Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 87 of 91
Found at i:19708222 original size:16 final size:16
Alignment explanation
Indices: 19708201--19708236 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
19708191 CCGACATGCT
19708201 CTCTCACTTGATATTA
1 CTCTCACTTGATATTA
19708217 CTCTCACTTGATATTA
1 CTCTCACTTGATATTA
19708233 CTCT
1 CTCT
19708237 TCTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.28, G:0.06, T:0.44
Consensus pattern (16 bp):
CTCTCACTTGATATTA
Found at i:19708266 original size:17 final size:16
Alignment explanation
Indices: 19708240--19708273 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19708230 TTACTCTTCT
19708240 TTTATTTATTTACTCA
1 TTTATTTATTTACTCA
*
19708256 TTTATTTTATTTATTCA
1 TTTA-TTTATTTACTCA
19708273 T
1 T
19708274 ACTTCTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTATTTACTCA
Found at i:19711436 original size:11 final size:11
Alignment explanation
Indices: 19711422--19711455 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
19711412 GATTTTTTCC
19711422 TTTTATTTTAT
1 TTTTATTTTAT
19711433 TTTTATTTTAT
1 TTTTATTTTAT
19711444 TTTTA-TTTAT
1 TTTTATTTTAT
19711454 TT
1 TT
19711456 AATTCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:19719976 original size:26 final size:25
Alignment explanation
Indices: 19719903--19720006 Score: 128
Period size: 23 Copynumber: 4.3 Consensus size: 25
19719893 AGGATAAAAA
*
19719903 TAAAAGAGATTTA-TT-TCTTTCAT
1 TAAAAGAGATTTATTTCTCTTTAAT
19719926 TAAAAGAGATTTATTTCT-TTT-AT
1 TAAAAGAGATTTATTTCTCTTTAAT
19719949 TAAAAGAGATTTATTATCTCTTTAAT
1 TAAAAGAGATTTATT-TCTCTTTAAT
* *
19719975 TAAAAGAGATTTCTTTTATCTTTAA-
1 TAAAAGAGATTT-ATTTCTCTTTAAT
19720000 TAAAAGA
1 TAAAAGA
19720007 TGACACACAC
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
23 30 0.41
24 8 0.11
25 11 0.15
26 22 0.30
27 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (25 bp):
TAAAAGAGATTTATTTCTCTTTAAT
Found at i:19723345 original size:16 final size:16
Alignment explanation
Indices: 19723306--19723338 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19723296 GAATTGAGAG
19723306 AGAACCTTATTTACAA
1 AGAACCTTATTTACAA
*
19723322 AGAACCTTCTTTACAA
1 AGAACCTTATTTACAA
19723338 A
1 A
19723339 TAGCCTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (16 bp):
AGAACCTTATTTACAA
Found at i:19725265 original size:19 final size:19
Alignment explanation
Indices: 19725241--19725282 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
19725231 TGTTTAGTTT
19725241 GTTATTATTTTATTCATTA
1 GTTATTATTTTATTCATTA
19725260 GTTATTATTTTATTCATTA
1 GTTATTATTTTATTCATTA
19725279 GTTA
1 GTTA
19725283 ATTAGGACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (19 bp):
GTTATTATTTTATTCATTA
Found at i:19733603 original size:6 final size:6
Alignment explanation
Indices: 19733592--19733619 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19733582 TGAAGGGTTT
19733592 AGGGCA AGGGCA AGGGCA AGGGCA AGGG
1 AGGGCA AGGGCA AGGGCA AGGGCA AGGG
19733620 AAAGATGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.54, T:0.00
Consensus pattern (6 bp):
AGGGCA
Found at i:19735045 original size:18 final size:18
Alignment explanation
Indices: 19735022--19735100 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 18
19735012 AGCGACGTGC
*
19735022 TTAAAAAATAATTATTTA
1 TTAAAAAATAATAATTTA
* * *
19735040 TT--AAAATTATGTATATA
1 TTAAAAAATAAT-AATTTA
*
19735057 TTAAAAAATATAAGAATTTA
1 TT-AAAAA-ATAATAATTTA
* *
19735077 TTAAAAATTAAAAATTTA
1 TTAAAAAATAATAATTTA
19735095 TTAAAA
1 TTAAAA
19735101 TTAATTTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
16 7 0.15
17 7 0.15
18 17 0.35
19 5 0.10
20 9 0.19
21 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TTAAAAAATAATAATTTA
Found at i:19735080 original size:20 final size:19
Alignment explanation
Indices: 19735055--19735100 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
19735045 ATTATGTATA
*
19735055 TATTAAAAAATATAAGAATT
1 TATTAAAAAAT-TAAAAATT
19735075 TATT-AAAAATTAAAAATT
1 TATTAAAAAATTAAAAATT
19735093 TATTAAAA
1 TATTAAAA
19735101 TTAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 11 0.46
19 9 0.38
20 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
TATTAAAAAATTAAAAATT
Found at i:19736928 original size:19 final size:20
Alignment explanation
Indices: 19736901--19736938 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19736891 ATGGCACGCA
*
19736901 AATCTATGCAAGT-ATACAC
1 AATCGATGCAAGTAATACAC
19736920 AATCGATGCAAGTAATACA
1 AATCGATGCAAGTAATACA
19736939 GTAGTGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (20 bp):
AATCGATGCAAGTAATACAC
Found at i:19753393 original size:13 final size:13
Alignment explanation
Indices: 19753375--19753408 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19753365 AGCATTGTGA
**
19753375 AAAGAAAATAATG
1 AAAGAAAATAAAC
19753388 AAAGAAAATAAAC
1 AAAGAAAATAAAC
19753401 AAAGAAAA
1 AAAGAAAA
19753409 GTGGAGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAC
Found at i:19754700 original size:28 final size:28
Alignment explanation
Indices: 19754660--19754725 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
19754650 AAATAAAGAA
* *
19754660 AAGGAAAAATGACTCAAAGTGGCTAATT
1 AAGGGAAAATGACTCAAAGTAGCTAATT
*
19754688 AAGGGAAAATGACTCAAAGTAGTTAATT
1 AAGGGAAAATGACTCAAAGTAGCTAATT
19754716 AAGGGAAAAT
1 AAGGGAAAAT
19754726 AAATGGATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (28 bp):
AAGGGAAAATGACTCAAAGTAGCTAATT
Found at i:19755563 original size:14 final size:15
Alignment explanation
Indices: 19755536--19755564 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19755526 TTTTTTTATT
19755536 TAAACTTCTAAATTA
1 TAAACTTCTAAATTA
19755551 TAAACTT-TAAATTA
1 TAAACTTCTAAATTA
19755565 ATATTTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAACTTCTAAATTA
Found at i:19756128 original size:5 final size:5
Alignment explanation
Indices: 19756099--19756159 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
19756089 AGTGCACCTA
*
19756099 AAAAT ATAAA- AAAAT AATTAT AAAAT AAAAT AAAAT AAAAT --AAT AAAAGT
1 AAAAT A-AAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T
19756149 AATAAT AAAAT
1 AA-AAT AAAAT
19756160 TAAAGAGGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 26 0.55
6 13 0.28
7 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:19756154 original size:12 final size:11
Alignment explanation
Indices: 19756099--19756159 Score: 63
Period size: 10 Copynumber: 5.5 Consensus size: 11
19756089 AGTGCACCTA
*
19756099 AAAAT-ATAAA
1 AAAATAATAAT
*
19756109 AAAATAATTAT
1 AAAATAATAAT
19756120 AAAATAA-AAT
1 AAAATAATAAT
19756130 AAAATAAAATAAT
1 AAAAT--AATAAT
19756143 AAAAGTAATAAT
1 AAAA-TAATAAT
19756155 AAAAT
1 AAAAT
19756160 TAAAGAGGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
10 12 0.28
11 11 0.26
12 12 0.28
13 7 0.16
14 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:19758147 original size:23 final size:23
Alignment explanation
Indices: 19758121--19758166 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
19758111 CGACCGGACA
19758121 AGTAAAGGTGGTATTTTCTTAAT
1 AGTAAAGGTGGTATTTTCTTAAT
*
19758144 AGTAAATGTGGTATTTTCTTAAT
1 AGTAAAGGTGGTATTTTCTTAAT
19758167 CTTCTGGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (23 bp):
AGTAAAGGTGGTATTTTCTTAAT
Found at i:19759925 original size:31 final size:30
Alignment explanation
Indices: 19759878--19759935 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
19759868 CTCAGTTTGG
* *
19759878 TTTTGAAACTTCTTCTAGGATATCTTTTTT
1 TTTTGAAAATTCTTCTAAGATATCTTTTTT
19759908 TTTTGAAGAATTCTTCTAAGATATCTTT
1 TTTTGAA-AATTCTTCTAAGATATCTTT
19759936 AAATGTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (30 bp):
TTTTGAAAATTCTTCTAAGATATCTTTTTT
Found at i:19761384 original size:14 final size:15
Alignment explanation
Indices: 19761357--19761419 Score: 67
Period size: 14 Copynumber: 4.2 Consensus size: 15
19761347 GTTTTAAAAT
19761357 TAATGAAAGTAAATAAA
1 TAATGAAA--AAATAAA
19761374 TAAT-AAAAAATAAA
1 TAATGAAAAAATAAA
* *
19761388 TATTGAATAAA-AAA
1 TAATGAAAAAATAAA
*
19761402 TAATGAGAAAATAAA
1 TAATGAAAAAATAAA
19761417 TAA
1 TAA
19761420 AATAAATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 21 0.54
15 11 0.28
16 3 0.08
17 4 0.10
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (15 bp):
TAATGAAAAAATAAA
Found at i:19761387 original size:18 final size:18
Alignment explanation
Indices: 19761366--19761404 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19761356 TTAATGAAAG
19761366 TAAATAAAT-AATAAAAAA
1 TAAAT-AATGAATAAAAAA
*
19761384 TAAATATTGAATAAAAAA
1 TAAATAATGAATAAAAAA
19761402 TAA
1 TAA
19761405 TGAGAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAATAATGAATAAAAAA
Found at i:19764367 original size:90 final size:89
