Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007072.1 Hibiscus syriacus cultivar Beakdansim tig00018415_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: 290543
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2613 original size:14 final size:14
Alignment explanation
Indices: 2594--2620 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2584 GTACTTCCAC
2594 TACAAATATATATT
1 TACAAATATATATT
2608 TACAAATATATAT
1 TACAAATATATAT
2621 AGATCACGAA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
TACAAATATATATT
Found at i:8030 original size:42 final size:42
Alignment explanation
Indices: 7984--8082 Score: 171
Period size: 42 Copynumber: 2.4 Consensus size: 42
7974 CAGCATCCTC
* **
7984 GGAGATCTTCTCATTGGCCTTTGTCTGCGTTGCTTCCAGCTT
1 GGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAGCTT
8026 GGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAGCTT
1 GGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAGCTT
8068 GGAGATCTTCTCATT
1 GGAGATCTTCTCATT
8083 CACCGCTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.38
Consensus pattern (42 bp):
GGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAGCTT
Found at i:10343 original size:16 final size:16
Alignment explanation
Indices: 10322--10355 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
10312 TCTTTAAACA
10322 CACAATTAAGAAGTTG
1 CACAATTAAGAAGTTG
10338 CACAATTAAGAAGTTG
1 CACAATTAAGAAGTTG
10354 CA
1 CA
10356 TAGGTTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (16 bp):
CACAATTAAGAAGTTG
Found at i:10603 original size:2 final size:2
Alignment explanation
Indices: 10596--10621 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10586 TTTATCCCCA
10596 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10622 TGCAGAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12509 original size:14 final size:14
Alignment explanation
Indices: 12490--12517 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12480 TCATCAATAG
12490 CACTAATCCACTGA
1 CACTAATCCACTGA
12504 CACTAATCCACTGA
1 CACTAATCCACTGA
12518 AGGGATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.21
Consensus pattern (14 bp):
CACTAATCCACTGA
Found at i:14031 original size:23 final size:23
Alignment explanation
Indices: 14005--14060 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
13995 TGAGTATAAA
14005 ATTATAAGTTTATCCCTTAAAAT
1 ATTATAAGTTTATCCCTTAAAAT
14028 ATTATAAGTTTATCCCTTAAAAT
1 ATTATAAGTTTATCCCTTAAAAT
14051 ATTATAAGTT
1 ATTATAAGTT
14061 CACTCCTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (23 bp):
ATTATAAGTTTATCCCTTAAAAT
Found at i:16055 original size:23 final size:23
Alignment explanation
Indices: 16029--16080 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
16019 TTATCAGGAT
16029 CTGGGTCTGGA-CCGGGTCGGGTC
1 CTGGGTC-GGATCCGGGTCGGGTC
*
16052 CTGGGTCGGATCCGGGTTGGGTC
1 CTGGGTCGGATCCGGGTCGGGTC
16075 CTGGGT
1 CTGGGT
16081 TGGTTTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.04, C:0.23, G:0.48, T:0.25
Consensus pattern (23 bp):
CTGGGTCGGATCCGGGTCGGGTC
Found at i:16083 original size:12 final size:12
Alignment explanation
Indices: 16029--16080 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 12
16019 TTATCAGGAT
* *
16029 CTGGGTCTGGAC
1 CTGGGTCGGGTC
16041 C-GGGTCGGGTC
1 CTGGGTCGGGTC
*
16052 CTGGGTCGGATC
1 CTGGGTCGGGTC
*
16064 C-GGGTTGGGTC
1 CTGGGTCGGGTC
16075 CTGGGT
1 CTGGGT
16081 TGGTTTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.04, C:0.23, G:0.48, T:0.25
Consensus pattern (12 bp):
CTGGGTCGGGTC
Found at i:17102 original size:335 final size:333
Alignment explanation
Indices: 16465--17416 Score: 973
Period size: 335 Copynumber: 2.8 Consensus size: 333
16455 CATTAAGTAC
* * * *
16465 TACAAGTTATTGAAAATAACCAATTAAGGGTAACCTCCAAAATGGAAACCAAACGCATTGAG-AA
1 TACATGTTATTGAAAATAACCAATTAAGGGTAATCTCCAAAATAGAAAGCAAACG-ATTGAGCAA
* * * * *
16529 TTACTTATCATTTACCAAAGAACACCTAACTATTTCATTTTTAACGTTCATAACCAATGGAATTA
65 TTACTTATCA-TTACCAAACAACACCTAACTGTTCCATTTTTAACATTCA-AACCAAT-GAA-CA
* * * * * *
16594 TGAAAATAAAACACTACTCTTTACTGAAGTCAGGTGACAAAAGCAAGTTCTTTTGCAAAGTGAAA
126 TG-AAAT-----ACTACCCTTTACTGAACTCAGATGACAAAAGCAGGTTCTTTAGCACAGTG-AA
* * * * *
16659 AAAATTGTTTCAAGTTTCCGTTTTTCTCCAATTTTTCTTTACTTTCTCGGTAACCAAACAGGAAG
184 ACAATTGTTTCAAGTTTCCGTTTTCCTCCGATTTTTCTTTACTTTATCGGTAACCAAACACGAAG
* * *
16724 TGAACTAACTGTAGTCAATTGAGAGAAATGTTAAGGGAATGTGGCCAAATGATGAAAAAAAATAG
249 TGAACTAACTGTAGTCAAATGAGAGAAATGATAAGGGAATGTGGCCAAATAATGAAAAAAAATAG
*
16789 CATTG-TCTGAAGGCGTTAAG
314 CATTGCTC-GAAGGCATTAAG
*
16809 TACATGTTATTGAAAATAACCAATTAAGGGTAATCTCCAAAATAAGAAAGCAAACGAATTGAGCG
1 TACATGTTATTGAAAATAACCAATTAAGGGTAATCTCCAAAAT-AGAAAGCAAACG-ATTGAGCA
* * * *
16874 ATTACTTATCA-CACCAAACAGCACTTACCTGTTCCATTTTTTAACATTCGAAACCAATGAACAT
64 ATTACTTATCATTACCAAACAACACCTAACTGTTCCA-TTTTTAACATTC-AAACCAATGAACAT
* * *
16938 GAAATGCTACCCTTAACTGAACTCAGATGACAAAAGCAGGTTCTTTAGCACGGTGAAACAATTGT
127 GAAATACTACCCTTTACTGAACTCAGATGACAAAAGCAGGTTCTTTAGCACAGTGAAACAATTGT
* * * * *
17003 TTCAAGTTTCCATTTTCCTGCGATTTTT-TTTATTTTATTGGTAACCAAACACGAAGTGAATTAA
192 TTCAAGTTTCCGTTTTCCTCCGATTTTTCTTTACTTTATCGGTAACCAAACACGAAGTGAACTAA
* * * * * *
17067 TTGTAGTCAAATGTGAGAAATGATGAGGTAATGTGGTCAAATAATGAATAAAAATAGCATTGCTC
257 CTGTAGTCAAATGAGAGAAATGATAAGGGAATGTGGCCAAATAATGAAAAAAAATAGCATTGCTC
**
17132 GAATTCATTAAG
322 GAAGGCATTAAG
* * *
17144 TACTACGTGTTATTGAAAATAACCAATTTAAGGCTAATCTCC----TA-TATG---A-GATTGA-
1 TAC-A--TGTTATTGAAAATAACCAA-TTAAGGGTAATCTCCAAAATAGAAAGCAAACGATTGAG
* *
17199 CAATCACTTATCATTTACCAAACAACACCTAACTGTTCCATTCTTAACATTCAAAACCAATGAAC
62 CAATTACTTATCA-TTACCAAACAACACCTAACTGTTCCATTTTTAACATTC-AAACCAATGAAC
* * * *
17264 ATAAAATACTACCCTTTTGCTGAACTCAGATGAACAAAAGCAGGTTCTTTATCACAGTGGAACAA
125 ATGAAATACTACCC-TTTACTGAACTCAGATG-ACAAAAGCAGGTTCTTTAGCACAGTGAAACAA
* * * ** ***
17329 TTGTTTTCAACTTTCCGTTTTCCTCCGATTTTCCTTAACTCGCA-CGGTAACCAAATGGGAAGTG
188 TTG-TTTCAAGTTTCCGTTTTCCTCCGATTTTTCTTTACT-TTATCGGTAACCAAACACGAAGTG
*
17393 AACTAACTGTCA-TCAAGTGAGAGA
251 AACTAACTGT-AGTCAAATGAGAGA
17417 CAATAAGGTA
Statistics
Matches: 511, Mismatches: 80, Indels: 46
0.80 0.13 0.07
Matches are distributed among these distances:
327 11 0.02
328 40 0.08
329 37 0.07
330 33 0.06
331 25 0.05
332 38 0.07
333 4 0.01
334 1 0.00
335 97 0.19
336 36 0.07
337 41 0.08
338 19 0.04
339 14 0.03
342 4 0.01
343 3 0.01
344 62 0.12
345 34 0.07
346 12 0.02
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (333 bp):
TACATGTTATTGAAAATAACCAATTAAGGGTAATCTCCAAAATAGAAAGCAAACGATTGAGCAAT
TACTTATCATTACCAAACAACACCTAACTGTTCCATTTTTAACATTCAAACCAATGAACATGAAA
TACTACCCTTTACTGAACTCAGATGACAAAAGCAGGTTCTTTAGCACAGTGAAACAATTGTTTCA
AGTTTCCGTTTTCCTCCGATTTTTCTTTACTTTATCGGTAACCAAACACGAAGTGAACTAACTGT
AGTCAAATGAGAGAAATGATAAGGGAATGTGGCCAAATAATGAAAAAAAATAGCATTGCTCGAAG
GCATTAAG
Found at i:18078 original size:2 final size:2
Alignment explanation
Indices: 18071--18132 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
18061 TTTTATTGAG
18071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18113 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
18133 CAAAACGCCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18420 original size:22 final size:21
Alignment explanation
Indices: 18395--18446 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
18385 CCCATTTTTG
18395 TTTAAAAT-AATATTTTTAAAAT
1 TTTAAAATCAA-A-TTTTAAAAT
* *
18417 TTTAGAATCCAATTTTAAAAT
1 TTTAAAATCAAATTTTAAAAT
*
18438 TTTTAAATC
1 TTTAAAATC
18447 TACTCGTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 16 0.64
22 8 0.32
23 1 0.04
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTAAAATCAAATTTTAAAAT
Found at i:25983 original size:181 final size:176
Alignment explanation
Indices: 25679--26037 Score: 610
Period size: 181 Copynumber: 2.0 Consensus size: 176
25669 AGGAATCGTC
25679 CCTGTTGAAGAATGAAATTCACAAACAACAAAATAAACTATACATTTTTAGACAAATAATAATAA
1 CCTGTTGAAGAATGAAATTCACAAACAACAAAATAAACTATACATTTTTAGACAAATAATAATAA
*
25744 TAAAAATCCAATATTACGAAATCCCAGCTTAAGGCATGCATAAGCCTTTCCAAAAGTAAGTAAAA
66 TAAAAATCCAATATTACAAAATCCCAGCTTAAGGCATGCATAAGCCTTTCC--AA--AAGTAAAA
*
25809 CATAGTGTGATCCTAGTCTATTCAACACATAAAGGGATAGCAGTATTCTAT
127 CATAGTGTGATCCTAGTCTATACAACACATAAAGGGATAGCAGT-TTCTAT
* * *
25860 CCTGTTGAAGAATGAAATTCACAACCAACAAGATAAACTATACATTTTTAGCCAAATAATAATAA
1 CCTGTTGAAGAATGAAATTCACAAACAACAAAATAAACTATACATTTTTAGACAAATAATAATAA
*
25925 TACAAATCCAATATTACAAAATCCCAGCTTAAGGCATGCATAAGCCTTTCCAAAAGTAAAACATA
66 TAAAAATCCAATATTACAAAATCCCAGCTTAAGGCATGCATAAGCCTTTCCAAAAGTAAAACATA
*
25990 GTGTGATCCTAGTCTATACAACACATAAAGGGATAGTAGTTTCTAT
131 GTGTGATCCTAGTCTATACAACACATAAAGGGATAGCAGTTTCTAT
26036 CC
1 CC
26038 AAAAGTCGCA
Statistics
Matches: 171, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
176 8 0.05
177 50 0.29
179 2 0.01
181 111 0.65
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.26
Consensus pattern (176 bp):
CCTGTTGAAGAATGAAATTCACAAACAACAAAATAAACTATACATTTTTAGACAAATAATAATAA
TAAAAATCCAATATTACAAAATCCCAGCTTAAGGCATGCATAAGCCTTTCCAAAAGTAAAACATA
GTGTGATCCTAGTCTATACAACACATAAAGGGATAGCAGTTTCTAT
Found at i:28509 original size:2 final size:2
Alignment explanation
Indices: 28502--28531 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28492 GACTCTGTTC
*
28502 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28532 TAACAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:31438 original size:14 final size:14
Alignment explanation
Indices: 31419--31457 Score: 64
Period size: 12 Copynumber: 2.9 Consensus size: 14
31409 ATACTTCCAC
31419 TACAAATATATATT
1 TACAAATATATATT
31433 TAC-AA-ATATATT
1 TACAAATATATATT
31445 TACAAATATATAT
1 TACAAATATATAT
31458 AGATCACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.43
13 4 0.17
14 9 0.39
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (14 bp):
TACAAATATATATT
Found at i:32165 original size:15 final size:15
Alignment explanation
Indices: 32137--32349 Score: 313
Period size: 15 Copynumber: 14.3 Consensus size: 15
32127 GCTTTGATCT
*
32137 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
32152 TCTACAGGATTTTCA
1 TCTTCAGGATTTTCA
32167 TCTT-AGGATTTTCA
1 TCTTCAGGATTTTCA
*
32181 CCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
32196 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
