Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009576.1 Hibiscus syriacus cultivar Beakdansim tig00116944_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: 1684752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1025493 original size:23 final size:23
Alignment explanation
Indices: 1025457--1025507 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1025447 GGAATCGATA
1025457 CCCC-TTGAAGGGGAACCGATTT
1 CCCCTTTGAAGGGGAACCGATTT
*
1025479 CCCCTTTGAATGGGAACCGATTT
1 CCCCTTTGAAGGGGAACCGATTT
1025502 CCCCTT
1 CCCCTT
1025508 ACGGGTTCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.27
Consensus pattern (23 bp):
CCCCTTTGAAGGGGAACCGATTT
Found at i:1027727 original size:24 final size:24
Alignment explanation
Indices: 1027688--1027745 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
1027678 TCCAGAGGGA
1027688 ACCGATT--CCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCCAAGGGGGT
1027710 ACCGATTCCCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCCAAGGGGGT
1027734 ACCGATTCCCCC
1 ACCGATTCCCCC
1027746 TGAATGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 7 0.21
24 27 0.79
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (24 bp):
ACCGATTCCCCCCCCCAAGGGGGT
Found at i:1027824 original size:23 final size:23
Alignment explanation
Indices: 1027787--1027843 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1027777 CTCGAAGGGA
1027787 ACCGATT-CCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCAAGGGGGT
1027809 ACCGATTCCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCAAGGGGGT
1027832 ACCGATTCCCCC
1 ACCGATTCCCCC
1027844 TGAATGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 7 0.21
23 27 0.79
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.14
Consensus pattern (23 bp):
ACCGATTCCCCCCCCAAGGGGGT
Found at i:1027897 original size:99 final size:98
Alignment explanation
Indices: 1027683--1027917 Score: 454
Period size: 98 Copynumber: 2.4 Consensus size: 98
1027673 GATTGTCCAG
1027683 AGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCCCCCAAGGGGGTACCGATTCCCCCTG
1 AGGGAACCGATTCCCCCCCAAGGGGGTACCGATT-CCCCCCCCAAGGGGGTACCGATTCCCCCTG
1027748 AATGGTTTGGCTCCGAGAAAAACAGAATGCTCGA
65 AATGGTTTGGCTCCGAGAAAAACAGAATGCTCGA
1027782 AGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCCCCAAGGGGGTACCGATTCCCCCTGA
1 AGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCCCCAAGGGGGTACCGATTCCCCCTGA
1027847 ATGGTTTGGCTCCGAGAAAAACAGAATGCTCGA
66 ATGGTTTGGCTCCGAGAAAAACAGAATGCTCGA
1027880 AGGGAACCGATT-CCCCCCAAGGGGGTACCGATTCCCCC
1 AGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCC
1027918 TGATCAACGG
Statistics
Matches: 136, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
97 26 0.19
98 76 0.56
99 34 0.25
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (98 bp):
AGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCCCCAAGGGGGTACCGATTCCCCCTGA
ATGGTTTGGCTCCGAGAAAAACAGAATGCTCGA
Found at i:1030973 original size:21 final size:21
Alignment explanation
Indices: 1030900--1030975 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
1030890 TAGAATTTGC
*
1030900 CCCGAATGAACACATATATGT
1 CCCGAATGACCACATATATGT
* * * * *
1030921 CTCGAAAGACAACATAGATAT
1 CCCGAATGACCACATATATGT
*
1030942 CTCGAATGACCACATATATGT
1 CCCGAATGACCACATATATGT
*
1030963 CCCGAAGGACCAC
1 CCCGAATGACCAC
1030976 TCCTTAAGGA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (21 bp):
CCCGAATGACCACATATATGT
Found at i:1031269 original size:31 final size:30
Alignment explanation
Indices: 1031234--1031294 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
1031224 CATGTCACAT
1031234 ATTCACA-TATTCATATCACATAAGCATGTAA
1 ATTCACAGT-TTCATATCACATAA-CATGTAA
* * *
1031265 ATTCATAGTTTCTTATCACGTAACATGTAA
1 ATTCACAGTTTCATATCACATAACATGTAA
1031295 TACATACAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 7 0.27
31 18 0.69
32 1 0.04
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (30 bp):
ATTCACAGTTTCATATCACATAACATGTAA
Found at i:1034024 original size:20 final size:21
Alignment explanation
Indices: 1033970--1034032 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1033960 TATTCCCCTG
1033970 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1033994 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1034014 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1034033 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1037819 original size:22 final size:21
Alignment explanation
Indices: 1037777--1037816 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1037767 GAGTTTGTTT
*
1037777 TCATTTTTGAATTTTGAAACA
1 TCATTTTTGAATTTTAAAACA
1037798 TCATTTTT-ATATTTTAAAA
1 TCATTTTTGA-ATTTTAAAA
1037817 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTGAATTTTAAAACA
Found at i:1040825 original size:21 final size:20
Alignment explanation
Indices: 1040801--1040848 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1040791 AAATATTATG
* *
1040801 TACTTTAACTATGTATTTTTT
1 TACTATAACTATG-ACTTTTT
1040822 TACTATAACTATGACTTTTT
1 TACTATAACTATGACTTTTT
1040842 TAACTAT
1 T-ACTAT
1040849 GTTTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (20 bp):
TACTATAACTATGACTTTTT
Found at i:1040856 original size:14 final size:15
Alignment explanation
Indices: 1040827--1040860 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1040817 TTTTTTACTA
1040827 TAACTATGACTTTTT
1 TAACTATGACTTTTT
*
1040842 TAACTATG-TTTTTT
1 TAACTATGACTTTTT
1040856 TAACT
1 TAACT
1040861 TGTATTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (15 bp):
TAACTATGACTTTTT
Found at i:1041394 original size:19 final size:18
Alignment explanation
Indices: 1041365--1041405 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 18
1041355 AATTAAAGAT
1041365 TTTTCATTTGTCTTTACATA
1 TTTTCATTTG--TTTACATA
1041385 TTTT-ATTTGTTTACATA
1 TTTTCATTTGTTTACATA
1041402 TTTT
1 TTTT
1041406 TTAAAGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.57
19 5 0.24
20 4 0.19
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTCATTTGTTTACATA
Found at i:1041407 original size:19 final size:20
Alignment explanation
Indices: 1041363--1041408 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
1041353 TTAATTAAAG
*
1041363 ATTTTTCATTTGTCTTTACAT
1 ATTTTTTATTTG-CTTTACAT
1041384 A--TTTTATTTG-TTTACAT
1 ATTTTTTATTTGCTTTACAT
1041401 ATTTTTTA
1 ATTTTTTA
1041409 AAGTTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 8 0.36
19 13 0.59
21 1 0.05
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (20 bp):
ATTTTTTATTTGCTTTACAT
Found at i:1043045 original size:29 final size:29
Alignment explanation
Indices: 1043006--1043072 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
1042996 ATGTGGCTCT
* *
1043006 TCATTCGTCATTTCTCGATGATGAATGGC
1 TCATTCTTCATTTCTCGATGACGAATGGC
1043035 TCATTCTTCATTTCTCGATGACGAATGGC
1 TCATTCTTCATTTCTCGATGACGAATGGC
1043064 TCATTCTTC
1 TCATTCTTC
1043073 TCGCTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.40
Consensus pattern (29 bp):
TCATTCTTCATTTCTCGATGACGAATGGC
Found at i:1044854 original size:2 final size:2
Alignment explanation
Indices: 1044843--1045272 Score: 65
Period size: 2 Copynumber: 218.5 Consensus size: 2
1044833 TTGAAACAAT
* *
1044843 TA TA -A TA TA TA TA TA TA TA -A AA CTA TA TA TA T- TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
1044883 AA CTA TA T- TG TG TA TA TA TA AA GTA TA TA TA TA AA CTA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * *
1044925 TA TA AA CTA TA TA GTT TA TA TT TA TA T- TA T- TA TA TA CTA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
1044966 TA TA AA CTA TA TA -A TT TA T- TA -A TA TA AA T- TA TA TA GT- TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
1045005 -A TA TA TA AA T- TA TA TA TGA -A TCA TA TT TA AA TA TA TA CA -A
1 TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA TA TA TA TA TA
* * * *
1045045 CT- TA TA TT TA TA TA T- TA TG TA TA -A T- TA TA AA T- TT TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
1045083 TA CTA TG TA TA AA T- TA TG TT TA TA TGA TC TA TA TA GA TA AA CTA
1 TA -TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA -TA
* * * * * *
1045127 TA TA TG TA TA AA CTA TA AA AA GTA TA TA GTT TA TA -A AA TA TA
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* *
1045169 -A TT TA TA T- TA -A TA TA GTA TA TA TA TA TA TA TA AA 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
* * * * *
1045208 TA TG TA TA AA CTA TA TA AA CTA TA TA GTT TA TA AA T- TA TA -A
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
*
1045249 TT TA TA T- TA -A TA TA GTA TA TA TA T
1 TA TA TA TA TA TA TA TA -TA TA TA TA T
1045273 GTATGTATAA
Statistics
Matches: 301, Mismatches: 74, Indels: 106
0.63 0.15 0.22
Matches are distributed among these distances:
1 30 0.10
2 243 0.81
3 28 0.09
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1044911 original size:13 final size:13
Alignment explanation
Indices: 1044895--1044937 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
1044885 CTATATTGTG
*
1044895 TATATATAAAGTA
1 TATATATAAACTA
1044908 TATATATAAACTA
1 TATATATAAACTA
1044921 TATATATAAACTA
1 TATATATAAACTA
1044934 TATA
1 TATA
1044938 GTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:1044969 original size:11 final size:11
Alignment explanation
Indices: 1044847--1044978 Score: 59
Period size: 11 Copynumber: 12.5 Consensus size: 11
1044837 AACAATTATA
1044847 ATATATATA-T
1 ATATATATACT
*
1044857 ATATA-AAACT
1 ATATATATACT
1044867 ATATATAT--T
1 ATATATATACT
* *
1044876 ATGTATAAACT
1 ATATATATACT
* *
1044887 ATATTGTGTA-T
1 ATA-TATATACT
*
1044898 ATATAAAGTA-T
1 ATATATA-TACT
*
1044909 ATATATAAACT
1 ATATATATACT
1044920 ATATATATAAACT
1 ATATATAT--ACT
1044933 ATATAGT-T--T
1 ATATA-TATACT
* *
1044942 ATATTTATATT
1 ATATATATACT
1044953 AT-TATATACT
1 ATATATATACT
*
1044963 ATATATAAACT
1 ATATATATACT
1044974 ATATA
1 ATATA
1044979 ATTTATTAAT
Statistics
Matches: 90, Mismatches: 18, Indels: 27
0.67 0.13 0.20
Matches are distributed among these distances:
8 1 0.01
9 15 0.17
10 21 0.23
11 40 0.44
12 3 0.03
13 9 0.10
14 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (11 bp):
ATATATATACT
Found at i:1045007 original size:18 final size:20
Alignment explanation
Indices: 1044922--1045020 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 20
1044912 TATAAACTAT
* *
1044922 ATATATAAACTATATAGTTT
1 ATATATAAATTATATAGTTA
* *
1044942 ATATTTATATTAT-TA-TATA
