Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 92 of 136
Found at i:30645430 original size:113 final size:112
Alignment explanation
Indices: 30645232--30645478 Score: 352
Period size: 113 Copynumber: 2.2 Consensus size: 112
30645222 TGTTTGCTTG
* * *
30645232 CTGTCATAAATTGAATTAAAGCTGTTGTTTGAGTGTTTCAAATTGAGCATTTTCATACTGTCTTA
1 CTGTCATAAATTGAATTAAAGTTGGTGTTTGAGTGTATCAAATTGAGCATTTTCATACTGTCTTA
* *
30645297 AATTGAATCAAGCTACTATTTTAGTGTTTCAAATTGAGCATT-TTCATA
66 AATTAAATCAAGCTACTA-TTTAATGTTTCAAATTGAGCATTATT-ATA
* *
30645345 CTGTCATAAATTGAATTAAAGTTGGTGTTTTAGTGTATCAAATTGAGCATTTTCATGCTGTCTTA
1 CTGTCATAAATTGAATTAAAGTTGGTGTTTGAGTGTATCAAATTGAGCATTTTCATACTGTCTTA
* * * *
30645410 AATTAAATTAAGCTGCTATTTAATGTTTCAAATTGAGTATTATTATG
66 AATTAAATCAAGCTACTATTTAATGTTTCAAATTGAGCATTATTATA
* *
30645457 CTGTCCTAAATTAAATTAAAGT
1 CTGTCATAAATTGAATTAAAGT
30645479 GTTGCTTCAG
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
112 43 0.36
113 77 0.64
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (112 bp):
CTGTCATAAATTGAATTAAAGTTGGTGTTTGAGTGTATCAAATTGAGCATTTTCATACTGTCTTA
AATTAAATCAAGCTACTATTTAATGTTTCAAATTGAGCATTATTATA
Found at i:30645525 original size:112 final size:113
Alignment explanation
Indices: 30645232--30645516 Score: 281
Period size: 113 Copynumber: 2.5 Consensus size: 113
30645222 TGTTTGCTTG
* * * * * * * * * * *
30645232 CTGTCATAAATTGAATTAAAGCTGTTGTTTGAGTGTTTCAAATTGAGCATTTTCATACTGTCTTA
1 CTGTCATAAATTAAATTAAAGTTGGTGCTTCAGTGTATCAAAGTAAGCATTTTCATGCTATCTAA
* *
30645297 AATTGAATCAAGCTACTATTTTAGTGTTTCAAATTGAGCATTTTCATA
66 AATTAAATCAAGCTACTATTTTAATGTTTCAAATTGAGCATTTTCATA
* * * * * * *
30645345 CTGTCATAAATTGAATTAAAGTTGGTGTTTTAGTGTATCAAATTGAGCATTTTCATGCTGTCTTA
1 CTGTCATAAATTAAATTAAAGTTGGTGCTTCAGTGTATCAAAGTAAGCATTTTCATGCTATCTAA
* * * *
30645410 AATTAAATTAAGCTGCTA-TTTAATGTTTCAAATTGAGTATTATT-ATG
66 AATTAAATCAAGCTACTATTTTAATGTTTCAAATTGAGCATT-TTCATA
* * *
30645457 CTGTCCTAAATTAAATTAAAG-TGTTGCTTCAGTGTCTCAAAGTAAGCATTATT-ATGCTAT
1 CTGTCATAAATTAAATTAAAGTTGGTGCTTCAGTGTATCAAAGTAAGCATT-TTCATGCTAT
30645517 TGAAAAATTG
Statistics
Matches: 150, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
111 29 0.19
112 44 0.29
113 77 0.51
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (113 bp):
CTGTCATAAATTAAATTAAAGTTGGTGCTTCAGTGTATCAAAGTAAGCATTTTCATGCTATCTAA
AATTAAATCAAGCTACTATTTTAATGTTTCAAATTGAGCATTTTCATA
Found at i:30652689 original size:18 final size:17
Alignment explanation
Indices: 30652656--30652694 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
30652646 TTTTATAAAT
30652656 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
30652674 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
30652691 TGTG
1 TGTG
30652695 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:30652946 original size:23 final size:23
Alignment explanation
Indices: 30652920--30653064 Score: 236
Period size: 23 Copynumber: 6.3 Consensus size: 23
30652910 AGTGTTATTG
30652920 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
30652943 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
30652966 TTCAGTGGTGGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
30652989 TTCAGTGGTGGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
30653012 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
30653035 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
30653058 ATCAGTG
1 ATCAGTG
30653065 TGGCACTTAT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 114 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:30654988 original size:75 final size:76
Alignment explanation
Indices: 30654891--30655040 Score: 230
Period size: 77 Copynumber: 2.0 Consensus size: 76
30654881 AAAAATCCTC
* * * *
30654891 AAACTTTTTTAAAAAAGCAATTAAGTCCCT-TTTTTTTTGCACTCATTTGGGCACTTGAACTTTC
1 AAACCTTTTCAAAAAAGCAATTAAGCCCCTATTTTTTTTGCACTCAATTGGGCACTTGAACTTTC
30654955 AAAATGCATTG
66 AAAATGCATTG
* *
30654966 AAACCTTTTCAAAAAAGTAATTAAGCCCCTACTTTTTTTTGCACTCAATTGGGTACTTGAACTTT
1 AAACCTTTTCAAAAAAGCAATTAAGCCCCTA-TTTTTTTTGCACTCAATTGGGCACTTGAACTTT
30655031 CAAAATGCAT
65 CAAAATGCAT
30655041 AAAAAAGACC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 26 0.39
77 41 0.61
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (76 bp):
AAACCTTTTCAAAAAAGCAATTAAGCCCCTATTTTTTTTGCACTCAATTGGGCACTTGAACTTTC
AAAATGCATTG
Found at i:30655126 original size:9 final size:11
Alignment explanation
Indices: 30655094--30655123 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
30655084 AGCTTTTATT
*
30655094 AAAAATTAGAA
1 AAAAATTATAA
30655105 AAAAATTATAA
1 AAAAATTATAA
30655116 AAAAATTA
1 AAAAATTA
30655124 AAATCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:30655347 original size:19 final size:18
Alignment explanation
Indices: 30655325--30655360 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30655315 ATAAAAAATA
*
30655325 TAAAGAAATATAAAATTAG
1 TAAAAAAAT-TAAAATTAG
30655344 TAAAAAAATTAAAATTA
1 TAAAAAAATTAAAATTA
30655361 TCGTACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (18 bp):
TAAAAAAATTAAAATTAG
Found at i:30655356 original size:18 final size:19
Alignment explanation
Indices: 30655295--30655360 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
30655285 TATAAAATTT
* *
30655295 TATAAAGTT-GTAAGAAAAT
1 TATAAAATTAGTAA-AAAAA
* *
30655314 TATAAAAAATA-TAAAGAAA
1 TAT-AAAATTAGTAAAAAAA
30655333 TATAAAATTAGTAAAAAAA
1 TATAAAATTAGTAAAAAAA
30655352 T-TAAAATTA
1 TATAAAATTA
30655361 TCGTACCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 14 0.37
19 17 0.45
20 7 0.18
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.29
Consensus pattern (19 bp):
TATAAAATTAGTAAAAAAA
Found at i:30665765 original size:23 final size:23
Alignment explanation
Indices: 30665737--30665791 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
30665727 ATTTGTTAGA
30665737 AAGCATTATTGTTTAATTTGGCG
1 AAGCATTATTGTTTAATTTGGCG
* *
30665760 AAGCATGATTTTTGTTTAATTTTGCG