32211 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
32226 TCTTCAGGA-TTTCA
1 TCTTCAGGATTTTCA
*
32240 TCTTCAGGATTTCCA
1 TCTTCAGGATTTTCA
32255 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
*
32270 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
32285 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
* *
32300 CCTTCAGTATTTTCA
1 TCTTCAGGATTTTCA
*
32315 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
32330 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
*
32345 CCTTC
1 TCTTC
32350 CTCGATCATT
Statistics
Matches: 183, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
14 27 0.15
15 156 0.85
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (15 bp):
TCTTCAGGATTTTCA
Found at i:32228 original size:59 final size:60
Alignment explanation
Indices: 32137--32349 Score: 322
Period size: 59 Copynumber: 3.6 Consensus size: 60
32127 GCTTTGATCT
* *
32137 TCTTCAGAATTTTCATCTACAGGATTTTCATCTT-AGGATTTTCACCTTCAGGATTTTCA
1 TCTTCAGAATTTTCATCTTCAGAATTTTCATCTTCAGGATTTTCACCTTCAGGATTTTCA
* * * *
32196 TCTTCAGGATTTTCATCTTCAGGATTTTCATCTTCAGGA-TTTCATCTTCAGGATTTCCA
1 TCTTCAGAATTTTCATCTTCAGAATTTTCATCTTCAGGATTTTCACCTTCAGGATTTTCA
* * *
32255 TCTTCAGGATTTTCATCTTCAGAATTTTCATCTTCAGAATTTTCACCTTCAGTATTTTCA
1 TCTTCAGAATTTTCATCTTCAGAATTTTCATCTTCAGGATTTTCACCTTCAGGATTTTCA
*
32315 TCTTCAGAATTTTCATCTTCAGAATTTTCACCTTC
1 TCTTCAGAATTTTCATCTTCAGAATTTTCATCTTC
32350 CTCGATCATT
Statistics
Matches: 141, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
59 87 0.62
60 54 0.38
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (60 bp):
TCTTCAGAATTTTCATCTTCAGAATTTTCATCTTCAGGATTTTCACCTTCAGGATTTTCA
Found at i:33611 original size:55 final size:56
Alignment explanation
Indices: 33511--33628 Score: 229
Period size: 56 Copynumber: 2.1 Consensus size: 56
33501 ATTCATACTG
33511 GAAAAAATATTTCATAGAAAATAAAAGAAACATAAAACCAAAAGAATTGAAGTTAA
1 GAAAAAATATTTCATAGAAAATAAAAGAAACATAAAACCAAAAGAATTGAAGTTAA
33567 GAAAAAATATTTCATAGAAAATAAAAGAAACAT-AAACCAAAAGAATTGAAGTTAA
1 GAAAAAATATTTCATAGAAAATAAAAGAAACATAAAACCAAAAGAATTGAAGTTAA
33622 GAAAAAA
1 GAAAAAA
33629 CTTCTTTCAA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 29 0.47
56 33 0.53
ACGTcount: A:0.64, C:0.07, G:0.11, T:0.19
Consensus pattern (56 bp):
GAAAAAATATTTCATAGAAAATAAAAGAAACATAAAACCAAAAGAATTGAAGTTAA
Found at i:36969 original size:42 final size:42
Alignment explanation
Indices: 36861--36958 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
36851 TTGCAGCATC
* **
36861 CTCGGAGATCTTCTCATTGGCCTTTGTCTGCGTTGCTTCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
* *
36903 CTTGGAGGTCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
36945 CTCGGAGATCTTCT
1 CTCGGAGATCTTCT
36959 TATTCACCTC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.11, C:0.28, G:0.24, T:0.37
Consensus pattern (42 bp):
CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
Found at i:43144 original size:92 final size:93
Alignment explanation
Indices: 42985--43172 Score: 353
Period size: 92 Copynumber: 2.0 Consensus size: 93
42975 ATTTCGTTAA
42985 AAACTTCATCTGAAAAATATGTCACACCAATATAGAAACGTCTTACTAAAACACCTTCTACATAA
1 AAACTTCATCTGAAAAATATGTCACACCAATATAGAAACGTCTTACTAAAACACCTTCTACATAA
43050 CATATCTTAATTAAAAGAGTGTTGTTTTT
66 CATATCTTAATT-AAAGAGTGTTGTTTTT
43079 AAACTTCATCTG-AAAA-ATGTCACACCAATATAGAAACGTCTTACTAAAACACCTTCTACATAA
1 AAACTTCATCTGAAAAATATGTCACACCAATATAGAAACGTCTTACTAAAACACCTTCTACATAA
43142 CATATCTTAATTAAAGAGTGTTGTTTTT
66 CATATCTTAATTAAAGAGTGTTGTTTTT
43170 AAA
1 AAA
43173 AATAAAATTA
Statistics
Matches: 94, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
91 19 0.20
92 59 0.63
93 4 0.04
94 12 0.13
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (93 bp):
AAACTTCATCTGAAAAATATGTCACACCAATATAGAAACGTCTTACTAAAACACCTTCTACATAA
CATATCTTAATTAAAGAGTGTTGTTTTT
Found at i:45519 original size:81 final size:82
Alignment explanation
Indices: 45380--45533 Score: 249
Period size: 81 Copynumber: 1.9 Consensus size: 82
45370 GTATCTACCG
* * *
45380 GCACCAATACCACATAAAATGGCGGGGGAAAATAGTAAAAATCTCAACTGCCCTGGGAAGGAGGG
1 GCACCAATACCACAT-AAATGGCGGGGCAAAATAGAAAAAATCTCAACTACCCTGGGAAGGAGGG
45445 CAATAATTATAACTACTA
65 CAATAATTATAACTACTA
45463 GCACCAATACCACAT-AA-GGCGGGGCAAAATAGAAAAAAATCTCAACTACCCTGGGAAGGAGGG
1 GCACCAATACCACATAAATGGCGGGGCAAAATAG-AAAAAATCTCAACTACCCTGGGAAGGAGGG
45526 CAATAATT
65 CAATAATT
45534 CAAAGGCAGA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
80 14 0.21
81 38 0.57
83 15 0.22
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (82 bp):
GCACCAATACCACATAAATGGCGGGGCAAAATAGAAAAAATCTCAACTACCCTGGGAAGGAGGGC
AATAATTATAACTACTA
Found at i:47268 original size:2 final size:2
Alignment explanation
Indices: 47261--47303 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
47251 AAGGTGTTTG
47261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47303 A
1 A
47304 ACGACGTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62907 original size:36 final size:35
Alignment explanation
Indices: 62856--62987 Score: 141
Period size: 36 Copynumber: 3.8 Consensus size: 35
62846 TTTATATTTC
*
62856 ATTTTC-AAAAATGAACTTCTTACATATTAAATAA
1 ATTTTCTAAAAGTGAACTTCTTACATATTAAATAA
62890 ATTTTACTAAAAGTGAACTTCTTACATATTAAATAA
1 ATTTT-CTAAAAGTGAACTTCTTACATATTAAATAA
* *
62926 A-TTTC-AATA-T-ATA-TTCTTACATATTAAATTA
1 ATTTTCTAAAAGTGA-ACTTCTTACATATTAAATAA
*
62957 ATTTCTCTAAAAGTGAAAACTTCTTAAATAT
1 ATTT-TCTAAAAGTG--AACTTCTTACATAT
62988 ATATACTTTA
Statistics
Matches: 82, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
31 19 0.23
32 4 0.05
33 5 0.06
34 9 0.11
35 5 0.06
36 28 0.34
37 1 0.01
38 11 0.13
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (35 bp):
ATTTTCTAAAAGTGAACTTCTTACATATTAAATAA
Found at i:66284 original size:42 final size:42
Alignment explanation
Indices: 66235--66332 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
66225 TTGCAGCATT
* **
66235 CTCGGAGATCTTCTCATTGGCCTTTGTCTGCGTTGCTTCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
*
66277 CTTGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
66319 CTCGGAGATCTTCT
1 CTCGGAGATCTTCT
66333 TATCCACCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.12, C:0.28, G:0.23, T:0.37
Consensus pattern (42 bp):
CTCGGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAG
Found at i:78553 original size:15 final size:15
Alignment explanation
Indices: 78533--78622 Score: 144
Period size: 15 Copynumber: 6.0 Consensus size: 15
78523 GATTTGATTT
*
78533 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
**
78548 TCTTCAAAATTTTCA
1 TCTTCAGGATTTTCA
*
78563 TCTTCAGGATTTTTA
1 TCTTCAGGATTTTCA
78578 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
78593 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
78608 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
78623 CCAATAGAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 70 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (15 bp):
TCTTCAGGATTTTCA
Found at i:80126 original size:59 final size:58
Alignment explanation
Indices: 79993--80162 Score: 182
Period size: 60 Copynumber: 2.9 Consensus size: 58
79983 ATGATTTTTT
* * *
79993 TAAATTAGTCCAT-AAACTTTTAAATATTTCAATTTCATCCATAAATTATGATTATCATTC
1 TAAATTAGTCC-TCAAACTTTTAAACATTTCAATTTCATCC-CAAATTAT-ATCATCATTC
* * * * *
80053 TAAATTTG-CACTCAAACTTTTAAACATTTTATTTTCATTCCCAAACTATATCCTCATTC
1 TAAATTAGTC-CTCAAACTTTTAAACATTTCAATTTCA-TCCCAAATTATATCATCATTC
* *
80112 TAAATTAGTCCTCAAACTATTTCACCATTTCAATTTCATCCCAAATTATAT
1 TAAATTAGTCCTCAAACT-TTTAAACATTTCAATTTCATCCCAAATTATAT
80163 GTATATATTA
Statistics
Matches: 91, Mismatches: 14, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
59 37 0.41
60 51 0.56
61 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (58 bp):
TAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCAAATTATATCATCATTC
Found at i:80403 original size:60 final size:60
Alignment explanation
Indices: 80325--80471 Score: 179
Period size: 60 Copynumber: 2.5 Consensus size: 60
80315 TAGGGGATAG
* *
80325 TTTAAAATGAGGT-TCATAGTTTGAGGATGGAATTGGAATGTTCAAAAATTGAAGGACTAA
1 TTTAAAATGA-GTATCATAGTTTGAGGATGAAATTGGAATATTCAAAAATTGAAGGACTAA
* * * * * *
80385 TTTAAAATTAGTATCATAGTTTGAGAATTAAATTGGAATATTCAAAAGTTTAGGGACTAA
1 TTTAAAATGAGTATCATAGTTTGAGGATGAAATTGGAATATTCAAAAATTGAAGGACTAA
* * *
80445 TTTAGAATGAGAATCATGGTTTGAGGA
1 TTTAAAATGAGTATCATAGTTTGAGGA
80472 CATATAACAC
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 2 0.03
60 71 0.97
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (60 bp):
TTTAAAATGAGTATCATAGTTTGAGGATGAAATTGGAATATTCAAAAATTGAAGGACTAA
Found at i:87004 original size:14 final size:14
Alignment explanation
Indices: 86985--87011 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
86975 ATACTTCCAC
86985 TACAAATATATATT
1 TACAAATATATATT
86999 TACAAATATATAT
1 TACAAATATATAT
87012 AGATCACGAA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
TACAAATATATATT
Found at i:87676 original size:15 final size:15
Alignment explanation
Indices: 87656--87720 Score: 85
Period size: 15 Copynumber: 4.3 Consensus size: 15
87646 GCTGTGATCT
*
87656 TCTTCAGGATTTTCA
1 TCTTCAGAATTTTCA
*
87671 TCTTCATAATTTTCA
1 TCTTCAGAATTTTCA
* *
87686 TCTTTAGGATTTTCA
1 TCTTCAGAATTTTCA
87701 TCTTCAGAATTTTCA
1 TCTTCAGAATTTTCA
*
87716 ACTTC
1 TCTTC
87721 CTCGATCATG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.49
Consensus pattern (15 bp):
TCTTCAGAATTTTCA
Found at i:87695 original size:30 final size:30
Alignment explanation
Indices: 87656--87720 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
87646 GCTGTGATCT
*
87656 TCTTCAGGATTTTCATCTTCATAATTTTCA
1 TCTTCAGGATTTTCATCTTCAGAATTTTCA
*
87686 TCTTTAGGATTTTCATCTTCAGAATTTTCA
1 TCTTCAGGATTTTCATCTTCAGAATTTTCA
*
87716 ACTTC
1 TCTTC
87721 CTCGATCATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.49
Consensus pattern (30 bp):
TCTTCAGGATTTTCATCTTCAGAATTTTCA
Found at i:89073 original size:33 final size:33
Alignment explanation
Indices: 89036--89142 Score: 90
Period size: 33 Copynumber: 3.1 Consensus size: 33
89026 TCATTTTCAT
*
89036 TTTTAAAATTTTAACTCTTACATATTAAATAAA
1 TTTTAAAATTATAACTCTTACATATTAAATAAA
* *
89069 TTTTACTAAAAGTGAAAACTTCTTACATATTAAATAAA
1 -TTT--TAAAA-TTATAAC-TCTTACATATTAAATAAA
* * * *
