Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 205 of 213
Found at i:61330876 original size:18 final size:18
Alignment explanation
Indices: 61330852--61330940 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 18
61330842 CTCAACTACT
*
61330852 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
61330870 ATATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* *
61330888 GTATACGTAAATAGTATC
1 GTATACGTGAATAGTACC
**
61330906 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
*
61330924 GTATACGTAAATAGTAC
1 GTATACGTGAATAGTAC
61330941 TGTAAACGGT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:61330911 original size:36 final size:36
Alignment explanation
Indices: 61330852--61330940 Score: 133
Period size: 36 Copynumber: 2.5 Consensus size: 36
61330842 CTCAACTACT
* *
61330852 GTATACGTGAACAGTACCATATACGTGAATAGTGCC
1 GTATACGTAAATAGTACCATATACGTGAATAGTGCC
* * *
61330888 GTATACGTAAATAGTATCGTATACGTGAATAGTGTC
1 GTATACGTAAATAGTACCATATACGTGAATAGTGCC
61330924 GTATACGTAAATAGTAC
1 GTATACGTAAATAGTAC
61330941 TGTAAACGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (36 bp):
GTATACGTAAATAGTACCATATACGTGAATAGTGCC
Found at i:61334733 original size:14 final size:14
Alignment explanation
Indices: 61334714--61334745 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
61334704 TAATAATGAG
61334714 AATACCAATTTTAT
1 AATACCAATTTTAT
61334728 AATACCAATTTTAT
1 AATACCAATTTTAT
61334742 AATA
1 AATA
61334746 ATAATATCAA
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:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (14 bp):
AATACCAATTTTAT
Found at i:61334749 original size:20 final size:20
Alignment explanation
Indices: 61334726--61334768 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
61334716 TACCAATTTT
61334726 ATAATACCAATTTTATAATA
1 ATAATACCAATTTTATAATA
* *
61334746 ATAATATCAATTTTATAGTA
1 ATAATACCAATTTTATAATA
61334766 ATA
1 ATA
61334769 TTGATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAATACCAATTTTATAATA
Found at i:61337020 original size:44 final size:44
Alignment explanation
Indices: 61336962--61337420 Score: 209
Period size: 44 Copynumber: 10.5 Consensus size: 44
61336952 ATCTACTTCG
* * * *
61336962 CTGCAACCTCAAGGAGATGAGATTTGTAGTTTTAATCAGCTCCA
1 CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* * *
61337006 CT-CTAACTTCAAGGAGATAAGATTTATGGCTTTAATCTGTTCCA
1 CTGC-AACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* * * * *
61337050 CTGCAACTTTAAGGAGATATGGTTT-TA---AT-AT--GCTCTA
1 CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* * * * ** *
61337087 CTACAACTTCAAAGAGATAAGAGTTACTATCTTCT-ATTTGTTCCA
1 CTGCAACTTCAAGGAGATAAGATTTA-TAGCTT-TAATCAGCTCCA
* * * * * *
61337132 TTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCTA
1 CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* * * * * *
61337176 TTGCAACTT-TAGAGAGATAAGATTTACTATCTTCAATCTGCTCTA
1 CTGCAACTTCAAG-GAGATAAGATTTA-TAGCTTTAATCAGCTCCA
* * * *
61337221 CTGCAACTTCAAGGAGATAAGATTTATTGCTTCAATCTGCTCTA
1 CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* * *
61337265 TTGCAACTT-TAGAGAGATAAGATTTGTAGCTTTAAT---CT--A
1 CTGCAACTTCAAG-GAGATAAGATTTATAGCTTTAATCAGCTCCA
* * * * * *
61337304 -TTCCACTTCAAGGAAATAAGACTTACTACGGTAGATTTAATCCGATCCA
1 CTGCAACTTCAAGGAGATAAGA-TT--TA---TAGCTTTAATCAGCTCCA
* * * * *
61337353 CTGCAACTTCAATGG-TATAGGATTTGTAGCTTCAATCTGCTCCA
1 CTGCAACTTCAA-GGAGATAAGATTTATAGCTTTAATCAGCTCCA
*
61337397 CTGTAACTTC-AGTGAGATAAGATT
1 CTGCAACTTCAAG-GAGATAAGATT
61337421 CGCTATGATG
Statistics
Matches: 318, Mismatches: 66, Indels: 62
0.71 0.15 0.14
Matches are distributed among these distances:
37 23 0.07
38 14 0.04
39 9 0.03
40 1 0.00
41 3 0.01
42 1 0.00
43 10 0.03
44 171 0.54
45 63 0.20
46 2 0.01
47 2 0.01
49 3 0.01
50 14 0.04
51 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (44 bp):
CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
Found at i:61337094 original size:37 final size:37
Alignment explanation
Indices: 61337030--61337105 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 37
61337020 AGATAAGATT
* * * * *
61337030 TATGGCTTTAATCTGTTCCACTGCAACTTTAAGGAGA
1 TATGGCTTTAATATGCTCCACTACAACTTCAAAGAGA
* *
61337067 TATGGTTTTAATATGCTCTACTACAACTTCAAAGAGA
1 TATGGCTTTAATATGCTCCACTACAACTTCAAAGAGA
61337104 TA
1 TA
61337106 AGAGTTACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (37 bp):
TATGGCTTTAATATGCTCCACTACAACTTCAAAGAGA
Found at i:61337226 original size:45 final size:45
Alignment explanation
Indices: 61337080--61337289 Score: 248
Period size: 44 Copynumber: 4.7 Consensus size: 45
61337070 GGTTTTAATA
* * * * * *
61337080 TGCTCTACTACAACTTCAAAGAGATAAGAGTTACTATCTTCTATT
1 TGCTCTATTGCAACTTCAGAGAGATAAGATTTACTATCTTCAATC
* * * * *
61337125 TGTTCCATTGCAACTTCAGGGAGATAAGATTT-GTAGCTTCAATC
1 TGCTCTATTGCAACTTCAGAGAGATAAGATTTACTATCTTCAATC
*
61337169 TGCTCTATTGCAACTTTAGAGAGATAAGATTTACTATCTTCAATC
1 TGCTCTATTGCAACTTCAGAGAGATAAGATTTACTATCTTCAATC
*
61337214 TGCTCTACTGCAACTTCA-AGGAGATAAGATTTA-T-TGCTTCAATC
1 TGCTCTATTGCAACTTCAGA-GAGATAAGATTTACTAT-CTTCAATC
*
61337258 TGCTCTATTGCAACTTTAGAGAGATAAGATTT
1 TGCTCTATTGCAACTTCAGAGAGATAAGATTT
61337290 GTAGCTTTAA
Statistics
Matches: 140, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
43 1 0.01
44 74 0.53
45 65 0.46
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (45 bp):
TGCTCTATTGCAACTTCAGAGAGATAAGATTTACTATCTTCAATC
Found at i:61337231 original size:89 final size:89
Alignment explanation
Indices: 61337080--61337289 Score: 303
Period size: 89 Copynumber: 2.4 Consensus size: 89
61337070 GGTTTTAATA
* * * * * * * * * *
61337080 TGCTCTACTACAACTTCAAAGAGATAAGAGTTACTATCTTCTATTTGTTCCATTGCAACTTCAGG
1 TGCTCTATTGCAACTTTAGAGAGATAAGATTTACTATCTTCAATCTGCTCCACTGCAACTTCAAG
*
61337145 GAGATAAGATTTGTAGCTTCAATC
66 GAGATAAGATTTATAGCTTCAATC
*
61337169 TGCTCTATTGCAACTTTAGAGAGATAAGATTTACTATCTTCAATCTGCTCTACTGCAACTTCAAG
1 TGCTCTATTGCAACTTTAGAGAGATAAGATTTACTATCTTCAATCTGCTCCACTGCAACTTCAAG
*
61337234 GAGATAAGATTTATTGCTTCAATC
66 GAGATAAGATTTATAGCTTCAATC
61337258 TGCTCTATTGCAACTTTAGAGAGATAAGATTT
1 TGCTCTATTGCAACTTTAGAGAGATAAGATTT
61337290 GTAGCTTTAA
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 108 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (89 bp):
TGCTCTATTGCAACTTTAGAGAGATAAGATTTACTATCTTCAATCTGCTCCACTGCAACTTCAAG
GAGATAAGATTTATAGCTTCAATC
Found at i:61349030 original size:17 final size:17
Alignment explanation
Indices: 61348996--61349066 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
61348986 TAATAATGAG
61348996 AATACCAA-TTT-T-AT
1 AATACCAATTTTATAAT
61349010 AATACCAATTTTATAATAAT
1 AATACCAA-TTT-T-ATAAT
*
61349030 AATATCAATTTTATAAT
1 AATACCAATTTTATAAT
* *
61349047 AATATCGATTTTATAAT
1 AATACCAATTTTATAAT
61349064 AAT
1 AAT
61349067 GGTACTAATC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.16
16 2 0.04
17 25 0.51
18 1 0.02
19 4 0.08
20 9 0.18
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.44
Consensus pattern (17 bp):
AATACCAATTTTATAAT
Found at i:61349031 original size:20 final size:19
Alignment explanation
Indices: 61349008--61349066 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
61348998 TACCAATTTT
61349008 ATAATACCAATTTTATAATA
1 ATAATA-CAATTTTATAATA
61349028 ATAATATCAATTTTATAATA
1 ATAATA-CAATTTTATAATA
*
61349048 AT-AT-CGATTTTATAATA
1 ATAATACAATTTTATAATA
61349065 AT
1 AT
61349067 GGTACTAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 14 0.38
19 2 0.05
20 21 0.57
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (19 bp):
ATAATACAATTTTATAATA
Found at i:61349047 original size:14 final size:14
Alignment explanation
Indices: 61348996--61349027 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
61348986 TAATAATGAG
61348996 AATACCAATTTTAT
1 AATACCAATTTTAT
61349010 AATACCAATTTTAT
1 AATACCAATTTTAT
61349024 AATA
1 AATA
61349028 ATAATATCAA
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:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (14 bp):
AATACCAATTTTAT
Found at i:61350851 original size:62 final size:62
Alignment explanation
Indices: 61350775--61350899 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
61350765 TTGGGTTGAC
61350775 ATTTTATAAATGGATTGGACTGTTTATTGGACTTTTATTCATTTAGTTTTGTTTATTATATT
1 ATTTTATAAATGGATTGGACTGTTTATTGGACTTTTATTCATTTAGTTTTGTTTATTATATT
61350837 ATTTTATAAATGGATTGGACTGTTTATTGGACTTTTATTCATTTAGTTTTGTTTATTATATT
1 ATTTTATAAATGGATTGGACTGTTTATTGGACTTTTATTCATTTAGTTTTGTTTATTATATT
61350899 A
1 A
61350900 CTTTGTGTGC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (62 bp):
ATTTTATAAATGGATTGGACTGTTTATTGGACTTTTATTCATTTAGTTTTGTTTATTATATT
Found at i:61355360 original size:94 final size:94
Alignment explanation
Indices: 61355107--61355619 Score: 510
Period size: 94 Copynumber: 5.5 Consensus size: 94
61355097 GTGAAACCAC
* * * * * *
61355107 AAATCCTATACCTCTGAAGTTGTAGTGGGTCAGATTGAAATC-ACCACAGTAAATCTTTTCTCCC
1 AAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATT-AAATCTACCATAGTGAATCTTATCTCCC
* * * *
61355171 TAAAGTTGCAGTAGAGCAGATCGAAGCTAC
65 TGAAGTTGCAGTGGAGCAGATTGAAGCTAA
* **
61355201 AAATCCTGTACCCCCTGAAA-TTGCAGTGGGT--G---GGATCTACCATAGTGAATCTTATCTCC
1 AAATCCTATA-CCCCT-AAAGTTGCAGTGGGTCAGATTAAATCTACCATAGTGAATCTTATCTCC
* *
61355260 CAGAAGTTGTAGTGGAGCAGATTGAAGCTAA
64 CTGAAGTTGCAGTGGAGCAGATTGAAGCTAA
* * *
61355291 AAATCCTAAACCCCTAAAGTTGCAGTGGGTCAGATTAGATCTACCATAGTGAATCTTATCTCCTT
1 AAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTAAATCTACCATAGTGAATCTTATCTCCCT
*
61355356 GAAGTTGTAGTGGAGCAGATTGAAGCTAA
66 GAAGTTGCAGTGGAGCAGATTGAAGCTAA
* * * * *
61355385 AAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAATCTACCATAGCGAATCTTATCTCTCT
1 AAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTAAATCTACCATAGTGAATCTTATCTCCCT
