Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009574.1 Hibiscus syriacus cultivar Beakdansim tig00116939_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: 2686660
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:2174926 original size:20 final size:20
Alignment explanation
Indices: 2174901--2174975 Score: 98
Period size: 20 Copynumber: 3.7 Consensus size: 20
2174891 TGCAGAAGAG
2174901 TCGCAACGAGAGAAATGAAA
1 TCGCAACGAGAGAAATGAAA
* *
2174921 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGA-AA
*
2174941 TCTGCAACGAGAAAAATGAAA
1 TC-GCAACGAGAGAAATGAAA
2174962 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2174976 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 6 0.13
20 24 0.51
21 11 0.23
22 6 0.13
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAAATGAAA
Found at i:2174979 original size:14 final size:14
Alignment explanation
Indices: 2174960--2175016 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2174950 AGAAAAATGA
2174960 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2174974 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2174993 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2175007 AATCGCAACG
1 AATCGCAACG
2175017 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2174999 original size:33 final size:32
Alignment explanation
Indices: 2174954--2175021 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 32
2174944 GCAACGAGAA
2174954 AAATGAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAATCGCAACGAGAGAATCGCAACGCG
2174986 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATG-AAATCGCAACGAGAGAATCGCAACGCG
2175019 AAA
1 AAA
2175022 CCAAAATCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 5 0.14
33 30 0.86
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.09
Consensus pattern (32 bp):
AAATGAAATCGCAACGAGAGAATCGCAACGCG
Found at i:2175028 original size:33 final size:33
Alignment explanation
Indices: 2174959--2175029 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2174949 GAGAAAAATG
**
2174959 AAATCGCAACGAGAGAATCGCAACGCGAAATGA
1 AAATCGCAACGAGAGAATCGCAACGCGAAACCA
2174992 AAATCGCAACGAGAGAATCGCAACGCGAAACCA
1 AAATCGCAACGAGAGAATCGCAACGCGAAACCA
2175025 AAATC
1 AAATC
2175030 TCATTGCGAT
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:0.46, C:0.24, G:0.21, T:0.08
Consensus pattern (33 bp):
AAATCGCAACGAGAGAATCGCAACGCGAAACCA
Found at i:2175068 original size:14 final size:14
Alignment explanation
Indices: 2175049--2175105 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2175039 TTTCATTTCG
2175049 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2175063 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2175082 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2175096 CGTTGCGATT
1 CGTTGCGATT
2175106 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2175080 original size:33 final size:33
Alignment explanation
Indices: 2175028--2175154 Score: 157
Period size: 33 Copynumber: 3.6 Consensus size: 33
2175018 GAAACCAAAA
*
2175028 TCTCATTGCGA-TTTCATTTCGCGTTGCGATTC
1 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
2175060 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
1 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
*
2175093 TCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTC
1 TCTCGTTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTC
2175134 TCTCGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTC
2175155 AACCAAAAGA
Statistics
Matches: 84, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
32 10 0.12
33 38 0.45
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.25
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (33 bp):
TCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
Found at i:2175116 original size:21 final size:21
Alignment explanation
Indices: 2175090--2175154 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2175080 CGCGTTGCGA
2175090 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2175111 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2175131 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
2175152 TTC
1 TTC
2175155 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2175694 original size:32 final size:31
Alignment explanation
Indices: 2175658--2175778 Score: 145
Period size: 32 Copynumber: 3.7 Consensus size: 31
2175648 TAGTTTACTT
*
2175658 TCGCAACACGAAACTTAAAATCGCAACG-AGAA
1 TCGCAACGCGAAAC--AAAATCGCAACGAAGAA
*
2175690 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAA-CAAAATCGCAACGA-AGAA
* *
2175723 TCGCAACGCGAAACCAAATCGCAACGACAAAA
1 TCGCAACGCGAAACAAAATCGCAACGA-AGAA
2175755 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAA-CAAAATCGCA
2175779 TTGCGATTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
31 12 0.15
32 41 0.52
33 26 0.33
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (31 bp):
TCGCAACGCGAAACAAAATCGCAACGAAGAA
Found at i:2175726 original size:14 final size:13
Alignment explanation
Indices: 2175706--2175762 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 13
2175696 CGCGAAATGA
2175706 AAATCGCAACGAC
1 AAATCGCAACGAC
2175719 AGAATCGCAACGCGAAACC
1 A-AATCGCAA--CG--A-C
2175738 AAATCGCAACGAC
1 AAATCGCAACGAC
2175751 AAAATCGCAACG
1 -AAATCGCAACG
2175763 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.05
14 20 0.54
16 4 0.11
18 9 0.24
19 2 0.05
ACGTcount: A:0.46, C:0.30, G:0.18, T:0.07
Consensus pattern (13 bp):
AAATCGCAACGAC
Found at i:2175744 original size:18 final size:18
Alignment explanation
Indices: 2175721--2175778 Score: 70
Period size: 14 Copynumber: 3.4 Consensus size: 18
2175711 GCAACGACAG
2175721 AATCGCAACGCGAAACCA
1 AATCGCAACGCGAAACCA
*
2175739 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAACCA
2175753 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACC-A
2175772 AATCGCA
1 AATCGCA
2175779 TTGCGATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 11 0.33
16 4 0.12
18 10 0.30
19 8 0.24
ACGTcount: A:0.47, C:0.31, G:0.16, T:0.07
Consensus pattern (18 bp):
AATCGCAACGCGAAACCA
Found at i:2175796 original size:19 final size:19
Alignment explanation
Indices: 2175774--2175945 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
2175764 GAAACCAAAA
*
2175774 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2175793 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2175807 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2175826 TCGCATTGCG---TTC-TG
1 TCGCGTTGCGATTTTCATT
2175841 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2175858 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
2175877 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
2175896 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
2175915 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2175935 TCGTGTTGCGA
1 TCGCGTTGCGA
2175946 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 17, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
13 6 0.05
14 10 0.08
15 2 0.02
16 9 0.07
17 5 0.04
19 80 0.65
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2175850 original size:32 final size:33
Alignment explanation
Indices: 2175779--2175870 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
2175769 CAAAATCGCA
2175779 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2175812 TTGCGATTTTCATTTCGCATTGCG-TTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2175844 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2175871 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2176834 original size:169 final size:171
Alignment explanation
Indices: 2176553--2176893 Score: 634
Period size: 169 Copynumber: 2.0 Consensus size: 171
2176543 GAGAGTTGGC
*
2176553 TCTCGTATAAGTTACCGGCCAGTACCATTCCGGTATCGGAAGTGGAGAGGAGACAACTACCAGAC
1 TCTCGTATAAGTTACCGGCCAGTACCATTCCGGTATCGGAAGTGGAGAGGAGACAACAACCAGAC
2176618 ACAATTCTGGATAACACCCTTTGGGCTAAGACCGCAGTTGATTTTATCTACATGAGC-GAGCCAG
66 ACAATTCTGGATAACACCCTTTGGGCTAAGACCGCAGTTGATTTTATCTACATGAGCGGAGCCAG
2176682 GGGTGTTTCACTGAC-TATGCAAGCTCACGATGATATCTAT
131 GGGTGTTTCACTGACATATGCAAGCTCACGATGATATCTAT
*
2176722 TCTCGTATAAGTTACCGGCCAGTACCATTCCGGTATCGGAAGTGGAGAGGAGA-GACAACCAGAC
1 TCTCGTATAAGTTACCGGCCAGTACCATTCCGGTATCGGAAGTGGAGAGGAGACAACAACCAGAC
2176786 ACAATTCTGGATAACACCCTTTGGGCTAAGACCGCAGTTGATTTTTATCTACATGAGCGGAGCCA
66 ACAATTCTGGATAACACCCTTTGGGCTAAGACCGCAGTTGA-TTTTATCTACATGAGCGGAGCCA
2176851 GGGGTGTTTCACTGACATATGCAAGCTCACGATGATATCTAT
130 GGGGTGTTTCACTGACATATGCAAGCTCACGATGATATCTAT
2176893 T
1 T
2176894 TGTTGCTTGA
Statistics
Matches: 167, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
168 50 0.30
169 69 0.41
170 22 0.13
171 26 0.16
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (171 bp):
TCTCGTATAAGTTACCGGCCAGTACCATTCCGGTATCGGAAGTGGAGAGGAGACAACAACCAGAC
ACAATTCTGGATAACACCCTTTGGGCTAAGACCGCAGTTGATTTTATCTACATGAGCGGAGCCAG
GGGTGTTTCACTGACATATGCAAGCTCACGATGATATCTAT
Found at i:2178016 original size:13 final size:14
Alignment explanation
Indices: 2178000--2178034 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2177990 ATTGTTTAAT
2178000 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
2178013 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2178027 TGATTTGT
1 TGATTTGT
2178035 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2178156 original size:20 final size:19
Alignment explanation
Indices: 2178139--2178237 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
2178129 CAAAATGACT
