Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 114 of 292
Found at i:34732896 original size:40 final size:40
Alignment explanation
Indices: 34732769--34732898 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
34732759 TTGCTGGAAA
* *
34732769 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
34732809 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
34732849 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
34732889 TTATATCCGG
1 TTATATCCGG
34732899 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:34739816 original size:15 final size:15
Alignment explanation
Indices: 34739796--34739864 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
34739786 GTATCTTGGG
34739796 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
34739811 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
34739826 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
34739841 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
34739856 TTTCTTTAT
1 TTTCTTTAT
34739865 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:34739865 original size:30 final size:30
Alignment explanation
Indices: 34739787--34739874 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
34739777 CATAGTATCG
* * * *
34739787 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
34739817 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
34739847 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
34739875 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:34742308 original size:46 final size:46
Alignment explanation
Indices: 34742258--34742433 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
34742248 ATGGTTGGCA
34742258 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
34742304 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
34742349 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
34742397 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
34742434 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:34742413 original size:93 final size:93
Alignment explanation
Indices: 34742254--34742425 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
34742244 TAGGATGGTT
* *
34742254 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
34742319 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
34742347 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
34742412 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
34742426 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:34746558 original size:10 final size:10
Alignment explanation
Indices: 34746543--34746569 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
34746533 TAAGTTGAAG
34746543 TTGAGCTGAT
1 TTGAGCTGAT
34746553 TTGAGCTGAT
1 TTGAGCTGAT
34746563 TTGAGCT
1 TTGAGCT
34746570 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:34748563 original size:28 final size:28
Alignment explanation
Indices: 34748531--34748588 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
34748521 CTTAAGTCCT
34748531 ATTGTTTATCTTCTCCTTTGGGTAACCA
1 ATTGTTTATCTTCTCCTTTGGGTAACCA
34748559 ATTGTTTATCTTCTCCTTTGGGTAACCA
1 ATTGTTTATCTTCTCCTTTGGGTAACCA
34748587 AT
1 AT
34748589 CTTGTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.47
Consensus pattern (28 bp):
ATTGTTTATCTTCTCCTTTGGGTAACCA
Found at i:34749398 original size:26 final size:26
Alignment explanation
Indices: 34749369--34749442 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
34749359 CATATACTGA
* *
34749369 TACTGGCAACTTTGTTGC-ATTACTAT
1 TACTGGCAGCTTTGCTGCGA-TACTAT
* *
34749395 TACTGGCAGCTCTGCTGCGATATTAT
1 TACTGGCAGCTTTGCTGCGATACTAT
*
34749421 TACTGGCAGCTTTACTGCGATA
1 TACTGGCAGCTTTGCTGCGATA
34749443 TTGGTGTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 40 0.98
27 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCGATACTAT
Found at i:34749443 original size:26 final size:26
Alignment explanation
Indices: 34749392--34749444 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
34749382 GTTGCATTAC
*
34749392 TATTACTGGCAGCTCTGCTGCGATAT
1 TATTACTGGCAGCTCTACTGCGATAT
*
34749418 TATTACTGGCAGCTTTACTGCGATAT
1 TATTACTGGCAGCTCTACTGCGATAT
34749444 T
1 T
34749445 GGTGTGTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (26 bp):
TATTACTGGCAGCTCTACTGCGATAT
Found at i:34753405 original size:15 final size:15
Alignment explanation
Indices: 34753373--34753401 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34753363 ATTTTCTATG
34753373 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
34753388 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
34753402 ATTTTCATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:34758379 original size:20 final size:21
Alignment explanation
Indices: 34758354--34758392 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
34758344 TCGAATGTAC
34758354 TTTTCATATACA-CATATAAT
1 TTTTCATATACATCATATAAT
*
34758374 TTTTCATTTACATCATATA
1 TTTTCATATACATCATATA
34758393 TGATTTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTCATATACATCATATAAT
Found at i:34758659 original size:41 final size:42
Alignment explanation
Indices: 34758583--34758706 Score: 155
Period size: 41 Copynumber: 2.9 Consensus size: 42
34758573 TCCTAGACGT
*
34758583 GGTCTTACATGCT-ATCACATATCGATGCCACTGTCCCAGACAG
1 GGTCTTACACG-TAATCACATATCGATGCCA-TGTCCCAGACAG
* *
34758626 GGTCTTACACG-AATCAAATAT-GATGCCGATGTCCCAGACAT
1 GGTCTTACACGTAATCACATATCGATGCC-ATGTCCCAGACAG
*
34758667 GGTCTTACACGTAATCACATCTCGATGCCAATGTCCCAGA
1 GGTCTTACACGTAATCACATATCGATGCC-ATGTCCCAGA
34758707 TGTGGTCTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
41 28 0.39
42 17 0.24
43 26 0.37
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGTAATCACATATCGATGCCATGTCCCAGACAG
Found at i:34758713 original size:43 final size:43
Alignment explanation
Indices: 34758564--34758716 Score: 179
Period size: 43 Copynumber: 3.6 Consensus size: 43
34758554 ATATCGTACA
* * *
34758564 ATGCCAACGTCCTAGACGTGGTCTTACATGCT-ATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-TAATCACATATCG
* *
34758607 ATGCCACTGTCCCAGACAG-GGTCTTACACG-AATCAAATAT-G
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* * *
34758648 ATGCCGATGTCCCAGACATGGTCTTACACGTAATCACATCTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
34758691 ATGCCAATGTCCCAGATGTGGTCTTA
1 ATGCCAATGTCCCAGACGTGGTCTTA
34758717 TAGGAGAACA
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
41 27 0.29
42 16 0.17
43 48 0.52
44 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:34762638 original size:13 final size:13
Alignment explanation
Indices: 34762622--34762648 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34762612 ATCATATGAC
34762622 TATATCATCATCA
1 TATATCATCATCA
34762635 TATATCATCATCA
1 TATATCATCATCA
34762648 T
1 T
34762649 TATGTCAAAT
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:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATCATCATCA
Found at i:34764325 original size:27 final size:27
Alignment explanation
Indices: 34764295--34764353 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
34764285 AAAGTACTCC
*
34764295 CGATTTACAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
34764322 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
34764349 TGATT
1 CGATT
34764354 GTGAAATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:34764426 original size:54 final size:54
Alignment explanation
Indices: 34764358--34764553 Score: 250
Period size: 54 Copynumber: 3.6 Consensus size: 54
34764348 TTGATTGTGA
* * * * *
34764358 AATTACTGAAATACCCCTGTAGGGTAGAATTTCTGAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * *
34764412 AATTACTGAAATACCCTTATAGGATAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* *
34764466 AATTA-TCGAAATACCCTTTTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * * *
34764520 AATTACCGAGATACCCTTGTGGGGTAAAATTACC
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACC
34764554 ATTTTGCCCC
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 121 0.99
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (54 bp):
AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
Found at i:34764553 original size:27 final size:27
Alignment explanation
Indices: 34764358--34764553 Score: 221
Period size: 27 Copynumber: 7.3 Consensus size: 27
34764348 TTGATTGTGA
* *
34764358 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * * * *
34764385 AATTTCTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
34764412 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
34764439 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
34764466 AATTATCGAAATACCCTTTTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
34764493 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
34764520 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAG
34764547 AATTACC
1 AATTACC
34764554 ATTTTGCCCC
Statistics
Matches: 144, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 144 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGTAGGGTAG
Found at i:34764790 original size:27 final size:26
Alignment explanation
