Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 136 of 161
Found at i:42338738 original size:24 final size:24
Alignment explanation
Indices: 42338706--42338752 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42338696 CTAAATTTAT
*
42338706 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
42338730 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
42338753 ATTTCCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:42339471 original size:94 final size:94
Alignment explanation
Indices: 42339350--42339537 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 94
42339340 AAAATTGCAA
42339350 GTTAGTCCCTCAAAATTCTTCACCTTTTCAATTTGGTTCTAATTCATCCATTTTCTTTAGTTTCT
1 GTTAGTCCCTCAAAATTCTTCACCTTTTCAATTTGGTTCTAATTCATCCATTTTCTTTAGTTTCT
42339415 AGATTATTCCACCCTTAAAATATTTACAC
66 AGATTATTCCACCCTTAAAATATTTACAC
*
42339444 GTTAGTCCCTCAAAATTCTTCATCTTTTCAATTTGGTTCTAATTCATCCATTTTCTTTAGTTTCT
1 GTTAGTCCCTCAAAATTCTTCACCTTTTCAATTTGGTTCTAATTCATCCATTTTCTTTAGTTTCT
42339509 AGATTATTCCACCCTTAAAATATTTACAC
66 AGATTATTCCACCCTTAAAATATTTACAC
42339538 TATTGGTCCT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (94 bp):
GTTAGTCCCTCAAAATTCTTCACCTTTTCAATTTGGTTCTAATTCATCCATTTTCTTTAGTTTCT
AGATTATTCCACCCTTAAAATATTTACAC
Found at i:42341550 original size:11 final size:13
Alignment explanation
Indices: 42341534--42341567 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
42341524 AATTTCATGA
42341534 AAAAATTTCG-T-
1 AAAAATTTCGTTC
42341545 AAAAATTTCGTTC
1 AAAAATTTCGTTC
42341558 AAAAATTTCG
1 AAAAATTTCG
42341568 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:42342946 original size:102 final size:101
Alignment explanation
Indices: 42342770--42343113 Score: 424
Period size: 102 Copynumber: 3.4 Consensus size: 101
42342760 TATCGATGAA
* * * *
42342770 CACGTGTATTGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTG-ATGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTA-GTA
* *
42342834 CTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
65 CTAAGTGAAGGCTACTATGTGTACCGA-AAACTTTGGT
* *
42342872 CACGTGTGTAGTATTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* *
42342937 TAAGTGAAGGCTACTATGTGTACCGAAAATTTTTTGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAA-CTTTGGT
* *** * *
42342974 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* * * * *
42343038 TATGTAAAGGCTACTACGTGAACCGTAAAAC-TTGAT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAACTTTGGT
* *
42343074 CACGTGTGTAGTACAATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
42343114 ATGATAAAAG
Statistics
Matches: 212, Mismatches: 26, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
100 39 0.18
101 43 0.20
102 129 0.61
103 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAACTTTGGT
Found at i:42343040 original size:50 final size:50
Alignment explanation
Indices: 42342770--42343107 Score: 322
Period size: 51 Copynumber: 6.7 Consensus size: 50
42342760 TATCGATGAA
* * * * * ***
42342770 CACGTGTATTGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * * * *
42342821 CACATGTG-ATGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
1 CACGTGTGTA-GTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGGT
* * * ***
42342872 CACGTGTGTAGTATTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * * * *
42342923 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAATTTTTTGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA--CTTGGT
*
42342974 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
* *
42343024 CACGTGTGTAGTACTATGTAAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
*
42343074 CACGTGTGTAGTACAATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
42343108 TATCGAATGA
Statistics
Matches: 235, Mismatches: 43, Indels: 19
0.79 0.14 0.06
Matches are distributed among these distances:
49 4 0.02
50 86 0.37
51 137 0.58
52 7 0.03
53 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:42344953 original size:18 final size:18
Alignment explanation
Indices: 42344932--42344967 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42344922 TGAACATATA
*
42344932 ATTGTATTTGGTTGAAAT
1 ATTGAATTTGGTTGAAAT
*
42344950 ATTGAATTTGTTTGAAAT
1 ATTGAATTTGGTTGAAAT
42344968 TGTGTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (18 bp):
ATTGAATTTGGTTGAAAT
Found at i:42345372 original size:16 final size:16
Alignment explanation
Indices: 42345343--42345376 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42345333 ACTATTTAAT
42345343 AATATAAAAAATTCTC
1 AATATAAAAAATTCTC
* *
42345359 AATATCAAAGATTCTC
1 AATATAAAAAATTCTC
42345375 AA
1 AA
42345377 CTAACTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (16 bp):
AATATAAAAAATTCTC
Found at i:42347433 original size:45 final size:42
Alignment explanation
Indices: 42347359--42347481 Score: 122
Period size: 41 Copynumber: 2.9 Consensus size: 42
42347349 ATATGTGTTC
* **
42347359 TCGTGTAAGACCACGTCTGGGATGATGGCATCGATATATGTAAT
1 TCGTGTAAGACCATGTCTGGGACAATGGCATCGATAT-T-TAAT
* ** *
42347403 TACGTGTAAGACCATGTCTAGGACCTTGGCATCG-TATTTGAT
1 T-CGTGTAAGACCATGTCTGGGACAATGGCATCGATATTTAAT
* * *
42347445 TCGTGTAAAACCCTGTCTGGGACAGTGGCATCGATAT
1 TCGTGTAAGACCATGTCTGGGACAATGGCATCGATAT
42347482 GAGATAGCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 27 0.41
42 7 0.11
43 1 0.02
44 4 0.06
45 27 0.41
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTGGGACAATGGCATCGATATTTAAT
Found at i:42351755 original size:19 final size:20
Alignment explanation
Indices: 42351723--42351762 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42351713 TAATTTTTTT
* *
42351723 TTAAATTATTTAAAT-TTAA
1 TTAAAATATATAAATATTAA
42351742 TTAAAATATATAAATATTAA
1 TTAAAATATATAAATATTAA
42351762 T
1 T
42351763 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAAATATATAAATATTAA
Found at i:42352821 original size:20 final size:20
Alignment explanation
Indices: 42352781--42352830 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
42352771 TTTCCTATAA
42352781 TTATAA-TTTCAAAACATATT
1 TTATAATTTTCAAAACATA-T
*
42352801 TTATAATTTTGAAAACA-AT
1 TTATAATTTTCAAAACATAT
42352820 TTATGAATTTT
1 TTAT-AATTTT
42352831 AAGATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
21 9 0.33
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (20 bp):
TTATAATTTTCAAAACATAT
Found at i:42352848 original size:28 final size:31
Alignment explanation
Indices: 42352817--42352873 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
42352807 TTTTGAAAAC
42352817 AATTTATGA-A-TTTTAA-GATTTTTTAATA
1 AATTTATGATATTTTTAATGATTTTTTAATA
*
42352845 AATTTATGATATTTTTAATTATTTTTTAA
1 AATTTATGATATTTTTAATGATTTTTTAA
42352874 CCATGGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 1 0.04
30 6 0.24
31 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (31 bp):
AATTTATGATATTTTTAATGATTTTTTAATA
Found at i:42356315 original size:23 final size:23
Alignment explanation
Indices: 42356278--42356322 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
42356268 TGCCCATATC
* *
42356278 TCTACTAGTATTAAATCATTTAT
1 TCTACTACTACTAAATCATTTAT
*
42356301 TCTACTACTACTAAATCTTTTA
1 TCTACTACTACTAAATCATTTA
42356323 GGGTGTGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (23 bp):
TCTACTACTACTAAATCATTTAT
Found at i:42360034 original size:13 final size:13
Alignment explanation
Indices: 42360016--42360046 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
42360006 CATTATTCCC
42360016 TTTCTCTATAATA
1 TTTCTCTATAATA
42360029 TTTCTCTATAATA
1 TTTCTCTATAATA
42360042 TTTCT
1 TTTCT
42360047 TATTCCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTCTCTATAATA
Found at i:42364957 original size:45 final size:45
Alignment explanation
Indices: 42364898--42364988 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
42364888 TATATCACTC
* * *
42364898 TTATTATTCTCCATATTATCATTTATATTGTTATTATTCTCTTTG
1 TTATTATTCCCCATATTATCATTTATACTCTTATTATTCTCTTTG
* * * *
42364943 TTATTGTTCCCCATATTATTATTTGTACTCTTATTATTGTCTTTG
1 TTATTATTCCCCATATTATCATTTATACTCTTATTATTCTCTTTG
42364988 T
1 T
42364989 CATGCATGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (45 bp):
TTATTATTCCCCATATTATCATTTATACTCTTATTATTCTCTTTG
Found at i:42384040 original size:3 final size:3
Alignment explanation
Indices: 42384034--42384063 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42384024 TCTCTCTCAA
42384034 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
42384064 CAAAAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42392828 original size:15 final size:15
Alignment explanation
Indices: 42392808--42392842 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
42392798 ATTATAGGTG
42392808 AAGTAAATTTTGGAT
1 AAGTAAATTTTGGAT
42392823 AAGTAAATTTTGGAT
1 AAGTAAATTTTGGAT
42392838 AAGTA
1 AAGTA
42392843 CTTTAGCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (15 bp):
AAGTAAATTTTGGAT
Found at i:42393031 original size:21 final size:21
Alignment explanation
Indices: 42393006--42393053 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
42392996 GGATGATAAT
*
42393006 ATAAAAT-GAAGATTAATTTAA
1 ATAAAATGGAA-ATTAATTAAA
* *
42393027 GTAAATTGGAAATTAATTAAA
1 ATAAAATGGAAATTAATTAAA
42393048 ATAAAA
1 ATAAAA
42393054 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
ATAAAATGGAAATTAATTAAA
Found at i:42396364 original size:74 final size:74
Alignment explanation
Indices: 42396243--42396391 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
42396233 ACTCTTATCA
42396243 TTTTCTCTCCTTTTATCATTATAACTTGGGATGATTTACTTTTATGTATTATGATAGAAAATAAT
1 TTTTCTCTCCTTTTATCATTATAACTTGGGATGATTTACTTTTATGTATTATGATAGAAAATAAT
42396308 AGTCTCTTC
66 AGTCTCTTC
*
42396317 TTTTCTCTCCTTTTATCATTCTAACTTGGGATGATTTACTTTTATGTATTATGATAGAAAATAAT
1 TTTTCTCTCCTTTTATCATTATAACTTGGGATGATTTACTTTTATGTATTATGATAGAAAATAAT
42396382 AGTCTCTTC
66 AGTCTCTTC
42396391 T
1 T
42396392 ATTTTATTTC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (74 bp):
TTTTCTCTCCTTTTATCATTATAACTTGGGATGATTTACTTTTATGTATTATGATAGAAAATAAT
AGTCTCTTC
Found at i:42400972 original size:91 final size:91
Alignment explanation
Indices: 42400832--42401013 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
