Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 62 of 65
Found at i:12199043 original size:33 final size:34
Alignment explanation
Indices: 12198981--12199056 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
12198971 ACTTAATTCG
* *
12198981 CGTTGTGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCACATTGCGATTCTCT
12199015 CGTTGCGATTTTCA-TTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCACATTGCGATTCTCT
12199048 CGTTGCGAT
1 CGTTGCGAT
12199057 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 27 0.68
34 13 0.32
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCACATTGCGATTCTCT
Found at i:12199181 original size:14 final size:15
Alignment explanation
Indices: 12199162--12199199 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
12199152 CATCAATTAA
12199162 ACAAATCAAT-ATTT
1 ACAAATCAATCATTT
*
12199176 ACAAATC-ATCTTTT
1 ACAAATCAATCATTT
12199190 ACAAATCAAT
1 ACAAATCAAT
12199200 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:12200680 original size:42 final size:41
Alignment explanation
Indices: 12200574--12200684 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 41
12200564 TCTAGAATGT
* *
12200574 TGGGAG-GGACCTCTTCAACGATGACAGGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGCCTCTTGAACGA
* ** *
12200615 TGGGAGAGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACA-GGGCCTCTTGAACGA
12200657 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
12200685 TGAGTCGGGC
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 20 0.35
42 34 0.60
43 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (41 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGCCTCTTGAACGA
Found at i:12201198 original size:20 final size:20
Alignment explanation
Indices: 12201175--12201250 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
12201165 TTGCAACGCT
*
12201175 AAAATGACTATCGCAACATG
1 AAAATGACTATCGCAACACG
**
12201195 AAAATGACTATCGCAATGCG
1 AAAATGACTATCGCAACACG
**
12201215 AAAATGACTATCGCAATGCG
1 AAAATGACTATCGCAACACG
**
12201235 AATTTGACTATCGCAA
1 AAAATGACTATCGCAA
12201251 TGCGAATTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (20 bp):
AAAATGACTATCGCAACACG
Found at i:12201219 original size:40 final size:40
Alignment explanation
Indices: 12201175--12201256 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
12201165 TTGCAACGCT
*
12201175 AAAATGACTATCGCAACATGAAAATGACTATCGCAATGCG
1 AAAATGACTATCGCAACACGAAAATGACTATCGCAATGCG
** **
12201215 AAAATGACTATCGCAATGCGAATTTGACTATCGCAATGCG
1 AAAATGACTATCGCAACACGAAAATGACTATCGCAATGCG
12201255 AA
1 AA
12201257 TTCAACTATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (40 bp):
AAAATGACTATCGCAACACGAAAATGACTATCGCAATGCG
Found at i:12201251 original size:20 final size:20
Alignment explanation
Indices: 12201199--12201270 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
12201189 AACATGAAAA
**
12201199 TGACTATCGCAATGCGAAAA
1 TGACTATCGCAATGCGAATT
12201219 TGACTATCGCAATGCGAATT
1 TGACTATCGCAATGCGAATT
12201239 TGACTATCGCAATGCGAATT
1 TGACTATCGCAATGCGAATT
**
12201259 CAACTATCGCAA
1 TGACTATCGCAA
12201271 CGAGAGAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (20 bp):
TGACTATCGCAATGCGAATT
Found at i:12201325 original size:20 final size:20
Alignment explanation
Indices: 12201296--12201443 Score: 141
Period size: 20 Copynumber: 7.8 Consensus size: 20
12201286 GCGATTTTCA
* * *
12201296 TTTCGTATTGCGATAATCAA
1 TTTCGCATTGCGATAGTCAT
*
12201316 ATTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
12201336 TTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
* **
12201356 TTTCGCGTTGCGATTTTCA-
1 TTTCGCATTGCGATAGTCAT
*
12201375 TTTCGCATTACGAT--T-A-
1 TTTCGCATTGCGATAGTCAT
*
12201391 TCTCG--TTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
*
12201409 ATTT-GCGTTGCGATAGTCAT
1 -TTTCGCATTGCGATAGTCAT
12201429 TTTCGCATTGCGATA
1 TTTCGCATTGCGATA
12201444 ATAAACTATT
Statistics
Matches: 106, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
14 6 0.06
16 6 0.06
17 2 0.02
18 1 0.01
19 17 0.16
20 74 0.70
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTCGCATTGCGATAGTCAT
Found at i:12203335 original size:20 final size:20
Alignment explanation
Indices: 12203312--12203380 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
12203302 CTGAAACTTT
12203312 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
12203332 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
**
12203352 CTATCGCAACACG-AAATGA
1 AAATCGCAACACGAAAATGA
12203371 AAATCGCAAC
1 AAATCGCAAC
12203381 GACAGAATCG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 14 0.31
20 31 0.69
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:12203779 original size:22 final size:22
Alignment explanation
Indices: 12203715--12203780 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
12203705 TGACCGTGAA
* *
12203715 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* * *
12203737 TGATATCGTTGGAGATTGGGAC
1 TGATTTCGTCGGAGATGGGGAC
12203759 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
12203781 GAATGTCTCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:12204000 original size:20 final size:20
Alignment explanation
Indices: 12203977--12204070 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
12203967 CGATAGTCAG
12203977 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
12203997 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
12204018 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
12204038 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
12204058 ATTCGCATTGCGA
1 ATTCGCATTGCGA
12204071 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 49 0.75
21 16 0.25
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:12204030 original size:41 final size:40
Alignment explanation
Indices: 12203959--12204070 Score: 152
Period size: 41 Copynumber: 2.8 Consensus size: 40
12203949 GTTATGTAAA
** *
12203959 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTTCAAATTCGCATTGCGATTTACGTAT
*
12203999 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTT-CAAATTCGCATTGCGATTTACGTAT
* **
12204040 TCGCATTGCGATTTACGTATTCGCATTGCGA
1 TCGCATTGCGATTTTCAAATTCGCATTGCGA
12204071 ATTAGGAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 26 0.41
41 37 0.59
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (40 bp):
TCGCATTGCGATTTTCAAATTCGCATTGCGATTTACGTAT
Found at i:12204090 original size:21 final size:21
Alignment explanation
Indices: 12204060--12204112 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
12204050 ATTTACGTAT
*
12204060 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
12204081 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
12204102 TCGCAATGCGA
1 TCGCAATGCGA
12204113 TAGTCAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:12204091 original size:61 final size:61
Alignment explanation
Indices: 12203977--12204091 Score: 167
Period size: 61 Copynumber: 1.9 Consensus size: 61
12203967 CGATAGTCAG
* * * **
12203977 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAATGCGATTTACGT
**
12204038 ATTCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCGCAATGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAATGCGA
12204092 ATTTGGAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (61 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAATGCGATTTACGT
Found at i:12210034 original size:21 final size:21
Alignment explanation
Indices: 12209917--12210054 Score: 70
Period size: 21 Copynumber: 6.8 Consensus size: 21
12209907 AAATGACCAA
*
12209917 CAAAATCGCAACGCGA--TCC
1 CAAAATCGCAACGCGATTTTC
* ** *
12209936 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGATTTTC
12209956 CAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGATT-TTC
* * ** *
12209977 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGATTTTC
* ***
12209998 CAAATTCGCGTTGCGATTTTC
1 CAAAATCGCAACGCGATTTTC
* * *
12210019 CAGAATCGCAACGCGAATAT-
1 CAAAATCGCAACGCGATTTTC
*
12210039 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
12210055 ACACATAAAT
Statistics
Matches: 86, Mismatches: 28, Indels: 9
0.70 0.23 0.07
Matches are distributed among these distances:
18 1 0.01
19 11 0.13
20 28 0.33
21 44 0.51
22 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
CAAAATCGCAACGCGATTTTC
Found at i:12210083 original size:20 final size:20
Alignment explanation
Indices: 12210022--12210250 Score: 239
Period size: 20 Copynumber: 11.4 Consensus size: 20
12210012 GATTTTCCAG
* ** *
12210022 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
12210042 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
12210062 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
12210082 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12210102 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12210122 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
12210142 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12210162 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
12210182 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
12210202 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
12210222 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
12210242 AATCACAAC
1 AATCGCAAC
12210251 ACTGAAATTT
Statistics
Matches: 177, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 173 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:12210672 original size:20 final size:19
Alignment explanation
Indices: 12210605--12210679 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 19
12210595 GTGTTTCAAA
12210605 GAAATTGAAAATCGCAATGC
1 GAAA-TGAAAATCGCAATGC
12210625 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
* *
12210642 --CA-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
*
12210658 GGAAATGAAAATCGCATTGC
1 -GAAATGAAAATCGCAATGC
12210678 GA
1 GA
12210680 TTCTCTCGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 1 0.02
17 1 0.02
19 15 0.34
20 16 0.36
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:12210749 original size:53 final size:53
Alignment explanation