* *
61355450 GAAGTTGCAGTGGAGCAAGA-TAAAACTACA
66 GAAGTTGCAGTGGAGC-AGATTGAAGCTA-A
* * * * * * * *
61355480 AATTCC-ATACCCCTAAAGTTGCAATGGAT-TGATTAAAACTA-CAGTGGCGAATTTTATCTCCC
1 AAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTAAATCTACCA-TAGTGAATCTTATCTCCC
* * * *
61355542 TAAAGTTACAGTGGAGCAAGA-TAAAGCTAC
65 TGAAGTTGCAGTGGAGC-AGATTGAAGCTAA
* * *
61355572 AATTCCTATATCCCTAAAGTTGGAGTGGGTCAGATTAAATCTACCATA
1 AAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTAAATCTACCATA
61355620 TAAAGCAGAT
Statistics
Matches: 352, Mismatches: 52, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
88 3 0.01
89 19 0.05
90 51 0.14
91 1 0.00
92 8 0.02
93 70 0.20
94 173 0.49
95 25 0.07
96 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (94 bp):
AAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTAAATCTACCATAGTGAATCTTATCTCCCT
GAAGTTGCAGTGGAGCAGATTGAAGCTAA
Found at i:61355423 original size:44 final size:44
Alignment explanation
Indices: 61355262--61355412 Score: 137
Period size: 44 Copynumber: 3.3 Consensus size: 44
61355252 TTATCTCCCA
* *
61355262 GAAGTTGTAGTGGAGCAGATTGAAGCTAAAAATCCTAAACCCCT
1 GAAGTTGCAGTGGAGCAGATTGAAGCTAAAAATCCTATACCCCT
* * * *
61355306 AAAGTTGCAGTGG-GTCAGATT-AGATCTACCATAGTGAATCTTAT-CTCCTT
1 GAAGTTGCAGTGGAG-CAGATTGA-AGCTA--A-A---AATCCTATAC-CCCT
*
61355356 GAAGTTGTAGTGGAGCAGATTGAAGCTAAAAATCCTATACCCCT
1 GAAGTTGCAGTGGAGCAGATTGAAGCTAAAAATCCTATACCCCT
61355400 GAAGTTGCAGTGG
1 GAAGTTGCAGTGG
61355413 GTCGGATTGA
Statistics
Matches: 83, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
43 2 0.02
44 43 0.52
45 1 0.01
46 1 0.01
47 2 0.02
48 1 0.01
49 1 0.01
50 30 0.36
51 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (44 bp):
GAAGTTGCAGTGGAGCAGATTGAAGCTAAAAATCCTATACCCCT
Found at i:61355979 original size:17 final size:16
Alignment explanation
Indices: 61355957--61355990 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61355947 CCGAAACCAG
61355957 AAATAAATAAACAAAAA
1 AAATAAA-AAACAAAAA
*
61355974 AAATAAAAACCAAAAA
1 AAATAAAAAACAAAAA
61355990 A
1 A
61355991 TAAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAAACAAAAA
Found at i:61357403 original size:15 final size:14
Alignment explanation
Indices: 61357385--61357442 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 14
61357375 ATTATTGTCG
61357385 TTATTATTTTTATTT
1 TTATTATTTTT-TTT
61357400 TTATTATTTTTCTTGT
1 TTATTATTTTT-TT-T
* *
61357416 TATTTTATTATTTCTT
1 T-TATTATT-TTTTTT
61357432 TTATTATTTTT
1 TTATTATTTTT
61357443 GGTACTTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 3 0.08
15 19 0.53
16 4 0.11
17 7 0.19
18 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (14 bp):
TTATTATTTTTTTT
Found at i:61357423 original size:20 final size:20
Alignment explanation
Indices: 61357398--61357441 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
61357388 TTATTTTTAT
*
61357398 TTTTATTATTT-TTCTTGTTA
1 TTTTATTATTTCTT-TTATTA
61357418 TTTTATTATTTCTTTTATTA
1 TTTTATTATTTCTTTTATTA
61357438 TTTT
1 TTTT
61357442 TGGTACTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTATTATTTCTTTTATTA
Found at i:61357548 original size:3 final size:3
Alignment explanation
Indices: 61357540--61357580 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
61357530 TTATGTTCTG
61357540 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
61357581 AGTATTCCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:61361403 original size:18 final size:16
Alignment explanation
Indices: 61361382--61361420 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
61361372 AATAATGGAA
61361382 ATATATAAAAACATGT
1 ATATATAAAAACATGT
**
61361398 ATATATAAAAGTATGT
1 ATATATAAAAACATGT
61361414 ATATATA
1 ATATATA
61361421 TAAATTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:61370266 original size:12 final size:12
Alignment explanation
Indices: 61370249--61370286 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
61370239 TCATTTAATA
61370249 ATCAAGTCTTTC
1 ATCAAGTCTTTC
61370261 ATCAAGT-TTTC
1 ATCAAGTCTTTC
61370272 AATCAAG-CTTTC
1 -ATCAAGTCTTTC
61370284 ATC
1 ATC
61370287 TTCTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (12 bp):
ATCAAGTCTTTC
Found at i:61370461 original size:15 final size:17
Alignment explanation
Indices: 61370436--61370467 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
61370426 ATTTAACCCT
61370436 CTCCAAATATG-CTCAA
1 CTCCAAATATGCCTCAA
61370452 CTCC-AATATGCCTCAA
1 CTCCAAATATGCCTCAA
61370468 ACTTTAGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.25
Consensus pattern (17 bp):
CTCCAAATATGCCTCAA
Found at i:61378235 original size:12 final size:12
Alignment explanation
Indices: 61378218--61378279 Score: 85
Period size: 12 Copynumber: 5.2 Consensus size: 12
61378208 TCATTCAATA
61378218 ATCAAGTCTTTC
1 ATCAAGTCTTTC
61378230 ATCAAGT-TTTC
1 ATCAAGTCTTTC
61378241 AATCAAGTCTTTC
1 -ATCAAGTCTTTC
61378254 ATCAAGT-TTTC
1 ATCAAGTCTTTC
61378265 AATCAA-TCTTTC
1 -ATCAAGTCTTTC
61378277 ATC
1 ATC
61378280 TTCTAAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
11 12 0.26
12 30 0.65
13 4 0.09
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (12 bp):
ATCAAGTCTTTC
Found at i:61378246 original size:24 final size:24
Alignment explanation
Indices: 61378217--61378279 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
61378207 TTCATTCAAT
61378217 AATCAAGTCTTTCATCAAGTTTTC
1 AATCAAGTCTTTCATCAAGTTTTC
61378241 AATCAAGTCTTTCATCAAGTTTTC
1 AATCAAGTCTTTCATCAAGTTTTC
61378265 AATCAA-TCTTTCATC
1 AATCAAGTCTTTCATC
61378280 TTCTAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
23 9 0.23
24 30 0.77
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.41
Consensus pattern (24 bp):
AATCAAGTCTTTCATCAAGTTTTC
Found at i:61385408 original size:32 final size:27
Alignment explanation
Indices: 61385393--61385445 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
61385383 CACCACTTAA
61385393 TCGGGGAATCAGCACTTAGCAACCCCT
1 TCGGGGAATCAGCACTTAGCAACCCCT
*
61385420 TGGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
61385446 CTTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17
Consensus pattern (27 bp):
TCGGGGAATCAGCACTTAGCAACCCCT
Found at i:61385543 original size:103 final size:104
Alignment explanation
Indices: 61385362--61385626 Score: 415
Period size: 103 Copynumber: 2.6 Consensus size: 104
61385352 AACCGTTATT
* * * *
61385362 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
* ** *
61385427 ATCAGCACTTAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
61385465 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
61385530 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
61385569 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
61385627 TTATGTACAA
Statistics
Matches: 148, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
103 82 0.55
104 66 0.45
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:61385988 original size:30 final size:29
Alignment explanation
Indices: 61385954--61386018 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
61385944 TAATCCACCA
61385954 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
61385984 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
61386014 CCCAA
1 CCCAA
61386019 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:61385992 original size:31 final size:30
Alignment explanation
Indices: 61385961--61386018 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
61385951 CCACCCAACT
61385961 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
61385991 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
61386019 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:61388357 original size:128 final size:128
Alignment explanation
Indices: 61388204--61388455 Score: 414
Period size: 128 Copynumber: 2.0 Consensus size: 128
61388194 AGATAATGTT
*
61388204 TTTCTTCTGTCTACTCCACTACTGCTTAGGGAGATAAGACTGGATGCAATCTGCTCTACTGCAAC
1 TTTCTTCTGTCTACTCCACTACTGCTTAGGGAGATAAGACTGGATGCAATCTGCTCTACTACAAC
* * * * *
61388269 TTCAGAGAGATAAGATTTGTGGTTTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCGG
66 TTCAGAGAGATAAGATCTGTGGTTTTCAATCTGCTCCACTACTGCTTAGAGAAATAAGATCGG
* * * *
61388332 TTTCTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGCGATTTGCTCTACTACAAC
1 TTTCTTCTGTCTACTCCACTACTGCTTAGGGAGATAAGACTGGATGCAATCTGCTCTACTACAAC
61388397 TTCAGAGAGATAAGATCTGTGGTTTTCAATCTGCTCCACTACTGCTTAGAGAAATAAGA
66 TTCAGAGAGATAAGATCTGTGGTTTTCAATCTGCTCCACTACTGCTTAGAGAAATAAGA
61388456 CTTGATGTGA
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
128 114 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (128 bp):
TTTCTTCTGTCTACTCCACTACTGCTTAGGGAGATAAGACTGGATGCAATCTGCTCTACTACAAC
TTCAGAGAGATAAGATCTGTGGTTTTCAATCTGCTCCACTACTGCTTAGAGAAATAAGATCGG
Found at i:61388439 original size:85 final size:85
Alignment explanation
Indices: 61388341--61388504 Score: 265
Period size: 85 Copynumber: 1.9 Consensus size: 85
61388331 GTTTCTTTTG
* * *
61388341 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGCGATTTGCTCTACTACAACTTCAGAGAG
1 TCTGCTCCACTACTGCTTAGAGAAATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAG
61388406 ATAAGATCTGTGGTTTTCAA
66 ATAAGATCTGTGGTTTTCAA
* * *
61388426 TCTGCTCCACTACTGCTTAGAGAAATAAGACTTGATGTGATCTGCTCTACTGCAACTTCAGAGAG
1 TCTGCTCCACTACTGCTTAGAGAAATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAG
*
61388491 ATAAGATTTGTGGT
66 ATAAGATCTGTGGT
61388505 CTATAGCTTC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 72 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (85 bp):
TCTGCTCCACTACTGCTTAGAGAAATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAG
ATAAGATCTGTGGTTTTCAA
Found at i:61388469 original size:40 final size:40
Alignment explanation
Indices: 61388217--61388496 Score: 141
