Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 166 of 255
Found at i:54426533 original size:37 final size:37
Alignment explanation
Indices: 54426478--54426564 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
54426468 CACAAGTAGG
* ** *
54426478 CCAACCGA-AACACGCCAAACGCTCATAAGTGGTAAT
1 CCAACCGATAACACGCCAAACACTCATAAAAGCTAAT
* *
54426514 CCAACCAATAACATGCCAAACACTCATAAAAGCTAAT
1 CCAACCGATAACACGCCAAACACTCATAAAAGCTAAT
54426551 CCAACCGATAACAC
1 CCAACCGATAACAC
54426565 ACCTATTTAC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 7 0.17
37 35 0.83
ACGTcount: A:0.44, C:0.32, G:0.10, T:0.14
Consensus pattern (37 bp):
CCAACCGATAACACGCCAAACACTCATAAAAGCTAAT
Found at i:54431515 original size:8 final size:8
Alignment explanation
Indices: 54431502--54431535 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
54431492 AGTCCCTAAT
54431502 TCACAAAA
1 TCACAAAA
54431510 TCACAAAA
1 TCACAAAA
*
54431518 TCAAAAAA
1 TCACAAAA
54431526 TACACAAAA
1 T-CACAAAA
54431535 T
1 T
54431536 TTCCTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.65, C:0.21, G:0.00, T:0.15
Consensus pattern (8 bp):
TCACAAAA
Found at i:54448490 original size:44 final size:44
Alignment explanation
Indices: 54448442--54448530 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
54448432 TATATACACA
54448442 ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
1 ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
54448486 ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
1 ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
54448530 A
1 A
54448531 AACCTATCAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (44 bp):
ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
Found at i:54451832 original size:28 final size:25
Alignment explanation
Indices: 54451801--54451860 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
54451791 TTCCATATTA
*
54451801 TCACATCATTTCATATACTATTATCAAT
1 TCACATCATTT--TATACCATT-TCAAT
54451829 TCACA--ATTTTATACCATTTCAAT
1 TCACATCATTTTATACCATTTCAAT
*
54451852 TCAAATCAT
1 TCACATCAT
54451861 ACATTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 9 0.32
24 8 0.29
25 2 0.07
26 4 0.14
28 5 0.18
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
TCACATCATTTTATACCATTTCAAT
Found at i:54464217 original size:7 final size:7
Alignment explanation
Indices: 54464207--54464231 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54464197 AGAAAAAGAG
54464207 AAAAAAT
1 AAAAAAT
54464214 AAAAAAT
1 AAAAAAT
54464221 AAAAAAT
1 AAAAAAT
54464228 AAAA
1 AAAA
54464232 TAAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:54467463 original size:25 final size:25
Alignment explanation
Indices: 54467435--54467504 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
54467425 CTCTTTTAAT
*
54467435 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
54467460 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
54467485 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
54467505 AGCACTTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:54467739 original size:27 final size:27
Alignment explanation
Indices: 54467709--54467775 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
54467699 GGGGCAAAAT
**
54467709 GGTAATTTTACCCCGCAAGGGTATCTC
1 GGTAATTTTACCCCAAAAGGGTATCTC
* * *
54467736 GGTAATTCTACCCTAAAAGGGTATTTC
1 GGTAATTTTACCCCAAAAGGGTATCTC
*
54467763 GATAATTTTACCC
1 GGTAATTTTACCC
54467776 TACAGGGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (27 bp):
GGTAATTTTACCCCAAAAGGGTATCTC
Found at i:54467776 original size:27 final size:27
Alignment explanation
Indices: 54467724--54467849 Score: 173
Period size: 27 Copynumber: 4.7 Consensus size: 27
54467714 TTTTACCCCG
* **
54467724 CAAGGGTATCTCGGTAATTCTACCCTA
1 CAAGGGTATTTCAATAATTCTACCCTA
* * *
54467751 AAAGGGTATTTCGATAATTTTACCCTA
1 CAAGGGTATTTCAATAATTCTACCCTA
*
54467778 CAGGGGTATTTCAATAATTCTACCCTA
1 CAAGGGTATTTCAATAATTCTACCCTA
*
54467805 C-AGGGTATTTCCATAATTCTACCCTA
1 CAAGGGTATTTCAATAATTCTACCCTA
54467831 CAAGGGTATTTCAATAATT
1 CAAGGGTATTTCAATAATT
54467850 TTGTAAATCA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
26 24 0.28
27 63 0.72
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (27 bp):
CAAGGGTATTTCAATAATTCTACCCTA
Found at i:54467829 original size:53 final size:54
Alignment explanation
Indices: 54467724--54467849 Score: 182
Period size: 53 Copynumber: 2.4 Consensus size: 54
54467714 TTTTACCCCG
* ** * *
54467724 CAAGGGTATCTCGGTAATTCTACCCTAAAAGGGTATTTCGATAATTTTACCCTA
1 CAAGGGTATTTCAATAATTCTACCCTAAAAGGGTATTTCCATAATTCTACCCTA
* *
54467778 CAGGGGTATTTCAATAATTCTACCCT-ACAGGGTATTTCCATAATTCTACCCTA
1 CAAGGGTATTTCAATAATTCTACCCTAAAAGGGTATTTCCATAATTCTACCCTA
54467831 CAAGGGTATTTCAATAATT
1 CAAGGGTATTTCAATAATT
54467850 TTGTAAATCA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 42 0.66
54 22 0.34
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (54 bp):
CAAGGGTATTTCAATAATTCTACCCTAAAAGGGTATTTCCATAATTCTACCCTA
Found at i:54467861 original size:27 final size:27
Alignment explanation
Indices: 54467831--54468182 Score: 262
Period size: 27 Copynumber: 13.0 Consensus size: 27
54467821 TTCTACCCTA
** **
54467831 CAAGGGTATTTCAATAATTTTGTAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAT
*** **
54467858 CAAGGGTAAAACGGTAATTTTGTAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAT
** *
54467885 TTAGGGTACTTT-GGTAATTTTTACAAGT
1 CAAGGGTA-TTTCGGTAA-TTTTACAAAT
* * * *
54467913 CGAGAGTATTTCAGTAATTTTAAAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAT
** **
54467940 TGAGGGTATTTTAGTAATTTTACAAA-
1 CAAGGGTATTTCGGTAATTTTACAAAT
* *
54467966 CTGAGGGTATTTCGATAATTTTACAAAT
1 C-AAGGGTATTTCGGTAATTTTACAAAT
* *
54467994 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAT
* * ** *
54468021 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAT
* *
54468048 CAAGGGTATTTTGGTAATTTTACAAGT
1 CAAGGGTATTTCGGTAATTTTACAAAT
* *
54468075 CAAGGGTATTTCAGTAATTTCACAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAT
* *
54468102 CAGGGGTATTTTGGT-ATTTTCACAAA-
1 CAAGGGTATTTCGGTAATTTT-ACAAAT
* * *
54468128 CTAGGGGTATTTTGGTAATTTTACAAAC
1 C-AAGGGTATTTCGGTAATTTTACAAAT
* **
54468156 CAACGGTATTTTAGTAATTTTACAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAT
54468183 TGAGGGCATT
Statistics
Matches: 265, Mismatches: 51, Indels: 18
0.79 0.15 0.05
Matches are distributed among these distances:
26 5 0.02
27 237 0.89
28 23 0.09
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTCGGTAATTTTACAAAT
Found at i:54468026 original size:81 final size:80
Alignment explanation
Indices: 54467886--54468202 Score: 359
Period size: 81 Copynumber: 3.9 Consensus size: 80
54467876 TTTGTAAATT
* * * * * *
54467886 TAGGGTACTTTGGTAATTTTTACAAGTCGAGAGTATTTCAGTAATTTTAAAAATTGAGGGTATTT
1 TAGGGTATTTTGGTAA-TTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTT
54467951 TAGTAATTTTACAAAC
65 TAGTAATTTTACAAAC
* * ** *
54467967 TGAGGGTATTTCGATAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACCGAGGGTATTT
1 T-AGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTT
* **
54468032 TGGTAATTTTGTAAACC
65 TAGTAATTTTACAAA-C
* * *
54468049 AAGGGTATTTTGGTAATTTTACAAGTCAAGGGTATTTCAGTAATTTCACAAATC-AGGGGTATTT
1 TAGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGA-GGGTATTT
*
54468113 TGGT-ATTTTCACAAAC
65 TAGTAATTTT-ACAAAC
* * * * *
54468129 TAGGGGTATTTTGGTAATTTTACAAACCAACGGTATTTTAGTAATTTTACAAATTGAGGGCATTT
1 TA-GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTT
54468194 TAGTAATTT
65 TAGTAATTT
54468203 GGTAAACTAA
Statistics
Matches: 196, Mismatches: 33, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
80 8 0.04
81 170 0.87
82 18 0.09
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (80 bp):
TAGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTT
AGTAATTTTACAAAC
Found at i:54468193 original size:27 final size:27
Alignment explanation
Indices: 54467918--54468202 Score: 268
Period size: 27 Copynumber: 10.6 Consensus size: 27
54467908 CAAGTCGAGA
* * ***
54467918 GTATTTCAGTAATTTTAAAAATTGAGG
1 GTATTTTAGTAATTTTACAAACCAAGG
**
54467945 GTATTTTAGTAATTTTACAAACTGAGG
1 GTATTTTAGTAATTTTACAAACCAAGG
* *
54467972 GTA-TTTCGATAATTTTACAAATCAAGG
1 GTATTTTAG-TAATTTTACAAACCAAGG
* *
54467999 GTATTTTGGTAATTTTACAAACCGAGG
1 GTATTTTAGTAATTTTACAAACCAAGG
* **
54468026 GTATTTTGGTAATTTTGTAAACCAAGG
1 GTATTTTAGTAATTTTACAAACCAAGG
* **
54468053 GTATTTTGGTAATTTTACAAGTCAAGG
1 GTATTTTAGTAATTTTACAAACCAAGG
* * * *
54468080 GTATTTCAGTAATTTCACAAATCAGGG
1 GTATTTTAGTAATTTTACAAACCAAGG
* * *
54468107 GTATTTTGGT-ATTTTCACAAACTAGGG
1 GTATTTTAGTAATTTT-ACAAACCAAGG
* *
54468134 GTATTTTGGTAATTTTACAAACCAACG
1 GTATTTTAGTAATTTTACAAACCAAGG
***
54468161 GTATTTTAGTAATTTTACAAATTGAGG
1 GTATTTTAGTAATTTTACAAACCAAGG
*
54468188 GCATTTTAGTAATTT
1 GTATTTTAGTAATTT
54468203 GGTAAACTAA
Statistics
Matches: 218, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
26 8 0.04
27 201 0.92
28 9 0.04
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
GTATTTTAGTAATTTTACAAACCAAGG
Found at i:54468194 original size:54 final size:54
Alignment explanation
Indices: 54467887--54468202 Score: 307
Period size: 54 Copynumber: 5.8 Consensus size: 54
54467877 TTGTAAATTT
* * * ** * ***
54467887 AGGGTACTTTGGTAATTTTTAC-AAGTCGAGAGTATTTCAGTAATTTTAAAAATTG
1 AGGGTATTTTGGTAA-TTTTACAAACT-GAGGGTATTTTGGTAATTTTACAAACCA
* * * *
54467942 AGGGTATTTTAGTAATTTTACAAACTGAGGGTATTTCGATAATTTTACAAATCA
1 AGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTTGGTAATTTTACAAACCA
* **
54467996 AGGGTATTTTGGTAATTTTACAAACCGAGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTTGGTAATTTTACAAACCA
* * ** * *
54468050 AGGGTATTTTGGTAATTTTAC-AAGTCAAGGGTATTTCAGTAATTTCACAAATCA
1 AGGGTATTTTGGTAATTTTACAAACT-GAGGGTATTTTGGTAATTTTACAAACCA
*
54468104 GGGGTATTTTGGT-ATTTTCACAAACT-AGGGGTATTTTGGTAATTTTACAAACCA
1 AGGGTATTTTGGTAATTTT-ACAAACTGA-GGGTATTTTGGTAATTTTACAAACCA
* * * * *
54468158 ACGGTATTTTAGTAATTTTACAAATTGAGGGCATTTTAGTAATTT
1 AGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTTGGTAATTT
54468203 GGTAAACTAA
Statistics
Matches: 217, Mismatches: 37, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
53 8 0.04
54 184 0.85
55 25 0.12
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTTGGTAATTTTACAAACCA
Found at i:54470845 original size:16 final size:16
Alignment explanation
Indices: 54470801--54470853 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 16
54470791 GTGTTCTTGG
54470801 TTCTTTTG-ATTTTTT
1 TTCTTTTGTATTTTTT
* *
54470816 TTATTTTAATTATTTTTT
1 TTCTTTT--GTATTTTTT
54470834 TTCTTTTGTATTTTTT
1 TTCTTTTGTATTTTTT
54470850 TTCT
1 TTCT
54470854 CTTCTCGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 6 0.19
16 12 0.39
18 13 0.42
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (16 bp):
TTCTTTTGTATTTTTT
Found at i:54471883 original size:60 final size:60
Alignment explanation
Indices: 54471814--54471937 Score: 212
Period size: 60 Copynumber: 2.1 Consensus size: 60
54471804 GTCATTATCA
*
54471814 ATATGCTATCATTATTCTCATCAATGTATTGTCATCATTAGTTTCTATTTTATTATTATT
1 ATATGCTATCATTATTCTCATCAATGTATTGTCATCATTAGTCTCTATTTTATTATTATT
* * *
54471874 ATATGCTATCATTATTCTCATTAATGTATTGTGATTATTAGTCTCTATTTTATTATTATT
1 ATATGCTATCATTATTCTCATCAATGTATTGTCATCATTAGTCTCTATTTTATTATTATT
54471934 ATAT
1 ATAT
54471938 TATTACTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.54
Consensus pattern (60 bp):
ATATGCTATCATTATTCTCATCAATGTATTGTCATCATTAGTCTCTATTTTATTATTATT
Found at i:54472150 original size:27 final size:26
Alignment explanation
Indices: 54472039--54472191 Score: 120
Period size: 24 Copynumber: 6.0 Consensus size: 26
54472029 TACCATTATT
* *
54472039 ATTATCATATATTTTATATTATTTT--
1 ATTATTATATATATTAT-TTATTTTAA
* * *
54472064 ATT-TTACATATGTTATTTCTTTTAA
1 ATTATTATATATATTATTTATTTTAA
* * *
54472089 ACTATTATACATATTGTTTATTTTGAA
1 ATTATTATATATATTATTTATTTT-AA
