Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 143 of 770
Found at i:42104035 original size:48 final size:48
Alignment explanation
Indices: 42103975--42104149 Score: 167
Period size: 48 Copynumber: 3.6 Consensus size: 48
42103965 TATGTGCGCT
* * *
42103975 AGTGTTAGACCATGTCTGGGACATGGCGTCGGCTACAATATGAGATCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACGATATGAGATCC
* * * * * * *
42104023 AGTGTAAGACCATGTTTGGAACATGGCATCAGCAATGTTGTGAGAGT-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACGATATGAGA-TCC
* * * *
42104071 AGTGTAAGACCATGTCTAGGACACGGCATCGGCGT-CGATATGTG-TGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TACGATATGAGAT-CC
*
42104119 AGTGTAAGACCATGTTTGGGACATGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
42104150 ACAATTCACC
Statistics
Matches: 99, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
46 1 0.01
48 97 0.98
49 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACGATATGAGATCC
Found at i:42104143 original size:96 final size:96
Alignment explanation
Indices: 42103975--42104148 Score: 244
Period size: 96 Copynumber: 1.8 Consensus size: 96
42103965 TATGTGCGCT
* * * *
42103975 AGTGTTAGACCATGTCTGGGACATGGCGTCGGCTACAATATGAGATCCAGTGTAAGACCATGTTT
1 AGTGTAAGACCATGTCTAGGACACGGCATCGGCTACAATATGAGATCCAGTGTAAGACCATGTTT
42104040 GGAACATGGCATCAGCAATGTTGTGAGAGTC
66 GGAACATGGCATCAGCAATGTTGTGAGAGTC
* * *
42104071 AGTGTAAGACCATGTCTAGGACACGGCATCGGCGT-CGATATGTG-TGCTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTAGGACACGGCATCGGC-TACAATATGAGAT-CCAGTGTAAGACCATGT
*
42104134 TTGGGACATGGCATC
64 TTGGAACATGGCATC
42104149 GACAATTCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
95 1 0.01
96 66 0.97
97 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTAGGACACGGCATCGGCTACAATATGAGATCCAGTGTAAGACCATGTTT
GGAACATGGCATCAGCAATGTTGTGAGAGTC
Found at i:42107816 original size:29 final size:28
Alignment explanation
Indices: 42107784--42107886 Score: 107
Period size: 29 Copynumber: 3.6 Consensus size: 28
42107774 GGGACGAGAT
* *
42107784 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* * *
42107813 TGGCACTAAGTGTGTGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
42107842 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
42107871 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
42107887 TGATTGAGTA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
28 3 0.05
29 56 0.93
30 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:42114346 original size:39 final size:39
Alignment explanation
Indices: 42114292--42114489 Score: 315
Period size: 39 Copynumber: 5.1 Consensus size: 39
42114282 AATTTTATTA
* * *
42114292 CCAGCACAAAGCCTGCGGGACTTTAGCTCGGATACATTT
1 CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGATACATTT
*
42114331 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGATACATTT
* * *
42114370 CCAACACGAAGCCTGCGGGTCTTTAGCCTGGATATATTT
1 CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGATACATTT
*
42114409 CCAGCACGAAGCCTGCGGGTCTTTAGCCCAGATACATTT
1 CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGATACATTT
*
42114448 CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGATATATTT
1 CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGATACATTT
42114487 CCA
1 CCA
42114490 TACACATTTC
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 147 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.24
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGATACATTT
Found at i:42118694 original size:48 final size:48
Alignment explanation
Indices: 42118635--42118808 Score: 183
Period size: 48 Copynumber: 3.6 Consensus size: 48
42118625 ATGTGCATTG
* *
42118635 GTGTAAGACCATG-CTTGGGACATGGCGTCGGCTACAATATGAGAGCCA
1 GTGTAAGACCATGTC-TGGGACATGGCATCGGCTACGATATGAGAGCCA
* * * * * * *
42118683 GTGTAAGACCATGTTTGGAACATGGCATCAGCAATGTTGTGAGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCTACGATATGAGAGCCA
* * * *
42118731 GTGTAAGACCATGTCTAGGACATGGCATCAGTG-T-CGATATGTGTGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATC-G-GCTACGATATGAGAGCCA
42118779 GTGTAAGACCATGTCTGGGACATGGCATCG
1 GTGTAAGACCATGTCTGGGACATGGCATCG
42118809 ACAATTCACC
Statistics
Matches: 102, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
47 1 0.01
48 100 0.98
50 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCTACGATATGAGAGCCA
Found at i:42119872 original size:28 final size:28
Alignment explanation
Indices: 42119832--42119890 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
42119822 GTTGAGACAT
* *
42119832 GGGCGTGTCCTGGTCGTGTGGGGAACAC
1 GGGCGTGTCCTGGCCGTATGGGGAACAC
42119860 GGGCGTGTCCTGGCCGTATGGGGAACAC
1 GGGCGTGTCCTGGCCGTATGGGGAACAC
42119888 GGG
1 GGG
42119891 TCATGAAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (28 bp):
GGGCGTGTCCTGGCCGTATGGGGAACAC
Found at i:42128004 original size:40 final size:40
Alignment explanation
Indices: 42127896--42128005 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
42127886 ATTGAATGAT
* * * * *
42127896 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
* * *
42127936 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
42127976 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
42128006 AAATTGTGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
Found at i:42131132 original size:26 final size:26
Alignment explanation
Indices: 42131077--42131152 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
42131067 TTCTCATTTC
* **
42131077 ATTTTA-CCCTCAACAAAATTTTGATG
1 ATTTTACCCCT-AATAAAATTTTGACA
* **
42131103 ATTTTACCCTTGGTAAAATTTTGACA
1 ATTTTACCCCTAATAAAATTTTGACA
*
42131129 ATTTTGCCCCTAATAAAATTTTGA
1 ATTTTACCCCTAATAAAATTTTGA
42131153 GAAAATATGT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 36 0.92
27 3 0.08
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (26 bp):
ATTTTACCCCTAATAAAATTTTGACA
Found at i:42131325 original size:18 final size:18
Alignment explanation
Indices: 42131315--42131353 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
42131305 ATTTTCTTTA
42131315 TTATTTCCATTTCCATTT
1 TTATTTCCATTTCCATTT
*
42131333 TTATTTCTATTTCCAATTT
1 TTATTTCCATTTCC-ATTT
42131352 TT
1 TT
42131354 GAAACTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTTCCATTTCCATTT
Found at i:42132418 original size:29 final size:29
Alignment explanation
Indices: 42132376--42132434 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42132366 TGTGCCATCC
42132376 ATACGACTGAGACACACTCCCGTGTCTCT
1 ATACGACTGAGACACACTCCCGTGTCTCT
42132405 ATACGACTGAGACACACTCCCGTGTCTCT
1 ATACGACTGAGACACACTCCCGTGTCTCT
42132434 A
1 A
42132435 CTCGTGTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.24
Consensus pattern (29 bp):
ATACGACTGAGACACACTCCCGTGTCTCT
Found at i:42139378 original size:29 final size:29
Alignment explanation
Indices: 42139333--42139397 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
42139323 TAATTTAATG
*
42139333 CACATCATCTCTGTTCATATTCATCAATT
1 CACATCATCTCTATTCATATTCATCAATT
*
42139362 CACATTATCTCTATTCATATTCATCAATT
1 CACATCATCTCTATTCATATTCATCAATT
42139391 CACATCA
1 CACATCA
42139398 CAAACTTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.02, T:0.40
Consensus pattern (29 bp):
CACATCATCTCTATTCATATTCATCAATT
Found at i:42142713 original size:40 final size:40
Alignment explanation
Indices: 42142647--42142813 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
42142637 AAATTGAATG
* * *
42142647 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
42142686 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
42142726 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
42142766 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
42142806 ATATCCGG
1 ATATCCGG
42142814 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:42148574 original size:29 final size:29
Alignment explanation
Indices: 42148532--42148615 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
42148522 GTATTTTTTT
**
42148532 TTTCCAGCTTGCACACTTAGTGCCAAATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
*
42148561 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
42148590 TTTCCAGCACGCACACTTAGTGCCAA
1 TTTCCAGCACGCACACTTAGTGCCAA
42148616 TCTCGACACC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCAAATA
Found at i:42161790 original size:33 final size:30
Alignment explanation
Indices: 42161745--42161814 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
42161735 AAATATATAT
*
42161745 ATATATATATATATAAATAATAGTATTAGAA
1 ATATATATATATATAAATAATAATATTA-AA
* *
42161776 ATCATATAGTATATATAACTGATAATATTAAA
1 AT-ATATA-TATATATAAATAATAATATTAAA
42161808 ATATATA
1 ATATATA
42161815 CATAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
32 9 0.26
33 18 0.53
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
ATATATATATATATAAATAATAATATTAAA
Found at i:42162038 original size:3 final size:3
Alignment explanation
Indices: 42162030--42162077 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
42162020 ACAAGGATAT
42162030 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42162078 TTGAAACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42162187 original size:3 final size:3
Alignment explanation
Indices: 42162179--42162221 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
42162169 AATGTATTTC
42162179 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
42162222 TTGAAATGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42162714 original size:11 final size:11
Alignment explanation
Indices: 42162698--42162732 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
42162688 GAAAAAAAAA
42162698 GAAGAGAGAGG
1 GAAGAGAGAGG
42162709 GAAGAGAGAGG
1 GAAGAGAGAGG
42162720 G-AGAGAGAAGG
1 GAAGAGAG-AGG
42162731 GA
1 GA
42162733 GGGGAATCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAGG
Found at i:42162827 original size:11 final size:11
Alignment explanation
Indices: 42162811--42162861 Score: 93
