGTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTA
1 TTGAGCTCGGGCAGCCGAGTATTTTAGTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTA
*** *
3236133 AGCCTTTTAATTTTTGTTTTTTTCAAAATC-ACTCATATTGCGAGAAATGAG
66 AGCCTTTT-ATTTTTGTTTTTCAAAAAATCAACTCATATTGCAAGAAATGAG
*
3236184 TTGAGGCTCGGGCACGCCGAGGTATTTTTAGTTTTGTTTTAAATTGACTCATATTGCGAGAGGTG
1 TTGA-GCTCGGGCA-GCCGA-GTA-TTTTAG-TATGTTTTAAATTGACTCATATTGCGAGAGGTG
**
3236249 AGTTAAGCCTTTTATTTTTGTTTTTCAAAAAATCAAACTCATATTGCAAGAGGTGAG
61 AGTTAAGCCTTTTATTTTTGTTTTTCAAAAAATC-AACTCATATTGCAAGAAATGAG
3236306 TTGAGCTCG
1 TTGAGCTCG
3236315 CTCACATGCT
Statistics
Matches: 116, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
115 4 0.03
116 2 0.02
117 6 0.05
118 5 0.04
119 3 0.03
120 24 0.21
121 50 0.43
122 22 0.19
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (116 bp):
TTGAGCTCGGGCAGCCGAGTATTTTAGTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTA
AGCCTTTTATTTTTGTTTTTCAAAAAATCAACTCATATTGCAAGAAATGAG
Found at i:3236539 original size:87 final size:85
Alignment explanation
Indices: 3236277--3236539 Score: 268
Period size: 90 Copynumber: 3.0 Consensus size: 85
3236267 TGTTTTTCAA
*
3236277 AAAATCAAACTCATATTGCAAGAGGTGAGTTGAGCTC-GCTCACATGCTGAGGTATTTTCAATTT
1 AAAATC-AACTCATATTGCAAGAGGTGAGTTGAGCTCAGC-CACACGCTGAGGTATTTTCAATTT
* * *
3236341 ATGTTTTTTTCAATCCTATGCTTTTC
64 CTG-TTTTAT-AATTCTAT--TTTTC
* *
3236367 AAAATCAACTCTATATTGCGAGAGGTGAGTTGAGCCTCAAG--GCACGCTGAGGTATTTTCAATT
1 AAAATCAACTC-ATATTGCAAGAGGTGAGTTGAG-CTC-AGCCACACGCTGAGGTATTTTCAATT
*
3236430 TCTGCTTTACT-ATTCTACTTTTTC
63 TCTGTTTTA-TAATTCTA-TTTTTC
* *
3236454 -AAATCAATCTCATATTGCAAGAGGATGAGTTGAGTCTCAGCCACACGCTGAGGT-CTTTCAAAT
1 AAAATCAA-CTCATATTGCAAGAGG-TGAGTTGAG-CTCAGCCACACGCTGAGGTATTTTCAATT
3236517 TCTGTTTTATAATTTCTATTTTT
63 TCTGTTTTATAA-TTCTATTTTT
3236540 TAATTCTGTG
Statistics
Matches: 148, Mismatches: 13, Indels: 27
0.79 0.07 0.14
Matches are distributed among these distances:
86 22 0.15
87 41 0.28
88 21 0.14
89 9 0.06
90 51 0.34
91 3 0.02
93 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (85 bp):
AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCTCAGCCACACGCTGAGGTATTTTCAATTTCT
GTTTTATAATTCTATTTTTC
Found at i:3236708 original size:52 final size:54
Alignment explanation
Indices: 3236627--3236834 Score: 249
Period size: 52 Copynumber: 4.0 Consensus size: 54
3236617 TCAATTTCTA
*
3236627 CTTTTCAATTTCTGTTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCT-ATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
3236681 CTTTT-AATTTCTATTTTC-AAAACCAACTCATATTGCGAGAGGTGAG-TGAGC
1 CTTTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
3236732 C--TT---TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTA-TTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
3236783 CTTTTGCCAAATTCTGTTTTCAAAAATCAACTCATA-T-CGAGAAGTGAGTTGA
1 CTTTT--CAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
3236835 CTTGGCTCAC
Statistics
Matches: 137, Mismatches: 6, Indels: 22
0.83 0.04 0.13
Matches are distributed among these distances:
47 6 0.04
48 5 0.04
49 2 0.01
50 27 0.20
51 12 0.09
52 32 0.23
53 9 0.07
54 19 0.14
55 1 0.01
56 15 0.11
57 5 0.04
58 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (54 bp):
CTTTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:3237154 original size:29 final size:29
Alignment explanation
Indices: 3237109--3237164 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
3237099 TTGACCCCTA
* *
3237109 AAACTTTCCTAAATTCA-TTTGACCCTGT
1 AAACTTTACTAAATTCACTTAGACCCTGT
*
3237137 AAACTTTATTAAATTTCACTTAGACCCT
1 AAACTTTACTAAA-TTCACTTAGACCCT
3237165 AACTTCATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 11 0.48
29 4 0.17
30 8 0.35
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.39
Consensus pattern (29 bp):
AAACTTTACTAAATTCACTTAGACCCTGT
Found at i:3237586 original size:3 final size:3
Alignment explanation
Indices: 3237578--3237623 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
3237568 GCTAGACTTT
*
3237578 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
3237624 AGAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3237596 original size:10 final size:10
Alignment explanation
Indices: 3237581--3237609 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3237571 AGACTTTGAA
3237581 GAAGAAGAAG
1 GAAGAAGAAG
3237591 GAAGAAGAAG
1 GAAGAAGAAG
3237601 GAAGAAGAA
1 GAAGAAGAA
3237610 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:3237596 original size:13 final size:13
Alignment explanation
Indices: 3237578--3237623 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
3237568 GCTAGACTTT
3237578 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
3237591 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
3237604 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
3237615 GAAGAAGAA
1 GAAGAAGAA
3237624 AGAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:3237621 original size:24 final size:24
Alignment explanation
Indices: 3237578--3237637 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3237568 GCTAGACTTT
* *
3237578 GAAGAAGAAGA-AGGAAGAAGAAG
1 GAAGAAGAAAAGAGGAAGAAGAAA
3237601 GAAGAAGAAAAGAGGAAGAAGAAA
1 GAAGAAGAAAAGAGGAAGAAGAAA
* *
3237625 GAAAAAAAAAAGA
1 GAAGAAGAAAAGA
3237638 AAAATCCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (24 bp):
GAAGAAGAAAAGAGGAAGAAGAAA
Found at i:3237749 original size:11 final size:11
Alignment explanation
Indices: 3237719--3237749 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3237709 GCAGCCCAAG
3237719 AAAAAAAAACA
1 AAAAAAAAACA
*
3237730 AAATAAAAACA
1 AAAAAAAAACA
3237741 AAAAAAAAA
1 AAAAAAAAA
3237750 AACAAGCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.06, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:3237906 original size:6 final size:6
Alignment explanation
Indices: 3237895--3237956 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
3237885 CAGCAGAGAA
* * **
3237895 AAAAAG AAAAAG AAAAAG ---AAG AAAAAG AGAAGG AAAAAG AAGGA-
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
3237939 AAAAAG AAAAAAG AAAAA
1 AAAAAG -AAAAAG AAAAA
3237957 AGAGGTTCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
3 3 0.07
5 3 0.07
6 31 0.72
7 6 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3237911 original size:7 final size:7
Alignment explanation
Indices: 3237894--3237959 Score: 55
Period size: 7 Copynumber: 9.1 Consensus size: 7
3237884 CCAGCAGAGA
3237894 AAAAAAG
1 AAAAAAG
3237901 -AAAAAG
1 AAAAAAG
3237907 AAAAAGAAG
1 -AAAA-AAG
3237916 AAAAAGAG
1 AAAAA-AG
*
3237924 AAGGAAA-
1 AA-AAAAG
* *
3237931 AAGAAGG
1 AAAAAAG
3237938 AAAAAAG
1 AAAAAAG
3237945 AAAAAAG
1 AAAAAAG
3237952 AAAAAAG
1 AAAAAAG
3237959 A
1 A
3237960 GGTTCAATTC
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
6 9 0.18
7 23 0.47
8 12 0.24
9 5 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3237921 original size:21 final size:21
Alignment explanation
Indices: 3237891--3237956 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 21
3237881 GGCCCAGCAG
3237891 AGAA-AAAAAGAAAAAGAAAA
1 AGAAGAAAAAGAAAAAGAAAA
* *
3237911 AGAAGAAAAAGAGAAGGAAAA
1 AGAAGAAAAAGAAAAAGAAAA
3237932 AGAAGGAAAAAAGAAAAAAGAAAA
1 AGAA-G-AAAAAG-AAAAAGAAAA
3237956 A
1 A
3237957 AGAGGTTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.11
21 18 0.47
22 1 0.03
23 6 0.16
24 9 0.24
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAGAAAAAGAAAA
Found at i:3237935 original size:10 final size:10
Alignment explanation
Indices: 3237906--3237942 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
3237896 AAAAGAAAAA
3237906 GAAAAAGAAG
1 GAAAAAGAAG
*
3237916 AAAAAGAGAAG
1 GAAAA-AGAAG
3237927 GAAAAAGAAG
1 GAAAAAGAAG
3237937 GAAAAA
1 GAAAAA
3237943 AGAAAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
GAAAAAGAAG
Found at i:3238485 original size:18 final size:18
Alignment explanation
Indices: 3238464--3238530 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
3238454 AAAATTTTTC
3238464 GTGTTTTCAAAAATTCCT
1 GTGTTTTCAAAAATTCCT
* *
3238482 GTG-TTGCAAAAATTTTCAT
