Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005637.1 Hibiscus syriacus cultivar Beakdansim tig00013142_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: 575832
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:8296 original size:84 final size:85
Alignment explanation
Indices: 8177--8348 Score: 256
Period size: 84 Copynumber: 2.0 Consensus size: 85
8167 ACGCAAATGC
* * *
8177 GTCATAAATTTATGACGCGTATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATG
1 GTCATAAATTTATGACACGCATTTATGACTTACATTACGCGTCATTGAAGCCCCCGTCATAAATG
* * *
8242 AAGATGTCACACATTTGTGT
66 AAAATGACACACATTCGTGT
* * *
8262 GTCATAAATTTATGGCACGCA-TTATGACTTACATTACGTGTCATTGAAGCCCCTGTCATAAATG
1 GTCATAAATTTATGACACGCATTTATGACTTACATTACGCGTCATTGAAGCCCCCGTCATAAATG
8326 AAAATGACACACATTCGTGT
66 AAAATGACACACATTCGTGT
8346 GTC
1 GTC
8349 GTGATTGTAT
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 60 0.77
85 18 0.23
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (85 bp):
GTCATAAATTTATGACACGCATTTATGACTTACATTACGCGTCATTGAAGCCCCCGTCATAAATG
AAAATGACACACATTCGTGT
Found at i:18252 original size:18 final size:19
Alignment explanation
Indices: 18213--18255 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
18203 TACTAGACTT
*
18213 ATTAAATTATTAATACATA
1 ATTAAATTATTAATACAAA
*
18232 ATTAAATT-TTAATCCAAA
1 ATTAAATTATTAATACAAA
18250 ATTAAA
1 ATTAAA
18256 AAAATGCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAATTATTAATACAAA
Found at i:18775 original size:2 final size:2
Alignment explanation
Indices: 18768--18799 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18758 TTAACTCTTA
18768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18800 TTGACTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18868 original size:23 final size:21
Alignment explanation
Indices: 18831--18874 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
18821 AATTTTAGTC
*
18831 ATTAAATTTTTAAAAAAGTTAA
1 ATTAAA-TTTTAAAAAAATTAA
18853 ATTATAATTTTAAAAAAATTAA
1 ATTA-AATTTTAAAAAAATTAA
18875 TAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTAAATTTTAAAAAAATTAA
Found at i:22732 original size:22 final size:22
Alignment explanation
Indices: 22682--22724 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
22672 AGATTAAAAT
22682 TAGGAAATATAAAGATTTTTCC
1 TAGGAAATATAAAGATTTTTCC
22704 TAGGAAATATAAAGATTTTTC
1 TAGGAAATATAAAGATTTTTC
22725 TTGGGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (22 bp):
TAGGAAATATAAAGATTTTTCC
Found at i:23238 original size:18 final size:18
Alignment explanation
Indices: 23215--23257 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
23205 AATTACATTC
23215 TTAATTATT-TATATTTAT
1 TTAATT-TTATATATTTAT
*
23233 TTAATTTTATTTATTTAT
1 TTAATTTTATATATTTAT
*
23251 TTCATTT
1 TTAATTT
23258 AATTAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTAATTTTATATATTTAT
Found at i:23245 original size:14 final size:14
Alignment explanation
Indices: 23221--23264 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
23211 ATTCTTAATT
23221 ATTTATATTTATTTA
1 ATTT-TATTTATTTA
23236 ATTTTATTTATTT-
1 ATTTTATTTATTTA
* *
23249 ATTTCATTTAATTA
1 ATTTTATTTATTTA
23263 AT
1 AT
23265 GTATGTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 11 0.42
15 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTTATTTATTTA
Found at i:24528 original size:19 final size:19
Alignment explanation
Indices: 24504--24543 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
24494 ATCATTTTTG
* *
24504 TTTTCTAATTTTTTTGGCT
1 TTTTCTAATTATTTTGCCT
*
24523 TTTTCTCATTATTTTGCCT
1 TTTTCTAATTATTTTGCCT
24542 TT
1 TT
24544 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.15, G:0.07, T:0.68
Consensus pattern (19 bp):
TTTTCTAATTATTTTGCCT
Found at i:24983 original size:16 final size:17
Alignment explanation
Indices: 24948--24984 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
24938 TAAAAGAATT
24948 ATGAAAAGATAAATAAA
1 ATGAAAAGATAAATAAA
24965 ATGAAAAGATAAA-AAA
1 ATGAAAAGATAAATAAA
24981 ATGA
1 ATGA
24985 TGAAAGAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (17 bp):
ATGAAAAGATAAATAAA
Found at i:32300 original size:51 final size:51
Alignment explanation
Indices: 32227--32339 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
32217 GTAACTACTG
* * ** *
32227 AGTAAAATAATAATAAACTAAAGATAATGTTTTGACTCTGTCCTACTTCCT
1 AGTAAAATAATAATAAACTAAAGATAAGGTTTTAACTCAATCCTAATTCCT
* * *
32278 AGTAAAATAATAGTAAATTAAAGATAAGGTTTTAACTCAATCTTAATTCCT
1 AGTAAAATAATAATAAACTAAAGATAAGGTTTTAACTCAATCCTAATTCCT
*
32329 AATAAAATAAT
1 AGTAAAATAAT
32340 GAATCTAAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (51 bp):
AGTAAAATAATAATAAACTAAAGATAAGGTTTTAACTCAATCCTAATTCCT
Found at i:46161 original size:46 final size:42
Alignment explanation
Indices: 46088--46229 Score: 148
Period size: 46 Copynumber: 3.3 Consensus size: 42
46078 TATAAAATCT
* *
46088 CTTACCATTTATCCCATAAGCTAGTAAGCTTATTTATCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTATC--AATA
*
46132 CTTACCATTTAAATTCCATAAGCTCGTAAGTTTATTTTATCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTA-TTTAT-CA-ATA
* *
46179 CTTGCCA-TTATT-AATAAGCTCGTAAGCTTATTT-TC-ATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTATCAATA
46217 CTTACCATTTATT
1 CTTACCATTTATT
46230 AACCAATACC
Statistics
Matches: 85, Mismatches: 7, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
38 9 0.11
39 5 0.06
40 1 0.01
41 1 0.01
42 3 0.04
43 16 0.19
44 13 0.15
46 22 0.26
47 14 0.16
48 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.42
Consensus pattern (42 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTATCAATA
Found at i:48691 original size:25 final size:25
Alignment explanation
Indices: 48654--48704 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
48644 GGACTAAAAG
48654 TATAATTTCCAAAAGTTAGGTGTTT
1 TATAATTTCCAAAAGTTAGGTGTTT
*
48679 TATAATTTTCAAAAGTTAGGTGTTT
1 TATAATTTCCAAAAGTTAGGTGTTT
48704 T
1 T
48705 GATCTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (25 bp):
TATAATTTCCAAAAGTTAGGTGTTT
Found at i:50250 original size:20 final size:20
Alignment explanation
Indices: 50169--50246 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
50159 CCGTTAAGCA
*
50169 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
*
50189 GGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCTGTACCCCCT
* *
50209 GGGGGGAATCTATACCCCTT
1 GGGGGGAATCTGTACCCCCT
50229 GGGGGGAATCTGTACCCC
1 GGGGGGAATCTGTACCCC
50247 TTGGACAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:51723 original size:19 final size:20
Alignment explanation
Indices: 51680--51727 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
51670 TCTAAATCCT
*
51680 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
51700 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
51719 TTTTCAAAA
1 TTTTCAAAA
51728 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:54929 original size:22 final size:22
Alignment explanation
Indices: 54901--54946 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
54891 ACTGGTTATT
54901 ATATATATGACATTTATCATGA
1 ATATATATGACATTTATCATGA
* **
54923 ATATATATTATGTTTATCATGA
1 ATATATATGACATTTATCATGA
54945 AT
1 AT
54947 GTTATTTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (22 bp):
ATATATATGACATTTATCATGA
Found at i:56578 original size:48 final size:48
Alignment explanation
Indices: 56522--56617 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
56512 AGTTCTTTAT
56522 AACTTAGTTTCTTCCTTGTTGTTTAAGATACTATCCATAGCCCTTCCA
1 AACTTAGTTTCTTCCTTGTTGTTTAAGATACTATCCATAGCCCTTCCA
56570 AACTTAGTTTCTTCCTTGTTGTTTAAGATACTATCCATAGCCCTTCCA
1 AACTTAGTTTCTTCCTTGTTGTTTAAGATACTATCCATAGCCCTTCCA
56618 TTGTTTCTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (48 bp):
AACTTAGTTTCTTCCTTGTTGTTTAAGATACTATCCATAGCCCTTCCA
Found at i:60121 original size:20 final size:20
Alignment explanation
Indices: 60083--60119 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60073 TGTCCAACAA
*
60083 CATGAATCTTCATTCAAACT
1 CATGAATCTTCATCCAAACT
60103 CATGAATCTTCA-CCAAA
1 CATGAATCTTCATCCAAA
60120 ACATACAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (20 bp):
CATGAATCTTCATCCAAACT
Found at i:65726 original size:17 final size:18
Alignment explanation
Indices: 65697--65730 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
65687 ACAAGAAAAT
65697 TAAAACAAACAAGGGATC
1 TAAAACAAACAAGGGATC
65715 TAAAAC-AACAAGGGAT
1 TAAAACAAACAAGGGAT
65731 AAAAAACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.15, G:0.18, T:0.12
Consensus pattern (18 bp):
TAAAACAAACAAGGGATC
Found at i:65736 original size:17 final size:18
Alignment explanation
Indices: 65698--65737 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
65688 CAAGAAAATT
**
65698 AAAACAAACAAGGGATCT
1 AAAACAAACAAGGGATAA
65716 AAAAC-AACAAGGGATAA
1 AAAACAAACAAGGGATAA
65733 AAAAC
1 AAAAC
65738 CAAATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.07
Consensus pattern (18 bp):
AAAACAAACAAGGGATAA
Found at i:68170 original size:2 final size:2
Alignment explanation
Indices: 68165--68201 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
68155 TTTTGTTTGC
68165 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68202 TAATAACTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:68612 original size:55 final size:55
Alignment explanation
Indices: 68548--69222 Score: 804
Period size: 55 Copynumber: 12.3 Consensus size: 55
68538 GGGAGTTAGA
* * *
68548 ACTCCAACAATCTTCTACAATCGTGTCTGCTCCCTATTCCTTCAGAAAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* * * * * * *
68603 TCTCGAACAAGT-TTCTACAAACGAGT-TCGCTCCCTTTTTCTTTCAGGGAGTAT-AG
1 ACTCGAACAA-TCTTCAACAATCGTGTCT-GCTCCC-TATTCCTTCAGAGAGTATAAG
** * ** *
68658 AACTAAAACAATATTCTGCAATCGTGTCTGCTCCCTATTCCTTGAGAGAGTATAAG
1 -ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* *
68714 ACTCGAACAATCTTCAACAATCATGTATGCTCCCTATTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* *
68769 ACTCGAACAATCTTCAACAACCGTGTTTGCTCCCTATTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* * *
68824 ACTCGAACAATCTTCAACAATCGTGTATGCTCCCAATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* * * * *
68879 ACTTGAACAATCTTCAACAATCGTGTCTACTCTCTATTCCTTTAGAGAATATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* * * * **
68934 ACTCGGAC-ATCTTCAATAATCATGTCTGCTCCCTATTTCTTTGGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* *
68988 ATTCGAACAATCTTCAACAATCGTGTCTGCTTCCTATTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* * * * *
69043 ACTCAAACAATCTTCAACAATAGTTTCTACTCCCTATTCCTTCAGAGAGTAAAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
** *
69098 ACTTTAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* * * * * * *
69153 ACTCGAACAATCTTCAATAATCGGGTTTGCTCCCTCTTTCTTTAGGGAGTAT-AG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
69207 AACTCGAACAA-CTTCA
1 -ACTCGAACAATCTTCA
69223 GCAAACGGGT
Statistics
Matches: 531, Mismatches: 80, Indels: 19
0.84 0.13 0.03
Matches are distributed among these distances:
54 53 0.10
55 436 0.82
56 41 0.08
57 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
Found at i:68668 original size:56 final size:56
Alignment explanation
Indices: 68449--68674 Score: 185
Period size: 56 Copynumber: 4.1 Consensus size: 56
68439 GAAAAGAGTC
* * * * * *
68449 TTCTAAAAACGGGTTCGCTCCCTATCTCTTTCAAGGCGTATAGAACTCAAAA-AATA
1 TTCTACAAACGAGTTCGCTCCCTTTTTCTTTCAGGGAGTATAGAACT-AAAACAATA
* * * ** *
68505 TTCTGCAAATGAGTTCGCTCCCTCTTTCTTTCAGGGAGT-TAGAACTCCAACAATC
1 TTCTACAAACGAGTTCGCTCCCTTTTTCTTTCAGGGAGTATAGAACTAAAACAATA
* * * * ** * **
68560 TTCTACAATCGTG-TCTGCTCCC-TATTCCTTCAGAAAGTATA-AGTCTCGAACAAGT-