Alignment explanation
Indices: 19764253--19764426 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 89
19764243 TCCCGAATAT
* * * * *
19764253 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAGTAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAATTAA
19764318 GGTAACTTGGATATAAAAGAATTA
66 GGTAACTTGGATATAAAAGAATTA
19764342 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAATTA
*
19764407 AGGTAACTTGGCTATAAAAG
65 AGGTAACTTGGATATAAAAG
19764427 GGTGTGTTAG
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 71 0.91
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAATTAA
GGTAACTTGGATATAAAAGAATTA
Found at i:19773948 original size:2 final size:2
Alignment explanation
Indices: 19773941--19773982 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
19773931 CAATTTTCTG
* *
19773941 AT AT AT AT AT AT AT AT AT AT AA AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19773983 CTTATGAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:19776944 original size:29 final size:29
Alignment explanation
Indices: 19776902--19776959 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
19776892 TCTCTGCAAA
*
19776902 TTTTTTTTCTATTCCTTTGGTGCTAAAAG
1 TTTTTTTTCTATTCCTTTGGTGATAAAAG
19776931 TTTTTTTTCTATTCCTTTGGTGATAAAAG
1 TTTTTTTTCTATTCCTTTGGTGATAAAAG
19776960 AAGAGCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.55
Consensus pattern (29 bp):
TTTTTTTTCTATTCCTTTGGTGATAAAAG
Found at i:19780762 original size:2 final size:2
Alignment explanation
Indices: 19780755--19780787 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19780745 GCATTTAATC
19780755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19780788 GAACTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19787751 original size:5 final size:5
Alignment explanation
Indices: 19787730--19787803 Score: 57
Period size: 5 Copynumber: 14.8 Consensus size: 5
19787720 TAATAATATG
* *
19787730 ATAA- ATAAT AT-AT ATAAT ATAAT AT--T ATACT ATAAT ATAAT ATATGT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
*
19787777 ACAAT ATAATAT ATAAT ATACAT ATAA
1 ATAAT AT-A-AT ATAAT ATA-AT ATAA
19787804 ATATTTTCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
3 3 0.05
4 8 0.14
5 32 0.56
6 10 0.18
7 4 0.07
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:19787751 original size:18 final size:17
Alignment explanation
Indices: 19787719--19787803 Score: 79
Period size: 16 Copynumber: 5.1 Consensus size: 17
19787709 ATAATAAACC
*
19787719 ATAATA-ATATGATA-A
1 ATAATATATATAATATA
19787734 ATAATATATATAATATA
1 ATAATATATATAATATA
*
19787751 ATATTATACTATAATATA
1 ATAATATA-TATAATATA
* *
19787769 AT-ATATGTACAATATA
1 ATAATATATATAATATA
19787785 AT-ATATAATATACATATA
1 ATAATAT-ATATA-ATATA
19787803 A
1 A
19787804 ATATTTTCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.10
16 21 0.36
17 14 0.24
18 17 0.29
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAATATATATAATATA
Found at i:19787787 original size:34 final size:32
Alignment explanation
Indices: 19787730--19787833 Score: 92
Period size: 32 Copynumber: 3.2 Consensus size: 32
19787720 TAATAATATG
* *
19787730 ATAA-ATAATATA-TATAATATAATATTATACT
1 ATAATATAATATATTACAATATAATA-TATAAT
19787761 ATAATATAATATATGTACAATATAATATATAAT
1 ATAATATAATATAT-TACAATATAATATATAAT
*
19787794 ATACATATAA-ATATTTTCAA-A-AACTATATAAT
1 ATA-ATATAATATA-TTACAATATAA-TATATAAT
19787826 ATATATAT
1 ATA-ATAT
19787834 TTTCAAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
31 6 0.10
32 24 0.38
33 15 0.24
34 18 0.29
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (32 bp):
ATAATATAATATATTACAATATAATATATAAT
Found at i:19787828 original size:26 final size:27
Alignment explanation
Indices: 19787792--19787842 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
19787782 ATAATATATA
19787792 ATATACATATAAATATTTTCAAAAACT
1 ATATACATATAAATATTTTCAAAAACT
*
19787819 ATATA-ATATATATATTTTCAAAAA
1 ATATACATATAAATATTTTCAAAAA
19787843 TGTTTTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATACATATAAATATTTTCAAAAACT
Found at i:19787908 original size:37 final size:37
Alignment explanation
Indices: 19787802--19788099 Score: 362
Period size: 39 Copynumber: 8.1 Consensus size: 37
19787792 ATATACATAT
* *
19787802 AAATATTTTCAAAAACTATATAATATATATATTTTCAA
1 AAATGTTTTCAAAAACTATATATTATATATATTTTC-A
**
19787840 AAATGTTTTTGAAAACTATATATTATATATATGTTTTCA
1 AAATGTTTTCAAAAACTATATATTATATATA--TTTTCA
*
19787879 AAATGTTTTCAAAAACTATATATTATATATATATTCA
1 AAATGTTTTCAAAAACTATATATTATATATATTTTCA
19787916 AAATGTTTTCAAAAACTATATATTATATATA---T--
1 AAATGTTTTCAAAAACTATATATTATATATATTTTCA
19787948 --A--TTTTCAAAAACTATATATTATATATATATTTTCA
1 AAATGTTTTCAAAAACTATATA-T-TATATATATTTTCA
19787983 AAATGTTTTCAAAAACTATATATTATATATATATTTTCA
1 AAATGTTTTCAAAAACTATATA-T-TATATATATTTTCA
* * * *
19788022 AAAAGTTTTCAAAAACCATATATTATATATGTTTTAA
1 AAATGTTTTCAAAAACTATATATTATATATATTTTCA
*
19788059 AAATATTTTCAAAAACTATATATTATATATATATTTTCA
1 AAATGTTTTCAAAAACTATATA-T-TATATATATTTTCA
19788098 AA
1 AA
19788100 TATATATATA
Statistics
Matches: 229, Mismatches: 16, Indels: 29
0.84 0.06 0.11
Matches are distributed among these distances:
28 17 0.07
29 1 0.00
30 9 0.04
33 1 0.00
34 1 0.00
37 68 0.30
38 29 0.13
39 98 0.43
40 5 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
AAATGTTTTCAAAAACTATATATTATATATATTTTCA
Found at i:19787952 original size:28 final size:28
Alignment explanation
Indices: 19787921--19787985 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
19787911 ATTCAAAATG
19787921 TTTTCAAAAACTATATATTATATATATA
1 TTTTCAAAAACTATATATTATATATATA
19787949 TTTTCAAAAACTATATATTATATATATA
1 TTTTCAAAAACTATATATTATATATATA
19787977 TTTTCAAAA
1 TTTTCAAAA
19787986 TGTTTTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTTCAAAAACTATATATTATATATATA
Found at i:19788007 original size:143 final size:144
Alignment explanation
Indices: 19787798--19788120 Score: 510
Period size: 143 Copynumber: 2.3 Consensus size: 144
19787788 TATAATATAC
* **
19787798 ATATAAATATTTTCAAAAACTATATA--ATATATATATTTTCAAAAATGTTTTTGAAAACTATAT
1 ATATATATATTTTCAAAAACTATATATTATATATATATTTTCAAAAATGTTTTCAAAAACTATAT
* * * * *
19787861 ATTATATATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTCAAAATGTTTTC
66 ATTATATATATATTTTCAAAAAGTTTTCAAAAACCATATATTATATATATATTAAAAATATTTTC
19787926 AAAAACTATATATT
131 AAAAACTATATATT
19787940 ATATATATATTTTCAAAAACTATATATTATATATATATTTTC-AAAATGTTTTCAAAAACTATAT
1 ATATATATATTTTCAAAAACTATATATTATATATATATTTTCAAAAATGTTTTCAAAAACTATAT
* *
19788004 ATTATATATATATTTTCAAAAAGTTTTCAAAAACCATATATTATATATGTTTTAAAAATATTTTC
66 ATTATATATATATTTTCAAAAAGTTTTCAAAAACCATATATTATATATATATTAAAAATATTTTC
19788069 AAAAACTATATATT
131 AAAAACTATATATT
*
19788083 ATATATATATTTTCAAATA-TATATATATATATATATAT
1 ATATATATATTTTCAAAAACTATATAT-TATATATATAT
19788121 ATATATATAT
Statistics
Matches: 167, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
142 32 0.19
143 121 0.72
144 14 0.08
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (144 bp):
ATATATATATTTTCAAAAACTATATATTATATATATATTTTCAAAAATGTTTTCAAAAACTATAT
ATTATATATATATTTTCAAAAAGTTTTCAAAAACCATATATTATATATATATTAAAAATATTTTC
AAAAACTATATATT
Found at i:19788087 original size:2 final size:2
Alignment explanation
Indices: 19788075--19788136 Score: 83
Period size: 2 Copynumber: 31.5 Consensus size: 2
19788065 TTTCAAAAAC
* *
19788075 TA TA TA T- TA TA TA TA TA T- TT TCA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
19788116 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
19788137 GTATTAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19788092 original size:28 final size:28
Alignment explanation
Indices: 19788061--19788120 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
19788051 TGTTTTAAAA
19788061 ATATTTTCAAAAACTATATAT-TATATAT
1 ATATTTTCAAAAA-TATATATATATATAT
*
19788089 ATATTTTCAAATATATATATATATATAT
1 ATATTTTCAAAAATATATATATATATAT
19788117 ATAT
1 ATAT
19788121 ATATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATTTTCAAAAATATATATATATATAT
Found at i:19788119 original size:76 final size:75
Alignment explanation
Indices: 19787818--19788128 Score: 327
Period size: 76 Copynumber: 4.2 Consensus size: 75
19787808 TTTCAAAAAC
* * ** * *
19787818 TATATAATATATATATTTTCAAAAATGTTTTTGAAAACTATATATTATATATATGTTTTCAAAAT
1 TATATATTATATATATTTT-AAAAATATTTTCAAAAACTATATATTATATATATATTTTCAAAAA
* * *
19787883 GTTTTCAAAAA
65 GTTATCATATA
* * *
19787894 CTATATATTATATATATATTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTC-AAAA
1 -TATATATTATATATATTTTAAAAATATTTTCAAAAACTATATATTATATATATATTTTCAAAAA
19787958 ---A-C-TATA
65 GTTATCATATA
* *
19787964 TAT-TA-TATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCAAAAAG
1 TATATATTATATATATTTTAAAAATATTTTCAAAAACTATATATTATATATATATTTTCAAAAAG