1 GTGTTTTCAAAAA--TTCCT
3238501 GT-TTTTCAAAAATT-CT
1 GTGTTTTCAAAAATTCCT
3238517 CGTGTTTTCAAAAA
1 -GTGTTTTCAAAAA
3238531 AAATTCCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 12 0.30
18 13 0.32
19 14 0.35
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.43
Consensus pattern (18 bp):
GTGTTTTCAAAAATTCCT
Found at i:3238561 original size:18 final size:18
Alignment explanation
Indices: 3238454--3238704 Score: 166
Period size: 17 Copynumber: 14.3 Consensus size: 18
3238444 TAAAAATCGG
*
3238454 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
3238472 AAAAA--TTCCTGTGTTGC
1 AAAAATTTTCGTGT-TTTC
*
3238489 AAAAATTTTCATGTTTTTC
1 AAAAATTTTCGTG-TTTTC
*
3238508 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** ***
3238526 AAAAAAAATTCCAATTTTC
1 -AAAAATTTTCGTGTTTTC
*
3238545 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
3238563 TAAAAA-CTTC-TGTGTTTC
1 -AAAAATTTTCGTGT-TTTC
3238581 AAAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
3238598 TAAAATTTTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
*
3238615 AAAAATTTTCTTGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
3238633 -AAATTTTTCGT-ATTTA
1 AAAAATTTTCGTGTTTTC
**
3238649 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
3238667 -AAAA-TTCCAGTG-TTTC
1 AAAAATTTTC-GTGTTTTC
*
3238683 AAAATTTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
3238700 AAAAA
1 AAAAA
3238705 AAAATTCCCG
Statistics
Matches: 176, Mismatches: 41, Indels: 33
0.70 0.16 0.13
Matches are distributed among these distances:
16 14 0.08
17 83 0.47
18 41 0.23
19 37 0.21
20 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:3252659 original size:67 final size:68
Alignment explanation
Indices: 3252555--3252710 Score: 181
Period size: 67 Copynumber: 2.3 Consensus size: 68
3252545 GAGATGATAG
** * * * * *
3252555 ACGACGTCGAGACGAGCAAGGTGTAGTGCGTCAAGATGACGCAACGTCCTTGGCAACGAAGTAAG
1 ACGACGTCGAGACGAGCAAGGTGTAGCACGTCAAGATGACACAACATCCTTAGCAACCAAGCAAG
3252620 GCT
66 GCT
* * **
3252623 ACGATGTCGAGACGAGC-AGGTGTAGCACGTCGAGATGACATGACATCCTTAGCAACCAAGCAAG
1 ACGACGTCGAGACGAGCAAGGTGTAGCACGTCAAGATGACACAACATCCTTAGCAACCAAGCAAG
3252687 GCT
66 GCT
* *
3252690 ACGACATCGTGACGAG-AAGGT
1 ACGACGTCGAGACGAGCAAGGT
3252711 ATGCCACATC
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
67 57 0.78
68 16 0.22
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (68 bp):
ACGACGTCGAGACGAGCAAGGTGTAGCACGTCAAGATGACACAACATCCTTAGCAACCAAGCAAG
GCT
Found at i:3255380 original size:18 final size:20
Alignment explanation
Indices: 3255354--3255393 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
3255344 TTTAATTAAA
3255354 ATAATAAAAATA-ATTAATT
1 ATAATAAAAATATATTAATT
*
3255373 AT-A-AAAAATATTTTAATT
1 ATAATAAAAATATATTAATT
3255391 ATA
1 ATA
3255394 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
17 7 0.39
18 9 0.50
19 2 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATAAAAATATATTAATT
Found at i:3255381 original size:17 final size:18
Alignment explanation
Indices: 3255359--3255393 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3255349 TTAAAATAAT
3255359 AAAAATA-ATTAATTATA
1 AAAAATATATTAATTATA
*
3255376 AAAAATATTTTAATTATA
1 AAAAATATATTAATTATA
3255394 TTTTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATATATTAATTATA
Found at i:3255404 original size:12 final size:12
Alignment explanation
Indices: 3255380--3255430 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3255370 ATTATAAAAA
3255380 ATATTTT-AATT
1 ATATTTTAAATT
3255391 ATATTTTAAATT
1 ATATTTTAAATT
** *
3255403 ATAAATTATATT
1 ATATTTTAAATT
3255415 ATATTCTTAATATT
1 ATATT-TTAA-ATT
3255429 AT
1 AT
3255431 GTGCTAAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
11 7 0.23
12 16 0.52
13 3 0.10
14 5 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATTTTAAATT
Found at i:3261143 original size:31 final size:32
Alignment explanation
Indices: 3261080--3261146 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
3261070 ACTTAATAGC
* * *
3261080 CAATGACTTAAACAAAATTTTTTTGAATAATT
1 CAATGACTTAAACAAAATATTTCTAAATAATT
*
3261112 CAATGACTTAAATAAAA-ATTTCTAAATAATT
1 CAATGACTTAAACAAAATATTTCTAAATAATT
3261143 CAAT
1 CAAT
3261147 AATAGTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.37
Consensus pattern (32 bp):
CAATGACTTAAACAAAATATTTCTAAATAATT
Found at i:3263138 original size:16 final size:16
Alignment explanation
Indices: 3263117--3263150 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3263107 TTATAATCAT
3263117 AATTAATATATT-AATA
1 AATTAAT-TATTGAATA
3263133 AATTAATTATTGAATA
1 AATTAATTATTGAATA
3263149 AA
1 AA
3263151 ATATAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTAATTATTGAATA
Found at i:3263739 original size:23 final size:24
Alignment explanation
Indices: 3263696--3263740 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3263686 AAATTTAAAA
3263696 AAATTAAATATAAAAAATATATAT
1 AAATTAAATATAAAAAATATATAT
3263720 AAATT-AAT-TAAAAAAGTATAT
1 AAATTAAATATAAAAAA-TATAT
3263741 TTTTTTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATTAAATATAAAAAATATATAT
Found at i:3270353 original size:17 final size:17
Alignment explanation
Indices: 3270320--3270357 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3270310 TTGTTTTTTT
3270320 ATTAAAAAATAACATTA
1 ATTAAAAAATAACATTA
*
3270337 GATTAAAAAGTAA-ATTA
1 -ATTAAAAAATAACATTA
3270354 ATTA
1 ATTA
3270358 TTTTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 4 0.21
18 11 0.58
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (17 bp):
ATTAAAAAATAACATTA
Found at i:3284633 original size:8 final size:8
Alignment explanation
Indices: 3284620--3284672 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
3284610 CGGCCAGCAG
3284620 AAAAAAGA
1 AAAAAAGA
3284628 AAAAAAG-
1 AAAAAAGA
*
3284635 AAAAGAGA
1 AAAAAAGA
*
3284643 GAAAAAGA
1 AAAAAAGA
*
3284651 AAAAAGAAA
1 AAAAA-AGA
3284660 AAAAAAGA
1 AAAAAAGA
3284668 AAAAA
1 AAAAA
3284673 GAGGTTCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
7 6 0.16
8 24 0.65
9 7 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:3284638 original size:15 final size:15
Alignment explanation
Indices: 3284618--3284674 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
3284608 AACGGCCAGC
3284618 AGAAAAAAGAAAAAA
1 AGAAAAAAGAAAAAA
* *
3284633 AGAAAAGAGAGAAAA
1 AGAAAAAAGAAAAAA
3284648 AGAAAAAAGAAAAAAAA
1 AGAAAAAAG--AAAAAA
3284665 AGAAAAAAGA
1 AGAAAAAAGA
3284675 GGTTCAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 22 0.61
17 14 0.39
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAAAAAAGAAAAAA
Found at i:3284647 original size:17 final size:17
Alignment explanation
Indices: 3284625--3284675 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
3284615 AGCAGAAAAA
3284625 AGAAAAAAAGAAAAGAG
1 AGAAAAAAAGAAAAGAG
3284642 AGAAAAAGAA-AAAAGA-
1 AGAAAAA-AAGAAAAGAG
*
3284658 A-AAAAAAAGAAAAAAG
1 AGAAAAAAAGAAAAGAG
3284674 AG
1 AG
3284676 GTTCAATTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 2 0.07
17 13 0.45
18 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAGAAAAGAG
Found at i:3284661 original size:23 final size:23
Alignment explanation
Indices: 3284621--3284671 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
3284611 GGCCAGCAGA
* *
3284621 AAAAAGAAAAAAAGAAAAGAGAG
1 AAAAAGAAAAAAAGAAAAAAAAG
3284644 AAAAAG-AAAAAAGAAAAAAAAAG
1 AAAAAGAAAAAAAG-AAAAAAAAG
3284667 AAAAA
1 AAAAA
3284672 AGAGGTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAAAGAAAAAAAAG
Found at i:3284674 original size:7 final size:7
Alignment explanation
Indices: 3284618--3284662 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
3284608 AACGGCCAGC
3284618 AGAAAAA
1 AGAAAAA
3284625 AGAAAAAA
1 AG-AAAAA
*
3284633 AGAAAAG
1 AGAAAAA
3284640 AGAGAAAA
1 AGA-AAAA
3284648 AGAAAAA
1 AGAAAAA
3284655 AGAAAAA
1 AGAAAAA
3284662 A
1 A
3284663 AAAGAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 21 0.62
8 13 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:3284840 original size:16 final size:17
Alignment explanation
