Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_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: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1114044 original size:20 final size:21
Alignment explanation
Indices: 1114003--1114057 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
1113993 ATGCAATTAG
1114003 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
1114024 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
1114044 TGCATCCATGCATC
1 TGCATCGATGCATC
1114058 AAGTCTGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:1117803 original size:33 final size:33
Alignment explanation
Indices: 1117751--1117839 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
1117741 CCAGTAAACA
* *
1117751 TATTATCTGGTAATCTTACATTCTCATTAACCC
1 TATTCTCTGATAATCTTACATTCTCATTAACCC
*
1117784 TATTCTCTGATAATCTTACATTCTCATTAACTC
1 TATTCTCTGATAATCTTACATTCTCATTAACCC
*
1117817 TATTCTCTGATAATCTTATATTC
1 TATTCTCTGATAATCTTACATTC
1117840 CCACTAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.46
Consensus pattern (33 bp):
TATTCTCTGATAATCTTACATTCTCATTAACCC
Found at i:1118684 original size:201 final size:199
Alignment explanation
Indices: 1118291--1118861 Score: 813
Period size: 201 Copynumber: 2.8 Consensus size: 199
1118281 AAAATTGAAT
* *
1118291 CTCAGTTGGTAAGAGCGCAAGGCTCTTAACCTTGTGGTCGTGGGATCGTGTCCCACGGTGGGTAA
1 CTCAGTTGGTAA-A-CGCAAGGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCATGGTGGGTAA
* * * * * * *
1118356 TTCATAATTATGACTGCCGGAGGTCTCCCACGAAAGCTGCTATCAACTTGACGTTGGGGTAGCCT
64 TTCATAATTCTGACTGTCGGAGGTCTCCCACGGAAGCTGCTCTCAACCTGGCGTTGGGGCAGCCT
* * * * *
1118421 ACTATCCTACCTCTCACTTACTCCATTACATATGAGAATAGGGTCAGCTAATTTTAGAATTGCTC
129 ACTATCCTACCTCTCCCTTACACCATTACATATGGGAATAGGGTCAGCAAATTTTAGAATTGCCC
1118486 GTCCAG
194 GTCCAG
* *
1118492 CTCAGTTGGTACAACGCAAGGCTCTTAACATTGTGGTCGTGGGATCGAGTCCCATGGGGGGTAAT
1 CTCAGTTGGTA-AACGCAAGGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCATGGTGGGTAAT
1118557 TCATAATTTCTGACTGTCGGAGGTCTCCCACGGAAGCTGCTCTCAACCTGGCGTTGGGGGCAGCC
65 TCATAA-TTCTGACTGTCGGAGGTCTCCCACGGAAGCTGCTCTCAACCTGGCGTT-GGGGCAGCC
* * *
1118622 TACTATCCTACCTCTCCCTTACCCCATTATATATGGGAATAGGGTTAGCAAATTTT-GAATTGCC
128 TACTATCCTACCTCTCCCTTACACCATTACATATGGGAATAGGGTCAGCAAATTTTAGAATTGCC
1118686 CGTCCAG
193 CGTCCAG
* * ** *
1118693 CTCAGTTGGTAGAGCGCAAGACTCTTAACCTTGTGGTATTGGGATCGAGTCCCATGGTGGGCAAT
1 CTCAGTTGGTA-AACGCAAGGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCATGGTGGGTAAT
* * * *
1118758 TCATAATTCTGATTGTCAGAGGTCTCTCACGGAAGCTGCTCTCAACCTGGCGTTGGGGCAACCTA
65 TCATAATTCTGACTGTCGGAGGTCTCCCACGGAAGCTGCTCTCAACCTGGCGTTGGGGCAGCCTA
*
1118823 CTATCCTACCTC-CCCTTACACCATCACATATGGGAATAG
130 CTATCCTACCTCTCCCTTACACCATTACATATGGGAATAG
1118862 ACCCTATCTT
Statistics
Matches: 334, Mismatches: 33, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
198 24 0.07
199 22 0.07
200 98 0.29
201 131 0.39
202 59 0.18
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (199 bp):
CTCAGTTGGTAAACGCAAGGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCATGGTGGGTAATT
CATAATTCTGACTGTCGGAGGTCTCCCACGGAAGCTGCTCTCAACCTGGCGTTGGGGCAGCCTAC
TATCCTACCTCTCCCTTACACCATTACATATGGGAATAGGGTCAGCAAATTTTAGAATTGCCCGT
CCAG
Found at i:1119090 original size:49 final size:44
Alignment explanation
Indices: 1119018--1119148 Score: 142
Period size: 41 Copynumber: 2.9 Consensus size: 44
1119008 TTTAGGGTTT
** *
1119018 CTAATTTTTAAATCTCACCTTTTATATTTATAATCGATATTAAAGGGCC
1 CTAATTTTTAAATCTCATATTTTACATTTATAATCGATATT-----GCC
* *
1119067 TTAATTTTTAAATCTCATATTTTACATTTATAATTG--A-TGCC
1 CTAATTTTTAAATCTCATATTTTACATTTATAATCGATATTGCC
*
1119108 CTAATTTTTAAATATCATATTTTACATTTATAATCGATATT
1 CTAATTTTTAAATCTCATATTTTACATTTATAATCGATATT
1119149 TGAGGCTCAT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
41 36 0.51
43 1 0.01
44 1 0.01
46 1 0.01
47 1 0.01
49 31 0.44
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.48
Consensus pattern (44 bp):
CTAATTTTTAAATCTCATATTTTACATTTATAATCGATATTGCC
Found at i:1119209 original size:43 final size:43
Alignment explanation
Indices: 1119148--1119320 Score: 158
Period size: 43 Copynumber: 4.0 Consensus size: 43
1119138 TAATCGATAT
1119148 TTGAGGCTCA-TAATTTTTTCAATC-ATACTTTTTACCTTTATAA
1 TTGAGG-TCACTAATTTTTTCAATCTA-ACTTTTTACCTTTATAA
* * * *
1119191 TTGAGGTCACTAATTTTTTTAATCTTACTTTCTACCTTTATAG
1 TTGAGGTCACTAATTTTTTCAATCTAACTTTTTACCTTTATAA
** *
1119234 TTGAAATTC-CTAATTTTTT-AAGCTAACTTTTTA-CTATTATAA
1 TTG-AGGTCACTAATTTTTTCAATCTAACTTTTTACCT-TTATAA
* * * * * *
1119276 TCGAGGCCCCAAATTTTTTCAATCTCACTTTTTACTTTTATAA
1 TTGAGGTCACTAATTTTTTCAATCTAACTTTTTACCTTTATAA
1119319 TT
1 TT
1119321 TATGACCCTA
Statistics
Matches: 104, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
41 4 0.04
42 30 0.29
43 66 0.63
44 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (43 bp):
TTGAGGTCACTAATTTTTTCAATCTAACTTTTTACCTTTATAA
Found at i:1122185 original size:124 final size:124
Alignment explanation
Indices: 1121965--1122209 Score: 427
Period size: 124 Copynumber: 2.0 Consensus size: 124
1121955 GAGTATGCCC
** * *
1121965 ACAATTTTATTTATTTGAAATTGTAAAAGCATGTCTTTTAATGTGCCGGTTCTGCTTCAATATTT
1 ACAATTTTATTTATTTGAAATTGTAAAAGCATGTCTTTTAATGTGCCAATTCTGATACAATATTT
1122030 TTGAATATATATTATCTGTTTTGAAGGTTGCAATTAAGAAAATGAAGAAGAAATATCCG
66 TTGAATATATATTATCTGTTTTGAAGGTTGCAATTAAGAAAATGAAGAAGAAATATCCG
* **
1122089 ACAATTTTATTTATTTGAAATTGTGAAAGCATGTCTTTTAATGTGTTAATTCTGATACAATATTT
1 ACAATTTTATTTATTTGAAATTGTAAAAGCATGTCTTTTAATGTGCCAATTCTGATACAATATTT
1122154 TTGAATATATATTATCTGTTTTGAAGGTTGCAATTAAGAAAATGAAGAAGAAATAT
66 TTGAATATATATTATCTGTTTTGAAGGTTGCAATTAAGAAAATGAAGAAGAAATAT
1122210 TACACATGGA
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 114 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.41
Consensus pattern (124 bp):
ACAATTTTATTTATTTGAAATTGTAAAAGCATGTCTTTTAATGTGCCAATTCTGATACAATATTT
TTGAATATATATTATCTGTTTTGAAGGTTGCAATTAAGAAAATGAAGAAGAAATATCCG
Found at i:1126634 original size:36 final size:36
Alignment explanation
Indices: 1126587--1126700 Score: 219
Period size: 36 Copynumber: 3.1 Consensus size: 36
1126577 TTGCGTCTGC
1126587 ATTGTGTAGTTTCTTTCTGTAACTGCAACTTGGCAT
1 ATTGTGTAGTTTCTTTCTGTAACTGCAACTTGGCAT
1126623 ATTGTGTAGTTTCTTTCTGTAACTGCAACTTGGCAT
1 ATTGTGTAGTTTCTTTCTGTAACTGCAACTTGGCAT
1126659 ATTGTGTAGTTTCTTTCTGTAACTGCAACTTGGCAT
1 ATTGTGTAGTTTCTTTCTGTAACTGCAACTTGGCAT
1126695 ACTTGT
1 A-TTGT
1126701 ATCATCCTCT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
36 73 0.95
37 4 0.05
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (36 bp):
ATTGTGTAGTTTCTTTCTGTAACTGCAACTTGGCAT
Found at i:1133230 original size:15 final size:15
Alignment explanation
Indices: 1133210--1133242 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1133200 TTAGCTGGGT
*
1133210 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGAC
1133225 GGGCGGATGCGGGAC
1 GGGCGGATGCGGGAC
1133240 GGG
1 GGG
1133243 TAATGTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.67, T:0.06
Consensus pattern (15 bp):
GGGCGGATGCGGGAC
Found at i:1137239 original size:21 final size:21
Alignment explanation
Indices: 1137213--1137265 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1137203 GTTTCCAGAT
1137213 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
* *
1137234 TCGCAACGCGAACTTTGACTA
1 TCGCAACGCGAACATCGACTA
*
1137255 TCGCAATGCGA
1 TCGCAACGCGA
1137266 TTTTCCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:1137787 original size:25 final size:25
Alignment explanation
Indices: 1137758--1137813 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
1137748 GTTGATTCAG
1137758 TTGTTTTAAGGTGCATGATTGTTAA
1 TTGTTTTAAGGTGCATGATTGTTAA
1137783 TTGTTTTAAGGTGCATGATTGTTAA
1 TTGTTTTAAGGTGCATGATTGTTAA
1137808 TTGTTT
1 TTGTTT
1137814 CCTGAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.21, C:0.04, G:0.23, T:0.52
Consensus pattern (25 bp):
TTGTTTTAAGGTGCATGATTGTTAA
Found at i:1137930 original size:21 final size:22
Alignment explanation
Indices: 1137905--1137953 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
1137895 ATTTTGGACT
1137905 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAACCGAACTTGGAATAA
1137926 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAAC-CGAACTTGGAATAA
1137949 ATCGC
1 ATCGC
1137954 TTGGAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 7 0.27
23 19 0.73
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (22 bp):
ATCGCAACCGAACTTGGAATAA
Found at i:1137991 original size:21 final size:21
Alignment explanation
Indices: 1137967--1138053 Score: 133
Period size: 21 Copynumber: 4.2 Consensus size: 21
1137957 GAATAAATAT
1137967 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCG
*
1137988 CAACGCGAACTTCGACTATTG
1 CAACGCGAACTTCGACTATCG
*
1138009 CAA--CGAACTTGGACTATCG
1 CAACGCGAACTTCGACTATCG
*
1138028 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTCGACTATCG
1138049 CAACG
1 CAACG
1138054 AATTTGGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
19 17 0.28
21 44 0.72
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (21 bp):
CAACGCGAACTTCGACTATCG
Found at i:1138024 original size:40 final size:40
Alignment explanation
Indices: 1137972--1138061 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
1137962 AATATCAACG
* *
1137972 CGAACTTCGACTATCGCAACGCGAACTTCGACTATTGCAA
1 CGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAA
*
1138012 CGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAA
1 CGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAA
*
1138052 CGAATTTGGA
1 CGAACTTGGA
1138062 AAATCACATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (40 bp):
CGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAA
Found at i:1138116 original size:21 final size:21
Alignment explanation
Indices: 1138070--1138117 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1138060 GAAAATCACA
*
1138070 TTGCAATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
*
1138091 TTGCGATAGTCGATGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
1138112 TTGCGA
1 TTGCGA
1138118 ATCTAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCG
Found at i:1144363 original size:21 final size:22
Alignment explanation
Indices: 1144319--1144372 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1144309 AAAAGAAAAA
* *
1144319 AAATAATAAAAATATTATTAAT
1 AAATAATAAAAATAATAATAAT
*
1144341 -AATAATAAAAATAATAATCAT
1 AAATAATAAAAATAATAATAAT
1144362 AAATAAATAAA
1 AAAT-AATAAA
1144373 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 18 0.67
22 3 0.11
23 6 0.22
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATAATAAAAATAATAATAAT
Found at i:1144853 original size:32 final size:32
Alignment explanation
Indices: 1144805--1144923 Score: 89
Period size: 32 Copynumber: 3.7 Consensus size: 32
1144795 AGGTACGATT
*
1144805 CCCTTCGTCGTGAAGTTGAAACCGTGGATGAC
1 CCCTTCGTCGTAAAGTTGAAACCGTGGATGAC
* * * * *
1144837 CCCTTCGTTGTAAAGTTG-AGCCTTGAATTGGATA
1 CCCTTCGTCGTAAAGTTGAAACCGTGGA-T-GA-C
* * *
1144871 TCCTTCGTCGTGAAA-TTGAAACTGTGGATGGC
1 CCCTTCGTCGT-AAAGTTGAAACCGTGGATGAC
* *
1144903 CCCTTCGTTGTGAAGTTGAAA
1 CCCTTCGTCGTAAAGTTGAAA
1144924 TCCAATGTAA
Statistics
Matches: 64, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
31 8 0.12
32 32 0.50
33 3 0.05
34 13 0.20
35 8 0.12
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (32 bp):
CCCTTCGTCGTAAAGTTGAAACCGTGGATGAC
Found at i:1145405 original size:252 final size:252
Alignment explanation
Indices: 1144912--1145736 Score: 1317
Period size: 252 Copynumber: 3.3 Consensus size: 252
1144902 CCCCTTCGTT
* * * *
1144912 GTGAAGTTGAAATCCAATGTAAGTTGCGCTGTTACGAGGCCAATATCCTTCGCCGTGAAGTTGAA
1 GTGAAGTTGAAATCCAA-GTAAATTGCACTGTTCCGAGGCCAATATCCTTCACCGTGAAGTTGAA
* *
1144977 ATTAACTCTGAAACTGGAAAATTTGTTGACAGACACTCATTCTTTGAGTTGGATATCCTTCATCG
65 ATTAACTCTGAAACTGGAAAATTTGTTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCG
* *
1145042 TGAAGTTGAAATCCAATATGGAGATGGATGTTGCTTGTGTGCACGATTTCCTTCATCGTGAAGTT
130 TGAAGTTGAAATCCAATATGGAGATGGATGCTGCTTGTGTGCACGATTTCCTTCGTCGTGAAGTT
* *
1145107 GAAACCGCTGGTGGCCCCTTCGTCGTGAAGTTGAGCCTGAAATTGGATATCCTTCATC
195 GAAACCGCGGGTGGCCCCTTCGTCGTGAAGTTGAGCCTGGAATTGGATATCCTTCATC
* *
1145165 GTGAAGTTGAAATCCAAGTAAATTGCACTGTTCCGAGGCTAATATCCTTCACTGTGAAGTTGAAA
1 GTGAAGTTGAAATCCAAGTAAATTGCACTGTTCCGAGGCCAATATCCTTCACCGTGAAGTTGAAA
* * *
1145230 TTGACTCTGAAACTAGAAAATTTGTTGACAGACACTCCTTCTTTGAGTTCGATATCCTTCGTCGT
66 TTAACTCTGAAACTGGAAAATTTGTTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGT
*
1145295 GAAGTTGAAATCCAATATGGAGATGAATGCTGCTTGTGTGCACGATTTCCTTCGTCGTGAAGTTG
131 GAAGTTGAAATCCAATATGGAGATGGATGCTGCTTGTGTGCACGATTTCCTTCGTCGTGAAGTTG
* *
1145360 AAACCGCGGGTGGTCCATTCGTCGTGAAGTTGAGCCTGGAATTGGATATCCTTCATC
196 AAACCGCGGGTGGCCCCTTCGTCGTGAAGTTGAGCCTGGAATTGGATATCCTTCATC
* *
1145417 GTGAAGTTGAAATCCAAGTAAATTGCGCTGTTCCGAGGCCAATATCCTTCACCATGAAGTTGAAA
1 GTGAAGTTGAAATCCAAGTAAATTGCACTGTTCCGAGGCCAATATCCTTCACCGTGAAGTTGAAA
* *
1145482 TTAACTCTGATATTGGAAAATTTGTTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGT
66 TTAACTCTGAAACTGGAAAATTTGTTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGT
1145547 GAAGTTGAAATCCAATATGGAGATGGATGCTGCTTGTGTGCACGATTTCCTTCGTCGTGAAGTTG
131 GAAGTTGAAATCCAATATGGAGATGGATGCTGCTTGTGTGCACGATTTCCTTCGTCGTGAAGTTG
* *
1145612 AAACCGCGGGTGGCCCCTTCGTCGTGAAGTTAAGCCTGAGAATTGGATATCCTTCGTC
196 AAACCGCGGGTGGCCCCTTCGTCGTGAAGTTGAGCCTG-GAATTGGATATCCTTCATC
* * * * * * * * * **
1145670 GTGAAGTTGAAATTCGAGTAAGTTGTATTGCTCCAAGTCAAATATCCTTCGTCGTGAAGTTGAAA
1 GTGAAGTTGAAATCCAAGTAAATTGCACTGTTCCGAGGCCAATATCCTTCACCGTGAAGTTGAAA
1145735 TT
66 TT
1145737 GGTTCTGGAA
Statistics
Matches: 526, Mismatches: 45, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
252 437 0.83
253 89 0.17
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (252 bp):
GTGAAGTTGAAATCCAAGTAAATTGCACTGTTCCGAGGCCAATATCCTTCACCGTGAAGTTGAAA
TTAACTCTGAAACTGGAAAATTTGTTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGT
GAAGTTGAAATCCAATATGGAGATGGATGCTGCTTGTGTGCACGATTTCCTTCGTCGTGAAGTTG
AAACCGCGGGTGGCCCCTTCGTCGTGAAGTTGAGCCTGGAATTGGATATCCTTCATC
Found at i:1145899 original size:106 final size:105
Alignment explanation
Indices: 1145705--1146374 Score: 814
Period size: 106 Copynumber: 6.5 Consensus size: 105
1145695 TATTGCTCCA
* * * *
1145705 AGTCAAATATCCTTCG-TCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAG
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTGGG-AATTGTTTGTTGACAA
* *
1145769 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTG
64 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
* * * *
1145811 AGTCCAATGTCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTAGGGAATTGTTTGTTGACAGT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACT-GGGAATTGTTTGTTGACAAT
* *
1145876 CAGCCGCCACTTCATCGTGAAGTTGAGCTTGTGTTGTCTTG
65 CAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
* * * *
1145917 AGTCTAATA----TC-C--TG-AGTTAAAATTGACTCTGAAA----G--TTATTTGTTGACAATC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAATTGTTTGTTGACAATC
* * *
1145968 AGCTGCCCCTTCATCGTGAAGTTGAGCTTGTGTTATCTTG
66 AGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
* * * * * * * *
1146008 GGACCAATATCATTCGCTGTGAAGTTGAAATTGGTTCTAAAATTGGGAAATTATTTGTTGACAGT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG-AATTGTTTGTTGACAAT
1146073 CAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGTTGTCTTG
65 CAGCCGCCCCTTCGTC-GTGAAGTTGAGCTTGTGTTGTCTTG
* * * *
1146114 AGTCAAATATTCTTCGCTATGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA-TTGTTTGTTGACAAT
* *
1146179 CAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
65 CAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
*
1146220 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA-TTGTTTGTTGACAAT
* *
1146285 CAGTCGCCTCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
65 CAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
* * *
1146326 AGTCCAATATCCTTTGTTGTGAGGTTGAAATTGGCTCTGAAACTGGGAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA
1146375 GCCCCTTCGT
Statistics
Matches: 492, Mismatches: 52, Indels: 40
0.84 0.09 0.07
Matches are distributed among these distances:
91 57 0.12
93 1 0.00
95 2 0.00
96 1 0.00
98 19 0.04
99 18 0.04
101 1 0.00
102 2 0.00
103 1 0.00
105 3 0.01
106 383 0.78
107 4 0.01
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAATTGTTTGTTGACAATC
AGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
Found at i:1150769 original size:2 final size:2
Alignment explanation
Indices: 1150762--1150795 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1150752 GATTAAACTA
1150762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1150796 CCAAATAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1153543 original size:48 final size:48
Alignment explanation
Indices: 1153467--1153565 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
1153457 TTATGATATC
* *
1153467 TCATATCAACTTATTCGAGCATGTCCATGCATTTCTAGTCTTACTCAA
1 TCATATCAACTTATTCAAGCATGACCATGCATTTCTAGTCTTACTCAA
1153515 TCATATCAACTTATTCAAGCATGACCATGCATTTCTAGTCTTACTCAA
1 TCATATCAACTTATTCAAGCATGACCATGCATTTCTAGTCTTACTCAA
1153563 TCA
1 TCA
1153566 AGTGGCCTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (48 bp):
TCATATCAACTTATTCAAGCATGACCATGCATTTCTAGTCTTACTCAA
Found at i:1155086 original size:2 final size:2
Alignment explanation
Indices: 1155079--1155105 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1155069 TTAGGCGATC
1155079 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 A
1155106 ACATGTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1156449 original size:32 final size:32
Alignment explanation
Indices: 1156412--1156475 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1156402 TGGACATAGC
*
1156412 CATCTCCGGTTGTTATGCGACAAGAGGGCCAT
1 CATCTCCGGTTGTCATGCGACAAGAGGGCCAT
1156444 CATCTCCGGTTGTCATGCGACAAGAGGGCCAT
1 CATCTCCGGTTGTCATGCGACAAGAGGGCCAT
1156476 TATGCCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Consensus pattern (32 bp):
CATCTCCGGTTGTCATGCGACAAGAGGGCCAT
Found at i:1164001 original size:29 final size:29
Alignment explanation
Indices: 1163959--1164015 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1163949 AGTGTTGGCC
*
1163959 GTAGGTCGCCATGCACTCTGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
1163988 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
1164016 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.32, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:1164178 original size:20 final size:19
Alignment explanation
Indices: 1164153--1164212 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
1164143 GCATAGATCG
1164153 CTCGGTTGCCCTCGGATGGC
1 CTCGGTTG-CCTCGGATGGC
1164173 CTC-G--G--TCGGATGGC
1 CTCGGTTGCCTCGGATGGC
*
1164187 CTCGGATGCTCTCGGATGGC
1 CTCGGTTGC-CTCGGATGGC
1164207 CTCGGT
1 CTCGGT
