Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 190 of 196
Found at i:56403530 original size:231 final size:230
Alignment explanation
Indices: 56403036--56403552 Score: 759
Period size: 230 Copynumber: 2.2 Consensus size: 230
56403026 AAGTTGTGAA
*
56403036 GAAAACGGCGCCGTTTTCTTATTACATTTAGTGGCGTTTTATACAAAACGCCGCAACTATGTTTT
1 GAAAACGGCGCCGTTTTCTTATTACATTTAGTGGCGTTTTA-ATAAAACGCCGCAACTATGTTTT
* * * * ** *
56403101 CTTTGTTACGGGAACGGCGTTGTTTTCCATTGTTATTAGTGGCGTTACACCCAAAACGCCGCAAA
65 CTTTGTTACAGAAACGGCATCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCGCAAA
* *
56403166 TATATTTTAAAGATTACACGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCATT
130 TATATTTTAAAGATTACACGAGTTTACGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACT
* *
56403231 TATATATAAACGTCGCAAACTCGAAATGGTGTTACG
195 TATATATAAACGCCGCAAAATCGAAATGGTGTTACG
* * * *
56403267 AAAAATGACGCCGTTTTCTTATTACATTTAGTGGCGTTTTAGATAAAACGCCGCAAGTATGTTTT
1 GAAAACGGCGCCGTTTTCTTATTACATTTAGTGGCGTTTTA-ATAAAACGCCGCAACTATGTTTT
*
56403332 CTTTGTTACAGAAACGGCATCGTTTT-CAAGGATATTTGTGGCGTTACACCCAAAACGCCGCAAA
65 CTTTGTTACAGAAACGGCATCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCGCAAA
* * *
56403396 TATATTTTAAAGATTACAGGAGTTTACTTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCT
130 TATATTTTAAAGATTACACGAGTTTACGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACT
56403461 TATATATAAACGCCGCAAAATCGAAATGGTGTTACG
195 TATATATAAACGCCGCAAAATCGAAATGGTGTTACG
* *** *
56403497 GAAAACGGCGCCGTTTACTTAGTTGGTTTTAGTGGCGCTTTT-ATTAAACGCCGCAA
1 GAAAACGGCGCCGTTTTCTTA-TTACATTTAGTGGCG-TTTTAATAAAACGCCGCAA
56403553 ATTTGCATTA
Statistics
Matches: 255, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
230 158 0.62
231 93 0.36
232 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (230 bp):
GAAAACGGCGCCGTTTTCTTATTACATTTAGTGGCGTTTTAATAAAACGCCGCAACTATGTTTTC
TTTGTTACAGAAACGGCATCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCGCAAAT
ATATTTTAAAGATTACACGAGTTTACGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACTT
ATATATAAACGCCGCAAAATCGAAATGGTGTTACG
Found at i:56403903 original size:19 final size:19
Alignment explanation
Indices: 56403881--56403924 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
56403871 CAGACATCTC
*
56403881 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* *
56403900 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
56403919 CCCCAA
1 CCCCAA
56403925 CGTAGTCCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.43, G:0.02, T:0.23
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:56405998 original size:39 final size:39
Alignment explanation
Indices: 56405941--56406830 Score: 185
Period size: 37 Copynumber: 23.7 Consensus size: 39
56405931 TACAATTTCT
56405941 TAACTTATATAATATTAAGATAACTTATATAATATTACA
1 TAACTTATATAATATTAAGATAACTTATATAATATTACA
* * * * *
56405980 TAACTTATATCATGTTAAGATAA--AAAATCGA-ATTACA
1 TAACTTATATAATATTAAGATAACTTATAT-AATATTACA
* * * *
56406017 TAACTTATATAATATTAATATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** * * *
56406057 TCAAATT-T-CGA-ATT-ACATAACTTATACAATAATA-A
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * * * *
56406092 GGTAAAATT-TCT-A-ATT-ACATAACTTATACAATATTAAGA
1 --T-AACTTATATAATATTAAGATAACTTATATAATATT-ACA
** *** * *
56406131 TAAAAT-TCCGA-ATT-ACATAACTTATATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* * * **
56406168 TTACTTTTATAATATTAAGATCAAATT-T-CGA-ATTACA
1 TAACTTATATAATATTAAGAT-AACTTATATAATATTACA
* * *
56406205 TAACTTATATAATATT-ACATAACTTACGTACAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTA--TATAATATT-ACA
* ** * * *
56406246 TAAAATT-T-CGA-ATT-ACATAAGTTATATAATATTAAGA
1 T-AACTTATATAATATTAAGATAACTTATATAATATT-ACA
* * * **
56406283 TTACTTTTATAATATTAAGATCAAATT-T-CGA-ATTACA
1 TAACTTATATAATATTAAGAT-AACTTATATAATATTACA
* ** *
56406320 TAACTTATATAATTTTCCG-TAACTTATATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** *
56406359 TAAAATT-T-CGA-ATT-ACATAACTTATATAATATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * * **
56406395 TAACTTATACAATATTAAGGTAAGATT-T-CGA-ATTACA
1 TAACTTATATAATATTAAGATAA-CTTATATAATATTACA
* * * *
56406432 TAACTCATACAATATTAAGATTACTTATATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* * * *
56406472 TTACTTTTATAATATTAAGATCAAATT-T-TGA-ATTACA
1 TAACTTATATAATATTAAGAT-AACTTATATAATATTACA
* ** *
56406509 TAACTTATATAATTTTCCG-TAACTTATATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* * * *
56406548 TAAAATT-TCT-A-ATT-ACATAACTTACATAA-ATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * * *
56406583 TAACTTATACAATATTAAGGTAAGATT-T-CAA-ATTACA
1 TAACTTATATAATATTAAGATAA-CTTATATAATATTACA
* * * *
56406620 TAACTCATACAATATTAAGATTACTTATATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* * * *
56406660 TAAAATT-TCT-A-ATT-ACATAACTTACATAAT-TTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * * **
56406695 TAACTTATACAATATTAAGGTAAGATT-T-CGA-ATTACA
1 TAACTTATATAATATTAAGATAA-CTTATATAATATTACA
* * *
56406732 TAACTCATACAATATTAAGATTAA-TTATATAATATTAAGA
1 TAACTTATATAATATTAAGA-TAACTTATATAATATT-ACA
* * * *
56406772 TAAAATT-TCT-A-ATT-ACATAACTTACATAA-ATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
*
56406807 TAACTTACATAA-ATTAA-ATAACTT
1 TAACTTATATAATATTAAGATAACTT
56406831 GCATAACTTA
Statistics
Matches: 617, Mismatches: 158, Indels: 155
0.66 0.17 0.17
Matches are distributed among these distances:
34 12 0.02
35 29 0.05
36 51 0.08
37 309 0.50
38 52 0.08
39 81 0.13
40 54 0.09
41 25 0.04
42 4 0.01
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (39 bp):
TAACTTATATAATATTAAGATAACTTATATAATATTACA
Found at i:56406074 original size:57 final size:56
Alignment explanation
Indices: 56405960--56406087 Score: 168
Period size: 57 Copynumber: 2.3 Consensus size: 56
56405950 TAATATTAAG
* *
56405960 ATAACTTATATAATATTACATAACTTATATCATGTTAAGATAAAAAATCGAATTAC
1 ATAACTTATATAATATTACATAACTTATATAATATTAAGATAAAAAATCGAATTAC
* * **
56406016 ATAACTTATATAATATTA-ATATTACTTTTATAATATTAAGATCAAATTTCGAATTAC
1 ATAACTTATATAATATTACATA--ACTTATATAATATTAAGATAAAAAATCGAATTAC
*
56406073 ATAACTTATACAATA
1 ATAACTTATATAATA
56406088 ATAAGGTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
55 3 0.05
56 18 0.29
57 42 0.67
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (56 bp):
ATAACTTATATAATATTACATAACTTATATAATATTAAGATAAAAAATCGAATTAC
Found at i:56406101 original size:37 final size:37
Alignment explanation
Indices: 56406047--56406168 Score: 190
Period size: 37 Copynumber: 3.3 Consensus size: 37
56406037 TTACTTTTAT
*
56406047 AATATTAAGATCAAATTTCGAATTACATAACTTATAC
1 AATATTAAGATAAAATTTCGAATTACATAACTTATAC
* * *
56406084 AATAATAAGGTAAAATTTCTAATTACATAACTTATAC
1 AATATTAAGATAAAATTTCGAATTACATAACTTATAC
* *
56406121 AATATTAAGATAAAATTCCGAATTACATAACTTATAT
1 AATATTAAGATAAAATTTCGAATTACATAACTTATAC
56406158 AATATTAAGAT
1 AATATTAAGAT
56406169 TACTTTTATA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (37 bp):
AATATTAAGATAAAATTTCGAATTACATAACTTATAC
Found at i:56406208 original size:131 final size:120
Alignment explanation
Indices: 56406105--56406795 Score: 561
Period size: 112 Copynumber: 5.9 Consensus size: 120
56406095 AAAATTTCTA
56406105 ATTACATAACTTATACAATATTAAGATAAAATTCCGAATTACATAACTTATATAATATTAAGATT
1 ATTACATAACTTATACAATATTAAGATAAAATT-CGAATTACATAACTTATATAATATTAAGATT
56406170 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAAC-T-T-ATATAATATTAC
65 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATAATATAATATTAC
* * * *
56406223 ATAAC-TTAC--GTACAATATTAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATT
1 ATTACATAACTTATACAATATTAAGATAAAA-TTCGAATTACATAACTTATATAATATTAAGATT
56406285 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAAC-T-T-ATAT-A-ATT--
65 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATAATATAATATTAC
* * * * *
56406334 -TTCCGTAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATT-ACATA
1 ATTACATAACTTATACAATATTAAGATAAAA-TTCGAATTACATAACTTATATAATATTAAGATT
* * * * *
56406397 ACTTATACAATATTAAGGT-AAGATTTCGAATTACATAACTCATACAATATTAAGATTAC
65 ACTTTTATAATATTAAGATCAA-ATTTCGAATTACATAACT--TATAATA-TAATATTAC
* * * * *
56406456 TTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTTGAATTACATAACTTATATAA
1 --AT-T-ACA-T---A--ACTTATACAATATTAAGAT-AAAATTCGAATTACATAACTTATATAA
* ** * * * * *
56406521 TTTTCCG-TAACTTATATAATATTAAGATAAAATTTCTAATTACATAAC---T--TA-CATA--A
55 TATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATAATATAATATTA
56406577 -
120 C
* * * * *
56406577 ATTACATAACTTATACAATATTAAGGTAAGATTTCAAATTACATAACTCATACAATATTAAGATT
1 ATTACATAACTTATACAATATTAAGATAA-AATTCGAATTACATAACTTATATAATATTAAGATT
* * * *
56406642 ACTTATATAATATTAAGATAAAATTTCTAATTACATAAC-T-T-ACAT-A-A-T--
65 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATAATATAATATTAC
* * * *
56406690 -TTACATAACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATT
1 ATTACATAACTTATACAATATTAAGATAA-AATTCGAATTACATAACTTATATAATATTAAGATT
* * * *
56406754 AATTATATAATATTAAGATAAAATTTCTAATTACATAACTTA
65 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTA
56406796 CATAAATTAC
Statistics
Matches: 490, Mismatches: 46, Indels: 78
0.80 0.07 0.13
Matches are distributed among these distances:
110 4 0.01
111 46 0.09
112 177 0.36
113 51 0.10
114 3 0.01
115 94 0.19
116 3 0.01
117 8 0.02
118 6 0.01
119 3 0.01
120 3 0.01
122 1 0.00
124 2 0.00
125 1 0.00
126 3 0.01
128 1 0.00
131 1 0.00
133 78 0.16
134 5 0.01
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (120 bp):
ATTACATAACTTATACAATATTAAGATAAAATTCGAATTACATAACTTATATAATATTAAGATTA
CTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATAATATAATATTAC
Found at i:56406246 original size:115 final size:113
Alignment explanation
Indices: 56406105--56406472 Score: 542
Period size: 115 Copynumber: 3.2 Consensus size: 113
56406095 AAAATTTCTA
*
56406105 ATTACATAACTTATACAATATTAAGATAAAATTCCGAATTACATAACTTATATAATATTAAGATT
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
56406170 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
66 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
*
56406218 ATTACATAACTTACGTACAATATTAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGA
1 ATTACATAACTTA--TACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGA
56406283 TTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
64 TTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
* * * * * *
56406333 TTTCCGTAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATT-ACATA
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
* * * * *
56406397 ACTTATACAATATTAAGGT-AAGATTTCGAATTACATAACTCATACAAT
66 ACTTTTATAATATTAAGATCAA-ATTTCGAATTACATAACTTATATAAT
* * *
56406445 ATTAAGATTACTTATATAATATTAAGAT
1 ATT-ACATAACTTATACAATATTAAGAT
56406473 TACTTTTATA
Statistics