1 ATATATAAATTATATAGT-TA
* *
1044961 CTATATATAAACTATATAATTTA
1 --ATATATAAATTATAT-AGTTA
*
1044984 TTAATATAAATTATATAGTTA
1 AT-ATATAAATTATATAGTTA
1045005 ATATATAAATTATATA
1 ATATATAAATTATATA
1045021 TGAATCATAT
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
18 1 0.02
19 3 0.05
20 24 0.39
21 16 0.26
22 13 0.21
23 3 0.05
24 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATATAAATTATATAGTTA
Found at i:1045019 original size:11 final size:11
Alignment explanation
Indices: 1044895--1045073 Score: 63
Period size: 11 Copynumber: 16.4 Consensus size: 11
1044885 CTATATTGTG
1044895 TATATATAAAGT
1 TATATATAAA-T
1044907 ATATATATAAACT
1 -TATATATAAA-T
*
1044920 ATATATATAAAC
1 -TATATATAAAT
1044932 TATATAGT---T
1 TATATA-TAAAT
* *
1044941 TATATTTATAT
1 TATATATAAAT
* *
1044952 TAT-TATATAC
1 TATATATAAAT
*
1044962 TATATATAAAC
1 TATATATAAAT
**
1044973 TATATAATTTAT
1 TATAT-ATAAAT
1044985 TA-ATATAAAT
1 TATATATAAAT
1044995 TATATAGT---T
1 TATATA-TAAAT
*
1045004 AATATATAAAT
1 TATATATAAAT
*
1045015 TATATATGAAT
1 TATATATAAAT
* *
1045026 CATATTTAAA-
1 TATATATAAAT
* *
1045036 TATATACAACT
1 TATATATAAAT
*
1045047 TATATTTATATAT
1 TATA--TATAAAT
*
1045060 TATGTAT-AAT
1 TATATATAAAT
1045070 TATA
1 TATA
1045074 AATTTTATAT
Statistics
Matches: 124, Mismatches: 28, Indels: 31
0.68 0.15 0.17
Matches are distributed among these distances:
8 2 0.02
9 11 0.09
10 25 0.20
11 50 0.40
12 7 0.06
13 29 0.23
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (11 bp):
TATATATAAAT
Found at i:1045129 original size:13 final size:15
Alignment explanation
Indices: 1045111--1045143 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1045101 TTTATATGAT
1045111 CTATATA-G-ATAAA
1 CTATATATGTATAAA
1045124 CTATATATGTATAAA
1 CTATATATGTATAAA
1045139 CTATA
1 CTATA
1045144 AAAAGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 1 0.06
15 10 0.56
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (15 bp):
CTATATATGTATAAA
Found at i:1045183 original size:15 final size:15
Alignment explanation
Indices: 1045150--1045262 Score: 54
Period size: 15 Copynumber: 7.3 Consensus size: 15
1045140 TATAAAAAGT
* *
1045150 ATATAGTTTATA-AA
1 ATATAATTTATATTA
1045164 ATATAATTTATATTA
1 ATATAATTTATATTA
* *
1045179 ATATAGTATATATATA
1 ATATAATTTATAT-TA
*
1045195 TATATAAATTATA-TA
1 -ATATAATTTATATTA
* ** *
1045210 TGTATAAACTATATAA
1 -ATATAATTTATATTA
1045226 ACTATATAGTTTATA--A
1 A-TATA-A-TTTATATTA
1045242 ATTATAATTTATATTA
1 A-TATAATTTATATTA
1045258 ATATA
1 ATATA
1045263 GTATATATAT
Statistics
Matches: 76, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
14 17 0.22
15 30 0.39
16 15 0.20
17 10 0.13
18 4 0.05
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:1045195 original size:79 final size:79
Alignment explanation
Indices: 1045112--1045272 Score: 277
Period size: 79 Copynumber: 2.0 Consensus size: 79
1045102 TTATATGATC
*
1045112 TATATAGATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAAATATAATTTATAT
1 TATATAGATAAACTATATATGTATAAACTATAAAAACTATATAGTTTATAAAATATAATTTATAT
1045177 TAATATAGTATATA
66 TAATATAGTATATA
* * * *
1045191 TATATATATAAATTATATATGTATAAACTATATAAACTATATAGTTTATAAATTATAATTTATAT
1 TATATAGATAAACTATATATGTATAAACTATAAAAACTATATAGTTTATAAAATATAATTTATAT
1045256 TAATATAGTATATA
66 TAATATAGTATATA
1045270 TAT
1 TAT
1045273 GTATGTATAA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (79 bp):
TATATAGATAAACTATATATGTATAAACTATAAAAACTATATAGTTTATAAAATATAATTTATAT
TAATATAGTATATA
Found at i:1045301 original size:79 final size:77
Alignment explanation
Indices: 1045112--1045319 Score: 240
Period size: 79 Copynumber: 2.6 Consensus size: 77
1045102 TTATATGATC
* *
1045112 TATATAGATAAACT-ATATATGTATAAACTATAAAAAGTATATAGTTTATAAAATATAATTTATA
1 TATATATATAAA-TAATATAAG-ATAAACTATAAAAA-TATATAGTTTATAAAATATAATTTATA
1045176 TTAATATAGTATATA
63 TTAATATAGTATATA
* * * *
1045191 TATATATATAAATTATATATGTATAAACTATATAAACTATATAGTTTATAAATTATAATTTATAT
1 TATATATATAAATAATATAAG-ATAAACTATA-AAAATATATAGTTTATAAAATATAATTTATAT
1045256 TAATATAGTATATA
64 TAATATAGTATATA
* * * *
1045270 TATGTATGTATAACTAATATAAG-TAATCTATAGAATATATATAGTTTATA
1 TA--TATATATAAATAATATAAGATAAACTATA-AAAATATATAGTTTATA
1045320 GAAACACTAT
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
78 1 0.01
79 95 0.83
80 3 0.03
81 15 0.13
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (77 bp):
TATATATATAAATAATATAAGATAAACTATAAAAATATATAGTTTATAAAATATAATTTATATTA
ATATAGTATATA
Found at i:1045379 original size:7 final size:7
Alignment explanation
Indices: 1045369--1045449 Score: 72
Period size: 7 Copynumber: 11.6 Consensus size: 7
1045359 TAGTTTATAA
1045369 AAACCCT
1 AAACCCT
*
1045376 AAACACT
1 AAACCCT
* *
1045383 AAATCTT
1 AAACCCT
1045390 AAACCCT
1 AAACCCT
**
1045397 AAATGCT
1 AAACCCT
1045404 AAACCCT
1 AAACCCT
*
1045411 AAACTCT
1 AAACCCT
*
1045418 AAACCAT
1 AAACCCT
* *
1045425 AAATCTT
1 AAACCCT
*
1045432 AAACCTT
1 AAACCCT
1045439 AAACCCT
1 AAACCCT
1045446 AAAC
1 AAAC
1045450 ATTATGCATA
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 57 1.00
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:1045420 original size:28 final size:27
Alignment explanation
Indices: 1045374--1045449 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 27
1045364 TATAAAAACC
* *
1045374 CTAAACACTAAA-TCTTAAACCCTAAAT
1 CTAAACCCTAAACTC-TAAACCATAAAT
1045401 GCTAAACCCTAAACTCTAAACCATAAAT
1 -CTAAACCCTAAACTCTAAACCATAAAT
* *
1045429 CTTAAACCTTAAACCCTAAAC
1 C-TAAACCCTAAACTCTAAAC
1045450 ATTATGCATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.02
28 39 0.93
29 2 0.05
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (27 bp):
CTAAACCCTAAACTCTAAACCATAAAT
Found at i:1045541 original size:35 final size:36
Alignment explanation
Indices: 1045471--1045544 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
1045461 ATAATAGTTA
* *
1045471 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTATAGTACA-GTATACATATAAACT
* *
1045508 ATATATGTAACTTATAGTACA-TATATATATAAACT
1 ATATATGTAACCTATAGTACAGTATACATATAAACT
1045543 AT
1 AT
1045545 GTATAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 14 0.42
37 19 0.58
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.39
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACAGTATACATATAAACT
Found at i:1045554 original size:57 final size:56
Alignment explanation
Indices: 1045471--1045633 Score: 204
Period size: 55 Copynumber: 2.9 Consensus size: 56
1045461 ATAATAGTTA
* * * *
1045471 ATATATGTAACCTATAGTATATGTATACATGTAAACTATATATGTAACTTATAGTACAT
1 ATATATATAAACTAT-GTATATGTAT--ATATAAACTATATATGTAACCTATAGTACAT
* *
1045530 ATATATATAAACTATGTATA-GTATATATAAACTATATATATAACCTATAGTATAT
1 ATATATATAAACTATGTATATGTATATATAAACTATATATGTAACCTATAGTACAT
*
1045585 ATATATATACAATCTATTTATATGT-TATATAAACTATATATGTAACCTA
1 ATATATATA-AA-CTATGTATATGTATATATAAACTATATATGTAACCTA
1045634 CAGTTTATAA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
55 36 0.39
56 2 0.02
57 35 0.38
58 7 0.08
59 13 0.14
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (56 bp):
ATATATATAAACTATGTATATGTATATATAAACTATATATGTAACCTATAGTACAT
Found at i:1045556 original size:20 final size:20
Alignment explanation
Indices: 1045531--1045625 Score: 81
Period size: 20 Copynumber: 4.9 Consensus size: 20
1045521 ATAGTACATA
*
1045531 TATATATAAACTATGTATAG
1 TATATATAAACTATATATAG
1045551 TATATATAAACTATATATA-
1 TATATATAAACTATATATAG
** * *
1045570 TA-ACCTATAGTATATATA-
1 TATATATAAACTATATATAG
* * *
1045588 TATATACAATCTATTTATATG
1 TATATATAAACTATATATA-G
1045609 T-TATATAAACTATATAT
1 TATATATAAACTATATAT
1045626 GTAACCTACA
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
18 14 0.25
19 11 0.19
20 31 0.54
21 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (20 bp):
TATATATAAACTATATATAG
Found at i:1045567 original size:13 final size:13
Alignment explanation
Indices: 1045551--1045585 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1045541 CTATGTATAG
1045551 TATATATAAACTA
1 TATATATAAACTA
*
1045564 TATATATAACCTA
1 TATATATAAACTA
1045577 TAGTATATA
1 TA-TATATA
1045586 TATATATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:1045571 original size:33 final size:33
Alignment explanation
Indices: 1045529--1045591 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1045519 TTATAGTACA
1045529 TATATATATAAACTAT-GTATAGTATATATAAAC
1 TATATATATAAACTATAGTATA-TATATATAAAC
*
1045562 TATATATATAACCTATAGTATATATATATA
1 TATATATATAAACTATAGTATATATATATA
1045592 TACAATCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (33 bp):
TATATATATAAACTATAGTATATATATATAAAC
Found at i:1045587 original size:55 final size:57
Alignment explanation
Indices: 1045502--1045642 Score: 198
Period size: 57 Copynumber: 2.5 Consensus size: 57
1045492 TGTATACATG
* *
1045502 TAAACTATATATGTAACTTATAGTACATATATATATA-AA-CTATGTATA-GTATATA
1 TAAACTATATATGTAACCTATAGTATATATATATATACAATCTATGTATATGT-TATA
* *
1045557 TAAACTATATATATAACCTATAGTATATATATATATACAATCTATTTATATGTTATA
1 TAAACTATATATGTAACCTATAGTATATATATATATACAATCTATGTATATGTTATA
* *
1045614 TAAACTATATATGTAACCTACAGTTTATA
1 TAAACTATATATGTAACCTATAGTATATA
1045643 AACAATAGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
55 34 0.45
56 2 0.03
57 38 0.50
58 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (57 bp):
TAAACTATATATGTAACCTATAGTATATATATATATACAATCTATGTATATGTTATA
Found at i:1045694 original size:21 final size:21
Alignment explanation
Indices: 1045668--1045741 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
1045658 TAGTGTACTA
*
1045668 TATAGTTTATACTTTATAACC
1 TATAGTTTATACTTTATAAAC
* *
1045689 TATAGTATATAATTTATAAAC
1 TATAGTTTATACTTTATAAAC
* *
1045710 TATAGCTTATACTTTATAAAT
1 TATAGTTTATACTTTATAAAC
1045731 TATAGTTTATA
1 TATAGTTTATA
1045742 TTAATGTACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (21 bp):
TATAGTTTATACTTTATAAAC
Found at i:1045778 original size:22 final size:21
Alignment explanation
Indices: 1045728--1045778 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
1045718 ATACTTTATA
1045728 AATTATAGTTTATATTAATGT
1 AATTATAGTTTATATTAATGT
*
1045749 ACTATATAGTTTATATTAATGTT
1 AAT-TATAGTTTATATTAATG-T
1045772 AATTATA
1 AATTATA
1045779 TTAACTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 21 0.81
23 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (21 bp):
AATTATAGTTTATATTAATGT
Found at i:1045789 original size:15 final size:15
Alignment explanation
Indices: 1045752--1045802 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
