Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 58 of 222
Found at i:17475234 original size:22 final size:22
Alignment explanation
Indices: 17475209--17475260 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
17475199 AAAAATTTCT
*
17475209 TTTAAAATATAT-TTTATAAAAA
1 TTTAAAATATATAATTAT-AAAA
17475231 TTTAAAATATATAATTATAAAA
1 TTTAAAATATATAATTATAAAA
17475253 TTCTAAAA
1 TT-TAAAA
17475261 AGGTATACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATATATAATTATAAAA
Found at i:17477596 original size:22 final size:22
Alignment explanation
Indices: 17477571--17477613 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17477561 GAGATCCCCT
* *
17477571 AGAAAAAGTATAGAAAACTAAG
1 AGAAAAACTAGAGAAAACTAAG
*
17477593 AGAAAACCTAGAGAAAACTAA
1 AGAAAAACTAGAGAAAACTAA
17477614 ATCTAAAACT
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:0.63, C:0.09, G:0.16, T:0.12
Consensus pattern (22 bp):
AGAAAAACTAGAGAAAACTAAG
Found at i:17486537 original size:12 final size:12
Alignment explanation
Indices: 17486520--17486545 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17486510 CAAAATAGGC
17486520 TTTTAGCGGCGT
1 TTTTAGCGGCGT
17486532 TTTTAGCGGCGT
1 TTTTAGCGGCGT
17486544 TT
1 TT
17486546 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:17486645 original size:40 final size:40
Alignment explanation
Indices: 17486552--17486658 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
17486542 GTTTGGATAA
** **
17486552 AAAACGCCGCTAAAGATTGAGCATTAGCGGCACTTTTTGG
1 AAAACGCCGCTAAAGATTGAGCATTAGTAGCACTTCATGG
* ** *
17486592 AAAACACTACTAAAGATTGAGCATTAGTAGCGCTTCATGG
1 AAAACGCCGCTAAAGATTGAGCATTAGTAGCACTTCATGG
* *
17486632 AAAACGCCGCTAAATA-TAAGCATTAGT
1 AAAACGCCGCTAAAGATTGAGCATTAGT
17486659 GGCGTTTTTC
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
39 10 0.19
40 44 0.81
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATTGAGCATTAGTAGCACTTCATGG
Found at i:17486782 original size:41 final size:41
Alignment explanation
Indices: 17486725--17487046 Score: 500
Period size: 41 Copynumber: 7.9 Consensus size: 41
17486715 CTTTCGGAGA
* *
17486725 TTTAGCGGCGTTTTTGAGAAAGTGCCGCTAATGCTCAGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* ** *
17486766 TTTAGCGGCGTTTTTGATAAAGCGCCGCTAAAACTAGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* * **
17486807 TTTAGCGGCGTTTTTGGGGAAGCGCCGCTAATGCTTTGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* *
17486848 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
*
17486889 TTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
17486930 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
*
17486971 TTTAGCGGCTTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* *
17487012 TTTAGTGGCGTTTTTGATAAAGCGCCGCTAATGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCT
17487047 TAGGGATTTA
Statistics
Matches: 256, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 256 1.00
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
Found at i:17487233 original size:14 final size:14
Alignment explanation
Indices: 17487214--17487325 Score: 64
Period size: 14 Copynumber: 7.4 Consensus size: 14
17487204 TATCACTATA
*
17487214 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
17487228 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
*
17487242 GTTTAGAGTTTAAT-
1 GTTTAGGGTTT-ATG
*
17487256 GTTTAGGTGTTACCATTTTAAG
1 GTTTAGG-G-------TTTATG
* *
17487278 GTTTATGGATTATG
1 GTTTAGGGTTTATG
*
17487292 AGTTTAGGGATTATG
1 -GTTTAGGGTTTATG
17487307 GTTTAGGGTTTATG
1 GTTTAGGGTTTATG
17487321 GTTTA
1 GTTTA
17487326 AATGCTGGGG
Statistics
Matches: 76, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
14 49 0.64
15 16 0.21
21 2 0.03
22 9 0.12
ACGTcount: A:0.21, C:0.02, G:0.29, T:0.48
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:17487302 original size:15 final size:14
Alignment explanation
Indices: 17487277--17487325 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
17487267 ACCATTTTAA
*
17487277 GGTTTATGGATTAT
1 GGTTTAGGGATTAT
17487291 GAGTTTAGGGATTAT
1 G-GTTTAGGGATTAT
*
17487306 GGTTTAGGGTTTAT
1 GGTTTAGGGATTAT
17487320 GGTTTA
1 GGTTTA
17487326 AATGCTGGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:17487344 original size:7 final size:7
Alignment explanation
Indices: 17487272--17487325 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
17487262 GTGTTACCAT
*
17487272 TTTAAGG
1 TTTATGG
17487279 TTTATGG
1 TTTATGG
*
17487286 ATTATGAG
1 TTTATG-G
*
17487294 TTTAGGG
1 TTTATGG
*
17487301 ATTATGG
1 TTTATGG
*
17487308 TTTAGGG
1 TTTATGG
17487315 TTTATGG
1 TTTATGG
17487322 TTTA
1 TTTA
17487326 AATGCTGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (7 bp):
TTTATGG
Found at i:17487401 original size:64 final size:64
Alignment explanation
Indices: 17487272--17487412 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 64
17487262 GTGTTACCAT
* * *
17487272 TTTAAGGTTTATGGATTATGAGTTTAGGGATTATGGTTTAGGGTTTATGGTTTAAATGCTGGGG
1 TTTAAGGTTTATGGATTATGAGTTAAGGGATTATGGTTTAGGGTTTAGGGTTTAAATGCTAGGG
* * * * *
17487336 TTTAAGGTTTA-GAGGTTATGTGTTAAGGGTTTGTGGGTTTAGGGTTTTAGGGTTT-TA-GCTAG
1 TTTAAGGTTTATG-GATTATGAGTTAAGGGATTAT-GGTTTAGGG-TTTAGGGTTTAAATGCTAG
17487398 GG
63 GG
17487400 TTT-AGGTTTATGG
1 TTTAAGGTTTATGG
17487413 TTTAGATTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
63 9 0.14
64 37 0.57
65 10 0.15
66 9 0.14
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.45
Consensus pattern (64 bp):
TTTAAGGTTTATGGATTATGAGTTAAGGGATTATGGTTTAGGGTTTAGGGTTTAAATGCTAGGG
Found at i:17487455 original size:16 final size:16
Alignment explanation
Indices: 17487434--17487466 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17487424 TAGTGTTTTC
17487434 TAATTTA-TATATTAAT
1 TAATTTATTAT-TTAAT
17487450 TAATTTATTATTTAAT
1 TAATTTATTATTTAAT
17487466 T
1 T
17487467 GTAAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATTTATTATTTAAT
Found at i:17487613 original size:18 final size:18
Alignment explanation
Indices: 17487569--17487623 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
17487559 CTTATCCCAT
*
17487569 TCCGGTTCAGCATTTTTAA
1 TCCGGTTCAG-TTTTTTAA
*
17487588 TGCTCGGTTCAGTTTTTTTA
1 T-C-CGGTTCAGTTTTTTAA
*
17487608 TCCGGTTCAATTTTTT
1 TCCGGTTCAGTTTTTT
17487624 GATTGTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 13 0.42
19 2 0.06
20 8 0.26
21 8 0.26
ACGTcount: A:0.15, C:0.18, G:0.16, T:0.51
Consensus pattern (18 bp):
TCCGGTTCAGTTTTTTAA
Found at i:17488113 original size:24 final size:25
Alignment explanation
Indices: 17488080--17488127 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
17488070 TTAAAATGAA
17488080 TTTTAAAATATTT-TAAACTTTTAT
1 TTTTAAAATATTTATAAACTTTTAT
* *
17488104 TTTTATAATATTTATATACTTTTA
1 TTTTAAAATATTTATAAACTTTTA
17488128 AAGAAAAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTAAAATATTTATAAACTTTTAT
Found at i:17492139 original size:43 final size:43
Alignment explanation
Indices: 17492092--17492258 Score: 201
Period size: 43 Copynumber: 3.9 Consensus size: 43
17492082 GCAATTGTAA
* * * *
17492092 AAAAAGAGTCGCTAAAGGCCTTGACCTATAGCGGCGTTTGTGG
1 AAAAAGCGCCGCTAAAGGCCTTGATCTATAGCGGCGTTTTTGG
* *
17492135 AAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTTTGG
1 AAAAAGCGCCGCTAAAGGCCTTGATCTATAGCGGCGTTTTTGG
* * ** *
17492178 GAAAAGCGCCGGTAAAGATCTTGATCTATAGTGGCGTTTTTGG
1 AAAAAGCGCCGCTAAAGGCCTTGATCTATAGCGGCGTTTTTGG
* *
17492221 GAAAAGCGCTGCTAAAGGTCC-TGATCTATAGCGGCGTT
1 AAAAAGCGCCGCTAAAGG-CCTTGATCTATAGCGGCGTT
17492259 GACAACAGTG
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 107 0.99
44 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (43 bp):
AAAAAGCGCCGCTAAAGGCCTTGATCTATAGCGGCGTTTTTGG
Found at i:17496046 original size:20 final size:18
Alignment explanation
Indices: 17495972--17496070 Score: 60
Period size: 19 Copynumber: 5.3 Consensus size: 18
17495962 ATAATATTGT
*
17495972 TTTAATAGTTTAATATTAA
1 TTTAATA-TTAAATATTAA
* * *
17495991 ATTAA-ATTTAATACTTAT
1 TTTAATATTAAATA-TTAA
* **
17496009 TTTAATAGTATTTTATTAA
1 TTTAATATTA-AATATTAA
17496028 TTTAATATTAAAGTGATT-A
1 TTTAATATTAAA-T-ATTAA
17496047 TCTTAATATTAAAT-TTAA
1 T-TTAATATTAAATATTAA
17496065 TTTAAT
1 TTTAAT
17496071 GTTTATCTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
17 14 0.23
18 10 0.16
19 22 0.35
20 16 0.26
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTAATATTAAATATTAA
Found at i:17497836 original size:19 final size:19
Alignment explanation
Indices: 17497809--17497861 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
17497799 ATTATTTAAA
*
17497809 TAATTTTAATTTTA-ATTAT
1 TAATATTAATTTTATATT-T
17497828 TAATATTAATATTTATATTT
1 TAATATTAAT-TTTATATTT
*
17497848 TAAAATTATATTTT
1 TAATATTA-ATTTT
17497862 TAAGAAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 9 0.31
20 15 0.52
21 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATATTAATTTTATATTT
Found at i:17497841 original size:27 final size:27
Alignment explanation
Indices: 17497781--17497850 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 27
17497771 ATACTATCAC
*
17497781 AATTTTTATTTTAAAATTATTATTTAAAT
1 AATTTATATTTT--AATTATTATTTAAAT
17497810 AATTT-TAATTTTAATTATTAATATT-AAT
1 AATTTAT-ATTTTAATTATT-AT-TTAAAT
17497838 -ATTTATATTTTAA
1 AATTTATATTTTAA
17497851 AATTATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
27 18 0.49
28 7 0.19
29 12 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
AATTTATATTTTAATTATTATTTAAAT
Found at i:17497856 original size:13 final size:14
Alignment explanation
Indices: 17497787--17497861 Score: 66
Period size: 13 Copynumber: 5.4 Consensus size: 14
17497777 TCACAATTTT
17497787 TATTTTAA-AATTA
1 TATTTTAATAATTA
* *
17497800 TTATTTAAATAATTT
1 -TATTTTAATAATTA
*
17497815 TAATTTTAATTATTA
1 T-ATTTTAATAATTA
* *
17497830 -ATATTAATATTTA
1 TATTTTAATAATTA
17497843 TATTTTAA-AATTA
1 TATTTTAATAATTA
17497856 TATTTT
1 TATTTT
17497862 TAAGAAGTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
13 20 0.42
14 14 0.29
15 14 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTAATAATTA
Found at i:17507348 original size:40 final size:40
Alignment explanation
Indices: 17507293--17507372 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
17507283 TAGAAGGCAA
* *
17507293 TCGACAACAACTTGATTAACAGATTTGGAGTGACCGTATT
1 TCGACAACAACTTGATCAACAGATTTAGAGTGACCGTATT
* *
17507333 TCGACAACAACTTGATCAATAGATTTAGAGTGACTGTATT
1 TCGACAACAACTTGATCAACAGATTTAGAGTGACCGTATT
