Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002152.1 Hibiscus syriacus cultivar Beakdansim tig00004394_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: 118575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4167 original size:2 final size:2
Alignment explanation
Indices: 4160--4186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4150 ATCAGGCATC
4160 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
4187 TCTACCTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10294 original size:18 final size:18
Alignment explanation
Indices: 10271--10316 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
10261 GTATAAAATA
10271 GCGGTTGCGGCATTTGTC
1 GCGGTTGCGGCATTTGTC
10289 GCGGTTGCGGCATTTGTC
1 GCGGTTGCGGCATTTGTC
10307 GCGGTTGCGG
1 GCGGTTGCGG
10317 TTGTAGTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.22, G:0.43, T:0.30
Consensus pattern (18 bp):
GCGGTTGCGGCATTTGTC
Found at i:14334 original size:8 final size:8
Alignment explanation
Indices: 14321--14351 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
14311 GAACCGGCCA
14321 GAACCGTT
1 GAACCGTT
14329 GAACCGTT
1 GAACCGTT
14337 GAACCGTT
1 GAACCGTT
14345 CGAACCG
1 -GAACCG
14352 GACCGACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.19
Consensus pattern (8 bp):
GAACCGTT
Found at i:15433 original size:32 final size:32
Alignment explanation
Indices: 15391--15451 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
15381 TTAATATCAC
*
15391 CCCTTAACACCGAAACTTCTTTCACCACTTCA
1 CCCTCAACACCGAAACTTCTTTCACCACTTCA
***
15423 CCCTCAACACCTCTACTTCTTTCACCACT
1 CCCTCAACACCGAAACTTCTTTCACCACT
15452 CCATCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.25, C:0.44, G:0.02, T:0.30
Consensus pattern (32 bp):
CCCTCAACACCGAAACTTCTTTCACCACTTCA
Found at i:17804 original size:20 final size:19
Alignment explanation
Indices: 17758--17804 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
17748 TCCGGTATCA
*
17758 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
17777 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
17798 TTTTACC
1 TTTTACC
17805 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:17951 original size:20 final size:20
Alignment explanation
Indices: 17925--17970 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
17915 CACTTTTAAA
17925 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
17944 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
17965 TTTACC
1 TTTACC
17971 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:18436 original size:228 final size:226
Alignment explanation
Indices: 18035--18481 Score: 765
Period size: 228 Copynumber: 2.0 Consensus size: 226
18025 TTAAAACTGC
18035 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACTACAATAT
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACTACAATAT
**
18100 TAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATT
66 TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
* *
18165 TAGCATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAAG
*
18230 TATGGACACTTTTATAAAAATGATATATACTT
195 TATGGACACTTTTATAAAAAAGATATATACTT
18262 TTTTGAAAGTTATGTAATTTATGTTTCAAATTT-TTTAATAGTGTTTCAT-TTTTCCACCTACAA
1 TTTT-AAAGTTATGTAATTTATGTTTC-AATTTATTTAATAGTGTTTCATGTTTTCCA-CTACAA
*
18325 TATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATT
63 TATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATT
*
18390 ATTTAG-ATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAAT
128 ATTTAGCA-TTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAAT
18454 AAGTATGGACACTTTTATAAAAAAGATA
192 AAGTATGGACACTTTTATAAAAAAGATA
18482 GATAATTTAC
Statistics
Matches: 209, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
227 49 0.23
228 155 0.74
229 5 0.02
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (226 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACTACAATAT
TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAGT
ATGGACACTTTTATAAAAAAGATATATACTT
Found at i:18932 original size:20 final size:21
Alignment explanation
Indices: 18907--18960 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
18897 TTTTATTCAC
* *
18907 GAAATATAAGATTTTCAG-TA
1 GAAATAAAAGATTATCAGTTA
18927 GAAATAAAAGATTATCAGTTA
1 GAAATAAAAGATTATCAGTTA
18948 G-AATAAAA-ATTAT
1 GAAATAAAAGATTAT
18961 AAGGGAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.31
Consensus pattern (21 bp):
GAAATAAAAGATTATCAGTTA
Found at i:19179 original size:32 final size:31
Alignment explanation
Indices: 19098--19179 Score: 83
Period size: 37 Copynumber: 2.4 Consensus size: 31
19088 ATAATATTAC
19098 AAATTATAAAATATTTATATATTTTCTTTAAA
1 AAATTA-AAAATATTTATATATTTTCTTTAAA
* *
19130 AAATTAAATTCATAATATTTATATAATTTTTTTTATA
1 AAATT-AA---A-AATATTTATAT-ATTTTCTTTAAA
19167 AAATTAAAAATAT
1 AAATTAAAAATAT
19180 AAAAAATGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
32 11 0.26
33 2 0.05
35 1 0.02
36 13 0.31
37 15 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
AAATTAAAAATATTTATATATTTTCTTTAAA
Found at i:24103 original size:36 final size:37
Alignment explanation
Indices: 24028--24103 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
24018 TTTTTATATT
*
24028 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* *
24065 TTTAATTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
24101 TTT
1 TTT
24104 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 13 0.37
36 13 0.37
37 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:24285 original size:20 final size:20
Alignment explanation
Indices: 24247--24286 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
24237 TAATCCTATT
**
24247 CACTGGTAATCTTTTATTCC
1 CACTGGTAATCTTACATTCC
