Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007790.1 Hibiscus syriacus cultivar Beakdansim tig00110076_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: 2956777
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:916350 original size:39 final size:38
Alignment explanation
Indices: 916307--916525 Score: 258
Period size: 39 Copynumber: 5.6 Consensus size: 38
916297 TCCTTTTTTC
* * *
916307 TCTTCAGATTATGAACTCTTTCTGCCTCTTCAAACTAGT
1 TCTTCAGATTATGAACTCTTT-TTCCTCTTCAGACGAGT
* * * *
916346 TCTTCAAATTATGAACTCCTTCTGCCTCTTCAGATGAGT
1 TCTTCAGATTATGAACT-CTTTTTCCTCTTCAGACGAGT
*
916385 TCTTCAGATTATGAACTCATTTTTTTCTCTTCAGACGAGT
1 TCTTCAGATTATGAACTC--TTTTTCCTCTTCAGACGAGT
*
916425 TCTTCAGATTATGAACACCTTTTTCCTCTTCAGACGAGT
1 TCTTCAGATTATGAAC-TCTTTTTCCTCTTCAGACGAGT
* * *
916464 TCTTCAAATTATGAACTCCTTTTTTCTCTTCGGACGAGT
1 TCTTCAGATTATGAACT-CTTTTTCCTCTTCAGACGAGT
* *
916503 TATTCAGATTATGAACTCCTTTT
1 TCTTCAGATTATGAACTCTTTTT
916526 GGAAATGTTT
Statistics
Matches: 156, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
38 6 0.04
39 114 0.73
40 35 0.22
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (38 bp):
TCTTCAGATTATGAACTCTTTTTCCTCTTCAGACGAGT
Found at i:916437 original size:79 final size:78
Alignment explanation
Indices: 916307--916523 Score: 299
Period size: 79 Copynumber: 2.8 Consensus size: 78
916297 TCCTTTTTTC
* ** * * *
916307 TCTTCAGATTATGAACTCTTTCTGCCTCTTCAAACTAGTTCTTCAAATTATGAACTCCTTCTGCC
1 TCTTCAGATTATGAACTCTTTTTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTGCC
*
916372 TCTTCAGATGAGT
66 TCTTCAGACGAGT
* * *
916385 TCTTCAGATTATGAACTCATTTTTTTCTCTTCAGACGAGTTCTTCAGATTATGAACACCTTTTTC
1 TCTTCAGATTATGAACTC-TTTTTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTGC
916450 CTCTTCAGACGAGT
65 CTCTTCAGACGAGT
* * * *
916464 TCTTCAAATTATGAACTCCTTTTTTCTCTTCGGACGAGTTATTCAGATTATGAACTCCTT
1 TCTTCAGATTATGAACTCTTTTTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTT
916524 TTGGAAATGT
Statistics
Matches: 123, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
78 56 0.46
79 67 0.54
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (78 bp):
TCTTCAGATTATGAACTCTTTTTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCTGCC
TCTTCAGACGAGT
Found at i:916515 original size:118 final size:118
Alignment explanation
Indices: 916307--916525 Score: 323
Period size: 118 Copynumber: 1.9 Consensus size: 118
916297 TCCTTTTTTC
* *
916307 TCTTCAGATTATGAACTCTTTCTGCCTCTTCAAACTAGTTCTTCAAATTATGAACTCCTTCTGCC
1 TCTTCAGATTATGAACCCTTTCTGCCTCTTCAAACGAGTTCTTCAAATTATGAACTCCTTCTGCC
* *
916372 TCTTCAGATGAGTTCTTCAGATTATGAACTCATTTTTTTCTCTTCAGACGAGT
66 TCTTCAGACGAGTTATTCAGATTATGAACTCATTTTTTTCTCTTCAGACGAGT
* * * **
916425 TCTTCAGATTATGAACACCTTT-TTCCTCTTCAGACGAGTTCTTCAAATTATGAACTCCTTTTTT
1 TCTTCAGATTATGAAC-CCTTTCTGCCTCTTCAAACGAGTTCTTCAAATTATGAACTCCTTCTGC
* *
916489 CTCTTCGGACGAGTTATTCAGATTATGAACTCCTTTT
65 CTCTTCAGACGAGTTATTCAGATTATGAACTCATTTT
916526 GGAAATGTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
118 85 0.96
119 4 0.04
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (118 bp):
TCTTCAGATTATGAACCCTTTCTGCCTCTTCAAACGAGTTCTTCAAATTATGAACTCCTTCTGCC
TCTTCAGACGAGTTATTCAGATTATGAACTCATTTTTTTCTCTTCAGACGAGT
Found at i:916641 original size:47 final size:47
Alignment explanation
Indices: 916567--916919 Score: 314
Period size: 47 Copynumber: 7.7 Consensus size: 47
916557 GATAAATTGT
* * *
916567 TTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCGGAGGC
1 TTTTTGAAAACATCCTGCACTGAAGGTCTTATGAATGACCCGAAGGC
* * *
916614 TTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCAGAAGGC
1 TTTTTGAAAACATCCTGCACTGAAGGTCTTATGAATGACCCGAAGGC
* * * * ** ***
916661 -TTTT---AACATCTTGCACCGGAGGTCTTA-CAGATGACCAAAATTTT
1 TTTTTGAAAACATCCTGCACTGAAGGTCTTATGA-ATGACCCGAA-GGC
* * * * *
916705 TTTTTG-AAACATCCTGCACTGTAGGTCTTATGGATGGCCCAAATGAC
1 TTTTTGAAAACATCCTGCACTGAAGGTCTTATGAATGACCCGAA-GGC
* *
916752 TTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGC
1 TTTTTGAAAACATCCTGCACTGAAGGTCTTATGAATGACCCGAAGGC
* *
916799 TTTTTGAAAACATCATGCACTGAAGGTCTTA-CAGATGACCCGAAGG-
1 TTTTTGAAAACATCCTGCACTGAAGGTCTTATGA-ATGACCCGAAGGC
* * ** *
916845 -TTTTGTAAACATCATGCACTGAAGGTCTTACAAATGACCCGAATG-
1 TTTTTGAAAACATCCTGCACTGAAGGTCTTATGAATGACCCGAAGGC
* *
916890 -TTTTGAAAACATCATGCACTAAAGGTCTTA
1 TTTTTGAAAACATCCTGCACTGAAGGTCTTA
916920 CAGATGTGGG
Statistics
Matches: 260, Mismatches: 37, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
43 29 0.11
45 72 0.28
46 5 0.02
47 119 0.46
48 35 0.13
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (47 bp):
TTTTTGAAAACATCCTGCACTGAAGGTCTTATGAATGACCCGAAGGC
Found at i:916770 original size:138 final size:140
Alignment explanation
Indices: 916560--916919 Score: 396
Period size: 137 Copynumber: 2.6 Consensus size: 140
916550 CAAGCGAGAT
** *
916560 AAATTGTTTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCGGAGGCTTTTTGAAAAC
1 AAATTGTTTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCAAAGACTTTTTGAAAAC
* *
916625 ATCCTGCACTGTAGGTCTTATGGATGACCAGAAGGC-TTTT-AACATCTTGCACCGGAGGTCTTA
66 ATCCTGCACTGTAGGTCTTATGGATGACCAGAAGGCTTTTTAAACATCATGCACCGAAGGTCTTA
916688 CAGATGACCA
131 CAGATGACCA
** * * * *
916698 AAATT-TTTTTTTGAAACATCCTGCACTGTAGGTCTTATGGATGGCCCAAATGACTTTTTGAAAA
1 AAATTGTTTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCAAA-GACTTTTTGAAAA
* *
916762 CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTC
65 CATCCTGCACTGTAGGTCTTATGGATGACCAGAAGGCTTTTT--AAACATCATGCACCGAAGGTC
*
916827 TTACAGATGACCC
128 TTACAGATGACCA
* * * ** ** *
916840 GAA-GGTTTTGT--AAACATCATGCACTGAAGGTCTTACAAATGACCC---GAATGTTTTGAAAA
1 AAATTGTTTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCAAAGACT-TTTTGAAAA
* **
916899 CATCATGCACTAAAGGTCTTA
65 CATCCTGCACTGTAGGTCTTA
916920 CAGATGTGGG
Statistics
Matches: 188, Mismatches: 27, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
136 3 0.02
137 64 0.34
138 53 0.28
139 4 0.02
140 28 0.15
142 36 0.19
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (140 bp):
AAATTGTTTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCAAAGACTTTTTGAAAAC
ATCCTGCACTGTAGGTCTTATGGATGACCAGAAGGCTTTTTAAACATCATGCACCGAAGGTCTTA
CAGATGACCA
Found at i:916902 original size:185 final size:183
Alignment explanation
Indices: 916567--916919 Score: 465
Period size: 185 Copynumber: 1.9 Consensus size: 183
916557 GATAAATTGT
* *
916567 TTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCGGAGGCTTTTTGAAAACATCCTGC
1 TTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCGAAGGCTTTTTGAAAACATCATGC
* ** * * *
916632 ACTGTAGGTCTTATGGATGACCAGAAGGCTTTTAACATCTTGCACCGGAGGTCTTACAGATGACC
66 ACTGAAGGTCTTACAGATGACCAGAAGGCTTTTAACATCATGCACCGAAGGTCTTACAAATGACC
* * **
916697 AAAATTTTTTTTTGAAACATCCTGCACTGTAGGTCTTATGGATGGCCCAAATGAC
131 AAAA--TTGTTTTGAAACATCATGCACTAAAGGTCTTATGGATGGCCCAAATGAC
* * * *
916752 TTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAAAACATCATGC
1 TTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCGAAGGCTTTTTGAAAACATCATGC
* * *
916817 ACTGAAGGTCTTACAGATGACCCGAAGGTTTTGTAAACATCATGCACTGAAGGTCTTACAAATGA
66 ACTGAAGGTCTTACAGATGACCAGAAGGCTTT-T-AACATCATGCACCGAAGGTCTTACAAATGA
**
916882 CCCGAA-TGTTTTGAAAACATCATGCACTAAAGGTCTTA
129 CCAAAATTGTTTTG-AAACATCATGCACTAAAGGTCTTA
916920 CAGATGTGGG
Statistics
Matches: 144, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
184 6 0.04
185 107 0.74
186 1 0.01
187 30 0.21
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (183 bp):
TTTTTCAAAACATCCGGCACTGAAGGTCTTATGAATGACCCGAAGGCTTTTTGAAAACATCATGC
ACTGAAGGTCTTACAGATGACCAGAAGGCTTTTAACATCATGCACCGAAGGTCTTACAAATGACC
AAAATTGTTTTGAAACATCATGCACTAAAGGTCTTATGGATGGCCCAAATGAC
Found at i:917716 original size:22 final size:22
Alignment explanation
Indices: 917571--917713 Score: 162
Period size: 22 Copynumber: 6.5 Consensus size: 22
917561 TAAAGCTTTT
* *
917571 ATCTTTGAAAAGATAATCTATC
1 ATCTTTGAAGAGAGAATCTATC
*
917593 ATATTTGAAGAGAGAATCTATC
1 ATCTTTGAAGAGAGAATCTATC
* * * *
917615 ATGTTTGTAGAGAGGATATATC
1 ATCTTTGAAGAGAGAATCTATC
* *
917637 ATCATTGAAGAGAGGATCTATC
1 ATCTTTGAAGAGAGAATCTATC
* *
917659 ATCTTTGAAGAGAGGACCTATC
1 ATCTTTGAAGAGAGAATCTATC
*
917681 ATCTTTGAAGA-ATGAATTTATC
1 ATCTTTGAAGAGA-GAATCTATC
917703 ATCTTTGAAGA
1 ATCTTTGAAGA
917714 ATGTAGATGT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
21 1 0.01
22 103 0.99
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (22 bp):
ATCTTTGAAGAGAGAATCTATC
Found at i:926328 original size:29 final size:27
Alignment explanation
Indices: 926275--926338 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
926265 TTATTTTACC
* *
926275 CTAAATATATAAAACATACAAGT-AATGA
1 CTAAAT-TATAAAAAATAAAAGTAAAT-A
926303 CTAAATTATAAATAAATAAAATGTAAATA
1 CTAAATTATAAA-AAATAAAA-GTAAATA
926332 CTAAATT
1 CTAAATT
926339 GAAATAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 6 0.19
28 12 0.39
29 10 0.32
30 3 0.10
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.30
Consensus pattern (27 bp):
CTAAATTATAAAAAATAAAAGTAAATA
Found at i:928329 original size:21 final size:21
Alignment explanation
Indices: 928305--928344 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
928295 TGATGGAAAG
928305 GTTAAGACCTTTCGATGAATA
1 GTTAAGACCTTTCGATGAATA
** *
928326 GTTAATTCCTTTTGATGAA
1 GTTAAGACCTTTCGATGAA
928345 GAGATTTGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (21 bp):
GTTAAGACCTTTCGATGAATA
Found at i:934359 original size:11 final size:11
Alignment explanation
Indices: 934323--934360 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
934313 CAATTGGACA
934323 AAATTAAGTCT
1 AAATTAAGTCT
*
934334 ATATTAA-TCT
1 AAATTAAGTCT
934344 AAAATTAAGTCT
1 -AAATTAAGTCT
934356 AAATT
1 AAATT
934361 CATCCTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (11 bp):
AAATTAAGTCT
Found at i:934905 original size:33 final size:32
Alignment explanation
Indices: 934863--934927 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
934853 ATCAATCCTT
* * *
934863 ATCATTTTCATTC-TTTATTTTATTTATCATTC
1 ATCATTTTCAGTCATATA-TTTATTCATCATTC
934895 ATCATCTTTCAGTCATATATTTATTCATCATTC
1 ATCAT-TTTCAGTCATATATTTATTCATCATTC
934928 TTTTAAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 5 0.18
33 20 0.71
34 3 0.11
ACGTcount: A:0.25, C:0.18, G:0.02, T:0.55
Consensus pattern (32 bp):
ATCATTTTCAGTCATATATTTATTCATCATTC
Found at i:935800 original size:12 final size:12
