Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 136 of 208
Found at i:41620361 original size:8 final size:8
Alignment explanation
Indices: 41620348--41620415 Score: 59
Period size: 8 Copynumber: 8.8 Consensus size: 8
41620338 ACCACATTTT
41620348 AATAAACA
1 AATAAACA
*
41620356 AATAAACG
1 AATAAACA
*
41620364 AA-ACA-A
1 AATAAACA
***
41620370 AATAATTG
1 AATAAACA
41620378 AATAAACA
1 AATAAACA
*
41620386 AACAAACA
1 AATAAACA
*
41620394 AACAAACA
1 AATAAACA
41620402 AATAAACA
1 AATAAACA
41620410 AATAAA
1 AATAAA
41620416 TCGATCACAT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 42 0.89
ACGTcount: A:0.72, C:0.13, G:0.03, T:0.12
Consensus pattern (8 bp):
AATAAACA
Found at i:41620416 original size:4 final size:4
Alignment explanation
Indices: 41620381--41620411 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
41620371 ATAATTGAAT
*
41620381 AAAC AAAC AAAC AAAC AAAC AAAT AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
41620412 TAAATCGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.19, G:0.00, T:0.03
Consensus pattern (4 bp):
AAAC
Found at i:41620416 original size:12 final size:12
Alignment explanation
Indices: 41620378--41620416 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
41620368 AAAATAATTG
41620378 AATAAACAAACA
1 AATAAACAAACA
*
41620390 AACAAACAAACA
1 AATAAACAAACA
*
41620402 AATAAACAAATA
1 AATAAACAAACA
41620414 AAT
1 AAT
41620417 CGATCACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.10
Consensus pattern (12 bp):
AATAAACAAACA
Found at i:41622486 original size:40 final size:40
Alignment explanation
Indices: 41622436--41622886 Score: 275
Period size: 40 Copynumber: 10.8 Consensus size: 40
41622426 GTCTCTTCTG
*
41622436 TCTGCTCCACTACTGCTTACGGAGATAAGACTGGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGA
* * *
41622476 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C--TGGATGTGA
** * * * **
41622519 TCTGCTCCACTACAACTTCAGGGAGATAGGA-TTGATTTCT
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTGGATGTGA
* *
41622559 TCTGTGTGTTCCACTACTGCTTAGGGAGATAAGACTGGATGCGA
1 TC----TGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGA
* * *
41622603 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT--GGATGTGA
* * * * * *
41622646 TCCGCTCCACT-GTAACTTCAGGGAGATAGGA-TTGATTTCTTCTG-
1 TCTGCTCCACTACT-GCTT-AGGGAGATAAGACTGGA-----TGTGA
* *
41622690 TCTGCTCCACTACTGCTTAAGGAGATAAGACTGGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGA
* * * * *
41622730 TCTGCTCCACTGCTGCTTAAGGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C--TGGATGTGA
* ** * * *
41622773 TCTGCTCCACTGCAACTTCAGGGAGATATGA-TTGATTTCTTCTG-
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTGGA-----TGTGA
* * *
41622817 TCTGCTCCACTACCGTTTAGGGAGATAAGACTGAATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGA
41622857 TCTGCTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
41622887 TCAGTGGTTT
Statistics
Matches: 314, Mismatches: 64, Indels: 66
0.71 0.14 0.15
Matches are distributed among these distances:
39 5 0.02
40 123 0.39
41 4 0.01
42 2 0.01
43 92 0.29
44 83 0.26
45 5 0.02
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGA
Found at i:41622585 original size:87 final size:85
Alignment explanation
Indices: 41622476--41622887 Score: 278
Period size: 87 Copynumber: 4.9 Consensus size: 85
41622466 CTGGATGTGA
41622476 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCACTACAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCACTACAACTT-AGG
*
41622541 GAGATAGGATTGATTTCTTCTG
65 GAGATAAGATTGATTT-TTCTG
* * * *** **
41622563 TGTGTTCCACTACTGCTTAGGGAGATAAGA-C--TGGATGCGATCTGCTCCACTACTGCTTAGGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCACTACAACTTAGGG
** **
41622625 AGATAAGATCTGCGGTTTT-AA
66 AGATAAGAT-TG-ATTTTTCTG
* * * * ** **
41622646 TCCGCTCCACT-GTAACTTCAGGGAGATAGGAT-TGAT--TTCTTCTGTCTGCTCCACTACTGCT
1 TCTGCTCCACTACT-GCTT-AGGGAGATAAGATCTG-TGGTT-TT-AATCTGCTCCACTACAACT
* * *
41622707 TAAGGAGATAAGACTGGA---TGC-G
61 TAGGGAGATAAGA-TTGATTTTTCTG
* * *
41622729 ATCTGCTCCACTGCTGCTTAAGGAGATAAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAG
1 -TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCACTACAACTT-AG
*
41622794 GGAGATATGATTGATTTCTTCTG
64 GGAGATAAGATTGATTT-TTCTG
* * ** * * **
41622817 TCTGCTCCACTACCGTTTAGGGAGATAAGA-C--TGAATGTGATCTGCTCCACTACTGCTTAGGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCACTACAACTTAGGG
41622879 AGATAAGAT
66 AGATAAGAT
41622888 CAGTGGTTTT
Statistics
Matches: 247, Mismatches: 55, Indels: 50
0.70 0.16 0.14
Matches are distributed among these distances:
82 1 0.00
83 66 0.27
84 83 0.34
85 6 0.02
86 2 0.01
87 87 0.35
88 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (85 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCACTACAACTTAGGG
AGATAAGATTGATTTTTCTG
Found at i:41622609 original size:127 final size:127
Alignment explanation
Indices: 41622383--41622937 Score: 903
Period size: 127 Copynumber: 4.4 Consensus size: 127
41622373 ATAGGATTTA
* * * *
41622383 TGGTTTTAATCTGCTCCACTGAAACTTAAGGGAGATAGGATTGGTCTCTTCTGTCTGCTCCACTA
1 TGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTA
* *
41622448 CTGCTTACGGAGATAAGACTGGATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
66 CTGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
* * *
41622510 TGGTTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGATTGATTTCTTCTGTGTGTTCCACTA
1 TGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTA
41622575 CTGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
66 CTGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
* * *
41622637 CGGTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTA
1 TGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTA
* * *
41622702 CTGCTTAAGGAGATAAGACTGGATGCGATCTGCTCCACTGCTGCTTAAGGAGATAAGATCTG
66 CTGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
*
41622764 TGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATATGATTGATTTCTTCTGTCTGCTCCACTA
1 TGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTA
* * * * *
41622829 CCGTTTAGGGAGATAAGACTGAATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCAG
66 CTGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
* *
41622891 TGGTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGATTT
1 TGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGATTT
41622938 TTTTCTTTAT
Statistics
Matches: 395, Mismatches: 33, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
127 395 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (127 bp):
TGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCCACTA
CTGCTTAGGGAGATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
Found at i:41623118 original size:100 final size:100
Alignment explanation
Indices: 41622941--41623556 Score: 851
Period size: 100 Copynumber: 6.2 Consensus size: 100
41622931 TTGATTTTTT
* * * * * * *
41622941 TCTTTATAATTGTAATGTCGGGGAA-CACGATTCATCGTTGTAGCTTCAAT-TAGTTCCACTGCA
1 TCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCT-GCTCCACTGCA
* * *
41623004 CCACCA-AGGAAGTAAGATTCGCCGTTGCAGCTTCAA
65 CCGCCAGA-AAAGTAAGATTCGCCGTTGCGGCTTCAA
*
41623040 TCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGTTTTAATCTGCTCCACTGCAC
1 TCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCAC
*
41623105 CGCCAGAAAAGTAAGATTCACCGTTGCGGCTTCAA
66 CGCCAGAAAAGTAAGATTCGCCGTTGCGGCTTCAA
* ** * * * *
41623140 TATTTGAAATTACAATGTCGGGGAAGCAAGATTCGCCATCGTAGCTTTAATTTGCTCCACTGCAC
1 TCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCAC
* * *
41623205 CGCCAGGAAAGTAAGATTCGCTGTTGCAGCTTCAA
66 CGCCAGAAAAGTAAGATTCGCCGTTGCGGCTTCAA
* * *
41623240 TATTTTTAATTGCAATGTTGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCAC
1 TCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCAC
* *
41623305 CACCAGAAAAGTAAGATTTGCCGTTGCGGCTTCAA
66 CGCCAGAAAAGTAAGATTCGCCGTTGCGGCTTCAA
* * *
41623340 TCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCACCGTCATAGCTTTAATCTGCTCCACTGCAT
1 TCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCAC
*
41623405 CGCCAGAAAATTAAGATTCGCCGTTGCGGCTTCAA
66 CGCCAGAAAAGTAAGATTCGCCGTTGCGGCTTCAA
* * * * *
41623440 TCTTTTAAATTGCAATGTCGGGGAAGCAATATTCGCCATCGTAGCTTTAATCTGCTCCATTGCAC
1 TCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCAC
* *
41623505 CGCCAGGAAAGTAAGATTCGCCATTGCGGCTTCAA
66 CGCCAGAAAAGTAAGATTCGCCGTTGCGGCTTCAA
41623540 TCTTTTTAATTGCAATG
1 TCTTTTTAATTGCAATG
41623557 GTGGGTATGA
Statistics
Matches: 460, Mismatches: 54, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
99 23 0.05
100 435 0.95
101 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (100 bp):
TCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCAC
CGCCAGAAAAGTAAGATTCGCCGTTGCGGCTTCAA
Found at i:41623522 original size:300 final size:299
Alignment explanation
Indices: 41622947--41623561 Score: 937
Period size: 300 Copynumber: 2.1 Consensus size: 299
41622937 TTTTTCTTTA
* * * * * *
41622947 TAATTGTAATGTCGGGGAACACGATTCATCGTTGTAGCTTCAATTAGTTCCACTGCACCACCAAG
1 TAATTGCAATGTTGGGGAACAAGATTCACCGTCGTAGCTTCAATTAGCTCCACTGCACCACCAAG
* *
41623012 GAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACC
66 AAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCACC
* *
41623077 GTCGTAGTTTTAATCTGCTCCACTGCACCGCCAGAAAAGTAAGATTCACCGTTGCGGCTTCAATA
131 GTCATAGCTTTAATCTGCTCCACTGCACCGCCAGAAAAGTAAGATTCACCGTTGCGGCTTCAATA
*
41623142 TTTGAAATTACAATGTCGGGGAAGCAAGATTCGCCATCGTAGCTTTAATTTGCTCCACTGCACCG
196 TTTGAAATTACAATGTCGGGGAAGCAAGATTCGCCATCGTAGCTTTAATCTGCTCCACTGCACCG
**
41623207 CCAGGAAAGTAAGATTCGCTGTTGCAGCTTCAATATTTT
261 CCAGGAAAGTAAGATTCGCCATTGCAGCTTCAATATTTT
* *
41623246 TAATTGCAATGTTGGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCT-GCTCCACTGCACCACC-
1 TAATTGCAATGTTGGGGAA-CAAGATTCACCGTCGTAGCTTCAAT-TAGCTCCACTGCACCACCA
* *
41623309 AGAAAAGTAAGATTTGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTC
64 AG-AAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTC
* * *
41623374 ACCGTCATAGCTTTAATCTGCTCCACTGCATCGCCAGAAAATTAAGATTCGCCGTTGCGGCTTCA
128 ACCGTCATAGCTTTAATCTGCTCCACTGCACCGCCAGAAAAGTAAGATTCACCGTTGCGGCTTCA
* * * * *
41623439 ATCTTTTAAATTGCAATGTCGGGGAAGCAATATTCGCCATCGTAGCTTTAATCTGCTCCATTGCA
193 ATATTTGAAATTACAATGTCGGGGAAGCAAGATTCGCCATCGTAGCTTTAATCTGCTCCACTGCA
* *
41623504 CCGCCAGGAAAGTAAGATTCGCCATTGCGGCTTCAATCTTTT
258 CCGCCAGGAAAGTAAGATTCGCCATTGCAGCTTCAATATTTT
*
41623546 TAATTGCAATGGTGGG
1 TAATTGCAATGTTGGG
41623562 TATGAATAAC
Statistics
Matches: 285, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
299 19 0.07
300 265 0.93
301 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (299 bp):
TAATTGCAATGTTGGGGAACAAGATTCACCGTCGTAGCTTCAATTAGCTCCACTGCACCACCAAG
AAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCACC
GTCATAGCTTTAATCTGCTCCACTGCACCGCCAGAAAAGTAAGATTCACCGTTGCGGCTTCAATA
TTTGAAATTACAATGTCGGGGAAGCAAGATTCGCCATCGTAGCTTTAATCTGCTCCACTGCACCG
CCAGGAAAGTAAGATTCGCCATTGCAGCTTCAATATTTT
Found at i:41624560 original size:5 final size:5
Alignment explanation
Indices: 41624552--41624594 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
41624542 TTTTTCGTTC
* *
41624552 TTCTT TTCTT TTCTTT TTCTT TTCAT TT-TT TTCTT TTTTT TTC
1 TTCTT TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT TTCTT TTC
41624595 AAGTGAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.09
5 24 0.75
6 5 0.16
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:41624582 original size:19 final size:18
Alignment explanation
Indices: 41624536--41624594 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 18
41624526 GGCCTCTCCT
*
41624536 TTTTCTTTTTTCGTTCTTC
1 TTTTCTTTTTTC-TTTTTC
41624555 TTTTC--TTTTCTTTTTC
1 TTTTCTTTTTTCTTTTTC
41624571 TTTTCATTTTTTTCTTTTT-
1 TTTTC--TTTTTTCTTTTTC
41624590 TTTTC
1 TTTTC
41624595 AAGTGAAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 10 0.29
17 5 0.14
19 10 0.29
20 10 0.29
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTTTC
Found at i:41625037 original size:18 final size:18
Alignment explanation
Indices: 41625013--41625084 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
41625003 CCCGGTAGAG
41625013 TTTTTTT-ATTTTTTTCT
1 TTTTTTTGATTTTTTTCT
* * *
41625030 CATTTTTTGCTTTTTTACT
1 -TTTTTTTGATTTTTTTCT
41625049 TTTTTTTGCATTTTTTTCT
1 TTTTTTTG-ATTTTTTTCT
*
41625068 TTTTTTTTACTTTTTTT
1 TTTTTTTGA-TTTTTTT
41625085 ACCTCCACTG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 14 0.32
19 30 0.68
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTTTTGATTTTTTTCT
Found at i:41625062 original size:38 final size:36
Alignment explanation
Indices: 41625013--41625083 Score: 97
Period size: 38 Copynumber: 1.9 Consensus size: 36
41625003 CCCGGTAGAG
*
41625013 TTTTTTTATTTTTTTCTCATTTTTTGCTTTTTTACT
1 TTTTTTTATTTTTTTCTCATTTTTTACTTTTTTACT
**
41625049 TTTTTTTGCATTTTTTTCTTTTTTTTTACTTTTTT
1 TTTTTTT--ATTTTTTTCTCATTTTTTACTTTTTT
41625084 TACCTCCACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 7 0.23
38 23 0.77
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.80
Consensus pattern (36 bp):
TTTTTTTATTTTTTTCTCATTTTTTACTTTTTTACT
Found at i:41625082 original size:27 final size:26
Alignment explanation
Indices: 41625014--41625072 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
41625004 CCGGTAGAGT
41625014 TTTTTTATTTTTTTCT-CATTTTTTGC
1 TTTTTTATTTTTTT-TGCATTTTTTGC
*
41625040 TTTTTTACTTTTTTTTGCATTTTTTTC
1 TTTTTTA-TTTTTTTTGCATTTTTTGC
41625067 TTTTTT
1 TTTTTT
41625073 TTTACTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.80
Consensus pattern (26 bp):
TTTTTTATTTTTTTTGCATTTTTTGC
Found at i:41628452 original size:8 final size:8
Alignment explanation
Indices: 41628439--41628506 Score: 59
Period size: 8 Copynumber: 8.8 Consensus size: 8
41628429 ACCACATTTT
41628439 AATAAACA
1 AATAAACA
*
41628447 AATAAACG
1 AATAAACA
*
41628455 AA-ACA-A
1 AATAAACA
***
41628461 AATAATTG
1 AATAAACA
41628469 AATAAACA
1 AATAAACA
*
41628477 AACAAACA
1 AATAAACA
*
41628485 AACAAACA
1 AATAAACA
41628493 AATAAACA
1 AATAAACA
41628501 AATAAA
1 AATAAA
41628507 TCGATCACAT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 42 0.89
ACGTcount: A:0.72, C:0.13, G:0.03, T:0.12
Consensus pattern (8 bp):
AATAAACA
Found at i:41628507 original size:4 final size:4
Alignment explanation
Indices: 41628472--41628502 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
41628462 ATAATTGAAT
*
41628472 AAAC AAAC AAAC AAAC AAAC AAAT AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
41628503 TAAATCGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.19, G:0.00, T:0.03
Consensus pattern (4 bp):
AAAC
Found at i:41628507 original size:12 final size:12
Alignment explanation
Indices: 41628469--41628507 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
41628459 AAAATAATTG
41628469 AATAAACAAACA
1 AATAAACAAACA
*
41628481 AACAAACAAACA
1 AATAAACAAACA
*
41628493 AATAAACAAATA
1 AATAAACAAACA
41628505 AAT
1 AAT
41628508 CGATCACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.10
Consensus pattern (12 bp):
AATAAACAAACA
Found at i:41638028 original size:69 final size:69
Alignment explanation
Indices: 41637917--41638047 Score: 181
Period size: 69 Copynumber: 1.9 Consensus size: 69
41637907 CTTTTTTGTC
* * * * *
41637917 GTATTAGTTTTGTCTCATAAATTGAAAAATTAAATATAAAATATAAGGTTTTAACTTAATTATGT
1 GTATTAGTATTGTCTCACAAATTAAAAAATTAAATACAAAATATAAGATTTTAACTTAATTATGT
41637982 ATTT
66 ATTT
* * **
41637986 GTATTAGTATTGTTTGACAAATTAAAAAATTATGTACAAAATATAAGATTTTAACTTAATTA
1 GTATTAGTATTGTCTCACAAATTAAAAAATTAAATACAAAATATAAGATTTTAACTTAATTA
41638048 CGTGGACTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (69 bp):
GTATTAGTATTGTCTCACAAATTAAAAAATTAAATACAAAATATAAGATTTTAACTTAATTATGT
ATTT
Found at i:41642307 original size:18 final size:17
Alignment explanation
Indices: 41642284--41642337 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
41642274 GATTAATAAC
41642284 AAAGAAAAAACAGAAAAG
1 AAAGAAAAAAC-GAAAAG
*
41642302 AAAGAAAAAACGACAGAG
1 AAAGAAAAAACGA-AAAG
*
41642320 AAA-AAAAGACGAAAAG
1 AAAGAAAAAACGAAAAG
41642336 AA
1 AA
41642338 CACCTTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 5 0.16
17 10 0.31
18 17 0.53
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAACGAAAAG
Found at i:41644743 original size:12 final size:12
Alignment explanation
Indices: 41644722--41644761 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
41644712 CACACGGACG
*
41644722 TGTGCCAGGCCA
1 TGTGCGAGGCCA
41644734 TGTG-GTAGGCCA
1 TGTGCG-AGGCCA
41644746 TGTGCGAGGCCA
1 TGTGCGAGGCCA
41644758 TGTG
1 TGTG
41644762 TGACACACGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 24 0.96
13 1 0.04
ACGTcount: A:0.15, C:0.23, G:0.40, T:0.23
Consensus pattern (12 bp):
TGTGCGAGGCCA
Found at i:41646956 original size:18 final size:18
Alignment explanation
Indices: 41646933--41646974 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
41646923 ATAAAAATTC
*
41646933 ACTTTCTGTTTGTTTGTT
1 ACTTTCTGTTTGTTTATT
41646951 ACTTTCTGTTTGTTTATT
1 ACTTTCTGTTTGTTTATT
41646969 ACTTTC
1 ACTTTC
41646975 AGGTAACCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.14, G:0.12, T:0.64
Consensus pattern (18 bp):
ACTTTCTGTTTGTTTATT
Found at i:41655787 original size:38 final size:38
Alignment explanation
Indices: 41655743--41655820 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
41655733 ACACAATCAC
*
41655743 CTTACCTACTAAACGAGTAACGACAGAACCACACCTCT
1 CTTACCTACTAAACGAGTAACGACAGAACCACACCGCT
* *
41655781 CTTACCTACTAAACGAGTAACGGCAGAGCCACACCGCT
1 CTTACCTACTAAACGAGTAACGACAGAACCACACCGCT
41655819 CT
1 CT
41655821 AATGCTAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.35, G:0.14, T:0.18
Consensus pattern (38 bp):
CTTACCTACTAAACGAGTAACGACAGAACCACACCGCT
Found at i:41656325 original size:21 final size:21
Alignment explanation
Indices: 41656299--41656338 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41656289 TACCCCTTAA
41656299 ATCCCTTAA-TTAACTCCCCTT
1 ATCCC-TAATTTAACTCCCCTT
*
41656320 ATCCCTAATTTCACTCCCC
1 ATCCCTAATTTAACTCCCC
41656339 AACCATCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (21 bp):
ATCCCTAATTTAACTCCCCTT
Found at i:41666224 original size:3 final size:3
Alignment explanation
Indices: 41666216--41666247 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41666206 AAGTATGAAC
41666216 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41666248 GAAGAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41670925 original size:15 final size:15
Alignment explanation
Indices: 41670905--41670954 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
41670895 GGGGTAGGAC
*
41670905 ATGATATGATATAAT
1 ATGATAAGATATAAT
* * *
41670920 ATGATACGGTATATT
1 ATGATAAGATATAAT
41670935 ATGATAAGATATAAT
1 ATGATAAGATATAAT
*
41670950 TTGAT
1 ATGAT
41670955 GAAAAATCTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (15 bp):
ATGATAAGATATAAT
Found at i:41673470 original size:41 final size:41
Alignment explanation
Indices: 41673413--41673507 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
41673403 GGTCAACATG
* *
41673413 CCCATGTGAGGGGGAGACATGCCCGTATGAGGAAACACACA
1 CCCATGTGAGAGGGAGACACGCCCGTATGAGGAAACACACA
* * *
41673454 CCCATGTGAGAGGGAGACACGCTCGTGTGAGGAAACACACG
1 CCCATGTGAGAGGGAGACACGCCCGTATGAGGAAACACACA
*
41673495 CCCGTGTGAGAGG
1 CCCATGTGAGAGG
41673508 AGGCACACGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.28, C:0.24, G:0.35, T:0.13
Consensus pattern (41 bp):
CCCATGTGAGAGGGAGACACGCCCGTATGAGGAAACACACA
Found at i:41673514 original size:22 final size:22
Alignment explanation
Indices: 41673448--41673525 Score: 56
Period size: 22 Copynumber: 3.7 Consensus size: 22
41673438 TATGAGGAAA
* *
41673448 CACACACCCATGTGAGAGG-GAG
1 CACACGCCCGTGTGAGAGGAG-G
* **
41673470 -ACACGCTCGTGT--GAGGAAA
1 CACACGCCCGTGTGAGAGGAGG
41673489 CACACGCCCGTGTGAGAGGAGG
1 CACACGCCCGTGTGAGAGGAGG
* *
41673511 CACACGGCTGTGTGA
1 CACACGCCCGTGTGA
41673526 CTAAGGCATA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
19 4 0.10
20 11 0.26
21 9 0.21
22 18 0.43
ACGTcount: A:0.27, C:0.26, G:0.35, T:0.13
Consensus pattern (22 bp):
CACACGCCCGTGTGAGAGGAGG
Found at i:41675352 original size:2 final size:2
Alignment explanation
Indices: 41675347--41675386 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
41675337 CTCTCTCTCC
41675347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41675387 GAGACAAGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41676948 original size:14 final size:14
Alignment explanation
Indices: 41676929--41676958 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41676919 ATTTCGGATT
41676929 ATCCAAATCCACAA
1 ATCCAAATCCACAA
*
41676943 ATCCAAGTCCACAA
1 ATCCAAATCCACAA
41676957 AT
1 AT
41676959 TATCGAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.33, G:0.03, T:0.17
Consensus pattern (14 bp):
ATCCAAATCCACAA
Found at i:41677431 original size:114 final size:113
Alignment explanation
Indices: 41677259--41677900 Score: 604
Period size: 113 Copynumber: 5.6 Consensus size: 113
41677249 CGTAGCGTTC
* * * * * *
41677259 TGGTCTTGATGTATATTGGAATTAGTGGCGCTTACGAA-CAAACGCCGGTAATGCATAGTATTAG
1 TGGTCTTGATGTATATTAGAATTAGTGGCGCTTA-TAAGAAAACGCCGCTAAAGTATAGTATTAG
*
41677323 CGGCGCTTAGCAG-AAGCGCCGCAAAAGATGTTAACCAAAACGCAGAGTT
65 CGGCGCTTAGC-GTAAGCGCCGCAAAAGATCTTAACCAAAACGCAGAGTT
* * *
41677372 TGGTCTTGATGTATATTACAATTAGTGGCGCTTATAAAGAAAACGCCGCTAATGTATAGTACTAG
1 TGGTCTTGATGTATATTAGAATTAGTGGCGCTTAT-AAGAAAACGCCGCTAAAGTATAGTATTAG
* * * *
41677437 CGGCGCTGAGCGTTAAACGCCGCAAAACATCTTAACCAAAACGCAGCGTTT
65 CGGCGCTTAGCG-TAAGCGCCGCAAAAGATCTTAACCAAAACGCAGAG-TT