Period size: 11 Copynumber: 4.5 Consensus size: 11
42162801 TAAATTTTTT
42162811 TTTTTTGTATA
1 TTTTTTGTATA
42162822 TTTTTTGTATA
1 TTTTTTGTATA
42162833 TTTTTTGTATA
1 TTTTTTGTATA
42162844 TCTTTTTGTATA
1 T-TTTTTGTATA
42162856 TTTTTT
1 TTTTTT
42162862 TATGTTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
11 28 0.72
12 11 0.28
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.75
Consensus pattern (11 bp):
TTTTTTGTATA
Found at i:42162849 original size:23 final size:22
Alignment explanation
Indices: 42162811--42162869 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
42162801 TAAATTTTTT
42162811 TTTTTTGTATATTTTTTGTATA
1 TTTTTTGTATATTTTTTGTATA
42162833 TTTTTTGTATATCTTTTTGTATA
1 TTTTTTGTATAT-TTTTTGTATA
*
42162856 TTTTTT-TATGTTTT
1 TTTTTTGTATATTTT
42162870 AATATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 3 0.09
22 16 0.46
23 16 0.46
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (22 bp):
TTTTTTGTATATTTTTTGTATA
Found at i:42162878 original size:34 final size:34
Alignment explanation
Indices: 42162812--42162878 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
42162802 AAATTTTTTT
* *
42162812 TTTTTGTATATTTTTTGTATATTTTTTGTATATC
1 TTTTTGTATATTTTTTGTATATTTTATATATATC
*
42162846 TTTTTGTATATTTTTT-TATGTTTTAATATATAT
1 TTTTTGTATATTTTTTGTATATTTT-ATATATAT
42162879 ATAGGTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.21, C:0.01, G:0.07, T:0.70
Consensus pattern (34 bp):
TTTTTGTATATTTTTTGTATATTTTATATATATC
Found at i:42164306 original size:2 final size:2
Alignment explanation
Indices: 42164299--42164332 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42164289 TGTTTTCATA
42164299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42164333 GGATTCCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42170029 original size:40 final size:40
Alignment explanation
Indices: 42169971--42170187 Score: 305
Period size: 40 Copynumber: 5.5 Consensus size: 40
42169961 TGGATGATAA
* *
42169971 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
42170011 CCGGGCTAAGTCCTGAAGGTATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
42170051 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
42170091 CCGGGCTAAGTCCCGAAGGCATTGGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
42170131 CCGGGCTATGTCCTGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
42170170 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
42170188 TACTTGGCTT
Statistics
Matches: 159, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
38 14 0.09
39 14 0.09
40 131 0.82
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42175339 original size:31 final size:31
Alignment explanation
Indices: 42175280--42175341 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
42175270 GAGTTTGATC
*
42175280 ATATAGCACTAAGTGTGCGAGCTGAATATAT
1 ATATAGCACTAAGTGTGCGAGCTCAATATAT
42175311 ATATAGCACTAAGTGTGCG-GACTCAATATAT
1 ATATAGCACTAAGTGTGCGAG-CTCAATATAT
42175342 GCTTTTGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (31 bp):
ATATAGCACTAAGTGTGCGAGCTCAATATAT
Found at i:42181416 original size:40 final size:40
Alignment explanation
Indices: 42181361--42181563 Score: 338
Period size: 40 Copynumber: 5.1 Consensus size: 40
42181351 TGGATGATAA
*
42181361 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
42181401 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
42181441 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
42181481 CCGGGCTAAGTCCCGAAGGCATTGGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
42181521 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
42181560 CCGG
1 CCGG
42181564 TTAAATCCGA
Statistics
Matches: 155, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
38 2 0.01
39 16 0.10
40 137 0.88
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42197388 original size:20 final size:21
Alignment explanation
Indices: 42197349--42197391 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
42197339 TAAACATAAA
42197349 AATAGAAATAAAACTAAAAAT
1 AATAGAAATAAAACTAAAAAT
* *
42197370 AATAG-AATGAAATTAAAAAT
1 AATAGAAATAAAACTAAAAAT
42197390 AA
1 AA
42197392 AAATAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (21 bp):
AATAGAAATAAAACTAAAAAT
Found at i:42197394 original size:7 final size:6
Alignment explanation
Indices: 42197332--42197398 Score: 62
Period size: 6 Copynumber: 10.8 Consensus size: 6
42197322 GTCTAAAATC
* * * * *
42197332 ATAACA ATAAAC ATAAAA ATAGAA ATAAAA CTAAAA ATAATAGA ATGAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAA-A-A ATAAAA
*
42197382 TTAAAA ATAAAA ATAAA
1 ATAAAA ATAAAA ATAAA
42197399 TGATAAATGG
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
6 42 0.88
7 2 0.04
8 4 0.08
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:42199425 original size:39 final size:40
Alignment explanation
Indices: 42199304--42199442 Score: 174
Period size: 40 Copynumber: 3.5 Consensus size: 40
42199294 GGATATAACG
* * *
42199304 ACTCGCTCAAATGCCTTCGGGAC-AAACCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAACCCAGGTT-TAGTA
* *
42199344 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAACCCAGGTTTAGTA
* *
42199384 ACTCGCACAAATGCCTTCGGG-CTTAACCCAGATTTATTA
1 ACTCGCACAAATGCCTTCGGGACTTAACCCAGGTTTAGTA
* *
42199423 ACTCGCACGAACGCCTTCGG
1 ACTCGCACAAATGCCTTCGG
42199443 ATCTTAGTCC
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 33 0.38
40 46 0.52
41 9 0.10
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAACCCAGGTTTAGTA
Found at i:42202094 original size:19 final size:20
Alignment explanation
Indices: 42202060--42202098 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
42202050 ATGACAGATG
*
42202060 TAATATAAGAATAATAACAA
1 TAATATAAGAAAAATAACAA
42202080 TAATA-AAGAAAAATAACAA
1 TAATATAAGAAAAATAACAA
42202099 GTAACTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (20 bp):
TAATATAAGAAAAATAACAA
Found at i:42202291 original size:40 final size:40
Alignment explanation
Indices: 42202247--42202322 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
42202237 TAGCAGCACA
* *
42202247 TAAAAACAGAAAAGAAA-AGAAAAATA-ATTAATAATACTAG
1 TAAAAACA-AAAA-AAATAAAAAAATATAATAATAATACTAG
*
42202287 TAAAAATAAAAAAAATAAAAAAATATAATAATAATA
1 TAAAAACAAAAAAAATAAAAAAATATAATAATAATA
42202323 AACCAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
38 3 0.10
39 12 0.39
40 16 0.52
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (40 bp):
TAAAAACAAAAAAAATAAAAAAATATAATAATAATACTAG
Found at i:42202655 original size:24 final size:25
Alignment explanation
Indices: 42202602--42202663 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
42202592 TCCTTATTTC
42202602 ATTAAAT-AAAAAATTTGAAAATAT
1 ATTAAATCAAAAAATTTGAAAATAT
* *
42202626 AATAAATCAAATACATTT-AAAA-AT
1 ATTAAATCAAA-AAATTTGAAAATAT
*
42202650 ATTAAAACAAAAAA
1 ATTAAATCAAAAAA
42202664 CAAATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.06
24 17 0.55
25 7 0.23
26 5 0.16
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (25 bp):
ATTAAATCAAAAAATTTGAAAATAT
Found at i:42203364 original size:11 final size:11
Alignment explanation
Indices: 42203348--42203392 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
42203338 CCACAAAAGT
42203348 AGCACCAAAAC
1 AGCACCAAAAC
42203359 AGCACCAAAAC
1 AGCACCAAAAC
* *
42203370 AACATCAAAAC
1 AGCACCAAAAC
*
42203381 AGCTCCAAAAC
1 AGCACCAAAAC
42203392 A
1 A
42203393 TCACAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.56, C:0.33, G:0.07, T:0.04
Consensus pattern (11 bp):
AGCACCAAAAC
Found at i:42203401 original size:22 final size:22
Alignment explanation
Indices: 42203353--42203400 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
42203343 AAAGTAGCAC
42203353 CAAAACAGCACCAAAACAACAT
1 CAAAACAGCACCAAAACAACAT
* *
42203375 CAAAACAGCTCCAAAACATCA-
1 CAAAACAGCACCAAAACAACAT
42203396 CAAAA
1 CAAAA
42203401 AAAAAGCACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.58, C:0.31, G:0.04, T:0.06
Consensus pattern (22 bp):
CAAAACAGCACCAAAACAACAT
Found at i:42206458 original size:47 final size:47
Alignment explanation
Indices: 42206389--42206872 Score: 772
Period size: 47 Copynumber: 10.3 Consensus size: 47
42206379 CCCTTCGGGA
* * * * *
42206389 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42206436 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42206483 CTTATCACATATATGCACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42206530 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42206577 CTTGTCACTTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42206624 CTTGTCACTTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42206671 CTTGTCACTTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42206718 CTTGTCACTTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42206765 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42206812 CTTGTCACTTATATACAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42206858 CTTATCACATATATA
1 CTTATCACATATATA
42206873 TATCTCATAC
Statistics
Matches: 420, Mismatches: 17, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
46 40 0.10
47 380 0.90
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42206492 original size:22 final size:22
Alignment explanation
Indices: 42206464--42206539 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
42206454 TTTCACATTC
42206464 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * * *
42206486 ATCACATATATGCACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
42206510 CATCACATTGGCCATTAGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
42206533 ATCACAT
1 ATCACAT
42206540 ATATACACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 17 0.43
23 6 0.15
24 6 0.15
25 11 0.28
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:42211554 original size:20 final size:20
Alignment explanation
Indices: 42211529--42211575 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