2178139 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2178159 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2178178 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2178192 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2178211 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2178231 ATCGCAA
1 ATCGCAA
2178238 CGAGAGATCG
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 29 0.41
20 26 0.37
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2178268 original size:52 final size:53
Alignment explanation
Indices: 2178139--2178255 Score: 211
Period size: 53 Copynumber: 2.2 Consensus size: 53
2178129 CAAAATGACT
2178139 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2178192 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG-
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2178244 ATCGCAATGCGA
1 ATCGCAATGCGA
2178256 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 31 0.49
53 32 0.51
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:2178300 original size:20 final size:19
Alignment explanation
Indices: 2178245--2178474 Score: 258
Period size: 20 Copynumber: 12.7 Consensus size: 19
2178235 CAACGAGAGA
*
2178245 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2178264 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
2178282 TCCGCATTACGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
2178302 TACGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
2178319 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2178336 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2178355 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
2178375 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
2178392 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2178409 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2178428 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
2178446 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
2178462 TCGCATTGCGATT
1 TCGCATTGCGATT
2178475 CTCTCGTTGC
Statistics
Matches: 182, Mismatches: 10, Indels: 38
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.13
16 12 0.07
17 13 0.07
18 15 0.08
19 56 0.31
20 63 0.35
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2178375 original size:73 final size:73
Alignment explanation
Indices: 2178251--2178446 Score: 367
Period size: 73 Copynumber: 2.7 Consensus size: 73
2178241 GAGATCGCAA
*
2178251 TGCGATTTTCATTTCGCATTGCGA-TTTCATTTCCGCATTACGATTTTCATTTACGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTACGCATTGCGAT
2178315 TCTCTCGT
66 TCTCTCGT
*
2178323 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTACGCATTGCGAT
2178388 TCTCTCGT
66 TCTCTCGT
2178396 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT
2178447 GTTGGGATTT
Statistics
Matches: 121, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
72 24 0.20
73 97 0.80
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (73 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTACGCATTGCGAT
TCTCTCGT
Found at i:2178414 original size:53 final size:53
Alignment explanation
Indices: 2178341--2178474 Score: 225
Period size: 53 Copynumber: 2.5 Consensus size: 53
2178331 TCATTTCGCA
2178341 TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCATTGCGATTCTCAT-G
*
2178395 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATG
*
2178448 TTGGGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2178475 CTCTCGTTGC
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
53 61 0.79
54 16 0.21
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATG
Found at i:2178461 original size:34 final size:34
Alignment explanation
Indices: 2178345--2178474 Score: 108
Period size: 34 Copynumber: 3.7 Consensus size: 34
2178335 TTCGCATTGC
*
2178345 GATTTTCATTTCCGCATTGCGATTTTCAT-TTCCG
1 GATTTTCATTTCCGCATTGCGATTTTCATGTT-GG
* * *
2178379 CA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCGCATTGC
1 GATTTTC-ATT-TC-CGCATTGCGATTTTCA--T-G--TTGG
2178418 GATTTTCATTTCCGCATTGCGATTTTCATGTTGG
1 GATTTTCATTTCCGCATTGCGATTTTCATGTTGG
2178452 GATTTTCATTT-CGCATTGCGATT
1 GATTTTCATTTCCGCATTGCGATT
2178475 CTCTCGTTGC
Statistics
Matches: 77, Mismatches: 7, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
33 15 0.19
34 30 0.39
35 2 0.03
36 4 0.05
37 3 0.04
38 2 0.03
39 16 0.21
40 5 0.06
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (34 bp):
GATTTTCATTTCCGCATTGCGATTTTCATGTTGG
Found at i:2178496 original size:33 final size:33
Alignment explanation
Indices: 2178414--2178488 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 33
2178404 TCATTTCGCA
*
2178414 TTGCGATTTTCATTTCCGCATTGCGATTTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCATG
*
2178448 TTGGGATTTTCATTTCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCAT-G
2178481 TTGCGATT
1 TTGCGATT
2178489 GTAATTTCCG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 22 0.59
34 14 0.38
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATG
Found at i:2178503 original size:53 final size:54
Alignment explanation
Indices: 2178291--2178507 Score: 184
Period size: 53 Copynumber: 4.1 Consensus size: 54
2178281 TTCCGCATTA
* * **
2178291 CGATTTTCATTTACGCATTGCGATTCTCTC-GTTGCG-ATTTTC-ATTT-CGCATTG
1 CGATTTTCATTTACGCATTGCGATT-T-TCAGTTCCGCA-TTGCGATTTCCGTGTTG
* *
2178344 CGATTTTCATTTCCGCATTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGTTG
1 CGATTTTCATTTACGCATTGCGATTTTCAGTTCCGCATTGCGATTTC-CGT-GTTG
* * *
2178398 CGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTG
1 CGATTTTCATTTACGCATTGCGATTTTCAGTTCCGCATTGCGATTTCCGTGTTG
* * **
2178451 GGATTTTCATTT-CGCATTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGTGTTG
1 CGATTTTCATTTACGCATTGCGATT-T-TCAGTTCCGCATTGCGATTTCCGTGTTG
2178504 CGAT
1 CGAT
2178508 AGTCAAATGC
Statistics
Matches: 139, Mismatches: 15, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
51 2 0.01
52 10 0.07
53 101 0.73
54 24 0.17
55 2 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.45
Consensus pattern (54 bp):
CGATTTTCATTTACGCATTGCGATTTTCAGTTCCGCATTGCGATTTCCGTGTTG
Found at i:2180924 original size:24 final size:24
Alignment explanation
Indices: 2180890--2180936 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2180880 CTGAAACATC
2180890 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2180914 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2180937 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2181548 original size:20 final size:20
Alignment explanation
Indices: 2181525--2181746 Score: 221
Period size: 20 Copynumber: 11.1 Consensus size: 20
2181515 AGTGTTGTGC
* *
2181525 TTTACAGATTCTCGTTGCGA
1 TTTACGGATTCGCGTTGCGA
** *
2181545 TTTACGGATTATCGTTACGA
1 TTTACGGATTCGCGTTGCGA
* *
2181565 TTTACAGATTCTCGTTGCGA
1 TTTACGGATTCGCGTTGCGA
**
2181585 TTTACGGATTATCGTTGCGA
1 TTTACGGATTCGCGTTGCGA
*
2181605 TTTACGGATACGCGTTGCGA
1 TTTACGGATTCGCGTTGCGA
* * *
2181625 TATACGGATACGCATTGCGA
1 TTTACGGATTCGCGTTGCGA
* *
2181645 TTTACGGATACGCGTTGCTA
1 TTTACGGATTCGCGTTGCGA
* * *
2181665 TTTACGGATACACGTTGCGG
1 TTTACGGATTCGCGTTGCGA
*
2181685 TTTACGGATACGCGTTGCGA
1 TTTACGGATTCGCGTTGCGA
*
2181705 TTTATGTG-TTCGCGTTGCGA
1 TTTACG-GATTCGCGTTGCGA
* **
2181725 TTTTCATATTCGCGTTGCGA
1 TTTACGGATTCGCGTTGCGA
2181745 TT
1 TT
2181747 CTGGAAAATC
Statistics
Matches: 173, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 172 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
TTTACGGATTCGCGTTGCGA
Found at i:2186539 original size:22 final size:19
Alignment explanation
Indices: 2186497--2186534 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2186487 TTGTTGAGTC
*
2186497 TTTCGATTATGATTATTAA
1 TTTCGATTAGGATTATTAA
2186516 TTTCGATTAGGATTATTAA
1 TTTCGATTAGGATTATTAA
2186535 AAATTACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (19 bp):
TTTCGATTAGGATTATTAA
Found at i:2186729 original size:28 final size:28
Alignment explanation
Indices: 2186697--2186753 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2186687 CTCTCCGTTT
* * * *
2186697 ACATTATGTTTTCAAGTTAGTGCTTGAA
1 ACATTATGTTGTAAAGTCAATGCTTGAA
2186725 ACATTATGTTGTAAAGTCAATGCTTGAA
1 ACATTATGTTGTAAAGTCAATGCTTGAA
2186753 A
1 A
2186754 ACAACGACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (28 bp):
ACATTATGTTGTAAAGTCAATGCTTGAA
Found at i:2187678 original size:31 final size:30
Alignment explanation
Indices: 2187642--2187711 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
2187632 AAGTTTTAAA
* *
2187642 TGTAACAAATTGCTCACTAATATTATCAATT
1 TGTAACAAATTGCTAACTAAT-GTATCAATT
* *
2187673 TGTAACAAATTGGTAACTAATGTATCGATT
1 TGTAACAAATTGCTAACTAATGTATCAATT
*
2187703 TATAACAAA
1 TGTAACAAA
2187712 ATGGTCATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 15 0.44
31 19 0.56
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (30 bp):
TGTAACAAATTGCTAACTAATGTATCAATT
Found at i:2187711 original size:30 final size:31
Alignment explanation
Indices: 2187644--2187716 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
2187634 GTTTTAAATG
* * * *
2187644 TAACAAATTGCTCACTAATATTATCAATTTG
1 TAACAAATTGGTAACTAATAGTATCAATTTA
*
2187675 TAACAAATTGGTAACTAAT-GTATCGATTTA
1 TAACAAATTGGTAACTAATAGTATCAATTTA
*
2187705 TAACAAAATGGT
1 TAACAAATTGGT
2187717 CATTCTATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 19 0.53
31 17 0.47
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (31 bp):
TAACAAATTGGTAACTAATAGTATCAATTTA
Found at i:2192382 original size:15 final size:15
Alignment explanation