Indices: 34764752--34764831 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
34764742 CGGAGGAAGC
34764752 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
34764779 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * *
34764805 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
34764832 ATTGACCGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.19
27 39 0.81
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:34765167 original size:27 final size:27
Alignment explanation
Indices: 34765145--34765200 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
34765135 TAGGTGGGTT
*
34765145 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
34765172 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
34765199 TG
1 TG
34765201 TTACGAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:34765369 original size:6 final size:6
Alignment explanation
Indices: 34765360--34765525 Score: 168
Period size: 6 Copynumber: 27.8 Consensus size: 6
34765350 CTGTCACGTA
* *
34765360 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATACTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG
* *
34765408 ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG A-TCTG -TCACCTA ATTCTG
1 ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
*
34765456 ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG
34765504 -TTACTG ATTCTG ATT-TG ATTCT
1 ATT-CTG ATTCTG ATTCTG ATTCT
34765526 CATTTTGGTT
Statistics
Matches: 135, Mismatches: 10, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
5 18 0.13
6 107 0.79
7 8 0.06
8 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:34765399 original size:30 final size:30
Alignment explanation
Indices: 34765339--34765525 Score: 245
Period size: 30 Copynumber: 6.2 Consensus size: 30
34765329 CATTCACATT
* *
34765339 TGATTCTGATTCTGTCACGTAATTCTGATTC
1 TGATTCTGATTCTGTTAC-TAATACTGATTC
34765370 TGATTCTGATTCTGTTACTAATACTGATTC
1 TGATTCTGATTCTGTTACTAATACTGATTC
**
34765400 TGATTCTGATTCTGATT-CTGTTACTGATTC
1 TGATTCTGATTCTG-TTACTAATACTGATTC
* *
34765430 TGATTCTGA-TCTGTCACCTAATTCTGATTC
1 TGATTCTGATTCTGTTA-CTAATACTGATTC
*
34765460 TGATTCTGATTCTGTTACTAATATTGATTC
1 TGATTCTGATTCTGTTACTAATACTGATTC
* *
34765490 TGATTCTGATTCTGTTACTGATTCTGATT-
1 TGATTCTGATTCTGTTACTAATACTGATTC
34765519 TGATTCT
1 TGATTCT
34765526 CATTTTGGTT
Statistics
Matches: 138, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.01
29 11 0.08
30 101 0.73
31 25 0.18
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (30 bp):
TGATTCTGATTCTGTTACTAATACTGATTC
Found at i:34771882 original size:19 final size:19
Alignment explanation
Indices: 34771851--34771896 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
34771841 TACACGGCCT
*
34771851 AAGG-ACACGGGCATGACA
1 AAGGTACACAGGCATGACA
*
34771869 AAGGTACACAGGCATGTCA
1 AAGGTACACAGGCATGACA
34771888 AAGGTACAC
1 AAGGTACAC
34771897 GGGCGTACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (19 bp):
AAGGTACACAGGCATGACA
Found at i:34774562 original size:3 final size:3
Alignment explanation
Indices: 34774554--34774975 Score: 130
Period size: 3 Copynumber: 142.7 Consensus size: 3
34774544 ATATATAATG
* * * *
34774554 TAA TAA TAA TAG TAA TAA T-A CAA TAA TAA TAA TAA -AG CAA -AA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
34774598 TAG CAA TAA TAA TACA TTAA TAA GAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
34774644 TAG GAA -AA -AA TAA T-A TAT TAAA GAA TAA TTA TAG TAA -AA -AA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * * *
34774685 TAA -AA GTAA AAA TAA TAA TAA TAA TAA TAT TAA TAA AAA GAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
34774730 TAA AAA TAA AAA TAA TGAA T-A TAA TAG TAA CATA TAA TAA TAA TGGAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA T--AA
* * * * *
34774778 TAA CAC TAA TAA TAA AAA T-A TAGA -AGA TAA CAA AAA TAA TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TA-A
* ** * * * * *
34774823 TAA TAA TGA T-A TGT TAA CAA TAA TGA TTA TAA -AA AAA TAGA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* ** * * * *
34774867 TAA TAA TGTA TGAA TAA TAA T-A TGC TAA AAA TAG CAA TAG TAA -AA
1 TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
34774912 -AA AAA TAG TAA TAA TAA AAA TAA AAA TTA T-A TAAA TAA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
34774956 TAA TAA TAA CAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
34774976 TTAAAATTAA
Statistics
Matches: 305, Mismatches: 84, Indels: 60
0.68 0.19 0.13
Matches are distributed among these distances:
2 37 0.12
3 241 0.79
4 22 0.07
5 5 0.02
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:34774578 original size:17 final size:17
Alignment explanation
Indices: 34774558--34774642 Score: 54
Period size: 17 Copynumber: 4.9 Consensus size: 17
34774548 ATAATGTAAT
34774558 AATAATAGTAATAATAC
1 AATAATAGTAATAATAC
*
34774575 AATAATAATAATAA-AGC
1 AATAATAGTAATAATA-C
*
34774592 AAAAAATAGCAATAATAATAC
1 -AATAATAG---TAATAATAC
*
34774613 ATTAATAAG-AATAAT--
1 AATAAT-AGTAATAATAC
34774628 AATAATA-TAATAATA
1 AATAATAGTAATAATA
34774643 ATAGGAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 20
0.67 0.08 0.25
Matches are distributed among these distances:
14 7 0.13
15 5 0.09
16 1 0.02
17 20 0.38
18 6 0.11
20 4 0.08
21 9 0.17
22 1 0.02
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (17 bp):
AATAATAGTAATAATAC
Found at i:34774625 original size:20 final size:20
Alignment explanation
Indices: 34774538--34774792 Score: 81
Period size: 20 Copynumber: 12.7 Consensus size: 20
34774528 GTATATGCAA
*
34774538 AAGAA-AATATATAATGTAAT
1 AAGAATAATA-ATAATATAAT
* * *
34774558 AATAATAGTAATAATACAAT
1 AAGAATAATAATAATATAAT
* * *
34774578 AATAATAATAA-AGCAAAAAAT
1 AAGAATAATAATA--ATATAAT
34774599 -AGCAATAATAATACAT-TAAT
1 AAG-AATAATAATA-ATATAAT
34774619 AAGAATAATAATAATATAAT
1 AAGAATAATAATAATATAAT
* * *
34774639 AATAATAGGAAAAAATAATATATT
1 AAGAAT----AATAATAATATAAT
34774663 AAAGAATAAT--T-ATAGTAA-
1 -AAGAATAATAATAATA-TAAT
34774681 AA-AATAA-AAGTAA-A-AAT
1 AAGAATAATAA-TAATATAAT
*
34774698 AATAATAATAATAATATTAAT
1 AAGAATAATAATAATA-TAAT
* *
34774719 AAAAAGAATAATAA-A-AAT
1 AAGAATAATAATAATATAAT
* *
34774737 AAAAATAATGAAT-ATAATAGT
1 AAGAATAAT-AATAAT-ATAAT
* **
34774758 AACATATAATAATAATGGAAT
1 AAGA-ATAATAATAATATAAT
* *
34774779 AACACTAATAATAA
1 AAGAATAATAATAA
34774793 AAATATAGAA
Statistics
Matches: 181, Mismatches: 25, Indels: 58
0.69 0.09 0.22
Matches are distributed among these distances:
16 7 0.04
17 4 0.02
18 25 0.14
19 13 0.07
20 56 0.31
21 51 0.28
22 8 0.04
24 12 0.07
25 5 0.03
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (20 bp):
AAGAATAATAATAATATAAT
Found at i:34774671 original size:31 final size:28
Alignment explanation
Indices: 34774636--34774704 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 28
34774626 ATAATAATAT
*
34774636 AATAATAATAGGAAAAAATAATATATTAAA
1 AATAATAATAGGAAAAAATAA-A-AGTAAA
* *
34774666 GAATAATTATAGTAAAAAATAAAAGTAAA
1 -AATAATAATAGGAAAAAATAAAAGTAAA
34774695 AATAATAATA
1 AATAATAATA
34774705 ATAATAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.26
29 5 0.15
30 1 0.03
31 19 0.56
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (28 bp):
AATAATAATAGGAAAAAATAAAAGTAAA
Found at i:34774917 original size:19 final size:19
Alignment explanation
Indices: 34774893--34774936 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
34774883 ATAATATGCT
*
34774893 AAAAATAGCAATAGTAAAA
1 AAAAATAGCAATAATAAAA
*
34774912 AAAAATAGTAATAATAAAA
1 AAAAATAGCAATAATAAAA
34774931 ATAAAA
1 A-AAAA
34774937 ATTATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (19 bp):
AAAAATAGCAATAATAAAA
Found at i:34774920 original size:13 final size:15
Alignment explanation
Indices: 34774902--34774933 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
34774892 TAAAAATAGC
34774902 AATAGTAA-AA-AAA
1 AATAGTAATAATAAA
34774915 AATAGTAATAATAAA
1 AATAGTAATAATAAA
34774930 AATA
1 AATA
34774934 AAAATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 2 0.12
15 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (15 bp):
AATAGTAATAATAAA
Found at i:34776754 original size:129 final size:132
Alignment explanation
Indices: 34776601--34776903 Score: 452
Period size: 129 Copynumber: 2.3 Consensus size: 132
34776591 CGTTACATGG
* *
34776601 AGATAAGATTTGCCATCTTTGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTGCAATTCCTC
1 AGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTCCTC
* * *
34776666 ATCCT-GCTCCACTACTACTCAGGGAGATAAGGTTAGTGGCTTAAAT-T-TT-CCTACTACTTTA
66 A-CCTCGCTCCACTACTACTCAGGGAGATAAGGCTAGTGGCTTAAATCTCTTCCCTACTACCTCA
34776727 GGA
130 GGA
* * *
34776730 AGATAAGATTTGCAATCTTCGATCTGCTCCATTACTGCTTAGGGAGATAAGATCTGCAATTCCTT
1 AGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTCCTC
* *
34776795 AGCTCGCTCCACTACTATTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCA
66 ACCTCGCTCCACTACTACTCAGGGAGATAAGGCTAGTGGCTTAAATCT-CTTCCCTACTACCTCA
34776860 GGA
130 GGA
* *
34776863 AAATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTA
1 AGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTA
34776904 AGGAAATGAG
Statistics
Matches: 155, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
128 2 0.01
129 100 0.65
130 1 0.01
132 2 0.01
133 50 0.32
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (132 bp):
AGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTCCTC
ACCTCGCTCCACTACTACTCAGGGAGATAAGGCTAGTGGCTTAAATCTCTTCCCTACTACCTCAG
GA
Found at i:34776788 original size:44 final size:44
Alignment explanation
Indices: 34776599--34776825 Score: 150
Period size: 45 Copynumber: 5.2 Consensus size: 44
34776589 GTCGTTACAT
* * * * *
34776599 GGAGATAAGATTTGCCATCTTTGATCTGCTTCACTACTGCTTAG
1 GGAGATAAGATCTGCAATCTTCGATCTGCTCCACTACTACTTAG
* *
34776643 GGAGATAAGATCTGCAATTCCTC-ATCCTGCTCCACTACTACTCAG
1 GGAGATAAGATCTGCAA-TCTTCGAT-CTGCTCCACTACTACTTAG
* * ** *
34776688 GGAGATAAGGT-T--AGTGGCTTAAAT-T--TTC-CTACTACTTTAG
1 GGAGATAAGATCTGCAAT--CTTCGATCTGCTCCACTACTAC-TTAG
* * * *
34776728 GAAGATAAGATTTGCAATCTTCGATCTGCTCCATTACTGCTTAG
1 GGAGATAAGATCTGCAATCTTCGATCTGCTCCACTACTACTTAG
* *
34776772 GGAGATAAGATCTGCAATTCCTTAGCTC-GCTCCACTACTA-TTCAG
1 GGAGATAAGATCTGCAA-T-CTTCGATCTGCTCCACTACTACTT-AG
34776817 GGAGATAAG
1 GGAGATAAG
34776826 GCTAGTGGCT
Statistics
Matches: 140, Mismatches: 27, Indels: 31
0.71 0.14 0.16
Matches are distributed among these distances:
39 7 0.05
40 14 0.10
41 7 0.05
42 3 0.02
43 4 0.03
44 43 0.31
45 56 0.40
46 6 0.04
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
GGAGATAAGATCTGCAATCTTCGATCTGCTCCACTACTACTTAG
Found at i:34787399 original size:51 final size:50
Alignment explanation
Indices: 34787284--34787519 Score: 203
Period size: 49 Copynumber: 4.7 Consensus size: 50
34787274 TTGTGAGGTT
* * * * *
34787284 ACGTGTGTAGTACTAAGTTCAGGCTACGACGTGTACCGAATTA-TTGGTC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCAATAATTTGGTC
* * * * *
34787333 GCATGTGTAGTACTAAGTACAGGCTACTATGCGTACCCAATAACTTTGATC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCAATAA-TTTGGTC
* * ** *
34787384 ACGTGTGTAGTACTAAGTGCTGGCTACTATGTGTA-TCAGATGGTTAGGTC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCA-ATAATTTGGTC
* * * * **
34787434 ACGTGTATAGTACTAAGTGCAAGCTACTACGTATACCGGATAA-TTGGTTGC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCAATAATTTGG-T-C
*
34787485 AC--GTGTAGTACTAAGTGCAGGCTACTATGCGTACC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACC
34787520 AGATAGCTTT
Statistics
Matches: 146, Mismatches: 35, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
49 66 0.45
50 40 0.27
51 40 0.27
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (50 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCAATAATTTGGTC
Found at i:34793606 original size:11 final size:10
Alignment explanation
Indices: 34793584--34793613 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
34793574 CACCCTCCTT
34793584 CTTTTTCTTC
1 CTTTTTCTTC
34793594 CTTTTTCTCTC
1 CTTTTTCT-TC
34793605 CTTTTTCTT
1 CTTTTTCTT
34793614 TTTTCCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
CTTTTTCTTC
Found at i:34797381 original size:30 final size:30
Alignment explanation
Indices: 34797347--34797404 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
34797337 TAGGCACTTC
*
34797347 CACACGGAT-GATCCACACGCCCGTGTGTGA
1 CACACGGATAGAT-CACACACCCGTGTGTGA
*
34797377 CACACGGGTAGATCACACACCCGTGTGT
1 CACACGGATAGATCACACACCCGTGTGT
34797405 CATGGCCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (30 bp):
CACACGGATAGATCACACACCCGTGTGTGA
Found at i:34802417 original size:43 final size:43
Alignment explanation
Indices: 34802353--34802439 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
34802343 ATATGTGATT
**
34802353 TCGATATGTGTTTACGAGTAAGACC-CTATCTAGGACAGTGGCA
1 TCGATATGTGACTACGAGTAAGACCAC-ATCTAGGACAGTGGCA
* *
34802396 TCGATATGTGACTAC-ATGTAAGACCACGTCTAGGACATTGGCA
1 TCGATATGTGACTACGA-GTAAGACCACATCTAGGACAGTGGCA
34802439 T
1 T
34802440 TGTATGATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 1 0.03
43 36 0.95
44 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
TCGATATGTGACTACGAGTAAGACCACATCTAGGACAGTGGCA
Found at i:34809824 original size:13 final size:13
Alignment explanation
Indices: 34809806--34809841 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
34809796 CATAAATCAC
34809806 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
*
34809819 TTTTTTTTTCGAA
1 TTTTTTTTTTGAA
34809832 TTTTTTTTTT
1 TTTTTTTTTT
34809842 CAAACTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:34809841 original size:14 final size:14
Alignment explanation
Indices: 34809806--34809842 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
34809796 CATAAATCAC
34809806 TTTTTTTTTT-GAA
1 TTTTTTTTTTCGAA
34809819 -TTTTTTTTTCGAA
1 TTTTTTTTTTCGAA
34809832 TTTTTTTTTTC
1 TTTTTTTTTTC
34809843 AAACTTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
13 3 0.14
14 10 0.45
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.78
Consensus pattern (14 bp):
TTTTTTTTTTCGAA
Found at i:34813626 original size:31 final size:31
Alignment explanation
Indices: 34813583--34813666 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
34813573 TTAGTCTTGA
34813583 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
* *
34813613 TATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
34813644 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
34813667 ACTGTAAACG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 4 0.08
31 46 0.92
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTCCATAAAT
Found at i:34813737 original size:42 final size:42
Alignment explanation
Indices: 34813690--34813781 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
34813680 TGGCCCTTAG
* * *
34813690 GCCCATTTCTATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACAAGTAATGTCAATGAATGTATGCAA
34813732 GCCCATTTCAATATCACAAGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACAAGTAATGTCAATGAATGTATGCAA
*
34813774 GCCAATTT
1 GCCCATTT
34813782 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACAAGTAATGTCAATGAATGTATGCAA
Found at i:34813965 original size:25 final size:25
Alignment explanation
Indices: 34813929--34813997 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
34813919 CTCTTTTAAT
34813929 AACT-GGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
34813953 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
34813978 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
34813998 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 4 0.10
25 33 0.80
26 4 0.10
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:34814955 original size:27 final size:28
Alignment explanation
Indices: 34814925--34815032 Score: 107
Period size: 27 Copynumber: 3.9 Consensus size: 28
34814915 GTAAATCTAC
34814925 AAACCAAGGGTATTT-TAGTAATTTTGT
1 AAACCAAGGGTATTTCTAGTAATTTTGT
* *
34814952 AAACCAATGGTATTTCTA-TAATTTTTT
1 AAACCAAGGGTATTTCTAGTAATTTTGT
**
34814979 AAAAGTTAAGGGTATTTCT-GTAATTTTGT
1 -AAA-CCAAGGGTATTTCTAGTAATTTTGT
* * *
34815008 AAATCAGGGGTATTT-TGGTAATTTT
1 AAACCAAGGGTATTTCTAGTAATTTT
34815033 TCAAATTGAG
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
26 1 0.01
27 40 0.59
28 8 0.12
29 19 0.28
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.44
Consensus pattern (28 bp):
AAACCAAGGGTATTTCTAGTAATTTTGT
Found at i:34815030 original size:56 final size:54
Alignment explanation
Indices: 34814930--34815113 Score: 144
Period size: 54 Copynumber: 3.4 Consensus size: 54
34814920 TCTACAAACC
*
34814930 AAGGGTATTT-TAGTAATTTTGTAAACCAATGGTATTTCTATAATTTTTTAAAAGTT
1 AAGGGTATTTCT-GTAATTTTGTAAACCAAGGGTATTTCTATAA-TTTTTAAAA-TT
* * * *
34814986 AAGGGTATTTCTGTAATTTTGTAAATCAGGGGTATTT-TGGTAATTTTTCAAATT
1 AAGGGTATTTCTGTAATTTTGTAAACCAAGGGTATTTCT-ATAATTTTTAAAATT
* *** * ** *
34815040 GAGGGTATTTC-GATAATTTCACAAACCAATGGTATTTCGGTAA-TTTTACAAACT
1 AAGGGTATTTCTG-TAATTTTGTAAACCAAGGGTATTTCTATAATTTTTA-AAATT
*
34815094 AGGGGTATTT-TGGTAATTTT
1 AAGGGTATTTCT-GTAATTTT
34815114 ACAAACTAGG
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
53 5 0.05
54 52 0.50
55 10 0.10
56 35 0.34
57 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.43
Consensus pattern (54 bp):
AAGGGTATTTCTGTAATTTTGTAAACCAAGGGTATTTCTATAATTTTTAAAATT
Found at i:34815106 original size:81 final size:80
Alignment explanation
Indices: 34814989--34815137 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 80
34814979 AAAAGTTAAG
* ** * * * *
34814989 GGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTTCAAATTGAGGGTATTTCGAT
1 GGTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACT-AGGGCATTTCAAT
34815054 AATTTCACAAACCAAT
65 AATTTCACAAACCAAT
34815070 GGTATTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAGGGCATTTCAAT
1 GGTATTTCGGTAATTTTACAAATC-AGGGGTATTTTGGTAATTTTACAAACTAGGGCATTTCAAT
34815134 AATT
65 AATT
34815138 GGTAAACTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
80 16 0.27
81 44 0.73
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (80 bp):
GGTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAACTAGGGCATTTCAATA
ATTTCACAAACCAAT
Found at i:34815119 original size:27 final size:27
