Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 36 of 75
Found at i:11317342 original size:24 final size:23
Alignment explanation
Indices: 11317297--11317342 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
11317287 TACCTTTTCA
**
11317297 TTATACTTTATTTTGATTAATTT
1 TTATACTTTATTTTGAAAAATTT
*
11317320 TTATAACTTTATTTTTAAAAATT
1 TTAT-ACTTTATTTTGAAAAATT
11317343 CGATTTTCGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATACTTTATTTTGAAAAATTT
Found at i:11320663 original size:2 final size:2
Alignment explanation
Indices: 11320656--11320680 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11320646 ATACCTAACC
11320656 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11320681 CCATTCCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11329752 original size:9 final size:9
Alignment explanation
Indices: 11329715--11329756 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
11329705 ACTCATAACC
11329715 ATAAAAA-A
1 ATAAAAATA
*
11329723 ATAAAACTA
1 ATAAAAATA
*
11329732 AGTAATAATA
1 A-TAAAAATA
11329742 ATAAAAATA
1 ATAAAAATA
11329751 ATAAAA
1 ATAAAA
11329757 GTCAACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 6 0.21
9 15 0.54
10 7 0.25
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
ATAAAAATA
Found at i:11329920 original size:72 final size:72
Alignment explanation
Indices: 11329883--11330319 Score: 858
Period size: 72 Copynumber: 6.1 Consensus size: 72
11329873 ATAAAAATAA
11329883 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
1 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
11329948 AAAATAA
66 AAAATAA
11329955 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
1 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
11330020 AAAATAA
66 AAAATAA
11330027 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
1 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
11330092 AAAATAA
66 AAAATAA
11330099 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
1 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
11330164 AAAATAA
66 AAAATAA
11330171 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
1 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
11330236 AAAATAA
66 AAAATAA
11330243 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAAT-
1 GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
11330307 AAAATAA
66 AAAATAA
11330314 GGAAAA
1 -GAAAA
11330320 AGAAGGGGAA
Statistics
Matches: 364, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
71 7 0.02
72 357 0.98
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (72 bp):
GAAAACACATGATAATAAATATAATAATAATATAAATAAGAATAACAAATAAATAAATAAAAATA
AAAATAA
Found at i:11329927 original size:21 final size:20
Alignment explanation
Indices: 11329896--11330310 Score: 165
Period size: 21 Copynumber: 19.6 Consensus size: 20
11329886 AACACATGAT
* *
11329896 AATAAATATAATAATAATATA
1 AATAAAAATAAAAATAA-ATA
*
11329917 AATAAGAATAACAAATAAATA
1 AATAAAAATAA-AAATAAATA
*
11329938 AATAAAAATAAAAATAAGAAAACA
1 AATAAAAATAAAAAT----AAATA
11329962 CATGATAATAAATATAATAATAATATA
1 -A--ATAA-AAATA-AA-AATAA-ATA
*
11329989 AATAAGAATAACAAATAAATA
1 AATAAAAATAA-AAATAAATA
*
11330010 AATAAAAATAAAAAT-AAGA
1 AATAAAAATAAAAATAAATA
* * * *
11330029 AA-ACACATGATAATAAATA
1 AATAAAAATAAAAATAAATA
* * *
11330048 TAATAATAATATAAAT-AA-G
1 -AATAAAAATAAAAATAAATA
11330067 AATAACAAAT--AAATAAATAAA
1 AATAA-AAATAAAAATAAAT--A
11330088 AATAAAAATAAGAAA-ACACATGA
1 AATAAAAATAA-AAATA-A-AT-A
* *
11330111 TAATAAATATAATAATAATATA
1 -AATAAAAATAAAAATAA-ATA
*
11330133 AATAAGAATAACAAATAAATA
1 AATAAAAATAA-AAATAAATA
*
11330154 AATAAAAATAAAAAT-AAGA
1 AATAAAAATAAAAATAAATA
* * * *
11330173 AA-ACACATGATAATAAATA
1 AATAAAAATAAAAATAAATA
* * *
11330192 TAATAATAATATAAAT-AA-G
1 -AATAAAAATAAAAATAAATA
11330211 AATAACAAAT--AAATAAATAAA
1 AATAA-AAATAAAAATAAAT--A
11330232 AATAAAAATAAGAAA-ACACATGA
1 AATAAAAATAA-AAATA-A-AT-A
* *
11330255 TAATAAATATAATAATAATATA
1 -AATAAAAATAAAAATAA-ATA
*
11330277 AATAAGAATAACAAATAAATA
1 AATAAAAATAA-AAATAAATA
11330298 AATAAAAATAAAA
1 AATAAAAATAAAA
11330311 TAAGGAAAAA
Statistics
Matches: 295, Mismatches: 54, Indels: 91
0.67 0.12 0.21
Matches are distributed among these distances:
17 8 0.03
18 30 0.10
19 22 0.07
20 30 0.10
21 101 0.34
22 25 0.08
23 25 0.08
24 34 0.12
25 1 0.00
26 3 0.01
27 6 0.02
28 5 0.02
29 2 0.01
30 3 0.01
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (20 bp):
AATAAAAATAAAAATAAATA
Found at i:11337294 original size:16 final size:17
Alignment explanation
Indices: 11337263--11337296 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11337253 CCATTATCTT
*
11337263 TTTTTTCCATTATTTAA
1 TTTTTTCCACTATTTAA
11337280 TTTTTTCCACT-TTTAA
1 TTTTTTCCACTATTTAA
11337296 T
1 T
11337297 CGTAGCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTCCACTATTTAA
Found at i:11350365 original size:20 final size:20
Alignment explanation
Indices: 11350342--11350380 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11350332 TTTATATTTA
11350342 TTTTTAAAGATTTTT-TTAAT
1 TTTTTAAA-ATTTTTGTTAAT
*
11350362 TTTTTAGAATTTTTGTTAA
1 TTTTTAAAATTTTTGTTAA
11350381 GAAAACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTTAAAATTTTTGTTAAT
Found at i:11350945 original size:27 final size:28
Alignment explanation
Indices: 11350908--11350961 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
11350898 CATTAAAGTT
11350908 AAAAAAAGAATTTCAATTA-TCCCAAAA
1 AAAAAAAGAATTTCAATTATTCCCAAAA
11350935 AAAAAAAGAATTTCAATTATTCCCAAA
1 AAAAAAAGAATTTCAATTATTCCCAAA
11350962 TTTTAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.24
Consensus pattern (28 bp):
AAAAAAAGAATTTCAATTATTCCCAAAA
Found at i:11353081 original size:10 final size:10
Alignment explanation
Indices: 11353062--11353091 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
11353052 AGGTGGTTGG
11353062 TTAGTGGGAT
1 TTAGTGGGAT
*
11353072 TTAGTAGGAT
1 TTAGTGGGAT
11353082 TTAGTGGGAT
1 TTAGTGGGAT
11353092 ATGGGTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (10 bp):
TTAGTGGGAT
Found at i:11353783 original size:36 final size:36
Alignment explanation
Indices: 11353742--11353819 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 36
11353732 TTTTTGCAGC
* * *
11353742 CGTGTGGAGAACATGGCCATATGAAATCATGCATGT
1 CGTGTGGAGAACACGACCATATGAAATCATGCAGGT
* * * *
11353778 CGTGTGGGGCACACGACCATGTGAAATCATGTAGGT
1 CGTGTGGAGAACACGACCATATGAAATCATGCAGGT
11353814 CGTGTG
1 CGTGTG
11353820 AGTAAACTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (36 bp):
CGTGTGGAGAACACGACCATATGAAATCATGCAGGT
Found at i:11353868 original size:36 final size:36
Alignment explanation
Indices: 11353828--11353929 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
11353818 TGAGTAAACT
* * *
11353828 GTGTGAGGCACACGACCATGTGAAATCATGTAGTCC
1 GTGTGAGGCACACGACCGTGTGAAATCATATAGGCC
11353864 GTGTGAGGCACACGACCGTGTGAAATCATATAGGCC
1 GTGTGAGGCACACGACCGTGTGAAATCATATAGGCC
* * **
11353900 TTGTGGGGCACACGGTCGTGTGAAATCATA
1 GTGTGAGGCACACGACCGTGTGAAATCATA
11353930 CAGATCGTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (36 bp):
GTGTGAGGCACACGACCGTGTGAAATCATATAGGCC
Found at i:11362753 original size:38 final size:37
Alignment explanation
Indices: 11362687--11362766 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 37
11362677 TCATGGAACG
* * * *
11362687 GTTATCTACTAGTCCTTTGGGGCCACACTGTGACGAC
1 GTTATCTACTAGTCCTTTAGAGACACACTATGACGAC
* *
11362724 AGTTATCTACTAGTCCTTTAGAGAGACACTATGATGAC
1 -GTTATCTACTAGTCCTTTAGAGACACACTATGACGAC
11362762 GTTAT
1 GTTAT
11362767 ATAGATCCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 5 0.14
38 31 0.86
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (37 bp):
GTTATCTACTAGTCCTTTAGAGACACACTATGACGAC
Found at i:11364728 original size:28 final size:28
Alignment explanation
Indices: 11364631--11364712 Score: 146
Period size: 28 Copynumber: 2.9 Consensus size: 28
11364621 AAAACATATA
* *
11364631 AAAATGGAAGCCTTTATCGCAATCTATG
1 AAAATGGAAGCCTTTGTGGCAATCTATG
11364659 AAAATGGAAGCCTTTGTGGCAATCTATG
1 AAAATGGAAGCCTTTGTGGCAATCTATG
11364687 AAAATGGAAGCCTTTGTGGCAATCTA
1 AAAATGGAAGCCTTTGTGGCAATCTA
11364713 AGGAAAGGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (28 bp):
AAAATGGAAGCCTTTGTGGCAATCTATG
Found at i:11365798 original size:66 final size:66
Alignment explanation
Indices: 11365728--11365859 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 66
11365718 GATAACTAAA
* *
11365728 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTGGCATTATAAAAGTTGAAAATAGA
1 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTAGCATTATAAAAGTTAAAAATAGA
11365793 T
66 T
11365794 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTAGCATTATAAAAGTTAAAAATAGA
1 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTAGCATTATAAAAGTTAAAAATAGA
11365859 T
66 T
11365860 CAATATAGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (66 bp):
AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTAGCATTATAAAAGTTAAAAATAGA
T
Found at i:11366113 original size:18 final size:17
Alignment explanation
Indices: 11366073--11366115 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
11366063 AATACTTTAA
*
11366073 ATAT-AAAATTATAAAT
1 ATATAAAAATAATAAAT
*
11366089 GTATAAAAATAATATAAT
1 ATATAAAAATAATA-AAT
11366107 ATATAAAAA
1 ATATAAAAA
11366116 AACTGCCACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATATAAAAATAATAAAT
Found at i:11370316 original size:15 final size:15
Alignment explanation
Indices: 11370280--11370322 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
11370270 ACAAAAAATG
* *
11370280 TATAAAATTATTAAA
1 TATAAAAATATAAAA
11370295 TATTAAAAATATAAAA
1 TA-TAAAAATATAAAA
*
11370311 TATAAATATATA
1 TATAAAAATATA
11370323 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAAAATATAAAA
Found at i:11372474 original size:59 final size:59
Alignment explanation
Indices: 11372408--11372533 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 59
11372398 AACTATGTAT
* * **
11372408 ATAACCAACAAAAC-ATACCTAAAACATAATCATTATTTACCAT-TTAAAACCGTACCTAA
1 ATAACCAACAAAACAAT-CATAAAACATAATCATTATTTACCATCAT-AAACCACACCTAA
* * * * *