1 AAGC---ATTATTGTTTAATTTGGCG
30665786 AAGCAT
1 AAGCAT
30665792 GATTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 6 0.22
26 21 0.78
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (23 bp):
AAGCATTATTGTTTAATTTGGCG
Found at i:30665776 original size:26 final size:26
Alignment explanation
Indices: 30665745--30665795 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
30665735 GAAAGCATTA
30665745 TTGTTTAATTTGGCGAAGCATGATTT
1 TTGTTTAATTTGGCGAAGCATGATTT
*
30665771 TTGTTTAATTTTGCGAAGCATGATT
1 TTGTTTAATTTGGCGAAGCATGATT
30665796 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.47
Consensus pattern (26 bp):
TTGTTTAATTTGGCGAAGCATGATTT
Found at i:30671858 original size:6 final size:6
Alignment explanation
Indices: 30671847--30671881 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
30671837 GGTTTTCTCC
30671847 AAAATG AAAATG AAAATG AAAATGG AGAAATG AAA
1 AAAATG AAAATG AAAATG AAAAT-G A-AAATG AAA
30671882 TCATTTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:30671891 original size:63 final size:64
Alignment explanation
Indices: 30671796--30671924 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 64
30671786 GAACAAAATT
*
30671796 AAATAAAAATGGAGAAATAGGAAATATTTGGAAAT-TATGAAGGTTTTCTCCAAAATG-AAAATG
1 AAATAAAAATGGAGAAATA-GAAATATTTGGAAATGAATG-AGGTTTTCTCCAAAATGTAAAATG
30671859 A
64 A
* * *
30671860 AAATGAAAATGGAGAAAT-GAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGTGAAATGA
1 AAATAAAAATGGAGAAATAGAAAT-ATTTGGAAATGAATGAGGTTTTCTCCAAAATGTAAAATGA
30671924 A
1 A
30671925 TTCATTTGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
62 5 0.09
63 26 0.45
64 27 0.47
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (64 bp):
AAATAAAAATGGAGAAATAGAAATATTTGGAAATGAATGAGGTTTTCTCCAAAATGTAAAATGA
Found at i:30671921 original size:44 final size:44
Alignment explanation
Indices: 30671873--30671959 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
30671863 TGAAAATGGA
** * *
30671873 GAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGT
1 GAAATGAAATCATTTGGAAATGAATAAGGATTTCTCAAAAATGT
*
30671917 GAAATGAATTCATTTGGAAATGAATAAGGATTTCTCAAAAATG
1 GAAATGAAATCATTTGGAAATGAATAAGGATTTCTCAAAAATG
30671960 ATCGGAAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (44 bp):
GAAATGAAATCATTTGGAAATGAATAAGGATTTCTCAAAAATGT
Found at i:30674033 original size:25 final size:25
Alignment explanation
Indices: 30673944--30674029 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
30673934 CACAGCTTTT
* *
30673944 ATGAGCATCCCAATATTTGGCTCTC
1 ATGAGCTTCCCAATAATTGGCTCTC
* * *
30673969 ACGAGCTTCTCAATTAA-TGGCTCTT
1 ATGAGCTTCCCAA-TAATTGGCTCTC
* * *
30673994 ATGAGCTTCTCGATAATTGGCTCGC
1 ATGAGCTTCCCAATAATTGGCTCTC
30674019 ATGAGCTTCCC
1 ATGAGCTTCCC
30674030 GATATACAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
24 3 0.06
25 44 0.90
26 2 0.04
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCAATAATTGGCTCTC
Found at i:30680213 original size:15 final size:15
Alignment explanation
Indices: 30680193--30680222 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30680183 TTCACTATTA
*
30680193 TGTCTTTTGTGTTTT
1 TGTCTTTTATGTTTT
30680208 TGTCTTTTATGTTTT
1 TGTCTTTTATGTTTT
30680223 GCATGCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.07, G:0.17, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATGTTTT
Found at i:30684410 original size:11 final size:11
Alignment explanation
Indices: 30684394--30684419 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30684384 CCTCCCTCTT
30684394 CCTTCGTTCTA
1 CCTTCGTTCTA
30684405 CCTTCGTTCTA
1 CCTTCGTTCTA
30684416 CCTT
1 CCTT
30684420 TGCCTCCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.38, G:0.08, T:0.46
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:30689203 original size:16 final size:16
Alignment explanation
Indices: 30689182--30689217 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
30689172 GATTTGCTAT
30689182 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
30689198 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
30689214 TACA
1 TACA
30689218 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:30694574 original size:21 final size:20
Alignment explanation
Indices: 30694550--30694750 Score: 91
Period size: 21 Copynumber: 9.7 Consensus size: 20
30694540 ATTTAGCTCT
*
30694550 TATGAGCTTCTGTTTAACTC
1 TATGAGCTTCTGTTCAACTC
* * * *
30694570 ATATGAGTTTTTGCTCAGCTC
1 -TATGAGCTTCTGTTCAACTC
30694591 TATTGAGCTTCTGTTCAACTC
1 TA-TGAGCTTCTGTTCAACTC
* * *
30694612 TTATAAGTTTCCGTTCAACTC
1 -TATGAGCTTCTGTTCAACTC
* * *
30694633 TATTAAGCTTCTGTTTAACCC
1 TA-TGAGCTTCTGTTCAACTC
* *
30694654 TTATG-GCTTTTCGTTCAGCTC
1 -TATGAGCTTCT-GTTCAACTC
** * *
30694675 TTACAAGCTTCTGTGCAACCC
1 -TATGAGCTTCTGTTCAACTC
* * * * * *
30694696 TTATGGGTTTCTTTTTAGCTTT
1 -TATGAGCTTCTGTTCAAC-TC
*
30694718 TATGAGCTTCTGTTCAGCT-
1 TATGAGCTTCTGTTCAACTC
30694737 TATGAGCTTCTGTT
1 TATGAGCTTCTGTT
30694751 AACGATATAC
Statistics
Matches: 132, Mismatches: 41, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
19 14 0.11
20 10 0.08
21 99 0.75
22 9 0.07
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (20 bp):
TATGAGCTTCTGTTCAACTC
Found at i:30694591 original size:42 final size:42
Alignment explanation
Indices: 30694554--30694688 Score: 148
Period size: 42 Copynumber: 3.2 Consensus size: 42
30694544 AGCTCTTATG
* * * *
30694554 AGCTTCTGTTTAACTCATATGAGTTTTTGCTCAGCTCTATTG
1 AGCTTCTGTTTAACTCTTATGAGTTTTCGTTCAGCTCTATTA
* * * *
30694596 AGCTTCTGTTCAACTCTTATAAGTTTCCGTTCAACTCTATTA
1 AGCTTCTGTTTAACTCTTATGAGTTTTCGTTCAGCTCTATTA
* *
30694638 AGCTTCTGTTTAACCCTTATG-GCTTTTCGTTCAGCTCT-TACA
1 AGCTTCTGTTTAACTCTTATGAG-TTTTCGTTCAGCTCTAT-TA
30694680 AGCTTCTGT
1 AGCTTCTGT
30694689 GCAACCCTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 2 0.03
42 75 0.97
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (42 bp):
AGCTTCTGTTTAACTCTTATGAGTTTTCGTTCAGCTCTATTA
