Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 75 of 135
Found at i:22676241 original size:147 final size:146
Alignment explanation
Indices: 22675996--22676420 Score: 579
Period size: 147 Copynumber: 2.9 Consensus size: 146
22675986 TTGTTTGATT
* *
22675996 AAAAAAAATCACTACTTTACTTCAAAATTCAAACTTTTATTTCGAAATAGTTTAAAAAAATCAAA
1 AAAAAAAATCACTATTTTACTT-AAAAATCAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAA
* * *
22676061 ACTTTATTAAAAATTTAAACTTTTTCTTAAAAATCACTAAAAAAACATA-TAT-TTTTTAAAAAT
64 ACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACATATTATATTTTTAAAAAT
*
22676124 ATAAATTTTCTCTTTTTA
129 ATAAAATTTCTCTTTTTA
* *
22676142 AAAAAAAATCACTATTTTGCTTAAAAACCAAAACTTTTATTTCGAAATAGTTAGAAAAAAATCAA
1 AAAAAAAATCACTATTTTACTTAAAAATC-AAACTTTTATTTCGAAATAGTT--AAAAAAATCAA
*
22676207 AACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAAACATATTTTTATTTTTAAA
63 AACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAAACATA-TTATATTTTTAAA
*
22676272 AATATAAAATTTCTCTTTTTT
126 AATATAAAATTTCTCTTTTTA
* * * *
22676293 AAAGAAAATCACTATTTTTACTTAAAAATTTAAATTTTTATTTCGAAATAGTTAAAAAAAT-TAA
1 AAAAAAAATCACTA-TTTTACTTAAAAA-TCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAA
* * *
22676357 ATTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAACAGATTTTTATTTTTAAAAA
64 ACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACATA-TTATATTTTTAAAAA
22676421 CAGATATCGT
Statistics
Matches: 252, Mismatches: 18, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
145 7 0.03
146 40 0.16
147 72 0.29
148 11 0.04
149 39 0.15
150 10 0.04
151 40 0.16
152 33 0.13
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.40
Consensus pattern (146 bp):
AAAAAAAATCACTATTTTACTTAAAAATCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAC
TTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACATATTATATTTTTAAAAATAT
AAAATTTCTCTTTTTA
Found at i:22676777 original size:6 final size:6
Alignment explanation
Indices: 22676736--22676762 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
22676726 AACCCAAAAA
22676736 AATAAG AATAAG AATAAG AATAAG AAT
1 AATAAG AATAAG AATAAG AATAAG AAT
22676763 GATGATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.19
Consensus pattern (6 bp):
AATAAG
Found at i:22677202 original size:42 final size:42
Alignment explanation
Indices: 22677156--22677443 Score: 436
Period size: 42 Copynumber: 6.9 Consensus size: 42
22677146 CCTCTATGCT
* *
22677156 TAGGCCTCTAATTACAATGAAAAGTAAATGGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * *
22677198 TAGGCCTCCAAATGTAATGAAAAATAAATGGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
22677240 TAGGCCTCTAAATGCAATGAAAAGTAAACGGGCCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
22677282 TAGGCCTCTAAATGCAATGAAAAGTAAAT-GAGCCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGA-CCTCCACACC
*
22677324 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
22677366 TAGACCTCTAATTGCAATGAAAAGTAAATGGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
22677408 T-GAGCCTTTAAATGCAATGAAAAGTAAATGGGCCTC
1 TAG-GCCTCTAAATGCAATGAAAAGTAAATGGACCTC
22677444 TAAATGCGAT
Statistics
Matches: 223, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
41 2 0.01
42 219 0.98
43 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (42 bp):
TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
Found at i:22677352 original size:126 final size:126
Alignment explanation
Indices: 22677156--22677708 Score: 719
Period size: 126 Copynumber: 4.5 Consensus size: 126
22677146 CCTCTATGCT
* * * * *
22677156 TAGGCCTCTAATTACAATGAAAAGTAAATG-GACCTCCACACCTAGGCCTCCAAATGTAATGAAA
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGAG-CCTCCACACCTGGGCCTCTAAATGCAATGAAA
* *
22677220 AATAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAACGGGCCTCCACACC
65 AGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
22677282 TAGGCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
* * *
22677347 GTAAATGGACCTCCACACCTAGACCTCTAATTGCAATGAAAAGTAAATGGACCTCCACACC
66 GTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
* *
22677408 T-GAGCCTTTAAATGCAATGAAAAG----T-A------A-A--TGGGCCTCTAAATGCGATGAAA
1 TAG-GCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACCTGGGCCTCTAAATGCAATGAAA
* *
22677458 AGTAAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGAGCCTCCACACC
65 AGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
* * * * *
22677520 TAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTGGGCCTCTAAATGCAATTAAAA
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
* *
22677585 GTAGATGGACCTCCACACCT-GTGCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACC
66 GTAAATGGACCTCCACACCTAG-GCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
* * * *
22677646 TAGGCCTCTAAAAGTAATGAAAAGTAAATG-GACCTCTACACCTAGGCCTCTAAATGCAATGAA
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGAG-CCTCCACACCTGGGCCTCTAAATGCAATGAA
22677709 TGCTTTCTTT
Statistics
Matches: 375, Mismatches: 33, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
112 96 0.26
113 1 0.00
114 1 0.00
115 1 0.00
116 1 0.00
117 1 0.00
121 1 0.00
122 1 0.00
123 1 0.00
124 1 0.00
125 2 0.01
126 267 0.71
127 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (126 bp):
TAGGCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACCTGGGCCTCTAAATGCAATGAAAA
GTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
Found at i:22677455 original size:28 final size:28
Alignment explanation
Indices: 22677411--22677471 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
22677401 CCACACCTGA
*
22677411 GCCTTTAAATGCAATGAAAAGTAAATGG
1 GCCTCTAAATGCAATGAAAAGTAAATGG
*
22677439 GCCTCTAAATGCGATGAAAAGTAAATGG
1 GCCTCTAAATGCAATGAAAAGTAAATGG
*
22677467 ACCTC
1 GCCTC
22677472 CACACCTAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (28 bp):
GCCTCTAAATGCAATGAAAAGTAAATGG
Found at i:22677457 original size:70 final size:70
Alignment explanation
Indices: 22677370--22677513 Score: 227
Period size: 70 Copynumber: 2.1 Consensus size: 70
22677360 CACACCTAGA
* *
22677370 CCTCTAATTGCAATGAAAAGTAAATGGACCTCCACACCT-GAGCCTTTAAATGCAATGAAAAGTA
1 CCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAG-GCCTCTAAATGCAATGAAAAGTA
*
22677434 AATGGG
65 AATGAG
* *
22677440 CCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAA
1 CCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAA
22677505 ATGAG
66 ATGAG
22677510 CCTC
1 CCTC
22677514 CACACCTAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
70 67 0.99
71 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (70 bp):
CCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAA
ATGAG
Found at i:22677485 original size:42 final size:42
Alignment explanation
Indices: 22677438--22677708 Score: 384
Period size: 42 Copynumber: 6.5 Consensus size: 42
22677428 AAAGTAAATG
*
22677438 GGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTA
*
22677480 GGCCTCTAAATGCGATGAAAAGTAAAT-GAGCCTCCACACCTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGA-CCTCCACACCTA
* * * * *
22677522 GGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTA
* *
22677564 GGCCTCTAAATGCAATTAAAAGTAGATGGACCTCCACACCT-
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTA
* *
22677605 GTGCCTCTAAATGCGATGAAAAGTAAATGGGCCTCCACACCTA
1 G-GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTA
* * *
22677648 GGCCTCTAAAAGTAATGAAAAGTAAATGGACCTCTACACCTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTA
22677690 GGCCTCTAAATGCAATGAA
1 GGCCTCTAAATGCAATGAA
22677709 TGCTTTCTTT
Statistics
Matches: 203, Mismatches: 22, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
41 3 0.01
42 198 0.98
43 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (42 bp):
GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTA
Found at i:22677532 original size:112 final size:111
Alignment explanation
Indices: 22677324--22677683 Score: 418
Period size: 112 Copynumber: 3.1 Consensus size: 111
22677314 CCTCCACACC
* * *
22677324 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGACCTCTAATTGCAATGAAAA
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAA
* *
22677389 GTAAATGGACCTCCACACCT-GAGCCTTTAAATGCAATGAAAAGTAAA
66 GTAAATGG-CCTCCACACCTAG-GCCTCTAAATGAAATGAAAAGTAAA
*
22677436 TGGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAA
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAA
* *
22677501 GTAAATGAGCCTCCACACCTAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACC
66 GTAAATG-GCCTCCACACCTAGGCCTCTAAATGAAAT----GA-AAA-G----T--A-A-A
* *
22677562 TGGGCCTCTAAATGCAATTAAAAGTAGATGGACCTCCACACCT-GTGCCTCTAAATGCGATGAAA
1 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAG-GCCTCTAAATGCGATGAAA
* *
22677626 AGTAAATGGGCCTCCACACCTAGGCCTCTAAAAGTAATGAAAAGTAAA
65 AGTAAAT-GGCCTCCACACCTAGGCCTCTAAATGAAATGAAAAGTAAA
*
22677674 TGGACCTCTA
1 TGGGCCTCTA
22677684 CACCTAGGCC
Statistics
Matches: 214, Mismatches: 16, Indels: 36
0.80 0.06 0.14
Matches are distributed among these distances:
112 101 0.47
113 3 0.01
114 1 0.00
116 2 0.01
117 3 0.01
118 1 0.00
120 1 0.00
121 3 0.01
122 2 0.01
124 1 0.00
125 2 0.01
126 93 0.43
127 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (111 bp):
TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAA
GTAAATGGCCTCCACACCTAGGCCTCTAAATGAAATGAAAAGTAAA
Found at i:22677587 original size:196 final size:196
Alignment explanation
Indices: 22677242--22677639 Score: 643
Period size: 196 Copynumber: 2.0 Consensus size: 196
22677232 TCCACACCTA
*
22677242 GGCCTCTAAATGCAATGAAAAGTAAACGGGCCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
1 GGCCTCTAAATGCAATGAAAAGTAAACGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
* * * * *
22677307 AAATGAGCCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGACC
66 AAATGAGCCTCCACACCTAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTAGACC
* *
22677372 TCTAATTGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTTTAAATGCAATGAAAAGTAAAT
131 TCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAAT
22677437 G
196 G
* * *
22677438 GGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGT
