Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 127 of 153
Found at i:40248528 original size:25 final size:25
Alignment explanation
Indices: 40248480--40248605 Score: 85
Period size: 25 Copynumber: 5.1 Consensus size: 25
40248470 TTCATGTATA
* * *
40248480 CTCATACGAGCTGTA-AACGAGAAG
1 CTCATCCGAGCTGAATAACGGGAAG
* *
40248504 CTCCTCCTAGCTGAATAACGGGAAG
1 CTCATCCGAGCTGAATAACGGGAAG
* * *
40248529 CTCATGCGAGCTGAGTAATGGGAAG
1 CTCATCCGAGCTGAATAACGGGAAG
* * ***
40248554 CTCATGCGAGCT-AAGTATCAATAAG
1 CTCATCCGAGCTGAA-TAACGGGAAG
* * *
40248579 CTCATGCGAGCTAAATATCGGGAAG
1 CTCATCCGAGCTGAATAACGGGAAG
40248604 CT
1 CT
40248606 TATGTGAGCT
Statistics
Matches: 80, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
24 12 0.15
25 66 0.82
26 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (25 bp):
CTCATCCGAGCTGAATAACGGGAAG
Found at i:40248614 original size:25 final size:25
Alignment explanation
Indices: 40248512--40248616 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 25
40248502 AGCTCCTCCT
* *
40248512 AGCTGAATAACGGGAAGCTCATGCG
1 AGCTAAATATCGGGAAGCTCATGCG
* *
40248537 AGCTGAGTAAT-GGGAAGCTCATGCG
1 AGCTAAAT-ATCGGGAAGCTCATGCG
* ***
40248562 AGCTAAGTATCAATAAGCTCATGCG
1 AGCTAAATATCGGGAAGCTCATGCG
* *
40248587 AGCTAAATATCGGGAAGCTTATGTG
1 AGCTAAATATCGGGAAGCTCATGCG
40248612 AGCTA
1 AGCTA
40248617 TGGCATGTAC
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
24 2 0.03
25 63 0.95
26 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (25 bp):
AGCTAAATATCGGGAAGCTCATGCG
Found at i:40250092 original size:47 final size:47
Alignment explanation
Indices: 40249983--40250093 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
40249973 CCCGGATAAG
*
40249983 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
40250030 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
40250077 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
40250094 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:40250865 original size:4 final size:4
Alignment explanation
Indices: 40250856--40250884 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
40250846 CCCTTTTCTA
40250856 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
40250885 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:40252992 original size:42 final size:42
Alignment explanation
Indices: 40252941--40253143 Score: 327
Period size: 42 Copynumber: 4.8 Consensus size: 42
40252931 GTTTACAAAC
40252941 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
40252983 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
40253025 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGGA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
40253067 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AGG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA-A
* * *
40253109 AAAAATGCCGCTAAATATCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
40253144 TTTTTTTTCT
Statistics
Matches: 151, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
42 151 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:40253176 original size:43 final size:42
Alignment explanation
Indices: 40252943--40253239 Score: 209
Period size: 42 Copynumber: 7.1 Consensus size: 42
40252933 TTACAAACAA
* * * **** *
40252943 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAA
1 AAACGCCGCTAAAGAACATGTTCTTTAGTGGCGATTTTTTAC
* * * **** *
40252985 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAA
1 AAACGCCGCTAAAGAACATGTTCTTTAGTGGCGATTTTTTAC
* * * **** *
40253027 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGGAAA
1 AAACGCCGCTAAAGAACATGTTCTTTAGTGGCGATTTTTTAC
* * **** *
40253069 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAGGAA
1 AAACGCCGCTAAAGAACATGTTCTTTAGTGGCGATTTTTTAC
* * * * * *
40253111 AAATGCCGCTAAATATCATGTTCTTTAGCGGCGTTTTTTTTC
1 AAACGCCGCTAAAGAACATGTTCTTTAGTGGCGATTTTTTAC
*
40253153 TAAGCGCCGCTAAAGAACATGTTCTTTAGTGGC-ATTTTTTAC
1 -AAACGCCGCTAAAGAACATGTTCTTTAGTGGCGATTTTTTAC
* * *
40253195 AAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTTTTATAC
1 AAACGCCGCTAAAGAACATGTTCTTTAGTGGCGATTTTTTAC
40253237 AAA
1 AAA
40253240 AACGCCACTA
Statistics
Matches: 226, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
41 30 0.13
42 169 0.75
43 27 0.12
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGTTCTTTAGTGGCGATTTTTTAC
Found at i:40253199 original size:126 final size:126
Alignment explanation
Indices: 40252941--40253230 Score: 350
Period size: 126 Copynumber: 2.3 Consensus size: 126
40252931 GTTTACAAAC
*
40252941 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGT
* *
40253006 TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGGA
66 TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTAGGA
* * *
40253067 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AGGAAAAATGCCGCTAAATATCATG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA-AAAAAACGCCGCTAAAGATCATG
* ****** * * ****
40253131 TTCTTTAGCGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATGTTCTTTAGTGGC-ATTTTTT
65 TTCTTTAGCGGCG-CTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTAGGA
* * *
40253193 ACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
40253231 TTATACAAAA
Statistics
Matches: 140, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
125 1 0.01
126 108 0.77
127 31 0.22
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (126 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGT
TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGATTAGGA
Found at i:40253622 original size:21 final size:21
Alignment explanation
Indices: 40253554--40253624 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
40253544 TTTTGCTCTA
* *
40253554 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
40253575 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
40253596 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
40253617 CTCTGCTT
1 CTCTGCTT
40253625 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.45, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:40259097 original size:18 final size:18
Alignment explanation
Indices: 40259074--40259518 Score: 135
Period size: 18 Copynumber: 25.5 Consensus size: 18
40259064 AATTACAATG
40259074 GTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
40259092 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
40259110 GTAAG-T-TGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
*
40259128 GT-A-TTGTGTAAG-T-T
1 GTAAGTTATGTAAGTTAT
40259142 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
40259160 GTAAG-T-TGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
*
40259176 -TATGTATTATGTAAG-T-T
1 GTAAG--TTATGTAAGTTAT
*
40259193 GTAAGTTAAATGT-A-TTGT
1 GTAAGTT--ATGTAAGTTAT
40259211 GTAAG-T-TGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259229 GT-A-TTATGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259247 GT-A-TTATGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259265 GT-A-TTATGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259283 GT-A-TTATGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259301 GT-A-TTATGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259319 GT-A-TTATGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259337 GT-A-TTATGTAAG-T-T
1 GTAAGTTATGTAAGTTAT
*
40259351 GTAAGTTAT-TATGTATTAT
1 GTAAGTTATGTAAG--TTAT
*
40259370 GTAAGTAATGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259390 GT-A-TTATGTAAG-T-T
1 GTAAGTTATGTAAGTTAT
*
40259404 GTAAGTTAT-TATGTATTAT
1 GTAAGTTATGTAAG--TTAT
*
40259423 GTAAGTAATGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259443 GT-A-TTATGTAAG-T-T
1 GTAAGTTATGTAAGTTAT
*
40259457 GTAAGTTAT-TATGTATTAT
1 GTAAGTTATGTAAG--TTAT
*
40259476 GTAAGTAATGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
40259496 GT-A-TTATGTAAG-T-T
1 GTAAGTTATGTAAGTTAT
40259510 GTAAGTTAT
1 GTAAGTTAT
40259519 TATGTATTAT
Statistics
Matches: 351, Mismatches: 16, Indels: 122
0.72 0.03 0.25
Matches are distributed among these distances:
14 24 0.07
15 20 0.06
16 28 0.08
17 17 0.05
18 200 0.57
19 37 0.11
20 25 0.07
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (18 bp):
GTAAGTTATGTAAGTTAT
Found at i:40259318 original size:72 final size:72
Alignment explanation
Indices: 40259217--40259509 Score: 319
Period size: 72 Copynumber: 4.1 Consensus size: 72
40259207 TTGTGTAAGT
40259217 TGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTAAA
1 TGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTAAA
40259282 TGTATTA
66 TGTATTA
*
40259289 TGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTGTA
1 TGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTT-AA
40259354 A-GTTATTA
65 ATG-TATTA
* *
40259362 TGT-A-TT--ATGTAAGTAATGTAAGTTAAATGTATTATGTAAGTTGTAA-GTTATTATGT-A-T
1 TGTAAGTTAAATGT-A-TTATGTAAGTTAAATGTATTATGTAAGTT-AAATG-TATTATGTAAGT
*
40259420 T--ATGTAAGTAA
62 TAAATGT-A-TTA
* *
40259431 TGTAAGTTAAATGTATTATGTAAGTTGTAA-GTTATTATGT-A-TT--ATGTAAGTAATGTAAGT
1 TGTAAGTTAAATGTATTATGTAAGTT-AAATG-TATTATGTAAGTTAAATGT-A-TTATGTAAGT
40259491 TAAATGTATTA
62 TAAATGTATTA
40259502 TGTAAGTT
1 TGTAAGTT
40259510 GTAAGTTATT
Statistics
Matches: 191, Mismatches: 8, Indels: 45
0.78 0.03 0.18
Matches are distributed among these distances:
67 4 0.02
68 4 0.02
69 14 0.07
70 7 0.04
71 58 0.30
72 86 0.45
73 18 0.09
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (72 bp):
TGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTAAATGTATTATGTAAGTTAAA
TGTATTA
Found at i:40259404 original size:53 final size:52
Alignment explanation
Indices: 40259079--40259528 Score: 582
Period size: 53 Copynumber: 8.6 Consensus size: 52
40259069 CAATGGTAAG
*
40259079 TTATGTAAGTTATGTAAGTTA-AATGTATTATGTAAGT-TGTAAGTTAAATGTA
1 TTATGTAAG-T-TGTAAGTTATTATGTATTATGTAAGTATGTAAGTTAAATGTA
* * *
40259131 TTGTGTAAGTTGTAAGTTA-AATGTATTATGTAAGT-TGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTATGTAAGTTA-AATGTA
* *
40259182 TTATGTAAGTTGTAAGTTA-AATGTATTGTGTAAGT-TGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTATGTAAGTTAAATGTA
* *
40259232 TTATGTAAG-T-TAAATGTATTATGTAAGTTAAATGT-ATTATGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGT-TATTATGT-A-TT--ATGTAAGTATGTAAGTTAAATGTA
* *
40259286 TTATGTAAG-T-TAAATGTATTATGTAAGTTAAATGT-ATTATGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGT-TATTATGT-A-TT--ATGTAAGTATGTAAGTTAAATGTA
40259340 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTAATGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGT-ATGTAAGTTAAATGTA
