Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 53 of 82
Found at i:19435694 original size:114 final size:114
Alignment explanation
Indices: 19435494--19435755 Score: 335
Period size: 114 Copynumber: 2.3 Consensus size: 114
19435484 CGTTATGATA
* * *
19435494 TTACATGTCATGTACAAAAACCTGTGACAAGCTATGGTTAGTGTATTACACGCTATGTACAAAAA
1 TTACATGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGTGTATTACACGCTATATACAAAAA
* * * *
19435559 TATGTGATACGTCATGTACAAAAACCTATGACAAGTTATGATTAACTTG
66 TATGTGACACGTCATATACAAAAACCTATGACAAGCTATGATTAACGTG
* * * * * *
19435608 TTACATGCCATGTACAAAAACTTGTGATATGCCGTGGTTAGTGTGTTACATGCTATATACAAAAA
1 TTACATGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGTGTATTACACGCTATATACAAAAA
* * *
19435673 TATGTGACACGTCATATACAAAAACTTGTGACAAGCTATGATTAGCGTG
66 TATGTGACACGTCATATACAAAAACCTATGACAAGCTATGATTAACGTG
* * * **
19435722 TTACACGCTATATACAAAAATATGTGACAAGCCA
1 TTACATGCCATGTACAAAAACCTGTGACAAGCCA
19435756 AGTACAAAAT
Statistics
Matches: 124, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
114 124 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (114 bp):
TTACATGCCATGTACAAAAACCTGTGACAAGCCATGGTTAGTGTATTACACGCTATATACAAAAA
TATGTGACACGTCATATACAAAAACCTATGACAAGCTATGATTAACGTG
Found at i:19435840 original size:183 final size:183
Alignment explanation
Indices: 19435500--19435840 Score: 459
Period size: 183 Copynumber: 1.9 Consensus size: 183
19435490 GATATTACAT
* * * *
19435500 GTCATGTACAAAAACCTGTGACAAGCTATGGTTAGTGTATTACACGCTATGTACAAAAATATGTG
1 GTCATATACAAAAACCTGTGACAAGCTATGATTAGCGTATTACACGCTATATACAAAAATATGTG
* * * * * * * *
19435565 ATACGTCATGTACAAAAACCTATGACAAGTTATGATTAACTTGTTACATGCCATGTACAAAAACT
66 ACAAGCCAAGTACAAAAACCTATGACAAGCTATGATTAACATGTTACACGCCATATACAAAAACT
* * * *
19435630 TGTGATATGCCGTGGTTAGTGTGTTACATGCTATATACAAAAATATGTGACAC
131 TGTGACAAGCCATGATTAGTGTGTTACATGCTATATACAAAAATATGTGACAC
* *
19435683 GTCATATACAAAAACTTGTGACAAGCTATGATTAGCGTGTTACACGCTATATACAAAAATATGTG
1 GTCATATACAAAAACCTGTGACAAGCTATGATTAGCGTATTACACGCTATATACAAAAATATGTG
* * * **
19435748 ACAAGCCAAGTACAAAATCCTGTGACAAGCTATGGTTAGGATGTTACACGCCATATACAAAAACT
66 ACAAGCCAAGTACAAAAACCTATGACAAGCTATGATTAACATGTTACACGCCATATACAAAAACT
19435813 TGTGACAAGCCATGATTAG-GTTGTTACA
131 TGTGACAAGCCATGATTAGTG-TGTTACA
19435841 CGCCATGTTG
Statistics
Matches: 134, Mismatches: 23, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
182 1 0.01
183 133 0.99
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (183 bp):
GTCATATACAAAAACCTGTGACAAGCTATGATTAGCGTATTACACGCTATATACAAAAATATGTG
ACAAGCCAAGTACAAAAACCTATGACAAGCTATGATTAACATGTTACACGCCATATACAAAAACT
TGTGACAAGCCATGATTAGTGTGTTACATGCTATATACAAAAATATGTGACAC
Found at i:19435855 original size:45 final size:45
Alignment explanation
Indices: 19435758--19435846 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
19435748 ACAAGCCAAG
* * * *
19435758 TACAAAATCCTGTGACAAGCTATGGTTAGGATGTTACACGCCATA
1 TACAAAAACTTGTGACAAGCCATGATTAGGATGTTACACGCCATA
*
19435803 TACAAAAACTTGTGACAAGCCATGATTAGGTTGTTACACGCCAT
1 TACAAAAACTTGTGACAAGCCATGATTAGGATGTTACACGCCAT
19435847 GTTGAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (45 bp):
TACAAAAACTTGTGACAAGCCATGATTAGGATGTTACACGCCATA
Found at i:19435869 original size:31 final size:29
Alignment explanation
Indices: 19435832--19435972 Score: 143
Period size: 31 Copynumber: 4.9 Consensus size: 29
19435822 CCATGATTAG
19435832 GTTGTTACACGCCATGTTGAAAAAAAATACT
1 GTTGTTACACGCCATGTTGAAAAAAAA-A-T
19435863 GTTGTTACACGCCATG-T--AAAAAAAAT
1 GTTGTTACACGCCATGTTGAAAAAAAAAT
*
19435889 G-TGTTACACGTCATGGTT---AAAAAAAT
1 GTTGTTACACGCCAT-GTTGAAAAAAAAAT
*
19435915 GTTGTTACATGCCATGTTGAAAAAAAAAATATT
1 GTTGTTACACGCCATGTTG--AAAAAAAA-A-T
*
19435948 GTTGTTACACGCCATATTGAAAAAA
1 GTTGTTACACGCCATGTTGAAAAAA
19435973 TATTATTATT
Statistics
Matches: 95, Mismatches: 5, Indels: 20
0.79 0.04 0.17
Matches are distributed among these distances:
25 12 0.13
26 15 0.16
27 13 0.14
28 7 0.07
30 1 0.01
31 28 0.29
32 1 0.01
33 18 0.19
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (29 bp):
GTTGTTACACGCCATGTTGAAAAAAAAAT
Found at i:19435883 original size:27 final size:26
Alignment explanation
Indices: 19435832--19435940 Score: 121
Period size: 27 Copynumber: 4.0 Consensus size: 26
19435822 CCATGATTAG
19435832 GTTGTTACACGCCATGTTGAAAAAAAATACT
1 GTTGTTACACGCCATGTT---AAAAAA-A-T
*
19435863 GTTGTTACACGCCATGTAAAAAAAAT
1 GTTGTTACACGCCATGTTAAAAAAAT
*
19435889 G-TGTTACACGTCATGGTTAAAAAAAT
1 GTTGTTACACGCCAT-GTTAAAAAAAT
*
19435915 GTTGTTACATGCCATGTTGAAAAAAA
1 GTTGTTACACGCCATGTT-AAAAAAA
19435941 AAATATTGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
25 12 0.17
26 16 0.23
27 19 0.27
28 6 0.09
31 17 0.24
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (26 bp):
GTTGTTACACGCCATGTTAAAAAAAT
Found at i:19435956 original size:33 final size:31
Alignment explanation
Indices: 19435832--19435972 Score: 106
Period size: 33 Copynumber: 4.8 Consensus size: 31
19435822 CCATGATTAG
* * *
19435832 GTTGTTACACGCCATGTTGAAAAAAAATACT
1 GTTGTTACACGCCATATTGAAAAAAAAAAAT
*
19435863 GTTGTTACACGCC--A-TG--TAAAAAAAAT
1 GTTGTTACACGCCATATTGAAAAAAAAAAAT
* *
19435889 G-TGTTACACGTCATGGTT-----AAAAAAAT
1 GTTGTTACACGCCAT-ATTGAAAAAAAAAAAT
* *
19435915 GTTGTTACATGCCATGTTGAAAAAAAAAATATT
1 GTTGTTACACGCCATATTGAAAAAAAAAA-A-T
19435948 GTTGTTACACGCCATATTGAAAAAA
1 GTTGTTACACGCCATATTGAAAAAA
19435973 TATTATTATT
Statistics
Matches: 88, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
25 10 0.11
26 20 0.23
27 11 0.12
28 2 0.02
29 1 0.01
31 19 0.22
32 1 0.01
33 24 0.27
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (31 bp):
GTTGTTACACGCCATATTGAAAAAAAAAAAT
Found at i:19435984 original size:29 final size:28
Alignment explanation
Indices: 19435938--19436004 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 28
19435928 ATGTTGAAAA
* * *
19435938 AAAAAATATTGTTGTTACACGCCATATT
1 AAAAAATATTATTATTACACGACATATT
19435966 GAAAAAATATTATTATTACACGACATATT
1 -AAAAAATATTATTATTACACGACATATT
*
19435995 CAAAAATATT
1 AAAAAATATT
19436005 TTGTTATACT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 9 0.26
29 25 0.74
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (28 bp):
AAAAAATATTATTATTACACGACATATT
Found at i:19441023 original size:30 final size:30
Alignment explanation
Indices: 19440989--19441047 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
19440979 GCAATAGAAT
*
19440989 TGAATCACATTCTTTATT-AATTAATTTAAA
1 TGAATCACATTC-ATATTAAATTAATTTAAA
* *
19441019 TGAATCATATTCATATTAAATTGATTTAA
1 TGAATCACATTCATATTAAATTAATTTAA
19441048 CTCCACAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (30 bp):
TGAATCACATTCATATTAAATTAATTTAAA
Found at i:19443126 original size:30 final size:30
Alignment explanation
Indices: 19443086--19443148 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
19443076 AGTTAATGAG
19443086 CATATCTGTCATGAT-CCTCAGCATATCTAT
1 CATATCTGTCATGATCCCT-AGCATATCTAT
* *
19443116 CATATTTGTCATGATCCCTAGCATATCTGT
1 CATATCTGTCATGATCCCTAGCATATCTAT
19443146 CAT
1 CAT
19443149 GATCCCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.38
Consensus pattern (30 bp):
CATATCTGTCATGATCCCTAGCATATCTAT
Found at i:19443146 original size:21 final size:21
Alignment explanation
Indices: 19443116--19443156 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19443106 GCATATCTAT
*
19443116 CATATTTGTCATGATCCCTAG
1 CATATCTGTCATGATCCCTAG
19443137 CATATCTGTCATGATCCCTA
1 CATATCTGTCATGATCCCTA
19443157 TTATCCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (21 bp):
CATATCTGTCATGATCCCTAG
Found at i:19443183 original size:34 final size:35
Alignment explanation
Indices: 19443138--19443204 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
19443128 GATCCCTAGC
* *
19443138 ATATCTGTCATGA-TCCCTATTATCCTTCATTATG
1 ATATCTATCATGATTCCCTAATATCCTTCATTATG
19443172 ATATCTATCATGATTCCCTAATATCCTTCATTA
1 ATATCTATCATGATTCCCTAATATCCTTCATTA
19443205 CTTCCCCTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.43
Consensus pattern (35 bp):
ATATCTATCATGATTCCCTAATATCCTTCATTATG
Found at i:19444634 original size:21 final size:21
Alignment explanation
Indices: 19444595--19444635 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19444585 TGAAGGATAA
* *
19444595 TGGGGATTATAACAGATATGT
1 TGGGGATCATAACAAATATGT
*
19444616 TGGGGATCATGACAAATATG
1 TGGGGATCATAACAAATATG
19444636 CTGGAGTGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.29
Consensus pattern (21 bp):
TGGGGATCATAACAAATATGT
Found at i:19448460 original size:21 final size:20
Alignment explanation
Indices: 19448435--19448473 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
19448425 TAAGTCAAAA
19448435 AGCATATTTATCATGATCTCC
1 AGCATATTTATCAT-ATCTCC
*
19448456 AGCATATTTGTCATATCT
1 AGCATATTTATCATATCT
19448474 GTCATGATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (20 bp):
AGCATATTTATCATATCTCC
Found at i:19448619 original size:23 final size:24
Alignment explanation
Indices: 19448579--19448631 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
19448569 TATTTTTTAA
*
19448579 TTTAATTTTAATTATTTTTTATCT
1 TTTAATTTTAATTATTTTTAATCT
*
19448603 TTTAATTTTTATT-TTTTTAATCT
1 TTTAATTTTAATTATTTTTAATCT
*
19448626 ATTAAT
1 TTTAAT
19448632 AAGACTACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTAATTTTAATTATTTTTAATCT
Found at i:19477614 original size:29 final size:27
Alignment explanation
Indices: 19477548--19477616 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
19477538 AAAAAAATTT
* *
19477548 AAATAAGTTTTTATTTTTTATTATATTT
1 AAATAA-TTTTTATTTTTTATTATAATC
* *
19477576 AATTATATTTTTATATTTTTATTTTAAATC
1 AAATA-ATTTTTAT-TTTTTATTAT-AATC
19477606 AAATAATTTTT
1 AAATAATTTTT
19477617 TTAATTAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 11 0.33
29 16 0.48
30 6 0.18
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (27 bp):
AAATAATTTTTATTTTTTATTATAATC
Found at i:19477901 original size:29 final size:29
Alignment explanation
Indices: 19477823--19477902 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
19477813 AGTTATTAAT
*
19477823 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTTAA-ATAAAATAAAAA
* ** *
19477853 TATAAAAACTTGA-TCGAATAGAATAAAAGA
1 TATAAAAA-TTTATTTAAATAAAATAAAA-A
19477883 -ATAAAAATTTATTTAAATAA
