Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 17 of 17
Found at i:3645072 original size:21 final size:23
Alignment explanation
Indices: 3645046--3645097 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
3645036 TCGAAAATTT
3645046 AAAATTATTA-AATATTTAA-AA
1 AAAATTATTATAATATTTAATAA
* *
3645067 AAAATTA-TATATTTTTTAATAA
1 AAAATTATTATAATATTTAATAA
3645089 AAAATTATT
1 AAAATTATT
3645098 TTTTTCTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.08
21 14 0.54
22 9 0.35
23 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATTATTATAATATTTAATAA
Found at i:3645109 original size:20 final size:21
Alignment explanation
Indices: 3645086--3645129 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3645076 TATTTTTTAA
*
3645086 TAAAAAATTATTT-TTTTCTC
1 TAAAAAATTATTTCGTTTCTC
**
3645106 TAAAATTTTATTTCGTTTCTC
1 TAAAAAATTATTTCGTTTCTC
3645127 TAA
1 TAA
3645130 GTTTAAACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (21 bp):
TAAAAAATTATTTCGTTTCTC
Found at i:3645285 original size:19 final size:19
Alignment explanation
Indices: 3645261--3645306 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3645251 AAAAAATGAT
3645261 TAAAATTAATAACAAAAAG
1 TAAAATTAATAACAAAAAG
* * *
3645280 TAAAATATACTTATAAAAAG
1 TAAAAT-TAATAACAAAAAG
3645300 TAAAATT
1 TAAAATT
3645307 TTAATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAAATTAATAACAAAAAG
Found at i:3648583 original size:19 final size:19
Alignment explanation
Indices: 3648561--3648605 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3648551 TAAATATTCT
*
3648561 TGATTTTTATAGTAAACTG
1 TGATATTTATAGTAAACTG
*
3648580 TGATATTTATAGTAAATTG
1 TGATATTTATAGTAAACTG
3648599 TGATATT
1 TGATATT
3648606 GACTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (19 bp):
TGATATTTATAGTAAACTG
Found at i:3654702 original size:20 final size:21
Alignment explanation
Indices: 3654679--3654722 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3654669 TATTTTTTAA
*
3654679 TAAAAAATTATTT-TTTTCTC
1 TAAAAAATTATTTCGTTTCTC
**
3654699 TAAAATTTTATTTCGTTTCTC
1 TAAAAAATTATTTCGTTTCTC
3654720 TAA
1 TAA
3654723 GTTTAAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (21 bp):
TAAAAAATTATTTCGTTTCTC
Found at i:3654877 original size:19 final size:19
Alignment explanation
Indices: 3654855--3654900 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3654845 AATAGATGAT
3654855 TAAAATTAATAACAAAAAG
1 TAAAATTAATAACAAAAAG
* * *
3654874 TAAAATATACTTATAAAAAG
1 TAAAAT-TAATAACAAAAAG
3654894 TAAAATT
1 TAAAATT
3654901 TTAATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAAATTAATAACAAAAAG
Found at i:3656392 original size:29 final size:29
Alignment explanation
Indices: 3656344--3656401 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
3656334 TGATTTTATG
3656344 TTAGGGGATAAACTTAAACTTATAAAATT
1 TTAGGGGATAAACTTAAACTTATAAAATT
* * *
3656373 TTAGGGGATGAATTTGAACTTATAAAATT
1 TTAGGGGATAAACTTAAACTTATAAAATT
3656402 CTAAAGAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.36
Consensus pattern (29 bp):
TTAGGGGATAAACTTAAACTTATAAAATT
Found at i:3658234 original size:19 final size:19
Alignment explanation
Indices: 3658212--3658256 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3658202 TAAATATTAT
*
3658212 TGATTTTTATAGTAAACTG
1 TGATATTTATAGTAAACTG
*
3658231 TGATATTTATAGTAAATTG
1 TGATATTTATAGTAAACTG
3658250 TGATATT
1 TGATATT
3658257 AACTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (19 bp):
TGATATTTATAGTAAACTG
Found at i:3665033 original size:19 final size:19
Alignment explanation
Indices: 3665011--3665055 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3665001 TAAATATTCT
*
3665011 TGATTTTTATAGTAAACTG
1 TGATATTTATAGTAAACTG
*
3665030 TGATATTTATAGTAAATTG
1 TGATATTTATAGTAAACTG
3665049 TGATATT
1 TGATATT
3665056 GATTTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (19 bp):
TGATATTTATAGTAAACTG
Found at i:3671819 original size:20 final size:20
Alignment explanation
Indices: 3671794--3671844 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3671784 ATTATATTGA
*
3671794 TTAATAAATTTTATAATTAT
1 TTAATAAATTTAATAATTAT
*
3671814 TTAATAAATTTAATGATTAT
1 TTAATAAATTTAATAATTAT
*
3671834 TTTAT-AATTTA
1 TTAATAAATTTA
3671845 TGTAAGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAATAAATTTAATAATTAT
Found at i:3675867 original size:152 final size:153
Alignment explanation
Indices: 3675571--3675877 Score: 566
Period size: 152 Copynumber: 2.0 Consensus size: 153
3675561 TCATTTCGCT
3675571 ACGTTTTTGTTGGTTATGAAGTTGTCTGTGTGATTAAAGCTAAAATAAAAGGATAATGATTATAT
1 ACGTTTTTGTTGGTTATGAAGTTGTCTGTGTGATTAAAGCTAAAATAAAAGGATAATGATTATAT
3675636 TGTCTGTTTTTGAAATTTTATATAAGATTTTTCCTTCCTGTTTGCATATTTGTTAATTAAAGGGC
66 TGTCTGTTTTTGAAATTTTATATAAGATTTTTCCTTCCTGTTTGCATATTTGTTAATTAAAGGGC
3675701 TTTGGCTGAATTCTTTTATTTCA
131 TTTGGCTGAATTCTTTTATTTCA
3675724 ACGTTTTTGTT-GTTATGAAGTTGTCTGTGTGATTAAAGCTAAAATAAAAGGATAATGATTATAT
1 ACGTTTTTGTTGGTTATGAAGTTGTCTGTGTGATTAAAGCTAAAATAAAAGGATAATGATTATAT
*
3675788 TGTCTTTTTTTTGAAATTTTATATAAGA-TTTTCCTTCCTGTTTGC-TATTTGTTAATTAAAGGG
66 TGTC-TGTTTTTGAAATTTTATATAAGATTTTTCCTTCCTGTTTGCATATTTGTTAATTAAAGGG
3675851 CTTTGGCTGAATTTCTTTTATTTCA
130 CTTTGGCTGAA-TTCTTTTATTTCA
3675876 AC
1 AC
3675878 AGGATGAAGG
Statistics
Matches: 151, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
151 29 0.19
152 89 0.59
153 33 0.22
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.48
Consensus pattern (153 bp):
ACGTTTTTGTTGGTTATGAAGTTGTCTGTGTGATTAAAGCTAAAATAAAAGGATAATGATTATAT
TGTCTGTTTTTGAAATTTTATATAAGATTTTTCCTTCCTGTTTGCATATTTGTTAATTAAAGGGC
TTTGGCTGAATTCTTTTATTTCA
Found at i:3684824 original size:28 final size:26
Alignment explanation
Indices: 3684788--3684849 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 26
3684778 CAAACACGTC
* *
3684788 CCCGTTTAGCATAAACGGTTTTCCCGT
1 CCCGTTTAGCATAAACGATTCT-CCGT
3684815 CTCCGTTTAGCATAAACGATTCTCCGT
1 C-CCGTTTAGCATAAACGATTCTCCGT
3684842 CCCGTTTA
1 CCCGTTTA
3684850 ATTCGATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 7 0.22
27 6 0.19
28 19 0.59
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (26 bp):
CCCGTTTAGCATAAACGATTCTCCGT
Found at i:3685943 original size:97 final size:96
Alignment explanation
Indices: 3685823--3686009 Score: 295
Period size: 97 Copynumber: 1.9 Consensus size: 96
3685813 ACAAATTCAA
* ** * *
3685823 ATATAATATTTATTTAAATGATATCAAATTAT-TTATTATTTAAATTCATTCGTCGATTAATCTC
1 ATATAATATTTACTTAAATGATATCAAATT-TCTTACAACTTAAATTCATTCGTAGATTAATCTC
3685887 TGCATCTTTAAACATTCTAATAACCTAAAAAT
