Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 130 of 167
Found at i:43544732 original size:43 final size:42
Alignment explanation
Indices: 43544635--43544736 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 42
43544625 ATCGAGATAT
* *
43544635 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTAA
1 GATTACATGTAAGACCATGGCTGGGACATTGGCATCG-ATTAA
43544678 GATTACATGTAAGACCATGGCTGGGACATTGGCATCG-TTAA
1 GATTACATGTAAGACCATGGCTGGGACATTGGCATCGATTAA
* *
43544719 TCGATTTCGTGTAAGACC
1 --GATTACATGTAAGACC
43544737 TTGTCCGAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
41 4 0.08
43 49 0.92
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
GATTACATGTAAGACCATGGCTGGGACATTGGCATCGATTAA
Found at i:43549814 original size:112 final size:109
Alignment explanation
Indices: 43549683--43550000 Score: 399
Period size: 111 Copynumber: 2.9 Consensus size: 109
43549673 ACACTAGAGG
* * * * *
43549683 CATTTAAAAAAAAATTGGGTGCTGGCAAATAGATGGCCGACACTAAGTATATTTTTCTGCTCTCA
1 CATTT-AAAAAAAATTGGGTGCTGGCAAGTAGATGGCCGGCACCAAGTATATTTTTCGGCTCCCA
*
43549748 AGGCTTTTTTTTTTTTACTTTGGGACACTGATAGCCGGCACCAATGT
65 AGGC--TTTTTTTTTTACTTTGGGACACTGATAGCCAGCACCAATGT
*
43549795 CATTTTTAAAAAAAA-TGGGTGCTGGCAAGTAGATAGCCGGCACCAAGTATATGTTTT-GGCTCC
1 CA--TTTAAAAAAAATTGGGTGCTGGCAAGTAGATGGCCGGCACCAAGTATAT-TTTTCGGCTCC
* * *
43549858 CAAGACTTTTTTTTTTACTTTGGGACACTGATGGCCAGCACCGATGT
63 CAAGGCTTTTTTTTTTACTTTGGGACACTGATAGCCAGCACCAATGT
* *
43549905 CATTTAAAAAAAATTTTGGGTGCGGGCCAGTAGATGGCCGGCACCAAGTATA-TTTTCGGCTCCC
1 CATTTAAAAAAAA--TTGGGTGCTGGCAAGTAGATGGCCGGCACCAAGTATATTTTTCGGCTCCC
* * *
43549969 AATGCACTTTTTTTTTACTTTGGGACATTGAT
64 AAGGC-TTTTTTTTTTACTTTGGGACACTGAT
43550001 TGTTGGCACC
Statistics
Matches: 181, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
108 11 0.06
109 4 0.02
110 50 0.28
111 57 0.31
112 44 0.24
113 12 0.07
114 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (109 bp):
CATTTAAAAAAAATTGGGTGCTGGCAAGTAGATGGCCGGCACCAAGTATATTTTTCGGCTCCCAA
GGCTTTTTTTTTTACTTTGGGACACTGATAGCCAGCACCAATGT
Found at i:43554432 original size:26 final size:26
Alignment explanation
Indices: 43554412--43554469 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
43554402 CCCGATATAT
43554412 GGCTCTTCATGAGCTTCCCGATTAAA
1 GGCTCTTCATGAGCTTCCCGATTAAA
** ** *
43554438 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTCTTCATGAGCTTCCCGATTAAA
43554464 GGCTCT
1 GGCTCT
43554470 CCGGAGCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCCGATTAAA
Found at i:43560216 original size:21 final size:21
Alignment explanation
Indices: 43560193--43560231 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43560183 AAATTATCTT
43560193 TTTTTTC-CATTTAAATTTAA
1 TTTTTTCTCATTTAAATTTAA
*
43560213 TTTTTTCTCATTTCAATTT
1 TTTTTTCTCATTTAAATTT
43560232 TTTTCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTCTCATTTAAATTTAA
Found at i:43560216 original size:22 final size:22
Alignment explanation
Indices: 43560177--43560231 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
43560167 TCATTCCATT
* *
43560177 TCATTTAAA-TTATCTTTTTTT
1 TCATTTAAATTTATATTTTTTC
43560198 TCCATTTAAATTTA-ATTTTTTC
1 T-CATTTAAATTTATATTTTTTC
*
43560220 TCATTTCAATTT
1 TCATTTAAATTT
43560232 TTTTCATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.38
22 15 0.52
23 3 0.10
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (22 bp):
TCATTTAAATTTATATTTTTTC
Found at i:43560234 original size:18 final size:18
Alignment explanation
Indices: 43560191--43560287 Score: 58
Period size: 18 Copynumber: 5.2 Consensus size: 18
43560181 TTAAATTATC
*
43560191 TTTTTTTTC-CATTTAAA
1 TTTTTTTTCTCATTTCAA
43560208 TTTAATTTTTTCTCATTTCAA
1 -TT--TTTTTTCTCATTTCAA
*
43560229 -TTTTTTTCAT-ATAGCTCATA
1 TTTTTTTTC-TCAT--TTCA-A
* *
43560249 TTTTTTTTTTCATTTCAG
1 TTTTTTTTCTCATTTCAA
43560267 TTTTTGTTT-TCATTTCAA
1 TTTTT-TTTCTCATTTCAA
43560285 TTT
1 TTT
43560288 ATAATTTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
17 9 0.14
18 19 0.30
19 10 0.16
20 9 0.14
21 16 0.25
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTTTTTCTCATTTCAA
Found at i:43560379 original size:28 final size:27
Alignment explanation
Indices: 43560312--43560382 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
43560302 TTTAAACTTC
* *
43560312 CATTCCATTTCATAATAATTACAAATT
1 CATTTCATTTCATATTAATTACAAATT
43560339 CATTTCATTTCATATTAATTACAAATT
1 CATTTCATTTCATATTAATTACAAATT
43560366 ACATTTCATTTCATATT
1 -CATTTCATTTCATATT
43560383 TATTTAACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (27 bp):
CATTTCATTTCATATTAATTACAAATT
Found at i:43560398 original size:28 final size:28
Alignment explanation
Indices: 43560312--43560399 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 28
43560302 TTTAAACTTC
* *
43560312 CATTCCATTTCATAATAATTACAAA-TT
1 CATTTCATTTCATATTAATTACAAATTT
*
43560339 CATTTCATTTCATATTAATTACAAATTA
1 CATTTCATTTCATATTAATTACAAATTT
* *
43560367 CATTTCATTTCATATTTATTTA-ACATTT
1 CATTTCATTTCATA-TTAATTACAAATTT
43560395 CATTT
1 CATTT
43560400 ATTAATTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 23 0.43
28 24 0.45
29 6 0.11
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (28 bp):
CATTTCATTTCATATTAATTACAAATTT
Found at i:43560504 original size:16 final size:17
Alignment explanation
Indices: 43560477--43560511 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
43560467 GTAGTCTCAT
43560477 TTCAATTTTTTTTTCAA
1 TTCAATTTTTTTTTCAA
43560494 TTCAA-TTTTTTTTCAA
1 TTCAATTTTTTTTTCAA
43560510 TT
1 TT
43560512 TATTTCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCAATTTTTTTTTCAA
Found at i:43560595 original size:25 final size:24
Alignment explanation
Indices: 43560557--43560603 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
43560547 TCAATTACAT
*
43560557 TTTATTTAAATTTTGTCATATTTTA
1 TTTATTTAAATTTTCTCA-ATTTTA
**
43560582 TTTATTTATTTTTTCTCAATTT
1 TTTATTTAAATTTTCTCAATTT
43560604 AAATATCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTATTTAAATTTTCTCAATTTTA
Found at i:43560828 original size:17 final size:16
Alignment explanation
Indices: 43560806--43560837 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
43560796 CTTTTGTTTT
43560806 CATTTCATTTTAATTTC
1 CATTTCA-TTTAATTTC
43560823 CATTTCATTTAATTT
1 CATTTCATTTAATTT
43560838 ATCTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
CATTTCATTTAATTTC
Found at i:43560863 original size:45 final size:47
Alignment explanation
Indices: 43560796--43560912 Score: 132
Period size: 50 Copynumber: 2.5 Consensus size: 47
43560786 ATCCTTTCAA
* * * *
43560796 CTTTTGTTTT-CATTTCATTTTAA-TTTC-CATTTCATTTAATTTAT
1 CTTTTTTTTTCCATTTAAATTTAATTTTCTCATTTCATTTAAATTAT
*
43560840 CTTTTTTTTTCCATTTAAATTTAATTTCTTTCTCATTTTATTTAAATTAT
1 CTTTTTTTTTCCATTTAAATTTAA--T-TTTCTCATTTCATTTAAATTAT
*
43560890 CTTTTTTTTTCCATTTTAATTTA
1 CTTTTTTTTTCCATTTAAATTTA
43560913 TGTTTTTCCC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
44 9 0.15
45 11 0.18
49 4 0.07
50 37 0.61
ACGTcount: A:0.21, C:0.13, G:0.01, T:0.65
Consensus pattern (47 bp):
CTTTTTTTTTCCATTTAAATTTAATTTTCTCATTTCATTTAAATTAT
Found at i:43560905 original size:23 final size:23
Alignment explanation
Indices: 43560828--43560919 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 23
43560818 ATTTCCATTT
*
43560828 CATTTAATTTATCTTTTTTTTTC
1 CATTTAAATTATCTTTTTTTTTC
43560851 CATTTAAATTTAAT-TTCTTTCTCATTT-
1 CATTTAAA-TT-ATCTT-TTT-T--TTTC
*
43560878 TATTTAAATTATCTTTTTTTTTC
1 CATTTAAATTATCTTTTTTTTTC
* *
43560901 CATTTTAATTTATGTTTTT
1 CA-TTTAAATTATCTTTTT
43560920 CCCATATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
22 3 0.05
23 8 0.15
24 19 0.35
25 10 0.18
26 5 0.09
27 7 0.13
28 3 0.05
ACGTcount: A:0.22, C:0.11, G:0.01, T:0.66
Consensus pattern (23 bp):
CATTTAAATTATCTTTTTTTTTC
Found at i:43560918 original size:21 final size:21
Alignment explanation
Indices: 43560894--43560934 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
43560884 AATTATCTTT
* *
43560894 TTTTTTCCATTTTAATTTATG
1 TTTTTCCCATATTAATTTATG
43560915 TTTTTCCCATATTAATTTAT
1 TTTTTCCCATATTAATTTAT
43560935 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTCCCATATTAATTTATG
Found at i:43560933 original size:50 final size:50
Alignment explanation
Indices: 43560822--43560933 Score: 147
Period size: 50 Copynumber: 2.2 Consensus size: 50
43560812 ATTTTAATTT
* *
43560822 CCATTTCATTTAATTTATCTTTTTTTTTCCATTTAAATTTAATTTCTTTC
1 CCATTTAATTTAAATTATCTTTTTTTTTCCATTTAAATTTAATTTCTTTC
* * *
43560872 TCATTTTATTTAAATTATCTTTTTTTTTCCATTTTAATTT-ATGTT-TTTC
1 CCATTTAATTTAAATTATCTTTTTTTTTCCATTTAAATTTAAT-TTCTTTC
43560921 CCATATTAATTTA
1 CCAT-TTAATTTA
43560934 TATATTTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
49 9 0.17
50 45 0.83
ACGTcount: A:0.23, C:0.13, G:0.01, T:0.62
Consensus pattern (50 bp):
CCATTTAATTTAAATTATCTTTTTTTTTCCATTTAAATTTAATTTCTTTC
Found at i:43560941 original size:23 final size:21
Alignment explanation
Indices: 43560894--43560941 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
43560884 AATTATCTTT
* * *
43560894 TTTTTTCCATTTTAATTTATG
1 TTTTTCCCATATTAATTTATA
43560915 TTTTTCCCATATTAATTTATA
1 TTTTTCCCATATTAATTTATA
43560936 TATTTT
1 T-TTTT