42211519 AACCTGCAAA
* *
42211529 AAGAAGATGCAGTAGTGAAG
1 AAGAAGATGCAGCAGTAAAG
*
42211549 AAGAAGATGTAGCAGTAAAG
1 AAGAAGATGCAGCAGTAAAG
42211569 AAGAAGA
1 AAGAAGA
42211576 AGAAGAAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.32, T:0.13
Consensus pattern (20 bp):
AAGAAGATGCAGCAGTAAAG
Found at i:42217604 original size:40 final size:40
Alignment explanation
Indices: 42217536--42217738 Score: 329
Period size: 40 Copynumber: 5.1 Consensus size: 40
42217526 CCGGATTTAA
* *
42217536 CCGGATATAGCT-ACTCGCTC-AATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42217575 CCGGATATAGTAACTCACACCAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
42217615 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
42217655 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42217695 CTGGATATAATAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
42217735 CCGG
1 CCGG
42217739 TTATCATCCA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
38 1 0.01
39 16 0.10
40 137 0.89
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42221568 original size:27 final size:27
Alignment explanation
Indices: 42221538--42221706 Score: 212
Period size: 27 Copynumber: 6.3 Consensus size: 27
42221528 GGGGTAAAAT
* * *
42221538 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
42221565 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
42221592 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
42221619 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
42221646 AGTAAATCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
42221673 GGTAATTCTACCTTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
42221700 AGTAATT
1 GGTAATT
42221707 TAACAAATCA
Statistics
Matches: 123, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 123 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:42221584 original size:54 final size:54
Alignment explanation
Indices: 42221539--42221707 Score: 250
Period size: 54 Copynumber: 3.1 Consensus size: 54
42221529 GGGTAAAATG
* *
42221539 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTTTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
* *
42221593 GT-ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTT-TACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
* * * *
42221647 GTAAATCTACCCTACAGGGGTATTTCGGTAATTCTACCTTATAGGGGTATTTCA
1 GTAATTTTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
42221701 GTAATTT
1 GTAATTT
42221708 AACAAATCAG
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
53 4 0.04
54 95 0.94
55 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (54 bp):
GTAATTTTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
Found at i:42221719 original size:54 final size:53
Alignment explanation
Indices: 42221539--42221733 Score: 237
Period size: 54 Copynumber: 3.6 Consensus size: 53
42221529 GGGTAAAATG
* * *
42221539 GTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCA
1 GTAA-TTTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
* * * *
42221593 GTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCA
1 GTAATT-TACCCTACAGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
* *
42221647 GTAAATCTACCCTACAGGGGTATTTCGGTAATTCTACCTTATAGGGGTATTTCA
1 GT-AATTTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
* ** *
42221701 GTAATTTAACAAATCAGGGGTATTTTGGTAATT
1 GTAATTTACCCTA-CAGGGGTATTTCGGTAATT
42221734 TTTCTAATCG
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
53 9 0.07
54 111 0.91
55 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (53 bp):
GTAATTTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCA
Found at i:42221722 original size:81 final size:81
Alignment explanation
Indices: 42221552--42221725 Score: 206
Period size: 81 Copynumber: 2.1 Consensus size: 81
42221542 ATTTTACCCC
* * * * *
42221552 ACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATT
1 ACAAGGGTATTTCAGTAAATCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATT
* * **
42221617 TCGGTAATTCTACCCT
66 TCAGTAATTCTAACAA
* * * *
42221633 ACAAGGGTATTTCAGTAAATCTACCCTACAGGGGTATTTCGGTAATTCTACCTTATAGGGGTATT
1 ACAAGGGTATTTCAGTAAATCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATT
42221698 TCAGTAATT-TAACAA
66 TCAGTAATTCTAACAA
*
42221713 ATCAGGGGTATTT
1 A-CAAGGGTATTT
42221726 TGGTAATTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 4 0.05
81 74 0.95
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (81 bp):
ACAAGGGTATTTCAGTAAATCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATT
TCAGTAATTCTAACAA
Found at i:42221742 original size:27 final size:27
Alignment explanation
Indices: 42221661--42221761 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 27
42221651 ATCTACCCTA
* *
42221661 CAGGGGTATTTCGGTAATTCTACCTTAT
1 CAGGGGTATTTCGGTAATT-TAACTAAT
* *
42221689 -AGGGGTATTTCAGTAATTTAACAAAT
1 CAGGGGTATTTCGGTAATTTAACTAAT
* **
42221715 CAGGGGTATTTTGGTAATTTTTCTAAT
1 CAGGGGTATTTCGGTAATTTAACTAAT
* *
42221742 C-GAGGGTATTTTGGCAATTT
1 CAG-GGGTATTTCGGTAATTT
42221762 CATAAACCAG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
26 6 0.10
27 55 0.90
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.41
Consensus pattern (27 bp):
CAGGGGTATTTCGGTAATTTAACTAAT
Found at i:42221794 original size:26 final size:26
Alignment explanation
Indices: 42221720--42221787 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
42221710 CAAATCAGGG
* * *
42221720 GTATTTTGGTAATTTTTC-TAATCGAGG
1 GTATTTTGGTAA--TTTCATAAACCAGA
*
42221747 GTATTTTGGCAATTTCATAAACCAGA
1 GTATTTTGGTAATTTCATAAACCAGA
42221773 GTATTTTGGTAATTT
1 GTATTTTGGTAATTT
42221788 GGTAAACTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 4 0.11
26 20 0.57
27 11 0.31
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.46
Consensus pattern (26 bp):
GTATTTTGGTAATTTCATAAACCAGA
Found at i:42221801 original size:26 final size:26
Alignment explanation
Indices: 42221747--42221803 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
42221737 CTAATCGAGG
*
42221747 GTATTTTGGCAATTTCATAAACCAGA
1 GTATTTTGGCAATTTCATAAACCAAA
* ** *
42221773 GTATTTTGGTAATTTGGTAAACTAAA
1 GTATTTTGGCAATTTCATAAACCAAA
42221799 GTATT
1 GTATT
42221804 CTAAACAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (26 bp):
GTATTTTGGCAATTTCATAAACCAAA
Found at i:42223971 original size:69 final size:69
Alignment explanation
Indices: 42223875--42224056 Score: 301
Period size: 69 Copynumber: 2.6 Consensus size: 69
42223865 ACAGATATAT
* * * * *
42223875 ATATATATGTGGCAAAGCCACCAGATTGCAGTGAGGCTGCCAGATATTGTGACGAAGTCACTAGA
1 ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTAACGAAGTCACCAGA
42223940 ACAG
66 ACAG
*
42223944 ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGTTGCCAGATATTGTAACGAAGTCACCAGA
1 ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTAACGAAGTCACCAGA
42224009 ACAG
66 ACAG
*
42224013 ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTACCAGA
1 ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGA
42224057 ACGCTTCCTC
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 105 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.20
Consensus pattern (69 bp):
ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTAACGAAGTCACCAGA
ACAG
Found at i:42224748 original size:54 final size:54
Alignment explanation
Indices: 42224690--42224860 Score: 240
Period size: 54 Copynumber: 3.2 Consensus size: 54
42224680 GGGCAAAATG
* *
42224690 GTAATTTTACCCCACAAGGGTATCTT-GGTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTTTACCCTACAAGGGTAT-TTCGGTAATTCTACCCTACAGGGGTATTTCA
42224744 GTAATTCTTA-CCTACAAGGGTATTTCGGTAATTCTACCCTACA-GGGTATTTCA
1 GTAATT-TTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* * * * *
42224797 GTAAATCTACCCTACAGGGGTATTTCGGTAATTCTACCATACAGGGGTATTTTA
1 GTAATTTTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
42224851 GTAATTTTAC
1 GTAATTTTAC
42224861 AAATTAGAGG
Statistics
Matches: 104, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
52 2 0.02
53 47 0.45
54 52 0.50
55 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (54 bp):
GTAATTTTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
Found at i:42224811 original size:80 final size:81
Alignment explanation
Indices: 42224689--42224848 Score: 236
Period size: 80 Copynumber: 2.0 Consensus size: 81
42224679 GGGGCAAAAT
* * *
42224689 GGTAATTTTACCCCACAAGGGTATCTTGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTTA
1 GGTAATTCTACCCCACAAGGGTATCTTAGTAAATCTACCCTACAGGGGTATTTCGGTAATTC-TA
42224754 CC-TACAAGGGTATTTC
65 CCATACAAGGGTATTTC
*
42224770 GGTAATTCTACCCTAC-AGGGTAT-TTCAGTAAATCTACCCTACAGGGGTATTTCGGTAATTCTA
1 GGTAATTCTACCCCACAAGGGTATCTT-AGTAAATCTACCCTACAGGGGTATTTCGGTAATTCTA
*
42224833 CCATACAGGGGTATTT
65 CCATACAAGGGTATTT
42224849 TAGTAATTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
79 6 0.08
80 52 0.72
81 14 0.19
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (81 bp):
GGTAATTCTACCCCACAAGGGTATCTTAGTAAATCTACCCTACAGGGGTATTTCGGTAATTCTAC
CATACAAGGGTATTTC
Found at i:42224818 original size:53 final size:55
Alignment explanation
Indices: 42224696--42224854 Score: 227
Period size: 53 Copynumber: 2.9 Consensus size: 55
42224686 AATGGTAATT
* * *
42224696 TTACCCCACAAGGGTATCTT-GGTAATTCTACCCTACAGGGGTATTTCGGTAATTC
1 TTACCCTACAAGGGTAT-TTCGGTAATTCTACCCTACAGGGGTATTTCAGTAAATC
42224751 TTA-CCTACAAGGGTATTTCGGTAATTCTACCCTACA-GGGTATTTCAGTAAATC
1 TTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAAATC
* * *
42224804 -TACCCTACAGGGGTATTTCGGTAATTCTACCATACAGGGGTATTTTAGTAA
1 TTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAA
42224855 TTTTACAAAT
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
52 2 0.02
53 48 0.51
54 42 0.44
55 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (55 bp):
TTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAAATC
Found at i:42224856 original size:27 final size:27
Alignment explanation
Indices: 42224689--42224848 Score: 218
Period size: 27 Copynumber: 6.0 Consensus size: 27
42224679 GGGGCAAAAT
* * *
42224689 GGTAATTTTACCCCACAAGGGTATCTT-
1 GGTAATTCTACCCTACAGGGGTAT-TTC
42224716 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42224743 GGTAATTCTTA-CCTACAAGGGTATTTC
1 GGTAATTC-TACCCTACAGGGGTATTTC
42224770 GGTAATTCTACCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42224796 AGTAAATCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42224823 GGTAATTCTACCATACAGGGGTATTT
1 GGTAATTCTACCCTACAGGGGTATTT
42224849 TAGTAATTTT
Statistics
Matches: 120, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
26 28 0.23
27 90 0.75
28 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:42224873 original size:54 final size:52
Alignment explanation
Indices: 42224705--42224883 Score: 182
Period size: 54 Copynumber: 3.3 Consensus size: 52
42224695 TTTACCCCAC
* * *
42224705 AAGGGTATCTT-GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTTACCTAC
1 AAGGGTAT-TTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATT-TTA-CAAT
* * **
42224759 AAGGGTATTTCGGTAATTCTACCCTACA-GGGTATTTCAGTAAATCTACCCT
1 AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTTTACAAT
* *
42224810 ACAGGGGTATTTCGGTAATTCTACCATACAGGGGTATTTTAGTAATTTTACAAAT
1 A-A-GGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTTTAC-AAT
* *
42224865 TAGAGGTATTTTGGTAATT
1 AAG-GGTATTTCGGTAATT
42224884 TGTTGAACTA
Statistics
Matches: 105, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
51 2 0.02
52 3 0.03
53 42 0.40
54 57 0.54
55 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (52 bp):
AAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTTTACAAT
Found at i:42231929 original size:13 final size:13
Alignment explanation
Indices: 42231911--42231936 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42231901 ACGAGGGCTC
42231911 CTTCGTTCCTTTG
1 CTTCGTTCCTTTG
42231924 CTTCGTTCCTTTG
1 CTTCGTTCCTTTG
42231937 TGGATCTCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.15, T:0.54
Consensus pattern (13 bp):
CTTCGTTCCTTTG
Found at i:42243003 original size:7 final size:7
Alignment explanation
Indices: 42242991--42243018 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
42242981 GGATGATTAG
42242991 GGGATGA
1 GGGATGA
42242998 GGGATGA
1 GGGATGA
42243005 GGGATGA
1 GGGATGA
42243012 GGGATGA
1 GGGATGA
42243019 TTAGAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.57, T:0.14
Consensus pattern (7 bp):
GGGATGA
Found at i:42247004 original size:93 final size:93
Alignment explanation
Indices: 42246892--42247062 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
42246882 GCCCATAAGT
*
42246892 GAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
42246956 ATGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
* *
42246985 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
42247050 CGAGTTCGGATGC
66 CGAGCTCGGATGC
42247063 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 70 0.97
94 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:42247054 original size:46 final size:46
Alignment explanation
Indices: 42246884--42247059 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
42246874 TGTAACCCGC
*
42246884 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCAT
* * *
42246930 CCATAAGTGAACTCAGACTCAACTCAATGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
42246976 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
42247023 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
42247060 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 66 0.62
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:42252310 original size:19 final size:19
Alignment explanation
Indices: 42252288--42252324 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
42252278 ACTATCACCG
42252288 ACCATAATCAAATTTGTTC
1 ACCATAATCAAATTTGTTC
42252307 ACCATAATCAAATTTGTT
1 ACCATAATCAAATTTGTT
42252325 AATAACTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (19 bp):
ACCATAATCAAATTTGTTC
Found at i:42253911 original size:3 final size:3
Alignment explanation
Indices: 42253903--42253950 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
42253893 AAAACTGCAA
42253903 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG
42253949 AA
1 AA
42253951 TCCAGGTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42257743 original size:14 final size:14
Alignment explanation
Indices: 42257724--42257775 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
42257714 TTGTAATGTA
42257724 TGTTTTTATGTTAC
1 TGTTTTTATGTTAC
*
42257738 TGTTTTTCGATAATGTA-
1 TGTTTTT--AT-GT-TAC
42257755 TGTTTTTATGTTAC
1 TGTTTTTATGTTAC
42257769 TGTTTTT
1 TGTTTTT
42257776 CGATAATGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
13 2 0.06
14 15 0.48
15 2 0.06
16 2 0.06
17 8 0.26
18 2 0.06
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.63
Consensus pattern (14 bp):
TGTTTTTATGTTAC
Found at i:42257755 original size:31 final size:31
Alignment explanation
Indices: 42257717--42257783 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
42257707 GAAATGATTG
42257717 TAATGTATGTTTTTATGTTACTGTTTTTCGA
1 TAATGTATGTTTTTATGTTACTGTTTTTCGA
42257748 TAATGTATGTTTTTATGTTACTGTTTTTCGA
1 TAATGTATGTTTTTATGTTACTGTTTTTCGA
42257779 TAATG
1 TAATG
42257784 CTCTGTAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.21, C:0.06, G:0.16, T:0.57
Consensus pattern (31 bp):
TAATGTATGTTTTTATGTTACTGTTTTTCGA
Found at i:42258217 original size:51 final size:51
Alignment explanation
Indices: 42258158--42258258 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
42258148 AATGTTTGCA
42258158 TAGCTATATTTTCCCCGAAGTTTGATGCACAAATCACTTTTTTCTTAGGTT
1 TAGCTATATTTTCCCCGAAGTTTGATGCACAAATCACTTTTTTCTTAGGTT
42258209 TAGCTATATTTTCCCCGAAGTTTGATGCACAAATCACTTTTTTCTTAGGT
1 TAGCTATATTTTCCCCGAAGTTTGATGCACAAATCACTTTTTTCTTAGGT
42258259 GGAAGTTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.43
Consensus pattern (51 bp):
TAGCTATATTTTCCCCGAAGTTTGATGCACAAATCACTTTTTTCTTAGGTT
Found at i:42261750 original size:45 final size:44
Alignment explanation
Indices: 42261699--42261829 Score: 155
Period size: 45 Copynumber: 3.0 Consensus size: 44
42261689 TTTGTTTTTC
*
42261699 ATAAAAGATAATTGAAAATTTAAAAATTTGTCCACATTTAAAATG
1 ATAAAAGATAATTGAAAA-TTAAAAATTTGTTCACATTTAAAATG
* *
42261744 ATAAAAGATAATTAAAAAATTAAAAATTTGTTCACGTTTAAAATG
1 ATAAAAGATAATT-GAAAATTAAAAATTTGTTCACATTTAAAATG
* *
42261789 ACAATAACATAA--G---ATTAAAAATTTGTTCACATTTAAAATG
1 ATAA-AAGATAATTGAAAATTAAAAATTTGTTCACATTTAAAATG
42261829 A
1 A
42261830 CAATAACATA
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
40 27 0.35
45 40 0.52
46 10 0.13
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (44 bp):
ATAAAAGATAATTGAAAATTAAAAATTTGTTCACATTTAAAATG
Found at i:42261806 original size:40 final size:40
Alignment explanation
Indices: 42261762--42261839 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
42261752 TAATTAAAAA
*
42261762 ATTAAAAATTTGTTCACGTTTAAAATGACAATAACATAAG
1 ATTAAAAATTTGTTCACATTTAAAATGACAATAACATAAG
42261802 ATTAAAAATTTGTTCACATTTAAAATGACAATAACATA
1 ATTAAAAATTTGTTCACATTTAAAATGACAATAACATA
42261840 GGACATAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (40 bp):
ATTAAAAATTTGTTCACATTTAAAATGACAATAACATAAG
Found at i:42276681 original size:8 final size:8
Alignment explanation
Indices: 42276670--42276803 Score: 60
Period size: 8 Copynumber: 17.2 Consensus size: 8
42276660 TTAATAATAT
42276670 TTATATTA
1 TTATATTA
42276678 TTATA-T-
1 TTATATTA
42276684 TTATATTA
1 TTATATTA
*
42276692 ATATATTTCGA
1 TTATA-TT--A
*
42276703 TT-TATAAA
1 TTATAT-TA
42276711 TCTATATT-
1 T-TATATTA
42276719 TCTATATTA
1 T-TATATTA
42276728 TT-TATT-
1 TTATATTA
*
42276734 TTATTATTC
1 TTA-TATTA
*
42276743 TATCTATTA
1 T-TATATTA
42276752 TTATATTA
1 TTATATTA
42276760 TCTAT-TTA
1 T-TATATTA
42276768 -TATATTA
1 TTATATTA
42276775 TT-T-TTA
1 TTATATTA
42276781 -TATATTA
1 TTATATTA
42276788 TTATA-TA
1 TTATATTA
42276795 -TATATTA
1 TTATATTA
42276802 TT
1 TT
42276804 TCTATTTAGT
Statistics
Matches: 98, Mismatches: 7, Indels: 42
0.67 0.05 0.29
Matches are distributed among these distances:
5 1 0.01
6 18 0.18
7 17 0.17
8 40 0.41
9 14 0.14
10 6 0.06
11 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:42276741 original size:15 final size:14
Alignment explanation
Indices: 42276725--42276870 Score: 85
Period size: 13 Copynumber: 10.5 Consensus size: 14
42276715 TATTTCTATA
42276725 TTATTTATT-TTA-
1 TTATTTATTATTAT
42276737 TTATTCTATCTATTA-
1 TTATT-TAT-TATTAT
42276752 TTA--TATTATCTAT
1 TTATTTATTAT-TAT
*
42276765 TTATATATTATT-T
1 TTATTTATTATTAT
*
42276778 TTATATATTATTAT
1 TTATTTATTATTAT
* *
42276792 ATATATATTATT-T
1 TTATTTATTATTAT
*
42276805 CTATTTAGTTATTAT
1 TTATTTA-TTATTAT
*
42276820 TTAGTTATTATT-T
1 TTATTTATTATTAT
* *
42276833 ATATTTAGTA-TAT
1 TTATTTATTATTAT
42276846 TTAGAATTTATTATTAT
1 TT---ATTTATTATTAT
42276863 TTAATTTA
1 TT-ATTTA
42276871 AGTTAAATAG
Statistics
Matches: 109, Mismatches: 10, Indels: 27
0.75 0.07 0.18
Matches are distributed among these distances:
11 3 0.03
12 11 0.10
13 35 0.32
14 24 0.22
15 24 0.22
16 7 0.06
17 5 0.05
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:42276755 original size:23 final size:23
Alignment explanation
Indices: 42276715--42276837 Score: 81
Period size: 23 Copynumber: 5.0 Consensus size: 23
42276705 TATAAATCTA
*
42276715 TATTTCTATATTATTTATTT-TAT
1 TATTTATATATTA-TTATTTATAT
* *
42276738 TATTCTATCTATTATTATATTAT-C
1 TATT-TATATATTATTAT-TTATAT
*
42276762 TATTTATATATTATTTTTATATAT
1 TATTTATATATTATTATT-TATAT
*
42276786 TA-TTATATATATATTATTTCTATT
1 TATTTATATAT-TATTATTTATA-T
*
42276810 TAGTTATTATTTAGTTATTATTTATAT
1 TA--T-TTATATA-TTATTATTTATAT
42276837 T
1 T
42276838 TAGTATATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.01
23 33 0.42