Alignment explanation
Indices: 935783--935807 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
935773 ATTTATTATT
935783 AAAAAACAAAAA
1 AAAAAACAAAAA
935795 AAAAAACAAAAA
1 AAAAAACAAAAA
935807 A
1 A
935808 TTATAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:935867 original size:57 final size:58
Alignment explanation
Indices: 935805--935933 Score: 151
Period size: 57 Copynumber: 2.3 Consensus size: 58
935795 AAAAAACAAA
*
935805 AAATTATAATAAAAGGCTAAA-C-TTTT-GAAATTTACAACAAAGGACAAAATATT-TTAG
1 AAATTATAATAAAAGGATAAATCTTTTTAGAAA-TTACAACAAAGG--AAAATATTATTAG
* * * *
935862 AAATTATAAT-GAAGGATAAATCTTTTTAGAAATTACAATAAAGGAGAATTTTATTAG
1 AAATTATAATAAAAGGATAAATCTTTTTAGAAATTACAACAAAGGAAAATATTATTAG
935919 AAATTATAATAAAAG
1 AAATTATAATAAAAG
935934 ACAAAAGTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
56 14 0.23
57 25 0.41
58 18 0.30
59 4 0.07
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (58 bp):
AAATTATAATAAAAGGATAAATCTTTTTAGAAATTACAACAAAGGAAAATATTATTAG
Found at i:935876 original size:29 final size:28
Alignment explanation
Indices: 935827--936056 Score: 105
Period size: 29 Copynumber: 7.9 Consensus size: 28
935817 AAGGCTAAAC
*
935827 TTTT-GAAATTTACAACAAAGGACAAAATA
1 TTTTAGAAA-TTACAATAAAGGA-AAAATA
* * * *
935856 TTTTAGAAATTATAATGAAGGATAAATCT
1 TTTTAGAAATTACAATAAAGGAAAAAT-A
* *
935885 TTTTAGAAATTACAATAAAGG-AGAATT
1 TTTTAGAAATTACAATAAAGGAAAAATA
* *
935912 TTATTAGAAATTATAATAAAAGACAAAAGTA
1 TT-TTAGAAATTACAATAAAGGA-AAAA-TA
* *
935943 -TTTATAAATTACAAT-AAGGTACGAAAGTA
1 TTTTAGAAATTACAATAAAGG-A--AAAATA
** *
935972 TTTATCTAAATTACAATAAAGTACAAAACTA
1 TTT-TAGAAATTACAATAAAGGA-AAAA-TA
* *
936003 TTTCT--AAATTAAAATAAAGTACAAAA-A
1 TTT-TAGAAATTACAATAAAGGA-AAAATA
* * *
936030 TGTTTATAAATTAAAATAAAGTAAAAA
1 T-TTTAGAAATTACAATAAAGGAAAAA
936057 AACTATTTCT
Statistics
Matches: 162, Mismatches: 24, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
27 6 0.04
28 33 0.20
29 84 0.52
30 16 0.10
31 20 0.12
32 3 0.02
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.32
Consensus pattern (28 bp):
TTTTAGAAATTACAATAAAGGAAAAATA
Found at i:935929 original size:28 final size:29
Alignment explanation
Indices: 935805--935931 Score: 104
Period size: 29 Copynumber: 4.4 Consensus size: 29
935795 AAAAAACAAA
*
935805 AAATTATAATAAAAGGCTAAA-C-TTTT-G
1 AAATTATAAT-AAAGGATAAATCTTTTTAG
* * * *
935832 AAATTTACAACAAAGGACAAAAT-ATTTTAG
1 AAA-TTATAATAAAGGA-TAAATCTTTTTAG
*
935862 AAATTATAATGAAGGATAAATCTTTTTAG
1 AAATTATAATAAAGGATAAATCTTTTTAG
* *
935891 AAATTACAATAAAGGA-GAAT-TTTATTAG
1 AAATTATAATAAAGGATAAATCTTT-TTAG
935919 AAATTATAATAAA
1 AAATTATAATAAA
935932 AGACAAAAGT
Statistics
Matches: 80, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
27 11 0.14
28 31 0.39
29 34 0.43
30 4 0.05
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (29 bp):
AAATTATAATAAAGGATAAATCTTTTTAG
Found at i:936057 original size:29 final size:29
Alignment explanation
Indices: 935919--936115 Score: 200
Period size: 29 Copynumber: 6.7 Consensus size: 29
935909 ATTTTATTAG
* * *
935919 AAATTATAATAAAAG-ACAAAAGTATTTAT
1 AAATTAAAAT-AAAGTACAAAAATATTTCT
* * * *
935948 AAATTACAATAAGGTACGAAAGTATTTATCT
1 AAATTAAAATAAAGTACAAAAATA-TT-TCT
* *
935979 AAATTACAATAAAGTACAAAACTATTTCT
1 AAATTAAAATAAAGTACAAAAATATTTCT
* *
936008 AAATTAAAATAAAGTACAAAAATGTTTAT
1 AAATTAAAATAAAGTACAAAAATATTTCT
*
936037 AAATTAAAATAAAGTAAAAAAACTATTTCT
1 AAATTAAAATAAAGTACAAAAA-TATTTCT
* * *
936067 AAAATAGAATAAAGTACAAAACTATTTCT
1 AAATTAAAATAAAGTACAAAAATATTTCT
*
936096 AAATTACAAT-AAGTACAAAA
1 AAATTAAAATAAAGTACAAAA
936116 TTTAAAATTA
Statistics
Matches: 144, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
28 13 0.09
29 81 0.56
30 27 0.19
31 23 0.16
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATTAAAATAAAGTACAAAAATATTTCT
Found at i:936078 original size:59 final size:59
Alignment explanation
Indices: 935936--936115 Score: 193
Period size: 59 Copynumber: 3.1 Consensus size: 59
935926 AATAAAAGAC
* * * * * * * *
935936 AAAAGTATTTATAAATTACAATAAGGTACGAAAGTATTTATCTAAATTACAATAAAGT-AC
1 AAAACTATTTCTAAAATAAAATAAAGTACAAAAATATTTA--TAAATTACAATAAAGTAAA
* * *
935996 AAAACTATTTCTAAATTAAAATAAAGTACAAAAATGTTTATAAATTAAAATAAAGTAAA
1 AAAACTATTTCTAAAATAAAATAAAGTACAAAAATATTTATAAATTACAATAAAGTAAA
* * * *
936055 AAAACTATTTCTAAAATAGAATAAAGTACAAAACTATTTCTAAATTACAAT-AAGTACA
1 AAAACTATTTCTAAAATAAAATAAAGTACAAAAATATTTATAAATTACAATAAAGTAAA
936113 AAA
1 AAA
936116 TTTAAAATTA
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
58 24 0.23
59 46 0.45
60 33 0.32
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (59 bp):
AAAACTATTTCTAAAATAAAATAAAGTACAAAAATATTTATAAATTACAATAAAGTAAA
Found at i:936101 original size:88 final size:89
Alignment explanation
Indices: 935919--936115 Score: 249
Period size: 88 Copynumber: 2.2 Consensus size: 89
935909 ATTTTATTAG
* * * * ** * *
935919 AAATTATAATAAAAG-ACAAAAGTATTTATAAATTACAATAAGGTACGAAAGTATTTATCTAAAT
1 AAATTAAAAT-AAAGTACAAAAATATTTATAAATTAAAATAAAGTAAAAAACTATTTATCTAAAA
935983 TACAATAAAGTACAAAACTATTTCT
65 TACAATAAAGTACAAAACTATTTCT
*
936008 AAATTAAAATAAAGTACAAAAATGTTTATAAATTAAAATAAAGTAAAAAAACTA-TT-TCTAAAA
1 AAATTAAAATAAAGTACAAAAATATTTATAAATTAAAATAAAGT-AAAAAACTATTTATCTAAAA
*
936071 TAGAATAAAGTACAAAACTATTTCT
65 TACAATAAAGTACAAAACTATTTCT
*
936096 AAATTACAAT-AAGTACAAAA
1 AAATTAAAATAAAGTACAAAA
936116 TTTAAAATTA
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
87 10 0.11
88 43 0.45
89 36 0.38
90 6 0.06
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (89 bp):
AAATTAAAATAAAGTACAAAAATATTTATAAATTAAAATAAAGTAAAAAACTATTTATCTAAAAT
ACAATAAAGTACAAAACTATTTCT
Found at i:951334 original size:41 final size:41
Alignment explanation
Indices: 951284--951362 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
951274 CGAAGTATCT
*
951284 AATCAGGAAATTAAATAAATCCTTGAGAAGGTTGTAAATCC
1 AATCAGGAAATTAAATAAATCATTGAGAAGGTTGTAAATCC
*
951325 AATCGGGAAATTAAATAAATCATTGAGAAGGTTGTAAA
1 AATCAGGAAATTAAATAAATCATTGAGAAGGTTGTAAA
951363 CCCATCTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.27
Consensus pattern (41 bp):
AATCAGGAAATTAAATAAATCATTGAGAAGGTTGTAAATCC
Found at i:953317 original size:20 final size:20
Alignment explanation
Indices: 953243--953319 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
953233 AAAATATATC
* * *
953243 TATAGTTAATTAAGTATATA
1 TATATTTAATTAATTAAATA
*
953263 TAT-TTTAA-TAATCCTGAATA
1 TATATTTAATTAAT--TAAATA
*
953283 TTTAATTTCAATTAATTAAATA
1 TAT-ATTT-AATTAATTAAATA
953305 TATATTTAATTAATT
1 TATATTTAATTAATT
953320 TGGAATAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
18 3 0.07
19 4 0.09
20 17 0.39
21 4 0.09
22 10 0.23
23 2 0.05
24 4 0.09
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (20 bp):
TATATTTAATTAATTAAATA
Found at i:960088 original size:89 final size:90
Alignment explanation
Indices: 959934--960113 Score: 269
Period size: 89 Copynumber: 2.0 Consensus size: 90
959924 TAATAATCCT
* *
959934 GATTATTTAATTTCAATTAATTAAATACAGATTTAATTAATTTGAAATAATAAAATCCCTGATAT
1 GATTATTAAATTTCAATTAATTAAATACAGATTTAATTAATTTGAAATAATAAAATCCCTAATAT
959999 GAT-TA-GGTAACTTGGATATAAAAG
66 G-TCTAGGGTAACTTGGATATAAAAG
*
960023 GATTATTAAA-TTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAT-CCTAAT
1 GATTATTAAATTTC-AATTAATTAAATACAGATTTAATTAATTTGAAATAAT-AAAATCCCTAAT
*
960086 ATGTCTAGGGTAACTTGGCTATAAAAG
64 ATGTCTAGGGTAACTTGGATATAAAAG
960113 G
1 G
960114 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
88 4 0.05
89 55 0.66
90 24 0.29
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.38
Consensus pattern (90 bp):
GATTATTAAATTTCAATTAATTAAATACAGATTTAATTAATTTGAAATAATAAAATCCCTAATAT
GTCTAGGGTAACTTGGATATAAAAG
Found at i:965650 original size:34 final size:33
Alignment explanation
Indices: 965561--965659 Score: 117
Period size: 35 Copynumber: 2.9 Consensus size: 33
965551 GCCCACCATA
* *
965561 TACACTAAGTGTCTTGGGTATAGACTCTAGTGT
1 TACACTAAGTGTCTTGGGTATACACTCTAGTGC
* *
965594 TATGAACTAAGTGTCTTAGGTATACACTCTAGTGCC
1 TA--CACTAAGTGTCTTGGGTATACACTCTAGTG-C
* *
965630 TACACTAAGTGTATGGGGTATACACTCTAG
1 TACACTAAGTGTCTTGGGTATACACTCTAG
965660 AAATAAATCG
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
33 2 0.04
34 24 0.44
35 27 0.49
36 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (33 bp):
TACACTAAGTGTCTTGGGTATACACTCTAGTGC
Found at i:967838 original size:7 final size:7
Alignment explanation
Indices: 967826--967856 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
967816 GGTCAAAAAA
967826 GTCAACG
1 GTCAACG
967833 GTCAACG
1 GTCAACG
967840 GTCAACG
1 GTCAACG
967847 GTCAACG
1 GTCAACG
967854 GTC
1 GTC
967857 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:967906 original size:29 final size:29
Alignment explanation
Indices: 967874--967961 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
967864 GTCGGGTCAA
* *
967874 CGGTCAAAACCGATTCAGACCGGTCAAAC
1 CGGTCAGAACCGATTCAAACCGGTCAAAC
* *
967903 CGGTTC-GAACCGGTTGAAACCGGTCAAAC
1 CGG-TCAGAACCGATTCAAACCGGTCAAAC
* * *
967932 CGGTCAGAACCGGTTGAAAACCGGTTAAAC
1 CGGTCAGAACCGATT-CAAACCGGTCAAAC
967962 TGGTTTCCAG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.04
29 34 0.68
30 14 0.28
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (29 bp):
CGGTCAGAACCGATTCAAACCGGTCAAAC
Found at i:967944 original size:19 final size:19
Alignment explanation
Indices: 967874--967945 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
967864 GTCGGGTCAA
*
967874 CGGTCAAAACCGATTCAG-AC
1 CGGTC-AAACCG-GTCAGAAC
967894 CGGTCAAACCGGTTC-GAAC
1 CGGTCAAACCGG-TCAGAAC
*
967913 CGGTTGAAACCGGTCA-AAC
1 CGG-TCAAACCGGTCAGAAC
967932 CGGTCAGAACCGGT
1 CGGTCA-AACCGGT
967946 TGAAAACCGG
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.07
19 28 0.64
20 13 0.30
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.15
Consensus pattern (19 bp):
CGGTCAAACCGGTCAGAAC
Found at i:967966 original size:9 final size:9
Alignment explanation
Indices: 967892--967966 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 9
967882 ACCGATTCAG
*
967892 ACCGGTCAA
1 ACCGGTTAA
*
967901 ACCGGTTCGA
1 ACCGGTT-AA
967911 ACCGGTTGAA
1 ACCGGTT-AA
*
967921 ACCGGTCAA
1 ACCGGTTAA
*
967930 ACCGGTCAGA
1 ACCGGTTA-A
967940 ACCGGTTGAAA
1 ACCGGTT--AA
967951 ACCGGTTAA
1 ACCGGTTAA
*
967960 ACTGGTT
1 ACCGGTT
967967 TCCAGCAGCC
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
9 24 0.44