11372467 ATAACCAACCAATCAATCATAGAACATATTCATTATTTGCCATCATAAACCACACCTAA
1 ATAACCAACAAAACAATCATAAAACATAATCATTATTTACCATCATAAACCACACCTAA
11372526 ATAACCAA
1 ATAACCAA
11372534 TACATAATCA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 53 0.95
60 3 0.05
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (59 bp):
ATAACCAACAAAACAATCATAAAACATAATCATTATTTACCATCATAAACCACACCTAA
Found at i:11373306 original size:41 final size:41
Alignment explanation
Indices: 11373241--11373387 Score: 145
Period size: 41 Copynumber: 3.5 Consensus size: 41
11373231 CAATGTTTCA
* * *
11373241 CACACTAAATGCCATCGCATAGCCGAAGCTAT-TATAATCTCG
1 CACACTAAGTGCCAT-ACATAGCCGAAGCTATCT-CAATCTCG
* * *
11373283 CACACTAAGTGTCTTACATAGCCGAAGCTATCTCAGTCTCG
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCAATCTCG
* *
11373324 CACACTAAGTGCCATAAATAGCCGAATTAGCTATCTCAA-ATCG
1 CACACTAAGTGCCATACATAGCCG-A--AGCTATCTCAATCTCG
* *
11373367 CACACTAAGTGCTAAACATAG
1 CACACTAAGTGCCATACATAG
11373388 TCGATTAATC
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
41 42 0.48
42 14 0.16
43 21 0.24
44 10 0.11
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (41 bp):
CACACTAAGTGCCATACATAGCCGAAGCTATCTCAATCTCG
Found at i:11390574 original size:540 final size:540
Alignment explanation
Indices: 11389556--11390635 Score: 1998
Period size: 540 Copynumber: 2.0 Consensus size: 540
11389546 GTTTGTGACT
* * * *
11389556 GTCGCACTTTCACTGGTGGTCGTGGCAGGTGTTGTCGCCCACGAGTTCAATGTTAGATTTGTGGC
1 GTCGCACTTTCACTGGTGGCCGTGGAAGATGTTGTCGCACACGAGTTCAATGTTAGATTTGTGGC
11389621 AGATTTGGTCACGTGGCTCAATGGTGGCTTTACCATTTTAATCACAAATATGATAATTCTCCTTT
66 AGATTTGGTCACGTGGCTCAATGGTGGCTTTACCATTTTAATCACAAATATGATAATTCTCCTTT
11389686 GGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGCGGGGTTTTGTATGCCTA
131 GGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGCGGGGTTTTGTATGCCTA
*
11389751 CGGAGAGTACTCACGGTGGTCATGGTGGCTTTACTTTTCCCTGGCTGTTCCTGGTCAGGTCGAGT
196 CGGAGAGTACTCACAGTGGTCATGGTGGCTTTACTTTTCCCTGGCTGTTCCTGGTCAGGTCGAGT
*
11389816 CGTATTTGCCAATGGTGTCACCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCTCAT
261 CGTATTTGCCAATGGTGTCACCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCCCAT
*
11389881 GCGACCACCTGAATGAAGATCCCTAGGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATGC
326 GCGACCACCTGAATGAAGATCCCTAAGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATGC
11389946 AGGCCATCATTTTGGGCCACTTGGAGGCGTTACTAGGCCAATAGGGGCAGACCAAGCTTCTGGGC
391 AGGCCATCATTTTGGGCCACTTGGAGGCGTTACTAGGCCAATAGGGGCAGACCAAGCTTCTGGGC
11390011 CATGCACTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCAG
456 CATGCACTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCAG
11390076 CAGGTTGGGCCTGGTCATGG
521 CAGGTTGGGCCTGGTCATGG
11390096 GTCGCACTTTCACTGGTGGCCGTGGAAGATGTTGTCGCACACGAGTTCAATGTTAGATTTGTGGC
1 GTCGCACTTTCACTGGTGGCCGTGGAAGATGTTGTCGCACACGAGTTCAATGTTAGATTTGTGGC
* * *
11390161 AGATTTGGTCACGTGGCTCAATGGTGTCTTTACCATTTTAATCGCAAATATGATAATTCTCTTTT
66 AGATTTGGTCACGTGGCTCAATGGTGGCTTTACCATTTTAATCACAAATATGATAATTCTCCTTT
*
11390226 GGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGTGGGGTTTTGTATGCCTA
131 GGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGCGGGGTTTTGTATGCCTA
* * *
11390291 CGGAGAGTACTCATAGTGGTCATGGTGGCTTTACTTTTCCTTGGTTGTTCCTGGTCAGGTCGAGT
196 CGGAGAGTACTCACAGTGGTCATGGTGGCTTTACTTTTCCCTGGCTGTTCCTGGTCAGGTCGAGT
*
11390356 CGTATTTGCCAATGGTGTCATCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCCCAT
261 CGTATTTGCCAATGGTGTCACCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCCCAT
11390421 GCGACCACCTGAATGAAGATCCCTAAGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATGC
326 GCGACCACCTGAATGAAGATCCCTAAGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATGC
*
11390486 AGGCCATCATTTTGGGCCACTTGGAGGCGTTACTGGGCCAATAGGGGCAGACCAAGCTTCTGGGC
391 AGGCCATCATTTTGGGCCACTTGGAGGCGTTACTAGGCCAATAGGGGCAGACCAAGCTTCTGGGC
*
11390551 CATGCGCTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCAG
456 CATGCACTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCAG
*
11390616 TAGGTTGGGCCTGGTCATGG
521 CAGGTTGGGCCTGGTCATGG
11390636 TGGTATCGGG
Statistics
Matches: 522, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
540 522 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.31
Consensus pattern (540 bp):
GTCGCACTTTCACTGGTGGCCGTGGAAGATGTTGTCGCACACGAGTTCAATGTTAGATTTGTGGC
AGATTTGGTCACGTGGCTCAATGGTGGCTTTACCATTTTAATCACAAATATGATAATTCTCCTTT
GGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGCGGGGTTTTGTATGCCTA
CGGAGAGTACTCACAGTGGTCATGGTGGCTTTACTTTTCCCTGGCTGTTCCTGGTCAGGTCGAGT
CGTATTTGCCAATGGTGTCACCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCCCAT
GCGACCACCTGAATGAAGATCCCTAAGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATGC
AGGCCATCATTTTGGGCCACTTGGAGGCGTTACTAGGCCAATAGGGGCAGACCAAGCTTCTGGGC
CATGCACTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCAG
CAGGTTGGGCCTGGTCATGG
Found at i:11402338 original size:120 final size:120
Alignment explanation
Indices: 11402115--11402352 Score: 415
Period size: 120 Copynumber: 2.0 Consensus size: 120
11402105 AGACTATTAT
*
11402115 AGAAATATATTAAAGTTTGGTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
1 AGAAATATATTAAAGCTTGGTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
* * *
11402180 ATGATCATAAAGTTAGTGATATCAAAAAGTGCAGTTTTAGAACCCCATTTTCAAA
66 ATGATCATAAAGTTAGTGATATCAAAAAGTACAATTTTAGAACACCATTTTCAAA
*
11402235 AGAAATATATTAAAGCTTGTTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
1 AGAAATATATTAAAGCTTGGTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
11402300 ATGATCATAAAGTTAGTGATATCGAAAAA-TACAATTTTAGAACACCATTTTCA
66 ATGATCATAAAGTTAGTGATATC-AAAAAGTACAATTTTAGAACACCATTTTCA
11402353 TAAACTGAGA
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
120 107 0.96
121 5 0.04
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (120 bp):
AGAAATATATTAAAGCTTGGTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
ATGATCATAAAGTTAGTGATATCAAAAAGTACAATTTTAGAACACCATTTTCAAA
Found at i:11404491 original size:22 final size:22
Alignment explanation
Indices: 11404460--11404542 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
11404450 AATTGGTTGA
*
11404460 GTTTGGTTAGTTGATGAACTAT
1 GTTTGATTAGTTGATGAACTAT
* * *
11404482 GTTTGCTTAGTTGATG-AGTTT
1 GTTTGATTAGTTGATGAACTAT
* **
11404503 GTGTTTATTAAATGATGAACTAT
1 GT-TTGATTAGTTGATGAACTAT
*
11404526 GTTTGTTTAGTTGATGA
1 GTTTGATTAGTTGATGA
11404543 GTACATAGGT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
21 5 0.11
22 36 0.78
23 5 0.11
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (22 bp):
GTTTGATTAGTTGATGAACTAT
Found at i:11404542 original size:25 final size:25
Alignment explanation
Indices: 11404471--11404542 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 25
11404461 TTTGGTTAGT
*
11404471 TGATGAACTATGTTTGCTTAGTTGA
1 TGATGAACTATGTTTGTTTAGTTGA
* *
11404496 TGA-G---T-T-TGTGTTTA-TTAAA
1 TGATGAACTATGTTTGTTTAGTT-GA
11404515 TGATGAACTATGTTTGTTTAGTTGA
1 TGATGAACTATGTTTGTTTAGTTGA
11404540 TGA
1 TGA
11404543 GTACATAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 16
0.62 0.09 0.29
Matches are distributed among these distances:
18 2 0.06
19 10 0.29
20 2 0.06
21 1 0.03
23 1 0.03
24 2 0.06
25 14 0.41
26 2 0.06
ACGTcount: A:0.25, C:0.04, G:0.24, T:0.47
Consensus pattern (25 bp):
TGATGAACTATGTTTGTTTAGTTGA
Found at i:11414002 original size:29 final size:28
Alignment explanation
Indices: 11413938--11414002 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
11413928 AATATACCCG
* ***
11413938 TTTTCTCATTTTAGTACCTAAACTTTTT
1 TTTTCTCAATTTAGTACCTAAACTTCAA
*
11413966 TTTGTCTCAATTTAGTACCTAAAGTATCAA
1 TTT-TCTCAATTTAGTACCTAAACT-TCAA
11413996 TTTTCTC
1 TTTTCTC
11414003 TACTTTTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.10
29 23 0.77
30 4 0.13
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (28 bp):
TTTTCTCAATTTAGTACCTAAACTTCAA
Found at i:11414143 original size:7 final size:7
Alignment explanation
Indices: 11414133--11414190 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
11414123 TTTAAATTAA
11414133 AAATATT
1 AAATATT
11414140 AAAT-TT
1 AAATATT
*
11414146 AAAGTA-A
1 AAA-TATT
11414153 AAATA-T
1 AAATATT
11414159 AAAT-TT
1 AAATATT
11414165 ATAATATT
1 A-AATATT
11414173 AAATATT
1 AAATATT
11414180 AAAATATT
1 -AAATATT
11414188 AAA
1 AAA
11414191 AAAGACTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
6 13 0.30
7 20 0.47
8 10 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:11414161 original size:19 final size:20
Alignment explanation
Indices: 11414122--11414165 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
11414112 AATTAGGTTT
*
11414122 ATTTAAATTAAAAATATTAA
1 ATTTAAAGTAAAAATATTAA
11414142 ATTTAAAGTAAAAATA-TAA
1 ATTTAAAGTAAAAATATTAA
11414161 ATTTA
1 ATTTA
11414166 TAATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTTAAAGTAAAAATATTAA
Found at i:11420676 original size:11 final size:11
Alignment explanation
Indices: 11420660--11420698 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
11420650 ACTACTATAT
11420660 ATTACTATTAA
1 ATTACTATTAA
*
11420671 ATTACTACTCTAT
1 ATTACTA-T-TAA
11420684 ATTACTATTAA
1 ATTACTATTAA
11420695 ATTA
1 ATTA
11420699 AGTTAGAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 13 0.54
12 2 0.08
13 9 0.38
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTACTATTAA
Found at i:11420684 original size:24 final size:24
Alignment explanation
Indices: 11420649--11420698 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
11420639 GGATCAACCC
11420649 TACTACTATATATTACTATTAAAT
1 TACTACTATATATTACTATTAAAT
*
11420673 TACTACTCTATATTACTATTAAAT
1 TACTACTATATATTACTATTAAAT
11420697 TA
1 TA
11420699 AGTTAGAGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (24 bp):
TACTACTATATATTACTATTAAAT
Found at i:11420689 original size:13 final size:12
Alignment explanation
Indices: 11420649--11420690 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
11420639 GGATCAACCC
11420649 TACTACTATATAT
1 TACTACT-TATAT
*
11420662 TACTA-TTAAAT
1 TACTACTTATAT
11420673 TACTACTCTATAT
1 TACTACT-TATAT