1 TTCTACAAACGAGTTC-GCTCCCTTTTTCTTTCAGGGAGTATAGA-ACTAAAACAA-TA
68615 TTCTACAAACGAGTTCGCTCCCTTTTTCTTTCAGGGAGTATAGAACTAAAACAATA
1 TTCTACAAACGAGTTCGCTCCCTTTTTCTTTCAGGGAGTATAGAACTAAAACAATA
68671 TTCT
1 TTCT
68675 GCAATCGTGT
Statistics
Matches: 130, Mismatches: 31, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
54 16 0.12
55 53 0.41
56 60 0.46
57 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (56 bp):
TTCTACAAACGAGTTCGCTCCCTTTTTCTTTCAGGGAGTATAGAACTAAAACAATA
Found at i:68747 original size:166 final size:166
Alignment explanation
Indices: 68447--69222 Score: 676
Period size: 165 Copynumber: 4.7 Consensus size: 166
68437 TTGAAAAGAG
* * * * *
68447 TCTTCTAA-AAACGGGTTCGCTCCCTATCTCTTTCAAGGCGTAT-AGAACTCAAAA-AATATTCT
1 TCTTC-AACAAACGAGTTCGCTCCCTATTTCTTTCAGGGAGTATAAG-ACT-AAAACAATATTCA
* * * * * * *
68509 GCAAAT-GAGT-TCGCTCCCTCTTTCTTTCAGGGAGT-T-AGAACTCCAACAATCTTCTACAATC
63 AC-AATCGTGTCT-GCTCCCT-ATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATC
* * *
68570 GTGTCTGCTCCCTATTCCTTCAGAAAGTATAAGTCTCGAACAA
124 ATGTCTACTCCCTATTCCTTCAGAAAGTATAAGACTCGAACAA
* * **
68613 GT-TTCTACAAACGAGTTCGCTCCCTTTTTCTTTCAGGGAGTAT-AGAACTAAAACAATATTCTG
1 -TCTTCAACAAACGAGTTCGCTCCCTATTTCTTTCAGGGAGTATAAG-ACTAAAACAATATTCAA
* *
68676 CAATCGTGTCTGCTCCCTATTCCTTGAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTA
64 CAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTC
* *
68741 TGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAA
129 TACTCCCTATTCCTTCAGAAAGTATAAGACTCGAACAA
* * * * * ** *
68779 TCTTCAACAACCGTGTTTGCTCCCTA-TTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
1 TCTTCAACAAACGAGTTCGCTCCCTATTTCTTTCAGGGAGTATAAGACTAAAACAATATTCAACA
* * * * *
68843 ATCGTGTATGCTCCCAATTTCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCTA
66 ATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCTA
* * *
68908 CTCTCTATTCCTTTAGAGAA-TATAAGACTCGGAC-A
131 CTCCCTATTCCTTCAGA-AAGTATAAGACTCGAACAA
* * * ** *
68943 TCTTCAATAATC-A-TGTCTGCTCCCTATTTCTTT--GGAGAGTATAAGATTCGAACAATCTTCA
1 TCTTCAACAAACGAGT-TC-GCTCCCTATTTCTTTCAGG-GAGTATAAGACTAAAACAATATTCA
* * *
69004 ACAATCGTGTCTGCTTCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAAT-AGTT
63 ACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCA-TG
* * **
69068 TCTACTCCCTATTCCTTCAGAGAGTAAAAGACTTTAACAA
127 TCTACTCCCTATTCCTTCAGAAAGTATAAGACTCGAACAA
* * * ** * *
69108 TCTTCAACAATCGTG-TCTGCTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAAT
1 TCTTCAACAAACGAGTTC-GCTCCCTATTTCTTTCAGGGAGTATAAGACTAAAACAATATTCAAC
* * * * * *
69171 AATCGGGTTTGCTCCCTCTTTCTTTAGGGAGTAT-AGAACTCGAACAA-CTTCA
65 AATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCA
69223 GCAAACGGGT
Statistics
Matches: 512, Mismatches: 76, Indels: 45
0.81 0.12 0.07
Matches are distributed among these distances:
162 1 0.00
163 3 0.01
164 136 0.27
165 226 0.44
166 142 0.28
167 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (166 bp):
TCTTCAACAAACGAGTTCGCTCCCTATTTCTTTCAGGGAGTATAAGACTAAAACAATATTCAACA
ATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCTA
CTCCCTATTCCTTCAGAAAGTATAAGACTCGAACAA
Found at i:69026 original size:274 final size:274
Alignment explanation
Indices: 68677--69175 Score: 813
Period size: 274 Copynumber: 1.8 Consensus size: 274
68667 AATATTCTGC
*
68677 AATCGTGTCTGCTCCCTATTCCTTGAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTAT
1 AATCATGTCTGCTCCCTATTCCTTGAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTAT
* * *
68742 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAACCGTGTT-TGCTCCCTAT
66 GCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAACAGT-TTCTACTCCCTAT
*
68806 TCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTATGCTCCCAATTTCTTCAGAG
130 TCCTTCAGAGAGTAAAAGACTCGAACAATCTTCAACAATCGTGTATGCTCCCAATTTCTTCAGAG
*
68871 AGTATAAGACTTGAACAATCTTCAACAATCGTGTCTACTCTCTATTCCTTTAGAGAATATAAGAC
195 AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTACTCTCTATTCCTTTAGAGAATATAAGAC
68936 TCGGACATCTTCAAT
260 TCGGACATCTTCAAT
* * * *
68951 AATCATGTCTGCTCCCTATTTCTTTG-GAGAGTATAAGATTCGAACAATCTTCAACAATCGTGTC
1 AATCATGTCTGCTCCCTA-TTCCTTGAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTA
* *
69015 TGCTTCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATAGTTTCTACTCCCTAT
65 TGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAACAGTTTCTACTCCCTAT
** * *
69080 TCCTTCAGAGAGTAAAAGACTTTAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAG
130 TCCTTCAGAGAGTAAAAGACTCGAACAATCTTCAACAATCGTGTATGCTCCCAATTTCTTCAGAG
*
69145 AGTATAAGACTCGAACAATCTTCAATAATCG
195 AGTATAAGACTCGAACAATCTTCAACAATCG
69176 GGTTTGCTCC
Statistics
Matches: 206, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
273 2 0.01
274 198 0.96
275 6 0.03
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (274 bp):
AATCATGTCTGCTCCCTATTCCTTGAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTAT
GCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAACAGTTTCTACTCCCTATT
CCTTCAGAGAGTAAAAGACTCGAACAATCTTCAACAATCGTGTATGCTCCCAATTTCTTCAGAGA
GTATAAGACTCGAACAATCTTCAACAATCGTGTCTACTCTCTATTCCTTTAGAGAATATAAGACT
CGGACATCTTCAAT
Found at i:69362 original size:107 final size:107
Alignment explanation
Indices: 69176--69376 Score: 271
Period size: 107 Copynumber: 1.9 Consensus size: 107
69166 TCAATAATCG
* *
69176 GGTTTGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAACTTCAGCAAACGGGTTCGTTCCC
1 GGTTTGCTCCCTCTTTCTTTAGGGAGTATAAAACTCGAACAACTTCAGCAAACGGGTTCGCTCCC
69241 TTTTCTTTAGGGAGTA-AGGAACTCAAACATATTCTTGAAACA
66 TTTTCTTTAGGGAGTATA-GAACTCAAACATATTCTTGAAACA
* ***** *
69283 GGTTTGCTCCCTCTTTCTTTAGGGAGTATAAAACTCGAACATCTTCTTTTTACGGGTTTGCTCCA
1 GGTTTGCTCCCTCTTTCTTTAGGGAGTATAAAACTCGAACAACTTCAGCAAACGGGTTCGCTCC-
* *
69348 TTTTTCTTTA-GGAGTATAGAACTCGAACA
65 CTTTTCTTTAGGGAGTATAGAACTCAAACA
69377 ATCTTCTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
107 71 0.88
108 10 0.12
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (107 bp):
GGTTTGCTCCCTCTTTCTTTAGGGAGTATAAAACTCGAACAACTTCAGCAAACGGGTTCGCTCCC
TTTTCTTTAGGGAGTATAGAACTCAAACATATTCTTGAAACA
Found at i:69381 original size:54 final size:55
Alignment explanation
Indices: 69125--69386 Score: 261
Period size: 54 Copynumber: 4.9 Consensus size: 55
69115 CAATCGTGTC
* * * **
69125 TGCTCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTC-AATAATCGGGTT
1 TGCTCCCTCTTTCTTTAGGGAGTATAGA-ACTCGAACAATCTTCTTTTAA-CGGGTT
****
69180 TGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAA-CTTCAGCAAACGGGTT
1 TGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTCTTTTAACGGGTT
* * * * ** *
69234 CGTTCCCT-TTTCTTTAGGGAGTA-AGGAACTCAAAC-ATATTCTTGAAACAGGTT
1 TGCTCCCTCTTTCTTTAGGGAGTATA-GAACTCGAACAATCTTCTTTTAACGGGTT
* *
69287 TGCTCCCTCTTTCTTTAGGGAGTATAAAACTCGAAC-ATCTTCTTTTTACGGGTT
1 TGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTCTTTTAACGGGTT
* *
69341 TGCTCCATTTTTCTTTA-GGAGTATAGAACTCGAACAATCTTCTTTT
1 TGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTCTTTT
69387 GCTTCACTAC
Statistics
Matches: 174, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
52 2 0.01
53 58 0.33
54 77 0.44
55 36 0.21
56 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (55 bp):
TGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACAATCTTCTTTTAACGGGTT
Found at i:69748 original size:36 final size:37
Alignment explanation
Indices: 69682--69840 Score: 214
Period size: 36 Copynumber: 4.4 Consensus size: 37
69672 ACTCTTCTAA
* *
69682 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTCAGT
1 GAAGGCTTAAGATGGACTTGCTTCACTACTCTTCAGT
* *
69719 GAAGGCTTAAGATGG-CTTGCTTCATTACTCTTCGGT
1 GAAGGCTTAAGATGGACTTGCTTCACTACTCTTCAGT
* *
69755 GAAGGCTTAAGATGGAC-TGATTCACTACTCATCAGT
1 GAAGGCTTAAGATGGACTTGCTTCACTACTCTTCAGT
* * * *
69791 GAATGCTTAAGATGGATTTACTTCACTACTCTTCGGT
1 GAAGGCTTAAGATGGACTTGCTTCACTACTCTTCAGT
69828 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
69841 AGAATTGCCC
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
36 63 0.60
37 42 0.40
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (37 bp):
GAAGGCTTAAGATGGACTTGCTTCACTACTCTTCAGT
Found at i:69838 original size:73 final size:73
Alignment explanation
Indices: 69682--69840 Score: 230
Period size: 73 Copynumber: 2.2 Consensus size: 73
69672 ACTCTTCTAA
* * * * * *
69682 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGCTTGCTTCATTAC
1 GAAGGCTTAAGATGGATCTGATTCACTACTCATCAGTGAAGGCTTAAGATGGCTTACTTCACTAC
69747 TCTTCGGT
66 TCTTCGGT
* *
69755 GAAGGCTTAAGATGGA-CTGATTCACTACTCATCAGTGAATGCTTAAGATGGATTTACTTCACTA
1 GAAGGCTTAAGATGGATCTGATTCACTACTCATCAGTGAAGGCTTAAGATGG-CTTACTTCACTA
69819 CTCTTCGGT
65 CTCTTCGGT
69828 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
69841 AGAATTGCCC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 31 0.40
73 46 0.60
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (73 bp):
GAAGGCTTAAGATGGATCTGATTCACTACTCATCAGTGAAGGCTTAAGATGGCTTACTTCACTAC
TCTTCGGT
Found at i:74733 original size:114 final size:114
Alignment explanation
Indices: 74533--74760 Score: 411
Period size: 114 Copynumber: 2.0 Consensus size: 114
74523 ATATTCGACA
* *
74533 TCGAATTGAATAGATGTGCTTTGAATCTTTGAGACTTTGTTCTTCTAATAGGTTCGAGTAGAAAC
1 TCGAATCGAATAGATGTGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTTCGAGTAGAAAC
*
74598 ATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTGCATGTATCATTCC
66 ATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTACATGTATCATTCC
* *
74647 TCGAATCGAATAGATGTTCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTTTGAGTAGAAAC
1 TCGAATCGAATAGATGTGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTTCGAGTAGAAAC
74712 ATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTACATGTATCATTCC
66 ATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTACATGTATCATTCC
74761 CCCACTCTTC
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (114 bp):
TCGAATCGAATAGATGTGCTTTGAATCTTCGAGACTTTGTTCTTCTAATAGGTTCGAGTAGAAAC
ATTAGTCCAAAGAAGCATGTATTATGGACTCTGGTACATGTATCATTCC
Found at i:79892 original size:106 final size:106
Alignment explanation
Indices: 79707--79921 Score: 331
Period size: 106 Copynumber: 2.0 Consensus size: 106
79697 TTGTCCTCCT
* * *
79707 TGGTATGAATGTATTTATCCCTTGAGTCAACATCTTGGCCTTTGTACCTTTAAAGGAATTCTTCA
1 TGGTATGAATGTATCTATCCCTTGAGTCAACATCTTGGACTTTGCACCTTTAAAGGAATTCTTCA
79772 ATCAACTTCAAATCTCTTCATTCATCAGGTGCCCTTCTTCA
66 ATCAACTTCAAATCTCTTCATTCATCAGGTGCCCTTCTTCA
* * * *
79813 TGGTATGACTGTATCTATCCCTTTAGTCAATATCTTGGACTTTGCACCTTTAAAGGAATTCTTTA
1 TGGTATGAATGTATCTATCCCTTGAGTCAACATCTTGGACTTTGCACCTTTAAAGGAATTCTTCA
* * **
79878 ATCAGCTTCAAATCTCTTCATTCATCGGGTGTTCTTCTTCA
66 ATCAACTTCAAATCTCTTCATTCATCAGGTGCCCTTCTTCA
79919 TGG
1 TGG
79922 ATCGTTTGAA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.40
Consensus pattern (106 bp):
TGGTATGAATGTATCTATCCCTTGAGTCAACATCTTGGACTTTGCACCTTTAAAGGAATTCTTCA
ATCAACTTCAAATCTCTTCATTCATCAGGTGCCCTTCTTCA
Found at i:80849 original size:18 final size:18
Alignment explanation
Indices: 80826--80868 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
80816 ATTAAAATGT
80826 AAACAAGAAATTTAAAAC
1 AAACAAGAAATTTAAAAC
**
80844 AAACAAGGGATTTAAAAC
1 AAACAAGAAATTTAAAAC
80862 AAACAAG
1 AAACAAG
80869 GGATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.63, C:0.12, G:0.12, T:0.14
Consensus pattern (18 bp):
AAACAAGAAATTTAAAAC
Found at i:80869 original size:18 final size:18
Alignment explanation
Indices: 80835--80872 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
80825 TAAACAAGAA
80835 ATTTAAAACAAACAAGGG
1 ATTTAAAACAAACAAGGG
80853 ATTTAAAACAAACAAGGG
