Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 136 of 318
Found at i:42174847 original size:21 final size:21
Alignment explanation
Indices: 42174822--42174866 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
42174812 ATTCAAATTG
42174822 TAAGTGGTTTTATATTTTATT
1 TAAGTGGTTTTATATTTTATT
42174843 TAAGTGGTTTTATATTTTATT
1 TAAGTGGTTTTATATTTTATT
42174864 TAA
1 TAA
42174867 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (21 bp):
TAAGTGGTTTTATATTTTATT
Found at i:42176160 original size:18 final size:19
Alignment explanation
Indices: 42176137--42176175 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
42176127 TATTTTGAAA
42176137 TTTTAATA-CTTCAAAATT
1 TTTTAATATCTTCAAAATT
*
42176155 TTTTAATATGTTCAAAATT
1 TTTTAATATCTTCAAAATT
42176174 TT
1 TT
42176176 AATATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTTAATATCTTCAAAATT
Found at i:42176175 original size:17 final size:17
Alignment explanation
Indices: 42176134--42176180 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
42176124 AAATATTTTG
42176134 AAATTTTAATA-CTTCA
1 AAATTTTAATATCTTCA
*
42176150 AAATTTTTTAATATGTTCA
1 AAA--TTTTAATATCTTCA
42176169 AAATTTTAATAT
1 AAATTTTAATAT
42176181 ATTTTGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 3 0.11
17 9 0.33
18 8 0.30
19 7 0.26
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATTTTAATATCTTCA
Found at i:42176262 original size:17 final size:17
Alignment explanation
Indices: 42176236--42176272 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
42176226 TAATATTTTC
42176236 TTTAACATATTTAAAAT
1 TTTAACATATTTAAAAT
*
42176253 TTTAATATATTTAAAAT
1 TTTAACATATTTAAAAT
42176270 TTT
1 TTT
42176273 TTAAGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAACATATTTAAAAT
Found at i:42176295 original size:26 final size:28
Alignment explanation
Indices: 42176252--42176309 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 28
42176242 ATATTTAAAA
* * *
42176252 TTTTAATATATTTAAAATTTTTTAAGTT
1 TTTTAATAAATTTAAAATATATTAAGTT
*
42176280 TTTTAA-AAATTT-AAATATATTAATTT
1 TTTTAATAAATTTAAAATATATTAAGTT
42176306 TTTT
1 TTTT
42176310 TCTCTTTACC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 15 0.58
27 5 0.19
28 6 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTAATAAATTTAAAATATATTAAGTT
Found at i:42176367 original size:13 final size:13
Alignment explanation
Indices: 42176349--42176375 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42176339 TATATTAAAA
42176349 TTTTAAAATATAT
1 TTTTAAAATATAT
42176362 TTTTAAAATATAT
1 TTTTAAAATATAT
42176375 T
1 T
42176376 GAACATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAAATATAT
Found at i:42176448 original size:19 final size:20
Alignment explanation
Indices: 42176419--42176458 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42176409 AACATTTTTT
**
42176419 AATATATTTAATTTTTTAAA
1 AATATATTTAAAATTTTAAA
42176439 AATATA-TTAAAATTTTAAA
1 AATATATTTAAAATTTTAAA
42176458 A
1 A
42176459 TTGGTTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATATTTAAAATTTTAAA
Found at i:42176450 original size:62 final size:61
Alignment explanation
Indices: 42176380--42176498 Score: 220
Period size: 62 Copynumber: 1.9 Consensus size: 61
42176370 TATATTGAAC
*
42176380 ATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTAATTTTTTAAAAAT
1 ATATTAAAATTTTAAAATTGGTTATACTTAAC-CTTTTTAATATATTTAATTTTTTAAAAAT
42176442 ATATTAAAATTTTAAAATTGGTTATACTTAACCTTTTTAATATATTTAATTTTTTAA
1 ATATTAAAATTTTAAAATTGGTTATACTTAACCTTTTTAATATATTTAATTTTTTAA
42176499 TATATTTCAT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 24 0.43
62 32 0.57
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (61 bp):
ATATTAAAATTTTAAAATTGGTTATACTTAACCTTTTTAATATATTTAATTTTTTAAAAAT
Found at i:42176490 original size:18 final size:17
Alignment explanation
Indices: 42176464--42176505 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
42176454 TAAAATTGGT
*
42176464 TATACTTAACCTTTTTAA
1 TATATTTAA-CTTTTTAA
*
42176482 TATATTTAATTTTTTAA
1 TATATTTAACTTTTTAA
42176499 TATATTT
1 TATATTT
42176506 CATTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTAACTTTTTAA
Found at i:42176516 original size:18 final size:17
Alignment explanation
Indices: 42176475--42176513 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
42176465 ATACTTAACC
42176475 TTTTTAATATATTTAAT
1 TTTTTAATATATTTAAT
*
42176492 TTTTTAATATATTTCAT
1 TTTTTAATATATTTAAT
42176509 TTTTT
1 TTTTT
42176514 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTAATATATTTAAT
Found at i:42194515 original size:21 final size:20
Alignment explanation
Indices: 42194482--42194525 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
42194472 TAATAATATA
*
42194482 AAACAAATGCATAAGGGAAAT
1 AAACAAATACATAA-GGAAAT
* *
42194503 AAACGAATACATAAGTAAAT
1 AAACAAATACATAAGGAAAT
42194523 AAA
1 AAA
42194526 AGAAAAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (20 bp):
AAACAAATACATAAGGAAAT
Found at i:42194621 original size:3 final size:3
Alignment explanation
Indices: 42194615--42194717 Score: 57
Period size: 3 Copynumber: 34.3 Consensus size: 3
42194605 AATATTGATG
* * * *
42194615 ATA ATA ATA ATA A-A AGTA ATA ATA AGA ATA TTA AT- ATT TTA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *** ** * *
42194659 ATA GTG ATA ATA ATA ATA GCG ACG ATA ATA ATA ATG ATA ATA ACA ACTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
42194708 ATA ATA ATA A
1 ATA ATA ATA A
42194718 CGATAATGCA
Statistics
Matches: 75, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
2 4 0.05
3 67 0.89
4 4 0.05
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:42194921 original size:34 final size:35
Alignment explanation
Indices: 42194855--42194921 Score: 86
Period size: 34 Copynumber: 1.9 Consensus size: 35
42194845 ATTTAGTTAA
*
42194855 AAAATAATAATAACGTATAGGTAAATACAAAAAGG
1 AAAATAATAATAACGTATAGGTAAATAAAAAAAGG
42194890 AAAAT-ATAATAACAGTAATA-GT-AATAAAAAAA
1 AAAATAATAATAAC-GT-ATAGGTAAATAAAAAAA
42194922 TACAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 17 0.59
35 9 0.31
36 3 0.10
ACGTcount: A:0.64, C:0.04, G:0.10, T:0.21
Consensus pattern (35 bp):
AAAATAATAATAACGTATAGGTAAATAAAAAAAGG
Found at i:42195162 original size:29 final size:29
Alignment explanation
Indices: 42195100--42195164 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
42195090 AAAGAAAACA
*
42195100 AATATATGATAGTATGTACATAATATATC
1 AATATATGATAGTATGTACATAAAATATC
* *
42195129 TATATATG-TATGTATGTATTATAAAATAT-
1 AATATATGATA-GTATGTA-CATAAAATATC
42195158 AATATAT
1 AATATAT
42195165 ATGCATACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 2 0.07
29 20 0.67
30 8 0.27
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (29 bp):
AATATATGATAGTATGTACATAAAATATC
Found at i:42199338 original size:25 final size:25
Alignment explanation
Indices: 42199310--42199389 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
42199300 TGCTCCAGGC
42199310 CGTGTCACACGCCCGTGTTCCAAGT
1 CGTGTCACACGCCCGTGTTCCAAGT
* * * * *
42199335 CGTGTAACTCGCCTGTGTTCCAGGC
1 CGTGTCACACGCCCGTGTTCCAAGT
42199360 CGTGTCACACGCCCGTGTTCCAAGT
1 CGTGTCACACGCCCGTGTTCCAAGT
42199385 CGTGT
1 CGTGT
42199390 AACTCTTGAA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (25 bp):
CGTGTCACACGCCCGTGTTCCAAGT
Found at i:42199360 original size:50 final size:50
Alignment explanation
Indices: 42199297--42199394 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
42199287 AGCCGTGTCA
42199297 CTGTGCTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTCGC
1 CTGTGCTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTCGC
*
42199347 CTGTGTTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTC
1 CTGTGCTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTC
42199395 TTGAATTAGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.14, C:0.35, G:0.26, T:0.26
Consensus pattern (50 bp):
CTGTGCTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTCGC
Found at i:42199623 original size:25 final size:25
Alignment explanation
Indices: 42199595--42199670 Score: 107
Period size: 25 Copynumber: 3.0 Consensus size: 25
42199585 CCCTGTCACA
42199595 CGCCCGTGTTCCAAGTCGTGTAACT
1 CGCCCGTGTTCCAAGTCGTGTAACT
* * * * *
42199620 CGCCTGTGTTCCAGGCCGTGTCACA
1 CGCCCGTGTTCCAAGTCGTGTAACT
42199645 CGCCCGTGTTCCAAGTCGTGTAACT
1 CGCCCGTGTTCCAAGTCGTGTAACT
42199670 C
1 C
42199671 TTGAATTAGC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.14, C:0.34, G:0.25, T:0.26
Consensus pattern (25 bp):
CGCCCGTGTTCCAAGTCGTGTAACT
Found at i:42199627 original size:50 final size:50
Alignment explanation
Indices: 42199573--42199670 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
42199563 AGCCGTGTCA
42199573 CTGTGTTCCAGGCCCTGTCACACGCCCGTGTTCCAAGTCGTGTAACTCGC
1 CTGTGTTCCAGGCCCTGTCACACGCCCGTGTTCCAAGTCGTGTAACTCGC
*
42199623 CTGTGTTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTC
1 CTGTGTTCCAGGCCCTGTCACACGCCCGTGTTCCAAGTCGTGTAACTC
42199671 TTGAATTAGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.14, C:0.35, G:0.24, T:0.27
Consensus pattern (50 bp):
CTGTGTTCCAGGCCCTGTCACACGCCCGTGTTCCAAGTCGTGTAACTCGC
Found at i:42199743 original size:276 final size:276
Alignment explanation
Indices: 42199204--42199802 Score: 1071
Period size: 276 Copynumber: 2.2 Consensus size: 276
42199194 GGTCACACGA
* * * * * * *
42199204 CCGTGTGGCCAGGCTGTGTGCCTCACACGGTTGAGACACAC-GCC-CG--TATCTCAGGACATGT
1 CCGTGTTGCCAGGCCGTGTGCCACACACGGATGAGTCACACTTCCGTGTCTATCTCAGGACATGT
