Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:200751 original size:22 final size:22
Alignment explanation
Indices: 200723--200765 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
200713 AACGGTCAAC
200723 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
200745 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
200766 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:200786 original size:19 final size:18
Alignment explanation
Indices: 200762--200869 Score: 119
Period size: 19 Copynumber: 5.7 Consensus size: 18
200752 GGTCGGGTCG
200762 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
200780 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
*
200799 GATTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
200818 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
200838 GGTCGAAACCGGTCAAACC
1 GGTC-AGACCGGTCAAACC
200857 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
200870 TGAAAACCGG
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
18 4 0.05
19 59 0.78
20 13 0.17
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:200809 original size:10 final size:9
Alignment explanation
Indices: 200762--200869 Score: 74
Period size: 10 Copynumber: 11.3 Consensus size: 9
200752 GGTCGGGTCG
200762 GGTCAGACC
1 GGTCAGACC
*
200771 GGTCAAACC
1 GGTCAGACC
200780 GGCTCAGACC
1 GG-TCAGACC
*
200790 GGTCAAACC
1 GGTCAGACC
*
200799 GATTCAGACC
1 G-GTCAGACC
*
200809 GGTCAAACC
1 GGTCAGACC
200818 GGTTC-GAACC
1 GG-TCAG-ACC
* *
200828 GGTTGAAACC
1 GG-TCAGACC
*
200838 GGTCGAAACC
1 GGTC-AGACC
*
200848 GGTCAAACC
1 GGTCAGACC
200857 GGTCAGAACC
1 GGTCAG-ACC
200867 GGT
1 GGT
200870 TGAAAACCGG
Statistics
Matches: 80, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
9 36 0.45
10 44 0.55
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAGACC
Found at i:200838 original size:20 final size:19
Alignment explanation
Indices: 200813--200890 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 19
200803 CAGACCGGTC
200813 AAACCGGTTCGAACCGGTTG
1 AAACCGG-TCGAACCGGTTG
*
200833 AAACCGGTCGAAACCGG-TC
1 AAACCGGTCG-AACCGGTTG
200852 AAACCGGTCAGAACCGGTTG
1 AAACCGGTC-GAACCGGTTG
**
200872 AAAACCGGTTAAACCGGTT
1 -AAACCGGTCGAACCGGTT
200891 TCCAGCAGCC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 19 0.38
20 23 0.46
21 8 0.16
ACGTcount: A:0.31, C:0.26, G:0.27, T:0.17
Consensus pattern (19 bp):
AAACCGGTCGAACCGGTTG
Found at i:200838 original size:29 final size:28
Alignment explanation
Indices: 200763--200889 Score: 105
Period size: 29 Copynumber: 4.4 Consensus size: 28
200753 GTCGGGTCGG
* * *
200763 GTCAGACCGGTCAAACCGGCTCAGACCG
1 GTCAAACCGGTCAAACCGGTTCAAACCG
* *
200791 GTCAAACCGATTCAGACCGG-TCAAACCG
1 GTCAAACCG-GTCAAACCGGTTCAAACCG
* *
200819 GTTCGAACCGGTTGAAACCGG-TCGAAACCG
1 G-TCAAACCGG-TCAAACCGGTTC-AAACCG
*
200849 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTT-CAAACCG
*
200879 GTTAAACCGGT
1 GTCAAACCGGT
200890 TTCCAGCAGC
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
28 18 0.22
29 38 0.47
30 24 0.30
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTCAAACCG
Found at i:200849 original size:39 final size:37
Alignment explanation
Indices: 200762--200889 Score: 134
Period size: 39 Copynumber: 3.3 Consensus size: 37
200752 GGTCGGGTCG
* *
200762 GGTCAGACCGGTCAAACCGGCTC-AGACCGG-TCAAACC
1 GGTCAAACCGGTCAAACCGG-TCGA-ACCGGTTGAAACC
* *
200799 GATTCAGACCGGTCAAACCGGTTCGAACCGGTTGAAACC
1 G-GTCAAACCGGTCAAACCGG-TCGAACCGGTTGAAACC
200838 GGTCGAAACCGGTCAAACCGGTCAGAACCGGTTGAAAACC
1 GGTC-AAACCGGTCAAACCGGTC-GAACCGGTTG-AAACC
*
200878 GGTTAAACCGGT
1 GGTCAAACCGGT
200890 TTCCAGCAGC
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
37 1 0.01
38 29 0.37
39 41 0.52
40 8 0.10
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (37 bp):
GGTCAAACCGGTCAAACCGGTCGAACCGGTTGAAACC
Found at i:207006 original size:20 final size:20
Alignment explanation
Indices: 206964--207006 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
206954 TTATTTTCAT
* *
206964 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
206984 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
207004 TTT
1 TTT
207007 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:209044 original size:46 final size:45
Alignment explanation
Indices: 208946--209051 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 45
208936 GTGCACTAAG
* *
208946 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
208991 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
209037 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
209052 TGTATGTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 29 0.54
46 22 0.41
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:209126 original size:65 final size:63
Alignment explanation
Indices: 208992--209137 Score: 154
Period size: 65 Copynumber: 2.3 Consensus size: 63
208982 AATAGCCAGA
** *
208992 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATTGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCAATGCATGGTAT
* *
209057 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATATAAT-TCATGGTGCATCAATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCAATGCATGGTA
209119 TT
63 -T
*
209121 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
209138 CTCTGAAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.04
63 4 0.06
64 20 0.29
65 42 0.61
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCAATGCATGGTAT
Found at i:215434 original size:20 final size:21
Alignment explanation
Indices: 215395--215435 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
215385 GAGTTTATTT
215395 TCATTTTTCAATTTTGAAAAA
1 TCATTTTTCAATTTTGAAAAA
215416 TCATTTTT-ATATTTT-AAAAA
1 TCATTTTTCA-ATTTTGAAAAA
215436 CAATTTCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAAAA
Found at i:217538 original size:91 final size:90
Alignment explanation
Indices: 217377--217549 Score: 212
Period size: 91 Copynumber: 1.9 Consensus size: 90
217367 GTGCGCTAAG
*
217377 AGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAATAGCCTGAGTGCATCGATGAATGGTCT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTT-AAATAGCCTGAGTGCATCGATGAATGGTCT
*
217442 TGTGCAT-AGATGCATCAAATGCACTA
65 GGTGCATCAG-TGCATCAAATGCACTA
* *
217468 AGTGCATCGATGCATAAAATGCATTCGATGTTCAATT-AAT-TCCATG-GTGCATCGATGCATGG
1 AGTGCATCGATGCATAAAATGCATTCGATGTT---TTAAATAGCC-TGAGTGCATCGATGAATGG
217530 AT-TGGTGCATCAGTGCATCA
62 -TCTGGTGCATCAGTGCATCA
217550 CTTTGAAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
91 62 0.86
92 8 0.11
94 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (90 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTAAATAGCCTGAGTGCATCGATGAATGGTCTG
GTGCATCAGTGCATCAAATGCACTA
Found at i:219008 original size:6 final size:6
Alignment explanation
Indices: 218997--219021 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
218987 TAAAATTTTA
218997 AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG A
219022 TTCTCTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:221582 original size:15 final size:15
Alignment explanation
Indices: 221562--221606 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
221552 GCTGGGTGGG
*
221562 CGGATGTGGGGCGGA
1 CGGATGCGGGGCGGA
* *
221577 CGGATGCGGAGCGGG
1 CGGATGCGGGGCGGA
*
221592 TGGATGCGGGGCGGA
1 CGGATGCGGGGCGGA
221607 TGCGGGGCGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.60, T:0.11
Consensus pattern (15 bp):
CGGATGCGGGGCGGA
Found at i:221609 original size:11 final size:11
Alignment explanation
Indices: 221559--221616 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
221549 TTAGCTGGGT
*
221559 GGGCGGATGTG
1 GGGCGGATGCG
221570 GGGCGGA--CG
1 GGGCGGATGCG
*
221579 GATGCGGA-GC-
1 G-GGCGGATGCG
*
221589 GGGTGGATGCG
1 GGGCGGATGCG
221600 GGGCGGATGCG
1 GGGCGGATGCG
221611 GGGCGG
1 GGGCGG
221617 GTAATGTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
9 6 0.16
10 8 0.21
11 24 0.63
ACGTcount: A:0.10, C:0.16, G:0.64, T:0.10
Consensus pattern (11 bp):
GGGCGGATGCG
Found at i:223409 original size:54 final size:55
Alignment explanation
Indices: 223323--223446 Score: 171
Period size: 54 Copynumber: 2.3 Consensus size: 55
223313 GTACCCCCTT
* * **
223323 GGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-CAAAACTGTTTA
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTA
** *
223377 GGGGGGAATCGGTTCCCTCCGAGCATTTTGGAAATCTCGGGGCCAAAACCATTTA
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTA
223432 -GGGGGAATCGGTTCC
1 GGGGGGAATCGGTTCC
223447 TCCTATGGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 52 0.84
55 10 0.16
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (55 bp):
GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTA
Found at i:224115 original size:17 final size:17
Alignment explanation
Indices: 224093--224136 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
224083 TTCATAAATC
224093 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
224110 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
224127 -AAATATCCAA
1 CAAA-ATCCAA
224137 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:224128 original size:9 final size:8
Alignment explanation
Indices: 224088--224138 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
224078 CACCATTCAT
224088 AAATCC-A
1 AAATCCAA
