Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 124 of 141
Found at i:39622859 original size:44 final size:44
Alignment explanation
Indices: 39622770--39622877 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 44
39622760 ACAAACCCTG
* * *
39622770 TCTCTCTGAAGTTGCAGTAGAGTAGATTGAAATAACAAACCTTA
1 TCTCTCTAAAGTTGCAGTAGAGCAGATTGAAATAACAAACATTA
* * * * *
39622814 TCTCTCTAAAATTGCAGTAGAGCAGGTTGAAGTTACTAACATTA
1 TCTCTCTAAAGTTGCAGTAGAGCAGATTGAAATAACAAACATTA
* * *
39622858 TCCCCCTAAAGTTCCAGTAG
1 TCTCTCTAAAGTTGCAGTAG
39622878 GGCAAGTAGA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (44 bp):
TCTCTCTAAAGTTGCAGTAGAGCAGATTGAAATAACAAACATTA
Found at i:39623290 original size:136 final size:136
Alignment explanation
Indices: 39623046--39623354 Score: 442
Period size: 136 Copynumber: 2.3 Consensus size: 136
39623036 AGATAGCGAG
* *
39623046 TCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACATATCTTATCTCTCTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACATATCGTATCTCTCTAA
39623111 AATTATAGTACAGCAGATCATATCAAACATCATCTCCCTGAAGTTGCAG-TGAGGCAGGTTGAAA
66 AATTATAGTACAGCAGATCATATCAAACATCATCTCCCTGAAGTTGCAGTTG-GGCAGGTTGAAA
39623175 TTACGAA
130 TTACGAA
* * * *
39623182 TCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGTTATAAATTAC-TGATCGTATCTCTCTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAT-ATCGTATCTCTCTA
* * * * *
39623246 AAGTTATAGTAGAGTAGATCATATCAAACTTCATCTCCCTGAAGTTGCAGTTGGGCAGGTTGACA
65 AAATTATAGTACAGCAGATCATATCAAACATCATCTCCCTGAAGTTGCAGTTGGGCAGGTTGAAA
*
39623311 TTACGAG
130 TTACGAA
* * * *
39623318 TCTTATCTCCTTGAAGTTACAGTGGAGCAGACTGAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG
39623355 ATAGCAAACC
Statistics
Matches: 154, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
135 1 0.01
136 151 0.98
137 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (136 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACATATCGTATCTCTCTAA
AATTATAGTACAGCAGATCATATCAAACATCATCTCCCTGAAGTTGCAGTTGGGCAGGTTGAAAT
TACGAA
Found at i:39625053 original size:3 final size:3
Alignment explanation
Indices: 39625045--39625094 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
39625035 TCATTTTACA
* * * *
39625045 TAT TAT TAT TAC TAT TA- TAT TA- TAT TAT TAT AAA TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39625091 TAT T
1 TAT T
39625095 TACTCAACTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:39625395 original size:6 final size:6
Alignment explanation
Indices: 39625384--39625428 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
39625374 NNNNNNNNNG
39625384 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATA
39625429 TCCTATTGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:39626397 original size:18 final size:18
Alignment explanation
Indices: 39626372--39626423 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
39626362 CGTTTCCATC
*
39626372 AAAT-TGAACATCATTTG
1 AAATGTGAACATCATTTA
39626389 AAATGTGAACATCATTTA
1 AAATGTGAACATCATTTA
39626407 AAATGTGAACATCATTT
1 AAATGTGAACATCATTT
39626424 CTGATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 4 0.12
18 29 0.88
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
AAATGTGAACATCATTTA
Found at i:39628845 original size:13 final size:12
Alignment explanation
Indices: 39628819--39628844 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39628809 TAAATTAAAA
39628819 TTCCTTTTTTTT
1 TTCCTTTTTTTT
39628831 TTCCTTTTTTTT
1 TTCCTTTTTTTT
39628843 TT
1 TT
39628845 TGTATTTGTT
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTCCTTTTTTTT
Found at i:39640238 original size:7 final size:7
Alignment explanation
Indices: 39640226--39640278 Score: 65
Period size: 7 Copynumber: 7.4 Consensus size: 7
39640216 ATATATATAT
39640226 ATGAAAA
1 ATGAAAA
39640233 ATGAAAAA
1 ATG-AAAA
39640241 ATG-AAA
1 ATGAAAA
39640247 ATGAAAA
1 ATGAAAA
39640254 ATGAAAAA
1 ATG-AAAA
39640262 ATGAAAA
1 ATGAAAA
39640269 A-GTAAAA
1 ATG-AAAA
39640276 ATG
1 ATG
39640279 GAGAGGCTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 7 0.17
7 19 0.46
8 15 0.37
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:39640240 original size:8 final size:8
Alignment explanation
Indices: 39640229--39640269 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
39640219 TATATATATG
39640229 AAAAATGA
1 AAAAATGA
39640237 AAAAATG-
1 AAAAATGA
39640244 -AAAATG-
1 AAAAATGA
39640250 AAAAATGA
1 AAAAATGA
39640258 AAAAATGA
1 AAAAATGA
39640266 AAAA
1 AAAA
39640270 GTAAAAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 6 0.19
8 19 0.61
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAATGA
Found at i:39640249 original size:14 final size:13
Alignment explanation
Indices: 39640230--39640260 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
39640220 ATATATATGA
39640230 AAAATGAAAAAATG
1 AAAATG-AAAAATG
39640244 AAAATGAAAAATG
1 AAAATGAAAAATG
39640257 AAAA
1 AAAA
39640261 AATGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:39640251 original size:21 final size:21
Alignment explanation
Indices: 39640226--39640278 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
39640216 ATATATATAT
39640226 ATGAAAAATGAAAAAATGAAA
1 ATGAAAAATGAAAAAATGAAA
39640247 ATGAAAAATGAAAAAATGAAA
1 ATGAAAAATGAAAAAATGAAA
*
39640268 AAGTAAAAATG
1 ATG-AAAAATG
39640279 GAGAGGCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
ATGAAAAATGAAAAAATGAAA
Found at i:39641651 original size:50 final size:50
Alignment explanation
Indices: 39641593--39642037 Score: 357
Period size: 50 Copynumber: 8.9 Consensus size: 50
39641583 GCAGTGGAAC
* * *
39641593 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTACAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * ** *
39641643 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCTAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCC-CGAC-ATTGCAGTTAAAA
* * * * *
39641693 AGATTAAAGCCACATCAATAAATCTTGATTCCTCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * *
39641743 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCCAAGCGA-TGCAG-CAGAAC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGA-C-ATTGCAGTTA-AAA
* *
39641793 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * ** *
39641843 AGATTAAAGCTACAACAGTGAATCTTAC-TCCCCAGGCGATAT--AGTGGAAC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCC-GAC-AT-TGCAGTTAAAA
* *
39641893 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * ** * * * **
39641943 AGATTAAAGCTACAACAGTGAATCTTACTTCCCTGGCGGTACAATGAAGT
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* *
39641993 AGATTAAAGCCACAACGGTGAATCTTGTTTCCCCGACATTGCAGT
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGT
39642038 CAGACAGAAG
Statistics
Matches: 297, Mismatches: 82, Indels: 32
0.72 0.20 0.08
Matches are distributed among these distances:
48 1 0.00
49 19 0.06
50 257 0.87
51 19 0.06
52 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:39641740 original size:100 final size:100
Alignment explanation
Indices: 39641567--39642037 Score: 710
Period size: 100 Copynumber: 4.7 Consensus size: 100
39641557 AATACCAGTT
* *
39641567 TTACTTCCCAGGTGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
*
39641632 TACAGTTAAAAAGATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* ** * * *
39641667 TTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCAATAAATCTTGATTCCTCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
39641732 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* **
39641767 TTACTCCCCAAGCGATGCAGCAGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
*
39641832 TGCAGTTAAAAAGATTAAAGCTACAACAGTGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
**
39641867 TTACTCCCCAGGCGATATAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
*
39641932 TGCAGTTAAAAAGATTAAAGCTACAACAGTGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * * * * * * *
39641967 TTACTTCCCTGGCGGTACAAT-GAAGTAGATTAAAGCCACAACGGTGAATCTTGTTTCCCCGACA
1 TTACTCCCCAGGCGATGCAGTGGAA-CAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACA
39642031 TTGCAGT
65 TTGCAGT
39642038 CAGACAGAAG
Statistics
Matches: 338, Mismatches: 32, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
99 3 0.01
100 335 0.99
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (100 bp):
TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
Found at i:39643499 original size:3 final size:3
Alignment explanation
Indices: 39643491--39643537 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
39643481 TTCAGTAATG
* *
39643491 TTA TTA TTAA TCTA TTA TTA TTA TCA AT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39643537 T
1 T
39643538 CACCGTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 1 0.03
3 31 0.84
4 4 0.11
5 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:39643513 original size:17 final size:17
Alignment explanation
Indices: 39643491--39643533 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
39643481 TTCAGTAATG
39643491 TTATTATTAATCTATTA
1 TTATTATTAATCTATTA
* *
39643508 TTATTATCAATTTATTA
1 TTATTATTAATCTATTA
39643525 TTATTATTA
1 TTATTATTA
39643534 TTATCACCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTATTAATCTATTA
Found at i:39644876 original size:47 final size:46
Alignment explanation
Indices: 39644795--39644929 Score: 109
Period size: 47 Copynumber: 2.9 Consensus size: 46
39644785 GGTTTCGACA
* *
39644795 ATAAATTTAAAAAT-A--TTAATGATAAATTTGAAATAGAT-ATACATG
1 ATAAA-TTAAAAATAATGTTAACGATAAATTTAAAATA-ATAATA-ATG
* * * *
39644840 ATAGATTTAAAATAATGTTAACGATGAATTTAAAATAATAATATTG
1 ATAAATTAAAAATAATGTTAACGATAAATTTAAAATAATAATAATG
** *
39644886 ATAAATTAAAAATAAT-AAAACATGATAAATCTAAAATAATAATA
1 ATAAATTAAAAATAATGTTAAC--GATAAATTTAAAATAATAATA
39644930 TACAATACAC
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
44 7 0.10
45 8 0.11
46 18 0.25
47 39 0.54
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.33
Consensus pattern (46 bp):
ATAAATTAAAAATAATGTTAACGATAAATTTAAAATAATAATAATG
Found at i:39644921 original size:24 final size:22
Alignment explanation
Indices: 39644869--39644927 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 22
39644859 AACGATGAAT
* *
39644869 TTAAAATAATAATATTGATAAA
1 TTAAAATAATAAAAATGATAAA
39644891 TTAAAAATAATAAAACATGATAAA
1 TT-AAAATAATAAAA-ATGATAAA
39644915 TCTAAAATAATAA
1 T-TAAAATAATAA
39644928 TATACAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.06
23 11 0.34
24 18 0.56
25 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (22 bp):
TTAAAATAATAAAAATGATAAA
