Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001371.1 Hibiscus syriacus cultivar Beakdansim tig00002683_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 365156
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:176222 original size:63 final size:62
Alignment explanation
Indices: 176149--176267 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 62
176139 GGTGTTTGAG
*
176149 TGCATGGATGCACTAC-ATGGTGCATCAATGCACTAGTGCA-GGTGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTACAAGGGTGCATCAATGCAC---TGCAGGGTGCATGGATGCACTGCAGGGA
**
176212 TGCATGGATGCACTACAAGGGTGCATGGATGCACTGCAGGGGTGCATGGATGCACT
1 TGCATGGATGCACTACAAGGGTGCATCAATGCACTGCA-GGGTGCATGGATGCACT
176268 TTGACACCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 4 0.08
63 32 0.64
64 14 0.28
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (62 bp):
TGCATGGATGCACTACAAGGGTGCATCAATGCACTGCAGGGTGCATGGATGCACTGCAGGGA
Found at i:177222 original size:20 final size:20
Alignment explanation
Indices: 177199--177352 Score: 195
Period size: 20 Copynumber: 7.7 Consensus size: 20
177189 CGCAAACACA
177199 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
177219 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
177239 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
177259 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
177279 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* **
177299 TAAATCGCAACG-ATAATCAT
1 TAAATCGCAACGCGT-ATCCG
*
177319 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
177339 TAAATCGCAACGCG
1 TAAATCGCAACGCG
177353 ATATTTAAAG
Statistics
Matches: 116, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
19 1 0.01
20 115 0.99
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:177224 original size:60 final size:59
Alignment explanation
Indices: 177160--177353 Score: 194
Period size: 60 Copynumber: 3.2 Consensus size: 59
177150 TCAGTTTCCA
** *
177160 AAATCGCAACGCGAATATGAAAATCGCAACGCAAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCAAACA-ATAAATCGCAACGCGTATCCGT
* * * **** *
177220 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGC-AAACAATAAATCGCAACGCGTATCCGT
* * * *
177280 ATATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCATTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCA-AA-CAATAAATCGCAACGCGT-ATCCGT
177340 AAATCGCAACGCGA
1 AAATCGCAACGCGA
177354 TATTTAAAGC
Statistics
Matches: 108, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
59 2 0.02
60 105 0.97
61 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (59 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGCAAACAATAAATCGCAACGCGTATCCGT
Found at i:177774 original size:33 final size:33
Alignment explanation
Indices: 177735--177805 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
177725 TTCACTTAGA
* *
177735 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
177768 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
177801 TTTCA
1 TTTCA
177806 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:177911 original size:21 final size:20
Alignment explanation
Indices: 177885--177990 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
177875 TGCAGAAGAG
177885 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
177906 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
177926 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
177947 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
177961 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
177980 TCGCAACGAGA
1 TCGCAACGAGA
177991 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:177929 original size:20 final size:21
Alignment explanation
Indices: 177883--177961 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
177873 TTTGCAGAAG
*
177883 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
177905 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
177924 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
177946 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
177962 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:177942 original size:41 final size:38
Alignment explanation
Indices: 177878--177994 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
177868 TTCAATTTGC
* *
177878 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
177916 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
177957 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
177990 AGAAT
1 AGAAT
177995 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:177967 original size:14 final size:14
Alignment explanation
Indices: 177948--178001 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
177938 AAATGAAAAG
177948 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
177962 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
177981 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
177995 CGCAACG
1 CGCAACG
178002 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:177977 original size:33 final size:33
Alignment explanation
Indices: 177937--178006 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
177927 CGCAACGAGA
177937 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
177970 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
178003 GAAA
1 GAAA
178007 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:178013 original size:33 final size:33
Alignment explanation
Indices: 177943--178017 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
177933 GAGAGAAATG
* **
177943 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
177976 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
178009 AAAATCGCA
1 AAAATCGCA
178018 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:178035 original size:19 final size:19
Alignment explanation
Indices: 178013--178110 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
178003 GAAACCAAAA
*
178013 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
178032 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
178046 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
178065 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
178079 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
178098 TCGCGTTGCGATT
1 TCGCGTTGCGATT
178111 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:178054 original size:14 final size:14
Alignment explanation
Indices: 178035--178124 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
178025 TTTCATTTCG
178035 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
178049 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
178068 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
178082 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
178099 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
178115 CGTTGCGATT
1 CGTTGCGATT
178125 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:178060 original size:33 final size:33
Alignment explanation
Indices: 178018--178132 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
178008 CAAAATCGCA
178018 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
178051 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
178084 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
178117 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
178133 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:180321 original size:93 final size:93
Alignment explanation
Indices: 179830--180302 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
179820 TAGATTGCTT
* *
179830 AGTAAATTTATTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179895 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
179923 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179988 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
180016 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
180081 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
180109 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
180174 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
180202 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
180267 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
180294 AGTAAATTT
1 AGTAAATTT
180303 ATCCATTCAA
Statistics
Matches: 375, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
92 30 0.08
93 345 0.92
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:180386 original size:19 final size:19
Alignment explanation
Indices: 180346--180474 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
180336 TAGTTTACTT
* *
180346 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
180366 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
180385 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
180404 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
180418 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
180437 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
180451 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
180470 TCGCA
1 TCGCA
180475 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:180420 original size:33 final size:32
Alignment explanation
Indices: 180382--180474 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
180372 CGCGAAACCA
**
180382 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
180414 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
180447 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
180475 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:180472 original size:52 final size:52
Alignment explanation
Indices: 180346--180474 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
180336 TAGTTTACTT
* **
180346 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
180398 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
180451 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
180475 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:180492 original size:19 final size:19
Alignment explanation
Indices: 180470--180604 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
180460 GAAACCAAAA
*
180470 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