224095 AAATCCAA
1 AAATCCAA
*
224103 CAATCCACA
1 AAATCCA-A
224112 AAAT-CAA
1 AAATCCAA
224119 ACAATCCAA
1 A-AATCCAA
224128 AATATCCAA
1 AA-ATCCAA
224137 AA
1 AA
224139 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:226137 original size:20 final size:21
Alignment explanation
Indices: 226089--226150 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
226079 TTCCCCTATG
226089 GGGGGGAATCGGTTCCTCTTCAAA
1 GGGGGGAATCGGTTCC-C-TC-AA
226113 GGGGGGAATCGGTTCCCTC-A
1 GGGGGGAATCGGTTCCCTCAA
* *
226133 GGGGGGGATCGATTCCCT
1 GGGGGGAATCGGTTCCCT
226151 ATGCACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.47
22 2 0.06
23 1 0.03
24 16 0.44
ACGTcount: A:0.16, C:0.23, G:0.39, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:231994 original size:75 final size:76
Alignment explanation
Indices: 231910--232107 Score: 274
Period size: 75 Copynumber: 2.6 Consensus size: 76
231900 CCGTTGTACA
* * * *
231910 AGGGGGAATCGGTACCCCCT-TGGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
**
231974 -CAAAACTGTTT
65 CCAAAACCATTT
* *
231985 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
232050 CAAAACCATTT
66 CAAAACCATTT
* * *
232061 ATGGGGAATCGATTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
232108 ATCTGTAATT
Statistics
Matches: 110, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
75 56 0.51
76 54 0.49
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (76 bp):
AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
CAAAACCATTT
Found at i:232077 original size:76 final size:75
Alignment explanation
Indices: 231910--232112 Score: 264
Period size: 76 Copynumber: 2.7 Consensus size: 75
231900 CCGTTGTACA
* * * * * *
231910 AGGGGGAATCGGTACCCCCT-TGGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGAATCGATTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
**
231974 CAAAACTGTTT
65 CAAAACCATTT
* *
231985 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 AGGGGGAATCGATTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG-
232050 CAAAACCATTT
65 CAAAACCATTT
* * *
232061 ATGGGGAATCGATTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 AGGGGGAATCGATTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTG
232113 TAATTTTTGG
Statistics
Matches: 114, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
75 56 0.49
76 58 0.51
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (75 bp):
AGGGGGAATCGATTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
AAAACCATTT
Found at i:233470 original size:20 final size:22
Alignment explanation
Indices: 233421--233474 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
233411 TAATGTAATA
233421 GGGTATCGATACCATAGTATAG
1 GGGTATCGATACCATAGTATAG
** *
233443 TAGTATCGATACCAT-G-GTAG
1 GGGTATCGATACCATAGTATAG
233463 GGGTATCGATAC
1 GGGTATCGATAC
233475 TATTAATCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 13 0.48
21 1 0.04
22 13 0.48
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (22 bp):
GGGTATCGATACCATAGTATAG
Found at i:234151 original size:82 final size:81
Alignment explanation
Indices: 234053--234382 Score: 464
Period size: 82 Copynumber: 4.0 Consensus size: 81
234043 GTTCTAAAAT
* * *
234053 AAAAGATTAATGGCCTAACTATGCATTTTACAGAAATGTGTTAATTATGCCAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAACTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAGG
234118 TTAAATACCTTTGAGTA
65 TTAAATACCTTTGAGTA
* *
234135 AAAAGATTAATGGCCTAACTGTGCATTTGACAGAAAGGTGTTAATTATGCCAGTTAGATGAAATG
1 AAAAGATTAATGGCCTAACTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAGG
234200 TTAAATACCTTTGAGTA
65 TTAAATACCTTTGAGTA
* * *
234217 AAAAGATTAATGACCTAACTTTGCATTTGACAGAAAGATGTCAATTATGCTAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAACTGTGCATTTGACAGAAAG-TGTCAATTATGCCAGTTAGATGAAAGG
*
234282 TTAAATACATTTGAGT-
65 TTAAATACCTTTGAGTA
* * * * **
234298 AAAAGATTATTGGCCTAACTGTGCATATGGCAGGAAAGTGTCAATGATGAAAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAACTGTGCATTTGACA-GAAAGTGTCAATTATGCCAGTTAGATGAAAGG
* *
234363 CTAAATACCTTTGGGTA
65 TTAAATACCTTTGAGTA
234380 AAA
1 AAA
234383 TACTAAATGC
Statistics
Matches: 224, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
81 65 0.29
82 159 0.71
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (81 bp):
AAAAGATTAATGGCCTAACTGTGCATTTGACAGAAAGTGTCAATTATGCCAGTTAGATGAAAGGT
TAAATACCTTTGAGTA
Found at i:234513 original size:46 final size:46
Alignment explanation
Indices: 234442--234748 Score: 443
Period size: 46 Copynumber: 6.6 Consensus size: 46
234432 TTTGAAATTA
* *
234442 AAGGCATGAAAGGATGACATCAATGAAATGCATGAAAGGATGCATT
1 AAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
*
234488 AAGGCATGAAAGGAGGCCATAAATGAAATGCATGAAAGGATGCATTT
1 AAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCA-TT
* * *
234535 AAGACATGAAAGGATGCCATAAATTAAATGCATGAAATGATGCATT
1 AAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
** * *
234581 AAGGCATGAAAGGATGTGATAAATGAAATGCATGAAAGAATTCATT
1 AAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
*
234627 AAGGCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATGCATT
1 AAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
* * ** *
234673 AAGGCAAGAAATGATGCCATAAATGAAATAAATAAAAGGATGCATT
1 AAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
*
234719 AAAGGCATGAAAGGATGCCATAAAGGAAAT
1 -AAGGCATGAAAGGATGCCATAAATGAAAT
234749 TAATGAATAA
Statistics
Matches: 233, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
46 165 0.71
47 68 0.29
ACGTcount: A:0.46, C:0.09, G:0.24, T:0.21
Consensus pattern (46 bp):
AAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATT
Found at i:234544 original size:21 final size:21
Alignment explanation
Indices: 234518--234596 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 21
234508 AAATGAAATG
234518 CATGAAAGGATGCATTTAAGA
1 CATGAAAGGATGCATTTAAGA
234539 CATGAAAGGATGCCATAAATTAA-A
1 CATGAAAGGATG-CAT---TTAAGA
* *
234563 TGCATGAAATGATGCA-TTAAGG
1 --CATGAAAGGATGCATTTAAGA
234585 CATGAAAGGATG
1 CATGAAAGGATG
234597 TGATAAATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
20 11 0.23
21 16 0.33
22 3 0.06
24 1 0.02
25 6 0.12
26 11 0.23
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.23
Consensus pattern (21 bp):
CATGAAAGGATGCATTTAAGA
Found at i:234755 original size:139 final size:140
Alignment explanation
Indices: 234438--234748 Score: 455
Period size: 139 Copynumber: 2.2 Consensus size: 140
234428 TCTATTTGAA
* *
234438 ATTAAAGGCATGAAAGGATGACATCAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAG
1 ATTAAAGGCATGAAAGGATGACATAAATGAAATGCATGAAAGAATGCATTAAGGCATGAAAGGAG
* * **
234503 GCCATAAATGAAATGCATGAAAGGATGCATTTAAGACATGAAAGGATGCCATAAATTAAATGCAT
66 GCCATAAATGAAATGCATGAAAGGATGCATTTAAGACAAGAAAGGATGCCATAAATGAAATAAAT
* *
234568 GAAATGATGC
131 AAAAGGATGC
** * *
234578 ATT-AAGGCATGAAAGGATGTGATAAATGAAATGCATGAAAGAATTCATTAAGGCATGAAAGGAT
1 ATTAAAGGCATGAAAGGATGACATAAATGAAATGCATGAAAGAATGCATTAAGGCATGAAAGGAG
* * *
234642 GTCATAAATGAAATGCATGAAAGGATGCA-TTAAGGCAAGAAATGATGCCATAAATGAAATAAAT
66 GCCATAAATGAAATGCATGAAAGGATGCATTTAAGACAAGAAAGGATGCCATAAATGAAATAAAT
234706 AAAAGGATGC
131 AAAAGGATGC
* *
234716 ATTAAAGGCATGAAAGGATGCCATAAAGGAAAT
1 ATTAAAGGCATGAAAGGATGACATAAATGAAAT
234749 TAATGAATAA
Statistics
Matches: 152, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
138 40 0.26
139 109 0.72
140 3 0.02
ACGTcount: A:0.46, C:0.09, G:0.24, T:0.21
Consensus pattern (140 bp):
ATTAAAGGCATGAAAGGATGACATAAATGAAATGCATGAAAGAATGCATTAAGGCATGAAAGGAG
GCCATAAATGAAATGCATGAAAGGATGCATTTAAGACAAGAAAGGATGCCATAAATGAAATAAAT
AAAAGGATGC
Found at i:242432 original size:55 final size:55
Alignment explanation
Indices: 242371--242549 Score: 225
Period size: 55 Copynumber: 3.3 Consensus size: 55
242361 TCAGATCAAT
* * * * *
242371 TTTGGAAGACGAGTATGATCTACTCTTCTTTCAGGGAGATAAGACTCGAGAAGTC
1 TTTGGAAAACGGGTATGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATC
* * * *
242426 TTTGGAAAATGGGTTTGCTCCACTCTTCTTTCATGGAGATAAGACTTGAGAAATC
1 TTTGGAAAACGGGTATGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATC
* * * *
242481 TTTTGAACACGGGTCTGCTCCATTCTTCTTTCAGGGAGATAAGACTCGAGAAATC
1 TTTGGAAAACGGGTATGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATC
242536 TTCT-GAAAACGGGT
1 TT-TGGAAAACGGGT
242550 TCACTCCCAA
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
55 105 0.99
56 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (55 bp):
TTTGGAAAACGGGTATGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATC
Found at i:242591 original size:55 final size:55
Alignment explanation
Indices: 242532--242648 Score: 153
Period size: 55 Copynumber: 2.1 Consensus size: 55
242522 AGACTCGAGA
**
242532 AATCTTCTGAAAACGGGTTCACTCCCAATTATTTCAAGGAGTATAAAACTTGAAC
1 AATCTTCTGAAAACGGGTTCACTCCCAATTATTTCAAGGAGTATAAAACTCAAAC
* * * * * * *
242587 AATCTTTTGAAAATGGGTTCTCTCCCTATTCTTTCAGGGAGTATAGAACTCAAAC
1 AATCTTCTGAAAACGGGTTCACTCCCAATTATTTCAAGGAGTATAAAACTCAAAC
242642 AATCTTC
1 AATCTTC
242649 AACAAATGTG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (55 bp):
AATCTTCTGAAAACGGGTTCACTCCCAATTATTTCAAGGAGTATAAAACTCAAAC
Found at i:242591 original size:110 final size:109
Alignment explanation
Indices: 242393--242627 Score: 280
Period size: 110 Copynumber: 2.1 Consensus size: 109
242383 GTATGATCTA