Found at i:39645770 original size:19 final size:20
Alignment explanation
Indices: 39645739--39645777 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
39645729 TTGATTTCTT
39645739 TTTTCCTCCCTTTACACTGA
1 TTTTCCTCCCTTTACACTGA
39645759 TTTTCC-CCCTTTACACTGA
1 TTTTCCTCCCTTTACACTGA
39645778 CTTCCTCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.15, C:0.36, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTTCCTCCCTTTACACTGA
Found at i:39646545 original size:54 final size:55
Alignment explanation
Indices: 39646463--39646580 Score: 229
Period size: 54 Copynumber: 2.2 Consensus size: 55
39646453 ATAGCTCGTA
39646463 AAAATATAAGAATAAAAAAAATATTTTAAAAATTTATTATCCTTTTAAAAATAAT
1 AAAATATAAGAATAAAAAAAATATTTTAAAAATTTATTATCCTTTTAAAAATAAT
39646518 AAAATATAAG-ATAAAAAAAATATTTTAAAAATTTATTATCCTTTTAAAAATAAT
1 AAAATATAAGAATAAAAAAAATATTTTAAAAATTTATTATCCTTTTAAAAATAAT
39646572 AAAATATAA
1 AAAATATAA
39646581 AATTTATTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 53 0.84
55 10 0.16
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (55 bp):
AAAATATAAGAATAAAAAAAATATTTTAAAAATTTATTATCCTTTTAAAAATAAT
Found at i:39646675 original size:20 final size:22
Alignment explanation
Indices: 39646637--39646680 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
39646627 ATTTTATTCA
39646637 TTTTTATAATTCTTGTATAATT
1 TTTTTATAATTCTTGTATAATT
*
39646659 TTTTTATGATT-TT-TATAATT
1 TTTTTATAATTCTTGTATAATT
39646679 TT
1 TT
39646681 ATACCACGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 2 0.10
22 10 0.48
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTTATAATTCTTGTATAATT
Found at i:39647965 original size:17 final size:18
Alignment explanation
Indices: 39647926--39647982 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
39647916 ACTCCCCCTA
*
39647926 TTTACTTTCCCTCAAAC-T
1 TTTA-TTTCCCCCAAACTT
39647944 TTTA-TTCCCCCAAACTT
1 TTTATTTCCCCCAAACTT
39647961 TTTATTTCCCCCTTAAACTT
1 TTTATTTCCCCC--AAACTT
39647981 TT
1 TT
39647983 ACTTCTCACC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
16 10 0.29
17 5 0.15
18 11 0.32
20 8 0.24
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTATTTCCCCCAAACTT
Found at i:39649968 original size:383 final size:384
Alignment explanation
Indices: 39649252--39650018 Score: 1527
Period size: 383 Copynumber: 2.0 Consensus size: 384
39649242 TTATATATAT
39649252 CTATTTAATTTTGTTAGATTTTTATTTTAATTTAATTGTAATTGAAATAGACCTGTCTATGGGTC
1 CTATTTAATTTTGTTAGATTTTTATTTTAATTTAATTGTAATTGAAATAGACCTGTCTATGGGTC
39649317 GGGCCGAATGGTTCGCCCGAAAAGTGGGAGGATTTGGGTAAAAATTAGGCTCAAAAAATGTGTTT
66 GGGCCGAATGGTTCGCCCGAAAAGTGGGAGGATTTGGGTAAAAATTAGGCTCAAAAAATGTGTTT
39649382 GGACAAAAAATGAGGCCGATTTAAAAAACAAGCCGAGCCTCAGTCAAGGTTTTTTTTGCTTGAGT
131 GGACAAAAAATGAGGCCGATTTAAAAAACAAGCCGAGCCTCAGTCAAGGTTTTTTTTGCTTGAGT
39649447 CCGGCCCGACCTGAATATGCAAAAAAGAAAAAGAAAACATGTTGTTTTCTTTTATTTTCTTTTAT
196 CCGGCCCGACCTGAATATGCAAAAAAGAAAAAGAAAACATGTTGTTTTCTTTTATTTTCTTTTAT
39649512 TGTTTTGATGCTATTTTCTTAATTTTTTTTTCACTATTGTGCCACAATTTCACTATTATATTGTT
261 TGTTTTGATGCTATTTTCTTAATTTTTTTTTCACTATTGTGCCACAATTTCACTATTATATTGTT
39649577 ACTATTTTGTTGTTATTGTTGGCTAATTTACTAAAAAAAGTTTTTTTAAAAAATTACCG
326 ACTATTTTGTTGTTATTGTTGGCTAATTTACTAAAAAAAGTTTTTTTAAAAAATTACCG
39649636 CTATTTAA-TTTGTTAGATTTTTATTTTAATTTAATTGTAATTGAAATAGACCTGTCTATGGGTC
1 CTATTTAATTTTGTTAGATTTTTATTTTAATTTAATTGTAATTGAAATAGACCTGTCTATGGGTC
39649700 GGGCCGAATGGTTCGCCCGAAAAGTGGGAGGATTTGGGTAAAAATTAGGCTCAAAAAATGTGTTT
66 GGGCCGAATGGTTCGCCCGAAAAGTGGGAGGATTTGGGTAAAAATTAGGCTCAAAAAATGTGTTT
39649765 GGACAAAAAATGAGGCCGATTTAAAAAACAAGCCGAGCCTCAGTCAAGGTTTTTTTTGCTTGAGT
131 GGACAAAAAATGAGGCCGATTTAAAAAACAAGCCGAGCCTCAGTCAAGGTTTTTTTTGCTTGAGT
39649830 CCGGCCCGACCTGAATATGCAAAAAAGAAAAAGAAAACATGTTGTTTTCTTTTATTTTCTTTTAT
196 CCGGCCCGACCTGAATATGCAAAAAAGAAAAAGAAAACATGTTGTTTTCTTTTATTTTCTTTTAT
39649895 TGTTTTGATGCTATTTTCTTAATTTTTTTTTCACTATTGTGCCACAATTTCACTATTATATTGTT
261 TGTTTTGATGCTATTTTCTTAATTTTTTTTTCACTATTGTGCCACAATTTCACTATTATATTGTT
39649960 ACTATTTTGTTGTTATTGTTGGCTAATTTACTAAAAAAAGTTTTTTTAAAAAATTACCG
326 ACTATTTTGTTGTTATTGTTGGCTAATTTACTAAAAAAAGTTTTTTTAAAAAATTACCG
39650019 AAATGGGCCG
Statistics
Matches: 383, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
383 375 0.98
384 8 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (384 bp):
CTATTTAATTTTGTTAGATTTTTATTTTAATTTAATTGTAATTGAAATAGACCTGTCTATGGGTC
GGGCCGAATGGTTCGCCCGAAAAGTGGGAGGATTTGGGTAAAAATTAGGCTCAAAAAATGTGTTT
GGACAAAAAATGAGGCCGATTTAAAAAACAAGCCGAGCCTCAGTCAAGGTTTTTTTTGCTTGAGT
CCGGCCCGACCTGAATATGCAAAAAAGAAAAAGAAAACATGTTGTTTTCTTTTATTTTCTTTTAT
TGTTTTGATGCTATTTTCTTAATTTTTTTTTCACTATTGTGCCACAATTTCACTATTATATTGTT
ACTATTTTGTTGTTATTGTTGGCTAATTTACTAAAAAAAGTTTTTTTAAAAAATTACCG
Found at i:39658301 original size:28 final size:28
Alignment explanation
Indices: 39658261--39658515 Score: 210
Period size: 28 Copynumber: 9.4 Consensus size: 28
39658251 NNNNNNNNNN
39658261 AATTTAATTAAAAACCCTAACCTAACCT
1 AATTTAATTAAAAACCCTAACCTAACCT
39658289 AATTTAATT-AAAACCCTAA-CT----T
1 AATTTAATTAAAAACCCTAACCTAACCT
*
39658311 AACTTAATTAAAAACCCTAACCCTAACCCT
1 AATTTAATTAAAAACCCTAA-CCTAA-CCT
** *
39658341 AACCTAATT-TAAACCCTAACCATAACCT
1 AATTTAATTAAAAACCCTAACC-TAACCT
*
39658369 AATTTAATTAAAGACCCTAACCCTAACCT
1 AATTTAATTAAAAACCCTAA-CCTAACCT
* *******
39658398 AACTTAATTAAAAACCCTAACNNNNNNN
1 AATTTAATTAAAAACCCTAACCTAACCT
**** ***
39658426 NNNNTAATTAAAAACCCTAACCTAGTTT
1 AATTTAATTAAAAACCCTAACCTAACCT
39658454 AATTTAATTAAAAA--C---CCTAACCT
1 AATTTAATTAAAAACCCTAACCTAACCT
39658477 AATTTAATTAAAAACCCTAACCTAACCT
1 AATTTAATTAAAAACCCTAACCTAACCT
39658505 AATTTAATTAA
1 AATTTAATTAA
39658516 TGTAAAAACC
Statistics
Matches: 177, Mismatches: 34, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
22 9 0.05
23 29 0.16
25 3 0.02
26 3 0.02
27 10 0.06
28 68 0.38
29 44 0.25
30 11 0.06
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.28
Consensus pattern (28 bp):
AATTTAATTAAAAACCCTAACCTAACCT
Found at i:39658307 original size:22 final size:23
Alignment explanation
Indices: 39658264--39658337 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 23
39658254 NNNNNNNAAT
39658264 TTAATTAAAAACCCTAACCTAAC
1 TTAATTAAAAACCCTAACCTAAC
* *
39658287 CTAATTTAATTAAAACCCTAACTTAAC
1 TTAA-TT-A--AAAACCCTAACCTAAC
39658314 TTAATTAAAAACCCTAACCCTAAC
1 TTAATTAAAAACCCTAA-CCTAAC
39658338 CCTAACCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
23 13 0.31
24 7 0.17
25 2 0.05
26 2 0.05
27 18 0.43
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (23 bp):
TTAATTAAAAACCCTAACCTAAC
Found at i:39658337 original size:29 final size:29
Alignment explanation
Indices: 39658300--39658418 Score: 168
Period size: 29 Copynumber: 4.1 Consensus size: 29
39658290 ATTTAATTAA
*
39658300 AACCCTAACTTAACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* *
39658329 AACCCTAACCCTAACCTAATT-TAAACCCT
1 AACCCTAA-CCTAACTTAATTAAAAACCCT
* * *
39658358 AACCATAACCTAATTTAATTAAAGACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
39658387 AACCCTAACCTAACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
39658416 AAC
1 AAC
39658419 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
28 10 0.13
29 57 0.74
30 10 0.13
ACGTcount: A:0.44, C:0.30, G:0.01, T:0.25
Consensus pattern (29 bp):
AACCCTAACCTAACTTAATTAAAAACCCT
Found at i:39658355 original size:23 final size:23
Alignment explanation
Indices: 39658329--39658375 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
39658319 TAAAAACCCT
*
39658329 AACCCTAACCCTAACCTAATTTA
1 AACCCTAACCATAACCTAATTTA
39658352 AACCCTAACCATAACCTAATTTA
1 AACCCTAACCATAACCTAATTTA
39658375 A
1 A
39658376 TTAAAGACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.26
Consensus pattern (23 bp):
AACCCTAACCATAACCTAATTTA
Found at i:39658359 original size:52 final size:53
Alignment explanation
Indices: 39658264--39658418 Score: 190
Period size: 58 Copynumber: 2.9 Consensus size: 53
39658254 NNNNNNNAAT
*
39658264 TTAATTAAAAACCCTAA-CCTAACCTAATTTAATTAAAACCCTAAC-T-TAAC
1 TTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAACCCTAACATATAAC
* * *
39658314 TTAATTAAAAACCCTAACCCTAACCCTAACCTAATTTAAACCCTAACCATAACCTAAT
1 TTAATTAAAAACCCTAACCCTAA-CCTAACTTAATTAAAACCCTAA-CAT-A--TAAC
*
39658372 TTAATTAAAGACCCTAACCCTAACCTAACTTAATTAAAAACCCTAAC
1 TTAATTAAAAACCCTAACCCTAACCTAACTTAATT-AAAACCCTAAC
39658419 NNNNNNNNNN
Statistics
Matches: 89, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
50 17 0.19
51 5 0.06
52 19 0.21
53 1 0.01
54 1 0.01
57 12 0.13
58 34 0.38
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.27
Consensus pattern (53 bp):
TTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAACCCTAACATATAAC
Found at i:39658472 original size:23 final size:23
Alignment explanation
Indices: 39658430--39658501 Score: 99
Period size: 23 Copynumber: 2.9 Consensus size: 23
39658420 NNNNNNNNNN
39658430 TAATTAAAAACCCTAACCTAGTTTAATT
1 TAATTAAAAACCCTAACC-----TAATT
39658458 TAATTAAAAACCCTAACCTAATT
1 TAATTAAAAACCCTAACCTAATT
39658481 TAATTAAAAACCCTAACCTAA
1 TAATTAAAAACCCTAACCTAA
39658502 CCTAATTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
23 26 0.59
28 18 0.41
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (23 bp):
TAATTAAAAACCCTAACCTAATT
Found at i:39658507 original size:23 final size:23
Alignment explanation
Indices: 39658458--39658508 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
39658448 TAGTTTAATT
**
39658458 TAATTAAAAACCCTAACCTAATT
1 TAATTAAAAACCCTAACCTAACC
39658481 TAATTAAAAACCCTAACCTAACC
1 TAATTAAAAACCCTAACCTAACC
39658504 TAATT
1 TAATT
39658509 TAATTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (23 bp):
TAATTAAAAACCCTAACCTAACC
Found at i:39675672 original size:24 final size:24
Alignment explanation
Indices: 39675644--39675695 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39675634 TTAGTAAGTC
* *
39675644 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
39675668 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
39675692 AAAT
1 AAAT
39675696 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:39678254 original size:18 final size:19
Alignment explanation
Indices: 39678233--39678268 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39678223 GTACAAGTTC
39678233 TATTTTCCTTTT-TATTTT
1 TATTTTCCTTTTATATTTT
*
39678251 TATTTTTCTTTTATATTT
1 TATTTTCCTTTTATATTT
39678269 AAAAACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (19 bp):
TATTTTCCTTTTATATTTT
Found at i:39679103 original size:18 final size:19
Alignment explanation
Indices: 39679077--39679115 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
