Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009014.1 Hibiscus syriacus cultivar Beakdansim tig00112402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3470424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1502559 original size:24 final size:24
Alignment explanation
Indices: 1502527--1502591 Score: 121
Period size: 24 Copynumber: 2.7 Consensus size: 24
1502517 ATGTATAATA
1502527 TCAACTGAAGCTTCATCCGCAGAT
1 TCAACTGAAGCTTCATCCGCAGAT
*
1502551 TCAACTGAAGCTTCATCCGCATAT
1 TCAACTGAAGCTTCATCCGCAGAT
1502575 TCAACTGAAGCTTCATC
1 TCAACTGAAGCTTCATC
1502592 AACAAGCTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (24 bp):
TCAACTGAAGCTTCATCCGCAGAT
Found at i:1506473 original size:20 final size:21
Alignment explanation
Indices: 1506430--1506473 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1506420 TATTTACATG
* *
1506430 TATTTATTTAAGTATATATTA
1 TATTTATTTAAGTACATATGA
*
1506451 TATTTATTT-TGTACATATGA
1 TATTTATTTAAGTACATATGA
1506471 TAT
1 TAT
1506474 ATACAATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TATTTATTTAAGTACATATGA
Found at i:1506940 original size:21 final size:20
Alignment explanation
Indices: 1506916--1506955 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1506906 TGAATTTATG
1506916 GATTAAAAAATTTTATTTTTA
1 GATTAAAAAA-TTTATTTTTA
**
1506937 GATTTCAAAATTTATTTTT
1 GATTAAAAAATTTATTTTT
1506956 CAAAAATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
GATTAAAAAATTTATTTTTA
Found at i:1507866 original size:29 final size:29
Alignment explanation
Indices: 1507823--1507905 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1507813 CTCACCTAAC
1507823 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1507853 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1507882 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1507906 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1512629 original size:29 final size:29
Alignment explanation
Indices: 1512586--1512668 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1512576 CTCACCTAAC
1512586 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1512616 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1512645 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1512669 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1522937 original size:2 final size:2
Alignment explanation
Indices: 1522926--1522977 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1522916 TTACACCATT
*
1522926 TA TA -A TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1522967 TA TA TA TA TA T
1 TA TA TA TA TA T
1522978 TATTACCATA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1533396 original size:12 final size:12
Alignment explanation
Indices: 1533362--1533408 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1533352 CATTTTCTCC
1533362 TTTTTA-ATTT-
1 TTTTTATATTTA
*
1533372 TTTTTAAATTTTA
1 TTTTTATA-TTTA
*
1533385 TTTTTTTATTTA
1 TTTTTATATTTA
1533397 TTTTTATATTTA
1 TTTTTATATTTA
1533409 AATTTAGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 6 0.19
11 1 0.03
12 18 0.58
13 6 0.19
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATATTTA
Found at i:1546100 original size:42 final size:42
Alignment explanation
Indices: 1546043--1546146 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
1546033 TCTGTGAAGG
* * * * *
1546043 CTTAAAAATTACCCGACGGATTTAATCATCACGCTCGAAAGA
1 CTTACAAATGACCCGAAGGATTTAAGCATCACGCTCAAAAGA
*
1546085 CTTACAAATGACCCGAAGGATTTAAGCATCATGCTCAAAAGA
1 CTTACAAATGACCCGAAGGATTTAAGCATCACGCTCAAAAGA
** *
1546127 CTTACTGATGGCCCGAAGGA
1 CTTACAAATGACCCGAAGGA
1546147 CTTATACATT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
CTTACAAATGACCCGAAGGATTTAAGCATCACGCTCAAAAGA
Found at i:1546483 original size:172 final size:173
Alignment explanation
Indices: 1546122--1546491 Score: 548
Period size: 173 Copynumber: 2.1 Consensus size: 173
1546112 ATCATGCTCA
* * * *
1546122 AAAGACTTACTGATGGCCCGAAGGACTTATACATTGTGAAATTTTGAAAATCGCGTTCTTCGTTT
1 AAAGGCTTACAGATGACCCGAAGGACTTATACATTGTGAAATTTTGAAAATCGCATTCTTCGTTT
* ** *
1546187 TCAAATATTTCATCTTTTCTAAACATTGTTTTTTCATTTTCAAATTCATGTGAAAACATCCTACC
66 TCAAAAATTTCATCTTTTCTAAACATCATTTTCTCATTTTCAAATTCATGTGAAAACATCCTACC
*
1546252 CGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCT
131 CGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGATCT
*
1546295 AAAGGCTTACAGATGACCTGAAGGACTTATA-AGTTGTGAAATTTTGAAAATCGCATTCTTCGTT
1 AAAGGCTTACAGATGACCCGAAGGACTTATACA-TTGTGAAATTTTGAAAATCGCATTCTTCGTT
**
1546359 TTCAAAAATTTCATCTTTT-TAAAACATCATTTTCTCATTTTC-CTTTCATGTGAAAACATCCTA
65 TTCAAAAATTTCATCTTTTCT-AAACATCATTTTCTCATTTTCAAATTCATGTGAAAACATCCTA
* * * *
1546422 CCCTATGGTTTTATGGATTGCCCGAAGGACTTATCATCTTGATCT
129 CCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGATCT
*
1546467 AAAGGCTTATAGATGACCCGAAGGA
1 AAAGGCTTACAGATGACCCGAAGGA
1546492 TTTAAATATC
Statistics
Matches: 177, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
172 84 0.47
173 93 0.53
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (173 bp):
AAAGGCTTACAGATGACCCGAAGGACTTATACATTGTGAAATTTTGAAAATCGCATTCTTCGTTT
TCAAAAATTTCATCTTTTCTAAACATCATTTTCTCATTTTCAAATTCATGTGAAAACATCCTACC
CGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGATCT
Found at i:1546749 original size:42 final size:42
Alignment explanation
Indices: 1546652--1546753 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
1546642 AGGTTTTATG
* * * *
1546652 GATGGCCCGAAGGACTTATCATCTTGCTCTTAAAGGCTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCTGAAAGACTTACA
* * * * *
1546694 GATGACCCAAAGGATTTAAGCATCATGCTC-GAAAGACTTCCT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCTGAAAGACTTACA
1546736 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
1546754 TAAATTATGA
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
41 1 0.02
42 36 0.77
43 10 0.21
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCTGAAAGACTTACA
Found at i:1546754 original size:216 final size:215
Alignment explanation
Indices: 1546284--1546868 Score: 834
Period size: 214 Copynumber: 2.7 Consensus size: 215
1546274 AAGGACTTAT
* * * * * * *
1546284 CATCTTGCTCTAAAGGCTTACAGATGACCTGAAGGACTTATAAGTTGTGAAATTTTGAAAATCGC
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGC
* * * **
1546349 ATTCTTCGTTTTCAAAAATTTCATCTTTTTAAAACATCATTTTCTCATTTTC-CTTTCATGTGAA
66 ATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAA
* * * *
1546413 AACATCCTACCCTATGGTTTTATGGATTGCCCGAAGGACTTATCATCTTGATCTAAAGGCTTATA
131 AACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGATCTAAAGGCTTACA
*
1546478 GATGACCCGAAGGATTTAAA
196 GATGACCCAAAGGATTTAAA
* *
1546498 TATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTATAAATTGTGAAATTTTGAAAATCGC
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGC
* *
1546563 ATTCTTCATTTTAAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAA
66 ATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAA
*
1546628 AACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTTAAAGGCTTAC
131 AACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGATC-TAAAGGCTTAC
*
1546693 AGATGACCCAAAGGATTTAAG
195 AGATGACCCAAAGGATTTAAA
* * **
1546714 CATCATGCTCGAAAGACTTCCTGATGGCCCGAAGGACTTATAAATTATGAAATTTTGAAAATAAC
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGC
* * * * *
1546779 A-T-TTCGTTTTCAAGAATTCCATCTTCTTAAAACTTCATTTATTCGTTTTCAAATTCATATGAA
66 ATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAA
* *
1546842 AACATCTTATCCGAAGGTTTTATGGAT
131 AACATCCTACCCGAAGGTTTTATGGAT
1546869 AGATTTGCTT
Statistics
Matches: 331, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
214 182 0.55
215 60 0.18
216 89 0.27
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (215 bp):
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGC
ATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAA
AACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGATCTAAAGGCTTACA
GATGACCCAAAGGATTTAAA
Found at i:1547140 original size:37 final size:35
Alignment explanation
Indices: 1546873--1547379 Score: 382
Period size: 37 Copynumber: 13.9 Consensus size: 35
1546863 ATGGATAGAT
*
1546873 TTGCTTCACTAGTCTTCGGTGAAGGCTTAAGATG-
1 TTGCTTCACTATTCTTCGGTGAAGGCTTAAGATGA
* * * *
1546907 GTGCTTCACTACTCATCTGTGAAGGCTTAAGATG-
1 TTGCTTCACTATTCTTCGGTGAAGGCTTAAGATGA
* * * *
1546941 GTGTTTCACTACTCTTCTGTGAAGGCTTAAGATGA
1 TTGCTTCACTATTCTTCGGTGAAGGCTTAAGATGA
1546976 TTGCTTCACTATTC-TCTGGTGAAGGCTTAAGATGA
1 TTGCTTCACTATTCTTC-GGTGAAGGCTTAAGATGA
* * * * *
1547011 TTACTTCACTACTGTCCGGTGAAGGCTTAAGATGGT
1 TTGCTTCACTATTCTTCGGTGAAGGCTTAAGAT-GA
** *
1547047 TTGCTTCACTCCTCTTTGGTGAAGGCTTAAGATTGA
1 TTGCTTCACTATTCTTCGGTGAAGGCTTAAGA-TGA
* *
1547083 TTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGAA
1 TTGCTTCACTATTCTTCGGTGAAGGCTTAAGATG-A
* * *
1547119 TTTGCTTCACTATTCTCCAGTGAAGGCTTAGGATGGA
1 -TTGCTTCACTATTCTTCGGTGAAGGCTTAAGAT-GA
1547156 TTTGCTTCACTATTC-TCAGGTGAAGGCTTAAGATGGAA
1 -TTGCTTCACTATTCTTC-GGTGAAGGCTTAAGAT-G-A
* *
1547194 TTGCTTCACTCATT-TTTGGTGAAGGCTTAAGATTGCC
1 TTGCTTCACT-ATTCTTCGGTGAAGGCTTAAGA-TG-A
* ** * * * **
1547231 CTG-TGGACTTAATCATCATGCTCAGAAGGCTTGCTGATGGA
1 TTGCTTCAC-TATTCTTC--GGT--GAAGGCTT-AAGAT-GA
* * * *
1547272 TTTACTTCACTACTCTTTGGTGAAGGCTTAGGATGGA
1 -TTGCTTCACTATTCTTCGGTGAAGGCTTAAGAT-GA
1547309 TTTGCTTCACTATTC-TCAGGTGAAGGCTTAAGATGGAA
1 -TTGCTTCACTATTCTTC-GGTGAAGGCTTAAGAT-G-A
*
1547347 TTGCTTCACTCATT-TCCGGTGAAGGCTTAAGAT
1 TTGCTTCACT-ATTCTTCGGTGAAGGCTTAAGAT
1547380 TCCCCTGAGG
Statistics
Matches: 388, Mismatches: 58, Indels: 51
0.78 0.12 0.10
Matches are distributed among these distances:
34 64 0.16
35 57 0.15
36 67 0.17
37 155 0.40
38 20 0.05
39 2 0.01
40 2 0.01
41 9 0.02
42 9 0.02
43 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (35 bp):
TTGCTTCACTATTCTTCGGTGAAGGCTTAAGATGA
Found at i:1547280 original size:79 final size:77
Alignment explanation
Indices: 1547177--1547416 Score: 229
Period size: 79 Copynumber: 3.1 Consensus size: 77
1547167 ATTCTCAGGT
1547177 GAAGGCTTAAGATGGAATTGCTTCACTCATTTTTGGTGAAGGCTTAAGATTGCCCTGTGGACTTA
1 GAAGGCTTAAGATGGAATTGCTTCACTCATTTTTGGTGAAGGCTTAAGATTGCCCTGTGGACTTA
1547242 ATCATCATGCTC
66 ATCATCATGCTC
** * * * * * *** **
1547254 AGAAGGCTTGCTGATGGATTTACTTCACT-ACTCTTTGGTGAAGGCTTAGGATGGATTTGCTTCA
1 -GAAGGCTT-AAGATGGAATTGCTTCACTCA-TTTTTGGTGAAGGCTTAAGATTGCCCTG-TGGA
* *
1547318 C-TATTC-TCA-GGT-
62 CTTAATCATCATGCTC
** * *
1547330 GAAGGCTTAAGATGGAATTGCTTCACTCATTTCCGGTGAAGGCTTAAGATTCCCCTGAGGACTTA
1 GAAGGCTTAAGATGGAATTGCTTCACTCATTTTTGGTGAAGGCTTAAGATTGCCCTGTGGACTTA
1547395 ATCATCATGCTC
66 ATCATCATGCTC
*
1547407 GGAAGACTTA
1 -GAAGGCTTA
1547417 TTGATGGCCC
Statistics
Matches: 120, Mismatches: 33, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
73 2 0.02
74 38 0.32
75 12 0.10
76 2 0.02
77 2 0.02
78 20 0.17
79 41 0.34
80 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (77 bp):
GAAGGCTTAAGATGGAATTGCTTCACTCATTTTTGGTGAAGGCTTAAGATTGCCCTGTGGACTTA
ATCATCATGCTC
Found at i:1547314 original size:153 final size:151
Alignment explanation
Indices: 1546961--1547416 Score: 554
Period size: 153 Copynumber: 3.1 Consensus size: 151
1546951 ACTCTTCTGT
* * *
1546961 GAAGGCTTAAGATG-A-TTGCTTCACTATTCTCTGGTGAAGGCTTAAGAT-GA-TTACTTCACTA
1 GAAGGCTTAAGATGAATTTACTTCACTATTCTCTGGTGAAGGCTTAGGATGGATTTGCTTCACTA
* * * * * * **
1547022 CTGTCCGGTGAAGGCTTAAGATGG-TTTGCTTCACTCCTCTTTGGTGAAGGCTTAAGATTG-ATT
66 TTCTCAGGTGAAGGCTTAAGATGGAATTGCTTCACTCATTTTTGGTGAAGGCTTAAGATTGCCCT
** * *
1547085 GCTTCAC-TACTCTTCA-G-T-
131 G-TGGACTTAATCATCATGCTC
* **
1547103 GAAGGCTTAAGATGAATTTGCTTCACTATTCTCCAGTGAAGGCTTAGGATGGATTTGCTTCACTA
1 GAAGGCTTAAGATGAATTTACTTCACTATTCTCTGGTGAAGGCTTAGGATGGATTTGCTTCACTA