65 TGCATCTTTAAACATTCTAATAACCTAAAAAT
*
3685919 ATATAATATTTTACTTAAATGATATCAAATTTCTTACAACTTAAATTCATTCGTAGGTTAATCTC
1 ATATAATA-TTTACTTAAATGATATCAAATTTCTTACAACTTAAATTCATTCGTAGATTAATCTC
3685984 TGCATCTTTAAACATTCTAATAACCT
65 TGCATCTTTAAACATTCTAATAACCT
3686010 CCTAAAAATC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
96 9 0.11
97 74 0.89
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (96 bp):
ATATAATATTTACTTAAATGATATCAAATTTCTTACAACTTAAATTCATTCGTAGATTAATCTCT
GCATCTTTAAACATTCTAATAACCTAAAAAT
Found at i:3686783 original size:32 final size:33
Alignment explanation
Indices: 3686742--3686807 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
3686732 CGTGGCTTCG
3686742 TACCAGTAGCCTAAATTCAATGC-TCATTTATA
1 TACCAGTAGCCTAAATTCAATGCTTCATTTATA
3686774 TACCAGTAGCCTAAATTCAATGCTTCATTTATA
1 TACCAGTAGCCTAAATTCAATGCTTCATTTATA
3686807 T
1 T
3686808 GAACGACCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 23 0.70
33 10 0.30
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (33 bp):
TACCAGTAGCCTAAATTCAATGCTTCATTTATA
Found at i:3687330 original size:29 final size:29
Alignment explanation
Indices: 3687297--3687387 Score: 155
Period size: 29 Copynumber: 3.1 Consensus size: 29
3687287 TCGTCAATCC
*
3687297 CTCCGGGCGACCTTGTAGGTCGCCATGAA
1 CTCCGGGCGACCTTGTAGGTCGCCATGCA
3687326 CTCCGGGCGACCTTGTAGGTCGCCATGCA
1 CTCCGGGCGACCTTGTAGGTCGCCATGCA
* *
3687355 CTCCTGGCGACCTTGTAGGTCACCATGCA
1 CTCCGGGCGACCTTGTAGGTCGCCATGCA
3687384 CTCC
1 CTCC
3687388 CTCATTCTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.15, C:0.35, G:0.27, T:0.22
Consensus pattern (29 bp):
CTCCGGGCGACCTTGTAGGTCGCCATGCA
Found at i:3687470 original size:14 final size:14
Alignment explanation
Indices: 3687451--3687482 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3687441 TCAGATAGCT
3687451 TCGGTCGGATGCCC
1 TCGGTCGGATGCCC
3687465 TCGGTCGGATGCCC
1 TCGGTCGGATGCCC
3687479 TCGG
1 TCGG
3687483 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.34, G:0.38, T:0.22
Consensus pattern (14 bp):
TCGGTCGGATGCCC
Found at i:3689268 original size:43 final size:43
Alignment explanation
Indices: 3689163--3689268 Score: 113
Period size: 43 Copynumber: 2.5 Consensus size: 43
3689153 CAATATGTAC
* * * * *
3689163 CGATATTTAGCGGCATTTGTCTTAAAAATGCCGCAATAGGTGT
1 CGATATTTAGCGGCATTTTTATCAAAAATGCCACAATAAGTGT
* * * *
3689206 CAATATTTAGTGGCGTTTTTATCACAAATGCCACAATAAGTGT
1 CGATATTTAGCGGCATTTTTATCAAAAATGCCACAATAAGTGT
* *
3689249 TGATATTTTGCGGCATTTTT
1 CGATATTTAGCGGCATTTTT
3689269 TTATGAAAAC
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (43 bp):
CGATATTTAGCGGCATTTTTATCAAAAATGCCACAATAAGTGT
Found at i:3689390 original size:44 final size:44
Alignment explanation
Indices: 3689275--3689552 Score: 271
Period size: 44 Copynumber: 6.4 Consensus size: 44
3689265 TTTTTTATGA
* * * *
3689275 AAACGTCG-TAATATGTCTGGTATTTAGCGGCGTTTTTAGGGTAAAA
1 AAACGTCGCT-ATAGGTCTGGTATATAGCGGCGTTTTTA-GG-ATAC
* **
3689321 AAACGTCGCTATAGGACTGAAATATAGCGGCGTTTTTAGGATAC
1 AAACGTCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* * *
3689365 AAACGTCGCGATAGGTCAGGTATATAGCGGTGTTTTTAGGATAC
1 AAACGTCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* *
3689409 AAACGCCACTATAGGT-TAGGTATATAGCGGCGTTTTTAGGATAC
1 AAACGTCGCTATAGGTCT-GGTATATAGCGGCGTTTTTAGGATAC
* * * * *
3689453 AAAGGCCGCGATAGGTC-GCTATATAGCGGCATTTTTAGGATAC
1 AAACGTCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
* * * * *
3689496 AAACGCCGCTAAAAGT-TGGTACATAGCGGCGTTTTT--TATAC
1 AAACGTCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
*
3689537 AAACGTCGCAATAGGT
1 AAACGTCGCTATAGGT
3689553 GTTAATATTT
Statistics
Matches: 193, Mismatches: 35, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
41 16 0.08
43 52 0.27
44 91 0.47
45 2 0.01
46 31 0.16
47 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (44 bp):
AAACGTCGCTATAGGTCTGGTATATAGCGGCGTTTTTAGGATAC
Found at i:3694472 original size:83 final size:83
Alignment explanation
Indices: 3694326--3694662 Score: 278
Period size: 83 Copynumber: 4.1 Consensus size: 83
3694316 GTTTTAATAT
* * * * * * **
3694326 AAACGCCA-TGATAAACAACA-TATTGCGGCGTTT-TTAGGACAAATGTCGCTATATTATTACTC
1 AAACGCCACT-ATAAACAATACTATTGCGGCGTTTGTT-TGATAAACGCCGCTAAATTACCACTC
* * *
3694388 TATTAAGGCATTTTTTGCAC
64 TATTAAGGCGTTTGTTGAAC
* **
3694408 AAACGCCACTATAAACAATACTATTGTGGCGTTTGTTTGATAAACGCCGCTAAATTACTTCTCTA
1 AAACGCCACTATAAACAATACTATTGCGGCGTTTGTTTGATAAACGCCGCTAAATTACCACTCTA
*
3694473 -T-AGCGTCGTTTGTTAAAC
66 TTAAG-G-CGTTTGTTGAAC
* * * * * *
3694491 AAACGCCACTATAAACAACACTATAGCGGCATTTGTGT-AAAAATGCCGCTAAATTACCACTCTA
1 AAACGCCACTATAAACAATACTATTGCGGCGTTTGTTTGATAAACGCCGCTAAATTACCACTCTA
* *
3694555 TTACGGCGTTTGTTGAAA
66 TTAAGGCGTTTGTTGAAC
* * *
3694573 AAACGCCACTATAAAC-ATATCTATTACGGCG-TT-TTAGCTATAATCGCCGCTAAATTACCACT
1 AAACGCCACTATAAACAATA-CTATTGCGGCGTTTGTTTG--ATAAACGCCGCTAAATTACCACT
* * * *
3694635 CTATTACGACGTTTGTTTAAA
63 CTATTAAGGCGTTTGTTGAAC
3694656 AAACGCC
1 AAACGCC
3694663 GCTAAAATAT
Statistics
Matches: 208, Mismatches: 36, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
80 1 0.00
81 6 0.03
82 75 0.36
83 123 0.59
84 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (83 bp):
AAACGCCACTATAAACAATACTATTGCGGCGTTTGTTTGATAAACGCCGCTAAATTACCACTCTA
TTAAGGCGTTTGTTGAAC
Found at i:3694579 original size:165 final size:164
Alignment explanation
Indices: 3694326--3694662 Score: 371
Period size: 165 Copynumber: 2.0 Consensus size: 164
3694316 GTTTTAATAT
* * * * * * **
3694326 AAACGCCATGATAAACAACATATTGCGGCGTTTTTAGGACAAATGTCGCTATATTATTACTCTAT
1 AAACGCCATGATAAACAACATATAGCGGCATTTGTAGGAAAAATGCCGCTAAATTACCACTCTAT
* * * ** *
3694391 TAAGGCATTTTTTGCACAAACGCCACTATAAACA-ATACTATTGTGGCGTTTGTTTG-ATAAACG
66 TAAGGCATTTGTTGAAAAAACGCCACTATAAACATAT-CTATTACGGCG-TT-TTAGCATAAACG
** *
3694454 CCGCTAAATTACTTCTCTA-TAGCGTCGTTTG-TTAAA
128 CCGCTAAATTACCACTCTATTA-CGACGTTTGTTTAAA
*
3694490 CAAACGCCACT-ATAAACAACACTATAGCGGCATTTGT-GTAAAAATGCCGCTAAATTACCACTC
1 -AAACGCCA-TGATAAACAACA-TATAGCGGCATTTGTAGGAAAAATGCCGCTAAATTACCACTC
* * *
3694553 TATTACGGCGTTTGTTGAAAAAACGCCACTATAAACATATCTATTACGGCGTTTTAGCTATAATC
63 TATTAAGGCATTTGTTGAAAAAACGCCACTATAAACATATCTATTACGGCGTTTTAGC-ATAAAC
3694618 GCCGCTAAATTACCACTCTATTACGACGTTTGTTTAAA
127 GCCGCTAAATTACCACTCTATTACGACGTTTGTTTAAA
3694656 AAACGCC
1 AAACGCC
3694663 GCTAAAATAT
Statistics
Matches: 144, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
163 3 0.02
164 2 0.01
165 117 0.81
166 22 0.15
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (164 bp):