1 GGCCTCTAAATGCAATGAAAAGTAAACGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
* *
22677503 AAATGAGCCTCCACACCTAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTGGGCC
66 AAATGAGCCTCCACACCTAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTAGACC
* * * *
22677568 TCTAAATGCAATTAAAAGTAGATGGACCTCCACACCTGTGCCTCTAAATGCGATGAAAAGTAAAT
131 TCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAAT
22677633 G
196 G
22677634 GGCCTC
1 GGCCTC
22677640 CACACCTAGG
Statistics
Matches: 185, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 185 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (196 bp):
GGCCTCTAAATGCAATGAAAAGTAAACGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
AAATGAGCCTCCACACCTAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTAGACC
TCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAGTAAAT
G
Found at i:22677632 original size:238 final size:238
Alignment explanation
Indices: 22677200--22677683 Score: 747
Period size: 238 Copynumber: 2.0 Consensus size: 238
22677190 TCCACACCTA
* *
22677200 GGCCTCCAAATGTAATGAAAAATAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
1 GGCCTCTAAATGCAATGAAAAATAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
* * * * *
22677265 AAACGGGCCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACCTGGGCC
66 AAACGAGCCTCCACACCTAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTGGGCC
*
22677330 TCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGACCTCTAATTGCAATGAAAAGTAAAT
131 TCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGACCTCTAAATGCAATGAAAAGTAAAT
* *
22677395 GGACCTCCACACCT-GAGCCTTTAAATGCAATGAAAAGTAAATG
196 GGACCTCCACACCTAG-GCCTCTAAAAGCAATGAAAAGTAAATG
* * *
22677438 GGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGT
1 GGCCTCTAAATGCAATGAAAAATAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
*
22677503 AAATGAGCCTCCACACCTAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTGGGCC
66 AAACGAGCCTCCACACCTAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTGGGCC
* * * *
22677568 TCTAAATGCAATTAAAAGTAGATGGACCTCCACACCT-GTGCCTCTAAATGCGATGAAAAGTAAA
131 TCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAG-ACCTCTAAATGCAATGAAAAGTAAA
* *
22677632 TGGGCCTCCACACCTAGGCCTCTAAAAGTAATGAAAAGTAAATG
195 TGGACCTCCACACCTAGGCCTCTAAAAGCAATGAAAAGTAAATG
*
22677676 GACCTCTA
1 GGCCTCTA
22677684 CACCTAGGCC
Statistics
Matches: 223, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
237 1 0.00
238 221 0.99
239 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (238 bp):
GGCCTCTAAATGCAATGAAAAATAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGT
AAACGAGCCTCCACACCTAGGCCTCTAAATGAAATAAAAAATAAATGAACCTCCACACCTGGGCC
TCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGACCTCTAAATGCAATGAAAAGTAAAT
GGACCTCCACACCTAGGCCTCTAAAAGCAATGAAAAGTAAATG
Found at i:22678130 original size:10 final size:10
Alignment explanation
Indices: 22678110--22678172 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
22678100 TTGCTCTCTC
22678110 TTTCTATTTTT
1 TTTCTA-TTTT
22678121 TTTCTATTTT
1 TTTCTATTTT
22678131 TTTCTATTTT
1 TTTCTATTTT
* *
22678141 CTTC---TCT
1 TTTCTATTTT
*
22678148 TTTCTTTTTT
1 TTTCTATTTT
*
22678158 TTTGTATTTT
1 TTTCTATTTT
22678168 TTTCT
1 TTTCT
22678173 TTGATTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
7 5 0.12
10 31 0.74
11 6 0.14
ACGTcount: A:0.06, C:0.13, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTCTATTTT
Found at i:22678157 original size:27 final size:27
Alignment explanation
Indices: 22678120--22678172 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
22678110 TTTCTATTTT
22678120 TTTTCTATTTTTTTCTATTTTCTTCTC
1 TTTTCTATTTTTTTCTATTTTCTTCTC
* * *
22678147 TTTTCTTTTTTTTTGTATTTTTTTCT
1 TTTTCTATTTTTTTCTATTTTCTTCT
22678173 TTGATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.06, C:0.13, G:0.02, T:0.79
Consensus pattern (27 bp):
TTTTCTATTTTTTTCTATTTTCTTCTC
Found at i:22685886 original size:17 final size:17
Alignment explanation
Indices: 22685855--22685887 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22685845 CAAACACTTA
22685855 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
22685872 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
22685888 AGTCCGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:22690198 original size:4 final size:4
Alignment explanation
Indices: 22690191--22690221 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
22690181 ACAAATGAGC
*
22690191 GAAT GAAT GAAT GAAT GAGT GAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
22690222 ATTTAGGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:22704142 original size:149 final size:149
Alignment explanation
Indices: 22703550--22704397 Score: 1215
Period size: 149 Copynumber: 5.6 Consensus size: 149
22703540 TCTTCTTCTT
* * * * * * *
22703550 TTTTTAAAAATCAAAAGTTT-TCATTTGATTAAACAAAAAACACTACTTTACTTAAAAATCCAAA
1 TTTTTAAAAATCTAAACTTTCTC-TTT-TTTAAA-GAAAATCACTATTTTACTTAAAAATTCAAA
22703614 CTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAA
63 CTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAA
*
22703679 TAA-TTAAAAAAC-AATTTTTA
128 TAACTAAAAAAACAAATTTTTA
* *
22703699 TTTTTTAAAAAAATCTAAACTTTCTTTTTTTTTAAAAGAAAATCACTATTTTACTTAAAAATCCA
1 -TTTTT--AAAAATCTAAACTTTC-TCTTTTTT-AAAGAAAATCACTATTTTACTTAAAAATTCA
*
22703764 AACTTTTATTTCGAAATAGTTAGAAAAAAATCAAAACTTTGTTAAAAATTTAAATTTTTTCTTTA
61 AACTTTTATTTCGAAATAGTTA-AAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTA
22703829 AAATAACTAAAAAAACATAGATTTTTA
125 AAATAACTAAAAAAACA-A-ATTTTTA
* * *
22703856 TTTTTAAAAATATAAATTTTCTCTTTTTTAAAGAAAATCACTATTTTTACTTAAAAATTCAAATT
1 TTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTA-TTTTACTTAAAAATTCAAACT
* *
22703921 TTTATTTCGAAATAATTAAAAAAAATCAAAACTTTGTTAAAAATTTAAATTTTTTCTTTAAAATA
65 TTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATA
22703986 ACT-AAAAAACAAATTTTTA
130 ACTAAAAAAACAAATTTTTA
* *
22704005 TTTTTAAAAATCTAAACTTTCTCTTTTTTAAATAAAATCACTATTTTGCTTAAAAATTCAAACTT
1 TTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTCAAACTT
* * *
22704070 TTATTTCGAAATAGTTAAAAAAAATCAAACCTTTATTAAAAATTTAAACTTTTTCTTTAATATAA
66 TTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAA
*
22704135 CTAAAAAAACAGATTTTTA
131 CTAAAAAAACAAATTTTTA
* * *
22704154 TTTTTAAAAATATAAATTTTCTCTTTTTTAAAGAAAATCACTATTTTATTTAAAAATTCAAACTT
1 TTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTCAAACTT
* * * *
22704219 TTATTTCGAAATAGTT--AAAAAATCAAAAATTTATTAAAAAGTTAAA-ATTTTCTTTAAAATAA
66 TTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAA
*
22704281 CTAAAAAAACATATTTTTA
131 CTAAAAAAACAAATTTTTA
* * *
22704300 TTTTTAAAAATCTAAACTTTCTCTTTTCTAAAGAAAATCACTATTTTGCTTAAAAAATCAAAGCT
1 TTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTCAAA-CT
*
22704365 TTTATTTCGAAATTATTTAAAAAAAATCAAAAC
65 TTTATTTCGAAA-TAGTTAAAAAAAATCAAAAC
22704398 ATTTCCCATA
Statistics
Matches: 637, Mismatches: 45, Indels: 32
0.89 0.06 0.04
Matches are distributed among these distances:
146 88 0.14
147 41 0.06
148 86 0.14
149 138 0.22
150 18 0.03
151 8 0.01
152 126 0.20
153 96 0.15
154 23 0.04
156 6 0.01
157 7 0.01
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (149 bp):
TTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTCAAACTT
TTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAA
CTAAAAAAACAAATTTTTA
Found at i:22709824 original size:17 final size:17
Alignment explanation
Indices: 22709797--22709840 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
22709787 ATTATAATTT
*
22709797 CATTAATTTTTT-TAAAT
1 CATTAATTTTTTAT-AAC
22709814 CATATAATTTTTTATAAC
1 CAT-TAATTTTTTATAAC
22709832 CATTAATTT
1 CATTAATTT
22709841 AAATACCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.38
18 14 0.58
19 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (17 bp):
CATTAATTTTTTATAAC
Found at i:22710513 original size:19 final size:20
Alignment explanation
Indices: 22710489--22710528 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
22710479 TTAGTAATGC
22710489 TTTTATC-TCAAAAGTG-TTT
1 TTTTATCAT-AAAAGTGCTTT
22710508 TTTTATCATAAAAGTGCTTT
1 TTTTATCATAAAAGTGCTTT
22710528 T
1 T
22710529 GAAAAGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTTATCATAAAAGTGCTTT
Found at i:22715008 original size:34 final size:34
Alignment explanation
Indices: 22714965--22715033 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
22714955 ATGTTCTGAG
22714965 ATCTGTCAGTAGTAGCAACAACTAGATCTAAACT
1 ATCTGTCAGTAGTAGCAACAACTAGATCTAAACT
22714999 ATCTGTCAGTAGTAGCAACAACTAGATCTAAACT
1 ATCTGTCAGTAGTAGCAACAACTAGATCTAAACT
22715033 A
1 A
22715034 ACTATCTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (34 bp):
ATCTGTCAGTAGTAGCAACAACTAGATCTAAACT
Found at i:22726142 original size:21 final size:21
Alignment explanation
Indices: 22726118--22726160 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
22726108 GAACTAAATT
*
22726118 CTCCCTCGAAAATTAATAAAA
1 CTCCCTCGAAAATTAACAAAA
*
22726139 CTCCTTCGAAAATTAACAAAA
1 CTCCCTCGAAAATTAACAAAA
22726160 C
1 C
22726161 AAGGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.23
Consensus pattern (21 bp):
CTCCCTCGAAAATTAACAAAA
Found at i:22746110 original size:15 final size:15
Alignment explanation
Indices: 22746090--22746119 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22746080 GCTTAGAAAA
22746090 TGCAAGCACTAATGT
1 TGCAAGCACTAATGT
*
22746105 TGCAAGCACTCATGT
1 TGCAAGCACTAATGT
22746120 AGCGAACACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (15 bp):
TGCAAGCACTAATGT
Found at i:22747745 original size:21 final size:21
Alignment explanation
Indices: 22747719--22747759 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
22747709 AGTTTTTATG
22747719 GTCAGATAAGATCTTTCTGTA
1 GTCAGATAAGATCTTTCTGTA
22747740 GTCAGATAAGATCTTTCTGT
1 GTCAGATAAGATCTTTCTGT
22747760 CGAGATGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (21 bp):
GTCAGATAAGATCTTTCTGTA
Found at i:22754126 original size:10 final size:10
Alignment explanation
Indices: 22754100--22754160 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
22754090 CCCATCCTTA
*
22754100 TTTCTTTATC
1 TTTCTTTTTC