17507373 CTGATAACGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (40 bp):
TCGACAACAACTTGATCAACAGATTTAGAGTGACCGTATT
Found at i:17508153 original size:23 final size:23
Alignment explanation
Indices: 17508108--17508153 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
17508098 CTTCTATTAA
*
17508108 TTATTATAAATTTTAATGATTTT
1 TTATTATAAATTTTAATCATTTT
*
17508131 TTATTATAAATTTTTATC-TTTT
1 TTATTATAAATTTTAATCATTTT
17508153 T
1 T
17508154 AATAATTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TTATTATAAATTTTAATCATTTT
Found at i:17509227 original size:26 final size:26
Alignment explanation
Indices: 17509192--17509242 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
17509182 ACCAATATCG
* *
17509192 CAGCATAGCTGCCAGTAGTAAAAATA
1 CAGCAGAGCTGCCAATAGTAAAAATA
* *
17509218 CAGCAGAGCTGTCAATAGTCAAAAT
1 CAGCAGAGCTGCCAATAGTAAAAAT
17509243 GGCTAAGAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (26 bp):
CAGCAGAGCTGCCAATAGTAAAAATA
Found at i:17509280 original size:22 final size:22
Alignment explanation
Indices: 17509250--17509301 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
17509240 AATGGCTAAG
* * *
17509250 AGCCGTAAACAGGATAGCTATA
1 AGCCATAAACAGAATAGCTACA
* *
17509272 AGCTATAAACAGAATGGCTACA
1 AGCCATAAACAGAATAGCTACA
17509294 AGCCATAA
1 AGCCATAA
17509302 GTACAGTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (22 bp):
AGCCATAAACAGAATAGCTACA
Found at i:17509363 original size:32 final size:33
Alignment explanation
Indices: 17509291--17509559 Score: 225
Period size: 32 Copynumber: 8.4 Consensus size: 33
17509281 CAGAATGGCT
* * *
17509291 ACAAGCCATAAGT-ACAGTAATGTGATTGGCAC
1 ACAAGCCATCAGTAACAGTAATATGATCGGCAC
* *
17509323 A-AAGCCATCAGTAGCAGTGATATGATCGGCAC
1 ACAAGCCATCAGTAACAGTAATATGATCGGCAC
** * *
17509355 ACAA-CCATCAGTAATGGTAACATGATCAGCAC
1 ACAAGCCATCAGTAACAGTAATATGATCGGCAC
* *
17509387 A-AAGCCATCAGTAACAGTGATATGATCAGCAC
1 ACAAGCCATCAGTAACAGTAATATGATCGGCAC
*
17509419 AC-AGCCATCAGTAACAGTGAA-ATGATTGGCAC
1 ACAAGCCATCAGTAACAGT-AATATGATCGGCAC
** **
17509451 AC-AGCCATTGGTAATGGTAATATGATCGGCAC
1 ACAAGCCATCAGTAACAGTAATATGATCGGCAC
* * * *
17509483 A-AAACCATCAGTAACGGTATTATGATCGACAC
1 ACAAGCCATCAGTAACAGTAATATGATCGGCAC
* ** * * *
17509515 A-AATCCATCAGTAATGGTACTACGGTCGGCAC
1 ACAAGCCATCAGTAACAGTAATATGATCGGCAC
17509547 A-AAGCCATCAGTA
1 ACAAGCCATCAGTA
17509560 GCATCGCAGC
Statistics
Matches: 194, Mismatches: 36, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
31 14 0.07
32 177 0.91
33 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (33 bp):
ACAAGCCATCAGTAACAGTAATATGATCGGCAC
Found at i:17509465 original size:96 final size:94
Alignment explanation
Indices: 17509293--17509528 Score: 276
Period size: 96 Copynumber: 2.5 Consensus size: 94
17509283 GAATGGCTAC
* * * * *
17509293 AAGCCATAAGT-ACAGTAATGTGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACAC
1 AAGCCATCAGTAACAGT-ATATGA-TCGCACAAAGCCATCAGTAACAGTGAAATGATCGGCACAC
17509357 AACCATCAGTAATGGTAACATGATCAGCACA
64 AACCATCAGTAATGGTAACATGATCAGCACA
* *
17509388 AAGCCATCAGTAACAGTGATATGATCAGCACACAGCCATCAGTAACAGTGAAATGATTGGCACAC
1 AAGCCATCAGTAACAGT-ATATGATC-GCACAAAGCCATCAGTAACAGTGAAATGATCGGCACAC
* ** * *
17509453 AGCCATTGGTAATGGTAATATGATCGGCACA
64 AACCATCAGTAATGGTAACATGATCAGCACA
* * *
17509484 AAACCATCAGTAACGGTATTATGATCGACACAAATCCATCAGTAA
1 AAGCCATCAGTAACAGTA-TATGATCG-CACAAAGCCATCAGTAA
17509529 TGGTACTACG
Statistics
Matches: 120, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
95 13 0.11
96 107 0.89
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (94 bp):
AAGCCATCAGTAACAGTATATGATCGCACAAAGCCATCAGTAACAGTGAAATGATCGGCACACAA
CCATCAGTAATGGTAACATGATCAGCACA
Found at i:17509546 original size:96 final size:96
Alignment explanation
Indices: 17509319--17509559 Score: 263
Period size: 96 Copynumber: 2.5 Consensus size: 96
17509309 AATGTGATTG
* * * *
17509319 GCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAATGGTAACATGATCAG
1 GCACAAAGCCATCAGTAACAGTGAAACGATCGGCACACAGCCATCAGTAATGGTAACATGATCAG
*
17509384 CACAAAGCCATCAGTAACAGTGATATGATCA
66 CACAAAACCATCAGTAACAGTGATATGATCA
* * * ** * *
17509415 GCACACAGCCATCAGTAACAGTGAAATGATTGGCACACAGCCATTGGTAATGGTAATATGATCGG
1 GCACAAAGCCATCAGTAACAGTGAAACGATCGGCACACAGCCATCAGTAATGGTAACATGATCAG
*
17509480 CACAAAACCATCAGTAACGGT-ATTATGATC-
66 CACAAAACCATCAGTAACAGTGA-TATGATCA
* ** * * *
17509510 GACACAAATCCATCAGTAATGGT-ACTACGGTCGGCACAAAGCCATCAGTA
1 G-CACAAAGCCATCAGTAACAGTGA-AACGATCGGCACACAGCCATCAGTA
17509560 GCATCGCAGC
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
95 3 0.03
96 117 0.98
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (96 bp):
GCACAAAGCCATCAGTAACAGTGAAACGATCGGCACACAGCCATCAGTAATGGTAACATGATCAG
CACAAAACCATCAGTAACAGTGATATGATCA
Found at i:17509594 original size:26 final size:26
Alignment explanation
Indices: 17509565--17509616 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
17509555 CAGTAGCATC
17509565 GCAGCAAAGCTGCCAGTAAAAATATA
1 GCAGCAAAGCTGCCAGTAAAAATATA
*
17509591 GCAGCAAAGCTGCCAGTAATAATATA
1 GCAGCAAAGCTGCCAGTAAAAATATA
17509617 TGTGGCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAAAAATATA
Found at i:17509801 original size:23 final size:23
Alignment explanation
Indices: 17509730--17509817 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 23
17509720 GCCATGCTCA
* * *
17509730 AAATCAGTCATTCAAATCACAGAC
1 AAATCAGTCATT-TAACCATAGAC
** *
17509754 AAATCAGTCATACCAAACATAGAC
1 AAATCAGTCAT-TTAACCATAGAC
17509778 AAATCAGTCATTTAACCATAGAC
1 AAATCAGTCATTTAACCATAGAC
* *
17509801 AAAACAATCATTTAACC
1 AAATCAGTCATTTAACC
17509818 TCGAGGGAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
23 24 0.44
24 30 0.56
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.22
Consensus pattern (23 bp):
AAATCAGTCATTTAACCATAGAC
Found at i:17509916 original size:53 final size:53
Alignment explanation
Indices: 17509833--17509966 Score: 175
Period size: 53 Copynumber: 2.5 Consensus size: 53
17509823 GGAAAAAATA
* * *
17509833 GTCA-TTTACCCACCAGGGCATTACGGTCATTTTACCCTACAGGG-GATTACG
1 GTCATTTTACCCACAAGGGCATTACGATCATTTTACCCTACAGGGACATTACG
17509884 GTCATTTTACCCGACAAGGGCATTACGATCATTTTACCCTACAGGGACATTACG
1 GTCATTTTACCC-ACAAGGGCATTACGATCATTTTACCCTACAGGGACATTACG
* * *
17509938 GT-ATTTTATCCTACAGGGGTATTACGATC
1 GTCATTTTA-CCCACAAGGGCATTACGATC
17509967 CAAATATCGA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
51 4 0.05
52 7 0.10
53 52 0.71
54 10 0.14
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (53 bp):
GTCATTTTACCCACAAGGGCATTACGATCATTTTACCCTACAGGGACATTACG
Found at i:17509961 original size:26 final size:27
Alignment explanation
Indices: 17509833--17509963 Score: 164
Period size: 26 Copynumber: 5.0 Consensus size: 27
17509823 GGAAAAAATA
17509833 GTCA-TTTACCC-ACCA-GGGCATTACG
1 GTCATTTTACCCTA-CAGGGGCATTACG
17509858 GTCATTTTACCCTACAGGGG-ATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
17509884 GTCATTTTACCCGACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
17509911 ATCATTTTACCCTACAGGGACATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
17509938 GT-ATTTTATCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
17509964 ATCCAAATAT
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.04
26 54 0.59
27 34 0.37
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:17511253 original size:39 final size:39
Alignment explanation
Indices: 17511199--17511276 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
17511189 CTCTTAGAAA
17511199 GAAGCATCGGGTATTCGACACTTCATAACAAAGTTTGTT
1 GAAGCATCGGGTATTCGACACTTCATAACAAAGTTTGTT
17511238 GAAGCATCGGGTATTCGACACTTCATAACAAAGTTTGTT
1 GAAGCATCGGGTATTCGACACTTCATAACAAAGTTTGTT
17511277 CGCTTTGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (39 bp):
GAAGCATCGGGTATTCGACACTTCATAACAAAGTTTGTT
Found at i:17517099 original size:13 final size:13
Alignment explanation
Indices: 17517081--17517110 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17517071 TATAAAATTA
*
17517081 TAAAATATTTTCT
1 TAAAATATTTTAT
17517094 TAAAATATTTTAT
1 TAAAATATTTTAT
17517107 TAAA
1 TAAA
17517111 TTCAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAAATATTTTAT
Found at i:17518345 original size:15 final size:15
Alignment explanation
Indices: 17518297--17518346 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
17518287 ATCATGTTTA
*
17518297 CACTTTCATTTTGAT
1 CACTTTCATTTTGGT
17518312 CAC--TCAACTTTTAGGT
1 CACTTTC-A-TTTT-GGT
17518328 CACTTTCATTTTGGT
1 CACTTTCATTTTGGT
17518343 CACT
1 CACT
17518347 AAAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
13 2 0.07
14 1 0.03
15 14 0.48
16 9 0.31
17 1 0.03
18 2 0.07
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.46
Consensus pattern (15 bp):
CACTTTCATTTTGGT
Found at i:17519151 original size:30 final size:29
Alignment explanation
Indices: 17519125--17519184 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
17519115 AGAATTGGAT
* *
17519125 CAAATTAAAATTTCATGTATAAAATTGCA
1 CAAAATAAAAGTTCATGTATAAAATTGCA
* *
17519154 CAAAATCAAAGTTCATGTATACAATTGCA
1 CAAAATAAAAGTTCATGTATAAAATTGCA
17519183 CA
1 CA
17519185 TTAAACCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (29 bp):
CAAAATAAAAGTTCATGTATAAAATTGCA
Found at i:17522090 original size:45 final size:45
Alignment explanation
Indices: 17522041--17522235 Score: 273
Period size: 45 Copynumber: 4.3 Consensus size: 45
17522031 TCGGCCATGG
* * * *
17522041 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
17522086 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* * * * *
17522131 TGCTTCCTCAAATTCTTTCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
17522176 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCGAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
17522221 TGCTTCCTTAATTTC
1 TGCTTCCTTAATTTC
17522236 ATGCCGTTCA
Statistics
Matches: 133, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (45 bp):
TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
Found at i:17522598 original size:20 final size:20
Alignment explanation
Indices: 17522575--17522621 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
17522565 AACTGAGCTT
*
17522575 GAATGAGCTGACTTGAGCAC
1 GAATGAGCTAACTTGAGCAC
*
17522595 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
17522615 GAATGAG
1 GAATGAG
17522622 TTGAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:17526568 original size:58 final size:57
Alignment explanation
Indices: 17526478--17526602 Score: 241
Period size: 58 Copynumber: 2.2 Consensus size: 57
