Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 47 of 135
Found at i:18885814 original size:37 final size:37
Alignment explanation
Indices: 18885771--18885841 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
18885761 TCATTTTTTT
18885771 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
18885808 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
18885842 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:18886556 original size:29 final size:28
Alignment explanation
Indices: 18886475--18886577 Score: 138
Period size: 27 Copynumber: 3.7 Consensus size: 28
18886465 TTGTTTTTTT
**
18886475 TTATATATATTTTGGTAAATAAAAAAAGT
1 TTATA-ATATTTTGGTAAATAAAAAAAAA
18886504 TTAT-ATATTTTGGTAAAT-AAAAAAAA
1 TTATAATATTTTGGTAAATAAAAAAAAA
18886530 TTATAATATTTTGGTAAATAAAAAAAAA
1 TTATAATATTTTGGTAAATAAAAAAAAA
* *
18886558 GTTGTAATATTTTGATAAAT
1 -TTATAATATTTTGGTAAAT
18886578 TTTTATTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
26 10 0.15
27 28 0.42
28 8 0.12
29 21 0.31
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.41
Consensus pattern (28 bp):
TTATAATATTTTGGTAAATAAAAAAAAA
Found at i:18887779 original size:31 final size:31
Alignment explanation
Indices: 18887744--18887805 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
18887734 GCCCAGTAAA
* * * *
18887744 TTAAATAAAAATTTTTGAATAGTTCAGTGAC
1 TTAAATAAAAACTTTCGAATAGATCAATGAC
*
18887775 TTAAATGAAAACTTTCGAATAGATCAATGAC
1 TTAAATAAAAACTTTCGAATAGATCAATGAC
18887806 CAAAATTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (31 bp):
TTAAATAAAAACTTTCGAATAGATCAATGAC
Found at i:18901540 original size:28 final size:27
Alignment explanation
Indices: 18901499--18901566 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
18901489 TCATGTTACT
* *
18901499 TTTTTTTTTAATTTT-ATTAACTTTTTA
1 TTTTTTGTGAATTTTAATTAA-TTTTTA
18901526 TATTTTTGTGAATTTTGAATTAATTTTTA
1 T-TTTTTGTGAATTTT-AATTAATTTTTA
18901555 TTTTTTGTGAAT
1 TTTTTTGTGAAT
18901567 ATTTTCATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 1 0.03
28 23 0.64
29 7 0.19
30 5 0.14
ACGTcount: A:0.24, C:0.01, G:0.07, T:0.68
Consensus pattern (27 bp):
TTTTTTGTGAATTTTAATTAATTTTTA
Found at i:18901945 original size:6 final size:6
Alignment explanation
Indices: 18901934--18901958 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18901924 AATTAATTTA
18901934 TTATGG TTATGG TTATGG TTATGG T
1 TTATGG TTATGG TTATGG TTATGG T
18901959 GGAGGGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TTATGG
Found at i:18902347 original size:6 final size:6
Alignment explanation
Indices: 18902336--18902362 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18902326 TGGTGCGTTT
18902336 CTTTCC CTTTCC CTTTCC CTTTCC CTT
1 CTTTCC CTTTCC CTTTCC CTTTCC CTT
18902363 CACCCCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTTCC
Found at i:18903943 original size:3 final size:3
Alignment explanation
Indices: 18903935--18903992 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
18903925 GCATACTTCC
* * * *
18903935 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TGA TGA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18903983 TAA TAA TAA T
1 TAA TAA TAA T
18903993 GTGTTCCTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:18908250 original size:29 final size:29
Alignment explanation
Indices: 18908208--18908266 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
18908198 AAACGTGACG
18908208 TTGTCACCTGCTACTTAATTAAATTTCAC
1 TTGTCACCTGCTACTTAATTAAATTTCAC
*
18908237 TTGTCACCTGCTACTTATTTAAATTTCAC
1 TTGTCACCTGCTACTTAATTAAATTTCAC
18908266 T
1 T
18908267 GAAAGTGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.44
Consensus pattern (29 bp):
TTGTCACCTGCTACTTAATTAAATTTCAC
Found at i:18912044 original size:92 final size:94
Alignment explanation
Indices: 18911935--18912105 Score: 249
Period size: 95 Copynumber: 1.8 Consensus size: 94
18911925 TCTTTTTATA
* * * * *
18911935 AACACACTCGGTGCCATTCAC-G-ACTAC-AAAGAATGAACTATTCTTCATTTTAAATTCAATGC
1 AACACACTCGGTCCCATTCACAGTACGACAAAAGAACGAACTATTCTT-AATATAAATTCAATGC
18911997 AAACGCAACGCATCTTCAGGAGATTCATAG
65 AAACGCAACGCATCTTCAGGAGATTCATAG
*
18912027 AACACACTCGGTCCCATTCACGAGTACGACAAAAGAACGAATTATTCTTAATATAAATTCAATGC
1 AACACACTCGGTCCCATTCAC-AGTACGACAAAAGAACGAACTATTCTTAATATAAATTCAATGC
18912092 AAACGCAACGCATC
65 AAACGCAACGCATC
18912106 ATCATCAGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
92 20 0.29
94 1 0.01
95 32 0.46
96 16 0.23
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (94 bp):
AACACACTCGGTCCCATTCACAGTACGACAAAAGAACGAACTATTCTTAATATAAATTCAATGCA
AACGCAACGCATCTTCAGGAGATTCATAG
Found at i:18914416 original size:364 final size:365
Alignment explanation
Indices: 18913747--18914477 Score: 1455
Period size: 364 Copynumber: 2.0 Consensus size: 365
18913737 ACAAATAAAA
18913747 TTTAAGGAATAGACTAATTTATACATTTCAAAATACATAAAAATTAATTTACTCATTTTTTAATA
1 TTTAAGGAATAGACTAATTTATACATTTCAAAATACATAAAAATTAATTTACTCATTTTTTAATA
18913812 AAAAGCCGAAATGCAATTCATTTTCTCTTATACTTTTACCATGAAAATACTATATTTAAAACCAC
66 AAAAGCCGAAATGCAATTCATTTTCTCTTATACTTTTACCATGAAAATACTATATTTAAAACCAC
18913877 CTATTCTACTCCAAAATAATATTAAAAAATCACCCCATTTTAAGGTGAACTAACTTTTAAAAATG
131 CTATTCTACTCCAAAATAATATTAAAAAATCACCCCATTTTAAGGTGAACTAACTTTTAAAAATG
18913942 AATTTGGTAAAGTTTTAGATGATTCTAATAAATTTTTTATATGATTTTAGCAATATTTTTGGAGG
196 AATTTGGTAAAGTTTTAGATGATTCTAATAAATTTTTTATATGATTTTAGCAATATTTTTGGAGG
18914007 TAGAATTAAATTGTTTATTTTTATGATAATAAAAATATAATTTTATCATTTTAACAACTTATATC
261 TAGAATTAAATTGTTTATTTTTATGATAATAAAAATATAATTTTATCATTTTAACAACTTATATC
18914072 TTTATAATTTTTAAAGGGTTAAATCAAA-TTTTATTATTT
326 TTTATAATTTTTAAAGGGTTAAATCAAATTTTTATTATTT
18914111 TTTAAGGAATAGACTAATTTATACATTTCAAAATACATAAAAATTAATTTACTCATTTTTTAATA
1 TTTAAGGAATAGACTAATTTATACATTTCAAAATACATAAAAATTAATTTACTCATTTTTTAATA
18914176 AAAAGCCGAAATGCAATTCATTTTCTCTTATACTTTTACCATGAAAATACTATATTTAAAACCAC
66 AAAAGCCGAAATGCAATTCATTTTCTCTTATACTTTTACCATGAAAATACTATATTTAAAACCAC
18914241 CTATTCTACTCCAAAATAATATTAAAAAATCACCCCATTTTAAGGTGAACTAACTTTTAAAAATG
131 CTATTCTACTCCAAAATAATATTAAAAAATCACCCCATTTTAAGGTGAACTAACTTTTAAAAATG
18914306 AATTTGGTAAAGTTTTAGATGATTCTAATAAATTTTTTATATGATTTTAGCAATATTTTTGGAGG
196 AATTTGGTAAAGTTTTAGATGATTCTAATAAATTTTTTATATGATTTTAGCAATATTTTTGGAGG
18914371 TAGAATTAAATTGTTTATTTTTATGATAATAAAAATATAATTTTATCATTTTAACAACTTATATC
261 TAGAATTAAATTGTTTATTTTTATGATAATAAAAATATAATTTTATCATTTTAACAACTTATATC
18914436 TTTATAATTTTTAAAGGGTTAAATCAAATTTTTATTATTT
326 TTTATAATTTTTAAAGGGTTAAATCAAATTTTTATTATTT
18914476 TT
1 TT
18914478 GGGAGAACAA
Statistics
Matches: 366, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
364 353 0.96
365 13 0.04
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (365 bp):
TTTAAGGAATAGACTAATTTATACATTTCAAAATACATAAAAATTAATTTACTCATTTTTTAATA
AAAAGCCGAAATGCAATTCATTTTCTCTTATACTTTTACCATGAAAATACTATATTTAAAACCAC
CTATTCTACTCCAAAATAATATTAAAAAATCACCCCATTTTAAGGTGAACTAACTTTTAAAAATG
AATTTGGTAAAGTTTTAGATGATTCTAATAAATTTTTTATATGATTTTAGCAATATTTTTGGAGG
TAGAATTAAATTGTTTATTTTTATGATAATAAAAATATAATTTTATCATTTTAACAACTTATATC
TTTATAATTTTTAAAGGGTTAAATCAAATTTTTATTATTT
Found at i:18916874 original size:24 final size:24
Alignment explanation
Indices: 18916847--18916893 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
18916837 TGGTGTGGCA
*
18916847 ACAGGAGTTGATGATGAAGCAGCT
1 ACAGGAGTTGATGATGAAACAGCT
18916871 ACAGGAGTTGATGATGAAACAGC
1 ACAGGAGTTGATGATGAAACAGC
18916894 ATCAGATGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (24 bp):
ACAGGAGTTGATGATGAAACAGCT
Found at i:18926720 original size:21 final size:21
Alignment explanation
Indices: 18926681--18926721 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18926671 CCACAAGAAA
* * *
18926681 CCTCTTTATAAATATATTTCT
1 CCTCTTTACAAAGAGATTTCT
18926702 CCTCTTTACAAAGAGATTTC
1 CCTCTTTACAAAGAGATTTC
18926722 ATAGGGAAAA