* *
54472116 ACTT-TTATATACATTTTTGTATTTTAA
1 A-TTATTATATATATTATT-TATTTTAA
* *
54472143 ATTATTATGTATATTATTTACTTT-A
1 ATTATTATATATATTATTTATTTTAA
54472168 A-TATTATATATATTATTTATTTTA
1 ATTATTATATATATTATTTATTTTA
54472192 GACCTTTTTA
Statistics
Matches: 100, Mismatches: 20, Indels: 16
0.74 0.15 0.12
Matches are distributed among these distances:
23 6 0.06
24 30 0.30
25 7 0.07
26 22 0.22
27 28 0.28
28 7 0.07
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (26 bp):
ATTATTATATATATTATTTATTTTAA
Found at i:54472400 original size:20 final size:22
Alignment explanation
Indices: 54472360--54472402 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54472350 TACTTAGTCA
54472360 AAATTGTTTAATCATTTATTTC
1 AAATTGTTTAATCATTTATTTC
*
54472382 AAATTGTTTTAT-A-TTATTTC
1 AAATTGTTTAATCATTTATTTC
54472402 A
1 A
54472403 TTCTTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (22 bp):
AAATTGTTTAATCATTTATTTC
Found at i:54473603 original size:47 final size:47
Alignment explanation
Indices: 54473532--54473934 Score: 698
Period size: 47 Copynumber: 8.6 Consensus size: 47
54473522 CCCTTCGGGA
* * * * * *
54473532 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
54473579 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54473626 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54473673 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54473720 CTTATCACATATATACACTTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54473767 CTTATCACATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54473814 CTTATCACATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54473861 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54473908 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
54473935 TATTCAACTA
Statistics
Matches: 344, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 344 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54473610 original size:25 final size:25
Alignment explanation
Indices: 54473582--54473660 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
54473572 ACTCGGCCCT
54473582 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
54473607 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
54473629 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
54473654 ATCACAT
1 ATCACAT
54473661 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:54477476 original size:28 final size:28
Alignment explanation
Indices: 54477444--54477500 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
54477434 CCTTCGTTCC
54477444 ATACGAGGTCTTACATGAATCTTGTTTT
1 ATACGAGGTCTTACATGAATCTTGTTTT
54477472 ATACGAGGTCTTACATGAATCTTGTTTT
1 ATACGAGGTCTTACATGAATCTTGTTTT
54477500 A
1 A
54477501 CTCACTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (28 bp):
ATACGAGGTCTTACATGAATCTTGTTTT
Found at i:54477825 original size:39 final size:40
Alignment explanation
Indices: 54477782--54478128 Score: 515
Period size: 40 Copynumber: 8.8 Consensus size: 40
54477772 CCAGCATGAT
* * * *
54477782 TGCTCTTCGGGACCTAG-CCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * * *
54477821 TGCTCTTCGGG-TTTAGCACGGATATATCACTAGTATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
54477860 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
54477900 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCGCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
54477940 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
54477980 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
54478020 TGCTCTTC-GGACTTAG-CCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
54478058 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
54478097 TGCTCTTCGGGACTTAGCCCAGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
54478129 CTCAATTCTC
Statistics
Matches: 281, Mismatches: 23, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
38 40 0.14
39 75 0.27
40 166 0.59
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:54479611 original size:47 final size:47
Alignment explanation
Indices: 54479542--54479668 Score: 202
Period size: 47 Copynumber: 2.7 Consensus size: 47
54479532 CTTCGGGACT
* * *
54479542 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGCCC
* *
54479589 TATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCT
1 TATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGCCC
54479636 TATCACATATATACACTTTCACATTCATC-CATT
1 TATCACATATATACACTTTCACATTCATCACATT
54479669 TACATTTCAT
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 4 0.05
47 71 0.95
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGCCC
Found at i:54479819 original size:122 final size:136
Alignment explanation
Indices: 54479674--54479942 Score: 404
Period size: 122 Copynumber: 2.1 Consensus size: 136
54479664 CCATTTACAT
54479674 TTCATTCATCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC-A
1 TTCATTCATCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
54479738 TTA-G-C-TATCACATATAT-CAC-TCAC-TC-C-AT-GCATTAG-CTTATCACATATATACAC-
66 TTAGGCCTTATCACATATATACACTTCACATCACAATGGCATTAGCCTTATCACATATATACACT
54479792 TTCACA
131 TTCACA
54479798 TTCA-TCA-CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
1 TTCATTCATCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
54479861 TTAGGCCTTATCACATATATACACTTTCACATTCATCAATGGCATTAGCCTTATCACATATATAC
66 TTAGGCCTTATCACATATATACAC-TTCACA-TCA-CAATGGCATTAGCCTTATCACATATATAC
54479926 ACTTTCACA
128 ACTTTCACA
*
54479935 TTTATTCA
1 TTCATTCA
54479943 ACTATACTTC
Statistics
Matches: 128, Mismatches: 1, Indels: 18
0.87 0.01 0.12
Matches are distributed among these distances:
122 54 0.42
123 7 0.05
124 5 0.04
125 1 0.01
126 12 0.09
127 3 0.02
129 4 0.03
131 2 0.02
133 1 0.01
134 2 0.02
135 7 0.05
136 18 0.14
137 9 0.07
138 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.34
Consensus pattern (136 bp):
TTCATTCATCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
TTAGGCCTTATCACATATATACACTTCACATCACAATGGCATTAGCCTTATCACATATATACACT
TTCACA
Found at i:54479858 original size:47 final size:47
Alignment explanation
Indices: 54479774--54479936 Score: 282
Period size: 47 Copynumber: 3.6 Consensus size: 47
54479764 CATGCATTAG
54479774 CTTATCACATATATACAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54479820 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54479867 CTTATCACATATATACACTTTCACATTCATCA-AT-GG-CATTA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54479910 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
54479937 TATTCAACTA
Statistics
Matches: 114, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
43 29 0.25
44 4 0.04
45 2 0.02
46 20 0.18
47 59 0.52
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54483236 original size:15 final size:15
Alignment explanation
Indices: 54483216--54483248 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54483206 TTCGTGGACC
54483216 AAAACT-AATGATTTT
1 AAAACTAAATG-TTTT
54483231 AAAACTAAATGTTTT
1 AAAACTAAATGTTTT
54483246 AAA
1 AAA
54483249 GGTGATCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
AAAACTAAATGTTTT
Found at i:54493186 original size:205 final size:205
Alignment explanation
Indices: 54492813--54493525 Score: 1072
Period size: 205 Copynumber: 3.5 Consensus size: 205
54492803 AGCATAACAA
* *
54492813 ATCTGGCCTTCAGATG-TTATACTGAAGCTGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
1 ATCTCGCCTTCAGATGTTTATACTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
* *
54492877 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGAGATTACGATGAAGCAAATCTAAGATGAT
66 GAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTAAGATGAT
54492942 TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
131 TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
54493007 CACATAGCAG
196 CACATAGCAG
* * *
54493017 ATCTCGCCTTCGGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTGTTTATAAG
1 ATCTCGCCTTCAGATGTTTATACTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
* *
54493082 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTATGATGAAGCAAATCTAAGATGAT
66 GAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTAAGATGAT
* * * * *
54493147 TTATCATCTCTGTATTGTCAAAGAATGAATCGCAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
131 TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
*
54493212 CACACAGCAG
196 CACATAGCAG
* * * *
54493222 ATCTCGCCTTCGGCTGTTTATGCTGAAGCGGATCCAAGATGGTTTGGAATCCTTGTGTTTACAAG
1 ATCTCGCCTTCAGATGTTTATACTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
* * * *
54493287 GAACAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
66 GAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTAAGATGAT
* * * *
54493352 TTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCA-TTTCAATGGAGAGCAG
131 TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTT-GATGGAGAGCAG
*
54493416 ATACATAGCAG
195 ACACATAGCAG
* * * *
54493427 ATCT-GATCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACA
1 ATCTCG-CCTTCAGATGTTTATACTGAAGC-GGATCCAAGATGGTTTGGCATCCTTGTGTTTACA
* *
54493491 AGGAACAAATCGAAGACATAGCAGATTTGACTTTC
64 AGGAACAAATCGAAGACATAGCTGATTTGGCTTTC
54493526 GGATGTTCCC
Statistics
Matches: 461, Mismatches: 44, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
204 18 0.04
205 381 0.83
206 62 0.13
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (205 bp):
ATCTCGCCTTCAGATGTTTATACTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
GAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTAAGATGAT
TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
CACATAGCAG
Found at i:54493751 original size:44 final size:43
Alignment explanation
Indices: 54493589--54493752 Score: 145
Period size: 44 Copynumber: 3.7 Consensus size: 43
54493579 CGACGGAGAG
* *
54493589 CAGATCGAAGAGATCAGCATGGCATCCCTGTGCTTATAGGGAA
1 CAGATCGAAGATAGCAGCATGGCATCCCTGTGCTTATAGGGAA
* * *
54493632 CAAGTTGGAA-ATAGCAG-ATTTGGCATCCCTGTGTTTATAGGGAA
1 C-AGATCGAAGATAGCAGCA--TGGCATCCCTGTGCTTATAGGGAA
* * * * *
54493676 CAAATCGAAGATAGCAGGTC-TGACATTCCTGTGCTTACAGTGAA
1 CAGATCGAAGATAGCA-G-CATGGCATCCCTGTGCTTATAGGGAA
**
54493720 GCAGATCGAAGATTTCAGCATGGCATCCCTGTG
1 -CAGATCGAAGATAGCAGCATGGCATCCCTGTG
54493753 AACAGATCGA
Statistics
Matches: 94, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
42 1 0.01
43 12 0.13
44 67 0.71
45 14 0.15
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (43 bp):
CAGATCGAAGATAGCAGCATGGCATCCCTGTGCTTATAGGGAA
Found at i:54494428 original size:20 final size:20
Alignment explanation
Indices: 54494405--54494446 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
54494395 GTTCTTTTGA
*
54494405 TTTTTTATTTATTTTTTT-TC
1 TTTTGTATTT-TTTTTTTCTC
54494425 TTTTGTATTTTTTTTTTCTC
1 TTTTGTATTTTTTTTTTCTC
54494445 TT
1 TT
54494447 CTCGAATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTGTATTTTTTTTTTCTC
Found at i:54495456 original size:10 final size:10
Alignment explanation
Indices: 54495441--54495493 Score: 65
Period size: 10 Copynumber: 5.2 Consensus size: 10
54495431 CATTAGTTTC
54495441 TATTTATTAT
1 TATTTATTAT
54495451 TATTTATTAT
1 TATTTATTAT
54495461 TA-TTATGTAT
1 TATTTAT-TAT
54495471 CTATTTATT-T
1 -TATTTATTAT
54495481 TATTATATTAT
1 TATT-TATTAT
54495492 TA
1 TA
54495494 CTATTGCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.21
10 20 0.53
11 6 0.16
12 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TATTTATTAT
Found at i:54495515 original size:3 final size:3
Alignment explanation
Indices: 54495444--54495498 Score: 51
Period size: 3 Copynumber: 17.7 Consensus size: 3
54495434 TAGTTTCTAT
54495444 TTA TTA TTA TTTA TTA TTA TTA TGTA TCTA TTTA TT- TTA TTA -TA TTA
1 TTA TTA TTA -TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA TTA TTA TTA
*
54495491 TTA CTA TT
1 TTA TTA TT
54495499 GCTATCATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
2 4 0.09
3 29 0.66
4 10 0.23