40259393 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTAATGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGT-ATGTAAGTTAAATGTA
40259446 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTAATGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGT-ATGTAAGTTAAATGTA
40259499 TTATGTAAGTTGTAAGTTATTATGTATTAT
1 TTATGTAAGTTGTAAGTTATTATGTATTAT
40259529 TTAATAAAAT
Statistics
Matches: 375, Mismatches: 11, Indels: 23
0.92 0.03 0.06
Matches are distributed among these distances:
48 4 0.01
49 3 0.01
50 52 0.14
51 53 0.14
52 12 0.03
53 156 0.42
54 82 0.22
55 9 0.02
56 4 0.01
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.46
Consensus pattern (52 bp):
TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTATGTAAGTTAAATGTA
Found at i:40259498 original size:11 final size:9
Alignment explanation
Indices: 40259368--40259490 Score: 50
Period size: 9 Copynumber: 13.9 Consensus size: 9
40259358 ATTATGTATT
40259368 ATGTAAGTA
1 ATGTAAGTA
40259377 ATGTAAGTTAA
1 ATGTAAG-T-A
*
40259388 ATGT-A-TT
1 ATGTAAGTA
40259395 ATGTAAGT-
1 ATGTAAGTA
*
40259403 -TGTAAGTT
1 ATGTAAGTA
*
40259411 AT-TATGTA
1 ATGTAAGTA
40259419 TTATGTAAGTA
1 --ATGTAAGTA
40259430 ATGTAAGTTAA
1 ATGTAAG-T-A
*
40259441 ATGT-A-TT
1 ATGTAAGTA
40259448 ATGTAAGT-
1 ATGTAAGTA
*
40259456 -TGTAAGTT
1 ATGTAAGTA
*
40259464 AT-TATGTA
1 ATGTAAGTA
40259472 TTATGTAAGTA
1 --ATGTAAGTA
40259483 ATGTAAGT
1 ATGTAAGT
40259491 TAAATGTATT
Statistics
Matches: 88, Mismatches: 8, Indels: 36
0.67 0.06 0.27
Matches are distributed among these distances:
7 22 0.25
8 12 0.14
9 26 0.30
10 8 0.09
11 20 0.23
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.44
Consensus pattern (9 bp):
ATGTAAGTA
Found at i:40259806 original size:13 final size:13
Alignment explanation
Indices: 40259788--40259858 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
40259778 ATTTATAATT
40259788 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
40259801 ATTTAAGTAACAT
1 ATTTAAGTAATAA
40259814 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
40259827 ATTTAAGTAACAT
1 ATTTAAGTAATAA
40259840 ATTTAAGTAATAA
1 ATTTAAGTAATAA
40259853 ATTTAA
1 ATTTAA
40259859 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:40259817 original size:26 final size:26
Alignment explanation
Indices: 40259787--40259858 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
40259777 TATTTATAAT
40259787 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
40259813 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
40259839 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
40259859 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:40259885 original size:17 final size:17
Alignment explanation
Indices: 40259863--40259906 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
40259853 ATTTAAACAA
40259863 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
40259880 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
40259897 ATTTTAGTAA
1 ATTTTAGTAA
40259907 TAAATTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:40261266 original size:11 final size:11
Alignment explanation
Indices: 40261250--40261289 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
40261240 GATGATAATA
40261250 CATTAGTTACC
1 CATTAGTTACC
40261261 CATTAGTTACC
1 CATTAGTTACC
40261272 CATTAGTTACC
1 CATTAGTTACC
40261283 CA-TAGTT
1 CATTAGTT
40261290 TGAGATATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 5 0.17
11 24 0.83
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (11 bp):
CATTAGTTACC
Found at i:40262596 original size:84 final size:84
Alignment explanation
Indices: 40262489--40263193 Score: 1329
Period size: 84 Copynumber: 8.4 Consensus size: 84
40262479 ATTAACACCG
* * *
40262489 TTTTGTGGCGTTTTTGGTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCGTTT
1 TTTTGTGGCGTTTTTAG-AAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTT
40262554 TCGTGGTCTGGAATTGCATT
65 TCGTGGTCTGGAATTGCATT
40262574 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
40262639 CGTGGTCTGGAATTGCATT
66 CGTGGTCTGGAATTGCATT
40262658 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
40262723 CGTGGTCTGGAATTGCATT
66 CGTGGTCTGGAATTGCATT
40262742 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
40262807 CGTGGTCTGGAATTGCATT
66 CGTGGTCTGGAATTGCATT
40262826 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
40262891 CGTGGTCTGGAATTGCATT
66 CGTGGTCTGGAATTGCATT
40262910 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
40262975 CGTGGTCTGGAATTGCATT
66 CGTGGTCTGGAATTGCATT
40262994 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
40263059 CGTGGTCTGGAATTGCATT
66 CGTGGTCTGGAATTGCATT
40263078 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
1 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
40263143 CGTGGTCTGGAATTGCATT
66 CGTGGTCTGGAATTGCATT
* * ***
40263162 ATTTGTGGCATTTTCCTAAAAACGCCACTAAA
1 TTTTGTGGCGTTTTTAGAAAAACGCCACTAAA
40263194 AGTTTAACTA
Statistics
Matches: 612, Mismatches: 8, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
84 596 0.97
85 16 0.03
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (84 bp):
TTTTGTGGCGTTTTTAGAAAAACGCCACTAAATATTACAGCTGCGAACAGAAACGACACCGTTTT
CGTGGTCTGGAATTGCATT
Found at i:40263594 original size:12 final size:12
Alignment explanation
Indices: 40263577--40263602 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40263567 TTAAAATAGC
40263577 ACGACCTCTTTT
1 ACGACCTCTTTT
40263589 ACGACCTCTTTT
1 ACGACCTCTTTT
40263601 AC
1 AC
40263603 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.35, G:0.08, T:0.38
Consensus pattern (12 bp):
ACGACCTCTTTT
Found at i:40264376 original size:112 final size:112
Alignment explanation
Indices: 40264215--40264580 Score: 583
Period size: 112 Copynumber: 3.3 Consensus size: 112
40264205 AACACCTAGA
* *
40264215 TTAGCGGCGCTTTACAAAAAACGCCACTAA-TGCCCCCCCAAAGGACACAAAACGGCACCGTCTG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGT-CCCCCCCAAAGGCCACAAAACGGCACCGTCTG
* * * * * ** *
40264279 GGAGTATTATTTGCGGCATTTTTTATAAGCGCTGCTAATGTTCACTCT
65 GGTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
*
40264327 TTAACGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
40264392 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
40264439 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
40264504 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
66 GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
* *
40264551 TTAGCGGCGCTTTTA-ATTAAACGCCGCTAA
1 TTAGCGGCGC-TTTACAATAAACGCCACTAA
40264581 TGCTCACTCT
Statistics
Matches: 238, Mismatches: 14, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
112 233 0.98
113 5 0.02
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (112 bp):
TTAGCGGCGCTTTACAATAAACGCCACTAAGTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
GTGTATTATTTGCGGCGTTATCTATAAACGCCACTAATGCTCACTCT
Found at i:40264573 original size:40 final size:40
Alignment explanation
Indices: 40264528--40264604 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
40264518 GCGTTATCTA
*
40264528 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTAAT
1 TAAACGCCACTAATGCTCACTCTTTAGCAGCGCTTTTAAT
*
40264568 TAAACGCCGCTAATGCTCACTCTTTAGCAGCGCTTTT
1 TAAACGCCACTAATGCTCACTCTTTAGCAGCGCTTTT
40264605 GCTCCAAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (40 bp):
TAAACGCCACTAATGCTCACTCTTTAGCAGCGCTTTTAAT
Found at i:40271013 original size:21 final size:22
Alignment explanation
Indices: 40270974--40271014 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40270964 TTACTAAATA
40270974 ATTTAAATATATGAAATATGCC
1 ATTTAAATATATGAAATATGCC
*
40270996 ATTTAAGTATAT-AAATATG
1 ATTTAAATATATGAAATATG
40271015 GGAGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (22 bp):
ATTTAAATATATGAAATATGCC
Found at i:40283799 original size:20 final size:21
Alignment explanation
Indices: 40283776--40283816 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
40283766 AAAAGGGGAA
40283776 TATGTT-CTAAAAAAAAAAGG
1 TATGTTACTAAAAAAAAAAGG
*
40283796 TATGTTGACTAAAAAGAAAAG
1 TATGTT-ACTAAAAAAAAAAG
40283817 AAAGAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (21 bp):
TATGTTACTAAAAAAAAAAGG
Found at i:40285075 original size:79 final size:79
Alignment explanation
Indices: 40284944--40285102 Score: 273
Period size: 79 Copynumber: 2.0 Consensus size: 79
40284934 AAAATATGAT
*
40284944 TCTAAAAAATCCAATCATAAACTCATTTCAAAATTTGTTAAGGTGATATCCCATGGAATTTGATT
1 TCTAAAAAATCCAATCATAAACTCATTTCAAAATTTGTTAAGGTGATATCCCATGGAATTTAATT
40285009 TTCATGATCTGTTG
66 TTCATGATCTGTTG
* * **
40285023 TCTAACAAATCCAGTCATAAACTCATTTTGAAATTTGTTAAGGTGATATCCCATGGAATTTAATT
1 TCTAAAAAATCCAATCATAAACTCATTTCAAAATTTGTTAAGGTGATATCCCATGGAATTTAATT
40285088 TTCATGATCTGTTG
66 TTCATGATCTGTTG
40285102 T
1 T
40285103 GTGTGGATAG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (79 bp):
TCTAAAAAATCCAATCATAAACTCATTTCAAAATTTGTTAAGGTGATATCCCATGGAATTTAATT
TTCATGATCTGTTG
Found at i:40285272 original size:42 final size:42
Alignment explanation
Indices: 40285200--40285415 Score: 254
Period size: 42 Copynumber: 5.1 Consensus size: 42
40285190 GGAAAGCATT
* *
40285200 CATTACATTTAG-AGACCCAGGTGTGAAGGTCCATTTACTTTG
1 CATTGCATTTAGAAG-CCCAGGTGTGGAGGTCCATTTACTTTG
* * *
40285242 CATTGCATTTAGAATCCTAGGTATGGAGGTCCATTTACTTTG
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
* * * * *
40285284 CATTGCATTTGGAATCCCAAGTGTGGAGGTCGATTTACTTTT
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
* * * *
40285326 CATTGCATTTAGAGGCCTAGGTGTGGAGGTCTATTTACTTTT
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
* * *
40285368 CATTGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTAATTTTG
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTT-ACTTTG
40285411 CATTG
1 CATTG
40285416 TATATGAAAG
Statistics
Matches: 152, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 142 0.93
43 10 0.07
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (42 bp):
CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
Found at i:40285439 original size:84 final size:85
Alignment explanation
Indices: 40285198--40285415 Score: 280
Period size: 84 Copynumber: 2.6 Consensus size: 85
40285188 AAGGAAAGCA
* * * *
40285198 TTCATTACATTTAGAGACCCAGGTGTGAAGGTCCATTT-ACTTTGCATTGCATTTAGAATCCTAG
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTAATTTTGCATTGCATTTAGAAGCCTAG
* *
40285262 GTATGGAGGTCCATTTACTT
66 GTGTGGAGGTCTATTTACTT
* * * * * *
40285282 TGCATTGCATTTGGA-ATCCCAAGTGTGGAGGTCGATTTACTTTT-CATTGCATTTAGAGGCCTA