Found at i:30694874 original size:12 final size:13
Alignment explanation
Indices: 30694844--30694882 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
30694834 AAGTAAGAGA
30694844 ATGATATGTAT-T
1 ATGATATGTATAT
30694856 ATGATATGTATAT
1 ATGATATGTATAT
*
30694869 AT-ATATATATAT
1 ATGATATGTATAT
30694881 AT
1 AT
30694883 CAATATCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 22 0.88
13 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (13 bp):
ATGATATGTATAT
Found at i:30704502 original size:27 final size:27
Alignment explanation
Indices: 30704437--30704495 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
30704427 AGCAGATCAC
* *
30704437 ATATAACCCTATCTGTATAGCGTGTAA
1 ATATTACCCTATCTATATAGCGTGTAA
30704464 ATATTACCCTATCTATATAGCGTGTAA
1 ATATTACCCTATCTATATAGCGTGTAA
30704491 ATATT
1 ATATT
30704496 CTCCTATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (27 bp):
ATATTACCCTATCTATATAGCGTGTAA
Found at i:30711925 original size:2 final size:2
Alignment explanation
Indices: 30711920--30711951 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
30711910 ATGTATGTAT
30711920 AC AC AC AC AC AC AC AC AC AC ATC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC A-C AC AC AC AC A
30711952 TATATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:30713997 original size:39 final size:39
Alignment explanation
Indices: 30713873--30714026 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 39
30713863 AGCGGCATTT
* *
30713873 TTAGCGGCGTTTGT-ATAAAAAACGCCGCTAAAAATTGAGCA
1 TTAGCGGCGTTT-TCA-AGAAAACGCCGC-AAAAAATGAGCA
* * * * *
30713914 TTAGAGGCGCTTT-ACGTAAAACGCCGCTAAAGATCGAGCA
1 TTAGCGGCGTTTTCAAG-AAAACGCCGCAAAAAAT-GAGCA
* *
30713954 TTAGCGGCGTTTCCAAGAAAGCGCCGCAAAAAATGAGCA
1 TTAGCGGCGTTTTCAAGAAAACGCCGCAAAAAATGAGCA
30713993 TTAGCGGCGTTTTTCTAA-AAAACGCCGCAAAAAA
1 TTAGCGGCG-TTTTC-AAGAAAACGCCGCAAAAAA
30714027 CCTAAGCCCA
Statistics
Matches: 92, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
39 18 0.20
40 60 0.65
41 14 0.15
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGTTTTCAAGAAAACGCCGCAAAAAATGAGCA
Found at i:30714136 original size:41 final size:41
Alignment explanation
Indices: 30714065--30714342 Score: 342
Period size: 41 Copynumber: 6.8 Consensus size: 41
30714055 CTTTCGAGGA
* * *
30714065 TTTAGCGGCG-TTTTTGAAAAAGTGTCGCTAATGCTCGGGTC
1 TTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTCGGGTC
* * * *
30714106 TTTAGCGGCGCTTTTCCCAAAACGCAGCTAATGCTCTGGTC
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
* * * * *
30714147 TTCAGCGGCGCTTTTTTACAAGCACCGCTAATGCTCGGGTC
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
* * * *
30714188 TTTAGCGGCGCTTTGTCAAAATCGCCGCTAAAGCTTGGGTC
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
* * *
30714229 TTCAGCGGCGCTTTTTCAAAAAGCGCCGCTAATGCTTGGGTT
1 TTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTCGGGTC
*
30714271 TTTAGCGGTGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
*
30714312 TTTAGCGACGCTTTTTCAAAAACGCCGCTAA
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAA
30714343 AGCTTTAGCG
Statistics
Matches: 200, Mismatches: 35, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
41 155 0.77
42 45 0.22
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
Found at i:30714308 original size:124 final size:123
Alignment explanation
Indices: 30714090--30714347 Score: 347
Period size: 124 Copynumber: 2.1 Consensus size: 123
30714080 GAAAAAGTGT
* * * *
30714090 CGCTAATGCTCGGGTCTTTAGCGGCGCTTTTCCCAAAACGCAGCTAATGCTCTGGTCTTCAGCGG
1 CGCTAAAGCTTGGGTCTTCAGCGGCGCTTTTCCAAAAACGCAGCTAATGCTCTGGTCTTCAGCGG
* * * * *
30714155 CGCTTTTTTACAAGCACCGCTAATGCTCGGGTCTTTAGCGGCGCTTTGTCAAAATCGC
66 CGCTTTTTCAAAAACACCGCTAATGCTCGGGTCTTTAGCGACGCTTTGTCAAAAACGC
* * * *
30714213 CGCTAAAGCTTGGGTCTTCAGCGGCGCTTTTTCAAAAAGCGCCGCTAATGCT-TGGGTTTTTAGC
1 CGCTAAAGCTTGGGTCTTCAGCGGCGCTTTTCCAAAAA-CGCAGCTAATGCTCT-GGTCTTCAGC
* * *
30714277 GGTGCTTTTTCAAAAACGCCGCTAATGCTCGGGTCTTTAGCGACGCTTTTTCAAAAACGC
64 GGCGCTTTTTCAAAAACACCGCTAATGCTCGGGTCTTTAGCGACGCTTTGTCAAAAACGC
30714337 CGCTAAAGCTT
1 CGCTAAAGCTT
30714348 TAGCGGCGTT
Statistics
Matches: 117, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
123 34 0.29
124 83 0.71
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (123 bp):
CGCTAAAGCTTGGGTCTTCAGCGGCGCTTTTCCAAAAACGCAGCTAATGCTCTGGTCTTCAGCGG
CGCTTTTTCAAAAACACCGCTAATGCTCGGGTCTTTAGCGACGCTTTGTCAAAAACGC
Found at i:30714366 original size:33 final size:35
Alignment explanation
Indices: 30714311--30714376 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
30714301 ATGCTCGGGT
*
30714311 CTTTAGCGACGCTTTTTCAAAAA-CGCCGCTAAAG
1 CTTTAGCGACGCTTTTTCAAAAAGCACCGCTAAAG
* *
30714345 CTTTAGCGGCG-TTTTTGAAAAAGCACCGCTAA
1 CTTTAGCGACGCTTTTTCAAAAAGCACCGCTAA
30714377 TCCCAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (35 bp):
CTTTAGCGACGCTTTTTCAAAAAGCACCGCTAAAG
Found at i:30716467 original size:43 final size:42
Alignment explanation
Indices: 30716413--30716763 Score: 441
Period size: 43 Copynumber: 8.2 Consensus size: 42
30716403 TTTTCGTGAC
* *
30716413 CTTTAGTGGCGTTTTTAGGGAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAAGGTCCTGGT
** * ** *
30716456 CACTCGCGGCGTTTGTCGAAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAAGGTCCTGGT
* *
30716499 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTG-TGGGAAAGCGCCGCTAAAGGTCCTGGT
* *
30716542 TTTTAGCGGCGTTTGTTGGCAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTG-TGGGAAAGCGCCGCTAAAGGTCCTGGT
* * *
30716585 TTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCCTCGT
1 CTTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCCTGGT
* *
30716628 CTTTAGCGGCGTTCGTGGGGAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAAGGTCCTGGT
*
30716671 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTG-TGGGAAAGCGCCGCTAAAGGTCCTGGT
* **
30716714 CTTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTAATGGT
1 CTTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCCTGGT
30716757 CTTTAGC
1 CTTTAGC
30716764 AGTGTTTTTT
Statistics
Matches: 272, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
42 6 0.02
43 261 0.96
44 5 0.02
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (42 bp):
CTTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCCTGGT
Found at i:30716525 original size:86 final size:86
Alignment explanation
Indices: 30716413--30716763 Score: 497
Period size: 86 Copynumber: 4.1 Consensus size: 86
30716403 TTTTCGTGAC
* * ** * * *
30716413 CTTTAGTGGCGTTT-TTAGGGAAAGCGCCGCTAAAGGTCCTGGTCACTCGCGGCGTTTGTCGAAA
1 CTTTAGCGGCGTTTGTT-GGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAA
30716477 AAGCGCCGCTAAAGGTCTTGGT
65 AAGCGCCGCTAAAGGTCTTGGT
* * * *
30716499 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCTTGGTTTTTAGCGGCGTTTGTTGGCAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
*
30716564 AGCGCCGCTAAAGGTCCTGGT
66 AGCGCCGCTAAAGGTCTTGGT
* * * * * *
30716585 TTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCCTCGTCTTTAGCGGCGTTCGTGGGGAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
30716650 AGCGCCGCTAAAGGTCTTGGT
66 AGCGCCGCTAAAGGTCTTGGT
30716671 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
* **
30716736 AGCGCTGCTAAAGGTAATGGT
66 AGCGCCGCTAAAGGTCTTGGT
30716757 CTTTAGC
1 CTTTAGC
30716764 AGTGTTTTTT
Statistics
Matches: 234, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 232 0.99
87 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (86 bp):
CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
AGCGCCGCTAAAGGTCTTGGT
Found at i:30716608 original size:129 final size:129
Alignment explanation
Indices: 30716413--30716763 Score: 515
Period size: 129 Copynumber: 2.7 Consensus size: 129
30716403 TTTTCGTGAC
* * ** * * *
30716413 CTTTAGTGGCGTTT-TTAGGGAAAGCGCCGCTAAAGGTCCTGGTCACTCGCGGCGTTTGTCGAAA
1 CTTTAGCGGCGTTTGTT-GGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAA
* * *
30716477 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCTTGGT
65 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTCGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* * *
30716542 TTTTAGCGGCGTTTGTTGGCAAAGCGCCGCTAAAGGTCCTGGTTTTTAGCGGCGTTTGTGGGAAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
* * * *
30716607 AGCGTCGCTAAAGGTCCTCGTCTTTAGCGGCGTTCGTGGGGAAAGCGCCGCTAAAGGTCTTGGT
66 AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTCGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
30716671 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
* *
30716736 AGCGCTGCTAAAGGTAATGGTCTTTAGC
66 AGCGCCGCTAAAGGTCATGGTCTTTAGC
30716764 AGTGTTTTTT
Statistics
Matches: 198, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
129 196 0.99
130 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (129 bp):
CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTCGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:30716843 original size:22 final size:22
Alignment explanation
Indices: 30716815--30716857 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
30716805 TAGCGGCGCT
*
30716815 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
30716837 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
30716858 GTTTTGGTGT
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:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:30718571 original size:61 final size:61
Alignment explanation
Indices: 30718468--30718586 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 61
30718458 TATTCCAGAT
* * *
30718468 GATTTATTTATACCATAAATATATCAGAATCTCCATAGTGTAAGACAACTATTAGAAAGGA
1 GATTTATTTATACCATAAAAATATCAGAATCTCCATACTGTAAGACAACTACTAGAAAGGA
* ***
30718529 GATTTATTTGTACCATAAAAATATCAGAATCTTTGTACTGTAAGACAACTACTAGAAA
1 GATTTATTTATACCATAAAAATATCAGAATCTCCATACTGTAAGACAACTACTAGAAA
30718587 AGAGTTATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (61 bp):
GATTTATTTATACCATAAAAATATCAGAATCTCCATACTGTAAGACAACTACTAGAAAGGA
Found at i:30732035 original size:25 final size:25
Alignment explanation
Indices: 30731980--30732037 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
30731970 CTCCCAACTG
* *
30731980 ATGTTGAAAAATTTTCAAATCTGAA
1 ATGTTTAAAAATTTCCAAATCTGAA
* *
30732005 ATGTTTAAAAATTTCCAAATTTGGA
1 ATGTTTAAAAATTTCCAAATCTGAA
30732030 ATGTTTAA
1 ATGTTTAA
30732038 TTAGCATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (25 bp):
ATGTTTAAAAATTTCCAAATCTGAA
Found at i:30732590 original size:21 final size:24
Alignment explanation
Indices: 30732557--30732606 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
30732547 CTACGAGCTT
30732557 TTTTAGAATTATTT-AATT-T-AA
1 TTTTAGAATTATTTCAATTATAAA
30732578 TTTT-GAATATATTTCAATTATAAA
1 TTTTAGAAT-TATTTCAATTATAAA
30732602 TTTTA
1 TTTTA
30732607 TTACACTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 4 0.17
21 9 0.38
22 4 0.17
23 1 0.04
24 6 0.25
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTAGAATTATTTCAATTATAAA
Found at i:30735543 original size:31 final size:31
Alignment explanation
Indices: 30735505--30735640 Score: 117
Period size: 31 Copynumber: 4.5 Consensus size: 31
30735495 TTCTTGGTCC
30735505 AATTTGGTACAC-AAACTTGACACTTTTTCCT
1 AATTTGGTAC-CTAAACTTGACACTTTTTCCT
*
30735536 AATTTGGTACCTAAACTTGACACTTTTTCTT
1 AATTTGGTACCTAAACTTGACACTTTTTCCT
* * *
30735567 AAGTTGGTACTTAATA-TT-----TTTTGGGATAC-
1 AATTTGGTACCTAA-ACTTGACACTTTT----TCCT
*
30735596 AATTTGGTACCTAAACTTGACTCTTTTTCCT
1 AATTTGGTACCTAAACTTGACACTTTTTCCT
30735627 AATTTGGTACCTAA
1 AATTTGGTACCTAA
30735641 TCTTTTTTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
26 4 0.05
28 1 0.01
29 14 0.17
30 4 0.05
31 56 0.67
32 1 0.01
34 4 0.05
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCT
Found at i:30735600 original size:60 final size:60
Alignment explanation
Indices: 30735536--30735648 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