22754110 ATTTCTTTTTC
1 -TTTCTTTTTC
22754121 TTTCTTTTTC
1 TTTCTTTTTC
*
22754131 CTTC--TTTC
1 TTTCTTTTTC
*
22754139 TTT-TTCCTTC
1 TTTCTT-TTTC
22754149 TTTCTTTTTC
1 TTTCTTTTTC
22754159 TT
1 TT
22754161 CAAATTTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 6 0.15
10 24 0.59
11 11 0.27
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:22754137 original size:14 final size:14
Alignment explanation
Indices: 22754118--22754158 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
22754108 TCATTTCTTT
22754118 TTCTTTCTTTTTCC
1 TTCTTTCTTTTTCC
22754132 TTCTTTCTTTTTCC
1 TTCTTTCTTTTTCC
22754146 TTCTTTCTTTTTC
1 TTCTTTCTTTTTC
22754159 TTCAAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCTTTCTTTTTCC
Found at i:22754159 original size:24 final size:24
Alignment explanation
Indices: 22754094--22754160 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
22754084 TGCCGTCCCA
* *
22754094 TCCTTATTTCTTTATCATTTCTTTT
1 TCCTTCTTTCTTTTTC-TTTCTTTT
* *
22754119 TCTTTCTTT-TTCCTTCTTTCTTTT
1 TCCTTCTTTCTT-TTTCTTTCTTTT
22754143 TCCTTCTTTCTTTTTCTT
1 TCCTTCTTTCTTTTTCTT
22754161 CAAATTTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 23 0.68
25 11 0.32
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (24 bp):
TCCTTCTTTCTTTTTCTTTCTTTT
Found at i:22754685 original size:14 final size:15
Alignment explanation
Indices: 22754658--22754692 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
22754648 TTAAAAACCT
22754658 AACCAAACCCAATTG
1 AACCAAACCCAATTG
22754673 AACCAAA-CCAATTG
1 AACCAAACCCAATTG
22754687 AACCAA
1 AACCAA
22754693 GTCCAACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.51, C:0.31, G:0.06, T:0.11
Consensus pattern (15 bp):
AACCAAACCCAATTG
Found at i:22754743 original size:11 final size:11
Alignment explanation
Indices: 22754716--22754755 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
22754706 CAAGTCAAAT
*
22754716 CGTTGACCAAC
1 CGTTGACCGAC
* *
22754727 CATTGATCGAC
1 CGTTGACCGAC
22754738 CGTTGACCGAC
1 CGTTGACCGAC
22754749 CGTTGAC
1 CGTTGAC
22754756 TTTAACCGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.23
Consensus pattern (11 bp):
CGTTGACCGAC
Found at i:22754782 original size:27 final size:27
Alignment explanation
Indices: 22754746--22754802 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
22754736 ACCGTTGACC
*
22754746 GACCGTTGACTTTAACCGTTGACCATT
1 GACCGTTGACGTTAACCGTTGACCATT
* * *
22754773 GACCGTTGACGTTGATCGTTGACCGTT
1 GACCGTTGACGTTAACCGTTGACCATT
22754800 GAC
1 GAC
22754803 TTTGGCCGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (27 bp):
GACCGTTGACGTTAACCGTTGACCATT
Found at i:22754785 original size:20 final size:20
Alignment explanation
Indices: 22754762--22754835 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
22754752 TGACTTTAAC
*
22754762 CGTTGACCATTGACCGTTGA
1 CGTTGACCGTTGACCGTTGA
*
22754782 CGTTGATCGTTGACCGTTGA
1 CGTTGACCGTTGACCGTTGA
* *
22754802 CTTTGGCCGTTGACCGTTGA
1 CGTTGACCGTTGACCGTTGA
* *
22754822 CTTTGACTGTTGAC
1 CGTTGACCGTTGAC
22754836 TGTTTTTTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGACCGTTGACCGTTGA
Found at i:22754792 original size:7 final size:7
Alignment explanation
Indices: 22754735--22754835 Score: 81
Period size: 7 Copynumber: 15.4 Consensus size: 7
22754725 ACCATTGATC
22754735 GACCGTT
1 GACCGTT
22754742 GACC---
1 GACCGTT
22754746 GACCGTT
1 GACCGTT
*
22754753 GA-CTTT
1 GACCGTT
*
22754759 AACCGTT
1 GACCGTT
*
22754766 GACCATT
1 GACCGTT
22754773 GACCGTT
1 GACCGTT
22754780 GA-CGTT
1 GACCGTT
*
22754786 GATCGTT
1 GACCGTT
22754793 GACCGTT
1 GACCGTT
*
22754800 GA-CTTT
1 GACCGTT
*
22754806 GGCCGTT
1 GACCGTT
22754813 GACCGTT
1 GACCGTT
*
22754820 GA-CTTT
1 GACCGTT
*
22754826 GACTGTT
1 GACCGTT
22754833 GAC
1 GAC
22754836 TGTTTTTTGA
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
4 4 0.05
6 19 0.26
7 50 0.68
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.33
Consensus pattern (7 bp):
GACCGTT
Found at i:22754836 original size:13 final size:13
Alignment explanation
Indices: 22754746--22754836 Score: 67
Period size: 13 Copynumber: 6.8 Consensus size: 13
22754736 ACCGTTGACC
22754746 GACCGTTGACTTT
1 GACCGTTGACTTT
* *
22754759 AACCGTTGACCATT
1 GACCGTTGA-CTTT
*
22754773 GACCGTTGACGTT
1 GACCGTTGACTTT
* *
22754786 GATCGTTGACCGTT
1 GACCGTTGA-CTTT
* * *
22754800 GA-CTTTGGCCGTT
1 GACCGTT-GACTTT
22754813 GACCGTTGACTTT
1 GACCGTTGACTTT
*
22754826 GACTGTTGACT
1 GACCGTTGACT
22754837 GTTTTTTGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
13 42 0.67
14 21 0.33
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.35
Consensus pattern (13 bp):
GACCGTTGACTTT
Found at i:22760149 original size:26 final size:26
Alignment explanation
Indices: 22760113--22760166 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
22760103 CAGAGATAGT
22760113 TCGTCTTCATAGGGTACCGTTATCTA
1 TCGTCTTCATAGGGTACCGTTATCTA
22760139 TCGTCTTCATAGGGTACCGTTATCTA
1 TCGTCTTCATAGGGTACCGTTATCTA
22760165 TC
1 TC
22760167 ATCTCTGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.39
Consensus pattern (26 bp):
TCGTCTTCATAGGGTACCGTTATCTA
Found at i:22761316 original size:10 final size:10
Alignment explanation
Indices: 22761290--22761336 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
22761280 CCCATCCTTA
*
22761290 TTTCTTTATC
1 TTTCTTTTTC
22761300 ATTTCTTTTTC
1 -TTTCTTTTTC
22761311 TTTCTTTTTC
1 TTTCTTTTTC
*
22761321 CTTCTTTCTT-
1 TTTCTTT-TTC
22761331 TTTCTT
1 TTTCTT
22761337 CAAATTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 21 0.66
11 11 0.34
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:22761327 original size:14 final size:14
Alignment explanation
Indices: 22761308--22761334 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22761298 TCATTTCTTT
22761308 TTCTTTCTTTTTCC
1 TTCTTTCTTTTTCC
22761322 TTCTTTCTTTTTC
1 TTCTTTCTTTTTC
22761335 TTCAAATTTC
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:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTTTCTTTTTCC
Found at i:22761860 original size:14 final size:15
Alignment explanation
Indices: 22761833--22761867 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
22761823 TTAAAAACCT
22761833 AACCAAACCCAATTG
1 AACCAAACCCAATTG
22761848 AACCAAA-CCAATTG
1 AACCAAACCCAATTG
22761862 AACCAA
1 AACCAA
22761868 GTCCAACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.51, C:0.31, G:0.06, T:0.11
Consensus pattern (15 bp):
AACCAAACCCAATTG
Found at i:22761990 original size:20 final size:19
Alignment explanation
Indices: 22761951--22762022 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
22761941 GTTTACTTTA
22761951 ACCGTTGA-TGTTGATCGTTG
1 ACCGTTGACT-TTGA-CGTTG
*
22761971 ACCGTTGACTTTGGCAGTTG
1 ACCGTTGACTTTGAC-GTTG
* * *
22761991 ATCGTTGACTATTGACCTGG
1 ACCGTTGACT-TTGACGTTG
22762011 ACCGTTGACTTT
1 ACCGTTGACTTT
22762023 TTTTGAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 3 0.07
20 35 0.81
21 5 0.12
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (19 bp):
ACCGTTGACTTTGACGTTG
Found at i:22762018 original size:27 final size:27
Alignment explanation
Indices: 22761960--22762010 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
22761950 AACCGTTGAT
* *
22761960 GTTGATCGTTGACCGTTGACTTTGGCA
1 GTTGATCGTTGACCATTGACTCTGGCA
*
22761987 GTTGATCGTTGACTATTGAC-CTGG
1 GTTGATCGTTGACCATTGACTCTGG
22762011 ACCGTTGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 3 0.14
27 18 0.86
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (27 bp):
GTTGATCGTTGACCATTGACTCTGGCA
Found at i:22777173 original size:18 final size:18
Alignment explanation
Indices: 22777150--22777189 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
22777140 TTGAAAACTT
22777150 TTTGAAAAGGATATCCGA
1 TTTGAAAAGGATATCCGA
22777168 TTTGAAAAGGATATCCGA
1 TTTGAAAAGGATATCCGA
22777186 TTTG
1 TTTG
22777190 CATGAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (18 bp):
TTTGAAAAGGATATCCGA
Found at i:22777906 original size:59 final size:59
Alignment explanation
Indices: 22777773--22778240 Score: 708
Period size: 59 Copynumber: 7.9 Consensus size: 59
22777763 TTGACTTTTG
** * *
22777773 GGGGTAAAAAT-GTAATTTTTGGTGAAATTAGGGTTAAAAAATGGAATGTTGGAAAGTTTA
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAAATGGGATTTTGGAAAGTTTA
* *
22777833 GGGGTAAAACGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
* * * * * *
22777892 AGGGTAAAATGGTAATTTTTGATGAAATAGGAGTTAAAAATAGGATTTTGGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
* * *
22777950 GAGGGTAAAATGGTAATTTATGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTG
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
*
22778010 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
* * *
22778069 GGGGTAAAATAGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTGA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
*
22778128 -GGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
22778186 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAG
22778241 CTTGGGACTA
Statistics
Matches: 374, Mismatches: 30, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
58 56 0.15
59 287 0.77
60 31 0.08
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
Found at i:22780164 original size:17 final size:17
Alignment explanation
Indices: 22780142--22780204 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 17
22780132 TCTTAAATGT
22780142 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
22780159 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
* **
22780175 ATTTAAAATTAATTCAA
1 ATTTAAATTTAAAACAA
*
22780192 ACTT-AATTTAAAA
1 ATTTAAATTTAAAA
22780205 TCCAAGTTGG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:22780188 original size:27 final size:27
Alignment explanation
Indices: 22780145--22780197 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
22780135 TAAATGTATT
* *
22780145 TAAATTTAAAACAAATTTAAATTTAAA
1 TAAATTTAAAACAAATTCAAACTTAAA
**
22780172 TAAATTTAAAATTAATTCAAACTTAA
1 TAAATTTAAAACAAATTCAAACTTAA
22780198 TTTAAAATCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (27 bp):
TAAATTTAAAACAAATTCAAACTTAAA
Found at i:22780829 original size:6 final size:6
