Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009616.1 Hibiscus syriacus cultivar Beakdansim tig00117002_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: 692457
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:145640 original size:12 final size:12
Alignment explanation
Indices: 145609--145640 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
145599 GGGATACCTG
*
145609 TTTCCCCCCGAT
1 TTTCCCCGCGAT
145621 TTTCCCCGCGAT
1 TTTCCCCGCGAT
145633 TTTCCCCG
1 TTTCCCCG
145641 ATTACCCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.47, G:0.12, T:0.34
Consensus pattern (12 bp):
TTTCCCCGCGAT
Found at i:151318 original size:15 final size:16
Alignment explanation
Indices: 151277--151318 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
151267 TATTTCATGC
*
151277 TATGTGATA-ATGATC
1 TATGTGATATATGATA
151292 TATGTGATTATATGA-A
1 TATGTGA-TATATGATA
151308 TATGTGATATA
1 TATGTGATATA
151319 AGCTATGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 11 0.46
16 9 0.38
17 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (16 bp):
TATGTGATATATGATA
Found at i:151439 original size:23 final size:23
Alignment explanation
Indices: 151404--151544 Score: 92
Period size: 23 Copynumber: 6.1 Consensus size: 23
151394 GAGTCGAGGG
*
151404 TTCTACGCAGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
* * **
151427 TTCTACGTGGTCCTTTGGGACTT
1 TTCTACGCGGTCCTTCGGGACAA
* *
151450 TTCTACGCGGTCTTTCGAGACATA
1 TTCTACGCGGTCCTTCGGGACA-A
* * * *
151474 TT-TATGTGGTCCTTCGGAACAT
1 TTCTACGCGGTCCTTCGGGACAA
*
151496 TTCTACGTGG-CACTTCGGTG-CATA
1 TTCTACGCGGTC-CTTCGG-GACA-A
*
151520 TTCTACGCGG-CACTTCGGTACAA
1 TTCTACGCGGTC-CTTCGGGACAA
151543 TT
1 TT
151545 TATATGAGCA
Statistics
Matches: 90, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
22 3 0.03
23 66 0.73
24 21 0.23
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.35
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:151483 original size:46 final size:46
Alignment explanation
Indices: 151404--151502 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 46
151394 GAGTCGAGGG
* * * *
151404 TTCTACGCAGTCCTTCGGGACAATTCTACGTGGTCCTTTGGGACTT
1 TTCTACGCAGTCCTTCGAGACAATTCTACGTGGTCCTTCGGAACAT
* * *
151450 TTCTACGCGGTCTTTCGAGACATATT-TATGTGGTCCTTCGGAACAT
1 TTCTACGCAGTCCTTCGAGACA-ATTCTACGTGGTCCTTCGGAACAT
151496 TTCTACG
1 TTCTACG
151503 TGGCACTTCG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 42 0.93
47 3 0.07
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.36
Consensus pattern (46 bp):
TTCTACGCAGTCCTTCGAGACAATTCTACGTGGTCCTTCGGAACAT
Found at i:154829 original size:21 final size:21
Alignment explanation
Indices: 154805--154866 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
154795 TAATTTTGAA
154805 AAAATGGTTTTCAAAGTTTGG
1 AAAATGGTTTTCAAAGTTTGG
154826 AAAAT-G-TTTC----TTT-G
1 AAAATGGTTTTCAAAGTTTGG
154840 AAAATGGTTTTCAAAGTTTGG
1 AAAATGGTTTTCAAAGTTTGG
*
154861 TAAATG
1 AAAATG
154867 TTTCTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 14
0.69 0.02 0.29
Matches are distributed among these distances:
14 6 0.18
15 4 0.12
16 4 0.12
19 4 0.12
20 4 0.12
21 11 0.33
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (21 bp):
AAAATGGTTTTCAAAGTTTGG
Found at i:154916 original size:72 final size:69
Alignment explanation
Indices: 154771--154914 Score: 175
Period size: 72 Copynumber: 2.1 Consensus size: 69
154761 TGAAATTATT
*
154771 AAAATGGTTTTCAAGTTTGGTAACTAATTTTGAAAAAATGGTTTTCAAAGTTTGGAAAATGTTTC
1 AAAATGGTTTTCAAGTTTGGTAAATAATTTTGAAAAAATGGTTTTCAAAGTTTGGAAAATGTTTC
*
154836 TTTG
66 GTTG
** * * *
154840 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-AAAAATAGTTTTTCAAAGTTTGGTAGATG
1 AAAATGGTTTTC-AAGTTTGGTAAAT-AAT-TTTGAAAAAAT-GGTTTTCAAAGTTTGGAAAATG
154904 TTT-GTTG
62 TTTCGTTG
154911 AAAA
1 AAAA
154915 ATAATAATGA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
69 12 0.19
70 12 0.19
71 14 0.22
72 26 0.41
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.42
Consensus pattern (69 bp):
AAAATGGTTTTCAAGTTTGGTAAATAATTTTGAAAAAATGGTTTTCAAAGTTTGGAAAATGTTTC
GTTG
Found at i:154917 original size:36 final size:36
Alignment explanation
Indices: 154771--154916 Score: 176
Period size: 35 Copynumber: 4.1 Consensus size: 36
154761 TGAAATTATT
* **
154771 AAAATGGTTTTC-AAGTTTGGTAACT-AAT-TTTGAA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-A
*
154805 AAAATGGTTTTCAAAGTTTGGAAAATGTTTCTTTG-
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
154840 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
* * *
154876 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
154912 AAAAT
1 AAAAT
154917 AATAATGAGA
Statistics
Matches: 99, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
34 12 0.12
35 45 0.45
36 15 0.15
37 27 0.27
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
Found at i:159454 original size:21 final size:21
Alignment explanation
Indices: 159430--159490 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
159420 AACTTTGAAA
159430 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
159451 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
159465 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
159486 AAATG
1 AAATG
159491 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:159521 original size:37 final size:37
Alignment explanation
Indices: 159422--159540 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
159412 TGGTAACCAA
159422 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
159459 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
159494 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
159531 -GTTGAAAAAT
1 CTTTGAAAAAT
159541 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:163135 original size:6 final size:6
Alignment explanation
Indices: 163124--163159 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
163114 AAAAATGATA
163124 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC
163160 ATACTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
TTCCCC
Found at i:165359 original size:23 final size:22
Alignment explanation
Indices: 165332--165380 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
165322 ATTATAATTA
165332 AATTATAATTCT-ATTAAAAGTAT
1 AATTA-AATTCTAATTAAAAGT-T
* *
165355 AATTAAATTTTAATTAATAGTT
1 AATTAAATTCTAATTAAAAGTT
165377 AATT
1 AATT
165381 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
AATTAAATTCTAATTAAAAGTT
Found at i:165580 original size:32 final size:32
Alignment explanation
Indices: 165544--165607 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
165534 TCATTTTTCT
*
165544 TTTCTTTTCGTCTC-AATTGTTATGTTGTAACA
1 TTTCTTTTCGTCTCGAATTGTTAT-ATGTAACA
*
165576 TTTCTTTTCGTCTCGGATTGTTATATGTAACA
1 TTTCTTTTCGTCTCGAATTGTTATATGTAACA
165608 AAATGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.52
Consensus pattern (32 bp):
TTTCTTTTCGTCTCGAATTGTTATATGTAACA
Found at i:178782 original size:24 final size:24
Alignment explanation
Indices: 178754--178803 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
178744 CTTCAATTAT
178754 TATTCATAAAGGATAAATTAGCAA
1 TATTCATAAAGGATAAATTAGCAA
178778 TATTCATAAAGGATAAATTAGCAA
1 TATTCATAAAGGATAAATTAGCAA
178802 TA
1 TA
178804 ATTTCATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (24 bp):
TATTCATAAAGGATAAATTAGCAA
Found at i:188677 original size:15 final size:15
Alignment explanation
Indices: 188657--188686 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
188647 AGCTTAATAT
*
188657 TTTTTTTCAAATTTA
1 TTTTTTTAAAATTTA
188672 TTTTTTTAAAATTTA
1 TTTTTTTAAAATTTA
188687 CATTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTTAAAATTTA
Found at i:189355 original size:32 final size:31
Alignment explanation
Indices: 189314--189378 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
189304 TTTGTTTCAC
* * *
189314 TAAAAATATTTTTTAAATATTTTTTGTAAAA
1 TAAAAATATTTTTTAAAAATGTTTTATAAAA
189345 TAAAATATATTTTTTAAAAATGTTTTATAAAA
1 TAAAA-ATATTTTTTAAAAATGTTTTATAAAA
189377 TA
1 TA
189379 TATTTTACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 5 0.17
32 25 0.83
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (31 bp):
TAAAAATATTTTTTAAAAATGTTTTATAAAA
Found at i:189375 original size:13 final size:14
Alignment explanation
Indices: 189344--189385 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
189334 TTTTTGTAAA
189344 ATAAAATATATTTT
1 ATAAAATATATTTT
* *
189358 TTAAAA-ATGTTTT
1 ATAAAATATATTTT
189371 ATAAAATATATTTT
1 ATAAAATATATTTT
189385 A
1 A
189386 CGGTGTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
ATAAAATATATTTT
Found at i:189897 original size:23 final size:21
Alignment explanation
Indices: 189863--189906 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
189853 TGAGTATTTT
189863 TATTATAATATTAACAAATATTA
1 TATTATAATATT-A-AAATATTA
*
189886 TATTATATTATTAAAATATTA
1 TATTATAATATTAAAATATTA
189907 AAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 11 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTATAATATTAAAATATTA
Found at i:192422 original size:6 final size:6
Alignment explanation
Indices: 192411--193347 Score: 1700
Period size: 6 Copynumber: 156.5 Consensus size: 6
192401 AAATTTATAC
192411 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
192459 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
192507 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
192555 ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
192601 ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
192647 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
192695 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