17526468 TTCCAGACTC
17526478 TTTTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAAA
1 TTTTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGC-AA
17526536 TTTTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAA
1 TTTTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAA
17526593 TTTTTTTTTT
1 TTTTTTTTTT
17526603 ACAAAACCAT
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
57 12 0.18
58 55 0.82
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.48
Consensus pattern (57 bp):
TTTTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAA
Found at i:17527274 original size:45 final size:45
Alignment explanation
Indices: 17527225--17527419 Score: 291
Period size: 45 Copynumber: 4.3 Consensus size: 45
17527215 TCGGCCATGG
* * * *
17527225 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
*
17527270 TGCTTCCTTAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* * * *
17527315 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
17527360 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCGAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
17527405 TGCTTCCTTAATTTC
1 TGCTTCCTTAATTTC
17527420 ATGCCGTTCA
Statistics
Matches: 135, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 135 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (45 bp):
TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
Found at i:17527782 original size:20 final size:20
Alignment explanation
Indices: 17527759--17527805 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
17527749 AACTGAGCTT
*
17527759 GAATGAGCTGACTTGAGCAC
1 GAATGAGCTAACTTGAGCAC
*
17527779 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
17527799 GAATGAG
1 GAATGAG
17527806 TTGAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:17543381 original size:22 final size:21
Alignment explanation
Indices: 17543328--17543381 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
17543318 ATTAAATATG
*
17543328 ATTAAAATAAAAATAATAGAA
1 ATTAAATTAAAAATAATAGAA
**
17543349 A-TAGCTGTAAAAATAAATAGAA
1 ATTAAAT-TAAAAAT-AATAGAA
17543371 ATTAAATTAAA
1 ATTAAATTAAA
17543382 TCGAATAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
20 2 0.08
21 8 0.32
22 12 0.48
23 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (21 bp):
ATTAAATTAAAAATAATAGAA
Found at i:17547100 original size:16 final size:16
Alignment explanation
Indices: 17547079--17547117 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17547069 TTTTAATAAA
17547079 ATTAAAACTAATTATT
1 ATTAAAACTAATTATT
* *
17547095 ATTAAAATTAATTGTT
1 ATTAAAACTAATTATT
*
17547111 AGTAAAA
1 ATTAAAA
17547118 TCATCAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTAAAACTAATTATT
Found at i:17547103 original size:22 final size:23
Alignment explanation
Indices: 17547050--17547105 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
17547040 CCCGTTTTTA
* *
17547050 ATTAAAATTAAAATTATATTTTT
1 ATTAAAATTAAAACTATATTATT
*
17547073 AATAAAATTAAAACTA-ATTATT
1 ATTAAAATTAAAACTATATTATT
17547095 ATTAAAATTAA
1 ATTAAAATTAA
17547106 TTGTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTATT
Found at i:17551057 original size:27 final size:28
Alignment explanation
Indices: 17551004--17551062 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
17550994 ATATTACTTA
* **
17551004 TTTTATACTTTTATATATACATTATTTG
1 TTTTATACTTATATATATACACCATTTG
* *
17551032 TTTTAT-CTTATATATATATACCATTTT
1 TTTTATACTTATATATATACACCATTTG
17551059 TTTT
1 TTTT
17551063 GTGTACATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTATACTTATATATATACACCATTTG
Found at i:17552506 original size:14 final size:14
Alignment explanation
Indices: 17552489--17552532 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
17552479 AATCATATAT
17552489 TTTATGTTTAAATA
1 TTTATGTTTAAATA
*
17552503 TTTAT-TTGAAA-A
1 TTTATGTTTAAATA
*
17552515 ATTATGTTTAAATA
1 TTTATGTTTAAATA
17552529 TTTA
1 TTTA
17552533 CTCGGCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 5 0.21
13 10 0.42
14 9 0.38
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTTATGTTTAAATA
Found at i:17557051 original size:18 final size:19
Alignment explanation
Indices: 17557030--17557069 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
17557020 ATCTTTCTTT
17557030 TCTCTCAAGTCTCTTAA-C
1 TCTCTCAAGTCTCTTAAGC
* *
17557048 TCTCTCAATTTTCTTAAGC
1 TCTCTCAAGTCTCTTAAGC
17557067 TCT
1 TCT
17557070 TGTTTTGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.20, C:0.30, G:0.05, T:0.45
Consensus pattern (19 bp):
TCTCTCAAGTCTCTTAAGC
Found at i:17561112 original size:23 final size:23
Alignment explanation
Indices: 17561065--17561115 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
17561055 ACCTACTTTC
* * *
17561065 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGAGATA
*
17561088 TTACAGTAGTAATTTTTGAGATA
1 TTACAGTAGTAATTTTCGAGATA
17561111 TTACA
1 TTACA
17561116 ACTACACAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGATA
Found at i:17564042 original size:21 final size:21
Alignment explanation
Indices: 17564016--17564071 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
17564006 AACAGCGGTG
*
17564016 GCGGTGAGATTAGTTACTATA
1 GCGGTGAGATTAGATACTATA
* *
17564037 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTATA
17564058 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
17564072 AACAGCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTATA
Found at i:17564849 original size:113 final size:113
Alignment explanation
Indices: 17564651--17564878 Score: 402
Period size: 113 Copynumber: 2.0 Consensus size: 113
17564641 AGAATATATC
17564651 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACAGTAAAACAAGAGTCCAGGTAGCA
1 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACAGTAAAACAAGAGTCCAGGTAGCA
* *
17564716 TTTATTACAGTTCTTAATACAATATATGATTACTATCAGTGTGTTGTG
66 TATATTACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
* * *
17564764 CCCATACCTATTCCTAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCTAGGTAGCA
1 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACAGTAAAACAAGAGTCCAGGTAGCA
*
17564829 TATATTACAGTTTTTAATACAATATATGATTACTATCAGTATGTTGTG
66 TATATTACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
17564877 CC
1 CC
17564879 ATGATTGAAG
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (113 bp):
CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACAGTAAAACAAGAGTCCAGGTAGCA
TATATTACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
Found at i:17567482 original size:21 final size:22
Alignment explanation
Indices: 17567456--17567508 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
17567446 AAAAGAGAAT
17567456 GAAAAAAAAAAAGAA-A-AAAA
1 GAAAAAAAAAAAGAACATAAAA
**
17567476 GGAAAAATTAAAAGAACATAAAA
1 -GAAAAAAAAAAAGAACATAAAA
17567499 GAAAAAAAAA
1 GAAAAAAAAA
17567509 TTAAATTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 13 0.50
22 9 0.35
23 4 0.15
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (22 bp):
GAAAAAAAAAAAGAACATAAAA
Found at i:17568403 original size:15 final size:15
Alignment explanation
Indices: 17568383--17568417 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
17568373 TACGATCCCT
17568383 CTTTATATTGTGTTA
1 CTTTATATTGTGTTA
17568398 CTTTATATTGTGTTA
1 CTTTATATTGTGTTA
*
17568413 TTTTA
1 CTTTA
17568418 AAATTACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.63
Consensus pattern (15 bp):
CTTTATATTGTGTTA
Found at i:17570826 original size:44 final size:44
Alignment explanation
Indices: 17570778--17570890 Score: 208
Period size: 44 Copynumber: 2.6 Consensus size: 44
17570768 GTTTTAATCC
*
17570778 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAGTCT
1 GCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTCAGTCT
17570822 GCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTCAGTCT
1 GCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTCAGTCT
*
17570866 ACTCCACTGCAACTTCAAGGAGATA
1 GCTCCACTGCAACTTCAAGGAGATA
17570891 AGAATGGATG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTCAGTCT
Found at i:17570974 original size:44 final size:44
Alignment explanation
Indices: 17570770--17570980 Score: 169
Period size: 44 Copynumber: 4.9 Consensus size: 44
17570760 GATTCATCGT
* *
17570770 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGC
* * * *
17570814 TTCAGTCTGCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGC
* * * * * *
17570858 TTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGA--A-TGGA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGC
* * * * * * * * * *
17570899 TGTGATTTACTCTACTACAACTTTAGAGAGATAAGATCT-GTGGT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TAGTAGC
* *
17570943 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
17570981 CGCCATTGCG
Statistics
Matches: 134, Mismatches: 29, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
41 28 0.21
42 1 0.01
43 1 0.01
44 104 0.78
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGC
Found at i:17571085 original size:50 final size:50
Alignment explanation
Indices: 17570994--17571610 Score: 404
Period size: 50 Copynumber: 12.4 Consensus size: 50
17570984 CATTGCGGTC
* * * * *
17570994 TCAATTGCAATGTCAGGGAA-CACGATTCGCAGTCGTAGCTTTAATCTTT
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * * * * * *
17571043 TCCACTGCACTGCCAGGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTT
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * * * **
17571093 TTAATTGCAATGTCAGGGAA-CAAGATTCGCAGTTGTAGCTTCAGTCTGA
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * * * * * * *
17571142 TCCACTAC-ATCGCCAGGAAAGTAAGATTCGTCGTTGCGGCTTCAATCTTT
1 TCAATTGCAAT-GTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * * * *
17571192 TTAATTGCAATGTCGGGGAA-CAAGATTCGCCATT-TGAGCTTTAATCTGT
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG-GCTTCAATCTTT
* * *** * *
17571241 TCCACTGCAACACCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * * * * *
17571291 TAAATTGCAATATTAGGGAAGCAAGATTCACCGTTGCGGCTTCAATATTT
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * * ** * * **
17571341 TAAATTGCAATATCAGGGAAGCAAGATTCACCGTCATAGCTTTAATCTGC
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * * * ** * *
17571391 TCCATTGTACTGCCAGGGAAGTGAGATTCACCGTTGTGGCTTCAATATTT
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * * * **
17571441 TTAATTGCAATGTCGGGGAA-CAAGATTCGCTGTTGTAGCTTCAATCTGA
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * * * *
17571490 TCCACTGC-ATCGCCAGGAAAGTAAGACTT-GCCGTTGTGGCTTCAATCTTT
1 TCAATTGCAAT-GTCAGGGAAGCAAGA-TTCGCCGTTGTGGCTTCAATCTTT
* * * * * **
17571540 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGC
1 TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
* * *
17571590 TCCACTGCACTGTCAGGGAAG
1 TCAATTGCAATGTCAGGGAAG
17571611 GTAACTTCAT
Statistics
Matches: 419, Mismatches: 137, Indels: 23
0.72 0.24 0.04
Matches are distributed among these distances:
48 5 0.01
49 116 0.28
50 291 0.69
51 7 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (50 bp):
TCAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTT
Found at i:17571167 original size:99 final size:98
Alignment explanation
Indices: 17570996--17571319 Score: 434
Period size: 99 Copynumber: 3.3 Consensus size: 98
17570986 TTGCGGTCTC
* * *
17570996 AATTGCAATGTCAGGGAACACGATTCGCAGTCGTAGCTTTAATCTTTTCCACTGCACTGCCAGGG
1 AATTGCAATGTCAGGGAACAAGATTCGCAGTTGTAGCTTTAATCTGTTCCACTGCAC-GCCAGGG
* * *
17571061 AAGTAAGATTCACCGTTGTGGCTTTAATCTTTTT
65 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTT
* * * * *
17571095 AATTGCAATGTCAGGGAACAAGATTCGCAGTTGTAGCTTCAGTCTGATCCACTACATCGCCAGGA
1 AATTGCAATGTCAGGGAACAAGATTCGCAGTTGTAGCTTTAATCTGTTCCACTGCA-CGCCAGGG
*
17571160 AAGTAAGATTCGTCGTTGCGGCTTCAATCTTTTT
65 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTT
* * *
17571194 AATTGCAATGTCGGGGAACAAGATTCGCCATTTG-AGCTTTAATCTGTTCCACTGCAACACCAGG
1 AATTGCAATGTCAGGGAACAAGATTCG-CAGTTGTAGCTTTAATCTGTTCCACTGC-ACGCCAGG
*
17571258 GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTA
64 GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTT
* *
17571293 AATTGCAATATTAGGGAAGCAAGATTC
1 AATTGCAATGTCAGGGAA-CAAGATTC
17571320 ACCGTTGCGG
Statistics
Matches: 196, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
99 181 0.92
100 15 0.08
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (98 bp):
AATTGCAATGTCAGGGAACAAGATTCGCAGTTGTAGCTTTAATCTGTTCCACTGCACGCCAGGGA
AGTAAGATTCGCCGTTGCGGCTTCAATCTTTTT
Found at i:17571496 original size:249 final size:248
Alignment explanation
Indices: 17571056--17571573 Score: 668
Period size: 249 Copynumber: 2.1 Consensus size: 248
17571046 ACTGCACTGC
* * * * * *
17571056 CAGGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCAGGGAACAAGATTC
1 CAGGGAAGCAAGATTCACCGTTGCGGCTTCAATATTTTAAATTGCAATATCAGGGAACAAGATTC
* ** * **
17571121 GCAGTTGTAGCTTCAGTCTGATCCACTACATCGCCAGGAAAGTAAGATTCGTCGTTGCGGCTTCA
66 ACAGTCATAGCTTCAATCTGATCCACTACATCGCCAGGAAAGTAAGATTCACCGTTGCGGCTTCA
* * *
17571186 ATCTTTTTAATTGCAATGTCGGGGAACAAGATTCGCCATTTGAGCTTTAATCTGTTCCACTGCAA
131 ATATTTTTAATTGCAATGTCGGGGAACAAGATTCGCCATTTGAGCTTCAATCTGATCCACTGCAA
*
17571251 CACCAGGGAAGTAAGA-TTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATAT
196 CACCAGGAAAGTAAGACTT-GCCGTTGCGGCTTCAATCTTTTAAATTGCAATAT
*
17571304 TAGGGAAGCAAGATTCACCGTTGCGGCTTCAATATTTTAAATTGCAATATCAGGGAAGCAAGATT
1 CAGGGAAGCAAGATTCACCGTTGCGGCTTCAATATTTTAAATTGCAATATCAGGGAA-CAAGATT
* * * * * * *
17571369 CACCGTCATAGCTTTAATCTGCTCCATTGTAC-T-GCCAGGGAAGTGAGATTCACCGTTGTGGCT
65 CACAGTCATAGCTTCAATCTGATCCA--CTACATCGCCAGGAAAGTAAGATTCACCGTTGCGGCT
17571432 TCAATATTTTTAATTGCAATGTCGGGGAACAAGATTCG-C-TGTTGTAGCTTCAATCTGATCCAC
128 TCAATATTTTTAATTGCAATGTCGGGGAACAAGATTCGCCAT-TTG-AGCTTCAATCTGATCCAC
* * * * *
17571495 TGCATCGCCAGGAAAGTAAGACTTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGT
191 TGCAACACCAGGAAAGTAAGACTTGCCGTTGCGGCTTCAATCTTTTAAATTGCAATAT
* *
17571553 CGGGGAAGCAAGATTCGCCGT
1 CAGGGAAGCAAGATTCACCGT
17571574 CGTAGCTTTA
Statistics
Matches: 232, Mismatches: 32, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
247 1 0.00
248 54 0.23
249 171 0.74
250 3 0.01
251 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (248 bp):
CAGGGAAGCAAGATTCACCGTTGCGGCTTCAATATTTTAAATTGCAATATCAGGGAACAAGATTC
ACAGTCATAGCTTCAATCTGATCCACTACATCGCCAGGAAAGTAAGATTCACCGTTGCGGCTTCA
ATATTTTTAATTGCAATGTCGGGGAACAAGATTCGCCATTTGAGCTTCAATCTGATCCACTGCAA
CACCAGGAAAGTAAGACTTGCCGTTGCGGCTTCAATCTTTTAAATTGCAATAT
Found at i:17571949 original size:24 final size:24
Alignment explanation
Indices: 17571895--17571952 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
17571885 TGGATTGCCC
17571895 CCACTGTAATCTTCAAAGCTCAAT
1 CCACTGTAATCTTCAAAGCTCAAT
** * * *
17571919 CTGCTGTAATCTTCAAGGTTCAGT
1 CCACTGTAATCTTCAAAGCTCAAT
17571943 CCACTGTAAT
1 CCACTGTAAT
17571953 TTTGGGACAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGCTCAAT
Found at i:17586053 original size:23 final size:23
Alignment explanation
Indices: 17586026--17586124 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
17586016 AGTGTTATTG
17586026 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
17586049 TTCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
17586072 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
17586095 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
17586118 ATTAGTG
1 ATCAGTG
17586125 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:17590724 original size:20 final size:19
Alignment explanation
Indices: 17590701--17590755 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
17590691 TTAAAATTTT
17590701 AAAAATATTTAAAAATC-CAA
1 AAAAAT-TTTAAAAATCTC-A
*
17590721 AAAAATTATAAAAAATCTCA
1 AAAAATT-TTAAAAATCTCA
*
17590741 AAGAATTTTAAAAAT
1 AAAAATTTTAAAAAT
17590756 ATGTTTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 8 0.27
20 21 0.70
21 1 0.03
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATTTTAAAAATCTCA
Found at i:17590785 original size:17 final size:18
Alignment explanation
Indices: 17590763--17590796 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17590753 AATATGTTTT
*
17590763 GTTTTTTGAAA-TTTTAG
1 GTTTTTAGAAACTTTTAG
17590780 GTTTTTAGAAACTTTTA
1 GTTTTTAGAAACTTTTA
17590797 TAATTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (18 bp):
GTTTTTAGAAACTTTTAG
Found at i:17590876 original size:20 final size:20
Alignment explanation
Indices: 17590817--17590877 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
17590807 AAAAAATTAA
*
17590817 AAATTTTATGGATTTTTTTA
1 AAATTTTATGGATTTTTTTG
* *
17590837 AAATTTTAGGGATTTCTTTG
1 AAATTTTATGGATTTTTTTG
* * *
17590857 CATTTTTATGAATTTTTTTG
1 AAATTTTATGGATTTTTTTG
17590877 A
1 A
17590878 TGTTTTTAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.57
Consensus pattern (20 bp):
AAATTTTATGGATTTTTTTG
Found at i:17591146 original size:9 final size:9
Alignment explanation
Indices: 17591134--17591158 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17591124 TTTTTTTAGT
17591134 TTTTTAAAA
1 TTTTTAAAA
17591143 TTTTTAAAA
1 TTTTTAAAA
17591152 TTTTTAA
1 TTTTTAA
17591159 GTGAATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:17594108 original size:19 final size:20
Alignment explanation
Indices: 17594076--17594114 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
17594066 TTAAATATAA
17594076 ATTTTGCAACTTTTATAAAAT
1 ATTTTGCAACTTTTA-AAAAT
17594097 ATTTTG-AA-TTTTAAAAAT
1 ATTTTGCAACTTTTAAAAAT
17594115 TTTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 2 0.11
21 6 0.33
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTTTGCAACTTTTAAAAAT
Found at i:17598508 original size:13 final size:13
Alignment explanation
Indices: 17598472--17598509 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
17598462 AAATAAACAA
17598472 TTAATAGAATCAG
1 TTAATAGAATCAG
17598485 TTAATCA-AATCAG
1 TTAAT-AGAATCAG
17598498 TTAATAGAATCA
1 TTAATAGAATCA
17598510 ATTGGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 21 0.91
14 1 0.04
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (13 bp):
TTAATAGAATCAG
Found at i:17601846 original size:20 final size:22
Alignment explanation
Indices: 17601801--17601848 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
17601791 AAATGAACAT
* *
17601801 ATAAATAAATATATAAATGAAC
1 ATAAATAAATATATAAAGGAAA
17601823 ATAAA-AAATA-ATAAAGGAAA
1 ATAAATAAATATATAAAGGAAA
17601843 ATAAAT
1 ATAAAT
17601849 GAAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 13 0.57
21 5 0.22
22 5 0.22
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (22 bp):
ATAAATAAATATATAAAGGAAA
Found at i:17602150 original size:3 final size:3
Alignment explanation
Indices: 17602142--17602216 Score: 55
Period size: 3 Copynumber: 24.7 Consensus size: 3
17602132 TAGATGAAGA
* * *
17602142 AAT AAT AAT AAT AACT AAT AAT AAC AAT AAT AAT AAA AGAT GAT AA-
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * *
17602188 AAT ATT AAA AAT AAT GAAG AA- AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
17602217 AAATGCTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
2 4 0.07
3 46 0.82
4 6 0.11
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:17603203 original size:20 final size:21
Alignment explanation
Indices: 17603180--17603226 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
17603170 GTTTTTGGGC
*
17603180 TGGGTTTTAATTTT-TCT-TTT
1 TGGGTTGTAATTTTAT-TGTTT
*
17603200 TGGGCTGTAATTTTATTGTTT
1 TGGGTTGTAATTTTATTGTTT
17603221 TGGGTT
1 TGGGTT
17603227 AGGTCTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.11, C:0.04, G:0.23, T:0.62
Consensus pattern (21 bp):
TGGGTTGTAATTTTATTGTTT
Found at i:17608095 original size:99 final size:99
Alignment explanation
Indices: 17607924--17608125 Score: 334
Period size: 99 Copynumber: 2.0 Consensus size: 99
17607914 CTCAACCTCA
* * * * *
17607924 ACTACCTCAGAATCTCAACTCCATCGAAACTCTACCACACAACCGAGCAAAAATAACTTCCATGC
1 ACTACCTCAGAATCTCAACTACACCAAAACTCTACCACACAACCGAGCAAAAATAACATCCACGC
17607989 TCGCGCAGGGATTCAAACACAATACCTCCAACAC
66 TCGCGCAGGGATTCAAACACAATACCTCCAACAC
*
17608023 ACTACCTCAGAATC-CTAACTACACCAAAACTCTATCACACAACCGAGCAAAAATAACATCCACG
1 ACTACCTCAGAATCTC-AACTACACCAAAACTCTACCACACAACCGAGCAAAAATAACATCCACG
17608087 CTCGCGCAGGGATTCAAACACAATACCTCCAACAC
65 CTCGCGCAGGGATTCAAACACAATACCTCCAACAC
17608122 ACTA
1 ACTA
17608126 ACTCCCTTAC
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 1 0.01
99 95 0.99
ACGTcount: A:0.39, C:0.35, G:0.09, T:0.16
Consensus pattern (99 bp):
ACTACCTCAGAATCTCAACTACACCAAAACTCTACCACACAACCGAGCAAAAATAACATCCACGC
TCGCGCAGGGATTCAAACACAATACCTCCAACAC
Found at i:17608553 original size:32 final size:32
Alignment explanation
Indices: 17608513--17608591 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
17608503 AATGTAAATT
**
17608513 ATTAATTTATTATATTT-TAAGTAA-ATTTTTA
1 ATTAATTTATTATATTTATAA-TAATATTTAAA
* *
17608544 TTGTAATTTATAATATTTATAATAATATTTAAA