Matches: 232, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
111 2 0.01
112 45 0.19
113 77 0.33
115 108 0.47
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (113 bp):
ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
Found at i:56406373 original size:56 final size:57
Alignment explanation
Indices: 56406110--56406472 Score: 498
Period size: 57 Copynumber: 6.4 Consensus size: 57
56406100 TTCTAATTAC
* *
56406110 ATAACTTATACAATATTAAGATAAAATTCCGAATTACATAACTTATATAATATTAAG
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
* * * *
56406167 ATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATT-AC
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
* *
56406223 ATAACTTACGTACAATATTAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAG
1 ATAACTTA--TATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
* * * * **
56406282 ATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATTTTCCG
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
*
56406339 -TAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATT-AC
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
* * * * *
56406394 ATAACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAG
1 ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
*
56406451 ATTACTTATATAATATTAAGAT
1 ATAACTTATATAATATTAAGAT
56406473 TACTTTTATA
Statistics
Matches: 266, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
56 104 0.39
57 112 0.42
58 43 0.16
59 7 0.03
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (57 bp):
ATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAG
Found at i:56406477 original size:189 final size:188
Alignment explanation
Indices: 56406267--56406660 Score: 743
Period size: 189 Copynumber: 2.1 Consensus size: 188
56406257 ATTACATAAG
56406267 TTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAA
1 TTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAA
*
56406332 TTTTCCGTAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTACATA
66 TTTTCCGTAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTACATAA-ATTACATA
*
56406397 ACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATTAC
130 ACTTATACAATATTAAGGTAAGATTTCAAATTACATAACTCATACAATATTAAGATTAC
*
56406456 TTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTTGAATTACATAACTTATATAA
1 TTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAA
*
56406521 TTTTCCGTAACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTACATAA
66 TTTTCCGTAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTACATAAATTACATAA
56406586 CTTATACAATATTAAGGTAAGATTTCAAATTACATAACTCATACAATATTAAGATTAC
131 CTTATACAATATTAAGGTAAGATTTCAAATTACATAACTCATACAATATTAAGATTAC
56406644 TTATATAATATTAAGAT
1 TTATATAATATTAAGAT
56406661 AAAATTTCTA
Statistics
Matches: 201, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
188 83 0.41
189 118 0.59
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.40
Consensus pattern (188 bp):
TTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAA
TTTTCCGTAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTACATAAATTACATAA
CTTATACAATATTAAGGTAAGATTTCAAATTACATAACTCATACAATATTAAGATTAC
Found at i:56406515 original size:57 final size:57
Alignment explanation
Indices: 56406454--56406827 Score: 419
Period size: 57 Copynumber: 6.7 Consensus size: 57
56406444 TATTAAGATT
* * *
56406454 ACTTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTT-TGAATTACATA
1 ACTTATATAATATTAAGATAACTTATATAATATTAAGATAAAATTTCT-AATTACATA
* **
56406511 ACTTATATAATTTTCCG-TAACTTATATAATATTAAGATAAAATTTCTAATTACATA
1 ACTTATATAATATTAAGATAACTTATATAATATTAAGATAAAATTTCTAATTACATA
* * * * * *
56406567 ACTTACATAA-ATT-ACATAACTTATACAATATTAAGGTAAGATTTCAAATTACATA
1 ACTTATATAATATTAAGATAACTTATATAATATTAAGATAAAATTTCTAATTACATA
* * *
56406622 ACTCATACAATATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATA
1 ACTTATATAATATTAAGATAACTTATATAATATTAAGATAAAATTTCTAATTACATA
* * * * * *
56406679 ACTTACATAAT-TT-ACATAACTTATACAATATTAAGGTAAGATTTCGAATTACATA
1 ACTTATATAATATTAAGATAACTTATATAATATTAAGATAAAATTTCTAATTACATA
* *
56406734 ACTCATACAATATTAAGATTAA-TTATATAATATTAAGATAAAATTTCTAATTACATA
1 ACTTATATAATATTAAGA-TAACTTATATAATATTAAGATAAAATTTCTAATTACATA
* * *
56406791 ACTTACATAA-ATT-ACATAACTTACATAA-ATTAA-ATAA
1 ACTTATATAATATTAAGATAACTTATATAATATTAAGATAA
56406828 CTTGCATAAC
Statistics
Matches: 264, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
53 4 0.02
54 8 0.03
55 97 0.37
56 53 0.20
57 99 0.38
58 3 0.01
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.39
Consensus pattern (57 bp):
ACTTATATAATATTAAGATAACTTATATAATATTAAGATAAAATTTCTAATTACATA
Found at i:56406574 original size:9 final size:9
Alignment explanation
Indices: 56406560--56406589 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
56406550 AAATTTCTAA
56406560 TTACATAAC
1 TTACATAAC
*
56406569 TTACATAAA
1 TTACATAAC
56406578 TTACATAAC
1 TTACATAAC
56406587 TTA
1 TTA
56406590 TACAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
TTACATAAC
Found at i:56406611 original size:55 final size:55
Alignment explanation
Indices: 56406474--56406854 Score: 398
Period size: 55 Copynumber: 6.9 Consensus size: 55
56406464 TATTAAGATT
* * * * * *
56406474 ACTTTTATAATATTAAGATCAAATTT-TGAATTACATAACTTATATAATTTTCCGTA
1 ACTTATATAATATTAAGATAAAATTTCT-AATTACATAACTTACATAA-ATTACATA
56406530 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTACATA
1 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTACATA
* * * * * * *
56406585 ACTTATACAATATTAAGGTAAGATTTCAAATTACATAACTCATACA-ATATTAAGATT
1 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACT--TACATAAATT-ACATA
*
56406642 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAATTTACATA
1 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTACATA
* * * * * *
56406697 ACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACA-ATATTAAGATTA
1 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACT--TACATAAATT-ACA-TA
56406755 A-TTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTACATA
1 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTACATA
* * * *
56406809 ACTTACATAA-ATTAA-AT-AACTTGCATAACTTAAATAACTTACATAA
1 ACTTATATAATATTAAGATAAAATTTC-TAA-TTACATAACTTACATAA
56406855 CACATAACCT
Statistics
Matches: 274, Mismatches: 38, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
52 5 0.02
53 5 0.02
54 24 0.09
55 97 0.35
56 56 0.20
57 84 0.31
58 3 0.01
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (55 bp):
ACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTACATA
Found at i:56406686 original size:9 final size:9
Alignment explanation
Indices: 56406672--56406701 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
56406662 AAATTTCTAA
56406672 TTACATAAC
1 TTACATAAC
*
56406681 TTACATAAT
1 TTACATAAC
56406690 TTACATAAC
1 TTACATAAC
56406699 TTA
1 TTA
56406702 TACAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (9 bp):
TTACATAAC
Found at i:56406742 original size:300 final size:303
Alignment explanation
Indices: 56406150--56406772 Score: 977
Period size: 300 Copynumber: 2.1 Consensus size: 303
56406140 GAATTACATA
56406150 ACTTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATAT
1 ACTTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATAT
* *
56406215 AATATTACATAACTTACGTACAATATTAAGATAAAATTTCGAATTACATAAGTTATATAATATTA
66 AATATTACATAACTTAC-TACAATATTAAGATAAAATTTCGAATTACATAACTTACATAATATTA
* * * * * * * * **
56406280 AGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATTTTCCGTAACTT
130 ACATAACTTATACAATATTAAGATCAAATTTCAAATTACATAACTCATACAATATTAAGTAACTT
*
56406345 ATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTACATAACTTATACAATAT
195 ATATAATATTAAGATAAAATTTCGAATTACATAACTTACATAATATTACATAACTTATACAATAT
56406410 TAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATT
260 TAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATT
*
56406454 ACTTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTTGAATTACATAACTTATAT
1 ACTTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATAT
* * * * *
56406519 AATTTTCCGTAACTTA-TATAATATTAAGATAAAATTTCTAATTACATAACTTACATAA-ATT-A
66 AATATTACATAACTTACTACAATATTAAGATAAAATTTCGAATTACATAACTTACATAATATTAA
* *
56406581 CATAACTTATACAATATTAAGGT-AAGATTTCAAATTACATAACTCATACAATATTAAGATTACT
131 CATAACTTATACAATATTAAGATCAA-ATTTCAAATTACATAACTCATACAATATTAAG-TAACT
*
56406645 TATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAT-TTACATAACTTATACAATA
194 TATATAATATTAAGATAAAATTTCGAATTACATAACTTACATAATATTACATAACTTATACAATA
56406709 TTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATT
259 TTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATT
*
56406754 AATTATATAATATTAAGAT
1 ACTTATATAATATTAAGAT
56406773 AAAATTTCTA
Statistics
Matches: 294, Mismatches: 23, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
299 2 0.01
300 127 0.43
301 50 0.17
302 38 0.13
304 77 0.26
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.39
Consensus pattern (303 bp):
ACTTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATAT
AATATTACATAACTTACTACAATATTAAGATAAAATTTCGAATTACATAACTTACATAATATTAA
CATAACTTATACAATATTAAGATCAAATTTCAAATTACATAACTCATACAATATTAAGTAACTTA
TATAATATTAAGATAAAATTTCGAATTACATAACTTACATAATATTACATAACTTATACAATATT
AAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATT
Found at i:56406784 original size:20 final size:20
Alignment explanation
Indices: 56405945--56406775 Score: 80
Period size: 20 Copynumber: 44.0 Consensus size: 20
56405935 ATTTCTTAAC
*
56405945 TTATATAATATTAAGATAAC
1 TTATATAATATTAAGATAAA
* *
56405965 TTATATAATATT-ACATAAC
1 TTATATAATATTAAGATAAA
* *
56405984 TTATATCATGTTAAGATAAA
1 TTATATAATATTAAGATAAA
* * * *
56406004 --AAATCGA-ATT-ACATAAC
1 TTATAT-AATATTAAGATAAA
* * *
56406021 TTATATAATATTAATATTAC
1 TTATATAATATTAAGATAAA
*
56406041 TTTTATAATATTAAGATCAAA
1 TTATATAATATTAAGAT-AAA
** * *
56406062 TT-T-CGA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* * *
56406078 TTATACAATAATAAGGTAAAA
1 TTATATAATATTAAGAT-AAA
* * *
56406099 TT-TCT-A-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
*
56406115 TTATACAATATTAAGATAAA
1 TTATATAATATTAAGATAAA
* *** * *
56406135 AT-TCCGA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* *
56406152 TTATATAATATTAAGATTAC
1 TTATATAATATTAAGATAAA
*
56406172 TTTTATAATATTAAGATCAAA
1 TTATATAATATTAAGAT-AAA
** * *
56406193 TT-T-CGA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* *
56406209 TTATATAATATT-ACATAAC
1 TTATATAATATTAAGATAAA
*
56406228 TTACGTACAATATTAAGATAAAA
1 TTA--TATAATATTAAGAT-AAA
** * *
56406251 TT-T-CGA-ATT-ACATAAG
1 TTATATAATATTAAGATAAA
* *
56406267 TTATATAATATTAAGATTAC
1 TTATATAATATTAAGATAAA
*
56406287 TTTTATAATATTAAGATCAAA
1 TTATATAATATTAAGAT-AAA
** * *
56406308 TT-T-CGA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* ** *