180489 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
180505 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
180522 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
180538 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
180555 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
180574 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
180594 TCGTGTTGCGA
1 TCGCGTTGCGA
180605 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:180511 original size:14 final size:14
Alignment explanation
Indices: 180492--180548 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
180482 TTTCATTTCG
180492 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
180506 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
180523 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
180539 CGTTGCGATT
1 CGTTGCGATT
180549 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:180517 original size:33 final size:33
Alignment explanation
Indices: 180475--180567 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
180465 CAAAATCGCA
*
180475 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
180508 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
180541 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
180568 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:182547 original size:14 final size:14
Alignment explanation
Indices: 182528--182563 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
182518 ATTGTTTAAT
182528 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
182542 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
182556 TGATTTGT
1 TGATTTGT
182564 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:182738 original size:20 final size:19
Alignment explanation
Indices: 182670--182750 Score: 109
Period size: 19 Copynumber: 4.5 Consensus size: 19
182660 AAAATTGACT
182670 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
182689 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
182703 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
182722 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
182742 ATCGCAATG
1 ATCGCAATG
182751 GGAGAATCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.37
20 18 0.33
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:182785 original size:19 final size:19
Alignment explanation
Indices: 182757--182924 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
182747 AATGGGAGAA
* *
182757 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
* *
182776 TCGCATTGCGA---TAATC
1 TCGCATTGCGATTTTCATT
182792 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
182809 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
182828 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
182844 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
182861 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
182880 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
182896 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
182913 TCCGCATTGCGA
1 T-CGCATTGCGA
182925 AATGTAATGG
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 18 0.14
16 21 0.17
17 18 0.14
18 2 0.02
19 60 0.48
20 6 0.05
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:182820 original size:52 final size:52
Alignment explanation
Indices: 182757--182924 Score: 291
Period size: 52 Copynumber: 3.2 Consensus size: 52
182747 AATGGGAGAA
* * **
182757 TCGCAATGCGATTTTAATTTCGCATTGCGATAATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
182809 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
182861 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
182913 TCCGCATTGCGA
1 T-CGCATTGCGA
182925 AATGTAATGG
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 101 0.91
53 10 0.09
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:182903 original size:33 final size:33
Alignment explanation
Indices: 182763--182924 Score: 141
Period size: 33 Copynumber: 4.7 Consensus size: 33
182753 AGAATCGCAA
* **
182763 TGCGATTTTAATTTCGCATTGCGATAATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
182796 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
182834 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
182867 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
182900 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
182925 AATGTAATGG
Statistics
Matches: 102, Mismatches: 15, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 49 0.48
34 10 0.10
35 3 0.03
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:183007 original size:19 final size:19
Alignment explanation
Indices: 182983--183080 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
182973 AAAATTGACT
182983 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
183002 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
183021 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
183035 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
183054 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
183074 ATCGCAA
1 ATCGCAA
183081 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:183112 original size:53 final size:53
Alignment explanation
Indices: 182983--183099 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
182973 AAAATTGACT
182983 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
183035 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
183088 ATCGCAATGCGA
1 ATCGCAATGCGA
183100 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:185430 original size:12 final size:12
Alignment explanation
Indices: 185413--185437 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
185403 TCTTCGGGGA
185413 CTTTTTCTTCTT
1 CTTTTTCTTCTT
185425 CTTTTTCTTCTT
1 CTTTTTCTTCTT
185437 C
1 C
185438 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:186368 original size:20 final size:20
Alignment explanation
Indices: 186340--186589 Score: 232
Period size: 20 Copynumber: 12.5 Consensus size: 20
186330 AAATTTCAGT
* * *
186340 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
186360 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
186380 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
186400 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
** **
186420 GTTGCGATTTACATATTATC
1 GTTGCGATTTACGGATTCGC
*
186440 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
186460 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
186480 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* * *
186500 GTTGCAATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
186520 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
186540 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
186560 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
186580 GTTGCGATTT
1 GTTGCGATTT
186590 TGGAAAATCG
Statistics
Matches: 196, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 195 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:186606 original size:21 final size:21
Alignment explanation
Indices: 186576--186658 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
186566 ATTTTCATAT
*
186576 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
186597 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
186618 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
186639 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
186659 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:186649 original size:42 final size:43
Alignment explanation
Indices: 186556--186654 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
186546 ATTTATGTGT
* *
186556 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
186597 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
186639 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
186655 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:188729 original size:19 final size:18
Alignment explanation
Indices: 188701--188746 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
188691 GAAGTAAATG
*
188701 ATAAGTTCGGACTAAAAAA
1 ATAAGATCGGACT-AAAAA
*
188720 ATAAGATCGGACTAAATA
1 ATAAGATCGGACTAAAAA
188738 ATAAGATCG
1 ATAAGATCG
188747 AACATAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (18 bp):
ATAAGATCGGACTAAAAA
Found at i:188742 original size:18 final size:18
Alignment explanation
Indices: 188695--188746 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
188685 ATGATTGAAG
* *
188695 TAAATGATAAGTTCGGAC
1 TAAATAATAAGATCGGAC
*
188713 TAAAAAAATAAGATCGGAC
1 T-AAATAATAAGATCGGAC
188732 TAAATAATAAGATCG
1 TAAATAATAAGATCG
188747 AACATAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (18 bp):
TAAATAATAAGATCGGAC
Found at i:190710 original size:82 final size:80
Alignment explanation
Indices: 190455--190767 Score: 405
Period size: 80 Copynumber: 3.9 Consensus size: 80
190445 TGTAAGTTCT
* * *
190455 TACGGACCTAAGGATATTTTGGGTAGG-CCCAAGGCATATCCTTAGGTTGGTTACCTTTGTTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTGTG
*
190519 TGCATAAGGTAACCC
66 TGCTTAAGGTAACCC
* * *
190534 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTC
1 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTGTG
190599 TGCTTAAGGTAACCC
66 TGCTTAAGGTAACCC
* * * * * *
190614 TACGTATCTAAGGATGTCCTTGGGTA-GACCCAAGGTATATGCTTAGGTTGGTTCCCTTTTTGAT
1 TACGGACCTAAGGATAT-CTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCC--TTTGTT
190678 GTGTGCTTAAGGTAACCC
63 GTGTGCTTAAGGTAACCC
* * * *
190696 TACGGATCTAAGGATATCCTTGAGTAGGCCCCTAGGTATATCCTTAGGTTGGCTCCCCTTTTGTT
1 TACGGACCTAAGGATAT-CTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGG-TTCCC-TTTGTT
190761 GTGTGCT
63 GTGTGCT
190768 GAGGGCAAGC
Statistics
Matches: 205, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
79 26 0.13
80 88 0.43
81 8 0.04
82 44 0.21
83 35 0.17
84 4 0.02
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (80 bp):
TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTGTG
TGCTTAAGGTAACCC
Found at i:192380 original size:19 final size:20
Alignment explanation
Indices: 192337--192384 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
192327 TCTAAATCCT
*
