Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 47 of 226
Found at i:19755329 original size:12 final size:12
Alignment explanation
Indices: 19755296--19755330 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
19755286 TTCTACCGGA
*
19755296 AATGAAGGAAGG
1 AATGAAGGAGGG
19755308 AATGAAGGAGGG
1 AATGAAGGAGGG
19755320 AATGAAGGAGG
1 AATGAAGGAGG
19755331 AGATAGAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.09
Consensus pattern (12 bp):
AATGAAGGAGGG
Found at i:19755903 original size:19 final size:18
Alignment explanation
Indices: 19755860--19755905 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
19755850 AAATTTTTAT
*
19755860 ATATAAAAT-TATATAAA
1 ATATAAAATATAAATAAA
*
19755877 AT-TTAAATATAAATATAA
1 ATATAAAATATAAATA-AA
19755895 ATATAAAATAT
1 ATATAAAATAT
19755906 CCTTAAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.22
17 7 0.30
18 4 0.17
19 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATAAAATATAAATAAA
Found at i:19755904 original size:13 final size:13
Alignment explanation
Indices: 19755870--19755905 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
19755860 ATATAAAATT
*
19755870 ATATAAAATTTAA
1 ATATAAAATATAA
19755883 ATAT-AAATATAA
1 ATATAAAATATAA
19755895 ATATAAAATAT
1 ATATAAAATAT
19755906 CCTTAAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATAAAATATAA
Found at i:19761501 original size:18 final size:20
Alignment explanation
Indices: 19761480--19761520 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
19761470 AAAATATTTA
*
19761480 TTTTCATGT-TTTTA-GTAT
1 TTTTCATGTATTATATGTAT
*
19761498 TTTTGATGTATTATATGTAT
1 TTTTCATGTATTATATGTAT
19761518 TTT
1 TTT
19761521 AAAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.66
Consensus pattern (20 bp):
TTTTCATGTATTATATGTAT
Found at i:19762463 original size:3 final size:3
Alignment explanation
Indices: 19762457--19762508 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
19762447 ATCAAAACAA
19762457 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
19762503 AAT AAT
1 AAT AAT
19762509 TCAAACTCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:19767857 original size:25 final size:26
Alignment explanation
Indices: 19767806--19767853 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
19767796 TTTAAAATAC
*
19767806 TTTTAAAATATTTTTATTTTTGTTAT
1 TTTTAAAATATTTTTATTTGTGTTAT
19767832 TTTTAAAATA-TTTT-TTTGTGTT
1 TTTTAAAATATTTTTATTTGTGTT
19767854 TATTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 4 0.19
26 10 0.48
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (26 bp):
TTTTAAAATATTTTTATTTGTGTTAT
Found at i:19773311 original size:42 final size:42
Alignment explanation
Indices: 19773260--19773377 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
19773250 CCCTAACGAG
* **
19773260 TTTCAGTTCAGCTCTTTTGAGCTTCAGTTTTACCCTTATGGAT
1 TTTC-GTTCAGCTCTTATGAGCTTCAGTTCAACCCTTATGGAT
* *
19773303 TTTCGTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATGGGT
1 TTTCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTTATGGAT
* * * * * *
19773345 TTCCGTTTAGCACTTATGTGCTTCTGTGCAACC
1 TTTCGTTCAGCTCTTATGAGCTTCAGTTCAACC
19773378 TTAGGGCTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (42 bp):
TTTCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTTATGGAT
Found at i:19773330 original size:21 final size:21
Alignment explanation
Indices: 19773306--19773368 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
19773296 TATGGATTTT
*
19773306 CGTTCAGCTCTTATGAGCTTC
1 CGTTCAGCACTTATGAGCTTC
* * * *
19773327 CGTTCAACCCTTATGGGTTTC
1 CGTTCAGCACTTATGAGCTTC
* *
19773348 CGTTTAGCACTTATGTGCTTC
1 CGTTCAGCACTTATGAGCTTC
19773369 TGTGCAACCT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (21 bp):
CGTTCAGCACTTATGAGCTTC
Found at i:19776292 original size:21 final size:22
Alignment explanation
Indices: 19776260--19776304 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
19776250 ATTTTCACAC
19776260 CAAAATTTGGACAGCATATATA
1 CAAAATTTGGACAGCATATATA
* *
19776282 CAAAA-TTGGACTGCATTTATA
1 CAAAATTTGGACAGCATATATA
19776303 CA
1 CA
19776305 TCAAAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (22 bp):
CAAAATTTGGACAGCATATATA
Found at i:19776336 original size:47 final size:47
Alignment explanation
Indices: 19776260--19776655 Score: 582
Period size: 47 Copynumber: 8.5 Consensus size: 47
19776250 ATTTTCACAC
* * *
19776260 CAAAATTTGGACAGCATAT--ATACAAAATTGGACTGCATTTATACAT
1 CAAAAATT-GACAGCATATACATATATAATTGGACTGCATTTATACAT
*
19776306 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACGT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
19776353 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* * * **
19776400 CAAAAATTGACAGCATATACATAAATATTTGGACTGCATTTGTGTAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* * * * **
19776447 CAAAATTTGACAGCATATACATAAATATTTGGACTGCATTTGTGTAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
19776494 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACGT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
19776541 CAAAAATTGACAGCATATACATATATAATTGGACTGC-CTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
19776587 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
19776634 CAAAATTTGACAGCATATACAT
1 CAAAAATTGACAGCATATACAT
19776656 TCATTTACTC
Statistics
Matches: 324, Mismatches: 23, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
45 10 0.03
46 51 0.16
47 263 0.81
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (47 bp):
CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
Found at i:19776931 original size:14 final size:15
Alignment explanation
Indices: 19776893--19776941 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
19776883 TCACCATGCA
* *
19776893 CATATATATACATTAC
1 CATATAAATAC-TAAC
19776909 CATATAAATACTAAC
1 CATATAAATACTAAC
19776924 CATA-AAATACTAATC
1 CATATAAATACTAA-C
19776939 CAT
1 CAT
19776942 GATTAAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 9 0.30
15 11 0.37
16 10 0.33
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (15 bp):
CATATAAATACTAAC
Found at i:19777736 original size:43 final size:43
Alignment explanation
Indices: 19777648--19777771 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
19777638 AGCTAGTACA
* *** * *
19777648 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-CCG
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA-AGTCG
19777691 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAAAACACAAGTCG
1 ATGCCGAC-GTCCCAGAC-GTGGTCTTACACAAAAACACAAGTCG
*
19777734 ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA
19777772 TATCGGAGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 4 0.06
43 63 0.90
44 3 0.04
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (43 bp):
ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACAAGTCG
Found at i:19779681 original size:42 final size:42
Alignment explanation
Indices: 19779620--19779733 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 42
19779610 AGTTAACTCA
* * * *
19779620 TATGAGTTTCCGTCTAACCCTAACGTG-TTTCAATTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTAACGGGTTTTC-ATTCAGCTCT
* * * *
19779662 TTTGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTAACGGGTTTTCATTCAGCTCT
* * * *
19779704 TATGAGCTTCCGTTCAACCCTTATGGGTTT
1 TATGAGCTTCAGTTTAACCCTAACGGGTTT
19779734 CCGTTTAGCA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 56 0.93
43 4 0.07
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTAACGGGTTTTCATTCAGCTCT
Found at i:19779707 original size:21 final size:21
Alignment explanation
Indices: 19779681--19779749 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
19779671 CAGTTTAACC
* *
19779681 CTTATGGGTTTTCGTTCAGCT
1 CTTATGGGTTTCCGTTCAGCA
* * * *
19779702 CTTATGAGCTTCCGTTCAACC
1 CTTATGGGTTTCCGTTCAGCA
*
19779723 CTTATGGGTTTCCGTTTAGCA
1 CTTATGGGTTTCCGTTCAGCA
19779744 CTTATG
1 CTTATG
19779750 TGCTTCTGTG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (21 bp):
CTTATGGGTTTCCGTTCAGCA
Found at i:19779748 original size:42 final size:42
Alignment explanation
Indices: 19779653--19779755 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 42
19779643 CGTGTTTCAA
* * * *
19779653 TTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTTCG
1 TTCAGCACTTATGAGCTTCAGTTCAACCCTTATGGGTTTCCG
* *
19779695 TTCAGCTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCCG
1 TTCAGCACTTATGAGCTTCAGTTCAACCCTTATGGGTTTCCG
* *
19779737 TTTAGCACTTATGTGCTTC
1 TTCAGCACTTATGAGCTTC
19779756 TGTGCAGCCT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (42 bp):
TTCAGCACTTATGAGCTTCAGTTCAACCCTTATGGGTTTCCG
Found at i:19782607 original size:50 final size:50
Alignment explanation
Indices: 19782532--19782729 Score: 252
Period size: 50 Copynumber: 3.8 Consensus size: 50