39679067 ATTTTTTTAT
39679077 TCGAGTTAATC-CGAATAAC
1 TCGAGTTAA-CACGAATAAC
39679096 TCGA-TTAACACGAATAAC
1 TCGAGTTAACACGAATAAC
39679114 TC
1 TC
39679116 AAATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 14 0.74
19 4 0.21
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (19 bp):
TCGAGTTAACACGAATAAC
Found at i:39680876 original size:37 final size:36
Alignment explanation
Indices: 39680815--39680884 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
39680805 AATATGAGAA
39680815 TTTAAAAAAAAACACGAGAATTTTGAAACACGATTT
1 TTTAAAAAAAAACACGAGAATTTTGAAACACGATTT
*
39680851 TTTAAAAAAAAACACG-GAAGTTTTTGAATCACGA
1 TTTAAAAAAAAACACGAGAA--TTTTGAAACACGA
39680885 GAATTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 3 0.10
36 16 0.52
37 12 0.39
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (36 bp):
TTTAAAAAAAAACACGAGAATTTTGAAACACGATTT
Found at i:39680891 original size:17 final size:16
Alignment explanation
Indices: 39680860--39681170 Score: 149
Period size: 18 Copynumber: 17.5 Consensus size: 16
39680850 TTTTAAAAAA
*
39680860 AAACACGGAAGTTTTTG
1 AAACAC-GAAATTTTTG
*
39680877 AATCACGAGAATTTTTG
1 AAACACGA-AATTTTTG
*
39680894 AAAAACCGAAAATTTTTG
1 AAACA-CG-AAATTTTTG
*
39680912 AAAACACTAAGATTTTTG
1 -AAACACGAA-ATTTTTG
39680930 AAACACGACAATTTTTG
1 AAACACGA-AATTTTTG
* *
39680947 AAACACAATAATTTTTTTTTA
1 AAACACGA-AA----TTTTTG
* *
39680968 AAACACAAAATTTTTTTA
1 AAACACGAAA--TTTTTG
*
39680986 AAACACGAAAATTTGTG
1 AAACACG-AAATTTTTG
*
39681003 AAACACGAGAATTGTTG
1 AAACACGA-AATTTTTG
39681020 AAAACACGAAAATTTTTG
1 -AAACACG-AAATTTTTG
* *
39681038 AAAATATGAAAATTTTTG
1 -AAACACG-AAATTTTTG
39681056 TAAACACGAAAATTTTTTTG
1 -AAACACG-AAA--TTTTTG
*
39681076 AAACAGAGAAATTTTTAG
1 AAACA-CGAAATTTTT-G
*
39681094 AAAACATGAAATTTTTTTG
1 -AAACACGAAA--TTTTTG
* *
39681113 AATCACTGGAA-TTTTG
1 AAACAC-GAAATTTTTG
39681129 AAAACACG-AATTTTTG
1 -AAACACGAAATTTTTG
* *
39681145 AAACACCGGAATTTTTTA
1 AAACA-C-GAAATTTTTG
39681163 AAACACGA
1 AAACACGA
39681171 GGATTTTTTT
Statistics
Matches: 238, Mismatches: 29, Indels: 55
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.03
16 17 0.07
17 69 0.29
18 92 0.39
19 26 0.11
20 14 0.06
21 13 0.05
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (16 bp):
AAACACGAAATTTTTG
Found at i:39680927 original size:36 final size:35
Alignment explanation
Indices: 39680871--39681170 Score: 188
Period size: 36 Copynumber: 8.4 Consensus size: 35
39680861 AACACGGAAG
* *
39680871 TTTTTG-AATCACGAGAATTTTTGAAAAACCGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAAA-CGAAAA
* * * *
39680906 TTTTTGAAAACACTAAGATTTTTGAAACACGACAA
1 TTTTTGAAAACACGAAAATTTTTGAAAAACGAAAA
*
39680941 TTTTTG-AAACAC-AATAATTTTTTTTTAAAACAC-AAAA
1 TTTTTGAAAACACGAA-AA---TTTTTGAAAA-ACGAAAA
* * * *
39680978 TTTTTTTAAAACACGAAAATTTGTGAAACACGAGAA
1 -TTTTTGAAAACACGAAAATTTTTGAAAAACGAAAA
* *
39681014 TTGTTGAAAACACGAAAATTTTTGAAAATATGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAA-ACGAAAA
* *
39681050 TTTTTGTAAACACGAAAATTTTTTTGAAACA-GAGAAA
1 TTTTTGAAAACACGAAAA--TTTTTGAAAAACGA-AAA
* * ** *
39681087 TTTTTAGAAAACATGAAATTTTTTTGAATCACTG-GAA
1 TTTTT-GAAAACACGAAA-ATTTTTGAAAAAC-GAAAA
* *
39681124 -TTTTGAAAACACG--AATTTTTGAAACACCG-GAA
1 TTTTTGAAAACACGAAAATTTTTGAAA-AACGAAAA
*
39681156 TTTTTTAAAACACGA
1 TTTTTGAAAACACGA
39681171 GGATTTTTTT
Statistics
Matches: 209, Mismatches: 35, Indels: 43
0.73 0.12 0.15
Matches are distributed among these distances:
32 12 0.06
33 16 0.08
34 7 0.03
35 51 0.24
36 54 0.26
37 32 0.15
38 26 0.12
39 9 0.04
40 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAAAACGAAAA
Found at i:39680961 original size:16 final size:17
Alignment explanation
Indices: 39680871--39680962 Score: 71
Period size: 17 Copynumber: 5.3 Consensus size: 17
39680861 AACACGGAAG
* * *
39680871 TTTTTGAATCACGAGAA
1 TTTTTGAAACACAACAA
*
39680888 TTTTTGAAAAACCGAA-AA
1 TTTTTGAAACA-C-AACAA
*
39680906 TTTTTGAAAACACTAA-GA
1 TTTTTG-AAACAC-AACAA
*
39680924 TTTTTGAAACACGACAA
1 TTTTTGAAACACAACAA
*
39680941 TTTTTGAAACACAATAA
1 TTTTTGAAACACAACAA
39680958 TTTTT
1 TTTTT
39680963 TTTTAAAACA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
16 1 0.02
17 36 0.59
18 19 0.31
19 5 0.08
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (17 bp):
TTTTTGAAACACAACAA
Found at i:39681090 original size:18 final size:18
Alignment explanation
Indices: 39680871--39681114 Score: 150
Period size: 18 Copynumber: 13.4 Consensus size: 18
39680861 AACACGGAAG
* *
39680871 TTTTTGAATCACGAGAA-
1 TTTTTGAAACACGAAAAT
*
39680888 TTTTTGAAAAACCGAAAA-
1 TTTTTGAAACA-CGAAAAT
* *
39680906 TTTTTGAAAACACTAAGA-
1 TTTTTG-AAACACGAAAAT
*
39680924 TTTTTGAAACACGACAA-
1 TTTTTGAAACACGAAAAT
39680941 TTTTTGAAACAC-AATAATTTT
1 TTTTTGAAACACGAA-AA---T
*
39680962 TTTTTAAAACAC-AAAATT
1 TTTTTGAAACACGAAAA-T
*
39680980 TTTTTAAAACACGAAAA-
1 TTTTTGAAACACGAAAAT
* *
39680997 TTTGTGAAACACGAGAA-
1 TTTTTGAAACACGAAAAT
*
39681014 TTGTTGAAAACACGAAAA-
1 TTTTTG-AAACACGAAAAT
* *
39681032 TTTTTGAAAATATGAAAA-
1 TTTTTG-AAACACGAAAAT
39681050 TTTTTGTAAACACGAAAATT
1 TTTTTG-AAACACGAAAA-T
39681070 TTTTTGAAACA-GAGAAAT
1 TTTTTGAAACACGA-AAAT
* * *
39681088 TTTTAGAAAACATGAAATT
1 TTTTTG-AAACACGAAAAT
39681107 TTTTTGAA
1 TTTTTGAA
39681115 TCACTGGAAT
Statistics
Matches: 187, Mismatches: 26, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.01
17 49 0.26
18 85 0.45
19 29 0.16
20 10 0.05
21 13 0.07
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (18 bp):
TTTTTGAAACACGAAAAT
Found at i:39681145 original size:32 final size:33
Alignment explanation
Indices: 39680860--39681170 Score: 105
Period size: 35 Copynumber: 8.8 Consensus size: 33
39680850 TTTTAAAAAA
*
39680860 AAACA-CGGAAGTTTTTG-AATCACGAGAATTTTTG
1 AAACACCGGAA-TTTTTGAAAACAC--GAATTTTTG
* * *
39680894 AAAAACCGAAAATTTTTGAAAACACTAAGATTTTTG
1 AAACACCG-GAATTTTTGAAAACAC-GA-ATTTTTG
* ** *
39680930 AAACA-CGACAATTTTTGAAACACAATAATTTTTTTTT
1 AAACACCG-GAATTTTTGAAA-ACACGAA---TTTTTG
** * *
39680967 AAA-ACACAAAATTTTTTTAAAACACGAAAATTTGTG
1 AAACAC-CGGAA-TTTTTGAAAACACG--AATTTTTG
*
39681003 AAACA-CGAGAATTGTTGAAAACACGAAAATTTTTG
1 AAACACCG-GAATTTTTGAAAACACG--AATTTTTG
** * *
39681038 AAA-ATATGAAAATTTTTGTAAACACGAAAATTTTTTTG
1 AAACA-CCG-GAATTTTTGAAAACACG--AA--TTTTTG
** * *
39681076 AAACAGAGAAATTTTTAGAAAACATGAAATTTTTTTG
1 AAACACCGGAATTTTT-GAAAACACG-AA--TTTTTG
* *
39681113 AATCACTGGAA-TTTTGAAAACACGAATTTTTG
1 AAACACCGGAATTTTTGAAAACACGAATTTTTG
*
39681145 AAACACCGGAATTTTTTAAAACACGA
1 AAACACCGGAATTTTTGAAAACACGA
39681171 GGATTTTTTT
Statistics
Matches: 217, Mismatches: 38, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
32 15 0.07
33 13 0.06
34 8 0.04
35 57 0.26
36 55 0.25
37 40 0.18
38 26 0.12
39 3 0.01
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (33 bp):
AAACACCGGAATTTTTGAAAACACGAATTTTTG
Found at i:39681666 original size:8 final size:8
Alignment explanation
Indices: 39681653--39681751 Score: 94
Period size: 8 Copynumber: 11.9 Consensus size: 8
39681643 TTGGGCCCCT
39681653 TTTTTTTC
1 TTTTTTTC
*
39681661 TTTTTTCC
1 TTTTTTTC
39681669 TTTTTTTCCC
1 TTTTTTT--C
39681679 TTCTTTTTC
1 TT-TTTTTC
*
39681688 CTTTTTTC
1 TTTTTTTC
39681696 TTTTTTTTC
1 -TTTTTTTC
39681705 TTTTCTTCTC
1 TTTT-TT-TC
*
39681715 TTTTCTT-
1 TTTTTTTC
39681722 TTTTTTTC
1 TTTTTTTC
39681730 -TTTTTTC
1 TTTTTTTC
*
39681737 TCTTTTTC
1 TTTTTTTC
39681745 TTTTTTT
1 TTTTTTT
39681752 TTGGACTGGG
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
7 13 0.17
8 36 0.48
9 12 0.16
10 9 0.12
11 5 0.07
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:39681672 original size:17 final size:17
Alignment explanation
Indices: 39681650--39681753 Score: 90
Period size: 17 Copynumber: 6.0 Consensus size: 17
39681640 AACTTGGGCC
39681650 CCTTTTTTTTCTTTTTT
1 CCTTTTTTTTCTTTTTT
*
39681667 CCTTTTTTTCCCTTCTTTTT
1 CCTTTTTTT-TC-T-TTTTT
39681687 CCTTTTTTCTT-TTTTTT
1 CCTTTTTT-TTCTTTTTT
* *
39681704 -C-TTTTCTTCTCTTTT
1 CCTTTTTTTTCTTTTTT
*
39681719 CTTTTTTTTTCTTTTTT
1 CCTTTTTTTTCTTTTTT
39681736 CTCTTTTTCTTT-TTTTTT
1 C-CTTTTT-TTTCTTTTTT
39681754 GGACTGGGCT
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.03
15 9 0.13
16 1 0.01
17 27 0.39
18 13 0.19
19 4 0.06
20 13 0.19
21 1 0.01
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
CCTTTTTTTTCTTTTTT
Found at i:39681718 original size:25 final size:24
Alignment explanation
Indices: 39681679--39681752 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
39681669 TTTTTTTCCC
*
39681679 TTCTTTTTCCT-TTTTTCTTTTTT
1 TTCTTTTTTCTCTTTTTCTTTTTT
39681702 TTCTTTTCTTCTC-TTTTCTTTTTTT
1 TTCTTTT-TTCTCTTTTTC-TTTTTT
39681727 TTCTTTTTTCTCTTTTTCTTTTTT
1 TTCTTTTTTCTCTTTTTCTTTTTT
39681751 TT
1 TT
39681753 TGGACTGGGC
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
23 7 0.15
24 21 0.46
25 18 0.39
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
TTCTTTTTTCTCTTTTTCTTTTTT
Found at i:39681743 original size:10 final size:10
Alignment explanation
Indices: 39681651--39681743 Score: 65
Period size: 9 Copynumber: 9.6 Consensus size: 10
39681641 ACTTGGGCCC
39681651 CTTTTTTT-T
1 CTTTTTTTCT
39681660 C-TTTTTTC-
1 CTTTTTTTCT
*
39681668 CTTTTTTTCC
1 CTTTTTTTCT
39681678 CTTCTTTTTC-
1 CTT-TTTTTCT
39681688 C-TTTTTTCT
1 CTTTTTTTCT
39681697 -TTTTTTTCT
1 CTTTTTTTCT
* *
39681706 TTTCTTCTCTTTT
1 CTT-TT-T-TTCT
*
39681719 CTTTTTTTTT
1 CTTTTTTTCT
39681729 C-TTTTTTCT
1 CTTTTTTTCT
39681738 CTTTTT
1 CTTTTT
39681744 CTTTTTTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 21
0.74 0.03 0.22
Matches are distributed among these distances:
8 13 0.19
9 25 0.36
10 15 0.21
11 9 0.13
12 3 0.04
13 5 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:39681752 original size:10 final size:10
Alignment explanation
Indices: 39681652--39681753 Score: 70
Period size: 10 Copynumber: 10.4 Consensus size: 10
39681642 CTTGGGCCCC
39681652 TTTTTTTTC-
1 TTTTTTTTCT
*
39681661 -TTTTTTCCT
1 TTTTTTTTCT
**
39681670 TTTTTTCCCT
1 TTTTTTTTCT
* *
39681680 TCTTTTTCCT
1 TTTTTTTTCT
39681690 TTTTTCTTT-T
1 TTTTT-TTTCT
39681700 TTTTCTTTTCT
1 TTTT-TTTTCT
* *
39681711 TCTCTTTTCT
1 TTTTTTTTCT
39681721 TTTTTTTTC-
1 TTTTTTTTCT
*
39681730 TTTTTTCTCT
1 TTTTTTTTCT
39681740 TTTTCTTTT-T
1 TTTT-TTTTCT
39681750 TTTT
1 TTTT
39681754 GGACTGGGCT
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
8 7 0.09
9 8 0.11
10 50 0.68
11 9 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:39682084 original size:3 final size:3
Alignment explanation
Indices: 39682078--39682149 Score: 103
Period size: 3 Copynumber: 24.0 Consensus size: 3