1547168 TTCTCAGGTGAAGGCTTAAGATGGAATTGCTTCACTCATTTTTGGTGAAGGCTTAAGATTGCCCT
66 TTCTCAGGTGAAGGCTTAAGATGGAATTGCTTCACTCATTTTTGGTGAAGGCTTAAGATTGCCCT
1547233 GTGGACTTAATCATCATGCTC
131 GTGGACTTAATCATCATGCTC
** * * *
1547254 AGAAGGCTTGCTGATGGATTTACTTCACTACTCTTTGGTGAAGGCTTAGGATGGATTTGCTTCAC
1 -GAAGGCTT-AAGATGAATTTACTTCACTATTCTCTGGTGAAGGCTTAGGATGGATTTGCTTCAC
** *
1547319 TATTCTCAGGTGAAGGCTTAAGATGGAATTGCTTCACTCATTTCCGGTGAAGGCTTAAGATTCCC
64 TATTCTCAGGTGAAGGCTTAAGATGGAATTGCTTCACTCATTTTTGGTGAAGGCTTAAGATTGCC
*
1547384 CTGAGGACTTAATCATCATGCTC
129 CTGTGGACTTAATCATCATGCTC
*
1547407 GGAAGACTTA
1 -GAAGGCTTA
1547417 TTGATGGCCC
Statistics
Matches: 271, Mismatches: 31, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
142 14 0.05
143 1 0.00
144 30 0.11
145 2 0.01
146 31 0.11
147 36 0.13
148 9 0.03
149 1 0.00
150 1 0.00
152 8 0.03
153 138 0.51
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (151 bp):
GAAGGCTTAAGATGAATTTACTTCACTATTCTCTGGTGAAGGCTTAGGATGGATTTGCTTCACTA
TTCTCAGGTGAAGGCTTAAGATGGAATTGCTTCACTCATTTTTGGTGAAGGCTTAAGATTGCCCT
GTGGACTTAATCATCATGCTC
Found at i:1547642 original size:42 final size:41
Alignment explanation
Indices: 1547545--1547650 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
1547535 ACCCGAAGGT
* * * *
1547545 CTTA-TGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGG
1 CTTACTGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
* * * *
1547585 CTTACAGATGACCCGAAGGATTTACGCATCATGTTCGAAAGA
1 CTTACTGATGGCCCGAAGGACTTA-GCATCATGCTCGAAAGA
1547627 CTTACTGATGGCCCGAAGGACTTA
1 CTTACTGATGGCCCGAAGGACTTA
1547651 TAAATTGTGA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 4 0.08
41 16 0.30
42 33 0.62
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (41 bp):
CTTACTGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:1547858 original size:43 final size:41
Alignment explanation
Indices: 1547759--1547866 Score: 119
Period size: 43 Copynumber: 2.6 Consensus size: 41
1547749 ACCCGACGAT
* * * * *
1547759 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGG
1 CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
* *
1547800 CTTATAGATGACCCGAAGGATTTAAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT--AGCATCATGCTCGAAAGA
1547843 CTTACT-GATGGCCCGAAGGACTTA
1 CTTA-TAGATGGCCCGAAGGACTTA
1547867 CAAATCGTGA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
41 21 0.38
43 33 0.60
44 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:1550243 original size:25 final size:22
Alignment explanation
Indices: 1550185--1550227 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1550175 AAATAAAGCA
1550185 AAGAAAATGAAAGCACTCAAAG
1 AAGAAAATGAAAGCACTCAAAG
*
1550207 AAGAAATTGAAAGCACTCAAA
1 AAGAAAATGAAAGCACTCAAA
1550228 AAGGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.14, G:0.16, T:0.12
Consensus pattern (22 bp):
AAGAAAATGAAAGCACTCAAAG
Found at i:1557605 original size:10 final size:9
Alignment explanation
Indices: 1557592--1557698 Score: 79
Period size: 10 Copynumber: 10.7 Consensus size: 9
1557582 TTTTATTATT
1557592 TTTTATTTTC
1 TTTT-TTTTC
1557602 TTTTCTTTTTC
1 -TTT-TTTTTC
*
1557613 TCTTTTTCTC
1 T-TTTTTTTC
*
1557623 TTTTTCTCTC
1 TTTTT-TTTC
*
1557633 TTTTTCTTC
1 TTTTTTTTC
1557642 TTTTTTTCTTC
1 -TTTTTT-TTC
1557653 TTTTTTCTTC
1 TTTTTT-TTC
1557663 TTTTTTCTTC
1 TTTTTT-TTC
*
1557673 TTTTTCTTC
1 TTTTTTTTC
1557682 TTCTTTTTTCC
1 TT-TTTTTT-C
1557693 TTTTTT
1 TTTTTT
1557699 ATTTCATTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
9 11 0.13
10 55 0.66
11 16 0.19
12 1 0.01
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1557618 original size:8 final size:8
Alignment explanation
Indices: 1557605--1557697 Score: 74
Period size: 8 Copynumber: 11.9 Consensus size: 8
1557595 TATTTTCTTT
1557605 TCTTTTTC
1 TCTTTTTC
1557613 TCTTTTTC
1 TCTTTTTC
1557621 TCTTTTTC
1 TCTTTTTC
1557629 TCTCTTTT-
1 TCT-TTTTC
1557637 TCTTCTTT-
1 TCTT-TTTC
1557645 T-TTTCTTC
1 TCTTT-TTC
1557653 T-TTTTTC
1 TCTTTTTC
1557660 TTCTTTTT-
1 -TCTTTTTC
*
1557668 TCTTCTTTT
1 TCTT-TTTC
*
1557677 TCTTCTTC
1 TCTTTTTC
1557685 T-TTTTTC
1 TCTTTTTC
1557692 -CTTTTT
1 TCTTTTT
1557698 TATTTCATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 19
0.77 0.03 0.20
Matches are distributed among these distances:
6 1 0.01
7 22 0.30
8 37 0.51
9 13 0.18
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TCTTTTTC
Found at i:1557621 original size:19 final size:19
Alignment explanation
Indices: 1557597--1557710 Score: 94
Period size: 20 Copynumber: 5.8 Consensus size: 19
1557587 TTATTTTTTA
1557597 TTTTCTTTTCTTTTTCTCT
1 TTTTCTTTTCTTTTTCTCT
* *
1557616 TTTTCTCTT-TTTCTCTCT
1 TTTTCTTTTCTTTTTCTCT
1557634 TTTTCTTCTT-TTTTTCTTCT
1 TTTTCTT-TTCTTTTTC-TCT
*
1557654 TTTT-TCTTCTTTTTTCTTCT
1 TTTTCTTTTC-TTTTTC-TCT
1557674 TTTTCTTCTTCTTTTT-TCCT
1 TTTTCTT-TTCTTTTTCT-CT
1557694 TTTT-TATTTCATTTTTC
1 TTTTCT-TTTC-TTTTTC
1557711 GAGTGTAGTA
Statistics
Matches: 79, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
18 16 0.20
19 21 0.27
20 33 0.42
21 6 0.08
22 3 0.04
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTCTCT
Found at i:1557627 original size:32 final size:30
Alignment explanation
Indices: 1557591--1557703 Score: 97
Period size: 28 Copynumber: 3.7 Consensus size: 30
1557581 TTTTTATTAT
1557591 TTTTTATTTTCTTTTCTTTTTCTCTTTTTCTC
1 TTTTT-TTTTCTTTT-TTTTTCTCTTTTTCTC
* * *
1557623 TTTTTCTCTC-TTTTTCTTCT-TTTTT-TC
1 TTTTTTTTTCTTTTTTTTTCTCTTTTTCTC
* *
1557650 TTCTTTTTTCTTCTTTTTTCTTCTTTTTCTTC
1 TTTTTTTTTCTTTTTTTTTC-TCTTTTTC-TC
*
1557682 TTCTTTTTTCCTTTTTTATTTC
1 TT-TTTTTTTCTTTTTT-TTTC
1557704 ATTTTTCGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
27 9 0.14
28 12 0.19
29 7 0.11
30 8 0.13
31 3 0.05
32 9 0.14
33 11 0.17
34 4 0.06
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (30 bp):
TTTTTTTTTCTTTTTTTTTCTCTTTTTCTC
Found at i:1557665 original size:40 final size:38
Alignment explanation
Indices: 1557607--1557698 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 38
1557597 TTTTCTTTTC
*
1557607 TTTTTCTC-TTTTTCTC-TTTTTCTCTCTTTTTCTTCTT
1 TTTTTTTCTTTTTTCTCTTTTTTCT-TCTTTTTCTTCTT
1557644 TTTTTCTTCTTTTTTCTTCTTTTTTCTTCTTTTTCTTCTT
1 TTTTT-TTCTTTTTTC-TCTTTTTTCTTCTTTTTCTTCTT
*
1557684 CTTTTTTCCTTTTTT
1 -TTTTTTTCTTTTTT
1557699 ATTTCATTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
37 5 0.10
38 2 0.04
39 6 0.12
40 23 0.48
41 12 0.25
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (38 bp):
TTTTTTTCTTTTTTCTCTTTTTTCTTCTTTTTCTTCTT
Found at i:1557710 original size:32 final size:29
Alignment explanation
Indices: 1557597--1557698 Score: 106
Period size: 29 Copynumber: 3.5 Consensus size: 29
1557587 TTATTTTTTA
*
1557597 TTTTCTTTTCTTTTTC-TCTTTTTC-TC-T
1 TTTTCTTCT-TTTTTCTTCTTTTTCTTCTT
1557624 TTTTC-TCTCTTTTTCTTCTTTTTTTCTTCTT
1 TTTTCTTCT-TTTTTCTTC--TTTTTCTTCTT
1557655 TTTTCTTCTTTTTTCTTCTTTTTCTTCTT
1 TTTTCTTCTTTTTTCTTCTTTTTCTTCTT
1557684 CTTTT-TTCCTTTTTT
1 -TTTTCTT-CTTTTTT
1557699 ATTTCATTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 13
0.82 0.01 0.16
Matches are distributed among these distances:
26 9 0.14
27 7 0.11
29 19 0.29
30 13 0.20
31 15 0.23
32 3 0.05
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTTCTTCTTTTTTCTTCTTTTTCTTCTT
Found at i:1573303 original size:26 final size:26
Alignment explanation
Indices: 1573274--1573340 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
1573264 ATCCTTCAAT
* **
1573274 TTTTCTAAAATTTCTATTTGATCTGA
1 TTTTCCAAAATTTCTATTCAATCTGA
*
1573300 TTTTCCAAATTTTCTATTCAATCTGA
1 TTTTCCAAAATTTCTATTCAATCTGA
* *
1573326 TTTACCGAAATTTCT
1 TTTTCCAAAATTTCT
1573341 CGAACTTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (26 bp):
TTTTCCAAAATTTCTATTCAATCTGA
Found at i:1585923 original size:17 final size:17
Alignment explanation
Indices: 1585903--1585941 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1585893 ATAAAGTTTA
1585903 CCAAATACGAAAGTCTC
1 CCAAATACGAAAGTCTC
1585920 CCAAATACGAAAGTCTC
1 CCAAATACGAAAGTCTC
1585937 CCAAA
1 CCAAA
1585942 ATGCATACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.31, G:0.10, T:0.15
Consensus pattern (17 bp):
CCAAATACGAAAGTCTC
Found at i:1587590 original size:21 final size:21
Alignment explanation
Indices: 1587564--1587605 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1587554 CCAAAATGGG
*
1587564 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1587585 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1587606 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1587754 original size:18 final size:18
Alignment explanation
Indices: 1587712--1587777 Score: 87
Period size: 19 Copynumber: 3.6 Consensus size: 18
1587702 TAGCCTCGGG
*
1587712 TTACTGTTCAAACAGTGAA
1 TTACTGTTCAAATAGT-AA
*
1587731 TTACTGTTCAAATAGTAT
1 TTACTGTTCAAATAGTAA
1587749 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAATAGT-AA
*
1587768 TTACTATTCA
1 TTACTGTTCA
1587778 TAAAAACATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.40
19 25 0.60
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (18 bp):
TTACTGTTCAAATAGTAA
Found at i:1588019 original size:54 final size:53
Alignment explanation
Indices: 1587932--1588537 Score: 528
Period size: 54 Copynumber: 11.2 Consensus size: 53
1587922 ACATAGTTCA
* * ** *
1587932 ACACATAGTGACTATACGGTCATTCATAAACTTATTATGAATTCTGTGGGTTGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTCT-TAGGTTGC
* * *** * * * *
1587986 ACACTTAGTGCCGATACGGTTGTTCATAAACTTATCATGAATTTTGTGGGCTGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTCT-TAGGTTGC
* * * * *
1588040 ACA-ATTAATGCCTATAC--AATTGTTCATAAACTTATTATGAATTCAATGGGTTTGC
1 ACACA-TAGTGCCAATACGGAA--ATTCATAAACTTATTATGAATTC-TTAGG-TTGC
* *
1588095 ACACATTA-TGCCAATACGGAAATTCATAAACTAATTATGAATTTATTAGGTTGC
1 ACACA-TAGTGCCAATACGGAAATTCATAAACTTATTATGAA-TTCTTAGGTTGC
* *
1588149 ACACATAGTGCTAATACGGAAATTCATAAACTTATTATGAATTCCGTT-GGTTTGG
1 ACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATT-C-TTAGG-TTGC
* * * * ** * * *
1588204 ACACTTAATACCGATACAAAAATTTATAAACTAATTATGAATTTCTTA-ATTGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAA-TTCTTAGGTTGC
* * * * *
1588257 ATACATAGTGCCAATACAGACATTCATCAACTTATTATGAATTTCTTAAGTTGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAA-TTCTTAGGTTGC
*
1588311 ACACACT-GTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
1 ACACA-TAGTGCCAATACGGAAATTCATAAACTTATTATGAA-TTCTTAGGTTGC
* * *
1588365 ACAAACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAA-TTCTTAGGTTGC
* * *
1588419 ACACATAGTGCAAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAA-TTCTTAGGTT-GC
** ** *
1588474 ACACA-A-TGCCAATACAAAAATTCATAAACTTATTACAAATTTCTTAAGTTGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAA-TTCTTAGGTTGC
1588526 ACACATAGTGCC
1 ACACATAGTGCC
1588538 CATTCGGTAA
Statistics
Matches: 468, Mismatches: 63, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
52 7 0.01
53 86 0.18
54 284 0.61
55 81 0.17
56 8 0.02
57 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (53 bp):
ACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTCTTAGGTTGC
Found at i:1616613 original size:3 final size:3
Alignment explanation
Indices: 1616605--1616633 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1616595 CATGTTCTTG
1616605 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1616634 ATACCTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1623612 original size:21 final size:21
Alignment explanation
Indices: 1623586--1623625 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1623576 CAGAACCCCA
*
1623586 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
1623607 GGGGGGAATCGATTCCCCT
1 GGGGGGAATCGATTCCCCT