Alignment explanation
Indices: 22780818--22780864 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
22780808 AGATTGGAAG
* * *
22780818 AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA ATTGGA ATTGAA AGTGA
1 AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGA
22780865 TATGAATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (6 bp):
AGTGAA
Found at i:22786888 original size:11 final size:11
Alignment explanation
Indices: 22786868--22786913 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
22786858 AGGTCACGTG
*
22786868 ACTGATGTGGC
1 ACTGACGTGGC
22786879 ACTGACGTGGC
1 ACTGACGTGGC
* * *
22786890 GCTGATGTGGT
1 ACTGACGTGGC
22786901 ACTGACGTGGC
1 ACTGACGTGGC
22786912 AC
1 AC
22786914 GTGCTGACAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.17, C:0.22, G:0.37, T:0.24
Consensus pattern (11 bp):
ACTGACGTGGC
Found at i:22786895 original size:22 final size:22
Alignment explanation
Indices: 22786869--22786911 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
22786859 GGTCACGTGA
22786869 CTGATGTGGCACTGACGTGGCG
1 CTGATGTGGCACTGACGTGGCG
*
22786891 CTGATGTGGTACTGACGTGGC
1 CTGATGTGGCACTGACGTGGC
22786912 ACGTGCTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.40, T:0.26
Consensus pattern (22 bp):
CTGATGTGGCACTGACGTGGCG
Found at i:22787394 original size:38 final size:39
Alignment explanation
Indices: 22787342--22787437 Score: 110
Period size: 38 Copynumber: 2.5 Consensus size: 39
22787332 TTTGCCCCAC
*
22787342 GATTGCATGTCTTCAATCTGCC-CTTTGATTAG-GGTAAAA
1 GATTGGATGTCTTCAATCTGCCTC-TTGA-TAGAGGTAAAA
* * *
22787381 GATTGGATG-CTTCAATTTGCCTCTTGATCGAGGTAAGA
1 GATTGGATGTCTTCAATCTGCCTCTTGATAGAGGTAAAA
22787419 GATT-GATGTCTTCAATCTG
1 GATTGGATGTCTTCAATCTG
22787438 TCTTCTGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
37 6 0.12
38 34 0.69
39 9 0.18
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (39 bp):
GATTGGATGTCTTCAATCTGCCTCTTGATAGAGGTAAAA
Found at i:22787577 original size:77 final size:77
Alignment explanation
Indices: 22787447--22787951 Score: 624
Period size: 77 Copynumber: 6.5 Consensus size: 77
22787437 GTCTTCTGAT
* * *
22787447 TTGGATTCTTCTATCTG-CTCCATGATCGAGGTAAGAGACTGCATGTCTTCAATCTGCCGTCTGA
1 TTGGATTCTTCAATCTGCCT-CATGATCGGGGTAAGAGACTGCATGTCTTCAATCTGCCTTCTGA
22787511 TTAAGGTAAGAGA
65 TTAAGGTAAGAGA
* * * *
22787524 TTAGATTCTTCAATTTGCCTCATGATCGGGGTAAGAGACTGCATGTATTCAATCTGCATTCTGAT
1 TTGGATTCTTCAATCTGCCTCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTGCCTTCTGAT
22787589 TAAGGTAAGAGA
66 TAAGGTAAGAGA
* * * ** *
22787601 TTGGATTCTTCAATCTTCC-CTATGATCGAGGTAAGAGATCGGTGTGTCTTCAATTTGCCTTCTG
1 TTGGATTCTTCAATCTGCCTC-ATGATCGGGGTAAGAGA-CTGCATGTCTTCAATCTGCCTTCTG
22787665 ATTAAGGTAAGAGA
64 ATTAAGGTAAGAGA
* * **
22787679 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGTGTGTCTTCAATCTGCCTTCTGA
1 TTGGATTCTTCAATCTGCCTCATGATCGGGGTAAGAGA-CTGCATGTCTTCAATCTGCCTTCTGA
22787744 TTAAGGTAAGAGA
65 TTAAGGTAAGAGA
* *
22787757 TTGGATTCGTCAATCTGCCTCATGATCAGGGTAAGAGA-TAGCATGTCTTCAATCTGCCTTCTGA
1 TTGGATTCTTCAATCTGCCTCATGATCGGGGTAAGAGACT-GCATGTCTTCAATCTGCCTTCTGA
22787821 TTAAGGTAAGAGA
65 TTAAGGTAAGAGA
* * * * * *
22787834 TTAGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGCCTGTCTTTAAATCTGTCCTT-TA
1 TTGGATTCTTCAATCTGCCTCATGATCGGGGTAAGAGACTGCATGTC-TTCAATCTG-CCTTCTG
*
22787898 ATTAGGGTAAGAGA
64 ATTAAGGTAAGAGA
* * * *
22787912 TTTGGATGCTTCGATCTTCC-CTATGATCAGGGTAAGAGAC
1 -TTGGATTCTTCAATCTGCCTC-ATGATCGGGGTAAGAGAC
22787952 CTGTAAAATA
Statistics
Matches: 378, Mismatches: 40, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
76 1 0.00
77 174 0.46
78 167 0.44
79 36 0.10
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (77 bp):
TTGGATTCTTCAATCTGCCTCATGATCGGGGTAAGAGACTGCATGTCTTCAATCTGCCTTCTGAT
TAAGGTAAGAGA
Found at i:22787680 original size:78 final size:78
Alignment explanation
Indices: 22787447--22787950 Score: 587
Period size: 78 Copynumber: 6.5 Consensus size: 78
22787437 GTCTTCTGAT
* * *
22787447 TTGGATTCTTCTATCTGCTCC-ATGATCGAGGTAAGAGA-CTGCATGTCTTCAATCTGCCGTCTG
1 TTGGATTCTTCAATCTTC-CCTATGATCGAGGTAAGAGATCTGCATGTCTTCAATCTGCCTTCTG
22787510 ATTAAGGTAAGAGA
65 ATTAAGGTAAGAGA
* * * * *
22787524 TTAGATTCTTCAAT-TTGCCTCATGATCGGGGTAAGAGA-CTGCATGTATTCAATCTGCATTCTG
1 TTGGATTCTTCAATCTTCCCT-ATGATCGAGGTAAGAGATCTGCATGTCTTCAATCTGCCTTCTG
22787587 ATTAAGGTAAGAGA
65 ATTAAGGTAAGAGA
* ** *
22787601 TTGGATTCTTCAATCTTCCCTATGATCGAGGTAAGAGATCGGTGTGTCTTCAATTTGCCTTCTGA
1 TTGGATTCTTCAATCTTCCCTATGATCGAGGTAAGAGATCTGCATGTCTTCAATCTGCCTTCTGA
22787666 TTAAGGTAAGAGA
66 TTAAGGTAAGAGA
* * * * **
22787679 TTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGTGTGTCTTCAATCTGCCTTCTGA
1 TTGGATTCTTCAATCTTCCCTATGATCGAGGTAAGAGATCTGCATGTCTTCAATCTGCCTTCTGA
22787744 TTAAGGTAAGAGA
66 TTAAGGTAAGAGA
* * *
22787757 TTGGATTCGTCAATC-TGCCTCATGATC-AGGGTAAGAGAT-AGCATGTCTTCAATCTGCCTTCT
1 TTGGATTCTTCAATCTTCCCT-ATGATCGA-GGTAAGAGATCTGCATGTCTTCAATCTGCCTTCT
22787819 GATTAAGGTAAGAGA
64 GATTAAGGTAAGAGA
* * * * * *
22787834 TTAGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT-TGCCTGTCTTTAAATCTGTCCTT-T
1 TTGGATTCTTCAATCTTCCCTATGATCGAGGTAAGAGATCTGCATGTC-TTCAATCTG-CCTTCT
* *
22787897 AATTAGGGTAAGAGA
64 GATTAAGGTAAGAGA
* *
22787912 TTTGGATGCTTCGATCTTCCCTATGATC-AGGGTAAGAGA
1 -TTGGATTCTTCAATCTTCCCTATGATCGA-GGTAAGAGA
22787951 CCTGTAAAAT
Statistics
Matches: 369, Mismatches: 46, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
75 2 0.01
76 1 0.00
77 165 0.45
78 166 0.45
79 35 0.09
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (78 bp):
TTGGATTCTTCAATCTTCCCTATGATCGAGGTAAGAGATCTGCATGTCTTCAATCTGCCTTCTGA
TTAAGGTAAGAGA
Found at i:22787804 original size:155 final size:154
Alignment explanation
Indices: 22787447--22787950 Score: 662
Period size: 155 Copynumber: 3.2 Consensus size: 154
22787437 GTCTTCTGAT
* *
22787447 TTGGATTCTTCTATCTGCTCC-ATGATCGAGGTAAGAGACTGCATGTCTTCAATCTGCCGTCTGA
1 TTGGATTCTTCAATCTGC-CCTATGATCGAGGTAAGAGA-TGCATGTCTTCAATCTGCCTTCTGA
* * *
22787511 TTAAGGTAAGAGATTAGATTCTTCAATTTGCCTCATGATCGGGGTAAGAGA-CTGCATGTATTCA
64 TTAAGGTAAGAGATTAGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGATCTGCATGTCTTCA
*
22787575 ATCTGCATTCTGATTAAGGTAAGAGA
129 ATCTGCCTTCTGATTAAGGTAAGAGA
* ** *
22787601 TTGGATTCTTCAATCTTCCCTATGATCGAGGTAAGAGATCGGTGTGTCTTCAATTTGCCTTCTGA
1 TTGGATTCTTCAATCTGCCCTATGATCGAGGTAAGAGAT--GCATGTCTTCAATCTGCCTTCTGA
* * **
22787666 TTAAGGTAAGAGATTGGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGTGTGTCTTCA
64 TTAAGGTAAGAGATTAGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGATCTGCATGTCTTCA
22787731 ATCTGCCTTCTGATTAAGGTAAGAGA
129 ATCTGCCTTCTGATTAAGGTAAGAGA
*
22787757 TTGGATTCGTCAATCTG-CCTCATGATC-AGGGTAAGAGATAGCATGTCTTCAATCTGCCTTCTG
1 TTGGATTCTTCAATCTGCCCT-ATGATCGA-GGTAAGAGAT-GCATGTCTTCAATCTGCCTTCTG
*
22787820 ATTAAGGTAAGAGATTAGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGAT-TGCCTGTCTTT
63 ATTAAGGTAAGAGATTAGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGATCTGCATGTC-TT
* * *
22787884 AAATCTGTCCTT-TAATTAGGGTAAGAGA
127 CAATCTG-CCTTCTGATTAAGGTAAGAGA
* * *
22787912 TTTGGATGCTTCGATCTTCCCTATGATC-AGGGTAAGAGA
1 -TTGGATTCTTCAATCTGCCCTATGATCGA-GGTAAGAGA
22787951 CCTGTAAAAT
Statistics
Matches: 309, Mismatches: 31, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
153 3 0.01
154 38 0.12
155 166 0.54
156 99 0.32
157 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (154 bp):
TTGGATTCTTCAATCTGCCCTATGATCGAGGTAAGAGATGCATGTCTTCAATCTGCCTTCTGATT
AAGGTAAGAGATTAGATTCTTCAATCTGCCCCATGATCGGGGTAAGAGATCTGCATGTCTTCAAT
CTGCCTTCTGATTAAGGTAAGAGA
Found at i:22789693 original size:37 final size:37
Alignment explanation
Indices: 22789643--22789717 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
22789633 AATGACTTTC
22789643 CATAGTGGACCAGTAATAACCAAATCTCATTATTTGT
1 CATAGTGGACCAGTAATAACCAAATCTCATTATTTGT
22789680 CATAGTGGACCAGTAATAACCAAATCTCATTATTTGT
1 CATAGTGGACCAGTAATAACCAAATCTCATTATTTGT
22789717 C
1 C
22789718 GAGCTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (37 bp):
CATAGTGGACCAGTAATAACCAAATCTCATTATTTGT
Found at i:22806326 original size:26 final size:25
Alignment explanation
Indices: 22806297--22806372 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 25
22806287 TCTGAAGAAT
22806297 TATACTAAACTGGCTCGTAAGAGCGA
1 TATACT-AACTGGCTCGTAAGAGCGA
* * *
22806323 TATACTGAATTGGCTCGTAGGAACGA
1 TATACT-AACTGGCTCGTAAGAGCGA
* *
22806349 TATCCTAACTGGGCTCGTATGAGC
1 TATACTAACT-GGCTCGTAAGAGC
22806373 TAAATTTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 3 0.07
26 38 0.93
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (25 bp):
TATACTAACTGGCTCGTAAGAGCGA
Found at i:22808214 original size:20 final size:21
Alignment explanation
Indices: 22808182--22808229 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
22808172 GTATGGGTTA
*
22808182 AATTAAGAGTAAATAAAT-TT
1 AATTAAGAGTAAAAAAATGTT
22808202 AATTAAG-GTTAAAAAAATGGTT
1 AATTAAGAG-TAAAAAAAT-GTT
22808224 AATTAA
1 AATTAA
22808230 AGCTTAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
22 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (21 bp):
AATTAAGAGTAAAAAAATGTT
Found at i:22809224 original size:51 final size:51
Alignment explanation
Indices: 22809099--22809278 Score: 254
Period size: 51 Copynumber: 3.5 Consensus size: 51
22809089 AAGAAAGGGC
* *
22809099 CCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGACTGT-AGGGT
1 CCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGA-T-TAAAGGT
*
22809151 CCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGT
1 CCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGT
* * *
22809202 CCAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGT
1 CCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGT
** *
22809253 GTGATGACTTAGTGTCATCGTGAGTA
1 CCGATGACTAAGTGTCATCGTGAGTA
22809279 TTAAATGAAA
Statistics
Matches: 116, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
50 1 0.01
51 74 0.64
52 41 0.35
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
CCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGT
Found at i:22809884 original size:50 final size:50
Alignment explanation
