Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 89 of 141
Found at i:28863752 original size:20 final size:20
Alignment explanation
Indices: 28863723--28863760 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28863713 ATAATTATAT
* *
28863723 TAATTGTATATGTTAAATAA
1 TAATTATATATATTAAATAA
28863743 TAATTATATATATTAAAT
1 TAATTATATATATTAAAT
28863761 CATCAACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TAATTATATATATTAAATAA
Found at i:28863851 original size:15 final size:16
Alignment explanation
Indices: 28863833--28863863 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28863823 TATATTTATG
28863833 ATAAAT-TTTTTTAAT
1 ATAAATATTTTTTAAT
28863848 ATAAATATTTTTTAAT
1 ATAAATATTTTTTAAT
28863864 GTGTTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATATTTTTTAAT
Found at i:28865176 original size:15 final size:16
Alignment explanation
Indices: 28865158--28865188 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28865148 TATATTTATG
28865158 ATAAAT-TTTTTTAAT
1 ATAAATATTTTTTAAT
28865173 ATAAATATTTTTTAAT
1 ATAAATATTTTTTAAT
28865189 GTGTTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATATTTTTTAAT
Found at i:28869813 original size:32 final size:32
Alignment explanation
Indices: 28869776--28869844 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
28869766 AGTCATTGGT
*
28869776 CTCGTGTTTGTTGCTGTTTCGGTTTAGGTAAG
1 CTCGTGTTTGTTGCTGTTTCGATTTAGGTAAG
28869808 CTCGTGTTTGTTGCTGTTTCGATTTAGGTAAG
1 CTCGTGTTTGTTGCTGTTTCGATTTAGGTAAG
28869840 CTCGT
1 CTCGT
28869845 ATAATGATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.10, C:0.14, G:0.29, T:0.46
Consensus pattern (32 bp):
CTCGTGTTTGTTGCTGTTTCGATTTAGGTAAG
Found at i:28875949 original size:20 final size:20
Alignment explanation
Indices: 28875921--28875969 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
28875911 GAATCTTTGA
* *
28875921 TTTTCTTTCTATCTTTGTTG
1 TTTTATTTCTATCCTTGTTG
*
28875941 TTTTATTTCTTTCCTTGTTG
1 TTTTATTTCTATCCTTGTTG
*
28875961 TTTTGTTTC
1 TTTTATTTC
28875970 CTTGCAGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.04, C:0.14, G:0.10, T:0.71
Consensus pattern (20 bp):
TTTTATTTCTATCCTTGTTG
Found at i:28876418 original size:21 final size:21
Alignment explanation
Indices: 28876392--28876446 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
28876382 CGAAGGCTGC
*
28876392 ACAGAAGCACATAAGTGCTAA
1 ACAGAAGCACATAAGGGCTAA
* * * *
28876413 ACAGAAACCCGTAAGGGTTAA
1 ACAGAAGCACATAAGGGCTAA
*
28876434 ACAGAAGCTCATA
1 ACAGAAGCACATA
28876447 GCAGCTGAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (21 bp):
ACAGAAGCACATAAGGGCTAA
Found at i:28876536 original size:42 final size:41
Alignment explanation
Indices: 28876416--28876536 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 41
28876406 GTGCTAAACA
* *
28876416 GAAACCCGTAAGGGTTAAACAGAAGCTCATAGCAGCTGAATG
1 GAAACCCATAAGGGTTAAACAGAAGCTCATAG-AGTTGAATG
* * * *
28876458 GAAATCTATAAGGGTTAAACTGAAGCTCAAAAGAGTTGAATG
1 GAAACCCATAAGGGTTAAACAGAAGCTC-ATAGAGTTGAATG
* *
28876500 GAAGCCCATAAGGGTTAAACAGAAACTCATATGAGTT
1 GAAACCCATAAGGGTTAAACAGAAGCTCATA-GAGTT
28876537 AACAGAAGCT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.03
42 60 0.92
43 3 0.05
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (41 bp):
GAAACCCATAAGGGTTAAACAGAAGCTCATAGAGTTGAATG
Found at i:28876647 original size:24 final size:24
Alignment explanation
Indices: 28876615--28876662 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
28876605 TACTTAGGTA
*
28876615 ATTTGCCATCAATTCATCATTTGC
1 ATTTACCATCAATTCATCATTTGC
28876639 ATTTACCATCAATTCATCATTTGC
1 ATTTACCATCAATTCATCATTTGC
28876663 CACAGAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (24 bp):
ATTTACCATCAATTCATCATTTGC
Found at i:28881164 original size:25 final size:25
Alignment explanation
Indices: 28881130--28881194 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
28881120 CATTTCACAG
28881130 CTCGTGTGAGCATTTA-CAGTTACAA
1 CTCGTGTGAGCATTTATC-GTTACAA
* *
28881155 CTCGTGTGAGCAATTATCGTTATAA
1 CTCGTGTGAGCATTTATCGTTACAA
*
28881180 CTCGTGTGATCATTT
1 CTCGTGTGAGCATTT
28881195 TCCCTCGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 34 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (25 bp):
CTCGTGTGAGCATTTATCGTTACAA
Found at i:28888818 original size:28 final size:29
Alignment explanation
Indices: 28888782--28888845 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
28888772 AAAGGAATGT
* * * **
28888782 CTTTGTGGCAATTTCTG-TAAATGGATGC
1 CTTTATGGCAATCTCTGTTAAAAGGACAC
*
28888810 CTTTATGGCTATCTCTGTTAAAAGGACAC
1 CTTTATGGCAATCTCTGTTAAAAGGACAC
28888839 CTTTATG
1 CTTTATG
28888846 ACTCTCTTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (29 bp):
CTTTATGGCAATCTCTGTTAAAAGGACAC
Found at i:28895184 original size:18 final size:18
Alignment explanation
Indices: 28895161--28895221 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
28895151 TACTAGCTAA
28895161 TATTGATCAGCAAAGTGG
1 TATTGATCAGCAAAGTGG
* * **
28895179 TATTGATTTA-C-AGGCTAA
1 TATTGA-TCAGCAAAG-TGG
28895197 TATTGATCAGCAAAGTGG
1 TATTGATCAGCAAAGTGG
28895215 TATTGAT
1 TATTGAT
28895222 GATAGAAGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
17 4 0.13
18 23 0.74
19 4 0.13
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (18 bp):
TATTGATCAGCAAAGTGG
Found at i:28903262 original size:21 final size:21
Alignment explanation
Indices: 28903236--28903278 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28903226 CGCGAATCAA
28903236 TTTTTTATATTAAA-AAAATAT
1 TTTTTTAT-TTAAATAAAATAT
*
28903257 TTTTTTGTTTAAATAAAATAT
1 TTTTTTATTTAAATAAAATAT
28903278 T
1 T
28903279 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTTATTTAAATAAAATAT
Found at i:28903287 original size:20 final size:20
Alignment explanation
Indices: 28903245--28903287 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
28903235 ATTTTTTATA
**
28903245 TTAAAAAAATATTTTTTTGT
1 TTAAAAAAATATTAATTTGT
28903265 TTAAATAAAATATTAATTT-T
1 TTAAA-AAAATATTAATTTGT
28903285 TTA
1 TTA
28903288 TTTTTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTAAAAAAATATTAATTTGT
Found at i:28903865 original size:17 final size:17
Alignment explanation
Indices: 28903845--28903883 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28903835 GAAAAGAGAG
28903845 AAAGGAGAAAAAAAAAA
1 AAAGGAGAAAAAAAAAA
* *
28903862 AAAGAAGAAAGAAAAAA
1 AAAGGAGAAAAAAAAAA
28903879 AAAGG
1 AAAGG
28903884 TAATGTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAGGAGAAAAAAAAAA
Found at i:28903870 original size:24 final size:23
Alignment explanation
Indices: 28903836--28903881 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
28903826 AGAGAGAAAG
28903836 AAAAGAGAGAAAGGAGAAAAAAAAA
1 AAAAGAGAGAAA-GA-AAAAAAAAA
28903861 AAAAGA-AGAAAGAAAAAAAAA
1 AAAAGAGAGAAAGAAAAAAAAA
28903882 GGTAATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 2 0.10
24 5 0.24
25 6 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (23 bp):
AAAAGAGAGAAAGAAAAAAAAAA
Found at i:28904109 original size:60 final size:60
Alignment explanation
Indices: 28904044--28904162 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
28904034 TTGCTTTTTA
* * *
28904044 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTTG
28904104 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
28904163 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTTG
Found at i:28904989 original size:202 final size:202
Alignment explanation
Indices: 28904643--28905044 Score: 795
Period size: 202 Copynumber: 2.0 Consensus size: 202
28904633 ACAAGTAGGA
28904643 TATGAATCTTCGAATTCCATTTAATGCACTTTTAGGGAATTTTTTTATTGTAGGTAAATTAGGGA
1 TATGAATCTTCGAATTCCATTTAATGCACTTTTAGGGAATTTTTTTATTGTAGGTAAATTAGGGA
28904708 ATCTTCGAATTCCATTTAATGCACTTTTAGGTAGTTTTGGTCGTGTTTTGTTTCTGAAATTTGAA
66 ATCTTCGAATTCCATTTAATGCACTTTTAGGTAGTTTTGGTCGTGTTTTGTTTCTGAAATTTGAA
*
28904773 ATAATTTATTGTATTTTTTGAAACAAATTAAATGAATTCATTTTTTTAATTGCAGATTTGCAGTA
131 ATAATTTATTGTATTTTTTGAAACAAATTAAATGAATTCATTTTTTTAATTGCAGATTTGCAGCA
28904838 AATGGAT
196 AATGGAT
28904845 TATGAATCTTCGAATTCCATTTAATGCACTTTTAGGGAATTTTTTTATTGTAGGTAAATTAGGGA
1 TATGAATCTTCGAATTCCATTTAATGCACTTTTAGGGAATTTTTTTATTGTAGGTAAATTAGGGA
28904910 ATCTTCGAATTCCATTTAATGCACTTTTAGGTAGTTTTGGTCGTGTTTTGTTTCTGAAATTTGAA
66 ATCTTCGAATTCCATTTAATGCACTTTTAGGTAGTTTTGGTCGTGTTTTGTTTCTGAAATTTGAA
28904975 ATAATTTATTGTATTTTTTGAAACAAATTAAATGAATTCATTTTTTTAATTGCAGATTTGCAGCA
131 ATAATTTATTGTATTTTTTGAAACAAATTAAATGAATTCATTTTTTTAATTGCAGATTTGCAGCA
28905040 AATGG
196 AATGG
28905045 GTTCTTTGAT
Statistics
Matches: 199, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 199 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.45
Consensus pattern (202 bp):
TATGAATCTTCGAATTCCATTTAATGCACTTTTAGGGAATTTTTTTATTGTAGGTAAATTAGGGA
ATCTTCGAATTCCATTTAATGCACTTTTAGGTAGTTTTGGTCGTGTTTTGTTTCTGAAATTTGAA
ATAATTTATTGTATTTTTTGAAACAAATTAAATGAATTCATTTTTTTAATTGCAGATTTGCAGCA
AATGGAT
Found at i:28906585 original size:6 final size:6
Alignment explanation
Indices: 28906574--28906615 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
28906564 GCATCATGCA
* *
28906574 CCAGAG CCAGAG CTAGAG CCAGAG CCAGAG CCGGAG CCAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
28906616 ACGGAACTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.31, C:0.31, G:0.36, T:0.02
Consensus pattern (6 bp):
CCAGAG
Found at i:28906815 original size:33 final size:34
Alignment explanation
Indices: 28906754--28906856 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 34
28906744 AGTCATCCTA
* * **
28906754 GCTC-GTATCCACTTCAGTACTCTGCTCCTTCCG
1 GCTCTGTATACACCTCAGTACTCCACTCCTTCCG
* **
28906787 GCTC-GTATATACCTCAGTACTCCACTCCTTTTG
1 GCTCTGTATACACCTCAGTACTCCACTCCTTCCG
* * *
28906820 GC-CTGTATCCACCGCCGTACTCCACTCCTTCCG
1 GCTCTGTATACACCTCAGTACTCCACTCCTTCCG
28906853 GCTC
1 GCTC
28906857 AAGTTCATCG
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
32 1 0.02
33 53 0.96
34 1 0.02
ACGTcount: A:0.14, C:0.41, G:0.15, T:0.31
Consensus pattern (34 bp):
GCTCTGTATACACCTCAGTACTCCACTCCTTCCG
Found at i:28910351 original size:27 final size:26
Alignment explanation
Indices: 28910313--28910370 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