1623626 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1623634 original size:23 final size:22
Alignment explanation
Indices: 1623608--1623666 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
1623598 TTCCCCTGTG
1623608 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TCAAA
* *
1623631 GGGGGAATCGGTT-CCCTCATA
1 GGGGGAATCGATTCCCCTCAAA
*
1623652 -GGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
1623667 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 10 0.32
21 6 0.19
22 3 0.10
23 12 0.39
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTCAAA
Found at i:1630224 original size:20 final size:20
Alignment explanation
Indices: 1630199--1630249 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1630189 CTAGTAAGAG
1630199 TATCGATACTCAACCCACAT
1 TATCGATACTCAACCCACAT
1630219 TATCGATACTCAACCCACAT
1 TATCGATACTCAACCCACAT
1630239 TATCGATACTC
1 TATCGATACTC
1630250 CCTTGAGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.27
Consensus pattern (20 bp):
TATCGATACTCAACCCACAT
Found at i:1635686 original size:23 final size:21
Alignment explanation
Indices: 1635653--1635719 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 21
1635643 TAGTTTACCC
1635653 TGTTTGTTTTAACTCAATATATT
1 TGTTTG-TTTAA-TCAATATATT
*
1635676 TGTTTGATTTAATTAATAT-TT
1 TGTTTG-TTTAATCAATATATT
*
1635697 T-TTTGTTAAAATCAATATGATT
1 TGTTTGTT-TAATCAATAT-ATT
1635719 T
1 T
1635720 AACTTCAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 3 0.08
22 9 0.24
23 11 0.30
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (21 bp):
TGTTTGTTTAATCAATATATT
Found at i:1635849 original size:22 final size:23
Alignment explanation
Indices: 1635798--1635849 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
1635788 GGATGGTTAA
1635798 AATAATATTTTAAAATTATAATT
1 AATAATATTTTAAAATTATAATT
* *
1635821 AAT-ATATTTTAAATTTATCA-T
1 AATAATATTTTAAAATTATAATT
1635842 AATAATAT
1 AATAATAT
1635850 GAGTTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 19 0.73
23 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AATAATATTTTAAAATTATAATT
Found at i:1635941 original size:59 final size:60
Alignment explanation
Indices: 1635868--1636031 Score: 187
Period size: 59 Copynumber: 2.8 Consensus size: 60
1635858 TACATCATTG
*
1635868 TCCCTAAACTATGACCCTCATTTTAAATTAGTCCCTAAACTTTTGAATATT-TCAATTTCA
1 TCCCTAAACTATGACCCTCATTTTAAATTAGTCCCTAAACTTTTGAACATTCT-AATTTCA
* * * * *
1635928 TCCC-AAACTATGACTCTCATTCTAAATCTA-T-CCTTAACTCTTGAACATTCTAATTTTA
1 TCCCTAAACTATGACCCTCATTTTAAAT-TAGTCCCTAAACTTTTGAACATTCTAATTTCA
* *
1635986 TCCCTAAACTATGACCCTC-TTTCTAAATTGGTCCCCAAA-TTTTGAA
1 TCCCTAAACTATGACCCTCATTT-TAAATTAGTCCCTAAACTTTTGAA
1636032 AGTTTTTGTG
Statistics
Matches: 86, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
58 28 0.33
59 48 0.56
60 10 0.12
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.38
Consensus pattern (60 bp):
TCCCTAAACTATGACCCTCATTTTAAATTAGTCCCTAAACTTTTGAACATTCTAATTTCA
Found at i:1637542 original size:54 final size:54
Alignment explanation
Indices: 1637440--1637576 Score: 136
Period size: 54 Copynumber: 2.5 Consensus size: 54
1637430 CCCGATGTCC
** ** *
1637440 CAATACTCACACCAAACGGAATCAATCACGTAAGGTGCATGAATCTAAACGTCT
1 CAATACTCACACCAAACAAAATCAATCACGTAAAATGCATGAACCTAAACGTCT
* *
1637494 CAATACTCACACCAAACAAAA-CTAGTCACGTAAAATG-ATCGAACCTAAAGGTCT
1 CAATACTCACACCAAACAAAATC-AATCACGTAAAATGCAT-GAACCTAAACGTCT
* * *
1637548 CATTACTTAC-CTCAAACAAAATAAATCAC
1 CAATACTCACAC-CAAACAAAATCAATCAC
1637577 ATGAGGTGGA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
53 4 0.06
54 64 0.94
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (54 bp):
CAATACTCACACCAAACAAAATCAATCACGTAAAATGCATGAACCTAAACGTCT
Found at i:1637818 original size:2 final size:2
Alignment explanation
Indices: 1637811--1637841 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1637801 TAGAAATCTT
1637811 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1637842 TTACAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1638043 original size:6 final size:6
Alignment explanation
Indices: 1638025--1638057 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1638015 CGTCAGTCAA
*
1638025 AATGTC AAAGTC AATGTC AATGTC AATGTC AAT
1 AATGTC AATGTC AATGTC AATGTC AATGTC AAT
1638058 ATGAACCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (6 bp):
AATGTC
Found at i:1639608 original size:69 final size:70
Alignment explanation
Indices: 1639470--1639616 Score: 172
Period size: 69 Copynumber: 2.1 Consensus size: 70
1639460 GGTAAAAGAC
* *
1639470 CATGCATATAATCATCAGCAGCAAGCCATGTATATCATGCATATAATCACCAGTAGTAAACACAT
1 CATGCATATAATCATCAGCAGCAAGCCATG-ATATCATGCATATAATCACCAATAGCAAACACAT
1639535 GTATAT
65 GTATAT
* * * * * ***
1639541 CATGCATATAATCATCA-TATCAAGAGCATG-TATCATGCATGTAATCATCAATAGCAAGTGCAT
1 CATGCATATAATCATCAGCAGCAAG-CCATGATATCATGCATATAATCACCAATAGCAAACACAT
1639604 GTATAT
65 GTATAT
1639610 CATGCAT
1 CATGCAT
1639617 GGGAATATCA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
69 39 0.60
70 5 0.08
71 21 0.32
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (70 bp):
CATGCATATAATCATCAGCAGCAAGCCATGATATCATGCATATAATCACCAATAGCAAACACATG
TATAT
Found at i:1639617 original size:36 final size:35
Alignment explanation
Indices: 1639470--1639616 Score: 156
Period size: 36 Copynumber: 4.2 Consensus size: 35
1639460 GGTAAAAGAC
** *
1639470 CATGCATATAATCATCAGCAGCAAGCCATGTATAT
1 CATGCATATAATCATCAATAGCAAGGCATGTATAT
* * * **
1639505 CATGCATATAATCACCAGTAGTAAACACATGTATAT
1 CATGCATATAATCATCAATAG-CAAGGCATGTATAT
*
1639541 CATGCATATAATCATC-ATATCAAGAGCATG--TAT
1 CATGCATATAATCATCAATAGCAAG-GCATGTATAT
*
1639574 CATGCATGTAATCATCAATAGCAAGTGCATGTATAT
1 CATGCATATAATCATCAATAGCAAG-GCATGTATAT
1639610 CATGCAT
1 CATGCAT
1639617 GGGAATATCA
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
33 18 0.19
34 14 0.15
35 25 0.27
36 36 0.39
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (35 bp):
CATGCATATAATCATCAATAGCAAGGCATGTATAT
Found at i:1640530 original size:51 final size:51
Alignment explanation
Indices: 1640454--1640892 Score: 452
Period size: 51 Copynumber: 8.6 Consensus size: 51
1640444 ATCACAGACC
* * *
1640454 TTTAACACATTATTCCAGTAATGAACTTATCATTGAATTACACCAGTGAAA
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACCAGTGAAA
* * ** * *
1640505 TTTAACACATTATTCTAGCAATGAACATATCACCGACTTACACTAGTTAAA
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACCAGTGAAA
* * * * * * *
1640556 TTTGACACATTATTCTAGTAATAAACTTATCACTAACTTGCACCAGT-AAA
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACCAGTGAAA
*
1640606 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACTAGTGAAA
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACCAGTGAAA
* * * *
1640657 TTTATCACATTATTCTACCAATGAACTTATCAATGACTTACACTAGTTG-AA
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACCAG-TGAAA
* * * * * * * *
1640708 TTGAACACAATATTCCAACAATAAACTTATCACTCACTTACACTAGTTAAA
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACCAGTGAAA
* * * * *
1640759 TTTAACATATTATTTCATCAATGGACTTATCAATGACTTACATCAGTGAAA
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACCAGTGAAA
** * * *
1640810 TTTAACACATTATTCCATTAATCAACTTATC-ATTATCTTACACCAGTTAAA
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGA-CTTACACCAGTGAAA
* * * *
1640861 TTTAACATATAATTCCAGCACTAAACTTATCA
1 TTTAACACATTATTCCAGCAATGAACTTATCA
1640893 CTTATCACTG
Statistics
Matches: 321, Mismatches: 62, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
50 46 0.14
51 273 0.85
52 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (51 bp):
TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACCAGTGAAA
Found at i:1640662 original size:26 final size:25
Alignment explanation
Indices: 1640627--1640703 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
1640617 ATTCCAGCAA
1640627 TGAACTTATCAATGACTTACACTAG
1 TGAACTTATCAATGACTTACACTAG
* * * *
1640652 TGAAATTTATCACATTA-TT-CTACCAA
1 TG-AACTTATCA-ATGACTTAC-ACTAG
1640678 TGAACTTATCAATGACTTACACTAG
1 TGAACTTATCAATGACTTACACTAG
1640703 T
1 T
1640704 TGAATTGAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
24 3 0.08
25 17 0.44
26 16 0.41
27 3 0.08
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (25 bp):
TGAACTTATCAATGACTTACACTAG
Found at i:1640731 original size:152 final size:153
Alignment explanation
Indices: 1640454--1640894 Score: 541
Period size: 152 Copynumber: 2.9 Consensus size: 153
1640444 ATCACAGACC
* * * *
1640454 TTTAACACATTATTCCAGTAATGAACTTATCATTGAATTACACCAGTGAAATTTAACACATTATT
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACTAGTGAAATTTAACACATTATT
* * ** * * *
1640519 CTAGCAATGAACATATCACCGACTTACACTAGTTAAATTTG-ACACATTATTCTAGTAATAAACT
66 CTACCAATGAACTTATCAATGACTTACACTAGTTAAA-TTGAACACAATATTCCAGCAATAAACT
*
1640583 TATCACTAACTTGCACCAG-TAAA
130 TATCACTAACTTACACCAGTTAAA
*
1640606 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACTAGTGAAATTTATCACATTATT
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACTAGTGAAATTTAACACATTATT
* *
1640671 CTACCAATGAACTTATCAATGACTTACACTAGTTGAATTGAACACAATATTCCAACAATAAACTT
66 CTACCAATGAACTTATCAATGACTTACACTAGTTAAATTGAACACAATATTCCAGCAATAAACTT
* *
1640736 ATCACTCACTTACACTAGTTAAA
131 ATCACTAACTTACACCAGTTAAA
* * * *
1640759 TTTAACATATTATTTCATCAATGGACTTATCAATGACTTACA-TCAGTGAAATTTAACACATTAT
1 TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACT-AGTGAAATTTAACACATTAT
* ** * * * * * *
1640823 TCCATTAATCAACTTATC-ATTATCTTACACCAGTTAAATTTAACA-TATAATTCCAGCACTAAA
65 TCTACCAATGAACTTATCAATGA-CTTACACTAGTTAAATTGAACACAAT-ATTCCAGCAATAAA
1640886 CTTATCACT
128 CTTATCACT
1640895 TATCACTGAC
Statistics
Matches: 251, Mismatches: 33, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
151 3 0.01
152 133 0.53
153 115 0.46
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (153 bp):
TTTAACACATTATTCCAGCAATGAACTTATCAATGACTTACACTAGTGAAATTTAACACATTATT
CTACCAATGAACTTATCAATGACTTACACTAGTTAAATTGAACACAATATTCCAGCAATAAACTT
ATCACTAACTTACACCAGTTAAA
Found at i:1640925 original size:58 final size:55
Alignment explanation
Indices: 1640846--1641003 Score: 153
Period size: 51 Copynumber: 2.9 Consensus size: 55
1640836 TTATCATTAT
* ** *
1640846 CTTACACCAGTTAAATTTAACATATAATTCCAGCACTAAACTTATCACTTATCACTGA
1 CTTACACCAGTCAAACGTAACATATAATTCCAGCACTAAACTTATCACTTA-CA--AA
* * * *
1640904 CTTACCCCAGTCAAACGTAACATATAATTCCAG-AATTAA--TCTCA-TTACAAA
1 CTTACACCAGTCAAACGTAACATATAATTCCAGCACTAAACTTATCACTTACAAA
* ** *
1640955 CTTACACTAGTCAAATTTAACATATAATTCCAGCACTAAACTCATCACT
1 CTTACACCAGTCAAACGTAACATATAATTCCAGCACTAAACTTATCACT
1641004 GACTATCCTA
Statistics
Matches: 80, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
51 30 0.38
52 4 0.05
53 2 0.03
54 6 0.08
55 5 0.06
57 4 0.05
58 29 0.36
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.30
Consensus pattern (55 bp):
CTTACACCAGTCAAACGTAACATATAATTCCAGCACTAAACTTATCACTTACAAA
Found at i:1640979 original size:51 final size:51
Alignment explanation
Indices: 1640896--1641066 Score: 204
Period size: 51 Copynumber: 3.4 Consensus size: 51
1640886 CTTATCACTT
* * * **
1640896 ATCACTGACTTACCCCAGTCAAACGTAACATATAATTCCAGAATTAATCTC
1 ATCACAGACTTACACTAGTCAAATTTAACATATAATTCCAGAATTAATCTC
* * * * *
1640947 ATTACAAACTTACACTAGTCAAATTTAACATATAATTCCAGCACTAAACTC
1 ATCACAGACTTACACTAGTCAAATTTAACATATAATTCCAGAATTAATCTC
*
1640998 ATCACTGAC-TATC-CTAGTCAAATTTAACATATAATTCCA-ACATTAATCTC
1 ATCACAGACTTA-CACTAGTCAAATTTAACATATAATTCCAGA-ATTAATCTC
1641048 ATCACAGACTTACACTAGT
1 ATCACAGACTTACACTAGT
1641067 TGCAACACCC
Statistics
Matches: 99, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
50 44 0.44
51 55 0.56
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.30
Consensus pattern (51 bp):
ATCACAGACTTACACTAGTCAAATTTAACATATAATTCCAGAATTAATCTC