1 ATTTAAAACAAACAAGGG
80871 AT
1 AT
80873 AAAAAACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.18
Consensus pattern (18 bp):
ATTTAAAACAAACAAGGG
Found at i:80878 original size:18 final size:18
Alignment explanation
Indices: 80839--80879 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
80829 CAAGAAATTT
**
80839 AAAACAAACAAGGGATTT
1 AAAACAAACAAGGGATAA
80857 AAAACAAACAAGGGATAA
1 AAAACAAACAAGGGATAA
80875 AAAAC
1 AAAAC
80880 CAAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.63, C:0.12, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAACAAACAAGGGATAA
Found at i:83360 original size:2 final size:2
Alignment explanation
Indices: 83355--83398 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
83345 TTTTGTTTGC
*
83355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83397 AT
1 AT
83399 TAATAACTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90028 original size:19 final size:19
Alignment explanation
Indices: 90004--90054 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
89994 CAAGCCAGAC
90004 TGCATCGATGCATGGTCTG
1 TGCATCGATGCATGGTCTG
90023 TGCATCGATGCATGGTCTG
1 TGCATCGATGCATGGTCTG
* *
90042 TACATCAATGCAT
1 TGCATCGATGCAT
90055 AAAATGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCATGGTCTG
Found at i:90173 original size:64 final size:65
Alignment explanation
Indices: 90022--90182 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 65
90012 TGCATGGTCT
*
90022 GTGCATCGATGCATGG-TCT-GTACATCAATGCATAAAATGCATTCGATGTTTTCATAAAATCTG
1 GTGCATCGATGCATGGAT-TGGTGCATCAATGCATAAAATGCATTCGATGTTTTCATAAAATCTG
90085 A
65 A
* * *
90086 GTGCATCGATGCATGGA--GAGTGCATCGATGCATAAAATGCATTCGATG--TTCA-ATTATTCA
1 GTGCATCGATGCATGGATTG-GTGCATCAATGCATAAAATGCATTCGATGTTTTCATA-AAATC-
90146 TTG-
63 -TGA
* *
90149 GTGCATTGATGCATGGATTGGTGCATCAGTGCAT
1 GTGCATCGATGCATGGATTGGTGCATCAATGCAT
90183 TCCTTTGAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
61 1 0.01
62 7 0.09
63 16 0.20
64 57 0.70
65 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATGGATTGGTGCATCAATGCATAAAATGCATTCGATGTTTTCATAAAATCTGA
Found at i:94206 original size:18 final size:18
Alignment explanation
Indices: 94183--94221 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
94173 AATTACATTC
94183 TTAATTATT-TATATTTAT
1 TTAATT-TTATATATTTAT
*
94201 TTAATTTTATTTATTTAT
1 TTAATTTTATATATTTAT
94219 TTA
1 TTA
94222 TTTCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTAATTTTATATATTTAT
Found at i:94222 original size:22 final size:24
Alignment explanation
Indices: 94183--94233 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
94173 AATTACATTC
94183 TTAATTATTTATATTTATTTAATT
1 TTAATTATTTATATTTATTTAATT
*
94207 TTATTTATTTATTTATTTCATTTAATT
1 TTAATTATTTA--TATTT-ATTTAATT
94234 AATGTATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
26 5 0.22
27 8 0.35
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
TTAATTATTTATATTTATTTAATT
Found at i:109700 original size:20 final size:20
Alignment explanation
Indices: 109677--109714 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
109667 GTTTTTTTTA
*
109677 CTTTTTTCTTATTTCTTTGC
1 CTTTTTTATTATTTCTTTGC
*
109697 CTTTTTTATTTTTTCTTT
1 CTTTTTTATTATTTCTTT
109715 TATTTTCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (20 bp):
CTTTTTTATTATTTCTTTGC
Found at i:114883 original size:19 final size:20
Alignment explanation
Indices: 114840--114886 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
114830 TAAAAAGCTA
*
114840 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAGTGTT
114860 GAAATTGATGTTAG-GATG-T
1 GAAATTGATGTTAGAG-TGTT
114879 GAAATTGA
1 GAAATTGA
114887 GTCATTTCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (20 bp):
GAAATTGATGTTAGAGTGTT
Found at i:116855 original size:21 final size:20
Alignment explanation
Indices: 116831--116872 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
116821 TGCAAACTAT
116831 TAATATAGTCAGTA-TCAAATA
1 TAATATAGT-A-TATTCAAATA
*
116852 TAATTTAGTATATTCAAATA
1 TAATATAGTATATTCAAATA
116872 T
1 T
116873 TATGATACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 9 0.47
21 8 0.42
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (20 bp):
TAATATAGTATATTCAAATA
Found at i:120208 original size:13 final size:13
Alignment explanation
Indices: 120190--120216 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
120180 TGTGAGCTAC
120190 ACTTAAGCTCATA
1 ACTTAAGCTCATA
120203 ACTTAAGCTCATA
1 ACTTAAGCTCATA
120216 A
1 A
120217 TTGTATTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTAAGCTCATA
Found at i:120763 original size:20 final size:21
Alignment explanation
Indices: 120726--120769 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
120716 TGTCCAAGAG
**
120726 CATGAATCTTCATTAAAAC-T
1 CATGAATCTTCACCAAAACAT
120746 CATGAATCTTCACCAAAACAT
1 CATGAATCTTCACCAAAACAT
120767 CAT
1 CAT
120770 TTTCAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (21 bp):
CATGAATCTTCACCAAAACAT
Found at i:122382 original size:81 final size:81
Alignment explanation
Indices: 122201--122750 Score: 630
Period size: 81 Copynumber: 6.9 Consensus size: 81
122191 GTTGCACTAA
* * *
122201 TGTCAATTATGCCAGTTAGATGAACAGTTAAATATTGTTGAG-AAAAGAATAATGACCTAACTGT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
* *
122265 TCATTTGACAACAAGG
66 GCATTTGGCAACAAGG
* * *
122281 TGTCAATTATGCTAGTTAGATGAATGGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTGT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
* *
122346 GCATTTGGCAAAAAAG
66 GCATTTGGCAACAAGG
* * * * * *
122362 TGTTAATTATACCAGATAGATGAACAGTTAAATATCGTTGAGTAAAAGAATAATTGTCTAACT-T
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
*
122426 GCATTTGGCATA-AATG
66 GCATTTGGCA-ACAAGG
* * * * * *
122442 TGTTAATTATGCAAGTTAGATGAACGGTTAAATACCGTTGACTAAAAGAAAAATGGTCTAACTGT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
*
122507 GCATTTGGCAGCAAGG
66 GCATTTGGCAACAAGG
** * *
122523 TGTCAATTATGCCAGTTAGATGAACAATTAAATATCGTTGGGTAAAAGAATAATGGCCT-ATTGT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
*
122587 GCATTTGGCAGCAAGG
66 GCATTTGGCAACAAGG
** * * * *
122603 TGTCAATTATG-CAGAAAGATGAATGATTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTCT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
*
122667 ACATTTGGCAGA-AA--
66 GCATTTGGCA-ACAAGG
* * * * * * * *
122681 TGTCAATTATTCCAGTTAGATTAACGGTTAAACATTGTTGAGTAAAATAATAATGGACTCACTCT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
122746 GCATT
66 GCATT
122751 GATAGAAAAG
Statistics
Matches: 400, Mismatches: 63, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
78 10 0.03
79 87 0.22
80 151 0.38
81 152 0.38
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (81 bp):
TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
GCATTTGGCAACAAGG
Found at i:122472 original size:80 final size:81
Alignment explanation
Indices: 122201--122750 Score: 637
Period size: 80 Copynumber: 6.9 Consensus size: 81
122191 GTTGCACTAA
* * *
122201 TGTCAATTATGCCAGTTAGATGAACAGTTAAATATTGTTGAG-AAAAGAATAATGACCTAACTGT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
* *
122265 TCATTTGACA-ACAAGG
66 GCATTTGGCAGA-AAGG
* * *
122281 TGTCAATTATGCTAGTTAGATGAATGGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTGT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
* *
122346 GCATTTGGCAAAAAAG
66 GCATTTGGCAGAAAGG
* * * * * *
122362 TGTTAATTATACCAGATAGATGAACAGTTAAATATCGTTGAGTAAAAGAATAATTGTCTAACT-T
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
* *
122426 GCATTTGGCATAAATG
66 GCATTTGGCAGAAAGG
* * * * * *
122442 TGTTAATTATGCAAGTTAGATGAACGGTTAAATACCGTTGACTAAAAGAAAAATGGTCTAACTGT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
*
122507 GCATTTGGCAGCAAGG
66 GCATTTGGCAGAAAGG
** * *
122523 TGTCAATTATGCCAGTTAGATGAACAATTAAATATCGTTGGGTAAAAGAATAATGGCCT-ATTGT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
*
122587 GCATTTGGCAGCAAGG
66 GCATTTGGCAGAAAGG
** * * * *
122603 TGTCAATTATG-CAGAAAGATGAATGATTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTCT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
*
122667 ACATTTGGCAGAAA--
66 GCATTTGGCAGAAAGG
* * * * * * * *
122681 TGTCAATTATTCCAGTTAGATTAACGGTTAAACATTGTTGAGTAAAATAATAATGGACTCACTCT
1 TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
122746 GCATT
66 GCATT
122751 GATAGAAAAG
Statistics
Matches: 401, Mismatches: 64, Indels: 11
0.84 0.13 0.02
Matches are distributed among these distances:
78 10 0.02
79 87 0.22
80 153 0.38
81 150 0.37
82 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (81 bp):
TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGT
GCATTTGGCAGAAAGG
Found at i:122482 original size:161 final size:160
Alignment explanation
Indices: 122201--122734 Score: 675
Period size: 161 Copynumber: 3.3 Consensus size: 160
122191 GTTGCACTAA
*
122201 TGTCAATTATGCCAGTTAGATGAACAGTTAAATATTGTTGAG-AAAAGAATAA-TGACCTAACTG
1 TGTCAATTATGCCAGTTAGATGAACAGTTAAATATCGTTGAGTAAAAGAATAATTG-CCTAACTG
* *
122264 TTCATTTGACAACAAGGTGTCAATTATGCTAGTTAGATGAATGGTTAAATACCGTTGAGTAAAAG
65 TGCATTTGGCAA-AAGGTGTCAATTATGC-AGTTAGATGAATGGTTAAATACCGTTGAGTAAAAG
122329 AATAATGGCCTAACTGTGCATTTGGCAAAAAAG
128 AATAATGGCCTAACTGTGCATTTGGCAAAAAAG
* * * *
122362 TGTTAATTATACCAGATAGATGAACAGTTAAATATCGTTGAGTAAAAGAATAATTGTCTAACT-T
1 TGTCAATTATGCCAGTTAGATGAACAGTTAAATATCGTTGAGTAAAAGAATAATTGCCTAACTGT
* * * *
122426 GCATTTGGCATAAATGTGTTAATTATGCAAGTTAGATGAACGGTTAAATACCGTTGACTAAAAGA
66 GCATTTGGCA-AAAGGTGTCAATTATGC-AGTTAGATGAATGGTTAAATACCGTTGAGTAAAAGA
* * ** *
122491 AAAATGGTCTAACTGTGCATTTGGCAGCAAGG
129 ATAATGGCCTAACTGTGCATTTGGCAAAAAAG
* * * *
122523 TGTCAATTATGCCAGTTAGATGAACAATTAAATATCGTTGGGTAAAAGAATAATGGCCT-ATTGT
1 TGTCAATTATGCCAGTTAGATGAACAGTTAAATATCGTTGAGTAAAAGAATAATTGCCTAACTGT
* ** *
122587 GCATTTGGCAGCAAGGTGTCAATTATGCAGAAAGATGAATGATTAAATACCGTTGAGTAAAAGAA
66 GCATTTGGCA-AAAGGTGTCAATTATGCAGTTAGATGAATGGTTAAATACCGTTGAGTAAAAGAA
* * *
122652 TAATGGCCTAACTCTACATTTGGC-AGAAA-
130 TAATGGCCTAACTGTGCATTTGGCAAAAAAG
* * * * * *
122681 TGTCAATTATTCCAGTTAGATTAACGGTTAAACATTGTTGAGTAAAATAATAAT
1 TGTCAATTATGCCAGTTAGATGAACAGTTAAATATCGTTGAGTAAAAGAATAAT
122735 GGACTCACTC
Statistics
Matches: 320, Mismatches: 49, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
158 46 0.14
159 2 0.01
160 54 0.17
161 199 0.62
162 17 0.05
163 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (160 bp):
TGTCAATTATGCCAGTTAGATGAACAGTTAAATATCGTTGAGTAAAAGAATAATTGCCTAACTGT
GCATTTGGCAAAAGGTGTCAATTATGCAGTTAGATGAATGGTTAAATACCGTTGAGTAAAAGAAT
AATGGCCTAACTGTGCATTTGGCAAAAAAG
Found at i:127336 original size:20 final size:20
Alignment explanation
Indices: 127286--127379 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
127276 TATGTAGAGT
* *
127286 AGTATCGATACCAATTCAAGTG
1 AGTATCGATACCAA--GAAGGG
* *
127308 -GTATGGATACCAAGAGGGG
1 AGTATCGATACCAAGAAGGG
127327 AGTATCGATACCAAGAAGGG
1 AGTATCGATACCAAGAAGGG
127347 AGTATCGATACCAAGAAGGG
1 AGTATCGATACCAAGAAGGG
127367 AGTATCGATACCA
1 AGTATCGATACCA
127380 TGATGTTGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 3 0.05
20 50 0.77
21 12 0.18
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (20 bp):
AGTATCGATACCAAGAAGGG
Found at i:127392 original size:40 final size:39
Alignment explanation
Indices: 127286--127395 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 39
127276 TATGTAGAGT
* * *
127286 AGTATCGATACCAATTCAAGTGGTATGGATACCAAGAGGGG
1 AGTATCGATACCAA--GAAGTGGTATCGATACCAAGAAGGG
*
127327 AGTATCGATACCAAGAAGGGAGTATCGATACCAAGAAGGG
1 AGTATCGATACCAAGAAGTG-GTATCGATACCAAGAAGGG
* *
127367 AGTATCGATACCATGATGTTGGTATCGAT
1 AGTATCGATACCAAGAAG-TGGTATCGAT