1 TATAAAAATTTATTTAAATAA
19477903 TTCAAAGAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
28 3 0.08
29 21 0.55
30 11 0.29
31 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.34
Consensus pattern (29 bp):
TATAAAAATTTATTTAAATAAAATAAAAA
Found at i:19481691 original size:2 final size:2
Alignment explanation
Indices: 19481679--19481709 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
19481669 CAAATATGAA
19481679 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
19481710 GTAAAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19490111 original size:41 final size:42
Alignment explanation
Indices: 19490066--19490148 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 42
19490056 CCTCAGCTTA
* *
19490066 GTCAACTTGATCAATCTTTTCTAATTATATTTATATC-CTTG
1 GTCAACTTCATCAATCTTCTCTAATTATATTTATATCTCTTG
* *
19490107 GTCAACTTCATCTATCTTCTCTAATTATATTTCTATCTCTTG
1 GTCAACTTCATCAATCTTCTCTAATTATATTTATATCTCTTG
19490149 ACCTCTATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 33 0.89
42 4 0.11
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.49
Consensus pattern (42 bp):
GTCAACTTCATCAATCTTCTCTAATTATATTTATATCTCTTG
Found at i:19491281 original size:90 final size:90
Alignment explanation
Indices: 19491128--19491304 Score: 336
Period size: 90 Copynumber: 2.0 Consensus size: 90
19491118 ATATTATTTT
*
19491128 ATTGCTTGTATTATTGTATTTAAGTTATATTAATGTCAATTTGTCTTTTTTCTTATTTATCAAGT
1 ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTGTCTTTTTTCTTATTTATCAAGT
19491193 ACTAGGATTGATAAACTAGTCTGTA
66 ACTAGGATTGATAAACTAGTCTGTA
19491218 ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTGTCTTTTTTCTTATTTATCAAGT
1 ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTGTCTTTTTTCTTATTTATCAAGT
*
19491283 ACTATGATTGATAAACTAGTCT
66 ACTAGGATTGATAAACTAGTCT
19491305 ACATGTACTT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (90 bp):
ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTGTCTTTTTTCTTATTTATCAAGT
ACTAGGATTGATAAACTAGTCTGTA
Found at i:19494415 original size:12 final size:12
Alignment explanation
Indices: 19494398--19494430 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
19494388 ATTTGGTTGG
19494398 TAAGAATAATTT
1 TAAGAATAATTT
19494410 TAAGAATAA-TT
1 TAAGAATAATTT
*
19494421 AAAGAATAAT
1 TAAGAATAAT
19494431 GAATAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (12 bp):
TAAGAATAATTT
Found at i:19494648 original size:22 final size:22
Alignment explanation
Indices: 19494623--19494694 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
19494613 AAATACAAAC
*
19494623 ATATTTTTGTTATAATTTAATA
1 ATATTTTTATTATAATTTAATA
* * **
19494645 ATATTTGTATTAGAAGATAATTA
1 ATATTTTTATTATAATTTAA-TA
*
19494668 A-ATCTTTTATTATAATTAAATA
1 ATAT-TTTTATTATAATTTAATA
19494690 ATATT
1 ATATT
19494695 GAATACTAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
22 21 0.57
23 16 0.43
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (22 bp):
ATATTTTTATTATAATTTAATA
Found at i:19494766 original size:41 final size:44
Alignment explanation
Indices: 19494720--19494812 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
19494710 AAATATATTC
* *
19494720 TTTATTAAATTTAAATAAT-ACA-AAATAATATTCTTTATTATA
1 TTTATTAAATTCAAATAATAACATAAATAATATTCTTTATAATA
* *
19494762 -TTATTATATTCAAATAATAATATTAAATAATATTCTTTATAATA
1 TTTATTAAATTCAAATAATAACA-TAAATAATATTCTTTATAATA
19494806 TTTATTA
1 TTTATTA
19494813 TAGCTAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
41 16 0.37
42 2 0.05
44 19 0.44
45 6 0.14
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (44 bp):
TTTATTAAATTCAAATAATAACATAAATAATATTCTTTATAATA
Found at i:19494803 original size:22 final size:22
Alignment explanation
Indices: 19494742--19494807 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
19494732 AAATAATACA
*
19494742 AAATAATATTCTTTATTATATT
1 AAATAATATTCTTTATAATATT
* * *
19494764 --ATTATATTCAAATAATAATATT
1 AAATAATATTC--TTTATAATATT
19494786 AAATAATATTCTTTATAATATT
1 AAATAATATTCTTTATAATATT
19494808 TATTATAGCT
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
20 8 0.24
22 17 0.52
24 8 0.24
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATAATATTCTTTATAATATT
Found at i:19494830 original size:41 final size:43
Alignment explanation
Indices: 19494731--19494835 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 43
19494721 TTATTAAATT
* * *
19494731 TAAATAATACAAAATAATATTCTTTATTATATTATTATATTCA
1 TAAATAATACTAAATAATATTCTTTATAATATTATTATATGCA
* *
19494774 AATAATAATATTAAATAATATTCTTTATAATATTTATTATA-GC-
1 TA-AATAATACTAAATAATATTCTTTATAATA-TTATTATATGCA
19494817 TAAATAATA-TAAAT-ATATT
1 TAAATAATACTAAATAATATT
19494836 AAATGATATT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
40 5 0.09
41 5 0.09
42 7 0.13
43 2 0.04
44 27 0.50
45 8 0.15
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.46
Consensus pattern (43 bp):
TAAATAATACTAAATAATATTCTTTATAATATTATTATATGCA
Found at i:19496058 original size:2 final size:2
Alignment explanation
Indices: 19496051--19496075 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19496041 AAGATTTTTG
19496051 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19496076 TCCTCTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19499782 original size:15 final size:15
Alignment explanation
Indices: 19499762--19499797 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
19499752 AAAAACGAAA
19499762 AAAAATCCACAAATG
1 AAAAATCCACAAATG
*
19499777 AAAAAT-CTCAAATG
1 AAAAATCCACAAATG
19499791 AAAAATC
1 AAAAATC
19499798 TTAGTGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.61, C:0.17, G:0.06, T:0.17
Consensus pattern (15 bp):
AAAAATCCACAAATG
Found at i:19502144 original size:17 final size:16
Alignment explanation
Indices: 19502111--19502144 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19502101 GGAGGTGTGT
19502111 GTGTGTGTGGTGGGGGG
1 GTGTGTGTGG-GGGGGG
*
19502128 NTGTGTGTGGGGGGGG
1 GTGTGTGTGGGGGGGG
19502144 G
1 G
19502145 GCGGGGGGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 1
0.83 0.11 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.00, G:0.71, T:0.26
Consensus pattern (16 bp):
GTGTGTGTGGGGGGGG
Found at i:19505356 original size:18 final size:18
Alignment explanation
Indices: 19505320--19505357 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19505310 GAAGGTAAAA
19505320 CTAAAAATAAATTGTTAC
1 CTAAAAATAAATTGTTAC
*
19505338 CTAATAAATATATTG-TAC
1 CTAA-AAATAAATTGTTAC
19505356 CT
1 CT
19505358 TTAATGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (18 bp):
CTAAAAATAAATTGTTAC
Found at i:19516920 original size:35 final size:35
Alignment explanation
Indices: 19516868--19517075 Score: 220
Period size: 35 Copynumber: 5.9 Consensus size: 35
19516858 AGTCTTTAAG
**
19516868 AAGCCCAATTAACTTAATTATTTAATTTAATCAATT
1 AAGCCCAA-TAACTTAATTAAATAATTTAATCAATT
*
19516904 AAGCCCAATAACTTAATTAAATAATTTAATTAATT
1 AAGCCCAATAACTTAATTAAATAATTTAATCAATT
* *
19516939 AAGCCCAACAATTTAATTAAATAATTTTAATCAATT
1 AAGCCCAATAACTTAATTAAATAA-TTTAATCAATT
* * *
19516975 AGGCCCAATGACTTAATTAAACAAATTTAATCAATT
1 AAGCCCAATAACTTAATTAAA-TAATTTAATCAATT
* * * * *
19517011 AGGCTCAATGACTTAATTAAACAATTTAATTAATT
1 AAGCCCAATAACTTAATTAAATAATTTAATCAATT
* * * *
19517046 ACA-CTCAATGATTTAATTAAACAATTTAAT
1 A-AGCCCAATAACTTAATTAAATAATTTAAT
19517076 TAAACAATTT
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
35 85 0.56
36 66 0.43
37 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (35 bp):
AAGCCCAATAACTTAATTAAATAATTTAATCAATT
Found at i:19516968 original size:71 final size:70
Alignment explanation
Indices: 19516868--19517078 Score: 217
Period size: 71 Copynumber: 3.0 Consensus size: 70
19516858 AGTCTTTAAG
* *** * *
19516868 AAGCCCAATTAACTTAATTATTTAATTTAATCAATTAAGCCCAATAACTTAATTAAATAATTTAA
1 AAGCCCAA-CAACTTAATTAAACAATTTAATCAATTAAGCCCAATGACTTAATTAAAAAATTTAA
19516933 TTAATT
65 TTAATT
* * *
19516939 AAGCCCAACAATTTAATTAAATAATTTTAATCAATTAGGCCCAATGACTTAATTAAACAAATTTA
1 AAGCCCAACAACTTAATTAAACAA-TTTAATCAATTAAGCCCAATGACTTAATTAAA-AAATTTA
*
19517004 ATCAATT
64 ATTAATT
* * ** * * * *
19517011 AGGCTCAATGACTTAATTAAACAATTTAATTAATTACA-CTCAATGATTTAATTAAACAATTTAA
1 AAGCCCAACAACTTAATTAAACAATTTAATCAATTA-AGCCCAATGACTTAATTAAAAAATTTAA
19517075 TTAA
65 TTAA
19517079 ACAATTTTAA
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
70 22 0.19
71 65 0.56
72 30 0.26
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (70 bp):
AAGCCCAACAACTTAATTAAACAATTTAATCAATTAAGCCCAATGACTTAATTAAAAAATTTAAT
TAATT
Found at i:19517089 original size:14 final size:13
Alignment explanation
Indices: 19517056--19517085 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19517046 ACACTCAATG
19517056 ATTTAATTAAACA
1 ATTTAATTAAACA
19517069 ATTTAATTAAACA
1 ATTTAATTAAACA
19517082 ATTT
1 ATTT
19517086 TAATCAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
ATTTAATTAAACA
Found at i:19519526 original size:61 final size:61
Alignment explanation
Indices: 19519420--19519574 Score: 229
Period size: 61 Copynumber: 2.5 Consensus size: 61
19519410 GTGACAAATG
* * **
19519420 CAACCGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCATGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGTAGTGCACATACCGACAATGATGCTGTCATGATAATTA
* * * * *
19519481 CAACCGTGCATGTGCGGAGTGGGTAGTGTACATACCGACAGTGATGTTGTCGTGATAGTTA
1 CAACCGTGCATGTGCGGAGTGGGTAGTGCACATACCGACAATGATGCTGTCATGATAATTA
19519542 CAACCGTGCATGTGCGGAGTGGGTAGTGCACAT
1 CAACCGTGCATGTGCGGAGTGGGTAGTGCACAT
19519575 GCCGGTGATG
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 84 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (61 bp):
CAACCGTGCATGTGCGGAGTGGGTAGTGCACATACCGACAATGATGCTGTCATGATAATTA
Found at i:19522118 original size:24 final size:24
Alignment explanation
Indices: 19522086--19522132 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
19522076 CAATCAAACA
* *
19522086 ATGAGGTGTCACATATATTTGTAC
1 ATGACGTGTAACATATATTTGTAC
* *
19522110 ATGACGTGTAACATGTTTTTGTA
1 ATGACGTGTAACATATATTTGTA
19522133 TATCGTGTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (24 bp):
ATGACGTGTAACATATATTTGTAC
Found at i:19524509 original size:2 final size:2
Alignment explanation
Indices: 19524502--19524543 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19524492 AAGTTGCCAA