Indices: 12210669--12210786 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
12210659 GAAATGAAAA
12210669 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA-TT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
12210722 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
12210775 TCGCATTGCGAT
1 TCGCATTGCGAT
12210787 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 16 0.25
53 48 0.75
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
Found at i:12210795 original size:20 final size:19
Alignment explanation
Indices: 12210688--12210786 Score: 136
Period size: 20 Copynumber: 5.4 Consensus size: 19
12210678 GATTCTCTCG
12210688 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
12210708 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
12210727 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
12210741 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
12210760 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
12210780 TTGCGAT
1 TTGCGAT
12210787 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 22 0.31
20 29 0.41
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:12210912 original size:14 final size:14
Alignment explanation
Indices: 12210893--12210929 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12210883 CATCAATTAC
12210893 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12210907 ACAAATCATCTTTT
1 ACAAATCAACTTTT
12210921 ACAAATCAA
1 ACAAATCAA
12210930 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:12212897 original size:19 final size:19
Alignment explanation
Indices: 12212855--12213027 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
12212845 TAGTTTACTC
* *
12212855 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
12212875 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
12212894 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
12212913 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
12212932 TCGCAACGCAAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
12212951 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
12212965 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
12212984 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
12212998 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
12213017 TCGCAATGCGA
1 TCGCAACGCGA
12213028 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.06
17 6 0.05
18 1 0.01
19 81 0.64
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:12212966 original size:14 final size:14
Alignment explanation
Indices: 12212949--12213005 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
12212939 GCAAAATGAA
*
12212949 AATCGCAACGACAG
1 AATCGCAACGAAAG
12212963 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
12212980 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
12212996 AATCGCAACG
1 AATCGCAACG
12213006 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:12212968 original size:33 final size:33
Alignment explanation
Indices: 12212930--12213022 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
12212920 GCGAAACCAA
*
12212930 AATCGCAACGCAAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
12212963 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
12212996 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
12213023 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:12213019 original size:52 final size:53
Alignment explanation
Indices: 12212871--12213027 Score: 142
Period size: 52 Copynumber: 2.9 Consensus size: 53
12212861 CACGAAACTT
* * *
12212871 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACC
1 AAAATCGCAACGC---A-GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACC
* ** * **
12212928 AAAATCGCAACGCA-A-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATG
1 AAAATCGCAACGCAGAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACC
*
12212980 AAAATCGCAACG-AGAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AAAATCGCAACGCAGAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
12213028 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
50 8 0.10
51 5 0.06
52 41 0.51
53 4 0.05
54 10 0.12
57 13 0.16
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (53 bp):
AAAATCGCAACGCAGAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACC
Found at i:12213039 original size:19 final size:19
Alignment explanation
Indices: 12213017--12213058 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
12213007 GAAATGAAAA
12213017 TCGCAATGCGATTTTGGTT
1 TCGCAATGCGATTTTGGTT
**
12213036 TCGCGTTGCGATTTTGGTT
1 TCGCAATGCGATTTTGGTT
12213055 TCGC
1 TCGC
12213059 GTTGCGATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.43
Consensus pattern (19 bp):
TCGCAATGCGATTTTGGTT
Found at i:12213059 original size:19 final size:19
Alignment explanation
Indices: 12213023--12213067 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
12213013 AAAATCGCAA
12213023 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
12213042 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
12213061 TGCGATT
1 TGCGATT
12213068 CTGTCATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.07, C:0.16, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:12213083 original size:33 final size:33
Alignment explanation
Indices: 12213041--12213132 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
12213031 TGGTTTCGCG
* *
12213041 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCA
1 TTGCGATTTTAGTTTCGCGTTGCGATTCTCTCA
*
12213074 TTGCGATTTTCA-TTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTT-AGTTTCGCGTTGCGATTCTCTCA
*
12213107 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTT-AGTTTCGCGTTGCGA
12213133 AAGTAAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
33 40 0.77
34 12 0.23
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTAGTTTCGCGTTGCGATTCTCTCA
Found at i:12213098 original size:19 final size:19
Alignment explanation
Indices: 12213023--12213100 Score: 76
Period size: 19 Copynumber: 4.4 Consensus size: 19
12213013 AAAATCGCAA
*
12213023 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCGTTTCGCGT
*
12213042 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCGTTTCGCGT
* *
12213061 TGCGA--TTC-TGT--CAT
1 TGCGATTTTCGTTTCGCGT
*
12213075 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCGTTTCGCGT
12213094 TGCGATT
1 TGCGATT
12213101 CTCTCGTTGC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
19 33 0.67
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCGTTTCGCGT
Found at i:12215079 original size:20 final size:20
Alignment explanation
Indices: 12215048--12215130 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
12215038 TTTTGGTTGA
12215048 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
12215068 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
12215088 AAATGAAAATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
12215108 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
12215128 AAT
1 AAT
12215131 CGCAACGCGA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 18 0.34
20 20 0.38
21 15 0.28
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:12215111 original size:19 final size:19
Alignment explanation
Indices: 12215046--12215159 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
12215036 TCTTTTGGTT
*
12215046 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
12215065 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
12215087 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
12215106 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
12215123 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
12215139 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
12215158 GA
1 GA
12215160 TTTTGGTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 33 0.43
20 12 0.16
21 12 0.16
22 4 0.05
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:12215207 original size:21 final size:21
Alignment explanation
Indices: 12215182--12215255 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
12215172 GTTGCGATTC
12215182 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
12215203 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
12215224 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
12215245 TCTCGTTGCGA
1 TCTCGTTGCGA
12215256 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:12215377 original size:33 final size:33
Alignment explanation
Indices: 12215335--12215405 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
12215325 AATACTAACT
*
12215335 TGAAAATCGCAACGAGAGAATAGCAACGTGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
*
12215368 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
12215401 TGAAA
1 TGAAA
12215406 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:12215391 original size:14 final size:14
Alignment explanation
Indices: 12215339--12215395 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
12215329 CTAACTTGAA
12215339 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
12215353 AATAGCAACGTGAAATGAA
1 AATCGCAAC--G--A-GAG
12215372 AATCGCAACGAGAG
1 AATCGCAACGAGAG
12215386 AATCGCAACG
1 AATCGCAACG
12215396 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 20 0.59
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:12215810 original size:20 final size:20
Alignment explanation
Indices: 12215785--12215977 Score: 201
Period size: 20 Copynumber: 9.6 Consensus size: 20
12215775 CTTTAAAAAT
12215785 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
12215805 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
12215825 TGTCGTTGTGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
12215846 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
***
12215866 CATATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
12215886 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
12215906 CACGTGGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
12215926 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
12215946 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
12215966 CGCGTTGCGATT
1 CGCGTTGCGATT