24267 CACTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
24287 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.40
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCC
Found at i:27678 original size:68 final size:68
Alignment explanation
Indices: 27599--27736 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 68
27589 AACTCTCAAT
*
27599 CACCTAGTATTGAACACTTATATCTTAACATTCATAATACTCGAACTCGAAATTTTAAGGAATAA
1 CACCTAATATTGAACACTTATATCTTAACATTCATAATACTCGAACTCGAAATTTTAAGGAATAA
27664 CAA
66 CAA
* * *
27667 CACCTAATATTGAATACTTATATCTTAACATTCATGATACTCGAACTCGAAATTTTAAGGAATGA
1 CACCTAATATTGAACACTTATATCTTAACATTCATAATACTCGAACTCGAAATTTTAAGGAATAA
27732 CAA
66 CAA
27735 CA
1 CA
27737 ACCCCTCTAC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (68 bp):
CACCTAATATTGAACACTTATATCTTAACATTCATAATACTCGAACTCGAAATTTTAAGGAATAA
CAA
Found at i:28737 original size:26 final size:26
Alignment explanation
Indices: 28670--28738 Score: 90
Period size: 25 Copynumber: 2.7 Consensus size: 26
28660 ATTTATTTTT
28670 TAAAAAAAAT-TAAAAATATTACTAAA
1 TAAAAAAAATCT-AAAATATTACTAAA
28696 TAAAATAAAATC-AAAAT-TTACTAAA
1 TAAAA-AAAATCTAAAATATTACTAAA
28721 TAAAAAAAACTCTAAAAT
1 TAAAAAAAA-TCTAAAAT
28739 CTTTTATTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
24 4 0.10
25 15 0.38
26 15 0.38
27 5 0.13
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (26 bp):
TAAAAAAAATCTAAAATATTACTAAA
Found at i:28933 original size:9 final size:9
Alignment explanation
Indices: 28915--28949 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
28905 TATATTATGC
28915 TTTT-AATT
1 TTTTGAATT
28923 TTTTGAATT
1 TTTTGAATT
28932 TTTTGAATT
1 TTTTGAATT
*
28941 TTTTTAATT
1 TTTTGAATT
28950 AAACCTCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (9 bp):
TTTTGAATT
Found at i:29267 original size:29 final size:29
Alignment explanation
Indices: 29235--29290 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
29225 TAGGGGGACG
*
29235 AACTTGAATTTATAAAATT-TCAGGGGGTA
1 AACTTGAACTTATAAAATTCT-AGGGGGTA
29264 AACTTGAACTTATAAAATTCTAGGGGG
1 AACTTGAACTTATAAAATTCTAGGGGG
29291 AGCTAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (29 bp):
AACTTGAACTTATAAAATTCTAGGGGGTA
Found at i:31174 original size:14 final size:14
Alignment explanation
Indices: 31155--31181 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31145 GGAGACCCTT
31155 AAAATTTCAATTTG
1 AAAATTTCAATTTG
31169 AAAATTTCAATTT
1 AAAATTTCAATTT
31182 TAGACCCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
AAAATTTCAATTTG
Found at i:51171 original size:117 final size:117
Alignment explanation
Indices: 50965--51204 Score: 426
Period size: 117 Copynumber: 2.1 Consensus size: 117
50955 ACCCTTTTCG
* *
50965 TTTCCACCATGGAAACCAGGGAATGTGGACCTCATGGCATCATTACCATCAAAACACACAGAAAC
1 TTTCCACCATGCAAACCAGGGAATGTGGACCTCATGACATCATTACCATCAAAACACACAGAAAC
*
51030 TTGCTGTGGCAAAGATTGAAACCCTTCATTAAACCCTTCATATGAATTATAT
66 TTGCTGTGGCAAAGATTGAAACCCTTCATTAAACCCTTCATATGAACTATAT
*
51082 TTTCCACCATGCAAACCAGGGAATGTGGACCTCATGACATCATTACCATCAAAACACACAGAAAT
1 TTTCCACCATGCAAACCAGGGAATGTGGACCTCATGACATCATTACCATCAAAACACACAGAAAC
* *
51147 TTGCTGTGGCGAAGATTGAAACCCTTCGTTAAACCCTTCATATGAACTATAT
66 TTGCTGTGGCAAAGATTGAAACCCTTCATTAAACCCTTCATATGAACTATAT
51199 TTTCCA
1 TTTCCA
51205 GCGTTATAAG
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (117 bp):
TTTCCACCATGCAAACCAGGGAATGTGGACCTCATGACATCATTACCATCAAAACACACAGAAAC
TTGCTGTGGCAAAGATTGAAACCCTTCATTAAACCCTTCATATGAACTATAT
Found at i:54244 original size:35 final size:35
Alignment explanation
Indices: 54198--54270 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
54188 TGAGTTTAAT
* *
54198 GAGCAAAGAGTCGAGCACCGAACTTAATGAGCAAC
1 GAGCAAAGAGTCCAGCACCGAACTTAACGAGCAAC
* * * *
54233 GAGCAATGAGTCCAGCAGCGAGCTTAACGAGCACC
1 GAGCAAAGAGTCCAGCACCGAACTTAACGAGCAAC
54268 GAG
1 GAG
54271 TTTAACGAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.29, T:0.11
Consensus pattern (35 bp):
GAGCAAAGAGTCCAGCACCGAACTTAACGAGCAAC
Found at i:54270 original size:16 final size:16
Alignment explanation
Indices: 54246--54281 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
54236 CAATGAGTCC
*
54246 AGCAGCGAGCTTAACG
1 AGCACCGAGCTTAACG
*
54262 AGCACCGAGTTTAACG
1 AGCACCGAGCTTAACG
54278 AGCA
1 AGCA
54282 ACAAGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.14
Consensus pattern (16 bp):
AGCACCGAGCTTAACG
Found at i:54288 original size:16 final size:17
Alignment explanation
Indices: 54256--54299 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
54246 AGCAGCGAGC
* *
54256 TTAACGAGCACCGAG-T
1 TTAACGAGCAACAAGTT
54272 TTAACGAGCAACAAGTT
1 TTAACGAGCAACAAGTT
54289 TTAACGAGCAA
1 TTAACGAGCAA
54300 GAATCGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (17 bp):
TTAACGAGCAACAAGTT
Found at i:60969 original size:2 final size:2
Alignment explanation
Indices: 60962--61000 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
60952 TTACCTTTAT
60962 TA 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 TA T
61001 GAGAGAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62607 original size:9 final size:9
Alignment explanation
Indices: 62584--62618 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
62574 ATGAATAAAA
62584 TTCTCCTCC
1 TTCTCCTCC
**
62593 CCCTCCTCC
1 TTCTCCTCC
62602 TTCTCCTCC
1 TTCTCCTCC
62611 TTCTCCTC
1 TTCTCCTC
62619 GAGTAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (9 bp):
TTCTCCTCC
Found at i:63615 original size:2 final size:2
Alignment explanation
Indices: 63608--63641 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
63598 TAGGCTTGTA
63608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