AAACGCCATGATAAACAACATATAGCGGCATTTGTAGGAAAAATGCCGCTAAATTACCACTCTAT
TAAGGCATTTGTTGAAAAAACGCCACTATAAACATATCTATTACGGCGTTTTAGCATAAACGCCG
CTAAATTACCACTCTATTACGACGTTTGTTTAAA
Found at i:3694596 original size:41 final size:40
Alignment explanation
Indices: 3694408--3694606 Score: 115
Period size: 41 Copynumber: 4.8 Consensus size: 40
3694398 TTTTTTGCAC
** *
3694408 AAACGCCACTATAAACAATACTATTGTGGCGTTTGTTTG-AT
1 AAACGCCACTATAAACAAT-CTATTACGGCGTTTG-TTGAAA
* * * *
3694449 AAACGCCGCTA-AATTAC-TTCTCTATAGCGTCGTTTGTT-AAA
1 AAACGCCACTATAA--ACAATCTAT-TA-CGGCGTTTGTTGAAA
* * *
3694490 CAAACGCCACTATAAACAACACTA-TAGCGGCATTTG-TGTAA
1 -AAACGCCACTATAAACAA-TCTATTA-CGGCGTTTGTTGAAA
* * *
3694531 AAATGCCGCTA-AATTACCACTCTATTACGGCGTTTGTTGAAA
1 AAACGCCACTATAA--A-CAATCTATTACGGCGTTTGTTGAAA
3694573 AAACGCCACTATAAACATATCTATTACGGCGTTT
1 AAACGCCACTATAAACA-ATCTATTACGGCGTTT
3694607 TAGCTATAAT
Statistics
Matches: 118, Mismatches: 23, Indels: 34
0.67 0.13 0.19
Matches are distributed among these distances:
39 2 0.02
40 17 0.14
41 57 0.48
42 36 0.31
43 6 0.05
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (40 bp):
AAACGCCACTATAAACAATCTATTACGGCGTTTGTTGAAA
Found at i:3700273 original size:2 final size:2
Alignment explanation
Indices: 3700268--3700295 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3700258 ACTTTTTTTA
3700268 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
3700296 TAATTTGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3701219 original size:40 final size:37
Alignment explanation
Indices: 3701157--3701231 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 37
3701147 TAATGTTAAA
*
3701157 TTTTAAATGGGGTACTAAAATGAAATAAAAATTAAATT
1 TTTTAAATGGGGTACTAAAATG-AACAAAAATTAAATT
* *
3701195 TTTTATATGAGGGTTACTAGAATGAACAAAAATTAAA
1 TTTTAAATG-GGG-TACTAAAATGAACAAAAATTAAA
3701232 CTTTAAGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 8 0.25
39 15 0.47
40 9 0.28
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (37 bp):
TTTTAAATGGGGTACTAAAATGAACAAAAATTAAATT
Found at i:3701979 original size:2 final size:2
Alignment explanation
Indices: 3701974--3702011 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3701964 CCCTCTCTCG
3701974 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
3702012 GTTATTGGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3712507 original size:14 final size:14
Alignment explanation
Indices: 3712490--3712518 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3712480 CAATTTAAGT
3712490 GAGACCATTTTAAA
1 GAGACCATTTTAAA
3712504 GAGACCATTTTAAA
1 GAGACCATTTTAAA
3712518 G
1 G
3712519 CACAAAATAG
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:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (14 bp):
GAGACCATTTTAAA
Found at i:3712757 original size:20 final size:20
Alignment explanation
Indices: 3712715--3712759 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3712705 TAATTAGCGG
* * *
3712715 TGCGAATTTGAAAATCGCGT
1 TGCGAATTTAAAAATCACAT
3712735 TGCGAATTTAAAAATCACAT
1 TGCGAATTTAAAAATCACAT
3712755 TGCGA
1 TGCGA
3712760 TAGTACTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (20 bp):
TGCGAATTTAAAAATCACAT
Found at i:3712825 original size:20 final size:20
Alignment explanation
Indices: 3712800--3712860 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
3712790 ACCGATATAG
*
3712800 GTAAACAATACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
* *
3712820 GTAAACAGTATTATTGCAAT
1 GTAAACAGTACTATCGCAAT
*
3712840 ATAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
3712860 G
1 G
3712861 CGATTTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:3712877 original size:19 final size:20
Alignment explanation
Indices: 3712853--3712900 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
3712843 AACAGTACTA
* *
3712853 TCGCAATGCGATTTT-TAAT
1 TCGCAACGCGATTTTCAAAT
3712872 TCGCAACGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
3712892 TCGCAACGC
1 TCGCAACGC
3712901 TAATTACCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:3712941 original size:20 final size:20
Alignment explanation
Indices: 3712916--3712976 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
3712906 ACCGATATAG
*
3712916 GTAAACAGTATTATCGCAAT
1 GTAAACAGTACTATCGCAAT
3712936 GTAAACAGTACTATCGCAAT
1 GTAAACAGTACTATCGCAAT
* *
3712956 ATAAACAGTACTATTGCAAT
1 GTAAACAGTACTATCGCAAT
3712976 G
1 G
3712977 CGATTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (20 bp):
GTAAACAGTACTATCGCAAT
Found at i:3712975 original size:116 final size:117
Alignment explanation
Indices: 3712768--3712997 Score: 408
Period size: 116 Copynumber: 2.0 Consensus size: 117
3712758 GATAGTACTG
*
3712768 TTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAATGTAAACAGTATTA
1 TTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAATGTAAACAGTACTA
*
3712833 TTGCAATATAAACAGTACTATCGCAATGCGATTTTT-AATTCGCAACGCGAT
66 TCGCAATATAAACAGTACTATCGCAATGCGATTTTTAAATTCGCAACGCGAT
* *
3712884 TTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTATTATCGCAATGTAAACAGTACTA
1 TTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAATGTAAACAGTACTA
*
3712949 TCGCAATATAAACAGTACTATTGCAATGCGATTTTTAAATTCGCAACGC
66 TCGCAATATAAACAGTACTATCGCAATGCGATTTTTAAATTCGCAACGC
3712998 TAATTACCGA
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
116 96 0.89
117 12 0.11
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (117 bp):
TTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAATGTAAACAGTACTA
TCGCAATATAAACAGTACTATCGCAATGCGATTTTTAAATTCGCAACGCGAT
Found at i:3713015 original size:97 final size:96
Alignment explanation
Indices: 3712820--3713031 Score: 273
Period size: 97 Copynumber: 2.2 Consensus size: 96
3712810 CTATCGCAAT
* * * ****
3712820 GTAAACAGTATTATTGCAATATAAACAGTACTATCGCAATGCGATTTTTAATTCGCAACGCGATT
1 GTAAACAGTATTATCGCAATATAAACAGTACTATCGCAATACAAACAGTAATTCGCAACGCGATT
*
3712885 TTCAAATTCGCAACGCTAATTACCGATATAG
66 TTCAAATTCGCAACGCTAATTACCGAGATAG
* * *
3712916 GTAAACAGTATTATCGCAATGTAAACAGTACTATCGCAATATAAACAGTACTATT-GCAATGCGA
1 GTAAACAGTATTATCGCAATATAAACAGTACTATCGCAATACAAACAGTA--ATTCGCAACGCGA
*
3712980 TTTTTAAATTCGCAACGCTAATTACCGAGATAG
64 TTTTCAAATTCGCAACGCTAATTACCGAGATAG
* *
3713013 GTAAACAGAACTATCGCAA
1 GTAAACAGTATTATCGCAA
3713032 CGCGATTTTC
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
96 41 0.41
97 56 0.56
98 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (96 bp):
GTAAACAGTATTATCGCAATATAAACAGTACTATCGCAATACAAACAGTAATTCGCAACGCGATT
TTCAAATTCGCAACGCTAATTACCGAGATAG
Found at i:3713026 original size:57 final size:57