28910303 CCACCATTCA
*
28910313 CGCCTCTGAGTTAGGCACAACTAGTC
1 CGCCTCTGAGTTAAGCACAACTAGTC
* *
28910339 GCGCCTTTGAGTTAAGCTCAACTAGTC
1 -CGCCTCTGAGTTAAGCACAACTAGTC
28910366 CGCCT
1 CGCCT
28910371 ATCAAATAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (26 bp):
CGCCTCTGAGTTAAGCACAACTAGTC
Found at i:28910745 original size:192 final size:194
Alignment explanation
Indices: 28910409--28910791 Score: 603
Period size: 192 Copynumber: 2.0 Consensus size: 194
28910399 TCTATACCCG
*
28910409 GGTTATATACTGACCCGAGAAAAAAATTAATAATATTTTATTAAACGAGAAAAAATAAAATATTT
1 GGTTATATACTGACCCGAGAAAAAAATTAATAATATTTTATTAAACAAGAAAAAATAAAATATTT
* * * *
28910474 TAATATAAAAATTTGATTCGCGCCTGTCAGATAGGCGCAATTAAAGAAACGTACCATTTCGGTAA
66 TAATATAAAAAATTGATTCGCGCCTGTCAGATAGGCACAATTAAAGAAACATACCATTTCGATAA
* *
28910539 TTAATTTAGCTGACAACCTATTTAGGTATTTAAA-TTTTTTTAATATATTTGGGCAAAAAACCT
131 TTAATCTAGCTGACAACCTATTTAGGTATTTAAATTTTTTTTAATATATTTGAGCAAAAAACCT
* *
28910602 GGTTATATACTGATCCGGGAAAAAAA-TAATAATATTTTATTAAAACAAG-AAAAA-AAAATATT
1 GGTTATATACTGACCCGAGAAAAAAATTAATAATATTTTATT-AAACAAGAAAAAATAAAATATT
* * *
28910664 TTAATATAAAAAATTGATTCGTGCCTGTCAGATAGGTACGATTAAAGAAAACATACCATTTCGAT
65 TTAATATAAAAAATTGATTCGCGCCTGTCAGATAGGCACAATTAAAG-AAACATACCATTTCGAT
*
28910729 AATTAATCTAGCTGACAACCTATTTAGGTATTTAAATTTTTTTTAATATATTTGAGTAAAAAA
129 AATTAATCTAGCTGACAACCTATTTAGGTATTTAAATTTTTTTTAATATATTTGAGCAAAAAA
28910792 AACCCCTCAA
Statistics
Matches: 174, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
191 50 0.29
192 70 0.40
193 54 0.31
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (194 bp):
GGTTATATACTGACCCGAGAAAAAAATTAATAATATTTTATTAAACAAGAAAAAATAAAATATTT
TAATATAAAAAATTGATTCGCGCCTGTCAGATAGGCACAATTAAAGAAACATACCATTTCGATAA
TTAATCTAGCTGACAACCTATTTAGGTATTTAAATTTTTTTTAATATATTTGAGCAAAAAACCT
Found at i:28912872 original size:14 final size:14
Alignment explanation
Indices: 28912855--28912882 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28912845 CTTTCTTGGG
28912855 AAATTCTACTTGTC
1 AAATTCTACTTGTC
28912869 AAATTCTACTTGTC
1 AAATTCTACTTGTC
28912883 GTTTGGAATG
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:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
AAATTCTACTTGTC
Found at i:28915825 original size:7 final size:7
Alignment explanation
Indices: 28915814--28915853 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
28915804 TCCTCAATCC
28915814 TCAATTT
1 TCAATTT
*
28915821 CCAATTT
1 TCAATTT
*
28915828 TCTATTT
1 TCAATTT
28915835 TCAATTT
1 TCAATTT
*
28915842 TTAATTT
1 TCAATTT
28915849 TCAAT
1 TCAAT
28915854 CCTCAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (7 bp):
TCAATTT
Found at i:28915859 original size:21 final size:21
Alignment explanation
Indices: 28915807--28915860 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
28915797 TTCCCAATCC
28915807 TCAATCCTCAATTTCCAATTT
1 TCAATCCTCAATTTCCAATTT
* ** **
28915828 TCTATTTTCAATTTTTAATTT
1 TCAATCCTCAATTTCCAATTT
28915849 TCAATCCTCAAT
1 TCAATCCTCAAT
28915861 AATTTTTTAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (21 bp):
TCAATCCTCAATTTCCAATTT
Found at i:28917668 original size:54 final size:54
Alignment explanation
Indices: 28917596--28917825 Score: 208
Period size: 54 Copynumber: 4.1 Consensus size: 54
28917586 TTACAAGCAT
* * * * * * ** *
28917596 CACAACACGCACACTCATTCCCCACATCATCACCTTCAGCTTCGATTTATTTTA
1 CACAACATGCGCAATCATTCCCTACATCAACACATTCAGCACCAATTTATTTTA
* *
28917650 TACAACATGCGCAATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTA
1 CACAACATGCGCAATCATTCCCTACATCAACACATTCAGCACCAATTTATTTTA
* * ** **
28917704 CACAAGCATCATGACACGCACATTCATTCCCTACATCATCACCTTCAGCTTCGGTTTATTTTA
1 CAC-A--A-CATG---CGCA-A-TCATTCCCTACATCAACACATTCAGCACCAATTTATTTTA
* *
28917767 TACAACATGCGCAATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTA
1 CACAACATGCGCAATCATTCCCTACATCAACACATTCAGCACCAATTTATTTTA
28917821 CACAA
1 CACAA
28917826 ACATCACGAC
Statistics
Matches: 139, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
54 82 0.59
55 2 0.01
56 4 0.03
57 1 0.01
58 4 0.03
59 4 0.03
60 1 0.01
61 4 0.03
62 2 0.01
63 35 0.25
ACGTcount: A:0.31, C:0.32, G:0.07, T:0.30
Consensus pattern (54 bp):
CACAACATGCGCAATCATTCCCTACATCAACACATTCAGCACCAATTTATTTTA
Found at i:28917741 original size:63 final size:61
Alignment explanation
Indices: 28917659--28917862 Score: 226
Period size: 63 Copynumber: 3.4 Consensus size: 61
28917649 ATACAACATG
28917659 CGCA-ATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTACACAAGCATCATGACA
1 CGCACATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTACACAA-CATCATGACA
* * * ** ** *
28917720 CGCACATTCATTCCCTACATCATCACCTTCAGCTTCGGTTTATTTTATAC-A-A-CATG---
1 CGCACA-TCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTACACAACATCATGACA
*
28917776 CGCA-ATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTACACAAACATCACGACA
1 CGCACATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTACAC-AACATCATGACA
*
28917837 CGCACAATCATTCCCTGTATCAACAC
1 CGCAC-ATCATTCCCTGCATCAACAC
28917863 CTTCTCTAGG
Statistics
Matches: 114, Mismatches: 18, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
54 35 0.31
55 1 0.01
56 5 0.04
57 1 0.01
58 3 0.03
59 4 0.04
60 1 0.01
61 8 0.07
62 2 0.02
63 54 0.47
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (61 bp):
CGCACATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTACACAACATCATGACA
Found at i:28917782 original size:117 final size:117
Alignment explanation
Indices: 28917588--28917866 Score: 468
Period size: 117 Copynumber: 2.4 Consensus size: 117
28917578 TTTTTTTGTT
* * *
28917588 ACAAGCATCACAACACGCACACTCATTCCCCACATCATCACCTTCAGCTTCGATTTATTTTATAC
1 ACAAGCATCACGACACGCACAATCATTCCCTACATCATCACCTTCAGCTTCGATTTATTTTATAC
28917653 AACATGCGCAATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTAC
66 AACATGCGCAATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTAC
* * *
28917705 ACAAGCATCATGACACGCACATTCATTCCCTACATCATCACCTTCAGCTTCGGTTTATTTTATAC
1 ACAAGCATCACGACACGCACAATCATTCCCTACATCATCACCTTCAGCTTCGATTTATTTTATAC
28917770 AACATGCGCAATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTAC
66 AACATGCGCAATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTAC
* ** *
28917822 ACAAACATCACGACACGCACAATCATTCCCTGTATCAACACCTTC
1 ACAAGCATCACGACACGCACAATCATTCCCTACATCATCACCTTC
28917867 TCTAGGGATA
Statistics
Matches: 151, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 151 1.00
ACGTcount: A:0.32, C:0.33, G:0.08, T:0.28
Consensus pattern (117 bp):
ACAAGCATCACGACACGCACAATCATTCCCTACATCATCACCTTCAGCTTCGATTTATTTTATAC
AACATGCGCAATCATTCCCTGCATCAACACATTCAGCACCAATTTATTTTAC
Found at i:28919927 original size:30 final size:30
Alignment explanation
Indices: 28919886--28919954 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
28919876 CTAAAAAGAA
*
28919886 AATATATTTTGTTTAACTTGACTTGCAAGC
1 AATATATTTTGTTTAAATTGACTTGCAAGC
*
28919916 AATACATTTTGTTTAAATTGACTTGCAAGC
1 AATATATTTTGTTTAAATTGACTTGCAAGC
28919946 AATATATTT
1 AATATATTT
28919955 AAATCTTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (30 bp):
AATATATTTTGTTTAAATTGACTTGCAAGC
Found at i:28922052 original size:41 final size:37
Alignment explanation
Indices: 28921950--28922053 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 37
28921940 AATTCGAAGT
**** *
28921950 AGTAAATTGACACTCAGTGTCTCATTGGTTAAACCGA
1 AGTAAATTGACACTCAGTGTCTCATCAAATAAACCAA
* * * *
28921987 AGTAAATTGGCATTGAGTGCCTCATCAAATAAATCCAA
1 AGTAAATTGACACTCAGTGTCTCATCAAATAAA-CCAA
28922025 AGTGATAAATTGACACTCAGTGTCTCATC
1 A--G-TAAATTGACACTCAGTGTCTCATC
28922054 GGCTCGAAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
37 25 0.50
38 4 0.08
40 1 0.02
41 20 0.40
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (37 bp):
AGTAAATTGACACTCAGTGTCTCATCAAATAAACCAA
Found at i:28922940 original size:13 final size:14
Alignment explanation
Indices: 28922922--28922956 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
28922912 AAGGTCGTGC
28922922 TTTTC-TTCTTTCT
1 TTTTCTTTCTTTCT
28922935 TTTTCTTTCTTTC-
1 TTTTCTTTCTTTCT
28922948 TTTTCTTTC
1 TTTTCTTTC
28922957 CAAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:28924415 original size:50 final size:50
Alignment explanation
Indices: 28924357--28924456 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
28924347 GACTCCAATG
28924357 AAATGAGCTGATTTTGTAAGTCGATCAACAATCACCCATAAAAAAATTTT
1 AAATGAGCTGATTTTGTAAGTCGATCAACAATCACCCATAAAAAAATTTT
28924407 AAATGAGCTGATTTTGTAAGTCGATCAACAATCACCCATAAAAAAATTTT
1 AAATGAGCTGATTTTGTAAGTCGATCAACAATCACCCATAAAAAAATTTT
28924457 CTTACTTGCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (50 bp):
AAATGAGCTGATTTTGTAAGTCGATCAACAATCACCCATAAAAAAATTTT
Found at i:28926724 original size:26 final size:25
Alignment explanation
Indices: 28926689--28926756 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 25
28926679 CCATCAATTC
*
28926689 ATAATCGGGAATGCTCATACGAGCACAT
1 ATAAT-GGGAA-GCTCATACAAGC-CAT
* *
28926717 A-AATGGGAAGCTCTTTCAAGCCAT
1 ATAATGGGAAGCTCATACAAGCCAT
28926741 ATAATGGGAAGCTCAT
1 ATAATGGGAAGCTCAT
28926757 GTGAGCCATG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.11
25 22 0.63
26 5 0.14
27 3 0.09
28 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (25 bp):
ATAATGGGAAGCTCATACAAGCCAT
Found at i:28926763 original size:25 final size:25
Alignment explanation
Indices: 28926689--28926779 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
28926679 CCATCAATTC
*
28926689 ATAATCGGGAATGCTCATACGAGCACAT
1 ATAAT-GGGAA-GCTCATATGAGC-CAT
* *
28926717 A-AATGGGAAGCTC-TTTCAAGCCAT
1 ATAATGGGAAGCTCATAT-GAGCCAT
*
28926741 ATAATGGGAAGCTCATGTGAGCCAT
1 ATAATGGGAAGCTCATATGAGCCAT
* * *
28926766 GTAACGGAAAGCTC
1 ATAATGGGAAGCTC
28926780 CGGAGAGCCT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
24 5 0.10
25 36 0.69
26 7 0.13
27 3 0.06
28 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (25 bp):
ATAATGGGAAGCTCATATGAGCCAT
Found at i:28926872 original size:25 final size:25
Alignment explanation
Indices: 28926841--28926900 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
28926831 CGAGCTAATA
*
28926841 TCGGGAAGCTCCGGAGAGCCTTTAAT
1 TCGGGAAGCTCCGAAGAGCCTTT-AT