1045742 TTAATGTACT
*
1045752 ATATAGTTTATATTA
1 ATATAATTTATATTA
*
1045767 ATGTTAA-TTATATTA
1 AT-ATAATTTATATTA
1045782 ACTATAATTTATATTA
1 A-TATAATTTATATTA
1045798 ATATA
1 ATATA
1045803 GTATATTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:1045839 original size:65 final size:67
Alignment explanation
Indices: 1045752--1045973 Score: 214
Period size: 65 Copynumber: 3.4 Consensus size: 67
1045742 TTAATGTACT
* * * **
1045752 ATATAGTTTATATTAATGTTAATTATATTAACTATAATTTATATTAATATAGTATATTGTTTATA
1 ATATAGTCTATATTAATATTAATTATATTAACTATAATTTATATTAATATACTATATAATTTATA
1045817 A-
66 AC
*
1045818 ACTAT-G-CTATATTAATATTAATTATATTAACTATAGTTTATA--AACTATACTATATAATTTA
1 A-TATAGTCTATATTAATATTAATTATATTAACTATAATTTATATTAA-TATACTATATAATTTA
1045879 TAAC
64 TAAC
* * *
1045883 ATATAGTTTATATTAATATTAACTT-TA-TAGACTATATTTTATATTAATATTAATAT-TAA-TT
1 ATATAGTCTATATTAATATTAA-TTATATTA-ACTATAATTTATATTAATA-TACTATATAATTT
*
1045944 ATAAT
63 ATAAC
* *
1045949 ATATAAT-TATTTTAATATT-ATTATA
1 ATATAGTCTATATTAATATTAATTATA
1045974 AATAGTTTAT
Statistics
Matches: 133, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
63 4 0.03
64 22 0.17
65 48 0.36
66 42 0.32
67 10 0.08
68 7 0.05
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (67 bp):
ATATAGTCTATATTAATATTAATTATATTAACTATAATTTATATTAATATACTATATAATTTATA
AC
Found at i:1045924 original size:31 final size:31
Alignment explanation
Indices: 1045825--1045935 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 31
1045815 TAAACTATGC
1045825 TATATTAATATTAA-TTATATTAAC-TATAGTT
1 TATATTAATATTAACTT-TA-TAACATATAGTT
*
1045856 TATAAACTATACTATATAA-TTTATAACATATAGTT
1 TAT--A-T-TAATAT-TAACTTTATAACATATAGTT
*
1045891 TATATTAATATTAACTTTATAGAC-TATATTT
1 TATATTAATATTAACTTTATA-ACATATAGTT
1045922 TATATTAATATTAA
1 TATATTAATATTAA
1045936 TATTAATTAT
Statistics
Matches: 69, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
30 3 0.04
31 34 0.49
32 3 0.04
33 2 0.03
34 5 0.07
35 17 0.25
36 5 0.07
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (31 bp):
TATATTAATATTAACTTTATAACATATAGTT
Found at i:1048413 original size:21 final size:21
Alignment explanation
Indices: 1048377--1048435 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
1048367 TCCACTTGGG
*
1048377 GGGGAATCGGTA-CCCCTAGA
1 GGGGAATCTGTACCCCCTAGA
*
1048397 GGGGAATCTGTACCCCCTAGG
1 GGGGAATCTGTACCCCCTAGA
1048418 GGGGAATCTGTACCCCCT
1 GGGGAATCTGTACCCCCT
1048436 GGACATTCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 11 0.31
21 25 0.69
ACGTcount: A:0.20, C:0.29, G:0.32, T:0.19
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTAGA
Found at i:1049803 original size:14 final size:14
Alignment explanation
Indices: 1049784--1049810 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1049774 TTATTGAACT
1049784 AAATGAATTATTTA
1 AAATGAATTATTTA
1049798 AAATGAATTATTT
1 AAATGAATTATTT
1049811 TTCTTTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
AAATGAATTATTTA
Found at i:1049943 original size:19 final size:20
Alignment explanation
Indices: 1049900--1049947 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1049890 TCTAAATCCT
*
1049900 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1049920 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1049939 TTTTCAAAA
1 TTTTCAAAA
1049948 GAAAATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1051294 original size:21 final size:20
Alignment explanation
Indices: 1051204--1051293 Score: 121
Period size: 19 Copynumber: 4.5 Consensus size: 20
1051194 AGGGGAATAG
*
1051204 GTACCCACTGGGGGGAATCT
1 GTACCCCCTGGGGGGAATCT
*
1051224 GT-TCCCCTGGGGGGAATCT
1 GTACCCCCTGGGGGGAATCT
* *
1051243 GT-TCCCCTGGGGGGAATCG
1 GTACCCCCTGGGGGGAATCT
1051262 GTACCCCCTGGAGGGGAATCT
1 GTACCCCCTGG-GGGGAATCT
1051283 GTACCCCCTGG
1 GTACCCCCTGG
1051294 ACATTCTGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 35 0.56
20 9 0.14
21 19 0.30
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21
Consensus pattern (20 bp):
GTACCCCCTGGGGGGAATCT
Found at i:1053393 original size:23 final size:23
Alignment explanation
Indices: 1053367--1053420 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1053357 CTTAATACAG
*
1053367 GATGCTTGCTGAATTGATGCAAT
1 GATGCTTGCTGAATTGATACAAT
* *
1053390 GATGCTTGCTGAATTGGTACATT
1 GATGCTTGCTGAATTGATACAAT
1053413 GATGCTTG
1 GATGCTTG
1053421 TCGGTTCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (23 bp):
GATGCTTGCTGAATTGATACAAT
Found at i:1056146 original size:16 final size:16
Alignment explanation
Indices: 1056125--1056156 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1056115 TACAAGATGT
1056125 TTCTCTAAACCTATTC
1 TTCTCTAAACCTATTC
1056141 TTCTCTAAACCTATTC
1 TTCTCTAAACCTATTC
1056157 ACTAACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (16 bp):
TTCTCTAAACCTATTC
Found at i:1056625 original size:23 final size:23
Alignment explanation
Indices: 1056599--1056652 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1056589 CTTAATACAG
*
1056599 GATGCTTGCTGAATTGATGCAAT
1 GATGCTTGCTGAATTGATACAAT
* *
1056622 GATGCTTGCTGAATTGGTACATT
1 GATGCTTGCTGAATTGATACAAT
1056645 GATGCTTG
1 GATGCTTG
1056653 TCGGTTCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (23 bp):
GATGCTTGCTGAATTGATACAAT
Found at i:1060851 original size:19 final size:19
Alignment explanation
Indices: 1060820--1060936 Score: 74
Period size: 19 Copynumber: 6.5 Consensus size: 19
1060810 AATATAATTT
1060820 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTATAA
1060838 ATAATATAAAGAATT-TGAA
1 ATAATATAAAGAATTAT-AA
* *
1060857 TTAATATAAA-AATCA-AA
1 ATAATATAAAGAATTATAA
*
1060874 GTTATAATATACA-AATTAT-A
1 ---ATAATATAAAGAATTATAA
1060894 AT--T-T-AAGAATTATAA
1 ATAATATAAAGAATTATAA
* *
1060909 AAAATATAAAGAATTGTAA
1 ATAATATAAAGAATTATAA
*
1060928 TTAATATAA
1 ATAATATAA
1060937 CAAATAAATT
Statistics
Matches: 76, Mismatches: 10, Indels: 25
0.68 0.09 0.23
Matches are distributed among these distances:
13 1 0.01
14 7 0.09
15 3 0.04
17 5 0.07
18 12 0.16
19 35 0.46
20 13 0.17
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (19 bp):
ATAATATAAAGAATTATAA
Found at i:1060863 original size:37 final size:36
Alignment explanation
Indices: 1060821--1060936 Score: 107
Period size: 37 Copynumber: 3.2 Consensus size: 36
1060811 ATATAATTTA
1060821 TAATATAAGAATTATAAATAATATAAAGAATTTGAAT
1 TAATATAAGAATTATAAATAATATAAAGAA-TTGAAT
* * *
1060858 TAATATAAAAATCA-AAGTTATAATATACA-AATT--A-
1 TAATATAAGAATTATAA---ATAATATAAAGAATTGAAT
* *
1060892 TAATTTAAGAATTATAAAAAATATAAAGAATTGTAAT
1 TAATATAAGAATTATAAATAATATAAAGAATTG-AAT
1060929 TAATATAA
1 TAATATAA
1060937 CAAATAAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
32 8 0.13
33 4 0.07
34 11 0.18
35 3 0.05
36 3 0.05
37 21 0.34
38 2 0.03
39 9 0.15
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (36 bp):
TAATATAAGAATTATAAATAATATAAAGAATTGAAT
Found at i:1060894 original size:71 final size:71
Alignment explanation
Indices: 1060805--1060941 Score: 206
Period size: 71 Copynumber: 1.9 Consensus size: 71
1060795 AATTTAGTGA
* * *
1060805 TTATAAATATAATTTATAATATAAGAATTATAAATAATATAAAGAATT-TGAATTAATATAA-AA
1 TTATAAATACAAATTATAATATAAGAATTATAAAAAATATAAAGAATTGT-AATTAATATAACAA
1060868 ATCAAAG
65 ATCAAAG
*
1060875 TTATAATATACAAATTATAATTTAAGAATTATAAAAAATATAAAGAATTGTAATTAATATAACAA
1 TTATAA-ATACAAATTATAATATAAGAATTATAAAAAATATAAAGAATTGTAATTAATATAACAA
1060940 AT
65 AT
1060942 AAATTTAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
70 6 0.10
71 49 0.82
72 5 0.08
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (71 bp):
TTATAAATACAAATTATAATATAAGAATTATAAAAAATATAAAGAATTGTAATTAATATAACAAA
TCAAAG
Found at i:1060992 original size:27 final size:26
Alignment explanation
Indices: 1060940--1060993 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1060930 AATATAACAA
* *
1060940 ATAAATTTAATTATCATAAGTTTATT
1 ATAAATTTAAATAACATAAGTTTATT
1060966 ATAAATTTAAAATAACATAA-TTATATT
1 ATAAATTT-AAATAACATAAGTT-TATT
1060993 A
1 A
1060994 ATTATAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
ATAAATTTAAATAACATAAGTTTATT
Found at i:1063047 original size:210 final size:210
Alignment explanation
Indices: 1062650--1063349 Score: 945
Period size: 210 Copynumber: 3.3 Consensus size: 210
1062640 AATGTGTCAC
* * *
1062650 CACCTACAATTGTTGGATACGTGGATTGTGTGCACTTCAAATAAATGGACAGAAGCAACAAGCTT
1 CACCTACAATTGTTTGATACATGGA-T-TGTGCAGTTCAAATAAATGGACAGAAGCAACAAGCTT
* * * * * *
1062715 GCTCGATAGTATGATGAACGAAAGTGTCCGTCCTGATGTAGTGACTTTCAGTTCTTTAATCGATG
64 GCTCGATAGAATGATGAATGAAGGTGTCCATCCTGATGTAGTGACTTTCAATTCTTTAATCAATG
*
1062780 CTTTATGCAAGGAAAAGAGAACAGAAGAAGCCATTTCCATGTTGGAAATAATGAGTCAGAGAAAT
129 CTTTATGCAAGGAAAAGAGAACAGAAGAAGCCATTTCCATGTTGGAACTAATGAGTCAGAGAAAT
* *
1062845 GTAAAACCTAACGTTGT
194 GTAAAACCTGACATTGT
*
1062862 CATCTACAATTGTTTGATACATGGATTGTGCAGTTCAAATAAATGGACAGAAGCAACAAGCTTGC
1 CACCTACAATTGTTTGATACATGGATTGTGCAGTTCAAATAAATGGACAGAAGCAACAAGCTTGC
* * *
1062927 TCGATAGGATGATGAGTGAAGGTGTCCATCCTGATGTTGTGACTTTCAATTCTTTAATCAATGCT
66 TCGATAGAATGATGAATGAAGGTGTCCATCCTGATGTAGTGACTTTCAATTCTTTAATCAATGCT
1062992 TTATGCAAGGAAAAGAGAACAGAAGAAGCCATTTCCATGTTGGAACTAATGAGTCAGAGAAATGT
131 TTATGCAAGGAAAAGAGAACAGAAGAAGCCATTTCCATGTTGGAACTAATGAGTCAGAGAAATGT
*
1063057 AAAACCTGACTTTGT
196 AAAACCTGACATTGT
* * * *
1063072 CACCCACAATTGTTTGATACATGCATTGTGCAGTTCAAATAATTGGACAGAAGCGACAAGCTTGC
1 CACCTACAATTGTTTGATACATGGATTGTGCAGTTCAAATAAATGGACAGAAGCAACAAGCTTGC
* ** *
1063137 TCAATAGAATGATGAATGAAGGAATCCATCCTGATGTAGTAACTTTCAATTCTTTAATCAATGCT
66 TCGATAGAATGATGAATGAAGGTGTCCATCCTGATGTAGTGACTTTCAATTCTTTAATCAATGCT
* ** * * * * * *
1063202 TTATGCAAGGAAAAGAGGATTGAAGAAGCGATTACCATGTTTGAACTGATGGGT-ATAAGAAATG
131 TTATGCAAGGAAAAGAGAACAGAAGAAGCCATTTCCATGTTGGAACTAATGAGTCA-GAGAAATG
*
1063266 TTAAACCTGACATTGT
195 TAAAACCTGACATTGT
* * * * ** ****
1063282 TACCTACACTTCTTTAATACATGGATTGTGCAAATCAGGCCAATGCGA-AGAAGCAACAAGCTTG
1 CACCTACAATTGTTTGATACATGGATTGTGCAGTTCAAATAAATG-GACAGAAGCAACAAGCTTG
1063346 CTCG
65 CTCG
1063350 GTAAGATGGT
Statistics
Matches: 433, Mismatches: 53, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
209 1 0.00
210 407 0.94
211 3 0.01
212 22 0.05
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (210 bp):
CACCTACAATTGTTTGATACATGGATTGTGCAGTTCAAATAAATGGACAGAAGCAACAAGCTTGC
TCGATAGAATGATGAATGAAGGTGTCCATCCTGATGTAGTGACTTTCAATTCTTTAATCAATGCT
TTATGCAAGGAAAAGAGAACAGAAGAAGCCATTTCCATGTTGGAACTAATGAGTCAGAGAAATGT