30735526 ACTTTTTCCT
* *
30735536 AATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGGTACTTAATATTTTTTGGGATAC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATATTTTTTGGGATAC
* * *
30735596 AATTTGGTACCTAAACTTGACTCTTTTTCCTAATTTGGTACCTAATCTTTTTT
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATATTTTTT
30735649 TTTGTTCGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (60 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATATTTTTTGGGATAC
Found at i:30736606 original size:20 final size:23
Alignment explanation
Indices: 30736547--30736606 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
30736537 ATCTTAGAAA
* *
30736547 TAAATATAATTTATTAAAAGTAT
1 TAAAAATATTTTATTAAAAGTAT
*
30736570 TAAAAATATGTTA--AAAA-TAT
1 TAAAAATATTTTATTAAAAGTAT
30736590 T-AAAAT-TTTTATTAAAA
1 TAAAAATATTTTATTAAAA
30736607 CAAAATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 4 0.13
19 5 0.16
20 8 0.26
21 4 0.13
23 10 0.32
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
TAAAAATATTTTATTAAAAGTAT
Found at i:30742962 original size:20 final size:20
Alignment explanation
Indices: 30742918--30742963 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
30742908 CCCTTGATTT
*
30742918 TTTTATGAAATATATAGCATA
1 TTTTATGAAATAAATA-CATA
30742939 -TTTATGTAAATAAATA-ATA
1 TTTTATG-AAATAAATACATA
30742958 TTTTAT
1 TTTTAT
30742964 AAAAGAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (20 bp):
TTTTATGAAATAAATACATA
Found at i:30750192 original size:38 final size:38
Alignment explanation
Indices: 30750150--30750226 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
30750140 AAAATGGTTT
*
30750150 AAAAATTAAAA-ATTAAAAAATGTTCTTAAAAATTCAAA
1 AAAAATTAAAATATTAAAAAAT-ATCTTAAAAATTCAAA
* * *
30750188 AAAAATTAAAATTTTTAAAAATATCTTCAAAATTCAAA
1 AAAAATTAAAATATTAAAAAATATCTTAAAAATTCAAA
30750226 A
1 A
30750227 TATAAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.31
Consensus pattern (38 bp):
AAAAATTAAAATATTAAAAAATATCTTAAAAATTCAAA
Found at i:30753899 original size:29 final size:28
Alignment explanation
Indices: 30753842--30753898 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
30753832 TATAACACTT
** *
30753842 TTTTATATTTTTAGAGATCAGAGTAAAA
1 TTTTATATTTTTAGAGAAAAGAATAAAA
30753870 TTTTATTATTTTTAGAGAAAAAGAATAAA
1 TTTTA-TATTTTTAGAG-AAAAGAATAAA
30753899 TGTTTTCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 11 0.46
30 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (28 bp):
TTTTATATTTTTAGAGAAAAGAATAAAA
Found at i:30756915 original size:2 final size:2
Alignment explanation
Indices: 30756910--30756952 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
30756900 GTTTTTTACC
30756910 TA TA TA -A TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30756949 TA TA
1 TA TA
30756953 CTGAGATGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:30757057 original size:2 final size:2
Alignment explanation
Indices: 30757052--30757094 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
30757042 GTTTTTTACC
30757052 TA TA TA -A TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30757091 TA TA
1 TA TA
30757095 CTGAGATGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:30757109 original size:142 final size:142
Alignment explanation
Indices: 30756853--30757130 Score: 538
Period size: 142 Copynumber: 2.0 Consensus size: 142
30756843 TGATATTTAA
*
30756853 TTTTGAGATATAATAATGAATAAACAACCAATGAAGTTAAAAAGGGGGTTTTTTACCTATATAAT
1 TTTTGAGATATAATAATAAATAAACAACCAATGAAGTTAAAAAGGGGGTTTTTTACCTATATAAT
*
30756918 ATAATATAATATATATATATATATATATATATATACTGAGATGGCATGTTTCACAAATTATGTAT
66 ATAATATAATATATATATATATATATATATATATACTGAGATGGCATGTTTCAAAAATTATGTAT
30756983 TAAAATAGTTAG
131 TAAAATAGTTAG
30756995 TTTTGAGATATAATAATAAATAAACAACCAATGAAGTTAAAAAGGGGGTTTTTTACCTATATAAT
1 TTTTGAGATATAATAATAAATAAACAACCAATGAAGTTAAAAAGGGGGTTTTTTACCTATATAAT
30757060 ATAATATAATATATATATATATATATATATATATACTGAGATGGCATGTTTCAAAAATTATGTAT
66 ATAATATAATATATATATATATATATATATATATACTGAGATGGCATGTTTCAAAAATTATGTAT
30757125 TAAAAT
131 TAAAAT
30757131 GGTACATTTA
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 134 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (142 bp):
TTTTGAGATATAATAATAAATAAACAACCAATGAAGTTAAAAAGGGGGTTTTTTACCTATATAAT
ATAATATAATATATATATATATATATATATATATACTGAGATGGCATGTTTCAAAAATTATGTAT
TAAAATAGTTAG
Found at i:30759606 original size:14 final size:14
Alignment explanation
Indices: 30759587--30759621 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
30759577 TGACTTTTTT
*
30759587 TTCTAATGATACTA
1 TTCTAACGATACTA
30759601 TTCTAACGATACTA
1 TTCTAACGATACTA
30759615 TTCTAAC
1 TTCTAAC
30759622 ATGTTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:30760241 original size:12 final size:12
Alignment explanation
Indices: 30760224--30760257 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30760214 TTGGGGCATA
*
30760224 CGAGCCAGTGCC
1 CGAGCCAGAGCC
30760236 CGAGCCAGAGCC
1 CGAGCCAGAGCC
*
30760248 TGAGCCAGAG
1 CGAGCCAGAG
30760258 TAGAAGCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.35, G:0.35, T:0.06
Consensus pattern (12 bp):
CGAGCCAGAGCC
Found at i:30760868 original size:48 final size:48
Alignment explanation
Indices: 30760812--30760903 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
30760802 CAACATTACA
* *
30760812 ACATTACAAGACTAAAACTTGGAACAAATTTTGTAATATAAATTAAAT
1 ACATTACAAGACTAAAAATTGGAACAAACTTTGTAATATAAATTAAAT
* *
30760860 ACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAATT
1 ACATTACAAGACTAAAAATTGGAACAAACTTTGTAATATAAATT
30760904 TTGTTATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (48 bp):
ACATTACAAGACTAAAAATTGGAACAAACTTTGTAATATAAATTAAAT
Found at i:30760913 original size:62 final size:62
Alignment explanation
Indices: 30760837--30761087 Score: 416
Period size: 62 Copynumber: 4.1 Consensus size: 62
30760827 AACTTGGAAC
* *