127396 TCCATTTGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
39 4 0.07
40 41 0.68
41 15 0.25
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (39 bp):
AGTATCGATACCAAGAAGTGGTATCGATACCAAGAAGGG
Found at i:127914 original size:55 final size:55
Alignment explanation
Indices: 127824--127949 Score: 146
Period size: 55 Copynumber: 2.3 Consensus size: 55
127814 TGCACGAAGG
* * * * ** *
127824 GTGCAAAAACTTAATAAATTCATACTAAGTGTATGAATTTATGTATGGGCACTTTGT
1 GTGC-AAAAC-TAAGAAATCCATACTAAGTATATGAATTTACGTATGAACACTATGT
* *
127881 GTGCAAAACTAAGAAATCCATACTAAGTATATGAATTTCCGTATGAATACTATGT
1 GTGCAAAACTAAGAAATCCATACTAAGTATATGAATTTACGTATGAACACTATGT
127936 GTGCAAAA-TAAGAA
1 GTGCAAAACTAAGAA
127950 GGTTTATTGC
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
54 6 0.10
55 45 0.75
56 5 0.08
57 4 0.07
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (55 bp):
GTGCAAAACTAAGAAATCCATACTAAGTATATGAATTTACGTATGAACACTATGT
Found at i:128202 original size:68 final size:67
Alignment explanation
Indices: 128088--128405 Score: 345
Period size: 68 Copynumber: 4.7 Consensus size: 67
128078 AAAGATTAAT
* * * **
128088 AGGCCTAACTGTGAATTTGACATAAAAGTGTCATTTATTCTTGTTAGATGAAAGGATACA-TGCC
1 AGGCCTAACTGTGCATTTGACA-AAAAATGTCATTTATGCCAGTTAGATGAAAGGATA-AGTGCC
128152 TTTG
64 TTTG
* * * *
128156 GGGCCTAACTGTGCATTTGATAGAAAAATGTCATTTATGCCAGTTAGATGAAA-AACTAAGTGCT
1 AGGCCTAACTGTGCATTTGACA-AAAAATGTCATTTATGCCAGTTAGATGAAAGGA-TAAGTGCC
128220 TTTG
64 TTTG
* * *
128224 AGGCCTAACAGTGCATTTGACAAAAAGGAT-TCATTTATGCCAGTTAGATGAAAAGCTAAGTGCC
1 AGGCCTAACTGTGCATTTGACAAAAA--ATGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCC
128288 TTTG
64 TTTG
* * * *
128292 AGGCCTAACTGTGCATTTGACAAAAAGGTGTCATTAATGCCAGTAAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAAAAA-ATGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCCT
*
128357 TTT
65 TTG
* * * * *
128360 AGGCCTAACTGTGCATTTGGCCGAAAGATGTCAATTATGCTAGTTA
1 AGGCCTAACTGTGCATTT-GACAAAAAATGTCATTTATGCCAGTTA
128406 AATAAACAGT
Statistics
Matches: 213, Mismatches: 30, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
67 8 0.04
68 198 0.93
69 7 0.03
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (67 bp):
AGGCCTAACTGTGCATTTGACAAAAAATGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCCTT
TG
Found at i:128733 original size:162 final size:161
Alignment explanation
Indices: 128361--128759 Score: 475
Period size: 162 Copynumber: 2.5 Consensus size: 161
128351 GTGCCTTTTA
* * * * * * *
128361 GGCCTAACTGTGCATTTGGCCGAAAGATGTCAATTATGCTAGTTAAATAAACAGTT-AATATTGT
1 GGCCTAACTGTGCATTTGG-CAAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAATGT
128425 TGAGTAAAAGAATAATGGCCTAACTGTGCATTTGGAAACAAGATGTCAATTATGCTAGTTAAATG
65 TGAGTAAAAGAATAATGGCCTAACTGTGCATTTGGAAACAAGATGTCAATTATGCTAGTTAAATG
***
128490 AATGGTTAAATATCGTTGTGTAAAAGAATAAT
130 AATGGTTAAATATCGTTAACTAAAAGAATAAT
** * * ** *
128522 TCCCTAATTGTGTATTTGG-AAGAATGGTGTTGATTATGCCAGATAGATGAACGGTTAAATAATG
1 GGCCTAACTGTGCATTTGGCAA-AA-GGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAATG
* *
128586 TTGAGTAAAAGAATAATGGCCTAACTGTGCATTTTGTAGAA-ATG-TGTCAATTATG-TCAGTTA
64 TTGAGTAAAAGAATAATGGCCTAACTGTGCA-TTTGGA-AACAAGATGTCAATTATGCT-AGTTA
*
128648 GATGAATGGTTAAATATCGTTAACTAAAAGAATAAT
126 AATGAATGGTTAAATATCGTTAACTAAAAGAATAAT
* * * * *
128684 GGCCTAACTGTGCATTTGGCAACAAGGTGTCAATTATACCAGTTAGATGAACGATTAAACACTAT
1 GGCCTAACTGTGCATTTGGCAA-AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAATGT
128749 TGAGTAAAAGA
65 TGAGTAAAAGA
128760 TGAATGGTTA
Statistics
Matches: 198, Mismatches: 33, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
159 1 0.01
160 2 0.01
161 39 0.20
162 143 0.72
163 11 0.06
164 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (161 bp):
GGCCTAACTGTGCATTTGGCAAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAATGTT
GAGTAAAAGAATAATGGCCTAACTGTGCATTTGGAAACAAGATGTCAATTATGCTAGTTAAATGA
ATGGTTAAATATCGTTAACTAAAAGAATAAT
Found at i:128766 original size:81 final size:79
Alignment explanation
Indices: 128361--128759 Score: 415
Period size: 81 Copynumber: 4.9 Consensus size: 79
128351 GTGCCTTTTA
* * * * * *
128361 GGCCTAACTGTGCATTTGGCCGAAAGATGTCAATTATGCTAGTTAAATAAACAGTT-AATATTGT
1 GGCCTAACTGTGCATTTGG-CAAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-TGT
128425 TGAGTAAAAGAATAAT
64 TGAGTAAAAGAATAAT
* * * * *
128441 GGCCTAACTGTGCATTTGGAAACAAGATGTCAATTATGCTAGTTAAATGAATGGTTAAATATCGT
1 GGCCTAACTGTGCATTTGGCAA-AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAT-GT
*
128506 TGTGTAAAAGAATAAT
64 TGAGTAAAAGAATAAT
** * * ** *
128522 TCCCTAATTGTGTATTTGG-AAGAATGGTGTTGATTATGCCAGATAGATGAACGGTTAAATAATG
1 GGCCTAACTGTGCATTTGGCAA-AA-GGTGTCAATTATGCCAGTTAGATGAACGGTTAAAT-ATG
128586 TTGAGTAAAAGAATAAT
63 TTGAGTAAAAGAATAAT
* * * * *
128603 GGCCTAACTGTGCATTTTGTAGAAATGTGTCAATTATGTCAGTTAGATGAATGGTTAAATATCGT
1 GGCCTAACTGTGCATTTGGCA-AAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAT-GT
* *
128668 TAACTAAAAGAATAAT
64 TGAGTAAAAGAATAAT
* * * *
128684 GGCCTAACTGTGCATTTGGCAACAAGGTGTCAATTATACCAGTTAGATGAACGATTAAACACTAT
1 GGCCTAACTGTGCATTTGGCAA-AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-TGT
128749 TGAGTAAAAGA
64 TGAGTAAAAGA
128760 TGAATGGTTA
Statistics
Matches: 266, Mismatches: 43, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
79 1 0.00
80 57 0.21
81 201 0.76
82 6 0.02
83 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (79 bp):
GGCCTAACTGTGCATTTGGCAAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATGTTG
AGTAAAAGAATAAT
Found at i:128795 original size:29 final size:29
Alignment explanation
Indices: 128728--128788 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
128718 TATACCAGTT
* *
128728 AGATGAACGATTAAACACTATTGAGTAAA
1 AGATGAATGGTTAAACACTATTGAGTAAA
128757 AGATGAATGGTTAAACACTATTGAGTAAA
1 AGATGAATGGTTAAACACTATTGAGTAAA
128786 AGA
1 AGA
128789 ATAATGGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.25
Consensus pattern (29 bp):
AGATGAATGGTTAAACACTATTGAGTAAA
Found at i:134772 original size:20 final size:19
Alignment explanation
Indices: 134727--134777 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
134717 TCGATTCAAG
*
134727 TGGTATCGATACCAAGAGC
1 TGGTATCGATACCAAGAGA
* *
134746 GGAGTATCGATACCATGATGA
1 TG-GTATCGATACCAAGA-GA
134767 TGGTATCGATA
1 TGGTATCGATA
134778 TCATTTGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 23 0.88
21 2 0.08
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (19 bp):
TGGTATCGATACCAAGAGA
Found at i:135274 original size:55 final size:57
Alignment explanation
Indices: 135202--135358 Score: 189
Period size: 55 Copynumber: 2.8 Consensus size: 57
135192 ATGGAACTAA
* * *
135202 GTGTGCAAAAACTTAAGAAATTCATATTAAGTGTATTAATTTCTGTATAGGCACT-T-T
1 GTGTGC-AAAAC-TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGCACTATAT
* * *
135259 GTGTGCAAAACTAAGAAATTCATACTGAGTGTATGAATTTCCGTATGGGTACTATAT
1 GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGCACTATAT
* *
135316 ATGTG--AAA-TAAGAAATTCATACCAAGTGTATGAATTTCCGTAT
1 GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
135359 TGAAAATATA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
54 33 0.37
55 39 0.44
56 6 0.07
57 11 0.12
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (57 bp):
GTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGCACTATAT
Found at i:135369 original size:54 final size:52
Alignment explanation
Indices: 135270--135376 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 52
135260 TGTGCAAAAC
** **
135270 TAAGAAATTCATACTGAGTGTATGAATTTCCGTATGGGTACTATATATGTGAAA
1 TAAGAAATTCATACCAAGTGTATGAATTTCCGTAT-GG-AAAATATATGTGAAA
*
135324 TAAGAAATTCATACCAAGTGTATGAATTTCCGTATTGAAAATATATGTGAAA
1 TAAGAAATTCATACCAAGTGTATGAATTTCCGTATGGAAAATATATGTGAAA
135376 T
1 T
135377 TATTAGAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 14 0.29
53 1 0.02
54 33 0.69
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (52 bp):
TAAGAAATTCATACCAAGTGTATGAATTTCCGTATGGAAAATATATGTGAAA
Found at i:135644 original size:68 final size:68
Alignment explanation
Indices: 135535--135858 Score: 486
Period size: 68 Copynumber: 4.8 Consensus size: 68
135525 AAAGATTAAT
* *
135535 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTGGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
135600 TTG
66 TTG
* * *
135603 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATGTATGCCAGTTAGATAAAAGGCTAAGTGTCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
135668 TTG
66 TTG
* * * * * *
135671 AGGCCTAATTGCGCATTTGACAGAAAGGAGTAATTTATGCCTGTTAGATGAAAGACTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
135736 TTG
66 TTG
*
135739 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATTCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
135804 TTG
66 TTG
** * * **
135807 AGGCCTAACTGTGCATTTGGTAGAAAAGTGTCAATTATTTCAGTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
135859 TGATTAAATG
Statistics
Matches: 230, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 230 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:135948 original size:81 final size:81
Alignment explanation
Indices: 135808--136369 Score: 673
Period size: 81 Copynumber: 6.9 Consensus size: 81
135798 GTGCCTTTGA
* ** * * ** *
135808 GGCCTAACTGTGCATTTGGTAGAAAAGTGTCAATTATTTCAGTTAGATGAATGATTAAATGCCTT
1 GGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAACGT
*
135873 TGAATAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * ** * *
135889 GACCTAATTGTGCATTTGGCAGTAAGGTGTCAATTATGCCAGTTAGATGAAATGCTAAATACCGT
1 GGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAACGT
*
135954 TGAGTACAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * *
135970 GACCTAATTGTACATTTGGTAGAAAGGTGTCAATTATGCCAGTTACATGAACGGTTAAATATCGT
1 GGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAACGT
136035 TGAG-AAGAAGAATAAT
66 TGAGTAA-AAGAATAAT
** * *
136051 GGCCTAACTACGCATTTGGTAGAAACGTGTCAATTATGCCTGTTAGATGAACGGTTAAAT-ACTG
1 GGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAAC-G
136115 TTGAGTAAAAGAATAAT
65 TTGAGTAAAAGAATAAT
* * * * * *
136132 GGCCTAACTGTCCATTTGGCAGCAAGGTGTCAGTTATTCCAGTTAGATGAACGGTTAAATATCGT
1 GGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAACGT
136197 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * *
136213 GGCCTAACTGTGCATTTGGCAGCAAGGTGTCAATTATGCTAGTTTGATGAACTGTTAAAT-ACTG
1 GGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAAC-G
136277 TTGAGTAAAAGAATAAT
65 TTGAGTAAAAGAATAAT
* * ** *
136294 GGCGTAACTGTGCATTTGGTAGAAAGTTGTCAATTATGTTAGTTAGATGAACGGTTAAA-CACTG
1 GGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAAC-G
136358 TTGAGTAAAAGA
65 TTGAGTAAAAGA
136370 TGAACATTTA
Statistics
Matches: 418, Mismatches: 57, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
80 3 0.01
81 412 0.99
82 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (81 bp):
GGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAACGT
TGAGTAAAAGAATAAT
Found at i:136242 original size:243 final size:241
Alignment explanation
Indices: 135808--136369 Score: 743
Period size: 243 Copynumber: 2.3 Consensus size: 241
135798 GTGCCTTTGA
* * * * *
135808 GGCCTAACTGTGCATTTGGTAGAAAAGTGTCAATTATTTCAGTTAGATGAATGATTAAATGCCT-
1 GGCCTAACTGTGCATTTGGTAG-AAAGTGTCAATTA-TGCTGTTAGATGAACGGTTAAAT-ACTG
* * * *
135872 TTGAATAAAAGAATAATGACCTAATTGTGCATTTGGCAGTAAGGTGTCAATTATGCCAGTTAGAT
63 TTGAGTAAAAGAATAATGACCTAACTGTCCATTTGGCAGCAAGGTGTCAATTATGCCAGTTAGAT
* * * *
135937 GAAATGCTAAATACCGTTGAGTACAAGAATAATGACCTAATTGTACATTTGGTAGAAAGGTGTCA
128 GAAAGGCTAAATACCGTTGAGTAAAAGAATAATGACCTAACTGTACATTTGGCAGAAAGGTGTCA