12215978 CTGGAAAATC
Statistics
Matches: 142, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
20 125 0.88
21 17 0.12
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:12217308 original size:27 final size:27
Alignment explanation
Indices: 12217278--12217486 Score: 267
Period size: 27 Copynumber: 7.7 Consensus size: 27
12217268 CTCTTCCACC
* * * *
12217278 CCGGCGTTTGGAGCTCTTTCTTCAACA
1 CCGGCGTTTGGAACTCCTTCCTCGACA
* *
12217305 CCGGCGTTTGGTACTCCGTCCTCGACA
1 CCGGCGTTTGGAACTCCTTCCTCGACA
12217332 CCGGCGTTTGGAACT-CTGTCCTCGACA
1 CCGGCGTTTGGAACTCCT-TCCTCGACA
*
12217359 CCGGCTTTTGGAACTCCTTCCTCGACA
1 CCGGCGTTTGGAACTCCTTCCTCGACA
*
12217386 CCGGCTTTTGGAACTCCTTCCTCGACA
1 CCGGCGTTTGGAACTCCTTCCTCGACA
* * *
12217413 CCTGCTTTTGGAACTCCTTCATCGACA
1 CCGGCGTTTGGAACTCCTTCCTCGACA
* * *
12217440 CCCGCGTTTGGGACTCCGTCCTCGACA
1 CCGGCGTTTGGAACTCCTTCCTCGACA
*
12217467 CCCGCGTTTGGAACTCCTTC
1 CCGGCGTTTGGAACTCCTTC
12217487 TACACCATCT
Statistics
Matches: 162, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 159 0.98
28 2 0.01
ACGTcount: A:0.14, C:0.36, G:0.22, T:0.29
Consensus pattern (27 bp):
CCGGCGTTTGGAACTCCTTCCTCGACA
Found at i:12218968 original size:120 final size:120
Alignment explanation
Indices: 12218755--12218974 Score: 422
Period size: 120 Copynumber: 1.8 Consensus size: 120
12218745 ATCAAAAAAA
12218755 GAAATGGGAGAGATCTGGCTGAACAGTGTTGTATGTTGTAAGTTTTGTTGCAAGTTTTTTTGGAA
1 GAAATGGGAGAGATCTGGCTGAACAGTGTTGTATGTTGTAAGTTTTGTTGCAAGTTTTTTTGGAA
12218820 GAAAAGTAATGAATGTGGTCAAAGATACAAGAGTTAAAAGAATATTTTGCCAATT
66 GAAAAGTAATGAATGTGGTCAAAGATACAAGAGTTAAAAGAATATTTTGCCAATT
* *
12218875 GAAATGGGAGAGATCTGGCTGAACAGTGTTGTATGTTTTAAGTTTTGTTGCTAGTTTTTTTGGAA
1 GAAATGGGAGAGATCTGGCTGAACAGTGTTGTATGTTGTAAGTTTTGTTGCAAGTTTTTTTGGAA
12218940 GAAAAGTAATGAATGTGGTCAAAGATACAAGAGTT
66 GAAAAGTAATGAATGTGGTCAAAGATACAAGAGTT
12218975 CTATGAGTAC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 98 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (120 bp):
GAAATGGGAGAGATCTGGCTGAACAGTGTTGTATGTTGTAAGTTTTGTTGCAAGTTTTTTTGGAA
GAAAAGTAATGAATGTGGTCAAAGATACAAGAGTTAAAAGAATATTTTGCCAATT
Found at i:12222926 original size:18 final size:19
Alignment explanation
Indices: 12222884--12222931 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
12222874 CCTTCTGAGG
*
12222884 GTATCGATACTCTACCCTCA
1 GTATCGATACTC-ACCATCA
*
12222904 GTATCGATACTC-CCATGA
1 GTATCGATACTCACCATCA
12222922 GTATCGATAC
1 GTATCGATAC
12222932 CAAATTTGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
20 12 0.46
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (19 bp):
GTATCGATACTCACCATCA
Found at i:12223355 original size:16 final size:16
Alignment explanation
Indices: 12223333--12223373 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
12223323 TTAGTATTAT
12223333 CTGACCTGTTATGAA-
1 CTGACCTGTTATGAAG
12223348 CTTGACCTGTTATGAAG
1 C-TGACCTGTTATGAAG
12223365 CTGACCTGT
1 CTGACCTGT
12223374 AATTGACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (16 bp):
CTGACCTGTTATGAAG
Found at i:12223828 original size:23 final size:24
Alignment explanation
Indices: 12223798--12223847 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
12223788 TTTTTATGTA
12223798 ATAATTAA-TTAATAA-TTT-AAAT
1 ATAATTAACTTAA-AATTTTAAAAT
12223820 ATAATTTAACTTAAAATTTTAAAAT
1 ATAA-TTAACTTAAAATTTTAAAAT
12223845 ATA
1 ATA
12223848 TATAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 6 0.25
24 7 0.29
25 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATTAACTTAAAATTTTAAAAT
Found at i:12223925 original size:20 final size:19
Alignment explanation
Indices: 12223893--12223942 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
12223883 AATTTTAAAA
12223893 GAAAGATTG-TTTTTGGGAGG
1 GAAA-ATTGATTTTT-GGAGG
12223913 GAAAATTGATTTTTGGAGG
1 GAAAATTGATTTTTGGAGG
*
12223932 AAAAATTGATT
1 GAAAATTGATT
12223943 AAAAGAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (19 bp):
GAAAATTGATTTTTGGAGG
Found at i:12223956 original size:31 final size:31
Alignment explanation
Indices: 12223921--12223981 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
12223911 GGGAAAATTG
*
12223921 ATTTTTGGAGGAAAAATTGATTAAAAGAAAT
1 ATTTTTGAAGGAAAAATTGATTAAAAGAAAT
* *
12223952 ATTTTTTAAGGAAAATTTGATTAAAAGAAA
1 ATTTTTGAAGGAAAAATTGATTAAAAGAAA
12223982 GAACGTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.34
Consensus pattern (31 bp):
ATTTTTGAAGGAAAAATTGATTAAAAGAAAT
Found at i:12223960 original size:16 final size:16
Alignment explanation
Indices: 12223931--12223981 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
12223921 ATTTTTGGAG
*
12223931 GAAAAATTGATTAAAA
1 GAAAATTTGATTAAAA
* *
12223947 GAAATATTT--TTTAAG
1 GAAA-ATTTGATTAAAA
12223962 GAAAATTTGATTAAAA
1 GAAAATTTGATTAAAA
12223978 GAAA
1 GAAA
12223982 GAACGTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 12 0.44
17 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (16 bp):
GAAAATTTGATTAAAA
Found at i:12224274 original size:14 final size:14
Alignment explanation
Indices: 12224255--12224299 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
12224245 TGTTTATATA
12224255 TATATATACTTATG
1 TATATATACTTATG
*
12224269 TATATATGC---T-
1 TATATATACTTATG
12224279 TATATATACTTATG
1 TATATATACTTATG
12224293 TATATAT
1 TATATAT
12224300 GTTTATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
10 8 0.32
11 1 0.04
13 1 0.04
14 15 0.60
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (14 bp):
TATATATACTTATG
Found at i:12224318 original size:24 final size:24
Alignment explanation
Indices: 12224255--12224310 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
12224245 TGTTTATATA
12224255 TATATATACTTATGTATATATGCT
1 TATATATACTTATGTATATATGCT
*
12224279 TATATATACTTATGTATATATGTT
1 TATATATACTTATGTATATATGCT
12224303 TATATATA
1 TATATATA
12224311 TTTGTGTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (24 bp):
TATATATACTTATGTATATATGCT
Found at i:12225344 original size:2 final size:2
Alignment explanation
Indices: 12225337--12225369 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12225327 TCGAATCCGA
12225337 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12225370 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12225374 original size:2 final size:2
Alignment explanation
Indices: 12225369--12225398 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12225359 ACACACACAC
12225369 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
12225399 TAAACTTATA
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:12225434 original size:19 final size:19
Alignment explanation
Indices: 12225410--12225451 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12225400 AAACTTATAT
* *
12225410 TCATACTTATGTATATACA
1 TCATACATATGTACATACA
*
12225429 TCATACATATGTACATATA
1 TCATACATATGTACATACA
12225448 TCAT
1 TCAT
12225452 TGATTAATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (19 bp):
TCATACATATGTACATACA
Found at i:12227519 original size:42 final size:42
Alignment explanation
Indices: 12227440--12227521 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
12227430 ATGGAACTTG
* * *
12227440 AAAAATATAATGATAAAAACTTGATATCAATATTTTTTTTTA
1 AAAAATATAATGATAAAAACTTGATACCAACACTTTTTTTTA
* * * *
12227482 AAAAATATTATGATAGAAACTTGATACCAGCCCTTTTTTT
1 AAAAATATAATGATAAAAACTTGATACCAACACTTTTTTT
12227522 AAATAAAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (42 bp):
AAAAATATAATGATAAAAACTTGATACCAACACTTTTTTTTA
Found at i:12227948 original size:10 final size:10
Alignment explanation
Indices: 12227929--12228014 Score: 54
Period size: 10 Copynumber: 8.4 Consensus size: 10
12227919 TTCGGTAATT
*
12227929 TGTTCGTTTA
1 TGTTCATTTA
12227939 TGTTCATTTA
1 TGTTCATTTA
*
12227949 TGTTCGTTCGTTTA
1 ---T-GTTCATTTA
12227963 TGTTCATTTA
1 TGTTCATTTA
*
12227973 CT-TTCATTTG
1 -TGTTCATTTA
12227983 TG-T-ATGTT-
1 TGTTCAT-TTA
*
12227991 CGTTCATTTA
1 TGTTCATTTA
12228001 TGTTCATTTA
1 TGTTCATTTA
12228011 TGTT
1 TGTT
12228015 GTAGCAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
8 3 0.05
9 7 0.12
10 39 0.65
11 2 0.03
13 1 0.02
14 8 0.13
ACGTcount: A:0.14, C:0.12, G:0.15, T:0.59
Consensus pattern (10 bp):
TGTTCATTTA
Found at i:12227988 original size:24 final size:24
Alignment explanation
Indices: 12227931--12227991 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
12227921 CGGTAATTTG
* *
12227931 TTCGTTTATGTTCATTTATGTTCG
1 TTCGTGTATGTTCATTTATGTTCA
*
12227955 TTCGTTTATGTTCATTTACT-TTCA
1 TTCGTGTATGTTCATTTA-TGTTCA
*
12227979 TTTGTGTATGTTC
1 TTCGTGTATGTTC
12227992 GTTCATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.59
Consensus pattern (24 bp):
TTCGTGTATGTTCATTTATGTTCA
Found at i:12228440 original size:23 final size:23
Alignment explanation
Indices: 12228379--12228466 Score: 87
Period size: 23 Copynumber: 4.0 Consensus size: 23
12228369 TGGTGTTGTG
12228379 GTTTATGTTCATTTATGT-TCGTTT
1 GTTTATGTTCATTTAT-TAT-GTTT
*
12228403 GTTT-TCTTCA--T-TTATGTTT
1 GTTTATGTTCATTTATTATGTTT
12228422 GTTTATGTTCATTTATTATGTTT
1 GTTTATGTTCATTTATTATGTTT
* * *
12228445 GTTTATATTCGTTTATTGTGTT
1 GTTTATGTTCATTTATTATGTT
12228467 CATTCACATC
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
19 9 0.17
20 7 0.13
21 1 0.02
22 1 0.02
23 32 0.59
24 4 0.07
ACGTcount: A:0.14, C:0.07, G:0.15, T:0.65
Consensus pattern (23 bp):
GTTTATGTTCATTTATTATGTTT
Found at i:12234326 original size:36 final size:37
Alignment explanation
Indices: 12234260--12234331 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
12234250 AAAGAATTCA
*
12234260 AGGGGTACCGATACCTTGAAGGACAATATCGATACCC
1 AGGGATACCGATACCTTGAAGGACAATATCGATACCC
*
12234297 AGGGATACCGATACCTT-AAGGA-AGGTATCGATACC
1 AGGGATACCGATACCTTGAAGGACA-ATATCGATACC
12234332 ATCTTGAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 1 0.03
36 15 0.47
37 16 0.50
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (37 bp):
AGGGATACCGATACCTTGAAGGACAATATCGATACCC
Found at i:12235851 original size:18 final size:18
Alignment explanation
Indices: 12235828--12235862 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12235818 AGGGATTAAC
*