56406324 TTATATAATTTTCCG-TAAC
1 TTATATAATATTAAGATAAA
56406343 TTATATAATATTAAGATAAAA
1 TTATATAATATTAAGAT-AAA
** * *
56406364 TT-T-CGA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* *
56406380 TTATATAATATT-ACATAAC
1 TTATATAATATTAAGATAAA
* *
56406399 TTATACAATATTAAGGTAAGA
1 TTATATAATATTAAGATAA-A
** * *
56406420 TT-T-CGA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* * * *
56406436 TCATACAATATTAAGATTAC
1 TTATATAATATTAAGATAAA
* *
56406456 TTATATAATATTAAGATTAC
1 TTATATAATATTAAGATAAA
*
56406476 TTTTATAATATTAAGATCAAA
1 TTATATAATATTAAGAT-AAA
* * *
56406497 TT-T-TGA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* ** *
56406513 TTATATAATTTTCCG-TAAC
1 TTATATAATATTAAGATAAA
56406532 TTATATAATATTAAGATAAAA
1 TTATATAATATTAAGAT-AAA
* * *
56406553 TT-TCT-A-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* * *
56406569 TTACATAA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* *
56406587 TTATACAATATTAAGGTAAGA
1 TTATATAATATTAAGATAA-A
* * *
56406608 TT-T-CAA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* * * *
56406624 TCATACAATATTAAGATTAC
1 TTATATAATATTAAGATAAA
56406644 TTATATAATATTAAGATAAAA
1 TTATATAATATTAAGAT-AAA
* * *
56406665 TT-TCT-A-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* * *
56406681 TTACATAAT-TT-ACATAAC
1 TTATATAATATTAAGATAAA
* *
56406699 TTATACAATATTAAGGTAAGA
1 TTATATAATATTAAGATAA-A
** * *
56406720 TT-T-CGA-ATT-ACATAAC
1 TTATATAATATTAAGATAAA
* * *
56406736 TCATACAATATTAAGATTAA
1 TTATATAATATTAAGATAAA
56406756 TTATATAATATTAAGATAAA
1 TTATATAATATTAAGATAAA
56406776 ATTTCTAATT
Statistics
Matches: 577, Mismatches: 160, Indels: 148
0.65 0.18 0.17
Matches are distributed among these distances:
16 39 0.07
17 61 0.11
18 96 0.17
19 139 0.24
20 194 0.34
21 41 0.07
22 3 0.01
23 4 0.01
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (20 bp):
TTATATAATATTAAGATAAA
Found at i:56406798 original size:9 final size:9
Alignment explanation
Indices: 56406784--56407047 Score: 242
Period size: 9 Copynumber: 30.1 Consensus size: 9
56406774 AAATTTCTAA
56406784 TTACATAAC
1 TTACATAAC
*
56406793 TTACATAAA
1 TTACATAAC
56406802 TTACATAAC
1 TTACATAAC
*
56406811 TTACATAAA
1 TTACATAAC
*
56406820 TTAAATAAC
1 TTACATAAC
*
56406829 TTGCATAAC
1 TTACATAAC
*
56406838 TTAAATAAC
1 TTACATAAC
56406847 TTACATAAC
1 TTACATAAC
56406856 --ACATAACC
1 TTACATAA-C
* *
56406864 TT-CCTAGC
1 TTACATAAC
* *
56406872 TTACATTAT
1 TTACATAAC
*
56406881 TTAGATAA-
1 TTACATAAC
*
56406889 -TACATAGC
1 TTACATAAC
*
56406897 CTACATAAC
1 TTACATAAC
56406906 TTACATAAC
1 TTACATAAC
*
56406915 TTACATAAA
1 TTACATAAC
*
56406924 TTAAATAAC
1 TTACATAAC
56406933 TTACATAAC
1 TTACATAAC
*
56406942 TTACATAAA
1 TTACATAAC
*
56406951 TTAAATAAC
1 TTACATAAC
56406960 TTACATAAC
1 TTACATAAC
56406969 TTACATAAC
1 TTACATAAC
*
56406978 TCACATAA-
1 TTACATAAC
*
56406986 -TACACAAC
1 TTACATAAC
56406994 TTACATAAC
1 TTACATAAC
56407003 TTACATAA-
1 TTACATAAC
56407011 -TACATAAC
1 TTACATAAC
* *
56407019 ATT-CCTATC
1 -TTACATAAC
*
56407028 ATATCATAAC
1 TTA-CATAAC
56407038 TTACATAAC
1 TTACATAAC
56407047 T
1 T
56407048 CATTTGTAGT
Statistics
Matches: 202, Mismatches: 40, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
7 23 0.11
8 5 0.02
9 167 0.83
10 7 0.03
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.33
Consensus pattern (9 bp):
TTACATAAC
Found at i:56409017 original size:21 final size:21
Alignment explanation
Indices: 56408991--56409061 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
56408981 CTACAACTTA
*
56408991 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
56409012 AAGCAGCGGCTGTAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
56409033 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
56409054 AAGCAGAG
1 AAGCAGAG
56409062 CAGAACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:56409469 original size:42 final size:42
Alignment explanation
Indices: 56409423--56409623 Score: 278
Period size: 42 Copynumber: 4.7 Consensus size: 42
56409413 AAAAAACGCT
* * *
56409423 GCTAAAG-ACAATGCTCTTTAGTGGCGTTTCTTTCAAAGCGCC
1 GCTAAAGAAC-ATGGTCTTTAGCGGCGTTTTTTTCAAAGCGCC
* *
56409465 GCTAAAGAACATGGTTTTTAGCGGCGTTTTTTTCTAAGCGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCAAAGCGCC
* *
56409507 GCTAAAGAACATGGTCTTTAGCGGCATTTTTTTTATAAGCGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCA-AAGCGCC
* *
56409550 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTTAACGCGCC
1 GCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTTCAAAGCGCC
*
56409593 GCTAAAGAACATGGTCTTTAGTGGCGTTTTT
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTT
56409624 GTTGTAAACG
Statistics
Matches: 144, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
42 70 0.49
43 65 0.45
44 9 0.06
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (42 bp):
GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCAAAGCGCC
Found at i:56409552 original size:43 final size:43
Alignment explanation
Indices: 56409423--56409637 Score: 285
Period size: 43 Copynumber: 5.0 Consensus size: 43
56409413 AAAAAACGCT
* * * *
56409423 GCTAAAG-ACAATGCTCTTTAGTGGCGTTTCTTTCA-AAGCGCC
1 GCTAAAGAAC-ATGGTCTTTAGCGGCGTTTTTTTTATAAGCGCC
* *
56409465 GCTAAAGAACATGGTTTTTAGCGGCG-TTTTTTTCTAAGCGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTATAAGCGCC
*
56409507 GCTAAAGAACATGGTCTTTAGCGGCATTTTTTTTATAAGCGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTATAAGCGCC
56409550 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTT-TAACGCGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTATAA-GCGCC
* * * *
56409593 GCTAAAGAACATGGTCTTTAGTGGCGTTTTTGTTGTAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTATAAGCGCC
56409636 GC
1 GC
56409638 AAACGTTTTC
Statistics
Matches: 155, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
41 5 0.03
42 54 0.35
43 93 0.60
44 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (43 bp):
GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTATAAGCGCC
Found at i:56409636 original size:86 final size:83
Alignment explanation
Indices: 56409423--56409637 Score: 297
Period size: 85 Copynumber: 2.5 Consensus size: 83
56409413 AAAAAACGCT
* * * *
56409423 GCTAAAG-ACAATGCTCTTTAGTGGCGTTTCTTTCAAAGCGCCGCTAAAGAACATGGTTTTTAGC
1 GCTAAAGAAC-ATGGTCTTTAGTGGCGTTTTTTTTAAA-CGCCGCTAAAGAACATGGTCTTTAGC
56409487 GGCGTTTTTTTCTAAGCGCC
64 GGCGTTTTTTTCTAAGCGCC
* *
56409507 GCTAAAGAACATGGTCTTTAGCGGCATTTTTTTTATAAGCGCCGCTAAAGAACATGGTCTTTAGC
1 GCTAAAGAACATGGTCTTTAGTGGCGTTTTTTTTA-AA-CGCCGCTAAAGAACATGGTCTTTAGC
*
56409572 GGCGTTTTTTTTTAACGCGCC
64 GGCGTTTTTTTCTAA-GCGCC
56409593 GCTAAAGAACATGGTCTTTAGTGGCGTTTTTGTTGTAAACGCCGC
1 GCTAAAGAACATGGTCTTTAGTGGCGTTTTT-TT-TAAACGCCGC
56409638 AAACGTTTTC
Statistics
Matches: 117, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
84 27 0.23
85 44 0.38
86 40 0.34
87 4 0.03
88 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (83 bp):
GCTAAAGAACATGGTCTTTAGTGGCGTTTTTTTTAAACGCCGCTAAAGAACATGGTCTTTAGCGG
CGTTTTTTTCTAAGCGCC
Found at i:56410072 original size:25 final size:25
Alignment explanation
Indices: 56410025--56410087 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
56410015 ATACCACTAT
* *
56410025 GTTTTAACTTTATCTTGAATTTTGCA
1 GTTTTAA-TTTTTATTGAATTTTGCA
* *
56410051 GTTTTAATTTTTATTGATTTTTGCC
1 GTTTTAATTTTTATTGAATTTTGCA
*
56410076 GCTTTAATTTTT
1 GTTTTAATTTTT
56410088 TTTATTGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.19, C:0.10, G:0.11, T:0.60
Consensus pattern (25 bp):
GTTTTAATTTTTATTGAATTTTGCA
Found at i:56410555 original size:23 final size:23
Alignment explanation
Indices: 56410529--56410574 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
56410519 AAATTTAACC
* *
56410529 ATATTTAT-AAAATATAATGACAA
1 ATATTAATCAAAATAAAAT-ACAA
56410552 ATATTAATCAAAATAAAATACAA
1 ATATTAATCAAAATAAAATACAA
56410575 TGATAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
ATATTAATCAAAATAAAATACAA
Found at i:56416861 original size:4 final size:4
Alignment explanation
Indices: 56416854--56416898 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
56416844 AAATAAATAA
*
56416854 AAAG AAAG AAAG AAAG AAAG AAAAG AAAAG AAA- AAGG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG -AAAG -AAAG AAAG AAAG AAAG AAAG
56416899 GAAGGAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 2 0.05
4 26 0.70
5 9 0.24
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:56416893 original size:21 final size:21
Alignment explanation
Indices: 56416853--56416897 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
56416843 AAAATAAATA
56416853 AAAAGAAAGAAAGAAAGAAAG
1 AAAAGAAAGAAAGAAAGAAAG
*
56416874 AAAAGAAAAGAAA-AAGGAAAG
1 AAAAG-AAAGAAAGAAAGAAAG
56416895 AAA
1 AAA
56416898 GGAAGGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AAAAGAAAGAAAGAAAGAAAG
Found at i:56417354 original size:5 final size:5
Alignment explanation
Indices: 56417341--56417384 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
56417331 GAAATATGCA
* *
56417341 ATTGA ATTGT ATTGT AATGT ATTGT ATTGT ATTGT ATTGT ATTG
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTG
56417385 ATGAATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (5 bp):
ATTGT
Found at i:56420506 original size:11 final size:11
Alignment explanation
Indices: 56420490--56420514 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56420480 GCGATTATTG
56420490 TATTTATTGTA
1 TATTTATTGTA
56420501 TATTTATTGTA
1 TATTTATTGTA
56420512 TAT
1 TAT
56420515 AAAGGGACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TATTTATTGTA
Found at i:56422926 original size:40 final size:40
Alignment explanation
Indices: 56422843--56422919 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
56422833 AATTATGGAA
* * *
56422843 TACTGAATATTGTTTTGAGTACTGAATTGAATTGTGAAGT
1 TACTAAATATTGTTATGAGTACTGAATTGAACTGTGAAGT
* *
56422883 TACTAAATATTGTTATGTGTACTGCATTGAACTGTGA
1 TACTAAATATTGTTATGAGTACTGAATTGAACTGTGA
56422920 GATTACTGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.42
Consensus pattern (40 bp):
TACTAAATATTGTTATGAGTACTGAATTGAACTGTGAAGT
Found at i:56423182 original size:45 final size:45
Alignment explanation
Indices: 56423132--56423283 Score: 182
Period size: 45 Copynumber: 3.4 Consensus size: 45
56423122 TGCCGACTAC
* *
56423132 TGTTACTGTTACTCTTACCGATTC-AGCACATTGTGTGTCGAATAA
1 TGTTACTGTTACTGTTACCGATTCGA-CACTTTGTGTGTCGAATAA
* * *
56423177 TGTTACTATTACTGTTACCGATTCGACACTTTGTGTGTCAAATAC
1 TGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAA
* * * * *
56423222 TGTTACCG-TATTGTTACAGATTCGACACTTTGTGTGTTGAATAT
1 TGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAA
*
56423266 TGTTACGGTTACTGTTAC
1 TGTTACTGTTACTGTTAC
56423284 TGCTACCTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
44 38 0.42
45 52 0.57