19524502 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19524544 TATTATACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19525350 original size:1 final size:1
Alignment explanation
Indices: 19525346--19525379 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
19525336 TCACCCCCTT
* *
19525346 CCCCCACCCCCCGCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
19525380 GCCCAAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.03, C:0.94, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:19528501 original size:15 final size:16
Alignment explanation
Indices: 19528481--19528510 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19528471 TATACGTTCG
19528481 AAAAACAAAA-AAAAA
1 AAAAACAAAAGAAAAA
19528496 AAAAACAAAAGAAAA
1 AAAAACAAAAGAAAA
19528511 GCCAAAGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAGAAAAA
Found at i:19533802 original size:12 final size:12
Alignment explanation
Indices: 19533780--19533810 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19533770 TATATTATAT
19533780 ATTTTTT-AATA
1 ATTTTTTAAATA
19533791 ATTTTTTAAATA
1 ATTTTTTAAATA
19533803 ATTTTTTA
1 ATTTTTTA
19533811 TTAAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTTTAAATA
Found at i:19533814 original size:15 final size:14
Alignment explanation
Indices: 19533781--19533820 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
19533771 ATATTATATA
19533781 TTTTTT-AATAA--
1 TTTTTTAAATAATT
19533792 TTTTTTAAATAATT
1 TTTTTTAAATAATT
19533806 TTTTATTAAATAATT
1 TTTT-TTAAATAATT
19533821 AATATAANTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.24
12 5 0.20
14 4 0.16
15 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTTAAATAATT
Found at i:19534823 original size:2 final size:2
Alignment explanation
Indices: 19534816--19534865 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
19534806 GGGGAAAAGA
19534816 AT AT AT AT AT AT AT AT A- AT AT AT AT AT -T AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19534855 AT AT AT AT AT A
1 AT AT AT AT AT A
19534866 ATGTATGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19535670 original size:269 final size:269
Alignment explanation
Indices: 19535201--19535706 Score: 640
Period size: 269 Copynumber: 1.9 Consensus size: 269
19535191 TACCAGCTGA
* * * *
19535201 GAGCATTATCTCTATGATGTAAGATTCACGTCTACGTGAGAACCGTGACATCCTCCCCCACTTCA
1 GAGCATTATCTCCATGATATAAGATTCACATCCACGTGAGAACCGTGACATCCTCCCCCACTTCA
* * * * *
19535266 ACAAGAGTCCATTATCTTTAGTGGTACATTGCTAATACTCAAAGTCCGCTCTGATACCAATTGTT
66 ACAAGAGTCCACTATCTTCAGTGATACATTACTAATACTCAAAGTCCGCTCTGATACCAATTGTC
* * * **
19535331 ACGATCCACACTAACCCTTGTGAGGTATTGTCTGTTTTAACTCATTAGCCTAATGGTTTTATCCC
131 ACGATCCACACTAACCCTTGTAAGGTATTATCTGTTTCAACTCATTAGCCTAACAGTTTTATCCC
*
19535396 ACAAAAGA-GACCTCACAAGTTAAAAGTGATGTGAACCTTTATGTTTTCAGTAGACTTTGTGGTT
196 ACAAAAGATG-CCTCACAAGTTAAAAGTGACGTGAACCTTTATGTTTTCAGTAGACTTTGTGGTT
19535460 CATCCATTGG
260 CATCCATTGG
** *
19535470 GAGCATTATCTCCATGATATTGGATTCACATCCACGTGA-AGACCGTGACATCCTCCCTCACTTC
1 GAGCATTATCTCCATGATATAAGATTCACATCCACGTGAGA-ACCGTGACATCCTCCCCCACTTC
* * * * * *
19535534 AACAAGGGTTCACTATCTTCGGTGATATATTACTAATACTCAGAGTCTGCTCTGATACCAATTGT
65 AACAAGAGTCCACTATCTTCAGTGATACATTACTAATACTCAAAGTCCGCTCTGATACCAATTGT
* * * * * ** * *
19535599 CGCGGTCCACACTAATCCTTGTAAGGTATTATCTGTTTC-AGTCCATTGGTTTCACAGTTTTGTC
130 CACGATCCACACTAACCCTTGTAAGGTATTATCTGTTTCAACT-CATTAGCCTAACAGTTTTATC
* * *
19535663 TCACAAAAGATGCCTCACAGGTTCAAAGTGACGTGAACCTTTAT
194 CCACAAAAGATGCCTCACAAGTTAAAAGTGACGTGAACCTTTAT
19535707 ATTCACAGTA
Statistics
Matches: 198, Mismatches: 36, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
268 3 0.02
269 194 0.98
270 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (269 bp):
GAGCATTATCTCCATGATATAAGATTCACATCCACGTGAGAACCGTGACATCCTCCCCCACTTCA
ACAAGAGTCCACTATCTTCAGTGATACATTACTAATACTCAAAGTCCGCTCTGATACCAATTGTC
ACGATCCACACTAACCCTTGTAAGGTATTATCTGTTTCAACTCATTAGCCTAACAGTTTTATCCC
ACAAAAGATGCCTCACAAGTTAAAAGTGACGTGAACCTTTATGTTTTCAGTAGACTTTGTGGTTC
ATCCATTGG
Found at i:19536812 original size:368 final size:364
Alignment explanation
Indices: 19535469--19536812 Score: 1046
Period size: 366 Copynumber: 3.7 Consensus size: 364
19535459 TCATCCATTG
* * ** * * *
19535469 GGAGCATTATCTCCATGATATTG-GATTCACATCCACGTGAA-GACCGTGACATCCTCCCTCACT
1 GGAGCATTATCTCTATGAT-GTGAGATTCATGTCCACG-CAAGGACCGTGACATCTTCCCCCACT
* ** ** * * * * *
19535532 TCAACAAGGGTTCACTATCTTCGGTGATATATTACTAATACTCAGAG-TCTGCTCTGATACCAAT
64 TCAACAAGGGTCCACTATCTTTAGTGGCATATTGCTAGTACTCAAAGTTC-GCTCTAATATCAAT
* * * * * * * * **
19535596 TGTCGCGGTCCACACTAATCCTTGT-AAGGTATTATCTG-TTTCAGTCC-ATTGGTTTCAC-AGT
128 TGTCACGGTCCACACCAATCCCTGTGAA-GTATTGT-TGTTTTGA-CCCGCTAGCCTT-ACGA-T
* * * * * *
19535657 TTTGTCTCACAAAAGATGCCTCACAGGTTCAAA-GT-GACGTGAACCTTTATATTCACAGTATCA
188 TTTGTCCCACAAAAGGTACCTCACAAGTT-AAAGGTAG-TGTGAACCCTTATATTCACAGTATCA
* * * * *
19535720 CTCTAGTATATAACCA-ATGAGAAAATTCATGGCTCTCCTCTTTAGGACCATGACATCTATTCTT
251 CTCTAATACATAACCATATG-G--GATTCATGGCTCTCCTTTTTAGGACCATGACATCTACTCTT
* * * * * * *
19535784 ACTTTTCACT-ACCCGTTTTTTTTTTCGATGTGGGACTTTGTAGCTCACTCGCTA
313 ACTCTTCATTGA---GATTTTTTCTTCGATGTGAGATTTTGTGGCTCACTCGCTA
* * * * * * *** *
19535838 GGAGCATTATCTCTATGATGTGAGATTTATGTTCATGCAAGAACCATGACATCCTCCTTTACTTT
1 GGAGCATTATCTCTATGATGTGAGATTCATGTCCACGCAAGGACCGTGACATCTTCCCCCACTTC
* * ** * * * * *
19535903 AATAAGGGTCCACTATCTTAAGTAACATATTGCTAATACTCAAAGTCCGCTATAAAATCCATTGT
66 AACAAGGGTCCACTATCTTTAGTGGCATATTGCTAGTACTCAAAGTTCGCTCTAATATCAATTGT
* * * * * *
19535968 CACGGTCCACACTAA-CCCTTATGAGGTATTATATGTTTTGACCCG-TTGACCTTACGATTTTAT
131 CACGGTCCACACCAATCCC-TGTGAAGTATTGT-TGTTTTGACCCGCTAG-CCTTACGATTTTGT
* *
19536031 CCCACAAAAGGTACTTAAC-AGATTAAAGGTAGTGTGAACCCTTATATTCACAGTATCACT-TAA
193 CCCACAAAAGGTACCTCACAAG-TTAAAGGTAGTGTGAACCCTTATATTCACAGTATCACTCTAA
* * * * * * * * *
19536094 GTGCATAGCCAATGTGGGATTCATGGCTTTCCTTTCTAAGATCATGACATCTACCCTTACTCCTC
257 -TACATAACC-ATATGGGATTCATGGCTCTCCTTTTTAGGACCATGACATCTACTCTTACTCTTC
** * * *
19536159 ATTG-GCAGCTTTTCTTCGATGTGAGATTTTATGGCTCACCCGCTG
320 ATTGAG-ATTTTTTCTTCGATGTGAGATTTTGTGGCTCACTCGCTA
* * * * * *
19536204 GGAGCATTATTTCTATGATGTGAGATTCGA-GTCCAC-AAGAGGACCGTAATATCCTT-TCCCAT
1 GGAGCATTATCTCTATGATGTGAGATTC-ATGTCCACGCA-AGGACCGTGACAT-CTTCCCCCAC
* * * * *
19536266 TTCAACAAGGGTCCACTAT-TCTTAATGGCATATTGTTAGTACTCAAAGTTCGTTCTGATACCAA
63 TTCAACAAGGGTCCACTATCT-TTAGTGGCATATTGCTAGTACTCAAAGTTCGCTCTAATATCAA
* * * * * *
19536330 TTGTCATGGTCCACACCAATCCTTGTAAAGTATTGTTCGTTTTGGCCTGCTA-TCTTAGCGATTT
127 TTGTCACGGTCCACACCAATCCCTGTGAAGTATTGTT-GTTTTGACCCGCTAGCCTTA-CGATTT
* * * * *
19536394 TGTCCCATAAAAGGTGCCTCACAAATTAAAAGCG-A-TATGAACCCTTATATTCTCAGTATCACT
190 TGTCCCACAAAAGGTACCTCACAAGTT-AAAG-GTAGTGTGAACCCTTATATTCACAGTATCACT
* *
19536457 CTAATACATAACCATTATGGGATTCATTGCTC-CTCTTTTTAGGACCATGACATCCACTCTTACT
253 CTAATACATAACCA-TATGGGATTCATGGCTCTC-CTTTTTAGGACCATGACATCTACTCTTACT
* *
19536521 CTTCATTGAGAATTTTTTCTTCGATGTAAGATTTTGTGGCTCACTCACTA
316 CTTCATTGAG-ATTTTTTCTTCGATGTGAGATTTTGTGGCTCACTCGCTA
19536571 GGAGCATTATCTCTATGATGTGAGATTCATGTCCACGCAAGGACCGTGACATCTTCCCCCCACTT
1 GGAGCATTATCTCTATGATGTGAGATTCATGTCCACGCAAGGACCGTGACATCTT-CCCCCACTT
* * * * *
19536636 CAACAATGGTCCACTATCTTTAGTGGCACATTACTAGTACTCAGAGTTCGCTCTAATATCAATTA
65 CAACAAGGGTCCACTATCTTTAGTGGCATATTGCTAGTACTCAAAGTTCGCTCTAATATCAATTG
* * * * *
19536701 TCACAGTCCACACCAATCCCTGTGAAGTGTTGTCTGCTCTGACCCGCTAGCCTCACCG-TTTTGT
130 TCACGGTCCACACCAATCCCTGTGAAGTATTGT-TGTTTTGACCCGCTAGCCTTA-CGATTTTGT
*** *
19536765 CCCACAAAAAAAACCTCACAAGTTAAAGGTAGTGTGAACCTTTATATT
193 CCCACAAAAGGTACCTCACAAGTTAAAGGTAGTGTGAACCCTTATATT
19536813 TTCAGTAAAT
Statistics
Matches: 759, Mismatches: 175, Indels: 83
0.75 0.17 0.08
Matches are distributed among these distances:
365 10 0.01
366 260 0.34
367 97 0.13
368 189 0.25
369 189 0.25
370 12 0.02
371 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (364 bp):
GGAGCATTATCTCTATGATGTGAGATTCATGTCCACGCAAGGACCGTGACATCTTCCCCCACTTC
AACAAGGGTCCACTATCTTTAGTGGCATATTGCTAGTACTCAAAGTTCGCTCTAATATCAATTGT
CACGGTCCACACCAATCCCTGTGAAGTATTGTTGTTTTGACCCGCTAGCCTTACGATTTTGTCCC
ACAAAAGGTACCTCACAAGTTAAAGGTAGTGTGAACCCTTATATTCACAGTATCACTCTAATACA
TAACCATATGGGATTCATGGCTCTCCTTTTTAGGACCATGACATCTACTCTTACTCTTCATTGAG
ATTTTTTCTTCGATGTGAGATTTTGTGGCTCACTCGCTA
Found at i:19538427 original size:640 final size:632
Alignment explanation
Indices: 19537255--19538456 Score: 1336
Period size: 640 Copynumber: 1.9 Consensus size: 632
19537245 TAAGAGGACT
* * *
19537255 GTGACATCCTCTCTCATTTTCATAAGGGTCCACTGTCCTCAATGACATATTGCTAGTATTTAGAG
1 GTGACATCCTCTCTCATTTTCATAAGGGTCCACTGTCCTCAATGACATAGTGCTAATACTTAGAG
* * * * *
19537320 TCCGCTCTGATACCAATTGTCACGGTCCACACTAATCCTTATGAGATATTGTTCGCTTTGACCCG
66 TCCACTCTGATACCAATTGTCACGGTCCACACCAAACCTTATGAGATATTGTACGCTTTGACCCA
* * * ** *
19537385 CTGACTTAAAGATTTTATCTCATAAAAGGTACCTCATAGGTAAAAGGTGATGTGAACCCTTATAT
131 CTGACCTAAAGATTTTATCTCACAAAAGGTACCTCACAAATAAAAGGTGATATGAACCCTTATAT
* *
19537450 TCTCAGTATCACTCTAGTACATAACCAATGTGGGATTCATTACTCCTCTCTAGGACCATGACATC
196 TCACAGTATCACTCTAGTACATAACCAATGTGGGATTCATTACCCCTCTCTAGGACCATGACATC
** * * * ** *
19537515 CATTCTTACTCTCGTTGAGAGTTTTCCCTTCGATGTGAGACTTTGTGACTTATCTGTTGGGAATA
261 CACCCTTACTCTCGTAGAGAGTTTTCCCTTCGATGTGAGACTTTATGACTCATCACTAGGGAATA
* *
19537580 CTATCTCTATGATGTGAGATTCACGTCTACGCGAAGATCATGACATCTTCCCCCACTTCAAAAAA
326 -TATCTCTATGATGTGAGATTCACGTCTACGCGAAGACCATGACATCATCCCCCACTTCAAAAAA
* * ** * *
19537645 AGTCCACTGTTCTTAGTGGCATATTGCTAGTACTCAGAGTTCGTTTTGATACCAATTGTCATGGT
390 AGTCCACTGATCTTAGTAGCATATTGCTAAAACTCAGAGTTCGCTTTGATACCAATTGTCACGGT
* * * **
19537710 CCACACCAACCCCTGTTAAGTATTACCTGCTTTGGCCCTCTAACCTCATGGTTTTGTATTACAAA
455 CCACACCAACCCCTGTTAAGTATTACCTGCTTAGGCCATCTAACCTCACGGTTTTGTACCACAAA
19537775 AGGGACCTCACAAGTTAAAAGT-GATGTGAAACCTTATATTCTTAGTAGACTTTATGGTTCACTC
520 AGGGACCTCACAAGTTAAAAGTGGA-GTGAAACCTTATATTCTTAGTAGACTTTATGGTTCACTC
19537839 GTTGGGAGCATTATCTTTATGATGTGAGATTCGTATCTACGCGAAGACC
584 GTTGGGAGCATTATCTTTATGATGTGAGATTCGTATCTACGCGAAGACC
* *
19537888 GTGACATCCTC-CTCCA-TTTCAATAAGGGTCCACTGTCCTCAGTGACATAGTGCTAATACTTAT
1 GTGACATCCTCTCT-CATTTTC-ATAAGGGTCCACTGTCCTCAATGACATAGTGCTAATACTTAG
* * * *
19537951 AGTCTACTCTGATACCCATTGTCACGGTCCACACCAACCCACCTTTATGAGGTATTGTACGTTTT