89107 TTTCAATA-TATATATTCTTACATAGTAAATAAA
1 TTTTAAAATTATA-ACTCTTACATATTAAATAAA
89140 TTT
1 TTT
89143 CTCTAAAAGT
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
33 22 0.37
34 4 0.07
35 3 0.05
36 5 0.08
37 7 0.12
38 18 0.31
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (33 bp):
TTTTAAAATTATAACTCTTACATATTAAATAAA
Found at i:89093 original size:38 final size:37
Alignment explanation
Indices: 89051--89169 Score: 140
Period size: 38 Copynumber: 3.3 Consensus size: 37
89041 AAATTTTAAC
89051 TCTTACATATTAAATAAATTTTACTAAAAGTGAAAACT
1 TCTTACATATTAAATAAATTTT-CTAAAAGTGAAAACT
* *
89089 TCTTACATATTAAATAAA-TTTC-AATA-T-ATATA-T
1 TCTTACATATTAAATAAATTTTCTAAAAGTGA-AAACT
*
89122 TCTTACATAGTAAATAAATTTCTCTAAAAGTGAAAACT
1 TCTTACATATTAAATAAATTT-TCTAAAAGTGAAAACT
*
89160 TCTTAAATAT
1 TCTTACATAT
89170 ATATACTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
33 19 0.28
34 5 0.07
35 5 0.07
36 4 0.06
37 6 0.09
38 28 0.42
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.39
Consensus pattern (37 bp):
TCTTACATATTAAATAAATTTTCTAAAAGTGAAAACT
Found at i:92450 original size:42 final size:42
Alignment explanation
Indices: 92342--92439 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
92332 TTGCAGCATC
* * **
92342 CTCGGAGATCTTCTCATTGGCCTTTGTCTGCGTTGCTTCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGGCTGCGTTGAATCCAG
* *
92384 CTTGGAGGTCTTCTCATTGGCCTCTGGCTGCGTTGAATCCAG
1 CTCGGAGATCTTCTCATTGGCCTCTGGCTGCGTTGAATCCAG
92426 CTCGGAGATCTTCT
1 CTCGGAGATCTTCT
92440 TATTCACCTC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.11, C:0.28, G:0.26, T:0.36
Consensus pattern (42 bp):
CTCGGAGATCTTCTCATTGGCCTCTGGCTGCGTTGAATCCAG
Found at i:97442 original size:8 final size:8
Alignment explanation
Indices: 97423--97478 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
97413 AAATATATAA
97423 ATTTTA-T
1 ATTTTATT
97430 A-TTTATT
1 ATTTTATT
97437 ATTTTATT
1 ATTTTATT
*
97445 ATTTTATA
1 ATTTTATT
*
97453 AATTTATT
1 ATTTTATT
97461 ATTTT-TAT
1 ATTTTAT-T
*
97469 ATTATATT
1 ATTTTATT
97477 AT
1 AT
97479 AAGTTTAAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
6 4 0.10
7 4 0.10
8 31 0.77
9 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
ATTTTATT
Found at i:97471 original size:27 final size:27
Alignment explanation
Indices: 97432--97485 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
97422 AATTTTATAT
*
97432 TTATTATTTTATTATTTTATAAATTTA
1 TTATTATTTTATTATATTATAAATTTA
*
97459 TTATT-TTTATATTATATTATAAGTTTA
1 TTATTATTT-TATTATATTATAAATTTA
97486 AGGGTCACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
TTATTATTTTATTATATTATAAATTTA
Found at i:98730 original size:23 final size:22
Alignment explanation
Indices: 98683--98732 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
98673 AGGGGTTGAG
**
98683 TAAAAAAAATTTTATATATTTT
1 TAAAAAAAATTTTATATATACT
98705 TAAAAAAAATATTTAT-TAATACT
1 TAAAAAAAAT-TTTATAT-ATACT
98728 TAAAA
1 TAAAA
98733 TGAAATTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAAAAATTTTATATATACT
Found at i:102547 original size:558 final size:554
Alignment explanation
Indices: 101245--103435 Score: 2648
Period size: 557 Copynumber: 3.9 Consensus size: 554
101235 GTTATATGGA
*
101245 GTCCACGTTTATTTAAATAATGGT-CCGTCGTCGATTAGTCTTTGTCTTCCATATGGTGGAGTCT
1 GTCCACGTTTATTTAAATAATGGTCCCCTCGTCGATTAGTCTTTGTCTTCCATATGGTGGAGTCT
*
101309 TCATCATTAATTCATTACAAACAAGTTGATCTCATTTGTGTCTCTCATCTCCTATTATTTTGGTC
66 TCATCATTAATTCATTACAAACAAGTTGATCCCATTTGTGTCTCTCATCT-CTATTATTTTGGTC
101374 TTTATGGATAAACTTGAACCTTCATGAACAACCCTACCAATCCAACGCAAAACCATTGCAATCAA
130 TTTATGGATAAACTTGAACCTTCATGAACAACCCTACCAATCCAACGCAAAACCATTGCAATCAA
* * * * *
101439 CCTTGTTTTATCTGAATAAATAAACTGCACAATTAATCACCCTCTTATTACCTCGTTTATGTTTT
195 CCATGTTTTATATGAATAAATAAACTACACAATTAGTCACCCACTTATTACCTCGTTTATGTTTT
* * * * * * * * *
101504 -GTTCACTCAACTATCTTTTTTTTTTATAAAATCATAACAAATGTTATGTTTTATTTCTGTTTTA
260 AG-TCACCCAA-TTTC-ATTTTTTTTACAAAATCATATCAAACGTTATGTTTTGTTTTTGTTTTG
** * * * * * *
101568 ATCATTTATTGATAGATTTATA-TGTTGATTAAATAGAACTGGTGATGTTATAATGGTATAATAA
322 ATCATCCACTGATAGATTTA-ACCGTTGACTAAACAGAACCGGTGATGTTATATTGGTATAATAA
* * * * * * *
101632 TAATTTTAATTCGCAAAACTTACATATTCTATCAAATTGATCTTAATTCTAAAAAGATTACTTTT
386 CAACTTTAGTCCACAAAACTTACATATTCTATCAAATTGATCCTAATTCTAAAAAGATTACTCTT
* * *
101697 GATATTTTAAAATCACACCAATTTAATCCCTCTTCAAACACACATTTAATAATTTGTTTACAAAC
451 GATATTTTAAAATCACACCAACTTAATCCCTCTTTAAACACACATTTAATAATTTGTTTACAAAT
* *
101762 AGCAAGTCTTGGTCGACCAACTAACAGAGCCAGACAGGG
516 AGCAAGTCTTGGTCGTCCAACTAAAAGAGCCAGACAGGG
** * * * *
101801 GTCCATTTTTATTTAAATAATGGTCCCCTCGTCGTTTAGTTTTTGTCTTCCATCTGGTGGGGTCT
1 GTCCACGTTTATTTAAATAATGGTCCCCTCGTCGATTAGTCTTTGTCTTCCATATGGTGGAGTCT
*
101866 TCATCATTAATTCATTACAAACAAGTTGATCCCATTTGTGTTTCTCATCTCTATTATTTTGGTCT
66 TCATCATTAATTCATTACAAACAAGTTGATCCCATTTGTGTCTCTCATCTCTATTATTTTGGTCT
*
101931 TTATGGATAAACGTGAACCTTCATGAACAACCCTACCAATCCAACGCAAAACCATTGCAATCAAC
131 TTATGGATAAACTTGAACCTTCATGAACAACCCTACCAATCCAACGCAAAACCATTGCAATCAAC
* * *
101996 CATGTTTTATATGATTATATATAAACTACACAATTAGCCACCCACTTATTATCTCG-TTATGTTT
196 CATGTTTTATATGA--ATAAATAAACTACACAATTAGTCACCCACTTATTACCTCGTTTATGTTT
* *
102060 TAGTCACCCAATTTTATTTTTTTTCTACAAAATCATATCAATCGTTATGTTTTGTTTTTGTTTTG
259 TAGTCACCCAATTTCA-TTTTTTT-TACAAAATCATATCAAACGTTATGTTTTGTTTTTGTTTTG
* * * ** **
102125 ATCATCCACTAATAGATTTAACCATTGATTAAACAGAACTAGTGATGTTGCATTGGTATAATAAC
322 ATCATCCACTGATAGATTTAACCGTTGACTAAACAGAACCGGTGATGTTATATTGGTATAATAAC
*
102190 AACTTTAGTCCACAAAACTTACACATTCTATCAAATTGATCCTAATTCTAAAAAAGATTACTCTT
387 AACTTTAGTCCACAAAACTTACATATTCTATCAAATTGATCCTAATTCT-AAAAAGATTACTCTT
* * * *
102255 AATATTTTAAAATCACACCAATTTAATCCCGCTTTAAACACGCATTTAATAATTTGTTTACAAAT
451 GATATTTTAAAATCACACCAACTTAATCCCTCTTTAAACACACATTTAATAATTTGTTTACAAAT
*
102320 AGCAAGTCTTGGTTGTCCAACTAAAAGAGCCAGACAGGGG
516 AGCAAGTCTTGGTCGTCCAACTAAAAGAGCCAGACA-GGG
*
102360 GTCCACGTTTATTTAAATAATGGTCCCCTCGTTGATTAGTCTTTGTCTTCCATATGGTGGAGTCT
1 GTCCACGTTTATTTAAATAATGGTCCCCTCGTCGATTAGTCTTTGTCTTCCATATGGTGGAGTCT
* *
102425 TCATCATTAATTCATTACAATCAAGTTGATCTCATTTGTGTCTCTCATCTCTATTATTTTGGTCT
66 TCATCATTAATTCATTACAAACAAGTTGATCCCATTTGTGTCTCTCATCTCTATTATTTTGGTCT
* * * * * ***
102490 TTACGGATAAATTTAAACCTTAATGAAC-ACCCTTACCATTCCAATTTAAAA-CATTGCAATCAA
131 TTATGGATAAACTTGAACCTTCATGAACAACCC-TACCAATCCAACGCAAAACCATTGCAATCAA
102553 CCATGTTTTATATGAATACATATAAACTACACAATTAGTCACCCACTTATTACCTCAGTTTATGT
195 CCATGTTTTATATGAATA-A-ATAAACTACACAATTAGTCACCCACTTATTACCTC-GTTTATGT
* * * *
102618 TTTAATCACCCAATTATCATTTTTTTTACAAAATTATATCAAACATTATGTTTTCTTTTTGCGTT
257 TTTAGTCACCCAATT-TCATTTTTTTTACAAAATCATATCAAACGTTATGTTTTGTTTTT--GTT
* * * * * * *
102683 GATTATATCAAACAATTAGTCACCGATGGATTTAACCGTTGACTAAATAGAACCGGTGATTTTGT
319 --TT-GAT----C-A-T--CCACTGATAGATTTAACCGTTGACTAAACAGAACCGGTGATGTTAT
* * * *
102748 ATTGGTATAATAATAACTTTAGTCCACGAAATTTACATATTCTATCAAATTGATCATAATT-TCA
373 ATTGGTATAATAACAACTTTAGTCCACAAAACTTACATATTCTATCAAATTGATCCTAATTCT-A
* * * * *
102812 GAAAGATTACTCTTTGATATTTTAAAAGCACACCAACTTAATCTCTTTTTAAACACACATTTAAG
437 AAAAGATTACTC-TTGATATTTTAAAATCACACCAACTTAATCCCTCTTTAAACACACATTTAAT
* ** * * * ** ** ***
102877 AAGTTGCATAGGTTTACATGCAACTTATG-AGGGGTAGATGGTGGAGAGGAAAAGAAATAGA-A-
501 AA-TT---T--GTTTACA---AA--TA-GCAAGTCTTGGTCGTCCA-ACTAAAAGAGCCAGACAG
**
102939 AA
553 GG
** * ** * * *
102941 GAACAC----ATTTAAATCAT-GTCCCCCTCGTCGATTAGTCTTCATCTTCGATATCGTGGGGTC
1 GTCCACGTTTATTTAAATAATGGT-CCCCTCGTCGATTAGTCTTTGTCTTCCATATGGTGGAGTC
* *
103001 TTCATCAATTAATTCATTACAAACAAGTTGATCCCATTTGTATCTCTCCTCTCTATTATTTTGGT
65 TTCATC-ATTAATTCATTACAAACAAGTTGATCCCATTTGTGTCTCTCATCTCTATTATTTTGGT
*
103066 CTTTATGGATAAACTTGAACCTTCATGAACAGCCCTACCAATCCAACGCAAAACCATTGCAATCA
129 CTTTATGGATAAACTTGAACCTTCATGAACAACCCTACCAATCCAACGCAAAACCATTGCAATCA
* * * ** *
103131 ACCTTGTTTTATCTGAATAAATAAACTGCACAATTAGTCACCCACTTATTATATTGTTTATGTTT
194 ACCATGTTTTATATGAATAAATAAACTACACAATTAGTCACCCACTTATTACCTCGTTTATGTTT
* * *
103196 TAGTTACCCAGCTATCATTTTTTTTACAAAATCATATCAAACGTTATGTTTTGTTTTTGTTTTGA
259 TAGTCACCCA-ATTTCATTTTTTTTACAAAATCATATCAAACGTTATGTTTTGTTTTTGTTTTGA
* * * *
103261 CCATCCACTGATAGATTTAACTGTTGACTAAACATAACCGGTGATTTTATATTGGTATAATAACA
323 TCATCCACTGATAGATTTAACCGTTGACTAAACAGAACCGGTGATGTTATATTGGTATAATAACA
103326 ACTTTAGTCCACAAAACTTACATATTCTATCAAATTGATCCTAATTCTAAAAAGATTACTCTTGA
388 ACTTTAGTCCACAAAACTTACATATTCTATCAAATTGATCCTAATTCTAAAAAGATTACTCTTGA
* *
103391 TATTTTAAAATCACATCAACTTAATCCCTCTTTAAACACGCATTT
453 TATTTTAAAATCACACCAACTTAATCCCTCTTTAAACACACATTT
103436 TAGAAGTTGC
Statistics
Matches: 1407, Mismatches: 180, Indels: 90
0.84 0.11 0.05
Matches are distributed among these distances:
556 126 0.09
557 226 0.16
558 206 0.15
559 191 0.14
560 27 0.02
561 5 0.00
562 44 0.03
563 110 0.08
564 3 0.00
565 1 0.00
566 1 0.00
567 1 0.00
568 1 0.00
569 1 0.00
570 1 0.00
571 14 0.01
572 139 0.10
573 2 0.00
574 3 0.00
576 62 0.04
577 82 0.06
578 102 0.07
579 31 0.02
581 6 0.00
583 11 0.01
584 11 0.01
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (554 bp):
GTCCACGTTTATTTAAATAATGGTCCCCTCGTCGATTAGTCTTTGTCTTCCATATGGTGGAGTCT
TCATCATTAATTCATTACAAACAAGTTGATCCCATTTGTGTCTCTCATCTCTATTATTTTGGTCT
TTATGGATAAACTTGAACCTTCATGAACAACCCTACCAATCCAACGCAAAACCATTGCAATCAAC
CATGTTTTATATGAATAAATAAACTACACAATTAGTCACCCACTTATTACCTCGTTTATGTTTTA
GTCACCCAATTTCATTTTTTTTACAAAATCATATCAAACGTTATGTTTTGTTTTTGTTTTGATCA
TCCACTGATAGATTTAACCGTTGACTAAACAGAACCGGTGATGTTATATTGGTATAATAACAACT
TTAGTCCACAAAACTTACATATTCTATCAAATTGATCCTAATTCTAAAAAGATTACTCTTGATAT
TTTAAAATCACACCAACTTAATCCCTCTTTAAACACACATTTAATAATTTGTTTACAAATAGCAA
GTCTTGGTCGTCCAACTAAAAGAGCCAGACAGGG
Found at i:103723 original size:2 final size:2
Alignment explanation
Indices: 103716--103743 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
103706 CTTTATCCCA
103716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
103744 TGCAGAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105452 original size:18 final size:19
Alignment explanation
Indices: 105421--105472 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
105411 ATCATACTAA
*
105421 ATTTTTTGTAATTTTT-CGG
1 ATTTTTTAT-ATTTTTCCGG
*
105440 ATTTTTTATATTTTTCCTG
1 ATTTTTTATATTTTTCCGG
105459 ATTTTTTTATATTT
1 A-TTTTTTATATTT
105473 ATAAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 6 0.21