Indices: 3284814--3284851 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3284804 TTATATTTAT
3284814 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
3284831 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
3284847 ATTTT
1 ATTTT
3284852 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:3285066 original size:16 final size:16
Alignment explanation
Indices: 3285015--3285068 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
3285005 CGTGCTTTTA
3285015 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
3285031 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
3285049 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
3285065 AAAA
1 AAAA
3285069 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:3285079 original size:17 final size:17
Alignment explanation
Indices: 3284992--3285512 Score: 129
Period size: 17 Copynumber: 30.2 Consensus size: 17
3284982 AAAATTGTAA
* *
3284992 TTTCAATAATCCTCGTG
1 TTTCAAAAATTCTCGTG
* *
3285009 CTTTTAAAAATTCTCATG
1 -TTTCAAAAATTCTCGTG
3285027 TTTCAAAAA-TCTTCGTG
1 TTTCAAAAATTC-TCGTG
*
3285044 TTTTC-AAAATTCTAGTG
1 -TTTCAAAAATTCTCGTG
* *
3285061 TTTCAAAAATTTTCTTG
1 TTTCAAAAATTCTCGTG
*
3285078 TTTTCAGAAAAAATTTTCGTG
1 -TTTC---AAAAATTCTCGTG
* * *
3285099 TTTTATAAATT-TCCGTAT
1 TTTCAAAAATTCT-CGT-G
* *
3285117 TTTCAAAAAATCAT-GTC
1 TTTCAAAAATTC-TCGTG
*
3285134 TTTC-AAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
*
3285150 TTTTCAAAAAAAATGAC-CGTG
1 -TTTC---AAAAAT-TCTCGTG
3285171 TTTCAAAAATT-TCCGTG
1 TTTCAAAAATTCT-CGTG
** * *
3285188 TTAAAAAAAAATCTTCGTAT
1 TT-TCAAAAATTC-TCGT-G
*
3285208 TTTCAAAAAAAAT-TCGTG
1 TTTC--AAAAATTCTCGTG
3285226 TTTC-AAAA-TCTTCGTG
1 TTTCAAAAATTC-TCGTG
3285242 TTTTC-AAAATT-TCGGTG
1 -TTTCAAAAATTCTC-GTG
* * *
3285259 TTTTAAAGATTTTCGTG
1 TTTCAAAAATTCTCGTG
*
3285276 TTTTCAAAAACTC-CGGTG
1 -TTTCAAAAATTCTC-GTG
* ***
3285294 ATTTAAAAAAAAATCGT-
1 -TTTCAAAAATTCTCGTG
3285311 TTTCTAAAAAATT-TCCGTG
1 TTTC--AAAAATTCT-CGTG
** *
3285330 TTTTGAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
* *
3285347 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
* *
3285364 TTTTAAAAATTCTCGTA
1 TTTCAAAAATTCTCGTG
*
3285381 TTT--TAAATT-T--T-
1 TTTCAAAAATTCTCGTG
* *
3285392 TTTAAGAAAAAAT-T-GTG
1 TTT--CAAAAATTCTCGTG
* * *
3285409 TTTCAAAAAATGTCTTG
1 TTTCAAAAATTCTCGTG
*
3285426 TTTTAAAAATTCTCGTG
1 TTTCAAAAATTCTCGTG
* *
3285443 TTTCAAAAAATGTCGTG
1 TTTCAAAAATTCTCGTG
* *
3285460 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
***
3285477 TTTTTGAAATT-TCCGTG
1 TTTCAAAAATTCT-CGTG
3285494 TTT-AAAAATTCTCGTG
1 TTTCAAAAATTCTCGTG
3285510 TTT
1 TTT
3285513 TTAAAAAAAA
Statistics
Matches: 382, Mismatches: 69, Indels: 106
0.69 0.12 0.19
Matches are distributed among these distances:
11 3 0.01
12 1 0.00
14 2 0.01
15 22 0.06
16 42 0.11
17 186 0.49
18 76 0.20
19 11 0.03
20 11 0.03
21 28 0.07
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:3285120 original size:72 final size:72
Alignment explanation
Indices: 3285025--3285186 Score: 186
Period size: 72 Copynumber: 2.2 Consensus size: 72
3285015 AAAATTCTCA
* * * * *
3285025 TGTTTCAAAAATCTT-CGTGTTTTC-AAAATTC-TAGTGTTTCAAAAATTTTCTTGTTTTCAGAA
1 TGTTTCAAAAAT-TTCCGTATTTTCAAAAAATCAT-GTCTTTC-AAAATTTTCGTGTTTTCAAAA
***
3285087 AAAATTTTCG
63 AAAATGACCG
* *
3285097 TGTTTTATAAATTTCCGTATTTTCAAAAAATCATGTCTTTCAAAATTTTCGTGTTTTCAAAAAAA
1 TGTTTCAAAAATTTCCGTATTTTCAAAAAATCATGTCTTTCAAAATTTTCGTGTTTTCAAAAAAA
3285162 ATGACCG
66 ATGACCG
3285169 TGTTTCAAAAATTTCCGT
1 TGTTTCAAAAATTTCCGT
3285187 GTTAAAAAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
71 2 0.03
72 60 0.80
73 12 0.16
74 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (72 bp):
TGTTTCAAAAATTTCCGTATTTTCAAAAAATCATGTCTTTCAAAATTTTCGTGTTTTCAAAAAAA
ATGACCG
Found at i:3285278 original size:34 final size:32
Alignment explanation
Indices: 3285214--3285519 Score: 158
Period size: 34 Copynumber: 9.2 Consensus size: 32
3285204 GTATTTTCAA
* * *
3285214 AAAAAATTCGTGTTTCAAAATCTTCGTGTTTT
1 AAAAATTTCGTGTTTTAAAATTTTCGTGTTTT
*
3285246 CAAAATTTCGGTGTTTTAAAGATTTTCGTGTTTT
1 AAAAATTTC-GTGTTTTAAA-ATTTTCGTGTTTT
* * * ***
3285280 CAAAAACTCCGGTGATTTAAAAAAAAATCGT-TTTCT
1 -AAAAATTTC-GTG-TTT-TAAAATTTTCGTGTTT-T
3285316 AAAAAATTTCCGTGTTTTGAAAATTTTCGTGTTTT
1 -AAAAATTT-CGTGTTTT-AAAATTTTCGTGTTTT
* *
3285351 AAAAATTTTCGTGTTTTAAAAATTCTCGTATTTT
1 AAAAA-TTTCGTGTTTT-AAAATTTTCGTGTTTT
* ** *
3285385 --AAATTT--T-TTTAAGAAAAAATT-GTGTTTCA
1 AAAAATTTCGTGTTT--TAAAATTTTCGTGTTT-T
* * * *
3285414 AAAAATGTCTTGTTTTAAAAATTCTCGTGTTTCA
1 AAAAATTTCGTGTTTT-AAAATTTTCGTGTTT-T
*
3285448 AAAAATGTCGTGTTTTAAAAATTTTCGTGTTTT
1 AAAAATTTCGTGTTTT-AAAATTTTCGTGTTTT
** * *
3285481 TGAAATTTCCGTGTTTAAAAATTCTCGTGTTTTT
1 AAAAATTT-CGTGTTTTAAAATTTTCGTG-TTTT
3285515 AAAAA
1 AAAAA
3285520 AAAACTTTCA
Statistics
Matches: 210, Mismatches: 42, Indels: 42
0.71 0.14 0.14
Matches are distributed among these distances:
28 8 0.04
29 6 0.03
31 8 0.04
32 10 0.05
33 31 0.15
34 94 0.45
35 28 0.13
36 21 0.10
37 4 0.02
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.45
Consensus pattern (32 bp):
AAAAATTTCGTGTTTTAAAATTTTCGTGTTTT
Found at i:3285468 original size:51 final size:49
Alignment explanation
Indices: 3285157--3285520 Score: 151
Period size: 51 Copynumber: 7.1 Consensus size: 49
3285147 GTGTTTTCAA
* * * *
3285157 AAAAAATGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAAATCTTCGTATTTT
1 AAAAAATG-TCGTGTTTTAAAAATTTCCGTGTT--TAAAAAA--TTCGTGTTTT
* * *
3285211 CAAAAAAAAT-TCGTG-TTTCAAAATCTT-CGTGTTTTCAAAATTTCGGTGTTTT
1 ---AAAAAATGTCGTGTTTTAAAAAT-TTCCGTG-TTTAAAAAATTC-GTGTTTT
* * * * *
3285263 AAAGATTTTCGTGTTTTCAAAAA-CTCCGGTGATTTAAAAAAAAATCGT-TTTCT
1 AAAAAATGTCGTGTTTT-AAAAATTTCC-GTG-TTT--AAAAAATTCGTGTTT-T
* * * *
3285316 AAAAAATTTCCGTGTTTTGAAAATTTTCGTGTTTTAAAAATTTTCGTGTTTT
1 AAAAAATGT-CGTGTTTTAAAAATTTCCGTG-TTTAAAAA-ATTCGTGTTTT
* * * *
3285368 AAAAATTCTCGTATTTT--AAATTT---T-TTTAAGAAAAAATT-GTGTTTC
1 AAAAAATGTCGTGTTTTAAAAATTTCCGTGTTT---AAAAAATTCGTGTTTT
*
3285413 AAAAAATGTCTTGTTTTAAAAA-TTCTCGTGTTTCAAAAAATGTCGTGTTTT
1 AAAAAATGTCGTGTTTTAAAAATTTC-CGTGTTT-AAAAAAT-TCGTGTTTT
* * ** *
3285464 AAAAATTTTCGTGTTTTTGAAATTTCCGTGTTTAAAAATTCTCGTGTTTTT
1 AAAAAATGTCGTGTTTTAAAAATTTCCGTGTTTAAAAAAT-TCGTG-TTTT
3285515 AAAAAA
1 AAAAAA
3285521 AAACTTTCAT
Statistics
Matches: 236, Mismatches: 42, Indels: 64
0.69 0.12 0.19
Matches are distributed among these distances:
44 3 0.01
45 19 0.08
46 5 0.02
47 8 0.03
49 18 0.08
50 19 0.08
51 61 0.26
52 34 0.14
53 27 0.11
54 27 0.11
55 8 0.03
57 7 0.03
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (49 bp):
AAAAAATGTCGTGTTTTAAAAATTTCCGTGTTTAAAAAATTCGTGTTTT
Found at i:3285533 original size:20 final size:19
Alignment explanation
Indices: 3285510--3285547 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3285500 AATTCTCGTG
3285510 TTTTTAAAAAAAAACTTTCA
1 TTTTTAAAAAAAAA-TTTCA
*
3285530 TTTTTTAAAAAAAATTTC
1 TTTTTAAAAAAAAATTTC
3285548 GTGCTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTTAAAAAAAAATTTCA
Found at i:3285558 original size:16 final size:17
Alignment explanation
Indices: 3285539--3285575 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3285529 ATTTTTTAAA
3285539 AAAAATT-TCGTG-CTT
1 AAAAATTCTCGTGTCTT
*
3285554 CAAAATTCTCGTGTCTT
1 AAAAATTCTCGTGTCTT
3285571 AAAAA
1 AAAAA
3285576 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (17 bp):
AAAAATTCTCGTGTCTT
Found at i:3287297 original size:17 final size:17
Alignment explanation
Indices: 3287275--3287308 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3287265 GTGAAAACTT
3287275 TTTCAAGAAAAAATCAC
1 TTTCAAGAAAAAATCAC
3287292 TTTCAAGAAAAAATCAC
1 TTTCAAGAAAAAATCAC
3287309 GGGCAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.24
Consensus pattern (17 bp):
TTTCAAGAAAAAATCAC
Found at i:3290815 original size:17 final size:16
Alignment explanation
Indices: 3290780--3290822 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3290770 ATTGACTGAT
*
3290780 TAATTTAAATTCGAAA
1 TAATTTAAATTCAAAA
*
3290796 TAATTTATACTTCAAAA
1 TAATTTA-AATTCAAAA
*
3290813 TAATTCAAAT
1 TAATTTAAAT