30760837 AAATTTTGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
* *
30760899 AAATTTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
* * * *
30760961 AAATTTTG-T-TATAAATTAAATATATTATAGCATTAAAAATTGGATCAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
30761021 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
30761083 AAATT
1 AAATT
30761088 AGGTACATTG
Statistics
Matches: 174, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
60 54 0.31
61 2 0.01
62 118 0.68
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (62 bp):
AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
Found at i:30760996 original size:122 final size:123
Alignment explanation
Indices: 30760837--30761087 Score: 423
Period size: 122 Copynumber: 2.0 Consensus size: 123
30760827 AACTTGGAAC
*
30760837 AAATTTTGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAA
1 AAATTTTGT-ATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAA
30760902 TTTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
65 TTTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
* * * *
30760961 AAATTTTGT-TATAAATTAAATATATTATAGCATTAAAAATTGGATCAAACTTTGTAATATAAAT
1 AAATTTTGTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
* *
30761025 TTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
66 TTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
30761083 AAATT
1 AAATT
30761088 AGGTACATTG
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
122 111 0.93
124 9 0.08
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (123 bp):
AAATTTTGTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
TTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
Found at i:30765539 original size:24 final size:23
Alignment explanation
Indices: 30765494--30765554 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
30765484 ATTTTTTAAC
30765494 TTTAA-AATATTTTTTTTAATTTT
1 TTTAATAAT-TTTTTTTTAATTTT
30765517 TTTAATAATTTTTATTTTAATTTT
1 TTTAATAATTTTT-TTTTAATTTT
**
30765541 TAAAATAATTTTTT
1 TTTAATAATTTTTT
30765555 GGTATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 10 0.29
24 24 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAATAATTTTTTTTTAATTTT
Found at i:30765542 original size:12 final size:11
Alignment explanation
Indices: 30765503--30765541 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
30765493 CTTTAAAATA
30765503 TTTTTTTTAAT
1 TTTTTTTTAAT
*
30765514 TTTTTTAATAAT
1 TTTTTT-TTAAT
30765526 TTTTATTTTAAT
1 TTTT-TTTTAAT
30765538 TTTT
1 TTTT
30765542 AAAATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 16 0.67
13 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:30765549 original size:12 final size:12
Alignment explanation
Indices: 30765510--30765553 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
30765500 ATATTTTTTT
*
30765510 TAATTTTTTTAA
1 TAATTTTTATAA
**
30765522 TAATTTTTATTT
1 TAATTTTTATAA
*
30765534 TAATTTTTAAAA
1 TAATTTTTATAA
30765546 TAATTTTT
1 TAATTTTT
30765554 TGGTATTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TAATTTTTATAA
Found at i:30783070 original size:20 final size:20
Alignment explanation
Indices: 30783045--30783089 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
30783035 GCAAATTTCG
30783045 GGTAAAATTGAATTAATTCA
1 GGTAAAATTGAATTAATTCA
*
30783065 GGTAAAATTGAATTAATTCG
1 GGTAAAATTGAATTAATTCA
30783085 GGTAA
1 GGTAA
30783090 CAGACCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.33
Consensus pattern (20 bp):
GGTAAAATTGAATTAATTCA
Found at i:30789903 original size:13 final size:13
Alignment explanation
Indices: 30789885--30789910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30789875 AGTTAGTAGT
30789885 TATTCTGTTAAAG
1 TATTCTGTTAAAG
30789898 TATTCTGTTAAAG
1 TATTCTGTTAAAG
30789911 AAGCTAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TATTCTGTTAAAG
Found at i:30796890 original size:18 final size:20
Alignment explanation
Indices: 30796867--30796906 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
30796857 TAGAAATAGT
30796867 AATTAAAAT-AT-TTTTTTA
1 AATTAAAATGATATTTTTTA
*
30796885 AATTAAACTGATATTTTTTA
1 AATTAAAATGATATTTTTTA
30796905 AA
1 AA
30796907 AATATATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
AATTAAAATGATATTTTTTA
Found at i:30800766 original size:20 final size:21
Alignment explanation
Indices: 30800726--30800792 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 21
30800716 ATTTTATAAT
30800726 TTTTTAAAAATATAAATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTGAAA
*
30800750 TTTTTACAAA-TATTTTG-AA
1 TTTTTAAAAATTATTTTGAAA
30800769 -TTTTAAAAATTATTTT-AAA
1 TTTTTAAAAATTATTTTGAAA
30800788 TTTTT
1 TTTTT
30800793 CTGTAACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.21
19 10 0.26
20 10 0.26
22 1 0.03
24 9 0.24
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (21 bp):
TTTTTAAAAATTATTTTGAAA
Found at i:30802579 original size:23 final size:24
Alignment explanation
Indices: 30802553--30802633 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 24
30802543 TTCATAGTTT
30802553 TAAA-ATTATATTATTATATTATG
1 TAAACATTATATTATTATATTATG
*
30802576 TAAA-ATTATATCATGTATTATTATTG
1 TAAACATTATATTAT-TA-TATTA-TG
*
30802602 TAATACATAATA-TATTA-ATTAT-
1 TAA-ACATTATATTATTATATTATG
*
30802624 TAAATATTAT
1 TAAACATTAT
30802634 TTTTTTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
21 5 0.10
22 3 0.06
23 14 0.29
24 6 0.12
25 5 0.10
26 7 0.15
27 3 0.06
28 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
TAAACATTATATTATTATATTATG
Found at i:30802598 original size:15 final size:15
Alignment explanation
Indices: 30802561--30802599 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
30802551 TTTAAAATTA
*
30802561 TATTATTATATTATG
1 TATTATTATATCATG
**
30802576 TAAAATTATATCATG
1 TATTATTATATCATG
30802591 TATTATTAT
1 TATTATTAT
30802600 TGTAATACAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (15 bp):
TATTATTATATCATG