Indices: 22809813--22809912 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
22809803 CATGTATGTT
22809813 TCGGTAGAAGTGCAGGGTAAGAGAGAGGTTATACATTGACTTGAGTTGTA
1 TCGGTAGAAGTGCAGGGTAAGAGAGAGGTTATACATTGACTTGAGTTGTA
22809863 TCGGTAGAAGTGCAGGGTAAGAGAGAGGTTATACATTGACTTGAGTTGTA
1 TCGGTAGAAGTGCAGGGTAAGAGAGAGGTTATACATTGACTTGAGTTGTA
22809913 ATTGTGAGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.08, G:0.34, T:0.28
Consensus pattern (50 bp):
TCGGTAGAAGTGCAGGGTAAGAGAGAGGTTATACATTGACTTGAGTTGTA
Found at i:22815402 original size:20 final size:21
Alignment explanation
Indices: 22815370--22815417 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
22815360 GTATGGGTTA
*
22815370 AATTAAGAGTAAATAAAT-TT
1 AATTAAGAGTAAAAAAATGTT
22815390 AATTAAG-GTTAAAAAAATGGTT
1 AATTAAGAG-TAAAAAAAT-GTT
22815412 AATTAA
1 AATTAA
22815418 AGCTTAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
22 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (21 bp):
AATTAAGAGTAAAAAAATGTT
Found at i:22816410 original size:51 final size:51
Alignment explanation
Indices: 22816280--22816519 Score: 266
Period size: 51 Copynumber: 4.6 Consensus size: 51
22816270 GCTATAAACA
* * * * *
22816280 AAAGAGTCCGATGACTAAGCGCCATCGTGAGCAAATGAATCTTTTATGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
22816332 ACAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 A-AAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
22816384 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATTCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* ** * **
22816435 AAAGGTCCGATGACTTAGTGTCATCGTGAGTGTATGAATTCCTATACGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
* *
22816487 AAGAGATCCGATGATTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
22816520 TTAAATGAAA
Statistics
Matches: 159, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
51 80 0.50
52 52 0.33
53 26 0.16
54 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:22816483 original size:103 final size:103
Alignment explanation
Indices: 22816280--22816519 Score: 288
Period size: 103 Copynumber: 2.3 Consensus size: 103
22816270 GCTATAAACA
* * * * * *
22816280 AAAGAGTCCGATGACTAAGCGCCATCGTGAGCAAATGAATCTTTTATGGATTACAGGGTCCGATG
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCTATGATGGATTACAAGGTCCGATG
* **
22816345 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
65 ACTAAGTGTCATCGTGAGTAAATGAATCCTATACGGAAC
22816384 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT-TCATGATGGATTA-AAGGTCCGATG
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCT-ATGATGGATTACAAGGTCCGATG
* **
22816447 ACTTAGTGTCATCGTGAGTGTATGAATTCCTATACGGAAC
65 ACTAAGTGTCATCGTGAGTAAATGAA-TCCTATACGGAAC
* *
22816487 AAGAGATCCGATGATTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
22816520 TTAAATGAAA
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
102 34 0.29
103 53 0.45
104 30 0.25
105 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (103 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCTATGATGGATTACAAGGTCCGATGA
CTAAGTGTCATCGTGAGTAAATGAATCCTATACGGAAC
Found at i:22818394 original size:6 final size:6
Alignment explanation
Indices: 22818369--22818407 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
22818359 ACAATTCATA
* * *
22818369 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
22818408 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:22823071 original size:60 final size:59
Alignment explanation
Indices: 22822988--22823113 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 59
22822978 TAAATCTAAA
* * *** * * *
22822988 AAAAAATCAACAAATTTAGCCCTCATTGTTTCAAAAATTAATT-ATTTTAGTTTGAATTCT
1 AAAAATTCAACAAATTTAACCCTCAACATTTAAAAAATT--TTCAATTTAGTTTAAATTCT
*
22823048 AAAAATTCAATAAATTTAACCCTCAACATTTAAAAAATTTTCAATTTAGTTTAAATTCT
1 AAAAATTCAACAAATTTAACCCTCAACATTTAAAAAATTTTCAATTTAGTTTAAATTCT
22823107 AAAAATT
1 AAAAATT
22823114 TAGAAAAAAG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
58 2 0.04
59 22 0.39
60 32 0.57
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (59 bp):
AAAAATTCAACAAATTTAACCCTCAACATTTAAAAAATTTTCAATTTAGTTTAAATTCT
Found at i:22823639 original size:21 final size:22
Alignment explanation
Indices: 22823615--22823655 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
22823605 GAATCATTTG
*
22823615 ATATAT-TTTTCTTTTTTTAAT
1 ATATATGTTTTCGTTTTTTAAT
*
22823636 ATATATGTTTTGGTTTTTTA
1 ATATATGTTTTCGTTTTTTA
22823656 TTTATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.68
Consensus pattern (22 bp):
ATATATGTTTTCGTTTTTTAAT
Found at i:22823661 original size:23 final size:22
Alignment explanation
Indices: 22823610--22823665 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
22823600 TTTTTGAATC
*
22823610 ATTTGATATATTTTTCTTTTTTT
1 ATTT-ATATATTTTTCGTTTTTT
* *
22823633 A-ATATATATGTTTTGGTTTTTT
1 ATTTATATAT-TTTTCGTTTTTT
22823655 ATTTATA-ATTT
1 ATTTATATATTT
22823666 ATGTACGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
21 8 0.30
22 14 0.52
23 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (22 bp):
ATTTATATATTTTTCGTTTTTT
Found at i:22824524 original size:16 final size:16
Alignment explanation
Indices: 22824495--22824529 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
22824485 TTTCTCAAAA
**
22824495 CCCCAATTTTTGAAAT
1 CCCCAATTCATGAAAT
22824511 CCCCAATTCATGAAAT
1 CCCCAATTCATGAAAT
22824527 CCC
1 CCC
22824530 TAAAATATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.34, G:0.06, T:0.29
Consensus pattern (16 bp):
CCCCAATTCATGAAAT
Found at i:22824668 original size:266 final size:268
Alignment explanation
Indices: 22824170--22824711 Score: 989
Period size: 266 Copynumber: 2.0 Consensus size: 268
22824160 CGGGAAAAAA
*
22824170 CCCCTAAATCATTGTGAAATCCCAAATCTTAAAATCTTAATTTCTCAAAACCCTAATTTTTGAAA
1 CCCCTAAATCATTGTGAAATCCCAAATCTTAAAATCTTAATTTCTCAAAACCCCAATTTTTGAAA
22824235 TCCCCAATTCATGAAATCCCTAAAATATTCAGCAATCTCCTATTTGAATCATTTGAATCATTGAT
66 TCCCCAATTCATGAAATCCCTAAAATATTCAGCAATCTCC----T---TCATTTGAATCATTGAT
22824300 TGAGGGATTTTTTTTACATCCTTAATCCCTTATTCCCAAATCATGAAATCCCATAATTTCCAGAA
124 TGAGGGATTTTTTTTACATCCTTAATCCCTTATTCCCAAATCATGAAATCCCATAATTTCCAGAA
*
22824365 ATTGTTATTTTTCCTCCTTATCGTCTGAAATCATGAATTTAGGAAATTTTCTCAAATTTGAATCA
189 ATTGTTATTTTTCCTCCTTATCGTCTAAAATCATGAATTTAGGAAATTTTCTCAAATTTGAATCA
22824430 CATAGTTCGAATAGT
254 CATAGTTCGAATAGT
22824445 CCCCTAAATCATTGTGAAATCCCAAATCTTAAAATCTTAATTTCTCAAAACCCCAATTTTTGAAA
1 CCCCTAAATCATTGTGAAATCCCAAATCTTAAAATCTTAATTTCTCAAAACCCCAATTTTTGAAA
22824510 TCCCCAATTCATGAAATCCCTAAAATATTCAGCAATCTCC-T-ATTTGAATCATTGATTGAGGGA
66 TCCCCAATTCATGAAATCCCTAAAATATTCAGCAATCTCCTTCATTTGAATCATTGATTGAGGGA
22824573 TTTTTTTTACATCCTTAATCCCTTATTCCCAAATCATGAAATCCCATAATTTCCAGAAATTGTTA
131 TTTTTTTTACATCCTTAATCCCTTATTCCCAAATCATGAAATCCCATAATTTCCAGAAATTGTTA
22824638 TTTTTCCTCCTTATCGTCTAAAATCATGAATTTAGGAAATTTTCTCAAATTTGAATCACATAGTT
196 TTTTTCCTCCTTATCGTCTAAAATCATGAATTTAGGAAATTTTCTCAAATTTGAATCACATAGTT
22824703 CGAATAGT
261 CGAATAGT
22824711 C
1 C
22824712 AGGCTAGAGG
Statistics
Matches: 265, Mismatches: 2, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
266 160 0.60
267 1 0.00
275 104 0.39
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.37
Consensus pattern (268 bp):
CCCCTAAATCATTGTGAAATCCCAAATCTTAAAATCTTAATTTCTCAAAACCCCAATTTTTGAAA
TCCCCAATTCATGAAATCCCTAAAATATTCAGCAATCTCCTTCATTTGAATCATTGATTGAGGGA
TTTTTTTTACATCCTTAATCCCTTATTCCCAAATCATGAAATCCCATAATTTCCAGAAATTGTTA
TTTTTCCTCCTTATCGTCTAAAATCATGAATTTAGGAAATTTTCTCAAATTTGAATCACATAGTT
CGAATAGT
Found at i:22824903 original size:17 final size:17
Alignment explanation
Indices: 22824883--22824941 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
22824873 TCAAAGATGC
*
22824883 GAGCTCACCAAAACTGT
1 GAGCTCACCAAAACTGA
* * *
22824900 GAGCTCACCAAGATTGC
1 GAGCTCACCAAAACTGA
22824917 GAGCTCACC-AAACATGA
1 GAGCTCACCAAAAC-TGA
22824934 GAGCTCAC
1 GAGCTCAC
22824942 TTGCGAGCTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 2 0.06
17 33 0.94
ACGTcount: A:0.34, C:0.31, G:0.20, T:0.15
Consensus pattern (17 bp):
GAGCTCACCAAAACTGA
Found at i:22824918 original size:34 final size:33
Alignment explanation
Indices: 22824876--22824941 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
22824866 CATAGAATCA
*
22824876 AAGATGCGAGCTCACCAAA-ACTGTGAGCTCACC
1 AAGATGCGAGCTCACCAAACA-TGAGAGCTCACC
22824909 AAGATTGCGAGCTCACCAAACATGAGAGCTCAC
1 AAGA-TGCGAGCTCACCAAACATGAGAGCTCAC
22824942 TTGCGAGCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.13
34 25 0.83
35 1 0.03
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (33 bp):
AAGATGCGAGCTCACCAAACATGAGAGCTCACC
Found at i:22826253 original size:25 final size:23
Alignment explanation
Indices: 22826225--22826270 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
22826215 GTTGGATCCA
22826225 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
22826250 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
22826271 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:22827269 original size:20 final size:20
Alignment explanation
Indices: 22827244--22827284 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
22827234 CTCAGACATA
*
22827244 TTTTTTCCTC-AATTTTCTT
1 TTTTTTTCTCAAATTTTCTT
*
22827263 TTTTTTTTTCAAATTTTCTT
1 TTTTTTTCTCAAATTTTCTT
22827283 TT
1 TT
22827285 CGACTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTTCTCAAATTTTCTT
Found at i:22828234 original size:10 final size:10
Alignment explanation
Indices: 22828219--22828246 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
22828209 ATAAAAATAA
22828219 AAATGAAATG
1 AAATGAAATG
22828229 AAATGAAATG
1 AAATGAAATG
22828239 AAATGAAA
1 AAATGAAA
22828247 CTAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (10 bp):
AAATGAAATG
Found at i:22828291 original size:8 final size:9
Alignment explanation
Indices: 22828273--22828325 Score: 54
Period size: 10 Copynumber: 5.7 Consensus size: 9
22828263 ATATGCTATT
*
22828273 TTTTTTGAA
1 TTTTTTCAA
22828282 -TTTTTCAA
1 TTTTTTCAA
22828290 TTTTTTTCAA
1 -TTTTTTCAA
22828300 TTTTTTTCAA
1 -TTTTTTCAA
*
22828310 TTTTTTTTAA
1 -TTTTTTCAA
22828320 TTTTTT
1 TTTTTT