19 11 0.38
20 12 0.41
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (19 bp):
ATTTTTTATATTTTTCCGG
Found at i:108352 original size:56 final size:56
Alignment explanation
Indices: 108291--108431 Score: 219
Period size: 56 Copynumber: 2.5 Consensus size: 56
108281 GGGCCCTCCA
* * *
108291 AAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTGTTGTCATTAATAAGTAT
1 AAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
*
108347 AAAAATAGGGGTCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
1 AAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
* * *
108403 AAAAATAAGGCCCCCGAAATCGAATATAT
1 AAAAATAGGGGCCCCGAAATCGAGTATAT
108432 ATAGAAAATA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 77 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (56 bp):
AAAAATAGGGGCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCAT
Found at i:110798 original size:13 final size:14
Alignment explanation
Indices: 110770--110806 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
110760 TTTTTAGGGA
110770 AAAAAATTAAATAT
1 AAAAAATTAAATAT
*
110784 AAAATATTAAA-AT
1 AAAAAATTAAATAT
110797 AAAAAATTAA
1 AAAAAATTAA
110807 TTCTAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAAATTAAATAT
Found at i:111698 original size:7 final size:7
Alignment explanation
Indices: 111686--111731 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
111676 GCCTATAAAT
111686 TTTTTTC
1 TTTTTTC
111693 TTTTTTC
1 TTTTTTC
111700 TTTTTTC
1 TTTTTTC
111707 TTTTTTC
1 TTTTTTC
111714 TTTTTTC
1 TTTTTTC
111721 TTTTTTC
1 TTTTTTC
111728 TTTT
1 TTTT
111732 GGACTTTGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTC
Found at i:112250 original size:2 final size:2
Alignment explanation
Indices: 112245--112279 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
112235 GGATGAACAC
112245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112280 ATAATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112709 original size:17 final size:19
Alignment explanation
Indices: 112687--112729 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 19
112677 GTAGGATAAA
112687 TTATTTTATTTA-CTA-TT
1 TTATTTTATTTATCTATTT
*
112704 TTA-TTTATTTATGTATTT
1 TTATTTTATTTATCTATTT
112722 TTATTTTA
1 TTATTTTA
112730 GTCACTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 5 0.23
19 4 0.18
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATTTTATTTATCTATTT
Found at i:115709 original size:34 final size:34
Alignment explanation
Indices: 115664--115730 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
115654 AATAGGAATT
*
115664 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATG
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATG
115699 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
115731 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATG
Found at i:116595 original size:12 final size:12
Alignment explanation
Indices: 116578--116625 Score: 87
Period size: 12 Copynumber: 4.0 Consensus size: 12
116568 CAATCAACTG
*
116578 GTACATGCATAC
1 GTACATACATAC
116590 GTACATACATAC
1 GTACATACATAC
116602 GTACATACATAC
1 GTACATACATAC
116614 GTACATACATAC
1 GTACATACATAC
116626 ATACGTGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (12 bp):
GTACATACATAC
Found at i:116600 original size:4 final size:4
Alignment explanation
Indices: 116579--116629 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
116569 AATCAACTGG
* * * *
116579 TACA TGCA TACG TACA TACA TACG TACA TACA TACG TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
116627 TAC
1 TAC
116630 GTGTTGAGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:119105 original size:18 final size:18
Alignment explanation
Indices: 119084--119118 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
119074 AACCGGTCAA
119084 TTAACTGAATTAACCAAC
1 TTAACTGAATTAACCAAC
*
119102 TTAATTGAATTAACCAA
1 TTAACTGAATTAACCAA
119119 AATTATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (18 bp):
TTAACTGAATTAACCAAC
Found at i:122970 original size:12 final size:12
Alignment explanation
Indices: 122955--122989 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
122945 TTAAATTTAG
122955 ATTTATTTTAAT
1 ATTTATTTTAAT
122967 ATTTATTTTAAT
1 ATTTATTTTAAT
122979 ATTTAGTTTTA
1 ATTTA-TTTTA
122990 GGGTAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (12 bp):
ATTTATTTTAAT
Found at i:127397 original size:18 final size:17
Alignment explanation
Indices: 127369--127402 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
127359 TTTATTCTAA
127369 TTTAAATTTAGATTTAT
1 TTTAAATTTAGATTTAT
*
127386 TTTAATATTTAGTTTTA
1 TTTAA-ATTTAGATTTA
127403 GGGTAAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTAAATTTAGATTTAT
Found at i:130181 original size:29 final size:29
Alignment explanation
Indices: 130139--130197 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
130129 ATTTTCACCT
130139 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
130168 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
130197 A
1 A
130198 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:134861 original size:29 final size:29
Alignment explanation
Indices: 134819--134877 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
134809 ATTTTCACCT
134819 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
134848 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
134877 A
1 A
134878 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:143649 original size:12 final size:12
Alignment explanation
Indices: 143640--143677 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
143630 ATCTGTATCC
143640 GTATCCGTATAT
1 GTATCCGTATAT
*
143652 GTATCTGTATAT
1 GTATCCGTATAT
143664 GTATCCGTATAT
1 GTATCCGTATAT
143676 GT
1 GT
143678 TTATGTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (12 bp):
GTATCCGTATAT
Found at i:143661 original size:24 final size:24
Alignment explanation
Indices: 143629--143677 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
143619 GATGCATACC
*
143629 TATCTGTATCCGTATCCGTATATG
1 TATCTGTATACGTATCCGTATATG
*
143653 TATCTGTATATGTATCCGTATATG
1 TATCTGTATACGTATCCGTATATG
143677 T
1 T
143678 TTATGTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (24 bp):
TATCTGTATACGTATCCGTATATG
Found at i:150253 original size:17 final size:17
Alignment explanation
Indices: 150211--150253 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
150201 TAAAATTTCA
150211 AAATTAATTAAATAAAT
1 AAATTAATTAAATAAAT
*
150228 AATTTAATTCAAA-AAAT
1 AAATTAATT-AAATAAAT
*
150245 AAATAAATT
1 AAATTAATT
150254 TCAGAGCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTAATTAAATAAAT
Found at i:151239 original size:67 final size:67
Alignment explanation
Indices: 151131--151259 Score: 258
Period size: 67 Copynumber: 1.9 Consensus size: 67
151121 GTGATCAAAT
151131 AATTCGAATATGAAGGGCTTTAACTTAACTCAATCATATAGGTTGATTTTCTTTTAAATTCGATC
1 AATTCGAATATGAAGGGCTTTAACTTAACTCAATCATATAGGTTGATTTTCTTTTAAATTCGATC
151196 AC
66 AC
151198 AATTCGAATATGAAGGGCTTTAACTTAACTCAATCATATAGGTTGATTTTCTTTTAAATTCG
1 AATTCGAATATGAAGGGCTTTAACTTAACTCAATCATATAGGTTGATTTTCTTTTAAATTCG
151260 GGTCTGGGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (67 bp):
AATTCGAATATGAAGGGCTTTAACTTAACTCAATCATATAGGTTGATTTTCTTTTAAATTCGATC
AC
Found at i:153823 original size:20 final size:20
Alignment explanation
Indices: 153798--153835 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
153788 TTTGGTTCAC
153798 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
153818 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
153836 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:153845 original size:16 final size:18
Alignment explanation
Indices: 153798--153848 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
153788 TTTGGTTCAC
153798 GGAATGTAAGATTACCAGTG
1 GGAA-GTAAGATTACCAG-G
153818 GGAATGTAAGATTACCA-G
1 GGAA-GTAAGATTACCAGG
153836 GGAA-TAAGATTAC
1 GGAAGTAAGATTAC
153849 TGGGAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 5 0.16
20 17 0.55
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGG
Found at i:157311 original size:42 final size:42
Alignment explanation
Indices: 157191--157321 Score: 172
Period size: 42 Copynumber: 3.1 Consensus size: 42
157181 TACAAATCTG
* * *
157191 TTGCGGCGTTTGTTGGAAAAACGTCAATATAGATTAAACCTA
1 TTGCGGCGTTTGTTGGAAAAAAGTCAATATAGATTAACCCAA
* ** *
157233 TTGTGGCGTTTGTTGGAAAAAAACCAATATAAATTAACCCAA
1 TTGCGGCGTTTGTTGGAAAAAAGTCAATATAGATTAACCCAA
* * *
157275 TTGCGGCGTTTGTTGGAAAAATGTCACTATAGATTAACCCAC
1 TTGCGGCGTTTGTTGGAAAAAAGTCAATATAGATTAACCCAA
157317 TTGCG
1 TTGCG
157322 ACATTTGTAT
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (42 bp):
TTGCGGCGTTTGTTGGAAAAAAGTCAATATAGATTAACCCAA
Found at i:162453 original size:20 final size:20
Alignment explanation
Indices: 162425--162463 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
162415 CGGTAAAGCG
162425 TTACCTAAAATATTATTTTT
1 TTACCTAAAATATTATTTTT
* *
162445 TTACTTAAAATGTTATTTT
1 TTACCTAAAATATTATTTT
162464 CGCTAACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
TTACCTAAAATATTATTTTT
Found at i:168522 original size:2 final size:2
Alignment explanation
Indices: 168517--168547 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
168507 ATTAAAAAAT
168517 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
168548 AATAATAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:170556 original size:2 final size:2
Alignment explanation
Indices: 170549--170596 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
170539 TATGTTTGTC
*
170549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
170591 TA TA TA
1 TA TA TA
170597 CACGATGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:170715 original size:2 final size:2
Alignment explanation
Indices: 170708--170776 Score: 93
Period size: 2 Copynumber: 34.5 Consensus size: 2
170698 TTAGATTCCA
* * * * *
170708 AT AT AT AT AA AC AC AT AT AT AC AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
170750 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
170777 GTGGTGTACA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:172225 original size:17 final size:17
Alignment explanation
Indices: 172203--172235 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