* * * * * *
41677488 TGGTCTTGATGTATACTATAATTAGTGGCG-TT-TAAGGAAAACGTCACTAAAGGATAGTAATAG
1 TGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAA-GAAAACGCCGCTAAAGTATAGTATTAG
* * * * * * *
41677551 CAGCGTTTGGTGGTAAGCGCCTCAAAATATCTTAACCAAAACGGAGAGTT
65 CGGCGCTTAG-CGTAAGCGCCGCAAAAGATCTTAACCAAAACGCAGAGTT
* * *
41677601 TGGTCTTGAGGTATATTAGAATTAGTGGCGCTTACT-GGAAAACGCCGCTAAAGTATAGTAGTAG
1 TGGTCTTGATGTATATTAGAATTAGTGGCGCTTA-TAAGAAAACGCCGCTAAAGTATAGTATTAG
* * * *
41677665 CGGCG-TTTGTGGAAACCGCCGC-AAAGTATCTTAACCAAAACGCAGAGTT
65 CGGCGCTTAG-CGTAAGCGCCGCAAAAG-ATCTTAACCAAAACGCAGAGTT
* * * * *
41677714 TGGTCTTGAGGTATATTAGAATTAGTGGCGCTTAT-TGAAAAACGCCGCTAATGGT-TACTATTT
1 TGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAG-AAAACGCCGCTAA-AGTATAGTATTA
* * * *
41677777 GCGGCGCTTTTG-GTAAGCGCCGCAAAAAGATATTAACGAAAACACA-ACGTT
64 GCGGCGC-TTAGCGTAAGCGCCGC-AAAAGATCTTAACCAAAACGCAGA-GTT
* * ** ** *
41677828 TGGTTCTTGATGTATACTGGAATTAGTGGCGCACATGGGAAAACGCCGCTAAAGCATAGTATTAG
1 TGG-TCTTGATGTATATTAGAATTAGTGGCGCTTATAAGAAAACGCCGCTAAAGTATAGTATTAG
*
41677893 CGTCGCTT
65 CGGCGCTT
41677901 TTCCCAAAAT
Statistics
Matches: 443, Mismatches: 65, Indels: 41
0.81 0.12 0.07
Matches are distributed among these distances:
112 5 0.01
113 168 0.38
114 145 0.33
115 93 0.21
116 32 0.07
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (113 bp):
TGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAGAAAACGCCGCTAAAGTATAGTATTAGC
GGCGCTTAGCGTAAGCGCCGCAAAAGATCTTAACCAAAACGCAGAGTT
Found at i:41678576 original size:80 final size:79
Alignment explanation
Indices: 41678415--41678578 Score: 188
Period size: 80 Copynumber: 2.1 Consensus size: 79
41678405 TTCGGTGTCA
* * * *
41678415 GGTTAGGCTTTAGGGTTTAGATTAATTAGTGTGTTTTAATTTTTATAAAATATGGTTTAAGGGTA
1 GGTTAGGATTTAGGGTTTAGATTAATTAATATGTTTTAATTTTTATAAAATAAGGTTTAAGGGTA
**
41678480 GGGGTTAGGGATTCG
66 GGAATTAGGGA-TCG
* * *
41678495 GGTTAGGATTTAGGGTTTTGATTAATTAATATTTTTTAATTTATGTATTAAATAAGGTTT-AGGG
1 GGTTAGGATTTAGGGTTTAGATTAATTAATATGTTTTAATTT-T-TATAAAATAAGGTTTAAGGG
*
41678559 TTAGTAATTAGGG-TCG
64 -TAGGAATTAGGGATCG
41678575 GGTT
1 GGTT
41678579 TATGGGTTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
80 44 0.62
81 5 0.07
82 22 0.31
ACGTcount: A:0.26, C:0.02, G:0.27, T:0.45
Consensus pattern (79 bp):
GGTTAGGATTTAGGGTTTAGATTAATTAATATGTTTTAATTTTTATAAAATAAGGTTTAAGGGTA
GGAATTAGGGATCG
Found at i:41679655 original size:43 final size:43
Alignment explanation
Indices: 41679592--41679677 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
41679582 AGCGACTGCG
*
41679592 TTTTGACTTATATTTAGTGGCGCTTAGTTTAAAACGCCGCAAA
1 TTTTGACTTATATTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
*
41679635 TTTTGACTTATAGTTT-GTGGCGCTTTGCTTAAAACGCCGCAAA
1 TTTTGACTTATA-TTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
41679678 AATGTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 37 0.93
44 3 0.08
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (43 bp):
TTTTGACTTATATTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
Found at i:41681040 original size:10 final size:10
Alignment explanation
Indices: 41681025--41681063 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
41681015 GTTTCGGGTA
41681025 AATTTTATAT
1 AATTTTATAT
41681035 AATTTTATAT
1 AATTTTATAT
* *
41681045 AATTGTATTT
1 AATTTTATAT
41681055 AATTTTATA
1 AATTTTATA
41681064 ATTATTCGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
AATTTTATAT
Found at i:41681544 original size:13 final size:13
Alignment explanation
Indices: 41681528--41681586 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
41681518 TTACTAAAAT
*
41681528 TTACTTTAATATA
1 TTACTTAAATATA
*
41681541 TTACTTGAATATA
1 TTACTTAAATATA
41681554 TTACTTAAATA-A
1 TTACTTAAATATA
*
41681566 TTTACTTAAATACA
1 -TTACTTAAATATA
41681580 TTACTTA
1 TTACTTA
41681587 CTAAAATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
12 1 0.02
13 40 0.95
14 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:41681655 original size:49 final size:47
Alignment explanation
Indices: 41681558--41681656 Score: 128
Period size: 49 Copynumber: 2.1 Consensus size: 47
41681548 AATATATTAC
***
41681558 TTAAATAATTTACTTAAATACATTACTTACTAAAATTTGTTTAAATA
1 TTAAATAATTTACTTAAATACATTACTTACTAAAATTTAAGTAAATA
*
41681605 TTAAATACA-TTACTTAAATATACATTACTTACTAAAATTTAAGTATATA
1 TTAAATA-ATTTACTT-AA-ATACATTACTTACTAAAATTTAAGTAAATA
41681654 TTA
1 TTA
41681657 CATTACTTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
47 13 0.29
48 3 0.07
49 29 0.64
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (47 bp):
TTAAATAATTTACTTAAATACATTACTTACTAAAATTTAAGTAAATA
Found at i:41681659 original size:45 final size:45
Alignment explanation
Indices: 41681558--41681665 Score: 116
Period size: 45 Copynumber: 2.4 Consensus size: 45
41681548 AATATATTAC
41681558 TTAAATA-ATTTACTT-AAATACATTACTTACTAAAATTTGTTTAAATA
1 TTAAATACA-TTACTTAAAATACATTACTTACTAAAA--T-TTTAAATA
*
41681605 TTAAATACATTACTTAAATATACATTACTTACTAAAA-TTTAAGTA
1 TTAAATACATTACTTAAA-ATACATTACTTACTAAAATTTTAAATA
*
41681650 -TATATTACATTACTTA
1 TTA-AATACATTACTTA
41681666 CATAACTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
44 2 0.04
45 19 0.35
47 13 0.24
48 3 0.05
49 18 0.33
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (45 bp):
TTAAATACATTACTTAAAATACATTACTTACTAAAATTTTAAATA
Found at i:41681717 original size:19 final size:18
Alignment explanation
Indices: 41681683--41681718 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41681673 TGTTAAAATA
*
41681683 TATTATATTTTCAATATT
1 TATTATATTTTAAATATT
41681701 TATTATATTTTTAAATAT
1 TATTATA-TTTTAAATAT
41681719 ATTTTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATATTTTAAATATT
Found at i:41681898 original size:13 final size:13
Alignment explanation
Indices: 41681865--41681933 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
41681855 AACATATTTT
41681865 TTAC-TAAA-ATA
1 TTACTTAAATATA
*
41681876 -TACTTTAATATA
1 TTACTTAAATATA
*
41681888 TTACTTGAATATA
1 TTACTTAAATATA
41681901 TTACTTAAATA-A
1 TTACTTAAATATA
*
41681913 TTTACTTAAATACA
1 -TTACTTAAATATA
41681927 TTACTTA
1 TTACTTA
41681934 CTAAAATTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
10 3 0.06
11 3 0.06
12 4 0.08
13 39 0.78
14 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.45
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:41681981 original size:347 final size:343
Alignment explanation
Indices: 41681343--41682043 Score: 1285
Period size: 347 Copynumber: 2.0 Consensus size: 343
41681333 AAAGTTAATA
41681343 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAA
1 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAA
41681408 ATATATATTGTTAAGTAATAATTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTA
66 ATATATATTGTTAAGTAATAATTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTA
*
41681473 AGTATATTCTACATGACTTACATATAACTTACTAAAACATATTTTTTACTAAAATTTACTTTAAT
131 AGTATATTCTACATGACTTACATATAACTTACTAAAACATATTTTTTACTAAAATATACTTTAAT
*
41681538 ATATTACTTGAATATATTACTTAAATAATTTACTTAAATACATTACTTACTAAAATTTGTTTAAA
196 ATATTACTTGAATATATTACTTAAATAATTTACTTAAATACATTACTTACTAAAATTTGTCTAAA
41681603 TATTAAATACATTACTTAAATATACATTACTTACTAAAATTTAAGTATATATTACATTACTTACA
261 TATTAAATACATTACTTAAATATACATTACTTACTAAAATTTAAGTATATATTACATTACTTACA
41681668 TAACTTGTTAAAATATAT
326 TAACTTGTTAAAATATAT
*
41681686 TATATTTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAAACAT
1 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATT--A-AT
*
41681751 ATATATATATATTGTTAAGTAATAATTTTTTAAAATTGATATCTTACATTACTTAAATATATATT
63 A-AAATATATATTGTTAAGTAATAATTTTTTAAAATTGATATCTTACATTACTTAAATATATATT
* *
41681816 TTTAAGTATATTCTACATGACTTACATATTACTTGCTAAAACATATTTTTTACTAAAATATACTT
127 TTTAAGTATATTCTACATGACTTACATATAACTTACTAAAACATATTTTTTACTAAAATATACTT
41681881 TAATATATTACTTGAATATATTACTTAAATAATTTACTTAAATACATTACTTACTAAAATTTGTC
192 TAATATATTACTTGAATATATTACTTAAATAATTTACTTAAATACATTACTTACTAAAATTTGTC
* * *
41681946 TAAATTTTAAATACATTACTTAATTATATATTACTTACTAAAATTTAAGTATATATTACATTACT
257 TAAATATTAAATACATTACTTAAATATACATTACTTACTAAAATTTAAGTATATATTACATTACT
41682011 TACATAACTTGTTAAAATATAT
322 TACATAACTTGTTAAAATATAT
41682033 TATAATTTCAA
1 TATAATTTCAA
41682044 AAATAATTAT
Statistics
Matches: 344, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
343 58 0.17
345 1 0.00
346 3 0.01
347 282 0.82
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (343 bp):
TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAA
ATATATATTGTTAAGTAATAATTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTA
AGTATATTCTACATGACTTACATATAACTTACTAAAACATATTTTTTACTAAAATATACTTTAAT
ATATTACTTGAATATATTACTTAAATAATTTACTTAAATACATTACTTACTAAAATTTGTCTAAA
TATTAAATACATTACTTAAATATACATTACTTACTAAAATTTAAGTATATATTACATTACTTACA
TAACTTGTTAAAATATAT
Found at i:41682252 original size:39 final size:38
Alignment explanation
Indices: 41682209--41682311 Score: 136
Period size: 38 Copynumber: 2.7 Consensus size: 38
41682199 CTTACATGTT
* ** *
41682209 AACTTACATAATACATGACTTTTATA-AAATTTTTATATA
1 AACTTACATAATACATTACTTACATATAAA--CTTATATA
*
41682248 AACTTACATAATACATTACTTACATATTAACTTATATA
1 AACTTACATAATACATTACTTACATATAAACTTATATA
41682286 AACTTACATAATACATTACTTACATA
1 AACTTACATAATACATTACTTACATA
41682312 GCATACATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
38 33 0.57
39 23 0.40
40 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.01, T:0.40
Consensus pattern (38 bp):
AACTTACATAATACATTACTTACATATAAACTTATATA
Found at i:41682319 original size:18 final size:16
Alignment explanation
Indices: 41682248--41682327 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 16
41682238 TTTTTATATA
41682248 AACTTACATAATACAT
1 AACTTACATAATACAT
* *
41682264 TACTTACATATTAACTTATAT
1 AACTTAC--A-TAA--TACAT
41682285 AAACTTACATAATACAT
1 -AACTTACATAATACAT
*
41682302 TACTTACATAGCATACAT
1 AACTTACATA--ATACAT
41682320 AACTTACA
1 AACTTACA
41682328 CGACTTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
16 15 0.30
17 4 0.08
18 14 0.28
19 6 0.12
20 1 0.02
21 4 0.08
22 6 0.12
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:41682327 original size:9 final size:9
Alignment explanation
Indices: 41682248--41682500 Score: 140
Period size: 9 Copynumber: 28.8 Consensus size: 9
41682238 TTTTTATATA
41682248 AACTTACAT
1 AACTTACAT
41682257 AA--TACAT
1 AACTTACAT
*
41682264 TACTTACATATT
1 AACTTAC--A-T
*
41682276 AACTTATAT
1 AACTTACAT
41682285 AAACTTACAT
1 -AACTTACAT
41682295 AA--TACAT
1 AACTTACAT
*
41682302 TACTTACAT
1 AACTTACAT
* *
41682311 AGCATACAT
1 AACTTACAT
*
41682320 AACTTACAC
1 AACTTACAT
* *
41682329 GACTTAAAT
1 AACTTACAT
41682338 AA--TACA-
1 AACTTACAT
41682344 AAGCTTACAT
1 AA-CTTACAT
41682354 AACTTACAT
1 AACTTACAT
* *
41682363 AACCTAAAT
1 AACTTACAT