**
28926867 T-GGGAAGCTCTTAAGAGCCTTTAT
1 TCGGGAAGCTCCGAAGAGCCTTTAT
28926891 TCGGGAAGCT
1 TCGGGAAGCT
28926901 TCGAGGAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.10
25 26 0.87
26 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (25 bp):
TCGGGAAGCTCCGAAGAGCCTTTAT
Found at i:28927006 original size:24 final size:24
Alignment explanation
Indices: 28926979--28927048 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 24
28926969 CAATCAGGAT
28926979 GCTCCGAAGAGCTATTAACGGGAA
1 GCTCCGAAGAGCTATTAACGGGAA
* *
28927003 GCT-CGCAAGAACCATATAACGGGAA
1 GCTCCG-AAGAGCTAT-TAACGGGAA
* *
28927028 GCTCATG-AGAGCTAATAACGG
1 GCTC-CGAAGAGCTATTAACGG
28927049 AATGCTCTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 2 0.06
24 16 0.44
25 17 0.47
27 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.27, T:0.16
Consensus pattern (24 bp):
GCTCCGAAGAGCTATTAACGGGAA
Found at i:28928212 original size:136 final size:136
Alignment explanation
Indices: 28927998--28928269 Score: 535
Period size: 136 Copynumber: 2.0 Consensus size: 136
28927988 TATTATATAA
28927998 TATAATATATATACTTAACACTTAAAGTTTTATTTTGTAATATATATAATAAATTCACAAAAAAA
1 TATAATATATATACTTAACACTTAAAGTTTTATTTTGTAATATATATAATAAATTCACAAAAAAA
28928063 AAATCTACCTTATGCCGCCTCATAAAGAAACAATGGTATAATTGTTTCTTTAGTCCCGTTAATTT
66 AAATCTACCTTATGCCGCCTCATAAAGAAACAATGGTATAATTGTTTCTTTAGTCCCGTTAATTT
28928128 TTCTTT
131 TTCTTT
*
28928134 TATAATATATATATTTAACACTTAAAGTTTTATTTTGTAATATATATAATAAATTCACAAAAAAA
1 TATAATATATATACTTAACACTTAAAGTTTTATTTTGTAATATATATAATAAATTCACAAAAAAA
28928199 AAATCTACCTTATGCCGCCTCATAAAGAAACAATGGTATAATTGTTTCTTTAGTCCCGTTAATTT
66 AAATCTACCTTATGCCGCCTCATAAAGAAACAATGGTATAATTGTTTCTTTAGTCCCGTTAATTT
28928264 TTCTTT
131 TTCTTT
28928270 AATCTTTAAC
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (136 bp):
TATAATATATATACTTAACACTTAAAGTTTTATTTTGTAATATATATAATAAATTCACAAAAAAA
AAATCTACCTTATGCCGCCTCATAAAGAAACAATGGTATAATTGTTTCTTTAGTCCCGTTAATTT
TTCTTT
Found at i:28946255 original size:40 final size:40
Alignment explanation
Indices: 28946211--28946345 Score: 134
Period size: 37 Copynumber: 3.4 Consensus size: 40
28946201 ACAAGTTTGG
28946211 CACCCAGTGCCTCATCGGATAATTCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGATAATTCAAAGTAGTAAATTGA
* * * * * *
28946251 CACCCAGTGTCTCCTCGGTTAA-ACCAA--AGTAAATTGG
1 CACCCAGTGCCTCATCGGATAATTCAAAGTAGTAAATTGA
* * *
28946288 CACCTAGTGCCTCATCGAATAATTCCGAAGT-GATAAATTGA
1 CACCCAGTGCCTCATCGGATAATT-CAAAGTAG-TAAATTGA
*
28946329 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
28946346 ACTAAAAGTC
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
37 26 0.35
39 6 0.08
40 20 0.27
41 22 0.30
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGGATAATTCAAAGTAGTAAATTGA
Found at i:28947240 original size:14 final size:14
Alignment explanation
Indices: 28947221--28947278 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
28947211 GCGTTTCTTC
28947221 TTTCTTTTTCTTTA
1 TTTCTTTTTCTTTA
28947235 TTTC-TTTTCTTTCCAA
1 TTTCTTTTTCTTT---A
* *
28947251 TTTTGTTTTTCTTTC
1 -TTTCTTTTTCTTTA
28947266 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
28947279 TATTATACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
13 8 0.22
14 16 0.44
16 1 0.03
17 3 0.08
18 8 0.22
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTTCTTTA
Found at i:28952510 original size:46 final size:48
Alignment explanation
Indices: 28952457--28952551 Score: 131
Period size: 50 Copynumber: 2.0 Consensus size: 48
28952447 AATTATAGAA
*
28952457 AAATTTTAAATTCTATTC-A-GAGTTTTATAATTTCAAAACAAAATAC
1 AAATTTTAAATTCTAGTCAATGAGTTTTATAATTTCAAAACAAAATAC
**
28952503 AAATTTTAAATTCTAGTCAGAATGAGTTTTATGCTTTCAAAACAAAATA
1 AAATTTTAAATTCTAGTC--AATGAGTTTTATAATTTCAAAACAAAATA
28952552 AAAAATCTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
46 17 0.40
49 1 0.02
50 24 0.57
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (48 bp):
AAATTTTAAATTCTAGTCAATGAGTTTTATAATTTCAAAACAAAATAC
Found at i:28953270 original size:10 final size:9
Alignment explanation
Indices: 28953231--28953350 Score: 86
Period size: 10 Copynumber: 13.1 Consensus size: 9
28953221 CATGTGGCAA
28953231 AAAAATTAT
1 AAAAATTAT
28953240 AAAAA--AT
1 AAAAATTAT
*
28953247 AAAAATCAAT
1 AAAAAT-TAT
*
28953257 AAAAGTTAT
1 AAAAATTAT
28953266 AAAAATTATT
1 AAAAATTA-T
**
28953276 AAATTTTAAT
1 AAAAATT-AT
*
28953286 AAAAA-TAG
1 AAAAATTAT
*
28953294 AAAAA-TAG
1 AAAAATTAT
28953302 AAAAATTTAT
1 AAAAA-TTAT
28953312 AAAAATTTAT
1 AAAAA-TTAT
28953322 AAAAATTTAT
1 AAAAA-TTAT
*
28953332 AAAAATTGT
1 AAAAATTAT
*
28953341 AAAAAATAT
1 AAAAATTAT
28953350 A
1 A
28953351 TATATAAAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
7 7 0.08
8 14 0.15
9 26 0.28
10 44 0.48
11 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:28953327 original size:20 final size:19
Alignment explanation
Indices: 28953231--28953385 Score: 92
Period size: 20 Copynumber: 8.2 Consensus size: 19
28953221 CATGTGGCAA
28953231 AAAAATTATAAAAA---AT
1 AAAAATTATAAAAATTTAT
* *
28953247 AAAAATCA-ATAAAAGTTAT
1 AAAAATTATA-AAAATTTAT
* *
28953266 AAAAATTATTAAATTTTAAT
1 AAAAATTATAAAAATTT-AT
* *
28953286 AAAAA-TAGAAAAA--TAG
1 AAAAATTATAAAAATTTAT
28953302 AAAAATTTATAAAAATTTAT
1 AAAAA-TTATAAAAATTTAT
*
28953322 AAAAATTTATAAAAATTGTAA
1 AAAAA-TTATAAAAATT-TAT
*
28953343 AAAATATATATATAAAATATAT
1 AAAA-AT-TATA-AAAATTTAT
* *
28953365 AGAAA-TATAAAATTTTAT
1 AAAAATTATAAAAATTTAT
28953383 AAA
1 AAA
28953386 GTCGTAAGAA
Statistics
Matches: 107, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
15 1 0.01
16 17 0.16
17 1 0.01
18 16 0.15
19 23 0.21
20 26 0.24
21 8 0.07
22 10 0.09
23 5 0.05
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAATTATAAAAATTTAT
Found at i:28953481 original size:11 final size:12
Alignment explanation
Indices: 28953457--28953481 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28953447 TATCGTTATT
28953457 AAAAATTAGAAA
1 AAAAATTAGAAA
28953469 AAAAATTAGAAA
1 AAAAATTAGAAA
28953481 A
1 A
28953482 TGCATCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAATTAGAAA
Found at i:28953758 original size:11 final size:11
Alignment explanation
Indices: 28953738--28953772 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28953728 CTTTATAAAA
28953738 TTTTACAATTT
1 TTTTACAATTT
*
28953749 TTTTATAATTT
1 TTTTACAATTT
*
28953760 TTTTACGATTT
1 TTTTACAATTT
28953771 TT
1 TT
28953773 CTAATTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTTACAATTT
Found at i:28953758 original size:19 final size:19
Alignment explanation
Indices: 28953701--28953760 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
28953691 TTTATATTTC
*
28953701 TTTACATTTTTTTTATAAT
1 TTTACAATTTTTTTATAAT
* * *
28953720 TTT-C-ATGACTTTATAAAAT
1 TTTACAAT--TTTTTTATAAT
28953739 TTTACAATTTTTTTATAAT
1 TTTACAATTTTTTTATAAT
28953758 TTT
1 TTT
28953761 TTTACGATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
17 1 0.03
18 1 0.03
19 25 0.83
20 1 0.03
21 2 0.07
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTACAATTTTTTTATAAT
Found at i:28953762 original size:21 final size:22
Alignment explanation
Indices: 28953729--28953772 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28953719 TTTTCATGAC
28953729 TTTATAA-AATTTTACAATTTT
1 TTTATAATAATTTTACAATTTT
** *
28953750 TTTATAATTTTTTTACGATTTT
1 TTTATAATAATTTTACAATTTT
28953772 T
1 T
28953773 CTAATTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTATAATAATTTTACAATTTT
Found at i:28953849 original size:19 final size:20
Alignment explanation
Indices: 28953815--28953860 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
28953805 ATATTTATAT
28953815 TTTTTATGAAAATTTAATCA
1 TTTTTATGAAAATTTAATCA
* * *
28953835 TTTTTAT-AAATTTTACTGA
1 TTTTTATGAAAATTTAATCA
28953854 TTTTTAT
1 TTTTTAT
28953861 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTTATGAAAATTTAATCA
Found at i:28956758 original size:19 final size:18
Alignment explanation
Indices: 28956722--28956770 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
28956712 TATTTTAAAA
28956722 ATTAAAAATCATTAAATTT
1 ATTAAAAAT-ATTAAATTT
*
28956741 ATTAAAAATATATTAATTT
1 ATTAAAAATAT-TAAATTT
*
28956760 -TAAAAAATATT
1 ATTAAAAATATT
28956771 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 11 0.41
19 15 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAAAAATATTAAATTT
Found at i:28959282 original size:3 final size:3
Alignment explanation
Indices: 28959274--28959314 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28959264 ATGAGCTTTA
28959274 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
28959315 GTCTTTGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:28961593 original size:24 final size:23
Alignment explanation
Indices: 28961526--28961591 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
28961516 ACCATATTTG
* * *
28961526 GACAGCTTTTATACA-TAAATTT
1 GACAGCATTTATACACCAAATTA
*
28961548 GAACAGCATTTATATACCAAATTA
1 G-ACAGCATTTATACACCAAATTA
28961572 GACAGCATTT-TCACACCAAA
1 GACAGCATTTAT-ACACCAAA
28961592 ATTTGGATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.06
23 28 0.78
24 6 0.17
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (23 bp):
GACAGCATTTATACACCAAATTA
Found at i:28961618 original size:23 final size:23
Alignment explanation
Indices: 28961591--28961634 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28961581 TTCACACCAA
28961591 AATTTGGATAGCATAAATACATC
1 AATTTGGATAGCATAAATACATC
* *
28961614 AATTTGGGTAGCATATATACA
1 AATTTGGATAGCATAAATACA
28961635 ACAGTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (23 bp):
AATTTGGATAGCATAAATACATC
Found at i:28961642 original size:23 final size:23
Alignment explanation
Indices: 28961591--28961642 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
28961581 TTCACACCAA
*
28961591 AATTTGGATAGCATAAATACATC
1 AATTTGGATAGCATAAATACAAC
* *
28961614 AATTTGGGTAGCATATATACAAC
1 AATTTGGATAGCATAAATACAAC
*
28961637 AGTTTG
1 AATTTG
28961643 AGCAACATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
AATTTGGATAGCATAAATACAAC
Found at i:28961695 original size:23 final size:23
Alignment explanation
Indices: 28961665--28961806 Score: 162
Period size: 23 Copynumber: 6.1 Consensus size: 23