42400822 CTCATGCGTA
42400832 CATAGTCCATCATCCACTTAGGATTAAGGTGTGTCACACTATGAACATCACAAGTGAACAAATTC
1 CATAGTCCATCATCCACTTAGGATTAAGGTGTGTCACACTATGAACATCACAAGTGAACAAATTC
42400897 ATAAACGGATCTAAGATCTATTCTAC
66 ATAAACGGATCTAAGATCTATTCTAC
*
42400923 CATAGTCCATCATCCACTTAGGATTAAGGTGTGTCACACTATGAACATCACAAGTGAACAAATTT
1 CATAGTCCATCATCCACTTAGGATTAAGGTGTGTCACACTATGAACATCACAAGTGAACAAATTC
42400988 ATAAACGGATCTAAGATCTATTCTAC
66 ATAAACGGATCTAAGATCTATTCTAC
42401014 TTGGGTCTGA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.28
Consensus pattern (91 bp):
CATAGTCCATCATCCACTTAGGATTAAGGTGTGTCACACTATGAACATCACAAGTGAACAAATTC
ATAAACGGATCTAAGATCTATTCTAC
Found at i:42402991 original size:83 final size:83
Alignment explanation
Indices: 42402864--42403021 Score: 226
Period size: 83 Copynumber: 1.9 Consensus size: 83
42402854 TACCTGAATC
* * *
42402864 GCTCGAGGCGACTGCAAACCTTTCAAGAGGTCGATAAATGATCGAATTACTCCATAGGGTAAAAT
1 GCTCGAGGCGACTGCAAACCTTTCAAGAGGTCAATAAATGATCGAATTACCCCACAGGGTAAAAT
*
42402929 GACCAAATTACCTAAGTT
66 CACCAAATTACCTAAGTT
* * ** *
42402947 GCTCGAGGCGACTGCAGATCTTTTGAGAGGTCAATAAATGATCGAATTACCCCACATGGTAAAAT
1 GCTCGAGGCGACTGCAAACCTTTCAAGAGGTCAATAAATGATCGAATTACCCCACAGGGTAAAAT
*
42403012 CACCGAATTA
66 CACCAAATTA
42403022 ACCCCATAGG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
83 65 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (83 bp):
GCTCGAGGCGACTGCAAACCTTTCAAGAGGTCAATAAATGATCGAATTACCCCACAGGGTAAAAT
CACCAAATTACCTAAGTT
Found at i:42403034 original size:27 final size:27
Alignment explanation
Indices: 42402982--42403202 Score: 205
Period size: 27 Copynumber: 8.3 Consensus size: 27
42402972 AGAGGTCAAT
* * * *
42402982 AAATGATCG-AATTACCCCACATGGTA
1 AAATGACCGAAATAACCCCATAGGGTA
* *
42403008 AAATCACCGAATTAACCCCATAGGGTA
1 AAATGACCGAAATAACCCCATAGGGTA
*
42403035 AAATGACCG-AATTACCCTCATAGGGTA
1 AAATGACCGAAATAACCC-CATAGGGTA
* * * * *
42403062 AAATGACTGAATTACCCCCACAGGATA
1 AAATGACCGAAATAACCCCATAGGGTA
* * *
42403089 AAATGATCGAAAT-ACCCCACAGGTTA
1 AAATGACCGAAATAACCCCATAGGGTA
* * *
42403115 AAATAACCGAAATATCCCTATAGGGTA
1 AAATGACCGAAATAACCCCATAGGGTA
* *
42403142 AAATGACCGAAATATCCCTATAGGGTA
1 AAATGACCGAAATAACCCCATAGGGTA
* * *
42403169 AAATAACCAAAATAACCCCATTGGGTA
1 AAATGACCGAAATAACCCCATAGGGTA
42403196 AAATGAC
1 AAATGAC
42403203 TGTTATGACC
Statistics
Matches: 158, Mismatches: 33, Indels: 7
0.80 0.17 0.04
Matches are distributed among these distances:
26 35 0.22
27 118 0.75
28 5 0.03
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATAACCCCATAGGGTA
Found at i:42403182 original size:54 final size:53
Alignment explanation
Indices: 42403004--42403202 Score: 227
Period size: 54 Copynumber: 3.7 Consensus size: 53
42402994 TACCCCACAT
* * *
42403004 GGTAAAATCACCGAATTAACCCCATAGGGTAAAATGACCGAATTACCCTCATAG
1 GGTAAAATAACCGAAATAACCCCATAGGGTAAAATGACCGAAATACCCT-ATAG
* * * * * * * * *
42403058 GGTAAAATGACTGAATTACCCCCACAGGATAAAATGATCGAAATACCCCACAG
1 GGTAAAATAACCGAAATAACCCCATAGGGTAAAATGACCGAAATACCCTATAG
* * *
42403111 GTTAAAATAACCGAAATATCCCTATAGGGTAAAATGACCGAAATATCCCTATAG
1 GGTAAAATAACCGAAATAACCCCATAGGGTAAAATGACCGAAATA-CCCTATAG
* *
42403165 GGTAAAATAACCAAAATAACCCCATTGGGTAAAATGAC
1 GGTAAAATAACCGAAATAACCCCATAGGGTAAAATGAC
42403203 TGTTATGACC
Statistics
Matches: 119, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
53 39 0.33
54 80 0.67
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (53 bp):
GGTAAAATAACCGAAATAACCCCATAGGGTAAAATGACCGAAATACCCTATAG
Found at i:42403201 original size:107 final size:107
Alignment explanation
Indices: 42402982--42403188 Score: 283
Period size: 107 Copynumber: 1.9 Consensus size: 107
42402972 AGAGGTCAAT
* * * *
42402982 AAATGATCGAATTACCCCACATGGTAAAATCACCGAATTAACCCCATAGGGTAAAATGACCGAAT
1 AAATGATCGAAATACCCCACATGGTAAAATAACCGAAATAACCCCATAGGGTAAAATGACCGAAA
* ** * *
42403047 TACCCTCATAGGGTAAAATGACTGAATTACCCCCACAGGATA
66 TACCCTCATAGGGTAAAATAACCAAAATAACCCCACAGGATA
* *
42403089 AAATGATCGAAATACCCCACA-GGTTAAAATAACCGAAATATCCCTATAGGGTAAAATGACCGAA
1 AAATGATCGAAATACCCCACATGG-TAAAATAACCGAAATAACCCCATAGGGTAAAATGACCGAA
42403153 ATATCCCT-ATAGGGTAAAATAACCAAAATAACCCCA
65 ATA-CCCTCATAGGGTAAAATAACCAAAATAACCCCA
42403189 TTGGGTAAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 2 0.02
107 81 0.93
108 4 0.05
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (107 bp):
AAATGATCGAAATACCCCACATGGTAAAATAACCGAAATAACCCCATAGGGTAAAATGACCGAAA
TACCCTCATAGGGTAAAATAACCAAAATAACCCCACAGGATA
Found at i:42403445 original size:26 final size:26
Alignment explanation
Indices: 42403409--42403489 Score: 101
Period size: 26 Copynumber: 3.1 Consensus size: 26
42403399 TTTGCCACAT
*
42403409 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
42403435 ATACTGATACTGGCAGCTCTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* * *
42403461 ATGCT-ATTACTAGCAACTTTGCTGCG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
42403487 ATA
1 ATA
42403490 TTGGTGTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 46 0.98
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.32
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:42403596 original size:28 final size:27
Alignment explanation
Indices: 42403564--42403617 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
42403554 TGTTGGCTGG
42403564 ATTGGGCTAAGGCCCACACTGTTACTGT
1 ATTGGGCTAAGGCCCACACTG-TACTGT
*
42403592 ATTGGGCTAAGGCCCACATTGTACTG
1 ATTGGGCTAAGGCCCACACTGTACTG
42403618 GTACTGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (27 bp):
ATTGGGCTAAGGCCCACACTGTACTGT
Found at i:42407274 original size:25 final size:25
Alignment explanation
Indices: 42407246--42407294 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
42407236 TAAGCTTTCC
*
42407246 GATTTACAGCTCGTGA-GAGCATACT
1 GATTCACAGCTCGT-ATGAGCATACT
*
42407271 GATTCATAGCTCGTATGAGCATAC
1 GATTCACAGCTCGTATGAGCATAC
42407295 ATAAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (25 bp):
GATTCACAGCTCGTATGAGCATACT
Found at i:42422414 original size:11 final size:11
Alignment explanation
Indices: 42422400--42422447 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
42422390 ATATACAATT
*
42422400 AATAACAACAA
1 AATAATAACAA
*
42422411 AATATTAACAA
1 AATAATAACAA
* *
42422422 TATAATAACGA
1 AATAATAACAA
*
42422433 AATGATAACAA
1 AATAATAACAA
42422444 AATA
1 AATA
42422448 GCAACGAAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.21
Consensus pattern (11 bp):
AATAATAACAA
Found at i:42422422 original size:31 final size:32
Alignment explanation
Indices: 42422363--42422425 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
42422353 ATAGTAGCAA
*
42422363 AATTAATAACGAAACAAAAGTTATACAATATAC
1 AATTAATAAC-AAACAAAAATTATACAATATAC
42422396 AATTAATAAC-AACAAAATATTA-ACAATATA
1 AATTAATAACAAACAAAA-ATTATACAATATA
42422426 ATAACGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 15 0.54
32 3 0.11
33 10 0.36
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.25
Consensus pattern (32 bp):
AATTAATAACAAACAAAAATTATACAATATAC
Found at i:42422435 original size:22 final size:22
Alignment explanation
Indices: 42422400--42422460 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
42422390 ATATACAATT
*
42422400 AATAACAACAAAATATTAACAA
1 AATAACAACGAAATATTAACAA
* *
42422422 TATAATAACGAAATGA-TAACAA
1 AATAACAACGAAAT-ATTAACAA
*
42422444 AATAGCAACGAAATATT
1 AATAACAACGAAATATT
42422461 TGACTTGGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.61, C:0.11, G:0.07, T:0.21
Consensus pattern (22 bp):
AATAACAACGAAATATTAACAA
Found at i:42422913 original size:25 final size:25
Alignment explanation
Indices: 42422868--42422918 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
42422858 GGTTAATTAG
* *
42422868 AGTTTAAGTGGGAAACTAAAAACCA
1 AGTTTAACTGGGAAACGAAAAACCA
*
42422893 AGTTTAACTGGGAGAA-GAAAAGCCA
1 AGTTTAACTGGGA-AACGAAAAACCA
42422918 A
1 A
42422919 AATAAACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (25 bp):
AGTTTAACTGGGAAACGAAAAACCA
Found at i:42423226 original size:25 final size:23
Alignment explanation
Indices: 42423182--42423232 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
42423172 TAAAAGCTGA
* *
42423182 AAATAAATTAATAAAAATTAGTT
1 AAATAAATTAAGAAAAATTAATT
42423205 AAATAAATCTGAAGAAAAATTAATT
1 AAATAAAT-T-AAGAAAAATTAATT
42423230 AAA
1 AAA
42423233 CTAAGCTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 8 0.33
24 1 0.04
25 15 0.62
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (23 bp):
AAATAAATTAAGAAAAATTAATT
Found at i:42427181 original size:23 final size:23
Alignment explanation
Indices: 42427155--42427662 Score: 201
Period size: 22 Copynumber: 21.4 Consensus size: 23
42427145 CAACTCTGTT
* *
42427155 TTGGACAGCAATTATTCAACAAA
1 TTGGACAGCAATTATACATCAAA
*
42427178 TTGGACAGCAATAATATGC-TCAAA
1 TTGGACAGCAAT--TATACATCAAA
*
42427202 ATGGACAGC-ATTATACATCAAA
1 TTGGACAGCAATTATACATCAAA
* * *
42427224 TTAGACAGCTTAAATATAC-CCAAAA
1 TTGGACAGC--AATTATACATC-AAA
* *
42427249 TTGGACAGCAGCTTAAATATACTCACAA
1 TTGGACAGCA-ATT--ATACA-TCA-AA
42427277 TTGGACAGC-ATTATACATCAAA
1 TTGGACAGCAATTATACATCAAA
* *
42427299 TTAGACAGCTTAAATATAC-TCACAA
1 TTGGACAGC--AATTATACATCA-AA
* *
42427324 TTGGACAGC-ATTATATATTAAA
1 TTGGACAGCAATTATACATCAAA
* *
42427346 ATGGACAGC-ATCAATACACTCAAAA
1 TTGGACAGCAAT-TATACA-TC-AAA
* *
42427371 TTGGACAAC-ATTATACATTAAA
1 TTGGACAGCAATTATACATCAAA
* *
42427393 ATGGACAGC-ATCAGTACACTCAAAA
1 TTGGACAGCAATTA-TACA-TC-AAA
* * *
42427418 TTGGACAAC-ATTACACATTAAA
1 TTGGACAGCAATTATACATCAAA
* *
42427440 ATGGA-A-CAATAATATGC-TCAAA
1 TTGGACAGCAAT--TATACATCAAA
*
42427462 ATGGACAGC-ATTATACATCAAA
1 TTGGACAGCAATTATACATCAAA
* * *
42427484 TTAGACAGCTTAAATATAC-CCAAAA
1 TTGGACAGC--AATTATACATC-AAA
* *
42427509 TTGGACAGCAGCTTAAATATACTCAAAA
1 TTGGACAGCA-ATT--ATACA-TC-AAA
* *
42427537 TTGGACAGC-ATTACACATTAAA
1 TTGGACAGCAATTATACATCAAA
* *
42427559 ATGGACAGC-ATCAATACACTCAAAA
1 TTGGACAGCAAT-TATACA-TC-AAA
* *
42427584 TTGAACAGC-ATTATACATTAAA
1 TTGGACAGCAATTATACATCAAA
* *
42427606 ATGGACAGC-ATCAATACACTCAAAA
1 TTGGACAGCAAT-TATACA-TC-AAA
*
42427631 TTGGACAGC-ATTATACATTAAA
1 TTGGACAGCAATTATACATCAAA
*
42427653 ATGGACAGCA
1 TTGGACAGCA
42427663 TCAATACACT