* * ** ** *
242393 CTCTTCTTTCAGGGAGATAAGACTCGAGAAGTCTTTGGAAAATGGGTTTGCTCCACTCTTCTTTC
1 CTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGGGTTCACTCCACAATTATTTC
* * *
242458 ATGGAGATAAGACTTGAGAAATCTTTTGAACACGGG-TCTGCTCC
66 AAGGAGATAAAACTTGAGAAATCTTTTGAAAACGGGTTCT-CTCC
*
242502 ATTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTCT-GAAAACGGGTTCACTCC-CAATTATT
1 -CTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTT-TGGAAAACGGGTTCACTCCACAATTATT
*
242565 TCAAGGAGTATAAAACTTGA-ACAATCTTTTGAAAATGGGTTCTCTCC
64 TCAAGGAG-ATAAAACTTGAGA-AATCTTTTGAAAACGGGTTCTCTCC
*
242612 CTATTCTTTCAGGGAG
1 CTCTTCTTTCAGGGAG
242628 TATAGAACTC
Statistics
Matches: 107, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
109 27 0.25
110 76 0.71
111 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (109 bp):
CTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGGGTTCACTCCACAATTATTTC
AAGGAGATAAAACTTGAGAAATCTTTTGAAAACGGGTTCTCTCC
Found at i:242656 original size:55 final size:55
Alignment explanation
Indices: 242541--242695 Score: 143
Period size: 55 Copynumber: 2.8 Consensus size: 55
242531 AAATCTTCTG
* * * * ** **
242541 AAAACGGGTTCACTCCCAATTATTTCAAGGAGTATAAAACTTGAACAATCTTTTG
1 AAAATGGGTTCTCTCCCAATTCTTTCAAGGAGTATAGAACTCAAACAATCTTTCA
* *
242596 AAAATGGGTTCTCTCCCTATTCTTTCAGGGAGTATAGAACTCAAACAATC-TTCA
1 AAAATGGGTTCTCTCCCAATTCTTTCAAGGAGTATAGAACTCAAACAATCTTTCA
* * * * *
242650 ACAAATGTG-TCTATTCCCCATTCTTTTAAGGAGTATAGGACTCAAA
1 A-AAATGGGTTCT-CTCCCAATTCTTTCAAGGAGTATAGAACTCAAA
242696 AATTTATTTG
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 6 0.07
55 76 0.93
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (55 bp):
AAAATGGGTTCTCTCCCAATTCTTTCAAGGAGTATAGAACTCAAACAATCTTTCA
Found at i:242782 original size:37 final size:37
Alignment explanation
Indices: 242701--242856 Score: 156
Period size: 37 Copynumber: 4.2 Consensus size: 37
242691 TCAAAAATTT
* * * * *
242701 ATTTGCTTCAATACTCTCCCTTGAAGGC-TAAAATTG
1 ATTTGCTTCACTACTATTCCGTGAAGGCTTAAGATTG
242737 ATTTGCTTCACTACTATTCCGTGAAGGCTTAAGATTG
1 ATTTGCTTCACTACTATTCCGTGAAGGCTTAAGATTG
* * * * **
242774 ACTTGCTTCACTACTCTTTCATGAATACTTAAGATTG
1 ATTTGCTTCACTACTATTCCGTGAAGGCTTAAGATTG
*
242811 ATTTG-TTCCACCACTCATT-CGTGAAGGCTTAAGATTG
1 ATTTGCTT-CACTACT-ATTCCGTGAAGGCTTAAGATTG
*
242848 ATTTTCTTC
1 ATTTGCTTC
242857 GAAGGTTGAC
Statistics
Matches: 98, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
36 26 0.27
37 68 0.69
38 4 0.04
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (37 bp):
ATTTGCTTCACTACTATTCCGTGAAGGCTTAAGATTG
Found at i:246932 original size:8 final size:8
Alignment explanation
Indices: 246909--246944 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
246899 AAAAGGAGAT
*
246909 ATATATAT
1 ATATATAC
*
246917 ATACATAC
1 ATATATAC
246925 ATATATAC
1 ATATATAC
246933 ATATATAC
1 ATATATAC
246941 ATAT
1 ATAT
246945 GGGAGAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:247650 original size:74 final size:74
Alignment explanation
Indices: 247499--247684 Score: 212
Period size: 74 Copynumber: 2.5 Consensus size: 74
247489 TAAATAGGGA
* * * *** * *
247499 GGTACCGATACCCCTCATAGGGTGTACCGATACCACTATGCCAATTTTGGTTCTGAGAAAAACAG
1 GGTACCGATACCCCTCATA-GG-GTACCGATACCCCTATACAAACAATGGCTCCGAGAAAAACAG
* *
247564 ATTGCTCAATG
64 AATGCCCAATG
*
247575 GGTACCGATACCCCTCATAGGGTACCAATACCCCTATACAAACAATGGCTCCGAGAAAAACAGAA
1 GGTACCGATACCCCTCATAGGGTACCGATACCCCTATACAAACAATGGCTCCGAGAAAAACAGAA
*
247640 TGCCCTATG
66 TGCCCAATG
* *
247649 GGTACCGATACCCC-CTTAGAGGTATCGATACCCCTA
1 GGTACCGATACCCCTCATAG-GGTACCGATACCCCTA
247685 GACATTTAAC
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
73 4 0.04
74 69 0.73
75 2 0.02
76 19 0.20
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (74 bp):
GGTACCGATACCCCTCATAGGGTACCGATACCCCTATACAAACAATGGCTCCGAGAAAAACAGAA
TGCCCAATG
Found at i:256060 original size:54 final size:52
Alignment explanation
Indices: 255997--256114 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 52
255987 CTTATAGGGT
* * * * *
255997 GTACCGATACCCATATGCCAATTTTGGTTCTGAGAAAAATAGATTGCTCAATGG
1 GTACCGATACCCATATGCAAATCTTGGCTCTGAGAAAAACAGAAT-CT-AATGG
* *
256051 GTACCGATACCCCTATGCAAATCTTGGCTCTGAGAAAAACATAATCTAATGG
1 GTACCGATACCCATATGCAAATCTTGGCTCTGAGAAAAACAGAATCTAATGG
*
256103 GTACTGATACCC
1 GTACCGATACCC
256115 CCTTAGAGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 16 0.29
53 2 0.04
54 38 0.68
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
GTACCGATACCCATATGCAAATCTTGGCTCTGAGAAAAACAGAATCTAATGG
Found at i:265270 original size:3 final size:3
Alignment explanation
Indices: 265262--265306 Score: 72
Period size: 3 Copynumber: 14.3 Consensus size: 3
265252 TTTGATAACA
265262 AAT AAT AAT AATT AAT AAT AAT AATT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AA-T AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
265307 TTAACCCTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:265272 original size:13 final size:13
Alignment explanation
Indices: 265256--265311 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 13
265246 TTATTTTTTG
*
265256 ATAACAAATAATA
1 ATAACTAATAATA
*
265269 ATAATTAATAATA
1 ATAACTAATAATA
*
265282 ATAATTAATAATA
1 ATAACTAATAATA
265295 ATAA-TAATAATA
1 ATAACTAATAATA
*
265307 TTAAC
1 ATAAC
265312 CCTGACAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
12 11 0.28
13 28 0.72
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAACTAATAATA
Found at i:279672 original size:2 final size:2
Alignment explanation
Indices: 279653--279720 Score: 118
Period size: 2 Copynumber: 33.5 Consensus size: 2
279643 TAAATGCGTG
*
279653 TA TA TA TCA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
279696 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 T
279721 GTACAATAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 61 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:284020 original size:2 final size:2
Alignment explanation
Indices: 284013--284050 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
284003 TAAAATTACA
284013 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
284051 TAATTATACA
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:285762 original size:4 final size:4
Alignment explanation
Indices: 285753--285789 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
285743 CTTGAACAAA
285753 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
285790 CAGAAAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:293462 original size:8 final size:8
Alignment explanation
Indices: 293449--293481 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
293439 CGGTGAAGGT
293449 ACTGGTTC
1 ACTGGTTC
*
293457 ATTGGTTC
1 ACTGGTTC
293465 ACTGGTTC
1 ACTGGTTC
293473 ACTGGTTC
1 ACTGGTTC
293481 A
1 A
293482 ATCGGGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.39
Consensus pattern (8 bp):
ACTGGTTC
Found at i:295982 original size:18 final size:19
Alignment explanation
Indices: 295955--295990 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
295945 CCGATTTGCC
*
295955 TAAAATAAAT-GAAAAAAG
1 TAAAAAAAATAGAAAAAAG
295973 TAAAAAAAATAGAAAAAA
1 TAAAAAAAATAGAAAAAA
295991 TATGGGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (19 bp):
TAAAAAAAATAGAAAAAAG
Found at i:296827 original size:6 final size:7
Alignment explanation
Indices: 296810--296839 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
296800 TTTAAATATT
296810 TTTTTTA
1 TTTTTTA
296817 TTTTTTA
1 TTTTTTA
296824 TTTTTTA
1 TTTTTTA
296831 TTTTTTA
1 TTTTTTA
296838 TT
1 TT
296840 AATAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:297834 original size:189 final size:190
Alignment explanation
Indices: 297500--297870 Score: 687
Period size: 189 Copynumber: 2.0 Consensus size: 190
297490 AAAGAAGCAG
297500 AGATCTCCCTTTCATTCCTCAATCATCTAAATCTAACATTTACTTGGTTTTTTAATGCAAAACAT
1 AGATCTCCCTTTCATTCCTCAATCATCTAAATCTAACATTTACTTGGTTTTTTAATGCAAAACAT
297565 TCTCCCAGCCCCATGCTTACTGTTAATACTTCTAGTCTCAAACAGCTCCCTGAAAAACAGTTCAT
66 TCTCCCAGCCCCATGCTTACTGTTAATACTTCTAGTCTCAAACAGCTCCCTGAAAAACAGTTCAT
297630 AAAGAAGGAAAAAAAAAACAG-AAAA-AAAAT-AACAAAAGGAGAAAAATCATTAATATCAA
131 AAAGAAGG--AAAAAAAACAGAAAAATAAAATAAACAAAAGGAGAAAAATCATTAATATCAA
297689 AGATCTCCCTTTCATTCCTCAATCATCTAAATCTAACATTTACTTGGTTTTTTAATGCAAAACAT
1 AGATCTCCCTTTCATTCCTCAATCATCTAAATCTAACATTTACTTGGTTTTTTAATGCAAAACAT
297754 TCTCCCAGCCCCATGCTTACTGTTAATACTTCTAGTCTCAAACAGCTCCCTGAAAAACAGTTCAT
66 TCTCCCAGCCCCATGCTTACTGTTAATACTTCTAGTCTCAAACAGCTCCCTGAAAAACAGTTCA-
297819 TAAAGAAGG-AAAAAAACAGAAAAATAAAATAAACAAAAGGAGAAAAATCATT
130 TAAAGAAGGAAAAAAAACAGAAAAATAAAATAAACAAAAGGAGAAAAATCATT
297871 TATTAATATC
Statistics
Matches: 178, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
187 10 0.06
188 4 0.02
189 134 0.75
190 30 0.17
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (190 bp):
AGATCTCCCTTTCATTCCTCAATCATCTAAATCTAACATTTACTTGGTTTTTTAATGCAAAACAT
TCTCCCAGCCCCATGCTTACTGTTAATACTTCTAGTCTCAAACAGCTCCCTGAAAAACAGTTCAT
AAAGAAGGAAAAAAAACAGAAAAATAAAATAAACAAAAGGAGAAAAATCATTAATATCAA
Found at i:298602 original size:3 final size:3
Alignment explanation
Indices: 298596--298638 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
298586 ATTAGTAATA
*
298596 ATT ATT ATT A-T ATT ATT ATT ATT -TC ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