Period size: 40 Copynumber: 6.7 Consensus size: 40
61388207 CTTCTGTCTA
* * **
61388217 CTCCACTACTGCTTAGGGAGATAAGACTGGATGCAATCTG
1 CTCCACTACTGCTTAGAGAGATAAGACTTGATGTGATCTG
* * ** *
61388257 CTCTACTGCAACTTCAGAGAGATAAGATTTG-TGGTTTTCGATCTG
1 CTCCACTACTGCTT-AGAGAGATAAGACTTGAT-G---T-GATCTG
* * ** *
61388302 CTCCACTATTGCTTAGGGAGATAAGATCGGTTTCTTTTG-TCTG
1 CTCCACTACTGCTTAGAGAGATAAGA-C---TTGATGTGATCTG
* * * *
61388345 CTCCACTACTGCTTAGGGAGATAAGACTGGATGCGATTTG
1 CTCCACTACTGCTTAGAGAGATAAGACTTGATGTGATCTG
* ** * * *
61388385 CTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTCAATCTG
1 CTCCACTACTGCTT-AGAGAGATAAGA-CT-T-GATGT-GATCTG
*
61388430 CTCCACTACTGCTTAGAGAAATAAGACTTGATGTGATCTG
1 CTCCACTACTGCTTAGAGAGATAAGACTTGATGTGATCTG
* * **
61388470 CTCTACTGCAACTTCAGAGAGATAAGA
1 CTCCACTACTGCTT-AGAGAGATAAGA
61388497 TTTGTGGTCT
Statistics
Matches: 175, Mismatches: 47, Indels: 35
0.68 0.18 0.14
Matches are distributed among these distances:
39 3 0.02
40 40 0.23
41 39 0.22
42 4 0.02
43 31 0.18
44 25 0.14
45 30 0.17
48 2 0.01
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (40 bp):
CTCCACTACTGCTTAGAGAGATAAGACTTGATGTGATCTG
Found at i:61388675 original size:100 final size:100
Alignment explanation
Indices: 61388518--61389078 Score: 773
Period size: 100 Copynumber: 5.6 Consensus size: 100
61388508 TAGCTTCTCT
* * * *
61388518 TTTTAAACTGCAATGTCGGGGAA-CAAGATTCGTTGTTGTAGCTTCAATCTGTTCCACTGCACTG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTG
* * * * * *
61388582 CCAGGGAAGTAGGATTCACCGTTGTGGCTTCAATA
66 CTAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATC
* ** * * *
61388617 TTTTAAATTGCAATATCGGGGAAGCAAGATTCGCCATCGTAGCTTTAATCTACTCCACTGTACTG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTG
* * *
61388682 CTAGAAAAGTAAGATTCGCCATTGCGGCTTCAGTC
66 CTAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATC
* * *
61388717 TTTTTAATTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTGCTCTACTGCACTG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTG
* * * *
61388782 CTAGGAAAGTAAGATTCGTCGTTCCGACTTCAATA
66 CTAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATC
* * * *
61388817 TTTTATATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAACTTTAATCTGCTCCACTACACCG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTG
61388882 CTAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATC
66 CTAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATC
* * *
61388917 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTTAATCTACTCCACTGCACCG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTG
* *
61388982 CTAGGAAAGTAAGATTCGTCGTTGCGACTTCAATC
66 CTAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATC
* * *
61389017 TTTTAAATTGTAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTTAATCTGCCCCACTGCA
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCA
61389079 TCGCCAGGGA
Statistics
Matches: 405, Mismatches: 56, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
99 21 0.05
100 384 0.95
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (100 bp):
TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTG
CTAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATC
Found at i:61388792 original size:50 final size:50
Alignment explanation
Indices: 61388738--61388999 Score: 165
Period size: 50 Copynumber: 5.2 Consensus size: 50
61388728 AATGTCGGGG
*
61388738 AAGTAAGATTCGCTGTTGTAGCTTTAATCTGCTCTACTGCACTGCTAGGA
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTGCTAGGA
* * ** ** * * * *
61388788 AAGTAAGATTCG-TCGTTCCG-A-CTTCAATATTTTATATTGCAATG-TCGGGG
1 AAGTAAGATTCGCT-GTT--GTAGCTTTAATCTGCTCCACTGCACTGCT-AGGA
* * * *
61388838 AAGCAAGATTCGCTGTTGTAACTTTAATCTGCTCCACTACACCGCTAGGA
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTGCTAGGA
* ** * ** ** * * * *
61388888 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATG-TCGGGG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTGCT-AGGA
* * * *
61388938 AAGCAAGATTCACTGTTGTAGCTTTAATCTACTCCACTGCACCGCTAGGA
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTGCTAGGA
61388988 AAGTAAGATTCG
1 AAGTAAGATTCG
61389000 TCGTTGCGAC
Statistics
Matches: 147, Mismatches: 55, Indels: 20
0.66 0.25 0.09
Matches are distributed among these distances:
48 1 0.01
49 4 0.03
50 137 0.93
51 4 0.03
52 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (50 bp):
AAGTAAGATTCGCTGTTGTAGCTTTAATCTGCTCCACTGCACTGCTAGGA
Found at i:61389425 original size:24 final size:24
Alignment explanation
Indices: 61389374--61389427 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
61389364 TTGCCCCCAT
**
61389374 TGTAATCTTCAAAGTTCAATCCGT
1 TGTAATCTTCAAAGTTCAATCCAC
* * *
61389398 TGTAATCTTCAAGGTTGAGTCCAC
1 TGTAATCTTCAAAGTTCAATCCAC
61389422 TGTAAT
1 TGTAAT
61389428 TTAGGGACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (24 bp):
TGTAATCTTCAAAGTTCAATCCAC
Found at i:61390355 original size:15 final size:15
Alignment explanation
Indices: 61390335--61390370 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
61390325 CTCCTTTTTC
*
61390335 TTTTTTGTTCTTCTT
1 TTTTTTCTTCTTCTT
*
61390350 TTTTTTCTTTTTCTT
1 TTTTTTCTTCTTCTT
61390365 TTTTTT
1 TTTTTT
61390371 TTGAAGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (15 bp):
TTTTTTCTTCTTCTT
Found at i:61399948 original size:38 final size:38
Alignment explanation
Indices: 61399901--61399979 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
61399891 GAGAAGGGGA
*
61399901 TTGACACCTCGACTTAAGGGTGGCGGT-AAGGGAGTTGG
1 TTGACACCTCGACTCAAGGGTGGCGGTAAAGGG-GTTGG
* * *
61399939 TTGAGACCTCGGCTCAGGGGTGGCGGTAAAGGGGTTGG
1 TTGACACCTCGACTCAAGGGTGGCGGTAAAGGGGTTGG
61399977 TTG
1 TTG
61399980 GGGCTTCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 31 0.86
39 5 0.14
ACGTcount: A:0.18, C:0.15, G:0.43, T:0.24
Consensus pattern (38 bp):
TTGACACCTCGACTCAAGGGTGGCGGTAAAGGGGTTGG
Found at i:61400614 original size:13 final size:13
Alignment explanation
Indices: 61400598--61400637 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
61400588 TTTTTCTGCA
61400598 TTTTTAAATTTAT
1 TTTTTAAATTTAT
* *
61400611 TTTTTAATTTTAA
1 TTTTTAAATTTAT
*
61400624 ATTTTAAATTTAT
1 TTTTTAAATTTAT
61400637 T
1 T
61400638 CAATAATACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTAAATTTAT
Found at i:61401533 original size:14 final size:13
Alignment explanation
Indices: 61401513--61401544 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
61401503 TGATTTTTAA
61401513 TTTTAAAAAATAT
1 TTTTAAAAAATAT
61401526 TGTTTAAAAAATAT
1 T-TTTAAAAAATAT
61401540 TTTTA
1 TTTTA
61401545 TAACTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:61401913 original size:30 final size:33
Alignment explanation
Indices: 61401853--61401918 Score: 93
Period size: 30 Copynumber: 2.1 Consensus size: 33
61401843 ACATGATTTT
*
61401853 TTTAAATAATTATAAAAATATTATAGAAAATTA
1 TTTAAATAACTATAAAAATATTATAGAAAATTA
*
61401886 TTTAAA-AACTATTAAAAT-TTA-AGAAAATTA
1 TTTAAATAACTATAAAAATATTATAGAAAATTA
61401916 TTT
1 TTT
61401919 GATACACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 12 0.39
31 3 0.10
32 10 0.32
33 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (33 bp):
TTTAAATAACTATAAAAATATTATAGAAAATTA
Found at i:61404219 original size:9 final size:9
Alignment explanation
Indices: 61404202--61404238 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
61404192 TGAGTTCTCG
61404202 AATTCGAAT
1 AATTCGAAT
*
61404211 AACTCGAAT
1 AATTCGAAT
61404220 AATTCGAAT
1 AATTCGAAT
61404229 AATTCGAAT
1 AATTCGAAT
61404238 A
1 A
61404239 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:61404489 original size:30 final size:31
Alignment explanation
Indices: 61404455--61404514 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
61404445 AAACCTTTTA
*
61404455 TTTTCCTCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTCC-CCTAAAACTTTTACTCCCTTCCCAC
*
61404485 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
61404515 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.08
30 19 0.73
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:61411105 original size:250 final size:251
Alignment explanation
Indices: 61410629--61411115 Score: 662
Period size: 250 Copynumber: 1.9 Consensus size: 251
61410619 TTCGAATGGA
*
61410629 TTTGAGCCAGATCCTAATGAGCTCACCGGATGAGCTCGAAGACCAAGCTCACAGGTCGAGCTCGC
1 TTTGAGCCAGATCCTAATGAGCTCACAGGATGAGCTCGAAGACCAAGCTCACAGGTCGAGCTCGC
* * *
61410694 TCTCCTACCAGGTTACATGTGCATAAGACTGTATAAACAAATGTTGAGTCTAGAGTAGGAAGTGT
66 TCTCCTACAAGGTTACACGTGCATAAGACTGTATAAACAAATGTTGAATCTAGAGTAGGAAGTGT
* * * *
61410759 TAATATGCATGAAGCCTACTTAGCATGTCAAGTCAATGAACAGTTTCCATATAATATAAATATGC
131 TAATATGCATGAAGCCTACCTAACATGTCAAGTCAATGAACAGTATCCATATAATATAAATATAC
* *
61410824 AGACAACACTACCTAGAGGAG-ATAGAGAAAAACACTCAACATTTGGGAGTTGAGAT
196 AGACAACACTACCTAAAGGAGAACAGA-AAAAACACTCAACATTTGGGAGTTGAGAT
* * * *
61410880 TTTG-GCCAGATCCTAATGAGCTCGCAGGATGAGCTCGTAGACCAAGCTCATAGGTCGAGCTTGC
1 TTTGAGCCAGATCCTAATGAGCTCACAGGATGAGCTCGAAGACCAAGCTCACAGGTCGAGCTCGC
* * **
61410944 TCTCCTGCAAGGTTACACGTGCATAATACTGTATAAACACGTGTTGAATCTAGAGTAGGATATGT
66 TCTCCTACAAGGTTACACGTGCATAAGACTGTATAAACAAATGTTGAATCTAGAGTAGGA-A-GT
* * * *
61411009 GTCT-GTATGCATGAAGTCTACCTAACATGTCATA-TCAATGAACAGTATCTATATCATATAAAT
129 GT-TAATATGCATGAAGCCTACCTAACATGTCA-AGTCAATGAACAGTATCCATATAATATAAAT
* *
61411072 ATACAGATACCACTA-CTGAAAGGAG-ACAGAAAAAACACTCAACA
192 ATACAGACAACACTACCT-AAAGGAGAACAGAAAAAACACTCAACA
61411116 AGTGTAAACT
Statistics
Matches: 207, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
250 108 0.52
251 21 0.10
252 76 0.37
253 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (251 bp):
TTTGAGCCAGATCCTAATGAGCTCACAGGATGAGCTCGAAGACCAAGCTCACAGGTCGAGCTCGC
TCTCCTACAAGGTTACACGTGCATAAGACTGTATAAACAAATGTTGAATCTAGAGTAGGAAGTGT
