Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 7 of 24
Found at i:910959 original size:166 final size:164
Alignment explanation
Indices: 910568--911023 Score: 395
Period size: 166 Copynumber: 2.8 Consensus size: 164
910558 TCATGAGTTT
* * * *
910568 TTTTTTATTTTTT-CTTGAAATCCCTCTATTTTTGAAATACGGAGTTTGCTACTTCGTAAATATT
1 TTTTTCATTTTTTCCTTGAAATCCCT-TATTTTTGAAATACAGAGTTTTCTACTACGTAAAT-TT
* * * * * * * *
910632 TTCAGGGG-TGCTTTTCTCGGTTCAAAATTTTTAATATTCACCAAATATTATCATTTAATTCATA
64 TT-TGGGGAGGATTTTCTCGATTTAAAATTTTTAAAATTCAACAAATATTATAATTTAATTCATA
* * * * *
910696 GCAAATTATTTTTAAAAATTTTATTTATTTTCTTGAG
128 CCAAATTATTTTTAAAAATTTTATTTATTTCCATCAA
* * ** * * * * *
910733 TTTTTCATTTTTTCCTTGAAATCCCATGTTTCCGAAATACATAATTTTTTTCTCCGTAAATTTTT
1 TTTTTCATTTTTTCCTTGAAATCCCTTATTTTTGAAATACAGAGTTTTCTACTACGTAAATTTTT
*
910798 TGGGGAGGATTTTCATCGATTTAAAATTTTTAAAATTCATCAAATATTATAATTTAA-T-A-ACC
66 TGGGGAGGATTTTC-TCGATTTAAAATTTTTAAAATTCAACAAATATTATAATTTAATTCATACC
*
910860 ATTTTATTATTTTTGAAAAATTCCTT-TTTA-TTCCATCAA
130 A---AATTATTTTT-AAAAATT--TTATTTATTTCCATCAA
* * * *
910899 TTTTTCATTTTTTCCTTGAAATCTCTTATTTTTGAAAAACCGAGTTTTCTACTACGTAAATATTT
1 TTTTTCATTTTTTCCTTGAAATCCCTTATTTTTGAAATACAGAGTTTTCTACTACGTAAATTTTT
* * * * * * * * *
910964 TCGGAAGAATTTTTCTCAATTTAACATTTTTGAAATTCAAAAAATATTATTATTAAATTC
66 TGGGGAGGA-TTTTCTCGATTTAAAATTTTTAAAATTCAACAAATATTATAATTTAATTC
911024 CTATTAAATC
Statistics
Matches: 230, Mismatches: 49, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
162 3 0.01
163 5 0.02
164 11 0.05
165 83 0.36
166 116 0.50
167 10 0.04
168 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (164 bp):
TTTTTCATTTTTTCCTTGAAATCCCTTATTTTTGAAATACAGAGTTTTCTACTACGTAAATTTTT
TGGGGAGGATTTTCTCGATTTAAAATTTTTAAAATTCAACAAATATTATAATTTAATTCATACCA
AATTATTTTTAAAAATTTTATTTATTTCCATCAA
Found at i:914728 original size:28 final size:28
Alignment explanation
Indices: 914662--914752 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 28
914652 TGTTCCATCA
* * *
914662 TTATTGATTTCCCTTTCTTTGTTATTTT
1 TTATTGATTTCCCTTTCCTTGATATTTC
* * *
914690 TTACTGTTTTCCTTTTCCTTGATATTTC
1 TTATTGATTTCCCTTTCCTTGATATTTC
* * * *
914718 TTGTTGATTT-CGTTTCCTTCATCTTTC
1 TTATTGATTTCCCTTTCCTTGATATTTC
914745 TTATTGAT
1 TTATTGAT
914753 CGTATTAATC
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 21 0.42
28 29 0.58
ACGTcount: A:0.11, C:0.18, G:0.09, T:0.63
Consensus pattern (28 bp):
TTATTGATTTCCCTTTCCTTGATATTTC
Found at i:917810 original size:21 final size:21
Alignment explanation
Indices: 917785--917837 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
917775 TGAGATGAAT
*
917785 TTTTATATTAATATTTATAT-A
1 TTTTATATTAA-ATTTAAATAA
917806 TTTTATAATTAAATTTAAATAA
1 TTTTAT-ATTAAATTTAAATAA
*
917828 ATTTATATTA
1 TTTTATATTA
917838 TTTTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATATTAAATTTAAATAA
Found at i:918120 original size:15 final size:15
Alignment explanation
Indices: 918100--918148 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
918090 AATATATATT
918100 ATAAATTTTATATAA
1 ATAAATTTTATATAA
918115 ATAAATTATTA-ATATA
1 ATAAATT-TTATATA-A
* *
918131 TTAAAATTTATATAA
1 ATAAATTTTATATAA
918146 ATA
1 ATA
918149 TAAAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAATTTTATATAA
Found at i:918152 original size:33 final size:33
Alignment explanation
Indices: 918093--918157 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
918083 CAATACGAAT
*
918093 ATATATTATAAATTTTATATAAATAAATTATTA
1 ATATATTATAAATTTTATATAAATAAAATATTA
918126 ATATATTA-AAA-TTTATATAAATATAAAATATT
1 ATATATTATAAATTTTATAT-AA-ATAAAATATT
918158 TTAAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.24
32 5 0.17
33 17 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATATTATAAATTTTATATAAATAAAATATTA
Found at i:919943 original size:24 final size:26
Alignment explanation
Indices: 919915--919970 Score: 89
Period size: 24 Copynumber: 2.2 Consensus size: 26
919905 AAGAATAAAT
919915 TTTAAATTAAT-TATTAAAT-TATTA
1 TTTAAATTAATATATTAAATATATTA
*
919939 TTTAAATTAATATTTTAAATATATTA
1 TTTAAATTAATATATTAAATATATTA
919965 TTTAAA
1 TTTAAA
919971 AATAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 11 0.38
25 7 0.24
26 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTAAATTAATATATTAAATATATTA
Found at i:919952 original size:12 final size:12
Alignment explanation
Indices: 919915--919970 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
919905 AAGAATAAAT
919915 TTTAAATTAAT-
1 TTTAAATTAATA
*
919926 TATTAAATTATTA
1 T-TTAAATTAATA
919939 TTTAAATTAATA
1 TTTAAATTAATA
*
919951 TTTTAAATATATTA
1 -TTTAAAT-TAATA
919965 TTTAAA
1 TTTAAA
919971 AATAAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 1 0.03
12 19 0.50
13 14 0.37
14 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTAAATTAATA
Found at i:920110 original size:15 final size:16
Alignment explanation
Indices: 920079--920118 Score: 64
Period size: 15 Copynumber: 2.5 Consensus size: 16
920069 ACATGAGGTA
920079 AAAAATAATTAAAAATT
1 AAAAA-AATTAAAAATT
920096 AAAAAAATT-AAAATT
1 AAAAAAATTAAAAATT
920111 AAAAAAAT
1 AAAAAAAT
920119 AAAGCTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.61
16 4 0.17
17 5 0.22
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAAAATTAAAAATT
Found at i:923476 original size:22 final size:22
Alignment explanation
Indices: 923426--923479 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
923416 TATAATTATT
*
923426 TTTAAA-TAAA-AATAATTTTA
1 TTTAAATTAAATAATAATTTAA
*
923446 -TTATTATTAAATAATAATTTAA
1 TTTA-AATTAAATAATAATTTAA
923468 TTTAAATTAAAT
1 TTTAAATTAAAT
923480 GTCACCGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 1 0.04
21 4 0.15
22 16 0.59
23 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATTAAATAATAATTTAA
Found at i:927013 original size:38 final size:39
Alignment explanation
Indices: 926971--927049 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 39
926961 GTTTATATAG
*
926971 ATTTTTATTTAGATTTTAATTGGGTTT-GATTTAAGTTT
1 ATTTTTAGTTAGATTTTAATTGGGTTTGGATTTAAGTTT
*
927009 ATTTTTAGTTAGATTTTAATTGGGTTTGGGTTTAAGTTT
1 ATTTTTAGTTAGATTTTAATTGGGTTTGGATTTAAGTTT
927048 AT
1 AT
927050 ATAGATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 26 0.68
39 12 0.32
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (39 bp):
ATTTTTAGTTAGATTTTAATTGGGTTTGGATTTAAGTTT
Found at i:927061 original size:45 final size:44
Alignment explanation
Indices: 926927--927063 Score: 160
Period size: 45 Copynumber: 3.2 Consensus size: 44
926917 CTTTGTTTTT
* * * *
926927 TTTTTAATTAGGTTTTGATTGAGTTTAGGTTTAAGTTTATATAGA
1 TTTTTAGTTAGATTTTAATTGGGTTT-GGTTTAAGTTTATATAGA
* *
926972 TTTTTATTTAGATTTTAATTGGGTTTGATTTAAG--T-T-T--A
1 TTTTTAGTTAGATTTTAATTGGGTTTGGTTTAAGTTTATATAGA
927010 TTTTTAGTTAGATTTTAATTGGGTTTGGGTTTAAGTTTATATAGA
1 TTTTTAGTTAGATTTTAATTGGGTTT-GGTTTAAGTTTATATAGA
927055 TTTTTAGTT
1 TTTTTAGTT
927064 GGTATTAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
38 26 0.33
39 7 0.09
40 1 0.01
41 2 0.03
42 2 0.03
43 1 0.01
44 7 0.09
45 32 0.41
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.57
Consensus pattern (44 bp):
TTTTTAGTTAGATTTTAATTGGGTTTGGTTTAAGTTTATATAGA
Found at i:927119 original size:21 final size:20
Alignment explanation
Indices: 927083--927133 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
927073 TAAACTTAAC
* * *
927083 TTTTAAATTTAATTTATATT
1 TTTTAAATATAATTTAAATA
*
927103 TTATTAAATATATTTTAAATA
1 TT-TTAAATATAATTTAAATA
927124 TTTTAAATAT
1 TTTTAAATAT
927134 TAAATTCGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAATATAATTTAAATA
Found at i:931875 original size:21 final size:21
Alignment explanation
Indices: 931851--931891 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
931841 TATTTAAATT
931851 AATTTTAAATAAAAATTTTAA
1 AATTTTAAATAAAAATTTTAA
* *
931872 AATTTTAAATCATAATTTTA
1 AATTTTAAATAAAAATTTTA
931892 CTTAAACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTTTAAATAAAAATTTTAA
Found at i:933122 original size:6 final size:7
Alignment explanation
Indices: 933103--933129 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
933093 ATGAAAACAC
933103 ATAAAAA
1 ATAAAAA
933110 ATAAAAA
1 ATAAAAA
933117 ATAAAAA
1 ATAAAAA
933124 ATAAAA
1 ATAAAA
933130 TCAAATACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:934030 original size:20 final size:21
Alignment explanation
Indices: 933988--934040 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
933978 TTCAACAATT
933988 TGTATCGATACAATAAGGCAA
1 TGTATCGATACAATAAGGCAA
*
934009 TGTATCGATA-TATAAGTG-AA
1 TGTATCGATACAATAAG-GCAA
*
934029 TGGATCGATACA
1 TGTATCGATACA
934041 TGCCCGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (21 bp):
TGTATCGATACAATAAGGCAA
Found at i:937795 original size:21 final size:22
Alignment explanation
Indices: 937744--937799 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
937734 AAAACAATGG
* *
937744 TAGCT-GTGAAATTAGTTACTA
1 TAGCTAGTGAGATTAGATACTA
*
937765 TAGCTA-TGAGATTAGATACTG
1 TAGCTAGTGAGATTAGATACTA
937786 TAG-TAGTGAGATTA
1 TAGCTAGTGAGATTA
937800 AAATTAGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (22 bp):
TAGCTAGTGAGATTAGATACTA
Found at i:940079 original size:19 final size:19
Alignment explanation
Indices: 940055--940109 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
940045 TGAAAATGGT
940055 CTTTTTAGGTAATCAAATC