298639 ACTTACATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 5 0.14
3 30 0.86
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:298612 original size:11 final size:11
Alignment explanation
Indices: 298596--298638 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
298586 ATTAGTAATA
298596 ATTATTATTAT
1 ATTATTATTAT
298607 ATTATTATTAT
1 ATTATTATTAT
298618 -TTCATTATTATT
1 ATT-ATTATTA-T
298630 ATTA-TATTA
1 ATTATTATTA
298639 ACTTACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.07
11 23 0.79
12 2 0.07
13 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:298615 original size:14 final size:14
Alignment explanation
Indices: 298596--298638 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
298586 ATTAGTAATA
298596 ATTATTATTATATT
1 ATTATTATTATATT
298610 ATTATTATT-TCATT
1 ATTATTATTAT-ATT
298624 ATTATTATTATATT
1 ATTATTATTATATT
298638 A
1 A
298639 ACTTACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:299247 original size:19 final size:19
Alignment explanation
Indices: 299225--299263 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
299215 AGAAACCCCG
*
299225 AAAAAAAAAAGAAAATGAA
1 AAAAAAAAAAGAAAAGGAA
*
299244 AAAATAAAAAGAAAAGGAA
1 AAAAAAAAAAGAAAAGGAA
299263 A
1 A
299264 GAAGAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAGGAA
Found at i:321549 original size:62 final size:62
Alignment explanation
Indices: 321452--321576 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
321442 TATTGATGTT
321452 CTACGATGTTGTTGATATAGTCATTGCTTAAACAATAGTCTGCATCGCCAAATTTGCAAGAA
1 CTACGATGTTGTTGATATAGTCATTGCTTAAACAATAGTCTGCATCGCCAAATTTGCAAGAA
321514 CTACGATGTTGTTGATATAGTCATTGCTTAAACAATAGTCTGCATCGCCAAATTTGCAAGAA
1 CTACGATGTTGTTGATATAGTCATTGCTTAAACAATAGTCTGCATCGCCAAATTTGCAAGAA
321576 C
1 C
321577 AATAGTCAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (62 bp):
CTACGATGTTGTTGATATAGTCATTGCTTAAACAATAGTCTGCATCGCCAAATTTGCAAGAA
Found at i:325079 original size:21 final size:21
Alignment explanation
Indices: 325055--325094 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
325045 ACTACAAAAC
325055 CTGCTAAAAATCCTACAGCCA
1 CTGCTAAAAATCCTACAGCCA
* *
325076 CTGCTGAAATTCCTACAGC
1 CTGCTAAAAATCCTACAGC
325095 ATTTGTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.23
Consensus pattern (21 bp):
CTGCTAAAAATCCTACAGCCA
Found at i:327739 original size:31 final size:31
Alignment explanation
Indices: 327704--327763 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
327694 TCATCAAAGC
* *
327704 TGTTTTTATGGTCATTGAGGAAGGAATAAGT
1 TGTTTTTATGGCCATTGAAGAAGGAATAAGT
327735 TGTTTTTATGGCCATTGAAGAAGGAATAA
1 TGTTTTTATGGCCATTGAAGAAGGAATAA
327764 AGCTTAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.37
Consensus pattern (31 bp):
TGTTTTTATGGCCATTGAAGAAGGAATAAGT
Found at i:329638 original size:23 final size:23
Alignment explanation
Indices: 329608--329663 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
329598 CATTTTGTCC
* *
329608 GGTAGCAATAATAGTTGGATTAT
1 GGTAGCAATAATAGCTGCATTAT
*
329631 GGTAGCAATTATAGCTGCATTAT
1 GGTAGCAATAATAGCTGCATTAT
* *
329654 TGCAGCAATA
1 GGTAGCAATA
329664 GTTTGATCCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (23 bp):
GGTAGCAATAATAGCTGCATTAT
Found at i:331031 original size:22 final size:23
Alignment explanation
Indices: 331001--331047 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
330991 TCGAATGTAT
*
331001 AAACGAACGATAAACAAACATTA
1 AAACGAACGATAAACAAACACTA
* *
331024 AAAC-AACGCTAAACGAACACTA
1 AAACGAACGATAAACAAACACTA
331046 AA
1 AA
331048 TGAACATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.11
Consensus pattern (23 bp):
AAACGAACGATAAACAAACACTA
Found at i:331064 original size:12 final size:12
Alignment explanation
Indices: 331047--331112 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
331037 CGAACACTAA
331047 ATGAACATGTTC
1 ATGAACATGTTC
* **
331059 ATGAACATATAA
1 ATGAACATGTTC
*
331071 ATGAACACGTTC
1 ATGAACATGTTC
* **
331083 GTGAACAT-TAA
1 ATGAACATGTTC
331094 ATGAACATGTTC
1 ATGAACATGTTC
*
331106 GTGAACA
1 ATGAACA
331113 ATAAATAAAT
Statistics
Matches: 38, Mismatches: 15, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
11 8 0.21
12 30 0.79
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (12 bp):
ATGAACATGTTC
Found at i:331064 original size:23 final size:23
Alignment explanation
Indices: 331038--331118 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
331028 AACGCTAAAC
*
331038 GAACACTAAATGAACATGTTCAT
1 GAACAATAAATGAACATGTTCAT
* *
331061 GAACATATAAATGAACACGTTCGT
1 GAACA-ATAAATGAACATGTTCAT
* *
331085 GAACATTAAATGAACATGTTCGT
1 GAACAATAAATGAACATGTTCAT
331108 GAACAATAAAT
1 GAACAATAAAT
331119 AAATGAACAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 31 0.61
24 20 0.39
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (23 bp):
GAACAATAAATGAACATGTTCAT
Found at i:332151 original size:24 final size:24
Alignment explanation
Indices: 332124--332180 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
332114 AACAACACAT
*
332124 GTGGATGATAGCTTATCATAAGTG
1 GTGGATGATAGCTCATCATAAGTG
*
332148 GTGGATGATAGCTCATCGTAAGTG
1 GTGGATGATAGCTCATCATAAGTG
* *
332172 TTTGATGAT
1 GTGGATGAT
332181 TATGCTATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.35
Consensus pattern (24 bp):
GTGGATGATAGCTCATCATAAGTG
Found at i:335867 original size:29 final size:29
Alignment explanation
Indices: 335834--335895 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
335824 ATATTTTTTA
* * * *
335834 ACAACTTGTAGTGCTAGGGTATGGATTAT
1 ACAACTTGCAGTGCCAGGGTAAGAATTAT
*
335863 ACAACTTGCAGTTCCAGGGTAAGAATTAT
1 ACAACTTGCAGTGCCAGGGTAAGAATTAT
335892 ACAA
1 ACAA
335896 GACAATATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (29 bp):
ACAACTTGCAGTGCCAGGGTAAGAATTAT
Found at i:337200 original size:96 final size:96
Alignment explanation
Indices: 337036--337229 Score: 388
Period size: 96 Copynumber: 2.0 Consensus size: 96
337026 GATTTTTGCA
337036 TTTCAAGCGCCAAAAATCTCGGCCGACTGGTAATCTCGTCGGCGCGTGATTTTCACTCATTGTTA
1 TTTCAAGCGCCAAAAATCTCGGCCGACTGGTAATCTCGTCGGCGCGTGATTTTCACTCATTGTTA
337101 TCGGTGGCCCTTGAGCTTCTGGGATTTGATC
66 TCGGTGGCCCTTGAGCTTCTGGGATTTGATC
337132 TTTCAAGCGCCAAAAATCTCGGCCGACTGGTAATCTCGTCGGCGCGTGATTTTCACTCATTGTTA
1 TTTCAAGCGCCAAAAATCTCGGCCGACTGGTAATCTCGTCGGCGCGTGATTTTCACTCATTGTTA
337197 TCGGTGGCCCTTGAGCTTCTGGGATTTGATC
66 TCGGTGGCCCTTGAGCTTCTGGGATTTGATC
337228 TT
1 TT
337230 AGTCGTTGGA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (96 bp):
TTTCAAGCGCCAAAAATCTCGGCCGACTGGTAATCTCGTCGGCGCGTGATTTTCACTCATTGTTA
TCGGTGGCCCTTGAGCTTCTGGGATTTGATC
Found at i:337755 original size:2 final size:2
Alignment explanation
Indices: 337748--337780 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
337738 TTTCAAAAAC
337748 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 T
337781 GTTTTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:338466 original size:72 final size:72
Alignment explanation
Indices: 338376--338531 Score: 208
Period size: 72 Copynumber: 2.2 Consensus size: 72
338366 TCCTTTGCCA
* * *
338376 TGAAGTTGAGTCAGTCTATTGGGCATTA-TATCTTTCATCGTGAAGTTG-GAATCGTAGGTGACT
1 TGAAGTTGAGTCAATCTATTGGGCA-CAGTATCCTTCATCGTGAAGTTGAG-ATCGTAGGTGACT
338439 CATTCATCG
64 CATTCATCG
* * *
338448 TGAAGTTGAGTTAATCTATTGGTCACAGTATCCTTCGTCGTGAAGTTGAGATCGTAGGTGACTCA
1 TGAAGTTGAGTCAATCTATTGGGCACAGTATCCTTCATCGTGAAGTTGAGATCGTAGGTGACTCA
*
338513 TTCGTCG
66 TTCATCG
*
338520 TGAAATTGAGTC
1 TGAAGTTGAGTC
338532 TAAATTGAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
71 1 0.01
72 71 0.97
73 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (72 bp):
TGAAGTTGAGTCAATCTATTGGGCACAGTATCCTTCATCGTGAAGTTGAGATCGTAGGTGACTCA
TTCATCG
Found at i:343364 original size:2 final size:2
Alignment explanation
Indices: 343357--343384 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
343347 ATACAGAAGA
343357 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
343385 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:343389 original size:2 final size:2
Alignment explanation
Indices: 343384--343408 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
343374 TATATATATA
343384 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
343409 ATGCGCGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:346496 original size:24 final size:24
Alignment explanation
Indices: 346460--346547 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
346450 GAGGCATGTA
*
346460 CTTTTGCAACAGATGAAACTTGTG
1 CTTTTGCAGCAGATGAAACTTGTG
346484 CTTTTGCAGCAGATGAAACTTGTG
1 CTTTTGCAGCAGATGAAACTTGTG
* * *
346508 CTTTTGCAGCAAATGAAGCTTGTT
1 CTTTTGCAGCAGATGAAACTTGTG
* *
346532 ATTTTGCAGAAGATGA
1 CTTTTGCAGCAGATGA
346548 GTCCCCTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (24 bp):
CTTTTGCAGCAGATGAAACTTGTG
Found at i:349222 original size:12 final size:12
Alignment explanation
Indices: 349207--349240 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
349197 AGTAAAATAT
349207 AAATAAAAATCA
1 AAATAAAAATCA
* *
349219 AAATAATAATGA
1 AAATAAAAATCA
349231 AAATAAAAAT
1 AAATAAAAAT
349241 TCCTACCCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (12 bp):
AAATAAAAATCA
Found at i:350367 original size:26 final size:26
Alignment explanation
Indices: 350337--350389 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