28961655 ACACCAAAAC
28961665 TGGACAGCATATATGCAACAAAT
1 TGGACAGCATATATGCAACAAAT
* * * *
28961688 TGGGCAGCATTTAAGCATAAAAAT
1 TGGACAGCATATATGCA-ACAAAT
*
28961712 TGGACAGCATATATGTAACAAAT
1 TGGACAGCATATATGCAACAAAT
*
28961735 TGGACAGCATATATGTAACAAAT
1 TGGACAGCATATATGCAACAAAT
* * *
28961758 TGGATAGCATTTAAT-CATCAAAAT
1 TGGACAGCATAT-ATGCAAC-AAAT
28961782 TGGACAGCATATATG-AACAAAT
1 TGGACAGCATATATGCAACAAAT
28961804 TGG
1 TGG
28961807 TTCAACTCAT
Statistics
Matches: 99, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
22 7 0.07
23 58 0.59
24 34 0.34
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (23 bp):
TGGACAGCATATATGCAACAAAT
Found at i:28961699 original size:47 final size:48
Alignment explanation
Indices: 28961623--28961744 Score: 131
Period size: 47 Copynumber: 2.6 Consensus size: 48
28961613 CAATTTGGGT
* ** * * * *
28961623 AGCATATATACAACAGTTTGAGCAACATTTTTA-CACCAAAACTGGAC
1 AGCATATATGCAACAAATTGGGCAGCATTTTAAGCACAAAAACTGGAC
* *
28961670 AGCATATATGCAACAAATTGGGCAGCA-TTTAAGCATAAAAATTGGAC
1 AGCATATATGCAACAAATTGGGCAGCATTTTAAGCACAAAAACTGGAC
* *
28961717 AGCATATATGTAACAAATTGGACAGCAT
1 AGCATATATGCAACAAATTGGGCAGCAT
28961745 ATATGTAACA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 4 0.06
47 58 0.94
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (48 bp):
AGCATATATGCAACAAATTGGGCAGCATTTTAAGCACAAAAACTGGAC
Found at i:28961742 original size:70 final size:69
Alignment explanation
Indices: 28961665--28961806 Score: 230
Period size: 70 Copynumber: 2.0 Consensus size: 69
28961655 ACACCAAAAC
*
28961665 TGGACAGCATATATGCAACAAATTGGGCAGCATTTAAGCATAAAAATTGGACAGCATATATGTAA
1 TGGACAGCATATATGCAACAAATTGGACAGCATTTAAGCATAAAAATTGGACAGCATATATG-AA
28961730 CAAAT
65 CAAAT
* * * *
28961735 TGGACAGCATATATGTAACAAATTGGATAGCATTTAATCATCAAAATTGGACAGCATATATGAAC
1 TGGACAGCATATATGCAACAAATTGGACAGCATTTAAGCATAAAAATTGGACAGCATATATGAAC
28961800 AAAT
66 AAAT
28961804 TGG
1 TGG
28961807 TTCAACTCAT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
69 10 0.15
70 57 0.85
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (69 bp):
TGGACAGCATATATGCAACAAATTGGACAGCATTTAAGCATAAAAATTGGACAGCATATATGAAC
AAAT
Found at i:28962766 original size:43 final size:42
Alignment explanation
Indices: 28962653--28962777 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 42
28962643 AACTCTTACA
* * * *
28962653 ATGCCAACGTCCTAGACGTGGTCTTACATGTAATCACGTATCG
1 ATGCCAACGTCCCAGAAGTGGTCTTACACGTAA-CACATATCG
*
28962696 ATGCC-ACTGTCCCAGACAG-GGTGTTACACGTAA-ACATAAGTCG
1 ATGCCAAC-GTCCCAGA-AGTGGTCTTACACGTAACACAT-A-TCG
*
28962739 ATGCCAACGTCCCAGATGTGGTCTTACACGATAACACAT
1 ATGCCAACGTCCCAGAAGTGGTCTTACACG-TAACACAT
28962778 CTCAGAAATC
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
41 3 0.04
42 4 0.06
43 50 0.75
44 6 0.09
45 4 0.06
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGAAGTGGTCTTACACGTAACACATATCG
Found at i:28963941 original size:14 final size:15
Alignment explanation
Indices: 28963922--28963950 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28963912 TCACGAAACT
28963922 TTCACACAT-ATAAA
1 TTCACACATAATAAA
28963936 TTCACACATAATAAA
1 TTCACACATAATAAA
28963951 CATAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:28983632 original size:24 final size:23
Alignment explanation
Indices: 28983601--28983651 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
28983591 CATAATTATC
*
28983601 AAGTTGGCATAGTATAAAATATT
1 AAGTTGGCATAGTACAAAATATT
28983624 AAGTCTGGCATAGTACAAAATATT
1 AAGT-TGGCATAGTACAAAATATT
28983648 AAGT
1 AAGT
28983652 AAAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (23 bp):
AAGTTGGCATAGTACAAAATATT
Found at i:28993242 original size:3 final size:3
Alignment explanation
Indices: 28993234--28993270 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
28993224 TTGTCGCTCT
28993234 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28993271 GACAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28993794 original size:12 final size:12
Alignment explanation
Indices: 28993777--28993802 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28993767 CTTATTAAAC
28993777 GTGATTATTCTT
1 GTGATTATTCTT
28993789 GTGATTATTCTT
1 GTGATTATTCTT
28993801 GT
1 GT
28993803 TGATGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.19, T:0.58
Consensus pattern (12 bp):
GTGATTATTCTT
Found at i:28995634 original size:14 final size:14
Alignment explanation
Indices: 28995617--28995649 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28995607 TAACCATTTT
*
28995617 TATTTTTACTTTAA
1 TATTTTTAATTTAA
28995631 TATTTTTAATTTAA
1 TATTTTTAATTTAA
28995645 T-TTTT
1 TATTTT
28995650 ACATTCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTTTAATTTAA
Found at i:28997614 original size:32 final size:33
Alignment explanation
Indices: 28997567--28997631 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
28997557 CTTGTCGAAA
28997567 CCATTTTTTATTTTTGGAAAAAAAACAAAAATT
1 CCATTTTTTATTTTTGGAAAAAAAACAAAAATT
28997600 CCATTTTTTA-TTTTGGAAAAAAAACAAAAATT
1 CCATTTTTTATTTTTGGAAAAAAAACAAAAATT
28997632 AGTTGTCGAC
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:0.46, C:0.09, G:0.06, T:0.38
Consensus pattern (33 bp):
CCATTTTTTATTTTTGGAAAAAAAACAAAAATT
Found at i:29018387 original size:32 final size:31
Alignment explanation
Indices: 29018307--29018387 Score: 92
Period size: 34 Copynumber: 2.5 Consensus size: 31
29018297 ATACATGTAC
*
29018307 ATATATAAAAAA-AATTATATACATATATAT
1 ATATATAAAAAATAATTACATACATATATAT
* *
29018337 AGATTATGAAAAAGATAATTACATATATATATAT
1 ATA-TAT-AAAAA-ATAATTACATACATATATAT
29018371 ATATATAAACAAATAAT
1 ATATATAAA-AAATAAT
29018388 AATAATTACA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
30 2 0.05
31 3 0.07
32 13 0.31
33 6 0.14
34 18 0.43
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (31 bp):
ATATATAAAAAATAATTACATACATATATAT
Found at i:29018812 original size:19 final size:20
Alignment explanation
Indices: 29018788--29018836 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 20
29018778 AAATCATATA
29018788 ATCTAAGATTGC-ATATCAT
1 ATCTAAGATTGCAATATCAT
29018807 ATCTAAGATTGCATATATCAT
1 ATCTAAGATTGCA-ATATCAT
29018828 ATCTAAGAT
1 ATCTAAGAT
29018837 CATATCTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 12 0.43
21 16 0.57
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (20 bp):
ATCTAAGATTGCAATATCAT
Found at i:29018856 original size:14 final size:12
Alignment explanation
Indices: 29018823--29018848 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29018813 GATTGCATAT
29018823 ATCATATCTAAG
1 ATCATATCTAAG
29018835 ATCATATCTAAG
1 ATCATATCTAAG
29018847 AT
1 AT
29018849 TGCATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:29018992 original size:15 final size:14
Alignment explanation
Indices: 29018962--29018991 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29018952 GGACTTAGAC
*
29018962 TTGGTTTTATTATT
1 TTGGGTTTATTATT
29018976 TTGGGTTTATTATT
1 TTGGGTTTATTATT
29018990 TT
1 TT
29018992 TTTGTGAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.17, T:0.70
Consensus pattern (14 bp):
TTGGGTTTATTATT
Found at i:29030914 original size:5 final size:6
Alignment explanation
Indices: 29030900--29030924 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29030890 TTTCAAAACA
29030900 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
29030925 CCGAAAGCTT
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:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:29043095 original size:50 final size:50
Alignment explanation
Indices: 29042971--29043156 Score: 196
Period size: 50 Copynumber: 3.7 Consensus size: 50
29042961 GATAATAACA
* * * * **
29042971 TGCCAAAGCCATGTCCCAGAAATGGTCTTACAAGGGATGTT-TCGTG-TAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATGTTGG
* * *
29043020 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATGTTGG
* ** ** *
29043070 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATGTTGG
* *
29043120 GGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
29043157 TCTCTTTACC
Statistics
Matches: 113, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
48 3 0.03
49 36 0.32
50 74 0.65
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATGTTGG
Found at i:29047167 original size:5 final size:6
Alignment explanation
Indices: 29047153--29047177 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29047143 ATATAAAATG
29047153 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
29047178 CCGGAAGCTT
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:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:29048141 original size:17 final size:18
Alignment explanation
Indices: 29048109--29048143 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29048099 CCACGATGTT
29048109 CGCCCGTGTGGGCCCACA
1 CGCCCGTGTGGGCCCACA
29048127 CGCCCGTGT-GGCCCACA
1 CGCCCGTGTGGGCCCACA
29048144 TGACCCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.46, G:0.31, T:0.11
Consensus pattern (18 bp):
CGCCCGTGTGGGCCCACA
Found at i:29053687 original size:22 final size:22
Alignment explanation
Indices: 29053660--29053952 Score: 586
Period size: 22 Copynumber: 13.3 Consensus size: 22
29053650 CTCTCTAATC
29053660 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053682 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053704 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053726 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053748 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053770 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053792 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053814 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053836 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053858 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053880 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053902 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053924 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
29053946 CTCTCAA
1 CTCTCAA
29053953 ACCCATATTT
Statistics
Matches: 271, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 271 1.00