*
42199265 AACAATCGAAATAGGGTCACATAGCCGTGTCACTGTGCTCCAGGCCGTGTCACACGCCCGTGTTC
66 AACAATCGAAATAGGGTCACATAGCCGTGTCACTGTGCTCCAGGCCCTGTCACACGCCCGTGTTC
42199330 CAAGTCGTGTAACTCGCCTGTGTTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTC
131 CAAGTCGTGTAACTCGCCTGTGTTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTC
*
42199395 TTGAATTAGCCCCATACGCCTGTGTGCTAGGCCATGTAACTGTCTGGCTTGGATGCAATAAAACC
196 TTGAATTAGCCCCATACGCCTGTGTGCTAGGCCATGTAACTGTCTAGCTTGGATGCAATAAAACC
42199460 TACAGGGGACGCATGG
261 TACAGGGGACGCATGG
*
42199476 CCGTGTTGCCAGGCCGTGTGCCACACACGGATGAGTCACACTTCCGTGTCTATCTCAGGCCATGT
1 CCGTGTTGCCAGGCCGTGTGCCACACACGGATGAGTCACACTTCCGTGTCTATCTCAGGACATGT
*
42199541 AACAATCGAAATAGGGTCACATAGCCGTGTCACTGTGTTCCAGGCCCTGTCACACGCCCGTGTTC
66 AACAATCGAAATAGGGTCACATAGCCGTGTCACTGTGCTCCAGGCCCTGTCACACGCCCGTGTTC
42199606 CAAGTCGTGTAACTCGCCTGTGTTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTC
131 CAAGTCGTGTAACTCGCCTGTGTTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTC
42199671 TTGAATTAGCCCCATACGCCTGTGTGCTAGGCCATGTAACTGTCTAGCTTGGATGCAATAAAACC
196 TTGAATTAGCCCCATACGCCTGTGTGCTAGGCCATGTAACTGTCTAGCTTGGATGCAATAAAACC
42199736 TACAGGGGACGCATGG
261 TACAGGGGACGCATGG
42199752 CCGTGTTGCCAGGCCGTGTGCCACACACGGATGAGTCACACTTCCGTGTCT
1 CCGTGTTGCCAGGCCGTGTGCCACACACGGATGAGTCACACTTCCGTGTCT
42199803 CAGGCTATGT
Statistics
Matches: 312, Mismatches: 11, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
272 36 0.12
273 2 0.01
274 1 0.00
276 273 0.88
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.24
Consensus pattern (276 bp):
CCGTGTTGCCAGGCCGTGTGCCACACACGGATGAGTCACACTTCCGTGTCTATCTCAGGACATGT
AACAATCGAAATAGGGTCACATAGCCGTGTCACTGTGCTCCAGGCCCTGTCACACGCCCGTGTTC
CAAGTCGTGTAACTCGCCTGTGTTCCAGGCCGTGTCACACGCCCGTGTTCCAAGTCGTGTAACTC
TTGAATTAGCCCCATACGCCTGTGTGCTAGGCCATGTAACTGTCTAGCTTGGATGCAATAAAACC
TACAGGGGACGCATGG
Found at i:42204329 original size:32 final size:32
Alignment explanation
Indices: 42204293--42204357 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
42204283 TATATGCATT
42204293 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
42204325 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
42204357 T
1 T
42204358 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:42211352 original size:17 final size:18
Alignment explanation
Indices: 42211330--42211363 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42211320 ATATTCATAA
42211330 TTATATATATA-ATTGTT
1 TTATATATATATATTGTT
*
42211347 TTATATTTATATATTGT
1 TTATATATATATATTGT
42211364 ATGCATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
TTATATATATATATTGTT
Found at i:42229247 original size:93 final size:93
Alignment explanation
Indices: 42229088--42229259 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
42229078 GTCCATAAGT
* * * *
42229088 GAACTCGGACTCAACTCAAAGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACACAACTCAAAGAGCTCAGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
42229153 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
42229181 GAACTCGGACACAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACACAACTCAAAGAGCTCAGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
*
42229246 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
42229260 CAAATATCCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCGGACACAACTCAAAGAGCTCAGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:42229252 original size:46 final size:44
Alignment explanation
Indices: 42229079--42229249 Score: 164
Period size: 46 Copynumber: 3.7 Consensus size: 44
42229069 ATGTAACCCG
* *
42229079 TCCATAAGTGAACTCGGACTCAACTCAAAGAGCTCGGGCGTTCGCA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTC--GCATTCGCA
* * *
42229125 TCCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGATGC-CTA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGCATTCGC-A
* *** * *
42229169 GTTACATCTCTCGAACTCGGACACAACTCAACGAGTTCAGACATTCGCA
1 --TCCATAAGT-GAACTCGGACTCAACTCAACGAGCTC-G-CATTCGCA
42229218 TCCATAAGTGAACTCGGACTCAACTCAACGAG
1 TCCATAAGTGAACTCGGACTCAACTCAACGAG
42229250 TTCGGATGCC
Statistics
Matches: 99, Mismatches: 19, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 60 0.61
47 28 0.28
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.20
Consensus pattern (44 bp):
TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGCATTCGCA
Found at i:42231982 original size:12 final size:12
Alignment explanation
Indices: 42231931--42232090 Score: 102
Period size: 12 Copynumber: 13.3 Consensus size: 12
42231921 AAAATTGTAC
*
42231931 ATAATAATAAATA
1 ATAA-AATATATA
42231944 ATAAAATA-ATA
1 ATAAAATATATA
*
42231955 A-AATAATAAAATA
1 ATAA-AAT-ATATA
42231968 ATAAAATATATA
1 ATAAAATATATA
42231980 ATAAAA-A-ATA
1 ATAAAATATATA
*
42231990 AAAAAATATAATGA
1 ATAAAATAT-AT-A
* *
42232004 ATCATATATATA
1 ATAAAATATATA
42232016 ATAAAATGATATA
1 ATAAAAT-ATATA
*
42232029 AT-ATAT-TATA
1 ATAAAATATATA
*
42232039 A-AGAATATA-A
1 ATAAAATATATA
*
42232049 ATAAAATGTATA
1 ATAAAATATATA
*
42232061 ATAAAATATGAAAA
1 ATAAAATAT--ATA
*
42232075 ATAATATATATA
1 ATAAAATATATA
42232087 ATAA
1 ATAA
42232091 TTTTTTATAT
Statistics
Matches: 116, Mismatches: 16, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
10 19 0.16
11 17 0.15
12 39 0.34
13 22 0.19
14 19 0.16
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (12 bp):
ATAAAATATATA
Found at i:42231986 original size:29 final size:27
Alignment explanation
Indices: 42231931--42232090 Score: 109
Period size: 26 Copynumber: 6.0 Consensus size: 27
42231921 AAAATTGTAC
*
42231931 ATAATAATAAATAATAA-A-ATAATAAA
1 ATAATAAAAAATAA-AATATATAATAAA
42231957 ATAATAAAATAATAAAATATATAATAAA
1 ATAATAAAA-AATAAAATATATAATAAA
* * *
42231985 A-AATAAAAAAATATAATGA-ATCATATAT
1 ATAAT-AAAAAATAAAAT-ATATAATA-AA
* * *
42232013 ATAATAAAATGATATAATATATTAT-AA
1 ATAATAAAA-AATAAAATATATAATAAA
* * *
42232040 AGAAT-ATAAATAAAATGTATAATAAA
1 ATAATAAAAAATAAAATATATAATAAA
* *
42232066 AT-ATGAAAAATAATATATATAATAA
1 ATAATAAAAAATAAAATATATAATAA
42232091 TTTTTTATAT
Statistics
Matches: 106, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
25 13 0.12
26 32 0.30
27 26 0.25
28 21 0.20
29 14 0.13
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAATAAAAAATAAAATATATAATAAA
Found at i:42231992 original size:7 final size:8
Alignment explanation
Indices: 42231933--42231997 Score: 91
Period size: 8 Copynumber: 8.5 Consensus size: 8
42231923 AATTGTACAT
42231933 AATAAT-A
1 AATAATAA
42231940 AATAATAA
1 AATAATAA
42231948 AATAATAA
1 AATAATAA
42231956 AATAATAA
1 AATAATAA
42231964 AATAATAA
1 AATAATAA
*
42231972 AAT-ATAT
1 AATAATAA
42231979 AATAA-AA
1 AATAATAA
*
42231986 AATAAAAA
1 AATAATAA
42231994 AATA
1 AATA
42231998 TAATGAATCA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
7 18 0.34
8 35 0.66
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAATAA
Found at i:42232163 original size:29 final size:27
Alignment explanation
Indices: 42232121--42232176 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
42232111 TTTATAGTAA
*
42232121 AAATAAATAATATATAAAATATTCAAAAT
1 AAATAAATAATATA-AAAAAATT-AAAAT
**
42232150 AAATAAATTCTATAAAAAAATTAAAAT
1 AAATAAATAATATAAAAAAATTAAAAT
42232177 GGACTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 7 0.29
29 12 0.50
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (27 bp):
AAATAAATAATATAAAAAAATTAAAAT
Found at i:42235862 original size:33 final size:32
Alignment explanation
Indices: 42235813--42235875 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
42235803 CTCGCTGCAA
* *
42235813 TCTGGTGGCTTTGCCACATATATATATATCTAT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTAT
*
42235846 TCTGGTGGCCTAGCCACAATATCTATATCT
1 TCTGGTGGCCTAGCCACAATATATATATCT
42235876 GGTGACTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTAT
Found at i:42243308 original size:26 final size:27
Alignment explanation
Indices: 42243279--42243338 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
42243269 CCACATATAT
*
42243279 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
42243305 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
42243332 ATATCTG
1 ATATCTG
42243339 GCAGCCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:42244154 original size:46 final size:46
Alignment explanation
Indices: 42244083--42244203 Score: 206
Period size: 46 Copynumber: 2.6 Consensus size: 46
42244073 TACATTTCAC
**
42244083 GAACTCGGACTCAACTCAATAAGTTCAGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGT
* *
42244129 GAACTCGGACTCAACTCAACGAGTTCGGACATTCTCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGT
42244175 GAACTCGGACTCAACTCAACGAGTTCAGA
1 GAACTCGGACTCAACTCAACGAGTTCAGA
42244204 TGCCCAAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGT
Found at i:42256358 original size:28 final size:26
Alignment explanation
Indices: 42256300--42256360 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
42256290 TAATATATAT
*
42256300 AATAATATTTCACGCAAATATAACAAC
1 AATAA-ATTTCACGCAAATATAAAAAC
42256327 -ATAAATTTCCACGCAAATATATAAAAC
1 AATAAATTT-CACGCAAATATA-AAAAC
42256354 AATAAAT
1 AATAAAT
42256361 AACATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 4 0.13
26 16 0.53
27 4 0.13
28 6 0.20
ACGTcount: A:0.54, C:0.16, G:0.03, T:0.26
Consensus pattern (26 bp):
AATAAATTTCACGCAAATATAAAAAC
Found at i:42257361 original size:22 final size:21
Alignment explanation
Indices: 42257326--42257401 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