5 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:54495752 original size:27 final size:25
Alignment explanation
Indices: 54495597--54495758 Score: 100
Period size: 27 Copynumber: 6.4 Consensus size: 25
54495587 TATTATTATC
*
54495597 ATATATTTTATATTATTTT-A-TTTT
1 ATATATATTAT-TTATTTTAACTTTT
* * * *
54495621 ACATATGTTATTTCTTTTAAACTATT
1 ATATATATTATTTATTTT-AACTTTT
* *
54495647 ATACATATTGTTTATTTTGAAACTTTT
1 ATATATATTATTTATTTT--AACTTTT
* * *
54495674 ATATACATTTTTGTATTTTAAATTATT
1 ATATATATTATT-TATTTTAACTT-TT
* * *
54495701 ATGTATATTA-TTACTTTAA-TATT
1 ATATATATTATTTATTTTAACTTTT
54495724 ATATATATTATTTATTTTAGACCTTTT
1 ATATATATTATTTATTTTA-A-CTTTT
54495751 ATAT-TATT
1 ATATATATT
54495759 TTAAATTGTC
Statistics
Matches: 106, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
23 17 0.16
24 17 0.16
25 9 0.08
26 25 0.24
27 32 0.30
28 6 0.06
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (25 bp):
ATATATATTATTTATTTTAACTTTT
Found at i:54505353 original size:6 final size:6
Alignment explanation
Indices: 54505315--54505513 Score: 124
Period size: 6 Copynumber: 32.3 Consensus size: 6
54505305 AAGAAACATT
* * * *
54505315 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAAA ATCAGA ATCAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* *
54505363 ATCAGA TGAT-AGA ATCAAA ATCCA-A ATCAGA ATCAGA ATTAGGTA A-CAGA
1 ATCAGA --ATCAGA ATCAGA AT-CAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
* * * *
54505413 ATCAGA ATCAGT ATCAGGTA A-CAAA ATCAGA ATCAGA ACCAGA ATCAAA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * *
54505462 ATTAGGTA A-CAGA ATCAGA ATCAGT ATCAGGTA A-CAAA ATCAGA ATCAGA
1 ATCA-G-A ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA
54505512 AT
1 AT
54505514 GTGAATGCAA
Statistics
Matches: 149, Mismatches: 25, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
5 13 0.09
6 113 0.76
7 15 0.10
8 8 0.05
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:54505384 original size:37 final size:37
Alignment explanation
Indices: 54505336--54505513 Score: 123
Period size: 37 Copynumber: 4.6 Consensus size: 37
54505326 AATCAAAATG
* *
54505336 AGAATCAAAATCAGAATCAGAATCAAAATCAGATGAT
1 AGAATCAAAATCAGAATCAGAATCAAAATCAGATAAC
* * *
54505373 AGAATCAAAATCCA-AATCAGAATCAGAATTAGGTAAC
1 AGAATCAAAAT-CAGAATCAGAATCAAAATCAGATAAC
* *
54505410 AGAATCAGAATCAGTATCAGGTAA-CAAAATCAGAATCAGAACC
1 AGAATCAAAATCAGAATCA-G-AATCAAAATCAG-AT---AA-C
* * *
54505453 AGAATCAAAATTAGGTAA-CAGAATCAGAATCAG-TATC
1 AGAATCAAAATCA-G-AATCAGAATCAAAATCAGATAAC
54505490 AGGTAA-CAAAATCAGAATCAGAAT
1 A-G-AATCAAAATCAGAATCAGAAT
54505514 GTGAATGCAA
Statistics
Matches: 110, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
36 4 0.04
37 52 0.47
38 19 0.17
39 5 0.05
41 1 0.01
42 4 0.04
43 21 0.19
44 3 0.03
45 1 0.01
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (37 bp):
AGAATCAAAATCAGAATCAGAATCAAAATCAGATAAC
Found at i:54505415 original size:25 final size:25
Alignment explanation
Indices: 54505386--54505450 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
54505376 ATCAAAATCC
*
54505386 AAATCAGAATCAGAATTAGGTAACA
1 AAATCAGAATCAGAATCAGGTAACA
* *
54505411 GAATCAGAATCAGTATCAGGTAACA
1 AAATCAGAATCAGAATCAGGTAACA
54505436 AAATCAGAATCAGAA
1 AAATCAGAATCAGAA
54505451 CCAGAATCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.18
Consensus pattern (25 bp):
AAATCAGAATCAGAATCAGGTAACA
Found at i:54505422 original size:62 final size:62
Alignment explanation
Indices: 54505347--54505512 Score: 199
Period size: 62 Copynumber: 2.7 Consensus size: 62
54505337 GAATCAAAAT
* * * * *
54505347 CAGAATCAGAATCAAAATCAGATGATAGAATCAAAATCCA-AATCAGAATCAGAATTAGGTAA
1 CAGAATCAGAATCAAAATCAGATAACAAAATCAAAAT-CAGAACCAGAATCAAAATTAGGTAA
** * *
54505409 CAGAATCAGAATCAGTATCAGGTAACAAAATCAGAATCAGAACCAGAATCAAAATTAGGTAA
1 CAGAATCAGAATCAAAATCAGATAACAAAATCAAAATCAGAACCAGAATCAAAATTAGGTAA
** * *
54505471 CAGAATCAGAATCAGTATCAGGTAACAAAATCAGAATCAGAA
1 CAGAATCAGAATCAAAATCAGATAACAAAATCAAAATCAGAA
54505513 TGTGAATGCA
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
61 2 0.02
62 92 0.98
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.18
Consensus pattern (62 bp):
CAGAATCAGAATCAAAATCAGATAACAAAATCAAAATCAGAACCAGAATCAAAATTAGGTAA
Found at i:54505480 original size:25 final size:25
Alignment explanation
Indices: 54505347--54505509 Score: 90
Period size: 25 Copynumber: 6.6 Consensus size: 25
54505337 GAATCAAAAT
* *
54505347 CAGAATCAGAATCAAAATCAGATGA
1 CAGAATCAGAATCAAAATCAGGTAA
* * *
54505372 TAGAATCAAAATCCAAATCA-G-AA
1 CAGAATCAGAATCAAAATCAGGTAA
* *
54505395 TCAGAATTAGGTAA-CAGAATCA-G-AA
1 -CAGAATCA-G-AATCAAAATCAGGTAA
*
54505420 TCAGTATCAGGTAA-CAAAATCA-G-AA
1 -CAGAATCA-G-AATCAAAATCAGGTAA
* *
54505445 TCAGAACCAGAATCAAAATTAGGTAA
1 -CAGAATCAGAATCAAAATCAGGTAA
**
54505471 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAAAATCAGGTAA
*
54505496 CAAAATCAGAATCA
1 CAGAATCAGAATCA
54505510 GAATGTGAAT
Statistics
Matches: 111, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
23 3 0.03
24 14 0.13
25 90 0.81
26 4 0.04
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.18
Consensus pattern (25 bp):
CAGAATCAGAATCAAAATCAGGTAA
Found at i:54505680 original size:27 final size:26
Alignment explanation
Indices: 54505632--54505722 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 26
54505622 ACGAGGCTGC
*
54505632 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
54505659 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
54505685 CAGATATATATATGTGGCGAAGCCACCAGAA
1 CAG----ATAT-TGTGACGAAGCCACCAGAA
54505716 CAGATAT
1 CAGATAT
54505723 ATATATGTGG
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
26 4 0.08
27 25 0.47
30 4 0.08
31 20 0.38
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:54505710 original size:31 final size:31
Alignment explanation
Indices: 54505662--54505745 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
54505652 CCAGATACAG
* *
54505662 ATAT-TGTGGCTAGGCCACCAGAACAGATAT
1 ATATATGTGGCGAAGCCACCAGAACAGATAT
54505692 ATATATGTGGCGAAGCCACCAGAACAGATAT
1 ATATATGTGGCGAAGCCACCAGAACAGATAT
54505723 ATATATGTGGCGAAGCCACCAGA
1 ATATATGTGGCGAAGCCACCAGA
54505746 TTGCAGCGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 4 0.08
31 47 0.92
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (31 bp):
ATATATGTGGCGAAGCCACCAGAACAGATAT
Found at i:54505723 original size:27 final size:27
Alignment explanation
Indices: 54505635--54505745 Score: 98
Period size: 31 Copynumber: 3.8 Consensus size: 27
54505625 AGGCTGCCAG
* *
54505635 ATATTGTGACGAAGTCACCAGATACAG-
1 ATATTGTGGCGAAGCCACCAGA-ACAGA
* *
54505662 ATATTGTGGCTAGGCCACCAGAACAGATA
1 ATATTGTGGCGAAGCCACCAGAACAG--A
54505691 TATATATGTGGCGAAGCCACCAGAACAGATA
1 -ATAT-TGTGGCGAAGCCACCAGAACAG--A
54505722 TATATATGTGGCGAAGCCACCAGA
1 -ATAT-TGTGGCGAAGCCACCAGA
54505746 TTGCAGCGAG
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.05
27 18 0.25
30 4 0.05
31 47 0.64
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (27 bp):
ATATTGTGGCGAAGCCACCAGAACAGA
Found at i:54506087 original size:27 final size:27
Alignment explanation
Indices: 54506057--54506303 Score: 254
Period size: 27 Copynumber: 9.3 Consensus size: 27
54506047 GGGGTAAAAT
* *
54506057 GGTAATTTTAACCC-ACAAGGGTATCTC
1 GGTAATTCT-ACCCTACAAGGGTATTTC
54506084 GGTAATTCTACCCTAC-AGTGGTATTTC
1 GGTAATTCTACCCTACAAG-GGTATTTC
* *
54506111 AGTAATTCTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
54506138 GGTATTTCTA-CC--CAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
54506162 GGTATTTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
54506189 AGTAATTCTACCCTAC-AGGAGTATTTC
1 GGTAATTCTACCCTACAAGG-GTATTTC
* * * *
54506216 GATATTTCTACCCTACAGGGGTATTTA
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
54506243 GGTATTTCTACACTACAAGGATATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
54506270 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
54506297 GATAATT
1 GGTAATT
54506304 TTATAAATCG
Statistics
Matches: 184, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
24 21 0.11
25 2 0.01
26 10 0.05
27 148 0.80
28 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:54506201 original size:78 final size:77
Alignment explanation
Indices: 54506072--54506300 Score: 305
Period size: 78 Copynumber: 2.9 Consensus size: 77
54506062 TTTTAACCCA
* * * *
54506072 CAAGGGTATCTCGGTAATTCTACCCTACAGTGGTATTTCAGTAATTCTACCCTACATGGGTATTT
1 CAAGGGTATTTCGGTATTTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACA-GGGTATTT
*
54506137 CGGTATTTCTACC
65 CGATATTTCTACC
54506150 CAAGGGTATTTCGGTATTTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGAGTATTT
1 CAAGGGTATTTCGGTATTTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGG-GTATTT
54506215 CGATATTTCTACC
65 CGATATTTCTACC
* * * * * *
54506228 CTACAGGGGTATTTAGGTATTTCTACACTACAAGGATATTTTGGTATTTCTACCCTACAAGGGTA
1 C-A-A-GGGTATTTCGGTATTTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTAC-AGGGTA
54506293 TTTCGATA
62 TTTCGATA
54506301 ATTTTATAAA
Statistics
Matches: 135, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
77 2 0.01
78 71 0.53
79 1 0.01
80 1 0.01
81 57 0.42
82 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (77 bp):
CAAGGGTATTTCGGTATTTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGTATTTC
GATATTTCTACC
Found at i:54506383 original size:27 final size:27
Alignment explanation
Indices: 54506353--54506417 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
54506343 GGTACTTTGG
*
54506353 TAATTTTGCAAGTCGAGGGTATCTCAA
1 TAATTTTACAAGTCGAGGGTATCTCAA
* * *
54506380 TAATTTTACAGGTCGAGGGTATTTCAG
1 TAATTTTACAAGTCGAGGGTATCTCAA
*
54506407 TAATTTCACAA
1 TAATTTTACAA
54506418 ATCAGGGGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (27 bp):
TAATTTTACAAGTCGAGGGTATCTCAA
Found at i:54506426 original size:27 final size:27
Alignment explanation
Indices: 54506395--54506662 Score: 329
Period size: 27 Copynumber: 9.9 Consensus size: 27
54506385 TTACAGGTCG
** * * *
54506395 AGGGTATTTCAGTAATTTCACAAATCA
1 AGGGTATTTTGGTAATTTTATAAACCA
* *
54506422 GGGGTATTTTGGTAATTTTATAAACTA
1 AGGGTATTTTGGTAATTTTATAAACCA
* *
54506449 GGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTATAAACCA
*
54506476 AGGGTATTTTAGTAATTTTATAAACCA
1 AGGGTATTTTGGTAATTTTATAAACCA
*
54506503 AGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTATAAACCA
*
54506530 AGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTATAAACCA
* * *
54506557 AGAGTATTTTCGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTATAAACCA
* *
54506584 AGGGTATTTTGGTAATTTTACAAACTA
1 AGGGTATTTTGGTAATTTTATAAACCA
* * *
54506611 GGGGTATTTTGGTGATTTTACAAACCA
1 AGGGTATTTTGGTAATTTTATAAACCA
* * *
54506638 GGGGTATTTTAGTAATTTGATAAAC
1 AGGGTATTTTGGTAATTTTATAAAC
54506663 TAAAGTATTC
Statistics
Matches: 213, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 213 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTATAAACCA
Found at i:54506454 original size:81 final size:80
Alignment explanation
Indices: 54506335--54506655 Score: 212
Period size: 81 Copynumber: 4.0 Consensus size: 80
54506325 GTAATTCTGT
* ** * * *** *
54506335 AAATCAGGGGTACTTTGGTAATTTTGCAAGTCGAGGGTATCTCAATAATTTTACAGGTCGAGGGT
1 AAATCAGGGGTATTTTGGTAATTTTTAAACTAG-GGGTATCTCAATAATTTTACAAACCAAGGGT
54506400 ATTTCAGTAATTTCAC
65 ATTTCAGTAATTTCAC
* *** **
54506416 AAATCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGGTAATTTTGTAAACCAAGGGT
1 AAATCAGGGGTATTTTGGTAATTTT-TAAACTAGGGGTATCTCAATAATTTTACAAACCAAGGGT
* * *
54506481 ATTTTAGTAATTTTAT
65 ATTTCAGTAATTTCAC
* * * * * *** ** *
54506497 AAACCAAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTGTAAACCAAGAGT
1 AAATCAGGGGTATTTTGGTAATTTT-TAAACTAGGGGTATCTCAATAATTTTACAAACCAAGGGT
***
54506562 ATTTTC-GTAATTTTGT
65 A-TTTCAGTAATTTCAC
* * * * *** * *
54506578 AAACCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTGATTTTACAAACCAGGGGT
1 AAATCAGGGGTATTTTGGTAATTTT-TAAACTAGGGGTATCTCAATAATTTTACAAACCAAGGGT
*
54506643 ATTTTAGTAATTT
65 ATTTCAGTAATTT
54506656 GATAAACTAA
Statistics
Matches: 201, Mismatches: 36, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
80 3 0.01
81 191 0.95
82 7 0.03
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (80 bp):
AAATCAGGGGTATTTTGGTAATTTTTAAACTAGGGGTATCTCAATAATTTTACAAACCAAGGGTA
TTTCAGTAATTTCAC
Found at i:54506662 original size:81 final size:81
Alignment explanation
Indices: 54506395--54506662 Score: 376
Period size: 81 Copynumber: 3.3 Consensus size: 81
54506385 TTACAGGTCG
* * * * *
54506395 AGGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
1 AGGGTATTTTAGTAATTTGATAAACCAAGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
54506460 GTAATTTTGTAAACCA
66 GTAATTTTGTAAACCA
* * * *
54506476 AGGGTATTTTAGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTG
1 AGGGTATTTTAGTAATTTGATAAACCAAGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
54506541 GTAATTTTGTAAACCA
66 GTAATTTTGTAAACCA
* * *
54506557 AGAGTATTTTCGTAATTTTG-TAAACCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTT
1 AGGGTATTTTAGTAA-TTTGATAAACCAAGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTT
* **
54506621 GGTGATTTTACAAACCA
65 GGTAATTTTGTAAACCA
*
54506638 GGGGTATTTTAGTAATTTGATAAAC
1 AGGGTATTTTAGTAATTTGATAAAC
54506663 TAAAGTATTC
Statistics
Matches: 164, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
80 4 0.02
81 157 0.96
82 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (81 bp):
AGGGTATTTTAGTAATTTGATAAACCAAGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTG
GTAATTTTGTAAACCA
Found at i:54509025 original size:6 final size:6
Alignment explanation
Indices: 54508999--54509140 Score: 105
Period size: 6 Copynumber: 23.0 Consensus size: 6
54508989 AATCAGGTGA
* *
54508999 CAGAAT CAAAAT CCA-AAT CAGAAT CAGAAT TAGGTAA- CAGAAT CAGAAT
1 CAGAAT CAGAAT -CAGAAT CAGAAT CAGAAT CA-G-AAT CAGAAT CAGAAT
* * * *
54509048 CAGTAT CAGGTAA- CAGAAT CAGAAT CAGAAC CAGAAT CAAAAT TAGGTAA-
1 CAGAAT CA-G-AAT CAGAAT CAGAAT CAGAAT CAGAAT CAGAAT CA-G-AAT
*
54509098 CAGAAT CAGAAT CAGTAT CAGGTAA- CAGAAT CAGAAT CAGAAT
1 CAGAAT CAGAAT CAGAAT CA-G-AAT CAGAAT CAGAAT CAGAAT
54509141 GTGAATGCAA
Statistics
Matches: 109, Mismatches: 13, Indels: 28
0.73 0.09 0.19
Matches are distributed among these distances:
5 10 0.09
6 82 0.75
7 11 0.10
8 6 0.06
ACGTcount: A:0.49, C:0.16, G:0.17, T:0.18
Consensus pattern (6 bp):
CAGAAT
Found at i:54509041 original size:19 final size:19
Alignment explanation
Indices: 54509017--54509109 Score: 91
Period size: 19 Copynumber: 4.6 Consensus size: 19
54509007 AAATCCAAAT
54509017 CAGAATCAGAATTAGGTAA
1 CAGAATCAGAATTAGGTAA
54509036 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAG-A--A-T-T-AGGTAA
*
54509061 CAGAATCAGAATCA-G-AA
1 CAGAATCAGAATTAGGTAA
*
54509078 CCAGAATCAAAATTAGGTAA
1 -CAGAATCAGAATTAGGTAA
54509098 CAGAATCAGAAT
1 CAGAATCAGAAT
54509110 CAGTATCAGG
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
17 2 0.03
18 13 0.21
19 22 0.36
20 3 0.05
21 1 0.02
22 2 0.03
23 1 0.02
24 2 0.03
25 15 0.25
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (19 bp):
CAGAATCAGAATTAGGTAA
Found at i:54509042 original size:25 final size:25
Alignment explanation
Indices: 54509014--54509077 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
54509004 TCAAAATCCA
*
54509014 AATCAGAATCAGAATTAGGTAACAG
1 AATCAGAATCAGAATCAGGTAACAG
*
54509039 AATCAGAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAGGTAACAG
54509064 AATCAGAATCAGAA
1 AATCAGAATCAGAA
54509078 CCAGAATCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (25 bp):
AATCAGAATCAGAATCAGGTAACAG
Found at i:54509064 original size:62 final size:63
Alignment explanation
Indices: 54508990--54509139 Score: 243
Period size: 62 Copynumber: 2.4 Consensus size: 63
54508980 TAAAATGAGA
* * * *
54508990 ATCAGGTGACAGAATCAAAATCCA-AATCAGAATCAGAATTAGGTAACAGAATCAGAATCAGT
1 ATCAGGTAACAGAATCAGAATCCAGAACCAGAATCAAAATTAGGTAACAGAATCAGAATCAGT
54509052 ATCAGGTAACAGAATCAGAAT-CAGAACCAGAATCAAAATTAGGTAACAGAATCAGAATCAGT
1 ATCAGGTAACAGAATCAGAATCCAGAACCAGAATCAAAATTAGGTAACAGAATCAGAATCAGT
54509114 ATCAGGTAACAGAATCAGAAT-CAGAA
1 ATCAGGTAACAGAATCAGAATCCAGAA
54509140 TGTGAATGCA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
61 2 0.02
62 81 0.98
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (63 bp):
ATCAGGTAACAGAATCAGAATCCAGAACCAGAATCAAAATTAGGTAACAGAATCAGAATCAGT
Found at i:54509077 original size:37 final size:37
Alignment explanation
Indices: 54509036--54509118 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
54509026 AATTAGGTAA
**
54509036 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAAT
1 CAGAATCAGAATCAAAATCAGGTAACAGAATCAGAAT
* *
54509073 CAGAACCAGAATCAAAATTAGGTAACAGAATCAGAAT
1 CAGAATCAGAATCAAAATCAGGTAACAGAATCAGAAT
*
54509110 CAGTATCAG
1 CAGAATCAG
54509119 GTAACAGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (37 bp):
CAGAATCAGAATCAAAATCAGGTAACAGAATCAGAAT
Found at i:54509107 original size:25 final size:25
Alignment explanation
Indices: 54509073--54509136 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
54509063 GAATCAGAAT
* *
54509073 CAGAACCAGAATCAAAATTAGGTAA
1 CAGAATCAGAATCAAAATCAGGTAA
**
54509098 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAAAATCAGGTAA
54509123 CAGAATCAGAATCA
1 CAGAATCAGAATCA
54509137 GAATGTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (25 bp):
CAGAATCAGAATCAAAATCAGGTAA
Found at i:54509307 original size:27 final size:26
Alignment explanation
Indices: 54509259--54509318 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
54509249 ACGAGGCTGC
*
54509259 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
54509286 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
54509312 CAGATAT
1 CAGATAT
54509319 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:54509363 original size:71 final size:67
Alignment explanation
Indices: 54509286--54509427 Score: 176
Period size: 67 Copynumber: 2.1 Consensus size: 67
54509276 TCACCAGATA
* * * * *
54509286 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAAATTACAGCGA
54509351 GGCTGC
62 GGCTGC
* * *
54509357 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACTAAATTACAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAAATTACAGCGAGGCT
54509422 GC
66 GC
54509424 CAGA
1 CAGA
54509428 ACGCTTCCTC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
67 38 0.60
71 25 0.40
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAAATTACAGCGAGGCT
GC
Found at i:54509684 original size:27 final size:27
Alignment explanation
Indices: 54509653--54509904 Score: 298
Period size: 27 Copynumber: 9.3 Consensus size: 27
54509643 GGGGTAAAAT
* *
54509653 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* * *
54509680 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
54509707 AGTAATTTTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
54509734 AGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* *
54509761 GGTAATTCTACCCTACAAGGGTATTTT
1 GGTAATTTTACCCTACAAGGGTATTTC
** *
54509788 AATAATTCTACCCTAC-AGGCGTATTTC
1 GGTAATTTTACCCTACAAGG-GTATTTC
*
54509815 GGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
54509842 GGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
54509869 GGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
54509896 GGTAATTTT
1 GGTAATTTT
54509905 GTAAATCAAG
Statistics
Matches: 201, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
26 10 0.05
27 182 0.91
28 9 0.04
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:54509700 original size:54 final size:54
Alignment explanation
Indices: 54509653--54509902 Score: 333
Period size: 54 Copynumber: 4.6 Consensus size: 54
54509643 GGGGTAAAAT
* *
54509653 GGTAATTTTACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* * * *
54509707 AGTAATTTTACCCTACAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* * * *
54509761 GGTAATTCTACCCTACAAGGGTATTTTAATAATTCTACCCTACAGGCGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* * * *
54509815 GGT-ATTTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
*
54509869 GGT-ATTTCTACCCTACAAGGGTATTTCGGTAATT
1 GGTAATTT-TACCCTACAAGGGTATTTCAGTAATT
54509903 TTGTAAATCA
Statistics
Matches: 171, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 3 0.02
54 168 0.98
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (54 bp):
GGTAATTTTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
Found at i:54509914 original size:27 final size:27
Alignment explanation
Indices: 54509884--54510422 Score: 544
Period size: 27 Copynumber: 20.0 Consensus size: 27
54509874 TTCTACCCTA
* * *
54509884 CAAGGGTATTTCGGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAC
**** * * *
54509911 CAAGGGTAAAACGGTAATTCTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * * **
54509938 CAGGGGTACTTTGGTAATTTTGTAAGT
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * *** * **
54509965 CGAGGGTGTTTCAATAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54509992 CGAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * *
54510019 TAAGGGTATTTTGATAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510046 CATGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510073 TAGGGGTATTTTGGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510100 AAAGGGTATTTTAGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510127 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510154 TAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510181 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510208 CAAGGGTATTTTAGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510235 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510262 CAAGGGTATTTTTGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510289 CAAGGATATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510316 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
*
54510343 CAAGGGTATTTTGG-AATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
54510369 C-AGGTGTATTTTGGTGATTTTACAAA-
1 CAAGG-GTATTTTGGTAATTTTATAAAC
* *
54510395 CTAGGGATATTTTGGTAATTTGATAAAC
1 CAAGGG-TATTTTGGTAATTTTATAAAC
54510423 TAAAGTATTC
Statistics
Matches: 432, Mismatches: 75, Indels: 9
0.84 0.15 0.02
Matches are distributed among these distances:
25 3 0.01
26 22 0.05
27 407 0.94
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTATAAAC
Found at i:54509926 original size:54 final size:54
Alignment explanation
Indices: 54509644--54509931 Score: 163
Period size: 54 Copynumber: 5.3 Consensus size: 54
54509634 AAAACCCTAG
* * * * * ** *
54509644 GGGTAAAATGGTAATTT-TACCCCACAAGGGTATCTCAGTAATTCTACCCTACAG
1 GGGTAAAACGGT-ATTTCTACCCTACAAGGGTATTTCGGTATTTCTACAATACAA
*** * * * **
54509698 GGGTATTTCAGTAATTT-TACCCTACAGGGGTATTTCAGTATTTCTACCCTACAA
1 GGGTAAAACGGT-ATTTCTACCCTACAAGGGTATTTCGGTATTTCTACAATACAA
*** * *** * **
54509752 GGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAATAATTCTACCCTAC-A
1 GGGTAAAACGGTATTTCTACCCTACAAGGGTATTTCGGTATTTCTACAATACAA
*** * **
54509805 GGCGTATTTCGGTATTTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAA
1 GG-GTAAAACGGTATTTCTACCCTACAAGGGTATTTCGGTATTTCTACAATACAA
*** *
54509860 GGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTAATTTTGTA-AAT-CAA
1 GGGTAAAACGGTATTTCTACCCTACAAGGGTATTTCGGT-A-TTTCTACAATACAA
*
54509914 GGGTAAAACGGTAATTCT
1 GGGTAAAACGGTATTTCT
54509932 GTAAATCAGG
Statistics
Matches: 199, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
53 6 0.03
54 183 0.92
55 5 0.03
56 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (54 bp):
GGGTAAAACGGTATTTCTACCCTACAAGGGTATTTCGGTATTTCTACAATACAA
Found at i:54509926 original size:81 final size:81
Alignment explanation
Indices: 54509657--54509899 Score: 339
Period size: 81 Copynumber: 3.0 Consensus size: 81