192337 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
192357 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
192376 TTTTCAAAA
1 TTTTCAAAA
192385 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:193827 original size:21 final size:20
Alignment explanation
Indices: 193736--193898 Score: 168
Period size: 21 Copynumber: 7.8 Consensus size: 20
193726 CGGTGTTTGC
* *
193736 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGTAGG
*
193756 GTGCATCGATGCACTAGT-GCAG
1 GTGCATGGATGCACT-GTAG--G
193778 GTGCATGGATGCACTAGT-GCAG
1 GTGCATGGATGCACT-GTAG--G
193800 GTGCATGGATGCACTGTAGG
1 GTGCATGGATGCACTGTAGG
*
193820 GATGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTGTAGG
*
193841 GATGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTGTAGG
193862 GATGCATGGATGCACTGTAGGG
1 G-TGCATGGATGCACTGTA-GG
*
193884 GTGAATGGATGCACT
1 GTGCATGGATGCACT
193899 TTGACACCCT
Statistics
Matches: 130, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
20 16 0.12
21 73 0.56
22 41 0.32
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGTAGG
Found at i:193999 original size:29 final size:29
Alignment explanation
Indices: 193978--194035 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
193968 AAACTTTGAA
193978 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
194007 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
194036 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:194025 original size:30 final size:30
Alignment explanation
Indices: 193978--194037 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
193968 AAACTTTGAA
193978 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
194007 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
194038 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:197846 original size:561 final size:561
Alignment explanation
Indices: 196783--197896 Score: 1919
Period size: 561 Copynumber: 2.0 Consensus size: 561
196773 ATATATATTT
* * *
196783 AATACGTGTATCTATTTATTTTTTAGTATTCTCTCCGTCCCACTAAATGTGCCCATTATTAACTT
1 AATACGTGTATCCATTTATTTCTTAGTACTCTCTCCGTCCCACTAAATGTGCCCATTATTAACTT
196848 TTAAAAGGTCAAAAAATTTAAACTTTGACCATTATTATTTTAAATATTTTAAACAATTAAATTTT
66 TTAAAAGGTCAAAAAATTTAAACTTTGACCATTATTATTTTAAATATTTTAAACAATTAAATTTT
* * * *
196913 ATAAAATATATAGGGTAAATTACACTATTCCTCACTGAACTTTATTCTCTCTCCTATTTTACCTA
131 ATAAAATATATACGGTAAATTACACTATTCCTAACTAAACTTTACTCTCTCTCCTATTTTACCTA
* * *
196978 TTGTACTTTCAGTTTTCTAATTTACTCATGTAACTTTCGAATTGCTCATGTTCTTGGTCACTTTG
196 TTGTACTTTCAGTTTTCTAATTTACTCACGTAACTTTCGAATTGCTCATGTTCTTGGCCACTCTG
197043 AATTATTTTATTATTATTTTGATATGACATGACATTTTTATTATTATTAAAATATGAAAGTAATT
261 AATTATTTTATTATTATTTTGATATGACATGACATTTTTATTATTATTAAAATATGAAAGTAATT
197108 TAAAATAAATGATAAAATAATATTTTATTATCTTTAAATTTAAAAACATTTAACATAATCACTGC
326 TAAAATAAATGATAAAATAATATTTTATTATCTTTAAATTTAAAAACATTTAACATAATCACTGC
*
197173 CCACTGTTAAACAGAGTTCACCATCATCGACCTTCAGAACCGACAATCGTTCGATATCAAATTTC
391 CCACTGTTAAACAGAGTTAACCATCATCGACCTTCAGAACCGACAATCGTTCGATATCAAATTTC
* *
197238 ATAGATCGCTTGGCCTTGACCTTCTGATTTCGAATATGGTTGTTGTTTCACCGAAAAATGTCTCA
456 ATAGATCGCTTCGCCTTGACCTTCTGATTTCGAATATGGTGGTTGTTTCACCGAAAAATGTCTCA
*
197303 GAACCCCGTGAATCTCGATCAAAATATTTCGGTATATAGCC
521 AAACCCCGTGAATCTCGATCAAAATATTTCGGTATATAGCC
* *
197344 AATACGTGTATCCATTTGTTTCTTAGTACTCTCTCCGTCCCACTAAATGTGTCCATTATTAACTT
1 AATACGTGTATCCATTTATTTCTTAGTACTCTCTCCGTCCCACTAAATGTGCCCATTATTAACTT
*
197409 TTAAAATGTCAAAAAAATTTAAACTTTGACCATTATTATTTTAAATATTTTAAACAATTAAATTT
66 TTAAAAGGTC-AAAAAATTTAAACTTTGACCATTATTATTTTAAATATTTTAAACAATTAAATTT
* *
197474 TATAAAATATATACGGTAAATTGCACTATTCTTAACTAAACTTTACTCTCTCTCCTATTTTACCT
130 TATAAAATATATACGGTAAATTACACTATTCCTAACTAAACTTTACTCTCTCTCCTATTTTACCT
*
197539 ATTGTACTTTCAGTCTTTCTAATTTACTCACGTAACTTTCGAATTGTTCATG-TC-TGGCCACTC
195 ATTGTACTTTCAGT-TTTCTAATTTACTCACGTAACTTTCGAATTGCTCATGTTCTTGGCCACTC
197602 TGAATTATTTTATTATTATTTTGATATGACATGACATTTTTATTATTATTAAAATATGAAAGTAA
259 TGAATTATTTTATTATTATTTTGATATGACATGACATTTTTATTATTATTAAAATATGAAAGTAA
*
197667 TTTAAAATAAATGATAAAATAATATTTTATTATCTTTAAATTTAAAAACATTTAACATAATCATT
324 TTTAAAATAAATGATAAAATAATATTTTATTATCTTTAAATTTAAAAACATTTAACATAATCACT
* *
197732 GCCCACTGTTAACCAGAGTTAACCATCATC-AGCCTTCAGAACCGACAATCGTTCGATCTCAAAT
389 GCCCACTGTTAAACAGAGTTAACCATCATCGA-CCTTCAGAACCGACAATCGTTCGATATCAAAT
* * * * * *
197796 TTCATGGGTTGCTTCGCCTTGACCTTCTGATTTCGAATATGGTGGTTGTTTCATCGGAAAATGTT
453 TTCATAGATCGCTTCGCCTTGACCTTCTGATTTCGAATATGGTGGTTGTTTCACCGAAAAATGTC
197861 TCAAAACCCCGTGAATCTCGATCAAAATATTTCGGT
518 TCAAAACCCCGTGAATCTCGATCAAAATATTTCGGT
197897 TTCCTCACTT
Statistics
Matches: 521, Mismatches: 29, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
560 1 0.00
561 356 0.68
562 129 0.25
563 35 0.07
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (561 bp):
AATACGTGTATCCATTTATTTCTTAGTACTCTCTCCGTCCCACTAAATGTGCCCATTATTAACTT
TTAAAAGGTCAAAAAATTTAAACTTTGACCATTATTATTTTAAATATTTTAAACAATTAAATTTT
ATAAAATATATACGGTAAATTACACTATTCCTAACTAAACTTTACTCTCTCTCCTATTTTACCTA
TTGTACTTTCAGTTTTCTAATTTACTCACGTAACTTTCGAATTGCTCATGTTCTTGGCCACTCTG
AATTATTTTATTATTATTTTGATATGACATGACATTTTTATTATTATTAAAATATGAAAGTAATT
TAAAATAAATGATAAAATAATATTTTATTATCTTTAAATTTAAAAACATTTAACATAATCACTGC
CCACTGTTAAACAGAGTTAACCATCATCGACCTTCAGAACCGACAATCGTTCGATATCAAATTTC
ATAGATCGCTTCGCCTTGACCTTCTGATTTCGAATATGGTGGTTGTTTCACCGAAAAATGTCTCA
AAACCCCGTGAATCTCGATCAAAATATTTCGGTATATAGCC
Found at i:202065 original size:12 final size:12
Alignment explanation
Indices: 202038--202107 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
202028 ACAGAGATAT
* *
202038 CAGAAATCAAAA
1 CAGAATTCAGAA
*
202050 CAGAATTCAGAT
1 CAGAATTCAGAA
202062 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
202074 CAGAATCCAGAT
1 CAGAATTCAGAA
*
202086 CAGAAATCAGAA
1 CAGAATTCAGAA
202098 CAGAATTCAG
1 CAGAATTCAG
202108 GTAATGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:202070 original size:24 final size:24
Alignment explanation
Indices: 202036--202144 Score: 123
Period size: 24 Copynumber: 4.5 Consensus size: 24
202026 AAACAGAGAT
*
202036 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
202060 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
202084 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
202108 GTAATG-TATCAGAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
*
202131 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
202145 TAAAATGTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
23 1 0.01
24 68 0.97
25 1 0.01
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:202100 original size:48 final size:47
Alignment explanation
Indices: 202036--202144 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 47
202026 AAACAGAGAT
* *
202036 ATCAGAAATCAAAACAGAATTCAGATCA-GATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAATG-TATCAGAACAGAATCCA
* *
202083 GATCAGAAATCAGAACAGAATTCAGGTAATGTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAATGTATCAGAACAGAATCCA
*
202131 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
202145 TAAAATGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAATGTATCAGAACAGAATCCA
Found at i:207157 original size:24 final size:24
Alignment explanation
Indices: 207130--207201 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
207120 AAACGGAGAT
* *
207130 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
207154 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
207178 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
207202 GTAATGTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:207201 original size:12 final size:12
Alignment explanation
Indices: 207132--207201 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
207122 ACGGAGATAT
* *
207132 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
207144 CATAATTCAGAT
1 CAGAATTCAGAA
207156 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
207168 CAGAATCCAGAT
1 CAGAATTCAGAA
*
207180 CAGAAATCAGAA
1 CAGAATTCAGAA
207192 CAGAATTCAG
1 CAGAATTCAG
207202 GTAATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:207212 original size:48 final size:48
Alignment explanation
Indices: 207130--207221 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
207120 AAACGGAGAT
* *
207130 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
* * *
207178 ATCAGAAATCAGAACAGAATTCAGGTAATG-TATCATAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGATAA-GATATCAGAACAGAAT
207222 TCAAGTCGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
48 37 0.97
49 1 0.03
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
Found at i:212221 original size:24 final size:24
Alignment explanation
Indices: 212194--212288 Score: 113
Period size: 24 Copynumber: 4.0 Consensus size: 24
212184 AAACGGAGAT
*
212194 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
212218 ATCA-AATATCAGAACAGAATCCAG
1 ATCAGAA-ATCAGAACAGAATTCAG
212242 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
212266 GTAATG-TATCAGAACAGAATTCA
1 ATCA-GAAATCAGAACAGAATTCA
212289 AGTTGGAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.03
24 57 0.92
25 3 0.05
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:212265 original size:12 final size:12
Alignment explanation
Indices: 212196--212265 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
212186 ACGGAGATAT
* *
212196 CAGAAATCAAAA
1 CAGAATTCAGAA
*
212208 CAGAATTCAGAT
1 CAGAATTCAGAA
212220 CA-AATATCAGAA
1 CAGAAT-TCAGAA
* *
212232 CAGAATCCAGAT
1 CAGAATTCAGAA
*
212244 CAGAAATCAGAA
1 CAGAATTCAGAA
212256 CAGAATTCAG
1 CAGAATTCAG
212266 GTAATGTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 3 0.07
12 40 0.87
13 3 0.07
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:212265 original size:48 final size:48
Alignment explanation
Indices: 212194--212285 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
212184 AAACGGAGAT
212194 ATCAGAAATCAAAACAGAATTCAGATCAA-ATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAT-AATATATCAGAACAGAATCCAG
* * *
212242 ATCAGAAATCAGAACAGAATTCAGGTAATGTATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGATAATATATCAGAACAGAAT
212286 TCAAGTTGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 2 0.05