3290823 AAATAATTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (16 bp):
TAATTTAAATTCAAAA
Found at i:3293240 original size:13 final size:13
Alignment explanation
Indices: 3293224--3293248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3293214 AAAAAAAGAA
3293224 AAAAAACACACAC
1 AAAAAACACACAC
3293237 AAAAAACACACA
1 AAAAAACACACA
3293249 TATTGTATAC
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:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACACACAC
Found at i:3294775 original size:2 final size:2
Alignment explanation
Indices: 3294770--3294795 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3294760 TAAAAGCCTA
3294770 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3294796 TAAATATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3294867 original size:12 final size:12
Alignment explanation
Indices: 3294850--3294887 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3294840 TATAGAAAAT
3294850 ATGATAATAATA
1 ATGATAATAATA
*
3294862 ATGATAGTAAATA
1 ATGATAAT-AATA
3294875 ATG-TAATAATA
1 ATGATAATAATA
3294886 AT
1 AT
3294888 AGTAATGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 6 0.26
12 10 0.43
13 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:3294873 original size:24 final size:24
Alignment explanation
Indices: 3294841--3294887 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3294831 ATGTATATGT
3294841 ATAGAAAAT-ATGATAATAATAATG
1 ATAGAAAATAATG-TAATAATAATG
*
3294865 ATAGTAAATAATGTAATAATAAT
1 ATAGAAAATAATGTAATAATAAT
3294888 AGTAATGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (24 bp):
ATAGAAAATAATGTAATAATAATG
Found at i:3296519 original size:89 final size:89
Alignment explanation
Indices: 3296391--3296974 Score: 631
Period size: 89 Copynumber: 6.6 Consensus size: 89
3296381 ATAAGACTTG
* * * * *
3296391 TATCTTCGATCTACTT--CGCCACCTATATGGGAAGACAAGATCTACTATCTTTGATCTACTTCA
1 TATCTTCGATCTACTTCACGCCA-ATACAT--GAAGACAAGATCTGCTATCTTCGATCTACTTCG
** *
3296454 CTGCCAATACAGGAAGACAAGATCTGC
63 CCACCAATATAGGAAGACAAGATCTGC
* * *
3296481 TATCTTCGATCTACTTTACGCCAATACATGAAGACAAGATCTTCTTTCTTCGATCTACTTCGCCA
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCA
* * *
3296546 CCAGTATGGGAAGACAAGATTTGC
66 CCAATATAGGAAGACAAGATCTGC
* * * * * * * * *
3296570 -ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTTGATCTACTTCACG
1 TATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCC
* * *
3296634 A-CAATACATGAAGACAAGATTTGC
65 ACCAATATAGGAAGACAAGATCTGC
* * * *** *
3296658 TTTCTTCGATCTACTTTGC-CACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGC
1 TATCTTCGATCTAC-TT-CACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGC
* *
3296721 TACCAATATAGGAAGACATGATCTGC
64 CACCAATATAGGAAGACAAGATCTGC
* *
3296747 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCATCGATCTACTTCGCCA
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCA
* *
3296812 CCAGTATGGGAAGACAAGATCTGC
66 CCAATATAGGAAGACAAGATCTGC
* * *
3296836 TATCTTTGATCTACTTCACGCCAATACATGAAGATAAGATTTGCTATCTTCGATCTACTTCGCCA
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCA
* * *
3296901 CCAGTATGGGAAGACAATATCTGC
66 CCAATATAGGAAGACAAGATCTGC
* * * *
3296925 TTTCTTCGATCTACTTCACGCCAATACGTGAAGACAATATCTGCTTTCTT
1 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTT
3296975 TCAACCTGCC
Statistics
Matches: 418, Mismatches: 67, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
87 1 0.00
88 73 0.17
89 315 0.75
90 19 0.05
91 5 0.01
92 5 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (89 bp):
TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCA
CCAATATAGGAAGACAAGATCTGC
Found at i:3296639 original size:133 final size:134
Alignment explanation
Indices: 3296393--3296941 Score: 764
Period size: 133 Copynumber: 4.1 Consensus size: 134
3296383 AAGACTTGTA
* * * *
3296393 TCTTCGATCTACTTCGCCACCTA-TATGGGAAGACAAGATCTACTATCTTTGATCTACTTCACTG
1 TCTTCGATCTACTTCGCCACC-AGTATGGGAAGACAAGATCTGCTATCTTCGATCCACTTCACTA
* *
3296457 CCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTTACGCCAATACATGAAGACAAGATC
65 CCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGACAATACATGAAGACAAGATC
*
3296522 TTCTT
130 TGCTT
* *
3296527 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATTTGC-ATCTTCGATCCACTTCGCTAC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCCACTTCACTAC
* * * *
3296591 CAATATAGGAAGACAGGATCTGCTATCTTTGATCTACTTCACGACAATACATGAAGACAAGATTT
66 CAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGACAATACATGAAGACAAGATCT
3296656 GCTT
131 GCTT
* *
3296660 TCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTAC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCCACTTCACTAC
* * *
3296724 CAATATAGGAAGACATGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
66 CAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGACAATACATGAAGACAAGATCT
3296789 GCTT
131 GCTT
* * * *
3296793 TCATCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCAC-GC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCCACTTCACTAC
* * * * * * *** *
3296857 CAATACATGAAGATAAGATTTGCTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATC
66 CAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGA-CAATACATGAAGACAAGATC
3296922 TGCTT
130 TGCTT
3296927 TCTTCGATCTACTTC
1 TCTTCGATCTACTTC
3296942 ACGCCAATAC
Statistics
Matches: 373, Mismatches: 39, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
133 285 0.76
134 88 0.24
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (134 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCCACTTCACTAC
CAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGACAATACATGAAGACAAGATCT
GCTT
Found at i:3298158 original size:14 final size:14
Alignment explanation
Indices: 3298130--3298177 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
3298120 AGCCTCTCCA
3298130 TTTT-ACTTTTCCAT
1 TTTTCACTTTT-CAT
*
3298144 TTTTCAGTTTTCA-
1 TTTTCACTTTTCAT
3298157 TTTTCACTATTTCAT
1 TTTTCACT-TTTCAT
3298172 TTTTCA
1 TTTTCA
3298178 TCTCATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 7 0.24
14 11 0.38
15 11 0.38
ACGTcount: A:0.17, C:0.19, G:0.02, T:0.62
Consensus pattern (14 bp):
TTTTCACTTTTCAT
Found at i:3301045 original size:19 final size:20
Alignment explanation
Indices: 3301021--3301067 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3301011 TAGCGGTGTT
* *
3301021 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
3301040 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
3301060 -AATGCAAA
1 TAATGCAAA
3301068 AAGAGACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:3302905 original size:24 final size:25
Alignment explanation
Indices: 3302848--3302907 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
3302838 ATATATATAT
* *
3302848 AAAATATAAAGTATATAAAAGTGAA
1 AAAATATAAAATATATAAAAGAGAA
*
3302873 AAAAAATAAAATA-ATAAAAGAGAA
1 AAAATATAAAATATATAAAAGAGAA
* *
3302897 CATATATAAAA
1 AAAATATAAAA
3302908 ACGTATGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 18 0.62
25 11 0.38
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (25 bp):
AAAATATAAAATATATAAAAGAGAA
Found at i:3303087 original size:12 final size:12
Alignment explanation
Indices: 3303070--3303107 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3303060 TATAGAAAAT
3303070 ATGATAATAATA
1 ATGATAATAATA
*
3303082 ATGATAGTAAATA
1 ATGATAAT-AATA
3303095 ATG-TAATAATA
1 ATGATAATAATA
3303106 AT
1 AT
3303108 AGTAATGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 6 0.26
12 10 0.43
13 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:3303093 original size:24 final size:24
Alignment explanation
Indices: 3303061--3303107 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3303051 ATGTATATGT
3303061 ATAGAAAAT-ATGATAATAATAATG
1 ATAGAAAATAATG-TAATAATAATG
*
3303085 ATAGTAAATAATGTAATAATAAT
1 ATAGAAAATAATGTAATAATAAT
3303108 AGTAATGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (24 bp):
ATAGAAAATAATGTAATAATAATG
Found at i:3310796 original size:44 final size:45
Alignment explanation
Indices: 3310748--3311064 Score: 147
Period size: 44 Copynumber: 7.2 Consensus size: 45