39682068 TTCTCTTTTT
*
39682078 TTC TTC TT- TT- TTC TTC TTT TTCC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC
39682122 TTC TTC TTC TTC TTTC TTC TTC TTC TTC
1 TTC TTC TTC TTC -TTC TTC TTC TTC TTC
39682150 AAACCCTAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 4 0.06
3 55 0.86
4 5 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:39682099 original size:9 final size:9
Alignment explanation
Indices: 39682065--39682149 Score: 89
Period size: 9 Copynumber: 9.0 Consensus size: 9
39682055 ATAATTTTAT
*
39682065 TTTTTCTCTT
1 TTTTTCT-TC
39682075 TTTTTCTTC
1 TTTTTCTTC
39682084 TTTTTTCTTC
1 -TTTTTCTTC
39682094 TTTTTCCTTC
1 TTTTT-CTTC
*
39682104 TTCTTCTTC
1 TTTTTCTTC
*
39682113 TTCTTCTTC
1 TTTTTCTTC
*
39682122 TTCTTCTTC
1 TTTTTCTTC
39682131 TTCTTTCTTC
1 TT-TTTCTTC
*
39682141 TTCTTCTTC
1 TTTTTCTTC
39682150 AAACCCTAGT
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
9 36 0.53
10 32 0.47
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:39682531 original size:30 final size:30
Alignment explanation
Indices: 39682497--39682622 Score: 116
Period size: 30 Copynumber: 4.2 Consensus size: 30
39682487 GGCCAAAACA
*
39682497 TAATTTTGAGAAAATTTAGGGGTCAAAATG
1 TAATTTTCAGAAAATTTAGGGGTCAAAATG
* *
39682527 TAA-TTTCA-AAATTTTGATGGGTCAAAATG
1 TAATTTTCAGAAAATTT-AGGGGTCAAAATG
* * * *
39682556 TAA-TTTCAAAAAATTTTAGGGCTTAAAATA
1 TAATTTTCAGAAAA-TTTAGGGGTCAAAATG
*
39682586 TAATTTT-AGGAAAATTTAAGGGTCAAAATG
1 TAATTTTCA-GAAAATTTAGGGGTCAAAATG
*
39682616 TATTTTT
1 TAATTTT
39682623 TTTTTATTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
28 6 0.08
29 24 0.31
30 37 0.48
31 10 0.13
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (30 bp):
TAATTTTCAGAAAATTTAGGGGTCAAAATG
Found at i:39682634 original size:9 final size:9
Alignment explanation
Indices: 39682620--39682655 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
39682610 AAAATGTATT
39682620 TTTTTTTTA
1 TTTTTTTTA
39682629 TTTTTTTTA
1 TTTTTTTTA
*
39682638 TTTTTTTGA
1 TTTTTTTTA
*
39682647 ATTTTTTTA
1 TTTTTTTTA
39682656 AAAAGCACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:39683097 original size:79 final size:79
Alignment explanation
Indices: 39682814--39683577 Score: 877
Period size: 79 Copynumber: 9.7 Consensus size: 79
39682804 TTGAAAGTAT
* * * *
39682814 CTCGGCGTGT-AGCCCGAGGCTCAACTCACCTCTAGCATTATGAGTTTATTTATGAAAAACAGAA
1 CTCGGCGTGTGA-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAA
39682878 ATTTAAAAG--ATAC
65 ATTTAAAAGAAATAC
***
39682891 CTCGATATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAA
* *
39682956 ATTTAAAAAAAAATAT
65 ATTT-AAAAGAAATAC
*
39682972 CTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
39683037 TTTAAAAGAAATAC
66 TTTAAAAGAAATAC
* * **
39683051 CTGGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTAAAAAAAAACAGA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT--TGAAAAACAGA
*
39683116 AA-TT--GA-AAATAC
64 AATTTAAAAGAAATAC
* * *
39683128 CTCAGC--GTGACCCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGA
* *
39683191 AA--TAAAAAAAATAT
64 AATTTAAAAGAAATAC
* * * ** *
39683205 CTCAGCGTGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATTTTACAAAAAATAGAA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TGAAAAACAGAA
39683270 ATTT---A-AAATAC
65 ATTTAAAAGAAATAC
* * * *
39683281 CTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTAATTTTTTTGAAAAACAGA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGA
*
39683344 AATTTAAAAGAAATAT
64 AATTTAAAAGAAATAC
* ** *
39683360 CTCGGCATGTGACCAAAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTGAAAAAACAGA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAAACAGA
39683425 AA-TTAATAA-AAATAC
64 AATTTAA-AAGAAATAC
*
39683440 CTCGGCGTGT-AGCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAA
1 CTCGGCGTGTGA-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAA
39683504 ATTTAAAAGAAATAC
65 ATTTAAAAGAAATAC
* * * * *
39683519 CTTGGCGTGAG-TCCGAGGCTCAACTCACATCTTGCAATATGAGTTGATTTTTGGAAAAA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAAA
39683578 AAAAACAGAA
Statistics
Matches: 591, Mismatches: 64, Indels: 62
0.82 0.09 0.09
Matches are distributed among these distances:
74 37 0.06
75 61 0.10
76 16 0.03
77 75 0.13
78 77 0.13
79 139 0.24
80 74 0.13
81 112 0.19
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (79 bp):
CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
TTTAAAAGAAATAC
Found at i:39683476 original size:314 final size:309
Alignment explanation
Indices: 39682793--39683569 Score: 965
Period size: 314 Copynumber: 2.5 Consensus size: 309
39682783 TTTTTATTTG
* * * * *
39682793 AAAAATAGAAATTGAAAGTATCTCGGCGTGTAGCCCGAGGCTCAACTCACCTCTAGCATTATGAG
1 AAAAACAGAAATTAAAAATACCTCGGCGTGTAGCCCGAGGCTCAACTCACCTCTCGCATTATGAG
* * ** * ** *
39682858 TTTA-TTTATGAAAAACAGAAATTTAAAAGATACCTCGATATGTGACCCGAGGCTCAACTCACCT
66 TTGATTTTTTGAAAAACAGAAATAAAAAAAATACCTCG-CGTGTGTCCCGAGGCTCAACTCACCT
** * * *
39682922 CTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTTAAAAAAAAATATCTCGGCGTGTGGCCC
130 CTCGCAATATGAGTTGATTTTACAAAAAACAGAAATTT----AAAAATACCTCAGCG-GTGACCC
*
39682987 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACC
190 GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAACAGAAATTTAAAAGAAATACC
* * **
39683052 TGGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTAAAA
255 TCGGCATGTGACCAAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTAAAA
* * *
39683107 AAAAACAGAAATTGAAAATACCTCAGCGTG-A-CCCGAGGCTCAACTCACTTCTCGCATTATGAG
1 AAAAACAGAAATTAAAAATACCTCGGCGTGTAGCCCGAGGCTCAACTCACCTCTCGCATTATGAG
*
39683170 TTGATTTTTTTGAAAAACAGAAATAAAAAAAATATCTCAGCGTGTGTCCCGAGGCTCAACTCACC
66 TTGA-TTTTTTGAAAAACAGAAATAAAAAAAATACCTC-GCGTGTGTCCCGAGGCTCAACTCACC
* *
39683235 TCTCGCAATATGAGTTTATTTTACAAAAAATAGAAATTT-AAAATACCTCAGC-GTGACCCGAGG
129 TCTCGCAATATGAGTTGATTTTACAAAAAACAGAAATTTAAAAATACCTCAGCGGTGACCCGAGG
* * *
39683298 CTCAACTCACCTCTCGTATTATGAGTTAATTTTTTTGAAAAACAGAAATTTAAAAGAAATATCTC
194 CTCAACTCACCTCTCGCAATATGAGTTAA--TTTTTGAAAAACAGAAATTTAAAAGAAATACCTC
* * ***
39683363 GGCATGTGACCAAAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTGA
257 GGCATGTGACCAAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTAAAA
* *
39683416 AAAAACAGAAATTAATAAAAATACCTCGGCGTGTAGCTCGAGGCTCAACTCACCTCTCGCAATAT
1 AAAAACAGAAA-T--TAAAAATACCTCGGCGTGTAGCCCGAGGCTCAACTCACCTCTCGCATTAT
* * *
39683481 GAGTTGA-TTTTTGAAAAACAGAAATTTAAAAGAAATACCTTGGCGTGAGT-CCGAGGCTCAACT
63 GAGTTGATTTTTTGAAAAACAGAAA--TAAAAAAAATACC-TCGCGTGTGTCCCGAGGCTCAACT
* *
39683544 CACATCTTGCAATATGAGTTGATTTT
125 CACCTCTCGCAATATGAGTTGATTTT
39683570 TGGAAAAAAA
Statistics
Matches: 403, Mismatches: 47, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
307 36 0.09
309 99 0.25
310 1 0.00
312 66 0.16
313 38 0.09
314 161 0.40
315 2 0.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (309 bp):
AAAAACAGAAATTAAAAATACCTCGGCGTGTAGCCCGAGGCTCAACTCACCTCTCGCATTATGAG
TTGATTTTTTGAAAAACAGAAATAAAAAAAATACCTCGCGTGTGTCCCGAGGCTCAACTCACCTC
TCGCAATATGAGTTGATTTTACAAAAAACAGAAATTTAAAAATACCTCAGCGGTGACCCGAGGCT
CAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCA
TGTGACCAAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTAAAA
Found at i:39692621 original size:50 final size:50
Alignment explanation
Indices: 39692514--39692648 Score: 189
Period size: 50 Copynumber: 2.7 Consensus size: 50
39692504 CATGCCAAAA
* ** * * *
39692514 CCATGTCTCAGACATGGTCTTACATGGGATGTTCTCATGTCGGTGCCCAGG
1 CCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAACG
*
39692565 CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
*
39692615 CCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCT
39692649 TTACCCAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 48 0.64
51 27 0.36
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
Found at i:39692764 original size:13 final size:13
Alignment explanation
Indices: 39692743--39692772 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39692733 GCTTGGATCA
39692743 TCATCAAATAAAT
1 TCATCAAATAAAT
*
39692756 TCATGAAATAAAT
1 TCATCAAATAAAT
39692769 TCAT
1 TCAT
39692773 AGTTGTTGGA
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:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:39695595 original size:33 final size:34
Alignment explanation
Indices: 39695555--39695632 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
39695545 TTGGTAGGTT
* *
39695555 TAGGGTTTAAGGTTTTTTAAAT-AATAAATTAAAA
1 TAGGTTTTAAGG-GTTTTAAATAAATAAATTAAAA
** *
39695589 TAGGTTTTTTGGGTTTTAAATAAATAAATTAAAT
1 TAGGTTTTAAGGGTTTTAAATAAATAAATTAAAA
39695623 TAGGATTTTA
1 TAGG-TTTTA
39695633 TTTTTTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
33 8 0.22
34 24 0.67
35 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (34 bp):
TAGGTTTTAAGGGTTTTAAATAAATAAATTAAAA
Found at i:39695639 original size:33 final size:30
Alignment explanation
Indices: 39695567--39695646 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 30
39695557 GGGTTTAAGG
39695567 TTTTTTAAATAATAAATTAAAATAGGTTTT
1 TTTTTTAAATAATAAATTAAAATAGGTTTT
*
39695597 TTGGGTTTTAAATAAATAAATTAAATTAGGATTTT
1 TT---TTTTAAAT-AATAAATTAAAATAGG-TTTT
39695632 ATTTTTTAAAATAAT
1 -TTTTTT-AAATAAT
39695647 TTTGTGTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
30 2 0.05
33 15 0.36
34 19 0.45
35 4 0.10
36 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (30 bp):
TTTTTTAAATAATAAATTAAAATAGGTTTT
Found at i:39695645 original size:34 final size:31
Alignment explanation
Indices: 39695567--39695641 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 31
39695557 GGGTTTAAGG
39695567 TTTTTTAAAT-AATAAATTAAAATAGGTTTT
1 TTTTTTAAATAAATAAATTAAAATAGGTTTT
*
39695597 TTGGGTTTTAAATAAATAAATTAAATTAGGATTTT
1 TT---TTTTAAATAAATAAATTAAAATAGG-TTTT
39695632 ATTTTTTAAA
1 -TTTTTTAAA
39695642 ATAATTTTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
30 2 0.05
33 15 0.39
34 15 0.39
35 4 0.11
36 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.49
Consensus pattern (31 bp):
TTTTTTAAATAAATAAATTAAAATAGGTTTT
Found at i:39695896 original size:126 final size:124
Alignment explanation
Indices: 39695730--39695969 Score: 322
Period size: 126 Copynumber: 1.9 Consensus size: 124
39695720 GAAAACATAA
* * *
39695730 TTTTGAGAAAACGATTCTGAAAAGATAATGTAAAAAATGCTCCAAGCAGGATGCACTGTCAGTAA
1 TTTTGAGAAAACGATTCTGAAAAGATAATGTAAAAAATGCTCCAAGAAGGATACACTGTCAGCAA
* *
39695795 AATTACTGAAAAAAGCTCCCACGTGGACACTATTTTTCTACAGTAGTTCCTAAAAAAGTAT
66 AATTACTG--AAAAGCTCCCACATGGACACTATTTTTCCACAGTAGTTCCTAAAAAAGTAT