10 22 0.40
11 8 0.15
12 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:974897 original size:24 final size:24
Alignment explanation
Indices: 974869--974916 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
974859 GAAAAGATTA
974869 ACGTCGTTTAATGCTCGGTCAAAG
1 ACGTCGTTTAATGCTCGGTCAAAG
974893 ACGTCGTTTAATGCTCGGTCAAAG
1 ACGTCGTTTAATGCTCGGTCAAAG
974917 CCATTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (24 bp):
ACGTCGTTTAATGCTCGGTCAAAG
Found at i:998498 original size:20 final size:21
Alignment explanation
Indices: 998460--998498 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
998450 CATCATGGCC
998460 TTTGTAGAAGCCATGAAATCT
1 TTTGTAGAAGCCATGAAATCT
*
998481 TTTGTCGAAGCCAT-AAAT
1 TTTGTAGAAGCCATGAAAT
998499 TCCTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (21 bp):
TTTGTAGAAGCCATGAAATCT
Found at i:1003807 original size:35 final size:34
Alignment explanation
Indices: 1003761--1003856 Score: 129
Period size: 35 Copynumber: 2.8 Consensus size: 34
1003751 CCACCATATA
*
1003761 CACTAAGTGTCTTGGATATACACTCTAGTGTAATG
1 CACTAAGTGTCTTGGGTATACACTCTAGTG-AATG
**
1003796 CACTAAGTGTCTTGGGTATACACTCTAGTGCCTG
1 CACTAAGTGTCTTGGGTATACACTCTAGTGAATG
** *
1003830 CACTAAAAGTCTAGGGTATACACTCTA
1 CACTAAGTGTCTTGGGTATACACTCTA
1003857 CTACGAATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
34 26 0.47
35 29 0.53
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (34 bp):
CACTAAGTGTCTTGGGTATACACTCTAGTGAATG
Found at i:1003847 original size:34 final size:35
Alignment explanation
Indices: 1003777--1003856 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 35
1003767 GTGTCTTGGA
** *
1003777 TATACACTCTAGTGTAATGCACTAAGTGTCTTGGG
1 TATACACTCTAGTGTAATGCACTAAAAGTCTAGGG
**
1003812 TATACACTCTAGTG-CCTGCACTAAAAGTCTAGGG
1 TATACACTCTAGTGTAATGCACTAAAAGTCTAGGG
1003846 TATACACTCTA
1 TATACACTCTA
1003857 CTACGAATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 26 0.65
35 14 0.35
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (35 bp):
TATACACTCTAGTGTAATGCACTAAAAGTCTAGGG
Found at i:1004544 original size:20 final size:20
Alignment explanation
Indices: 1004519--1004558 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1004509 ATTCAATTTT
1004519 ACATTCTAACATTAATTTCA
1 ACATTCTAACATTAATTTCA
*
1004539 ACATTCTAACCTTAATTTCA
1 ACATTCTAACATTAATTTCA
1004559 TGCTTAGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACATTCTAACATTAATTTCA
Found at i:1009203 original size:40 final size:40
Alignment explanation
Indices: 1009158--1009237 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
1009148 ACATAAATGT
* * * *
1009158 AAATGAGTAACACTATTTAAGGCATTATGACCACTTTACC
1 AAATGAGTAACAATAATCAAGGCATTATGACAACTTTACC
* *
1009198 AAATGAGTAACAATAATCAATGCATTATGATAACTTTACC
1 AAATGAGTAACAATAATCAAGGCATTATGACAACTTTACC
1009238 TGATATTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (40 bp):
AAATGAGTAACAATAATCAAGGCATTATGACAACTTTACC
Found at i:1010940 original size:19 final size:20
Alignment explanation
Indices: 1010916--1010959 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1010906 AAAATAATCC
1010916 AATTTC-ATATTCTAACATA
1 AATTTCAATATTCTAACATA
*
1010935 AATTTCAATATTCTAACATT
1 AATTTCAATATTCTAACATA
1010955 AATTT
1 AATTT
1010960 ATAGCGTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTCAATATTCTAACATA
Found at i:1012422 original size:122 final size:122
Alignment explanation
Indices: 1012199--1012439 Score: 358
Period size: 122 Copynumber: 2.0 Consensus size: 122
1012189 AATTTTATTG
* * *
1012199 TGTTACATAGCCCATGTAATACAAAAATGCTCCCCATGGAATTTCTTTTAAAAAAGAATATGATA
1 TGTTACATAGCCCATGAAATACAAAAATGCTCCCCATGGAATTTCATTTAAAAAAGAATAGGATA
* *
1012264 TTATGCTAGTTTAAGGAGTGGGGCTAAAAATCTAGAAAACCCCATATGGATTTTAGGT
66 TTATGCTAGTTTAAGGAGTAGGGCTAAAAATCTAG-AAACCACATATGGATTTTAGGT
* * * * *
1012322 TGTTACATAGCCCATGAAATATAAACATGCTCCGCATGGAATTT-ATTTCAAAAATAATAGGATA
1 TGTTACATAGCCCATGAAATACAAAAATGCTCCCCATGGAATTTCATTTAAAAAAGAATAGGATA
* *
1012386 TTATGCTAGTTTAAGGAGTAGGGCTAAATATCTAGAAACCACATATGGTTTTTA
66 TTATGCTAGTTTAAGGAGTAGGGCTAAAAATCTAGAAACCACATATGGATTTTA
1012440 TGTGAGAACT
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
121 17 0.16
122 49 0.46
123 40 0.38
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (122 bp):
TGTTACATAGCCCATGAAATACAAAAATGCTCCCCATGGAATTTCATTTAAAAAAGAATAGGATA
TTATGCTAGTTTAAGGAGTAGGGCTAAAAATCTAGAAACCACATATGGATTTTAGGT
Found at i:1013612 original size:19 final size:20
Alignment explanation
Indices: 1013590--1013680 Score: 59
Period size: 19 Copynumber: 4.8 Consensus size: 20
1013580 AGAAACTAGG
1013590 TTTTAGGTTGGAAACCA-AT
1 TTTTAGGTTGGAAACCAGAT
*** *
1013609 TTTTTTATT-GAAAGCTAGAT
1 TTTTAGGTTGGAAA-CCAGAT
*
1013629 TTTT--GTCTGGAAACCA-AA
1 TTTTAGGT-TGGAAACCAGAT
* *
1013647 TTTTAGATTAGAAACCAGA-
1 TTTTAGGTTGGAAACCAGAT
1013666 TTTTAGGTTGGAAAC
1 TTTTAGGTTGGAAAC
1013681 TATATTTTCT
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
18 10 0.19
19 32 0.59
20 12 0.22
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (20 bp):
TTTTAGGTTGGAAACCAGAT
Found at i:1013678 original size:38 final size:38
Alignment explanation
Indices: 1013580--1013680 Score: 116
Period size: 38 Copynumber: 2.7 Consensus size: 38
1013570 TTTTGTGTTG
* * **
1013580 AGAAACTAGGTTTTAGGTTGGAAACCAATTTTTTTATT
1 AGAAACTAGATTTTAGGTTGGAAACCAAATTTTAGATT
*
1013618 -GAAAGCTAGATTTT-TGTCTGGAAACCAAATTTTAGATT
1 AGAAA-CTAGATTTTAGGT-TGGAAACCAAATTTTAGATT
*
1013656 AGAAACCAGATTTTAGGTTGGAAAC
1 AGAAACTAGATTTTAGGTTGGAAAC
1013681 TATATTTTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
37 6 0.12
38 40 0.77
39 6 0.12
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (38 bp):
AGAAACTAGATTTTAGGTTGGAAACCAAATTTTAGATT
Found at i:1013688 original size:19 final size:19
Alignment explanation
Indices: 1013636--1013680 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1013626 GATTTTTGTC
1013636 TGGAAACCAAATTTTAGAT
1 TGGAAACCAAATTTTAGAT
* * *
1013655 TAGAAACCAGATTTTAGGT
1 TGGAAACCAAATTTTAGAT
1013674 TGGAAAC
1 TGGAAAC
1013681 TATATTTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (19 bp):
TGGAAACCAAATTTTAGAT
Found at i:1017810 original size:44 final size:44
Alignment explanation
Indices: 1017747--1017862 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 44
1017737 GTAAGCATGC
*
1017747 AAATAAGCTTACGAGCTTAT-GAAATATTTGCAAGTA-TATGGTAA
1 AAATAAGCTTACGAGCTTATGGAAATA-TGGCAAGTATTATGGT-A
* * *
1017791 AAATAAGCTTACGAGCTTATGGGACAA-ATGGTAATTATTTTGGTA
1 AAATAAGCTTACGAGCTTAT-GGA-AATATGGCAAGTATTATGGTA
1017836 AAATAAGCTTACGAGCTTATGGAAATA
1 AAATAAGCTTACGAGCTTATGGAAATA
1017863 AATGGTAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
43 2 0.03
44 24 0.38
45 27 0.43
46 8 0.13
47 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAAATATGGCAAGTATTATGGTA
Found at i:1018235 original size:12 final size:12
Alignment explanation
Indices: 1018218--1018254 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1018208 TTTTCAGAAA
1018218 TTACTGTAGCAG
1 TTACTGTAGCAG
1018230 TTACTGTAGCAG
1 TTACTGTAGCAG
**
1018242 GCACTGTAGCAG
1 TTACTGTAGCAG
1018254 T
1 T
1018255 GCATCCATAC
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:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (12 bp):
TTACTGTAGCAG
Found at i:1018775 original size:16 final size:17
Alignment explanation
Indices: 1018751--1018783 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1018741 AAACTAAAGA
1018751 AAAAGGTTG-AAAGAAG
1 AAAAGGTTGAAAAGAAG
*
1018767 AAAATGTTGAAAAGAAG
1 AAAAGGTTGAAAAGAAG
1018784 GTCGAGATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (17 bp):
AAAAGGTTGAAAAGAAG
Found at i:1028712 original size:116 final size:118
Alignment explanation
Indices: 1028501--1028731 Score: 340
Period size: 116 Copynumber: 2.0 Consensus size: 118
1028491 CAACTACCAA
* * * *
1028501 AGCTGTTACAACATGTTAATTTTTTTGGATTACCATCTAGCATTATACAGTTTCCTGTAATTAAT
1 AGCTGTTACAACATGTTAA-TCTTTTAGATTACCAGCTAGCATTATACAGTTTCCAGTAATTAAT
* * * **
1028566 CTGACCAATTTTAAAATTATTTTACCTATAAATATGTTTT-AAAATTCTCTTTC
65 CTAACCAATTTAAAAATTATTTTACATATAAATACATTTTAAAAATTCTCTTTC
*
1028619 AGCTGTTACAACATGTTAA-CTTTTAGATTACCAGCTAGCATTATACAGTTTCCAGTAATTAGTC
1 AGCTGTTACAACATGTTAATCTTTTAGATTACCAGCTAGCATTATACAGTTTCCAGTAATTAATC
*
1028683 TAACCAATTTAAAAATTATTTTGCATATAAATACATTTTAAAAATTCTC
66 TAACCAATTTAAAAATTATTTTACATATAAATACATTTTAAAAATTCTC
1028732 ATTTTAGTTT
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
116 73 0.72
117 9 0.09
118 19 0.19
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.42
Consensus pattern (118 bp):
AGCTGTTACAACATGTTAATCTTTTAGATTACCAGCTAGCATTATACAGTTTCCAGTAATTAATC
TAACCAATTTAAAAATTATTTTACATATAAATACATTTTAAAAATTCTCTTTC
Found at i:1029772 original size:65 final size:64
Alignment explanation
Indices: 1029703--1029828 Score: 182
Period size: 65 Copynumber: 2.0 Consensus size: 64
1029693 ACTAATTACA
* *
1029703 TTCGATGTTTCAA-AAGAGCCAAGAGTGCATCGATGCATGGTCTGTGCATCAGTACATAAAATGC
1 TTCGATGTTTCAATAA-AACCAAGAGTGCATCGATGCATGGT-TGTGCATCAGTACACAAAATGC
1029767 T
64 T
* * *
1029768 TTCGATGTTTCAATAAAATCAAGAGTGCATCGATGTATGGTTGTGCATCGGTACACAAAAT
1 TTCGATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGTTGTGCATCAGTACACAAAAT
1029829 ACATTCGAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 18 0.33
65 35 0.64
66 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (64 bp):
TTCGATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGTTGTGCATCAGTACACAAAATGCT
Found at i:1030423 original size:16 final size:16
Alignment explanation
Indices: 1030402--1030432 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1030392 TAATTGGTCA
*
1030402 TAAATGATCTAAAATG
1 TAAATGATCCAAAATG
1030418 TAAATGATCCAAAAT
1 TAAATGATCCAAAAT
1030433 CTAACATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (16 bp):
TAAATGATCCAAAATG
Found at i:1030519 original size:25 final size:26
Alignment explanation
Indices: 1030482--1030545 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 26
1030472 TCATTCAAAC
1030482 AAACGAAAC-ATCCAAACT-ATATTCA
1 AAAC-AAACAATCCAAACTAATATTCA
1030507 AAACAAACAATCCAAACTAAATATTCA
1 AAACAAACAATCCAAACT-AATATTCA
1030534 AAATCCAAACAA
1 AAA--CAAACAA
1030546 ACGAAGCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.12
25 13 0.38
27 10 0.29
29 7 0.21
ACGTcount: A:0.58, C:0.23, G:0.02, T:0.17
Consensus pattern (26 bp):
AAACAAACAATCCAAACTAATATTCA