172193 GAAATCTTCA
*
172203 TTAATTAAAACTATATG
1 TTAATTAAAACGATATG
172220 TTAATTAAAACGATAT
1 TTAATTAAAACGATAT
172236 TTTTTGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (17 bp):
TTAATTAAAACGATATG
Found at i:172629 original size:12 final size:12
Alignment explanation
Indices: 172592--172629 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
172582 ACTTTAAAAT
172592 AATATTTTTATA
1 AATATTTTTATA
* *
172604 AA-ATTATAATA
1 AATATTTTTATA
172615 AATATTTTTATA
1 AATATTTTTATA
172627 AAT
1 AAT
172630 TAAATTTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATATTTTTATA
Found at i:173097 original size:40 final size:37
Alignment explanation
Indices: 173049--173137 Score: 99
Period size: 43 Copynumber: 2.3 Consensus size: 37
173039 TAATAATTAT
173049 TAAT-TTATTAATAAATAATAAAAAATAATAAATTAACTAA
1 TAATATTATTAATAAATAAT--AAAAT-AT-AATTAACTAA
* *
173089 TATATTATTTTTAATAAATAATAAAATATTATTAACTAA
1 TA-A-TATTATTAATAAATAATAAAATATAATTAACTAA
173128 TAATATTATT
1 TAATATTATT
173138 TTAATACCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
37 6 0.14
38 1 0.02
39 11 0.26
40 4 0.09
41 6 0.14
42 1 0.02
43 14 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (37 bp):
TAATATTATTAATAAATAATAAAATATAATTAACTAA
Found at i:173108 original size:43 final size:40
Alignment explanation
Indices: 173030--173143 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 40
173020 TTCAAAAACT
*
173030 AAATCTAAA-TAA-TAAT-TATTAATTTATTAATAAATAATAAA
1 AAATATAAATTAACTAATATATT-ATTT-TTAATAAATAAT--A
173071 AAATAATAAATTAACTAATATATTATTTTTAATAAATAATA
1 AAAT-ATAAATTAACTAATATATTATTTTTAATAAATAATA
*
173112 AAATAT-TATTAACTAATAATATTA-TTTTAATA
1 AAATATAAATTAACTAAT-ATATTATTTTTAATA
173144 CCAAAAAAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
39 18 0.27
40 8 0.12
41 9 0.14
42 4 0.06
43 15 0.23
44 8 0.12
45 4 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (40 bp):
AAATATAAATTAACTAATATATTATTTTTAATAAATAATA
Found at i:173141 original size:18 final size:18
Alignment explanation
Indices: 173081--173141 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 18
173071 AAATAATAAA
173081 TTAACTAAT-ATATTATTT
1 TTAACTAATAATATTA-TT
*
173099 TTAA-TAAATAATAAAATATT
1 TTAACT-AATAAT--ATTATT
173119 ATTAACTAATAATATTATT
1 -TTAACTAATAATATTATT
173138 TTAA
1 TTAA
173142 TACCAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
17 1 0.03
18 11 0.31
19 7 0.20
20 2 0.06
21 13 0.37
22 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAACTAATAATATTATT
Found at i:173256 original size:21 final size:21
Alignment explanation
Indices: 173230--173270 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
173220 TTTTTTAGTG
*
173230 AGCTTAACGAGCAACGAGTCT
1 AGCTTAACAAGCAACGAGTCT
173251 AGCTTAACAAGCAACGAGTC
1 AGCTTAACAAGCAACGAGTC
173271 GAGTTGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (21 bp):
AGCTTAACAAGCAACGAGTCT
Found at i:179153 original size:140 final size:140
Alignment explanation
Indices: 178780--180333 Score: 2035
Period size: 140 Copynumber: 11.2 Consensus size: 140
178770 AAAAACACAA
* * *
178780 TGTTACTCTCCCATCTTC-A-ATATCTCTCTTATGCTCTAAGTCATGTTACATTCATCAACTAGC
1 TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGC
* * *
178843 TCTCGTAGCTCAGTTGATCAGAGCACCCGTTTTGTAAGCGGGAGGTCTTGAGTTCAACTCTCAAC
66 TCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAAC
*
178908 AAAAGCATAG
131 AAGAGCATAG
* * * * * *
178918 TGTTACTCTCTCATATTTAATAT-TATCTCTTATTCTCTAACTCATGTTACATTTATCAGTTAGC
1 TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGC
* *
178982 TCTCGTAGCTCAGTTGGTCAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTTAACTCTCAAC
66 TCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAAC
*
179047 AAAAGCATAG
131 AAGAGCATAG
* * *
179057 TGTTACTCTCTCATCTTCAATATATCTCTCTTATTCTCTAATTCATGTTACATTCATCAGTTAGC
1 TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGC
* ** *
179122 TCTCGTAGCTCAGTTGGTTAGAGCACTCGTTTAGTAAGCGGGAGGTCTTGAGTTTGACTATCAAC
66 TCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAAC
*
179187 AAGAGCATGG
131 AAGAGCATAG
* * *
179197 TGTTAGTCTCTTATCTTCAATATATATCTCTTTTATGCTCTAACTCATGTTACATTCATCAATTA
1 TGTTACTCTCTCATCTTC-A-ATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTA
* * *
179262 GCTATTGTAGCTCAGTTGGTTAGAGCACCCATTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCA
64 GCTCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCA
* *
179327 ACAAAAACATAG
129 ACAAGAGCATAG
179339 TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGC
1 TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGC
* * * * ** * *
179404 TGTTGTAGCTTAGTTGGTCAGAGCACTTGTTTAGTAAGCAGGAGGTCTTGAGTTCAACTCGCAAC
66 TCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAAC
* * *
179469 AAAATCATGG
131 AAGAGCATAG
* * * * * **
179479 TGTCACTCTCTCTTCTTCAATATATATATCTTATTCTCTAACTCATGTTACATTCATCAGGTAGC
1 TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGC
* * * * **
179544 TCTTGTAGCTCAGTTGGTTAGAGTACCCGTTTAGTAAGCGAGAGGTATTGAGTTTGACTCTCAAC
66 TCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAAC
*
179609 AAGAGCATGG
131 AAGAGCATAG
* *
179619 TGTTACTCTCACATCTTCAATATATATCTCTTTTATGCTCTAACTCATGTTACATTCATC-A--A
1 TGTTACTCTCTCATCTTC-A-ATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTA
* *
179681 ----T--TAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGTGGGAGGTCTTGAATTCAACTCTCA
64 GCTCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCA
*
179740 ACAAGATCATAG
129 ACAAGAGCATAG
* * ** * * *
179752 TGTTACTCTCTTATCTTCAATATATCTCTTTTATTATCCAACCCATGTTACATTCATCAGTTAGC
1 TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGC
* * * **
179817 TCTCGTAGCTTAGTTGGTTAGAGCACTCGTTTAGTAAGCGGAAGGTCTTGAGTTTGACTCTCAAC
66 TCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAAC
179882 AAGAGCAT-G
131 AAGAGCATAG
* * *
179891 ATATTACTATCTCATCTTCAATATATCTATCTTATGCTCTAACTCATGTTACATTCATCAATTAG
1 -TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAG
* * *
179956 CTCTCGTAGCAT-AGTTGGTCAAAGCACCCGTTTAGTAAGTGGGAGGTCTTGAGTTCAACTCTCA
65 CTCTCGTAGC-TCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCA
180020 ACAAGAG-AGTAG
129 ACAAGAGCA-TAG
* * * *
180032 TGTTACTTTCTTATCTTCAATATATCTCTCTTATTCTCTAACTCATGTTACATTCATCAATTAAC
1 TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGC
* * * * * * *
180097 TCTCGTAGCTCAGATGGTTAGAGCACCTGTTTAGTAATCTGGAAGTCTTGAGCTT-GACTCTAAA
66 TCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAG-TTCAACTCTCAA
180161 CAAGAGCAT-G
130 CAAGAGCATAG
*
180171 ATGTTACTCTCTCATCTTCAATATATCTATCTTATGCTCTAACTCATGTTACATTCATCAATTAG
1 -TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAG
* * * *
180236 TTCTCGTAGCTTAGTTGGTTATAGCACCTGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAA
65 CTCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAA
180301 CAAGAGCATAG
130 CAAGAGCATAG
*
180312 TGTTACTCTCTCATCTTTAATA
1 TGTTACTCTCTCATCTTCAATA
180334 GAATGCTTAA
Statistics
Matches: 1237, Mismatches: 153, Indels: 50
0.86 0.11 0.03
Matches are distributed among these distances:
131 35 0.03
132 1 0.00
133 77 0.06
134 1 0.00
135 1 0.00
138 16 0.01
139 136 0.11
140 803 0.65
141 9 0.01
142 158 0.13
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (140 bp):
TGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGC
TCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAAC
AAGAGCATAG
Found at i:179918 original size:553 final size:549
Alignment explanation
Indices: 178782--180333 Score: 2088
Period size: 553 Copynumber: 2.8 Consensus size: 549
178772 AAACACAATG
* * *
178782 TTACTCTCCCATCTTC-A-ATATCTCTCTTATGCTCTAAGTCATGTTACATTCATCAACTAGCTC
1 TTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGCTC
* * *
178845 TCGTAGCTCAGTTGATCAGAGCACCCGTTTTGTAAGCGGGAGGTCTTGAGTTCAACTCTCAACAA
66 TCGTAGCTTAGTTGGTCAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAACAA
* * * *
178910 AAGCATAGTGTTACTCTCTCATATTTAATAT-TATCTCTTATTCTCTAACTCATGTTACATTTAT
131 AA-CATAGTGTTACTCTCTCTTCTTCAATATATATCTCTTATTCTCTAACTCATGTTACATTCAT
* *
178974 CAGTTAGCTCTCGTAGCTCAGTTGGTCAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTTAA
195 CAGTTAGCTCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGC-GGAGGTCTTGAGTTTGA
* * * *
179039 CTCTCAACAAAAGCATAGTGTTACTCTCTCATCTTCAATATATCTCTCTTATTCTCTAATTCATG
259 CTCTCAACAAGAGCATGGTGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATG
*
179104 TTACATTCATCAGTTAGCTCTCGTAGCTCAGTTGGTTAGAGCACTCGTTTAGTAAGCGGGAGGTC
324 TTACATTCATCA---A----T--TAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTC
** * * *
179169 TTGAGTTTGACTATCAACAAGAGCATGGTGTTAGTCTCTTATCTTCAATATATATCTCTTTTATG
380 TTGAGTTCAACTCTCAACAAGAGCATAGTGTTACTCTCTTATCTTC-A-ATATATCTCTTTTATG
* * * *
179234 CTCTAACTCATGTTACATTCATCAATTAGCTATTGTAGCTCAGTTGGTTAGAGCACCCATTTAGT
443 ATCCAACCCATGTTACATTCATCAATTAGCTATCGTAGCTCAGTTGGTTAGAGCACCCATTTAGT
* *
179299 AAGCGGGAGGTCTTGAGTTCAACTCTCAACAAAAACATAGTG
508 AAGCGGAAGGTCTTGAGTTCAACTCTCAACAAAAACATAGTA
*
179341 TTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGCTG
1 TTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGCTC
* ** * *
179406 TTGTAGCTTAGTTGGTCAGAGCACTTGTTTAGTAAGCAGGAGGTCTTGAGTTCAACTCGCAACAA
66 TCGTAGCTTAGTTGGTCAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAACAA
* * *
179471 AATCATGGTGTCACTCTCTCTTCTTCAATATATATATCTTATTCTCTAACTCATGTTACATTCAT
131 AA-CATAGTGTTACTCTCTCTTCTTCAATATATATCTCTTATTCTCTAACTCATGTTACATTCAT
* * * *
179536 CAGGTAGCTCTTGTAGCTCAGTTGGTTAGAGTACCCGTTTAGTAAGCGAGAGGTATTGAGTTTGA
195 CAGTTAGCTCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCG-GAGGTCTTGAGTTTGA
* *
179601 CTCTCAACAAGAGCATGGTGTTACTCTCACATCTTCAATATATATCTCTTTTATGCTCTAACTCA
259 CTCTCAACAAGAGCATGGTGTTACTCTCTCATCTTC-A-ATATATCTCTCTTATGCTCTAACTCA
* *
179666 TGTTACATTCATCAATTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGTGGGAGGTCTTGAATT
322 TGTTACATTCATCAATTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTT
* *
179731 CAACTCTCAACAAGATCATAGTGTTACTCTCTTATCTTCAATATATCTCTTTTATTATCCAACCC
387 CAACTCTCAACAAGAGCATAGTGTTACTCTCTTATCTTCAATATATCTCTTTTATGATCCAACCC
* * * * *
179796 ATGTTACATTCATCAGTTAGCTCTCGTAGCTTAGTTGGTTAGAGCACTCGTTTAGTAAGCGGAAG
452 ATGTTACATTCATCAATTAGCTATCGTAGCTCAGTTGGTTAGAGCACCCATTTAGTAAGCGGAAG
** * *
179861 GTCTTGAGTTTGACTCTCAACAAGAGCAT-GATA