1 AT-TAATTTATTATATTTATAATAATATTTAAA
17608577 ATTAATTTATTATAT
1 ATTAATTTATTATAT
17608592 AAAATAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 1 0.03
32 29 0.74
33 9 0.23
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (32 bp):
ATTAATTTATTATATTTATAATAATATTTAAA
Found at i:17613811 original size:26 final size:25
Alignment explanation
Indices: 17613752--17613803 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
17613742 GATAACATTG
17613752 AATTTTTGAATTTTTATATTTTTAA
1 AATTTTTGAATTTTTATATTTTTAA
*
17613777 AATCATTTTTAATTTTT-TATTTTTAA
1 AAT--TTTTGAATTTTTATATTTTTAA
17613803 A
1 A
17613804 GAGTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 10 0.42
27 11 0.46
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
AATTTTTGAATTTTTATATTTTTAA
Found at i:17621494 original size:61 final size:61
Alignment explanation
Indices: 17621387--17621916 Score: 412
Period size: 61 Copynumber: 8.6 Consensus size: 61
17621377 TCCAATGTTA
* *** * * ***
17621387 AAATCAATTTAGCAATATATATTGATATACGAACCAAATTCAGCAATGTATATTTATATAC
1 AAATCAATTTAGCAATGTATAACCATATACGAATCAATTTCAGCAATGTATAACCATATAC
* * * * * *
17621448 AAATCAATTTGGCAACGTATAACCATATACGAATCAAGTTCGGCAATGTATAATCATATAA
1 AAATCAATTTAGCAATGTATAACCATATACGAATCAATTTCAGCAATGTATAACCATATAC
* * * * *
17621509 AAATTAAATTCAGTAATGTATAACCATATACGAATCAA-TTCGGCAACT-TATATCCATATAC
1 AAA-TCAATTTAGCAATGTATAACCATATACGAATCAATTTCAGCAA-TGTATAACCATATAC
* * * * * * * *
17621570 AATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTTAGCAATATATAATCATATAC
1 AAATCAATTT-AGCAATGTATAACCATATACGAATCAATTTCAGCAATGTATAACCATATAC
** * *
17621632 AAATCAATTCGGCAACT-TATATCCATATAC-AATTCAATTTCAACAATGTATAACCATATAC
1 AAATCAATTTAGCAA-TGTATAACCATATACGAA-TCAATTTCAGCAATGTATAACCATATAC
* * * * *
17621693 AAATTAATTTCAGAAATGTACAACCATATACGAATCAA-TTCGGCAACT-TATATCCATATAC
1 AAATCAATTT-AGCAATGTATAACCATATACGAATCAATTTCAGCAA-TGTATAACCATATAC
* ** * * * **
17621754 AATTCAATTTCAGCAATGTATAACCATATAAAAATTAGTTTCAGCAATGTACAATTATATAC
1 AAATCAATTT-AGCAATGTATAACCATATACGAATCAATTTCAGCAATGTATAACCATATAC
* * *
17621816 AAATCAA-TTCGACAACT-TATATCCATATAC-AATTCAATTTCAACAATGTATAACCATATAC
1 AAATCAATTTAG-CAA-TGTATAACCATATACGAA-TCAATTTCAGCAATGTATAACCATATAC
* * * * *
17621877 AAATTAATTTCAGTAATGTACAATCATATACAAATCAATT
1 AAATCAATTT-AGCAATGTATAACCATATACGAATCAATT
17621917 CGACAACTCA
Statistics
Matches: 368, Mismatches: 81, Indels: 39
0.75 0.17 0.08
Matches are distributed among these distances:
60 10 0.03
61 235 0.64
62 118 0.32
63 5 0.01
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (61 bp):
AAATCAATTTAGCAATGTATAACCATATACGAATCAATTTCAGCAATGTATAACCATATAC
Found at i:17621499 original size:31 final size:31
Alignment explanation
Indices: 17621387--17621916 Score: 452
Period size: 31 Copynumber: 17.3 Consensus size: 31
17621377 TCCAATGTTA
* ***
17621387 AAATCAATTT-AGCAATATATATTGATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
* * * ***
17621417 GAACCAAATTCAGCAATGTATATTTATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
* *
17621448 AAATCAATTT-GGCAACGTATAACCATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
* * * * *
17621478 GAATCAAGTTCGGCAATGTATAATCATATAA
1 AAATCAATTTCAGCAATGTATAACCATATAC
* * *
17621509 AAATTAAATTCAGTAATGTATAACCATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
* * *
17621540 GAATCAA-TTCGGCAACT-TATATCCATATAC
1 AAATCAATTTCAGCAA-TGTATAACCATATAC
* * *
17621570 AATTCAATTTCAACAATGTATAACCATGTAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
* * * *
17621601 AAATTAATTTTAGCAATATATAATCATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
* *
17621632 AAATCAA-TTCGGCAACT-TATATCCATATAC
1 AAATCAATTTCAGCAA-TGTATAACCATATAC
* *
17621662 AATTCAATTTCAACAATGTATAACCATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
* * *
17621693 AAATTAATTTCAGAAATGTACAACCATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
* * *
17621724 GAATCAA-TTCGGCAACT-TATATCCATATAC
1 AAATCAATTTCAGCAA-TGTATAACCATATAC
* *
17621754 AATTCAATTTCAGCAATGTATAACCATATAA
1 AAATCAATTTCAGCAATGTATAACCATATAC
* * * **
17621785 AAATTAGTTTCAGCAATGTACAATTATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
*
17621816 AAATCAA-TTC-GACAACT-TATATCCATATAC
1 AAATCAATTTCAG-CAA-TGTATAACCATATAC
* *
17621846 AATTCAATTTCAACAATGTATAACCATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
* * * *
17621877 AAATTAATTTCAGTAATGTACAATCATATAC
1 AAATCAATTTCAGCAATGTATAACCATATAC
17621908 AAATCAATT
1 AAATCAATT
17621917 CGACAACTCA
Statistics
Matches: 393, Mismatches: 91, Indels: 31
0.76 0.18 0.06
Matches are distributed among these distances:
29 1 0.00
30 123 0.31
31 269 0.68
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (31 bp):
AAATCAATTTCAGCAATGTATAACCATATAC
Found at i:17621555 original size:92 final size:92
Alignment explanation
Indices: 17621425--17621961 Score: 734
Period size: 92 Copynumber: 5.8 Consensus size: 92
17621415 ACGAACCAAA
* * * * * * *
17621425 TTCAGCAATGTATATTTATATACAAATCAATTTGGCAACGTATAACCATATACGAA-TCAAGTTC
1 TTCAGCAATGTACAATCATATACAAATCAATTCGGCAACTTATATCCATATAC-AATTCAATTTC
** * *
17621489 GGCAATGTATAATCATATAAAAATTAAA
65 AACAATGTATAACCATATAAAAATTAAT
* * * *
17621517 TTCAGTAATGTATAACCATATACGAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCA
1 TTCAGCAATGTACAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCA
* *
17621582 ACAATGTATAACCATGTACAAATTAAT
66 ACAATGTATAACCATATAAAAATTAAT
* * *
17621609 TTTAGCAATATATAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCA
1 TTCAGCAATGTACAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCA
*
17621674 ACAATGTATAACCATATACAAATTAAT
66 ACAATGTATAACCATATAAAAATTAAT
* * *
17621701 TTCAGAAATGTACAACCATATACGAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCA
1 TTCAGCAATGTACAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCA
* *
17621766 GCAATGTATAACCATATAAAAATTAGT
66 ACAATGTATAACCATATAAAAATTAAT
* *
17621793 TTCAGCAATGTACAATTATATACAAATCAATTCGACAACTTATATCCATATACAATTCAATTTCA
1 TTCAGCAATGTACAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCA
*
17621858 ACAATGTATAACCATATACAAATTAAT
66 ACAATGTATAACCATATAAAAATTAAT
* * * * * *
17621885 TTCAGTAATGTACAATCATATACAAATCAATTCGACAACTCATATCCATATGCAAATCAATTTCG
1 TTCAGCAATGTACAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCA
*
17621950 ATAATGTATAAC
66 ACAATGTATAAC
17621962 TATAAACAAT
Statistics
Matches: 399, Mismatches: 45, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
91 2 0.01
92 397 0.99
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (92 bp):
TTCAGCAATGTACAATCATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCA
ACAATGTATAACCATATAAAAATTAAT
Found at i:17621934 original size:61 final size:60
Alignment explanation
Indices: 17621442--17621970 Score: 364
Period size: 61 Copynumber: 8.7 Consensus size: 60
17621432 ATGTATATTT
* * * * *
17621442 ATATACAAATCAATTT-GGCAACGTATAACCATATACGAATCAAGTTCGGCAATGTATAAT-C
1 ATATACAAATTAATTTCAGCAATGTATAACCATATACAAATCAA-TTCGACAAT-TAT-ATCC
* * * * *
17621503 ATATAAAAATTAAATTCAGTAATGTATAACCATATACGAATCAATTCGGCAACTTATATCC
1 ATATACAAATTAATTTCAGCAATGTATAACCATATACAAATCAATTCGACAA-TTATATCC
* * * **
17621564 ATATAC-AATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTTAGCAATATATAAT-C
1 ATATACAAATT-AATTTCAGCAATGTATAACCATATACAAATCAATTCGA-CAAT-TAT-ATCC
* * * * * *
17621626 ATATACAAATCAA-TTCGGCAACT-TATATCCATATACAATTCAATTTCAACAATGTATAACC
1 ATATACAAATTAATTTCAGCAA-TGTATAACCATATACAAATCAA-TTCGACAAT-TATATCC
* * * *
17621687 ATATACAAATTAATTTCAGAAATGTACAACCATATACGAATCAATTCGGCAACTTATATCC
1 ATATACAAATTAATTTCAGCAATGTATAACCATATACAAATCAATTCGACAA-TTATATCC
* * * * *
17621748 ATATAC-AATTCAATTTCAGCAATGTATAACCATATAAAAATTAGTTTC-AGCAATGTACAAT-T
1 ATATACAAATT-AATTTCAGCAATGTATAACCATATACAAATCA-ATTCGA-CAAT-TA-TATCC
* * * * *
17621810 ATATACAAATCAA-TTC-GACAACT-TATATCCATATACAATTCAATTTCAACAATGTATAACC
1 ATATACAAATTAATTTCAG-CAA-TGTATAACCATATACAAATCAA-TTCGACAAT-TATATCC
* * * *
17621871 ATATACAAATTAATTTCAGTAATGTACAATCATATACAAATCAATTCGACAACTCATATCC
1 ATATACAAATTAATTTCAGCAATGTATAACCATATACAAATCAATTCGACAA-TTATATCC
* * * * *
17621932 ATATGCAAATCAATTTC-GATAATGTATAACTATAAACAA
1 ATATACAAATTAATTTCAG-CAATGTATAACCATATACAA
17621971 TTCGAATTTG
Statistics
Matches: 368, Mismatches: 70, Indels: 60
0.74 0.14 0.12
Matches are distributed among these distances:
60 14 0.04
61 236 0.64
62 107 0.29
63 11 0.03
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (60 bp):
ATATACAAATTAATTTCAGCAATGTATAACCATATACAAATCAATTCGACAATTATATCC
Found at i:17624317 original size:21 final size:22
Alignment explanation
Indices: 17624259--17624367 Score: 116
Period size: 23 Copynumber: 5.0 Consensus size: 22
17624249 CCTGATCAGT
17624259 ATACGACACAT-AAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
****
17624280 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATAAAGTGCCTGA
*
17624300 ATACGACACATAAAGTGCTTGA
1 ATACGACACATAAAGTGCCTGA
*
17624322 GATACGACACATAAAGTGCTTGA
1 -ATACGACACATAAAGTGCCTGA
*
17624345 TGTACGACACATAAAGTGCCTGA
1 -ATACGACACATAAAGTGCCTGA
17624368 TCGACAAAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
20 10 0.14
21 20 0.27
22 1 0.01
23 42 0.58
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGA
Found at i:17624617 original size:36 final size:37
Alignment explanation
Indices: 17624563--17624639 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
17624553 AAATTCATAT
* *
17624563 TTCAATTCAATTTCACTTTTTCACTTTCAA-TCACAA
1 TTCAATTCAATTTCACTTTTCCACTTTCAAGTCAAAA
*
17624599 TTCAATTCAAATTT-ACTTTTCCATTTTCAAGTCAAAA
1 TTCAATTC-AATTTCACTTTTCCACTTTCAAGTCAAAA
17624636 TTCA
1 TTCA
17624640 TTTTAATTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 22 0.61
37 14 0.39
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.44
Consensus pattern (37 bp):
TTCAATTCAATTTCACTTTTCCACTTTCAAGTCAAAA
Found at i:17625354 original size:11 final size:11
Alignment explanation
Indices: 17625338--17625366 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
17625328 AAAAATTTAG
17625338 TTTTTCCTTTT
1 TTTTTCCTTTT
17625349 TTTTT-CTTTT
1 TTTTTCCTTTT
17625359 TTTTTCCT
1 TTTTTCCT
17625367 GCTCTGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCCTTTT
Found at i:17626137 original size:16 final size:16
Alignment explanation
Indices: 17626113--17626143 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17626103 TTTTAAATTT
17626113 TTATATTAAAAAAAAC
1 TTATATTAAAAAAAAC
*
17626129 TTATTTTAAAAAAAA
1 TTATATTAAAAAAAA
17626144 TTACACTTGT