350327 AAATTGAATA
350337 AAATTAATATATAGAGGTAAAATTAC
1 AAATTAATATATAGAGGTAAAATTAC
*
350363 AAATTAATATTTAGAGGTAAAATTAC
1 AAATTAATATATAGAGGTAAAATTAC
350389 A
1 A
350390 CTTGGTGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (26 bp):
AAATTAATATATAGAGGTAAAATTAC
Found at i:351711 original size:2 final size:2
Alignment explanation
Indices: 351706--351748 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
351696 TTTTAAAAAC
351706 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
351748 T
1 T
351749 TGAAAATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:351802 original size:37 final size:36
Alignment explanation
Indices: 351768--351957 Score: 106
Period size: 38 Copynumber: 5.5 Consensus size: 36
351758 TATGTTTTCA
351768 AAAACTATAT-TATATATGTTTTCAAAAAC-CGTTTTTTT
1 AAAACTATATAT-TATATGTTTTCAAAAACACG---TTTT
* *
351806 AAATCTATATATTATATGATTTT-AAAAACAATGTTTT
1 AAAACTATATATTATATG-TTTTCAAAAAC-ACGTTTT
*
351843 TAAACTATATATTATATGTTTTC-AAAA-AC----T
1 AAAACTATATATTATATGTTTTCAAAAACACGTTTT
* * *
351873 ---AC-AT-TA-TATATGTTTTCAAACACCA-TTTTA
1 AAAACTATATATTATATGTTTTCAAA-AACACGTTTT
* **
351903 AAAACTATATATTATATGTTTTCAAATATCATTTTTT
1 AAAACTATATATTATATGTTTTCAAA-AACACGTTTT
351940 AAAAACTATATATTATAT
1 -AAAACTATATATTATAT
351958 CTTCGAAAAC
Statistics
Matches: 122, Mismatches: 10, Indels: 40
0.71 0.06 0.23
Matches are distributed among these distances:
24 11 0.09
25 4 0.03
26 3 0.02
27 3 0.02
30 1 0.01
33 2 0.02
34 3 0.02
35 2 0.02
36 25 0.20
37 24 0.20
38 38 0.31
39 5 0.04
40 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (36 bp):
AAAACTATATATTATATGTTTTCAAAAACACGTTTT
Found at i:351814 original size:38 final size:37
Alignment explanation
Indices: 351769--351871 Score: 138
Period size: 38 Copynumber: 2.8 Consensus size: 37
351759 ATGTTTTCAA
** *
351769 AAACTATAT-TATATATGTTTTCAAAAACCGTTTTTTT
1 AAACTATATAT-TATATGTTTTCAAAAACAATGTTTTT
351806 AAATCTATATATTATATGATTTT-AAAAACAATGTTTTT
1 AAA-CTATATATTATATG-TTTTCAAAAACAATGTTTTT
351844 AAACTATATATTATATGTTTTCAAAAAC
1 AAACTATATATTATATGTTTTCAAAAAC
351872 TACATTATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
36 4 0.07
37 23 0.39
38 27 0.46
39 5 0.08
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.46
Consensus pattern (37 bp):
AAACTATATATTATATGTTTTCAAAAACAATGTTTTT
Found at i:351893 original size:22 final size:22
Alignment explanation
Indices: 351836--351893 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
351826 TTTAAAAACA
* *
351836 ATGTTTTTAAACTATATATTAT
1 ATGTTTTCAAACTACATATTAT
351858 ATGTTTTCAAAAACTACAT-TATAT
1 ATGTTTTC--AAACTACATAT-TAT
351882 ATGTTTTCAAAC
1 ATGTTTTCAAAC
351894 ACCATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 11 0.35
23 1 0.03
24 19 0.61
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (22 bp):
ATGTTTTCAAACTACATATTAT
Found at i:351940 original size:38 final size:37
Alignment explanation
Indices: 351861--351957 Score: 126
Period size: 36 Copynumber: 2.6 Consensus size: 37
351851 ATATTATATG
* *
351861 TTTTCAAAAACTACAT-TATATATGTTTTCAAACACCA
1 TTTTTAAAAACTATATAT-TATATGTTTTCAAACACCA
* *
351898 -TTTTAAAAACTATATATTATATGTTTTCAAATATCA
1 TTTTTAAAAACTATATATTATATGTTTTCAAACACCA
351934 TTTTTTAAAAACTATATATTATAT
1 -TTTTTAAAAACTATATATTATAT
351958 CTTCGAAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
36 30 0.57
37 1 0.02
38 22 0.42
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (37 bp):
TTTTTAAAAACTATATATTATATGTTTTCAAACACCA
Found at i:351975 original size:26 final size:27
Alignment explanation
Indices: 351946--352010 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
351936 TTTTAAAAAC
351946 TATATAT-TATATCTTCGAAAACT-TTA
1 TATATATATATATCTTCG-AAACTATTA
* * *
351972 TATAT-TATATATTTTTGAAATTATTA
1 TATATATATATATCTTCGAAACTATTA
351998 TATATATATATAT
1 TATATATATATAT
352011 ATTATCATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 5 0.15
26 21 0.64
27 7 0.21
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (27 bp):
TATATATATATATCTTCGAAACTATTA
Found at i:353498 original size:2 final size:2
Alignment explanation
Indices: 353491--353522 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
353481 TATGCACTGT
353491 TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
353523 CCCATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:353744 original size:81 final size:81
Alignment explanation
Indices: 353643--353892 Score: 383
Period size: 81 Copynumber: 3.1 Consensus size: 81
353633 AAACATTTAG
* * * * *
353643 TCTTTTACCCAAAGGTATTTAACCTTTCTTCTAACTGGCATAATTTACACCTTTCTTTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
*
353708 ACAGCTAGGCCATTAA
66 ACAACTAGGCCATTAA
* * *
353724 TCTTTTACTCAAAGGTATTTATCCTTTCATCTAACTTACATACTTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
*
353789 ACAACTAGGACATTAA
66 ACAACTAGGCCATTAA
*
353805 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
*
353870 ACAACAAGGCCATTAA
66 ACAACTAGGCCATTAA
*
353886 TATTTTA
1 TCTTTTA
353893 TTTTGGAATA
Statistics
Matches: 152, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 152 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
ACAACTAGGCCATTAA
Found at i:354217 original size:20 final size:20
Alignment explanation
Indices: 354192--354362 Score: 108
Period size: 20 Copynumber: 7.7 Consensus size: 20
354182 TCATTTATGT
*
354192 CATCCTTTCATGCCTTAATA
1 CATCCTTTCATGCCTTAATG
*
354212 CATCCTTTCATGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
* *
354238 CATCCTTTCAAGCTTTAATG
1 CATCCTTTCATGCCTTAATG
*
354258 CATCCTTTCATGCATTTCATTTATG
1 CATCCTTTCATGC----C-TTAATG
* *
354283 ACACCCTTTCATGTCTTAATG
1 -CATCCTTTCATGCCTTAATG
*
354304 CATCCTTTCATGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
354330 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
354350 CATCCTTTCATGC
1 CATCCTTTCATGC
354363 ATTTCATTTA
Statistics
Matches: 118, Mismatches: 15, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
20 51 0.43
21 13 0.11
22 2 0.02
24 2 0.02
25 13 0.11
26 37 0.31
ACGTcount: A:0.21, C:0.27, G:0.09, T:0.43
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:354242 original size:46 final size:46
Alignment explanation
Indices: 354179--354373 Score: 327
Period size: 46 Copynumber: 4.2 Consensus size: 46
354169 TTATTCATTA
* *
354179 ATTTCATTTATGTCATCCTTTCATGCCTTAATACATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
354225 ATTTCATTTATGGCATCCTTTCAAGCTTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
354271 ATTTCATTTATGACACCCTTTCATGTCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
354317 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
354363 ATTTCATTTAT
1 ATTTCATTTAT
354374 TAATTCATTT
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 137 1.00
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.45
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:354270 original size:12 final size:12
Alignment explanation
Indices: 354250--354364 Score: 52
Period size: 12 Copynumber: 9.9 Consensus size: 12
354240 TCCTTTCAAG
*
354250 CTTTAATGCATC
1 CTTTCATGCATC
354262 CTTTCATGCATTTC
1 CTTTCATGCA--TC
* *
354276 ATTT-ATGACACC
1 CTTTCATG-CATC
354288 CTTTCATG--T-
1 CTTTCATGCATC
*
354297 C-TTAATGCATC
1 CTTTCATGCATC
354308 CTTTCATGCATTTC
1 CTTTCATGCA--TC
*
354322 ATTT-ATGGCATC
1 CTTTCAT-GCATC
354334 CTTTCATG---C
1 CTTTCATGCATC
*
354343 C-TTAATGCATC
1 CTTTCATGCATC
354354 CTTTCATGCAT
1 CTTTCATGCAT
354365 TTCATTTATT
Statistics
Matches: 76, Mismatches: 11, Indels: 32
0.64 0.09 0.27
Matches are distributed among these distances:
8 10 0.13
9 3 0.04
10 1 0.01
11 3 0.04
12 34 0.45
13 10 0.13
14 15 0.20
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (12 bp):
CTTTCATGCATC
Found at i:356349 original size:21 final size:21
Alignment explanation
Indices: 356323--356363 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
356313 AACGGTTATA
356323 TTTATTAAATATTTTAAATAT
1 TTTATTAAATATTTTAAATAT
* *
356344 TTTATTAATTATTTTTAATA
1 TTTATTAAATATTTTAAATA
356364 AGTGTTACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTATTAAATATTTTAAATAT
Found at i:360236 original size:14 final size:14
Alignment explanation
Indices: 360217--360244 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
360207 TTGATTTTAA
360217 AACATTTAAAATAT
1 AACATTTAAAATAT
360231 AACATTTAAAATAT
1 AACATTTAAAATAT
360245 TCAGTCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
AACATTTAAAATAT
Found at i:361102 original size:425 final size:423
Alignment explanation
Indices: 360311--361159 Score: 1600
Period size: 425 Copynumber: 2.0 Consensus size: 423
360301 ATTACTATTA
360311 CAAAACCCTTTTTAAAATAAATTTGATAAAGCAATCCAACATATATAATGTACATGCCACTAGTA
1 CAAAACCCTTTTTAAAATAAATTTGATAAAGCAATCCAACATATATAATGTACATGCCACTAGTA
360376 GGTCAAAGTTAGGATGTCTTACTAATACTATCGGTAGGTTTGGTTTTGTATAAATGTTGGAAAGC
66 GGTCAAAGTTAGGATGTCTTACTAATACTATCGGTAGGTTTGGTTTTGTATAAATGTTGGAAAGC
360441 TCCTCAGTTCACGACCTCTACTTTATTCAAACCTACACATGAAATAATCACGCGCTAAGTAAAAC
131 TCCTCAGTTCACGACCTCTACTTTATTCAAACCTACACATGAAATAATCACGCGCTAAGTAAAAC
360506 TTAGTGAGGCATAATATAAAATAAGCGATAAACATTAATTTCAAACATAATGTAATTTAAAACCG
196 TTAGTGAGGCATAATATAAAATAAGCGATAAACATTAATTTCAAACATAATGTAATTTAAAACCG
360571 TAAATTAAATATAAGAAACAAACTGTAATTTAAATAAAAACATTAAACTTCAAACCTGGATAGTC
261 TAAATTAAATATAAGAAACAAACTGTAATTTAAATAAAAACATTAAACTTCAAACCTGGATAGTC