43560942 AATCTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTCCCATATTAATTTATA
Found at i:43564530 original size:110 final size:111
Alignment explanation
Indices: 43564331--43564574 Score: 357
Period size: 110 Copynumber: 2.2 Consensus size: 111
43564321 TAGTGTTGGC
*
43564331 GCCATCAGTGTCCCAAAGTAAAAAAAAAAAGTGCATTGGGAGCTGAAAAATGTACTTGGTGCCGA
1 GCCATCAGTGTCCCAAAGT----AAAAAAAGTGCATTAGGAGCTGAAAAATGTACTTGGTGCCGA
* * * *
43564396 CCATCTACTGGCTAACATCGAAAATTTTTTTTTAAATGACACTGATGCCG
62 CCATCTACTGGCCAACACCCAAAATTTTTTTTTAAATGACACTGATGCAG
43564446 GCCATCAGTGTCCCAAAGT-AAAAAAGTGCATTAGGAG-TAGAAAAATGTACTTGGTGCCGACCA
1 GCCATCAGTGTCCCAAAGTAAAAAAAGTGCATTAGGAGCT-GAAAAATGTACTTGGTGCCGACCA
* *
43564509 TCTACTGGCCAGCACCCAAAATTTTTTTTTAAATGACACTGGTGCAG
65 TCTACTGGCCAACACCCAAAATTTTTTTTTAAATGACACTGATGCAG
*
43564556 GCCATCAGTATCCCAAAGT
1 GCCATCAGTGTCCCAAAGT
43564575 TAAATAATAA
Statistics
Matches: 120, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
109 1 0.01
110 100 0.83
115 19 0.16
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (111 bp):
GCCATCAGTGTCCCAAAGTAAAAAAAGTGCATTAGGAGCTGAAAAATGTACTTGGTGCCGACCAT
CTACTGGCCAACACCCAAAATTTTTTTTTAAATGACACTGATGCAG
Found at i:43565652 original size:26 final size:28
Alignment explanation
Indices: 43565623--43565678 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
43565613 GTTTTACAAA
*
43565623 ATAACTTTA-TATAAAA-TTATGTCTTT
1 ATAACTTTAGTATAAAAGTTACGTCTTT
43565649 ATAACTTTATGTATAAAAGTTACGTCTTT
1 ATAACTTTA-GTATAAAAGTTACGTCTTT
43565678 A
1 A
43565679 CAACACAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 9 0.35
28 7 0.27
29 10 0.38
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (28 bp):
ATAACTTTAGTATAAAAGTTACGTCTTT
Found at i:43567350 original size:18 final size:17
Alignment explanation
Indices: 43567326--43567360 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
43567316 ATTAAGAGTT
43567326 ATTTTTTTAACTTCATG
1 ATTTTTTTAACTTCATG
*
43567343 ATTTTTTTAACTTTATG
1 ATTTTTTTAACTTCATG
43567360 A
1 A
43567361 ATTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (17 bp):
ATTTTTTTAACTTCATG
Found at i:43569254 original size:23 final size:24
Alignment explanation
Indices: 43569215--43569260 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
43569205 ATATTATGTG
**
43569215 ATTATATATAATTTATT-TTTAAT
1 ATTATATATAAAATATTGTTTAAT
43569238 ATTATATATAAAATATTGTTTAA
1 ATTATATATAAAATATTGTTTAA
43569261 AAATGTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTATATATAAAATATTGTTTAAT
Found at i:43569349 original size:18 final size:18
Alignment explanation
Indices: 43569309--43569356 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
43569299 ATTTTTTTAA
* *
43569309 AAAAATAAAATATTATAT
1 AAAAATAAAAAAGTATAT
* *
43569327 GAAAATAAAAAAGTATCT
1 AAAAATAAAAAAGTATAT
43569345 AAAAATAAAAAA
1 AAAAATAAAAAA
43569357 AAGTATTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAAATAAAAAAGTATAT
Found at i:43569508 original size:19 final size:19
Alignment explanation
Indices: 43569464--43569530 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
43569454 TCATATATAA
43569464 TATATAAATAATT-AAAT-T
1 TATATAAA-AATTAAAATAT
*
43569482 TTTA-AAAAATTAAAATAT
1 TATATAAAAATTAAAATAT
* *
43569500 TATATAAAAATAAAAAAAT
1 TATATAAAAATTAAAATAT
*
43569519 TATCTAAAAATT
1 TATATAAAAATT
43569531 TTAAAAAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 4 0.10
17 7 0.17
18 7 0.17
19 22 0.55
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATAAAAATTAAAATAT
Found at i:43569547 original size:180 final size:180
Alignment explanation
Indices: 43569237--43569606 Score: 575
Period size: 180 Copynumber: 2.1 Consensus size: 180
43569227 TTATTTTTAA
* *
43569237 TATT-ATATATAAAATATTGTTTAAAAATGTAAACAAATCATATATAATATGTAAATAATTCAAT
1 TATTCATAAATAAAATATTGTTTAAAAATGTAAACAAATCATATATAATATATAAATAATTCAAT
* *
43569301 TTTTTTAAAAAAATAAAATATTATATGAAAATAAAAAAGTATCTAAAAATAAAAAAAAGTATTTA
66 ATTTTTAAAAAAATAAAATATTATATAAAAATAAAAAAGTATCTAAAAATAAAAAAAAGTATTTA
43569366 ACTTTTAAAAATTGAAAAAACTTAATTTTTCAAAAATACATTCTAATTTT
131 ACTTTTAAAAATTGAAAAAACTTAATTTTTCAAAAATACATTCTAATTTT
* *
43569416 TATTCATAAATAAAATATTGTTTAAAATTTTAAACAAATCATATATAATATATAAATAATT-AA-
1 TATTCATAAATAAAATATTGTTTAAAAATGTAAACAAATCATATATAATATATAAATAATTCAAT
* * **
43569479 ATTTTTAAAAAATTAAAATATTATATAAAAATAAAAAAATTATCTAAAAATTTTAAAAAAGTATT
66 ATTTTTAAAAAAATAAAATATTATATAAAAAT-AAAAAAGTATCTAAAAA-TAAAAAAAAGTATT
* **
43569544 TAACTTTTAAAATTTGAAAAAACTTAATTTTTCAAAAATGTATTCTAATTTT
129 TAACTTTTAAAAATTGAAAAAACTTAATTTTTCAAAAATACATTCTAATTTT
*
43569596 TTTTCATAAAT
1 TATTCATAAAT
43569607 TTTAATTTTT
Statistics
Matches: 174, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
178 29 0.17
179 22 0.13
180 123 0.71
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (180 bp):
TATTCATAAATAAAATATTGTTTAAAAATGTAAACAAATCATATATAATATATAAATAATTCAAT
ATTTTTAAAAAAATAAAATATTATATAAAAATAAAAAAGTATCTAAAAATAAAAAAAAGTATTTA
ACTTTTAAAAATTGAAAAAACTTAATTTTTCAAAAATACATTCTAATTTT
Found at i:43569804 original size:23 final size:23
Alignment explanation
Indices: 43569766--43569836 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 23
43569756 TTTTTATATA
43569766 ATATTT-TA-ATTTTTAAACTTT
1 ATATTTATATATTTTTAAACTTT
*
43569787 ATATTTATATATTTTTAAATTTT
1 ATATTTATATATTTTTAAACTTT
** *
43569810 ATA-AAATATATTTTTTAACTTT
1 ATATTTATATATTTTTAAACTTT
43569832 -TATTT
1 ATATTT
43569837 TTTTGAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
21 8 0.20
22 17 0.43
23 15 0.38
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTTATATATTTTTAAACTTT
Found at i:43569818 original size:22 final size:23
Alignment explanation
Indices: 43569774--43569834 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
43569764 TAATATTTTA
* **
43569774 ATTTTTAAACTTTATATTTATAT
1 ATTTTTAAATTTTATATAAATAT
43569797 ATTTTTAAATTTTATA-AAATAT
1 ATTTTTAAATTTTATATAAATAT
*
43569819 ATTTTTTAACTTTTAT
1 A-TTTTTAAATTTTAT
43569835 TTTTTTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 5 0.15
23 28 0.85
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTTAAATTTTATATAAATAT
Found at i:43570421 original size:17 final size:17
Alignment explanation
Indices: 43570399--43570486 Score: 65
Period size: 14 Copynumber: 5.0 Consensus size: 17
43570389 CTTGGGCAGT
43570399 AGAAGAATAAGAGAAAA
1 AGAAGAATAAGAGAAAA
43570416 AGAAGAATAAGAGAAGAAACAA
1 AGAAGAAT-A-AG-AG-AA-AA
* *
43570438 AGAAGAAGAATAAGAAAA
1 AGAAGAATAA-GAGAAAA
* *
43570456 AGAAGAGTATGAG---A
1 AGAAGAATAAGAGAAAA
43570470 AGAAGAATAAGAGAAAA
1 AGAAGAATAAGAGAAAA
43570487 TGGAAGGAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
14 12 0.22
17 11 0.20
18 10 0.19
19 4 0.07
20 5 0.09
21 3 0.06
22 9 0.17
ACGTcount: A:0.67, C:0.01, G:0.25, T:0.07
Consensus pattern (17 bp):
AGAAGAATAAGAGAAAA
Found at i:43572375 original size:51 final size:51
Alignment explanation
Indices: 43572278--43572379 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
43572268 ATAACTAAGT
* * * *
43572278 TATCCGGATGAAATATGAAGCTCTTGTTGAAACTAGAGCAATAAAGTAATA
1 TATCCGGATGAAATATGAAGCTCTTGTTGAAACCAAAACAACAAAGTAATA
* *
43572329 TATCCGGATGAAATATGAAGTTCTTGTTGAAGCCAAAACAACAAAGTAATA
1 TATCCGGATGAAATATGAAGCTCTTGTTGAAACCAAAACAACAAAGTAATA
43572380 ATTCTAGATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (51 bp):
TATCCGGATGAAATATGAAGCTCTTGTTGAAACCAAAACAACAAAGTAATA
Found at i:43573001 original size:23 final size:23
Alignment explanation
Indices: 43572963--43573009 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
43572953 AGGATTTATA
43572963 ATATTCCGGATGTGTTTGGGCTGG
1 ATATTCCGGATGTGTTTGGG-TGG
*
43572987 ATATTCTGG-TGTGTTTGGGTGG
1 ATATTCCGGATGTGTTTGGGTGG
43573009 A
1 A
43573010 ATCCGCGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 10 0.45
24 8 0.36
ACGTcount: A:0.13, C:0.09, G:0.38, T:0.40
Consensus pattern (23 bp):
ATATTCCGGATGTGTTTGGGTGG
Found at i:43574205 original size:12 final size:12
Alignment explanation
Indices: 43574188--43574243 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
43574178 TGGGAGAAAG
43574188 AAGATGAAGAGA
1 AAGATGAAGAGA
43574200 AAGATG-AGA-A
1 AAGATGAAGAGA
43574210 GAAGATGAAGAGA
1 -AAGATGAAGAGA
43574223 AAGATG-AGAAGA
1 AAGATGAAG-AGA
43574235 AA-ATGAAGA
1 AAGATGAAGA
43574244 AAAATCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 1 0.03
11 15 0.38
12 22 0.56
13 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.09
Consensus pattern (12 bp):
AAGATGAAGAGA
Found at i:43574213 original size:23 final size:23
Alignment explanation
Indices: 43574185--43574243 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
43574175 TTGTGGGAGA
43574185 AAGAAGATGAAGAGAAAGATGAG
1 AAGAAGATGAAGAGAAAGATGAG
43574208 AAGAAGATGAAGAGAAAGATGAG
1 AAGAAGATGAAGAGAAAGATGAG
*
43574231 AAGAAAATGAAGA
1 AAGAAGATGAAGA
43574244 AAAATCATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.08
Consensus pattern (23 bp):
AAGAAGATGAAGAGAAAGATGAG
Found at i:43574417 original size:30 final size:31
Alignment explanation
Indices: 43574364--43574432 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
43574354 ACTGTTAATC
* * *
43574364 AGTGACTATTTTGTCACTTTTTTATAACGTT-