48 38 0.95
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAATATATCAGAACAGAATCCAG
Found at i:212300 original size:24 final size:23
Alignment explanation
Indices: 212198--212302 Score: 63
Period size: 24 Copynumber: 4.4 Consensus size: 23
212188 GGAGATATCA
* *
212198 GAAATCAAAACAGAATTC-AGATC
1 GAAATCAGAACAGAATTCAAG-TT
* * *
212221 AAATATCAGAACAGAA-TCCAGATCA
1 GAA-ATCAGAACAGAATTCAAG-T-T
*
212246 GAAATCAGAACAGAATTCAGGTAAT
1 GAAATCAGAACAGAATTCAAGT--T
*
212271 G-TATCAGAACAGAATTCAAGTT
1 GAAATCAGAACAGAATTCAAGTT
212293 GGAAATCAGA
1 -GAAATCAGA
212303 TAAAATATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
22 1 0.02
23 5 0.08
24 52 0.81
25 6 0.09
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (23 bp):
GAAATCAGAACAGAATTCAAGTT
Found at i:221394 original size:20 final size:21
Alignment explanation
Indices: 221369--221418 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
221359 AAACCCTTCT
221369 CCAAATCTTT-CTCTTTCAAC
1 CCAAATCTTTGCTCTTTCAAC
* *
221389 CCAAATTTTTGTTCTTTCAAC
1 CCAAATCTTTGCTCTTTCAAC
*
221410 TCATAATCT
1 CCA-AATCT
221419 CTCAAACAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.38
21 11 0.46
22 4 0.17
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (21 bp):
CCAAATCTTTGCTCTTTCAAC
Found at i:221901 original size:168 final size:168
Alignment explanation
Indices: 221668--222009 Score: 463
Period size: 168 Copynumber: 2.0 Consensus size: 168
221658 CAACTTCACC
* *
221668 TCTTTACATTGCTGCTCACATTGCTTTACACTAAACTCAAAATCTCTACGACGTTCTCCCAAAGC
1 TCTTTCCATTGCTGCTCACATTGCTTTACACTAAACTCAAAATATCTACGACGTTCTCCCAAAGC
* * *
221733 CTTTTCTTCCAACTCAAACTCCATATACCGCTTCTGAAAA-CTCTCCTCTTTCAACCCAAATT-T
66 CTTTTCTTCCAACTCAAACTCCATACACCGCTTCTCAAAATC-CGCCTCTTTCAACCCAAATTGT
** *
221796 CTGTTCTTTCAACTCATAATCTCTCATGCAGTTGTCCAAT
130 -TCCTCTTTCAACTCATAATCTCTCAAGCAGTTGTCCAAT
* * * * * * *
221836 TTTTTCCATTGCTGCTCACATTGTTTTACATTAAAGTCAAGATATCTACGGCGTTCTTCCAAAGC
1 TCTTTCCATTGCTGCTCACATTGCTTTACACTAAACTCAAAATATCTACGACGTTCTCCCAAAGC
* * * *
221901 CTTTTCTTCCGACTCAAACTCCATACATCGCTTCTCAAAATCCGCCTCTTTCAGCCTAAATTGTT
66 CTTTTCTTCCAACTCAAACTCCATACACCGCTTCTCAAAATCCGCCTCTTTCAACCCAAATTGTT
* *
221966 CCTCTTTCAACTCATACTCTCTCAAGCATTTGTCCAAT
131 CCTCTTTCAACTCATAATCTCTCAAGCAGTTGTCCAAT
222004 TCTTTC
1 TCTTTC
222010 TCTTTCAACC
Statistics
Matches: 150, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
168 148 0.99
169 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.08, T:0.37
Consensus pattern (168 bp):
TCTTTCCATTGCTGCTCACATTGCTTTACACTAAACTCAAAATATCTACGACGTTCTCCCAAAGC
CTTTTCTTCCAACTCAAACTCCATACACCGCTTCTCAAAATCCGCCTCTTTCAACCCAAATTGTT
CCTCTTTCAACTCATAATCTCTCAAGCAGTTGTCCAAT
Found at i:221979 original size:231 final size:227
Alignment explanation
Indices: 221759--222484 Score: 612
Period size: 231 Copynumber: 3.1 Consensus size: 227
221749 AACTCCATAT
* *
221759 ACCGCTTCTG-AAAACTCTCCTCTTTCAACCCAAATT-TCTGTTCTTTCAACTCATAATCTCTCA
1 ACCGCTTCTGCAAATCT-TTCTCTTTCAACCCAAATTCTCTGTTCTTTCAACTCATAATCTC-CA
* * *
221822 TGCAGTTGTCCAATTTTTTCCATTGCTGCTCACATTGTTTTACATTAAAGTCAAGATATCTACGG
64 TGCACTTATCCAATTTTTTCCA-TGCTGCTCACATTGTTTTACATCAAAGTCAAGATATCTACGG
* * *
221887 CGTTCTTCCAAAGCCTTTTCTTCCGACTCAAACTCCATACATCGCTTCTCAAAATCCGCCTCTTT
128 CGTTCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCATACAACGCTTC-CAAAA-CCTCCTCTTT
* *
221952 CAGCCTAAATTGTTCCTCTTTCAACTCATACTCTCTCA
191 CAGCC-AAATTGCTCTTCTTTCAACTCATACTCTCTCA
* ** * * * * * * ** **
221990 AGCATTTGTCCAATTCTTTCTCTTTCAACCGAACTTCCTCCAACTGATCTTT-TGC-CATTTTCT
1 ACCGCTTCTGCAAATCTTTCTCTTTCAACCCAAATT-CT----CTGTTCTTTCAACTCATAATCT
* * * *
222053 CCAT-CAACTTAACC--TCTTTACGC-TGCTGCTCACATT-TTTTA-ATACAAAGTTCAAGATCT
61 CCATGC-ACTTATCCAATTTTTTC-CATGCTGCTCACATTGTTTTACAT-CAAAG-TCAAGATAT
* *
222112 CTACGGCGTTCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCACACACCGCTTCCGAAAACTCTC
122 CTACGGCGTTCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCATACAACGCTTCC-AAAAC-CTC
* *
222177 CTCTTTCACCCCAAATTGCTCTTCTTTCGACTCATACTCTCTCAA
185 CTCTTTCA-GCCAAATTGCTCTTCTTTCAACTCATACTCTCTC-A
* * * * * * *
222222 ACC-CTTCTCCAGATCTTTCTCTTTCAACACAAATTGT-TGTTCTTTCAACTCATACTCTAGCAA
1 ACCGCTTCTGCAAATCTTTCTCTTTCAACCCAAATTCTCTGTTCTTTCAACTCATAATCT-CCAT
* * * * * *** * * *
222285 GCACTTCTCCAAATCTTTCCAATGCTTCTCGCATTGTTTTACATGGCATTCAAGATTTCTACGAC
65 GCACTTATCCAATTTTTTCC-ATGCTGCTCACATTGTTTTACATCAAAGTCAAGATATCTACGGC
* * * *
222350 GTTCTTCCAAAGCTTTTTCTTCCAACTCAAACTCCATAAAACGTTTCCCAAAACCCTTCTCTTTC
129 GTTCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCATACAACGCTT-CCAAAA-CCTCCTCTTTC
* *
222415 AGTCCAAATTGCTCTTCTTTCAACTCGTAGTCTCTCA
192 AG-CCAAATTGCTCTTCTTTCAACTCATACTCTCTCA
* ** * *
222452 AGCAATTCTCCAAATCTTTTTCTTTCAACCCAA
1 ACCGCTTCTGCAAATCTTTCTCTTTCAACCCAA
222485 CTTCCTCCCA
Statistics
Matches: 391, Mismatches: 75, Indels: 58
0.75 0.14 0.11
Matches are distributed among these distances:
225 7 0.02
226 1 0.00
227 6 0.02
228 8 0.02
229 4 0.01
230 18 0.05
231 295 0.75
232 23 0.06
233 5 0.01
234 8 0.02
235 7 0.02
236 1 0.00
237 8 0.02
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (227 bp):
ACCGCTTCTGCAAATCTTTCTCTTTCAACCCAAATTCTCTGTTCTTTCAACTCATAATCTCCATG
CACTTATCCAATTTTTTCCATGCTGCTCACATTGTTTTACATCAAAGTCAAGATATCTACGGCGT
TCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCATACAACGCTTCCAAAACCTCCTCTTTCAGCC
AAATTGCTCTTCTTTCAACTCATACTCTCTCA
Found at i:222082 original size:399 final size:399
Alignment explanation
Indices: 221379--222223 Score: 1205
Period size: 399 Copynumber: 2.1 Consensus size: 399
221369 CCAAATCTTT
* *
221379 CTCTTTCAACCCAAATTTTTGTTCTTTCAACTCATAATCTCTCAAACAGTTGTCCAGTTTTTTCC
1 CTCTTTCAACCCAAATTTCTGTTCTTTCAACTCATAATCTCTCAAACAGTTGTCCAATTTTTTCC
* * * * *
221444 ATTGCTGCTCACCTTGTTTTACATTAAATTCAAGATATGTACGACGTTCTGCCAAATCCTTTTTT
66 ATTGCTGCTCACATTGTTTTACATTAAAGTCAAGATATCTACGACGTTCTGCCAAAGCCTTTTCT
* * * * *
221509 TCCGACTCAAACTCCAGACATCGCTTCTCAAAGTCCTCCTCTTTCAGCCTAATTTGCTCTTTTTT
131 TCCGACTCAAACTCCAGACATCGCTTCTCAAAATCCGCCTCTTTCAGCCTAAATTGCTCCTCTTT
* *
221574 CAACTCATACTCTCTCAAGTTCTTCTTCAAATCTTTCTCTTTCAACCCAACTTCCTCCAACCTAT
196 CAACTCATACTCTCTCAAGATCTTCTCCAAATCTTTCTCTTTCAACCCAACTTCCTCCAACCTAT
* ** * *
221639 CTTTTACTGATATCTCTGTCAACTTCACCTCTTTACATTGCTGCTCACATTGCTTT-ACACTAAA
261 CTTTTACTCATATCTCCATCAACTTAACCTCTTTACACTGCTGCTCACATT-CTTTAACAC-AAA
* *
221703 -CTCAAAATCTCTACGACGTTCTCCCAAAGCCTTTTCTTCCAACTCAAACTCCATATACCGCTTC
324 GCTCAAAATCTCTACGACGTTCTCCCAAAGCCTTTTCTTCCAACTCAAACTCCACACACCGCTTC
*
221767 TGAAAACTCTC
389 CGAAAACTCTC
**
221778 CTCTTTCAACCCAAATTTCTGTTCTTTCAACTCATAATCTCTCATGCAGTTGTCCAATTTTTTCC
1 CTCTTTCAACCCAAATTTCTGTTCTTTCAACTCATAATCTCTCAAACAGTTGTCCAATTTTTTCC
* *
221843 ATTGCTGCTCACATTGTTTTACATTAAAGTCAAGATATCTACGGCGTTCTTCCAAAGCCTTTTCT
66 ATTGCTGCTCACATTGTTTTACATTAAAGTCAAGATATCTACGACGTTCTGCCAAAGCCTTTTCT
* *
221908 TCCGACTCAAACTCCATACATCGCTTCTCAAAATCCGCCTCTTTCAGCCTAAATTGTTCCTCTTT
131 TCCGACTCAAACTCCAGACATCGCTTCTCAAAATCCGCCTCTTTCAGCCTAAATTGCTCCTCTTT
* * *
221973 CAACTCATACTCTCTCAAGCAT-TTGTCCAATTCTTTCTCTTTCAACCGAACTTCCTCCAA-CTG
196 CAACTCATACTCTCTCAAG-ATCTTCTCCAAATCTTTCTCTTTCAACCCAACTTCCTCCAACCT-
* * * * *
222036 ATCTTTTGC-CATTTTCTCCATCAACTTAACCTCTTTACGCTGCTGCTCACATTTTTTAATACAA
259 ATCTTTTACTCA-TATCTCCATCAACTTAACCTCTTTACACTGCTGCTCACATTCTTTAACACAA
* * * *
222100 AGTTCAAGATCTCTACGGCGTTCTTCCAAAGCCTTTTCTTCCAACTCAAACTCCACACACCGCTT
323 AGCTCAAAATCTCTACGACGTTCTCCCAAAGCCTTTTCTTCCAACTCAAACTCCACACACCGCTT
222165 CCGAAAACTCTC
388 CCGAAAACTCTC
* * * * *
222177 CTCTTTCACCCCAAATTGCTCTTCTTTCGACTCATACTCTCTCAAAC
1 CTCTTTCAACCCAAATTTCTGTTCTTTCAACTCATAATCTCTCAAAC
222224 CCTTCTCCAG
Statistics
Matches: 394, Mismatches: 47, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
398 9 0.02
399 384 0.97
400 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.08, T:0.37
Consensus pattern (399 bp):
CTCTTTCAACCCAAATTTCTGTTCTTTCAACTCATAATCTCTCAAACAGTTGTCCAATTTTTTCC
ATTGCTGCTCACATTGTTTTACATTAAAGTCAAGATATCTACGACGTTCTGCCAAAGCCTTTTCT
TCCGACTCAAACTCCAGACATCGCTTCTCAAAATCCGCCTCTTTCAGCCTAAATTGCTCCTCTTT
CAACTCATACTCTCTCAAGATCTTCTCCAAATCTTTCTCTTTCAACCCAACTTCCTCCAACCTAT
CTTTTACTCATATCTCCATCAACTTAACCTCTTTACACTGCTGCTCACATTCTTTAACACAAAGC
TCAAAATCTCTACGACGTTCTCCCAAAGCCTTTTCTTCCAACTCAAACTCCACACACCGCTTCCG
AAAACTCTC
Found at i:222244 original size:63 final size:63
Alignment explanation
Indices: 222177--222303 Score: 164
Period size: 63 Copynumber: 2.0 Consensus size: 63
222167 GAAAACTCTC
* * * ** * *
222177 CTCTTTCACCCCAAATTGCTCTTCTTTCGACTCATACTCTCTCAAACCCTTCTCCAGATCTTT
1 CTCTTTCAACACAAATTGCTCTTCTTTCAACTCATACTCTAGCAAACACTTCTCCAAATCTTT
* * *
222240 CTCTTTCAACACAAATTGTTGTTCTTTCAACTCATACTCTAGCAAGCACTTCTCCAAATCTTT
1 CTCTTTCAACACAAATTGCTCTTCTTTCAACTCATACTCTAGCAAACACTTCTCCAAATCTTT
222303 C
1 C
222304 CAATGCTTCT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.38
Consensus pattern (63 bp):
CTCTTTCAACACAAATTGCTCTTCTTTCAACTCATACTCTAGCAAACACTTCTCCAAATCTTT
Found at i:222553 original size:231 final size:226
Alignment explanation
Indices: 221851--222569 Score: 636
Period size: 231 Copynumber: 3.1 Consensus size: 226
221841 CCATTGCTGC
* * *
221851 TCACATTGTTTTACATTAAAGTCAAGATATCTACGGCGTTCTTCCAAAGCCTTTTCTTCCGACTC
1 TCACATTGTTTTACA-TACATTCAAGATATCTACGGCGTTCTTCCAAAGCCTTTTCTTCCAACTC
* * * * * *
221916 AAACTCCATACATCGCTTCTCAAAATCCGCCTCTTTCAGCCTAAATTGTTCCTCTTTCAACTCAT
65 AAACTCCATACAACGCTTCCCAAAACCCTCCTCTTTCAGCC-AAATTGCTCTTCTTTCAACTCAT
* * * * * *
221981 ACTCTCTCAAGCATTTGTCCAATTCTTTCTCTTTCAACCGAACTTCCTCCAAC-TGATCTTTTGC
129 ACTCTCTCAAGCAATTCTCCAAATCTTTCTCTTTCAACCCAACTTCCTCC-ACTTG-TTTTTTAC
* *
222045 CATTTTCTCCATCAACTTAACCTCTTTACGCTGCTGC-
192 CATTTTCTCCATCAA-TTTACCTCTTTAAG-TGCT-CT
*
222082 TCACATT-TTTTA-ATACAAAGTTCAAGATCTCTACGGCGTTCTTCCAAAGCCTTTTCTTCCAAC
1 TCACATTGTTTTACATAC--A-TTCAAGATATCTACGGCGTTCTTCCAAAGCCTTTTCTTCCAAC
* * * * * *
222145 TCAAACTCCACACACCGCTTCCGAAAACTCTCCTCTTTCACCCCAAATTGCTCTTCTTTCGACTC
63 TCAAACTCCATACAACGCTTCCCAAAACCCTCCTCTTTCA-GCCAAATTGCTCTTCTTTCAACTC
* ** * * * * *
222210 ATACTCTCTCAAACCCTTCTCCAGATCTTTCTCTTTCAACACAA-AT--T---GTTGTTCTTTCA
127 ATACTCTCTCAAGCAATTCTCCAAATCTTTCTCTTTCAACCCAACTTCCTCCACTTGTT-TTT-T