AAAACCTGACATTGT
Found at i:1068511 original size:2 final size:2
Alignment explanation
Indices: 1068506--1068582 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
1068496 TACAATATTC
1068506 AT AT AT AT 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 AT AT AT AT
1068548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1068583 CTTTAAAATA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1068745 original size:21 final size:21
Alignment explanation
Indices: 1068721--1068763 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1068711 GTCCATATTG
1068721 AAATCATAATATAAATAATAT
1 AAATCATAATATAAATAATAT
* * *
1068742 AAATCTTTATTTAAATAATAT
1 AAATCATAATATAAATAATAT
1068763 A
1 A
1068764 CGGAAACCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATCATAATATAAATAATAT
Found at i:1069325 original size:29 final size:29
Alignment explanation
Indices: 1069252--1069439 Score: 168
Period size: 29 Copynumber: 6.6 Consensus size: 29
1069242 ATCAACCATT
* * * *
1069252 TTACACAATTATCACCCTTTTAAGAAATAT
1 TTACAAAAATATCACCCTTTTTA-AAATAA
*
1069282 TTA-AAAAATAGCACCCTTTTTAAAATAA
1 TTACAAAAATATCACCCTTTTTAAAATAA
** *
1069310 TTATGAAACTATCACCC-TTTTAAAATAA
1 TTACAAAAATATCACCCTTTTTAAAATAA
**
1069338 TTACAAAAATATCA--CTTTTTTTAATAA
1 TTACAAAAATATCACCCTTTTTAAAATAA
** * *
1069365 TTATGAAAATAACACCATTTTTAAAATAA
1 TTACAAAAATATCACCCTTTTTAAAATAA
* * *
1069394 TTACCAAAATATCACCATTTTAAAAATAA
1 TTACAAAAATATCACCCTTTTTAAAATAA
* *
1069423 TAACTAAAATATCACCC
1 TTACAAAAATATCACCC
1069440 GGTCAACGGT
Statistics
Matches: 128, Mismatches: 26, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 20 0.16
28 30 0.23
29 74 0.58
30 3 0.02
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (29 bp):
TTACAAAAATATCACCCTTTTTAAAATAA
Found at i:1069470 original size:18 final size:18
Alignment explanation
Indices: 1069447--1069482 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1069437 CCCGGTCAAC
1069447 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1069465 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1069483 AGTTGTAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1077922 original size:17 final size:17
Alignment explanation
Indices: 1077897--1077935 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1077887 ATTTTGAATT
*
1077897 TTTTTTGGAATGTTTGA
1 TTTTGTGGAATGTTTGA
*
1077914 TTTTGTGGATTGTTTGA
1 TTTTGTGGAATGTTTGA
*
1077931 CTTTG
1 TTTTG
1077936 AATTTGTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.03, G:0.26, T:0.59
Consensus pattern (17 bp):
TTTTGTGGAATGTTTGA
Found at i:1078617 original size:20 final size:21
Alignment explanation
Indices: 1078577--1078631 Score: 85
Period size: 20 Copynumber: 2.6 Consensus size: 21
1078567 CTCAGATGGA
1078577 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATT-CCCCCCAAGGGGGT
*
1078599 ACCGATTCCCGCC-AGGGGGT
1 ACCGATTCCCCCCAAGGGGGT
1078619 ACCGATTCCCCCC
1 ACCGATTCCCCCC
1078632 CACTGTTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 19 0.61
21 5 0.16
22 7 0.23
ACGTcount: A:0.16, C:0.44, G:0.25, T:0.15
Consensus pattern (21 bp):
ACCGATTCCCCCCAAGGGGGT
Found at i:1085270 original size:43 final size:43
Alignment explanation
Indices: 1085209--1085299 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
1085199 TCCAAGGTAT
*
1085209 GTTGCATATGAAATCTTCTTTTTCAATGCCATATGATAAACAA
1 GTTGCATACGAAATCTTCTTTTTCAATGCCATATGATAAACAA
*
1085252 GTTGCATACGAAATCTTCTTTTTCAATGCCATATGATAAACAT
1 GTTGCATACGAAATCTTCTTTTTCAATGCCATATGATAAACAA
1085295 GTTGC
1 GTTGC
1085300 TTCTGGTCGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (43 bp):
GTTGCATACGAAATCTTCTTTTTCAATGCCATATGATAAACAA
Found at i:1093548 original size:24 final size:24
Alignment explanation
Indices: 1093520--1093569 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1093510 ATCCACAATT
1093520 ATAAACATGTACATTTAATGTATA
1 ATAAACATGTACATTTAATGTATA
*
1093544 ATAAACATGTATATTTAATGTATA
1 ATAAACATGTACATTTAATGTATA
1093568 AT
1 AT
1093570 GCTATTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (24 bp):
ATAAACATGTACATTTAATGTATA
Found at i:1095153 original size:16 final size:15
Alignment explanation
Indices: 1095128--1095158 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1095118 AAGCATGATG
1095128 TAATAAACAATAATA
1 TAATAAACAATAATA
1095143 TAATAAAACAATAATA
1 TAAT-AAACAATAATA
1095159 AAATTCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAATAAACAATAATA
Found at i:1097109 original size:24 final size:23
Alignment explanation
Indices: 1097082--1097141 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 23
1097072 TACCCTATAG
1097082 GGTACCAATACCCCTA-TACAAAGA
1 GGTACCAATACCCCTAGTAC-AA-A
* * *
1097106 GGTATCGATA--CCTAGTTCAAA
1 GGTACCAATACCCCTAGTACAAA
1097127 GGTACCAATACCCCT
1 GGTACCAATACCCCT
1097142 TATGTTAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
21 9 0.32
22 6 0.21
23 5 0.18
24 8 0.29
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (23 bp):
GGTACCAATACCCCTAGTACAAA
Found at i:1103026 original size:21 final size:22
Alignment explanation
Indices: 1103002--1103056 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1102992 CCCTTGCTAG
*
1103002 GTATCGATACTTATTTAAA-GT
1 GTATCGATACCTATTTAAATGT
* *
1103023 GTATCAATACCCTCTTTAAATGT
1 GTATCGATA-CCTATTTAAATGT
1103046 GTATCGATACC
1 GTATCGATACC
1103057 CCTCGATGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 8 0.29
22 10 0.36
23 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (22 bp):
GTATCGATACCTATTTAAATGT
Found at i:1103049 original size:23 final size:22
Alignment explanation
Indices: 1103015--1103057 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1103005 TCGATACTTA
1103015 TTTAAAGTGTATCAATACCCTC
1 TTTAAAGTGTATCAATACCCTC
*
1103037 TTTAAATGTGTATCGATACCC
1 TTTAAA-GTGTATCAATACCC
1103058 CTCGATGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (22 bp):
TTTAAAGTGTATCAATACCCTC
Found at i:1106729 original size:22 final size:22
Alignment explanation
Indices: 1106704--1106782 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
1106694 AGAGGTACCG
1106704 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
*
1106726 ATACCCCTATGAATGGGTATCG
1 ATACCCCTATGAATGGGTATCA
*
1106748 ATACCTCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
*
1106770 ATACACCTATGAA
1 ATACCCCTATGAA
1106783 GGCTCAAAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTATCA
Found at i:1106765 original size:44 final size:44
Alignment explanation
Indices: 1106697--1106782 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
1106687 AATATTAAGA
*
1106697 GGTACCGATACCCCTATGAATGGGTATCAATACCCCTATGAATG
1 GGTACCGATACCCCTATGAATGGGTATCAATACACCTATGAATG
* *
1106741 GGTATCGATACCTCTATGAATGGGTATCAATACACCTATGAA
1 GGTACCGATACCCCTATGAATGGGTATCAATACACCTATGAA
1106783 GGCTCAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (44 bp):
GGTACCGATACCCCTATGAATGGGTATCAATACACCTATGAATG
Found at i:1107278 original size:33 final size:33
Alignment explanation
Indices: 1107241--1107310 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1107231 TTTTGTAAAG
* *
1107241 GGGAAAGGTTCTAGCTGATCCCGTGAAAAGCTA
1 GGGAAAGGTTCTAGCTGAGCCCGTGAAAAACTA
* *
1107274 GGGAAAGGTTCTAGTTTAGCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTGAGCCCGTGAAAAACTA
1107307 GGGA
1 GGGA
1107311 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTGAGCCCGTGAAAAACTA
Found at i:1108276 original size:17 final size:16
Alignment explanation
Indices: 1108241--1108342 Score: 71
Period size: 17 Copynumber: 5.9 Consensus size: 16
1108231 TTAATTTATG
1108241 TCTGATAAATGTAAAATA
1 TCTGAT-AATGT-AAATA
1108259 TCTGATATATGTAAATA
1 TCTGATA-ATGTAAATA
* *
1108276 TCTGATGAATAT-ATTCA
1 TCTGAT-AATGTAAAT-A
*
1108293 TCTGATATCTGTAAATA
1 TCTGATA-ATGTAAATA
* *
1108310 TGTGATAATTGAAAATCA
1 TCTGATAA-TGTAAAT-A
1108328 TCTGATAACTGTAAA
1 TCTGATAA-TGTAAA
1108343 CATTTAGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
16 3 0.05
17 37 0.56
18 26 0.39
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (16 bp):
TCTGATAATGTAAATA
Found at i:1108334 original size:35 final size:34
Alignment explanation
Indices: 1108241--1108342 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 34
1108231 TTAATTTATG
*
1108241 TCTGATAAATGTAAAAT-ATCTGATATATGTAAATA
1 TCTGAT-AATG-AAAATCATCTGATATCTGTAAATA
* *
1108276 TCTGATGAAT-ATATTCATCTGATATCTGTAAATA
1 TCTGAT-AATGAAAATCATCTGATATCTGTAAATA
* *
1108310 TGTGATAATTGAAAATCATCTGATAACTGTAAA
1 TCTGATAA-TGAAAATCATCTGATATCTGTAAA
1108343 CATTTAGAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
33 5 0.09
34 23 0.41
35 28 0.50
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (34 bp):
TCTGATAATGAAAATCATCTGATATCTGTAAATA
Found at i:1108473 original size:19 final size:20
Alignment explanation
Indices: 1108435--1108473 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1108425 AGAAATATTC
**
1108435 CATACTAAAAATTTATAAAT
1 CATACTAAAAAAATATAAAT
1108455 CATACTAAAAAAATA-AAAT
1 CATACTAAAAAAATATAAAT
1108474 GAGGTTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (20 bp):
CATACTAAAAAAATATAAAT
Found at i:1115109 original size:23 final size:23
Alignment explanation
Indices: 1115076--1115143 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1115066 AATCTTATAT
1115076 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1115099 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* * *
1115122 GGCATTTTGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1115144 AGATGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1117330 original size:17 final size:19
Alignment explanation
Indices: 1117310--1117347 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1117300 TATAAAAGTT
1117310 AAAAGGATAAA-GA-ATGA
1 AAAAGGATAAATGATATGA
*
1117327 AAAAGTATAAATGATATGA
1 AAAAGGATAAATGATATGA
1117346 AA
1 AA
1117348 GGAATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 2 0.11
19 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.18, T:0.18
Consensus pattern (19 bp):
AAAAGGATAAATGATATGA
Found at i:1118039 original size:15 final size:15
Alignment explanation
Indices: 1118019--1118092 Score: 79
Period size: 15 Copynumber: 5.3 Consensus size: 15
1118009 GGTGACGAAT
1118019 ATTATGAACGAATAG
1 ATTATGAACGAATAG
*
1118034 ATTATG-ACG-A-GG
1 ATTATGAACGAATAG
*
1118046 ATTATGAACAAATAG
1 ATTATGAACGAATAG
*
1118061 ATTATG-ACG-A-GG
1 ATTATGAACGAATAG
1118073 ATTATGAACGAATAG
1 ATTATGAACGAATAG
1118088 ATTAT