Alignment explanation
Indices: 34814988--34815124 Score: 127
Period size: 27 Copynumber: 5.1 Consensus size: 27
34814978 TAAAAGTTAA
**
34814988 GGGTATTTCT-GTAATTTTGTAAA-TCAG
1 GGGTATTT-TGGTAATTTTACAAACT-AG
* *
34815015 GGGTATTTTGGTAATTTTTCAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * * * *
34815041 AGGGTATTTCGATAATTTCACAAACCAA
1 -GGGTATTTTGGTAATTTTACAAACTAG
* *
34815069 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
34815096 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
34815123 GG
1 GG
34815125 CATTTCAATA
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.02
27 88 0.98
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:34817199 original size:31 final size:31
Alignment explanation
Indices: 34817053--34817199 Score: 251
Period size: 31 Copynumber: 4.8 Consensus size: 31
34817043 TTAGTCTTGA
*
34817053 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
34817083 CATATCACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
34817114 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
34817145 CATATCACTGGGCAGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
34817176 CATATCACTGGGTCGAAGCCTTTT
1 CATATCACTGGGCCGAAGCCTTTT
34817200 TGTAAACGGT
Statistics
Matches: 112, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 5 0.04
31 107 0.96
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:34818701 original size:40 final size:40
Alignment explanation
Indices: 34818627--34818848 Score: 367
Period size: 40 Copynumber: 5.6 Consensus size: 40
34818617 AACCCAAGTA
* *
34818627 CCTTCGGGATTTAG-CCGGATATAG-CAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
34818666 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
34818706 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
34818746 CCTTTGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
34818786 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
34818826 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
34818849 CATTCGAATA
Statistics
Matches: 171, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 12 0.07
40 156 0.91
41 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:34823577 original size:40 final size:40
Alignment explanation
Indices: 34823385--34823570 Score: 261
Period size: 40 Copynumber: 4.7 Consensus size: 40
34823375 TCGAATGATG
* * *
34823385 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
34823425 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34823465 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
34823505 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
34823546 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
34823571 AACGAGTAGC
Statistics
Matches: 134, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
39 1 0.01
40 123 0.92
41 10 0.07
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:34823577 original size:80 final size:80
Alignment explanation
Indices: 34823385--34823603 Score: 270
Period size: 80 Copynumber: 2.8 Consensus size: 80
34823375 TCGAATGATG
* * **
34823385 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAAGATCCGAAGGCATT
34823449 TGTGCGAGTTACTAAA
65 TGTGCGAGTTACTAAA
* *
34823465 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGAT-CCGAAGGCATT
34823529 TGTGCGAGTTACTATAA
65 TGTGCGAGTTACTA-AA
* **
34823546 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAA-ACTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAGA-TCCGAAGG
34823604 TACGTGATTC
Statistics
Matches: 122, Mismatches: 11, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
79 16 0.13
80 97 0.80
81 9 0.07
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:34831624 original size:40 final size:40
Alignment explanation
Indices: 34831526--34831711 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
34831516 TCGAATGATG
* * * * *
34831526 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGATTATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* **
34831566 TTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
34831606 TCCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
34831646 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
34831687 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
34831712 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 117 0.92
41 9 0.07
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:34838430 original size:40 final size:40
Alignment explanation
Indices: 34838355--34838574 Score: 351
Period size: 40 Copynumber: 5.6 Consensus size: 40
34838345 AACCCAAGTA
*
34838355 CCTTCGGGATTTAG-CCGGATATAG-CAACTCA-CACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-T-AGCACAAATG
* *
34838394 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
34838434 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
34838474 CCTTC-GGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
34838513 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
34838553 CCTT-GGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
34838575 CATTCGAATA
Statistics
Matches: 170, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
39 69 0.41
40 98 0.58
41 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:34838491 original size:79 final size:79
Alignment explanation
Indices: 34838355--34838574 Score: 347
Period size: 79 Copynumber: 2.8 Consensus size: 79
34838345 AACCCAAGTA
* *
34838355 CCTTCGGGATTTAG-CCGGATATAG-CAACTCA-CACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACT-AGCACAAATGCCTTC-GGACTTAGCCCGGATAT
34838417 AGTCAATAGCACAAAAG
63 AGTCAATAGCACAAAAG
34838434 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGACTTAGCCCGGATATAGT
*
34838499 CAATAGCACAAATG
66 CAATAGCACAAAAG
* *
34838513 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATGCCTTGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGACTTAGCCCGGATAT
34838575 CATTCGAATA
Statistics
Matches: 133, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
79 106 0.80
80 26 0.20
81 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGACTTAGCCCGGATATAGT
CAATAGCACAAAAG
Found at i:34840630 original size:25 final size:25
Alignment explanation
Indices: 34840602--34840671 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
34840592 CTCTTTTAAT
34840602 AACTGGGGAAAAGCCC-TTTCTGATA
1 AACTGGGGAAAAGCCCTTTTC-GATA
* * *
34840627 AACTAGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGAAAAGCCCTTTTCGATA
* *
34840652 AACTGGGGTAGAGCCCTTTT
1 AACTGGGGAAAAGCCCTTTT
34840672 AGCATTTCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 34 0.89
26 4 0.11
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGAAAAGCCCTTTTCGATA
Found at i:34841163 original size:27 final size:28
Alignment explanation
Indices: 34841133--34841240 Score: 116
Period size: 27 Copynumber: 3.9 Consensus size: 28
34841123 GTAAATCTAC
34841133 AAACCAAGGGTATTT-TAGTAATTTTGT
1 AAACCAAGGGTATTTCTAGTAATTTTGT
* *
34841160 AAACCAATGGTATTTCTA-TAATTTTTT
1 AAACCAAGGGTATTTCTAGTAATTTTGT
**
34841187 AAAAGTTAAGGGTATTTCT-GTAATTTTGT
1 -AAA-CCAAGGGTATTTCTAGTAATTTTGT
* *
34841216 AAATCAGGGGTATTT-TAGTAATTTT
1 AAACCAAGGGTATTTCTAGTAATTTT
34841241 TCAAATTGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
26 1 0.01
27 40 0.59
28 8 0.12
29 19 0.28
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.44
Consensus pattern (28 bp):
AAACCAAGGGTATTTCTAGTAATTTTGT
Found at i:34841228 original size:56 final size:55
Alignment explanation
Indices: 34841138--34841266 Score: 149
Period size: 56 Copynumber: 2.3 Consensus size: 55
34841128 TCTACAAACC
*
34841138 AAGGGTATTT-TAGTAATTTTGTAAACCAATGGTATTTCTA-TAATTTTTTAAAAGTT-
1 AAGGGTATTTCT-GTAATTTTGTAAACCAAGGGTATTT-TAGTAA-TTTTTAAAA-TTG
* * *
34841194 AAGGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTAGTAATTTTTCAAATTG
1 AAGGGTATTTCTGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTTAAAATTG
*
34841249 AA-GGTATTTCGGTAATTT
1 AAGGGTATTTCTGTAATTT
34841267 CACAAACCAG
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
54 17 0.26
55 12 0.18
56 35 0.54
57 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (55 bp):
AAGGGTATTTCTGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTTAAAATTG
Found at i:34841246 original size:27 final size:27
Alignment explanation
Indices: 34841140--34841326 Score: 89
Period size: 27 Copynumber: 6.9 Consensus size: 27
34841130 TACAAACCAA
* *
34841140 GGGTATTTTAGTAATTTTGT-AAACCAA
1 GGGTATTTTAGTAATTTT-TCAAATCAG
* * * *
34841167 TGGTATTTCTA-TAATTTTTTAAAAGTTAA
1 GGGTATTT-TAGTAA-TTTTTCAAA-TCAG
34841196 GGGTATTTCT-GTAATTTTGT-AAATCAG
1 GGGTATTT-TAGTAATTTT-TCAAATCAG
*
34841223 GGGTATTTTAGTAATTTTTCAAAT-TG
1 GGGTATTTTAGTAATTTTTCAAATCAG
* ** ** *
34841249 AAGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTAGTAATTTTTCAAATCAG
* ** *
34841277 TGGTATTTCGGTAATTTTACAAA-CTAG
1 GGGTATTTTAGTAATTTTTCAAATC-AG
* *
34841304 GGGTATTTTGGTAATTTTACAAA
1 GGGTATTTTAGTAATTTTTCAAA
34841327 CTAGGGCATT
Statistics
Matches: 131, Mismatches: 18, Indels: 22
0.77 0.11 0.13
Matches are distributed among these distances:
26 4 0.03
27 95 0.73
28 17 0.13
29 15 0.11
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTTCAAATCAG
Found at i:34841282 original size:54 final size:53
Alignment explanation
Indices: 34841141--34841327 Score: 151
Period size: 54 Copynumber: 3.4 Consensus size: 53
34841131 ACAAACCAAG
** ** * *
34841141 GGTATTTTAGTAATTTTGTAAACCAATGGTATTTCTA-TAATTTTTTAAAAGTTAA
1 GGTATTTCGGTAATTTTACAAACCAGTGGTATTT-TAGTAA-TTTTTCAAA-TTAA
* ** * *
34841196 GGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTAGTAATTTTTCAAATTGAA
1 -GGTATTTCGGTAATTTTACAAACCAGTGGTATTTTAGTAATTTTTCAAATT-AA
* ** * * *
34841251 GGTATTTCGGTAATTTCACAAACCAGTGGTATTTCGGTAATTTTACAAACTAGG
1 GGTATTTCGGTAATTTTACAAACCAGTGGTATTTTAGTAATTTTTCAAATTA-A
*
34841305 GGTATTTTGGTAATTTTACAAAC
1 GGTATTTCGGTAATTTTACAAAC
34841328 TAGGGCATTT
Statistics
Matches: 109, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
53 1 0.01
54 64 0.59
55 12 0.11
56 32 0.29
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.43
Consensus pattern (53 bp):
GGTATTTCGGTAATTTTACAAACCAGTGGTATTTTAGTAATTTTTCAAATTAA
Found at i:34841345 original size:26 final size:26
Alignment explanation
Indices: 34841195--34841338 Score: 128
Period size: 27 Copynumber: 5.4 Consensus size: 26
34841185 TTAAAAGTTA
* **
34841195 AGGGTATTTCTGTAATTTTGTAAA-T
1 AGGGTATTTCGGTAATTTTACAAACT
** * *
34841220 CAGGGGTATTTTAGTAATTTTTCAAATT
1 -A-GGGTATTTCGGTAATTTTACAAACT
* * *
34841248 GAAGGTATTTCGGTAATTTCACAAACC
1 -AGGGTATTTCGGTAATTTTACAAACT
34841275 AGTGGTATTTCGGTAATTTTACAAACT
1 AG-GGTATTTCGGTAATTTTACAAACT
*
34841302 AGGGGTATTTTGGTAATTTTACAAACT
1 A-GGGTATTTCGGTAATTTTACAAACT
*
34841329 AGGGCATTTC
1 AGGGTATTTC
34841339 AATAATTGGT
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
26 9 0.09
27 84 0.88
28 3 0.03
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.40
Consensus pattern (26 bp):
AGGGTATTTCGGTAATTTTACAAACT
Found at i:34848919 original size:18 final size:18
Alignment explanation
Indices: 34848880--34848965 Score: 84
Period size: 18 Copynumber: 4.7 Consensus size: 18
34848870 GGAGAAAAAT
* *
34848880 AAAAGAAAAAGAACG-AA
1 AAAAGAAAAAGAAAGTGA
*
34848897 AAAAGAACAAGAAAGTGA
1 AAAAGAAAAAGAAAGTGA
*
34848915 AAAAGAAAAAGAGAGTGAA
1 AAAAGAAAAAGAAAGTG-A
* *
34848934 AGAAAGGAAAAACAAATTGA
1 A-AAA-GAAAAAGAAAGTGA
34848954 AAAAGAAAAAGA
1 AAAAGAAAAAGA
34848966 TTTCAAGCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
17 13 0.23
18 23 0.41
19 5 0.09
20 5 0.09
21 10 0.18
ACGTcount: A:0.71, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAAGTGA
Found at i:34848961 original size:39 final size:35
Alignment explanation
Indices: 34848880--34848965 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 35
34848870 GGAGAAAAAT
* *
34848880 AAAAGAAAAAGAACGAAAAAAGAACAAGAAAGTGA
1 AAAAGAAAAAGAACGAAAAAAGAAAAACAAAGTGA
* *
34848915 AAAAGAAAAAGAGAGTGAAAGAAAGGAAAAACAAATTGA
1 AAAAGAAAAAGA-A-CGAAA-AAA-GAAAAACAAAGTGA
34848954 AAAAGAAAAAGA
1 AAAAGAAAAAGA
34848966 TTTCAAGCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 12 0.28
36 1 0.02
37 4 0.09
38 3 0.07
39 23 0.53
ACGTcount: A:0.71, C:0.03, G:0.21, T:0.05
Consensus pattern (35 bp):
AAAAGAAAAAGAACGAAAAAAGAAAAACAAAGTGA
Found at i:34849977 original size:23 final size:21
Alignment explanation
Indices: 34849951--34849994 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
34849941 GTGTTTTATG
34849951 TGTTTAAAAGTGTTTAATATGCA
1 TGTTTAAAAGTG-TTAAT-TGCA
* *
34849974 TGTTTTAATGTGTTAATTGCA
1 TGTTTAAAAGTGTTAATTGCA
34849995 GGTGTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 10 0.53
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.48
Consensus pattern (21 bp):
TGTTTAAAAGTGTTAATTGCA
Found at i:34853899 original size:29 final size:29
Alignment explanation
Indices: 34853866--34853938 Score: 146
Period size: 29 Copynumber: 2.5 Consensus size: 29
34853856 GTGACGAGAT
34853866 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
34853895 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
34853924 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
34853939 GAAATCGAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:34869942 original size:11 final size:11
Alignment explanation
Indices: 34869926--34869955 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
34869916 CAGCTCGGGT
34869926 CCAGCTCACTA
1 CCAGCTCACTA
*
34869937 CTAGCTCACTA
1 CCAGCTCACTA
34869948 CCAGCTCA
1 CCAGCTCA
34869956 TGGGTCCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.43, G:0.10, T:0.20
Consensus pattern (11 bp):
CCAGCTCACTA
Found at i:34871541 original size:26 final size:26
Alignment explanation
Indices: 34871512--34871561 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
34871502 TTATAATATG
* *
34871512 AAAAATGACTATTTTA-CCCCTAGGT
1 AAAAATGACCATTATACCCCCTAGGT
34871537 AAAAATGACCATTATACCCCCTAGG
1 AAAAATGACCATTATACCCCCTAGG
34871562 GTTTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (26 bp):
AAAAATGACCATTATACCCCCTAGGT
Found at i:34871627 original size:11 final size:11
Alignment explanation
Indices: 34871598--34871650 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
34871588 ATATTGTTAT
34871598 ACATGATATG-
1 ACATGATATGC
*
34871608 ACATAATATGC
1 ACATGATATGC
34871619 ACATGATATG-
1 ACATGATATGC
** *
34871629 TTATGAGATGC
1 ACATGATATGC
34871640 ACATGATATGC
1 ACATGATATGC
34871651 TATGATATAC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (11 bp):
ACATGATATGC
Found at i:34871654 original size:21 final size:21
Alignment explanation
Indices: 34871598--34871655 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
34871588 ATATTGTTAT
* *
34871598 ACATGATATGAC-ATAATATGC
1 ACATGATATG-CTATGAGATGC
*
34871619 ACATGATATGTTATGAGATGC
1 ACATGATATGCTATGAGATGC
34871640 ACATGATATGCTATGA
1 ACATGATATGCTATGA
34871656 TATACTCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (21 bp):
ACATGATATGCTATGAGATGC
Found at i:34871738 original size:24 final size:24
Alignment explanation
Indices: 34871706--34871752 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
34871696 AGGAATTACG
**
34871706 AAAAAGGCTTTGCC-CCAGTTATT
1 AAAAAGGCTAGGCCTCCAGTTATT
34871729 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAA-AGGCTAGGCCTCCAGTTAT
34871753 ATGATAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 8 0.40
25 8 0.40
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (24 bp):
AAAAAGGCTAGGCCTCCAGTTATT
Found at i:34879901 original size:16 final size:16
Alignment explanation
Indices: 34879882--34879912 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34879872 CTTCTTCACT
34879882 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
34879898 TACTTACTTACTTAA
1 TACTCACTTACTTAA
34879913 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:34879918 original size:20 final size:20
Alignment explanation
Indices: 34879879--34879918 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
34879869 AAACTTCTTC
* *
34879879 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
34879899 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
34879919 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:34880357 original size:55 final size:54
Alignment explanation
Indices: 34880102--34880357 Score: 253
Period size: 55 Copynumber: 4.8 Consensus size: 54
34880092 ACGCGGGTAC
* * *
34880102 CTTACC-ATTGCCATGACTTGTCATGGTCTTACGTGGTATCCTT---TT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
* * *
34880151 CTTACC-ATTTCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTA-GAAA
* * * * *
34880204 CTCACCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCC-TTACC-T-TAGAAA
* * * *
34880259 CTTATCAA-TGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTAGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
*
34880312 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTTA
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTA
34880358 AACCCTAATG
Statistics
Matches: 171, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
49 39 0.23
52 4 0.02
53 43 0.25
54 12 0.07
55 71 0.42
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
Found at i:34883675 original size:16 final size:16
Alignment explanation
Indices: 34883656--34883723 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
34883646 AAAACAAAAG
34883656 AAGAAAA-AATAAGAAA
1 AAGAAAACAA-AAGAAA
*
34883672 AAGAAAACAAAAGAGA
1 AAGAAAACAAAAGAAA
** *
34883688 GTGAAAAGAAAAAGAACA
1 AAGAAAA-CAAAAGAA-A
*
34883706 AAGAAAA-AGAAGAAA
1 AAGAAAACAAAAGAAA
34883721 AAG
1 AAG
34883724 GAAAGAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
15 4 0.10
16 23 0.56
17 8 0.20
18 6 0.15
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (16 bp):
AAGAAAACAAAAGAAA
Found at i:34883684 original size:29 final size:33
Alignment explanation
Indices: 34883646--34883712 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 33
34883636 AGATTGTAAA
*
34883646 AAAACAAAAGA-A-GAAAA-AATAAGAA-AAAG
1 AAAACAAAAGAGAGGAAAAGAAAAAGAACAAAG
34883675 AAAACAAAAGAGAGTGAAAAGAAAAAGAACAAAG
1 AAAACAAAAGAGAG-GAAAAGAAAAAGAACAAAG
34883709 AAAA
1 AAAA