1164213 CGGATGGCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
14 12 0.36
15 1 0.03
17 2 0.06
19 1 0.03
20 17 0.52
ACGTcount: A:0.07, C:0.32, G:0.37, T:0.25
Consensus pattern (19 bp):
CTCGGTTGCCTCGGATGGC
Found at i:1164183 original size:14 final size:14
Alignment explanation
Indices: 1164164--1164225 Score: 70
Period size: 14 Copynumber: 4.0 Consensus size: 14
1164154 TCGGTTGCCC
1164164 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1164178 TCGGATGGCCTCGGATG
1 TCGGATGGCCTC-G--G
1164195 CTCTCGGATGGCCTCGG
1 ---TCGGATGGCCTCGG
1164212 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1164226 ATGCCCAGCG
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
14 26 0.62
15 1 0.02
17 2 0.05
19 1 0.02
20 12 0.29
ACGTcount: A:0.08, C:0.29, G:0.40, T:0.23
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:1164201 original size:34 final size:34
Alignment explanation
Indices: 1164153--1164231 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
1164143 GCATAGATCG
*
1164153 CTCGGTTGCCCTCGGATGGCCTCGGTCGGATGGC
1 CTCGGATGCCCTCGGATGGCCTCGGTCGGATGGC
*
1164187 CTCGGATGCTCTCGGATGGCCTCGGTCGGATGGC
1 CTCGGATGCCCTCGGATGGCCTCGGTCGGATGGC
1164221 CTCGGATGCCC
1 CTCGGATGCCC
1164232 AGCGTGTTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.08, C:0.33, G:0.37, T:0.23
Consensus pattern (34 bp):
CTCGGATGCCCTCGGATGGCCTCGGTCGGATGGC
Found at i:1164228 original size:10 final size:10
Alignment explanation
Indices: 1164178--1164211 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1164168 ATGGCCTCGG
1164178 TCGGATGGCC
1 TCGGATGGCC
1164188 TCGGAT-GCTC
1 TCGGATGGC-C
1164198 TCGGATGGCC
1 TCGGATGGCC
1164208 TCGG
1 TCGG
1164212 TCGGATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:1166526 original size:36 final size:37
Alignment explanation
Indices: 1166486--1166559 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
1166476 TTTTATTATT
*
1166486 TCGGGTCGG-GTTTTTAATTCAT-ATATTCGGGTCGGG
1 TCGGGTCGGTGTTTTTAAGT-ATGATATTCGGGTCGGG
* *
1166522 TCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGTGTTTTTAAGTATGATATTCGGGTCGGG
1166559 T
1 T
1166560 AGAGTTCGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 10 0.30
37 23 0.70
ACGTcount: A:0.12, C:0.12, G:0.35, T:0.41
Consensus pattern (37 bp):
TCGGGTCGGTGTTTTTAAGTATGATATTCGGGTCGGG
Found at i:1166859 original size:194 final size:199
Alignment explanation
Indices: 1166545--1166946 Score: 600
Period size: 194 Copynumber: 2.0 Consensus size: 199
1166535 TTTAAGTGTG
* * *
1166545 ATATTCGGGTCGGGTAGAGTTCGGGTTTATGGTGAAAAATACCCGACCCGAAAATATATATAATT
1 ATATTCGGGTCGGGTAGAGTACGGGTTTAGGGTGAAAAATA--C-ACCCGAAAAAATATATAATT
* *
1166610 TTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTCTATATAA-TTTTTTTCAATTAAG
63 TTACCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAG
*
1166674 TCATTGTTTTTATTGAAT-AAAAT-ATTTTTTTTATTATTTCGGGTCG-GTTCGGGTCGGATTTC
128 TCAATGTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGTG-TCGGGTCGGATTTC
1166736 TAATTCAT
192 TAATTCAT
* *
1166744 ATATTCGGGTCGGGTCGGGTACGGGTTTAGGGTGAAAAA-A-ACCCGAAAAAATATATAATTTTA
1 ATATTCGGGTCGGGTAGAGTACGGGTTTAGGGTGAAAAATACACCCGAAAAAATATATAATTTTA
*
1166807 CCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATACTTTTTTTTTCAATTAAGTC
66 CCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATA-ATTTTTTTTCAATTAAGTC
* * * *
1166872 AATGTTTTTATTGAATAAAAATAATTTTTTTTATTATTTTGTGTCGTGTGGGGTCGGGTTTCTAA
130 AATGTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGTGTCGGGTCGGATTTCTAA
1166937 TTCAT
195 TTCAT
1166942 ATATT
1 ATATT
1166947 GAATAAAAAT
Statistics
Matches: 185, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
194 65 0.35
196 32 0.17
197 5 0.03
198 47 0.25
199 36 0.19
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.42
Consensus pattern (199 bp):
ATATTCGGGTCGGGTAGAGTACGGGTTTAGGGTGAAAAATACACCCGAAAAAATATATAATTTTA
CCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCA
ATGTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGTGTCGGGTCGGATTTCTAAT
TCAT
Found at i:1171569 original size:31 final size:31
Alignment explanation
Indices: 1171502--1171569 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
1171492 TATTAATTTT
*
1171502 TTTTTAATTTGATCACTTAATTATTATCATA
1 TTTTTAATTTGATCACTTAATTAATATCATA
* *
1171533 ATTTTATTTTGATCA-TTAAATTAATA-CTATA
1 TTTTTAATTTGATCACTT-AATTAATATC-ATA
1171564 TTTTTA
1 TTTTTA
1171570 CTTTACATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (31 bp):
TTTTTAATTTGATCACTTAATTAATATCATA
Found at i:1172147 original size:14 final size:16
Alignment explanation
Indices: 1172128--1172159 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1172118 GCAGAGATTT
1172128 TTAAATT-TT-TTATA
1 TTAAATTATTATTATA
1172142 TTAAATTATTATTATA
1 TTAAATTATTATTATA
1172158 TT
1 TT
1172160 TCTGAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAAATTATTATTATA
Found at i:1173521 original size:20 final size:21
Alignment explanation
Indices: 1173498--1173541 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1173488 TTTTAAATTA
*
1173498 ATAAAAATTATTA-TCTAATG
1 ATAAAAATTAATATTCTAATG
*
1173518 ATAAATATTAATATTCTAATG
1 ATAAAAATTAATATTCTAATG
1173539 ATA
1 ATA
1173542 TATTTGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
ATAAAAATTAATATTCTAATG
Found at i:1174571 original size:14 final size:14
Alignment explanation
Indices: 1174560--1174593 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1174550 CTTAAAACAC
1174560 TAAACCTTAAACTA
1 TAAACCTTAAACTA
*
1174574 TAAACCTTAACCT-
1 TAAACCTTAAACTA
1174587 TAAACCT
1 TAAACCT
1174594 AAAAATTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAACCTTAAACTA
Found at i:1174743 original size:15 final size:15
Alignment explanation
Indices: 1174706--1174749 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1174696 CATTTCATTT
* *
1174706 TCATTAAACCTTAAA
1 TCATAAAACCATAAA
*
1174721 TC-TAAAACCCTAAA
1 TCATAAAACCATAAA
1174735 TCATAAAACCATAAA
1 TCATAAAACCATAAA
1174750 CCTTGAACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (15 bp):
TCATAAAACCATAAA
Found at i:1174819 original size:7 final size:7
Alignment explanation
Indices: 1174809--1174885 Score: 58
Period size: 7 Copynumber: 11.3 Consensus size: 7
1174799 CCTAAACATG
1174809 AACCTTA
1 AACCTTA
1174816 AACC-TA
1 AACCTTA
1174822 AA--TGTA
1 AACCT-TA
1174828 AA-CTTAA
1 AACCTT-A
1174835 AACACT-A
1 AAC-CTTA
1174842 AACCTTA
1 AACCTTA
1174849 AA-CTATA
1 AACCT-TA
1174856 AACCTTA
1 AACCTTA
1174863 AACCTTA
1 AACCTTA
*
1174870 AACCCTA
1 AACCTTA
*
1174877 AACCCTA
1 AACCTTA
1174884 AA
1 AA
1174886 TTATAAACCC
Statistics
Matches: 60, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
6 13 0.22
7 43 0.72
8 2 0.03
9 2 0.03
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.23
Consensus pattern (7 bp):
AACCTTA
Found at i:1174862 original size:274 final size:270
Alignment explanation
Indices: 1174323--1174867 Score: 986
Period size: 274 Copynumber: 2.0 Consensus size: 270
1174313 TTCATATATT
1174323 AATTAGGCTACAAGTTTTTGATGAATTCCATTCCGAGGTGATAATGTCTCACCCATAACATAAAC
1 AATTAGGCTACAAGTTTTTGATGAATTCCATTCCGAGGTGATAATGTCTCACCCATAACATAAAC
1174388 TATATGAGAATCCTAATAAAATGATTAAATAAATCATTTCATTTCATTAAACCTTAAATCAAAAC
66 TATATGAGAATCCTAATAAAATGATTAAATAAATCATTTCATTTCATTAAACCTTAAATCAAAAC
1174453 CCTAAATCATAAAACCATAACCTGAACCTAAGCCTTAAACAGTAGACTTAAACCCTAAACCCTAA
131 CCTAAATCATAAAACCATAACCTGAACCTAAGCCTTAAACAGTAGACTTAAACCCTAAACCCTAA
1174518 GGCCTAAACATGAACCTAAACCTAAATGTAAACTTAAAACACTAAACCTTAAACTATAAACCTTA
196 GGCCTAAACATGAACCTAAACCTAAATGTAAACTTAAAACACTAAACCTTAAACTAT-AA-C--A
1174583 ACCTTAAACCTAAA
257 ACCTTAAACCTAAA
1174597 AATTAGGCTACAAGTTTTTGATGAATTCCATTCCGAGGTGATAATGTCTCACCCATAACATAAAC
1 AATTAGGCTACAAGTTTTTGATGAATTCCATTCCGAGGTGATAATGTCTCACCCATAACATAAAC
1174662 TATATGAGAATCCTAATAAAATGATTAAATAAATCATTTCATTTTCATTAAACCTTAAATCTAAA
66 TATATGAGAATCCTAATAAAATGATTAAATAAATCATTTCA-TTTCATTAAACCTTAAATC-AAA
1174727 ACCCTAAATCATAAAACCATAAACCTTGAACCTAAGCCTTAAACAGTAGATCTTAAACCCTAAAC
129 ACCCTAAATCATAAAACCAT-AACC-TGAACCTAAGCCTTAAACAGTAGA-CTTAAACCCTAAAC
1174792 CCTAAGGCCTAAACATGAACCTTAAACCTAAATGTAAACTTAAAACACTAAACCTTAAACTAT-A
191 CCTAAGGCCTAAACATGAACC-TAAACCTAAATGTAAACTTAAAACACTAAACCTTAAACTATAA
1174856 -AACCTTAAACCT
255 CAACCTTAAACCT
1174868 TAAACCCTAA
Statistics
Matches: 265, Mismatches: 0, Indels: 12
0.96 0.00 0.04
Matches are distributed among these distances:
274 118 0.45
275 19 0.07
276 23 0.09
277 4 0.02
278 25 0.09
279 35 0.13
280 41 0.15
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (270 bp):
AATTAGGCTACAAGTTTTTGATGAATTCCATTCCGAGGTGATAATGTCTCACCCATAACATAAAC
TATATGAGAATCCTAATAAAATGATTAAATAAATCATTTCATTTCATTAAACCTTAAATCAAAAC
CCTAAATCATAAAACCATAACCTGAACCTAAGCCTTAAACAGTAGACTTAAACCCTAAACCCTAA
GGCCTAAACATGAACCTAAACCTAAATGTAAACTTAAAACACTAAACCTTAAACTATAACAACCT
TAAACCTAAA
Found at i:1174878 original size:21 final size:21
Alignment explanation
Indices: 1174834--1174935 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 21
1174824 TGTAAACTTA
* **
1174834 AAACACTAAACCTTAAACTAT
1 AAACCCTAAACCTTAAACCCT
*
1174855 AAACCTTAAACCTTAAACCCT
1 AAACCCTAAACCTTAAACCCT
*
1174876 AAACCCTAAA-TTATAAACCCT
1 AAACCCTAAACCT-TAAACCCT
* * *
1174897 AAACAC-AAACTTTAAATCCT
1 AAACCCTAAACCTTAAACCCT
*
1174917 AAAACCCTAAACCCTAAAC
1 -AAACCCTAAACCTTAAAC
1174936 TATAAACTAC
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
20 11 0.17
21 46 0.71
22 8 0.12
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCCTAAACCTTAAACCCT
Found at i:1174899 original size:7 final size:7
Alignment explanation
Indices: 1174834--1174935 Score: 71
Period size: 7 Copynumber: 14.6 Consensus size: 7
1174824 TGTAAACTTA
*
1174834 AAACACT
1 AAACCCT
*
1174841 AAACCTT
1 AAACCCT
**
1174848 AAACTAT
1 AAACCCT
*
1174855 AAACCTT
1 AAACCCT
*
1174862 AAACCTT
1 AAACCCT
1174869 AAACCCT
1 AAACCCT
1174876 AAACCCT
1 AAACCCT
***
1174883 AAATTAT
1 AAACCCT
1174890 AAACCCT
1 AAACCCT
*
1174897 AAACAC-
1 AAACCCT
**
1174903 AAACTTT
1 AAACCCT
*
1174910 AAATCCT
1 AAACCCT
1174917 AAAACCCT
1 -AAACCCT
1174925 AAACCCT
1 AAACCCT
1174932 AAAC
1 AAAC
1174936 TATAAACTAC
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
6 4 0.05
7 63 0.86
8 6 0.08
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:1174928 original size:35 final size:35
Alignment explanation
Indices: 1174889--1174962 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
1174879 CCCTAAATTA
** *
1174889 TAAACCCTAAAC-ACAAACTTTAAATCCTAAAACCC
1 TAAACCCTAAACTACAAACTACAAATACT-AAACCC
*
1174924 TAAACCCTAAACTATAAACTACAAATACTAAACCC
1 TAAACCCTAAACTACAAACTACAAATACTAAACCC
1174959 TAAA
1 TAAA
1174963 TAATGATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 22 0.65
36 12 0.35
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.20
Consensus pattern (35 bp):
TAAACCCTAAACTACAAACTACAAATACTAAACCC
Found at i:1176949 original size:17 final size:17
Alignment explanation
Indices: 1176927--1177034 Score: 117
Period size: 17 Copynumber: 5.9 Consensus size: 17
1176917 AGGTTCAAAT
1176927 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
*
1176944 TCGAGTTCGAGTTTGAA
1 TCGAGTTCGAGCTTGAA
*
1176961 TCGAGTTTGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
1176978 TCGAGCTCAAATTCGAGCTTGAA
1 TCGAG------TTCGAGCTTGAA
*
1177001 TCGAGTTCGAGCTTCAA
1 TCGAGTTCGAGCTTGAA
*
1177018 TCGAGCTCGAGTCTTGA
1 TCGAGTTCGAG-CTTGA
1177035 GCTTCAATCG
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
17 57 0.74
18 4 0.05
23 16 0.21
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (17 bp):
TCGAGTTCGAGCTTGAA
Found at i:1177004 original size:40 final size:40
Alignment explanation
Indices: 1176949--1177025 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
1176939 TTGAATCGAG
* * *
1176949 TTCGAGTTTGAATCGAGTTTGAGCTTGAATCGAGCTCAAA
1 TTCGAGCTTGAATCGAGTTCGAGCTTCAATCGAGCTCAAA
1176989 TTCGAGCTTGAATCGAGTTCGAGCTTCAATCGAGCTC
1 TTCGAGCTTGAATCGAGTTCGAGCTTCAATCGAGCTC
1177026 GAGTCTTGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (40 bp):
TTCGAGCTTGAATCGAGTTCGAGCTTCAATCGAGCTCAAA
Found at i:1177038 original size:24 final size:23
Alignment explanation
Indices: 1177001--1177049 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
1176991 CGAGCTTGAA
1177001 TCGAGTTCGAGCTTCAATCGAGC
1 TCGAGTTCGAGCTTCAATCGAGC
*
1177024 TCGAGTCTTGAGCTTCAATCGAGC
1 TCGAGT-TCGAGCTTCAATCGAGC
1177048 TC
1 TC
1177050 ATGAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (23 bp):
TCGAGTTCGAGCTTCAATCGAGC
Found at i:1185121 original size:21 final size:21
Alignment explanation
Indices: 1185097--1185137 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1185087 ATTAATAATA
1185097 TATTATGTAAATGTTTCGATT
1 TATTATGTAAATGTTTCGATT
1185118 TATTATGTAAATGTTTCGAT
1 TATTATGTAAATGTTTCGAT
1185138 ATAATGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (21 bp):
TATTATGTAAATGTTTCGATT
Found at i:1185146 original size:19 final size:19
Alignment explanation
Indices: 1185096--1185147 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 19
1185086 AATTAATAAT
1185096 ATATTATGTAAATGTTTCG
1 ATATTATGTAAATGTTTCG
1185115 ATTTATTATGTAAATGTTTCG
1 A--TATTATGTAAATGTTTCG
*
1185136 ATATAATGTAAA
1 ATATTATGTAAA
1185148 AATTATAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 11 0.37
21 19 0.63
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (19 bp):
ATATTATGTAAATGTTTCG
Found at i:1188065 original size:21 final size:21
Alignment explanation
Indices: 1187977--1188070 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1187967 TATGGTATAA
*
1187977 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1187998 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1188019 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1188040 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1188061 AACCCTGCGG
1 AACCCTGCGG
1188071 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1188100 original size:21 final size:21
Alignment explanation
Indices: 1188074--1188121 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1188064 CCTGCGGAGA
*
1188074 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1188095 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1188116 GGGCAT
1 TGGCAT
1188122 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1189869 original size:14 final size:14
Alignment explanation
Indices: 1189818--1189870 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1189808 AATAATAATT
1189818 ATATAAATATTATTTA
1 ATATAAATA-TA-TTA
*
1189834 ATAATAAAATATATTT
1 AT-AT-AAATATATTA
*
1189850 ACATAAATATATTA
1 ATATAAATATATTA
1189864 ATATAAA
1 ATATAAA
1189871 AAATAATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 15 0.48
15 2 0.06
16 5 0.16
17 4 0.13
18 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATAAATATATTA
Found at i:1193975 original size:2 final size:2
Alignment explanation
Indices: 1193968--1194045 Score: 140
Period size: 2 Copynumber: 39.5 Consensus size: 2
1193958 TCCCAATAAT
1193968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1194009 GA TA 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 TA TA T
1194046 GTTAAAAGTA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1195993 original size:2 final size:2
Alignment explanation
Indices: 1195893--1195973 Score: 121
Period size: 2 Copynumber: 40.5 Consensus size: 2
1195883 TTTATTGCTA
1195893 AT AT GAT AT -T AT AT AT AT CAT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
*
1195935 AT AT AT AT AT CT 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 AT AT AT AT AT A
1195974 ATTATTGAAG
Statistics
Matches: 73, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.03
2 67 0.92
3 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1199830 original size:14 final size:15
Alignment explanation
Indices: 1199777--1199831 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
1199767 GAGAAATAAT
* *
1199777 AAAAAATTATAATTA
1 AAAAAAATATAAGTA
*
1199792 AACAAAAT-TAAGTA
1 AAAAAAATATAAGTA
*
1199806 AATACAAATATAA-TA
1 AA-AAAAATATAAGTA
1199821 AAAAAAATATA
1 AAAAAAATATA
1199832 TCGATGCCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 15 0.47
15 14 0.44
16 3 0.09
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (15 bp):
AAAAAAATATAAGTA
Found at i:1201948 original size:111 final size:111
Alignment explanation
Indices: 1201811--1202016 Score: 394
Period size: 111 Copynumber: 1.9 Consensus size: 111
1201801 ATTACAAAAA
1201811 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
1201876 AATTAAAACATTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
1201922 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
1201987 AATTAAAACTTTAAAATGTTACCGTATCAG
66 AATTAAAACATTAAAATGTTACCGTATCAG
1202017 TAAGTGTTGA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 93 1.00
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:1206849 original size:2 final size:2
Alignment explanation
Indices: 1206842--1206877 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1206832 TTCAAACATA
*
1206842 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1206878 CACATCCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1215401 original size:16 final size:16
Alignment explanation
Indices: 1215380--1215412 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1215370 TAATAAATAG
1215380 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1215396 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1215412 A
1 A
1215413 AAAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1215493 original size:10 final size:10
Alignment explanation
Indices: 1215478--1215552 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1215468 CATTTAATAA
1215478 ATAAACGAAC
1 ATAAACGAAC
1215488 ATAAACGAAC
1 ATAAACGAAC
1215498 ----ACGAAC
1 ATAAACGAAC
1215504 ATAAACGAAC
1 ATAAACGAAC
** *
1215514 ACGAAC-ATAA
1 ATAAACGA-AC
1215524 ATGAACACGAAC
1 AT-AA-ACGAAC
1215536 ATAAACGAAC
1 ATAAACGAAC
1215546 ATAAACG
1 ATAAACG
1215553 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1215503 original size:16 final size:16
Alignment explanation
Indices: 1215482--1215546 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1215472 TAATAAATAA
1215482 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1215498 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1215514 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1215530 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1215546 A
1 A
1215547 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1216297 original size:14 final size:14
Alignment explanation
Indices: 1216280--1216335 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
1216270 AATGAACATA
*
1216280 AACGAACATAATCG
1 AACGAACATAACCG
1216294 AACGAACAT-A---
1 AACGAACATAACCG
1216304 AACGAACATAACCG
1 AACGAACATAACCG
1216318 AACGAACATAACCG
1 AACGAACATAACCG
1216332 AACG
1 AACG
1216336 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1216300 original size:24 final size:24