1 CTTTTTAGGTAATCAAATC
***
940074 CTTTTTTTTAGGTAATTGGATC
1 C---TTTTTAGGTAATCAAATC
940096 CTTTTTAGGTAATC
1 CTTTTTAGGTAATC
940110 CGTGTCACCA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 13 0.45
22 16 0.55
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.49
Consensus pattern (19 bp):
CTTTTTAGGTAATCAAATC
Found at i:940186 original size:27 final size:27
Alignment explanation
Indices: 940151--940234 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
940141 CATCTTTTCC
*
940151 TTTTAAGTCCATAACTCCATGGCACCT
1 TTTTAAGTCCACAACTCCATGGCACCT
*
940178 TTTTAAGTCCACAACTCCATGGCACCC
1 TTTTAAGTCCACAACTCCATGGCACCT
* * *
940205 CTTTAAGTTCACAACTCCGTGGCA-CT
1 TTTTAAGTCCACAACTCCATGGCACCT
940231 TTTT
1 TTTT
940235 CCCTTTCAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 4 0.08
27 46 0.92
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCATGGCACCT
Found at i:940228 original size:54 final size:55
Alignment explanation
Indices: 940108--940234 Score: 134
Period size: 58 Copynumber: 2.3 Consensus size: 55
940098 TTTTAGGTAA
* * * * *
940108 TCCGTGTCACCATTTTAAGTCCACAACTCGTGGCATCTTTTCCTTTTAAGTCCATAAC
1 TCCGTGGCACCTTTTTAAGTCCACAACTCATGGCATC---TCCCTTTAAGTCCACAAC
* *
940166 TCCATGGCACCTTTTTAAGTCCACAACTCCATGGCA-C-CCCTTTAAGTTCACAAC
1 TCCGTGGCACCTTTTTAAGTCCACAACT-CATGGCATCTCCCTTTAAGTCCACAAC
940220 TCCGTGGCA-CTTTTT
1 TCCGTGGCACCTTTTT
940235 CCCTTTCAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
53 6 0.10
54 22 0.37
58 26 0.43
59 6 0.10
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (55 bp):
TCCGTGGCACCTTTTTAAGTCCACAACTCATGGCATCTCCCTTTAAGTCCACAAC
Found at i:940274 original size:34 final size:33
Alignment explanation
Indices: 940124--940366 Score: 183
Period size: 34 Copynumber: 7.7 Consensus size: 33
940114 TCACCATTTT
* *
940124 AAGTCCACAACT-CGTGGCA-TCTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTC
* * *
940155 AAGTCCATAACTCCATGGCAC---CTT--TTT-
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTC
* *
940182 AAGTCCACAACTCCATGGCAC-----CCCTTT-
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTC
* *
940209 AAGTTCACAACTCCGTGGCACTTTTTCCCTTTC
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTC
* * *
940242 AAGTCTACAACTCCGTGGTACCTTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CTTTTTTCCTTTC
* *
940276 AAGTCCACAACTCCATGGCACCCTTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA--CTTTTTTCCTTTC
* *
940311 AAGTCCACAACTCCGTGGTACTTTTTTCTTTTCC
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTT-C
*
940345 AAG-CCTATAACTCCGTGGCACT
1 AAGTCC-ACAACTCCGTGGCACT
940367 CCTTTTTAAA
Statistics
Matches: 177, Mismatches: 21, Indels: 25
0.79 0.09 0.11
Matches are distributed among these distances:
27 42 0.24
28 3 0.02
30 2 0.01
31 11 0.06
32 12 0.07
33 30 0.17
34 45 0.25
35 32 0.18
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (33 bp):
AAGTCCACAACTCCGTGGCACTTTTTTCCTTTC
Found at i:940301 original size:35 final size:34
Alignment explanation
Indices: 940206--940365 Score: 184
Period size: 34 Copynumber: 4.7 Consensus size: 34
940196 ATGGCACCCC
* *
940206 TTTAAGTTCACAACTCCGTGGCA-CTTTTTCCCT
1 TTTAAGTCCACAACTCCGTGGCACCTTTTTTCCT
* * *
940239 TTCAAGTCTACAACTCCGTGGTACCTTTTTTCCT
1 TTTAAGTCCACAACTCCGTGGCACCTTTTTTCCT
*
940273 TTTAAGTCCACAACTCCATGGCACCCTTTTTTCCT
1 TTTAAGTCCACAACTCCGTGGCA-CCTTTTTTCCT
*
940308 TTTAAGTCCACAACTCCGTGGTA-CTTTTTT-CT
1 TTTAAGTCCACAACTCCGTGGCACCTTTTTTCCT
*
940340 TTTCCAAG-CCTATAACTCCGTGGCAC
1 TTT--AAGTCC-ACAACTCCGTGGCAC
940366 TCCTTTTTAA
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
32 5 0.05
33 28 0.26
34 43 0.40
35 32 0.30
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (34 bp):
TTTAAGTCCACAACTCCGTGGCACCTTTTTTCCT
Found at i:940322 original size:69 final size:67
Alignment explanation
Indices: 940206--940373 Score: 207
Period size: 69 Copynumber: 2.5 Consensus size: 67
940196 ATGGCACCCC
* *
940206 TTTAAGTTCACAACTCCGTGGCA--CTTTTTCCCTTTCAAGTCTACAACTCCGTGGTACCTTTTT
1 TTTAAGTCCACAACTCCGTGGCACCCTTTTTCCCTTTCAAGTCCACAACTCCGTGGTA-CTTTTT
940269 TCCT
65 T-CT
* * *
940273 TTTAAGTCCACAACTCCATGGCACCCTTTTTTCCTTTTAAGTCCACAACTCCGTGGTACTTTTTT
1 TTTAAGTCCACAACTCCGTGGCACCCTTTTTCCCTTTCAAGTCCACAACTCCGTGGTACTTTTTT
940338 CT
66 CT
*
940340 TTTCCAAG-CCTATAACTCCGTGGCACTCCTTTTT
1 TTT--AAGTCC-ACAACTCCGTGGCAC-CCTTTTT
940374 AAAGCCCACA
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
67 26 0.30
68 9 0.10
69 46 0.52
70 7 0.08
ACGTcount: A:0.18, C:0.30, G:0.11, T:0.40
Consensus pattern (67 bp):
TTTAAGTCCACAACTCCGTGGCACCCTTTTTCCCTTTCAAGTCCACAACTCCGTGGTACTTTTTT
CT
Found at i:940412 original size:31 final size:31
Alignment explanation
Indices: 940367--940465 Score: 112
Period size: 32 Copynumber: 3.2 Consensus size: 31
940357 CCGTGGCACT
* *
940367 CCTTTTTAAAGCCCACACAAGTCGGTGGCAGC
1 CCTTTCTAAAGCCCACACAAGTCGGTGGCA-A
*
940399 CCTTTC-AAAGCCCACACAAG-CTGGTAGCAA
1 CCTTTCTAAAGCCCACACAAGTC-GGTGGCAA
* *
940429 CCTTTCTTAAAGCCCACGCAAGTCGGTGGTAA
1 CCTTTC-TAAAGCCCACACAAGTCGGTGGCAA
940461 CCTTT
1 CCTTT
940466 TCAAATCCCT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
30 7 0.12
31 20 0.35
32 29 0.51
33 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.23
Consensus pattern (31 bp):
CCTTTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:940439 original size:63 final size:63
Alignment explanation
Indices: 940367--940491 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
940357 CCGTGGCACT
* *
940367 CCTTTTTAAAGCCCACACAAGTCGGTGGCAGCCCTTTCAAAGCCC-ACACAAGCTGGTAGCAA
1 CCTTTTTAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCTAAACAAGCTGGTAGCAA
* * * * *
940429 CCTTTCTTAAAGCCCACGCAAGTCGGTGGTAACCTTTTCAAATCCCTAAACAAGTTGGTAGCA
1 CCTTT-TTAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCTAAACAAGCTGGTAGCA
940492 TCTCCTTCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 5 0.09
63 35 0.65
64 14 0.26
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (63 bp):
CCTTTTTAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCTAAACAAGCTGGTAGCAA
Found at i:940505 original size:63 final size:63
Alignment explanation
Indices: 940367--940507 Score: 160
Period size: 63 Copynumber: 2.2 Consensus size: 63
940357 CCGTGGCACT
* * *
940367 CCTTTTTAAAGCCCACACAAGTCGGTGGCAGCCCTTTCAAAGCCCACACAAGCTGGTAGCAAC
1 CCTTCTTAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCAAACAAGCTGGTAGCAAC
* * * * * * *
940430 CTTTCTTAAAGCCCACGCAAGTCGGTGGTAACCTTTTCAAATCCCTAAACAAGTTGGTAGCATC
1 CCTTCTTAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCC-AAACAAGCTGGTAGCAAC
940494 TCCTTC-T-AAGCCCA
1 -CCTTCTTAAAGCCCA
940508 ATATCGTTGG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 45 0.69
64 16 0.25
65 4 0.06
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (63 bp):
CCTTCTTAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCAAACAAGCTGGTAGCAAC
Found at i:940620 original size:43 final size:43
Alignment explanation
Indices: 940573--940874 Score: 172
Period size: 52 Copynumber: 6.4 Consensus size: 43
940563 TCTAATGCCA
* *
940573 CTGGCCTTGAATTAGCACATTGGTACCTTTAAGTCTAATATCG
1 CTGGCCTTGAATCAGCACATTGGTACCTTTAAGTCCAATATCG
* *
940616 CTGGCCTTGAATCAGCATCTTGGCACCTTTGTCATCTTTAAGTCCAATATCG
1 CTGGCCTTGAATCAGCA------CA--TTGGT-ACCTTTAAGTCCAATATCG
* *
940668 CTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCG
1 CTGGCCTTGAATCAGCACATTGGTACCTTTAAGTCCAATATCG
* * * * *
940711 TTGGCCTTGAATCAGCATATTGGCGTCTTTATCATCTTTAAGTTCAATGTCA
1 CTGGCCTTGAATCAGCACATT-G-G----TA-C--CTTTAAGTCCAATATCG
* * * * *
940763 TTGACCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCG
1 CTGGCCTTGAATCAGC--A----CA--TTGGT-ACCTTTAAGTCCAATATCG
* * *
940815 CTGGCTTTGAATCAGTACATTGGCACCTTTAAGTCCAATATCG
1 CTGGCCTTGAATCAGCACATTGGTACCTTTAAGTCCAATATCG
* *
940858 CTGACCTTAAATCAGCA
1 CTGGCCTTGAATCAGCA
940875 TATTAGAATC
Statistics
Matches: 199, Mismatches: 33, Indels: 54
0.70 0.12 0.19
Matches are distributed among these distances:
43 82 0.41
44 7 0.04
45 1 0.01
46 4 0.02
49 3 0.02
50 2 0.01
51 4 0.02
52 89 0.45
54 2 0.01
55 1 0.01
58 2 0.01
60 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (43 bp):
CTGGCCTTGAATCAGCACATTGGTACCTTTAAGTCCAATATCG
Found at i:940677 original size:52 final size:52
Alignment explanation
Indices: 940599--940844 Score: 253
Period size: 52 Copynumber: 4.9 Consensus size: 52
940589 ACATTGGTAC
*
940599 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATCTTGGCACCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATCTTGGCACCTTTGTCAT
*
940651 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCA-CATTGGCA-------C--
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATC-TTGGCACCTTTGTCAT
* * ** *
940694 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGTCTTTATCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATCTTGGCACCTTTGTCAT
* * ** * *
940746 CTTTAAGTTCAATGTCATTGACCTTGAATCAGCATATTGGCACCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATCTTGGCACCTTTGTCAT
* * *
940798 CTTTAAGTCCAATGTCGCTGGCTTTGAATCAGTA-CATTGGCACCTTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATC-TTGGCACCTTT
940845 AAGTCCAATA
Statistics
Matches: 162, Mismatches: 20, Indels: 24
0.79 0.10 0.12
Matches are distributed among these distances:
43 37 0.23
45 1 0.01
50 1 0.01
51 1 0.01
52 122 0.75