Found at i:1641031 original size:50 final size:50
Alignment explanation
Indices: 1640912--1641057 Score: 186
Period size: 50 Copynumber: 2.9 Consensus size: 50
1640902 GACTTACCCC
** * * *
1640912 AGTCAAACGTAACATATAATTCCAGAATTAATCTCATTACAAACT-TACACT
1 AGTCAAATTTAACATATAATTCCAGCATTAATCTCATCACAGACTAT-C-CT
* * *
1640963 AGTCAAATTTAACATATAATTCCAGCACTAAACTCATCACTGACTATCCT
1 AGTCAAATTTAACATATAATTCCAGCATTAATCTCATCACAGACTATCCT
*
1641013 AGTCAAATTTAACATATAATTCCAACATTAATCTCATCACAGACT
1 AGTCAAATTTAACATATAATTCCAGCATTAATCTCATCACAGACT
1641058 TACACTAGTT
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
50 43 0.52
51 38 0.46
52 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (50 bp):
AGTCAAATTTAACATATAATTCCAGCATTAATCTCATCACAGACTATCCT
Found at i:1641032 original size:101 final size:105
Alignment explanation
Indices: 1640846--1641066 Score: 290
Period size: 101 Copynumber: 2.1 Consensus size: 105
1640836 TTATCATTAT
* *
1640846 CTTACACCAGTTAAATTTAACATATAATTCCAGCACTAAACTTATCACTTATCACTGACTTACCC
1 CTTACACTAGTCAAATTTAACATATAATTCCAGCACTAAAC-T-T-AC-TATCACTGACTTACCC
*
1640911 CAGTCAAACGTAACATATAATTCCAGA-ATTAATCTCATTACAAA
62 CAGTCAAACGTAACATATAATTCCA-ACATTAATCTCATCACAAA
* *
1640955 CTTACACTAGTCAAATTTAACATATAATTCCAGCACTAAAC-T-C-ATCACTGAC-TATCCTAGT
1 CTTACACTAGTCAAATTTAACATATAATTCCAGCACTAAACTTACTATCACTGACTTACCCCAGT
** *
1641016 CAAATTTAACATATAATTCCAACATTAATCTCATCACAGA
66 CAAACGTAACATATAATTCCAACATTAATCTCATCACAAA
1641056 CTTACACTAGT
1 CTTACACTAGT
1641067 TGCAACACCC
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
100 1 0.01
101 52 0.50
102 9 0.09
104 1 0.01
106 1 0.01
109 39 0.38
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (105 bp):
CTTACACTAGTCAAATTTAACATATAATTCCAGCACTAAACTTACTATCACTGACTTACCCCAGT
CAAACGTAACATATAATTCCAACATTAATCTCATCACAAA
Found at i:1645040 original size:60 final size:60
Alignment explanation
Indices: 1644970--1645097 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 60
1644960 ATAGTCGGAT
* * * * *
1644970 GACCATTTTGTAACTTTTAATAGTCGAGGGACTGAACAAA-GAAACATCCTATAATTGGGG
1 GACCATTTTGTAACATTTAATAGTCAAGGGACTCAA-AAATGAAACATCATATAATTGAGG
* *
1645030 GACCATTTTGTAACATTTAATAGTCAAGGGACTCAAAAATGCAACATCATATAGTTGAGG
1 GACCATTTTGTAACATTTAATAGTCAAGGGACTCAAAAATGAAACATCATATAATTGAGG
1645090 GACCATTT
1 GACCATTT
1645098 GTGTGTTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 3 0.05
60 57 0.95
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (60 bp):
GACCATTTTGTAACATTTAATAGTCAAGGGACTCAAAAATGAAACATCATATAATTGAGG
Found at i:1646905 original size:8 final size:8
Alignment explanation
Indices: 1646892--1646923 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
1646882 TGAAACGTAT
1646892 GAATAATC
1 GAATAATC
1646900 GAATAATC
1 GAATAATC
1646908 GAATAATC
1 GAATAATC
1646916 GAATAATC
1 GAATAATC
1646924 ATTTTCGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (8 bp):
GAATAATC
Found at i:1653472 original size:12 final size:12
Alignment explanation
Indices: 1653455--1653480 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1653445 TTTTTGTCCA
1653455 TTTGTTTTTATT
1 TTTGTTTTTATT
1653467 TTTGTTTTTATT
1 TTTGTTTTTATT
1653479 TT
1 TT
1653481 ATTATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTGTTTTTATT
Found at i:1653487 original size:3 final size:3
Alignment explanation
Indices: 1653474--1653528 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
1653464 ATTTTTGTTT
*
1653474 TTA TT- TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1653520 TTA TTA TTA
1 TTA TTA TTA
1653529 ATAAATAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1655002 original size:2 final size:2
Alignment explanation
Indices: 1654990--1655021 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1654980 ATATCCTTCT
*
1654990 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1655022 CTTCATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1660063 original size:7 final size:7
Alignment explanation
Indices: 1660036--1660185 Score: 87
Period size: 7 Copynumber: 21.4 Consensus size: 7
1660026 ACACTTGAAG
1660036 AAAAGAA
1 AAAAGAA
*
1660043 AAATAAATA
1 AAA-AGA-A
1660052 AAAAGAA
1 AAAAGAA
*
1660059 AAAAGTTA
1 AAAAG-AA
*
1660067 GAAAG-A
1 AAAAGAA
1660073 AAAA-AA
1 AAAAGAA
*
1660079 AAAGGAA
1 AAAAGAA
*
1660086 AAAGGAA
1 AAAAGAA
*
1660093 AAAAGAG
1 AAAAGAA
*
1660100 AAAAGAG
1 AAAAGAA
*
1660107 AAAAGAG
1 AAAAGAA
*
1660114 AAAAGAG
1 AAAAGAA
1660121 AAAA-AA
1 AAAAGAA
1660127 AAAAG-A
1 AAAAGAA
1660133 AAAAGAA
1 AAAAGAA
1660140 AAGGAA-AA
1 AA--AAGAA
*
1660148 AAAGGAAA
1 AAAAG-AA
*
1660156 AAAAGGA
1 AAAAGAA
1660163 AAAAG-A
1 AAAAGAA
1660169 AAAAGAA
1 AAAAGAA
* *
1660176 TAAATAA
1 AAAAGAA
1660183 AAA
1 AAA
1660186 GGGGTCAAAG
Statistics
Matches: 116, Mismatches: 15, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
6 26 0.22
7 65 0.56
8 19 0.16
9 6 0.05
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:1660069 original size:27 final size:26
Alignment explanation
Indices: 1660051--1660136 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 26
1660041 AAAAATAAAT
1660051 AAAAAGAAAAAAGTTAGAAAGAAAAA
1 AAAAAGAAAAAAGTTAGAAAGAAAAA
* *
1660077 AAAAAGGAAAAAG---GAAA-AAAGA
1 AAAAAGAAAAAAGTTAGAAAGAAAAA
* * ** *
1660099 GAAAAGAGAAAAGAGAAAAGAGAAAAA
1 AAAAAGAAAAAAGTTAGAA-AGAAAAA
1660126 AAAAAGAAAAA
1 AAAAAGAAAAA
1660137 GAAAAGGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
22 14 0.30
23 4 0.09
25 2 0.04
26 13 0.28
27 13 0.28
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAAAAGTTAGAAAGAAAAA
Found at i:1660087 original size:48 final size:45
Alignment explanation
Indices: 1660035--1660172 Score: 109
Period size: 47 Copynumber: 2.9 Consensus size: 45
1660025 GACACTTGAA
*
1660035 GAAAAGAAAAATAAATAAAAAGAAAAAAGTTAGAA-AGAAAAAAAAAAG
1 GAAAAGAAAAA-AAA-AAAAAGAAAAAAG--AAAAGAGAAAAAAAAAAG
* *
1660083 GAAAAAGGAAAAAAGAGAAAAGAGAAAAGAGAAAAGAGAAAAAAAAAAG
1 G-AAAA-GAAAAAA-A-AAAAAAGAAAAAAGAAAAGAGAAAAAAAAAAG
* * *
1660132 AAAAAGAAAAGGAAAAAAAGGAAAAAAAGGAAAA-AGAAAAA
1 GAAAAGAAAA-AAAAAAAAAG-AAAAAA-GAAAAGAGAAAAA
1660173 GAATAAATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
46 5 0.07
47 18 0.24
48 14 0.19
49 18 0.24
50 18 0.24
51 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (45 bp):
GAAAAGAAAAAAAAAAAAAGAAAAAAGAAAAGAGAAAAAAAAAAG
Found at i:1660094 original size:14 final size:13
Alignment explanation
Indices: 1660071--1660187 Score: 79
Period size: 12 Copynumber: 9.1 Consensus size: 13
1660061 AAGTTAGAAA
1660071 GAAAAA-AAAAAG
1 GAAAAAGAAAAAG
*
1660083 GAAAAAGGAAAAAA
1 GAAAAA-GAAAAAG
1660097 GAGAAAAGAGAAAAG
1 GA-AAAAGA-AAAAG
1660112 AGAAAAGAGAAAAA-
1 -GAAAA-AGAAAAAG
1660126 -AAAAAGAAAAA-
1 GAAAAAGAAAAAG
*
1660137 GAAAAGGAAAAA-
1 GAAAAAGAAAAAG
*
1660149 -AAGGAA-AAAAAG
1 GAA-AAAGAAAAAG
1660161 GAAAAAGAAAAA-
1 GAAAAAGAAAAAG
*
1660173 GAATAAATAAAAAG
1 GAA-AAAGAAAAAG
1660187 G
1 G
1660188 GGTCAAAGAT
Statistics
Matches: 85, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
11 14 0.16
12 26 0.31
13 15 0.18
14 10 0.12
15 15 0.18
16 5 0.06
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (13 bp):
GAAAAAGAAAAAG
Found at i:1660096 original size:9 final size:9
Alignment explanation
Indices: 1660075--1660166 Score: 53
Period size: 9 Copynumber: 9.6 Consensus size: 9
1660065 TAGAAAGAAA
1660075 AAAAAAAGG
1 AAAAAAAGG
1660084 --AAAAAGG
1 AAAAAAAGG
*
1660091 AAAAAAGAGA
1 AAAAAA-AGG
*
1660101 AAAGAGAAAAG
1 AAA-A-AAAGG
* *
1660112 AGAAAAGAGAA
1 A-AAAAAAG-G
*
1660123 AAAAAAAAGA
1 AAAA-AAAGG
1660133 AAAAGAAAAGG
1 AAAA-AA-AGG
1660144 AAAAAAAGG
1 AAAAAAAGG
1660153 AAAAAAAGG
1 AAAAAAAGG
1660162 AAAAA
1 AAAAA
1660167 GAAAAAGAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
7 7 0.11
9 21 0.32
10 19 0.29
11 14 0.22
12 4 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:1660150 original size:55 final size:54
Alignment explanation
Indices: 1660052--1660186 Score: 136
Period size: 55 Copynumber: 2.5 Consensus size: 54
1660042 AAAATAAATA
* * * *
1660052 AAAAGAAAAAAGTTAGAAAGAAAAAA-AAAAGGAAAAAGGAAAAAAG-AGAAAAGAG
1 AAAAGAGAAAAG--AGAAAAAAAAAAGAAAAAGAAAAAGGAAAAAAGAAAAAAAG-G
1660107 AAAAGAGAAAAGAGAAAAAAAAAAGAAAAAG-AAAAGGAAAAAAAGGAAAAAAAGG
1 AAAAGAGAAAAGAGAAAAAAAAAAGAAAAAGAAAAAGG-AAAAAA-GAAAAAAAGG
1660162 AAAA-AGAAAA-AGAATAAATAAAAAG
1 AAAAGAGAAAAGAGAA-AAA-AAAAAG
1660187 GGGTCAAAGA
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
53 21 0.30
54 20 0.29
55 23 0.33
56 6 0.09
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (54 bp):
AAAAGAGAAAAGAGAAAAAAAAAAGAAAAAGAAAAAGGAAAAAAGAAAAAAAGG
Found at i:1662490 original size:19 final size:19
Alignment explanation
Indices: 1662466--1662502 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1662456 TTAAGGTTAG
1662466 ATACCCTTTAGAGGAGTAT
1 ATACCCTTTAGAGGAGTAT
1662485 ATACCCTTTAGAGGAGTA
1 ATACCCTTTAGAGGAGTA
1662503 CTCATGGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (19 bp):
ATACCCTTTAGAGGAGTAT
Found at i:1674620 original size:21 final size:21
Alignment explanation
Indices: 1674572--1674620 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1674562 TGAGCTATGG
* *
1674572 CTTTGAAGTAAGGCGCCTTGA
1 CTTTGAAGTAAAGCGCATTGA
* *
1674593 CTATGAAGTAAAGCTCATTGA
1 CTTTGAAGTAAAGCGCATTGA
*
1674614 TTTTGAA
1 CTTTGAA
1674621 TTGAAGTAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (21 bp):
CTTTGAAGTAAAGCGCATTGA
Found at i:1679031 original size:116 final size:117
Alignment explanation
Indices: 1678813--1679426 Score: 485
Period size: 116 Copynumber: 5.3 Consensus size: 117
1678803 ACAATTCAAC
* * * * ** * *
1678813 TTCCAATAGAATGGTTCATAATGAGAAGAACTCATTTGATAAGGGATAAGAAA-TTCATAATGAG
1 TTCCAGTAGAAGGGTTCATAATGAGAATAATTTGTTCGATAAGGGAGAA-AAAGTTCATAATGAG
* *
1678877 AA-AATTTTGTTCAACC-TTTGTCTCATTCATCACAAAAGGAGGTGGATCAATAT
65 AAGAA-CTTGTTCAACCTTTTGT-TCATTCATCACAGAAGGAGGTGGATCAATAT
** * * * *
1678930 TTTTAGTGGAAGGGTTCATAATGTGTATAATTTGTTCGATAAGGGA-AAAAAGTTCATGATGAGA
1 TTCCAGTAGAAGGGTTCATAATGAGAATAATTTGTTCGATAAGGGAGAAAAAGTTCATAATGAGA
* * *
1678994 AGAACTTGTTCAACCTATTGTTGATTCATCA-TGAAAGGAGGTGGATCAATAT
66 AGAACTTGTTCAACCTTTTGTTCATTCATCACAG-AAGGAGGTGGATCAATAT
* * * * * * * **
1679046 TTCCAGTAGAAGAGTTCATAATAAGAAGAACTTGTTCAATAAGGAAGAAGAAGTTCATAACAAGA
1 TTCCAGTAGAAGGGTTCATAATGAGAATAATTTGTTCGATAAGGGAGAAAAAGTTCATAATGAGA
** * *
1679111 AGAACTTGTTCAACCTTTTCATCATTCATCACAGAAGAAGATGGATC-ATAAT
66 AGAACTTGTTCAACCTTTTGTTCATTCATCACAGAAGGAGGTGGATCAAT-AT
* ** * * * *
1679163 TTCCAGTATAAGGGTTTGTAATGAGAATAATTCGTT-GATAAGTGAGAAGAAGTTCGTAATGAGA
1 TTCCAGTAGAAGGGTTCATAATGAGAATAATTTGTTCGATAAGGGAGAAAAAGTTCATAATGAGA
* * **
1679227 AGAACTTATTCAACCTTTTGCTCATTCATCACAGAAGGAGGTGGATCAGCAT
66 AGAACTTGTTCAACCTTTTGTTCATTCATCACAGAAGGAGGTGGATCAATAT
* * * * * * ** ** * * *
1679279 TTCTAATAGAAGGGTTCATAATAATAAAAACTCATTCGATAAGAAAGAAAAA-ATCATAATAAAA
1 TTCCAGTAGAAGGGTTCATAATGAGAATAATTTGTTCGATAAGGGAGAAAAAGTTCATAATGAGA
* * * * * * *
1679343 AGAACTCGTTCAATCTTTTTGCTCAAATTTATCACAGAAAGAAGTGGATCAACAT
66 AGAACTTGTTCAA-CCTTTTGTTC--ATTCATCACAGAAGGAGGTGGATCAATAT
*
1679398 TTCCAAAGT-GAA--GTTCATAACGAGAATAA
1 TTCC--AGTAGAAGGGTTCATAATGAGAATAA
1679427 CACTTCCAAA
Statistics
Matches: 392, Mismatches: 91, Indels: 27
0.77 0.18 0.05
Matches are distributed among these distances:
115 3 0.01
116 199 0.51
117 143 0.36
118 14 0.04
119 28 0.07
120 3 0.01
121 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (117 bp):
TTCCAGTAGAAGGGTTCATAATGAGAATAATTTGTTCGATAAGGGAGAAAAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGTTCATTCATCACAGAAGGAGGTGGATCAATAT
Found at i:1679121 original size:20 final size:20
Alignment explanation
Indices: 1679059--1679122 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
1679049 CAGTAGAAGA