64 AGTCCACTCTGATACCAATTGTCACGGTCCACACCAA---ACC-TTATGAGATATTGTACGCTTT
* * * * * * * * * *
19538016 GGCCCATTGGCCTCATGATTTTGTC-CTACAAAAGGTGCTTCACAAATTAAAGGTGGTATGAACC
125 GACCCACTGACCTAAAGATTTTATCTC-ACAAAAGGTACCTCACAAATAAAAGGTGATATGAACC
* * *
19538080 CTTATATTCACAGTATCACTTTAGTACATAGCCAATGTGGGATTCATGATTCCCCTCTCTAGGAC
189 CTTATATTCACAGTATCACTCTAGTACATAACCAATGTGGGATTCAT--TACCCCTCTCTAGGAC
* * * ** *
19538145 TATGACATCTACCCTTATTCTCCGCTAGA-AGTTTTCTTTTCGATGTGAGACTTTATGGCTCACT
252 CATGACATCCACCCTTACTCT-CG-TAGAGAGTTTTCCCTTCGATGTGAGACTTTATGACTCA-T
* * * * *
19538209 CACTAGGAGCAT-TATCTCTATGATGTGAGATTTATGT-TCATGCG-AGAACCGTGACATCATCC
314 CACTAGG-GAATATATCTCTATGATGTGAGATTCACGTCT-ACGCGAAG-ACCATGACATCATCC
** * *
19538271 CTTACTTC-AACAAGGATCCACT-ATCTTGAGTAGCATATTGCTAAAACTC-GAAG-TCTGCTTT
376 CCCACTTCAAAAAAAG-TCCACTGATCTT-AGTAGCATATTGCTAAAACTCAG-AGTTC-GCTTT
* ** * **
19538332 GATACCAATTGTCACGGTCCACATCC-ACCCTTG-TAAGGTATTGTCTGCTTAGGTTCAT-TGGC
437 GATACCAATTGTCACGGTCCACA-CCAACCCCTGTTAA-GTATTACCTGCTTAGG-CCATCTAAC
* * ** * *
19538394 TTCACGGTTTTGTCCCACAAAAGGGACCTCACAAGTTCCAGGTGGAGTGAACCCTTATATTCT
499 CTCACGGTTTTGTACCACAAAAGGGACCTCACAAGTTAAAAGTGGAGTGAAACCTTATATTCT
19538457 CAATATCTCT
Statistics
Matches: 463, Mismatches: 83, Indels: 39
0.79 0.14 0.07
Matches are distributed among these distances:
632 6 0.01
633 83 0.18
636 3 0.01
637 107 0.23
639 48 0.10
640 199 0.43
641 14 0.03
642 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (632 bp):
GTGACATCCTCTCTCATTTTCATAAGGGTCCACTGTCCTCAATGACATAGTGCTAATACTTAGAG
TCCACTCTGATACCAATTGTCACGGTCCACACCAAACCTTATGAGATATTGTACGCTTTGACCCA
CTGACCTAAAGATTTTATCTCACAAAAGGTACCTCACAAATAAAAGGTGATATGAACCCTTATAT
TCACAGTATCACTCTAGTACATAACCAATGTGGGATTCATTACCCCTCTCTAGGACCATGACATC
CACCCTTACTCTCGTAGAGAGTTTTCCCTTCGATGTGAGACTTTATGACTCATCACTAGGGAATA
TATCTCTATGATGTGAGATTCACGTCTACGCGAAGACCATGACATCATCCCCCACTTCAAAAAAA
GTCCACTGATCTTAGTAGCATATTGCTAAAACTCAGAGTTCGCTTTGATACCAATTGTCACGGTC
CACACCAACCCCTGTTAAGTATTACCTGCTTAGGCCATCTAACCTCACGGTTTTGTACCACAAAA
GGGACCTCACAAGTTAAAAGTGGAGTGAAACCTTATATTCTTAGTAGACTTTATGGTTCACTCGT
TGGGAGCATTATCTTTATGATGTGAGATTCGTATCTACGCGAAGACC
Found at i:19538510 original size:367 final size:366
Alignment explanation
Indices: 19537821--19538967 Score: 1074
Period size: 367 Copynumber: 3.1 Consensus size: 366
19537811 TATTCTTAGT
** * * *** * *
19537821 AGACTTTATGGTTCACTCGTTGGGAGCATTATCTTTATGATGTGAGATTCGTATCTACGCGA-AG
1 AGACTTTATGACTCACTCGCTGGGAGCATTATCTCTATGATGTGAGATTCACGTCCACACGAGA-
* * * * * * * *
19537885 ACCGTGACATC-CTCCTCCATTTCAATAAGGGTCCACTGTCCTCAGT-G-ACATAGTGCTAATAC
65 ACCGTGAAATCTC-CCTTCACTTCAACAAGAGTCCACTATCCTTAGTAGCACAT--TGCTAAAAC
* * * * * *
19537947 TTATAGTCTA-CTCTGATACCCATTGTCACGGTCCACACCAACCCACCTT-TATGAGGTATTGTA
127 TCAAAGTCCACCT-TGATACCAATTGTCACGATCCACACCAA--C-CCTTGTA--AGGTATTGTC
* ** * * * *
19538010 CGTTTTGGCCCATTGGCCTCATGATTTTGTCCTACAAAAGGTGCTTCACAAATTAAAGGTGGTA-
186 CGTCTTAACCCATTGGCCTCACGATTTTGTCCCACAAAAGG-GCCTCACAAGTTAAAGGTGG-AG
* * *
19538074 TGAACCCTTATATTCACAGTATCACTTTAGTACATAGCCAATGTGGGATTCAT-GATTCCCCTCT
249 TGAACCCTTATATTCTCAGTATCACTTTAGTACATAGCCAATGTGGGATTCATGGCTT-CCCTAT
* * *
19538138 CTAGGACTATGACATCTACCCTTATTCTCC-GCTAGAAGTTTTCTTTTCGATGTG
313 CTAGGACCATGACATCCACCCTTA-TCTCCAGATAGAAGTTTTCTTTTCGATGTG
* * * * * * **
19538192 AGACTTTATGGCTCACTCACTAGGAGCATTATCTCTATGATGTGAGATTTATGTTCATGCGAGAA
1 AGACTTTATGACTCACTCGCTGGGAGCATTATCTCTATGATGTGAGATTCACGTCCACACGAGAA
* *
19538257 CCGTGACATCATCCCTT-ACTTCAACAAG-GATCCACTAT-CTTGAGTAGCATATTGCTAAAACT
66 CCGTGAAATC-TCCCTTCACTTCAACAAGAG-TCCACTATCCTT-AGTAGCACATTGCTAAAACT
* ** * * *
19538319 CGAAGTCTGCTTTGATACCAATTGTCACGGTCCACATCC-ACCCTTGTAAGGTATTGTCTG-CTT
128 CAAAGTCCACCTTGATACCAATTGTCACGATCCACA-CCAACCCTTGTAAGGTATTGTCCGTCTT
*** * * **
19538382 AGGTTCATTGGCTTCACGGTTTTGTCCCACAAAAGGGACCTCACAAGTTCCAGGTGGAGTGAACC
192 A-ACCCATTGGCCTCACGATTTTGTCCCACAAAAGGG-CCTCACAAGTTAAAGGTGGAGTGAACC
* * *
19538447 CTTATATTCTCAATATCTCTTTAGTACATAACCAATGTGGGATTCATGGCTTCCCTATCTAGGAC
255 CTTATATTCTCAGTATCACTTTAGTACATAGCCAATGTGGGATTCATGGCTTCCCTATCTAGGAC
*
19538512 CATGACATCCACCCTTA-CTCCTA-ATTGAGAGTTTT-TTCTTCGATGTG
320 CATGACATCCACCCTTATCTCC-AGATAGA-AGTTTTCTT-TTCGATGTG
* * * *
19538559 GGACTTTATGACTCACTCGTTGGGAGCATTATCTCTATGTTGTGGGATTCACGTCCACACGAGAA
1 AGACTTTATGACTCACTCGCTGGGAGCATTATCTCTATGATGTGAGATTCACGTCCACACGAGAA
* * * * **
19538624 CCGTGAAATCTTCCTTCACTTCAATAAGAGTCCACTGTCCTTAGTGGCACATTGCTAGTACTCAA
66 CCGTGAAATCTCCCTTCACTTCAACAAGAGTCCACTATCCTTAGTAGCACATTGCTAAAACTCAA
*
19538689 AGTCCACCTTGATACCAATTGTCACGATCCACACCAACCCTTGTAAGGTATTGTCCGTTTTAACC
131 AGTCCACCTTGATACCAATTGTCACGATCCACACCAACCCTTGTAAGGTATTGTCCGTCTTAACC
** * * * * * *
19538754 CGCTAGCCTCACGATTTTGTCCCACAAAAAGTGCCTCATAGGTTAAAAGTGGTGT-AACCCCTTA
196 CATTGGCCTCACGATTTTGTCCCAC-AAAAGGGCCTCACAAGTTAAAGGTGGAGTGAA-CCCTTA
* * * * * * *
19538818 TATTCTCAGTATCACTCTAGTATATAGCCAATGTGAGATTCATGGC-TCCTTTTTCTAAGACCAC
259 TATTCTCAGTATCACTTTAGTACATAGCCAATGTGGGATTCATGGCTTCC-CTATCTAGGACCAT
*
19538882 GACATCCACCCTTA-CTCCCAGTTAGAAGTTTTCTTTTCGATGTG
323 GACATCCACCCTTATCT-CCAGATAGAAGTTTTCTTTTCGATGTG
* * *
19538926 AGACTTTGTGACTCATTCGCTGGGAGCATTATCTCCATGATG
1 AGACTTTATGACTCACTCGCTGGGAGCATTATCTCTATGATG
19538968 CAGGATTTGA
Statistics
Matches: 639, Mismatches: 108, Indels: 62
0.79 0.13 0.08
Matches are distributed among these distances:
365 4 0.01
366 21 0.03
367 450 0.70
368 27 0.04
369 3 0.00
370 3 0.00
371 119 0.19
372 8 0.01
373 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (366 bp):
AGACTTTATGACTCACTCGCTGGGAGCATTATCTCTATGATGTGAGATTCACGTCCACACGAGAA
CCGTGAAATCTCCCTTCACTTCAACAAGAGTCCACTATCCTTAGTAGCACATTGCTAAAACTCAA
AGTCCACCTTGATACCAATTGTCACGATCCACACCAACCCTTGTAAGGTATTGTCCGTCTTAACC
CATTGGCCTCACGATTTTGTCCCACAAAAGGGCCTCACAAGTTAAAGGTGGAGTGAACCCTTATA
TTCTCAGTATCACTTTAGTACATAGCCAATGTGGGATTCATGGCTTCCCTATCTAGGACCATGAC
ATCCACCCTTATCTCCAGATAGAAGTTTTCTTTTCGATGTG
Found at i:19544200 original size:2 final size:2
Alignment explanation
Indices: 19544193--19544225 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19544183 ATAAATTAGG
19544193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19544226 GAAATCATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19549503 original size:21 final size:20
Alignment explanation
Indices: 19549477--19549519 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
19549467 TAAAACTATG
*
19549477 TTTGATTGATTTTTTTTTATT
1 TTTGATTGA-TGTTTTTTATT
*
19549498 TTTGATTTATGTTTTTTATT
1 TTTGATTGATGTTTTTTATT
19549518 TT
1 TT
19549520 ATGCAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (20 bp):
TTTGATTGATGTTTTTTATT
Found at i:19553084 original size:86 final size:86
Alignment explanation
Indices: 19552939--19553790 Score: 1259
Period size: 86 Copynumber: 10.0 Consensus size: 86
19552929 CGATATGTTA
* * * *
19552939 TTAAGTTTACATCATAGTTAAAATAATATAAATTAATTTTACATTTGTTAGTTTATAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
19553004 TAATATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* * * * * *
19553025 TTAAGTTTGCATAATAGTTCAAGCAATATAAATTAATTTTACATTTTTTTGTTTATAAGTTTAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
*
19553090 TAGTATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* * *
19553111 TTAAATTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTAAAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
**
19553176 TAATATAAAAATTTTACCTAT
66 TAATATAAAAATTTTATATAT
* * *
19553197 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACAATTATTAGTTTACAAATTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
* *
19553262 TGATATTAAAATTTTATACT-T
66 TAATATAAAAATTTTATA-TAT
* * * *
19553283 TTAAGATTGTATCTTAGTTCAAGTAATATAAATTAATTATACATTTGTTAGTTTACAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
19553348 TAATATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
*
19553369 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTCA-TTTAAAAGTTCAA
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTT-AGTTTACAAGTTCAA
*
19553433 CTACTATAAAAATTTTATATAT
65 CTAATATAAAAATTTTATATAT
* * * *
19553455 TTAAGTTTACATTACAGTTCAAGTAATATAAATTAATTTTACATTGGTTAGTTTACAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
*
19553520 TAATATAAAAATATTATATAT
66 TAATATAAAAATTTTATATAT
* *
19553541 TTAAGTTTCCATCATAGTTCAAGTAATACAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
19553606 TAATATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* * * *
19553627 TTAAGTTTGCATCATACTTTAAGTAACATAAATTAATTTTACATTTATTAGTTTACAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
**
19553692 TAATATAAATTTTTTATATAT
66 TAATATAAAAATTTTATATAT
* *
19553713 TTAAGTTTGCAT--TA--T-AAGTTATATAAATTAATTTTACATTTGTTAGTTTACAAATTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
19553773 TAATATAAAAATTTTATA
66 TAATATAAAAATTTTATA
19553791 AGTACTATAA
Statistics
Matches: 693, Mismatches: 69, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
81 57 0.08
82 1 0.00
84 2 0.00
85 2 0.00
86 629 0.91
87 2 0.00
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (86 bp):
TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
TAATATAAAAATTTTATATAT
Found at i:19558769 original size:19 final size:18
Alignment explanation
Indices: 19558746--19558802 Score: 73
Period size: 16 Copynumber: 3.2 Consensus size: 18
19558736 TGAATTAGTA
19558746 GATTCATGTATCATTATT
1 GATTCATGTATCATTATT
* *
19558764 GTATTCATGAATCAGTA--
1 G-ATTCATGTATCATTATT
19558781 GATTCATGTATCATTATT
1 GATTCATGTATCATTATT
19558799 GATT
1 GATT
19558803 ACATACATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 13 0.41
17 1 0.03
18 5 0.16
19 13 0.41
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
GATTCATGTATCATTATT
Found at i:19558787 original size:16 final size:16
Alignment explanation
Indices: 19558735--19558793 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
19558725 TACTGCATAT
*
19558735 ATGAATTAGTAGATTC
1 ATGAATCAGTAGATTC
* *
19558751 ATGTATCATTATTGTATTC
1 ATGAATCAGTA--G-ATTC
19558770 ATGAATCAGTAGATTC
1 ATGAATCAGTAGATTC
*
19558786 ATGTATCA
1 ATGAATCA
19558794 TTATTGATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 19 0.56
17 1 0.03
18 1 0.03
19 13 0.38
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (16 bp):
ATGAATCAGTAGATTC