360636 AAGCCGTTGTTCCTTCTGAAAAACCTGAAAAATCATCATCTCA-GA-TTTATCAAAAATTATATA
326 AAGCCGTTGTTCCTTCTGAAAAACCTGAAAAATCATCATCTCATGATTTTATCAAAAATTATATA
360699 AGTC-ACATC-AATATCATAAATAACTTTTGTT
391 AGTCAACATCAAATATCATAAATAACTTTTGTT
360730 CAAAACCCTTTTTAAAATAAATTTGATAAAGCAATCCAACATATATAATGTACATGCCACTAGTA
1 CAAAACCCTTTTTAAAATAAATTTGATAAAGCAATCCAACATATATAATGTACATGCCACTAGTA
360795 GGTCAAAGTTAGGATGTCTTACTAATACTATCGGTAGGTTTGGTTTTGTATAAGATGTTGGAAAG
66 GGTCAAAGTTAGGATGTCTTACTAATACTATCGGTAGGTTTGGTTTTGTATAA-ATGTTGGAAAG
360860 CTCCTCAGTTCACGACCTCTACTTTATTCAAACCTACACATGAAAATAATCACGCGCTAAGTAAA
130 CTCCTCAGTTCACGACCTCTACTTTATTCAAACCTACACATG-AAATAATCACGCGCTAAGTAAA
360925 ACTTAGTGAGGCATAA-ATATAAATAAAGCGATATAAACATTAATTTCAAACATTAATGTAATTT
194 ACTTAGTGAGGCATAATATA-AAAT-AAGCG--ATAAACATTAATTTCAAACA-TAATGTAATTT
360989 AAAACCGTAAATTAAATATAAGAAACAAACTGTAATTTAAATAAAAACATTAAACTTCAAACCTG
254 AAAACCGTAAATTAAATATAAGAAACAAACTGTAATTTAAATAAAAACATTAAACTTCAAACCTG
361054 GATAGTCAAGCCGTTGTTCCTTCTGAAAAACCTGAAAAATCATCATCTCATGATTTTATCAAAAA
319 GATAGTCAAGCCGTTGTTCCTTCTGAAAAACCTGAAAAATCATCATCTCATGATTTTATCAAAAA
361119 TTATATAAGTCAACATCAAATATCATAAATAACTTTTGTT
384 TTATATAAGTCAACATCAAATATCATAAATAACTTTTGTT
361159 C
1 C
361160 TTTTCATTCA
Statistics
Matches: 419, Mismatches: 0, Indels: 12
0.97 0.00 0.03
Matches are distributed among these distances:
419 118 0.28
420 56 0.13
421 42 0.10
422 5 0.01
424 20 0.05
425 126 0.30
426 2 0.00
427 22 0.05
428 5 0.01
429 23 0.05
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (423 bp):
CAAAACCCTTTTTAAAATAAATTTGATAAAGCAATCCAACATATATAATGTACATGCCACTAGTA
GGTCAAAGTTAGGATGTCTTACTAATACTATCGGTAGGTTTGGTTTTGTATAAATGTTGGAAAGC
TCCTCAGTTCACGACCTCTACTTTATTCAAACCTACACATGAAATAATCACGCGCTAAGTAAAAC
TTAGTGAGGCATAATATAAAATAAGCGATAAACATTAATTTCAAACATAATGTAATTTAAAACCG
TAAATTAAATATAAGAAACAAACTGTAATTTAAATAAAAACATTAAACTTCAAACCTGGATAGTC
AAGCCGTTGTTCCTTCTGAAAAACCTGAAAAATCATCATCTCATGATTTTATCAAAAATTATATA
AGTCAACATCAAATATCATAAATAACTTTTGTT
Found at i:361601 original size:35 final size:36
Alignment explanation
Indices: 361560--361646 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 36
361550 TATTAATTTG
** *
361560 TATCTGATAACTGTAAAATATATAATATTTG-TAAT
1 TATCTGATAACTGTAAAATATATAATAACTGAAAAT
*
361595 TATCTGATAACTGT-AAATATATGATAACTGAAAAT
1 TATCTGATAACTGTAAAATATATAATAACTGAAAAT
*
361630 CATCTGATAACTGTAAA
1 TATCTGATAACTGTAAA
361647 CATTTAGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 13 0.29
35 30 0.67
36 2 0.04
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (36 bp):
TATCTGATAACTGTAAAATATATAATAACTGAAAAT
Found at i:361619 original size:17 final size:17
Alignment explanation
Indices: 361564--361646 Score: 85
Period size: 17 Copynumber: 4.8 Consensus size: 17
361554 AATTTGTATC
361564 TGATAACTGTAAAATATA
1 TGATAACTGT-AAATATA
* ** * *
361582 TAATATTTGTAATTATC
1 TGATAACTGTAAATATA
361599 TGATAACTGTAAATATA
1 TGATAACTGTAAATATA
* *
361616 TGATAACTGAAAATCATC
1 TGATAACTGTAAAT-ATA
361634 TGATAACTGTAAA
1 TGATAACTGTAAA
361647 CATTTAGAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
17 30 0.59
18 21 0.41
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (17 bp):
TGATAACTGTAAATATA
Found at i:367626 original size:40 final size:41
Alignment explanation
Indices: 367565--367641 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
367555 ACGGTGCTGG
* * *
367565 ACATTGATACACGAATGTACCAAAGTTGAACTGATAACTGA
1 ACATTGATACACAAATATACCAAAGCTGAACTGATAACTGA
367606 ACATTG-TACACAAATATACCAAAGCTGAACTGATAA
1 ACATTGATACACAAATATACCAAAGCTGAACTGATAA
367642 GTACTCACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 27 0.82
41 6 0.18
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.23
Consensus pattern (41 bp):
ACATTGATACACAAATATACCAAAGCTGAACTGATAACTGA
Found at i:370014 original size:24 final size:24
Alignment explanation
Indices: 369969--370020 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
369959 AGCATTTTTA
* *
369969 TTTTATTTTTTATATTTTTTATAG
1 TTTTACTTTTTATATTTCTTATAG
*
369993 TTTTACTTTTTAT-TTTCCTTATCG
1 TTTTACTTTTTATATTT-CTTATAG
370017 TTTT
1 TTTT
370021 CAAGTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTACTTTTTATATTTCTTATAG
Found at i:376006 original size:55 final size:54
Alignment explanation
Indices: 375935--376267 Score: 427
Period size: 55 Copynumber: 6.0 Consensus size: 54
375925 CCCATTACCA
* *
375935 ATACGGAAAATCATAAACTTATTATGAATTTCTTAATTTTGCACACAAAGTGCCC
1 ATAC-GAAATTCATAAACTCATTATGAATTTCTTAATTTTGCACACAAAGTGCCC
* * ***
375990 ATACAGAAATTTATAAACTTATTATGAATTTCTTAGCA-AAAGCACACAAAGTGCCC
1 ATAC-GAAATTCATAAACTCATTATGAATTTCTTA--ATTTTGCACACAAAGTGCCC
376046 ATACGAAAATTCATAAACTCATTATGAATTTC-TAAGTTTTGCACACAAAGTGCCC
1 ATACG-AAATTCATAAACTCATTATGAATTTCTTAA-TTTTGCACACAAAGTGCCC
* *
376101 ATACAAAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATAC-GAAATTCATAAACTCATTATGAATTTCTTAATTTTGCACACAAAGTGCCC
* *
376156 ATACGAAAATTCATAAACTCATTATGAATTTCTTAGTTTTTCACACAAAGTGCCC
1 ATACG-AAATTCATAAACTCATTATGAATTTCTTAATTTTGCACACAAAGTGCCC
* *
376211 ATATGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACATATAGTGCC
1 ATA-CGAAATTCATAAACTCATTATGAATTTCTTA-ATTTTGCACACA-A-AGTGCC
376268 GTTCGCTAAT
Statistics
Matches: 248, Mismatches: 18, Indels: 21
0.86 0.06 0.07
Matches are distributed among these distances:
53 1 0.00
55 183 0.74
56 56 0.23
57 2 0.01
58 6 0.02
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (54 bp):
ATACGAAATTCATAAACTCATTATGAATTTCTTAATTTTGCACACAAAGTGCCC
Found at i:376194 original size:110 final size:111
Alignment explanation
Indices: 375935--376267 Score: 499
Period size: 110 Copynumber: 3.0 Consensus size: 111
375925 CCCATTACCA
* *
375935 ATACGGAAAA-TCATAAACTTATTATGAATTTCTTAATTTTGCACACAAAGTGCCCATACAGAAA
1 ATAC-GAAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAA
* * ****
375999 TTTATAAACTTATTATGAATTTCTTAGCAAAAGCACACAAAGTGCCC
65 TTCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* *
376046 ATACGAAAATTCATAAACTCATTATGAATTTCTAAGTTTTGCACACAAAGTGCCCATACAAAAAT
1 ATACGAAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAAT
376111 TCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCC
66 TCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* **
376156 ATACGAAAATTCATAAACTCATTATGAATTTCTTAGTTTTTCACACAAAGTGCCCATATGGAAAT
1 ATACGAAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAAT
*
376221 TCATAAACTCATTATGAATTTCTTAGTTTTTGCACACATATAGTGCC
66 TCATAAACTCATTATGAATTTCTTAGCTTTTGCACACA-A-AGTGCC
376268 GTTCGCTAAT
Statistics
Matches: 203, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
110 106 0.52
111 90 0.44
112 1 0.00
113 6 0.03
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (111 bp):
ATACGAAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAAT
TCATAAACTCATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
Found at i:376707 original size:17 final size:18
Alignment explanation
Indices: 376669--376707 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
376659 TACTACACTA
*
376669 TGGTATCGATACTCCCTTT
1 TGGTATCGATAC-CCATTT
376688 TGGTATCGATA-CCATTT
1 TGGTATCGATACCCATTT
376705 TGG
1 TGG
376708 CATTTTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (18 bp):
TGGTATCGATACCCATTT
Found at i:377596 original size:40 final size:40
Alignment explanation
Indices: 377541--377621 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
377531 TGGGGTATTA
377541 CATTAAAGAAGGTGGTGAATCCAAGAAGGAAGGATTGGTC
1 CATTAAAGAAGGTGGTGAATCCAAGAAGGAAGGATTGGTC
*
377581 CATTAAAGAAGGTGGTGAATCCTAGAAGGAAGGATTGGTC
1 CATTAAAGAAGGTGGTGAATCCAAGAAGGAAGGATTGGTC
377621 C
1 C
377622 CTGAAGCTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (40 bp):
CATTAAAGAAGGTGGTGAATCCAAGAAGGAAGGATTGGTC
Found at i:379951 original size:37 final size:37
Alignment explanation
Indices: 379872--379979 Score: 118
Period size: 37 Copynumber: 3.0 Consensus size: 37
379862 AAGTATTAAA
** *
379872 ATGGTTTTC-AAGTTTGGT-AACCTACTTTGAAAAA-
1 ATGGTTTTCAAAGTTTGGTAAATTTTCTTTGAAAAAT
379906 ATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAAT
1 ATGGTTTTCAAAGTTTGGTAAAT-TTTCTTTGAAAAAT
* *
379944 A-GTTTTTCAAAGTTTGGTAGATTTT-TGTTGAAAAAT
1 ATGGTTTTCAAAGTTTGGTAAATTTTCT-TTGAAAAAT
379980 GATAATGGGA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
34 9 0.14
35 10 0.16
36 14 0.22
37 30 0.47
38 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (37 bp):
ATGGTTTTCAAAGTTTGGTAAATTTTCTTTGAAAAAT
Found at i:384500 original size:21 final size:21
Alignment explanation
Indices: 384476--384536 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
384466 AACTTTGAAA
384476 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
384497 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
384511 AAATGGTTTTAAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
384532 AAATG
1 AAATG
384537 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 3 0.10
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:384582 original size:36 final size:36
Alignment explanation
Indices: 384468--384587 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
384458 TGGTAACCAA
384468 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
384505 CTTTG-AAAATGGTTTTAAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
384540 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