Alignment explanation
Indices: 3712957--3713093 Score: 193
Period size: 57 Copynumber: 2.4 Consensus size: 57
3712947 TATCGCAATA
* * * * *
3712957 TAAACAGTACTATTGCAATGCGATTTTTAAATTCGCAACGCTAATTACCGAGATAGG
1 TAAACAGAACTATCGCAACGCGATTTTCAAATTCACAACGCTAATTACCGAGATAGG
* * *
3713014 TAAACAGAACTATCGCAACGCGATTTTCAAATTCACAACTCTAATTATCGATATAGG
1 TAAACAGAACTATCGCAACGCGATTTTCAAATTCACAACGCTAATTACCGAGATAGG
*
3713071 TAAACACAACTATCGCAACGCGA
1 TAAACAGAACTATCGCAACGCGA
3713094 ATTTGGAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 71 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (57 bp):
TAAACAGAACTATCGCAACGCGATTTTCAAATTCACAACGCTAATTACCGAGATAGG
Found at i:3718406 original size:29 final size:29
Alignment explanation
Indices: 3718325--3718428 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 29
3718315 ATTTTTCATT
* * *
3718325 TAAGTACTTAAAGTATTTTTTTAGTCAACA
1 TAAGTACCTAAAGTATTTTTTGA-TCAAAA
* ** *
3718355 TGAGTATATAAATTTATCTTTTTGATCAAAA
1 TAAGTACCTAAA-GTAT-TTTTTGATCAAAA
*
3718386 TAAGTACCTAAAGTATTTTTTGATTAAAA
1 TAAGTACCTAAAGTATTTTTTGATCAAAA
* *
3718415 TATGTATCTAAAGT
1 TAAGTACCTAAAGT
3718429 GTTCAATTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
29 24 0.41
30 12 0.20
31 17 0.29
32 6 0.10
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (29 bp):
TAAGTACCTAAAGTATTTTTTGATCAAAA
Found at i:3734045 original size:20 final size:20
Alignment explanation
Indices: 3734016--3734055 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3734006 TGTATTGAAG
*
3734016 AGGTATAGGAAAACAACATA
1 AGGTAGAGGAAAACAACATA
3734036 AGGTAGAGGAAAACAACATA
1 AGGTAGAGGAAAACAACATA
3734056 TGAGAACTAA
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:0.55, C:0.10, G:0.23, T:0.12
Consensus pattern (20 bp):
AGGTAGAGGAAAACAACATA
Found at i:3737126 original size:27 final size:27
Alignment explanation
Indices: 3737096--3737150 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
3737086 AAGACTTGCA
3737096 TTATAAATAAGTACCTAA-AGTATACCT
1 TTATAAATAAGTACCTAACA-TATACCT
3737123 TTATAAATAAGTACCTAACATATACCT
1 TTATAAATAAGTACCTAACATATACCT
3737150 T
1 T
3737151 CTTTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (27 bp):
TTATAAATAAGTACCTAACATATACCT
Found at i:3737213 original size:26 final size:28
Alignment explanation
Indices: 3737169--3737232 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 28
3737159 TTTAAATACC
3737169 TAAAGTATTTTTGAGTCAAAATAAGTACA
1 TAAAGTATTTTT-AGTCAAAATAAGTACA
*
3737198 TAAAGT-TTTTT-GTCAAAATAAGTACC
1 TAAAGTATTTTTAGTCAAAATAAGTACA
*
3737224 TAAACTATT
1 TAAAGTATT
3737233 CAAAAAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 19 0.59
27 2 0.06
28 5 0.16
29 6 0.19
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (28 bp):
TAAAGTATTTTTAGTCAAAATAAGTACA
Found at i:3737383 original size:31 final size:31
Alignment explanation
Indices: 3737312--3737386 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
3737302 TGAAAAATTG
*
3737312 AATACTTTAGGCACCTATTTTGATCTAAAAA
1 AATACTTTAGGTACCTATTTTGATCTAAAAA
3737343 AATACTTTAGGTACCTATTTTGA-CTAAAAA
1 AATACTTTAGGTACCTATTTTGATCTAAAAA
* *
3737373 GATAATTTTAGGTA
1 AAT-ACTTTAGGTA
3737387 TTTTTTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.22
31 31 0.77
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (31 bp):
AATACTTTAGGTACCTATTTTGATCTAAAAA
Found at i:3738592 original size:4 final size:4
Alignment explanation
Indices: 3738585--3738668 Score: 114
Period size: 4 Copynumber: 21.0 Consensus size: 4
3738575 TCACACACAC
* ** * *
3738585 ATGT ATGT ATAT ACAT ATGC ATGT ATGT ATGT ATGC ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
3738633 ATGT ATGT ATGT ATGT ATGT ATGC ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3738669 GAAGAAAGCT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 70 1.00
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:3749486 original size:10 final size:10
Alignment explanation
Indices: 3749457--3749519 Score: 69
Period size: 10 Copynumber: 6.5 Consensus size: 10
3749447 GCTCCTGGAA
3749457 AACCGGTTTG
1 AACCGGTTTG
*
3749467 -ACCAGTTTTG
1 AACC-GGTTTG
3749477 AACCGGTTTG
1 AACCGGTTTG
*
3749487 -ACCGGTTCG
1 AACCGGTTTG
3749496 AACCGGTTTG
1 AACCGGTTTG
*
3749506 -ACCGGTCTG
1 AACCGGTTTG
3749515 AACCG
1 AACCG
3749520 ACTGTTGACC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 19 0.43
10 22 0.50
11 3 0.07
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:3749500 original size:19 final size:19
Alignment explanation
Indices: 3749457--3749511 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
3749447 GCTCCTGGAA
* *
3749457 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
3749477 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
3749496 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
3749512 CTGAACCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:3749517 original size:19 final size:18
Alignment explanation
Indices: 3749457--3749519 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
3749447 GCTCCTGGAA
*
3749457 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-G-GTTG
3749477 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTT-G
3749496 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGT-TG
3749515 AACCG
1 AACCG
3749520 ACTGTTGACC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 2 0.05
19 24 0.60
20 14 0.35
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (18 bp):
AACCGGTTTGACCGGTTG
Found at i:3750500 original size:31 final size:30
Alignment explanation
Indices: 3750429--3750503 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
3750419 CTAATGTGAC
* * *
3750429 TCTTAGGTAGGCTCTGCGGCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGCCCTAAGATCAT
** **
3750459 TCTCGGGTAGGCCCTGCGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGCCCTAAGAT-CAT
3750490 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
3750504 CACGGCCCCG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 22 0.63
31 13 0.37
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.28
Consensus pattern (30 bp):
TCTTAGGTAGGCCCTGCGCCCTAAGATCAT
Found at i:3756013 original size:9 final size:9
Alignment explanation
Indices: 3755981--3756053 Score: 83
Period size: 10 Copynumber: 7.7 Consensus size: 9
3755971 CTCCTGAAAA
3755981 ACCGGTTTG
1 ACCGGTTTG
*
3755990 ACCAGTTTTG
1 ACC-GGTTTG
3756000 AACCGGTTTG
1 -ACCGGTTTG
*
3756010 ACCGGTTCG
1 ACCGGTTTG
3756019 AACCGGTTTG
1 -ACCGGTTTG
*
3756029 ACCGGTCTG
1 ACCGGTTTG
3756038 AACCGGTTTG
1 -ACCGGTTTG