Indices: 2192362--2192390 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2192352 TCAAGAAGGC
2192362 TAAAAAGAATAAGAA
1 TAAAAAGAATAAGAA
2192377 TAAAAAGAATAAGA
1 TAAAAAGAATAAGA
2192391 TACCTCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
TAAAAAGAATAAGAA
Found at i:2194832 original size:15 final size:15
Alignment explanation
Indices: 2194812--2194844 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2194802 CAAGAAAATT
2194812 CAAAATTTGATAGGG
1 CAAAATTTGATAGGG
*
2194827 CAAAATTTGATGGGG
1 CAAAATTTGATAGGG
2194842 CAA
1 CAA
2194845 GAAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.24
Consensus pattern (15 bp):
CAAAATTTGATAGGG
Found at i:2195014 original size:21 final size:22
Alignment explanation
Indices: 2194990--2195030 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2194980 CATGTCAAAG
2194990 AATTCAAGA-TCAAGAATCAGA
1 AATTCAAGATTCAAGAATCAGA
*
2195011 AATTCAAGATTCCAGAATCA
1 AATTCAAGATTCAAGAATCA
2195031 ATAGTCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (22 bp):
AATTCAAGATTCAAGAATCAGA
Found at i:2195317 original size:58 final size:58
Alignment explanation
Indices: 2195249--2195386 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 58
2195239 AACTTCAGGG
* * ** *
2195249 CGAATGATATCCAACTTAAAGTCAATTCGATGAAGCAGA-TTGAATTTCAACATCACAA
1 CGAAGGATATCCAACTCAAAACCAATTCGATGAAACA-ACTTGAATTTCAACATCACAA
* * * * *
2195307 CGAAGGATATCCAACTCAAAACCAATTTGGTGAAACAACCCTTGGATTTCAACTTCACGA
1 CGAAGGATATCCAACTCAAAACCAATTCGATGAAACAA--CTTGAATTTCAACATCACAA
*
2195367 CGAAGGATATCCAATTCAAA
1 CGAAGGATATCCAACTCAAA
2195387 GCTCAACTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 1 0.02
58 30 0.45
60 35 0.53
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (58 bp):
CGAAGGATATCCAACTCAAAACCAATTCGATGAAACAACTTGAATTTCAACATCACAA
Found at i:2195373 original size:60 final size:58
Alignment explanation
Indices: 2195227--2195386 Score: 169
Period size: 58 Copynumber: 2.7 Consensus size: 58
2195217 ACACAACACA
* * * * ** *
2195227 AGATTGGATTTCAACTTCAGGGCGAATGATATCCAACTTAAAGTCAATTCGATGAAGC
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTCGATGAAAC
* * * * *
2195285 AGATTGAATTTCAACATCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTCGATGAAAC
*
2195343 A-ACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAA
1 AGA---TTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAA
2195387 GCTCAACTTT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
57 1 0.01
58 47 0.57
60 35 0.42
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (58 bp):
AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTCGATGAAAC
Found at i:2195433 original size:66 final size:65
Alignment explanation
Indices: 2195351--2195564 Score: 202
Period size: 66 Copynumber: 3.4 Consensus size: 65
2195341 ACAACCCTTG
2195351 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTTACGAAGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAAC-TTACGAAGAATGAGCCATCCA
2195416 C
65 C
* * * * * *
2195417 GATTTCAACTTCACGACGAAGGATAT-C-A-T---GGC-C-AC--AAGCAGTAATATAACC--CT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTACGAAG-AAT-GAGCCATCC
**
2195470 TG
64 AC
*
2195472 GATTTTAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCAC-AACGAATGAGCCATCC
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTT-ACGAA-GAATGAGCCATCC
2195536 AC
64 AC
*
2195538 GATTTCAACTTCACGACAAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
2195565 GTGCCCACAA
Statistics
Matches: 113, Mismatches: 19, Indels: 32
0.69 0.12 0.20
Matches are distributed among these distances:
55 30 0.27
56 4 0.04
57 4 0.04
58 3 0.03
59 1 0.01
60 2 0.02
61 2 0.02
62 1 0.01
63 3 0.03
64 4 0.04
65 5 0.04
66 54 0.48
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.23
Consensus pattern (65 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTACGAAGAATGAGCCATCCAC
Found at i:2195690 original size:121 final size:121
Alignment explanation
Indices: 2195341--2195692 Score: 571
Period size: 121 Copynumber: 2.9 Consensus size: 121
2195331 ATTTGGTGAA
*
2195341 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTTACGAA-GAA
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCAC-AACGAA
* * * *
2195405 TGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGGCCACAAGCAGTAAT
65 TGAGCCATCCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAGCAGCAAT
* *
2195462 ATAACCCTTGGATTTTAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAT
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAT
2195527 GAGCCATCCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAGCAGCAAT
66 GAGCCATCCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAGCAGCAAT
* * * *
2195583 GCAACCCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCCAAGCTCAAGTTCACAACGAAT
1 ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAT
* *
2195648 GAGCCATCCACGATTTTAACTTCACGACAAAGGATATTGTGCCCA
66 GAGCCATCCACGATTTCAACTTCACGACAAAGGATATCGTGCCCA
2195693 ATGGATCGAC
Statistics
Matches: 215, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
120 2 0.01
121 213 0.99
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (121 bp):
ACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAT
GAGCCATCCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAGCAGCAAT
Found at i:2196645 original size:14 final size:14
Alignment explanation
Indices: 2196628--2196661 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2196618 GGTCTCGAAC
*
2196628 GAAAAAGATCGAGA
1 GAAAAAGATCAAGA
*
2196642 GAAAAATATCAAGA
1 GAAAAAGATCAAGA
2196656 GAAAAA
1 GAAAAA
2196662 CCATTCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.21, T:0.09
Consensus pattern (14 bp):
GAAAAAGATCAAGA
Found at i:2197745 original size:19 final size:19
Alignment explanation
Indices: 2197705--2197745 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2197695 AATTTTTTCT
*
2197705 AATTAATTAATTTGAAGCA
1 AATTAATTAATTTCAAGCA
2197724 AATTAATTAAATTTCAAG-A
1 AATTAATT-AATTTCAAGCA
2197743 AAT
1 AAT
2197746 GAATCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (19 bp):
AATTAATTAATTTCAAGCA
Found at i:2203581 original size:14 final size:14
Alignment explanation
Indices: 2203562--2203589 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2203552 TTTTTTTAAC
2203562 TAGCAACACAGGCG
1 TAGCAACACAGGCG
2203576 TAGCAACACAGGCG
1 TAGCAACACAGGCG
2203590 ATGAGAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.29, T:0.07
Consensus pattern (14 bp):
TAGCAACACAGGCG
Found at i:2206010 original size:41 final size:41
Alignment explanation
Indices: 2205965--2206176 Score: 253
Period size: 41 Copynumber: 5.1 Consensus size: 41
2205955 ACTTTAGCGC
* *
2205965 CGTTTTTATACAAACGCCGCTATAAACACGTAAGTTAGTGG
1 CGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGG
* * * *
2206006 CGTTTTTATACAAATGCCGTTATAGACATGTAATTTAGCGG
1 CGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGG
*
2206047 CGTTTTTATACAAACGCCGCTATAGACACGTACTTTAGTGG
1 CGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGG
* * *
2206088 CGTTTTTATACAAACGCCGCTATAGACTCATACTTTAGTGG
1 CGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGG
* * ** * * *
2206129 CGTTTGTGTTTAAAAACGATGCTATAGACTCGTACTTTAGCGG
1 CGTTT-T-TATACAAACGCCGCTATAGACACGTAATTTAGTGG
2206172 CGTTT
1 CGTTT
2206177 GTAAAAACAA
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
41 115 0.77
42 1 0.01
43 34 0.23
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (41 bp):
CGTTTTTATACAAACGCCGCTATAGACACGTAATTTAGTGG
Found at i:2206189 original size:43 final size:41
Alignment explanation
Indices: 2205831--2206195 Score: 229
Period size: 41 Copynumber: 8.8 Consensus size: 41
2205821 CAAATTGATA
* * * * * *
2205831 ACTTTAGCGGCGTTTTTATACAAAACGCCACAACAGAGTAGT
1 ACTTTAGCGGCGTTTTTAAAC-AAACGCCGCTATAGACTCGT
* * * ** *
2205873 ACTTTAGTGGCGTTTTTATACAAACGCCGCAATAGGTTCAT
1 ACTTTAGCGGCGTTTTTAAACAAACGCCGCTATAGACTCGT
** * * * *
2205914 -CCATAGTGGCATTTTTTAAACAAACGTCATGAC-ATAG--TAGT
1 ACTTTAGCGGC-GTTTTTAAACAAACG-C-CG-CTATAGACTCGT
* * * *
2205955 ACTTTAGCGCCGTTTTTATACAAACGCCGCTATAAACACGT
1 ACTTTAGCGGCGTTTTTAAACAAACGCCGCTATAGACTCGT
** * * * *
2205996 AAGTTAGTGGCGTTTTTATACAAATGCCGTTATAGACAT-GT
1 ACTTTAGCGGCGTTTTTAAACAAACGCCGCTATAGAC-TCGT
* * *
2206037 AATTTAGCGGCGTTTTTATACAAACGCCGCTATAGACACGT
1 ACTTTAGCGGCGTTTTTAAACAAACGCCGCTATAGACTCGT
* * *
2206078 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCAT
1 ACTTTAGCGGCGTTTTTAAACAAACGCCGCTATAGACTCGT
* * **
2206119 ACTTTAGTGGCGTTTGTGTTTAA-AAACGATGCTATAGACTCGT
1 ACTTTAGCGGCG-TT-T-TTAAACAAACGCCGCTATAGACTCGT
* *
2206162 ACTTTAGCGGCGTTTGTAAAAACAAACGTCGCTA
1 ACTTTAGCGGCGTTT-T-TAAACAAACGCCGCTA
2206196 AAGTTTAAAG
Statistics
Matches: 257, Mismatches: 51, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
38 1 0.00
39 4 0.02
40 9 0.04
41 163 0.63
42 33 0.13
43 43 0.17
44 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (41 bp):
ACTTTAGCGGCGTTTTTAAACAAACGCCGCTATAGACTCGT
Found at i:2210634 original size:21 final size:21
Alignment explanation
Indices: 2210577--2210635 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
2210567 TGATTTATTA
* *
2210577 TTATAGATTTTAAGTATCTTG
1 TTATGGATTTTAAGTTTCTTG
*
2210598 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTTAAGTTTCTTG
*
2210619 TTATGGATGTTAAGTTT
1 TTATGGATTTTAAGTTT
2210636 ATTGGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.02, G:0.20, T:0.54
Consensus pattern (21 bp):
TTATGGATTTTAAGTTTCTTG
Found at i:2210867 original size:43 final size:42
Alignment explanation
Indices: 2210801--2210908 Score: 157