* * *
19788027 TTTTCAAAAA
66 TTATCATATA
* * *
19788037 CCATATATTATATATGTTTTAAAAATATTTTCAAAAACTATATATTATATATATATTTTCAAATA
1 -TATATATTATATATATTTTAAAAATATTTTCAAAAACTATATATTATATATATATTTTCAAAAA
19788102 -TATAT-ATATA
65 GT-TATCATATA
19788112 TATATATATATATATAT
1 TATATAT-TATATATAT
19788129 ATATATATGT
Statistics
Matches: 199, Mismatches: 24, Indels: 24
0.81 0.10 0.10
Matches are distributed among these distances:
67 51 0.26
68 6 0.03
69 3 0.02
70 2 0.01
71 1 0.01
72 1 0.01
73 2 0.01
74 8 0.04
75 17 0.09
76 91 0.46
77 17 0.09
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (75 bp):
TATATATTATATATATTTTAAAAATATTTTCAAAAACTATATATTATATATATATTTTCAAAAAG
TTATCATATA
Found at i:19788951 original size:123 final size:123
Alignment explanation
Indices: 19788747--19789004 Score: 426
Period size: 123 Copynumber: 2.1 Consensus size: 123
19788737 CTTTTTCGTG
** * * *
19788747 AAGTTGAAATCATGGATGGTTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGTTGT
1 AAGTTGAAATTGTAGATGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTAGTTGT
*
19788812 GAAGTTGAAATCCAATCTTGTAAATTGCATCACTTCGAGTTTAATATCTTTCAATGTA
66 GAAGTTGAAATCCAATCTTGTAAATTGCATCACTTCGAGTTCAATATCTTTCAATGTA
19788870 AAGTTGAAATTGTAGATGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTAGTTGT
1 AAGTTGAAATTGTAGATGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTAGTTGT
* ** *
19788935 GAAGTTGAAATCCAATCTTGTAAATTGCATCGCTTCGAGTTCAATATCTTTCGCTGTG
66 GAAGTTGAAATCCAATCTTGTAAATTGCATCACTTCGAGTTCAATATCTTTCAATGTA
19788993 AAGTTGAAATTG
1 AAGTTGAAATTG
19789005 ACTCTAACAA
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 125 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (123 bp):
AAGTTGAAATTGTAGATGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTAGTTGT
GAAGTTGAAATCCAATCTTGTAAATTGCATCACTTCGAGTTCAATATCTTTCAATGTA
Found at i:19793351 original size:44 final size:44
Alignment explanation
Indices: 19793288--19793373 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
19793278 ATCCCACATG
19793288 GAATGAACGAAAATTAAATTCAAAAG-AGAATGAAACGAAGTACT
1 GAATGAACGAAAATTAAATTCAAAAGAAG-ATGAAACGAAGTACT
* * *
19793332 GAATGAAGGAAAATTAAATTCATAAGAAGATGAAATGAAGTA
1 GAATGAACGAAAATTAAATTCAAAAGAAGATGAAACGAAGTA
19793374 AGAAAATGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 36 0.95
45 2 0.05
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.20
Consensus pattern (44 bp):
GAATGAACGAAAATTAAATTCAAAAGAAGATGAAACGAAGTACT
Found at i:19813915 original size:20 final size:21
Alignment explanation
Indices: 19813890--19813928 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19813880 CTATTGGACC
19813890 AAAT-AACAAAAAAAGAAAGA
1 AAATAAACAAAAAAAGAAAGA
*
19813910 AAATAAATAAAAAAAGAAA
1 AAATAAACAAAAAAAGAAA
19813929 AATTAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (21 bp):
AAATAAACAAAAAAAGAAAGA
Found at i:19816446 original size:26 final size:27
Alignment explanation
Indices: 19816411--19816461 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
19816401 ATAATATATA
19816411 ATATACATATAAATATTTTCAAAAACT
1 ATATACATATAAATATTTTCAAAAACT
*
19816438 ATATA-ATATATATATTTTCAAAAA
1 ATATACATATAAATATTTTCAAAAA
19816462 TGTTTTCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATACATATAAATATTTTCAAAAACT
Found at i:19816447 original size:39 final size:40
Alignment explanation
Indices: 19816398--19816579 Score: 162
Period size: 39 Copynumber: 4.6 Consensus size: 40
19816388 TACAATATAA
*
19816398 TATATAATATATA-ATATACATATAAATATTTTCAAAAAC
1 TATATAATATATATATATACATATAAATGTTTTCAAAAAC
* * *
19816437 TATATAATATATATATTTTCA-A-AAATGTTTTCGAAAAC
1 TATATAATATATATATATACATATAAATGTTTTCAAAAAC
* * **
19816475 TATATATTATATATATGT-TTTCA-AAATGTTTTCAAAAAC
1 TATATAATATATATATATACAT-ATAAATGTTTTCAAAAAC
* * * *
19816514 TATATATTGTATATATGTTTTCA-A-AAATGTTTTCAAAAAC
1 TATATA--ATATATATATATACATATAAATGTTTTCAAAAAC
*
19816554 TATATATATATATATATATATATATA
1 TATATA-ATATATATATATACATATA
19816580 TATATATTCA
Statistics
Matches: 116, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
38 30 0.26
39 47 0.41
40 29 0.25
41 10 0.09
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (40 bp):
TATATAATATATATATATACATATAAATGTTTTCAAAAAC
Found at i:19816545 original size:12 final size:12
Alignment explanation
Indices: 19816528--19816552 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19816518 TATTGTATAT
19816528 ATGTTTTCAAAA
1 ATGTTTTCAAAA
19816540 ATGTTTTCAAAA
1 ATGTTTTCAAAA
19816552 A
1 A
19816553 CTATATATAT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:19816561 original size:2 final size:2
Alignment explanation
Indices: 19816554--19816586 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19816544 TTTCAAAAAC
19816554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19816587 TCAAAATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19816593 original size:92 final size:89
Alignment explanation
Indices: 19816475--19816658 Score: 296
Period size: 92 Copynumber: 2.0 Consensus size: 89
19816465 TTTCGAAAAC
* * * * *
19816475 TATATATTATATATATGTTTTCAAAATGTTTTCAAAAACTATATATTGTATATATGTTTTCAAAA
1 TATATATTATATATATATATTCAAAATGATTTCAAAAAATATATATTATATATATGTTTTC-AAA
19816540 ATGTTTTCAAAAACTATATATATATA
65 ATGTTTTCAAAAACTATATAT-TATA
19816566 TATATATATATATATATATATTCAAAATGATTTCAAAAAATATATATTATATATATGTTTTCAAA
1 TATATAT-TATATATATATATTCAAAATGATTTCAAAAAATATATATTATATATATGTTTTCAAA
19816631 ATGTTTTCAAAAACTATATATTATA
65 ATGTTTTCAAAAACTATATATTATA
19816656 TAT
1 TAT
19816659 GTTGAATAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
90 7 0.08
91 31 0.36
92 49 0.56
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (89 bp):
TATATATTATATATATATATTCAAAATGATTTCAAAAAATATATATTATATATATGTTTTCAAAA
TGTTTTCAAAAACTATATATTATA
Found at i:19816649 original size:37 final size:39
Alignment explanation
Indices: 19816565--19816658 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
19816555 ATATATATAT
* *
19816565 ATATATATATATATATATATATTCAAAATGATTTCAAAAA
1 ATATATAT-TATATATATGTTTTCAAAATGATTTCAAAAA
*
19816605 ATATATATTATATATATGTTTTCAAAATGTTTTCAAAAA
1 ATATATATTATATATATGTTTTCAAAATGATTTCAAAAA
*
19816644 CTATATATTATATAT
1 ATATATATTATATAT
19816659 GTTGAATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 42 0.84
40 8 0.16
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (39 bp):
ATATATATTATATATATGTTTTCAAAATGATTTCAAAAA
Found at i:19821209 original size:39 final size:39
Alignment explanation
Indices: 19821155--19821358 Score: 345
Period size: 39 Copynumber: 5.2 Consensus size: 39
19821145 ACAAAAAATA
* *
19821155 TTTTCAAAATGTTTTCAAAAAATATATAGTATATATATG
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATG
* *
19821194 TTTTCGAAATGTTTTCAAAAACTATATATTATATATATT
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATG
19821233 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATG
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATG
*
19821272 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATT
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATG
* *
19821311 TTTTCAAAATGTTTTTAAAAACTATATATTATATATATA
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATG
19821350 TTTTCAAAA
1 TTTTCAAAA
19821359 AAATTATATA
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 156 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (39 bp):
TTTTCAAAATGTTTTCAAAAACTATATATTATATATATG
Found at i:19823992 original size:74 final size:71
Alignment explanation
Indices: 19823908--19824191 Score: 265
Period size: 74 Copynumber: 3.8 Consensus size: 71
19823898 GTTTTTGAAA
*
19823908 ATATATTATATAGTTTTGAAAATGATTTTTG-AAAATATATATTATATAGTTTTGAAAACGATTG
1 ATATAATATATAGTTTTGAAAAT-ATTTTTGAAAAATATATATTATATAGTTTTGAAAAC-ATT-
19823972 TTAAAAGTAT
63 TTAAAA-TAT
* *
19823982 ATATAATATATAGTTTTTGAAAACA-TTTTGAAAAATATATAATATATAGTTTTGAAAACATTTT
1 ATATAATATATAG-TTTTGAAAATATTTTTGAAAAATATATATTATATAGTTTTGAAAACATTTT
*
19824046 -GAA-A-
65 AAAATAT
* *
19824050 ACAT-ATATATAGTTTTGAAAATATTTTTGAAAACATATATATAATATACAGTTTTTGAAAACAT
1 ATATAATATATAGTTTTGAAAATATTTTTGAAAA-ATATATAT--TATATAG-TTTTGAAAACAT
19824114 TTTGAAAAAAATAT
62 TTT----AAAATAT
* * * *
19824128 ATATAATATATAGTTTTTTTTGAAAAATATTTTTTTAAATATATATAATATATAGTTTAGAAAA
1 ATATAATATATAG----TTTTG-AAAATA-TTTTTGAAAAATATATATTATATAGTTTTGAAAA
19824192 TGTTTTTGAA
Statistics
Matches: 174, Mismatches: 15, Indels: 35
0.78 0.07 0.16
Matches are distributed among these distances:
66 10 0.06
67 17 0.10
68 10 0.06
69 1 0.01
70 6 0.03
71 17 0.10
72 2 0.01
73 8 0.05
74 40 0.23
75 9 0.05
76 2 0.01
77 1 0.01
78 3 0.02
79 8 0.05
81 8 0.05
82 6 0.03
83 5 0.03
84 13 0.07
85 8 0.05
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (71 bp):
ATATAATATATAGTTTTGAAAATATTTTTGAAAAATATATATTATATAGTTTTGAAAACATTTTA