3756048 ACCGGT
1 ACCGGT
3756054 CTGAACCGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 25 0.46
10 26 0.48
11 3 0.06
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3756054 original size:19 final size:19
Alignment explanation
Indices: 3755980--3756061 Score: 121
Period size: 19 Copynumber: 4.3 Consensus size: 19
3755970 GCTCCTGAAA
* *
3755980 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
3756000 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
3756019 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
3756038 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
3756057 AACCG
1 AACCG
3756062 ACTGTTGACC
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
18 1 0.02
19 44 0.75
20 14 0.24
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:3757104 original size:63 final size:63
Alignment explanation
Indices: 3757021--3757144 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
3757011 CTAATGTGAC
* ** * *
3757021 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* * *
3757084 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCATGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
3757145 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:3757891 original size:36 final size:36
Alignment explanation
Indices: 3757844--3757921 Score: 156
Period size: 36 Copynumber: 2.2 Consensus size: 36
3757834 CGATGAAAAG
3757844 GTTGTTGGTTATGGAGGGAAAGGGTTGATTGAAGGA
1 GTTGTTGGTTATGGAGGGAAAGGGTTGATTGAAGGA
3757880 GTTGTTGGTTATGGAGGGAAAGGGTTGATTGAAGGA
1 GTTGTTGGTTATGGAGGGAAAGGGTTGATTGAAGGA
3757916 GTTGTT
1 GTTGTT
3757922 TGTAACACCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.23, C:0.00, G:0.44, T:0.33
Consensus pattern (36 bp):
GTTGTTGGTTATGGAGGGAAAGGGTTGATTGAAGGA
Found at i:3764333 original size:32 final size:30
Alignment explanation
Indices: 3764296--3764360 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
3764286 TTGACTATAT
*
3764296 ATTCTTTTTGTATTGAA-TTTTATTCACTTTTA
1 ATTCTTTTT-TATAGAATTTTTA-T-ACTTTTA
*
3764328 ATTCTTTTTTATAGCATTTTTATACTTTTA
1 ATTCTTTTTTATAGAATTTTTATACTTTTA
3764358 ATT
1 ATT
3764361 ACAATTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 10 0.33
31 6 0.20
32 14 0.47
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.63
Consensus pattern (30 bp):
ATTCTTTTTTATAGAATTTTTATACTTTTA
Found at i:3764416 original size:10 final size:10
Alignment explanation
Indices: 3764401--3764458 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
3764391 ATTTTTTTTA
3764401 AAAAATCAAT
1 AAAAATCAAT
3764411 AAAAATACAAT
1 AAAAAT-CAAT
3764422 AAAAAAT-AATT
1 -AAAAATCAA-T
* *
3764433 AAAAGTGAAT
1 AAAAATCAAT
*
3764443 AAAATTCAAT
1 AAAAATCAAT
3764453 AAAAAT
1 AAAAAT
3764459 GTCAACTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 27 0.68
11 7 0.17
12 6 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAAATCAAT
Found at i:3764426 original size:21 final size:21
Alignment explanation
Indices: 3764399--3764458 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
3764389 TCATTTTTTT
3764399 TAAAAAATCAATAAAAATACAA
1 TAAAAAATCAATAAAAAT-CAA
* *
3764421 TAAAAAAT-AATTAAAAGTGAA
1 TAAAAAATCAA-TAAAAATCAA
*
3764442 T-AAAATTCAATAAAAAT
1 TAAAAAATCAATAAAAAT
3764459 GTCAACTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 11 0.34
21 7 0.22
22 14 0.44
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.23
Consensus pattern (21 bp):
TAAAAAATCAATAAAAATCAA
Found at i:3778915 original size:22 final size:22
Alignment explanation
Indices: 3778885--3778927 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3778875 TTATAAAATT
*
3778885 TTATTAAATAAATACAAAATAA
1 TTATAAAATAAATACAAAATAA
* *
3778907 TTATAAAATTATTACAAAATA
1 TTATAAAATAAATACAAAATA
3778928 GTTGTTGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (22 bp):
TTATAAAATAAATACAAAATAA
Found at i:3783946 original size:33 final size:34
Alignment explanation
Indices: 3783868--3783947 Score: 110
Period size: 33 Copynumber: 2.4 Consensus size: 34
3783858 AAATCTAACT
* *
3783868 TAGGGTTTATAATTTAGAGTTTTTAATTTAGGGG
1 TAGGGTTTATAATTTAGAGTTTTTAAGTTAGGGA
3783902 T-GAGGTTTATAATTTAGAG-TTTTAAGTTAGGGA
1 TAG-GGTTTATAATTTAGAGTTTTTAAGTTAGGGA
*
3783935 TAGGGTATATAAT
1 TAGGGTTTATAAT
3783948 AATGCAATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 23 0.56
34 18 0.44
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (34 bp):
TAGGGTTTATAATTTAGAGTTTTTAAGTTAGGGA
Found at i:3784045 original size:2 final size:2
Alignment explanation
Indices: 3784038--3784088 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3784028 TCAAGCCTAT
3784038 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
3784080 TA TA TA TA T
1 TA TA TA TA T
3784089 TTTTTTATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3787701 original size:26 final size:27
Alignment explanation
Indices: 3787672--3787727 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
3787662 TTTTATAATA
* *
3787672 ATAAATATTTTATAATTTT-AAAAATT
1 ATAAAAATTATATAATTTTAAAAAATT
*
3787698 ATAAAAATTATATATTTTTGAAAAAATT
1 ATAAAAATTATATAATTTT-AAAAAATT
3787726 AT
1 AT
3787728 TGAATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 16 0.64
28 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
ATAAAAATTATATAATTTTAAAAAATT
Found at i:3788196 original size:26 final size:28
Alignment explanation
Indices: 3788151--3788206 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
3788141 TTAAAATACA
3788151 ATAATTTTTTCAAAAATATATAAA-ATTT
1 ATAATTTTTTCAAAAATATA-AAATATTT
*
3788179 ATAA-TTTTT-AAAATTATAAAATATTT
1 ATAATTTTTTCAAAAATATAAAATATTT
3788205 AT
1 AT
3788207 TATTATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 3 0.12
26 14 0.54
27 5 0.19
28 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
ATAATTTTTTCAAAAATATAAAATATTT
Found at i:3788217 original size:26 final size:26
Alignment explanation
Indices: 3788162--3788218 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
3788152 TAATTTTTTC
*
3788162 AAAAA-TATATAAAATTTATAATTTT
1 AAAAATTATATAAAATTTATAATTAT
* *
3788187 TAAAATTATA-AAATATTTATTATTAT
1 AAAAATTATATAAA-ATTTATAATTAT
3788213 AAAAAT
1 AAAAAT
3788219 AAACTTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAAATTATATAAAATTTATAATTAT
Found at i:3789355 original size:19 final size:19
Alignment explanation
Indices: 3789328--3789376 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
3789318 TTAGAATACG
3789328 TATTAATTAT-GTGTATAATT
1 TATT-ATTATAGT-TATAATT
3789348 TATTATTATAGTTATAATT
1 TATTATTATAGTTATAATT
*
3789367 TTTTATTATA