384577 -GTTGAAAAATG
1 CTTTGAAAAATG
384588 ATAATGGGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 35 0.46
36 14 0.18
37 27 0.36
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:385015 original size:15 final size:15
Alignment explanation
Indices: 384995--385032 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
384985 TCAAGGTATC
*
384995 TTGCATAACATTGCA
1 TTGCATAACATTACA
385010 TTGCATAACATTACA
1 TTGCATAACATTACA
385025 TTGCATAA
1 TTGCATAA
385033 AATGTAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (15 bp):
TTGCATAACATTACA
Found at i:387466 original size:13 final size:13
Alignment explanation
Indices: 387450--387475 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
387440 CGTCTTCTAG
387450 CCCAAGAGACTTC
1 CCCAAGAGACTTC
387463 CCCAAGAGACTTC
1 CCCAAGAGACTTC
387476 GTTGTGAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCAAGAGACTTC
Found at i:388189 original size:106 final size:106
Alignment explanation
Indices: 388057--388797 Score: 1142
Period size: 106 Copynumber: 7.0 Consensus size: 106
388047 GCATTGTTCC
* * ** * *
388057 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
388121 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* *
388163 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
388228 CCAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* * * *
388269 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
388334 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* * *
388375 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
388440 CCAGCAGTCCCTTCATTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
* * *
388481 GAGTCCAATATCCTTCGCTATGAAGTTGAATTTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * **
388546 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGTGTTGTCAA
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
388587 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
388652 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
*
388693 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
388758 CCAGCTGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
388798 CAAGTGGCAC
Statistics
Matches: 591, Mismatches: 43, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
106 590 1.00
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
Found at i:389637 original size:16 final size:16
Alignment explanation
Indices: 389612--389650 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
389602 AATGTTTATG
**
389612 TTTC-AAGAGAAACTT
1 TTTCAAAGAGAAACGA
389627 TTTCAAAGAGAAACGA
1 TTTCAAAGAGAAACGA
389643 TTTCAAAG
1 TTTCAAAG
389651 GTTTTTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (16 bp):
TTTCAAAGAGAAACGA
Found at i:389962 original size:20 final size:20
Alignment explanation
Indices: 389934--389972 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
389924 AAATTTAGCA
389934 TCTTGCTGTTGAGTTAAGCT
1 TCTTGCTGTTGAGTTAAGCT
*
389954 TCTTTCTGTTGAGTTAAGC
1 TCTTGCTGTTGAGTTAAGC
389973 AACCAACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (20 bp):
TCTTGCTGTTGAGTTAAGCT
Found at i:390381 original size:24 final size:24
Alignment explanation
Indices: 390352--390412 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
390342 ATATCAAAAA
*
390352 AAGAGTTTTGAATGATCTTTAATC
1 AAGAGTTTTGAAAGATCTTTAATC
* *
390376 AAGAGTTTTGAAAGATGTTTAATT
1 AAGAGTTTTGAAAGATCTTTAATC
*
390400 AAAAGTTTTGAAA
1 AAGAGTTTTGAAA
390413 ATATTATCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (24 bp):
AAGAGTTTTGAAAGATCTTTAATC
Found at i:391333 original size:172 final size:173
Alignment explanation
Indices: 391031--391377 Score: 601
Period size: 172 Copynumber: 2.0 Consensus size: 173
391021 TAAATAGGCC
*
391031 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTTTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
391096 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
*
391161 ATTGTGCCTGATCAATCTCATAGTTTGAAGCTTGATGTGTCATTT
129 ATTGTGCCTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
391206 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
*
391268 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTTGAGTGAAGTGATTCAGTGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
*
391333 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCCTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
391378 TTTTAGGGAA
Statistics
Matches: 166, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
170 14 0.08
172 99 0.60
174 1 0.01
175 52 0.31
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGAT
TGTGCCTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:391449 original size:16 final size:18
Alignment explanation
Indices: 391425--391457 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
391415 TCTTTTTGAT
391425 TTTTGTTC-TTGTTTTTC
1 TTTTGTTCTTTGTTTTTC
391442 TTTT-TTCTTTGTTTTT
1 TTTTGTTCTTTGTTTTT
391458 TTGCTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (18 bp):
TTTTGTTCTTTGTTTTTC
Found at i:391465 original size:16 final size:15
Alignment explanation
Indices: 391424--391481 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
391414 TTCTTTTTGA
391424 TTTTTGTTC-TTGTTT
1 TTTTTGTTCTTTG-TT
*
391439 TTCTTTTTTCTTTGTT
1 TT-TTTGTTCTTTGTT
391455 TTTTTGCTTCTTT-TCT
1 TTTTTG-TTCTTTGT-T
391471 TTTTTGTTCTT
1 TTTTTGTTCTT
391482 GATTGAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 11 0.30
16 23 0.62
17 3 0.08
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTTGTTCTTTGTT
Found at i:392721 original size:8 final size:7
Alignment explanation
Indices: 392690--392723 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
392680 ATGAATGTAT
392690 ATGCAAA
1 ATGCAAA
392697 ATGCAAA
1 ATGCAAA
392704 ATGCAAA
1 ATGCAAA
392711 ATGCAAAA
1 ATGC-AAA
392719 ATGCA
1 ATGCA
392724 TGAGATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGCAAA
Found at i:396858 original size:27 final size:27
Alignment explanation
Indices: 396820--396879 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
396810 TGATGTACAA
*
396820 GAATTGGGAGCAAGGATAAGCAAAAGG
1 GAATTGGGAGCAAGAATAAGCAAAAGG
396847 GAATTGGGAGCAAGAATAAGCAAAAGG
1 GAATTGGGAGCAAGAATAAGCAAAAGG
396874 GAATTG
1 GAATTG
396880 TCGTGACATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.35, T:0.13
Consensus pattern (27 bp):
GAATTGGGAGCAAGAATAAGCAAAAGG
Found at i:400935 original size:19 final size:19
Alignment explanation
Indices: 400911--400951 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
400901 TTTTGTATTG
400911 AAAATGAATTGATTTTTGA
1 AAAATGAATTGATTTTTGA
400930 AAAATGAATTGATTTTTGA
1 AAAATGAATTGATTTTTGA
400949 AAA
1 AAA
400952 TTAGAGGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (19 bp):
AAAATGAATTGATTTTTGA
Found at i:409014 original size:23 final size:23
Alignment explanation
Indices: 408988--409077 Score: 117
Period size: 23 Copynumber: 3.9 Consensus size: 23
408978 ATCTTATATA
408988 GCACTTAGGTGCATTTCTACGCG
1 GCACTTAGGTGCATTTCTACGCG
409011 GCACTTAGGTGCATTTCTACGCG
1 GCACTTAGGTGCATTTCTACGCG
* * * * *
409034 GCACTTCGGTACAATTCTATGTG
1 GCACTTAGGTGCATTTCTACGCG
* *
409057 GCACTTTGGTGCATTTATACG
1 GCACTTAGGTGCATTTCTACG
409078 AGTTGTGGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (23 bp):
GCACTTAGGTGCATTTCTACGCG
Found at i:413191 original size:2 final size:2
Alignment explanation
Indices: 413184--413227 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
413174 GAAAATTGTT
413184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
413225 TA T
1 TA T
413228 TGCAAAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:419422 original size:45 final size:45
Alignment explanation
Indices: 419329--419435 Score: 151
Period size: 45 Copynumber: 2.4 Consensus size: 45
419319 GGAAGGTGCC
* * * *
419329 GATGTTATGTAACCTAAACCTCACCTGAGATACTTAGGAGGTGTT
1 GATGCTATGTAACCTAGACCTCACCTGAGATACTTAGGAGATGAT
*
419374 GATGCTATGTAACCTAGACCTCACCTGAGATACTTTGGAGATGAT
1 GATGCTATGTAACCTAGACCTCACCTGAGATACTTAGGAGATGAT
* *
419419 GATGCTGTGTGACCTAG
1 GATGCTATGTAACCTAG
419436 GTTTAACCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (45 bp):
GATGCTATGTAACCTAGACCTCACCTGAGATACTTAGGAGATGAT
Found at i:423200 original size:15 final size:16
Alignment explanation
Indices: 423180--423219 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 16
423170 TCCCCACTTG
423180 TCTTCTCTTCATTT-T
1 TCTTCTCTTCATTTCT
423195 TC-T-TCTTCATTTCT
1 TCTTCTCTTCATTTCT
423209 TCTTC-CTTCAT
1 TCTTCTCTTCAT
423220 CTCCTTCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 9 0.41
14 4 0.18
15 9 0.41
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.62
Consensus pattern (16 bp):
TCTTCTCTTCATTTCT
Found at i:423409 original size:21 final size:21
Alignment explanation
Indices: 423376--423437 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
423366 TCTCCATCCA
*
423376 AGCTTAAGGAGGTTGATTTTT
1 AGCTTAAGAAGGTTGATTTTT
*
423397 AGCTTGAGAAGGTTGATTTTT
1 AGCTTAAGAAGGTTGATTTTT
* * *
423418 AGCTAAAGGAGGTTCATTTT
1 AGCTTAAGAAGGTTGATTTT
423438 GGGATTCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.26, C:0.06, G:0.27, T:0.40
Consensus pattern (21 bp):
AGCTTAAGAAGGTTGATTTTT
Found at i:423861 original size:21 final size:21
Alignment explanation
Indices: 423811--423868 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