*
1679059 GTTCATAATAAGAAGAACTT
1 GTTCATAACAAGAAGAACTT
*
1679079 GTTCAATAAGGAAGAAGAA---
1 GTTC-ATAA-CAAGAAGAACTT
1679098 GTTCATAACAAGAAGAACTT
1 GTTCATAACAAGAAGAACTT
1679118 GTTCA
1 GTTCA
1679123 ACCTTTTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.22
18 4 0.11
19 4 0.11
20 9 0.24
21 4 0.11
22 8 0.22
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (20 bp):
GTTCATAACAAGAAGAACTT
Found at i:1679233 original size:233 final size:231
Alignment explanation
Indices: 1678813--1679426 Score: 607
Period size: 233 Copynumber: 2.6 Consensus size: 231
1678803 ACAATTCAAC
* * * * *
1678813 TTCCAATAGAATGGTTCATAATGAGAAGAACTCATTTGATAAGGGATAAGAAATTCATAATGAGA
1 TTCCAATAGAA-GGTTCATAATAAGAAGAACTCATTCGATAAGGAAGAAGAAATTCATAATAAGA
* * * ** *
1678878 A-AATTTTGTTCAACCTTTGTCTCATTCATCACAAAAGGAGGTGGATCAATATTTTTAGTGGAAG
65 AGAA-CTTGTTCAACCTTT-TCTCATTCATCACAAAAGAAGATGGATCAATATTTCCAGTAGAAG
* * * * *
1678942 GGTTCATAATGTGTATAATTTGTTCGATAAGGGAAAAAAGTTCATGATGAGAAGAACTTGTTCAA
128 GGTTCATAATGAGAATAATTCGTTCGATAAGGGAAAAAAGTTCATAATGAGAAGAACTTATTCAA
* * * *
1679007 CCTATTGTTGATTCATCA-TGAAAGGAGGTGGATCAATAT
193 CCTATTGCTCATTCATCACAG-AAGGAGGTGGATCAACAT
* ** * * *
1679046 TTCCAGTAGAAGAGTTCATAATAAGAAGAACTTGTTCAATAAGGAAGAAGAAGTTCATAACAAGA
1 TTCCAATAGAAG-GTTCATAATAAGAAGAACTCATTCGATAAGGAAGAAGAAATTCATAATAAGA
* *
1679111 AGAACTTGTTCAACCTTTTCATCATTCATCACAGAAGAAGATGGATC-ATAATTTCCAGTATAAG
65 AGAACTTGTTCAACCTTTTC-TCATTCATCACAAAAGAAGATGGATCAAT-ATTTCCAGTAGAAG
** * * *
1679175 GGTTTGTAATGAGAATAATTCGTT-GATAAGTGAGAAGAAGTTCGTAATGAGAAGAACTTATTCA
128 GGTTCATAATGAGAATAATTCGTTCGATAAGGGA-AAAAAGTTCATAATGAGAAGAACTTATTCA
* *
1679239 ACCTTTTGCTCATTCATCACAGAAGGAGGTGGATCAGCAT
192 ACCTATTGCTCATTCATCACAGAAGGAGGTGGATCAACAT
* * * * * *
1679279 TTCTAATAGAAGGGTTCATAATAATAAAAACTCATTCGATAAGAAAGAA-AAAATCATAATAAAA
1 TTCCAATAGAA-GGTTCATAATAAGAAGAACTCATTCGATAAGGAAGAAGAAATTCATAATAAGA
* * * *
1679343 AGAACTCGTTCAATCTTTTTGCTCAAATTTATCACAGAAAGAAG-TGGATCAACATTTCCAAAGT
65 AGAACTTGTTCAA-CCTTTT-CTC--ATTCATCACA-AAAGAAGATGGATCAATATTTCC--AGT
*
1679407 -GAA--GTTCATAACGAGAATAA
123 AGAAGGGTTCATAATGAGAATAA
1679427 CACTTCCAAA
Statistics
Matches: 310, Mismatches: 56, Indels: 29
0.78 0.14 0.07
Matches are distributed among these distances:
232 36 0.12
233 222 0.72
234 19 0.06
235 21 0.07
236 9 0.03
237 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (231 bp):
TTCCAATAGAAGGTTCATAATAAGAAGAACTCATTCGATAAGGAAGAAGAAATTCATAATAAGAA
GAACTTGTTCAACCTTTTCTCATTCATCACAAAAGAAGATGGATCAATATTTCCAGTAGAAGGGT
TCATAATGAGAATAATTCGTTCGATAAGGGAAAAAAGTTCATAATGAGAAGAACTTATTCAACCT
ATTGCTCATTCATCACAGAAGGAGGTGGATCAACAT
Found at i:1683915 original size:19 final size:20
Alignment explanation
Indices: 1683891--1683942 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
1683881 GGTTTTAAAT
*
1683891 CGGTTTTGACCAGTTTG-AC
1 CGGTTTTGACCAGTTCGAAC
* *
1683910 CGGTTTCGACCGGTTCGAAC
1 CGGTTTTGACCAGTTCGAAC
*
1683930 CGG-TCTGACCAGT
1 CGGTTTTGACCAGT
1683943 CTGAACCGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (20 bp):
CGGTTTTGACCAGTTCGAAC
Found at i:1683920 original size:10 final size:9
Alignment explanation
Indices: 1683869--1683939 Score: 52
Period size: 10 Copynumber: 7.3 Consensus size: 9
1683859 CAGCTGGAAA
1683869 ACCGGTTTG
1 ACCGGTTTG
*
1683878 ACCGGTTTTAA
1 ACCGG-TTT-G
*
1683889 ATCGGTTTTG
1 ACCGG-TTTG
*
1683899 ACCAGTTTG
1 ACCGGTTTG
1683908 ACCGGTTTCG
1 ACCGGTTT-G
*
1683918 ACCGGTTCG
1 ACCGGTTTG
*
1683927 AACCGGTCTG
1 -ACCGGTTTG
1683937 ACC
1 ACC
1683940 AGTCTGAACC
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 20 0.41
10 21 0.43
11 8 0.16
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1683996 original size:7 final size:7
Alignment explanation
Indices: 1683984--1684019 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1683974 GACCCGACCC
1683984 GACCGTT
1 GACCGTT
1683991 GACCGTT
1 GACCGTT
1683998 GACCGTT
1 GACCGTT
1684005 GACCG-T
1 GACCGTT
*
1684011 GACTGTT
1 GACCGTT
1684018 GA
1 GA
1684020 TCTCCTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.28
Consensus pattern (7 bp):
GACCGTT
Found at i:1684439 original size:10 final size:10
Alignment explanation
Indices: 1684424--1684449 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1684414 GATCGTTCGA
1684424 CAGCTCGACC
1 CAGCTCGACC
1684434 CAGCTCGACC
1 CAGCTCGACC
1684444 CAGCTC
1 CAGCTC
1684450 TTCTAGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (10 bp):
CAGCTCGACC
Found at i:1695241 original size:129 final size:130
Alignment explanation
Indices: 1694930--1695296 Score: 488
Period size: 131 Copynumber: 2.8 Consensus size: 130
1694920 TAATTCTAAG
** *
1694930 AGAGAAAATAATAATATCTAATTATTTCCAATCGATAATAAATGATCTCTCATGCCTTAAAGCAA
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGA-CTCTCATGCCTTAAAGCAA
* * * * *
1694995 TCATTTATTACTCCAATCGAAATGAAGATATATCACTATTTCATCTTAAGATTCAATATTGATTC
65 TCATTTATTACTCCAATCGAAATAAAGAGATATCACTATTTTATCTTAAAAATCAATATTGATTC
1695060 A
130 A
* * *
1695061 AGTGAAAATGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAA
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGA-CTCTCATGCCTTAAAGCAA
* * *
1695126 TCATTCATTTCTCCAATC-AAATAAAGAGATATCACTATTTTGTCTTAAAAATCAATATTGATTC
65 TCATTTATTACTCCAATCGAAATAAAGAGATATCACTATTTTATCTTAAAAATCAATATTGATTC
*
1695190 G
130 A
* * * *
1695191 AGAG-AAACGGTAATATCTAATTATTTCTAATCGAGAATAAATGACATCTCATGTCTTAAAACAA
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGAC-TCTCATGCCTTAAAGCAA
* *
1695255 TCATTTATTACTCCAACCGAAATGAAA-AGATATTACTATTTT
65 TCATTTATTACTCCAATCGAAAT-AAAGAGATATCACTATTTT
1695297 CAATATTGAG
Statistics
Matches: 208, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
128 1 0.00
129 67 0.32
130 61 0.29
131 79 0.38
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (130 bp):
AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACTCTCATGCCTTAAAGCAAT
CATTTATTACTCCAATCGAAATAAAGAGATATCACTATTTTATCTTAAAAATCAATATTGATTCA
Found at i:1697323 original size:3 final size:3
Alignment explanation
Indices: 1697308--1697400 Score: 89
Period size: 3 Copynumber: 31.3 Consensus size: 3
1697298 AAAAACCAAT
* * * * *
1697308 TAA TAA AAA TAA TAA T-A TAT TAA TAA TAA TAA CAT TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1697355 TAA TAA TAA TAA CAT TAA TAT TTA TAA TAA TAA TAA TAA AAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1697401 GGTGTAGGGA
Statistics
Matches: 69, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1697366 original size:27 final size:27
Alignment explanation
Indices: 1697328--1697393 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
1697318 AATAATATAT
1697328 TAATAATAATAACATTAATATTAATAA
1 TAATAATAATAACATTAATATTAATAA
*
1697355 TAATAATAATAACATTAATATTTATAA
1 TAATAATAATAACATTAATATTAATAA
1697382 TAATAATAATAA
1 TAATAATAATAA
1697394 AAATAATGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (27 bp):
TAATAATAATAACATTAATATTAATAA
Found at i:1697400 original size:27 final size:27
Alignment explanation
Indices: 1697308--1697400 Score: 116
Period size: 27 Copynumber: 3.5 Consensus size: 27
1697298 AAAAACCAAT
* *
1697308 TAATAAAAATAATA-ATATATTAATAA
1 TAATAAAAATAATATTTATAATAATAA
* * *
1697334 TAATAACATTAATATTAATAATAATAA
1 TAATAAAAATAATATTTATAATAATAA
* *
1697361 TAATAACATTAATATTTATAATAATAA
1 TAATAAAAATAATATTTATAATAATAA
1697388 TAATAAAAATAAT
1 TAATAAAAATAAT
1697401 GGTGTAGGGA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
26 12 0.21
27 46 0.79
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
TAATAAAAATAATATTTATAATAATAA
Found at i:1698981 original size:42 final size:42
Alignment explanation
Indices: 1698920--1699001 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
1698910 TTATTTTTTT
** *
1698920 TGGGAACCGAAATCAGAACCTATTGCACCGGTTCCTAAAAAA
1 TGGGAACCGAAATCAGAACCTATTAAACCAGTTCCTAAAAAA
* * * *
1698962 TGGGAATCGGAATCGGAACCTGTTAAACCAGTTCCTAAAA
1 TGGGAACCGAAATCAGAACCTATTAAACCAGTTCCTAAAA
1699002 TTTGGGATCC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (42 bp):
TGGGAACCGAAATCAGAACCTATTAAACCAGTTCCTAAAAAA
Found at i:1699544 original size:29 final size:29
Alignment explanation
Indices: 1699502--1699596 Score: 154
Period size: 29 Copynumber: 3.2 Consensus size: 29
1699492 CTAGTTTCAG
* *
1699502 GGTACCTGGTATTGGAACTGCTTTTAGCC
1 GGTACCCGGTATTGGAACCGCTTTTAGCC
*
1699531 GGTACCCGATATTGGAACCGCTTTTAGCC
1 GGTACCCGGTATTGGAACCGCTTTTAGCC
1699560 GGTACCCGGTATTGGAACCGCTTTTAGCC
1 GGTACCCGGTATTGGAACCGCTTTTAGCC
1699589 GGGTACCC
1 -GGTACCC
1699597 AACCAGTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 54 0.89
30 7 0.11
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.28
Consensus pattern (29 bp):
GGTACCCGGTATTGGAACCGCTTTTAGCC
Found at i:1704585 original size:18 final size:18
Alignment explanation
Indices: 1704562--1704607 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1704552 ACCGATTTCA
* *
1704562 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCATTG
1704580 ACCCGACCCGACCCATTG
1 ACCCGACCCGACCCATTG
*
1704598 ACCCGGCCCG
1 ACCCGACCCG
1704608 TTGACCTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCATTG
Found at i:1704608 original size:31 final size:31
Alignment explanation
Indices: 1704566--1704629 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1704556 ATTTCAACCC
*
1704566 GACCCGACCCGTTTACCCGACCCGACCCATT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
* * *
1704597 GACCCGGCCCGTTGACCTGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
1704628 GA
1 GA
1704630 TCGTTGACCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.17, C:0.45, G:0.22, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCATT
Found at i:1707124 original size:24 final size:24
Alignment explanation
Indices: 1707097--1707179 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
1707087 AATTATTTTA
*
1707097 TCTGATTTCCGACTTGAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
* * *
1707121 TCTGA-TACATTACCTGAATTCTGT
1 TCTGATTTC-TGACTTGAATTCTGT
*
1707145 TCTGATTTCTGA-TCTGGATTCTGT
1 TCTGATTTCTGACT-TGAATTCTGT
*
1707169 TCTGATATCTG
1 TCTGATTTCTG
1707180 TTCTGAATTC
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
23 2 0.04
24 43 0.91
25 2 0.04
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.46
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTCTGT
Found at i:1707149 original size:12 final size:12
Alignment explanation
Indices: 1707134--1707190 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
1707124 GATACATTAC
1707134 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1707146 CTGATTTCTGAT
1 CTGAATTCTGTT
*
1707158 CTGGATTCTGTT
1 CTGAATTCTGTT
1707170 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
1707182 CTGAATTCT
1 CTGAATTCT
1707191 ATTTTGATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1707198 original size:24 final size:24
Alignment explanation
Indices: 1707111--1707190 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
1707101 ATTTCCGACT
* *
1707111 TGAATTCTGTTCTGATA-CATTACC
1 TGAATTCTGTTCTGATATC-TGATC
*
1707135 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
1707159 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
1707183 TGAATTCT
1 TGAATTCT
1707191 ATTTTGATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 47 0.98
25 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:1709027 original size:6 final size:6
Alignment explanation
Indices: 1709018--1709105 Score: 122
Period size: 6 Copynumber: 14.7 Consensus size: 6
1709008 TATATATATA
* *
1709018 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCA TATACG
1 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG
* * **
1709066 TATGCA TATGCG TATGCA TATGAT TATGCG TATGCG TATG