Found at i:19558797 original size:35 final size:35
Alignment explanation
Indices: 19558712--19558799 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 35
19558702 CATTTATTGT
* * *
19558712 ATTCATATATCATTACTGCATATATGAATTAGTAG
1 ATTCATGTATCATTATTGCATATATGAATCAGTAG
*
19558747 ATTCATGTATCATTATTGTAT-TCATGAATCAGTAG
1 ATTCATGTATCATTATTGCATAT-ATGAATCAGTAG
19558782 ATTCATGTATCATTATTG
1 ATTCATGTATCATTATTG
19558800 ATTACATACA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 1 0.02
35 47 0.98
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (35 bp):
ATTCATGTATCATTATTGCATATATGAATCAGTAG
Found at i:19558823 original size:39 final size:36
Alignment explanation
Indices: 19558712--19558823 Score: 120
Period size: 35 Copynumber: 3.1 Consensus size: 36
19558702 CATTTATTGT
* * * *
19558712 ATTCATATATCATTACTG-CATATATGAATTAGTAG
1 ATTCATGTATCATTATTGTCATACATGAATAAGTAG
* *
19558747 ATTCATGTATCATTATTGT-ATTCATGAATCAGTAG
1 ATTCATGTATCATTATTGTCATACATGAATAAGTAG
*
19558782 ATTCATGTATCATTATTGATTACATACATGAATAAATAG
1 ATTCATGTATCATTATTG--T-CATACATGAATAAGTAG
19558821 ATT
1 ATT
19558824 TGATTATAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 47 0.73
37 1 0.02
39 16 0.25
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (36 bp):
ATTCATGTATCATTATTGTCATACATGAATAAGTAG
Found at i:19566228 original size:22 final size:22
Alignment explanation
Indices: 19566203--19566244 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
19566193 CTTCTTGATT
19566203 AAATTTTA-TATTTATTATTATA
1 AAATTTTATTATTT-TTATTATA
19566225 AAATTTTATTATTTTTATTA
1 AAATTTTATTATTTTTATTA
19566245 ATTAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AAATTTTATTATTTTTATTATA
Found at i:19568977 original size:5 final size:5
Alignment explanation
Indices: 19568967--19568996 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
19568957 TTCAGGGGGT
*
19568967 TTTTA TTTTA TTTTA TTTTA TTTTC TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
19568997 ATTGACTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:19570435 original size:4 final size:4
Alignment explanation
Indices: 19570426--19570475 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
19570416 CTTGTATCTC
* * * *
19570426 ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT ATAT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
19570474 AT
1 AT
19570476 GTATCTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:19570441 original size:10 final size:10
Alignment explanation
Indices: 19570426--19570475 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
19570416 CTTGTATCTC
19570426 ATATATATAT
1 ATATATATAT
19570436 ATATATATAT
1 ATATATATAT
* *
19570446 ATATGTATGT
1 ATATATATAT
*
19570456 ATATATATGT
1 ATATATATAT
*
19570466 ATGTATATAT
1 ATATATATAT
19570476 GTATCTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:19570445 original size:14 final size:14
Alignment explanation
Indices: 19570426--19570475 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
19570416 CTTGTATCTC
*
19570426 ATATATATATATAT
1 ATATATATATGTAT
19570440 ATATATATATGTAT
1 ATATATATATGTAT
*
19570454 GTATATATATGTAT
1 ATATATATATGTAT
*
19570468 GTATATAT
1 ATATATAT
19570476 GTATCTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:19570486 original size:12 final size:12
Alignment explanation
Indices: 19570445--19570487 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
19570435 TATATATATA
19570445 TATATGTATGTAT
1 TATATGTATGT-T
*
19570458 ATATATGTATGTA
1 -TATATGTATGTT
*
19570471 TATATGTATCTT
1 TATATGTATGTT
19570483 TATAT
1 TATAT
19570488 TCAGACGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 15 0.58
14 11 0.42
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (12 bp):
TATATGTATGTT
Found at i:19570696 original size:21 final size:20
Alignment explanation
Indices: 19570656--19570696 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
19570646 GTCCAGTTTC
*
19570656 TTTTCTAATTTTTCTTTCAA
1 TTTTCTAATTTTTCTCTCAA
*
19570676 TTTTCTTAATTTTTGTCTCAA
1 TTTTC-TAATTTTTCTCTCAA
19570697 AAAACTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.15, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTCTAATTTTTCTCTCAA
Found at i:19573106 original size:16 final size:17
Alignment explanation
Indices: 19573074--19573107 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19573064 TTATTCAAAT
19573074 GTGACTATTCAAATTAA
1 GTGACTATTCAAATTAA
*
19573091 GTGATTATTC-AATTAA
1 GTGACTATTCAAATTAA
19573107 G
1 G
19573108 ATATGACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (17 bp):
GTGACTATTCAAATTAA
Found at i:19578054 original size:16 final size:17
Alignment explanation
Indices: 19578023--19578056 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
19578013 TTATTCAGAT
19578023 GTGACTATTCAAATTAA
1 GTGACTATTCAAATTAA
*
19578040 GTGATTATT-AAATTAA
1 GTGACTATTCAAATTAA
19578056 G
1 G
19578057 ATATGACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
GTGACTATTCAAATTAA
Found at i:19583565 original size:43 final size:43
Alignment explanation
Indices: 19583504--19583590 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
19583494 CTAATTTATG
19583504 TAAATTTTATAGTTACATTTTATTTATAATGTTACTAAAAATA
1 TAAATTTTATAGTTACATTTTATTTATAATGTTACTAAAAATA
19583547 TAAATTTTATAGTTACATTTTATTTATAATGTTACTAAAAATA
1 TAAATTTTATAGTTACATTTTATTTATAATGTTACTAAAAATA
19583590 T
1 T
19583591 GTATATTGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (43 bp):
TAAATTTTATAGTTACATTTTATTTATAATGTTACTAAAAATA
Found at i:19586873 original size:23 final size:23
Alignment explanation
Indices: 19586829--19586876 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19586819 ATTACACCAC
*
19586829 AACAACAATATAAATACCACAAA
1 AACAACAATATAAATACAACAAA
*
19586852 AACAACAATATTACA-ACAACAAA
1 AACAACAATA-TAAATACAACAAA
19586875 AA
1 AA
19586877 AAACCCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.12
Consensus pattern (23 bp):
AACAACAATATAAATACAACAAA
Found at i:19587026 original size:2 final size:2
Alignment explanation
Indices: 19587019--19587059 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
19587009 GTGGCACACT
* *
19587019 AG AG AG AG AG AG AG AG AG AG AG AA AG AA AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19587060 AGAAGGAGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19588115 original size:16 final size:16
Alignment explanation
Indices: 19588096--19588126 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19588086 GAAATAGATA
19588096 AATATTTAAATTAATC
1 AATATTTAAATTAATC
*
19588112 AATATTTAATTTAAT
1 AATATTTAAATTAAT
19588127 AAGAAAATTA
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTTAAATTAATC
Found at i:19589823 original size:17 final size:16
Alignment explanation
Indices: 19589786--19589831 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
19589776 TTAATTATTA
19589786 ATTATTATTTTCATTTT
1 ATTATTATTTT-ATTTT
19589803 ATTATTATTTT-TTTAT
1 ATTATTATTTTATTT-T
19589819 CATTA-TATTTTAT
1 -ATTATTATTTTAT
19589832 ATTTGATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.12
16 7 0.27
17 16 0.62
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTATTATTTTATTTT
Found at i:19590160 original size:21 final size:21
Alignment explanation
Indices: 19590126--19590165 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19590116 TTTGAATTAT
*
19590126 TTTTATTTATTATTTTTATCC
1 TTTTATTTATTATTGTTATCC
19590147 TTTT-TTTATCTATTGTTAT
1 TTTTATTTAT-TATTGTTAT
19590166 TTATTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTATTTATTATTGTTATCC
Found at i:19590174 original size:14 final size:13
Alignment explanation
Indices: 19590121--19590183 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
19590111 ATATATTTGA
19590121 ATTATTTTTATTT
1 ATTATTTTTATTT
*
19590134 ATTATTTTTA-TC
1 ATTATTTTTATTT
* *
19590146 CTT-TTTTTATCT
1 ATTATTTTTATTT
*
19590158 ATTGTTATTTATTT
1 ATTATT-TTTATTT
19590172 ATTATTTTTATT
1 ATTATTTTTATT
19590184 GAATAACTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
11 6 0.15
12 5 0.12
13 18 0.45
14 11 0.28
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.73
Consensus pattern (13 bp):
ATTATTTTTATTT
Found at i:19591736 original size:20 final size:20
Alignment explanation
Indices: 19591690--19591737 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
19591680 CTCCACCTTT
* *
19591690 TTTTTTTCATTTTTTCTTTA
1 TTTTTTTCATTTTTTATTCA
19591710 TTATTTTT-ATTTTTTAATTCA
1 TT-TTTTTCATTTTTT-ATTCA
19591731 TTTTTTT
1 TTTTTTT
19591738 TGTTTATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTTCATTTTTTATTCA
Found at i:19591737 original size:21 final size:21
Alignment explanation
Indices: 19591689--19591738 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
19591679 TCTCCACCTT
* *
19591689 TTTTTTTTCATTTTTTCTTTA
1 TTTTTTTTCATTTTTTATTCA
*
19591710 TTATTTTT-ATTTTTTAATTCA
1 TTTTTTTTCATTTTTT-ATTCA
19591731 TTTTTTTT
1 TTTTTTTT
19591739 GTTTATGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTTCATTTTTTATTCA
Found at i:19591750 original size:13 final size:13
Alignment explanation
Indices: 19591734--19591777 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
19591724 TAATTCATTT
19591734 TTTTTGTTTATGA
1 TTTTTGTTTATGA
19591747 TTTTTGTTTATGA
1 TTTTTGTTTATGA
*
19591760 TTTTTG-TTATAA
1 TTTTTGTTTATGA
19591772 TTTTTG
1 TTTTTG
19591778 GTGTCTATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (13 bp):
TTTTTGTTTATGA
Found at i:19591944 original size:38 final size:37
Alignment explanation
Indices: 19591887--19592324 Score: 407
Period size: 38 Copynumber: 11.8 Consensus size: 37
19591877 TTTTTTTTTT
* * * * *
19591887 AATGAACTTCTCAAGATTGAGGTAATGACACTTTTAA
1 AATGAACTCCTCAAAACTGAGGCAACGACACTTTTAA
* * * * *
19591924 GAATAAACTCCTCAAAATTGAGGTAATGACACTTTAAA
1 -AATGAACTCCTCAAAACTGAGGCAACGACACTTTTAA
* * * * *
19591962 AATGAACTCCTCAAAGCTAAGACAACGAAACTTCTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGACACTT-TTAA
* *
19592000 AATGAACTCTTTAAAACTGAGGCAACGA-ACTTTTTAA
1 AATGAACTCCTCAAAACTGAGGCAACGACAC-TTTTAA
* * * * * *
19592037 AATAAACTCCTTAAACCTAAGGCAGA-GAGACTTTAAAA
1 AATGAACTCCTCAAAACTGAGGCA-ACGACACTTT-TAA
* * * * *
19592075 AATGAACGCCTCAAATCTAAGGGAACGAAACTTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGACACTTTT-AA
* * * *