46 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (45 bp):
TGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAA
Found at i:56426314 original size:241 final size:241
Alignment explanation
Indices: 56425891--56426373 Score: 939
Period size: 241 Copynumber: 2.0 Consensus size: 241
56425881 AAACCAACTA
56425891 ACTTGATCGATTTAGTGCTTGGATTAGGTCCGGGTAGAGAACAGGTAGGGGCGGTAGGCTTTTCA
1 ACTTGATCGATTTAGTGCTTGGATTAGGTCCGGGTAGAGAACAGGTAGGGGCGGTAGGCTTTTCA
56425956 CTTTAGCCGTTGTTATTCAAGGCCTTACTTTACTCGTTTAAATCTTTTTTGATCCCCTCATTCTT
66 CTTTAGCCGTTGTTATTCAAGGCCTTACTTTACTCGTTTAAATCTTTTTTGATCCCCTCATTCTT
56426021 TCTAGTTAGGGAGGCCGTAGATGAAATGATACGTTATAAGTCTAGATAATTAGAATGAAACTCTT
131 TCTAGTTAGGGAGGCCGTAGATGAAATGATACGTTATAAGTCTAGATAATTAGAATGAAACTCTT
*
56426086 TTTAGACTCAAAAATTTGAATTATCTTTGAATTTGGAATAGAAATG
196 TTTAGACTCAAAAATTTGAATTATCTTTGAATTCGGAATAGAAATG
*
56426132 ACTTGATCGATTTAGTGCTTGGATTAGGTTCGGGTAGAGAACAGGTAGGGGCGGTAGGCTTTTCA
1 ACTTGATCGATTTAGTGCTTGGATTAGGTCCGGGTAGAGAACAGGTAGGGGCGGTAGGCTTTTCA
*
56426197 CTTTAGCCGTTGTTATTCAAGGCCTTACTTTACTCGTTTAAATTTTTTTTGATCCCCTCATTCTT
66 CTTTAGCCGTTGTTATTCAAGGCCTTACTTTACTCGTTTAAATCTTTTTTGATCCCCTCATTCTT
56426262 TCTAGTTAGGGAGGCCGTAGATGAAATGATACGTTATAAGTCTAGATAATTAGAATGAAACTCTT
131 TCTAGTTAGGGAGGCCGTAGATGAAATGATACGTTATAAGTCTAGATAATTAGAATGAAACTCTT
56426327 TTTAGACTCAAAAATTTGAATTATCTTTGAATTCGGAATAGAAATG
196 TTTAGACTCAAAAATTTGAATTATCTTTGAATTCGGAATAGAAATG
56426373 A
1 A
56426374 ATGGAATAAT
Statistics
Matches: 239, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
241 239 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (241 bp):
ACTTGATCGATTTAGTGCTTGGATTAGGTCCGGGTAGAGAACAGGTAGGGGCGGTAGGCTTTTCA
CTTTAGCCGTTGTTATTCAAGGCCTTACTTTACTCGTTTAAATCTTTTTTGATCCCCTCATTCTT
TCTAGTTAGGGAGGCCGTAGATGAAATGATACGTTATAAGTCTAGATAATTAGAATGAAACTCTT
TTTAGACTCAAAAATTTGAATTATCTTTGAATTCGGAATAGAAATG
Found at i:56427180 original size:11 final size:11
Alignment explanation
Indices: 56427164--56427197 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
56427154 GGTGAGATTA
56427164 GATACTGTAGC
1 GATACTGTAGC
56427175 GATACTGTAGC
1 GATACTGTAGC
56427186 GATACTGTAGC
1 GATACTGTAGC
56427197 G
1 G
56427198 TGAGACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (11 bp):
GATACTGTAGC
Found at i:56432610 original size:17 final size:19
Alignment explanation
Indices: 56432583--56432619 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
56432573 TCAAAATTTT
56432583 AAAGAATAAAATA-CATAA
1 AAAGAATAAAATATCATAA
56432601 AAAG-ATAAAATATCATAA
1 AAAGAATAAAATATCATAA
56432619 A
1 A
56432620 TATAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAGAATAAAATATCATAA
Found at i:56432755 original size:3 final size:3
Alignment explanation
Indices: 56432743--56432777 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
56432733 TTGGGTGGAG
56432743 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56432778 TATTCAGCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:56433936 original size:3 final size:3
Alignment explanation
Indices: 56433928--56433967 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
56433918 CATGAGTACT
56433928 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
56433968 AATAATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:56440707 original size:25 final size:26
Alignment explanation
Indices: 56440679--56440737 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
56440669 AAAATATACT
56440679 AAAAATATT-AAAATAAATATTTCTC
1 AAAAATATTAAAAATAAATATTTCTC
* * *
56440704 AAAAA-ATTAAAAATAAATTTTTTTT
1 AAAAATATTAAAAATAAATATTTCTC
56440729 AAAAATATT
1 AAAAATATT
56440738 TATACTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.10
25 23 0.79
26 3 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (26 bp):
AAAAATATTAAAAATAAATATTTCTC
Found at i:56443278 original size:16 final size:17
Alignment explanation
Indices: 56443252--56443300 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 17
56443242 TTAAAATGAT
56443252 AAATTTT-TAATTTA-A
1 AAATTTTATAATTTATA
56443267 AAATTTTATAATTTATA
1 AAATTTTATAATTTATA
*
56443284 AAATTTTA-AATTAATA
1 AAATTTTATAATTTATA
56443300 A
1 A
56443301 TAAAATTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
15 7 0.23
16 15 0.48
17 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTTATAATTTATA
Found at i:56444972 original size:16 final size:15
Alignment explanation
Indices: 56444951--56444994 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 15
56444941 TGAATTTATC
56444951 GAAATAATTGATTTA
1 GAAATAATTGATTTA
56444966 GGAAATATATTTGATTTA
1 -GAAATA-A-TTGATTTA
*
56444984 AAAATAATTGA
1 GAAATAATTGA
56444995 AATGAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.16
16 7 0.28
17 6 0.24
18 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.39
Consensus pattern (15 bp):
GAAATAATTGATTTA
Found at i:56445298 original size:14 final size:15
Alignment explanation
Indices: 56445268--56445300 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
56445258 AATAATATTA
56445268 TAATAAACCTAAATT
1 TAATAAACCTAAATT
*
56445283 TAATAAA-CTAATTT
1 TAATAAACCTAAATT
56445297 TAAT
1 TAAT
56445301 GTTATCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAAACCTAAATT
Found at i:56450339 original size:31 final size:30
Alignment explanation
Indices: 56450249--56450341 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 30
56450239 CGCTAGTTGG
* *
56450249 ACTTAAA-AAAAATCTTT-AACAACTCAATG
1 ACTTAAATAAAAA-CTTTCAACAATTCAATT
* * * *
56450278 AGTTAAATAAAAACTTTCTAATAGTCCAATT
1 ACTTAAATAAAAACTTTC-AACAATTCAATT
56450309 ACTTAAATAAAAACTTTCAAACAATTCAATT
1 ACTTAAATAAAAACTTTC-AACAATTCAATT
56450340 AC
1 AC
56450342 CATTTCATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 10 0.20
30 5 0.10
31 35 0.70
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.31
Consensus pattern (30 bp):
ACTTAAATAAAAACTTTCAACAATTCAATT
Found at i:56454041 original size:46 final size:46
Alignment explanation
Indices: 56453974--56454109 Score: 227
Period size: 46 Copynumber: 3.0 Consensus size: 46
56453964 TGCTATAACT
* *
56453974 CAGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCACAACA
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACA
* *
56454020 CAGTATGGTTTTCTTCACTGAAACACTATACCTACTTTTCACAACT
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACA
*
56454066 CAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTCACAA
1 CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
56454110 ATTTCCATGA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 84 1.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (46 bp):
CAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAACA
Found at i:56454061 original size:24 final size:24
Alignment explanation
Indices: 56454033--56454107 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 24
56454023 TATGGTTTTC
56454033 TTCACTGAAACACTATACCTACTT
1 TTCACTGAAACACTATACCTACTT
* * **
56454057 TTCAC--AACTCAGTATGGCT--TT
1 TTCACTGAA-ACACTATACCTACTT
*
56454078 CTTCACTGAAACACCATACCTACTT
1 -TTCACTGAAACACTATACCTACTT
56454103 TTCAC
1 TTCAC
56454108 AAATTTCCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 12
0.63 0.16 0.21
Matches are distributed among these distances:
21 2 0.06
22 7 0.19
23 13 0.36
24 12 0.33
25 2 0.06
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (24 bp):
TTCACTGAAACACTATACCTACTT
Found at i:56455343 original size:17 final size:17
Alignment explanation
Indices: 56455321--56455368 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
56455311 AAATTCTTTT
56455321 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
*
56455338 TAAATCACAGAATTCAC
1 TAAATCACAAAATTCAC
*
56455355 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
56455369 TTCTAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:56455597 original size:41 final size:38
Alignment explanation
Indices: 56455519--56455595 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
56455509 AATAATATTT
56455519 TTTTATATTTTTTATTATAACGACTTAAACAAGCATCA
1 TTTTATATTTTTTATTATAACGACTTAAACAAGCATCA
56455557 TTTTATATTTTTTATTATAACGACTTAAACAAGCATCA
1 TTTTATATTTTTTATTATAACGACTTAAACAAGCATCA
56455595 T
1 T
56455596 CAAGTCACAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (38 bp):
TTTTATATTTTTTATTATAACGACTTAAACAAGCATCA
Found at i:56460499 original size:19 final size:18
Alignment explanation
Indices: 56460467--56460505 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
56460457 AAAAGTTACT
56460467 AAAATCATTAAATAATTAA
1 AAAATCATTAAATAA-TAA
56460486 AAAAGTCATT-AATAATAA
1 AAAA-TCATTAAATAATAA
56460504 AA
1 AA
56460506 TAAAAAGCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATCATTAAATAATAA
Found at i:56477801 original size:7 final size:7
Alignment explanation
Indices: 56477789--56477813 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56477779 TTTAAGATAG
56477789 TATTCTA
1 TATTCTA
56477796 TATTCTA
1 TATTCTA
56477803 TATTCTA
1 TATTCTA
56477810 TATT
1 TATT
56477814 AAGCCACGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTCTA
Found at i:56480325 original size:114 final size:113
Alignment explanation
Indices: 56480155--56480375 Score: 275
Period size: 114 Copynumber: 1.9 Consensus size: 113
56480145 AAACTTCGAA
** *
56480155 ACGTTCTAATTAATTTATCAAAATATCAATATAATATCAATCAAGTCATTCTATCAACCAAA-TC
1 ACGTTCTAACCAATTCATCAAAATATCAATATAATATCAATCAAGTCATTCTATCAACCAAACT-
* * *
56480219 GATGTAGAATATATTAAAAACACTTGTAT-TAAATTTTAAACACGCCAGC
65 AATGTAGAACATATTAAAAACACTTGCATCT-AATTTTAAACACGCCAGC
* * * * **
56480268 ACGTTCTAACCAATTCATCAAAATATTAGATATCATATCAATCATGTCTTTCTATCAACTTAACT
1 ACGTTCTAACCAATTCATCAAAATATCA-ATATAATATCAATCAAGTCATTCTATCAACCAAACT
* *
56480333 AATGTGGAACATATTAAAAACATTTGCATCTAATTTTAAACAC
65 AATGTAGAACATATTAAAAACACTTGCATCTAATTTTAAACAC
56480376 ACGTGCACTG
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
113 24 0.26
114 65 0.71
115 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.34
Consensus pattern (113 bp):
ACGTTCTAACCAATTCATCAAAATATCAATATAATATCAATCAAGTCATTCTATCAACCAAACTA
ATGTAGAACATATTAAAAACACTTGCATCTAATTTTAAACACGCCAGC
Found at i:56486433 original size:30 final size:30
Alignment explanation
Indices: 56486397--56486459 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
56486387 GCACGATAAA
*
56486397 CAACATTAGACAAATATCATAAAACCATTT
1 CAACATTAGACAAATATCATAAAACCAGTT
56486427 CAACATTAGACAAATATCATAAAACCAGTT
1 CAACATTAGACAAATATCATAAAACCAGTT
56486457 CAA
1 CAA
56486460 ACTTAATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.24
Consensus pattern (30 bp):
CAACATTAGACAAATATCATAAAACCAGTT
Found at i:56490770 original size:31 final size:31
Alignment explanation
Indices: 56490735--56490794 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
56490725 AATTTGGTTT
*
56490735 TTGAACTATTCGAA-TGTTTTCATTTAAGTAA