517 GTCTTGAGTTCAACTCTCAACAAAAACATAG-TA
* *
179894 TTACTATCTCATCTTCAATATATCTATCTTATGCTCTAACTCATGTTACATTCATCAATTAGCTC
1 TTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGCTC
* * *
179959 TCGTAGCATAGTTGGTCAAAGCACCCGTTTAGTAAGTGGGAGGTCTTGAGTTCAACTCTCAACAA
66 TCGTAGCTTAGTTGGTCAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAACAA
* * * *
180024 GAGAGTAGTGTTACTTTCT-TATCTTCAATATATCTCTCTTATTCTCTAACTCATGTTACATTCA
131 AACA-TAGTGTTACTCTCTCT-TCTTCAATATATATCTCTTATTCTCTAACTCATGTTACATTCA
* * * * * * *
180088 TCAATTAACTCTCGTAGCTCAGATGGTTAGAGCACCTGTTTAGTAATCTGGAAGTCTTGAGCTTG
194 TCAGTTAGCTCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGC-GGAGGTCTTGAGTTTG
* * *
180153 ACTCTAAACAAGAGCATGATGTTACTCTCTCATCTTCAATATATCTATCTTATGCTCTAACTCAT
258 ACTCTCAACAAGAGCATGGTGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCAT
* *
180218 GTTACATTCATCAATTAGTTCTCGTAGCTTAGTTGGTTATAGCACCTGTTTAGTAAGCGGGAGGT
323 GTTACATTCATCAATTAG----C-T--C--AGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGT
* *
180283 CTTGAGTTCAACTCTCAACAAGAGCATAGTGTTACTCTCTCATCTTTAATA
379 CTTGAGTTCAACTCTCAACAAGAGCATAGTGTTACTCTCTTATCTTCAATA
180334 GAATGCTTAA
Statistics
Matches: 876, Mismatches: 98, Indels: 37
0.87 0.10 0.04
Matches are distributed among these distances:
551 43 0.05
552 4 0.00
553 363 0.41
554 2 0.00
555 80 0.09
556 1 0.00
557 1 0.00
558 1 0.00
559 15 0.02
560 80 0.09
561 127 0.14
562 121 0.14
563 1 0.00
564 37 0.04
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (549 bp):
TTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTTACATTCATCAATTAGCTC
TCGTAGCTTAGTTGGTCAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAACTCTCAACAA
AACATAGTGTTACTCTCTCTTCTTCAATATATATCTCTTATTCTCTAACTCATGTTACATTCATC
AGTTAGCTCTCGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGAGGTCTTGAGTTTGACT
CTCAACAAGAGCATGGTGTTACTCTCTCATCTTCAATATATCTCTCTTATGCTCTAACTCATGTT
ACATTCATCAATTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCAAC
TCTCAACAAGAGCATAGTGTTACTCTCTTATCTTCAATATATCTCTTTTATGATCCAACCCATGT
TACATTCATCAATTAGCTATCGTAGCTCAGTTGGTTAGAGCACCCATTTAGTAAGCGGAAGGTCT
TGAGTTCAACTCTCAACAAAAACATAGTA
Found at i:181767 original size:2 final size:2
Alignment explanation
Indices: 181754--181784 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
181744 AACTATTAAT
*
181754 TA TA TC 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 T
181785 CGTCACTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:181959 original size:21 final size:20
Alignment explanation
Indices: 181931--181969 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
181921 TACAATCAAA
* *
181931 TAAAAAAATTGTAATATATT
1 TAAAAAAACTATAATATATT
181951 TAAACAAAACTATAATATA
1 TAAA-AAAACTATAATATA
181970 ATAAGAGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAAAAAACTATAATATATT
Found at i:182966 original size:21 final size:23
Alignment explanation
Indices: 182918--182967 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
182908 TAACTAAAAC
*
182918 TAATAATAAAATGAATAAAATTA
1 TAATTATAAAATGAATAAAATTA
*
182941 -GATTATAAAAT-AAT-AAATTA
1 TAATTATAAAATGAATAAAATTA
182961 TAATTAT
1 TAATTAT
182968 TATCAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 6 0.26
21 8 0.35
22 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
TAATTATAAAATGAATAAAATTA
Found at i:183521 original size:14 final size:16
Alignment explanation
Indices: 183485--183521 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
183475 TATTAATGTA
183485 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
183502 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
183517 T-AATA
1 TGAATA
183522 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:184186 original size:130 final size:130
Alignment explanation
Indices: 183982--184229 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
183972 AATTTTCTTC
* *
183982 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
184047 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
184112 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
184177 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
184230 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:184677 original size:35 final size:35
Alignment explanation
Indices: 184627--184702 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
184617 AATTGAATTT
* *
184627 AATTGAATTATTTTGG-AATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTGA-GGTTTAGAATGA
184662 AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
184697 AATTGA
1 AATTGA
184703 GGGCTGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
Found at i:192564 original size:21 final size:21
Alignment explanation
Indices: 192540--192605 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
192530 TTTTACAAGC
192540 ACAATGGTCCAAGTTCATTAA
1 ACAATGGTCCAAGTTCATTAA
** *
192561 ACAAT--TCCAAGCACCTTGAA
1 ACAATGGTCCAAGTTCATT-AA
*
192581 AGAA-GGTCCAAGTTCATTAA
1 ACAATGGTCCAAGTTCATTAA
192601 ACAAT
1 ACAAT
192606 TCCAAGATCA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 9 0.27
20 10 0.30
21 14 0.42
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (21 bp):
ACAATGGTCCAAGTTCATTAA
Found at i:192571 original size:19 final size:19
Alignment explanation
Indices: 192547--192616 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
192537 AGCACAATGG
192547 TCCAAGTTCATTAAACAAT
1 TCCAAGTTCATTAAACAAT
** * * *
192566 TCCAAGCACCTTGAAAGAAGG
1 TCCAAGTTCATT-AAACAA-T
192587 TCCAAGTTCATTAAACAAT
1 TCCAAGTTCATTAAACAAT
*
192606 TCCAAGATCAT
1 TCCAAGTTCAT
192617 AAAATGTATT
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
19 19 0.50
20 10 0.26
21 9 0.24
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (19 bp):
TCCAAGTTCATTAAACAAT
Found at i:201468 original size:34 final size:34
Alignment explanation
Indices: 201430--201498 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
201420 AAACTAAAAG
201430 TATGAAAGTGAGAGGACTAGAAAAGTTTTTCAAT
1 TATGAAAGTGAGAGGACTAGAAAAGTTTTTCAAT
*
201464 TATGAAAGTGAGAGGACTAGAATAGTTTTTCAAT
1 TATGAAAGTGAGAGGACTAGAAAAGTTTTTCAAT
201498 T
1 T
201499 CTGGTTGGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (34 bp):
TATGAAAGTGAGAGGACTAGAAAAGTTTTTCAAT
Found at i:202476 original size:31 final size:32
Alignment explanation
Indices: 202441--202518 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 32
202431 AAAATTTGTG
*
202441 TAAAATATTAATTTAAATCC-TAAACATTAGA
1 TAAAATATTAATTTAAACCCTTAAACATTAGA
* *
202472 TAAAATATCAATTT-AACCCTTAAACTTTAGA
1 TAAAATATTAATTTAAACCCTTAAACATTAGA
*
202503 TAAAATACTAATTTAA
1 TAAAATATTAATTTAA
202519 CCCATGAGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 4 0.10
31 35 0.88
32 1 0.03
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.36
Consensus pattern (32 bp):
TAAAATATTAATTTAAACCCTTAAACATTAGA
Found at i:203946 original size:26 final size:26
Alignment explanation
Indices: 203917--203975 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
203907 TTATAAGTTA
* * * *
203917 TATATATAAATTATGTTTATATGAAC
1 TATATATAAACTATATATATATAAAC
*
203943 TATATATAAACTATATATGTATAAAC
1 TATATATAAACTATATATATATAAAC
203969 TATATAT
1 TATATAT
203976 GCATAAACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (26 bp):
TATATATAAACTATATATATATAAAC
Found at i:203967 original size:15 final size:15
Alignment explanation
Indices: 203947--203988 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
203937 ATGAACTATA
203947 TATAAACTATATATG
1 TATAAACTATATATG
203962 TATAAACTATATATG
1 TATAAACTATATATG
*
203977 CATAAACT-TATA
1 TATAAACTATATA
203989 AACTATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (15 bp):
TATAAACTATATATG
Found at i:204157 original size:29 final size:29
Alignment explanation
Indices: 204117--204176 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
204107 TTTTTTTTTA
* *
204117 TTTGGGAATTTAGAGGGAAAATAGGAAAT
1 TTTGAGAATTTAAAGGGAAAATAGGAAAT
* *
204146 TTTGAGAATTTAAAGGGAAATTGGGAAAT
1 TTTGAGAATTTAAAGGGAAAATAGGAAAT
204175 TT
1 TT
204177 AGAGGGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (29 bp):
TTTGAGAATTTAAAGGGAAAATAGGAAAT
Found at i:204462 original size:12 final size:12
Alignment explanation
Indices: 204415--204465 Score: 84
Period size: 12 Copynumber: 4.2 Consensus size: 12
204405 ATATGTATAT
204415 ATGTATGTATGC
1 ATGTATGTATGC
* *
204427 ATGCATGTATGT
1 ATGTATGTATGC
204439 ATGTATGTATGC
1 ATGTATGTATGC
204451 ATGTATGTATGC
1 ATGTATGTATGC
204463 ATG
1 ATG
204466 CGTGCGTGCG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.41
Consensus pattern (12 bp):
ATGTATGTATGC
Found at i:204466 original size:4 final size:4
Alignment explanation
Indices: 204406--204461 Score: 76
Period size: 4 Copynumber: 14.0 Consensus size: 4
204396 TTTCTATATA
* * * *
204406 TATG TATA TATG TATG TATG CATG CATG TATG TATG TATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
204454 TATG TATG
1 TATG TATG
204462 CATGCGTGCG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:204471 original size:4 final size:4
Alignment explanation
Indices: 204464--204489 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
204454 TATGTATGCA
204464 TGCG TGCG TGCG TGCG TGCG TGCG TG
1 TGCG TGCG TGCG TGCG TGCG TGCG TG
204490 TGTGTATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.50, T:0.27
Consensus pattern (4 bp):
TGCG
Found at i:204507 original size:4 final size:4
Alignment explanation
Indices: 204492--204548 Score: 60
Period size: 4 Copynumber: 14.2 Consensus size: 4
204482 CGTGCGTGTG
* * * * * *
204492 TGTA TGTT TGTA TGTA TGTA TGTA TGTG TTTC TGCA TGTA TGTG TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
204540 TGTA TGTA T
1 TGTA TGTA T
204549 ATAAACTATA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.18, C:0.04, G:0.26, T:0.53
Consensus pattern (4 bp):
TGTA
Found at i:204851 original size:15 final size:15
Alignment explanation
Indices: 204826--204879 Score: 81
Period size: 15 Copynumber: 3.4 Consensus size: 15
204816 ATAAATTATG
204826 TATAGTATATATAAAC
1 TATA-TATATATAAAC
204842 TATATATATATATAACC
1 TATATATATATA-AA-C
204859 TATATATATATAAAC
1 TATATATATATAAAC
204874 TATATA
1 TATATA
204880 AAGTAAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.42
16 8 0.22
17 13 0.36