Found at i:30803317 original size:20 final size:21
Alignment explanation
Indices: 30803277--30803343 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 21
30803267 ATTTTATAAT
30803277 TTTTTAAAAATATAAATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTGAAA
*
30803301 TTTTTACAAA-TATTTTG-AA
1 TTTTTAAAAATTATTTTGAAA
30803320 -TTTTAAAAATTATTTT-AAA
1 TTTTTAAAAATTATTTTGAAA
30803339 TTTTT
1 TTTTT
30803344 CTGTAACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.21
19 10 0.26
20 10 0.26
22 1 0.03
24 9 0.24
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (21 bp):
TTTTTAAAAATTATTTTGAAA
Found at i:30804936 original size:18 final size:18
Alignment explanation
Indices: 30804909--30804950 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
30804899 TTAAGTCCAT
*
30804909 ATGCCAGTGTGAGCCCAC
1 ATGCCCGTGTGAGCCCAC
30804927 ATGCCCGTGTGAGCCCAC
1 ATGCCCGTGTGAGCCCAC
30804945 ATGCCC
1 ATGCCC
30804951 AGATTGGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.38, G:0.26, T:0.17
Consensus pattern (18 bp):
ATGCCCGTGTGAGCCCAC
Found at i:30815199 original size:46 final size:46
Alignment explanation
Indices: 30815132--30815225 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
30815122 CTTGGACTGT
* *
30815132 GTATTCGCCTGATTTGTTCCCTCGCCATATTAGAACATCCGGCTGC
1 GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
30815178 GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
1 GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
30815224 GT
1 GT
30815226 CCTGCTTACC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (46 bp):
GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
Found at i:30816900 original size:105 final size:101
Alignment explanation
Indices: 30816721--30816918 Score: 254
Period size: 105 Copynumber: 1.9 Consensus size: 101
30816711 AATTGACGGA
* * * * *
30816721 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTGAGCTTTGGCATTTTAA
1 TAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGGCATTCTAA
30816786 TGAACAGACCATAACTGAGTTATGGCACATTGAACG
66 TGAACAGACCATAACTGAGTTATGGCACATTGAACG
* *
30816822 TAAGACCATGGTTGGACCATGACAATATAGATACATGTGTAAGACCATAGCTGGGCTATGGCATT
1 TAAGACCATGGTTGGACCATGACAATAT--ATA-A-ATGTAAGACCATAGCTGAGCTATGGCATT
* * *
30816887 CTGATGATA-AGACCATAACTGGGTTGTGGCAC
62 CTAATGA-ACAGACCATAACTGAGTTATGGCAC
30816919 TACAAATGTA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 26 0.32
103 2 0.02
104 1 0.01
105 52 0.63
106 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGGCATTCTAA
TGAACAGACCATAACTGAGTTATGGCACATTGAACG
Found at i:30816931 original size:33 final size:32
Alignment explanation
Indices: 30816859--30816935 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
30816849 TAGATACATG
* * **
30816859 TGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGGCATACAAA
* *
30816891 TGATAAGACCATAACTGGGTTGTGGCACTACAAA
1 TG-TAAGACCATAACTGGGCTATGGCA-TACAAA
30816925 TGTAAGACCAT
1 TGTAAGACCAT
30816936 GGCAGAGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGGCATACAAA
Found at i:30816947 original size:105 final size:105
Alignment explanation
Indices: 30816754--30816952 Score: 251
Period size: 105 Copynumber: 1.9 Consensus size: 105
30816744 AATGTTTAAA
* * **
30816754 TGTAAGACCATAGCTGAGCTTTGGCATTTTAATGAACAGACCATAACTGAGTTATGGCACATTGA
1 TGTAAGACCATAGCTGAGCTATGGCATTCTAATGAACAGACCATAACTGAGTTATGGCACATCAA
**
30816819 ACGTAAGACCATGGTTGGACCATGACAATATAGATACATG
66 ACGTAAGACCATGGCAGGACCATGACAATATAGATACATG
* * * *
30816859 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATA-AGACCATAACTGGGTTGTGGCAC-TAC
1 TGTAAGACCATAGCTGAGCTATGGCATTCTAATGA-ACAGACCATAACTGAGTTATGGCACAT-C
*
30816922 AAATGTAAGACCATGGCA-GAGCCATGACAAT
64 AAACGTAAGACCATGGCAGGA-CCATGACAAT
30816953 GCATGTAATA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
104 3 0.04
105 76 0.95
106 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (105 bp):
TGTAAGACCATAGCTGAGCTATGGCATTCTAATGAACAGACCATAACTGAGTTATGGCACATCAA
ACGTAAGACCATGGCAGGACCATGACAATATAGATACATG
Found at i:30826041 original size:26 final size:26
Alignment explanation
Indices: 30825989--30826041 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
30825979 TCCATTGAAT
** *
30825989 ATAATTAAAATATATTAATTTATTTA
1 ATAATTAAAATATATTAATAAAATTA
* *
30826015 ATAATTTAAATATTTTAATAAAATTA
1 ATAATTAAAATATATTAATAAAATTA
30826041 A
1 A
30826042 AGCATTTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATAATTAAAATATATTAATAAAATTA
Found at i:30827486 original size:77 final size:78
Alignment explanation
Indices: 30827390--30827544 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
30827380 AAAATGAATA
30827390 TATATATATATATAAATTAAAATTAGAGAGATGTATTAAAATTTTAAAAATTCTCAAAACGCAAA
1 TATATATATATATAAATTAAAATTAGAGAGATGTATTAAAATTTTAAAAATTCTCAAAACGCAAA
30827455 AATGACGTGTAAT
66 AATGACGTGTAAT
30827468 TATATATATA-ATAAATTAAAATTAGAGAGATGTATTAAAATTTTAAAAATTCTCAAAACGCAAA
1 TATATATATATATAAATTAAAATTAGAGAGATGTATTAAAATTTTAAAAATTCTCAAAACGCAAA
30827532 AATGACGTGTAAT
66 AATGACGTGTAAT
30827545 GGTTATATTC
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 67 0.87
78 10 0.13
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.33
Consensus pattern (78 bp):
TATATATATATATAAATTAAAATTAGAGAGATGTATTAAAATTTTAAAAATTCTCAAAACGCAAA
AATGACGTGTAAT
Found at i:30831202 original size:3 final size:3
Alignment explanation
Indices: 30831194--30831262 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
30831184 NNNNNNNNNN
30831194 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30831242 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
30831263 GTTCGAGAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30835902 original size:19 final size:19
Alignment explanation
Indices: 30835878--30835916 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
30835868 TCAGCAAAGT
30835878 TAGCATTCTCAATCTACCA
1 TAGCATTCTCAATCTACCA
30835897 TAGCATTCTCAATCTACCA
1 TAGCATTCTCAATCTACCA
30835916 T