Alignment explanation
Indices: 1216260--1216334 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
1216250 GATTGGGTTA
*
1216260 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1216284 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
1216308 AACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
1216332 AAC
1 AAC
1216335 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1216334 original size:10 final size:10
Alignment explanation
Indices: 1216273--1216320 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1216263 ATAAATGAAT
1216273 GAACATAAAC
1 GAACATAAAC
1216283 GAACATAATCGAAC
1 GAACAT-A---AAC
1216297 GAACATAAAC
1 GAACATAAAC
*
1216307 GAACATAACC
1 GAACATAAAC
1216317 GAAC
1 GAAC
1216321 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1221839 original size:149 final size:151
Alignment explanation
Indices: 1221653--1221954 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 151
1221643 TTTATTAAAA
1221653 TATAATTTCTATAAGAATATGTATTAAAATATCAATTTTTTAACGGTACTCTCATAACAACATTT
1 TATAATTTCTATAAGAATATGTATTAAAATATCAATTTTTTAACGGTACTCTCATAACAACATTT
1221718 TTGAAAAATATAAACATAAACGTGTCGATTTATCATTCTATCATAAGAAAACAAATAAATTA-TT
66 TTGAAAAATATAAACATAAACGTGTCGATTTATCATTCTATCATAAGAAAACAAATAAATTATTT
1221782 TA-GGAAAATATATTTGGGCC
131 TATGGAAAATATATTTGGGCC
1221802 TATAATTTCTATAAGAATATGTATTAAAATATCAATTTTTTAACGGTACTCTCATAACAACATTT
1 TATAATTTCTATAAGAATATGTATTAAAATATCAATTTTTTAACGGTACTCTCATAACAACATTT
*
1221867 TTGGAAAATATAAACATAAACGTGTCGATTTATCATTCTATCATAAGAAAACAAATAAATTATTT
66 TTGAAAAATATAAACATAAACGTGTCGATTTATCATTCTATCATAAGAAAACAAATAAATTATTT
1221932 TATGGAAAATATATTTGGGCC
131 TATGGAAAATATATTTGGGCC
1221953 TA
1 TA
1221955 ATTTTAGTAT
Statistics
Matches: 150, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
149 126 0.84
150 4 0.03
151 20 0.13
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (151 bp):
TATAATTTCTATAAGAATATGTATTAAAATATCAATTTTTTAACGGTACTCTCATAACAACATTT
TTGAAAAATATAAACATAAACGTGTCGATTTATCATTCTATCATAAGAAAACAAATAAATTATTT
TATGGAAAATATATTTGGGCC
Found at i:1224426 original size:17 final size:17
Alignment explanation
Indices: 1224392--1224424 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
1224382 TCCAAAATAG
1224392 TTAATTATTAGATAAAAT
1 TTAA-TATTAGATAAAAT
1224410 TTAATATTA-ATAAAA
1 TTAATATTAGATAAAA
1224425 ATGTAATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAATATTAGATAAAAT
Found at i:1229262 original size:2 final size:2
Alignment explanation
Indices: 1229230--1229254 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1229220 AACAACATAA
1229230 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1229255 TCCACACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1232372 original size:32 final size:32
Alignment explanation
Indices: 1232314--1232384 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1232304 TTAACAGCTG
* * *
1232314 AGAGACT-AAAATCTAACGGATTGATAACATT
1 AGAGACTAAAAATCGAACAGATCGATAACATT
1232345 AGAGACTAAAAATCGAACAGATCGATAACATT
1 AGAGACTAAAAATCGAACAGATCGATAACATT
*
1232377 AAAGACTA
1 AGAGACTA
1232385 TTTCTCTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 7 0.20
32 28 0.80
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.21
Consensus pattern (32 bp):
AGAGACTAAAAATCGAACAGATCGATAACATT
Found at i:1234813 original size:24 final size:25
Alignment explanation
Indices: 1234775--1234827 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
1234765 GTACTTGATG
*
1234775 AATATAACCAGAATGCATATCACTT
1 AATATAACAAGAATGCATATCACTT
1234800 AATAT-ACAAGAATGCATATCACTT
1 AATATAACAAGAATGCATATCACTT
1234824 AATA
1 AATA
1234828 AACTATAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (25 bp):
AATATAACAAGAATGCATATCACTT
Found at i:1235899 original size:18 final size:18
Alignment explanation
Indices: 1235876--1235928 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1235866 ACTGAATATT
1235876 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1235894 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
1235912 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1235929 GATAATCCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1239924 original size:21 final size:23
Alignment explanation
Indices: 1239895--1239952 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1239885 CTTCTGACTT
*
1239895 TGAATACACTAAAATATCATCGA
1 TGAACACACTAAAATATCATCGA
1239918 TGAACACACTAAAATATCATCGA
1 TGAACACACTAAAATATCATCGA
1239941 TGAACACCACTA
1 TGAACA-CACTA
1239953 CGAATCGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 28 0.85
24 5 0.15
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (23 bp):
TGAACACACTAAAATATCATCGA
Found at i:1242973 original size:18 final size:18
Alignment explanation
Indices: 1242950--1242984 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1242940 ACTGAATATT
1242950 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1242968 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1242985 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1244090 original size:13 final size:13
Alignment explanation
Indices: 1244072--1244096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1244062 TCACACGCAC
1244072 AGAGAAGAAAAGA
1 AGAGAAGAAAAGA
1244085 AGAGAAGAAAAG
1 AGAGAAGAAAAG
1244097 TCTAGAACTC
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
AGAGAAGAAAAGA
Found at i:1248182 original size:19 final size:19
Alignment explanation
Indices: 1248158--1248195 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1248148 TATACATCAG
*
1248158 CTAACAGCTTCATCATTCA
1 CTAACAACTTCATCATTCA
1248177 CTAACAACTTCATCATTCA
1 CTAACAACTTCATCATTCA
1248196 ATAATTAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (19 bp):
CTAACAACTTCATCATTCA
Found at i:1252714 original size:176 final size:176
Alignment explanation
Indices: 1252420--1252773 Score: 600
Period size: 176 Copynumber: 2.0 Consensus size: 176
1252410 CTAAGTTTAA
* * * *
1252420 ACTTTCAATAACAACAGCAGTGATGTTAAAATCACCTCCAATGAGTCAAACACTACTTCCAACCA
1 ACTTTCAATAACAACAGCAATAATGTTAAAATCACCTCCAATGAGCCAAACACTACTTCCAACAA
* *
1252485 GAGAATCAACAGAAGTAAGTTGATGCCATAGTTCCCTCCTAACATATTTACCTCTCAAAATACCT
66 GAGAATCAACAGAAGTAAGTTGATACCATAGTTCCCTCCTAACATATTTACCTCCCAAAATACCT
* *
1252550 TGAAATAACTATCCCATTATTACTATCGTACACAGTAGAAATAACT
131 TGAAATAACTATCCCATTATTACTACCATACACAGTAGAAATAACT
1252596 ACTTTCAATAACAACAGCAATAATGTTAAAATCACCTCCAATGAGCCAAACACTACTTCCAACAA
1 ACTTTCAATAACAACAGCAATAATGTTAAAATCACCTCCAATGAGCCAAACACTACTTCCAACAA
* *
1252661 GAGAATCAACAGAAGTAAGTTGCTACCATAGTTCCCTCCTAACATATTTACCTCCCAAACTACCT
66 GAGAATCAACAGAAGTAAGTTGATACCATAGTTCCCTCCTAACATATTTACCTCCCAAAATACCT
**
1252726 TGAAATAACTATCCCATTATTGTTACCATACACAGTAGAAATAACT
131 TGAAATAACTATCCCATTATTACTACCATACACAGTAGAAATAACT
1252772 AC
1 AC
1252774 ATATTTACCT
Statistics
Matches: 166, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
176 166 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.26
Consensus pattern (176 bp):
ACTTTCAATAACAACAGCAATAATGTTAAAATCACCTCCAATGAGCCAAACACTACTTCCAACAA
GAGAATCAACAGAAGTAAGTTGATACCATAGTTCCCTCCTAACATATTTACCTCCCAAAATACCT
TGAAATAACTATCCCATTATTACTACCATACACAGTAGAAATAACT
Found at i:1258295 original size:66 final size:66
Alignment explanation
Indices: 1258179--1258303 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
1258169 GTCCCTTTTT
* *
1258179 TTCTTCTGGTTGGTGGGTACAGCTTCTCTCCCACGTTCCTCAGTAACAGTCGACTCGTTGGTGTT
1 TTCTTCGGGTTGGTGGGTACAGCTTCTCTCCCACGTCCCTCAGTAACAGTCGACTCGTTGGTGTT
1258244 C
66 C
* * * *
1258245 TTCTTCGGGTTGGTGGGTACAGTTTCTTTCCCACGTCCCTCGGTAGCAGTCGACTCGTT
1 TTCTTCGGGTTGGTGGGTACAGCTTCTCTCCCACGTCCCTCAGTAACAGTCGACTCGTT
1258304 CGAGTTCCCG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.11, C:0.27, G:0.26, T:0.36
Consensus pattern (66 bp):
TTCTTCGGGTTGGTGGGTACAGCTTCTCTCCCACGTCCCTCAGTAACAGTCGACTCGTTGGTGTT
C
Found at i:1259041 original size:23 final size:21
Alignment explanation
Indices: 1259015--1259091 Score: 77
Period size: 24 Copynumber: 3.5 Consensus size: 21
1259005 GTTTGCGAAA
1259015 ATGTTCGTTTAATGTTCACGAGC
1 ATGTTCGTTTAATGTT-ACGA-C
* *
1259038 ATGTTCGTTTATATGTTTGCGAAA
1 ATGTTCGTTTA-ATG-TTACG-AC
1259062 ATGTTCGTTTAATGTTA--AC
1 ATGTTCGTTTAATGTTACGAC
1259081 ATGTTCGTTTA
1 ATGTTCGTTTA
1259092 TATATTCAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
19 12 0.26
22 2 0.04
23 14 0.30
24 16 0.34
25 3 0.06
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.45
Consensus pattern (21 bp):
ATGTTCGTTTAATGTTACGAC
Found at i:1259053 original size:47 final size:43
Alignment explanation
Indices: 1258994--1259094 Score: 166
Period size: 47 Copynumber: 2.3 Consensus size: 43
1258984 AAGGTGTTCA
1258994 TTCGTTTATATGTTTGCGAAAATGTTCGTTTAATGTTCACGAGCATG
1 TTCGTTTATATGTTTGCGAAAATGTTCGTTTAATGTT-A--A-CATG
1259041 TTCGTTTATATGTTTGCGAAAATGTTCGTTTAATGTTAACATG
1 TTCGTTTATATGTTTGCGAAAATGTTCGTTTAATGTTAACATG
1259084 TTCGTTTATAT
1 TTCGTTTATAT
1259095 ATTCAGAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
43 15 0.28
44 1 0.02
46 1 0.02
47 37 0.69
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.47
Consensus pattern (43 bp):
TTCGTTTATATGTTTGCGAAAATGTTCGTTTAATGTTAACATG
Found at i:1259065 original size:24 final size:23
Alignment explanation
Indices: 1258994--1259077 Score: 114
Period size: 24 Copynumber: 3.6 Consensus size: 23
1258984 AAGGTGTTCA
1258994 TTCGTTTATATGTTTGCGAAAATG
1 TTCGTTTA-ATGTTTGCGAAAATG
** **
1259018 TTCGTTTAATGTTCACGAGCATG