** * * *
222269 ACTCATACTCTAGCAAGCACTTCT-CCAAATCTTTCCAA-TGCT-T
190 AC-CATTTTCT--CCATCAATT-TACC---TCTTT--AAGTGCTCT
* * * * *
222312 CTCGCATTGTTTTACATGGCATTCAAGATTTCTACGACGTTCTTCCAAAGCTTTTTCTTCCAACT
1 -TCACATTGTTTTACAT-ACATTCAAGATATCTACGGCGTTCTTCCAAAGCCTTTTCTTCCAACT
* * * *
222377 CAAACTCCATAAAACGTTTCCCAAAACCCTTCTCTTTCAGTCCAAATTGCTCTTCTTTCAACTCG
64 CAAACTCCATACAACGCTTCCCAAAACCCTCCTCTTTCAG-CCAAATTGCTCTTCTTTCAACTCA
* *
222442 TAGTCTCTCAAGCAATTCTCCAAATCTTTTTCTTTCAACCCAACTTCCTCCCACTTGTTTTTTAC
128 TACTCTCTCAAGCAATTCTCCAAATCTTTCTCTTTCAACCCAACTTCCT-CCACTTGTTTTTTAC
*
222507 CATTTTCTCCATCAATTTAGCCTCCTTAAGTTGCTCT
192 CATTTTCTCCATCAATTTA-CCTCTTTAAG-TGCTCT
*
222544 TCACATTGTTTTACACTAAATTCAAG
1 TCACATTGTTTTACA-TACATTCAAG
222570 GTCTTTACTG
Statistics
Matches: 384, Mismatches: 69, Indels: 70
0.73 0.13 0.13
Matches are distributed among these distances:
224 1 0.00
225 5 0.01
226 1 0.00
227 6 0.02
228 7 0.02
229 7 0.02
230 7 0.02
231 309 0.80
232 12 0.03
233 9 0.02
234 4 0.01
235 6 0.02
236 2 0.01
237 3 0.01
238 5 0.01
ACGTcount: A:0.24, C:0.31, G:0.08, T:0.37
Consensus pattern (226 bp):
TCACATTGTTTTACATACATTCAAGATATCTACGGCGTTCTTCCAAAGCCTTTTCTTCCAACTCA
AACTCCATACAACGCTTCCCAAAACCCTCCTCTTTCAGCCAAATTGCTCTTCTTTCAACTCATAC
TCTCTCAAGCAATTCTCCAAATCTTTCTCTTTCAACCCAACTTCCTCCACTTGTTTTTTACCATT
TTCTCCATCAATTTACCTCTTTAAGTGCTCT
Found at i:225302 original size:184 final size:182
Alignment explanation
Indices: 224833--225406 Score: 577
Period size: 185 Copynumber: 3.1 Consensus size: 182
224823 GTTACCAATA
* * **
224833 ACTAGGAAATTAGGTTGAGATCTAAAATGTTATAAGTTTCTTTAACAAATTCGGTTTGGACTTAA
1 ACTAAGAAATTAGGTTGAGATCT-GAATGTTATAAGTTT-TTTAACAAATTCGGTTTGGACCAAA
* * * * * * * *
224898 AATGTTACCGGAGTTTAGCACATGAGT--AAAAAATAGTTACAATGACAAAAATAAGCTGAAAGC
64 AATGTTACCGAAGTTTAACAAATGGGTCAAAAAAATAGCTACAGTAAC-AAAATAAGTTGAAAGC
* *** * * * *
224961 TAAAAAAATCATCAATCGCATTAACAAATCCGATTACACTCAAGAACACTATCGATC
128 TAAAAATATCATCAATCGCATTAACAAATCCGATT-GTGTCAA-AAAATTATTGGTC
* *
225018 GCTAAGAAATT-GTGTTAAGAT-TGAAT-TCTATAAGTTTTTTAACAAATTCGGTTTGGACCAAA
1 ACTAAGAAATTAG-GTTGAGATCTGAATGT-TATAAGTTTTTTAACAAATTCGGTTTGGACCAAA
* ** *
225080 AATGTTACCAAAGTTTAACAAACAGGTCAAAGAAAATAGCCACAGTAACAAAATAAGTTGAAA-C
64 AATGTTACCGAAGTTTAACAAATGGGTCAAA-AAAATAGCTACAGTAACAAAATAAGTTGAAAGC
*** * *
225144 CCGAAATATCATCAATCGCGTTAATAAATCCGATTGTGTCAAAAAAGTTATTGGTC
128 TAAAAATATCATCAATCGCATTAACAAATCCGATTGTGTCAAAAAA-TTATTGGTC
* * * *
225200 CCTAAGAAATTAGGTTGAGATCGTGAATGTTATAAGTTTTTTAACAAATTTGATTTTGGACCGAA
1 ACTAAGAAATTAGGTTGAGATC-TGAATGTTATAAGTTTTTTAACAAATTCG-GTTTGGACCAAA
* * *
225265 AATATTACCGAAGTTTAACAAATGGGTCAAAAAAATAGCTAC-GCTAATAAAATAAGTTGAAAGT
64 AATGTTACCGAAGTTTAACAAATGGGTCAAAAAAATAGCTACAG-TAACAAAATAAGTTGAAAGC
* * * *
225329 TAAAAATTTTATCAATCGCATTAACAAATCGGATTGTGTTAAAAAATATTATTGGTC
128 TAAAAATATCATCAATCGCATTAACAAATCCGATTGTG-TCAAAAA-ATTATTGGTC
* *
225386 ACTAAAAAATTAAGTTGAGAT
1 ACTAAGAAATTAGGTTGAGAT
225407 AAAAACTATA
Statistics
Matches: 319, Mismatches: 55, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
181 3 0.01
182 71 0.22
183 44 0.14
184 70 0.22
185 97 0.30
186 33 0.10
187 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (182 bp):
ACTAAGAAATTAGGTTGAGATCTGAATGTTATAAGTTTTTTAACAAATTCGGTTTGGACCAAAAA
TGTTACCGAAGTTTAACAAATGGGTCAAAAAAATAGCTACAGTAACAAAATAAGTTGAAAGCTAA
AAATATCATCAATCGCATTAACAAATCCGATTGTGTCAAAAAATTATTGGTC
Found at i:236137 original size:17 final size:17
Alignment explanation
Indices: 236115--236155 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
236105 TATCTAATAC
236115 GTTAACTGTTAACGATA
1 GTTAACTGTTAACGATA
236132 GTTAACTGTTAACGATA
1 GTTAACTGTTAACGATA
236149 GTTAACT
1 GTTAACT
236156 CGTGGTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (17 bp):
GTTAACTGTTAACGATA
Found at i:240220 original size:3 final size:3
Alignment explanation
Indices: 240212--240280 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
240202 TATCTAATTG
240212 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
240260 TTA -TA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
240281 GCTTATTTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:240805 original size:13 final size:13
Alignment explanation
Indices: 240787--240811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
240777 GGGTTCAGAG
240787 AAAAAAAAAAACC
1 AAAAAAAAAAACC
240800 AAAAAAAAAAAC
1 AAAAAAAAAAAC
240812 AGAGGATAGA
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACC
Found at i:240867 original size:24 final size:24
Alignment explanation
Indices: 240821--240867 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
240811 CAGAGGATAG
* **
240821 AGAAAAAAAAGAGAGATTCGAAAC
1 AGAAAAAAAAAAGAGAAACGAAAC
*
240845 AGAAAAAAAAAAGAGAAAGGAAA
1 AGAAAAAAAAAAGAGAAACGAAA
240868 GAGGAGAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.70, C:0.04, G:0.21, T:0.04
Consensus pattern (24 bp):
AGAAAAAAAAAAGAGAAACGAAAC
Found at i:241444 original size:19 final size:19
Alignment explanation
Indices: 241398--241444 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
241388 CATTAATTTG
*
241398 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
241418 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
241438 TATATTT
1 TATATTT
241445 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:243923 original size:31 final size:32
Alignment explanation
Indices: 243887--243948 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
243877 ATTTTACATG
243887 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
243918 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
243949 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:245158 original size:26 final size:25
Alignment explanation
Indices: 245127--245206 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
245117 CCAATTTTTG
245127 ACATTCTATCTCTTTGAGACCTTG-A
1 ACATTCT-TCTCTTTGAGACCTTGAA
* *
245152 A-A-TATTCT-TTT-CGACCTTGAA
1 ACATTCTTCTCTTTGAGACCTTGAA
*
245173 ACATTCCCTCTCTTTGAGACCTTGAA
1 ACATT-CTTCTCTTTGAGACCTTGAA
245199 ACATTCTT
1 ACATTCTT
245207 TCCACCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.16
21 5 0.12
22 4 0.09
23 3 0.07
24 4 0.09
25 6 0.14
26 14 0.33
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
ACATTCTTCTCTTTGAGACCTTGAA
Found at i:247740 original size:104 final size:101
Alignment explanation
Indices: 247554--247785 Score: 265
Period size: 104 Copynumber: 2.3 Consensus size: 101
247544 TGAGAATTTT
* ** * * *
247554 AAAACAAATTGCGTCTCGCTTGAGATATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCATT
1 AAAACAAATTTCGTCTCGCTTGAGA-CCTTTCCCTTTGAGATACAAATTTCGAATTTGATTCAAT
*
247619 TAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
65 TAAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* *
247659 AAAACAAATTTCGTCTCGCTTGAGACCTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACAT
1 AAAACAAATTTCGTCTCGCTTGAGACCTTTCCCTTTGAGATACAAATTTCGAATTTGATTCA-AT
* *
247724 T-AAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
65 TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
247760 AAAACAAACTTT-GTCTCGCTTGAGAC
1 AAAACAAA-TTTCGTCTCGCTTGAGAC
247786 AATTGCTCTA
Statistics
Matches: 112, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
100 2 0.02
101 22 0.20
102 7 0.06
103 4 0.04
104 51 0.46
105 26 0.23
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (101 bp):
AAAACAAATTTCGTCTCGCTTGAGACCTTTCCCTTTGAGATACAAATTTCGAATTTGATTCAATT
AAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:247782 original size:36 final size:36
Alignment explanation
Indices: 247737--247821 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
247727 ACAAAGTTGA
** *
247737 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTGCTCTAAAAACAAACTTTG
* *
247773 TCTCGCTTGAGACAATTGCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTGCTCTAAAAACAAACTTTG
*
247809 TCTCATTTGAGAC
1 TCTCACTTGAGAC
247822 TATATCTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 6 0.15
36 35 0.85
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTGCTCTAAAAACAAACTTTG
Found at i:248131 original size:27 final size:27
Alignment explanation
Indices: 248098--248232 Score: 155
Period size: 29 Copynumber: 4.8 Consensus size: 27
248088 AAGACAATTT
248098 CTTTTGAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAATCTTTGAGTTTGTTC
*
248125 CTCTTGAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAATCTTTGAGTTTGTTC
*
248152 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTG-A-AAAAATCTTTGAGTTTGTTC
* *
248181 CTTTTGAATAAAATTTTTTGAG-TTGTTT
1 CTTTTGAA-AAAA-TCTTTGAGTTTGTTC
*
248209 CGTTTGAAACAAAAATCTTTGAGT
1 CTTTTG--A-AAAAATCTTTGAGT
248233 CTATTTATTT
Statistics
Matches: 92, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
27 32 0.35
28 16 0.17
29 38 0.41
30 5 0.05
31 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (27 bp):
CTTTTGAAAAAATCTTTGAGTTTGTTC
Found at i:248182 original size:56 final size:56
Alignment explanation
Indices: 248098--248232 Score: 168
Period size: 56 Copynumber: 2.4 Consensus size: 56
248088 AAGACAATTT
248098 CTTTTG-AAAAAATCTTTGAGTTTGTTCCTCTTGAA-AAAA-TCTTTGAGTTTGTTC
1 CTTTTGAAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAATTCTTTGAG-TTGTTC
* * * *
248152 CTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAATTTTTTGAGTTGTTT
1 CTTTTGAA-AAAAATCTTTGAGTTTGTTCCTCTTGAATAAAATTCTTTGAGTTGTTC
*
248209 CGTTTGAAACAAAAATCTTTGAGT
1 CTTTTG-AA-AAAAATCTTTGAGT
248233 CTATTTATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
54 6 0.09
55 1 0.01
56 26 0.38
57 14 0.20
58 22 0.32
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (56 bp):
CTTTTGAAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAATTCTTTGAGTTGTTC
Found at i:248399 original size:29 final size:30
Alignment explanation
Indices: 248326--248532 Score: 123
Period size: 30 Copynumber: 6.4 Consensus size: 30
248316 TTGAGACAAT
* *
248326 TTTGTAAAAAAAAATCTTTGAGATTGTTTC
1 TTTGGAAACAAAAATCTTTGAGATTGTTTC
*
248356 TTTTGAAACAAAAATCTTTGAG-TTGGTTTC
1 TTTGGAAACAAAAATCTTTGAGATT-GTTTC
* * **
248386 TTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTC
1 TTTGGAAACAAAA------ATCT-TTGAGATTGTTTC
*
248423 TTTTGAAACAAAAATCTTTGAG-TCTGTTTC
1 TTTGGAAACAAAAATCTTTGAGAT-TGTTTC
* * **
248453 TTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTC
1 TTTGGAAACAAAA------ATCT-TTGAGATTGTTTC
*
248490 TTTTGAAACAAAAATCTTTGAG-TATGTTTC
1 TTTGGAAACAAAAATCTTTGAGAT-TGTTTC
248520 TTTGGAAACAAAA
1 TTTGGAAACAAAA
248533 TTTTGTCTCT
Statistics
Matches: 134, Mismatches: 24, Indels: 38
0.68 0.12 0.19
Matches are distributed among these distances:
29 4 0.03
30 76 0.57
31 6 0.04
36 6 0.04
37 40 0.30
38 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (30 bp):
TTTGGAAACAAAAATCTTTGAGATTGTTTC
Found at i:248432 original size:37 final size:37
Alignment explanation
Indices: 248382--248575 Score: 143
Period size: 37 Copynumber: 5.6 Consensus size: 37
248372 TTTGAGTTGG
248382 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* **
248419 TTTCTTTTGAAACAAAAATCTTTG--AGTC-T--G----
1 TTTCTTTGGAAAC-AAAAT-TTTGTCTCTCTTAAGATAA
248449 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* * * *
248486 TTTCTTTTGAAACAAAA------ATCT-TTGAG-TATG
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA-A
*
248516 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAT
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* *
248553 TTTCTTTTGAAAAAAAATCTTTG
1 TTTCTTTGGAAACAAAAT-TTTG
248576 AATCTGTTTC
Statistics
Matches: 120, Mismatches: 16, Indels: 41
0.68 0.09 0.23
Matches are distributed among these distances:
28 4 0.03
29 7 0.06
30 34 0.28
31 4 0.03
33 1 0.01
34 1 0.01
36 4 0.03
37 50 0.42
38 11 0.09
39 4 0.03
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:248460 original size:67 final size:67
Alignment explanation
Indices: 248352--248586 Score: 420
Period size: 67 Copynumber: 3.5 Consensus size: 67
248342 TTTGAGATTG
248352 TTTCTTTTGAAACAAAAATCTTTGAGT-TGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1 TTTCTTTTGAAACAAAAATCTTTGAGTCT-GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
248416 TAA
65 TAA
248419 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
248484 AA
66 AA
*
248486 TTTCTTTTGAAACAAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
*
248551 AT
66 AA
*
248553 TTTCTTTTGAAA-AAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT
248587 CTTAAAATGA
Statistics
Matches: 163, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
66 20 0.12
67 142 0.87
68 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:248659 original size:65 final size:66
Alignment explanation
Indices: 248351--248659 Score: 263
Period size: 67 Copynumber: 4.7 Consensus size: 66
248341 CTTTGAGATT
* * * *
248351 GTTTCTTTTGAAACAAAAATCTTTGAGT-TGGTTTCTTTGGAAACA-AAATTTTGTCTCTCTTAA
1 GTTTCTCTTGAAA-AAAAATCTTTGAATAT-GTTTCTTTTGAAA-ATAAATTTTGTATCTCTTAA
*
248414 GATA
63 GACA
* * * * * *
248418 ATTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACA-AAATTTTGTCTCTCTTAAG
1 GTTTCTCTTGAAA-AAAAATCTTTGAATATGTTTCTTTTGAAA-ATAAATTTTGTATCTCTTAAG
*
248482 ATA
64 ACA
* * * * *
248485 ATTTCTTTTGAAACAAAAATCTTTGAGTATGTTTCTTTGGAAACA-AAATTTTGTCTCTCTTAAG
1 GTTTCTCTTGAAA-AAAAATCTTTGAATATGTTTCTTTTGAAA-ATAAATTTTGTATCTCTTAAG
*
248549 ATA
64 ACA
* * * * * *
248552 TTTTCTTTTGAAAAAAAATCTTTGAATCTGTTTCTCTT-AAAATGAATTTTGTATCTCTTGAGAC
1 GTTTCTCTTGAAAAAAAATCTTTGAATATGTTTCTTTTGAAAATAAATTTTGTATCTCTTAAGAC
248616 A
66 A
**
248617 GTTTCTCTTG-AAGTAAATCTTTGAATATG-TTCATTTTGAAAAT
1 GTTTCTCTTGAAAAAAAATCTTTGAATATGTTTC-TTTTGAAAAT
248660 CTTTGAGTTT
Statistics
Matches: 221, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
63 3 0.01
64 20 0.09
65 34 0.15
66 21 0.10
67 142 0.64
68 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (66 bp):
GTTTCTCTTGAAAAAAAATCTTTGAATATGTTTCTTTTGAAAATAAATTTTGTATCTCTTAAGAC
A
Found at i:248855 original size:120 final size:120
Alignment explanation
Indices: 248687--248911 Score: 262
Period size: 120 Copynumber: 1.9 Consensus size: 120
248677 TTAACAAAAT
* * *
248687 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTAATGAAAAAC
1 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAA-
*
248752 TAA-CTTTTGAGATT-GTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGATC
65 AAATC-TTTGAG-TTGGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
* ** * **
248807 CATCTTTGAGTCTGTTTCTTTTGATACAAAAT-TT-TATCTCTTAAAGACAATTTCTTTTGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTAATGAAAA
* *
248870 AAAATCTTTGAGTTGGTTTCCTTTGAAACAAAATTTTGTCTC
64 AAAATCTTTGAGTTGGTTTCATTTGAAACAAAATTTGGTCTC
248912 TCGAGACAAC
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
118 2 0.02
119 28 0.32
120 54 0.61
121 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (120 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAAA
AATCTTTGAGTTGGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
Found at i:248889 original size:65 final size:64
Alignment explanation
Indices: 248808--248933 Score: 173
Period size: 65 Copynumber: 2.0 Consensus size: 64
248798 GATGTGATCC
* * *
248808 ATCTTTGAGTCTGTTTCTTTTGATACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAAA
* **
248873 ATCTTTGAGT-TGGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCT-GTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
248934 TACCCACCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
64 20 0.37
65 34 0.63
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (64 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAAA
Found at i:248970 original size:40 final size:40
Alignment explanation
Indices: 248915--248994 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
248905 TTGTCTCTCG
248915 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
248955 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
248995 CTATTAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
Found at i:249613 original size:28 final size:28
Alignment explanation
Indices: 249542--249623 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
249532 TAAAAATATC
* * *
249542 ATCTTTGAGTTTATTTTTCTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
** *
249570 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
249598 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTCTTGAAAC
249624 CATAACTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 43 0.93
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.50
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTCTTGAAACAA
Found at i:249704 original size:40 final size:40
Alignment explanation
Indices: 249649--250000 Score: 198
Period size: 40 Copynumber: 8.3 Consensus size: 40
249639 TGGCCAGCCG
* * * * *
249649 TCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAGACCAGACC
* * *
249689 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGACC
* * * *
249731 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGACC
* * *
249778 TCTTCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATC
1 TCCTCATCACGTATGAGCCGTGTCA-TCCCTAGACCAGACC
*
249818 TCTTCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGACC
* * * *
249859 GTCCTCATCACGTATGAACTGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGACC
* *
249906 TCTTCATCACGTATGAGCCGTGTCATTCTCC--GACCAGATC
1 TCCTCATCACGTATGAGCCGTGTCA-TC-CCTAGACCAGACC
*
249946 TCTTCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CC
1 TCCTCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGACC
249987 GTCCTCATCACGTA
1 -TCCTCATCACGTA
250001 GGAACCATGT
Statistics
Matches: 248, Mismatches: 32, Indels: 62
0.73 0.09 0.18
Matches are distributed among these distances:
37 2 0.01
38 4 0.02
39 2 0.01
40 89 0.36
41 2 0.01
42 44 0.18
43 36 0.15
44 3 0.01
46 58 0.23
47 8 0.03
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (40 bp):
TCCTCATCACGTATGAGCCGTGTCATCCCTAGACCAGACC
Found at i:249903 original size:128 final size:128
Alignment explanation
Indices: 249652--250047 Score: 620
Period size: 128 Copynumber: 3.1 Consensus size: 128
249642 CCAGCCGTCC
* * * * *
249652 TCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTC-AC
*
249716 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
64 CCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
249781 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
* *
249846 TAGATAACCAGCCGTCCTCATCACGTATGAACTGTGTTATCACCTTTAGATGGCCAGAACTCT
66 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
249909 TCATCACGTATGAGCCGTGTCATTCTCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
* * * * *
249974 TAGATAACCAGCCGTCCTCATCACGTAGGAACCATG---TCACCCTTAGACGACCCGAACTCT
66 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
250034 TCATCACGTATGAG
1 TCATCACGTATGAG
250048 TAGTGGCGTC
Statistics
Matches: 250, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
125 34 0.14
128 161 0.64
129 50 0.20
130 5 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (128 bp):
TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC
TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:250226 original size:3 final size:3
Alignment explanation
Indices: 250218--250293 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
250208 TATCTAATTG
250218 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
250266 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
250294 ATGCTTATTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:250320 original size:18 final size:18
Alignment explanation
Indices: 250222--250321 Score: 121
Period size: 18 Copynumber: 5.4 Consensus size: 18
250212 TAATTGTTAT
*
250222 TATTATTATTATTATTAT
1 TATTATTATTATTATTAA
*
250240 TATTATTATTATTATTAT
1 TATTATTATTATTATTAA
*
250258 TATTATTATTATTATTAT
1 TATTATTATTATTATTAA
250276 TATTATTATTATTATTATA
1 TATTATTATTATTATTA-A
* *
250295 TGCTTATTTATTGTTATTAA
1 T-ATTA-TTATTATTATTAA
250315 TA-TATTA
1 TATTATTA
250322 CAAATTTTTG
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
17 3 0.04
18 55 0.73
19 1 0.01
20 5 0.07
21 11 0.15
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (18 bp):
TATTATTATTATTATTAA
Found at i:251459 original size:19 final size:19
Alignment explanation
Indices: 251413--251459 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
251403 CATTAATTTG
*