AAATAT
Found at i:19824117 original size:39 final size:41
Alignment explanation
Indices: 19824054--19824145 Score: 136
Period size: 40 Copynumber: 2.3 Consensus size: 41
19824044 TTGAAAACAT
* *
19824054 ATATATAG-TTTTGAAAATATTTTTG-AAAACATATATATA
1 ATATATAGTTTTTGAAAACATTTTTGAAAAAAATATATATA
*
19824093 ATATACAGTTTTTGAAAACA-TTTTGAAAAAAATATATATA
1 ATATATAGTTTTTGAAAACATTTTTGAAAAAAATATATATA
19824133 ATATATAGTTTTT
1 ATATATAGTTTTT
19824146 TTTGAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
39 12 0.26
40 35 0.74
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (41 bp):
ATATATAGTTTTTGAAAACATTTTTGAAAAAAATATATATA
Found at i:19824120 original size:106 final size:110
Alignment explanation
Indices: 19823900--19824144 Score: 319
Period size: 106 Copynumber: 2.3 Consensus size: 110
19823890 AAAAATCAGT
* *
19823900 TTTTG-AAAATATAT--TATATAGTTTTGAAAATGATTTTTGAAAATATATATTATATAGTTTTG
1 TTTTGAAAAATATATAATATATAGTTTTGAAAATCATTTTTGAAAATACATATTATATAGTTTTG
* *
19823962 AAAACGATTGTTAAAAGTATATATAATATATAGTTTTTGAAAACA
66 AAAACGATTGTTAAAAATATATATAATATACAGTTTTTGAAAACA
19824007 TTTTGAAAAATATATAATATATAGTTTTGAAAA-CA-TTTTG-AAA-ACATA-TATATAGTTTTG
1 TTTTGAAAAATATATAATATATAGTTTTGAAAATCATTTTTGAAAATACATATTATATAGTTTTG
* *
19824067 AAAA-TATTTTTGAAAACATATATATAATATACAGTTTTTGAAAACA
66 AAAACGATTGTT-AAAA-ATATATATAATATACAGTTTTTGAAAACA
19824113 TTTTGAAAAAAATATATATAATATATAGTTTT
1 TTTTG---AAAA-ATATATAATATATAGTTTT
19824145 TTTTGAAAAA
Statistics
Matches: 123, Mismatches: 6, Indels: 15
0.85 0.04 0.10
Matches are distributed among these distances:
104 5 0.04
105 20 0.16
106 36 0.29
107 8 0.07
108 14 0.11
109 5 0.04
110 35 0.28
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (110 bp):
TTTTGAAAAATATATAATATATAGTTTTGAAAATCATTTTTGAAAATACATATTATATAGTTTTG
AAAACGATTGTTAAAAATATATATAATATACAGTTTTTGAAAACA
Found at i:19824147 original size:42 final size:40
Alignment explanation
Indices: 19824062--19824185 Score: 126
Period size: 40 Copynumber: 3.0 Consensus size: 40
19824052 ATATATATAG
* *
19824062 TTTTGAAAATATTTTTGAAAACATATATATAATATACAG--T
1 TTTTGAAAA-A-TTTTGAAAAAATATATATAATATATAGTTT
19824102 TTTTGAAAACATTTTGAAAAAAATATATATAATATATAGTTTT
1 TTTTGAAAA-ATTTTG-AAAAAATATATATAATATATAG-TTT
****
19824145 TTTTGAAAAATATTTTTTTAAATATATATAATATATAGTTT
1 TTTTGAAAAAT-TTTGAAAAAATATATATAATATATAGTTT
19824186 AGAAAATGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.07
40 30 0.42
41 3 0.04
42 21 0.29
43 13 0.18
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.47
Consensus pattern (40 bp):
TTTTGAAAAATTTTGAAAAAATATATATAATATATAGTTT
Found at i:19824147 original size:70 final size:70
Alignment explanation
Indices: 19824007--19824157 Score: 177
Period size: 71 Copynumber: 2.2 Consensus size: 70
19823997 TTTGAAAACA
* * * *
19824007 TTTTG-AAAA-ATATATAATATATAGTTTTGAAAACATTTTGAAAACATATATATAGTTTTGAAA
1 TTTTGAAAAATATATATAATATACAGTTTTGAAAACATTTTGAAAAAATATATATAGATATGAAA
19824070 A-TAT
66 ATTAT
19824074 TTTTGAAAACATATATATAATATACAGTTTTTGAAAACATTTTGAAAAAAATATATATA-ATAT-
1 TTTTGAAAA-ATATATATAATATACAG-TTTTGAAAACATTTTG-AAAAAATATATATAGATATG
* * *
19824137 ATAGTTTT
63 AAAATTAT
19824145 TTTTGAAAAATAT
1 TTTTGAAAAATAT
19824158 TTTTTTAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
67 5 0.07
68 3 0.04
69 1 0.01
70 20 0.28
71 29 0.41
72 13 0.18
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (70 bp):
TTTTGAAAAATATATATAATATACAGTTTTGAAAACATTTTGAAAAAATATATATAGATATGAAA
ATTAT
Found at i:19824191 original size:38 final size:36
Alignment explanation
Indices: 19823908--19824204 Score: 241
Period size: 36 Copynumber: 7.9 Consensus size: 36
19823898 GTTTTTGAAA
*
19823908 ATATATTATATAGTTTTGAAAATGATTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAAT-ATTTTT-AAAATAT
* *
19823946 ATAT--TATATAGTTTTGAAAACGATTGTTAAAAGTAT
1 ATATAATATATAGTTTTGAAAA-TATTTTTAAAA-TAT
* *
19823982 ATATAATATATAGTTTTTGAAAACATTTTGAAAA-AT
1 ATATAATATATAG-TTTTGAAAATATTTTTAAAATAT
* *
19824018 ATATAATATATAGTTTTGAAAACA-TTTT-GAA-A-
1 ATATAATATATAGTTTTGAAAATATTTTTAAAATAT
*
19824050 ACAT-ATATATAGTTTTGAAAATATTTTTGAAAACATAT
1 ATATAATATATAGTTTTGAAAATATTTTT--AAA-ATAT
* * *
19824088 ATATAATATACAGTTTTTGAAAACATTTTGAAAAAAATAT
1 ATATAATATATAG-TTTTGAAAATATTTT---TAAAATAT
*
19824128 ATATAATATATAGTTTTTTTTGAAAAATATTTTTTTAAATAT
1 ATATAATATATAG----TTTTG-AAAATA-TTTTTAAAATAT
* *
19824170 ATATAATATATAGTTTAGAAAATGTTTTTGAAAAT
1 ATATAATATATAGTTTTGAAAATATTTTT-AAAAT
19824205 TTGAAAATGT
Statistics
Matches: 215, Mismatches: 21, Indels: 47
0.76 0.07 0.17
Matches are distributed among these distances:
31 18 0.08
32 7 0.03
33 3 0.01
34 3 0.01
35 16 0.07
36 49 0.23
37 10 0.05
38 26 0.12
39 16 0.07
40 30 0.14
41 3 0.01
42 19 0.09
43 6 0.03
44 5 0.02
45 4 0.02
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAAATATTTTTAAAATAT
Found at i:19825362 original size:9 final size:9
Alignment explanation
Indices: 19825338--19825367 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
19825328 TCCCTAAATT
19825338 TCAATTTAA
1 TCAATTTAA
19825347 CTCAATTTAA
1 -TCAATTTAA
19825357 TCAATTTAA
1 TCAATTTAA
19825366 TC
1 TC
19825368 CTTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (9 bp):
TCAATTTAA
Found at i:19825391 original size:4 final size:4
Alignment explanation
Indices: 19825382--19825421 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
19825372 TAATTTTATC
19825382 TTTA TTTA TTTA TTTA TTTTA TTTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTT
19825422 TTGTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 22 0.65
5 9 0.26
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:19825407 original size:18 final size:17
Alignment explanation
Indices: 19825376--19825417 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
19825366 TCCTTTTAAT
19825376 TTTATCTTTATTTATTTA
1 TTTAT-TTTATTTATTTA
19825394 TTTATTTTATTTTATTTA
1 TTTATTTTA-TTTATTTA
19825412 TTTATT
1 TTTATT
19825418 ATTTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTATTTA
Found at i:19825428 original size:22 final size:22
Alignment explanation
Indices: 19825374--19825422 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
19825364 AATCCTTTTA
19825374 ATTTTATCTTTATTTATTTATTT
1 ATTTTAT-TTTATTTATTTATTT
19825397 ATTTTATTTTATTTATTTA-TT
1 ATTTTATTTTATTTATTTATTT
19825418 ATTTT
1 ATTTT
19825423 TGTTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 7 0.27
22 12 0.46
23 7 0.27
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (22 bp):
ATTTTATTTTATTTATTTATTT
Found at i:19826678 original size:107 final size:107
Alignment explanation
Indices: 19826492--19826705 Score: 324
Period size: 107 Copynumber: 2.0 Consensus size: 107
19826482 AAAACATACT
*
19826492 ATAAGTTAGGTAAATGTATTGCAAGTTTTAAAAGTTAGATGACCAAAATGCAAGCATCCTAAACG
1 ATAAGTTAGGTAAATGTATTGCAAGTTTTAAAAGTAAGATGACCAAAATGCAAGCATCCTAAACG
*
19826557 TTCGATGACCATTTATACAGTTTACCCTTAATTTAATTACAC
66 TTCGATGACCATTTATACAGTTTACCCTTAATTTAAGTACAC
* * *
19826599 ATAAGTTCA-GTAACTGTATTGTAAGTTTTAAAAGCTAAG-TGACCAAAATGTAAGCATCCTAAA
1 ATAAGTT-AGGTAAATGTATTGCAAGTTTTAAAAG-TAAGATGACCAAAATGCAAGCATCCTAAA
* * *
19826662 CGTTTGGTGACCATTTATATAGTTTACCCTTAATTTAAGTACAC
64 CGTTCGATGACCATTTATACAGTTTACCCTTAATTTAAGTACAC
19826706 TTATACATAA
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 93 0.96
108 4 0.04
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (107 bp):
ATAAGTTAGGTAAATGTATTGCAAGTTTTAAAAGTAAGATGACCAAAATGCAAGCATCCTAAACG
TTCGATGACCATTTATACAGTTTACCCTTAATTTAAGTACAC
Found at i:19827236 original size:31 final size:30
Alignment explanation
Indices: 19827162--19827237 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 30
19827152 AATATGGCTG
*
19827162 AGGGACTAAAATCAAATGGTAGTTAATGAT
1 AGGGACTAAAATCAAATGGTAGATAATGAT
*
19827192 AGAGGCACTAAAATCAAATGGATCA-ATAATGTT
1 AG-GG-ACTAAAATCAAATGG-T-AGATAATGAT
19827225 AGGGACTAAAATC
1 AGGGACTAAAATC
19827238 GAACATATCG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 2 0.05
31 11 0.28
32 17 0.43
33 9 0.22
34 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.24
Consensus pattern (30 bp):
AGGGACTAAAATCAAATGGTAGATAATGAT
Found at i:19845318 original size:21 final size:21
Alignment explanation
Indices: 19845292--19845342 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
19845282 AAATAGCTCG
19845292 GTATCGATACCCCTACTGAGA
1 GTATCGATACCCCTACTGAGA
19845313 GTATCGATACCCCTACTGAGA
1 GTATCGATACCCCTACTGAGA
19845334 GTATCGATA
1 GTATCGATA
19845343 ATCTACCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
GTATCGATACCCCTACTGAGA
Found at i:19848172 original size:19 final size:19
Alignment explanation
Indices: 19848159--19848206 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
19848149 TTGAAATTAG
19848159 GTATCGATACTGAAGTATA