63642 CATACGAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:63910 original size:14 final size:14
Alignment explanation
Indices: 63891--63930 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
63881 AATGAACATA
*
63891 AACGAACACGAACG
1 AACGAACACAAACG
*
63905 AACGAACATAAACG
1 AACGAACACAAACG
63919 AAC-AACACAAAC
1 AACGAACACAAAC
63931 AAAAAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.57, C:0.28, G:0.12, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:64202 original size:14 final size:14
Alignment explanation
Indices: 64183--64228 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
64173 GCCCTCTGTT
64183 CGAACATAAATGAA
1 CGAACATAAATGAA
64197 CGAACATAAATGAA
1 CGAACATAAATGAA
*
64211 CAAACATATAATCGAA
1 CGAACATA-AAT-GAA
64227 CG
1 CG
64229 TTCACGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 21 0.75
15 3 0.11
16 4 0.14
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:64473 original size:26 final size:26
Alignment explanation
Indices: 64439--64493 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
64429 ATAAAATATT
64439 TTTTGAACAATAATCCCCTTAGTAGA
1 TTTTGAACAATAATCCCCTTAGTAGA
64465 TTTTGAACAATAATCCCCTTAGTAGA
1 TTTTGAACAATAATCCCCTTAGTAGA
64491 TTT
1 TTT
64494 GTTAGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (26 bp):
TTTTGAACAATAATCCCCTTAGTAGA
Found at i:69467 original size:15 final size:15
Alignment explanation
Indices: 69447--69503 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
69437 AACCGGGTAT
69447 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
69462 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
69479 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
69494 CGGGTACCCG
1 CGGGTACCCG
69504 TAACATCCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:69483 original size:17 final size:16
Alignment explanation
Indices: 69447--69515 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
69437 AACCGGGTAT
**
69447 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
69462 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
69479 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
69494 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
69511 CGGGT
1 CGGGT
69516 CGGGACACGG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:69488 original size:32 final size:32
Alignment explanation
Indices: 69447--69515 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
69437 AACCGGGTAT
69447 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
69479 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
69511 CGGGT
1 CGGGT
69516 CGGGACACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:77520 original size:20 final size:21
Alignment explanation
Indices: 77495--77546 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
77485 TTTTCCCAAT
*
77495 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
77515 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
77536 TCGCAATGCGA
1 TCGCAATGCGA
77547 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:77560 original size:20 final size:20
Alignment explanation
Indices: 77535--77709 Score: 165
Period size: 20 Copynumber: 8.7 Consensus size: 20
77525 AATTGGGAAA
77535 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
77555 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
77575 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
77596 AGCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
77616 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
77636 TTCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
77656 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
77676 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
77696 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
77710 TTTCTAAGCG
Statistics
Matches: 132, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
19 4 0.03
20 103 0.78
21 23 0.17
22 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:77579 original size:61 final size:61
Alignment explanation
Indices: 77545--77709 Score: 174
Period size: 61 Copynumber: 2.7 Consensus size: 61
77535 ATCGCAATGC
* *
77545 GATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAAAGCGCAACGA
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATACAAAAGCGCAACGA
* * * *** *
77606 GATACTGACTTTCGCAACGCGATACTGACTTTCGCAATGCGATACTGAC--TTTCGCAACGC
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAAT-ACAAAAGCGCAACGA
* * *
77666 GATTCTGACTTTCGCAACGCGATAAT-ACATAATCGCAATGCGAT
1 GATACTGACTATCGCAACGCGATACTGAC-T-ATCGCAATGCGAT
77710 TTTCTAAGCG
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.02
60 32 0.36
61 53 0.60
62 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (61 bp):
GATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATACAAAAGCGCAACGA
Found at i:77905 original size:22 final size:22
Alignment explanation
Indices: 77877--77920 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
77867 CACTCTCTCA
77877 CCCATCT-CAGACGAAATCCGTC
1 CCCATCTCCAGA-GAAATCCGTC
*
77899 CCCATCTCCGGAGAAATCCGTC
1 CCCATCTCCAGAGAAATCCGTC
77921 TATCTCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGAGAAATCCGTC
Found at i:78237 original size:20 final size:20
Alignment explanation
Indices: 78183--78241 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
78173 GCGATTCTCT
**
78183 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
78203 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
78223 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
78242 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:79583 original size:18 final size:18
Alignment explanation
Indices: 79562--79606 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