Statistics
Matches: 367, Mismatches: 72, Indels: 92
0.69 0.14 0.17
Matches are distributed among these distances:
20 1 0.00
21 11 0.03
22 116 0.32
23 49 0.13
24 49 0.13
25 104 0.28
26 10 0.03
27 1 0.00
28 26 0.07
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (23 bp):
TTGGACAGCAATTATACATCAAA
Found at i:42427254 original size:47 final size:47
Alignment explanation
Indices: 42427155--42427258 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 47
42427145 CAACTCTGTT
* * * *
42427155 TTGGACAGCAATTATTCAACAAATTGGACAGCAATAATATGCTCAAAA
1 TTGGACAGC-ATTATACAACAAATTAGACAGCAATAATATACCCAAAA
* *
42427203 -TGGACAGCATTATACATCAAATTAGACAGC-TTAAATATACCCAAAA
1 TTGGACAGCATTATACAACAAATTAGACAGCAAT-AATATACCCAAAA
42427249 TTGGACAGCA
1 TTGGACAGCA
42427259 GCTTAAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
45 1 0.02
46 30 0.62
47 17 0.35
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.24
Consensus pattern (47 bp):
TTGGACAGCATTATACAACAAATTAGACAGCAATAATATACCCAAAA
Found at i:42427267 original size:28 final size:28
Alignment explanation
Indices: 42427229--42427286 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
42427219 TCAAATTAGA
42427229 CAGCTTAAATATACCCAAAATTGGACAG
1 CAGCTTAAATATACCCAAAATTGGACAG
* *
42427257 CAGCTTAAATATACTCACAATTGGACAG
1 CAGCTTAAATATACCCAAAATTGGACAG
42427285 CA
1 CA
42427287 TTATACATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (28 bp):
CAGCTTAAATATACCCAAAATTGGACAG
Found at i:42427290 original size:75 final size:71
Alignment explanation
Indices: 42427175--42427356 Score: 251
Period size: 75 Copynumber: 2.5 Consensus size: 71
42427165 ATTATTCAAC
*
42427175 AAATTGGACAGCAATAATATGCTCAAAATGGACAGCATTATACATCAAATTAGACAGCTTAAATA
1 AAATTGGACAGCAATAATATACTCAAAATGGACAGCATTATACATCAAATTAGACAGCTTAAATA
42427240 TACCCA
66 TACCCA
* *
42427246 AAATTGGACAGCAGCTTAAATATACTCACAATTGGACAGCATTATACATCAAATTAGACAGCTTA
1 AAATTGGACAGCA--AT-AATATACTCA-AAATGGACAGCATTATACATCAAATTAGACAGCTTA
*
42427311 AATATACTCA
62 AATATACCCA
* * *
42427321 CAATTGGACAGC-ATTATATA-TTAAAATGGACAGCAT
1 AAATTGGACAGCAATAATATACTCAAAATGGACAGCAT
42427357 CAATACACTC
Statistics
Matches: 98, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
69 12 0.12
70 2 0.02
71 18 0.18
72 1 0.01
73 1 0.01
74 9 0.09
75 55 0.56
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (71 bp):
AAATTGGACAGCAATAATATACTCAAAATGGACAGCATTATACATCAAATTAGACAGCTTAAATA
TACCCA
Found at i:42427319 original size:47 final size:47
Alignment explanation
Indices: 42427257--42427518 Score: 289
Period size: 47 Copynumber: 5.6 Consensus size: 47
42427247 AATTGGACAG
* * * *
42427257 CAGCTTAAATATACTCACAATTGGACAGCATTATACATCAAATTAGA
1 CAGCTTAAATATACTCAAAATTGGACAGCATTATACATTAAAATGGA
* *
42427304 CAGCTTAAATATACTCACAATTGGACAGCATTATATATTAAAATGGA
1 CAGCTTAAATATACTCAAAATTGGACAGCATTATACATTAAAATGGA
* * * *
42427351 CAGCATCAATACACTCAAAATTGGACAACATTATACATTAAAATGGA
1 CAGCTTAAATATACTCAAAATTGGACAGCATTATACATTAAAATGGA
* * * * * *
42427398 CAGCATCAGTACACTCAAAATTGGACAACATTACACATTAAAATGGA
1 CAGCTTAAATATACTCAAAATTGGACAGCATTATACATTAAAATGGA
* * * * *
42427445 -A-C-AATAATATGCTCAAAA-TGGACAGCATTATACATCAAATTAGA
1 CAGCTTA-AATATACTCAAAATTGGACAGCATTATACATTAAAATGGA
*
42427489 CAGCTTAAATATACCCAAAATTGGACAGCA
1 CAGCTTAAATATACTCAAAATTGGACAGCA
42427519 GCTTAAATAT
Statistics
Matches: 185, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
44 21 0.11
45 12 0.06
46 13 0.07
47 139 0.75
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.25
Consensus pattern (47 bp):
CAGCTTAAATATACTCAAAATTGGACAGCATTATACATTAAAATGGA
Found at i:42427372 original size:122 final size:122
Alignment explanation
Indices: 42427155--42427377 Score: 288
Period size: 122 Copynumber: 1.8 Consensus size: 122
42427145 CAACTCTGTT
* * *
42427155 TTGGACAGCAATTATTCAACAAATTGGACAGCAATAATATGCTCAAAATGGACAGCATTATACAT
1 TTGGACAGCAATTATACAACAAATTAGACAGCAATAATATACTCAAAATGGACAGCATTATACAT
* * *
42427220 CAAATTAGACAGCTTAAATATACCCAAAATTGGACAGCAGCTTAAATATACTCACAA
66 CAAAATAGACAGCATAAATACACCCAAAATTGGACAGCAGCTTAAATATACTCACAA
* * * *
42427277 TTGGACAGC-ATTATACATCAAATTAGACAGC-TTAAATATACTCACAATTGGACAGCATTATAT
1 TTGGACAGCAATTATACAACAAATTAGACAGCAAT-AATATACTCA-AAATGGACAGCATTATAC
* * * *
42427340 ATTAAAATGGACAGCATCAATACACTCAAAATTGGACA
64 ATCAAAATAGACAGCATAAATACACCCAAAATTGGACA
42427378 ACATTATACA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
120 1 0.01
121 28 0.33
122 56 0.66
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (122 bp):
TTGGACAGCAATTATACAACAAATTAGACAGCAATAATATACTCAAAATGGACAGCATTATACAT
CAAAATAGACAGCATAAATACACCCAAAATTGGACAGCAGCTTAAATATACTCACAA
Found at i:42427384 original size:94 final size:92
Alignment explanation
Indices: 42427264--42427518 Score: 325
Period size: 94 Copynumber: 2.8 Consensus size: 92
42427254 CAGCAGCTTA
* *
42427264 AATATACTCACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCACAATTGGA
1 AATATACTCAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAATTGGA
* *
42427329 CAGCATTATATATTAAAATGG-ACAGCAT
66 CAGCATTACACATTAAAATGGAACA--AT
* * * * * * * * *
42427357 CAATACACTCAAAATTGGACAACATTATACATTAAAATGGACAGCATCAGTACACTCAAAATTGG
1 -AATATACTCAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAATTGG
*
42427422 ACAACATTACACATTAAAATGGAACAAT
65 ACAGCATTACACATTAAAATGGAACAAT
* *
42427450 AATATGCTCAAAA-TGGACAGCATTATACATCAAATTAGACAGCTTAAATATACCCAAAATTGGA
1 AATATACTCAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAATTGGA
42427514 CAGCA
66 CAGCA
42427519 GCTTAAATAT
Statistics
Matches: 134, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
91 46 0.34
92 11 0.08
93 2 0.01
94 72 0.54
95 3 0.02
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (92 bp):
AATATACTCAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAATTGGA
CAGCATTACACATTAAAATGGAACAAT
Found at i:42427527 original size:28 final size:28
Alignment explanation
Indices: 42427489--42427546 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
42427479 TCAAATTAGA
42427489 CAGCTTAAATATACCCAAAATTGGACAG
1 CAGCTTAAATATACCCAAAATTGGACAG
*
42427517 CAGCTTAAATATACTCAAAATTGGACAG
1 CAGCTTAAATATACCCAAAATTGGACAG
42427545 CA
1 CA
42427547 TTACACATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (28 bp):
CAGCTTAAATATACCCAAAATTGGACAG
Found at i:42427559 original size:166 final size:167
Alignment explanation
Indices: 42427343--42427683 Score: 460
Period size: 166 Copynumber: 2.1 Consensus size: 167
42427333 ATTATATATT
* *
42427343 AAAATGGACAGCA---TCAATACACTCAAAATTGGACAACATTATACATTAAAATGGACAGCATC
1 AAAATGGACAGCAGCTTAAATACACTCAAAATTGGACAACATTACACATTAAAATGGACAGCATC
* * **
42427405 AGTACACTCAAAATTGGACAACATTACACATTAAAATGGA-ACAAT-AATATGCTCAAAA-TGGA
66 AATACACTCAAAATTGAACAACATTACACATTAAAATGGACAC-ATCAATACACTCAAAATTGGA
* * *
42427467 CAGCATTATACATCAAATTAGACAGCTTAAATATACCC
130 CAGCATTATACATCAAAATAGACAGCATAAATACACCC
* *
42427505 AAAATTGGACAGCAGCTTAAATATACTCAAAATTGGACAGCATTACACATTAAAATGGACAGCAT
1 AAAA-TGGACAGCAGCTTAAATACACTCAAAATTGGACAACATTACACATTAAAATGGACAGCAT
* *
42427570 CAATACACTCAAAATTGAACAGCATTATACATTAAAATGGACAGCATCAATACACTCAAAATTGG
65 CAATACACTCAAAATTGAACAACATTACACATTAAAATGGACA-CATCAATACACTCAAAATTGG
* * * *
42427635 ACAGCATTATACATTAAAATGGACAGCATCAATACACTC
129 ACAGCATTATACATCAAAATAGACAGCATAAATACACCC
42427674 AAAATGGACA
1 AAAATGGACA
42427684 TCAAATTTGG
Statistics
Matches: 154, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
162 4 0.03
163 9 0.06
166 81 0.53
167 3 0.02
168 18 0.12
169 39 0.25
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (167 bp):
AAAATGGACAGCAGCTTAAATACACTCAAAATTGGACAACATTACACATTAAAATGGACAGCATC
AATACACTCAAAATTGAACAACATTACACATTAAAATGGACACATCAATACACTCAAAATTGGAC
AGCATTATACATCAAAATAGACAGCATAAATACACCC
Found at i:42427583 original size:75 final size:74
Alignment explanation
Indices: 42427199--42427586 Score: 243
Period size: 75 Copynumber: 5.4 Consensus size: 74
42427189 TAATATGCTC
* * *
42427199 AAAATGGACAGCAT-TATACA-TC-AAATT--AGACAGCTTAAATATACCCAAAATTGGACAGCA
1 AAAATGGACAGCATCAATACACTCAAAATTGGACACAGCTTAAATATACTCAAAATTGGACAGCA
* *
42427259 GCTTAAATATACT
66 --TTACACAT--T
* * * *
42427272 CACAATTGGACAGCAT-TATACA-TC-AAATT--AGACAGCTTAAATATACTCACAATTGGACAG
1 -A-AAATGGACAGCATCAATACACTCAAAATTGGACACAGCTTAAATATACTCAAAATTGGACAG
* *
42427332 CATTATATATT
64 CATTACACATT
* *
42427343 AAAATGGACAGCATCAATACACTCAAAATTGGACA-A-C---ATTATACATTAAAA-TGGACAGC
1 AAAATGGACAGCATCAATACACTCAAAATTGGACACAGCTTAAATATAC-TCAAAATTGGACAGC
*
42427402 ATCAGTACAC-TC
65 AT---TACACATT
* * * *
42427414 AAAATTGGACA--A-CATTACACATTAAAA-TGGA-ACA--AT-AATATGCTCAAAA-TGGACAG
1 AAAA-TGGACAGCATCAATACAC-TCAAAATTGGACACAGCTTAAATATACTCAAAATTGGACAG
* *
42427470 CATTATACATC
64 CATTACACATT
* * * * * *
42427481 AAATTAGACAGCTTAAATATACCCAAAATTGGACAGCAGCTTAAATATACTCAAAATTGGACAGC
1 AAAATGGACAGCATCAATACACTCAAAATTGGACA-CAGCTTAAATATACTCAAAATTGGACAGC
42427546 ATTACACATT
65 ATTACACATT
42427556 AAAATGGACAGCATCAATACACTCAAAATTG
1 AAAATGGACAGCATCAATACACTCAAAATTG
42427587 AACAGCATTA
Statistics
Matches: 251, Mismatches: 37, Indels: 51
0.74 0.11 0.15
Matches are distributed among these distances:
66 9 0.04
67 5 0.02
68 5 0.02
69 64 0.25
70 22 0.09
71 10 0.04
72 15 0.06
73 9 0.04
74 15 0.06
75 97 0.39
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (74 bp):
AAAATGGACAGCATCAATACACTCAAAATTGGACACAGCTTAAATATACTCAAAATTGGACAGCA
TTACACATT
Found at i:42427584 original size:47 final size:47
Alignment explanation
Indices: 42427524--42427683 Score: 286
Period size: 47 Copynumber: 3.4 Consensus size: 47
42427514 CAGCAGCTTA
* *
42427524 AATATACTCAAAATTGGACAGCATTACACATTAAAATGGACAGCATC
1 AATACACTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATC
*
42427571 AATACACTCAAAATTGAACAGCATTATACATTAAAATGGACAGCATC
1 AATACACTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATC
42427618 AATACACTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATC
1 AATACACTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATC
42427665 AATACACTCAAAA-TGGACA
1 AATACACTCAAAATTGGACA
42427684 TCAAATTTGG
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
46 6 0.06
47 103 0.94