Found at i:1030542 original size:29 final size:28
Alignment explanation
Indices: 1030487--1030566 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 28
1030477 CAAACAAACG
1030487 AAAC-ATCCAAACT--ATATTCAAAA-C
1 AAACAATCCAAACTAAATATTCAAAATC
1030511 AAACAATCCAAACTAAATATTCAAAATCC
1 AAACAATCCAAACTAAATATTCAAAAT-C
* * * *
1030540 AAACAAACGAAGCCAAATATTCAAAAT
1 AAACAATCCAAACTAAATATTCAAAAT
1030567 GTTTAAACAC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 4 0.09
25 9 0.19
27 10 0.21
29 24 0.51
ACGTcount: A:0.56, C:0.23, G:0.03, T:0.19
Consensus pattern (28 bp):
AAACAATCCAAACTAAATATTCAAAATC
Found at i:1032010 original size:13 final size:13
Alignment explanation
Indices: 1031992--1032029 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1031982 TCCTAATGGG
1031992 CAATCTTTGAAAA
1 CAATCTTTGAAAA
*
1032005 CTATC-TTGAAAA
1 CAATCTTTGAAAA
*
1032017 CAATGTTTGAAAA
1 CAATCTTTGAAAA
1032030 ATCATAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (13 bp):
CAATCTTTGAAAA
Found at i:1035418 original size:50 final size:50
Alignment explanation
Indices: 1035343--1035442 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
1035333 ATGCTAACAG
*
1035343 TTCTAATTATCCCAAAAAGATCTATAT-GAATAAATTGTAATACTCTACTA
1 TTCTAATTAGCCCAAAAAGATCTATATAG-ATAAATTGTAATACTCTACTA
* *
1035393 TTCTAATTGGCCCAAAAAGATCTATATAGATCAATTGTAATACTCTACTA
1 TTCTAATTAGCCCAAAAAGATCTATATAGATAAATTGTAATACTCTACTA
1035443 GTTGATACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 45 0.98
51 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (50 bp):
TTCTAATTAGCCCAAAAAGATCTATATAGATAAATTGTAATACTCTACTA
Found at i:1039171 original size:13 final size:13
Alignment explanation
Indices: 1039153--1039193 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
1039143 CCTCGATTTG
1039153 TATACAAATAACA
1 TATACAAATAACA
1039166 TATACAAATAACA
1 TATACAAATAACA
1039179 TATACAAATAACA
1 TATACAAATAACA
1039192 TA
1 TA
1039194 GCCTCTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (13 bp):
TATACAAATAACA
Found at i:1041662 original size:48 final size:48
Alignment explanation
Indices: 1041591--1041690 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 48
1041581 CATAGTACTA
*
1041591 ATACGAAAAGGAAACATAGGCATTAAACAAAATCGATCGATAACCATC
1 ATACGAAAAGGAAACATAGGCATTAAACAAAATCGATAGATAACCATC
* * * *
1041639 ATACGAAAATGTAACTTATGCATTAAACAAAATCGATAGATAACCATC
1 ATACGAAAAGGAAACATAGGCATTAAACAAAATCGATAGATAACCATC
1041687 ATAC
1 ATAC
1041691 ACAAAGTATG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (48 bp):
ATACGAAAAGGAAACATAGGCATTAAACAAAATCGATAGATAACCATC
Found at i:1042722 original size:55 final size:55
Alignment explanation
Indices: 1042661--1043102 Score: 534
Period size: 55 Copynumber: 8.0 Consensus size: 55
1042651 CCCACTACCA
* * *
1042661 ATACGAAAATTCATAAACTTATCATGAATTTCTTAATTTTGAACATAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGCCC
* * * *
1042716 ATACGAAAATTCATAAACTTATTATGAATTTCTAACTTTTGCACACAAAGTACCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGCCC
* * * *
1042771 ATTCGAAAATTCATAAAATTACTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGCCC
** *
1042826 ATTTGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGCCC
* *
1042881 ATAC-AGAAATTCATAAACTTATTATGAATTTTTTAGTTTT-ACACACGAAGTGCCC
1 ATACGA-AAATTCATAAACTTATTATGAATTTCTTAGTTTTGA-ACACAAAGTGCCC
* * * * *
1042936 ATACGGAAATTCACAAACTTATTATGAATTTCTTAGTTTTGTACACAACGTGTCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGCCC
*** * * *
1042991 ATAC-AGGGCTTCATAAACTTATTATGAATTTCTTAGTTTAGAACACAAATTTCCC
1 ATACGA-AAATTCATAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGCCC
* * *
1043046 ATAC-AGAAATTCATAAACTTATTATGAATTTCTTTGTTAT-ACACATAAAGTGCCC
1 ATACGA-AAATTCATAAACTTATTATGAATTTCTTAGTTTTGA-ACACAAAGTGCCC
1043101 AT
1 AT
1043103 TTAGTAATCA
Statistics
Matches: 334, Mismatches: 47, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
54 2 0.01
55 332 0.99
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (55 bp):
ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGAACACAAAGTGCCC
Found at i:1059752 original size:55 final size:55
Alignment explanation
Indices: 1059707--1060367 Score: 1056
Period size: 55 Copynumber: 12.0 Consensus size: 55
1059697 CCCACTACCA
* *
1059707 ATACGGAACTTCATAAACTTATTATGAATTTCTTCA-TTTTTCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTT-AGTTTTGCACACAAAGTGCCC
* * * * *
1059762 ATACAGAAATTCATAAACTTATAATGAATTTC-TATGTTTTCCATAAAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTA-GTTTTGCACACAAAGTGCCC
* * * *
1059817 ATTCGAAAATTCATAAACTTACTATGAATTTCTTAGTTTTGCACATAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1059872 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
*
1059927 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* *
1059982 ATACGGAAATTCATAAACTTATTATGAATTTTTTAGTTTTGCACACAAAGTGCTC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
*
1060037 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * * *
1060092 TTACAGAAATTCGTAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
** * *
1060147 ATACAAAAATTCATACACTTATTATGAATTTCTTAGTTTTTCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
*
1060202 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
*
1060257 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAATGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
*
1060312 ATATGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1060367 A
1 A
1060368 ATTGGTAATC
Statistics
Matches: 560, Mismatches: 43, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
53 1 0.00
54 1 0.00
55 556 0.99
56 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (55 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
Found at i:1068372 original size:48 final size:48
Alignment explanation
Indices: 1068300--1068399 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
1068290 CATAGTACTG
*
1068300 ATACGAAAATGCAACATAGGCATTAAACAAAATCGATCGATAACCATC
1 ATACGAAAATGCAACATAGACATTAAACAAAATCGATCGATAACCATC
* *
1068348 ATACGAAAATGCAACTTATACATTAAACAAAATCGATCGATAACCATC
1 ATACGAAAATGCAACATAGACATTAAACAAAATCGATCGATAACCATC
1068396 ATAC
1 ATAC
1068400 ACAAAGTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (48 bp):
ATACGAAAATGCAACATAGACATTAAACAAAATCGATCGATAACCATC
Found at i:1076956 original size:81 final size:80
Alignment explanation
Indices: 1076817--1077802 Score: 1287
Period size: 81 Copynumber: 12.2 Consensus size: 80
1076807 ACTACTAAGA
* * * * * * *
1076817 ATTTAGTCTTTCACCCAAAGGCAGTTAATCCTTTCATCTAACTGGCATGAATGGCACCTTTCT-T
1 ATTTAATCTTTTACTCAAAGGTATTTAA-CCTTTCATCTAACTGGCATGATTGACACCTTTCTGT
* * * *
1076881 CCAAATGAACGTATATGA
65 -CAAATGCACG-CTAGGC
*
1076899 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCAAT-TAACTGGCATGATTGACACCTTTTTGT
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTC-ATCTAACTGGCATGATTGACACCTTTCTGT
1076963 CAAATGCACAGCTAGGC
65 CAAATGCAC-GCTAGGC
* *
1076980 ATTTAATCTTTTACTTAAAAGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
* * *
1077045 AAATCCAAAG-AAGGGC
66 AAATGC-ACGCTA-GGC
* *
1077061 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAAATGGCATGATTGACACCTTTTTGTC
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
*
1077126 AAATGCACAACTAGGC
66 AAATGCAC-GCTAGGC
* * * *
1077142 ATTTGAT-TTCTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTTAAACCTTTCTTT
1 ATTTAATCTT-TTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGT
* *
1077206 CAAATGCATAGCTAGAC
65 CAAATGCA-CGCTAGGC
* * * *
1077223 ATTTAATCTTTTACTTAAAGGTATTTAACCTTTAATATAACTGGCATGATTGACACATTTCTGTC
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
1077288 AAATGCACAGCTAGGC
66 AAATGCAC-GCTAGGC
* *
1077304 ATTTAATCTTTTACTCAAAGGTATTTAAACTTTCATCTAATTGGCATGATTGACACCTTTCTGTC
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
1077369 AAATGCACAGCTAGGC
66 AAATGCAC-GCTAGGC
* *
1077385 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAAATGGCATGATTGACACCTTTATGTC
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
*
1077450 AAATGCACATCTAGGC
66 AAATGCAC-GCTAGGC
* * * * *
1077466 ATTTTATTTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTTACACCTTTCTATC
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
* * *
1077531 AAATACATGTCTAGAC
66 AAATGCACG-CTAGGC
* * *
1077547 ATTTAATCTTTTACTTAAAGGTATTTAACCTTTAATCTAACTGGCATGATTGACACATTTCTGTC
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
* *
1077612 AAATGCACAACTAGAC
66 AAATGCAC-GCTAGGC
* * * *
1077628 ATTTAATCTTTTACTCAAAGGTATTTAAACTTTCATGTAATTGGCATAATTGACACCTTTCTGTC
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
* *
1077693 AAATACACATCTAGGC
66 AAATGCAC-GCTAGGC
*
1077709 ATTTAATTTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
1 ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
*
1077774 AAATGCAGAGCTAGGC
66 AAATGCA-CGCTAGGC
1077790 ATTTAATCTTTTA
1 ATTTAATCTTTTA
1077803 TTTTAAAACA
Statistics
Matches: 793, Mismatches: 96, Indels: 31
0.86 0.10 0.03
Matches are distributed among these distances:
80 6 0.01
81 756 0.95
82 31 0.04
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (80 bp):
ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTC
AAATGCACGCTAGGC
Found at i:1077539 original size:26 final size:26
Alignment explanation
Indices: 1077488--1077539 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1077478 ACTCAAAGGT
*
1077488 ATTTAACCTTTCATCTAACTAGCATG
1 ATTTAACCTTTCATCTAAATAGCATG
1077514 ATTTACACCTTTCTATC-AAATA-CATG
1 ATTTA-ACCTTTC-ATCTAAATAGCATG
1077540 TCTAGACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.39
27 11 0.48
28 3 0.13
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (26 bp):
ATTTAACCTTTCATCTAAATAGCATG
Found at i:1101809 original size:48 final size:49
Alignment explanation
Indices: 1101748--1101876 Score: 161
Period size: 48 Copynumber: 2.6 Consensus size: 49
1101738 AAATATTTCA
**
1101748 CTTAGGGTGAAAACCCGAAAGGGTTCCCTAAGTTAAATT-AAAAAAATG
1 CTTAGGGTGAAAACCCGAAAGGGCGCCCTAAGTTAAATTAAAAAAAATG
* * *
1101796 CTTATGGTGAAAACTCGAAAGGGCGCCCTAAGTTGAATTCAAAAAAAATG
1 CTTAGGGTGAAAACCCGAAAGGGCGCCCTAAGTTAAATT-AAAAAAAATG
* * * *
1101846 TTTAGGGTGAAAACCCAAAAAGGCGCTCTAA
1 CTTAGGGTGAAAACCCGAAAGGGCGCCCTAA
1101877 ATGGAAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
48 34 0.50
50 34 0.50
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (49 bp):
CTTAGGGTGAAAACCCGAAAGGGCGCCCTAAGTTAAATTAAAAAAAATG