1 ATTAT
1118093 AAAGTTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
12 14 0.30
13 7 0.15
14 7 0.15
15 19 0.40
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (15 bp):
ATTATGAACGAATAG
Found at i:1118049 original size:27 final size:27
Alignment explanation
Indices: 1118019--1118092 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
1118009 GGTGACGAAT
1118019 ATTATGAACGAATAGATTATGACGAGG
1 ATTATGAACGAATAGATTATGACGAGG
*
1118046 ATTATGAACAAATAGATTATGACGAGG
1 ATTATGAACGAATAGATTATGACGAGG
1118073 ATTATGAACGAATAGATTAT
1 ATTATGAACGAATAGATTAT
1118093 AAAGTTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (27 bp):
ATTATGAACGAATAGATTATGACGAGG
Found at i:1120642 original size:2 final size:2
Alignment explanation
Indices: 1120635--1120664 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1120625 ATTTGATTCC
1120635 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
1120665 TGCTTCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1130314 original size:18 final size:18
Alignment explanation
Indices: 1130291--1130327 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1130281 AGAACATTGG
1130291 TTGTGCTTCTACTTGTGT
1 TTGTGCTTCTACTTGTGT
1130309 TTGTGCTTCTACTTGTGT
1 TTGTGCTTCTACTTGTGT
1130327 T
1 T
1130328 CGGTTGTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (18 bp):
TTGTGCTTCTACTTGTGT
Found at i:1130803 original size:21 final size:21
Alignment explanation
Indices: 1130773--1130813 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1130763 AATTGTTAAA
* *
1130773 AAATATTAATGTTTTAGGTAG
1 AAATAATAATATTTTAGGTAG
1130794 AAATAATAATATTTTAGGTA
1 AAATAATAATATTTTAGGTA
1130814 ATTTTTTACA
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:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (21 bp):
AAATAATAATATTTTAGGTAG
Found at i:1131203 original size:19 final size:20
Alignment explanation
Indices: 1131172--1131212 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
1131162 TCGTATCCCT
1131172 GCCCTTAAAAAAAATCTAAA
1 GCCCTTAAAAAAAATCTAAA
*
1131192 GCCCTT-AAAAAATTCTAAA
1 GCCCTTAAAAAAAATCTAAA
1131211 GC
1 GC
1131213 AATGGTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.22
Consensus pattern (20 bp):
GCCCTTAAAAAAAATCTAAA
Found at i:1132542 original size:20 final size:20
Alignment explanation
Indices: 1132503--1132546 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1132493 AATATCAACT
* * *
1132503 AGAAGCAAGCATTATCAAAC
1 AGAAGCAAACAATATAAAAC
1132523 AGAAGCAAACAATATAAAAC
1 AGAAGCAAACAATATAAAAC
1132543 AGAA
1 AGAA
1132547 TAAAGTAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.11
Consensus pattern (20 bp):
AGAAGCAAACAATATAAAAC
Found at i:1134928 original size:63 final size:62
Alignment explanation
Indices: 1134825--1134981 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 62
1134815 TTAAATCAAT
* * ** ** * *
1134825 TGCTTCAGACAGTACATCATTTACATCCCCTTGCAAAAAAAACCATGGATAGTTTACATTAAA
1 TGCTTCTGACAGTATATCATTTACATCAAC-AACAAAAAAAACCAGGGATACTTTACATTAAA
* *
1134888 TGCTTCTGACAGTATATCATTTACATCAACAACAATAAAAAACTAGGGTTACTTTACATTAAA
1 TGCTTCTGACAGTATATCATTTACATCAACAACAA-AAAAAACCAGGGATACTTTACATTAAA
* * *
1134951 TGCTTCTAACAATATATCATTTATATCAACA
1 TGCTTCTGACAGTATATCATTTACATCAACA
1134982 GATTTATATA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
62 3 0.04
63 77 0.96
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (62 bp):
TGCTTCTGACAGTATATCATTTACATCAACAACAAAAAAAACCAGGGATACTTTACATTAAA
Found at i:1135246 original size:6 final size:6
Alignment explanation
Indices: 1135227--1135341 Score: 70
Period size: 6 Copynumber: 19.3 Consensus size: 6
1135217 TGGATTCCAT
* * ** * *
1135227 TTCGGG TTCAGG TTCGGG TTC-AG TTCGGG TTTAGG TTTGGG TTTGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
* * * * * * * * *
1135274 TTTGAG TTCGGG TTCGAG TTTGGG TTTGGG TTTGGG ATCGGA TTTGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
* *
1135322 TTTGGG TTCGAG TTCGGG TT
1 TTCGGG TTCGGG TTCGGG TT
1135342 AGGGGTAGAG
Statistics
Matches: 86, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
5 4 0.05
6 82 0.95
ACGTcount: A:0.07, C:0.09, G:0.43, T:0.42
Consensus pattern (6 bp):
TTCGGG
Found at i:1135270 original size:12 final size:12
Alignment explanation
Indices: 1135227--1135341 Score: 79
Period size: 12 Copynumber: 9.7 Consensus size: 12
1135217 TGGATTCCAT
**
1135227 TTCGGGTTCAGG
1 TTCGGGTTTGGG
**
1135239 TTCGGG-TTCAG
1 TTCGGGTTTGGG
*
1135250 TTCGGGTTTAGG
1 TTCGGGTTTGGG
*
1135262 TTTGGGTTTGGG
1 TTCGGGTTTGGG
* * *
1135274 TTTGAGTTCGGG
1 TTCGGGTTTGGG
*
1135286 TTCGAGTTTGGG
1 TTCGGGTTTGGG
*
1135298 TTTGGGTTTGGG
1 TTCGGGTTTGGG
* *
1135310 ATCGGATTTGGG
1 TTCGGGTTTGGG
* * *
1135322 TTTGGGTTCGAG
1 TTCGGGTTTGGG
1135334 TTCGGGTT
1 TTCGGGTT
1135342 AGGGGTAGAG
Statistics
Matches: 80, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
11 8 0.10
12 72 0.90
ACGTcount: A:0.07, C:0.09, G:0.43, T:0.42
Consensus pattern (12 bp):
TTCGGGTTTGGG
Found at i:1135284 original size:30 final size:30
Alignment explanation
Indices: 1135248--1135329 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
1135238 GTTCGGGTTC
1135248 AGTTCGGGTTTAGGTTTGGGTTTGGGTTTG
1 AGTTCGGGTTTAGGTTTGGGTTTGGGTTTG
*
1135278 AGTTCGGG-TTCGAGTTTGGGTTTGGGTTTG
1 AGTTCGGGTTTAG-GTTTGGGTTTGGGTTTG
* * * *
1135308 GGATCGGATTTGGGTTTGGGTT
1 AGTTCGGGTTTAGGTTTGGGTT
1135330 CGAGTTCGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
29 3 0.07
30 39 0.87
31 3 0.07
ACGTcount: A:0.07, C:0.05, G:0.44, T:0.44
Consensus pattern (30 bp):
AGTTCGGGTTTAGGTTTGGGTTTGGGTTTG
Found at i:1135294 original size:24 final size:23
Alignment explanation
Indices: 1135266--1135338 Score: 92
Period size: 24 Copynumber: 3.1 Consensus size: 23
1135256 TTTAGGTTTG
*
1135266 GGTTTGGGTTTGAGTTCGGGTTC
1 GGTTTGGGTTTGGGTTCGGGTTC
* *
1135289 GAGTTTGGGTTTGGGTTTGGGATC
1 G-GTTTGGGTTTGGGTTCGGGTTC
*
1135313 GGATTTGGGTTTGGGTTCGAGTTC
1 GG-TTTGGGTTTGGGTTCGGGTTC
1135337 GG
1 GG
1135339 GTTAGGGGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.05
24 40 0.95
ACGTcount: A:0.07, C:0.07, G:0.45, T:0.41
Consensus pattern (23 bp):
GGTTTGGGTTTGGGTTCGGGTTC
Found at i:1135776 original size:103 final size:101
Alignment explanation
Indices: 1135574--1135799 Score: 294
Period size: 103 Copynumber: 2.2 Consensus size: 101
1135564 AGGGAAGAAC
* * *
1135574 TGGGATGAACAC-GGACGAACACAGATGAATATTTGATTGTTTGATCGAAAAAACATGAAATTGT
1 TGGGATGAAC-CGGGATGAACACAGATGAATATTTGAGTGTTTGATCGAAAAAACATGAAATGGT
*
1135638 TTGGGTTTCAATGTTTTTTAAGATCAAATAAGGGTTT
65 TTGGGTTTCAATGTTTTTGAAGATCAAATAAGGGTTT
*
1135675 TAGGGATGAACCGGGATGAACACGGATGAATATTTTG-GTGTTTGATCGAAAAAAACATGAAATG
1 T-GGGATGAACCGGGATGAACACAGATGAATA-TTTGAGTGTTTGATCG-AAAAAACATGAAATG
*** *
1135739 GTTTGGGTTTTGGTGTTTTTGAAGATCAAATGAGGGTTT
63 GTTTGGGTTTCAATGTTTTTGAAGATCAAATAAGGGTTT
* *
1135778 TGGGAAAGAACTGGGATGAACA
1 TGGG-ATGAACCGGGATGAACA
1135800 AATGAAGAAC
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
101 2 0.02
102 39 0.36
103 68 0.62
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.31
Consensus pattern (101 bp):
TGGGATGAACCGGGATGAACACAGATGAATATTTGAGTGTTTGATCGAAAAAACATGAAATGGTT
TGGGTTTCAATGTTTTTGAAGATCAAATAAGGGTTT
Found at i:1136084 original size:62 final size:61
Alignment explanation
Indices: 1136006--1136143 Score: 204
Period size: 62 Copynumber: 2.2 Consensus size: 61
1135996 TCCTAGTTTT
*
1136006 AAATTTGTTCAATTTAGTCCAAATTTAATAATGCAATATATTAATTTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATAATACAATATATTAATTTAAGCTTCATATTTA
* * ** * *
1136067 AACTTTTTTTCAATTTAGTCCAAATTTAATGTTACAGTTTATTAATTTAAGCTTCATATTTA
1 AA-ATTTGTTCAATTTAGTCCAAATTTAATAATACAATATATTAATTTAAGCTTCATATTTA
1136129 AAATTTGTTCAATTT
1 AAATTTGTTCAATTT
1136144 GATCCTTATA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
61 13 0.19
62 54 0.81
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (61 bp):
AAATTTGTTCAATTTAGTCCAAATTTAATAATACAATATATTAATTTAAGCTTCATATTTA
Found at i:1136259 original size:18 final size:18
Alignment explanation
Indices: 1136236--1136595 Score: 205
Period size: 18 Copynumber: 20.2 Consensus size: 18
1136226 AACTTTTCAA
1136236 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
1136254 TATATAGTATATATATAC
1 TATATAGTTTATATATAC
*
1136272 TA-AT-GAATTATATA-A-
1 TATATAG-TTTATATATAC
*
1136287 TATATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* * *
1136305 CATATACTATATAGGTTATA-
1 TATATAGTTTATA---TATAC
* ** *
1136325 TATATTAATGCACTATATAA
1 TATA-TAGTTTA-TATATAC
*
1136345 TATATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* * *
1136363 CATATACTATATAGGTTATA-
1 TATATAGTTTATA---TATAC
* ** *
1136383 TATACTAATGAACTATATAA
1 TATA-TAGTTTA-TATATAC
1136403 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
**
1136421 TA-AT-G-AAATATATA-
1 TATATAGTTTATATATAC
*
1136435 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
1136453 CATATAGTTTATATATAT
1 TATATAGTTTATATATAC
1136471 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
***
1136489 TA-ATAAACTATATA-A-
1 TATATAGTTTATATATAC
*
1136504 TGTATAGTTTTATATATAC
1 TATATAG-TTTATATATAC
*
1136523 CATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
1136541 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
*
1136556 TATATAGTTTATATATAT
1 TATATAGTTTATATATAC
1136574 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
1136592 TATA
1 TATA
1136596 GTATAAATTA
Statistics
Matches: 257, Mismatches: 55, Indels: 60
0.69 0.15 0.16
Matches are distributed among these distances:
14 2 0.01
15 20 0.08
16 19 0.07
17 37 0.14
18 124 0.48
19 21 0.08
20 14 0.05
21 16 0.06
22 4 0.02
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:1136265 original size:58 final size:58
Alignment explanation
Indices: 1136174--1136579 Score: 325
Period size: 58 Copynumber: 7.5 Consensus size: 58
1136164 TTCTTTCAAT
* * * * * *
1136174 TAATATATATGTTTATAT-TAATAAATTAATATATATGTTATATATAGTAATGAACT-TT
1 TAATATATA-GTTTATATATACTATA-TACTATATAGGTTATATATACTAATGAACTATA
* *
1136232 TCAATATATAGTTTATATATAC--TATA-TA-GTA---TATATATACTAATGAATTATA
1 T-AATATATAGTTTATATATACTATATACTATATAGGTTATATATACTAATGAACTATA
* * * *
1136284 TAATATATAGTTTGTATATACCATATACTATATAGGTTATATATATTAATGCACTATA
1 TAATATATAGTTTATATATACTATATACTATATAGGTTATATATACTAATGAACTATA
* *
1136342 TAATATATAGTTTGTATATACCATATACTATATAGGTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTATATACTATATAGGTTATATATACTAATGAACTATA
* * **