1 TATTATTATA
3789377 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (19 bp):
TATTATTATAGTTATAATT
Found at i:3793797 original size:6 final size:6
Alignment explanation
Indices: 3793786--3793952 Score: 75
Period size: 6 Copynumber: 27.3 Consensus size: 6
3793776 CCTCGTTAAC
* * * * * *
3793786 CTCCTT CTCCTTCT CATCCTC CTCCTC CTCCTC CTCCTC CTCCTT CTCATC
1 CTCCTT CTCC-T-T C-TCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT
* * * * * * *
3793837 CTCCTC CTCCTT CTTCTT CTTCTT CTTCTT TTTCTT CTCCTC CTCCTT
1 CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT
* ** ** * * * *
3793885 CTTCTT CTTTTT CTTTTT CTTCTC CT-CTT CCTCCTC CTCCTT CTTCTT
1 CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT -CTCCTT CTCCTT CTCCTT
* *
3793933 CTCCTT CTTCTT CTTCTT CT
1 CTCCTT CTCCTT CTCCTT CT
3793953 TAAGTGTGAA
Statistics
Matches: 134, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
5 2 0.01
6 122 0.91
7 4 0.03
8 3 0.02
9 3 0.02
ACGTcount: A:0.01, C:0.46, G:0.00, T:0.53
Consensus pattern (6 bp):
CTCCTT
Found at i:3793805 original size:9 final size:9
Alignment explanation
Indices: 3793785--3793940 Score: 62
Period size: 9 Copynumber: 17.0 Consensus size: 9
3793775 CCCTCGTTAA
3793785 CCTCCTTCT
1 CCTCCTTCT
*
3793794 CCTTCTCATCCT
1 CC-TC-C-TTCT
*
3793806 CCTCCTCCT
1 CCTCCTTCT
*
3793815 CCTCCTCCT
1 CCTCCTTCT
3793824 CCTCCTTCT
1 CCTCCTTCT
* *
3793833 CATCCTCCT
1 CCTCCTTCT
3793842 CCTCCTTCT
1 CCTCCTTCT
* *
3793851 TCTTCTTCT
1 CCTCCTTCT
* * *
3793860 TCTTCTTTT
1 CCTCCTTCT
* * *
3793869 TCTTCTCCT
1 CCTCCTTCT
3793878 CCTCCTTCT
1 CCTCCTTCT
* * *
3793887 TCTTCTTTT
1 CCTCCTTCT
* **
3793896 TCTTTTTCT
1 CCTCCTTCT
*
3793905 TCTCC-TCTT
1 CCTCCTTC-T
*
3793914 CCTCCTCCT
1 CCTCCTTCT
*
3793923 CCTTCTTCT
1 CCTCCTTCT
*
3793932 TCTCCTTCT
1 CCTCCTTCT
3793941 TCTTCTTCTT
Statistics
Matches: 115, Mismatches: 27, Indels: 10
0.76 0.18 0.07
Matches are distributed among these distances:
8 2 0.02
9 101 0.88
10 4 0.03
11 3 0.03
12 5 0.04
ACGTcount: A:0.01, C:0.47, G:0.00, T:0.51
Consensus pattern (9 bp):
CCTCCTTCT
Found at i:3793808 original size:18 final size:18
Alignment explanation
Indices: 3793785--3793850 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
3793775 CCCTCGTTAA
*
3793785 CCTCCTTCTCCTTCTCAT
1 CCTCCTCCTCCTTCTCAT
3793803 CCTCCTCCTCC-TC-C-T
1 CCTCCTCCTCCTTCTCAT
3793818 CCTCCTCCTCCTTCTCAT
1 CCTCCTCCTCCTTCTCAT
3793836 CCTCCTCCTCCTTCT
1 CCTCCTCCTCCTTCT
3793851 TCTTCTTCTT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
15 12 0.27
16 3 0.07
17 3 0.07
18 26 0.59
ACGTcount: A:0.03, C:0.58, G:0.00, T:0.39
Consensus pattern (18 bp):
CCTCCTCCTCCTTCTCAT
Found at i:3793810 original size:3 final size:3
Alignment explanation
Indices: 3793785--3793847 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
3793775 CCCTCGTTAA
* * * *
3793785 CCT CCT TCT CCT TCT CAT CCT CCT CCT CCT CCT CCT CCT CCT CCT TCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
*
3793833 CAT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT
3793848 TCTTCTTCTT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.38
Consensus pattern (3 bp):
CCT
Found at i:3793852 original size:3 final size:3
Alignment explanation
Indices: 3793846--3793953 Score: 101
Period size: 3 Copynumber: 36.0 Consensus size: 3
3793836 CCTCCTCCTC
* * * *
3793846 CTT CTT CTT CTT CTT CTT CTT TTT CTT CTC CTC CTC CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * * * *
3793894 TTT CTT TTT CTT C-T CCT CTT CCTC CTC CTC CTT CTT CTT CTC CTT
1 CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT
3793939 CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT
3793954 AAGTGTGAAG
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.02
3 86 0.96
4 2 0.02
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:3793865 original size:33 final size:33
Alignment explanation
Indices: 3793785--3793935 Score: 131
Period size: 33 Copynumber: 4.5 Consensus size: 33
3793775 CCCTCGTTAA
*
3793785 CCTCCTTCTCCTTCTCATCCTCCTCCTCCTCCT
1 CCTCCTTCTTCTTCTCATCCTCCTCCTCCTCCT
* * *
3793818 CCTCCTCCTCCTTCTCATCCTCCTCCTCCTTCT
1 CCTCCTTCTTCTTCTCATCCTCCTCCTCCTCCT
* * ** * *
3793851 TCTTCTTCTTCTTCTTTTTCTTCTCCTCCTCCT
1 CCTCCTTCTTCTTCTCATCCTCCTCCTCCTCCT
* * * ** *
3793884 TCTTCTTCTTTTTCTTTTTCTTCTCCTCTTCCTCCT
1 CCTCCTTCTTCTTC-TCATC--CTCCTCCTCCTCCT
3793920 CCTCCTTCTTCTTCTC
1 CCTCCTTCTTCTTCTC
3793936 CTTCTTCTTC
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
33 68 0.71
34 4 0.04
35 1 0.01
36 23 0.24
ACGTcount: A:0.01, C:0.48, G:0.00, T:0.51
Consensus pattern (33 bp):
CCTCCTTCTTCTTCTCATCCTCCTCCTCCTCCT
Found at i:3793877 original size:36 final size:36
Alignment explanation
Indices: 3793837--3793949 Score: 147
Period size: 36 Copynumber: 3.1 Consensus size: 36
3793827 CCTTCTCATC
3793837 CTCCTCCTCCTTCTTCTTCTTCTTCTTCTTTTTCTT
1 CTCCTCCTCCTTCTTCTTCTTCTTCTTCTTTTTCTT
*
3793873 CTCCTCCTCCTTCTTCTTCTTTTTCTT-TTTCTTCTCCT
1 CTCCTCCTCCTTCTTCTTCTTCTTCTTCTTT-TTCT--T
* * *
3793911 CTTCCTCCTCCTCCTTCTTCTTCTCCTTCTTCTTCTT
1 C-TCCTCCTCCTTCTTCTTCTTCTTCTTCTTTTTCTT
3793948 CT
1 CT
3793950 TCTTAAGTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
35 3 0.04
36 31 0.46
37 2 0.03
38 2 0.03
39 27 0.40
40 2 0.03
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (36 bp):
CTCCTCCTCCTTCTTCTTCTTCTTCTTCTTTTTCTT
Found at i:3793892 original size:42 final size:42
Alignment explanation
Indices: 3793823--3793951 Score: 161
Period size: 42 Copynumber: 3.0 Consensus size: 42
3793813 CTCCTCCTCC
* * *
3793823 TCCTCCTTCTCATCCTCCTCCTCCTTCTTCTTCTTCTTCTTCT
1 TCCT-CTTCTCCTCCTCCTTCTTCTTCTTCTTCTTCTTCTTCT
** * *
3793866 TTTTCTTCTCCTCCTCCTTCTTCTTCTTTTTCTTTTTCTTC-
1 TCCTCTTCTCCTCCTCCTTCTTCTTCTTCTTCTTCTTCTTCT
*
3793907 TCCTCTTCCTCCTCCTCCTTCTTCTTCTCCTTCTTCTTCTTCT
1 TCCTCTT-CTCCTCCTCCTTCTTCTTCTTCTTCTTCTTCTTCT
3793950 TC
1 TC
3793952 TTAAGTGTGA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
41 5 0.07
42 63 0.88
43 4 0.06
ACGTcount: A:0.01, C:0.43, G:0.00, T:0.57
Consensus pattern (42 bp):
TCCTCTTCTCCTCCTCCTTCTTCTTCTTCTTCTTCTTCTTCT
Found at i:3793941 original size:9 final size:9
Alignment explanation
Indices: 3793825--3793952 Score: 80
Period size: 9 Copynumber: 14.2 Consensus size: 9
3793815 CCTCCTCCTC
3793825 CTCCTTC-T
1 CTCCTTCTT
* *
3793833 CATCCTCCTC
1 C-TCCTTCTT
3793843 CTCCTTCTT
1 CTCCTTCTT
*
3793852 CTTCTTCTT
1 CTCCTTCTT
* *
3793861 CTTCTTTTT
1 CTCCTTCTT
* * *
3793870 CTTCTCCTC
1 CTCCTTCTT
3793879 CTCCTTCTT
1 CTCCTTCTT
* *
3793888 CTTCTTTTT
1 CTCCTTCTT
**
3793897 CTTTTTCTT