Period size: 43 Copynumber: 2.6 Consensus size: 42
2210791 AGATAAATAG
*
2210801 CGGCGTTTG-AAAAATACGCCGCTAAATATCATAACATTTAC
1 CGGCGTTTGTAAAAAAACGCCGCTAAATATCATAACATTTAC
* * *
2210842 CGGCGTTTGTAATAAAAACGCCGCTAAATATCATTACCTTTAG
1 CGGCGTTTGTAA-AAAAACGCCGCTAAATATCATAACATTTAC
2210885 CGGCGTTTGT-AAAAAACGCCGCTA
1 CGGCGTTTGTAAAAAAACGCCGCTA
2210909 CAAAACATCA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
41 22 0.36
42 3 0.05
43 36 0.59
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (42 bp):
CGGCGTTTGTAAAAAAACGCCGCTAAATATCATAACATTTAC
Found at i:2210922 original size:41 final size:41
Alignment explanation
Indices: 2210798--2210935 Score: 172
Period size: 41 Copynumber: 3.3 Consensus size: 41
2210788 AAAAGATAAA
*
2210798 TAGCGGCGTTTG-AAAAATACGCCGCTAAATATCATAACATT
1 TAGCGGCGTTTGTAAAAA-ACGCCGCTAAATATCATAACCTT
* *
2210839 TACCGGCGTTTGTAATAAAAACGCCGCTAAATATCATTACCTT
1 TAGCGGCGTTTGT-A-AAAAACGCCGCTAAATATCATAACCTT
* *
2210882 TAGCGGCGTTTGTAAAAAACGCCGCTACAA-AACATCACCTT
1 TAGCGGCGTTTGTAAAAAACGCCGCTA-AATATCATAACCTT
*
2210923 CAGCGGCGTTTGT
1 TAGCGGCGTTTGT
2210936 GAACGAAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
41 45 0.52
42 3 0.03
43 34 0.40
44 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (41 bp):
TAGCGGCGTTTGTAAAAAACGCCGCTAAATATCATAACCTT
Found at i:2210930 original size:84 final size:86
Alignment explanation
Indices: 2210798--2210954 Score: 205
Period size: 84 Copynumber: 1.8 Consensus size: 86
2210788 AAAAGATAAA
* * *
2210798 TAGCGGCGTTTGAAAAATACGCCGCTAAATATCATAACATTTACCGGCGTTTGT-AA-TAAAAAC
1 TAGCGGCGTTTGAAAAATACGCCGCTAAATAACATAACATTCACCGGCGTTTGTGAACAAAAAAC
2210861 GCCGCTAAATATCATTACCTT
66 GCCGCTAAATATCATTACCTT
* * *
2210882 TAGCGGCGTTTGTAAAAA-ACGCCGCTACAA-AACATCACCTTCAGCGGCGTTTGTGAACGAAAA
1 TAGCGGCGTTTG-AAAAATACGCCGCTA-AATAACATAACATTCACCGGCGTTTGTGAAC-AAAA
2210945 AACGCCGCTA
63 AACGCCGCTA
2210955 CCTTTTGCGA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
84 40 0.65
85 9 0.15
87 13 0.21
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (86 bp):
TAGCGGCGTTTGAAAAATACGCCGCTAAATAACATAACATTCACCGGCGTTTGTGAACAAAAAAC
GCCGCTAAATATCATTACCTT
Found at i:2211778 original size:10 final size:10
Alignment explanation
Indices: 2211757--2211789 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2211747 TTAGCAAAAG
2211757 AAATTG-AAT
1 AAATTGAAAT
2211766 AAATTGAAAT
1 AAATTGAAAT
2211776 AAATTGAAAT
1 AAATTGAAAT
2211786 AAAT
1 AAAT
2211790 AAAAATAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (10 bp):
AAATTGAAAT
Found at i:2211795 original size:20 final size:19
Alignment explanation
Indices: 2211752--2211797 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
2211742 GGGGTTTAGC
* *
2211752 AAAAGAAATTGAATAAATT
1 AAAATAAATTGAATAAATA
*
2211771 GAAATAAATTGAAATAAATA
1 AAAATAAATTG-AATAAATA
2211791 AAAATAA
1 AAAATAA
2211798 GAAAAATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (19 bp):
AAAATAAATTGAATAAATA
Found at i:2212680 original size:41 final size:41
Alignment explanation
Indices: 2212593--2212680 Score: 124
Period size: 41 Copynumber: 2.2 Consensus size: 41
2212583 TAATTTCTAA
* *
2212593 ATAAAA-TAATAATAAAATAATCAAACTAAAAAACCTAAAT
1 ATAAAAGTAATAATAAAATAATCAAACCAAAAAACATAAAT
* *
2212633 AAAAAAGTAATAATAAAATAATCAAACCAAAAATCATAAAT
1 ATAAAAGTAATAATAAAATAATCAAACCAAAAAACATAAAT
*
2212674 CTAAAAG
1 ATAAAAG
2212681 GTTTATCGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 5 0.12
41 36 0.88
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.20
Consensus pattern (41 bp):
ATAAAAGTAATAATAAAATAATCAAACCAAAAAACATAAAT
Found at i:2222659 original size:18 final size:18
Alignment explanation
Indices: 2222636--2222673 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2222626 GTTTCAACAT
2222636 TTTGAATATTT-TGGAATG
1 TTTGAAT-TTTGTGGAATG
*
2222654 TTTGAATTTTGTGGATTG
1 TTTGAATTTTGTGGAATG
2222672 TT
1 TT
2222674 AAACTTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (18 bp):
TTTGAATTTTGTGGAATG
Found at i:2226296 original size:22 final size:22
Alignment explanation
Indices: 2226231--2226296 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 22
2226221 CCTACCAATA
*
2226231 AAATAATCAAACTAAAGATCAT
1 AAATAATCAAACTAAAAATCAT
* * *
2226253 AATTAA--AAAGTAATAAT-A-
1 AAATAATCAAACTAAAAATCAT
2226271 AAATAATCAAACTAAAAATCAT
1 AAATAATCAAACTAAAAATCAT
2226293 AAAT
1 AAAT
2226297 CTAAAAGGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
18 5 0.15
19 1 0.03
20 17 0.52
21 1 0.03
22 9 0.27
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (22 bp):
AAATAATCAAACTAAAAATCAT
Found at i:2227745 original size:17 final size:17
Alignment explanation
Indices: 2227704--2227745 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2227694 AAAAAAATAC
2227704 AATATATATATAATATA
1 AATATATATATAATATA
* *
2227721 AGTTTATATATAA-ACTA
1 AATATATATATAATA-TA
2227738 AATATATA
1 AATATATA
2227746 AACTATATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AATATATATATAATATA
Found at i:2227758 original size:13 final size:13
Alignment explanation
Indices: 2227726--2227750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2227716 ATATAAGTTT
2227726 ATATATAAACTAA
1 ATATATAAACTAA
2227739 ATATATAAACTA
1 ATATATAAACTA
2227751 TATTTATATT
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATATAAACTAA
Found at i:2227765 original size:18 final size:18
Alignment explanation
Indices: 2227742--2227794 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
2227732 AAACTAAATA
*
2227742 TATAAACTATATTTATAT
1 TATAAACTATATATATAT
2227760 TATAAACTATATAGT-TAT
1 TATAAACTATATA-TATAT
*
2227778 TATAAGCTATATATATA
1 TATAAACTATATATATA
2227795 AATTGTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (18 bp):
TATAAACTATATATATAT
Found at i:2227835 original size:13 final size:13
Alignment explanation
Indices: 2227810--2227846 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2227800 TGTTTATATG
2227810 AACTATATA--TA
1 AACTATATATGTA
2227821 AACTATATATGTA
1 AACTATATATGTA
*
2227834 AATTATATATGTA
1 AACTATATATGTA
2227847 TAAACTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 9 0.39
13 14 0.61
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (13 bp):
AACTATATATGTA
Found at i:2227853 original size:39 final size:39
Alignment explanation
Indices: 2227706--2227935 Score: 120
Period size: 39 Copynumber: 5.9 Consensus size: 39
2227696 AAAAATACAA
* *
2227706 TATATATATAATATAAGTTTATATATAAACTAAATATATAAAC
1 TATATATATAA-ATTA-TATATATATAAACT--ATATATAAAC
* * ** *
2227749 TATAT-T-TATATTATAAACTATAT-AGTTAT-TATAAGC
1 TATATATATAAATTATATA-TATATAAACTATATATAAAC
* * * *
2227785 TATATATATAAATTGTGTTTATATGAACTATATATAAAC
1 TATATATATAAATTATATATATATAAACTATATATAAAC
* *
2227824 TATATATGTAAATTATATATGTATAAACTATA-A-AAGTA-
1 TATATATATAAATTATATATATATAAACTATATATAA--AC
* * * * *
2227862 TATAGTTTATAAACTATAATTTATATATA-TATATATATA-
1 TATA-TATATAAATTAT-ATATATATAAACTATATATAAAC
* *
2227901 TATATATATATATATATATATATATATA-TATATAT
1 TATATATATAAAT-TATATATATATAAACTATATAT
2227936 TCAAAGTGAG
Statistics
Matches: 143, Mismatches: 32, Indels: 29
0.70 0.16 0.14
Matches are distributed among these distances:
36 11 0.08
37 10 0.07
38 38 0.27
39 58 0.41
40 17 0.12
41 3 0.02
42 1 0.01
43 5 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (39 bp):
TATATATATAAATTATATATATATAAACTATATATAAAC
Found at i:2227886 original size:23 final size:23
Alignment explanation
Indices: 2227833--2227894 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2227823 CTATATATGT
2227833 AAATTATATATGTATAAACTATA
1 AAATTATATATGTATAAACTATA
* *
2227856 AAAGTATATAGTTTATAAACTAT-
1 AAATTATATA-TGTATAAACTATA
* *
2227879 AATTTATATATATATA
1 AAATTATATATGTATA
2227895 TATATATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 5 0.15
23 17 0.52
24 11 0.33
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (23 bp):
AAATTATATATGTATAAACTATA
Found at i:2227890 original size:2 final size:2
Alignment explanation
Indices: 2227883--2227935 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2227873 AACTATAATT
2227883 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2227925 TA TA TA TA TA T
1 TA TA TA TA TA T
2227936 TCAAAGTGAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2227896 original size:24 final size:24
Alignment explanation
Indices: 2227813--2227935 Score: 96
Period size: 22 Copynumber: 5.1 Consensus size: 24
2227803 TTATATGAAC
*
2227813 TATATATAAACTATATATGTAAATTATA
1 TATATATAAACTATA-A--TATA-TATA
*
2227841 TATGTATAAACTATAA-A-AGTATA
1 TATATATAAACTATAATATA-TATA
* *
2227864 TAGTTTATAAACTATAATTTATATA
1 TA-TATATAAACTATAATATATATA
*
2227889 TATATATATA-TAT-ATATATATA
1 TATATATAAACTATAATATATATA
*
2227911 TATATATATA-TAT-ATATATATA
1 TATATATAAACTATAATATATATA
2227933 TAT
1 TAT
2227936 TCAAAGTGAG
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
22 33 0.39
23 10 0.12
24 20 0.24
25 6 0.07
26 1 0.01
27 1 0.01
28 14 0.16
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (24 bp):
TATATATAAACTATAATATATATA
Found at i:2228305 original size:2 final size:2
Alignment explanation
Indices: 2228298--2228451 Score: 99
Period size: 2 Copynumber: 78.5 Consensus size: 2
2228288 TTTATTTTTC
* * *
2228298 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TG TA TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
2228341 TA TG TA TA AA CTA TA TA -A AA TA TA TA GTT TA TA AA T- TA TA AA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