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:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (21 bp):
CCTCTTTACAAAGAGATTTCT
Found at i:18934950 original size:4 final size:4
Alignment explanation
Indices: 18934943--18934982 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
18934933 TATATATATC
*
18934943 TATG TATG TATG TATG TATG TATG TACG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
18934983 ACTGCCCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:18935750 original size:18 final size:18
Alignment explanation
Indices: 18935727--18935766 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
18935717 CAATTCATCG
*
18935727 ATATAAA-TCTATAGATAT
1 ATATAAATTCAATA-ATAT
18935745 ATATAAATTCAATAATAT
1 ATATAAATTCAATAATAT
18935763 ATAT
1 ATAT
18935767 CCAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (18 bp):
ATATAAATTCAATAATAT
Found at i:18939320 original size:26 final size:26
Alignment explanation
Indices: 18939270--18939329 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
18939260 CATAAATTAT
* *
18939270 GAAGCTCACAAAGAGCCTTTAATCGG
1 GAAGCTCACAAAGAGCCTATAATCGA
18939296 GAAGCTCACGAAA-AGCC-ATATATCGA
1 GAAGCTCAC-AAAGAGCCTATA-ATCGA
*
18939322 GATGCTCA
1 GAAGCTCA
18939330 TAAGAGCTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 24 0.83
27 3 0.10
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (26 bp):
GAAGCTCACAAAGAGCCTATAATCGA
Found at i:18939777 original size:5 final size:5
Alignment explanation
Indices: 18939749--18939787 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
18939739 AAATTTAGCA
* *
18939749 CAATT GAATA CAATT CATATT CAATT CAATT CAATT CAA
1 CAATT CAATT CAATT CA-ATT CAATT CAATT CAATT CAA
18939788 ATCCTAGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (5 bp):
CAATT
Found at i:18949779 original size:26 final size:27
Alignment explanation
Indices: 18949724--18949780 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
18949714 TATAGGGGTA
* * **
18949724 TGGTGCCTATTTGATAGGCGGCACTGG
1 TGGTGCCTATCTGATAGGCGACACCAG
18949751 TGGTG-CTATCTGATAGGCGACACCAG
1 TGGTGCCTATCTGATAGGCGACACCAG
18949777 TGGT
1 TGGT
18949781 ATTTTCCCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.28
Consensus pattern (27 bp):
TGGTGCCTATCTGATAGGCGACACCAG
Found at i:18950949 original size:17 final size:18
Alignment explanation
Indices: 18950923--18950956 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18950913 TTTGTCACAA
18950923 TTTATAATTAT-ATATTT
1 TTTATAATTATAATATTT
*
18950940 TTTATCATTATAATATT
1 TTTATAATTATAATATT
18950957 AAAGGAGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATAATTATAATATTT
Found at i:18952085 original size:2 final size:2
Alignment explanation
Indices: 18952078--18952123 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
18952068 ACAGTAGGTA
18952078 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18952120 CT CT
1 CT CT
18952124 TATTGCCACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18976568 original size:21 final size:22
Alignment explanation
Indices: 18976526--18976569 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
18976516 ACAATAATTT
*
18976526 TATTTATATTTTAAATTGTAAA
1 TATTTATATTTTAAAGTGTAAA
18976548 TATTTA-ATTTTTAAAGT-TAAA
1 TATTTATA-TTTTAAAGTGTAAA
18976569 T
1 T
18976570 TTATGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TATTTATATTTTAAAGTGTAAA
Found at i:18977683 original size:20 final size:21
Alignment explanation
Indices: 18977660--18977698 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18977650 AGCTATTCAA
18977660 ATAA-TATTTTTTGAATAGTT
1 ATAATTATTTTTTGAATAGTT
*
18977680 ATAATTCTTTTTTGAATAG
1 ATAATTATTTTTTGAATAG
18977699 GTGTCTTTAT
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:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (21 bp):
ATAATTATTTTTTGAATAGTT
Found at i:18979986 original size:21 final size:22
Alignment explanation
Indices: 18979959--18980016 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
18979949 AAATATGCTT
*
18979959 ATTTTTCGTTGACCTGTAAGTC
1 ATTTTCCGTTGACCTGTAAGTC
18979981 ATTTTCCGTTGACCTGTAAGTC
1 ATTTTCCGTTGACCTGTAAGTC
18980003 ATTTTCCGTTGACC
1 ATTTTCCGTTGACC
18980017 AAGCTGTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (22 bp):
ATTTTCCGTTGACCTGTAAGTC
Found at i:18990502 original size:13 final size:13
Alignment explanation
Indices: 18990486--18990510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18990476 TATTATATTC
18990486 TTTATTTTCTTTA
1 TTTATTTTCTTTA
18990499 TTTATTTTCTTT
1 TTTATTTTCTTT
18990511 TAATGTTTAT
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTCTTTA
Found at i:18995084 original size:48 final size:48
Alignment explanation
Indices: 18995013--18995107 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
18995003 TTCTTTGCTC
** **
18995013 AAAAACGCCTAAGTCAGCCTAACTTGCAGTAATAAAGGATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTCACAACAATAAAGGATTCAACAGT
*
18995061 AAAAACGCCTAAGTCAGCTTAACTCACAACAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCACAACAATAAAGGATTCAACAG
18995108 AATTCCCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCACAACAATAAAGGATTCAACAGT
Found at i:18995445 original size:35 final size:36
Alignment explanation
Indices: 18995405--18995476 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
18995395 TCTAGGATCA
18995405 CATATC-TCAAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
* *
18995440 CATATCTTCAAAAGATCACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
18995476 C
1 C
18995477 TCCAGAGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
Found at i:19018626 original size:14 final size:14
Alignment explanation
Indices: 19018607--19018638 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
19018597 AGTTATCTGA
19018607 AAAGGAACCATTCC
1 AAAGGAACCATTCC
19018621 AAAGGAACCATTCC
1 AAAGGAACCATTCC
19018635 AAAG
1 AAAG
19018639 CAGTTGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAGGAACCATTCC
Found at i:19023724 original size:1 final size:1
Alignment explanation
Indices: 19023718--19023889 Score: 344
Period size: 1 Copynumber: 172.0 Consensus size: 1
19023708 TCTACCCCTT
19023718 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
19023783 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
19023848 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
19023890 AAATGGAAAC
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 171 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:19025261 original size:15 final size:15
Alignment explanation
Indices: 19025241--19025273 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
19025231 ATCACTCTTT
19025241 TTTTAT-TTTTTAATC
1 TTTTATCTTTTT-ATC
19025256 TTTTATCTTTTTATC
1 TTTTATCTTTTTATC
19025271 TTT
1 TTT
19025274 CCAAGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATCTTTTTATC
Found at i:19036790 original size:18 final size:17
Alignment explanation
Indices: 19036758--19036793 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
19036748 ATTTTTCAAG
19036758 TTTTAAAATTTTGAATT
1 TTTTAAAATTTTGAATT
*
19036775 TTTTGAAATATTTGAATT
1 TTTTAAAAT-TTTGAATT
19036793 T
1 T
19036794 GGACTAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
TTTTAAAATTTTGAATT
Found at i:19040106 original size:33 final size:33
Alignment explanation
Indices: 19040053--19040130 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
19040043 TGGCCCTGCC
*
19040053 ATGGTCTTACACTCGTAATGCCATAACCCAGTT
1 ATGGTCTTACACTCGTAATGCCATAACCCAGCT
*
19040086 ATGGTCTTATCA-TCAG-AATGCCATAGCCCAGCT
1 ATGGTCTTA-CACTC-GTAATGCCATAACCCAGCT
19040119 ATGGTCTTACAC
1 ATGGTCTTACAC
19040131 GTATACATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
32 2 0.05
33 35 0.88
34 3 0.08
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (33 bp):
ATGGTCTTACACTCGTAATGCCATAACCCAGCT
Found at i:19040244 original size:105 final size:101
Alignment explanation