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:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TTATATTAAAAAAAAC
Found at i:17626233 original size:13 final size:13
Alignment explanation
Indices: 17626208--17626246 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
17626198 ATTATTTTTT
17626208 TAATTTT-AAATA
1 TAATTTTAAAATA
17626220 TAATTTTAAAATA
1 TAATTTTAAAATA
17626233 TACA-TTTAAAATA
1 TA-ATTTTAAAATA
17626246 T
1 T
17626247 TATAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.28
13 17 0.68
14 1 0.04
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATTTTAAAATA
Found at i:17626330 original size:13 final size:12
Alignment explanation
Indices: 17626312--17626344 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
17626302 ATGTTTTATA
17626312 ATATTAAAAAATT
1 ATATTAAAAAA-T
17626325 ATATTAAAAAAT
1 ATATTAAAAAAT
17626337 AT-TTAAAA
1 ATATTAAAA
17626345 CATACATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.30
12 3 0.15
13 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATATTAAAAAAT
Found at i:17626378 original size:22 final size:21
Alignment explanation
Indices: 17626332--17626406 Score: 53
Period size: 24 Copynumber: 3.3 Consensus size: 21
17626322 ATTATATTAA
*
17626332 AAAATATT-TAAAACATACATTT
1 AAAATATTATAAAACA-ACA-AT
17626354 AAAATATTATAAAACTAACAAT
1 AAAATATTATAAAAC-AACAAT
* *
17626376 AAAAAAATAAATAAAACAAACAAAT
1 -AAAATAT-TATAAAAC-AAC-AAT
17626401 AAAATA
1 AAAATA
17626407 AATAAAGGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 9 0.21
23 15 0.35
24 16 0.37
25 3 0.07
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATATTATAAAACAACAAT
Found at i:17626380 original size:23 final size:22
Alignment explanation
Indices: 17626331--17626404 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
17626321 AATTATATTA
*
17626331 AAAAATATT-TAAAACATACATT
1 AAAAATATTATAAAACA-ACAAT
*
17626353 TAAAATATTATAAAACTAACAAT
1 AAAAATATTATAAAAC-AACAAT
* *
17626376 AAAAAAATAAATAAAACAAACAAAT
1 AAAAATAT-TATAAAAC-AAC-AAT
17626401 AAAA
1 AAAA
17626405 TAAATAAAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
22 8 0.19
23 16 0.38
24 11 0.26
25 7 0.17
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAATATTATAAAACAACAAT
Found at i:17626389 original size:4 final size:4
Alignment explanation
Indices: 17626373--17626467 Score: 54
Period size: 4 Copynumber: 23.5 Consensus size: 4
17626363 TAAAACTAAC
* * * * *
17626373 AATA AAAA AATA AATAA AACA AACA AATAA AATA AATA AA-G GATA AATA
1 AATA AATA AATA AAT-A AATA AATA AAT-A AATA AATA AATA AATA AATA
* *
17626422 AATA AATA AACTGA AA-A AGTA AATA AAGA AA-A ACA-A AATA AATA AA
1 AATA AATA AA-T-A AATA AATA AATA AATA AATA A-ATA AATA AATA AA
17626468 ACGAAAAAGG
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
3 6 0.08
4 55 0.76
5 8 0.11
6 3 0.04
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (4 bp):
AATA
Found at i:17627212 original size:7 final size:7
Alignment explanation
Indices: 17627200--17627226 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17627190 AATATAACTC
17627200 AAAATTT
1 AAAATTT
17627207 AAAATTT
1 AAAATTT
17627214 AAAATTT
1 AAAATTT
17627221 AAAATT
1 AAAATT
17627227 AGTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:17627271 original size:15 final size:15
Alignment explanation
Indices: 17627253--17627294 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
17627243 CATATATATA
17627253 AAAAATTCGAAAAA-T
1 AAAAATT-GAAAAATT
*
17627268 AAAAATTAAAAAATT
1 AAAAATTGAAAAATT
17627283 AAAAATTGAAAA
1 AAAAATTGAAAA
17627295 TATAGAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAAATTGAAAAATT
Found at i:17627465 original size:18 final size:19
Alignment explanation
Indices: 17627433--17627478 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
17627423 TGTGTTTTTA
17627433 TTTTTTTATTGTTTG-AAT
1 TTTTTTTATTGTTTGAAAT
17627451 TTTTTATTATT-TTTGAAAT
1 TTTTT-TTATTGTTTGAAAT
*
17627470 TTTATTTAT
1 TTTTTTTAT
17627479 ATTCAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTTTTTATTGTTTGAAAT
Found at i:17627472 original size:17 final size:19
Alignment explanation
Indices: 17627431--17627475 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
17627421 AATGTGTTTT
*
17627431 TATTTTTTTATTGTTTGAA
1 TATTTTATTATTGTTTGAA
*
17627450 TTTTTTATTATT-TTTGAA
1 TATTTTATTATTGTTTGAA
17627468 -ATTTTATT
1 TATTTTATT
17627476 TATATTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 7 0.30
18 6 0.26
19 10 0.43
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (19 bp):
TATTTTATTATTGTTTGAA
Found at i:17634589 original size:29 final size:29
Alignment explanation
Indices: 17634554--17634764 Score: 171
Period size: 29 Copynumber: 7.2 Consensus size: 29
17634544 TCATCGACCA
17634554 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
* * * *
17634583 ATGAAAAGGGAT-GGTGACGACCATCGAATT
1 ATGAAAAGGGATAGCT-TCGGCTATCG-ATT
*
17634613 ATGAAAAGGGATAGCTTCGGCTATAGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
* *
17634642 ATGAAAAGGGAT-GGTGAT-GGCCATCGAATT
1 ATGAAAAGGGATAGCT--TCGGCTATCG-ATT
* * *
17634672 ATGTAAAGGGATAGCTTTGACTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
* * * * * *
17634701 ATGAAAAAGGAT-GGTGACGACCATCAATT
1 ATGAAAAGGGATAGCT-TCGGCTATCGATT
*
17634730 ATGAAAAGGGAAAGC-TCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
*
17634758 ACGAAAA
1 ATGAAAA
17634765 AAGATGGTGA
Statistics
Matches: 141, Mismatches: 31, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
28 21 0.15
29 73 0.52
30 43 0.30
31 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGATT
Found at i:17634631 original size:59 final size:59
Alignment explanation
Indices: 17634554--17634857 Score: 425
Period size: 59 Copynumber: 5.2 Consensus size: 59
17634544 TCATCGACCA
17634554 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAATT
* * *
17634613 ATGAAAAGGGATAGCTTCGGCTATAGATTATGAAAAGGGATGGTGATGGCCATCGAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAATT
* * * *
17634672 ATGTAAAGGGATAGCTTTGACTATCGATTATGAAAAAGGATGGTGACGACCATC-AATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAATT
* * ** *
17634730 ATGAAAAGGGAAAGC-TCGGCTATCGATTACGAAAAAAGATGGTGACGACCATTGAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAATT
* * * * * *
17634788 ATGAAAAGGGATAACTTTGACTATTGATTATAAAAAGGGATGGTGACGACCATC-AACT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAATT
17634846 ATGAAAAGGGAT
1 ATGAAAAGGGAT
17634858 GGTGACGACC
Statistics
Matches: 215, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
57 33 0.15
58 49 0.23
59 133 0.62
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (59 bp):
ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAATT
Found at i:17634806 original size:116 final size:117
Alignment explanation
Indices: 17634554--17634856 Score: 439
Period size: 116 Copynumber: 2.6 Consensus size: 117
17634544 TCATCGACCA
* * *
17634554 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAATTATGAAA
1 ATGAAAAGGGATAGCTTTGACTATCGATTATGAAAAAGGATGGTGACGACCATC-AATTATGAAA
* * ** * *
17634619 AGGGATAGCTTCGGCTATAGATTATGAAAAGGGATGGTGATGGCCATCGAATT
65 AGGGAAAGCTTCGGCTATAGATTACGAAAAAAGATGGTGACGACCATCGAATT
*
17634672 ATGTAAAGGGATAGCTTTGACTATCGATTATGAAAAAGGATGGTGACGACCATCAATTATGAAAA
1 ATGAAAAGGGATAGCTTTGACTATCGATTATGAAAAAGGATGGTGACGACCATCAATTATGAAAA
* *
17634737 GGGAAAGC-TCGGCTATCGATTACGAAAAAAGATGGTGACGACCATTGAATT
66 GGGAAAGCTTCGGCTATAGATTACGAAAAAAGATGGTGACGACCATCGAATT
* * *
17634788 ATGAAAAGGGATAACTTTGACTATTGATTAT-AAAAAGGGATGGTGACGACCATCAACTATGAAA
1 ATGAAAAGGGATAGCTTTGACTATCGATTATGAAAAA-GGATGGTGACGACCATCAATTATGAAA
17634852 AGGGA
65 AGGGA
17634857 TGGTGACGAC
Statistics
Matches: 168, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
115 5 0.03
116 95 0.57
117 18 0.11
118 50 0.30
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (117 bp):
ATGAAAAGGGATAGCTTTGACTATCGATTATGAAAAAGGATGGTGACGACCATCAATTATGAAAA
GGGAAAGCTTCGGCTATAGATTACGAAAAAAGATGGTGACGACCATCGAATT
Found at i:17635166 original size:21 final size:20
Alignment explanation
Indices: 17635129--17635167 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17635119 CTACAATTTG
*
17635129 AAAAATTCTAACTTTTTCCC
1 AAAAATTCTAACATTTTCCC
17635149 AAAAATTCTATACATTTTC
1 AAAAATTCTA-ACATTTTC
17635168 TATTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTCTAACATTTTCCC
Found at i:17637954 original size:18 final size:18
Alignment explanation
Indices: 17637931--17637967 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17637921 AATTCTTTTC
17637931 TTTCTATTATACTAGTAT
1 TTTCTATTATACTAGTAT
* *
17637949 TTTCTATTCTATTAGTAT
1 TTTCTATTATACTAGTAT
17637967 T
1 T
17637968 AAATTAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTCTATTATACTAGTAT
Found at i:17637980 original size:27 final size:27
Alignment explanation
Indices: 17637950--17638005 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
17637940 TACTAGTATT
17637950 TTCTATTCTATTAGTATTAAATTAGTA
1 TTCTATTCTATTAGTATTAAATTAGTA
*
17637977 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAAATTAGTA
17638004 TT
1 TT
17638006 AGTTAGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (27 bp):
TTCTATTCTATTAGTATTAAATTAGTA
Found at i:17637996 original size:6 final size:6
Alignment explanation
Indices: 17637958--17638028 Score: 59
Period size: 5 Copynumber: 13.2 Consensus size: 6
17637948 TTTTCTATTC
* * *
17637958 TATTAG TATTA- AATTAG TATT-C TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
17638002 TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG T
17638029 TAGTGATCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
4 4 0.07
5 27 0.48
6 25 0.45
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (6 bp):
TATTAG
Found at i:17638000 original size:11 final size:11
Alignment explanation
Indices: 17637986--17638032 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
17637976 ATTCTATTCT
17637986 ATTAGTATTAG
1 ATTAGTATTAG
17637997 ATTAGTATTAG
1 ATTAGTATTAG
17638008 -TTAG-ATTAG
1 ATTAGTATTAG
17638017 ATTAGTATTAG
1 ATTAGTATTAG
17638028 -TTAGT
1 ATTAGT
17638033 GATCCCGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 16 0.47
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:17638017 original size:20 final size:21
Alignment explanation
Indices: 17637987--17638032 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
17637977 TTCTATTCTA
17637987 TTAGTATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