12235828 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
12235846 AGTGGTTATTCGGGACA
1 AGTGGTCATTCGGGACA
12235863 AATATTCAGT
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:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:12238133 original size:19 final size:21
Alignment explanation
Indices: 12238101--12238139 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12238091 TGGAAATTAA
*
12238101 TGTTAGAGTGATG-AATTTGG
1 TGTTAGAATGATGAAATTTGG
12238121 TGTTAGAAT-ATGAAATTTG
1 TGTTAGAATGATGAAATTTG
12238140 ACTATTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (21 bp):
TGTTAGAATGATGAAATTTGG
Found at i:12239856 original size:18 final size:19
Alignment explanation
Indices: 12239823--12239858 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12239813 TGAAAATATG
12239823 AATCTGAAATTAAGTTATA
1 AATCTGAAATTAAGTTATA
12239842 AATCTGAAA-TAAGTTAT
1 AATCTGAAATTAAGTTAT
12239859 GAGTCCGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (19 bp):
AATCTGAAATTAAGTTATA
Found at i:12239945 original size:19 final size:19
Alignment explanation
Indices: 12239917--12239964 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
12239907 AGTACATATT
12239917 ATGAAAATGAAATGTGAAAG
1 ATGAAAATGAAA-GTGAAAG
*
12239937 -TGAATATGAAAGTGAAAG
1 ATGAAAATGAAAGTGAAAG
12239955 ATGAAAATGA
1 ATGAAAATGA
12239965 GATATGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (19 bp):
ATGAAAATGAAAGTGAAAG
Found at i:12241643 original size:39 final size:39
Alignment explanation
Indices: 12241589--12241670 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
12241579 CGAGTCAAAT
** *
12241589 ATATGCACCGTAGTGCTTACACAGAAGGTGGTACCCACC
1 ATATGCACCAAAGTGCTTACACAGAAGGTCGTACCCACC
* *
12241628 ATATGCACCAAAGTGCTTACACATAAGGTCGTGCCCACC
1 ATATGCACCAAAGTGCTTACACAGAAGGTCGTACCCACC
12241667 ATAT
1 ATAT
12241671 ACACTAGGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (39 bp):
ATATGCACCAAAGTGCTTACACAGAAGGTCGTACCCACC
Found at i:12243199 original size:65 final size:64
Alignment explanation
Indices: 12243089--12243244 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 64
12243079 TACACTTGGG
* * * * * *
12243089 GTGCATCGGTACACT-AATTACATTCGATGTTTCAAAAGAGCCAGGAGTGTATCGATGCATTATA
1 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAAAAGAACCAGGAGTGCAACGATGCA-TAGA
12243153 T
64 T
* * * *
12243154 GTGCATCGGTACATAAAATGCATTCGATGTTTTAATAA-AATCAGGAGTGCAACGATGCATGGCT
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCAA-AAGAACCAGGAGTGCAACGATGCATAGAT
*
12243218 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACATAAAATGCATTCGA
12243245 ATTAGGGTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 29 0.37
65 47 0.60
66 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATGCATTCGATGTTTCAAAAGAACCAGGAGTGCAACGATGCATAGAT
Found at i:12243574 original size:13 final size:13
Alignment explanation
Indices: 12243556--12243589 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
12243546 TAAGATTTTC
12243556 TTTGAAAATCAAT
1 TTTGAAAATCAAT
12243569 TTTG-AAATCAAT
1 TTTGAAAATCAAT
12243581 TTTGAAAAT
1 TTTGAAAAT
12243590 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:12245384 original size:13 final size:13
Alignment explanation
Indices: 12245349--12245386 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
12245339 TCCTAATGGG
12245349 CAATGTTTGAAAA
1 CAATGTTTGAAAA
*
12245362 TAAT-TTTGAAAA
1 CAATGTTTGAAAA
12245374 CAATGTTTGAAAA
1 CAATGTTTGAAAA
12245387 ATTATGATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:12245923 original size:23 final size:23
Alignment explanation
Indices: 12245892--12245962 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
12245882 TGCAGAGTGT
12245892 ATCGATGCACATTCAAAGAATGC
1 ATCGATGCACATTCAAAGAATGC
* * * *
12245915 ATCGGTGCACCTTCATAG--TGT
1 ATCGATGCACATTCAAAGAATGC
*
12245936 ATCGATGCATATTC-AAGAGATGC
1 ATCGATGCACATTCAAAGA-ATGC
12245959 ATCG
1 ATCG
12245963 GTACACTTTC
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
23 21 0.58
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (23 bp):
ATCGATGCACATTCAAAGAATGC
Found at i:12245950 original size:44 final size:44
Alignment explanation
Indices: 12245887--12245990 Score: 165
Period size: 44 Copynumber: 2.4 Consensus size: 44
12245877 TACACTGCAG
*
12245887 AGTGTATCGATGCACATTCAA-AGAATGCATCGGTGCACCTTCAT
1 AGTGTATCGATGCACATTCAAGAG-ATGCATCGGTACACCTTCAT
* *
12245931 AGTGTATCGATGCATATTCAAGAGATGCATCGGTACACTTTCAT
1 AGTGTATCGATGCACATTCAAGAGATGCATCGGTACACCTTCAT
12245975 AGTGTATCGATGCACA
1 AGTGTATCGATGCACA
12245991 GTGCACAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 53 0.96
45 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGAGATGCATCGGTACACCTTCAT
Found at i:12255056 original size:22 final size:21
Alignment explanation
Indices: 12255026--12255068 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
12255016 TCTCACTCAA
12255026 ATTCCAACA-TGTTCTAATTCCT
1 ATTCCAACACT-TTCT-ATTCCT
*
12255048 ATTCTAACACTTTCTATTCCT
1 ATTCCAACACTTTCTATTCCT
12255069 TAATTAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 12 0.63
23 1 0.05
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTCCAACACTTTCTATTCCT
Found at i:12256533 original size:54 final size:54
Alignment explanation
Indices: 12256447--12256813 Score: 494
Period size: 54 Copynumber: 6.8 Consensus size: 54
12256437 TGAATATTTC
*
12256447 AACTCATTAT-AATTTATGTGGTTTTGCACACATAGTGCTGATACGGTAATTCACA
1 AACTCATTATGAA-TTATGTGG-GTTGCACACATAGTGCTGATACGGTAATTCACA
* * *
12256502 AACTCATTATGAATTAAGTGGGTTGCACACATAGTG-TCGATACGATAATTCATA
1 AACTCATTATGAATTATGTGGGTTGCACACATAGTGCT-GATACGGTAATTCACA
* *
12256556 AACTCATTATGAATTATGTGTGTTACACACATAGTG-TCGATACGGTAATTCACA
1 AACTCATTATGAATTATGTGGGTTGCACACATAGTGCT-GATACGGTAATTCACA
*
12256610 AACTCATTATGAATTATGTGGGTTGCACACATAGTTCCT-ATACGGTAATTCACA
1 AACTCATTATGAATTATGTGGGTTGCACACATAG-TGCTGATACGGTAATTCACA
* *
12256664 AACTCATTATGAATTAAGTGGGTTGCACACATAGTGCTGATACGATAATTCACA
1 AACTCATTATGAATTATGTGGGTTGCACACATAGTGCTGATACGGTAATTCACA
* * *
12256718 AACTCATTATGAATTACT-TGGGTTGTACACATAGTG-TCGATACAGTAATTCATA
1 AACTCATTATGAATTA-TGTGGGTTGCACACATAGTGCT-GATACGGTAATTCACA
* * *
12256772 ATCTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATA
1 AACTCATTATGAATTATGTGGGTTGCACACATAGTGCTGATA
12256814 TGAATTACGT
Statistics
Matches: 279, Mismatches: 24, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
53 5 0.02
54 253 0.91
55 18 0.06
56 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (54 bp):
AACTCATTATGAATTATGTGGGTTGCACACATAGTGCTGATACGGTAATTCACA
Found at i:12256715 original size:162 final size:163
Alignment explanation
Indices: 12256447--12256806 Score: 559
Period size: 162 Copynumber: 2.2 Consensus size: 163
12256437 TGAATATTTC
* *
12256447 AACTCATTAT-AATTTATGTGGTTTTGCACACATAG-TGCTGATACGGTAATTCACAAACTCATT
1 AACTCATTATGAA-TTATGTGG-GTTGCACACATAGTTCCTGATACGGTAATTCACAAACTCATT
*
12256510 ATGAATTAAGTGGGTTGCACACATAGTGTCGATACGATAATTCATAAACTCATTATGAATTA-TG
64 ATGAATTAAGTGGGTTGCACACATAGTGTCGATACGATAATTCACAAACTCATTATGAATTACT-
* *
12256574 TGTGTTACACACATAGTGTCGATACGGTAATTCACA
128 TGGGTTACACACATAGTGTCGATACAGTAATTCACA
12256610 AACTCATTATGAATTATGTGGGTTGCACACATAGTTCCT-ATACGGTAATTCACAAACTCATTAT
1 AACTCATTATGAATTATGTGGGTTGCACACATAGTTCCTGATACGGTAATTCACAAACTCATTAT
12256674 GAATTAAGTGGGTTGCACACATAGTG-CTGATACGATAATTCACAAACTCATTATGAATTACTTG
66 GAATTAAGTGGGTTGCACACATAGTGTC-GATACGATAATTCACAAACTCATTATGAATTACTTG
** *
12256738 GGTTGTACACATAGTGTCGATACAGTAATTCATA
130 GGTTACACACATAGTGTCGATACAGTAATTCACA
* *
12256772 ATCTCATTATGAATTACGTGGGTTGCACACATAGT
1 AACTCATTATGAATTATGTGGGTTGCACACATAGT
12256807 GCCGATATGA
Statistics
Matches: 183, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
161 1 0.01
162 158 0.86
163 22 0.12
164 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (163 bp):
AACTCATTATGAATTATGTGGGTTGCACACATAGTTCCTGATACGGTAATTCACAAACTCATTAT
GAATTAAGTGGGTTGCACACATAGTGTCGATACGATAATTCACAAACTCATTATGAATTACTTGG
GTTACACACATAGTGTCGATACAGTAATTCACA
Found at i:12256821 original size:33 final size:33
Alignment explanation
Indices: 12256779--12256846 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
12256769 ATAATCTCAT
12256779 TATGAATTACGTGGGTTGCACACATAGTGCCGA
1 TATGAATTACGTGGGTTGCACACATAGTGCCGA
*
12256812 TATGAATTACGTGGGTTGCACACATAGTGTCGA
1 TATGAATTACGTGGGTTGCACACATAGTGCCGA
12256845 TA
1 TA
12256847 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (33 bp):
TATGAATTACGTGGGTTGCACACATAGTGCCGA
Found at i:12256871 original size:87 final size:87
Alignment explanation
Indices: 12256725--12256902 Score: 311
Period size: 87 Copynumber: 2.0 Consensus size: 87
12256715 ACAAACTCAT
* * * *
12256725 TATGAATTACTTGGGTTGTACACATAGTGTCGATACAGTAATTCATAATCTCATTATGAATTACG
1 TATGAATTACGTGGGTTGCACACATAGTGTCGATACAGTAATTCACAAACTCATTATGAATTACG
12256790 TGGGTTGCACACATAGTGCCGA
66 TGGGTTGCACACATAGTGCCGA
*
12256812 TATGAATTACGTGGGTTGCACACATAGTGTCGATACAGTAATTCACAAACTCGTTATGAATTACG
1 TATGAATTACGTGGGTTGCACACATAGTGTCGATACAGTAATTCACAAACTCATTATGAATTACG
12256877 TGGGTTGCACACATAGTGCCGA
66 TGGGTTGCACACATAGTGCCGA
12256899 TATG
1 TATG
12256903 GTAATTCACA
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (87 bp):
TATGAATTACGTGGGTTGCACACATAGTGTCGATACAGTAATTCACAAACTCATTATGAATTACG
TGGGTTGCACACATAGTGCCGA
Found at i:12256894 original size:54 final size:54
Alignment explanation
Indices: 12256812--12256976 Score: 258
Period size: 54 Copynumber: 3.1 Consensus size: 54
12256802 ATAGTGCCGA
* *
12256812 TATGAATTACGTGGGTTGCACACATAGTGTCGATACAGTAATTCACAAACTCGT
1 TATGAATTACGTGGGTTGCACACATAGTGCCGATACAGTAATTCACAAACTCAT
** *
12256866 TATGAATTACGTGGGTTGCACACATAGTGCCGATATGGTAATTCACAAAATCAT
1 TATGAATTACGTGGGTTGCACACATAGTGCCGATACAGTAATTCACAAACTCAT
* * *
12256920 TATGAATTACGTGGGTTGCACACATAATGCCGATGCAGTAATTCACAAACACAT
1 TATGAATTACGTGGGTTGCACACATAGTGCCGATACAGTAATTCACAAACTCAT
12256974 TAT
1 TAT
12256977 CCTTTGTCCC
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (54 bp):
TATGAATTACGTGGGTTGCACACATAGTGCCGATACAGTAATTCACAAACTCAT
Found at i:12256925 original size:141 final size:141
Alignment explanation