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.36
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATCTTGGCACCTTTGTCAT
Found at i:940685 original size:95 final size:94
Alignment explanation
Indices: 940576--940792 Score: 299
Period size: 95 Copynumber: 2.3 Consensus size: 94
940566 AATGCCACTG
* * * *
940576 GCCTTGAATTAGCACATTGGTACCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATCTTGGCA
1 GCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* *
940641 CCTTTGTCATCTTTAAGTCCAATATCGCTA
66 CCTTTATCATCTTTAAGTCCAATATC-ATA
* *
940671 GCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCG
1 GCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* * * *
940736 TCTTTATCATCTTTAAGTTCAATGTCATT
66 CCTTTATCATCTTTAAGTCCAATATCATA
*
940765 GACCTTGAATCAGCATATTGGCACCTTT
1 G-CCTTGAATCAGCACATTGGCACCTTT
940793 GTCATCTTTA
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
94 2 0.02
95 106 0.98
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (94 bp):
GCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
CCTTTATCATCTTTAAGTCCAATATCATA
Found at i:940792 original size:147 final size:147
Alignment explanation
Indices: 940620--940900 Score: 454
Period size: 147 Copynumber: 1.9 Consensus size: 147
940610 ATATCGCTGG
*
940620 CCTTGAATCAGCATCTTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCA
1 CCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCA
* * * * ** *
940685 CATTGGCACCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGTCTTTATCATCTTT
66 CATTGGCACCTTTAAGTCCAATATCGCTGACCTTAAATCAGCATATTAGAATCCTTATCATCTTT
940750 AAGTTCAATGTCATTGA
131 AAGTTCAATGTCATTGA
* * * *
940767 CCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCTTTGAATCAGTA
1 CCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCA
940832 CATTGGCACCTTTAAGTCCAATATCGCTGACCTTAAATCAGCATATTAGAATCCTTATCATCTTT
66 CATTGGCACCTTTAAGTCCAATATCGCTGACCTTAAATCAGCATATTAGAATCCTTATCATCTTT
940897 AAGT
131 AAGT
940901 CTAGTGTTGC
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
147 122 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (147 bp):
CCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCA
CATTGGCACCTTTAAGTCCAATATCGCTGACCTTAAATCAGCATATTAGAATCCTTATCATCTTT
AAGTTCAATGTCATTGA
Found at i:940845 original size:95 final size:95
Alignment explanation
Indices: 940746--940921 Score: 228
Period size: 95 Copynumber: 1.9 Consensus size: 95
940736 TCTTTATCAT
* * * * * * *
940746 CTTTAAGTTCAATGTCATTGACCTTGAATCAGCATATTGGCA-CCTTTGTCATCTTTAAGTCCAA
1 CTTTAAGTCCAATATCACTGACCTTAAATCAGCATATTAGAATCC-TTATCATCTTTAAGTCCAA
*
940810 TGTCGCTGGCTTTGAATCAGTACATTGGCAC
65 TGTCGCAGGCTTTGAATCAGTACATTGGCAC
* * *
940841 CTTTAAGTCCAATATCGCTGACCTTAAATCAGCATATTAGAATCCTTATCATCTTTAAGTCTAGT
1 CTTTAAGTCCAATATCACTGACCTTAAATCAGCATATTAGAATCCTTATCATCTTTAAGTCCAAT
*
940906 GTTGCAGGCTTTGAAT
66 GTCGCAGGCTTTGAAT
940922 TTGCACACTG
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
95 66 0.97
96 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (95 bp):
CTTTAAGTCCAATATCACTGACCTTAAATCAGCATATTAGAATCCTTATCATCTTTAAGTCCAAT
GTCGCAGGCTTTGAATCAGTACATTGGCAC
Found at i:940920 original size:147 final size:147
Alignment explanation
Indices: 940599--940921 Score: 436
Period size: 147 Copynumber: 2.2 Consensus size: 147
940589 ACATTGGTAC
* * * *
940599 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATCTTGGCACCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCTAATGTTGCAGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
* * *
940664 ATCGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCAT
66 ATCGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGACCTTAAATCAGCAT
* ** *
940729 ATTGGCGTCTTTATCAT
131 ATTAGAATCCTTATCAT
*
940746 CTTTAAGT-TCAATG-T-CATTGACCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCC
1 CTTTAAGTCT-AATGTTGCA--GGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCC
* * * *
940808 AATGTCGCTGGCTTTGAATCAGTACATTGGCACCTTTAAGTCCAATATCGCTGACCTTAAATCAG
63 AATATCGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGACCTTAAATCAG
940873 CATATTAGAATCCTTATCAT
128 CATATTAGAATCCTTATCAT
* *
940893 CTTTAAGTCTAGTGTTGCAGGCTTTGAAT
1 CTTTAAGTCTAATGTTGCAGGCCTTGAAT
940922 TTGCACACTG
Statistics
Matches: 151, Mismatches: 19, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
145 1 0.01
146 1 0.01
147 145 0.96
148 2 0.01
149 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (147 bp):
CTTTAAGTCTAATGTTGCAGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
ATCGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGACCTTAAATCAGCAT
ATTAGAATCCTTATCAT
Found at i:947936 original size:17 final size:17
Alignment explanation
Indices: 947916--947982 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
947906 AATTATATAT
947916 AAAT-TAATAATATATTA
1 AAATATAATAATAT-TTA
*
947933 AAATATAA-AATATTTT
1 AAATATAATAATATTTA
* *
947949 AAATATAATAATAATAA
1 AAATATAATAATATTTA
*
947966 AAAAATAA-AA-ATTTA
1 AAATATAATAATATTTA
947981 AA
1 AA
947983 CTCGAGCTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
15 5 0.12
16 12 0.29
17 21 0.51
18 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAATAATATTTA
Found at i:947940 original size:34 final size:33
Alignment explanation
Indices: 947902--947982 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
947892 AAATACATAT
* *
947902 TATAAATTATATATAAAT-TAATAATATATTAAAA
1 TATAAAATAT-TATAAATATAATAATA-ATAAAAA
*
947936 TATAAAATATTTTAAATATAATAATAATAAAAA
1 TATAAAATATTATAAATATAATAATAATAAAAA
*
947969 AATAAAA-ATT-TAAA
1 TATAAAATATTATAAA
947983 CTCGAGCTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 4 0.10
32 3 0.07
33 18 0.43
34 17 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (33 bp):
TATAAAATATTATAAATATAATAATAATAAAAA
Found at i:947952 original size:16 final size:18
Alignment explanation
Indices: 947909--947961 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
947899 TATTATAAAT
*
947909 TATATATAAAT-TAATAA
1 TATATTTAAATATAATAA
*
947926 TATATTAAAATATAA-AA
1 TATATTTAAATATAATAA
947943 TAT-TTTAAATATAATAA
1 TATATTTAAATATAATAA
947960 TA
1 TA
947962 ATAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 10 0.32
17 18 0.58
18 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATATTTAAATATAATAA
Found at i:948230 original size:17 final size:17
Alignment explanation
Indices: 948208--948265 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
948198 ATTATAAATT
948208 ATATATAAAAATTATTA
1 ATATATAAAAATTATTA
*
948225 ATATATTAAAATTTATATA
1 ATATA-TAAAAATTAT-TA
*
948244 A-ATATAAAATATTTTTA
1 ATATATAAAA-ATTATTA
948261 ATATA
1 ATATA
948266 ATAATAACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 13 0.38
18 18 0.53
19 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATAAAAATTATTA
Found at i:948249 original size:20 final size:21
Alignment explanation
Indices: 948186--948249 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 21
948176 ATATAGTATA
*
948186 ATATAAATATGTATTATAAATTAT
1 ATATAAAAAT-TA-TATAAA-TAT
948210 ATATAAAAATTAT-T-AATAT
1 ATATAAAAATTATATAAATAT
*
948229 AT-TAAAATTTATATAAATAT
1 ATATAAAAATTATATAAATAT
948249 A
1 A
948250 AAATATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 9 0.25
19 6 0.17
20 8 0.22
21 1 0.03
22 1 0.03
23 2 0.06
24 9 0.25
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATAAAAATTATATAAATAT
Found at i:949912 original size:28 final size:28
Alignment explanation
Indices: 949872--949929 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
949862 ATCTTGTAAG
949872 TATGTCTTACATAAAACCAATGGTTTGC
1 TATGTCTTACATAAAACCAATGGTTTGC
*
949900 TATGTCTTACATAAAACCAATGTTTTGC
1 TATGTCTTACATAAAACCAATGGTTTGC
949928 TA
1 TA
949930 CTTCAATCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (28 bp):
TATGTCTTACATAAAACCAATGGTTTGC
Found at i:952353 original size:22 final size:24
Alignment explanation
Indices: 952321--952364 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
952311 ATATCTCAAT
*
952321 TGATAAGTTTTT-TTA-TAAAACA
1 TGATAACTTTTTATTATTAAAACA
952343 TGATAACTTTTTATTATTAAAA
1 TGATAACTTTTTATTATTAAAA
952365 ATTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 3 0.16
24 5 0.26
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (24 bp):
TGATAACTTTTTATTATTAAAACA
Found at i:953760 original size:22 final size:22
Alignment explanation
Indices: 953710--953763 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
953700 ATAATTATTT
*
953710 TTTAAA-TAAA-AATAATTTTA
1 TTTAAATTAAATAATAATTTAA
*
953730 -TTATTATTAAATAATAATTTAA
1 TTTA-AATTAAATAATAATTTAA
953752 TTTAAATTAAAT
1 TTTAAATTAAAT
953764 GCTCCGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 1 0.04
21 4 0.15
22 16 0.59
23 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATTAAATAATAATTTAA
Found at i:960768 original size:24 final size:22
Alignment explanation
Indices: 960712--960760 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
960702 TGGACATGTT
*
960712 AAAAATGCATAAAACATAATAA
1 AAAAATGCATGAAACATAATAA
960734 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
960756 AAAAA
1 AAAAA
960761 AATGCATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:961727 original size:20 final size:20
Alignment explanation
Indices: 961680--961754 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
961670 AAAAAGACAT
*
961680 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