19782522 GATAATAACA
* * *
19782532 TGCCAAAGCCATGTCCCAGACATGGTCTTATAGGGGACATCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
19782582 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
19782632 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
19782687 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
19782730 TTACCCAAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
50 85 0.66
53 2 0.02
54 1 0.01
55 2 0.02
56 39 0.30
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:19782717 original size:106 final size:100
Alignment explanation
Indices: 19782539--19782729 Score: 283
Period size: 106 Copynumber: 1.9 Consensus size: 100
19782529 ACATGCCAAA
* *
19782539 GCCATGTCCCAGACATGGTCTTATAGGGGACATCTCATCTCGGTGCCAACGCCATGTCCCAGACA
1 GCCATGTCCCAGACATGGTCTTACAGGGGACATCTCATCTAGGTGCCAACGCCATGTCCCAGACA
19782604 TGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
66 TGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
* *
19782639 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGGATGCCAATGCCATGTCC
1 GCCATGTCCCAGACATGGTCTTACAGGGGACATCTC---ATC-T-AGG-TGCCAACGCCATGTCC
*
19782704 CAGACATGGTCTTACATGGGATCTCT
60 CAGACATGGTCTTACATGGGACCTCT
19782730 TTACCCAAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
100 34 0.43
103 3 0.04
104 1 0.01
105 2 0.03
106 40 0.50
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (100 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGACATCTCATCTAGGTGCCAACGCCATGTCCCAGACA
TGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
Found at i:19782845 original size:13 final size:13
Alignment explanation
Indices: 19782824--19782855 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19782814 GCTTGGATCA
*
19782824 TCATCAAATAAAT
1 TCATAAAATAAAT
19782837 TCATAAAATAAAT
1 TCATAAAATAAAT
19782850 TCATAA
1 TCATAA
19782856 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:19783102 original size:30 final size:30
Alignment explanation
Indices: 19783067--19783124 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19783057 CCTCGACTCT
*
19783067 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
19783097 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
19783125 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:19784686 original size:31 final size:30
Alignment explanation
Indices: 19784651--19784709 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
19784641 GGAGGTGGGA
*
19784651 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
19784682 TGGGAGGGAGTAAAAATTTTGGGGGAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAA
19784710 TAAAAAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:19784938 original size:9 final size:9
Alignment explanation
Indices: 19784924--19784951 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19784914 TATAGTTTGA
19784924 TATTCGAAT
1 TATTCGAAT
19784933 TATTCGAAT
1 TATTCGAAT
19784942 TATTCGAAT
1 TATTCGAAT
19784951 T
1 T
19784952 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19785021 original size:9 final size:9
Alignment explanation
Indices: 19785004--19785034 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19784994 TCGAGTTGAT
19785004 TCGAATAAC
1 TCGAATAAC
*
19785013 TCGATTAAC
1 TCGAATAAC
19785022 TCGAATAAC
1 TCGAATAAC
19785031 TCGA
1 TCGA
19785035 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:19788007 original size:2 final size:2
Alignment explanation
Indices: 19787995--19788033 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
19787985 AATTCGAGTA
19787995 AT AT A- 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
19788034 TGGTTGCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19790986 original size:18 final size:19
Alignment explanation
Indices: 19790951--19790988 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
19790941 ATTAATATAA
*
19790951 ATTAATAAAATTACATTTT
1 ATTAATAAAATAACATTTT
*
19790970 ATTAAT-AAATAATATTTT
1 ATTAATAAAATAACATTTT
19790988 A
1 A
19790989 GACCAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAATAAAATAACATTTT
Found at i:19791338 original size:23 final size:23
Alignment explanation
Indices: 19791312--19791368 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
19791302 TTTCTATGCA
* *
19791312 TTTTTATTATTGTTTCGCTGTCG
1 TTTTTAATATTGTTTCACTGTCG
** *
19791335 TTTTTAAGGTTGTTTCACTGTTG
1 TTTTTAATATTGTTTCACTGTCG
19791358 TTTTTAATATT
1 TTTTTAATATT
19791369 ATTTGGATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.61
Consensus pattern (23 bp):
TTTTTAATATTGTTTCACTGTCG
Found at i:19792456 original size:12 final size:12
Alignment explanation
Indices: 19792439--19792471 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
19792429 CGGTCTGTCC
19792439 ATATTAATTTTT
1 ATATTAATTTTT
19792451 ATATT-ATTTTT
1 ATATTAATTTTT
19792462 ATA-TAATTTT
1 ATATTAATTTT
19792472 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:19792632 original size:29 final size:30
Alignment explanation
Indices: 19792586--19792646 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
19792576 CTTAACAAAT
19792586 AAATGTCTCTAAAATAATAACAAAATTAAC
1 AAATGTCTCTAAAATAATAACAAAATTAAC
19792616 AAATGTCT-TAAAATAATAACAAAATTAAC
1 AAATGTCTCTAAAATAATAACAAAATTAAC
19792645 AA
1 AA
19792647 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGTCTCTAAAATAATAACAAAATTAAC
Found at i:19793926 original size:20 final size:22
Alignment explanation
Indices: 19793903--19793955 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
19793893 TATGTATTAG
*
19793903 AATTCTTAAAAAA-TA-ATAAA
1 AATTCTAAAAAAATTATATAAA
*
19793923 AATTGTAAAAAAATTATATAAA
1 AATTCTAAAAAAATTATATAAA
*
19793945 AAATCATAAAA
1 AATTC-TAAAA
19793956 GCTTGATCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.42
21 2 0.08
22 8 0.31
23 5 0.19
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (22 bp):
AATTCTAAAAAAATTATATAAA
Found at i:19794583 original size:29 final size:29
Alignment explanation
Indices: 19794480--19794583 Score: 77
Period size: 28 Copynumber: 3.6 Consensus size: 29
19794470 TTATAAAAAA
** * *
19794480 TTTAAATATTTTAAATATGTTGTATAATCT
1 TTTAAATATTTTTTATATTTTTTAT-ATCT
* * *
19794510 TATAAATATTTATTAGATTTTTT-TATACT
1 TTTAAATATTTTTTATATTTTTTATAT-CT
* * * *
19794539 TTT-AATAATATCTATATTTTTTATATTT
1 TTTAAATATTTTTTATATTTTTTATATCT
19794567 TTTAAATATTTTTTATA
1 TTTAAATATTTTTTATA
19794584 AATTTAAATC
Statistics
Matches: 54, Mismatches: 17, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
28 20 0.37
29 18 0.33
30 16 0.30
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTAAATATTTTTTATATTTTTTATATCT
Found at i:19802978 original size:7 final size:7
Alignment explanation
Indices: 19802966--19803017 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
19802956 CCAAAGCATC
19802966 AAAGAGA
1 AAAGAGA
19802973 AAAGAGA
1 AAAGAGA
19802980 AAAGAGA
1 AAAGAGA
*
19802987 AAAGGGA
1 AAAGAGA
*
19802994 AAAGGGA
1 AAAGAGA
19803001 AAAGAGA
1 AAAGAGA
*
19803008 AAAGGGA
1 AAAGAGA
19803015 AAA
1 AAA
19803018 AATGGGGTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (7 bp):
AAAGAGA
Found at i:19802990 original size:21 final size:21
Alignment explanation
Indices: 19802966--19803017 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
19802956 CCAAAGCATC
*
19802966 AAAGAGAAAAGAGAAAAGAGA
1 AAAGGGAAAAGAGAAAAGAGA
*
19802987 AAAGGGAAAAGGGAAAAGAGA
1 AAAGGGAAAAGAGAAAAGAGA
19803008 AAAGGGAAAA
1 AAAGGGAAAA
19803018 AATGGGGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
AAAGGGAAAAGAGAAAAGAGA
Found at i:19814799 original size:40 final size:40
Alignment explanation
Indices: 19814744--19814823 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
19814734 TGACCTTTTG
19814744 CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
1 CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
19814784 CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
1 CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
19814824 TCAAAACTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.45
Consensus pattern (40 bp):
CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
Found at i:19825533 original size:6 final size:6
Alignment explanation
Indices: 19825522--19825549 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19825512 ACACGTGTAC
19825522 ATATGT ATATGT ATATGT ATATGT ATAT
1 ATATGT ATATGT ATATGT ATATGT ATAT
19825550 ATACACGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:19826748 original size:23 final size:24
Alignment explanation
Indices: 19826722--19826774 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
19826712 TATTATAATT
19826722 TATTATTT-TTAGT-TTAATTTAAA
1 TATTATTTCTTAGTATTAA-TTAAA
19826745 TATT-TTTCTTAGTAAGTTAATTAAA
1 TATTATTTCTTAGT-A-TTAATTAAA
19826770 TATTA
1 TATTA