11420686 TACTA
1 TACTA
11420691 TTAAATTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
13 14 0.56
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (12 bp):
TACTACTTATAT
Found at i:11421124 original size:9 final size:8
Alignment explanation
Indices: 11421110--11421150 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 8
11421100 TACAATAAAT
11421110 AAATATATA
1 AAATATA-A
11421119 AAATATTAA
1 AAATA-TAA
11421128 AAATATAA
1 AAATATAA
11421136 AAATATTAA
1 AAATA-TAA
11421145 AAATAT
1 AAATAT
11421151 TCTTTATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 9 0.30
9 19 0.63
10 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AAATATAA
Found at i:11421138 original size:17 final size:18
Alignment explanation
Indices: 11421110--11421150 Score: 75
Period size: 17 Copynumber: 2.3 Consensus size: 18
11421100 TACAATAAAT
11421110 AAATATATAAAATATTAA
1 AAATATATAAAATATTAA
11421128 AAATATA-AAAATATTAA
1 AAATATATAAAATATTAA
11421145 AAATAT
1 AAATAT
11421151 TCTTTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATATAAAATATTAA
Found at i:11421151 original size:9 final size:9
Alignment explanation
Indices: 11421118--11421151 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
11421108 ATAAATATAT
11421118 AAAATATTA
1 AAAATATTA
11421127 AAAATA-TA
1 AAAATATTA
11421135 AAAATATTA
1 AAAATATTA
11421144 AAAATATT
1 AAAATATT
11421152 CTTTATTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATATTA
Found at i:11425134 original size:24 final size:24
Alignment explanation
Indices: 11425090--11425139 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
11425080 CGCAATAAAG
*
11425090 AATTTAAAAATTATCAAAAATCAA
1 AATTTAAAAAGTATCAAAAATCAA
* *
11425114 AATTATAAAAAGT-TCATAAATTAA
1 AATT-TAAAAAGTATCAAAAATCAA
11425138 AA
1 AA
11425140 AAAAAACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (24 bp):
AATTTAAAAAGTATCAAAAATCAA
Found at i:11429017 original size:22 final size:23
Alignment explanation
Indices: 11428974--11429017 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
11428964 AACTTGGTCA
* *
11428974 TTTTCCTATAAAAATAAGTTTTTT
1 TTTTCCTAT-AAAACAACTTTTTT
11428998 TTTTCCTAT-AAACAACTTTT
1 TTTTCCTATAAAACAACTTTT
11429018 AAAGCGTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
24 9 0.50
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTTCCTATAAAACAACTTTTTT
Found at i:11432988 original size:6 final size:6
Alignment explanation
Indices: 11432977--11433004 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
11432967 AATTAATAAA
11432977 GGCATG GGCATG GGCATG GGCATG GGCA
1 GGCATG GGCATG GGCATG GGCATG GGCA
11433005 ATAAAGTGAA
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:0.18, C:0.18, G:0.50, T:0.14
Consensus pattern (6 bp):
GGCATG
Found at i:11441186 original size:25 final size:25
Alignment explanation
Indices: 11441156--11441205 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
11441146 CTCATTTCCA
*
11441156 TTTCTCTTATTTGCCATTTCAATAT
1 TTTCTCATATTTGCCATTTCAATAT
*
11441181 TTTCTCATCTTTGCCATTTCAATAT
1 TTTCTCATATTTGCCATTTCAATAT
11441206 CAATCACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTCTCATATTTGCCATTTCAATAT
Found at i:11444903 original size:50 final size:50
Alignment explanation
Indices: 11444823--11445015 Score: 289
Period size: 50 Copynumber: 3.8 Consensus size: 50
11444813 ATTTGGGTAA
*
11444823 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAAATG
1 AGAGTTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAAATG
*
11444873 AGAGTTCCCATGTAAGACCATGTCTCGGACATGGCGTTGGCACCGAAATG
1 AGAGTTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAAATG
* * *
11444923 AGAGGTT-CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGA-GTTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAAATG
** *
11444973 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGTTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
11445016 TGTTATTATC
Statistics
Matches: 130, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
50 93 0.72
51 37 0.28
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGTTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAAATG
Found at i:11445879 original size:30 final size:30
Alignment explanation
Indices: 11445835--11445897 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
11445825 ACTTAACAAG
*
11445835 CAAATGCCTCTAAAATAATGACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
11445865 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
11445895 CAA
1 CAA
11445898 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:11453444 original size:44 final size:43
Alignment explanation
Indices: 11453348--11453686 Score: 218
Period size: 44 Copynumber: 7.8 Consensus size: 43
11453338 ACTTGATGCG
* * * *
11453348 ATCTGCTCTACTGCAACTTCAGAGAGGTAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATTACTTCA
* * * *
11453392 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-TACTTCA
* * *
11453436 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATT-TGCTTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT--TACTTCA
* * ** * * *
11453480 TTCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TT-ATTACTTCA
** * * ** * * *
11453524 GCCTGCTCTACTGCAACCTCAGGGAGATAAGA-CCTGA-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTACTTCA
** * * *
11453565 ATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATTACTTCA
* * * * * **
11453609 ATCCGCTACACTACAACTTTAGGGAGATAGGATTATCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-TACTTCA
*
11453653 ATCTACTCCACTGCAACTTCAGGGAGATAAGATT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
11453687 TGCCATCTTC
Statistics
Matches: 221, Mismatches: 64, Indels: 20
0.72 0.21 0.07
Matches are distributed among these distances:
40 1 0.00
41 27 0.12
43 9 0.04
44 176 0.80
45 7 0.03
47 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTACTTCA
Found at i:11453769 original size:217 final size:217
Alignment explanation
Indices: 11453335--11453755 Score: 542
Period size: 217 Copynumber: 1.9 Consensus size: 217
11453325 TATAGTTGGC
* ** * *
11453335 AAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGGTAAGATCTATTACTTTAATCCGCTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTA
*
11453400 CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTACTCCACTGCAACCTCAGGGAGATA
* * * *** ** * * *
11453465 AGATTTGCTTCTTCGTTCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTTAGCCTGC
131 AGATTTGCATCTTCGATCTGCCCCACTCTGACTTCAGCAAGATAAGACTTAATTTCTCAACCTAC
*
11453530 TCTACTGCAACCTCAGGGAGAT
196 TCCACTGCAACCTCAGGGAGAT
11453552 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTA
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTA
* * *
11453617 CACTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGCAACTTCAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTACTCCACTGCAACCTCAGGGAGATA
* * ** *
11453682 AGATTTGCCATCTTCGATCTGCTCCGCTACTG-CTT-AGACAAGATCTGTCTATAATTTC-CAAC
131 AGATTTG-CATCTTCGATCTGCCCCACT-CTGACTTCAG-CAAGATAAGACT-TAATTTCTCAAC
*
11453744 TTACTCCACTGC
192 CTACTCCACTGC
11453756 TGACTAGGGA
Statistics
Matches: 173, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
217 130 0.75
218 36 0.21
219 7 0.04
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (217 bp):
AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTA
CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTACTCCACTGCAACCTCAGGGAGATA
AGATTTGCATCTTCGATCTGCCCCACTCTGACTTCAGCAAGATAAGACTTAATTTCTCAACCTAC
TCCACTGCAACCTCAGGGAGAT
Found at i:11453830 original size:128 final size:124
Alignment explanation
Indices: 11453677--11454217 Score: 706
Period size: 128 Copynumber: 4.2 Consensus size: 124
11453667 AACTTCAGGG
*
11453677 AGATAAGATTTGCCATCTTCGATCTGCTCCGCTACTGCTT-AGACAAGATCTGTCTATAATTTCC
1 AGATAAGATTTGCC-GCTTCGATCTGCTCCGCTACTGCTTGAGACAAGATCTG----TAATTTCC
* * * *
11453741 AACTTACTCCACTGCTGACTAGGGAGATAGGACTTGTGGCTTAAATCTGCTTTCTTACACTTGA
61 AACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * *
11453805 AGATAAGATTCGCCGTCTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATTTGTAATTTCTA
1 AGATAAGATTTGCCG-CTTCGATCTGCTCCGCTACTGCTT---GAGACAAGATCTGTAATTTCCA
* *
11453870 ACCTACTCCACTGCTGACCAGAGACATAGGACTTGTGGCTTAAATCTACTTCCTTACACTTGA
62 ACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
*
11453933 AGATAAGATTTGCCGCTTTCGATTTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTTGCCGC-TTCGATCTGCTCCGCTACTGCTT---GAGACAAGATCTGTAATTTCCA
* * * * *
11453998 ACCTACTTCACTACTGACCAGGAACATAGGACTTGAGGCTTAAATCTGCTTTCTTACACTTGA
62 ACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * *
11454061 AGATAAGATTTACCGCTTTCGATCTGCTCCGTTACCGCTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTTGCCGC-TTCGATCTGCTCCGCTACTGCTT---GAGACAAGATCTGTAATTTCCA
* *
11454126 ACCTACTCCACTGCTAACCAGGGACATAGGACTTGTGGCTTGAATCTGCTTCCTTACACTTGA
62 ACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
*
11454189 AGATAAGATTTGTCGCTTCCGATCTGCTC
1 AGATAAGATTTGCCGCTT-CGATCTGCTC
11454218 TGTAATTTCT
Statistics
Matches: 370, Mismatches: 36, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
127 3 0.01
128 356 0.96
132 11 0.03
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (124 bp):
AGATAAGATTTGCCGCTTCGATCTGCTCCGCTACTGCTTGAGACAAGATCTGTAATTTCCAACCT
ACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
Found at i:11454132 original size:256 final size:253
Alignment explanation
Indices: 11453677--11454372 Score: 841
Period size: 256 Copynumber: 2.8 Consensus size: 253
11453667 AACTTCAGGG
*
11453677 AGATAAGATTTGCC-ATCTTCGATCTGCTCCGCTACTGCTTAGACAAGATCTGTCTATAATTTCC
1 AGATAAGATTTGCCGCT-TTCGATCTGCTCCGCTACTGCTTAGACAAGATCTG--T-TAATTTCC
* * * * * *
11453741 AACTTACTCCACTGCTGACTAGGGAGATAGGACTTGTGGCTTAAATCTGCTTTCTTACACTTGAA
62 AACCTACTCCACTACTGACCAGGAACATAGGACTTGAGGCTTAAATCTGCTTTCTTACACTTGAA
* * * * *
11453806 GATAAGATTCGCCGTCTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATTTGTAATTTCTAA
127 GATAAGATTCACCGTCTTCGATCTGCTCCGCTACCGCTTAGGGAGACAAGATCTGTAATTTCCAA
*
11453871 CCTACTCCACTGCTGACCAGAGACATAGGACTTGTGGCTTAAATCTACTTCCTTACACTTGA