1136400 TAATATATAGTTTATATATACTA-ATGA--A-ATA---TATATGTA-TAGTTTA-TATA
1 TAATATATAGTTTATATATACTATAT-ACTATATAGGTTATATATACTAATGAACTATA
** * *
1136450 TACCATATAG--T-T-TATA-TATAT--TATATAGTTTATATATACTAATAAACTATA
1 TAATATATAGTTTATATATACTATATACTATATAGGTTATATATACTAATGAACTATA
* * *
1136501 TAATGTATAG--T-T-T-TA-TATATACCATATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTATATACTATATAGGTTATATATACTAATGAACTATA
*
1136553 TAATATATAGTTTATATATATTATATA
1 TAATATATAGTTTATATATACTATATA
1136580 GTTTATATAT
Statistics
Matches: 290, Mismatches: 31, Indels: 54
0.77 0.08 0.14
Matches are distributed among these distances:
45 3 0.01
46 9 0.03
47 1 0.00
48 1 0.00
49 7 0.02
50 23 0.08
51 53 0.18
52 46 0.16
53 4 0.01
54 5 0.02
55 8 0.03
56 4 0.01
57 5 0.02
58 111 0.38
59 10 0.03
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (58 bp):
TAATATATAGTTTATATATACTATATACTATATAGGTTATATATACTAATGAACTATA
Found at i:1136284 original size:33 final size:32
Alignment explanation
Indices: 1136247--1136519 Score: 182
Period size: 33 Copynumber: 8.7 Consensus size: 32
1136237 ATATAGTTTA
* *
1136247 TATATACTATATAGTATATATATACTAATGAAT
1 TATATAATATATAGT-TATATATACTAATGAAC
*
1136280 TATATAATATATAG-T-T-TGTA-T-AT--AC
1 TATATAATATATAGTTATATATACTAATGAAC
* * * *
1136305 CATATACTATATAGGTTATATATATTAATGCAC
1 TATATAATATATA-GTTATATATACTAATGAAC
*
1136338 TATATAATATATAG-T-T-TGTA-T-AT--AC
1 TATATAATATATAGTTATATATACTAATGAAC
* *
1136363 CATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATA-GTTATATATACTAATGAAC
*
1136396 TATATAATATATAGTTTATATATACTAATGAAA
1 TATATAATATATAG-TTATATATACTAATGAAC
* **
1136429 TATAT-ATGTATAGTTTATATATACCATATAGTTTA-
1 TATATAATATATAG-TTATATATA-C-TA-A-TGAAC
* *
1136464 TATATATTATATAGTTTATATATACTAATAAAC
1 TATATAATATATAG-TTATATATACTAATGAAC
* *
1136497 TATATAATGTATAGTTTTATATA
1 TATATAATATATAGTTATATATA
1136520 TACCATATAG
Statistics
Matches: 192, Mismatches: 25, Indels: 47
0.73 0.09 0.18
Matches are distributed among these distances:
25 25 0.13
26 2 0.01
27 6 0.03
28 4 0.02
29 12 0.06
30 4 0.02
31 6 0.03
32 29 0.15
33 75 0.39
34 4 0.02
35 7 0.04
36 18 0.09
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (32 bp):
TATATAATATATAGTTATATATACTAATGAAC
Found at i:1136373 original size:25 final size:25
Alignment explanation
Indices: 1136339--1136387 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1136329 TTAATGCACT
* *
1136339 ATATAATATATAGTTTGTATATACC
1 ATATAATATATAGGTTATATATACC
*
1136364 ATATACTATATAGGTTATATATAC
1 ATATAATATATAGGTTATATATAC
1136388 TAATGAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (25 bp):
ATATAATATATAGGTTATATATACC
Found at i:1136479 original size:68 final size:70
Alignment explanation
Indices: 1136396--1136539 Score: 249
Period size: 68 Copynumber: 2.1 Consensus size: 70
1136386 ACTAATGAAC
1136396 TATATAATATATAGTTTATATATACTAATGAAA-TATAT-ATGTATAG-TTTATATATACCATAT
1 TATATAATATATAGTTTATATATACTAAT-AAACTATATAATGTATAGTTTTATATATACCATAT
1136458 AGTTTA
65 AGTTTA
*
1136464 TATATATTATATAGTTTATATATACTAATAAACTATATAATGTATAGTTTTATATATACCATATA
1 TATATAATATATAGTTTATATATACTAATAAACTATATAATGTATAGTTTTATATATACCATATA
1136529 GTTTA
66 GTTTA
1136534 TATATA
1 TATATA
1136540 CTAATGAACT
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
67 3 0.04
68 33 0.46
69 8 0.11
70 28 0.39
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (70 bp):
TATATAATATATAGTTTATATATACTAATAAACTATATAATGTATAGTTTTATATATACCATATA
GTTTA
Found at i:1136595 original size:9 final size:9
Alignment explanation
Indices: 1136443--1136738 Score: 67
Period size: 9 Copynumber: 32.8 Consensus size: 9
1136433 TATGTATAGT
1136443 TTATATATA
1 TTATATATA
**
1136452 CCATATAGT-
1 TTATATA-TA
1136461 TTATATATA
1 TTATATATA
1136470 TTATATAGT-
1 TTATATA-TA
1136479 TTATATATA
1 TTATATATA
* *
1136488 CTA-ATAAA
1 TTATATATA
*
1136496 CTATATA-A
1 TTATATATA
1136504 TGTATAGT-T-
1 T-TATA-TATA
1136513 TTATATATA
1 TTATATATA
**
1136522 CCATATAGT-
1 TTATATA-TA
1136531 TTATATATA
1 TTATATATA
*
1136540 CTA-ATGA-A
1 TTATAT-ATA
*
1136548 CTATATA-A
1 TTATATATA
1136556 -TATATAGT-
1 TTATATA-TA
1136564 TTATATATA
1 TTATATATA
1136573 TTATATAGT-
1 TTATATA-TA
1136582 TTATATATA
1 TTATATATA
*
1136591 CTATAGTATA
1 TTATA-TATA
*
1136601 -AAT-TATA
1 TTATATATA
1136608 TTATATA-A
1 TTATATATA
*
1136616 TATATAAATA
1 T-TATATATA
*
1136626 TCA-ACTATA
1 TTATA-TATA
*
1136635 GTATATAGT-
1 TTATATA-TA
* *
1136644 TTATATGGGTT
1 TTATAT--ATA
1136655 TTATATATA
1 TTATATATA
1136664 GTTCATATAT-
1 -TT-ATATATA
*
1136674 GTATATATA
1 TTATATATA
1136683 TATATAATATA
1 T-TAT-ATATA
*
1136694 GTATATATA
1 TTATATATA
*
1136703 -TAAACTATA
1 TTATA-TATA
1136712 GTT-TATATA
1 -TTATATATA
1136721 TATAGTATATA
1 T-TA-TATATA
*
1136732 CTATATA
1 TTATATA
1136739 AATAGTTTAT
Statistics
Matches: 215, Mismatches: 30, Indels: 84
0.65 0.09 0.26
Matches are distributed among these distances:
7 11 0.05
8 41 0.19
9 114 0.53
10 25 0.12
11 24 0.11
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (9 bp):
TTATATATA
Found at i:1136744 original size:18 final size:18
Alignment explanation
Indices: 1136428--1136738 Score: 111
Period size: 18 Copynumber: 17.3 Consensus size: 18
1136418 TACTAATGAA
* *
1136428 ATATATAT-GTATAGTTT
1 ATATATATAATATAGTAT
** *
1136445 ATATATACCATATAGTTT
1 ATATATATAATATAGTAT
* *
1136463 ATATATATTATATAGTTT
1 ATATATATAATATAGTAT
1136481 ATATATACTAATA-A--ACT
1 ATATATA-TAATATAGTA-T
*
1136498 ATATA-AT-GTATAGT-T
1 ATATATATAATATAGTAT
* *
1136513 TTATATATACCATATAGTTT
1 ATATATATA--ATATAGTAT
*
1136533 ATATATACTAATGA-A--CT
1 ATATATA-TAAT-ATAGTAT
*
1136550 ATATA-AT-ATATAGTTT
1 ATATATATAATATAGTAT
*
1136566 ATATATATTATATAGT-T
1 ATATATATAATATAGTAT
*
1136583 -TATATATACTATAGTAT
1 ATATATATAATATAGTAT
* * *
1136600 AAATTATATTATATAATAT
1 ATA-TATATAATATAGTAT
*
1136619 ATAAATATCAACTATAGTAT
1 ATATATAT-AA-TATAGTAT
* *
1136639 ATAGT-T-T-ATATGGGTTTT
1 ATA-TATATAATAT-AG-TAT
*
1136657 ATATATAGTTCATATATGTATAT
1 ATATATA--TAATATA-G--TAT
1136680 ATATATATAATATAGTAT
1 ATATATATAATATAGTAT
*
1136698 ATATATA-AACTATAGTTT
1 ATATATATAA-TATAGTAT
*
1136716 ATATATATAGTATA-TACT
1 ATATATATAATATAGTA-T
1136734 ATATA
1 ATATA
1136739 AATAGTTTAT
Statistics
Matches: 226, Mismatches: 32, Indels: 71
0.69 0.10 0.22
Matches are distributed among these distances:
13 1 0.00
14 5 0.02
15 8 0.04
16 26 0.12
17 29 0.13
18 84 0.37
19 30 0.13
20 20 0.09
21 9 0.04
22 5 0.02
23 9 0.04
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (18 bp):
ATATATATAATATAGTAT
Found at i:1136749 original size:18 final size:18
Alignment explanation
Indices: 1136677--1136749 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 18
1136667 CATATATGTA
1136677 TATATA-TATATAATATAG
1 TATATACTATATAA-ATAG
1136695 TATATA-TATA-AACTATAG
1 TATATACTATATAA--ATAG
1136713 T-T-TA-TATAT--ATAG
1 TATATACTATATAAATAG
1136726 TATATACTATATAAATAG
1 TATATACTATATAAATAG
*
1136744 TTTATA
1 TATATA
1136750 TAGTTCACTA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
13 5 0.11
14 1 0.02
15 2 0.04
16 11 0.23
17 3 0.06
18 25 0.53
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATACTATATAAATAG
Found at i:1136751 original size:2 final size:2
Alignment explanation
Indices: 1136396--1136738 Score: 81
Period size: 2 Copynumber: 165.0 Consensus size: 2
1136386 ACTAATGAAC
* * *
1136396 TA TA TA -A TA TA TA GTT TA TA TA TA CTA -A TGA AA TA TA TA TG
1 TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA T-A TA TA TA TA TA
* * * *
1136437 TA TA GTT TA TA TA TA CCA TA TA GTT TA TA TA TA T- TA TA TA GTT
1 TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * *
1136480 TA TA TA TA CTA -A TA AA CTA TA TA -A TG TA TA GT- TT TA TA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA
* *
1136520 TA CCA TA TA GTT TA TA TA TA CTA -A TGA -A CTA TA TA -A TA TA TA
1 TA -TA TA TA -TA TA TA TA TA -TA TA T-A TA -TA TA TA TA TA TA TA
* * *
1136562 GTT TA TA TA TA T- TA TA TA GTT TA TA TA TA CTA TA GTA TA AA T-
1 -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA -TA TA TA TA
* *
1136604 TA TA T- TA TA TA -A TA TA TA AA TA TCA -A CTA TA GTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA -TA TA TA -TA
* ** * *
1136645 TA TA TG GG T- TT TA TA TA TA GT- TCA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA
* *
1136687 TA -A TA TA GTA TA TA TA TA AA CTA TA GTT TA TA TA TA TA GTA TA
1 TA TA TA TA -TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA -TA TA
1136730 TA CTA TA TA
1 TA -TA TA TA
1136739 AATAGTTTAT
Statistics
Matches: 251, Mismatches: 43, Indels: 94
0.65 0.11 0.24
Matches are distributed among these distances:
1 17 0.07
2 195 0.78
3 39 0.16
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1136805 original size:20 final size:19
Alignment explanation
Indices: 1136782--1136921 Score: 75
Period size: 18 Copynumber: 7.5 Consensus size: 19
1136772 TATATAGGTC
1136782 ATATGTAAACTACATAGTTT
1 ATATGTAAACTA-ATAGTTT
*
1136802 ATA--T--A-T-ATAGTTC
1 ATATGTAAACTAATAGTTT
*
1136815 ATATGTAAACT-ATAGTTC
1 ATATGTAAACTAATAGTTT
*
1136833 ATATGTAAATATCAACTATAGTTT
1 ATATGT-AA-A-CTA--ATAGTTT
1136857 ATATGTAAACT-ATAG-TT
1 ATATGTAAACTAATAGTTT
*
1136874 AGTATATAAACTATATAGTTT
1 A-TATGTAAACTA-ATAGTTT
* *
1136895 ATATTTAAACT-ATAGTTC
1 ATATGTAAACTAATAGTTT
*
1136913 ATATATAAA
1 ATATGTAAA
1136922 TATTAATTAT
Statistics
Matches: 97, Mismatches: 8, Indels: 32
0.71 0.06 0.23
Matches are distributed among these distances:
13 9 0.09
15 2 0.02
16 1 0.01
17 4 0.04
18 42 0.43
19 2 0.02
20 17 0.18
21 5 0.05
22 1 0.01
23 2 0.02
24 12 0.12
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (19 bp):
ATATGTAAACTAATAGTTT
Found at i:1136830 original size:18 final size:18
Alignment explanation
Indices: 1136807--1136969 Score: 120
Period size: 18 Copynumber: 8.7 Consensus size: 18
1136797 AGTTTATATA
1136807 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
1136825 TATAGTTCATATGTAAATATCAAC
1 TATAGTTCATATG----TA--AAC
*
1136849 TATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
*
1136867 TATAGTT-AGTATATAAAC
1 TATAGTTCA-TATGTAAAC
* *
1136885 TATATAGTTTATATTTAAAC
1 --TATAGTTCATATGTAAAC
*
1136905 TATAGTTCATATATAAA-
1 TATAGTTCATATGTAAAC
*
1136922 TATTAATT-ATA-GTATATA-
1 TA-TAGTTCATATGTA-A-AC
*
1136940 TATAATTCATATGTAAAC
1 TATAGTTCATATGTAAAC
1136958 TATAGTTCATAT
1 TATAGTTCATAT
1136970 ATATAGTATA
Statistics
Matches: 121, Mismatches: 8, Indels: 32
0.75 0.05 0.20
Matches are distributed among these distances:
16 2 0.02
17 13 0.11
18 68 0.56
19 3 0.02
20 17 0.14
21 1 0.01
22 2 0.02
24 15 0.12
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:1136866 original size:42 final size:41
Alignment explanation
Indices: 1136806--1136940 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 41
1136796 TAGTTTATAT
* *
1136806 ATATAGTTCATATGTAAACTATAGTTCATATGTAAATATCA
1 ATATAGTTTATATGTAAACTATAGTTCATATATAAATATCA
*
1136847 ACTATAGTTTATATGTAAACTATAGTT-AGTATAT-AA-A-CT
1 A-TATAGTTTATATGTAAACTATAGTTCA-TATATAAATATCA
* *
1136886 ATATAGTTTATATTTAAACTATAGTTCATATATAAATATTA
1 ATATAGTTTATATGTAAACTATAGTTCATATATAAATATCA
*
1136927 ATTATAGTATATAT
1 A-TATAGTTTATAT
1136941 ATAATTCATA
Statistics
Matches: 80, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
38 29 0.36
39 5 0.06
40 2 0.03
41 5 0.06
42 39 0.49
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (41 bp):
ATATAGTTTATATGTAAACTATAGTTCATATATAAATATCA
Found at i:1136904 original size:38 final size:39
Alignment explanation
Indices: 1136805--1136922 Score: 150
Period size: 38 Copynumber: 3.0 Consensus size: 39
1136795 ATAGTTTATA
* *
1136805 TATATAGTTCATATGTAAACTATAGTTCATATGTAAATATC
1 TATATAGTTTATATGTAAACTATAGTTCATATAT-AA-ATC
*
1136846 AACTATAGTTTATATGTAAACTATAGTT-AGTATATAAA-C
1 TA-TATAGTTTATATGTAAACTATAGTTCA-TATATAAATC
*
1136885 TATATAGTTTATATTTAAACTATAGTTCATATATAAAT
1 TATATAGTTTATATGTAAACTATAGTTCATATATAAAT
1136923 ATTAATTATA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
38 32 0.47
39 3 0.04
40 1 0.01
41 4 0.06
42 28 0.41
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (39 bp):
TATATAGTTTATATGTAAACTATAGTTCATATATAAATC
Found at i:1136979 original size:18 final size:17
Alignment explanation
Indices: 1136905--1136979 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 17
1136895 ATATTTAAAC
* *
1136905 TATAGTTCATATATAAA
1 TATAATTCATATATATA
1136922 TATTAATT-ATAGTATATA
1 TA-TAATTCATA-TATATA
* *
1136940 TATAATTCATATGTAAA
1 TATAATTCATATATATA
*
1136957 CTATAGTTCATATATATA
1 -TATAATTCATATATATA
1136975 GTATA
1 -TATA
1136980 TAAATATAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
17 14 0.30
18 32 0.70
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (17 bp):
TATAATTCATATATATA
Found at i:1136990 original size:33 final size:32
Alignment explanation
Indices: 1136953--1137019 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
1136943 AATTCATATG
*
1136953 TAAACTATAGTTCATATATATAGTATATAAATA
1 TAAACTATAGTTCATATAAATAGTATA-AAATA
*
1136986 TAAACTATAGTTTATATAAATAGTATAAAATA
1 TAAACTATAGTTCATATAAATAGTATAAAATA
1137018 TA
1 TA
1137020 GTATATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (32 bp):
TAAACTATAGTTCATATAAATAGTATAAAATA
Found at i:1137010 original size:133 final size:131
Alignment explanation
Indices: 1136801--1137050 Score: 283
Period size: 133 Copynumber: 1.9 Consensus size: 131
1136791 CTACATAGTT
* * * ***
1136801 TATATATATAGTTCATATGTAAACTATAGTTCATATGTAAATATCAACTATAGTTTATATGTAAA
1 TATATATATAATTCATATGTAAACTATAGTTCATATATAAATATCAAATATAAACTATATGTAAA
** * * * *
1136866 CTATAGTTAGTATATAAACTATA-TAGTTTATATTTAAACTATAGTTCATATATAAATATTAATT
66 CTATAAATAGTATA-AAA-TATAGTA-TATAAATATAAACTATAATTCATATATAAATATTAATT
1136930 ATAG
128 ATAG
1136934 TATATATATAATTCATATGTAAACTATAGTTCATATATATAGTATAT-AAATATAAACTATA-GT
1 TATATATATAATTCATATGTAAACTATAGTTCATATATA-A--ATATCAAATATAAACTATATGT
** *
1136997 TTA-TATAAATAGTATAAAATATAGTATATAAATATAAACTATAATTTATATATA
63 AAACTATAAATAGTATAAAATATAGTATATAAATATAAACTATAATTCATATATA
1137051 TAGTATATAC
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
131 27 0.28
132 5 0.05
133 48 0.49
134 4 0.04
135 10 0.10
136 4 0.04
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (131 bp):
TATATATATAATTCATATGTAAACTATAGTTCATATATAAATATCAAATATAAACTATATGTAAA
CTATAAATAGTATAAAATATAGTATATAAATATAAACTATAATTCATATATAAATATTAATTATA
G
Found at i:1137019 original size:25 final size:25
Alignment explanation
Indices: 1136984--1137064 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
1136974 AGTATATAAA
1136984 TATAAACTATAGTTTATATAAATAG
1 TATAAACTATAGTTTATATAAATAG
*
1137009 TATAAAATATAG--TATAT-AA-A-
1 TATAAACTATAGTTTATATAAATAG
* *
1137029 TATAAACTATAATTTATATATATAG
1 TATAAACTATAGTTTATATAAATAG
*
1137054 TATATACTATA
1 TATAAACTATA
1137065 TAAATAGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
20 10 0.22
21 1 0.02
22 7 0.15
23 6 0.13
24 1 0.02
25 21 0.46
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.41
Consensus pattern (25 bp):
TATAAACTATAGTTTATATAAATAG
Found at i:1137022 original size:12 final size:13
Alignment explanation
Indices: 1136983--1137032 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1136973 TAGTATATAA
1136983 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
1136997 TTATATAA-ATAGT
1 ATATA-AATATAGT
1137010 ATA-AAATATAGT
1 ATATAAATATAGT
1137022 ATATAAATATA
1 ATATAAATATA
1137033 AACTATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:1137024 original size:45 final size:45
Alignment explanation
Indices: 1136970--1137057 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
1136960 TAGTTCATAT
*
1136970 ATATAGTATATAAATATAAACTATAGTTTATATAAATAGTATAAA
1 ATATAGTATATAAATATAAACTATAATTTATATAAATAGTATAAA
*
1137015 ATATAGTATATAAATATAAACTATAATTTATATATATAGTATA
1 ATATAGTATATAAATATAAACTATAATTTATATAAATAGTATA
1137058 TACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (45 bp):
ATATAGTATATAAATATAAACTATAATTTATATAAATAGTATAAA
Found at i:1137034 original size:20 final size:20
Alignment explanation
Indices: 1136970--1137070 Score: 85
Period size: 20 Copynumber: 4.8 Consensus size: 20
1136960 TAGTTCATAT
1136970 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
1136990 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
1137015 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
* * * * **
1137035 CTATAATTTATATATATAGT
1 ATATAGTATATAAATATAAA
*
1137055 ATATACTATATAAATA
1 ATATAGTATATAAATA
1137071 GTTTATATAG
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
20 37 0.58
21 1 0.02
22 7 0.11
23 7 0.11
24 1 0.02
25 11 0.17
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:1137064 original size:18 final size:18
Alignment explanation
Indices: 1137043--1137077 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1137033 AACTATAATT
*
1137043 TATATATATAGTATATAC
1 TATATAAATAGTATATAC
*
1137061 TATATAAATAGTTTATA
1 TATATAAATAGTATATA
1137078 TAGTTCACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATAAATAGTATATAC
Found at i:1137147 original size:9 final size:9
Alignment explanation
Indices: 1137118--1137148 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1137108 ATATGTAAAC
1137118 TATATAGTT
1 TATATAGTT
*
1137127 TACATAGTT
1 TATATAGTT
1137136 TATATAGTT
1 TATATAGTT
1137145 TATA
1 TATA
1137149 CATATAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (9 bp):
TATATAGTT
Found at i:1137193 original size:20 final size:20
Alignment explanation
Indices: 1137118--1137199 Score: 73
Period size: 20 Copynumber: 4.1 Consensus size: 20
1137108 ATATGTAAAC
*
1137118 TATATAGTTTAC--ATAGTT
1 TATATAGTTTACATATAGTA
1137136 TATATAGTTTATACATATAGT-
1 TATATAG-TT-TACATATAGTA
**
1137157 TCATAT-GTAAACTATATAGTA
1 T-ATATAGTTTAC-ATATAGTA
1137178 TATATAGTTTACATATAGTA
1 TATATAGTTTACATATAGTA
1137198 TA
1 TA
1137200 GGTTAGTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
18 7 0.13
19 4 0.08
20 25 0.48
21 7 0.13
22 9 0.17
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (20 bp):
TATATAGTTTACATATAGTA
Found at i:1137228 original size:11 final size:11
Alignment explanation
Indices: 1137176--1137229 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
1137166 AACTATATAG
1137176 TATATATAGTT
1 TATATATAGTT
* *
1137187 TACATATAGTA
1 TATATATAGTT
**
1137198 TAGGT-TAGTT
1 TATATATAGTT
1137208 TATAT-T-GTT
1 TATATATAGTT
1137217 TATATATAGTT
1 TATATATAGTT
1137228 TA
1 TA
1137230 AATACTACTA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
9 8 0.24
10 9 0.26
11 17 0.50
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (11 bp):
TATATATAGTT
Found at i:1137347 original size:22 final size:24
Alignment explanation
Indices: 1137313--1137445 Score: 87
Period size: 26 Copynumber: 5.3 Consensus size: 24
1137303 TTAAACCATA
*
1137313 TATATATATATAAACTATATAGTT
1 TATATATATATAAACTATATAATT
1137337 TATAT-TA-ATAAACTATATAATT
1 TATATATATATAAACTATATAATT
* * *
1137359 TATACAATATATATTA-TTTATAATT
1 TATA-TATATATA-AACTATATAATT
*
1137384 ATACATAATATATAAA-TATA-AATT
1 -TATAT-ATATATAAACTATATAATT
*
1137408 GTATAGGTTATATATAATTCATATATAATT
1 -TATA---TATATATAA-AC-TATATAATT
1137438 TATATATA
1 TATATATA
1137446 AACTATGTAC
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
22 18 0.21
23 2 0.02
24 14 0.16
25 15 0.18
26 23 0.27
27 1 0.01
29 8 0.09
30 4 0.05
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (24 bp):
TATATATATATAAACTATATAATT
Found at i:1137441 original size:9 final size:10
Alignment explanation
Indices: 1137365--1137446 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 10
1137355 AATTTATACA
1137365 ATATAT-ATT
1 ATATATAATT
*
1137374 ATTTATAATT
1 ATATATAATT
*
1137384 ATACATAATAT
1 ATATATAAT-T
1137395 ATAAATATAAATT
1 AT--ATAT-AATT
* **
1137408 GTATA-GGTT
1 ATATATAATT
1137417 ATATATAATT
1 ATATATAATT
1137427 CATATATAATTT
1 -ATATATAA-TT
1137439 ATATATAA
1 ATATATAA
1137447 ACTATGTACT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
9 11 0.20
10 12 0.22
11 22 0.40
12 2 0.04
13 5 0.09
14 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (10 bp):
ATATATAATT
Found at i:1137444 original size:13 final size:11
Alignment explanation
Indices: 1137415--1137446 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1137405 ATTGTATAGG
1137415 TTATATATAAT
1 TTATATATAAT
*
1137426 TCATATATAAT
1 TTATATATAAT
1137437 TTATATATAA
1 TTATATATAA
1137447 ACTATGTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TTATATATAAT
Found at i:1137526 original size:20 final size:19
Alignment explanation
Indices: 1137494--1137531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1137484 AAATTATATA
1137494 GTATTATAATTTATACATG
1 GTATTATAATTTATACATG
*
1137513 GTATCTATAGTTTATACAT
1 GTAT-TATAATTTATACAT
1137532 AATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (19 bp):
GTATTATAATTTATACATG
Found at i:1137541 original size:20 final size:20
Alignment explanation
Indices: 1137478--1137541 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 20