136002 ATTATGCCAGTTACATGAACGGTTAAATA-TCGTTGAG-AAGAAGAATAAT
193 ATTATGCCAGTTACATGAACGGTTAAATACT-GTTGAGTAA-AAGAATAAT
**
136051 GGCCTAACTACGCATTTGGTAGAAACGTGTCAATTATGCCTGTTAGATGAACGGTTAAATACTGT
1 GGCCTAACTGTGCATTTGGTAGAAA-GTGTCAATTATG-CTGTTAGATGAACGGTTAAATACTGT
* * *
136116 TGAGTAAAAGAATAATGGCCTAACTGTCCATTTGGCAGCAAGGTGTCAGTTATTCCAGTTAGATG
64 TGAGTAAAAGAATAATGACCTAACTGTCCATTTGGCAGCAAGGTGTCAATTATGCCAGTTAGATG
* * * * * *
136181 AACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAACTGTGCATTTGGCAGCAAGGTGTCAA
129 AAAGGCTAAATACCGTTGAGTAAAAGAATAATGACCTAACTGTACATTTGGCAGAAAGGTGTCAA
* ** *
136246 TTATGCTAGTTTGATGAACTGTTAAATACTGTTGAGTAAAAGAATAAT
194 TTATGCCAGTTACATGAACGGTTAAATACTGTTGAGTAAAAGAATAAT
* * *
136294 GGCGTAACTGTGCATTTGGTAGAAAGTTGTCAATTATGTTAGTTAGATGAACGGTTAAACACTGT
1 GGCCTAACTGTGCATTTGGTAGAAAG-TGTCAATTATGCT-GTTAGATGAACGGTTAAATACTGT
136359 TGAGTAAAAGA
64 TGAGTAAAAGA
136370 TGAACATTTA
Statistics
Matches: 279, Mismatches: 33, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
242 8 0.03
243 268 0.96
244 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (241 bp):
GGCCTAACTGTGCATTTGGTAGAAAGTGTCAATTATGCTGTTAGATGAACGGTTAAATACTGTTG
AGTAAAAGAATAATGACCTAACTGTCCATTTGGCAGCAAGGTGTCAATTATGCCAGTTAGATGAA
AGGCTAAATACCGTTGAGTAAAAGAATAATGACCTAACTGTACATTTGGCAGAAAGGTGTCAATT
ATGCCAGTTACATGAACGGTTAAATACTGTTGAGTAAAAGAATAAT
Found at i:136371 original size:29 final size:29
Alignment explanation
Indices: 136338--136398 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
136328 TATGTTAGTT
* *
136338 AGATGAACGGTTAAACACTGTTGAGTAAA
1 AGATGAACAGTTAAACACTGTTGAATAAA
*
136367 AGATGAACATTTAAACACTGTTGAATAAA
1 AGATGAACAGTTAAACACTGTTGAATAAA
136396 AGA
1 AGA
136399 GTAATGGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.25
Consensus pattern (29 bp):
AGATGAACAGTTAAACACTGTTGAATAAA
Found at i:137701 original size:21 final size:22
Alignment explanation
Indices: 137676--137717 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
137666 ATTGGGTGTT
137676 CAATGTTGAATTTTAA-TTATG
1 CAATGTTGAATTTTAAGTTATG
*
137697 CAATGTTGGATTTTAAGTTAT
1 CAATGTTGAATTTTAAGTTAT
137718 ATTGCTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (22 bp):
CAATGTTGAATTTTAAGTTATG
Found at i:139105 original size:24 final size:23
Alignment explanation
Indices: 139078--139123 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
139068 AGTTTAAAGA
*
139078 TTTTATTGGATTTATTTTTATTTG
1 TTTTAATGGATTTA-TTTTATTTG
*
139102 TTTTAATGTATTTATTTTATTT
1 TTTTAATGGATTTATTTTATTT
139124 TAATTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (23 bp):
TTTTAATGGATTTATTTTATTTG
Found at i:139134 original size:19 final size:20
Alignment explanation
Indices: 139093--139135 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
139083 TTGGATTTAT
*
139093 TTTTA-TTTGTTTTAATGTA
1 TTTTATTTTATTTTAATGTA
139112 -TTTATTTTATTTTAAT-TA
1 TTTTATTTTATTTTAATGTA
139130 TTTTAT
1 TTTTAT
139136 CTCACCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTATTTTATTTTAATGTA
Found at i:140815 original size:18 final size:18
Alignment explanation
Indices: 140792--140838 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
140782 GTTATACAAG
140792 TGTGACTATTCCAAGACT
1 TGTGACTATTCCAAGACT
140810 TGTGACTATTCCAAGACT
1 TGTGACTATTCCAAGACT
*
140828 TGTGCCTATTC
1 TGTGACTATTC
140839 TAGATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (18 bp):
TGTGACTATTCCAAGACT
Found at i:147697 original size:36 final size:36
Alignment explanation
Indices: 147618--147819 Score: 273
Period size: 36 Copynumber: 5.7 Consensus size: 36
147608 GAATTGCAGT
* * *
147618 ACTTCATTACTCTTCCGTGAA-GTTGGAAATG-ATG
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATGTTTG
**
147652 ACTTCACTACTCTTTTGTGAAGGTTGAAAATGTTTG
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATGTTTG
* *
147688 ACTTCACTACTCTTTCGTGAAGGTTGAAAATATTTG
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATGTTTG
* * *
147724 ACTTCACTACTCGTCCGTTAAGGTTTAAAATGTTTG
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATGTTTG
* * *
147760 ATTTCACTACTCTCCCGTGAAGGTTGAAAATATTTG
1 ACTTCACTACTCTTCCGTGAAGGTTGAAAATGTTTG
147796 ACTTCACTACTCTTCCGTGAAGGT
1 ACTTCACTACTCTTCCGTGAAGGT
147820 CAGAATCATG
Statistics
Matches: 146, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
34 18 0.12
35 9 0.06
36 119 0.82
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (36 bp):
ACTTCACTACTCTTCCGTGAAGGTTGAAAATGTTTG
Found at i:154398 original size:89 final size:89
Alignment explanation
Indices: 154144--154400 Score: 354
Period size: 92 Copynumber: 2.9 Consensus size: 89
154134 AAATTCGATC
* * * *
154144 TCCACGGAAGAGTAGTGGAAGCAAATTAACCTTGAATCTAATCTTCATGGAAGAGTAGTGAAACA
1 TCCATGGAAGAGTAGTGGAAGCAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGAAACA
*
154209 TATTCTTTGCAAGTCAATCCAATT
66 TATTCTTTCCAAGTCAATCCAATT
* * * * *
154233 TCCGCTGAAGAGTACGTAGTGGAAGCAAA-CAACCTTGAATTTGATCTTCACGGAAGATTAGTTA
1 TCC-ATGGA-AG-A-GTAGTGGAAGCAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGA
*
154297 AATATATTCTTTCCAAGTCAATCCAATT
62 AACATATTCTTTCCAAGTCAATCCAATT
*
154325 TCCATGGAAGAGTAGTGGTAGCAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGAAACA
1 TCCATGGAAGAGTAGTGGAAGCAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGAAACA
*
154390 GATTCTTTCCA
66 TATTCTTTCCA
154401 TGCAACCAAG
Statistics
Matches: 144, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
88 13 0.09
89 49 0.34
90 4 0.03
91 5 0.03
92 59 0.41
93 14 0.10
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (89 bp):
TCCATGGAAGAGTAGTGGAAGCAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGAAACA
TATTCTTTCCAAGTCAATCCAATT
Found at i:154682 original size:9 final size:9
Alignment explanation
Indices: 154644--154691 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
154634 TCTTGATTTG
*
154644 TTATAAGTA
1 TTATAATTA
*
154653 TTATAATAA
1 TTATAATTA
* *
154662 TAATAATAA
1 TTATAATTA
*
154671 TTATTATTA
1 TTATAATTA
154680 TTATAATTA
1 TTATAATTA
154689 TTA
1 TTA
154692 ATTTTTACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (9 bp):
TTATAATTA
Found at i:156092 original size:25 final size:25
Alignment explanation
Indices: 156050--156100 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
156040 TTATTAATAA
*
156050 TTATTAATATGATTATAATATAATT
1 TTATTAATAGGATTATAATATAATT
*
156075 TTATT-ATAGGATTAATAATATTATT
1 TTATTAATAGGATT-ATAATATAATT
156100 T
1 T
156101 AATATTATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (25 bp):
TTATTAATAGGATTATAATATAATT
Found at i:158812 original size:10 final size:11
Alignment explanation
Indices: 158790--158818 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
158780 TAAATTGACA
158790 AATTTATATTT
1 AATTTATATTT
158801 AATTTA-ATTT
1 AATTTATATTT
158811 AATTTATA
1 AATTTATA
158819 CAAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
AATTTATATTT
Found at i:158866 original size:27 final size:26
Alignment explanation
Indices: 158836--158896 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
158826 TAATACTACT
158836 TAATATATTATTTATTATAAATA-TAAA
1 TAATATA-TATTTATT-TAAATATTAAA
*
158863 TAATCCTATATTTATTTAAATATTAAA
1 TAAT-ATATATTTATTTAAATATTAAA
*
158890 TTATATA
1 TAATATA
158897 GGTTAAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 8 0.28
27 19 0.66
28 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (26 bp):
TAATATATATTTATTTAAATATTAAA
Found at i:159965 original size:25 final size:25
Alignment explanation
Indices: 159918--159982 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 25
159908 GGGTCTTGTA
159918 ATAAGTTAATAATAATATATATAATAT
1 ATAA-TTAAT-ATAATATATATAATAT
*
159945 -TATATTAATATAATA-AGTATATTAT
1 ATA-ATTAATATAATATA-TATAATAT
*
159970 ATAATAAATATAA
1 ATAATTAATATAA
159983 ACGACACTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 1 0.03
25 22 0.67
26 9 0.27
27 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
ATAATTAATATAATATATATAATAT
Found at i:159976 original size:16 final size:16
Alignment explanation
Indices: 159935--159981 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
159925 AATAATAATA
*
159935 TATATAAT-ATTATAT
1 TATATAATAAATATAT
*
159950 TAATATAATAAGTATAT
1 T-ATATAATAAATATAT
159967 TATATAATAAATATA
1 TATATAATAAATATA
159982 AACGACACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 1 0.04
16 20 0.71
17 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
TATATAATAAATATAT
Found at i:159982 original size:22 final size:22
Alignment explanation
Indices: 159941--159982 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
159931 AATATATATA
*
159941 ATATTATATTAATATAATAAGT
1 ATATTATATTAATAAAATAAGT
159963 ATATTATA-TAATAAATATAA
1 ATATTATATTAATAAA-ATAA
159983 ACGACACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATTATATTAATAAAATAAGT
Found at i:161706 original size:18 final size:18
Alignment explanation
Indices: 161683--161723 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
161673 ACAATTGTGA
161683 CTATTCCAAGACTTATGC
1 CTATTCCAAGACTTATGC
161701 CTATTCCAAGACTTATGC
1 CTATTCCAAGACTTATGC
161719 CTATT
1 CTATT
161724 TTAGATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (18 bp):
CTATTCCAAGACTTATGC
Found at i:165373 original size:19 final size:22
Alignment explanation
Indices: 165333--165376 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
165323 TTGTTCATTT
165333 TTATTATTAATTATATATATTA
1 TTATTATTAATTATATATATTA
165355 TTATTA-TAATTAT-TA-ATTA
1 TTATTATTAATTATATATATTA
165374 TTA
1 TTA
165377 CAAGCCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 2 0.09
21 7 0.32
22 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTATTAATTATATATATTA
Found at i:166639 original size:14 final size:15
Alignment explanation
Indices: 166620--166648 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
166610 ATATGATCCC
166620 TTAATTTT-AATATT
1 TTAATTTTAAATATT
166634 TTAATTTTAAATATT
1 TTAATTTTAAATATT
166649 ATTTTTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATTTTAAATATT
Found at i:172226 original size:35 final size:35
Alignment explanation
Indices: 172139--172236 Score: 100
Period size: 32 Copynumber: 3.0 Consensus size: 35
172129 AGAATGACAA
* * *
172139 AAACTTTTCAGT-GTCA-A-ATAACTTCATTTTAG
1 AAACTTTTCAGTAGTGATATATCACTTCATTTCAG
* *
172171 AAAC-TTT--GCAGTGATGTATCACTTCATTTCAG
1 AAACTTTTCAGTAGTGATATATCACTTCATTTCAG
*
172203 AAACTTTTCAGTAGTGATATATCAGTTCATTTCA
1 AAACTTTTCAGTAGTGATATATCACTTCATTTCA
172237 TAAAAACGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
29 1 0.02
30 3 0.06
31 3 0.06
32 21 0.40
33 3 0.06
35 21 0.40
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (35 bp):
AAACTTTTCAGTAGTGATATATCACTTCATTTCAG
Found at i:172316 original size:141 final size:140
Alignment explanation
Indices: 172058--172522 Score: 471
Period size: 140 Copynumber: 3.3 Consensus size: 140
172048 AATTCGGTGA
* * * * *
172058 CAGAAACTTTTCAGTAGTAATATATCACTTTATTTCAGAAAAAAAACCATTTCTCATAGGCCATT
1 CAGAAACTTTTCAGTAGTGATATATCACTTCATTTCA-TAAAAACATCATTTCTCATAGGCCATT
* * * * * *
172123 TAATACAGAAT-GACAAAAACTTTTCAGTGTCAAATAACTTCAT-TTTAGAAACTTTGCAGTGAT
65 TAATGCACAATGGA-AAAAACTTTTCAGTGCCCAATAACTTC-TCTTCAAAAACTTT-CAGTGAT
*
172186 GTATCACTTCATTT
127 ATATCACTTCATTT
* * *
172200 CAGAAACTTTTCAGTAGTGATATATCAGTTCATTTCATAAAAACGTTATTTCTCATAGGCCATTT
1 CAGAAACTTTTCAGTAGTGATATATCACTTCATTTCATAAAAACATCATTTCTCATAGGCCATTT
* * *
172265 AATGCACAATGGAAGAAACTTTTAAGTGCCCAATAACTTCTCTTCAAAAACTTTTCAGTAATATA
66 AATGCACAATGGAAAAAACTTTTCAGTGCCCAATAACTTCTCTTCAAAAAC-TTTCAGTGATATA
*
172330 TCAATTCATTT
130 TCACTTCATTT
**** * *
172341 -A-AAAAAAATCAATAGTG-TATATCA-TTCATTTAAATACAAAACATACATTTCTCATAGAG-C