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:29053988 original size:51 final size:51
Alignment explanation
Indices: 29053924--29054036 Score: 199
Period size: 51 Copynumber: 2.2 Consensus size: 51
29053914 TTCCAAAATT
29053924 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
* *
29053975 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTGAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
*
29054026 CCCTCAATTTC
1 CTCTCAATTTC
29054037 ATTTTTGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.28, C:0.29, G:0.01, T:0.42
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
Found at i:29054064 original size:10 final size:10
Alignment explanation
Indices: 29054051--29054102 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
29054041 TTGAAAATAA
*
29054051 TTTTAAATTC
1 TTTTAAATTT
*
29054061 TTTTATATTT
1 TTTTAAATTT
**
29054071 TTTTAAAATAA
1 TTTT-AAATTT
29054082 TTTTAAATTT
1 TTTTAAATTT
*
29054092 TTTTATATTT
1 TTTTAAATTT
29054102 T
1 T
29054103 CATCAATGGC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:29054079 original size:31 final size:31
Alignment explanation
Indices: 29054038--29054102 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
29054028 CTCAATTTCA
29054038 TTTTTGAAAATAATTTTAAATTCTTTTATAT
1 TTTTTGAAAATAATTTTAAATTCTTTTATAT
* *
29054069 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTGAAAATAATTTTAAATTCTTTTATAT
29054100 TTT
1 TTT
29054103 CATCAATGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTTGAAAATAATTTTAAATTCTTTTATAT
Found at i:29054864 original size:21 final size:19
Alignment explanation
Indices: 29054836--29054874 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
29054826 TAACGAGGTA
29054836 AATTTTATGTTACATTTTGG
1 AATTTTATG-TACATTTTGG
*
29054856 AATTATTATGTAGATTTTG
1 AATT-TTATGTACATTTTG
29054875 TAAGAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (19 bp):
AATTTTATGTACATTTTGG
Found at i:29055057 original size:7 final size:7
Alignment explanation
Indices: 29055045--29055069 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29055035 AGTCGATTGA
29055045 TATTTAG
1 TATTTAG
29055052 TATTTAG
1 TATTTAG
29055059 TATTTAG
1 TATTTAG
29055066 TATT
1 TATT
29055070 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:29055747 original size:18 final size:18
Alignment explanation
Indices: 29055721--29055755 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29055711 AAGCGTGTTT
* *
29055721 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
29055739 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
29055756 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:29057537 original size:23 final size:25
Alignment explanation
Indices: 29057507--29057650 Score: 129
Period size: 29 Copynumber: 5.6 Consensus size: 25
29057497 CCCTAACCCT
29057507 AACCCTAA-CCTAA-CTTAATTAAA
1 AACCCTAACCCTAACCTTAATTAAA
29057530 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACC----TTAATTAAA
*
29057559 AACCCTAACCCTAACCTAAATTAAA
1 AACCCTAACCCTAACCTTAATTAAA
*
29057584 TAA---AAACCCTAA-CTTAATTAAA
1 -AACCCTAACCCTAACCTTAATTAAA
**
29057606 AACCCTAACCAAAACCTAATTTAATTAAA
1 AACCCTAACCCTAACC----TTAATTAAA
29057635 AACCCTAACCCTAACC
1 AACCCTAACCCTAACC
29057651 CTAACCTAAC
Statistics
Matches: 98, Mismatches: 8, Indels: 24
0.75 0.06 0.18
Matches are distributed among these distances:
21 2 0.02
22 9 0.09
23 16 0.16
24 11 0.11
25 10 0.10
26 2 0.02
29 48 0.49
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (25 bp):
AACCCTAACCCTAACCTTAATTAAA
Found at i:29057600 original size:18 final size:18
Alignment explanation
Indices: 29057573--29057614 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
29057563 CTAACCCTAA
*
29057573 CCTAAATTAAATAAAAAC
1 CCTAACTTAAATAAAAAC
*
29057591 CCTAACTTAATTAAAAAC
1 CCTAACTTAAATAAAAAC
29057609 CCTAAC
1 CCTAAC
29057615 CAAAACCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (18 bp):
CCTAACTTAAATAAAAAC
Found at i:29057601 original size:47 final size:47
Alignment explanation
Indices: 29057544--29057643 Score: 155
Period size: 47 Copynumber: 2.1 Consensus size: 47
29057534 CTAACCCTAA
* **
29057544 CCTAATTTAATTAAAAACCCTAACCCTAACCTAAATTAAATAAAAAC
1 CCTAACTTAATTAAAAACCCTAACCAAAACCTAAATTAAATAAAAAC
* *
29057591 CCTAACTTAATTAAAAACCCTAACCAAAACCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAACCCTAACCAAAACCTAAATTAAATAAAAAC
29057638 CCTAAC
1 CCTAAC
29057644 CCTAACCCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (47 bp):
CCTAACTTAATTAAAAACCCTAACCAAAACCTAAATTAAATAAAAAC
Found at i:29057605 original size:76 final size:79
Alignment explanation
Indices: 29057515--29057726 Score: 271
Period size: 76 Copynumber: 2.8 Consensus size: 79
29057505 CTAACCCTAA
29057515 CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCT-A-A
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACA
29057578 A-TTAAATAAAAAC
66 ACTTAAATAAAAAC
**
29057591 CCTAACTTAATTAAAAACCCTAACCAAAACCTAATTTAATTAAAAACCCTAACCCTAACCCTAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA-CCTAA-
* *
29057656 CTAACTTGATTAAAAAC
64 C-AACTTAAATAAAAAC
** *
29057673 CCTAAC---CCT---AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACC
29057727 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
75 2 0.02
76 96 0.79
77 3 0.02
78 1 0.01
79 1 0.01
81 2 0.02
82 16 0.13
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (79 bp):
CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACA
ACTTAAATAAAAAC
Found at i:29057623 original size:29 final size:30
Alignment explanation
Indices: 29057586--29057679 Score: 109
Period size: 35 Copynumber: 3.0 Consensus size: 30
29057576 AAATTAAATA
29057586 AAAACCCTAACTTAATTAAAAACCCTAACC-
1 AAAA-CCTAACTTAATTAAAAACCCTAACCT
*
29057616 AAAACCTAATTTAATTAAAAACCCTAACCCT
1 AAAACCTAACTTAATTAAAAACCCTAA-CCT
*
29057647 AACCCTAACCTAACTTGATTAAAAACCCTAACC
1 AA----AACCTAACTTAATTAAAAACCCTAACC
29057680 CTAACCCTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
29 22 0.40
30 6 0.11
31 2 0.04
34 2 0.04
35 23 0.42
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (30 bp):
AAAACCTAACTTAATTAAAAACCCTAACCT
Found at i:29057685 original size:29 final size:29
Alignment explanation
Indices: 29056413--29057596 Score: 2152
Period size: 29 Copynumber: 40.4 Consensus size: 29
29056403 NNNNNNNNNN
*
29056413 AAAAACCCTAATCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056442 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056471 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056500 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056529 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056558 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056587 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056616 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056645 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056674 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056703 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056732 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056761 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056790 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056819 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056848 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056877 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056906 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056935 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056964 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29056993 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057022 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057051 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057080 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057109 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057138 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057167 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057196 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057225 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057254 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057283 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057312 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057341 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
* * *
29057370 AAAAACCCTAACTCTAACCTAACTTCATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057399 AAAAACCCTAACCCTAACCCTAACCTAATTTAATT
1 --AAA----AACCCTAACCCTAACCTAATTTAATT
* * *
29057434 AAATACCCTAACCCTAACCAAACTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
* * *
29057463 AAAAACCCAAACCCTAACCAAACTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057492 AAAAACCCTAACCCTAACCCTAACCTAACTTAATT
1 AAAAACCCTAACCCTAA-CCTAA--T---TTAATT
29057527 AAAAACCCTAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCCTAACCTAATTTAATT
* *
29057556 AAAAACCCTAACCCTAACCTAAATTAAAT
1 AAAAACCCTAACCCTAACCTAATTTAATT
29057585 AAAAACCCTAAC
1 AAAAACCCTAAC
29057597 TTAATTAAAA
Statistics
Matches: 1126, Mismatches: 17, Indels: 24
0.96 0.01 0.02
Matches are distributed among these distances:
29 1064 0.94
30 4 0.00
31 3 0.00
32 1 0.00
33 3 0.00
34 5 0.00
35 46 0.04
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAAACCCTAACCCTAACCTAATTTAATT
Found at i:29057701 original size:5 final size:6
Alignment explanation
Indices: 29057670--29057701 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
29057660 CTTGATTAAA
29057670 AACCCT AACCCT AACCCT AACCCT AA-CCT AAC
1 AACCCT AACCCT AACCCT AACCCT AACCCT AAC
29057702 TTAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:29061925 original size:124 final size:124
Alignment explanation
Indices: 29061581--29061916 Score: 620
Period size: 124 Copynumber: 2.7 Consensus size: 124
29061571 CCCAAACTTG
*
29061581 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
29061646 TAGAGGCGATTTTTTACTATTTGCTTAGAAACAACAAAAAAATTTATTTCTTACATGAC
66 TAGAGGCGATTTTTTACTATTTGCTTAGAAACAACAAAAAAATTTATTTCTTACATGAC
29061705 CTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
29061770 TAGAGGCGATTTTTTACTATTTGCTTAGAAACAACAAAAAAATTTATTTCTTACATGAC