42257316 AAAAGGTATC
* *
42257326 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
42257347 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
42257370 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
42257389 TGC-AATCATATCT
1 TACAAATCATATCT
42257402 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:42257418 original size:35 final size:37
Alignment explanation
Indices: 42257355--42257452 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
42257345 ATTACAAAAT
42257355 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
42257391 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
42257426 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
42257453 TGAAGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:42257460 original size:17 final size:19
Alignment explanation
Indices: 42257362--42257452 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
42257352 AATCATATCT
42257362 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42257381 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
42257399 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
42257416 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42257435 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
42257453 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:42259126 original size:15 final size:16
Alignment explanation
Indices: 42259102--42259144 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
42259092 CATATTTATT
42259102 ATATAATTCAATCAAA
1 ATATAATTCAATCAAA
*
42259118 ATA-AATTCAATCAAT
1 ATATAATTCAATCAAA
42259133 ATATAATTCAAT
1 ATATAATTCAAT
42259145 ATTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAATTCAATCAAA
Found at i:42259290 original size:17 final size:18
Alignment explanation
Indices: 42259246--42259292 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
42259236 AGCTTCCAAA
*
42259246 TCCTCATTCTCCCTTTTCT
1 TCCTCTTTC-CCCTTTTCT
**
42259265 TTTTCTTTCCCCTTTTCT
1 TCCTCTTTCCCCTTTTCT
42259283 TCCT-TTTCCC
1 TCCTCTTTCCC
42259293 GTTTGCTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 6 0.26
18 11 0.48
19 6 0.26
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (18 bp):
TCCTCTTTCCCCTTTTCT
Found at i:42259532 original size:20 final size:21
Alignment explanation
Indices: 42259509--42259556 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
42259499 TATAATTATT
* *
42259509 TAATTTATAAATATCT-TTTA
1 TAATTAATAAATATCTATTAA
42259529 TAATTAATAAATATCTATTAA
1 TAATTAATAAATATCTATTAA
42259550 TAATTAA
1 TAATTAA
42259557 ATACATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTAATAAATATCTATTAA
Found at i:42259955 original size:14 final size:14
Alignment explanation
Indices: 42259938--42259980 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
42259928 TCTTATAATA
42259938 TAATTATAATAAAT
1 TAATTATAATAAAT
42259952 TAATT-TAATATAAT
1 TAATTATAATA-AAT
*
42259966 TTATTACTAATAAAT
1 TAATTA-TAATAAAT
42259981 ATATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 12 0.48
15 3 0.12
16 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTATAATAAAT
Found at i:42265051 original size:15 final size:16
Alignment explanation
Indices: 42265027--42265069 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
42265017 CATATTTATT
42265027 ATATAATTCAATCAAA
1 ATATAATTCAATCAAA
*
42265043 ATA-AATTCAATCAAT
1 ATATAATTCAATCAAA
42265058 ATATAATTCAAT
1 ATATAATTCAAT
42265070 ATTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAATTCAATCAAA
Found at i:42265459 original size:20 final size:21
Alignment explanation
Indices: 42265436--42265483 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
42265426 TATAATTATT
* *
42265436 TAATTTATAAATATCT-TTTA
1 TAATTAATAAATATCTATTAA
42265456 TAATTAATAAATATCTATTAA
1 TAATTAATAAATATCTATTAA
42265477 TAATTAA
1 TAATTAA
42265484 ATACATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTAATAAATATCTATTAA
Found at i:42265882 original size:14 final size:14
Alignment explanation
Indices: 42265865--42265907 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
42265855 TCTTATAATA
42265865 TAATTATAATAAAT
1 TAATTATAATAAAT
42265879 TAATT-TAATATAAT
1 TAATTATAATA-AAT
*
42265893 TTATTACTAATAAAT
1 TAATTA-TAATAAAT
42265908 ATATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 12 0.48
15 3 0.12
16 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTATAATAAAT
Found at i:42266352 original size:3 final size:3
Alignment explanation
Indices: 42266344--42266422 Score: 76
Period size: 3 Copynumber: 26.0 Consensus size: 3
42266334 AAAATTGTAC
42266344 ATA ATA ATAA ATA ATAA ATA ATA A-A ATA ATA A-A ATA ATA A-A ATA
1 ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
42266388 TATA ATAA ATA ATA AAA ATA AT- ATA ATGA ATA ATA
1 -ATA AT-A ATA ATA ATA ATA ATA ATA AT-A ATA ATA
42266423 TATTATAAAG
Statistics
Matches: 65, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
2 8 0.12
3 42 0.65
4 15 0.23
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:42266356 original size:7 final size:7
Alignment explanation
Indices: 42266346--42266422 Score: 88
Period size: 7 Copynumber: 11.0 Consensus size: 7
42266336 AATTGTACAT
42266346 AATAATA
1 AATAATA
42266353 AATAATA
1 AATAATA
42266360 AATAATAA
1 AATAAT-A
42266368 AATAATAA
1 AATAAT-A
42266376 AATAAT-
1 AATAATA
42266382 AA-AATA
1 AATAATA
*
42266388 TATAATA
1 AATAATA
42266395 AATAATA
1 AATAATA
42266402 AA-AATA
1 AATAATA
*
42266408 ATATAATG
1 A-ATAATA
42266416 AATAATA
1 AATAATA
42266423 TATTATAAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
5 3 0.05
6 8 0.13
7 31 0.51
8 19 0.31
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (7 bp):
AATAATA
Found at i:42266375 original size:28 final size:28
Alignment explanation
Indices: 42266346--42266431 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 28
42266336 AATTGTACAT
42266346 AATAATAAATAATAAATAATAAAATAATAA
1 AATAAT-AATAATAAATAAT-AAATAATAA
*
42266376 AATAATAA-AATATATAATAAATAATAAA
1 AATAATAATAATAAATAATAAATAAT-AA
* * *
42266404 AATAAT-ATAATGAATAATATATTATAA
1 AATAATAATAATAAATAATAAATAATAA
42266431 A
1 A
42266432 GCATATAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
27 11 0.22
28 30 0.61
29 2 0.04
30 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (28 bp):
AATAATAATAATAAATAATAAATAATAA
Found at i:42266394 original size:12 final size:12
Alignment explanation
Indices: 42266377--42266481 Score: 80
Period size: 12 Copynumber: 8.8 Consensus size: 12
42266367 AAATAATAAA
42266377 ATAATAAAATAT
1 ATAATAAAATAT
42266389 ATAAT-AAATA-
1 ATAATAAAATAT
42266399 AT-A-AAAATAAT
1 ATAATAAAAT-AT
42266410 ATAATGAATAATAT
1 ATAAT-AA-AATAT
*
42266424 ATTATAAAGCATAT
1 ATAATAAA--ATAT
*
42266438 A-AATAAAATGT
1 ATAATAAAATAT
42266449 ATAATAAAATAT
1 ATAATAAAATAT
*
42266461 -GAA-AAAATAT
1 ATAATAAAATAT
42266471 ATATATAAAAT
1 ATA-ATAAAAT
42266482 TTTTTTATAT
Statistics
Matches: 74, Mismatches: 6, Indels: 25
0.70 0.06 0.24
Matches are distributed among these distances:
9 5 0.07
10 10 0.14
11 14 0.19
12 17 0.23
13 12 0.16
14 13 0.18
15 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (12 bp):
ATAATAAAATAT
Found at i:42266431 original size:35 final size:33
Alignment explanation
Indices: 42266344--42266431 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 33
42266334 AAAATTGTAC
*
42266344 ATAATAATAAATAATAAATAATAAAATAATAAA
1 ATAATAATATATAATAAATAATAAAATAATAAA
*
42266377 ATAATAAAATATATAATAAATAATAAAAATAATATA
1 ATAAT--AATATATAATAAATAAT-AAAATAATAAA
*
42266413 ATGAATAATATATTATAAA
1 AT-AATAATATATAATAAA
42266432 GCATATAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.10
35 28 0.58
36 12 0.25
37 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (33 bp):
ATAATAATATATAATAAATAATAAAATAATAAA
Found at i:42266548 original size:29 final size:27
Alignment explanation
Indices: 42266511--42266566 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
42266501 GTTTATAGTA
*
42266511 AAAATAAAT-AA-TATATAAAATATTT
1 AAAATAAATAAATTATATAAAAAATTT
*
42266536 AAAATAAATAAATTGTATAAAAAATTT
1 AAAATAAATAAATTATATAAAAAATTT
42266563 AAAA
1 AAAA
42266567 AGGACGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 9 0.33
26 2 0.07
27 16 0.59
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAATAAATAAATTATATAAAAAATTT
Found at i:42273642 original size:21 final size:21
Alignment explanation
Indices: 42273618--42273755 Score: 150
Period size: 21 Copynumber: 6.6 Consensus size: 21
42273608 GTGTTTTACT
*
42273618 TTCTGTTCAGCTCTTACAAGC
1 TTCTGTTCAGCTCTTACGAGC
* * ** *
42273639 TTCTATTCAACTCTTATAAGT
1 TTCTGTTCAGCTCTTACGAGC
* *
42273660 TTTTGTTCAGCTTTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * *
42273681 TTCTGTTCACCTCTTATGAGT
1 TTCTGTTCAGCTCTTACGAGC
* * *
42273702 TTTTGTTTAGCTCTTACGAGT
1 TTCTGTTCAGCTCTTACGAGC
42273723 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
42273744 TTCTGTTCAGCT
1 TTCTGTTCAGCT
42273756 TTCAAGCTTT
Statistics
Matches: 94, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 94 1.00
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:42273682 original size:42 final size:42
Alignment explanation
Indices: 42273621--42273755 Score: 171
Period size: 42 Copynumber: 3.2 Consensus size: 42
42273611 TTTTACTTTC
* * *
42273621 TGTTCAGCTCTTACAAGCTTCTATTCAACTCTTATAAGTTTT
1 TGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATGAGTTTT
* *
42273663 TGTTCAGCTTTTACGAGCTTCTGTTCACCTCTTATGAGTTTT