19826775 ATTGTTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
22 3 0.12
23 9 0.36
25 9 0.36
26 4 0.16
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (24 bp):
TATTATTTCTTAGTATTAATTAAA
Found at i:19827338 original size:22 final size:23
Alignment explanation
Indices: 19827313--19827361 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
19827303 TAATATTAGA
*
19827313 TTTAATTTT-TGTATTTTTATT-T
1 TTTAATTTTGTG-ATTTTAATTAT
19827335 TTTAATTTTGTGATTTTAATTAT
1 TTTAATTTTGTGATTTTAATTAT
19827358 TTTA
1 TTTA
19827362 TTTAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTAATTTTGTGATTTTAATTAT
Found at i:19829667 original size:58 final size:58
Alignment explanation
Indices: 19829568--19829678 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
19829558 TTTTAGGATT
* * *
19829568 TTCAAAAACTAACTTGAATAAAAAAAATTGAAATCTCAATATGAAAATATTTATCAAG
1 TTCAAAAACTAACTTGAATAAAAAAAATTCAAATCTCAATATAAAAAAATTTATCAAG
* * *
19829626 TTCAAAATCTAACTTTGAA-AAAAAAATTTCATA-CTCTAATATAAAAAAATTTA
1 TTCAAAAACTAAC-TTGAATAAAAAAAATTCAAATCTC-AATATAAAAAAATTTA
19829679 CCGAATTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 3 0.07
58 37 0.82
59 5 0.11
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (58 bp):
TTCAAAAACTAACTTGAATAAAAAAAATTCAAATCTCAATATAAAAAAATTTATCAAG
Found at i:19829838 original size:18 final size:18
Alignment explanation
Indices: 19829815--19829851 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
19829805 TTGATTTTCA
*
19829815 AATTCAAATAACTCGAAT
1 AATTCAAATAAATCGAAT
19829833 AATTCAAATAAATCGAAT
1 AATTCAAATAAATCGAAT
19829851 A
1 A
19829852 TCAGACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (18 bp):
AATTCAAATAAATCGAAT
Found at i:19830013 original size:18 final size:19
Alignment explanation
Indices: 19829990--19830025 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19829980 TCCCCATTAC
*
19829990 TTTCCCCC-AAATTTTTAT
1 TTTCCCCCTAAACTTTTAT
19830008 TTTCCCCCTAAACTTTTA
1 TTTCCCCCTAAACTTTTA
19830026 CTTCTCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTCCCCCTAAACTTTTAT
Found at i:19832516 original size:15 final size:16
Alignment explanation
Indices: 19832496--19832525 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19832486 TCTAAAATTA
19832496 TTTTTG-AGAAATAAG
1 TTTTTGAAGAAATAAG
19832511 TTTTTGAAGAAATAA
1 TTTTTGAAGAAATAA
19832526 TTAAGAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (16 bp):
TTTTTGAAGAAATAAG
Found at i:19837117 original size:8 final size:8
Alignment explanation
Indices: 19837106--19837131 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
19837096 TTATAAAAAA
19837106 TTAAAATT
1 TTAAAATT
19837114 TTAAAATT
1 TTAAAATT
19837122 TTAAAATT
1 TTAAAATT
19837130 TT
1 TT
19837132 TCTAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTAAAATT
Found at i:19838185 original size:16 final size:15
Alignment explanation
Indices: 19838144--19838187 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
19838134 AAAACTTGTA
19838144 ATTTTTAAT-ATATT
1 ATTTTTAATAATATT
*
19838158 A-TTTTAAAAATATAT
1 ATTTTTAATAATAT-T
19838173 ATTTTTAATAATATT
1 ATTTTTAATAATATT
19838188 TTGGAATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 6 0.24
14 5 0.20
15 3 0.12
16 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTTAATAATATT
Found at i:19839923 original size:15 final size:15
Alignment explanation
Indices: 19839899--19839932 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19839889 GTTCGATAAC
*
19839899 TTGAAAAATTAAGTG
1 TTGAAAAATTAAGAG
*
19839914 TTGAATAATTAAGAG
1 TTGAAAAATTAAGAG
19839929 TTGA
1 TTGA
19839933 GTTTTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (15 bp):
TTGAAAAATTAAGAG
Found at i:19846108 original size:99 final size:98
Alignment explanation
Indices: 19845954--19846142 Score: 265
Period size: 99 Copynumber: 1.9 Consensus size: 98
19845944 CCTTTGAGTC
* * *
19845954 AGTTTGTTGATATAACCTTGTGTGATTATTGCATTTCCTTTTTCTCTTGATAGTATGCTGTTTGT
1 AGTTTGTTGATATAACATTGTGTGATTATTGCAATTCCTTTTTCTCTTGAAAGTATGCTGTTTGT
19846019 GCATTAAACAAACAAAGTTAAAATTTGAAGTGTG
66 GCATTAAACAAAC-AAGTTAAAATTTGAAGTGTG
* * *
19846053 AGTTTGTTGATGTAACATCTG-GTGATTATTGCAATT-CTTTGTTGTCTTTAAAGTATGCTGTTT
1 AGTTTGTTGATATAACAT-TGTGTGATTATTGCAATTCCTTT-TTCTCTTGAAAGTATGCTGTTT
* *
19846116 GTGCATTAAAGAAACAAGTTGAAATTT
64 GTGCATTAAACAAACAAGTTAAAATTT
19846143 AAATTTTTGT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
98 15 0.19
99 63 0.79
100 2 0.03
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (98 bp):
AGTTTGTTGATATAACATTGTGTGATTATTGCAATTCCTTTTTCTCTTGAAAGTATGCTGTTTGT
GCATTAAACAAACAAGTTAAAATTTGAAGTGTG
Found at i:19858445 original size:25 final size:23
Alignment explanation
Indices: 19858412--19858457 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
19858402 TTTAATTTTA
*
19858412 GTTTTATATTTTTATTTTTAAAAT
1 GTTTTATA-TATTATTTTTAAAAT
19858436 GTTTTAATATATTATTTTTAAA
1 GTTTT-ATATATTATTTTTAAA
19858458 TCAATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (23 bp):
GTTTTATATATTATTTTTAAAAT
Found at i:19858771 original size:30 final size:30
Alignment explanation
Indices: 19858736--19858820 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
19858726 TTTAGATTCA
19858736 TTAAAATTTGATAAAAAAAATTTTGAG-CCC
1 TTAAAATTTGA-AAAAAAAATTTTGAGCCCC
* * ** *
19858766 TTAAAAGTTAAAAAAAAAAAATTGGGCCCC
1 TTAAAATTTGAAAAAAAAATTTTGAGCCCC
* * *
19858796 TTAAAATTAGAAAATAATATTTTGA
1 TTAAAATTTGAAAAAAAAATTTTGA
19858821 ATCATTTTTA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
29 12 0.29
30 29 0.71
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.31
Consensus pattern (30 bp):
TTAAAATTTGAAAAAAAAATTTTGAGCCCC
Found at i:19858794 original size:29 final size:29
Alignment explanation
Indices: 19858748--19858809 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
19858738 AAAATTTGAT
**
19858748 AAAAAAAATTTTGAG-CCCTTAAAAGTTAA
1 AAAAAAAAAATTGAGCCCCTTAAAA-TTAA
* *
19858777 AAAAAAAAAATTGGGCCCCTTAAAATTAG
1 AAAAAAAAAATTGAGCCCCTTAAAATTAA
19858806 AAAA
1 AAAA
19858810 TAATATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (29 bp):
AAAAAAAAAATTGAGCCCCTTAAAATTAA
Found at i:19861999 original size:5 final size:5
Alignment explanation
Indices: 19861989--19862014 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19861979 GAACAAATAT
19861989 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
19862015 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:19862114 original size:5 final size:5
Alignment explanation
Indices: 19862104--19862129 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19862094 CTCGAAAATT
19862104 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
19862130 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:19864944 original size:7 final size:7
Alignment explanation
Indices: 19864932--19864962 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
19864922 CTATGTAATA
19864932 AAAAATC
1 AAAAATC
19864939 AAAAATC
1 AAAAATC
19864946 AAAAATC
1 AAAAATC
19864953 AAAAATC
1 AAAAATC
19864960 AAA
1 AAA
19864963 GATGTTCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATC
Found at i:19868681 original size:33 final size:35
Alignment explanation
Indices: 19868619--19868684 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
19868609 GCTTTGAAAT
* * *
19868619 TTTTGAAGGTGAAGACCTTTTTTTTAACCTCAAAA
1 TTTTGAAGATGAAGACCTCTTTTTGAACCTCAAAA
19868654 TTTTGAAGATG-A-ACCTCTTTTTGAACCTCAA
1 TTTTGAAGATGAAGACCTCTTTTTGAACCTCAA
19868685 CTAATTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 17 0.61
34 1 0.04
35 10 0.36
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (35 bp):
TTTTGAAGATGAAGACCTCTTTTTGAACCTCAAAA
Found at i:19869260 original size:30 final size:31
Alignment explanation
Indices: 19869201--19869264 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
19869191 AATGAGTGAT
19869201 TGATTTATTACTTTTTGATAACGTTAATAAC
1 TGATTTATTACTTTTTGATAACGTTAATAAC
*
19869232 TGATTTCTTA-TTTTTCGA-AA-GTTAAATAAC
1 TGATTTATTACTTTTT-GATAACGTT-AATAAC
19869262 TGA
1 TGA
19869265 ATTGAAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 3 0.10
30 16 0.53
31 11 0.37
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (31 bp):
TGATTTATTACTTTTTGATAACGTTAATAAC
Found at i:19876468 original size:17 final size:17
Alignment explanation
Indices: 19876446--19876485 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
19876436 TGATGTAATT
19876446 GGGTTGATTGTATTCTC
1 GGGTTGATTGTATTCTC
19876463 GGGTTGATTGTATTCTC
1 GGGTTGATTGTATTCTC
19876480 GAGGTT
1 G-GGTT
19876486 AATTTATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.12, C:0.10, G:0.33, T:0.45
Consensus pattern (17 bp):
GGGTTGATTGTATTCTC
Found at i:19876493 original size:17 final size:17
Alignment explanation
Indices: 19876446--19876493 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