41682372 AA--TACATTAT
1 AACTTAC---AT
41682382 AACTTAC--
1 AACTTACAT
41682389 AACTTACAT
1 AACTTACAT
*
41682398 AACATACAT
1 AACTTACAT
* *
41682407 TACTTTCAT
1 AACTTACAT
41682416 AACTTACAT
1 AACTTACAT
*
41682425 AACTTACAC
1 AACTTACAT
*
41682434 AACTTAAAT
1 AACTTACAT
* *
41682443 AGCTTACTT
1 AACTTACAT
41682452 AA--TACAT
1 AACTTACAT
41682459 AACTTACAT
1 AACTTACAT
41682468 AACTT--AT
1 AACTTACAT
* *
41682475 ACACGTACCT
1 A-ACTTACAT
41682485 AACTTACAT
1 AACTTACAT
*
41682494 AATTTAC
1 AACTTAC
41682501 TTAATACATA
Statistics
Matches: 182, Mismatches: 38, Indels: 48
0.68 0.14 0.18
Matches are distributed among these distances:
6 2 0.01
7 33 0.18
8 3 0.02
9 117 0.64
10 17 0.09
11 1 0.01
12 9 0.05
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:41682353 original size:34 final size:34
Alignment explanation
Indices: 41682306--41682377 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
41682296 ATACATTACT
* * *
41682306 TACATAGCATACATAACTTACACGACTTAAATAA
1 TACAAAGCATACATAACTTACACAACCTAAATAA
* *
41682340 TACAAAGCTTACATAACTTACATAACCTAAATAA
1 TACAAAGCATACATAACTTACACAACCTAAATAA
41682374 TACA
1 TACA
41682378 TTATAACTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (34 bp):
TACAAAGCATACATAACTTACACAACCTAAATAA
Found at i:41688135 original size:21 final size:21
Alignment explanation
Indices: 41688109--41688154 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
41688099 GTACAACTTA
41688109 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
* *
41688130 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
41688151 AAGC
1 AAGC
41688155 GAAGGCCGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.22, G:0.48, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGGG
Found at i:41688551 original size:41 final size:41
Alignment explanation
Indices: 41688495--41688696 Score: 287
Period size: 42 Copynumber: 4.9 Consensus size: 41
41688485 GTTTTTGTAT
* *
41688495 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
* *
41688536 AAAAACGCCGCTAAAGACCATGTTCTTTAGCAGCGCTTAGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
* *
41688577 AGAAAACGCCGCTAAAGATCATCTTCTTTAGCGGCGCTTAAGA
1 A-AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT-AGA
* *
41688620 ATAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
* *
41688661 AATAAACGCCGCTAAAGAACATGATCTTTCGCGGCG
1 AA-AAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
41688697 TTTTTTTCTA
Statistics
Matches: 145, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
41 44 0.30
42 97 0.67
43 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA
Found at i:41689598 original size:29 final size:26
Alignment explanation
Indices: 41689544--41689609 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
41689534 CCTTTAGTTT
* *
41689544 AAGTAAATATTATTTTATGTTTAAAA
1 AAGTAAATAATATTTTATATTTAAAA
*
41689570 AAGTAAATAATATTTTAATAATTTCAAA
1 AAGTAAATAATATTTT-AT-ATTTAAAA
*
41689598 AATTATAATAAT
1 AAGTA-AATAAT
41689610 TAATAACATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 15 0.45
27 2 0.06
28 10 0.30
29 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (26 bp):
AAGTAAATAATATTTTATATTTAAAA
Found at i:41690835 original size:19 final size:18
Alignment explanation
Indices: 41690811--41690846 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41690801 AAAAAAGAAG
*
41690811 AAAAAGAAGGAGAGAAAGA
1 AAAAAGAAAGA-AGAAAGA
41690830 AAAAAGAAAGAAGAAAG
1 AAAAAGAAAGAAGAAAG
41690847 GGAAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAGAAGAAAGA
Found at i:41690856 original size:24 final size:24
Alignment explanation
Indices: 41690793--41690858 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
41690783 GGCTCGGCCC
41690793 GAAGA-AGAAA-AAAAGAAGAAAAA
1 GAAGAGAGAAAGAAAA-AAGAAAAA
41690816 GAAGGAGAGAAAGAAAAAAGAAAGAA
1 GAA-GAGAGAAAGAAAAAAGAAA-AA
*
41690842 GAA-AGGGAAAGAAAAAA
1 GAAGAGAGAAAGAAAAAA
41690859 TAGAAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 3 0.08
24 15 0.39
25 11 0.29
26 9 0.24
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
GAAGAGAGAAAGAAAAAAGAAAAA
Found at i:41690879 original size:28 final size:27
Alignment explanation
Indices: 41690797--41690879 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 27
41690787 CGGCCCGAAG
*
41690797 AAGAAAAAAAGAAGAAAAAGAAGGAGAGA
1 AAGAAAAAAAGAAAAAAAAGAA--AGAGA
* *
41690826 AAG-AAAAAAG--AAAGAAGAAAGGGA
1 AAGAAAAAAAGAAAAAAAAGAAAGAGA
*
41690850 AAGAAAAAATAGAAAAAAAAGAAATAGA
1 AAGAAAAAA-AGAAAAAAAAGAAAGAGA
41690878 AA
1 AA
41690880 AGTCAGTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 7 0.16
25 5 0.11
26 9 0.20
28 20 0.45
29 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (27 bp):
AAGAAAAAAAGAAAAAAAAGAAAGAGA
Found at i:41691217 original size:16 final size:15
Alignment explanation
Indices: 41691192--41691283 Score: 70
Period size: 15 Copynumber: 6.3 Consensus size: 15
41691182 GCAGCAGGCC
41691192 AAAAAA-AAGAAGAGA
1 AAAAAAGAAGAA-AGA
41691207 AAAAAAGAAG-AA-A
1 AAAAAAGAAGAAAGA
* * *
41691220 AGAATAGCAACCAAA-A
1 AAAAAAG-AA-GAAAGA
41691236 AGAAAAAGAAG--AGA
1 A-AAAAAGAAGAAAGA
*
41691250 AAAAAAGAAAAAAGA
1 AAAAAAGAAGAAAGA
41691265 AAAAAAGAAGAAAGA
1 AAAAAAGAAGAAAGA
41691280 AAAA
1 AAAA
41691284 GGGGCCCAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
13 15 0.25
14 5 0.08
15 28 0.46
16 9 0.15
17 4 0.07
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.01
Consensus pattern (15 bp):
AAAAAAGAAGAAAGA
Found at i:41691261 original size:26 final size:27
Alignment explanation
Indices: 41691204--41691282 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 27
41691194 AAAAAAGAAG
*
41691204 AGAAAAAAAGAAGAAAAGAATAGCAACCAAAA
1 AGAAAAAAAGAAG-AAAGAAAAG--A--AAAA
41691236 AGAAAAAGAAG-AGAAA-AAAAGAAAAA
1 AGAAAAA-AAGAAGAAAGAAAAGAAAAA
41691262 AGAAAAAAAGAAGAAAGAAAA
1 AGAAAAAAAGAAGAAAGAAAA
41691283 AGGGGCCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
25 3 0.07
26 16 0.37
27 4 0.09
28 1 0.02
30 4 0.09
31 3 0.07
32 9 0.21
33 3 0.07
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.01
Consensus pattern (27 bp):
AGAAAAAAAGAAGAAAGAAAAGAAAAA
Found at i:41691636 original size:21 final size:21
Alignment explanation
Indices: 41691611--41691650 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41691601 GAAAATATTC
*
41691611 AAAAATTTTCGTGTTTTAAAA
1 AAAAATTCTCGTGTTTTAAAA
41691632 AAAAATTCTCGTGTTTTAA
1 AAAAATTCTCGTGTTTTAA
41691651 TAGAATCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (21 bp):
AAAAATTCTCGTGTTTTAAAA
Found at i:41691803 original size:18 final size:18
Alignment explanation
Indices: 41691780--41692037 Score: 95
Period size: 18 Copynumber: 14.7 Consensus size: 18
41691770 TCAACAAATT
41691780 CGTGTTTCAAAAAATTTC
1 CGTGTTTCAAAAAATTTC
41691798 CGTGTTTTC-AAAAATTT-
1 CGTG-TTTCAAAAAATTTC
* *
41691815 CATG--TCCAAAAA-TTC
1 CGTGTTTCAAAAAATTTC
* * * *
41691830 TCGTATTTC-ATAAGTTTT
1 -CGTGTTTCAAAAAATTTC
*
41691848 AGTG-TT-AAAAAATTTTC
1 CGTGTTTCAAAAAA-TTTC
41691865 CGTGTTTTCAACAAAATTT-
1 CGTG-TTTCAA-AAAATTTC
*
41691884 -GTGTTTC-TAAAA-TTC
1 CGTGTTTCAAAAAATTTC
*
41691899 TCGTATTTC-AAAAATTTC
1 -CGTGTTTCAAAAAATTTC
41691917 TCGTGTTTCAAAAAATTT-
1 -CGTGTTTCAAAAAATTTC
*
41691935 CGTGTTTTCAAAAAAAATGTTT
1 CGTG-TTTC--AAAAAAT-TTC
* *
41691957 CGTGTTT-TAAAAATTTT
1 CGTGTTTCAAAAAATTTC
* *
41691974 CGTGTTTC--TAAAGTTC
1 CGTGTTTCAAAAAATTTC
* *
41691990 TCGTATTTC-AAAATTTTC
1 -CGTGTTTCAAAAAATTTC
* *
41692008 CGTATTTAAAAAAATTAT-
1 CGTGTTTCAAAAAATT-TC
*
41692026 TGTGTTTCAAAA
1 CGTGTTTCAAAA
41692038 TTCTCGTGTT
Statistics
Matches: 183, Mismatches: 29, Indels: 56
0.68 0.11 0.21
Matches are distributed among these distances:
14 6 0.03
15 9 0.05
16 12 0.07
17 56 0.31
18 60 0.33
19 15 0.08
20 12 0.07
21 9 0.05
22 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (18 bp):
CGTGTTTCAAAAAATTTC
Found at i:41691808 original size:19 final size:17
Alignment explanation
Indices: 41691780--41692019 Score: 104
Period size: 17 Copynumber: 13.8 Consensus size: 17
41691770 TCAACAAATT
41691780 CGTGTTTCAAAAAATTTC
1 CGTGTTTC-AAAAATTTC
41691798 CGTGTTTTCAAAAATTT-
1 CGTG-TTTCAAAAATTTC
* *
41691815 CATG-TCCAAAAA-TTC
1 CGTGTTTCAAAAATTTC
* * * *
41691830 TCGTATTTCATAAGTTTT
1 -CGTGTTTCAAAAATTTC
* *
41691848 AGTG-TTAAAAAATTTTC
1 CGTGTTTCAAAAA-TTTC
41691865 CGTGTTTTCAACAAAATTT-
1 CGTG-TTTC-A-AAAATTTC
*
41691884 -GTGTTTCTAAAA-TTC
1 CGTGTTTCAAAAATTTC
*
41691899 TCGTATTTCAAAAATTTC
1 -CGTGTTTCAAAAATTTC
41691917 TCGTGTTTCAAAAAATTT-
1 -CGTGTTTC-AAAAATTTC
*
41691935 CGTGTTTTCAAAAAAAATGTTT
1 CGTG-TTTC---AAAAAT-TTC
* *
41691957 CGTGTTTTAAAAATTTT
1 CGTGTTTCAAAAATTTC
* *
41691974 CGTGTTTC-TAAAGTTC
1 CGTGTTTCAAAAATTTC
* *
41691990 TCGTATTTCAAAATTTTC
1 -CGTGTTTCAAAAATTTC
*
41692008 CGTATTT-AAAAA
1 CGTGTTTCAAAAA
41692020 AATTATTGTG
Statistics
Matches: 170, Mismatches: 30, Indels: 46
0.69 0.12 0.19
Matches are distributed among these distances:
14 4 0.02
15 11 0.06
16 16 0.09
17 58 0.34
18 43 0.25
19 14 0.08
20 11 0.06
21 9 0.05
22 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (17 bp):
CGTGTTTCAAAAATTTC
Found at i:41691907 original size:17 final size:17
Alignment explanation
Indices: 41691887--41692044 Score: 79
Period size: 17 Copynumber: 8.9 Consensus size: 17
41691877 AAAATTTGTG
*
41691887 TTTCTAAAATTCTCGTA
1 TTTCAAAAATTCTCGTA
*
41691904 TTTCAAAAATTTCTCGTG
1 TTTCAAAAA-TTCTCGTA
*
41691922 TTTCAAAAAATT-TCGTGT
1 TTTC-AAAAATTCTCGT-A
* *
41691940 TTTCAAAAAAAATGTTTCGTG
1 TTTC---AAAAAT-TCTCGTA
* * *
41691961 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTA
* *
41691978 TTTCTAAAGTTCTCGTA
1 TTTCAAAAATTCTCGTA
*
41691995 TTTC-AAAATTTTCCGTA
1 TTTCAAAAATTCT-CGTA
* * * *
41692012 TTTAAAAAAATTATTGTG
1 TTT-CAAAAATTCTCGTA
41692030 TTTC-AAAATTCTCGT
1 TTTCAAAAATTCTCGT
41692045 GTTTTTTTAA
Statistics
Matches: 112, Mismatches: 19, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
16 15 0.13
17 42 0.38
18 28 0.25
19 12 0.11
20 7 0.06
21 4 0.04
22 4 0.04
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.46
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTA
Found at i:41691949 original size:20 final size:20
Alignment explanation
Indices: 41691926--41691969 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
41691916 CTCGTGTTTC
41691926 AAAAAA-TTTCGTGTTTTCAA
1 AAAAAAGTTTCGTGTTTT-AA
41691946 AAAAAATGTTTCGTGTTTTAA
1 AAAAAA-GTTTCGTGTTTTAA
41691967 AAA
1 AAA
41691970 TTTTCGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 11 0.50
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (20 bp):
AAAAAAGTTTCGTGTTTTAA
Found at i:41691991 original size:91 final size:91
Alignment explanation
Indices: 41691854--41692037 Score: 250
Period size: 91 Copynumber: 2.0 Consensus size: 91
41691844 TTTTAGTGTT
41691854 AAAAAATTTTCCGTGTTTTCAACAAAATTTGTGTTTCTAAAATTCTCGTATTTCAAAAATTTCTC