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (47 bp):
AATACACTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATC
Found at i:42427639 original size:122 final size:119
Alignment explanation
Indices: 42427410--42427640 Score: 320
Period size: 122 Copynumber: 1.9 Consensus size: 119
42427400 GCATCAGTAC
** *
42427410 ACTCAAAATTGGACAACATTACACATTAAAATGGAACAATAATATGCTCAAAATGGACAGCATTA
1 ACTCAAAATTGGACAACATTACACATTAAAATGGAACAATAATACACTCAAAATGAACAGCATTA
* * *
42427475 TACATCAAATTAGACAGCTTAAATATACCCAAAATTGGACAGCAGCTTAAATAT
66 TACATCAAAATAGACAGCATAAATACACCCAAAATTGGACAGCAGCTTAAATAT
*
42427529 ACTCAAAATTGGACAGCATTACACATTAAAATGG-ACAGCATCAATACACTCAAAATTGAACAGC
1 ACTCAAAATTGGACAACATTACACATTAAAATGGAACA--AT-AATACACTCAAAA-TGAACAGC
* * * *
42427593 ATTATACATTAAAATGGACAGCATCAATACACTCAAAATTGGACAGCA
62 ATTATACATCAAAATAGACAGCATAAATACACCCAAAATTGGACAGCA
42427641 TTATACATTA
Statistics
Matches: 97, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
118 3 0.03
119 33 0.34
120 2 0.02
121 11 0.11
122 48 0.49
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (119 bp):
ACTCAAAATTGGACAACATTACACATTAAAATGGAACAATAATACACTCAAAATGAACAGCATTA
TACATCAAAATAGACAGCATAAATACACCCAAAATTGGACAGCAGCTTAAATAT
Found at i:42427647 original size:260 final size:259
Alignment explanation
Indices: 42427186--42427683 Score: 870
Period size: 260 Copynumber: 1.9 Consensus size: 259
42427176 AATTGGACAG
42427186 CAATAATATGCTCAAAATGGACAGCATTATACATCAAATTAGACAGCTTAAATATACCCAAAATT
1 CAATAATATGCTCAAAATGGACAGCATTATACATCAAATTAGACAGCTTAAATATACCCAAAATT
* * * * *
42427251 GGACAGCAGCTTAAATATACTCACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATAT
66 GGACAGCAGCTTAAATATACTCAAAATTGGACAGCATTACACATCAAAATAGACAGCATAAATAC
* * *
42427316 ACTCACAATTGGACAGCATTATATATTAAAATGGACAGCATCAATACACTCAAAATTGGACAACA
131 ACTCAAAATTGAACAGCATTATACATTAAAATGGACAGCATCAATACACTCAAAATTGGACAACA
*
42427381 TTATACATTAAAATGGACAGCATCAGTACACTCAAAATTGGACAACATTACACATTAAAATGGAA
196 TTATACATTAAAATGGACAGCATCAATACACTCAAAA-TGGACAACATTACACATTAAAATGGAA
42427446 CAATAATATGCTCAAAATGGACAGCATTATACATCAAATTAGACAGCTTAAATATACCCAAAATT
1 CAATAATATGCTCAAAATGGACAGCATTATACATCAAATTAGACAGCTTAAATATACCCAAAATT
* * *
42427511 GGACAGCAGCTTAAATATACTCAAAATTGGACAGCATTACACATTAAAATGGACAGCATCAATAC
66 GGACAGCAGCTTAAATATACTCAAAATTGGACAGCATTACACATCAAAATAGACAGCATAAATAC
*
42427576 ACTCAAAATTGAACAGCATTATACATTAAAATGGACAGCATCAATACACTCAAAATTGGACAGCA
131 ACTCAAAATTGAACAGCATTATACATTAAAATGGACAGCATCAATACACTCAAAATTGGACAACA
42427641 TTATACATTAAAATGGACAGCATCAATACACTCAAAATGGACA
196 TTATACATTAAAATGGACAGCATCAATACACTCAAAATGGACA
42427684 TCAAATTTGG
Statistics
Matches: 225, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
259 6 0.03
260 219 0.97
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (259 bp):
CAATAATATGCTCAAAATGGACAGCATTATACATCAAATTAGACAGCTTAAATATACCCAAAATT
GGACAGCAGCTTAAATATACTCAAAATTGGACAGCATTACACATCAAAATAGACAGCATAAATAC
ACTCAAAATTGAACAGCATTATACATTAAAATGGACAGCATCAATACACTCAAAATTGGACAACA
TTATACATTAAAATGGACAGCATCAATACACTCAAAATGGACAACATTACACATTAAAATGGAA
Found at i:42428702 original size:28 final size:27
Alignment explanation
Indices: 42428670--42428768 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
42428660 TTAATAAGTA
*
42428670 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
* *
42428698 CGCACACTTAGTGCTT-TACCCTTATACT
1 CGCACACTTAGTGCTTATA--ATTAAACT
42428726 CGCACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
42428754 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42428769 AATCTCATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 55 0.89
29 3 0.05
30 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:42436933 original size:22 final size:20
Alignment explanation
Indices: 42436897--42436955 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
42436887 TGCTAGACCT
42436897 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
42436919 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
42436940 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
42436956 TTTTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:42436957 original size:11 final size:11
Alignment explanation
Indices: 42436937--42436996 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
42436927 TAAAAATTAA
42436937 AAAAAGTATTTT
1 AAAAA-TATTTT
42436949 AAAAATATTTT
1 AAAAATATTTT
***
42436960 AAAAATA-AAA
1 AAAAATATTTT
42436970 AAAAAGTATTTT
1 AAAAA-TATTTT
42436982 AAAAATATTTT
1 AAAAATATTTT
42436993 AAAA
1 AAAA
42436997 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 5 0.12
11 25 0.62
12 10 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:42436977 original size:33 final size:33
Alignment explanation
Indices: 42436922--42437005 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
42436912 ACCAAAAATT
*
42436922 TATTTTAAAAAT-TAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATAAAAAAAAAGTATTTTAAAAA
42436954 TATTTTAAAAATAAAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATAAAAAAAAAGTATTTTAAAAA
*
42436987 TATTTTAAAATTAAAAAAA
1 TATTTTAAAAATAAAAAAA
42437006 TTTAAAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 12 0.24
33 37 0.76
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (33 bp):
TATTTTAAAAATAAAAAAAAAGTATTTTAAAAA
Found at i:42437000 original size:17 final size:17
Alignment explanation
Indices: 42436980--42437024 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
42436970 AAAAAGTATT
42436980 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
42436997 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
42437013 ATAAATATATTT
1 TTAAAAATATTT
42437025 ATTATATCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:42438732 original size:107 final size:107
Alignment explanation
Indices: 42438545--42438862 Score: 483
Period size: 107 Copynumber: 3.0 Consensus size: 107
42438535 CCATACTTTG
* *
42438545 AAGTTTTAAAAGGATATTTGGTTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGTTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
* * *
42438610 GTTTCCTCAATTTTCCAAACACGAAGTATTGCCTTATTTTAA
66 GTTTCCTCGATTTTCCAAACGCGAAATATTGCCTTATTTTAA
* * * * *
42438652 GAGTTTAAAAAGGATATTTGGTTATTTGGTCAAACGAGAAGTCGAAAACCAACACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGTTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
*
42438717 GTTTCCTCGATTTTCCAAACGCGAAATATTGTCTTATTTTAA
66 GTTTCCTCGATTTTCCAAACGCGAAATATTGCCTTATTTTAA
* *
42438759 AAGTTTAAAAAAGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGTTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
* * * *
42438824 ATTTTCTTGATTTTCCAAACGCAAAATATTGCCTTATTT
66 GTTTCCTCGATTTTCCAAACGCGAAATATTGCCTTATTT
42438863 AGAAAAACTT
Statistics
Matches: 188, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 188 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (107 bp):
AAGTTTAAAAAGGATATTTGGTTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
GTTTCCTCGATTTTCCAAACGCGAAATATTGCCTTATTTTAA
Found at i:42439654 original size:13 final size:14
Alignment explanation
Indices: 42439636--42439666 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
42439626 TATATGAATT
42439636 TAAACCAAAT-AAA
1 TAAACCAAATAAAA
42439649 TAAACCAAATAAAA
1 TAAACCAAATAAAA
42439663 TAAA
1 TAAA
42439667 AACTTGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (14 bp):
TAAACCAAATAAAA
Found at i:42445624 original size:20 final size:20
Alignment explanation
Indices: 42445599--42445639 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
42445589 CTTCGGTAGT
*
42445599 ACTTTGGACGACAATAGAAA
1 ACTTTGGACAACAATAGAAA
42445619 ACTTTGGACAACAATAGAAA
1 ACTTTGGACAACAATAGAAA
42445639 A
1 A
42445640 TTTATTCGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (20 bp):
ACTTTGGACAACAATAGAAA
Found at i:42446300 original size:32 final size:32
Alignment explanation
Indices: 42446264--42446430 Score: 76
Period size: 32 Copynumber: 5.2 Consensus size: 32
42446254 TGATCACGAG
42446264 TCATTTGTCTAGGAAAAATGATTTAATTACTA
1 TCATTTGTCTAGGAAAAATGATTTAATTACTA
* * * ** * * *
42446296 TCA-TT-AC-ACGATAGAAAGTAACGTGATCACGA
1 TCATTTGTCTAGGA-A-AAA-TGATTTAATTACTA
42446328 GTCATTTGTCTAGGAAAAATGATTTAATTACTA
1 -TCATTTGTCTAGGAAAAATGATTTAATTACTA
* * * ** * * *
42446361 TCA-TT-AC-ACGATAGAAAGTAACGTGATCACGA
1 TCATTTGTCTAGGA-A-AAA-TGATTTAATTACTA
42446393 GTCATTTGTCTAGGAAAAATGATTTAATTACTA
1 -TCATTTGTCTAGGAAAAATGATTTAATTACTA
42446426 TCATT
1 TCATT
42446431 ACACGATAGA
Statistics
Matches: 89, Mismatches: 32, Indels: 28
0.60 0.21 0.19
Matches are distributed among these distances:
29 6 0.07
30 4 0.04
31 10 0.11
32 27 0.30
33 22 0.25
34 10 0.11
35 4 0.04
36 6 0.07
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (32 bp):
TCATTTGTCTAGGAAAAATGATTTAATTACTA
Found at i:42446336 original size:65 final size:65
Alignment explanation
Indices: 42446240--42446490 Score: 477
Period size: 65 Copynumber: 3.9 Consensus size: 65
42446230 GACATTAAAT
42446240 GATAGAAAGTAACGTGATCACGAGTCATTTGTCTAGGAAAAATGATTTAATTACTATCATTACAC
1 GATAGAAAGTAACGTGATCACGAGTCATTTGTCTAGGAAAAATGATTTAATTACTATCATTACAC
42446305 GATAGAAAGTAACGTGATCACGAGTCATTTGTCTAGGAAAAATGATTTAATTACTATCATTACAC
1 GATAGAAAGTAACGTGATCACGAGTCATTTGTCTAGGAAAAATGATTTAATTACTATCATTACAC
42446370 GATAGAAAGTAACGTGATCACGAGTCATTTGTCTAGGAAAAATGATTTAATTACTATCATTACAC
1 GATAGAAAGTAACGTGATCACGAGTCATTTGTCTAGGAAAAATGATTTAATTACTATCATTACAC
* *
42446435 GATAGAAAGTAACGTGATCACGAGTCATTTATCTAGG-AAAATGATGTAATTACTAT
1 GATAGAAAGTAACGTGATCACGAGTCATTTGTCTAGGAAAAATGATTTAATTACTAT
42446491 TTTTTAGTAA
Statistics
Matches: 184, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
64 18 0.10
65 166 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (65 bp):
GATAGAAAGTAACGTGATCACGAGTCATTTGTCTAGGAAAAATGATTTAATTACTATCATTACAC
Found at i:42448759 original size:14 final size:14
Alignment explanation
Indices: 42448742--42448826 Score: 55
Period size: 14 Copynumber: 6.1 Consensus size: 14
42448732 AAATACATAA
42448742 TCATACATGCAGAT
1 TCATACATGCAGAT
* *
42448756 TCATAAATG-TGAAT
1 TCATACATGCAG-AT
*
42448770 TCATACATGCGGAT
1 TCATACATGCAGAT
* **
42448784 TCATAGATATAGAT
1 TCATACATGCAGAT
* * **
42448798 CCATAAATGTGGAT