192743 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATACAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACAT--AT
192793 ACATAT ACATAT ACATAT ACATATAT ACATAT AC--AT ACATAT ACATAT
1 ACATAT ACATAT ACATAT AC--ATAT ACATAT ACATAT ACATAT ACATAT
192841 ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
192887 ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT ACATATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--ATAT
192935 ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
192981 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
193029 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
193077 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
193125 ACATAT ACATAT ACATACAT ACATAT ACATAT ACATATAT ACATAT ACATAT
1 ACATAT ACATAT ACAT--AT ACATAT ACATAT AC--ATAT ACATAT ACATAT
193177 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
193225 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
193273 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
193321 ACATAT ACATAT ACATAT ACATAT ACA
1 ACATAT ACATAT ACATAT ACATAT ACA
193348 CACACGCACA
Statistics
Matches: 909, Mismatches: 0, Indels: 44
0.95 0.00 0.05
Matches are distributed among these distances:
4 24 0.03
6 855 0.94
8 30 0.03
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:200613 original size:31 final size:31
Alignment explanation
Indices: 200578--200640 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
200568 CTTTTTCTTG
200578 ACAGAAAGGAGAATGAATTGGACAAAACCAT
1 ACAGAAAGGAGAATGAATTGGACAAAACCAT
* *
200609 ACAGAAAGGTGGATGAATTGGACAAAACCAT
1 ACAGAAAGGAGAATGAATTGGACAAAACCAT
200640 A
1 A
200641 AGTGTGGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.13, G:0.24, T:0.14
Consensus pattern (31 bp):
ACAGAAAGGAGAATGAATTGGACAAAACCAT
Found at i:202087 original size:2 final size:2
Alignment explanation
Indices: 202080--202109 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
202070 CCTATGTAAG
202080 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
202110 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:202114 original size:2 final size:2
Alignment explanation
Indices: 202109--202156 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
202099 ACACACACAC
202109 AT AT AT AT 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 AT AT AT AT
202151 AT AT AT
1 AT AT AT
202157 CACATACCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:203084 original size:20 final size:20
Alignment explanation
Indices: 203059--203101 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
203049 TTGTATTGTC
* *
203059 TTACAGATCGTGGTTGGTTT
1 TTACAGATCATGGTAGGTTT
203079 TTACAGATCATGGTAGGTTT
1 TTACAGATCATGGTAGGTTT
203099 TTA
1 TTA
203102 TAAATTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (20 bp):
TTACAGATCATGGTAGGTTT
Found at i:213304 original size:2 final size:2
Alignment explanation
Indices: 213297--213331 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
213287 GAGTGTAAAG
213297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
213332 GAAAAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:220462 original size:21 final size:20
Alignment explanation
Indices: 220422--220463 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
220412 CCAACTTACA
*
220422 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
220442 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
220463 A
1 A
220464 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:224938 original size:27 final size:27
Alignment explanation
Indices: 224900--224964 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
224890 GTATTGGAAG
*
224900 AAAGCTAGAATGTTTTGGGATGGTTTT
1 AAAGCTAGAATGCTTTGGGATGGTTTT
224927 AAAGCTAGAATGCTTTGGGATGGTTTT
1 AAAGCTAGAATGCTTTGGGATGGTTTT
*
224954 GAAGCTA-AATG
1 AAAGCTAGAATG
224965 AGTTAGGGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 4 0.11
27 32 0.89
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (27 bp):
AAAGCTAGAATGCTTTGGGATGGTTTT
Found at i:226267 original size:19 final size:19
Alignment explanation
Indices: 226245--226281 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
226235 ATATTCAATT
226245 AAATAAATTAAAATCAAGA
1 AAATAAATTAAAATCAAGA
* *
226264 AAATATATTATAATCAAG
1 AAATAAATTAAAATCAAG
226282 TGATGACACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
AAATAAATTAAAATCAAGA
Found at i:228248 original size:33 final size:33
Alignment explanation
Indices: 228211--228275 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
228201 TTCTATTTTA
228211 ATTAATATTTTAACAATAAGTGATTAAGGGTTG
1 ATTAATATTTTAACAATAAGTGATTAAGGGTTG
228244 ATTAATATTTTAACAATAAGTGATTAAGGGTT
1 ATTAATATTTTAACAATAAGTGATTAAGGGTT
228276 TGTTTGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (33 bp):
ATTAATATTTTAACAATAAGTGATTAAGGGTTG
Found at i:228601 original size:16 final size:18
Alignment explanation
Indices: 228580--228624 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
228570 TATTGTTATA
228580 ATTATA-TAAT-TATAAT
1 ATTATATTAATATATAAT
228596 ATTATATTAATATATAAT
1 ATTATATTAATATATAAT
*
228614 A-AATATTAATA
1 ATTATATTAATA
228625 AAATTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 13 0.50
18 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATATTAATATATAAT
Found at i:228635 original size:15 final size:17
Alignment explanation
Indices: 228586--228636 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
228576 TATAATTATA
*
228586 TAAT-TATAATATTATAT
1 TAATATATAATA-AATAT
228603 TAATATATAATAAATAT
1 TAATATATAATAAATAT
*
228620 TAATA-A-AATTAATAT
1 TAATATATAATAAATAT
228635 TA
1 TA
228637 TTTATTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 10 0.32
16 1 0.03
17 13 0.42
18 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATATAATAAATAT
Found at i:241085 original size:8 final size:8
Alignment explanation
Indices: 241072--241110 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
241062 CAACTCTTAC
241072 ATAATATA
1 ATAATATA
241080 ATAATATA
1 ATAATATA
*
241088 ATAATATG
1 ATAATATA
241096 ATAATA-A
1 ATAATATA
241103 ATAA-ATA
1 ATAATATA
241110 A
1 A
241111 AACGAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 1 0.04
7 6 0.21
8 21 0.75
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (8 bp):
ATAATATA
Found at i:245324 original size:18 final size:18
Alignment explanation
Indices: 245298--245332 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
245288 TCGAAAGGAC
*
245298 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
245316 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
245333 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:246912 original size:32 final size:31
Alignment explanation
Indices: 246839--246914 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
246829 CTAATGTGAC
* *
246839 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** * **
246870 TCTCGGGTAGGCCCTGTGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
246902 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
246915 TCACGACCCC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:254866 original size:19 final size:19
Alignment explanation
Indices: 254842--254899 Score: 116
Period size: 19 Copynumber: 3.1 Consensus size: 19
254832 TTAGAATGCT
254842 AAATTGAGTTAATTTGGGA
1 AAATTGAGTTAATTTGGGA
254861 AAATTGAGTTAATTTGGGA
1 AAATTGAGTTAATTTGGGA
254880 AAATTGAGTTAATTTGGGA
1 AAATTGAGTTAATTTGGGA
254899 A
1 A
254900 GTGATGAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (19 bp):
AAATTGAGTTAATTTGGGA
Found at i:255644 original size:25 final size:27
Alignment explanation
Indices: 255602--255666 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
255592 AGGTTTTTAT
255602 ATGATATTTTCTTAAAAATG-TATT-AGA
1 ATGAT-TTTT-TTAAAAATGATATTAAGA
* *
255629 ATGATTTTTTTTAAAATGATTTTAAAGA
1 ATGATTTTTTTAAAAATGATATT-AAGA
255657 ATGATTTTTT
1 ATGATTTTTT
255667 ATTGTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 8 0.24
26 7 0.21
27 5 0.15
28 13 0.39
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.51
Consensus pattern (27 bp):
ATGATTTTTTTAAAAATGATATTAAGA
Found at i:256844 original size:23 final size:22
Alignment explanation
Indices: 256792--256862 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
256782 AACAATTAGG
* *
256792 GGAATTATCTTTTGCA-ATTTA
1 GGAATTATCTTTTGGATTTTTA
*
256813 GCAGGATTATCTTTTGTGATTTTTA
1 G--GAATTATCTTTTG-GATTTTTA
*
256838 GGAATTATCTCTTAGGATTTTTA
1 GGAATTATCT-TTTGGATTTTTA
256861 GG
1 GG
256863 GTTTTTGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 1 0.03
23 30 0.75
24 4 0.10
25 5 0.12
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (22 bp):
GGAATTATCTTTTGGATTTTTA
Found at i:258775 original size:23 final size:23
Alignment explanation
Indices: 258749--258818 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
258739 GAGATTATAG
258749 CTAAAAAATTGCAAAGATAATTC
1 CTAAAAAATTGCAAAGATAATTC
*
258772 CT-AAAAATCAT-AAAAGATAA-TC
1 CTAAAAAAT--TGCAAAGATAATTC
*
258794 CTAATAAATTGCAAAAGATAATTC
1 CTAAAAAATTGC-AAAGATAATTC
258818 C
1 C
258819 CTTAATTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
21 1 0.03
22 10 0.26
23 23 0.61
24 4 0.11
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (23 bp):
CTAAAAAATTGCAAAGATAATTC
Found at i:258808 original size:45 final size:47
Alignment explanation
Indices: 258725--258818 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 47
258715 CCTCGAAAAC
* * * *
258725 CCTAAAAATCCTAAGAGATTATAGCTAAAAAATTGC-AAAGATAATT
1 CCTAAAAATCATAAAAGATAATACCTAAAAAATTGCAAAAGATAATT
*
258771 CCTAAAAATCATAAAAGATAAT-CCTAATAAATTGCAAAAGATAATT
1 CCTAAAAATCATAAAAGATAATACCTAAAAAATTGCAAAAGATAATT
258817 CC
1 CC