2228383 T- TA TA T- TA -A TA TA GTA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2228423 -A CTA -A TA TA AA TA -A TC TA TA TA TA TA TA T
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2228452 GGAATCCTAA
Statistics
Matches: 116, Mismatches: 23, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
1 8 0.07
2 102 0.88
3 6 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2228558 original size:17 final size:17
Alignment explanation
Indices: 2228531--2228588 Score: 89
Period size: 17 Copynumber: 3.2 Consensus size: 17
2228521 ATAAGCTATT
2228531 TATAGTATATATAAACTA
1 TATA-TATATATAAACTA
2228549 TATATATATATATAACCTA
1 TATATATATATA-AA-CTA
2228568 TATATATATATAAACTA
1 TATATATATATAAACTA
2228585 TATA
1 TATA
2228589 AAGTAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 15 0.39
18 8 0.21
19 15 0.39
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (17 bp):
TATATATATATAAACTA
Found at i:2228560 original size:19 final size:19
Alignment explanation
Indices: 2228520--2228588 Score: 88
Period size: 17 Copynumber: 3.7 Consensus size: 19
2228510 TACATGTATG
* *
2228520 TATAAGCTATTTATAGTATA
1 TATAAACTATATATA-TATA
2228540 TATAAACTATATATATATA
1 TATAAACTATATATATATA
*
2228559 TAT-AAC-CTATATATATA
1 TATAAACTATATATATATA
2228576 TATAAACTATATA
1 TATAAACTATATA
2228589 AAGTAAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
17 13 0.30
18 6 0.14
19 11 0.26
20 13 0.30
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (19 bp):
TATAAACTATATATATATA
Found at i:2228875 original size:35 final size:36
Alignment explanation
Indices: 2228807--2228880 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
2228797 ACAATAGTTA
*
2228807 ATATATGTAACCTATAGTATATGTATACATATAAACT
1 ATATATGTAACCTATAGTACATGTATA-ATATAAACT
* *
2228844 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACCTATAGTACATGTATAATATAAACT
2228879 AT
1 AT
2228881 GCATAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 10 0.29
37 24 0.71
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACATGTATAATATAAACT
Found at i:2228896 original size:20 final size:17
Alignment explanation
Indices: 2228871--2228924 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 17
2228861 TACATGTATG
2228871 TATAAACTATGCATAATATA
1 TATAAACTAT--AT-ATATA
2228891 TATAAACTATATATATA
1 TATAAACTATATATATA
2228908 TAT-AAC-ATATAGTATA
1 TATAAACTATATA-TATA
2228924 T
1 T
2228925 GTATATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.15
16 8 0.24
17 8 0.24
18 2 0.06
20 10 0.30
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (17 bp):
TATAAACTATATATATA
Found at i:2228929 original size:20 final size:20
Alignment explanation
Indices: 2228900--2228961 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
2228890 ATATAAACTA
*
2228900 TATATATATATAACATATA-G
1 TATATGTATATAA-ATATATG
*
2228920 TATATGTATATATAATATATT
1 TATATGTATATA-AATATATG
2228941 TATATGGTATATAAACTATAT
1 TATAT-GTATATAAA-TATAT
2228962 ATGTAACGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 16 0.44
21 8 0.22
22 12 0.33
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (20 bp):
TATATGTATATAAATATATG
Found at i:2228929 original size:22 final size:22
Alignment explanation
Indices: 2228898--2228962 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
2228888 ATATATAAAC
*
2228898 TATATATATATATAACATATAG
1 TATATGTATATATAACATATAG
* *
2228920 TATATGTATATATAATATAT-T
1 TATATGTATATATAACATATAG
2228941 TATATGGTATATA-AACTATATA
1 TATAT-GTATATATAAC-ATATA
2228963 TGTAACGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 7 0.19
22 29 0.81
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (22 bp):
TATATGTATATATAACATATAG
Found at i:2228963 original size:2 final size:2
Alignment explanation
Indices: 2228886--2228945 Score: 52
Period size: 2 Copynumber: 30.0 Consensus size: 2
2228876 ACTATGCATA
* * *
2228886 AT AT AT AT AA ACT AT AT AT AT AT AT A- AC AT AT AGT AT AT GT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
2228929 AT AT A- AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT
2228946 GGTATATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
1 2 0.04
2 42 0.89
3 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2229032 original size:21 final size:21
Alignment explanation
Indices: 2229006--2229058 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2228996 TAGTGTACTA
*
2229006 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAACC
* *
2229027 TATAGTATATAATTTATAATC
1 TATAGTTTATAATTTATAACC
2229048 TATAGTTTATA
1 TATAGTTTATA
2229059 TTAATGTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (21 bp):
TATAGTTTATAATTTATAACC
Found at i:2229168 original size:21 final size:21
Alignment explanation
Indices: 2229105--2229168 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2229095 CTTAACTATG
*
2229105 ATTTATATTAATATAGTATATA
1 ATTTATA-AAATATAGTATATA
* * *
2229127 GTTTATAAACTATACTATATA
1 ATTTATAAAATATAGTATATA
*
2229148 ATTTATAAAATATAGTTTATA
1 ATTTATAAAATATAGTATATA
2229169 TTAATATTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 28 0.82
22 6 0.18
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTTATAAAATATAGTATATA
Found at i:2229198 original size:31 final size:31
Alignment explanation
Indices: 2229149--2229304 Score: 101
Period size: 31 Copynumber: 5.0 Consensus size: 31
2229139 TACTATATAA
2229149 TTTATAAAATATAGTTTATATTAATATTAAT
1 TTTATAAAATATAGTTTATATTAATATTAAT
* * *
2229180 TTTATAGACTATATTTTATATTAATATTAAT
1 TTTATAAAATATAGTTTATATTAATATTAAT
* *
2229211 TACAAATTATAAACTATA--TTATATTAATA-TAAG
1 T-----TTATAAAATATAGTTTATATTAATATTAAT
* * *
2229244 TTAATATTAATATTA-ATTATATTAATATTAA-
1 TTTATA-AAATA-TAGTTTATATTAATATTAAT
* * *
2229275 TAT-TAATAT-TAATTTATATTAATATTAAT
1 TTTATAAAATATAGTTTATATTAATATTAAT
2229304 T
1 T
2229305 ATAAATAGTT
Statistics
Matches: 101, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
27 2 0.02
28 19 0.19
29 6 0.06
30 4 0.04
31 41 0.41
32 3 0.03
33 4 0.04
34 11 0.11
36 11 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (31 bp):
TTTATAAAATATAGTTTATATTAATATTAAT
Found at i:2229221 original size:88 final size:88
Alignment explanation
Indices: 2229069--2229268 Score: 215
Period size: 88 Copynumber: 2.4 Consensus size: 88
2229059 TTAATGTACT
* * * **
2229069 ATATAGTTTATATTAATGTTAATTATCTTAACTATGATTTATATTAATATAGTATATAGTTTATA
1 ATATAGTTTATATTAATATTAATTATCTTAACTATGATTTATATTAATATAATATACAAATTATA
2229134 AACTATACTATATAATTTATAAA
66 AACTATACTATATAATTTATAAA
2229157 ATATAGTTTATATTAATATTAATT-T-TATAGACTAT-ATTTTATATTAATATTAAT-TACAAAT
1 ATATAGTTTATATTAATATTAATTATCT-TA-ACTATGA-TTTATATTAATA-TAATATACAAAT
*
2229218 TATAAACTATA-T-TAT-A--T-TAAT
62 TATAAACTATACTATATAATTTATAAA
* *
2229239 ATA-AGTTAATATTAATATTAATTATATTAA
1 ATATAGTTTATATTAATATTAATTATCTTAA
2229269 TATTAATATT
Statistics
Matches: 99, Mismatches: 7, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
81 20 0.20
82 9 0.09
83 2 0.02
85 1 0.01
86 4 0.04
87 5 0.05
88 55 0.56
89 3 0.03
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (88 bp):
ATATAGTTTATATTAATATTAATTATCTTAACTATGATTTATATTAATATAATATACAAATTATA
AACTATACTATATAATTTATAAA
Found at i:2229221 original size:110 final size:109
Alignment explanation
Indices: 2229005--2229221 Score: 231
Period size: 110 Copynumber: 2.0 Consensus size: 109
2228995 TTAGTGTACT
* * * **
2229005 ATATAGTTTATACTTTATAACCTATAGTATATAATTTATAATCTATAGTTTATATTAATGTACTA
1 ATATAGTATATACTTTATAAACTATACTATATAATTTATAAAATATAGTTTATATTAATGTACTA
** * ** *
2229070 TATAGTTTATATTAATGTTAATTATCTTAACTATGATTTATATTA
66 TATAGACTATATTAATATTAATTA-CTTAACTACAAATTATATTA
* * *
2229115 ATATAGTATATAGTTTATAAACTATACTATATAATTTATAAAATATAGTTTATATTAATATTAAT
1 ATATAGTATATACTTTATAAACTATACTATATAATTTATAAAATATAGTTTATATTAAT-GT-AC
* * *
2229180 TTTATAGACTATATTTTATATTAA-TA-TTAATTACAAATTATA
64 TATATAGACTATA-TTAATATTAATTACTTAACTACAAATTATA
2229222 AACTATATTA
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
110 65 0.75
111 1 0.01
112 13 0.15
113 8 0.09
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (109 bp):
ATATAGTATATACTTTATAAACTATACTATATAATTTATAAAATATAGTTTATATTAATGTACTA
TATAGACTATATTAATATTAATTACTTAACTACAAATTATATTA
Found at i:2229252 original size:16 final size:15
Alignment explanation
Indices: 2229231--2229305 Score: 77
Period size: 16 Copynumber: 5.0 Consensus size: 15
2229221 AAACTATATT
2229231 ATATTAATATAAGTTA
1 ATATTAATATAA-TTA
2229247 ATATTAATATTAATT-
1 ATATTAATA-TAATTA
2229262 ATATT-A-AT-ATTA
1 ATATTAATATAATTA
*
2229274 ATATTAATATTAATTT
1 ATATTAATA-TAATTA
2229290 ATATTAATATTAATTA
1 ATATTAATA-TAATTA
2229306 TAAATAGTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
11 3 0.06
12 6 0.12
13 2 0.04
14 2 0.04
15 6 0.12
16 29 0.57
17 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATATTAATATAATTA
Found at i:2229253 original size:6 final size:6
Alignment explanation
Indices: 2229226--2229303 Score: 91
Period size: 6 Copynumber: 14.3 Consensus size: 6
2229216 ATTATAAACT
*
2229226 ATATT- ATATTA ATA-TA A-GTTA ATATTA ATATT- A-ATT- ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
2229268 ATATTA ATATTA ATATTA AT-TT- ATATTA ATATTA AT
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA AT
2229304 TATAAATAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 13
0.81 0.03 0.16
Matches are distributed among these distances:
4 6 0.09
5 19 0.30
6 39 0.61
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:2229278 original size:43 final size:42
Alignment explanation
Indices: 2229226--2229307 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 42