66 TAGAGGCGATTTTTTACTATTTGCTTAGAAACAACAAAAAAATTTATTTCTTACATGAC
* *
29061829 CTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCATAATTTCTCCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
29061894 TAGAAGCG-TTTTTATACTATTTG
66 TAGAGGCGATTTTT-TACTATTTG
29061917 ACCAGAAACG
Statistics
Matches: 207, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
123 5 0.02
124 202 0.98
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (124 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAGGCGATTTTTTACTATTTGCTTAGAAACAACAAAAAAATTTATTTCTTACATGAC
Found at i:29062218 original size:28 final size:29
Alignment explanation
Indices: 29062160--29062225 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
29062150 CGATTTCCCG
*
29062160 AAAAAT-GGCCCATTCCAGTAAATAATCA
1 AAAAATCGGCCCATTCCAGTAAATAATAA
* * *
29062188 AAAAATCGGCCCATTTCGGTAAAT-TTAA
1 AAAAATCGGCCCATTCCAGTAAATAATAA
*
29062216 AAAAAACGGC
1 AAAAATCGGC
29062226 TTTTTTTGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (29 bp):
AAAAATCGGCCCATTCCAGTAAATAATAA
Found at i:29064483 original size:17 final size:16
Alignment explanation
Indices: 29064452--29064485 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29064442 TAATAACCAA
29064452 TATTTTTTTTCGATTT
1 TATTTTTTTTCGATTT
*
29064468 TATTTTTATTTTGATTT
1 TATTTTT-TTTCGATTT
29064485 T
1 T
29064486 TTAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (16 bp):
TATTTTTTTTCGATTT
Found at i:29066890 original size:22 final size:21
Alignment explanation
Indices: 29066837--29066911 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
29066827 TAAGTATAAG
29066837 AATAATAAAT-AAAATAAAAA
1 AATAATAAATAAAAATAAAAA
*
29066857 AATTAGTAAAATAAAAATAAACAA
1 AA-TAAT-AAATAAAAATAAA-AA
* * *
29066881 TATAATAAATAATAATAAATA
1 AATAATAAATAAAAATAAAAA
29066902 AATAAATAAA
1 AAT-AATAAA
29066912 ATAGAAGGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.05
21 6 0.14
22 22 0.50
23 11 0.25
24 3 0.07
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (21 bp):
AATAATAAATAAAAATAAAAA
Found at i:29070656 original size:51 final size:50
Alignment explanation
Indices: 29070598--29070773 Score: 192
Period size: 51 Copynumber: 3.5 Consensus size: 50
29070588 TTTGGGGGTT
* * * * * *
29070598 TTCACATAGTACCACCCATGTTACTATTATCATTCGATACACGTAGTAGCC
1 TTCACATAGTACTACACATGTGACAATAAT-TTTCGATACACGTAGTAGCC
* * *
29070649 TTCACATAGTACTACACACGTGACCAA-AGATTTTCGGTACACATAGTAGCC
1 TTCACATAGTACTACACATGTGA-CAATA-ATTTTCGATACACGTAGTAGCC
* * *
29070700 TTCACTTACTACTACACATGTGACCATAATTTATCGATACACGTAGTAGCC
1 TTCACATAGTACTACACATGTGACAATAATTT-TCGATACACGTAGTAGCC
*
29070751 TTCACATAATACTACACATGTGA
1 TTCACATAGTACTACACATGTGA
29070774 TCATCGATAC
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
50 6 0.06
51 94 0.90
52 4 0.04
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (50 bp):
TTCACATAGTACTACACATGTGACAATAATTTTCGATACACGTAGTAGCC
Found at i:29078261 original size:51 final size:50
Alignment explanation
Indices: 29078203--29078423 Score: 200
Period size: 51 Copynumber: 4.4 Consensus size: 50
29078193 TTTGGGGGGT
* * * *
29078203 TTCACATAGTACCACTCATGTTACTATTATCATTCGATACACGTAGTAGCC
1 TTCACATAGTACTACACACGTGAC-ATTATCATTCGATACACGTAGTAGCC
* * *
29078254 TTCACATAGTACTACACACGTGATCAAGT-TCA--CGGTCCACGTAGTAGCC
1 TTCACATAGTACTACACACGTGA-C-ATTATCATTCGATACACGTAGTAGCC
* * * * *
29078303 TTCACATAGTACTACACACGTGACCA-AAGCTTTTCGGTACACATAGTAGCC
1 TTCACATAGTACTACACACGTGA-CATTATC-ATTCGATACACGTAGTAGCC
* * * *
29078354 TTCACTTAGTACTACACATGTGAACATTAT-TTATCGATACACGTAGTACCC
1 TTCACATAGTACTACACACGTG-ACATTATCAT-TCGATACACGTAGTAGCC
29078405 TTCACATAGTACTACACAC
1 TTCACATAGTACTACACAC
29078424 ATGATCATCG
Statistics
Matches: 139, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
48 2 0.01
49 39 0.28
50 2 0.01
51 91 0.65
52 5 0.04
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (50 bp):
TTCACATAGTACTACACACGTGACATTATCATTCGATACACGTAGTAGCC
Found at i:29078302 original size:49 final size:49
Alignment explanation
Indices: 29078240--29078430 Score: 231
Period size: 51 Copynumber: 3.8 Consensus size: 49
29078230 TATCATTCGA
*
29078240 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTCACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTACGG
* * *
29078289 TCCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTACGG
* * * * *
29078340 TACACATAGTAGCCTTCACTTAGTACTACACATGTGAACATTA-TTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCA--AGTTTA-CGG
* *
29078391 TACACGTAGTACCCTTCACATAGTACTACACACATGATCA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCA
29078431 TCGATACTTT
Statistics
Matches: 120, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
49 37 0.31
50 7 0.06
51 75 0.62
52 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (49 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTACGG
Found at i:29087654 original size:51 final size:50
Alignment explanation
Indices: 29087579--29087774 Score: 196
Period size: 51 Copynumber: 3.9 Consensus size: 50
29087569 CAATGATGAT
* * ** *
29087579 CGGTTCACATAGTAGCCTGTACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCA-TACCATC
* * * * * * *
29087630 TGATACACGTAGTACCCTACACATAGTACTACACACATGATCGAAACTATC
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGA-CCATACCATC
* * * * * *
29087681 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCATACCA-TC
29087731 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCAT
29087775 CACTTTAACT
Statistics
Matches: 112, Mismatches: 30, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.36
51 68 0.61
52 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCATACCATC
Found at i:29087794 original size:101 final size:99
Alignment explanation
Indices: 29087585--29087766 Score: 249
Period size: 101 Copynumber: 1.8 Consensus size: 99
29087575 TGATCGGTTC
* * *
29087585 ACATAGTAGCCTGTACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTACCCTAC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTACCCTAC
* *
29087650 ACATAGTACTACACACATGATCGAAACTATCCGGT
65 ACATAGTACTACACACATGATCCAAACTAACCGGT
* * *
29087685 ACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCT
1 A--CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTACCCT
29087749 ACACATAGTACTACACAC
63 ACACATAGTACTACACAC
29087767 GTGACCATCA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 5 0.07
101 35 0.48
102 33 0.45
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.24
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTACCCTACA
CATAGTACTACACACATGATCCAAACTAACCGGT
Found at i:29093219 original size:27 final size:27
Alignment explanation
Indices: 29093189--29093266 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
29093179 ACTTAACTTT
29093189 TAAACCATAAACCTAAACTCAAAACAC
1 TAAACCATAAACCTAAACTCAAAACAC
* * * *
29093216 TAAACCTTAAGCATTAAAGTC-AAACAC
1 TAAACCATAAAC-CTAAACTCAAAACAC
*
29093243 TAAACCCTAAATCCTAAAC-CAAAA
1 TAAACCATAAA-CCTAAACTCAAAA
29093267 TGCCAAATTC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 1 0.03
27 32 0.80
28 7 0.17
ACGTcount: A:0.53, C:0.27, G:0.03, T:0.18
Consensus pattern (27 bp):
TAAACCATAAACCTAAACTCAAAACAC
Found at i:29093297 original size:14 final size:14
Alignment explanation
Indices: 29093274--29093303 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29093264 AAATGCCAAA
*
29093274 TTCAAGGTTTTGGG
1 TTCAAAGTTTTGGG
29093288 TTCAAAGTTTTGGG
1 TTCAAAGTTTTGGG
29093302 TT
1 TT
29093304 TTGGGTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.30, T:0.47
Consensus pattern (14 bp):
TTCAAAGTTTTGGG
Found at i:29093340 original size:32 final size:32
Alignment explanation
Indices: 29093303--29093368 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
29093293 AGTTTTGGGT
* * ** *
29093303 TTTGGGTTTGGATTTAGGGTTCGAGGTTTGAG
1 TTTGGGTTTGAATTCACAGTTCAAGGTTTGAG
29093335 TTTGGGTTTGAATTCACAGTTCAAGGTTTGAG
1 TTTGGGTTTGAATTCACAGTTCAAGGTTTGAG
29093367 TT
1 TT
29093369 CGAGTTCACG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.44
Consensus pattern (32 bp):
TTTGGGTTTGAATTCACAGTTCAAGGTTTGAG
Found at i:29093363 original size:26 final size:26
Alignment explanation
Indices: 29093334--29093388 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
29093324 CGAGGTTTGA
* *
29093334 GTTTGGGTTTGAATTCAC-AGTTCAAG
1 GTTTGAGTTCGAATTCACGA-TTCAAG
*
29093360 GTTTGAGTTCGAGTTCACGATTCAAG
1 GTTTGAGTTCGAATTCACGATTCAAG
29093386 GTT
1 GTT
29093389 CAATCTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (26 bp):
GTTTGAGTTCGAATTCACGATTCAAG
Found at i:29093880 original size:19 final size:19
Alignment explanation
Indices: 29093856--29093909 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
29093846 AATCTTCAAG
29093856 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
29093875 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29093894 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
29093910 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29093885 original size:36 final size:36
Alignment explanation
Indices: 29093845--29093916 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 36
29093835 TATGGAAACA
29093845 TAATCTT-CA-AGGATATGCAATCTTAGATATGATATG
1 TAATCTTACATAGGATATGCAATCTTAGA-A-GATATG
* *
29093881 TAATCTTAGATATGATATGCAATCTTAGAAGATATG
1 TAATCTTACATAGGATATGCAATCTTAGAAGATATG
29093917 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.41
37 2 0.06
38 17 0.53
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (36 bp):
TAATCTTACATAGGATATGCAATCTTAGAAGATATG
Found at i:29093900 original size:38 final size:40
Alignment explanation
Indices: 29093856--29093932 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
29093846 AATCTTCAAG
29093856 GATATGCAATCTT-AGATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
*
29093894 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT--AAGATATGATTATGTAATCTTAGA
29093933 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 13 0.38
41 8 0.24
42 13 0.38
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
Found at i:29094087 original size:22 final size:19
Alignment explanation
Indices: 29094056--29094098 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
29094046 GGGAGTTGGG
*