258819 CTTAATTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.26
Consensus pattern (47 bp):
CCTAAAAATCATAAAAGATAATACCTAAAAAATTGCAAAAGATAATT
Found at i:263152 original size:60 final size:60
Alignment explanation
Indices: 263064--263225 Score: 218
Period size: 60 Copynumber: 2.7 Consensus size: 60
263054 GTTGAATGAC
* * * *
263064 CATTTTGTAACTTTTAATAGTCGAATGACTCAACAAAGCAACGCCCTATAGT-TAGGAGAT
1 CATTTTATAACTTTTAATAATCGGATGACTCAACAAAGCAACGCCCTATAGTCTA-GAGAA
*
263124 CATTTTATAACTTTTAATAATCGGATGACTCAACAAAGCAACGCTCTATAGTCTAGAGAA
1 CATTTTATAACTTTTAATAATCGGATGACTCAACAAAGCAACGCCCTATAGTCTAGAGAA
* * * * *
263184 CATTTTATAACTTTTAATATTCAGAAGAATCAACAAAACAAC
1 CATTTTATAACTTTTAATAATCGGATGACTCAACAAAGCAAC
263226 ATTCTATAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 89 0.98
61 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAATCGGATGACTCAACAAAGCAACGCCCTATAGTCTAGAGAA
Found at i:263232 original size:60 final size:59
Alignment explanation
Indices: 263064--263248 Score: 212
Period size: 60 Copynumber: 3.1 Consensus size: 59
263054 GTTGAATGAC
* * * *
263064 CATTTTGTAACTTTTAATAGTCGAATGACTCAACAAAGCAACGCCCTATAGTTAGGAGAT
1 CATTTTATAACTTTTAATAATCGAA-GACTCAACAAAGCAACGCTCTATAGTTAGGAGAA
*
263124 CATTTTATAACTTTTAATAATCGGATGACTCAACAAAGCAACGCTCTATAGTCTA-GAGAA
1 CATTTTATAACTTTTAATAATC-GAAGACTCAACAAAGCAACGCTCTATAGT-TAGGAGAA
* * * ** *
263184 CATTTTATAACTTTTAATATTCAGAAGAATCAACAAAACAACATTCTATAATT-GGACGAA
1 CATTTTATAACTTTTAATAATC-GAAGACTCAACAAAGCAACGCTCTATAGTTAGGA-GAA
263244 CATTT
1 CATTT
263249 ATGTACTTTA
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
59 3 0.03
60 101 0.94
61 4 0.04
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (59 bp):
CATTTTATAACTTTTAATAATCGAAGACTCAACAAAGCAACGCTCTATAGTTAGGAGAA
Found at i:264200 original size:15 final size:17
Alignment explanation
Indices: 264180--264211 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
264170 TAAGAATTAT
264180 ATTATA-AATT-TAAGA
1 ATTATACAATTATAAGA
264195 ATTATACAATTATAAGA
1 ATTATACAATTATAAGA
264212 TTTTATACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (17 bp):
ATTATACAATTATAAGA
Found at i:266814 original size:10 final size:10
Alignment explanation
Indices: 266786--266847 Score: 61
Period size: 11 Copynumber: 5.9 Consensus size: 10
266776 AATTATAAAA
*
266786 AATATAAAATA
1 AATA-AAAATG
266797 AATAAAAATG
1 AATAAAAATG
*
266807 CAATAAAAAAG
1 -AATAAAAATG
266818 AATTAAAAATG
1 AA-TAAAAATG
* *
266829 AATAAAATTC
1 AATAAAAATG
266839 AATAAAAAT
1 AATAAAAAT
266848 ATAATGTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 21 0.49
11 22 0.51
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (10 bp):
AATAAAAATG
Found at i:266933 original size:21 final size:21
Alignment explanation
Indices: 266895--266934 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
266885 AATATTATTT
* * *
266895 ATATAATATTAATTTTAAAAA
1 ATATAAAATAAATATTAAAAA
266916 ATATAAAATAAATATTAAA
1 ATATAAAATAAATATTAAA
266935 TTTTAATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAAATAAATATTAAAAA
Found at i:267475 original size:22 final size:22
Alignment explanation
Indices: 267450--267513 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
267440 TTTTAATATT
267450 TTAAAAAAATTAATT-TTAAAAG
1 TTAAAAAAATT-ATTATTAAAAG
*
267472 TT-AATAAA-TATTATTAAATA-
1 TTAAAAAAATTATTATTAAA-AG
267492 TTAAAAAAATTATTATTAAAAG
1 TTAAAAAAATTATTATTAAAAG
267514 AAAGACAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
19 3 0.09
20 8 0.23
21 12 0.34
22 12 0.34
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
TTAAAAAAATTATTATTAAAAG
Found at i:268820 original size:22 final size:22
Alignment explanation
Indices: 268792--268833 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
268782 CAAACGGTCG
268792 GAGATCAAACGTATTTAATTTA
1 GAGATCAAACGTATTTAATTTA
268814 GAGATCAAACGTATTTAATT
1 GAGATCAAACGTATTTAATT
268834 AAAAAATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
GAGATCAAACGTATTTAATTTA
Found at i:273384 original size:2 final size:2
Alignment explanation
Indices: 273379--273446 Score: 93
Period size: 2 Copynumber: 34.5 Consensus size: 2
273369 TTTATTTTAG
* * * *
273379 TA TA TA TA TA TT TT TA GA T- TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
273420 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
273447 GTGTTAATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:276802 original size:13 final size:14
Alignment explanation
Indices: 276771--276821 Score: 70
Period size: 13 Copynumber: 3.7 Consensus size: 14
276761 ATCAGAACAA
276771 AAAGAGAAAAAAAGC
1 AAAGAGAAAAAAA-C
*
276786 AAAGAGAAAATAA-
1 AAAGAGAAAAAAAC
276799 AAAGAGAAAAAAAC
1 AAAGAGAAAAAAAC
276813 AAAG-GAAAA
1 AAAGAGAAAA
276822 TTGAAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 17 0.52
14 4 0.12
15 12 0.36
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAGAAAAAAAC
Found at i:276802 original size:28 final size:26
Alignment explanation
Indices: 276769--276822 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 26
276759 CAATCAGAAC
276769 AAAAAGAGAAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAAA-CAAAG-GAAAAT
276797 AAAAAGAGAAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAAACAAAGGAAAAT
276823 TGAAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 6 0.23
27 5 0.19
28 15 0.58
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.04
Consensus pattern (26 bp):
AAAAAGAGAAAAAAACAAAGGAAAAT
Found at i:277967 original size:32 final size:31
Alignment explanation
Indices: 277931--278018 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 31
277921 AGGAACAATG
*
277931 AGGGCATCTTTGAAGATTCAACATCAAATGCT
1 AGGGCATTTTTG-AGATTCAACATCAAATGCT
* *
277963 AGGGCATTTTTTGAGATTTAACATCAAATGTT
1 AGGGCA-TTTTTGAGATTCAACATCAAATGCT
* *
277995 GGGGAATTTTTGAGATTCAACATC
1 AGGGCATTTTTGAGATTCAACATC
278019 GAATATTGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
31 17 0.35
32 27 0.55
33 5 0.10
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (31 bp):
AGGGCATTTTTGAGATTCAACATCAAATGCT
Found at i:278008 original size:31 final size:31
Alignment explanation
Indices: 277939--278032 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 31
277929 TGAGGGCATC
* * *
277939 TTTGAAGATTCAACATCAAATGCTAGGGCATTT
1 TTTG-AGATTCAACATCAAATG-TTGGGGAATT
*
277972 TTTGAGATTTAACATCAAATGTTGGGGAATT
1 TTTGAGATTCAACATCAAATGTTGGGGAATT
* *
278003 TTTGAGATTCAACATCGAATATT-GGGAATT
1 TTTGAGATTCAACATCAAATGTTGGGGAATT
278033 CAATATCCTG
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 7 0.13
31 27 0.50
32 16 0.30
33 4 0.07
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (31 bp):
TTTGAGATTCAACATCAAATGTTGGGGAATT
Found at i:278826 original size:39 final size:39
Alignment explanation
Indices: 278783--278863 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
278773 ATTTTCCAAG
*
278783 TTTTGTCTCTCTTGAGACAACTTCCCTTGAAACAAAAAA
1 TTTTGTCTCTCTTAAGACAACTTCCCTTGAAACAAAAAA
* ** * *
278822 TTTTGTCTCTCTTAAGATAGTTTTCCTTGAAACAAAATA
1 TTTTGTCTCTCTTAAGACAACTTCCCTTGAAACAAAAAA
278861 TTT
1 TTT
278864 GAATATGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.41
Consensus pattern (39 bp):
TTTTGTCTCTCTTAAGACAACTTCCCTTGAAACAAAAAA
Found at i:278973 original size:21 final size:21
Alignment explanation
Indices: 278949--279010 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
278939 GACAGTTTCT
278949 CTTGAAACAAATTTTGTCTCC
1 CTTGAAACAAATTTTGTCTCC
* *
278970 CTTGAGAC--A----GTTTCC
1 CTTGAAACAAATTTTGTCTCC
*
278985 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCC
279006 CTTGA
1 CTTGA
279011 GACAGTTTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 12 0.40
17 1 0.03
19 1 0.03
21 16 0.53
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.39
Consensus pattern (21 bp):
CTTGAAACAAATTTTGTCTCC
Found at i:278974 original size:36 final size:36
Alignment explanation
Indices: 278870--279031 Score: 227
Period size: 36 Copynumber: 4.5 Consensus size: 36
278860 ATTTGAATAT
*
278870 GTTTCCCTTGAAAAAAATTTCT-TCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTT-TGTCTCCCTTGAGACA
** * * *
278906 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACA
*
278943 GTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
278979 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
279015 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
279032 ATAATTGAAT
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
36 82 0.73
37 30 0.27
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:279028 original size:72 final size:73
Alignment explanation
Indices: 278870--279031 Score: 247
Period size: 73 Copynumber: 2.2 Consensus size: 73
278860 ATTTGAATAT
* ** * *
278870 GTTTCCCTTGAAAAAAATTTCTTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTCCCTTGAAACAAATTTCTTCTCCCTTGAGACAGTTTCCCTTGAAACTAAATTTTGTCTCTC
278935 TTGAGACA
66 TTGAGACA
*
278943 GTTTCTCTTGAAACAAATTT-TGTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCT
1 GTTTCCCTTGAAACAAATTTCT-TCTCCCTTGAGACAGTTTCCCTTGAAACTAAATTTTGTCTCT
279006 CTTGAGACA
65 CTTGAGACA
279015 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
279032 ATAATTGAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
72 38 0.47
73 43 0.53
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (73 bp):
GTTTCCCTTGAAACAAATTTCTTCTCCCTTGAGACAGTTTCCCTTGAAACTAAATTTTGTCTCTC
TTGAGACA
Found at i:279042 original size:174 final size:174
Alignment explanation
Indices: 278783--279169 Score: 621
Period size: 174 Copynumber: 2.2 Consensus size: 174
278773 ATTTTCCAAG
* ** * *
278783 TTTTGTCTCTCTTGAGACAACTTCCCTTGAAACAAAAAATTTTGTCTCTCTTAAGATAGTTTTCC