TAATATGCATGAAGCCTACCTAACATGTCAAGTCAATGAACAGTATCCATATAATATAAATATAC
AGACAACACTACCTAAAGGAGAACAGAAAAAACACTCAACATTTGGGAGTTGAGAT
Found at i:61412561 original size:3 final size:3
Alignment explanation
Indices: 61412539--61412585 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
61412529 TTTAATAAAA
* *
61412539 ATT ATT ATA ATA ATT A-T ATT ATT ATT AATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
61412584 AT
1 AT
61412586 AAAAGGGGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:61427471 original size:175 final size:175
Alignment explanation
Indices: 61427180--61427951 Score: 1287
Period size: 175 Copynumber: 4.4 Consensus size: 175
61427170 AAGATGGTGA
**
61427180 ATCTTATCTCCCTGAGATTACAATGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
* *
61427245 AGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
66 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
61427310 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* * *
61427355 ATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTAAGATTAT
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
* * *
61427420 AGTAGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAATTACAGTAGAGTAGATCGCATCAGG
66 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
* *
61427485 TCTTATCTCCCTGATATTACAGTGGAATAGACTGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
*
61427530 ATTTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTT-CCTCGAGATTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCT-GAGATTA
* *
61427594 CAATGGAA-AGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATTA
65 CAGTGGAACA-GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
* * * *
61427658 GGTCTTATCTCTCTGAGATTACAGTGGAACAGACCAAAAAATTACAG
129 GGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* *
61427705 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATTTCCCTGATATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
*
61427770 AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
61427835 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* * *
61427880 ATATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAACCAGTAATCCTATTTCTCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
61427945 AGTGGAA
66 AGTGGAA
61427952 TAGACCGAAG
Statistics
Matches: 553, Mismatches: 40, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
174 4 0.01
175 546 0.99
176 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (175 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
Found at i:61428009 original size:90 final size:90
Alignment explanation
Indices: 61427845--61428010 Score: 210
Period size: 90 Copynumber: 1.8 Consensus size: 90
61427835 TCTTATCTCC
* * *
61427845 CTGAGATTACAGTGGAATAGACCGAAGAATTACAGATATTATCTCCCTGAGATTACAGCGGAGCA
1 CTGAGATTACAGTGGAATAGACCGAAGAATTACAAATATTATCTCCCGGAGATTACAGCGGAACA
* *
61427910 GATTGAAACCAGTAATCCTATTTCT
66 GAGTAAAACCAGTAATCCTATTTCT
** * * *
61427935 CTGAGATTACAGTGGAATAGACCGAAGAATTTTAAATATTA-CTTCCCAGGCGA-TGCAGTGGAA
1 CTGAGATTACAGTGGAATAGACCGAAGAATTACAAATATTATC-TCCC-GGAGATTACAGCGGAA
61427998 CAGAGTAAAACCA
64 CAGAGTAAAACCA
61428011 CATCGGTGAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
89 1 0.02
90 60 0.94
91 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (90 bp):
CTGAGATTACAGTGGAATAGACCGAAGAATTACAAATATTATCTCCCGGAGATTACAGCGGAACA
GAGTAAAACCAGTAATCCTATTTCT
Found at i:61428042 original size:50 final size:50
Alignment explanation
Indices: 61427988--61428612 Score: 417
Period size: 50 Copynumber: 12.5 Consensus size: 50
61427978 TCCCAGGCGA
* *
61427988 TGCAGTGGAACAGAGTAAAACCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
** * * * * * * * * **
61428038 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGG
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* *
61428088 TGCAGTGGAACATATTAAAGCCACATCGATGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* ** * * * * ** * * * **
61428138 TACAGTTAAAAAGATTAAAGCTACAACAGCAAATCTTACTTCCCAGGCGG
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
*
61428188 TGCAGTGGAACATATTAAAGCC-CATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
** * * * * * * * * **
61428237 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGG
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* *
61428287 TGCAGTGGAACAGATTAAAGTCATATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
** * * * * ** * * ** * **
61428337 TGCAGTTAAAAAGATTAAAGCTACAACAGCAAATTTTACTTCCTAGGCGG
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* * * *
61428387 TGCAGTGGAACATATTAAAGTCACATAGGTGAATCTTGCTTCCTCGACAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* ** * * * * * * * * **
61428437 TACAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGG
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
*
61428487 TGCAGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
** * * * * * * * **
61428537 TGCAGTTAAAAAGATTAAA-CCTATAACAGCGAATCTTACTTCCCAGACGG
1 TGCAGTGGAACAGATTAAAGCC-ACATCGGTGAATCTTGCTTCCCCGACAT
*
61428587 TGCCGTGGAACAGATTAAAGCCACAT
1 TGCAGTGGAACAGATTAAAGCCACAT
61428613 TGTAGAACAG
Statistics
Matches: 403, Mismatches: 169, Indels: 6
0.70 0.29 0.01
Matches are distributed among these distances:
49 37 0.09
50 364 0.90
51 2 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (50 bp):
TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
Found at i:61428146 original size:100 final size:100
Alignment explanation
Indices: 61427973--61428612 Score: 1066
Period size: 100 Copynumber: 6.4 Consensus size: 100
61427963 ATTTTAAATA
* * *
61427973 TTACTTCCCAGGCGATGCAGTGGAACAGAGTAAAACCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
61428038 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* *
61428073 TTACTTCCCAGGCGGTGCAGTGGAACATATTAAAGCCACATCGATGAATCTTGCTTCCCCGACAT
1 TTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* *
61428138 TACAGTTAAAAAGATTAAAGCTACAACAGCAAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
*
61428173 TTACTTCCCAGGCGGTGCAGTGGAACATATTAAAGCC-CATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
61428237 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* *
61428272 TTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGTCATATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* *
61428337 TGCAGTTAAAAAGATTAAAGCTACAACAGCAAATT
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * * * *
61428372 TTACTTCCTAGGCGGTGCAGTGGAACATATTAAAGTCACATAGGTGAATCTTGCTTCCTCGACAT
1 TTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
*
61428437 TACAGTTAAAAAGATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
*
61428472 TTACTTCCCAGGCGGTGCAGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* *
61428537 TGCAGTTAAAAAGATTAAACCTATAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* *
61428572 TTACTTCCCAGACGGTGCCGTGGAACAGATTAAAGCCACAT
1 TTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAT
61428613 TGTAGAACAG
Statistics
Matches: 505, Mismatches: 34, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
99 94 0.19
100 411 0.81
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (100 bp):
TTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
Found at i:61432376 original size:18 final size:20
Alignment explanation
Indices: 61432349--61432387 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
61432339 CACGTTCTCC
*
61432349 TTTTGTTA-TTTATTTCTTT
1 TTTTGTTATTTTATTCCTTT
61432368 TTTTG-TATTTTATTCCTTT
1 TTTTGTTATTTTATTCCTTT
61432387 T
1 T
61432388 CTTTCCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.10, C:0.08, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTGTTATTTTATTCCTTT
Found at i:61438110 original size:15 final size:15
Alignment explanation
Indices: 61438090--61438120 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
61438080 AATAGAACGA
61438090 AATTTCCATTCATTT
1 AATTTCCATTCATTT
*
61438105 AATTTCTATTCATTT
1 AATTTCCATTCATTT
61438120 A
1 A
61438121 CGTACCTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTCCATTCATTT
Found at i:61440200 original size:51 final size:50
Alignment explanation
Indices: 61440112--61440416 Score: 234
Period size: 50 Copynumber: 5.8 Consensus size: 50
61440102 GATAATAACA
* * * *
61440112 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGAT-CTCTCATATCGG
** *
61440163 TGTCC-ATGCCATGTCCCAGACATGGTCTTATGGGGGATCTCTCATCTCGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCTCTCATATCGG
* * * **
61440213 TGCCAATTCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTTTTCGGTGCCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA--TCTC---TC-ATATCGG
* * * * *
61440269 TGCCAATGCCATGTCCCAGACATGGTCTTACACGAGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCTCTCATATCGG
* * * * * *
61440319 TGCCAACGCTATGTCCCAGACATGGTTTTTCATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCTCTCAT-A--TC--GG
* * * *
61440374 ATGCCAATTCCATGTCCCAGACATGGTTTTACATGGGACCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCTCT
61440417 TTACCCAAAT
Statistics
Matches: 206, Mismatches: 34, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
49 2 0.01
50 82 0.40
51 32 0.16
52 6 0.03
53 1 0.00
54 3 0.01
55 4 0.02
56 76 0.37
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCTCTCATATCGG
Found at i:61440275 original size:56 final size:52
Alignment explanation
Indices: 61440112--61440416 Score: 282
Period size: 56 Copynumber: 5.8 Consensus size: 52
61440102 GATAATAACA
* * ** *
61440112 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGT-TCTCATAT-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCT-ATCTCCGG
*** *
61440163 TGTCC-ATGCCATGTCCCAGACATGGTCTTATGGGGGATCTCTC-ATCT-CGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTATCTCCGG
* *
61440213 TGCCAATTCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTTTTCGGTGCCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-TATC--T-CCGG
* * *
61440269 TGCCAATGCCATGTCCCAGACATGGTCTTACACGAGACCTCTC-ATCT-TGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTATCTCCGG
* * * * *
61440319 TGCCAACGCTATGTCCCAGACATGGTTTTTCATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-T-ATCTC-CGG
* *
61440374 ATGCCAATTCCATGTCCCAGACATGGTTTTACATGGGACCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
61440417 TTACCCAAAT
Statistics
Matches: 210, Mismatches: 29, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
49 2 0.01
50 80 0.38
51 31 0.15
52 7 0.03
53 4 0.02
54 3 0.01
55 2 0.01
56 81 0.39
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.29
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTATCTCCGG
Found at i:61440311 original size:106 final size:100
Alignment explanation
Indices: 61440112--61440416 Score: 288
Period size: 106 Copynumber: 2.9 Consensus size: 100
61440102 GATAATAACA
* * **
61440112 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGTCCATGCCATGT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGGTGTCCATGCCATGT
*** * *
61440177 CCCAGACATGGTCTTATGGGGGATCTCTCATCTCGG
65 CCCAGACATGGTCTTACACGAGACCTCTCATCTCGG
** * *
61440213 TGCCAATTCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTTTTCGGTGCCGGTGCCAATGC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT----GT-CC-ATGC
*
61440278 CATGTCCCAGACATGGTCTTACACGAGACCTCTCATCTTGG
60 CATGTCCCAGACATGGTCTTACACGAGACCTCTCATCTCGG
* * * *
61440319 TGCCAACGCTATGTCCCAGACATGGTTTTTCATGGGACCTCTCATGATCTCAAGGATG-CCAATT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG-TGTCC-ATG
* * *
61440383 CCATGTCCCAGACATGGTTTTACATGGGACCTCT
59 CCATGTCCCAGACATGGTCTTACACGAGACCTCT
61440417 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
100 10 0.06
101 34 0.20
104 2 0.01
105 2 0.01
106 114 0.68
108 1 0.01
109 2 0.01
111 2 0.01
112 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.29
Consensus pattern (100 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCATGCCATGTC
CCAGACATGGTCTTACACGAGACCTCTCATCTCGG
Found at i:61446530 original size:20 final size:20
Alignment explanation
Indices: 61446489--61446530 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
61446479 AAAGTTGTAG
*
61446489 AAAATAAACAAAAAAAATAA
1 AAAATAAACAAAAAAAAGAA
*
61446509 AAAATAAA-AAAATAGAAGAA
1 AAAATAAACAAAA-AAAAGAA
61446529 AA
1 AA
61446531 TAAATAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.83, C:0.02, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAATAAACAAAAAAAAGAA
Found at i:61452738 original size:18 final size:18
Alignment explanation
Indices: 61452704--61452738 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61452694 TATTGAAAAT
*
61452704 GGAAGTGGAGAGAGAAAG
1 GGAAGTGGAAAGAGAAAG
*
61452722 GGAAGTGGAAAGGGAAA
1 GGAAGTGGAAAGAGAAA
61452739 TACAAAGGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.49, T:0.06
Consensus pattern (18 bp):
GGAAGTGGAAAGAGAAAG
Found at i:61454114 original size:25 final size:24
Alignment explanation
Indices: 61454062--61454122 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
61454052 CTGACCCAGC
*
61454062 CCAGCAGGC-CAGCCCAGCGCTCA
1 CCAGCAGGCTCAGCCCAGCGCCCA
*
61454085 CCAGCAGGCCTCAGCCCAGTGCCCA
1 CCAGCAGG-CTCAGCCCAGCGCCCA
*
61454110 GCAGCAGGCTCAG
1 CCAGCAGGCTCAG
61454123 AAGCACCCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.24
24 6 0.18
25 19 0.58
ACGTcount: A:0.21, C:0.44, G:0.28, T:0.07
Consensus pattern (24 bp):
CCAGCAGGCTCAGCCCAGCGCCCA
Found at i:61454182 original size:12 final size:11
Alignment explanation
Indices: 61454161--61454190 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
61454151 CCAACTGCAG
61454161 AAAAAAAAGAA
1 AAAAAAAAGAA
61454172 AAAAGAAAAGAA
1 AAAA-AAAAGAA
61454184 AAAAAAA
1 AAAAAAA
61454191 GCTCGAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:61458569 original size:20 final size:20
Alignment explanation
Indices: 61458533--61458570 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61458523 TTATTTTATT
*
61458533 TTTATTTTTATTTTTAAACC
1 TTTATTTTTATTATTAAACC
61458553 TTTA-TTTTATCTATTAAA
1 TTTATTTTTAT-TATTAAA
61458571 AAATATAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATTTTTATTATTAAACC
Found at i:61468142 original size:23 final size:23
Alignment explanation
Indices: 61468123--61468188 Score: 132
Period size: 23 Copynumber: 2.9 Consensus size: 23
61468113 ACTCTGATAT
61468123 GTAGCCGAAGCTACCACTGAAAC
1 GTAGCCGAAGCTACCACTGAAAC
61468146 GTAGCCGAAGCTACCACTGAAAC
1 GTAGCCGAAGCTACCACTGAAAC
61468169 GTAGCCGAAGCTACCACTGA
1 GTAGCCGAAGCTACCACTGA
61468189 TCAATAACAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (23 bp):
GTAGCCGAAGCTACCACTGAAAC
Found at i:61475229 original size:35 final size:35
Alignment explanation
Indices: 61475190--61475267 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
61475180 TAATATTTCG
*
61475190 ACAGCCTCGTAATCTAGAGAGCCCAACTCAAATTA
1 ACAGCCTCGCAATCTAGAGAGCCCAACTCAAATTA
61475225 ACAGCCTCGCAATCTAGAGAGCCCAACTCAAATTA
1 ACAGCCTCGCAATCTAGAGAGCCCAACTCAAATTA
61475260 ACAGCCTC
1 ACAGCCTC
61475268 AACCACGTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.36, C:0.32, G:0.14, T:0.18
Consensus pattern (35 bp):
ACAGCCTCGCAATCTAGAGAGCCCAACTCAAATTA
Found at i:61476731 original size:3 final size:3
Alignment explanation
Indices: 61476669--61476713 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
61476659 ACTAATTAGG
* *
61476669 TTA TTA TTA TTA CTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
61476714 GTAGTAGTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:61476849 original size:14 final size:14
Alignment explanation
Indices: 61476817--61476851 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
61476807 ATTATTATTG
* *
61476817 TATAATTACTTATC
1 TATATTTACTTATA
61476831 TATATTTACTTATA
1 TATATTTACTTATA
61476845 TATATTT
1 TATATTT
61476852 TTTATACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATTTACTTATA
Found at i:61488964 original size:24 final size:24
Alignment explanation
Indices: 61488909--61488970 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
61488899 TTTTATGTCC
*
61488909 AAAAATTACAGTGGATTGAAATTT
1 AAAAATTACAGTGGATTGAAACTT
* *
61488933 AAAAATTACAGTGGATTGGACCTT
1 AAAAATTACAGTGGATTGAAACTT
* *
61488957 GAAGATTACAGTGG
1 AAAAATTACAGTGG
61488971 GGGCAATCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (24 bp):
AAAAATTACAGTGGATTGAAACTT
Found at i:61489341 original size:45 final size:45
Alignment explanation
Indices: 61489284--61489774 Score: 660
Period size: 45 Copynumber: 10.9 Consensus size: 45
61489274 GAAGAATATT
* *
61489284 GCAGATCTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAATATA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* *
61489329 GCAGATCTTGTCTTCCTATATAGGCAGCGAAGTAGATCGAAGATA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* * * *
61489374 GCAAATCTTGTCTTCCTGTATTGGCAGTGATGTAGATCGAATATA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* * *
61489419 GTAGATCTTGTCTTCTTGTATTGGCAGCGAAATAGATCGAAGATA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* *
61489464 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTATATCAAAGATA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* *
61489509 GCAGGTCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCGAAGATA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* * * *
61489554 ACA-AGTCTTGTCTTCCTATATTGGCAGCAAAGTAGACCGAAGATA
1 GCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* * *
61489599 GCAAATCTTGTCTTCCTGCATTGGCAGAGAAGTAGATCGAAGATA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* *
61489644 GCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCAAAGATA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* * * * * *
61489689 ACAGGTTTTGTCTTCTTGTATTGACAACGAAGTAGATCGAAGATA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
* * * *
61489734 GCAGATCTTGTCTTCCTATACTGGCAGTGAAGCAGATCGAA
1 GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAA
61489775 AACACCAACC
Statistics
Matches: 385, Mismatches: 59, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
45 384 1.00
46 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (45 bp):
GCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATA
Found at i:61489838 original size:88 final size:88
Alignment explanation
Indices: 61489719--61489916 Score: 290
Period size: 88 Copynumber: 2.2 Consensus size: 88
61489709 TTGACAACGA
* * * *
61489719 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATACTGGCAGTGAAGCAGATCGAAAACACCA-A
1 AGTAGGTCGAAGATTGTAGATCTTGTCTTCCTATACTGGCAGTGAAGCAAATCGAAAACACCAGA
* *
61489783 CCTTATCTCCCTGAGCAGTAGTGG
66 CC-TATCTCCCTGAGCAGCAATGG
* * *
61489807 AGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAAATCGAAAACACCAGT
1 AGTAGGTCGAAGATTGTAGATCTTGTCTTCCTATACTGGCAGTGAAGCAAATCGAAAACACCAGA
61489872 CCTATCTCCCTGAGCAGCAATGG
66 CCTATCTCCCTGAGCAGCAATGG
*
61489895 AGTAGGTCGAAGATTGTGGATC
1 AGTAGGTCGAAGATTGTAGATC
61489917 CTGCCTCCCT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 96 0.98
89 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (88 bp):
AGTAGGTCGAAGATTGTAGATCTTGTCTTCCTATACTGGCAGTGAAGCAAATCGAAAACACCAGA
CCTATCTCCCTGAGCAGCAATGG
Found at i:61490201 original size:51 final size:51
Alignment explanation
Indices: 61490059--61490201 Score: 171
Period size: 51 Copynumber: 2.8 Consensus size: 51
61490049 AAGCGAAACG
* * *
61490059 GATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTGGCGTTACAGTGGAACA
1 GATTAAAGCTGAAGGCAGCGAATCTTATCTCCTTGGCATTACAGTGGAACA
* * * * * * *
61490110 GATTAAAGCTAAAAGTAGCGAATCTTGTTTTCC-TGACATTACAGTGGAGCA