961699 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
961720 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
961740 AATGTATCGATACAT
1 AATGTATCGATACAT
961755 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:961748 original size:40 final size:39
Alignment explanation
Indices: 961677--961754 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
961667 GGTAAAAAGA
* *
961677 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
961716 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
961755 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:962014 original size:18 final size:17
Alignment explanation
Indices: 961991--962024 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
961981 TTTGTTCTCC
961991 AAAAAAGCAAAAAAAAAA
1 AAAAAAG-AAAAAAAAAA
962009 AAAAAAGAAAAAAAAA
1 AAAAAAGAAAAAAAAA
962025 TTATTGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAAA
Found at i:962023 original size:9 final size:9
Alignment explanation
Indices: 961991--962023 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
961981 TTTGTTCTCC
961991 AAAAAAGCAA
1 AAAAAAG-AA
962001 AAAAAA-AA
1 AAAAAAGAA
962009 AAAAAAGAA
1 AAAAAAGAA
962018 AAAAAA
1 AAAAAA
962024 ATTATTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 8 0.36
10 6 0.27
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:962455 original size:99 final size:100
Alignment explanation
Indices: 962281--962482 Score: 318
Period size: 99 Copynumber: 2.0 Consensus size: 100
962271 ACGTACTTAA
* *
962281 TTTTTTGGTCATGGTTAGTAAGGTATAAATTTTTATGCTTAAAATTCCAATATGACTCCAGTAGT
1 TTTTTTGCTCATGGTTAGCAAGGTATAAATTTTTATGCTTAAAATTCCAATATGACTCCAGTAGT
* *
962346 TGCCTTTGACTTCTATTCCCAAGTTCTTTCTGATG
66 TGCCTTTGACTTCTACTCCCAAGTTCTTCCTGATG
*
962381 TTTTTTGCTCATGGTTAGCGAGGTATAAATTTTTATGCTT-AAATTCCACA-ATGACTCCAGTAG
1 TTTTTTGCTCATGGTTAGCAAGGTATAAATTTTTATGCTTAAAATTCCA-ATATGACTCCAGTAG
* *
962444 TTGCCTTTGACTTCTACTGCCAAGTTCTTCCTGGTG
65 TTGCCTTTGACTTCTACTCCCAAGTTCTTCCTGATG
962480 TTT
1 TTT
962483 ACTTCAATCT
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
99 56 0.60
100 38 0.40
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (100 bp):
TTTTTTGCTCATGGTTAGCAAGGTATAAATTTTTATGCTTAAAATTCCAATATGACTCCAGTAGT
TGCCTTTGACTTCTACTCCCAAGTTCTTCCTGATG
Found at i:962866 original size:42 final size:42
Alignment explanation
Indices: 962815--962903 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
962805 GTAGTAATAA
*
962815 TGCA-CCTTTTTAATCTTTATCAAAATTCAACTATACTATAC
1 TGCACCCTTTTTAATCTTTATCAAAATTCAACTATACTACAC
** * * *
962856 TGCACCCTTTTTTTTCTTTATCAAAATTGAGCTATCCTACAC
1 TGCACCCTTTTTAATCTTTATCAAAATTCAACTATACTACAC
962898 TGCACC
1 TGCACC
962904 ATTCAAATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 4 0.10
42 37 0.90
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (42 bp):
TGCACCCTTTTTAATCTTTATCAAAATTCAACTATACTACAC
Found at i:965246 original size:34 final size:34
Alignment explanation
Indices: 965186--965437 Score: 387
Period size: 34 Copynumber: 7.4 Consensus size: 34
965176 TTTTGTTAAG
* * *
965186 TGTATTAGGTGAAGCATGTTAAGTGTGTTAGGTGA
1 TGTATTTGGTG-AGAATGTTAGGTGTGTTAGGTGA
965221 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
965255 TGTATTTGGTGAGAATGTTAAGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
965289 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
965323 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
* * *
965357 TGTATTTGGTGAGAATATTAGATGTGTTAGGTAA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
* * *
965391 TGTATTTGGTGAAAATATTAGGTGTGTTAGGTAA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
* *
965425 TGTGTTAGGTGAG
1 TGTATTTGGTGAG
965438 TAAGATATTT
Statistics
Matches: 204, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
34 194 0.95
35 10 0.05
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.40
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:965274 original size:25 final size:25
Alignment explanation
Indices: 965245--965346 Score: 71
Period size: 25 Copynumber: 4.4 Consensus size: 25
965235 ATGTTAGGTG
965245 TGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGATGTATTTGGTGAGAA
* * *
965270 TGTTAAGTG-TG--TTAGGTGATGTA
1 TGTTAGGTGATGTATTTGGTGA-GAA
*
965293 T-TT-GGTGA-GAATGTTAGGT--G--
1 TGTTAGGTGATGTAT-TT-GGTGAGAA
965313 TGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGATGTATTTGGTGAGAA
965338 TGTTAGGTG
1 TGTTAGGTG
965347 TGTTAGGTGA
Statistics
Matches: 58, Mismatches: 6, Indels: 26
0.64 0.07 0.29
Matches are distributed among these distances:
20 1 0.02
21 9 0.16
22 17 0.29
23 8 0.14
24 3 0.05
25 20 0.34
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (25 bp):
TGTTAGGTGATGTATTTGGTGAGAA
Found at i:970204 original size:34 final size:34
Alignment explanation
Indices: 970166--970334 Score: 248
Period size: 34 Copynumber: 5.0 Consensus size: 34
970156 TAGGTGAAGC
*
970166 ATGTTAAGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
970200 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
*
970234 ATGTTAGGTGTGTTAGGTGATATATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
* * * *
970268 ATATTAGATGTGTTAGGTAATGTATTTGGTGAAA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
* * * *
970302 ATATTAGGTGTGTTAGGTAATGTGTTAGGTGAG
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAG
970335 TAAGATATTT
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 124 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (34 bp):
ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
Found at i:973974 original size:20 final size:21
Alignment explanation
Indices: 973951--973995 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
973941 AGATTAATTT
973951 AAATTATTATTTA-TT-AATAA
1 AAATTATT-TTTATTTAAATAA
973971 AAA-TATTTTTATTTAAATAA
1 AAATTATTTTTATTTAAATAA
973991 AAATT
1 AAATT
973996 TAAAACTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 11 0.50
21 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTATTTTTATTTAAATAA
Found at i:973996 original size:18 final size:20
Alignment explanation
Indices: 973951--973993 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
973941 AGATTAATTT
*
973951 AAATTATTATTTATTAATAAA
1 AAATTTTTATTTA-TAATAAA
973972 AATATTTTTATTTA-AATAAA
1 AA-ATTTTTATTTATAATAAA
973992 AA
1 AA
973994 TTTAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 2 0.10
22 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTTTTATTTATAATAAA
Found at i:976080 original size:21 final size:21
Alignment explanation
Indices: 976031--976080 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
976021 ATGATAGATG
*
976031 TGAAATTAGTTACTATAGCTA
1 TGAAATTAGATACTATAGCTA
*
976052 T-AAGATTAGATACTGTAG-TAA
1 TGAA-ATTAGATACTATAGCT-A
976073 TGAAATTA
1 TGAAATTA
976081 AAATTAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.12
21 19 0.79
22 2 0.08
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (21 bp):
TGAAATTAGATACTATAGCTA
Found at i:977227 original size:28 final size:27
Alignment explanation
Indices: 977195--977247 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
977185 TTTTGGTTAA
*
977195 TTCTTACTGATTTCATTTTCCTTGATAT
1 TTCTTACTGATTTCA-CTTCCTTGATAT
*
977223 TTCTTATTGATTTCACTTCCTTGAT
1 TTCTTACTGATTTCACTTCCTTGAT
977248 CTTTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.57
Consensus pattern (27 bp):
TTCTTACTGATTTCACTTCCTTGATAT
Found at i:977256 original size:27 final size:28
Alignment explanation
Indices: 977195--977258 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
977185 TTTTGGTTAA
* *
977195 TTCTTACTGATTTCATTTTCCTTGATAT
1 TTCTTATTGATTTCATCTTCCTTGATAT
*
977223 TTCTTATTGATTTCA-CTTCCTTGATCT
1 TTCTTATTGATTTCATCTTCCTTGATAT
*
977250 TTTTTATTG
1 TTCTTATTG
977259 GTCTTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.16, C:0.17, G:0.08, T:0.59
Consensus pattern (28 bp):
TTCTTATTGATTTCATCTTCCTTGATAT
Found at i:978536 original size:23 final size:23
Alignment explanation
Indices: 978505--978548 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
978495 AGATAATAGC
978505 GACATAAAGAA-CCGTGCATGTT
1 GACATAAAGAACCCGTGCATGTT
978527 GACATTAAAGAACCCGTGCATG
1 GACA-TAAAGAACCCGTGCATG
978549 GAGATATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 9 0.45
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (23 bp):
GACATAAAGAACCCGTGCATGTT
Found at i:982658 original size:28 final size:28
Alignment explanation
Indices: 982626--982689 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
982616 AAAAAAATTA
*
982626 AAATTTAAA-AATAATAATTTTAAATTTT
1 AAATTTAAATAA-AAAAATTTTAAATTTT
982654 AAA-TTACAATAAAAAAATTTTAAATTTT
1 AAATTTA-AATAAAAAAATTTTAAATTTT
*
982682 AAGTTTAA
1 AAATTTAA
982690 GTTTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 3 0.10
28 23 0.74
29 5 0.16
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
AAATTTAAATAAAAAAATTTTAAATTTT
Found at i:983137 original size:18 final size:17
Alignment explanation
Indices: 983095--983163 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 17
983085 AAATATCTAT
*
983095 TATAAATTTTATATAAA
1 TATAAAATTTATATAAA
983112 T-T---ATTTAT-TAATA
1 TATAAAATTTATATAA-A
983125 TATTAAAATTTATATAAA
1 TA-TAAAATTTATATAAA
983143 TATAAAATATT-T-TAAA
1 TATAAAAT-TTATATAAA
983159 TATAA
1 TATAA
983164 TAATAATACA
Statistics