1 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATG
1709106 TATTTTATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (6 bp):
TATGCG
Found at i:1715268 original size:127 final size:126
Alignment explanation
Indices: 1715103--1715353 Score: 360
Period size: 127 Copynumber: 2.0 Consensus size: 126
1715093 CTTTTACTAA
* *
1715103 TTCATTAATTATATGCTTTTGACAAGAGGCAAGATTAAACCTTCCATGTCCCATCCAACCCCAAA
1 TTCATTAATTATATGCTTTTCACAAGAGGCAAGATTAAACCTTCCATGTCCCATCCAAACCCAAA
* * * *
1715168 AGAATCATTGTTGGGCTACTCACCC-AGAAGTAACACTGGGATTGAACTTTGACATCAAATAC
66 AGAACCATTGTTGGGCTACTCACCCGA-AAGTAACACCGGGACTGAAATTTGACAT-AAATAC
* ** ** *
1715230 TTCATTAATTATATGCTTTTCACAAGAGGCAATATTAAACCTTCTGTGTCCCATCCAAAGTCGAA
1 TTCATTAATTATATGCTTTTCACAAGAGGCAAGATTAAACCTTCCATGTCCCATCCAAACCCAAA
*
1715295 AGAACCATTGTTGGGCTCCTCACCCGAAAGTAACACCGGGACTGAAATTTGACATAAAT
66 AGAACCATTGTTGGGCTACTCACCCGAAAGTAACACCGGGACTGAAATTTGACATAAAT
1715354 TCCCCAGCCT
Statistics
Matches: 110, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
126 4 0.04
127 105 0.95
128 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (126 bp):
TTCATTAATTATATGCTTTTCACAAGAGGCAAGATTAAACCTTCCATGTCCCATCCAAACCCAAA
AGAACCATTGTTGGGCTACTCACCCGAAAGTAACACCGGGACTGAAATTTGACATAAATAC
Found at i:1715934 original size:22 final size:22
Alignment explanation
Indices: 1715896--1715961 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
1715886 GCAAGAAAGG
*
1715896 AAAGGAAAAATAGAGAAAGGAAA
1 AAAGGAAAAA-AAAGAAAGGAAA
*
1715919 AAAGGAAAAAAAAGAAAAGAAA
1 AAAGGAAAAAAAAGAAAGGAAA
* *
1715941 GAA-GAAGAAAGAAG-AAGGAAA
1 AAAGGAA-AAAAAAGAAAGGAAA
1715962 GAAAACTGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 9 0.24
22 18 0.49
23 10 0.27
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.02
Consensus pattern (22 bp):
AAAGGAAAAAAAAGAAAGGAAA
Found at i:1715948 original size:10 final size:10
Alignment explanation
Indices: 1715929--1715964 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
1715919 AAAGGAAAAA
1715929 AAAGAA-AAG
1 AAAGAAGAAG
1715938 AAAGAAGAAG
1 AAAGAAGAAG
1715948 AAAGAAGAAGG
1 AAAGAAGAA-G
1715959 AAAGAA
1 AAAGAA
1715965 AACTGATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.24
10 12 0.48
11 7 0.28
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAAGAAGAAG
Found at i:1718064 original size:42 final size:41
Alignment explanation
Indices: 1718011--1718134 Score: 115
Period size: 42 Copynumber: 3.0 Consensus size: 41
1718001 TCCAAAATTT
* *
1718011 ATAAGTCCTTCGGGCCAT-TAGTAAGTCTTCCGAGCATGATG
1 ATAAATCCTTCGGGCCATCT-GTAAGTCTTCCGAGCAAGATG
* * *
1718052 CTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCTGTAAGTCTTCCGAGCAAGATG
* * * ** * *
1718094 ATAAGTCCTTCGGACGATCCATAAGTCTTTCGTGCAAGATG
1 ATAAATCCTTCGGGCCATCTGTAAGTCTTCCGAGCAAGATG
1718135 TTTTTCAAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 33 0.49
42 34 0.50
43 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCTGTAAGTCTTCCGAGCAAGATG
Found at i:1718098 original size:21 final size:20
Alignment explanation
Indices: 1718074--1718134 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1718064 GGGTCATCTG
1718074 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCTTTCG-GCAAGATGA
* * *
1718095 TAAGTCCTTCGG-ACGATCCA
1 TAAGTCTTTCGGCAAGAT-GA
1718115 TAAGTCTTTCGTGCAAGATG
1 TAAGTCTTTCG-GCAAGATG
1718135 TTTTTCAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
19 4 0.13
20 12 0.39
21 11 0.35
22 4 0.13
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (20 bp):
TAAGTCTTTCGGCAAGATGA
Found at i:1718352 original size:37 final size:37
Alignment explanation
Indices: 1718303--1719296 Score: 260
Period size: 37 Copynumber: 26.1 Consensus size: 37
1718293 CCTCTGGGCC
* * *
1718303 ATCTTAAGCCTTCACCAAAGAGTAATGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* * *
1718340 ATCTAAAACCTTCACCGAAGAGTAGTAAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* *
1718377 ATATTAAGCCTTCACCGAATAGTAGTAAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* * *
1718414 ATCTTAAGCCTTCACTGATGAGTAGTGAAGCAAATTC-
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAA-TCA
* * * * *** **** *
1718451 ATCAGTAAGCCTTCCGAGCATGATGATTAAGT-CCTCCGGGCC
1 ATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTAAAGCAAATCA
* * *
1718493 ATCTTAAGCCTTCACCAAAGACTAGT-GAGACAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAG-CAAATCA
* *
1718530 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTC-
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAA-TCA
* * * * * **** ****
1718567 ATCAGTAAGCTTTCCGAGCATGATGATTAAGTCCTCCGGGCCA
1 ATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTAAAGCAAATCA
* * * *
1718610 A-CTAAAGCCTTCACCGAAGAGTAGTGAAGAAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* *
1718646 ATCTTAAGGCTTCACCGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* * * * *
1718683 ATCTTAAGCTTTCACTGATGAGTAATGAAGCAAATTC-
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAA-TCA
* * * * * *** **** *
1718720 ATCAGTAAACCTTCTGAGCATGATGATTAAGT-CCTCCGGGCC
1 ATC-TTAAGCCTTC--A-C-CGAAGAGT-AGTAAAGCAAATCA
* *
1718762 ATCTTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* **
1718799 ATCTTAAGCCTTCACTGAAGAGTAGTGCAGCAAATTC-
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAA-TCA
* * * * *** ** * *
1718836 ATCAGTAAGCCTTCCGAGCATGATGATTAAGT-CCTCCGAGCC
1 ATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTAAAGCAAATCA
* *
1718878 ATCTTAAACCTTCACCAAAGAGTAGTGAAA-CAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGT-AAAGCAAATCA
* *
1718915 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTC-
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAA-TCA
** * * * * ** *** *
1718952 ATAAGTAAGCCTTCCGAGCATGATGATTAAGTCATTC-GGGCC
1 AT-CTTAAGCCTT-C-A-C-CGAAGAGT-AGTAAAGCAAATCA
* * *
1718994 ATCTTAAGCCTTTACTGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* **
1719031 ATCTTAAGTCTTCACTAAAGAGTAGTAAAGCAAATTC-
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAA-TCA
* * * *
1719068 ATCAGTAAGCCTT--CCG-AGCATGATAATTAAGTC--CTCCGGA
1 ATC-TTAAGCCTTCACCGAAG-A-G-TAGTAAAG-CAAAT-C--A
* * * * * *
1719108 CCATCTTAAGCCTTCTCCAAATAGTACTGAAGAAAATCA
1 --ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* * * *
1719147 ATCTTAAGCCTTCGCCGAAGAGTAATGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* * * * *
1719184 ATTTTAAGCATTCACCGAAGAGTAGTGAAGTAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* * * *
1719221 ATTTTAAGCCTTCACCGAAGAGTAGTGAAGTAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
* * * *
1719258 ATCTTAAGCCTTCATCGAAGAGTGGTGAAGAAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
1719295 AT
1 AT
1719297 ATCGAGTCTG
Statistics
Matches: 703, Mismatches: 189, Indels: 130
0.69 0.18 0.13
Matches are distributed among these distances:
35 2 0.00
36 24 0.03
37 451 0.64
38 69 0.10
39 11 0.02
40 8 0.01
41 61 0.09
42 55 0.08
43 21 0.03
44 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCA
Found at i:1718539 original size:116 final size:116
Alignment explanation
Indices: 1718375--1718680 Score: 472
Period size: 116 Copynumber: 2.6 Consensus size: 116
1718365 TAAAGCAAAT
* * * *
1718375 CCATATTAAGCCTTCACCGAATAGTAGT-AAAGCAAATCAATCTTAAGCCTTCACTGATGAGTAG
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAGA-CAAATCAATCTTAAGCCTTCACTGAAGAGTAG
1718439 TGAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGG
65 TGAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGG
* *
1718491 CCATCTTAAGCCTTCACCAAAGACTAGTGAGACAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAGACAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
*
1718556 GAAGCAAATTCATCAGTAAGCTTTCCGAGCATGATGATTAAGTCCTCCGGG
66 GAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGG
* * * * *
1718607 CCAACTAAAGCCTTCACCGAAGAGTAGTGAAGA-AAATCCATCTTAAGGCTTCACCGAAGAGTAG
1 CCATCTTAAGCCTTCACCGAAGAGTAGTG-AGACAAATCAATCTTAAGCCTTCACTGAAGAGTAG
1718671 TGAAGCAAAT
65 TGAAGCAAAT
1718681 CAATCTTAAG
Statistics
Matches: 174, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
116 169 0.97
117 5 0.03
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (116 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAGACAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
GAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGG
Found at i:1718650 original size:153 final size:153
Alignment explanation
Indices: 1718491--1718833 Score: 508
Period size: 153 Copynumber: 2.2 Consensus size: 153
1718481 GTCCTCCGGG
*
1718491 CCATCTTAAGCCTTCACCAAAGACTAGTG-AGACAAATCAATCTTAAGCCTTCACTGAAGAGTAG
1 CCATCTTAAGCCTTCACCAAAGACTAGTGAAG-CAAATCAATCTTAAGCCTTCACTGAAGAGTAA
* *
1718555 TGAAGCAAATTCATCAGTAAGCTTTCCGAGCATGATGATTAAGTCCTCCGGGCCAACTAAAGCCT
65 TGAAGCAAATTCATCAGTAAACCTTCCGAGCATGATGATTAAGTCCTCCGGGCCAACTAAAGCCT
1718620 TCACCGAAGAGTAGTGAAGAAAAT
130 TCACCGAAGAGTAGTGAAGAAAAT
* * * * *
1718644 CCATCTTAAGGCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCTTTCACTGATGAGTAAT
1 CCATCTTAAGCCTTCACCAAAGACTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAAT
* * *
1718709 GAAGCAAATTCATCAGTAAACCTTCTGAGCATGATGATTAAGTCCTCCGGGCCATCTTAAGCCTT
66 GAAGCAAATTCATCAGTAAACCTTCCGAGCATGATGATTAAGTCCTCCGGGCCAACTAAAGCCTT
* *
1718774 CATCGAAGAGTAGTGAAGCAAAT
131 CACCGAAGAGTAGTGAAGAAAAT
* ** * *
1718797 CAATCTTAAGCCTTCACTGAAGAGTAGTGCAGCAAAT
1 CCATCTTAAGCCTTCACCAAAGACTAGTGAAGCAAAT
1718834 TCATCAGTAA
Statistics
Matches: 172, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
153 170 0.99
154 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (153 bp):
CCATCTTAAGCCTTCACCAAAGACTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAAT
GAAGCAAATTCATCAGTAAACCTTCCGAGCATGATGATTAAGTCCTCCGGGCCAACTAAAGCCTT
CACCGAAGAGTAGTGAAGAAAAT
Found at i:1718764 original size:116 final size:116
Alignment explanation
Indices: 1718644--1719181 Score: 806
Period size: 116 Copynumber: 4.6 Consensus size: 116
1718634 TGAAGAAAAT
* * * *
1718644 CCATCTTAAGGCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCTTTCACTGATGAGTAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
* *
1718709 GAAGCAAATTCATCAGTAAACCTTCTGAGCATGATGATTAAGTCCTCCGGG
66 GAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGG
*
1718760 CCATCTTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
* *
1718825 GCAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGAG
66 GAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGG
* * *
1718876 CCATCTTAAACCTTCACCAAAGAGTAGTGAAACAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
* * *
1718941 GAAGCAAATTCATAAGTAAGCCTTCCGAGCATGATGATTAAGTCATTCGGG
66 GAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGG
* * * *
1718992 CCATCTTAAGCCTTTACTGAAGAGTAGTGAAGCAAATCAATCTTAAGTCTTCACTAAAGAGTAGT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
* * *
1719057 AAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATAATTAAGTCCTCCGGA
66 GAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGG
* * * * * * * *
1719108 CCATCTTAAGCCTTCTCCAAATAGTACTGAAGAAAATCAATCTTAAGCCTTCGCCGAAGAGTAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
1719173 GAAGCAAAT
66 GAAGCAAAT
1719182 CCATTTTAAG
Statistics
Matches: 378, Mismatches: 44, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
116 378 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (116 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGT
GAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGGG
Found at i:1718768 original size:232 final size:232
Alignment explanation
Indices: 1718530--1719181 Score: 567
Period size: 232 Copynumber: 2.8 Consensus size: 232
1718520 AGACAAATCA
* * *
1718530 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTC-ATCAGTAAGCTTTCCGAGCATGATGAT