3310738 AAGATAGCAG
* * *
3310748 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGATGA-CAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACCAA
* * * *
3310792 ATCTTATCTTTCC-AAG-A-TAGTTGGAAGCAGATTTAAG-CCACCCA
1 ATCTTATC-TCCCTAAGCAGTAG-TGG-AGCAGATTAAAGACGACCAA
** * * * * * * * * *
3310836 GCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGA-TAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACCAA
*
3310880 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATTAAAGACGA-CAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACCAA
* * * *
3310924 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGACCAA
** ** * * * * * * *
3310968 GCCTTATCTCCCCGAGCAGTAGTGTAGTAGGTTGAAGA-TAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACCAA
* **
3311012 ATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGA-CAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACCAA
*
3311056 ATATTATCT
1 ATCTTATCT
3311065 TTCCAAGATA
Statistics
Matches: 195, Mismatches: 60, Indels: 36
0.67 0.21 0.12
Matches are distributed among these distances:
42 7 0.04
43 16 0.08
44 153 0.78
45 13 0.07
46 6 0.03
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (45 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACCAA
Found at i:3310978 original size:132 final size:132
Alignment explanation
Indices: 3310738--3311155 Score: 658
Period size: 132 Copynumber: 3.2 Consensus size: 132
3310728 CAGATCAGTA
* *
3310738 AAGATAGCAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGATGACAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTT
*
3310803 CCAAGATAGTTGGAAGCAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
66 CCAAGATAGTAGGAAGCAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
3310868 TG
131 TG
* *
3310870 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATTAAAGACGACAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTT
* * * * *
3310935 CCAAGATAGTGGGAAGCAGATTTAAGCCACCCAGCCTTATCTCCCCGAGCAGTAGTGTAGTAGGT
66 CCAAGATAGTAGGAAGCAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
3311000 TG
131 TG
* * *
3311002 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGACAAATATTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTT
* * *
3311067 CCAAGATAGTAGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAACAGCAGGGGAGTAGGT
66 CCAAGATAGTAGGAAGCAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
3311132 TG
131 TG
* *
3311134 AAGATCA-CAAATCCTATCTCCC
1 AAGAT-AGCAGATCTTATCTCCC
3311156 CGACGTTGCA
Statistics
Matches: 261, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
132 260 1.00
133 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (132 bp):
AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTT
CCAAGATAGTAGGAAGCAGATTTAAGCCACCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
TG
Found at i:3312583 original size:19 final size:21
Alignment explanation
Indices: 3312561--3312606 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
3312551 TTATTGTTAC
3312561 TTTTATTTTTATAC-TTAT-T
1 TTTTATTTTTATACTTTATGT
3312580 TTTTATTTTTATACTTTATGT
1 TTTTATTTTTATACTTTATGT
3312601 TTTTAT
1 TTTTAT
3312607 ATACATGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 14 0.56
20 4 0.16
21 7 0.28
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATTTTTATACTTTATGT
Found at i:3312854 original size:4 final size:4
Alignment explanation
Indices: 3312845--3312886 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
3312835 TAATTTCAAG
3312845 TTAT TTA- TT-T TTAT CTTACT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT -TTA-T TTAT TTAT TTAT TTAT TTAT TT
3312887 CCTTGCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 4 0.12
4 23 0.68
5 6 0.18
6 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:3315052 original size:10 final size:11
Alignment explanation
Indices: 3315026--3315056 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
3315016 TGTTCTACAT
3315026 ACAAATAAAAC
1 ACAAATAAAAC
3315037 ACAAATAAAA-
1 ACAAATAAAAC
3315047 ACAAATAAAA
1 ACAAATAAAA
3315057 GGGAAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (11 bp):
ACAAATAAAAC
Found at i:3315884 original size:23 final size:23
Alignment explanation
Indices: 3315844--3315896 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3315834 ATATATATAT
3315844 ATATATTTTTAAACGAATATTTTC
1 ATAT-TTTTTAAACGAATATTTTC
* * *
3315868 TTATTTTTTTAATGAATATTTTC
1 ATATTTTTTAAACGAATATTTTC
3315891 ATATTT
1 ATATTT
3315897 ATATGTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (23 bp):
ATATTTTTTAAACGAATATTTTC
Found at i:3320463 original size:31 final size:31
Alignment explanation
Indices: 3320425--3320485 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3320415 GTATCAAAAC
*
3320425 AAACATTAAAACCAAACTCAAATACCAAATT
1 AAACATTAAAACCAAACCCAAATACCAAATT
* *
3320456 AAACATTAAAATCAAACCCAAGTACCAAAT
1 AAACATTAAAACCAAACCCAAATACCAAAT
3320486 GGTATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.57, C:0.23, G:0.02, T:0.18
Consensus pattern (31 bp):
AAACATTAAAACCAAACCCAAATACCAAATT
Found at i:3322118 original size:19 final size:18
Alignment explanation
Indices: 3322095--3322141 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
3322085 TAAGTTGTAC
3322095 TTTTAATTTTTTATATAA
1 TTTTAATTTTTTATATAA
**
3322113 TATTTAATAATTTATATAA
1 T-TTTAATTTTTTATATAA
3322132 TTTT-ATTTTT
1 TTTTAATTTTT
3322142 CTAATTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAATTTTTTATATAA
Found at i:3322138 original size:22 final size:22
Alignment explanation
Indices: 3322113--3322179 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
3322103 TTTTATATAA
3322113 TATTTAATAATTTATATAATTT
1 TATTTAATAATTTATATAATTT
** *
3322135 TATTTTTCTAATTT-TCTAATTT
1 TA-TTTAATAATTTATATAATTT
* *
3322157 TTTTGTAATATTTTA-ATAATTT
1 TATT-TAATAATTTATATAATTT
3322179 T
1 T
3322180 TAAAGAAATT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 2 0.06
22 23 0.68
23 9 0.26
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (22 bp):
TATTTAATAATTTATATAATTT
Found at i:3322789 original size:29 final size:30
Alignment explanation
Indices: 3322728--3322791 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
3322718 AATATATTTT
**
3322728 TTAAGGGCTTAATTGATTGGCAACTTTGGA
1 TTAAGGGCTTAATTGATTGGCAACTTTCAA
*
3322758 TTAAGGG-TTAAATTGATT-GCAATTTTCAA
1 TTAAGGGCTT-AATTGATTGGCAACTTTCAA
3322787 TTAAG
1 TTAAG
3322792 AATTTAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (30 bp):
TTAAGGGCTTAATTGATTGGCAACTTTCAA
Found at i:3322800 original size:29 final size:30
Alignment explanation
Indices: 3322736--3322804 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
3322726 TTTTAAGGGC
** **
3322736 TTAATTGATTGGCAACTTTGGATTAAGGGT
1 TTAATTGATTGGCAACTTTCAATTAAGAAT
* *
3322766 TAAATTGATT-GCAATTTTCAATTAAGAAT
1 TTAATTGATTGGCAACTTTCAATTAAGAAT
3322795 TTAATTGATT
1 TTAATTGATT
3322805 TTTTAAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.43
Consensus pattern (30 bp):
TTAATTGATTGGCAACTTTCAATTAAGAAT
Found at i:3329665 original size:94 final size:94
Alignment explanation
Indices: 3329553--3329859 Score: 258
Period size: 94 Copynumber: 3.3 Consensus size: 94
3329543 TAGTGGCTTC
3329553 AATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACTGC
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACTGC
* *
3329618 AACCTCAAAGGTATAGGATTCATCGTTTT
66 AACTTCAAAGGCATAGGATTCATCGTTTT
* * * * ** *
3329647 AATCTGCTCCACTGCAACTTCAGGGAGATAGGA----TTA--GTAGCTTCAATCTG-CTCCGCTA
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGAC-CTACTG
* * * * * *
3329705 TAATTTC-AGGGAGATAAGAGTTGCTATC--TTC
65 CAACTTCAAAGG-CATAGGA-TT-C-ATCGTTTT
* ** * * * * *
3329736 AGTCTACTCCACTGCAACTTCAGAGAGATAAAACTTGATATGATAGATTTAATCCGACCTACTGC
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACTGC
*
3329801 AACTTCAGAGGCAT-GTGATTCATCGTTTT
66 AACTTCAAAGGCATAG-GATTCATCGTTTT
*
3329830 AATCCGTTCCACTGCAACTTCAGGGAGATA
1 AATCCGCTCCACTGCAACTTCAGGGAGATA
3329860 GGATCGGTGG
Statistics
Matches: 158, Mismatches: 39, Indels: 32
0.69 0.17 0.14
Matches are distributed among these distances:
87 4 0.03
88 24 0.15
89 32 0.20
90 4 0.03
91 3 0.02
92 3 0.02
93 3 0.02
94 60 0.38
95 22 0.14
96 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (94 bp):
AATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACTGC
AACTTCAAAGGCATAGGATTCATCGTTTT
Found at i:3329678 original size:44 final size:44
Alignment explanation
Indices: 3329383--3330277 Score: 240
Period size: 44 Copynumber: 19.7 Consensus size: 44
3329373 TTTAACCTGT
* * *
3329383 TCCACTGCAACTTCAGGGAAATAAGATTCA-C-TATCCTTAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCATCGT-T--TCAATCTGC
* * * *
3329428 TCCACTGCAACTTCAGTGAGATAAGACTTGTAAC--TTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TT-CATCGTTTCAATCTGC
* * ** * *
3329472 TCCACTGCAAGTTCAGGGAGATAAGACTT-GTAATTTCAACCCGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTCATCGTTTCAATCTGC
* * * * *
3329516 CCCATTGCAACTTCAGGGAGATAAGATT-AGTGGCTTCAATCCGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCA-TCGTTTCAATCTGC
* * *
3329560 TCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGAC
1 TCCACTGCAACTTCAGGGAGATAAGA--T-TCATCGT---TTCAATCTG-C
* * * * * *
3329611 -CTACTGCAACCTCAAAGG-TATAGGATTCATCGTTTTAATCTGC
1 TCCACTGCAACTTC-AGGGAGATAAGATTCATCGTTTCAATCTGC
* * *
3329654 TCCACTGCAACTTCAGGGAGATAGGATT-AGTAGCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCA-TCGTTTCAATCTGC
* ** * * *
3329698 TCCGCTATAATTTCAGGGAGATAAGAGTTGCTATC--TTCAGTCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TT-C-ATCGTTTCAATCTGC
* * * *
3329743 TCCACTGCAACTTCAGAGAGATAAAACTTGATATGATAGATTT-AATCCGAC
1 TCCACTGCAACTTCAGGGAGAT--AA---GAT-TCATCG-TTTCAATCTG-C
* * ** * * *
3329794 -CTACTGCAACTTCAGAGG-CATGTGATTCATCGTTTTAATCCGT
1 TCCACTGCAACTTCAG-GGAGATAAGATTCATCGTTTCAATCTGC
* * * *
3329837 TCCACTGCAACTTCAGGGAGATAGGA-TCGGTGGCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTC-ATCGTTTCAATCTGC
* * * * *
3329881 TCCACTGCAACTTTAGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGAT-T--C---A-TCGT---TTCAATCTGC
** * * * * *
3329935 TCCACTGCAACGCCAAGGAAATAAGATTC-GCTGTCTTTAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCATC-GT-TTCAATCTGC
* * * * *
3329980 TCCACTGCAACTTCAGAGAGATAAGACTTGTAAC--TTCAACCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TT-CATCGTTTCAATCTGC
* * * *
3330024 TCCACTGCAACTTTAGGGAGATAA-ATT--TTGCTAT-GATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCATCG-TTTCAATCTGC
* * * * **
3330065 TCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTATAGCTTT-AATCTAT
1 TCCACTGCAACTTCAGGGAGATAAG-------ATTCATCG-TTTCAATCTGC
* * * * ** *
3330116 TCCACTGCAACTTTAGGAAAATAAGATTCGCTATTTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTC-ATCGTTTCAATCTGC
* * *
3330161 TCGACTGCAACTTCATGGAGATAAGACTTGTATC--TTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TT-CATCGTTTCAATCTGC
* * * * *
3330205 CCCACTGCAACTTCAGGGGGATAAGATT-AGTGGCTTCAATATGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCA-TCGTTTCAATCTGC
* **
3330249 TCCACTACCTCTTCAGGGAGATAAGATTC
1 TCCACTGCAACTTCAGGGAGATAAGATTC
3330278 GCCATGATGA
Statistics
Matches: 626, Mismatches: 152, Indels: 144
0.68 0.16 0.16
Matches are distributed among these distances:
41 26 0.04
42 4 0.01
43 17 0.03
44 316 0.50
45 111 0.18
46 10 0.02
47 15 0.02
48 8 0.01
49 4 0.01
50 45 0.07
51 40 0.06
53 1 0.00
54 29 0.05
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTCATCGTTTCAATCTGC
Found at i:3329905 original size:183 final size:183
Alignment explanation
Indices: 3329559--3329906 Score: 511
Period size: 183 Copynumber: 1.9 Consensus size: 183
3329549 CTTCAATCCG
* * * * *
3329559 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTTAATCTGACCTACTGCAACCTC
1 CTCCACTGCAACTTCAGAGAGATAAAACTTGATATGATAGATTTAATCCGACCTACTGCAACCTC
* * *
3329624 AAAGGTATAGGATTCATCGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCT
66 AAAGGCATAGGATTCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCAGTAGCT
* * *
3329689 TCAATCTGCTCCGCTATAATTTCAGGGAGATAAGAGTTGCTATCTTCAGTCTA
131 TCAATCTGCTCCACTACAATTTCAGGAAGATAAGAGTTGCTATCTTCAGTCTA
*
3329742 CTCCACTGCAACTTCAGAGAGATAAAACTTGATATGATAGATTTAATCCGACCTACTGCAACTTC
1 CTCCACTGCAACTTCAGAGAGATAAAACTTGATATGATAGATTTAATCCGACCTACTGCAACCTC
* * * *
3329807 AGAGGCAT-GTGATTCATCGTTTTAATCCGTTCCACTGCAACTTCAGGGAGATAGGATCGGTGGC
66 AAAGGCATAG-GATTCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCAGTAGC
*
3329871 TTCAATCTGCTCCACTGCAACTTT-AGGAAGATAAGA
130 TTCAATCTGCTCCACTACAA-TTTCAGGAAGATAAGA
3329907 TCTGCCATAA
Statistics
Matches: 146, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
182 1 0.01
183 142 0.97
184 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (183 bp):
CTCCACTGCAACTTCAGAGAGATAAAACTTGATATGATAGATTTAATCCGACCTACTGCAACCTC
AAAGGCATAGGATTCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCAGTAGCT
TCAATCTGCTCCACTACAATTTCAGGAAGATAAGAGTTGCTATCTTCAGTCTA
Found at i:3330002 original size:99 final size:98
Alignment explanation
Indices: 3329827--3330005 Score: 234
Period size: 99 Copynumber: 1.8 Consensus size: 98
3329817 GATTCATCGT
** * * * *
3329827 TTTAATCCGTTCCACTGCAACTTCAGGGAGATAGGATCGGTGGCTTCAATCTGCTCCACTGCAAC
1 TTTAATCCGTTCCACTGCAACGCCAAGGAAATAAGATCGCTGGCTTCAATCTGCTCCACTGCAAC
*
3329892 TTTAGGAAGATAAGATCTGCCATAATTTGTAGC
66 TTCAGGAAGATAAGATCTGCCATAATTTGTAGC
* * * *
3329925 TTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTTAGTCTGCTCCACTGCAA
1 TTTAATCCGTTCCACTGCAACGCCAAGGAAATAAGA-TCGCTGGCTTCAATCTGCTCCACTGCAA
3329990 CTTCA-GAGAGATAAGA
65 CTTCAGGA-AGATAAGA
3330006 CTTGTAACTT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
98 32 0.47
99 36 0.53
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (98 bp):
TTTAATCCGTTCCACTGCAACGCCAAGGAAATAAGATCGCTGGCTTCAATCTGCTCCACTGCAAC
TTCAGGAAGATAAGATCTGCCATAATTTGTAGC
Found at i:3330146 original size:181 final size:182
Alignment explanation
Indices: 3329875--3330228 Score: 466
Period size: 181 Copynumber: 1.9 Consensus size: 182
3329865 GGTGGCTTCA
* * *
3329875 ATCTGCTCCACTGCAACTTTAGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCAC
1 ATCTGCTCCACTGCAACTTCAGGAAGATAAGATCT--CATAATTTATAGCTTTAATCTATTCCAC
*
3329940 TGCAACGCCAAGGAAATAAGATTCGCTGTCTTT-AGTCTGCTCCACTGCAACTTCA-GAGAGATA
64 TGCAACGCCAAGGAAATAAGATTCGCTAT-TTTCAGTCTGCTCCACTGCAACTTCATG-GAGATA
* *
3330003 AGACTTGTAACTTCAACCTACTCCACTGCAACTTTAGGGAGATAAATTTTGCTATG
127 AGACTTGTAACTTCAACCTACCCCACTGCAACTTCAGGGAGATAAATTTTGCTATG
* * *
3330059 ATCTGCTCTACTGCAACTTCA-GAGAGATAAGATCT-TTTATTTATAGCTTTAATCTATTCCACT
1 ATCTGCTCCACTGCAACTTCAGGA-AGATAAGATCTCATAATTTATAGCTTTAATCTATTCCACT
*** *
3330122 GCAAC-TTTAGGAAAATAAGATTCGCTATTTTCAGTCTGCTCGACTGCAACTTCATGGAGATAAG
65 GCAACGCCAAGG-AAATAAGATTCGCTATTTTCAGTCTGCTCCACTGCAACTTCATGGAGATAAG
* * * *
3330186 ACTTGTATCTTCAATCTGCCCCACTGCAACTTCAGGGGGATAA
129 ACTTGTAACTTCAACCTACCCCACTGCAACTTCAGGGAGATAA
3330229 GATTAGTGGC
Statistics
Matches: 149, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
180 6 0.04
181 110 0.74
182 1 0.01
183 2 0.01
184 30 0.20
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (182 bp):
ATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTCATAATTTATAGCTTTAATCTATTCCACTG
CAACGCCAAGGAAATAAGATTCGCTATTTTCAGTCTGCTCCACTGCAACTTCATGGAGATAAGAC
TTGTAACTTCAACCTACCCCACTGCAACTTCAGGGAGATAAATTTTGCTATG
Found at i:3331190 original size:22 final size:22
Alignment explanation
Indices: 3331164--3331205 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3331154 GCCTCTCTTT
3331164 TTTCTTTTTT-TTTTTGTTTTCG
1 TTTCTTTTTTCTTTTT-TTTTCG
3331186 TTTCTTTTTTCTTTTTTTTT
1 TTTCTTTTTTCTTTTTTTTT
3331206 AAAATGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.86
Consensus pattern (22 bp):
TTTCTTTTTTCTTTTTTTTTCG
Found at i:3339991 original size:20 final size:21
Alignment explanation
Indices: 3339966--3340008 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
3339956 CCAAATCTAC
*
3339966 TTTATAAAAATT-TTAAAAAT
1 TTTATAAAAATTCATAAAAAT
3339986 TTTATAAAAATTCATAAAAAT
1 TTTATAAAAATTCATAAAAAT
3340007 TT
1 TT
3340009 CCACTTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTATAAAAATTCATAAAAAT
Found at i:3339993 original size:11 final size:10
Alignment explanation
Indices: 3339966--3340008 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
3339956 CCAAATCTAC
3339966 TTTATAAAAA
1 TTTATAAAAA
3339976 TTT-TAAAAA
1 TTTATAAAAA
3339985 TTTTATAAAAA
1 -TTTATAAAAA
*
3339996 TTCATAAAAA
1 TTTATAAAAA
3340006 TTT
1 TTT
3340009 CCACTTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 6 0.21
10 17 0.59
11 6 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:3343674 original size:21 final size:20
Alignment explanation
Indices: 3343648--3343688 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3343638 AATATATATA
* *
3343648 TATAATATTTTTAATTTTTTT
1 TATAAT-TTTTGAAATTTTTT
3343669 TATAATTTTTGAAATTTTTT
1 TATAATTTTTGAAATTTTTT
3343689 AGTTTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TATAATTTTTGAAATTTTTT
Found at i:3344489 original size:19 final size:20
Alignment explanation
Indices: 3344453--3344494 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3344443 TTATTATTCA
* *
3344453 TTTAATATTAAGAGATAAAT
1 TTTAAAATTAAGACATAAAT
3344473 TTTAAAATT-AGACATAAAT
1 TTTAAAATTAAGACATAAAT
3344492 TTT
1 TTT
3344495 GATTTAACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (20 bp):
TTTAAAATTAAGACATAAAT
Found at i:3344775 original size:29 final size:30
Alignment explanation
Indices: 3344733--3344813 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
3344723 GATCTAGATC
* *
3344733 AAATTAAAATTTCATGTATAAAATTGTACA-
1 AAATCAAAA-TTCATGTATAAAATTGCACAT
*
3344763 AAATCAAAATTCATGTATACAATTGCACATT
1 AAATCAAAATTCATGTATAAAATTGCACA-T
*
3344794 AAATCATAGA-TCATGTATAA
1 AAATCA-AAATTCATGTATAA
3344814 TTTTAGGATT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.42
30 8 0.19
31 15 0.35
32 2 0.05
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (30 bp):
AAATCAAAATTCATGTATAAAATTGCACAT
Found at i:3348756 original size:19 final size:19
Alignment explanation
Indices: 3348712--3348761 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3348702 ATGGATAATT
3348712 ATTTTGTACACAAATAGTAA
1 ATTTTGTACACAAATA-TAA
*
3348732 ATTTTGTACCCAAAT-TAA
1 ATTTTGTACACAAATATAA
3348750 GATTTTGT-CACA
1 -ATTTTGTACACA
3348762 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.22
19 7 0.26
20 14 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (19 bp):
ATTTTGTACACAAATATAA
Found at i:3349877 original size:64 final size:64
Alignment explanation
Indices: 3349781--3349908 Score: 195
Period size: 64 Copynumber: 2.0 Consensus size: 64
3349771 AAAATGATTA
* * * * *
3349781 AATTAAAATACAGAGATTAAATTCACAGTTTTTA-TAAAGTTAAAATTTAACCTTAATTTATTTG
1 AATTAAAATAAAAAAATTAAATCCACAATTTTTATTAAA-TTAAAATTTAACCTTAATTTATTTG
3349845 AATTAAAATAAAAAAATTAAATCCACAATTTTTATTAAATTAAAATTTAACCTTAATTTATTTG
1 AATTAAAATAAAAAAATTAAATCCACAATTTTTATTAAATTAAAATTTAACCTTAATTTATTTG
3349909 CCTATCTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 54 0.93
65 4 0.07
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (64 bp):
AATTAAAATAAAAAAATTAAATCCACAATTTTTATTAAATTAAAATTTAACCTTAATTTATTTG
Found at i:3351611 original size:13 final size:13
Alignment explanation
Indices: 3351593--3351620 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3351583 GAAATACATA
3351593 TCTTAGATCCAAG
1 TCTTAGATCCAAG
3351606 TCTTAGATCCAAG
1 TCTTAGATCCAAG
3351619 TC
1 TC
3351621 GATTTGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (13 bp):
TCTTAGATCCAAG
Found at i:3352492 original size:32 final size:32
Alignment explanation
Indices: 3352454--3352519 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
3352444 TACCTTGTTG
*
3352454 TTTTATGTAATCTATGCAAGTTGTTGGTTATC
1 TTTTATGTAATCTATGCAAGTTGTCGGTTATC
3352486 TTTTATGTAATCTATGCAAGTTGTCGGTTATC
1 TTTTATGTAATCTATGCAAGTTGTCGGTTATC
3352518 TT
1 TT
3352520 AGGATTGAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (32 bp):
TTTTATGTAATCTATGCAAGTTGTCGGTTATC
Found at i:3359099 original size:6 final size:6
Alignment explanation
Indices: 3359088--3359128 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
3359078 ACTCAACTGG
3359088 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAG
1 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAG
3359129 CTCCATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.51, T:0.17
Consensus pattern (6 bp):
TGGAGA
Found at i:3362386 original size:21 final size:21
Alignment explanation
Indices: 3362360--3362412 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3362350 CGCTGTTTCT
* *
3362360 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACA
*
3362381 AATCTCACTGCTACAGTAACA
1 AATCTCACCGCTACAGTAACA
3362402 AATCTCACCGC
1 AATCTCACCGC
3362413 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.36, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACA
Found at i:3366668 original size:23 final size:23
Alignment explanation
Indices: 3366592--3366770 Score: 213
Period size: 23 Copynumber: 8.0 Consensus size: 23
3366582 CCTGATCAGT
3366592 ATACGACACAT-AAGTGCCTG--
1 ATACGACACATAAAGTGCCTGAA
** * *
3366612 ATACGACACACGAGGTGCCTAAA
1 ATACGACACATAAAGTGCCTGAA
* *
3366635 ATACGACACATGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
* *
3366658 ATACGACACATAAAGCGCCTGAT
1 ATACGACACATAAAGTGCCTGAA
* * *
3366681 ATACAACACATAAAATACCTGAA
1 ATACGACACATAAAGTGCCTGAA
* *
3366704 ATATGACACATAAAGTGGCTGAA
1 ATACGACACATAAAGTGCCTGAA
3366727 ATA-GACACATAAAGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
3366749 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
3366771 TCGGCATAGC
Statistics
Matches: 135, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
20 10 0.07
21 7 0.05
22 21 0.16
23 97 0.72
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:3369308 original size:19 final size:19
Alignment explanation
Indices: 3369267--3369308 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3369257 ATTGAATTTG
* * *
3369267 AAAATTGGACCCAAGATCG
1 AAAATTGAACCCAAGAACC
3369286 AAAATTGAACCCAAGAACC
1 AAAATTGAACCCAAGAACC
3369305 AAAA
1 AAAA
3369309 CCCAGGACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.12
Consensus pattern (19 bp):
AAAATTGAACCCAAGAACC
Found at i:3369697 original size:31 final size:30
Alignment explanation
Indices: 3369662--3369760 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 30
3369652 TGTTTTAATG
3369662 AATTTAATATTTATCTAGATAGTATTTTATT
1 AATTTAATATTTATCTAGATA-TATTTTATT
* * **
3369693 AATTTAATATTAATAT-GATATATTAAATTT
1 AATTTAATATTTATCTAGATATATTTTA-TT
* *
3369723 AATTTAATATTTATCTAGATAATGTTTTAGT
1 AATTTAATATTTATCTAGAT-ATATTTTATT
3369754 AATTTAA
1 AATTTAA
3369761 GATTAATGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
29 5 0.09
30 20 0.36
31 25 0.45
32 5 0.09
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (30 bp):
AATTTAATATTTATCTAGATATATTTTATT
Found at i:3373905 original size:9 final size:9
Alignment explanation
Indices: 3373891--3373924 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
3373881 CCAACATACT
*
3373891 GTCAGTCTA
1 GTCAGTCCA
3373900 GTCAGTCCA
1 GTCAGTCCA
3373909 GTCAGTCCA
1 GTCAGTCCA
3373918 GTCAGTC
1 GTCAGTC
3373925 ACATCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (9 bp):
GTCAGTCCA
Found at i:3374890 original size:18 final size:19
Alignment explanation
Indices: 3374839--3374893 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
3374829 ATTACAAAAT
3374839 AATTCAAAATAATTT-TCAAA
1 AATTCAAAAT-ATTTAT-AAA
3374859 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
3374878 AATTCTAAA-ATTTATA
1 AATTCAAAATATTTATA
3374894 TTTTTAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 7 0.21
19 15 0.45
20 11 0.33
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:3377662 original size:4 final size:4
Alignment explanation
Indices: 3377649--3377695 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
3377639 TTCATTCATC
* *
3377649 TATT TAATT TATT TATT T-TT TTTAT TATC TATT TATT TATT TATT TA
1 TATT T-ATT TATT TATT TATT TAT-T TATT TATT TATT TATT TATT TA
3377696 CCTATTACTC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
3 3 0.08
4 27 0.73