29094056 GAGTAATAATAATTCTTAA
1 GAGTACTAATAATTCTTAA
29094075 GAGTACTAATAATTCTTAA
1 GAGTACTAATAATTCTTAA
29094094 GAGTA
1 GAGTA
29094099 TTTACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (19 bp):
GAGTACTAATAATTCTTAA
Found at i:29098989 original size:6 final size:6
Alignment explanation
Indices: 29098974--29099031 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
29098964 GATGATGGAA
* * * *
29098974 AAAAAG AAAAGAA AAAAAG AAAAAAG AAAAAG AAAAAT AAAGAAG AAGAGG
1 AAAAAG AAAA-AG AAAAAG -AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG
29099025 AAAAAG A
1 AAAAAG A
29099032 GAGGCCAAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
6 26 0.63
7 15 0.37
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:29099010 original size:13 final size:12
Alignment explanation
Indices: 29098972--29099020 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 12
29098962 ATGATGATGG
29098972 AAAAAAAGAAAA
1 AAAAAAAGAAAA
29098984 GAAAAAAAGAAAA
1 -AAAAAAAGAAAA
29098997 AAGAAAAAGAAAA
1 AA-AAAAAGAAAA
*
29099010 ATAAAGAAGAA
1 A-AAAAAAGAA
29099021 GAGGAAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
12 2 0.06
13 30 0.91
14 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:29100117 original size:44 final size:44
Alignment explanation
Indices: 29100045--29100131 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
29100035 CGATGACCCC
* **
29100045 AGTCCTATCTCCCTGGTCATTAGAGGAATAGGTTGAAGATTGTA
1 AGTCCTATCTCCCTAGTCAGCAGAGGAATAGGTTGAAGATTGTA
* *
29100089 AGTCCTATCTCCCTAGTTAGCAGTGGAATAGGTTGAAGATTGT
1 AGTCCTATCTCCCTAGTCAGCAGAGGAATAGGTTGAAGATTGT
29100132 GAATCTTACT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (44 bp):
AGTCCTATCTCCCTAGTCAGCAGAGGAATAGGTTGAAGATTGTA
Found at i:29100412 original size:167 final size:167
Alignment explanation
Indices: 29100132--29100522 Score: 489
Period size: 167 Copynumber: 2.3 Consensus size: 167
29100122 TGAAGATTGT
* * * ** * * *
29100132 GAATCTTACTTCCCTGACGTTATAGCGGAGTAGATTAAAGTTGAGGGCAGCGAATCTTATCTCCC
1 GAATCTTACTTCCCTGACGTTGTAGCGGAGCAGATTGAAG-CCACGACAGTGAATCTTATCTCCC
*
29100197 TGGCGTTAAGACTTGAAATAGCTGAAGCAGAGTGGATTAAAGCTGTGGGCAGCGAATCCTATCTC
65 TGGCGTTAAGACTTGAAATAGCTGAAGCAGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTC
* *
29100262 TTTGGCATTACAGTGAAATAGATTGAAGCCAAAACGGC
130 TTTGGCATTACAGTGAAACAGATTAAAGCCAAAACGGC
*
29100300 GATTCTTACTTCCCTGACGTTGTAGCGGAGCAGATTGAAGCCACGACAGTGAATCTTATCTCCCT
1 GAATCTTACTTCCCTGACGTTGTAGCGGAGCAGATTGAAGCCACGACAGTGAATCTTATCTCCCT
* * * ** *
29100365 GGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCGGATTGAAGCTGTGGGCAGCGAATCCTATCTCT
66 GGCGTTAAGACTTGAAATAGCTGAAGCAGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCT
* * ***
29100430 TTGGCATTACAGTGGAGCAGATTAAAGCTGCAACGGC
131 TTGGCATTACAGTGAAACAGATTAAAGCCAAAACGGC
* * * * *
29100467 GAATCTTAC-TCCGTGAGCAG-TGTAGTGGAACAGATTGAAGCTACGACGGTGAATCT
1 GAATCTTACTTCCCTGA-C-GTTGTAGCGGAGCAGATTGAAGCCACGACAGTGAATCT
29100523 CGTTTCCCCA
Statistics
Matches: 192, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
166 6 0.03
167 149 0.78
168 37 0.19
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (167 bp):
GAATCTTACTTCCCTGACGTTGTAGCGGAGCAGATTGAAGCCACGACAGTGAATCTTATCTCCCT
GGCGTTAAGACTTGAAATAGCTGAAGCAGAGCGGATTAAAGCTGTGGGCAGCGAATCCTATCTCT
TTGGCATTACAGTGAAACAGATTAAAGCCAAAACGGC
Found at i:29100621 original size:91 final size:92
Alignment explanation
Indices: 29100486--29100927 Score: 555
Period size: 101 Copynumber: 4.6 Consensus size: 92
29100476 TCCGTGAGCA
*
29100486 GTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTCGTTTCCCCAACATTGCAATTGAAGCCA
1 GTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTCGTTTCCCCAACATTGCAATTGAAGCCA
* * *
29100551 CAATC-ACGAATTTTAGTTCTCTGGCG
66 CAAACGACGAATTTTACTTCCCTGGCG
* *
29100577 GTGTAGTGGAACAGATTGAAGCTACGGCGGCGAATCTCGTTTCCCTAACATTGCAATTAAAAAGA
1 GTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTCGTTTCCCCAACATTGC--------A-A
** *
29100642 TTGAAGCCACAAACGGTGAATTTTACTTCCCTAGCG
57 TTGAAGCCACAAACGACGAATTTTACTTCCCTGGCG
*
29100678 GTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTCGTTTCCCCAACATTGCAATTGAAGCCA
1 GTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTCGTTTCCCCAACATTGCAATTGAAGCCA
* * *
29100743 CAATC-ACGAATTTTAGTTCTCTGGCG
66 CAAACGACGAATTTTACTTCCCTGGCG
*
29100769 GTGTAGTGGAACAGATTGAAGCTACGGCGGCGAATCTCGTTTCCCCAACATTGCAATTAAAAAGA
1 GTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTCGTTTCCCCAACATTGC--------A-A
* *
29100834 TTGAAGCCGCAAACGGCGAATTTTACTTCCCTGGCG
57 TTGAAGCCACAAACGACGAATTTTACTTCCCTGGCG
*
29100870 GTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATT
1 GTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTCGTTTCCCCAACATTGCAATT
29100928 TAAAAGACTG
Statistics
Matches: 304, Mismatches: 27, Indels: 39
0.82 0.07 0.11
Matches are distributed among these distances:
91 119 0.39
92 17 0.06
93 2 0.01
99 2 0.01
100 27 0.09
101 137 0.45
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.26
Consensus pattern (92 bp):
GTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTCGTTTCCCCAACATTGCAATTGAAGCCA
CAAACGACGAATTTTACTTCCCTGGCG
Found at i:29100715 original size:101 final size:100
Alignment explanation
Indices: 29100541--29100940 Score: 557
Period size: 101 Copynumber: 4.1 Consensus size: 100
29100531 CAACATTGCA
* * * *
29100541 ATTGAAGCCACAATCACGAATTTTAGTTCTCTGGCGGTGTAGTGGAACAGATTGAAGCTACGGCG
1 ATTGAAGCCACAAACACGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGACG
*
29100606 GCGAATCTCGTTTCCCTAACATTGCAATTAAAAAG
66 GCGAATCTCGTTTCCCCAACATTGCAATTAAAAAG
** *
29100641 ATTGAAGCCACAAACGGTGAATTTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCTACGAC
1 ATTGAAGCCACAAAC-ACGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGAC
*
29100706 GGTGAATCTCGTTTCCCCAACATTGC--------A-
65 GGCGAATCTCGTTTCCCCAACATTGCAATTAAAAAG
* * * *
29100733 ATTGAAGCCACAATCACGAATTTTAGTTCTCTGGCGGTGTAGTGGAACAGATTGAAGCTACGGCG
1 ATTGAAGCCACAAACACGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGACG
29100798 GCGAATCTCGTTTCCCCAACATTGCAATTAAAAAG
66 GCGAATCTCGTTTCCCCAACATTGCAATTAAAAAG
* *
29100833 ATTGAAGCCGCAAACGGCGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGAC
1 ATTGAAGCCACAAAC-ACGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGAC
* *
29100898 GGCGAATCTTGTTTCCCCAACATTGCAATTTAAAAG
65 GGCGAATCTCGTTTCCCCAACATTGCAATTAAAAAG
*
29100934 ACTGAAG
1 ATTGAAG
29100941 ATGACAAGTC
Statistics
Matches: 263, Mismatches: 26, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
91 68 0.26
92 14 0.05
93 1 0.00
99 1 0.00
100 27 0.10
101 152 0.58
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (100 bp):
ATTGAAGCCACAAACACGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGACG
GCGAATCTCGTTTCCCCAACATTGCAATTAAAAAG
Found at i:29100725 original size:192 final size:192
Alignment explanation
Indices: 29100461--29100927 Score: 837
Period size: 192 Copynumber: 2.4 Consensus size: 192
29100451 TTAAAGCTGC
* * *
29100461 AACGGCGAATCTTAC-TCCGTGAGCAGTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTCG
1 AACGGCGAATTTTACTTCCCT-AGCGGTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTCG
29100525 TTTCCCCAACATTGCAATTGAAGCCACAATCACGAATTTTAGTTCTCTGGCGGTGTAGTGGAACA
65 TTTCCCCAACATTGCAATTGAAGCCACAATCACGAATTTTAGTTCTCTGGCGGTGTAGTGGAACA
*
29100590 GATTGAAGCTACGGCGGCGAATCTCGTTTCCCTAACATTGCAATTAAAAAGATTGAAGCCACA
130 GATTGAAGCTACGGCGGCGAATCTCGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACA
*
29100653 AACGGTGAATTTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTCGT
1 AACGGCGAATTTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTCGT
29100718 TTCCCCAACATTGCAATTGAAGCCACAATCACGAATTTTAGTTCTCTGGCGGTGTAGTGGAACAG
66 TTCCCCAACATTGCAATTGAAGCCACAATCACGAATTTTAGTTCTCTGGCGGTGTAGTGGAACAG
*
29100783 ATTGAAGCTACGGCGGCGAATCTCGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCCGCA
131 ATTGAAGCTACGGCGGCGAATCTCGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACA
* * *
29100845 AACGGCGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGT
1 AACGGCGAATTTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTCGT
29100910 TTCCCCAACATTGCAATT
66 TTCCCCAACATTGCAATT
29100928 TAAAAGACTG
Statistics
Matches: 264, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
192 260 0.98
193 4 0.02
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (192 bp):
AACGGCGAATTTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTCGT
TTCCCCAACATTGCAATTGAAGCCACAATCACGAATTTTAGTTCTCTGGCGGTGTAGTGGAACAG
ATTGAAGCTACGGCGGCGAATCTCGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACA
Found at i:29100940 original size:50 final size:50
Alignment explanation
Indices: 29100781--29100940 Score: 131
Period size: 50 Copynumber: 3.2 Consensus size: 50
29100771 GTAGTGGAAC
* *
29100781 AGATTGAAGCTACGGCGGCGAATCTCGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
** * * ** *** ** * * ** *
29100831 AGATTGAAGCCGCAAACGGCGAATTTTACTTCCCTGGCGGTGTAGTGGAAC
1 AGATTGAAGCTAC-GACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
*
29100882 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTTAAA
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
*
29100932 AGACTGAAG
1 AGATTGAAG
29100941 ATGACAAGTC
Statistics
Matches: 74, Mismatches: 35, Indels: 2
0.67 0.32 0.02
Matches are distributed among these distances:
50 42 0.57
51 32 0.43
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (50 bp):
AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
Found at i:29101485 original size:19 final size:19
Alignment explanation
Indices: 29101461--29101514 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
29101451 NNNNNNCAAG
29101461 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
29101480 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29101499 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
29101515 AGATATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29111163 original size:17 final size:18
Alignment explanation
Indices: 29111141--29111174 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29111131 CTCAACAACC
29111141 AAAGGTATTGTC-CCTGG
1 AAAGGTATTGTCTCCTGG
*