1 AGTGACTGTTTTGTCAATTTTTTA-AAAGTTG
43574395 AGTGACTGTTTTGT-AATTTTTTAAAAGTTG
1 AGTGACTGTTTTGTCAATTTTTTAAAAGTTG
43574425 AGTGACTG
1 AGTGACTG
43574433 AAATAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 16 0.47
31 13 0.38
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.48
Consensus pattern (31 bp):
AGTGACTGTTTTGTCAATTTTTTAAAAGTTG
Found at i:43581194 original size:45 final size:45
Alignment explanation
Indices: 43581126--43581299 Score: 249
Period size: 45 Copynumber: 3.9 Consensus size: 45
43581116 AAGAGGTGGA
**
43581126 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
* * *
43581171 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
* * *
43581216 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
* * *
43581261 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCA
43581300 CCATGGCCGA
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 117 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
Found at i:43587836 original size:89 final size:86
Alignment explanation
Indices: 43587681--43587858 Score: 284
Period size: 89 Copynumber: 2.0 Consensus size: 86
43587671 CACCTCACCC
* * *
43587681 AATTATAGTTTTAATCTTCTATTTACGCAGTGGTGTATTTTTCTTAAGGTATGAACTTGACTTGG
1 AATTATAGTTTTAATCTTCTATTTACGCAGCGGTGTATTTTTCTTAAGGTATAAACTTGACCTGG
43587746 AATACCTATATTTTAAATAAATTA
66 -A-A-CTATATTTTAAATAAATTA
* *
43587770 AATTATAGTTTTAATCTTTTATTTATGCAGCGGTGTATTTTTCTTAAGGTATAAACTTGACCTGG
1 AATTATAGTTTTAATCTTCTATTTACGCAGCGGTGTATTTTTCTTAAGGTATAAACTTGACCTGG
43587835 AACTATATTTTAAATAAATTA
66 AACTATATTTTAAATAAATTA
43587856 AAT
1 AAT
43587859 ATGTACGGAA
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
86 22 0.26
87 1 0.01
88 1 0.01
89 60 0.71
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.45
Consensus pattern (86 bp):
AATTATAGTTTTAATCTTCTATTTACGCAGCGGTGTATTTTTCTTAAGGTATAAACTTGACCTGG
AACTATATTTTAAATAAATTA
Found at i:43587902 original size:19 final size:19
Alignment explanation
Indices: 43587880--43587942 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
43587870 ATTTATATTA
43587880 TTTTACTAAATTAATTAAT
1 TTTTACTAAATTAATTAAT
*
43587899 TTTTAC-ACAATATAATTTTAT
1 TTTTACTA-AAT-TAA-TTAAT
* * *
43587920 TTTGAATAAGTTAATTAAT
1 TTTTACTAAATTAATTAAT
43587939 TTTT
1 TTTT
43587943 GTCCAATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 6 0.18
21 10 0.29
22 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTTACTAAATTAATTAAT
Found at i:43587936 original size:40 final size:39
Alignment explanation
Indices: 43587877--43587961 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 39
43587867 AAAATTTATA
*
43587877 TTATTTTACTAAATTAATTAATTTTT-ACACAATATAATT
1 TTATTTTAATAAATTAATTAATTTTTGAC-CAATATAATT
* *
43587916 TTATTTTGAATAAGTTAATTAATTTTTGTCCAATATAATT
1 TTATTTT-AATAAATTAATTAATTTTTGACCAATATAATT
43587956 TCTATT
1 T-TATT
43587962 AGTAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
39 7 0.17
40 28 0.70
41 5 0.12
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (39 bp):
TTATTTTAATAAATTAATTAATTTTTGACCAATATAATT
Found at i:43594122 original size:22 final size:21
Alignment explanation
Indices: 43594084--43594135 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
43594074 TAAAAATTCC
* *
43594084 AAAATT-TATATTTTTTTGAA
1 AAAATTATAAATTTTTTTTAA
43594104 AAAATTATAAATTTTTTTTAA
1 AAAATTATAAATTTTTTTTAA
*
43594125 AAAATTCTAAA
1 AAAATTATAAA
43594136 GAATATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATTATAAATTTTTTTTAA
Found at i:43596963 original size:44 final size:44
Alignment explanation
Indices: 43596915--43597001 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
43596905 AAGTAAAATA
* *
43596915 GAAGTTGTGCTAATTATACATTTAAAAATAATTATAATATAATC
1 GAAGTTGTGATAATAATACATTTAAAAATAATTATAATATAATC
* * *
43596959 GAAGTTGTTATAATAATACATTTTAAAATAATTATAATTTAAT
1 GAAGTTGTGATAATAATACATTTAAAAATAATTATAATATAAT
43597002 ATACATTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (44 bp):
GAAGTTGTGATAATAATACATTTAAAAATAATTATAATATAATC
Found at i:43609353 original size:19 final size:19
Alignment explanation
Indices: 43609329--43609368 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43609319 TATACATTTT
43609329 AACTTT-TACTTATTATAAA
1 AACTTTCTACTTATT-TAAA
*
43609348 AACTTTCTAGTTATTTAAA
1 AACTTTCTACTTATTTAAA
43609367 AA
1 AA
43609369 TAATTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (19 bp):
AACTTTCTACTTATTTAAA
Found at i:43610435 original size:28 final size:29
Alignment explanation
Indices: 43610402--43610456 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
43610392 AAAATGTCCA
*
43610402 TTTTTC-TCGTTCAAAATTAATAAAATCC
1 TTTTTCGTAGTTCAAAATTAATAAAATCC
43610430 TTTTTCGTAGTTCAAAATTAATAAAAT
1 TTTTTCGTAGTTCAAAATTAATAAAAT
43610457 ATAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (29 bp):
TTTTTCGTAGTTCAAAATTAATAAAATCC
Found at i:43615745 original size:15 final size:15
Alignment explanation
Indices: 43615722--43615751 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43615712 TCCAGTGACA
43615722 CCACAGCCTCCACCT
1 CCACAGCCTCCACCT
*
43615737 CCACCGCCTCCACCT
1 CCACAGCCTCCACCT
43615752 AATAGAACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.63, G:0.07, T:0.13
Consensus pattern (15 bp):
CCACAGCCTCCACCT
Found at i:43629719 original size:46 final size:46
Alignment explanation
Indices: 43629659--43629932 Score: 478
Period size: 46 Copynumber: 6.0 Consensus size: 46
43629649 TTTGACATGA
* * * * * *
43629659 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
43629705 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
43629751 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
43629797 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
43629843 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
43629889 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
43629933 AGAGCACACT
Statistics
Matches: 221, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
45 4 0.02
46 217 0.98
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:43632027 original size:17 final size:16
Alignment explanation
Indices: 43632005--43632044 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
43631995 AATTTTTCCC
*
43632005 TTTTTCCTTCTTTCCTT
1 TTTTTCCTTCCTT-CTT
43632022 TTTTTCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
43632038 TCTTTCC
1 TTTTTCC
43632045 CCTGCTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:43632100 original size:16 final size:17
Alignment explanation
Indices: 43632069--43632114 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
43632059 TCATCCTTTC
*
43632069 TTTCTTTTTCTATTCTT
1 TTTCTTTTTATATTCTT
43632086 TTTCTTTTTAT-TTCTT
1 TTTCTTTTTATATTCTT
* *
43632102 TTACTTTATATAT
1 TTTCTTTTTATAT
43632115 ATATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTCTTTTTATATTCTT
Found at i:43632103 original size:10 final size:10
Alignment explanation
Indices: 43632065--43632102 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
43632055 CGTTTCATCC
43632065 TTTCTTTCTT
1 TTTCTTTCTT
43632075 TTTCTATTCTT
1 TTTCT-TTCTT
43632086 TTTCTTT-TT
1 TTTCTTTCTT
43632095 ATTTCTTT
1 -TTTCTTT
43632103 TACTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.08
10 14 0.54
11 10 0.38
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:43634401 original size:91 final size:91
Alignment explanation
Indices: 43634278--43634485 Score: 285
Period size: 91 Copynumber: 2.3 Consensus size: 91
43634268 TTGATTTTAG
* *
43634278 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
43634342 TATTTAAT-ATTAATTATTTTAAATTGTA
64 TATGTAATAATT-ATTATTTTAAATTATA
* *
43634370 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
43634435 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
43634461 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
43634486 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
91 83 0.80
92 21 0.20
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:43634527 original size:17 final size:17
Alignment explanation
Indices: 43634502--43634535 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43634492 ATTATTTTAA
*
43634502 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
43634519 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
43634536 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:43634537 original size:15 final size:16
Alignment explanation
Indices: 43634502--43634540 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
43634492 ATTATTTTAA
*
43634502 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
43634519 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
43634534 ATTTAAT
1 ATTTAAT
43634541 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:43634544 original size:17 final size:18
Alignment explanation
Indices: 43634506--43634545 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
43634496 TTTTAAATTT
*
43634506 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
43634524 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
43634540 TATTAA
1 TATTAA
43634546 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:43634655 original size:16 final size:16
Alignment explanation