22828326 TCATCTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 7 0.17
9 6 0.15
10 27 0.68
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTTTCAA
Found at i:22828326 original size:20 final size:20
Alignment explanation
Indices: 22828270--22828339 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
22828260 TAAATATGCT
22828270 ATTTTTTTTGAA--TTTTTCA
1 ATTTTTTTT-AATTTTTTTCA
*
22828289 ATTTTTTTCAATTTTTTTCA
1 ATTTTTTTTAATTTTTTTCA
22828309 ATTTTTTTTAATTTTTTTC-
1 ATTTTTTTTAATTTTTTTCA
22828328 ATCTTTTTTTAA
1 AT-TTTTTTTAA
22828340 AAAATTAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.04
19 10 0.22
20 34 0.74
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.71
Consensus pattern (20 bp):
ATTTTTTTTAATTTTTTTCA
Found at i:22828336 original size:10 final size:10
Alignment explanation
Indices: 22828282--22828328 Score: 85
Period size: 10 Copynumber: 4.7 Consensus size: 10
22828272 TTTTTTTGAA
22828282 TTTTTCAATT
1 TTTTTCAATT
22828292 TTTTTCAATT
1 TTTTTCAATT
22828302 TTTTTCAATT
1 TTTTTCAATT
*
22828312 TTTTTTAATT
1 TTTTTCAATT
22828322 TTTTTCA
1 TTTTTCA
22828329 TCTTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTCAATT
Found at i:22831552 original size:25 final size:23
Alignment explanation
Indices: 22831520--22831565 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
22831510 GTTAGATCCA
22831520 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
22831545 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
22831566 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:22833895 original size:28 final size:28
Alignment explanation
Indices: 22833854--22833909 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
22833844 GATATCCGAT
*
22833854 TTACTCCCTATTGACCCAAAGGTCATGC
1 TTACTCCCTATTGACCCAAAGGCCATGC
*
22833882 TTACTCCCTGTTGACCCAAAGGCCATGC
1 TTACTCCCTATTGACCCAAAGGCCATGC
22833910 CTGTTACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (28 bp):
TTACTCCCTATTGACCCAAAGGCCATGC
Found at i:22836497 original size:21 final size:20
Alignment explanation
Indices: 22836459--22836497 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
22836449 TTTTCTCTTG
22836459 ATTTCTATGCTTGTATGTTC
1 ATTTCTATGCTTGTATGTTC
22836479 ATTTCTTATGTCTTG-ATGT
1 ATTTC-TATG-CTTGTATGT
22836498 GTCTTTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (20 bp):
ATTTCTATGCTTGTATGTTC
Found at i:22838422 original size:92 final size:91
Alignment explanation
Indices: 22838312--22838499 Score: 229
Period size: 92 Copynumber: 2.1 Consensus size: 91
22838302 AAATTTTTTC
** *
22838312 AAAAAAAGTAATTAAGCCCCTT-CTTTTTTTTTAC-ACTCAATT-GAGCACTTGAACTTTTAAAA
1 AAAAAAAACAATTAAG-CCCTTAC-TTTTTTTTACTACTCAATTGGA-CACTTGAACTTTCAAAA
22838374 TGCATAAAAAAGACCCTCAAACTTCTTTAA
63 TGCATAAAAAAGACCCTCAAACTT-TTTAA
* * *
22838404 AAAAAAAACAATTAAGCCCTTACTTTTTTTTCCTACTCAATTGGATACTTGAACTTTCAAAATGT
1 AAAAAAAACAATTAAGCCCTTACTTTTTTTTACTACTCAATTGGACACTTGAACTTTCAAAATGC
* * * *
22838469 TTCAAAAAGACCCTCAAAGTTTTTCA
66 ATAAAAAAGACCCTCAAACTTTTTAA
22838495 AAAAA
1 AAAAA
22838500 GCAATTAAAC
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
91 23 0.28
92 58 0.70
93 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (91 bp):
AAAAAAAACAATTAAGCCCTTACTTTTTTTTACTACTCAATTGGACACTTGAACTTTCAAAATGC
ATAAAAAAGACCCTCAAACTTTTTAA
Found at i:22838573 original size:19 final size:19
Alignment explanation
Indices: 22838542--22838588 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
22838532 AAAAAAAGGT
*
22838542 ATAAAAA-AATAAATTTTA
1 ATAAAAATATTAAATTTTA
22838560 ATAAAAATATTAAATTTTA
1 ATAAAAATATTAAATTTTA
22838579 ATAAAAATAT
1 ATAAAAATAT
22838589 AAAAACTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAAAATATTAAATTTTA
Found at i:22838987 original size:9 final size:9
Alignment explanation
Indices: 22838948--22839053 Score: 81
Period size: 9 Copynumber: 11.6 Consensus size: 9
22838938 TTTATAAAAG
22838948 TTTATAATT
1 TTTATAATT
*
22838957 TTTTTATATT
1 TTTATA-ATT
*
22838967 TCTAT-ATAT
1 TTTATAAT-T
22838976 TTTATAATT
1 TTTATAATT
**
22838985 TTTACGATT
1 TTTATAATT
*
22838994 TTTATAAAAT
1 TTTAT-AATT
*
22839004 TTTACAATT
1 TTTATAATT
22839013 TTTAT-ATT
1 TTTATAATT
*
22839021 TTTATGATT
1 TTTATAATT
*
22839030 TTTATATTTT
1 TTTATA-ATT
*
22839040 TTTCTAATT
1 TTTATAATT
22839049 TTTAT
1 TTTAT
22839054 TAAAATTTAA
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
8 10 0.14
9 43 0.58
10 21 0.28
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTATAATT
Found at i:22838994 original size:17 final size:17
Alignment explanation
Indices: 22838957--22839040 Score: 80
Period size: 17 Copynumber: 4.8 Consensus size: 17
22838947 GTTTATAATT
* *
22838957 TTTTTATATTTCTA-TA
1 TTTTTATATTTTTACGA
22838973 TATTTTATAATTTTTACGA
1 T-TTTTAT-ATTTTTACGA
* *
22838992 TTTTTATAAAATTTTACAA
1 TTTTTAT--ATTTTTACGA
*
22839011 TTTTTATATTTTTATGA
1 TTTTTATATTTTTACGA
22839028 TTTTTATATTTTT
1 TTTTTATATTTTT
22839041 TTCTAATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.02
17 26 0.46
18 12 0.21
19 18 0.32
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTATATTTTTACGA
Found at i:22839049 original size:36 final size:38
Alignment explanation
Indices: 22838965--22839053 Score: 103
Period size: 36 Copynumber: 2.4 Consensus size: 38
22838955 TTTTTTTATA
22838965 TTTCTATATATTTTATAATTTTTACGATTTTTATAAAATT
1 TTTCTA-AT-TTTTATAATTTTTACGATTTTTATAAAATT
* * **
22839005 TTAC-AATTTTTAT-ATTTTTATGATTTTTAT-ATTTT
1 TTTCTAATTTTTATAATTTTTACGATTTTTATAAAATT
22839040 TTTCTAATTTTTAT
1 TTTCTAATTTTTAT
22839054 TAAAATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
35 6 0.14
36 25 0.58
37 6 0.14
38 2 0.05
39 1 0.02
40 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (38 bp):
TTTCTAATTTTTATAATTTTTACGATTTTTATAAAATT
Found at i:22839326 original size:90 final size:90
Alignment explanation
Indices: 22839127--22839344 Score: 291
Period size: 90 Copynumber: 2.4 Consensus size: 90
22839117 ATAAAACCAA
** * *
22839127 GGGCTTAATTGCTTTTTTTTTTAAAGTTTGAGGGTC-CTTTTAATGCATTTTAAAAGTTCAAGTA
1 GGGCTTAATTGC-TTTTTTTGAAAAGTTTGAGGGTCTTTTTTAATGCAGTTTAAAAGTTCAAGTA
* * *
22839191 CCCAATTGAGTGAGAAAAAAAAGTAG
65 CCCAAATGAGTGACAAAAAAAAGAAG
* *
22839217 GGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGTCTTTTTTGATGCAGTTTGAAAGTTCAAGTA
1 GGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGGGTCTTTTTTAATGCAGTTTAAAAGTTCAAGTA
*
22839282 CCCAAATGAGTG-CAAGAAAAAGAAG
65 CCCAAATGAGTGACAAAAAAAAGAAG
22839307 GGGCTTAATTGCTTTTTTTGAGAAAG-TTGAGGG-CTTTT
1 GGGCTTAATTGCTTTTTTTGA-AAAGTTTGAGGGTCTTTT
22839345 ACACCCTTAA
Statistics
Matches: 115, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
88 5 0.04
89 17 0.15
90 55 0.48
91 38 0.33
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (90 bp):
GGGCTTAATTGCTTTTTTTGAAAAGTTTGAGGGTCTTTTTTAATGCAGTTTAAAAGTTCAAGTAC
CCAAATGAGTGACAAAAAAAAGAAG
Found at i:22843036 original size:64 final size:64
Alignment explanation
Indices: 22842935--22843060 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 64
22842925 TAACGGGTGA
22842935 AAAAGCTCAATGTTCAAGCCAGGTCGTGGACTTAGACAAAGTG-ACCCTTTAAGCCCCTTTTTGT
1 AAAAGCTCAATGTTCAAGCCAGGTCGTGGACTTAGACAAAGTGAACCC-TTAAGCCCCTTTTTGT
* *
22842999 AAAAGCTCAATGTTCAAGCCAGGTCGTGGACTTAGACAAGGTGAACCCTTAAGCCCTTTTTT
1 AAAAGCTCAATGTTCAAGCCAGGTCGTGGACTTAGACAAAGTGAACCCTTAAGCCCCTTTTT
22843061 TTTTAATTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 55 0.93
65 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (64 bp):
AAAAGCTCAATGTTCAAGCCAGGTCGTGGACTTAGACAAAGTGAACCCTTAAGCCCCTTTTTGT
Found at i:22844415 original size:22 final size:21
Alignment explanation
Indices: 22844369--22844415 Score: 51
Period size: 23 Copynumber: 2.1 Consensus size: 21
22844359 TTAAATTTTG
*
22844369 AAATTTTAAAAATAATGCAATT
1 AAATTTTAAAAATAA-GAAATT
22844391 AAATTCTTAAAAATAA-AAATAT
1 AAATT-TTAAAAATAAGAAAT-T
22844413 AAA
1 AAA
22844416 AACTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 3 0.14
22 9 0.41
23 10 0.45
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (21 bp):
AAATTTTAAAAATAAGAAATT
Found at i:22851876 original size:13 final size:13
Alignment explanation
Indices: 22851858--22851884 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22851848 TTAACTCAAA
22851858 ATTTATTTACTCG
1 ATTTATTTACTCG
22851871 ATTTATTTACTCG
1 ATTTATTTACTCG
22851884 A
1 A
22851885 AATTCAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTTATTTACTCG
Found at i:22854102 original size:21 final size:21
Alignment explanation
Indices: 22854055--22854104 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
22854045 GAGTTTTTAA
* *
22854055 TATCGGTAGAAGTATGACTTG
1 TATCGGTAGAAGTATCACCTG
*
22854076 TTTCGGTAGAAGT-TACACCTG
1 TATCGGTAGAAGTAT-CACCTG
22854097 TATCGGTA
1 TATCGGTA
22854105 AAACTTTCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (21 bp):
TATCGGTAGAAGTATCACCTG
Found at i:22854750 original size:14 final size:14
Alignment explanation
Indices: 22854733--22854773 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
22854723 TTTAAACTCT
22854733 AAAAGATAAATACA
1 AAAAGATAAATACA
22854747 AAAAGAT-AA-ACA
1 AAAAGATAAATACA
*
22854759 TAAAG-TAAATACA
1 AAAAGATAAATACA
22854772 AA
1 AA
22854774 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.39
13 6 0.26
14 7 0.30
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAGATAAATACA
Found at i:22854788 original size:19 final size:19
Alignment explanation
Indices: 22854764--22854806 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
22854754 AAACATAAAG
22854764 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
22854783 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
22854802 TAAAT
1 TAAAT
22854807 CTTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:22854826 original size:5 final size:5
Alignment explanation
Indices: 22854816--22854840 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
22854806 TCTTAATAAA
22854816 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
22854841 CAAGTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:22859490 original size:4 final size:4
Alignment explanation
Indices: 22859477--22859566 Score: 120
Period size: 4 Copynumber: 23.8 Consensus size: 4