Found at i:1103658 original size:28 final size:28
Alignment explanation
Indices: 1103606--1103663 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1103596 AAATACGTAT
* *
1103606 AATATATAGTTTTTAAAATGGTTTTGAA
1 AATATATAGTTTTTAAAATAGTTTTAAA
* * *
1103634 AATATATGGTTTTTAAATTATTTTTAAA
1 AATATATAGTTTTTAAAATAGTTTTAAA
1103662 AA
1 AA
1103664 CTGTATAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (28 bp):
AATATATAGTTTTTAAAATAGTTTTAAA
Found at i:1103678 original size:39 final size:36
Alignment explanation
Indices: 1103634--1103918 Score: 165
Period size: 37 Copynumber: 7.9 Consensus size: 36
1103624 TGGTTTTGAA
*
1103634 AATATAT-GGTTTTTAAATTATTTTTAAAAACTGTAT
1 AATATATAGGTTTTTAAATTATTTTTGAAAAC-GTAT
* * * *
1103670 AAATATATAGTTTTTTAAATATAATTTTGAAAGCATAT
1 -AATATATAGGTTTTTAAAT-TATTTTTGAAAACGTAT
* **
1103708 AATATATAGTTTTTTAAAACGATTTTTGAAAACGTAT
1 AATATATAGGTTTTT-AAATTATTTTTGAAAACGTAT
* ** * **
1103745 AATATATATAGTGTTTTAAAACGATTTTTGAGAATATAT
1 -A-ATATATAG-GTTTTTAAATTATTTTTGAAAACGTAT
* * * *
1103784 AGTATATAGTTTTTTAAAATATTTTTGAAAACATAT
1 AATATATAGGTTTTTAAATTATTTTTGAAAACGTAT
* ** *
1103820 AATATATA-GTTTTAAAAAAATTATTTTAAAAC----
1 AATATATAGGTTTTTAAATTATT-TTTGAAAACGTAT
* *
1103852 -ATATATA-GTTTTTAAAATGATTTTTTTTAAAACGTAT
1 AATATATAGGTTTTT-AAAT--TATTTTTGAAAACGTAT
* * *
1103889 AATTTATA-GTTTTTAAAATATCTTTGAAAA
1 AATATATAGGTTTTTAAATTATTTTTGAAAA
1103919 TTGTATATAA
Statistics
Matches: 197, Mismatches: 36, Indels: 32
0.74 0.14 0.12
Matches are distributed among these distances:
31 12 0.06
32 3 0.02
33 9 0.05
34 2 0.01
35 20 0.10
36 36 0.18
37 45 0.23
38 30 0.15
39 36 0.18
40 4 0.02
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (36 bp):
AATATATAGGTTTTTAAATTATTTTTGAAAACGTAT
Found at i:1103683 original size:37 final size:36
Alignment explanation
Indices: 1103634--1103832 Score: 195
Period size: 37 Copynumber: 5.4 Consensus size: 36
1103624 TGGTTTTGAA
* * * *
1103634 AATATAT-GGTTTTTAAATTATTTTTAAAAACTGTAT
1 AATATATAGTTTTTTAAACTATTTTTGAAAAC-ATAT
*
1103670 AAATATATAGTTTTTTAAA-TATAATTTTGAAAGCATAT
1 -AATATATAGTTTTTTAAACTAT--TTTTGAAAACATAT
* *
1103708 AATATATAGTTTTTTAAAACGATTTTTGAAAACGTAT
1 AATATATAGTTTTTT-AAACTATTTTTGAAAACATAT
* * * *
1103745 AATATATATAGTGTTTTAAAACGATTTTTGAGAATATAT
1 -A-ATATATAGT-TTTTTAAACTATTTTTGAAAACATAT
* *
1103784 AGTATATAGTTTTTTAAAATATTTTTGAAAACATAT
1 AATATATAGTTTTTTAAACTATTTTTGAAAACATAT
1103820 AATATATAGTTTT
1 AATATATAGTTTT
1103833 AAAAAAATTA
Statistics
Matches: 136, Mismatches: 18, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
36 33 0.24
37 45 0.33
38 17 0.12
39 37 0.27
40 4 0.03
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (36 bp):
AATATATAGTTTTTTAAACTATTTTTGAAAACATAT
Found at i:1103762 original size:76 final size:75
Alignment explanation
Indices: 1103634--1103827 Score: 225
Period size: 76 Copynumber: 2.6 Consensus size: 75
1103624 TGGTTTTGAA
* ** * * *
1103634 AATATAT-GGTTTTTAAATTATTTTTAAAAACTGTATAA-ATATATAGTTTTTTAAATA-TAATT
1 AATATATAGTTTTTTAAAAGATTTTTGAAAAC-GTATAATATATATAGTGTTTTAAA-ACGAATT
1103696 TTGA-AAGCATAT
64 TTGAGAA-CATAT
*
1103708 AATATATAGTTTTTTAAAACGATTTTTGAAAACGTATAATATATATAGTGTTTTAAAACGATTTT
1 AATATATAGTTTTTTAAAA-GATTTTTGAAAACGTATAATATATATAGTGTTTTAAAACGAATTT
*
1103773 TGAGAATATAT
65 TGAGAACATAT
* * *
1103784 AGTATATAGTTTTTTAAAATATTTTTGAAAACATATAATATATA
1 AATATATAGTTTTTTAAAAGATTTTTGAAAACGTATAATATATA
1103828 GTTTTAAAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
74 7 0.07
75 39 0.38
76 56 0.54
77 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (75 bp):
AATATATAGTTTTTTAAAAGATTTTTGAAAACGTATAATATATATAGTGTTTTAAAACGAATTTT
GAGAACATAT
Found at i:1103858 original size:76 final size:74
Alignment explanation
Indices: 1103634--1103858 Score: 208
Period size: 76 Copynumber: 3.0 Consensus size: 74
1103624 TGGTTTTGAA
* * * ** * *
1103634 AATATAT-GGTTTTTAAATTATTTTTAAAAACTGTATAAATATATAGTTTTTTAAATATAATTTT
1 AATATATAGTTTTTTAAAATATTTTTGAAAAC-GTATAAATATATAGTTTTAAAAAAATTATTTT
*
1103698 GAAAGC-ATAT
65 -AAAACAATAT
* **
1103708 AATATATAGTTTTTTAAAACGATTTTTGAAAACGTATAATATATATAGTGTTTTAAAACGATT-T
1 AATATATAGTTTTTTAAAA-TATTTTTGAAAACGTATAA-ATATATA--GTTTTAAAAAAATTAT
* * *
1103772 TTGAGAA-TATAT
62 TTTAAAACAATAT
* *
1103784 AGTATATAGTTTTTTAAAATATTTTTGAAAACATAT-AATATATAGTTTTAAAAAAATTATTTTA
1 AATATATAGTTTTTTAAAATATTTTTGAAAACGTATAAATATATAGTTTTAAAAAAATTATTTTA
1103848 AAACATATAT
66 AAACA-ATAT
1103858 A
1 A
1103859 GTTTTTAAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 18
0.76 0.12 0.11
Matches are distributed among these distances:
71 12 0.10
72 6 0.05
73 7 0.06
74 13 0.11
75 30 0.25
76 42 0.34
77 3 0.02
78 9 0.07
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (74 bp):
AATATATAGTTTTTTAAAATATTTTTGAAAACGTATAAATATATAGTTTTAAAAAAATTATTTTA
AAACAATAT
Found at i:1103955 original size:16 final size:15
Alignment explanation
Indices: 1103934--1103963 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1103924 TATAATATGA
1103934 TTTTTTGAAAACATAT
1 TTTTTTG-AAACATAT
1103950 TTTTTTGAAACATA
1 TTTTTTGAAACATA
1103964 GTATATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (15 bp):
TTTTTTGAAACATAT
Found at i:1103989 original size:21 final size:20
Alignment explanation
Indices: 1103952--1103990 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1103942 AAACATATTT
*
1103952 TTTTGAAACATAGTATATGA
1 TTTTGAAACATAATATATGA
*
1103972 TTTTGAAAATATAATATAT
1 TTTTG-AAACATAATATAT
1103991 TATATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTTGAAACATAATATATGA
Found at i:1104007 original size:24 final size:23
Alignment explanation
Indices: 1103971--1104017 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1103961 ATAGTATATG
1103971 ATTTTGAAAATATA-ATATATTAT
1 ATTTTGAAAATATATAT-TATTAT
*
1103994 ATTTTTAAATATATATATTATTAT
1 ATTTTGAAA-ATATATATTATTAT
1104018 TGTTGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 11 0.52
25 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTTGAAAATATATATTATTAT
Found at i:1104070 original size:15 final size:15
Alignment explanation
Indices: 1104030--1104072 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1104020 TTGTTATTTA
*
1104030 TTTATTTATTTTCTT
1 TTTATTCATTTTCTT
*
1104045 TTTATTTATTTTCTT
1 TTTATTCATTTTCTT
1104060 TTT-TCTCATTTTC
1 TTTAT-TCATTTTC
1104073 AGGTTCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 1 0.04
15 25 0.96
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTCATTTTCTT
Found at i:1104070 original size:19 final size:15
Alignment explanation
Indices: 1104030--1104062 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1104020 TTGTTATTTA
1104030 TTTATTTATTTTCTT
1 TTTATTTATTTTCTT
1104045 TTTATTTATTTTCTT
1 TTTATTTATTTTCTT
1104060 TTT
1 TTT
1104063 TCTCATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTATTTTCTT
Found at i:1105975 original size:31 final size:30
Alignment explanation
Indices: 1105913--1105977 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
1105903 TAATGGCTCC
* *
1105913 GTGACTAAAATATAATAATTGATAACGTAA
1 GTGACTAAAATATAATAATCGATAACATAA
* * *
1105943 GTGAGTAAAATTTAATAAATCGATAATATAA
1 GTGACTAAAATATAAT-AATCGATAACATAA
1105974 GTGA
1 GTGA
1105978 TCAAAACATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.48
31 15 0.52
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (30 bp):
GTGACTAAAATATAATAATCGATAACATAA
Found at i:1110170 original size:60 final size:60
Alignment explanation
Indices: 1110079--1110217 Score: 219
Period size: 60 Copynumber: 2.3 Consensus size: 60
1110069 GGTAAACTAC
* * *
1110079 ACAAAT-GGTCACTAATGTTTGAGTAAGTTTTTGTTTTCC-CACTAAAGTTTCAAAAGTA
1 ACAAATGGGTCACTAATGTTTAAGTAAGTTTTTGTTTTCCTCACTAAAGTTTAAAAAATA
1110137 ACAAATCGGGTCACTAATGTTTAAGTAAGTTTTTGTTTTCCTCACTAAAGTTTAAAAAATA
1 ACAAAT-GGGTCACTAATGTTTAAGTAAGTTTTTGTTTTCCTCACTAAAGTTTAAAAAATA
*
1110198 ACAAATTGGTCACTAATGTT
1 ACAAATGGGTCACTAATGTT
1110218 ATCGATTTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
58 6 0.08
60 45 0.61
61 23 0.31
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (60 bp):
ACAAATGGGTCACTAATGTTTAAGTAAGTTTTTGTTTTCCTCACTAAAGTTTAAAAAATA
Found at i:1110271 original size:31 final size:31
Alignment explanation
Indices: 1110196--1110273 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
1110186 GTTTAAAAAA
* * ** *
1110196 TAACAAATTGGTCACTAATGTTATCGATTTG
1 TAACAAATAGATCACTAACATTATCGATTAG
* *
1110227 TAACAAATGGATCACTAACATTATTGATTAG
1 TAACAAATAGATCACTAACATTATCGATTAG
*
1110258 TAATAAATAGATCACT
1 TAACAAATAGATCACT
1110274 CAACGTTAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (31 bp):
TAACAAATAGATCACTAACATTATCGATTAG
Found at i:1114781 original size:22 final size:21
Alignment explanation
Indices: 1114756--1114801 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 21
1114746 TATTTTTTTT
1114756 TATACTAACTTTGATATTTATA
1 TATACTAACTTTGATATTTA-A
1114778 TATACTAACTTTGATATTTAA
1 TATACTAACTTTGATATTTAA
1114799 TAT
1 TAT
1114802 TTATAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (21 bp):
TATACTAACTTTGATATTTAA
Found at i:1117427 original size:23 final size:23
Alignment explanation
Indices: 1117401--1117449 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
1117391 TATTAATTTT
1117401 TAAACTATTATAAG-AAT-AAAATA
1 TAAA-TATT-TAAGTAATGAAAATA
1117424 TAAATATTTAAGTTAATGAAAATA
1 TAAATATTTAAG-TAATGAAAATA
1117448 TA
1 TA
1117450 TATTTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 4 0.17
23 7 0.30
24 8 0.35
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (23 bp):
TAAATATTTAAGTAATGAAAATA
Found at i:1118872 original size:13 final size:13
Alignment explanation
Indices: 1118837--1118951 Score: 62
Period size: 13 Copynumber: 8.9 Consensus size: 13
1118827 AAATATAATA
1118837 TATATAATATAAAT
1 TATAT-ATATAAAT
1118851 T-TATATATAAAT
1 TATATATATAAAT
* *
1118863 TATATGTATAAAC
1 TATATATATAAAT
*
1118876 TATAT-T-TATAT
1 TATATATATAAAT
*
1118887 TATAAACTATATAA-
1 TATATA-TATA-AAT
**
1118901 T-TAT-TATAAGC
1 TATATATATAAAT
1118912 TATATATATAAAT
1 TATATATATAAAT
* * *
1118925 TATGTTTATATGAAC
1 TA--TATATATAAAT
1118940 TATATATATAAA
1 TATATATATAAA
1118952 AACTATAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
10 1 0.01
11 12 0.16
12 13 0.17
13 35 0.46
14 4 0.05
15 11 0.14
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (13 bp):
TATATATATAAAT
Found at i:1118873 original size:30 final size:31