24 24 0.31
25 1 0.01
27 2 0.03
28 16 0.21
29 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTTATATATTATTATTTATAT
Found at i:42276809 original size:44 final size:47
Alignment explanation
Indices: 42276715--42276846 Score: 129
Period size: 47 Copynumber: 2.9 Consensus size: 47
42276705 TATAAATCTA
* * *
42276715 TATTTCTATATTATTTATTTTATTATTCTATCTATTATTATATTATC
1 TATTTATATATTATTTATTTTATTATTATATATATTATTATATTATC
42276762 TATTTATATATTATTT-TTATATATTATTATATATA-TA-T-TATT-TC
1 TATTTATATATTATTTATT-T-TATTATTATATATATTATTATATTATC
* *
42276806 TATTTAGT-TATTATTTA-GTTATTATT-TATAT-TTAGTATATT
1 TATTTA-TATATTATTTATTTTATTATTATATATATTATTATATT
42276847 TAGAATTTAT
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
41 7 0.09
42 8 0.11
43 5 0.07
44 16 0.22
45 5 0.07
46 3 0.04
47 18 0.24
48 12 0.16
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (47 bp):
TATTTATATATTATTTATTTTATTATTATATATATTATTATATTATC
Found at i:42276820 original size:11 final size:11
Alignment explanation
Indices: 42276806--42276833 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
42276796 ATATTATTTC
42276806 TATTTAGTTAT
1 TATTTAGTTAT
42276817 TATTTAGTTAT
1 TATTTAGTTAT
42276828 TATTTA
1 TATTTA
42276834 TATTTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (11 bp):
TATTTAGTTAT
Found at i:42276837 original size:28 final size:28
Alignment explanation
Indices: 42276757--42276846 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 28
42276747 TATTATTATA
* *
42276757 TTATCTATTTATATATTATTTTTATATA-
1 TTAT-TATTTATATATTATTTATATTTAG
* *
42276785 TTATTATATATATATTATTTCTATTTAG
1 TTATTATTTATATATTATTTATATTTAG
42276813 TTATTATTTAGT-TATTATTTATATTTAG
1 TTATTATTTA-TATATTATTTATATTTAG
42276841 TATATT
1 T-TATT
42276847 TAGAATTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 20 0.37
28 29 0.54
29 5 0.09
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.63
Consensus pattern (28 bp):
TTATTATTTATATATTATTTATATTTAG
Found at i:42276882 original size:31 final size:32
Alignment explanation
Indices: 42276824--42276931 Score: 114
Period size: 31 Copynumber: 3.4 Consensus size: 32
42276814 TATTATTTAG
* **
42276824 TTATTATTTATATTT-AGTATATTTAGAATTTA
1 TTATTATTTA-ATTTAAGTATAATTAGAATAAA
*
42276856 TTATTATTTAATTTAAGT-TAAATAGAA-AAA
1 TTATTATTTAATTTAAGTATAATTAGAATAAA
* *
42276886 TTAATAATTTAATTTAAGTATAATTAAAATAAA
1 TT-ATTATTTAATTTAAGTATAATTAGAATAAA
42276919 TTATTAATTTAAT
1 TTATT-ATTTAAT
42276932 AATTTAGTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
30 3 0.05
31 26 0.41
32 22 0.35
33 12 0.19
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (32 bp):
TTATTATTTAATTTAAGTATAATTAGAATAAA
Found at i:42283769 original size:24 final size:20
Alignment explanation
Indices: 42283724--42283763 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42283714 GTTCCATGAG
42283724 AATGAGTTACTTGGCAATTC
1 AATGAGTTACTTGGCAATTC
42283744 AATGAGTTACTTGGCAATTC
1 AATGAGTTACTTGGCAATTC
42283764 GTTCAAGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
AATGAGTTACTTGGCAATTC
Found at i:42289908 original size:6 final size:6
Alignment explanation
Indices: 42289885--42290000 Score: 67
Period size: 6 Copynumber: 18.8 Consensus size: 6
42289875 TATCAAAACT
* * * * *
42289885 AGAATC AAAATG AGAATC AGAATC AGAATC AG-GTGAC AGAATT AGAATT
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * * * *
42289934 AAAATC AGAATT AGAATT AG-GTGAC AGAATC AGAATC AGTATC AGGTAA-C
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC A-G-AATC
42289984 AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAAT
42290001 GTGAATGCAA
Statistics
Matches: 85, Mismatches: 16, Indels: 18
0.71 0.13 0.15
Matches are distributed among these distances:
5 4 0.05
6 70 0.82
7 8 0.09
8 3 0.04
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:42289926 original size:19 final size:19
Alignment explanation
Indices: 42289902--42289972 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
42289892 AAATGAGAAT
42289902 CAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAGGTGA
* * **
42289921 CAGAATTAGAATTA--AAA
1 CAGAATCAGAATCAGGTGA
* *
42289938 TCAGAATTAGAATTAGGTGA
1 -CAGAATCAGAATCAGGTGA
42289958 CAGAATCAGAATCAG
1 CAGAATCAGAATCAG
42289973 TATCAGGTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
17 1 0.02
18 14 0.34
19 25 0.61
20 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.21
Consensus pattern (19 bp):
CAGAATCAGAATCAGGTGA
Found at i:42289926 original size:37 final size:37
Alignment explanation
Indices: 42289885--42289991 Score: 117
Period size: 37 Copynumber: 2.9 Consensus size: 37
42289875 TATCAAAACT
* *
42289885 AGAATCAAAATGAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGAATCAGGTGAC
* * * * *
42289922 AGAATTAGAATTAAAATCAGAATTAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGAATCAGGTGAC
*
42289959 AGAATCAGAATCAGTATCAGGTAA-CAGAATCAG
1 AGAATCAGAATCAGAATCA-G-AATCAGAATCAG
42289992 AATCAGAATG
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
37 46 0.82
38 8 0.14
39 2 0.04
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.21
Consensus pattern (37 bp):
AGAATCAGAATCAGAATCAGAATCAGAATCAGGTGAC
Found at i:42289964 original size:25 final size:25
Alignment explanation
Indices: 42289936--42290000 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
42289926 TTAGAATTAA
* * *
42289936 AATCAGAATTAGAATTAGGTGACAG
1 AATCAGAATCAGAATCAGGTAACAG
*
42289961 AATCAGAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAGGTAACAG
42289986 AATCAGAATCAGAAT
1 AATCAGAATCAGAAT
42290001 GTGAATGCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (25 bp):
AATCAGAATCAGAATCAGGTAACAG
Found at i:42290158 original size:27 final size:26
Alignment explanation
Indices: 42290118--42290253 Score: 164
Period size: 27 Copynumber: 5.0 Consensus size: 26
42290108 AACATGGCTG
* * *
42290118 CCAGAACAAATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
42290144 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
*
42290171 CCAGAACAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGGCAGAGCCA
42290198 CCAGAAACAGAATATTGTGGCAGAGCCA
1 CCAG-AACAG-ATATTGTGGCAGAGCCA
* * *
42290226 CCAGAATCAGATAATGTAGCAAAGCCA
1 CCAGAA-CAGATATTGTGGCAGAGCCA
42290253 C
1 C
42290254 TTAACAGAAT
Statistics
Matches: 97, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
26 12 0.12
27 57 0.59
28 25 0.26
29 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:42290252 original size:55 final size:54
Alignment explanation
Indices: 42290142--42290253 Score: 163
Period size: 55 Copynumber: 2.1 Consensus size: 54
42290132 GTGACAGAGT
* * * *
42290142 CACCAGATACAGATATTGTGGCAGAGCCACCAGAACAGATATTTGTGGCATAGC
1 CACCAGAAACAGATATTGTGGCAGAGCCACCAGAACAGATATATGTAGCAAAGC
42290196 CACCAGAAACAGAATATTGTGGCAGAGCCACCAGAATCAGATA-ATGTAGCAAAGC
1 CACCAGAAACAG-ATATTGTGGCAGAGCCACCAGAA-CAGATATATGTAGCAAAGC
42290251 CAC
1 CAC
42290254 TTAACAGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 11 0.21
55 35 0.67
56 6 0.12
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (54 bp):
CACCAGAAACAGATATTGTGGCAGAGCCACCAGAACAGATATATGTAGCAAAGC
Found at i:42290406 original size:27 final size:27
Alignment explanation
Indices: 42290376--42290427 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
42290366 ATTCGTCAAC
*
42290376 AAATATGTTAGGCAC-ATAGCCATAGGT
1 AAATACGTTAGGCACGA-AGCCATAGGT
*
42290403 AAATACGTTTGGCACGAAGCCATAG
1 AAATACGTTAGGCACGAAGCCATAG
42290428 TCAAGATGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (27 bp):
AAATACGTTAGGCACGAAGCCATAGGT
Found at i:42290459 original size:22 final size:22
Alignment explanation
Indices: 42290411--42290469 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
42290401 GTAAATACGT
*
42290411 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
42290433 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
42290455 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
42290470 CGAAAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:42290515 original size:20 final size:20
Alignment explanation
Indices: 42290486--42290533 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
42290476 CGGGTCTATA
42290486 ATCGACACGAAGCCCACAAT
1 ATCGACACGAAGCCCACAAT
*
42290506 ATCGATACGAAGCCCACAAT
1 ATCGACACGAAGCCCACAAT
*
42290526 AACGACAC
1 ATCGACAC
42290534 ACAGTCTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.33, G:0.15, T:0.10
Consensus pattern (20 bp):
ATCGACACGAAGCCCACAAT
Found at i:42290866 original size:27 final size:27
Alignment explanation
Indices: 42290817--42291255 Score: 538
Period size: 27 Copynumber: 16.3 Consensus size: 27
42290807 GGGGCAAAAT
* * *
42290817 GGTAATTTTACCCCAC-GAGGGTATCTC
1 GGTAATTCTACCCTACAG-GGGTATTTC
* *
42290844 GGTAATTCTACCCTACAGAGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
42290871 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42290898 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** *
42290925 AATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42290952 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42290979 GGTAATTCTACCTTACATGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42291006 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42291033 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42291060 GGTAATTCTACCTTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
42291087 AATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42291114 GGTAATTCTACCTTACAGGAGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
42291141 AGTAATTCTAACCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
42291168 GATAATTCTACCTTACAGGAGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42291195 AGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42291222 GGTAATTCTACCTTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
42291249 GGTAATT
1 GGTAATT
42291256 TTTCTAATCG
Statistics