17638008 TTAG-ATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
17638028 TTAGT
1 TTAGT
17638033 GATCCCGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (21 bp):
TTAGTATTAGATTAGTATTAG
Found at i:17642302 original size:29 final size:28
Alignment explanation
Indices: 17642282--17642577 Score: 193
Period size: 29 Copynumber: 10.1 Consensus size: 28
17642272 GGCTTCGGCT
*
17642282 ATCGATTATGAAAAGGAATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGT-ACGACC
* *
17642311 ATCAATTATGAAAAGGGATGGGACGACC
1 ATCGATTATGAAAAGGGATGGTACGACC
* * ** * *
17642339 ATCGAAGTATGAAAAGGGATAGCTTTGGCT
1 ATCG-ATTATGAAAAGGGAT-GGTACGACC
* *
17642369 ATTGATTATGAAAAGGGATGGTGATGACC
1 ATCGATTATGAAAAGGGATGGT-ACGACC
* *
17642398 ATCAATTATGAAAATGGG-TGGTGATGACC
1 ATCGATTATGAAAA-GGGATGGT-ACGACC
* * * * *
17642427 ATCGAATTATGAAAAGGGAAAGCTTCGGCT
1 ATCG-ATTATGAAAAGGG-ATGGTACGACC
*
17642457 ATCGATTATGAAAAGGGATGGTGATGACC
1 ATCGATTATGAAAAGGGATGGT-ACGACC
* * * * *
17642486 ATTGAATTATGAAAAGGGATAGCTTCGGCT
1 ATCG-ATTATGAAAAGGGAT-GGTACGACC
*
17642516 ATTGATTAT-AAAATGGGAAT-GTGACGACC
1 ATCGATTATGAAAA-GGG-ATGGT-ACGACC
* *
17642545 ATCAACTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGT-ACGACC
17642574 ATCG
1 ATCG
17642578 TGATTCCACT
Statistics
Matches: 206, Mismatches: 46, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
28 21 0.10
29 129 0.63
30 52 0.25
31 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (28 bp):
ATCGATTATGAAAAGGGATGGTACGACC
Found at i:17642464 original size:88 final size:87
Alignment explanation
Indices: 17642273--17642505 Score: 360
Period size: 88 Copynumber: 2.7 Consensus size: 87
17642263 AATAGGGATG
* *
17642273 GCTTCGGCTATCGATTATGAAAAGGAATGGTGACGACCATCAATTATGAAAAGGGATGGGACGAC
1 GCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATCAATTATGAAAAGGGATGGGACGAC
*
17642338 CATCGAAGTATGAAAAGGGATA
66 CATCGAAGTATGAAAAGGGAAA
* * *
17642360 GCTTTGGCTATTGATTATGAAAAGGGATGGTGATGACCATCAATTATGAAAATGGG-TGGTGATG
1 GCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATCAATTATGAAAA-GGGATGG-GACG
*
17642424 ACCATCGAATTATGAAAAGGGAAA
64 ACCATCGAAGTATGAAAAGGGAAA
*
17642448 GCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATTGAATTATGAAAAGGGAT
1 GCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCA-TCAATTATGAAAAGGGAT
17642506 AGCTTCGGCT
Statistics
Matches: 132, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
87 51 0.39
88 68 0.52
89 13 0.10
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.25
Consensus pattern (87 bp):
GCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATCAATTATGAAAAGGGATGGGACGAC
CATCGAAGTATGAAAAGGGAAA
Found at i:17642510 original size:59 final size:58
Alignment explanation
Indices: 17642260--17642564 Score: 248
Period size: 59 Copynumber: 5.2 Consensus size: 58
17642250 TCATCGACCA
* * * *
17642260 ATGAATAGGGATGGCTTCGGCTATCGATTATGAAAAGGAATGGTGACGACCA-TCAATT
1 ATGAAAAGGGAT-GCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATTGAATT
*** * * * * * * *
17642318 ATGAAAAGGGATGGGACGACCATCGAAGTATGAAAAGGGATAGCT-TTGGCTATTG-ATT
1 ATGAAAAGGGATGCTTCGGCTATCG-ATTATGAAAAGGGAT-GGTGATGACCATTGAATT
* * * * *
17642376 ATGAAAAGGGATGGTGAT-GACCATCAATTATGAAAATGGG-TGGTGATGACCATCGAATT
1 ATGAAAAGGGATGCT--TCGGCTATCGATTATGAAAA-GGGATGGTGATGACCATTGAATT
*
17642435 ATGAAAAGGGAAAGCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATTGAATT
1 ATGAAAAGGG-ATGCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATTGAATT
* * * *
17642494 ATGAAAAGGGATAGCTTCGGCTATTGATTAT-AAAATGGGAAT-GTGACGACCA-TCAACT
1 ATGAAAAGGGAT-GCTTCGGCTATCGATTATGAAAA-GGG-ATGGTGATGACCATTGAATT
17642552 ATGAAAAGGGATG
1 ATGAAAAGGGATG
17642565 GTGACGACCA
Statistics
Matches: 199, Mismatches: 34, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
57 11 0.06
58 85 0.43
59 98 0.49
60 5 0.03
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.25
Consensus pattern (58 bp):
ATGAAAAGGGATGCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATTGAATT
Found at i:17642524 original size:88 final size:87
Alignment explanation
Indices: 17642273--17642576 Score: 330
Period size: 88 Copynumber: 3.5 Consensus size: 87
17642263 AATAGGGATG
* **
17642273 GCTTCGGCTATCGATTATGAAAAGGAATGGTGACGACCATCAATTATGAAAAGGGATGGGACGAC
1 GCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCAATTATGAAAAGGGATGGTTCGAC
* *
17642338 CATCGAAGTATGAAAAGGGATA
66 CATCGAATTATGAAAAGGGAAA
* * *
17642360 GCTTTGGCTATTGATTATGAAAAGGGATGGTGATGACCATCAATTATGAAAATGGG-TGGTGAT-
1 GCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCAATTATGAAAA-GGGATGGT--TC
17642423 GACCATCGAATTATGAAAAGGGAAA
63 GACCATCGAATTATGAAAAGGGAAA
* * *
17642448 GCTTCGGCTATCGATTATGAAAAGGGATGGTGATGACCATTGAATTATGAAAAGGGATAGCTTCG
1 GCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCA-TCAATTATGAAAAGGGAT-GGTTCG
* * * *
17642513 GCTATTG-ATTAT-AAAATGGGAAT
64 ACCATCGAATTATGAAAA-GGGAAA
* * * * *
17642536 G-TGACGACCATCAACTATGAAAAGGGATGGTGACGACCATC
1 GCT-TCGGCTATCGATTATGAAAAGGGATGGTGACGACCATC
17642577 GTGATTCCAC
Statistics
Matches: 185, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
87 57 0.31
88 108 0.58
89 18 0.10
90 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (87 bp):
GCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCAATTATGAAAAGGGATGGTTCGAC
CATCGAATTATGAAAAGGGAAA
Found at i:17649568 original size:13 final size:14
Alignment explanation
Indices: 17649539--17649572 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
17649529 CATCCACCAT
*
17649539 CAAAATACATTCAA
1 CAAAATACATCCAA
17649553 CAAAAT-CATCCAA
1 CAAAATACATCCAA
17649566 CAAAATA
1 CAAAATA
17649573 AAACTATCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.18
Consensus pattern (14 bp):
CAAAATACATCCAA
Found at i:17652420 original size:19 final size:18
Alignment explanation
Indices: 17652393--17652431 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
17652383 ATCCCCACCA
17652393 TTAACTCTTTCATTACAAT
1 TTAACTC-TTCATTACAAT
*
17652412 TTAATTCTTCATTACAAT
1 TTAACTCTTCATTACAAT
17652430 TT
1 TT
17652432 TGTTCCCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAACTCTTCATTACAAT
Found at i:17652990 original size:48 final size:47
Alignment explanation
Indices: 17652935--17653076 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 47
17652925 AATATACCAC
*
17652935 ATAATATACATACATTAAACATGACATACATAATATACAAACATAAT
1 ATAATATACATACATTAAACATAACATACATAATATACAAACATAAT
* *
17652982 AGTAATATA-ACACA-T-AACA-AACATACA-AATATACATACATAAT
1 A-TAATATACATACATTAAACATAACATACATAATATACAAACATAAT
*
17653025 ATAATA-ACAATACATAACATAACATAACATACATACAAATATACAAACATAA
1 ATAATATAC-ATACAT--TA-AACATAACATACAT---AATATACAAACATAA
17653077 CAATAAACAT
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
41 1 0.01
42 5 0.07
43 20 0.26
44 7 0.09
45 4 0.05
46 1 0.01
47 5 0.07
48 11 0.14
49 8 0.11
53 14 0.18
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.24
Consensus pattern (47 bp):
ATAATATACATACATTAAACATAACATACATAATATACAAACATAAT
Found at i:17652990 original size:60 final size:56
Alignment explanation
Indices: 17652915--17653182 Score: 178
Period size: 60 Copynumber: 4.7 Consensus size: 56
17652905 ACAGTCATAC
* * *
17652915 ACATAACAATAATATACCACATAATATACATACATTAAACATGACATACATAATATACAA
1 ACATAACAATAATATAACACATAACAAACATAC---AAACAT-ACATACATAATATACAA
* * *
17652975 ACATAATAGTAATATAACACATAACAAACATACAAATATACATACATAATATA-ATA
1 ACATAACAATAATATAACACATAACAAACATACAAACATACATACATAATATACA-A
* * * * * *
17653031 ACA-ATAC-ATAACAT-A-ACATAACATACATACAAATATACAAACATAACA-ATAA
1 ACATA-ACAATAATATAACACATAACAAACATACAAACATACATACATAATATACAA
*
17653083 ACATAACATACATATATAACA-AT-ACATAACATAACATAACATACATACA-AATATACAA
1 ACATAACA-ATA-ATATAACACATAACA-AACAT-ACA-AACATACATACATAATATACAA
* * * * *
17653141 GCACAACAGTAAACATAACATACAT-ACAAATATACAAACATA
1 ACATAACAAT-AATATAAC--ACATAACAAACATACAAACATA
17653183 ACAGTAAACA
Statistics
Matches: 166, Mismatches: 25, Indels: 37
0.73 0.11 0.16
Matches are distributed among these distances:
52 7 0.04
53 32 0.19
54 3 0.02
55 13 0.08
56 26 0.16
57 24 0.14
58 23 0.14
59 5 0.03
60 33 0.20
ACGTcount: A:0.58, C:0.18, G:0.01, T:0.22
Consensus pattern (56 bp):
ACATAACAATAATATAACACATAACAAACATACAAACATACATACATAATATACAA
Found at i:17653055 original size:37 final size:35
Alignment explanation
Indices: 17652998--17653304 Score: 246
Period size: 37 Copynumber: 8.7 Consensus size: 35
17652988 ATAACACATA
* *
17652998 ACAAACAT-ACA-AATAT-ACATACATA-ATATAAT
1 ACAAACATAACATAACATAACATACATACAAAT-AT
17653030 AACAATACATAACATAACATAACATACATACAAATAT
1 -ACAA-ACATAACATAACATAACATACATACAAATAT
*
17653067 ACAAACATAACAATAAACATAACATACAT--ATATA-
1 ACAAACATAAC-AT-AACATAACATACATACAAATAT
17653101 ACAATACATAACATAACATAACATACATACAAATAT
1 ACAA-ACATAACATAACATAACATACATACAAATAT
* *
17653137 ACAAGCACAACAGTAAACATAACATACATACAAATAT
1 ACAAACATAACA-T-AACATAACATACATACAAATAT
* * * *
17653174 ACAAACATAACAGTAAACATATCATCCACACATAACAAT
1 ACAAACATAACA-T-AACATAACATACATACA-AA-TAT
*
17653213 ACATAACATAATAGTAAACATAACATACATAC--ATA-
1 ACA-AACATAACA-T-AACATAACATACATACAAATAT
* *
17653248 ACAAAACATAACAT-ACATAATATACATA-ACAATTT
1 AC-AAACATAACATAACATAACATACATACA-AATAT
*
17653283 AAAAACATAACAT-ACAT-ACATA
1 ACAAACATAACATAACATAACATA
17653305 AACAATAAAG
Statistics
Matches: 231, Mismatches: 22, Indels: 42
0.78 0.07 0.14
Matches are distributed among these distances:
32 13 0.06
33 22 0.10
34 28 0.12
35 42 0.18
36 17 0.07
37 75 0.32
38 5 0.02
39 5 0.02
40 24 0.10
ACGTcount: A:0.58, C:0.19, G:0.01, T:0.21
Consensus pattern (35 bp):
ACAAACATAACATAACATAACATACATACAAATAT
Found at i:17653109 original size:70 final size:71
Alignment explanation
Indices: 17652991--17653294 Score: 304
Period size: 70 Copynumber: 4.3 Consensus size: 71
17652981 TAGTAATATA
*
17652991 ACAC-ATA-ACAAACAT-ACAAATATACAT-ACATA-ATATAATAACAATACATAACATAACATA
1 ACACAATATACAAACATAAC-AATAAACATAACATACATAT-ATAACAATACATAACATAACATA
17653051 ACATACAT
64 ACATACAT
17653059 ACA-AATATACAAACATAACAATAAACATAACATACATATATAACAATACATAACATAACATAAC
1 ACACAATATACAAACATAACAATAAACATAACATACATATATAACAATACATAACATAACATAAC
17653123 ATACAT
66 ATACAT
* * * *
17653129 ACA-AATATACAAGCACAACAGTAAACATAACATACATACAAATATACAA-ACATAACAGTAAAC
1 ACACAATATACAAACATAACAATAAACATAACATACAT--ATATA-ACAATACATAACA-T-AAC
* * *
17653192 ATATCATCCAC
61 ATAACATACAT
* * * * * *
17653203 ACATAACAATACATAACATAATAGTAAACATAACATACATACATAACAAAACATAACAT-ACATA
1 ACACAA-TATACA-AACATAACAATAAACATAACATACATATATAACAATACATAACATAACATA
*