1 TCATACATGCAGAT
*
42448812 TCATACATACAGAT
1 TCATACATGCAGAT
42448826 T
1 T
42448827 GATAGACACA
Statistics
Matches: 52, Mismatches: 17, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
13 1 0.02
14 50 0.96
15 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (14 bp):
TCATACATGCAGAT
Found at i:42448802 original size:28 final size:28
Alignment explanation
Indices: 42448726--42448825 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 28
42448716 GTTCGTTTAA
*
42448726 ATTCATAAATACATA-AT-CATACATGCAG
1 ATTCATAAAT--ATAGATCCATACATGCGG
* *
42448754 ATTCATAAATGT-GAATTCATACATGCGG
1 ATTCATAAATATAG-ATCCATACATGCGG
* * *
42448782 ATTCATAGATATAGATCCATAAATGTGG
1 ATTCATAAATATAGATCCATACATGCGG
* *
42448810 ATTCATACATACAGAT
1 ATTCATAAATATAGAT
42448826 TGATAGACAC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
26 1 0.02
27 2 0.03
28 55 0.93
29 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (28 bp):
ATTCATAAATATAGATCCATACATGCGG
Found at i:42448832 original size:42 final size:42
Alignment explanation
Indices: 42448725--42448832 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 42
42448715 CGTTCGTTTA
* * * * ** *
42448725 AATTCATAAATACATAATCATACATGCAGATTCATAAATGTG
1 AATTCATACATACAGATTCATAGATATAGATCCATAAATGTG
* *
42448767 AATTCATACATGCGGATTCATAGATATAGATCCATAAATGTG
1 AATTCATACATACAGATTCATAGATATAGATCCATAAATGTG
* *
42448809 GATTCATACATACAGATTGATAGA
1 AATTCATACATACAGATTCATAGA
42448833 CACAGATTAT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (42 bp):
AATTCATACATACAGATTCATAGATATAGATCCATAAATGTG
Found at i:42449528 original size:54 final size:54
Alignment explanation
Indices: 42449407--42449534 Score: 139
Period size: 54 Copynumber: 2.4 Consensus size: 54
42449397 AGGTTACATG
* ** ** *
42449407 GCCGTGTCGTAGGCCGTGTGCCAGACCGTGTAACTTTCTAACTTGTGACACACG
1 GCCGTGTCGTAGGCCGTGTGCCAAACCGTGTAACTCACTAACTTGACACACACA
* * * *
42449461 GCCGTGTAGTAGGCCGTGTGCTAAACCGTGTAACTCAGTGACTTGACACACACA
1 GCCGTGTCGTAGGCCGTGTGCCAAACCGTGTAACTCACTAACTTGACACACACA
* * *
42449515 GCCGTATCTTAGGCCATGTG
1 GCCGTGTCGTAGGCCGTGTG
42449535 AAAATTACAT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (54 bp):
GCCGTGTCGTAGGCCGTGTGCCAAACCGTGTAACTCACTAACTTGACACACACA
Found at i:42450923 original size:54 final size:54
Alignment explanation
Indices: 42450865--42450985 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 54
42450855 TCCACACCCG
* *
42450865 TGTAACTCACTGAGATGCCTCACACGCTAGTGTATTAGGCCGTGTGCTAGGCAA
1 TGTAACTCACTGAGATGCCACACACGCTAGTGTACTAGGCCGTGTGCTAGGCAA
* * * * * * ***
42450919 TGTAACTCTCTGAGTTGCCACACATGTTCGTGTGCTAGGCCGTGTGCTAGGTTG
1 TGTAACTCACTGAGATGCCACACACGCTAGTGTACTAGGCCGTGTGCTAGGCAA
42450973 TGTAACTCACTGA
1 TGTAACTCACTGA
42450986 CTTGAAACAC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (54 bp):
TGTAACTCACTGAGATGCCACACACGCTAGTGTACTAGGCCGTGTGCTAGGCAA
Found at i:42456454 original size:49 final size:49
Alignment explanation
Indices: 42456395--42456530 Score: 146
Period size: 49 Copynumber: 2.8 Consensus size: 49
42456385 ACCAGTGGCC
* * *
42456395 GCCAACCTGGTTAACAACTAACATGTCCTACTAGTGGCCCAACATACAT
1 GCCAATCTGGTTAGCAACTAACATGTCCTACTAGTGGCCCAACACACAT
* * * * **
42456444 GCCAATCTGGTTAGCAACTAGCATGCCCTACTAGTGGTCCATCACATTT
1 GCCAATCTGGTTAGCAACTAACATGTCCTACTAGTGGCCCAACACACAT
* * * * *
42456493 GTCATTCTAGTTTGCAACTAACATGTCCTACCAGTGGC
1 GCCAATCTGGTTAGCAACTAACATGTCCTACTAGTGGC
42456531 TATTTATCTC
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (49 bp):
GCCAATCTGGTTAGCAACTAACATGTCCTACTAGTGGCCCAACACACAT
Found at i:42459932 original size:33 final size:33
Alignment explanation
Indices: 42459873--42459955 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
42459863 TACACATATA
* * **
42459873 CATATATATTATAGAAAACATGACCCAAAAACG
1 CATATATATTATATATAACAAAACCCAAAAACG
* *
42459906 CATATATATTATATATAACAAAACCCATATACG
1 CATATATATTATATATAACAAAACCCAAAAACG
42459939 -ATTATATATTATATATA
1 CA-TATATATTATATATA
42459956 TACACATACC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.31
Consensus pattern (33 bp):
CATATATATTATATATAACAAAACCCAAAAACG
Found at i:42460777 original size:140 final size:138
Alignment explanation
Indices: 42460598--42461154 Score: 830
Period size: 138 Copynumber: 4.0 Consensus size: 138
42460588 TAGAAAAATG
* * *
42460598 AATTATATTCTTTCCAAATGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTTTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
42460663 TATAAATATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTTTATGAAACAAATT
66 TATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
42460728 CATATATATT
131 C--ATATATT
* *
42460738 AATTATATTTTTTCCTAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTTTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
42460803 TATAAATGTTTATATTAATAAATTCGGTAAAATATATACGATTAATATTTCGTATGAATCAAATT
66 TATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
42460868 CATATATT
131 CATATATT
* ** *
42460876 AATTATATTATTTCCAAAAGAATATTAATTTTAAT-TCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTTTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * * *
42460940 TATAACTGTTTATATGAATAAATTCTGTAATATATATAGAATTAATATTTTGTATGAATCAAATT
66 TATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
42461005 CATATATT
131 CATATATT
* * * *
42461013 AAATATATTGTTTT-CAAAAGAATATTAATTTCCAAGTCTTTTATATTTTTACTGAAATTAATTA
1 AATTATATT-TTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTA
* *
42461077 ATATCACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
65 ATATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
42461142 TCATATATT
130 TCATATATT
42461151 AATT
1 AATT
42461155 TTATCTATGT
Statistics
Matches: 376, Mismatches: 39, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
137 119 0.32
138 137 0.36
140 120 0.32
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (138 bp):
AATTATATTTTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:42461102 original size:275 final size:277
Alignment explanation
Indices: 42460598--42461154 Score: 863
Period size: 275 Copynumber: 2.0 Consensus size: 277
42460588 TAGAAAAATG
* * * *
42460598 AATTATATTCTTTCCAAATGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTAATGTCTTTTATATTTTGACCAAAATTAATTAA
* *
42460663 TATAAATATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTTTATGAAACAAATT
66 TATAAATATTTATATGAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAAACAAATT
* * *
42460728 CATATATATTAATTATATTTTTTCCTAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGA
131 CA-ATATATTAAATATATTTTTTCCAAAAGAATATTAATTTCCAAGTCTTTTATATTTTGATCGA
* *
42460793 AATTAATTAATATAAATGTTTATATTAATAAATTCGGTAAAATATATACGATTAATATTTCGTAT
195 AATTAATTAATATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTCGTAT
42460858 GAATCAAATTCATATATT
260 GAATCAAATTCATATATT
42460876 AATTATATTATTTCCAAAAGAATATTAATTTTAAT-TCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTAATGTCTTTTATATTTTGACCAAAATTAATTAA
* * * * *
42460940 TATAACTGTTTATATGAATAAATTCTG-TAATATATATAGAATTAATATTTTGTATGAATCAAAT
66 TATAAATATTTATATGAATAAATTC-GATAAAATATATACAATTAATATTTTGTATGAAACAAAT
*
42461004 TC-ATATATTAAATATATTGTTTT-CAAAAGAATATTAATTTCCAAGTCTTTTATATTTTTA-CT
130 TCAATATATTAAATATATT-TTTTCCAAAAGAATATTAATTTCCAAGTCTTTTATATTTTGATC-
* * *
42461066 GAAATTAATTAATATCACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGT
193 GAAATTAATTAATATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTCGT
42461131 ATGAATCAAATTCATATATT
258 ATGAATCAAATTCATATATT
42461151 AATT
1 AATT
42461155 TTATCTATGT
Statistics
Matches: 256, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
274 1 0.00
275 133 0.52
276 4 0.02
277 85 0.33
278 33 0.13
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (277 bp):
AATTATATTATTTCCAAAAGAATATTAATTTTAATGTCTTTTATATTTTGACCAAAATTAATTAA
TATAAATATTTATATGAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAAACAAATT
CAATATATTAAATATATTTTTTCCAAAAGAATATTAATTTCCAAGTCTTTTATATTTTGATCGAA
ATTAATTAATATAAATATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTCGTATG
AATCAAATTCATATATT
Found at i:42463061 original size:45 final size:44
Alignment explanation
Indices: 42463002--42463129 Score: 159
Period size: 45 Copynumber: 2.9 Consensus size: 44
42462992 TGTTTACCAT
* * *
42463002 GATGTCATATCATCTTTCAGCCATGGTCTTACTAATTTATATCAC
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCATTT-TATCAC
* * * *
42463047 GATG-CTATAGCATCTTTTAGCTATGGTCTTACTCATCCTTGTCAT
1 GATGTC-ATAGCATCTTTCAGCTATGGTCTTACTCAT-TTTATCAC
42463092 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCATTT
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCATTT
42463130 CAAGCGTATA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
44 2 0.03
45 67 0.94
46 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (44 bp):
GATGTCATAGCATCTTTCAGCTATGGTCTTACTCATTTTATCAC
Found at i:42465366 original size:20 final size:20
Alignment explanation
Indices: 42465293--42465367 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
42465283 TGTCTTTCTA
*
42465293 TTTAAATCAATT-ATGTTTCTG
1 TTTAAATCGATTCAT-TTT-TG
*
42465314 TTTGAATCGATTCATTTTTG
1 TTTAAATCGATTCATTTTTG
* *
42465334 TTTAAACCAATTC-TTTGTTG
1 TTTAAATCGATTCATTT-TTG
*
42465354 TTTAATTCGATTCA
1 TTTAAATCGATTCA
42465368 AACTCCAACA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.07
20 25 0.58
21 13 0.30
22 2 0.05
ACGTcount: A:0.25, C:0.12, G:0.11, T:0.52
Consensus pattern (20 bp):
TTTAAATCGATTCATTTTTG
Found at i:42471096 original size:44 final size:44
Alignment explanation
Indices: 42471032--42471124 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 44
42471022 TTGACCAGCC
* *
42471032 TCTTTCCCATGTTCTTCTTTGTTTCTTGTAGCACCTAAGCTTTT
1 TCTTTCCCATGTCCTCCTTTGTTTCTTGTAGCACCTAAGCTTTT
*
42471076 TCTTTCCCTTGTCCTCCTTTGTTTCTTGTAGCACCTAAGCTTTT
1 TCTTTCCCATGTCCTCCTTTGTTTCTTGTAGCACCTAAGCTTTT
42471120 TCTTT
1 TCTTT
42471125 TCTTGATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.10, C:0.27, G:0.11, T:0.53
Consensus pattern (44 bp):
TCTTTCCCATGTCCTCCTTTGTTTCTTGTAGCACCTAAGCTTTT
Found at i:42472152 original size:13 final size:13
Alignment explanation