1 AAAAAATTTTCCGTGTTTTCAACAAAATTTGTGTTTCTAAAATTCTCGTATTTCAAAAATTTC-C
* *
41691919 GTGTTTCAAAAAATT-TCGTGTTTTCAA
65 GTATTTAAAAAAATTATCGTG-TTTCAA
* * *
41691946 AAAAAATGTTT-CGTGTTTT-AA-AAATTTTCGTGTTTCTAAAGTTCTCGTATTTCAAAATTTTC
1 AAAAAAT-TTTCCGTGTTTTCAACAAAATTT-GTGTTTCTAAAATTCTCGTATTTCAAAAATTTC
*
41692008 CGTATTTAAAAAAATTATTGTGTTTCAA
64 CGTATTTAAAAAAATTATCGTGTTTCAA
41692036 AA
1 AA
41692038 TTCTCGTGTT
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
90 28 0.34
91 37 0.45
92 15 0.18
93 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (91 bp):
AAAAAATTTTCCGTGTTTTCAACAAAATTTGTGTTTCTAAAATTCTCGTATTTCAAAAATTTCCG
TATTTAAAAAAATTATCGTGTTTCAA
Found at i:41692020 original size:51 final size:51
Alignment explanation
Indices: 41691948--41692044 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
41691938 GTTTTCAAAA
* * *
41691948 AAAATGTTTCGTGTTT-TAAAAATT-TTCGTGTTTCTAAAGTTCTCGTATTTC
1 AAAATGTTTCGTATTTAAAAAAATTATT-GTGTTTC-AAAATTCTCGTATTTC
41691999 AAAAT-TTTCCGTATTTAAAAAAATTATTGTGTTTCAAAATTCTCGT
1 AAAATGTTT-CGTATTTAAAAAAATTATTGTGTTTCAAAATTCTCGT
41692045 GTTTTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
50 3 0.08
51 21 0.52
52 14 0.35
53 2 0.05
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (51 bp):
AAAATGTTTCGTATTTAAAAAAATTATTGTGTTTCAAAATTCTCGTATTTC
Found at i:41704347 original size:74 final size:74
Alignment explanation
Indices: 41703924--41704560 Score: 632
Period size: 75 Copynumber: 8.5 Consensus size: 74
41703914 CAAGAAATAT
*** * * *
41703924 TTTTCAATTTCTGTTTTT-TTTAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCT-TGGGCAC
1 TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCAC
41703987 A-TGCCAAGGTA
66 ACTG---AGGTA
* * *
41703998 TTTCTCAATTTCTGTTTTTCAAAAAAATTAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTC
1 TTT-TCAATTTCTGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTC
* *
41704063 ATATCCTAAGGTA
64 ACA--CTGAGGTA
* * * *
41704076 TTTTCAATTTCTATTTTTC-AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGCCAC
1 TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCAC
41704140 ACTGAGGTA
66 ACTGAGGTA
* * * *
41704149 TTTTCAATTTCTGCTTTTCAAAAATATCAACTAATATTGCGAGAGGTAAGTTGAGCCTCAGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAA-ATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCA
41704214 CACTGAGGTA
65 CACTGAGGTA
* *
41704224 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTCA
1 TTTTCAATTTCTGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCA
41704289 CATGCTGAGGTA
65 CA--CTGAGGTA
* *
41704301 TATTTTAA-TT-T-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTG
1 T-TTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGG-T-
*
41704363 CACACCGAGGTA
63 CACACTGAGGTA
* ** * *
41704375 TTTTTAATTTC--TTTTAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGCTAT
1 TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-AGGT-C
* * *
41704438 ACGCCGAGGAA
64 ACACTGAGGTA
* * * * *
41704449 TTTTTAATTTCTGTTTTTC-AAAAATCAACTTATATTGCAAGAGGTGAGTTGAGCCTTAGGTC-C
1 TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCAC
* *
41704512 TATGTCGAGGTGT
66 -A-CT-GAGGT-A
* **
41704525 TTTTCAATTTCTATTTTTC-AAATGTCAACTCATAAT
1 TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAAT
41704561 CTGATAAGTG
Statistics
Matches: 480, Mismatches: 59, Indels: 46
0.82 0.10 0.08
Matches are distributed among these distances:
72 1 0.00
73 30 0.06
74 124 0.26
75 204 0.43
76 44 0.09
77 58 0.12
78 18 0.04
81 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (74 bp):
TTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCAC
ACTGAGGTA
Found at i:41704639 original size:15 final size:15
Alignment explanation
Indices: 41704619--41704648 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
41704609 TCAAGCTTTC
41704619 AAAAAATATAGACAAA
1 AAAAAAT-TAGACAAA
41704635 AAAAAATTAGACAA
1 AAAAAATTAGACAA
41704649 TCGAACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATTAGACAAA
Found at i:41704944 original size:30 final size:29
Alignment explanation
Indices: 41704895--41705026 Score: 88
Period size: 30 Copynumber: 4.4 Consensus size: 29
41704885 CAAAAAATAT
*
41704895 AAATTACATTTT-AGTCCCTAAACTTTTCAA
1 AAATTACATTTTGA-CCCCTAAA-TTTTCAA
* *
41704925 AAATTACATTTTGACCCCTAATTTTTTCTA
1 AAATTACATTTTGACCCCTAA-ATTTTCAA
* * * * **
41704955 AATTTACATCTTAACCCCTAATAATTT-GT
1 AAATTACATTTTGACCCCTAA-ATTTTCAA
* * * *
41704984 AAATTACATTTAGACCCTTAAAATTTCTAG
1 AAATTACATTTTGACCCCTAAATTTTC-AA
41705014 AAATTACATTTTG
1 AAATTACATTTTG
41705027 GCCACATATT
Statistics
Matches: 80, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
28 5 0.06
29 16 0.20
30 58 0.73
31 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.42
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAATTTTCAA
Found at i:41705000 original size:29 final size:29
Alignment explanation
Indices: 41704925--41705024 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 29
41704915 AACTTTTCAA
* **
41704925 AAATTACATTTTGACCCCTAATTTTTTCT
1 AAATTACATTTAGACCCCTAATAATTTCT
*
41704954 AAATTTACATCTTA-ACCCCTAATAATTTGT
1 AAA-TTACAT-TTAGACCCCTAATAATTTCT
*
41704984 AAATTACATTTAGACCCTTAA-AATTTCT
1 AAATTACATTTAGACCCCTAATAATTTCT
41705012 AGAAATTACATTT
1 --AAATTACATTT
41705025 TGGCCACATA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
28 9 0.15
29 16 0.27
30 33 0.55
31 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (29 bp):
AAATTACATTTAGACCCCTAATAATTTCT
Found at i:41706149 original size:13 final size:13
Alignment explanation
Indices: 41706131--41706155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41706121 AGCAGGCCAA
41706131 AAAAAAAGAAGAG
1 AAAAAAAGAAGAG
41706144 AAAAAAAGAAGA
1 AAAAAAAGAAGA
41706156 AAAGAATAGC
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAGAG
Found at i:41706150 original size:16 final size:16
Alignment explanation
Indices: 41706129--41706220 Score: 62
Period size: 16 Copynumber: 5.2 Consensus size: 16
41706119 GCAGCAGGCC
*
41706129 AAAAAAAAAGAAGAGA
1 AAAAAAAAAGAAAAGA
*
41706145 AAAAAAGAAGAAAAGA
1 AAAAAAAAAGAAAAGA
41706161 ATAGCAACCAAAAAGAAAAAGA
1 A-A--AA--AAAAAG-AAAAGA
41706183 AGAGGAAAAAAAGAAAA-A
1 A-A--AAAAAAAGAAAAGA
41706201 ATAAAAAAAAG-AAAGA
1 A-AAAAAAAAGAAAAGA
41706217 AAAA
1 AAAA
41706221 GGGGCCCAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
15 6 0.10
16 25 0.40
17 1 0.02
18 3 0.05
19 6 0.10
20 6 0.10
21 5 0.08
22 11 0.17
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAGAAAAGA
Found at i:41706158 original size:21 final size:20
Alignment explanation
Indices: 41706132--41706220 Score: 83
Period size: 20 Copynumber: 4.2 Consensus size: 20
41706122 GCAGGCCAAA
41706132 AAAAAAGAAGAGAAAAAAAG
1 AAAAAAGAAGAGAAAAAAAG
*
41706152 AAGAAAAGAATAGCAACCAAAAAG
1 AA-AAAAGAAGAG-AA--AAAAAG
41706176 -AAAAAGAAGAGGAAAAAAAG
1 AAAAAAGAAGA-GAAAAAAAG
* *
41706196 AAAAAATAA-AAAAAAGAAAG
1 AAAAAAGAAGAGAAAA-AAAG
41706216 AAAAA
1 AAAAA
41706221 GGGGCCCAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
19 4 0.07
20 18 0.31
21 16 0.28
22 12 0.21
23 2 0.03
24 6 0.10
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAAGAAGAGAAAAAAAG
Found at i:41706578 original size:20 final size:19
Alignment explanation
Indices: 41706545--41706583 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
41706535 GAAAATATTC
*
41706545 AAAAAATTTTGTGTTTTAA
1 AAAAAATTTCGTGTTTTAA
41706564 AAAAAATTCTCGTGTTTTAA
1 AAAAAATT-TCGTGTTTTAA
41706584 TAGAATCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (19 bp):
AAAAAATTTCGTGTTTTAA
Found at i:41706820 original size:17 final size:17
Alignment explanation
Indices: 41706800--41706842 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
41706790 AAAATTTGTG
41706800 TTTCTAAAA-TTCTCGTA
1 TTTC-AAAATTTCTCGTA
*
41706817 TTTCAAAAATTTCTCGTG
1 TTTC-AAAATTTCTCGTA
41706835 TTTCAAAA
1 TTTCAAAA
41706843 AATTTCGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (17 bp):
TTTCAAAATTTCTCGTA
Found at i:41706850 original size:17 final size:17
Alignment explanation
Indices: 41706703--41706860 Score: 105
Period size: 18 Copynumber: 9.2 Consensus size: 17
41706693 CTAAAAAAAT
*
41706703 AAAAAAATTCGTGTTTC
1 AAAAAATTTCGTGTTTC
*
41706720 -AAAAATTTCATG--TC
1 AAAAAATTTCGTGTTTC
* *
41706734 CAAAAATTCTCGTATTTC
1 AAAAAATT-TCGTGTTTC
* * *
41706752 ATAAATTTTTGTG-TT-
1 AAAAAATTTCGTGTTTC
41706767 AAAAAATTTTCCGTGTTTTC
1 AAAAAA-TTT-CGTG-TTTC
41706787 AACAAAATTT-GTGTTTC
1 AA-AAAATTTCGTGTTTC
* *
41706804 -TAAAATTCTCGTATTTC
1 AAAAAATT-TCGTGTTTC
*
41706821 AAAAATTTCTCGTGTTTC
1 AAAAAATT-TCGTGTTTC
41706839 AAAAAATTTCGTGTTTTC
1 AAAAAATTTCGTG-TTTC
41706857 AAAA
1 AAAA
41706861 TAAAAAAAGT
Statistics
Matches: 109, Mismatches: 18, Indels: 27
0.71 0.12 0.18
Matches are distributed among these distances:
14 2 0.02
15 17 0.16
16 19 0.17
17 21 0.19
18 39 0.36
19 2 0.02
20 5 0.05
21 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTC
Found at i:41706861 original size:35 final size:33
Alignment explanation
Indices: 41706703--41706861 Score: 89
Period size: 35 Copynumber: 4.7 Consensus size: 33
41706693 CTAAAAAAAT
* * *
41706703 AAAAAAATTCGTG-TTTCAAAAATTTCATG-TC
1 AAAAAATTTCGTGATTTCAAAATTTTCGTGTTC
* *
41706734 CAAAAATTCTCGT-ATTTCATAAATTTTTGTGTT-
1 AAAAAATT-TCGTGATTTCA-AAATTTTCGTGTTC
* *
41706767 AAAAAATTTTCCGTGTTTTCAACAAAATTT-GTGTTTC
1 AAAAAA-TTT-CGTGATTTC-A-AAATTTTCGTG-TTC
*
41706804 -TAAAATTCTCGT-ATTTCAAAAATTTCTCGTGTTTC
1 AAAAAATT-TCGTGATTTC-AAAATTT-TCGTG-TTC
*
41706839 AAAAAATTTCGTGTTTTCAAAAT
1 AAAAAATTTCGTGATTTCAAAAT
41706862 AAAAAAAGTT
Statistics
Matches: 99, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
31 6 0.06
32 9 0.09
33 19 0.19
34 13 0.13
35 28 0.28
36 24 0.24
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (33 bp):
AAAAAATTTCGTGATTTCAAAATTTTCGTGTTC
Found at i:41706868 original size:24 final size:25
Alignment explanation
Indices: 41706839--41706886 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
41706829 CTCGTGTTTC
41706839 AAAAAA-TTTCGTGTTTTCAAAATA
1 AAAAAAGTTTCGTGTTTTCAAAATA
41706863 AAAAAAGTTTCGTGTTTTCAAAAT
1 AAAAAAGTTTCGTGTTTTCAAAAT
41706887 TTCCGTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (25 bp):
AAAAAAGTTTCGTGTTTTCAAAATA
Found at i:41706885 original size:17 final size:16
Alignment explanation
Indices: 41706865--41706923 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
41706855 TCAAAATAAA
41706865 AAAAGTTTCGTGTTTTC
1 AAAAGTTTCGTG-TTTC
41706882 AAAA-TTTCCGTGTTTC
1 AAAAGTTT-CGTGTTTC
* *
41706898 TAAAGTTCTCGTATTTC
1 AAAAGTT-TCGTGTTTC
*
41706915 AAAATTTTC
1 AAAAGTTTC
41706924 CGTATTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 12 0.34
17 22 0.63
18 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (16 bp):
AAAAGTTTCGTGTTTC