54509647 TAAAATGGTA
* * * *
54509657 ATTT-TACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCAGTAATTT-TACCC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGT-ATTTCTACCC
* *
54509720 TACAGGGGTATTTCAGT
65 TACAAGGGTATTTCGGT
* * *
54509737 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAATAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTATTTCTACCCT
54509802 AC-AGGCGTATTTCGGT
66 ACAAGG-GTATTTCGGT
* * *
54509818 ATTTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGGTATTTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTATTTCTACCCT
54509883 ACAAGGGTATTTCGGT
66 ACAAGGGTATTTCGGT
54509899 A
1 A
54509900 ATTTTGTAAA
Statistics
Matches: 144, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
80 9 0.06
81 132 0.92
82 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (81 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTATTTCTACCCT
ACAAGGGTATTTCGGT
Found at i:54514296 original size:33 final size:33
Alignment explanation
Indices: 54514179--54514289 Score: 159
Period size: 33 Copynumber: 3.4 Consensus size: 33
54514169 TACTCTTTGT
* *
54514179 TTGGTGTGTTGGTTGGACTAGCTCTTATAAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
*
54514212 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
* * *
54514245 TTGGTGTGCTGCTTGGATTAGCTCTTCTGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
*
54514278 TTAGTGTGTTGG
1 TTGGTGTGTTGG
54514290 AGGGATTGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.15, C:0.12, G:0.32, T:0.41
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
Found at i:54520476 original size:26 final size:26
Alignment explanation
Indices: 54520447--54520501 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
54520437 TAATAAATTT
54520447 TTTAAGTAATTGCATGAATTGAATGG
1 TTTAAGTAATTGCATGAATTGAATGG
54520473 TTTAAGTAATTGCATGAATTGAATGG
1 TTTAAGTAATTGCATGAATTGAATGG
54520499 TTT
1 TTT
54520502 TCTTTTGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.42
Consensus pattern (26 bp):
TTTAAGTAATTGCATGAATTGAATGG
Found at i:54533053 original size:117 final size:118
Alignment explanation
Indices: 54532845--54533075 Score: 374
Period size: 117 Copynumber: 2.0 Consensus size: 118
54532835 ACCTTGATGC
* * *
54532845 TTTGATTCGTTCATGATAGATTGATTTCGAGGCAATATGAAGAGCAACTTAATTATGGCACCAAA
1 TTTGATTCGTTCATGATAGATTCATTTCGAGGCAATATGAACAGAAACTTAATTATGGCACCAAA
*
54532910 ATTTTGCTAGTGGTGTATGCTCCAATCCAA-TTCAATTAACAGATGTTAAAAG
66 ATTTTGCTAGTGATGTATGCTCCAATCCAATTTCAATTAACAGATGTTAAAAG
* * *
54532962 TTTGATTCTTTCATGATAGTTTCATTTCGAGGCAATATGAACAGAAACTTAATTATGGTACCAAA
1 TTTGATTCGTTCATGATAGATTCATTTCGAGGCAATATGAACAGAAACTTAATTATGGCACCAAA
* *
54533027 GTTTTGCTAGTGATGTATGCTTCAATCCAATTTCAATTAACAGATGTTA
66 ATTTTGCTAGTGATGTATGCTCCAATCCAATTTCAATTAACAGATGTTA
54533076 TATCCACATG
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
117 86 0.83
118 18 0.17
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (118 bp):
TTTGATTCGTTCATGATAGATTCATTTCGAGGCAATATGAACAGAAACTTAATTATGGCACCAAA
ATTTTGCTAGTGATGTATGCTCCAATCCAATTTCAATTAACAGATGTTAAAAG
Found at i:54542318 original size:13 final size:13
Alignment explanation
Indices: 54542300--54542324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54542290 CCTCCATCAG
54542300 TTCCTTTTTCTTC
1 TTCCTTTTTCTTC
54542313 TTCCTTTTTCTT
1 TTCCTTTTTCTT
54542325 TTATGTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCCTTTTTCTTC
Found at i:54544907 original size:21 final size:21
Alignment explanation
Indices: 54544883--54544949 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
54544873 CACATGGTCA
* *
54544883 TGTGCATGGGTCACACAGCCT
1 TGTGGATGGGTCACACGGCCT
54544904 TGTGGATGGGTCACACGGCCT
1 TGTGGATGGGTCACACGGCCT
* *
54544925 TGTGGATAGGTCACACGGCCG
1 TGTGGATGGGTCACACGGCCT
54544946 TGTG
1 TGTG
54544950 TCCAAACCGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (21 bp):
TGTGGATGGGTCACACGGCCT
Found at i:54550884 original size:39 final size:40
Alignment explanation
Indices: 54550783--54550967 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
54550773 TCGAATGATG
* * *
54550783 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
54550822 ATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
54550863 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
54550902 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
54550941 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54550968 AATGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:54550989 original size:79 final size:79
Alignment explanation
Indices: 54550839--54551000 Score: 186
Period size: 79 Copynumber: 2.1 Consensus size: 79
54550829 CTAAGATCCA
** **
54550839 AAGGCATTTGTGCGAGTTACTAATTTCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATC
1 AAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATC
*
54550904 CGGGTTAAGTCCCG
66 CGGGTTAAATCCCG
* * * *
54550918 AAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGCTAT
1 AAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAA
*
54550981 ATCC-GGTTAAATTCCG
63 ATCCGGGTTAAATCCCG
54550997 AAGG
1 AAGG
54551001 TACGTGATTC
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 45 0.64
80 23 0.33
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATC
CGGGTTAAATCCCG
Found at i:54556818 original size:757 final size:757
Alignment explanation
Indices: 54555358--54556873 Score: 2764
Period size: 757 Copynumber: 2.0 Consensus size: 757
54555348 CACATGAGAA
* *
54555358 AAATTATCCGACCCATGATCTCGAACTAGCTGCCATCGTATTCGCTTTAAAAATATGGCGACATT
1 AAATTATCCAACCCATGATCTCGAACTAGCCGCCATCGTATTCGCTTTAAAAATATGGCGACATT
* *
54555423 ACTTATTTGGTGAAAAGTGCTATGTATTTTCGGATCATAAAAGTCTCAAATATTTGATGACTCAA
66 ACTTATTTGGTGAAAAGTGCCATGTATTTTCGGATCACAAAAGTCTCAAATATTTGATGACTCAA
54555488 AGAGACTTAAATCTGCGACAAAGACGTTGGCTTGAGTTGTTGAAAGATTACGAGCTTGTCATTGA
131 AGAGACTTAAATCTGCGACAAAGACGTTGGCTTGAGTTGTTGAAAGATTACGAGCTTGTCATTGA
54555553 TTACCACCCGGGAAAGGCTAATGTGGTTGCGGACGCCTTAAGCCAGAAATCACTGTTTGCTTTAC
196 TTACCACCCGGGAAAGGCTAATGTGGTTGCGGACGCCTTAAGCCAGAAATCACTGTTTGCTTTAC
54555618 GAGCGATGAATGTGCACTTGTCTGTTCTACCCAACAATGTGTTAGTAGCTGAATTAAAGGCCAAA
261 GAGCGATGAATGTGCACTTGTCTGTTCTACCCAACAATGTGTTAGTAGCTGAATTAAAGGCCAAA
* *
54555683 CCATTATTGATTCGTCAAATTCGTGAAGCTCAGAAAGTCGACGATGAATTGGTTGCAAAATGGGC
326 CCATCATTGATTCGTCAAATTCGTGAAGCTCAGAAAGTCGACGATGAATTGGTTGCAAAACGGGC
*
54555748 TGAATGTGTTCCGAATATGGAATCCGAATTTCAAATTGATGATGACGATTGTTTGAGGTTCAGAA
391 TGAATGTATTCCGAATATGGAATCCGAATTTCAAATTGATGATGACGATTGTTTGAGGTTCAGAA
54555813 GTCGGTTGTGTGTTCCAAGAAATTCAGAACTCATTTCGATGATTCTGAACGAAGCCCATTGTAGC
456 GTCGGTTGTGTGTTCCAAGAAATTCAGAACTCATTTCGATGATTCTGAACGAAGCCCATTGTAGC
*
54555878 CGAATGTCAATTCACCCGGGGAGTACGAAAATGTACAACGATTTGAAACGTCGATTTTGGTGGCA
521 CGAATGTCAATTCACCCGGGGAGTAAGAAAATGTACAACGATTTGAAACGTCGATTTTGGTGGCA
* *
54555943 TGGTATGAAATGAGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCAACAAGTGAAAGCGG
586 TGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCAACAAGTGAAAGCAG
*
54556008 AACATCAAGTGCCTTCAGGATTACTTCAGCCGATCATGATACCTGACTGGAAATGGGATCGAGTC
651 AACATCAAGTGCCTTCAGGATTACTTCAGCCGATCATGATACCCGACTGGAAATGGGATCGAGTC
54556073 ACAATGGACTTTGTGTCCGGACTGCCATTGTCAGCAAGTAAG
716 ACAATGGACTTTGTGTCCGGACTGCCATTGTCAGCAAGTAAG
* * * *
54556115 AAATTATCCAACTCATGATCTCGAGCTAGCCGCCATCGTATTTGCTTTGAAAATATGGCGACATT
1 AAATTATCCAACCCATGATCTCGAACTAGCCGCCATCGTATTCGCTTTAAAAATATGGCGACATT
* *
54556180 ATTTGTTTGGTGAAAAGTGCCATGTATTTTCGGATCACAAAAGTCTCAAATATTTGATGACTCAA
66 ACTTATTTGGTGAAAAGTGCCATGTATTTTCGGATCACAAAAGTCTCAAATATTTGATGACTCAA
54556245 AGAGACTTAAATCTGCGACAAAGACGTTGGCTTGAGTTGTTGAAAGATTACGAGCTTGTCATTGA
131 AGAGACTTAAATCTGCGACAAAGACGTTGGCTTGAGTTGTTGAAAGATTACGAGCTTGTCATTGA
* * * *
54556310 TTACCACCCGGGAAAGGCTAATGTGGTTGCGGATGCCTTAAGCCGGAAATCGCTGTTTGTTTTAC
196 TTACCACCCGGGAAAGGCTAATGTGGTTGCGGACGCCTTAAGCCAGAAATCACTGTTTGCTTTAC
* *
54556375 GAGCGATGAATGTGCGCTTGTCTGTTCTACCCGACAATGTGTTAGTAGCTGAATTAAAGGCCAAA
261 GAGCGATGAATGTGCACTTGTCTGTTCTACCCAACAATGTGTTAGTAGCTGAATTAAAGGCCAAA
*
54556440 CCATCATTGATTCGTCAAATTCGTGAAGCTCATAAAGTCGACGATGAATTGGTTGCAAAACGGGC
326 CCATCATTGATTCGTCAAATTCGTGAAGCTCAGAAAGTCGACGATGAATTGGTTGCAAAACGGGC
54556505 TGAATGTATTCCGAATATGGAATCCGAATTTCAAATTGATGATGACGATTGTTTGAGGTTCAGAA
391 TGAATGTATTCCGAATATGGAATCCGAATTTCAAATTGATGATGACGATTGTTTGAGGTTCAGAA
*
54556570 GTCGGTTGTGTGTTCCAAGAAATTCAGAACTCATTTCGATGATTCTGAACGAAGCTCATTGTAGC
456 GTCGGTTGTGTGTTCCAAGAAATTCAGAACTCATTTCGATGATTCTGAACGAAGCCCATTGTAGC
*
54556635 CGAATGTCAATTCACCCGGGGAGTAAGAAAATGTACAACGATTTGAAACGTCGGTTTTGGTGGCA
521 CGAATGTCAATTCACCCGGGGAGTAAGAAAATGTACAACGATTTGAAACGTCGATTTTGGTGGCA
*
54556700 TGGTATGAAACGGGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCAACAAGTGAAAGCAG
586 TGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCAACAAGTGAAAGCAG
*
54556765 AACATCAAGTGCCTTCAGGATTACTTCAGCCGA-CAATGATACCCGAGTGGAAATGGGATCGAGT
651 AACATCAAGTGCCTTCAGGATTACTTCAGCCGATC-ATGATACCCGACTGGAAATGGGATCGAGT
54556829 CACAATGGACTTTGTGTCCGGACTGCCATTGTCAGCAAGTAAG
715 CACAATGGACTTTGTGTCCGGACTGCCATTGTCAGCAAGTAAG
54556872 AA
1 AA
54556874 GGATGCGATT
Statistics
Matches: 730, Mismatches: 28, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
756 1 0.00
757 729 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (757 bp):
AAATTATCCAACCCATGATCTCGAACTAGCCGCCATCGTATTCGCTTTAAAAATATGGCGACATT
ACTTATTTGGTGAAAAGTGCCATGTATTTTCGGATCACAAAAGTCTCAAATATTTGATGACTCAA
AGAGACTTAAATCTGCGACAAAGACGTTGGCTTGAGTTGTTGAAAGATTACGAGCTTGTCATTGA
TTACCACCCGGGAAAGGCTAATGTGGTTGCGGACGCCTTAAGCCAGAAATCACTGTTTGCTTTAC
GAGCGATGAATGTGCACTTGTCTGTTCTACCCAACAATGTGTTAGTAGCTGAATTAAAGGCCAAA
CCATCATTGATTCGTCAAATTCGTGAAGCTCAGAAAGTCGACGATGAATTGGTTGCAAAACGGGC
TGAATGTATTCCGAATATGGAATCCGAATTTCAAATTGATGATGACGATTGTTTGAGGTTCAGAA
GTCGGTTGTGTGTTCCAAGAAATTCAGAACTCATTTCGATGATTCTGAACGAAGCCCATTGTAGC
CGAATGTCAATTCACCCGGGGAGTAAGAAAATGTACAACGATTTGAAACGTCGATTTTGGTGGCA
TGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTTAATATGTCAACAAGTGAAAGCAG
AACATCAAGTGCCTTCAGGATTACTTCAGCCGATCATGATACCCGACTGGAAATGGGATCGAGTC
ACAATGGACTTTGTGTCCGGACTGCCATTGTCAGCAAGTAAG
Found at i:54559830 original size:39 final size:40
Alignment explanation
Indices: 54559722--54559905 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
54559712 TCGAATGATG
* * *
54559722 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
54559761 ATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
54559802 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
54559841 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
54559880 AACCGAGCTATGTCCCGAAGGCATTT
1 -TCCGGGCTAAGTCCCGAAGGCATTT
54559906 AAACGAGTAG
Statistics
Matches: 122, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 77 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:54559928 original size:79 final size:79
Alignment explanation
Indices: 54559778--54559939 Score: 177
Period size: 79 Copynumber: 2.1 Consensus size: 79
54559768 CTAAGATCCA
* * ***
54559778 AAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATC
1 AAGGCATTTGTGCGAGTTACTAATACCGAGCTAAGCCCGAAGGCATTGAAACGAGTTACTAAATC
*
54559843 CGGGTTAAGTCCCG
66 CGGGTTAAATCCCG
* * *
54559857 AAGGCATTTGTGCGAGTTACT-ATAACCGAGCTATGTCCCGAAGGCATTTAAACGAG-TAGCTAT
1 AAGGCATTTGTGCGAGTTACTAAT-ACCGAGCTAAG-CCCGAAGGCATTGAAACGAGTTA-CTAA
* *
54559920 GTCC-GGTTAAATTCCG
63 ATCCGGGTTAAATCCCG
54559936 AAGG
1 AAGG
54559940 TACGTGATTC
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
78 2 0.03
79 45 0.65
80 22 0.32
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGTTACTAATACCGAGCTAAGCCCGAAGGCATTGAAACGAGTTACTAAATC
CGGGTTAAATCCCG
Found at i:54562560 original size:46 final size:46
Alignment explanation
Indices: 54562493--54562621 Score: 186
Period size: 46 Copynumber: 2.8 Consensus size: 46
54562483 TGTAACCCAC
* * * * *
54562493 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACAT
*
54562539 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACAT
* *
54562585 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
54562622 TGCTCAACCA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACAT
Found at i:54565660 original size:26 final size:25
Alignment explanation
Indices: 54565631--54565784 Score: 166
Period size: 26 Copynumber: 5.9 Consensus size: 25
54565621 ATGTTACTGA
* *
54565631 TTAGCAGGTTTTGAGCTAGTGATTAG
1 TTAGCAGGCTTTGAGC-CGTGATTAG
* *
54565657 TTAGCAGGCTTTGAGCTTGTGACT-G
1 TTAGCAGGCTTTGAGC-CGTGATTAG
54565682 ATTAGCAGGCTTTGAGCCGGTGATTAG
1 -TTAGCAGGCTTTGAGCC-GTGATTAG
*
54565709 TTAGTAGGCTTTGAGCCGATGATTAG
1 TTAGCAGGCTTTGAGCCG-TGATTAG
*
54565735 TTAGTAGGCTTTGAGCCGATGATTAG
1 TTAGCAGGCTTTGAGCCG-TGATTAG
* *
54565761 TTAGTAGGCTTTGAGTCGGTGATT
1 TTAGCAGGCTTTGAG-CCGTGATT
54565785 TATATAACAT
Statistics
Matches: 116, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
25 2 0.02
26 111 0.96
27 3 0.03
ACGTcount: A:0.21, C:0.12, G:0.32, T:0.36
Consensus pattern (25 bp):
TTAGCAGGCTTTGAGCCGTGATTAG
Found at i:54565705 original size:52 final size:52
Alignment explanation
Indices: 54565626--54565775 Score: 196
Period size: 52 Copynumber: 2.9 Consensus size: 52
54565616 TGAGTATGTT
* ** * *
54565626 ACTGATTAGCAGGTTTTGAGCTAGTGATTAGTTAGCAGGCTTTGAGCTTG-TG
1 ACTGATTAGCAGGCTTTGAGCCGGTGATTAGTTAGTAGGCTTTGAGC-CGATG
54565678 ACTGATTAGCAGGCTTTGAGCCGGTGATTAGTTAGTAGGCTTTGAGCCGATG
1 ACTGATTAGCAGGCTTTGAGCCGGTGATTAGTTAGTAGGCTTTGAGCCGATG
* * *
54565730 A-TTAGTTAGTAGGCTTTGAGCCGATGATTAGTTAGTAGGCTTTGAG
1 ACTGA-TTAGCAGGCTTTGAGCCGGTGATTAGTTAGTAGGCTTTGAG
54565776 TCGGTGATTT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 3 0.03
52 85 0.97
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (52 bp):
ACTGATTAGCAGGCTTTGAGCCGGTGATTAGTTAGTAGGCTTTGAGCCGATG
Found at i:54578017 original size:45 final size:45
Alignment explanation
Indices: 54577953--54578126 Score: 223
Period size: 45 Copynumber: 3.9 Consensus size: 45
54577943 ATCGTACGAC
*
54577953 ACTATTTGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
1 ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
* *
54577998 ACTATTCGGGCCTTTGAGCCTAGTAGGCTACAATGCCGGTGAGAT
1 ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
54578043 ACTATTCGGG-CTTTCGAGCCTAGCAGGCTATAATGCCGGTGA-A-
1 ACTATTCGGGCCTTT-GAGCCTAGCAGGCTATAATGCCGGTGAGAT
** * * *
54578086 AGGATATCGGGCC-TCGAGTCTAGCAGGCGA-AATGCCGGTGA
1 ACTAT-TCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
54578127 ATGAATTCGG
Statistics
Matches: 116, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
42 11 0.09
43 16 0.14
44 11 0.09
45 78 0.67
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (45 bp):
ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
Found at i:54591438 original size:30 final size:30
Alignment explanation
Indices: 54591403--54591462 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
54591393 GGTGCAGGGG
*
54591403 ACACACGGCCTA-ACCACATGTCCGTGTGTC
1 ACACACGGCCTAGA-CACATGCCCGTGTGTC
*
54591433 ACACACGGTCTAGACACATGCCCGTGTGTC
1 ACACACGGCCTAGACACATGCCCGTGTGTC
54591463 TGCCCATGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.23, C:0.35, G:0.22, T:0.20
Consensus pattern (30 bp):
ACACACGGCCTAGACACATGCCCGTGTGTC
Found at i:54594078 original size:145 final size:145
Alignment explanation
Indices: 54593882--54594153 Score: 499
Period size: 145 Copynumber: 1.9 Consensus size: 145
54593872 CTCAAGGTAC
* * *
54593882 TTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGTACCCTTCATGTAAATAATTTATAGA
1 TTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGA
*
54593947 AAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGCAT
66 AAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGCAT
54594012 TTCAAGTTCGCACAT
131 TTCAAGTTCGCACAT
*
54594027 TTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATAGA
1 TTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGA
54594092 AAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATG
66 AAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATG
54594154 TACTTTAAAC
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
145 122 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (145 bp):
TTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGA
AAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGCAT
TTCAAGTTCGCACAT
Found at i:54594170 original size:29 final size:30
Alignment explanation
Indices: 54594131--54594209 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
54594121 CTTAATAATC
54594131 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
54594161 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
54594190 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
54594210 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:54600486 original size:22 final size:23
Alignment explanation
Indices: 54600470--54600514 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
54600460 AATTCATGCC
54600470 ACAAAATATACCAATTCATCATCA
1 ACAAAATATACCAATTCATCA-CA
*
54600494 ACAAAATGTACCAATTCATCA
1 ACAAAATATACCAATTCATCA
54600515 ACCTTATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (23 bp):
ACAAAATATACCAATTCATCACA
Found at i:54600514 original size:21 final size:21
Alignment explanation
Indices: 54600460--54600516 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
54600450 ATTATCATAT
*
54600460 AATTCATGCCACAAAATATACC
1 AATTCAT-CAACAAAATATACC
*
54600482 AATTCATCATCAACAAAATGTACC
1 AA-T--TCATCAACAAAATATACC
54600506 AATTCATCAAC
1 AATTCATCAAC
54600517 CTTATACCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 8 0.27
22 2 0.07
23 2 0.07
24 14 0.47
25 4 0.13
ACGTcount: A:0.46, C:0.26, G:0.04, T:0.25
Consensus pattern (21 bp):
AATTCATCAACAAAATATACC
Found at i:54601457 original size:42 final size:42
Alignment explanation
Indices: 54601425--54601528 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 42
54601415 TAGCTTAGCT
54601425 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCTAGAC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCTAGAC
* * *
54601467 ATGGTCTTACACGAATCTCATATCGATGCAAATGTCCCAGTC
1 ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCTAGAC
*
54601509 ATGGTCTTACATGAATCTCA
1 ATGGTCTTACACGAATCTCA
54601529 CATCCCGATA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGGTCTTACACGAATCTCATATCGATGCCAATGTCCTAGAC
Found at i:54605261 original size:189 final size:189
Alignment explanation
Indices: 54604941--54605318 Score: 666
Period size: 189 Copynumber: 2.0 Consensus size: 189
54604931 CAAAATCTGG
54604941 GTGTTACAACTCTCCACCCTTTAGGGATTTTCGTCCCCGAAAATCTTACCAGAAAAGTGGTCTTC
1 GTGTTACAACTCTCCACCCTTTAGGGATTTTCGTCCCCGAAAATCTTACCAGAAAAGTGGTCTTC
* * * * *
54605006 ACTTAGATTCCTCAGTCTCATAGTCGATACCAAAGTACCTTTGCTCAGGTGGTGCCTCCAATACA
66 ACTTAGATTCCTCAATCTCATACTCAATACCAAAGTACCTTCGCTCAGGCGGTGCCTCCAATACA
54605071 TCTCTTTAATTTCTCATATGATCTGAAAGCTTACGGACTCAACTCCCAATTGTTCTTAA
131 TCTCTTTAATTTCTCATATGATCTGAAAGCTTACGGACTCAACTCCCAATTGTTCTTAA
* * * *
54605130 GTGTTACAACTCTCCCCCCTTTAGGGATTTTTGTCTCCGAAAATCTTACCGGAAAAGTGGTCTTC
1 GTGTTACAACTCTCCACCCTTTAGGGATTTTCGTCCCCGAAAATCTTACCAGAAAAGTGGTCTTC
*
54605195 ACTTAGATTCCTCAATCTCATTCTCAATACCAAAGTACCTTCGCTCAGGCGGTGCCTCCAATACA
66 ACTTAGATTCCTCAATCTCATACTCAATACCAAAGTACCTTCGCTCAGGCGGTGCCTCCAATACA
54605260 TCTCTTTAATTTCTCATATGATCTGAAAGCTTACGGACTCAACTCCCAATTGTTCTTAA
131 TCTCTTTAATTTCTCATATGATCTGAAAGCTTACGGACTCAACTCCCAATTGTTCTTAA
54605319 ATTTTCAAAG
Statistics
Matches: 179, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
189 179 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (189 bp):
GTGTTACAACTCTCCACCCTTTAGGGATTTTCGTCCCCGAAAATCTTACCAGAAAAGTGGTCTTC
ACTTAGATTCCTCAATCTCATACTCAATACCAAAGTACCTTCGCTCAGGCGGTGCCTCCAATACA
TCTCTTTAATTTCTCATATGATCTGAAAGCTTACGGACTCAACTCCCAATTGTTCTTAA
Found at i:54612811 original size:11 final size:11
Alignment explanation
Indices: 54612795--54612827 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
54612785 GTCTCTGCCC
54612795 GTGTGCCCAAT
1 GTGTGCCCAAT
54612806 GTGTGCCCAAT
1 GTGTGCCCAAT
54612817 GTGTGCCCAAT
1 GTGTGCCCAAT
54612828 TCTGAGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (11 bp):
GTGTGCCCAAT
Found at i:54616027 original size:24 final size:23
Alignment explanation
Indices: 54616000--54616046 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
54615990 AACAATTTGC
*
54616000 ACCCATGACCAAAGCATCAAAAAA
1 ACCCATGACCAAAGAAT-AAAAAA
*
54616024 ACCCTTGACCAAAGAATAAAAAA
1 ACCCATGACCAAAGAATAAAAAA
54616047 CATACCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.55, C:0.26, G:0.09, T:0.11
Consensus pattern (23 bp):
ACCCATGACCAAAGAATAAAAAA
Found at i:54619375 original size:29 final size:29
Alignment explanation
Indices: 54619341--54619408 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
54619331 ATGAGAGCTT
*
54619341 TTGTGGCTATATCTATTAAGTGGACGCCC
1 TTGTGGCTATATCTATTAAGTAGACGCCC
* * * *
54619370 TTGTGGCTATATTTATTATGTAGATGCCT
1 TTGTGGCTATATCTATTAAGTAGACGCCC
54619399 TTGTGGCTAT
1 TTGTGGCTAT
54619409 TTATCTGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.43
Consensus pattern (29 bp):
TTGTGGCTATATCTATTAAGTAGACGCCC
Found at i:54619424 original size:28 final size:28
Alignment explanation
Indices: 54619340--54619469 Score: 108
Period size: 27 Copynumber: 4.6 Consensus size: 28
54619330 TATGAGAGCT
*
54619340 TTTGTGGCTA--TATCTATTAAGTGGACGCC
1 TTTGTGGCTATTTATCTATT---TGGATGCC
* * *
54619369 CTTGTGGCTATATTTAT-TATGTAGATGCC
1 TTTGTGGC--TATTTATCTATTTGGATGCC
*
54619398 TTTGTGGCTATTTATCTGTTTGGATGCC
1 TTTGTGGCTATTTATCTATTTGGATGCC
54619426 TTTGTGGCTATCTTA--TATTTGGATGCC
1 TTTGTGGCTAT-TTATCTATTTGGATGCC
* *
54619453 TTTTTGGCTATCTATCT
1 TTTGTGGCTATTTATCT
54619470 TTGATCTAGT
Statistics
Matches: 82, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
26 2 0.02
27 28 0.34
28 21 0.26
29 23 0.28
31 2 0.02
32 3 0.04
33 3 0.04
ACGTcount: A:0.16, C:0.15, G:0.22, T:0.47
Consensus pattern (28 bp):
TTTGTGGCTATTTATCTATTTGGATGCC
Found at i:54619461 original size:55 final size:56
Alignment explanation
Indices: 54619361--54619469 Score: 141
Period size: 55 Copynumber: 1.9 Consensus size: 56
54619351 ATCTATTAAG
*
54619361 TGGACGCCCTTGTGGCTATATTTATTATGTAGATGCCTTTGTGGCTATTTATCTGTT
1 TGGACGCCCTTGTGGCTATATTTATTATG-AGATGCCTTTGTGGCTATCTATCTGTT
* * * *
54619418 TGGATGCCTTTGTGGCTATCTTATATT-TG-GATGCCTTTTTGGCTATCTATCT
1 TGGACGCCCTTGTGGCTATATT-TATTATGAGATGCCTTTGTGGCTATCTATCT
54619470 TTGATCTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 21 0.46
57 21 0.46
58 4 0.09
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.47
Consensus pattern (56 bp):
TGGACGCCCTTGTGGCTATATTTATTATGAGATGCCTTTGTGGCTATCTATCTGTT
Found at i:54623695 original size:34 final size:34
Alignment explanation
Indices: 54623623--54623705 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
54623613 CAATTCAGTA
* *
54623623 ACAGT-TCAGTTTCAGTTAGGGCCTTAGCCCATT
1 ACAGTATCAGTATCAGTTAGGGCCTAAGCCCATT
54623656 ACAGTATCAGTATCAGTGT-GGGCCTAAGCCCATCT
1 ACAGTATCAGTATCAGT-TAGGGCCTAAGCCCAT-T
*
54623691 -CAGTAACAGTA-CAGT
1 ACAGTATCAGTATCAGT
54623706 ATAGATATGC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
33 9 0.20
34 33 0.75
35 2 0.05
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (34 bp):
ACAGTATCAGTATCAGTTAGGGCCTAAGCCCATT
Found at i:54626316 original size:31 final size:31
Alignment explanation
Indices: 54626281--54626344 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
54626271 ATTTACCATT
54626281 TTGAACTAAACCCCCTCGAGGGCTAAATTTC
1 TTGAACTAAACCCCCTCGAGGGCTAAATTTC
54626312 TTGAACTAAACCCCCTCGAGGGCTAAATTTC
1 TTGAACTAAACCCCCTCGAGGGCTAAATTTC
54626343 TT
1 TT
54626345 TCTCAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (31 bp):
TTGAACTAAACCCCCTCGAGGGCTAAATTTC
Found at i:54630270 original size:237 final size:237