423801 ATCACTTTTC
* * *
423811 AAAAGGATCGATCCCTTGGAG
1 AAAAAGATCGATCCCTCGAAG
423832 AAAAAGATCGATCCCTCGAAG
1 AAAAAGATCGATCCCTCGAAG
* * *
423853 GAAATGATCAATCCCT
1 AAAAAGATCGATCCCT
423869 TCTTTGTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (21 bp):
AAAAAGATCGATCCCTCGAAG
Found at i:424988 original size:45 final size:45
Alignment explanation
Indices: 424931--425035 Score: 156
Period size: 45 Copynumber: 2.3 Consensus size: 45
424921 GGAAGGTATC
* * * *
424931 GATGCTATGTGACCTGGACCTCGCCTGAGATACTTGGGAGGTGCT
1 GATGCTATGTGACCCGGACCTCGCATGAGATACTTGGGAGATACT
424976 GATGCTATGTGACCCGGACCTCGCATGAGATACTTGGGAGATACT
1 GATGCTATGTGACCCGGACCTCGCATGAGATACTTGGGAGATACT
* *
425021 GATGATGTGTGACCC
1 GATGCTATGTGACCC
425036 AAGTCTACCC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (45 bp):
GATGCTATGTGACCCGGACCTCGCATGAGATACTTGGGAGATACT
Found at i:431934 original size:17 final size:18
Alignment explanation
Indices: 431912--431956 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
431902 TACAACAAAA
431912 TTTATTTTC-TCACTACT
1 TTTATTTTCGTCACTACT
*
431929 TTTA-TTTCGTCACTTCT
1 TTTATTTTCGTCACTACT
431946 TTTA-TTTCGTC
1 TTTATTTTCGTC
431957 GCTAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.13, C:0.22, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTATTTTCGTCACTACT
Found at i:431994 original size:30 final size:31
Alignment explanation
Indices: 431958--432028 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
431948 TATTTCGTCG
*
431958 CTAAATATTTT-TTATAACTTTTTACTGTGA
1 CTAAATATTTTATTACAACTTTTTACTGTGA
* *
431988 CTAAATAATTTTATTACAATTTTTTATTGTGA
1 CTAAAT-ATTTTATTACAACTTTTTACTGTGA
**
432020 AAAAATATT
1 CTAAATATT
432029 ATTTGTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 6 0.18
31 8 0.24
32 20 0.59
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.51
Consensus pattern (31 bp):
CTAAATATTTTATTACAACTTTTTACTGTGA
Found at i:432012 original size:32 final size:30
Alignment explanation
Indices: 431958--432045 Score: 79
Period size: 32 Copynumber: 2.8 Consensus size: 30
431948 TATTTCGTCG
*
431958 CTAAATATTTTTTATAACTTTTTACTGTGA
1 CTAAATATTTTTTACAACTTTTTACTGTGA
* *
431988 CTAAATAATTTTATTACAATTTTTTATTGTGA
1 CTAAAT-ATTTT-TTACAACTTTTTACTGTGA
**
432020 AAAAATATTATTTGTCACAA-TTTTTA
1 CTAAATATT-TTT-T-ACAACTTTTTA
432046 TAACGAGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
30 6 0.12
31 9 0.19
32 29 0.60
33 4 0.08
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (30 bp):
CTAAATATTTTTTACAACTTTTTACTGTGA
Found at i:432123 original size:32 final size:33
Alignment explanation
Indices: 432050--432123 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 33
432040 TTTTTATAAC
* * *
432050 GAGAAATTAATATTTGTTATAAATTTTTATTTT
1 GAGAAAATAATATTTGTCATAAATTGTTATTTT
**
432083 GATTAAATAA-ATTTGTCA-AAAGTTGTTATTTT
1 GAGAAAATAATATTTGTCATAAA-TTGTTATTTT
432115 GAGAAAATA
1 GAGAAAATA
432124 TTGTGAAGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
31 3 0.09
32 23 0.70
33 7 0.21
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (33 bp):
GAGAAAATAATATTTGTCATAAATTGTTATTTT
Found at i:432365 original size:197 final size:196
Alignment explanation
Indices: 431983--432392 Score: 500
Period size: 197 Copynumber: 2.1 Consensus size: 196
431973 AACTTTTTAC
* **
431983 TGTGACTAAATAATTTTATTACAATTTTTTATTGTGAAAAAATATTATTTGTCACAATTTTTATA
1 TGTGACTAAATAAATTTATTACAATTGATTATTGTGAAAAAATATTATTTGTCACAATTTTTATA
* * * * * *
432048 ACGAGAAATTAATATTTGTTATAAATTTTTATTTTGATTAAATAAATTTGTCAAAAGTTGTTATT
66 ACGAGAAATTAATACTTATTATAAATTTTTATTATAACTAAATAAATTTATCAAAAGTTGTTATT
* *
432113 TTGAGAAAATATTGTGAAGAAATAAATTTAACATAAATTTTTATTTTGACTAAATTTAA-TGTTA
131 TTGAGAAAATATTGTGAAGAAATAAATTTAACATAAATTTTTAGTTTAACTAAATTTAATTGTTA
432177 T
196 T
* * * *
432178 TGTGACTAAATAAATTTGTTATAATTGATTATTGTGAAAAACTATTATTTGTCATAACTTTTTAT
1 TGTGACTAAATAAATTTATTACAATTGATTATTGTGAAAAAATATTATTTGTCACAA-TTTTTAT
** ** * *
432243 ATTGAGAAATTAATACTTATTAT-AATTTGTTATTATAACTATTTAAAATTTATCATAATTTGTT
65 AACGAGAAATTAATACTTATTATAAATTT-TTATTATAACTAAAT-AAATTTATCAAAAGTTGTT
* * ** * *
432307 ATTTTGATAAAATATTTTGACTAAATAAATTTGACATAAGTTTTTAGTTTAACTAAATTTAATTT
128 ATTTTGAGAAAATATTGTGAAGAAATAAATTTAACATAAATTTTTAGTTTAACTAAATTTAA-TT
432372 GTTAT
192 GTTAT
* * *
432377 TTTGTCTATATAAATT
1 TGTGACTAAATAAATT
432393 ATCATAATTT
Statistics
Matches: 180, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
195 55 0.31
196 36 0.20
197 70 0.39
199 19 0.11
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (196 bp):
TGTGACTAAATAAATTTATTACAATTGATTATTGTGAAAAAATATTATTTGTCACAATTTTTATA
ACGAGAAATTAATACTTATTATAAATTTTTATTATAACTAAATAAATTTATCAAAAGTTGTTATT
TTGAGAAAATATTGTGAAGAAATAAATTTAACATAAATTTTTAGTTTAACTAAATTTAATTGTTA
T
Found at i:432402 original size:31 final size:31
Alignment explanation
Indices: 432366--432461 Score: 183
Period size: 31 Copynumber: 3.1 Consensus size: 31
432356 TAACTAAATT
*
432366 TAATTTGTTATTTTGTCTATATAAATTATCA
1 TAATTTGTTATTTTGTCTAAATAAATTATCA
432397 TAATTTGTTATTTTGTCTAAATAAATTATCA
1 TAATTTGTTATTTTGTCTAAATAAATTATCA
432428 TAATTTGTTATTTTGTCTAAATAAATTATCA
1 TAATTTGTTATTTTGTCTAAATAAATTATCA
432459 TAA
1 TAA
432462 ATTATCTTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (31 bp):
TAATTTGTTATTTTGTCTAAATAAATTATCA
Found at i:433455 original size:79 final size:78
Alignment explanation
Indices: 433228--433502 Score: 388
Period size: 78 Copynumber: 3.5 Consensus size: 78
433218 AAAGGGGCTA
** *
433228 CAAATGTTTCGGAATAACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAA
1 CAAATGTTTCGGAACGACAAAAAGAAGACAATGCTGAAGATCAAGGGAAAAGAAACGAGGCAAAA
* *
433293 CAAAAAGTGATTG
66 CAAAAAGAGACTG
* * * *
433306 CAAGTGTTTTGGAGCGACAAAAAGAAGACAATGTTGAAGATCAAGGGAAAAGAAACGAGGCAAAA
1 CAAATGTTTCGGAACGACAAAAAGAAGACAATGCTGAAGATCAAGGGAAAAGAAACGAGGCAAAA
433371 CAAAAAGAGACTG
66 CAAAAAGAGACTG
** * * * *
433384 CAAATGTTTCCAAACAAAAAAAAAGAAGACAATGCTGAAGATCAAGTGAAAGGAAACGAGGCAAA
1 CAAATGTTTCGGAAC-GACAAAAAGAAGACAATGCTGAAGATCAAGGGAAAAGAAACGAGGCAAA
433449 ACAAAAAGAGACTG
65 ACAAAAAGAGACTG
* *
433463 TAAATGTTTCGGAACGACAGAAAGAAGACAATGCTGAAGA
1 CAAATGTTTCGGAACGACAAAAAGAAGACAATGCTGAAGA
433503 ACAACCTGTT
Statistics
Matches: 171, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
78 101 0.59
79 70 0.41
ACGTcount: A:0.50, C:0.12, G:0.24, T:0.13
Consensus pattern (78 bp):
CAAATGTTTCGGAACGACAAAAAGAAGACAATGCTGAAGATCAAGGGAAAAGAAACGAGGCAAAA
CAAAAAGAGACTG
Found at i:435104 original size:29 final size:29
Alignment explanation
Indices: 435071--435136 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
435061 TTTTTTTCAT
435071 ATTGATTAAAATATATAACTACAAAAATA
1 ATTGATTAAAATATATAACTACAAAAATA
*
435100 ATTGATTAAAATATATAACTATAAAAATA
1 ATTGATTAAAATATATAACTACAAAAATA
435129 ATTGATTA
1 ATTGATTA
435137 CCAAAAACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (29 bp):
ATTGATTAAAATATATAACTACAAAAATA
Found at i:445332 original size:24 final size:24
Alignment explanation
Indices: 445302--445356 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
445292 TAGAAATTTG
* *
445302 ATTGAAGCTTAAAATTTGAGTTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
445326 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
445350 ATTGAAG
1 ATTGAAG
445357 TGAAAGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:450094 original size:14 final size:14
Alignment explanation
Indices: 450075--450107 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
450065 AAGAAAAGAA
450075 GAAAAAATGAAAAT
1 GAAAAAATGAAAAT
450089 GAAAAAATGAAAAT
1 GAAAAAATGAAAAT
450103 -AAAAA
1 GAAAAA
450108 TAAAAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (14 bp):
GAAAAAATGAAAAT
Found at i:450127 original size:7 final size:7
Alignment explanation
Indices: 450117--450161 Score: 55
Period size: 6 Copynumber: 7.1 Consensus size: 7
450107 ATAAAAAGAG
450117 AGAGAAA
1 AGAGAAA
450124 AGAGAAA
1 AGAGAAA
450131 AGAGAAA
1 AGAGAAA
450138 A-A-AAA
1 AGAGAAA
450143 AGA-AAA
1 AGAGAAA
450149 AGA-AAA
1 AGAGAAA
450155 A-AGAAA
1 AGAGAAA
450161 A
1 A
450162 CTGAAATGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
6 16 0.44
7 15 0.42
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AGAGAAA
Found at i:450150 original size:6 final size:6
Alignment explanation
Indices: 450064--450161 Score: 53
Period size: 6 Copynumber: 16.3 Consensus size: 6
450054 AATTACACCT
* * * * *
450064 AAAG-A AAAGAA GAA-AA AATGAA AATGAA AAA-ATGA AAATAA AAATAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA--A AAAGAA AAAGAA
* *
450111 AAAGAG AGAG-A AAAGAGA AAAGAGA AAA-AA AAAGAA AAAGAAA AAAGAA
1 AAAGAA AAAGAA AAAGA-A AAAGA-A AAAGAA AAAGAA AAAG-AA AAAGAA
450160 AA
1 AA
450162 CTGAAATGAG
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
5 15 0.20
6 38 0.51
7 21 0.28
8 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:454478 original size:20 final size:20
Alignment explanation
Indices: 454453--454510 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
454443 GAGTGATTAT
454453 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
454473 CAGTGGTCCTTCGGGAC--A
1 CAGTGGTCCTTCGGGACAAA
*
454491 CAGTGGTCCTTCGAGACAAA
1 CAGTGGTCCTTCGGGACAAA
454511 TATTCAGTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 17 0.49
20 18 0.51
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Done.