19876436 TGATGTAATT
*
19876446 GGGTTGATTGTATTCTC
1 GGGTTAATTGTATTCTC
*
19876463 GGGTTGATTGTATTCTC
1 GGGTTAATTGTATTCTC
19876480 GAGGTTAATT-TATT
1 G-GGTTAATTGTATT
19876494 AGTAACTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 22 0.76
18 7 0.24
ACGTcount: A:0.17, C:0.08, G:0.27, T:0.48
Consensus pattern (17 bp):
GGGTTAATTGTATTCTC
Found at i:19878484 original size:21 final size:21
Alignment explanation
Indices: 19878474--19878590 Score: 171
Period size: 21 Copynumber: 5.6 Consensus size: 21
19878464 TTATCCCTTT
19878474 CGAGCTTCTGTTCAGCTCTTA
1 CGAGCTTCTGTTCAGCTCTTA
19878495 CGAGCTTCTGTTCAGCTCTTA
1 CGAGCTTCTGTTCAGCTCTTA
19878516 CGAGCTTCTGTTCAGCTCTTA
1 CGAGCTTCTGTTCAGCTCTTA
* *
19878537 TGAGCTTCTGTTCAACTCTTA
1 CGAGCTTCTGTTCAGCTCTTA
* * * *
19878558 TGAGTTTCTATTAAGCTCTTA
1 CGAGCTTCTGTTCAGCTCTTA
*
19878579 TGAGCTTCTGTT
1 CGAGCTTCTGTT
19878591 GGCATTTTCA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 88 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
CGAGCTTCTGTTCAGCTCTTA
Found at i:19887534 original size:31 final size:29
Alignment explanation
Indices: 19887482--19887553 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 29
19887472 TTCTTTACAT
*
19887482 ATGTATAATTGAATCAAAATCAAAGTTTC
1 ATGTATAATTGAATCAAAATCAAAATTTC
* *
19887511 ATGTATATATTTGAATTACAATCAAAATTTC
1 ATGTATA-A-TTGAATCAAAATCAAAATTTC
19887542 ATAGGTATAATT
1 AT--GTATAATT
19887554 ACACCAAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 7 0.19
30 1 0.03
31 22 0.61
32 1 0.03
33 5 0.14
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (29 bp):
ATGTATAATTGAATCAAAATCAAAATTTC
Found at i:19889728 original size:23 final size:23
Alignment explanation
Indices: 19889698--19889742 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19889688 TAGTGTAATT
*
19889698 AAATTGATTCCTACGTTAAGCAC
1 AAATTGATTCCTACATTAAGCAC
19889721 AAATTGATTCCTACATTAAGCA
1 AAATTGATTCCTACATTAAGCA
19889743 TTGGATCTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (23 bp):
AAATTGATTCCTACATTAAGCAC
Found at i:19890384 original size:33 final size:31
Alignment explanation
Indices: 19890347--19890413 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
19890337 GTTAACTTTC
* * *
19890347 TTTATATATCTTTTAGATTTTTTTTTGGAAATT
1 TTTATAAATATTTT-GAATTTTTTTT-GAAATT
*
19890380 TTTATAAATATTTTGAATTTTTTTTGTAATT
1 TTTATAAATATTTTGAATTTTTTTTGAAATT
19890411 TTT
1 TTT
19890414 GTTGAGAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 8 0.27
32 10 0.33
33 12 0.40
ACGTcount: A:0.25, C:0.01, G:0.07, T:0.66
Consensus pattern (31 bp):
TTTATAAATATTTTGAATTTTTTTTGAAATT
Found at i:19897083 original size:15 final size:16
Alignment explanation
Indices: 19897053--19897090 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
19897043 TCGGGAAAGC
*
19897053 ACGTCCAATTAAAAAT
1 ACGTCCAATAAAAAAT
19897069 ACGTCCAA-AAAAAAT
1 ACGTCCAATAAAAAAT
*
19897084 ATGTCCA
1 ACGTCCA
19897091 GCTAGATACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.21
Consensus pattern (16 bp):
ACGTCCAATAAAAAAT
Found at i:19902011 original size:7 final size:7
Alignment explanation
Indices: 19901999--19902028 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
19901989 GCTGACCAGC
19901999 TGGTCTA
1 TGGTCTA
19902006 TGGTCTA
1 TGGTCTA
19902013 TGGTCTA
1 TGGTCTA
19902020 TGGTCTA
1 TGGTCTA
19902027 TG
1 TG
19902029 CAGTTGATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.43
Consensus pattern (7 bp):
TGGTCTA
Found at i:19910955 original size:5 final size:5
Alignment explanation
Indices: 19910945--19910971 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19910935 ATAATTTTTT
19910945 TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA
19910972 TCGAGATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:19917154 original size:26 final size:24
Alignment explanation
Indices: 19917123--19917181 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
19917113 TTATACTGAA
19917123 ATTAAAACAACAATAATATACAAAAT
1 ATTAAAACAAC-AT-ATATACAAAAT
* *
19917149 ATTAAAAC-TCATTTATACAAAAT
1 ATTAAAACAACATATATACAAAAT
*
19917172 ATTAAGACAA
1 ATTAAAACAA
19917182 ATCTCATGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 17 0.61
24 2 0.07
25 1 0.04
26 8 0.29
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (24 bp):
ATTAAAACAACATATATACAAAAT
Found at i:19933786 original size:129 final size:127
Alignment explanation
Indices: 19933653--19933947 Score: 387
Period size: 128 Copynumber: 2.3 Consensus size: 127
19933643 TCTATATTTG
* ** *
19933653 ATAAATATAATTATTTATATATGTAATATATAAACATAAAACAATGCTATATCAATAATTGTATT
1 ATAAATATAATTATTT-TATATGCAATATATAAACATAAAACAATAATATATAAATAATTGTATT
* * **
19933718 TATAAAAATTGATTCAAATTAAAATTTTTTATATAAAATTACACAAAATCAAAATTCAAATATA
65 T-TAAAAATTGAATCAAATCAAAATTTCGTATATAAAATTACACAAAATCAAAATTCAAATATA
* * * *
19933782 ATAAATAAAATTATTTTTATATACAATATATAAACCTAAAATAATAATATATAAATAATTGTATT
1 ATAAATATAATTA-TTTTATATGCAATATATAAACATAAAACAATAATATATAAATAATTGTATT
* * *
19933847 TTTAAAATTGAATCAAATCAAAATTTCGTATATAAAATTATACAAAATTAAAATTCAAATATA
65 TTAAAAATTGAATCAAATCAAAATTTCGTATATAAAATTACACAAAATCAAAATTCAAATATA
* * *
19933910 ATAAACATAACTA-TTCATATGCAATATATAAA-ATAAAA
1 ATAAATATAATTATTTTATATGCAATATATAAACATAAAA
19933948 TAAACACTCT
Statistics
Matches: 144, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
125 5 0.03
126 17 0.12
128 65 0.45
129 54 0.38
130 3 0.02
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.37
Consensus pattern (127 bp):
ATAAATATAATTATTTTATATGCAATATATAAACATAAAACAATAATATATAAATAATTGTATTT
TAAAAATTGAATCAAATCAAAATTTCGTATATAAAATTACACAAAATCAAAATTCAAATATA
Found at i:19934738 original size:30 final size:30
Alignment explanation
Indices: 19934648--19934738 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
19934638 ATCACGAGTA
19934648 GTTTCTGGGTTTTAAAGATAGATTTATACC
1 GTTTCTGGGTTTTAAAGATAGATTTATACC
*
19934678 ATTTCTGGGTTTTAAAGATAGATTTATACC
1 GTTTCTGGGTTTTAAAGATAGATTTATACC
*
19934708 GTTTCTGGGTTTTAAAGACAGATTTATACC
1 GTTTCTGGGTTTTAAAGATAGATTTATACC
19934738 G
1 G
19934739 ATCTCCTTGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (30 bp):
GTTTCTGGGTTTTAAAGATAGATTTATACC
Found at i:19945902 original size:47 final size:47
Alignment explanation
Indices: 19945833--19945926 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
19945823 TAAGTTAATA
19945833 ACAAAGCAATATTCTAGATAAAAGTACGAGAATTTGGGTCCACCATT
1 ACAAAGCAATATTCTAGATAAAAGTACGAGAATTTGGGTCCACCATT
19945880 ACAAAGCAATATTCTAGATAAAAGTACGAGAATTTGGGTCCACCATT
1 ACAAAGCAATATTCTAGATAAAAGTACGAGAATTTGGGTCCACCATT
19945927 CTATCCTCCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (47 bp):
ACAAAGCAATATTCTAGATAAAAGTACGAGAATTTGGGTCCACCATT
Found at i:19947928 original size:6 final size:6
Alignment explanation
Indices: 19947917--19947947 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
19947907 CAATAAATAA
19947917 TTATAT TTATAT TTATAT TTATAT TTATAT T
1 TTATAT TTATAT TTATAT TTATAT TTATAT T
19947948 AAATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:19947957 original size:18 final size:18
Alignment explanation
Indices: 19947910--19947957 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
19947900 TATAATACAA
19947910 TAAATAATTATATTTATAT
1 TAAATAA-TATATTTATAT
* *
19947929 T-TATATTTATATTTATAT
1 TAAATA-ATATATTTATAT
19947947 TAAATAATATA
1 TAAATAATATA
19947958 ACATAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAATAATATATTTATAT
Found at i:19948101 original size:35 final size:35
Alignment explanation
Indices: 19948026--19948092 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
19948016 AATAAAATTT
19948026 AAATATTTTTAAATTATATTCATAATAAAATATCA
1 AAATATTTTTAAATTATATTCATAATAAAATATCA
*
19948061 AAATATTTTATAAATTATATTTA-AATAAAATA
1 AAATATTTT-TAAATTATATTCATAATAAAATA
19948093 ATGAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 18 0.60
36 12 0.40
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (35 bp):
AAATATTTTTAAATTATATTCATAATAAAATATCA
Found at i:19957952 original size:2 final size:2
Alignment explanation
Indices: 19957945--19957980 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19957935 TACTGTTCTT
19957945 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19957981 ACTCAGCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:19959669 original size:25 final size:25
Alignment explanation
Indices: 19959619--19959666 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
19959609 TAACTGTTAC
*
19959619 AGAAAATTATTATAAAGAATTAAAT
1 AGAAAATTATTATAAAGAATAAAAT
*
19959644 AGAAAATTGTT-TAAAGAATAAAA
1 AGAAAATTATTATAAAGAATAAAA
19959667 ATAAAGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.29
Consensus pattern (25 bp):
AGAAAATTATTATAAAGAATAAAAT
Found at i:19974310 original size:18 final size:18