Indices: 42472130--42472159 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42472120 TTTAAACTTT
*
42472130 AAAAAGCAAAAAA
1 AAAAAACAAAAAA
42472143 AAAAAACAAAAAA
1 AAAAAACAAAAAA
42472156 AAAA
1 AAAA
42472160 GAAGAAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAA
Found at i:42473911 original size:43 final size:44
Alignment explanation
Indices: 42473851--42473937 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
42473841 AATCTGATTG
*
42473851 TTGTTTTATCTATTTTC-TGATTGATGCAAATATTGTTGATGTA
1 TTGTTTTATCTATTTTCTTGATTGATGCAAATATTCTTGATGTA
*
42473894 TTGTTTTATTCTA-TTTCTTGATTGATGCAAATTTTCTTGATGTA
1 TTGTTTTA-TCTATTTTCTTGATTGATGCAAATATTCTTGATGTA
42473938 GACTGATCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 12 0.30
44 28 0.70
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.55
Consensus pattern (44 bp):
TTGTTTTATCTATTTTCTTGATTGATGCAAATATTCTTGATGTA
Found at i:42491615 original size:102 final size:101
Alignment explanation
Indices: 42491434--42491618 Score: 255
Period size: 101 Copynumber: 1.8 Consensus size: 101
42491424 AGTTGCTAGG
* * * * * * *
42491434 TCACGTGTGTAGTACTATGTGTAGGCTACTACATGTACTGGAATGATAGGTCGCATGTGCAGTAC
1 TCACGTATATAGTACTATGTGCAGACTACTACATGTACTCGAATGAAAGGTCACATGTGCAGTAC
42491499 CATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 CATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* *
42491535 TCACGTATATAGTACTATGTGCAGACTACTACGTGTA-TCGAATGAAAATGGTCACATGTGTAGT
1 TCACGTATATAGTACTATGTGCAGACTACTACATGTACTCGAATG-AAA-GGTCACATGTGCAGT
*
42491599 ACTATGTGCAGGCTACTATG
64 ACCATGTGCAGGCTACTATG
42491619 TGAATTGGGT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
100 6 0.08
101 34 0.47
102 32 0.44
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (101 bp):
TCACGTATATAGTACTATGTGCAGACTACTACATGTACTCGAATGAAAGGTCACATGTGCAGTAC
CATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:42507679 original size:19 final size:20
Alignment explanation
Indices: 42507639--42507679 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
42507629 TGTAATTATC
*
42507639 CATTATATATATCCCATAAT
1 CATTATATATATCACATAAT
42507659 CATT-TATATAT-ACATATAT
1 CATTATATATATCACATA-AT
42507678 CA
1 CA
42507680 AATGCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 11 0.58
20 4 0.21
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (20 bp):
CATTATATATATCACATAAT
Found at i:42507766 original size:41 final size:41
Alignment explanation
Indices: 42507709--42507817 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
42507699 TTTAACATAT
*
42507709 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTA-A
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTC-AGA
*
42507750 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
42507791 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
42507818 AAGTCCGAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 1 0.02
41 62 0.98
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:42507836 original size:41 final size:40
Alignment explanation
Indices: 42507709--42507854 Score: 154
Period size: 41 Copynumber: 3.6 Consensus size: 40
42507699 TTTAACATAT
* *
42507709 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTAA
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTAT-A
* *
42507750 TCACCGGCACTTAGCCTGCTAGGTTTATAA-CCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTA-AAGCCTGATT-ATA
* *
42507791 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCC-GAATTATT
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAG-CCTG-ATTATA
*
42507832 TCACCGAC-CTTAAGCCTGCTAGG
1 TCACCGGCACTT-AGCCTGCTAGG
42507855 TTTTAAACCT
Statistics
Matches: 89, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
40 5 0.06
41 78 0.88
42 6 0.07
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTATA
Found at i:42507848 original size:82 final size:82
Alignment explanation
Indices: 42507709--42507866 Score: 207
Period size: 82 Copynumber: 1.9 Consensus size: 82
42507699 TTTAACATAT
* * * *
42507709 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCTAATCACCGGCACTTAGCCTGCTAGG-
1 TCACCGGCACTTAGCCTGCTAGACTTAAAGCCTGATTATAATCACCGACACTTAGCCTGCTAGGT
42507773 TTTATAACCTGATTCAGA
66 TTTA-AACCTGATTCAGA
*
42507791 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCC-GAATTAT-TTCACCGAC-CTTAAGCCTGCTA
1 TCACCGGCACTTAGCCTGCTAGACTTAAAG-CCTG-ATTATAATCACCGACACTT-AGCCTGCTA
42507853 GGTTTTAAACCTGA
63 GGTTTTAAACCTGA
42507867 AAATTTCAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
81 3 0.04
82 54 0.81
83 10 0.15
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (82 bp):
TCACCGGCACTTAGCCTGCTAGACTTAAAGCCTGATTATAATCACCGACACTTAGCCTGCTAGGT
TTTAAACCTGATTCAGA
Found at i:42513163 original size:6 final size:6
Alignment explanation
Indices: 42513152--42513180 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42513142 TTGATACAAA
42513152 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
42513181 CTAATATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:42517968 original size:18 final size:19
Alignment explanation
Indices: 42517942--42517984 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
42517932 TGAGCAGGAA
42517942 AGTGAGGAACAGGAA-AGG
1 AGTGAGGAACAGGAAGAGG
* *
42517960 AGTGGGGAAGAGGAAGAGG
1 AGTGAGGAACAGGAAGAGG
*
42517979 AATGAG
1 AGTGAG
42517985 AAGAGGATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.42, C:0.02, G:0.49, T:0.07
Consensus pattern (19 bp):
AGTGAGGAACAGGAAGAGG
Found at i:42520874 original size:26 final size:26
Alignment explanation
Indices: 42520836--42520886 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
42520826 CTTGTTGCGT
*
42520836 CCTCAGAATGACACCAATATGACTTG
1 CCTCAGAACGACACCAATATGACTTG
* * *
42520862 CCTCGGAACGACACCATTGTGACTT
1 CCTCAGAACGACACCAATATGACTT
42520887 TCCTTGAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (26 bp):
CCTCAGAACGACACCAATATGACTTG
Found at i:42523949 original size:16 final size:17
Alignment explanation
Indices: 42523928--42523959 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42523918 AAATATGCAA
42523928 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
42523944 TCACATAACTTCATAT
1 TCACATAACTTCATAT
42523960 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:42524187 original size:43 final size:42
Alignment explanation
Indices: 42524120--42524290 Score: 127
Period size: 43 Copynumber: 4.0 Consensus size: 42
42524110 GACTCGTATA
* * *
42524120 ATGCCGAC-GTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCC-ACTGTCCCAGAAG-GGTCTTACATGAAAACACATATCG
* * * *
42524163 ATGCCACTGTCTCAGATAGGGTCTTACA-CAAATCAAATA-CG
1 ATGCCACTGTCCCAGA-AGGGTCTTACATGAAAACACATATCG
* * * *
42524204 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCG
1 ATGCCACTGTCCCAGA-AGGGTCTTACATGAAAACACATA-TCG
* *
42524247 ATGACAAC-GTCCCAGACGTGGTCTTACATGAAAACACATATCG
1 ATG-CCACTGTCCCAGAAG-GGTCTTACATGAAAACACATATCG
42524290 A
1 A
42524291 AATCCTATGT
Statistics
Matches: 101, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
41 27 0.27
42 15 0.15
43 55 0.54
44 4 0.04
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
ATGCCACTGTCCCAGAAGGGTCTTACATGAAAACACATATCG
Found at i:42529453 original size:34 final size:35
Alignment explanation
Indices: 42529405--42529477 Score: 130
Period size: 34 Copynumber: 2.1 Consensus size: 35
42529395 ACAAGGAGAA
42529405 AAAGAAAAAAATTAGGGCTCATGCTATTATTTTGT
1 AAAGAAAAAAATTAGGGCTCATGCTATTATTTTGT
*
42529440 AAAG-AAAAAATTAGGGTTCATGCTATTATTTTGT
1 AAAGAAAAAAATTAGGGCTCATGCTATTATTTTGT
42529474 AAAG
1 AAAG
42529478 CTTCAATTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 33 0.89
35 4 0.11
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (35 bp):
AAAGAAAAAAATTAGGGCTCATGCTATTATTTTGT
Found at i:42530216 original size:22 final size:22
Alignment explanation
Indices: 42530191--42530267 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
42530181 TAGTGCCTAG
* *
42530191 CAGGATTAGTGTCGGTTTTATT
1 CAGGCTTAGTGTCGGTATTATT
* *
42530213 CAGGCTTAATGCCGGTATTATT
1 CAGGCTTAGTGTCGGTATTATT
* *
42530235 CAGTCTTAGTGTCGGTGTTATT
1 CAGGCTTAGTGTCGGTATTATT
42530257 CAGGCTTAGTG
1 CAGGCTTAGTG
42530268 CCTAGCAGGC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.40
Consensus pattern (22 bp):
CAGGCTTAGTGTCGGTATTATT
Found at i:42530563 original size:43 final size:43
Alignment explanation
Indices: 42530515--42530677 Score: 195
Period size: 43 Copynumber: 3.8 Consensus size: 43
42530505 TTATGTGAAA
* * *
42530515 AAACGCCGCTATAGAGCATGATCTTTAGCGACGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
*
42530558 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
* * * * *
42530601 AAACGCCGATAAAATAACATGATCTTTGGTGGCGC-TTTACCCAC
1 AAACGCCGCT-AAAGAACATGATCTTTAGCGGCGCTTTTA-TCAC
*
42530645 AAACGCCGCTAAAGATCATG-TCTTTTAGCGGCG
1 AAACGCCGCTAAAGAACATGATC-TTTAGCGGCG
42530678 TTTACAAAAA
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.02
43 68 0.67
44 32 0.31
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
Found at i:42532363 original size:41 final size:41
Alignment explanation
Indices: 42532304--42532456 Score: 209
Period size: 41 Copynumber: 3.7 Consensus size: 41
42532294 TAAAATGTTT
* * *
42532304 TTAGCGGTGCTTTTTCAAAAACGCCGCTAAAGCTC-CCAGCA
1 TTAGCGGCGCTTTCTCAAAAACGCCACTAAAGC-CACCAGCA
*
42532345 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCACCAGCA
1 TTAGCGGCGCTTTCTCAAAAACGCCACTAAAGCCACCAGCA
* * *
42532386 TTAGTGACGCTTTCTCAAAAATGCCACTAAAGCCACCAGCA
1 TTAGCGGCGCTTTCTCAAAAACGCCACTAAAGCCACCAGCA
* *
42532427 TTAGCGGTGCTTTTTCAAAAACGCCACTAA
1 TTAGCGGCGCTTTCTCAAAAACGCCACTAA
42532457 TGCTTGGTTC
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 1 0.01
41 99 0.99
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (41 bp):
TTAGCGGCGCTTTCTCAAAAACGCCACTAAAGCCACCAGCA
Found at i:42532480 original size:82 final size:82
Alignment explanation
Indices: 42532303--42532499 Score: 216
Period size: 82 Copynumber: 2.4 Consensus size: 82
42532293 ATAAAATGTT
*
42532303 TTTAGCGGTGCTTTTTCAAAAACGCCGCTAAAGCTCCCAGCATTAGCGGCGCTTTCTCAAAAACG
1 TTTAGCGATGCTTTTTCAAAAACGCCGCTAAAGCTCCCAGCATTAGCGGCGCTTTCTCAAAAACG
*
42532368 CCGCTAAAGCCACCAGC
66 CCACTAAAGCCACCAGC