1 TGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATGAGTTTT
* * * * * *
42273705 TGTTTAGCTCTTACGAGTTTCTGTTCAGCTCTTACGAGCTTC
1 TGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATGAGTTTT
42273747 TGTTCAGCT
1 TGTTCAGCT
42273756 TTCAAGCTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (42 bp):
TGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATGAGTTTT
Found at i:42276770 original size:36 final size:37
Alignment explanation
Indices: 42276703--42276777 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 37
42276693 TATTACAAAA
*
42276703 TCTTACCCGGACATAATCTCCACACGAAGTCATCGGG
1 TCTTACCCGGACATAATCCCCACACGAAGTCATCGGG
*
42276740 TCTTACCCGGACA-AATCCCCACACGTAGTCATCGGG
1 TCTTACCCGGACATAATCCCCACACGAAGTCATCGGG
42276776 TC
1 TC
42276778 CTTAGAACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 23 0.64
37 13 0.36
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (37 bp):
TCTTACCCGGACATAATCCCCACACGAAGTCATCGGG
Found at i:42276976 original size:47 final size:47
Alignment explanation
Indices: 42276898--42277160 Score: 382
Period size: 47 Copynumber: 5.6 Consensus size: 47
42276888 CCCTTCGGGA
* * * * * **
42276898 CTTATCACATTTATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* *
42276945 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
**
42276992 CTTATCACGCATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
** *
42277039 CTTATCACGCATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
42277086 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
42277133 CTTATCACATATATATACACTTTCACAT
1 CTTATCAC--ATATATACACTTTCACAT
42277161 ATGGGTTTAA
Statistics
Matches: 197, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
47 179 0.91
49 18 0.09
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
Found at i:42278592 original size:13 final size:13
Alignment explanation
Indices: 42278574--42278598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42278564 TACTAAATTT
42278574 TCATGGATTCAAG
1 TCATGGATTCAAG
42278587 TCATGGATTCAA
1 TCATGGATTCAA
42278599 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:42281102 original size:40 final size:40
Alignment explanation
Indices: 42281058--42281173 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 40
42281048 GAATACATGT
* * *
42281058 CACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGAACCTAGCCCGGATATAA
* * ***
42281098 CACCAGCACGAATGCTCTTCGGAACTTAGTCCGGATACCT
1 CACCAGCACGAATGCTCTTCGGAACCTAGCCCGGATATAA
* **
42281138 CACTAGCACGAATGCTCTTCGGAATTTAGCCCGGAT
1 CACCAGCACGAATGCTCTTCGGAACCTAGCCCGGAT
42281174 TTAGTAACTC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGAACCTAGCCCGGATATAA
Found at i:42281645 original size:29 final size:29
Alignment explanation
Indices: 42281606--42281684 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
42281596 CTTAATAATC
*
42281606 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
42281636 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
42281665 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
42281685 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:42281727 original size:43 final size:43
Alignment explanation
Indices: 42281666--42281811 Score: 274
Period size: 43 Copynumber: 3.4 Consensus size: 43
42281656 TGCATTTCAA
42281666 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
42281709 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
42281752 GCTCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
42281795 GCTCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
42281812 TGAAAACCAA
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 102 1.00
ACGTcount: A:0.27, C:0.34, G:0.15, T:0.24
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:42283724 original size:37 final size:37
Alignment explanation
Indices: 42283664--42283739 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
42283654 TATTACGAAA
* *
42283664 TCTTACCCGGACATAATCTCCACACGAAGTCATCGGG
1 TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGG
*
42283701 TCTTACCCGGACAAAATCCCCACACGTAGTCATCGGG
1 TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGG
42283738 TC
1 TC
42283740 CTTAGAACTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.21
Consensus pattern (37 bp):
TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGG
Found at i:42283938 original size:47 final size:47
Alignment explanation
Indices: 42283860--42284169 Score: 467
Period size: 47 Copynumber: 6.6 Consensus size: 47
42283850 CCCTTCGGGA
* * * * * **
42283860 CTTATCACATTTATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* *
42283907 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
**
42283954 CTTATCACGCATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
** *
42284001 CTTATCACGCATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
*
42284048 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
42284095 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
42284142 CTTATCACATATATATACACTTTCACAT
1 CTTATCAC--ATATATACACTTTCACAT
42284170 ATGGGTTTAA
Statistics
Matches: 244, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
47 226 0.93
49 18 0.07
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
Found at i:42285602 original size:13 final size:13
Alignment explanation
Indices: 42285584--42285608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42285574 TACTAAATTT
42285584 TCATGGATTCAAG
1 TCATGGATTCAAG
42285597 TCATGGATTCAA
1 TCATGGATTCAA
42285609 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:42293285 original size:7 final size:6
Alignment explanation
Indices: 42293273--42293328 Score: 53
Period size: 7 Copynumber: 9.0 Consensus size: 6
42293263 ATAAATTTTA
*
42293273 TTATAT GTTATAT TTTTAT TATATAT ATTATAT TTATAT TT-TA- TTATAT
1 TTATAT -TTATAT TTATAT T-TATAT -TTATAT TTATAT TTATAT TTATAT
42293322 GTTATAT
1 -TTATAT
42293329 ATTTTTTACT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 2 0.05
5 4 0.10
6 14 0.33
7 21 0.50
8 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (6 bp):
TTATAT
Found at i:42293303 original size:20 final size:20
Alignment explanation
Indices: 42293274--42293362 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
42293264 TAAATTTTAT
* *
42293274 TATATGTTATATTTTTATTA
1 TATATATTATATTTTTACTA
**
42293294 TATATATTATATTTATATTTTA
1 TATATATTATATTT-T-TACTA
*
42293316 TTATATGTTATATATTTTTTACTA
1 -TATAT-AT-TATA-TTTTTACTA
*
42293340 TATATATTATTTTTTTACTA
1 TATATATTATATTTTTACTA
42293360 TAT
1 TAT
42293363 TTTTATATGT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
20 25 0.45
21 4 0.07
22 5 0.09
23 10 0.18
24 4 0.07
25 5 0.09
26 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TATATATTATATTTTTACTA
Found at i:42293319 original size:25 final size:24
Alignment explanation
Indices: 42293239--42293349 Score: 84
Period size: 27 Copynumber: 4.5 Consensus size: 24
42293229 ATGAAAAATA
* *
42293239 ATATATATTATTATATACATCTTTAT
1 ATATATATTA-TATTTATAT-TTTAT
* *
42293265 AAATTTTATTATATGTTATATTTTTATT
1 ATA-TATATTATAT-TTATA-TTTTA-T
42293293 ATATATATTATATTTATATTTTAT
1 ATATATATTATATTTATATTTTAT
* *
42293317 -TATATGTTATA--TATTTTTTACT
1 ATATATATTATATTTATATTTTA-T
42293339 ATATATATTAT
1 ATATATATTAT
42293350 TTTTTTACTA
Statistics
Matches: 70, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
21 8 0.11
22 1 0.01
23 19 0.27
24 1 0.01
25 5 0.07
26 10 0.14
27 22 0.31
28 4 0.06
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (24 bp):
ATATATATTATATTTATATTTTAT
Found at i:42293335 original size:21 final size:21
Alignment explanation
Indices: 42293268--42293477 Score: 102
Period size: 21 Copynumber: 10.1 Consensus size: 21
42293258 TCTTTATAAA
42293268 TTTTATTATATGTTATAT-TT
1 TTTTATTATATGTTATATATT
* *
42293288 TTATTATATATAT-TATATTTATA
1 TT-TTAT-TATATGT-TATATATT
42293311 TTTTATTATATGTTATATATT
1 TTTTATTATATGTTATATATT
* *
42293332 TTTTACTATAT-ATAT-TATTT
1 TTTTATTATATGTTATATA-TT
* * *
42293352 TTTTACTATAT-TTTTATATG
1 TTTTATTATATGTTATATATT
***
42293372 TAAAATTACT-TGTTATATCA-T
1 TTTTATTA-TATGTTATAT-ATT
42293393 TTTTATTAT-T-TTATATATT
1 TTTTATTATATGTTATATATT
** *
42293412 ACTTATCATATTGTTCATATTATT
1 TTTTATTATA-TGTT-ATA-TATT
* * **
42293436 ATATATT-T-TGTT-TATAAA
1 TTTTATTATATGTTATATATT
42293454 TTTTATTATATGTTATATATT
1 TTTTATTATATGTTATATATT
42293475 TTT
1 TTT
42293478 CCACCTATTA
Statistics
Matches: 141, Mismatches: 30, Indels: 37
0.68 0.14 0.18
Matches are distributed among these distances:
18 8 0.06
19 18 0.13
20 32 0.23
21 51 0.36
22 17 0.12
23 7 0.05
24 8 0.06
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (21 bp):
TTTTATTATATGTTATATATT
Found at i:42293737 original size:16 final size:16
Alignment explanation
Indices: 42293718--42293752 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
42293708 AAACATCTTT
*
42293718 ATTTTTATTTTATTTG
1 ATTTTTATTTTATATG
42293734 ATTTTTATTTTATATG
1 ATTTTTATTTTATATG
42293750 ATT
1 ATT
42293753 ATAATTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
ATTTTTATTTTATATG
Found at i:42296020 original size:25 final size:26
Alignment explanation
Indices: 42295976--42296026 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
42295966 ATATTTGTTT
* *
42295976 TTATGTTTTTAAATATATTTTATTTA
1 TTATATTTTTAAATAAATTTTATTTA
42296002 TTATATTTTTAAA-AAATTTTATTTA
1 TTATATTTTTAAATAAATTTTATTTA
42296027 ATGAAATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTATATTTTTAAATAAATTTTATTTA