1 GTATCGATACTGAAGTATA
*
19848178 GTATAGATACTGAAGTATA
1 GTATCGATACTGAAGTATA
19848197 GTATCGATAC
1 GTATCGATAC
19848207 CATAAGGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (19 bp):
GTATCGATACTGAAGTATA
Found at i:19848931 original size:21 final size:21
Alignment explanation
Indices: 19848907--19848983 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
19848897 GGTTCTACGC
19848907 GATCCTTCGAGACATATATGT
1 GATCCTTCGAGACATATATGT
* * * * *
19848928 GATCTTTCGGGATAATTCTATGA
1 GATCCTTCGAGA-CA-TATATGT
* *
19848951 GGTCCTTCGGGACATATATGT
1 GATCCTTCGAGACATATATGT
*
19848972 GGTCCTTCGAGA
1 GATCCTTCGAGA
19848984 AAATTTTATA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
21 26 0.60
22 2 0.05
23 15 0.35
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (21 bp):
GATCCTTCGAGACATATATGT
Found at i:19852966 original size:44 final size:44
Alignment explanation
Indices: 19852898--19852981 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
19852888 AGTCGAGGGT
* *
19852898 TCTACGCGGTCCTTCGAGATATATATGTGATCCTTCGGGACAAA
1 TCTACGAGGTCCTTCGAGACATATATGTGATCCTTCGGGACAAA
* * *
19852942 TCTACGAGGTCCTTCGGGACATATATGTGGTCCTTTGGGA
1 TCTACGAGGTCCTTCGAGACATATATGTGATCCTTCGGGA
19852982 TAATTTTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (44 bp):
TCTACGAGGTCCTTCGAGACATATATGTGATCCTTCGGGACAAA
Found at i:19852975 original size:21 final size:21
Alignment explanation
Indices: 19852905--19852981 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
19852895 GGTTCTACGC
* *
19852905 GGTCCTTCGAGATATATATGT
1 GGTCCTTCGGGACATATATGT
* * * *
19852926 GATCCTTCGGGACAAATCTACGA
1 GGTCCTTCGGGAC--ATATATGT
19852949 GGTCCTTCGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
*
19852970 GGTCCTTTGGGA
1 GGTCCTTCGGGA
19852982 TAATTTTATA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
21 26 0.60
23 17 0.40
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (21 bp):
GGTCCTTCGGGACATATATGT
Found at i:19860198 original size:20 final size:19
Alignment explanation
Indices: 19860133--19860200 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
19860123 GGCATTCATG
*
19860133 AGGTATCGATACATGAA-GA
1 AGGTATCGATACCT-AAGGA
*
19860152 ACAGTATCGATACC-AAGG-
1 A-GGTATCGATACCTAAGGA
*
19860170 -GGTACCGATACCTTAAGGA
1 AGGTATCGATACC-TAAGGA
19860189 AGGTATCGATAC
1 AGGTATCGATAC
19860201 AATTTTTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
16 10 0.26
18 6 0.16
19 2 0.05
20 20 0.53
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.21
Consensus pattern (19 bp):
AGGTATCGATACCTAAGGA
Found at i:19860306 original size:21 final size:23
Alignment explanation
Indices: 19860254--19860308 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
19860244 ACCTAAGCAT
19860254 GGTACCGATACCTCAACTAGGGA
1 GGTACCGATACCTCAACTAGGGA
* * * *
19860277 AGTATCGATACC-CTAC-AGGGG
1 GGTACCGATACCTCAACTAGGGA
19860298 GGTACCGATAC
1 GGTACCGATAC
19860309 TTTAAGAAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 13 0.50
22 3 0.12
23 10 0.38
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
GGTACCGATACCTCAACTAGGGA
Found at i:19867287 original size:10 final size:10
Alignment explanation
Indices: 19867272--19867297 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19867262 TTTTATTTCA
19867272 AAAATTTTGG
1 AAAATTTTGG
19867282 AAAATTTTGG
1 AAAATTTTGG
19867292 AAAATT
1 AAAATT
19867298 CTTCTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (10 bp):
AAAATTTTGG
Found at i:19867693 original size:22 final size:22
Alignment explanation
Indices: 19867661--19867742 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
19867651 CAGAACCTCC
* *
19867661 AGGGGGTATCGATTCCCCTACA
1 AGGGGGAATCGATTCCCCTTCA
* *
19867683 GGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
19867706 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
* *
19867728 AGGGGGTATCTATTC
1 AGGGGGAATCGATTC
19867743 ACTCTGCACT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 30 0.59
23 21 0.41
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:19867710 original size:23 final size:22
Alignment explanation
Indices: 19867661--19867733 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
19867651 CAGAACCTCC
* * *
19867661 AGGGGGTATCGATTCCCCTACA
1 AGGGGGAATCGGTTCCCCTTCA
*
19867683 GGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTC-A
19867706 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGGTTCCCCTTCA
19867728 AGGGGG
1 AGGGGG
19867734 TATCTATTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
22 24 0.53
23 21 0.47
ACGTcount: A:0.19, C:0.25, G:0.36, T:0.21
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTCA
Found at i:19876535 original size:18 final size:18
Alignment explanation
Indices: 19876512--19876547 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19876502 TCTCTCAAGT
19876512 TCCTCTTAGAATTGCTAA
1 TCCTCTTAGAATTGCTAA
*
19876530 TCCTCTTAGGATTGCTAA
1 TCCTCTTAGAATTGCTAA
19876548 AAAACCATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (18 bp):
TCCTCTTAGAATTGCTAA
Found at i:19877307 original size:134 final size:134
Alignment explanation
Indices: 19877094--19877940 Score: 931
Period size: 134 Copynumber: 6.3 Consensus size: 134
19877084 AGATCAAGAA
* * *
19877094 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGAATGAATCGAGGTAGACTTGTGCCACTGTTACT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * * * *
19877159 CA-AGGAAGATCAAATCT-TAAAAGAGACGGATCTGTTTCGCTTTTTCTTGAGGTAAAATTAGAT
66 CAGA-GAAGATCAAATCTGTAAAAGAGA-GGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGAT
19877222 TTGGGG
129 TTGGGG
* * *
19877228 ATGTTAATTCATTCAACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * * * *
19877293 CAGAGAATATCAAATCT-TGAAAGAGAGGGATATGTTTCTCTTCTTCTTGAGGGAAAATCATATA
66 CAGAGAAGATCAAATCTGTAAAAGAGA-GGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGAT-
19877357 TT-GGG
129 TTGGGG
* *
19877362 ACGTTGATTCATTCCACCGTTAC-TCATGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTAC
1 ACGTTGATTCATTCCACTGTT-CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTAC
* * * * * *
19877426 TCAGGGAATATCAAATCT-TGAAAGAGAGAGATTTGTTCCGCTTCTTCTTAAGGGAAAATCAAAT
65 TCAGAGAAGATCAAATCTGTAAAAGAGAG-GATATGTTCCGCTTCTTCTTGAGGGAAAATCAGAT
*
19877490 ATGGGG
129 TTGGGG
* * *
19877496 ACGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCATTGTTCCT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * *
19877561 CAGGGAAGATCAAATCTGGAAAAAAAGAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGAT
66 CAGAGAAGATCAAATCT-GTAAAAGAGA-GGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGAT
19877626 CTT-GGG
129 -TTGGGG
* * *** * * *
19877632 ATGTTGATTCATTCTACTGTTCTTCAGGGAAGATTGAATCGAATAAGACATGTTTCACTGTTCCT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
** * * *
19877697 CA-AGAAGATCAAATCTGGGGGAAA-A-AGGATCTGATCCGCTTCTTCTTGAGGGAAAATCATAT
66 CAGAGAAGATCAAATCT--GTAAAAGAGAGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGAT
*
19877759 ATGGGG
129 TTGGGG
* * * * * * *
19877765 ACATTGATTCATTCCACTGTTCTTCAAGGAAGATTAAATCGAGCCAGACTTGTTTCATTGTTCCT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
* * * * * * * *
19877830 CAGGGAAGATCAAATCTGGAAAAAAAGAGGAATTTGCTCCACTTCTTCTTAAGGGAAAATAAGAT
66 CAGAGAAGATCAAATCT-GTAAAAGAGAGG-ATATGTTCCGCTTCTTCTTGAGGGAAAATCAGAT
*
19877895 CTGGGG
129 TTGGGG
* * *
19877901 ACATTGATTCATTCCACCGTTCTTCAAGGAAGATTGAATC
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATC
19877941 AAGTTTGATT
Statistics
Matches: 619, Mismatches: 78, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
132 1 0.00
133 101 0.16
134 319 0.52
135 21 0.03
136 175 0.28
137 2 0.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (134 bp):
ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACT
CAGAGAAGATCAAATCTGTAAAAGAGAGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATTT
GGGG
Found at i:19877798 original size:269 final size:267
Alignment explanation
Indices: 19877094--19877940 Score: 1074
Period size: 269 Copynumber: 3.1 Consensus size: 267
19877084 AGATCAAGAA
* * *
19877094 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGAATGAATCGAGGTAGACTTGTGCCACTGTTACT
1 ACGTTGATTCATTCCACCGTTCTTCAGGGAAGATTGAATCGA-GTAGACTTGTTCCACTGTTACT
* * * * * * *
19877159 CAAGGAAGATCAAATCTTAAAAGAGACGGATCTGTTTCGCTTTTTCTTGAGGTAAAATTAGATTT
65 CAA-GAAGATCAAATCTTGAAAGAGA-GGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAAATAT
* * * *
19877224 GGGGATGTTAATTCATTCAACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGT
128 GGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCATTGT
* * * * * * *
19877289 TACTCAGAGAATATCAAATCTTG--AAAGAGAGGGATATGTTTCTCTTCTTCTTGAGGGAAAATC
193 TCCTCAGGGAAGATCAAATCTGGAAAAAAAGAGGGATATGTTCCACTTCTTCTTGAGGGAAAATC
* *