192 CCTACTCCACTGCTAACCAGAGACATAGGACTTGTGGCTTAAATCTACTTCCTTACACTTGA
*
11453933 AGATAAGATTTGCCGCTTTCGATTTGCTCCGCTACTGCTTAGGGAGACAAGATCTG-TAATTTCC
1 AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTT----AGACAAGATCTGTTAATTTCC
*
11453997 AACCTACTTCACTACTGACCAGGAACATAGGACTTGAGGCTTAAATCTGCTTTCTTACACTTGAA
62 AACCTACTCCACTACTGACCAGGAACATAGGACTTGAGGCTTAAATCTGCTTTCTTACACTTGAA
* *
11454062 GATAAGATTTACCG-CTTTCGATCTGCTCCGTTACCGCTTAGGGAGACAAGATCTGTAATTTCCA
127 GATAAGATTCACCGTC-TTCGATCTGCTCCGCTACCGCTTAGGGAGACAAGATCTGTAATTTCCA
* * *
11454126 ACCTACTCCACTGCTAACCAGGGACATAGGACTTGTGGCTTGAATCTGCTTCCTTACACTTGA
191 ACCTACTCCACTGCTAACCAGAGACATAGGACTTGTGGCTTAAATCTACTTCCTTACACTTGA
*
11454189 AGATAAGATTT---G---TCG--CT--TCCG--A-T-C-T-G-C----TCTG-TAATTTCTAACC
1 AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTTAGACAAGATCTGTTAATTTCCAACC
* * * * *
11454232 TACTCCACTACTAACCAGGGAA-ATAGGACTTGTGGCTTGAATCTGCTTCCTTACACTTGAAGGT
66 TACTCCACTACTGACCA-GGAACATAGGACTTGAGGCTTAAATCTGCTTTCTTACACTTGAAGAT
* **
11454296 AAGATTCACCGTCTTTGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACC
130 AAGATTCACCGTCTTCGATCTGCTCCGCTACCGCTTAGGGAGACAAGATCTGTAATTT-CCAACC
*
11454361 TATTCCACTGCT
194 TACTCCACTGCT
11454373 GGTCAGGGAG
Statistics
Matches: 397, Mismatches: 34, Indels: 42
0.84 0.07 0.09
Matches are distributed among these distances:
231 119 0.30
232 22 0.06
235 1 0.00
236 1 0.00
241 1 0.00
242 1 0.00
243 1 0.00
244 1 0.00
246 4 0.01
248 1 0.00
250 3 0.01
253 1 0.00
255 1 0.00
256 227 0.57
257 1 0.00
260 12 0.03
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (253 bp):
AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTTAGACAAGATCTGTTAATTTCCAACC
TACTCCACTACTGACCAGGAACATAGGACTTGAGGCTTAAATCTGCTTTCTTACACTTGAAGATA
AGATTCACCGTCTTCGATCTGCTCCGCTACCGCTTAGGGAGACAAGATCTGTAATTTCCAACCTA
CTCCACTGCTAACCAGAGACATAGGACTTGTGGCTTAAATCTACTTCCTTACACTTGA
Found at i:11454292 original size:103 final size:103
Alignment explanation
Indices: 11454113--11454301 Score: 342
Period size: 103 Copynumber: 1.8 Consensus size: 103
11454103 GGAGACAAGA
* *
11454113 TCTGTAATTTCCAACCTACTCCACTGCTAACCAGGGACATAGGACTTGTGGCTTGAATCTGCTTC
1 TCTGTAATTTCCAACCTACTCCACTACTAACCAGGGAAATAGGACTTGTGGCTTGAATCTGCTTC
11454178 CTTACACTTGAAGATAAGATTTGTCGCTTCCGATCTGC
66 CTTACACTTGAAGATAAGATTTGTCGCTTCCGATCTGC
*
11454216 TCTGTAATTTCTAACCTACTCCACTACTAACCAGGGAAATAGGACTTGTGGCTTGAATCTGCTTC
1 TCTGTAATTTCCAACCTACTCCACTACTAACCAGGGAAATAGGACTTGTGGCTTGAATCTGCTTC
*
11454281 CTTACACTTGAAGGTAAGATT
66 CTTACACTTGAAGATAAGATT
11454302 CACCGTCTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 82 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (103 bp):
TCTGTAATTTCCAACCTACTCCACTACTAACCAGGGAAATAGGACTTGTGGCTTGAATCTGCTTC
CTTACACTTGAAGATAAGATTTGTCGCTTCCGATCTGC
Found at i:11455684 original size:7 final size:7
Alignment explanation
Indices: 11455665--11455716 Score: 61
Period size: 7 Copynumber: 7.0 Consensus size: 7
11455655 TTAGCCTCTC
11455665 CATTTTT
1 CATTTTT
11455672 -ACTTTTT
1 CA-TTTTT
11455679 CATTTTTT
1 CA-TTTTT
11455687 CATTTTT
1 CATTTTT
11455694 CATTTTTT
1 CA-TTTTT
11455702 CATTTTT
1 CATTTTT
11455709 CATATTTT
1 CAT-TTTT
11455717 TTTGACTCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
6 1 0.03
7 20 0.50
8 19 0.47
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:11455685 original size:8 final size:8
Alignment explanation
Indices: 11455674--11455717 Score: 65
Period size: 7 Copynumber: 5.6 Consensus size: 8
11455664 CCATTTTTAC
11455674 TTTTTCAT
1 TTTTTCAT
11455682 TTTTTCA-
1 TTTTTCAT
11455689 TTTTTCAT
1 TTTTTCAT
11455697 TTTTTCA-
1 TTTTTCAT
11455704 TTTTTCAT
1 TTTTTCAT
11455712 ATTTTT
1 -TTTTT
11455718 TTGACTCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 14 0.42
8 14 0.42
9 5 0.15
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCAT
Found at i:11455692 original size:15 final size:15
Alignment explanation
Indices: 11455665--11455717 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
11455655 TTAGCCTCTC
*
11455665 CATTTTTAC-TTTTT
1 CATTTTTTCATTTTT
11455679 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
11455694 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
11455709 CATATTTTT
1 CAT-TTTTT
11455718 TTGACTCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 8 0.22
15 23 0.64
16 5 0.14
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (15 bp):
CATTTTTTCATTTTT
Found at i:11470331 original size:3 final size:3
Alignment explanation
Indices: 11470323--11470354 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11470313 AGTCCCCTTT
11470323 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11470355 TTTTTTTTAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11470511 original size:12 final size:12
Alignment explanation
Indices: 11470494--11470522 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
11470484 TATGCATACC
11470494 TACATATTTTAA
1 TACATATTTTAA
11470506 TACATATTTTAA
1 TACATATTTTAA
11470518 TACAT
1 TACAT
11470523 TCATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
TACATATTTTAA
Found at i:11471746 original size:39 final size:40
Alignment explanation
Indices: 11471645--11471748 Score: 106
Period size: 44 Copynumber: 2.5 Consensus size: 40
11471635 GGTTCGCTGT
11471645 AATGGAATAGATGTGTAATAGTAATTCAATTGTTTGGTTG
1 AATGGAATAGATGTGTAATAGTAATTCAATTGTTTGGTTG
* *
11471685 AATGGAATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTG
1 AATGGAATAG-AT-G---TGTAATAGTAATTCAAT-TGTTTGGTTG
11471729 AATGGAAT-GATGTTGTAATA
1 AATGGAATAGATG-TGTAATA
11471749 ACATAAGGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
39 7 0.13
40 9 0.16
41 3 0.05
42 3 0.05
43 2 0.04
44 22 0.40
45 9 0.16
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (40 bp):
AATGGAATAGATGTGTAATAGTAATTCAATTGTTTGGTTG
Found at i:11471822 original size:6 final size:6
Alignment explanation
Indices: 11471811--11471839 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11471801 AGGTAGATGA
11471811 TTATTG TTATTG TTATTG TTATTG TTATT
1 TTATTG TTATTG TTATTG TTATTG TTATT
11471840 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
TTATTG
Found at i:11471972 original size:56 final size:56
Alignment explanation
Indices: 11471857--11471980 Score: 144
Period size: 56 Copynumber: 2.2 Consensus size: 56
11471847 AATAAGATTA
* *
11471857 TTAATATAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* * *
11471915 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATAAATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
*
11471971 TTACTAAAAT
1 TTAATAAAAT
11471981 CATNNNNNNN
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
55 4 0.07
56 29 0.51
57 18 0.32
58 6 0.11
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (56 bp):
TTAATAAAATAATAAATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:11473841 original size:372 final size:375
Alignment explanation
Indices: 11473276--11474027 Score: 1357
Period size: 372 Copynumber: 2.0 Consensus size: 375
11473266 TGTGAATATT
*
11473276 AGAGTATTGAGTTTAGGGTTTATGATGTGGGTTATGGTGTTTTAGGTTTAGGGTTTAGGAGTTTG
1 AGAGAATTGAGTTTAGGGTTTATGATGTGGGTTATGGTGTTTTAGGTTTAGGGTTTAGGAGTTTG
11473341 GGGTTTAAGATTTGGGCTGCTTTAGTCATGTTAAGAGGTTAATTACTGCTTTAAGGGTTTATGCT
66 GGGTTTAAGA-----GCTGCTTTAGTCATGTTAAGAGGTTAATTACTGCTTTAAGGGTTTATGCT
11473406 TGTGGTTAACGGTTTGCAGTTTATAATTTAACGTTTACAATGCATGGTTTTGGGGTATGGGCGAT
126 TGTGGTTAACGGTTTGCAGTTTATAATTTAACGTTTACAATGCATGGTTTTGGGGTATGGGCGAT
**
11473471 TTTGGGTTTAATGACTTTTTTGGTACCAATTTGAAAAAAATGACAAATACGTATTGTTTTTTAAT
191 TTAAGGTTTAATGACTTTTTTGGTACCAATTTGAAAAAAATGACAAATACGTATTGTTTTTTAAT
11473536 TATTATTATGATACTATAGTTCTAAGTGACACAAATGACTAGTTTACTAATTAATGACGAATGAC
256 TATTATTATGATACTATAGTTCTAAGTGACACAAATGACTAGTTTACTAATTAATGACGAATGAC
11473601 ATATTTATATGTTATATATGATGAAACAAATTATTTTAATATTG-GTTATTTACA
321 ATATTTATATGTTATATATGATGAAACAAATTATTTTAATATTGTGTTATTTACA
* *
11473655 AGAGAATTGAGTTTAGGGTTTATGATGTGGGTTATGGTGTTTTGGGTTTATGGTTTAGGAGTTTG
1 AGAGAATTGAGTTTAGGGTTTATGATGTGGGTTATGGTGTTTTAGGTTTAGGGTTTAGGAGTTTG
*
11473720 GGGTTT-AGA-CTGCTTTAGTCATGTTAAGAGGTTAATTACTGCTTTAGGGGTTTATGCTTGTGG
66 GGGTTTAAGAGCTGCTTTAGTCATGTTAAGAGGTTAATTACTGCTTTAAGGGTTTATGCTTGTGG
* * *
11473783 TTAACGGTTTGCAGTTTATAATTTAACGTTTCCAATGTATGGTTTTGGGGTTTGGGCGATTTAAG
131 TTAACGGTTTGCAGTTTATAATTTAACGTTTACAATGCATGGTTTTGGGGTATGGGCGATTTAAG
11473848 GTTTAATGACTTTTTTGGTACCAATTTGAAAAAAATGACAAATACGTATTGTTTTTTAATTATTA
196 GTTTAATGACTTTTTTGGTACCAATTTGAAAAAAATGACAAATACGTATTGTTTTTTAATTATTA
11473913 TTATGATACTATAGTTCTAAGTGACACAAATGACTAGTTTACTAATTAATGACGAATGACATATT
261 TTATGATACTATAGTTCTAAGTGACACAAATGACTAGTTTACTAATTAATGACGAATGACATATT
11473978 TATATGTTATATATGATGAAACAAATTATTTTAATATTGTGTTATTTACA
326 TATATGTTATATATGATGAAACAAATTATTTTAATATTGTGTTATTTACA
11474028 TATATATATT
Statistics
Matches: 363, Mismatches: 9, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
372 282 0.78
373 10 0.03
378 3 0.01
379 68 0.19
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.42
Consensus pattern (375 bp):
AGAGAATTGAGTTTAGGGTTTATGATGTGGGTTATGGTGTTTTAGGTTTAGGGTTTAGGAGTTTG
GGGTTTAAGAGCTGCTTTAGTCATGTTAAGAGGTTAATTACTGCTTTAAGGGTTTATGCTTGTGG
TTAACGGTTTGCAGTTTATAATTTAACGTTTACAATGCATGGTTTTGGGGTATGGGCGATTTAAG
GTTTAATGACTTTTTTGGTACCAATTTGAAAAAAATGACAAATACGTATTGTTTTTTAATTATTA
TTATGATACTATAGTTCTAAGTGACACAAATGACTAGTTTACTAATTAATGACGAATGACATATT
TATATGTTATATATGATGAAACAAATTATTTTAATATTGTGTTATTTACA
Found at i:11474953 original size:44 final size:44
Alignment explanation
Indices: 11474890--11474984 Score: 154
Period size: 44 Copynumber: 2.2 Consensus size: 44
11474880 GAAATTCTTG
* *
11474890 CTCCTTCTTGCCCAATTTCTTGAATTCCCAAATCCGTAAATCGC
1 CTCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGC
* *
11474934 CTCCTTCTTGCCGAATTTCTTGAAATCCGAAATCCCTAAATCGC
1 CTCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGC
11474978 CTCCTTC
1 CTCCTTC
11474985 CTCCTTCCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.22, C:0.35, G:0.09, T:0.34
Consensus pattern (44 bp):
CTCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGC
Found at i:11483023 original size:43 final size:43