1 GATTAAAGCTGAAGGCAGCGAATCTT-ATCTCCTTGGCATTACAGTGGAACA
*
61490161 GATTAAAGCTGAAGGCAGCGAATCTTATGTCCTTGGCATTA
1 GATTAAAGCTGAAGGCAGCGAATCTTATCTCCTTGGCATTA
61490202 AAGTTGAAGA
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
50 4 0.05
51 67 0.91
52 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (51 bp):
GATTAAAGCTGAAGGCAGCGAATCTTATCTCCTTGGCATTACAGTGGAACA
Found at i:61490319 original size:45 final size:44
Alignment explanation
Indices: 61490260--61490519 Score: 174
Period size: 45 Copynumber: 5.9 Consensus size: 44
61490250 GAAGATGGCA
* * *
61490260 AATCATATCCCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
* * * *
61490304 AAGTCTTATCTCCCTGAAGTTACAGAGGAGCAGACT-GA-CTAAAACC
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT--AA-C
* * * *
61490350 AATCTTATTTCCTTGAAGTTGCAGTGGAACAGATTGAAGCTATA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-AC
* * * * * *
61490394 AAT-TACAGACTCTCTGAAGTTGCAATAGAGCAGGTTGAAA--TAAC
1 AATCT-TA-TCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTAAC
* * * **
61490438 AAAT-TTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGCTATT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
* *
61490482 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
61490520 ATTATGAAAT
Statistics
Matches: 161, Mismatches: 40, Indels: 30
0.70 0.17 0.13
Matches are distributed among these distances:
42 2 0.01
43 27 0.17
44 41 0.25
45 82 0.51
46 7 0.04
47 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAAC
Found at i:61492093 original size:3 final size:3
Alignment explanation
Indices: 61492075--61492170 Score: 70
Period size: 3 Copynumber: 31.7 Consensus size: 3
61492065 ATCCTTTTTC
* * * *
61492075 TAT TGT TAT T-T TAT TAT TAT TA- AACT AAT TAGT TTAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T T-AT TAT TAT TAT
* * * * *
61492121 TAT TAT CAT CAT CAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61492169 TA
1 TA
61492171 CATTTCCATT
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
2 3 0.04
3 66 0.87
4 6 0.08
5 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:61492499 original size:18 final size:19
Alignment explanation
Indices: 61492460--61492549 Score: 57
Period size: 18 Copynumber: 5.0 Consensus size: 19
61492450 ATATATATAC
*
61492460 ATACTTATATATATTTTTT
1 ATACTTATATATATTTTAT
61492479 ATACTT-TATA-ATTTTAAT
1 ATACTTATATATATTTT-AT
* * ** *
61492497 ATACATATATACA-TACAC
1 ATACTTATATATATTTTAT
*
61492515 ATACTTATATATCTTTT-T
1 ATACTTATATATATTTTAT
*
61492533 ATA-TTTTATA-ATTTTAT
1 ATACTTATATATATTTTAT
61492550 TCATTTTCTT
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
16 4 0.08
17 12 0.23
18 24 0.45
19 12 0.23
20 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (19 bp):
ATACTTATATATATTTTAT
Found at i:61495138 original size:14 final size:16
Alignment explanation
Indices: 61495098--61495141 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
61495088 TTTTCAACAT
*
61495098 AAATTAAACTGAATTCA
1 AAATTAAA-TAAATTCA
61495115 AAATTAAATAAATT-A
1 AAATTAAATAAATTCA
61495130 AAA-TAAATAAAT
1 AAATTAAATAAAT
61495142 ATGAGTTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 5 0.19
17 8 0.31
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (16 bp):
AAATTAAATAAATTCA
Found at i:61496463 original size:27 final size:30
Alignment explanation
Indices: 61496424--61496482 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
61496414 ATTTCTAACT
*
61496424 TATACATGCA-TT-TTTATATAGTATATATA
1 TATACAT-CATTTCTTTATATAATATATATA
61496453 TATACAT-ATTTCTTTATATAATATATATA
1 TATACATCATTTCTTTATATAATATATATA
61496482 T
1 T
61496483 GTGTTCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 1 0.04
28 2 0.07
29 24 0.89
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (30 bp):
TATACATCATTTCTTTATATAATATATATA
Found at i:61496825 original size:28 final size:26
Alignment explanation
Indices: 61496778--61496838 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
61496768 TTTACGTACA
*
61496778 TATATATACCTATATACATACATTTTTT
1 TATATATACATATATACAT--ATTTTTT
* * *
61496806 TGTATATACATATTTTCATATTTTTT
1 TATATATACATATATACATATTTTTT
61496832 TATATAT
1 TATATAT
61496839 TTAACAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 13 0.46
28 15 0.54
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.56
Consensus pattern (26 bp):
TATATATACATATATACATATTTTTT
Found at i:61504299 original size:27 final size:28
Alignment explanation
Indices: 61504268--61504321 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
61504258 ATTTTTTGTA
*
61504268 ATTTTTATAATTAAAT-TTAAATAAAAT
1 ATTTTAATAATTAAATATTAAATAAAAT
* *
61504295 ATTTTAATCATTAAATATTAATTAAAA
1 ATTTTAATAATTAAATATTAAATAAAA
61504322 ATATAAGCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTTAATAATTAAATATTAAATAAAAT
Found at i:61514470 original size:18 final size:18
Alignment explanation
Indices: 61514447--61514482 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
61514437 TTTTTTATTT
61514447 GTATAATGATAAATTTAA
1 GTATAATGATAAATTTAA
61514465 GTATAATGATAAATTTAA
1 GTATAATGATAAATTTAA
61514483 CTCTCAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATAATGATAAATTTAA
Found at i:61518205 original size:26 final size:26
Alignment explanation
Indices: 61518166--61518215 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
61518156 TCTTCATTGT
61518166 TTTTGAAAACTGCTATGGAAAAATGC
1 TTTTGAAAACTGCTATGGAAAAATGC
* * * *
61518192 TTTTGAGAAGTGCTTTTGAAAAAT
1 TTTTGAAAACTGCTATGGAAAAAT
61518216 TCGAGTGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (26 bp):
TTTTGAAAACTGCTATGGAAAAATGC
Found at i:61525732 original size:9 final size:9
Alignment explanation
Indices: 61525715--61525751 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
61525705 TATAGTTTGA
*
61525715 TATTAGAAT
1 TATTCGAAT
61525724 TATTCGAAT
1 TATTCGAAT
*
61525733 TATTCGAGT
1 TATTCGAAT
61525742 TATTCGAAT
1 TATTCGAAT
61525751 T
1 T
61525752 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:61528857 original size:20 final size:20
Alignment explanation
Indices: 61528797--61528857 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
61528787 CCGAATTATA
*
61528797 TATTAAATATATATGTTTATT
1 TATTAAATATATATATTT-TT
* *
61528818 T-TT-AATCAAATATACTTTT
1 TATTAAAT-ATATATATTTTT
61528837 TATTAAATATATATATTTTT
1 TATTAAATATATATATTTTT
61528857 T
1 T
61528858 GGACTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 6 0.19
20 22 0.69
21 4 0.12
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTAAATATATATATTTTT
Found at i:61542339 original size:18 final size:18
Alignment explanation
Indices: 61542293--61542340 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
61542283 TTAATTATTT
*
61542293 TTTAAAATTTAAAAAAAA
1 TTTAAAAATTAAAAAAAA
** * *
61542311 TCCAAATATTAAAAATAA
1 TTTAAAAATTAAAAAAAA
61542329 TTTAAAAATTAA
1 TTTAAAAATTAA
61542341 TTGTTGATGT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTAAAAATTAAAAAAAA
Found at i:61543486 original size:38 final size:38
Alignment explanation
Indices: 61543407--61543483 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 38
61543397 TAATCTAACC
* *
61543407 TAAAATATTTATTATATTTATTTGTGTTTTTAATATTA
1 TAAAATATTTATTATATTTATTAGTGCTTTTAATATTA
61543445 TAAAATATTTATTATATTTATGATAGTGCTTTTCAATAT
1 TAAAATATTTATTATATTTAT--TAGTGCTTTT-AATAT
61543484 AAATGATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 21 0.62
40 8 0.24
41 5 0.15
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (38 bp):
TAAAATATTTATTATATTTATTAGTGCTTTTAATATTA
Found at i:61557889 original size:34 final size:34
Alignment explanation
Indices: 61557833--61557898 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
61557823 TACTGTATAT
* *
61557833 ATGAACAGTACCATCTACGTAAATAGTATCGTGG
1 ATGAACAATACCATATACGTAAATAGTATCGTGG
* *
61557867 ATGAACAATACCGTATATGTAAATAGTATCGT
1 ATGAACAATACCATATACGTAAATAGTATCGT
61557899 AAATAGTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (34 bp):
ATGAACAATACCATATACGTAAATAGTATCGTGG
Found at i:61559833 original size:20 final size:20
Alignment explanation
Indices: 61559796--61559841 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
61559786 AATGGGCATG
* *
61559796 AATTATTATTTAAATAATGA
1 AATTATTATCTAAATAATCA
**
61559816 AATTATTATCTACTTAATCA
1 AATTATTATCTAAATAATCA
61559836 AATTAT
1 AATTAT
61559842 AAAAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTATTATCTAAATAATCA
Found at i:61561569 original size:28 final size:29
Alignment explanation
Indices: 61561537--61561592 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
61561527 TGATGCAATT
61561537 TGCAATGTAT-ACATGA-ATTTTGATTTTG
1 TGCAAT-TATAACATGATATTTTGATTTTG
*
61561565 TGCAATTTTGAACATGATATTTTGATTT
1 TGCAATTAT-AACATGATATTTTGATTT
61561593 GATTCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 6 0.25
29 6 0.25
30 10 0.42
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (29 bp):
TGCAATTATAACATGATATTTTGATTTTG
Found at i:61561593 original size:29 final size:30
Alignment explanation
Indices: 61561547--61561603 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
61561537 TGCAATGTAT
61561547 ACATGAATTTTGATTTTG-TGCAATTTTGA
1 ACATGAATTTTGATTTTGATGCAATTTTGA
*
61561576 ACATGATATTTTGA-TTTGATTCAATTTT
1 ACATGA-ATTTTGATTTTGATGCAATTTT
61561604 TTTTAGCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (30 bp):
ACATGAATTTTGATTTTGATGCAATTTTGA
Found at i:61561763 original size:31 final size:33
Alignment explanation
Indices: 61561728--61561789 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
61561718 ATGTGTAGAA
*
61561728 TTGAATCAAAAT-TAAAGTTT-TATGTATATTT
1 TTGAATCAAAATCAAAAGTTTATATGTATATTT
*
61561759 TTGAATTAAAATCAAAAGTTTAATATGTATA
1 TTGAATCAAAATCAAAAGTTT-ATATGTATA
61561790 ATTGCACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 11 0.42