Indices: 19040071--19040261 Score: 274
Period size: 105 Copynumber: 1.9 Consensus size: 101
19040061 ACACTCGTAA
* * * *
19040071 TGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACACGTATA
1 TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTACGATCTTACACGTAAA
19040136 CATTTACTGCCATGGTCCAACCATGGTCTTACGTTTAAGG
66 CA--T--TGCCATGGTCCAACCATGGTCTTACGTTTAAGG
* * **
19040176 TGCCATAACCCAGTTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTACGATCTTACATTTAAA
1 TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTACGATCTTACACGTAAA
19040241 CATTGCCATGGTCCAACCATG
66 CATTGCCATGGTCCAACCATG
19040262 ATCTGATCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 18 0.23
103 1 0.01
105 59 0.76
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (101 bp):
TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTACGATCTTACACGTAAA
CATTGCCATGGTCCAACCATGGTCTTACGTTTAAGG
Found at i:19050107 original size:22 final size:21
Alignment explanation
Indices: 19050049--19050107 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
19050039 AAATGACAGT
*
19050049 AAAACAATGAGAAAATAGCAAG
1 AAAACAA-CAGAAAATAGCAAG
**
19050071 AAAACAACAGCAAAATAGTGAG
1 AAAACAACAG-AAAATAGCAAG
*
19050093 GAAACAACAAGAAAA
1 AAAACAAC-AGAAAA
19050108 CAACTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.64, C:0.12, G:0.17, T:0.07
Consensus pattern (21 bp):
AAAACAACAGAAAATAGCAAG
Found at i:19054214 original size:31 final size:31
Alignment explanation
Indices: 19054176--19054239 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
19054166 CAAGTCATGT
19054176 TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
1 TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
19054207 TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
1 TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
19054238 TT
1 TT
19054240 AACATTTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (31 bp):
TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
Found at i:19057586 original size:9 final size:9
Alignment explanation
Indices: 19057572--19057602 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19057562 GTTAAACGAA
19057572 TCGAGTTAT
1 TCGAGTTAT
*
19057581 TCGAGTTAA
1 TCGAGTTAT
19057590 TCGAGTTAT
1 TCGAGTTAT
19057599 TCGA
1 TCGA
19057603 ATCAACTCGA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:19058482 original size:5 final size:5
Alignment explanation
Indices: 19058472--19058497 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19058462 GAACAAATAT
19058472 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
19058498 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:19059126 original size:7 final size:7
Alignment explanation
Indices: 19059114--19059139 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19059104 TAATTATCAA
19059114 CATGAAC
1 CATGAAC
19059121 CATGAAC
1 CATGAAC
19059128 CATGAAC
1 CATGAAC
19059135 CATGA
1 CATGA
19059140 CATACTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (7 bp):
CATGAAC
Found at i:19061273 original size:20 final size:23
Alignment explanation
Indices: 19061244--19061292 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
19061234 AGTGTGACGA
*
19061244 GTCG-CAAAA-GATCTAGTC-CC
1 GTCGACAAAAGGACCTAGTCTCC
19061264 GT-GACAAAAGGACCTAGTCTCC
1 GTCGACAAAAGGACCTAGTCTCC
19061286 GTCGACA
1 GTCGACA
19061293 GGGTTTGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 7 0.29
21 8 0.33
22 4 0.17
23 4 0.17
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (23 bp):
GTCGACAAAAGGACCTAGTCTCC
Found at i:19062164 original size:1 final size:1
Alignment explanation
Indices: 19062158--19062203 Score: 83
Period size: 1 Copynumber: 46.0 Consensus size: 1
19062148 AAGACGGAGA
*
19062158 GGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
19062204 AGGGAAGGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.00, G:0.98, T:0.00
Consensus pattern (1 bp):
G
Found at i:19062184 original size:23 final size:23
Alignment explanation
Indices: 19062153--19062200 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
19062143 TTTCTAAGAC
19062153 GGAGAGGGGGGGGGGGGGGGGGG
1 GGAGAGGGGGGGGGGGGGGGGGG
*
19062176 GGAGGGGGGGGGGGGGGGGGGGG
1 GGAGAGGGGGGGGGGGGGGGGGG
19062199 GG
1 GG
19062201 GGGAGGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.06, C:0.00, G:0.94, T:0.00
Consensus pattern (23 bp):
GGAGAGGGGGGGGGGGGGGGGGG
Found at i:19062194 original size:26 final size:26
Alignment explanation
Indices: 19062158--19062207 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
19062148 AAGACGGAGA
19062158 GGGGGGGGGGGGGGGGGGGGAGGGGG
1 GGGGGGGGGGGGGGGGGGGGAGGGGG
19062184 GGGGGGGGGGGGGGGGGGGGAGGG
1 GGGGGGGGGGGGGGGGGGGGAGGG
19062208 AAGGAGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.04, C:0.00, G:0.96, T:0.00
Consensus pattern (26 bp):
GGGGGGGGGGGGGGGGGGGGAGGGGG
Found at i:19070576 original size:31 final size:31
Alignment explanation
Indices: 19070538--19070600 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
19070528 GAGTCTTGAC
19070538 CTTATGCAAATATTCTTTAACATTTAAACTA
1 CTTATGCAAATATTCTTTAACATTTAAACTA
19070569 CTTATGCAAATATTCTTTAACATTTAAACTA
1 CTTATGCAAATATTCTTTAACATTTAAACTA
19070600 C
1 C
19070601 CTTTCTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.41
Consensus pattern (31 bp):
CTTATGCAAATATTCTTTAACATTTAAACTA
Found at i:19072232 original size:57 final size:54
Alignment explanation
Indices: 19072144--19072255 Score: 161
Period size: 57 Copynumber: 2.0 Consensus size: 54
19072134 CCACATTAGA
*
19072144 AGATTTAACAAAGTATAAAGGCCAATCATGTCATAATCTTTTTTTTTTATCAAATTC
1 AGATTTAACAAAGTATAAAGGCCAATCATGTCATAA-C--TTTTTATTATCAAATTC
* * *
19072201 AGATTTAATAATGTATAAAGGCCAATTATGTCATAACTTTTTATTATCAAATTC
1 AGATTTAACAAAGTATAAAGGCCAATCATGTCATAACTTTTTATTATCAAATTC
19072255 A
1 A
19072256 ACCTTAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 17 0.33
56 1 0.02
57 33 0.65
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (54 bp):
AGATTTAACAAAGTATAAAGGCCAATCATGTCATAACTTTTTATTATCAAATTC
Found at i:19075049 original size:24 final size:24
Alignment explanation
Indices: 19075021--19075068 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19075011 TTGTTTTGTG
19075021 GCAAAGGATGAATTGACGGAAAAT
1 GCAAAGGATGAATTGACGGAAAAT
19075045 GCAAAGGATGAATTGACGGAAAAT
1 GCAAAGGATGAATTGACGGAAAAT
19075069 TACCCAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.29, T:0.17
Consensus pattern (24 bp):
GCAAAGGATGAATTGACGGAAAAT
Found at i:19077446 original size:23 final size:23
Alignment explanation
Indices: 19077420--19077494 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
19077410 ATAAGTGCAA
*
19077420 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
19077443 CACTGAAATGTAGCCGAAGCTAA
1 CACTGAAATGTAGCCGAAGCTAC
*
19077466 CACTGAAACGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
19077489 CACTGA
1 CACTGA
19077495 TCAATAACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:19077595 original size:8 final size:8
Alignment explanation
Indices: 19077582--19077610 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
19077572 ACCCGGGACT
19077582 CACTGTAA
1 CACTGTAA
19077590 CACTGTAA
1 CACTGTAA
19077598 CACTGTAA
1 CACTGTAA
19077606 CACTG
1 CACTG
19077611 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:19078799 original size:45 final size:46
Alignment explanation
Indices: 19078707--19078844 Score: 210
Period size: 45 Copynumber: 3.0 Consensus size: 46
19078697 ACATTGCTAT
* *
19078707 AACTCAGTATGG-TTTCCTTCACTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGCTTT-CTTCACTGAAACACCATACCTACTTTTCAC
*
19078753 AACTCAGTATGGCTTTCTTCACCG-AACACCATACCTACTTTTCAC
1 AACTCAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
19078798 AACTCAGTAT-GCTTTCTTCACTGAAACACCATACCTATTTTTCAC
1 AACTCAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTCAC
19078843 AA
1 AA
19078845 TTTGCCATAG
Statistics
Matches: 85, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
44 12 0.14
45 51 0.60
46 19 0.22
47 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:19080116 original size:16 final size:17
Alignment explanation
Indices: 19080070--19080117 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
19080060 AAATTCTTTT
19080070 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
19080087 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
19080104 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
19080118 TTATAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:19080367 original size:42 final size:42
Alignment explanation
Indices: 19080275--19080406 Score: 122
Period size: 42 Copynumber: 3.2 Consensus size: 42
19080265 TCTCACGAGC
* * * *
19080275 TTCTGTT-AACTCATATGAGTTTCAGTTTAACACTTATGGGT
1 TTCTGTTCAGCTCCTATGAGCTTCAGTTTAACCCTTATGGGT
** * * * * *
19080316 TTCCATTCAGTTCTTTTGAGCTTCGGTTTAACCCTTATGAGT
1 TTCTGTTCAGCTCCTATGAGCTTCAGTTTAACCCTTATGGGT
* * * *
19080358 TTCTGTTCAGCTCCTACGAGCTCCCGTTCAACCCTTATGGGT
1 TTCTGTTCAGCTCCTATGAGCTTCAGTTTAACCCTTATGGGT
19080400 TTCTGTT
1 TTCTGTT
19080407 TAGCACTTAT
Statistics
Matches: 70, Mismatches: 20, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
41 5 0.07
42 65 0.93
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (42 bp):
TTCTGTTCAGCTCCTATGAGCTTCAGTTTAACCCTTATGGGT
Found at i:19085409 original size:132 final size:133
Alignment explanation
Indices: 19085242--19085506 Score: 523
Period size: 132 Copynumber: 2.0 Consensus size: 133
19085232 GGTAAGTTTG
19085242 TTAAAATTTACTTTAGGATTAATTAGATAATTTTATTTTTTTGGCACTATTAAATTATTAAATTA
1 TTAAAATTTACTTTAGGATTAATTAGATAATTTTATTTTTTTGGCACTATTAAATTATTAAATTA
19085307 TTTATCATTTATTTACTTTTTAGGGTTTTGTAATTTCCAATAGCACTTGTAAATTAT-CATGAAC
66 TTTATCATTTATTTACTTTTTAGGGTTTTGTAATTTCCAATAGCACTTGTAAATTATCCATGAAC
19085371 AAT
131 AAT
19085374 TTAAAATTTACTTTAGGATTAATTAGATAATTTTATTTTTTTGGCACTATTAAATTATTAAATTA
1 TTAAAATTTACTTTAGGATTAATTAGATAATTTTATTTTTTTGGCACTATTAAATTATTAAATTA
19085439 TTTATCATTTATTTACTTTTTAGGGTTTTGTAATTTCCAATAGCACTTGTAAATTATCCATGAAC
66 TTTATCATTTATTTACTTTTTAGGGTTTTGTAATTTCCAATAGCACTTGTAAATTATCCATGAAC
19085504 AAT
131 AAT
19085507 AATTTTGATA
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
132 122 0.92
133 10 0.08
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (133 bp):
TTAAAATTTACTTTAGGATTAATTAGATAATTTTATTTTTTTGGCACTATTAAATTATTAAATTA
TTTATCATTTATTTACTTTTTAGGGTTTTGTAATTTCCAATAGCACTTGTAAATTATCCATGAAC
AAT
Found at i:19103933 original size:2 final size:2
Alignment explanation
Indices: 19103926--19103952 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19103916 CAAGAAAATT
19103926 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19103953 CAGTTCGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19118104 original size:23 final size:23
Alignment explanation
Indices: 19118069--19118119 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
19118059 AAGCAACATA
19118069 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
*
19118092 TGTAATA-CTCCGAAATTTACTAC
1 TGTAATATC-CCGAAAATTACTAC
*
19118115 AGTAA
1 TGTAA
19118120 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:19121036 original size:13 final size:14
Alignment explanation
Indices: 19121011--19121037 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19121001 CTTTTCAAAA
19121011 AAAAATCATTTTTC
1 AAAAATCATTTTTC
19121025 AAAAATCATTTTT
1 AAAAATCATTTTT
19121038 GGAAACTATT
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:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAATCATTTTTC
Found at i:19137477 original size:28 final size:27
Alignment explanation
Indices: 19137453--19137505 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
19137443 CTTAAAACTT
* *
19137453 AAAAAATTAAAGTAGATATATAAAAATC
1 AAAAAATTAAA-TAAAAATATAAAAATC
*
19137481 ATAAAATTAAATAAAAATATAAAAA
1 AAAAAATTAAATAAAAATATAAAAA
19137506 CGTTTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAAAATTAAATAAAAATATAAAAATC
Found at i:19142158 original size:51 final size:51
Alignment explanation
Indices: 19142063--19142489 Score: 793
Period size: 51 Copynumber: 8.4 Consensus size: 51
19142053 TGAGTACTTC
* *
19142063 TGATCAGTGACAAGTGATAAGTGGTAG-TTTAGCTGCACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
* *
19142113 TGATAAGTGACAAGTGATAAGTGATAGCTTTAGCTGCACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
19142164 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
19142215 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
19142266 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
19142317 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
19142368 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
*
19142419 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCAGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
*
19142470 TGACAAGTGACAAGTGATAA
1 TGATAAGTGACAAGTGATAA
19142490 ATGTGATTCG
Statistics
Matches: 370, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
50 25 0.07
51 345 0.93
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (51 bp):
TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
Found at i:19143132 original size:39 final size:40
Alignment explanation
Indices: 19143089--19143167 Score: 151
Period size: 39 Copynumber: 2.0 Consensus size: 40
19143079 TAATGCCTCG
19143089 TACCTTATTCCGGTGTTGGATACGGGTAA-GGGTGTTACA
1 TACCTTATTCCGGTGTTGGATACGGGTAAGGGGTGTTACA
19143128 TACCTTATTCCGGTGTTGGATACGGGTAAGGGGTGTTACA
1 TACCTTATTCCGGTGTTGGATACGGGTAAGGGGTGTTACA
19143168 AACATGATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 29 0.74
40 10 0.26
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.33
Consensus pattern (40 bp):
TACCTTATTCCGGTGTTGGATACGGGTAAGGGGTGTTACA
Found at i:19151598 original size:42 final size:43
Alignment explanation
Indices: 19151521--19151629 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 43
19151511 CAATGCCAAA
* * * *
19151521 TCCCAGAC-GTGGTCTTACATGTAATCCAATAACGATGCCACTG
1 TCCCAGACAG-GGTCTTACACGTAATCCAATAACGATACAAATG
*
19151564 TCCCAGACAGGGTCTTACACGTAAT-C-ATATACGATACAAATT
1 TCCCAGACAGGGTCTTACACGTAATCCAATA-ACGATACAAATG
*
19151606 TCCCAGACATGGTCTTACACGTAA
1 TCCCAGACAGGGTCTTACACGTAA
19151630 ATCTCAAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 3 0.05
42 32 0.55
43 22 0.38
44 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
TCCCAGACAGGGTCTTACACGTAATCCAATAACGATACAAATG
Found at i:19152778 original size:16 final size:14
Alignment explanation
Indices: 19152743--19152770 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19152733 CACAAACGAT
19152743 AAAATTTTCACACA
1 AAAATTTTCACACA
19152757 AAAATTTTCACACA
1 AAAATTTTCACACA
19152771 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTTTCACACA
Found at i:19153830 original size:30 final size:31
Alignment explanation
Indices: 19153796--19153853 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
19153786 TTTTACGAGC
*
19153796 TTAGGGGCAAAATCATAATTTTG-TAAAACT
1 TTAGGGGCAAAAACATAATTTTGCTAAAACT
19153826 TTAGGGGCAAAAACATAATTTTGCTAAA
1 TTAGGGGCAAAAACATAATTTTGCTAAA
19153854 GTATGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (31 bp):
TTAGGGGCAAAAACATAATTTTGCTAAAACT
Found at i:19154231 original size:45 final size:45
Alignment explanation
Indices: 19154170--19154264 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
19154160 TACTATGTGA
* *
19154170 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
* * * *
19154215 ACCGGACATTATTGATTAATAAGGTGGTTGTTATGTTCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
19154260 ACCGA
1 ACCGA
19154265 GTATATGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:19159806 original size:2 final size:2
Alignment explanation
Indices: 19159799--19159843 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