* * * *
39695856 TTTTGAGAAGAC-AGTTCTGAACAA-ATAGTGTCAAAAATGCTTCAAGAAGGATACACTGTCAGC
1 TTTTGAGAAAACGA-TTCTGAA-AAGATAATGTAAAAAATGCTCCAAGAAGGATACACTGTCAGC
* * *
39695919 AAAATTATTGAAAAGCTCCCACATGGACTCTCTTTTTCCACAGTAGTTCCT
64 AAAATTACTGAAAAGCTCCCACATGGACACTATTTTTCCACAGTAGTTCCT
39695970 GTTTGGCCCT
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
124 37 0.37
125 1 0.01
126 60 0.60
127 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (124 bp):
TTTTGAGAAAACGATTCTGAAAAGATAATGTAAAAAATGCTCCAAGAAGGATACACTGTCAGCAA
AATTACTGAAAAGCTCCCACATGGACACTATTTTTCCACAGTAGTTCCTAAAAAAGTAT
Found at i:39699030 original size:25 final size:26
Alignment explanation
Indices: 39698989--39699037 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
39698979 ATTTCTATTT
*
39698989 TATTAAAAATATAAAAAATAAATTAC
1 TATTAAAAATATAAAAAACAAATTAC
*
39699015 TATT-AAAATATTAAAAACAAATT
1 TATTAAAAATATAAAAAACAAATT
39699038 TTATTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
TATTAAAAATATAAAAAACAAATTAC
Found at i:39700325 original size:13 final size:13
Alignment explanation
Indices: 39700307--39700331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39700297 TAATTTATAT
39700307 GTGTGAAAATTTC
1 GTGTGAAAATTTC
39700320 GTGTGAAAATTT
1 GTGTGAAAATTT
39700332 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:39701489 original size:44 final size:42
Alignment explanation
Indices: 39701459--39701573 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 42
39701449 TTGAGATTTG
*
39701459 CGTGTAAGACCATGTCTGGGACATTAGCATCGTATATGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTA
* * *
39701501 CGTGTAAGACCCTGTCTGGGACAGTGGCATCGTTATTTGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTA
* * * *
39701544 CATATAAGACCACGTCAGGGACATTGGCAT
1 CGTGTAAGACCATGTCTGGGACATTGGCAT
39701574 TGTACGATCT
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 29 0.47
43 33 0.53
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTA
Found at i:39703390 original size:22 final size:22
Alignment explanation
Indices: 39703364--39703410 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
39703354 TATTCCAACA
39703364 TAACTCGCCGAATGGTTCCACC
1 TAACTCGCCGAATGGTTCCACC
39703386 TAACTCGCCGAATGGTTCCACC
1 TAACTCGCCGAATGGTTCCACC
39703408 TAA
1 TAA
39703411 TCAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (22 bp):
TAACTCGCCGAATGGTTCCACC
Found at i:39707491 original size:44 final size:44
Alignment explanation
Indices: 39707446--39707637 Score: 231
Period size: 44 Copynumber: 4.2 Consensus size: 44
39707436 TCACTTTTCC
*
39707446 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACATGTCC
1 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACATGTCA
* *
39707490 CTGATCAGATAAGTGCAGCTAAAGCTACCACTTATCACTTGTCA
1 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACATGTCA
* * *
39707534 TTGATCAGATAACTGTAGCTAAAGCTATCACTTATCACTTGTCACTTGTCA
1 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCA-----CA--TGTCA
* * * *
39707585 CTGATCAGATAAGTGTAGTTGAAGCTACTACTTATCACTTGTCA
1 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACATGTCA
39707629 CTGATCAGA
1 CTGATCAGA
39707638 AGTACTCAAA
Statistics
Matches: 126, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
44 88 0.70
46 1 0.01
49 1 0.01
51 36 0.29
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (44 bp):
CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACATGTCA
Found at i:39707529 original size:51 final size:50
Alignment explanation
Indices: 39707474--39707629 Score: 180
Period size: 51 Copynumber: 3.2 Consensus size: 50
39707464 CTAAAGCTAC
* *
39707474 CACTTATCACATGTCCCTGATCAGATAAGTGCAGCTAAAGCTACCACTTAT
1 CACTTGTCACATGT-CCTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
* *
39707525 CACTTGT--CA--T--TGATCAGATAACTGTAGCTAAAGCTATCACTTAT
1 CACTTGTCACATGTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
* * * *
39707569 CACTTGTCACTTGTCACTGATCAGATAAGTGTAGTTGAAGCTACTACTTAT
1 CACTTGTCACATGTC-CTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
39707620 CACTTGTCAC
1 CACTTGTCAC
39707630 TGATCAGAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
44 38 0.43
46 1 0.01
47 1 0.01
48 1 0.01
49 2 0.02
51 45 0.51
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (50 bp):
CACTTGTCACATGTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
Found at i:39707612 original size:95 final size:88
Alignment explanation
Indices: 39707430--39707637 Score: 254
Period size: 95 Copynumber: 2.3 Consensus size: 88
39707420 TCGTATTTAT
* * * * *
39707430 CACTTTTCACTTTTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACATGTCCCTGAT
1 CACTTATCACTTGTCACTGATCAGATAACTGTAGCTAAAGCTACCACTTATCACATGTCACTGAT
39707495 CAGATAAGTGCAGCTAAAGCTAC
66 CAGATAAGTGCAGCTAAAGCTAC
* *
39707518 CACTTATCACTTGTCATTGATCAGATAACTGTAGCTAAAGCTATCACTTATCACTTGTCACTTGT
1 CACTTATCACTTGTCACTGATCAGATAACTGTAGCTAAAGCTACCACTTATCA-----CA--TGT
* * *
39707583 CACTGATCAGATAAGTGTAGTTGAAGCTAC
59 CACTGATCAGATAAGTGCAGCTAAAGCTAC
*
39707613 TACTTATCACTTGTCACTGATCAGA
1 CACTTATCACTTGTCACTGATCAGA
39707638 AGTACTCAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
88 47 0.47
93 2 0.02
95 52 0.51
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (88 bp):
CACTTATCACTTGTCACTGATCAGATAACTGTAGCTAAAGCTACCACTTATCACATGTCACTGAT
CAGATAAGTGCAGCTAAAGCTAC
Found at i:39718552 original size:25 final size:25
Alignment explanation
Indices: 39718524--39718573 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
39718514 AGGTTAAGAG
39718524 TTAAATTTATTATTATACCTTATAC
1 TTAAATTTATTATTATACCTTATAC
*
39718549 TTAAATTTATTATTATATCTTATAC
1 TTAAATTTATTATTATACCTTATAC
39718574 AAAAAACACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAAATTTATTATTATACCTTATAC
Found at i:39725147 original size:25 final size:24
Alignment explanation
Indices: 39725110--39725161 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
39725100 AATGTTATAA
* *
39725110 AAAATTATAAAAT-AAAAATTAATT
1 AAAATTACAAAATGAAAAAAT-ATT
39725134 AAAATTACATAAATGAAAAAATATT
1 AAAATTACA-AAATGAAAAAATATT
39725159 AAA
1 AAA
39725162 TAATATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATTACAAAATGAAAAAATATT
Found at i:39725370 original size:13 final size:13
Alignment explanation
Indices: 39725346--39725377 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
39725336 AGAGAGCTTT
39725346 GAGAAA-TTTAGA
1 GAGAAATTTTAGA
39725358 GAGAAATTTTAGA
1 GAGAAATTTTAGA
39725371 GA-AAATT
1 GAGAAATT
39725378 GAAGAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (13 bp):
GAGAAATTTTAGA
Found at i:39728019 original size:19 final size:20
Alignment explanation
Indices: 39727990--39728027 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
39727980 ATAAGTTGAG
*
39727990 ATGATTTAAATTTTAAATTT
1 ATGATTTAAATATTAAATTT
39728010 ATGA-TTAAATATTAAATT
1 ATGATTTAAATATTAAATT
39728028 AGGGACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
ATGATTTAAATATTAAATTT
Found at i:39729807 original size:7 final size:7
Alignment explanation
Indices: 39729795--39729819 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39729785 AGTCGATTGA
39729795 TATTTAG
1 TATTTAG
39729802 TATTTAG
1 TATTTAG
39729809 TATTTAG
1 TATTTAG
39729816 TATT
1 TATT
39729820 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:39730495 original size:18 final size:18
Alignment explanation
Indices: 39730469--39730503 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39730459 AGGTGCGTTT
*
39730469 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
39730487 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
39730504 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:39731652 original size:17 final size:18
Alignment explanation
Indices: 39731611--39731652 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
39731601 TTTACTAACC
* *
39731611 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
39731629 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
39731646 ATTAATA
1 ATTAATA
39731653 ATTTCATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:39731654 original size:116 final size:116
Alignment explanation
Indices: 39731348--39731635 Score: 524
Period size: 116 Copynumber: 2.5 Consensus size: 116
39731338 NNNNNNNNNN
* *
39731348 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACA
1 TAATTGTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACA
* *
39731413 TTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
66 TTCACATAATGTTAAATTTGGAAAAATGTTTTAACTGGTACTAACAATTAA
39731464 TAATTGTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACA
1 TAATTGTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACA
39731529 TTCACATAATGTTAAATTTGGAAAAATGTTTTAACTGGTACTAACAATTAA
66 TTCACATAATGTTAAATTTGGAAAAATGTTTTAACTGGTACTAACAATTAA
*
39731580 TAATTGTATATAATTTAATAA-TTTACTAACCATTAATACAATTTTTTGACTTAATA
1 TAATTGTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGACTTAATA
39731636 CAATTTATCA
Statistics
Matches: 167, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
115 35 0.21
116 132 0.79
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (116 bp):
TAATTGTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACA
TTCACATAATGTTAAATTTGGAAAAATGTTTTAACTGGTACTAACAATTAA
Found at i:39736346 original size:126 final size:125
Alignment explanation
Indices: 39736056--39736408 Score: 469
Period size: 126 Copynumber: 2.8 Consensus size: 125
39736046 CCCAAACATG
** * *
39736056 CTACTGTAGCAAAATTGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAG
1 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTTTCAAATAGCATCCT-G
* * *
39736121 -TATAAGTGATTTTATATTATTTGCTCAGAAACATCAAAAAAAAATTATTTCTTACATGAC
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* * * * *
39736181 CTACTGTAGCAAAAGCGCG-CTGACAAGGCCGCAATTTCACAAATTCTTTTTAAATAGCGTCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACAAGGGCGCGATTTCACAAATTCTTTTCAAATAGCATCCTG
* * * * *
39736245 CTAGAACCGATTTTATACTATTTGCTCAGAAACGTGAAAAAAATAATTATTTCTTCCGTGAC
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTACATGAC
*
39736307 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATT-TTTCTCAAATACCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTT-TCAAATAGCATCCTG
**
39736371 CTAGAAGCGATTTTATATTATTTTATCAGAAACGTCAA
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAA
39736409 CTCGAAATTA
Statistics
Matches: 195, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
124 2 0.01
125 91 0.47
126 101 0.52
127 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTTTCAAATAGCATCCTGC
TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:39737126 original size:26 final size:27
Alignment explanation
Indices: 39737082--39737132 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
39737072 TGCCAATCCT
39737082 TTCTTTTAATTTTATAATATGATATTC
1 TTCTTTTAATTTTATAATATGATATTC
* *
39737109 TTCTTTT-ATTTTTTAATATTATAT
1 TTCTTTTAATTTTATAATATGATAT
39737133 ATTACAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (27 bp):
TTCTTTTAATTTTATAATATGATATTC
Found at i:39740308 original size:3 final size:3
Alignment explanation
Indices: 39740300--39740326 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39740290 TTGGTAAAAT
39740300 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
39740327 GTTTAGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:39742389 original size:17 final size:17
Alignment explanation
Indices: 39742369--39742410 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
39742359 TTTGAAAGCG
39742369 GAAAGAAAAAGAAAAAC
1 GAAAGAAAAAGAAAAAC
*
39742386 GAAAGAAAAAGAAAAAG
1 GAAAGAAAAAGAAAAAC
39742403 GAAAGAAA
1 GAAAGAAA
39742411 GAAAGAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAAGAAAAAC
Found at i:39744820 original size:4 final size:4
Alignment explanation
Indices: 39744811--39744867 Score: 87
Period size: 4 Copynumber: 14.2 Consensus size: 4
39744801 ATTGAGTAGC
* * *
39744811 ATGT ATGT ATGT ACGT ATGT ATGT ACGT ATGT ATGT ATGT AGGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39744859 ATGT ATGT A
1 ATGT ATGT A
39744868 ACGGGGGCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.44
Consensus pattern (4 bp):
ATGT
Found at i:39751996 original size:66 final size:66
Alignment explanation
Indices: 39751914--39752042 Score: 258
Period size: 66 Copynumber: 2.0 Consensus size: 66
39751904 TTATCACGAT
39751914 TGTAATGCAGTTGCTTGCACTTAAATATTATTATTTTATGCATATGTATATATTTATTTTTTTTC
1 TGTAATGCAGTTGCTTGCACTTAAATATTATTATTTTATGCATATGTATATATTTATTTTTTTTC
39751979 A
66 A
39751980 TGTAATGCAGTTGCTTGCACTTAAATATTATTATTTTATGCATATGTATATATTTATTTTTTT
1 TGTAATGCAGTTGCTTGCACTTAAATATTATTATTTTATGCATATGTATATATTTATTTTTTT
39752043 CATATTTAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (66 bp):
TGTAATGCAGTTGCTTGCACTTAAATATTATTATTTTATGCATATGTATATATTTATTTTTTTTC
A
Found at i:39752091 original size:44 final size:45
Alignment explanation
Indices: 39752032--39752121 Score: 173
Period size: 44 Copynumber: 2.0 Consensus size: 45
39752022 TATGTATATA
39752032 TTTATTTTTTTCATATTTAATAATTGAATAATAATTAATTTTTAT
1 TTTATTTTTTTCATATTTAATAATTGAATAATAATTAATTTTTAT
39752077 TTTA-TTTTTTCATATTTAATAATTGAATAATAATTAATTTTTAT
1 TTTATTTTTTTCATATTTAATAATTGAATAATAATTAATTTTTAT
39752121 T
1 T
39752122 ACTCCTGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 41 0.91
45 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (45 bp):
TTTATTTTTTTCATATTTAATAATTGAATAATAATTAATTTTTAT
Found at i:39760660 original size:37 final size:35
Alignment explanation
Indices: 39760539--39760662 Score: 124
Period size: 36 Copynumber: 3.4 Consensus size: 35
39760529 ATATATGTTG
*
39760539 CTTACATTTTATATCACCAATAAGTGGTTTACA-CT
1 CTTACATTTTATATCATCAATAA-TGGTTTACACCT
* * *** *
39760574 CTTTCCATTTTATATCATCAACAAACAATTTACACTT
1 C-TTACATTTTATATCATCAA-TAATGGTTTACACCT
39760611 CTTACATTTTATATCATCAATGAATGGTTTCACACCT
1 CTTACATTTTATATCATCAAT-AATGGTTT-ACACCT
*
39760648 CTTACGTTTTATATC
1 CTTACATTTTATATC
39760663 GCCAAAAGAT
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
35 1 0.01
36 46 0.66
37 23 0.33
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (35 bp):
CTTACATTTTATATCATCAATAATGGTTTACACCT
Found at i:39764097 original size:33 final size:32
Alignment explanation
Indices: 39764037--39764118 Score: 123
Period size: 33 Copynumber: 2.6 Consensus size: 32
39764027 TAATAACTTT
*
39764037 CATAT-ACATATAC-TTTTTTTATCATATTTC
1 CATATAACATGTACATTTTTTTATCATATTTC
39764067 CATATAACATGTACATTTTTCTTATCATATTTC
1 CATATAACATGTACATTTTT-TTATCATATTTC
*
39764100 CATATAACATGTTCATTTT
1 CATATAACATGTACATTTT
39764119 CATAACAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 5 0.11
31 7 0.15
32 5 0.11
33 30 0.64
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.50
Consensus pattern (32 bp):
CATATAACATGTACATTTTTTTATCATATTTC
Found at i:39766176 original size:25 final size:25
Alignment explanation
Indices: 39766146--39766202 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
39766136 GGGATGCTCC
*
39766146 GAAGCTCACAAGAAATATTTAACGA
1 GAAGCTCACAAGAAACATTTAACGA
** * *
39766171 GAAGCTCGTAAGAACCATTTAACGG
1 GAAGCTCACAAGAAACATTTAACGA
39766196 GAAGCTC
1 GAAGCTC
39766203 GTGAGAGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (25 bp):
GAAGCTCACAAGAAACATTTAACGA
Found at i:39769850 original size:21 final size:20
Alignment explanation
Indices: 39769820--39769861 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
39769810 AAAATATTAA
*
39769820 TAATATTATTATCTAATATAT
1 TAATAATATTAT-TAATATAT
*
39769841 TAATAATATTATTAATTTAT
1 TAATAATATTATTAATATAT
39769861 T
1 T
39769862 TACATCCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATAATATTATTAATATAT
Found at i:39771174 original size:41 final size:41
Alignment explanation
Indices: 39771115--39771517 Score: 410
Period size: 41 Copynumber: 9.6 Consensus size: 41
39771105 TAATGTAAGG
* ** * * *
39771115 GGTTGCTAAGTGCAGATTCCCCAAATCATTGATCAAAAAGA
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTATAAAGT
* *
39771156 GGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTATAAAGT
* * * *
39771197 GGTTGCTAAGTGTTGATTCCACCGTATCCTTGATTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTAT-AAAGT
* * *
39771240 GGTTGCTATGTGCTGATTCCCCGTATCGTTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTATAAAGT
* * * *
39771281 GGTTGCTAAGTGCTGATTCCGTCGTATCCTTGATTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTAT-AAAGT
* *
39771324 GGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTATAAAGT
* * * *
39771365 GGTTGCTAAGTGCTGATTCCATCGTATCCTTGATTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTAT-AAAGT
* * *
39771408 GGTCGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTATAAAGT
* * ** * *
39771449 GGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATGAGGT
1 GGTTGCTAAGTGCTGATTCC-CC-GTAT-CATTGATTATAAAGT
39771493 GGTTGCTAAGTGCTGATTCCACCGT
1 GGTTGCTAAGTGCTGATTCC-CCGT
39771518 GTAACGGTTA
Statistics
Matches: 300, Mismatches: 53, Indels: 16
0.81 0.14 0.04
Matches are distributed among these distances:
41 116 0.39
42 82 0.27
43 68 0.23
44 34 0.11
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCCCGTATCATTGATTATAAAGT
Found at i:39771257 original size:84 final size:84
Alignment explanation
Indices: 39771151--39771472 Score: 581
Period size: 84 Copynumber: 3.8 Consensus size: 84
39771141 CATTGATCAA
* *
39771151 AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
39771216 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
*
39771235 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCGTTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
**
39771300 CGTCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
39771319 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
*
39771384 CATCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
*
39771403 AAAGGGGTCGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
39771468 CACCG
66 CACCG
39771473 GGATCCTTTG
Statistics
Matches: 229, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 229 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
CACCGTATCCTTGATTGTG
Found at i:39774459 original size:35 final size:35
Alignment explanation
Indices: 39774419--39774488 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
39774409 TTGGAAATTG
39774419 ATAGTACTATATGTTTTGTGATTATTCGTGGCTAA
1 ATAGTACTATATGTTTTGTGATTATTCGTGGCTAA
39774454 ATAGTACTATATGTTTTGTGATTATTCGTGGCTAA
1 ATAGTACTATATGTTTTGTGATTATTCGTGGCTAA
39774489 CATTGACCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (35 bp):
ATAGTACTATATGTTTTGTGATTATTCGTGGCTAA
Found at i:39774931 original size:43 final size:43
Alignment explanation
Indices: 39774877--39774985 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
39774867 ATAGATTATA
* * *
39774877 CTTCGATATATCTGATGTTGCACCGTGTGTGCCAGTATAATTG
1 CTTCGGTATATCCGATGATGCACCGTGTGTGCCAGTATAATTG
* ** *
39774920 CTTTGGTATATCCGATGATGCATTGTGTGTGCTAGTATAATTG
1 CTTCGGTATATCCGATGATGCACCGTGTGTGCCAGTATAATTG
39774963 CTTCGGTATATCCGATGATGCAC
1 CTTCGGTATATCCGATGATGCAC
39774986 TTGCGTGCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (43 bp):
CTTCGGTATATCCGATGATGCACCGTGTGTGCCAGTATAATTG
Found at i:39775051 original size:42 final size:42
Alignment explanation
Indices: 39774905--39775088 Score: 190
Period size: 42 Copynumber: 4.3 Consensus size: 42
39774895 TGCACCGTGT
* * *
39774905 GTGCCAGTATAATTGCTTTGGTATATCCGATGATGCATTGTGT
1 GTGCTAGTATAATTGCTTTGGTATATCCGATGATGCACT-TGC
*
39774948 GTGCTAGTATAATTGCTTCGGTATATCCGATGATGCACTTGC
1 GTGCTAGTATAATTGCTTTGGTATATCCGATGATGCACTTGC
* * * * * *
39774990 GTGCAAATATATTTTCTTTGGTACATCC-ATTGATGCACTTAC
1 GTGCTAGTATAATTGCTTTGGTATATCCGA-TGATGCACTTGC
* * * *
39775032 GTGCTAGCATAATTGCTTTGGTTTATTCGATGATGCACTACGC
1 GTGCTAGTATAATTGCTTTGGTATATCCGATGATGCACT-TGC
* *
39775075 ATGCCAGTATAATT
1 GTGCTAGTATAATT
39775089 TATTCGTCTT
Statistics
Matches: 114, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
41 1 0.01
42 64 0.56
43 49 0.43
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (42 bp):
GTGCTAGTATAATTGCTTTGGTATATCCGATGATGCACTTGC
Found at i:39775879 original size:16 final size:16
Alignment explanation
Indices: 39775858--39775888 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39775848 GTCAAATTTG
39775858 GTATATAAAGTTATGT
1 GTATATAAAGTTATGT
*
39775874 GTATATGAAGTTATG
1 GTATATAAAGTTATG
39775889 GTTTAATGGT
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:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (16 bp):
GTATATAAAGTTATGT
Found at i:39783291 original size:9 final size:9
Alignment explanation
Indices: 39783277--39783367 Score: 53
Period size: 9 Copynumber: 10.0 Consensus size: 9
39783267 TAGGATATTA
39783277 TTATATTTT
1 TTATATTTT
*
39783286 TTATATATT
1 TTATATTTT
* *
39783295 TAATAATTT
1 TTATATTTT
*
39783304 TTATGTTTTT
1 TTAT-ATTTT
*
39783314 TTAATAATTT
1 TT-ATATTTT
39783324 TTATATTTT
1 TTATATTTT
*
39783333 CTGA-ATTTT
1 -TTATATTTT
*
39783342 TTGAAATTTT
1 TT-ATATTTT
*
39783352 ATAT-TTTT
1 TTATATTTT
39783360 TTA-ATTTT
1 TTATATTTT
39783368 AAAAAATAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 13