1 TTGAACTATTCAAACT-TTTTCATTTAAGTAA
*
56490766 TTGAACTATTCAAACTTTTTTATTTAAGT
1 TTGAACTATTCAAACTTTTTCATTTAAGT
56490795 CACTAGGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (31 bp):
TTGAACTATTCAAACTTTTTCATTTAAGTAA
Found at i:56493711 original size:15 final size:15
Alignment explanation
Indices: 56493691--56493720 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56493681 ATAAATCCAG
56493691 AAAAAAAAACTTTAA
1 AAAAAAAAACTTTAA
56493706 AAAAAAAAACTTTAA
1 AAAAAAAAACTTTAA
56493721 CCTTCTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAAAAACTTTAA
Found at i:56500035 original size:12 final size:12
Alignment explanation
Indices: 56500018--56500049 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
56500008 CAGTGTCTTC
56500018 TAATTACACAAT
1 TAATTACACAAT
56500030 TAATTACACAAT
1 TAATTACACAAT
*
56500042 TAAGTACA
1 TAATTACA
56500050 TATGGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (12 bp):
TAATTACACAAT
Found at i:56503084 original size:31 final size:31
Alignment explanation
Indices: 56503026--56503085 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
56503016 CTTTACTTTG
*
56503026 GTCAAGTTTAGTCATTGCAATTTTCAAATAT
1 GTCAAGTTTAGTCATTGCAATTCTCAAATAT
* *
56503057 GTCAATTTTAGTCATTAG-ACTTCTCAAAT
1 GTCAAGTTTAGTCATT-GCAATTCTCAAAT
56503086 TTTGAAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (31 bp):
GTCAAGTTTAGTCATTGCAATTCTCAAATAT
Found at i:56504275 original size:9 final size:9
Alignment explanation
Indices: 56504259--56504319 Score: 104
Period size: 9 Copynumber: 6.8 Consensus size: 9
56504249 GGTATTTTTC
56504259 GGTAATTCG
1 GGTAATTCG
*
56504268 GTTAATTCG
1 GGTAATTCG
*
56504277 GTTAATTCG
1 GGTAATTCG
56504286 GGTAATTCG
1 GGTAATTCG
56504295 GGTAATTCG
1 GGTAATTCG
56504304 GGTAATTCG
1 GGTAATTCG
56504313 GGTAATT
1 GGTAATT
56504320 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.38
Consensus pattern (9 bp):
GGTAATTCG
Found at i:56512592 original size:5 final size:5
Alignment explanation
Indices: 56512582--56512607 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56512572 AAATGTATAA
56512582 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
56512608 CTCATGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:56516546 original size:13 final size:14
Alignment explanation
Indices: 56516481--56516549 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 14
56516471 TTATTGCTTT
56516481 ATATAAATATAATAA
1 ATATAAAT-TAATAA
*
56516496 ATAT-AAGTAATAA
1 ATATAAATTAATAA
* **
56516509 TGTCATTAAAAGAATAA
1 -AT-A-TAAATTAATAA
56516526 ATATAAATTAATAA
1 ATATAAATTAATAA
56516540 A-ATAAATTAA
1 ATATAAATTAA
56516550 AAGCAAAATG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
13 15 0.35
14 13 0.30
15 6 0.14
16 2 0.05
17 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (14 bp):
ATATAAATTAATAA
Found at i:56532062 original size:12 final size:11
Alignment explanation
Indices: 56532034--56532075 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
56532024 ATTTTTTTAA
56532034 TTTTAAAATAC
1 TTTTAAAATAC
56532045 TTTTAAAATAC
1 TTTTAAAATAC
56532056 TTTTTAAAAT--
1 -TTTTAAAATAC
56532066 TTTTAAAATA
1 TTTTAAAATA
56532076 AGTTTTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.31
11 11 0.38
12 9 0.31
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:56532071 original size:21 final size:22
Alignment explanation
Indices: 56532034--56532075 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
56532024 ATTTTTTTAA
56532034 TTTTAAAATACTTTTAAAATACT
1 TTTTAAAATA-TTTTAAAATACT
56532057 TTTTAAAAT-TTTTAAAATA
1 TTTTAAAATATTTTAAAATA
56532076 AGTTTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAATATTTTAAAATACT
Found at i:56533905 original size:16 final size:16
Alignment explanation
Indices: 56533886--56533926 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
56533876 AATTTGATAC
56533886 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
56533902 AATTTTGATAACAATT
1 AATTTTAATAACAATT
*
56533918 AGTTTTAAT
1 AATTTTAAT
56533927 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:56533928 original size:22 final size:23
Alignment explanation
Indices: 56533900--56533961 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
56533890 TTAATAACAA
* * *
56533900 TTAATTTTGATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
56533922 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
56533945 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
56533962 ACTGGCCGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 15 0.43
23 14 0.40
24 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:56551876 original size:26 final size:27
Alignment explanation
Indices: 56551836--56551891 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
56551826 TTGAACTTGC
*
56551836 ATTTTTAAAACTAAAAA-AAAACCTAA
1 ATTTTTAAAACTAAAAATAAAAACTAA
56551862 ATTTCTTAAAA-TAAAAATAAAAACTAA
1 ATTT-TTAAAACTAAAAATAAAAACTAA
56551889 ATT
1 ATT
56551892 CTAAATATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (27 bp):
ATTTTTAAAACTAAAAATAAAAACTAA
Found at i:56555933 original size:27 final size:27
Alignment explanation
Indices: 56555889--56556018 Score: 104
Period size: 27 Copynumber: 4.7 Consensus size: 27
56555879 GTGTTCAAGT
56555889 AAAAAAAAACAT-AGGTACTTAATTTGA
1 AAAAAAAAAC-TCAGGTACTTAATTTGA
* * *
56555916 AAAAAAAAACTCATGTAC-CAAATTGA
1 AAAAAAAAACTCAGGTACTTAATTTGA
** * *
56555942 TCATTAAAGCTAAACTCAAGTGCTTAATTTGA
1 --A--AAA-AAAAACTCAGGTACTTAATTTGA
56555974 AAAAAAAAACAT-AGGTACTTAATTTGA
1 AAAAAAAAAC-TCAGGTACTTAATTTGA
*
56556001 AAAAAAAAACTCATGTAC
1 AAAAAAAAACTCAGGTAC
56556019 CAAATTGATC
Statistics
Matches: 80, Mismatches: 14, Indels: 18
0.71 0.12 0.16
Matches are distributed among these distances:
26 8 0.10
27 47 0.59
28 5 0.06
30 4 0.05
31 10 0.12
32 6 0.08
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.25
Consensus pattern (27 bp):
AAAAAAAAACTCAGGTACTTAATTTGA
Found at i:56555982 original size:85 final size:85
Alignment explanation
Indices: 56555889--56556055 Score: 334
Period size: 85 Copynumber: 2.0 Consensus size: 85
56555879 GTGTTCAAGT
56555889 AAAAAAAAACATAGGTACTTAATTTGAAAAAAAAAACTCATGTACCAAATTGATCATTAAAGCTA
1 AAAAAAAAACATAGGTACTTAATTTGAAAAAAAAAACTCATGTACCAAATTGATCATTAAAGCTA
56555954 AACTCAAGTGCTTAATTTGA
66 AACTCAAGTGCTTAATTTGA
56555974 AAAAAAAAACATAGGTACTTAATTTGAAAAAAAAAACTCATGTACCAAATTGATCATTAAAGCTA
1 AAAAAAAAACATAGGTACTTAATTTGAAAAAAAAAACTCATGTACCAAATTGATCATTAAAGCTA
56556039 AACTCAAGTGCTTAATT
66 AACTCAAGTGCTTAATT
56556056 GGGACAAATG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (85 bp):
AAAAAAAAACATAGGTACTTAATTTGAAAAAAAAAACTCATGTACCAAATTGATCATTAAAGCTA
AACTCAAGTGCTTAATTTGA
Found at i:56556142 original size:31 final size:33
Alignment explanation
Indices: 56556101--56556166 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
56556091 AACCTAGGTA
*
56556101 TAGATTTGAATATTGAAACC-AAATTCAAGTAC
1 TAGATTTGAATATTGAAACCAAAACTCAAGTAC
* *
56556133 TAGA-TTGAATTTTGAAGCCAAAACTCAAGTAC
1 TAGATTTGAATATTGAAACCAAAACTCAAGTAC
56556165 TA
1 TA
56556167 AATAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
TAGATTTGAATATTGAAACCAAAACTCAAGTAC
Found at i:56567978 original size:117 final size:117
Alignment explanation
Indices: 56567552--56568139 Score: 840
Period size: 117 Copynumber: 4.9 Consensus size: 117
56567542 AAAGAAAAAC
* * * * *
56567552 AACAACAACAAGAAGAAAACTATTGGTGGTGAACATATTATTGAAGGGTTAAGTGATAACAAGGT
1 AACAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGT
* *
56567617 TGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTGCAATG
66 TGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAACG
* *
56567669 AACAAGAAGAAG-AG--AACTATTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAAGGT
1 AACAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGT
56567731 TGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAACGAAGAAG
66 TGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAAC------G
* * ** *
56567789 AAGAAGAAGAAGAAGAAAACTATTGGTAGTGAACATTGTATTGAAGGGTTAAGTGATAGCAGGGT
1 AACAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGT
* *
56567854 TGAAATGGAAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTTCAACG
66 TGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAACG
* *
56567906 AAGAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGCAAGGT
1 AACAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGT
*
56567971 TGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATG
66 TGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAACG
* * * *
56568023 AACAAGAAGAAGAAGAAAACTATTGGTGGTGAGCAGAGTATTGAAGTGTTTAGTAATAGCAAGGT
1 AACAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGT
56568088 TGAAATGGAAGATCCCCTTAAAGCCAAGCCTAAACGTGGTCGGCCAAAGGGT
66 TGAAATGGAAGATCCCCTT------AAGCCTAAACGTGGTCGGCCAAAGGGT
56568140 TCAAAGAATA
Statistics
Matches: 429, Mismatches: 27, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
114 96 0.22
116 2 0.00
117 199 0.46
120 12 0.03
121 2 0.00
123 118 0.28
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.20
Consensus pattern (117 bp):
AACAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGT
TGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAACG
Found at i:56568020 original size:240 final size:235
Alignment explanation
Indices: 56567522--56568143 Score: 876
Period size: 237 Copynumber: 2.6 Consensus size: 235
56567512 TAAGGGTAAG
* * * * *
56567522 CGTGGTAGGCCAAAGGGTTCAAAGAAAAACAACAACAACAAGAAGAAAACTATTGGTGGTGAACA
1 CGTGGTCGGCCAAAGGG-TCAACG-AAAAGAACAAGAAGAAGAAGAAAACTATTGGTGGTGAACA
*
56567587 TAT-TATTGAAGGGTTAAGTGATAACAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGT
64 T-TGTATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGT
* * * *
56567651 CGGCCAAAGGGTGCAATGAACAAGAAGAAGAGAACTATTGGTGGTGAACAGATTATTGAAGGGTT
128 CGGCCAAAGGGTTCAACGAACAAGAAGAAGAGAACTATTGGTGGTGAACAAAGTATTGAAGGGTT
56567716 AAGTGATAACAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
193 AAGTGATAACAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
* *
56567759 CGTGGTCGGCCAAAGGGTACAACGAAGAAGAAGAAGAAGAAGAAGAAAACTATTGGTAGTGAACA
1 CGTGGTCGGCCAAAGGGT-CAACGAA-AAGAACAAGAAGAAGAAGAAAACTATTGGTGGTGAACA
* *
56567824 TTGTATTGAAGGGTTAAGTGATAGCAGGGTTGAAATGGAAAATCCCCTTAAGCCTAAACGTGGTC
64 TTGTATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTC
*
56567889 GGCCAAAGGGTTCAACGAAGAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGG
129 GGCCAAAGGGTTCAACGAACAAGAAGAAG-AG--AACTATTGGTGGTGAACAAAGTATTGAAGGG
*
56567954 TTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
191 TTAAGTGATAACAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
* * **
56567999 CGTGGTCGGCCAAAGGGT--AC--AATGAACAAGAAGAAGAAGAAAACTATTGGTGGTGAGCAGA
1 CGTGGTCGGCCAAAGGGTCAACGAAAAGAACAAGAAGAAGAAGAAAACTATTGGTGGTGAACATT
* * *