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC---AAATTTTGTCTCTCTTAAGACAGTTTCCC
* * * *
278848 TTGAAACAAAATATTTGAATATGTTTCCCTTGAAAAAAATTTCTTCTCCCTTGAGACAGTTTCTT
63 TTGAAACAAAATAATTGAATATGTTTCCCTTGAAAAAAATTCCGTCTCCCTTGAGACAATTTCTT
278913 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
128 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
*
278960 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTCCCTTG
* **
279025 AAACAAAATAATTGAATATGTTTTCCTTGAAACTAATTCCGTCTCCCTTGAGACAATTTCTTTTG
66 AAACAAAATAATTGAATATGTTTCCCTTGAAAAAAATTCCGTCTCCCTTGAGACAATTTCTTTTG
279090 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
131 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
*
279134 TTTTGTCTTCCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
279170 ATAATTGAAT
Statistics
Matches: 196, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
174 166 0.85
177 30 0.15
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (174 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTCCCTTG
AAACAAAATAATTGAATATGTTTCCCTTGAAAAAAATTCCGTCTCCCTTGAGACAATTTCTTTTG
GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
Found at i:279059 original size:138 final size:138
Alignment explanation
Indices: 278917--279403 Score: 723
Period size: 138 Copynumber: 3.5 Consensus size: 138
278907 TTTCTTTTGG
* * * *
278917 AACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGT
1 AACTAA-TTTCGTCTCCCTTGAGACAATTTCTTTTGAAACTAAATTTTGTCTCCCTTGAGACAGT
* *
278981 TTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATATGT
65 TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGT
279046 TTTCCTTGA
130 TTTCCTTGA
* * * *
279055 AACTAATTCCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTT
1 AACTAATTTCGTCTCCCTTGAGACAATTTCTTTTGAAACTAAATTTTGTCTCCCTTGAGACAGTT
279120 TCTCTTGAAACAAATTTTGTCT-TCCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGT
66 TCTCTTGAAACAAATTTTGTCTCT-CTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGT
279184 TTTCCTTGA
130 TTTCCTTGA
* * *
279193 AACTAATTTCGTCTCCCTTGAGACAATTT-TTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTT
1 AACTAATTTCGTCTCCCTTGAGACAATTTCTTTTGAAACTAAATTTTGTCTCCCTTGAGACAGTT
** * **
279257 TCTCTAAAAACAAATTTTGTCTCCCTT-AGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTT
66 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGTT
*
279321 TTCTTTGA
131 TTCCTTGA
* *
279329 AACTAATTTCGTCTCCCCTGAGACATTTTCTTTT-AGAACTAAATTTTGTCTCCCTTGAGACAGT
1 AACTAATTTCGTCTCCCTTGAGACAATTTCTTTTGA-AACTAAATTTTGTCTCCCTTGAGACAGT
279393 TTCTCTTGAAA
65 TTCTCTTGAAA
279404 TATAAACATT
Statistics
Matches: 320, Mismatches: 24, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
136 69 0.22
137 125 0.39
138 126 0.39
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (138 bp):
AACTAATTTCGTCTCCCTTGAGACAATTTCTTTTGAAACTAAATTTTGTCTCCCTTGAGACAGTT
TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGTT
TTCCTTGA
Found at i:279120 original size:102 final size:102
Alignment explanation
Indices: 278944--279133 Score: 283
Period size: 102 Copynumber: 1.9 Consensus size: 102
278934 CTTGAGACAG
** *
278944 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTT
279009 GAGACAGTTTCCCTTGAAACAAAATAATTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATAATTGAATATGT
* ** * *
279046 TTTC-CTTGAAACTAATTCCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCCCTTGAAAC-AAATTTTGTCTCTCT
*
279110 TGAGACAGTTTCTCTTGAAACAAA
65 TGAGACAGTTTCCCTTGAAACAAA
279134 TTTTGTCTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 37 0.47
102 41 0.53
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATAATTGAATATGT
Found at i:279148 original size:36 final size:36
Alignment explanation
Indices: 279046--279169 Score: 135
Period size: 36 Copynumber: 3.4 Consensus size: 36
279036 TTGAATATGT
* ** * *
279046 TTTC-CTTGAAACTAATTCCGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTTCCTTGAGACAG
* * *
279081 TTTCTTTTGGAACTAAGTTTTGTC-TCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTTC-CTTGAGACAG
279118 TTTCTCTTGAAACAAATTTTGTCTTCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTTCCTTGAGACAG
*
279154 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
279170 ATAATTGAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
35 4 0.05
36 41 0.56
37 28 0.38
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTTCCTTGAGACAG
Found at i:279368 original size:137 final size:138
Alignment explanation
Indices: 278917--279403 Score: 746
Period size: 137 Copynumber: 3.5 Consensus size: 138
278907 TTTCTTTTGG
* * * * *
278917 AACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGT
1 AACTAA-TTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGT
* * *
278981 TTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATATGT
65 TTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGT
279046 TTTCCTTGA
130 TTTCCTTGA
* * *
279055 AACTAATTCCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTT
1 AACTAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTT
*
279120 TCTCTTGAAACAAATTTTGTCTTCCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGTT
66 TCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGTT
279185 TTCCTTGA
131 TTCCTTGA
* *
279193 AACTAATTTCGTCTCCCTTGAGACAATTT-TTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTT
1 AACTAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTT
** **
279257 TCTCTAAAAACAAATTTTGTCTCCCTT-AGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTT
66 TCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGTT
*
279321 TTCTTTGA
131 TTCCTTGA
* * *
279329 AACTAATTTCGTCTCCCCTGAGACATTTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTT
1 AACTAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTT
279394 TCTCTTGAAA
66 TCTCTTGAAA
279404 TATAAACATT
Statistics
Matches: 321, Mismatches: 26, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
136 69 0.21
137 126 0.39
138 126 0.39
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (138 bp):
AACTAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTT
TCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTGTT
TTCCTTGA
Found at i:279380 original size:37 final size:35
Alignment explanation
Indices: 279319--279403 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 35
279309 TTTGAATCTG
279319 TTTTCTTTGAAACTAATTTCGTCTCCCCTGAGACA
1 TTTTCTTTGAAACTAATTTCGTCTCCCCTGAGACA
* * *
279354 TTTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACA
1 TTTTCTTTGA-AACT-AATTTCGTCTCCCCTGAGACA
*
279391 GTTTCTCTTGAAA
1 TTTTCT-TTGAAA
279404 TATAAACATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 9 0.21
36 4 0.10
37 26 0.62
38 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.44
Consensus pattern (35 bp):
TTTTCTTTGAAACTAATTTCGTCTCCCCTGAGACA
Found at i:279431 original size:102 final size:100
Alignment explanation
Indices: 279228--279472 Score: 253
Period size: 102 Copynumber: 2.4 Consensus size: 100
279218 ATTTTTTTGG
* *
279228 AACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTAAAAACAAATTTTGTCTCCCTTAGACAGTTT
1 AACTAA-TTTTGTCTCCCCTGAGACAGTTTCTCTAAAAACAAATTTTGTCTCCCTTAGACAGTTT
* * * * *
279293 CCCTTGAAACAAAATCTTTGAATCTGTTTTCTTTGA
65 CCCTTGAAACAAAATCATTGAAACTATTTCCCTTGA
* * * * *
279329 AACTAATTTCGTCTCCCCTGAGACATTTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTT
1 AACTAATTTTGTCTCCCCTGAGACAGTTTCTCTAAAAAC-AAATTTTGTCTCCCTT-AGACAGTT
* *
279394 TCTCTTGAAATATAAA-CATTGAAAAC-ATTTCCCTTGA
64 TCCCTTGAAACA-AAATCATTG-AAACTATTTCCCTTGA
* * * *
279431 AA-TGAATTTTGTCTCTCTTGAGATAGTTTCTCTTAAAACAAA
1 AACT-AATTTTGTCTCCCCTGAGACAGTTTCTCTAAAAACAAA
279473 ATCTTTGAAT
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
100 26 0.22
101 26 0.22
102 60 0.51
103 6 0.05
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (100 bp):
AACTAATTTTGTCTCCCCTGAGACAGTTTCTCTAAAAACAAATTTTGTCTCCCTTAGACAGTTTC
CCTTGAAACAAAATCATTGAAACTATTTCCCTTGA
Found at i:279490 original size:65 final size:65
Alignment explanation
Indices: 279369--279520 Score: 171
Period size: 65 Copynumber: 2.3 Consensus size: 65
279359 TTTTAGAACT
* * *
279369 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAACATTTCCCTTGAAAC
* * * * **** *
279434 GAATTTTGTCTCTCTTGAGATAGTTTCTCTTAAAACA-AAATCTTTGAATTTGTTTCCTTTGAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAA-CATTGAAAACATTTCCCTTGAAA
279498 C
65 C
*
279499 AAATTTCGTCTCCCTTGAGACA
1 AAATTTTGTCTCCCTTGAGACA
279521 TTTTTTTGGA
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
64 3 0.04
65 67 0.96
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (65 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAACATTTCCCTTGAAAC
Found at i:279605 original size:166 final size:167
Alignment explanation
Indices: 279269--279644 Score: 553
Period size: 166 Copynumber: 2.3 Consensus size: 167
279259 TCTAAAAACA
* * * * *
279269 AATTTTGTCTCCCTT-AGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCTTTGAAACT
1 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCTTTGAAACA
*
279333 AATTTCGTCTCCCCTGAGACATTTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTC
66 AATTTCGTCTCCCCTGAGACATTTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTA
* *
279398 TTGAAATATAAACATTGAAAACATTTCCCTTGAAATG
131 TTGAAACATAAACATTAAAAACATTTCCCTTGAAATG
* *
279435 AATTTTGTCTCTCTTGAGATAGTTTCTCTTAAAACAAAATCTTTGAATTTGTTTCCTTTGAAACA
1 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCTTTGAAACA
* * * * * *
279500 AATTTCGTCTCCCTTGAGACA-TTT-TTTTGGAACTAAGTTTTGTCTCTCTTGATATAGTTTCTA
66 AATTTCGTCTCCCCTGAGACATTTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTA
279563 TTGCAAACATAAACATTAAAAACATTTCCCTTGAAATG
131 TTG-AAACATAAACATTAAAAACATTTCCCTTGAAATG