Matches: 43, Mismatches: 1, Indels: 17
0.70 0.02 0.28
Matches are distributed among these distances:
12 3 0.07
13 7 0.16
15 1 0.02
16 10 0.23
17 8 0.19
18 11 0.26
19 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATAAAATTTATATAAA
Found at i:983156 original size:20 final size:19
Alignment explanation
Indices: 983104--983154 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
983094 TTATAAATTT
*
983104 TATATAAATTATTTATTAA
1 TATATAAAATATTTATTAA
*
983123 TATATTAAA-ATTTATATAA
1 TATATAAAATATTTAT-TAA
983142 -ATATAAAATATTT
1 TATATAAAATATTT
983155 TAAATATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATAAAATATTTATTAA
Found at i:987298 original size:17 final size:18
Alignment explanation
Indices: 987257--987290 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
987247 TACTTTTATA
987257 AAGTA-AATTTATTTTTG
1 AAGTATAATTTATTTTTG
987274 AAGTATAATTTATTTTT
1 AAGTATAATTTATTTTT
987291 ATTTATAAAA
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:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (18 bp):
AAGTATAATTTATTTTTG
Found at i:987322 original size:18 final size:17
Alignment explanation
Indices: 987262--987332 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
987252 TTATAAAGTA
*
987262 AATTTATTTTTGAAGTAT
1 AATTTATTTTT-AAATAT
**
987280 AATTTATTTTTATTTAT
1 AATTTATTTTTAAATAT
**
987297 AAAAATATTTTTAAATAT
1 -AATTTATTTTTAAATAT
987315 AATTATATGTATTTAAAT
1 AATT-TAT-T-TTTAAAT
987333 TTTATAAGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
17 6 0.15
18 27 0.66
19 1 0.02
20 7 0.17
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
AATTTATTTTTAAATAT
Found at i:987453 original size:74 final size:73
Alignment explanation
Indices: 987328--987512 Score: 175
Period size: 73 Copynumber: 2.6 Consensus size: 73
987318 TATATGTATT
* * * * *
987328 TAAATT-TTATAAGATATGA--T-TTTTTATTTATATATATTTTAATTTAATTTTTTGTTTGATT
1 TAAATTATTTTAAGATATGATTTATTTTTATTTGTA-AAATTTTAATTTAATTTTTAGGTTGATT
* *
987389 ATATAAGTTT
65 ATAGAAG-TA
* * * *
987399 TAAAATT-TTTTAAGATGTGGTTTATTTTTATTTGTAGAATTTTAAATTT-GTTTTTAGGTTGAT
1 T-AAATTATTTTAAGATATGATTTATTTTTATTTGTAAAATTTT-AATTTAATTTTTAGGTTGAT
*
987462 TATAGGAGTA
64 TATAGAAGTA
*
987472 TAAATTATTTTAAGGTATGATTTATTTTTATTTGTAAAATT
1 TAAATTATTTTAAGATATGATTTATTTTTATTTGTAAAATT
987513 AGTTTGATTT
Statistics
Matches: 92, Mismatches: 16, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
71 1 0.01
72 20 0.22
73 32 0.35
74 23 0.25
75 16 0.17
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (73 bp):
TAAATTATTTTAAGATATGATTTATTTTTATTTGTAAAATTTTAATTTAATTTTTAGGTTGATTA
TAGAAGTA
Found at i:987695 original size:34 final size:35
Alignment explanation
Indices: 987657--987760 Score: 108
Period size: 34 Copynumber: 3.1 Consensus size: 35
987647 ATACGAGTTT
*
987657 AAATTTTTAAA-ATATAATTTATTTTTATTTGTAA
1 AAATTTTTAAAGATATAATTTATTTTTATTTATAA
** * * *
987691 AAA--TTTAAATTTATATTTTAGTTTGA-TTATAA
1 AAATTTTTAAAGATATAATTTATTTTTATTTATAA
* *
987723 GAGTTTTTAAAGATATAATTTATTTTTATTTATAA
1 AAATTTTTAAAGATATAATTTATTTTTATTTATAA
987758 AAA
1 AAA
987761 ATTAAATTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
32 12 0.23
33 12 0.23
34 21 0.40
35 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (35 bp):
AAATTTTTAAAGATATAATTTATTTTTATTTATAA
Found at i:987728 original size:72 final size:72
Alignment explanation
Indices: 987644--987835 Score: 231
Period size: 67 Copynumber: 2.8 Consensus size: 72
987634 TTTTTTTATA
*
987644 ATTATACGAGTTTAAATTTTTAAAATATAATTTATTTTTATTTGTAAAAATTTAAATTTATATTT
1 ATTATAAGAGTTTAAATTTTTAAAATATAATTTATTTTTATTTGTAAAAATTTAAATTTATATTT
*
987709 TAGTTTG
66 TAATTTG
* *
987716 ATTATAAGAG------TTTTTAAAGATATAATTTATTTTTATTTATAAAAAATTAAATTTATATT
1 ATTATAAGAGTTTAAATTTTTAAA-ATATAATTTATTTTTATTTGTAAAAATTTAAATTTATATT
987775 TTAATTTG
65 TTAATTTG
* * * *
987783 GTTATAAAAATTTAAAATTTTAAAATATTAA-TTA-TTTT-TTTGTAAAAATTTAA
1 ATTATAAGAGTTTAAATTTTTAAAATA-TAATTTATTTTTATTTGTAAAAATTTAA
987836 TTTTTTTAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
66 8 0.08
67 52 0.51
70 13 0.13
71 4 0.04
72 15 0.15
73 10 0.10
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.52
Consensus pattern (72 bp):
ATTATAAGAGTTTAAATTTTTAAAATATAATTTATTTTTATTTGTAAAAATTTAAATTTATATTT
TAATTTG
Found at i:988644 original size:14 final size:14
Alignment explanation
Indices: 988625--988674 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
988615 TTAAAAAAAA
988625 TAAAAAATATATTT
1 TAAAAAATATATTT
**
988639 TAAAAAATAT-TAA
1 TAAAAAATATATTT
*
988652 TAAAAAATATAATT
1 TAAAAAATATATTT
988666 TAAAAAATA
1 TAAAAAATA
988675 AAAAATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 11 0.37
14 19 0.63
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAAAATATATTT
Found at i:988648 original size:12 final size:12
Alignment explanation
Indices: 988627--988674 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
988617 AAAAAAAATA
988627 AAAAATATATTTT
1 AAAAA-ATATTTT
*
988640 AAAAAATATTAAT
1 AAAAAATATT-TT
988653 AAAAAATATAATTT
1 AAAAAATAT--TTT
988667 AAAAAATA
1 AAAAAATA
988675 AAAAATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 5 0.17
13 15 0.50
14 9 0.30
15 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAAATATTTT
Found at i:988655 original size:27 final size:27
Alignment explanation
Indices: 988623--988674 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
988613 TTTTAAAAAA
*
988623 AATAAAAAATATATTTTAAAAAATATT
1 AATAAAAAATATAATTTAAAAAATATT
988650 AATAAAAAATATAATTTAAAAAATA
1 AATAAAAAATATAATTTAAAAAATA
988675 AAAAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AATAAAAAATATAATTTAAAAAATATT
Found at i:996440 original size:100 final size:100
Alignment explanation
Indices: 996316--996518 Score: 316
Period size: 100 Copynumber: 2.0 Consensus size: 100
996306 TGTACTTAAT
*
996316 TTTTTTGATCATGGCTAGTAAGGTATAAATTTTTATGCTTAAAATTCCACAATGACTCCAGTAGC
1 TTTTTTGATCATGGCTAGTAAGGTATAAATTCTTATGCTTAAAATTCCACAATGACTCCAGTAGC
* *
996381 TGCCTTCGACTTCTATTAGCAAGTTCTCCCGGGTG
66 TGCCTTCGACTTCTATGACCAAGTTCTCCCGGGTG
* * * *
996416 TTTTTTGGTCATGGTTGGTAAGGTATAAATTCTTATGCTTAAAATTCCACAATGACTCCAGTAGT
1 TTTTTTGATCATGGCTAGTAAGGTATAAATTCTTATGCTTAAAATTCCACAATGACTCCAGTAGC
* * *
996481 TGCCTTTGACTTCTATGACCAAGTTCTTCCTGGTG
66 TGCCTTCGACTTCTATGACCAAGTTCTCCCGGGTG
996516 TTT
1 TTT
996519 ACTTCAATCT
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (100 bp):
TTTTTTGATCATGGCTAGTAAGGTATAAATTCTTATGCTTAAAATTCCACAATGACTCCAGTAGC
TGCCTTCGACTTCTATGACCAAGTTCTCCCGGGTG
Found at i:997229 original size:68 final size:68
Alignment explanation
Indices: 997120--997259 Score: 262
Period size: 68 Copynumber: 2.1 Consensus size: 68
997110 GCTAAGCAGA
*
997120 TACCAAAAGGCAGAATCGTGGCTTATTTAATCTAAATGTCTGGGAGTACGAATAAGGGAATAATT
1 TACCAAAAGGCAGAATCATGGCTTATTTAATCTAAATGTCTGGGAGTACGAATAAGGGAATAATT
997185 AGC
66 AGC
*
997188 TACCAAAAGGCAGAATCATGGCTTATTTAATCTAAATGTCTGGGAGTATGAATAAGGGAATAATT
1 TACCAAAAGGCAGAATCATGGCTTATTTAATCTAAATGTCTGGGAGTACGAATAAGGGAATAATT
997253 AGC
66 AGC
997256 TACC
1 TACC
997260 TGATTCGTCT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (68 bp):
TACCAAAAGGCAGAATCATGGCTTATTTAATCTAAATGTCTGGGAGTACGAATAAGGGAATAATT
AGC
Found at i:998899 original size:16 final size:16
Alignment explanation
Indices: 998864--998916 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
998854 AGTTGAAAGT
998864 AATTTAATAAAAAGTTTA
1 AATTTAA-AAAAA-TTTA
*
998882 AATTTAAAATAATTTA
1 AATTTAAAAAAATTTA
*
998898 AATTTAAAAAAAATTA
1 AATTTAAAAAAATTTA
998914 AAT
1 AAT
998917 ATAAGGTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 21 0.66
17 4 0.12
18 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTTAAAAAAATTTA
Found at i:998982 original size:16 final size:18
Alignment explanation
Indices: 998958--998998 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
998948 ATTTAAATTT
*
998958 AATATTAAAA-ATAAA-A
1 AATAATAAAATATAAATA
998974 AATAATAAAATTATAAATA
1 AATAATAAAA-TATAAATA
998993 AATAAT
1 AATAAT
998999 TTTTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
18 5 0.24
19 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAATAAAATATAAATA
Found at i:999006 original size:17 final size:17
Alignment explanation
Indices: 998984--999018 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
998974 AATAATAAAA
998984 TTAT-AAATAAATAATTT
1 TTATAAAATAAA-AATTT
999001 TTATAAAATAAAAATTT
1 TTATAAAATAAAAATTT
999018 T
1 T
999019 AATTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTATAAAATAAAAATTT
Found at i:999137 original size:21 final size:22
Alignment explanation
Indices: 999111--999151 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
999101 ATAATTTATA
999111 AAAAAT-TATATC-ATAAAATTT
1 AAAAATAT-TATCAATAAAATTT
999132 AAAAATATTATCAATAAAAT
1 AAAAATATTATCAATAAAAT
999152 ATATTATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAATATTATCAATAAAATTT
Found at i:999702 original size:9 final size:10
Alignment explanation
Indices: 999664--999707 Score: 54
Period size: 9 Copynumber: 4.2 Consensus size: 10
999654 ATTAAATAAG
999664 TTTTTAAATA
1 TTTTTAAATA
999674 TTTTATAAAATA
1 TTTT-T-AAATA
999686 TATTTTAAAT-
1 T-TTTTAAATA
999696 TTTTTAAATA
1 TTTTTAAATA
999706 TT
1 TT
999708 AATTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.27
10 7 0.23
11 5 0.17
12 7 0.23