* * * * * * * *
42532385 ATTAGTGACGCTTTCTCAAAAATGCCACTAAAGC-CACCAGCATTAGCGGTGCTTTTTCAAAAAC
1 TTTAGCGATGCTTTTTCAAAAACGCCGCTAAAGCTC-CCAGCATTAGCGGCGCTTTCTCAAAAAC
* ******
42532449 GCCACTAATGCTTGGTTC
65 GCCACTAAAGCCACCAGC
*
42532467 TTTAGCGTTGCTTTTTCAAAAACGCCGCTAAAG
1 TTTAGCGATGCTTTTTCAAAAACGCCGCTAAAG
42532500 ACCCGAAAGG
Statistics
Matches: 90, Mismatches: 24, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
81 1 0.01
82 89 0.99
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (82 bp):
TTTAGCGATGCTTTTTCAAAAACGCCGCTAAAGCTCCCAGCATTAGCGGCGCTTTCTCAAAAACG
CCACTAAAGCCACCAGC
Found at i:42550065 original size:92 final size:91
Alignment explanation
Indices: 42549908--42550116 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
42549898 TTGATTTTAG
* * *
42549908 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
42549973 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
42550000 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
42550064 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
42550092 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
42550117 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:42550079 original size:24 final size:25
Alignment explanation
Indices: 42550044--42550091 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
42550034 TTATGAAATT
42550044 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
42550068 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
42550092 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:42550281 original size:18 final size:17
Alignment explanation
Indices: 42550253--42550287 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42550243 ATTATTAAGA
*
42550253 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42550270 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42550288 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42550538 original size:45 final size:44
Alignment explanation
Indices: 42550449--42550543 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
42550439 TTACACCTCT
*
42550449 ATTACATTCAACCAAACACAGGATTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
*** *
42550493 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGA-TTACTATTACACCTCTATTCC
42550538 ATTACA
1 ATTACA
42550544 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 20 0.44
45 25 0.56
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
Found at i:42550543 original size:16 final size:16
Alignment explanation
Indices: 42550522--42550559 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
42550512 TTGATTTGCT
*
42550522 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
42550538 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
42550554 AATACA
1 ATTACA
42550560 GCGAACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:42552133 original size:33 final size:32
Alignment explanation
Indices: 42552092--42552158 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 32
42552082 GAAAAGACAG
42552092 AGAAAGAGAACAAA-AAAATTACTTTAAAA-AAAA
1 AGAAAGAGAA-AAACAAAA-TA-TTTAAAATAAAA
42552125 AGAAAGAGAAAAACTAAAATATTTAAAATAAAA
1 AGAAAGAGAAAAAC-AAAATATTTAAAATAAAA
42552158 A
1 A
42552159 TATCTGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
32 10 0.32
33 17 0.55
34 4 0.13
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.16
Consensus pattern (32 bp):
AGAAAGAGAAAAACAAAATATTTAAAATAAAA
Found at i:42553869 original size:6 final size:6
Alignment explanation
Indices: 42553852--42553888 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
42553842 GAGTGATGGT
*
42553852 TTTA-G TTT-TG TTTATG TTTTTG TTTATG TTTATG TTT
1 TTTATG TTTATG TTTATG TTTATG TTTATG TTTATG TTT
42553889 TGGTGTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 7 0.25
6 21 0.75
ACGTcount: A:0.11, C:0.00, G:0.16, T:0.73
Consensus pattern (6 bp):
TTTATG
Found at i:42553881 original size:18 final size:17
Alignment explanation
Indices: 42553850--42553889 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
42553840 AGGAGTGATG
42553850 GTTTTAGTTTTGTTTAT
1 GTTTTAGTTTTGTTTAT
*
42553867 GTTTTTGTTTATGTTTAT
1 GTTTTAGTTT-TGTTTAT
42553885 GTTTT
1 GTTTT
42553890 GGTGTTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.10, C:0.00, G:0.17, T:0.72
Consensus pattern (17 bp):
GTTTTAGTTTTGTTTAT
Found at i:42563241 original size:20 final size:19
Alignment explanation
Indices: 42563196--42563244 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
42563186 TAATATAAGT
42563196 TTAAAAT-ATTAAAAGAAA
1 TTAAAATAATTAAAAGAAA
*
42563214 TAAAAATAATTAATAA-ATAA
1 TTAAAATAATTAA-AAGA-AA
42563234 TTAAAATAATT
1 TTAAAATAATT
42563245 TTTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 6 0.23
19 6 0.23
20 14 0.54
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TTAAAATAATTAAAAGAAA
Found at i:42563292 original size:5 final size:5
Alignment explanation
Indices: 42563282--42563306 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42563272 CATTTTACCT
42563282 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
42563307 TCCATTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:42568195 original size:45 final size:47
Alignment explanation
Indices: 42568144--42568239 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 47
42568134 CATATAGAAC
* * * *
42568144 TATACTTCTTTTATTT-TATT-TTAGAATAAGGTTTTTCAATCTTAT
1 TATACTTCATCTATTTATATTATTAGAATAAGGTGTTTCAACCTTAT
42568189 TATACTTCATCTATTTGATATTGATTAGAATAAGGTGTTTCAACCTTAT
1 TATACTTCATCTATTT-ATATT-ATTAGAATAAGGTGTTTCAACCTTAT
42568238 TA
1 TA
42568240 CACTCCTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 14 0.33
47 4 0.09
49 25 0.58
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.51
Consensus pattern (47 bp):
TATACTTCATCTATTTATATTATTAGAATAAGGTGTTTCAACCTTAT
Found at i:42574744 original size:13 final size:13
Alignment explanation
Indices: 42574728--42574793 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
42574718 TTTAAACCAA
42574728 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
42574741 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
42574754 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
42574767 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
42574780 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
42574793 A
1 A
42574794 TTGCCAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
12 4 0.09
13 39 0.83
14 4 0.09
ACGTcount: A:0.38, C:0.29, G:0.06, T:0.27
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:42575758 original size:25 final size:25
Alignment explanation
Indices: 42575724--42575775 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
42575714 CTTGATGATG
*
42575724 GAAGATTCCACTTATAATTTTTAAT
1 GAAGATTCCACTTATAATTGTTAAT
42575749 GAAGATTCCACTTATAATTGTTAAT
1 GAAGATTCCACTTATAATTGTTAAT
42575774 GA
1 GA
42575776 TGGATTAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (25 bp):
GAAGATTCCACTTATAATTGTTAAT
Found at i:42576067 original size:11 final size:12
Alignment explanation
Indices: 42576043--42576067 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42576033 ATTTGTAAAA
42576043 TTTTTAAAGTTT
1 TTTTTAAAGTTT
42576055 TTTTTAAAGTTT
1 TTTTTAAAGTTT
42576067 T
1 T
42576068 CATTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTTAAAGTTT
Found at i:42576969 original size:30 final size:30
Alignment explanation
Indices: 42576927--42577044 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
42576917 ACGGACGGGT
* *
42576927 AACCTCGATATAATGTCATCTTGTGTGAGC
1 AACCTGGATATAATGTCAGCTTGTGTGAGC
*
42576957 AACCTGGTTATAATGTCAGCTTGTGTGAGC
1 AACCTGGATATAATGTCAGCTTGTGTGAGC
* * * * *
42576987 AACATTGAAATATTGTCAGCTTATGTGAGC
1 AACCTGGATATAATGTCAGCTTGTGTGAGC
* * * *
42577017 AACCTTGAAATATTGTCAGCTTATGTGA
1 AACCTGGATATAATGTCAGCTTGTGTGA
42577045 ACATTTCATT
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (30 bp):
AACCTGGATATAATGTCAGCTTGTGTGAGC
Found at i:42589140 original size:28 final size:28
Alignment explanation
Indices: 42589108--42589162 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
42589098 ATGGTTTGAA
*
42589108 TTATTTTTA-ACTAAGTTTTCTGGATTTT
1 TTATTTTTAGACTAAGCTTT-TGGATTTT
42589136 TTATTTTTAGACTAAGCTTTTGGATTT
1 TTATTTTTAGACTAAGCTTTTGGATTT
42589163 GATTTTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.13, T:0.58
Consensus pattern (28 bp):
TTATTTTTAGACTAAGCTTTTGGATTTT
Found at i:42602612 original size:11 final size:11
Alignment explanation
Indices: 42602582--42602656 Score: 62
Period size: 11 Copynumber: 6.7 Consensus size: 11
42602572 AAACTAATCC
42602582 TCTCTCAATTAT
1 TCTCTCAATT-T
*
42602594 TTTCTCAATTT
1 TCTCTCAATTT
42602605 TCTCTCAATTT
1 TCTCTCAATTT
* * *
42602616 GCTTTCAAGTT
1 TCTCTCAATTT
*
42602627 GCTCTCAATTT
1 TCTCTCAATTT
* *
42602638 CCT-TCCAAATT
1 TCTCT-CAATTT
42602649 TCTCTCAA
1 TCTCTCAA
42602657 ATCCATATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
10 1 0.02
11 40 0.78
12 10 0.20
ACGTcount: A:0.21, C:0.27, G:0.04, T:0.48
Consensus pattern (11 bp):
TCTCTCAATTT
Found at i:42602759 original size:19 final size:19
Alignment explanation
Indices: 42602714--42602750 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42602704 TTAAATCCCT
42602714 ATTTTTAATTATTTTAAAA
1 ATTTTTAATTATTTTAAAA
**
42602733 AAATTTAATTATTTTAAA
1 ATTTTTAATTATTTTAAA
42602751 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTTAATTATTTTAAAA
Found at i:42603881 original size:7 final size:7
Alignment explanation
Indices: 42603869--42603894 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42603859 TAGTCGATTG
42603869 GTATTTA
1 GTATTTA
42603876 GTATTTA
1 GTATTTA
42603883 GTATTTA
1 GTATTTA
42603890 GTATT
1 GTATT
42603895 ACGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:42605147 original size:8 final size:8
Alignment explanation
Indices: 42605134--42605177 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
42605124 AATTTATTAA
42605134 AAATTTAT
1 AAATTTAT
42605142 AAATTTAT
1 AAATTTAT
42605150 AAATTATAATT
1 AAATT-T-A-T
42605161 AAATTTAT
1 AAATTTAT
42605169 -AATTTAT
1 AAATTTAT
42605176 AA
1 AA
42605178 TTAAATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 7 0.22