1 TTCATTGCATTTAGAGA-CCCAGGTGTGGAGGTCCATTTAATTTTGCATTGCATTTAGAAGCCTA
40285345 GGTGTGGAGGTCTATTTACTT
65 GGTGTGGAGGTCTATTTACTT
* *
40285366 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTAATTTTGCATTG
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTAATTTTGCATTG
40285416 TATATGAAAG
Statistics
Matches: 112, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
83 1 0.01
84 103 0.92
85 8 0.07
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (85 bp):
TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTAATTTTGCATTGCATTTAGAAGCCTAG
GTGTGGAGGTCTATTTACTT
Found at i:40285439 original size:126 final size:126
Alignment explanation
Indices: 40285198--40285461 Score: 307
Period size: 126 Copynumber: 2.1 Consensus size: 126
40285188 AAGGAAAGCA
* * *
40285198 TTCATTACATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAATCCTAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAAGCCCAGG
* * * * * *
40285263 TATGGAGGTCCATTTACTTTGCATTGCATTTGGAATCCCAAGTGTGGAGGTCG-ATTTACTT
66 TATGGAGGTCCATTTACTTTGCATTGCATATGAAAGCACAAGTGTGGAGGT-GTAATTACAT
* * * * * *
40285324 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCTATTTACTTTTCATTGCATTTAGAGGCCCAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAAGCCCAGG
* * * * *
40285389 TGTGGAGGTCTATTTAATTTTGCATTGTATATGAAAGCACATGTGT-GAGGTGTAATTACAT
66 TATGGAGGTCCATTT-ACTTTGCATTGCATATGAAAGCACAAGTGTGGAGGTGTAATTACAT
40285450 TTCATCTGCATT
1 TTCAT-TGCATT
40285462 CTCATTTCAA
Statistics
Matches: 115, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
125 1 0.01
126 85 0.74
127 29 0.25
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (126 bp):
TTCATTGCATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAAGCCCAGG
TATGGAGGTCCATTTACTTTGCATTGCATATGAAAGCACAAGTGTGGAGGTGTAATTACAT
Found at i:40285869 original size:15 final size:15
Alignment explanation
Indices: 40285849--40285888 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
40285839 AAGGGCCCAA
*
40285849 ATCATTATTACTATT
1 ATCATTATTACTACT
*
40285864 ATCATTACTACTACT
1 ATCATTATTACTACT
*
40285879 ATTATTATTA
1 ATCATTATTA
40285889 ATAAATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (15 bp):
ATCATTATTACTACT
Found at i:40286395 original size:19 final size:18
Alignment explanation
Indices: 40286355--40286397 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
40286345 TAAAGCTTTG
* * *
40286355 ATTTTTAAGAAAAATAGT
1 ATTTTTAAAAAAAAGAGA
40286373 ATTTTTAAAAAAAAGAGA
1 ATTTTTAAAAAAAAGAGA
*
40286391 AATTTTA
1 ATTTTTA
40286398 GATTTTTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (18 bp):
ATTTTTAAAAAAAAGAGA
Found at i:40288445 original size:20 final size:19
Alignment explanation
Indices: 40288398--40288450 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
40288388 TTACTAGCCC
40288398 CCGTACTCTTATGTAGGCA
1 CCGTACTCTTATGTAGGCA
* * *
40288417 ACTTACTCTTATGTAGGCCT
1 CCGTACTCTTATGTAGG-CA
40288437 CCGTACTCTTATGT
1 CCGTACTCTTATGT
40288451 TAGTAAGTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (19 bp):
CCGTACTCTTATGTAGGCA
Found at i:40301305 original size:23 final size:22
Alignment explanation
Indices: 40301273--40301315 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
40301263 TAATATCTCA
*
40301273 ACATTTCATACCATTCAATAAG
1 ACATTTCATACCATGCAATAAG
*
40301295 ACATTCTCATATCATGCAATA
1 ACATT-TCATACCATGCAATA
40301316 TAATTATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (22 bp):
ACATTTCATACCATGCAATAAG
Found at i:40307592 original size:27 final size:27
Alignment explanation
Indices: 40307547--40307896 Score: 337
Period size: 27 Copynumber: 13.0 Consensus size: 27
40307537 CACCGAGACC
40307547 CCGAAATACCC-CATAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* *
40307573 CCGAAATATCCTCATAGGGTAAATTGA
1 CCGAAATACCCTCATAGGGTAAAATGA
** * *
40307600 CTAAAATACCCCCATAAGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* * * *
40307627 CCAAAATACCCCCATATGGTAAAATAA
1 CCGAAATACCCTCATAGGGTAAAATGA
* *
40307654 TCGAAATACCCCCATAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* * * *
40307681 CAGCAATACCCTTATAGTGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* * * *
40307708 CCAAAATACCCCCATGGGGTAAAATAA
1 CCGAAATACCCTCATAGGGTAAAATGA
* *
40307735 TCGAAATACCCTCACAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
** * * *
40307762 TTGAAATACCCTTATAAGATAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
*
40307789 CCAAAATACCC-CATAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* *
40307815 CCAAAATACCCTCGTAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* * *
40307842 CTGAAATA-CCTCTGTAGGGTAGAATGA
1 CCGAAATACCCTC-ATAGGGTAAAATGA
** * *
40307869 CAAAAATACCCTGATAGGGTCAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
40307896 C
1 C
40307897 TGTTCTACCC
Statistics
Matches: 264, Mismatches: 56, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
26 37 0.14
27 224 0.85
28 3 0.01
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (27 bp):
CCGAAATACCCTCATAGGGTAAAATGA
Found at i:40307690 original size:81 final size:81
Alignment explanation
Indices: 40307550--40307893 Score: 390
Period size: 81 Copynumber: 4.3 Consensus size: 81
40307540 CGAGACCCCG
* * * *
40307550 AAATA-CCCCATAGGGTAAAATGACCGAAATATCCTCATAGGGTAAATTGACTA-AAATACCCCC
1 AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGAC-AGAAATACCCCT
40307613 ATAAGGTAAAATGACCA
65 ATAAGGTAAAATGACCA
* * * * *
40307630 AAATACCCCCATATGGTAAAATAATCGAAATACCCCCATAGGGTAAAATGACAGCAATACCCTTA
1 AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCTA
40307695 T-AGTGTAAAATGACCA
66 TAAG-GTAAAATGACCA
* * * ** *
40307711 AAATACCCCCATGGGGTAAAATAATCGAAATACCCTCACAGGGTAAAATGATTGAAATACCCTTA
1 AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCTA
*
40307776 TAAGATAAAATGACCA
66 TAAGGTAAAATGACCA
* * * * * *
40307792 AAATA-CCCCATAGGGTAAAATGACCAAAATACCCTCGTAGGGTAAAATGACTGAAATACCTCTG
1 AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCTA
* * *
40307856 TAGGGTAGAATGACAA
66 TAAGGTAAAATGACCA
** *
40307872 AAATACCCTGATAGGGTCAAAT
1 AAATACCCCCATAGGGTAAAAT
40307894 GACTGTTCTA
Statistics
Matches: 225, Mismatches: 34, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
80 74 0.33
81 149 0.66
82 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (81 bp):
AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCTA
TAAGGTAAAATGACCA
Found at i:40307906 original size:134 final size:135
Alignment explanation
Indices: 40307549--40307924 Score: 321
Period size: 134 Copynumber: 2.8 Consensus size: 135
40307539 CCGAGACCCC
* * * * * *
40307549 GAAATACCC-CATAGGGTAAAATGACCGAAATATCCTCATAGGGTAAATTGA-CTAAAATACCCC
1 GAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATC-AAAATACCCT
* * ** * * * * * * *
40307612 CATAAGGTAAAATGACCAAAATACCCCCATATGGTAAAATAATCGAAATACCCCCATAGGGTAAA
65 CACAGGGTAAAATGACTGAAATACCCCTAGAAGATAAAATGACCAAAATACCCCCATAGGGTAAA
40307677 ATGACA
130 ATGACA
* * * * *
40307683 GCAATACCCTTATAGTGTAAAATGACCAAAATACCCCCATGGGGTAAAATAATCGAAATACCCTC
1 GAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATCAAAATACCCTC
* * *
40307748 ACAGGGTAAAATGATTGAAATACCCTTATAAGATAAAATGACCAAAATA-CCCCATAGGGTAAAA
66 ACAGGGTAAAATGACTGAAATACCCCTAGAAGATAAAATGACCAAAATACCCCCATAGGGTAAAA
40307812 TGACCA
131 TGA-CA
* ** * ** * *
40307818 -AAATACCCTCGTAGGGTAAAATGACTGAAATACCTCTGTAGGGTAGAATGA-CAAAAATACCCT
1 GAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATC-AAAATACCCT
* * * *** * *
40307881 GATAGGGTCAAATGACTGTTCTACCCCTAGGAGATGAAATGACC
65 CACAGGGTAAAATGACTGAAATACCCCTAGAAGATAAAATGACC
40307925 GTTATAGTCT
Statistics
Matches: 191, Mismatches: 47, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
133 1 0.01
134 107 0.56
135 82 0.43
136 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (135 bp):
GAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATCAAAATACCCTC
ACAGGGTAAAATGACTGAAATACCCCTAGAAGATAAAATGACCAAAATACCCCCATAGGGTAAAA
TGACA
Found at i:40310260 original size:25 final size:25
Alignment explanation
Indices: 40310165--40310260 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
40310155 TACTGATTTT
* * *
40310165 AGCTCGTATGAGCTTACCGCTACTT-
1 AGCTCGAAGGAGCTTACCGTTA-TTC
* *
40310190 AGCTC-ACATGAGCTTACTGTTATTC
1 AGCTCGA-AGGAGCTTACCGTTATTC
** *
40310215 AGCTCGGTGGAGCTTATCGTTATTC
1 AGCTCGAAGGAGCTTACCGTTATTC
40310240 AGCTCGAAGGAGCTTACCGTT
1 AGCTCGAAGGAGCTTACCGTT
40310261 TACAACTCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
24 2 0.04
25 55 0.96
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (25 bp):
AGCTCGAAGGAGCTTACCGTTATTC
Found at i:40315733 original size:20 final size:20
Alignment explanation
Indices: 40315693--40315733 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
40315683 GGTTGAGATC
40315693 GGTTTGCTGTAATTTGAAATT
1 GGTTTGCTGT-ATTTGAAATT
40315714 GGTTTGCTGT-TTTAGAAATT
1 GGTTTGCTGTATTT-GAAATT
40315734 TAATTCGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 6 0.32
21 10 0.53
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (20 bp):
GGTTTGCTGTATTTGAAATT
Found at i:40322738 original size:15 final size:16
Alignment explanation
Indices: 40322710--40322742 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40322700 TTTGGAAAGG
40322710 TTTTTGATATAGTGAT
1 TTTTTGATATAGTGAT
*
40322726 TTTTTTATA-AGTGAT
1 TTTTTGATATAGTGAT
40322741 TT
1 TT
40322743 ATTAAGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (16 bp):
TTTTTGATATAGTGAT
Found at i:40323994 original size:25 final size:25
Alignment explanation
Indices: 40323957--40324104 Score: 126
Period size: 25 Copynumber: 6.0 Consensus size: 25
40323947 GTCATTAGGG
*
40323957 TTACCGAT-TTTAGCTCGTATGAGC
1 TTACCGTTATTTAGCTCGTATGAGC
* * **
40323981 TTACTGTTACTTAGCTCACATGAGC
1 TTACCGTTATTTAGCTCGTATGAGC
* * *
40324006 TTACCATTATTTAGCTTAG-AGGAGC
1 TTACCGTTATTTAGC-TCGTATGAGC
*
40324031 TTACCGTTATTTAGCTCGTAAGAGC
1 TTACCGTTATTTAGCTCGTATGAGC
* *
40324056 TTACCGTT-TATAGCTCGTAAGAGC
1 TTACCGTTATTTAGCTCGTATGAGC
*
40324080 ATACCG--ATTTAGAGCTCGTATGAGC
1 TTACCGTTATTT--AGCTCGTATGAGC
40324105 ATACATGTAC
Statistics
Matches: 100, Mismatches: 18, Indels: 11
0.78 0.14 0.09
Matches are distributed among these distances:
23 2 0.02
24 28 0.28
25 69 0.69
26 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (25 bp):
TTACCGTTATTTAGCTCGTATGAGC
Found at i:40328251 original size:6 final size:6
Alignment explanation
Indices: 40328240--40328266 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40328230 TACTCACACA
40328240 GGCACG GGCACG GGCACG GGCACG GGC
1 GGCACG GGCACG GGCACG GGCACG GGC