Indices: 43634634--43634675 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
43634624 TTATTAAATT
*
43634634 ATATATTTTAATTATA
1 ATATATTTTAATAATA
43634650 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
43634665 AT-TATGTTTAA
1 ATATAT-TTTAA
43634676 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:43634660 original size:15 final size:15
Alignment explanation
Indices: 43634625--43634666 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43634615 TTAAGAATTT
*
43634625 TATTAAATTAT-ATA
1 TATTTAATTATAATA
43634639 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
43634653 TATTTAATAATAAT
1 TATTTAATTATAAT
43634667 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:43634782 original size:154 final size:156
Alignment explanation
Indices: 43634612--43634922 Score: 572
Period size: 154 Copynumber: 2.0 Consensus size: 156
43634602 AGAATTTTAT
*
43634612 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
43634677 TATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATAAT
66 TATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAAT
43634740 AATTTACCAAAACAAATTTATGCTAA
131 AATTTACCAAAACAAATTTATGCTAA
43634766 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
43634831 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
66 TATGATTAAATTATTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAATAA
* *
43634896 TCATTTACCAAAACAAATTTCTGCTAA
130 TAATTTACCAAAACAAATTTATGCTAA
43634923 GGGTATTCTA
Statistics
Matches: 151, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
154 89 0.59
155 2 0.01
157 60 0.40
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (156 bp):
TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
TATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAAT
AATTTACCAAAACAAATTTATGCTAA
Found at i:43634803 original size:18 final size:17
Alignment explanation
Indices: 43634775--43634809 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43634765 ATTATTAAGA
*
43634775 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43634792 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43634810 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43634843 original size:75 final size:75
Alignment explanation
Indices: 43634612--43634845 Score: 208
Period size: 75 Copynumber: 3.1 Consensus size: 75
43634602 AGAATTTTAT
*
43634612 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
43634677 TATGATTAAA
66 TATGATTAAA
* ** * * * * * * ***
43634687 TTATTTATTATTGATATTAATCTTATTAAAATTTAAATAACAATA-A--CAATAATAATT-TACC
1 TTATTAAGAATT-TTATTAA-ATTA-TATATTTTAATTAA-AATATATTTAATAATAATTATGTT
* * *
43634748 AAAACA-AATTTATGCTAA
62 TAAATATGA-TTA----AA
43634766 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
43634831 TATGATTAAA
66 TATGATTAAA
43634841 TTATT
1 TTATT
43634846 TATTATTGAT
Statistics
Matches: 114, Mismatches: 31, Indels: 28
0.66 0.18 0.16
Matches are distributed among these distances:
74 1 0.01
75 28 0.25
76 28 0.25
77 6 0.05
78 27 0.24
79 23 0.20
80 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (75 bp):
TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
TATGATTAAA
Found at i:43635075 original size:16 final size:16
Alignment explanation
Indices: 43635054--43635110 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
43635044 ACACAGCTTT
*
43635054 TCCATTACACCTCTAT
1 TCCATTACACCTCTAA
*
43635070 TTCATTACACCTCTAA
1 TCCATTACACCTCTAA
*
43635086 TCCAATACACCTCTAA
1 TCCATTACACCTCTAA
*
43635102 TCCAATACA
1 TCCATTACA
43635111 GCGAACCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.32
Consensus pattern (16 bp):
TCCATTACACCTCTAA
Found at i:43635186 original size:27 final size:27
Alignment explanation
Indices: 43635149--43635203 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
43635139 GCCCGTTTGG
*
43635149 CCCCTAGCCCAAAACCCATTTTCTAAC
1 CCCCTAGCCCAAAACCCATATTCTAAC
*
43635176 CCCCTAGCCCAAAACCTATATTCTAAC
1 CCCCTAGCCCAAAACCCATATTCTAAC
43635203 C
1 C
43635204 TACAAAGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.44, G:0.04, T:0.22
Consensus pattern (27 bp):
CCCCTAGCCCAAAACCCATATTCTAAC
Found at i:43636329 original size:25 final size:23
Alignment explanation
Indices: 43636277--43636340 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 23
43636267 TTACCTTTTT
*
43636277 TATTTTAAATATTATTGATTATTC
1 TATTTT-ACTATTATTGATTATTC
**
43636301 TATTTTTGTATTATT-ATTATTAGC
1 TATTTTACTATTATTGATTATT--C
43636325 ATATTTTACTATTATT
1 -TATTTTACTATTATT
43636341 TAGACATCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 6 0.18
23 7 0.21
24 7 0.21
25 13 0.39
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (23 bp):
TATTTTACTATTATTGATTATTC
Found at i:43636532 original size:18 final size:19
Alignment explanation
Indices: 43636506--43636558 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 19
43636496 TTATACCATG
43636506 TATATATA-TATATATTTT
1 TATATATATTATATATTTT
* *
43636524 TATAAATATTATATATATT
1 TATATATATTATATATTTT
43636543 TA-ATATATTATATATT
1 TATATATATTATATATT
43636559 GTGTACATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATATATTATATATTTT
Found at i:43636998 original size:12 final size:12
Alignment explanation
Indices: 43636976--43637029 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
43636966 ATATATTGTA
*
43636976 TATTCTTACTAT
1 TATTATTACTAT
*
43636988 TATCATTACTA-
1 TATTATTACTAT
*
43636999 TATTTATTATTAT
1 TA-TTATTACTAT
*
43637012 TATTATTATTAT
1 TATTATTACTAT
43637024 TATTAT
1 TATTAT
43637030 AGCAATCCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTACTAT
Found at i:43637010 original size:3 final size:3
Alignment explanation
Indices: 43637002--43637029 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43636992 ATTACTATAT
43637002 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43637030 AGCAATCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43643567 original size:46 final size:46
Alignment explanation
Indices: 43643465--43643649 Score: 273
Period size: 46 Copynumber: 3.9 Consensus size: 46
43643455 TTTGACATGA
* * * *
43643465 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTCATTTTC-TGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTA--CA--CA-TTTCATATCACGT
43643515 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
*
43643561 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
43643607 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
43643650 GATAGCACAC
Statistics
Matches: 129, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
45 4 0.03
46 97 0.75
48 2 0.02
50 26 0.20
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
Found at i:43645373 original size:16 final size:18
Alignment explanation
Indices: 43645344--43645379 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
43645334 TCATCCTTTC
43645344 TTTCTTTTTCTATT-CTT
1 TTTCTTTTTCTATTCCTT
43645361 TTTCTTTTT-TATTCCTT
1 TTTCTTTTTCTATTCCTT
43645378 TT
1 TT
43645380 ACTATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCTTTTTCTATTCCTT
Found at i:43654334 original size:19 final size:19
Alignment explanation
Indices: 43654293--43654334 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
43654283 GATTTGTTTT
*
43654293 TTTATTTTTGAATTATAGT
1 TTTATTTTTGAATTATAGA
43654312 TTTATTTTATGAATT-TAGA
1 TTTATTTT-TGAATTATAGA
43654331 TTTA
1 TTTA
43654335 AAAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (19 bp):
TTTATTTTTGAATTATAGA
Found at i:43661838 original size:39 final size:39
Alignment explanation
Indices: 43661784--43661884 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
43661774 GCTCTAATGA
*
43661784 GCTTCAGTTAGCCTTCGGGCTTTCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
43661823 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* **
43661862 GCTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
43661885 AGATCACGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.11, C:0.25, G:0.26, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:43661866 original size:21 final size:21
Alignment explanation
Indices: 43661802--43661866 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 21
43661792 TAGCCTTCGG
*
43661802 GCTTTCGTTTAGCACTTGTGT
1 GCTTCCGTTTAGCACTTGTGT
*
43661823 GCTTCAG-TTAGC-CTTCG-G-
1 GCTTCCGTTTAGCACTT-GTGT
43661841 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCGTTTAGCACTTGTGT
43661862 GCTTC
1 GCTTC
43661867 AGCTAGATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 6 0.17
19 10 0.28
20 10 0.28
21 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.42
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTGTGT
Found at i:43663425 original size:24 final size:26
Alignment explanation
Indices: 43663390--43663445 Score: 98
Period size: 24 Copynumber: 2.2 Consensus size: 26
43663380 TTTAAAATCT
43663390 TTTTCATAAATATTTCAAAAAAAA-G
1 TTTTCATAAATATTTCAAAAAAAATG
43663415 TTTTCAT-AATATTTCAAAAAAAATG
1 TTTTCATAAATATTTCAAAAAAAATG
43663440 TTTTCA
1 TTTTCA
43663446 AGTAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 16 0.53
25 14 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (26 bp):
TTTTCATAAATATTTCAAAAAAAATG
Found at i:43683305 original size:49 final size:45
Alignment explanation