Alignment explanation
Indices: 19974287--19974329 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
19974277 ATTTAAGGTG
19974287 TAATTAATTTAAATTT-TT
1 TAATTAA-TTAAATTTATT
19974305 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
19974323 TAATTAA
1 TAATTAA
19974330 AAACCTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:19979923 original size:14 final size:15
Alignment explanation
Indices: 19979901--19979977 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
19979891 CAATCAAACA
19979901 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
19979915 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
19979930 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
19979950 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
19979964 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
19979978 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:19979942 original size:20 final size:20
Alignment explanation
Indices: 19979917--19979956 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19979907 AATATTTTCC
*
19979917 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
19979937 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
19979957 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:19979962 original size:34 final size:35
Alignment explanation
Indices: 19979905--19979971 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
19979895 CAAACACCAG
*
19979905 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
19979940 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
19979972 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:19983743 original size:17 final size:17
Alignment explanation
Indices: 19983721--19983761 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
19983711 TTCCGCCAAA
19983721 GATTCGATAAATTATTT
1 GATTCGATAAATTATTT
19983738 GATTCGATAAATTATTT
1 GATTCGATAAATTATTT
19983755 GATTCGA
1 GATTCGA
19983762 GTTTTCCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (17 bp):
GATTCGATAAATTATTT
Found at i:19993220 original size:3 final size:3
Alignment explanation
Indices: 19993212--19993240 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19993202 GACAATCTGA
19993212 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19993241 ATATCTATTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19993896 original size:3 final size:3
Alignment explanation
Indices: 19993890--19993921 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19993880 GTTAGTATTA
19993890 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
19993922 AGTATTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:19995090 original size:28 final size:31
Alignment explanation
Indices: 19995032--19995090 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
19995022 ATATATAGTT
19995032 TTTATACTATTTATAAAAGTTATAATAATAA
1 TTTATACTATTTATAAAAGTTATAATAATAA
* *
19995063 TTTATA-TA-TTAT-AATGTTATTATAATAA
1 TTTATACTATTTATAAAAGTTATAATAATAA
19995091 AAAGGAACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 14 0.54
29 4 0.15
30 2 0.08
31 6 0.23
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (31 bp):
TTTATACTATTTATAAAAGTTATAATAATAA
Found at i:19996047 original size:41 final size:41
Alignment explanation
Indices: 19995944--19996101 Score: 176
Period size: 41 Copynumber: 3.8 Consensus size: 41
19995934 GATATGTATT
*
19995944 TTCGTGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTGTGTA
1 TTCGTGTAAGACCACGTCTGGGACATTGGCATCGTA-TT-TG-A
* *
19995987 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGA
1 TTCGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGA
* * * *
19996028 TTTGTGTAAGACC-CTGTCTGGGACAGTGGCATCATATGTGA
1 TTCGTGTAAGACCAC-GTCTGGGACATTGGCATCGTATTTGA
* *
19996069 TTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TT-CGTGTAAGACCACGTCTGGGACATTGGCAT
19996102 TGTACGAGCC
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
41 37 0.38
42 26 0.27
43 34 0.35
44 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (41 bp):
TTCGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGA
Found at i:19996101 original size:83 final size:84
Alignment explanation
Indices: 19995947--19996101 Score: 212
Period size: 83 Copynumber: 1.9 Consensus size: 84
19995937 ATGTATTTTC
* *
19995947 GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTATACGTGTAAGACCATGTCTGGGACA
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTATACATGTAAGACCACGTCTGGGACA
19996012 TTGGCATCGTATTTGATTT
66 TTGGCATCGTATTTGATTT
19996031 GTGTAAGACC-CTGTCTGGGACAG-TGGCATC-A-TATGTG-ATTACATGTAAGACCACGTCTGG
1 GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGTA-TACATGTAAGACCACGTCTGG
*
19996091 GACGTTGGCAT
62 GACATTGGCAT
19996102 TGTACGAGCC
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
82 2 0.03
83 35 0.55
84 26 0.41
85 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.30
Consensus pattern (84 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTATACATGTAAGACCACGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:19996292 original size:16 final size:17
Alignment explanation
Indices: 19996263--19996294 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19996253 TGAATTGATG
19996263 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
19996280 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
19996295 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:20001643 original size:159 final size:158
Alignment explanation
Indices: 20001197--20001654 Score: 401
Period size: 161 Copynumber: 2.9 Consensus size: 158
20001187 GCAAGTTGAA
* * * * * *
20001197 AAAAAAGTTAGTAAAAAAATCTTACTTCGGCCATTTATTCGTA-TTTTTTCTCCGCATTTTATTC
1 AAAATAGTTAGTAAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCACATTTTATTA
**
20001261 CTTTAAAAAATATCAT-AATTTCTAATTTTATAATTTTACATTATTTCAGTGCATAATATTTGAA
66 CTTTAAAAAATATCATAAATTAGT-ATTTTATAATTTTACATTATTTCAGTGCATAATATTTGAA
* * *
20001325 ATTTATTAATCTAGTGTGTTATTTAAATT
130 ATTTATTAATCTAATGTATTATTGAAATT
** * ** * ** * * * * *
20001354 AATTTGGTGTAAAAAAAAACCCTTACCCCTGCCCTTTGCTCGTATTATTTTCTCGA-TTTTTATT
1 AAAATAGT-TAGTAAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCACATTTTATT
* * * ** * * ** *
20001418 ACTTTAAATAAAAATAT-ATTATTCTCGTATTTTATTGTTTTAAATTATTTCAGTACATTTTCTT
65 ACTTT--A-AAAAATATCATAAAT-TAGTATTTTATAATTTTACATTATTTCAGTGCATAATATT
* *
20001482 TGAAATATT-TTGTAT-TAAT-TATT-TCTGAATTTT
126 TGAAAT-TTATT-AATCTAATGTATTAT-TGAA-ATT
* *
20001515 AAAATAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCACATTTTATTA
1 AAAATAGTTAGTAAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCACATTTTATTA
* *
20001580 CTTTAAAAAATATCATAAACTTAGTTTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAA
66 CTTTAAAAAATATCATAAA-TTAGTATTTTATAATTTTACATTATTTCAGTGCATAATATTTGAA
20001645 ATTTATTAAT
130 ATTTATTAAT
20001655 TTAGTGTGTT
Statistics
Matches: 225, Mismatches: 61, Indels: 29
0.71 0.19 0.09
Matches are distributed among these distances:
157 4 0.02
158 48 0.21
159 52 0.23
160 46 0.20
161 69 0.31
162 6 0.03
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (158 bp):
AAAATAGTTAGTAAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCACATTTTATTA
CTTTAAAAAATATCATAAATTAGTATTTTATAATTTTACATTATTTCAGTGCATAATATTTGAAA
TTTATTAATCTAATGTATTATTGAAATT
Found at i:20002174 original size:17 final size:18
Alignment explanation
Indices: 20002147--20002182 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
20002137 TTAAACACAC
20002147 AAATATTACAAAAAAATT
1 AAATATTACAAAAAAATT
20002165 AAAT-TTACAAAAAAATT
1 AAATATTACAAAAAAATT
20002182 A
1 A
20002183 CCTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATATTACAAAAAAATT
Found at i:20002243 original size:31 final size:28
Alignment explanation
Indices: 20002194--20002250 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
20002184 CTTTTTTTTC
20002194 TTTTTTTTCCTTCCTTTCCTCTTCTTCT
1 TTTTTTTTCCTTCCTTTCCTCTTCTTCT
*
20002222 TTTTTTTTCTCTTCTCATTTCCTTTTCTT
1 TTTTTTTTC-CTTC-C-TTTCCTCTTCTT
20002251 TCCTTCTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 4 0.16
30 1 0.04
31 11 0.44
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTTTTTCCTTCCTTTCCTCTTCTTCT
Found at i:20002244 original size:36 final size:38
Alignment explanation
Indices: 20002204--20002274 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 38
20002194 TTTTTTTTCC
20002204 TTCCTTTCCTCTT-CTTCTTT-TT-TTTTCTCTTCTCAT
1 TTCCTTTCCT-TTCCTTCTTTCTTCTTTTCTCTTCTCAT
*
20002240 TTCCTTTTCTTTCCTTCTTTCTTCTTTTCTCTTCT
1 TTCCTTTCCTTTCCTTCTTTCTTCTTTTCTCTTCT
20002275 TCTTCTTTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 2 0.06
36 16 0.52
37 2 0.06
38 11 0.35
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (38 bp):
TTCCTTTCCTTTCCTTCTTTCTTCTTTTCTCTTCTCAT