Alignment explanation
Indices: 11482964--11483663 Score: 1201
Period size: 43 Copynumber: 16.3 Consensus size: 43
11482954 GTTTTTGAAC
* * * * * * *
11482964 AAGCGCCGCTATAGAACATTA-CTTTTAGCGGCGTTTTCTCCCA
1 AAGCGCCGCTAAAGAACGTGATC-TTTAGCGGCTTTTTTTTCCT
* * *
11483007 AAGCGCCGCTAAAGAACATGATCTTTAGTGGC--GTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483048 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483091 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483134 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483177 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483220 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483263 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483306 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483349 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483392 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483435 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483478 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
11483521 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
* *
11483564 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGC-GTTTTTTCAT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
* * * *
11483606 AAGCGCCGCTAAAGAACATGATCTTTAGCTGCGTTTTTTTCTAT
1 AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTC-CT
*
11483650 AAGCGCCGCAAAAG
1 AAGCGCCGCTAAAG
11483664 TTAGCGACGT
Statistics
Matches: 636, Mismatches: 16, Indels: 9
0.96 0.02 0.01
Matches are distributed among these distances:
41 35 0.06
42 38 0.06
43 547 0.86
44 16 0.03
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACGTGATCTTTAGCGGCTTTTTTTTCCT
Found at i:11485277 original size:49 final size:49
Alignment explanation
Indices: 11485205--11485308 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
11485195 AGAAAAAAAC
* * *
11485205 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
11485254 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
*
11485303 ATATTA
1 AAATTA
11485309 TAACACATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.33
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
Found at i:11495145 original size:87 final size:87
Alignment explanation
Indices: 11494997--11495171 Score: 323
Period size: 87 Copynumber: 2.0 Consensus size: 87
11494987 AGCGCTATCG
11494997 TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCATTTTTTTTAGTCTACCATCTTCAGT
1 TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCATTTTTTTTAGTCTACCATCTTCAGT
*
11495062 TCGATTGGAATGGGTGAGAAGA
66 TCGATTGGAATGGGTAAGAAGA
* *
11495084 TGCGTTGAGCAAAATTCCTAACCATCAATGCAAATGCTCATTTTTTTTAGTCTACCTTCTTCAGT
1 TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCATTTTTTTTAGTCTACCATCTTCAGT
11495149 TCGATTGGAATGGGTAAGAAGA
66 TCGATTGGAATGGGTAAGAAGA
11495171 T
1 T
11495172 TTCTTTTTGA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (87 bp):
TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCATTTTTTTTAGTCTACCATCTTCAGT
TCGATTGGAATGGGTAAGAAGA
Found at i:11496869 original size:44 final size:46
Alignment explanation
Indices: 11496816--11496908 Score: 118
Period size: 46 Copynumber: 2.1 Consensus size: 46
11496806 TACAACATCT
*
11496816 ATTCCATTCAACCAAA-TACAAAAATACT-ATTACAACTCTATTCC
1 ATTCCATTCAACCAAACAACAAAAATACTAATTACAACTCTATTCC
* ** * *
11496860 ATTCCATTCAACGAAACAACTGAATTACTAATTATAACTCTATTCC
1 ATTCCATTCAACCAAACAACAAAAATACTAATTACAACTCTATTCC
11496906 ATT
1 ATT
11496909 ACAGCTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 15 0.37
45 8 0.20
46 18 0.44
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.32
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAACAAAAATACTAATTACAACTCTATTCC
Found at i:11496919 original size:16 final size:16
Alignment explanation
Indices: 11496890--11496940 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
11496880 TGAATTACTA
*
11496890 ATTATAACTCTATTCC
1 ATTACAACTCTATTCC
* * *
11496906 ATTACAGCTTTATTAC
1 ATTACAACTCTATTCC
*
11496922 ATTATAACTCTATTCC
1 ATTACAACTCTATTCC
11496938 ATT
1 ATT
11496941 CTCCCTAACC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.02, T:0.45
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:11497212 original size:26 final size:25
Alignment explanation
Indices: 11497165--11497215 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
11497155 TTAGATGGAT
11497165 GATTATTGTTATTAAAATTTTAATAG
1 GATTATTGTTA-TAAAATTTTAATAG
11497191 GATTATTGTTA-AAAATAATTTAATA
1 GATTATTGTTATAAAAT--TTTAATA
11497216 AAAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
26 18 0.78
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (25 bp):
GATTATTGTTATAAAATTTTAATAG
Found at i:11497219 original size:14 final size:14
Alignment explanation
Indices: 11497200--11497228 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11497190 GGATTATTGT
11497200 TAAAAATAATTTAA
1 TAAAAATAATTTAA
11497214 TAAAAATAATTTAA
1 TAAAAATAATTTAA
11497228 T
1 T
11497229 CATATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAATAATTTAA
Found at i:11518564 original size:119 final size:120
Alignment explanation
Indices: 11518352--11518591 Score: 473
Period size: 119 Copynumber: 2.0 Consensus size: 120
11518342 CACTAATCAC
11518352 TTAACTAACGCGCCAGTTTTAGCATACCCATATTGATGTTTTAAACTTTCATTTATTCTTGGTTT
1 TTAACTAACGCGCCAGTTTTAGCATACCCATATTGATGTTTTAAACTTTCATTTATTCTTGGTTT
11518417 AAATAAAATTATTTTTTTATACTTTAAATAAAAACATAAAAATTAAAAAAAATAT
66 AAATAAAATTATTTTTTTATACTTTAAATAAAAACATAAAAATTAAAAAAAATAT
11518472 TTAACTAACG-GCCAGTTTTAGCATACCCATATTGATGTTTTAAACTTTCATTTATTCTTGGTTT
1 TTAACTAACGCGCCAGTTTTAGCATACCCATATTGATGTTTTAAACTTTCATTTATTCTTGGTTT
11518536 AAATAAAATTATTTTTTTATACTTTAAATAAAAACATAAAAATTAAAAAAAATAT
66 AAATAAAATTATTTTTTTATACTTTAAATAAAAACATAAAAATTAAAAAAAATAT
11518591 T
1 T
11518592 CTTTAAAAAA
Statistics
Matches: 120, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 110 0.92
120 10 0.08
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (120 bp):
TTAACTAACGCGCCAGTTTTAGCATACCCATATTGATGTTTTAAACTTTCATTTATTCTTGGTTT
AAATAAAATTATTTTTTTATACTTTAAATAAAAACATAAAAATTAAAAAAAATAT
Found at i:11518650 original size:17 final size:18
Alignment explanation
Indices: 11518583--11518652 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 18
11518573 AAAAATTAAA
11518583 AAAAATATTCTTTAAAAAAT
1 AAAAATA-T-TTTAAAAAAT
*
11518603 AAAAAAATTTATGAAAAAAT
1 AAAAATATTT-T-AAAAAAT
* *
11518623 AAAACT-CTTT-AAAAAT
1 AAAAATATTTTAAAAAAT
11518639 AAAAATATTTTAAA
1 AAAAATATTTTAAA
11518653 TATATAAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
16 11 0.28
17 3 0.08
18 5 0.12
19 4 0.10
20 17 0.43
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (18 bp):
AAAAATATTTTAAAAAAT
Found at i:11519946 original size:17 final size:18
Alignment explanation
Indices: 11519879--11519948 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 18
11519869 AAAAATTAAA
11519879 AAAAATATTCTTTAAAAAAT
1 AAAAATA-T-TTTAAAAAAT
*
11519899 AAAAAAATTTATGAAAAAAT
1 AAAAATATTT-T-AAAAAAT
* *
11519919 AAAACT-CTTT-AAAAAT
1 AAAAATATTTTAAAAAAT
11519935 AAAAATATTTTAAA
1 AAAAATATTTTAAA
11519949 TATATAAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
16 11 0.28
17 3 0.08
18 5 0.12
19 4 0.10
20 17 0.43
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (18 bp):
AAAAATATTTTAAAAAAT
Found at i:11520409 original size:14 final size:16
Alignment explanation
Indices: 11520381--11520434 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
11520371 ATTTAAACAA
* *
11520381 AAAAACATAAAAATTT
1 AAAAATATATAAATTT
*
11520397 AAAAAT-TATAATTTT
1 AAAAATATATAAATTT
* *
11520412 TAAAATATATAAAATT
1 AAAAATATATAAATTT
11520428 AAAAATA
1 AAAAATA
11520435 AAAATTCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATATATAAATTT
Found at i:11520431 original size:31 final size:31
Alignment explanation
Indices: 11520382--11520463 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
11520372 TTTAAACAAA
* * *
11520382 AAAACATAAAAATTTAAAAATTATAATT-TTT
1 AAAATATAAAAA-TTAAAAATAAAAATTCTTT
11520413 AAAATATATAAAATTAAAAATAAAAATTCTTT
1 AAAATATA-AAAATTAAAAATAAAAATTCTTT
11520445 AAAAT-TCAAAAATTAAAAA
1 AAAATAT-AAAAATTAAAAA
11520464 AATGATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 32 0.71
32 13 0.29
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAATATAAAAATTAAAAATAAAAATTCTTT
Found at i:11520477 original size:31 final size:32
Alignment explanation
Indices: 11520382--11520498 Score: 82
Period size: 31 Copynumber: 3.6 Consensus size: 32
11520372 TTTAAACAAA
* * *
11520382 AAAACATA-AAAATTTAAAAATTATAA-TTTTT
1 AAAATATATAAAA-TTAAAAATAAAAATTTTTT
*
11520413 AAAATATATAAAATTAAAAATAAAAATTCTTT
1 AAAATATATAAAATTAAAAATAAAAATTTTTT
* *
11520445 AAAAT-TCA-AAAATTAAAAA-AATGATTTTTTT
1 AAAATAT-ATAAAATTAAAAATAA-AAATTTTTT
*
11520476 AAAAATATTTTAAAATATAAAAA
1 -AAAATA-TATAAAAT-TAAAAA
11520499 ATTCCAAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
30 2 0.03
31 36 0.52
32 19 0.28
34 6 0.09
35 6 0.09
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (32 bp):
AAAATATATAAAATTAAAAATAAAAATTTTTT
Found at i:11523016 original size:23 final size:23
Alignment explanation
Indices: 11522986--11523032 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
11522976 ATAGTGATGA
*
11522986 TACATAGAAATAGTAAACTATTT
1 TACATAGAAACAGTAAACTATTT
11523009 TACATAGAAACAGTAAACTATTT
1 TACATAGAAACAGTAAACTATTT
11523032 T
1 T
11523033 TTAAAGTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.34
Consensus pattern (23 bp):
TACATAGAAACAGTAAACTATTT
Found at i:11525188 original size:84 final size:84
Alignment explanation
Indices: 11525092--11525260 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
11525082 ATGAGTCCCT
11525092 CTACCTTTGTAGCTTTTGGCTCTAGAATGGGTGAGTCGACCCTCCTTGCACCACTATCCTCACCT
1 CTACCTTTGTAGCTTTTGGCTCTAGAATGGGTGAGTCGACCCTCCTTGCACCACTATCCTCACCT
11525157 CTCTCATTGATACCATGTA
66 CTCTCATTGATACCATGTA
11525176 CTACCTTTGTAGCTTTTGGCTCTAGAATGGGTGAGTCGACCCTCCTTGCACCACTATCCTCACCT
1 CTACCTTTGTAGCTTTTGGCTCTAGAATGGGTGAGTCGACCCTCCTTGCACCACTATCCTCACCT
11525241 CTCTCATTGATACCATGTA
66 CTCTCATTGATACCATGTA