251413 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
251433 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
251453 TATATTT
1 TATATTT
251460 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:256686 original size:18 final size:19
Alignment explanation
Indices: 256646--256689 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
256636 GTTGGTTTAC
* *
256646 GGAATATAAGATTATTAGTA
1 GGAATAAAAAATTATTAG-A
256666 GGAATAAAAAATTATTA-A
1 GGAATAAAAAATTATTAGA
256684 GGAATA
1 GGAATA
256690 GGATTAATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (19 bp):
GGAATAAAAAATTATTAGA
Found at i:256910 original size:37 final size:39
Alignment explanation
Indices: 256832--256911 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 39
256822 AACAAGTTGA
*
256832 AAAATATTTATATATTTTCTTTAAAAAAATTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAAATTAAAATCAT
*
256871 AAAATATATTATA-ATTTT-TTT-ACAAAATTAAAAAT-AT
1 AAAATAT-TTATATATTTTCTTTAAAAAAATT-AAAATCAT
256908 AAAA
1 AAAA
256912 AGATTTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 13 0.35
38 7 0.19
39 12 0.32
40 5 0.14
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAAATTAAAATCAT
Found at i:258080 original size:22 final size:22
Alignment explanation
Indices: 258052--258124 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
258042 TTTAAATTTA
*
258052 AAATATAAAAGTATTAAAAAAT
1 AAATATAAAAATATTAAAAAAT
* **
258074 AAGTATAAAAATACCAAAAAAT
1 AAATATAAAAATATTAAAAAAT
* * * *
258096 AAAAATTAAATTATTAAAAATT
1 AAATATAAAAATATTAAAAAAT
*
258118 ATATATA
1 AAATATA
258125 TATTATTATT
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (22 bp):
AAATATAAAAATATTAAAAAAT
Found at i:260049 original size:18 final size:18
Alignment explanation
Indices: 260028--260062 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
260018 TTGAAATTTT
260028 TATTATTAAAAAAATATA
1 TATTATTAAAAAAATATA
*
260046 TATTATTTAAAAAATAT
1 TATTATTAAAAAAATAT
260063 TTTTCTAAAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATTATTAAAAAAATATA
Found at i:268325 original size:19 final size:20
Alignment explanation
Indices: 268281--268326 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
268271 AGAGAACCGG
268281 CGGTTCACACCGGTTTTCAGC
1 CGGTTCACACCGGTTTT-AGC
* *
268302 TGGTTCACCCCGGTTTT-GC
1 CGGTTCACACCGGTTTTAGC
268321 CGGTTC
1 CGGTTC
268327 TCAACTGGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 7 0.32
21 15 0.68
ACGTcount: A:0.09, C:0.33, G:0.26, T:0.33
Consensus pattern (20 bp):
CGGTTCACACCGGTTTTAGC
Found at i:268570 original size:27 final size:27
Alignment explanation
Indices: 268525--268579 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
268515 CCAACCCGAT
* * *
268525 CCGACCCGAAAATTTTATATCATTCAC
1 CCGACCCGAAAAATATATACCATTCAC
*
268552 CCGACCCGAAAAATATATACCCTTCAC
1 CCGACCCGAAAAATATATACCATTCAC
268579 C
1 C
268580 TAACCCGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.35, G:0.07, T:0.24
Consensus pattern (27 bp):
CCGACCCGAAAAATATATACCATTCAC
Found at i:268585 original size:27 final size:27
Alignment explanation
Indices: 268528--268587 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
268518 ACCCGATCCG
* * * *
268528 ACCCGAAAATTTTATATCATTCACCCG
1 ACCCGAAAAATATATACCATTCACCCA
* *
268555 ACCCGAAAAATATATACCCTTCACCTA
1 ACCCGAAAAATATATACCATTCACCCA
268582 ACCCGA
1 ACCCGA
268588 CTTTTTTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.23
Consensus pattern (27 bp):
ACCCGAAAAATATATACCATTCACCCA
Found at i:272685 original size:28 final size:28
Alignment explanation
Indices: 272634--272687 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
272624 ACTATGATTA
* * *
272634 TTTTTAAGAATTGGTTCGATAGTATAAT
1 TTTTTAAGAATTGATTCAACAGTATAAT
*
272662 TTTTTAAGTATTGATTCAACAGTATA
1 TTTTTAAGAATTGATTCAACAGTATA
272688 GTATATACAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (28 bp):
TTTTTAAGAATTGATTCAACAGTATAAT
Found at i:275311 original size:38 final size:40
Alignment explanation
Indices: 275265--275439 Score: 142
Period size: 42 Copynumber: 4.3 Consensus size: 40
275255 TTTTCTAAAC
275265 AAACGCCACTAATGTAACGTGAAATTGC-C-TTTCTTCAA
1 AAACGCCACTAATGTAACGTGAAATTGCACATTTCTTCAA
* * * *
275303 AAATGCCACTAATGTTACGTGAAGTTGCGACATTTTCTTTAA
1 AAACGCCACTAATGTAACGTGAAATTGC-ACA-TTTCTTCAA
* * ** * *
275345 AAACGCCACTAATATAACATGAAATTGTGGCGTTT-TAACAA
1 AAACGCCACTAATGTAACGTGAAATTG-CACATTTCT-TCAA
* * *
275386 AAACACCACTAATGTAACATGAAATTGCAGAGTTCTCTTC-A
1 AAACGCCACTAATGTAACGTGAAATTGCACA-TT-TCTTCAA
275427 AAACTGCCACTAA
1 AAAC-GCCACTAA
275440 AGTACGAGCT
Statistics
Matches: 105, Mismatches: 22, Indels: 16
0.73 0.15 0.11
Matches are distributed among these distances:
38 25 0.24
40 2 0.02
41 37 0.35
42 40 0.38
43 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (40 bp):
AAACGCCACTAATGTAACGTGAAATTGCACATTTCTTCAA
Found at i:275353 original size:42 final size:38
Alignment explanation
Indices: 275265--275413 Score: 129
Period size: 38 Copynumber: 3.7 Consensus size: 38
275255 TTTTCTAAAC
275265 AAACGCCACTAATGTAACGTGAAATTGCCTTTCTTCAA
1 AAACGCCACTAATGTAACGTGAAATTGCCTTTCTTCAA
* * * *
275303 AAATGCCACTAATGTTACGTGAAGTTGCGACATTTTCTTTAA
1 AAACGCCACTAATGTAACGTGAAATTGC--C--TTTCTTCAA
* * * *
275345 AAACGCCACTAATATAACATGAAATTGTGGCGTTT-TAACAA
1 AAACGCCACTAATGTAACGTGAAA-T-T-GCCTTTCT-TCAA
* *
275386 AAACACCACTAATGTAACATGAAATTGC
1 AAACGCCACTAATGTAACGTGAAATTGC
275414 AGAGTTCTCT
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
38 27 0.30
39 1 0.01
40 3 0.03
41 27 0.30
42 27 0.30
43 1 0.01
44 1 0.01
45 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (38 bp):
AAACGCCACTAATGTAACGTGAAATTGCCTTTCTTCAA
Found at i:282458 original size:21 final size:20
Alignment explanation
Indices: 282428--282467 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
282418 TTTAAAAATT
282428 TTAAAATTTAAATACTAAAA
1 TTAAAATTTAAATACTAAAA
*
282448 TTAATAATTTAGATACTAAA
1 TTAA-AATTTAAATACTAAA
282468 TACGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (20 bp):
TTAAAATTTAAATACTAAAA
Found at i:285624 original size:19 final size:19
Alignment explanation
Indices: 285600--285646 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
285590 TTTGTTATGA
*
285600 GTTTTAATAGTAAAACTAT
1 GTTTTAACAGTAAAACTAT
285619 GTTTTAACAGTAAAACTAT
1 GTTTTAACAGTAAAACTAT
285638 GTTTTAACA
1 GTTTTAACA
285647 AACTCAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (19 bp):
GTTTTAACAGTAAAACTAT
Found at i:289392 original size:11 final size:11
Alignment explanation
Indices: 289376--289402 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
289366 AAACATTACT
289376 ATTCTTGAAGA
1 ATTCTTGAAGA
289387 ATTCTTGAAGA
1 ATTCTTGAAGA
289398 ATTCT
1 ATTCT
289403 CAATATCTGT
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:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (11 bp):
ATTCTTGAAGA
Found at i:289892 original size:20 final size:21
Alignment explanation
Indices: 289867--289912 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
289857 GTTGTGGTCG
*
289867 TTTCTAGCCG-TTGGGGATGA
1 TTTCTAGCCGTTTGAGGATGA
*
289887 TTTCTAGCCGTTTGAGGATGT
1 TTTCTAGCCGTTTGAGGATGA
289908 TTTCT
1 TTTCT
289913 CTGCAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.43
Consensus pattern (21 bp):
TTTCTAGCCGTTTGAGGATGA
Found at i:296317 original size:14 final size:14
Alignment explanation
Indices: 296300--296351 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
296290 GTTAAAAAAA
296300 TATTATTAAATTAT
1 TATTATTAAATTAT
296314 TATTATTAAATTAT
1 TATTATTAAATTAT
* *
296328 TATTATTAATTTTAG
1 TATTATTAA-ATTAT
296343 TATTATTAA
1 TATTATTAA
296352 GTGTGTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TATTATTAAATTAT
Found at i:309447 original size:7 final size:7
Alignment explanation
Indices: 309425--309486 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
309415 AAAAGGGAAC
*
309425 AAATAAA
1 AAATGAA
309432 AAGATGAA
1 AA-ATGAA
309440 AAATGAAA
1 AAATG-AA
309448 AAATG-A
1 AAATGAA
*
309454 AAA-GGA
1 AAATGAA
309460 AAA--AA
1 AAATGAA
309465 AAATGAA
1 AAATGAA
309472 AAATGAA
1 AAATGAA
*
309479 AAAAGAA
1 AAATGAA
309486 A
1 A
309487 TGAAAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 5 0.11
6 8 0.17
7 21 0.45
8 13 0.28
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (7 bp):
AAATGAA
Found at i:309449 original size:17 final size:17
Alignment explanation
Indices: 309429--309484 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
309419 GGGAACAAAT
309429 AAAAAGATGAAAAATG-
1 AAAAAGATGAAAAATGA
*
309445 AAAAA-ATG-AAAAGGAA
1 AAAAAGATGAAAAATG-A
*
309461 AAAAAAATGAAAAATGA
1 AAAAAGATGAAAAATGA
309478 AAAAAGA
1 AAAAAGA
309485 AATGAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 5 0.15
15 3 0.09
16 10 0.30
17 10 0.30
18 5 0.15
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (17 bp):
AAAAAGATGAAAAATGA
Found at i:309449 original size:32 final size:32
Alignment explanation
Indices: 309413--309483 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
309403 GCTTGAAGAA
* *
309413 AAAAAAGGGAACAA-ATAAAAAGATGAAAAATG
1 AAAAAAGGGAA-AAGAAAAAAAAATGAAAAATG
*
309445 AAAAAA-TGAAAAGGAAAAAAAAATGAAAAATG
1 AAAAAAGGGAAAA-GAAAAAAAAATGAAAAATG
309477 AAAAAAG
1 AAAAAAG
309484 AAATGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 2 0.06
31 3 0.09
32 28 0.85
ACGTcount: A:0.73, C:0.01, G:0.17, T:0.08
Consensus pattern (32 bp):
AAAAAAGGGAAAAGAAAAAAAAATGAAAAATG
Found at i:309481 original size:19 final size:18
Alignment explanation
Indices: 309445--309493 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
309435 ATGAAAAATG
*
309445 AAAAAATG-AAAAGGAAA
1 AAAAAATGAAAAAGAAAA
309462 AAAAAATGAAAAATGAAAA
1 AAAAAATGAAAAA-GAAAA
*
309481 AAGAAATGAAAAA
1 AAAAAATGAAAAA
309494 ATAAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.29
18 4 0.14
19 16 0.57
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (18 bp):
AAAAAATGAAAAAGAAAA
Found at i:309481 original size:25 final size:26
Alignment explanation
Indices: 309438--309511 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 26
309428 TAAAAAGATG
309438 AAAAATGAAAAAATG-AAAAGGAAA-A
1 AAAAATG-AAAAATGAAAAAGGAAAGA
*