40328267 TGGGACACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.52, T:0.00
Consensus pattern (6 bp):
GGCACG
Found at i:40328693 original size:39 final size:39
Alignment explanation
Indices: 40328637--40328714 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
40328627 TAGGTTTGCA
40328637 AAGTGTTTTGAGAATAGGATAGGTGATGGATCGGCTAAG
1 AAGTGTTTTGAGAATAGGATAGGTGATGGATCGGCTAAG
* *
40328676 AAGTGTTTT-AGGGATAGGATAGGTGATGGCTCGGCTAAG
1 AAGTGTTTTGA-GAATAGGATAGGTGATGGATCGGCTAAG
40328715 GATAAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.28, C:0.06, G:0.37, T:0.28
Consensus pattern (39 bp):
AAGTGTTTTGAGAATAGGATAGGTGATGGATCGGCTAAG
Found at i:40328768 original size:18 final size:18
Alignment explanation
Indices: 40328745--40328781 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
40328735 ATGAAGATAG
40328745 CAGGAATGGATAGGTAAA
1 CAGGAATGGATAGGTAAA
40328763 CAGGAATGGATAGGTAAA
1 CAGGAATGGATAGGTAAA
40328781 C
1 C
40328782 TTAAGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.08, G:0.32, T:0.16
Consensus pattern (18 bp):
CAGGAATGGATAGGTAAA
Found at i:40330409 original size:13 final size:13
Alignment explanation
Indices: 40330391--40330416 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40330381 TCCCAATATA
40330391 GCTCATTACTTTC
1 GCTCATTACTTTC
40330404 GCTCATTACTTTC
1 GCTCATTACTTTC
40330417 CAGTTGATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (13 bp):
GCTCATTACTTTC
Found at i:40333125 original size:18 final size:18
Alignment explanation
Indices: 40333102--40333196 Score: 87
Period size: 18 Copynumber: 5.6 Consensus size: 18
40333092 TCTTCACACA
40333102 TTTCTTTTTCAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
*
40333120 TCTCTTTTTC-A-CTCGT-
1 TTTCTTTTTCAAGCTC-TC
40333136 TTTC-TTTTCAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
* *
40333153 TTTCCTTTTC-A-CTCGC
1 TTTCTTTTTCAAGCTCTC
40333169 TTTC-TTTTCAAAGCTCTC
1 TTTCTTTTTC-AAGCTCTC
*
40333187 TTTCCTTTTC
1 TTTCTTTTTC
40333197 TTGCTCACAC
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
15 10 0.16
16 16 0.25
17 11 0.17
18 22 0.34
19 5 0.08
ACGTcount: A:0.09, C:0.31, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTCTTTTTCAAGCTCTC
Found at i:40333143 original size:16 final size:16
Alignment explanation
Indices: 40333122--40333176 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
40333112 AAGCTCTCTC
40333122 TCTTTTTCACTCGTTT
1 TCTTTTTCACTCGTTT
40333138 TC-TTTTCAAGCTC-TCTT
1 TCTTTTTC-A-CTCGT-TT
* *
40333155 TCCTTTTCACTCGCTT
1 TCTTTTTCACTCGTTT
40333171 TCTTTT
1 TCTTTT
40333177 CAAAGCTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
15 5 0.16
16 14 0.44
17 8 0.25
18 5 0.16
ACGTcount: A:0.07, C:0.29, G:0.05, T:0.58
Consensus pattern (16 bp):
TCTTTTTCACTCGTTT
Found at i:40333144 original size:33 final size:33
Alignment explanation
Indices: 40333102--40333196 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
40333092 TCTTCACACA
* * *
40333102 TTTCTTTTTCAAGCTCTCTCTCTTTTTCACTCGT
1 TTTC-TTTTCAAGCTCTCTTTCCTTTTCACTCGC
40333136 TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCGC
1 TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCGC
40333169 TTTCTTTTCAAAGCTCTCTTTCCTTTTC
1 TTTCTTTTC-AAGCTCTCTTTCCTTTTC
40333197 TTGCTCACAC
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 35 0.61
34 22 0.39
ACGTcount: A:0.09, C:0.31, G:0.05, T:0.55
Consensus pattern (33 bp):
TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCGC
Found at i:40333145 original size:15 final size:15
Alignment explanation
Indices: 40333125--40333178 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
40333115 CTCTCTCTCT
40333125 TTTTCACTCGTTTTC
1 TTTTCACTCGTTTTC
40333140 TTTTCAAGCTC-TCTTTCC
1 TTTTC-A-CTCGT-TTT-C
*
40333158 TTTTCACTCGCTTTC
1 TTTTCACTCGTTTTC
40333173 TTTTCA
1 TTTTCA
40333179 AAGCTCTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
15 12 0.36
16 8 0.24
17 7 0.21
18 6 0.18
ACGTcount: A:0.09, C:0.30, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTTCACTCGTTTTC
Found at i:40333288 original size:33 final size:33
Alignment explanation
Indices: 40333223--40333288 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
40333213 TTGCTCTCAA
**
40333223 TCTCTTTTTCTTTTTCAATTCTTTTGTTTCATT
1 TCTCTTTTTCTTTTTCAATTCTTTTGACTCATT
*
40333256 TCTCTTTTTCTTTTT-ATTTCTTTTTGACTCATT
1 TCTCTTTTTCTTTTTCAATTC-TTTTGACTCATT
40333289 CTTTCATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (33 bp):
TCTCTTTTTCTTTTTCAATTCTTTTGACTCATT
Found at i:40340887 original size:4 final size:4
Alignment explanation
Indices: 40340880--40340909 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
40340870 AATTAATCAA
*
40340880 TCAT TCAT TCAT CCAT TCAT TCAT TCAT TC
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TC
40340910 GCTCATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (4 bp):
TCAT
Found at i:40350172 original size:9 final size:9
Alignment explanation
Indices: 40350158--40350271 Score: 86
Period size: 9 Copynumber: 12.7 Consensus size: 9
40350148 CAAGTTTGGG
*
40350158 CATGCACTC
1 CATGCATTC
40350167 CATGCATTC
1 CATGCATTC
***
40350176 CATGCAAAA
1 CATGCATTC
*
40350185 CATGCTTTC
1 CATGCATTC
40350194 CATGCATTC
1 CATGCATTC
* ***
40350203 CACGCAAAA
1 CATGCATTC
40350212 CATGCATTC
1 CATGCATTC
40350221 CATGCATTC
1 CATGCATTC
**
40350230 CATGCAACC
1 CATGCATTC
*
40350239 CATGCATTT
1 CATGCATTC
*
40350248 CATGCGA-AC
1 CATGC-ATTC
*
40350257 CATGCATCC
1 CATGCATTC
40350266 CATGCA
1 CATGCA
40350272 ATTTGCTACA
Statistics
Matches: 78, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
8 1 0.01
9 76 0.97
10 1 0.01
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.25
Consensus pattern (9 bp):
CATGCATTC
Found at i:40350196 original size:27 final size:27
Alignment explanation
Indices: 40350158--40350252 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
40350148 CAAGTTTGGG
*
40350158 CATGCACTCCATGCATTCCATGCAAAA
1 CATGCATTCCATGCATTCCATGCAAAA
* *
40350185 CATGCTTTCCATGCATTCCACGCAAAA
1 CATGCATTCCATGCATTCCATGCAAAA
**
40350212 CATGCATTCCATGCATTCCATGCAACC
1 CATGCATTCCATGCATTCCATGCAAAA
*
40350239 CATGCATTTCATGC
1 CATGCATTCCATGC
40350253 GAACCATGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.28, C:0.34, G:0.12, T:0.26
Consensus pattern (27 bp):
CATGCATTCCATGCATTCCATGCAAAA
Found at i:40350259 original size:27 final size:27
Alignment explanation
Indices: 40350158--40350271 Score: 104
Period size: 27 Copynumber: 4.2 Consensus size: 27
40350148 CAAGTTTGGG
* * **
40350158 CATGCACTCCATGCATTCCATGCAAAA
1 CATGCATTCCATGCATACCATGCAACC
* * * **
40350185 CATGCTTTCCATGCATTCCACGCAAAA
1 CATGCATTCCATGCATACCATGCAACC
*
40350212 CATGCATTCCATGCATTCCATGCAACC
1 CATGCATTCCATGCATACCATGCAACC
* *
40350239 CATGCATTTCATGCGA-ACCATGCATCC
1 CATGCATTCCATGC-ATACCATGCAACC
40350266 CATGCA
1 CATGCA
40350272 ATTTGCTACA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
27 75 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.25
Consensus pattern (27 bp):
CATGCATTCCATGCATACCATGCAACC
Found at i:40350434 original size:41 final size:41
Alignment explanation
Indices: 40350387--40350470 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
40350377 GTTTAGACAT
*
40350387 TTTAAATGTGTGTCTTAAATACTGCACTTTAATTATAAGTC
1 TTTAAATATGTGTCTTAAATACTGCACTTTAATTATAAGTC
* *
40350428 TTTAAATATGTGTCTTAAATATTGCACTTTAATTATATGTC
1 TTTAAATATGTGTCTTAAATACTGCACTTTAATTATAAGTC
40350469 TT
1 TT
40350471 AGTTCTTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (41 bp):
TTTAAATATGTGTCTTAAATACTGCACTTTAATTATAAGTC
Found at i:40352133 original size:37 final size:37
Alignment explanation
Indices: 40352092--40352166 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
40352082 CCCCAAAAAG
40352092 AATGATGCTTGGGGTGGTGGTGTGCCCAATATAACAT
1 AATGATGCTTGGGGTGGTGGTGTGCCCAATATAACAT
*
40352129 AATGATGCTTGGGGTGGTGGTGTGCCCAATCTAACAT
1 AATGATGCTTGGGGTGGTGGTGTGCCCAATATAACAT
40352166 A
1 A
40352167 CCAAGCTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (37 bp):
AATGATGCTTGGGGTGGTGGTGTGCCCAATATAACAT
Found at i:40353619 original size:27 final size:27
Alignment explanation
Indices: 40353579--40353673 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
40353569 CGAGTTTAGG
* *
40353579 CATGCACTCTATGCATTCTATGAAAAA
1 CATGCATTCCATGCATTCTATGAAAAA
* ** *
40353606 CCTGCATTCCATGCGCTCTATGTAAAA
1 CATGCATTCCATGCATTCTATGAAAAA
* * * **
40353633 CATGCATTTCATGCATTCCATGCAACC
1 CATGCATTCCATGCATTCTATGAAAAA
*
40353660 CATGCATTTCATGC
1 CATGCATTCCATGC
40353674 GAATGCATCC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (27 bp):
CATGCATTCCATGCATTCTATGAAAAA
Found at i:40356472 original size:20 final size:19
Alignment explanation
Indices: 40356447--40356560 Score: 93
Period size: 20 Copynumber: 5.7 Consensus size: 19
40356437 CATGCGGTTT
40356447 AGCTCACTTGAGCTCAAGTC
1 AGCTCA-TTGAGCTCAAGTC
*
40356467 AGCTCATTTGAGCTCAAGTA
1 AGCTCA-TTGAGCTCAAGTC
*
40356487 AGCTCATTCAAGCTCAAGTC
1 AGCTCATT-GAGCTCAAGTC
* * * *
40356507 GGCTTATTTAAGCTCAATTC
1 AGCTCA-TTGAGCTCAAGTC
* * * *
40356527 AACTTATTCGAGCTCAATTT
1 AGCTCATT-GAGCTCAAGTC
40356547 AGCTCATTGAGCTC
1 AGCTCATTGAGCTC
40356561 GTTATTAGCT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
19 10 0.13
20 66 0.85
21 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (19 bp):
AGCTCATTGAGCTCAAGTC
Found at i:40356491 original size:40 final size:40
Alignment explanation
Indices: 40356457--40356554 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 40
40356447 AGCTCACTTG
*
40356457 AGCTCAAGTCAGCTCATTTGAGCTCAAGTAAGCTCATTCA
1 AGCTCAAGTCAGCTCATTTAAGCTCAAGTAAGCTCATTCA
* * * * *
40356497 AGCTCAAGTCGGCTTATTTAAGCTCAATTCAA-CTTATTCG
1 AGCTCAAGTCAGCTCATTTAAGCTCAAGT-AAGCTCATTCA
* *
40356537 AGCTCAATTTAGCTCATT
1 AGCTCAAGTCAGCTCATT
40356555 GAGCTCGTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 45 0.96
41 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (40 bp):
AGCTCAAGTCAGCTCATTTAAGCTCAAGTAAGCTCATTCA
Found at i:40358098 original size:15 final size:16
Alignment explanation
Indices: 40358078--40358117 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
40358068 GAAGAAATTT
40358078 CAAAAAAAAAGT-GAG
1 CAAAAAAAAAGTCGAG
40358093 C-AAAAAAAA-TCGAG
1 CAAAAAAAAAGTCGAG
40358107 CAAAAAAAAAG
1 CAAAAAAAAAG
40358118 AATTGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 12 0.55
15 9 0.41
ACGTcount: A:0.70, C:0.10, G:0.15, T:0.05
Consensus pattern (16 bp):
CAAAAAAAAAGTCGAG
Found at i:40359216 original size:18 final size:18