56568060 GTATTGAAGTGTTTAGTAATAGCAAGGTTGAAATGGAAGATCCCCTTAAAGCCAAGCCTAAACGT
66 GTATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTT------AAGCCTAAACGT
56568125 GGTCGGCCAAAGGGTTCAA
125 GGTCGGCCAAAGGGTTCAA
56568144 AGAATAAACA
Statistics
Matches: 346, Mismatches: 27, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
234 76 0.22
235 1 0.00
236 4 0.01
237 141 0.41
238 2 0.01
240 122 0.35
ACGTcount: A:0.39, C:0.14, G:0.28, T:0.20
Consensus pattern (235 bp):
CGTGGTCGGCCAAAGGGTCAACGAAAAGAACAAGAAGAAGAAGAAAACTATTGGTGGTGAACATT
GTATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGG
CCAAAGGGTTCAACGAACAAGAAGAAGAGAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAG
TGATAACAAGGTTGAAATGGAAGATCCCCTTAAGCCTAAA
Found at i:56587823 original size:30 final size:30
Alignment explanation
Indices: 56587789--56587860 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
56587779 GGAATTGTAA
56587789 TATAATTAATAAGGTGTACTATATAATATT
1 TATAATTAATAAGGTGTACTATATAATATT
56587819 TATAATTAATAAGGTGTACTATATAATATT
1 TATAATTAATAAGGTGTACTATATAATATT
56587849 TAT-ATATAATAA
1 TATAAT-TAATAA
56587861 ATATATATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 2 0.05
30 39 0.95
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (30 bp):
TATAATTAATAAGGTGTACTATATAATATT
Found at i:56594761 original size:18 final size:18
Alignment explanation
Indices: 56594738--56594774 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
56594728 TAGTTGTGTT
*
56594738 TGAATCCAAACTCATATC
1 TGAATCCAAACCCATATC
56594756 TGAATCCAAACCCATATC
1 TGAATCCAAACCCATATC
56594774 T
1 T
56594775 CACCGATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (18 bp):
TGAATCCAAACCCATATC
Found at i:56594833 original size:21 final size:21
Alignment explanation
Indices: 56594786--56594836 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
56594776 ACCGATGTTT
* * *
56594786 CTAATCTCATTACTACAGTAT
1 CTAATCTCATCACTACAATAA
* *
56594807 CCAATCTCATCGCTACAATAA
1 CTAATCTCATCACTACAATAA
56594828 CTAATCTCA
1 CTAATCTCA
56594837 CCGCCACCAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.31
Consensus pattern (21 bp):
CTAATCTCATCACTACAATAA
Found at i:56597480 original size:51 final size:51
Alignment explanation
Indices: 56597421--56597517 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
56597411 TTATATATTT
* *
56597421 TGTGTAAATATTGC-ATGATAAATTTGTTGAAT-TAGAACCAATTTGATAGCA
1 TGTGTAAATATTGCGA-GATAAATTTGTTAAATCAAG-ACCAATTTGATAGCA
* *
56597472 TGTGTAAATGTTGCGAGCTAAATTTGTTAAATCAAGACCAATTTGA
1 TGTGTAAATATTGCGAGATAAATTTGTTAAATCAAGACCAATTTGA
56597518 CAGAAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
51 37 0.93
52 3 0.08
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (51 bp):
TGTGTAAATATTGCGAGATAAATTTGTTAAATCAAGACCAATTTGATAGCA
Found at i:56598926 original size:29 final size:30
Alignment explanation
Indices: 56598887--56598958 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
56598877 ACTTTCGAAT
* *
56598887 ATTT-AAAATTTAGTTCTTAT-ATTTTTAT
1 ATTTAAAAATTTAGTCCTTATAATTTTTAG
* * *
56598915 TTTTAAAAATTTAATCCTTTTAATTTTTAG
1 ATTTAAAAATTTAGTCCTTATAATTTTTAG
56598945 ATTTAAAAATTTAG
1 ATTTAAAAATTTAG
56598959 ATCTAATTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 3 0.09
29 13 0.37
30 19 0.54
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (30 bp):
ATTTAAAAATTTAGTCCTTATAATTTTTAG
Found at i:56609319 original size:25 final size:27
Alignment explanation
Indices: 56609248--56609319 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 27
56609238 TAAATAAAAA
56609248 AATAAAATAGTATATTAATAT-ATATAAGT
1 AATAAAAT--TATA-TAATATAATATAAGT
56609277 AATAAAATTATA-AA-ATAATATAA-T
1 AATAAAATTATATAATATAATATAAGT
56609301 AAT-AAATTATATAATATAA
1 AATAAAATTATATAATATAA
56609320 ATAGTTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
23 8 0.20
24 8 0.20
25 12 0.30
27 4 0.10
29 8 0.20
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
AATAAAATTATATAATATAATATAAGT
Found at i:56609748 original size:20 final size:19
Alignment explanation
Indices: 56609723--56609763 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
56609713 AACATAATGA
* *
56609723 TATATAATATATATTTTTAT
1 TATATAAT-TACATATTTAT
56609743 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
56609762 TA
1 TA
56609764 GTTGATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:56613532 original size:83 final size:83
Alignment explanation
Indices: 56613390--56613550 Score: 277
Period size: 83 Copynumber: 1.9 Consensus size: 83
56613380 GTAACAATAA
**
56613390 GTTGAAAACGAAAGGAAGAATAGAGATTTACTAATTGTTGAGACCTATTTAACACAGTTTCCTCA
1 GTTGAAAACGAAAGGAAGAATAGAGATTTACTAAACGTTGAGACCTATTTAACACAGTTTCCTCA
56613455 AAACAGTAGCACTTTGTT
66 AAACAGTAGCACTTTGTT
* *
56613473 GTTGAAAACGACAGGAAGAATAGAGATTTACTAAACGTTGAGACCTATTTAACATAGTTTCCTCA
1 GTTGAAAACGAAAGGAAGAATAGAGATTTACTAAACGTTGAGACCTATTTAACACAGTTTCCTCA
*
56613538 AAATAGTAGCACT
66 AAACAGTAGCACT
56613551 ATGTGTAACA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (83 bp):
GTTGAAAACGAAAGGAAGAATAGAGATTTACTAAACGTTGAGACCTATTTAACACAGTTTCCTCA
AAACAGTAGCACTTTGTT
Found at i:56616338 original size:14 final size:14
Alignment explanation
Indices: 56616319--56616350 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
56616309 TCCAATCACC
56616319 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
56616333 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
56616347 GGGC
1 GGGC
56616351 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:56621453 original size:14 final size:14
Alignment explanation
Indices: 56621434--56621465 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
56621424 TCCAATCACC
56621434 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
56621448 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
56621462 GGGC
1 GGGC
56621466 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:56624157 original size:23 final size:23
Alignment explanation
Indices: 56624131--56624295 Score: 163
Period size: 23 Copynumber: 7.2 Consensus size: 23
56624121 ATAAGTGCCA
56624131 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
** **
56624154 CACTGATACATAGCCTTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
56624177 CACTGAAATGTAGCCAAATCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
56624200 CACTGATACGTAGCC-ATAGCTAG
1 CACTGATATGTAGCCGA-AGCTAC
* *
56624223 CACTGAAATGTAG-CTAGAGCTAC
1 CACTGATATGTAGCCGA-AGCTAC
* *
56624246 CACTGATATGTAACCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
56624269 CACTGAAATATAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
56624292 CACT
1 CACT
56624296 AATCAATAAC
Statistics
Matches: 113, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
22 2 0.02
23 110 0.97
24 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:56624188 original size:46 final size:46
Alignment explanation
Indices: 56624131--56624295 Score: 215
Period size: 46 Copynumber: 3.6 Consensus size: 46
56624121 ATAAGTGCCA
* * *
56624131 CACTGATATGTAGCCGAAGCTACCACTGATACATAGCCTTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
* * *
56624177 CACTGAAATGTAGCCAAATCTACCACTGATACGTAGCCATAGCTAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
* * * *
56624223 CACTGAAATGTAG-CTAGAGCTACCACTGATATGTAACCGTAGCTAC
1 CACTGAAATGTAGCCGA-AGCTACCACTGATACGTAGCCATAGCTAC
*
56624269 CACTGAAATATAGCCGAAGCTACCACT
1 CACTGAAATGTAGCCGAAGCTACCACT
56624296 AATCAATAAC
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
45 2 0.02
46 99 0.96
47 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
Found at i:56624290 original size:69 final size:69
Alignment explanation
Indices: 56624131--56624295 Score: 181
Period size: 69 Copynumber: 2.4 Consensus size: 69
56624121 ATAAGTGCCA
* * * *
56624131 CACTGATATGTAGCCGAAGCTACCACTGATACATAGCCTTAGCTACCACTGAAATGTAGCCAAAT
1 CACTGATATGTAGCCGAAGCTACCACTGAAACATAGCCTGAGCTACCACTGAAATGTAACCAAAG
56624196 CTAC
66 CTAC
* * ** * **
56624200 CACTGATACGTAGCC-ATAGCTAGCACTGAAATGTAG-CTAGAGCTACCACTGATATGTAACCGT
1 CACTGATATGTAGCCGA-AGCTACCACTGAAACATAGCCT-GAGCTACCACTGAAATGTAACCAA
56624263 AGCTAC
64 AGCTAC
* *
56624269 CACTGAAATATAGCCGAAGCTACCACT
1 CACTGATATGTAGCCGAAGCTACCACT
56624296 AATCAATAAC
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
68 3 0.04
69 74 0.95
70 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (69 bp):
CACTGATATGTAGCCGAAGCTACCACTGAAACATAGCCTGAGCTACCACTGAAATGTAACCAAAG
CTAC
Found at i:56624549 original size:18 final size:17
Alignment explanation
Indices: 56624523--56624561 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
56624513 ATTTTCCTTC
56624523 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
56624540 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
56624558 CACA
1 CACA
56624562 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:56630805 original size:47 final size:47
Alignment explanation
Indices: 56630736--56630830 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
56630726 ATGCCGCTGT
56630736 AAGGATGAGGTTCGCGAGAATGTGCTCTCTGAAATGGAAATGTGCGC
1 AAGGATGAGGTTCGCGAGAATGTGCTCTCTGAAATGGAAATGTGCGC
56630783 AAGGATGAGGTTCGCGAGAATGTGCTCTCTGAAATGGAAATGTGCGC
1 AAGGATGAGGTTCGCGAGAATGTGCTCTCTGAAATGGAAATGTGCGC
56630830 A
1 A
56630831 CACATGAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (47 bp):
AAGGATGAGGTTCGCGAGAATGTGCTCTCTGAAATGGAAATGTGCGC
Found at i:56631892 original size:24 final size:24
Alignment explanation
Indices: 56631865--56631912 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
56631855 CATTTATATG
56631865 TTTAAAAATAATAAAA-ATATTTTA
1 TTTAAAAAT-ATAAAATATATTTTA
*
56631889 TTTAAATATATAAAATTATATTTT
1 TTTAAAAATATAAAA-TATATTTT
56631913 TGTTATCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTAAAAATATAAAATATATTTTA
Found at i:56632020 original size:14 final size:14
Alignment explanation
Indices: 56632001--56632031 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
56631991 GAAACTTGAA
56632001 AAGAAAGATTCTGG
1 AAGAAAGATTCTGG
56632015 AAGAAAGATTCTGG
1 AAGAAAGATTCTGG
56632029 AAG
1 AAG
56632032 TCTCGCTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.29, T:0.19
Consensus pattern (14 bp):
AAGAAAGATTCTGG
Found at i:56635901 original size:25 final size:25
Alignment explanation
Indices: 56635873--56635921 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
56635863 AGAGAAAAGT
*
56635873 TTAAAGAACATAAAATAAAAAAAAA
1 TTAAAGAACATAAAACAAAAAAAAA
** *
56635898 TTAAATTACTTAAAACAAAAAAAA
1 TTAAAGAACATAAAACAAAAAAAA
56635922 TATGAGAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.20
Consensus pattern (25 bp):
TTAAAGAACATAAAACAAAAAAAAA
Found at i:56638352 original size:26 final size:25
Alignment explanation
Indices: 56638306--56638359 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
56638296 AGTTTATTTT