Alignment explanation
Indices: 1118834--1118899 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
1118824 AAAAAATATA
*
1118834 ATATATATAATA-TAAATTTATA-TATAAATT
1 ATATATATAA-ACTAAATTTATATTATAAACT
* *
1118864 ATATGTATAAACTATATTTATATTATAAACT
1 ATATATATAAACTAAATTTATATTATAAACT
1118895 ATATA
1 ATATA
1118900 ATTATTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 18 0.60
31 11 0.37
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (31 bp):
ATATATATAAACTAAATTTATATTATAAACT
Found at i:1118892 original size:18 final size:18
Alignment explanation
Indices: 1118862--1118921 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
1118852 TATATATAAA
1118862 TTATATGTATAAACTATAT
1 TTATAT-TATAAACTATAT
1118881 TTATATTATAAACTATA-
1 TTATATTATAAACTATAT
* *
1118898 TAATTATTATAAGCTATAT
1 TTA-TATTATAAACTATAT
*
1118917 ATATA
1 TTATA
1118922 AATTATGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.06
18 26 0.74
19 7 0.20
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (18 bp):
TTATATTATAAACTATAT
Found at i:1118926 original size:20 final size:18
Alignment explanation
Indices: 1118869--1118927 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
1118859 AAATTATATG
*
1118869 TATAAACTATAT-TTATAT
1 TATAAACTATATAATA-AT
*
1118887 TATAAACTATATAATTAT
1 TATAAACTATATAATAAT
*
1118905 TATAAGCTATATATATAAAT
1 TATAAACTATATA-AT-AAT
1118925 TAT
1 TAT
1118928 GTTTATATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 26 0.76
19 3 0.09
20 5 0.15
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (18 bp):
TATAAACTATATAATAAT
Found at i:1118949 original size:15 final size:15
Alignment explanation
Indices: 1118835--1118958 Score: 73
Period size: 15 Copynumber: 8.3 Consensus size: 15
1118825 AAAAATATAA
1118835 TATATATAATATAAA-
1 TATATAT-ATATAAAC
1118850 T-T-TATATATAAA-
1 TATATATATATAAAC
*
1118862 T-TATATGTATAAAC
1 TATATATATATAAAC
1118876 TATATTTATATTATAAAC
1 TATA--TATA-TATAAAC
*
1118894 TATATAATTATTATAAGC
1 TATAT-A-TA-TATAAAC
*
1118912 --TATATATATAAAT
1 TATATATATATAAAC
* * *
1118925 TATGTTTATATGAAC
1 TATATATATATAAAC
*
1118940 TATATATATAAAAAC
1 TATATATATATAAAC
1118955 TATA
1 TATA
1118959 AAAAGTATAT
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
12 9 0.10
13 17 0.20
14 4 0.05
15 28 0.33
16 4 0.05
17 4 0.05
18 20 0.23
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.44
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:1119144 original size:19 final size:19
Alignment explanation
Indices: 1119112--1119189 Score: 97
Period size: 19 Copynumber: 4.2 Consensus size: 19
1119102 CTGAGAAATT
*
1119112 TTGAGAATATAG-GG-AAA
1 TTGAGAATTTAGAGGAAAA
*
1119129 TTGAGAATTTAGAGGGAAA
1 TTGAGAATTTAGAGGAAAA
*
1119148 TTAAGAATTTAGAGGAAAA
1 TTGAGAATTTAGAGGAAAA
* *
1119167 TTGAAAATTTATAGGAAAA
1 TTGAGAATTTAGAGGAAAA
1119186 TTGA
1 TTGA
1119190 AAAAATTTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.21
18 2 0.04
19 40 0.75
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.28
Consensus pattern (19 bp):
TTGAGAATTTAGAGGAAAA
Found at i:1119196 original size:21 final size:19
Alignment explanation
Indices: 1119126--1119202 Score: 93
Period size: 19 Copynumber: 3.9 Consensus size: 19
1119116 GAATATAGGG
* *
1119126 AAATTGAGAATTTAGAGGG
1 AAATTGAAAATTTAGAGGA
1119145 AAATT-AAGAATTTAGAGGA
1 AAATTGAA-AATTTAGAGGA
*
1119164 AAATTGAAAATTTATAGGA
1 AAATTGAAAATTTAGAGGA
1119183 AAATTGAAAAAATTTAGAGG
1 AAATTG--AAAATTTAGAGG
1119203 TAATAGAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.02
19 36 0.72
20 2 0.04
21 11 0.22
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (19 bp):
AAATTGAAAATTTAGAGGA
Found at i:1119420 original size:2 final size:2
Alignment explanation
Indices: 1119413--1119599 Score: 135
Period size: 2 Copynumber: 96.0 Consensus size: 2
1119403 TTTAATTTTC
* *
1119413 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * * *
1119456 TG TA TA AA CTA TA TA -A AA TA TA TA GTT TA TA AA T- TA TA -A TT
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
1119497 TA TA T- TA -A TA TA GTA TA TA TA TA TG TA TG TA TA -A CTA -A TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
1119537 TA -A GTA -A TC TA TA GA T- 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
1119577 TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1119600 GAAATACTAT
Statistics
Matches: 145, Mismatches: 23, Indels: 34
0.72 0.11 0.17
Matches are distributed among these distances:
1 11 0.08
2 127 0.88
3 7 0.05
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1120001 original size:14 final size:14
Alignment explanation
Indices: 1119958--1120049 Score: 55
Period size: 14 Copynumber: 6.6 Consensus size: 14
1119948 TAAATTACAG
1119958 AAACCCTAAAT-TCT
1 AAACCCTAAATCT-T
* *
1119972 AAA-CCTTAATCAT
1 AAACCCTAAATCTT
*
1119985 AAACTCTAAATCTT
1 AAACCCTAAATCTT
** * *
1119999 AAACTTTAAACCAT
1 AAACCCTAAATCTT
*
1120013 AAACACTAAA-CTCT
1 AAACCCTAAATCT-T
* *
1120027 AAACCCTAAACCCT
1 AAACCCTAAATCTT
1120041 AAACCCTAA
1 AAACCCTAA
1120050 TGTATTTATA
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
13 11 0.18
14 49 0.80
15 1 0.02
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (14 bp):
AAACCCTAAATCTT
Found at i:1120022 original size:21 final size:21
Alignment explanation
Indices: 1119998--1120049 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1119988 CTCTAAATCT
*
1119998 TAAACTTTAAACCATAAACAC
1 TAAACTCTAAACCATAAACAC
* *
1120019 TAAACTCTAAACCCTAAACCC
1 TAAACTCTAAACCATAAACAC
*
1120040 TAAACCCTAA
1 TAAACTCTAA
1120050 TGTATTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAACTCTAAACCATAAACAC
Found at i:1120046 original size:7 final size:7
Alignment explanation
Indices: 1120005--1120049 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
1119995 TCTTAAACTT
*
1120005 TAAACCA
1 TAAACCC
*
1120012 TAAACAC
1 TAAACCC
*
1120019 TAAACTC
1 TAAACCC
1120026 TAAACCC
1 TAAACCC
1120033 TAAACCC
1 TAAACCC
1120040 TAAACCC
1 TAAACCC
1120047 TAA
1 TAA
1120050 TGTATTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:1120185 original size:14 final size:14
Alignment explanation
Indices: 1120166--1120212 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1120156 ATTTTTTCTT
1120166 TATATAAATTAAAC
1 TATATAAATTAAAC
1120180 TATAT-AATT----
1 TATATAAATTAAAC
1120189 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1120203 TATATTAATT
1 TATATAAATT
1120213 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:1120191 original size:23 final size:24
Alignment explanation
Indices: 1120164--1120213 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1120154 TTATTTTTTC
1120164 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1120187 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1120211 TTT
1 TTT
1120214 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1120474 original size:16 final size:16
Alignment explanation
Indices: 1120455--1120487 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1120445 AAATATAAGA
1120455 TCAGGTTAAAAACAGG
1 TCAGGTTAAAAACAGG
*
1120471 TCAGGTTGAAAACAGG
1 TCAGGTTAAAAACAGG
1120487 T
1 T
1120488 AGGGTAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.21
Consensus pattern (16 bp):
TCAGGTTAAAAACAGG
Found at i:1124699 original size:17 final size:17
Alignment explanation
Indices: 1124677--1124719 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
1124667 GTAGGAGTCT
1124677 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
1124694 TTTTCTTATTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
1124712 TTTT-TTTT
1 TTTTCTTTT
1124720 GTTGTAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:1125172 original size:36 final size:36
Alignment explanation
Indices: 1125118--1125238 Score: 161
Period size: 36 Copynumber: 3.3 Consensus size: 36
1125108 TGGCGTGAAA
** * * *
1125118 GTGATGGACTATGGTGATGTTATAGGCGTGAAAATG
1 GTGATGGAAGATGATGATGATATAGGCGTGATAATG
*
1125154 GTGATGGAAGGTGATGATGATATAGGCGTGATAATG
1 GTGATGGAAGATGATGATGATATAGGCGTGATAATG
* *
1125190 GTGATGGAATATGGTGATGATATAGGCGTGATAATG
1 GTGATGGAAGATGATGATGATATAGGCGTGATAATG
1125226 GTGATGGATAGAT
1 GTGATGGA-AGAT
1125239 TGTATCTTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 71 0.96
37 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30
Consensus pattern (36 bp):
GTGATGGAAGATGATGATGATATAGGCGTGATAATG
Found at i:1128755 original size:14 final size:15
Alignment explanation
Indices: 1128736--1128770 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
1128726 CTATCTTTTG
1128736 CTTTTGATTTTC-TT
1 CTTTTGATTTTCTTT
1128750 CTTTTGATTTTCTTT
1 CTTTTGATTTTCTTT
1128765 CTTTTG
1 CTTTTG
1128771 CACTCCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.06, C:0.14, G:0.09, T:0.71
Consensus pattern (15 bp):
CTTTTGATTTTCTTT
Found at i:1129288 original size:36 final size:36
Alignment explanation
Indices: 1129237--1129357 Score: 161
Period size: 36 Copynumber: 3.3 Consensus size: 36
1129227 TGGCGTGAAA
** * * *
1129237 GTGATGGACTATGGTGATGTTATAGGTGTGAAAATG
1 GTGATGGAAGATGGTGATGATATAGGCGTGATAATG
*
1129273 GTGATGGAAGGTGGTGATGATATAGGCGTGATAATG
1 GTGATGGAAGATGGTGATGATATAGGCGTGATAATG
**
1129309 GTGATGGATTATGGTGATGATATAGGCGTGATAATG
1 GTGATGGAAGATGGTGATGATATAGGCGTGATAATG
1129345 GTGATGGATAGAT
1 GTGATGGA-AGAT
1129358 TGTATCTTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
36 71 0.97
37 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.38, T:0.31
Consensus pattern (36 bp):
GTGATGGAAGATGGTGATGATATAGGCGTGATAATG
Found at i:1132857 original size:6 final size:6
Alignment explanation
Indices: 1132846--1132883 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
1132836 TTGCTTCACC
1132846 TTTCTT TTTCTT TTTCTTT TCTTCTT TTTC-T TTTCTT T
1 TTTCTT TTTCTT TTTC-TT T-TTCTT TTTCTT TTTCTT T
1132884 CTTTTGCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 15 0.52
7 6 0.21
8 3 0.10
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:1132872 original size:14 final size:15
Alignment explanation
Indices: 1132852--1132888 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
1132842 CACCTTTCTT
1132852 TTTCTTTTTCTTTTC
1 TTTCTTTTTCTTTTC
1132867 -TTCTTTTTCTTTTC
1 TTTCTTTTTCTTTTC
1132881 TTTCTTTT
1 TTTCTTTT
1132889 GCACTCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTTCTTTTC
Found at i:1133396 original size:36 final size:36
Alignment explanation
Indices: 1133353--1133469 Score: 173