Alignment explanation
Indices: 40359195--40359229 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40359185 GAGTGGGGGT
40359195 GAAAA-AAAATCTGAAAAC
1 GAAAAGAAAAT-TGAAAAC
40359213 GAAAAGAAAATTGAAAA
1 GAAAAGAAAATTGAAAA
40359230 TGAGATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.06, G:0.14, T:0.11
Consensus pattern (18 bp):
GAAAAGAAAATTGAAAAC
Found at i:40361020 original size:10 final size:9
Alignment explanation
Indices: 40361005--40361122 Score: 67
Period size: 10 Copynumber: 12.0 Consensus size: 9
40360995 CATTTGGTTT
40361005 AGCTCACTTG
1 AGCTCA-TTG
40361015 AGCTCAAGTT-
1 AGCTC-A-TTG
40361025 AGCTCATTCG
1 AGCTCATT-G
* *
40361035 AGCTCAAGTC
1 AGCTC-ATTG
40361045 AGCTCATTCG
1 AGCTCATT-G
* *
40361055 AGCTCAAGTC
1 AGCTC-ATTG
40361065 AGCTCATTCG
1 AGCTCATT-G
* *
40361075 AGCTCAAATC
1 AGCTC-ATTG
40361085 AGCTCATTCG
1 AGCTCATT-G
*
40361095 AGCTCAATTT
1 AGCTC-ATTG
40361105 AGCTCATTG
1 AGCTCATTG
40361114 AGCTCATTG
1 AGCTCATTG
40361123 TTAGCTCTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 21
0.70 0.13 0.18
Matches are distributed among these distances:
8 2 0.02
9 19 0.23
10 50 0.60
11 12 0.14
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (9 bp):
AGCTCATTG
Found at i:40361028 original size:20 final size:20
Alignment explanation
Indices: 40361003--40361129 Score: 168
Period size: 20 Copynumber: 6.3 Consensus size: 20
40360993 CTCATTTGGT
40361003 TTAGCTCACTT-GAGCTCAAG
1 TTAGCTCA-TTCGAGCTCAAG
40361023 TTAGCTCATTCGAGCTCAAG
1 TTAGCTCATTCGAGCTCAAG
*
40361043 TCAGCTCATTCGAGCTCAAG
1 TTAGCTCATTCGAGCTCAAG
* *
40361063 TCAGCTCATTCGAGCTCAAA
1 TTAGCTCATTCGAGCTCAAG
* *
40361083 TCAGCTCATTCGAGCTCAAT
1 TTAGCTCATTCGAGCTCAAG
*
40361103 TTAGCTCATT-GAGCTCATTG
1 TTAGCTCATTCGAGCTCA-AG
40361123 TTAGCTC
1 TTAGCTC
40361130 TTTAGTTCAT
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
19 9 0.09
20 90 0.91
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (20 bp):
TTAGCTCATTCGAGCTCAAG
Found at i:40372258 original size:8 final size:8
Alignment explanation
Indices: 40372242--40372275 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
40372232 CAGGTATTCC
*
40372242 AAAAGAAA
1 AAAATAAA
40372250 AAAATAAAA
1 AAAAT-AAA
40372259 AAAATAAA
1 AAAATAAA
40372267 AAAATAAA
1 AAAATAAA
40372275 A
1 A
40372276 TGTCTAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (8 bp):
AAAATAAA
Found at i:40372261 original size:9 final size:9
Alignment explanation
Indices: 40372247--40372275 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
40372237 ATTCCAAAAG
40372247 AAAAAAATA
1 AAAAAAATA
40372256 AAAAAAAT-
1 AAAAAAATA
40372264 AAAAAAATA
1 AAAAAAATA
40372273 AAA
1 AAA
40372276 TGTCTAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:40372267 original size:17 final size:17
Alignment explanation
Indices: 40372242--40372275 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40372232 CAGGTATTCC
40372242 AAAAGAAAAAAATAAAA
1 AAAAGAAAAAAATAAAA
*
40372259 AAAATAAAAAAATAAAA
1 AAAAGAAAAAAATAAAA
40372276 TGTCTAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAAAATAAAA
Found at i:40375251 original size:168 final size:168
Alignment explanation
Indices: 40374973--40375314 Score: 666
Period size: 168 Copynumber: 2.0 Consensus size: 168
40374963 TGCTCGAAAG
* *
40374973 TTAAAGTTACAAAACAGTCCTTGATCACTTTTAAGCTAGGGAATTACGAGGATGAGGTATGGTGT
1 TTAAAGTTACAAAACAGTCCTTGATCACGTTTAAGCTAGGGAATTACGAGGATGAGGTATGGTGC
40375038 GATGTGGTCCCAATGCATGCGACACACTTGCTCCTTAGATGGCCTTGGTAATTTGATCGTGATGT
66 GATGTGGTCCCAATGCATGCGACACACTTGCTCCTTAGATGGCCTTGGTAATTTGATCGTGATGT
40375103 TACACACCAAGGTAAGCTCAATAGATACTCTCTTGTGT
131 TACACACCAAGGTAAGCTCAATAGATACTCTCTTGTGT
40375141 TTAAAGTTACAAAACAGTCCTTGATCACGTTTAAGCTAGGGAATTACGAGGATGAGGTATGGTGC
1 TTAAAGTTACAAAACAGTCCTTGATCACGTTTAAGCTAGGGAATTACGAGGATGAGGTATGGTGC
40375206 GATGTGGTCCCAATGCATGCGACACACTTGCTCCTTAGATGGCCTTGGTAATTTGATCGTGATGT
66 GATGTGGTCCCAATGCATGCGACACACTTGCTCCTTAGATGGCCTTGGTAATTTGATCGTGATGT
40375271 TACACACCAAGGTAAGCTCAATAGATACTCTCTTGTGT
131 TACACACCAAGGTAAGCTCAATAGATACTCTCTTGTGT
40375309 TTAAAG
1 TTAAAG
40375315 GCTGAAATTC
Statistics
Matches: 172, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 172 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (168 bp):
TTAAAGTTACAAAACAGTCCTTGATCACGTTTAAGCTAGGGAATTACGAGGATGAGGTATGGTGC
GATGTGGTCCCAATGCATGCGACACACTTGCTCCTTAGATGGCCTTGGTAATTTGATCGTGATGT
TACACACCAAGGTAAGCTCAATAGATACTCTCTTGTGT
Found at i:40378501 original size:27 final size:30
Alignment explanation
Indices: 40378465--40378546 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 30
40378455 GAATATAAAG
40378465 GGGGTTGCTAAGTGCTGATTCCC-C-CA-A
1 GGGGTTGCTAAGTGCTGATTCCCACTCATA
*
40378492 GGGGTTGCTAAGTGCTGATTCCCTGACTCATT
1 GGGGTTGCTAAGTGCTGATTCCC--ACTCATA
40378524 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
40378547 ACCGTATCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 23 0.48
30 1 0.02
31 2 0.04
32 2 0.04
33 20 0.42
ACGTcount: A:0.16, C:0.22, G:0.30, T:0.32
Consensus pattern (30 bp):
GGGGTTGCTAAGTGCTGATTCCCACTCATA
Found at i:40378604 original size:105 final size:105
Alignment explanation
Indices: 40378464--40378655 Score: 312
Period size: 105 Copynumber: 1.8 Consensus size: 105
40378454 TGAATATAAA
* * * * * *
40378464 GGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCTGACTCATTGGTGG
1 GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGG
*
40378529 TTGCTAAGTGCTGATTCCACCGTATCTTTGAATGTAAAAG
66 TTGCTAAGTGCTGAATCCACCGTATCTTTGAATGTAAAAG
40378569 GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGG
1 GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGG
*
40378634 TTGCTAAGTTCTGAATCCACCG
66 TTGCTAAGTGCTGAATCCACCG
40378656 ATAACGGACA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 79 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (105 bp):
GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGG
TTGCTAAGTGCTGAATCCACCGTATCTTTGAATGTAAAAG
Found at i:40381240 original size:49 final size:49
Alignment explanation
Indices: 40381159--40381252 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
40381149 ATCTCAGTTG
*
40381159 CGAGCATCAACGAACCAATTTCGGGAGAGAACGAATTACAAGCCCGTTA
1 CGAGCATCAACGAACCAATTTCAGGAGAGAACGAATTACAAGCCCGTTA
* *
40381208 CGAGCATCAACGAACCAATTTCAGGAGCGAACGGATTACAAGCCC
1 CGAGCATCAACGAACCAATTTCAGGAGAGAACGAATTACAAGCCC
40381253 AAGTTCTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.15
Consensus pattern (49 bp):
CGAGCATCAACGAACCAATTTCAGGAGAGAACGAATTACAAGCCCGTTA
Found at i:40384373 original size:11 final size:11
Alignment explanation
Indices: 40384352--40384387 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
40384342 TAAAACCTGC
40384352 TAAAA-CAAAT
1 TAAAAGCAAAT
40384362 TAAAAGCAAAT
1 TAAAAGCAAAT
*
40384373 TTAAAGCAAAT
1 TAAAAGCAAAT
40384384 TAAA
1 TAAA
40384388 CACACAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.64, C:0.08, G:0.06, T:0.22
Consensus pattern (11 bp):
TAAAAGCAAAT
Found at i:40385650 original size:22 final size:21
Alignment explanation
Indices: 40385625--40385666 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
40385615 TTAAATAAAT
*
40385625 TTTAGTTAATTTAGTTTAAGTA
1 TTTAATTAATTTAG-TTAAGTA
40385647 TTTAATTAATTTAGTTAAGT
1 TTTAATTAATTTAGTTAAGT
40385667 GTTAAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTTAGTTAAGTA
Found at i:40386927 original size:28 final size:28
Alignment explanation
Indices: 40386885--40386947 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
40386875 CTATTCACTA
40386885 ACAGT-ACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
*
40386912 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
40386940 ACAGTAAC
1 ACAGTAAC
40386948 CAATACAGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:40387330 original size:27 final size:27
Alignment explanation
Indices: 40387300--40387700 Score: 358
Period size: 27 Copynumber: 14.9 Consensus size: 27
40387290 GGGTATAACA
*
40387300 GTCATTTTACCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *** * **
40387327 GTCATTCTACCCTGCAGAGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
40387354 GCCATTTTACCCTACGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
40387381 GTCATTTTACCCTATGGTGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTTG
40387408 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * ** **
40387435 GTCATTTTATCTTATAAGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
40387462 ATCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
40387489 ATTATTTTACCCTATGGGGGGATTCTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
40387516 GTCATTTTACACTATGAGGGTATTGCT-
1 GTCATTTTACCCTATGGGGGTATT-TTG
*
40387543 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
40387570 ATTATTTTACCATATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * **
40387597 GTCATTTTACCTTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
40387624 GTTAATTTATCCTATGGGGATATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
40387651 GTAATTTTATCCTAT--GGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
*
40387676 TTCATTTTACCCTATGGGGGTATTT
1 GTCATTTTACCCTATGGGGGTATTT
40387701 GGGCTCTCGA
Statistics
Matches: 295, Mismatches: 75, Indels: 8
0.78 0.20 0.02
Matches are distributed among these distances:
25 21 0.07
27 272 0.92
28 2 0.01
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTTG
Found at i:40387682 original size:25 final size:25
Alignment explanation
Indices: 40387629--40387692 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
40387619 TTTCAGTTAA
*
40387629 TTTATCCTATGGGGATATTTTGGTAAT
1 TTTATCCTAT--GGATATTTCGGTAAT
* *
40387656 TTTATCCTATGGATATTTCGTTCAT
1 TTTATCCTATGGATATTTCGGTAAT
*
40387681 TTTACCCTATGG
1 TTTATCCTATGG
40387693 GGGTATTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 23 0.70
27 10 0.30
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.48
Consensus pattern (25 bp):
TTTATCCTATGGATATTTCGGTAAT
Found at i:40395537 original size:33 final size:34
Alignment explanation
Indices: 40395486--40395560 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
40395476 AGAGTTAAAC
*
40395486 AAATTAATTACTAACACTTATTTAAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
40395520 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
40395553 AATTTAAT
1 AAATTAAT
40395561 AAACCAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:40396707 original size:27 final size:27
Alignment explanation
Indices: 40396675--40396727 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