34883713 AGAAGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 11 0.34
30 1 0.03
32 5 0.16
33 7 0.22
34 8 0.25
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.03
Consensus pattern (33 bp):
AAAACAAAAGAGAGGAAAAGAAAAAGAACAAAG
Found at i:34883710 original size:13 final size:13
Alignment explanation
Indices: 34883692--34883716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34883682 AAGAGAGTGA
34883692 AAAGAAAAAGAAC
1 AAAGAAAAAGAAC
34883705 AAAGAAAAAGAA
1 AAAGAAAAAGAA
34883717 GAAAAAGGAA
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:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAC
Found at i:34886971 original size:101 final size:99
Alignment explanation
Indices: 34886772--34886972 Score: 267
Period size: 99 Copynumber: 2.0 Consensus size: 99
34886762 TATGTAGCCA
* * * * *
34886772 AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 AACTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGGTACACA
** *
34886837 TAGTAGCCTGTACTTAGTACTACACACGTGACCT
66 TAGTAGCCTACACTTAGTACTACACACGCGACCT
* * * *
34886871 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACG
1 AACTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCAGGTACA
*
34886936 CATAGTAGCCTACACTTAGTACTACACATGCGACCT
64 CATAGTAGCCTACACTTAGTACTACACACGCGACCT
34886972 A
1 A
34886973 GCTACATATA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 42 0.48
100 3 0.03
101 42 0.48
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (99 bp):
AACTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGGTACACA
TAGTAGCCTACACTTAGTACTACACACGCGACCT
Found at i:34887031 original size:64 final size:66
Alignment explanation
Indices: 34886961--34887112 Score: 184
Period size: 68 Copynumber: 2.3 Consensus size: 66
34886951 TTAGTACTAC
* * *
34886961 ACATGCGACCTAGCTACATAT-A-TCCTGTAGCTCTCTTGT-CTACATGGTGTACACATAGTATC
1 ACATGCGACCTAGCTACATATAAGTCCTGTAGCTCTCTTGTAC-ACATGATGTACACATAGCACC
34887023 AT
65 AT
* * * *
34887025 CCATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTACACATGATGTGCACTTAGCAC
1 ACATGCGACCTAGCTACAT-ATAA-GTCCTGTAGCTCTCTTGTACACATGATGTACACATAGCAC
34887090 CAT
64 CAT
*
34887093 ACATGTGACCTAGCTACATA
1 ACATGCGACCTAGCTACATA
34887113 CTATTTGTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
64 18 0.24
65 2 0.03
66 1 0.01
67 1 0.01
68 51 0.69
69 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (66 bp):
ACATGCGACCTAGCTACATATAAGTCCTGTAGCTCTCTTGTACACATGATGTACACATAGCACCA
T
Found at i:34887812 original size:30 final size:30
Alignment explanation
Indices: 34887778--34887838 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
34887768 TCCTTAACTC
34887778 AAACTTTTGCAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
34887808 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
34887838 A
1 A
34887839 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:34890570 original size:30 final size:30
Alignment explanation
Indices: 34890536--34890632 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
34890526 TAAACTAAAA
*
34890536 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
34890566 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
34890596 TGAGCTAAGGTTTAGCTTGTGAGCTAAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
34890625 ATGAGCTA
1 -TGAGCTA
34890633 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:34899420 original size:20 final size:20
Alignment explanation
Indices: 34899361--34899423 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
34899351 AAATGAAAAA
*
34899361 GAAATGAGCTGAAGCGAGCT
1 GAAATGAGCTCAAGCGAGCT
* *
34899381 AAAATCGAGCTCAAACGAGCT
1 GAAAT-GAGCTCAAGCGAGCT
*
34899402 GAAATGAGCTCAAGTGAGCT
1 GAAATGAGCTCAAGCGAGCT
34899422 GA
1 GA
34899424 TTGCTAGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.16
Consensus pattern (20 bp):
GAAATGAGCTCAAGCGAGCT
Found at i:34901907 original size:21 final size:21
Alignment explanation
Indices: 34901861--34901923 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
34901851 TCAGCTCCAA
**
34901861 TCAGCTCACTTGAG-TTCATT
1 TCAGCTCGTTTGAGCTTCATT
*
34901881 TCAGCTCGTTTGAGCTTGATT
1 TCAGCTCGTTTGAGCTTCATT
* *
34901902 TTAGCTCGTTTCAGC-TCATT
1 TCAGCTCGTTTGAGCTTCATT
34901922 TC
1 TC
34901924 TTTTTCATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (21 bp):
TCAGCTCGTTTGAGCTTCATT
Found at i:34904390 original size:21 final size:20
Alignment explanation
Indices: 34904366--34904413 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
34904356 AAAAGAAATG
*
34904366 AGCTGAAACGAGCTAAAATCA
1 AGCTCAAACGAGCTAAAA-CA
*
34904387 AGCTCAAACGAGCTGAAACA
1 AGCTCAAACGAGCTAAAACA
34904407 AGCTCAA
1 AGCTCAA
34904414 GTGAGCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (20 bp):
AGCTCAAACGAGCTAAAACA
Found at i:34904419 original size:20 final size:21
Alignment explanation
Indices: 34904366--34904422 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
34904356 AAAAGAAATG
* *
34904366 AGCTGAAACGAGCTAAAATCA
1 AGCTCAAACGAGCTGAAATCA
34904387 AGCTCAAACGAGCTGAAA-CA
1 AGCTCAAACGAGCTGAAATCA
**
34904407 AGCTCAAGTGAGCTGA
1 AGCTCAAACGAGCTGA
34904423 TTGGAGCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (21 bp):
AGCTCAAACGAGCTGAAATCA
Found at i:34904999 original size:27 final size:26
Alignment explanation
Indices: 34904957--34905012 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
34904947 ATATAGCTTA
34904957 AATGTGTCTAGTTTA-GGACATCAATTT
1 AATGTGTCTAGTTTAGGGACA--AATTT
34904984 AATGTGTCTA-TCTTAGGGACAAATTT
1 AATGTGTCTAGT-TTAGGGACAAATTT
34905010 AAT
1 AAT
34905013 TGTTGCTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 9 0.33
27 13 0.48
28 5 0.19
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (26 bp):
AATGTGTCTAGTTTAGGGACAAATTT
Found at i:34906788 original size:10 final size:10
Alignment explanation
Indices: 34906763--34906802 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
34906753 CCAGCTCAAC
*
34906763 TCAGCTCATT
1 TCAGCTCGTT
* *
34906773 TGAGCTTGTT
1 TCAGCTCGTT
34906783 TCAGCTCGTT
1 TCAGCTCGTT
34906793 TCAGCTCGTT
1 TCAGCTCGTT
34906803 CTTTATTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.42
Consensus pattern (10 bp):
TCAGCTCGTT
Found at i:34908213 original size:10 final size:10
Alignment explanation
Indices: 34908188--34908227 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
34908178 CCAGCTCAAC
*
34908188 TCAGCTCATT
1 TCAGCTCGTT
* *
34908198 TGAGCTTGTT
1 TCAGCTCGTT
34908208 TCAGCTCGTT
1 TCAGCTCGTT
34908218 TCAGCTCGTT
1 TCAGCTCGTT
34908228 CTTTATTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.42
Consensus pattern (10 bp):
TCAGCTCGTT
Found at i:34910771 original size:6 final size:5
Alignment explanation
Indices: 34910747--34910813 Score: 55
Period size: 5 Copynumber: 12.8 Consensus size: 5
34910737 ACGAGAAAAC
* * *
34910747 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACA AAATAA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA
*
34910794 AAAGA AAAGA GAAGCA AAAG
1 AAAGA AAAGA AAAG-A AAAG
34910814 GCAAGTAAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
4 3 0.06
5 29 0.58
6 18 0.36
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (5 bp):
AAAGA
Found at i:34910796 original size:25 final size:25
Alignment explanation
Indices: 34910751--34910799 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
34910741 GAAAACAAAG
*
34910751 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAACAAAAA-CAAAAGAAGA
34910777 AAAAGAAAACAAAATA-AAAAGAA
1 AAAAGAAAACAAAA-ACAAAAGAA
34910800 AAGAGAAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAGAAAACAAAAACAAAAGAAGA
Found at i:34910894 original size:12 final size:12
Alignment explanation
Indices: 34910872--34910896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34910862 TTTGAAAAAC
34910872 AAAAAGAAAATG
1 AAAAAGAAAATG
34910884 AAAAAGAAAATG
1 AAAAAGAAAATG
34910896 A
1 A
34910897 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:34910903 original size:18 final size:18
Alignment explanation
Indices: 34910863--34910916 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
34910853 GAAAAAGCCT
* *
34910863 TTGAAAAACAAAAAGAAA
1 TTGAAAAAGAAAATGAAA
* *
34910881 ATGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAATGAAA
*
34910899 TTGAAAAAGAGAATGAAA
1 TTGAAAAAGAAAATGAAA
34910917 AAGAGTTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.13
Consensus pattern (18 bp):
TTGAAAAAGAAAATGAAA
Found at i:34910928 original size:30 final size:30
Alignment explanation
Indices: 34910872--34910953 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
34910862 TTTGAAAAAC
**
34910872 AAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
* ***
34910902 AAAAAGAGAATGAAAAAGAGTTTGAGAGAG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
** *
34910932 AAAAAGAATGTGAACAAGAAAA
1 AAAAAGAAAATGAAAAAGAAAA
34910954 AATAGTGGAA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.63, C:0.01, G:0.23, T:0.12
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGAGAG
Found at i:34914315 original size:15 final size:15
Alignment explanation