32 7 0.27
34 8 0.31
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (33 bp):
TTGAATCAAAATCAAAAGTTTATATGTATATTT
Found at i:61561942 original size:54 final size:54
Alignment explanation
Indices: 61561884--61561996 Score: 226
Period size: 54 Copynumber: 2.1 Consensus size: 54
61561874 CACAGAATCT
61561884 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
61561938 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
61561992 TTCAA
1 TTCAA
61561997 CTTGGAATAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.18
Consensus pattern (54 bp):
TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
Found at i:61564990 original size:16 final size:16
Alignment explanation
Indices: 61564957--61564990 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61564947 AGTATATGTT
* *
61564957 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
61564973 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
61564989 AA
1 AA
61564991 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:61567816 original size:21 final size:21
Alignment explanation
Indices: 61567790--61567830 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61567780 AGACGAGCAA
* *
61567790 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
61567811 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
61567831 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:61569768 original size:16 final size:16
Alignment explanation
Indices: 61569735--61569768 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61569725 GGAGATTGTT
* *
61569735 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
61569751 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
61569767 AA
1 AA
61569769 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:61573753 original size:31 final size:31
Alignment explanation
Indices: 61573712--61573775 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
61573702 TTCTCGCAAT
*
61573712 GTAAACGTTCTTACAATATTACTTATCTTCA
1 GTAAACGTTCTTACAATACTACTTATCTTCA
*
61573743 GTAAATGTTCTTACAATACTACTTATCTTCA
1 GTAAACGTTCTTACAATACTACTTATCTTCA
61573774 GT
1 GT
61573776 TTGAACTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (31 bp):
GTAAACGTTCTTACAATACTACTTATCTTCA
Found at i:61573858 original size:15 final size:15
Alignment explanation
Indices: 61573834--61573865 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
61573824 TATGCATGCA
*
61573834 AAATATAAAAGACAT
1 AAATACAAAAGACAT
61573849 AAATACAAAAGACAT
1 AAATACAAAAGACAT
61573864 AA
1 AA
61573866 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:61583581 original size:3 final size:3
Alignment explanation
Indices: 61583573--61583631 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
61583563 AAGAAACCAA
61583573 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61583621 AAT AAT AAT AA
1 AAT AAT AAT AA
61583632 AGGGGAAGCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:61593577 original size:27 final size:28
Alignment explanation
Indices: 61593536--61593605 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
61593526 TTTGTAATAT
*
61593536 ATATTGTCAAATGAGCATA-GTCTAGGCG
1 ATATTGGC-AATGAGCATAGGTCTAGGCG
* *
61593564 ATATTGGCAATGAGGATAGGTGTAGGCG
1 ATATTGGCAATGAGCATAGGTCTAGGCG
61593592 ATATTGGCAATGAG
1 ATATTGGCAATGAG
61593606 TGCATTGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.27
Consensus pattern (28 bp):
ATATTGGCAATGAGCATAGGTCTAGGCG
Found at i:61606435 original size:14 final size:12
Alignment explanation
Indices: 61606407--61606439 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
61606397 TGTGAAACCC
61606407 ATATATTTTGGT
1 ATATATTTTGGT
*
61606419 ATATATTTTGGG
1 ATATATTTTGGT
61606431 ATATATTTT
1 ATATATTTT
61606440 AAAGTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (12 bp):
ATATATTTTGGT
Found at i:61606554 original size:41 final size:41
Alignment explanation
Indices: 61606503--61606582 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
61606493 ATATTTTATT
61606503 TTATCATTTAGTAGTTTATTAGAATAAGGAAATTATTTTCC
1 TTATCATTTAGTAGTTTATTAGAATAAGGAAATTATTTTCC
* *
61606544 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTT
1 TTATCATTTAGTAGTTTATTAGAATAAGGAAATTATTTT
61606583 TCTAATTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (41 bp):
TTATCATTTAGTAGTTTATTAGAATAAGGAAATTATTTTCC
Found at i:61610294 original size:24 final size:24
Alignment explanation
Indices: 61610266--61610314 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
61610256 TTCCCAATTG
61610266 AGTTATAACTCTTTTCTCTATTTA
1 AGTTATAACTCTTTTCTCTATTTA
61610290 AGTTATAACTCTTTTCTCTATTTA
1 AGTTATAACTCTTTTCTCTATTTA
61610314 A
1 A
61610315 ATTCAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.53
Consensus pattern (24 bp):
AGTTATAACTCTTTTCTCTATTTA
Found at i:61625735 original size:15 final size:16
Alignment explanation
Indices: 61625705--61625737 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61625695 AGATGACTAT
*
61625705 ATAAAAAATTTAATAA
1 ATAAAAAATGTAATAA
61625721 ATAAAAAATGT-ATAA
1 ATAAAAAATGTAATAA
61625736 AT
1 AT
61625738 TTATTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAAAAAATGTAATAA
Found at i:61634715 original size:20 final size:20
Alignment explanation
Indices: 61634674--61634715 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
61634664 ATAAATTTAA
* *
61634674 TTATCAATGTTTGCATTTTT
1 TTATCAATGTTGGCATTATT
61634694 TTATCAAT-TTGGCAATTATT
1 TTATCAATGTTGGC-ATTATT
61634714 TT
1 TT
61634716 TATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (20 bp):
TTATCAATGTTGGCATTATT
Found at i:61635154 original size:20 final size:19
Alignment explanation
Indices: 61635129--61635186 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
61635119 TTTAAAAAAT
*
61635129 ATTTTTAAAAATTGTTATAA
1 ATTTTTAAAAATTATTA-AA
61635149 ATTTTTAAAACATTATTAAA
1 ATTTTTAAAA-ATTATTAAA
*
61635169 ATTTATAAAAA-TATTAAA
1 ATTTTTAAAAATTATTAAA
61635187 TAAAGTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.20
19 1 0.03
20 21 0.60
21 6 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTTTTAAAAATTATTAAA
Found at i:61635634 original size:11 final size:11
Alignment explanation
Indices: 61635618--61635657 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
61635608 AAAAATAAAC
61635618 ATTTTTTTTAA
1 ATTTTTTTTAA
61635629 A-TTTTTTTAA
1 ATTTTTTTTAA
*
61635639 ATTTTTTTT-T
1 ATTTTTTTTAA
61635649 ATTTTTTTT
1 ATTTTTTTT
61635658 CTTGACGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
ATTTTTTTTAA
Found at i:61638045 original size:4 final size:4
Alignment explanation
Indices: 61638030--61638072 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
61638020 TAAAAGCGGC
* * *
61638030 TGTA TTTA TGTA TGTA TGTA TGTA TGTG TGTG TGTA TTGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -TGTA TG
61638073 CTGAGTTGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (4 bp):
TGTA
Found at i:61638204 original size:4 final size:4
Alignment explanation
Indices: 61638195--61638265 Score: 97
Period size: 4 Copynumber: 17.8 Consensus size: 4
61638185 TAAAAGCAGC
* *
61638195 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGCA TGTA TGTA TGCA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* **
61638243 TATA TGTA TGTA CATA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGT
61638266 GTATGCGTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.27, C:0.04, G:0.23, T:0.46
Consensus pattern (4 bp):
TGTA
Found at i:61643034 original size:14 final size:14
Alignment explanation
Indices: 61643015--61643044 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
61643005 AGAAGAGACG
61643015 TGCTAAAAGTAGCA
1 TGCTAAAAGTAGCA
61643029 TGCTAAAAGTAGCA
1 TGCTAAAAGTAGCA
61643043 TG
1 TG
61643045 GAGGACTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (14 bp):
TGCTAAAAGTAGCA
Found at i:61644988 original size:42 final size:42
Alignment explanation
Indices: 61644836--61645143 Score: 146
Period size: 43 Copynumber: 7.3 Consensus size: 42
61644826 CTGGCATAGC
* ** * *
61644836 AGTGCATCATTAGAT-AACCGAAAG-AAAGATACTGGCACAAA
1 AGTGCATCATCAGATAAACC-AAAGCAATCATACTGACACATA
* * * * *
61644877 TAGTGCATCATCAGACAATCTGAAA-CAGTTATACTGGCACACAT-
1 -AGTGCATCATCAGATAAAC-CAAAGCAATCATACT-G-ACACATA
* ** * * * *
61644921 AGTGCATGATTGGATAAAACGAAGCAATCATATTGGCACATA
1 AGTGCATCATCAGATAAACCAAAGCAATCATACTGACACATA
**
61644963 AGTGCATCATC-GAATTTACCAAAGCAAAT-ATACTGACACATA
1 AGTGCATCATCAG-ATAAACCAAAGC-AATCATACTGACACATA
* *
61645005 AGGTACATCATCAGATAAACCGAAGCAATCATACTGACACATA
1 A-GTGCATCATCAGATAAACCAAAGCAATCATACTGACACATA
* * ** * * * * *
61645048 AGTGTATAATTGGA-AGTACCAAAGTAAAT-ATATTAACACACGA
1 AGTGCATCATCAGATA-AACCAAAG-CAATCATACTGACACA-TA
* ** **
61645091 GGTGCATCATTGGATAAACTGAAGCAATCATACTGACACATA
1 AGTGCATCATCAGATAAACCAAAGCAATCATACTGACACATA
61645133 AGTGCATCATC
1 AGTGCATCATC
61645144 TAATAGACCG
Statistics
Matches: 193, Mismatches: 56, Indels: 34
0.68 0.20 0.12
Matches are distributed among these distances:
41 7 0.04
42 84 0.44
43 95 0.49
44 3 0.02
45 4 0.02
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (42 bp):
AGTGCATCATCAGATAAACCAAAGCAATCATACTGACACATA
Found at i:61645130 original size:43 final size:42
Alignment explanation
Indices: 61644915--61645142 Score: 185
Period size: 42 Copynumber: 5.4 Consensus size: 42
61644905 TTATACTGGC
* * *
61644915 ACACAT-AGTGCATGATTGGATAAAACGAAGCAATCATATTG
1 ACACATAAGTGCATCATTGGATAAACCGAAGCAATCATACTG
* * * ** *
61644956 GCACATAAGTGCATCATCGAATTTACCAAAGCAAAT-ATACTG
1 ACACATAAGTGCATCATTGGATAAACCGAAGC-AATCATACTG
* **
61644998 ACACATAAGGTACATCATCAGATAAACCGAAGCAATCATACTG
1 ACACATAA-GTGCATCATTGGATAAACCGAAGCAATCATACTG
* * * * * * *
61645041 ACACATAAGTGTATAATTGGA-AGTACCAAAGTAAAT-ATATTA