Alignment explanation
Indices: 54629855--54630329 Score: 932
Period size: 237 Copynumber: 2.0 Consensus size: 237
54629845 GGTCCTCGAG
54629855 ACCCTAAAATATGAAATTGAAACGGTTCAGGAACAAACCGGAATCAATAAAAATTTTCTGATCAC
1 ACCCTAAAATATGAAATTGAAACGGTTCAGGAACAAACCGGAATCAATAAAAATTTTCTGATCAC
54629920 TTAAACAAATCAAACAATTCATTTCATCTTTCATAAATAAACTATCCATCTGCGTCATAGTCACT
66 TTAAACAAATCAAACAATTCATTTCATCTTTCATAAATAAACTATCCATCTGCGTCATAGTCACT
54629985 AAATAAATCATAACTCGAGTTACGAAACTCAAAATTCAAATTTATAAATTTTCTCTGAAACTAGA
131 AAATAAATCATAACTCGAGTTACGAAACTCAAAATTCAAATTTATAAATTTTCTCTGAAACTAGA
54630050 CTCATATATCTTCTTACTTAATTTGTTTCATAATTTTTTGTC
196 CTCATATATCTTCTTACTTAATTTGTTTCATAATTTTTTGTC
*
54630092 ACCCTAAAATATGAAATTGAAACGGTTCAGGAATAAACCGGAATCAATAAAAATTTTCTGATCAC
1 ACCCTAAAATATGAAATTGAAACGGTTCAGGAACAAACCGGAATCAATAAAAATTTTCTGATCAC
*
54630157 TTAAACAAATCAAACAATTCATTTCATCTTTCATAAATAAACTATTCATCTGCGTCATAGTCACT
66 TTAAACAAATCAAACAATTCATTTCATCTTTCATAAATAAACTATCCATCTGCGTCATAGTCACT
54630222 AAATAAATCATAACTCGAGTTACGAAACTCAAAATTCAAATTTATAAATTTTCTCTGAAACTAGA
131 AAATAAATCATAACTCGAGTTACGAAACTCAAAATTCAAATTTATAAATTTTCTCTGAAACTAGA
54630287 CTCATATATCTTCTTACTTAATTTGTTTCATAATTTTTTGTC
196 CTCATATATCTTCTTACTTAATTTGTTTCATAATTTTTTGTC
54630329 A
1 A
54630330 AGCCAATTAG
Statistics
Matches: 236, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
237 236 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (237 bp):
ACCCTAAAATATGAAATTGAAACGGTTCAGGAACAAACCGGAATCAATAAAAATTTTCTGATCAC
TTAAACAAATCAAACAATTCATTTCATCTTTCATAAATAAACTATCCATCTGCGTCATAGTCACT
AAATAAATCATAACTCGAGTTACGAAACTCAAAATTCAAATTTATAAATTTTCTCTGAAACTAGA
CTCATATATCTTCTTACTTAATTTGTTTCATAATTTTTTGTC
Found at i:54631588 original size:55 final size:53
Alignment explanation
Indices: 54631472--54631657 Score: 153
Period size: 55 Copynumber: 3.4 Consensus size: 53
54631462 CCATGTCTCA
* *
54631472 ACATGGTCTTTCATGGTATCCTTGCCTTATGAACTCACCAATGCCACGCCTTG
1 ACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATGCCACGCCTTG
* * * * * *
54631525 GCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTTATCAATGCGATGTCTTG
1 ACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTCACCAATGCCACGCCTTG
* * * * *
54631580 ACATGGTCTTACATGGTA-CACTTGTCTTA-GAAACCTTACCAATTTCCATGCCTTG
1 ACATGGTCTTACATGGGATC-CTTGCCTTATG-AA-CTCACCAA-TGCCACGCCTTG
* *
54631635 GCATGGTCTTACATGGTATCCTT
1 ACATGGTCTTACATGGGATCCTT
54631658 AAACCCTAAT
Statistics
Matches: 109, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
52 2 0.02
53 27 0.25
54 8 0.07
55 70 0.64
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (53 bp):
ACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATGCCACGCCTTG
Found at i:54640197 original size:40 final size:40
Alignment explanation
Indices: 54640160--54640291 Score: 169
Period size: 40 Copynumber: 3.3 Consensus size: 40
54640150 GCTACTCGTT
**
54640160 CAAATGCCTTCGGGACATAGTCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
* *
54640200 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
54640240 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
54640279 CAAATGCCTTCGG
1 CAAATGCCTTCGG
54640292 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.42
40 46 0.55
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:54640279 original size:79 final size:82
Alignment explanation
Indices: 54640160--54640344 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
54640150 GCTACTCGTT
* * * *
54640160 CAAATGCCTTCGGGACATAGTCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
54640223 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
54640240 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
54640303 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
54640320 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54640345 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.59
80 34 0.38
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:54651488 original size:16 final size:16
Alignment explanation
Indices: 54651469--54651499 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54651459 CTTCTTCACT
54651469 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
54651485 TACTTACTTACTTAA
1 TACTCACTTACTTAA
54651500 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:54651505 original size:20 final size:20
Alignment explanation
Indices: 54651466--54651505 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54651456 AAACTTCTTC
* *
54651466 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
54651486 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
54651506 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:54651861 original size:55 final size:55
Alignment explanation
Indices: 54651794--54651993 Score: 289
Period size: 55 Copynumber: 3.6 Consensus size: 55
54651784 CTTATGACAA
* * *
54651794 TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA-CTTATCAA-
1 TGCCATGCCTTGGCATGGTCTTACATGGTATCCTTT-CC-T-TAGAAACCTTACCAAT
* * *
54651849 TGCGATGTCTTGGCATGGTCTTACATGGTATCCTTTCCTTAGAAATCTTACCAAT
1 TGCCATGCCTTGGCATGGTCTTACATGGTATCCTTTCCTTAGAAACCTTACCAAT
*
54651904 TGCCATGCCTTGACATGGTCTTACATGGTATCCTTTCCTTAGAAACCTTACCAAT
1 TGCCATGCCTTGGCATGGTCTTACATGGTATCCTTTCCTTAGAAACCTTACCAAT
54651959 TGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 TGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
54651994 AAACCCTAAT
Statistics
Matches: 132, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
53 5 0.04
54 8 0.06
55 114 0.86
56 5 0.04
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (55 bp):
TGCCATGCCTTGGCATGGTCTTACATGGTATCCTTTCCTTAGAAACCTTACCAAT
Found at i:54654638 original size:48 final size:47
Alignment explanation
Indices: 54654567--54654795 Score: 250
Period size: 48 Copynumber: 4.8 Consensus size: 47
54654557 GAGGGTAAAT
54654567 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-TCAC
* * * *
54654615 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCA-TGATG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATTCA-C
* *
54654662 TGGTCGATGCCATGTCCCAGACATGGTCTTACACTAG-TGCACATATCAAC
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT-CTCAT-TC-AC
* * * * *
54654712 -ACTGATGCCATGTTCCAGACATGGTCTTACACTGGCTCTCATGTC-G
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-TCAC
*
54654758 TGGCCGATGCCATGTCCCAGACATGGTCTTACGCTAGC
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
54654796 ACACATATCA
Statistics
Matches: 149, Mismatches: 23, Indels: 18
0.78 0.12 0.09
Matches are distributed among these distances:
46 2 0.01
47 2 0.01
48 142 0.95
49 1 0.01
50 1 0.01
51 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (47 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATTCAC
Found at i:54654734 original size:96 final size:96
Alignment explanation
Indices: 54654568--54654805 Score: 338
Period size: 96 Copynumber: 2.5 Consensus size: 96
54654558 AGGGTAAATT
* * *
54654568 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC-ACTGCCGATGCCATGTCCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-TCACATATCAACTACCGATGCCATGTCCC
54654632 AAACATGGTCTTACACTGGCTCTCATGAT-GTG
65 AAACATGGTCTTACACTGGCTCTCATG-TCGTG
* * *
54654664 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGTGCACATATCAAC-ACTGATGCCATGTTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGT-CACATATCAACTACCGATGCCATGTCCC
*
54654728 AGACATGGTCTTACACTGGCTCTCATGTCGTG
65 AAACATGGTCTTACACTGGCTCTCATGTCGTG
* *
54654760 GCCGATGCCATGTCCCAGACATGGTCTTACGCTAGCACACATATCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-TCACATATCA
54654806 CCCAAATGAC
Statistics
Matches: 128, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
95 2 0.02
96 124 0.97
97 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGTCACATATCAACTACCGATGCCATGTCCCA
AACATGGTCTTACACTGGCTCTCATGTCGTG
Found at i:54663888 original size:45 final size:45
Alignment explanation
Indices: 54663824--54663915 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
54663814 CCTAGACTAG
* *
54663824 TAGTTTAAAGTAAGCAAGCAAATGCCCAATTAAAATTTAAATCCA
1 TAGTTTAAAGTAAACAAGCAAATGCCCAATTAAAACTTAAATCCA
54663869 TAGTTTAAAGTAAACAAGCAAATGCCCAATTAAAACTTAAATCCA
1 TAGTTTAAAGTAAACAAGCAAATGCCCAATTAAAACTTAAATCCA
54663914 TA
1 TA
54663916 AAAGGCCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (45 bp):
TAGTTTAAAGTAAACAAGCAAATGCCCAATTAAAACTTAAATCCA
Found at i:54672860 original size:26 final size:27
Alignment explanation
Indices: 54672809--54672864 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
54672799 CTAGCCTAAG
* *
54672809 AATAGTGGGGTTTTGTTTTAATTAACT
1 AATAATGGGGTTTTGTTTTAACTAACT
54672836 AATAATGGGG-TTTGTTTTAACTAACT
1 AATAATGGGGTTTTGTTTTAACTAACT
54672862 AAT
1 AAT
54672865 TAACTAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (27 bp):
AATAATGGGGTTTTGTTTTAACTAACT
Found at i:54677322 original size:21 final size:21
Alignment explanation
Indices: 54677271--54677322 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
54677261 TTTTTCCTAG
*
54677271 GATG-TTAATTGAATTAAATT
1 GATGATTAAATGAATTAAATT
*
54677291 GA-GTATGAAATGAATTAAATT
1 GATG-ATTAAATGAATTAAATT
54677312 GATGATTAAAT
1 GATGATTAAAT
54677323 TCATTTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 2 0.08
21 22 0.85
22 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.38
Consensus pattern (21 bp):
GATGATTAAATGAATTAAATT
Found at i:54681061 original size:43 final size:43
Alignment explanation
Indices: 54680960--54681124 Score: 174
Period size: 43 Copynumber: 3.8 Consensus size: 43
54680950 CAATGCCATA
* * * * **
54680960 TCCCAGATATGGTCTTACATGTTATCACA-TATCGACGCCATTG
1 TCCCAGACATGGTCTTACATGTAATCATAGTA-CGATGCCAACG
* * * *
54681003 GCCCACACA-GTGTCTTACACGAAATCATAGTACGATGCCAACG
1 TCCCAGACATG-GTCTTACATGTAATCATAGTACGATGCCAACG
* *
54681046 TCCCAGACATGGTCTTACATGTAATC-TCAATACAATGCCAACG
1 TCCCAGACATGGTCTTACATGTAATCAT-AGTACGATGCCAACG
54681089 TCCCAGACATGGTCTTACATGTAATCATAGTACGAT
1 TCCCAGACATGGTCTTACATGTAATCATAGTACGAT
54681125 AACCTAGTGT
Statistics
Matches: 99, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
42 2 0.02
43 93 0.94
44 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACATGTAATCATAGTACGATGCCAACG
Found at i:54688708 original size:43 final size:43
Alignment explanation
Indices: 54688661--54688769 Score: 139
Period size: 43 Copynumber: 2.5 Consensus size: 43
54688651 TCGACGACAC
* * **
54688661 TGTCCCAGACAGGGTCTTACATGAAATCAT-AATACGATGCCAA
1 TGTCCTAGACATGGTCTTACATGAAATC-TCAATAAAATGCCAA
* * *
54688704 TGTCCTAGACATGGTCTTATACGTAATCTCAATAAAATGCCAA
1 TGTCCTAGACATGGTCTTACATGAAATCTCAATAAAATGCCAA
54688747 TGTCCTAGACATGGTCTTACATG
1 TGTCCTAGACATGGTCTTACATG
54688770 TTATCACAAC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (43 bp):
TGTCCTAGACATGGTCTTACATGAAATCTCAATAAAATGCCAA
Found at i:54698725 original size:13 final size:13
Alignment explanation
Indices: 54698707--54698731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54698697 ACAAACAATC
54698707 AAATTTTCATACG
1 AAATTTTCATACG
54698720 AAATTTTCATAC
1 AAATTTTCATAC
54698732 ATACTAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
AAATTTTCATACG
Found at i:54703803 original size:42 final size:43
Alignment explanation
Indices: 54703690--54703809 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 43
54703680 CAAAAATCTC
* * * * * *
54703690 ATACAATGCCAACGTCCCAGACGTAGTCTTACA-TATAATCAA
1 ATACGATGCCAACGTCCAAAACGTGGTCTTACACGATAACCAA
* *
54703732 ATATCGATGCC-ACTGTCCTATAC-TGGGTCTTACACGA-AACCAA
1 ATA-CGATGCCAAC-GTCCAAAACGT-GGTCTTACACGATAACCAA
54703775 ATACGATGCCAACGTCCAAAACGTGGTCTTACACG
1 ATACGATGCCAACGTCCAAAACGTGGTCTTACACG
54703810 TAAATCATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
42 31 0.48
43 32 0.50
44 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (43 bp):
ATACGATGCCAACGTCCAAAACGTGGTCTTACACGATAACCAA
Found at i:54707956 original size:43 final size:42
Alignment explanation