Indices: 12256671--12256953 Score: 435
Period size: 141 Copynumber: 2.0 Consensus size: 141
12256661 ACAAACTCAT
*
12256671 TATGAATTAAGTGGGTTGCACACATAGTGCTGATACGATAATTCACAAACTCATTATGAATTACT
1 TATGAATTAAGTGGGTTGCACACATAGTGCTGATACGATAATTCACAAACTCATTATGAATTACG
* * * **
12256736 TGGGTTGTACACATAGTGTCGATACAGTAATTCATAATCTCATTATGAATTACGTGGGTTGCACA
66 TGGGTTGCACACATAGTGCCGATACAGTAATTCACAAAATCATTATGAATTACGTGGGTTGCACA
*
12256801 CATAGTGCCGA
131 CATAATGCCGA
* *
12256812 TATGAATTACGTGGGTTGCACACATAGTG-TCGATAC-AGTAATTCACAAACTCGTTATGAATTA
1 TATGAATTAAGTGGGTTGCACACATAGTGCT-GATACGA-TAATTCACAAACTCATTATGAATTA
**
12256875 CGTGGGTTGCACACATAGTGCCGATATGGTAATTCACAAAATCATTATGAATTACGTGGGTTGCA
64 CGTGGGTTGCACACATAGTGCCGATACAGTAATTCACAAAATCATTATGAATTACGTGGGTTGCA
12256940 CACATAATGCCGA
129 CACATAATGCCGA
12256953 T
1 T
12256954 GCAGTAATTC
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
140 2 0.02
141 127 0.98
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (141 bp):
TATGAATTAAGTGGGTTGCACACATAGTGCTGATACGATAATTCACAAACTCATTATGAATTACG
TGGGTTGCACACATAGTGCCGATACAGTAATTCACAAAATCATTATGAATTACGTGGGTTGCACA
CATAATGCCGA
Found at i:12260052 original size:29 final size:29
Alignment explanation
Indices: 12260010--12260068 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
12260000 ATTTTCACCT
*
12260010 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
12260039 AACTAAATTGATGTAAGCAATAACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
12260068 A
1 A
12260069 GTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATAACATCAA
Found at i:12265973 original size:13 final size:13
Alignment explanation
Indices: 12265955--12265983 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12265945 CTCACCAACA
12265955 TTTTTTTCT-GTT
1 TTTTTTTCTGGTT
12265967 TTTTTTTCTGGTT
1 TTTTTTTCTGGTT
12265980 TTTT
1 TTTT
12265984 AATCTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (13 bp):
TTTTTTTCTGGTT
Found at i:12266445 original size:66 final size:66
Alignment explanation
Indices: 12266355--12266820 Score: 196
Period size: 66 Copynumber: 7.2 Consensus size: 66
12266345 AGAAATTCTA
* * * * * *
12266355 TGGGGAGCTTTGGTTCAATATGATCAATTTTCGCTTCTGATAAACAACCGACATTAAGGGTTTGC
1 TGGGGAGCTTTGCTTCAATATGATCAATTTCCACTTCTGATAAACAACCAACATTAAAGGATTGC
12266420 G
66 G
* ** * *
12266421 TGGGGAGCTTTGCTTC-GTAGTGATCGGTTTCCACTTCTGATACACGACCAACATTAAAGGATTG
1 TGGGGAGCTTTGCTTCAATA-TGATCAATTTCCACTTCTGATAAACAACCAACATTAAAGGATTG
*
12266485 TG
65 CG
* * * * * * ** * * * *
12266487 TGGGAAGCTTTACTTTACTGTGATCAGTTTCTGCTTCTGATACACGATCAAC----AAGTGATTT
1 TGGGGAGCTTTGCTTCAATATGATCAATTTCCACTTCTGATAAACAACCAACATTAAAG-GATTG
*
12266548 TG
65 CG
* * * ** * * * * ** *
12266550 TAGGGAGTTTTACTTCTTTGTGATCAGTTTTCACTTCTGATACATGACCAACATTAATGGATT-C
1 TGGGGAGCTTTGCTTCAATATGATCAATTTCCACTTCTGATAAACAACCAACATTAAAGGATTGC
*
12266614 TA
66 -G
** * ** * *
12266616 TGGGGAATTTTGTTTCGGTATGATCAA-TT--ACTTCTGATACACAACCAACATTAAAGGATTGT
1 TGGGGAGCTTTGCTTCAATATGATCAATTTCCACTTCTGATAAACAACCAACATTAAAGGATTGC
12266678 G
66 G
* ** * * * * ** * * *
12266679 TGGGGAGCTTTACTTCGTTGTGATCAGTTTCCACTTCTGACACATGATCAACATGAAGGGATT-C
1 TGGGGAGCTTTGCTTCAATATGATCAATTTCCACTTCTGATAAACAACCAACATTAAAGGATTGC
*
12266743 TA
66 -G
* ** * * * * * ** * *
12266745 TGGGAAATTTTGGTTCGATATGATCAGTTTCCACTTTTGATACACGGCCGACATTAAAGGATTGA
1 TGGGGAGCTTTGCTTCAATATGATCAATTTCCACTTCTGATAAACAACCAACATTAAAGGATTGC
12266810 G
66 G
12266811 TGGGGAGCTT
1 TGGGGAGCTT
12266821 GACTTTGCTG
Statistics
Matches: 302, Mismatches: 84, Indels: 28
0.73 0.20 0.07
Matches are distributed among these distances:
62 3 0.01
63 95 0.31
64 2 0.01
65 4 0.01
66 195 0.65
67 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (66 bp):
TGGGGAGCTTTGCTTCAATATGATCAATTTCCACTTCTGATAAACAACCAACATTAAAGGATTGC
G
Found at i:12266587 original size:63 final size:62
Alignment explanation
Indices: 12266440--12266602 Score: 161
Period size: 63 Copynumber: 2.5 Consensus size: 62
12266430 TTGCTTCGTA
* *
12266440 GTGATCGGTTTCCACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGAAGCTTTACTTTAC
1 GTGATCAGTTTTCACTTCTGATACACGACCAAC----AAGGATTGTGTGGGAAGCTTTACTTTAC
12266505 T
62 T
* * * * *
12266506 GTGATCAG-TTTCTGCTTCTGATACACGATCAACAAGTGATTTTGTAGGG-AGTTTTACTTCT-T
1 GTGATCAGTTTTC-ACTTCTGATACACGACCAACAAG-GATTGTGT-GGGAAGCTTTACTT-TAC
12266568 T
62 T
*
12266569 GTGATCAGTTTTCACTTCTGATACATGACCAACA
1 GTGATCAGTTTTCACTTCTGATACACGACCAACA
12266603 TTAATGGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
62 3 0.04
63 43 0.52
64 8 0.10
65 3 0.04
66 25 0.30
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (62 bp):
GTGATCAGTTTTCACTTCTGATACACGACCAACAAGGATTGTGTGGGAAGCTTTACTTTACT
Found at i:12266649 original size:63 final size:65
Alignment explanation
Indices: 12266570--12266807 Score: 210
Period size: 66 Copynumber: 3.6 Consensus size: 65
12266560 TACTTCTTTG
* * * *
12266570 TGATCAGTTTTCACTTCTGATACATGACCAACATTAATGGATTCTATGGGGAATTTTGTTTCGGT
1 TGATCAG-ATTCACTTCTGATACATGACCAACATTAAAGGATTCTATGGGGAATTTTGCTTCGAT
12266635 A
65 A
** * * ** * * *
12266636 TGATCA-ATT-ACTTCTGATACACAACCAACATTAAAGGATTGTGTGGGGAGCTTTACTTCGTTG
1 TGATCAGATTCACTTCTGATACATGACCAACATTAAAGGATTCTATGGGGAATTTTGCTTCGATA
* * * * * * *
12266699 TGATCAGTTTCCACTTCTGACACATGATCAACATGAAGGGATTCTATGGGAAATTTTGGTTCGAT
1 TGATCAGATT-CACTTCTGATACATGACCAACATTAAAGGATTCTATGGGGAATTTTGCTTCGAT
12266764 A
65 A
* * * * *
12266765 TGATCAGTTTCCACTTTTGATACACGGCCGACATTAAAGGATT
1 TGATCAGATT-CACTTCTGATACATGACCAACATTAAAGGATT
12266808 GAGTGGGGAG
Statistics
Matches: 133, Mismatches: 36, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
63 49 0.37
64 4 0.03
66 80 0.60
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (65 bp):
TGATCAGATTCACTTCTGATACATGACCAACATTAAAGGATTCTATGGGGAATTTTGCTTCGATA
Found at i:12266667 original size:192 final size:192
Alignment explanation
Indices: 12266453--12267120 Score: 534
Period size: 192 Copynumber: 3.4 Consensus size: 192
12266443 ATCGGTTTCC
* * *
12266453 ACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGAAGCTTTACTTTACTGTGATCAGTTTC
1 ACTTCTGATACACAACCAACATTAAAGGATTGTGTGGG-AGCTTTACTTCATTGTGATCAGTTTC
* ** *
12266518 TGCTTCTGATACACGATCAAC-AAGTGATTTTGTAGGGAGTTTTACTTCTTTGTGATCAGTTTTC
65 TGCTTCTGATACACGATCAACTAAGGGATTTTGTAGGGAGTTTTACTTCGATATGATCAGTTTTC
* *
12266582 ACTTCTGATACATGACCAACATTAATGGATTCTATGGGGAATTTTGTTTCGGTATGATCAA-TT
130 ACTTCTGATACATGACCAACATTAA-GGATTCTATGGGGAACTTTGTTTCGATATGATCAATTT
*
12266645 ACTTCTGATACACAACCAACATTAAAGGATTGTGTGGGGAGCTTTACTTCGTTGTGATCAGTTTC
1 ACTTCTGATACACAACCAACATTAAAGGATTGTGT-GGGAGCTTTACTTCATTGTGATCAGTTTC
** * * * * * **
12266710 CACTTCTGACACATGATCAACATGAAGGGATTCTAT-GGGAAATTTTGGTTCGATATGATCAGTT
65 TGCTTCTGATACACGATCAAC-T-AAGGGATTTTGTAGGG-AGTTTTACTTCGATATGATCAGTT
* * * * * * * * * *
12266774 TCCACTTTTGATACACGGCCGACATTAAAGGATT-GAGTGGGGAGC-TTGACTTT-GCTGTGGTC
127 TTCACTTCTGATACATGACCAACATT-AAGGATTCTA-TGGGGAACTTTG--TTTCGATATGATC
*
12266836 AACTT
188 AATTT
* ** * *
12266841 -CTTCTGATACACAACCAAC----AAGTGATTTTGTTGGGAGCTTTGGTTCA-AGATGATCAATT
1 ACTTCTGATACACAACCAACATTAAAG-GATTGTG-TGGGAGCTTTACTTCATTG-TGATCAGTT
* * * * * * * *
12266900 TTTGCTTCAGATACACGATCAACATTAAGGGATTGTGTGGGGAGCTTTATTTCGCTATTATCAGT
63 TCTGCTTCTGATACACGATCAAC--TAAGGGATTTTGTAGGGAGTTTTACTTCGATATGATCAGT
* * * * * * *
12266965 TTTCATTTCTGACACATGACCAACATTCAGAGATTCTGA-GGGAAACTTTGCTCCAATATGATCA
126 TTTCACTTCTGATACATGACCAACATTAAG-GATTCT-ATGGGGAACTTTGTTTCGATATGATCA
12267029 ATTTCT
189 A-TT-T
* * * * * ** *
12267035 ATTTCTGGTACACGACCATCATTAAAGGATTGTATGAGGAGCTTTACTTTGTTGTGACCAGTTTC
1 ACTTCTGATACACAACCAACATTAAAGGATTGTGTG-GGAGCTTTACTTCATTGTGATCAGTTTC
*
12267100 TGCTTCTGATACCCGATCAAC
65 TGCTTCTGATACACGATCAAC
12267121 ATGTGGTCTT
Statistics
Matches: 364, Mismatches: 83, Indels: 52
0.73 0.17 0.10
Matches are distributed among these distances:
191 7 0.02
192 180 0.49
193 12 0.03
194 9 0.02
195 101 0.28
196 7 0.02
197 2 0.01
198 42 0.12
199 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (192 bp):
ACTTCTGATACACAACCAACATTAAAGGATTGTGTGGGAGCTTTACTTCATTGTGATCAGTTTCT
GCTTCTGATACACGATCAACTAAGGGATTTTGTAGGGAGTTTTACTTCGATATGATCAGTTTTCA
CTTCTGATACATGACCAACATTAAGGATTCTATGGGGAACTTTGTTTCGATATGATCAATTT
Found at i:12266847 original size:258 final size:258
Alignment explanation
Indices: 12266349--12267294 Score: 736
Period size: 258 Copynumber: 3.6 Consensus size: 258
12266339 ACATTAAGAA
* * * * *
12266349 ATTCTATGGGGAGCTTTGGTTCAATATGATCAATTTTCGCTTCTGATAAACAACCGACATTAAGG
1 ATTCT-TGGGGAGCTTTGGTTCAGTATGATCAA-TTT-GCTTCTGATACACAATCAACATTAAAG
* * * * * *
12266414 GTTTGCGTGGGGAGCTTTGCTTCG-TAGTGATCGGTTTCCACTTCTGATACACGACCAACATTAA
63 GATTGTGTGGGGAGCTTTACTTCGCT-GTGATCAGTTTCCACTTCTGACACATGACCAACATTAA
* * * ** * * * ***
12266478 AGGATTGTGTGGGAAGCTTTACTT-TACTGTGATCAGTTTCTGCTTCTGATACACG---ATCA--
127 GGGATTCTATGGGAAATTTTGCTTCGA-TATGATCAGTTTCCATTTCTGATACACGACCATCATT
* * * * ** * *
12266537 ACAAGTGATT-T-TGTAGGGAGTTTTACTTCT-TTGTGATCAGTTTTCACTTCTGATACATGACC
191 A-AAG-GATTGTATG-A-GGAGCTTGACTT-TGCTGTGACCA-TACT-GCTTCTGATACACGACC
*
12266599 AACATTAATGG
249 AACA-TAGTGG
** * * * *
12266610 ATTCTATGGGGAATTTTGTTTCGGTATGATCAA-TTACTTCTGATACACAACCAACATTAAAGGA
1 ATTCT-TGGGGAGCTTTGGTTCAGTATGATCAATTTGCTTCTGATACACAATCAACATTAAAGGA
* * *
12266674 TTGTGTGGGGAGCTTTACTTCGTTGTGATCAGTTTCCACTTCTGACACATGATCAACATGAAGGG
65 TTGTGTGGGGAGCTTTACTTCGCTGTGATCAGTTTCCACTTCTGACACATGACCAACATTAAGGG
* *
12266739 ATTCTATGGGAAATTTTGGTTCGATATGATCAGTTTCCACTTT-TGATACACGGCCGA-CATTAA
130 ATTCTATGGGAAATTTTGCTTCGATATGATCAGTTTCCA-TTTCTGATACACGACC-ATCATTAA
* ** * *
12266802 AGGATTG-AGTGGGGAGCTTGACTTTGCTGTGGTCA-ACTTCTTCTGATACACAACCAACA-AGT
193 AGGATTGTA-TGAGGAGCTTGACTTTGCTGTGACCATACTGCTTCTGATACACGACCAACATAGT
12266864 -G
257 GG
* *
12266865 ATT-TTGTTGGGAGCTTTGGTTCAAG-ATGATCAATTTTTGCTTCAGATACACGATCAACATTAA
1 ATTCTTG--GGGAGCTTTGGTTC-AGTATGATCAA--TTTGCTTCTGATACACAATCAACATTAA
* * * * * * *
12266928 GGGATTGTGTGGGGAGCTTTATTTCGCTATTATCAGTTTTCATTTCTGACACATGACCAACATTC
61 AGGATTGTGTGGGGAGCTTTACTTCGCTGTGATCAGTTTCCACTTCTGACACATGACCAACATTA
* * * * * * *
12266993 AGAGATTCTGA-GGGAAACTTTGCTCCAATATGATCAATTTCTATTTCTGGTACACGACCATCAT