Found at i:42298202 original size:23 final size:22
Alignment explanation
Indices: 42298172--42298214 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
42298162 CTTAGTTAAC
42298172 ATTTATAT-TACTATTAATGTAAA
1 ATTTATATATA-TATT-ATGTAAA
42298195 ATTTATATATATATTATGTA
1 ATTTATATATATATTATGTA
42298215 TTTTGAGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 12 0.63
24 2 0.11
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (22 bp):
ATTTATATATATATTATGTAAA
Found at i:42322338 original size:28 final size:28
Alignment explanation
Indices: 42322272--42322399 Score: 175
Period size: 28 Copynumber: 4.5 Consensus size: 28
42322262 CATGAGATTG
* * **
42322272 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
42322301 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
42322329 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
42322358 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
42322386 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
42322400 GACTTACTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 45 0.51
29 44 0.49
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:42322361 original size:57 final size:57
Alignment explanation
Indices: 42322272--42322399 Score: 186
Period size: 57 Copynumber: 2.2 Consensus size: 57
42322262 CATGAGATTG
*
42322272 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * *
42322329 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
*
42322386 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
42322400 GACTTACTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:42342822 original size:27 final size:28
Alignment explanation
Indices: 42342738--42342835 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
42342728 CATGAGATTG
* * * *
42342738 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
42342767 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
42342795 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
42342822 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
42342836 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:42342846 original size:27 final size:27
Alignment explanation
Indices: 42342766--42342848 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
42342756 TAAATTGTAC
* *
42342766 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
42342794 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
42342821 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
42342848 A
1 A
42342849 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:42344565 original size:21 final size:21
Alignment explanation
Indices: 42344541--42344593 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
42344531 CCTAATATTG
42344541 AAATCCTAAATCCTAAACATA
1 AAATCCTAAATCCTAAACATA
* * * *
42344562 AAATTCTAAACCCTAAACTTT
1 AAATCCTAAATCCTAAACATA
*
42344583 AAACCCTAAAT
1 AAATCCTAAAT
42344594 TAATTAGATA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATCCTAAATCCTAAACATA
Found at i:42347866 original size:33 final size:33
Alignment explanation
Indices: 42347826--42347892 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
42347816 CGTGTTTGGA
42347826 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
1 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
42347859 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
1 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
42347892 T
1 T
42347893 TTAGCCTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (33 bp):
TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
Found at i:42360433 original size:26 final size:26
Alignment explanation
Indices: 42360397--42360450 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
42360387 TCAAGAAGTA
42360397 AAAAAAACACTATCACCCAAATTCAC
1 AAAAAAACACTATCACCCAAATTCAC
42360423 AAAAAAACACTATCACCCAAATTCAC
1 AAAAAAACACTATCACCCAAATTCAC
42360449 AA
1 AA
42360451 TAGAAGCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.56, C:0.30, G:0.00, T:0.15
Consensus pattern (26 bp):
AAAAAAACACTATCACCCAAATTCAC
Found at i:42370359 original size:24 final size:24
Alignment explanation
Indices: 42370327--42370372 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
42370317 AGTATTTTTT
42370327 TTGCTAAATTCTTTATATGACCAG
1 TTGCTAAATTCTTTATATGACCAG
*
42370351 TTGCTAAATTCTTTATGTGACC
1 TTGCTAAATTCTTTATATGACC
42370373 GATTAGCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (24 bp):
TTGCTAAATTCTTTATATGACCAG
Found at i:42373100 original size:126 final size:126
Alignment explanation
Indices: 42372786--42373292 Score: 784
Period size: 126 Copynumber: 4.0 Consensus size: 126
42372776 TTTCTGCAAG
* * * *
42372786 AATAATTCTGAGCAGACGTTTCTGGAA-AAATAGTGTCGGAAAATGTTTCAAGCAGGATGCACAG
1 AATAATTCTGAGTAGACGTTTCT-GAACAAATAGTGTC-GAAAACGCTTCAAGCAGGATGCACTG
* * *
42372850 TCAGCAAAATTTTTGGAAAAAACTCCCACGTGGACGCTCTTTCGCTACAGTAGTTCGTGG-AA
64 TCAGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
* * * *
42372912 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCTAAAACACTTCAAGCAGGATGCACTGTT
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
* * *
42372977 GGAAAAATTTATGGAAAAAGCTCTCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
66 AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
* *
42373038 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAATGCTTCAAGCAGGATACACTGTC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
* *
42373103 AGCAAAATTTCTGGAAAAAGCTCCTACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
66 AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
* * *
42373164 AATAATTCTGAGTAGACGTTTTTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
*
42373229 AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
42373290 AAT
1 AAT
42373293 GAGGCTATAA
Statistics
Matches: 346, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
125 77 0.22
126 269 0.78
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
Found at i:42376817 original size:18 final size:18
Alignment explanation
Indices: 42376781--42376818 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42376771 GGAAAAGGAA
* *
42376781 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAAGAT
42376799 ACATATAAGGGCTAAGAT
1 ACATATAAGGGCTAAGAT
42376817 AC
1 AC
42376819 TCACCTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGCTAAGAT
Found at i:42378631 original size:15 final size:15
Alignment explanation
Indices: 42378608--42378639 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42378598 GGATTTTTTT
*
42378608 AATTTAAAAAAATTA
1 AATTAAAAAAAATTA
42378623 AATTAAAAAAAATTA
1 AATTAAAAAAAATTA
42378638 AA
1 AA
42378640 CAAAGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATTAAAAAAAATTA
Found at i:42378662 original size:11 final size:11
Alignment explanation
Indices: 42378643--42378699 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
42378633 AATTAAACAA
*
42378643 AGAATTTTGAT
1 AGAAATTTGAT
42378654 AGAAATTTGAT
1 AGAAATTTGAT
* *
42378665 AGAATTTTGAG
1 AGAAATTTGAT
*
42378676 A-AAATTTCA-
1 AGAAATTTGAT
42378685 ATGAAATTTGAT
1 A-GAAATTTGAT
42378697 AGA
1 AGA
42378700 TTTTTGAAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 1 0.03
10 6 0.16
11 29 0.78
12 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.37
Consensus pattern (11 bp):
AGAAATTTGAT
Found at i:42378668 original size:22 final size:21
Alignment explanation
Indices: 42378642--42378699 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
42378632 AAATTAAACA
*
42378642 AAGAATTTTGATAGAAATTTG
1 AAGAATTTTGATAGAAATTTC
*
42378663 ATAGAATTTTGAGA-AAATTTC
1 A-AGAATTTTGATAGAAATTTC
*
42378684 AATGAAATTTGATAGA
1 AA-GAATTTTGATAGA
42378700 TTTTTGAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.03
21 17 0.57
22 12 0.40
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (21 bp):
AAGAATTTTGATAGAAATTTC
Found at i:42381109 original size:28 final size:28
Alignment explanation
Indices: 42381052--42381113 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
42381042 TGACATTCAC
* *
42381052 TCTCCCAAATATTTCACATACAAAAAAA
1 TCTCTCAAATATTTCACATAAAAAAAAA
42381080 TCTCTCAAATATTTCA-A-AAAAAAATTAA
1 TCTCTCAAATATTTCACATAAAAAAA--AA
42381108 TCTCTC
1 TCTCTC
42381114 CAAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 6 0.20
27 1 0.03
28 23 0.77
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.31
Consensus pattern (28 bp):
TCTCTCAAATATTTCACATAAAAAAAAA
Found at i:42381996 original size:19 final size:20
Alignment explanation
Indices: 42381959--42381996 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42381949 CCTTTAAAAT
42381959 AATAAGATTATTAACAATAA
1 AATAAGATTATTAACAATAA
42381979 AATAAG-TT-TTATACAATA
1 AATAAGATTATTA-ACAATA
42381997 TCCAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 8 0.47
20 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
AATAAGATTATTAACAATAA
Found at i:42394164 original size:7 final size:7
Alignment explanation
Indices: 42394152--42394176 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42394142 GTAGTCTAGT
42394152 GGCCGGA
1 GGCCGGA
42394159 GGCCGGA
1 GGCCGGA
42394166 GGCCGGA
1 GGCCGGA
42394173 GGCC
1 GGCC
42394177 AGGGCAGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.32, G:0.56, T:0.00
Consensus pattern (7 bp):
GGCCGGA
Found at i:42394822 original size:21 final size:21
Alignment explanation
Indices: 42394798--42394852 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
42394788 CTTACAAATT