Period size: 36 Copynumber: 3.2 Consensus size: 36
1133343 TTGGCGTGAA
* *
1133353 GTGATGGACTATGGTGATGTTATAGGCGTGAAAATG
1 GTGATGGACTATGGTGATGATATAGGCGTGATAATG
* *
1133389 GTGATGGA-TGGTGGTGATGATATAGGCTTGATAATG
1 GTGATGGACT-ATGGTGATGATATAGGCGTGATAATG
*
1133425 GTGATGGATTATGGTGATGATATAGGCGTGATAATG
1 GTGATGGACTATGGTGATGATATAGGCGTGATAATG
1133461 GTGATGGAC
1 GTGATGGAC
1133470 AGATTGTATC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 1 0.01
36 70 0.97
37 1 0.01
ACGTcount: A:0.26, C:0.04, G:0.38, T:0.32
Consensus pattern (36 bp):
GTGATGGACTATGGTGATGATATAGGCGTGATAATG
Found at i:1135012 original size:36 final size:35
Alignment explanation
Indices: 1134951--1135144 Score: 135
Period size: 36 Copynumber: 5.8 Consensus size: 35
1134941 CTTTAGGGAT
**
1134951 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AATTTGTTTCAAGAGAAACAATCTCAAGA-AGACAA
* * *
1134987 AACTTGATTCAAGGGAAACAATCTC---AA-A-AA
1 AATTTGTTTCAAGAGAAACAATCTCAAGAAGACAA
** *
1135017 GGTTTGTTTCAAGAGAAAC-ATCTCAAGAAAGACAG
1 AATTTGTTTCAAGAGAAACAATCTCAAG-AAGACAA
*
1135052 AATTTGTTTCAAGGGAAACAATCTC-A-AAG----
1 AATTTGTTTCAAGAGAAACAATCTCAAGAAGACAA
* * *
1135081 ATTTCTGTTCCAAGAGAAA-ATGTCTCAAGAGAGACAA
1 AATT-TGTTTCAAGAGAAACA-ATCTCAAGA-AGACAA
*
1135118 AATTTGTTTCAAGGGAAACAATCTCAA
1 AATTTGTTTCAAGAGAAACAATCTCAA
1135145 AGGTTATGTT
Statistics
Matches: 119, Mismatches: 22, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
29 9 0.08
30 32 0.27
31 2 0.02
32 2 0.02
33 8 0.07
34 1 0.01
35 18 0.15
36 43 0.36
37 4 0.03
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (35 bp):
AATTTGTTTCAAGAGAAACAATCTCAAGAAGACAA
Found at i:1135028 original size:30 final size:32
Alignment explanation
Indices: 1134994--1135079 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 32
1134984 CAAAACTTGA
1134994 TTCAAGGGAAACAATCTCAAAAAG-G-TTTGT
1 TTCAAGGGAAACAATCTCAAAAAGAGATTTGT
*
1135024 TTCAAGAGAAAC-ATCTCAAGAAAGACAGAATTTGT
1 TTCAAGGGAAACAATCTCAA-AAAG--AG-ATTTGT
1135059 TTCAAGGGAAACAATCTCAAA
1 TTCAAGGGAAACAATCTCAAA
1135080 GATTTCTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
29 7 0.15
30 15 0.32
33 1 0.02
35 17 0.36
36 7 0.15
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.23
Consensus pattern (32 bp):
TTCAAGGGAAACAATCTCAAAAAGAGATTTGT
Found at i:1135134 original size:66 final size:65
Alignment explanation
Indices: 1134953--1135164 Score: 295
Period size: 65 Copynumber: 3.2 Consensus size: 65
1134943 TTAGGGATAA
* * * *
1134953 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGATTCAAGGGAAACAATCTCAAAAAG
1 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGA-
1135018 G
65 G
* *
1135019 TTTGTTTCAAGAGAAACA--TCTCAAGAAAGACAGAATTTGTTTCAAGGGAAACAATCTCAAAGA
1 TTTGTTTCAAGAGAAA-ATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGA
*
1135082 T
65 G
*
1135083 TTCTGTTCCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG-
1 TT-TGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGA
1135147 G
65 G
1135148 TTATGTTTCAAGAGAAA
1 TT-TGTTTCAAGAGAAA
1135165 CTATTTTGAA
Statistics
Matches: 129, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
64 3 0.02
65 68 0.53
66 58 0.45
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (65 bp):
TTTGTTTCAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAG
Found at i:1136711 original size:25 final size:24
Alignment explanation
Indices: 1136653--1136710 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
1136643 CTTTTATTTT
1136653 AAAAATTTTGAAAAATATCAATTA
1 AAAAATTTTGAAAAATATCAATTA
* *
1136677 AAAGAATTTTGAAAAATGTTTAA-TA
1 AAA-AATTTTGAAAAAT-ATCAATTA
1136702 AAAAATTTT
1 AAAAATTTT
1136711 TTTAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.30
25 18 0.60
26 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (24 bp):
AAAAATTTTGAAAAATATCAATTA
Found at i:1142040 original size:110 final size:110
Alignment explanation
Indices: 1141909--1142134 Score: 425
Period size: 110 Copynumber: 2.1 Consensus size: 110
1141899 CATAAGTGAA
1141909 CCATGTGTTTATATGTATATGTGATATGTGATCTATATGACAATGAGCTATGTGAAAGAACTATG
1 CCATGTGTTTATATGTATATGTGATATGTGATCTATATGACAATGAGCTATGTGAAAGAACTATG
*
1141974 TGACTAGGTAAATATGTGAATGTGTGATAACAAAAATATTAATGC
66 TGACTAGGTAAATATATGAATGTGTGATAACAAAAATATTAATGC
*
1142019 CCATGTGTTTATATGTATATGTGATATGTGATTTATATGACAATGAGCTATGTGAAAGAACTATG
1 CCATGTGTTTATATGTATATGTGATATGTGATCTATATGACAATGAGCTATGTGAAAGAACTATG
*
1142084 TGACTAGGTAAATATATGAATGTGTGATAACATAAATATTAATGC
66 TGACTAGGTAAATATATGAATGTGTGATAACAAAAATATTAATGC
1142129 CCATGT
1 CCATGT
1142135 TATGTGTCCT
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 113 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.35
Consensus pattern (110 bp):
CCATGTGTTTATATGTATATGTGATATGTGATCTATATGACAATGAGCTATGTGAAAGAACTATG
TGACTAGGTAAATATATGAATGTGTGATAACAAAAATATTAATGC
Found at i:1142362 original size:23 final size:23
Alignment explanation
Indices: 1142317--1142362 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1142307 ACATTTTATA
*
1142317 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
* *
1142340 TGGCACTTTGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
1142363 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:1151700 original size:32 final size:32
Alignment explanation
Indices: 1151663--1151736 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 32
1151653 TGCCTGAAGA
1151663 AAAAAATAAAGAAAAAAAGAAGAAG-AGAAAAT
1 AAAAAATAAAGAAAAAAA-AAGAAGAAGAAAAT
1151695 -AAAAA-AAAGAAAAAAAAAGAAGAAGAAAAT
1 AAAAAATAAAGAAAAAAAAAGAAGAAGAAAAT
1151725 AAATAAATAAAG
1 AAA-AAATAAAG
1151737 GAGGGTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
29 6 0.16
30 18 0.47
31 7 0.18
32 3 0.08
33 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (32 bp):
AAAAAATAAAGAAAAAAAAAGAAGAAGAAAAT
Found at i:1151721 original size:16 final size:16
Alignment explanation
Indices: 1151674--1151723 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
1151664 AAAAATAAAG
1151674 AAAAAAAGAAGAAGAGA
1 AAAAAAAGAAGAAGA-A
1151691 AAATAAAA-AA-AAGAA
1 AAA-AAAAGAAGAAGAA
1151706 AAAAAAAGAAGAAGAA
1 AAAAAAAGAAGAAGAA
1151722 AA
1 AA
1151724 TAAATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.13
15 6 0.20
16 11 0.37
17 5 0.17
18 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAGAAGAA
Found at i:1153177 original size:135 final size:135
Alignment explanation
Indices: 1152935--1153257 Score: 484
Period size: 135 Copynumber: 2.4 Consensus size: 135
1152925 CTAAATCTTA
* * * * * * *
1152935 AGATTTGGTTTTCTTGAAGAGCAACGAAGTAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAT
1 AGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTTCCTAAAGAGCAG
* *
1153000 TGAAGTGGATCAAAAATTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGTGGATCAGATTCTTCTT
66 TGAAGTGGATCAAAAATTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTT
1153065 CTTTC
131 CTTTC
* *
1153070 AGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTTCTTAAAGAGTAG
1 AGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTTCCTAAAGAGCAG
* *
1153135 TGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCCTCTAAAGAGTAGCGGAGCAGATTCTTCTT
66 TGAAGTGGATCAAAAATTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTT
1153200 CTTTC
131 CTTTC
* * * * *
1153205 AGATTTAGTCTTCCTGAAGAGCAGCAAAGGAAATCAAGTTCGCTTTAATCTTT
1 AGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTT
1153258 TTGAAGAACA
Statistics
Matches: 170, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 170 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (135 bp):
AGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTTCCTAAAGAGCAG
TGAAGTGGATCAAAAATTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTT
CTTTC
Found at i:1159387 original size:68 final size:68
Alignment explanation
Indices: 1159278--1159415 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
1159268 TACTTATATG
1159278 TTATGATACTGATTTTGTTTTCAATTTAAACAAATCTCGCTAACCATATATGATATACATATATA
1 TTATGATACTGATTTTGTTTTCAATTTAAACAAATCTCGCTAACCATATATGATATACATATATA
1159343 TTT
66 TTT
1159346 TTATGATACTGATTTTGTTTTCAATTTAAACAAATCTCGCTAACCATATATGATATACATATATA
1 TTATGATACTGATTTTGTTTTCAATTTAAACAAATCTCGCTAACCATATATGATATACATATATA
1159411 TTT
66 TTT
1159414 TT
1 TT
1159416 CATATTCAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (68 bp):
TTATGATACTGATTTTGTTTTCAATTTAAACAAATCTCGCTAACCATATATGATATACATATATA
TTT
Found at i:1161014 original size:24 final size:22
Alignment explanation
Indices: 1160986--1161030 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1160976 TGTTAAATCA
*
1160986 TAAAAATAAATATTTTTATATTG
1 TAAAAATAAAT-TATTTATATTG
*
1161009 TAAAAATAAGTTATTTATATTG
1 TAAAAATAAATTATTTATATTG
1161031 AGTTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
TAAAAATAAATTATTTATATTG
Found at i:1163447 original size:20 final size:20
Alignment explanation
Indices: 1163418--1163456 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1163408 AGAGCTCATA
*
1163418 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1163438 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1163457 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1165253 original size:85 final size:85
Alignment explanation
Indices: 1165136--1165294 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
1165126 ATTATGACAC
* * * *
1165136 ATGACACACATTTATGACGCGCATTGCATGTCATTAAAGCCCCCGTCATAATTGAAAATGACACA
1 ATGACACACATGTATGACGCACATTACATGTCATTAAAGCCCCCGTCATAAATGAAAATGACACA
*
1165201 CATTTGTGTGTCATAAATTT
66 CATTCGTGTGTCATAAATTT
** * * * *
1165221 ATGACACACATGTATGACTTACATTACGTGTCATTGAAGCTCCCGTCATAAATGAAGATGACACA
1 ATGACACACATGTATGACGCACATTACATGTCATTAAAGCCCCCGTCATAAATGAAAATGACACA
1165286 CATTCGTGT
66 CATTCGTGT
1165295 ATTGTGATTG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 63 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (85 bp):
ATGACACACATGTATGACGCACATTACATGTCATTAAAGCCCCCGTCATAAATGAAAATGACACA
CATTCGTGTGTCATAAATTT
Found at i:1173420 original size:157 final size:158
Alignment explanation
Indices: 1173134--1173443 Score: 613
Period size: 157 Copynumber: 2.0 Consensus size: 158
1173124 TATTTTACTT
1173134 CTTCTTGGAATGATACTCGGGGTATAATCAAATTAACATCGCACTAGAGGACCAGGAGAAGACTA
1 CTTCTTGGAATGATACTCGGGGTATAATCAAATTAACATCGCACTAGAGGACCAGGAGAAGACTA
1173199 CGTTCACGTGTCCCTATGACACTTATGCTTTCTGGAGGATGCCTTTTGGACTCTATAATGTTTGA