Matches: 359, Mismatches: 52, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
27 358 1.00
28 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:42291255 original size:54 final size:54
Alignment explanation
Indices: 42290818--42291247 Score: 592
Period size: 54 Copynumber: 8.0 Consensus size: 54
42290808 GGGCAAAATG
* * * * * *
42290818 GTAATTTTACCCCAC-GAGGGTATCTCGGTAATTCTACCCTACAGAGGTATTTTA
1 GTAATTCTACCCTACAG-GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* * * * *
42290872 GTATTTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* * *
42290926 ATAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* * * * *
42290980 GTAATTCTACCTTACATGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
*
42291034 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* *
42291088 ATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGAGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
* * * * *
42291142 GTAATTCTAACCTATAGGGGTATTTTGATAATTCTACCTTACAGGAGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
*
42291196 GTAATTCTACCTTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTT
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTT
42291248 TGGTAATTTT
Statistics
Matches: 330, Mismatches: 45, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
54 330 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (54 bp):
GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCA
Found at i:42291270 original size:27 final size:27
Alignment explanation
Indices: 42291240--42291310 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
42291230 TACCTTACAG
*
42291240 GGGTATTTTGGTAATTTTTCTAATCGA
1 GGGTATTTTGGTAATTTTGCTAATCGA
*
42291267 GGGTATTTTGGTAATTTTGCTAATCGT
1 GGGTATTTTGGTAATTTTGCTAATCGA
* * *
42291294 GGCTGTTTTAGTAATTT
1 GGGTATTTTGGTAATTT
42291311 GGTAAACTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTGCTAATCGA
Found at i:42292214 original size:24 final size:25
Alignment explanation
Indices: 42292182--42292242 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
42292172 TGTTACATTT
**
42292182 GAGCTTACTGTTCT-CAGCT-TGTCA
1 GAGCTTACTGTTCTCCAGCTCAAT-A
42292206 GAGCTTACTGTT-TCCAGCTCAATA
1 GAGCTTACTGTTCTCCAGCTCAATA
42292230 GAGCTTACTGTTC
1 GAGCTTACTGTTC
42292243 ATCATCTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 1 0.03
24 30 0.94
25 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (25 bp):
GAGCTTACTGTTCTCCAGCTCAATA
Found at i:42295252 original size:13 final size:13
Alignment explanation
Indices: 42295234--42295258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42295224 GTAAGTGATT
42295234 TTGATGATTTTTC
1 TTGATGATTTTTC
42295247 TTGATGATTTTT
1 TTGATGATTTTT
42295259 GTACTTTTAG
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:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:42296147 original size:49 final size:47
Alignment explanation
Indices: 42296024--42296198 Score: 131
Period size: 49 Copynumber: 3.6 Consensus size: 47
42296014 TCATAAAGGA
* * * *
42296024 AGCCAGTGTAAGACCATGTCTGGGACCTGGCACCGGGA-TGGATATGCGA-G
1 AGCCAGTGTAAGACCATCTCTGGGACATGGCAAC--GACTCGATA--C-ATG
* * * * * *
42296074 AGCTAGTGTAACACTATGTTTGGGACATGGCATCGACCTCGATGACGAT-
1 AGCCAGTGTAAGACCATCTCTGGGACATGGCAACGA-CTCGAT-AC-ATG
* *
42296123 AGTCAGTGTAAGACCATCTCTGGGACATGGCAACGACTTGATACATG
1 AGCCAGTGTAAGACCATCTCTGGGACATGGCAACGACTCGATACATG
* *
42296170 AGCCAGTGTAAGACCATGTTTGGGACATG
1 AGCCAGTGTAAGACCATCTCTGGGACATG
42296199 ACATTGGTAT
Statistics
Matches: 102, Mismatches: 18, Indels: 13
0.77 0.14 0.10
Matches are distributed among these distances:
46 2 0.02
47 28 0.27
48 7 0.07
49 32 0.31
50 32 0.31
51 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (47 bp):
AGCCAGTGTAAGACCATCTCTGGGACATGGCAACGACTCGATACATG
Found at i:42302846 original size:13 final size:13
Alignment explanation
Indices: 42302828--42302852 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42302818 GTAAGTGATT
42302828 TTGATGATTTTTC
1 TTGATGATTTTTC
42302841 TTGATGATTTTT
1 TTGATGATTTTT
42302853 GTACTTTTAG
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:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:42303685 original size:94 final size:99
Alignment explanation
Indices: 42303567--42303793 Score: 252
Period size: 94 Copynumber: 2.3 Consensus size: 99
42303557 ATATTATGAG
* * * *
42303567 AGCCAGTGTCAGACCATGTCTGGGACATGGCATCGGCAT-TA-AGACGAGAGCTAGTGTAATAT-
1 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATGGATAGACGAGAGCTAGTGTAAGATC
* * * *
42303629 GTGTCTGGGACATG-CATCGGCCTTG-TAAAG-T
66 ATATCTGGGACATGACATCGACCTCGATAAAGAT
* * *
42303660 AAGCC-GATGTAAGACCATGTTTGGGACATGGCATGGGCATGGATATACGAGAGCTTGTGTAAGA
1 -AGCCAG-TGTAAGACCATGTTTGGGACATGGCATCGGCATGGATAGACGAGAGCTAGTGTAAGA
* * *
42303724 TCATATTTGGGACATGACATCGACCTCGATGACGAT
64 TCATATCTGGGACATGACATCGACCTCGATAAAGAT
*
42303760 AGTCAGTGTAAGACCATGTTTGGGACATGGCATC
1 AGCCAGTGTAAGACCATGTTTGGGACATGGCATC
42303794 AACTTGAGAC
Statistics
Matches: 109, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
93 1 0.01
94 34 0.31
95 1 0.01
96 18 0.17
97 11 0.10
98 9 0.08
99 33 0.30
100 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (99 bp):
AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATGGATAGACGAGAGCTAGTGTAAGATC
ATATCTGGGACATGACATCGACCTCGATAAAGAT
Found at i:42303782 original size:49 final size:49
Alignment explanation
Indices: 42303667--42303840 Score: 167
Period size: 47 Copynumber: 3.6 Consensus size: 49
42303657 AGTAAGCCGA
* * * * * * *
42303667 TGTAAGACCATGTTTGGGACATGGCATGGGCATGGATATACGAGAGCTTG
1 TGTAAGACCATGTTTGGGACATGGCATCGACCTCGAT-GACGATAGCTAG
* * *
42303717 TGTAAGATCATATTTGGGACATGACATCGACCTCGATGACGATAG-TCAG
1 TGTAAGACCATGTTTGGGACATGGCATCGACCTCGATGACGATAGCT-AG
* *
42303766 TGTAAGACCATGTTTGGGACATGGCATC-AACTTGA-GAC-ATGAGCTAG
1 TGTAAGACCATGTTTGGGACATGGCATCGACCTCGATGACGAT-AGCTAG
* *
42303813 TGTAAGACCATGTCTAGGACATGGCATC
1 TGTAAGACCATGTTTGGGACATGGCATC
42303841 AGTATTATAC
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
46 2 0.02
47 33 0.32
48 7 0.07
49 32 0.31
50 30 0.29
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (49 bp):
TGTAAGACCATGTTTGGGACATGGCATCGACCTCGATGACGATAGCTAG
Found at i:42306318 original size:14 final size:14
Alignment explanation
Indices: 42306299--42306335 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
42306289 AACTTTCAAG
42306299 ATAATTCAAAACTC
1 ATAATTCAAAACTC
42306313 ATAATTCAAAACTC
1 ATAATTCAAAACTC
42306327 ATATATTCA
1 ATA-ATTCA
42306336 TATTCCGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATTCAAAACTC
Found at i:42306618 original size:85 final size:85
Alignment explanation
Indices: 42306515--42306753 Score: 361
Period size: 85 Copynumber: 2.8 Consensus size: 85
42306505 TTAACATGTA
* * * *
42306515 TAACCATGGCATATCCACTTAGCAGCACATTACATGTTTAATCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
42306580 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
* * * * *
42306600 TAACCGTTGCATACCCACTTAGCATCATGTTACATGTTTAACCATGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
*
42306665 CGTTAATGACTCAATATATG
66 CGTTAATGAATCAATATATG
* * *
42306685 TAACTGTGGCATATCCACTTAGCACCACGTTACACGTATAACCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
42306750 CGTT
66 CGTT
42306754 TTTTCATTCC
Statistics
Matches: 137, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 137 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
CGTTAATGAATCAATATATG
Found at i:42309016 original size:15 final size:15
Alignment explanation
Indices: 42308998--42309039 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
42308988 GAAGTCCAGA
42308998 ATAAGGAAATCCAAG
1 ATAAGGAAATCCAAG
* *
42309013 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
42309028 ATAAGGAAATCC
1 ATAAGGAAATCC
42309040 CATTTACAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:42312336 original size:38 final size:38
Alignment explanation
Indices: 42312293--42312447 Score: 184
Period size: 38 Copynumber: 3.8 Consensus size: 38
42312283 TTAACTTGTA
42312293 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTT
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTT
* * *
42312331 TAACCGTGGTATATCCACTTGGCACCACGTTAATGAATCAATATAT
1 TAACCGTGGCATATCCACTTAGCACCACG-T--T--A-C-ATGT-T
*
42312377 GTAACCGTGGCATATCCACTTAGCACCACTTTACATGTT
1 -TAACCGTGGCATATCCACTTAGCACCACGTTACATGTT
*
42312416 TAACCGTGGTATATCCACTTAGCACCACGTTA
1 TAACCGTGGCATATCCACTTAGCACCACGTTA
42312448 ATGACTCAAT
Statistics
Matches: 99, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
38 57 0.58
39 2 0.02
40 3 0.03
41 2 0.02
42 1 0.01
43 1 0.01
44 2 0.02
45 3 0.03
46 2 0.02
47 26 0.26
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (38 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATGTT
Found at i:42312382 original size:47 final size:47
Alignment explanation
Indices: 42312331--42312542 Score: 253
Period size: 47 Copynumber: 4.7 Consensus size: 47
42312321 GTTACATGTT
*
42312331 TAACCGTGGTATATCCACTTGGCACCACGTTAATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* *
42312378 TAACCGTGGCATATCCACTTAGCACCAC-TT--T--A-C-ATGT-T-
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
*
42312416 TAACCGTGGTATATCCACTTAGCACCACGTTAATGACTCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
** * * * *
42312463 TAACCGTGGCGTATCCGCTTAGCACCATGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
*
42312511 TAATCGTGGTATATCCACTTAGCACCACGTTA
1 TAACCGTGGTATATCCACTTAGCACCACGTTA
42312543 CACGTATAAT
Statistics
Matches: 137, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
38 27 0.20
39 3 0.02
40 3 0.02
41 2 0.01
42 1 0.01
44 2 0.01
45 3 0.02
46 3 0.02
47 54 0.39
48 39 0.28
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (47 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
Found at i:42312441 original size:85 final size:85
Alignment explanation
Indices: 42312293--42312499 Score: 353