40396665 CTTGTCTGTT
40396675 TCTTTTTCACTCTCAATCTCTTTTTTC
1 TCTTTTTCACTCTCAATCTCTTTTTTC
* **
40396702 TCTTTTTCATTCTCTTTCTCTTTTTT
1 TCTTTTTCACTCTCAATCTCTTTTTT
40396728 GATTTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (27 bp):
TCTTTTTCACTCTCAATCTCTTTTTTC
Found at i:40397575 original size:11 final size:11
Alignment explanation
Indices: 40397559--40397584 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40397549 TTAGAAAGTG
40397559 TAAAGGATGAA
1 TAAAGGATGAA
40397570 TAAAGGATGAA
1 TAAAGGATGAA
40397581 TAAA
1 TAAA
40397585 AGCAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (11 bp):
TAAAGGATGAA
Found at i:40412186 original size:21 final size:21
Alignment explanation
Indices: 40412162--40412201 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40412152 TACTCCGACT
*
40412162 CTTCCTCCTCTTCTTCCTCCA
1 CTTCCTCCTCCTCTTCCTCCA
40412183 CTTCCTCCTCCTCTTCCTC
1 CTTCCTCCTCCTCTTCCTC
40412202 TTCCAAGAGT
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:0.03, C:0.55, G:0.00, T:0.42
Consensus pattern (21 bp):
CTTCCTCCTCCTCTTCCTCCA
Found at i:40412199 original size:12 final size:12
Alignment explanation
Indices: 40412164--40412201 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
40412154 CTCCGACTCT
*
40412164 TCCTCCTCTTCT
1 TCCTCCTCTTCC
*
40412176 TCCTCCACTTCC
1 TCCTCCTCTTCC
40412188 TCCTCCTCTTCC
1 TCCTCCTCTTCC
40412200 TC
1 TC
40412202 TTCCAAGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.55, G:0.00, T:0.42
Consensus pattern (12 bp):
TCCTCCTCTTCC
Found at i:40416254 original size:20 final size:20
Alignment explanation
Indices: 40416229--40416268 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40416219 AAGTTCTTTC
*
40416229 ACACTGATAGCACAAAACAA
1 ACACTGACAGCACAAAACAA
40416249 ACACTGACAGCACAAAACAA
1 ACACTGACAGCACAAAACAA
40416269 GAAATACTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.28, G:0.10, T:0.07
Consensus pattern (20 bp):
ACACTGACAGCACAAAACAA
Found at i:40417582 original size:2 final size:2
Alignment explanation
Indices: 40417575--40417605 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40417565 GTCTCGCTTG
40417575 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40417606 TTTGCGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:40417804 original size:25 final size:25
Alignment explanation
Indices: 40417751--40417805 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
40417741 AACTTACACT
* * *
40417751 GCGATGCAGCAGAGGACTGTTGACG
1 GCGATGCAGCAGAGGACTATCGACA
*
40417776 GCGATGCAGCAGAGGATTATCGACA
1 GCGATGCAGCAGAGGACTATCGACA
40417801 GCGAT
1 GCGAT
40417806 ACAACAGACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.36, T:0.16
Consensus pattern (25 bp):
GCGATGCAGCAGAGGACTATCGACA
Found at i:40418094 original size:41 final size:40
Alignment explanation
Indices: 40417956--40418095 Score: 129
Period size: 41 Copynumber: 3.5 Consensus size: 40
40417946 TTTATGGGCA
*
40417956 AAACGTCGCTATTGCTTTACC-TTTAGCGGCGTTTTTTCAT
1 AAACGTCGCTATTGCTTTACCTTTTA-TGGCGTTTTTTCAT
* * * * *** *
40417996 AAACGCCGCTATTGCTTTACCTTTTGTAGCGATTATGAGAA
1 AAACGTCGCTATTGCTTTACCTTTTATGGCG-TTTTTTCAT
* * *
40418037 AAATGTCACTACTGCTTTACCTTTTATGGCGTTTTTCTCAT
1 AAACGTCGCTATTGCTTTACCTTTTATGGCGTTTTT-TCAT
*
40418078 AAACGTCGTTATTGCTTT
1 AAACGTCGCTATTGCTTT
40418096 TCTTATTGCG
Statistics
Matches: 73, Mismatches: 24, Indels: 5
0.72 0.24 0.05
Matches are distributed among these distances:
40 26 0.36
41 47 0.64
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (40 bp):
AAACGTCGCTATTGCTTTACCTTTTATGGCGTTTTTTCAT
Found at i:40418723 original size:16 final size:18
Alignment explanation
Indices: 40418692--40418726 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
40418682 ACGGAATTAG
40418692 ATTTGGGTTGAGAAAATT
1 ATTTGGGTTGAGAAAATT
40418710 ATTT-GGTT-AGAAAATT
1 ATTTGGGTTGAGAAAATT
40418726 A
1 A
40418727 ATTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (18 bp):
ATTTGGGTTGAGAAAATT
Found at i:40424449 original size:26 final size:26
Alignment explanation
Indices: 40424401--40424505 Score: 69
Period size: 25 Copynumber: 4.2 Consensus size: 26
40424391 ACATACCACA
* * **
40424401 GCTCTTTATGAGCGTCCTAATATATG
1 GCTCTTCATGAGCTTCCCGATATATG
40424427 GCTCTTCATGAGCTTCCCG--ATATG
1 GCTCTTCATGAGCTTCCCGATATATG
* * *
40424451 GCTC-GCTTGAACTTCCTC-ATATATG
1 GCTCTTCATGAGCTTCC-CGATATATG
* * *
40424476 GCTATTCA-GAGCTTCCTGATA-ATA
1 GCTCTTCATGAGCTTCCCGATATATG
40424500 GCTCTT
1 GCTCTT
40424506 TAGAGTTACC
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
23 9 0.15
24 17 0.28
25 18 0.30
26 16 0.27
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (26 bp):
GCTCTTCATGAGCTTCCCGATATATG
Found at i:40424588 original size:23 final size:23
Alignment explanation
Indices: 40424558--40424614 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
40424548 TTTTATGAGT
*
40424558 TTCCTGTTATAGCCCAGATAAGC
1 TTCCTGTTACAGCCCAGATAAGC
40424581 TTCCTGTTACAGCCCAGATAAGC
1 TTCCTGTTACAGCCCAGATAAGC
40424604 TTCCTGTTACA
1 TTCCTGTTACA
40424615 TGGCTCACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.32
Consensus pattern (23 bp):
TTCCTGTTACAGCCCAGATAAGC
Found at i:40431957 original size:20 final size:20
Alignment explanation
Indices: 40431932--40431971 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40431922 GTCAAATTAT
*
40431932 AAAGTCTTAACTATGGTATA
1 AAAGTCTTAACAATGGTATA
40431952 AAAGTCTTAACAATGGTATA
1 AAAGTCTTAACAATGGTATA
40431972 TATATGTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
AAAGTCTTAACAATGGTATA
Found at i:40438066 original size:14 final size:14
Alignment explanation
Indices: 40438049--40438114 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
40438039 CCCGAACACC
*
40438049 AAACCATGAACCTT
1 AAACCATAAACCTT
* *
40438063 AAACC-TCAAACATC
1 AAACCAT-AAACCTT
40438077 AAACCATAAACCTT
1 AAACCATAAACCTT
*
40438091 AAACCTTAAACAC-T
1 AAACCATAAAC-CTT
*
40438105 AAACCTTAAA
1 AAACCATAAA
40438115 TTCAAGCTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.02
14 40 0.93
15 2 0.05
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.20
Consensus pattern (14 bp):
AAACCATAAACCTT
Found at i:40438067 original size:7 final size:7
Alignment explanation
Indices: 40438057--40438114 Score: 64
Period size: 7 Copynumber: 8.3 Consensus size: 7
40438047 CCAAACCATG
40438057 AACCTTA
1 AACCTTA
*
40438064 AACCTCA
1 AACCTTA
* *
40438071 AACATCA
1 AACCTTA
*
40438078 AACCATA
1 AACCTTA
40438085 AACCTTA
1 AACCTTA
40438092 AACCTTA
1 AACCTTA
40438099 AACAC-TA
1 AAC-CTTA
40438106 AACCTTA
1 AACCTTA
40438113 AA
1 AA
40438115 TTCAAGCTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
6 1 0.02
7 41 0.95
8 1 0.02
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (7 bp):
AACCTTA
Found at i:40438079 original size:28 final size:28
Alignment explanation
Indices: 40438043--40438114 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
40438033 TTGAACCCCG
*
40438043 AACACCAAACCATGAACCTTAAACCTCA
1 AACACCAAACCATAAACCTTAAACCTCA
* *
40438071 AACATCAAACCATAAACCTTAAACCTTA
1 AACACCAAACCATAAACCTTAAACCTCA
* *
40438099 AACACTAAACCTTAAA
1 AACACCAAACCATAAA
40438115 TTCAAGCTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.18
Consensus pattern (28 bp):
AACACCAAACCATAAACCTTAAACCTCA
Found at i:40444550 original size:28 final size:28
Alignment explanation
Indices: 40444518--40444574 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
40444508 TATGTACAAA
40444518 AATCATGTAATTAAGCATAATTTCACAG
1 AATCATGTAATTAAGCATAATTTCACAG
*
40444546 AATCATGTAATTAAGCATAATTTCTCAG
1 AATCATGTAATTAAGCATAATTTCACAG
40444574 A
1 A
40444575 CTTTAAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (28 bp):
AATCATGTAATTAAGCATAATTTCACAG
Found at i:40449138 original size:19 final size:20
Alignment explanation
Indices: 40449114--40449151 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40449104 ATTATTATAC
*
40449114 TTATTATTACT-TTAGTTTA
1 TTATTATAACTATTAGTTTA
40449133 TTATTATAACTATTAGTTT
1 TTATTATAACTATTAGTTT
40449152 TACTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
TTATTATAACTATTAGTTTA
Found at i:40453082 original size:27 final size:27
Alignment explanation
Indices: 40453052--40453119 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
40453042 GAAAGAACTA
40453052 CTTTTGTGGCATACTCTAAATGGATTG
1 CTTTTGTGGCATACTCTAAATGGATTG
* * * *
40453079 CTTTTGTGACGTACTCTGAATGGGTTG
1 CTTTTGTGGCATACTCTAAATGGATTG
* *
40453106 CCTTAGTGGCATAC
1 CTTTTGTGGCATAC
40453120 CATGATAAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (27 bp):
CTTTTGTGGCATACTCTAAATGGATTG
Found at i:40461350 original size:21 final size:22
Alignment explanation
Indices: 40461324--40461366 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
40461314 TACTACATAT
40461324 AATATTTAAATCATT-TTTAAA
1 AATATTTAAATCATTGTTTAAA
* *
40461345 AATATTTGAATTATTGTTTAAA
1 AATATTTAAATCATTGTTTAAA
40461367 TAAGTAGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
AATATTTAAATCATTGTTTAAA
Found at i:40469801 original size:1 final size:1
Alignment explanation
Indices: 40469749--40469781 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
40469739 TTATCATGGC
*
40469749 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40469782 GGAANNNNNN
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:40471348 original size:1 final size:1
Alignment explanation
Indices: 40471342--40472138 Score: 1594
Period size: 1 Copynumber: 797.0 Consensus size: 1
40471332 TTTCTTAAGC
40471342 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471407 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471472 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471537 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471602 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471667 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471732 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471797 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471862 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471927 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40471992 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40472057 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40472122 TTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTT
40472139 GTGGAGCTCA
Statistics
Matches: 796, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 796 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40475311 original size:3 final size:3
Alignment explanation