1 CTCCTTCTT
3793906 CTCC-TCTT
1 CTCCTTCTT
* *
3793914 CCTCCTCCTC
1 -CTCCTTCTT
*
3793924 CTTCTTCTT
1 CTCCTTCTT
3793933 CTCCTTCTT
1 CTCCTTCTT
*
3793942 CTTCTTCTT
1 CTCCTTCTT
3793951 CT
1 CT
3793953 TAAGTGTGAA
Statistics
Matches: 91, Mismatches: 25, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
8 5 0.05
9 83 0.91
10 3 0.03
ACGTcount: A:0.01, C:0.42, G:0.00, T:0.57
Consensus pattern (9 bp):
CTCCTTCTT
Found at i:3802873 original size:3 final size:3
Alignment explanation
Indices: 3802865--3802894 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3802855 TTCACACAGT
3802865 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
3802895 CATTCTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3803636 original size:30 final size:31
Alignment explanation
Indices: 3803579--3803645 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
3803569 AAAAATTTAA
* *
3803579 AGTTTAGGTACGAAAACGAACTAAAACTGAT
1 AGTTTAAGTACGAAAACGAACTAAAACTAAT
*
3803610 AGTTTAAGTACTAAAACGAA-TAAAACTAAT
1 AGTTTAAGTACGAAAACGAACTAAAACTAAT
3803640 AGTTTA
1 AGTTTA
3803646 GATATTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (31 bp):
AGTTTAAGTACGAAAACGAACTAAAACTAAT
Found at i:3808398 original size:10 final size:10
Alignment explanation
Indices: 3808383--3808412 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3808373 AATAAATATA
3808383 GTTTGTTCGT
1 GTTTGTTCGT
*
3808393 GTTTGTTCAT
1 GTTTGTTCGT
3808403 GTTTGTTCGT
1 GTTTGTTCGT
3808413 TAAAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.03, C:0.10, G:0.27, T:0.60
Consensus pattern (10 bp):
GTTTGTTCGT
Found at i:3808455 original size:24 final size:24
Alignment explanation
Indices: 3808420--3808477 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
3808410 CGTTAAAATG
* *
3808420 ATAAACGAACACAAACGAACGAAT
1 ATAAACGAACACAAACAAACGAAC
* *
3808444 ATAAACGGACACAAATAAACGAAC
1 ATAAACGAACACAAACAAACGAAC
3808468 ATAAACGAAC
1 ATAAACGAAC
3808478 GAACATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.59, C:0.21, G:0.12, T:0.09
Consensus pattern (24 bp):
ATAAACGAACACAAACAAACGAAC
Found at i:3808483 original size:14 final size:14
Alignment explanation
Indices: 3808423--3808486 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
3808413 TAAAATGATA
*
3808423 AACGAACACAAACG
1 AACGAACATAAACG
*
3808437 AACGAATATAAACG
1 AACGAACATAAACG
*
3808451 GAC--ACA-AATA--
1 AACGAACATAA-ACG
3808461 AACGAACATAAACG
1 AACGAACATAAACG
3808475 AACGAACATAAA
1 AACGAACATAAA
3808487 ATTAATTGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
10 2 0.05
11 2 0.05
12 7 0.18
13 2 0.05
14 26 0.67
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.08
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:3809130 original size:51 final size:50
Alignment explanation
Indices: 3809037--3809137 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 50
3809027 ATTTATAAAT
* *
3809037 TTGATACCTTAAAATTTATATTTTTTAAATTTGACACCTAAAATAAATTTG
1 TTGACACCTTAAAA-TTATATTTTTTAAACTTGACACCTAAAATAAATTTG
* *
3809088 TTGACACCTTAAAA-TATTTTTTTTAAAGCTTGACACTTTAAAATAAATTT
1 TTGACACCTTAAAATTATATTTTTTAAA-CTTGACAC-CTAAAATAAATTT
3809138 TCTAACTCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
49 12 0.27
50 7 0.16
51 25 0.57
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.45
Consensus pattern (50 bp):
TTGACACCTTAAAATTATATTTTTTAAACTTGACACCTAAAATAAATTTG
Found at i:3816935 original size:31 final size:29
Alignment explanation
Indices: 3816872--3816946 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
3816862 GATGTATCGT
3816872 TTATACCACTGAACTTTCAATTTTGTCAA
1 TTATACCACTGAACTTTCAATTTTGTCAA
* *
3816901 TTATAGCACTGAACTTT-GATTTTCGTTTCAA
1 TTATACCACTGAACTTTCAATTTT-G--TCAA
*
3816932 TTATACCACTAAACT
1 TTATACCACTGAACT
3816947 ATTAAATCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 5 0.13
29 17 0.44
31 17 0.44
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (29 bp):
TTATACCACTGAACTTTCAATTTTGTCAA
Found at i:3819969 original size:293 final size:293
Alignment explanation
Indices: 3819389--3819979 Score: 922
Period size: 293 Copynumber: 2.0 Consensus size: 293
3819379 CTAAACTATC
* * * *
3819389 AATTTTAGTTTGTTTTAGTATTTAAACTTTTAATTCTTTCAAAATCATATATGATATTTAGTTTT
1 AATTTTAGTCTGTTGTAGTATTTAAACTTTCAATTCTTTCAAAATCATACATGATATTTAGTTTT
* *
3819454 TGTTTCATTTTATTGCCTGACATTAAAAACTTAACGCATATAGTACATAAACTATCAATTTTGGT
66 TGTTTCATTTTAGTACCTGACATTAAAAACTTAACGCATATAGTACATAAACTATCAATTTTGGT
*
3819519 TTGTTTTAGTACCTAAACTTTTATTTTATTTTTTCAAAAACTAACATTAAATTTTAAATTGTGTA
131 TTGTTTTAGTACCCAAACTTTTATTTTATTTTTTCAAAAACTAACATTAAATTTTAAATTGTGTA
* ** * *
3819584 CTAAAATGAAACAAAGCTAAGTTTTAGGTATAGTTTTGAAAAATTAAAAGTTTAGGTACTGAAAC
196 CTAAAATGAAACAAAACTAAACTTTAAGTATAGTTTTGAAAAATTAAAAGTTTAGGTACTGAAAA
**
3819649 ATTTCAAATTAATAATTTAAGTACTAAATACGT
261 ATACCAAATTAATAATTTAAGTACTAAATACGT
3819682 AATTTTAGTCTGTTGTAGTATTTAAACTTTCAATTCTTTCAAAATCATACATGATATTTAGTTTT
1 AATTTTAGTCTGTTGTAGTATTTAAACTTTCAATTCTTTCAAAATCATACATGATATTTAGTTTT
* * * * * *
3819747 TGTTTTATTTTAGTATCTGACGTTAAAAACTTAATGCATTTAGTACCTAAACTATCAATTTTGGT
66 TGTTTCATTTTAGTACCTGACATTAAAAACTTAACGCATATAGTACATAAACTATCAATTTTGGT
3819812 TTGTTTTAGTACCCAAACTTTTAATTTT-TTTTTTCAAAAACTAA-AGTTAAATTTTGAAA-TGT
131 TTGTTTTAGTACCCAAACTTTT-ATTTTATTTTTTCAAAAACTAACA-TTAAATTTT-AAATTGT
3819874 GTACTAAAATGAAACAAAAACTAAACTTTAAGTATAGTTTTGAAAAATTAAAAGTTTAGGTACT-
193 GTACTAAAATGAAAC-AAAACTAAACTTTAAGTATAGTTTTGAAAAATTAAAAGTTTAGGTACTG
3819938 AAAAATACCAAAATTAATAATTTAA-TACTAAATACGT
257 AAAAATACC-AAATTAATAATTTAAGTACTAAATACGT
3819975 AATTT
1 AATTT
3819980 ACCCTTGTAA
Statistics
Matches: 273, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
292 1 0.00
293 205 0.75
294 67 0.25
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (293 bp):
AATTTTAGTCTGTTGTAGTATTTAAACTTTCAATTCTTTCAAAATCATACATGATATTTAGTTTT
TGTTTCATTTTAGTACCTGACATTAAAAACTTAACGCATATAGTACATAAACTATCAATTTTGGT
TTGTTTTAGTACCCAAACTTTTATTTTATTTTTTCAAAAACTAACATTAAATTTTAAATTGTGTA
CTAAAATGAAACAAAACTAAACTTTAAGTATAGTTTTGAAAAATTAAAAGTTTAGGTACTGAAAA
ATACCAAATTAATAATTTAAGTACTAAATACGT
Found at i:3821235 original size:21 final size:21
Alignment explanation
Indices: 3821209--3821283 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
3821199 CCCTGCGACA
*
3821209 GTGGCATCTGAACTGAATATG
1 GTGGCATCTGAACTGGATATG
* * *
3821230 GTGGCATATGAAATGGATGTG
1 GTGGCATCTGAACTGGATATG
* * * *
3821251 GTGGTATTTGACCTGGATACG
1 GTGGCATCTGAACTGGATATG
*
3821272 GTGGAATCTGAA
1 GTGGCATCTGAA
3821284 ATGACTGTGG
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.29