* *
279601 AATTTTGTATCTCTTGAGATAGGTTCTCTTGAAACAAAAT-TTTG
1 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTG
279645 TCTCCCTTGA
Statistics
Matches: 189, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
165 40 0.21
166 86 0.46
167 63 0.33
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (167 bp):
AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCTTTGAAACA
AATTTCGTCTCCCCTGAGACATTTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTA
TTGAAACATAAACATTAAAAACATTTCCCTTGAAATG
Found at i:279644 original size:37 final size:37
Alignment explanation
Indices: 279601--279673 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
279591 CCTTGAAATG
* *
279601 AATTTTGTATCTCTTGAGATAGGTTCTCTTGAAACAA
1 AATTTTGTATCCCTTGAGACAGGTTCTCTTGAAACAA
* *
279638 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTATCCCTTGAGACAGGTTCTCTTGAAACA
279674 TAAACATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (37 bp):
AATTTTGTATCCCTTGAGACAGGTTCTCTTGAAACAA
Found at i:279692 original size:102 final size:101
Alignment explanation
Indices: 279537--279776 Score: 365
Period size: 102 Copynumber: 2.4 Consensus size: 101
279527 TGGAACTAAG
* * * *
279537 TTTTGTCTCTCTTGATATAGTTTCTATTGCAAACATAAACATTAAAAACATTTCCCTTGAAATGA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTG-AAACATAAACATTAAAAACATTTCCCTTGAAATGA
*
279602 ATTTTGTATCTCTTGAGATAGGTTCTCTTGAAACAAAA
65 ATTTTGTATCTCTTGAGATAGGTTCCCTTGAAA-AAAA
*
279640 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAA
*
279705 TTTTGTCTCTCTTGAGATAGGTTCCCTTGAAAAAAA
66 TTTTGTATCTCTTGAGATAGGTTCCCTTGAAAAAAA
* * *
279741 -ATTGTCTCCATTGAGACAGTTTCTCTTGAAGCATAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAA
279777 TGTTGAGTTA
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
100 33 0.26
101 4 0.03
102 65 0.51
103 25 0.20
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (101 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAA
TTTTGTATCTCTTGAGATAGGTTCCCTTGAAAAAAA
Found at i:283452 original size:17 final size:16
Alignment explanation
Indices: 283421--283454 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
283411 CACGTGAGGA
283421 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
283437 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
283454 T
1 T
283455 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:298028 original size:2 final size:2
Alignment explanation
Indices: 298021--298056 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
298011 GGTCCTGTAA
298021 AT 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 AT
298057 GGGTATATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:301654 original size:21 final size:21
Alignment explanation
Indices: 301629--301704 Score: 118
Period size: 21 Copynumber: 3.6 Consensus size: 21
301619 TCATACCAAG
**
301629 GACGAGAAGATTATTCATAAA
1 GACGAGAAGACCATTCATAAA
301650 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
301671 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
301692 GAC-ATGAAGACCA
1 GACGA-GAAGACCA
301705 CTTCGCATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 1 0.02
21 51 0.98
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (21 bp):
GACGAGAAGACCATTCATAAA
Found at i:301973 original size:7 final size:7
Alignment explanation
Indices: 301951--301982 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
301941 TAACACCTCG
301951 TGCA-TT
1 TGCATTT
301957 TGCA-TT
1 TGCATTT
301963 TGCATTT
1 TGCATTT
301970 TGCATTT
1 TGCATTT
301977 TGCATT
1 TGCATT
301983 GCATGTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 10 0.40
7 15 0.60
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (7 bp):
TGCATTT
Found at i:304284 original size:12 final size:11
Alignment explanation
Indices: 304263--304292 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
304253 ATGTATAAAG
304263 AGAAAAAGAAA
1 AGAAAAAGAAA
304274 AGAAGAAAGAAA
1 AGAA-AAAGAAA
304286 AGAAAAA
1 AGAAAAA
304293 AATTGGAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:305810 original size:124 final size:124
Alignment explanation
Indices: 305598--305822 Score: 326
Period size: 124 Copynumber: 1.8 Consensus size: 124
305588 GTTGGGGCAC
* * *
305598 GACTGAACCCACATCATGTTGAGATGGCAAGATTCAGACCAAGGAGGCATGAAGAATGAGCCTTA
1 GACTGAACCCACATCATATTGAGATGGCAAGATTCAGACCAAGAAGGCATGAAGAATAAGCCTTA
* * *
305663 CAATTTGAGGTGATGAGGCATTTTGAAGGCTCGTACTAGTTAAGACACTGATGGGGAAT
66 CAATCTGAGATGATGAGGCATTTTGAAGGCCCGTACTAGTTAAGACACTGATGGGGAAT
* * *
305722 GACTGAACCCACATCATATTGAGA-GGACAAGATTTAGACCAAGAAGGCATTAAGAGTAAGCCTT
1 GACTGAACCCACATCATATTGAGATGG-CAAGATTCAGACCAAGAAGGCATGAAGAATAAGCCTT
* * *
305786 ACAATCTGAGATGTTGGGGTATTTTGAAGGCCCGTAC
65 ACAATCTGAGATGATGAGGCATTTTGAAGGCCCGTAC
305823 CAATATAAGA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 2 0.02
124 86 0.98
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.24
Consensus pattern (124 bp):
GACTGAACCCACATCATATTGAGATGGCAAGATTCAGACCAAGAAGGCATGAAGAATAAGCCTTA
CAATCTGAGATGATGAGGCATTTTGAAGGCCCGTACTAGTTAAGACACTGATGGGGAAT
Found at i:307680 original size:54 final size:54
Alignment explanation
Indices: 307599--308222 Score: 924
Period size: 54 Copynumber: 11.4 Consensus size: 54
307589 AGTGAAGCAA
* **
307599 AAGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * * * *
307653 AAGAATATGTTCGAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCTGTAAG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
*
307707 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCTGTAAG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* *
307761 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGTAGCGAACTCGTAAG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* *
307815 AAGAAGATTCTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCTGTAAG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * * **
307869 AAGAAGGTTTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACTCGTTTG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
*
307923 AAGAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAAGCGAGCCCGTAAG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCG-A---A-CCCGTAAG
* * *
307982 AAGAAGATTCTCGAGTTCTATACTTCCTGAAGAAAGAAGGAGAGAACCCGTAAG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* *
308036 AAGAAGATTTTTTGAGTTCTATACTTCCTGAAGAAAGAGGAAGCGAACCCGTAAG
1 AAGAAGA-TTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * **
308091 AAGAAGATTTTCGAGTTCTCTACTCCCTGAAGAAAGATAGAGCGAACCCGTAAG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* *
308145 AAGAAGATTATCGAGTTCTATACTTCTTGAAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
308199 AAGAAGATTTTCGAGTTCTATACT
1 AAGAAGATTTTCGAGTTCTATACT
308223 GTCGTAACCG
Statistics
Matches: 512, Mismatches: 52, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
54 414 0.81
55 51 0.10
58 2 0.00
59 45 0.09
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (54 bp):
AAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAG
Found at i:308674 original size:55 final size:53
Alignment explanation
Indices: 308615--308717 Score: 127
Period size: 55 Copynumber: 1.9 Consensus size: 53
308605 CCAAGGAAAT
* * *
308615 AAATGAAA-CCAATAATAATAAACATAAAATAATTGGATGAAACAAATATAAAAGA
1 AAATGAAATCCAATAA-AATAAA-ATAAAATAAAT-GAAGAAAAAAATATAAAAGA
**
308670 AAATGAAATTGAATAAAATAAAATAAAATAAATGAAGAAAAAAATATA
1 AAATGAAATCCAATAAAATAAAATAAAATAAATGAAGAAAAAAATATA
308718 TATACCAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
53 13 0.31
54 10 0.24
55 14 0.33
56 5 0.12
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (53 bp):
AAATGAAATCCAATAAAATAAAATAAAATAAATGAAGAAAAAAATATAAAAGA
Found at i:308833 original size:31 final size:29
Alignment explanation
Indices: 308798--308909 Score: 84
Period size: 31 Copynumber: 3.6 Consensus size: 29
308788 AACTAAAAAC
308798 ATAATGAAAATAAATAAATAGTATAAATAAA
1 ATAAT-AAAATAAATAAATA-TATAAATAAA
* *
308829 ATAATAAAATAATAAAAAATATATAAA-AAT
1 ATAATAAAAT-A-AATAAATATATAAATAAA
* *
308859 ATATGTATAATATAATAAA-ATACTAAATAATA
1 ATA-ATAAAATA-AATAAATATA-TAAATAA-A
*
308891 ACAATAATAATAAATAAAT
1 ATAATAA-AATAAATAAAT
308910 GAAAAATAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
29 3 0.05
30 21 0.33
31 27 0.42
32 13 0.20
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (29 bp):
ATAATAAAATAAATAAATATATAAATAAA
Found at i:308834 original size:8 final size:8
Alignment explanation
Indices: 308823--308900 Score: 56
Period size: 8 Copynumber: 9.6 Consensus size: 8
308813 AAATAGTATA
308823 AATAAAAT
1 AATAAAAT
308831 AATAAAAT
1 AATAAAAT
308839 AATAAAA-
1 AATAAAAT
*
308846 AAT-ATAT
1 AATAAAAT
308853 AA-AAATAT
1 AATAAA-AT
*
308861 ATGTATAATAT
1 A---ATAAAAT
308872 AATAAAAT
1 AATAAAAT
*
308880 ACT-AAAT
1 AATAAAAT
308887 AATAACAAT
1 AATAA-AAT
308896 AATAA
1 AATAA
308901 TAAATAAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
6 2 0.04
7 12 0.22
8 27 0.49
9 8 0.15
11 4 0.07
12 2 0.04
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (8 bp):
AATAAAAT
Found at i:308902 original size:15 final size:14
Alignment explanation
Indices: 308798--308908 Score: 52
Period size: 14 Copynumber: 7.6 Consensus size: 14
308788 AACTAAAAAC
308798 ATAATGAAAATAAATAA
1 ATAAT-AAAAT-AAT-A
*
308815 ATAGTATAAATAA-A
1 ATAATA-AAATAATA
308829 ATAATAAAATAATA
1 ATAATAAAATAATA
*
308843 A-AA-AATATATAAAA
1 ATAATAA-A-ATAATA
**
308857 AT-ATATGTATAAT-
1 ATAATA-AAATAATA
*
308870 ATAATAAAATACTAA
1 ATAATAAAATAAT-A
308885 ATAATAACAATAATA
1 ATAATAA-AATAATA
308900 ATAAATAAA
1 AT-AATAAA
308909 TGAAAAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 26
0.67 0.09 0.24
Matches are distributed among these distances:
12 2 0.03