66 CGTTCACGTGTCCCTATGACACTTATGCTTTCTGGAGGATGCCTTTTGGACTCTATAATGTTTGA
1173264 TAA-CTTTCAACTCTGCATGCAATTTTA
131 TAACCTTTCAACTCTGCATGCAATTTTA
1173291 CTTCTTGGAATGATACTCGGGGTATAATCAAATTAACATCGCACTAGAGGACCAGGAGAAGACTA
1 CTTCTTGGAATGATACTCGGGGTATAATCAAATTAACATCGCACTAGAGGACCAGGAGAAGACTA
1173356 CGTTCACGTGTCCCTATGACACTTATGCTTTCTGGAGGATGCCTTTTGGACTCTATAATGTTTGA
66 CGTTCACGTGTCCCTATGACACTTATGCTTTCTGGAGGATGCCTTTTGGACTCTATAATGTTTGA
1173421 TAACCTTTCAACTCTGCATGCAA
131 TAACCTTTCAACTCTGCATGCAA
1173444 GCCATAGTTT
Statistics
Matches: 152, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 133 0.88
158 19 0.12
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (158 bp):
CTTCTTGGAATGATACTCGGGGTATAATCAAATTAACATCGCACTAGAGGACCAGGAGAAGACTA
CGTTCACGTGTCCCTATGACACTTATGCTTTCTGGAGGATGCCTTTTGGACTCTATAATGTTTGA
TAACCTTTCAACTCTGCATGCAATTTTA
Found at i:1188975 original size:13 final size:13
Alignment explanation
Indices: 1188957--1188985 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1188947 AAATGAATAC
1188957 AATTTTAAATTAA
1 AATTTTAAATTAA
1188970 AATTTTAAATTAA
1 AATTTTAAATTAA
1188983 AAT
1 AAT
1188986 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTTTAAATTAA
Found at i:1201461 original size:140 final size:138
Alignment explanation
Indices: 1201226--1201481 Score: 336
Period size: 140 Copynumber: 1.8 Consensus size: 138
1201216 GATTTTAACC
* * *
1201226 AATTATTGAATCAAATAATCAAATAGACCATCGGGCACTAAGACGAGGTATAAATCAATTATTCC
1 AATTATTAAATCAAATAATCAAATAGACCATCGGGCACTAAGACGAGGTACAAATCAAATATTCC
* * * **
1201291 TTAAATTAAAGGACTAAAAGTAAAATTAAGCCTAAAGTGGAGGCTCTAATTAATAATCCTATTTA
66 TTAAATTAAAGGAATAAAAGTAAAAGTAAG-CTAAAATAAAGGCTCTAATTAATAATCCTATTTA
1201356 ATTATGTCT
130 ATTATGTCT
* * * *
1201365 AATTATTAAATCGAATAATTGAAATGGACCATCGGGCATTAAGACGAGG-ACCAAATCAAATATT
1 AATTATTAAATCAAATAA-TCAAATAGACCATCGGGCACTAAGACGAGGTA-CAAATCAAATATT
* *
1201429 CCTTAAATTAAGGGAAT-AAAGTGAAAGGTAAGCTAAAATAAAGGCTCTAATTA
64 CCTTAAATTAAAGGAATAAAAGT-AAAAGTAAGCTAAAATAAAGGCTCTAATTA
1201482 TCTATGTACA
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
139 40 0.40
140 60 0.60
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (138 bp):
AATTATTAAATCAAATAATCAAATAGACCATCGGGCACTAAGACGAGGTACAAATCAAATATTCC
TTAAATTAAAGGAATAAAAGTAAAAGTAAGCTAAAATAAAGGCTCTAATTAATAATCCTATTTAA
TTATGTCT
Found at i:1203787 original size:25 final size:21
Alignment explanation
Indices: 1203770--1203814 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
1203760 AAAATACAAG
*
1203770 AGAAAAAGAACGAAAAAAAGAAA
1 AGAAAAA-AAC-AAAAAAATAAA
*
1203793 AGAAAAAAACAATAAAATAAA
1 AGAAAAAAACAAAAAAATAAA
1203814 A
1 A
1203815 AAATCCCCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 3 0.15
23 7 0.35
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.04
Consensus pattern (21 bp):
AGAAAAAAACAAAAAAATAAA
Found at i:1203788 original size:13 final size:13
Alignment explanation
Indices: 1203748--1203801 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
1203738 TTCGAAAACC
1203748 AAAAAGAAAAG--
1 AAAAAGAAAAGAA
* * *
1203759 AAAAATACAAGAG
1 AAAAAGAAAAGAA
*
1203772 AAAAAG-AACGAA
1 AAAAAGAAAAGAA
1203784 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
1203797 AAAAA
1 AAAAA
1203802 CAATAAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
11 9 0.27
12 9 0.27
13 15 0.45
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:1203816 original size:23 final size:24
Alignment explanation
Indices: 1203759--1203816 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
1203749 AAAAGAAAAG
* *
1203759 AAAAATACAAGAGAAAAAGAACGA
1 AAAAATAAAAAAGAAAAAGAACGA
*
1203783 AAAAA-AGAAAAGAAAAA-AAC-A
1 AAAAATAAAAAAGAAAAAGAACGA
1203804 ATAAAATAAAAAA
1 A-AAAATAAAAAA
1203817 ATCCCCGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.07
22 7 0.24
23 15 0.52
24 5 0.17
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.05
Consensus pattern (24 bp):
AAAAATAAAAAAGAAAAAGAACGA
Found at i:1205935 original size:18 final size:18
Alignment explanation
Indices: 1205901--1205936 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1205891 CAAATTAGTC
**
1205901 ATAATTGTTTTTTAAAAT
1 ATAATTGTTTTAAAAAAT
1205919 ATAATTGTTTTAAAAAAT
1 ATAATTGTTTTAAAAAAT
1205937 GGTTATGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
ATAATTGTTTTAAAAAAT
Found at i:1210278 original size:155 final size:155
Alignment explanation
Indices: 1210041--1210327 Score: 368
Period size: 155 Copynumber: 1.9 Consensus size: 155
1210031 ATTTTTACCT
* * * * *
1210041 AAACAAAATTGATCTCATTTGAGATTGTTCTCTCCAAACAAATTTTATCTCGCTTGAGACATGTT
1 AAACAAAATTGATCTCACTTGAGATTGCTCTCTCCAAACAAATTTTACCTCACTTGAGACATCTT
** *
1210106 CTTTTGTAGCATAAACATTTGAGATTGTTTCTCACAAAACAAA-TTTCGTCTCGCTTGATACAGT
66 CTTAAGTAGCATAAACATTTGAGATTGTTTCTCACAAAACAAAGTTTCGTCTCGCTTGAGACAGT
1210170 TTTTCCAAAAATATTGAAAATTTTG
131 TTTTCCAAAAATATTGAAAATTTTG
*
1210195 AAACAAAATTGATCTCACTTGAGATTGCTCT-TCTCAATACAAATTTTGCCTCACTTGAGACAAT
1 AAACAAAATTGATCTCACTTGAGATTGCTCTCTC-CAA-ACAAATTTTACCTCACTTGAGAC-AT
**** *
1210259 CTTCCTTAAG-A-CACT-AACATTTGAGATTGTTTCTTTTGAAATAAAGTTTCGTCTCGCTTGAG
63 CTT-CTTAAGTAGCA-TAAACATTTGAGATTGTTTCTCACAAAACAAAGTTTCGTCTCGCTTGAG
1210321 ACAGTTT
126 ACAGTTT
1210328 CCCTTGAAAC
Statistics
Matches: 113, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
153 2 0.02
154 32 0.28
155 47 0.42
156 28 0.25
157 4 0.04
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (155 bp):
AAACAAAATTGATCTCACTTGAGATTGCTCTCTCCAAACAAATTTTACCTCACTTGAGACATCTT
CTTAAGTAGCATAAACATTTGAGATTGTTTCTCACAAAACAAAGTTTCGTCTCGCTTGAGACAGT
TTTTCCAAAAATATTGAAAATTTTG
Found at i:1213722 original size:3 final size:3
Alignment explanation
Indices: 1213708--1213770 Score: 56
Period size: 3 Copynumber: 20.3 Consensus size: 3
1213698 TTTTCATTTC
* ** *
1213708 ATT ATC ATT ATT ATT AAA ATT ATT ATT ATT AAT ATT AATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT-T ATT
1213755 ATT ATT -TT GATT ATT A
1 ATT ATT ATT -ATT ATT A
1213771 AATAAATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 38 0.79
4 8 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1214325 original size:22 final size:20
Alignment explanation
Indices: 1214284--1214324 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1214274 GAACGAGAGG
*
1214284 AGACAGAGAGAAATCCAAAA
1 AGACAGAGAGAAACCCAAAA
*
1214304 AGACAGAGAGCAACCCAAAA
1 AGACAGAGAGAAACCCAAAA
1214324 A
1 A
1214325 ACAAAAAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.20, G:0.20, T:0.02
Consensus pattern (20 bp):
AGACAGAGAGAAACCCAAAA
Found at i:1214334 original size:19 final size:20
Alignment explanation
Indices: 1214298--1214335 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1214288 AGAGAGAAAT
* *
1214298 CCAAAAAGACAGAGAGCAAC
1 CCAAAAAGACAAAAAGCAAC
1214318 CCAAAAA-ACAAAAAGCAA
1 CCAAAAAGACAAAAAGCAA
1214336 TAAAAAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.63, C:0.24, G:0.13, T:0.00
Consensus pattern (20 bp):
CCAAAAAGACAAAAAGCAAC
Found at i:1215414 original size:40 final size:40
Alignment explanation
Indices: 1215362--1215520 Score: 268
Period size: 40 Copynumber: 4.0 Consensus size: 40
1215352 TTTTTTTATA
1215362 AATAAATATTTTACTTTTATAAATTATATATATTATTTTT
1 AATAAATATTTTACTTTTATAAATTATATATATTATTTTT
*
1215402 AATAAATATTTTACTTTTATAAATTATATTTATTATTTTT
1 AATAAATATTTTACTTTTATAAATTATATATATTATTTTT
* *
1215442 AAATAAATATTTTACTTTTATAAACTATATATA-T-TTTTA
1 -AATAAATATTTTACTTTTATAAATTATATATATTATTTTT
1215481 AATAAATATTTTACTTTTATAAATTATATATATTATTTTT
1 AATAAATATTTTACTTTTATAAATTATATATATTATTTTT
1215521 TAATGTTTTA
Statistics
Matches: 110, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
38 31 0.28
39 5 0.05
40 44 0.40
41 30 0.27
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (40 bp):
AATAAATATTTTACTTTTATAAATTATATATATTATTTTT
Found at i:1215519 original size:79 final size:81
Alignment explanation
Indices: 1215346--1215520 Score: 284
Period size: 79 Copynumber: 2.2 Consensus size: 81
1215336 CCATTTTCTG
* * *
1215346 ATATAT-TTTTTTTATAAATAAATATTTTACTTTTATAAATTATATATATTATTTTTAATAAATA
1 ATATATATTATTTT-TAAATAAATATTTTACTTTTATAAACTATATATATTATTTTAAATAAATA
1215410 TTTTACTTTTATAAATT
65 TTTTACTTTTATAAATT
*
1215427 ATATTTATTATTTTTAAATAAATATTTTACTTTTATAAACTATATATA-T-TTTTAAATAAATAT
1 ATATATATTATTTTTAAATAAATATTTTACTTTTATAAACTATATATATTATTTTAAATAAATAT
1215490 TTTACTTTTATAAATT
66 TTTACTTTTATAAATT
1215506 ATATATATTATTTTT
1 ATATATATTATTTTT
1215521 TAATGTTTTA
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
79 43 0.49
80 1 0.01
81 38 0.43
82 6 0.07
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (81 bp):
ATATATATTATTTTTAAATAAATATTTTACTTTTATAAACTATATATATTATTTTAAATAAATAT
TTTACTTTTATAAATT
Found at i:1215541 original size:41 final size:40
Alignment explanation
Indices: 1215346--1215524 Score: 231
Period size: 40 Copynumber: 4.4 Consensus size: 40
1215336 CCATTTTCTG
*
1215346 ATATATTTTTTTTATAAATAAATATTTTACTTTTATAAATTAT
1 ATATATTATTTTT-T-AAT-AATATTTTACTTTTATAAATTAT
1215389 ATATATTA-TTTTTAATAAATATTTTACTTTTATAAATTAT
1 ATATATTATTTTTTAAT-AATATTTTACTTTTATAAATTAT
* * *
1215429 ATTTATTATTTTTAAATAAATATTTTACTTTTATAAA--CT
1 ATATATTATTTTTTAAT-AATATTTTACTTTTATAAATTAT
*
1215468 ATATA-TATTTTTAAATAAATATTTTACTTTTATAAATTAT
1 ATATATTATTTTTTAAT-AATATTTTACTTTTATAAATTAT
1215508 ATATATTATTTTTTAAT
1 ATATATTATTTTTTAAT
1215525 GTTTTATTAA
Statistics
Matches: 125, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
38 31 0.25
39 5 0.04
40 40 0.32
41 38 0.30
42 4 0.03
43 7 0.06
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (40 bp):
ATATATTATTTTTTAATAATATTTTACTTTTATAAATTAT
Found at i:1215545 original size:29 final size:31
Alignment explanation
Indices: 1215495--1215553 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
1215485 AATATTTTAC
1215495 TTTTATAAATTATATATATTATTTTTTAATG
1 TTTTATAAATTATATATATTATTTTTTAATG
* *
1215526 TTTTATTAA-TATTTAT-TTATTTTTTAAT
1 TTTTATAAATTATATATATTATTTTTTAAT
1215554 ATTAAGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 6 0.23
31 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (31 bp):
TTTTATAAATTATATATATTATTTTTTAATG
Found at i:1215646 original size:2 final size:2
Alignment explanation
Indices: 1215639--1215670 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1215629 AAATAAATAA
1215639 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1215671 TTTCTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.