19159789 TTCCTTTTGT
19159799 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T- TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19159837 TA -A TA TA
1 TA TA TA TA
19159844 AAAACATACT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 5 0.13
2 33 0.87
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19159820 original size:16 final size:16
Alignment explanation
Indices: 19159799--19159843 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 16
19159789 TTCCTTTTGT
19159799 TATATATATATATATA
1 TATATATATATATATA
19159815 TATATATA-ATATAT-
1 TATATATATATATATA
19159829 TA-ATA-ATATA-ATA
1 TATATATATATATATA
19159842 TA
1 TA
19159844 AAAACATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 2 0.07
15 6 0.22
16 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATATATATATA
Found at i:19163435 original size:24 final size:24
Alignment explanation
Indices: 19163408--19163462 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
19163398 TCCGATGCTT
19163408 CCCGTTAATTGCTCTTCGAAGCTA
1 CCCGTTAATTGCTCTTCGAAGCTA
* *
19163432 CCCGTTAATTGCTCTTTGGAGCTA
1 CCCGTTAATTGCTCTTCGAAGCTA
*
19163456 CCAGTTA
1 CCCGTTA
19163463 TAGGCTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (24 bp):
CCCGTTAATTGCTCTTCGAAGCTA
Found at i:19164301 original size:30 final size:29
Alignment explanation
Indices: 19164262--19164328 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
19164252 TTTTTTATTT
* **
19164262 AAATAACCCAAATAATTTAATTAAGTACCA
1 AAATGACCCAAAT-ATTTAATTAAACACCA
** *
19164292 AAATGACCCACCTTTTTAATTAAACACCA
1 AAATGACCCAAATATTTAATTAAACACCA
19164321 AAATGACC
1 AAATGACC
19164329 TAAAATCTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.25
Consensus pattern (29 bp):
AAATGACCCAAATATTTAATTAAACACCA
Found at i:19165111 original size:40 final size:41
Alignment explanation
Indices: 19165058--19165142 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 41
19165048 AAAAATATAT
*
19165058 ATTAAGTACATAAATTCATGAATGTGTACTAAAATTAAAAA
1 ATTAAGTACATAAATTCATAAATGTGTACTAAAATTAAAAA
* *
19165099 ATTAA-TATATAAATTTATAAATGTGTACTAAAATTAAAAA
1 ATTAAGTACATAAATTCATAAATGTGTACTAAAATTAAAAA
19165139 ATTA
1 ATTA
19165143 TAACCAACAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 36 0.88
41 5 0.12
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (41 bp):
ATTAAGTACATAAATTCATAAATGTGTACTAAAATTAAAAA
Found at i:19165132 original size:20 final size:20
Alignment explanation
Indices: 19165078--19165140 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
19165068 TAAATTCATG
19165078 AATGTGTACTAAAATTAAAA
1 AATGTGTACTAAAATTAAAA
* * *
19165098 AAT-TAATA-TATAAATTTATA
1 AATGT-GTACTA-AAATTAAAA
19165118 AATGTGTACTAAAATTAAAA
1 AATGTGTACTAAAATTAAAA
19165138 AAT
1 AAT
19165141 TATAACCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (20 bp):
AATGTGTACTAAAATTAAAA
Found at i:19166391 original size:22 final size:24
Alignment explanation
Indices: 19166339--19166397 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 24
19166329 ATATCTTTAA
19166339 AAATAAT-TTA-AAAATCATAATT
1 AAATAATATTATAAAATCATAATT
*
19166361 TAA-AATATTATAAAA-CA-AATT
1 AAATAATATTATAAAATCATAATT
19166382 AAATAATATT-TAAAAT
1 AAATAATATTATAAAAT
19166398 ATTAAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 14 0.45
22 13 0.42
23 4 0.13
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAATATTATAAAATCATAATT
Found at i:19166602 original size:9 final size:9
Alignment explanation
Indices: 19166588--19166620 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
19166578 TAATAACAAT
19166588 AAATAAATA
1 AAATAAATA
19166597 AAATAAATA
1 AAATAAATA
19166606 AACA-AAATA
1 AA-ATAAATA
19166615 AAATAA
1 AAATAA
19166621 GAAAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (9 bp):
AAATAAATA
Found at i:19166603 original size:13 final size:13
Alignment explanation
Indices: 19166574--19166616 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
19166564 AAATTTTTTA
*
19166574 AAATTAATAACAAT
1 AAATAAATAA-AAT
19166588 AAATAAATAAAAT
1 AAATAAATAAAAT
*
19166601 AAATAAACAAAAT
1 AAATAAATAAAAT
19166614 AAA
1 AAA
19166617 ATAAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:19166642 original size:17 final size:18
Alignment explanation
Indices: 19166618--19166682 Score: 69
Period size: 17 Copynumber: 3.5 Consensus size: 18
19166608 CAAAATAAAA
19166618 TAAGAAAAAAGAAAAAACT
1 TAAG-AAAAAGAAAAAACT
19166637 TAA-AAAAAGAAAAAACTT
1 TAAGAAAAAGAAAAAAC-T
* *
19166655 TAAAGAAAAAGACAAAAGT
1 T-AAGAAAAAGAAAAAACT
*
19166674 TAATAAAAA
1 TAAGAAAAA
19166683 AATAAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 13 0.32
18 9 0.22
19 7 0.17
20 11 0.28
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (18 bp):
TAAGAAAAAGAAAAAACT
Found at i:19166683 original size:20 final size:21
Alignment explanation
Indices: 19166622--19166690 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 21
19166612 ATAAAATAAG
19166622 AAAAAAGAAAAAAC--T--TA
1 AAAAAAGAAAAAACGTTAATA
*
19166639 AAAAAAGAAAAAACTTTAA-A
1 AAAAAAGAAAAAACGTTAATA
* *
19166659 GAAAAAGACAAAA-GTTAATA
1 AAAAAAGAAAAAACGTTAATA
*
19166679 AAAAAATAAAAA
1 AAAAAAGAAAAA
19166691 TAAAAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 14 0.34
19 5 0.12
20 22 0.54
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.13
Consensus pattern (21 bp):
AAAAAAGAAAAAACGTTAATA
Found at i:19166689 original size:18 final size:17
Alignment explanation
Indices: 19166585--19166689 Score: 56
Period size: 18 Copynumber: 5.9 Consensus size: 17
19166575 AATTAATAAC
* *
19166585 AATAAATAAATAAAATA
1 AATAAAAAAATAAAATT
19166602 AATAAACAAAATAAAA-T
1 AATAAA-AAAATAAAATT
* *
19166619 AAGAAAAAAGAAAAAACTT
1 AATAAAAAA-ATAAAA-TT
19166638 AA-AAAAAGAA-AAAACTTT
1 AATAAAAA-AATAAAA--TT
*
19166656 AA-AGAAAAAGACAAAAGTT
1 AATA-AAAAA-ATAAAA-TT
19166675 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
19166690 ATAAAAAATA
Statistics
Matches: 71, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
16 3 0.04
17 20 0.28
18 25 0.35
19 18 0.25
20 5 0.07
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (17 bp):
AATAAAAAAATAAAATT
Found at i:19178531 original size:16 final size:17
Alignment explanation
Indices: 19178510--19178543 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
19178500 GGATAATTCT
19178510 AAAAATAAAAAAT-ATA
1 AAAAATAAAAAATCATA
*
19178526 AAAAATGAAAAATCATA
1 AAAAATAAAAAATCATA
19178543 A
1 A
19178544 TATATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAAAAAATCATA
Found at i:19181027 original size:5 final size:5
Alignment explanation
Indices: 19181017--19181041 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19181007 TTAATATTTT
19181017 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
19181042 CCTAAACTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:19183165 original size:42 final size:42
Alignment explanation
Indices: 19183106--19183189 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
19183096 AAATGATTGC
*
19183106 TCCTTCCAAACTTTCATAAAAAAATTAATAAAGAAAAAAAAA
1 TCCTTCCAAACTTTCATAAAAAAATTAATAAAAAAAAAAAAA
19183148 TCCTTCCAAACTTTCATAAAAAAATTAATAAAAAAAAAAAAA
1 TCCTTCCAAACTTTCATAAAAAAATTAATAAAAAAAAAAAAA
19183190 AAAAAACAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.61, C:0.14, G:0.01, T:0.24
Consensus pattern (42 bp):
TCCTTCCAAACTTTCATAAAAAAATTAATAAAAAAAAAAAAA
Found at i:19192694 original size:18 final size:18
Alignment explanation
Indices: 19192671--19192706 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19192661 CTTATATAGG
19192671 TGGAAAAGAGCTGCCTAA
1 TGGAAAAGAGCTGCCTAA
19192689 TGGAAAAGAGCTGCCTAA
1 TGGAAAAGAGCTGCCTAA
19192707 CTCTAGCTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.17
Consensus pattern (18 bp):
TGGAAAAGAGCTGCCTAA
Found at i:19208272 original size:21 final size:21
Alignment explanation