13 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:999713 original size:21 final size:23
Alignment explanation
Indices: 999666--999714 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
999656 TAAATAAGTT
*
999666 TTTAAATATTTTATAAAATATAT
1 TTTAAATATTTTATAAAATATAA
999689 TTTAAAT-TTTT-T-AAATATTAA
1 TTTAAATATTTTATAAAATA-TAA
999710 TTTAA
1 TTTAA
999715 TTTATTCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 4 0.17
23 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAAATATTTTATAAAATATAA
Found at i:999982 original size:27 final size:30
Alignment explanation
Indices: 999928--999987 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 30
999918 ATTAAATATA
999928 TTAAAAATATAATAATATAATAAAAATTTAT
1 TTAAAAATATAATAATAT-ATAAAAATTTAT
*
999959 TTAAAAAT-TAATAAT-T-TAATAATTTAT
1 TTAAAAATATAATAATATATAAAAATTTAT
999986 TT
1 TT
999988 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 12 0.43
29 1 0.04
30 7 0.25
31 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TTAAAAATATAATAATATATAAAAATTTAT
Found at i:1000603 original size:24 final size:25
Alignment explanation
Indices: 1000574--1000636 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
1000564 TCGATGATAT
* *
1000574 TAAATATGTTTA-TCAAATATAATA
1 TAAATATATTTATTAAAATATAATA
*
1000598 TAAATAAATTTATTAAAATATAATA
1 TAAATATATTTATTAAAATATAATA
1000623 TAATATATAATTTA
1 TAA-ATAT-ATTTA
1000637 AATTTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 10 0.31
25 14 0.44
26 3 0.09
27 5 0.16
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAATATATTTATTAAAATATAATA
Found at i:1000683 original size:33 final size:33
Alignment explanation
Indices: 1000589--1000685 Score: 100
Period size: 32 Copynumber: 3.1 Consensus size: 33
1000579 ATGTTTATCA
1000589 AATATAATATA-AA-T-AAATTTAT-TAAAATAT
1 AATATAATATATAATTAAAATTTATAT-AAATAT
*
1000619 AATATAATATATAATTTAAATTTATAT-AATAT
1 AATATAATATATAATTAAAATTTATATAAATAT
*
1000651 GAATGATTA-ATAT-ATTAAAATTTATATAAATAT
1 -AAT-ATAATATATAATTAAAATTTATATAAATAT
1000684 AA
1 AA
1000686 AATATTTTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
30 11 0.19
31 2 0.03
32 21 0.36
33 20 0.34
34 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (33 bp):
AATATAATATATAATTAAAATTTATATAAATAT
Found at i:1000721 original size:17 final size:16
Alignment explanation
Indices: 1000678--1000741 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 16
1000668 AAATTTATAT
1000678 AAATATAAAATATTTTAAA
1 AAATATAAAATA---TAAA
1000697 AGAATATAATAATATAAA
1 A-AATATAA-AATATAAA
1000715 AAATAT-AAATATAATA
1 AAATATAAAATATAA-A
1000731 AACATATAAAA
1 AA-ATATAAAA
1000742 ATTAACACTC
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.17
16 4 0.10
17 9 0.22
18 8 0.20
19 1 0.03
20 7 0.17
21 4 0.10
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
AAATATAAAATATAAA
Found at i:1000725 original size:18 final size:18
Alignment explanation
Indices: 1000678--1000725 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1000668 AAATTTATAT
* *
1000678 AAATATAAAATATTTTAAA
1 AAATAT-AAATAATATAAA
1000697 AGAATAT-AATAATATAAA
1 A-AATATAAATAATATAAA
1000715 AAATATAAATA
1 AAATATAAATA
1000726 TAATAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.20
18 14 0.56
19 1 0.04
20 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATATAAATAATATAAA
Found at i:1000731 original size:18 final size:18
Alignment explanation
Indices: 1000678--1000732 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
1000668 AAATTTATAT
**
1000678 AAATATAAAATATTTTAAA
1 AAATAT-AAATATAATAAA
1000697 AGAATAT-AATA-ATATAAA
1 A-AATATAAATATA-ATAAA
1000715 AAATATAAATATAATAAA
1 AAATATAAATATAATAAA
1000733 CATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
17 5 0.17
18 18 0.60
19 2 0.07
20 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATATAAATATAATAAA
Found at i:1007361 original size:30 final size:30
Alignment explanation
Indices: 1007327--1007392 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1007317 GTTGAACAAA
*
1007327 TAGTATGAGTTTTTATTTTTCTTAAAATAT
1 TAGTATGAGTTTTCATTTTTCTTAAAATAT
1007357 TAGTATGAGTTTTCATTTTTCTTAAAATAT
1 TAGTATGAGTTTTCATTTTTCTTAAAATAT
1007387 TAGTAT
1 TAGTAT
1007393 TCGATAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.55
Consensus pattern (30 bp):
TAGTATGAGTTTTCATTTTTCTTAAAATAT
Found at i:1007765 original size:21 final size:21
Alignment explanation
Indices: 1007741--1007786 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1007731 TAGCTGTAAA
* *
1007741 ATTAGTTACTATAACTGTGAG
1 ATTAGATACTATAACAGTGAG
* *
1007762 ATTAGATACTGTAGCAGTGAG
1 ATTAGATACTATAACAGTGAG
1007783 ATTA
1 ATTA
1007787 AAATTAGTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (21 bp):
ATTAGATACTATAACAGTGAG
Found at i:1008377 original size:66 final size:66
Alignment explanation
Indices: 1008261--1008388 Score: 152
Period size: 66 Copynumber: 1.9 Consensus size: 66
1008251 TTATCCTTAT
* * *
1008261 TGATTACTATTAGGACTGTGATTAAGATTGCCCTTTTTTAGTCATAACTCTACTA-ATTTTAGTT
1 TGATTACTATTAAGACTGTGATTAAGATTGCCCTTTTTTAATCAGAACTCTA-TAGATTTTAGTT
1008325 AA
65 AA
* * * * *
1008327 TGATTACTGTTAAGACTGTGATTAGGATTG-TCTTTGTTTAATTAGGACTCTATAGATTTTAG
1 TGATTACTATTAAGACTGTGATTAAGATTGCCCTTT-TTTAATCAGAACTCTATAGATTTTAG
1008389 GCCTATACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
65 6 0.12
66 46 0.88
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (66 bp):
TGATTACTATTAAGACTGTGATTAAGATTGCCCTTTTTTAATCAGAACTCTATAGATTTTAGTTA
A
Found at i:1008795 original size:13 final size:13
Alignment explanation
Indices: 1008777--1008801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1008767 ATCACCTATA
1008777 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
1008790 AAAAAAAGAAAA
1 AAAAAAAGAAAA
1008802 AAAGTGTTTT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:1008934 original size:28 final size:26
Alignment explanation
Indices: 1008872--1008938 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 26
1008862 GTTCCCTCAT
*
1008872 TGTTGATTTCCCTTCTTTTGATATTTC
1 TGTTGATTT-CATTCTTTTGATATTTC
*
1008899 TCTCTGATTTCATTCTCTTTGATATTTC
1 TGT-TGATTTCATTCT-TTTGATATTTC
1008927 TAGTTGATTTCA
1 T-GTTGATTTCA
1008939 CTTCCTTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 7 0.21
28 26 0.76
29 1 0.03
ACGTcount: A:0.15, C:0.18, G:0.10, T:0.57
Consensus pattern (26 bp):
TGTTGATTTCATTCTTTTGATATTTC
Found at i:1009378 original size:6 final size:6
Alignment explanation
Indices: 1009369--1009399 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1009359 GAGGAAGAAG
*
1009369 ATGATT ATGATT ATGATT GTGATT ATGATT A
1 ATGATT ATGATT ATGATT ATGATT ATGATT A
1009400 GAGTAGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (6 bp):
ATGATT
Found at i:1010794 original size:18 final size:19
Alignment explanation
Indices: 1010771--1010813 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1010761 AGGATAGCTA
1010771 AAAAAAGTAAGATG-A-AAG
1 AAAAAAGTAAG-TGCACAAG
*
1010789 AAAAAATTAAGTGCACAAG
1 AAAAAAGTAAGTGCACAAG
1010808 AAAAAA
1 AAAAAA
1010814 AGAGTGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 11 0.50
19 9 0.41
ACGTcount: A:0.67, C:0.05, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAAAAGTAAGTGCACAAG
Found at i:1011853 original size:13 final size:13
Alignment explanation
Indices: 1011835--1011859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1011825 ATTTTGCTTA
1011835 GTATCGATACATT
1 GTATCGATACATT
1011848 GTATCGATACAT
1 GTATCGATACAT
1011860 AAACTGGCAG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1013818 original size:13 final size:13
Alignment explanation
Indices: 1013800--1013829 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1013790 GATACATGGC
1013800 ACATTGTATCGAT
1 ACATTGTATCGAT
1013813 ACATTGTATCGAT
1 ACATTGTATCGAT
1013826 ACAT
1 ACAT
1013830 AATGAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:1016031 original size:17 final size:18
Alignment explanation
Indices: 1016011--1016044 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1016001 ATATTCAATT
1016011 AATTATTAT-ATTTTATG
1 AATTATTATAATTTTATG
*
1016028 AATTTTTATAATTTTAT
1 AATTATTATAATTTTAT
1016045 TTAATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
AATTATTATAATTTTATG
Found at i:1016140 original size:25 final size:24
Alignment explanation
Indices: 1016112--1016167 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
1016102 ATATTAAAAA
*
1016112 TTATTATATATTTAATATAATTTAT
1 TTATTATATAATT-ATATAATTTAT
*
1016137 TTATTTATATAATTATATATTTTAT
1 TTA-TTATATAATTATATAATTTAT
1016162 TT-TTAT
1 TTATTAT
1016168 GTTTGTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 4 0.14
25 15 0.54
26 9 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATTATATAATTATATAATTTAT
Found at i:1016144 original size:8 final size:8
Alignment explanation
Indices: 1016115--1016167 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
1016105 TTAAAAATTA
1016115 TTATATAT
1 TTATATAT
1016123 TTAATATAAT
1 TT-ATAT-AT
*
1016133 TTATTTAT
1 TTATATAT
*
1016141 TTATATAA
1 TTATATAT
1016149 TTATATAT
1 TTATATAT
*
1016157 TT-TATTT
1 TTATATAT
1016164 TTAT
1 TTAT
1016168 GTTTGTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
7 6 0.16
8 20 0.54
9 7 0.19
10 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATATAT
Found at i:1016160 original size:17 final size:17
Alignment explanation