Found at i:41706927 original size:17 final size:16
Alignment explanation
Indices: 41706878--41706934 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
41706868 AGTTTCGTGT
*
41706878 TTTCAAAATTTCCGTG
1 TTTCAAAATTTCCGTA
* *
41706894 TTTCTAAAGTTCTCGTA
1 TTTCAAAATTTC-CGTA
41706911 TTTCAAAATTTTCCGTA
1 TTTCAAAA-TTTCCGTA
41706928 TTT-AAAA
1 TTTCAAAA
41706935 AAAAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 14 0.41
17 17 0.50
18 3 0.09
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.46
Consensus pattern (16 bp):
TTTCAAAATTTCCGTA
Found at i:41713984 original size:23 final size:23
Alignment explanation
Indices: 41713958--41714003 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
41713948 AATAAAGGAG
*
41713958 ATAAACACAAAATTAGGATTTTC
1 ATAAACACAAAATCAGGATTTTC
*
41713981 ATAAACATAAAATCAGGATTTTC
1 ATAAACACAAAATCAGGATTTTC
41714004 GATGATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (23 bp):
ATAAACACAAAATCAGGATTTTC
Found at i:41714160 original size:13 final size:13
Alignment explanation
Indices: 41714121--41714162 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
41714111 TTGGATAAAA
*
41714121 AATTATTATACTT
1 AATTATTATATTT
41714134 AATT-TTAT-TATT
1 AATTATTATAT-TT
41714146 AATTATTATATTT
1 AATTATTATATTT
41714159 AATT
1 AATT
41714163 TTTGAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 10 0.40
13 14 0.56
14 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
AATTATTATATTT
Found at i:41715412 original size:17 final size:16
Alignment explanation
Indices: 41715369--41715413 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
41715359 TTAAATTTTT
41715369 ATATAATTTTTAAAAA
1 ATATAATTTTTAAAAA
41715385 A-ATTATATTTTTAAAAA
1 ATA-TA-ATTTTTAAAAA
*
41715402 ATATAAGTTTTA
1 ATATAATTTTTA
41715414 GAATTTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 14 0.56
18 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATAATTTTTAAAAA
Found at i:41715438 original size:19 final size:20
Alignment explanation
Indices: 41715409--41715464 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
41715399 AAAATATAAG
*
41715409 TTTTAGAATTTCTATAAA-TA
1 TTTTAGAATTT-TAAAAATTA
41715429 TTTT-GAATTTTAAAAATTA
1 TTTTAGAATTTTAAAAATTA
*
41715448 TTTTCAAAATTTTAAAA
1 TTTT-AGAATTTTAAAA
41715465 TTACTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 5 0.16
19 12 0.39
20 4 0.13
21 10 0.32
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTAGAATTTTAAAAATTA
Found at i:41715480 original size:20 final size:20
Alignment explanation
Indices: 41715434--41715480 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
41715424 AAATATTTTG
* *
41715434 AATTTTAAAAATTATTTTCA
1 AATTTTTAAAATTACTTTCA
*
41715454 AAATTTTAAAATTACTTT-A
1 AATTTTTAAAATTACTTTCA
41715473 ATATTTTT
1 A-ATTTTT
41715481 GTAATTTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTTTAAAATTACTTTCA
Found at i:41715807 original size:77 final size:77
Alignment explanation
Indices: 41715680--41715835 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
41715670 AACTCAAATT
41715680 TAAATTTTTTTTCGATTTTTCAAATCGAATCGAATTTTACTCACCCTTAGGAGAGGCCCAAAACC
1 TAAATTTTTTTTCGATTTTTCAAATCGAATCGAATTTTACTCACCCTTAGGAGAGGCCCAAAACC
41715745 CCTCATAATACA
66 CCTCATAATACA
41715757 TAAATTTTTTTTCGATTTTTCAAATCGAATCGAATTTTACTCACCCTTAGGAGAGGCCCAAAACC
1 TAAATTTTTTTTCGATTTTTCAAATCGAATCGAATTTTACTCACCCTTAGGAGAGGCCCAAAACC
41715822 CCTCATAATACA
66 CCTCATAATACA
41715834 TA
1 TA
41715836 TAGGGGGCGA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (77 bp):
TAAATTTTTTTTCGATTTTTCAAATCGAATCGAATTTTACTCACCCTTAGGAGAGGCCCAAAACC
CCTCATAATACA
Found at i:41723126 original size:29 final size:29
Alignment explanation
Indices: 41723084--41723140 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
41723074 TGTGTCAGGC
41723084 TGTGTGGCAAACCGTGTGAGCCACACGGT
1 TGTGTGGCAAACCGTGTGAGCCACACGGT
*
41723113 TGTGTGGCAAACCGTGTGGGCCACACGG
1 TGTGTGGCAAACCGTGTGAGCCACACGG
41723141 CCTAGATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (29 bp):
TGTGTGGCAAACCGTGTGAGCCACACGGT
Found at i:41750786 original size:10 final size:10
Alignment explanation
Indices: 41750771--41750856 Score: 54
Period size: 9 Copynumber: 9.8 Consensus size: 10
41750761 CAAAATAACT
41750771 TTAAAAATTA
1 TTAAAAATTA
*
41750781 TT-AAAAGTA
1 TTAAAAATTA
41750790 ---AAAA-TA
1 TTAAAAATTA
*
41750796 TAAAAAATTA
1 TTAAAAATTA
41750806 -T-AAAATTA
1 TTAAAAATTA
41750814 TTAAAAATTA
1 TTAAAAATTA
41750824 -TAAAAACTTA
1 TTAAAAA-TTA
41750834 -T--AAATT-
1 TTAAAAATTA
41750840 TTAAAAA-TA
1 TTAAAAATTA
41750849 TTAAAAAT
1 TTAAAAAT
41750857 GCTTATAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 24
0.70 0.02 0.27
Matches are distributed among these distances:
6 2 0.03
7 7 0.11
8 11 0.18
9 27 0.44
10 15 0.24
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:41750819 original size:18 final size:17
Alignment explanation
Indices: 41750790--41750896 Score: 81
Period size: 18 Copynumber: 5.8 Consensus size: 17
41750780 ATTAAAAGTA
*
41750790 AAAATATAAAAAATTAT
1 AAAATATTAAAAATTAT
41750807 AAAATTATTAAAAATTAT
1 AAAA-TATTAAAAATTAT
* *
41750825 AAAA-ACTTATAAATTTT
1 AAAATA-TTAAAAATTAT
41750842 AAAAATATTAAAAATGCTTAT
1 -AAAATATTAAAAA---TTAT
*
41750863 AAAAAATTCTAAATAATTAT
1 AAAATA-T-TAAA-AATTAT
*
41750883 AAAATAATAAAAAT
1 AAAATATTAAAAAT
41750897 AAAACATATA
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
16 1 0.01
17 16 0.22
18 30 0.42
19 1 0.01
20 14 0.19
21 4 0.06
22 4 0.06
23 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.34
Consensus pattern (17 bp):
AAAATATTAAAAATTAT
Found at i:41750861 original size:28 final size:27
Alignment explanation
Indices: 41750788--41750865 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
41750778 TTATTAAAAG
*
41750788 TAAAAATA-TAAAAAATTATAAAATTAT
1 TAAAAATATTAAAAACTTAT-AAATTAT
41750815 TAAAAAT-TATAAAAACTTATAAATT-T
1 TAAAAATAT-TAAAAACTTATAAATTAT
41750841 TAAAAATATTAAAAATGCTTATAAA
1 TAAAAATATTAAAAA--CTTATAAA
41750866 AAATTCTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
26 14 0.31
27 13 0.29
28 18 0.40
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
TAAAAATATTAAAAACTTATAAATTAT
Found at i:41750880 original size:10 final size:10
Alignment explanation
Indices: 41750794--41750890 Score: 53
Period size: 10 Copynumber: 10.0 Consensus size: 10
41750784 AAAGTAAAAA
*
41750794 TATAAAAAAT
1 TATAAATAAT
41750804 TAT-AA-AAT
1 TATAAATAAT
41750812 TATTAAA-AAT
1 TA-TAAATAAT
41750822 TATAAA-AACT
1 TATAAATAA-T
*
41750832 TATAAAT-TT
1 TATAAATAAT
*
41750841 TAAAAAT-AT
1 TATAAATAAT
* **
41750850 TAAAAATGCT
1 TATAAATAAT
*
41750860 TATAAAAAAT
1 TATAAATAAT
*
41750870 TCTAAATAAT
1 TATAAATAAT
41750880 TATAAAATAAT
1 TAT-AAATAAT
41750891 AAAAATAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
8 5 0.07
9 24 0.34
10 34 0.49
11 7 0.10
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (10 bp):
TATAAATAAT
Found at i:41750911 original size:66 final size:64
Alignment explanation
Indices: 41750794--41750920 Score: 141
Period size: 66 Copynumber: 1.9 Consensus size: 64
41750784 AAAGTAAAAA
* * * *
41750794 TATAAAAAATTATAAAATTATTAAAAATTATAAAAACTTATAAATTTTAAAAATATTAAAAATGC
1 TATAAAAAATTATAAAATAATTAAAAATAATAAAAAC-TAAAAATTAT-AAAATATTAAAAATGC
41750859 T
64 T
* *
41750860 TATAAAAAATTCT-AAATAATTATAAAATAATAAAAA-TAAAACATATATAAAATATTTAAAA
1 TATAAAAAATTATAAAATAATTA-AAAATAATAAAAACTAAAA-AT-TATAAAATATTAAAAA
41750921 CCTTTTATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
64 4 0.08
65 22 0.42
66 26 0.50
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (64 bp):
TATAAAAAATTATAAAATAATTAAAAATAATAAAAACTAAAAATTATAAAATATTAAAAATGCT
Found at i:41751569 original size:24 final size:24
Alignment explanation
Indices: 41751542--41751600 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
41751532 TAAATGATTT
* *
41751542 TTTTATAATTTCTAATTTTTTTAG-
1 TTTTATAATTTATAA-TTTATTAGA
41751566 TTTTATAATATTATAATTTATTAGA
1 TTTTATAAT-TTATAATTTATTAGA
41751591 TTTTA-AATTT
1 TTTTATAATTT
41751601 TTTTATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.06
24 19 0.61
25 10 0.32
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (24 bp):
TTTTATAATTTATAATTTATTAGA
Found at i:41752026 original size:17 final size:17
Alignment explanation
Indices: 41752004--41752038 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41751994 TCTTTGGTTG
41752004 ATTGACCTTATCAAATC
1 ATTGACCTTATCAAATC
41752021 ATTGACCTTATCAAATC
1 ATTGACCTTATCAAATC
41752038 A
1 A
41752039 ATAATAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (17 bp):
ATTGACCTTATCAAATC
Found at i:41758584 original size:22 final size:22
Alignment explanation
Indices: 41758559--41758602 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41758549 AAAATATAAT
*
41758559 AGATATTAGTTGAATAGTTATG
1 AGATATTAGTTGAATAATTATG
41758581 AGATATTAGTTGAATAATTATG
1 AGATATTAGTTGAATAATTATG
41758603 TCTCTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (22 bp):
AGATATTAGTTGAATAATTATG
Found at i:41762028 original size:22 final size:24
Alignment explanation
Indices: 41761976--41762028 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
41761966 AATGGCAAGC
*
41761976 TTCATTTTTCCTTTTAATTTTGTT
1 TTCATTTTTCCTTTTAATTTTATT
*
41762000 TTC-TTTTT-CTTTTTA-TTTATT
1 TTCATTTTTCCTTTTAATTTTATT
41762021 TTCATTTT
1 TTCATTTT
41762029 CGATTAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 10 0.38
23 5 0.19
24 3 0.12
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.75
Consensus pattern (24 bp):
TTCATTTTTCCTTTTAATTTTATT
Found at i:41762261 original size:21 final size:21
Alignment explanation
Indices: 41762230--41762282 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
41762220 TCGTGTATCA
* *
41762230 TTTTAAGTTTTCATA-TATTG
1 TTTTAAATTTTAATACTATTG
41762250 TTATTAAATTTTAATACTTATTG
1 TT-TTAAATTTTAATAC-TATTG
41762273 TTTT-AATTTT
1 TTTTAAATTTT
41762283 GTGATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 17 0.61
22 2 0.07
23 7 0.25
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (21 bp):
TTTTAAATTTTAATACTATTG
Found at i:41762618 original size:12 final size:11
Alignment explanation
Indices: 41762586--41762628 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
41762576 TTTTGCTAAC
41762586 ATTATTATA-T
1 ATTATTATATT
41762596 ATATATCTATATT
1 AT-TAT-TATATT
41762609 ATTATATATATT
1 ATTAT-TATATT
41762621 ATTATTAT
1 ATTATTAT
41762629 GTTTTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 2 0.07
11 6 0.21
12 18 0.62
13 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTATTATATT
Found at i:41762638 original size:15 final size:15
Alignment explanation
Indices: 41762586--41762628 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
41762576 TTTTGCTAAC
41762586 ATTATTATATATATAT
1 ATTATTAT-TATATAT
*
41762602 CTATATTATTATATAT