126 AGGGATTCT-ATGGGAAATTTTGCTTCGATATGATCAGTTTCCATTTCTGATACACGACCATCAT
* * * * *
12267057 TAAAGGATTGTATGAGGAGCTTTACTTTGTTGTGACCAGTTTCTGCTTCTGATACCCGATCAACA
190 TAAAGGATTGTATGAGGAGCTTGACTTTGCTGTGACCA--TACTGCTTCTGATACACGACCAACA
12267122 T-GTGG
253 TAGTGG
* * * *
12267127 --TCTTGTAGGGAGCTTTGGGTCAGTATGATCAATTTTTGCTTCTGGTACACAATCGACAATAAA
1 ATTCTTG--GGGAGCTTTGGTTCAGTATGATCAA--TTTGCTTCTGATACACAATCAACATTAAA
* * * *
12267190 GGATTGTGTGGGGAGCTTTGCTTCACTGTGATCAGTTTCCACTTCTGACATATGACCACCATTAA
62 GGATTGTGTGGGGAGCTTTACTTCGCTGTGATCAGTTTCCACTTCTGACACATGACCAACATTAA
* *
12267255 GGGATTCTAT--GAAGAGTTTTGTTTCGTTATGATCAGTTTC
127 GGGATTCTATGGGAA-A-TTTTGCTTCGATATGATCAGTTTC
12267295 TGATACATTA
Statistics
Matches: 550, Mismatches: 102, Indels: 66
0.77 0.14 0.09
Matches are distributed among these distances:
253 2 0.00
254 1 0.00
255 23 0.04
256 3 0.01
257 4 0.01
258 289 0.53
259 12 0.02
260 6 0.01
261 202 0.37
262 5 0.01
263 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (258 bp):
ATTCTTGGGGAGCTTTGGTTCAGTATGATCAATTTGCTTCTGATACACAATCAACATTAAAGGAT
TGTGTGGGGAGCTTTACTTCGCTGTGATCAGTTTCCACTTCTGACACATGACCAACATTAAGGGA
TTCTATGGGAAATTTTGCTTCGATATGATCAGTTTCCATTTCTGATACACGACCATCATTAAAGG
ATTGTATGAGGAGCTTGACTTTGCTGTGACCATACTGCTTCTGATACACGACCAACATAGTGG
Found at i:12267058 original size:132 final size:131
Alignment explanation
Indices: 12266307--12267265 Score: 616
Period size: 129 Copynumber: 7.4 Consensus size: 131
12266297 TTTACTTTAT
* * * * * * *
12266307 TGTGATCAGTTTCCACTCCTGACACGTGACCGACATTAAGAAATTCTATGGGGAGCTTTGGTTCA
1 TGTGATCAGTTTTCACTTCTGACACATGACCAACATTAAG-GATTCTATGGGAAACTTTGGTTCA
* * * * * * * **
12266372 ATATGATCAATTT-TCGCTTCTGATAAACAACCGACATTAAGGGTTTGCGTGGGGAGCTTTGCTT
65 ATATGATCAATTTCT-ACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGGAGCTTTATTT
12266436 CG-
129 CGC
* * * * * * * ** *
12266438 TAGTGATCGGTTTCCACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGAAGCTTTACTTT
1 T-GTGATCAGTTTTCACTTCTGACACATGACCAACATT-AAGGATTCTATGGGAAACTTTGGTTC
* * * * * * * * *
12266503 ACTGTGATCAGTTTCTGCTTCTGATACACGATCAAC----AAGTGATTTTGTAGGGAGTTTTACT
64 AATATGATCAATTTCTACTTCTGATACACGACCAACATTAAAG-GATTGTGTGGGGAGCTTTATT
**
12266564 TCTT
128 TCGC
* * * * *
12266568 TGTGATCAGTTTTCACTTCTGATACATGACCAACATTAATGGATTCTATGGGGAATTTTGTTTCG
1 TGTGATCAGTTTTCACTTCTGACACATGACCAACATTAA-GGATTCTATGGGAAACTTTGGTTCA
* * *
12266633 GTATGATCAA--T-TACTTCTGATACACAACCAACATTAAAGGATTGTGTGGGGAGCTTTACTTC
65 ATATGATCAATTTCTACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGGAGCTTTATTTC
*
12266695 GT
130 GC
* * * * *
12266697 TGTGATCAGTTTCCACTTCTGACACATGATCAACATGAAGGGATTCTATGGGAAATTTTGGTTCG
1 TGTGATCAGTTTTCACTTCTGACACATGACCAACATTAA-GGATTCTATGGGAAACTTTGGTTCA
* * * * * * *
12266762 ATATGATCAGTTTCCACTTTTGATACACGGCCGACATTAAAGGATTGAGTGGGGAGCTTGACTTT
65 ATATGATCAATTTCTACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGGAGCTTTA-TTT
12266827 -GC
129 CGC
* ** * ** * * *
12266829 TGTGGTCA-ACTT--CTTCTGATACACAACCAAC---AAGTGATTTTGTTGGG-AGCTTTGGTTC
1 TGTGATCAGTTTTCACTTCTGACACATGACCAACATTAAG-GATTCT-ATGGGAAACTTTGGTTC
* * * * * *
12266887 AAGATGATCAATTTTTGCTTCAGATACACGATCAACATTAAGGGATTGTGTGGGGAGCTTTATTT
64 AATATGATCAATTTCTACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGGAGCTTTATTT
12266952 CGC
129 CGC
* * * * * *
12266955 TATTATCAGTTTTCATTTCTGACACATGACCAACATTCAGAGATTCTGA-GGGAAACTTTGCTCC
1 TGTGATCAGTTTTCACTTCTGACACATGACCAACATTAAG-GATTCT-ATGGGAAACTTTGGTTC
* * * * *
12267019 AATATGATCAATTTCTATTTCTGGTACACGACCATCATTAAAGGATTGTATGAGGAGCTTTACTT
64 AATATGATCAATTTCTACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGGAGCTTTA-TT
*
12267084 T-GT
128 TCGC
* * * ** * * * * *
12267087 TGTGACCAG-TTTCTGCTTCTGATACCCGATCAACATGT--GGTCTTGTA-GGG-AGCTTTGGGT
1 TGTGATCAGTTTTC-ACTTCTGACACATGACCAACAT-TAAGG-ATTCTATGGGAAACTTTGGTT
* * * * * * * * **
12267147 CAGTATGATCAATTTTTGCTTCTGGTACACAATCGACAATAAAGGATTGTGTGGGGAGCTTTGCT
63 CAATATGATCAATTTCTACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGGAGCTTTATT
*
12267212 TCAC
128 TCGC
* * *
12267216 TGTGATCAGTTTCCACTTCTGACATATGACCACCATTAAGGGATTCTATG
1 TGTGATCAGTTTTCACTTCTGACACATGACCAACATTAA-GGATTCTATG
12267266 AAGAGTTTTG
Statistics
Matches: 631, Mismatches: 163, Indels: 68
0.73 0.19 0.08
Matches are distributed among these distances:
125 4 0.01
126 89 0.14
127 7 0.01
128 7 0.01
129 270 0.43
130 16 0.03
131 17 0.03
132 211 0.33
133 10 0.02
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (131 bp):
TGTGATCAGTTTTCACTTCTGACACATGACCAACATTAAGGATTCTATGGGAAACTTTGGTTCAA
TATGATCAATTTCTACTTCTGATACACGACCAACATTAAAGGATTGTGTGGGGAGCTTTATTTCG
C
Found at i:12271149 original size:2 final size:2
Alignment explanation
Indices: 12271142--12271170 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12271132 CATCTAAATC
12271142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12271171 AAGTGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12272973 original size:10 final size:10
Alignment explanation
Indices: 12272958--12272992 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
12272948 ATCACATCAT
12272958 ATTCTTTCAA
1 ATTCTTTCAA
12272968 ATTCTTTCAA
1 ATTCTTTCAA
*
12272978 ATTCTCTCAA
1 ATTCTTTCAA
12272988 ATTCT
1 ATTCT
12272993 CTATCTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (10 bp):
ATTCTTTCAA
Found at i:12273073 original size:17 final size:17
Alignment explanation
Indices: 12273032--12273077 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
12273022 TTTTAATATT
*
12273032 ATATATTTAATTTATTTA
1 ATAT-TTTACTTTATTTA
*
12273050 AGCATTTTACTTTATTTA
1 A-TATTTTACTTTATTTA
12273068 ATATTTTACT
1 ATATTTTACT
12273078 AATATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.33
18 14 0.58
19 2 0.08
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (17 bp):
ATATTTTACTTTATTTA
Found at i:12274227 original size:18 final size:18
Alignment explanation
Indices: 12274201--12274235 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12274191 CAGCAGCCAC
*
12274201 CGCAGCCATTTATGATGT
1 CGCAGCCATATATGATGT
*
12274219 CGCATCCATATATGATG
1 CGCAGCCATATATGATG
12274236 CCGTCGTCTT
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:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (18 bp):
CGCAGCCATATATGATGT
Found at i:12274601 original size:9 final size:9
Alignment explanation
Indices: 12274587--12274618 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
12274577 TGCTCAGGAT
12274587 GACAACGAC
1 GACAACGAC
12274596 GACAACGAC
1 GACAACGAC
*
12274605 GACGACGAC
1 GACAACGAC
12274614 GACAA
1 GACAA
12274619 TGGTGATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.31, G:0.25, T:0.00
Consensus pattern (9 bp):
GACAACGAC
Found at i:12274818 original size:26 final size:24
Alignment explanation
Indices: 12274747--12274818 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
12274737 TTATATTTGT
12274747 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
12274772 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
12274794 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
12274819 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:12275760 original size:23 final size:23
Alignment explanation
Indices: 12275734--12275778 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
12275724 CACCACAGCT
* *
12275734 CGTATAAATGCACTGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
12275757 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
12275779 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:12276500 original size:64 final size:63
Alignment explanation
Indices: 12276367--12276523 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
12276357 TAATGAAGGT
* * * ** *
12276367 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
12276431 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
12276493 G
63 G
*
12276494 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
12276524 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:12282571 original size:24 final size:24
Alignment explanation
Indices: 12282544--12282643 Score: 76
Period size: 24 Copynumber: 4.2 Consensus size: 24
12282534 GATATTAGAA
* *
12282544 ATCAAAATATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
12282568 ATCAGAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
12282592 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
12282616 GTCAAAATAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
12282640 ATCA
1 ATCA
12282644 GATAAAATAT
Statistics
Matches: 57, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
23 2 0.04
24 53 0.93
25 2 0.04
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:12285131 original size:13 final size:13
Alignment explanation
Indices: 12285113--12285137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12285103 TCCGGTCAAC
12285113 GGTCAACGGGTCG
1 GGTCAACGGGTCG
12285126 GGTCAACGGGTC
1 GGTCAACGGGTC
12285138 ATGTCGGGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:12285166 original size:30 final size:31
Alignment explanation
Indices: 12285113--12285189 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
12285103 TCCGGTCAAC
* *
12285113 GGTCAACGGGTCGGGTCAACGGGTCATGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCAGGTCG
* *
12285144 GGTCAACGGGT-TGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCAGGTCG
*
12285174 GGTCAATGGGTCGGGT
1 GGTCAACGGGTCGGGT
12285190 CGGGTTGTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 25 0.64
31 14 0.36
ACGTcount: A:0.16, C:0.18, G:0.45, T:0.21
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCAGGTCG
Found at i:12287354 original size:24 final size:24
Alignment explanation
Indices: 12287327--12287433 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
12287317 AAACGGAGAT
*
12287327 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
12287351 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
12287375 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
12287399 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
12287423 ATCAGAAATCA
1 ATCAGAAATCA