Indices: 19208214--19208300 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
19208204 CCTGATCAGT
19208214 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* ** *
19208234 AAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
*
19208255 ATACGACACATAAAGTGCCCGAG
1 ATACGACACATAAAGTG-CC-TG
19208278 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
19208299 AT
1 AT
19208301 CGGCAAAGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.16
21 24 0.44
22 4 0.07
23 18 0.33
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:19208284 original size:23 final size:23
Alignment explanation
Indices: 19208214--19208296 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 23
19208204 CCTGATCAGT
*
19208214 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCCGAG
** * *
19208235 A-ACGACACACGAGGTG-CC-TG
1 ATACGACACATAAAGTGCCCGAG
19208255 ATACGACACATAAAGTGCCCGAG
1 ATACGACACATAAAGTGCCCGAG
19208278 ATACGACACATAAAGTGCC
1 ATACGACACATAAAGTGCC
19208297 TGATCGGCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 10 0.20
21 17 0.35
22 2 0.04
23 20 0.41
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCCGAG
Found at i:19208296 original size:44 final size:41
Alignment explanation
Indices: 19208214--19208300 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 41
19208204 CCTGATCAGT
* * *
19208214 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCCGAAACGACACACAAAGTGCCTG
*
19208255 ATACGACACATAAAGTGCCCGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCCGA-A-ACGACACACAAAGTGCCTG
19208299 AT
1 AT
19208301 CGGCAAAGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 11 0.28
42 9 0.23
43 1 0.03
44 18 0.46
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (41 bp):
ATACGACACATAAGTGCCCGAAACGACACACAAAGTGCCTG
Found at i:19208651 original size:16 final size:16
Alignment explanation
Indices: 19208625--19208664 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
19208615 TTAATAACAA
*
19208625 TACTTATCTTA-TATT
1 TACTTACCTTATTATT
19208640 TCACTTACCTTATTATT
1 T-ACTTACCTTATTATT
19208657 TACTTACC
1 TACTTACC
19208665 ATACACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.73
17 5 0.23
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (16 bp):
TACTTACCTTATTATT
Found at i:19208947 original size:13 final size:13
Alignment explanation
Indices: 19208931--19208956 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19208921 TTGCTTTTTC
19208931 TAATAATATAATA
1 TAATAATATAATA
19208944 TAATAATATAATA
1 TAATAATATAATA
19208957 GTTTTACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:19209073 original size:5 final size:5
Alignment explanation
Indices: 19209063--19209090 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
19209053 TTTGTTTATT
19209063 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
19209091 TATATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:19209590 original size:9 final size:9
Alignment explanation
Indices: 19209573--19209637 Score: 53
Period size: 9 Copynumber: 6.9 Consensus size: 9
19209563 TTTAGTCATG
*
19209573 ATTCTAAAA
1 ATTCAAAAA
19209582 ATTCAAAAA
1 ATTCAAAAA
*
19209591 ATATAAATTAAA
1 AT-TCAA--AAA
19209603 ATTCAAAAA
1 ATTCAAAAA
19209612 ATTCAAAAA
1 ATTCAAAAA
19209621 TACTT--AAAA
1 -A-TTCAAAAA
19209630 ATTCAAAA
1 ATTCAAAA
19209638 TTTATAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 29 0.63
10 4 0.09
11 5 0.11
12 5 0.11
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (9 bp):
ATTCAAAAA
Found at i:19210271 original size:31 final size:30
Alignment explanation
Indices: 19210235--19210311 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
19210225 ATTTTAACGG
* *
19210235 TAGAGTGACTAAAATTAAGAACTTATTTAA
1 TAGAGTGACTAAAATTAACAACTTATCTAA
* *
19210265 TGAGAGTGACTAAAATTGACAATTTATCTAA
1 T-AGAGTGACTAAAATTAACAACTTATCTAA
19210296 TATGAGTGACTAAAAT
1 TA-GAGTGACTAAAAT
19210312 AATTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 2 0.05
31 39 0.95
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (30 bp):
TAGAGTGACTAAAATTAACAACTTATCTAA
Found at i:19210779 original size:18 final size:17
Alignment explanation
Indices: 19210758--19210799 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
19210748 AAAAAATTAT
19210758 TTTAAAAATTAAAACAAA
1 TTTAAAAATTAAAA-AAA
*
19210776 TTT-AAAATTTAAAAAA
1 TTTAAAAATTAAAAAAA
19210792 TTTAAAAA
1 TTTAAAAA
19210800 AAGTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 13 0.59
18 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TTTAAAAATTAAAAAAA
Found at i:19210794 original size:16 final size:17
Alignment explanation
Indices: 19210762--19210798 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
19210752 AATTATTTTA
19210762 AAAATTAAAACAAATTT
1 AAAATTAAAACAAATTT
*
19210779 AAAATTTAAA-AAATTT
1 AAAATTAAAACAAATTT
19210795 AAAA
1 AAAA
19210799 AAAGTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATTAAAACAAATTT
Found at i:19210824 original size:23 final size:22
Alignment explanation
Indices: 19210782--19210823 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19210772 CAAATTTAAA
19210782 ATTTAAAAAATTTAAAAAAAGT
1 ATTTAAAAAATTTAAAAAAAGT
* *
19210804 ATTTTAAAATTTTAAAAAAA
1 ATTTAAAAAATTTAAAAAAA
19210824 ATAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATTTAAAAAATTTAAAAAAAGT
Found at i:19212461 original size:17 final size:18
Alignment explanation
Indices: 19212439--19212472 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19212429 CACTATGTTT
19212439 GGTTGGCACC-CCTAATC
1 GGTTGGCACCACCTAATC
*
19212456 GGTTGGCCCCACCTAAT
1 GGTTGGCACCACCTAAT
19212473 ACCTCTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (18 bp):
GGTTGGCACCACCTAATC
Found at i:19212666 original size:11 final size:11
Alignment explanation
Indices: 19212650--19212675 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19212640 CGCCTCTTCT
19212650 TTCGTTCTACC
1 TTCGTTCTACC
19212661 TTCGTTCTACC
1 TTCGTTCTACC
19212672 TTCG
1 TTCG
19212676 CCTCCCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.35, G:0.12, T:0.46
Consensus pattern (11 bp):
TTCGTTCTACC
Found at i:19213798 original size:18 final size:19
Alignment explanation
Indices: 19213775--19213810 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19213765 CTGAACCGAG
*
19213775 ACTAATTT-TTATTCTCAA
1 ACTAATTTCATATTCTCAA
19213793 ACTAATTTCATATTCTCA
1 ACTAATTTCATATTCTCA
19213811 TTCCATTCCC
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:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (19 bp):
ACTAATTTCATATTCTCAA
Found at i:19240714 original size:2 final size:2
Alignment explanation
Indices: 19240707--19240746 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
19240697 GACACTGGAA
19240707 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
19240747 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19253909 original size:2 final size:2
Alignment explanation
Indices: 19253902--19253948 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
19253892 AACCATTCTT
*
19253902 TC TC TC TC TC TC TC TG 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 TC TC TC
19253944 TC TC T
1 TC TC T
19253949 TTTTGAAAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:19255235 original size:2 final size:2
Alignment explanation
Indices: 19255228--19255293 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
19255218 AGGCTTAAAC
19255228 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA G-
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
19255268 GA GA G- GA GA GA GA GA GA GA GA CA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
19255294 GAGGGGAAGG
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 56 0.95
ACGTcount: A:0.47, C:0.02, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19256245 original size:20 final size:22
Alignment explanation