2229216 ATTATAAACT
2229226 ATATTATATTAATA-TAAGTTAATATTAATATTAATTATATTA
1 ATATTATATTAATATTAA-TTAATATTAATATTAATTATATTA
*
2229268 ATATTAATATTAATATTAATTTATATTAATATTAATTATA
1 ATATT-ATATTAATATTAATTAATATTAATATTAATTATA
2229308 AATAGTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 5 0.14
43 29 0.78
44 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (42 bp):
ATATTATATTAATATTAATTAATATTAATATTAATTATATTA
Found at i:2229377 original size:6 final size:6
Alignment explanation
Indices: 2229366--2229435 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
2229356 AAATATAAAG
* *
2229366 ATTAAT ATTAAT ATTAAT A-T-A- ATTAAT ATTAATT ATAAAT ATT-TT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAA-T ATTAAT ATTAAT
* *
2229411 ATTAAT ATAAAT AGTTTAT ATTAAT
1 ATTAAT ATTAAT A-TTAAT ATTAAT
2229436 GTTCTCATCA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 6 0.12
6 32 0.64
7 9 0.18
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (6 bp):
ATTAAT
Found at i:2229392 original size:15 final size:16
Alignment explanation
Indices: 2229372--2229403 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2229362 AAAGATTAAT
2229372 ATTAATATTAA-TATA
1 ATTAATATTAATTATA
2229387 ATTAATATTAATTATA
1 ATTAATATTAATTATA
2229403 A
1 A
2229404 ATATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAATATTAATTATA
Found at i:2229392 original size:21 final size:22
Alignment explanation
Indices: 2229366--2229407 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2229356 AAATATAAAG
*
2229366 ATTAATATTAA-TATTAATATA
1 ATTAATATTAATTATAAATATA
2229387 ATTAATATTAATTATAAATAT
1 ATTAATATTAATTATAAATAT
2229408 TTTATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAATATTAATTATAAATATA
Found at i:2229421 original size:17 final size:19
Alignment explanation
Indices: 2229357--2229435 Score: 74
Period size: 18 Copynumber: 4.2 Consensus size: 19
2229347 AATAATTTAA
* *
2229357 AATATAAAGA-TTAATATT
1 AATATAAATAGTTTATATT
* *
2229375 AATATTAATATAATTAATATT
1 AATA-TAA-ATAGTTTATATT
2229396 AATTATAAATA-TTT-TATT
1 AA-TATAAATAGTTTATATT
2229414 AATATAAATAGTTTATATT
1 AATATAAATAGTTTATATT
2229433 AAT
1 AAT
2229436 GTTCTCATCA
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
17 8 0.15
18 13 0.25
19 12 0.23
20 5 0.09
21 13 0.25
22 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AATATAAATAGTTTATATT
Found at i:2229930 original size:3 final size:3
Alignment explanation
Indices: 2229914--2229966 Score: 61
Period size: 3 Copynumber: 16.3 Consensus size: 3
2229904 GATTTAAAAA
*
2229914 TAT TATT TATT TAT TAT TAC TAT TAT TAT TAT TATT TAT TAT TATT TAT
1 TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TA-T TAT
2229963 TAT T
1 TAT T
2229967 TTTTTATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 32 0.71
4 13 0.29
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2229939 original size:9 final size:8
Alignment explanation
Indices: 2229914--2229965 Score: 58
Period size: 7 Copynumber: 6.8 Consensus size: 8
2229904 GATTTAAAAA
2229914 TATTAT-T
1 TATTATAT
2229921 TATT-TAT
1 TATTATAT
2229928 TATTACTAT
1 TATTA-TAT
2229937 TATTATTAT
1 TATTA-TAT
2229946 TATT-TAT
1 TATTATAT
2229953 TATTAT-T
1 TATTATAT
2229960 TATTAT
1 TATTAT
2229966 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
6 1 0.03
7 23 0.57
8 1 0.03
9 15 0.38
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTATAT
Found at i:2229954 original size:10 final size:10
Alignment explanation
Indices: 2229914--2229996 Score: 79
Period size: 10 Copynumber: 8.8 Consensus size: 10
2229904 GATTTAAAAA
2229914 TATTATTTATT
1 TATTATTTA-T
*
2229925 TATTA-TTAC
1 TATTATTTAT
2229934 TATTA-TTAT
1 TATTATTTAT
2229943 TATTATTTAT
1 TATTATTTAT
2229953 TATTATTTAT
1 TATTATTTAT
2229963 TATT-TTT-T
1 TATTATTTAT
* *
2229971 TATTTTTTTT
1 TATTATTTAT
2229981 TATT-TTT-T
1 TATTATTTAT
*
2229989 TTTTATTT
1 TATTATTT
2229997 TTTTTAGACC
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
8 9 0.14
9 25 0.38
10 26 0.40
11 5 0.08
ACGTcount: A:0.23, C:0.01, G:0.00, T:0.76
Consensus pattern (10 bp):
TATTATTTAT
Found at i:2229975 original size:25 final size:25
Alignment explanation
Indices: 2229919--2229996 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
2229909 AAAAATATTA
*
2229919 TTTATTTATTATTA-CTATTATTATT
1 TTTATTTATTATTATTTATTATT-TT
*
2229944 ATTATTTATTATTATTTATTATTTT
1 TTTATTTATTATTATTTATTATTTT
*
2229969 TTTA-TT-TT-TT-TTTATTTTTTT
1 TTTATTTATTATTATTTATTATTTT
2229990 TTTATTT
1 TTTATTT
2229997 TTTTTAGACC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 14 0.30
22 4 0.09
23 2 0.04
24 2 0.04
25 18 0.38
26 7 0.15
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTATTTATTATTATTTATTATTTT
Found at i:2229996 original size:11 final size:11
Alignment explanation
Indices: 2229958--2230001 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
2229948 TTTATTATTA
*
2229958 TTTATTATTTT
1 TTTATTTTTTT
2229969 TTTA-TTTTTT
1 TTTATTTTTTT
2229979 TTTATTTTTTT
1 TTTATTTTTTT
2229990 TTTATTTTTTT
1 TTTATTTTTTT
2230001 T
1 T
2230002 AGACCCCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:2229996 original size:21 final size:21
Alignment explanation
Indices: 2229936--2230001 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 21
2229926 ATTATTACTA
* *
2229936 TTATTATTATTATTTATTATTAT
1 TTATTATT-TT-TTTATTTTTTT
2229959 TTATTATTTTTTTATTTTTTT
1 TTATTATTTTTTTATTTTTTT
*
2229980 TTATTTTTTTTTTATTTTTTT
1 TTATTATTTTTTTATTTTTTT
2230001 T
1 T
2230002 AGACCCCATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 30 0.75
22 2 0.05
23 8 0.20
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (21 bp):
TTATTATTTTTTTATTTTTTT
Found at i:2231386 original size:18 final size:17
Alignment explanation
Indices: 2231357--2231397 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
2231347 TTATTTAATA
*
2231357 TATTTTTTATTTTGTTT
1 TATTTTTTATTTTATTT
2231374 TATTTTCTTATTTTATTT
1 TATTTT-TTATTTTATTT
2231392 TATTTT
1 TATTTT
2231398 AATTCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (17 bp):
TATTTTTTATTTTATTT
Found at i:2231429 original size:11 final size:11
Alignment explanation
Indices: 2231413--2231438 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2231403 TTTTTCTATG
2231413 ATTTATTTATT
1 ATTTATTTATT
2231424 ATTTATTTATT
1 ATTTATTTATT
2231435 ATTT
1 ATTT
2231439 CTTATCACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:2234971 original size:23 final size:23
Alignment explanation
Indices: 2234945--2234989 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2234935 CACCACAGCT
*
2234945 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
2234968 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2234990 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:2235227 original size:149 final size:149
Alignment explanation
Indices: 2234968--2235271 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
2234958 CGAAGTGCCC
* *
2234968 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
2235033 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
2235098 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
2235117 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
2235182 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
2235247 CATATGTCTCGAAGAACCG
131 CATATGTCCCGAAGAACCG
2235266 CGTAGA
1 CGTAGA
2235272 CCCTCGACTC
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:2236288 original size:18 final size:18
Alignment explanation
Indices: 2236267--2236301 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2236257 TCCCATCTAG
2236267 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2236285 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2236302 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:2236908 original size:21 final size:21
Alignment explanation
Indices: 2236884--2236928 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2236874 TCTTGTTCGT
* *
2236884 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2236905 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2236926 TTG
1 TTG
2236929 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2238791 original size:32 final size:32
Alignment explanation
Indices: 2238747--2238822 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
2238737 AGGAACAACG
* * *
2238747 GGGGCACCTTTGAAGATTTAACATCAAATATT
1 GGGGCATCTTTGAAGATTCAACATCAAATATC
* * *
2238779 GGGGCATTTTTGAAGATTCAATATCGAATATC
1 GGGGCATCTTTGAAGATTCAACATCAAATATC
2238811 GGGGCATCTTTG
1 GGGGCATCTTTG
2238823 GGGATTCGAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (32 bp):
GGGGCATCTTTGAAGATTCAACATCAAATATC
Found at i:2239595 original size:110 final size:105
Alignment explanation
Indices: 2239456--2239736 Score: 348
Period size: 110 Copynumber: 2.6 Consensus size: 105
2239446 ACGAAGGGGC
2239456 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA-ACAACACAAGCT
* * *
2239521 CAGCTTCACAATGAAGGGGCGACTGATTGTCAACAAACAACT
65 CAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAA-T
** * * **
2239563 TT-TTAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTAAACTCAAAACAACACA
1 TTCCCAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC-AAACAACACA
* * *
2239627 AGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAAT
61 AGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
* * *
2239672 TTCCCAGTTTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGAAACAATACAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC-AAACAACACAAGCT
2239737 TGGATTTCAA
Statistics