19592113 AATAAACTCCTCAAAGCTGAGGTAATGACACTTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGACACTTTT-AA
* *
19592151 AATGAACTCTTCAAAGCTGAGGCAACGA-ACTTTTAA
1 AATGAACTCCTCAAAACTGAGGCAACGACACTTTTAA
* *
19592187 AATGAACTCCTCAAAACTGAGGCAATGAGACTTTTAA
1 AATGAACTCCTCAAAACTGAGGCAACGACACTTTTAA
* **
19592224 AATAAACTCCTCAAAGTTGAGGCAACGA-ACTTTTAA
1 AATGAACTCCTCAAAACTGAGGCAACGACACTTTTAA
*
19592260 AATGAACTCCTCAAAACTGAGGCAATGACACTTTTAA
1 AATGAACTCCTCAAAACTGAGGCAACGACACTTTTAA
* *
19592297 AATGAACTCTTCAAAACTGAGGTAACGA
1 AATGAACTCCTCAAAACTGAGGCAACGA
19592325 AACCTTTTTT
Statistics
Matches: 336, Mismatches: 55, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
36 59 0.18
37 127 0.38
38 150 0.45
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.25
Consensus pattern (37 bp):
AATGAACTCCTCAAAACTGAGGCAACGACACTTTTAA
Found at i:19605345 original size:12 final size:12
Alignment explanation
Indices: 19605328--19605355 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19605318 ATAATAAAAA
19605328 ATATATATTCTT
1 ATATATATTCTT
19605340 ATATATATTCTT
1 ATATATATTCTT
19605352 ATAT
1 ATAT
19605356 TCTTGTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATATATTCTT
Found at i:19620486 original size:19 final size:19
Alignment explanation
Indices: 19620462--19620499 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19620452 CCATTTAACT
*
19620462 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
19620481 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
19620500 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:19621829 original size:10 final size:11
Alignment explanation
Indices: 19621815--19621856 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
19621805 AAAAAAATTC
19621815 AAAAAAATAAT
1 AAAAAAATAAT
19621826 AAAAAAAT-AT
1 AAAAAAATAAT
19621836 AAAATAAAATAAT
1 -AAA-AAAATAAT
19621849 GAAAAAAA
1 -AAAAAAA
19621857 AAAAGAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 2 0.07
11 11 0.41
12 9 0.33
13 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:19621844 original size:23 final size:22
Alignment explanation
Indices: 19621805--19621856 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 22
19621795 ACCCATTTTA
*
19621805 AAAAAAATTCAAAAAAATAAT-
1 AAAAAAATTAAAAAAAATAATG
19621826 AAAAAAATATAAAATAAAATAATG
1 AAAAAAAT-TAAAA-AAAATAATG
19621850 AAAAAAA
1 AAAAAAA
19621857 AAAAGAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.30
22 4 0.15
23 8 0.30
24 7 0.26
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (22 bp):
AAAAAAATTAAAAAAAATAATG
Found at i:19623452 original size:14 final size:13
Alignment explanation
Indices: 19623432--19623486 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 13
19623422 TGAAAAAGAT
19623432 AAAAAAATAAATAA
1 AAAAAAATAAAT-A
19623446 CAAAAAATATATAATA
1 -AAAAAA-ATA-AATA
19623462 AATAAAAATAAATA
1 AA-AAAAATAAATA
*
19623476 ATAAAAATAAA
1 AAAAAAATAAA
19623487 CTTCATAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 9 0.25
14 5 0.14
15 11 0.31
16 8 0.22
17 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAAATAAATA
Found at i:19623461 original size:17 final size:16
Alignment explanation
Indices: 19623432--19623482 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
19623422 TGAAAAAGAT
19623432 AAAAAA-ATA-AATAA
1 AAAAAATATATAATAA
19623446 CAAAAAATATATAATAA
1 -AAAAAATATATAATAA
*
19623463 ATAAAAATAAATAATAA
1 A-AAAAATATATAATAA
19623480 AAA
1 AAA
19623483 TAAACTTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 20 0.62
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAAATATATAATAA
Found at i:19626434 original size:13 final size:13
Alignment explanation
Indices: 19626416--19626440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19626406 TTTCAGAAAA
19626416 TTTATAAAATCAT
1 TTTATAAAATCAT
19626429 TTTATAAAATCA
1 TTTATAAAATCA
19626441 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:19634149 original size:4 final size:4
Alignment explanation
Indices: 19634140--19634170 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
19634130 ATTTTGTGTA
19634140 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
19634171 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:19636188 original size:71 final size:74
Alignment explanation
Indices: 19636017--19636213 Score: 247
Period size: 71 Copynumber: 2.7 Consensus size: 74
19636007 GGTAAGTTTC
* * * * * *
19636017 TAGTTGGCTAACCATATTTCTTAGTCTATTAAGTTTTCTCTATCTCGCAACCAAATTCTCTAACG
1 TAGTTGGCTAACTATATTTCTTAGTCGATTAAGTATTCTCTGTCTTGCAATCAAATTCTCTAACG
19636082 ATGAGCTTT
66 ATGAGCTTT
* * * * * *
19636091 TAGCTGGCTAATTATATTTCTGAGTCGATTAAGTCTTCTATGTCTTGCAATCAAATT-T-T-TCG
1 TAGTTGGCTAACTATATTTCTTAGTCGATTAAGTATTCTCTGTCTTGCAATCAAATTCTCTAACG
19636153 ATGAGCTTT
66 ATGAGCTTT
* *
19636162 TAGTTGGCTAACTATACTTCTTAGTCGATTAAGTATTCTCTGTCTTACAATC
1 TAGTTGGCTAACTATATTTCTTAGTCGATTAAGTATTCTCTGTCTTGCAATC
19636214 TCCTTTACTC
Statistics
Matches: 105, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
71 56 0.53
72 1 0.01
73 1 0.01
74 47 0.45
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (74 bp):
TAGTTGGCTAACTATATTTCTTAGTCGATTAAGTATTCTCTGTCTTGCAATCAAATTCTCTAACG
ATGAGCTTT
Found at i:19637640 original size:65 final size:65
Alignment explanation
Indices: 19637513--19637643 Score: 199
Period size: 65 Copynumber: 2.0 Consensus size: 65
19637503 GTTTCACCTG
* *
19637513 CCTTAGGGTTTTTTGCTATCTACCTCATTCTTTCCTTCCTGTCCCTTGTTCCTCCTATCTTTCCA
1 CCTTAGGGTTTTTTGCTATCTACCTCATTCTTTCCTTCCTGTCCCTTGTACCTCCTAACTTTCCA
* * * * *
19637578 CCTTAGGGTTTTTTGCTATCTACCTCGTTCTTTCCTTCTTGTCCGTTGTACTTTCTAACTTTCCA
1 CCTTAGGGTTTTTTGCTATCTACCTCATTCTTTCCTTCCTGTCCCTTGTACCTCCTAACTTTCCA
19637643 C
1 C
19637644 AATCACGTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.10, C:0.31, G:0.11, T:0.48
Consensus pattern (65 bp):
CCTTAGGGTTTTTTGCTATCTACCTCATTCTTTCCTTCCTGTCCCTTGTACCTCCTAACTTTCCA
Found at i:19642148 original size:14 final size:14
Alignment explanation
Indices: 19642129--19642155 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19642119 TTCAGACTAT
19642129 TTATTGGTTTCTTC
1 TTATTGGTTTCTTC
19642143 TTATTGGTTTCTT
1 TTATTGGTTTCTT
19642156 TTTACATCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.15, T:0.67
Consensus pattern (14 bp):
TTATTGGTTTCTTC
Found at i:19642421 original size:3 final size:3
Alignment explanation
Indices: 19642415--19642443 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19642405 AATAATAATA
19642415 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19642444 CCTTTTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19650199 original size:13 final size:13
Alignment explanation
Indices: 19650181--19650205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19650171 CAGAACATAG
19650181 AAAATACATAAAT
1 AAAATACATAAAT
19650194 AAAATACATAAA
1 AAAATACATAAA
19650206 AGATTGTTGA
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:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATACATAAAT
Found at i:19655244 original size:29 final size:30
Alignment explanation
Indices: 19655198--19655254 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
19655188 TTAGATAGTC
19655198 TTGAATTCTAATTAGACT-AGAATATTTTGT
1 TTGAATTCTAATTAGACTAAG-ATATTTTGT
* *
19655228 TTGAA-TCTAGTTTGACTAAGATATTTT
1 TTGAATTCTAATTAGACTAAGATATTTT
19655255 ATTATAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TTGAATTCTAATTAGACTAAGATATTTTGT
Found at i:19658831 original size:2 final size:2
Alignment explanation
Indices: 19658824--19658941 Score: 168
Period size: 2 Copynumber: 59.0 Consensus size: 2
19658814 TACATCCATT
19658824 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
19658867 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A NTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
19658909 TA TA TA TA GA CA TA CA AA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19658942 CGCACACAAA
Statistics
Matches: 106, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
1 2 0.02
2 101 0.95
3 3 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:19666173 original size:28 final size:28
Alignment explanation
Indices: 19666110--19666165 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
19666100 TCTCAATAAA
19666110 GTATTATTGTAATAAAAAACTTTAGTAC
1 GTATTATTGTAATAAAAAACTTTAGTAC
19666138 GTATTATTGTAATAAAAAACTTTAGTAC
1 GTATTATTGTAATAAAAAACTTTAGTAC
19666166 TTTATATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (28 bp):
GTATTATTGTAATAAAAAACTTTAGTAC
Found at i:19666289 original size:20 final size:20
Alignment explanation
Indices: 19666250--19666299 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
19666240 AATCTATTTT
* *
19666250 ATATACT-ATCAAATAATCA
1 ATATACTAATAAAAAAATCA
19666269 ATATACTAATAAAAAAATCA
1 ATATACTAATAAAAAAATCA
*
19666289 ACATAC-AATAA
1 ATATACTAATAA
19666300 TTCGTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (20 bp):
ATATACTAATAAAAAAATCA
Found at i:19666699 original size:18 final size:19
Alignment explanation
Indices: 19666670--19666709 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
19666660 ATTATACTCT
19666670 TTATTAATTTTTATAATAA
1 TTATTAATTTTTATAATAA
* *
19666689 TTATT-ATTTTTTTATTAA
1 TTATTAATTTTTATAATAA
19666707 TTA
1 TTA
19666710 AAAAAAGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTAATTTTTATAATAA
Found at i:19669557 original size:11 final size:11
Alignment explanation
Indices: 19669534--19669572 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
19669524 TAGAACTAAT
19669534 TTTATTATTAAA
1 TTTATT-TTAAA
19669546 TTTATTTTAAA
1 TTTATTTTAAA
*
19669557 TTGTATTTAAAA
1 TT-TATTTTAAA
19669569 TTTA
1 TTTA
19669573 ATATAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:19670373 original size:33 final size:33
Alignment explanation
Indices: 19670307--19670373 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
19670297 ATGAATAAAT
* * *
19670307 AGAATAAAAATTAAAAAAATAATAATAATTGAA
1 AGAATAAAAATAAAAAAAATAAAAATAAGTGAA
19670340 AGAA-AAAAATAAAAAAAATAAAAATTAAGTGAA
1 AGAATAAAAATAAAAAAAATAAAAA-TAAGTGAA
19670373 A
1 A
19670374 CATATGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.19
Consensus pattern (33 bp):
AGAATAAAAATAAAAAAAATAAAAATAAGTGAA
Found at i:19673778 original size:20 final size:20