Indices: 19256208--19256248 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
19256198 GGGAACGGGC
19256208 AAGGGGAAGAGTAGCAAAAGAA
1 AAGGGGAAGAGTAGCAAAAGAA
19256230 AAGGGGAA-AG-AGCAAAAGA
1 AAGGGGAAGAGTAGCAAAAGA
19256249 CTGACATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.37, T:0.02
Consensus pattern (22 bp):
AAGGGGAAGAGTAGCAAAAGAA
Found at i:19261928 original size:2 final size:2
Alignment explanation
Indices: 19261921--19261950 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19261911 TCATTCATGA
19261921 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
19261951 ATGTATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:19272966 original size:11 final size:11
Alignment explanation
Indices: 19272950--19272974 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19272940 ATTTTTTAAC
19272950 TTTAAAATACT
1 TTTAAAATACT
19272961 TTTAAAATACT
1 TTTAAAATACT
19272972 TTT
1 TTT
19272975 TTTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:19272995 original size:41 final size:41
Alignment explanation
Indices: 19272934--19273053 Score: 192
Period size: 40 Copynumber: 3.0 Consensus size: 41
19272924 AATATTTTTA
* *
19272934 TTTTTT-A-TTTTTTAACTTTAAAATACTTTTAAAATACTT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTT
*
19272973 TTTTTTAATTTTTTTAATTTTAAAATTTTTTTAAAATAC-T
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTT
19273013 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTT
19273054 NNNNNNNNNN
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
39 6 0.08
40 40 0.54
41 28 0.38
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (41 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTT
Found at i:19273026 original size:8 final size:9
Alignment explanation
Indices: 19272972--19273033 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 9
19272962 TTAAAATACT
19272972 TTTTTTTAA
1 TTTTTTTAA
19272981 TTTTTTTAA
1 TTTTTTTAA
**
19272990 -TTTTAAAA
1 TTTTTTTAA
19272998 TTTTTTTAAAATA
1 TTTTTTT---A-A
19273011 CTTTTTTTAA
1 -TTTTTTTAA
19273021 TTTTTTTAA
1 TTTTTTTAA
19273030 TTTT
1 TTTT
19273034 AAAATATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 6 0.14
9 26 0.60
10 1 0.02
11 1 0.02
12 1 0.02
13 1 0.02
14 7 0.16
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:19279737 original size:20 final size:20
Alignment explanation
Indices: 19279714--19279762 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
19279704 AGACCCATCC
19279714 ATATTATTTTTAATTTTTTT
1 ATATTATTTTTAATTTTTTT
*
19279734 ATATCATTTTT-ATTTTTTT
1 ATATTATTTTTAATTTTTTT
19279753 -TATT-TTTTTA
1 ATATTATTTTTA
19279763 CTTATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.19
18 3 0.12
19 8 0.31
20 10 0.38
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
ATATTATTTTTAATTTTTTT
Found at i:19285806 original size:21 final size:20
Alignment explanation
Indices: 19285772--19285811 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19285762 AAATTAAAAT
*
19285772 CGAAAGAGAAATTAAATTAAC
1 CGAAAGACAAATT-AATTAAC
*
19285793 CGAAAGACACATTAATTAA
1 CGAAAGACAAATTAATTAA
19285812 AATTCAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (20 bp):
CGAAAGACAAATTAATTAAC
Found at i:19290872 original size:21 final size:21
Alignment explanation
Indices: 19290840--19290907 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
19290830 GAGCTAAATA
19290840 GAAACCCATAAGGGTTGAACG
1 GAAACCCATAAGGGTTGAACG
* * * *
19290861 GAAGCTCATAAGAGCTGAACG
1 GAAACCCATAAGGGTTGAACG
* *
19290882 GAAACCCATTAGGGTTGAACA
1 GAAACCCATAAGGGTTGAACG
19290903 GAAAC
1 GAAAC
19290908 TTATATGAGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (21 bp):
GAAACCCATAAGGGTTGAACG
Found at i:19290875 original size:42 final size:42
Alignment explanation
Indices: 19290813--19290926 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
19290803 GCTTGAAGGC
* * *
19290813 TGAACAGAATCTCATGAGAGCTAAATAGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * *
19290855 TGAACGGAAGCTCATAAGAGCTGAACGGAAACCCATTAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * *
19290897 TGAACAGAAACTTATATGAGTTAAACAGAA
1 TGAACAGAAGCTCATAAGAGCTAAACAGAA
19290927 GCTTGTGAGA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:19291151 original size:45 final size:45
Alignment explanation
Indices: 19291091--19291183 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
19291081 CTTCAAATTC
*
19291091 ATAATTTAACAATATTCTATTTTTCAACAACATGCTAAATACATA
1 ATAATTTAACAATATTCTATTTTTCAACAACATACTAAATACATA
* *
19291136 ATAATTTAACAATATTCTATTTTTCAATAATATACTAAATACATA
1 ATAATTTAACAATATTCTATTTTTCAACAACATACTAAATACATA
19291181 ATA
1 ATA
19291184 TTATTCATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (45 bp):
ATAATTTAACAATATTCTATTTTTCAACAACATACTAAATACATA
Found at i:19292247 original size:132 final size:133
Alignment explanation
Indices: 19292094--19292358 Score: 523
Period size: 132 Copynumber: 2.0 Consensus size: 133
19292084 AGATGATGAG
19292094 AATTCTTCATCTCATCATCTTTCTTTCCTTATATACTAAATAAAATAATAATAAAATAAAAAATA
1 AATTCTTCATCTCATCATCTTTCTTTCCTTATATACTAAATAAAATAATAATAAAATAAAAAATA
19292159 TATATATAATTAAAAGTCAAATCAAAATATTAATAAACTATTATTTATTTAATTAATCTAAAATA
66 TATATATAATTAAAAGTCAAATCAAAATATTAATAAACTATTATTTATTTAATTAATCTAAAATA
19292224 TCA
131 TCA
19292227 AATTCTTCAT-TCATCATCTTTCTTTCCTTATATACTAAATAAAATAATAATAAAATAAAAAATA
1 AATTCTTCATCTCATCATCTTTCTTTCCTTATATACTAAATAAAATAATAATAAAATAAAAAATA
19292291 TATATATAATTAAAAGTCAAATCAAAATATTAATAAACTATTATTTATTTAATTAATCTAAAATA
66 TATATATAATTAAAAGTCAAATCAAAATATTAATAAACTATTATTTATTTAATTAATCTAAAATA
19292356 TCA
131 TCA
19292359 CCAACATCAT
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
132 122 0.92
133 10 0.08
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (133 bp):
AATTCTTCATCTCATCATCTTTCTTTCCTTATATACTAAATAAAATAATAATAAAATAAAAAATA
TATATATAATTAAAAGTCAAATCAAAATATTAATAAACTATTATTTATTTAATTAATCTAAAATA
TCA
Found at i:19293169 original size:18 final size:20
Alignment explanation
Indices: 19293148--19293188 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
19293138 AAAATATTTA
*
19293148 TTTTGATAT-TT-TTAATAT
1 TTTTGATATATTATAAATAT
19293166 TTTTGATATATTATAAATAT
1 TTTTGATATATTATAAATAT
19293186 TTT
1 TTT
19293189 AAAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTGATATATTATAAATAT
Found at i:19302301 original size:47 final size:44
Alignment explanation
Indices: 19302210--19302306 Score: 122
Period size: 47 Copynumber: 2.1 Consensus size: 44
19302200 CACTTAATTC
*
19302210 TAATAAAGATAATAATTTATAACAATAAACATCATATATAAACT
1 TAATAAAGATAATAATTTATAACAATAAACATCATACATAAACT
* * * *
19302254 TAATAAAGAATATCTAATTTGATAATAATAAATATTATACATAAACT
1 TAATAAAG-ATA-ATAATTT-ATAACAATAAACATCATACATAAACT
19302301 TAATAA
1 TAATAA
19302307 CAAGCCATGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 8 0.18
45 3 0.07
46 6 0.13
47 28 0.62
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (44 bp):
TAATAAAGATAATAATTTATAACAATAAACATCATACATAAACT
Found at i:19324565 original size:26 final size:27
Alignment explanation
Indices: 19324536--19324586 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
19324526 TTTAGTGAAA
19324536 ATTAAAAAAAT-ATTTATT-ATAATTCT
1 ATTAAAAAAATAATTT-TTAATAATTCT
*
19324562 ATTAAAAATATAATTTTTAATAATT
1 ATTAAAAAAATAATTTTTAATAATT
19324587 TTAAGTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTAAAAAAATAATTTTTAATAATTCT
Found at i:19324590 original size:24 final size:23
Alignment explanation
Indices: 19324563--19324622 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
19324553 TATAATTCTA
19324563 TTAAAAATATAATTTTTAATAATT
1 TTAAAAATATAATTTTTAAT-ATT
*
19324587 TTAAGTAA-ATAA-TTTTAATATT
1 TTAA-AAATATAATTTTTAATATT
*
19324609 TT-AAAATTTAATTT
1 TTAAAAATATAATTT
19324623 GAATATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
20 2 0.07
21 4 0.13
22 7 0.23
23 7 0.23
24 8 0.27
25 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAAAAATATAATTTTTAATATT
Found at i:19325666 original size:30 final size:32
Alignment explanation
Indices: 19325631--19325690 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
19325621 AAAATGATAA
*
19325631 AATTTTAGT-AATGTACTTTTCAA-TTTGATT
1 AATTTTAATCAATGTACTTTTCAACTTTGATT
* *
19325661 AATTTTAATCATTGTACTTTTTAACTTTGA
1 AATTTTAATCAATGTACTTTTCAACTTTGA
19325691 AATTTCATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.32
31 12 0.48
32 5 0.20
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (32 bp):
AATTTTAATCAATGTACTTTTCAACTTTGATT
Found at i:19337919 original size:43 final size:42
Alignment explanation
Indices: 19337841--19337949 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 42
19337831 GAAACAAATA
*
19337841 AAAATTATAAAATAT-AAAATATATATATGTGTATATA-CAT
1 AAAATTATAAAATATAAAAATATATATATGTATATATATCAT
* **
19337881 AAAATTATAAAAATATGAAAAATATATGTATGTATATATATTTT
1 AAAATTAT-AAAATAT-AAAAATATATATATGTATATATATCAT
19337925 AAAATTATAAAATATAAAAATATAT
1 AAAATTATAAAATATAAAAATATAT
19337950 CTAAGTATGT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
40 8 0.13
41 7 0.11
42 10 0.16
43 27 0.44
44 9 0.15
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.38
Consensus pattern (42 bp):
AAAATTATAAAATATAAAAATATATATATGTATATATATCAT
Found at i:19338098 original size:3 final size:3
Alignment explanation
Indices: 19338090--19338134 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
19338080 NNNNNNNNNN
19338090 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19338135 CAACAACAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19340276 original size:51 final size:51
Alignment explanation
Indices: 19340200--19340364 Score: 260
Period size: 51 Copynumber: 3.3 Consensus size: 51
19340190 ACTTTTGATC
*
19340200 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATGTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
19340251 AGTGACAAGTGATAAGTAGTAGCTTCAGTTGCACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* * *
19340302 AGTGGCAAGTGATAAGTGGTAGCTT-AGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
19340352 AGTGATAAGTGAT
1 AGTGACAAGTGAT
19340365 CATACGTAAG
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 33 0.32
51 71 0.68
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:19343170 original size:75 final size:75
Alignment explanation
Indices: 19343045--19343208 Score: 231
Period size: 75 Copynumber: 2.2 Consensus size: 75
19343035 ATTCATGTAT
* * **
19343045 GCTCATACGAACTGAATAACGGGAAGCTCATGCGAGCTAAATAACGGGAAACTCATGTGAGCTGT
1 GCTCATACGAGCTGAATAACGGGAAGCTCATGCGAGCTAAATAACAGGAAACTCATGTGAGCTAA
19343110 ATAAT-GGGAA
66 AT-ATCGGGAA
* * * *
19343120 GCTCATACGAGCTGAGTATCGGGAAGCTCATGCGAGCTAAGTATCAGGAAACTCATGTGAGCTAA
1 GCTCATACGAGCTGAATAACGGGAAGCTCATGCGAGCTAAATAACAGGAAACTCATGTGAGCTAA
19343185 ATATCGGGAA
66 ATATCGGGAA
*
19343195 GCTCATAAGAGCTG
1 GCTCATACGAGCTG
19343209 TGGTGTATCC
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 2 0.03
75 77 0.97
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (75 bp):
GCTCATACGAGCTGAATAACGGGAAGCTCATGCGAGCTAAATAACAGGAAACTCATGTGAGCTAA
ATATCGGGAA
Found at i:19343207 original size:25 final size:25
Alignment explanation
Indices: 19343045--19343200 Score: 152
Period size: 25 Copynumber: 6.2 Consensus size: 25
19343035 ATTCATGTAT
* * * *
19343045 GCTCATACGAACTGAATAACGGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
*
19343070 GCTCATGCGAGCTAAATAACGGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
* * **
19343095 ACTCATGTGAGCTGTATAAT-GGGAA
1 GCTCATGCGAGCTAAAT-ATCGGGAA
* * *
19343120 GCTCATACGAGCTGAGTATCGGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
* *
19343145 GCTCATGCGAGCTAAGTATCAGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
* *
19343170 ACTCATGTGAGCTAAATATCGGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
19343195 GCTCAT
1 GCTCAT
19343201 AAGAGCTGTG
Statistics
Matches: 108, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
24 2 0.02
25 105 0.97
26 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (25 bp):
GCTCATGCGAGCTAAATATCGGGAA
Found at i:19345174 original size:18 final size:17
Alignment explanation
Indices: 19345149--19345192 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
19345139 ATATACATAC
* *
19345149 ATACTTATATTTTTTAT
1 ATACTTATAATTATTAT
19345166 ATACTTTATAATTATTAT
1 ATAC-TTATAATTATTAT
*
19345184 ATACATATA
1 ATACTTATA
19345193 TATATACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (17 bp):
ATACTTATAATTATTAT
Found at i:19352236 original size:5 final size:5
Alignment explanation
Indices: 19352228--19352257 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
19352218 ATCAAATCAG
19352228 TCACC TCACC TCACC TCACC TCACC TCACC
1 TCACC TCACC TCACC TCACC TCACC TCACC
19352258 CCATCTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
TCACC
Found at i:19352265 original size:15 final size:15
Alignment explanation
Indices: 19352229--19352265 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
19352219 TCAAATCAGT
*
19352229 CACCTCACCTCACCT
1 CACCTCACCTCACCC
19352244 CACCTCACCTCACCC
1 CACCTCACCTCACCC
*
19352259 CATCTCA
1 CACCTCA
19352266 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.59, G:0.00, T:0.19
Consensus pattern (15 bp):
CACCTCACCTCACCC
Found at i:19353349 original size:21 final size:22
Alignment explanation
Indices: 19353310--19353350 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19353300 TTACTAAATA
19353310 ATTTAAATATATGAAATATGCC
1 ATTTAAATATATGAAATATGCC
*
19353332 ATTTAAGTATAT-AAATATG
1 ATTTAAATATATGAAATATG
19353351 GGAGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (22 bp):
ATTTAAATATATGAAATATGCC
Found at i:19370624 original size:22 final size:23
Alignment explanation
Indices: 19370594--19370653 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
19370584 TTTTCAGGTA
* *
19370594 CTTCAATTTTTT-TTCAATGTTC
1 CTTCTATTTTTTGTTCAATGTGC
*
19370616 CTTCTATTTCTTTGTTGAATGTGC
1 CTTCTATTT-TTTGTTCAATGTGC
*
19370640 CCTCT-TTTTTTGTT
1 CTTCTATTTTTTGTT
19370654 TTTTTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 14 0.44
23 6 0.19
24 12 0.38
ACGTcount: A:0.12, C:0.18, G:0.10, T:0.60
Consensus pattern (23 bp):
CTTCTATTTTTTGTTCAATGTGC
Found at i:19376870 original size:16 final size:17
Alignment explanation
Indices: 19376849--19376882 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19376839 ATGTCTAGAT
19376849 AAATT-ATTAATTGAGG
1 AAATTAATTAATTGAGG
19376865 AAATTAGATTAATTGAGG
1 AAATTA-ATTAATTGAGG
19376883 GGTTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
18 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (17 bp):
AAATTAATTAATTGAGG
Found at i:19379855 original size:40 final size:40
Alignment explanation
Indices: 19379780--19380066 Score: 273
Period size: 40 Copynumber: 7.2 Consensus size: 40
19379770 ATTTTATGAC
* *
19379780 TTTACCAAAATATTTAACAA-TTACCAATAATTCTAAAGA
1 TTTACCAAAATATCTAACAATTTACCAATAATTCTAACGA
* * *
19379819 TTTATCAAAATATTTAACAATTTACCAATAATTCTAAGGA
1 TTTACCAAAATATCTAACAATTTACCAATAATTCTAACGA
** * *
19379859 TTTACCAAAATATCTAATGATTTACCAATATTTCTAAGGA
1 TTTACCAAAATATCTAACAATTTACCAATAATTCTAACGA
* * * *
19379899 TATACCAATATATCTAACAATTTGCCAA-AATTTTTAACGA
1 TTTACCAAAATATCTAACAATTTACCAATAA-TTCTAACGA
19379939 TTTACCAATAAT-TCTAACAATTTACCAA-AATATCTAACGA
1 TTTACCAA-AATATCTAACAATTTACCAATAAT-TCTAACGA
* ** * *
19379979 TTTACCAATAAT-TTTAAGGATTTATCAA-AATATCTAACGC
1 TTTACCAA-AATATCTAACAATTTACCAATAAT-TCTAACGA
* ** *
19380019 TTTACCAAAATTTCTAATGATTTATCAA-AATATCTAACGA
1 TTTACCAAAATATCTAACAATTTACCAATAAT-TCTAACGA
19380059 TTTACCAA
1 TTTACCAA
19380067 TATTTATGAG
Statistics
Matches: 216, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
39 24 0.11
40 190 0.88
41 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (40 bp):
TTTACCAAAATATCTAACAATTTACCAATAATTCTAACGA
Done.