Matches: 146, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
106 51 0.35
107 2 0.01
108 2 0.01
109 3 0.02
110 86 0.59
111 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (105 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAACAACACAAGCTC
AACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAAT
Found at i:2239980 original size:124 final size:124
Alignment explanation
Indices: 2239733--2240108 Score: 576
Period size: 124 Copynumber: 3.0 Consensus size: 124
2239723 AAACAATACA
*
2239733 AGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAAGGCTCAACTTCACAACGAAGGAG
1 AGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTT-AAGGCTCAACTTCACAACGAAGGGG
* * * *
2239798 CCATCCGCGGGTTTCAACTTCATGACGAAGGGAATCGTGCTCATCACTAACATTCATCTTC
65 CCATCCAC-GGTTTCAACTTCACGAAGAAGGGAATCGTGCTCACCACTAACATTCATCTTC
*
2239859 AGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGATCAACTTCACAACGAAGGGGC
1 AGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAAGGGGC
* * *
2239924 CATCCACGGTTTCAACTTCACGATGAAGGAAATCGTGCTCACCATTAACATTCATCTTC
66 CATCCACGGTTTCAACTTCACGAAGAAGGGAATCGTGCTCACCACTAACATTCATCTTC
* *
2239983 AGCTTGGATTTCAACTTCATGACGAAGGATATTCAAG-TAGAGGCTCAACTTCACAACGAATGGG
1 AGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTA-AGGCTCAACTTCACAACGAAGGGG
* * *
2240047 TCATCCACGGTTTCAACTTCACGAAGAAGGGAATCGTACCCACCAGC-AACATTCATCTTC
65 CCATCCACGGTTTCAACTTCACGAAGAAGGGAATCGTGCTCACCA-CTAACATTCATCTTC
2240107 AG
1 AG
2240109 GAACAAGCAG
Statistics
Matches: 231, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
123 2 0.01
124 160 0.69
125 30 0.13
126 39 0.17
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (124 bp):
AGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAAGGGGC
CATCCACGGTTTCAACTTCACGAAGAAGGGAATCGTGCTCACCACTAACATTCATCTTC
Found at i:2240415 original size:84 final size:84
Alignment explanation
Indices: 2240273--2240530 Score: 365
Period size: 84 Copynumber: 3.1 Consensus size: 84
2240263 GAAACACCAA
* * * * *
2240273 ACCTTCGAGTTCGATTACACTTAGCTCCAAGACACGTCATTTGCAATATAGCTTAAGGCACGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAGCTTAAGGCACGAAG
2240338 GGCTATTTGCCAACCAAAG
66 GGCTATTTGCCAACCAAAG
* * *
2240357 ACCTTCGAGTTCAACTACGCTCATCTCCAAGGCACATCATTTGCAATATAGCTCAAGGCACGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAGCTTAAGGCACGAAG
* *
2240422 GGCTATTTTCCAACCAAAT
66 GGCTATTTGCCAACCAAAG
* * *
2240441 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATTGCTTAAGTCGA-GAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAGCTTAAGGC-ACGAA
* *
2240505 GGGTTATCTGCCAACCAAAG
65 GGGCTATTTGCCAACCAAAG
2240525 ACCTTC
1 ACCTTC
2240531 TATTTCATTC
Statistics
Matches: 153, Mismatches: 20, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
84 152 0.99
85 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (84 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAGCTTAAGGCACGAAG
GGCTATTTGCCAACCAAAG
Found at i:2240775 original size:3 final size:3
Alignment explanation
Indices: 2240769--2240815 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
2240759 ATTTATTTAT
* * *
2240769 TTA TTA TTA CTA TTA TT- TTA TTT TTA TTA TTTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
2240814 TT
1 TT
2240816 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2240786 original size:16 final size:15
Alignment explanation
Indices: 2240756--2240822 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 15
2240746 GTTTAAAAAA
2240756 ATTATT-TATTTATTT
1 ATTATTATA-TTATTT
2240771 ATTATTACTATTATTTT
1 ATTATTA-TATTA-TTT
2240788 ATT-TT-TATTATTT
1 ATTATTATATTATTT
*
2240801 ATTATTATTAATATTT
1 ATTATTA-TATTATTT
*
2240817 TTTATT
1 ATTATT
2240823 TTTGTAGGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
13 6 0.14
14 7 0.16
15 6 0.14
16 17 0.39
17 8 0.18
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTATTATATTATTT
Found at i:2240800 original size:30 final size:31
Alignment explanation
Indices: 2240760--2240817 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
2240750 AAAAAAATTA
*
2240760 TTTATTTATTTATTATTACTATTATTTTATT
1 TTTATTTATTTATTATTACTAATATTTTATT
*
2240791 TTTA-TTATTTATTATTATTAATATTTT
1 TTTATTTATTTATTATTACTAATATTTT
2240818 TTATTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (31 bp):
TTTATTTATTTATTATTACTAATATTTTATT
Found at i:2242200 original size:5 final size:5
Alignment explanation
Indices: 2242186--2242234 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
2242176 TTAATATATT
* *
2242186 TTTTA TTTTTG TTTTA TTTTA TTTTA -TTT- TCTTA TTTTA TTTTA TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
2242235 ATTTGTTCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
4 5 0.14
5 28 0.76
6 4 0.11
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:2242220 original size:18 final size:17
Alignment explanation
Indices: 2242186--2242233 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
2242176 TTAATATATT
*
2242186 TTTTATTTT-TGTTTTA
1 TTTTATTTTATTTTTTA
2242202 TTTTATTTTATTTTCTTA
1 TTTTATTTTATTTT-TTA
2242220 TTTTATTTTATTTT
1 TTTTATTTTATTTT
2242234 AATTTGTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 9 0.31
17 3 0.10
18 17 0.59
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.81
Consensus pattern (17 bp):
TTTTATTTTATTTTTTA
Found at i:2242222 original size:13 final size:13
Alignment explanation
Indices: 2242204--2242228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2242194 TTGTTTTATT
2242204 TTATTTTATTTTC
1 TTATTTTATTTTC
2242217 TTATTTTATTTT
1 TTATTTTATTTT
2242229 ATTTTAATTT
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:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTC
Found at i:2242264 original size:11 final size:11
Alignment explanation
Indices: 2242248--2242273 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2242238 TGTTCCTTTG
2242248 ATTTATTTATT
1 ATTTATTTATT
2242259 ATTTATTTATT
1 ATTTATTTATT
2242270 ATTT
1 ATTT
2242274 CTTATATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:2242675 original size:13 final size:14
Alignment explanation
Indices: 2242657--2242706 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
2242647 CAACTAATGC
2242657 AACATG-AATTAAT
1 AACATGCAATTAAT
*
2242670 AACATGCAA-T-AC
1 AACATGCAATTAAT
*
2242682 CACATG-AATTAAT
1 AACATGCAATTAAT
2242695 AACATGCAATTA
1 AACATGCAATTA
2242707 TTATTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 2 0.07
12 7 0.24
13 13 0.45
14 7 0.24
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (14 bp):
AACATGCAATTAAT
Found at i:2243533 original size:23 final size:24
Alignment explanation
Indices: 2243505--2243555 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 24
2243495 TTATTTTTTC
2243505 TTTACATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
2243528 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
2243552 TTTA
1 TTTA
2243556 AATTTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:2243610 original size:23 final size:24
Alignment explanation
Indices: 2243584--2243654 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 24
2243574 TGCCAATATT
2243584 TTTATTAATAAT-ATTTTATATAA
1 TTTATTAATAATAATTTTATATAA
*
2243607 TTTA-TATTTAAATAATTTTAT-TAA
1 TTTATTA-AT-AATAATTTTATATAA
2243631 TTTTATT-A-AATAATTTTATATAA
1 -TTTATTAATAATAATTTTATATAA
2243654 T
1 T
2243655 AGGTCTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
22 14 0.35
23 8 0.20
24 6 0.15
25 11 0.28
26 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTATTAATAATAATTTTATATAA
Found at i:2243889 original size:16 final size:16
Alignment explanation
Indices: 2243846--2243900 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2243836 CGGATCATTT
2243846 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* * * **
2243862 ACATGTCGGGTTCATC
1 ACAGGTCAGGTTAAAA
*
2243878 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
2243894 ACAGGTC
1 ACAGGTC
2243901 GGGTAATACC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:2245007 original size:43 final size:42
Alignment explanation
Indices: 2244960--2245157 Score: 200
Period size: 43 Copynumber: 4.6 Consensus size: 42
2244950 ATACCGTAAT
* *
2244960 AGGTCAAGATCTATAGCAGCGTTGTTGGAAAAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTT-TTGGAACAAACGCCGCAAA
* * *
2245003 AGGTCGATATCTATAGTGGCGTTTTGGAACAAACGCCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTGGAACAAACG-CCGCAAA
*** * * *
2245046 AGGTTGGGATCTATAGCGGCATTTTTTAGATACAAATGCCGCAAA
1 AGGTCAAGATCTATAGCGGC--GTTTTGGA-ACAAACGCCGCAAA
* * *
2245091 AGGTCAAGATCTATAGCGGCGTTTTCGGAATAAACGCTGCCAA
1 AGGTCAAGATCTATAGCGGCGTTTT-GGAACAAACGCCGCAAA
*
2245134 AGGT-TAGATCTATAGCGGCGTTTT
1 AGGTCAAGATCTATAGCGGCGTTTT
2245158 TTGTCATAAA
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
42 30 0.23
43 60 0.47
44 2 0.02
45 30 0.23
46 6 0.05
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (42 bp):
AGGTCAAGATCTATAGCGGCGTTTTGGAACAAACGCCGCAAA
Found at i:2245103 original size:88 final size:87
Alignment explanation
Indices: 2244995--2245159 Score: 233
Period size: 88 Copynumber: 1.9 Consensus size: 87
2244985 TGGAAAAAAC
* * * *
2244995 GCCGCAAAAGGTCGATATCTATAGTGGCGTTTT-GGAACAAACGCCCGCAAAAGGTTGGGATCTA
1 GCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTCGGAACAAACG-CCGCAAAAGGTT-AGATCTA
2245059 TAGCGGCATTTTTTAGATACAAAT
64 TAGCGGCATTTTTTAGATACAAAT
* * *
2245083 GCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTCGGAATAAACGCTGCCAAAGGTTAGATCTATA
1 GCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTCGGAACAAACGCCGCAAAAGGTTAGATCTATA