Indices: 43683237--43683333 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 45
43683227 TCTTATAGAG
* *
43683237 AACATATGGAAAGCATT-AAACACGCTATATTCTTTCTAAAAAGAATTAT
1 AACATATGGAAAACATTAAAAAACG-T-T-TT-TTT-TAAAAAGAATTAT
43683286 AACATATGGAAAACATTAAAAAACGTTTTTTTTAAAAAGAATTAT
1 AACATATGGAAAACATTAAAAAACGTTTTTTTTAAAAAGAATTAT
43683331 AAC
1 AAC
43683334 TACCATGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
45 16 0.36
46 3 0.07
47 2 0.04
48 1 0.02
49 17 0.38
50 6 0.13
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.31
Consensus pattern (45 bp):
AACATATGGAAAACATTAAAAAACGTTTTTTTTAAAAAGAATTAT
Found at i:43684842 original size:18 final size:18
Alignment explanation
Indices: 43684819--43684855 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
43684809 CGAAACCATT
43684819 CCACATTGTAGCCTATAG
1 CCACATTGTAGCCTATAG
43684837 CCACATTGTAGCCTATAG
1 CCACATTGTAGCCTATAG
43684855 C
1 C
43684856 ACGAGCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (18 bp):
CCACATTGTAGCCTATAG
Found at i:43686551 original size:13 final size:13
Alignment explanation
Indices: 43686530--43686596 Score: 60
Period size: 13 Copynumber: 5.8 Consensus size: 13
43686520 GTGGAGTGGT
*
43686530 TGGGATGGTTTAG
1 TGGGGTGGTTTAG
43686543 TGGGGTGG--T--
1 TGGGGTGGTTTAG
43686552 TGGGGTGGTTTAG
1 TGGGGTGGTTTAG
43686565 TGGGGTGG--T--
1 TGGGGTGGTTTAG
*
43686574 TGGAGTGGTTTAG
1 TGGGGTGGTTTAG
43686587 TGGGGTGGTT
1 TGGGGTGGTT
43686597 GGAGTGAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
9 15 0.35
11 4 0.09
13 24 0.56
ACGTcount: A:0.07, C:0.00, G:0.55, T:0.37
Consensus pattern (13 bp):
TGGGGTGGTTTAG
Found at i:43686599 original size:22 final size:22
Alignment explanation
Indices: 43686519--43686602 Score: 134
Period size: 22 Copynumber: 3.8 Consensus size: 22
43686509 TTTGTAGGCA
*
43686519 AGTGGAGTGGTTGG-GATGGTTT
1 AGTGGGGTGGTTGGAG-TGGTTT
*
43686541 AGTGGGGTGGTTGGGGTGGTTT
1 AGTGGGGTGGTTGGAGTGGTTT
43686563 AGTGGGGTGGTTGGAGTGGTTT
1 AGTGGGGTGGTTGGAGTGGTTT
43686585 AGTGGGGTGGTTGGAGTG
1 AGTGGGGTGGTTGGAGTG
43686603 AAGATATTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
22 58 0.98
23 1 0.02
ACGTcount: A:0.10, C:0.00, G:0.56, T:0.35
Consensus pattern (22 bp):
AGTGGGGTGGTTGGAGTGGTTT
Found at i:43686718 original size:16 final size:15
Alignment explanation
Indices: 43686677--43686721 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
43686667 CTTTGGAGGT
** *
43686677 TGTTGGGTTTTGGGC
1 TGTTGGGTTTTTAGA
43686692 TGTTGGGTTTTTAGA
1 TGTTGGGTTTTTAGA
43686707 TGTTGGGCTTTTTAG
1 TGTTGGG-TTTTTAG
43686722 CCCGGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.07, C:0.04, G:0.38, T:0.51
Consensus pattern (15 bp):
TGTTGGGTTTTTAGA
Found at i:43687460 original size:206 final size:206
Alignment explanation
Indices: 43687092--43688175 Score: 1891
Period size: 206 Copynumber: 5.3 Consensus size: 206
43687082 CAAATCTGCT
* * * * *
43687092 TCTTCAATTTGTTACTTGTAAGCACAAGGATGCCAAATCGTCTTGGATCTTGCTTCTGTATAAAC
1 TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTATAAAC
* * *
43687157 ATTTGAAGGCCAGATCTGCTATGTATCTGCTTTCCGTCGAAATGGAGATACCAGACTTCGACTTG
66 ATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGACTTCGACTTG
*
43687222 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACACGAAAGCCA
131 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
* *
43687287 AATTAGCTATA
196 AATCAGCTATG
* *
43687298 TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATAATCTTGGATCTTGCTTCAATATAAAC
1 TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTATAAAC
* * *
43687363 ATTTAAAGGCCAGATCTGCTATGTATCTACTCTCCGTCGAAATGGAGATGCCAGACTTCGACTTG
66 ATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGACTTCGACTTG
43687428 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
131 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
*
43687493 AATCAGCTATA
196 AATCAGCTATG
*
43687504 TCTTCGATTTGCTCATTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTATAAAC
1 TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTATAAAC
43687569 ATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGACTTCGACTTG
66 ATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGACTTCGACTTG
43687634 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
131 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
43687699 AATCAGCTATG
196 AATCAGCTATG
* *
43687710 TCTTCGATTTGCTCATTGTAAGCACAAGGATGACAAATCATCTTGGATCTTGCTTCAGTATAAAC
1 TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTATAAAC
*
43687775 ATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTAGAAATGGAGATGCCAGACTTCGACTTG
66 ATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGACTTCGACTTG
43687840 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
131 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
43687905 AATCAGCTATG
196 AATCAGCTATG
* * *
43687916 TCTTCGATTTGCTCCTTGCAAGCATAAGGATGCCAAATCATATTGGATCTTGCTTCAGTATAAAC
1 TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTATAAAC
* * *
43687981 ATCTGAAGGCCAAATCTGCTATCTATCTGCTCTCTGTCGAAATGGAGATGCCAGACTTCGACTTG
66 ATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGACTTCGACTTG
43688046 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
131 TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
43688111 AATCAGCTATG
196 AATCAGCTATG
* * *
43688122 TCTTCGATTTGCTCCTTGGAAGTACAAGGATGCCAAACCATCTTGGATC-TGCTT
1 TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTT
43688176 TAGCCAGATC
Statistics
Matches: 842, Mismatches: 36, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
205 5 0.01
206 837 0.99
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (206 bp):
TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTATAAAC
ATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGACTTCGACTTG
TTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCACGCGAAAGCCA
AATCAGCTATG
Found at i:43697486 original size:23 final size:23
Alignment explanation
Indices: 43697458--43697542 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
43697448 CAAAAAAAAG
43697458 AAAATATAATAATAATAATAGTA
1 AAAATATAATAATAATAATAGTA
* * *
43697481 AAAATACAATAGTAATAATAATGA
1 AAAATATAATAATAATAATAGT-A
* *
43697505 AAAGGTATTATAAT-ATAATAGTA
1 AAA-ATATAATAATAATAATAGTA
* *
43697528 ACAATGATGATAATA
1 AAAAT-ATAATAATA
43697543 GTGGTATTAG
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
22 1 0.02
23 29 0.62
24 11 0.23
25 6 0.13
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.29
Consensus pattern (23 bp):
AAAATATAATAATAATAATAGTA
Found at i:43697853 original size:13 final size:13
Alignment explanation
Indices: 43697835--43697867 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
43697825 AAAAGAAACC
43697835 TCTTTTGCTTTAA
1 TCTTTTGCTTTAA
*
43697848 TCTTTTGCTTTGA
1 TCTTTTGCTTTAA
43697861 TCTTTTG
1 TCTTTTG
43697868 ATTAATCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.15, G:0.12, T:0.64
Consensus pattern (13 bp):
TCTTTTGCTTTAA
Found at i:43698000 original size:22 final size:22
Alignment explanation
Indices: 43697969--43698039 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
43697959 TTTGTAGGCA
*
43697969 AGTGGAGTGGTTGGGATGGTTT
1 AGTGGGGTGGTTGGGATGGTTT
*
43697991 AGTGGGGTGGTTGGGGTGGTTT
1 AGTGGGGTGGTTGGGATGGTTT
43698013 AGTGGGGTGGTT-GGAGTGGTTT
1 AGTGGGGTGGTTGGGA-TGGTTT
43698035 AGTGG
1 AGTGG
43698040 AGTAGTTTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 2 0.04
22 43 0.96
ACGTcount: A:0.10, C:0.00, G:0.55, T:0.35
Consensus pattern (22 bp):
AGTGGGGTGGTTGGGATGGTTT
Found at i:43698001 original size:13 final size:13
Alignment explanation
Indices: 43697980--43698059 Score: 59
Period size: 13 Copynumber: 6.8 Consensus size: 13
43697970 GTGGAGTGGT
*
43697980 TGGGATGGTTTAG
1 TGGGGTGGTTTAG
43697993 TGGGGTGG--T--
1 TGGGGTGGTTTAG
43698002 TGGGGTGGTTTAG
1 TGGGGTGGTTTAG
43698015 TGGGGTGG--T--
1 TGGGGTGGTTTAG
*
43698024 TGGAGTGGTTTAG
1 TGGGGTGGTTTAG
* *
43698037 TGGAGTAGTTTAG
1 TGGGGTGGTTTAG
*
43698050 TAGGGTGGTT
1 TGGGGTGGTT
43698060 GGAGTGAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
13 34 0.64
ACGTcount: A:0.11, C:0.00, G:0.51, T:0.38
Consensus pattern (13 bp):
TGGGGTGGTTTAG
Found at i:43698183 original size:16 final size:15
Alignment explanation
Indices: 43698142--43698186 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
43698132 CTTTCGAGGT
** *
43698142 TGTTGGGTTTTGGGC
1 TGTTGGGTTTTTAGA
43698157 TGTTGGGTTTTTAGA
1 TGTTGGGTTTTTAGA
43698172 TGTTGGGCTTTTTAG
1 TGTTGGG-TTTTTAG
43698187 CCCGGGCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.07, C:0.04, G:0.38, T:0.51
Consensus pattern (15 bp):
TGTTGGGTTTTTAGA
Found at i:43699057 original size:29 final size:29
Alignment explanation
Indices: 43699025--43699082 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
43699015 ACACCCACAA
* *
43699025 GTAGGGTTGTAAATAAACTAAGCTTGAAT
1 GTAGGGCTATAAATAAACTAAGCTTGAAT
*
43699054 GTAGGGCTATAAATGAACTAAGCTTGAAT
1 GTAGGGCTATAAATAAACTAAGCTTGAAT
43699083 AAATAAACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (29 bp):
GTAGGGCTATAAATAAACTAAGCTTGAAT
Found at i:43709015 original size:27 final size:27