22859467 AAAATTGAAG
*
22859477 GAAA -AAA GAAA GAAA -AAA GAGA GAGAA -AAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA
22859523 GAAA GAAA GAAA G-AA -AAA GAAA GAAA GAAA GAAA GAAA -AAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
22859567 GAAGGAAGAA
Statistics
Matches: 77, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
3 15 0.19
4 61 0.79
5 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:22859955 original size:21 final size:20
Alignment explanation
Indices: 22859925--22859964 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
22859915 AATTTACTTT
22859925 AATTTAATTTTGTTAGTTAGC
1 AATTTAATTTTGTT-GTTAGC
*
22859946 AATTTTATTTTGTTGTTAG
1 AATTTAATTTTGTTGTTAG
22859965 TAGTAGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (20 bp):
AATTTAATTTTGTTGTTAGC
Found at i:22861912 original size:43 final size:43
Alignment explanation
Indices: 22861830--22861913 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 43
22861820 ATTAACATGT
* ** *
22861830 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAACTATATTACTTGACTCGTACTAATATGATTGCATGTTAC
* *
22861873 TAAACTATATTACTTTACTCTTACTAATAT-ATTGACATGTT
1 TAAACTATATTACTTGACTCGTACTAATATGATTG-CATGTT
22861914 GTTAATTGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.09
43 31 0.91
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (43 bp):
TAAACTATATTACTTGACTCGTACTAATATGATTGCATGTTAC
Found at i:22862511 original size:21 final size:21
Alignment explanation
Indices: 22862485--22862531 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
22862475 ACGAGCCATC
*
22862485 GCAATACTTTACTCCTCCCGG
1 GCAATACTCTACTCCTCCCGG
22862506 GCAATACTCTACTCCTCCCGG
1 GCAATACTCTACTCCTCCCGG
22862527 GCAAT
1 GCAAT
22862532 TGGACCCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCGG
Found at i:22865832 original size:4 final size:4
Alignment explanation
Indices: 22865812--22865889 Score: 90
Period size: 4 Copynumber: 19.5 Consensus size: 4
22865802 AACACATTAC
* *
22865812 CTTT CTTT AC-TT C-TT CTTT CTTT CCTCT CCTT C-TT CTTT CCTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT -CTTT CTTT
22865860 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
22865890 CGTTTATTTG
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
3 7 0.11
4 51 0.77
5 8 0.12
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:22867390 original size:21 final size:21
Alignment explanation
Indices: 22867342--22867390 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
22867332 CTAGTGTTGA
* *
22867342 TTCTACCGATACAAGTGACAC
1 TTCTACCGAAACAAGTCACAC
* **
22867363 TTTTACCGAAACAAGTCATGC
1 TTCTACCGAAACAAGTCACAC
22867384 TTCTACC
1 TTCTACC
22867391 AATACTAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (21 bp):
TTCTACCGAAACAAGTCACAC
Found at i:22868120 original size:18 final size:18
Alignment explanation
Indices: 22868090--22868153 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
22868080 CTCATGTGAT
*
22868090 CCAGTATGATCAAACGAG
1 CCAGTATGCTCAAACGAG
*
22868108 CCAATATGCTCAAACGAG
1 CCAGTATGCTCAAACGAG
** * *
22868126 TTAGTATGCTCAAGCAAG
1 CCAGTATGCTCAAACGAG
22868144 CCAGTATGCT
1 CCAGTATGCT
22868154 ATTCCTTCCG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (18 bp):
CCAGTATGCTCAAACGAG
Found at i:22869139 original size:34 final size:34
Alignment explanation
Indices: 22869101--22869168 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
22869091 TACAATTTAG
22869101 TCTTTTTTACTTGATTAACTATCTAAACAATAAA
1 TCTTTTTTACTTGATTAACTATCTAAACAATAAA
22869135 TCTTTTTTACTTGATTAACTATCTAAACAATAAA
1 TCTTTTTTACTTGATTAACTATCTAAACAATAAA
22869169 ATTTCATAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (34 bp):
TCTTTTTTACTTGATTAACTATCTAAACAATAAA
Found at i:22869325 original size:23 final size:24
Alignment explanation
Indices: 22869294--22869359 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
22869284 AAAAACCGAG
*
22869294 CAGTACTAATCAGAGAGCAC-ACA
1 CAGTGCTAATCAGAGAGCACGACA
*
22869317 CAGTGCTAATAACAGAGAGCACGAGA
1 CAGTGCTAAT--CAGAGAGCACGACA
*
22869343 C-GTGCTAAACAGAGAGC
1 CAGTGCTAATCAGAGAGC
22869360 GCGCTAGTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 17 0.46
25 17 0.46
26 3 0.08
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (24 bp):
CAGTGCTAATCAGAGAGCACGACA
Found at i:22869338 original size:25 final size:23
Alignment explanation
Indices: 22869299--22869359 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
22869289 CCGAGCAGTA
*
22869299 CTAATCAGAGAGCAC-ACACAGTG
1 CTAAACAGAGAGCACGACAC-GTG
*
22869322 CTAATAACAGAGAGCACGAGACGTG
1 CT-A-AACAGAGAGCACGACACGTG
22869347 CTAAACAGAGAGC
1 CTAAACAGAGAGC
22869360 GCGCTAGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 12 0.36
24 2 0.06
25 16 0.48
26 3 0.09
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (23 bp):
CTAAACAGAGAGCACGACACGTG
Found at i:22871480 original size:5 final size:5
Alignment explanation
Indices: 22871470--22871496 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
22871460 TTGATTATAG
22871470 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
22871497 TTGATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:22878855 original size:21 final size:20
Alignment explanation
Indices: 22878810--22878856 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
22878800 TAATATGAAA
22878810 TTTTAATTAAAAGATAAATT
1 TTTTAATTAAAAGATAAATT
* *
22878830 ATTTAATTTAAAAGATAATTT
1 TTTTAA-TTAAAAGATAAATT
22878851 TTTTAA
1 TTTTAA
22878857 CTGTAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTTAATTAAAAGATAAATT
Found at i:22878887 original size:22 final size:22
Alignment explanation
Indices: 22878844--22878892 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
22878834 AATTTAAAAG
* *
22878844 ATAA-TTTTTTTAACTGTAATA
1 ATAATTTTTTTTAAATATAATA
22878865 ATTAATTTTTTTTAAATAT-ATA
1 A-TAATTTTTTTTAAATATAATA
22878887 ATAATT
1 ATAATT
22878893 ATTATGAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 7 0.29
23 11 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
ATAATTTTTTTTAAATATAATA
Found at i:22878990 original size:113 final size:113
Alignment explanation
Indices: 22878768--22878993 Score: 294
Period size: 113 Copynumber: 2.0 Consensus size: 113
22878758 ATAATATAAG
* * * *
22878768 TATATAATAATTATTGTGAAGTGATTTGAAATTAATATGAAATTTTAATTAAAAGATAAATTATT
1 TATATAATAATTATTATGAAGTGATTTGAAAATAATATGAAAATTTAACTAAAAGATAAATTATT
** * **
22878833 TAATTTAAAAGATAATTTTTTTAACTGTAATAATTAATTTTTTTTAAA
66 TAATTTAAAAGATAATTTTTACAACTGTAATAATAAATAATTTTTAAA
* * * *
22878881 TATATAATAATTATTATGAAGTGATTTGAAAATAATATTAAAATTTAACTAATATATAAATTGTT
1 TATATAATAATTATTATGAAGTGATTTGAAAATAATATGAAAATTTAACTAAAAGATAAATTATT
*
22878946 TAATTTAAAAGATAATTATTTGACAAC-GTGAT-ATAAATAATTTTTAAA
66 TAATTTAAAAGATAATT-TTT-ACAACTGTAATAATAAATAATTTTTAAA
22878994 AATTTATTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
113 87 0.90
114 7 0.07
115 3 0.03
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (113 bp):
TATATAATAATTATTATGAAGTGATTTGAAAATAATATGAAAATTTAACTAAAAGATAAATTATT
TAATTTAAAAGATAATTTTTACAACTGTAATAATAAATAATTTTTAAA
Found at i:22879742 original size:7 final size:7
Alignment explanation
Indices: 22879730--22879755 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
22879720 TCCTATACTC
22879730 TCAATTT
1 TCAATTT
22879737 TCAATTT
1 TCAATTT
22879744 TCAATTT
1 TCAATTT
22879751 TCAAT
1 TCAAT
22879756 CCTCAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (7 bp):
TCAATTT
Found at i:22884620 original size:52 final size:51
Alignment explanation
Indices: 22884538--22884726 Score: 261
Period size: 52 Copynumber: 3.6 Consensus size: 51
22884528 CACTTCATTT
* * * * * *
22884538 ATATACTAACGATGACTCAGAGCCACCGGACCTTATAATCCGCAAGGGATTC
1 ATATACTCACGATGACACAGAGTCATCGGACCTT-TAATCCGTAAAGGATTC
*
22884590 GTATACTCACGATGACACAGAGTCATCGGACCTCTTAATCCGTAAAGGATTC
1 ATATACTCACGATGACACAGAGTCATCGGACCT-TTAATCCGTAAAGGATTC
* *
22884642 ATATACTCACAATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGATTC
1 ATATACTCACGATGACACAGAGTCATCGGACC-TTTAATCCGTAAAGGATTC
*
22884694 ATATACTCACGATGACACATAGTCATCGGACCT
1 ATATACTCACGATGACACAGAGTCATCGGACCT
22884727 CTTCGTTTAT
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
51 1 0.01
52 121 0.98
53 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (51 bp):
ATATACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAAAGGATTC
Found at i:22887050 original size:21 final size:21
Alignment explanation
Indices: 22887012--22887060 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
22887002 TTTTAGTACT
* * *
22887012 GGTAGAAGCATGATTTGTTTC
1 GGTAGAAGCATCACTTGTATC
*
22887033 GGTAGAAGCTTCACTTGTATC
1 GGTAGAAGCATCACTTGTATC
*
22887054 AGTAGAA
1 GGTAGAA
22887061 CTGTCATAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33
Consensus pattern (21 bp):
GGTAGAAGCATCACTTGTATC
Found at i:22898233 original size:15 final size:15
Alignment explanation
Indices: 22898199--22898233 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
22898189 GTTTGATAAA
*
22898199 TTGAAAAATTAAGTG
1 TTGAAAAATTAAGGG
*
22898214 CTGAAAAATTAAGGG
1 TTGAAAAATTAAGGG
22898229 TTGAA
1 TTGAA
22898234 TATTTTAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.29
Consensus pattern (15 bp):
TTGAAAAATTAAGGG
Found at i:22900734 original size:46 final size:46
Alignment explanation
Indices: 22900682--22900769 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
22900672 TAGGGAAATA
* *
22900682 AAAACCTAATACAATAAGGAAAATAACTAAAACTAAAACTCTTAAT
1 AAAACCTAATACAATAAAGAAAATAAATAAAACTAAAACTCTTAAT
* * * *
22900728 AAAACCTGATATAATAAAGAAATTAAATAAATCTAAAACTCT
1 AAAACCTAATACAATAAAGAAAATAAATAAAACTAAAACTCT
22900770 AATTGCAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.58, C:0.14, G:0.05, T:0.24
Consensus pattern (46 bp):
AAAACCTAATACAATAAAGAAAATAAATAAAACTAAAACTCTTAAT
Found at i:22909213 original size:10 final size:9
Alignment explanation
Indices: 22909182--22909223 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
22909172 GTTCCCCTTA
*
22909182 TATTTTATT
1 TATTTTAAT
*
22909191 TA-TTTATT
1 TATTTTAAT
22909199 TATTTTACAT
1 TATTTTA-AT
22909209 TATTTTAAT