19877352 ATATATTGGG
258 AGATCTTGGG
* *
19877362 ACGTTGATTCATTCCACCGTTAC-TCATGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTAC
1 ACGTTGATTCATTCCACCGTT-CTTCAGGGAAGATTGAATCGA-GTAGACTTGTTCCACTGTTAC
* * * *
19877426 TCAGGGAATATCAAATCTTGAAAGAGAGAGATTTGTTCCGCTTCTTCTTAAGGGAAAATCAAATA
64 TCA-AGAAGATCAAATCTTGAAAGAGAG-GATCTGTTCCGCTTCTTCTTGAGGGAAAATCAAATA
*
19877491 TGGGGACGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCATTG
127 TGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCATTG
*
19877556 TTCCTCAGGGAAGATCAAATCTGGAAAAAAAGAGGGATATGTTCCGCTTCTTCTTGAGGGAAAAT
192 TTCCTCAGGGAAGATCAAATCTGGAAAAAAAGAGGGATATGTTCCACTTCTTCTTGAGGGAAAAT
19877621 CAGATCTTGGG
257 CAGATCTTGGG
* * * * * * *
19877632 ATGTTGATTCATTCTACTGTTCTTCAGGGAAGATTGAATCGAATAAGACATGTTTCACTGTTCCT
1 ACGTTGATTCATTCCACCGTTCTTCAGGGAAGATTGAATCGAGT-AGACTTGTTCCACTGTTACT
* * *
19877697 CAAGAAGATCAAATCTGGGGGAAA-A-AGGATCTGATCCGCTTCTTCTTGAGGGAAAATCATATA
65 CAAGAAGATCAAATCT---TGAAAGAGAGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAAATA
* * * * *
19877760 TGGGGACATTGATTCATTCCACTGTTCTTCAAGGAAGATTAAATCGAGCCAGACTTGTTTCATTG
127 TGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCATTG
* * * *
19877825 TTCCTCAGGGAAGATCAAATCTGGAAAAAAAGAGGAATTTGCTCCACTTCTTCTTAAGGGAAAAT
192 TTCCTCAGGGAAGATCAAATCTGGAAAAAAAGAGGGATATGTTCCACTTCTTCTTGAGGGAAAAT
* *
19877890 AAGATCTGGGG
257 CAGATCTTGGG
* *
19877901 ACATTGATTCATTCCACCGTTCTTCAAGGAAGATTGAATC
1 ACGTTGATTCATTCCACCGTTCTTCAGGGAAGATTGAATC
19877941 AAGTTTGATT
Statistics
Matches: 505, Mismatches: 64, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
267 1 0.00
268 188 0.37
269 209 0.41
270 102 0.20
271 1 0.00
272 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (267 bp):
ACGTTGATTCATTCCACCGTTCTTCAGGGAAGATTGAATCGAGTAGACTTGTTCCACTGTTACTC
AAGAAGATCAAATCTTGAAAGAGAGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAAATATGGG
GACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCATTGTTCC
TCAGGGAAGATCAAATCTGGAAAAAAAGAGGGATATGTTCCACTTCTTCTTGAGGGAAAATCAGA
TCTTGGG
Found at i:19878581 original size:41 final size:41
Alignment explanation
Indices: 19878518--19878605 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
19878508 TATGGATGGT
* * * *
19878518 CCGAAGGACTTATCATCTTGCTCGAAAGACTTGCGAATGAC
1 CCGAAGGACTTAACATCATGCTCGAAAGAATTACGAATGAC
* * *
19878559 CCGAAGGATTTAACATCATGCTCGAAAGAATTACTAATGGC
1 CCGAAGGACTTAACATCATGCTCGAAAGAATTACGAATGAC
19878600 CCGAAG
1 CCGAAG
19878606 AATGGAAACT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (41 bp):
CCGAAGGACTTAACATCATGCTCGAAAGAATTACGAATGAC
Found at i:19880289 original size:23 final size:23
Alignment explanation
Indices: 19880256--19880300 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19880246 TGTTTTATAT
19880256 GTTCACAAACATGTTCGTTTAGC
1 GTTCACAAACATGTTCGTTTAGC
*
19880279 GTTCACGAACATGTTCGTTTAG
1 GTTCACAAACATGTTCGTTTAG
19880301 AATTTGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
GTTCACAAACATGTTCGTTTAGC
Found at i:19884238 original size:16 final size:16
Alignment explanation
Indices: 19884219--19884272 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
19884209 CTTTCATGTC
19884219 TTTTTTTTTCGAACAG
1 TTTTTTTTTCGAACAG
*
19884235 TTTTTTTTTCGAACTG
1 TTTTTTTTTCGAACAG
*
19884251 CTATTTTTTTC-AACA-
1 -TTTTTTTTTCGAACAG
19884266 TTTTTTT
1 TTTTTTT
19884273 GTGATGGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.18
16 18 0.55
17 9 0.27
ACGTcount: A:0.17, C:0.13, G:0.07, T:0.63
Consensus pattern (16 bp):
TTTTTTTTTCGAACAG
Found at i:19891763 original size:19 final size:20
Alignment explanation
Indices: 19891736--19891780 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
19891726 ATTAGCAACA
*
19891736 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGATCCTATC
*
19891755 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
19891775 TAATAA
1 TAATAA
19891781 CTAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:19891764 original size:20 final size:20
Alignment explanation
Indices: 19891739--19891778 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19891729 AGCAACATAA
*
19891739 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
19891759 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
19891779 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:19891821 original size:20 final size:21
Alignment explanation
Indices: 19891792--19891831 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19891782 TAATAGAATA
*
19891792 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
19891813 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
19891832 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:19891875 original size:52 final size:52
Alignment explanation
Indices: 19891737--19891884 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
19891727 TTAGCAACAT
19891737 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
19891788 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
**
19891841 AATAAAAACTGATTCTATCTAATTAAAACGGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
19891885 TTTAATTTAG
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 3 0.03
52 44 0.47
53 46 0.49
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:19891878 original size:20 final size:20
Alignment explanation
Indices: 19891845--19891883 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19891835 TAATAGAATA
* *
19891845 AAAACTGATTCTATCTAATT
1 AAAACGGATCCTATCTAATT
19891865 AAAACGGATCCTATCTAAT
1 AAAACGGATCCTATCTAAT
19891884 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAACGGATCCTATCTAATT
Found at i:19896481 original size:19 final size:20
Alignment explanation
Indices: 19896454--19896498 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
19896444 ATTAGCAACA
*
19896454 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGATCCTATC
*
19896473 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
19896493 TAATAA
1 TAATAA
19896499 CTAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:19896482 original size:20 final size:20
Alignment explanation
Indices: 19896457--19896496 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19896447 AGCAACATAA
*
19896457 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
19896477 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
19896497 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:19896539 original size:20 final size:21
Alignment explanation
Indices: 19896510--19896549 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19896500 TAATAGAATA
*
19896510 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
19896531 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
19896550 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:19896593 original size:52 final size:52
Alignment explanation
Indices: 19896455--19896602 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
19896445 TTAGCAACAT
19896455 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
19896506 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
**
19896559 AATAAAAACTGATTCTATCTAATTAAAACGGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
19896603 TTTAATTTAG
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 3 0.03
52 44 0.47
53 46 0.49
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:19896596 original size:20 final size:20
Alignment explanation
Indices: 19896563--19896601 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19896553 TAATAGAATA
* *
19896563 AAAACTGATTCTATCTAATT
1 AAAACGGATCCTATCTAATT
19896583 AAAACGGATCCTATCTAAT
1 AAAACGGATCCTATCTAAT
19896602 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAACGGATCCTATCTAATT
Found at i:19902427 original size:17 final size:18
Alignment explanation
Indices: 19902407--19902440 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19902397 AAATTGAGGG
19902407 TTTTT-AAAAATAAATTA
1 TTTTTAAAAAATAAATTA
19902424 TTTTTAAAAAATAAATT
1 TTTTTAAAAAATAAATT
19902441 TCTAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTTAAAAAATAAATTA
Found at i:19908842 original size:30 final size:31
Alignment explanation
Indices: 19908806--19908874 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
19908796 AAATTTAAAG
19908806 ATTGACCCAAAC-CAAAAAT-ATCAATCCGAT
1 ATTGACCC-AACTCAAAAATAATCAATCCGAT
* *
19908836 ATTGACCCGACTCAAAAATCAATCGATCCGAT
1 ATTGACCCAACTCAAAAAT-AATCAATCCGAT
19908868 ATTGACC
1 ATTGACC
19908875 TGACCTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 15 0.44
32 17 0.50
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.22
Consensus pattern (31 bp):
ATTGACCCAACTCAAAAATAATCAATCCGAT
Found at i:19908870 original size:32 final size:32
Alignment explanation
Indices: 19908829--19908991 Score: 150