Found at i:20002261 original size:4 final size:4
Alignment explanation
Indices: 20002245--20002327 Score: 68
Period size: 4 Copynumber: 21.0 Consensus size: 4
20002235 CTCATTTCCT
* *
20002245 TTTC TTTC CTTC TTTC -TTC TTTTC TCTTC -TTC -TTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC -TTTC T-TTC TTTC TTTC TTTC TTTC TTTC
*
20002290 TTTC TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC
20002328 CCTCTCCTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
3 13 0.20
4 42 0.64
5 10 0.15
6 1 0.02
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:20002276 original size:41 final size:40
Alignment explanation
Indices: 20002199--20002328 Score: 104
Period size: 41 Copynumber: 3.1 Consensus size: 40
20002189 TTTTCTTTTT
* * * *
20002199 TTTCCTTCCTTTCCTCTTC-TTCTTTTTTTTTCTCTTC-TC
1 TTTCCTTCTTTTTC-CTTCTTTCTTCTTTTCTCTCTTCTTC
20002238 ATTTCCTT-TTCTTTCCTTCTTTCTTCTTTTCTCTTCTTCTTC
1 -TTTCCTTCTT-TTTCCTTCTTTCTTCTTTTCTC-TCTTCTTC
* * *
20002280 TTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCTTTCTTTCTTTC
1 TTTCCTTCTTTTTCCTTCTTT-CT-TCTTTTCTCTC-TTC-TTC
20002324 TTTCC
1 TTTCC
20002329 CTCTCCTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
39 5 0.07
40 21 0.28
41 22 0.30
42 8 0.11
43 10 0.14
44 8 0.11
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (40 bp):
TTTCCTTCTTTTTCCTTCTTTCTTCTTTTCTCTCTTCTTC
Found at i:20002276 original size:59 final size:59
Alignment explanation
Indices: 20002213--20002326 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
20002203 CTTCCTTTCC
* *
20002213 TCTTCTTCTTT-TT-TTTTCTCTTCTCATTTCCTTTTCTTTCCTTCTTTC-TTCTTTTCTCT
1 TCTTCTTCTTTCTTCTTTT-TCTT-TC-TTTCCTCTCCTTTCCTTCTTTCTTTCTTTTCTCT
*
20002272 TCTTCTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCTTTCTTTCTTTCTTT
1 TCTTCTTCTTT-CTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTCTTTCTTTCTTT
20002327 CCCTCTCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
59 30 0.62
60 8 0.17
61 6 0.12
62 4 0.08
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (59 bp):
TCTTCTTCTTTCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTCTTTCTTTCTTTTCTCT
Found at i:20002284 original size:31 final size:30
Alignment explanation
Indices: 20002207--20002326 Score: 113
Period size: 31 Copynumber: 4.0 Consensus size: 30
20002197 TTTTTCCTTC
* *
20002207 CTTTCCTCTTC-TT-CTTTTTTTTTCTCTTCT
1 CTTTCCTCTTCTTTCCTTCTTTCTTCT-TT-T
*
20002237 CATTTCCTTTTCTTTCCTTCTTTCTTCTTTT
1 C-TTTCCTCTTCTTTCCTTCTTTCTTCTTTT
*
20002268 CTCTTCTTCTTCTTTCCTTCTTT-TTC-TTT
1 CT-TTCCTCTTCTTTCCTTCTTTCTTCTTTT
* *
20002297 CTTTCCTCTCCTTTCTTTCTTTCTTTCTTT
1 CTTTCCTCTTCTTTCCTTCTTTC-TTCTTT
20002327 CCCTCTCCTT
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
28 17 0.23
29 5 0.07
30 8 0.11
31 31 0.41
32 4 0.05
33 10 0.13
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (30 bp):
CTTTCCTCTTCTTTCCTTCTTTCTTCTTTT
Found at i:20002400 original size:27 final size:27
Alignment explanation
Indices: 20002370--20002473 Score: 154
Period size: 27 Copynumber: 3.9 Consensus size: 27
20002360 TATTATCAAC
*
20002370 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGTATTGGCACCTT
*
20002397 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGTATTGGCACCTT
* *
20002424 TGGTGTCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGTATTGGCACCTT
**
20002451 TGGTGCCGCCAATGCCATTGGCA
1 TGGTGCCGCCAATGGTATTGGCA
20002474 TGACCAGTGT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (27 bp):
TGGTGCCGCCAATGGTATTGGCACCTT
Found at i:20002559 original size:27 final size:26
Alignment explanation
Indices: 20002520--20002589 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 26
20002510 CAGGTTTTTT
*
20002520 TTATATATTTTGGTAAATAAAAAAAT
1 TTATATATTTTGGTAAATAAAAAAAA
20002546 TGTATATATTTTGGTAAATAAAAAAAA
1 T-TATATATTTTGGTAAATAAAAAAAA
*
20002573 TTATAACATTTTGGTAA
1 TTAT-ATATTTTGGTAA
20002590 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.10
27 36 0.90
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (26 bp):
TTATATATTTTGGTAAATAAAAAAAA
Found at i:20003056 original size:95 final size:95
Alignment explanation
Indices: 20002890--20003800 Score: 1453
Period size: 95 Copynumber: 9.6 Consensus size: 95
20002880 CAAGCATCAC
*
20002890 ATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
* * *
20002955 GAGGAAGCAAGATCCGTTGTTGTAGCTTCA
66 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
* * * *
20002985 ATCTGTTCCACTACAACACTAGAAAAGTAAAATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
*
20003050 GGGGAAGCAAGATTCGCTGCTGTAGCTTCA
66 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
* *
20003080 ATCTGTTCCACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCT
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
*
20003145 AGGGAAGCAAGATCCGCTGCTGTAGCTTCA
66 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
* *
20003175 ATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTTCC
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
*
20003240 GGGGAAGCAAGATCCGCTGCTATAGCTTCA
66 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
*
20003270 ATCTGTTCCACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
*
20003335 AGGGAAGCAAGATCCGCTGCTGTAGCTTCA
66 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
* * * *
20003365 ATATGTTTCACTGCAACGCTAGGAAAGCAAGATCTGCTGTTGTAGCTTCAATCTTTTTAACTGCC
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
*
20003430 GGGGAAGCAAGATCCGCTGTTGTAGCTTCA
66 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
*
20003460 ATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
20003525 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
66 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
* * * * * *
20003555 ATCTGTTCCAGTGTAATGCTAGGAAAATAAGATTCGTTGTTGTAGCTTCAATCTTTTTAACTGCC
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
*
20003620 AGGGAAGCAAGATCCGCTGCTGTAGCTTCA
66 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
* * * *
20003650 ATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTTAATCTTTTTAATTGCA
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
* *
20003715 AGGGAAGCAAGATCCGCTGTTGTAGCTTCA
66 GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
** * * *
20003745 ATCTGTTCCACTGCAACAATAAGAAAGTAAGATTCACTGTTGTAGCTTCAATCTTT
1 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTT
20003801 CTAATTGCAA
Statistics
Matches: 749, Mismatches: 67, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 749 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (95 bp):
ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCC
GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
Found at i:20003810 original size:50 final size:50
Alignment explanation
Indices: 20002890--20003810 Score: 664
Period size: 50 Copynumber: 19.3 Consensus size: 50
20002880 CAAGCATCAC
* *
20002890 ATCTGTT-TCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAAC-ATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * *
20002940 ATCT-TTTTAACTGC--C-GAGG-AAGCAAGATCCGTTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * *
20002985 ATCTGTTC-CACTACAACACTAGAAAAGTAAAATCCGCTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAACA-TAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * * * *
20003035 ATCT-TTTTAACTGC--C--GGGGAAGCAAGATTCGCTGCTGTAGCTTCA
1 ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
*
20003080 ATCTGTTC-CACTGCAATGC-TAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAA--CATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * *
20003130 ATCT-TTTTAACTG---C-TAGGGAAGCAAGATCCGCTGCTGTAGCTTCA
1 ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* *
20003175 ATCTGTT-TCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAAC-ATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * * * * *
20003225 ATCT-TTTTAACTTC--C--GGGGAAGCAAGATCCGCTGCTATAGCTTCA
1 ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
*
20003270 ATCTGTTC-CACTGCAATGC-TAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAA--CATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * *
20003320 ATCT-TTTTAACTGC--C--AGGGAAGCAAGATCCGCTGCTGTAGCTTCA
1 ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * * *
20003365 ATATGTT-TCACTGCAACGCTAGGAAAGCAAGATCTGCTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAAC-ATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * *
20003415 ATCT-TTTTAACTGC--C--GGGGAAGCAAGATCCGCTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
*
20003460 ATCTGTTC-CACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAACA-TAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * * *
20003510 ATCT-TTTTAACTGC--C--GGGGAAGCAAGATCCGCTGCTGTAGCTTCA
1 ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * * * *
20003555 ATCTGTTC-CAGTGTAATGC-TAGGAAAATAAGATTCGTTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAA--CATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * *
20003605 ATCT-TTTTAACTGC--C--AGGGAAGCAAGATCCGCTGCTGTAGCTTCA
1 ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * *
20003650 ATCTGTT-TCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTTA
1 ATCTGTTCTAACTGCAAC-ATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * *
20003700 ATCT-TTTTAATTG---CA-AGGGAAGCAAGATCCGCTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
* * * *
20003745 ATCTGTTC-CACTGCAACAATAAGAAAGTAAGATTCACTGTTGTAGCTTCA
1 ATCTGTTCTAACTGCAAC-ATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
*
20003795 ATCT-TTCTAATTGCAA
1 ATCTGTTCTAACTGCAA
20003811 TGTATGGTTT
Statistics
Matches: 686, Mismatches: 121, Indels: 128
0.73 0.13 0.14
Matches are distributed among these distances:
45 308 0.45
46 23 0.03
47 5 0.01
48 7 0.01
49 27 0.04
50 316 0.46
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (50 bp):
ATCTGTTCTAACTGCAACATAGGAAAGTAAGATCCGCTGTTGTAGCTTCA
Found at i:20004966 original size:44 final size:43
Alignment explanation
Indices: 20004901--20005006 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
20004891 TGCCTCGATC
*
20004901 TGAT-CAAAATTTGAGCTGCTCTAATCACCACCATGCCCCAATT
1 TGATCCAAAATTTGAGCCGCTCTAATCA-CACCATGCCCCAATT
* * ** * *
20004944 TGATCCAAAATTTAAGCCGCTCTGATCACTTCGTGCCCCATTT
1 TGATCCAAAATTTGAGCCGCTCTAATCACACCATGCCCCAATT
*
20004987 TGTTCCAAAATTTGAGCCGC
1 TGATCCAAAATTTGAGCCGC
20005007 CCTTTTTTGG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 33 0.62
44 20 0.38
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.30
Consensus pattern (43 bp):
TGATCCAAAATTTGAGCCGCTCTAATCACACCATGCCCCAATT
Found at i:20005142 original size:15 final size:15
Alignment explanation
Indices: 20005093--20005141 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
20005083 TTTCCTTTTA
*
20005093 TTTTCTCTTCTTCTTC
1 TTTTCT-TTCTTCTTT
*
20005109 TTCTCTTTCTTCTTT
1 TTTTCTTTCTTCTTT
20005124 TTTTCTTTCTT-TTT
1 TTTTCTTTCTTCTTT
20005138 TTTT
1 TTTT
20005142 TGTATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 7 0.23
15 18 0.60
16 5 0.17
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCTTTCTTCTTT
Found at i:20010135 original size:9 final size:9
Alignment explanation
Indices: 20010121--20010166 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
20010111 TATAGTTTGA
20010121 TATTCGAAT
1 TATTCGAAT
20010130 TATTCGAAT
1 TATTCGAAT
20010139 TATTCGAAT
1 TATTCGAAT
*
20010148 TATTCGAGT
1 TATTCGAAT
20010157 TATTCGAAT
1 TATTCGAAT
20010166 T
1 T
20010167 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20010237 original size:9 final size:9
Alignment explanation
Indices: 20010220--20010250 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20010210 TCGAGTTGAT
20010220 TCGAATAAC
1 TCGAATAAC
*
20010229 TCGATTAAC
1 TCGAATAAC
20010238 TCGAATAAC
1 TCGAATAAC
20010247 TCGA
1 TCGA
20010251 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:20011284 original size:21 final size:21
Alignment explanation
Indices: 20011260--20011299 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20011250 TAACATAAAA
*
20011260 TAATATATAATATACATATTT
1 TAATATATAAAATACATATTT
*
20011281 TAATATATAAAATATATAT
1 TAATATATAAAATACATAT
20011300 ATATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATATATAAAATACATATTT
Found at i:20011476 original size:3 final size:3
Alignment explanation
Indices: 20011470--20011600 Score: 194
Period size: 3 Copynumber: 43.7 Consensus size: 3
20011460 CAATAATACC
* * * *
20011470 AAT AAT ATT AAT GAAT -AT AAA AAT AAT AAT AGT AA- AGAC AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
20011515 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20011563 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20011601 AATTGCCAAG
Statistics
Matches: 117, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
2 3 0.03
3 110 0.94
4 4 0.03
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20012323 original size:12 final size:12
Alignment explanation
Indices: 20012296--20012332 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
20012286 TTTCTTAAGG
*
20012296 AAATAAAAT-CA
1 AAATAAAATAAA
20012307 AAATAAAATAAA
1 AAATAAAATAAA
20012319 AAATAAAATAAA
1 AAATAAAATAAA
20012331 AA
1 AA
20012333 CTTTGCGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:20012332 original size:11 final size:11
Alignment explanation
Indices: 20012296--20012332 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
20012286 TTTCTTAAGG
*
20012296 AAATAAAATCA
1 AAATAAAATAA
20012307 AAATAAAATAAA
1 AAATAAAAT-AA
20012319 AAATAAAATAA
1 AAATAAAATAA
20012330 AAA
1 AAA
20012333 CTTTGCGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:20016913 original size:22 final size:23
Alignment explanation
Indices: 20016880--20016923 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
20016870 GTGATGATGT
20016880 TATCTTATAAATACGTT-AAATC
1 TATCTTATAAATACGTTGAAATC
*
20016902 TATCTTGA-AAATATGTTGAAAT
1 TATCTT-ATAAATACGTTGAAAT
20016924 TGATTGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
TATCTTATAAATACGTTGAAATC
Found at i:20017469 original size:8 final size:8
Alignment explanation
Indices: 20017456--20017492 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
20017446 TATGGTCTTA
20017456 CACATAAT
1 CACATAAT
20017464 CACATAAT
1 CACATAAT
20017472 CACATAAT
1 CACATAAT
20017480 CACATAA-
1 CACATAAT
20017487 CACATA
1 CACATA
20017493 CCGATGCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (8 bp):
CACATAAT
Found at i:20017600 original size:43 final size:43
Alignment explanation
Indices: 20017539--20017639 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
20017529 CACTTATCAT
* *
20017539 TTATCTCTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCAC
1 TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTACCAC
20017582 TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTACCAC
1 TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTACCAC
* *
20017625 TTATCGCTTATCACT
1 TTATCACTTGTCACT
20017640 TGTCACTTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (43 bp):
TTATCACTTGTCACTGATCAAATAAGTGTAGCTAAGCTACCAC
Found at i:20017645 original size:7 final size:7
Alignment explanation
Indices: 20017635--20017667 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
20017625 TTATCGCTTA
20017635 TCACTTG
1 TCACTTG
20017642 TCACTTG
1 TCACTTG
20017649 TCACTTG
1 TCACTTG
20017656 TCACTTG
1 TCACTTG
20017663 TCACT
1 TCACT
20017668 GATCAGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.12, T:0.42
Consensus pattern (7 bp):
TCACTTG
Found at i:20021240 original size:17 final size:18
Alignment explanation
Indices: 20021208--20021243 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
20021198 AATCAGAGGA
20021208 GGGATTTTCCTTTGATTT
1 GGGATTTTCCTTTGATTT
*
20021226 GGGATTTT-TTTTGATTT
1 GGGATTTTCCTTTGATTT
20021243 G
1 G
20021244 TCATAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.11, C:0.06, G:0.25, T:0.58
Consensus pattern (18 bp):
GGGATTTTCCTTTGATTT
Found at i:20024524 original size:6 final size:7
Alignment explanation
Indices: 20024507--20024533 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
20024497 GGGCTCGAAG
20024507 AAAAAAT
1 AAAAAAT
20024514 AAAAAAT
1 AAAAAAT
20024521 AAAAAAT
1 AAAAAAT
20024528 AAAAAA
1 AAAAAA
20024534 AGGCTCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:20031149 original size:25 final size:25
Alignment explanation
Indices: 20031117--20031184 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
20031107 CTCTCAAGCC
** *
20031117 ATATAACGGGAAGCTCATGTGAGCT
1 ATATAACGGGAAGCTCATCCGAGAT
* *
20031142 ATATAACGAGAAGCTTATCCGAGAT
1 ATATAACGGGAAGCTCATCCGAGAT
* *
20031167 GTATAACAGGAAGCTCAT
1 ATATAACGGGAAGCTCAT
20031185 AAAAGCCATA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (25 bp):
ATATAACGGGAAGCTCATCCGAGAT
Found at i:20031397 original size:25 final size:26
Alignment explanation
Indices: 20031369--20031425 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
20031359 CTCGTAGGAA
20031369 CTATATAAT-GGGAAGCTCAAGAGAG
1 CTATATAATCGGGAAGCTCAAGAGAG
* * *
20031394 CTAT-TTATCGGGATGCTCATGAGAG
1 CTATATAATCGGGAAGCTCAAGAGAG
20031419 CTA-ATAA
1 CTATATAA
20031426 CAGGATGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (26 bp):
CTATATAATCGGGAAGCTCAAGAGAG
Found at i:20031612 original size:21 final size:21
Alignment explanation
Indices: 20031586--20031627 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20031576 TAAATTTAAC
*
20031586 TCAATTTAATAAAATTCACAT
1 TCAATTCAATAAAATTCACAT
* *
20031607 TCAATTCCATCAAATTCACAT
1 TCAATTCAATAAAATTCACAT
20031628 CTTAGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (21 bp):