1 AT-TATTATTATATAT
41762618 ATTATTATTAT
1 ATTATTATTAT
41762629 GTTTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.38
16 9 0.38
17 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATATAT
Found at i:41765402 original size:19 final size:19
Alignment explanation
Indices: 41765378--41765415 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41765368 ACTACTGTCA
*
41765378 CCCACCATAATCAAATTTG
1 CCCACCATAATAAAATTTG
*
41765397 CCCACCGTAATAAAATTTG
1 CCCACCATAATAAAATTTG
41765416 TTATTAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (19 bp):
CCCACCATAATAAAATTTG
Found at i:41767462 original size:24 final size:24
Alignment explanation
Indices: 41767435--41767485 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
41767425 TACTTGGGTA
*
41767435 ATTTGCAGTCAATTCATCCTTTAC
1 ATTTGCAGTCAATTCATCATTTAC
* *
41767459 ATTTTCCGTCAATTCATCATTTAC
1 ATTTGCAGTCAATTCATCATTTAC
41767483 ATT
1 ATT
41767486 CGTAGTGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.24, G:0.06, T:0.45
Consensus pattern (24 bp):
ATTTGCAGTCAATTCATCATTTAC
Found at i:41767547 original size:33 final size:33
Alignment explanation
Indices: 41767491--41767648 Score: 88
Period size: 33 Copynumber: 4.7 Consensus size: 33
41767481 ACATTCGTAG
* ** *
41767491 TGCCATAACCCAGTTATGTTCTTATCATTAGAA
1 TGCCATAGCCCAACTATGGTCTTATCATTAGAA
41767524 TGCCATAGCCCAACTATGGTCTTA-CATATA-AA
1 TGCCATAGCCCAACTATGGTCTTATCAT-TAGAA
* * * * * * * *
41767556 TACTATCATGGTCCAACCATGGTATTAT-GTTCATAG
1 TGC---CATAGCCCAACTATGGTCTTATCATT-AGAA
* * ** *
41767592 TGCCATAACTCAGTTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAACTATGGTCTTATCATTAGAA
*
41767625 TGCCATAGTCCAACTATGGTCTTA
1 TGCCATAGCCCAACTATGGTCTTA
41767649 CAAATAAGCA
Statistics
Matches: 88, Mismatches: 29, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
32 7 0.08
33 57 0.65
34 2 0.02
35 19 0.22
36 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (33 bp):
TGCCATAGCCCAACTATGGTCTTATCATTAGAA
Found at i:41767667 original size:101 final size:101
Alignment explanation
Indices: 41767479--41767718 Score: 354
Period size: 101 Copynumber: 2.4 Consensus size: 101
41767469 AATTCATCAT
* * * *
41767479 TTACATTCGTAGTGCCATAACCCAGTTATGTTCTTATCATTAGAATGCCATAGCCCAACTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
* * *
41767544 CTTACATATAAATACTATCATGGTCCAACCATGGTA
66 CTTACAAATAAACACTACCATGGTCCAACCATGGTA
* * *
41767580 TTATGTTCATAGTGCCATAACTCAGTTATGGTCTTATCATCAGAATGCCATAGTCCAACTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
* *
41767645 CTTACAAATAAGCACTGCCATGGTCCAACCATGGTA
66 CTTACAAATAAACACTACCATGGTCCAACCATGGTA
* *
41767681 TTACGTTCATAGTACCATAACCCAATTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
41767719 CGTCAATTCA
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 123 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
CTTACAAATAAACACTACCATGGTCCAACCATGGTA
Found at i:41769636 original size:11 final size:11
Alignment explanation
Indices: 41769620--41769669 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
41769610 TACTAAATAA
41769620 AATAATAAAAT
1 AATAATAAAAT
41769631 AATAATAAAAT
1 AATAATAAAAT
* *
41769642 ATCTCATTAAAAT
1 A-AT-AATAAAAT
*
41769655 ATTAATAAAAT
1 AATAATAAAAT
41769666 AATA
1 AATA
41769670 TTTATCTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 22 0.69
12 2 0.06
13 8 0.25
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:41772539 original size:5 final size:5
Alignment explanation
Indices: 41772519--41772565 Score: 62
Period size: 5 Copynumber: 9.4 Consensus size: 5
41772509 CTTTGGAAAT
41772519 TATGA TAT-A T-TGA TATGA TATGA TATGA TATGA TATGTAA TATGA TA
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATG--A TATGA TA
41772566 GGGAATTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 28 0.74
7 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (5 bp):
TATGA
Found at i:41775601 original size:17 final size:18
Alignment explanation
Indices: 41775570--41775606 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
41775560 TTTAAAATGC
*
41775570 AAGAGAAGAATAAAAAGA
1 AAGAGAAGAAAAAAAAGA
41775588 AAGA-AAGAAAAAAAAGA
1 AAGAGAAGAAAAAAAAGA
41775605 AA
1 AA
41775607 ATTGTGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (18 bp):
AAGAGAAGAAAAAAAAGA
Found at i:41781898 original size:25 final size:25
Alignment explanation
Indices: 41781869--41781928 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
41781859 TTAATTAGTA
*
41781869 TAAAATATTAATAATTTAAT-AAAT
1 TAAAATATTAATAATTAAATAAAAT
41781893 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATT-AATAATTAAATAAAAT
41781919 TAAAAT-TTAA
1 TAAAATATTAA
41781929 GAGAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
24 6 0.19
25 20 0.65
26 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
TAAAATATTAATAATTAAATAAAAT
Found at i:41784001 original size:3 final size:3
Alignment explanation
Indices: 41783993--41784025 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
41783983 AATTAGATAT
41783993 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41784026 ATTAGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41784855 original size:12 final size:12
Alignment explanation
Indices: 41784810--41784856 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
41784800 TGTATGTATA
*
41784810 ATTGAATTGTAT
1 ATTGAATTGAAT
*
41784822 ATTGATTTGAAT
1 ATTGAATTGAAT
41784834 -TTGAAATTGAAT
1 ATTG-AATTGAAT
*
41784846 ATTGACTTGAA
1 ATTGAATTGAA
41784857 AAAAAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 3 0.10
12 23 0.79
13 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (12 bp):
ATTGAATTGAAT
Found at i:41785813 original size:30 final size:31
Alignment explanation
Indices: 41785789--41785847 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
41785779 GTAAATACTC
**
41785789 AAAATTTGAGGGATTAA-AGTGTAAATATGA
1 AAAATTTGAGGGACCAATAGTGTAAATATGA
*
41785819 AAAATTTGATGGACCAATAGTGTAAATAT
1 AAAATTTGAGGGACCAATAGTGTAAATAT
41785848 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (31 bp):
AAAATTTGAGGGACCAATAGTGTAAATATGA
Found at i:41789599 original size:50 final size:49
Alignment explanation
Indices: 41789438--41789770 Score: 244
Period size: 50 Copynumber: 6.6 Consensus size: 49
41789428 CGATCTCGTA
* * * * * *
41789438 TAAGACCATGTCTGGGACATGGTATCGACATCGATATGTGA-G-CCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCA-TG
*
41789486 TAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTC-CATG
**
41789542 TAAGACCATGTCTGGGACATGGGGTTGGCACCGAGATGAGAGGTGCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT-CCATG
* * * *
41789592 TAAGACCATTTCTGGGACATGACGTTGGCACCGGGATGAGAGGTCC-TCCG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCAT--G
* * * **
41789642 TAAGACCATGTCTGGGACATGGCATGGGCACTGATATGAGAACTCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC-CATG
* * * * * * **
41789692 TAAGACCATATCTGGGATATGACATTCGCA--GTACATGAAACATCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTC-CATG
* * *
41789741 TAGGACCATGTTTGGGACATGGCTTTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
41789771 TGTTATTATC
Statistics
Matches: 231, Mismatches: 39, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
48 29 0.13
49 38 0.16
50 116 0.50
51 4 0.02
52 1 0.00
53 3 0.01
54 5 0.02
55 2 0.01
56 31 0.13
57 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (49 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCATG
Found at i:41791283 original size:23 final size:23
Alignment explanation
Indices: 41791252--41791299 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
41791242 GGAGAAATGC
* *
41791252 AATATCCCAAAAATTACTACTGT
1 AATACCCCAAAAATTACTACAGT
41791275 AATACCCCAAAAATTACTACAGT
1 AATACCCCAAAAATTACTACAGT
41791298 AA
1 AA
41791300 GAAAGTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (23 bp):
AATACCCCAAAAATTACTACAGT
Found at i:41793756 original size:44 final size:43
Alignment explanation
Indices: 41793558--41794260 Score: 274
Period size: 44 Copynumber: 15.4 Consensus size: 43
41793548 CAAATAATAG
* * * * *
41793558 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCATA-T-CAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTACAA
* * * ** * * *
41793599 ACCTTATCTGCCTGAAGTTGTAGTGGAATAGGTTAAAAATAAACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGT--ACAA
*
41793645 ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGACGGGCTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-A---G-TACAA
* *
41793694 ATCTTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAGTCACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-ACAA
* * * *
41793738 ACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TACAA
** *
41793782 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGCAGATTAAAACAACGA
1 ATCTTATCTCCCTGAAGTTGCAGT-G-G-A----GCAGATT-AAAGTACAA
* * * * *
41793833 ATCCTATACGT--CTGAGGTTGCAGTAGG-TCGGATTAAATCTACCATAGCA
1 ATCTTAT-C-TCCCTGAAGTTGCAGT-GGAGCAGATTAAA-GTA-C--A--A
* * * **
41793882 AGTTTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAACCACAA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGTACAA
* * * *** *
41793927 A--TTATCCCCCTGAAGTTGCAGTGGGGTAGGCCGAAA-TCACGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTAAAGT-ACAA
* * * * * *
41793969 GTCTTATCTCCCTAAAGTTGTAGTAGAGCAGACTGAAGATAGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TA-CAA
* * * * ** *
41794014 ATCTTATTTCCTTGAAATTGTAGTGGAATAGATTAAGGCTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TACAA
* * * *
41794058 ATTAGAATTGGATCTCCCTAAAGTTGCAAT-GAGGCAGATTGAAAATACAA
1 A-T---CTT--ATCTCCCTGAAGTTGCAGTGGA-GCAGATT-AAAGTACAA
* * *
41794108 GTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TA-CAA
* * * * *
41794153 ATCTTATCTCCCTGAAATTGCAGTAGAACATATTAAAGCTATAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TACAA
* * *
41794197 A-CTTTATCTCCCTGAATTTGCAGTGGAGCAGATTGAAGATAGCGA
1 ATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TA-CAA
*
41794242 ATCTTATTTCCCTGAAGTT
1 ATCTTATCTCCCTGAAGTT
41794261 ATAGAAAAGC
Statistics
Matches: 491, Mismatches: 117, Indels: 104
0.69 0.16 0.15
Matches are distributed among these distances:
41 26 0.05
42 31 0.06
43 14 0.03
44 156 0.32
45 92 0.19
46 35 0.07
47 4 0.01
48 5 0.01
49 45 0.09
50 44 0.09
51 35 0.07
52 3 0.01
53 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTACAA
Found at i:41793764 original size:93 final size:88
Alignment explanation
Indices: 41793647--41794260 Score: 278
Period size: 89 Copynumber: 6.7 Consensus size: 88
41793637 ATAAACCAAT
* *
41793647 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGACGGGCTACAAATCTTATCTCCTTAAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-----TACAAATCTTATCTCCCTAAAGT
41793712 TGCAGTGGAGCAGATTAAAGTCACAAAC
61 TGCAGTGGAGCAGATTAAAGTCACAAAC