309463 AAAAATGAAAAATGAAAAAAGAAATGA
1 AAAAATGAAAAATGAAAAAGGAAA-GA
*
309490 AAAAAT-AAAAAGAGAAAAAGGA
1 AAAAATGAAAAA-TGAAAAAGGA
309512 GGGTTTGAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.17
25 15 0.36
26 5 0.12
27 15 0.36
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (26 bp):
AAAAATGAAAAATGAAAAAGGAAAGA
Found at i:309499 original size:19 final size:19
Alignment explanation
Indices: 309448--309506 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
309438 AAAAATGAAA
*
309448 AAATG-AAAAGGAAAAAA-
1 AAATGAAAAATGAAAAAAG
309465 AAATGAAAAATGAAAAAAG
1 AAATGAAAAATGAAAAAAG
309484 AAATGAAAAAAT-AAAAAGAG
1 AAATG-AAAAATGAAAAA-AG
309504 AAA
1 AAA
309507 AAGGAGGGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
17 5 0.14
18 11 0.30
19 10 0.27
20 11 0.30
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (19 bp):
AAATGAAAAATGAAAAAAG
Found at i:310647 original size:136 final size:136
Alignment explanation
Indices: 310361--310708 Score: 522
Period size: 136 Copynumber: 2.6 Consensus size: 136
310351 GGTGAACCAG
** *
310361 CATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATAAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* * *
310426 AG-A-AGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTTGCTTGAAG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
*
310489 GATCAG
131 GATCAA
* **
310495 TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATAAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* *
310560 AGAAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACACCTCGCTTGAGG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
310625 GATCAA
131 GATCAA
* ** *
310631 CATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCAAAC-GAGGAAGAAGAAGTTCATAATG
1 CATTTCCAATAAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
*
310695 AGAAGAACTTGTTC
66 AGAAGAGCTTGTTC
310709 AACTTCGCAT
Statistics
Matches: 196, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
134 65 0.33
135 35 0.18
136 96 0.49
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (136 bp):
CATTTCCAATAAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
GATCAA
Found at i:311072 original size:91 final size:92
Alignment explanation
Indices: 310957--311123 Score: 275
Period size: 91 Copynumber: 1.8 Consensus size: 92
310947 AAAGAGATGG
310957 ATCAACATTTCCAATGGAGAGTTCATAAT-AAGAAGAACTCATCCAAT-GAGAGAGAAGAAGTTC
1 ATCAACATTTCCAATGGAGAGTTCATAATGAA-AAGAACTCATCCAATAGAGAGAGAAGAAGTTC
311020 ATAATGAGAAGAACTTGTTCAACTTCGC
65 ATAATGAGAAGAACTTGTTCAACTTCGC
* * * *
311048 ATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCAATAGAGAGAGAAGAAGTTCA
311113 TAATGAGAAGA
66 TAATGAGAAGA
311124 GTTTTTTTGA
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
91 41 0.59
92 29 0.41
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (92 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCAATAGAGAGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACTTCGC
Found at i:311512 original size:14 final size:14
Alignment explanation
Indices: 311493--311543 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
311483 GGTTAAAAAA
311493 ATTATTAAATTATT
1 ATTATTAAATTATT
311507 ATTATTAAATTATT
1 ATTATTAAATTATT
* *
311521 ATTATTAATTTTAGT
1 ATTATTAA-ATTATT
311536 ATTATTAA
1 ATTATTAA
311544 GTGTGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTATTAAATTATT
Found at i:317683 original size:18 final size:18
Alignment explanation
Indices: 317660--317700 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
317650 GATTGGTGTT
317660 GCTTGAGTTGTATGTTTG
1 GCTTGAGTTGTATGTTTG
317678 GCTTGAGTTGTATGTTTG
1 GCTTGAGTTGTATGTTTG
317696 GCTTG
1 GCTTG
317701 TTTGTAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.07, G:0.34, T:0.49
Consensus pattern (18 bp):
GCTTGAGTTGTATGTTTG
Found at i:320904 original size:2 final size:2
Alignment explanation
Indices: 320857--320890 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
320847 TTTTTAAAGA
320857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
320891 TAAAAAGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322953 original size:60 final size:60
Alignment explanation
Indices: 322889--323079 Score: 258
Period size: 60 Copynumber: 3.2 Consensus size: 60
322879 AAAGCCGGCT
* * * *
322889 AAGGATTTAAAGTGGAAGCCAAGGAATGATATGTACTATGAGGAGGGATTAAAGCCAAAG
1 AAGGATGTAGAGTGGAAGCCAAGGAAGGATATGTACTATGAGGAGGAATTAAAGCCAAAG
* * *
322949 AAGGATGTAGAGTGGAAGCCAAGGAAGGATATGAACTATGAAGAGAAATTAAAGCCAAAG
1 AAGGATGTAGAGTGGAAGCCAAGGAAGGATATGTACTATGAGGAGGAATTAAAGCCAAAG
* * * *
323009 AAGGATGCAGAGCT-GAAGCTAAGTAAGGATATGTTCTATGAGGAGGAATTAAAGCCAAAG
1 AAGGATGTAGAG-TGGAAGCCAAGGAAGGATATGTACTATGAGGAGGAATTAAAGCCAAAG
*
323069 AAGGATTTAGA
1 AAGGATGTAGA
323080 ACCGAAGCTG
Statistics
Matches: 114, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 113 0.99
61 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.30, T:0.19
Consensus pattern (60 bp):
AAGGATGTAGAGTGGAAGCCAAGGAAGGATATGTACTATGAGGAGGAATTAAAGCCAAAG
Found at i:330707 original size:16 final size:17
Alignment explanation
Indices: 330675--330708 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
330665 ATAAAAAGAG
330675 TATTTTATCTTACTTTT
1 TATTTTATCTTACTTTT
330692 TATTTT-TCTTA-TTTT
1 TATTTTATCTTACTTTT
330707 TA
1 TA
330709 AAGAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 5 0.29
17 6 0.35
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTATCTTACTTTT
Found at i:336015 original size:36 final size:36
Alignment explanation
Indices: 335968--336039 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
335958 CAAATTTGGT
335968 AACTGAACTTTACTCTCTCTTATTTTACTCACTGTA
1 AACTGAACTTTACTCTCTCTTATTTTACTCACTGTA
* * *
336004 AACTGAACTTTATTCTCTTTTATTTTACTCATTGTA
1 AACTGAACTTTACTCTCTCTTATTTTACTCACTGTA
336040 CTTTAAATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.49
Consensus pattern (36 bp):
AACTGAACTTTACTCTCTCTTATTTTACTCACTGTA
Found at i:341841 original size:10 final size:10
Alignment explanation
Indices: 341826--341854 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
341816 GCAAGAGTTT
341826 TGATTTTAAA
1 TGATTTTAAA
341836 TGATTTTAAA
1 TGATTTTAAA
341846 TGATTTTAA
1 TGATTTTAA
341855 GTTTTCTATG
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:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (10 bp):
TGATTTTAAA
Found at i:342609 original size:21 final size:22
Alignment explanation
Indices: 342576--342634 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
342566 GATTGAATAG
** *
342576 AGAAAATCTATAAGAAAGGAGT
1 AGAAAATAAATAAGAAAGGAAT
*
342598 A-AAAATAAATAACAAAGGAAT
1 AGAAAATAAATAAGAAAGGAAT
* *
342619 AGAAAATGAAGAAGAA
1 AGAAAATAAATAAGAA
342635 GAGTTTTAGC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.64, C:0.03, G:0.19, T:0.14
Consensus pattern (22 bp):
AGAAAATAAATAAGAAAGGAAT
Found at i:346692 original size:32 final size:31
Alignment explanation
Indices: 346629--346700 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
346619 TTAATATGAT
* *
346629 AAATTTAATGAAAATTTGTAATAATTTAATA
1 AAATTTAATGAAAATTTATAATAATTCAATA
**
346660 AAATTTAATGATTATTCTATAATAATTCAATA
1 AAATTTAATGAAAATT-TATAATAATTCAATA
*
346692 AAATGTAAT
1 AAATTTAAT
346701 TTATAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 14 0.40
32 21 0.60
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (31 bp):
AAATTTAATGAAAATTTATAATAATTCAATA
Found at i:348930 original size:24 final size:25
Alignment explanation
Indices: 348896--348946 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
348886 TGATATGTAT
* *
348896 ATATATTTATAGTTATTTATTTTTC
1 ATATATTTATAGTTATTCATATTTC
*
348921 ATAT-TTTATATTTATTCATATTTC
1 ATATATTTATAGTTATTCATATTTC
348945 AT
1 AT
348947 TCATTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (25 bp):
ATATATTTATAGTTATTCATATTTC
Found at i:351553 original size:16 final size:16
Alignment explanation
Indices: 351515--351553 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
351505 CCTTTTAGAA
*
351515 CTTAAATTGACTAGCT
1 CTTAAATTGACAAGCT
* *
351531 CTAAAATTGACAAGGT
1 CTTAAATTGACAAGCT
351547 CTTAAAT
1 CTTAAAT
351554 GTATATAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (16 bp):
CTTAAATTGACAAGCT
Found at i:353722 original size:25 final size:25
Alignment explanation
Indices: 353693--353752 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
353683 TTCGGGTCGG
*
353693 GTCGGATCGGATTTCTAAGTTATAT
1 GTCGGGTCGGATTTCTAAGTTATAT
* *
353718 GTCGGGTTGAATTTCTAAGTTATAT
1 GTCGGGTCGGATTTCTAAGTTATAT
353743 GTCGGGTCGG
1 GTCGGGTCGG
353753 GGTGAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.12, G:0.30, T:0.38
Consensus pattern (25 bp):
GTCGGGTCGGATTTCTAAGTTATAT
Found at i:355570 original size:32 final size:32
Alignment explanation
Indices: 355534--355622 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
355524 AATAATGAAA
*
355534 ATTTTGTAATAATTTGATAAAATGTAATGATT
1 ATTTTATAATAATTTGATAAAATGTAATGATT
* ** * * *
355566 ATTTTATAACAATTCAATAAATTGTAATTAAT
1 ATTTTATAATAATTTGATAAAATGTAATGATT
* *
355598 AATTTATAATAATTTGA-CAAATGTA
1 ATTTTATAATAATTTGATAAAATGTA
355623 TTGGTTGTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
31 6 0.14
32 38 0.86
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (32 bp):
ATTTTATAATAATTTGATAAAATGTAATGATT
Found at i:356549 original size:15 final size:14
Alignment explanation
Indices: 356525--356555 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
356515 TTCTTTTTAG
356525 AGCTTAAATTGACT
1 AGCTTAAATTGACT
356539 AGCTCTAAATTGACT
1 AGCT-TAAATTGACT
356554 AG
1 AG
356556 ATCATAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (14 bp):
AGCTTAAATTGACT
Found at i:359090 original size:24 final size:24
Alignment explanation
Indices: 359058--359118 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
359048 CGGAGATATT
359058 AGAAATCAAAACAGAATCCAGATA
1 AGAAATCAAAACAGAATCCAGATA
* * * *
359082 AGATATCAAAATATAATCCAGATC
1 AGAAATCAAAACAGAATCCAGATA
*
359106 AGAAATCAGAACA
1 AGAAATCAAAACA
359119 AAATACTGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.16, G:0.11, T:0.16
Consensus pattern (24 bp):
AGAAATCAAAACAGAATCCAGATA
Done.