1 CAGAAACTTTTCAGTAGTGATATATCACTTCATTT-CATA-AAAACAT-CATTTCTCATAG-GCC
* * ** *
172401 ATTTAATGCACAATGAAAAAAACTTTTCAGTGCCCAATAACTTCACTTCTTAAACATTTTAGTGA
62 ATTTAATGCACAATGGAAAAAACTTTTCAGTGCCCAATAACTTCTCTTCAAAAAC-TTTCAGTGA
172466 TATATCAAC-TCATTT
126 TATATC-ACTTCATTT
* *
172481 CAGAAAACTTTTGAGTAGTGATATA-CACTTCATTTCAGAAAA
1 CAG-AAACTTTTCAGTAGTGATATATCACTTCATTTCATAAAA
172523 TTTCATAAAC
Statistics
Matches: 265, Mismatches: 45, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
137 7 0.03
138 10 0.04
139 17 0.06
140 82 0.31
141 82 0.31
142 42 0.16
143 14 0.05
144 11 0.04
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (140 bp):
CAGAAACTTTTCAGTAGTGATATATCACTTCATTTCATAAAAACATCATTTCTCATAGGCCATTT
AATGCACAATGGAAAAAACTTTTCAGTGCCCAATAACTTCTCTTCAAAAACTTTCAGTGATATAT
CACTTCATTT
Found at i:172433 original size:140 final size:141
Alignment explanation
Indices: 172105--172487 Score: 429
Period size: 141 Copynumber: 2.7 Consensus size: 141
172095 GAAAAAAAAC
* * * * * *
172105 CATTTCTCATAGGCCATTTAATACAGAATGACAAAAACTTTTCAGTGTCAAATAACTTCAT-TTT
1 CATTTCTCATAGGCCATTTAATGCACAATGAAAAAAACTTTTCAGTGCCCAATAACTTC-TCTTC
* * * * **** *
172169 AGAAACTTTGCAGTGATGTATCACTTCATTTCAGAAACTTTTCAGTAGTGATATATCAGTTCATT
65 AAAAACTTTTCAGTGATATATCAATTCATTTCAGAAAAAAATCAATAGTGATATATCAGTTCATT
* *
172234 TCATAAAAACGT
130 TAATAAAAACAT
* * * *
172246 TATTTCTCATAGGCCATTTAATGCACAATGGAAGAAACTTTTAAGTGCCCAATAACTTCTCTTCA
1 CATTTCTCATAGGCCATTTAATGCACAATGAAAAAAACTTTTCAGTGCCCAATAACTTCTCTTCA
*
172311 AAAACTTTTCAGTAATATATCAATTCATTT-A-AAAAAAATCAATAGTG-TATATCA-TTCATTT
66 AAAACTTTTCAGTGATATATCAATTCATTTCAGAAAAAAATCAATAGTGATATATCAGTTCATTT
172372 AAATACAAAACAT
131 -AATA-AAAACAT
*
172385 ACATTTCTCATAGAG-CATTTAATGCACAATGAAAAAAACTTTTCAGTGCCCAATAACTTCACTT
1 -CATTTCTCATAG-GCCATTTAATGCACAATGAAAAAAACTTTTCAGTGCCCAATAACTTCTCTT
** *
172449 CTTAAACATTTT-AGTGATATATCAACTCATTTCAGAAAA
64 CAAAAAC-TTTTCAGTGATATATCAATTCATTTCAGAAAA
172488 CTTTTGAGTA
Statistics
Matches: 203, Mismatches: 31, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
137 7 0.03
138 10 0.05
139 17 0.08
140 81 0.40
141 84 0.41
142 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (141 bp):
CATTTCTCATAGGCCATTTAATGCACAATGAAAAAAACTTTTCAGTGCCCAATAACTTCTCTTCA
AAAACTTTTCAGTGATATATCAATTCATTTCAGAAAAAAATCAATAGTGATATATCAGTTCATTT
AATAAAAACAT
Found at i:182308 original size:3 final size:3
Alignment explanation
Indices: 182300--182368 Score: 59
Period size: 3 Copynumber: 22.7 Consensus size: 3
182290 TATATTGCAA
* * * *
182300 AAT AAT AAT AAT AA- AATT AGT AAAT AAT AAT AAT AGT AAT TAT TAT
1 AAT AAT AAT AAT AAT AA-T AAT -AAT AAT AAT AAT AAT AAT AAT AAT
* *
182346 AAT GAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
182369 AAGTAATTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:182327 original size:16 final size:16
Alignment explanation
Indices: 182306--182338 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
182296 GCAAAATAAT
182306 AATAATAA-AATTAGTA
1 AATAATAATAA-TAGTA
182322 AATAATAATAATAGTA
1 AATAATAATAATAGTA
182338 A
1 A
182339 TTATTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
AATAATAATAATAGTA
Found at i:182963 original size:134 final size:134
Alignment explanation
Indices: 182651--182974 Score: 362
Period size: 134 Copynumber: 2.4 Consensus size: 134
182641 GAAGATTTTT
* ** * * * *
182651 TCGGTGGATGACACGGTTCATACAAGATGATGACATGTGACCATATTTA-GAGATGTTGATAACA
1 TCGGTGGATGACACGGTTCCTACGTGATGATGACGTCTGACCATCTTTAGGA-ATGATGATAACA
* * * * * *
182715 TGGTTCCTACGCGATGAGGATGGCTGGTTATCTAAGGGTGACACGACTCCTACTTGATTAAGAGA
65 CGATTCCTACACGATGAGGATGGATGGTTATCTAAGGGTGACACGACTCCTACGTGATGAAGAGA
182780 TCTGG
130 TCTGG
** * * * * *
182785 TCAATGGATGACATGGTTCCTACGTGATGAGGATGCCTGGCCATCTTTAGGAATGATGATAACAC
1 TCGGTGGATGACACGGTTCCTACGTGATGATGACGTCTGACCATCTTTAGGAATGATGATAACAC
* * * ** *
182850 GATTCCTACATGATGAGGATGGATGGTTATCTAAGGTTGACGCGGTTCCTACGTGATGAGGAGAT
66 GATTCCTACACGATGAGGATGGATGGTTATCTAAGGGTGACACGACTCCTACGTGATGAAGAGAT
182915 CTGG
131 CTGG
* * * *
182919 TCGGTGGATGACACGATTCCTACGTGATGATGAGGTCTGTCCATCTTTAGGGATGA
1 TCGGTGGATGACACGGTTCCTACGTGATGATGACGTCTGACCATCTTTAGGAATGA
182975 ATCATTTCAA
Statistics
Matches: 154, Mismatches: 35, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
134 152 0.99
135 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (134 bp):
TCGGTGGATGACACGGTTCCTACGTGATGATGACGTCTGACCATCTTTAGGAATGATGATAACAC
GATTCCTACACGATGAGGATGGATGGTTATCTAAGGGTGACACGACTCCTACGTGATGAAGAGAT
CTGG
Found at i:183059 original size:52 final size:52
Alignment explanation
Indices: 182991--183107 Score: 155
Period size: 52 Copynumber: 2.2 Consensus size: 52
182981 TCAAGAGAAA
* * *
182991 TTATCTCAAGACAGACAAAAC-GTATTTCGAGGGAAACAGACTCAAAGATTTT
1 TTATTTCAAGAGAGACAAAACTGTATTTCAAGGGAAACAGACTCAAAGA-TTT
* * *
183043 TTATTTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAATATTT
1 TTATTTCAAGAGAGACAAAACTGTATTTCAAGGGAAACAGACTCAAAGATTT
*
183095 TTGTTTCAAGAGA
1 TTATTTCAAGAGA
183108 AAATGTTTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 34 0.60
53 23 0.40
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (52 bp):
TTATTTCAAGAGAGACAAAACTGTATTTCAAGGGAAACAGACTCAAAGATTT
Found at i:183119 original size:67 final size:67
Alignment explanation
Indices: 183046--183240 Score: 281
Period size: 67 Copynumber: 3.0 Consensus size: 67
183036 AGATTTTTTA
183046 TTTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAATATTTTTGTTTCAAGAGAAAA
1 TTTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAATATTTTTGTTTCAAGAGAAAA
183111 TG
66 TG
* *
183113 TTTCAAGAGAGACAAGACTTTGTTTCAAGGGAAACAGACTC--ATA-TTTT-TTTCAAGAGAAAT
1 TTTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAATATTTTTGTTTCAAGAGAAAA
183174 TG
66 TG
** * * * * *
183176 CCTCAAGAGAGAAAAAACTTTGTTTCAAGAGAAGCAAACTCAAAGATTTTTGTTTCAAGAGAAAA
1 TTTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAATATTTTTGTTTCAAGAGAAAA
183241 AAATCTCAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
63 48 0.42
64 4 0.04
65 5 0.04
66 4 0.04
67 52 0.46
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (67 bp):
TTTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAATATTTTTGTTTCAAGAGAAAA
TG
Found at i:184003 original size:16 final size:15
Alignment explanation
Indices: 183982--184012 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
183972 AACATGTTAC
183982 ATGTGTTGATGTATGT
1 ATGTGTTGAT-TATGT
183998 ATGTGTTGATTATGT
1 ATGTGTTGATTATGT
184013 TTTCTCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (15 bp):
ATGTGTTGATTATGT
Found at i:195102 original size:16 final size:17
Alignment explanation
Indices: 195081--195113 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
195071 CGTCAAAAAA
195081 CATAAAA-TTGACTTTT
1 CATAAAATTTGACTTTT
195097 CATAAAATTTGACTTTT
1 CATAAAATTTGACTTTT
195114 TGGTCAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (17 bp):
CATAAAATTTGACTTTT
Found at i:196042 original size:6 final size:6
Alignment explanation
Indices: 196033--196064 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
196023 TAATTTAAAT
196033 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
196065 GGGTTGTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:196673 original size:2 final size:2
Alignment explanation
Indices: 196666--196699 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
196656 AAAAAGATTA
196666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
196700 TAATAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:196806 original size:8 final size:8
Alignment explanation
Indices: 196761--196815 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
196751 AATACATTTT
196761 TAAATAT-
1 TAAATATA
196768 T-AATAATA
1 TAAAT-ATA
*
196776 TAAAAATA
1 TAAATATA
*
196784 TAAATAAA
1 TAAATATA
196792 TAAATATA
1 TAAATATA
*
196800 TATATATA
1 TAAATATA
*
196808 TATATATA
1 TAAATATA
196816 ATGAATATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 32 0.80
9 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAAATATA
Found at i:196857 original size:28 final size:29
Alignment explanation
Indices: 196802--196857 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
196792 TAAATATATA
* *
196802 TATATATATATATAATGAATATGTAAAAGT
1 TATATATATATATAA-GAATAAGAAAAAGT
*
196832 TATATATATATATAA-CATAAGAAAAA
1 TATATATATATATAAGAATAAGAAAAA
196858 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
30 15 0.65
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (29 bp):
TATATATATATATAAGAATAAGAAAAAGT
Found at i:198319 original size:130 final size:128
Alignment explanation
Indices: 198087--198722 Score: 478
Period size: 130 Copynumber: 4.9 Consensus size: 128
198077 GAATCCAAAT
* * * * * *
198087 ATAT-TTCATTGTGAAGTTGAAATTTGACTTGAAAATCTATTGGAAAATAACTCT-ATGCTATTG
1 ATATCTTCATCGTGAAGTTGAAATCTGAC-TCAAAATCTGTTGGAAAATAACTCTCAT--TGTTA
* * ** * *
198150 AGTTAAGTTATGTTGTAGATAACTCCTCCATTGCGAGTTAAGTCAAAATTAGATGACTCAAGAAT
63 AGTTAAGCTATGTTGTAGATGACTCCTCCATTGCGAGTTAAGTCAATCTTGGATGACTCAAGACT
198215 G
128 G
* *
198216 ATATACTTCATCGTGAAGTTGAAATCTGACT-AAGAATGTGTTGGAAAATAACTTCTCATTGTTG
1 ATAT-CTTCATCGTGAAGTTGAAATCTGACTCAA-AATCTGTTGGAAAATAAC-TCTCATTGTTA
*** * * *
198280 AGTTAAGCTATGTTGTAGATGACTCCTCCATTGCGAGTTAAGTTGGTCTTGAATTACTCGAG-CT
63 AGTTAAGCTATGTTGTAGATGACTCCTCCATTGCGAGTTAAGTCAATCTTGGATGACTCAAGAC-
198344 TG
127 TG
** * * *
198346 ATATCTTTCGGCGTGAAGTTGAAATCTGACTCAAAATCTAG--GAAAAAATAGCTCCTCGTTGTT
1 ATATC-TTCATCGTGAAGTTGAAATCTGACTCAAAATCT-GTTG-GAAAATAACT-CTCATTGTT
* ** * * ** * ** * * *
198409 AAGTTTAGCTAAATTGTAGACGAATGGTCCATTGTGAGTTAAGTGGATTTTGGATGACTCGAGTC
62 AAGTTAAGCTATGTTGTAGATGACTCCTCCATTGCGAGTTAAGTCAATCTTGGATGACTCAAGAC
*
198474 TA
127 TG
* * * * *
198476 ATATCCTTTATCATGAAGTTGAAATCTGACTCCAAAAT-TG-TGATAAAATAGCTCATTATTGTT
1 ATAT-CTTCATCGTGAAGTTGAAATCTGACT-CAAAATCTGTTG-GAAAATAACTC-TCATTGTT
* * * * * * * * *
198539 AAGTTAAGTTTTTTTGTAAATTACTCCTCTAATGCAAGTTGAGTCAATCTTGGATGACTCAAGAC
62 AAGTTAAGCTATGTTGTAGATGACTCCTCCATTGCGAGTTAAGTCAATCTTGGATGACTCAAGAC
198604 TG
127 TG
* * * * * *
198606 ATATCGTTCATCGTGAAGTTAAAATCTGACTCAGAATCTGTTGCAAAACAAATCATCGTTGTTAA
1 ATATC-TTCATCGTGAAGTTGAAATCTGACTCAAAATCTGTTGGAAAATAACTC-TCATTGTTAA
* * * ** *
198671 CTTAAGGTATGTTGTAGATGACTCCTCTATTATGAGTTAAGTCAATTTTGGA
64 GTTAAGCTATGTTGTAGATGACTCCTCCATTGCGAGTTAAGTCAATCTTGGA
198723 CCCCAATTTT
Statistics
Matches: 399, Mismatches: 89, Indels: 37
0.76 0.17 0.07
Matches are distributed among these distances:
129 17 0.04
130 342 0.86
131 38 0.10
132 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (128 bp):
ATATCTTCATCGTGAAGTTGAAATCTGACTCAAAATCTGTTGGAAAATAACTCTCATTGTTAAGT
TAAGCTATGTTGTAGATGACTCCTCCATTGCGAGTTAAGTCAATCTTGGATGACTCAAGACTG
Found at i:202693 original size:148 final size:148
Alignment explanation
Indices: 202514--202781 Score: 446
Period size: 148 Copynumber: 1.8 Consensus size: 148
202504 AAAATTATTT
*
202514 ATAAAATTGAGAAATTTCAAATTTTAACAACTAAAATCATTTAAAAATAATGTTATATCAAAATC
1 ATAAAATTGAGAAATTGCAAATTTTAACAACTAAAATCATTTAAAAATAATGTTATATCAAAATC
202579 AAATGTTGGTTCAACAATCTCCCCCTTTTTGATATAACAAAACCTTTTGTGAAAATTTGCTCTTA
66 AAATGTTGGTTCAACAATCTCCCCCTTTTTGATATAACAAAACCTTTTGTGAAAATTTGCTCTTA
202644 CAAATTTGCCTTGATATA
131 CAAATTTGCCTTGATATA
* * * *
202662 ATAAAATTGATAAATTGCACATTTTAACAACTTAAATCATTTAAAAATAATGTTCTATCAAAATC
1 ATAAAATTGAGAAATTGCAAATTTTAACAACTAAAATCATTTAAAAATAATGTTATATCAAAATC
* * * * *
202727 AAATGTTTGTTGAACAGTCTTCCCGTTTTTGATATAACAAAACCTTTTGTGAAAA
66 AAATGTTGGTTCAACAATCTCCCCCTTTTTGATATAACAAAACCTTTTGTGAAAA
202782 ACTGCTTTTA
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