11525260 C
1 C
11525261 CAACAAGAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (84 bp):
CTACCTTTGTAGCTTTTGGCTCTAGAATGGGTGAGTCGACCCTCCTTGCACCACTATCCTCACCT
CTCTCATTGATACCATGTA
Found at i:11532827 original size:16 final size:16
Alignment explanation
Indices: 11532806--11532839 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
11532796 ATACAAGCAT
11532806 TTTCATTATGTTTTAG
1 TTTCATTATGTTTTAG
11532822 TTTCATTATGTTTTAG
1 TTTCATTATGTTTTAG
11532838 TT
1 TT
11532840 AAGTTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65
Consensus pattern (16 bp):
TTTCATTATGTTTTAG
Found at i:11535231 original size:23 final size:23
Alignment explanation
Indices: 11535205--11535250 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
11535195 ACAAACAACA
11535205 AATAATCTACTATTACTCCTACT
1 AATAATCTACTATTACTCCTACT
11535228 AATAATCTACTATTACTCCTACT
1 AATAATCTACTATTACTCCTACT
11535251 TCTAACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAATCTACTATTACTCCTACT
Found at i:11539550 original size:18 final size:17
Alignment explanation
Indices: 11539503--11539550 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
11539493 ACAAAAGAAG
*
11539503 ATTTAGAGGTTCTAAAA
1 ATTTAGAGGTTTTAAAA
11539520 AGTTTAGA-GTTTTAAAA
1 A-TTTAGAGGTTTTAAAA
11539537 ATTTAGAGGATTTT
1 ATTTAGAGG-TTTT
11539551 GAGACAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.22
17 11 0.41
18 10 0.37
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.42
Consensus pattern (17 bp):
ATTTAGAGGTTTTAAAA
Found at i:11551802 original size:22 final size:22
Alignment explanation
Indices: 11551776--11551830 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
11551766 TACAGAGGTG
11551776 ATGTCGAGACACACCAGGTCCT
1 ATGTCGAGACACACCAGGTCCT
* *
11551798 GTGTCGTGACACACCAGGTCCT
1 ATGTCGAGACACACCAGGTCCT
*
11551820 ATGTCGCGACA
1 ATGTCGAGACA
11551831 TCGATGGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.20
Consensus pattern (22 bp):
ATGTCGAGACACACCAGGTCCT
Found at i:11553050 original size:39 final size:39
Alignment explanation
Indices: 11553007--11553083 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
11552997 TCCATGTTAC
*
11553007 ATTGTCTTGTCACA-CTATTGATTTGATGATTGCTTCCAT
1 ATTGTCTTGTCACATC-ATTGATTTGATGATTACTTCCAT
* *
11553046 ATTGTCTTGTTACATCATTGATTTGATGGTTACTTCCA
1 ATTGTCTTGTCACATCATTGATTTGATGATTACTTCCA
11553084 AGTTGCAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 33 0.97
40 1 0.03
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.47
Consensus pattern (39 bp):
ATTGTCTTGTCACATCATTGATTTGATGATTACTTCCAT
Found at i:11556687 original size:40 final size:41
Alignment explanation
Indices: 11556626--11556706 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 41
11556616 TTTCTATTTG
11556626 TTATAGCAGTATTTTTAAAATATAATTTATTTCCAGACGAC
1 TTATAGCAGTATTTTTAAAATATAATTTATTTCCAGACGAC
11556667 TTATAGCAGT-TTTTTAAAATATAATTTATTTCCAGACGAC
1 TTATAGCAGTATTTTTAAAATATAATTTATTTCCAGACGAC
11556707 ATGTATTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 30 0.75
41 10 0.25
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (41 bp):
TTATAGCAGTATTTTTAAAATATAATTTATTTCCAGACGAC
Found at i:11559395 original size:29 final size:29
Alignment explanation
Indices: 11559348--11559438 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
11559338 AAAATTATTT
* *
11559348 AAAAA-ATTTAAAA-TGAATAAAAGTTATA
1 AAAAATATTTAAAATTTAATAAAA-ATATA
* *
11559376 AAAATTA-TTAAACTTTAATAAAAATATA
1 AAAAATATTTAAAATTTAATAAAAATATA
* *
11559404 AAAAATATTTAAAATTTAGTAAAAAGTAGA
1 AAAAATATTTAAAATTTAATAAAAA-TATA
11559434 AAAAA
1 AAAAA
11559439 ATATAAATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
28 19 0.37
29 24 0.47
30 8 0.16
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (29 bp):
AAAAATATTTAAAATTTAATAAAAATATA
Found at i:11559857 original size:8 final size:8
Alignment explanation
Indices: 11559829--11559868 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
11559819 TTTTATAGTT
11559829 TATTTTTC
1 TATTTTTC
11559837 TATTGTTTC
1 TATT-TTTC
11559846 -ATTTTTC
1 TATTTTTC
11559853 TATTTTTCC
1 TATTTTT-C
11559862 TATTTTT
1 TATTTTT
11559869 TTCTAGTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.14
8 13 0.45
9 12 0.41
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (8 bp):
TATTTTTC
Found at i:11559867 original size:16 final size:16
Alignment explanation
Indices: 11559815--11559860 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
11559805 AGTAAAATTA
*
11559815 CATTTTT-TATAGTTT
1 CATTTTTCTATTGTTT
11559830 -ATTTTTCTATTGTTT
1 CATTTTTCTATTGTTT
11559845 CATTTTTCTATT-TTT
1 CATTTTTCTATTGTTT
11559860 C
1 C
11559861 CTATTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 6 0.21
15 11 0.39
16 11 0.39
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (16 bp):
CATTTTTCTATTGTTT
Found at i:11561936 original size:17 final size:16
Alignment explanation
Indices: 11561914--11561965 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
11561904 ATAAGTTTAC
* *
11561914 AAAAATAATTATTTGAA
1 AAAAATTATT-TTTAAA
11561931 AAAAATTATTTTTAAA
1 AAAAATTATTTTTAAA
11561947 AAAAATTATTTTTTAAA
1 AAAAATTA-TTTTTAAA
11561964 AA
1 AA
11561966 GTAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAAATTATTTTTAAA
Found at i:11561948 original size:16 final size:16
Alignment explanation
Indices: 11561914--11561965 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
11561904 ATAAGTTTAC
* *
11561914 AAAAATAATTATTTGAA
1 AAAAATTATT-TTTAAA
11561931 AAAAATTATTTTTAAA
1 AAAAATTATTTTTAAA
*
11561947 AAAAATTATTTTTTAA
1 AAAAATTATTTTTAAA
11561963 AAA
1 AAA
11561966 GTAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 23 0.72
17 9 0.28
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAAATTATTTTTAAA
Found at i:11566754 original size:13 final size:13
Alignment explanation
Indices: 11566736--11566760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11566726 AAAAAATCAT
11566736 AAAAATTATAAAC
1 AAAAATTATAAAC
11566749 AAAAATTATAAA
1 AAAAATTATAAA
11566761 AAATTTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTATAAAC
Found at i:11572491 original size:26 final size:25
Alignment explanation
Indices: 11572449--11572507 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
11572439 TTACCCCCAA
*
11572449 TAAAATTTGACAATTTTACCCTTGG
1 TAAAATTTGACAATTTTACCATTGG
* * *
11572474 TAAAATCTTGACGATTTTTCTATTGG
1 TAAAAT-TTGACAATTTTACCATTGG
11572500 TAAAATTT
1 TAAAATTT
11572508 CAAGAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (25 bp):
TAAAATTTGACAATTTTACCATTGG
Found at i:11577486 original size:26 final size:27
Alignment explanation
Indices: 11577457--11577518 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
11577447 TATGCCCAAC
*
11577457 AAAATTTTGAA-AATTTTACCCTTGAT
1 AAAATTTTGAACAATTTTACCCCTGAT
* * *
11577483 AAAATTTT-AACGATTTTGCCCCTGGT
1 AAAATTTTGAACAATTTTACCCCTGAT
11577509 AAAATTTTGA
1 AAAATTTTGA
11577519 GAAAATATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.07
26 27 0.90
27 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (27 bp):
AAAATTTTGAACAATTTTACCCCTGAT
Found at i:11578639 original size:31 final size:30
Alignment explanation
Indices: 11578604--11578668 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
11578594 TTATTTAATA
11578604 CATTAAAGAAATTGAGTTTACGATAATTATT
1 CATTAAA-AAATTGAGTTTACGATAATTATT
* *
11578635 CATT--AATATTGAGTTTATGATAATTATT
1 CATTAAAAAATTGAGTTTACGATAATTATT
11578663 CATTAA
1 CATTAA
11578669 TATTAAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 25 0.83
29 1 0.03
31 4 0.13
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (30 bp):
CATTAAAAAATTGAGTTTACGATAATTATT
Found at i:11578645 original size:28 final size:28
Alignment explanation
Indices: 11578614--11578672 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
11578604 CATTAAAGAA
11578614 ATTGAGTTTACGATAATTATTCATTAAT
1 ATTGAGTTTACGATAATTATTCATTAAT
*
11578642 ATTGAGTTTATGATAATTATTCATTAAT
1 ATTGAGTTTACGATAATTATTCATTAAT
11578670 ATT
1 ATT
11578673 AAATGTCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (28 bp):
ATTGAGTTTACGATAATTATTCATTAAT
Found at i:11579506 original size:27 final size:27
Alignment explanation
Indices: 11579454--11579529 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 27
11579444 TAGGGTCTAG
*
11579454 GGGTTCTAAAAAAATAATATTGACGAGTT
1 GGGTTCTAAAAAAA-AAT-TTGACGAGAT
11579483 GGGTTCTGAAAAAAAAATTT-ACGAGAT
1 GGGTTCT-AAAAAAAAATTTGACGAGAT
*
11579510 GGGTTCTAAAGAAATAATTT
1 GGGTTCTAAA-AAAAAATTT
11579530 TGAAGAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 3 0.07
27 21 0.49
28 2 0.05
29 10 0.23
30 7 0.16
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (27 bp):
GGGTTCTAAAAAAAAATTTGACGAGAT
Found at i:11585977 original size:25 final size:24
Alignment explanation
Indices: 11585940--11586010 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 24
11585930 AAGAGCTTTT
*
11585940 CGTTATACAGCTCACATGAGCTTCC
1 CGTTATA-TGCTCACATGAGCTTCC
*
11585965 CGTTATATGGCTCGA-AAGAGCTTCC
1 CGTTATAT-GCTC-ACATGAGCTTCC
11585990 CGTTTATATGCTCACATGAGC
1 CG-TTATATGCTCACATGAGC
11586011 ATTTTTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 1 0.03
25 31 0.79
26 7 0.18
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (24 bp):
CGTTATATGCTCACATGAGCTTCC
Found at i:11590902 original size:18 final size:19
Alignment explanation
Indices: 11590879--11590915 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11590869 AAACGAATTA
*
11590879 TATTTTT-TCTCTTATTTT
1 TATTTTTATCTATTATTTT
11590897 TATTTTTATCTATTATTTT
1 TATTTTTATCTATTATTTT
11590916 GTTTTTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTTATCTATTATTTT
Found at i:11591732 original size:27 final size:25
Alignment explanation
Indices: 11591702--11591787 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 25
11591692 TGTTATTATT
11591702 ATTATTATTAATTAGTTTAATATTTTC
1 ATTATTATT-ATTA-TTTAATATTTTC
* *
11591729 ATTATTATTATTA-TTATTATTATC
1 ATTATTATTATTATTTAATATTTTC
* *
11591753 ATTATTATTATTATTACTACTACTTTC
1 ATTATTATTATTATT--TAATATTTTC
11591780 ATTATTAT
1 ATTATTAT