Indices: 40475303--40475328 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40475293 AAAAACAAAA
40475303 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
40475329 ACCCTACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40480556 original size:57 final size:57
Alignment explanation
Indices: 40480470--40481309 Score: 1558
Period size: 57 Copynumber: 14.8 Consensus size: 57
40480460 NNNNNNNAAT
** * *
40480470 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40480525 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40480582 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40480639 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40480696 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40480753 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40480810 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40480867 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40480924 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40480981 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40481038 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40481095 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
40481152 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
* * *
40481209 CATATCATATCTAAGATTATATATCATATCTAAGATTGCATATCATATCTAAGATTA
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
* * * * *
40481266 TATATTATATCTAAGATTGTATATCATATCTAAGATTGCATATC
1 CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATC
40481310 CCTGAAGATT
Statistics
Matches: 773, Mismatches: 10, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
55 6 0.01
56 1 0.00
57 766 0.99
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (57 bp):
CATATCATATCTAAGATTATATATTATATCTAAGATTGTATATCATATCTAAGATTG
Found at i:40486988 original size:22 final size:21
Alignment explanation
Indices: 40486953--40487076 Score: 75
Period size: 19 Copynumber: 6.2 Consensus size: 21
40486943 AAAGGGTATC
* *
40486953 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
40486974 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
40486997 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
40487016 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
40487035 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
40487054 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
40487073 TACA
1 TACA
40487077 TATCCCTGAA
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
17 2 0.02
19 56 0.64
21 5 0.06
22 15 0.17
23 10 0.11
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:40486996 original size:23 final size:22
Alignment explanation
Indices: 40486953--40487010 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40486943 AAAGGGTATC
* *
40486953 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40486974 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40486997 TGCATATCATATCT
1 TACAAATCATATCT
40487011 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40487013 original size:19 final size:19
Alignment explanation
Indices: 40486966--40487080 Score: 140
Period size: 19 Copynumber: 5.8 Consensus size: 19
40486956 AAATTAAATC
*
40486966 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
40486986 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
*
40487008 TCTAAGATTATATATCATA
1 TCTAAGATTACATATCATA
* *
40487027 TCTAAGATTATATATTATA
1 TCTAAGATTACATATCATA
*
40487046 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
40487065 TCTAAGATTACATATC
1 TCTAAGATTACATATC
40487081 CCTGAAGATT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
19 66 0.80
22 7 0.08
23 10 0.12
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:40487859 original size:18 final size:18
Alignment explanation
Indices: 40487823--40487859 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40487813 TCTTAATTTC
* *
40487823 TCTTCTCTCACACTTTTT
1 TCTTCTCTCAAACTCTTT
40487841 TCTTCTCTCAAACTCTTT
1 TCTTCTCTCAAACTCTTT
40487859 T
1 T
40487860 ATTTTTCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.32, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTCTCTCAAACTCTTT
Found at i:40500862 original size:84 final size:84
Alignment explanation
Indices: 40500755--40501722 Score: 1909
Period size: 84 Copynumber: 11.5 Consensus size: 84
40500745 CAAAGGATCC
* *
40500755 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40500820 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40500839 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40500904 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40500923 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40500988 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40501007 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40501072 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40501091 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40501156 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40501175 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40501240 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40501259 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40501324 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40501343 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40501408 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40501427 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40501492 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40501511 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40501576 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
40501595 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
40501660 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
*
40501679 CGGTGGAATCAGCACTTAACAACCACCTTATAATCAATGATACG
1 CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACG
40501723 AGTTCACATA
Statistics
Matches: 881, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 881 1.00
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (84 bp):
CGGTGGAATCAACACTTAACAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
CCTTTCACAATCAAGGATA
Found at i:40501807 original size:51 final size:51
Alignment explanation
Indices: 40501731--40501917 Score: 211
Period size: 51 Copynumber: 3.7 Consensus size: 51
40501721 CGAGTTCACA
* **
40501731 TAGTAGCCTACACATAGTACTACACATGTGACCATCA-CTATCCAATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT-AGCTATCCGGTACACG
* * * *
40501782 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATAGCTATCCGGTACACG
* * * *
40501833 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATAGCTATCCGGTACACG
*
40501883 TAGTAGCCTGCACACAGTACTACAC-TCGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACAT-GTGACCAT
40501918 CACTTTCACT
Statistics
Matches: 114, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 42 0.37
51 69 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATAGCTATCCGGTACACG
Found at i:40501906 original size:101 final size:101
Alignment explanation
Indices: 40501729--40501913 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
40501719 TACGAGTTCA
*
40501729 CATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCAATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCCAATACACGTAGTAGCCTGCA
*
40501794 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
65 CACAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * ***
40501831 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCCAATACACGTAGTAGCCTGCA
*
40501895 CACAGTACTACACTCGTGA
65 CACAGTACTACACACGTGA
40501914 CCATCACTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 1 0.01
101 40 0.54
102 33 0.45
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACTATCCAATACACGTAGTAGCCTGCAC
ACAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:40518181 original size:24 final size:24
Alignment explanation
Indices: 40518154--40518227 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
40518144 TTCGATGCAA
40518154 ATAAAAGTTGCTAATACAGTGTGG
1 ATAAAAGTTGCTAATACAGTGTGG
** ***
40518178 AT-AAA-CCGCTAAT-CAGTGCAA
1 ATAAAAGTTGCTAATACAGTGTGG
**
40518199 ATAAAAGTTGCTAATATGGTGTGG
1 ATAAAAGTTGCTAATACAGTGTGG
40518223 ATAAA
1 ATAAA
40518228 CCACTAAACA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
21 7 0.20
22 9 0.26
23 9 0.26
24 10 0.29
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (24 bp):
ATAAAAGTTGCTAATACAGTGTGG
Found at i:40518213 original size:45 final size:45
Alignment explanation
Indices: 40518119--40518242 Score: 169
Period size: 45 Copynumber: 2.7 Consensus size: 45
40518109 TAAAAACTAA
* *
40518119 TAATACAGTGAGGGTAAACCACTAATTC-GATGCAAATAAAAGTTGC
1 TAATACAGTGTGGATAAACCACTAA-TCAG-TGCAAATAAAAGTTGC
*
40518165 TAATACAGTGTGGATAAACCGCTAATCAGTGCAAATAAAAGTTGC
1 TAATACAGTGTGGATAAACCACTAATCAGTGCAAATAAAAGTTGC
** *
40518210 TAATATGGTGTGGATAAACCACTAAACAGTGCA
1 TAATACAGTGTGGATAAACCACTAATCAGTGCA
40518243 GACAAATTGC
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
45 47 0.67
46 23 0.33
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (45 bp):
TAATACAGTGTGGATAAACCACTAATCAGTGCAAATAAAAGTTGC
Found at i:40518739 original size:28 final size:27
Alignment explanation
Indices: 40518715--40518965 Score: 197
Period size: 28 Copynumber: 9.0 Consensus size: 27
40518705 CTTAAAATTT
*
40518715 TGGGTAAAATTGTAAAATCTAAAAATA
1 TGGGCAAAATTGTAAAATCTAAAAATA
*
40518742 AGGGCAAAACTT-TAAAATCTAAAAAATA
1 TGGGCAAAA-TTGTAAAATCT-AAAAATA
* *
40518770 TGGGCAAAATTGTAAAATTTAAAAAAA
1 TGGGCAAAATTGTAAAATCTAAAAATA
*
40518797 TGAG-AAATATTGTAAAATCTAAAAAATA
1 TGGGCAAA-ATTGTAAAATCT-AAAAATA
*
40518825 GGGGGCAAAATTGTAAAATCTAAAAAATA
1 -TGGGCAAAATTGTAAAATCT-AAAAATA
* *
40518854 TGAGCAAAATTGTAAAATTTAAAAA-A
1 TGGGCAAAATTGTAAAATCTAAAAATA
*
40518880 TAGGTG-AAAATTATAAAAT-TAGAAAAATA
1 T-GG-GCAAAATTGTAAAATCT--AAAAATA
* * * * * *
40518909 GGGGTAAAACTGTAAAAATTTTAAAGTA
1 TGGGCAAAATTGT-AAAATCTAAAAATA
* *
40518937 GGGGACAAAATTGTAAACTCTAATAAATA
1 TGGG-CAAAATTGTAAAATCTAA-AAATA
40518966 GGGGACACAT
Statistics
Matches: 181, Mismatches: 26, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
26 6 0.03
27 56 0.31
28 76 0.42
29 39 0.22
30 4 0.02
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (27 bp):
TGGGCAAAATTGTAAAATCTAAAAATA
Found at i:40518784 original size:55 final size:55
Alignment explanation
Indices: 40518720--40518965 Score: 225
Period size: 55 Copynumber: 4.4 Consensus size: 55
40518710 AATTTTGGGT
* *
40518720 AAAATTGTAAAATCTAAAAATAAGGGCAAAACTT-TAAAATCTAAAAAATATGGGC
1 AAAATTGTAAAATCTAAAAATAAGAGCAAAA-TTGTAAAATCTAAAAAATAGGGGC