17653267 ATATACAT
64 ACATACAT
* *
17653275 A-ACAATTTAAAAACATAACA
1 ACACAATATACAAACATAACA
17653295 TACATACATA
Statistics
Matches: 200, Mismatches: 22, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
68 6 0.03
69 24 0.12
70 75 0.38
71 7 0.04
72 22 0.11
73 5 0.03
74 19 0.09
75 14 0.07
76 5 0.03
77 23 0.12
ACGTcount: A:0.59, C:0.19, G:0.01, T:0.21
Consensus pattern (71 bp):
ACACAATATACAAACATAACAATAAACATAACATACATATATAACAATACATAACATAACATAAC
ATACAT
Found at i:17653170 original size:107 final size:110
Alignment explanation
Indices: 17653045--17653241 Score: 319
Period size: 107 Copynumber: 1.8 Consensus size: 110
17653035 TACATAACAT
* *
17653045 AACATAACATACATACAAATATACAAACATAACAATAAACATAACATACATATATAACAATACAT
1 AACATAACATACATACAAATATACAAACATAACAATAAACATAACATACACACATAACAATACAT
17653110 AACATAACA-T-AACAT-ACATACAAATATACAAGCACAACAGTA
66 AACATAACAGTAAACATAACATACAAATATACAAGCACAACAGTA
* * *
17653152 AACATAACATACATACAAATATACAAACATAACAGTAAACATATCATCCACACATAACAATACAT
1 AACATAACATACATACAAATATACAAACATAACAATAAACATAACATACACACATAACAATACAT
*
17653217 AACATAATAGTAAACATAACATACA
66 AACATAACAGTAAACATAACATACA
17653242 TACATAACAA
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
107 68 0.84
108 1 0.01
109 5 0.06
110 7 0.09
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (110 bp):
AACATAACATACATACAAATATACAAACATAACAATAAACATAACATACACACATAACAATACAT
AACATAACAGTAAACATAACATACAAATATACAAGCACAACAGTA
Found at i:17653291 original size:44 final size:40
Alignment explanation
Indices: 17653203--17653294 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
17653193 TATCATCCAC
* * * *
17653203 ACATAACAATACATAACATAATAGTAAACATAACATACAT
1 ACATAACAAAACATAACATAATAATAAACATAACATAAAA
*
17653243 ACATAACAAAACATAACATACATAATATACATAACAATTTAAAA
1 ACATAACAAAACATAACATA-ATAATAAACATAAC-A--TAAAA
17653287 ACATAACA
1 ACATAACA
17653295 TACATACATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
40 19 0.44
41 12 0.28
42 1 0.02
44 11 0.26
ACGTcount: A:0.60, C:0.17, G:0.01, T:0.22
Consensus pattern (40 bp):
ACATAACAAAACATAACATAATAATAAACATAACATAAAA
Found at i:17653935 original size:16 final size:16
Alignment explanation
Indices: 17653914--17653960 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
17653904 GTTTTCTTTC
*
17653914 AGATGAAGAGTTGTTT
1 AGATGAAGAATTGTTT
*
17653930 AGATGAAGAATCGTTT
1 AGATGAAGAATTGTTT
17653946 AGATGAAGAATTGTT
1 AGATGAAGAATTGTT
17653961 CATATTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (16 bp):
AGATGAAGAATTGTTT
Found at i:17657945 original size:106 final size:105
Alignment explanation
Indices: 17657756--17657946 Score: 271
Period size: 105 Copynumber: 1.8 Consensus size: 105
17657746 AATCCAAAAA
* *
17657756 TAATTTTATTTTAATAAATTTAATATTAAATTAAATTAAATATTTATCTGAATAGTATTTTAATA
1 TAATTTTATCTTAATAAATTTAATATTAAATTAAATTAAATATTTATCTGAATAGTATTATAATA
17657821 ATTTAATATGAAAGTGATTATCTTAATATTAAATGTAATT
66 ATTTAATATGAAAGTGATTATCTTAATATTAAATGTAATT
* *
17657861 TAATATTTATCTT-ATAGATTTAATATTAAATTTAATCT-AATATTTATCT-AGATAAGTATTAT
1 TAAT-TTTATCTTAATAAATTTAATATTAAATTAAAT-TAAATATTTATCTGA-AT-AGTATTAT
* *
17657923 ATTAATTTAATATTAAAGTGATTA
62 AATAATTTAATATGAAAGTGATTA
17657947 AACTTAATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
104 1 0.01
105 38 0.50
106 37 0.49
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (105 bp):
TAATTTTATCTTAATAAATTTAATATTAAATTAAATTAAATATTTATCTGAATAGTATTATAATA
ATTTAATATGAAAGTGATTATCTTAATATTAAATGTAATT
Found at i:17667627 original size:48 final size:50
Alignment explanation
Indices: 17667555--17667664 Score: 147
Period size: 49 Copynumber: 2.3 Consensus size: 50
17667545 ATTTTAACAT
*
17667555 ATTTAATATT-AAATTTAACTTAATACTTATCTTA-A-AAGTATTTTATTA
1 ATTTAATATTAAAATTTAACTTAATACTTATC-TAGATAAGTATTATATTA
* * *
17667603 ATTTAATATTAAAATTTATC-TAATATTTATCTAGATAATTATTATATTA
1 ATTTAATATTAAAATTTAACTTAATACTTATCTAGATAAGTATTATATTA
17667652 ATTTAATATTAAA
1 ATTTAATATTAAA
17667665 GTGATTAAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
47 2 0.04
48 21 0.38
49 32 0.58
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (50 bp):
ATTTAATATTAAAATTTAACTTAATACTTATCTAGATAAGTATTATATTA
Found at i:17680959 original size:25 final size:25
Alignment explanation
Indices: 17680931--17680978 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17680921 CTCGCAGGAA
*
17680931 CCATATAACGAGAAGCTCGAGAGGG
1 CCATATAACGAGAAGCTCAAGAGGG
* * *
17680956 CCATGTATCGAGATGCTCAAGAG
1 CCATATAACGAGAAGCTCAAGAG
17680979 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (25 bp):
CCATATAACGAGAAGCTCAAGAGGG
Found at i:17681339 original size:21 final size:20
Alignment explanation
Indices: 17681313--17681361 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
17681303 TAAATTTAAC
* *
17681313 TCAATTTAATACGATTCATAA
1 TCAATTCAATACAATTCA-AA
*
17681334 TCAATTCAATTCAATTCAAA
1 TCAATTCAATACAATTCAAA
17681354 TCAATTCA
1 TCAATTCA
17681362 CATTCTAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATTCAATACAATTCAAA
Found at i:17681357 original size:15 final size:16
Alignment explanation
Indices: 17681334--17681366 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17681324 CGATTCATAA
*
17681334 TCAATTCAATTCA-AT
1 TCAAATCAATTCACAT
17681349 TCAAATCAATTCACAT
1 TCAAATCAATTCACAT
17681365 TC
1 TC
17681367 TAGGAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.36
Consensus pattern (16 bp):
TCAAATCAATTCACAT
Found at i:17688276 original size:29 final size:31
Alignment explanation
Indices: 17688214--17688290 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 31
17688204 TTACAGAGAA
* *
17688214 TGCCACAGAGGC-TTT-CATTTGATAGATAT
1 TGCCACAAAGGCGTTTCCTTTTGATAGATAT
*
17688243 CGCCACAAAGGCGTTTCCTTTTGA-AGAT-T
1 TGCCACAAAGGCGTTTCCTTTTGATAGATAT
*
17688272 TGCCACAAAGTCG-TTCCTT
1 TGCCACAAAGGCGTTTCCTT
17688291 AACAGAGGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.15
29 22 0.54
30 7 0.17
31 6 0.15
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (31 bp):
TGCCACAAAGGCGTTTCCTTTTGATAGATAT
Found at i:17688405 original size:61 final size:61
Alignment explanation
Indices: 17688331--17688469 Score: 188
Period size: 61 Copynumber: 2.3 Consensus size: 61
17688321 TGGAGTTTTC
* * *
17688331 CCACAAAGGCATTCTTTAACATTTAGTAGTCACCACAAAGCCTTTCATGTCCAAAGTATTA
1 CCACAAAGGCATTCCTTAACATTCAGTACTCACCACAAAGCCTTTCATGTCCAAAGTATTA
* ** * * *
17688392 CCACAAAGGCATTCCTTAACATTCAGTACTCGCCACAAAGGTTTTCCTGTCCAGAGTATTG
1 CCACAAAGGCATTCCTTAACATTCAGTACTCACCACAAAGCCTTTCATGTCCAAAGTATTA
*
17688453 CCACAAAGGTATTCCTT
1 CCACAAAGGCATTCCTT
17688470 CCCCTAGTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (61 bp):
CCACAAAGGCATTCCTTAACATTCAGTACTCACCACAAAGCCTTTCATGTCCAAAGTATTA
Found at i:17698353 original size:74 final size:74
Alignment explanation
Indices: 17698232--17698404 Score: 258
Period size: 74 Copynumber: 2.3 Consensus size: 74
17698222 AGTTTACTGT
*
17698232 ATGGTACGTAGCTTCATAAATAAACGAGGTGATATGGTGACAGGTTAT-CTATTTCAGACCTTTA
1 ATGGTACGTAGCTTCATAAATAAACGAGGGGATATGGTGACAGGTTATGC-ATTTCAGACCTTTA
17698296 GAGTAAACAC
65 GAGTAAACAC
* * * *
17698306 ATGGTACGTAACTTCATAAATAAACTAGGGGATATGGTGACTGGTTATGCATTTCAGACTTTTAG
1 ATGGTACGTAGCTTCATAAATAAACGAGGGGATATGGTGACAGGTTATGCATTTCAGACCTTTAG
* *
17698371 AGTAGACGC
66 AGTAAACAC
*
17698380 ATGGTATGTAGCTTCATAAATAAAC
1 ATGGTACGTAGCTTCATAAATAAAC
17698405 CGTGGAAAGA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 88 0.99
75 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.31
Consensus pattern (74 bp):
ATGGTACGTAGCTTCATAAATAAACGAGGGGATATGGTGACAGGTTATGCATTTCAGACCTTTAG
AGTAAACAC
Found at i:17698906 original size:26 final size:27
Alignment explanation
Indices: 17698870--17698922 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 27
17698860 TCGGAAATAC
17698870 ATTTTAAAAATAA-AAAATAAAAAAGT
1 ATTTTAAAAATAATAAAATAAAAAAGT
17698896 ATTTTAAAAATAATTTAAAATAAAAAA
1 ATTTTAAAAATAA--TAAAATAAAAAA
17698923 ATAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 13 0.54
29 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
ATTTTAAAAATAATAAAATAAAAAAGT
Found at i:17698947 original size:13 final size:13
Alignment explanation
Indices: 17698931--17698955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17698921 AAATAAAAAA
17698931 ATTTATTATATAT
1 ATTTATTATATAT
17698944 ATTTATTATATA
1 ATTTATTATATA
17698956 AATACTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTATTATATAT
Found at i:17700640 original size:27 final size:27
Alignment explanation
Indices: 17700596--17700654 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
17700586 CTAACGAGAT
*
17700596 AAGAATATTGGTTCAACAATTAATGTA
1 AAGAATATTGATTCAACAATTAATGTA
*
17700623 AAGAATATTGATTGAACAATTAATGTA
1 AAGAATATTGATTCAACAATTAATGTA
17700650 AAGAA
1 AAGAA
17700655 GTTTTAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (27 bp):
AAGAATATTGATTCAACAATTAATGTA
Found at i:17701733 original size:24 final size:25
Alignment explanation
Indices: 17701701--17701753 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
17701691 AAAGCTAAAA
*
17701701 TTTTGGATAAAATGGAAATTTA-CT
1 TTTTGGATAAAATGGAAACTTATCT
* *
17701725 TTTTTGATAAATTGGAAACTTATCT
1 TTTTGGATAAAATGGAAACTTATCT
17701750 TTTT
1 TTTT
17701754 CTTCAATAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (25 bp):
TTTTGGATAAAATGGAAACTTATCT
Found at i:17710661 original size:21 final size:21
Alignment explanation
Indices: 17710637--17710680 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
17710627 CCCCTTTATT
* *
17710637 AACATAAAAAATTAAAATTTA
1 AACAGAAAAAATGAAAATTTA
* *
17710658 AACAGAATAAATGAAATTTTA
1 AACAGAAAAAATGAAAATTTA
17710679 AA
1 AA
17710681 AAAAATTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
AACAGAAAAAATGAAAATTTA
Found at i:17712320 original size:101 final size:102
Alignment explanation
Indices: 17712200--17712384 Score: 320
Period size: 101 Copynumber: 1.8 Consensus size: 102
17712190 AAAGTGATGG
*
17712200 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
17712263 ACTAGGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTAGGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
*
17712301 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
*
17712366 CTATGTGCAGGCTACTATG
66 CTAGGTGCAGGCTACTATG
17712385 TGAACCGGTA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
101 41 0.52
102 34 0.43
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTAGGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Done.