79552 TCCACTTCGG
**
79562 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTAACCCA
*
79580 GAGCTATCACCTAACCCA
1 GAGCCATCACCTAACCCA
79598 GAGCCATCA
1 GAGCCATCA
79607 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.42, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTAACCCA
Found at i:80142 original size:19 final size:20
Alignment explanation
Indices: 80088--80154 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
80078 TAGTTTACTT
* *
80088 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
80108 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
80128 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
80147 TCGCAACG
1 TCGCAACG
80155 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:80162 original size:14 final size:14
Alignment explanation
Indices: 80143--80201 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
80133 ATGCGAAATG
80143 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
80157 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
80176 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
80190 AAAATCGTAACG
1 AAAATCGCAACG
80202 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:80169 original size:33 final size:33
Alignment explanation
Indices: 80127--80218 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
80117 GGAAATGGCT
80127 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
80160 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
80193 ATCGTAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
80219 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:80181 original size:19 final size:19
Alignment explanation
Indices: 80127--80223 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
80117 GGAAATGGCT
80127 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
80146 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
80160 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
80179 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
80193 ATCGTAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
80212 ATCGCAATGCGA
1 ATCGCAATGCGA
80224 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.49
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:80265 original size:20 final size:20
Alignment explanation
Indices: 80249--80316 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
80239 GCGATTTTGT
**
80249 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
* *
80268 CATTGCGATAGCCATTTTCG
1 CGTTGCGATAGTCATTTTCG
80288 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
80308 CGTTGCGAT
1 CGTTGCGAT
80317 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 10 0.24
20 32 0.76
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:80326 original size:20 final size:20
Alignment explanation
Indices: 80263--80341 Score: 68
Period size: 20 Copynumber: 4.0 Consensus size: 20
80253 GCGATTTTCA
* ** *
80263 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGTAAG
* *
80283 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTAAG
**
80303 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATAGTAAG
* *
80323 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGATAGTAA
80342 ACTATTCTTC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTAAG
Found at i:80413 original size:27 final size:28
Alignment explanation
Indices: 80347--80415 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
80337 AGTAAACTAT
*
80347 TCTTCTTCTGGAATGTTTATATATGTTG
1 TCTTCTTCTGGAATGTTTATATAAGTTG
*
80375 TCTT-TT-T-AAATGTTTATATAAG-TG
1 TCTTCTTCTGGAATGTTTATATAAGTTG
80399 -CTTACTTCTGGAATGTT
1 TCTT-CTTCTGGAATGTT
80416 ATCTGAGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
23 3 0.09
24 2 0.06
25 15 0.44
26 2 0.06
27 8 0.24
28 4 0.12
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.52
Consensus pattern (28 bp):
TCTTCTTCTGGAATGTTTATATAAGTTG
Found at i:82206 original size:14 final size:14
Alignment explanation
Indices: 82187--82222 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
82177 ATTGTTTAAT
82187 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
82201 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
82215 TGATTTGT
1 TGATTTGT
82223 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:82386 original size:19 final size:19
Alignment explanation
Indices: 82362--82426 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
82352 GCAACGAGAG
82362 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
82381 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
82400 AATCGCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
82414 AATCGCAATGCGA
1 AATCGCAATGCGA
82427 TTTTCATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
14 11 0.26
15 2 0.05
16 1 0.02
17 1 0.02
19 27 0.64
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:82470 original size:20 final size:20
Alignment explanation
Indices: 82445--82502 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
82435 TCGCATTGCG
*
82445 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
82465 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
82485 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
82503 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:82925 original size:41 final size:41
Alignment explanation
Indices: 82806--82943 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 41
82796 AACTTTGAAA
* * *
82806 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** *
82847 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
* *
82887 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
82928 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