12287434 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:12287433 original size:48 final size:48
Alignment explanation
Indices: 12287327--12287435 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
12287317 AAACGGAGAT
* * * *
12287327 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
12287375 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
12287423 ATCAGAAATCAGA
1 ATCAGAAATCAGA
12287436 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:12289924 original size:13 final size:13
Alignment explanation
Indices: 12289906--12289930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12289896 TCCTGTCAAC
12289906 GGTCAACGGGTCG
1 GGTCAACGGGTCG
12289919 GGTCAACGGGTC
1 GGTCAACGGGTC
12289931 ATGTCGGGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:12289959 original size:30 final size:31
Alignment explanation
Indices: 12289906--12289982 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
12289896 TCCTGTCAAC
* *
12289906 GGTCAACGGGTCGGGTCAACGGGTCATGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCAGGTCG
* *
12289937 GGTCAACGGGT-TGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCAGGTCG
*
12289967 GGTCAATGGGTCGGGT
1 GGTCAACGGGTCGGGT
12289983 CGGGTTGTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 25 0.64
31 14 0.36
ACGTcount: A:0.16, C:0.18, G:0.45, T:0.21
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCAGGTCG
Found at i:12305249 original size:2 final size:2
Alignment explanation
Indices: 12305244--12305269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12305234 TATCTTATTC
12305244 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
12305270 CCACAAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12318957 original size:23 final size:24
Alignment explanation
Indices: 12318914--12318966 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
12318904 CCACTAGGGG
*
12318914 CTATGAAATTTGTCCCGAAGGACCA
1 CTATGAAA-TTGTCCCAAAGGACCA
*
12318939 CTATGAAA-TGTCCCAAAGGACTA
1 CTATGAAATTGTCCCAAAGGACCA
12318962 CTATG
1 CTATG
12318967 TCCCGAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 18 0.69
25 8 0.31
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (24 bp):
CTATGAAATTGTCCCAAAGGACCA
Found at i:12318969 original size:18 final size:18
Alignment explanation
Indices: 12318946--12318994 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
12318936 CCACTATGAA
* *
12318946 ATGTCCCAAAGGACTACT
1 ATGTCCCGAAGGACCACT
12318964 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
*
12318982 GTGTCCCGAAGGA
1 ATGTCCCGAAGGA
12318995 TCGCGTAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:12325769 original size:33 final size:33
Alignment explanation
Indices: 12325732--12325796 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
12325722 CTCATGTGCA
*
12325732 AAGTTGGCCACCTA-CAGAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCA-AGATGAATTTTCCAAT
12325765 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
12325797 CTTGCCAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
Found at i:12331128 original size:136 final size:136
Alignment explanation
Indices: 12330879--12331152 Score: 469
Period size: 136 Copynumber: 2.0 Consensus size: 136
12330869 GGAACAGTCA
* *
12330879 ATTGTCGTGAGGGAGCTTTGGTAGAATGAAAGGATGAAGCTCTCATGATAACTGTTAGGGGTTTA
1 ATTGTCGTGAGGGAGCCTTGGTAGAATGAAAGGAGGAAGCTCTCATGATAACTGTTAGGGGTTTA
* *
12330944 CTGGTTGGGATTGAACCAAGGGATTTAGAGGCACAAGCTTCGACAAGAGATTTTCCTTTAAAGGA
66 CGGGTTGAGATTGAACCAAGGGATTTAGAGGCACAAGCTTCGACAAGAGATTTTCCTTTAAA-GA
12331009 A-GGGTG
130 ATGGGTG
12331015 ATTGTCGTGAGGGAGCCTTGGTAGAATGAAAGGAGGAAGCTCTCATGATAACTGTTAGGGGTTTA
1 ATTGTCGTGAGGGAGCCTTGGTAGAATGAAAGGAGGAAGCTCTCATGATAACTGTTAGGGGTTTA
* * *
12331080 CGGGTTGAGATTGAACCAAGGGATTTAGAGGCACAAGCTTCGATAAGAGATTTTCTTTTAGAGAA
66 CGGGTTGAGATTGAACCAAGGGATTTAGAGGCACAAGCTTCGACAAGAGATTTTCCTTTAAAGAA
12331145 TGGGTG
131 TGGGTG
12331151 AT
1 AT
12331153 GTTGAGAAGC
Statistics
Matches: 130, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
135 3 0.02
136 127 0.98
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (136 bp):
ATTGTCGTGAGGGAGCCTTGGTAGAATGAAAGGAGGAAGCTCTCATGATAACTGTTAGGGGTTTA
CGGGTTGAGATTGAACCAAGGGATTTAGAGGCACAAGCTTCGACAAGAGATTTTCCTTTAAAGAA
TGGGTG
Found at i:12338856 original size:13 final size:13
Alignment explanation
Indices: 12338838--12338862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12338828 ATACTTACTT
12338838 AAATATTTAATTA
1 AAATATTTAATTA
12338851 AAATATTTAATT
1 AAATATTTAATT
12338863 TAGAATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTTAATTA
Found at i:12347005 original size:126 final size:125
Alignment explanation
Indices: 12346666--12347290 Score: 942
Period size: 126 Copynumber: 5.0 Consensus size: 125
12346656 GTACTATTCA
12346666 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTT-CCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
12346731 TATTATGTCACTTATG------GGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
65 TATTATGTCACTTATGTCCCCCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
12346786 CGTGAAGGCGCGTTCCAGGGGG-GCGTCTTCCATTATTTTGTCAGAGAATAGGTTATCATTGCCC
1 CGTGAAGGCGCGTTCC-GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* **
12346850 TATTATGTCACTTATGTCCCCCGGAAACTATTCATATCAATATATATTATTCCTTAGGGGAC
65 TATTATGTCACTTATGTCCCCCGG-AACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
12346912 CGTGAAGGTGCGTTCCTAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCC-GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
*
12346977 TATTATGTCACTTATATCCCCCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
65 TATTATGTCACTTATGTCCCCCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* * *
12347038 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA-TTTGTCAGAGAATATGTTATCATTACCA
1 CGTGAAGGCGCGTT-CCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* * * * * *
12347102 TATTATGTCACTTATGTCCACCGGGAACTATTTATGCCAATACATATTATTTCTTAGAGGAC
65 TATTATGTCACTTATGTCC-CCCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
12347164 CGTGAAGGCGCATTCGCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTC-CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
*
12347229 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCTTTAGGGGAC
65 TATTATGTCACTTATGTCCCCC-GGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
12347291 TTTAAAGCGC
Statistics
Matches: 453, Mismatches: 38, Indels: 21
0.88 0.07 0.04
Matches are distributed among these distances:
119 58 0.13
120 19 0.04
125 47 0.10
126 186 0.41
127 143 0.32
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (125 bp):
CGTGAAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTTATGTCCCCCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:12347499 original size:23 final size:23
Alignment explanation
Indices: 12347451--12347500 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
12347441 TGAAGTTTGA
* * *
12347451 ATAAATTAGATAAAATGTTATGG
1 ATAAATTAAATAAAATGTGAAGG
12347474 ATAAATTAAAT-AAATGTGAAGTG
1 ATAAATTAAATAAAATGTGAAG-G
12347497 ATAA
1 ATAA
12347501 GTTTATTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (23 bp):
ATAAATTAAATAAAATGTGAAGG
Found at i:12347751 original size:34 final size:32
Alignment explanation
Indices: 12347713--12347820 Score: 126
Period size: 34 Copynumber: 3.2 Consensus size: 32
12347703 TTAACTTCAA
* *
12347713 TTTAAAGTTAAATTTCGAATACTATACTTTATAT
1 TTTAAATTTAAATTT-GAATACTATA-TTTGTAT
*
12347747 TTTAAATTTAAATTATGAATAATATTATTTGTAT
1 TTTAAATTTAAATT-TGAATACTA-TATTTGTAT
*
12347781 TTTAATTTTAAATTTTGAATACTATAATTTGTAT
1 TTTAAATTTAAA-TTTGAATACTAT-ATTTGTAT
12347815 TTTAAA
1 TTTAAA
12347821 AACATTTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.02
34 58 0.91
35 5 0.08
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.52
Consensus pattern (32 bp):
TTTAAATTTAAATTTGAATACTATATTTGTAT
Found at i:12348365 original size:21 final size:21
Alignment explanation
Indices: 12348341--12348392 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12348331 TATGGTATAA
*
12348341 AACCCTGCGGGCTAGGTATGT
1 AACCCTGCGGGCTAGGAATGT
12348362 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
12348383 AACCCTGCGG
1 AACCCTGCGG
12348393 AGATGACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 22 0.79
22 3 0.11
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:12350238 original size:31 final size:31
Alignment explanation
Indices: 12350171--12350271 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
12350161 TAATTAGCAC
* * *
12350171 AAAAAATAATTA-ATTAATA-AATTTAAAT-
1 AAAAAATAATTATATAAATATTATTTTAATA
*
12350199 AAATAATAATTATATAAATATTATTTTAATA
1 AAAAAATAATTATATAAATATTATTTTAATA
* * *
12350230 AAAAAATAA-TATTTATATAATTATATTAATA
1 AAAAAATAATTATATAAAT-ATTATTTTAATA
*
12350261 TAAAATATAAT
1 -AAAAAATAAT
12350272 AACTATTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
28 11 0.19
29 6 0.10
30 14 0.24
31 19 0.33
32 8 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAAAATAATTATATAAATATTATTTTAATA
Found at i:12355237 original size:159 final size:159
Alignment explanation
Indices: 12354948--12355269 Score: 511
Period size: 159 Copynumber: 2.0 Consensus size: 159
12354938 GAAACCAACC
* * * *
12354948 TATAAAAATAAAGGAGATCTCTAATATTGTGGTAACTACAGAGGTATTAAACTATTCAGTCATAT
1 TATAAAAATAAAGGAGATCCCGAATATTGTGGTAACTACAGAGATATTAAACTATTCAGCCATAT
*
12355013 TATGAAGCTATGGGAAAGGATGATAGAGGCTAGGTTGAGACAGATTACTAGGTGTAGACACATGT
66 TATGAAGCTATGGAAAAGGATGATAGAGGCTAGGTTGAGACAGATTACTAGGTGTAGACACATGT
12355078 TTTTGTCCAGATATACAAAAATATTTTAT
131 TTTTGTCCAGATATACAAAAATATTTTAT
*
12355107 TATAAGAATAAAGGAGATCCCGAATATTGTGGTAACTACAGAGATATTAAACTACTT-AGCCATA
1 TATAAAAATAAAGGAGATCCCGAATATTGTGGTAACTACAGAGATATTAAACTA-TTCAGCCATA
* * * *
12355171 TTATGAAGCTATGGAAAAGGGTGATAGATGCTAGGTTGAGACATATTACTAGGTGTATACACATG
65 TTATGAAGCTATGGAAAAGGATGATAGAGGCTAGGTTGAGACAGATTACTAGGTGTAGACACATG
* * *
12355236 TTTTTGTTCGGGTATACAAAAATATTTTAT
130 TTTTTGTCCAGATATACAAAAATATTTTAT
12355266 TATA
1 TATA
12355270 TTATATTTAT
Statistics
Matches: 149, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