13 15 0.21
14 22 0.31
15 12 0.17
16 13 0.18
17 8 0.11
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (14 bp):
ATAATAAAATAATA
Found at i:308904 original size:19 final size:18
Alignment explanation
Indices: 308827--308907 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 18
308817 AGTATAAATA
*
308827 AAATAATAAAATAATAAA
1 AAATAATAAAATAATAAT
*
308845 AAATATATAAAA-ATATATGT
1 AAATA-ATAAAATA-ATA-AT
*
308865 ATAAT-ATAATAA-AATACT
1 A-AATAATAA-AATAATAAT
308883 AAATAATAACAATAATAAT
1 AAATAATAA-AATAATAAT
308902 AAATAA
1 AAATAA
308908 ATGAAAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
17 3 0.06
18 14 0.27
19 27 0.53
20 4 0.08
21 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.28
Consensus pattern (18 bp):
AAATAATAAAATAATAAT
Found at i:308906 original size:16 final size:16
Alignment explanation
Indices: 308809--308908 Score: 75
Period size: 16 Copynumber: 6.1 Consensus size: 16
308799 TAATGAAAAT
*
308809 AAATAAATAGTATAAATA
1 AAAT-AATAATAT-AATA
*
308827 AAATAATAAAATAATA
1 AAATAATAATATAATA
308843 AAA-AAT-ATATAA-A
1 AAATAATAATATAATA
308856 AATATATGTATAATATAATA
1 AA-ATA---ATAATATAATA
*
308876 AAATACTAA-ATAATA
1 AAATAATAATATAATA
308891 ACAATAATAATA-AATA
1 A-AATAATAATATAATA
308907 AA
1 AA
308909 TGAAAAATAA
Statistics
Matches: 68, Mismatches: 5, Indels: 21
0.72 0.05 0.22
Matches are distributed among these distances:
13 3 0.04
14 6 0.09
15 12 0.18
16 22 0.32
17 7 0.10
18 6 0.09
19 9 0.13
20 3 0.04
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
AAATAATAATATAATA
Found at i:309137 original size:23 final size:23
Alignment explanation
Indices: 309103--309149 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
309093 ACACAAAGAA
309103 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
309126 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
309149 A
1 A
309150 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:309606 original size:37 final size:37
Alignment explanation
Indices: 309557--309649 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
309547 ATGCTTGTGG
* * *
309557 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGAAAAACTCT
* * ** *
309594 ATTCTATTTTTAGGAGTTTGAATCCTAGAAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGAAAAACTCT
309631 ATCCTATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
309650 TAATCTTAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGAAAAACTCT
Found at i:310596 original size:106 final size:106
Alignment explanation
Indices: 310411--311686 Score: 1923
Period size: 106 Copynumber: 12.0 Consensus size: 106
310401 GCATTGTTCT
* * * * *
310411 GAGTCCAATATCC-TC-CTTCGTGAAGTTAAAATTTGCTCTGGAATCGGGAAATTATTTGTTGAC
1 GAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * * *
310474 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
310517 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATAT-TTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT-TGTTTGTTGACA
*
310581 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
310623 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
310688 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
310729 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
310794 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * ***
310835 GAGTCTAATATCCTTCACTATGAAGTTGAAATTGGCTCCGAAATTCAAAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
310900 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
310941 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTAGGAAATTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
311006 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
311047 GATTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACA
*
311111 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
311153 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
311218 CCATCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
311259 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
311324 CCAGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTC-G
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
311364 TGAGTCCAATAACCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 -GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
311429 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
311471 GAGTTCAATATCCTTTGTTGTGAAGTTTAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
311536 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
311577 GAGTCCAATATCCTTCGCTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * *
311642 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
311683 GAGT
1 GAGT
311687 GGCATGATAT
Statistics
Matches: 1075, Mismatches: 87, Indels: 16
0.91 0.07 0.01
Matches are distributed among these distances:
105 7 0.01
106 1061 0.99
107 7 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:313260 original size:16 final size:16
Alignment explanation
Indices: 313241--313302 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
313231 TTGTCCCTTT
313241 TTCTTTTTGAT-TTTTG
1 TTCTTTTT-ATGTTTTG
*
313257 TTCTTTTTTTGTTTTG
1 TTCTTTTTATGTTTTG
313273 TTCTTTTT-TGCTTCTT-
1 TTCTTTTTATG-TT-TTG
313289 TTCTTTTT-TGTTTT
1 TTCTTTTTATGTTTT
313303 TGCCCTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 2 0.05
15 5 0.12
16 33 0.79
17 2 0.05
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.79
Consensus pattern (16 bp):
TTCTTTTTATGTTTTG
Found at i:313264 original size:23 final size:22
Alignment explanation
Indices: 313228--313304 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
313218 TGCATGTGCT
* *
313228 TTTTTGTCCCTTTTTCTTTTTG
1 TTTTTGTTCTTTTTTCTTTTTG
313250 ATTTTTGTTCTTTTTT-TGTTTTG
1 -TTTTTGTTCTTTTTTCT-TTTTG
*
313273 TTCTTTTTTGCTTCTTTTCTTTTTTG
1 TT-TTTGTT-CTT-TTTTC-TTTTTG
313299 TTTTTG
1 TTTTTG
313305 CCCTTTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 3 0.07
23 23 0.52
24 3 0.07
25 7 0.16
26 7 0.16
27 1 0.02
ACGTcount: A:0.01, C:0.12, G:0.10, T:0.77
Consensus pattern (22 bp):
TTTTTGTTCTTTTTTCTTTTTG
Found at i:313290 original size:26 final size:26
Alignment explanation
Indices: 313251--313300 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
313241 TTCTTTTTGA
313251 TTTTTGTTCTTTTT-TTGTTTTGTTCT
1 TTTTTGTTCTTTTTCTT-TTTTGTTCT
313277 TTTTTGCTTC-TTTTCTTTTTTGTT
1 TTTTTG-TTCTTTTTCTTTTTTGTT
313301 TTTGCCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (26 bp):
TTTTTGTTCTTTTTCTTTTTTGTTCT
Found at i:318064 original size:2 final size:2
Alignment explanation
Indices: 318057--318086 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
318047 AAATAAAATA
318057 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
318087 ATAAAATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:318971 original size:55 final size:56
Alignment explanation
Indices: 318901--319405 Score: 751
Period size: 55 Copynumber: 9.2 Consensus size: 56
318891 CTCCATGAAG
* * * * *
318901 AATAGGGAACGGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAAG-
1 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGA
318956 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAG-
1 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGA
*
319011 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAAG-
1 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGA
*
319066 AATAGGGAGCATACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAG-
1 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGA
*
319121 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTTTG-AAGA
1 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGA
* * *
319176 AATAGGGAGCAGACACAATTGTTGAAGATTGTTCGAGTCTTATACTCTATG-AAGA
1 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGA
* * *
319231 AATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAATCTCATACTCTCTG-AAGA
1 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGA
* *
319286 AATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTG-AAGA
1 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGA
* * *
319341 AATAGAGAGCAAACACAATTATTGAAGATTATTCGAGT-TCTATACTGC-CTGAAAGA
1 AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTC-ATACT-CTCTGAAAGA
319397 AATAGGGAG
1 AATAGGGAG
319406 TGAACCCGTT
Statistics
Matches: 422, Mismatches: 24, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
54 5 0.01
55 404 0.96
56 13 0.03
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (56 bp):
AATAGGGAGCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGA
Found at i:323267 original size:65 final size:63
Alignment explanation
Indices: 323069--323278 Score: 191
Period size: 65 Copynumber: 3.3 Consensus size: 63
323059 TGCACTAAGA
* * *
323069 GTGCATCGATGCATCAAGTGCATTCGATGATTT-A-AAATAGC-CAGAGTGCATCGATGCATGGC
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAA-ATCTC--AGTGCATCGATGCATGGT
323131 TG
62 TG
*
323133 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAATGCATC-AGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGA-TGCATGGT-
323197 T-
62 TG
* **
323198 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
323261 TG
62 TG
*
323263 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
323279 CTCTGAAAAA
Statistics
Matches: 123, Mismatches: 11, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 51 0.41
65 60 0.49
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:323677 original size:36 final size:36
Alignment explanation
Indices: 323582--323692 Score: 120
Period size: 36 Copynumber: 3.1 Consensus size: 36
323572 GTTCTACGTT
* * *
323582 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
323618 ---GAAGTTTTTGCCCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAG-TTTTG-TCTCTCTTGAGACAGTTTCTCTTG