42394798 TTTATTATATATACATTTTAC
1 TTTATTATATATACATTTTAC
**
42394819 TTTA-TATATTATTTATTTTAC
1 TTTATTATA-TATACATTTTAC
*
42394840 TATATTTATATAT
1 TTTA-TTATATAT
42394853 GTAAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 17 0.61
22 3 0.11
23 4 0.14
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTATATATACATTTTAC
Found at i:42406981 original size:44 final size:44
Alignment explanation
Indices: 42406918--42407458 Score: 685
Period size: 44 Copynumber: 12.3 Consensus size: 44
42406908 TAGATCACCA
* * * * *
42406918 ATAGCTGATTTGGCATCTCTATATTGTCAGAGAGCAAATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
42406962 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * * *
42407006 AT-GATAGATTTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAG
1 ATAG-CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * * * *
42407050 ATAACAAATTTGGCATCTCTGTGTTGACAGAGAGCAGATCAAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* *
42407094 ATAGCAGATTTGGCGTCTCTGTATTGACGGAGAGCAGATTGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
*
42407138 ATAGCAGATTTGGCGTCTCTGTATTGACGGAGAGCAGATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* *
42407182 ATAACAGATTTGGCGTCTCTGTATT-ATCAGAGAGCAGATCAAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGA-CAGAGAGCAGATCGAAG
* *
42407226 ATAGCAGATTTGGCGTCTCTGTATTGACGGAGAGCATATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * * * *
42407270 ATAACAGATTTGGCGTCTCTATATTGACGGGGAGCATATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* *
42407314 ATAGTAGATTTGGCGTCTCTGTATTGACAGAGAGTAGATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * * *
42407358 ATAGCAGATTTGGCGTCT-TAGTATTGATAAAGAGCAGATTGAAA
1 ATAGCAGATTTGGCGTCTCT-GTATTGACAGAGAGCAGATCGAAG
* * * *
42407402 ATAACAGATTTTGCGTCTCTGTGTTAGA-TGAGGAGCAGATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATT-GACAGA-GAGCAGATCGAAG
42407447 ATAGCAGATTTG
1 ATAGCAGATTTG
42407459 ACATTTGTAT
Statistics
Matches: 433, Mismatches: 56, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
43 3 0.01
44 405 0.94
45 25 0.06
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (44 bp):
ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
Found at i:42407526 original size:90 final size:88
Alignment explanation
Indices: 42406948--42407538 Score: 348
Period size: 88 Copynumber: 6.7 Consensus size: 88
42406938 ATATTGTCAG
* * * * * *
42406948 AGAGCAAATCGAAGATAGCAGATTTGGCGTCTCTGTATT-GACAGAGAGCAGATCGAAGAT-GAT
1 AGAGCAGATTGAAAATAACAGATTTGGCGTCTCTGTATTAGACAG-GAGTAGATCGAAGATAG-C
* * *
42407011 AGATTTGGCATCTCT-GTATT-GTCAG
64 AGATTTGACATCT-TAGTATTCAT-AA
* * * * * * * *
42407036 AGAGCAAATCGAAGATAACAAATTTGGCATCTCTGTGTT-GACAGAGAGCAGATCAAAGATAGCA
1 AGAGCAGATTGAAAATAACAGATTTGGCGTCTCTGTATTAGACAG-GAGTAGATCGAAGATAGCA
* * * ***
42407100 GATTTGGCGTCTCT-GTATTGACGG
65 GATTTGACATCT-TAGTATTCATAA
* * * * *
42407124 AGAGCAGATTGAAGATAGCAGATTTGGCGTCTCTGTATT-GACGGAGAGCAGATCGAAGATAACA
1 AGAGCAGATTGAAAATAACAGATTTGGCGTCTCTGTATTAGACAG-GAGTAGATCGAAGATAGCA
* * *
42407188 GATTTGGCGTCTCT-GTATT-ATCAG
65 GATTTGACATCT-TAGTATTCAT-AA
* * * * * *
42407212 AGAGCAGA-TCAAAGATAGCAGATTTGGCGTCTCTGTATT-GACGGAGAGCATATCGAAGATAAC
1 AGAGCAGATTGAAA-ATAACAGATTTGGCGTCTCTGTATTAGACAG-GAGTAGATCGAAGATAGC
* * * ***
42407275 AGATTTGGCGTCTCTA-TATTGACGG
64 AGATTTGACATCT-TAGTATTCATAA
* * * * **
42407300 GGAGCATATCGAAGATAGTAGATTTGGCGTCTCTGTATT-GACAGAGAGTAGATCGAAGATAGCA
1 AGAGCAGATTGAAAATAACAGATTTGGCGTCTCTGTATTAGACAG-GAGTAGATCGAAGATAGCA
* * *
42407364 GATTTGGCGTCTTAGTATTGATAA
65 GATTTGACATCTTAGTATTCATAA
* * * *
42407388 AGAGCAGATTGAAAATAACAGATTTTGCGTCTCTGTGTTAGATGAGGAGCAGATCGAAGATAGCA
1 AGAGCAGATTGAAAATAACAGATTTGGCGTCTCTGTATTAGA-CAGGAGTAGATCGAAGATAGCA
* *
42407453 GATTTGACATTTGTATGT-TTACATCA
65 GATTTGACATCT-TA-GTATT-CATAA
* * * * *
42407479 A-AGCAGATTGAAGATGACAGATTTGGCCTCTCTGTATTAAACAAGGAGTAGATCAAAGAT
1 AGAGCAGATTGAAAATAACAGATTTGGCGTCTCTGTATTAGAC-AGGAGTAGATCGAAGAT
42407539 TTCAGCATGC
Statistics
Matches: 426, Mismatches: 63, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
87 6 0.01
88 326 0.77
89 33 0.08
90 55 0.13
91 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (88 bp):
AGAGCAGATTGAAAATAACAGATTTGGCGTCTCTGTATTAGACAGGAGTAGATCGAAGATAGCAG
ATTTGACATCTTAGTATTCATAA
Found at i:42408621 original size:20 final size:21
Alignment explanation
Indices: 42408596--42408647 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
42408586 TGCAGTGGCT
*
42408596 GGAGGCCGGAGGTCTG-GGCC
1 GGAGGCCGGAGGTCGGAGGCC
*
42408616 GGAGGCCGGAGGTCGGAGGTC
1 GGAGGCCGGAGGTCGGAGGCC
42408637 GG-GGCCGGAGG
1 GGAGGCCGGAGG
42408648 GCTTCCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.12, C:0.21, G:0.60, T:0.08
Consensus pattern (21 bp):
GGAGGCCGGAGGTCGGAGGCC
Found at i:42408622 original size:7 final size:7
Alignment explanation
Indices: 42408596--42408647 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
42408586 TGCAGTGGCT
42408596 GGAGGCC
1 GGAGGCC
*
42408603 GGAGGTC
1 GGAGGCC
*
42408610 TG-GGCC
1 GGAGGCC
42408616 GGAGGCC
1 GGAGGCC
*
42408623 GGAGGTC
1 GGAGGCC
*
42408630 GGAGGTC
1 GGAGGCC
42408637 GG-GGCC
1 GGAGGCC
42408643 GGAGG
1 GGAGG
42408648 GCTTCCCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
6 9 0.24
7 28 0.76
ACGTcount: A:0.12, C:0.21, G:0.60, T:0.08
Consensus pattern (7 bp):
GGAGGCC
Found at i:42408634 original size:27 final size:27
Alignment explanation
Indices: 42408596--42408647 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
42408586 TGCAGTGGCT
*
42408596 GGAGGCCGGAGGTCTGGGCCGGAGGCC
1 GGAGGCCGGAGGTCGGGGCCGGAGGCC
*
42408623 GGAGGTCGGAGGTCGGGGCCGGAGG
1 GGAGGCCGGAGGTCGGGGCCGGAGG
42408648 GCTTCCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.12, C:0.21, G:0.60, T:0.08
Consensus pattern (27 bp):
GGAGGCCGGAGGTCGGGGCCGGAGGCC
Found at i:42409189 original size:28 final size:28
Alignment explanation
Indices: 42409131--42409189 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
42409121 TTAGTCTTTT
*
42409131 TTATATGTATTTAATTTATTTTAAAATA
1 TTATATGTATTTAATTTATTTTAAAACA
42409159 TTATATGTA-TT-ATTTATTTTTATAAACA
1 TTATATGTATTTAATTTA-TTTTA-AAACA
42409187 TTA
1 TTA
42409190 GTTATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.18
27 7 0.25
28 16 0.57
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
TTATATGTATTTAATTTATTTTAAAACA
Found at i:42409229 original size:17 final size:15
Alignment explanation
Indices: 42409209--42409372 Score: 63
Period size: 13 Copynumber: 11.5 Consensus size: 15
42409199 AAAAATAATG
*
42409209 TATATTAGTTTTATTTA
1 TATATTA-TATTA-TTA
42409226 TATATTATATTATTA
1 TATATTATATTATTA
* *
42409241 TATA-TGT-TTCTTA
1 TATATTATATTATTA
*
42409254 TA-ATT-TTTTATTA
1 TATATTATATTATTA
*
42409267 TATA-TACATT-TTA
1 TATATTATATTATTA
*
42409280 CTTTA-TATATTATT-
1 -TATATTATATTATTA
*
42409294 TATTTTACTA-TATTTA
1 TATATTA-TATTA-TTA
*
42409310 TATATGTAAATTATTA
1 TATAT-TATATTATTA
42409326 TATA-T-TATTA-TA
1 TATATTATATTATTA
*
42409338 T-TATTTTATTATTA
1 TATATTATATTATTA
42409352 -ACTATT-TATTATGTA
1 TA-TATTATATTAT-TA
42409367 TA-ATTA
1 TATATTA
42409373 ACATTTTTTA
Statistics
Matches: 114, Mismatches: 13, Indels: 42
0.67 0.08 0.25
Matches are distributed among these distances:
11 2 0.02
12 6 0.05
13 30 0.26
14 29 0.25
15 19 0.17
16 17 0.15
17 11 0.10
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (15 bp):
TATATTATATTATTA
Found at i:42410714 original size:80 final size:85
Alignment explanation
Indices: 42410616--42410769 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
42410606 ATACTCGAAC
* *
42410616 CTAAAACCTCACATACACAAGCA-T-AA-AA-TAAATTTACTTGAAAATTTTTAATAATTCAAAA
1 CTAAAACCTCACATACACAACCACTAAACAAGTAAATTTACTTGAAAATTTTTAACAATTCAAAA
42410677 AGTTAAAATTTAATTGACCA
66 AGTTAAAATTTAATTGACCA
* **
42410697 CTAAAA-CTCACATACACAACCACTAAACCAAGTCAATTTACTTGGCAATTTTTAACAATTCAAA
1 CTAAAACCTCACATACACAACCACTAAA-CAAGTAAATTTACTTGAAAATTTTTAACAATTCAAA
42410761 AAGTTAAAA
65 AAGTTAAAA
42410770 ATTTTGGGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
80 15 0.24
81 7 0.11
82 2 0.03
84 2 0.03
85 37 0.59
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.29
Consensus pattern (85 bp):
CTAAAACCTCACATACACAACCACTAAACAAGTAAATTTACTTGAAAATTTTTAACAATTCAAAA
AGTTAAAATTTAATTGACCA
Found at i:42411006 original size:13 final size:12
Alignment explanation
Indices: 42410988--42411030 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
42410978 TATTCTATAT
42410988 AAATAAAATAAA
1 AAATAAAATAAA
42411000 AATATAACAATAAA
1 AA-ATAA-AATAAA
*
42411014 AAATATTAATAAA
1 AAATA-AAATAAA
42411027 AAAT
1 AAAT
42411031 TATCACTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 2 0.07
13 17 0.63
14 8 0.30
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:42419644 original size:18 final size:18
Alignment explanation
Indices: 42419611--42419646 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42419601 TAATTTATTT
*
42419611 TATAAATTTTTCTACATA
1 TATAAATTTATCTACATA
*
42419629 TATAAATTTATGTACATA
1 TATAAATTTATCTACATA
42419647 AGTCATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (18 bp):
TATAAATTTATCTACATA
Found at i:42421521 original size:18 final size:18
Alignment explanation
Indices: 42421500--42421566 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
42421490 AATCGGTTAA
*
42421500 TCAGTAACAATCATTTAT
1 TCAGTAACAGTCATTTAT
* * *
42421518 TCAGTATCAGTCGTTTAG
1 TCAGTAACAGTCATTTAT
*
42421536 TCAGTAACAGTCAATTAT
1 TCAGTAACAGTCATTTAT