1 TTCGTTTAATGTTTGCGAAAATG
1259041 TTCGTTTATATGTTTGCGAAAATG
1 TTCGTTTA-ATGTTTGCGAAAATG
1259065 TTCGTTTAATGTT
1 TTCGTTTAATGTT
1259078 AACATGTTCG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
23 24 0.47
24 27 0.53
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (23 bp):
TTCGTTTAATGTTTGCGAAAATG
Found at i:1266500 original size:19 final size:19
Alignment explanation
Indices: 1266451--1266507 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1266441 TTCTTTTTAC
1266451 ATTTATAATTTAA-TGAAT
1 ATTTATAATTTAATTGAAT
* *
1266469 ATATATAATTTTAATTGAGT
1 ATTTATAA-TTTAATTGAAT
*
1266489 ATTTTTAATTTAATT-AAT
1 ATTTATAATTTAATTGAAT
1266507 A
1 A
1266508 ATTTTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 10 0.31
19 12 0.38
20 10 0.31
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTTATAATTTAATTGAAT
Found at i:1266662 original size:18 final size:18
Alignment explanation
Indices: 1266614--1266662 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1266604 TATAAACTAG
1266614 TATTTAAA-ATATATTTA
1 TATTTAAATATATATTTA
*
1266631 TA-TAAATATATATATTTA
1 TATTTAA-ATATATATTTA
*
1266649 TATTTAAATGTATA
1 TATTTAAATATATA
1266663 AAAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 17 0.65
19 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TATTTAAATATATATTTA
Found at i:1266670 original size:29 final size:30
Alignment explanation
Indices: 1266629--1266687 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
1266619 AAAATATATT
*
1266629 TATATAAATATATATATT-TATATTTAAATG
1 TATATAAAAATATAT-TTATATATTTAAATG
1266659 TATA-AAAAATATATTTATATATTTAAATG
1 TATATAAAAATATATTTATATATTTAAATG
1266688 GATGAATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 2 0.07
29 21 0.78
30 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (30 bp):
TATATAAAAATATATTTATATATTTAAATG
Found at i:1267009 original size:19 final size:19
Alignment explanation
Indices: 1266981--1267021 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1266971 AATCTCATCA
1266981 TTTTCATTTTTCT-TTCTTT
1 TTTTCATTTTTCTATT-TTT
*
1267000 TTTTCTTTTTTCTATTTTT
1 TTTTCATTTTTCTATTTTT
1267019 TTT
1 TTT
1267022 GGGCATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTCATTTTTCTATTTTT
Found at i:1267124 original size:13 final size:13
Alignment explanation
Indices: 1267108--1267133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1267098 ATTTTAACCA
1267108 ACTTTTTTTGGAT
1 ACTTTTTTTGGAT
1267121 ACTTTTTTTGGAT
1 ACTTTTTTTGGAT
1267134 TTACCAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
ACTTTTTTTGGAT
Found at i:1267319 original size:21 final size:21
Alignment explanation
Indices: 1267254--1267324 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
1267244 GATTTACATA
*
1267254 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* *
1267275 TTCGCGATT----TATTCCAAG
1 TTCGCG-TTGCGATAGTCGAAG
1267293 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
1267312 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1267325 TTATTCTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
18 9 0.24
19 9 0.24
21 14 0.37
22 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:1267340 original size:21 final size:21
Alignment explanation
Indices: 1267278--1267366 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
1267268 GTCGAAGTTC
*
1267278 GCGATTTATTCCAAGTTCGTT
1 GCGATTTATTCCAAATTCGTT
* * *
1267299 GCGA--TAGTCGAAGTTCGCGTT
1 GCGATTTATTCCAAATT--CGTT
*
1267320 GCGATTTATTCTAAATTCGTT
1 GCGATTTATTCCAAATTCGTT
* *
1267341 GTGATTTATTCCAAGTTCGTT
1 GCGATTTATTCCAAATTCGTT
1267362 GCGAT
1 GCGAT
1267367 AGTCCAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
19 9 0.16
21 38 0.69
23 8 0.15
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.40
Consensus pattern (21 bp):
GCGATTTATTCCAAATTCGTT
Found at i:1268004 original size:6 final size:5
Alignment explanation
Indices: 1267956--1268000 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
1267946 CCGTCTCGTC
1267956 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
1268001 TGGTAGTTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 28 0.72
6 11 0.28
ACGTcount: A:0.00, C:0.20, G:0.56, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:1268032 original size:21 final size:20
Alignment explanation
Indices: 1268005--1268122 Score: 141
Period size: 21 Copynumber: 5.7 Consensus size: 20
1267995 TGGTCGTGGT
*
1268005 AGTTCGCATTGCGATAGTCG
1 AGTTCGCATTGCGATAGTCA
* *
1268025 ACTATCGCATTGCGAT-TTACA
1 AGT-TCGCATTGCGATAGT-CA
1268046 TA-TTCGCATTGCGATAGTCCA
1 -AGTTCGCATTGCGATAGT-CA
1268067 AGTTCGCATTGCGATAGTTCA
1 AGTTCGCATTGCGATAG-TCA
1268088 AGTTCGCATTGCGATAGTCGA
1 AGTTCGCATTGCGATAGTC-A
1268109 AGTTCGCATTGCGA
1 AGTTCGCATTGCGA
1268123 ATCTGGAAAC
Statistics
Matches: 86, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
20 18 0.21
21 66 0.77
22 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (20 bp):
AGTTCGCATTGCGATAGTCA
Found at i:1268105 original size:42 final size:42
Alignment explanation
Indices: 1268004--1268122 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
1267994 GTGGTCGTGG
* *
1268004 TAGTTCGCATTGCGATAGT-CGACTATCGCATTGCGATTTACA
1 TAGTTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATTTACA
1268046 TA-TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTT-CA
1 TAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGAT--TTACA
*
1268088 -AGTTCGCATTGCGATAGTCGAAGTTCGCATTGCGA
1 TAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGA
1268123 ATCTGGAAAC
Statistics
Matches: 70, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
41 29 0.41
42 39 0.56
43 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (42 bp):
TAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACA
Found at i:1269258 original size:25 final size:25
Alignment explanation
Indices: 1269226--1269275 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1269216 TATACTTTAC
1269226 CCATAATATAAATACTTTAATTCTA
1 CCATAATATAAATACTTTAATTCTA
*
1269251 CCATAATATAAATCCTTTAATTCTA
1 CCATAATATAAATACTTTAATTCTA
1269276 TAACCCTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (25 bp):
CCATAATATAAATACTTTAATTCTA
Found at i:1272473 original size:91 final size:91
Alignment explanation
Indices: 1272316--1272484 Score: 234
Period size: 91 Copynumber: 1.9 Consensus size: 91
1272306 AAAACTCATG
* * * *
1272316 TAACATTCTCGGTTGTAACCGGAATTACTATCAATTGTGTAACTTTTTAAAGTAGACAATGTAAC
1 TAACATTCTCGATTGTAACCGAAATTACTATCAATTGTATAACTTTTTAAAGTAGACAATGCAAC
1272381 ATTTTAGGTTAAAACTCATCGCAATA
66 ATTTTAGGTTAAAACTCATCGCAATA
* * *
1272407 TAACATTTTCGATTTTAACCGAAATTATTATCAATTGTATAACTTTTTAGAA-TAGACAA-GACA
1 TAACATTCTCGATTGTAACCGAAATTACTATCAATTGTATAACTTTTTA-AAGTAGACAATG-CA
*
1272470 ACATTTTATGTTAAA
64 ACATTTTAGGTTAAA
1272485 CCCATAGTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 65 0.96
92 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (91 bp):
TAACATTCTCGATTGTAACCGAAATTACTATCAATTGTATAACTTTTTAAAGTAGACAATGCAAC
ATTTTAGGTTAAAACTCATCGCAATA
Found at i:1273955 original size:12 final size:12
Alignment explanation
Indices: 1273938--1273984 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
1273928 GCATTGTTAG
*
1273938 AGTCGGAGGAGA
1 AGTCAGAGGAGA
*
1273950 AGTCGGAGGAGA
1 AGTCAGAGGAGA
1273962 AG--AG-GGAGA
1 AGTCAGAGGAGA
1273971 AGTCAGAGGAGA
1 AGTCAGAGGAGA
1273983 AG
1 AG
1273985 AGGAGGAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 7 0.23
10 1 0.03
11 2 0.06
12 21 0.68
ACGTcount: A:0.38, C:0.06, G:0.49, T:0.06
Consensus pattern (12 bp):
AGTCAGAGGAGA
Found at i:1273969 original size:21 final size:21
Alignment explanation
Indices: 1273945--1273987 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1273935 TAGAGTCGGA
*
1273945 GGAGAAGTCGGAGGAGAAGAG
1 GGAGAAGTCAGAGGAGAAGAG
1273966 GGAGAAGTCAGAGGAGAAGAG
1 GGAGAAGTCAGAGGAGAAGAG
1273987 G
1 G
1273988 AGGAACGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.51, T:0.05
Consensus pattern (21 bp):
GGAGAAGTCAGAGGAGAAGAG
Found at i:1279807 original size:17 final size:17
Alignment explanation
Indices: 1279785--1279829 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
1279775 AACGGTCAAC
1279785 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1279802 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1279819 GGTCAACGGTC
1 GGTCAACGGTC
1279830 AGAACCGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.13, C:0.24, G:0.44, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1286476 original size:13 final size:13
Alignment explanation
Indices: 1286460--1286485 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1286450 ATATTAAAAC
1286460 CAATAAAACAGTT
1 CAATAAAACAGTT
1286473 CAATAAAACAGTT
1 CAATAAAACAGTT
1286486 TTCGAATGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
CAATAAAACAGTT
Found at i:1286992 original size:17 final size:17
Alignment explanation
Indices: 1286970--1287007 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1286960 AACGGTCAAC
1286970 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1286987 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1287004 GGTC
1 GGTC
1287008 GGGTCAGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1286997 original size:7 final size:7
Alignment explanation
Indices: 1286950--1286980 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1286940 GTCAAAGAAA
1286950 GTCAACG
1 GTCAACG
1286957 GTCAACG
1 GTCAACG
1286964 GTCAACG
1 GTCAACG
1286971 GTCAACG