TCAATTCAATAAAATTCACAT
Found at i:20033146 original size:19 final size:18
Alignment explanation
Indices: 20033116--20033151 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20033106 CTTTTATGAA
20033116 TTATTTTTATTTATTTAT
1 TTATTTTTATTTATTTAT
*
20033134 TTATTTATTATTTCTTTA
1 TTATTT-TTATTTATTTA
20033152 CCTCTGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATTTTTATTTATTTAT
Found at i:20033447 original size:19 final size:20
Alignment explanation
Indices: 20033412--20033453 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
20033402 TCATTTCAAA
20033412 TTTTATCTATGTTTTATT-T
1 TTTTATCTATGTTTTATTAT
*
20033431 TTTTATGTA-GTTATTATTAT
1 TTTTATCTATGTT-TTATTAT
20033451 TTT
1 TTT
20033454 GTTCTTATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 13 0.65
20 4 0.20
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTTATCTATGTTTTATTAT
Found at i:20036354 original size:165 final size:165
Alignment explanation
Indices: 20036077--20036396 Score: 577
Period size: 165 Copynumber: 1.9 Consensus size: 165
20036067 TAAAAATGTT
*
20036077 AAATTGTAGAAAAATATGGAATTTTTATGATGACAAGGACTAAATTGTTAAACTTGAGAAAATAT
1 AAATTGTAGAAAAATATGGAATTTTTATGATGACAAGGACTAAATTGTCAAACTTGAGAAAATAT
* * *
20036142 GTGGATTAAATAGTAGAAGTGAAATTTATAGAAATTGATACGTGAAACAATATATTAATATAAAA
66 GTGGATAAAATAATAGAAGTGAAATATATAGAAATTGATACGTGAAACAATATATTAATATAAAA
20036207 TATGTGATTAAAGTGTAACAAGAAAGGAAACTGTG
131 TATGTGATTAAAGTGTAACAAGAAAGGAAACTGTG
*
20036242 AAATTGTAGAAAAATATGGATTTTTTATGATGACAAGGACTAAATTGTCAAACTTGAGAAAATAT
1 AAATTGTAGAAAAATATGGAATTTTTATGATGACAAGGACTAAATTGTCAAACTTGAGAAAATAT
* *
20036307 GTGGATAAAATAATATAAGTGAAATATATAGAAATTGATATGTGAAACAATATATTAATATAAAA
66 GTGGATAAAATAATAGAAGTGAAATATATAGAAATTGATACGTGAAACAATATATTAATATAAAA
20036372 TATGTGATTAAAGTGTAACAAGAAA
131 TATGTGATTAAAGTGTAACAAGAAA
20036397 TAAAAATGAT
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
165 148 1.00
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (165 bp):
AAATTGTAGAAAAATATGGAATTTTTATGATGACAAGGACTAAATTGTCAAACTTGAGAAAATAT
GTGGATAAAATAATAGAAGTGAAATATATAGAAATTGATACGTGAAACAATATATTAATATAAAA
TATGTGATTAAAGTGTAACAAGAAAGGAAACTGTG
Found at i:20044363 original size:19 final size:19
Alignment explanation
Indices: 20044336--20044374 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
20044326 CTTCACTTTA
20044336 CCCTCTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
*
20044355 CCCTTTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
20044374 C
1 C
20044375 TTCCTTCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.46, G:0.10, T:0.44
Consensus pattern (19 bp):
CCCTCTGCCTCTTCTGTTC
Found at i:20046815 original size:91 final size:91
Alignment explanation
Indices: 20046668--20046875 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
20046658 TTGATTTTAG
* *
20046668 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
20046733 ATTTAACATTAATTATTTTAAATTGTA
65 ATGTAACAATAATTATTTTAAATTATA
*
20046760 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
20046825 TGTAATAATAATTATTTTAAATTATA
66 TGTAACAATAATTATTTTAAATTATA
*
20046851 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
20046876 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAACAATAATTATTTTAAATTATA
Found at i:20046844 original size:26 final size:28
Alignment explanation
Indices: 20046790--20046850 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
20046780 TATTATCAAG
* *
20046790 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
20046818 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
20046844 AATTATA
1 AATTATA
20046851 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:20046850 original size:44 final size:43
Alignment explanation
Indices: 20046708--20046850 Score: 112
Period size: 44 Copynumber: 3.2 Consensus size: 43
20046698 GAATTTTATG
* * *
20046708 AAATTATATATCATTATTAAATTATATTTAACATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
20046752 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
20046799 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
20046843 AAATTATA
1 AAATTATA
20046851 CAAATTCATA
Statistics
Matches: 75, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 10 0.13
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:20046956 original size:59 final size:57
Alignment explanation
Indices: 20046887--20047077 Score: 147
Period size: 59 Copynumber: 3.2 Consensus size: 57
20046877 TTATAATTAT
*
20046887 TTTAAATTTTATTAAATCATTTATTTTAATTAAAATATATTTAATATTAATTATTTCAA
1 TTTATATTTTATTAAAT-ATTTATTTTAATTAAAATATATTTAATATTAATTATTT-AA
* * * * **
20046946 TTTATATTTTATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTA-TTAA
1 TTTATATTTTAT--TA-AATAT-TTAT--TTTAATTAAAAT-ATAT-TTAATATTAATTATTTAA
* * * *
20047010 --GA-ATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAA
1 TTTATATTTTATTAAA-TATTTATTTTAATTAAAATATATTTAATATTAATTAT-TTAA
20047066 TTTATATTTTAT
1 TTTATATTTTAT
20047078 AGTATTATAT
Statistics
Matches: 100, Mismatches: 18, Indels: 28
0.68 0.12 0.19
Matches are distributed among these distances:
54 10 0.10
55 4 0.04
56 12 0.12
58 5 0.05
59 23 0.23
61 11 0.11
62 7 0.07
64 11 0.11
65 6 0.06
66 11 0.11
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (57 bp):
TTTATATTTTATTAAATATTTATTTTAATTAAAATATATTTAATATTAATTATTTAA
Found at i:20046996 original size:130 final size:125
Alignment explanation
Indices: 20046852--20047183 Score: 445
Period size: 120 Copynumber: 2.7 Consensus size: 125
20046842 TAAATTATAC
* *
20046852 AAATTCATATAAGAAAATTTATTAGTTATAATTATTTTA-AATTTTATTAAATCATTTATTTTAA
1 AAATTCATATAAG-AAA-TTATTA--T-TAATTA-TTAAGAATTTTATTAAATCATATATTTTAA
*
20046916 TTAAAATATATTTAATATTAATTAT-TTCAATTTATATTTTATAGTATTATATATTATGATTTGA
60 TTAAAATATATTTAATAATAATTATGTT-AATTTATATTTTATAGTATTATATATTATGATTTGA
20046980 GT
124 GT
* *
20046982 AAATTCATATAAG--A--A-TATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAA
1 AAATTCATATAAGAAATTATTATTAATTATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
20047042 TATATTTAATAATAATTATGTTAATTTATATTTTATAGTATTATATATTATGATTTGAGT
66 TATATTTAATAATAATTATGTTAATTTATATTTTATAGTATTATATATTATGATTTGAGT
* * *
20047102 AAATTCATATAAG--A--A-TATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTATAA
1 AAATTCATATAAGAAATTATTATTAATTATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
20047162 TATATTTAATAATAATTATGTT
66 TATATTTAATAATAATTATGTT
20047184 TAAATATGAT
Statistics
Matches: 194, Mismatches: 6, Indels: 14
0.91 0.03 0.07
Matches are distributed among these distances:
119 3 0.02
120 171 0.88
121 3 0.02
123 2 0.01
124 1 0.01
127 1 0.01
130 13 0.07
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (125 bp):
AAATTCATATAAGAAATTATTATTAATTATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
TATATTTAATAATAATTATGTTAATTTATATTTTATAGTATTATATATTATGATTTGAGT
Found at i:20046999 original size:66 final size:64
Alignment explanation
Indices: 20046929--20047127 Score: 204
Period size: 66 Copynumber: 3.2 Consensus size: 64
20046919 AAATATATTT
20046929 AATATTAATTATTTCAATTTATATTTTATAGTATTATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AA-TTATATTTTATAGTATTATATATTATGATTTGAGTAAATTCATATAA
20046994 G
64 G
* * * * **
20046995 AATATTAATTA-TTAA-GA-ATTTTATTA-AATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTAATTATATTTTA-TAGTATTATATATTATGATTTGAGTAAATTCATATAAG
*
20047049 AATAATAATTATGTTAATTTATATTTTATAGTATTATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAA-TTATATTTTATAGTATTATATATTATGATTTGAGTAAATTCATATAA
20047114 G
64 G
*
20047115 AATATTGATTATT
1 AATATTAATTATT
20047128 AAGAATTTTA
Statistics
Matches: 104, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
54 10 0.10
55 4 0.04
56 5 0.05
57 2 0.02
58 4 0.04
59 17 0.16
60 8 0.08
61 17 0.16
62 4 0.04
63 2 0.02
64 3 0.03
65 7 0.07
66 21 0.20
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (64 bp):
AATATTAATTATTTAATTATATTTTATAGTATTATATATTATGATTTGAGTAAATTCATATAAG
Found at i:20047016 original size:120 final size:120
Alignment explanation
Indices: 20046891--20047183 Score: 525
Period size: 120 Copynumber: 2.4 Consensus size: 120
20046881 AATTATTTTA
* * * *
20046891 AATTTTATTAAATCATTTATTTTAATTAAAATATATTTAATATTAATTAT-TTCAATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
20046955 TATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
20047011 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
20047076 ATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
20047131 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
20047184 TAAATATGAT
Statistics
Matches: 167, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
120 165 0.99
121 2 0.01
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATTATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Done.