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:204983 original size:14 final size:14
Alignment explanation
Indices: 204955--205022 Score: 73
Period size: 14 Copynumber: 4.9 Consensus size: 14
204945 AGGTTTATAG
* *
204955 AAACCTTAAATCTT
1 AAACCATAAACCTT
*
204969 AAATCATAAACCTT
1 AAACCATAAACCTT
* *
204983 AAACCCTAAACTTT
1 AAACCATAAACCTT
* *
204997 AAACTATAAACATT
1 AAACCATAAACCTT
205011 AAACCATAAACC
1 AAACCATAAACC
205023 CTAATGAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (14 bp):
AAACCATAAACCTT
Found at i:204986 original size:7 final size:7
Alignment explanation
Indices: 204955--205022 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
204945 AGGTTTATAG
204955 AAACCTT
1 AAACCTT
*
204962 AAATCTT
1 AAACCTT
* *
204969 AAATCAT
1 AAACCTT
204976 AAACCTT
1 AAACCTT
*
204983 AAACCCT
1 AAACCTT
*
204990 AAACTTT
1 AAACCTT
204997 AAA-CTAT
1 AAACCT-T
*
205004 AAACATT
1 AAACCTT
*
205011 AAACCAT
1 AAACCTT
205018 AAACC
1 AAACC
205023 CTAATGAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
6 1 0.02
7 46 0.96
8 1 0.02
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (7 bp):
AAACCTT
Found at i:205856 original size:20 final size:19
Alignment explanation
Indices: 205833--205902 Score: 106
Period size: 18 Copynumber: 3.7 Consensus size: 19
205823 AATATGTATG
* *
205833 TATAAACCATGTATAGTATA
1 TATAAACTATATATA-TATA
205853 TATAAACTATATATATATA
1 TATAAACTATATATATATA
205872 TAT-AACTATATATATATA
1 TATAAACTATATATATATA
205890 TATAAACTATATA
1 TATAAACTATATA
205903 AAATATATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 18 0.38
19 16 0.34
20 13 0.28
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (19 bp):
TATAAACTATATATATATA
Found at i:205865 original size:18 final size:17
Alignment explanation
Indices: 205844--205902 Score: 82
Period size: 17 Copynumber: 3.2 Consensus size: 17
205834 ATAAACCATG
205844 TATAGTATATATAAACTA
1 TATA-TATATATAAACTA
205862 TATATATATATATAACTATA
1 TATATATATATA-AAC--TA
205882 TATATATATATAAACTA
1 TATATATATATAAACTA
205899 TATA
1 TATA
205903 AAATATATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
17 14 0.37
18 7 0.18
19 3 0.08
20 14 0.37
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (17 bp):
TATATATATATAAACTA
Found at i:205896 original size:37 final size:36
Alignment explanation
Indices: 205844--205932 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 36
205834 ATAAACCATG
*
205844 TATAGTATATATAAACTATATATATATATATAACTATA
1 TATAGTATATATAAACTATATA-AAATATATAACT-TA
*
205882 TATA-TATATATAAACTATATAAAATATATTACTTA
1 TATAGTATATATAAACTATATAAAATATATAACTTA
* *
205917 TATAGTTTATAAAAAC
1 TATAGTATATATAAAC
205933 ACTATGCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 6 0.13
36 19 0.41
37 17 0.37
38 4 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (36 bp):
TATAGTATATATAAACTATATAAAATATATAACTTA
Found at i:205908 original size:18 final size:18
Alignment explanation
Indices: 205844--205910 Score: 91
Period size: 18 Copynumber: 3.7 Consensus size: 18
205834 ATAAACCATG
*
205844 TATAGTATATATAAACTA
1 TATAATATATATAAACTA
205862 TAT-ATATATATATAACTA
1 TATAATATATATA-AACTA
205880 TATATATATATATAAACTA
1 TATA-ATATATATAAACTA
*
205899 TATAAAATATAT
1 TATAATATATAT
205911 TACTTATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.18
18 18 0.41
19 9 0.20
20 9 0.20
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (18 bp):
TATAATATATATAAACTA
Found at i:205910 original size:2 final size:2
Alignment explanation
Indices: 205844--205893 Score: 57
Period size: 2 Copynumber: 24.0 Consensus size: 2
205834 ATAAACCATG
*
205844 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA -A CTA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
205886 TA TA TA TA
1 TA TA TA TA
205894 AACTATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 1 0.02
2 37 0.88
3 4 0.10
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:206356 original size:25 final size:22
Alignment explanation
Indices: 206337--206376 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
206327 TAATTTATAT
206337 TTAAATAATTTTATTA-AATTA
1 TTAAATAATTTTATTATAATTA
206358 TTAAATAATTTTA-TATAAT
1 TTAAATAATTTTATTATAAT
206377 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAATAATTTTATTATAATTA
Found at i:206407 original size:20 final size:21
Alignment explanation
Indices: 206379--206433 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
206369 TATATAATAT
*
206379 GTATGTATAAAC-CATGTATA
1 GTATATATAAACACATGTATA
*
206399 GTATATATAAACTATATATGTATA
1 GTATATATAAAC---ACATGTATA
206423 GTATATATAAA
1 GTATATATAAA
206434 TATATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.38
24 18 0.62
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.38
Consensus pattern (21 bp):
GTATATATAAACACATGTATA
Found at i:206419 original size:24 final size:23
Alignment explanation
Indices: 206392--206440 Score: 89
Period size: 24 Copynumber: 2.1 Consensus size: 23
206382 TGTATAAACC
206392 ATGTATAGTATATATAAACTATAT
1 ATGTATAGTATATATAAA-TATAT
206416 ATGTATAGTATATATAAATATAT
1 ATGTATAGTATATATAAATATAT
206439 AT
1 AT
206441 AAACTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (23 bp):
ATGTATAGTATATATAAATATAT
Found at i:206524 original size:48 final size:49
Alignment explanation
Indices: 206434--206528 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 49
206424 TATATATAAA
* * **
206434 TATATATAAACTATATAAAATAAATTACTTATATAGTTTATAGAAACAC
1 TATACATAAACTATATAAAATAAATAAAGTATATAGTTTATAGAAACAC
*
206483 TATACATAAACTATATAAAGT-AATAAAGTATATAGTTTATAGAAAC
1 TATACATAAACTATATAAAATAAATAAAGTATATAGTTTATAGAAAC
206529 CGTAAACCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 22 0.54
49 19 0.46
ACGTcount: A:0.52, C:0.07, G:0.06, T:0.35
Consensus pattern (49 bp):
TATACATAAACTATATAAAATAAATAAAGTATATAGTTTATAGAAACAC
Found at i:206535 original size:7 final size:7
Alignment explanation
Indices: 206525--206555 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
206515 TAGTTTATAG
206525 AAACCGT
1 AAACCGT
206532 AAACCGT
1 AAACCGT
206539 AAACCGT
1 AAACCGT
*
206546 AAACCCT
1 AAACCGT
206553 AAA
1 AAA
206556 TTTTAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.48, C:0.29, G:0.10, T:0.13
Consensus pattern (7 bp):
AAACCGT
Found at i:207076 original size:16 final size:16
Alignment explanation
Indices: 207055--207125 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
207045 CGGATTATTT
207055 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
207071 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* * *
207087 ACAAGTTAGGTTGAAA
1 ACAGGTCAGGTTAAAA
* * *
207103 ATAGGTCAGATTGAAA
1 ACAGGTCAGGTTAAAA
207119 ACAGGTC
1 ACAGGTC
207126 GGGTAATACC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:209833 original size:30 final size:30
Alignment explanation
Indices: 209799--209879 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
209789 GATCTAGGGG
*
209799 TTAAATTGATTTTTATCTAAAGTGTAAGGT
1 TTAAATTGATTTTTATCTAAAATGTAAGGT
* * *
209829 TTAAATTGATATTTTACCTAAAATTTAGGGT
1 TTAAATTGAT-TTTTATCTAAAATGTAAGGT
*
209860 TTAAATT--TATTTATCTAAAA
1 TTAAATTGATTTTTATCTAAAA
209880 AGAATAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 10 0.23
29 1 0.02
30 10 0.23
31 23 0.52
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (30 bp):
TTAAATTGATTTTTATCTAAAATGTAAGGT
Found at i:210827 original size:51 final size:51
Alignment explanation
Indices: 210772--210873 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
210762 TGGCGAGTGC
210772 AGGAAATAGATATGTATGCCATTGACGAAATTCCTACGTCGGCTTATTAGT
1 AGGAAATAGATATGTATGCCATTGACGAAATTCCTACGTCGGCTTATTAGT
210823 AGGAAATAGATATGTATGCCATTGACGAAATTCCTACGTCGGCTTATTAGT
1 AGGAAATAGATATGTATGCCATTGACGAAATTCCTACGTCGGCTTATTAGT
210874 CTTACATATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (51 bp):
AGGAAATAGATATGTATGCCATTGACGAAATTCCTACGTCGGCTTATTAGT
Found at i:210853 original size:24 final size:24
Alignment explanation
Indices: 210774--210853 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
210764 GCGAGTGCAG
210774 GAAATAGATATGTATGCCATTGAC
1 GAAATAGATATGTATGCCATTGAC
*** * ** * *
210798 GAAATTCCTACGTCGGCTTATTAGTAG
1 GAAATAGATATGTATGC-CATT-G-AC
210825 GAAATAGATATGTATGCCATTGAC
1 GAAATAGATATGTATGCCATTGAC
210849 GAAAT
1 GAAAT
210854 TCCTACGTCG
Statistics
Matches: 37, Mismatches: 16, Indels: 6
0.63 0.27 0.10
Matches are distributed among these distances:
24 17 0.46
25 4 0.11
26 4 0.11
27 12 0.32
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (24 bp):
GAAATAGATATGTATGCCATTGAC
Found at i:224831 original size:8 final size:8
Alignment explanation
Indices: 224807--224841 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
224797 AAAAATTGTG
*
224807 TGTATGTA
1 TGTATGCA
*
224815 TGCATGCA
1 TGTATGCA
224823 TGTATGCA
1 TGTATGCA
224831 TGTATGCA
1 TGTATGCA
224839 TGT
1 TGT
224842 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (8 bp):
TGTATGCA
Found at i:224846 original size:2 final size:2
Alignment explanation
Indices: 224839--225142 Score: 248
Period size: 2 Copynumber: 152.0 Consensus size: 2
224829 CATGTATGCA
* *
224839 TG TG TG TG TG TG TG TG AG TG TG TG AG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * ** ** **
224881 TG TG TG TG TG CG CG CG CC TG TG TG TG TG CC TG TG TG TG TG CC
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
** * **
224923 TG TG TG TG TG CC TC TG TG TG TG TG TG TG TG TG CC TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
** ** * *
224965 TG CC TG TG TG TG TG TG TG TG TG CC TG TG TA TG TG TG TG TG TA
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* ** *
225007 TG TG TG CG CC TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * ** ** ** **
225049 CG CG CC TG TG TG TG TG CA TG TG TG TG TG CC TG TG TG TG TG CC
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
** *
225091 TG TG TG TG CA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG GG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
225133 TG GG TG TG TG
1 TG TG TG TG TG
225143 CCTCATGAAG
Statistics
Matches: 238, Mismatches: 64, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 238 1.00
ACGTcount: A:0.02, C:0.11, G:0.45, T:0.42
Consensus pattern (2 bp):
TG
Found at i:227487 original size:4 final size:4
Alignment explanation
Indices: 227478--227547 Score: 131