* * *
41793740 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAATCTTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTAAAGTTGCAG
* ** *
41793805 TGGAGCAGGTTGCAGATTA-AAAC
66 TGGAGCAGATTAAAG-TCACAAAC
** * * * * * * * *
41793828 AACGAATCCTATACGTCTGAGGTTGCAGTAGG-TCGGATTAAATCTACCATAGCAAGTTTTATCT
1 --CTTAT-C--T-C-CCTGAAGTTGCAGT-GGAGCAGATT-GA---A-GATA-CAAATCTTATCT
* * * **
41793892 CCCTGAAGTTGTAGTGGAGCAGACTAAAACCACAAA-
52 CCCTAAAGTTGCAGTGGAGCAGATTAAAGTCACAAAC
* * * *** * * *
41793928 -TTATCCCCCTGAAGTTGCAGTGGGGTAGGCCGAA-ATCACGAGTCTTATCTCCCTAAAGTTGTA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACAAATCTTATCTCCCTAAAGTTGCA
* * * *
41793991 GTAGAGCAGACTGAAGAT-AGCAAAT
65 GTGGAGCAGATTAAAG-TCA-CAAAC
* * * * ** * *
41794016 CTTATTTCCTTGAAATTGTAGTGGAATAGATT-AAGGCTACAAATTAGAATTGGATCTCCCTAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-GATACAAA-T---CTT--ATCTCCCTAAA
* * **
41794080 GTTGCAAT-GAGGCAGATTGAAAAT-ACAAGT
59 GTTGCAGTGGA-GCAGATT-AAAGTCACAAAC
* * *
41794110 CTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCAAATCTTATCTCCCTGAAA-TTGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAATCTTATCTCCCT-AAAGTTGC
* * * *
41794174 AGTAGAACATATTAAAG-CTATAAAC
64 AGTGGAGCAGATTAAAGTC-ACAAAC
* * * * *
41794199 TTTATCTCCCTGAATTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAATCTTATCTCCCTAAAGTT
41794261 ATAGAAAAGC
Statistics
Matches: 391, Mismatches: 91, Indels: 82
0.69 0.16 0.15
Matches are distributed among these distances:
86 38 0.10
87 5 0.01
88 49 0.13
89 99 0.25
90 10 0.03
91 6 0.02
92 13 0.03
93 39 0.10
94 37 0.09
95 47 0.12
96 6 0.02
97 2 0.01
99 1 0.00
100 4 0.01
101 35 0.09
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (88 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTAAAGTTGCAG
TGGAGCAGATTAAAGTCACAAAC
Found at i:41794154 original size:95 final size:95
Alignment explanation
Indices: 41793974--41794154 Score: 213
Period size: 94 Copynumber: 1.9 Consensus size: 95
41793964 CACGAGTCTT
* * * * *
41793974 ATCTCCCTAAAGTTGTAGTAGAGCAGACTGAAGATAGCAAATCTTATTTCCTTGAAATTGTAGTG
1 ATCTCCCTAAAGTTGCAATAGAGCAGACTGAAAATAGCAAATCTTATCTCCCTGAAATTGTAGTG
* * * *
41794039 GAATAGATTAAGGCTACAAATTAGAATTGG
66 GAACAGACTAAAGATACAAATTAGAATTGG
* * *
41794069 ATCTCCCTAAAGTTGCAAT-GAGGCAGATTGAAAATA-CAAGTCTTATCTCCCTGAAGTTGTAGT
1 ATCTCCCTAAAGTTGCAATAGA-GCAGACTGAAAATAGCAAATCTTATCTCCCTGAAATTGTAGT
*
41794132 GGAGCAGACTAAAGATAGCAAAT
65 GGAACAGACTAAAGATA-CAAAT
41794155 CTTATCTCCC
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
94 37 0.52
95 34 0.48
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (95 bp):
ATCTCCCTAAAGTTGCAATAGAGCAGACTGAAAATAGCAAATCTTATCTCCCTGAAATTGTAGTG
GAACAGACTAAAGATACAAATTAGAATTGG
Found at i:41794190 original size:45 final size:45
Alignment explanation
Indices: 41793970--41794257 Score: 187
Period size: 45 Copynumber: 6.3 Consensus size: 45
41793960 AAATCACGAG
* * * *
41793970 TCTTATCTCCCT-AAAGTTGTAGTAGAGCAGACTGAAGATAGCAAA
1 TCTTATCTCCCTGAAA-TTGCAGTGGAGCAGATTAAAGATAGCAAA
* * * ** * *
41794015 TCTTATTTCCTTGAAATTGTAGTGGAATAGATTAAGGCTA-CAAA
1 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATAGCAAA
* * *
41794059 TTAGAATTGGATCTCCCT-AAAGTTGCAAT-GAGGCAGATTGAAA-ATA-CAAG
1 -T---CTT--ATCTCCCTGAAA-TTGCAGTGGA-GCAGATT-AAAGATAGCAAA
* * *
41794109 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCAAA
1 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATAGCAAA
* * * * *
41794154 TCTTATCTCCCTGAAATTGCAGTAGAACATATTAAAGCTA-TAAA
1 TCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATAGCAAA
* * *
41794198 -CTTTATCTCCCTGAATTTGCAGTGGAGCAGATTGAAGATAGCGAA
1 TC-TTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATAGCAAA
*
41794243 TCTTATTTCCCTGAA
1 TCTTATCTCCCTGAA
41794258 GTTATAGAAA
Statistics
Matches: 184, Mismatches: 42, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
43 4 0.02
44 61 0.33
45 82 0.45
46 6 0.03
48 2 0.01
49 6 0.03
50 21 0.11
51 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (45 bp):
TCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATAGCAAA
Found at i:41795744 original size:26 final size:26
Alignment explanation
Indices: 41795685--41795771 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
41795675 TTTTACCATC
*
41795685 ATTTATTTTAAGTTTTTATATATATATT
1 ATTTATTTTAAGTTCTT-T-TATATATT
* *
41795713 ATTTATTTTAAGTTGTTTTACATATT
1 ATTTATTTTAAGTTCTTTTATATATT
* * *
41795739 ATTTATTTAAATTTCCTTTATATATT
1 ATTTATTTTAAGTTCTTTTATATATT
41795765 ATTTATT
1 ATTTATT
41795772 GTAAACTATT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
26 35 0.67
27 1 0.02
28 16 0.31
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (26 bp):
ATTTATTTTAAGTTCTTTTATATATT
Found at i:41795786 original size:26 final size:24
Alignment explanation
Indices: 41795703--41795789 Score: 66
Period size: 26 Copynumber: 3.4 Consensus size: 24
41795693 TAAGTTTTTA
* *
41795703 TATATATATTATTTATTTTAAGTTGT
1 TATATATATTATTTA-TTTAA-ATAT
* * *
41795729 TTTACATATTATTTATTTAAATTT
1 TATATATATTATTTATTTAAATAT
*
41795753 CCTTTATATATTATTTATTGTAAACTAT
1 --TATATATATTATTTATT-TAAA-TAT
41795781 TATATATAT
1 TATATATAT
41795790 CTTTCAAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
24 2 0.04
25 5 0.10
26 37 0.74
27 4 0.08
28 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (24 bp):
TATATATATTATTTATTTAAATAT
Found at i:41795821 original size:21 final size:21
Alignment explanation
Indices: 41795773--41795821 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 21
41795763 TTATTTATTG
41795773 TAAACTA-TTATATATATCTT
1 TAAACTATTTATATATATCTT
*
41795793 TCAA--ATTTATATATAT-TT
1 TAAACTATTTATATATATCTT
41795811 TAAAACTATTT
1 T-AAACTATTT
41795822 TGATATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 3 0.13
21 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAACTATTTATATATATCTT
Found at i:41795867 original size:25 final size:25
Alignment explanation
Indices: 41795829--41795920 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
41795819 TTTTGATATG
41795829 TTTTTTTA-TATTATTTATTTTAAA
1 TTTTTTTATTATTATTTATTTTAAA
* * *
41795853 TTTTTTTATTGTTATTTATTTTTAG
1 TTTTTTTATTATTATTTATTTTAAA
* * *
41795878 TTTTTTTATATTTTGTTTATTTGAAA
1 TTTTTTTAT-TATTATTTATTTTAAA
*
41795904 -CTTTTTATTACTTATTT
1 TTTTTTTATTA-TTATTT
41795921 TGAATCGTTC
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
24 9 0.17
25 34 0.63
26 11 0.20
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTTTTTATTATTATTTATTTTAAA
Found at i:41798215 original size:23 final size:23
Alignment explanation
Indices: 41798189--41798236 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
41798179 ATATAATTGA
41798189 GTATGTTGGTAAATGTTTGACAT
1 GTATGTTGGTAAATGTTTGACAT
41798212 GTATGTTGGTAAATGTTTGACAT
1 GTATGTTGGTAAATGTTTGACAT
41798235 GT
1 GT
41798237 CAGCGAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.27, T:0.44
Consensus pattern (23 bp):
GTATGTTGGTAAATGTTTGACAT
Found at i:41798877 original size:20 final size:20
Alignment explanation
Indices: 41798836--41798877 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
41798826 GAATTAATTC
* *
41798836 AAGAAATTGAGGAAATAGTT
1 AAGAAATTCAGGAAAGAGTT
41798856 AAGAAGATTCAGGAAAGA-TT
1 AAGAA-ATTCAGGAAAGAGTT
41798876 AA
1 AA
41798878 AGGCAGCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.24, T:0.21
Consensus pattern (20 bp):
AAGAAATTCAGGAAAGAGTT
Found at i:41798955 original size:19 final size:19
Alignment explanation
Indices: 41798931--41798975 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
41798921 TCGGACATTG
41798931 AGTATTTAGTCAGGGAAAA
1 AGTATTTAGTCAGGGAAAA
41798950 AGTATTTAGTCAGGGAAAA
1 AGTATTTAGTCAGGGAAAA
41798969 AGTATTT
1 AGTATTT
41798976 CTTAACTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.31
Consensus pattern (19 bp):
AGTATTTAGTCAGGGAAAA
Found at i:41799742 original size:28 final size:30
Alignment explanation
Indices: 41799711--41799766 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
41799701 TATGTTAATT
41799711 AATTATAAAATATATT-ATTAT-TTATTCA
1 AATTATAAAATATATTAATTATATTATTCA
* **
41799739 AATTGTAATTTATATTAATTATATTATT
1 AATTATAAAATATATTAATTATATTATT
41799767 ATATTATGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 13 0.57
29 5 0.22
30 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
AATTATAAAATATATTAATTATATTATTCA
Found at i:41800738 original size:11 final size:11
Alignment explanation
Indices: 41800718--41800746 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41800708 TCAAATCACT
41800718 TTTTAT-TAAA
1 TTTTATATAAA
41800728 TTTTATATAAA
1 TTTTATATAAA
41800739 TTTTATAT
1 TTTTATAT
41800747 TTAATAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTATATAAA
Found at i:41808892 original size:10 final size:11
Alignment explanation
Indices: 41808879--41808916 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
41808869 GAAAATAATC
41808879 AAATTTAA-TA
1 AAATTTAATTA
41808889 AAATTTAATTA
1 AAATTTAATTA
*
41808900 TAAAATTAATTA
1 -AAATTTAATTA
41808912 AAATT
1 AAATT
41808917 CATCATGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 8 0.33
11 6 0.25
12 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTTAATTA
Found at i:41809235 original size:22 final size:22
Alignment explanation
Indices: 41809210--41809254 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
41809200 AATTTTAAAT
41809210 TTTCAATATAAT-TATGCATATA
1 TTTCAATATAATATA-GCATATA
*
41809232 TTTCAATCTAATATAGCATATA
1 TTTCAATATAATATAGCATATA
41809254 T
1 T
41809255 CGGAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (22 bp):
TTTCAATATAATATAGCATATA
Found at i:41821438 original size:13 final size:13
Alignment explanation
Indices: 41821412--41821447 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
41821402 TGCATAAAAT
*
41821412 AAAAT-ATTCCTA
1 AAAATAATTCTTA
41821424 AAAATAATTCTTA
1 AAAATAATTCTTA
41821437 AAAATAATTCT
1 AAAATAATTCT
41821448 AAAGAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATAATTCTTA
Found at i:41831146 original size:72 final size:72
Alignment explanation
Indices: 41831023--41831165 Score: 182
Period size: 72 Copynumber: 2.0 Consensus size: 72
41831013 GGGGTTTGTT
* *
41831023 ATACTTACCATTTCTTTTTTCAAGGTCCACCATAAAGGTATTCCTTACAGATGATAGTCATAAGG
1 ATACTTACCATTTCTTTTTTCAAGGTCCACCACAAAGGTATTCCTTACAGATGATAGCCATAAGG
*
41831088 GCTTTCC
66 GATTTCC
* * * * *
41831095 ATACTTACCATTTCTTTCTTT-AGGGTTCGCCACAAAGGTGTTCCCTT-CAGATGATAGCCGTAA
1 ATACTTACCATTTCTTT-TTTCAAGGTCCACCACAAAGGTATT-CCTTACAGATGATAGCCATAA
41831158 GGGATTTC
64 GGGATTTC
41831166 TTTTAGACTG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 54 0.89
73 7 0.11
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (72 bp):
ATACTTACCATTTCTTTTTTCAAGGTCCACCACAAAGGTATTCCTTACAGATGATAGCCATAAGG
GATTTCC
Done.