1 GTCAACG
1286978 GTC
1 GTC
1286981 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1287005 original size:22 final size:23
Alignment explanation
Indices: 1286963--1287018 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
1286953 AACGGTCAAC
1286963 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC-ACGGTCGGGTCG
*
1286987 GGTCAACGGTC-GGGTCGGGTCG
1 GGTCAACGGTCACGGTCGGGTCG
1287009 GGTCAGACGG
1 GGTCA-ACGG
1287019 GTCAAATCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 15 0.50
23 4 0.13
24 11 0.37
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.16
Consensus pattern (23 bp):
GGTCAACGGTCACGGTCGGGTCG
Found at i:1287028 original size:19 final size:19
Alignment explanation
Indices: 1287006--1287043 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1286996 TCGGGTCGGG
* *
1287006 TCGGGTCAGACGGGTCAAA
1 TCGGCTCAGACCGGTCAAA
1287025 TCGGCTCAGACCGGTCAAA
1 TCGGCTCAGACCGGTCAAA
1287044 CCGGTTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (19 bp):
TCGGCTCAGACCGGTCAAA
Found at i:1288636 original size:12 final size:11
Alignment explanation
Indices: 1288609--1288658 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
1288599 TGTTAGATTC
*
1288609 GGAGGAGAAGTC
1 GGAGGAGAAG-A
1288621 GGAGGAGAAGA
1 GGAGGAGAAGA
*
1288632 -G-GGAGAAATA
1 GGAGGAG-AAGA
1288642 GGAGGAGAAGA
1 GGAGGAGAAGA
1288653 GGAGGA
1 GGAGGA
1288659 ACGAAGGAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 10 0.31
12 14 0.44
ACGTcount: A:0.42, C:0.02, G:0.52, T:0.04
Consensus pattern (11 bp):
GGAGGAGAAGA
Found at i:1288636 original size:21 final size:21
Alignment explanation
Indices: 1288612--1288654 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1288602 TAGATTCGGA
* *
1288612 GGAGAAGTCGGAGGAGAAGAG
1 GGAGAAATAGGAGGAGAAGAG
1288633 GGAGAAATAGGAGGAGAAGAG
1 GGAGAAATAGGAGGAGAAGAG
1288654 G
1 G
1288655 AGGAACGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.51, T:0.05
Consensus pattern (21 bp):
GGAGAAATAGGAGGAGAAGAG
Found at i:1290077 original size:73 final size:76
Alignment explanation
Indices: 1289958--1290106 Score: 250
Period size: 73 Copynumber: 2.0 Consensus size: 76
1289948 GCTCATGTTC
*
1289958 GTTTGTTTATTTGAGAAAATATTAATGTTTGATTCGTATTCATTTAATTTTTTA-TATTGTGTTC
1 GTTTGTTTATTTGAGAAAATATTAATGTTTGATTCGTATTCATTTAATTTTTTAGTATTGTATTC
1290022 GT-TT-GTTTG
66 GTGTTCGTTTG
**
1290031 GTTTGTTTATTTGAGAAGGTATTAATGTTTGATTCGTATTCATTTAATTTTTTAGTATTGTATTC
1 GTTTGTTTATTTGAGAAAATATTAATGTTTGATTCGTATTCATTTAATTTTTTAGTATTGTATTC
1290096 GTGTTCGTTTG
66 GTGTTCGTTTG
1290107 TATAGTGTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
73 52 0.74
74 11 0.16
75 2 0.03
76 5 0.07
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.56
Consensus pattern (76 bp):
GTTTGTTTATTTGAGAAAATATTAATGTTTGATTCGTATTCATTTAATTTTTTAGTATTGTATTC
GTGTTCGTTTG
Found at i:1294990 original size:35 final size:35
Alignment explanation
Indices: 1294943--1295038 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
1294933 AACATATTCA
*
1294943 TCAATTACATTCTAAACCGCAAAATT-CAAAATGCT
1 TCAATTACATTCTAAACCGC-AAATTCCAAAATACT
* *
1294978 TCAATT-CTATTCTAAACCTCAACTTCCAAAATACT
1 TCAATTAC-ATTCTAAACCGCAAATTCCAAAATACT
* * *
1295013 TCAATTACATGCTCAACCCCAAATTC
1 TCAATTACATTCTAAACCGCAAATTC
1295039 ATAATTCATT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
34 5 0.10
35 45 0.88
36 1 0.02
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.30
Consensus pattern (35 bp):
TCAATTACATTCTAAACCGCAAATTCCAAAATACT
Found at i:1295386 original size:148 final size:148
Alignment explanation
Indices: 1295196--1295491 Score: 495
Period size: 148 Copynumber: 2.0 Consensus size: 148
1295186 CTTAAATACA
1295196 CAATTCAATTTATAAAATAGTTGACTCAAACTTTTTTCGATTTGAGTTTATAAAATTTAAATCAA
1 CAATTCAATTTATAAAATAGTTGACTCAAACTTTTTTCGATTTGAGTTTATAAAATTTAAATCAA
* * * *
1295261 GTCGAATTGAATTAAATTTTCGAGTTTTTGTTTAAATTTAATTATAAATATTTATCATATTATAA
66 GACGAATTGAATTAAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATAATATAA
*
1295326 TATTATTTTATTATAATT
131 TATTATATTATTATAATT
* *
1295344 CAATTCATTTTATAAAATAGTTGACTCGAAA-TTTTTTTGATTTGAGTTTATAAAATTTAAATCA
1 CAATTCAATTTATAAAATAGTTGACTC-AAACTTTTTTCGATTTGAGTTTATAAAATTTAAATCA
* *
1295408 AGACGAATTGAATTGAATTTTTGAGTTTATGTTTAAATTTAATTATAAATATTTATAATAATATA
65 AGACGAATTGAATTAAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATAATATA
1295473 ATATTATATTATTATAATT
130 ATATTATATTATTATAATT
1295492 TAAATAGTTT
Statistics
Matches: 138, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
148 135 0.98
149 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (148 bp):
CAATTCAATTTATAAAATAGTTGACTCAAACTTTTTTCGATTTGAGTTTATAAAATTTAAATCAA
GACGAATTGAATTAAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATAATATAA
TATTATATTATTATAATT
Found at i:1295466 original size:16 final size:17
Alignment explanation
Indices: 1295447--1295489 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1295437 TGTTTAAATT
1295447 TAATTATAAATATT-TA
1 TAATTATAAATATTATA
*
1295463 TAATAATATAATATTATA
1 TAATTATA-AATATTATA
*
1295481 TTATTATAA
1 TAATTATAA
1295490 TTTAAATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 7 0.32
17 7 0.32
18 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTATAAATATTATA
Found at i:1295490 original size:16 final size:17
Alignment explanation
Indices: 1295449--1295490 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1295439 TTTAAATTTA
1295449 ATTATAAATATTTATAAT
1 ATTAT-AATATTTATAAT
* *
1295467 AATATAATA-TTATATT
1 ATTATAATATTTATAAT
1295483 ATTATAAT
1 ATTATAAT
1295491 TTAAATAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 4 0.19
18 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATAATATTTATAAT
Found at i:1296030 original size:36 final size:36
Alignment explanation
Indices: 1295973--1296058 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
1295963 AATGGATAAT
** * *
1295973 GAATTTTGGGTTGGGCA-TGTAATTGAAGTATTTTTT
1 GAATTTTGGGTTTAG-AGTGTAATTGAAGCATTTTTG
1296009 GAA-TTTGAGGTTTAGAGTGTAATTGAAGCATTTTTG
1 GAATTTTG-GGTTTAGAGTGTAATTGAAGCATTTTTG
1296045 GAATTTTGGGTTTA
1 GAATTTTGGGTTTA
1296059 TAAATTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
35 5 0.12
36 34 0.79
37 4 0.09
ACGTcount: A:0.24, C:0.02, G:0.28, T:0.45
Consensus pattern (36 bp):
GAATTTTGGGTTTAGAGTGTAATTGAAGCATTTTTG
Found at i:1296068 original size:36 final size:36
Alignment explanation
Indices: 1295989--1296068 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
1295979 TGGGTTGGGC
* * *
1295989 ATGTAATTGAAGTATTTTTTGAATTTGAGGTTTAGA
1 ATGTAATTGAAGCATTTTTGGAATTTGAGGTTTAAA
*
1296025 GTGTAATTGAAGCATTTTTGGAATTTTG-GGTTTATAA
1 ATGTAATTGAAGCATTTTTGGAA-TTTGAGGTTTA-AA
1296062 AT-TAATT
1 ATGTAATT
1296069 AATGACTGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.47
Consensus pattern (36 bp):
ATGTAATTGAAGCATTTTTGGAATTTGAGGTTTAAA
Found at i:1303774 original size:21 final size:21
Alignment explanation
Indices: 1303711--1303967 Score: 219
Period size: 20 Copynumber: 12.6 Consensus size: 21
1303701 TTTTCCTAAT
1303711 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
1303731 TCGCAACGCG-TTTACGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
1303751 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGTAAA
1303772 TCGCAATGCG-A-TA-GTCAGAA
1 TCGCAATGCGAATTACGT-A-AA
* * * * * *
1303792 TCGCATTACGATTTTCCTAAT
1 TCGCAATGCGAATTACGTAAA
* * *
1303813 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGAATTACGTAAA
** * * * *
1303833 TCGCGTTGCGATTTTCCTAAT
1 TCGCAATGCGAATTACGTAAA
1303854 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGTAAA
1303874 TCGCAATGCG-ATTACGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
1303894 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGTAAA
*
1303915 TCGCAATGC-AAATACGTAAA
1 TCGCAATGCGAATTACGTAAA
1303935 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGTAAA
*
1303955 TCGCAATGTGAAT
1 TCGCAATGCGAAT
1303968 CTGACTATCG
Statistics
Matches: 194, Mismatches: 31, Indels: 23
0.78 0.12 0.09
Matches are distributed among these distances:
18 1 0.01
19 4 0.02
20 123 0.63
21 63 0.32
22 2 0.01
23 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGAATTACGTAAA
Found at i:1303794 original size:41 final size:40
Alignment explanation
Indices: 1303711--1303967 Score: 115
Period size: 41 Copynumber: 6.3 Consensus size: 40
1303701 TTTTCCTAAT
* *
1303711 TCGCAATGCGAATACGTAAATCGCAACGCGTTTACGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCGTATACGTAAA
* *
1303751 TCGCAATGCGAATTAGGAAAATCGCAATGCG-ATA-GTCAGAA
1 TCGCAATGCGAA-TACGAAAATCGCAACGCGTATACGT-A-AA
* * * * ** * ** * *
1303792 TCGCATTACGATTTTCCTAATTCGCATTGCGATTTACGT-AT
1 TCGCAATGCGA-ATACGAAAATCGCAACGCG-TATACGTAAA
** * * ** * * *
1303833 TCGCGTTGCGATTTTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGA-ATACGAAAATCGCAACGCGTATACGTAAA
* * * * * *
1303874 TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCGTA-TACGTAAA
* * * *
1303915 TCGCAATGCAAATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCGTATACGTAAA
*
1303955 TCGCAATGTGAAT
1 TCGCAATGCGAAT
1303968 CTGACTATCG
Statistics
Matches: 174, Mismatches: 34, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
39 2 0.01
40 55 0.32
41 113 0.65
43 2 0.01
44 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAACGCGTATACGTAAA
Found at i:1303794 original size:61 final size:61
Alignment explanation
Indices: 1303711--1303967 Score: 186
Period size: 61 Copynumber: 4.2 Consensus size: 61