Indices: 1016114--1016161 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1016104 ATTAAAAATT
*
1016114 ATTATATATTTAATATA
1 ATTATATATTTTATATA
*
1016131 ATT-TATTTATTTATATA
1 ATTATATAT-TTTATATA
1016148 ATTATATATTTTAT
1 ATTATATATTTTAT
1016162 TTTTATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 18 0.69
18 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATATATTTTATATA
Found at i:1017602 original size:78 final size:78
Alignment explanation
Indices: 1017429--1017614 Score: 214
Period size: 79 Copynumber: 2.4 Consensus size: 78
1017419 ATGCATCAAT
* * * * *
1017429 ATGAAAGTTCCCCCATGACTCTAAAGACTCGGTATTAATGTAATATCACCCAAGTAAACCCTAAT
1 ATGAAAGTTCTCACATGACTCTAAAGACTCCGTATGAATGTAATATCACCCAAG-AAACCCTAAC
* *
1017494 GGACATGTATCAGT
65 GGACATATATCAGC
* *
1017508 ATGAAAGTTCTCACATGACTCTAAAGACTCCGTATGAATGTAATATCACTTCACG-AACCCTAAC
1 ATGAAAGTTCTCACATGACTCTAAAGACTCCGTATGAATGTAATATCAC-CCAAGAAACCCTAAC
*
1017572 GGACATATAT-TGAC
65 GGACATATATCAG-C
* * *
1017586 ATGAAAGTTTTCACATGACCCTAGAGACT
1 ATGAAAGTTCTCACATGACTCTAAAGACT
1017615 TGATATTAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
77 1 0.01
78 43 0.47
79 45 0.49
80 3 0.03
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (78 bp):
ATGAAAGTTCTCACATGACTCTAAAGACTCCGTATGAATGTAATATCACCCAAGAAACCCTAACG
GACATATATCAGC
Found at i:1017626 original size:78 final size:77
Alignment explanation
Indices: 1017429--1017635 Score: 220
Period size: 78 Copynumber: 2.6 Consensus size: 77
1017419 ATGCATCAAT
* * *
1017429 ATGAAAGTTCCCCCATGACTCTAAAGACTCGGTATTAATGTAATATCACCCAAGTAAACCCTAAT
1 ATGAAAGTTCTCACATGACTCTAAAGACTC-GTATTAATGTAATATCACCCAAG-AAACCCTAAC
* *
1017494 GGACATGTATCAGT
64 GGACATATATCAGC
* * *
1017508 ATGAAAGTTCTCACATGACTCTAAAGACTCCGTATGAATGTAATATCACTTCACG-AACCCTAAC
1 ATGAAAGTTCTCACATGACTCTAAAGACT-CGTATTAATGTAATATCAC-CCAAGAAACCCTAAC
*
1017572 GGACATATAT-TGAC
64 GGACATATATCAG-C
* * * * *
1017586 ATGAAAGTTTTCACATGACCCTAGAGACTTGATATTAATGTCATATCACC
1 ATGAAAGTTCTCACATGACTCTAAAGACTCG-TATTAATGTAATATCACC
1017636 TAATGAACTT
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
77 2 0.02
78 58 0.54
79 44 0.41
80 4 0.04
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (77 bp):
ATGAAAGTTCTCACATGACTCTAAAGACTCGTATTAATGTAATATCACCCAAGAAACCCTAACGG
ACATATATCAGC
Found at i:1017965 original size:59 final size:58
Alignment explanation
Indices: 1017892--1018212 Score: 308
Period size: 59 Copynumber: 5.4 Consensus size: 58
1017882 ACTATATGGT
* * ** *
1017892 CCTAAAATGTATGAAAAATGCTAAAGTGACCTTAGATTATGTAAAATAACCTAAATGGC
1 CCTAAAATGCATGAAAATTGCTAAA-TGACCTTAGATTACATAAAATAACCTAAATGAC
* * * *
1017951 CCTAAAATGCATGAATATTACTAAATAGTCCTTAAATTACATAAAATAACCTAAATGAC
1 CCTAAAATGCATGAAAATTGCTAAAT-GACCTTAGATTACATAAAATAACCTAAATGAC
* * * * *
1018010 CCTAAAATGTATGACAATTACTAAAT-AGCCTCTAGATCACATAAAATAACCTAAAGTTAC
1 CCTAAAATGCATGAAAATTGCTAAATGA-CCT-TAGATTACATAAAATAACCTAAA-TGAC
* * * * * * *
1018070 CTTAAAATGCATTATAATTGCAAAATAGTCCCTAGATTACATAAAATAACCTAAGTGAC
1 CCTAAAATGCATGAAAATTGCTAAAT-GACCTTAGATTACATAAAATAACCTAAATGAC
* * *
1018129 CCTAAAATGCATGAAAATTG-TCAAAT-AGTCTCTAGATTACATAAAATAACCT-AATTAG
1 CCTAAAATGCATGAAAATTGCT-AAATGA-CCT-TAGATTACATAAAATAACCTAAATGAC
*
1018187 CCTTAAATGCATGAAAATTGCTAAAT
1 CCTAAAATGCATGAAAATTGCTAAAT
1018213 TGCCCTTAAC
Statistics
Matches: 214, Mismatches: 38, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
58 31 0.14
59 137 0.64
60 44 0.21
61 2 0.01
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (58 bp):
CCTAAAATGCATGAAAATTGCTAAATGACCTTAGATTACATAAAATAACCTAAATGAC
Found at i:1017975 original size:29 final size:28
Alignment explanation
Indices: 1017942--1018035 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
1017932 GTAAAATAAC
*
1017942 CTAAATGGCCCTAAAATGCATGAATATTA
1 CTAAATGACCCTAAAATGCATGAA-ATTA
* * * * * *
1017971 CTAAATAGTCCTTAAATTACATAAAATAA
1 CTAAAT-GACCCTAAAATGCATGAAATTA
*
1018000 CCTAAATGACCCTAAAATGTATGACAATTA
1 -CTAAATGACCCTAAAATGCATGA-AATTA
1018030 CTAAAT
1 CTAAAT
1018036 AGCCTCTAGA
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
29 26 0.53
30 23 0.47
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (28 bp):
CTAAATGACCCTAAAATGCATGAAATTA
Found at i:1018123 original size:119 final size:117
Alignment explanation
Indices: 1017933--1018212 Score: 359
Period size: 119 Copynumber: 2.4 Consensus size: 117
1017923 TTAGATTATG
** * * *
1017933 TAAAATAACCTAAATGGCCCTAAAATGCATGAATATTACTAAATAGTCCTTAAATTACATAAAAT
1 TAAAATAACCTAAATTACCTTAAAATGCATGAA-ATTGCTAAATAGTCCCTAAATTACATAAAAT
* *
1017998 AACCTAAATGACCCTAAAATGTATGACAATTACT-AAATAGCCTCTAGATCACA
65 AACCTAAATGACCCTAAAATGCATGAAAATT-CTCAAATAGCCTCTAGATCACA
* * *
1018051 TAAAATAACCTAAAGTTACCTTAAAATGCATTATAATTGCAAAATAGTCCCTAGATTACATAAAA
1 TAAAATAACCTAAA-TTACCTTAAAATGCATGA-AATTGCTAAATAGTCCCTAAATTACATAAAA
* * * *
1018116 TAACCTAAGTGACCCTAAAATGCATGAAAATTGTCAAATAGTCTCTAGATTACA
64 TAACCTAAATGACCCTAAAATGCATGAAAATTCTCAAATAGCCTCTAGATCACA
1018170 TAAAATAACCT-AATTAGCCTT-AAATGCATGAAAATTGCTAAAT
1 TAAAATAACCTAAATTA-CCTTAAAATGCATG-AAATTGCTAAAT
1018213 TGCCCTTAAC
Statistics
Matches: 141, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
117 21 0.15
118 22 0.16
119 97 0.69
120 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.28
Consensus pattern (117 bp):
TAAAATAACCTAAATTACCTTAAAATGCATGAAATTGCTAAATAGTCCCTAAATTACATAAAATA
ACCTAAATGACCCTAAAATGCATGAAAATTCTCAAATAGCCTCTAGATCACA
Found at i:1018864 original size:12 final size:12
Alignment explanation
Indices: 1018843--1018877 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1018833 AGCTTTATCC
1018843 TTCTCT-TTTTT
1 TTCTCTCTTTTT
1018854 TTCTCTCTTTTT
1 TTCTCTCTTTTT
1018866 TTCTCTCTTTTT
1 TTCTCTCTTTTT
1018878 CCTTTCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTCTCTTTTT
Found at i:1018869 original size:23 final size:24
Alignment explanation
Indices: 1018843--1018891 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1018833 AGCTTTATCC
* *
1018843 TTCTCTTTTTTTTCTCT-CTTTTT
1 TTCTCTCTTTTTCCTCTCCTTTTT
*
1018866 TTCTCTCTTTTTCCTTTCCTTTTT
1 TTCTCTCTTTTTCCTCTCCTTTTT
1018890 TT
1 TT
1018892 TTTGTTGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCTCTCTTTTTCCTCTCCTTTTT
Found at i:1020247 original size:84 final size:84
Alignment explanation
Indices: 1020119--1020338 Score: 246
Period size: 84 Copynumber: 2.6 Consensus size: 84
1020109 TTTTGAAAAT
* * * * * *
1020119 TTTCTTAAATGCTTCAAATTTCACCATCAATAAAAAAAATCTTAAATGCTTCAAATG-CCTCTAC
1 TTTCTTAAATACTTCTAATTCCACCATTAATGAAAAAAATCTTAAATGCTTCAAATGTCC-CCAC
* *
1020183 CAAAGACTTGCTATGATAAC
65 CAAAAACTTGCTATGAGAAC
* * *
1020203 TTTCTTAAATACTTCTAATTCCACCATTAATGAAAAAAGTCTTAAATGCTTTAAATGTCCCCACT
1 TTTCTTAAATACTTCTAATTCCACCATTAATGAAAAAAATCTTAAATGCTTCAAATGTCCCCACC
* *
1020268 AAAAACTTGTTTTGAGAAC
66 AAAAACTTGCTATGAGAAC
* * * *
1020287 TTTCTTAAA-AGCTTTTGATTCCACCATTGATGAAAAAAAATCTTAAACGCTT
1 TTTCTTAAATA-CTTCTAATTCCACCATTAATG-AAAAAAATCTTAAATGCTT
1020339 TGGATGCGCC
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
83 1 0.01
84 95 0.83
85 19 0.17
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.35
Consensus pattern (84 bp):
TTTCTTAAATACTTCTAATTCCACCATTAATGAAAAAAATCTTAAATGCTTCAAATGTCCCCACC
AAAAACTTGCTATGAGAAC
Found at i:1023306 original size:15 final size:16
Alignment explanation
Indices: 1023286--1023315 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1023276 GCTTGAACTT
1023286 TTTTCTTT-TCTTCAA
1 TTTTCTTTCTCTTCAA
1023301 TTTTCTTTCTCTTCA
1 TTTTCTTTCTCTTCA
1023316 TAGCAGTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCTTTCTCTTCAA
Found at i:1023648 original size:24 final size:24
Alignment explanation
Indices: 1023616--1023664 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1023606 AGGATTACTT
1023616 TGGCCAGATCATTCTAATTCTAGA
1 TGGCCAGATCATTCTAATTCTAGA
1023640 TGGCCAGATCATTCTAATTCTAGA
1 TGGCCAGATCATTCTAATTCTAGA
1023664 T
1 T
1023665 CTTGCTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (24 bp):
TGGCCAGATCATTCTAATTCTAGA
Found at i:1024575 original size:18 final size:17
Alignment explanation
Indices: 1024544--1024578 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1024534 CATAATGCAT
1024544 AAAAAATATATATAAAA
1 AAAAAATATATATAAAA
*
1024561 AAAACAATATGTATAAAA
1 AAAA-AATATATATAAAA
1024579 GCTTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAAAATATATATAAAA
Found at i:1025213 original size:49 final size:49
Alignment explanation
Indices: 1025153--1025252 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
1025143 AATTGTTATG
1025153 GTTCACGATATGAGGTTTGGGGTTTGCCATTTAAATATGTTATCAAATT
1 GTTCACGATATGAGGTTTGGGGTTTGCCATTTAAATATGTTATCAAATT
1025202 GTTCACGATATGAGGTTTGGGGTTTGCCATTTAAATATGTTATCAAATT
1 GTTCACGATATGAGGTTTGGGGTTTGCCATTTAAATATGTTATCAAATT
1025251 GT
1 GT
1025253 CCCTTGAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (49 bp):
GTTCACGATATGAGGTTTGGGGTTTGCCATTTAAATATGTTATCAAATT
Found at i:1030580 original size:429 final size:429
Alignment explanation
Indices: 1029939--1030724 Score: 1475
Period size: 429 Copynumber: 1.8 Consensus size: 429
1029929 GCTTAGACCT
*
1029939 TCAAGTCCCTTATAAGTTTTTAAAACTTGGTTCATGACTAGAGTGATGTTAATGGACATTGCTTT
1 TCAAGTCCCTTATAAGTTTTTAAAACTTGGTTCATGACTAAAGTGATGTTAATGGACATTGCTTT
*
1030004 TTTGAACATGCTAGACATTTCATCATCTTTTCTTAGCAAATCAAACCAGTGCATCCCAAGTACTT