1 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTCAATC-GTAAGCCTT-C-A-C-TGAAGAG
** *** *
1718594 TAAGT-CCTCCGGGCCAACTA-AAGCCTT-C-A-C-CGAAGAGT-AGTGAAGAAAATCCATCTTA
61 T-AGTGCAGCAAAGCCAAC-AGAAGCCTTCCGAGCACGAAGAGTAAGT-AAGAAAAGCCATCTTA
** * * * *
1718652 AGGCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCTTTCACTGATGAGTAATGAAGCAAA
123 AACCTTCACCAAAGAGTAGTGAAACAAATCAATCTTAAGCCTTCACTGAAGAGTAATGAAGCAAA
* * *
1718717 TTCATCAGTAAACCTTCTGAGCATGATGATTAAGTCCTCCGGGCC
188 TTCATAAGTAAACCTTCCGAGCATGATGATTAAGTCATCCGGGCC
*
1718762 ATCTTAAGCCTTCA-TCGAAGAGTAGTGAAGCAAA-TCAATCTTAAGCCTTCACTGAAGAGTAGT
1 ATCTTAAGCCTTCACT-GAAGAGTAGTGAAGCAAATTCAATCGTAAGCCTTCACTGAAGAGTAGT
** * * * * ******
1718825 GCAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCGAGCCATCTTAAACCTT
65 GCAGCAAAGCCAACAG-AAGCCTTCCGAGCACGAAGAGTAAGTAAGAAAAGCCATCTTAAACCTT
*
1718890 CACCAAAGAGTAGTGAAACAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTCATA
129 CACCAAAGAGTAGTGAAACAAATCAATCTTAAGCCTTCACTGAAGAGTAATGAAGCAAATTCATA
* *
1718955 AGTAAGCCTTCCGAGCATGATGATTAAGTCATTCGGGCC
194 AGTAAACCTTCCGAGCATGATGATTAAGTCATCCGGGCC
* * * * *
1718994 ATCTTAAGCCTTTACTGAAGAGTAGTGAAGCAAA-TCAATCTTAAGTCTTCACTAAAGAGTAGTA
1 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTCAATCGTAAGCCTTCACTGAAGAGTAGTG
* ** * * * ****** *
1719058 AAGCAAATTCATCAGTAAGCCTTCCGAGCATGATA-ATTAAGT-CCTCCGGACCATCTTAAGCCT
66 CAGCAAAGCCAACAG-AAGCCTTCCGAGCACGA-AGAGTAAGTAAGAAAAG-CCATCTTAAACCT
* * * * *
1719121 TCTCCAAATAGTACTGAAGA-AAATCAATCTTAAGCCTTCGCCGAAGAGTAATGAAGCAAAT
128 TCACCAAAGAGTAGTGAA-ACAAATCAATCTTAAGCCTTCACTGAAGAGTAATGAAGCAAAT
1719182 CCATTTTAAG
Statistics
Matches: 355, Mismatches: 51, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
226 4 0.01
227 11 0.03
228 8 0.02
229 2 0.01
230 2 0.01
231 14 0.04
232 309 0.87
233 5 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (232 bp):
ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTCAATCGTAAGCCTTCACTGAAGAGTAGTG
CAGCAAAGCCAACAGAAGCCTTCCGAGCACGAAGAGTAAGTAAGAAAAGCCATCTTAAACCTTCA
CCAAAGAGTAGTGAAACAAATCAATCTTAAGCCTTCACTGAAGAGTAATGAAGCAAATTCATAAG
TAAACCTTCCGAGCATGATGATTAAGTCATCCGGGCC
Found at i:1718833 original size:269 final size:268
Alignment explanation
Indices: 1718345--1718949 Score: 980
Period size: 269 Copynumber: 2.2 Consensus size: 268
1718335 AATCAATCTA
* * * * *
1718345 AAACCTTCACCGAAGAGTAGTAAAGCAAATCCATATTAAGCCTTCACCGAATAGTAGTAAAGCAA
1 AAACCTTCACCGAAGAGTAGTGAAGAAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
* *
1718410 ATCAATCTTAAGCCTTCACTGATGAGTAGTGAAGCAAATTCATCAGTAAGCCTTCCGAGCATGAT
66 ATCAATCTTAAGCCTTCACTGATGAGTAATGAAGCAAATTCATCAGTAAACCTTCCGAGCATGAT
1718475 GATTAAGTCCTCCGGGCCATCTTAAGCCTTCACCAAAGACTAGTGAGACAAATCAATCTTAAGCC
131 GATTAAGTCCTCCGGGCCATCTTAAGCCTTCACCAAAGACTAGTGAGACAAATCAATCTTAAGCC
*
1718540 TTCACTGAAGAGTAGTGAAGCAAATTCATCAGTAAGCTTTCCGAGCATGATGATTAAGTCCTCCG
196 TTCACTGAAGAGTAGTGAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCG
*
1718605 GGCCAACT
261 AGCCAACT
*
1718613 AAAGCCTTCACCGAAGAGTAGTGAAGAAAATCCATCTTAAGGCTTCACCGAAGAGTAGTGAAGCA
1 AAA-CCTTCACCGAAGAGTAGTGAAGAAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
* *
1718678 AATCAATCTTAAGCTTTCACTGATGAGTAATGAAGCAAATTCATCAGTAAACCTTCTGAGCATGA
65 AATCAATCTTAAGCCTTCACTGATGAGTAATGAAGCAAATTCATCAGTAAACCTTCCGAGCATGA
* * *
1718743 TGATTAAGTCCTCCGGGCCATCTTAAGCCTTCATCGAAGAGTAGTGA-AGCAAATCAATCTTAAG
130 TGATTAAGTCCTCCGGGCCATCTTAAGCCTTCACCAAAGACTAGTGAGA-CAAATCAATCTTAAG
*
1718807 CCTTCACTGAAGAGTAGTGCAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTC
194 CCTTCACTGAAGAGTAGTGAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTC
*
1718872 CGAGCCATCTT
259 CGAGCCAAC-T
* * *
1718883 AAACCTTCACCAAAGAGTAGTGAA-ACAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCA
1 AAACCTTCACCGAAGAGTAGTGAAGA-AAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
1718947 AAT
65 AAT
1718950 TCATAAGTAA
Statistics
Matches: 312, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
268 5 0.02
269 303 0.97
270 4 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (268 bp):
AAACCTTCACCGAAGAGTAGTGAAGAAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
ATCAATCTTAAGCCTTCACTGATGAGTAATGAAGCAAATTCATCAGTAAACCTTCCGAGCATGAT
GATTAAGTCCTCCGGGCCATCTTAAGCCTTCACCAAAGACTAGTGAGACAAATCAATCTTAAGCC
TTCACTGAAGAGTAGTGAAGCAAATTCATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTCCG
AGCCAACT
Found at i:1719498 original size:9 final size:9
Alignment explanation
Indices: 1719477--1719509 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1719467 TAATAGTAAT
1719477 TATTATT-A
1 TATTATTAA
1719485 TATTATTAA
1 TATTATTAA
1719494 TATTATTAA
1 TATTATTAA
*
1719503 TACTATT
1 TATTATT
1719510 TATTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATTAA
Found at i:1723591 original size:18 final size:18
Alignment explanation
Indices: 1723568--1723607 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1723558 ACTTGATGGG
1723568 TTAGATTTAGATATAACT
1 TTAGATTTAGATATAACT
1723586 TTAGATTTAGATATAACT
1 TTAGATTTAGATATAACT
1723604 TTAG
1 TTAG
1723608 CTATAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (18 bp):
TTAGATTTAGATATAACT
Found at i:1725359 original size:4 final size:4
Alignment explanation
Indices: 1725318--1725583 Score: 277
Period size: 4 Copynumber: 67.0 Consensus size: 4
1725308 AGTTGTCAGG
* * * * * * *
1725318 TGTA CGTA TGTA CGTA TATA CGTA TGTA CGTT TGTA TGTA TGTG TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
1725366 TGTA TGTA TGTG TGTG TGTA TGTA TGTA TGTG TGCA TGTG TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * *
1725414 TGTA TGTA TGTA TGTA TG-- TGTG TGTA TGTG TGTG TGTA TGTG TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
1725460 TGTA TGTG TGTA TGTG TGTA TGTC TGTT TGTA TGTA TGTA TATA TAG-A
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-GTA
* *
1725508 TGTA TGTA TGTA TGTA TGTA TGTA CGTA CGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
1725556 TGTA TGTA TGTA TGTA CGTA CGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1725584 AGTACTGATT
Statistics
Matches: 218, Mismatches: 40, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.01
3 1 0.00
4 215 0.99
ACGTcount: A:0.21, C:0.04, G:0.29, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:1727009 original size:30 final size:30
Alignment explanation
Indices: 1726975--1727033 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
1726965 TCTTTCTCAA
1726975 CTTTGGATAAACAAGCTAACTGGGAATATC
1 CTTTGGATAAACAAGCTAACTGGGAATATC
1727005 CTTTGGATAAACAAGCTAACTGGGAATAT
1 CTTTGGATAAACAAGCTAACTGGGAATAT
1727034 TCCATCTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (30 bp):
CTTTGGATAAACAAGCTAACTGGGAATATC
Found at i:1733938 original size:17 final size:17
Alignment explanation
Indices: 1733918--1733989 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 17
1733908 AAGAAAAACA
1733918 AAAAAAAAAGAGCAAAG
1 AAAAAAAAAGAGCAAAG
*
1733935 AAAAACAAAGAGCAAAG
1 AAAAAAAAAGAGCAAAG
* *
1733952 -AGAAAAGA-AGCAAAG
1 AAAAAAAAAGAGCAAAG
* *
1733967 AAAGAAAAAACA-CAGAG
1 AAA-AAAAAAGAGCAAAG
1733984 AAAAAA
1 AAAAAA
1733990 GAATAAAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 7 0.16
16 9 0.20
17 28 0.62
18 1 0.02
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAGCAAAG
Found at i:1733958 original size:24 final size:24
Alignment explanation
Indices: 1733907--1733960 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1733897 AAAGAGAAGC
*
1733907 AAAGAAAAACAAAAAAAAAAGAGC
1 AAAGAAAAACAAAAAAAAAAGAGA
* **
1733931 AAAGAAAAACAAAGAGCAAAGAGA
1 AAAGAAAAACAAAAAAAAAAGAGA
1733955 AAAGAA
1 AAAGAA
1733961 GCAAAGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (24 bp):
AAAGAAAAACAAAAAAAAAAGAGA
Found at i:1733990 original size:32 final size:32
Alignment explanation
Indices: 1733916--1734001 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
1733906 CAAAGAAAAA
* * *
1733916 CAAAAAAAAAAG-AGCAAAGAAAAACAAAGAG
1 CAAAGAAAAAAGAAGCAAAGAAAAAAAAACAG
*
1733947 CAAAGAGAAAAGAAGCAAAGAAAGAAAAAACA-
1 CAAAGAAAAAAGAAGCAAAGAAA-AAAAAACAG
* *
1733979 CAGAGAAAAAAGAA-TAAAGAAAA
1 CAAAGAAAAAAGAAGCAAAGAAAA
1734002 TGGATCAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 1 0.02
31 17 0.37
32 22 0.48
33 6 0.13
ACGTcount: A:0.73, C:0.08, G:0.17, T:0.01
Consensus pattern (32 bp):
CAAAGAAAAAAGAAGCAAAGAAAAAAAAACAG
Found at i:1734898 original size:25 final size:24
Alignment explanation
Indices: 1734858--1734919 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
1734848 GGGGCAATAT
1734858 TTTTTCAAAATTTTTT-ATTAAACA
1 TTTTTCAAAATTTTTTAATT-AACA
*
1734882 TTTTTCAAAATTCTTTTAATTAATA
1 TTTTTCAAAATT-TTTTAATTAACA
1734907 TTTTT-AAAATTTT
1 TTTTTCAAAATTTT
1734920 GAAAATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
23 2 0.06
24 18 0.51
25 12 0.34
26 3 0.09
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTTCAAAATTTTTTAATTAACA
Found at i:1735366 original size:77 final size:77
Alignment explanation
Indices: 1735276--1735424 Score: 185
Period size: 77 Copynumber: 1.9 Consensus size: 77
1735266 AATTAATAAA
* *
1735276 TAAAATATTATTTAATTAATTCAAAA-TATATATATATTAAAGACTTATAATCTAAATTGCAATC
1 TAAAATATTATTTAATT-ATACAAAATTATATATA-ATTAAAGACTTATAATCTAAATTACAATC
1735340 -TTTAATGTTTATT
64 TTTTAATGTTTATT
* * * * * *
1735353 TAAAATTTTATTTAATTATACCAAATTATATATCAATTAAATAGTTGTAATCTAAATTACATTCT
1 TAAAATATTATTTAATTATACAAAATTATATAT-AATTAAAGACTTATAATCTAAATTACAATCT
1735418 TTTAATG
65 TTTAATG
1735425 CATACTTACT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
76 6 0.10
77 47 0.77
78 8 0.13
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (77 bp):
TAAAATATTATTTAATTATACAAAATTATATATAATTAAAGACTTATAATCTAAATTACAATCTT
TTAATGTTTATT
Found at i:1736621 original size:16 final size:16
Alignment explanation
Indices: 1736586--1736619 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1736576 ATTTTTGCTA
*
1736586 TTTAACTTTATGCACT
1 TTTAAATTTATGCACT
1736602 TTTAAATTTATGC-CT
1 TTTAAATTTATGCACT
1736617 TTT
1 TTT
1736620 TATTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAAATTTATGCACT
Found at i:1738453 original size:29 final size:29
Alignment explanation
Indices: 1738404--1738464 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1738394 TTTATACAAT
1738404 AAATAATTTTCAAGTAATTATTTT-CTATA
1 AAATAATTTTCAAGTAATTATTTTAC-ATA
1738433 AAATAATTTT--AGATAATTTATTTTACATA
1 AAATAATTTTCAAG-TAA-TTATTTTACATA
1738462 AAA
1 AAA
1738465 CATTATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 2 0.07
28 3 0.10
29 23 0.79
30 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (29 bp):
AAATAATTTTCAAGTAATTATTTTACATA
Found at i:1751098 original size:90 final size:90
Alignment explanation
Indices: 1750945--1751125 Score: 362
Period size: 90 Copynumber: 2.0 Consensus size: 90
1750935 ACACCTAAGA
1750945 GTGTTTGGAACAAACTTAAAGAAACTAATGAAGGAGGTGATAGAGTAAACAAAAGCAAAGCTCTT
1 GTGTTTGGAACAAACTTAAAGAAACTAATGAAGGAGGTGATAGAGTAAACAAAAGCAAAGCTCTT
1751010 GACTCTGAAAAAAGTTTTCTATGCT
66 GACTCTGAAAAAAGTTTTCTATGCT
1751035 GTGTTTGGAACAAACTTAAAGAAACTAATGAAGGAGGTGATAGAGTAAACAAAAGCAAAGCTCTT
1 GTGTTTGGAACAAACTTAAAGAAACTAATGAAGGAGGTGATAGAGTAAACAAAAGCAAAGCTCTT
1751100 GACTCTGAAAAAAGTTTTCTATGCT
66 GACTCTGAAAAAAGTTTTCTATGCT
1751125 G
1 G
1751126 CAGCTGAAGG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (90 bp):
GTGTTTGGAACAAACTTAAAGAAACTAATGAAGGAGGTGATAGAGTAAACAAAAGCAAAGCTCTT
GACTCTGAAAAAAGTTTTCTATGCT
Found at i:1753973 original size:27 final size:27
Alignment explanation
Indices: 1753939--1754054 Score: 94
Period size: 28 Copynumber: 4.2 Consensus size: 27
1753929 AACAAACCGA
*
1753939 GGAA-AAATATCATACATAACAGAT-GG