*
2245148 GCGGCGTTTTTT
66 GCGGCATTTTTT
2245160 GTCATAAACG
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
87 19 0.28
88 40 0.59
89 9 0.13
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (87 bp):
GCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTCGGAACAAACGCCGCAAAAGGTTAGATCTATA
GCGGCATTTTTTAGATACAAAT
Found at i:2245380 original size:21 final size:21
Alignment explanation
Indices: 2245356--2245399 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2245346 CATGACATCT
* *
2245356 ATAACAACAAACTTTAATTCC
1 ATAACAACAAACTTAAAATCC
*
2245377 ATAACAACCAACTTAAAATCC
1 ATAACAACAAACTTAAAATCC
2245398 AT
1 AT
2245400 CATAGTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
ATAACAACAAACTTAAAATCC
Found at i:2248015 original size:18 final size:18
Alignment explanation
Indices: 2247992--2248045 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
2247982 ACTCACTATA
2247992 AAATATATTAGTATTGAG
1 AAATATATTAGTATTGAG
** *
2248010 AAATATAAAAG-ATTAAG
1 AAATATATTAGTATTGAG
*
2248027 AAATTTCATTAGTATTGAG
1 AAATAT-ATTAGTATTGAG
2248046 TTCGCATACA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
17 10 0.37
18 12 0.44
19 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (18 bp):
AAATATATTAGTATTGAG
Found at i:2248819 original size:23 final size:23
Alignment explanation
Indices: 2248793--2248839 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2248783 GAATGTCTTT
2248793 TTAACAACAAAAGGGTCTATTTG
1 TTAACAACAAAAGGGTCTATTTG
**
2248816 TTAACAATGAAAGGGTCTATTTG
1 TTAACAACAAAAGGGTCTATTTG
2248839 T
1 T
2248840 AGGATGTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (23 bp):
TTAACAACAAAAGGGTCTATTTG
Found at i:2251569 original size:41 final size:40
Alignment explanation
Indices: 2251425--2251569 Score: 114
Period size: 41 Copynumber: 3.5 Consensus size: 40
2251415 AGATTAACCC
*
2251425 TATTGCGGCGTTTGTATAAAAATACCGCTAAAGTACTACTA
1 TATTGCGGCGTTTGT-TAAAAACACCGCTAAAGTACTACTA
* * * * **
2251466 TATTGCGGTGTTTATTGAAAAACACCACCAAA-TA-TGAACCC
1 TATTGCGGCGTTTGTT-AAAAACACCGCTAAAGTACT--ACTA
** * *
2251507 TATTATGGCATTTGAATAAAAACACCGCTAAAGTACTACTA
1 TATTGCGGCGTTTG-TTAAAAACACCGCTAAAGTACTACTA
*
2251548 TATTGCGACGTTTGTTGAAAAA
1 TATTGCGGCGTTTGTT-AAAAA
2251570 ATGCCACCAT
Statistics
Matches: 75, Mismatches: 22, Indels: 14
0.68 0.20 0.13
Matches are distributed among these distances:
39 1 0.01
40 4 0.05
41 66 0.88
42 3 0.04
43 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (40 bp):
TATTGCGGCGTTTGTTAAAAACACCGCTAAAGTACTACTA
Found at i:2251644 original size:83 final size:83
Alignment explanation
Indices: 2251341--2251789 Score: 433
Period size: 83 Copynumber: 5.4 Consensus size: 83
2251331 ATATAACAAA
* * * * * ****
2251341 CTATTGCGACATTTGTA-AAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTTTTTTTTTAA
1 CTATTACGGCATTTGTATAAAAACACCGCTAAAGTACTACTCTATTGCGGCG-TTTGTTGAAAAA
* *
2251405 ATGCCAATATAGATTAACC
65 ATGCCACTATAGATGAACC
* * * * * *
2251424 CTATTGCGGCGTTTGTATAAAAATACCGCTAAAGTACTACTATATTGCGGTGTTTATTGAAAAAC
1 CTATTACGGCATTTGTATAAAAACACCGCTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAA-
* * *
2251489 A--CCACCAAATATGAACC
65 ATGCCACTATAGATGAACC
* * * *
2251506 CTATTATGGCATTTGAATAAAAACACCGCTAAAGTACTACTATATTGCGACGTTTGTTGAAAAAA
1 CTATTACGGCATTTGTATAAAAACACCGCTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAA
*
2251571 TGCCACCATAGATGAACC
66 TGCCACTATAGATGAACC
** * ** * *
2251589 CTATTACAACATTTATATAAAAACACAACTAAAGTATTACTCTGTTGCGGCGTTTGTTGAAAAAA
1 CTATTACGGCATTTGTATAAAAACACCGCTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAA
*
2251654 AGCCACTATAGATGAACC
66 TGCCACTATAGATGAACC
* **
2251672 CTATTACGGCGTTTGTATAAAAA-ATGCCGCTATCGTACTACTCTATTGCGGCGTTTGTTG-AAA
1 CTATTACGGCATTTGTATAAAAACA--CCGCTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAA
* *
2251735 AATGTCACTATATATGAACC
64 AATGCCACTATAGATGAACC
* * * *
2251755 CTATTGCGG-AGTTTGTACAAAACCGCCGCTAAAGT
1 CTATTACGGCA-TTTGTATAAAAACACCGCTAAAGT
2251790 TACCATTTTG
Statistics
Matches: 298, Mismatches: 60, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
81 1 0.00
82 76 0.26
83 163 0.55
84 58 0.19
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (83 bp):
CTATTACGGCATTTGTATAAAAACACCGCTAAAGTACTACTCTATTGCGGCGTTTGTTGAAAAAA
TGCCACTATAGATGAACC
Found at i:2251682 original size:42 final size:42
Alignment explanation
Indices: 2251548--2251770 Score: 156
Period size: 42 Copynumber: 5.4 Consensus size: 42
2251538 AGTACTACTA
* *
2251548 TATTGCGACGTTTGTTGAAAAAATGCCACCATAGATGAACCC
1 TATTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACCC
* ** * * * * * *
2251590 TATTACAACATTTATAT-AAAAACA--CAACTAAAGTAT-TACTC
1 TATTGCGGCGTTTGT-TGAAAAA-ATGCCACTATAG-ATGAACCC
* *
2251631 TGTTGCGGCGTTTGTTGAAAAAAAGCCACTATAGATGAACCC
1 TATTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACCC
* * * *
2251673 TATTACGGCGTTTGTAT-AAAAAATGCCGCTATCG-T-ACTACTC
1 TATTGCGGCGTTTGT-TGAAAAAATGCCACTATAGATGA--ACCC
* *
2251715 TATTGCGGCGTTTGTTG-AAAAATGTCACTATATATGAACCC
1 TATTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACCC
*
2251756 TATTGCGGAGTTTGT
1 TATTGCGGCGTTTGT
2251771 ACAAAACCGC
Statistics
Matches: 136, Mismatches: 32, Indels: 27
0.70 0.16 0.14
Matches are distributed among these distances:
40 3 0.02
41 56 0.41
42 73 0.54
43 4 0.03
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (42 bp):
TATTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACCC
Found at i:2252471 original size:32 final size:30
Alignment explanation
Indices: 2252406--2252472 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 30
2252396 GCTCGACTCA
* * *
2252406 AACTCGAAATAAAAAATGAAACTCGATTGG
1 AACTCAAAATAAAAAATGAAACTCAATTCG
*
2252436 AACTCAAAATAAAAAATATGAAGCTCAATTCG
1 AACTCAAAAT-AAAAA-ATGAAACTCAATTCG
2252468 AACTC
1 AACTC
2252473 GAACAAACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 9 0.29
31 5 0.16
32 17 0.55
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.21
Consensus pattern (30 bp):
AACTCAAAATAAAAAATGAAACTCAATTCG
Found at i:2252710 original size:17 final size:17
Alignment explanation
Indices: 2252688--2252722 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2252678 TCATTAAGAA
2252688 TTCGAG-TCGAGTTCGAG
1 TTCGAGCTCGAG-TCGAG
2252705 TTCGAGCTCGAGTCGAG
1 TTCGAGCTCGAGTCGAG
2252722 T
1 T
2252723 CCATTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (17 bp):
TTCGAGCTCGAGTCGAG
Found at i:2256935 original size:18 final size:18
Alignment explanation
Indices: 2256912--2256946 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2256902 TTTAATCATT
2256912 AAAATTGATTTGGATGTA
1 AAAATTGATTTGGATGTA
2256930 AAAATTGATTTGGATGT
1 AAAATTGATTTGGATGT
2256947 GATTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (18 bp):
AAAATTGATTTGGATGTA
Found at i:2258349 original size:39 final size:40
Alignment explanation
Indices: 2258292--2258374 Score: 150
Period size: 39 Copynumber: 2.1 Consensus size: 40
2258282 TCCAATGAGT
2258292 GTTCCGAATTTCATATAGTCAAAAGTTGAAGAAATGAGCAA
1 GTTCCGAATTTCA-ATAGTCAAAAGTTGAAGAAATGAGCAA
2258333 GTTCCGAATTTC-ATAGTCAAAAGTTGAAGAAATGAGCAA
1 GTTCCGAATTTCAATAGTCAAAAGTTGAAGAAATGAGCAA
2258372 GTT
1 GTT
2258375 AGCACTGAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 30 0.71
41 12 0.29
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (40 bp):
GTTCCGAATTTCAATAGTCAAAAGTTGAAGAAATGAGCAA
Found at i:2258834 original size:35 final size:35
Alignment explanation
Indices: 2258729--2258840 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
2258719 TCTAAACTTT
* * *
2258729 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * * *
2258764 TAATTGAATTATTTTGGAATTTAGGATTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * *
2258799 AAATTGAATTACTTTGGAAATTGGGGTTTATAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
2258834 AAATTGA
1 AAATTGA
2258841 GGACTATTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
Found at i:2268459 original size:20 final size:20
Alignment explanation
Indices: 2268436--2268533 Score: 106
Period size: 20 Copynumber: 4.9 Consensus size: 20
2268426 CAAAATCGCA
*
2268436 GAATAGGTAAATTGCAATGC
1 GAATAGGTAAATCGCAATGC
2268456 GAATAGGTAAATCGCAATGC
1 GAATAGGTAAATCGCAATGC
* * *
2268476 GAATATGTAAATCGCAACGA
1 GAATAGGTAAATCGCAATGC
* * * *
2268496 TAATATGTAAATCACAACGC
1 GAATAGGTAAATCGCAATGC
**
2268516 GAATTTGTAAATCGCAAT
1 GAATAGGTAAATCGCAAT
2268534 ACAGAAGTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.24
Consensus pattern (20 bp):
GAATAGGTAAATCGCAATGC
Found at i:2268630 original size:20 final size:20
Alignment explanation
Indices: 2268607--2268673 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
2268597 ATTTTCTAAA
* *
2268607 TCGCAACTCGATTTTTGAA-T
1 TCGCAACACGAATTTT-AATT
2268627 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTAATT
* *
2268647 TCGCAACA--ACTTTTATTT
1 TCGCAACACGAATTTTAATT
2268665 TCGCAACAC
1 TCGCAACAC
2268674 AAATGTTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 16 0.39
19 2 0.05
20 23 0.56
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (20 bp):
TCGCAACACGAATTTTAATT
Found at i:2268854 original size:16 final size:16
Alignment explanation
Indices: 2268833--2268871 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2268823 TCCCCATCTC
* *
2268833 TAATTTTGTTTTTACA
1 TAATTTTATTTCTACA
*
2268849 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
2268865 TAATTTT
1 TAATTTT
2268872 TTAATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Done.