Indices: 54707909--54708059 Score: 119
Period size: 43 Copynumber: 3.5 Consensus size: 42
54707899 CTAGACGTGA
* *
54707909 TCTTACATGTAATCAAATATCGATGCCACCGTCCCAGACAGGG
1 TCTTACACGAAATCAAATATCGATGCCA-CGTCCCAGACAGGG
* * * * *
54707952 TCTTACACGAAATCAAATA-CAATACTGATGTCCCAGACATGG
1 TCTTACACGAAATCAAATATCGATGC-CACGTCCCAGACAGGG
* * *
54707994 TCTTACACGTAAATCATAA-GTCGATGCCAACGTCCCATAC-GTTG
1 TCTTACACG-AAATCA-AATATCGATGCC-ACGTCCCAGACAG-GG
* *
54708038 TCTTACATGAAATCACATATCG
1 TCTTACACGAAATCAAATATCG
54708060 GATCCTATGT
Statistics
Matches: 83, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
42 26 0.31
43 33 0.40
44 24 0.29
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (42 bp):
TCTTACACGAAATCAAATATCGATGCCACGTCCCAGACAGGG
Found at i:54709164 original size:13 final size:13
Alignment explanation
Indices: 54709146--54709171 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54709136 ACAAACAATC
54709146 AAATTTTCATACA
1 AAATTTTCATACA
54709159 AAATTTTCATACA
1 AAATTTTCATACA
54709172 TACTAATTCA
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTTTCATACA
Found at i:54710789 original size:15 final size:15
Alignment explanation
Indices: 54710757--54710785 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54710747 ATTTTCTGTG
54710757 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
54710772 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
54710786 ATTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:54715158 original size:46 final size:45
Alignment explanation
Indices: 54715089--54715263 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
54715079 TGTAACCCGC
* * *
54715089 CCATAAGTGAAATCGGACCCAACTCAACGAGCTCGGGCGTTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTAT
* *
54715135 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGT-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGTAT
* * * * * *
54715181 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTAT
*
54715228 CCATAAGTAAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
54715264 ATGCTCAACC
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
45 3 0.03
46 64 0.62
47 33 0.32
48 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGTAT
Found at i:54718823 original size:26 final size:26
Alignment explanation
Indices: 54718794--54718901 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
54718784 TGGTACAAAT
54718794 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
54718820 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54718846 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
54718872 TGATAATAGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54718898 TGAT
1 TGAT
54718902 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54739379 original size:13 final size:13
Alignment explanation
Indices: 54739363--54739387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54739353 TTAAATCAGT
54739363 TAATTAGTTTAAA
1 TAATTAGTTTAAA
54739376 TAATTAGTTTAA
1 TAATTAGTTTAA
54739388 TAAATAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:54744748 original size:17 final size:17
Alignment explanation
Indices: 54744728--54744794 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
54744718 TTATTTACTC
54744728 TTATTTTTTATTTTATT
1 TTATTTTTTATTTTATT
*
54744745 TTATTTTTCT-TTTGATT
1 TTATTTTT-TATTTTATT
* *
54744762 TT-TATTTTCATTTCAATT
1 TTAT-TTTTTATTT-TATT
54744780 TTATTATTTTATTTT
1 TTATT-TTTTATTTT
54744795 GAAAGACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
16 1 0.03
17 23 0.59
18 7 0.18
19 8 0.21
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (17 bp):
TTATTTTTTATTTTATT
Found at i:54752624 original size:29 final size:29
Alignment explanation
Indices: 54752582--54752753 Score: 256
Period size: 29 Copynumber: 6.0 Consensus size: 29
54752572 GCATGTATAT
54752582 GAATGTGATTTGGGCCTAATGGGCCATAC
1 GAATGTGATTTGGGCCTAATGGGCCATAC
* *
54752611 GAATATGATTTGGGCATAATGGGCCATAC
1 GAATGTGATTTGGGCCTAATGGGCCATAC
* *
54752640 GAATGTGATTTAGGCCTAATGGGCTATAC
1 GAATGTGATTTGGGCCTAATGGGCCATAC
54752669 GAATGTGATTTGGGCCTAATGGGCCATAC
1 GAATGTGATTTGGGCCTAATGGGCCATAC
* * *
54752698 GATTGTGATTTGGGCCTAATAGGCCATAT
1 GAATGTGATTTGGGCCTAATGGGCCATAC
* *
54752727 GAATGAGA-TTGGGCCTAGTGGGCCATA
1 GAATGTGATTTGGGCCTAATGGGCCATA
54752754 TGCATGTATG
Statistics
Matches: 128, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 17 0.13
29 111 0.87
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (29 bp):
GAATGTGATTTGGGCCTAATGGGCCATAC
Found at i:54758867 original size:29 final size:29
Alignment explanation
Indices: 54758810--54758895 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 29
54758800 TACTTGTATC
*
54758810 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCATATTCATA
54758838 TGGCCCATTAGGCCCAAATCACCTA-T-ATA
1 TGGCCCATTAGGCCCAAATCA--TATTCATA
* * *
54758867 TGGCCCATTAGACCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCATATTCATA
54758895 T
1 T
54758896 TCATGCTCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 22 0.45
29 22 0.45
30 1 0.02
31 2 0.04
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCATATTCATA
Found at i:54759148 original size:24 final size:23
Alignment explanation
Indices: 54759103--54759148 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
54759093 ACTGTAGCCA
* *
54759103 AACTTTTGACTTTTCGGCATTTC
1 AACTTTTGACTTTTCAGAATTTC
54759126 AACTTTTCGACTTTTCAGAATTT
1 AACTTTT-GACTTTTCAGAATTT
54759149 TGGCTTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (23 bp):
AACTTTTGACTTTTCAGAATTTC
Found at i:54759164 original size:16 final size:16
Alignment explanation
Indices: 54759145--54759188 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
54759135 ACTTTTCAGA
*
54759145 ATTTTGGCTTTTCGGC
1 ATTTAGGCTTTTCGGC
54759161 ATTTCAGG-TTTTCGGC
1 ATTT-AGGCTTTTCGGC
*
54759177 ATTTCGGCTTTT
1 ATTTAGGCTTTT
54759189 GCCGATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.09, C:0.18, G:0.23, T:0.50
Consensus pattern (16 bp):
ATTTAGGCTTTTCGGC
Found at i:54761024 original size:43 final size:43
Alignment explanation
Indices: 54760976--54761084 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 43
54760966 TATAAATGGC
* *
54760976 CTTACATGTTATCACATATCGATGCCACTATCCCAAACAGGGT
1 CTTACATGTAATCACATATCGATGCCAATATCCCAAACAGGGT
* * * * * * *
54761019 CTTACACGAAATCA-ATTAACAATGCCAATGTCCCAGACATGGT
1 CTTACATGTAATCACA-TATCGATGCCAATATCCCAAACAGGGT
*
54761062 CTTACATGTAATCACATCTCGAT
1 CTTACATGTAATCACATATCGAT
54761085 AACCTAATGT
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
42 1 0.02
43 48 0.96
44 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (43 bp):
CTTACATGTAATCACATATCGATGCCAATATCCCAAACAGGGT
Found at i:54763543 original size:40 final size:40
Alignment explanation
Indices: 54763475--54763655 Score: 182
Period size: 40 Copynumber: 4.5 Consensus size: 40
54763465 TATCTTGCAT
* * * * * *
54763475 ACTAAGTGTCGTACATAGTCGAAACTATCTCAAATCGCGC
1 ACTAAGTGCCATATATAGCCGAAGCTATCTCAAATCGCAC
* *
54763515 ACTAAGTGCCATATATAGCCAAAGCTATCTCAATTCTTGCAC
1 ACTAAGTGCCATATATAGCCGAAGCTATCTCAAATC--GCAC
**
54763557 ACTAAGTGCCATATATAGCCGAAGCTATCTCGATCTCGCAC
1 ACTAAGTGCCATATATAGCCGAAGCTATCTC-AAATCGCAC
* * * * * *
54763598 ATTAGGTGCCATTTATAGCTGAAGCTATGTCAAATCACAC
1 ACTAAGTGCCATATATAGCCGAAGCTATCTCAAATCGCAC
*
54763638 ACTAAGTGCCACATATAG
1 ACTAAGTGCCATATATAG
54763656 TTGAATTGTC
Statistics
Matches: 115, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
40 49 0.43
41 30 0.26
42 33 0.29
43 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (40 bp):
ACTAAGTGCCATATATAGCCGAAGCTATCTCAAATCGCAC
Found at i:54763564 original size:42 final size:41
Alignment explanation
Indices: 54763499--54763655 Score: 167
Period size: 42 Copynumber: 3.9 Consensus size: 41
54763489 ATAGTCGAAA
*
54763499 CTATCTCAAATC-GCGCACTAAGTGCCATATATAGCCAAAG
1 CTATCTCAAATCTGCACACTAAGTGCCATATATAGCCAAAG
* *
54763539 CTATCTCAATTCTTGCACACTAAGTGCCATATATAGCCGAAG
1 CTATCTCAAATC-TGCACACTAAGTGCCATATATAGCCAAAG
* * * * **
54763581 CTATCTC-GATCTCGCACATTAGGTGCCATTTATAGCTGAAG
1 CTATCTCAAATCT-GCACACTAAGTGCCATATATAGCCAAAG
* * *
54763622 CTATGTCAAATC-ACACACTAAGTGCCACATATAG
1 CTATCTCAAATCTGCACACTAAGTGCCATATATAG
54763656 TTGAATTGTC
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
40 29 0.30
41 32 0.33
42 36 0.37
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (41 bp):
CTATCTCAAATCTGCACACTAAGTGCCATATATAGCCAAAG
Found at i:54766232 original size:93 final size:93
Alignment explanation
Indices: 54766120--54766291 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
54766110 CGCCCATAAG
* *
54766120 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54766185 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
*
54766213 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
54766278 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
54766292 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:54766288 original size:46 final size:46
Alignment explanation
Indices: 54766113--54766288 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
54766103 TGTAACCCGC
* *
54766113 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
54766159 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* *
54766209 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
54766252 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
54766289 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.58
47 28 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:54779770 original size:49 final size:48
Alignment explanation
Indices: 54779424--54779833 Score: 202
Period size: 46 Copynumber: 8.7 Consensus size: 48
54779414 TTTGTGTGCT
* * * *
54779424 AGTGTAAGA-CATGTCTGGGATAT-GCATTGGCCAC-ATT-ATGAGAACC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGATTGATGAG--CC
* * * * * **
54779470 CGTGTAAGACCATGCCT-GGACATGGCATCAGCATTGAAACGA-GAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCG-ATTGATGAGCC
* *
54779517 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCGA--GATGTAAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGATTGATG--AGCC
* * * **
54779563 AGTGTAAGA-CATGTCTGGGACAT-GCATCAG-CTACGA--GATGTGGT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCT-CGATTGATGAGCC
* * * * *
54779607 AGTGTAAAACCATGTCTGGGACATGGCATCAGCACAT--ATAGATG-TCTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGC-C-TCGATTGATGAGC-C
* * * * *
54779655 AATATAAGACCAT-TCCTAGGACATGGCATCGACAC-AGATATG-TGAGAGCT
1 AGTGTAAGACCATGT-CTAGGACATGGCATCGGC-CTCGAT-TGAT--GAGCC
* *
54779705 AGTGTAAGACCATGTCT-GAGACATGGCGTCGGCCTCGATTTCGAT-AGTC
1 AGTGTAAGACCATGTCTAG-GACATGGCATCGGCCTCGA-TT-GATGAGCC
* * *
54779754 AGTGTAAGACCCTGTCTAGGACATGGCATC-GACTTGATTGATGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGATTGATGAGCC
54779801 AGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGC
54779834 ATTATACCCC
Statistics
Matches: 282, Mismatches: 48, Indels: 66
0.71 0.12 0.17
Matches are distributed among these distances:
43 2 0.01
44 10 0.04
45 17 0.06
46 77 0.27
47 63 0.22
48 41 0.15
49 36 0.13
50 31 0.11
51 4 0.01
52 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGATTGATGAGCC
Found at i:54784845 original size:42 final size:43
Alignment explanation
Indices: 54784739--54784848 Score: 125
Period size: 44 Copynumber: 2.6 Consensus size: 43
54784729 GGATATGTAT
* * * *
54784739 TTTCGTGTAAGACCATGTCTAGGACGTTCGCATCGACTTATGA
1 TTTCGTGTAAGACCCTGTCTGGGACATTCGCATCGAATTATGA
* * *
54784782 TTTATGTGTAAGACCAC-GTCTGGGACATTGGCATCTAATT-TGA
1 TTT-CGTGTAAGACC-CTGTCTGGGACATTCGCATCGAATTATGA
54784825 TTTCGTGTAAGACCCTGTCTGGGA
1 TTTCGTGTAAGACCCTGTCTGGGA
54784849 TAGTGAAATC
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.02
42 18 0.32
43 9 0.16
44 28 0.50
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (43 bp):
TTTCGTGTAAGACCCTGTCTGGGACATTCGCATCGAATTATGA
Done.