82944 ACCAATTCGC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.39
41 47 0.57
42 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:82940 original size:20 final size:20
Alignment explanation
Indices: 82826--82939 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
82816 GATTCTGTAT
*
82826 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
82846 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
82866 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
82886 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
82907 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
82927 TATCGCATTGCGA
1 TATCGCGTTGCGA
82940 TTTTACCAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:82954 original size:41 final size:41
Alignment explanation
Indices: 82806--82961 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 41
82796 AACTTTGAAA
* ** * * * *
82806 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* *** * *
82847 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* ** *
82887 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
82928 ATCGCATTGCGATTTTACCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
82962 TTACTTATTC
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
40 33 0.35
41 60 0.63
42 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
Found at i:82971 original size:20 final size:21
Alignment explanation
Indices: 82929--82977 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
82919 ATAGTCAGTA
82929 TCGCATTGCGATTTTACCAAT
1 TCGCATTGCGATTTTACCAAT
* **
82950 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
82970 TCGCATTG
1 TCGCATTG
82978 TGAATTGGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:83051 original size:21 final size:21
Alignment explanation
Indices: 83011--83051 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
83001 ACTGTAGACC
**
83011 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
83032 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
83052 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:84699 original size:21 final size:21
Alignment explanation
Indices: 84622--84714 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 21
84612 GCTATAATAT
*
84622 TATATTTTATAAAAAAATTGAA
1 TATATATTAT-AAAAAATTGAA
* ** **
84644 TATATATTATAATATTTTTTA
1 TATATATTATAAAAAATTGAA
* * *
84665 TATGTACT-T-CAAAATTGAA
1 TATATATTATAAAAAATTGAA
*
84684 TATATATTATAAAAAAATGAA
1 TATATATTATAAAAAATTGAA
84705 TATATATTAT
1 TATATATTAT
84715 TATATTTTAT
Statistics
Matches: 51, Mismatches: 18, Indels: 5
0.69 0.24 0.07
Matches are distributed among these distances:
19 10 0.20
20 2 0.04
21 30 0.59
22 9 0.18
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
TATATATTATAAAAAATTGAA
Found at i:88860 original size:28 final size:28
Alignment explanation
Indices: 88820--88873 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
88810 TTGTAAACGA
88820 GCCTATCAAAAGAAACTAAATTATGTGG
1 GCCTATCAAAAGAAACTAAATTATGTGG
*
88848 GCCTATCAAAAGAAACTAAGTTATGT
1 GCCTATCAAAAGAAACTAAATTATGT
88874 TATTATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (28 bp):
GCCTATCAAAAGAAACTAAATTATGTGG
Found at i:88978 original size:17 final size:17
Alignment explanation
Indices: 88956--88989 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88946 AGCTAATTTC
*
88956 GATTAACTAAAGATTAA
1 GATTAACAAAAGATTAA
88973 GATTAACAAAAGATTAA
1 GATTAACAAAAGATTAA
88990 AAGTCAGACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (17 bp):
GATTAACAAAAGATTAA
Found at i:93641 original size:127 final size:128
Alignment explanation
Indices: 93472--93721 Score: 333
Period size: 127 Copynumber: 2.0 Consensus size: 128
93462 GTGTCGATAA
* * * *
93472 ATTTTTAAAAGGTAACGACCCCAAAAACATCAAAACATATAATTATAATGTAATATGTAAATTTA
1 ATTTTCAAAAAGTAACGACCCCAAAAACATCAAAACAGATAATTATAATGTAATAGGTAAATTTA
* * *
93537 CAATGTAACCGGTATAAATATACCGGTTTTAT-AAAAAATATGTCTATAAGATGTATCTATAC
66 CAATATAACCGGTATAAATATACCGATTTTATGAAAAAATATGTCTACAAGATGTATCTATAC
* * *
93599 ATTTTCAAAAAGTATCGATCCCAAAAACATCAAAATC-GATAATTATAATGTAATAGGTAATTTT
1 ATTTTCAAAAAGTAACGACCCCAAAAACATCAAAA-CAGATAATTATAATGTAATAGGTAAATTT
** * * * *
93663 GTAATATAACTGGTATAAATATACCGATTTTATGAGAGAATATGTCTACAATATGTATC
65 ACAATATAACCGGTATAAATATACCGATTTTATGAAAAAATATGTCTACAAGATGTATC
93722 GACACTTTTT
Statistics
Matches: 105, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
127 83 0.79
128 22 0.21
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (128 bp):
ATTTTCAAAAAGTAACGACCCCAAAAACATCAAAACAGATAATTATAATGTAATAGGTAAATTTA
CAATATAACCGGTATAAATATACCGATTTTATGAAAAAATATGTCTACAAGATGTATCTATAC
Found at i:93749 original size:21 final size:20
Alignment explanation
Indices: 93712--93752 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
93702 ATATGTCTAC
93712 AATATGTATCGACACTTTTT
1 AATATGTATCGACACTTTTT
* *
93732 AATATTGTGTCGATACTTTTT
1 AATA-TGTATCGACACTTTTT
93753 GACCAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (20 bp):
AATATGTATCGACACTTTTT
Found at i:93943 original size:200 final size:200
Alignment explanation
Indices: 93595--94916 Score: 1696
Period size: 200 Copynumber: 6.8 Consensus size: 200
93585 AGATGTATCT
* * ** *
93595 ATACATTTTCAAAAAGTATCGATCCCAAAAACATCAAAATCGATAATTATAATGTAATAGGTAAT
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAAT
* * * *
93660 TTTGTAATATAACTGGTATAAATATACCGATTTTATGAGAGAATATGTCTACAATATGTATCGAC
66 TTTGTAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGAC
* * * *
93725 ACTTTTTAATATTGTGTCGATACTTTTTGACCAAAATTGATGTCAAAAAGGGTTAACACACAAAG
131 ACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAG
93790 TGTCG
196 TGTCG
* * *
93795 ATATATTTTCAAAAAGTTTCGATTTCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAAT
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAAT
* *
93860 TTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATTGAC
66 TTTGTAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGAC
* *
93925 ACTTTTTAATAGTGTGTCGATACTTTTTGTCTAGAATGGATGCCAAAAAGGGTTAACACACAAAG
131 ACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAG
93990 TGTCG
196 TGTCG
* * **
93995 ATATATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGCCAAT
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAAT
* *
94060 TTTGTAATATAACCGATATAAATATACC-AATTAAT--GAG---A-G---A-AACATGTATCGAC
66 TTTGTAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGAC
* ** * *
94114 ACTTTTTAATATTGTGTCGATATTTTTTGTCCAGAATGGATGCCAAAAAGGGTGGACAAATAAAG
131 ACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAG
94179 TGTCG
196 TGTCG
* ** * *
94184 ATACATTTTCAAAAAGTGTCGATCCCAAAAACATCAAAACCGATAATTATAAAGTAATAGTTAAT
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAAT
* * * * * *
94249 TTTTTAATATAACCAATATAAATATATCGGTTTTATGAGAGAATAGCTCTACAATATGTATCGAC
66 TTTGTAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGAC
* *
94314 ACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACGCACAAAG
131 ACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAG
94379 TGTCG
196 TGTCG
* *
94384 ATACATTTTCAAAAAGTGACGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAAT
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAAT
* * * *
94449 TTTGTAATATAACCGGTATAAATATACTGATTTTATGAGAGAATAAGTCTACAACATGTATCGAA
66 TTTGTAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGAC
* *
94514 ACTTTTTAATATTGT-TACGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTTAACGCACAAA
131 ACTTTTTAATATTGTGT-CGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAA
94578 GTGTCG
195 GTGTCG
* * *
94584 ATATATTTTCAAAAAGTGACGATTCCAAAAACATCGTAATCGATAATTATAATGTAATAGGTAAT
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAAT
* * * *
94649 TTTGTAATATAACCAATACAAATATACC-AGTTTTATGAGAGAATATGTCTACAACATATATCGA
66 TTTGTAATATAACCGATATAAATATACCGA-TTTTATGAGAGAATAGGTCTACAACATGTATCGA
* *
94713 CACTTTTTAATATTGTGTCGATAC----T-T------T--A--CCAAAAAGGGTGAACGA-ATAA
130 CACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAAC-ACACAA
94762 AGTGTCG
194 AGTGTCG
* * * *
94769 ATACATTTTCAAAAAGTGTGGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA-G----
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAAT
** * *
94829 ---GT-ATATAACTAATATAAATATATC-AGTTTTATGAGATAATAGGTCTACAACATGTATCGA
66 TTTGTAATATAACCGATATAAATATACCGA-TTTTATGAGAGAATAGGTCTACAACATGTATCGA
* *
94889 TACTTTTTAATATTGTGTTGATACTTTT
130 CACTTTTTAATATTGTGTCGATACTTTT
94917 AAATAACGCG
Statistics
Matches: 1002, Mismatches: 101, Indels: 58
0.86 0.09 0.05
Matches are distributed among these distances:
176 74 0.07
177 2 0.00
184 1 0.00
185 76 0.08
187 1 0.00
189 158 0.16
190 5 0.00
192 3 0.00
193 1 0.00
194 1 0.00
195 2 0.00
196 1 0.00
197 3 0.00
199 8 0.01
200 665 0.66
201 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (200 bp):
ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAAT
TTTGTAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGAC
ACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAG
TGTCG
Found at i:94332 original size:389 final size:390
Alignment explanation
Indices: 93595--94739 Score: 1605
Period size: 389 Copynumber: 2.9 Consensus size: 390
93585 AGATGTATCT
* ** * *
93595 ATACATTTTCAAAAAGTATCGATCCCAAAAACATCAAAATCGATAATTATAATGTAATAGGTAAT
1 ATACATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAAT
* *
93660 TTTGTAATATAACTGGTATAAATATACCGATTTTATGAGAGAATATGTCTACAATATGTATCGAC
66 TTTGTAATATAACCGGTATAAATATACC-ATTTTAT--GAG---A-G--TACAACATGTATCGAC
* * *
93725 ACTTTTTAATATTGTGTCGATACTTTTTGACCAAAATTGATGTCAAAAAGGGTTAACACACAAAG
122 ACTTTTTAATATTGTGTCGATACTTTTTGTCCAAAATGGATGCCAAAAAGGGTTAACACACAAAG
* *
93790 TGTCGATATATTTTCAAAAAGTTTCGATTTCAAAAACATCGTAACCGATAATTATAATGTAATAG
187 TGTCGATATATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAG
** *
93855 GTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTA
252 GTAATTTTGTAATATAACCAATATAAATATACCGGTTTTATGAGAGAATA-GTCTACAACATGTA
* * * *
93920 TTGACACTTTTTAATAGTGTGTCGATACTTTTTGTCTAGAATGGATGCCAAAAAGGGTTAACACA
316 TCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACACA
93985 CAAAGTGTCG
381 CAAAGTGTCG
* **
93995 ATATATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGCCAAT
1 ATACATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAAT
* * *
94060 TTTGTAATATAACCGATATAAATATACCAATTAATGAGAG-A-AACATGTATCGACACTTTTTAA
66 TTTGTAATATAACCGGTATAAATATACCATTTTATGAGAGTACAACATGTATCGACACTTTTTAA
* * ** * * *
94123 TATTGTGTCGATATTTTTTGTCCAGAATGGATGCCAAAAAGGGTGGACAAATAAAGTGTCGATAC
131 TATTGTGTCGATACTTTTTGTCCAAAATGGATGCCAAAAAGGGTTAACACACAAAGTGTCGATAT
* ** * * *
94188 ATTTTCAAAAAGTGTCGATCCCAAAAACATCAAAACCGATAATTATAAAGTAATAGTTAATTTTT
196 ATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAATTTTG
* *
94253 TAATATAACCAATATAAATATATCGGTTTTATGAGAGAATAGCTCTACAATATGTATCGACACTT
261 TAATATAACCAATATAAATATACCGGTTTTATGAGAGAATAG-TCTACAACATGTATCGACACTT
*
94318 TTTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACGCACAAAGTGTC
325 TTTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACACACAAAGTGTC
94383 G
390 G
94384 ATACATTTTCAAAAAGTGA-CGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAA
1 ATACATTTTCAAAAAGT-ATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAA
*
94448 TTTTGTAATATAACCGGTATAAATATACTGATTTTATGAGAGAATAAGTCTACAACATGTATCGA
65 TTTTGTAATATAACCGGTATAAATATAC-CATTTTAT--GAG----AG--TACAACATGTATCGA
* * *
94513 AACTTTTTAATATTGT-TACGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTTAACGCACAA
121 CACTTTTTAATATTGTGT-CGATACTTTTTGTCCAAAATGGATGCCAAAAAGGGTTAACACACAA
* *
94577 AGTGTCGATATATTTTCAAAAAGTGACGATTCCAAAAACATCGTAATCGATAATTATAATGTAAT
185 AGTGTCGATATATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAAT
* * *
94642 AGGTAATTTTGTAATATAACCAATACAAATATACCAGTTTTATGAGAGAATATGTCTACAACATA
250 AGGTAATTTTGTAATATAACCAATATAAATATACCGGTTTTATGAGAGAATA-GTCTACAACATG
94707 TATCGACACTTTTTAATATTGTGTCGATACTTT
314 TATCGACACTTTTTAATATTGTGTCGATACTTT
94740 ACCAAAAAGG
Statistics
Matches: 661, Mismatches: 69, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
388 1 0.00
389 338 0.51
390 7 0.01
392 3 0.00
393 1 0.00
394 1 0.00
396 2 0.00
397 3 0.00
399 7 0.01
400 297 0.45
401 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (390 bp):
ATACATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAAT
TTTGTAATATAACCGGTATAAATATACCATTTTATGAGAGTACAACATGTATCGACACTTTTTAA
TATTGTGTCGATACTTTTTGTCCAAAATGGATGCCAAAAAGGGTTAACACACAAAGTGTCGATAT
ATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGGTAATTTTG
TAATATAACCAATATAAATATACCGGTTTTATGAGAGAATAGTCTACAACATGTATCGACACTTT
TTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACACACAAAGTGTCG
Found at i:94338 original size:21 final size:20
Alignment explanation
Indices: 94301--94341 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
94291 ATAGCTCTAC
94301 AATATGTATCGACACTTTTT
1 AATATGTATCGACACTTTTT
* *
94321 AATATTGTGTCGATACTTTTT
1 AATA-TGTATCGACACTTTTT
94342 GTCCAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (20 bp):
AATATGTATCGACACTTTTT
Found at i:94780 original size:185 final size:176
Alignment explanation
Indices: 94556--94915 Score: 477
Period size: 176 Copynumber: 2.0 Consensus size: 176
94546 ATAATGGATG
* * * * *
94556 CCAAAAAGGGTTAACGCACAAAGTGTCGATATATTTTCAAAAAGTGACGATTCCAAAAACATCGT
1 CCAAAAAGGGTGAACGAACAAAGTGTCGATACATTTTCAAAAAGTGACGATCCCAAAAACATCGA
* *
94621 AATCGATAATTATAATGTAATAGGTAATTTTGTAATATAACCAATACAAATATACCAGTTTTATG
66 AACCCATAATTATAATGTAATA-G-------GT-ATATAACCAATACAAATATACCAGTTTTATG
*
94686 AGAGAATATGTCTACAACATATATCGACACTTTTTAATATTGTGTCGATACTTTA
122 AGAGAATAGGTCTACAACATATATCGACACTTTTTAATATTGTGTCGATACTTTA
* **
94741 CCAAAAAGGGTGAACGAATAAAGTGTCGATACATTTTCAAAAAGTGTGGATCCCAAAAACATCGA
1 CCAAAAAGGGTGAACGAACAAAGTGTCGATACATTTTCAAAAAGTGACGATCCCAAAAACATCGA
* * * *
94806 AACCCATAATTATAATGTAATAGGTATATAACTAATATAAATATATCAGTTTTATGAGATAATAG
66 AACCCATAATTATAATGTAATAGGTATATAACCAATACAAATATACCAGTTTTATGAGAGAATAG
* * *
94871 GTCTACAACATGTATCGATACTTTTTAATATTGTGTTGATACTTT
131 GTCTACAACATATATCGACACTTTTTAATATTGTGTCGATACTTT
94916 TAAATAACGC
Statistics
Matches: 157, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
176 77 0.49
177 2 0.01
184 1 0.01
185 77 0.49
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (176 bp):
CCAAAAAGGGTGAACGAACAAAGTGTCGATACATTTTCAAAAAGTGACGATCCCAAAAACATCGA
AACCCATAATTATAATGTAATAGGTATATAACCAATACAAATATACCAGTTTTATGAGAGAATAG
GTCTACAACATATATCGACACTTTTTAATATTGTGTCGATACTTTA
Found at i:96527 original size:17 final size:17
Alignment explanation
Indices: 96501--96534 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
96491 ATACGATTTA
* *
96501 TAATTTTGTATGTGATG
1 TAATTATGTATGAGATG
96518 TAATTATGTATGAGATG
1 TAATTATGTATGAGATG
96535 AGAAAAGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (17 bp):
TAATTATGTATGAGATG
Found at i:99469 original size:198 final size:199
Alignment explanation
Indices: 99157--99678 Score: 642
Period size: 198 Copynumber: 2.6 Consensus size: 199
99147 TATTGTCCCA
* * * *
99157 AACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCAAAA
1 AACGAGGTACAAGCATAAAGTGTCGATACATTTA--AAATTGTATCGATCCCAAAAACATCGAAA
* *
99221 CTGATAATTATAATGTAATAGGTAAATTTACAATGTAATCAATATAAATATACCGATTTTATGAG
64 C-GATAATTATAATGTAATAGGTAAATTTACAATGT-ACCAGTATAAATATACCGATTTTATGAG
* *
99286 AAAATA-GGTCAGCATAAAGTATCGACAC-TTGTTAAATTTGTGTCGATACATTTTTTCC-AT-A
127 AAAATATGGTCA-AATAAAGTATCAACACATT-TTAAATTTGTGTCGATA-ATTTTTTCCAATAA
99347 -ATGAATGCCC
189 TATGAATGCCC
* * * *
99357 AACGAGGTACAAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCCATAAACACCGAAACA
1 AACGAGGTACAAGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACG
* * * *
99422 AAAATTACAATGTGATAGGTAAATTTACAATGTACCCAGTATAAATATACCGGTTTTATGAGAAA
66 ATAATTATAATGTAATAGGTAAATTTACAATGTA-CCAGTATAAATATACCGATTTTATGAGAAA
* * * * * *
99487 ATATGTTTAAATAATGTATCAACACATTTTTAGTTTGTGTCGATATTTTTTTCCAGAATGAAATA
130 ATATGGTCAAATAAAGTATCAACACATTTTAAATTTGTGTCGATAATTTTTTCC--AAT--AATA
99552 TGAATGCCC
191 TGAATGCCC
* * *
99561 AACGAGGTTCAAGCATAAAGTGTCGATACATTTAAAATTTTATCGATCCAAAAAACATCGAAACC
1 AACGAGGTACAAGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAA-C
*
99626 GATAATTATAATGTAATAGGTAAATTTGCAATGTTACCAGTATAAATATACCG
65 GATAATTATAATGTAATAGGTAAATTTACAATG-TACCAGTATAAATATACCG
99679 GTTTACTTCG
Statistics
Matches: 276, Mismatches: 33, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
197 9 0.03
198 91 0.33
199 27 0.10
200 33 0.12
203 1 0.00
204 67 0.24
205 46 0.17
206 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (199 bp):
AACGAGGTACAAGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACG
ATAATTATAATGTAATAGGTAAATTTACAATGTACCAGTATAAATATACCGATTTTATGAGAAAA
TATGGTCAAATAAAGTATCAACACATTTTAAATTTGTGTCGATAATTTTTTCCAATAATATGAAT
GCCC
Found at i:99802 original size:87 final size:87
Alignment explanation
Indices: 99700--99862 Score: 274
Period size: 87 Copynumber: 1.9 Consensus size: 87
99690 AAATAGGTCA
*
99700 ATATAAGTGCTACCTATTACATTATATAAG-AGCTACCTAATATGTTATTGTACTTGATAATATT
1 ATATAAGCGCTACCTATTACATTATATAAGCA-CTACCTAATATGTTATTGTACTTGATAATATT
*
99764 TCCGGCTAAATGCCTATTTTATT
65 TCCAGCTAAATGCCTATTTTATT
*