Indices: 34914295--34914342 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
34914285 TCAAAGATGG
34914295 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
34914310 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
34914325 -TTTATGGATATAAA
1 GTTTATGGATATGAA
34914339 GTTT
1 GTTT
34914343 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:34914322 original size:29 final size:29
Alignment explanation
Indices: 34914289--34914348 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
34914279 AAGGATTCAA
* *
34914289 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
34914318 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
34914347 AG
1 AG
34914349 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:34918701 original size:16 final size:17
Alignment explanation
Indices: 34918669--34918702 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34918659 TATGTTCAAA
*
34918669 TTTTCAGATTTTATTTT
1 TTTTCAAATTTTATTTT
34918686 TTTTCAAATTTT-TTTT
1 TTTTCAAATTTTATTTT
34918702 T
1 T
34918703 GAAACTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTCAAATTTTATTTT
Found at i:34918944 original size:15 final size:15
Alignment explanation
Indices: 34918924--34918971 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
34918914 TCAAAGATGG
34918924 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
34918939 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
34918954 -TTTATGGATATAAA
1 GTTTATGGATATGAA
34918968 GTTT
1 GTTT
34918972 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:34918951 original size:29 final size:29
Alignment explanation
Indices: 34918918--34918977 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
34918908 AAGAATTCAA
* *
34918918 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
34918947 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
34918976 AG
1 AG
34918978 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:34920315 original size:136 final size:136
Alignment explanation
Indices: 34920048--34920332 Score: 500
Period size: 136 Copynumber: 2.1 Consensus size: 136
34920038 TATTGGGCCT
*
34920048 AAGCCCATTTAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAAATTACAATAAACTGGGCTTA
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAAATTACAATAAACTGGGCTTA
* * *
34920113 CCCCCTTATTCAGATAATAGTATGGCCCATAGGCCTATTTCAAAATACATGCAACATCAGTAAAC
66 CCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAAC
34920178 ATATGC
131 ATATGC
*
34920184 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAAATTACAATAAACTGGG-CTT
*
34920249 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
65 ACCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
34920313 CATATGC
130 CATATGC
34920320 AAGCCCATTTGGG
1 AAGCCCATTTGGG
34920333 GAGACTACTC
Statistics
Matches: 142, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
136 81 0.57
137 61 0.43
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAAATTACAATAAACTGGGCTTA
CCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAAC
ATATGC
Found at i:34922159 original size:26 final size:26
Alignment explanation
Indices: 34922123--34922258 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
34922113 CATGAAATTC
34922123 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
34922149 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
34922175 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
34922201 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
34922227 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
34922253 TTATCA
1 TTATCA
34922259 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:34924733 original size:40 final size:40
Alignment explanation
Indices: 34924606--34924735 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
34924596 TTGCTGGAAA
* * *
34924606 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
34924646 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
34924686 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
34924726 TTATATCCGG
1 TTATATCCGG
34924736 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:34940675 original size:124 final size:123
Alignment explanation
Indices: 34940451--34940676 Score: 301
Period size: 124 Copynumber: 1.8 Consensus size: 123
34940441 TGAATTATGT
* * * * * * * *
34940451 GAAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCG
1 GAAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATAACCG
**
34940516 GGCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTTGTGTTTGAGCCTTAGTAAC
66 GGCTAAGTCCCGAAGGCGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAAC
*
34940574 GAAAGTGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATAACT
1 GAAA-TGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATAACC
* * *
34940639 GGGCTAAGTCCCGAAGTC-TTTATTGCTGGAAATTATAT
65 GGGCTAAGTCCCGAAGGCGATTA-TGCTAGAAATTATAT
34940677 CCGAGTTAAG
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
123 7 0.08
124 80 0.92
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (123 bp):
GAAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATAACCG
GGCTAAGTCCCGAAGGCGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAAC
Found at i:34940798 original size:40 final size:40
Alignment explanation
Indices: 34940671--34940800 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
34940661 TTGCTGGAAA
* * * * *
34940671 TTATATCCGAGTTAAGACCCGAAGGCAATT-GTTCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTACGAGTGG
* * *
34940711 CTACATCCGGGCTAAGACCCGAAGGCATTCGTACGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTACGAGTGG
* *
34940751 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTACGA-GTGG
34940791 TTATATCCGG
1 TTATATCCGG
34940801 TTGTATTCCG
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
39 4 0.05
40 70 0.95
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTACGAGTGG
Found at i:34945614 original size:136 final size:136
Alignment explanation
Indices: 34945347--34945631 Score: 500
Period size: 136 Copynumber: 2.1 Consensus size: 136
34945337 TATTGGGCCT
** *
34945347 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAAATTACAATAAACTGGGCTTA
1 AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAAATTACAATAAACTGGGCTTA
* *
34945412 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCTATTTCAAAATACATGCAACATCAGTAAAC
66 GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAAC
34945477 ATATGC
131 ATATGC
*
34945483 AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAAATTACAATAAACTGGG-CTT
34945548 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
65 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
34945612 CATATGC
130 CATATGC
34945619 AAGCCCATTTGGG
1 AAGCCCATTTGGG
34945632 GAGACTACTC
Statistics
Matches: 142, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
136 79 0.56
137 63 0.44
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTAGGCCAGAGCCCTTTTCAAATTACAATAAACTGGGCTTA
GCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAAC
ATATGC
Found at i:34947450 original size:26 final size:26
Alignment explanation
Indices: 34947414--34947549 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
34947404 CATGAAATTC
34947414 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
34947440 TTATCATGAAATATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
34947466 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
34947492 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
34947518 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
34947544 TTATCA
1 TTATCA
34947550 ATTTGTATCA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 102 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:34951803 original size:30 final size:30
Alignment explanation
Indices: 34951769--34951865 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
34951759 AGCTCACTCC
34951769 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
34951799 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
34951829 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
34951859 TAGCTCA
1 TAGCTCA
34951866 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:34953704 original size:18 final size:19
Alignment explanation
Indices: 34953667--34953714 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
34953657 TAAAACACAA
*
34953667 TTAATT-ATTTAAGCTGAC
1 TTAATTAATTTAAGCTAAC
34953685 TTAATTAATTTAA-CTAAC
1 TTAATTAATTTAAGCTAAC
*
34953703 TTATTTAATTTA
1 TTAATTAATTTA
34953715 TTCTAGCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (19 bp):
TTAATTAATTTAAGCTAAC
Found at i:34956039 original size:25 final size:26
Alignment explanation
Indices: 34956002--34956053 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
34955992 TCAAACATGC
34956002 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
34956028 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
34956053 A
1 A
34956054 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:34957562 original size:26 final size:26
Alignment explanation
Indices: 34957531--34957638 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