0.69 0.17 0.15
Matches are distributed among these distances:
8 11 0.18
9 30 0.49
10 18 0.30
11 2 0.03
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.68
Consensus pattern (9 bp):
TTATATTTT
Found at i:39783316 original size:20 final size:20
Alignment explanation
Indices: 39783293--39783332 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
39783283 TTTTTATATA
*
39783293 TTTAATAATTTTTATGTTTT
1 TTTAATAATTTTTATATTTT
39783313 TTTAATAATTTTTATATTTT
1 TTTAATAATTTTTATATTTT
39783333 CTGAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTAATAATTTTTATATTTT
Found at i:39783374 original size:26 final size:26
Alignment explanation
Indices: 39783312--39783374 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
39783302 TTTTATGTTT
* *
39783312 TTTTAATAATTTTTATATTTTCTGAA
1 TTTTAAAAAATTTTATATTTTCTGAA
*** * *
39783338 TTTTTTGAAATTTTATATTTTTTTAA
1 TTTTAAAAAATTTTATATTTTCTGAA
39783364 TTTTAAAAAAT
1 TTTTAAAAAAT
39783375 AATTAATTGT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (26 bp):
TTTTAAAAAATTTTATATTTTCTGAA
Found at i:39786810 original size:18 final size:20
Alignment explanation
Indices: 39786787--39786831 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
39786777 TTACGAGTCC
39786787 ATAATATA-TA-TTATAAAA
1 ATAATATATTATTTATAAAA
39786805 ATAATATATTTATTTATAAAA
1 ATAATATA-TTATTTATAAAA
39786826 A-AATAT
1 ATAATAT
39786832 TATAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
20 7 0.29
21 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATATATTATTTATAAAA
Found at i:39786840 original size:21 final size:21
Alignment explanation
Indices: 39786797--39786840 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39786787 ATAATATATA
**
39786797 TTATAAAAATAATATATTTAT
1 TTATAAAAATAATATATAAAT
39786818 TTATAAAAA-AATATTATAAAT
1 TTATAAAAATAATA-TATAAAT
39786839 TT
1 TT
39786841 TTTTCATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATAAAAATAATATATAAAT
Found at i:39787379 original size:19 final size:20
Alignment explanation
Indices: 39787357--39787403 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39787347 ACTTATTTAG
*
39787357 ATTTTTTATCGT-ACTAATA
1 ATTTTTTATAGTAACTAATA
*
39787376 ATTTTTTATAGTAATTAATA
1 ATTTTTTATAGTAACTAATA
*
39787396 TTTTTTTA
1 ATTTTTTA
39787404 AATATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (20 bp):
ATTTTTTATAGTAACTAATA
Found at i:39787381 original size:20 final size:19
Alignment explanation
Indices: 39787357--39787401 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39787347 ACTTATTTAG
*
39787357 ATTTTTTATCGT-ACTAAT
1 ATTTTTTATAGTAACTAAT
*
39787375 AATTTTTTATAGTAATTAAT
1 -ATTTTTTATAGTAACTAAT
39787395 ATTTTTT
1 ATTTTTT
39787402 TAAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (19 bp):
ATTTTTTATAGTAACTAAT
Found at i:39792793 original size:37 final size:37
Alignment explanation
Indices: 39792751--39792842 Score: 130
Period size: 37 Copynumber: 2.5 Consensus size: 37
39792741 ATTAGGGTTG
* **
39792751 ATACAATCATCTATGAAAATAGATCCTTGTCTTCTGA
1 ATACAATCATCTATGAAAATAGATCCATGTCTTCCAA
* * *
39792788 CTACAATGATCTATGAAAATAGCTCCATGTCTTCCAA
1 ATACAATCATCTATGAAAATAGATCCATGTCTTCCAA
39792825 ATACAATCATCTATGAAA
1 ATACAATCATCTATGAAA
39792843 GTGATGATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (37 bp):
ATACAATCATCTATGAAAATAGATCCATGTCTTCCAA
Found at i:39796851 original size:2 final size:2
Alignment explanation
Indices: 39796844--39796874 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39796834 TTAGGTCAAA
39796844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39796875 AATACCAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39798289 original size:240 final size:242
Alignment explanation
Indices: 39797838--39798338 Score: 720
Period size: 240 Copynumber: 2.1 Consensus size: 242
39797828 TCTAATATCC
* * *
39797838 AATCCTCAAAACGCAAGTTAGATATTTGTAAATATTCGAATCTGCACTACTTGAAGAAGGGTTTG
1 AATCCTCAAAAAGCAAGTTAGATATTTGCAAATATTCAAATCTGCACTACTTGAAGAAGGGTTTG
* * * * *
39797903 GATCAATTTTGTGTTCGAATTGTTTTGGGTTCACGTGGTTTGAGTCAAGGATTTTTAAGTGGGTC
66 AATCAATTTTGTGTTCGAATTGTTTTGGGCTCAAGTAGTTTGAGTCAAGGATTTTTAAGTGGGCC
* * * *
39797968 ATTATTAGTTCAAGCCATTTTGGATATACGAGAACTAATATTCACTTTGAATTTACTAAGAATAG
131 ATTACTAGTTCAAGCCATTTTGGATATACAAGAACTAATATTCACTTTAAATTTACTAAGAATAA
39798033 TAATTAGAAAATCTGAATTTAAATATCAT-TCGAATCTACAATATCTG
196 TAATTAGAAAATCTGAATTTAAATATCATCTC-AATCTACAATATCTG
*
39798080 AATCCT-AAAAAGCAAGTTAGATATTTGCAAATATTCAAATCTGCACTACTTGGAGAAGGGTTTG
1 AATCCTCAAAAAGCAAGTTAGATATTTGCAAATATTCAAATCTGCACTACTTGAAGAAGGGTTTG
* * * *
39798144 AATTAATTTTGTGTTCGAGTT-TTTTGGGCTCAAGTAGTTTGAGTCTAGGATTTTTAGGTGGGCC
66 AATCAATTTTGTGTTCGAATTGTTTTGGGCTCAAGTAGTTTGAGTCAAGGATTTTTAAGTGGGCC
* * * * *
39798208 ATTGCTAGTTCAAGCCATTTTGGATATTCAAGAACTAATATTCACTTTAAATTTGCTAGGGATAA
131 ATTACTAGTTCAAGCCATTTTGGATATACAAGAACTAATATTCACTTTAAATTTACTAAGAATAA
* * *
39798273 TAATTATAATATCTGAATTTAAATATCATCTCAATCTACAATATATCAG
196 TAATTAGAAAATCTGAATTTAAATATCATCTCAATCTAC-A-ATATCTG
*
39798322 AATCCTCAAAATGCAAG
1 AATCCTCAAAAAGCAAG
39798339 GGAAATATCC
Statistics
Matches: 229, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
240 127 0.55
241 75 0.33
242 18 0.08
243 9 0.04
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (242 bp):
AATCCTCAAAAAGCAAGTTAGATATTTGCAAATATTCAAATCTGCACTACTTGAAGAAGGGTTTG
AATCAATTTTGTGTTCGAATTGTTTTGGGCTCAAGTAGTTTGAGTCAAGGATTTTTAAGTGGGCC
ATTACTAGTTCAAGCCATTTTGGATATACAAGAACTAATATTCACTTTAAATTTACTAAGAATAA
TAATTAGAAAATCTGAATTTAAATATCATCTCAATCTACAATATCTG
Found at i:39808943 original size:218 final size:212
Alignment explanation
Indices: 39808603--39809009 Score: 597
Period size: 218 Copynumber: 1.9 Consensus size: 212
39808593 AATTCATTGA
*
39808603 GCTCTTCTCATACCAACTGTTTGAGGTTTGAATTGCCTACTCAAATAACAACACTTCAAAGGCTT
1 GCTCTCCTCATACCAACTGTTTGAGGTTTGAATTGCCTACTCAAATAACAACACTTCAAAGGCTT
*
39808668 CTTTCAATAAGAAAGACAGTTCCCCCTTACAGGGTAGTGTTCTTACCCATTAAAACCGCTTAAGG
66 CTCTCAATAAGAAAGACAGTTCCCCCTTACAGGGTAGTGTTCTTACCCATTAAAACCGCTTAA-G
* *
39808733 AGTTGGTTCGAATCCCATCAAGACCAAAATGATAAAACATTTCCTTGGTGGACCTTAGACGCTCC
130 -G--GGTT-G-ATCCC-TCAAGACCAAAATGATAAAACATTTCCTTAGTGGACCTTAGAAGCTCC
39808798 CGATAAGCTCCATGAATCCTTTTG
189 CGATAAGCTCCATGAATCCTTTTG
* *
39808822 GCTCTCCTCATACCAACTGTTTGAGGTTTGAATTGCTTACTTAAA-AGAC-ACACTTCAAAGGCT
1 GCTCTCCTCATACCAACTGTTTGAGGTTTGAATTGCCTACTCAAATA-ACAACACTTCAAAGGCT
* *
39808885 TCTCTCAATAAGAAAGACAATTTCTCCC-TA-AGGGGTAGTGTTCTTACCCATTAAAACCGCTTA
65 TCTCTCAATAAGAAAGAC-AGTTCCCCCTTACA-GGGTAGTGTTCTTACCCATTAAAACCGCTTA
** *
39808948 AGGGGTTGATTTCTCAAGACCAAAATGATAAAACATTTCCTTAGTGGACTTTAGAAGCTCCC
128 AGGGGTTGATCCCTCAAGACCAAAATGATAAAACATTTCCTTAGTGGACCTTAGAAGCTCCC
39809010 ATCTTTTGAA
Statistics
Matches: 174, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
211 46 0.26
212 3 0.02
213 1 0.01
214 4 0.02
216 1 0.01
217 2 0.01
218 66 0.38
219 51 0.29
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (212 bp):
GCTCTCCTCATACCAACTGTTTGAGGTTTGAATTGCCTACTCAAATAACAACACTTCAAAGGCTT
CTCTCAATAAGAAAGACAGTTCCCCCTTACAGGGTAGTGTTCTTACCCATTAAAACCGCTTAAGG
GGTTGATCCCTCAAGACCAAAATGATAAAACATTTCCTTAGTGGACCTTAGAAGCTCCCGATAAG
CTCCATGAATCCTTTTG
Found at i:39813454 original size:23 final size:23
Alignment explanation
Indices: 39813428--39813484 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
39813418 TGAAATTTTG
39813428 ATTACATTTATTTTA-GTTTTAAA
1 ATTA-ATTTATTTTATGTTTTAAA
* *
39813451 ATTAAATATATTTTATTTTTTAAA
1 ATT-AATTTATTTTATGTTTTAAA
39813475 ATTAATTTAT
1 ATTAATTTAT
39813485 GTTTTCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTAATTTATTTTATGTTTTAAA
Found at i:39816920 original size:14 final size:14
Alignment explanation
Indices: 39816892--39816941 Score: 61
Period size: 13 Copynumber: 3.7 Consensus size: 14
39816882 ATTTATGTTC
39816892 TTTTC-TTAAATAA
1 TTTTCTTTAAATAA
39816905 TTGTTCTTTAAA-AA
1 TT-TTCTTTAAATAA
*
39816919 TTTTCTATAAATAA
1 TTTTCTTTAAATAA
39816933 TTTT-TTTAA
1 TTTTCTTTAA
39816942 TCTTTCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 14 0.44
14 13 0.41
15 5 0.16
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (14 bp):
TTTTCTTTAAATAA
Found at i:39827971 original size:2 final size:2
Alignment explanation
Indices: 39827964--39827991 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39827954 TTATAACCCC
39827964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39827992 CTTGTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39830592 original size:27 final size:27
Alignment explanation
Indices: 39830554--39830609 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
39830544 GGATTCGGCG
39830554 ACACACCGAACCAGGTAAAGTTTCTAA
1 ACACACCGAACCAGGTAAAGTTTCTAA
*
39830581 ACACGCCGAACCAGGTAAAGTTTCTAA
1 ACACACCGAACCAGGTAAAGTTTCTAA
39830608 AC
1 AC
39830610 CCTTCCCCCT
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:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (27 bp):
ACACACCGAACCAGGTAAAGTTTCTAA
Found at i:39831170 original size:13 final size:13
Alignment explanation
Indices: 39831152--39831178 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39831142 TATGAATTTG
39831152 GCCCATTGTAATT
1 GCCCATTGTAATT
39831165 GCCCATTGTAATT
1 GCCCATTGTAATT
39831178 G
1 G
39831179 GACTTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (13 bp):
GCCCATTGTAATT
Found at i:39831616 original size:44 final size:45
Alignment explanation
Indices: 39831543--39831634 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 45
39831533 GCTTGGGTAG
* * *
39831543 TAAGATTTGCTATTCTCAATCTGCCCCATTGCAACTTCAGGGGGA
1 TAAGACTTGCTATTCTCAATCTGCCCCATTGCAACCTCAGGGAGA
* * *
39831588 TAAGACTTGCT-TTCTCAGTCTGCTCCATTGTAACCTCAGGGAGA
1 TAAGACTTGCTATTCTCAATCTGCCCCATTGCAACCTCAGGGAGA
39831632 TAA
1 TAA
39831635 AACCTGATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 31 0.76
45 10 0.24
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (45 bp):
TAAGACTTGCTATTCTCAATCTGCCCCATTGCAACCTCAGGGAGA
Found at i:39831921 original size:88 final size:88
Alignment explanation
Indices: 39831768--39832115 Score: 448
Period size: 88 Copynumber: 4.0 Consensus size: 88
39831758 AAGATTTGCC
* * * *
39831768 GTCTTCGATCTGCTTTGCCGTC-AGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCTACT
1 GTCTTCGATCTGCTTCGCTGTCTA-TGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCACT
*
39831832 GCAACCGAGGGAGGCGAGGCTGGT
65 GCAACCGAGGGAGGCAAGGCTGGT
* * * * **
39831856 GTCTTCGATCTACTTCGCTGTCTACGCAGGAAGGCAAGATATGCTATCTTCAATTTGCTCCACTG