Alignment explanation
Indices: 19673733--19673770 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19673723 TTTTGACCCC
19673733 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
19673753 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
19673771 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:19673854 original size:28 final size:27
Alignment explanation
Indices: 19673823--19673875 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
19673813 TTTGGAGTAA
*
19673823 AAGGGTAAAATGGTAATTTTACCACCCC
1 AAGGGCAAAATGGTAATTTT-CCACCCC
*
19673851 AAGGGCAAAATTGTAATTTTCCACC
1 AAGGGCAAAATGGTAATTTTCCACC
19673876 ACCAGGACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (27 bp):
AAGGGCAAAATGGTAATTTTCCACCCC
Found at i:19677472 original size:11 final size:12
Alignment explanation
Indices: 19677448--19677478 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
19677438 AAAAAATATG
19677448 TTATTTTATTAA
1 TTATTTTATTAA
19677460 TTATTTT-TTAA
1 TTATTTTATTAA
19677471 TTATTTTA
1 TTATTTTA
19677479 AATATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTTATTAA
Found at i:19677811 original size:16 final size:16
Alignment explanation
Indices: 19677790--19677824 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19677780 TATGCATCAT
19677790 ATTTCTCATTTAATTA
1 ATTTCTCATTTAATTA
* *
19677806 ATTTCTTATTTACTTA
1 ATTTCTCATTTAATTA
19677822 ATT
1 ATT
19677825 ATATAATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTCTCATTTAATTA
Found at i:19678441 original size:407 final size:408
Alignment explanation
Indices: 19677467--19678480 Score: 1395
Period size: 407 Copynumber: 2.5 Consensus size: 408
19677457 TAATTATTTT
* * ** *
19677467 TTAATTATTTTAAATATTTAATTCATTGGTAAATAACAAATTAAAACACGTATTCATTAATTTGA
1 TTAATTACTTTAAATATTTAATTCATTGCTAAATAACAAATTAAAACATTTTTTCATTAATTTGA
* *
19677532 TTAGTCAAATTCTTTAATTACCCTTATACAACCTTAATTAAATTAACTAATTTTTATTTAATATA
66 TTAGTCAAATTCTTTAATTACCCTTATACAACCTTAATTAAATTAACTAATTTTAAATTAATATA
** * *
19677597 AATTTAATCATCAAATTAATTGCTCAATTATCCTCAACCTTACTTAAGTTAAATAATTTTAAAAT
131 AATTTAATCATTTAATTAATTGCTTAATTATCCTAAACCTTACTTAAGTTAAATAATTTTAAAAT
* * * *
19677662 TTTCTAAATTTACTAATTTAATTTATTATTAATGGCTAATACATGATTGTTTTTGTTCATTTAAA
196 TTTCTAAATTTACTAATTTAATTTATTATTAATGACTAATACATGATTATTTTTATTCACTTAAA
* *
19677727 TTATTTAATTAATTCCCCAAGCCCTAAACCCTAATTTAAATAAAATATATTATTATGCATCATAT
261 TTATTTAATTAATT---C---CCCTAAACCCTAATTTAAATAAAATATAATATTATGCATCACAT
* *
19677792 TTCTCATTTAATTAATTTCTTATTTACTTAATTATATAATAACACATTCCATTACTTAATTAACT
320 TACTCAGTTAATTAATTTCTTATTTAC---ATTATATAATAACACATTCCATTACTTAATTAACT
* *
19677857 AAATTATCTAATTAACTCATTAAATCC
382 AAATTATCTAATTAACTCAGTAAACCC
* *
19677884 TTAATTACTTTAAATATTTAATTTATTGCTAGATAACAAATTAAAACATTTTTTCATTAATTTGA
1 TTAATTACTTTAAATATTTAATTCATTGCTAAATAACAAATTAAAACATTTTTTCATTAATTTGA
* *
19677949 TTAGTCAAATTCTTTAATTACCCTTATACAACCTTAATTAAATTAACTAATTTTAAACTAATCTA
66 TTAGTCAAATTCTTTAATTACCCTTATACAACCTTAATTAAATTAACTAATTTTAAATTAATATA
* *
19678014 AATTTAATCATTCT-ATTAATTGCTTAATTACCCTAAACGTTACTTAAGTTAAATAATTTTAAAA
131 AATTTAATCATT-TAATTAATTGCTTAATTATCCTAAACCTTACTTAAGTTAAATAATTTTAAAA
* * * *
19678078 TTTTCTAAATTTATTAATTTAATTTATTGTTTAATTACTAATACATGATTATTTTTATTTACTTA
195 TTTTCTAAATTTACTAATTTAATTTATT-ATTAATGACTAATACATGATTATTTTTATTCACTTA
* * *
19678143 AATTATTTAATTAATT-CTCTAAACCTTAATTTAAATGAAATATAATATTATGCATCACATTACT
259 AATTATTTAATTAATTCCCCTAAACCCTAATTTAAATAAAATATAATATTATGCATCACATTACT
** *
19678207 CAGTTAATTAATTTCTTATTTAC-TTATATAATAACGTATTCCATTACTTAATTAACTGAATTAT
324 CAGTTAATTAATTTCTTATTTACATTATATAATAACACATTCCATTACTTAATTAACTAAATTAT
* *
19678271 TTAATTCACTCAGTAAACCC
389 CTAATTAACTCAGTAAACCC
* * * ** * *
19678291 TTAATTAGTTAAAATATTTAATTCATTGCTAAATAGCTGATTAAGACATTTTTTCATTAATTTGG
1 TTAATTACTTTAAATATTTAATTCATTGCTAAATAACAAATTAAAACATTTTTTCATTAATTTGA
* * * * * *
19678356 TTTGTAAAATTCTTTAATTACCCTAATACAACATTAATTAATTTAACTAATTTTAAATTAATTTA
66 TTAGTCAAATTCTTTAATTACCCTTATACAACCTTAATTAAATTAACTAATTTTAAATTAATATA
* * * * *
19678421 CATTTACTCGTTTAATTAATTGCTTAATTATCCTAACCCTTAATTAAGTTAAATAATTTT
131 AATTTAATCATTTAATTAATTGCTTAATTATCCTAAACCTTACTTAAGTTAAATAATTTT
19678481 TCTTATACAA
Statistics
Matches: 532, Mismatches: 62, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
406 1 0.00
407 219 0.41
411 64 0.12
417 203 0.38
418 45 0.08
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (408 bp):
TTAATTACTTTAAATATTTAATTCATTGCTAAATAACAAATTAAAACATTTTTTCATTAATTTGA
TTAGTCAAATTCTTTAATTACCCTTATACAACCTTAATTAAATTAACTAATTTTAAATTAATATA
AATTTAATCATTTAATTAATTGCTTAATTATCCTAAACCTTACTTAAGTTAAATAATTTTAAAAT
TTTCTAAATTTACTAATTTAATTTATTATTAATGACTAATACATGATTATTTTTATTCACTTAAA
TTATTTAATTAATTCCCCTAAACCCTAATTTAAATAAAATATAATATTATGCATCACATTACTCA
GTTAATTAATTTCTTATTTACATTATATAATAACACATTCCATTACTTAATTAACTAAATTATCT
AATTAACTCAGTAAACCC
Found at i:19679920 original size:13 final size:14
Alignment explanation
Indices: 19679893--19679923 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
19679883 AATTTTATTC
19679893 AAATAATTAAATTA
1 AAATAATTAAATTA
19679907 AAATAATT-AATTA
1 AAATAATTAAATTA
19679920 AAAT
1 AAAT
19679924 TAAAGCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATAATTAAATTA
Found at i:19681572 original size:46 final size:48
Alignment explanation
Indices: 19681516--19681626 Score: 115
Period size: 46 Copynumber: 2.4 Consensus size: 48
19681506 CAACGATAAT
* *
19681516 TCCGTTAATGATTCCATTG-GTATAT-TTATTAATCATTCCAATCGTC
1 TCCGTCAATGATTCCATTGTCTATATATTATTAATCATTCCAATCGTC
* *
19681562 TTCGTCAATGATT--A-TGTCTATATAGTTATTAATCATTCCAATTGTC
1 TCCGTCAATGATTCCATTGTCTATATA-TTATTAATCATTCCAATCGTC
***
19681608 TCCGTTGGTGATTCCATTG
1 TCCGTCAATGATTCCATTG
19681627 ATGACATAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
43 2 0.04
44 6 0.12
46 40 0.78
48 1 0.02
49 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (48 bp):
TCCGTCAATGATTCCATTGTCTATATATTATTAATCATTCCAATCGTC
Found at i:19687360 original size:32 final size:32
Alignment explanation
Indices: 19687323--19687484 Score: 137
Period size: 35 Copynumber: 4.9 Consensus size: 32
19687313 TTTTACACTA
* *
19687323 GTTTTTCACGGGCTAAACTAAAACCCAAAGTG
1 GTTTTTCACGGGCTCAACCAAAACCCAAAGTG
** *
19687355 GTTTTTCAAAGGCTCAACCACAACCTTTCACAA-TG
1 GTTTTTCACGGGCTCAACCAAAACC---CA-AAGTG
* *
19687390 GTTTTTCACGAGTTCAACCAAAACCCAAAGTG
1 GTTTTTCACGGGCTCAACCAAAACCCAAAGTG
** * *
19687422 GTTTTTCAAAGGCTCAACCACAACCTACAACAATG
1 GTTTTTCACGGGCTCAACCAAAACC--CAA-AGTG
* *
19687457 GTTTTTCAAGGGATCAACCAAAACCCAA
1 GTTTTTCACGGGCTCAACCAAAACCCAA
19687485 CAACTAGCTT
Statistics
Matches: 103, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
31 2 0.02
32 44 0.43
33 3 0.03
34 3 0.03
35 49 0.48
36 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (32 bp):
GTTTTTCACGGGCTCAACCAAAACCCAAAGTG
Found at i:19687413 original size:67 final size:67
Alignment explanation
Indices: 19687309--19687484 Score: 246
Period size: 67 Copynumber: 2.6 Consensus size: 67
19687299 GCTTAGTCAA
* * * * * *
19687309 AACCTTTTACACTAGTTTTTCACGGGCTAAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
19687374 AC
66 AC
* *
19687376 AACCTTTCACAATGGTTTTTCACGAGTTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
19687441 AC
66 AC
* *
19687443 AACC-TACAACAATGGTTTTTCAAGGGATCAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACCCAA
19687485 CAACTAGCTT
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 2 0.02
67 95 0.98
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:19699169 original size:14 final size:14
Alignment explanation
Indices: 19699152--19699187 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
19699142 GTTTAATTTT
* *
19699152 TTCAGTTCGGTTAG
1 TTCAGTTAGGATAG
19699166 TTCAGTTAGGATAG
1 TTCAGTTAGGATAG
19699180 TTCAGTTA
1 TTCAGTTA
19699188 TTAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (14 bp):
TTCAGTTAGGATAG
Found at i:19699370 original size:23 final size:24
Alignment explanation
Indices: 19699342--19699399 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
19699332 CATCTCCATC
19699342 TTATTTATT-ATAATTTTT-TACTA
1 TTATTTATTAAT-ATTTTTGTACTA
*
19699365 TTATTT-TTAATATTTTTGTAGTA
1 TTATTTATTAATATTTTTGTACTA
19699388 TTAATTTATTAA
1 TT-ATTTATTAA
19699400 AAAAATACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 8 0.27
23 14 0.47
24 4 0.13
25 4 0.13
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (24 bp):
TTATTTATTAATATTTTTGTACTA
Found at i:19700935 original size:19 final size:20
Alignment explanation
Indices: 19700908--19700947 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
19700898 GCCTCGAACT
19700908 AGATCAAATAGAG-AATTTA
1 AGATCAAATAGAGAAATTTA
* *
19700927 AGATGAAATTGAGAAATTTA
1 AGATCAAATAGAGAAATTTA
19700947 A
1 A
19700948 AGCCTCAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.28
Consensus pattern (20 bp):
AGATCAAATAGAGAAATTTA
Found at i:19701431 original size:11 final size:11
Alignment explanation
Indices: 19701414--19701457 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
19701404 TATGGCTGGC
19701414 CAAAGGAA-AA
1 CAAAGGAAGAA
19701424 CAAAAGGAAGAA
1 C-AAAGGAAGAA
19701436 CAAAGGAAG-A
1 CAAAGGAAGAA
19701446 -AAA-GAAGAA
1 CAAAGGAAGAA
19701455 CAA
1 CAA
19701458 GAACCCTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 4 0.13
11 15 0.50
12 3 0.10
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:19710711 original size:21 final size:21
Alignment explanation
Indices: 19710684--19710782 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
19710674 CTAATTTTTA
*
19710684 GACATTGCGTGATTGACTTTG
1 GACATTGCGTGACTGACTTTG
* *
19710705 GATATTGCTTGACTGACTTTG
1 GACATTGCGTGACTGACTTTG
*
19710726 GACATTGCGTGACT-AGTTGATAG
1 GACATTGCGTGACTGACTT--T-G
* *
19710749 G-CATTGCATGACTGATTTTG
1 GACATTGCGTGACTGACTTTG
* *
19710769 GAAATTACGTGACT
1 GACATTGCGTGACT
19710783 AGTTTTTAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
20 5 0.08
21 40 0.65
22 12 0.19
23 5 0.08
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.36
Consensus pattern (21 bp):
GACATTGCGTGACTGACTTTG
Found at i:19710763 original size:43 final size:44
Alignment explanation
Indices: 19710708--19710833 Score: 128
Period size: 47 Copynumber: 2.8 Consensus size: 44
19710698 GACTTTGGAT
* * *
19710708 ATTGCTTGACTGACTTTGGACATTGCGTGACTAGTTGAT-AGGC