1 TATTTTAAT
22909218 TATTTT
1 TATTTT
22909224 TTGTTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 8 0.27
9 14 0.47
10 8 0.27
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
TATTTTAAT
Found at i:22909245 original size:30 final size:31
Alignment explanation
Indices: 22909186--22909262 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
22909176 CCCTTATATT
* *
22909186 TTATTTATTTATTTATTTTACATTATTTTAA
1 TTATTTATTTATTTAATTTACATAATTTTAA
* *
22909217 TTATTT-TTTGTTTAATTTGCATAATTTTAA
1 TTATTTATTTATTTAATTTACATAATTTTAA
*
22909247 TTGTTTATTCTATTTA
1 TTATTTATT-TATTTA
22909263 TTATTTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 25 0.66
31 8 0.21
32 5 0.13
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (31 bp):
TTATTTATTTATTTAATTTACATAATTTTAA
Found at i:22920741 original size:19 final size:19
Alignment explanation
Indices: 22920705--22920741 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
22920695 TCATTCTAAA
22920705 ATATAACATCTTTGCATGC
1 ATATAACATCTTTGCATGC
22920724 ATATCAACATCTTT-CATG
1 ATAT-AACATCTTTGCATG
22920742 TACATTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (19 bp):
ATATAACATCTTTGCATGC
Found at i:22921118 original size:49 final size:49
Alignment explanation
Indices: 22920972--22921189 Score: 174
Period size: 49 Copynumber: 4.4 Consensus size: 49
22920962 AATCCTAGAG
* *
22920972 TTGAAGAGGGAAAGATTAAAGCCGCAACGATG-GATCTTACACCTTAAAA
1 TTGAAGAGGGAAAGATTAAAGCCACAAC-ATGTAATCTTACACCTTAAAA
* * * *** * * * *
22921021 TTAAAGAGGGATAGGTTAAAGCTGTAACA-GTTTACCTAACACCCTAAAA
1 TTGAAGAGGGAAAGATTAAAGCCACAACATG-TAATCTTACACCTTAAAA
*
22921070 TTGAAGAGGGAAAGATTAAAGCCACAA-ATGTAAATCTTACCCCTTAAAA
1 TTGAAGAGGGAAAGATTAAAGCCACAACATGT-AATCTTACACCTTAAAA
** * * * *
22921119 CCGAAGAGGGATAGATTGAAGCCACAATA-GTGAATCTCACACCTTAAAA
1 TTGAAGAGGGAAAGATTAAAGCCACAACATGT-AATCTTACACCTTAAAA
* * *
22921168 TCGAAGAAGGAAAGATTGAAGC
1 TTGAAGAGGGAAAGATTAAAGC
22921190 TGTAATGACG
Statistics
Matches: 134, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
47 1 0.01
48 3 0.02
49 129 0.96
50 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (49 bp):
TTGAAGAGGGAAAGATTAAAGCCACAACATGTAATCTTACACCTTAAAA
Found at i:22921161 original size:98 final size:98
Alignment explanation
Indices: 22921056--22921336 Score: 255
Period size: 98 Copynumber: 2.9 Consensus size: 98
22921046 AACAGTTTAC
* * * * *
22921056 CTAACACCCTAAAATTGAAGAGGGAAAGATTAAAGCCACAAATGTA-AATCTTACCCCTTAAAAC
1 CTAACACCATAAAATCGAAGAGGGAAAGATTGAAGCCACAAATG-ACAATCTAACACCTTAAAAC
*
22921120 CGAAGAGGGATAGATTGAAGCCACAATAGT-GAAT
65 CGAAGAGGGATAGATTGAAGCCACAATAATAG-AT
* * * *** * *
22921154 CTCACACCTTAAAATCGAAGAAGGAAAGATTGAAG-CTGTAATGACGGATCTAACACCTTAAAAT
1 CTAACACCATAAAATCGAAGAGGGAAAGATTGAAGCCACAAATGAC-AATCTAACACCTTAAAAC
* **
22921218 CGAAGATGGATAGATTGAAGCCGTAATAATAGAT
65 CGAAGAGGGATAGATTGAAGCCACAATAATAGAT
* * ** * *
22921252 CTAACGCCATAAAATCAAAGAGGGAAAGATTGAAGCCAC-AATGGAGGATCTAACACTTTAAAGC
1 CTAACACCATAAAATCGAAGAGGGAAAGATTGAAGCCACAAAT-GACAATCTAACACCTTAAAAC
* * * *
22921316 TGAAAAGGGAAATATTGAAGC
65 CGAAGAGGGATAGATTGAAGC
22921337 AGCAATGACA
Statistics
Matches: 146, Mismatches: 32, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
96 1 0.01
97 5 0.03
98 136 0.93
99 4 0.03
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (98 bp):
CTAACACCATAAAATCGAAGAGGGAAAGATTGAAGCCACAAATGACAATCTAACACCTTAAAACC
GAAGAGGGATAGATTGAAGCCACAATAATAGAT
Found at i:22921210 original size:49 final size:48
Alignment explanation
Indices: 22921056--22921313 Score: 196
Period size: 49 Copynumber: 5.3 Consensus size: 48
22921046 AACAGTTTAC
* * * * ** *
22921056 CTAACACCCTAAAATTGAAGAGGGAAAGATTAAAGCCACAAATGTA-AAT
1 CTAACACCTTAAAATCGAAGAAGGAAAGATTGAAGCC-GTAATG-AGGAT
* * * * * **
22921105 CTTACCCCTTAAAACCGAAGAGGGATAGATTGAAGCCACAAT-AGTGAAT
1 CTAACACCTTAAAATCGAAGAAGGAAAGATTGAAGCCGTAATGAG-G-AT
* *
22921154 CTCACACCTTAAAATCGAAGAAGGAAAGATTGAAGCTGTAATGACGGAT
1 CTAACACCTTAAAATCGAAGAAGGAAAGATTGAAGCCGTAATGA-GGAT
* * * *
22921203 CTAACACCTTAAAATCGAAGATGGATAGATTGAAGCCGTAATAATAGAT
1 CTAACACCTTAAAATCGAAGAAGGAAAGATTGAAGCCGTAATGA-GGAT
* * * * **
22921252 CTAACGCCATAAAATCAAAGAGGGAAAGATTGAAGCCACAATGGAGGAT
1 CTAACACCTTAAAATCGAAGAAGGAAAGATTGAAGCCGTAAT-GAGGAT
*
22921301 CTAACACTTTAAA
1 CTAACACCTTAAA
22921314 GCTGAAAAGG
Statistics
Matches: 166, Mismatches: 37, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
46 1 0.01
48 3 0.02
49 158 0.95
50 3 0.02
51 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.20
Consensus pattern (48 bp):
CTAACACCTTAAAATCGAAGAAGGAAAGATTGAAGCCGTAATGAGGAT
Found at i:22923161 original size:37 final size:37
Alignment explanation
Indices: 22923112--22923183 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
22923102 TTATATTTTA
22923112 TTTATTTATTTAATTTGCATGATTTTAATTATTTATT
1 TTTATTTATTTAATTTGCATGATTTTAATTATTTATT
*
22923149 TTTATTTGTTTAATTTGCATGATTTTAATTATTTA
1 TTTATTTATTTAATTTGCATGATTTTAATTATTTA
22923184 ATTGTTACTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.03, G:0.07, T:0.64
Consensus pattern (37 bp):
TTTATTTATTTAATTTGCATGATTTTAATTATTTATT
Found at i:22926434 original size:17 final size:18
Alignment explanation
Indices: 22926406--22926440 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
22926396 TTCAATATCT
22926406 CAAAATTAAAATTTAAAC
1 CAAAATTAAAATTTAAAC
22926424 CAAAA-TAAAATTTAAAC
1 CAAAATTAAAATTTAAAC
22926441 ATCTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (18 bp):
CAAAATTAAAATTTAAAC
Found at i:22935095 original size:10 final size:10
Alignment explanation
Indices: 22935080--22935109 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
22935070 GACAAACCCA
22935080 AAAAAAAAAG
1 AAAAAAAAAG
22935090 AAAAAAAAAG
1 AAAAAAAAAG
22935100 AAAAATAAAA
1 AAAAA-AAAA
22935110 ACCTCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:22938010 original size:43 final size:43
Alignment explanation
Indices: 22937962--22938214 Score: 274
Period size: 43 Copynumber: 5.9 Consensus size: 43
22937952 GTTAGCAGCA
* * * *
22937962 TTTGTGGGAAAAACGCCACTAAAGATCATGTTCTATAGCGGCG
1 TTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCG
* ** *
22938005 TTTGTGATAAAAGCGTTGCTAAAGACCATATTCTATAGCGGCG
1 TTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCG
* * * * *
22938048 TTTTTGAGAAAAGCACCGCTAAAGACCATGTTCTTTAGCAGTG
1 TTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCG
* ** *
22938091 TTTGTGATAAAAGCATCGCTAAAGACCATGTTCTTTAGCGGCG
1 TTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCG
* * * * *
22938134 TTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGGGGTG
1 TTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCG
* *
22938177 TTTATG-GAAAAAGCGCCGCCAAAGACCATGTTCTATAG
1 TTTGTGAG-AAAAGCGCCGCTAAAGACCATGTTCTATAG
22938215 TGGCATTTTT
Statistics
Matches: 176, Mismatches: 33, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 1 0.01
43 175 0.99
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
TTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCG
Found at i:22938078 original size:86 final size:86
Alignment explanation
Indices: 22937980--22938224 Score: 312
Period size: 86 Copynumber: 2.8 Consensus size: 86
22937970 AAAAACGCCA
* * * * *
22937980 CTAAAGATCATGTTCTATAGCGGCGTTTGTGATAAAAGCGTTGCTAAAGACCATATTCTATAGCG
1 CTAAAGACCATGTTCTTTAGCGGTGTTTGTGATAAAAGCGTCGCTAAAGACCATGTTCTATAGCG
22938045 GCGTTTTTGAGAAAAGCACCG
66 GCGTTTTTGAGAAAAGCACCG
* * *
22938066 CTAAAGACCATGTTCTTTAGCAGTGTTTGTGATAAAAGCATCGCTAAAGACCATGTTCTTTAGCG
1 CTAAAGACCATGTTCTTTAGCGGTGTTTGTGATAAAAGCGTCGCTAAAGACCATGTTCTATAGCG
* * **
22938131 GCGTTTGTGGGAAAAGTGCCG
66 GCGTTTTTGAGAAAAGCACCG
* * * * *
22938152 CTAAAGACCATGTTCTTTAGGGGTGTTTATGGA-AAAAGCGCCGCCAAAGACCATGTTCTATAGT
1 CTAAAGACCATGTTCTTTAGCGGTGTTTGT-GATAAAAGCGTCGCTAAAGACCATGTTCTATAGC
*
22938216 GGCATTTTT
65 GGCGTTTTT
22938225 CCTCATAAAT
Statistics
Matches: 136, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
86 134 0.99
87 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (86 bp):
CTAAAGACCATGTTCTTTAGCGGTGTTTGTGATAAAAGCGTCGCTAAAGACCATGTTCTATAGCG
GCGTTTTTGAGAAAAGCACCG
Found at i:22938841 original size:6 final size:6
Alignment explanation
Indices: 22938830--22938855 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22938820 ACCCAAGTTT
22938830 ATATAC ATATAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC AT
22938856 TTTTTCTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAC
Found at i:22950627 original size:19 final size:19
Alignment explanation
Indices: 22950603--22950644 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
22950593 TCAGCTATGA
22950603 ATTCAACTTGATTCTACTC
1 ATTCAACTTGATTCTACTC
*
22950622 ATTCAATTTGATTCTACTC
1 ATTCAACTTGATTCTACTC
22950641 ATTC
1 ATTC
22950645 GAGGTTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTCAACTTGATTCTACTC
Found at i:22951326 original size:11 final size:11
Alignment explanation
Indices: 22951310--22951339 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
22951300 CAAAGTGGTC
22951310 GAGAAATCTTT
1 GAGAAATCTTT
22951321 GAGAAATCTTT
1 GAGAAATCTTT
22951332 GAGAAATC
1 GAGAAATC
22951340 CTTTATAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (11 bp):
GAGAAATCTTT
Found at i:22953889 original size:15 final size:15
Alignment explanation
Indices: 22953850--22953883 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22953840 ACCTTTAAGC
* *
22953850 CCAAACCAAAGTGAA
1 CCAAACCCAATTGAA
22953865 CCAAACCCAATTGAA
1 CCAAACCCAATTGAA
22953880 CCAA
1 CCAA
22953884 GTCCAAACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.32, G:0.09, T:0.09
Consensus pattern (15 bp):
CCAAACCCAATTGAA
Found at i:22955098 original size:22 final size:22
Alignment explanation
Indices: 22955052--22955101 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
22955042 CAAAATTTAC
**
22955052 ATTATT-TTATTTTATTTATTT
1 ATTATTATTATTTTATTTATGG
22955073 ATTATTATTATTTTGATTT-TGG
1 ATTATTATTATTTT-ATTTATGG
22955095 ATTATTA
1 ATTATTA
22955102 ATATACTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 15 0.60
23 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (22 bp):
ATTATTATTATTTTATTTATGG
Done.