1303701 TTTTCCTAAT
*** * *
1303711 TCGCAATGCGAATACGT-AAATCGCAACGCGTTTACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATA-GTCAAATCGCAACGCAAATACGTAAATCGCAATGCGAATTACGTAAA
** * * * * * *
1303772 TCGCAATGCG-ATAGTCAGAATCGCATTACG-ATTTTCCTAATTCGCATTGCGATTTACGT-AT
1 TCGCAATGCGAATAGTCA-AATCGCA--ACGCAAATACGTAAATCGCAATGCGAATTACGTAAA
** ** * * *
1303833 TCGCGTTGCG-ATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAATGCG-ATTACGTAAA
1 TCGCAATGCGAATAGT-C-AAATCGCAACGCAAATACGTAAATCGCAATGCGAATTACGTAAA
** *
1303894 TCGCAATGCGAATTAGGAAAATCGCAATGCAAATACGTAAATCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAA-TAGTCAAATCGCAACGCAAATACGTAAATCGCAATGCGAATTACGTAAA
*
1303955 TCGCAATGTGAAT
1 TCGCAATGCGAAT
1303968 CTGACTATCG
Statistics
Matches: 152, Mismatches: 33, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
59 2 0.01
60 13 0.09
61 102 0.67
62 30 0.20
63 5 0.03
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (61 bp):
TCGCAATGCGAATAGTCAAATCGCAACGCAAATACGTAAATCGCAATGCGAATTACGTAAA
Found at i:1304599 original size:19 final size:19
Alignment explanation
Indices: 1304519--1304625 Score: 133
Period size: 20 Copynumber: 5.5 Consensus size: 19
1304509 TTCTAAACTT
**
1304519 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
1304539 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
*
1304559 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
1304579 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
1304598 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
1304617 AAAATCGCA
1 AAAATCGCA
1304626 TTGTGATTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
19 31 0.39
20 49 0.61
ACGTcount: A:0.51, C:0.21, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1304711 original size:20 final size:19
Alignment explanation
Indices: 1304630--1304719 Score: 135
Period size: 20 Copynumber: 4.6 Consensus size: 19
1304620 ATCGCATTGT
1304630 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
1304649 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
**
1304668 GATAGTCATTTCCGCGTTGC
1 GATTTTCATTT-CGCGTTGC
*
1304688 GATTTTCATTCTCTCGTTGC
1 GATTTTCATT-TCGCGTTGC
1304708 GATTTTCATTTC
1 GATTTTCATTTC
1304720 AACCAAAAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 30 0.47
20 33 0.52
21 1 0.02
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:1306555 original size:94 final size:94
Alignment explanation
Indices: 1306398--1306773 Score: 593
Period size: 94 Copynumber: 4.1 Consensus size: 94
1306388 TAGATTGCTT
* * * *
1306398 AGTAAATTTATTCGGTTGCTGTCAATACTGCT-AAA-CTGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAGT
1306459 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
1306488 AGTAAATTTATTCGGTTGCTGCCAATTCTGTTAAAATGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAGT
1306553 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1306582 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAGT
1306647 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
1306676 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAGT
1306741 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1306769 AGTAA
1 AGTAA
1306774 TGCAATCCAT
Statistics
Matches: 270, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
90 29 0.11
91 3 0.01
92 3 0.01
93 28 0.10
94 207 0.77
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1306943 original size:33 final size:33
Alignment explanation
Indices: 1306864--1306933 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1306854 TCTTTTGGTT
* * *
1306864 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGACAAAATCACAACGC
1306897 GAAATGAAAATCGCAACGACAAAATCACAACGC
1 GAAATGAAAATCGCAACGACAAAATCACAACGC
1306930 GAAA
1 GAAA
1306934 CTATAATCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.50, C:0.21, G:0.20, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGACAAAATCACAACGC
Found at i:1307025 original size:20 final size:19
Alignment explanation
Indices: 1306940--1307052 Score: 127
Period size: 19 Copynumber: 5.8 Consensus size: 19
1306930 GAAACTATAA
*
1306940 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
1306959 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
* *
1306978 TCGTGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
1306997 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
1307016 CTCTCGTTGCGATAGTCATTTT
1 -TCGCGTTGCGATTTTCA--TT
*
1307038 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
1307053 AAGTTCCAGA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 51 0.65
20 14 0.18
21 12 0.15
22 2 0.03
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.49
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1307529 original size:21 final size:21
Alignment explanation
Indices: 1307505--1307571 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1307495 TCATTCCTCG
1307505 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
1307526 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
1307547 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
1307568 AGAG
1 AGAG
1307572 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:1307529 original size:42 final size:42
Alignment explanation
Indices: 1307483--1307571 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
1307473 CCTATCGTTG
*
1307483 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
1307525 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
1307567 AAGAG
1 AAGAG
1307572 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.10
42 35 0.85
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:1308907 original size:14 final size:14
Alignment explanation
Indices: 1308888--1308923 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1308878 ATTGTTTAAT
1308888 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1308902 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1308916 TGATTTGT
1 TGATTTGT
1308924 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1309114 original size:33 final size:33
Alignment explanation
Indices: 1309072--1309264 Score: 332
Period size: 33 Copynumber: 5.8 Consensus size: 33
1309062 ACTAAATTCG
* *
1309072 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1309105 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* * *
1309138 CGTTGCGATTTTCATTTCGCTTTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1309171 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1309204 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1309237 CGTTACGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1309265 AGTCATTTCC
Statistics
Matches: 151, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 151 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1309283 original size:20 final size:19
Alignment explanation
Indices: 1309248--1309291 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1309238 GTTACGATTT
1309248 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
*
1309267 TCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
*
1309287 ACATT
1 TCATT
1309292 AAGATGATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1309330 original size:20 final size:20
Alignment explanation
Indices: 1309258--1309330 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
1309248 TCATTTCGCA
* *
1309258 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTACGTG
* *
1309278 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTACG-TG
*
1309298 ATTGCGA-ACGTCATTTTCGTG
1 -TTGCGATA-GTCATTTACGTG
1309319 TTGCGATAGTCA
1 TTGCGATAGTCA
1309331 AATGAATGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTACGTG
Found at i:1311836 original size:24 final size:24
Alignment explanation
Indices: 1311802--1311855 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1311792 CTGAAAAATC
1311802 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1311826 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1311850 ATCAAA
1 ATCAAA
1311856 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1311869 original size:24 final size:24
Alignment explanation
Indices: 1311802--1311869 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1311792 CTGAAAAATC
* * *
1311802 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1311826 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1311850 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1311870 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1312756 original size:21 final size:20
Alignment explanation
Indices: 1312717--1312787 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1312707 CAGAATCTCG
*
1312717 TTGCAATTTA-CTAAATCGCA
1 TTGCGATTTACCT-AATCGCA
* *
1312737 TTGCGGTTTTCCTAATTCGCA
1 TTGCGATTTACCTAA-TCGCA
* *
1312758 TTGTGATTTACGTAATCGCA
1 TTGCGATTTACCTAATCGCA
1312778 TTGCGATTTA
1 TTGCGATTTA
1312788 GGAAAATCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 23 0.56
21 18 0.44
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACCTAATCGCA
Found at i:1312797 original size:21 final size:20
Alignment explanation
Indices: 1312771--1312826 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
1312761 TGATTTACGT
*
1312771 AATCGCATTGCGATTTAGGAA
1 AATCGCAATGCGATTTAGG-A
* *
1312792 AATCGCAACGCGAATTTGGGA
1 AATCGCAATGCG-ATTTAGGA
1312813 AATCGCAATGCGAT
1 AATCGCAATGCGAT
1312827 AGTCAGAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 22 0.73
22 6 0.20
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGATTTAGGA
Done.