Period size: 85 Copynumber: 2.4 Consensus size: 85
42312283 TTAACTTGTA
* *
42312293 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTGGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACTTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
42312358 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
42312378 TAACCGTGGCATATCCACTTAGCACCACTTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACTTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
*
42312443 CGTTAATGACTCAATATATG
66 CGTTAATGAATCAATATATG
* *
42312463 TAACCGTGGCGTATCCGCTTAGCACCA-TGTTACATGT
1 TAACCGTGGCATATCCACTTAGCACCACT-TTACATGT
42312500 ATCAATATGT
Statistics
Matches: 116, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
84 1 0.01
85 115 0.99
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCACTTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
CGTTAATGAATCAATATATG
Found at i:42312519 original size:48 final size:48
Alignment explanation
Indices: 42312411--42312556 Score: 174
Period size: 48 Copynumber: 3.1 Consensus size: 48
42312401 ACCACTTTAC
* *
42312411 ATGTTTAACCGTGGTATATCCACTTAGCACCACGTTA-ATG-ACTCAAT
1 ATGTGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTA-TCAAT
* * * *
42312458 ATATGTAACCGTGGCGTATCCGCTTAGCACCATGTTACATGTATCAAT
1 ATGTGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
* * *
42312506 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACACGTAT-AAT
1 ATGTGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
42312553 -TGTG
1 ATGTG
42312557 GTATATCCAC
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
46 4 0.05
47 34 0.40
48 45 0.54
49 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (48 bp):
ATGTGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
Found at i:42312527 original size:133 final size:132
Alignment explanation
Indices: 42312331--42312576 Score: 357
Period size: 133 Copynumber: 1.9 Consensus size: 132
42312321 GTTACATGTT
* *
42312331 TAACCGTGGTATATCCACTTGGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
* * *
42312396 TTAGCACCACTTTACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAATGACTCAATATA
66 TTAGCACCACGTTACACGTATAACCGTGGTATATCCACTTAGCACCACGTTAATGACTCAATATA
42312461 TG
131 TG
* * * * * * *
42312463 TAACCGTGGCGTATCCGCTTAGCACCATGTTACATGTATCAATATGTGTAATCGTGGTATATCCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAACCGTGGCATATCCA
**
42312528 CTTAGCACCACGTTACACGTATAATTGTGGTATATCCACTTAGCACCAC
65 CTTAGCACCACGTTACACGTATAACCGTGGTATATCCACTTAGCACCAC
42312577 ATTTTTTCAT
Statistics
Matches: 99, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
132 27 0.27
133 72 0.73
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (132 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCAC
TTAGCACCACGTTACACGTATAACCGTGGTATATCCACTTAGCACCACGTTAATGACTCAATATA
TG
Found at i:42315348 original size:24 final size:23
Alignment explanation
Indices: 42315321--42315365 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
42315311 TGAGTACCCG
42315321 AAAACACAAAAAATGAGAACTAAT
1 AAAACACAAAAAATGA-AACTAAT
**
42315345 AAAAGTCAAAAAATGAAACTA
1 AAAACACAAAAAATGAAACTA
42315366 TCGACACCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.67, C:0.11, G:0.09, T:0.13
Consensus pattern (23 bp):
AAAACACAAAAAATGAAACTAAT
Found at i:42317867 original size:44 final size:42
Alignment explanation
Indices: 42317798--42317960 Score: 130
Period size: 43 Copynumber: 3.8 Consensus size: 42
42317788 CGATATGTGT
* ** * *
42317798 TTTCGTGTAAGAGCACATCTTGGACATTGGCATCG-ACTTCTGT
1 TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTA--TCTGA
* * *
42317841 TTTATGTGTAAGACCATGTCTGGGACATCGACATCGTATCTGA
1 TTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGTATCTGA
* * * * *
42317884 TTTCGTGTAAGACCCTGTCTGGGACAGTGGCATTGATGTTTGA
1 TTTCGTGTAAGACCATGTCTGGGACATTGGCATCG-TATCTGA
* * * *
42317927 TTGCATGTAAGACCACGTCTGGGACGTTGGCATC
1 TTTCGTGTAAGACCATGTCTGGGACATTGGCATC
42317961 ATATATGCTT
Statistics
Matches: 94, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
42 26 0.28
43 42 0.45
44 25 0.27
45 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (42 bp):
TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTATCTGA
Found at i:42318535 original size:23 final size:25
Alignment explanation
Indices: 42318509--42318559 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
42318499 TTTGGCTTGA
*
42318509 TTATGG-ATATGTT-TATGAATG-AG
1 TTATGGTATAAGTTATATG-ATGAAG
42318532 TTATGGTATAAGTTATATGATGAAG
1 TTATGGTATAAGTTATATGATGAAG
42318557 TTA
1 TTA
42318560 AGTTTATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.25
24 9 0.38
25 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (25 bp):
TTATGGTATAAGTTATATGATGAAG
Found at i:42325138 original size:30 final size:31
Alignment explanation
Indices: 42325090--42325147 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
42325080 TTTTCGAGCC
42325090 TAGGGGAAAAATCATAATTCTG-CAAAGGTT
1 TAGGGGAAAAATCATAATTCTGTCAAAGGTT
* ** *
42325120 TAGGGGCAAAATTGTAATTTTGTCAAAG
1 TAGGGGAAAAATCATAATTCTGTCAAAG
42325148 TTTGAGTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (31 bp):
TAGGGGAAAAATCATAATTCTGTCAAAGGTT
Found at i:42325970 original size:47 final size:47
Alignment explanation
Indices: 42325911--42326032 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
42325901 GCATTGGCAC
42325911 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
42325958 TAAGACAAGGATACCATGTGAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* * *
42326005 TAAGATAAAGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
42326033 CCAAGGCTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:42326192 original size:53 final size:54
Alignment explanation
Indices: 42326011--42326199 Score: 184
Period size: 55 Copynumber: 3.5 Consensus size: 54
42326001 TTGGTAAGAT
* * * *
42326011 AAAGATATCATGTAAGACCATGCCAAGGCT-TAGCATTGATAAGTTCTATAAGAC
1 AAAGATACCATGTAAGACCATGCCAAGG-TATGGCATTGATGAGTTCTATAAGGC
* * * * * ** *
42326065 AAGGAAATCATGGAAGACCATGTCAAGACATGGCATTGATGATTTACTATAAGGC
1 AAAGATACCATGTAAGACCATGCCAAGGTATGGCATTGATGAGTT-CTATAAGGC
* * *
42326120 AAAGGTCCCATGTAAGACCATGCCAAGGTATGGCATTGGTGAGTTC-ATAAGGC
1 AAAGATACCATGTAAGACCATGCCAAGGTATGGCATTGATGAGTTCTATAAGGC
* * *
42326173 AATGATACCACGTAAGACCATGTCAAG
1 AAAGATACCATGTAAGACCATGCCAAG
42326200 ACATGGAAAT
Statistics
Matches: 107, Mismatches: 26, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
53 29 0.27
54 36 0.34
55 42 0.39
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (54 bp):
AAAGATACCATGTAAGACCATGCCAAGGTATGGCATTGATGAGTTCTATAAGGC
Found at i:42326218 original size:53 final size:53
Alignment explanation
Indices: 42326078--42326219 Score: 158
Period size: 53 Copynumber: 2.6 Consensus size: 53
42326068 GAAATCATGG
* * * * *
42326078 AAGACCATGTCAAGACATGGCATTGATGATTTACTATAAGGCAAAGGTCCCATGT
1 AAGACCATGTCAAGACATGGCATTGGTGAGTT-C-ATAAGGCAAAGATACCACGT
* ** *
42326133 AAGACCATGCCAAGGTATGGCATTGGTGAGTTCATAAGGCAATGATACCACGT
1 AAGACCATGTCAAGACATGGCATTGGTGAGTTCATAAGGCAAAGATACCACGT
* * *
42326186 AAGACCATGTCAAGACATGGAAATGGTAAGTTCA
1 AAGACCATGTCAAGACATGGCATTGGTGAGTTCA
42326220 AAAAGGAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
53 44 0.61
54 1 0.01
55 27 0.38
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (53 bp):
AAGACCATGTCAAGACATGGCATTGGTGAGTTCATAAGGCAAAGATACCACGT
Found at i:42340697 original size:14 final size:15
Alignment explanation
Indices: 42340678--42340720 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
42340668 GCAACAAAAA
42340678 ATAAAAAGAAAAACT
1 ATAAAAAGAAAAACT
**
42340693 A-AAAACTAAAAACT
1 ATAAAAAGAAAAACT
42340707 ATAAGAAAGAAAAA
1 ATAA-AAAGAAAAA
42340721 TGAATAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 12 0.55
15 3 0.14
16 7 0.32
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (15 bp):
ATAAAAAGAAAAACT
Found at i:42342377 original size:86 final size:86
Alignment explanation
Indices: 42342230--42342388 Score: 187
Period size: 86 Copynumber: 1.8 Consensus size: 86
42342220 CAATGTCATA
* ** * * * * *
42342230 TCCCAAATATGGTCTTACATGTTATCACATATCGATGCCACTGTCCTGGACAAGGTTTTACACGA
1 TCCCAAACATGGTCTTACACATAATCACATATCAATGCCAATGTCCTAGACAAGGTCTTACACGA
42342295 AATCATATAACGATGCCAATG
66 AATCATATAACGATGCCAATG
* *
42342316 TCCCAAACATGGTCTTACACATAATCACA-ATACAATGCCAATGTACC-AGACATGGTCTTACAT
1 TCCCAAACATGGTCTTACACATAATCACATAT-CAATGCCAATGT-CCTAGACAAGGTCTTACAC
*
42342379 GTAATCATAT
64 GAAATCATAT
42342389 CTCGGTAATC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
85 2 0.03
86 56 0.93
87 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (86 bp):
TCCCAAACATGGTCTTACACATAATCACATATCAATGCCAATGTCCTAGACAAGGTCTTACACGA
AATCATATAACGATGCCAATG
Found at i:42342384 original size:43 final size:41
Alignment explanation
Indices: 42342238--42342385 Score: 134
Period size: 43 Copynumber: 3.5 Consensus size: 41
42342228 TATCCCAAAT
* * * *
42342238 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCTGGAC
1 ATGGTCTTACACGTAATCACATA-CGATGCCAATGTCC-AGAC
* * * * *
42342281 AAGGTTTTACACGAAATCATATAACGATGCCAATGTCCCAAAC
1 ATGGTCTTACACGTAATCACAT-ACGATGCCAATGT-CCAGAC
* *
42342324 ATGGTCTTACACATAATCACAATACAATGCCAATGTACCAGAC
1 ATGGTCTTACACGTAATCAC-ATACGATGCCAATGT-CCAGAC
*
42342367 ATGGTCTTACATGTAATCA
1 ATGGTCTTACACGTAATCA
42342386 TATCTCGGTA
Statistics
Matches: 83, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
43 78 0.94
44 5 0.06
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (41 bp):
ATGGTCTTACACGTAATCACATACGATGCCAATGTCCAGAC
Found at i:42344920 original size:26 final size:26
Alignment explanation
Indices: 42344884--42344943 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
42344874 TTATAAATAG
*
42344884 GTGCCAAATGCAAGAGTATGAGGCTA
1 GTGCCGAATGCAAGAGTATGAGGCTA
42344910 GTGCCGAATGCAAGAGTATGAGGCTA
1 GTGCCGAATGCAAGAGTATGAGGCTA
*