11591788 CGATATTTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
24 22 0.43
25 1 0.02
26 4 0.08
27 24 0.47
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (25 bp):
ATTATTATTATTATTTAATATTTTC
Found at i:11591787 original size:3 final size:3
Alignment explanation
Indices: 11591694--11591768 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
11591684 CCTTTTTGTG
* *
11591694 TTA TTA TTA TTA TTA TTAA TTA GT- TTA ATA TT- TTCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
11591739 TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11591769 CTACTACTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
2 3 0.05
3 54 0.87
4 5 0.08
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:11596439 original size:25 final size:25
Alignment explanation
Indices: 11596417--11596473 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
11596407 ATTGGCTCGT
11596417 AAGAGCTTCCCGTTATACAGCTCAC
1 AAGAGCTTCCCGTTATACAGCTCAC
* * ** *
11596442 ATGAGTTTCCCGTTATATGGCTCAA
1 AAGAGCTTCCCGTTATACAGCTCAC
11596467 AAGAGCT
1 AAGAGCT
11596474 ACTCGTTTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (25 bp):
AAGAGCTTCCCGTTATACAGCTCAC
Found at i:11600699 original size:76 final size:76
Alignment explanation
Indices: 11600600--11600837 Score: 226
Period size: 76 Copynumber: 3.1 Consensus size: 76
11600590 AGGACGTATA
*
11600600 CACACATTTAATATTGTCAGTTTATCCGACTAGCGCTGGACACAAATCTCTATTGGTTAA-TCTG
1 CACACATTTAATATTGTCAGTTTATCCGACTAGCGCTGGACACAAATCTCTATTAGTTAATTC-G
**
11600664 ACTAGTGTTGGG
65 ACTAGTACTGGG
* * ** * * * * * * *
11600676 CACATATTTAATATCGTTGGTTTATCCGATTAGTGTTGGGCATAAATCTTTATTAGTTAATTCGG
1 CACACATTTAATATTGTCAGTTTATCCGACTAGCGCTGGACACAAATCTCTATTAGTTAATTCGA
11600741 CTAGTACTGGG
66 CTAGTACTGGG
* * * * * * * ** *
11600752 CGCACATTTAATATTGTCAGTTTATCCGACTAGTGTTGGGCGCAAATCTTTGTCGGTTAATTCAA
1 CACACATTTAATATTGTCAGTTTATCCGACTAGCGCTGGACACAAATCTCTATTAGTTAATTCGA
*
11600817 CTAGTGCTGGG
66 CTAGTACTGGG
*
11600828 TACACATTTA
1 CACACATTTA
11600838 GTATCGTCGA
Statistics
Matches: 131, Mismatches: 30, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
76 129 0.98
77 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (76 bp):
CACACATTTAATATTGTCAGTTTATCCGACTAGCGCTGGACACAAATCTCTATTAGTTAATTCGA
CTAGTACTGGG
Found at i:11602380 original size:17 final size:17
Alignment explanation
Indices: 11602358--11602392 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11602348 AGTAAAAAAT
* *
11602358 GATAAAAGTATAATTTA
1 GATAAAAATAGAATTTA
11602375 GATAAAAATAGAATTTA
1 GATAAAAATAGAATTTA
11602392 G
1 G
11602393 GAAAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
GATAAAAATAGAATTTA
Found at i:11602481 original size:13 final size:13
Alignment explanation
Indices: 11602465--11602491 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11602455 AGCAGAGAAT
11602465 TGTGAGAAATGTG
1 TGTGAGAAATGTG
11602478 TGTGAGAAATGTG
1 TGTGAGAAATGTG
11602491 T
1 T
11602492 TGGGGGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (13 bp):
TGTGAGAAATGTG
Found at i:11604586 original size:53 final size:55
Alignment explanation
Indices: 11604487--11604595 Score: 134
Period size: 53 Copynumber: 2.0 Consensus size: 55
11604477 CATGTCAACA
* * * **
11604487 TTTAATTGATTTTTTAAATTTTAAAAAATATGTTTTTACACCTTTT-AAAATAAT
1 TTTAATTGATTTTTAAAATTTTAAAAAAAATGTTTTTAAAAATTTTAAAAATAAT
*
11604541 TTTAA-TGA-TTTTAAAATTTTAAAAATAAATTTTTTTAAAAATTTTAAAAATAAT
1 TTTAATTGATTTTTAAAATTTTAAAAA-AAATGTTTTTAAAAATTTTAAAAATAAT
11604595 T
1 T
11604596 AAATGTTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
52 16 0.34
53 17 0.36
54 14 0.30
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (55 bp):
TTTAATTGATTTTTAAAATTTTAAAAAAAATGTTTTTAAAAATTTTAAAAATAAT
Found at i:11614641 original size:31 final size:31
Alignment explanation
Indices: 11614606--11614665 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
11614596 GTTTTTTGAA
*
11614606 CTATTCAAAAGTTTTTATTTAAGTCACTGAG
1 CTATTCAAAAGTTTTTATTTAAATCACTGAG
*
11614637 CTATTCAAATGTTTTTATTTAAATCACTG
1 CTATTCAAAAGTTTTTATTTAAATCACTG
11614666 GGTTGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (31 bp):
CTATTCAAAAGTTTTTATTTAAATCACTGAG
Found at i:11614896 original size:6 final size:6
Alignment explanation
Indices: 11614881--11614912 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
11614871 ATTGAATTGT
11614881 AGAA-G AGAATG AGAATG AGAATG AGAATG AGA
1 AGAATG AGAATG AGAATG AGAATG AGAATG AGA
11614913 GCTTTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.53, C:0.00, G:0.34, T:0.12
Consensus pattern (6 bp):
AGAATG
Found at i:11615270 original size:21 final size:21
Alignment explanation
Indices: 11615246--11615288 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
11615236 TTTTTTCAAA
*
11615246 TCGAATCGAGTGAAATGAAAT
1 TCGAATCGAGTCAAATGAAAT
* * *
11615267 TCGAGTTGAGTCAAGTGAAAT
1 TCGAATCGAGTCAAATGAAAT
11615288 T
1 T
11615289 GTTCAAGTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (21 bp):
TCGAATCGAGTCAAATGAAAT
Found at i:11615399 original size:3 final size:3
Alignment explanation
Indices: 11615393--11615426 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11615383 TTCAAAGAAA
11615393 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11615427 TATTAGTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11615534 original size:19 final size:20
Alignment explanation
Indices: 11615510--11615556 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
11615500 ATATTCTTTA
*
11615510 GAATTTTTATAAA-TATTTT
1 GAATTTTTAAAAATTATTTT
11615529 GAATTTTTAAAAATTATTTT
1 GAATTTTTAAAAATTATTTT
*
11615549 AAATTTTT
1 GAATTTTT
11615557 TATTGTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
GAATTTTTAAAAATTATTTT
Found at i:11618206 original size:18 final size:18
Alignment explanation
Indices: 11618151--11618208 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 18
11618141 AGTTTTTTAA
11618151 TGTTTTTTGCTTAGAAAAT
1 TGTTTTTT-CTTAGAAAAT
*
11618170 TGTTTGTTTATTCAAAGAAAAT
1 TGTTT-TTTCTT---AGAAAAT
11618192 TGTTTTTTCTTAGAAAA
1 TGTTTTTTCTTAGAAAA
11618209 GATGTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 6 0.18
19 7 0.21
20 3 0.09
21 5 0.15
22 12 0.36
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (18 bp):
TGTTTTTTCTTAGAAAAT
Found at i:11618711 original size:33 final size:33
Alignment explanation
Indices: 11618647--11618712 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
11618637 TGACTATTGA
* * * * **
11618647 GGAGGGTGATGTTGAAGGGGTGGAAGTTGATGG
1 GGAGAGTGATGATGAAGGAGTAGAAACTGATGG
11618680 GGAGAGTGATGATGAAGGAGTAGAAACTGATGG
1 GGAGAGTGATGATGAAGGAGTAGAAACTGATGG
11618713 TGATGGTGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (33 bp):
GGAGAGTGATGATGAAGGAGTAGAAACTGATGG
Found at i:11621808 original size:16 final size:16
Alignment explanation
Indices: 11621787--11621825 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11621777 GTTTTTGGCT
11621787 TGTATAGCATGAATAG
1 TGTATAGCATGAATAG
** *
11621803 TGTATAGGGTGAATGG
1 TGTATAGCATGAATAG
11621819 TGTATAG
1 TGTATAG
11621826 ACTAATCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (16 bp):
TGTATAGCATGAATAG
Found at i:11622216 original size:212 final size:210
Alignment explanation
Indices: 11621849--11622272 Score: 679
Period size: 212 Copynumber: 2.0 Consensus size: 210
11621839 TTTTGTAAAG
* * *
11621849 TACATTTATCCAAATTGCAAAGGGGAAATCATATGCTTAAATGATCAAATTTGTCTTCTTAGTCT
1 TACATTTATCCAAATCGCAAAGGGGAAATCATATGCTTAAATGATCAAAGTCGTCTTCTTAGTCT
* *
11621914 TATGTTTATTGTTACTGCATTATTTATTAAGCTAAATTAAATTAGGCATAAACAACAAATATTAG
66 TATGTTTATTGTTACTACATTATTTACTAAGCTAAATTAAATTAGGCATAAACAACAAATATTAG
* * *
11621979 CCATTACTTCCAATCATTATGTTAAATTACATAAAAAAAACAACCAATATTGGTTAATCAACATT
131 CCATTACTTCCAAGCATAATGTTAAATTACAT--AAAAAACAACCAATATTGGTCAATCAACATT
*
11622044 TGCAACTGCTAGCTGCA
194 TGCAACTGCTAACTGCA
* * *
11622061 TACATTTATCCAAATCGCAATGGGGAAATCATATGCTTAAATTATCAAGGTCGTCCTT-TTAGTC
1 TACATTTATCCAAATCGCAAAGGGGAAATCATATGCTTAAATGATCAAAGTCGT-CTTCTTAGTC
*
11622125 TTATGTTTATTGTTACTACATTATTTACTAAGCTAAATTAAATTAGGCATAAACAACAAATATTG
65 TTATGTTTATTGTTACTACATTATTTACTAAGCTAAATTAAATTAGGCATAAACAACAAATATTA
* *
11622190 GTCATTACTTCCAAGCATAATGTTAAATTACATAAAAAACAACCAATATTTGTCAATCAACATTT
130 GCCATTACTTCCAAGCATAATGTTAAATTACATAAAAAACAACCAATATTGGTCAATCAACATTT
11622255 GCAACTGCTAACTGCA
195 GCAACTGCTAACTGCA
11622271 TA
1 TA
11622273 TGCCTCTTAC
Statistics
Matches: 196, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
210 47 0.24
212 146 0.74
213 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (210 bp):
TACATTTATCCAAATCGCAAAGGGGAAATCATATGCTTAAATGATCAAAGTCGTCTTCTTAGTCT
TATGTTTATTGTTACTACATTATTTACTAAGCTAAATTAAATTAGGCATAAACAACAAATATTAG
CCATTACTTCCAAGCATAATGTTAAATTACATAAAAAACAACCAATATTGGTCAATCAACATTTG
CAACTGCTAACTGCA
Found at i:11623377 original size:18 final size:18
Alignment explanation
Indices: 11623354--11623410 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
11623344 AAAGTTTTAG
11623354 GGATTTCAAGAATATTTT
1 GGATTTCAAGAATATTTT
* **
11623372 GGATTTGTAA-AAGT-TTAG
1 GGATTT-CAAGAA-TATTTT
11623390 GGATTTCAAGAATATTTT
1 GGATTTCAAGAATATTTT
11623408 GGA
1 GGA
11623411 ATGCTAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
17 3 0.10
18 23 0.79
19 3 0.10
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (18 bp):
GGATTTCAAGAATATTTT
Found at i:11623396 original size:36 final size:37
Alignment explanation
Indices: 11623336--11623410 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 37
11623326 CCAACGGTTT
11623336 GATTTGTAAAAGTTTTAGGGATTTCAAGAATATTTTG
1 GATTTGTAAAAGTTTTAGGGATTTCAAGAATATTTTG
11623373 GATTTGTAAAAG-TTTAGGGATTTCAAGAATATTTTG
1 GATTTGTAAAAGTTTTAGGGATTTCAAGAATATTTTG
11623409 GA
1 GA
11623411 ATGCTAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 26 0.68
37 12 0.32
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.41
Consensus pattern (37 bp):
GATTTGTAAAAGTTTTAGGGATTTCAAGAATATTTTG
Found at i:11623912 original size:16 final size:16
Alignment explanation
Indices: 11623891--11623925 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11623881 TGTTCTTTTA