* *
323653 AAACAAGTTTTGTCTCTCTTGAGACGGTTTCCCTTG
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
323689 AAAC
1 AAAC
323693 TTCAACCTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
33 2 0.03
34 5 0.08
35 21 0.34
36 25 0.41
37 5 0.08
38 3 0.05
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.40
Consensus pattern (36 bp):
AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:323926 original size:84 final size:84
Alignment explanation
Indices: 323784--324016 Score: 286
Period size: 84 Copynumber: 2.8 Consensus size: 84
323774 TTTGATTACA
* * ** * * *
323784 CTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGATGGGTTATTTGTCACCAAAA
1 CTCAGCTCCAA-GGCACATCATTTACAGCATAGCTCAAGGAAAGAAGGGTTATCTGTCAACAAAA
323849 GACCTTCGAGTTCGACTATG
65 GACCTTCGAGTTCGACTATG
* * * * * * ** *
323869 CTCAGCTCTAAGGGATATCATTTGCAGCGTAGCTTAAGTCAAGAAGGGTTATCTGTCAACTAAAG
1 CTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGAAAGAAGGGTTATCTGTCAACAAAAG
323934 ACCTTCGAGTTCGACTATG
66 ACCTTCGAGTTCGACTATG
* * *
323953 CTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGAAAGAAGAGCTATCTGTCAATAAAA
1 CTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGAAAGAAGGGTTATCTGTCAACAAAA
324017 TTGTCGAGTT
Statistics
Matches: 122, Mismatches: 26, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
84 113 0.93
85 9 0.07
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (84 bp):
CTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGAAAGAAGGGTTATCTGTCAACAAAAG
ACCTTCGAGTTCGACTATG
Found at i:324865 original size:14 final size:15
Alignment explanation
Indices: 324832--324870 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
324822 TACATTTACG
* *
324832 TTTTAATTATTATTA
1 TTTTATTTATTATAA
324847 TTTTATTTATT-TAA
1 TTTTATTTATTATAA
324861 TTTTATTTAT
1 TTTTATTTAT
324871 ACGCACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTATTATAA
Found at i:324982 original size:2 final size:2
Alignment explanation
Indices: 324977--325013 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
324967 TTTACTTTAG
324977 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
325014 GTTAATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:325218 original size:9 final size:9
Alignment explanation
Indices: 325200--325279 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
325190 TATTTTCTAG
325200 TATTTTATT
1 TATTTTATT
*
325209 TATTTCATT
1 TATTTTATT
*
325218 TACTTTTATG
1 TA-TTTTATT
* *
325228 GACTTTATT
1 TATTTTATT
325237 TA-TTTATTT
1 TATTTTA-TT
*
325246 TATGTCT-TT
1 TAT-TTTATT
325255 TATTTTATT
1 TATTTTATT
*
325264 TATTTTTTTT
1 TA-TTTTATT
325274 TATTTT
1 TATTTT
325280 TTTTTTCGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
8 6 0.11
9 33 0.60
10 14 0.25
11 2 0.04
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (9 bp):
TATTTTATT
Found at i:325261 original size:23 final size:23
Alignment explanation
Indices: 325207--325269 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
325197 TAGTATTTTA
*
325207 TTTATTTCATTTACTTTTATGGAC
1 TTTATTTTATTTA-TTTTATGGAC
*
325231 TTTA-TTTATTTATTTTAT-GTC
1 TTTATTTTATTTATTTTATGGAC
325252 TTTTATTTTATTTATTTT
1 -TTTATTTTATTTATTTT
325270 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 2 0.06
22 10 0.29
23 19 0.54
24 4 0.11
ACGTcount: A:0.19, C:0.06, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTATTTTATTTATTTTATGGAC
Found at i:325275 original size:10 final size:10
Alignment explanation
Indices: 325252--325284 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
325242 ATTTTATGTC
325252 TTTTA-TTTT
1 TTTTATTTTT
*
325261 ATTTATTTTT
1 TTTTATTTTT
325271 TTTTATTTTT
1 TTTTATTTTT
325281 TTTT
1 TTTT
325285 TCGTTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:325280 original size:9 final size:9
Alignment explanation
Indices: 325235--325305 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 9
325225 ATGGACTTTA
*
325235 TTTATTTAT
1 TTTATTTTT
* *
325244 TTTATGTCT
1 TTTATTTTT
*
325253 TTTATTTTA
1 TTTATTTTT
325262 TTTATTTTTT
1 TTTA-TTTTT
325272 TTTATTTTT
1 TTTATTTTT
325281 TTT-TTCGTTT
1 TTTATT--TTT
325291 CTTTATTTTT
1 -TTTATTTTT
325301 ATTTA
1 -TTTA
325306 ATTTACTTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
8 2 0.04
9 25 0.50
10 18 0.36
11 3 0.06
12 2 0.04
ACGTcount: A:0.14, C:0.04, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTATTTTT
Found at i:325341 original size:14 final size:13
Alignment explanation
Indices: 325231--325341 Score: 62
Period size: 14 Copynumber: 7.8 Consensus size: 13
325221 TTTTATGGAC
*
325231 TTTATTTATTTAT
1 TTTATTTTTTTAT
*
325244 TTTATGTCTTTTAT
1 TTTAT-TTTTTTAT
*
325258 TTTATTTATTTTTT
1 TTTATTT-TTTTAT
325272 TTTATTTTTTT-T
1 TTTATTTTTTTAT
** *
325284 TTCGTTTCTTTATT
1 TTTATTTTTTTA-T
*
325298 TTTATTTAATTTACT
1 TTTATTT-TTTTA-T
325313 TGTTATCGTTATTTTAT
1 T-TTAT--TT-TTTTAT
325330 TATTATTTTTTT
1 T-TTATTTTTTT
325342 CTTTGTCTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
12 9 0.12
13 10 0.13
14 33 0.43
15 8 0.10
16 4 0.05
17 6 0.08
18 7 0.09
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTATTTTTTTAT
Found at i:327052 original size:14 final size:14
Alignment explanation
Indices: 327031--327075 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
327021 ATTTTTTTAA
327031 TTTTATATTTAT-T
1 TTTTATATTTATAT
327044 TTCTTATA-TTATAT
1 TT-TTATATTTATAT
327058 TTTTATATTTATAT
1 TTTTATATTTATAT
327072 TTTT
1 TTTT
327076 TGTTTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATATTTATAT
Found at i:327655 original size:2 final size:2
Alignment explanation
Indices: 327610--327647 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
327600 ATTTTATTCA
327610 AT AT 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 AT AT
327648 TGTATATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:330214 original size:16 final size:16
Alignment explanation
Indices: 330189--330227 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
330179 TAGATAAGTT
* *
330189 CTTTTTGTTGCAATAG
1 CTTTTAGTTGCAAAAG
330205 CTTTTAGTTGCAAAAG
1 CTTTTAGTTGCAAAAG
330221 CTTTTAG
1 CTTTTAG
330228 CTTTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (16 bp):
CTTTTAGTTGCAAAAG
Found at i:330327 original size:16 final size:16
Alignment explanation
Indices: 330308--330338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
330298 GTTCTTTTTG
*
330308 TTGCAATAGCTTTTAT
1 TTGCAAAAGCTTTTAT
330324 TTGCAAAAGCTTTTA
1 TTGCAAAAGCTTTTA
330339 GCTTTTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (16 bp):
TTGCAAAAGCTTTTAT
Found at i:330328 original size:112 final size:112
Alignment explanation
Indices: 330129--330403 Score: 532
Period size: 112 Copynumber: 2.5 Consensus size: 112
330119 ATGTGTACTA
330129 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
330194 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
66 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
330241 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
*
330306 TGTTGCAATAGCTTTTATTTGCAAAAGCTTTTAGCTTTTAGAAACAT
66 TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
*
330353 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTATGTCCTAT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTAT
330404 GATTTTACTG
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 161 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (112 bp):
AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
TGTTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
Found at i:340193 original size:23 final size:23
Alignment explanation
Indices: 340124--340194 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
340114 GTGTTTGTTA
* *
340124 TTAATTTTTAAACAATTAAAATTT
1 TTAATATTTAAATAATT-AAATTT
* * * *
340148 TTAA-ATTTTAATTATGATTATTT
1 TTAATATTTAAATAATTA-AATTT
340171 TTAATATTTAAATAATTAAATTT
1 TTAATATTTAAATAATTAAATTT
340194 T
1 T
340195 ATAAAATATA
Statistics
Matches: 35, Mismatches: 10, Indels: 5
0.70 0.20 0.10
Matches are distributed among these distances:
22 1 0.03
23 20 0.57
24 14 0.40
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (23 bp):
TTAATATTTAAATAATTAAATTT
Found at i:340496 original size:15 final size:16
Alignment explanation
Indices: 340459--340497 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
340449 TTAACATTAC
*
340459 ATATAAAATTAAATAT
1 ATATAAATTTAAATAT
*
340475 ATTTAAATTTAAATA-
1 ATATAAATTTAAATAT
340490 ATATAAAT
1 ATATAAAT
340498 ATCATATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAAATTTAAATAT
Found at i:344201 original size:21 final size:21
Alignment explanation
Indices: 344118--344201 Score: 53
Period size: 21 Copynumber: 3.9 Consensus size: 21
344108 CAGAACCCCA
* *
344118 GGGGGTATCGATTCCC-CTGTG
1 GGGGGGATCGATTCCCTC-ATG
* **
344139 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGATT-CCC-TCATG
* * *
344163 GGGGGAATCGGTTTCCTCATG
1 GGGGGGATCGATTCCCTCATG
344184 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
344202 TGCACCAAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
21 23 0.49
22 8 0.17
23 10 0.21
24 5 0.11
25 1 0.02
ACGTcount: A:0.14, C:0.24, G:0.37, T:0.25
Consensus pattern (21 bp):
GGGGGGATCGATTCCCTCATG
Found at i:345308 original size:15 final size:15
Alignment explanation
Indices: 345288--345334 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
345278 GTAGGACCAT
345288 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
345303 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
345318 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
345333 TA
1 TA
345335 TTATACCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:345496 original size:12 final size:12