*
42421554 TCAGTAGCAGTCA
1 TCAGTAACAGTCA
42421567 GTTTTTAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (18 bp):
TCAGTAACAGTCATTTAT
Found at i:42421540 original size:36 final size:37
Alignment explanation
Indices: 42421500--42421570 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 37
42421490 AATCGGTTAA
* *
42421500 TCAGTAACAATCATTTATTCAGTATCAGTC-GTTTAG
1 TCAGTAACAATCAATTATTCAGTAGCAGTCAGTTTAG
*
42421536 TCAGTAACAGTCAATTATTCAGTAGCAGTCAGTTT
1 TCAGTAACAATCAATTATTCAGTAGCAGTCAGTTT
42421571 TTAATACTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (37 bp):
TCAGTAACAATCAATTATTCAGTAGCAGTCAGTTTAG
Found at i:42421705 original size:6 final size:6
Alignment explanation
Indices: 42421688--42421734 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
42421678 TACACTGTGT
* * *
42421688 CAGTAA CGGTAA CAGTAA CAGTAA TAGTAA CAGTAA TAGTAA CAGTA
1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
42421735 GCGGTACACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (6 bp):
CAGTAA
Found at i:42422100 original size:3 final size:3
Alignment explanation
Indices: 42422092--42422123 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42422082 ATTCAATACC
42422092 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
42422124 TACCATTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:42428521 original size:51 final size:53
Alignment explanation
Indices: 42428422--42428531 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 53
42428412 GAGCAGTAAC
* * *
42428422 AGTAATAGTAACAGTAGCGGTACACAAAGTACCTCATTGGAACAAATCC-AGAAT
1 AGTAACAGTAACAGTAGAGGTA-ACAAAGTACCTCATTGAAACAAATCCGA-AAT
*
42428476 AGTAACAGTAACAGTA-AGGT-ACAAAGTACCTC-TTCGAAACGAATCCGAAAT
1 AGTAACAGTAACAGTAGAGGTAACAAAGTACCTCATT-GAAACAAATCCGAAAT
42428527 AGTAA
1 AGTAA
42428532 TAGCAGTCGA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
50 2 0.04
51 29 0.58
52 1 0.02
53 3 0.06
54 15 0.30
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (53 bp):
AGTAACAGTAACAGTAGAGGTAACAAAGTACCTCATTGAAACAAATCCGAAAT
Found at i:42434607 original size:20 final size:20
Alignment explanation
Indices: 42434582--42434619 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42434572 TTAAATTAAA
*
42434582 TTTTTATAGATGTTTATTTT
1 TTTTTAAAGATGTTTATTTT
*
42434602 TTTTTAAATATGTTTATT
1 TTTTTAAAGATGTTTATT
42434620 ACATTATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (20 bp):
TTTTTAAAGATGTTTATTTT
Found at i:42435443 original size:15 final size:15
Alignment explanation
Indices: 42435425--42435477 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
42435415 AAAGTACTTT
42435425 TTTAATTTTATTTAA
1 TTTAATTTTATTTAA
* *
42435440 TTTAATTATATTCAA
1 TTTAATTTTATTTAA
** *
42435455 AATATTTTTATTTAAA
1 TTTAATTTTATTT-AA
42435471 TTTAATT
1 TTTAATT
42435478 ATAAATTATA
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
15 21 0.78
16 6 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAATTTTATTTAA
Found at i:42438519 original size:43 final size:42
Alignment explanation
Indices: 42438442--42438549 Score: 103
Period size: 43 Copynumber: 2.5 Consensus size: 42
42438432 TCACACATGT
* * * *
42438442 GGTTCACACCTAGGGGTTCGCACATAAGGGTTTGC-TCAAGTAA
1 GGTTCACACATA-GGGTTTGTACATAAGGCTTTGCAT-AAGTAA
*
42438485 GGTTCACACATAGGGTTTGTACATATAGGCTTTGCATAAGTAG
1 GGTTCACACATAGGGTTTGTACATA-AGGCTTTGCATAAGTAA
*
42438528 GGTTCGC-CTATAGAGGTTTGTA
1 GGTTCACAC-ATAG-GGTTTGTA
42438550 TGAGGGGTGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
42 12 0.22
43 34 0.62
44 9 0.16
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (42 bp):
GGTTCACACATAGGGTTTGTACATAAGGCTTTGCATAAGTAA
Found at i:42440979 original size:47 final size:47
Alignment explanation
Indices: 42440926--42441362 Score: 667
Period size: 47 Copynumber: 9.2 Consensus size: 47
42440916 AATTCTAAAT
42440926 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
42440973 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
42441020 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
42441068 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
42441117 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
42441164 TGCGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
42441213 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
42441260 CGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * * *
42441307 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
42441354 TGTGATAAG
1 TGTGATAAG
42441363 TCCCGAAGGG
Statistics
Matches: 357, Mismatches: 28, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
47 223 0.62
48 45 0.13
49 89 0.25
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.30
Consensus pattern (47 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:42441173 original size:96 final size:94
Alignment explanation
Indices: 42440926--42441362 Score: 667
Period size: 96 Copynumber: 4.6 Consensus size: 94
42440916 AATTCTAAAT
*
42440926 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTTAATGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
42440991 CCGATGTGATGAATGTGAAAGTGTATATA
66 CCGATGTGATGAATGTGAAAGTGTATATA
*
42441020 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
1 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
42441085 GCCGATGTGATGAATGTGAAAGTGTATATATA
65 GCCGATGTGATGAATGTGAAAGTG--TATATA
* * * *
42441117 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGCGATAAGGCCTAATAG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
42441182 CCGATGTGATGAATGTGAAAGTGTATATATA
66 CCGATGTGATGAATGTGAAAGTG--TATATA
* ** *
42441213 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGCGTGATAAGGCTTAATGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
42441278 CCGATGTGATGAATGTGAAAGTGTATATA
66 CCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * * *
42441307 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAATGTGATAAG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
42441363 TCCCGAAGGG
Statistics
Matches: 318, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
94 55 0.17
95 82 0.26
96 171 0.54
97 10 0.03
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.30
Consensus pattern (94 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
CCGATGTGATGAATGTGAAAGTGTATATA
Found at i:42441268 original size:143 final size:142
Alignment explanation
Indices: 42440926--42441362 Score: 700
Period size: 143 Copynumber: 3.1 Consensus size: 142
42440916 AATTCTAAAT
42440926 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTTAATGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTTAATGG
42440991 CCGATGTGATGAATGTGAAAGTGTATATATGTGAATAGGGCCTAATGGCCGATGTGATGAATGTG
66 CCGATGTGATGAATGTGAAAGTGTATATATGTG-ATAGGGCCTAATGGCCGATGTGATGAATGTG
42441056 AAAGTG-TATATA
130 AAAGTGATATATA
42441068 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAAT
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCTTAAT
* * * *
42441133 GGCCGATGTGATGAATGTGAAAGTGTATATGTGCGATAAGGCCTAATAGCCGATGTGATGAATGT
64 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGT
42441198 GAAAGTGTATATATA
129 GAAAGTG-ATATATA
* **
42441213 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGCGTGATAAGGCTTAATGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTTAATGG
* * * * *
42441278 CCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGA
66 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGA
42441343 AAGTGCATA-A-A
131 AAGTG-ATATATA
42441354 TGTGATAAG
1 TGTGATAAG
42441363 TCCCGAAGGG
Statistics
Matches: 274, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
141 10 0.04
142 42 0.15
143 121 0.44
144 55 0.20
145 46 0.17
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.30
Consensus pattern (142 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTTAATGG
CCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGA
AAGTGATATATA
Found at i:42441536 original size:37 final size:37
Alignment explanation
Indices: 42441480--42441558 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42441470 TCGAGCTCTA
* * *
42441480 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
42441517 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
42441554 AAGAC
1 AAGAC
42441559 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:42444387 original size:23 final size:23
Alignment explanation
Indices: 42444343--42444407 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
42444333 ATAATAGTTC
* * * * *
42444343 CTATAGGCTTCACATGATATTTT
1 CTATAGGGTTCGCATAACATTTA
42444366 CTATAGGGTTCGCATAACATTTA
1 CTATAGGGTTCGCATAACATTTA
42444389 CTAT-GGGATTCGCATAACA
1 CTATAGGG-TTCGCATAACA
42444408 GTTCTTATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 3 0.08
23 33 0.92
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (23 bp):
CTATAGGGTTCGCATAACATTTA
Found at i:42444735 original size:23 final size:23
Alignment explanation
Indices: 42444705--42444799 Score: 95
Period size: 23 Copynumber: 4.1 Consensus size: 23
42444695 GGTTTACACA
* *
42444705 ATAACAGTTCCTCTAGGGTTCGC
1 ATAACAGTTCCTATAGGGTTTGC
* *
42444728 ATAACAGTTACTATAAGGTTTGC
1 ATAACAGTTCCTATAGGGTTTGC
42444751 ATAAC-GATTCCTATA-GGTTTGGC
1 ATAACAG-TTCCTATAGGGTTT-GC
* * *
42444774 ATGATATTTCCTATAGGGTTTGC
1 ATAACAGTTCCTATAGGGTTTGC
42444797 ATA
1 ATA
42444800 TACTCATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
22 6 0.10
23 48 0.81
24 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (23 bp):
ATAACAGTTCCTATAGGGTTTGC