1 ACACATAAGTGCATCATTGGATA-AACCGAAG-CAATCATACTG
* * *
61645083 ACACACGAGGTGCATCATTGGATAAACTGAAGCAATCATACTG
1 ACACA-TAAGTGCATCATTGGATAAACCGAAGCAATCATACTG
61645126 ACACATAAGTGCATCAT
1 ACACATAAGTGCATCAT
61645143 CTAATAGACC
Statistics
Matches: 140, Mismatches: 38, Indels: 17
0.72 0.19 0.09
Matches are distributed among these distances:
41 6 0.04
42 69 0.49
43 64 0.46
44 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.23
Consensus pattern (42 bp):
ACACATAAGTGCATCATTGGATAAACCGAAGCAATCATACTG
Found at i:61645158 original size:85 final size:84
Alignment explanation
Indices: 61644914--61645158 Score: 253
Period size: 85 Copynumber: 2.9 Consensus size: 84
61644904 GTTATACTGG
* * * *
61644914 CACACATA-GTGCATGATTGGATAAAACGAAGCAATCATATTGGCACATAAGTGCATCATCGAAT
1 CACACA-AGGTGCATCATTGGAT-AAACGAAGCAATCATACTGACACATAAGTGCATCATCTAAT
** * *
61644978 TTACCAAAGCAAATATACTGA
64 AGACCAAAGTAAATATACTAA
* * ** * * *
61644999 CACATAAGGTACATCATCAGATAAACCGAAGCAATCATACTGACACATAAGTGTATAAT-TGGA-
1 CACACAAGGTGCATCATTGGATAAA-CGAAGCAATCATACTGACACATAAGTGCATCATCT-AAT
*
61645062 AGTACCAAAGTAAATATATTAA
64 AG-ACCAAAGTAAATATACTAA
*
61645084 CACACGAGGTGCATCATTGGATAAACTGAAGCAATCATACTGACACATAAGTGCATCATCTAATA
1 CACACAAGGTGCATCATTGGATAAAC-GAAGCAATCATACTGACACATAAGTGCATCATCTAATA
*
61645149 GACCGAAGTA
65 GACCAAAGTA
61645159 TAACCCGTAC
Statistics
Matches: 128, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
84 5 0.04
85 120 0.94
86 3 0.02
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (84 bp):
CACACAAGGTGCATCATTGGATAAACGAAGCAATCATACTGACACATAAGTGCATCATCTAATAG
ACCAAAGTAAATATACTAA
Found at i:61651165 original size:28 final size:25
Alignment explanation
Indices: 61651104--61651166 Score: 63
Period size: 30 Copynumber: 2.3 Consensus size: 25
61651094 ATAGTTGTGT
*
61651104 TTTTATTACTTTCATTTATATACTA
1 TTTTATTACTTTCACTTATATACTA
61651129 TAGTATTATTCCACTTTCACTTATATAGCTA
1 T--T-TTATT--ACTTTCACTTATATA-CTA
61651160 TTTTATT
1 TTTTATT
61651167 TCATTTTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
25 1 0.03
27 1 0.03
28 10 0.32
29 1 0.03
30 14 0.45
31 4 0.13
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTTATTACTTTCACTTATATACTA
Found at i:61653045 original size:20 final size:21
Alignment explanation
Indices: 61653022--61653072 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
61653012 CTCATATTAG
*
61653022 ATATTAACATAACATA-TAAA
1 ATATTAACATAACAAATTAAA
* *
61653042 ATATAAACCTAACAAATTAAA
1 ATATTAACATAACAAATTAAA
61653063 ATATT-ACATA
1 ATATTAACATA
61653073 TATTTAGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (21 bp):
ATATTAACATAACAAATTAAA
Found at i:61653588 original size:21 final size:21
Alignment explanation
Indices: 61653541--61653588 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
61653531 AATTTGTTAG
61653541 ATTTT-TATATATATTTTTCA
1 ATTTTATATATATATTTTTCA
* *
61653561 ATATTATATATATTTTTTTTC-
1 ATTTTATATATA-TATTTTTCA
61653582 ATTTTAT
1 ATTTTAT
61653589 CTCTGTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 7 0.30
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTATATATATATTTTTCA
Found at i:61654369 original size:23 final size:23
Alignment explanation
Indices: 61654341--61654387 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
61654331 AGAGGAAAGT
61654341 TTAAATAACATAAAAGAAAAAAA
1 TTAAATAACATAAAAGAAAAAAA
* * *
61654364 TTAAATTACTTAAAAGGAAAAAA
1 TTAAATAACATAAAAGAAAAAAA
61654387 T
1 T
61654388 ATAGGGATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (23 bp):
TTAAATAACATAAAAGAAAAAAA
Found at i:61654768 original size:20 final size:20
Alignment explanation
Indices: 61654743--61654782 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61654733 CGTAAAATGA
*
61654743 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
61654763 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
61654783 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:61654772 original size:34 final size:35
Alignment explanation
Indices: 61654728--61654794 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
61654718 CAGTAAAATA
* *
61654728 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
61654762 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
61654795 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:61655514 original size:111 final size:111
Alignment explanation
Indices: 61655320--61655541 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
61655310 TGATGAAGTA
61655320 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
1 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
61655385 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
61655431 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
1 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
61655496 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
61655542 CATGGTATTG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (111 bp):
TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
Found at i:61658935 original size:57 final size:55
Alignment explanation
Indices: 61658870--61658991 Score: 138
Period size: 57 Copynumber: 2.1 Consensus size: 55
61658860 GATAAAATTG
* * *
61658870 AATAGTTGGATAATCATTTTGTAAC-TCATATTTAGGTGACCAAAATAGAAATTTACT
1 AATAGTTGGATAAT-A--TTGTAACTTCATAGTTAGATGACCAAAAAAGAAATTTACT
* * *
61658927 AATAGTTGGATGATATTGTAACTTTTCATAGTTAGATGACTAAAAAATAAATTTACT
1 AATAGTTGGATAATATTGTAAC--TTCATAGTTAGATGACCAAAAAAGAAATTTACT
61658984 AATAGTTG
1 AATAGTTG
61658992 ACTGCCTACC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
54 7 0.12
56 1 0.02
57 48 0.86
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (55 bp):
AATAGTTGGATAATATTGTAACTTCATAGTTAGATGACCAAAAAAGAAATTTACT
Found at i:61659270 original size:2 final size:2
Alignment explanation
Indices: 61659263--61659305 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
61659253 GATTGTTTAA
61659263 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
61659305 T
1 T
61659306 TTTCGGTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:61660160 original size:15 final size:15
Alignment explanation
Indices: 61660142--61660193 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
61660132 AGAGGAAGAG
*
61660142 GAGGAAGTGGAAGTT
1 GAGGAAGTGGAAGTA
* * *
61660157 GAGGAAGAGGTAGAA
1 GAGGAAGTGGAAGTA
61660172 GAGGAAGTGGAAGTA
1 GAGGAAGTGGAAGTA
*
61660187 GAAGAAG
1 GAGGAAG
61660194 AAGAAGAAGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.46, T:0.12
Consensus pattern (15 bp):
GAGGAAGTGGAAGTA
Found at i:61660165 original size:24 final size:24
Alignment explanation
Indices: 61660133--61660179 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
61660123 TGAAGAAATA
*
61660133 GAGGAAGAGG-AGGAAGTGGAAGTT
1 GAGGAAGAGGTA-GAAGAGGAAGTT
61660157 GAGGAAGAGGTAGAAGAGGAAGT
1 GAGGAAGAGGTAGAAGAGGAAGT
61660180 GGAAGTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (24 bp):
GAGGAAGAGGTAGAAGAGGAAGTT
Found at i:61660176 original size:30 final size:30
Alignment explanation
Indices: 61660132--61660206 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
61660122 ATGAAGAAAT
* * *
61660132 AGAGGAAGAGGAGGAAGTGGAAGTTGAGGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA
*
61660162 AGAGGTAGAAGAGGAAGTGGAAGTAGAAGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA
*
61660192 AGAAGAAGAAGAGGA
1 AGAGGAAGAAGAGGA
61660207 CGAGGATGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.45, T:0.08
Consensus pattern (30 bp):
AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA
Found at i:61669939 original size:2 final size:2
Alignment explanation
Indices: 61669932--61669957 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61669922 TCATTTTCAT
61669932 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
61669958 AAAGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:61674413 original size:17 final size:17
Alignment explanation
Indices: 61674385--61674426 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
61674375 TAATAAATAA
*
61674385 AATTATCCAACCCAACTC
1 AATTA-CCAACCCAACCC
*
61674403 AATTACCAACCTAACCC
1 AATTACCAACCCAACCC
61674420 AATTACC
1 AATTACC
61674427 CAATCCAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.21
Consensus pattern (17 bp):
AATTACCAACCCAACCC
Found at i:61674463 original size:39 final size:39
Alignment explanation
Indices: 61674416--61674512 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
61674406 TACCAACCTA
* *
61674416 ACCCAATTACCCAATCCAGTAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
* *
61674455 ACCTAATTATCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
61674494 ACCCAATTA-CCAACCCAAT
1 ACCCAATTACCCAACCCAAT
61674513 TAATTTCAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 10 0.19
39 43 0.81
ACGTcount: A:0.46, C:0.30, G:0.03, T:0.21
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:61674543 original size:17 final size:17
Alignment explanation
Indices: 61674523--61674585 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
61674513 TAATTTCAAG
61674523 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
61674540 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
61674558 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
61674577 AATTATGTA
1 AATTATGTA
61674586 GTTATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:61674566 original size:37 final size:37
Alignment explanation
Indices: 61674520--61674594 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
61674510 AATTAATTTC
*
61674520 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
* *
61674557 AAGACTTATGTAATATTTTTAATTATGTAGTTATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
61674594 A
1 A
61674595 TTCGGGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
Done.