Period size: 4 Copynumber: 17.5 Consensus size: 4
227468 GTAAGCCTTA
*
227478 GTCT GTCT GTCT GTCT ATCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
227526 GTCT GTCT GTCT GTCT GTCT GT
1 GTCT GTCT GTCT GTCT GTCT GT
227548 ATGTATGTAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.01, C:0.24, G:0.24, T:0.50
Consensus pattern (4 bp):
GTCT
Found at i:227645 original size:4 final size:4
Alignment explanation
Indices: 227636--227673 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
227626 GTAAGCCTTA
227636 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GT
227674 ATGTATGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.00, C:0.24, G:0.26, T:0.50
Consensus pattern (4 bp):
GTCT
Found at i:227678 original size:4 final size:4
Alignment explanation
Indices: 227671--229902 Score: 4310
Period size: 4 Copynumber: 563.5 Consensus size: 4
227661 TCTGTCTGTC
227671 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
227719 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
227767 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
227815 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
227863 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
227911 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
227959 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228007 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228055 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228103 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228151 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228199 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228247 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228295 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228343 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228390 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228437 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228485 TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA --TA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228529 TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228575 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228622 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228670 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228718 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA --TA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228764 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228812 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228860 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228908 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
228956 TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229003 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA --TA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229049 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229097 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229145 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229193 TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229239 TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229285 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229333 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229381 TGTA TGTA TGTA TGTA TGTA TGTA TG-A TGTA TGTA TGTA TGT- TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229427 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229475 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229523 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229571 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229619 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229667 TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229713 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229761 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229809 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
229857 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
229903 ATTAGAAAGA
Statistics
Matches: 2206, Mismatches: 0, Indels: 44
0.98 0.00 0.02
Matches are distributed among these distances:
2 16 0.01
3 18 0.01
4 2172 0.98
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:227707 original size:158 final size:158
Alignment explanation
Indices: 227411--227726 Score: 551
Period size: 158 Copynumber: 2.0 Consensus size: 158
227401 CTTCGCTCGG
227411 GGGCGGGAATTCCCCCTAGTAGGAGTAGTAGTCTTGGGCAGAGATTAGCAATCATCCGTAAGCCT
1 GGGCGGGAATTCCCCCTAGTAGGAGTAGTAGTCTTGGGCAGAGATTAGCAATCATCCGTAAGCCT
* * * * * * *
227476 TAGTCTGTCTGTCTGTCTATCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC
66 TAGTCTGTCTGTCTGTCTATCTGTCTGTCTGTCTGTCTGTATGTATGTATGTATGTATGTATGTA
*
227541 TGTCTGTATGTATGTATGTATGTATGTA
131 TGTATGTATGTATGTATGTATGTATGTA
227569 GGGCGGGAATTCCCCCTAGTAGGAGTAGTAGTCTTGGGCAGAGATTAGCAATCATCCGTAAGCCT
1 GGGCGGGAATTCCCCCTAGTAGGAGTAGTAGTCTTGGGCAGAGATTAGCAATCATCCGTAAGCCT
*
227634 TAGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTATGTATGTATGTATGTATGTATGTA
66 TAGTCTGTCTGTCTGTCTATCTGTCTGTCTGTCTGTCTGTATGTATGTATGTATGTATGTATGTA
227699 TGTATGTATGTATGTATGTATGTATGTA
131 TGTATGTATGTATGTATGTATGTATGTA
227727 TGTATGTATG
Statistics
Matches: 149, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
158 149 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (158 bp):
GGGCGGGAATTCCCCCTAGTAGGAGTAGTAGTCTTGGGCAGAGATTAGCAATCATCCGTAAGCCT
TAGTCTGTCTGTCTGTCTATCTGTCTGTCTGTCTGTCTGTATGTATGTATGTATGTATGTATGTA
TGTATGTATGTATGTATGTATGTATGTA
Found at i:230733 original size:3 final size:3
Alignment explanation
Indices: 230725--230817 Score: 141
Period size: 3 Copynumber: 31.0 Consensus size: 3
230715 ATTAATTTAT
* * *
230725 TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
230773 TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
230818 AATATATATA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:230742 original size:24 final size:24
Alignment explanation
Indices: 230715--230818 Score: 122
Period size: 24 Copynumber: 4.2 Consensus size: 24
230705 TTTTACCCAT
230715 ATTAAT-TTATTTATTATTATTATA
1 ATTAATATTA-TTATTATTATTATA
230739 ATT-ATAATTATTATTATTATTATA
1 ATTAAT-ATTATTATTATTATTATA
*
230763 ATTATTATTATTATTATTATTATTATT
1 ATTA--A-TATTATTATTATTATTATA
* *
230790 ATAAATATTATTATTATTATTATT
1 ATTAATATTATTATTATTATTATA
230814 ATTAA
1 ATTAA
230819 ATATATATAT
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.03
24 43 0.61
25 4 0.06
27 21 0.30
28 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTAATATTATTATTATTATTATA
Found at i:230953 original size:15 final size:16
Alignment explanation
Indices: 230933--230974 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
230923 CCTAATCCCT
230933 AGCCGCCTCT-AATCC
1 AGCCGCCTCTGAATCC
**
230948 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGAATCC
230964 AGCCGCCTCTG
1 AGCCGCCTCTG
230975 CCTCCACCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.50, G:0.19, T:0.19
Consensus pattern (16 bp):
AGCCGCCTCTGAATCC
Found at i:230966 original size:16 final size:16
Alignment explanation
Indices: 230945--230984 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
230935 CCGCCTCTAA
230945 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
230961 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
230977 TCCA-CCGC
1 TCCAGCCGC
230985 TGCCACGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.07, C:0.57, G:0.17, T:0.17
Consensus pattern (16 bp):
TCCAGCCGCCTCTGCC
Found at i:232294 original size:24 final size:22
Alignment explanation
Indices: 232266--232310 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
232256 TATTCTGGTA
232266 TTTTAAAATTTAATAATTAAATTT
1 TTTTAAAATTTAAT--TTAAATTT
**
232290 TTTTATTATTTAATTTAAATT
1 TTTTAAAATTTAATTTAAATT
232311 AATATTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAAATTTAATTTAAATTT
Found at i:232909 original size:28 final size:27
Alignment explanation
Indices: 232878--232931 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
232868 TAATTCTTTC
* *
232878 TTTTCAAAATTTTTATATTTATTTATTA
1 TTTTCAAAATATTTATATGT-TTTATTA
*
232906 TTTTCATAATATTTATATGTTTTATT
1 TTTTCAAAATATTTATATGTTTTATT
232932 TTATTTGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTCAAAATATTTATATGTTTTATTA
Found at i:232936 original size:18 final size:18
Alignment explanation
Indices: 232886--232937 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
232876 TCTTTTCAAA
232886 ATTTTTATATTTATTTATT
1 ATTTTTAT-TTTATTTATT
* **
232905 ATTTTCATAATATTTA-T
1 ATTTTTATTTTATTTATT
232922 ATGTTTTATTTTATTT
1 AT-TTTTATTTTATTT
232938 GCAAGTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 3 0.12
18 16 0.62
19 7 0.27
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTATTTTATTTATT
Found at i:243603 original size:7 final size:7
Alignment explanation
Indices: 243570--243623 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
243560 ATTATGCTTG
243570 AAAAAGA
1 AAAAAGA
*
243577 AAGAAAAA
1 AA-AAAGA
*
243585 TAAAAATA
1 -AAAAAGA
243593 AAAAAG-
1 AAAAAGA
*
243599 GAAAAGA
1 AAAAAGA
243606 AAAAAGA
1 AAAAAGA
243613 AAAAAGA
1 AAAAAGA
243620 AAAA
1 AAAA
243624 GGGGGTCAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 5 0.13
7 24 0.62
8 8 0.21
9 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (7 bp):
AAAAAGA
Found at i:243603 original size:14 final size:14
Alignment explanation
Indices: 243570--243623 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 14
243560 ATTATGCTTG
*
243570 AAAAAGAAAGAAAAA
1 AAAAAGAAA-AAAGA
*
243585 TAAAAATAAAAAAG-
1 -AAAAAGAAAAAAGA
*
243599 GAAAAGAAAAAAGA
1 AAAAAGAAAAAAGA
243613 AAAAAGAAAAA
1 AAAAAGAAAAA
243624 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 11 0.34
14 10 0.31
15 3 0.09
16 8 0.25
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:243609 original size:20 final size:20
Alignment explanation
Indices: 243576--243624 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
243566 CTTGAAAAAG
* *
243576 AAAGAAAAA-TAAAAATAAA
1 AAAGAAAAAGAAAAAAGAAA
*
243595 AAAGGAAAAGAAAAAAGAAA
1 AAAGAAAAAGAAAAAAGAAA
243615 AAAGAAAAAG
1 AAAGAAAAAG
243625 GGGGTCAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAGAAA
Done.