*
56638306 TTATATAAAAATAAATTTAAAAAATA
1 TTATATAAAAATAAATCT-AAAAATA
*
56638332 TTATATATAAAATACA-CTAAAAATA
1 TTATATA-AAAATAAATCTAAAAATA
56638357 TTA
1 TTA
56638360 AAATAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.40
26 8 0.32
27 7 0.28
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
TTATATAAAAATAAATCTAAAAATA
Found at i:56638516 original size:11 final size:11
Alignment explanation
Indices: 56638502--56638529 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
56638492 TATCCAAATA
56638502 ATAATAACAAT
1 ATAATAACAAT
56638513 ATAATAACAAT
1 ATAATAACAAT
56638524 ATAATA
1 ATAATA
56638530 GCGAAATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATAACAAT
Found at i:56639261 original size:21 final size:22
Alignment explanation
Indices: 56639237--56639284 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
56639227 ATTTTGTTTT
*
56639237 ATTTTAATC-ATTTAATTA-TTA
1 ATTTT-ATCGATTTAATCATTTA
*
56639258 ATTTTTTCGATTTAATCATTTA
1 ATTTTATCGATTTAATCATTTA
56639280 ATTTT
1 ATTTT
56639285 TGAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 13 0.57
22 8 0.35
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTTATCGATTTAATCATTTA
Found at i:56639880 original size:10 final size:10
Alignment explanation
Indices: 56639865--56639890 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
56639855 GACCCACACC
56639865 ATAAAAAATT
1 ATAAAAAATT
56639875 ATAAAAAATT
1 ATAAAAAATT
56639885 ATAAAA
1 ATAAAA
56639891 TTATTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:56641949 original size:32 final size:32
Alignment explanation
Indices: 56641902--56641978 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
56641892 GTGTAAATTG
*
56641902 ATACATG-AACTTTGATT-CGGTGCAATTATAT
1 ATACATGAAACTTTGATTGCGGTGCAA-AATAT
* * *
56641933 ATACATGAAACTTTGATTGTGGTTCAAAATGT
1 ATACATGAAACTTTGATTGCGGTGCAAAATAT
56641965 ATACATGAAACTTT
1 ATACATGAAACTTT
56641979 CATTTTAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.17
32 27 0.68
33 6 0.15
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (32 bp):
ATACATGAAACTTTGATTGCGGTGCAAAATAT
Found at i:56644879 original size:22 final size:22
Alignment explanation
Indices: 56644773--56644879 Score: 53
Period size: 22 Copynumber: 4.8 Consensus size: 22
56644763 AACTTTTATA
* *
56644773 AATTTTATTATAGTAAAAATAT
1 AATTTTATTATTGTTAAAATAT
* *
56644795 AGTTTTATTATT-TTAATAGCTTAT
1 AATTTTATTATTGTTAA-A--ATAT
* *
56644819 ACTTTTA-TAGTTTTTAAAAT-T
1 AATTTTATTA-TTGTTAAAATAT
*
56644840 -ATTTT-TTTTTGAAATTAAAATAT
1 AATTTTATTATTG---TTAAAATAT
56644863 AATTTTATTATTGTTAA
1 AATTTTATTATTGTTAA
56644880 TTTAAAATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 24
0.65 0.10 0.25
Matches are distributed among these distances:
19 2 0.03
20 5 0.08
21 4 0.06
22 23 0.37
23 3 0.05
24 17 0.27
25 9 0.14
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (22 bp):
AATTTTATTATTGTTAAAATAT
Found at i:56650429 original size:17 final size:17
Alignment explanation
Indices: 56650407--56650440 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56650397 TATTAATATC
*
56650407 ATTTTAATAATTTGAAA
1 ATTTTAATAATTAGAAA
*
56650424 ATTTTATTAATTAGAAA
1 ATTTTAATAATTAGAAA
56650441 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTTTAATAATTAGAAA
Found at i:56652780 original size:21 final size:19
Alignment explanation
Indices: 56652738--56652782 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
56652728 ATAATTTTGG
* *
56652738 TAAATTTTACCCTTAATCT
1 TAAATTTTACCCTGAATAT
56652757 TAAATTTTAAACCCTGAATAT
1 TAAATTTT--ACCCTGAATAT
56652778 TAAAT
1 TAAAT
56652783 CCTGAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAATTTTACCCTGAATAT
Found at i:56652786 original size:14 final size:14
Alignment explanation
Indices: 56652763--56652797 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
56652753 ATCTTAAATT
56652763 TTAAACCCTGAATA
1 TTAAACCCTGAATA
* *
56652777 TTAAATCCTGAATC
1 TTAAACCCTGAATA
56652791 TTAAACC
1 TTAAACC
56652798 TTGAGCAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (14 bp):
TTAAACCCTGAATA
Found at i:56669297 original size:15 final size:16
Alignment explanation
Indices: 56669267--56669299 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
56669257 TTGATATATA
56669267 ATATTTGAAAATTTTT
1 ATATTTGAAAATTTTT
*
56669283 ATATTT-AATATTTTT
1 ATATTTGAAAATTTTT
56669298 AT
1 AT
56669300 TAAAGTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATATTTGAAAATTTTT
Found at i:56671560 original size:31 final size:31
Alignment explanation
Indices: 56671525--56671589 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
56671515 TCTAACATAC
56671525 AAAAACTAAATT-ACCTAAATTTGTAATAAAA
1 AAAAACTAAATTAACCTAAATTT-TAATAAAA
* *
56671556 AAAAACTAAATTCAACCTAACTTTTAATATAA
1 AAAAACTAAATT-AACCTAAATTTTAATAAAA
56671588 AA
1 AA
56671590 TTTTTGTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 12 0.40
32 9 0.30
33 9 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (31 bp):
AAAAACTAAATTAACCTAAATTTTAATAAAA
Found at i:56674560 original size:33 final size:33
Alignment explanation
Indices: 56674493--56674561 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
56674483 GAAACACCAT
*
56674493 CACCACCCACAAATACTGAACCACATATTGAAC
1 CACCACCCACAAATACTGAACCACATATTAAAC
*
56674526 CACCACCCATAAATACTGAACCACATGA-TAAAC
1 CACCACCCACAAATACTGAACCACAT-ATTAAAC
56674559 CAC
1 CAC
56674562 ATATTGAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.43, C:0.36, G:0.06, T:0.14
Consensus pattern (33 bp):
CACCACCCACAAATACTGAACCACATATTAAAC
Found at i:56676333 original size:13 final size:13
Alignment explanation
Indices: 56676315--56676363 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
56676305 AGGGGGGATG
56676315 TTAGTATATTAAA
1 TTAGTATATTAAA
**
56676328 TTAGTATATT-GC
1 TTAGTATATTAAA
56676340 TATAGTATATTAAA
1 T-TAGTATATTAAA
56676354 TTAGTATATT
1 TTAGTATATT
56676364 GCTAATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 1 0.03
13 28 0.93
14 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (13 bp):
TTAGTATATTAAA
Found at i:56676352 original size:26 final size:26
Alignment explanation
Indices: 56676316--56676367 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
56676306 GGGGGGATGT
56676316 TAGTATATTAAATTAGTATATTGCTA
1 TAGTATATTAAATTAGTATATTGCTA
56676342 TAGTATATTAAATTAGTATATTGCTA
1 TAGTATATTAAATTAGTATATTGCTA
56676368 ATTTAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (26 bp):
TAGTATATTAAATTAGTATATTGCTA
Found at i:56680652 original size:39 final size:40
Alignment explanation
Indices: 56680598--56680680 Score: 159
Period size: 39 Copynumber: 2.1 Consensus size: 40
56680588 ACTCTTATAT
56680598 TAATATTTAATATTTGATTGTTAGAATAAGAGCATTCT-G
1 TAATATTTAATATTTGATTGTTAGAATAAGAGCATTCTGG
56680637 TAATATTTAATATTTGATTGTTAGAATAAGAGCATTCTGG
1 TAATATTTAATATTTGATTGTTAGAATAAGAGCATTCTGG
56680677 TAAT
1 TAAT
56680681 TTAATAACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 38 0.88
40 5 0.12
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (40 bp):
TAATATTTAATATTTGATTGTTAGAATAAGAGCATTCTGG
Found at i:56685392 original size:18 final size:18
Alignment explanation
Indices: 56685364--56685401 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
56685354 TTATTGTATT
*
56685364 TTCATTTTGTTATTTTTAG
1 TTCATTTTGTT-TTTTAAG
56685383 TTCA-TTTGTTTTTTAAG
1 TTCATTTTGTTTTTTAAG
56685400 TT
1 TT
56685402 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (18 bp):
TTCATTTTGTTTTTTAAG
Found at i:56694814 original size:76 final size:76
Alignment explanation
Indices: 56694688--56694839 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
56694678 GAACTTGGGC
56694688 GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
1 GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
56694753 TTTCCTTCCTG
66 TTTCCTTCCTG
56694764 GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
1 GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
56694829 TTTCCTTCCTG
66 TTTCCTTCCTG
56694840 TTTTTATATA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (76 bp):
GCTAAATACATCTTCATTTTGCTAATTTTACTGGCTGGTTTGTAGGGATGTATATAAGATGCTGG
TTTCCTTCCTG
Found at i:56707019 original size:20 final size:20
Alignment explanation
Indices: 56706975--56707012 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56706965 AATACAATTT
56706975 ATATTTTAATAATAAATAAA
1 ATATTTTAATAATAAATAAA
56706995 ATATTTT-ATAATTAAATA
1 ATATTTTAATAA-TAAATA
56707013 GATTATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTTTAATAATAAATAAA
Found at i:56719019 original size:20 final size:20
Alignment explanation
Indices: 56718994--56719036 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
56718984 TAATTATAGT
56718994 AATTATATATGTTA-AATAAA
1 AATTATATAT-TTATAATAAA
*
56719014 AATTATATATTTATATTAAA
1 AATTATATATTTATAATAAA
56719034 AAT
1 AAT
56719037 CACTAACCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATTATATATTTATAATAAA
Found at i:56719191 original size:39 final size:41
Alignment explanation
Indices: 56719132--56719220 Score: 119
Period size: 39 Copynumber: 2.2 Consensus size: 41
56719122 AAAAATTATA
* * * *
56719132 TTTAATACAATAAAATATTTATTATA-TT-TGTTTGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTATGGTAGTGTTT
*
56719171 TTTAATATAATTAAACATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTATGGTAGTGTTT
56719212 TTTAATATA
1 TTTAATATA
56719221 TTTCTAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 23 0.53
40 2 0.05
41 18 0.42
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (41 bp):
TTTAATATAATAAAACATTTATTATATTTATGGTAGTGTTT
Found at i:56720335 original size:14 final size:15
Alignment explanation
Indices: 56720312--56720353 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
56720302 TCCAACATTA
*
56720312 GGTTTTGGGTTTTAG
1 GGTTTAGGGTTTTAG
*
56720327 GG-TTAGGGTTTAAG
1 GGTTTAGGGTTTTAG
56720341 GGTTTAGGGTTTT
1 GGTTTAGGGTTTT
56720354 GAAGAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (15 bp):
GGTTTAGGGTTTTAG
Found at i:56720777 original size:125 final size:125
Alignment explanation
Indices: 56720470--56720912 Score: 724
Period size: 125 Copynumber: 3.5 Consensus size: 125
56720460 GATAAAATCA
* * *
56720470 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAGTCACGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* *
56720535 AGGTCCTGGAAAAATAATTTCAAGTTGACGTTTCTAAGAAAATAGTATAAAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTAT-AAAAAACGCTTC
* * *
56720596 AAGCAAGATGCTTTATCAGAAGAATTTATGAAATCCCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * *
56720661 AGGTCCTGGAAAAATAATTTTGAGTTCACGTTTCTGAGTAAATAGTATAAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
* *
56720721 AAGCAGGATGCTTTATCAGAAGAATTTTTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAAT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* *