Alignment explanation
Indices: 43708985--43709053 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
43708975 AAAGAATGCC
* *
43708985 AAATTGTACATAAATAAATTTTAAAGA
1 AAATTATACATAAATAAATTTAAAAGA
* *
43709012 AAA-TATATATACAATTAATTTAAAAGA
1 AAATTATACATA-AATAAATTTAAAAGA
*
43709039 AAATATTTACATAAA
1 AAAT-TATACATAAA
43709054 ATAATTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
26 6 0.18
27 19 0.58
28 2 0.06
29 6 0.18
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (27 bp):
AAATTATACATAAATAAATTTAAAAGA
Found at i:43710989 original size:176 final size:176
Alignment explanation
Indices: 43710582--43711013 Score: 490
Period size: 176 Copynumber: 2.4 Consensus size: 176
43710572 CTCTACATCC
* * * * *
43710582 TCAGTCTGCTTCATTGCGACTTCAGGGAGATAAAATTTGTAATTTTGAACCTGCTCCACTGCAAC
1 TCAGTCTGCTTC-CTGCGACTTCAGGAAGATAAGACTTG-AATATTGAACCTGCTCCACTGCAAC
* * * * *
43710647 TTCAGGGAGACAAGGATGGTGGCTTAAATCTGCTCCATTGCCGATACACAGAGATAAGACTCGCC
64 CTCAGAGAGACAAGGATGGTAGCTTAAATCTGCTCCATTGCCGATACACAGAGATAAAACTCACC
** * *
43710712 GTCTTTGATCAACTCCACTTCTGCTTAGTGAGATAAGATCTATAAATT
129 GTCTACGATCAACTCCACTACTGCTTAGGGAGATAAGATCTATAAATT
* * * * * * *
43710760 TCAGTCTGCTTCCTGCAACTTCAGGAAGACAAGACTTGTATCTTCAACCTGCTCTC-TTGCTACC
1 TCAGTCTGCTTCCTGCGACTTCAGGAAGATAAGACTTGAATATTGAACCTGCTC-CACTGCAACC
* * * ** *
43710824 TCAGAGAGATAAGGTTGGTAG-TTAAAATCTGCTCCATTGTCGATACATGGAGATAAAATTCACC
65 TCAGAGAGACAAGGATGGTAGCTT-AAATCTGCTCCATTGCCGATACACAGAGATAAAACTCACC
** * *
43710888 GTCTACGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTT
129 GTCTACGATCAACTCCACTACTGCTTAGGGAGATAAGATCTATAAATT
* * *
43710936 TCAGTCTGCTTCCTGCGACTTCAGGAAGATAAGACTTGCATATTGAGCCTGCTCCACTGCAACTT
1 TCAGTCTGCTTCCTGCGACTTCAGGAAGATAAGACTTGAATATTGAACCTGCTCCACTGCAACCT
* *
43711001 CAGGGAGATAAGG
66 CAGAGAGACAAGG
43711014 CTTGTCACTT
Statistics
Matches: 211, Mismatches: 40, Indels: 8
0.81 0.15 0.03
Matches are distributed among these distances:
175 3 0.01
176 175 0.83
177 21 0.10
178 12 0.06
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (176 bp):
TCAGTCTGCTTCCTGCGACTTCAGGAAGATAAGACTTGAATATTGAACCTGCTCCACTGCAACCT
CAGAGAGACAAGGATGGTAGCTTAAATCTGCTCCATTGCCGATACACAGAGATAAAACTCACCGT
CTACGATCAACTCCACTACTGCTTAGGGAGATAAGATCTATAAATT
Found at i:43711001 original size:44 final size:43
Alignment explanation
Indices: 43710948--43711056 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 43
43710938 AGTCTGCTTC
* * * *
43710948 CTGCGACTTCAGGAAGATAAGACTTG-CATATTGAGCCTGCTCCA
1 CTGCAACTTCAGG-AGATAAGACTTGTCA-ATTCAACCTACTCCA
* *
43710992 CTGCAACTTCAGGGAGATAAGGCTTGTCACTTCAACCTACTCCA
1 CTGCAACTTCA-GGAGATAAGACTTGTCAATTCAACCTACTCCA
*
43711036 CAGCAACTTCAAGGAGATAAG
1 CTGCAACTTC-AGGAGATAAG
43711057 GTTTGCTATG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
44 50 0.91
45 5 0.09
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (43 bp):
CTGCAACTTCAGGAGATAAGACTTGTCAATTCAACCTACTCCA
Found at i:43711313 original size:205 final size:205
Alignment explanation
Indices: 43710954--43711370 Score: 825
Period size: 205 Copynumber: 2.0 Consensus size: 205
43710944 CTTCCTGCGA
*
43710954 CTTCAGGAAGATAAGACTTGCATATTGAGCCTGCTCCACTGCAACTTCAGGGAGATAAGGCTTGT
1 CTTCAGTAAGATAAGACTTGCATATTGAGCCTGCTCCACTGCAACTTCAGGGAGATAAGGCTTGT
43711019 CACTTCAACCTACTCCACAGCAACTTCAAGGAGATAAGGTTTGCTATGATCTGCTCTACTGCCAC
66 CACTTCAACCTACTCCACAGCAACTTCAAGGAGATAAGGTTTGCTATGATCTGCTCTACTGCCAC
43711084 TTTAGAGAGATAAGATATGTTTATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAA
131 TTTAGAGAGATAAGATATGTTTATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAA
43711149 GATTCGCTAT
196 GATTCGCTAT
43711159 CTTCAGTAAGATAAGACTTGCATATTGAGCCTGCTCCACTGCAACTTCAGGGAGATAAGGCTTGT
1 CTTCAGTAAGATAAGACTTGCATATTGAGCCTGCTCCACTGCAACTTCAGGGAGATAAGGCTTGT
43711224 CACTTCAACCTACTCCACAGCAACTTCAAGGAGATAAGGTTTGCTATGATCTGCTCTACTGCCAC
66 CACTTCAACCTACTCCACAGCAACTTCAAGGAGATAAGGTTTGCTATGATCTGCTCTACTGCCAC
43711289 TTTAGAGAGATAAGATATGTTTATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAA
131 TTTAGAGAGATAAGATATGTTTATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAA
43711354 GATTCGCTAT
196 GATTCGCTAT
43711364 CTTCAGT
1 CTTCAGT
43711371 CTGCTCCTCT
Statistics
Matches: 211, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 211 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (205 bp):
CTTCAGTAAGATAAGACTTGCATATTGAGCCTGCTCCACTGCAACTTCAGGGAGATAAGGCTTGT
CACTTCAACCTACTCCACAGCAACTTCAAGGAGATAAGGTTTGCTATGATCTGCTCTACTGCCAC
TTTAGAGAGATAAGATATGTTTATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAA
GATTCGCTAT
Found at i:43711434 original size:44 final size:44
Alignment explanation
Indices: 43711188--43711443 Score: 153
Period size: 44 Copynumber: 5.7 Consensus size: 44
43711178 GCATATTGAG
* *
43711188 CCTGCTCCACTGCAACTTCAGGGAGATAAGGCTTGTCACTTCAA
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATCACTTCAA
* * * * * *
43711232 CCTACTCCACAGCAACTTCAAGGAGATAAG-GTT-T-GCTAT-GA
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATCACT-TCAA
* * * * * * *
43711273 TCTGCTCTACTGCCACTTTAGAGAGATAAGATATGTTTATTTATAGCTTCAA
1 CCTGCTCCACTGCAACTTCAGGGAGATAAG--A--CTTA--T-CA-CTTCAA
* * * ** *
43711325 TCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTCAG
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATC-A-CTTCAA
* * * *
43711370 TCTGCTCCTCTACAACTTCAGGGAGATAAGACTTATCACTTTAA
1 CCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATCACTTCAA
43711414 CCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CCTGCTCCACTGCAACTTCAGGGAGATAAG
43711444 GTTTGTAATA
Statistics
Matches: 158, Mismatches: 39, Indels: 30
0.70 0.17 0.13
Matches are distributed among these distances:
41 25 0.16
42 2 0.01
43 2 0.01
44 58 0.37
45 34 0.22
46 5 0.03
47 2 0.01
49 1 0.01
50 1 0.01
51 1 0.01
52 27 0.17
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
CCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATCACTTCAA
Found at i:43716228 original size:21 final size:21
Alignment explanation
Indices: 43716186--43716229 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
43716176 GAAATGCAAG
* *
43716186 AAAAGAATATTTGCTTAAAAT
1 AAAAGAATATTTACTCAAAAT
*
43716207 AAAAGAATATTTACTCAGAAT
1 AAAAGAATATTTACTCAAAAT
43716228 AA
1 AA
43716230 GACATAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAAGAATATTTACTCAAAAT
Found at i:43723667 original size:27 final size:27
Alignment explanation
Indices: 43723637--43723705 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
43723627 AAAGAATGCC
* *
43723637 AAATTGTACATAAATAAATTTTAAAGA
1 AAATTATACATAAATAAATTTAAAAGA
*
43723664 AAA-TATATATACAATAAATTTAAAAGA
1 AAATTATACATA-AATAAATTTAAAAGA
*
43723691 AAATATTTACATAAA
1 AAAT-TATACATAAA
43723706 ATAATTTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
26 6 0.18
27 20 0.59
28 2 0.06
29 6 0.18
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (27 bp):
AAATTATACATAAATAAATTTAAAAGA
Found at i:43730832 original size:14 final size:14
Alignment explanation
Indices: 43730813--43730842 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43730803 TTATATCGAG
*
43730813 ACCAATCTAATTCA
1 ACCAATCCAATTCA
43730827 ACCAATCCAATTCA
1 ACCAATCCAATTCA
43730841 AC
1 AC
43730843 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (14 bp):
ACCAATCCAATTCA
Found at i:43751199 original size:16 final size:18
Alignment explanation
Indices: 43751161--43751200 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
43751151 TAAATTTTTT
*
43751161 ATATTATTTTTATATAAA
1 ATATAATTTTTATATAAA
43751179 A-ATAATTTTTA-A-AAA
1 ATATAATTTTTATATAAA
43751194 ATATAAT
1 ATATAAT
43751201 ACATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 9 0.45
18 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATAATTTTTATATAAA
Found at i:43753784 original size:17 final size:16
Alignment explanation
Indices: 43753762--43753796 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
43753752 ATTTATCCAA
43753762 ATATATTCAATGATTTT
1 ATATATT-AATGATTTT
*
43753779 ATATATTTATGATTTT
1 ATATATTAATGATTTT
43753795 AT
1 AT
43753797 TTGTGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (16 bp):
ATATATTAATGATTTT
Found at i:43759544 original size:18 final size:17
Alignment explanation
Indices: 43759502--43759545 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
43759492 AAAATATTAT
*
43759502 ATTATATTTAAGAAATAA
1 ATTAT-TTTAAAAAATAA
*
43759520 ATAATTTTAAAAAATAAA
1 ATTATTTTAAAAAAT-AA
43759538 ATTATTTT
1 ATTATTTT
43759546 TATCAACCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTATTTTAAAAAATAA
Found at i:43760549 original size:22 final size:21
Alignment explanation
Indices: 43760508--43760551 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
43760498 AAATAATTTA
43760508 TAATTAATTGTAAATTTAAAAT
1 TAATTAATTGTAAA-TTAAAAT
43760530 TAATTAATTTGTAACA-TAAAAT
1 TAATTAA-TTGTAA-ATTAAAAT
43760552 ATTGTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 6 0.30
24 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
TAATTAATTGTAAATTAAAAT
Found at i:43762184 original size:21 final size:21
Alignment explanation
Indices: 43762158--43762200 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