1 GGAACAAATA-CATACATAACAGATCAG
* * *
1753965 GGAACAAATCCCATACAGAACATATCAG
1 GGAACAAAT-ACATACATAACAGATCAG
* *
1753993 GAAACAAATGACATACATAACAGATCAA
1 GGAACAAAT-ACATACATAACAGATCAG
* *
1754021 GGAACAAA-ACCCACACATAACAGATCAA
1 GGAACAAATA--CATACATAACAGATCAG
1754049 GGAACA
1 GGAACA
1754055 CACCCATGAA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
26 5 0.07
27 16 0.22
28 52 0.71
ACGTcount: A:0.52, C:0.21, G:0.15, T:0.13
Consensus pattern (27 bp):
GGAACAAATACATACATAACAGATCAG
Found at i:1764583 original size:39 final size:39
Alignment explanation
Indices: 1764540--1764623 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
1764530 GGGTAAGTCT
* * *
1764540 TTACTGTAGACTCCTCTGCTTTGTGCACATGATAAGACC
1 TTACTGCAGACTCCTCTGCTTTATGCACAGGATAAGACC
* * *
1764579 TTACTGCAGGCTCCTCTGCTTTATGCACAGGTTAAGTCC
1 TTACTGCAGACTCCTCTGCTTTATGCACAGGATAAGACC
1764618 TTACTG
1 TTACTG
1764624 GGTGTACATG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (39 bp):
TTACTGCAGACTCCTCTGCTTTATGCACAGGATAAGACC
Found at i:1764834 original size:13 final size:13
Alignment explanation
Indices: 1764816--1764841 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1764806 ATTCAGACTA
1764816 TAGCAGACTAGGC
1 TAGCAGACTAGGC
1764829 TAGCAGACTAGGC
1 TAGCAGACTAGGC
1764842 ATCAGGAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (13 bp):
TAGCAGACTAGGC
Found at i:1764996 original size:38 final size:38
Alignment explanation
Indices: 1764952--1765025 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
1764942 CTGTATTATC
* * *
1764952 GGTATTTTGTTCCGTAAATGTTTTATACGGTTTTCTAT
1 GGTATTTTGATACGTAAATGTTTTATACAGTTTTCTAT
* * *
1764990 GGTATTTTGATATGTATATGTTTTATGCAGTTTTCT
1 GGTATTTTGATACGTAAATGTTTTATACAGTTTTCT
1765026 GACATATGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (38 bp):
GGTATTTTGATACGTAAATGTTTTATACAGTTTTCTAT
Found at i:1774894 original size:20 final size:19
Alignment explanation
Indices: 1774865--1774914 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
1774855 TGGGCCTGAC
*
1774865 GATATCGATACTAAGCCT-AT
1 GATATTGATACT-A-CCTAAT
1774885 GATATTGATACTACCTAAT
1 GATATTGATACTACCTAAT
1774904 GAGTATTGATA
1 GA-TATTGATA
1774915 ATTCCCTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 5 0.19
20 19 0.70
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATTGATACTACCTAAT
Found at i:1785395 original size:14 final size:14
Alignment explanation
Indices: 1785378--1785410 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1785368 GTTATTTACT
1785378 TATTTT-CTCTTCTC
1 TATTTTACT-TTCTC
1785392 TATTTTACTTTCTC
1 TATTTTACTTTCTC
1785406 TATTT
1 TATTT
1785411 CCAGTTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTACTTTCTC
Found at i:1796710 original size:105 final size:105
Alignment explanation
Indices: 1796556--1797397 Score: 1277
Period size: 105 Copynumber: 8.1 Consensus size: 105
1796546 GGAGGATATC
* *
1796556 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAACAAATTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
1796621 ATTTCGGGGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1796661 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACAGCTAGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* * * *
1796726 ATTTTAGAGCCGATTTCAACTTCACAGCAAAAGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1796766 ACTCCAGACAACGTAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGT---CAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
1796828 ATTTCGGAGCCGATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1796868 ACTCCAGACAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1796933 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1796973 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
** * * * *
1797038 ATTTTGGAGCCGATTTCAACTTCACAGCAAAGAATATCGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1797078 ACTCCAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
1797143 ATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1797183 ATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
1797248 ATTTCAGAGCTAATTTCAACTTCCCAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
1797288 ACTTCAGACAACGCAAGTTCAACTTCATGACGAAGGGACTGCTGGTTGTTAAC-A-AAGTT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* * * *
1797349 A-TTCAGAGTCAATTTTAACTTCACAGTGAAGGATATTAG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1797388 ACTCGAGACA
1 ACTCCAGACA
1797398 GCACAAACTT
Statistics
Matches: 672, Mismatches: 62, Indels: 11
0.90 0.08 0.01
Matches are distributed among these distances:
100 40 0.06
101 1 0.00
102 96 0.14
103 4 0.01
104 1 0.00
105 530 0.79
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1797121 original size:312 final size:313
Alignment explanation
Indices: 1796556--1797342 Score: 1317
Period size: 312 Copynumber: 2.5 Consensus size: 313
1796546 GGAGGATATC
* *
1796556 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAACAAATTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
1796621 ATTTCGGGGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
*
1796686 CACGACGAAGGGACAGCTAGTTGTCAACAACAACTTCCCAATTTTAGAGCCGATTTCAACTTCAC
131 CACGACGAAGGGACAGCTGGTTGTCAACAACAACTTCCCAATTTTAGAGCCGATTTCAACTTCAC
* * *
1796751 AGCAAAAGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGT-
196 AGCAAAAGATATCGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTA
* * *
1796815 CAACAACTTCCCAATTTCGGAGCCGATTTCAACTTCACAGCGAAGGATATTGG
261 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
*
1796868 ACTCCAGACAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1796933 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* * * *
1796998 CACGACGAAGGGACCGTTGGTTGTCAATAACAACTTCCCAATTTTGGAGCCGATTTCAACTTCAC
131 CACGACGAAGGGACAGCTGGTTGTCAACAACAACTTCCCAATTTTAGAGCCGATTTCAACTTCAC
*
1797063 AGC-AAAGAATATCGGACTCCAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
196 AGCAAAAG-ATATCGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
1797127 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
260 --ACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
*
1797183 ATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* * *
1797248 ATTTCAGAGCTAATTTCAACTTCCCAGCGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTT
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* * *
1797313 CATGACGAAGGGACTGCTGGTTGTTAACAA
131 CACGACGAAGGGACAGCTGGTTGTCAACAA
1797343 AGTTTCATTC
Statistics
Matches: 444, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
311 4 0.01
312 240 0.54
315 200 0.45
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (313 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACAGCTGGTTGTCAACAACAACTTCCCAATTTTAGAGCCGATTTCAACTTCAC
AGCAAAAGATATCGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTA
CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
Found at i:1799529 original size:14 final size:14
Alignment explanation
Indices: 1799512--1799544 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1799502 GTTATTTACT
1799512 TATTTT-CTCTTCTC
1 TATTTTACT-TTCTC
1799526 TATTTTACTTTCTC
1 TATTTTACTTTCTC
1799540 TATTT
1 TATTT
1799545 CCAGTTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTACTTTCTC
Found at i:1810313 original size:23 final size:23
Alignment explanation
Indices: 1810262--1810313 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1810252 ATGTGGCAAC
* *
1810262 AAATGGAGATGTTGTGGCAAAAT
1 AAATGGAGATGTCGTGACAAAAT
** *
1810285 GGATGGAGATGTCGTGACAAATT
1 AAATGGAGATGTCGTGACAAAAT
1810308 AAATGG
1 AAATGG
1810314 TGTTTAGTGC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.25
Consensus pattern (23 bp):
AAATGGAGATGTCGTGACAAAAT
Found at i:1813831 original size:20 final size:20
Alignment explanation
Indices: 1813802--1813844 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1813792 ATTCCACCAC
* *
1813802 ATGCAACTATATGCTGCTAA
1 ATGCAACTATATGATCCTAA
*
1813822 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
1813842 ATG
1 ATG
1813845 GCCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1816044 original size:22 final size:22
Alignment explanation
Indices: 1816018--1816089 Score: 99
Period size: 22 Copynumber: 3.3 Consensus size: 22
1816008 TAGCCTTCAT
*
1816018 GGGTATTGATACCCTTTCATAG
1 GGGTATTGATACCCATTCATAG
* * * *
1816040 GGGTATCGGTACCCATTCTTGG
1 GGGTATTGATACCCATTCATAG
1816062 GGGTATTGATACCCATTCATAG
1 GGGTATTGATACCCATTCATAG
1816084 GGGTAT
1 GGGTAT
1816090 CGGTACCTCT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (22 bp):
GGGTATTGATACCCATTCATAG
Found at i:1824368 original size:22 final size:22
Alignment explanation
Indices: 1824342--1824415 Score: 121
Period size: 22 Copynumber: 3.3 Consensus size: 22
1824332 AGCCTTTATG
*
1824342 GGGGTATTGATACCCTTTCATA
1 GGGGTATTGATACCCATTCATA
*
1824364 GGGGTATTGGTACCCATTCATA
1 GGGGTATTGATACCCATTCATA
1824386 GGGGGTATTGATACCCATTCATA
1 -GGGGTATTGATACCCATTCATA
1824409 GGGGTAT
1 GGGGTAT
1824416 CAGTATCTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 27 0.56
23 21 0.44
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (22 bp):
GGGGTATTGATACCCATTCATA
Found at i:1824394 original size:23 final size:23
Alignment explanation
Indices: 1824341--1824412 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1824331 GAGCCTTTAT
*
1824341 GGGGGTATTGATACCCTTTCATA
1 GGGGGTATTGATACCCATTCATA
*
1824364 -GGGGTATTGGTACCCATTCATA
1 GGGGGTATTGATACCCATTCATA
1824386 GGGGGTATTGATACCCATTCATA
1 GGGGGTATTGATACCCATTCATA
1824409 GGGG
1 GGGG
1824413 TATCAGTATC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 20 0.44
23 25 0.56
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (23 bp):
GGGGGTATTGATACCCATTCATA
Found at i:1825889 original size:43 final size:43
Alignment explanation
Indices: 1825818--1825918 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 43
1825808 TGCATTATCA
* *
1825818 CAAAATAAAAATTAGGAAATAAGTTGGAAAGCTAGTAATAGCTC
1 CAAAAT-AGAATTAGGAAATAAGTTGGAAAGATAGTAATAGCTC
* * * *
1825862 CAACATAGTATTAGGAAATAAGTTGGAAAGATGGTAATTGCTC
1 CAAAATAGAATTAGGAAATAAGTTGGAAAGATAGTAATAGCTC
*
1825905 TAAAATAGAATTAG
1 CAAAATAGAATTAG
1825919 ACATATTACC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
43 43 0.90
44 5 0.10
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.26
Consensus pattern (43 bp):
CAAAATAGAATTAGGAAATAAGTTGGAAAGATAGTAATAGCTC
Found at i:1827567 original size:31 final size:30
Alignment explanation
Indices: 1827532--1827598 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1827522 AACTGCTACA
* * *
1827532 CATTATCTAAATGTGAACCTTACATATTGTG
1 CATTATCTAAATG-CAACATGACATATTGTG
* *
1827563 CATTATTTGAATGCAACATGACATATTGTG
1 CATTATCTAAATGCAACATGACATATTGTG
1827593 CATTAT
1 CATTAT
1827599 TTGCATGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (30 bp):
CATTATCTAAATGCAACATGACATATTGTG
Found at i:1828671 original size:21 final size:21
Alignment explanation
Indices: 1828645--1828698 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1828635 AAAGTGAGTC
1828645 GTATCGATACCCTGGGGTCAA
1 GTATCGATACCCTGGGGTCAA
1828666 GTATCGATACCCTGGGGTCAA
1 GTATCGATACCCTGGGGTCAA
1828687 GTATCGATACCC
1 GTATCGATACCC
1828699 CTATGAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (21 bp):
GTATCGATACCCTGGGGTCAA
Found at i:1842271 original size:18 final size:18
Alignment explanation
Indices: 1842243--1842292 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
1842233 CAAGAGTTGA
1842243 GGGATTATAGTGGTCCTTC
1 GGGA-TATAGTGGTCCTTC
1842262 GGGATATAGTGGTCCTTC
1 GGGATATAGTGGTCCTTC
* *
1842280 AGGACATAGTGGT
1 GGGATATAGTGGT
1842293 TATTCGGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.32
Consensus pattern (18 bp):
GGGATATAGTGGTCCTTC
Done.