56720786 AGGTCTTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
* *
56720846 AAGCAGGATACTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
56720911 AG
66 AG
56720913 CATGTTTGGG
Statistics
Matches: 295, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
125 192 0.65
126 103 0.35
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
Found at i:56724050 original size:26 final size:26
Alignment explanation
Indices: 56724015--56724065 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
56724005 AATGTGAAAG
*
56724015 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
56724041 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
56724066 TTCATTGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:56724103 original size:102 final size:102
Alignment explanation
Indices: 56723937--56724190 Score: 385
Period size: 102 Copynumber: 2.5 Consensus size: 102
56723927 TGTATATAAA
** * * *
56723937 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
56724002 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
66 TGAAA--TGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
56724040 AGGGGTTGCTAAGTGCTGATTCCCCG-TTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TGATCCACCATATCT
56724103 TTGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
56724141 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGT-GT-GTGCTAAGTGC-TGAT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGAT
56724191 TCCCCGATTC
Statistics
Matches: 141, Mismatches: 6, Indels: 12
0.89 0.04 0.08
Matches are distributed among these distances:
98 1 0.01
99 2 0.01
100 37 0.26
101 33 0.23
102 43 0.30
103 25 0.18
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:56724183 original size:30 final size:32
Alignment explanation
Indices: 56724147--56724218 Score: 130
Period size: 30 Copynumber: 2.3 Consensus size: 32
56724137 CCCGAGGGGT
56724147 TGCTAAGTGCTGATTCCCCGATTCAGT-GT-G
1 TGCTAAGTGCTGATTCCCCGATTCAGTGGTGG
56724177 TGCTAAGTGCTGATTCCCCGATTCAGTGGTGG
1 TGCTAAGTGCTGATTCCCCGATTCAGTGGTGG
56724209 TGCTAAGTGC
1 TGCTAAGTGC
56724219 GAGATCCACC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 27 0.68
31 2 0.05
32 11 0.28
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (32 bp):
TGCTAAGTGCTGATTCCCCGATTCAGTGGTGG
Found at i:56730381 original size:14 final size:15
Alignment explanation
Indices: 56730357--56730385 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56730347 ACGGAAAATT
56730357 TTCGTAAAAATTTCG
1 TTCGTAAAAATTTCG
56730372 TTCG-AAAAATTTCG
1 TTCGTAAAAATTTCG
56730386 ACGTTTGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
TTCGTAAAAATTTCG
Found at i:56731551 original size:26 final size:26
Alignment explanation
Indices: 56731515--56731564 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
56731505 GAAATGTGAA
*
56731515 AGGGGTTGCTATGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
56731541 AGGGGTTGCTAAGTGCTGATTCCC
1 AGGGGTTGCTAAGTGCTGATTCCC
56731565 GATTCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.22, G:0.34, T:0.30
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:56731621 original size:101 final size:101
Alignment explanation
Indices: 56731439--56731798 Score: 561
Period size: 101 Copynumber: 3.6 Consensus size: 101
56731429 TGTATATAAA
** * * *
56731439 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
56731503 TTGAAATGTGAAA-GGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAA--TGAAAGGGGGTTGCTATGTGCTGATTCCCCG
56731541 AGGGGTTGCTAAGTGCTGATT-CCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
56731605 TGAAATGAAAGGGGGGTTGCTATGTGCTGATTCCCCG
66 TGAAATGAAA-GGGGGTTGCTATGTGCTGATTCCCCG
56731642 A-GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
56731706 TGAAATAAAAGGGGGTTGCTA--TGCTGATTCCCCG
66 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCG
* **
56731740 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
56731799 ATAACGGCTA
Statistics
Matches: 244, Mismatches: 9, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
98 14 0.06
99 59 0.24
100 30 0.12
101 121 0.50
102 20 0.08
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.31
Consensus pattern (101 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:56731651 original size:25 final size:25
Alignment explanation
Indices: 56731618--56731667 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
56731608 AATGAAAGGG
*
56731618 GGGTTGCTATGTGCTGATTCCCCGA
1 GGGTTGCTAAGTGCTGATTCCCCGA
56731643 GGGTTGCTAAGTGCTGATTCCCCGA
1 GGGTTGCTAAGTGCTGATTCCCCGA
56731668 TTCATTGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.30
Consensus pattern (25 bp):
GGGTTGCTAAGTGCTGATTCCCCGA
Found at i:56731748 original size:24 final size:26
Alignment explanation
Indices: 56731717--56731766 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
56731707 GAAATAAAAG
56731717 GGGGTTGCT-A-TGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
56731741 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
56731767 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 9 0.38
25 1 0.04
26 14 0.58
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:56733895 original size:16 final size:16
Alignment explanation
Indices: 56733874--56733907 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
56733864 GACTTAAAAG
56733874 TTAAAACTAATTGTTA
1 TTAAAACTAATTGTTA
*
56733890 TTAAAATTAATTGTTA
1 TTAAAACTAATTGTTA
56733906 TT
1 TT
56733908 GAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:56735357 original size:13 final size:13
Alignment explanation
Indices: 56735339--56735501 Score: 99
Period size: 13 Copynumber: 12.6 Consensus size: 13
56735329 CAAATTAAAT
56735339 GTATATTATAACA
1 GTATATTATAACA
*
56735352 GTATATTA-AA-T
1 GTATATTATAACA
* *
56735363 TTAAAAGTTA-AACA
1 GT-ATA-TTATAACA
* *
56735377 TTATATTAAAACA
1 GTATATTATAACA
* *
56735390 ATATAATTATAATA
1 GTAT-ATTATAACA
*
56735404 GTATATTAAAACA
1 GTATATTATAACA
* *
56735417 ATATATTA-AAAA
1 GTATATTATAACA
*
56735429 GTATATTTATAATA
1 GTATA-TTATAACA
*
56735443 GTATATTAAAACA
1 GTATATTATAACA
56735456 GTATATTATAA-A
1 GTATATTATAACA
56735468 -T-T-TTATAACA
1 GTATATTATAACA
56735478 GTATATTAGTAAAACA
1 GTATATTA-T--AACA
56735494 GTATATTA
1 GTATATTA
56735502 CATTAAAAAT
Statistics
Matches: 118, Mismatches: 18, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
9 6 0.05
10 2 0.02
11 3 0.03
12 16 0.14
13 58 0.49
14 21 0.18
16 12 0.10
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (13 bp):
GTATATTATAACA
Found at i:56735439 original size:39 final size:40
Alignment explanation
Indices: 56735372--56735463 Score: 141
Period size: 39 Copynumber: 2.3 Consensus size: 40
56735362 TTTAAAAGTT
*
56735372 AAACATTATATTAAAACAATATAATTATAATAGTATATTA
1 AAACAATATATTAAAACAATATAATTATAATAGTATATTA
* *
56735412 AAACAATATATTAAAA-AGTATATTTATAATAGTATATTA
1 AAACAATATATTAAAACAATATAATTATAATAGTATATTA
*
56735451 AAACAGTATATTA
1 AAACAATATATTA
56735464 TAAATTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (40 bp):
AAACAATATATTAAAACAATATAATTATAATAGTATATTA
Found at i:56735635 original size:15 final size:15
Alignment explanation
Indices: 56735615--56735648 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
56735605 AAACTAAAAT
*
56735615 TTAATGTGTTAGAAA
1 TTAATGTGTTACAAA
56735630 TTAATGTGTTACAAA
1 TTAATGTGTTACAAA
56735645 TTAA
1 TTAA
56735649 ATGTATATTT
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:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (15 bp):
TTAATGTGTTACAAA
Found at i:56735702 original size:13 final size:12
Alignment explanation
Indices: 56735684--56735778 Score: 73
Period size: 13 Copynumber: 7.2 Consensus size: 12
56735674 AATTTAAAAG
56735684 TTAAAAAATTATA
1 TTAAAAAA-TATA
56735697 TTAAAACAATATAA
1 TTAAAA-AATAT-A
* *
56735711 TTATAACAGTATA
1 TTA-AAAAATATA
56735724 TTAAAACAATATA
1 TTAAAA-AATATA
56735737 TTAAAAAATATA
1 TTAAAAAATATA
* *
56735749 TTTATAATAGTATA
1 -TTA-AAAAATATA
*
56735763 TTAAAACAGTATA
1 TTAAAA-AATATA
56735776 TTA
1 TTA
56735779 TAAATTTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
12 10 0.15
13 39 0.57
14 17 0.25
15 2 0.03
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (12 bp):
TTAAAAAATATA
Found at i:56735723 original size:27 final size:25
Alignment explanation
Indices: 56735693--56735778 Score: 91
Period size: 27 Copynumber: 3.3 Consensus size: 25
56735683 GTTAAAAAAT
56735693 TATATTAAAACAATATAATTATAACAG
1 TATATTAAAACAATAT-ATTA-AACAG
* *
56735720 TATATTAAAACAATATATTAAAAAA
1 TATATTAAAACAATATATTAAACAG
* * *
56735745 TATATTTATAATAGTATATTAAAACAG
1 TATA-TTAAAACAATATATT-AAACAG
56735772 TATATTA
1 TATATTA
56735779 TAAATTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
25 7 0.14
26 19 0.38
27 24 0.48
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (25 bp):
TATATTAAAACAATATATTAAACAG
Found at i:56735761 original size:39 final size:40
Alignment explanation
Indices: 56735684--56735778 Score: 140
Period size: 39 Copynumber: 2.4 Consensus size: 40
56735674 AATTTAAAAG
56735684 TTAAAA-AATTATATTAAAACAATATAATTATAACAGTATA
1 TTAAAACAA-TATATTAAAACAATATAATTATAACAGTATA
* *
56735724 TTAAAACAATATATTAAAA-AATATATTTATAATAGTATA
1 TTAAAACAATATATTAAAACAATATAATTATAACAGTATA
*
56735763 TTAAAACAGTATATTA
1 TTAAAACAATATATTA
56735779 TAAATTTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
39 33 0.65
40 16 0.31
41 2 0.04
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (40 bp):
TTAAAACAATATATTAAAACAATATAATTATAACAGTATA
Found at i:56735808 original size:13 final size:12
Alignment explanation
Indices: 56735688--56735816 Score: 66
Period size: 13 Copynumber: 10.1 Consensus size: 12
56735678 TAAAAGTTAA
56735688 AAAAT-TATATT
1 AAAATATATATT
*
56735699 AAAACAATATAATT
1 AAAA-TATAT-ATT
* *
56735713 ATAACAGTATATT
1 AAAATA-TATATT
*
56735726 AAAACAATATATT
1 AAAA-TATATATT
*
56735739 AAAAAATATATTT
1 AAAATATATA-TT
*
56735752 ATAATAGTATATT
1 AAAATA-TATATT
*
56735765 AAAACAGTATATT
1 AAAATA-TATATT
*
56735778 ATAAAT-TTTA-T
1 A-AAATATATATT
56735789 AACAATATATTATT
1 AA-AATATA-TATT
56735803 AAAATAGTATATT
1 AAAATA-TATATT
56735816 A
1 A
56735817 CATTAAAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
10 1 0.01
11 9 0.10
12 10 0.11
13 51 0.55
14 22 0.24
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (12 bp):
AAAATATATATT
Found at i:56735948 original size:15 final size:15
Alignment explanation
Indices: 56735928--56735961 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
56735918 AAACTAAAAT
*
56735928 TTAATGTGTTAGAAA
1 TTAATGTGTTACAAA
56735943 TTAATGTGTTACAAA
1 TTAATGTGTTACAAA
56735958 TTAA
1 TTAA
56735962 ATGTATATTT
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:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (15 bp):
TTAATGTGTTACAAA
Done.