1 ATTGCATGACTGACTTTGGAAATTGCGTGACTAGTTAATAAGGC
* *
19710751 ATTGCATGACTGATTTTGGAAATTACGTGACTAGTTTTTAATAAGGC
1 ATTGCATGACTGACTTTGGAAATTGCGTGACTAG---TTAATAAGGC
* * * **
19710798 ATTGCGTGATTAACTTTGGGTATTGCGTGACTAGTT
1 ATTGCATGACTGACTTTGGAAATTGCGTGACTAGTT
19710834 TCTGATAAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
43 30 0.45
44 2 0.03
46 4 0.06
47 31 0.46
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (44 bp):
ATTGCATGACTGACTTTGGAAATTGCGTGACTAGTTAATAAGGC
Found at i:19710816 original size:47 final size:47
Alignment explanation
Indices: 19710708--19710856 Score: 126
Period size: 47 Copynumber: 3.3 Consensus size: 47
19710698 GACTTTGGAT
* * * * *
19710708 ATTGCTTGACTGACTTTGGACATTGCGTGACTAG--T-TGAT-AGGC
1 ATTGCGTGACTAACTTTGGAAATTACGTGACTAGTTTCTAATAAGGC
* * * *
19710751 ATTGCATGACTGATTTTGGAAATTACGTGACTAGTTTTTAATAAGGC
1 ATTGCGTGACTAACTTTGGAAATTACGTGACTAGTTTCTAATAAGGC
* ** * * * *
19710798 ATTGCGTGATTAACTTTGGGTATTGCGTGACTAGTTTCTGATAAAGT
1 ATTGCGTGACTAACTTTGGAAATTACGTGACTAGTTTCTAATAAGGC
19710845 ATTGCGTGACTA
1 ATTGCGTGACTA
19710857 GTTGATAGGC
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
43 30 0.35
45 1 0.01
46 3 0.04
47 51 0.60
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (47 bp):
ATTGCGTGACTAACTTTGGAAATTACGTGACTAGTTTCTAATAAGGC
Found at i:19710893 original size:23 final size:22
Alignment explanation
Indices: 19710728--19710877 Score: 67
Period size: 22 Copynumber: 6.5 Consensus size: 22
19710718 TGACTTTGGA
19710728 CATTGCGTGACTAGTTGATAGG
1 CATTGCGTGACTAGTTGATAGG
* *
19710750 CATTGCATGACT-GATT--TTGG
1 CATTGCGTGACTAG-TTGATAGG
* * *
19710770 AAATTACGTGACTAGTTTTTAATAAGG
1 -CATTGCGTGACTAG---TTGAT-AGG
* * *
19710797 CATTGCGTGATTAACTT--TGGG
1 CATTGCGTGACT-AGTTGATAGG
* *
19710818 TATTGCGTGACTAGTTTCTGATAAAG
1 CATTGCGTGACTAG--T-TGAT-AGG
*
19710844 TATTGCGTGACTAGTTGATAGG
1 CATTGCGTGACTAGTTGATAGG
19710866 CATTGCGTGACT
1 CATTGCGTGACT
19710878 TGTTAGGAAG
Statistics
Matches: 94, Mismatches: 19, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
20 4 0.04
21 22 0.23
22 29 0.31
23 5 0.05
24 5 0.05
25 1 0.01
26 25 0.27
27 3 0.03
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.37
Consensus pattern (22 bp):
CATTGCGTGACTAGTTGATAGG
Found at i:19710984 original size:22 final size:22
Alignment explanation
Indices: 19710928--19710989 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
19710918 TCAGTCACAC
*
19710928 AATGTCTAAAAACT-GTCACGT
1 AATGACTAAAAACTAGTCACGT
* *
19710949 AATGCCT-AAAACTAATCACGT
1 AATGACTAAAAACTAGTCACGT
19710970 AATGACTAAAAACTAGTCAC
1 AATGACTAAAAACTAGTCAC
19710990 TTGGTGATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.17
21 18 0.51
22 11 0.31
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (22 bp):
AATGACTAAAAACTAGTCACGT
Found at i:19711975 original size:88 final size:89
Alignment explanation
Indices: 19711825--19712000 Score: 266
Period size: 88 Copynumber: 2.0 Consensus size: 89
19711815 TTGATATCTT
* * *
19711825 CATCCAATCAAGGTACTACTCTCGATCACGAGGATAAGATACTTAATATACAAATTTGGTCCTCT
1 CATCCAATCAAGATACTACTCTCGATCACAAGGACAAGATACTTAATATACAAATTTGGTCCTCT
*
19711890 CACCTGCATACAATTAATGAATTC
66 CACCTGCATACAATAAATGAATTC
* *
19711914 CATCCAATCAATGAT-CTACTCT-TATCACAAGGACAAGATACTTAATATACCAATTTGGTCCTC
1 CATCCAATCAA-GATACTACTCTCGATCACAAGGACAAGATACTTAATATACAAATTTGGTCCTC
*
19711977 TCACCTGGATACAATAAATGAATT
65 TCACCTGCATACAATAAATGAATT
19712001 TGGTCCTCAC
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 59 0.75
89 18 0.23
90 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (89 bp):
CATCCAATCAAGATACTACTCTCGATCACAAGGACAAGATACTTAATATACAAATTTGGTCCTCT
CACCTGCATACAATAAATGAATTC
Found at i:19723355 original size:20 final size:20
Alignment explanation
Indices: 19723330--19723375 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
19723320 ATGAGAGGAA
19723330 GAAGAAGAAGAAAAGCTGCT-
1 GAAGAAGAA-AAAAGCTGCTG
* *
19723350 GAAGAATAAAGAAGCTGCTG
1 GAAGAAGAAAAAAGCTGCTG
19723370 GAAGAA
1 GAAGAA
19723376 AGATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.50, C:0.09, G:0.30, T:0.11
Consensus pattern (20 bp):
GAAGAAGAAAAAAGCTGCTG
Found at i:19731073 original size:15 final size:15
Alignment explanation
Indices: 19731053--19731085 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19731043 ATCATTTAAT
19731053 CATTATGGTCATGAA
1 CATTATGGTCATGAA
*
19731068 CATTATGGTTATGAA
1 CATTATGGTCATGAA
19731083 CAT
1 CAT
19731086 GGAAAAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (15 bp):
CATTATGGTCATGAA
Found at i:19731180 original size:28 final size:27
Alignment explanation
Indices: 19731148--19731354 Score: 186
Period size: 28 Copynumber: 7.4 Consensus size: 27
19731138 CTAATAATAA
* *
19731148 GAATACTTTTAATCTACCATAAGTGGAT
1 GAATACTTTTAACCCACCA-AAGTGGAT
* *
19731176 GAATACTTTTAACCCACTAAAAGTAGAT
1 GAATACTTTTAACCCAC-CAAAGTGGAT
** *
19731204 GAATACTTTTAACCTTCCAAGAGTGGAA
1 GAATACTTTTAACCCACCAA-AGTGGAT
*
19731232 GAATACTTTTAACCCATCAAAAGTGGAT
1 GAATACTTTTAACCCA-CCAAAGTGGAT
*
19731260 GAATACTTTTAA-ACACCAAGAG-GGTAT
1 GAATACTTTTAACCCACCAA-AGTGG-AT
* ** *
19731287 GAGTACTTTTAACCCATTAAGAGTGAAT
1 GAATACTTTTAACCCACCAA-AGTGGAT
*
19731315 GAATACTCTTAACCCA-CAAGGAGTGGAT
1 GAATACTTTTAACCCACCAA--AGTGGAT
19731343 GAATACTTTTAA
1 GAATACTTTTAA
19731355 TTACCAGGAG
Statistics
Matches: 146, Mismatches: 25, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
26 5 0.03
27 21 0.14
28 115 0.79
29 5 0.03
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (27 bp):
GAATACTTTTAACCCACCAAAGTGGAT
Found at i:19731303 original size:55 final size:56
Alignment explanation
Indices: 19731148--19731354 Score: 235
Period size: 56 Copynumber: 3.7 Consensus size: 56
19731138 CTAATAATAA
* *
19731148 GAATACTTTTAATCTACCATA-AGTGGATGAATACTTTTAACCCA-CTAAAAGTAGAT
1 GAATACTTTTAAACTACCA-AGAGTGGATGAATACTTTTAACCCATC-AAAAGTGGAT
* * *
19731204 GAATACTTTTAACCTTCCAAGAGTGGAAGAATACTTTTAACCCATCAAAAGTGGAT
1 GAATACTTTTAAACTACCAAGAGTGGATGAATACTTTTAACCCATCAAAAGTGGAT
* * * *
19731260 GAATACTTTTAAAC-ACCAAGAG-GGTATGAGTACTTTTAACCCATTAAGAGTGAAT
1 GAATACTTTTAAACTACCAAGAGTGG-ATGAATACTTTTAACCCATCAAAAGTGGAT
* * *
19731315 GAATACTCTTAACCCA-CAAGGAGTGGATGAATACTTTTAA
1 GAATACTTTTAAACTACCAA-GAGTGGATGAATACTTTTAA
19731355 TTACCAGGAG
Statistics
Matches: 131, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
54 2 0.02
55 48 0.37
56 78 0.60
57 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (56 bp):
GAATACTTTTAAACTACCAAGAGTGGATGAATACTTTTAACCCATCAAAAGTGGAT
Found at i:19731327 original size:83 final size:83
Alignment explanation
Indices: 19731168--19731354 Score: 222
Period size: 83 Copynumber: 2.2 Consensus size: 83
19731158 AATCTACCAT
* *
19731168 AAGTGGATGAATACTTTTAACCCACTAAAAGTAGATGAATACTTTTAACCTTCCAAGAGTGGAAG
1 AAGTGGATGAATACTTTTAACACACCAAAAGTAGATGAATACTTTTAACCTT-CAAGAGTGGAAG
*
19731233 AATACTTTTAACCCATCAA-
65 AATACTCTTAACCCA-CAAG
* * *
19731252 AAGTGGATGAATACTTTTAA-ACACCAAGAG-GGTATGAGTACTTTTAACCCATT-AAGAGT-GA
1 AAGTGGATGAATACTTTTAACACACCAAAAGTAG-ATGAATACTTTTAA-CC-TTCAAGAGTGGA
19731313 ATGAATACTCTTAACCCACAAG
63 A-GAATACTCTTAACCCACAAG
*
19731335 GAGTGGATGAATACTTTTAA
1 AAGTGGATGAATACTTTTAA
19731355 TTACCAGGAG
Statistics
Matches: 91, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
82 7 0.08
83 60 0.66
84 22 0.24
85 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (83 bp):
AAGTGGATGAATACTTTTAACACACCAAAAGTAGATGAATACTTTTAACCTTCAAGAGTGGAAGA
ATACTCTTAACCCACAAG
Found at i:19733584 original size:19 final size:19
Alignment explanation
Indices: 19733557--19733602 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
19733547 AGGAGACAAG
*
19733557 ATAAAATTTT-TTGAATAAA
1 ATAATATTTTATT-AATAAA
19733576 ATAATATTTTATTAATAAA
1 ATAATATTTTATTAATAAA
19733595 ATAATATT
1 ATAATATT
19733603 AAAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATAATATTTTATTAATAAA
Found at i:19733970 original size:26 final size:26
Alignment explanation
Indices: 19733937--19734000 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
19733927 TCACTATTTA
*
19733937 GGGG-CAAAATGGTCATTTGCCACCT
1 GGGGACAAAATGATCATTTGCCACCT
*
19733962 GGGGACAAAATGATCATTTGTCACCT
1 GGGGACAAAATGATCATTTGCCACCT
19733988 GGGGACAAAATGA
1 GGGGACAAAATGA
19734001 AAATTTTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 4 0.11
26 32 0.89
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (26 bp):
GGGGACAAAATGATCATTTGCCACCT
Found at i:19734006 original size:26 final size:26
Alignment explanation
Indices: 19733951--19734006 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
19733941 CAAAATGGTC
**
19733951 ATTTGCCACCTGGGGACAAAATGATC
1 ATTTGCCACCTGGGGACAAAATGAAA
*
19733977 ATTTGTCACCTGGGGACAAAATGAAA
1 ATTTGCCACCTGGGGACAAAATGAAA
19734003 ATTT
1 ATTT
19734007 TTAGAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (26 bp):
ATTTGCCACCTGGGGACAAAATGAAA
Found at i:19734076 original size:20 final size:20
Alignment explanation
Indices: 19734030--19734068 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19734020 TTTTTGGCCC
*
19734030 AATTTGACTTATTTGAGTAT
1 AATTTGACTTATTGGAGTAT
19734050 AATTTGACTTATTGGAGTA
1 AATTTGACTTATTGGAGTA
19734069 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (20 bp):
AATTTGACTTATTGGAGTAT
Found at i:19762206 original size:23 final size:22
Alignment explanation
Indices: 19762180--19762222 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
19762170 TATTTAATTA
* *
19762180 TTATTTTCATTTTATTTTATTCT
1 TTATTATCATATT-TTTTATTCT
19762203 TTATTATCATATTTTTTATT
1 TTATTATCATATTTTTTATT
19762223 TTATTTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (22 bp):
TTATTATCATATTTTTTATTCT
Found at i:19762235 original size:27 final size:27
Alignment explanation
Indices: 19762188--19762251 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
19762178 TATTATTTTC
*
19762188 ATTTTATTTTA-TTCTTTATTATCATATT
1 ATTTTATTTTATTTCTTAATTA-C-TATT
19762216 -TTTTATTTTATTTC-TAATTACTATT
1 ATTTTATTTTATTTCTTAATTACTATT
19762241 ATTTT-TTTTAT
1 ATTTTATTTTAT
19762252 ACCTTACATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 10 0.30
26 5 0.15
27 15 0.45
28 3 0.09
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (27 bp):
ATTTTATTTTATTTCTTAATTACTATT
Done.