Found at i:42448371 original size:46 final size:45
Alignment explanation
Indices: 42448229--42448382 Score: 154
Period size: 46 Copynumber: 3.4 Consensus size: 45
42448219 CTGCTTTACA
* * * *
42448229 GCAACTTCAGAGAGATAAGGATTGTG-ACTTTGATCTT-CTCCACT
1 GCAACTTCAGAGAGATAA-GACTGGGTAATTTTATCTTGCTCCACT
* * *
42448273 GCAACTTCAAAGAGATAAGATCT-GCTAACTTTAGTC-TGCTCCACT
1 GCAACTTCAGAGAGATAAGA-CTGGGTAATTTTA-TCTTGCTCCACT
* * *
42448318 ACAACTTCAGGGAGATAAGACCTGGGTAATTTTATCTTGCTCTACT
1 GCAACTTCAGAGAGATAAGA-CTGGGTAATTTTATCTTGCTCCACT
42448364 GCAACTTCAGAGAGATAAG
1 GCAACTTCAGAGAGATAAG
42448383 GATTGGGGCT
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
43 2 0.02
44 23 0.26
45 30 0.34
46 33 0.38
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (45 bp):
GCAACTTCAGAGAGATAAGACTGGGTAATTTTATCTTGCTCCACT
Found at i:42448423 original size:44 final size:45
Alignment explanation
Indices: 42448230--42448559 Score: 234
Period size: 44 Copynumber: 7.4 Consensus size: 45
42448220 TGCTTTACAG
* * * *
42448230 CAACTTCAGAGAGATAAGGA-TTGTGACTTTGATCTTCTCCACTG
1 CAACTTCAGGGAGATAAGGACTTGTGACTTCGATCTGCTCCACTA
** * *
42448274 CAACTTCAAAGAGATAA-GA-TCTGCTAACTT-TAGTCTGCTCCACTA
1 CAACTTCAGGGAGATAAGGACT-TG-TGACTTCGA-TCTGCTCCACTA
* * * ** * *
42448319 CAACTTCAGGGAGATAA-GACCTGGGTAATTTTATCTTGCTCTACTG
1 CAACTTCAGGGAGATAAGGACTTGTG-ACTTCGATC-TGCTCCACTA
* * * *
42448365 CAACTTCAGAGAGATAAGGA-TTGGGGCTTCGATCTGTTCCACTA
1 CAACTTCAGGGAGATAAGGACTTGTGACTTCGATCTGCTCCACTA
* *
42448409 CAACTTTAGGGAGATAA-GATCTTCT-ATCTTC-AGTCTGCTCCACTA
1 CAACTTCAGGGAGATAAGGA-CTTGTGA-CTTCGA-TCTGCTCCACTA
* * * * *
42448454 CAACTTCAGGGAGATAA-GACTTGCT-ATTTCAACCCGCTCTACTA
1 CAACTTCAGGGAGATAAGGACTTG-TGACTTCGATCTGCTCCACTA
* * *
42448498 CAACTTCAGAGAGATAAGG-TTTGTGACTTCGATCTGCTCCACTG
1 CAACTTCAGGGAGATAAGGACTTGTGACTTCGATCTGCTCCACTA
42448542 CAACTTCAGGGAGATAAG
1 CAACTTCAGGGAGATAAG
42448560 ATCTTCAATC
Statistics
Matches: 227, Mismatches: 43, Indels: 32
0.75 0.14 0.11
Matches are distributed among these distances:
43 6 0.03
44 106 0.47
45 83 0.37
46 30 0.13
47 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (45 bp):
CAACTTCAGGGAGATAAGGACTTGTGACTTCGATCTGCTCCACTA
Found at i:42448553 original size:133 final size:135
Alignment explanation
Indices: 42448230--42448571 Score: 481
Period size: 135 Copynumber: 2.5 Consensus size: 135
42448220 TGCTTTACAG
* * **
42448230 CAACTTCAGAGAGATAAGGATTGTGACTTTGATCTTCTCCACTGCAACTTCAAAGAGATAAGATC
1 CAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATC
* * * * * * **
42448295 TGCTAACTTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCTGGGTAATTTTATCTTGCTC
66 TTCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCTGGCTAATTTCAACCCGCTC
*
42448360 TACTG
131 TACTA
* * * * *
42448365 CAACTTCAGAGAGATAAGGATTGGGGCTTCGATCTGTTCCACTACAACTTTAGGGAGATAAGATC
1 CAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATC
*
42448430 TTCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGA-CTTGCT-ATTTCAACCCGCTC
66 TTCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCTGGCTAATTTCAACCCGCTC
42448493 TACTA
131 TACTA
*
42448498 CAACTTCAGAGAGATAAGGTTTGTGACTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATC
1 CAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATC
*
42448563 TTCAATCTT
66 TTCTATCTT
42448572 TAGTTTTTTT
Statistics
Matches: 181, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
133 81 0.45
134 4 0.02
135 96 0.53
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (135 bp):
CAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATC
TTCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCTGGCTAATTTCAACCCGCTC
TACTA
Found at i:42459273 original size:127 final size:126
Alignment explanation
Indices: 42459126--42459443 Score: 429
Period size: 127 Copynumber: 2.5 Consensus size: 126
42459116 TAGTCCAACG
* * * *
42459126 AAAAACCGTAACCCAGCACGATAGGGCACAATGCCTCGAATTTCCAAACATTGAACATTGCGTTG
1 AAAAATCGAAACCCAGCACGATAGGGCACAATTCC-CGAATTTCCAAACATTGAACATTGCCTTG
* * * * *
42459191 CTTTAGAATTTATAAAACACGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAAATC
65 CTTTAAAATTTAGAAAACACAAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAATA
** * *
42459253 GGAAATCGAAACCCAACACGATAGGGCACGATTTCCCGAATTTCCAAACATTGAACATTGCCTTG
1 AAAAATCGAAACCCAGCACGATAGGGCAC-AATTCCCGAATTTCCAAACATTGAACATTGCCTTG
* *
42459318 TTTTAAAATTTGGAAAACACAAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAATA
65 CTTTAAAATTTAGAAAACACAAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAATA
* * * **
42459380 AAAAATCGAAACCCAGCACGATAGGACACGATTCCCCAAATTTCCAAACATCAAACATTGCCTT
1 AAAAATCGAAACCCAGCACGATAGGGCACAATT-CCCGAATTTCCAAACATTGAACATTGCCTT
42459444 CGTTTTAGGG
Statistics
Matches: 165, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
126 2 0.01
127 159 0.96
128 4 0.02
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.25
Consensus pattern (126 bp):
AAAAATCGAAACCCAGCACGATAGGGCACAATTCCCGAATTTCCAAACATTGAACATTGCCTTGC
TTTAAAATTTAGAAAACACAAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAATA
Found at i:42461638 original size:24 final size:24
Alignment explanation
Indices: 42461611--42461656 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42461601 TAGGTCTAGG
*
42461611 TTTTGGGCCATTGGGCT-ATGTATT
1 TTTTAGGCC-TTGGGCTGATGTATT
*
42461635 TTTTAGGTCTTGGGCTGATGTA
1 TTTTAGGCCTTGGGCTGATGTA
42461657 AATGGATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.13, C:0.11, G:0.30, T:0.46
Consensus pattern (24 bp):
TTTTAGGCCTTGGGCTGATGTATT
Found at i:42464940 original size:35 final size:35
Alignment explanation
Indices: 42464894--42464969 Score: 152
Period size: 35 Copynumber: 2.2 Consensus size: 35
42464884 GTCCAATAAC
42464894 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
1 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
42464929 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
1 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
42464964 GATCAA
1 GATCAA
42464970 CTAGAATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (35 bp):
GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
Found at i:42470978 original size:18 final size:18
Alignment explanation
Indices: 42470955--42470991 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42470945 TAGGGAACTC
42470955 TAAATCCTTCT-GGGATTT
1 TAAATCCTT-TAGGGATTT
42470973 TAAATCCTTTAGGGATTT
1 TAAATCCTTTAGGGATTT
42470991 T
1 T
42470992 TATATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (18 bp):
TAAATCCTTTAGGGATTT
Found at i:42474123 original size:15 final size:14
Alignment explanation
Indices: 42474099--42474130 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
42474089 CCACTATTGG
42474099 TTTCACTAACCCAA
1 TTTCACTAACCCAA
42474113 TTTCTACTAACCCAA
1 TTTC-ACTAACCCAA
42474128 TTT
1 TTT
42474131 TTGGGGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTCACTAACCCAA
Found at i:42490533 original size:21 final size:21
Alignment explanation
Indices: 42490507--42490548 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
42490497 TTGTTGCGAA
42490507 AATATGATTGCATGGTTTGGT
1 AATATGATTGCATGGTTTGGT
42490528 AATATGATTGCATGGTTTGGT
1 AATATGATTGCATGGTTTGGT
42490549 TATGTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.43
Consensus pattern (21 bp):
AATATGATTGCATGGTTTGGT
Found at i:42491596 original size:20 final size:20
Alignment explanation
Indices: 42491571--42491615 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
42491561 TTTTTCACTA
*
42491571 AATAGAGAAAATTAAAGCAG
1 AATAGAGAAAATGAAAGCAG
42491591 AATAGAGAAAATGAAAGCAG
1 AATAGAGAAAATGAAAGCAG
42491611 AATAG
1 AATAG
42491616 GGTAAGGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.22, T:0.13
Consensus pattern (20 bp):
AATAGAGAAAATGAAAGCAG
Found at i:42493163 original size:7 final size:7
Alignment explanation
Indices: 42493151--42493176 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42493141 TAAAAATTTA
42493151 AATATTC
1 AATATTC
42493158 AATATTC
1 AATATTC
42493165 AATATTC
1 AATATTC
42493172 AATAT
1 AATAT
42493177 GAAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:42494144 original size:42 final size:42
Alignment explanation
Indices: 42494097--42494183 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
42494087 TGCTAATATG
42494097 TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
1 TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
42494139 TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
1 TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
42494181 TAT
1 TAT
42494184 TAATATGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (42 bp):
TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
Found at i:42495793 original size:11 final size:11
Alignment explanation
Indices: 42495777--42495801 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42495767 TTGCAAGTTA
42495777 AATTTTATTTT
1 AATTTTATTTT
42495788 AATTTTATTTT
1 AATTTTATTTT
42495799 AAT
1 AAT
42495802 ATTACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
AATTTTATTTT
Found at i:42507739 original size:12 final size:12
Alignment explanation
Indices: 42507722--42507751 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42507712 CCGCGTGCTG
42507722 CCACACAGCCTA
1 CCACACAGCCTA
*
42507734 CCACACAGGCTA
1 CCACACAGCCTA
42507746 CCACAC
1 CCACAC
42507752 GCTAGTGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.50, G:0.10, T:0.07
Consensus pattern (12 bp):
CCACACAGCCTA
Done.