159 147 0.99
160 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (159 bp):
TATAAAAATAAAGGAGATCCCGAATATTGTGGTAACTACAGAGATATTAAACTATTCAGCCATAT
TATGAAGCTATGGAAAAGGATGATAGAGGCTAGGTTGAGACAGATTACTAGGTGTAGACACATGT
TTTTGTCCAGATATACAAAAATATTTTAT
Found at i:12355282 original size:4 final size:4
Alignment explanation
Indices: 12355261--12355296 Score: 54
Period size: 4 Copynumber: 8.5 Consensus size: 4
12355251 ACAAAAATAT
12355261 TTTA TTATA TTATA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TT-TA TT-TA TTTA TTTA TTTA TTTA TTTA TT
12355297 ATTATTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 22 0.71
5 9 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:12355300 original size:3 final size:3
Alignment explanation
Indices: 12355258--12355335 Score: 90
Period size: 3 Copynumber: 25.3 Consensus size: 3
12355248 TATACAAAAA
12355258 TAT T-T TAT TA- TAT TA- TATT TATT TATT TATT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TA-T TA-T TAT TAT TAT
12355302 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12355336 TACAGGCCCC
Statistics
Matches: 71, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 6 0.08
3 47 0.66
4 18 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:12355728 original size:17 final size:17
Alignment explanation
Indices: 12355706--12355751 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
12355696 TTTTATTCTT
*
12355706 TTTATTTCATTTATTTA
1 TTTATTTCATTTATATA
12355723 TTTATTT-ATTTTATATA
1 TTTATTTCA-TTTATATA
*
12355740 TATATTTCATTT
1 TTTATTTCATTT
12355752 TCTCCTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 1 0.04
17 23 0.92
18 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTCATTTATATA
Found at i:12355735 original size:13 final size:13
Alignment explanation
Indices: 12355705--12355751 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
12355695 GTTTTATTCT
12355705 TTTTATTTCATTTA
1 TTTTATTT-ATTTA
12355719 -TTTATTTATTTA
1 TTTTATTTATTTA
* *
12355731 TTTTATATATATA
1 TTTTATTTATTTA
*
12355744 TTTCATTT
1 TTTTATTT
12355752 TCTCCTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 5 0.18
13 23 0.82
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:12355829 original size:27 final size:26
Alignment explanation
Indices: 12355799--12355852 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
12355789 TTATATATAT
12355799 ATATATATATATATT-TATTTTTTATTA
1 ATAT-TAT-TATATTATATTTTTTATTA
12355826 ATATTATTATATTAATATTTTTTATTA
1 ATATTATTATATT-ATATTTTTTATTA
12355853 TTCTTTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.24
26 3 0.12
27 16 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATTATTATATTATATTTTTTATTA
Found at i:12356872 original size:39 final size:38
Alignment explanation
Indices: 12356809--12356883 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
12356799 ATTTGTTTTA
12356809 AATAAGCATGCGGAATAGAGATCATGTCCGGGTAGGAAT
1 AATAAGCATGCGGAATAGAGATCATGT-CGGGTAGGAAT
* ** * *
12356848 AATAAGCATGTGGGGTAGATATCATGTGGGGTAGGA
1 AATAAGCATGCGGAATAGAGATCATGTCGGGTAGGA
12356884 TTTTTCATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 8 0.26
39 23 0.74
ACGTcount: A:0.33, C:0.09, G:0.35, T:0.23
Consensus pattern (38 bp):
AATAAGCATGCGGAATAGAGATCATGTCGGGTAGGAAT
Found at i:12358941 original size:13 final size:13
Alignment explanation
Indices: 12358923--12358983 Score: 99
Period size: 13 Copynumber: 4.8 Consensus size: 13
12358913 TCAAGAACAA
12358923 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
12358936 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
12358949 AAAGAGAAAATAA-
1 AAAGAGAAAA-AAC
12358962 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
12358975 AAAG-GAAAA
1 AAAGAGAAAA
12358984 TTGAAGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.15
13 37 0.80
14 2 0.04
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:12359174 original size:69 final size:69
Alignment explanation
Indices: 12359056--12359193 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
12359046 GATTCAAACT
*
12359056 ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCACTTCACTCGAAGATCATAAAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCACTCCACTCGAAGATCATAAAGCA
12359121 TCAA
66 TCAA
* * *
12359125 ATGAGATTGATCAAGCACAATCATTTCTAAATCACTGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCACTCCACTCGAAGATCATAAAGCA
12359190 TCAA
66 TCAA
12359194 GAGACAGACG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCACTCCACTCGAAGATCATAAAGCA
TCAA
Found at i:12360153 original size:32 final size:32
Alignment explanation
Indices: 12360117--12360206 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
12360107 GCATCTTTAA
* *
12360117 AGATTCACCATCAAATGCTGAGGCATTTTTTG
1 AGATTCAACATCAAATACTGAGGCATTTTTTG
* * *
12360149 AGATTTAACATCAAATATTGGGGCATTTTTTG
1 AGATTCAACATCAAATACTGAGGCATTTTTTG
* * *
12360181 AGATTCAACATCGAATATTGGGGCAT
1 AGATTCAACATCAAATACTGAGGCAT
12360207 CTTTGGGAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (32 bp):
AGATTCAACATCAAATACTGAGGCATTTTTTG
Found at i:12360219 original size:32 final size:32
Alignment explanation
Indices: 12360117--12360220 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
12360107 GCATCTTTAA
* ** * **
12360117 AGATTCACCATCAAATGCTGAGGCATTTTTTG
1 AGATTCAACATCAAATATTGGGGCATTTTGGG
* **
12360149 AGATTTAACATCAAATATTGGGGCATTTTTTG
1 AGATTCAACATCAAATATTGGGGCATTTTGGG
*
12360181 AGATTCAACATCGAATATTGGGGCATCTTTGGG
1 AGATTCAACATCAAATATTGGGGCAT-TTTGGG
12360214 A-ATTCAA
1 AGATTCAA
12360221 TATCCTGATA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 57 0.92
33 5 0.08
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATTTTGGG
Found at i:12361434 original size:28 final size:28
Alignment explanation
Indices: 12361394--12361472 Score: 158
Period size: 28 Copynumber: 2.8 Consensus size: 28
12361384 GTGCTCACCA
12361394 TTGTCTCTCTTGAGACAGTTTCCAAGTT
1 TTGTCTCTCTTGAGACAGTTTCCAAGTT
12361422 TTGTCTCTCTTGAGACAGTTTCCAAGTT
1 TTGTCTCTCTTGAGACAGTTTCCAAGTT
12361450 TTGTCTCTCTTGAGACAGTTTCC
1 TTGTCTCTCTTGAGACAGTTTCC
12361473 CTTGAAACAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (28 bp):
TTGTCTCTCTTGAGACAGTTTCCAAGTT
Found at i:12361583 original size:30 final size:31
Alignment explanation
Indices: 12361523--12361583 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
12361513 TTTTGTCTCC
*
12361523 CTTGAGACAGTTTCTTTTAGAACTAAATTTT
1 CTTGAGACAATTTCTTTTAGAACTAAATTTT
12361554 CTTGAGACAATTTCTTTT-GAAAC-AAATTTT
1 CTTGAGACAATTTCTTTTAG-AACTAAATTTT
12361584 GTCCCTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (31 bp):
CTTGAGACAATTTCTTTTAGAACTAAATTTT
Found at i:12361604 original size:36 final size:36
Alignment explanation
Indices: 12361503--12361613 Score: 121
Period size: 36 Copynumber: 3.2 Consensus size: 36
12361493 TATCTTTTCC
12361503 TTGAAACAAATTTTGTCTCC-CTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTC-CCTCTTGAGACAGTTTCTT
*
12361539 TT-AGAACTAAA--TT-T---TCTTGAGACAATTTCTT
1 TTGA-AAC-AAATTTTGTCCCTCTTGAGACAGTTTCTT
*
12361570 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTT
12361606 TTGAAACA
1 TTGAAACA
12361614 CAAAAAAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
30 3 0.05
31 20 0.32
32 3 0.05
33 1 0.02
34 1 0.02
35 3 0.05
36 28 0.45
37 3 0.05
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.41
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTT
Found at i:12365334 original size:20 final size:20
Alignment explanation
Indices: 12365305--12365465 Score: 277
Period size: 20 Copynumber: 8.1 Consensus size: 20
12365295 GCATTGCGAA
* *
12365305 GTAAATAGTATTATCGCAAT
1 GTAAACAGTACTATCGCAAT
12365325 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
12365345 GTAAACAATACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
12365365 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
12365385 GTAAACAATACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
12365405 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
*
12365425 GTAAACAGTAATATCGCAAT
1 GTAAACAGTACTATCGCAAT
12365445 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
12365465 G
1 G
12365466 CGCTTTTCAA
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 133 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:12365527 original size:20 final size:20
Alignment explanation
Indices: 12365502--12365543 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12365492 ACCGATATAG
*
12365502 GTAAACATTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
12365522 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
12365542 GT
1 GT
12365544 GATTTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:12365541 original size:77 final size:77
Alignment explanation
Indices: 12365425--12365674 Score: 428
Period size: 77 Copynumber: 3.2 Consensus size: 77
12365415 CTATCGCAAT
* * *
12365425 GTAAACAGTAATATCGCAATGTAAACAGTACTATCGCAATGCGCTTTTCAAATTCGCAACGTTAA
1 GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
12365490 TTACCGATATAG
66 TTACCGATATAG
* *
12365502 GTAAACATTACTATCGCAATGTAAACAGTACTATCGCAATGTGATTTTCAAATTCGCAACGCTAA
1 GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
12365567 TTACCGATATAG
66 TTACCGATATAG
12365579 GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
1 GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
12365644 TTACCGATATAG
66 TTACCGATATAG
* **
12365656 ATAAACACAACTATCGCAA
1 GTAAACAGTACTATCGCAA
12365675 CGCGAATTTT
Statistics
Matches: 163, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 163 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (77 bp):
GTAAACAGTACTATCGCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
TTACCGATATAG
Found at i:12365604 original size:20 final size:20
Alignment explanation
Indices: 12365579--12365619 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12365569 ACCGATATAG
12365579 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
12365599 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
12365619 G
1 G
12365620 CGATTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Done.