29111158 AAAGGTTTTGTCTCCTG
1 AAAGGTATTGTCTCCTG
29111175 TGCTCTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (18 bp):
AAAGGTATTGTCTCCTGG
Found at i:29112559 original size:3 final size:3
Alignment explanation
Indices: 29112551--29112585 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29112541 ATGAGAGAGA
29112551 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
29112586 ATAGTGTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:29113695 original size:101 final size:103
Alignment explanation
Indices: 29113562--29113765 Score: 394
Period size: 101 Copynumber: 2.0 Consensus size: 103
29113552 AGATAAAAAA
29113562 AAAACATATATATATATATATATATATCTAACTCTAACTTTGTTAGGGCTTCATCCCATTCACTC
1 AAAACATATATATATATATATATATATCTAACTCTAACTTTGTTAGGGCTTCATCCCATTCACTC
29113627 TTCCAAATCCTTAAGTCTAATTTGCACCCTCGCAATAT
66 TTCCAAATCCTTAAGTCTAATTTGCACCCTCGCAATAT
29113665 AAAA-ATATAT-TATATATATATATATCTAACTCTAACTTTGTTAGGGCTTCATCCCATTCACTC
1 AAAACATATATATATATATATATATATCTAACTCTAACTTTGTTAGGGCTTCATCCCATTCACTC
29113728 TTCCAAATCCTTAAGTCTAATTTGCACCCTCGCAATAT
66 TTCCAAATCCTTAAGTCTAATTTGCACCCTCGCAATAT
29113766 GAAGCGCCAA
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
101 91 0.90
102 6 0.06
103 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (103 bp):
AAAACATATATATATATATATATATATCTAACTCTAACTTTGTTAGGGCTTCATCCCATTCACTC
TTCCAAATCCTTAAGTCTAATTTGCACCCTCGCAATAT
Found at i:29121891 original size:27 final size:25
Alignment explanation
Indices: 29121853--29122022 Score: 124
Period size: 27 Copynumber: 6.4 Consensus size: 25
29121843 TGCAAGTTGA
*
29121853 GTTCGCCAGTTGGTTTGGCGAGCTGGT
1 GTTCGCCAGTTGG-TT-GCGAACTGGT
* *
29121880 GTTCGCCAGTTGAGTTGTGAACTAGGG
1 GTTCGCCAGTTG-GTTGCGAACT-GGT
* * *
29121907 GTTCACTAGTTAAGTTGCGAACTGGT
1 GTTCGCCAGTT-GGTTGCGAACTGGT
* * *
29121933 GTTCGCCATTTGGTTTGGCGAGCTAGT
1 GTTCGCCAGTTGG-TT-GCGAACTGGT
* **
29121960 GTTCGCCAGTTGAATTATGAACTGGT
1 GTTCGCCAGTTG-GTTGCGAACTGGT
* *
29121986 GGTTCGCTAGTTGAGTTGCAAACTGGT
1 -GTTCGCCAGTTG-GTTGCGAACTGGT
29122013 GTTCGCCAGT
1 GTTCGCCAGT
29122023 CAAAAAGTCA
Statistics
Matches: 110, Mismatches: 26, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
25 1 0.01
26 32 0.29
27 76 0.69
28 1 0.01
ACGTcount: A:0.16, C:0.17, G:0.33, T:0.34
Consensus pattern (25 bp):
GTTCGCCAGTTGGTTGCGAACTGGT
Found at i:29121990 original size:80 final size:80
Alignment explanation
Indices: 29121853--29122022 Score: 261
Period size: 80 Copynumber: 2.1 Consensus size: 80
29121843 TGCAAGTTGA
* * *
29121853 GTTCGCCAGTTGGTTTGGCGAGCTGGTGTTCGCCAGTTGAGTTGTGAACTAGGGGTTCACTAGTT
1 GTTCGCCAGTTGGTTTGGCGAGCTAGTGTTCGCCAGTTGAATTATGAACTAGGGGTTCACTAGTT
*
29121918 AAGTTGCGAACTGGT
66 AAGTTGCAAACTGGT
* *
29121933 GTTCGCCATTTGGTTTGGCGAGCTAGTGTTCGCCAGTTGAATTATGAACT-GGTGGTTCGCTAGT
1 GTTCGCCAGTTGGTTTGGCGAGCTAGTGTTCGCCAGTTGAATTATGAACTAGG-GGTTCACTAGT
*
29121997 TGAGTTGCAAACTGGT
65 TAAGTTGCAAACTGGT
29122013 GTTCGCCAGT
1 GTTCGCCAGT
29122023 CAAAAAGTCA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 2 0.02
80 79 0.98
ACGTcount: A:0.16, C:0.17, G:0.33, T:0.34
Consensus pattern (80 bp):
GTTCGCCAGTTGGTTTGGCGAGCTAGTGTTCGCCAGTTGAATTATGAACTAGGGGTTCACTAGTT
AAGTTGCAAACTGGT
Found at i:29136775 original size:44 final size:44
Alignment explanation
Indices: 29136655--29137225 Score: 264
Period size: 44 Copynumber: 13.0 Consensus size: 44
29136645 TCTTGGTGCT
* * * *
29136655 CTTGCTTTCTTGAGTCTACTCCCCTGCAACTTCAGGGAAATAAGA
1 CTTGCTTACTT-AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * *
29136700 TTTTC-CATCTTCAGTCTGC-CTCACTGCAACTTCA-GGAGGATAAGA
1 CTTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGA
29136745 CTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 CTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * * * * * * *
29136789 CTAG-ATGC-GA-TCTACT-CTCTGTAACTTTAGAGAGATAAGA
1 CTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
** * * * *
29136829 TCCAAGGTT--TTAATCTGCTCCATTGCAACCTT-AGGGAGATAGGA
1 --CTTGCTTACTTAGTCTGCTCCACTGCAA-CTTCAGGGAGATAAGA
* * * * *
29136873 TTATCGGTT--TTAATCTGCCCCACTGCAACTTCAGGGAGATGAGA
1 CT-T-GCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * *
29136917 TTTGC-CATCTTCAGTCTGC-CTCATTGCAACTTCA-GGAGGATAAGA
1 CTTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGA
*
29136962 CTTACTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 CTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
** * **
29137006 TCCAAGGTT--TT-GATCCACTCCACTGCAACTTCAGGGAGATAAGA
1 --CTTGCTTACTTAG-TCTGCTCCACTGCAACTTCAGGGAGATAAGA
** * * * *
29137050 TCCAAGGTT--TTAATCTGCTCCATTGCAACCTT-AGGGAGATAGGA
1 --CTTGCTTACTTAGTCTGCTCCACTGCAA-CTTCAGGGAGATAAGA
* * * *
29137094 TTATCGGC-T--TTAATCTGTTCCACTGCAACGTCAGGGAGATAAGA
1 CT-T--GCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * *
29137138 TTTGC-CATCTTCAGTCTGC-CTCACTGCAACTTCA-GGAG--GAGA
1 CTTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTCAGGGAGATAAGA
29137180 CTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 CTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
29137224 CT
1 CT
29137226 AGATGCGATC
Statistics
Matches: 410, Mismatches: 72, Indels: 89
0.72 0.13 0.16
Matches are distributed among these distances:
40 20 0.05
41 27 0.07
42 21 0.05
43 17 0.04
44 222 0.54
45 98 0.24
46 5 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
CTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
Found at i:29137130 original size:221 final size:217
Alignment explanation
Indices: 29136678--29137265 Score: 903
Period size: 221 Copynumber: 2.7 Consensus size: 217
29136668 GTCTACTCCC
* *
29136678 CTGCAACTTCAGGGAAATAAGATTTTCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
1 CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
* * *
29136743 GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTC
66 GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACAAGATGCGATCCACTCAC
* *
29136808 TGTAACTTTAGAGAGATAAGATCCAAGGTTTTAATCTGCTCCATTGCAACCTTAGGGAGATAGGA
131 TGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCTGCTCCATTGCAACCTTAGGGAGATAGGA
*
29136873 TTATCGGTTTTAATCTGCCCCA
196 TTATCGGCTTTAATCTGCCCCA
* *
29136895 CTGCAACTTCAGGGAGATGAGATTTGCCATCTTCAGTCTGCCTCATTGCAACTTCAGGAGGATAA
1 CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
* * **
29136960 GACTTACTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATCCAAGGTTTTGATCCACT
66 GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA--CAA-GATGCGATCCACT
*
29137025 CCACTGCAACTTCAGGGAGATAAGATCCAAGGTTTTAATCTGCTCCATTGCAACCTTAGGGAGAT
128 -CACTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCTGCTCCATTGCAACCTTAGGGAGAT
**
29137090 AGGATTATCGGCTTTAATCTGTTCCA
192 AGGATTATCGGCTTTAATCTGCCCCA
*
29137116 CTGCAACGTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGG---A
1 CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
* ** *
29137178 GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTC
66 GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACAAGATGCGATCCACTCAC
* *
29137243 TGTAACTTCAAAGAGATAAGATC
131 TGCAACTTCAGAGAGATAAGATC
29137266 TGTGATTTTA
Statistics
Matches: 336, Mismatches: 31, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
214 22 0.07
215 8 0.02
216 2 0.01
217 106 0.32
218 46 0.14
219 2 0.01
220 9 0.03
221 141 0.42
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (217 bp):
CTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAA
GACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACAAGATGCGATCCACTCAC
TGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCTGCTCCATTGCAACCTTAGGGAGATAGGA
TTATCGGCTTTAATCTGCCCCA
Found at i:29153676 original size:23 final size:22
Alignment explanation
Indices: 29153633--29153755 Score: 117
Period size: 23 Copynumber: 5.5 Consensus size: 22
29153623 TTCATGATTA
*
29153633 GCCATAAAGG-TAATACAGAATAC
1 GCCACAAAGGCTAA-ACAGAAT-C
* *
29153656 ACCACAAAGGCTAAACCGAAT-
1 GCCACAAAGGCTAAACAGAATC
*
29153677 GCCACAAAGGCAAAACAGAATC
1 GCCACAAAGGCTAAACAGAATC
*
29153699 TGCCACAAAGGCTAAATAGAATGC
1 -GCCACAAAGGCTAAACAGAAT-C
* *
29153723 GCCACAAAGGCCAAATAGAAT-
1 GCCACAAAGGCTAAACAGAATC
*
29153744 GCCACCAAGGCT
1 GCCACAAAGGCT
29153756 TAGTGTTGAT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
21 28 0.33
23 53 0.62
24 4 0.05
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.11
Consensus pattern (22 bp):
GCCACAAAGGCTAAACAGAATC
Found at i:29153695 original size:44 final size:45
Alignment explanation
Indices: 29153633--29153743 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 45
29153623 TTCATGATTA
* * * *
29153633 GCCATAAAGGTAATACAGAATAC-ACCACAAAGGCTAAACCGAAT-
1 GCCACAAAGGCAAAACAGAAT-CTACCACAAAGGCTAAACAGAATC
* *
29153677 GCCACAAAGGCAAAACAGAATCTGCCACAAAGGCTAAATAGAATGC
1 GCCACAAAGGCAAAACAGAATCTACCACAAAGGCTAAACAGAAT-C
* *
29153723 GCCACAAAGGCCAAATAGAAT
1 GCCACAAAGGCAAAACAGAAT
29153744 GCCACCAAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 1 0.02
44 36 0.64
46 19 0.34
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (45 bp):
GCCACAAAGGCAAAACAGAATCTACCACAAAGGCTAAACAGAATC
Found at i:29153747 original size:44 final size:43
Alignment explanation
Indices: 29153657--29153755 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 43
29153647 ACAGAATACA
*
29153657 CCACAAAGGCTAAACCGAATGCCACAAAGGCAAAACAGAATCTG
1 CCACAAAGGCTAAACAGAATGCCACAAAGGCAAAACAGAA-CTG
* * *
29153701 CCACAAAGGCTAAATAGAATGCGCCACAAAGGCCAAATAGAA-TG
1 CCACAAAGGCTAAACAGAAT--GCCACAAAGGCAAAACAGAACTG
*
29153745 CCACCAAGGCT
1 CCACAAAGGCT
29153756 TAGTGTTGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 30 0.62
46 18 0.38
ACGTcount: A:0.43, C:0.27, G:0.19, T:0.10
Consensus pattern (43 bp):
CCACAAAGGCTAAACAGAATGCCACAAAGGCAAAACAGAACTG
Found at i:29154625 original size:24 final size:24
Alignment explanation
Indices: 29154598--29154645 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29154588 AAGAGAACAT
29154598 TTAATTTTAAAAAGAAGAACTAGA
1 TTAATTTTAAAAAGAAGAACTAGA
29154622 TTAATTTTAAAAAGAAGAACTAGA
1 TTAATTTTAAAAAGAAGAACTAGA
29154646 AAGTAGTATT
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:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (24 bp):
TTAATTTTAAAAAGAAGAACTAGA
Done.