Period size: 32 Copynumber: 5.1 Consensus size: 32
19908819 AAAAATATCA
* * * *
19908829 ATCCGATATTGACCCGACTCAAAAATCAATCG
1 ATCCGATATTGACCTGACCCGAAAATCAACCG
*
19908861 ATCCGATATTGACCTGACCTGAAAATCAACCG
1 ATCCGATATTGACCTGACCCGAAAATCAACCG
** * *
19908893 ATATGATTTTGACCTGACCCGAAAATAAACCG
1 ATCCGATATTGACCTGACCCGAAAATCAACCG
** * * **
19908925 ATATGATTTTGACCTGACCCGAAAACCAATAG
1 ATCCGATATTGACCTGACCCGAAAATCAACCG
*
19908957 ATCCGATATTGA-CTCGACCC-ATAAACCAACCG
1 ATCCGATATTGACCT-GACCCGA-AAATCAACCG
19908989 ATC
1 ATC
19908992 ATGTAACACC
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
31 3 0.03
32 107 0.97
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (32 bp):
ATCCGATATTGACCTGACCCGAAAATCAACCG
Found at i:19910779 original size:24 final size:24
Alignment explanation
Indices: 19910747--19910800 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
19910737 CACCATTGCT
*
19910747 CATATAATTTGCACAGAAGTGCCA
1 CATAGAATTTGCACAGAAGTGCCA
* * *
19910771 CGTAGAATTTGTACCGAAGTGCCA
1 CATAGAATTTGCACAGAAGTGCCA
19910795 CATAGA
1 CATAGA
19910801 TATGTCCTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (24 bp):
CATAGAATTTGCACAGAAGTGCCA
Found at i:19914598 original size:19 final size:19
Alignment explanation
Indices: 19914570--19914606 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19914560 TTTTCAATCC
*
19914570 ATATCAATTTGTTTAATTT
1 ATATCAATTTATTTAATTT
*
19914589 ATATCCATTTATTTAATT
1 ATATCAATTTATTTAATT
19914607 AGCCCAATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (19 bp):
ATATCAATTTATTTAATTT
Found at i:19914715 original size:24 final size:24
Alignment explanation
Indices: 19914683--19914736 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
19914673 CACCACTGCT
*
19914683 CATATAATTTGCACAGAAGTGCCA
1 CATAGAATTTGCACAGAAGTGCCA
* *
19914707 CGTAGAATTTGCACTGAAGTGCCA
1 CATAGAATTTGCACAGAAGTGCCA
19914731 CATAGA
1 CATAGA
19914737 TATGTCCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (24 bp):
CATAGAATTTGCACAGAAGTGCCA
Found at i:19914776 original size:24 final size:24
Alignment explanation
Indices: 19914728--19914808 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
19914718 CACTGAAGTG
* * *
19914728 CCACATAG-ATATGTCCCAAAGGA
1 CCACATAGAATTTGTCCCGAATGA
*
19914751 CCACGTAGAATTTGTCCCGAATGA
1 CCACATAGAATTTGTCCCGAATGA
19914775 CCACATAGAATTTGTCCCGAA-GAA
1 CCACATAGAATTTGTCCCGAATG-A
*
19914799 CCGCATAGAA
1 CCACATAGAA
19914809 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
23 8 0.16
24 42 0.84
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCGAATGA
Found at i:19915130 original size:2 final size:2
Alignment explanation
Indices: 19915123--19915151 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19915113 TTCACATAGA
19915123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19915152 CTCATAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19916218 original size:7 final size:7
Alignment explanation
Indices: 19916202--19916272 Score: 135
Period size: 7 Copynumber: 10.3 Consensus size: 7
19916192 AGTTTCCAGA
19916202 CTTT-TC
1 CTTTCTC
19916208 CTTTCTC
1 CTTTCTC
19916215 CTTTCTC
1 CTTTCTC
19916222 CTTTCTC
1 CTTTCTC
19916229 CTTTCTC
1 CTTTCTC
19916236 CTTTCTC
1 CTTTCTC
19916243 CTTTCTC
1 CTTTCTC
19916250 CTTTCTC
1 CTTTCTC
19916257 CTTTCTC
1 CTTTCTC
19916264 CTTTCTC
1 CTTTCTC
19916271 CT
1 CT
19916273 AATATCCCAT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 4 0.06
7 60 0.94
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
CTTTCTC
Found at i:19921088 original size:37 final size:37
Alignment explanation
Indices: 19921038--19921111 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
19921028 AAGGAAGTTT
19921038 TCTGGTTAAGTTTATCTCCAGAAGGTGCAATTCGACA
1 TCTGGTTAAGTTTATCTCCAGAAGGTGCAATTCGACA
* *
19921075 TCTGGTTAAGTTTATCTCCTGAAGGTGCAATTTGACA
1 TCTGGTTAAGTTTATCTCCAGAAGGTGCAATTCGACA
19921112 GCTGATCAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (37 bp):
TCTGGTTAAGTTTATCTCCAGAAGGTGCAATTCGACA
Found at i:19926817 original size:6 final size:6
Alignment explanation
Indices: 19926750--19926814 Score: 121
Period size: 6 Copynumber: 10.8 Consensus size: 6
19926740 AGACTATTAT
19926750 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC
*
19926798 ATAAAC ATAAAT ATAAA
1 ATAAAC ATAAAC ATAAA
19926815 TATTGTTGTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAC
Found at i:19927562 original size:20 final size:20
Alignment explanation
Indices: 19927537--19927610 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
19927527 TTTTCCCAAT
*
19927537 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
19927557 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
19927578 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
19927598 TCGCAACGCGAAT
1 TCGCAACGCGAAT
19927611 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:19927580 original size:21 final size:21
Alignment explanation
Indices: 19927554--19927624 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
19927544 GCGAATAAGT
19927554 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
19927575 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
19927595 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
19927616 AAATCGCAA
1 AAATCGCAA
19927625 TGTGATACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:19927582 original size:41 final size:41
Alignment explanation
Indices: 19927537--19927626 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
19927527 TTTTCCCAAT
19927537 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
19927578 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
19927619 TCGCAATG
1 TCGCAATG
19927627 TGATACTGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:19927642 original size:41 final size:41
Alignment explanation
Indices: 19927556--19927690 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
19927546 GAATAAGTAA
* * *
19927556 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAG-ATACTG-ACT
*
19927597 ATCGCAACGCGAATTGGGAAAATCGCAATGTGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
* * ** * *
19927638 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGAGATACTGACT
*
19927679 TTCGCAACGCGA
1 ATCGCAACGCGA
19927691 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
Found at i:19927685 original size:20 final size:20
Alignment explanation
Indices: 19927660--19927712 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
19927650 TAATAAAAAA
* *
19927660 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
19927680 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
19927700 TCGCAACGCGATA
1 TCGCAACGCGATA
19927713 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:19927928 original size:22 final size:22
Alignment explanation
Indices: 19927900--19927943 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19927890 CACTCTCTCA
19927900 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
19927922 CCCATCTCCGACGAAATTCGTC
1 CCCATCTCCGACGAAATCCGTC
19927944 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.43, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:19928232 original size:20 final size:20
Alignment explanation
Indices: 19928207--19928244 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19928197 CGATTCTCTC
19928207 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
19928227 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
19928245 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:19929585 original size:18 final size:18
Alignment explanation
Indices: 19929564--19929608 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
19929554 TCCACTTCGG
*
19929564 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
19929582 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
19929600 GAGCCATCA
1 GAGCCATCA
19929609 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:19930144 original size:19 final size:20
Alignment explanation
Indices: 19930090--19930156 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
19930080 TAGTTTACTT
* *
19930090 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
19930110 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
19930130 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
19930149 TCGCAACG
1 TCGCAACG
19930157 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:19930164 original size:14 final size:14
Alignment explanation
Indices: 19930145--19930202 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
19930135 ATGCGAAATG
19930145 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
19930159 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
19930175 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
19930191 AAAATCGCAACG
1 AAAATCGCAACG