8 15 0.47
9 2 0.06
10 2 0.06
11 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAATTTAT
Found at i:42605163 original size:19 final size:19
Alignment explanation
Indices: 42605141--42605194 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
42605131 TAAAAATTTA
*
42605141 TAAATTTATAAATTATAAT
1 TAAATTTATAATTTATAAT
42605160 TAAATTTATAATTTATAAT
1 TAAATTTATAATTTATAAT
42605179 TAAATTTATAATTTAT
1 TAAATTTATAATTTAT
42605195 TTGACAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAATTTATAATTTATAAT
Found at i:42605170 original size:12 final size:13
Alignment explanation
Indices: 42605138--42605191 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 13
42605128 TATTAAAAAT
42605138 TTATAAATTTATAAA
1 TTAT-AATTTAT-AA
42605153 TTATAA-TTA-AA
1 TTATAATTTATAA
42605164 TTTATAATTTATAA
1 -TTATAATTTATAA
42605178 TTA-AATTTATAA
1 TTATAATTTATAA
42605190 TT
1 TT
42605192 TATTTGACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.06
12 17 0.47
13 9 0.25
14 4 0.11
15 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTATAATTTATAA
Found at i:42605259 original size:22 final size:21
Alignment explanation
Indices: 42605225--42605310 Score: 120
Period size: 22 Copynumber: 4.0 Consensus size: 21
42605215 CCCTAACCTT
42605225 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
42605246 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
42605268 AACCCTAACCCTTAACATAAA
1 AACCCTAACCCTTAACTTAAA
42605289 AACCCCATAA-CCTTAATCTTAA
1 AA-CCC-TAACCCTTAA-CTTAA
42605311 CAAAAACTCT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
21 22 0.37
22 30 0.51
23 7 0.12
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:42605279 original size:43 final size:44
Alignment explanation
Indices: 42605225--42605310 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
42605215 CCCTAACCTT
* *
42605225 AACCCTAACCCTTAACTTAAAAACCCTA-AACCCTTAA-CTTAAA
1 AACCCTAACCCTTAACATAAAAACCCCATAA-CCTTAATCTTAAA
42605268 AACCCTAACCCTTAACATAAAAACCCCATAACCTTAATCTTAA
1 AACCCTAACCCTTAACATAAAAACCCCATAACCTTAATCTTAA
42605311 CAAAAACTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 32 0.82
44 7 0.18
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (44 bp):
AACCCTAACCCTTAACATAAAAACCCCATAACCTTAATCTTAAA
Found at i:42608690 original size:125 final size:124
Alignment explanation
Indices: 42608408--42608840 Score: 697
Period size: 124 Copynumber: 3.5 Consensus size: 124
42608398 TAAACATGCT
* * * * *
42608408 ACTGTAGGAAAAGCGCGTCCATGAGGGCGCGATTTCATAAATTCTTCTGATAAAGCATCATACTT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTACTT
* * * *
42608473 GAAGCGTTTTTATATTATTCGCTCAGAAACGTAAACTCGAAATTA-TTTTTCAGGACCT
66 GAAGCGTTTTTATACTATTCGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCA
* *
42608531 ACTGTAGCAAAAGCGCGTCCACGTAGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTACTT
*
42608596 GAAGCGTTTTTTATACTATTCGCTCAGAAATGTCAACTCAAAATTATTTTTTCAGGACCA
66 GAAGCG-TTTTTATACTATTCGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCA
*
42608656 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTACTT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTACTT
* **
42608721 GAAGCCTTTTTATACTATTTTCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCA
66 GAAGCGTTTTTATACTATTCGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCA
*
42608780 ACTATAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCT
42608841 GCTTTGATTT
Statistics
Matches: 287, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
123 64 0.22
124 144 0.50
125 79 0.28
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTACTT
GAAGCGTTTTTATACTATTCGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCA
Found at i:42609004 original size:22 final size:22
Alignment explanation
Indices: 42608964--42609006 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42608954 TTTTATCTAA
**
42608964 AACCCTAAAAACCTTAAACCTT
1 AACCCTAAAAACCCAAAACCTT
42608986 AACCCTAAAAACCCAAAACCT
1 AACCCTAAAAACCCAAAACCT
42609007 AATGGCGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (22 bp):
AACCCTAAAAACCCAAAACCTT
Found at i:42612015 original size:6 final size:6
Alignment explanation
Indices: 42612004--42612059 Score: 62
Period size: 6 Copynumber: 9.3 Consensus size: 6
42611994 TTTGGTACAC
* *
42612004 AGATGT AGATGT AGATGT AGATGT AAATGT AAATGT -GATTCGT AGATGT
1 AGATGT AGATGT AGATGT AGATGT AGATGT AGATGT AGA-T-GT AGATGT
42612053 A-ATGT AG
1 AGATGT AG
42612060 GGGATGGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 6 0.14
6 33 0.75
7 3 0.07
8 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.34
Consensus pattern (6 bp):
AGATGT
Found at i:42612152 original size:10 final size:10
Alignment explanation
Indices: 42612137--42612162 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
42612127 ATATTGTTAT
42612137 CATTTTATAC
1 CATTTTATAC
42612147 CATTTTATAC
1 CATTTTATAC
42612157 CATTTT
1 CATTTT
42612163 GTTAGTCTAT
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:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (10 bp):
CATTTTATAC
Found at i:42634172 original size:49 final size:49
Alignment explanation
Indices: 42634115--42634218 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
42634105 TCATGTGTTA
* * * *
42634115 TAATTTTATACAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
*
42634164 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATGTTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
42634213 TAATTT
1 TAATTT
42634219 GTTTCTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:42635424 original size:44 final size:46
Alignment explanation
Indices: 42635370--42635463 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
42635360 ATTACAACAT
* *
42635370 CATTCTATTCAACCAAACACAA-GAATA-CTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACAAAAGGAATACCTATTACGCCTCTATTC
*
42635414 CATTCCATTCAACCAAACAAAAGGATTACCTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACAAAAGGAATACCTATTACGCCTCTATTC
42635460 CATT
1 CATT
42635464 ACACCTCTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 20 0.44
45 4 0.09
46 21 0.47
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (46 bp):
CATTCCATTCAACCAAACAAAAGGAATACCTATTACGCCTCTATTC
Found at i:42635470 original size:16 final size:16
Alignment explanation
Indices: 42635445--42635482 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
42635435 AGGATTACCT
*
42635445 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
42635461 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
42635477 ATTACA
1 ATTACA
42635483 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:42636006 original size:27 final size:26
Alignment explanation
Indices: 42635939--42636030 Score: 80
Period size: 27 Copynumber: 3.3 Consensus size: 26
42635929 GTATCAGTAT
42635939 ATTAATGTTT-TAAATATAATTTATTATTAG
1 ATTAAT-TTTATAAATAT--TTTA-TATT-G
*
42635969 ATTTAAGTTTTA-AAATTTTTTTATATATG
1 A-TTAA-TTTTATAAA-TATTTTATAT-TG
42635998 ATTAATTTTATAAATATTTTATATTG
1 ATTAATTTTATAAATATTTTATATTG
42636024 ATTAATT
1 ATTAATT
42636031 AAAAGGTATG
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
26 9 0.17
27 14 0.26
28 7 0.13
29 5 0.09
30 6 0.11
31 10 0.19
32 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (26 bp):
ATTAATTTTATAAATATTTTATATTG
Found at i:42637324 original size:8 final size:8
Alignment explanation
Indices: 42637307--42637335 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
42637297 ATAGTTCTTG
42637307 TAAA-ATA
1 TAAATATA
42637314 TAAATATA
1 TAAATATA
42637322 TAAATATA
1 TAAATATA
42637330 TAAATA
1 TAAATA
42637336 AAATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TAAATATA
Found at i:42637803 original size:31 final size:30
Alignment explanation
Indices: 42637737--42637803 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
42637727 AGTTTATTTT
42637737 TTTTTATAATTTTTAAGAAGTTAGATTAAA
1 TTTTTATAATTTTTAAGAAGTTAGATTAAA
* *
42637767 ATTTTATCATTTTTAATGTAA-TTA-ATTTAAA
1 TTTTTATAATTTTTAA-G-AAGTTAGA-TTAAA
42637798 TTTTTA
1 TTTTTA
42637804 AATGACCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 15 0.48
31 14 0.45
32 2 0.06
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.55
Consensus pattern (30 bp):
TTTTTATAATTTTTAAGAAGTTAGATTAAA
Found at i:42648899 original size:110 final size:107
Alignment explanation
Indices: 42648707--42648902 Score: 266
Period size: 110 Copynumber: 1.8 Consensus size: 107
42648697 AAACTTGGCA
*
42648707 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGAGCACGTTCCTCGAATTTCCAAACGCAA
* *
42648772 AATATTGCCTTATTTTGAAATTTTTATGAAGGATATTAAGCC
66 AATATTGCCTCAATTTGAAATTTTTATGAAGGATATTAAGCC
* * ** * * *
42648814 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGAGCGTGTTTTCTCGAATTTCTAAATG
1 ATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGAGCACG-TTCCTCGAATTTCCAAACG
*
42648879 CTAAATATTGCCTCAATTTGAAAT
63 CAAAATATTGCCTCAATTTGAAAT
42648903 ATTCTCCTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
107 14 0.19
109 24 0.32
110 37 0.49
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (107 bp):
ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGAGCACGTTCCTCGAATTTCCAAACGCAA
AATATTGCCTCAATTTGAAATTTTTATGAAGGATATTAAGCC
Found at i:42649331 original size:16 final size:16
Alignment explanation
Indices: 42649253--42649319 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
42649243 AAAAACAGGA
42649253 AGAAAAAAATGTATAT
1 AGAAAAAAATGTATAT
* * * *
42649269 AGATATATATCTATAT
1 AGAAAAAAATGTATAT
42649285 AGAAAAAAATGTATAT
1 AGAAAAAAATGTATAT
42649301 AGAAAAAAATGTATAT
1 AGAAAAAAATGTATAT
42649317 AGA
1 AGA
42649320 TATATATGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.58, C:0.01, G:0.12, T:0.28
Consensus pattern (16 bp):
AGAAAAAAATGTATAT
Found at i:42649486 original size:17 final size:17
Alignment explanation
Indices: 42649464--42649496 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42649454 GAGTTTATAC
42649464 ATATAATGAT-TTAAAAT
1 ATATAAT-ATATTAAAAT
42649481 ATATAATATATTAAAA
1 ATATAATATATTAAAA
42649497 GAATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATATAATATATTAAAAT
Done.