1 GTCTTCGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCACTG
*
39831921 CAACCGAGGGAGGCAAGGCTGGG
66 CAACCGAGGGAGGCAAGGCTGGT
* * * *
39831944 GTCTTCGATCTGCTTCGCTGTTTATGCTGGAGGGCAAGATCTGCTATCTTTAACCCGCTCCACTG
1 GTCTTCGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCACTG
* *
39832009 CAACCGATGGAGGCAAGGCT-TT
66 CAACCGAGGGAGGCAAGGCTGGT
* * * * * *
39832031 GTTTTCGATTTGCTTCGCTGTCCATGTAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTG
1 GTCTTCGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCACTG
*
39832096 CAACCGATGGAGGCAAGGCT
66 CAACCGAGGGAGGCAAGGCT
39832116 TTGCTTTCGA
Statistics
Matches: 225, Mismatches: 34, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
87 76 0.34
88 148 0.66
89 1 0.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (88 bp):
GTCTTCGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCACTG
CAACCGAGGGAGGCAAGGCTGGT
Found at i:39832110 original size:175 final size:176
Alignment explanation
Indices: 39831800--39832115 Score: 463
Period size: 175 Copynumber: 1.8 Consensus size: 176
39831790 AGTACAGGAA
* * *
39831800 GGCAAGATCTGCTATCTTTAACCTGCTCTACTGCAACCGAGGGAGGCGAGGCTGGTGTCTTCGAT
1 GGCAAGATCTGCTATCTTTAACCCGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTGTCTTCGAT
* ***
39831865 CTACTTCGCTGTCTACGCAGGAAGGCAAGATATGCTATCTTCAATTTGCTCCACTGCAACCGAGG
66 CTACTTCGCTGTCCACGCAGGAAGGCAAGATATGCTATCTTCAACCAGCTCCACTGCAACCGAGG
39831930 GAGGCAAGGCTGGGGTCTTCGATCTGCTTCGCTGTTTATGCTGGAG
131 GAGGCAAGGCTGGGGTCTTCGATCTGCTTCGCTGTTTATGCTGGAG
* * *
39831976 GGCAAGATCTGCTATCTTTAACCCGCTCCACTGCAACCGATGGAGGCAAGGCT-TTGTTTTCGAT
1 GGCAAGATCTGCTATCTTTAACCCGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTGTCTTCGAT
* * * * * * * *
39832040 TTGCTTCGCTGTCCATGTAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG
66 CTACTTCGCTGTCCACGCAGGAAGGCAAGATATGCTATCTTCAACCAGCTCCACTGCAACCGAGG
39832105 GAGGCAAGGCT
131 GAGGCAAGGCT
39832116 TTGCTTTCGA
Statistics
Matches: 122, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
175 73 0.60
176 49 0.40
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (176 bp):
GGCAAGATCTGCTATCTTTAACCCGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTGTCTTCGAT
CTACTTCGCTGTCCACGCAGGAAGGCAAGATATGCTATCTTCAACCAGCTCCACTGCAACCGAGG
GAGGCAAGGCTGGGGTCTTCGATCTGCTTCGCTGTTTATGCTGGAG
Found at i:39832949 original size:26 final size:26
Alignment explanation
Indices: 39832888--39832968 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
39832878 AAGTTCAAGT
*
39832888 GAGCCA-T-ATCAGGAAGCTC-CGGA
1 GAGCCATTAATCAGGAAGCTCACGAA
* *
39832911 GTGCCATTAATCAGAAAGCTCACGAA
1 GAGCCATTAATCAGGAAGCTCACGAA
* *
39832937 GAGCCTTTAATCAGGAAGCTTACGAA
1 GAGCCATTAATCAGGAAGCTCACGAA
39832963 GAGCCA
1 GAGCCA
39832969 CATAACGGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
23 5 0.11
24 1 0.02
25 11 0.23
26 30 0.64
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACGAA
Found at i:39836178 original size:18 final size:18
Alignment explanation
Indices: 39836155--39836189 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39836145 AGTTTTAATA
* *
39836155 TTTAATTTGGTATTTAAG
1 TTTAATTAGGTACTTAAG
39836173 TTTAATTAGGTACTTAA
1 TTTAATTAGGTACTTAA
39836190 TTGATATGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.51
Consensus pattern (18 bp):
TTTAATTAGGTACTTAAG
Found at i:39841540 original size:14 final size:14
Alignment explanation
Indices: 39841511--39841556 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
39841501 AGTCCTTAAC
39841511 AAATACAGATAT-CA
1 AAAT-CAGATATACA
*
39841525 AAATCAGATGTACA
1 AAATCAGATATACA
*
39841539 AAAT-AGATATATA
1 AAATCAGATATACA
39841552 AAATC
1 AAATC
39841557 TTACCCTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.24
Consensus pattern (14 bp):
AAATCAGATATACA
Found at i:39844139 original size:42 final size:41
Alignment explanation
Indices: 39844090--39844176 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
39844080 TCATATAAGT
* *
39844090 TTTTGTTTAACCCTAATGGGTTTCTGGT-CAGCTCTTTTGAG
1 TTTTGTTTAACCCTAATGGGTTT-TCGTACAGCTCTTATGAG
*
39844131 CTTTTGTTTAACCCTTATGGGTTTTCGTACAGCTCTTATGAG
1 -TTTTGTTTAACCCTAATGGGTTTTCGTACAGCTCTTATGAG
39844173 TTTT
1 TTTT
39844177 CATTCTGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
41 7 0.17
42 34 0.83
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (41 bp):
TTTTGTTTAACCCTAATGGGTTTTCGTACAGCTCTTATGAG
Found at i:39846826 original size:21 final size:21
Alignment explanation
Indices: 39846800--39846840 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39846790 ACATTCAACC
* *
39846800 CTTATGAGTTTCTGTTTAGCA
1 CTTATGAGCTTCTGTATAGCA
*
39846821 CTTATGTGCTTCTGTATAGC
1 CTTATGAGCTTCTGTATAGC
39846841 CTTCGGGCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (21 bp):
CTTATGAGCTTCTGTATAGCA
Found at i:39849701 original size:27 final size:27
Alignment explanation
Indices: 39849670--39849729 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
39849660 GAGACTTGAC
*
39849670 GGGTGGAGGCGGTGAGTA-GACGGGTGG
1 GGGTGGAGGCGGGGAG-AGGACGGGTGG
* * *
39849697 TGGTGGTGGTGGGGAGAGGACGGGTGG
1 GGGTGGAGGCGGGGAGAGGACGGGTGG
39849724 GGGTGG
1 GGGTGG
39849730 TGAGCGCANN
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.12, C:0.05, G:0.67, T:0.17
Consensus pattern (27 bp):
GGGTGGAGGCGGGGAGAGGACGGGTGG
Found at i:39849704 original size:21 final size:21
Alignment explanation
Indices: 39849650--39849704 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
39849640 GGATTTTACT
* *
39849650 GGTGGTGGTGGAGACTTGACG
1 GGTGGTGGTGGTGACTAGACG
* * *
39849671 GGTGGAGGCGGTGAGTAGACG
1 GGTGGTGGTGGTGACTAGACG
39849692 GGTGGTGGTGGTG
1 GGTGGTGGTGGTG
39849705 GTGGGGAGAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.13, C:0.07, G:0.58, T:0.22
Consensus pattern (21 bp):
GGTGGTGGTGGTGACTAGACG
Found at i:39849973 original size:21 final size:20
Alignment explanation
Indices: 39849948--39850039 Score: 60
Period size: 21 Copynumber: 4.2 Consensus size: 20
39849938 NNNTGCGGGG
*
39849948 GGTGGGGGGGAGGGAGCCGGT
1 GGTGGGGGGGAGGGA-CAGGT
*
39849969 GGTGGTGGTGGTGAGTGGACGGGT
1 GGTGG-GG-GG-GAG-GGACAGGT
39849993 GG-GGGTGGGGAGGGCACAGGT
1 GGTGGG-GGGGAGGG-ACAGGT
* * *
39850014 GGTGGTGGGGATTGGACGGGT
1 GGTGGGGGGGA-GGGACAGGT
39850035 GGTGG
1 GGTGG
39850040 TAGGGAAGGG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
20 2 0.03
21 30 0.52
22 9 0.16
23 5 0.09
24 9 0.16
25 3 0.05
ACGTcount: A:0.10, C:0.07, G:0.66, T:0.17
Consensus pattern (20 bp):
GGTGGGGGGGAGGGACAGGT
Found at i:39850015 original size:42 final size:42
Alignment explanation
Indices: 39849969--39850063 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
39849959 GGGAGCCGGT
* *
39849969 GGTGGTGGTGGTGAGTGGACGGGTGGGGGT-GGGGAGGGCACA
1 GGTGGTGGTGGGGAGTGGACGGGTGGGGGTAGGGAAGGG-ACA
* * *
39850011 GGTGGTGGTGGGGATTGGACGGGTGGTGGTAGGGAAGGGACT
1 GGTGGTGGTGGGGAGTGGACGGGTGGGGGTAGGGAAGGGACA
*
39850053 GGTGGAGGTGG
1 GGTGGTGGTGG
39850064 AACCGGTGCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 39 0.85
43 7 0.15
ACGTcount: A:0.13, C:0.05, G:0.63, T:0.19
Consensus pattern (42 bp):
GGTGGTGGTGGGGAGTGGACGGGTGGGGGTAGGGAAGGGACA
Found at i:39850040 original size:21 final size:20
Alignment explanation
Indices: 39849969--39850063 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 20
39849959 GGGAGCCGGT
*
39849969 GGTGGTGGTGGTGAGTGGACG
1 GGTGGTGGTGGGGAG-GGACG
* *
39849990 GGTGGGGGTGGGGAGGGCACA
1 GGTGGTGGTGGGGAGGG-ACG
*
39850011 GGTGGTGGTGGGGATTGGACG
1 GGTGGTGGTGGGGA-GGGACG
* *
39850032 GGTGGTGGTAGGGAAGGGACT
1 GGTGGTGGT-GGGGAGGGACG
*
39850053 GGTGGAGGTGG
1 GGTGGTGGTGG
39850064 AACCGGTGCT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.07
21 51 0.84
22 6 0.10
ACGTcount: A:0.13, C:0.05, G:0.63, T:0.19
Consensus pattern (20 bp):
GGTGGTGGTGGGGAGGGACG
Found at i:39853479 original size:21 final size:21
Alignment explanation
Indices: 39853455--39853506 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
39853445 GATGGAGTTC
*
39853455 GTGGAGGTGGAGATTGTACTG
1 GTGGAGGTGGAGACTGTACTG
* *
39853476 GTGGGGGTGGGGACTGTACTG
1 GTGGAGGTGGAGACTGTACTG
* *
39853497 CTGGTGGTGG
1 GTGGAGGTGG
39853507 TGGTGGGGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.08, G:0.54, T:0.27
Consensus pattern (21 bp):
GTGGAGGTGGAGACTGTACTG
Found at i:39853526 original size:21 final size:21
Alignment explanation
Indices: 39853502--39853581 Score: 97
Period size: 21 Copynumber: 3.5 Consensus size: 21
39853492 TACTGCTGGT
*
39853502 GGTGGTGGTGGGGAGTGGACG
1 GGTGGTGGTGGGGAGTAGACG
39853523 GGTGGGGGTGGTGGTGGTGAGTAGACG
1 GGT---GGTGGT-G-GG-GAGTAGACG
39853550 GGTGGTGGTGGGGAGTAGACG
1 GGTGGTGGTGGGGAGTAGACG
39853571 GGTGGTGGTGG
1 GGTGGTGGTGG
39853582 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
21 23 0.44
22 2 0.04
23 1 0.02
24 12 0.23
25 1 0.02
26 2 0.04
27 11 0.21
ACGTcount: A:0.10, C:0.04, G:0.65, T:0.21
Consensus pattern (21 bp):
GGTGGTGGTGGGGAGTAGACG
Found at i:39853532 original size:27 final size:27
Alignment explanation
Indices: 39853474--39853560 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
39853464 GAGATTGTAC
* * * * *
39853474 TGGTGGGGGTGGGGACTGTACTGCTGG
1 TGGTGGTGGTGGGGAGTGGACGGGTGG
39853501 TGGTGGTGGTGGGGAGTGGACGGGTGG
1 TGGTGGTGGTGGGGAGTGGACGGGTGG
* * *
39853528 GGGTGGTGGTGGTGAGTAGACGGGTGG
1 TGGTGGTGGTGGGGAGTGGACGGGTGG
39853555 TGGTGG
1 TGGTGG
39853561 GGAGTAGACG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.08, C:0.06, G:0.62, T:0.24
Consensus pattern (27 bp):
TGGTGGTGGTGGGGAGTGGACGGGTGG
Found at i:39853580 original size:27 final size:27
Alignment explanation
Indices: 39853498--39853581 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
39853488 ACTGTACTGC
*
39853498 TGGTGGTGGTGGTGGGGAGTGGACGGG
1 TGGTGGTGGTGGTGGGGAGTAGACGGG
* *
39853525 TGGGGGTGGTGGTGGTGAGTAGAC---
1 TGGTGGTGGTGGTGGGGAGTAGACGGG
39853549 --G-GGTGGTGGTGGGGAGTAGACGGG
1 TGGTGGTGGTGGTGGGGAGTAGACGGG
39853573 TGGTGGTGG
1 TGGTGGTGG
39853582 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
21 19 0.40
22 1 0.02
26 1 0.02
27 26 0.55
ACGTcount: A:0.10, C:0.04, G:0.64, T:0.23
Consensus pattern (27 bp):
TGGTGGTGGTGGTGGGGAGTAGACGGG
Found at i:39856204 original size:16 final size:17
Alignment explanation
Indices: 39856185--39856224 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39856175 TCTTGAGGTA
*
39856185 AAATTAATTT-AAGTTT
1 AAATTAATTTAAAATTT
*
39856201 AAATTATTTTAAAATTT
1 AAATTAATTTAAAATTT
39856218 AAATTAA
1 AAATTAA
39856225 ACAAGTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAATTAATTTAAAATTT
Done.