34957521 TGAAATGCCC
*
34957531 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
34957557 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
34957583 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
34957609 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
34957635 ATCA
1 ATCA
34957639 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:34961941 original size:10 final size:10
Alignment explanation
Indices: 34961928--34961972 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
34961918 AAAAGAAATG
34961928 AGCTGAAACA
1 AGCTGAAACA
*
34961938 AGCTAAAATCA
1 AGCTGAAA-CA
* *
34961949 AGCTCAAACG
1 AGCTGAAACA
34961959 AGCTGAAACA
1 AGCTGAAACA
34961969 AGCT
1 AGCT
34961973 CAAGTGAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (10 bp):
AGCTGAAACA
Found at i:34961952 original size:21 final size:20
Alignment explanation
Indices: 34961928--34961975 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
34961918 AAAAGAAATG
*
34961928 AGCTGAAACAAGCTAAAATCA
1 AGCTCAAACAAGCTAAAA-CA
* *
34961949 AGCTCAAACGAGCTGAAACA
1 AGCTCAAACAAGCTAAAACA
34961969 AGCTCAA
1 AGCTCAA
34961976 GTGAGCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (20 bp):
AGCTCAAACAAGCTAAAACA
Found at i:34963072 original size:6 final size:6
Alignment explanation
Indices: 34963063--34963142 Score: 51
Period size: 6 Copynumber: 13.5 Consensus size: 6
34963053 TTTATCACAA
* * *
34963063 TTCTTT TTC-TT TTCTCT TTCATT TTC-TT TTC--T TTCTTT TTCATT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
* **
34963107 TTCAGTTCT TTCTTT TTCATT TTCACT TTCTTT TTC
1 TTC--TT-T TTCTTT TTCTTT TTCTTT TTCTTT TTC
34963143 CACTCTCATA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.07
5 10 0.17
6 38 0.64
7 2 0.03
8 1 0.02
9 4 0.07
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.71
Consensus pattern (6 bp):
TTCTTT
Found at i:34963103 original size:21 final size:21
Alignment explanation
Indices: 34963067--34963139 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
34963057 TCACAATTCT
*
34963067 TTTTCTTTTCTCTTTCATTTTC
1 TTTTC-TTTCTTTTTCATTTTC
34963089 TTTTCTTTCTTTTTCATTTTC
1 TTTTCTTTCTTTTTCATTTTC
**
34963110 AGTTCTTTCTTTTTCATTTTC
1 TTTTCTTTCTTTTTCATTTTC
*
34963131 ACTTTCTTT
1 -TTTTCTTT
34963140 TTCCACTCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
21 34 0.76
22 11 0.24
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (21 bp):
TTTTCTTTCTTTTTCATTTTC
Found at i:34963109 original size:27 final size:28
Alignment explanation
Indices: 34963063--34963142 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 28
34963053 TTTATCACAA
* *
34963063 TTCTTTTTC-TTTTCTCTTTCATTTTCT
1 TTCTCTTTCATTTTCACTTTCATTTTCT
* * *
34963090 TT-TCTTTCTTTTTCATTTTCA-GTTCT
1 TTCTCTTTCATTTTCACTTTCATTTTCT
* *
34963116 TTCTTTTTCATTTTCACTTTCTTTTTC
1 TTCTCTTTCATTTTCACTTTCATTTTC
34963143 CACTCTCATA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
26 11 0.27
27 27 0.66
28 3 0.07
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.71
Consensus pattern (28 bp):
TTCTCTTTCATTTTCACTTTCATTTTCT
Found at i:34966683 original size:10 final size:10
Alignment explanation
Indices: 34966670--34966714 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
34966660 AAAAGAAATG
34966670 AGCTGAAACA
1 AGCTGAAACA
*
34966680 AGCTAAAATCA
1 AGCTGAAA-CA
*
34966691 AGCTCAAACA
1 AGCTGAAACA
34966701 AGCTGAAACA
1 AGCTGAAACA
34966711 AGCT
1 AGCT
34966715 CAAGTGAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (10 bp):
AGCTGAAACA
Found at i:34966694 original size:21 final size:20
Alignment explanation
Indices: 34966670--34966717 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
34966660 AAAAGAAATG
*
34966670 AGCTGAAACAAGCTAAAATCA
1 AGCTCAAACAAGCTAAAA-CA
*
34966691 AGCTCAAACAAGCTGAAACA
1 AGCTCAAACAAGCTAAAACA
34966711 AGCTCAA
1 AGCTCAA
34966718 GTGAGCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (20 bp):
AGCTCAAACAAGCTAAAACA
Found at i:34968586 original size:14 final size:14
Alignment explanation
Indices: 34968567--34968611 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
34968557 AACTCATCTT
*
34968567 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
34968581 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
34968594 AATTTAATTTAATG
1 AGTTTAATTTAATG
34968608 AGTT
1 AGTT
34968612 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:34969618 original size:29 final size:29
Alignment explanation
Indices: 34969585--34969644 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
34969575 ATAACCAAAC
*
34969585 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
34969614 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
34969643 CT
1 CT
34969645 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:34969637 original size:15 final size:15
Alignment explanation
Indices: 34969591--34969638 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
34969581 AAACCTACAA
*
34969591 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
34969606 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
34969620 AAACTTCATATCCAT
1 AAACTTCATATCCAT
34969635 AAAC
1 AAAC
34969639 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:34972532 original size:21 final size:21
Alignment explanation
Indices: 34972508--34972549 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
34972498 ATCTAGGTTG
34972508 GACTACTTCAGGAGGTCTTTC
1 GACTACTTCAGGAGGTCTTTC
34972529 GACTACTTCAGGAGGTCTTTC
1 GACTACTTCAGGAGGTCTTTC
34972550 ACGTTGCTCT
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:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (21 bp):
GACTACTTCAGGAGGTCTTTC
Found at i:34973108 original size:11 final size:11
Alignment explanation
Indices: 34973088--34973152 Score: 75
Period size: 10 Copynumber: 6.3 Consensus size: 11
34973078 AATGTTCTAG
34973088 TTTC-AATTTT
1 TTTCGAATTTT
*
34973098 TTTCAAATTTT
1 TTTCGAATTTT
* *
34973109 TTTTGGA-TTT
1 TTTCGAATTTT
34973119 TTTCGAA-TTT
1 TTTCGAATTTT
34973129 TTTCGAATTTT
1 TTTCGAATTTT
34973140 TTTC-AATTTT
1 TTTCGAATTTT
34973150 TTT
1 TTT
34973153 TATTTTTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
10 31 0.65
11 17 0.35
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.68
Consensus pattern (11 bp):
TTTCGAATTTT
Found at i:34973119 original size:9 final size:9
Alignment explanation
Indices: 34973107--34973180 Score: 69
Period size: 9 Copynumber: 8.0 Consensus size: 9
34973097 TTTTCAAATT
*
34973107 TTTTTTGGA
1 TTTTTTGAA
34973116 TTTTTTCGAA
1 TTTTTT-GAA
34973126 TTTTTTCGAA
1 TTTTTT-GAA
*
34973136 TTTTTTTCAA
1 -TTTTTTGAA
**
34973146 TTTTTTTTA
1 TTTTTTGAA
*
34973155 TTTTTT-TA
1 TTTTTTGAA
34973163 TTTTTTGAA
1 TTTTTTGAA
34973172 TTTTTTGAA
1 TTTTTTGAA
34973181 ACTTTTTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
8 8 0.14
9 29 0.51
10 14 0.25
11 6 0.11
ACGTcount: A:0.18, C:0.04, G:0.08, T:0.70
Consensus pattern (9 bp):
TTTTTTGAA
Found at i:34973120 original size:21 final size:19
Alignment explanation
Indices: 34973095--34973160 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
34973085 TAGTTTCAAT
34973095 TTTTTTCAAATTTTTTTTGGA
1 TTTTTTC-AATTTTTTTT-GA
*
34973116 TTTTTTCGAA-TTTTTTCGAA
1 TTTTTTC-AATTTTTTTTG-A
34973136 TTTTTTTCAATTTTTTTT-A
1 -TTTTTTCAATTTTTTTTGA
34973155 TTTTTT
1 TTTTTT
34973161 TATTTTTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.15
19 2 0.05
20 9 0.23
21 22 0.56
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (19 bp):
TTTTTTCAATTTTTTTTGA
Found at i:34973153 original size:11 final size:10
Alignment explanation
Indices: 34973088--34973177 Score: 66
Period size: 10 Copynumber: 9.2 Consensus size: 10
34973078 AATGTTCTAG
34973088 TTTCAATTTT
1 TTTCAATTTT
34973098 TTTCAAATTTTT
1 TTTC-AA-TTTT
**
34973110 TTTGGA-TTT
1 TTTCAATTTT
34973119 TTTCGAA-TTT
1 TTTC-AATTTT
34973129 TTTCGAATTTT
1 TTTC-AATTTT
34973140 TTTCAATTTT
1 TTTCAATTTT
*
34973150 TTT-TATTTT
1 TTTCAATTTT
34973159 TTT--A-TTT
1 TTTCAATTTT
*
34973166 TTTGAATTTT
1 TTTCAATTTT
34973176 TT
1 TT
34973178 GAAACTTTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
7 6 0.09
8 1 0.01
9 15 0.22
10 29 0.43
11 10 0.15
12 7 0.10
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (10 bp):
TTTCAATTTT
Found at i:34975612 original size:21 final size:21
Alignment explanation
Indices: 34975571--34975612 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
34975561 TGGGCTAGCC
* *
34975571 GAATGGTCTTTTCAAGGAGCT
1 GAATGGACTTTTCAAGAAGCT
34975592 GAATGGACTTTT-AATGAAGCT
1 GAATGGACTTTTCAA-GAAGCT
34975613 AATAATGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (21 bp):
GAATGGACTTTTCAAGAAGCT
Found at i:34979553 original size:10 final size:10
Alignment explanation
Indices: 34979538--34979581 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
34979528 GCTGAAAGTA
*
34979538 AGCTCAATTG
1 AGCTCAAATG
34979548 AGCTCAAATG
1 AGCTCAAATG
* *
34979558 AGCTGAAACG
1 AGCTCAAATG
34979568 AGCTCAAATG
1 AGCTCAAATG
34979578 AGCT
1 AGCT
34979582 GAGTTGAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (10 bp):
AGCTCAAATG
Done.