11623891 TTGTTTTCATTTGATT
1 TTGTTTTCATTTGATT
* *
11623907 TTGTTTTCCTTTGTTT
1 TTGTTTTCATTTGATT
11623923 TTG
1 TTG
11623926 AAAAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.09, G:0.14, T:0.71
Consensus pattern (16 bp):
TTGTTTTCATTTGATT
Found at i:11629484 original size:5 final size:5
Alignment explanation
Indices: 11629476--11629504 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
11629466 AAAAAGGGGA
11629476 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
11629505 AAGAACCCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:11630014 original size:17 final size:17
Alignment explanation
Indices: 11629992--11630025 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11629982 AGATGATGAG
11629992 AAATGAAAAAGTGAAAA
1 AAATGAAAAAGTGAAAA
*
11630009 AAATGAAAAATTGAAAA
1 AAATGAAAAAGTGAAAA
11630026 GTAAAATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (17 bp):
AAATGAAAAAGTGAAAA
Found at i:11634778 original size:16 final size:16
Alignment explanation
Indices: 11634757--11634791 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11634747 TGTTCTTTTA
11634757 TTGTTTTCATTTGATT
1 TTGTTTTCATTTGATT
* *
11634773 TTGTTTTCCTTTGTTT
1 TTGTTTTCATTTGATT
11634789 TTG
1 TTG
11634792 AAAAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.09, G:0.14, T:0.71
Consensus pattern (16 bp):
TTGTTTTCATTTGATT
Found at i:11652803 original size:35 final size:35
Alignment explanation
Indices: 11652763--11652878 Score: 232
Period size: 35 Copynumber: 3.3 Consensus size: 35
11652753 GAGAGCGATT
11652763 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
1 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
11652798 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
1 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
11652833 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
1 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
11652868 GAGCAATACAT
1 GAGCAATACAT
11652879 AATTGAATCT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 81 1.00
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (35 bp):
GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
Found at i:11664788 original size:153 final size:153
Alignment explanation
Indices: 11664619--11664905 Score: 438
Period size: 153 Copynumber: 1.9 Consensus size: 153
11664609 TATTTAAATG
* * *
11664619 TTTATTTTTTACTTTATAACACCATGTCTAAAATG-GACATTTTATTTTTTAAAAGCACTTTTTG
1 TTTATTTGTTACTTTATAACACCATATCTAAAATGAG-CATTTTATTTCTTAAAAGCACTTTTTG
*
11664683 AC-GACAATACT-AACACTTAAATCTTAAA-CTAAACTTTTCAAAACTACTCCTCAAAATCACTT
65 ACAG-CAATACTAAACACTTAAATCTTAAATC-AAAATTTTCAAAACTACTCCTCAAAATCACTT
11664745 TTCTAAAATACTTTTTAAAATAGGCAT
128 TT-TAAAATACTTTTTAAAATAGGCAT
*
11664772 TTTATTTGTTACTTTATAACACCATATCTAAAATGAGCATTTTATTTCTTAAAATCACTTTTTGA
1 TTTATTTGTTACTTTATAACACCATATCTAAAATGAGCATTTTATTTCTTAAAAGCACTTTTTGA
* * *
11664837 CAGCAATACTAAACACTTAAATTTTAAATCAAAATTTTTAAAACTACTTCTCAAAATCACTTTTT
66 CAGCAATACTAAACACTTAAATCTTAAATCAAAATTTTCAAAACTACTCCTCAAAATCACTTTTT
11664902 AAAA
131 AAAA
11664906 GCACTTTGTC
Statistics
Matches: 122, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
153 72 0.59
154 49 0.40
155 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (153 bp):
TTTATTTGTTACTTTATAACACCATATCTAAAATGAGCATTTTATTTCTTAAAAGCACTTTTTGA
CAGCAATACTAAACACTTAAATCTTAAATCAAAATTTTCAAAACTACTCCTCAAAATCACTTTTT
AAAATACTTTTTAAAATAGGCAT
Found at i:11667533 original size:32 final size:33
Alignment explanation
Indices: 11667481--11667545 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
11667471 ACTCTAATTA
11667481 ATAGGCTTGAGTCCCATCCCTTTTGAGGCCATT
1 ATAGGCTTGAGTCCCATCCCTTTTGAGGCCATT
11667514 ATAGGCTTGA-TCCCATCCCTTTTGAGGCCATT
1 ATAGGCTTGAGTCCCATCCCTTTTGAGGCCATT
11667546 TTTACTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 22 0.69
33 10 0.31
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (33 bp):
ATAGGCTTGAGTCCCATCCCTTTTGAGGCCATT
Found at i:11672077 original size:27 final size:27
Alignment explanation
Indices: 11672044--11672186 Score: 160
Period size: 27 Copynumber: 5.3 Consensus size: 27
11672034 TCATCTCCTA
*
11672044 GGGTATTTTGGTCATTTTACCCTATGG
1 GGGTATTTCGGTCATTTTACCCTATGG
* *
11672071 GGGTATTTCGATCATTTTACCCTATAG
1 GGGTATTTCGGTCATTTTACCCTATGG
* **
11672098 CGGTATTTCAATCATTTTACCCTATGG
1 GGGTATTTCGGTCATTTTACCCTATGG
** * * *
11672125 GGGTATTTTAGTCATTTTATCTTATGA
1 GGGTATTTCGGTCATTTTACCCTATGG
* *
11672152 GGGTATTTCGGTCATTTTATCTTATGG
1 GGGTATTTCGGTCATTTTACCCTATGG
*
11672179 CGGTATTT
1 GGGTATTT
11672187 TTGTTATTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 100 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCCTATGG
Found at i:11672187 original size:54 final size:53
Alignment explanation
Indices: 11672042--11672199 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 53
11672032 TTTCATCTCC
* *
11672042 TAGGGTATTTTGGTCATTTTACCCTATGGGGGTA-TTTCGATCATTTTACCCTA
1 TAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTTAG-TCATTTTACCCTA
** * *
11672095 TAGCGGTATTTCAATCATTTTACCCTATGGGGGTATTTTAGTCATTTTATCTTA
1 TAG-GGTATTTCGGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTA
* * * * *
11672149 TGAGGGTATTTCGGTCATTTTATCTTATGGCGGTATTTTTGTTATTTTACC
1 T-AGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACC
11672200 TATTTTAAGG
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
53 3 0.03
54 79 0.90
55 6 0.07
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.47
Consensus pattern (53 bp):
TAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTA
Found at i:11674876 original size:37 final size:36
Alignment explanation
Indices: 11674781--11674876 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 36
11674771 GTCTCCAATT
* * *
11674781 TCACATTTTAATTCAATTTCACTTTTTCACTTCCAA
1 TCACAATTCAATTCAATTTCACTTTTCCACTTCCAA
* * *
11674817 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAA
1 TCACAATTCAATTC-AATTTCACTTTTCCACTTCCAA
*
11674854 GTCA-ATATTCATTTCAATTTCAC
1 -TCACA-ATTCAATTCAATTTCAC
11674877 ACGTATATTC
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
36 12 0.24
37 26 0.53
38 11 0.22
ACGTcount: A:0.31, C:0.24, G:0.01, T:0.44
Consensus pattern (36 bp):
TCACAATTCAATTCAATTTCACTTTTCCACTTCCAA
Found at i:11685139 original size:25 final size:25
Alignment explanation
Indices: 11685082--11685139 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
11685072 AGGGTCATAC
*
11685082 GGCCATGTCCCACCCCCATGTGCTA
1 GGCCGTGTCCCACCCCCATGTGCTA
** *
11685107 GGTTGTGTCCCACGCCCATGTGCTA
1 GGCCGTGTCCCACCCCCATGTGCTA
11685132 GGCCGTGT
1 GGCCGTGT
11685140 AACTCTCTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.12, C:0.36, G:0.28, T:0.24
Consensus pattern (25 bp):
GGCCGTGTCCCACCCCCATGTGCTA
Found at i:11692766 original size:51 final size:52
Alignment explanation
Indices: 11692686--11692784 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 52
11692676 TGAAATAGTT
* *
11692686 TGAAGTAGTTGCTTGTCGCTAAAGAATTGAGAAATTATATATA-TTGTGATC
1 TGAAGTAGGTGCTTGTCGATAAAGAATTGAGAAATTATATATAGTTGTGATC
* *
11692737 TGAAGTAGGTGCTTGTCTATAAA-ACATTGAGAATTTATATATAGTTGT
1 TGAAGTAGGTGCTTGTCGATAAAGA-ATTGAGAAATTATATATAGTTGT
11692785 AGTTTAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
50 1 0.02
51 37 0.88
52 4 0.10
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (52 bp):
TGAAGTAGGTGCTTGTCGATAAAGAATTGAGAAATTATATATAGTTGTGATC
Found at i:11695620 original size:16 final size:17
Alignment explanation
Indices: 11695601--11695632 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11695591 TTATGGAAGA
11695601 GAAATAA-TAGTTGGAT
1 GAAATAATTAGTTGGAT
11695617 GAAATAATTAGTTGGA
1 GAAATAATTAGTTGGA
11695633 ATAGATCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (17 bp):
GAAATAATTAGTTGGAT
Found at i:11703800 original size:41 final size:41
Alignment explanation
Indices: 11703743--11703930 Score: 295
Period size: 41 Copynumber: 4.6 Consensus size: 41
11703733 AGTAAGATGA
* *
11703743 TTCAGACTTTAAGTCTAGCAGGCTTGATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
* *
11703784 TTCAGACTTTACGTCTAGCAGGCTTGATGCCAGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
11703825 TTTAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
* *
11703866 TTCTGACTTTACGTCTAGCAGGCTTAATACCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
* *
11703907 TTCTGACTTTAAGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
11703931 AATTGCTGGT
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 138 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
Found at i:11703966 original size:123 final size:123
Alignment explanation
Indices: 11703747--11703984 Score: 275
Period size: 123 Copynumber: 1.9 Consensus size: 123
11703737 AGATGATTCA
* * * *
11703747 GACTTTAAGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCTTGAT
1 GACTTTAAGTCTAGCAGGCTTAATACCGGTGAAATATTTCAGACTTTAAGTCTAGCAGGCTTAAT
* * * *
11703812 GCCAGTGAAATATTTTAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTGAAATATTTCT
66 GCCAGTGAAATATATCAGACTTTAAGCCTAGCAGGC-TAAGTGCCGGTGAAATATTTCT
* *
11703870 GACTTTACGTCTAGCAGGCTTAATACCGGTGAAATATTTCTGACTTTAAGTCTAGCAGGC-TAAT
1 GACTTTAAGTCTAGCAGGCTTAATACCGGTGAAATATTTCAGACTTTAAGTCTAGCAGGCTTAA-
** * * ** *
11703934 TGCTGGTGTACTGA-ATCAGGTTTTAAGCCTAGCAGGCTAAGTGCTGGTGAA
65 TGCCAGTGAAAT-ATATCAGACTTTAAGCCTAGCAGGCTAAGTGCCGGTGAA
11703985 TCTGTTTAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
122 5 0.05
123 89 0.94
124 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (123 bp):
GACTTTAAGTCTAGCAGGCTTAATACCGGTGAAATATTTCAGACTTTAAGTCTAGCAGGCTTAAT
GCCAGTGAAATATATCAGACTTTAAGCCTAGCAGGCTAAGTGCCGGTGAAATATTTCT
Found at i:11706674 original size:22 final size:22
Alignment explanation
Indices: 11706648--11706689 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11706638 AATACGAGAA
11706648 AATATGGAACTAAAAAGAAATG
1 AATATGGAACTAAAAAGAAATG
* *
11706670 AATATGGAACTGAGAAGAAA
1 AATATGGAACTAAAAAGAAA
11706690 AGTTATCGAT
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:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (22 bp):
AATATGGAACTAAAAAGAAATG
Done.