Alignment explanation
Indices: 345479--345528 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
345469 TATCGTGTTC
345479 TCATATCACATG
1 TCATATCACATG
*
345491 TCATATCACATA
1 TCATATCACATG
345503 TCATATCACATG
1 TCATATCACATG
*
345515 AACATAT-ACATG
1 -TCATATCACATG
345527 TC
1 TC
345529 TTATGCATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 1 0.03
12 27 0.82
13 5 0.15
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (12 bp):
TCATATCACATG
Found at i:345930 original size:64 final size:64
Alignment explanation
Indices: 345822--345998 Score: 239
Period size: 64 Copynumber: 2.8 Consensus size: 64
345812 TAATGAAGGT
* ** * **
345822 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-GTCATTATTAATGGG
* ** *
345886 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAATGGG
*
345950 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT
345999 CTTTATTTTA
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 1 0.01
64 98 0.99
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAATGGG
Found at i:346019 original size:64 final size:64
Alignment explanation
Indices: 345822--346046 Score: 222
Period size: 64 Copynumber: 3.5 Consensus size: 64
345812 TAATGAAGGT
* ** ** * * *** *
345822 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * *
345886 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
345950 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
** *
346013 AGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
346047 ATTCAAATAA
Statistics
Matches: 138, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 3 0.02
64 130 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:352270 original size:15 final size:15
Alignment explanation
Indices: 352250--352296 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
352240 GTAGGACCAT
352250 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
352265 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
352280 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
352295 TA
1 TA
352297 TTATACCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:352458 original size:12 final size:12
Alignment explanation
Indices: 352441--352490 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
352431 TATCGTGTTC
352441 TCATATCACATG
1 TCATATCACATG
*
352453 TCATATCACATA
1 TCATATCACATG
352465 TCATATCACATG
1 TCATATCACATG
*
352477 AACATAT-ACATG
1 -TCATATCACATG
352489 TC
1 TC
352491 TTATGCATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 1 0.03
12 27 0.82
13 5 0.15
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (12 bp):
TCATATCACATG
Found at i:352892 original size:64 final size:64
Alignment explanation
Indices: 352784--352960 Score: 230
Period size: 64 Copynumber: 2.8 Consensus size: 64
352774 TAATGAAGGT
* ** * **
352784 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-GTCATTATTAATGGG
* * ** *
352848 ATGCATCGATGCACTCCTTATGCATCGATGTACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAATGGG
*
352912 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT
352961 CTTTATTTTA
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 1 0.01
64 96 0.99
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAATGGG
Found at i:352981 original size:64 final size:64
Alignment explanation
Indices: 352784--353008 Score: 213
Period size: 64 Copynumber: 3.5 Consensus size: 64
352774 TAATGAAGGT
* ** ** * * *** *
352784 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * * *
352848 ATGCATCGATGCACTCCTTATGCATCGATGTACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
352912 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
** *
352975 AGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
353009 ATTCAAATAA
Statistics
Matches: 136, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 3 0.02
64 128 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:357237 original size:22 final size:21
Alignment explanation
Indices: 357195--357234 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
357185 GAGCTTATTT
*
357195 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
357216 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
357235 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:369747 original size:20 final size:20
Alignment explanation
Indices: 369709--369748 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
369699 TATATTATTG
* *
369709 AAAAATCAAATTAATATTTT
1 AAAAAACAAATTAACATTTT
*
369729 AAAAAACAAATTTACATTTT
1 AAAAAACAAATTAACATTTT
369749 TAATAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAACAAATTAACATTTT
Found at i:374956 original size:24 final size:23
Alignment explanation
Indices: 374905--374969 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 23
374895 CTAACTAGCT
*
374905 CAACTAACCAGAAAC-G--AC-C
1 CAACTAACCAGAAACAGTTACAA
*
374924 CAACTAACCAGGAACAGTTACAA
1 CAACTAACCAGAAACAGTTACAA
374947 CAACTTAACCAGAAACAGTTACA
1 CAAC-TAACCAGAAACAGTTACA
374970 GCTAATCAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 14 0.37
20 1 0.03
22 2 0.05
23 4 0.11
24 17 0.45
ACGTcount: A:0.48, C:0.29, G:0.11, T:0.12
Consensus pattern (23 bp):
CAACTAACCAGAAACAGTTACAA
Found at i:376808 original size:21 final size:18
Alignment explanation
Indices: 376743--376791 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
376733 ATGATGATGA
376743 TGATGGTGAAGGTAGTGG
1 TGATGGTGAAGGTAGTGG
376761 TGATGGTGAAGGTAGTGG
1 TGATGGTGAAGGTAGTGG
376779 TGATGGTGAAGGT
1 TGATGGTGAAGGT
376792 GGTAGTGGCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.22, C:0.00, G:0.49, T:0.29
Consensus pattern (18 bp):
TGATGGTGAAGGTAGTGG
Found at i:378144 original size:21 final size:22
Alignment explanation
Indices: 378103--378144 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
378093 TAAAATTATT
*
378103 AACATGCATTTCATCATCAGTA
1 AACATGCAATTCATCATCAGTA
*
378125 AACATGCAATT-ATTATCAGT
1 AACATGCAATTCATCATCAGT
378145 GTTATTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
AACATGCAATTCATCATCAGTA
Found at i:378725 original size:15 final size:15
Alignment explanation
Indices: 378705--378752 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
378695 GAGGCTGCTG
378705 CAGAAACTTGAGGAA
1 CAGAAACTTGAGGAA
*
378720 CAGAAACTTGAGGAC
1 CAGAAACTTGAGGAA
*
378735 CAGAAACTTGTGGAA
1 CAGAAACTTGAGGAA
378750 CAG
1 CAG
378753 CAGATACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.27, T:0.15
Consensus pattern (15 bp):
CAGAAACTTGAGGAA
Found at i:380070 original size:361 final size:361
Alignment explanation
Indices: 379406--380123 Score: 1321
Period size: 361 Copynumber: 2.0 Consensus size: 361
379396 ATGTAGCATT
*
379406 CTCCTATAGGGCATTAACCTAGAAGTGGTCTTGCCACTGTATAGCCTATGCAATGTATTCCAAAT
1 CTCCTATAGGACATTAACCTAGAAGTGGTCTTGCCACTGTATAGCCTATGCAATGTATTCCAAAT
* *
379471 TTCAGCTGCAGTGTTAAGACCTATCAGATATAGGCACACTTCCTCACTAACAGTAGAGAGCAACC
66 TTCAGCTGCAGTGTTAACACCTATCAGATAGAGGCACACTTCCTCACTAACAGTAGAGAGCAACC
*
379536 ATGAGGCAAGAGCTCCACCTTGTTCCTCATACAATTTATATTCAGGGTTCAAACTAACTACACCA
131 ATGAGGCAAGAGCTCCACCTTGTTCCTCATACAATTCATATTCAGGGTTCAAACTAACTACACCA
* *
379601 TATGAAGTAACATACTGTGTAGGCCAAGAAACATGAGGATCTATATACTTTTGCAGTCTATGTGT
196 TATGAAGTAACATACTATGTAGGCCAAGAAACATGAGGATCTATATACTTCTGCAGTCTATGTGT
*
379666 TTTAATAGTGAGAAAAACCTGTTGATGCCATATCAAGTAGTTGTGATCATCTAAGGTAACATTAA
261 TTTAATAATGAGAAAAACCTGTTGATGCCATATCAAGTAGTTGTGATCATCTAAGGTAACATTAA
379731 TTTTCTTAGTAGAGAATAACCTATTAGGAGCAAGAG
326 TTTTCTTAGTAGAGAATAACCTATTAGGAGCAAGAG
*
379767 CTCCTATAGGACATTAACCTAGAAGTGGTCTTGCCACTGTATAGCCTATGTAATGTATTCCAAAT
1 CTCCTATAGGACATTAACCTAGAAGTGGTCTTGCCACTGTATAGCCTATGCAATGTATTCCAAAT
*
379832 TTCAGCTGCAGTGTTAACACCTATCAGAT-GAGGCAACACTTCCTCACTAACAGTAGAGAGCAGC
66 TTCAGCTGCAGTGTTAACACCTATCAGATAGAGGC-ACACTTCCTCACTAACAGTAGAGAGCAAC
*
379896 CATGAGGCAAGAGCTCCATCTTGTTCCTCATACAATTCATATTCAGGGTTCAAACTAACTACACC
130 CATGAGGCAAGAGCTCCACCTTGTTCCTCATACAATTCATATTCAGGGTTCAAACTAACTACACC
*
379961 ATCTGAAGTAACATACTATGTAGGCCAAGAAACATGAGGATCTATATACTTCTGCAGTCTATGTG
195 ATATGAAGTAACATACTATGTAGGCCAAGAAACATGAGGATCTATATACTTCTGCAGTCTATGTG
380026 TTTTAATAATGAGAAAAACCTGTTGATGCCATATCAAGTAGTTGTGATCATCTAAGGTAACATTA
260 TTTTAATAATGAGAAAAACCTGTTGATGCCATATCAAGTAGTTGTGATCATCTAAGGTAACATTA
380091 ATTTTCTTAGTAGAGAATAACCTATTAGGAGCA
325 ATTTTCTTAGTAGAGAATAACCTATTAGGAGCA
380124 GAGGAGGCAG
Statistics
Matches: 345, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
360 4 0.01
361 341 0.99
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (361 bp):
CTCCTATAGGACATTAACCTAGAAGTGGTCTTGCCACTGTATAGCCTATGCAATGTATTCCAAAT
TTCAGCTGCAGTGTTAACACCTATCAGATAGAGGCACACTTCCTCACTAACAGTAGAGAGCAACC
ATGAGGCAAGAGCTCCACCTTGTTCCTCATACAATTCATATTCAGGGTTCAAACTAACTACACCA
TATGAAGTAACATACTATGTAGGCCAAGAAACATGAGGATCTATATACTTCTGCAGTCTATGTGT
TTTAATAATGAGAAAAACCTGTTGATGCCATATCAAGTAGTTGTGATCATCTAAGGTAACATTAA
TTTTCTTAGTAGAGAATAACCTATTAGGAGCAAGAG
Found at i:381065 original size:24 final size:23
Alignment explanation
Indices: 381033--381078 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
381023 AGAAACGGCC
*
381033 CAACTAACCAGGAACAGTTACAA
1 CAACTAACCAGAAACAGTTACAA
381056 CAACTTAACCAGAAACAGTTACA
1 CAAC-TAACCAGAAACAGTTACA
381079 GCTAATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.48, C:0.26, G:0.11, T:0.15
Consensus pattern (23 bp):
CAACTAACCAGAAACAGTTACAA
Found at i:384907 original size:14 final size:13
Alignment explanation
Indices: 384888--384917 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
384878 TTAAAGTTTA
384888 TATTAATAGATATT
1 TATTAATA-ATATT
384902 TATTAATAATATT
1 TATTAATAATATT
384915 TAT
1 TAT
384918 CATTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
TATTAATAATATT
Done.