148 110 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (148 bp):
ATAAAATTGAGAAATTGCAAATTTTAACAACTAAAATCATTTAAAAATAATGTTATATCAAAATC
AAATGTTGGTTCAACAATCTCCCCCTTTTTGATATAACAAAACCTTTTGTGAAAATTTGCTCTTA
CAAATTTGCCTTGATATA
Found at i:212557 original size:125 final size:127
Alignment explanation
Indices: 212405--212727 Score: 330
Period size: 125 Copynumber: 2.6 Consensus size: 127
212395 AAACGGCTAG
* * * * *
212405 TCCATTGCGAGTTAAGTCAATTTTGGATTACTCGAGCCTGATATCCTTCAACGTGAAGTTGAAAT
1 TCCATTGTGAGTTAAGACAATCTTGGATGACTCGAGCCTGATATCCTTCATCGTGAAGTTGAAAT
* * * * *
212470 TTGACTAAAAAACTGTTAG-AAAATAAC-CCATCATTGTTAAGATATGTTGTAGATGA-TTTA-
66 CTGACTAAAAAACT-TTAGAAAAATAACTCC-TCATTGTTAAGATAAGTTATAGATGAGGTGAC
* * * * * *
212530 TCTATTGTGAGTTAAGACAATCTTGGATGACTTGAGACTGATATCATTCATCTTGAAGTTAAAAT
1 TCCATTGTGAGTTAAGACAATCTTGGATGACTCGAGCCTGATATCCTTCATCGTGAAGTTGAAAT
* * * * * * * * ** *
212595 CTGACTCATAATCTTTTGAAAAATAGCTCCTCGTTGTTGAGTTAAGTTATATTTTAGGTGAC
66 CTGACTAAAAAACTTTAGAAAAATAACTCCTCATTGTTAAGATAAGTTATAGATGAGGTGAC
* * *
212657 TCCATTGTGAGTTAAGCCAATCTTTGATGACTCGAGCATGATATCCTTCATCGTGAAGTTGAAAT
1 TCCATTGTGAGTTAAGACAATCTTGGATGACTCGAGCCTGATATCCTTCATCGTGAAGTTGAAAT
212722 CTGACT
66 CTGACT
212728 CGAAATCTAG
Statistics
Matches: 158, Mismatches: 36, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
124 3 0.02
125 89 0.56
126 4 0.03
127 62 0.39
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (127 bp):
TCCATTGTGAGTTAAGACAATCTTGGATGACTCGAGCCTGATATCCTTCATCGTGAAGTTGAAAT
CTGACTAAAAAACTTTAGAAAAATAACTCCTCATTGTTAAGATAAGTTATAGATGAGGTGAC
Found at i:212720 original size:252 final size:255
Alignment explanation
Indices: 212249--212727 Score: 630
Period size: 252 Copynumber: 1.9 Consensus size: 255
212239 TCATTGTTAA
* * * *
212249 GTTAAGCTATGTTGTAAATGAATCCTCTATTATGAGTTGGTCAATCTTGAATGACTTGAGCTTGA
1 GTTAAGATATGTTGTAAATGAATCATCTATTATGAGTTAGACAATCTTGAATGACTTGAGCTTGA
* *
212314 TATCATTCGTCGTGAAGTTAAGATCTGACTCAAAATCTAGGCTGAAAAATAGCTCCACGTTGTTG
66 TATCATTCATCGTGAAGTTAAAATCTGACTCAAAATCTA-GCTGAAAAATAGCTCCACGTTGTTG
* * * *
212379 AGTTAAGCTAAATTGTAAACGGCTAGTCCATTGCGAGTTAAGTCAATTTTGGATTACTCGAGCCT
130 AGTTAAGCTAAATTGTAAACGGCTACTCCATTGCGAGTTAAGCCAATTTTGGATGACTCGAGCAT
*
212444 GATATCCTTCAACGTGAAGTTGAAATTTGACTAAAAAACTGTTAGAAAATAACCCATCATT
195 GATATCCTTCAACGTGAAGTTGAAATCTGACTAAAAAACTGTTAGAAAATAACCCATCATT
* * * * *
212505 GTTAAGATATGTTGTAGATGATTTATCTATTGTGAGTTAAGACAATCTTGGATGACTTGAGAC-T
1 GTTAAGATATGTTGTAAATGAATCATCTATTATGAGTT-AGACAATCTTGAATGACTTGAG-CTT
* * ** *
212569 GATATCATTCATCTTGAAGTTAAAATCTGACTCATAATCT-TTTGAAAAATAGCTCCTCGTTGTT
64 GATATCATTCATCGTGAAGTTAAAATCTGACTCAAAATCTAGCTGAAAAATAGCTCCACGTTGTT
* * * *
212633 GAGTTAAGTTATATT-T-TA-GG-TGACTCCATTGTGAGTTAAGCCAATCTTT-GATGACTCGAG
129 GAGTTAAGCTAAATTGTAAACGGCT-ACTCCATTGCGAGTTAAGCCAAT-TTTGGATGACTCGAG
*
212693 CATGATATCCTTCATCGTGAAGTTGAAATCTGACT
192 CATGATATCCTTCAACGTGAAGTTGAAATCTGACT
212728 CGAAATCTAG
Statistics
Matches: 193, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
251 1 0.01
252 64 0.33
253 4 0.02
254 1 0.01
255 34 0.18
256 32 0.17
257 56 0.29
258 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (255 bp):
GTTAAGATATGTTGTAAATGAATCATCTATTATGAGTTAGACAATCTTGAATGACTTGAGCTTGA
TATCATTCATCGTGAAGTTAAAATCTGACTCAAAATCTAGCTGAAAAATAGCTCCACGTTGTTGA
GTTAAGCTAAATTGTAAACGGCTACTCCATTGCGAGTTAAGCCAATTTTGGATGACTCGAGCATG
ATATCCTTCAACGTGAAGTTGAAATCTGACTAAAAAACTGTTAGAAAATAACCCATCATT
Found at i:212835 original size:132 final size:129
Alignment explanation
Indices: 212136--213077 Score: 639
Period size: 132 Copynumber: 7.3 Consensus size: 129
212126 TATGTCTTAG
* * * * * * *
212136 ATGACTCCTCCATTGCGAGTTAAGACAATCTTGGATGACTTGAGGCTGATATCCTTCATAGTCAG
1 ATGACTACTCCATTGCGAGTTAAGTCAATTTTGGATGACTCGA-GCTGATATCCTTCATCGTGAA
* * * ** ** * **
212201 GTTAAAATTTGACTCATAATTTA-TTAAAAAATAGCTTTTCATTGTTAAGTTAAGCTATGTTGTA
65 GTTGAAATCTGACTCA-AATCTAGTTGGAAAATAGCTCCTCATTGTTGAGTTAAGCTAAATTGTA
212265 A
129 A
* * * ** * * * * * *
212266 ATGAATCCTCTATTATGAGTT-GGTCAATCTTGAATGACTTGAGCTTGATATCATTCGTCGTGAA
1 ATGACTACTCCATTGCGAGTTAAGTCAATTTTGGATGACTCGAGC-TGATATCCTTCATCGTGAA
* * * *
212330 GTT-AAGATCTGACTCAAAATCTAGGCTGAAAAATAGCTCCACGTTGTTGAGTTAAGCTAAATTG
65 GTTGAA-ATCTGACTC-AAATCTA-GTTGGAAAATAGCTCCTCATTGTTGAGTTAAGCTAAATTG
212394 TAA
127 TAA
* * * * *
212397 ACGGCTAGTCCATTGCGAGTTAAGTCAATTTTGGATTACTCGAGCCTGATATCCTTCAACGTGAA
1 ATGACTACTCCATTGCGAGTTAAGTCAATTTTGGATGACTCGAG-CTGATATCCTTCATCGTGAA
* * * * * * **
212462 GTTGAAATTTGACTAAAAAACT-GTTAGAAAATAAC-CCATCA---TT--GTTAAGATATGTTGT
65 GTTGAAATCTGACT-CAAATCTAGTTGGAAAATAGCTCC-TCATTGTTGAGTTAAGCTAAATTGT
*
212520 AG
128 AA
* * * * * * * *
212522 ATGATTTA-TCTATTGTGAGTTAAGACAATCTTGGATGACTTGAGACTGATATCATTCATCTTGA
1 ATGA-CTACTCCATTGCGAGTTAAGTCAATTTTGGATGACTCGAG-CTGATATCCTTCATCGTGA
* * * * * * *
212586 AGTTAAAATCTGACTCATAATCT-TTTGAAAAATAGCTCCTCGTTGTTGAGTTAAGTTATATTTT
64 AGTTGAAATCTGACTCA-AATCTAGTTGGAAAATAGCTCCTCATTGTTGAGTTAAGCTAAATTGT
*
212650 AG
128 AA
* * *
212652 GTG---ACTCCATTGTGAGTTAAGCCAATCTTT-GATGACTCGAGCATGATATCCTTCATCGTGA
1 ATGACTACTCCATTGCGAGTTAAGTCAAT-TTTGGATGACTCGAGC-TGATATCCTTCATCGTGA
* *
212713 AGTTGAAATCTGACTCGAAATCTAGGTTGGAAAATAGCTCCTCATTATTGAGTTAAGCTAAATTA
64 AGTTGAAATCTGACTC-AAATCTA-GTTGGAAAATAGCTCCTCATTGTTGAGTTAAGCTAAATTG
*
212778 CAA
127 TAA
** * * * * * *
212781 ACAACTTCTCCATTGCAAATTAAGTCGATTTTGGATGACTTGAGTCTGATATCCTTCATGGTGAA
1 ATGACTACTCCATTGCGAGTTAAGTCAATTTTGGATGACTCGAG-CTGATATCCTTCATCGTGAA
* * * * **
212846 GTTGAAATCAGACTCAAA-ATATGTTAGAAAATAGCTCCTCATTGTTAAGTTAAGCTATGTTGTA
65 GTTGAAATCTGACTCAAATCTA-GTTGGAAAATAGCTCCTCATTGTTGAGTTAAGCTAAATTGTA
212910 A
129 A
* * * * * * * *
212911 ATGACTACCCCTTTACGAGATAAGTCAA-TCTGGAATGACACGAGACTAATATCCTTCTTCGTGA
1 ATGACTACTCCATTGCGAGTTAAGTCAATTTTGG-ATGACTCGAG-CTGATATCCTTCATCGTGA
* * * *
212975 AGTTAAAATCTGACTCGAAATCTTAGTTGTAAAATATCTCATCGA-TGTTGAGTTAAGCTAAATT
64 AGTTGAAATCTGACTC-AAATC-TAGTTGGAAAATAGCTCCTC-ATTGTTGAGTTAAGCTAAATT
*
213039 -AAA
126 GTAA
* *
213042 TATGACT-CATACATTGTGAGTTAAGTCAATTTTGGA
1 -ATGACTAC-TCCATTGCGAGTTAAGTCAATTTTGGA
213078 AATACTTTCA
Statistics
Matches: 625, Mismatches: 150, Indels: 72
0.74 0.18 0.09
Matches are distributed among these distances:
124 1 0.00
125 89 0.14
126 6 0.01
127 67 0.11
128 9 0.01
129 88 0.14
130 138 0.22
131 58 0.09
132 158 0.25
133 11 0.02
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (129 bp):
ATGACTACTCCATTGCGAGTTAAGTCAATTTTGGATGACTCGAGCTGATATCCTTCATCGTGAAG
TTGAAATCTGACTCAAATCTAGTTGGAAAATAGCTCCTCATTGTTGAGTTAAGCTAAATTGTAA
Found at i:212847 original size:384 final size:385
Alignment explanation
Indices: 212147--212894 Score: 934
Period size: 384 Copynumber: 1.9 Consensus size: 385
212137 TGACTCCTCC
* * * *
212147 ATTGCGAGTTAAGACAATCTTGGATGACTTGAGGCTGATATCCTTCATAGTCAGGTTAAAATTTG
1 ATTGCGAGTTAAGACAATCTTGGATGACTTGAGACTGATATCATTCATAGTCAAGTTAAAATCTG
** * *
212212 ACTCATAATTTATTAAAAAATAGCTTTTCATTGTTAAGTTAAGCTATGTTGTAAATGAATCCTCT
66 ACTCATAATTTATTAAAAAATAGCTCCTCATTGTTAAGTTAAGCTATATTGTAAATGAA-CCTCC
* * * * *
212277 ATTATGAGTTGGTCAATCTTGAATGACTTGAGCTTGATATCATTCGTCGTGAAGTTAAGATCTGA
130 ATTATGAGTTAGCCAATCTTGAATGACTCGAGCATGATATCATTCATCGTGAAGTTAAGATCTGA
* * ** ** *
212342 CTCAAAATCTAGGCTGAAAAATAGCTCCACGTTGTTGAGTTAAGCTAAATTGTAAACGGCTAGTC
195 CTCAAAATCTAGGCTGAAAAATAGCTCCACATTATTGAGTTAAGCTAAATTACAAACAACTACTC
* * * **
212407 CATTGCGAGTTAAGTCAATTTTGGATTACTCGAGCCTGATATCCTTCAACGTGAAGTTGAAATTT
260 CATTGCAAATTAAGTCAATTTTGGATGACTCGAGCCTGATATCCTTCAACGTGAAGTTGAAATCA
212472 GACT-AAAAAACTGTTAGAAAATAAC-CCATCATTGTTAAGATATGTTGTAGATGATTTATCT
325 GACTCAAAAAA-TGTTAGAAAATAACTCC-TCATTGTTAAGATATGTTGTAGATGATTTATCT
* ** *
212533 ATTGTGAGTTAAGACAATCTTGGATGACTTGAGACTGATATCATTCATCTTGAAGTTAAAATCTG
1 ATTGCGAGTTAAGACAATCTTGGATGACTTGAGACTGATATCATTCATAGTCAAGTTAAAATCTG
* * * * * **
212598 ACTCATAATCTT-TTGAAAAATAGCTCCTCGTTGTTGAGTTAAGTTATATTTTAGGTG-A-CTCC
66 ACTCATAAT-TTATTAAAAAATAGCTCCTCATTGTTAAGTTAAGCTATATTGTAAATGAACCTCC
* *
212660 ATTGTGAGTTAAGCCAATCTTTG-ATGACTCGAGCATGATATCCTTCATCGTGAAGTTGAA-ATC
130 ATTATGAGTT-AGCCAATC-TTGAATGACTCGAGCATGATATCATTCATCGTGAAGTT-AAGATC
* * * * *
212723 TGACTCGAAATCTAGGTTGGAAAATAGCTCCTCATTATTGAGTTAAGCTAAATTACAAACAACTT
192 TGACTCAAAATCTAGGCTGAAAAATAGCTCCACATTATTGAGTTAAGCTAAATTACAAACAACTA
* * * **
212788 CTCCATTGCAAATTAAGTCGATTTTGGATGACTTGAGTCTGATATCCTTCATGGTGAAGTTGAAA
257 CTCCATTGCAAATTAAGTCAATTTTGGATGACTCGAGCCTGATATCCTTCAACGTGAAGTTGAAA
* *
212853 TCAGACTCAAAATATGTTAGAAAATAGCTCCTCATTGTTAAG
322 TCAGACTCAAAAAATGTTAGAAAATAACTCCTCATTGTTAAG
212895 TTAAGCTATG
Statistics
Matches: 306, Mismatches: 50, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
383 12 0.04
384 178 0.58
385 13 0.04
386 101 0.33
387 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (385 bp):
ATTGCGAGTTAAGACAATCTTGGATGACTTGAGACTGATATCATTCATAGTCAAGTTAAAATCTG
ACTCATAATTTATTAAAAAATAGCTCCTCATTGTTAAGTTAAGCTATATTGTAAATGAACCTCCA
TTATGAGTTAGCCAATCTTGAATGACTCGAGCATGATATCATTCATCGTGAAGTTAAGATCTGAC
TCAAAATCTAGGCTGAAAAATAGCTCCACATTATTGAGTTAAGCTAAATTACAAACAACTACTCC
ATTGCAAATTAAGTCAATTTTGGATGACTCGAGCCTGATATCCTTCAACGTGAAGTTGAAATCAG
ACTCAAAAAATGTTAGAAAATAACTCCTCATTGTTAAGATATGTTGTAGATGATTTATCT
Found at i:213042 original size:130 final size:128
Alignment explanation
Indices: 212548--213043 Score: 337
Period size: 130 Copynumber: 3.8 Consensus size: 128
212538 GAGTTAAGAC
** * * * * *
212548 AATCTTGGATGACTTGAGACTGATATCATTCATCTTGAAGTTAAAATCTGACTC-ATAATCT-TT
1 AATC-TGGATGACACGAGACTAATATCCTTCATCGTGAAGTTGAAATCTGACTCGA-AATCTAGT
* * * * ** * *** *
212611 TGAAAAATAGCTCCTCGTTGTTGAGTTAAGTTATATT--TTAGGTGACTCCATTGTGAGTTAAG-
64 TG-AAAATAGCTCCTCATTGTTGAGTTAAGCTAAATTAAATAACT-ACCCCATTACAAATTAAGT
*
212673 CC
127 CG
* * *
212675 AATCTTTGATGACTCGAG-CATGATATCCTTCATCGTGAAGTTGAAATCTGACTCGAAATCTAGG
1 AATC-TGGATGACACGAGAC-TAATATCCTTCATCGTGAAGTTGAAATCTGACTCGAAATCTA-G
* * * * *
212739 TTGGAAAATAGCTCCTCATTATTGAGTTAAGCTAAATTACAAACAACTTCTCCATTGCAAATTAA
63 TT-GAAAATAGCTCCTCATTGTTGAGTTAAGCTAAATT--AAATAACTACCCCATTACAAATTAA
212804 GTCG
125 GTCG
* * ** * * * * * *
212808 ATTTTGGATGACTTGAGTCTGATATCCTTCATGGTGAAGTTGAAATCAGACTCAAAATAT-GTTA
1 AATCTGGATGACACGAGACTAATATCCTTCATCGTGAAGTTGAAATCTGACTCGAAATCTAGTT-
* ** * * *
212872 GAAAATAGCTCCTCATTGTTAAGTTAAGCTATGTTGTAAATGACTACCCCTTTACGAGA-TAAGT
65 GAAAATAGCTCCTCATTGTTGAGTTAAGCTA-AAT-TAAATAACTACCCCATTAC-AAATTAAGT
212936 C-
127 CG
* *
212937 AATCTGGAATGACACGAGACTAATATCCTTCTTCGTGAAGTTAAAATCTGACTCGAAATCTTAGT
1 AATCTGG-ATGACACGAGACTAATATCCTTCATCGTGAAGTTGAAATCTGACTCGAAATC-TAGT
* *
213002 TGTAAAATATCTCATCGA-TGTTGAGTTAAGCTAAATTAAATA
64 TG-AAAATAGCTCCTC-ATTGTTGAGTTAAGCTAAATTAAATA
213044 TGACTCATAC
Statistics
Matches: 293, Mismatches: 57, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
126 1 0.00
127 52 0.18
128 1 0.00
129 37 0.13
130 98 0.33
131 6 0.02
132 91 0.31
133 7 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (128 bp):
AATCTGGATGACACGAGACTAATATCCTTCATCGTGAAGTTGAAATCTGACTCGAAATCTAGTTG
AAAATAGCTCCTCATTGTTGAGTTAAGCTAAATTAAATAACTACCCCATTACAAATTAAGTCG
Found at i:213068 original size:262 final size:259
Alignment explanation
Indices: 212533--213077 Score: 602
Period size: 262 Copynumber: 2.1 Consensus size: 259
212523 TGATTTATCT
* * * *
212533 ATTGTGAGTTAAGACAATCTTGGATGACTTGAGACTGATATCATTCATCTTGAAGTTAAAATCTG
1 ATTGTGAGTTAAGTCAATTTTGGATGACTTGAGACTGATATCATTCATCGTGAAGTTAAAATCAG
* * * * * * * **
212598 ACTCATAATCTTTTGAAAAATAGCTCCTCGTTGTTGAGTTAAGTTATATTTTAGGTGACTCCATT
66 ACTCAAAATATTTAGAAAAATAGCTCCTCATTGTTAAGTTAAGCTATATTGTAAATGACTCCATT
* * * * *
212663 GTGAGTTAAGCCAATCTTTGATGACTCGAGCATGATATCCTTCATCGTGAAGTTGAAATCTGACT