43762148 CTTAACGGGA
43762158 TAGTTGACGTGGCCAGTTAAC
1 TAGTTGACGTGGCCAGTTAAC
*
43762179 TAGTTGATGTGGCCAGTTAAC
1 TAGTTGACGTGGCCAGTTAAC
43762200 T
1 T
43762201 TGCCACATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (21 bp):
TAGTTGACGTGGCCAGTTAAC
Found at i:43762285 original size:22 final size:22
Alignment explanation
Indices: 43762260--43762310 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
43762250 GGTTGAGGTA
* *
43762260 AAAATAAGAATAGGAGAAGAAG
1 AAAAGAAGAAGAGGAGAAGAAG
43762282 AAAAGAAGAAGAGGAGAAGAAG
1 AAAAGAAGAAGAGGAGAAGAAG
*
43762304 AATAGAA
1 AAAAGAA
43762311 AATGGAGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (22 bp):
AAAAGAAGAAGAGGAGAAGAAG
Found at i:43763308 original size:20 final size:22
Alignment explanation
Indices: 43763283--43763324 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43763273 ACGAAGCTCC
*
43763283 TTCCA-TT-TTCTCTTTTTCTT
1 TTCCATTTCTTCTCTTATTCTT
43763303 TTCCATTTCTTCTCTTATTCTT
1 TTCCATTTCTTCTCTTATTCTT
43763325 CTTTTTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (22 bp):
TTCCATTTCTTCTCTTATTCTT
Found at i:43765074 original size:43 final size:42
Alignment explanation
Indices: 43765005--43765091 Score: 97
Period size: 43 Copynumber: 2.0 Consensus size: 42
43764995 AAAACATCGC
* * *
43765005 AAAAGATCATGTTTTTAGCGGTGTTTGT-AGTAAAAGTGCCTCT
1 AAAAGATCATGTTTATAGCGGCGTTTGTGAG-AAAA-TGCCACT
*
43765048 AAAA-ATCATGTTCTATAGTGGCGTTTGTGAGAAAATGCCACT
1 AAAAGATCATGTT-TATAGCGGCGTTTGTGAGAAAATGCCACT
43765090 AA
1 AA
43765092 CATTAACAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
42 16 0.42
43 20 0.53
44 2 0.05
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (42 bp):
AAAAGATCATGTTTATAGCGGCGTTTGTGAGAAAATGCCACT
Found at i:43767581 original size:44 final size:41
Alignment explanation
Indices: 43767454--43767643 Score: 177
Period size: 41 Copynumber: 4.6 Consensus size: 41
43767444 AATATTCGTA
* * * *
43767454 GCGTTTATGGGCAAAACGCCGCTATTGCTTTACCTTTAGAG
1 GCGTTTATGGGAAAAATGCCGCTATTGTTTTACCTTTAGCG
* * * * *
43767495 GCGTATATGAGAAAAATACTGCTATTGTTTTACCTTTTGCG
1 GCGTTTATGGGAAAAATGCCGCTATTGTTTTACCTTTAGCG
*
43767536 GCGTTTATGGGAAAAATGCGGCTATTGTTGTTATACCTTTAGCG
1 GCGTTTATGGGAAAAATGCCGCTATTG-T-TT-TACCTTTAGCG
* * * * *
43767580 GCGTTTA-GGGAAAAACGACGCTATT-TCTTTACTTTTTGTG
1 GCGTTTATGGGAAAAATGCCGCTATTGT-TTTACCTTTAGCG
**
43767620 GTATTTATGGGAAAAATGCCGCTA
1 GCGTTTATGGGAAAAATGCCGCTA
43767644 ACGCTGCTCC
Statistics
Matches: 120, Mismatches: 25, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
40 13 0.11
41 72 0.60
42 1 0.01
43 17 0.14
44 17 0.14
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.36
Consensus pattern (41 bp):
GCGTTTATGGGAAAAATGCCGCTATTGTTTTACCTTTAGCG
Found at i:43767617 original size:84 final size:82
Alignment explanation
Indices: 43767454--43767643 Score: 206
Period size: 84 Copynumber: 2.3 Consensus size: 82
43767444 AATATTCGTA
* * *
43767454 GCGTTTATGGGCAAAACGCCGCTATTGCTTTACCTTTAGAGGCGTATATGAGAAAAATACTGCTA
1 GCGTTTATGGGAAAAATGCCGCTATTGCTTTACCTTTAGAGGCGTATATGAGAAAAAGACTGCTA
43767519 TTGTTTTACCTTTTGCG
66 TTGTTTTACCTTTTGCG
* * * * *
43767536 GCGTTTATGGGAAAAATGCGGCTATTGTTGTTATACCTTTAGCGGCGTTTA-GGGAAAAACGAC-
1 GCGTTTATGGGAAAAATGCCGCTATTG--CTT-TACCTTTAGAGGCGTATATGAGAAAAA-GACT
* *
43767599 GCTATT-TCTTTACTTTTTGTG
62 GCTATTGT-TTTACCTTTTGCG
**
43767620 GTATTTATGGGAAAAATGCCGCTA
1 GCGTTTATGGGAAAAATGCCGCTA
43767644 ACGCTGCTCC
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
82 24 0.27
83 1 0.01
84 47 0.52
85 18 0.20
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.36
Consensus pattern (82 bp):
GCGTTTATGGGAAAAATGCCGCTATTGCTTTACCTTTAGAGGCGTATATGAGAAAAAGACTGCTA
TTGTTTTACCTTTTGCG
Found at i:43768345 original size:20 final size:20
Alignment explanation
Indices: 43768301--43768343 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
43768291 GTTGAACCGA
43768301 TTTAATAATTTTTTTAATTT
1 TTTAATAATTTTTTTAATTT
43768321 TTTAA-AATTTTTTATGAATTT
1 TTTAATAATTTTTT-T-AATTT
43768342 TT
1 TT
43768344 AATTAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTAATAATTTTTTTAATTT
Found at i:43769551 original size:22 final size:22
Alignment explanation
Indices: 43769506--43769548 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43769496 ATTAAATCTC
*
43769506 TTAAAATCTTAAAAAATTTTAA
1 TTAAAATCTTAAAAAATTTAAA
*
43769528 TTAAAATCTT-CAAAATTTAAA
1 TTAAAATCTTAAAAAATTTAAA
43769549 ATTTCTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATCTTAAAAAATTTAAA
Found at i:43769773 original size:21 final size:21
Alignment explanation
Indices: 43769747--43769798 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
43769737 ACGGTGGTGA
*
43769747 TGAGATTAGTTACTGTAGCGG
1 TGAGATTAGATACTGTAGCGG
* * *
43769768 TGAGATTGGATATTGTAGTGG
1 TGAGATTAGATACTGTAGCGG
43769789 TGAGATTAGA
1 TGAGATTAGA
43769799 AACAATGGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.35
Consensus pattern (21 bp):
TGAGATTAGATACTGTAGCGG
Found at i:43770426 original size:27 final size:28
Alignment explanation
Indices: 43770389--43770444 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
43770379 ATTTTATCAT
43770389 ATAAATTTAAAA-AATTAT-GAAAATGAC
1 ATAAATTTAAAATAATTATAG-AAATGAC
*
43770416 ATAACTTTAAAATTAATTATAGAAATGAC
1 ATAAATTTAAAA-TAATTATAGAAATGAC
43770445 CTTGTTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 11 0.44
29 13 0.52
30 1 0.04
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (28 bp):
ATAAATTTAAAATAATTATAGAAATGAC
Found at i:43776031 original size:45 final size:46
Alignment explanation
Indices: 43775982--43776078 Score: 169
Period size: 46 Copynumber: 2.1 Consensus size: 46
43775972 CTGTAATTTA
43775982 AATTTTCAAGTTTGT-ATTAATTTAATTATAACAAATGTTTGACTT
1 AATTTTCAAGTTTGTAATTAATTTAATTATAACAAATGTTTGACTT
* *
43776027 AATTTTCAAGTTTGTAATTAATTTAGTTATAGCAAATGTTTGACTT
1 AATTTTCAAGTTTGTAATTAATTTAATTATAACAAATGTTTGACTT
43776073 AATTTT
1 AATTTT
43776079 ATTTGAAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 15 0.31
46 34 0.69
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.49
Consensus pattern (46 bp):
AATTTTCAAGTTTGTAATTAATTTAATTATAACAAATGTTTGACTT
Found at i:43780573 original size:20 final size:20
Alignment explanation
Indices: 43780543--43780587 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
43780533 CTGTTTTATT
43780543 ATGGG-CCAACTGTATTAAA
1 ATGGGCCCAACTGTATTAAA
* *
43780562 ATGGGCCCAACTGTGTTAAT
1 ATGGGCCCAACTGTATTAAA
43780582 ATGGGC
1 ATGGGC
43780588 AAGACCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTAAA
Found at i:43780717 original size:28 final size:28
Alignment explanation
Indices: 43780616--43780729 Score: 81
Period size: 28 Copynumber: 3.9 Consensus size: 28
43780606 ACTTGTAATA
* * *
43780616 GGGCTACGGCCCAGACTGATACTGATAT
1 GGGCTAAGGCCCAGATTAATACTGATAT
* *
43780644 GGGCT-AGGCCCAGTATGCTCTGATATTG-TAAT
1 GGGCTAAGGCCCAG-A---T-TAATACTGAT-AT
*
43780676 AGGGCTATGGCCCAGATTAATACTGATAT
1 -GGGCTAAGGCCCAGATTAATACTGATAT
*
43780705 GGGCTAAGGCCCAG-TTAACACTGAT
1 GGGCTAAGGCCCAGATTAATACTGAT
43780730 TTCTGAATAG
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
27 17 0.25
28 19 0.28
29 8 0.12
30 2 0.03
31 1 0.01
32 9 0.13
33 6 0.09
34 7 0.10
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (28 bp):
GGGCTAAGGCCCAGATTAATACTGATAT
Found at i:43780750 original size:62 final size:61
Alignment explanation
Indices: 43780608--43780752 Score: 179
Period size: 61 Copynumber: 2.4 Consensus size: 61
43780598 ATATCTCGAC
* * *
43780608 TTGTAATAGGGCTACGGCCCAGACTGATACTGATATGGGCTAGGCCCAGTATGCTCTGATA
1 TTGTAATAGGGCTACGGCCCAGACTAATACTGATATGGGCTAGGCCCAGTATACACTGATA
* *
43780669 TTGTAATAGGGCTATGGCCCAGATTAATACTGATATGGGCTAAGGCCCAGT-TAACACTGAT-
1 TTGTAATAGGGCTACGGCCCAGACTAATACTGATATGGGCT-AGGCCCAGTAT-ACACTGATA
*
43780730 TTCTGAATAGGGCTTA-GGCCCAG
1 TTGT-AATAGGGC-TACGGCCCAG
43780753 TAAAGCTTGA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
61 42 0.57
62 30 0.41
63 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (61 bp):
TTGTAATAGGGCTACGGCCCAGACTAATACTGATATGGGCTAGGCCCAGTATACACTGATA
Found at i:43783901 original size:10 final size:10
Alignment explanation
Indices: 43783886--43783924 Score: 78
Period size: 10 Copynumber: 3.9 Consensus size: 10
43783876 GACAAGTTTG
43783886 AGAAACAAGA
1 AGAAACAAGA
43783896 AGAAACAAGA
1 AGAAACAAGA
43783906 AGAAACAAGA
1 AGAAACAAGA
43783916 AGAAACAAG
1 AGAAACAAG
43783925 TTTGAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.69, C:0.10, G:0.21, T:0.00
Consensus pattern (10 bp):
AGAAACAAGA
Found at i:43792059 original size:41 final size:41
Alignment explanation
Indices: 43792002--43792281 Score: 381
Period size: 41 Copynumber: 6.8 Consensus size: 41
43791992 GAATATAATA
* *
43792002 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
43792043 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
43792084 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
43792125 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
43792166 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
43792207 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TT
* * **
43792248 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