66 TTTGAACATGCTAGACATTTCATCATCTTTTCTTAGCAAATCAAACCAGTGCACCCCAAGTACTT
*
1030069 TCACACATGAAAACTACCTTCCAATGTTACATTTTTCAAGTATTTCTTGTAATTGTGACAAATTG
131 TCACACATGAAAACTACCTTCCAATGTTACATTTTTCAAGTATTTCTTGTAACTGTGACAAATTG
*
1030134 ATGAAAATTACCATTAGTTAGGACAACTCATATACTAGATTTCAATTCATATATGAAAGAGTATT
196 ATGAAAATTACCATTAGTTAGGACAACTCATATACTAGATTTCAATTCATATATGAAAGAGTATC
1030199 GTAAAAAATGTGTGCAGGCACATGGGCATGTAAATGGACTCTAATATGATATATAGATGAAGAAA
261 GTAAAAAATGTGTGCAGGCACATGGGCATGTAAATGGACTCTAATATGATATATAGATGAAGAAA
*
1030264 AATTATAAGGATGAAAAATACTATACAACATTATAAGTTTTTAAAACTTGGTTCATGACTAGAGT
326 AATTATAAGGATGAAAAATACTAAACAACATTATAAGTTTTTAAAACTTGGTTCATGACTAGAGT
1030329 GATGTTAATGGACATTCCTTTATTGAACATGCTAAACCC
391 GATGTTAATGGACATTCCTTTATTGAACATGCTAAACCC
1030368 TCAAGTCCCTTATAAGTTTTTAAAACTTGGTTCATGACTAAAGTGATGTTAATGGACATTGCTTT
1 TCAAGTCCCTTATAAGTTTTTAAAACTTGGTTCATGACTAAAGTGATGTTAATGGACATTGCTTT
*
1030433 TTTGAACATGCTAGACATTTCATCATCTTTTCTTAGCAAATCAAGCCAGTGCACCCCAAGTACTT
66 TTTGAACATGCTAGACATTTCATCATCTTTTCTTAGCAAATCAAACCAGTGCACCCCAAGTACTT
1030498 TCACACATGAAAAGCTACCTTCCAATGTTACATTTTTCAAGTATTTCTTGTAACTGTGACAAATT
131 TCACACATGAAAA-CTACCTTCCAATGTTACATTTTTCAAGTATTTCTTGTAACTGTGACAAATT
*
1030563 GATGAAAATTA-CATTAGTTAGGACAACTTATATACTAGATTTCAATTCATATATGAAAGAGTAT
195 GATGAAAATTACCATTAGTTAGGACAACTCATATACTAGATTTCAATTCATATATGAAAGAGTAT
*
1030627 CGTAAAAAATGTGTGCAGGCACATGGGCATGTAAATGGACTCTAATATGATATATAGCTGAAGAA
260 CGTAAAAAATGTGTGCAGGCACATGGGCATGTAAATGGACTCTAATATGATATATAGATGAAGAA
*
1030692 AAATTATGAGGATGAAAAATACTAAACAACATT
325 AAATTATAAGGATGAAAAATACTAAACAACATT
1030725 CGAAGATATA
Statistics
Matches: 347, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
429 286 0.82
430 61 0.18
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (429 bp):
TCAAGTCCCTTATAAGTTTTTAAAACTTGGTTCATGACTAAAGTGATGTTAATGGACATTGCTTT
TTTGAACATGCTAGACATTTCATCATCTTTTCTTAGCAAATCAAACCAGTGCACCCCAAGTACTT
TCACACATGAAAACTACCTTCCAATGTTACATTTTTCAAGTATTTCTTGTAACTGTGACAAATTG
ATGAAAATTACCATTAGTTAGGACAACTCATATACTAGATTTCAATTCATATATGAAAGAGTATC
GTAAAAAATGTGTGCAGGCACATGGGCATGTAAATGGACTCTAATATGATATATAGATGAAGAAA
AATTATAAGGATGAAAAATACTAAACAACATTATAAGTTTTTAAAACTTGGTTCATGACTAGAGT
GATGTTAATGGACATTCCTTTATTGAACATGCTAAACCC
Found at i:1031831 original size:21 final size:21
Alignment explanation
Indices: 1031806--1031847 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1031796 ATCAAAGCAT
*
1031806 TTCATTCTAAATCAACTCCAA
1 TTCATTCCAAATCAACTCCAA
*
1031827 TTCATTCCAAATCAATTCCAA
1 TTCATTCCAAATCAACTCCAA
1031848 AATTACAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (21 bp):
TTCATTCCAAATCAACTCCAA
Found at i:1036399 original size:19 final size:19
Alignment explanation
Indices: 1036375--1036422 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1036365 TTTATAAAAA
1036375 TTATTTTTAATTTT-TTTGT
1 TTATTTTT-ATTTTCTTTGT
*
1036394 TTATTTTCT-TTTTCTTTTT
1 TTATTTT-TATTTTCTTTGT
1036413 TTATTTTTAT
1 TTATTTTTAT
1036423 CTTTTTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.20
19 19 0.76
20 1 0.04
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.81
Consensus pattern (19 bp):
TTATTTTTATTTTCTTTGT
Found at i:1036425 original size:22 final size:23
Alignment explanation
Indices: 1036385--1036429 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1036375 TTATTTTTAA
* *
1036385 TTTTTTTGTTTATTTTCTTTTTC
1 TTTTTTTATTTATTATCTTTTTC
1036408 TTTTTTTATTT-TTATCTTTTTC
1 TTTTTTTATTTATTATCTTTTTC
1036430 ATAAATAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.82
Consensus pattern (23 bp):
TTTTTTTATTTATTATCTTTTTC
Found at i:1036519 original size:19 final size:18
Alignment explanation
Indices: 1036470--1036521 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
1036460 ATATTTTAAT
*
1036470 TTAAATTAATTTTATAAACA
1 TTAAA-TAA-TTTATAAAAA
1036490 TTAAATAATTTATAAAAA
1 TTAAATAATTTATAAAAA
1036508 TATACAAT-ATTTAT
1 T-TA-AATAATTTAT
1036522 TTACTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.34
19 11 0.38
20 8 0.28
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATAATTTATAAAAA
Found at i:1038194 original size:15 final size:15
Alignment explanation
Indices: 1038157--1038207 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
1038147 TAAAATATAT
*
1038157 TTTATTTATATAAAA
1 TTTATATATATAAAA
1038172 TTTA-ATATATTAATAA
1 TTTATATATA-TAA-AA
*
1038188 TTTATATTATATAAAT
1 TTTATA-TATATAAAA
1038204 TTTA
1 TTTA
1038208 AAATATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 4 0.13
15 7 0.23
16 11 0.37
17 4 0.13
18 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATATATAAAA
Found at i:1038198 original size:32 final size:33
Alignment explanation
Indices: 1038150--1038232 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
1038140 ATTATTTTAA
*
1038150 AATATATTT-TATTTATATAAAATTTAATATATT
1 AATATATTTATA-TTATATAAAATTTAAAATATT
*
1038183 AATA-ATTTATATTATATAAATTTTAAAATATT
1 AATATATTTATATTATATAAAATTTAAAATATT
* *
1038215 TATATATTTATATCATAT
1 AATATATTTATATTATAT
1038233 TAATATTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (33 bp):
AATATATTTATATTATATAAAATTTAAAATATT
Found at i:1038237 original size:25 final size:25
Alignment explanation
Indices: 1038209--1038259 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1038199 TAAATTTTAA
1038209 AATATT-TATATATTTATATCATATT
1 AATATTAT-TATATTTATATCATATT
* *
1038234 AATATTATTATTTTTATATTATATT
1 AATATTATTATATTTATATCATATT
1038259 A
1 A
1038260 TATGTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
AATATTATTATATTTATATCATATT
Found at i:1038292 original size:11 final size:11
Alignment explanation
Indices: 1038219--1038293 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
1038209 AATATTTATA
**
1038219 TATTTATATCA
1 TATTTATATTT
*
1038230 TATTAATATTAT
1 TATTTATATT-T
* *
1038242 TATTTTTATAT
1 TATTTATATTT
*
1038253 TATATTATATGT
1 TAT-TTATATTT
*
1038265 TAATTA-ATTT
1 TATTTATATTT
1038275 T-TTTATATTT
1 TATTTATATTT
1038285 TATTTATAT
1 TATTTATAT
1038294 CATACAATTA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
9 3 0.06
10 9 0.18
11 22 0.45
12 15 0.31
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (11 bp):
TATTTATATTT
Found at i:1043226 original size:32 final size:33
Alignment explanation
Indices: 1043160--1043248 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 33
1043150 TAAATAAAAT
*
1043160 AATTAAAATATAATAT-AATATTAATATATTTTAA
1 AATTAATAT-TAATATAAATATTAATATA-TTTAA
1043194 AATTAAT-TTAATATAAATTATTAATATA-TTAA
1 AATTAATATTAATATAAA-TATTAATATATTTAA
* *
1043226 AATTTATATAAATATAAAATATT
1 AATTAATATTAATAT-AAATATT
1043249 TAAATAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
32 16 0.33
33 13 0.27
34 19 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AATTAATATTAATATAAATATTAATATATTTAA
Found at i:1043243 original size:17 final size:16
Alignment explanation
Indices: 1043191--1043254 Score: 53
Period size: 15 Copynumber: 4.0 Consensus size: 16
1043181 TAATATATTT
* *
1043191 TAAAATTAATTTAATA
1 TAAAATTTATTAAATA
1043207 T-AAA-TTATTAATATA
1 TAAAATTTATTAA-ATA
1043222 TTAAAATTTATATAAATA
1 -TAAAATTTAT-TAAATA
*
1043240 TAAAATAT-TTAAATA
1 TAAAATTTATTAAATA
1043255 AAATTAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
14 5 0.12
15 12 0.30
16 3 0.08
17 10 0.25
18 7 0.17
19 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTTATTAAATA
Found at i:1043246 original size:27 final size:27
Alignment explanation
Indices: 1043198--1043252 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
1043188 TTTTAAAATT
*
1043198 AATTTAATATAAATTATTAATATATTAA
1 AATTTAATATAAATTATAAATAT-TTAA
1043226 AATTT-ATATAAA-TATAAAATATTTAA
1 AATTTAATATAAATTAT-AAATATTTAA
1043252 A
1 A
1043253 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 12 0.48
28 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTTAATATAAATTATAAATATTTAA
Found at i:1043280 original size:25 final size:25
Alignment explanation
Indices: 1043235--1043294 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
1043225 AAATTTATAT
*
1043235 AAATAT-AAAATATTTAAATAAAATTA
1 AAATATAAAAATAATT-AAT-AAATTA
*
1043261 AAATATAAAAATAATT-ATAATTTA
1 AAATATAAAAATAATTAATAAATTA
1043285 AATATATAAA
1 AA-ATATAAA
1043295 TTATTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 7 0.23
25 9 0.30
26 6 0.20
27 8 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATATAAAAATAATTAATAAATTA
Found at i:1043286 original size:17 final size:17
Alignment explanation
Indices: 1043221--1043288 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
1043211 TTATTAATAT
*
1043221 ATTAAAATTTATATAAA
1 ATTAAAATTTAAATAAA
*
1043238 TATAAAATATTTAAATAAA
1 -ATTAAA-ATTTAAATAAA
*
1043257 ATTAAAATATAAA-AATA
1 ATTAAAATTTAAATAA-A
*
1043274 ATTATAATTTAAATA
1 ATTAAAATTTAAATA
1043289 TATAAATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
16 2 0.05
17 18 0.44
18 11 0.27
19 10 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAAATTTAAATAAA
Found at i:1043287 original size:23 final size:22
Alignment explanation
Indices: 1043255--1043307 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
1043245 TATTTAAATA
*
1043255 AAATTAAAATATAAAAATAATT
1 AAATTTAAATATAAAAATAATT
* *
1043277 ATAATTTAAATATATAAATTATT
1 A-AATTTAAATATAAAAATAATT
1043300 AAATTTAA
1 AAATTTAA
1043308 TTTTTAACGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATTTAAATATAAAAATAATT
Done.