Consensus pattern (21 bp):
GTGGCATCTGAACTGGATATG
Found at i:3822360 original size:23 final size:23
Alignment explanation
Indices: 3822326--3822384 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
3822316 CTCATATAAA
*
3822326 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
3822349 TGCACCGTAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
3822372 TGCACCGAAGTGC
1 TGCACCGAAGTGC
3822385 TATATAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:3823543 original size:2 final size:2
Alignment explanation
Indices: 3823536--3823578 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3823526 GTAATATTTC
3823536 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
3823578 A
1 A
3823579 GATCTTATCG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3824108 original size:21 final size:21
Alignment explanation
Indices: 3824084--3824126 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3824074 TTTTGTTCGT
* *
3824084 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3824105 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3824126 T
1 T
3824127 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3827507 original size:23 final size:23
Alignment explanation
Indices: 3827473--3827531 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
3827463 CTCATATAAA
3827473 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
3827496 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
3827519 TGCACCGAAGTGC
1 TGCACCGAAGTGC
3827532 TATATAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3832598 original size:23 final size:23
Alignment explanation
Indices: 3832539--3832599 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
3832529 CTCATATAAA
*
3832539 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
* *
3832562 TGCACCGTAGTGCTGCGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
3832585 TGCACCGAAGTGCTA
1 TGCACCGAAGTGCTA
3832600 TATAAGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCTACGTAGAAT
Found at i:3834294 original size:21 final size:21
Alignment explanation
Indices: 3834270--3834312 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3834260 TTTTGTTCGT
*
3834270 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
3834291 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
3834312 T
1 T
3834313 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:3835456 original size:20 final size:21
Alignment explanation
Indices: 3835428--3835466 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3835418 TATTCAATGT
3835428 AAAAAAATTA-TTATATACTC
1 AAAAAAATTATTTATATACTC
*
3835448 AAAACAATTATTTATATAC
1 AAAAAAATTATTTATATAC
3835467 GAACTCAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAAATTATTTATATACTC
Found at i:3837219 original size:21 final size:22
Alignment explanation
Indices: 3837193--3837243 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
3837183 AATTCCCTTG
3837193 CCTGGTTTCGAA-ACCCTTGTA
1 CCTGGTTTCGAAGACCCTTGTA
* *
3837214 CTTGGTTTCGAAGCCCCTTGTA
1 CCTGGTTTCGAAGACCCTTGTA
3837236 CCTGGTTT
1 CCTGGTTT
3837244 TAAAACTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (22 bp):
CCTGGTTTCGAAGACCCTTGTA
Found at i:3837234 original size:22 final size:21
Alignment explanation
Indices: 3837176--3837243 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
3837166 TTTCAGCCTA
3837176 GTTTCGAAATTCCCTTG--CCTG
1 GTTTCGAAA--CCCTTGTACCTG
*
3837197 GTTTCGAAACCCTTGTACTTG
1 GTTTCGAAACCCTTGTACCTG
*
3837218 GTTTCGAAGCCCCTTGTACCTG
1 GTTTCGAA-ACCCTTGTACCTG
3837240 GTTT
1 GTTT
3837244 TAAAACTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.15
21 20 0.49
22 15 0.37
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (21 bp):
GTTTCGAAACCCTTGTACCTG
Found at i:3847977 original size:183 final size:183
Alignment explanation
Indices: 3847669--3848018 Score: 682
Period size: 183 Copynumber: 1.9 Consensus size: 183
3847659 CCCAATAATA
3847669 ACAGATTAAATGGTATCCGATTTTTATTTTTTTTCATCGACTACTCGTATTTCTAATTATAATTA
1 ACAGATTAAATGGTATCCGATTTTTATTTTTTTTCATCGACTACTCGTATTTCTAATTATAATTA
*
3847734 AATTACGCGAATTGACAGTATTACCCTCGTAGCTTTAGGGTTTTTTTTAAAAATCAAATAATTTT
66 AATTACGCGAATTGACAGTATTACCCTCGTAGCTTTAGGGTTTTTTTAAAAAATCAAATAATTTT
3847799 TTAATTATACGCGCGATTATATTTATTTAGATTTTTTAATTATACGCGAATTG
131 TTAATTATACGCGCGATTATATTTATTTAGATTTTTTAATTATACGCGAATTG
*
3847852 ACAGATTAAATGGTATCCGATTTTTATTTTTTTTCATCGACTATTCGTATTTCTAATTATAATTA
1 ACAGATTAAATGGTATCCGATTTTTATTTTTTTTCATCGACTACTCGTATTTCTAATTATAATTA
3847917 AATTACGCGAATTGACAGTATTACCCTCGTAGCTTTAGGGTTTTTTTAAAAAATCAAATAATTTT
66 AATTACGCGAATTGACAGTATTACCCTCGTAGCTTTAGGGTTTTTTTAAAAAATCAAATAATTTT
3847982 TTAATTATACGCGCGATTATATTTATTTAGATTTTTT
131 TTAATTATACGCGCGATTATATTTATTTAGATTTTTT
3848019 TATTCAATTA
Statistics
Matches: 165, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 165 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (183 bp):
ACAGATTAAATGGTATCCGATTTTTATTTTTTTTCATCGACTACTCGTATTTCTAATTATAATTA
AATTACGCGAATTGACAGTATTACCCTCGTAGCTTTAGGGTTTTTTTAAAAAATCAAATAATTTT
TTAATTATACGCGCGATTATATTTATTTAGATTTTTTAATTATACGCGAATTG
Found at i:3849152 original size:35 final size:35
Alignment explanation
Indices: 3849048--3849152 Score: 165
Period size: 35 Copynumber: 3.0 Consensus size: 35
3849038 GGGCTGATGT
* * *
3849048 ACATAGTTTTATTGGAAATCGTTGCACACTCGTTT
1 ACATAGTTTTAGTGGAAATCGTTGCACACTCATTA
**
3849083 ACATAGTTTTAGTAAAAATCGTTGCACACTCATTA
1 ACATAGTTTTAGTGGAAATCGTTGCACACTCATTA
3849118 ACATAGTTTTAGTGGAAATCGTTGCACACTCATTA
1 ACATAGTTTTAGTGGAAATCGTTGCACACTCATTA
3849153 TTTTAAGAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (35 bp):
ACATAGTTTTAGTGGAAATCGTTGCACACTCATTA
Found at i:3850932 original size:7 final size:8
Alignment explanation
Indices: 3850918--3850942 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3850908 AAAATATATA
3850918 AAATTTTT
1 AAATTTTT
3850926 AAATTTTT
1 AAATTTTT
3850934 AAATTTTT
1 AAATTTTT
3850942 A
1 A
3850943 GAAGAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AAATTTTT
Found at i:3854159 original size:22 final size:22
Alignment explanation
Indices: 3854131--3854208 Score: 147
Period size: 22 Copynumber: 3.5 Consensus size: 22
3854121 GATGATAAAC
3854131 GAAGCCATCAAGTTTGAAAAAT
1 GAAGCCATCAAGTTTGAAAAAT
*
3854153 GAAGCCATCAAGTTTGAAAAAC
1 GAAGCCATCAAGTTTGAAAAAT
3854175 GAAGCCATCAAGTTTGAAAAAT
1 GAAGCCATCAAGTTTGAAAAAT
3854197 GAAGCCATCAAG
1 GAAGCCATCAAG
3854209 AATATTGCAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (22 bp):
GAAGCCATCAAGTTTGAAAAAT
Done.