*
40518775 AAAATTGTAAAATTTAAAAA-AATGAG-AAATATTGTAAAATCTAAAAAATAGGGGGC
1 AAAATTGTAAAATCTAAAAATAA-GAGCAAA-ATTGTAAAATCTAAAAAATA-GGGGC
* * *
40518831 AAAATTGTAAAATCTAAAAAATATGAGCAAAATTGTAAAATTTAAAAAATAGGTG-
1 AAAATTGTAAAATCT-AAAAATAAGAGCAAAATTGTAAAATCTAAAAAATAGGGGC
* * * * * ** *
40518886 AAAATTATAAAAT-TAGAAAAATAGGGGTAAAACTGTAAAAAT-TTTAAAGTAGGGGAC
1 AAAATTGTAAAATCT--AAAAATAAGAGCAAAATTGT-AAAATCTAAAAAATAGGGG-C
*
40518943 AAAATTGTAAACTCTAATAAATA
1 AAAATTGTAAAATCTAA-AAATA
40518966 GGGGACACAT
Statistics
Matches: 159, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
54 8 0.05
55 75 0.47
56 28 0.18
57 43 0.27
58 5 0.03
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.26
Consensus pattern (55 bp):
AAAATTGTAAAATCTAAAAATAAGAGCAAAATTGTAAAATCTAAAAAATAGGGGC
Found at i:40518852 original size:84 final size:83
Alignment explanation
Indices: 40518720--40518925 Score: 285
Period size: 84 Copynumber: 2.5 Consensus size: 83
40518710 AATTTTGGGT
* *
40518720 AAAATTGTAAAATCT-AAAAATAAGGGCAAAACTT-TAAAATCTAAAAAATATGGGCAAAATTGT
1 AAAATTGTAAAATCTAAAAAATAGGGGCAAAA-TTGTAAAATCTAAAAAATATGAGCAAAATTGT
*
40518783 AAAATTTAAAAAA-ATGAG
65 AAAATTTAAAAAATAGGAG
40518801 AAATATTGTAAAATCTAAAAAATAGGGGGCAAAATTGTAAAATCTAAAAAATATGAGCAAAATTG
1 AAA-ATTGTAAAATCTAAAAAATA-GGGGCAAAATTGTAAAATCTAAAAAATATGAGCAAAATTG
*
40518866 TAAAATTTAAAAAATAGGTG
64 TAAAATTTAAAAAATAGGAG
* * *
40518886 AAAATTATAAAAT-TAGAAAAATAGGGGTAAAACTGTAAAA
1 AAAATTGTAAAATCTA-AAAAATAGGGGCAAAATTGTAAAA
40518926 ATTTTAAAGT
Statistics
Matches: 112, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
81 3 0.03
82 12 0.11
83 26 0.23
84 65 0.58
85 6 0.05
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.25
Consensus pattern (83 bp):
AAAATTGTAAAATCTAAAAAATAGGGGCAAAATTGTAAAATCTAAAAAATATGAGCAAAATTGTA
AAATTTAAAAAATAGGAG
Found at i:40519962 original size:77 final size:79
Alignment explanation
Indices: 40519863--40520194 Score: 249
Period size: 86 Copynumber: 4.0 Consensus size: 79
40519853 TATAACTTGG
* * *
40519863 ATTATTTAATTAAATCTTGTTTGGAAACAAAATC-AA-AATAAAATTTGTTAAATGG-TAGGAAT
1 ATTATTTAATTAAATCTCGTTTGGAAACAAAATCAAAGAATAAAATCTGTTAAACGGCT-GGAAT
40519925 AAATCCCGAAACATA
65 AAATCCCGAAACATA
* *
40519940 ATTATTTGATTAATTCTCGTTTGGAAACAAAATCAAAATGGAATAAAATCTGTTAAACGGCTGGA
1 ATTATTTAATTAAATCTCGTTTGGAAACAAAATC-AAA--GAATAAAATCTGTTAAACGGCTGGA
*
40520005 ATAAATCCCGAAACAGA
63 ATAAATCCCGAAACATA
* * * ** * * *
40520022 TTTTATTTAATTTAATTCTTGTTTACAAATAAAATAAAAAATAGAATAAAATCTGTTAAACGGCG
1 -ATTATTTAA-TTAAATCTCGTTTGGAAACAAAAT---CAA-AGAATAAAATCTGTTAAACGGCT
*
40520087 GGAATAAATCCCAAAACATA
60 GGAATAAATCCCGAAACATA
* * * * * * * * *
40520107 TTTTACTTAATTTTAATTCTCGCTTAGAAAAAAAATAAAAAAAGGAATAAAATCTATTGAACGGC
1 -ATTATTTAA--TTAAATCTCGTTTGGAAACAAAAT---CAAA-GAATAAAATCTGTTAAACGGC
* *
40520172 GGGAATAAATCCCAAAACA-A
59 TGGAATAAATCCCGAAACATA
40520192 ATT
1 ATT
40520195 TTATTCAATT
Statistics
Matches: 217, Mismatches: 24, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
77 31 0.14
79 2 0.01
82 36 0.17
83 8 0.04
84 22 0.10
85 50 0.23
86 67 0.31
87 1 0.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (79 bp):
ATTATTTAATTAAATCTCGTTTGGAAACAAAATCAAAGAATAAAATCTGTTAAACGGCTGGAATA
AATCCCGAAACATA
Found at i:40520170 original size:86 final size:85
Alignment explanation
Indices: 40519899--40520210 Score: 362
Period size: 86 Copynumber: 3.7 Consensus size: 85
40519889 ACAAAATCAA
* * ** * * *
40519899 AATAAAATTTGTTAAATGGTAGGAATAAATCCCGAAACATA-ATTATTTGA-TTAATTCTCGTTT
1 AATAAAATCTGTTAAACGGCGGGAATAAATCCCAAAACATATTTTATTTAATTTAATTCTCGTTT
* * * *
40519962 GGAAACAAAAT-CAAAATGG
66 AGAAAAAAAATAAAAAAAGG
* * * *
40519981 AATAAAATCTGTTAAACGGCTGGAATAAATCCCGAAACAGATTTTATTTAATTTAATTCTTGTTT
1 AATAAAATCTGTTAAACGGCGGGAATAAATCCCAAAACATATTTTATTTAATTTAATTCTCGTTT
* *
40520046 ACAAATAAAATAAAAAATA-G
66 AGAAAAAAAATAAAAAA-AGG
* *
40520066 AATAAAATCTGTTAAACGGCGGGAATAAATCCCAAAACATATTTTACTTAATTTTAATTCTCGCT
1 AATAAAATCTGTTAAACGGCGGGAATAAATCCCAAAACATATTTTATTTAA-TTTAATTCTCGTT
40520131 TAGAAAAAAAATAAAAAAAGG
65 TAGAAAAAAAATAAAAAAAGG
* * * *
40520152 AATAAAATCTATTGAACGGCGGGAATAAATCCCAAAACAAATTTTATTCAATTTTAATT
1 AATAAAATCTGTTAAACGGCGGGAATAAATCCCAAAACATATTTTATTTAA-TTTAATT
40520211 TTTATTTTCA
Statistics
Matches: 198, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
82 36 0.18
83 7 0.04
84 20 0.10
85 53 0.27
86 82 0.41
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (85 bp):
AATAAAATCTGTTAAACGGCGGGAATAAATCCCAAAACATATTTTATTTAATTTAATTCTCGTTT
AGAAAAAAAATAAAAAAAGG
Found at i:40523374 original size:17 final size:18
Alignment explanation
Indices: 40523331--40523374 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
40523321 TGGTTAGACT
40523331 TTTATTTATTTTTAATATA
1 TTTA-TTATTTTTAATATA
*
40523350 ATTA-TATTTTTAAT-TA
1 TTTATTATTTTTAATATA
40523366 TTTATTATT
1 TTTATTATT
40523375 GTTCATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
19 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTTTTAATATA
Found at i:40523992 original size:110 final size:110
Alignment explanation
Indices: 40523856--40524075 Score: 431
Period size: 110 Copynumber: 2.0 Consensus size: 110
40523846 CAATCCATAT
40523856 TTATAAACCTTATTTAAATTAATTTTAATTTTTAAATGCATAAAAAAATTAATTATTTAACTATT
1 TTATAAACCTTATTTAAATTAATTTTAATTTTTAAATGCATAAAAAAATTAATTATTTAACTATT
40523921 AAACACAAAAATTTTAAATGAGGTATTAACTATTTTCTTGTCCTA
66 AAACACAAAAATTTTAAATGAGGTATTAACTATTTTCTTGTCCTA
40523966 TTATAAACCTTATTTAAATTAATTTTAATTTTTAAATGCATAAAAAAATTAATTATTTAACTATT
1 TTATAAACCTTATTTAAATTAATTTTAATTTTTAAATGCATAAAAAAATTAATTATTTAACTATT
*
40524031 AAACACAAAAATTTTAAATGAGGTATTAATTATTTTCTTGTCCTA
66 AAACACAAAAATTTTAAATGAGGTATTAACTATTTTCTTGTCCTA
40524076 ACATACATTA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.44
Consensus pattern (110 bp):
TTATAAACCTTATTTAAATTAATTTTAATTTTTAAATGCATAAAAAAATTAATTATTTAACTATT
AAACACAAAAATTTTAAATGAGGTATTAACTATTTTCTTGTCCTA
Found at i:40529211 original size:15 final size:15
Alignment explanation
Indices: 40529187--40529220 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40529177 AAGGTTTTTT
*
40529187 GTGTCTTCAAATCAG
1 GTGTCCTCAAATCAG
40529202 GTGTCCTCAAATCAG
1 GTGTCCTCAAATCAG
40529217 GTGT
1 GTGT
40529221 GGGATCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (15 bp):
GTGTCCTCAAATCAG
Found at i:40529331 original size:29 final size:29
Alignment explanation
Indices: 40529290--40529363 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
40529280 ATGACCCCCT
40529290 TGTATGCG-AACCCTTATAGGAGAACCCA
1 TGTATGCGAAACCCTTATAGGAGAACCCA
* * *
40529318 TGTATGCGAAACCCCTATAGGCGAACCCT
1 TGTATGCGAAACCCTTATAGGAGAACCCA
*
40529347 TGTATGC-AAACCATTAT
1 TGTATGCGAAACCCTTAT
40529364 GAATGAAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.40
29 24 0.60
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (29 bp):
TGTATGCGAAACCCTTATAGGAGAACCCA
Found at i:40534490 original size:41 final size:41
Alignment explanation
Indices: 40534428--40534507 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
40534418 TGATCGAATG
* *
40534428 TAATTCAGACTTATTGTCTAGCAGGCTTGATGCCAGTGATA
1 TAATTCAGACTTATTGCCTAGCAGGCTTCATGCCAGTGATA
40534469 TAATTCAGA-TTCATTGCCTAGCAGGCTTCATGCCAGTGA
1 TAATTCAGACTT-ATTGCCTAGCAGGCTTCATGCCAGTGA
40534508 AATTATTCGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 2 0.06
41 34 0.94
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (41 bp):
TAATTCAGACTTATTGCCTAGCAGGCTTCATGCCAGTGATA
Found at i:40534531 original size:41 final size:41
Alignment explanation
Indices: 40534428--40534536 Score: 121
Period size: 41 Copynumber: 2.7 Consensus size: 41
40534418 TGATCGAATG
* * * *
40534428 TAATTCAGACTTATTGTCTAGCAGGCTTGATGCCAGTGATA
1 TAATTCAGACTCATAGTCTAGCAGGCTTCATGCCAGTGAAA
* * *
40534469 TAATTCAGATTCATTGCCTAGCAGGCTTCATGCCAGTGAAA
1 TAATTCAGACTCATAGTCTAGCAGGCTTCATGCCAGTGAAA
* *
40534510 TTATTCGGACT-ATAAGTCTAGCAGGCT
1 TAATTCAGACTCAT-AGTCTAGCAGGCT
40534537 AAAAGTCGGT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 2 0.04
41 55 0.96
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (41 bp):
TAATTCAGACTCATAGTCTAGCAGGCTTCATGCCAGTGAAA
Found at i:40542699 original size:43 final size:43
Alignment explanation
Indices: 40542652--40542739 Score: 142
Period size: 43 Copynumber: 2.0 Consensus size: 43
40542642 GTACACCTGT
40542652 TAGATCAGTTTACA-CACTCCTGTGAAAATGATAAATAGAGATC
1 TAGATCAGTTTA-ATCACTCCTGTGAAAATGATAAATAGAGATC
* *
40542695 TAGATCAGTTTAATCACTCCTGTTAAAATGATAAATAGATATC
1 TAGATCAGTTTAATCACTCCTGTGAAAATGATAAATAGAGATC
40542738 TA
1 TA
40542740 ACGTGAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 1 0.02
43 41 0.98
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.32
Consensus pattern (43 bp):
TAGATCAGTTTAATCACTCCTGTGAAAATGATAAATAGAGATC
Found at i:40543867 original size:28 final size:26
Alignment explanation
Indices: 40543816--40543867 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
40543806 ACTACCAATA
* *
40543816 TTTTTAATAAAATTTATTTTTTTATT
1 TTTTTAAAAAAATTTATTTGTTTATT
40543842 TTTTTAAAAATAATATTATTTGTTTA
1 TTTTTAAAAA-AAT-TTATTTGTTTA
40543868 GTGGTGCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 3 0.14
28 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTTAAAAAAATTTATTTGTTTATT
Found at i:40544238 original size:10 final size:11
Alignment explanation
Indices: 40544203--40544249 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
40544193 GTGTAGTTTG
*
40544203 TTTATTGTTAT
1 TTTAATGTTAT
* *
40544214 TTTTATGTTGTT
1 TTTAATGTT-AT
40544226 TTTAAT-TTAT
1 TTTAATGTTAT
40544236 TTTAATGTTAT
1 TTTAATGTTAT
40544247 TTT
1 TTT
40544250 GTTAGTTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
10 7 0.24
11 16 0.55
12 6 0.21
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (11 bp):
TTTAATGTTAT
Found at i:40552625 original size:3 final size:3
Alignment explanation
Indices: 40552619--40552652 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
40552609 AGCTAAACAA
40552619 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40552653 GAGCTAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40555501 original size:19 final size:18
Alignment explanation
Indices: 40555466--40555512 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 18
40555456 GGTGATCAAA
*
40555466 ATTATTTTTTATTTGTTT
1 ATTATTTATTATTTGTTT
40555484 ATTATTTATTATTTTGTTT
1 ATTATTTATTA-TTTGTTT
40555503 ATTATTTATT
1 ATTATTTATT
40555513 TTATAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (18 bp):
ATTATTTATTATTTGTTT
Done.