43792282 ATCTGTTTAA
Statistics
Matches: 222, Mismatches: 10, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
39 3 0.01
40 8 0.04
41 209 0.94
42 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:43794723 original size:23 final size:24
Alignment explanation
Indices: 43794695--43794745 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
43794685 ATTAATTGGA
* *
43794695 TAAATTCTGAATAT-TAAAAGTAT
1 TAAATTCTAAATATCTAAAAATAT
*
43794718 TAAATTTTAAATATCTAAAAATAT
1 TAAATTCTAAATATCTAAAAATAT
43794742 TAAA
1 TAAA
43794746 GATGGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
TAAATTCTAAATATCTAAAAATAT
Found at i:43795487 original size:21 final size:21
Alignment explanation
Indices: 43795461--43795501 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43795451 AGTAATATTA
43795461 CAGTAAAATTAGT-TATTGTAT
1 CAGTAAAATT-GTATATTGTAT
43795482 CAGTAAAATTGTATATTGTA
1 CAGTAAAATTGTATATTGTA
43795502 GCATTGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (21 bp):
CAGTAAAATTGTATATTGTAT
Found at i:43802109 original size:17 final size:17
Alignment explanation
Indices: 43802069--43802111 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
43802059 ATATTTAATT
* *
43802069 TAAAAATTATATATTAT
1 TAAAATTTATATATTAA
*
43802086 TATAAATTTATATTTTAA
1 TA-AAATTTATATATTAA
43802104 TAAAATTT
1 TAAAATTT
43802112 GAAACCGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAAATTTATATATTAA
Found at i:43806846 original size:19 final size:19
Alignment explanation
Indices: 43806822--43806858 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
43806812 CGTTCATGTG
*
43806822 TTTTAACAATACTAGTGGT
1 TTTTAACAATACAAGTGGT
43806841 TTTTAACAATACAAGTGG
1 TTTTAACAATACAAGTGG
43806859 AAACATGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTTAACAATACAAGTGGT
Found at i:43816703 original size:108 final size:108
Alignment explanation
Indices: 43816514--43816739 Score: 434
Period size: 108 Copynumber: 2.1 Consensus size: 108
43816504 ACTTAGCGTG
*
43816514 TTAACAGTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAGACAT
1 TTAACATTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAGACAT
*
43816579 TGTGTGTTTCTCTCATTACTTTACTCCTTATTCTACTTTGAAT
66 TGTGTGTTTCTCTCATTACTTTACTCCTTACTCTACTTTGAAT
43816622 TTAACATTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAGACAT
1 TTAACATTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAGACAT
43816687 TGTGTGTTTCTCTCATTACTTTACTCCTTACTCTACTTTGAAT
66 TGTGTGTTTCTCTCATTACTTTACTCCTTACTCTACTTTGAAT
43816730 TTAACATTTA
1 TTAACATTTA
43816740 TGTTTGTTCC
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 116 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (108 bp):
TTAACATTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAGACAT
TGTGTGTTTCTCTCATTACTTTACTCCTTACTCTACTTTGAAT
Found at i:43821599 original size:69 final size:69
Alignment explanation
Indices: 43821484--43821622 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
43821474 TACACAATTA
*
43821484 TCATATGTGGGTGTCTAATTTCATAATGTATGATACTGTCAGTAGCTCTAATTTTATGGGTGAAT
1 TCATATGTGGGTGTCTAATTTCATAATGTATGATACTGTCAATAGCTCTAATTTTATGGGTGAAT
43821549 TTTT
66 TTTT
*
43821553 TCATATGTGGGTGTCTAATTTCATAATGTATGATATTGTCAATAGCTCTAATTTTATGGGTGAAT
1 TCATATGTGGGTGTCTAATTTCATAATGTATGATACTGTCAATAGCTCTAATTTTATGGGTGAAT
43821618 TTTT
66 TTTT
43821622 T
1 T
43821623 TCCGGTTTAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.46
Consensus pattern (69 bp):
TCATATGTGGGTGTCTAATTTCATAATGTATGATACTGTCAATAGCTCTAATTTTATGGGTGAAT
TTTT
Found at i:43822265 original size:17 final size:17
Alignment explanation
Indices: 43822204--43822265 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
43822194 ACTTTAAAAT
*
43822204 AAAAAATATTTTTGAGA
1 AAAAAATATTTTTGAAA
* *
43822221 TAAAAATATTCTT--AA
1 AAAAAATATTTTTGAAA
* **
43822236 ACAAAATGCTTTTGAAA
1 AAAAAATATTTTTGAAA
43822253 AAAAAATATTTTT
1 AAAAAATATTTTT
43822266 CAAACACCAA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
15 9 0.28
17 23 0.72
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (17 bp):
AAAAAATATTTTTGAAA
Found at i:43822828 original size:16 final size:16
Alignment explanation
Indices: 43822794--43822836 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
43822784 AGCAGTATAG
*
43822794 ATATATAAAATCAATA
1 ATATATAAAATCAAAA
43822810 ATATATAAAAT-ATAAA
1 ATATATAAAATCA-AAA
43822826 ATATAGTAAAA
1 ATATA-TAAAA
43822837 AGATACGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 18 0.75
17 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
ATATATAAAATCAAAA
Found at i:43830810 original size:12 final size:12
Alignment explanation
Indices: 43830795--43830830 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
43830785 AAGAAAGGAG
43830795 AAGAGAAGAAAA
1 AAGAGAAGAAAA
*
43830807 AAGAGAAGGAAA
1 AAGAGAAGAAAA
*
43830819 AAGAAAAGAAAA
1 AAGAGAAGAAAA
43830831 GAGAAGGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAGAGAAGAAAA
Found at i:43830836 original size:22 final size:23
Alignment explanation
Indices: 43830784--43830837 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
43830774 AAATAAAGGG
*
43830784 AAAGA-AAGGAGAAGAGAAGAAA
1 AAAGAGAAGGAGAAAAGAAGAAA
43830806 AAAGAGAAGGA-AAAAGAA-AAGA
1 AAAGAGAAGGAGAAAAGAAGAA-A
43830828 AAAGAGAAGG
1 AAAGAGAAGG
43830838 TATAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 22 0.76
23 5 0.17
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (23 bp):
AAAGAGAAGGAGAAAAGAAGAAA
Found at i:43831205 original size:21 final size:21
Alignment explanation
Indices: 43831181--43831221 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
43831171 AAAAAATAAA
43831181 ATACCAAAATAGGTTGTTTGG
1 ATACCAAAATAGGTTGTTTGG
43831202 ATACCAAAATAGGTTGTTTG
1 ATACCAAAATAGGTTGTTTG
43831222 AAAGATTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (21 bp):
ATACCAAAATAGGTTGTTTGG
Found at i:43834040 original size:139 final size:140
Alignment explanation
Indices: 43833870--43834207 Score: 572
Period size: 140 Copynumber: 2.4 Consensus size: 140
43833860 TATTTCTAAA
* * * *
43833870 ATTTTTAAAATTTTCAGATTCTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTTTATCT
1 ATTTCTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTTATCT
43833935 TA-TTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCC
66 TATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCC
* *
43833999 CTTTTTTTGT
131 ATTTGTTTGT
*
43834009 ATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTTATCT
1 ATTTCTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTTATCT
*
43834074 TATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCT
66 TATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCC
43834139 ATTTGTTTGT
131 ATTTGTTTGT
*
43834149 A-TTCTTAAAATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTT
1 ATTTC-TAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTT
43834208 ATACTATTTT
Statistics
Matches: 187, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
139 65 0.35
140 122 0.65
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (140 bp):
ATTTCTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTTATCT
TATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCC
ATTTGTTTGT
Found at i:43834204 original size:13 final size:13
Alignment explanation
Indices: 43834186--43834228 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
43834176 TTAAAATATA
43834186 TTATTTTCGTATT
1 TTATTTTCGTATT
* *
43834199 TTATTTT-TTATA
1 TTATTTTCGTATT
*
43834211 CTATTTTCGTATT
1 TTATTTTCGTATT
43834224 TTATT
1 TTATT
43834229 GTATTTTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (13 bp):
TTATTTTCGTATT
Found at i:43834246 original size:46 final size:48
Alignment explanation
Indices: 43834166--43834313 Score: 135
Period size: 46 Copynumber: 3.1 Consensus size: 48
43834156 AAATTTTCGG
* * * * *
43834166 ATTTTAT-TTTTTAAAATATATTATTTTCGTATTTTATTTTTTATACT
1 ATTTTATATTTTCATAAGATATTTTTTTCATATTTTATTTTTTATACT
* * *
43834213 ATTTTCGTATTTT-AT-TG-TATTTTTTTCATATTTTATTTCTTT-TCCT
1 ATTTT-ATATTTTCATAAGATATTTTTTTCATATTTTATTT-TTTATACT
* *
43834259 ATTTTATTTTTTCATGAAGATATTTTTTTCATATTTTCTTTTTTTATACT
1 ATTTTATATTTTCAT-AAGATATTTTTTTCATATTTT-ATTTTTTATACT
43834309 ATTTT
1 ATTTT
43834314 TGTAAAATAG
Statistics
Matches: 80, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
45 5 0.06
46 29 0.36
47 8 0.10
48 3 0.04
49 24 0.30
50 11 0.14
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.68
Consensus pattern (48 bp):
ATTTTATATTTTCATAAGATATTTTTTTCATATTTTATTTTTTATACT
Found at i:43834261 original size:17 final size:16
Alignment explanation
Indices: 43834225--43834303 Score: 79
Period size: 16 Copynumber: 4.9 Consensus size: 16
43834215 TTTCGTATTT
*
43834225 TATTGTATTTTTTTCA
1 TATTTTATTTTTTTCA
*
43834241 TATTTTATTTCTTTTCC
1 TATTTTATTT-TTTTCA
43834258 TATTTTA-TTTTTTCA
1 TATTTTATTTTTTTCA
***
43834273 TGAAGATATTTTTTTCA
1 T-ATTTTATTTTTTTCA
*
43834290 TATTTTCTTTTTTT
1 TATTTTATTTTTTT
43834304 ATACTATTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.12
16 23 0.46
17 21 0.42
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.70
Consensus pattern (16 bp):
TATTTTATTTTTTTCA
Done.