131 GTGAGATAAGCCAATCTTGGATGACACGAGCATAATATCCTTCATCGTGAAGTTAAAATCTGACT
* *
212728 CGAAATCTAGGTTGGAAAATAGCTCCTCATTATTGAGTTAAGCTAAATTACAAACAACTTCTCC
196 CGAAATCTAGGTTGGAAAATAGCTCATCATTATTGAGTTAAGCTAAATTACAAACAACTTCTAC
** * * * * * *
212792 ATTGCAAATTAAGTCGATTTTGGATGACTTGAGTCTGATATCCTTCATGGTGAAGTTGAAATCAG
1 ATTGTGAGTTAAGTCAATTTTGGATGACTTGAGACTGATATCATTCATCGTGAAGTTAAAATCAG
*
212857 ACTCAAAATATGTTAG-AAAATAGCTCCTCATTGTTAAGTTAAGCTATGTTGTAAATGACTACCC
66 ACTCAAAATAT-TTAGAAAAATAGCTCCTCATTGTTAAGTTAAGCTATATTGTAAATGACT--CC
* * *
212921 CTT-TACGAGATAAGTCAATC-TGGAATGACACGAG-ACTAATATCCTTCTTCGTGAAGTTAAAA
128 ATTGT--GAGATAAGCCAATCTTGG-ATGACACGAGCA-TAATATCCTTCATCGTGAAGTTAAAA
* * * *
212983 TCTGACTCGAAATCTTA-GTTGTAAAATATCTCATCGA-TGTTGAGTTAAGCTAAATTA-AATAT
189 TCTGACTCGAAATC-TAGGTTGGAAAATAGCTCATC-ATTATTGAGTTAAGCTAAATTACAA-AC
*
213045 GAC-TCATAC
251 AACTTC-TAC
213054 ATTGTGAGTTAAGTCAATTTTGGA
1 ATTGTGAGTTAAGTCAATTTTGGA
213078 AATACTTTCA
Statistics
Matches: 234, Mismatches: 41, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
259 99 0.42
260 4 0.02
261 11 0.05
262 117 0.50
263 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (259 bp):
ATTGTGAGTTAAGTCAATTTTGGATGACTTGAGACTGATATCATTCATCGTGAAGTTAAAATCAG
ACTCAAAATATTTAGAAAAATAGCTCCTCATTGTTAAGTTAAGCTATATTGTAAATGACTCCATT
GTGAGATAAGCCAATCTTGGATGACACGAGCATAATATCCTTCATCGTGAAGTTAAAATCTGACT
CGAAATCTAGGTTGGAAAATAGCTCATCATTATTGAGTTAAGCTAAATTACAAACAACTTCTAC
Found at i:215167 original size:13 final size:14
Alignment explanation
Indices: 215151--215179 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
215141 AAACACATGC
215151 AAAAAAACA-AATA
1 AAAAAAACATAATA
215164 AAAAAAACATAATA
1 AAAAAAACATAATA
215178 AA
1 AA
215180 CAAGTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAAACATAATA
Found at i:225625 original size:2 final size:2
Alignment explanation
Indices: 225618--225660 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
225608 TTCACCAACT
225618 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
225660 T
1 T
225661 CACTGCCATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:229380 original size:3 final size:3
Alignment explanation
Indices: 229372--229444 Score: 85
Period size: 3 Copynumber: 24.3 Consensus size: 3
229362 GTATTTGTAT
* * * * *
229372 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATG ATA GTA TTT TTAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
229417 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
229445 CAGGACGAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.95
4 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:230818 original size:13 final size:13
Alignment explanation
Indices: 230800--230825 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
230790 AAAAAAGAAC
230800 AAAGTAAACAAAT
1 AAAGTAAACAAAT
230813 AAAGTAAACAAAT
1 AAAGTAAACAAAT
230826 CGGTGAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAGTAAACAAAT
Found at i:231814 original size:12 final size:12
Alignment explanation
Indices: 231797--231833 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
231787 CGGGATCACA
231797 TATGTATATATG
1 TATGTATATATG
*
231809 TATGTATATATA
1 TATGTATATATG
*
231821 TATATATATATG
1 TATGTATATATG
231833 T
1 T
231834 GAGTGTGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (12 bp):
TATGTATATATG
Found at i:236238 original size:2 final size:2
Alignment explanation
Indices: 236231--236278 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
236221 ATTAAAAGGC
236231 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
236273 TA TA TA
1 TA TA TA
236279 AGTACCCACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:236710 original size:32 final size:32
Alignment explanation
Indices: 236672--236732 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
236662 ACCCAAATTT
236672 TTTTCCTTAAAACCATACTCACTTCAAAAAAA
1 TTTTCCTTAAAACCATACTCACTTCAAAAAAA
236704 TTTTCCTTAAAACCATACTCACTTCAAAA
1 TTTTCCTTAAAACCATACTCACTTCAAAA
236733 TATTTATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (32 bp):
TTTTCCTTAAAACCATACTCACTTCAAAAAAA
Found at i:238413 original size:2 final size:2
Alignment explanation
Indices: 238406--238468 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
238396 GAAGGCAACA
238406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
238448 AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
238469 GATAAGTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:241936 original size:19 final size:19
Alignment explanation
Indices: 241914--241968 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
241904 GACTGTTTCC
241914 TACAGTCTGTTTTCTACTA
1 TACAGTCTGTTTTCTACTA
*
241933 TACAGTCTGTTTTCTTTCTA
1 TACAGTCTGTTTTC-TACTA
241953 T--AGTCTGATTTTCTAC
1 TACAGTCTG-TTTTCTAC
241969 ATGGTATCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.25
19 19 0.59
20 5 0.16
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (19 bp):
TACAGTCTGTTTTCTACTA
Found at i:245542 original size:26 final size:27
Alignment explanation
Indices: 245506--245568 Score: 110
Period size: 26 Copynumber: 2.3 Consensus size: 27
245496 AGAATTGGAC
245506 TTAGATGACAAGAAGAATTTTGAGATTT
1 TTAG-TGACAAGAAGAATTTTGAGATTT
245534 TT-GTGACAAGAAGAATTTTGAGATTT
1 TTAGTGACAAGAAGAATTTTGAGATTT
245560 TTAGTGACA
1 TTAGTGACA
245569 GTCAATCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 25 0.74
27 7 0.21
28 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (27 bp):
TTAGTGACAAGAAGAATTTTGAGATTT
Found at i:246379 original size:18 final size:19
Alignment explanation
Indices: 246340--246391 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
246330 TGTTTCCTAC
246340 AGTCTGTTTTCTACTATAT
1 AGTCTGTTTTCTACTATAT
* *
246359 AGTCTGTTTTCT-TTCTAT
1 AGTCTGTTTTCTACTATAT
246377 AGTCTGATTTTCTAC
1 AGTCTG-TTTTCTAC
246392 AGTTATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (19 bp):
AGTCTGTTTTCTACTATAT
Found at i:254368 original size:16 final size:15
Alignment explanation
Indices: 254337--254372 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
254327 TTTTATGAAT
254337 ATAAAAAATAAAATA
1 ATAAAAAATAAAATA
*
254352 ATAAAACAATAATATA
1 ATAAAA-AATAAAATA
254368 ATAAA
1 ATAAA
254373 TCTAGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
ATAAAAAATAAAATA
Found at i:262887 original size:17 final size:17
Alignment explanation
Indices: 262865--262904 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
262855 TTCAAGTCAT
262865 CACCCTGTACACTTCTA
1 CACCCTGTACACTTCTA
262882 CACCCTGTACACTTCTA
1 CACCCTGTACACTTCTA
262899 CACCCT
1 CACCCT
262905 TCATATGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.45, G:0.05, T:0.28
Consensus pattern (17 bp):
CACCCTGTACACTTCTA
Found at i:286333 original size:59 final size:59
Alignment explanation
Indices: 286237--286359 Score: 194
Period size: 59 Copynumber: 2.1 Consensus size: 59
286227 GAGAAAGGAC
286237 TTGTCAATGCTTCTTTATATGACCTTCCATCGATAAACTTGATGAAAAACTCCCTTCTG
1 TTGTCAATGCTTCTTTATATGACCTTCCATCGATAAACTTGATGAAAAACTCCCTTCTG
* * * *
286296 TTGTCAATGCTTCTTTATATGACCCTT-TATCGTTAAACTTGTTGAAAAACTCCCTTTTG
1 TTGTCAATGCTTCTTTATATGA-CCTTCCATCGATAAACTTGATGAAAAACTCCCTTCTG
286355 TTGTC
1 TTGTC
286360 GGCGTTCCTA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
59 55 0.93
60 4 0.07
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (59 bp):
TTGTCAATGCTTCTTTATATGACCTTCCATCGATAAACTTGATGAAAAACTCCCTTCTG
Found at i:295645 original size:14 final size:14
Alignment explanation
Indices: 295628--295656 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
295618 TTTTTACAAT
295628 TATTCATTAATTTC
1 TATTCATTAATTTC
295642 TATTCATTAATTTC
1 TATTCATTAATTTC
295656 T
1 T
295657 CCAAGGTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTCATTAATTTC
Found at i:296499 original size:20 final size:21
Alignment explanation
Indices: 296467--296510 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
296457 GTGCCTGTAA
*
296467 AAGGGGAAGAAGGTCAATTTC
1 AAGGGGAAGAAGGCCAATTTC
296488 AAGGGG-AGAAGGCCAATTTC
1 AAGGGGAAGAAGGCCAATTTC
296508 AAG
1 AAG
296511 ATCGAGTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.39, C:0.11, G:0.34, T:0.16
Consensus pattern (21 bp):
AAGGGGAAGAAGGCCAATTTC
Found at i:297248 original size:25 final size:25
Alignment explanation
Indices: 297220--297271 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
297210 AACTATAAAA
*
297220 GAAAAATAAATTCACATCATCTCAT
1 GAAAAAAAAATTCACATCATCTCAT
297245 GAAAAAAAAATTCACATCATCTCAT
1 GAAAAAAAAATTCACATCATCTCAT
297270 GA
1 GA
297272 TTGTCCAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (25 bp):
GAAAAAAAAATTCACATCATCTCAT
Found at i:299139 original size:24 final size:25
Alignment explanation
Indices: 299111--299166 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
299101 TTACAGAATC
*
299111 TTAGGCTA-ATTGTTAGGCTGATTA
1 TTAGGCTAGATTCTTAGGCTGATTA
*
299135 TTAGGC-AGATTCTTAGGGTGATTA
1 TTAGGCTAGATTCTTAGGCTGATTA
*
299159 TTATGCTA
1 TTAGGCTA
299167 CCTAGTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 25 0.93
25 1 0.04
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (25 bp):
TTAGGCTAGATTCTTAGGCTGATTA
Found at i:299145 original size:12 final size:12
Alignment explanation
Indices: 299111--299161 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
299101 TTACAGAATC
* *
299111 TTAGGCTAATTG
1 TTAGGCTGATTA
299123 TTAGGCTGATTA
1 TTAGGCTGATTA
* *
299135 TTAGGCAGATTC
1 TTAGGCTGATTA
*
299147 TTAGGGTGATTA
1 TTAGGCTGATTA
299159 TTA
1 TTA
299162 TGCTACCTAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.41
Consensus pattern (12 bp):
TTAGGCTGATTA
Found at i:301944 original size:60 final size:60
Alignment explanation
Indices: 301870--301984 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
301860 AAATTAATCC
* * * *
301870 TTAATCTTTTGAATATTTTAGATTCATCCTTAAATTATATCCTTCATTCTAAATTAGTTT
1 TTAAACTTTCGAATATTTTAGATTCATCCTTAAATCATAACCTTCATTCTAAATTAGTTT
*
301930 TTAAACTTTCGAATATTTTAGATTCATCCTTAAATCGTAACCTTCATTCTAAATT
1 TTAAACTTTCGAATATTTTAGATTCATCCTTAAATCATAACCTTCATTCTAAATT
301985 GATCCCCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.48
Consensus pattern (60 bp):
TTAAACTTTCGAATATTTTAGATTCATCCTTAAATCATAACCTTCATTCTAAATTAGTTT
Found at i:301963 original size:29 final size:29
Alignment explanation
Indices: 301853--301963 Score: 73
Period size: 29 Copynumber: 3.8 Consensus size: 29
301843 AATTTTATCT
* * *
301853 ATATTTTAAATTAATCCTTAATCTTTTGA
1 ATATTTTAAATTCATCCTTAAACTTTCGA
* * *
301882 ATATTTTAGATTCATCCTTAAATTATATC-C
1 ATATTTTAAATTCATCCTTAAACT-T-TCGA
* * **
301912 TTCATTCTAAATT-AGTTTTTAAACTTTCGA
1 AT-ATTTTAAATTCA-TCCTTAAACTTTCGA
*
301942 ATATTTTAGATTCATCCTTAAA
1 ATATTTTAAATTCATCCTTAAA
301964 TCGTAACCTT
Statistics
Matches: 58, Mismatches: 18, Indels: 12
0.66 0.20 0.14
Matches are distributed among these distances:
29 36 0.62
30 6 0.10
31 16 0.28
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.49
Consensus pattern (29 bp):
ATATTTTAAATTCATCCTTAAACTTTCGA
Found at i:302242 original size:31 final size:29
Alignment explanation
Indices: 302202--302284 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 29
302192 ATTGGAATGT
302202 TCAAAAGTTTAAGGACTAATTTAGAATAAGTC
1 TCAAAAGTTTAAGGACTAATTTAGAAT-A--C
* *
302234 TC-ATAGTTTAAGGA-TAAAATTAGAATAC
1 TCAAAAGTTTAAGGACT-AATTTAGAATAC
*
302262 TCAAAAGTTTAAGGACCAATTTA
1 TCAAAAGTTTAAGGACTAATTTA
302285 AAATGAGAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
28 3 0.07
29 16 0.37
30 2 0.05
31 20 0.47
32 2 0.05
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (29 bp):
TCAAAAGTTTAAGGACTAATTTAGAATAC
Done.