19930203 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:19930187 original size:32 final size:33
Alignment explanation
Indices: 19930129--19930219 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
19930119 GGAAATGGCT
19930129 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
19930162 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
19930194 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
19930220 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:19930255 original size:14 final size:14
Alignment explanation
Indices: 19930236--19930293 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
19930226 TTGTGTTTCG
19930236 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
19930250 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
19930266 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
19930282 CGTTGCGATTTT
1 CGTTGCGATTTT
19930294 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:19930270 original size:32 final size:33
Alignment explanation
Indices: 19930231--19930309 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
19930221 GCGATTTGTG
19930231 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
19930263 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
19930296 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
19930310 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:19930308 original size:19 final size:19
Alignment explanation
Indices: 19930250--19930367 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
19930240 GCGATTTTGT
19930250 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
19930268 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
19930282 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
19930301 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
19930321 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
19930340 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
19930360 TGTTGCGA
1 CGTTGCGA
19930368 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:19932260 original size:13 final size:13
Alignment explanation
Indices: 19932213--19932265 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
19932203 TTGATTGTTT
19932213 AATTGATTTGTAA
1 AATTGATTTGTAA
*
19932226 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
19932240 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
19932254 AATTGATATGTA
1 AATTGATTTGTA
19932266 CATAATTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:19932384 original size:33 final size:33
Alignment explanation
Indices: 19932339--19932452 Score: 147
Period size: 33 Copynumber: 3.3 Consensus size: 33
19932329 AAAACAGACT
* ***
19932339 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
19932372 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
19932410 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
19932443 ATCGCAATGC
1 ATCGCAATGC
19932453 AATTTTCATT
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
33 36 0.50
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 30 0.42
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:19932454 original size:19 final size:19
Alignment explanation
Indices: 19932368--19932435 Score: 136
Period size: 19 Copynumber: 3.6 Consensus size: 19
19932358 ATCGCAACGA
19932368 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
19932387 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
19932406 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
19932425 GAAAATCGCAA
1 GAAAATCGCAA
19932436 CGAGAAAATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:19932530 original size:20 final size:20
Alignment explanation
Indices: 19932473--19932530 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
19932463 TCGCATTGCG
* * *
19932473 ATTTTCTCGTTACGATAACC
1 ATTTTCGCGTTGCGATAGCC
19932493 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
19932513 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
19932531 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:19933034 original size:22 final size:22
Alignment explanation
Indices: 19933006--19933060 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
19932996 TATCACTCTC
19933006 TCCGACGACATTCATTCCAATA
1 TCCGACGACATTCATTCCAATA
*
19933028 TCCGACGACATTCGTTCCAATA
1 TCCGACGACATTCATTCCAATA
*
19933050 TCCAACGACAT
1 TCCGACGACAT
19933061 CCTTCCCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.25
Consensus pattern (22 bp):
TCCGACGACATTCATTCCAATA
Found at i:19933640 original size:24 final size:24
Alignment explanation
Indices: 19933613--19933666 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
19933603 GTATTCAAAA
* *
19933613 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
19933637 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
19933661 TTTGAT
1 TTTGAT
19933667 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:19936199 original size:33 final size:33
Alignment explanation
Indices: 19936157--19936283 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
19936147 GGAAATTACT
19936157 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* **
19936190 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
19936222 TTTCGCAATGCGAAATGAAAAT-AGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCA-CAACGAGAGA
*
19936256 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCACAACG
19936284 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:19936240 original size:66 final size:66
Alignment explanation
Indices: 19936158--19936290 Score: 232
Period size: 66 Copynumber: 2.0 Consensus size: 66
19936148 GAAATTACTA
*
19936158 TCGCAATGCGAAATGAAAATCA-CAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAA
1 TCGCAATGCGAAATGAAAAT-AGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAA
19936222 TT
65 TT
*
19936224 TCGCAATGCGAAATGAAAATAGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATAGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
19936289 T
66 T
19936290 T
1 T
19936291 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 1 0.02
66 63 0.98
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATAGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:19936305 original size:19 final size:20
Alignment explanation
Indices: 19936283--19936325 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
19936273 AAATCGCAAC
19936283 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
19936302 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
19936322 GCGA
1 GCGA
19936326 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:19936310 original size:14 final size:14
Alignment explanation
Indices: 19936311--19936344 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19936301 TGCGATTTTC
19936311 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
19936325 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
19936339 ATTTTC
1 ATTTTC
19936345 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:19936485 original size:14 final size:14
Alignment explanation
Indices: 19936466--19936504 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
19936456 CATCAATTAA
19936466 ACAAATCAATTTTT
1 ACAAATCAATTTTT
**
19936480 ACAAATCACCTTTT
1 ACAAATCAATTTTT
19936494 ACAAATCAATT
1 ACAAATCAATT
19936505 AAACAATCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:19937926 original size:21 final size:21
Alignment explanation
Indices: 19937860--19937926 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
19937850 GTGAATCGGG
*
19937860 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
19937880 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
19937902 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
19937923 CTCT
1 CTCT
19937927 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:19937945 original size:42 final size:41
Alignment explanation
Indices: 19937860--19937982 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
19937850 GTGAATCGGG
* * * * *
19937860 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
19937902 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
19937944 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
19937983 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:19940066 original size:33 final size:33
Alignment explanation
Indices: 19940009--19940107 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
19939999 ACGAGATAAT
* *
19940009 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACG-AGAAATGACTATCGCAACCA
*
19940043 GAGAATCGCAACGAGAAATGACTATCGCGACCA
1 GAGAATCGCAACGAGAAATGACTATCGCAACCA
* * **
19940076 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGAGAAATGACTATCGCAACC
19940108 GCGAAATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGAGAAATGACTATCGCAACCA
Done.