42344936 ATGCCGAA
1 GTGCCGAA
42344944 ATCTTTTGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (26 bp):
GTGCCGAATGCAAGAGTATGAGGCTA
Found at i:42345666 original size:16 final size:16
Alignment explanation
Indices: 42345647--42345689 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
42345637 AAATGCCAAA
42345647 ATGCAGAAAAGTCGAC
1 ATGCAGAAAAGTCGAC
42345663 ATGCAGAAAAGTCGAC
1 ATGCAGAAAAGTCGAC
*
42345679 ATGCCGAAAAG
1 ATGCAGAAAAG
42345690 CTAAAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.12
Consensus pattern (16 bp):
ATGCAGAAAAGTCGAC
Found at i:42345961 original size:29 final size:29
Alignment explanation
Indices: 42345906--42346029 Score: 110
Period size: 29 Copynumber: 4.3 Consensus size: 29
42345896 GTGAGCATGA
* *
42345906 ATATGAATGTGA-CTGGGCCTAACGGGCC
1 ATATAAATGTGATCTGGGCCTAATGGGCC
*
42345934 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATCTGGGCCTAATGGGCC
* * *
42345963 ATATATA-GTTGGTCTGGACCTAATGGGCC
1 ATATAAATG-TGATCTGGGCCTAATGGGCC
* * **
42345992 ATATGAATATGA-CTGGGTTTAATGGGCC
1 ATATAAATGTGATCTGGGCCTAATGGGCC
* *
42346020 AGATACATGT
1 ATATAAATGT
42346030 ATGTGAATTT
Statistics
Matches: 75, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
28 31 0.41
29 44 0.59
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (29 bp):
ATATAAATGTGATCTGGGCCTAATGGGCC
Found at i:42353699 original size:27 final size:28
Alignment explanation
Indices: 42353669--42353729 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
42353659 GTGAGGATGA
* *
42353669 ATATGAATGT-TCTGGGCTTAACGGGCC
1 ATATAAATGTATCTGGGCCTAACGGGCC
* *
42353696 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGT-ATCTGGGCCTAACGGGCC
42353725 ATATA
1 ATATA
42353730 CAGGTGGTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 9 0.32
29 19 0.68
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (28 bp):
ATATAAATGTATCTGGGCCTAACGGGCC
Found at i:42353723 original size:29 final size:29
Alignment explanation
Indices: 42353679--42353782 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 29
42353669 ATATGAATGT
* *
42353679 TCTGGGCTTAACGGGCCATATAAATGTGA
1 TCTGGGCCTAATGGGCCATATAAATGTGA
* * * *
42353708 TTTGGGCCTAATGGGCCATATACAGGTGG
1 TCTGGGCCTAATGGGCCATATAAATGTGA
* * * *
42353737 TCTGGACCTAGTGGGCCATATGAATATGA
1 TCTGGGCCTAATGGGCCATATAAATGTGA
*
42353766 -CTGGGCTTAATGGGCCA
1 TCTGGGCCTAATGGGCCA
42353783 GATATAGGTA
Statistics
Matches: 58, Mismatches: 17, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
28 14 0.24
29 44 0.76
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (29 bp):
TCTGGGCCTAATGGGCCATATAAATGTGA
Found at i:42362095 original size:29 final size:29
Alignment explanation
Indices: 42361994--42362087 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
42361984 GTGACGAGAT
42361994 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42362023 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42362052 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
42362081 CGGCACT
1 TGGCACT
42362088 GGGTGTGCGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:42362124 original size:58 final size:58
Alignment explanation
Indices: 42361990--42362117 Score: 170
Period size: 58 Copynumber: 2.2 Consensus size: 58
42361980 TACGGTGACG
* *
42361990 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
* **
42362047 ATATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGC-ATGCTCGAA
* *
42362105 GGGTATGGCACTA
1 AGATATGGCACTA
42362118 TATGTGCGGG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.05
58 57 0.93
59 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
Found at i:42381187 original size:43 final size:43
Alignment explanation
Indices: 42381139--42381242 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
42381129 TCAGATATAT
* * *
42381139 TCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGG
1 TCTTACATGTAATCACATAACGATGCCAATGTCCCAGACAGGG
* * * *
42381182 TCTTACACGAAATCATATAACGATGCCAATGTCCCAGACATGG
1 TCTTACATGTAATCACATAACGATGCCAATGTCCCAGACAGGG
*
42381225 TTTTACATGTAATCACAT
1 TCTTACATGTAATCACAT
42381243 CTCAGTAATC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (43 bp):
TCTTACATGTAATCACATAACGATGCCAATGTCCCAGACAGGG
Found at i:42382652 original size:202 final size:203
Alignment explanation
Indices: 42382299--42382705 Score: 753
Period size: 202 Copynumber: 2.0 Consensus size: 203
42382289 CTGTCCTTTA
*
42382299 TCTCAAATTGAGCTATTAAACGATAAAATTTTCTCACGAAATTTTCACACATATATATTCACATG
1 TCTCAAATTGAGCTATTAAACGATAAAATTATCTCACGAAATTTTCACACATATATATTCACATG
*
42382364 CTGTAAACACATAAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGTCTCAAAACCACT
66 CTGTAAACACA-AAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGGCTCAAAACCACT
42382429 ATTCCAATTTAGCTAGAATCAGACTGCTACAATTTCAAACTGGGTTCTGAAAGAAATATGTGAGC
130 ATTCCAATTTAGCTAGAATCAGACTGCTACAATTTCAAACTGGGTTCTGAAAGAAATATGTGAGC
42382494 TAGAGATTC
195 TAGAGATTC
42382503 TCTCAAATTGAGCTATTAAACGATAAAATTATCTCACGAAATTTTCACACATATATATTCACATG
1 TCTCAAATTGAGCTATTAAACGATAAAATTATCTCACGAAATTTTCACACATATATATTCACATG
*
42382568 TTGTAAACAC-AAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGGCTCAAAACCACTA
66 CTGTAAACACAAAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGGCTCAAAACCACTA
* *
42382632 TTCCAATTTAGCTAGAATCAGACTGTTATAATTTCAAACTGGGTTCTGAAAGAAATATGTGAGCT
131 TTCCAATTTAGCTAGAATCAGACTGCTACAATTTCAAACTGGGTTCTGAAAGAAATATGTGAGCT
42382697 AGAGATTC
196 AGAGATTC
42382705 T
1 T
42382706 TAGACAAGAA
Statistics
Matches: 198, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
202 125 0.63
204 73 0.37
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (203 bp):
TCTCAAATTGAGCTATTAAACGATAAAATTATCTCACGAAATTTTCACACATATATATTCACATG
CTGTAAACACAAAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGGCTCAAAACCACTA
TTCCAATTTAGCTAGAATCAGACTGCTACAATTTCAAACTGGGTTCTGAAAGAAATATGTGAGCT
AGAGATTC
Found at i:42390473 original size:22 final size:22
Alignment explanation
Indices: 42390448--42390506 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
42390438 CTTGAGTTGA
42390448 TGAACAGTAAGCTCTAACGAGC
1 TGAACAGTAAGCTCTAACGAGC
**
42390470 TGAA-ATGGTAAGCTCTATTGAGC
1 TGAACA--GTAAGCTCTAACGAGC
42390493 TGAACAGTAAGCTC
1 TGAACAGTAAGCTC
42390507 ATACAAGCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 1 0.03
22 12 0.38
23 18 0.56
24 1 0.03
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (22 bp):
TGAACAGTAAGCTCTAACGAGC
Found at i:42390480 original size:23 final size:23
Alignment explanation
Indices: 42390454--42390529 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
42390444 TTGATGAACA
42390454 GTAAGCTCTAACGAGCTGAAATG
1 GTAAGCTCTAACGAGCTGAAATG
**
42390477 GTAAGCTCTATTGAGCTGAACA--
1 GTAAGCTCTAACGAGCTGAA-ATG
*
42390499 GTAAGCTC-ATACAAGCTGAAATG
1 GTAAGCTCTA-ACGAGCTGAAATG
42390522 GTAAGCTC
1 GTAAGCTC
42390530 CAATGATTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.05
22 15 0.34
23 26 0.59
24 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (23 bp):
GTAAGCTCTAACGAGCTGAAATG
Found at i:42390515 original size:22 final size:21
Alignment explanation
Indices: 42390448--42390518 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 21
42390438 CTTGAGTTGA
42390448 TGAACAGTAAGCTCTAACGAGC
1 TGAACAGTAAGCTCT-ACGAGC
*
42390470 TGAA-ATGGTAAGCTCTATTGAGC
1 TGAACA--GTAAGCTCTA-CGAGC
*
42390493 TGAACAGTAAGCTCATACAAGC
1 TGAACAGTAAGCTC-TACGAGC
42390515 TGAA
1 TGAA
42390519 ATGGTAAGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
21 1 0.02
22 20 0.49
23 19 0.46
24 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (21 bp):
TGAACAGTAAGCTCTACGAGC
Found at i:42403231 original size:40 final size:40
Alignment explanation
Indices: 42403186--42403327 Score: 205
Period size: 40 Copynumber: 3.5 Consensus size: 40
42403176 ATAACCACAA
* * *
42403186 GCACAATTGCCTTCGAGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
42403226 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
42403266 GCACAAATGCCTTCGGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* *
42403306 GCATAAATGCCTTCGGGGCTTA
1 GCACAAATGCCTTCGGGTCTTA
42403328 GCCGGGTATC
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 92 0.98
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:42411312 original size:40 final size:40
Alignment explanation
Indices: 42411267--42411379 Score: 208
Period size: 40 Copynumber: 2.8 Consensus size: 40
42411257 ATAACCACAA
* *
42411267 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
42411307 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
42411347 GCACAAATGCCTTCGGGTCTTAACCCGGATATA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATA
42411380 ATCACTAGCA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:42411395 original size:40 final size:40
Alignment explanation
Indices: 42411251--42411413 Score: 202
Period size: 40 Copynumber: 4.1 Consensus size: 40
42411241 CGGAATTTAG
* * * *
42411251 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAAC
* *
42411291 CCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAAC
*
42411331 CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * *
42411371 CCGGATATAATC-ACTAGCATAAATGACTTCGGGGCTTAGC
1 CCGGATAT-AGCAACTAGCACAAATGCCTTCGGGTCTTAAC
42411411 CCG
1 CCG
42411414 AGTATCATTC
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 107 0.98
41 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:42413171 original size:30 final size:30
Alignment explanation
Indices: 42413135--42413235 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
42413125 GACAAGATTG
* * *
42413135 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
42413165 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
42413193 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
42413222 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42413236 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Done.