5 7 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:3377692 original size:16 final size:16
Alignment explanation
Indices: 3377646--3377692 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
3377636 TCATTCATTC
3377646 ATCTATTTAATTTATTT
1 ATCTATTT-ATTTATTT
3377663 AT-T-TTT-TTTA-TT
1 ATCTATTTATTTATTT
3377675 ATCTATTTATTTATTT
1 ATCTATTTATTTATTT
3377691 AT
1 AT
3377693 TTACCTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
12 4 0.15
13 5 0.19
14 3 0.12
15 7 0.27
16 5 0.19
17 2 0.08
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (16 bp):
ATCTATTTATTTATTT
Found at i:3377700 original size:20 final size:20
Alignment explanation
Indices: 3377658--3377701 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3377648 CTATTTAATT
* *
3377658 TATTTATTTTTTTTATTATC
1 TATTTATTTTTTATATTACC
3377678 TATTTATTTATTTAT-TTACC
1 TATTTATTT-TTTATATTACC
3377698 TATT
1 TATT
3377702 ACTCTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTATTTTTTATATTACC
Found at i:3381559 original size:19 final size:20
Alignment explanation
Indices: 3381525--3381574 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
3381515 CTTTTTTTTT
3381525 CATT-CATTTCATTCATCA-G
1 CATTACATTTCATTCAT-ATG
3381544 CATTACATTTCA-TCATATG
1 CATTACATTTCATTCATATG
*
3381563 CATTAAATTTCA
1 CATTACATTTCA
3381575 CAAAAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.04
19 20 0.71
20 7 0.25
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (20 bp):
CATTACATTTCATTCATATG
Found at i:3389086 original size:44 final size:43
Alignment explanation
Indices: 3389031--3389142 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 43
3389021 AATGCCATGT
* * **
3389031 CCCAGACATGGTCTTACATGGAAATCTTGTAA-CGATGCCAATAG
1 CCCAAACATGGTCTTACA-CGAAATC-TCAAATCGATGCCAATAG
* *
3389075 CCC-AGCTATGGTCTTACACGAAATCTCAAATCGATGTCAATAG
1 CCCAAAC-ATGGTCTTACACGAAATCTCAAATCGATGCCAATAG
3389118 CCCAAACATGGTCTTACACGAAATC
1 CCCAAACATGGTCTTACACGAAATC
3389143 ACACATCGGA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
42 3 0.05
43 39 0.67
44 16 0.28
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
CCCAAACATGGTCTTACACGAAATCTCAAATCGATGCCAATAG
Found at i:3389320 original size:31 final size:31
Alignment explanation
Indices: 3389284--3389414 Score: 167
Period size: 31 Copynumber: 4.3 Consensus size: 31
3389274 AATATATATC
* *
3389284 CATATACGAATCAAATTCAGCAATGTATAAT
1 CATATACAAATCAAATTCGGCAATGTATAAT
* *
3389315 CATATACAAATCAAATTCGACAATGTATATT
1 CATATACAAATCAAATTCGGCAATGTATAAT
* * *
3389346 TATAAACAATTCAAATTCGGCAATGTAT-AT
1 CATATACAAATCAAATTCGGCAATGTATAAT
*
3389376 -ATATACAAATCAAATTCGGCAATGTATAAAA
1 CATATACAAATCAAATTCGGCAATGTAT-AAT
3389407 CATATACA
1 CATATACA
3389415 TTTAAATTCA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
29 25 0.29
30 1 0.01
31 52 0.61
32 7 0.08
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (31 bp):
CATATACAAATCAAATTCGGCAATGTATAAT
Found at i:3389422 original size:60 final size:62
Alignment explanation
Indices: 3389294--3389424 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 62
3389284 CATATACGAA
***
3389294 TCAAATTCAGCAATGTATAATCATATACAAATCAAATTCGACAATGTATATTTATAAACAAT
1 TCAAATTCAGCAATGTATAATCATATACAAATCAAATTCGACAATGTATAAACATAAACAAT
* * *
3389356 TCAAATTCGGCAATGTAT-AT-ATATACAAATCAAATTCGGCAATGTATAAAACATATAC-AT
1 TCAAATTCAGCAATGTATAATCATATACAAATCAAATTCGACAATGTAT-AAACATAAACAAT
*
3389416 TTAAATTCA
1 TCAAATTCA
3389425 AAAACATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 35 0.58
61 8 0.13
62 17 0.28
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.32
Consensus pattern (62 bp):
TCAAATTCAGCAATGTATAATCATATACAAATCAAATTCGACAATGTATAAACATAAACAAT
Found at i:3391802 original size:44 final size:44
Alignment explanation
Indices: 3391753--3392096 Score: 165
Period size: 44 Copynumber: 7.5 Consensus size: 44
3391743 CTTCTTGAAT
* **
3391753 TTGCAGTGGAGCAAATTAGAGCTAAAAATATTATCTCCCTAAAG
1 TTGCAGTGGAGCAGATTAGAGCTACGAATATTATCTCCCTAAAG
* * * *
3391797 TTGCAGTGGAGTAGATT-GAAGCTACGAGTATTATCTCTCTGAAG
1 TTGCAGTGGAGCAGATTAG-AGCTACGAATATTATCTCCCTAAAG
* * * *
3391841 TTGCAGTAGAGTAGATT-GAAGCTACGAGTCTTATCTCCCTAAAG
1 TTGCAGTGGAGCAGATTAG-AGCTACGAATATTATCTCCCTAAAG
*** * * * * *
3391885 TTGCAGCCAAGCAGATTAAAGATAGCGAATCTTATTTCCCTGAAG
1 TTGCAGTGGAGCAGATTAGAGCTA-CGAATATTATCTCCCTAAAG
* * * * *
3391930 TTGCAGTGGAACAAATTAAAGCTACAAGTTACAGGTCTTATCTCCCTGAAG
1 TTGCAGTGGAGCAGATTAGAGCTAC--G--A-A--TATTATCTCCCTAAAG
* * * * * *
3391981 TTACAGTGGAACAGATTAAAGCTACGAGTTACAAATCTTATCACCTTGAAA-
1 TTGCAGTGGAGCAGATTAGAGCTAC--G-----AATATTATCTCCCT-AAAG
* * * * *
3392032 TTGCAGTGGAGTAGATT-GAAGCTATGAGTCTTATTTCCCTAAAG
1 TTGCAGTGGAGCAGATTAG-AGCTACGAATATTATCTCCCTAAAG
*
3392076 TTGTAGTGGAGCAGATTAGAG
1 TTGCAGTGGAGCAGATTAGAG
3392097 TGACAAACCC
Statistics
Matches: 237, Mismatches: 46, Indels: 34
0.75 0.15 0.11
Matches are distributed among these distances:
43 4 0.02
44 120 0.51
45 36 0.15
46 1 0.00
48 1 0.00
49 2 0.01
51 69 0.29
52 2 0.01
53 1 0.00
54 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (44 bp):
TTGCAGTGGAGCAGATTAGAGCTACGAATATTATCTCCCTAAAG
Found at i:3391990 original size:51 final size:51
Alignment explanation
Indices: 3391912--3392041 Score: 179
Period size: 51 Copynumber: 2.5 Consensus size: 51
3391902 AAAGATAGCG
*
3391912 AATCTTATTTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACA
** * * *
3391963 GGTCTTATCTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACGAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACA
* * *
3392014 AATCTTATCACCTTGAAATTGCAGTGGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGA
3392042 GTAGATTGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (51 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACA
Found at i:3392048 original size:51 final size:51
Alignment explanation
Indices: 3391912--3392060 Score: 172
Period size: 51 Copynumber: 2.9 Consensus size: 51
3391902 AAAGATAGCG
** * *
3391912 AATCTTATTTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACA
1 AATCTTATCACCCTGAAGTTGCAGTGGAACAGATTAAAGCTACGAGTTACA
** * *
3391963 GGTCTTATCTCCCTGAAGTTACAGTGGAACAGATTAAAGCTACGAGTTACA
1 AATCTTATCACCCTGAAGTTGCAGTGGAACAGATTAAAGCTACGAGTTACA
* * ** * *
3392014 AATCTTATCACCTTGAAATTGCAGTGGAGTAGATTGAAGCTATGAGT
1 AATCTTATCACCCTGAAGTTGCAGTGGAACAGATTAAAGCTACGAGT
3392061 CTTATTTCCC
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 82 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (51 bp):
AATCTTATCACCCTGAAGTTGCAGTGGAACAGATTAAAGCTACGAGTTACA
Found at i:3393738 original size:46 final size:44
Alignment explanation
Indices: 3393634--3393741 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3393624 TGTCTTTGAC
** * * *
3393634 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3393678 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3393724 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3393742 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3394163 original size:9 final size:9
Alignment explanation
Indices: 3394149--3394182 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3394139 TTCTATTCTG
3394149 TTTCTTTTC
1 TTTCTTTTC
3394158 TTTCTTTT-
1 TTTCTTTTC
*
3394166 TTTCTATTC
1 TTTCTTTTC
3394175 TTTCTTTT
1 TTTCTTTT
3394183 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:3394175 original size:17 final size:17
Alignment explanation
Indices: 3394149--3394182 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3394139 TTCTATTCTG
*
3394149 TTTCTTTTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
3394166 TTTCTATTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
3394183 GTTTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTATTCTTTCTTTT
Found at i:3394204 original size:5 final size:5
Alignment explanation
Indices: 3394191--3394262 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
3394181 TTGTTTTATG
3394191 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
3394239 CATAA TCATTAC TATAA TATAA TA
1 TATAA T-A-TAA TATAA TATAA TA
3394263 ATATTTTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (5 bp):
TATAA
Done.