1137468 TCAATAATTC
* *
1137478 ATATATAAATTAT--ATAGT
1 ATATATAATTTATACATAAT
**
1137496 AT-TATAATTTATACATGGT
1 ATATATAATTTATACATAAT
* *
1137515 ATCTATAGTTTATACATAAT
1 ATATATAATTTATACATAAT
1137535 ATATATA
1 ATATATA
1137542 TAATATATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
17 9 0.24
18 2 0.05
19 6 0.16
20 20 0.54
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (20 bp):
ATATATAATTTATACATAAT
Found at i:1137544 original size:11 final size:11
Alignment explanation
Indices: 1137525--1137582 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
1137515 ATCTATAGTT
*
1137525 TATACATAATA
1 TATATATAATA
1137536 TATATATAATA
1 TATATATAATA
*
1137547 TATAGTTTACATA
1 TATA-TATA-ATA
1137560 TAGTATATAATA
1 TA-TATATAATA
1137572 -ATATA-AATA
1 TATATATAATA
1137581 TA
1 TA
1137583 AACTATATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 4 0.10
10 5 0.12
11 15 0.38
12 6 0.15
13 8 0.20
14 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (11 bp):
TATATATAATA
Found at i:1137551 original size:29 final size:28
Alignment explanation
Indices: 1137518--1137576 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
1137508 ACATGGTATC
*
1137518 TATAGTTTATACATAATATATATATAATA
1 TATAGTTTACACATAATATATA-ATAATA
* *
1137547 TATAGTTTACATATAGTATATAATAATA
1 TATAGTTTACACATAATATATAATAATA
1137575 TA
1 TA
1137577 AATATAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (28 bp):
TATAGTTTACACATAATATATAATAATA
Found at i:1137640 original size:22 final size:21
Alignment explanation
Indices: 1137578--1137641 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
1137568 AATAATATAA
*
1137578 ATATAAACTATATAGTTTCTAT
1 ATATAAA-TATATAGTTTTTAT
*
1137600 ATAT-AATACGTATA--CTTTAT
1 ATATAAATA--TATAGTTTTTAT
1137620 ATATAAATTATATAGTTTTTAT
1 ATATAAA-TATATAGTTTTTAT
1137642 TACATATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
20 14 0.42
21 4 0.12
22 15 0.45
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (21 bp):
ATATAAATATATAGTTTTTAT
Found at i:1138469 original size:215 final size:216
Alignment explanation
Indices: 1137766--1138649 Score: 1348
Period size: 210 Copynumber: 4.2 Consensus size: 216
1137756 TGTTTAATTC
* * * *
1137766 ATTTAAATTT-TAATTTCATATTTGTTCAATTTAATCCTTAAAATTATATTTGCATCTAAAATTG
1 ATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTATATTTGCATCTGAAATTG
* * *
1137830 ACTCATACTTATTACTTATTTATATTTTTTAATTGACCCATAACTTTTTAAATGTGTATAATTTA
66 ACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTA
* *
1137895 GTACTTTTTTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATA
131 GTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATG
1137960 TGTGTTGTTTAATTTATTTAA
196 TGTGTTGTTTAATTTATTTAA
* *
1137981 ATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTCCATCTGAAATTG
1 ATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTATATTTGCATCTGAAATTG
* * * *
1138046 ACCCATACTTATAACTTATTTCTATTTTTTAATTGGCCCATAGCTTTTTAAATGGCTATAATTTA
66 ACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTA
*
1138111 GTACTTTTTTGTATTAATTTCAACCTCACAAATTTAAAATTATTTTGATTTGAT-CC-C-T---T
131 GTACTTTTTTGTATTAATTTCAACCTCAC-AATTTAAAATTATTTCGATTTGATCCCTCATCAAT
1138170 -TGTGTTGTTTAATTTATTTAA
195 GTGTGTTGTTTAATTTATTTAA
* ** * *
1138191 ATTTTTATTCATAATTTTATATTTGTTCAATTTAGTCCTCCAAATTATATTTGCATCTGAAATTG
1 ATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTATATTTGCATCTGAAATTG
* *
1138256 ACCCATACTTATTACATATTTATATTTTTTAATTGGCCCATAACTTTGTAAATGGGTATAATTTA
66 ACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTA
*
1138321 GTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTTATCAATG
131 GTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATG
1138385 TGTGTTGTTTAATTTATTTAA
196 TGTGTTGTTTAATTTATTTAA
* * *
1138406 ATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTATATTTGCATATGAAATTG
1 ATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTATATTTGCATCTGAAATTG
* * *
1138471 ACCCATACTTATTACTTATTTATA-TTTATATTTGGCCCATAACTTTTTAAATGGGCATAATTTA
66 ACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTA
*
1138535 GTACTTTTTTGTATTAATTTCAACCTCACAATTTAAACTTA--T---TTTGATCCCTCATCAATG
131 GTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATG
* *
1138595 TATGTTGTTTAAATTATTTAA
196 TGTGTTGTTTAATTTATTTAA
*
1138616 ATTTAAATTTGTAATTTCATATTTGTTCAATTTA
1 ATTTTAATTTGTAATTTCATATTTGTTCAATTTA
1138650 ATTCTTAAAT
Statistics
Matches: 616, Mismatches: 43, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
208 23 0.04
209 26 0.04
210 210 0.34
211 2 0.00
213 1 0.00
214 42 0.07
215 150 0.24
216 139 0.23
217 23 0.04
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (216 bp):
ATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAATTATATTTGCATCTGAAATTG
ACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTA
GTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATG
TGTGTTGTTTAATTTATTTAA
Found at i:1138603 original size:425 final size:426
Alignment explanation
Indices: 1137766--1138651 Score: 1386
Period size: 425 Copynumber: 2.1 Consensus size: 426
1137756 TGTTTAATTC
* *
1137766 ATTTAAATT-TTAATTTCATATTTGTTCAATTTAATCCTTAAAATTATATTTGCATCTAAAATTG
1 ATTTAAATTCATAATTTCATATTTGTTCAATTTAATCCTCAAAATTATATTTGCATCTAAAATTG
* * * *
1137830 ACTCATACTTATTACTTATTTATATTTTTTAATTGACCCATAACTTTTTAAATGTGTATAATTTA
66 ACCCATACTTATTACATATTTATATTTTTTAATTGACCCATAACTTTGTAAATGGGTATAATTTA
1137895 GTACTTTTTTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATA
131 GTACTTTTTTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATA
*
1137960 TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAA
196 TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAA
* * * *
1138025 TTATATTTCCATCTGAAATTGACCCATACTTATAACTTATTTCTATTTTTTAATTGGCCCATAGC
261 TTATATTTCCATATGAAATTGACCCATACTTATAACTTATTTATATTTTATAATTGGCCCATAAC
1138090 TTTTTAAATGGCTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAAATTTAAAATTATT
326 TTTTTAAATGGCTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAAATTTAAAATTATT
* * ** * * *
1138155 TTGATTTGATCCCTTTGTGTTGTTTAATTTATTTAA
391 TTGATCTCATCAATGTATGTTGTTTAAATTATTTAA
** * * * *
1138191 ATTTTTATTCATAATTTTATATTTGTTCAATTTAGTCCTCCAAATTATATTTGCATCTGAAATTG
1 ATTTAAATTCATAATTTCATATTTGTTCAATTTAATCCTCAAAATTATATTTGCATCTAAAATTG
*
1138256 ACCCATACTTATTACATATTTATATTTTTTAATTGGCCCATAACTTTGTAAATGGGTATAATTTA
66 ACCCATACTTATTACATATTTATATTTTTTAATTGACCCATAACTTTGTAAATGGGTATAATTTA
* * *
1138321 GTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTTATCAATG
131 GTACTTTTTTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATA
* *
1138385 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
196 TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAA
* * *
1138450 TTATATTTGCATATGAAATTGACCCATACTTATTACTTATTTATA-TTTATATTTGGCCCATAAC
261 TTATATTTCCATATGAAATTGACCCATACTTATAACTTATTTATATTTTATAATTGGCCCATAAC
*
1138514 TTTTTAAATGGGC-ATAATTTAGTACTTTTTTGTATTAATTTCAACCTCAC-AATTTAAACTTAT
326 TTTTTAAAT-GGCTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAAATTTAAAATTAT
1138577 TTTGATCCCTCATCAATGTATGTTGTTTAAATTATTTAA
390 TTTGAT--CTCATCAATGTATGTTGTTTAAATTATTTAA
**
1138616 ATTTAAATTTGTAATTTCATATTTGTTCAATTTAAT
1 ATTTAAATTCATAATTTCATATTTGTTCAATTTAAT
1138652 TCTTAAATTT
Statistics
Matches: 417, Mismatches: 40, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
423 18 0.04
424 62 0.15
425 224 0.54
426 113 0.27
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (426 bp):
ATTTAAATTCATAATTTCATATTTGTTCAATTTAATCCTCAAAATTATATTTGCATCTAAAATTG
ACCCATACTTATTACATATTTATATTTTTTAATTGACCCATAACTTTGTAAATGGGTATAATTTA
GTACTTTTTTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATA
TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTCAAAA
TTATATTTCCATATGAAATTGACCCATACTTATAACTTATTTATATTTTATAATTGGCCCATAAC
TTTTTAAATGGCTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAAATTTAAAATTATT
TTGATCTCATCAATGTATGTTGTTTAAATTATTTAA
Found at i:1139486 original size:56 final size:56
Alignment explanation
Indices: 1139425--1139536 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
1139415 TAATGTAAAA
*
1139425 CTATCAAATTGTAATTGTAAACATAATGTAAAAAATTCGATTAAAGTTTTAATGGC
1 CTATCAAATTGTAATTGTAAACATAATGTAAAAAATTCGATTAAAGTTGTAATGGC
1139481 CTATCAAATTGTAATTGTAAACATAATGTAAAAAATTCGATTAAAGTTGTAATGGC
1 CTATCAAATTGTAATTGTAAACATAATGTAAAAAATTCGATTAAAGTTGTAATGGC
1139537 AGTAATTTCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (56 bp):
CTATCAAATTGTAATTGTAAACATAATGTAAAAAATTCGATTAAAGTTGTAATGGC
Found at i:1140879 original size:20 final size:20
Alignment explanation
Indices: 1140854--1140988 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1140844 AATTGGGAAA
1140854 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1140874 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1140894 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1140915 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1140935 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1140955 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1140975 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1140989 TTTCTAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1140898 original size:61 final size:61
Alignment explanation
Indices: 1140851--1140982 Score: 165
Period size: 61 Copynumber: 2.2 Consensus size: 61
1140841 ACGAATTGGG
* * * * **
1140851 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACACGATAATAC
* * * *
1140912 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACACGATAATAC
*
1140973 ATAATCGCAA
1 AAAATCGCAA
1140983 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACACGATAATAC
Found at i:1141184 original size:22 final size:22
Alignment explanation
Indices: 1141156--1141199 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1141146 CACTCTCTCA
1141156 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1141178 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1141200 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1141502 original size:20 final size:20
Alignment explanation
Indices: 1141443--1141506 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
1141433 GCGATTTTAG
* *
1141443 TTTCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
1141463 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
1141483 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
1141503 TTTC
1 TTTC
1141507 AGAAACTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Done.