99787 ATATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATGTTTTTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
*
99852 CCAGTTAAATG
66 CCAGCTAAATG
99863 ATATAACATA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
87 70 0.99
88 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
CCAGCTAAATGCCTATTTTATT
Found at i:110270 original size:37 final size:36
Alignment explanation
Indices: 110163--110664 Score: 243
Period size: 38 Copynumber: 13.8 Consensus size: 36
110153 TTTTTGAATT
** * *
110163 TTTTTGAAAAATATA-ATATATAATTTTTTAGAAAACGG
1 TTTTTGAAAAATATATAT-TAT-ATAGTTT-GAAAATGA
* *
110201 TTTTTGAAAACATATA-A-TATACT-GTTTAAAAATCGG
1 TTTTTGAAAA-ATATATATTATA-TAGTTTGAAAAT-GA
*
110237 GTTTT-AAAAATATATATTATATAGCTTTGAAAATGA
1 TTTTTGAAAAATATATATTATATAG-TTTGAAAATGA
*
110273 TTTTTGAAAATATATATATTATATAGTTTGTAAATGA
1 TTTTTGAAAA-ATATATATTATATAGTTTGAAAATGA
*
110310 TTTTTGAAAAAATATATATAATATATAGTTTTTGAAAA-CA
1 TTTTTG-AAAAATATATAT--TATATAG--TTTGAAAATGA
* *
110350 -TTTTGAAAATATATATAATATATAGTTTTTTGAAAA-CA
1 TTTTTGAAAA-ATATATATTATATAG---TTTGAAAATGA
* *
110388 -TTTTGAAAATATATATAATATATAGTTTTTAAAA--A
1 TTTTTGAAAA-ATATATATTATATAG-TTTGAAAATGA
* *
110423 TATTTT-AAAAACTTATATAATATATAGTTTTGAAAA-CA
1 T-TTTTGAAAAA--TATATATTATATAG-TTTGAAAATGA
*
110461 -TTTT-AAAAACT-TATA-TATATAGTTTTG-AAATCA
1 TTTTTGAAAAA-TATATATTATATAG-TTTGAAAATGA
* *
110494 -TTTT-AAAAACT-TAATAATATATAGTTTTG-AAATCA
1 TTTTTGAAAAA-TAT-ATATTATATAG-TTTGAAAATGA
* *
110529 -TTTT-AAAAACT-TATA-TATATAGTTTTAAAA-CA
1 TTTTTGAAAAA-TATATATTATATAGTTTGAAAATGA
* * * *
110561 TTTTTCAAAACTATATAATATATAGTTTTGAAAA-CA
1 TTTTTGAAAAATATATATTATATAG-TTTGAAAATGA
* *
110597 TTTTTAAAAAATATATATATAATATATAGTTTTAAAATG-
1 TTTTT-GAAAA-ATATATAT--TATATAGTTTGAAAATGA
*
110636 TTTTTGAAAATATATATATTATATGGTTT
1 TTTTTGAAAA-ATATATATTATATAGTTT
110665 TTTGAAATAT
Statistics
Matches: 405, Mismatches: 24, Indels: 72
0.81 0.05 0.14
Matches are distributed among these distances:
32 8 0.02
33 41 0.10
34 23 0.06
35 50 0.12
36 64 0.16
37 77 0.19
38 90 0.22
39 37 0.09
40 8 0.02
41 7 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (36 bp):
TTTTTGAAAAATATATATTATATAGTTTGAAAATGA
Found at i:110522 original size:68 final size:69
Alignment explanation
Indices: 110330--110617 Score: 372
Period size: 68 Copynumber: 4.1 Consensus size: 69
110320 AATATATATA
*
110330 ATATATAGTTTTTGAAAACATTTTGAAAA-TATATATAATATATAGTTTTTTGAAAACATTTTGA
1 ATATATAGTTTTTGAAAACATTTTAAAAACT-TATATAATATATAG--TTTTGAAAACATTTT-A
110394 AAATATATAT
62 AAA-AT-TAT
* *
110404 AATATATAGTTTTTAAAAATATTTTAAAAACTTATATAATATATAGTTTTGAAAACATTTTAAAA
1 -ATATATAGTTTTTGAAAACATTTTAAAAACTTATATAATATATAGTTTTGAAAACATTTTAAAA
110469 ACTTAT
65 A-TTAT
* *
110475 ATATATAG-TTTTGAAATCATTTTAAAAACTTA-ATAATATATAGTTTTGAAATCATTTTAAAAA
1 ATATATAGTTTTTGAAAACATTTTAAAAACTTATATAATATATAGTTTTGAAAACATTTTAAAAA
110538 CTTAT
66 -TTAT
*
110543 ATATATAG-TTTT-AAAACATTTTTCAAAAC-TATATAATATATAGTTTTGAAAACATTTTTAAA
1 ATATATAGTTTTTGAAAACA-TTTTAAAAACTTATATAATATATAGTTTTGAAAACA-TTTTAAA
*
110605 AAATAT
64 AATTAT
110611 ATATATA
1 ATATATA
110618 ATATATAGTT
Statistics
Matches: 197, Mismatches: 11, Indels: 17
0.88 0.05 0.08
Matches are distributed among these distances:
67 7 0.04
68 87 0.44
69 30 0.15
70 8 0.04
71 4 0.02
72 5 0.03
73 15 0.08
75 40 0.20
76 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.44
Consensus pattern (69 bp):
ATATATAGTTTTTGAAAACATTTTAAAAACTTATATAATATATAGTTTTGAAAACATTTTAAAAA
TTAT
Found at i:110698 original size:3 final size:3
Alignment explanation
Indices: 110690--110740 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
110680 ATATATAAAA
* *
110690 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAGT TTT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
110735 TAT TAT
1 TAT TAT
110741 ATTTTTTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:110747 original size:15 final size:17
Alignment explanation
Indices: 110692--110762 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 17
110682 ATATAAAATA
110692 TTATTATTATTATTATT
1 TTATTATTATTATTATT
*
110709 GTTATTATTATTAGT-TT
1 -TTATTATTATTATTATT
110726 TTATT-TTATTATTATAT
1 TTATTATTATTATTAT-T
*
110743 TTTTTCATTAATTATT-TT
1 TTATT-ATT-ATTATTATT
110761 TT
1 TT
110763 GTTTTAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
15 7 0.16
16 6 0.13
17 7 0.16
18 16 0.36
19 3 0.07
20 6 0.13
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.70
Consensus pattern (17 bp):
TTATTATTATTATTATT
Found at i:110747 original size:21 final size:21
Alignment explanation
Indices: 110690--110746 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
110680 ATATATAAAA
*
110690 TATTATTATTATTATTATTGT
1 TATTATTATTATTTTTATTGT
110711 TATTATTATTAGTTTTTATT-T
1 TATTATTATTA-TTTTTATTGT
110732 TATTATTA-TATTTTT
1 TATTATTATTATTTTT
110747 TCATTAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.15
20 2 0.06
21 20 0.59
22 7 0.21
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TATTATTATTATTTTTATTGT
Found at i:112059 original size:4 final size:4
Alignment explanation
Indices: 112050--112083 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
112040 TTCCTTTTTC
112050 ATTT ATTT A-TT ATTT ATTT ATTT ATTT A-TT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
112084 CTTATCTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:112463 original size:18 final size:18
Alignment explanation
Indices: 112428--112463 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
112418 AAATCAAGTA
**
112428 ACATATTTATGTGTGTAC
1 ACATATTTATGTACGTAC
112446 ACATATTTATGTACGTAC
1 ACATATTTATGTACGTAC
112464 CTAGAGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (18 bp):
ACATATTTATGTACGTAC
Done.