1 T
30835917 CTTAAGCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (19 bp):
TAGCATTCTCAATCTACCA
Found at i:30837376 original size:3 final size:3
Alignment explanation
Indices: 30837370--30837412 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
30837360 AAAAAAAAAA
30837370 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AGAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG
30837413 GGAGACGGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:30837417 original size:7 final size:7
Alignment explanation
Indices: 30837371--30837417 Score: 50
Period size: 6 Copynumber: 7.4 Consensus size: 7
30837361 AAAAAAAAAA
30837371 AGAAGA-
1 AGAAGAG
30837377 AGAAGA-
1 AGAAGAG
30837383 AGAAGA-
1 AGAAGAG
30837389 AGAAGA-
1 AGAAGAG
30837395 AGAAGA-
1 AGAAGAG
30837401 AGAAGAG
1 AGAAGAG
*
30837408 AGAAGGG
1 AGAAGAG
30837415 AGA
1 AGA
30837418 CGGTAACCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
6 30 0.77
7 9 0.23
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (7 bp):
AGAAGAG
Found at i:30838498 original size:26 final size:26
Alignment explanation
Indices: 30838462--30838517 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
30838452 GTTTAATCAA
30838462 AGCATAATTTCGGTCCAAATTCATAC
1 AGCATAATTTCGGTCCAAATTCATAC
30838488 AGCATAATTTCGGTCCAAATTCATAC
1 AGCATAATTTCGGTCCAAATTCATAC
30838514 AGCA
1 AGCA
30838518 AGTTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (26 bp):
AGCATAATTTCGGTCCAAATTCATAC
Found at i:30841240 original size:17 final size:16
Alignment explanation
Indices: 30841220--30841264 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
30841210 AGTATTTTAA
30841220 TTTTTTATTTTATCTT
1 TTTTTTATTTTATCTT
* *
30841236 TTTTTAACTTTTTTCTT
1 TTTTTTA-TTTTATCTT
30841253 TTTCTTTATTTT
1 TTT-TTTATTTT
30841265 CCATTCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.25
17 15 0.62
18 3 0.12
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTATTTTATCTT
Found at i:30841240 original size:23 final size:24
Alignment explanation
Indices: 30841212--30841264 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
30841202 TCCTTTTGAG
30841212 TATTTTAA-TTTTTTATTTTATCTT
1 TATTTTAACTTTTTTATTTT-TCTT
*
30841236 T-TTTTAACTTTTTTCTTTTTCTT
1 TATTTTAACTTTTTTATTTTTCTT
30841259 TATTTT
1 TATTTT
30841265 CCATTCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (24 bp):
TATTTTAACTTTTTTATTTTTCTT
Found at i:30842278 original size:13 final size:13
Alignment explanation
Indices: 30842260--30842284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30842250 AGAAGAGAAT
30842260 GGGAAAAAAAAAA
1 GGGAAAAAAAAAA
30842273 GGGAAAAAAAAA
1 GGGAAAAAAAAA
30842285 CATAAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GGGAAAAAAAAAA
Found at i:30848402 original size:11 final size:11
Alignment explanation
Indices: 30848374--30848446 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
30848364 ATTAATCCTT
*
30848374 TCTCAATTATTT
1 TCTCAATT-TTC
30848386 TCTCAATTTTC
1 TCTCAATTTTC
*
30848397 TCTCAATTTCC
1 TCTCAATTTTC
* * *
30848408 TTTCAAATTGC
1 TCTCAATTTTC
*
30848419 TCTCAATTTCC
1 TCTCAATTTTC
*
30848430 T-TCCAAATTTC
1 TCT-CAATTTTC
30848441 TCTCAA
1 TCTCAA
30848447 ATCCATATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
10 1 0.02
11 39 0.80
12 9 0.18
ACGTcount: A:0.23, C:0.27, G:0.01, T:0.48
Consensus pattern (11 bp):
TCTCAATTTTC
Found at i:30848421 original size:22 final size:22
Alignment explanation
Indices: 30848396--30848446 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
30848386 TCTCAATTTT
*
30848396 CTCTCAATTTCCTTTCAAATTG
1 CTCTCAATTTCCTTCCAAATTG
*
30848418 CTCTCAATTTCCTTCCAAATTT
1 CTCTCAATTTCCTTCCAAATTG
30848440 CTCTCAA
1 CTCTCAA
30848447 ATCCATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.43
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAATTG
Found at i:30848471 original size:51 final size:51
Alignment explanation
Indices: 30848410--30848507 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
30848400 CAATTTCCTT
30848410 TCAAATTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAATC
1 TCAAATTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAATC
* * * *
30848461 TCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
30848508 TTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.45
Consensus pattern (51 bp):
TCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAATC
Found at i:30848483 original size:11 final size:11
Alignment explanation
Indices: 30848386--30848483 Score: 55
Period size: 11 Copynumber: 9.3 Consensus size: 11
30848376 TCAATTATTT
*
30848386 TCTCAATTTTC
1 TCTCAATTTCC
30848397 TCTCAATTTCC
1 TCTCAATTTCC
* * *
30848408 TTTCAAATTGC
1 TCTCAATTTCC
30848419 TCTCAATTTCC
1 TCTCAATTTCC
30848430 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
30848441 TCTCAA-ATCC
1 TCTCAATTTCC
* **
30848451 -AT--ATTTAA
1 TCTCAATTTCC
*
30848459 TCTCAATTTGC
1 TCTCAATTTCC
30848470 TCTCAATTTCC
1 TCTCAATTTCC
30848481 TCT
1 TCT
30848484 TAAATTTCTC
Statistics
Matches: 63, Mismatches: 16, Indels: 16
0.66 0.17 0.17
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.06
11 48 0.76
12 6 0.10
ACGTcount: A:0.23, C:0.29, G:0.02, T:0.46
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:30848537 original size:18 final size:17
Alignment explanation
Indices: 30848514--30848547 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30848504 ATTTTTAATT
30848514 ATTTTTTAAAAAATTTTA
1 ATTTTTT-AAAAATTTTA
*
30848532 ATTTTTTTAAAATTTT
1 ATTTTTTAAAAATTTT
30848548 TTAAATCGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTTAAAAATTTTA
Found at i:30851238 original size:135 final size:135
Alignment explanation
Indices: 30850985--30851254 Score: 369
Period size: 135 Copynumber: 2.0 Consensus size: 135
30850975 CGATTTGGGC
* * * *
30850985 ATGATCGGTTTGTATGGCCTGGATTCCTACACCATCCGCACAACTTGCCTTAACAGACTATTTCT
1 ATGATCGGCTTGTATGACCTAGATTCCTACACCATCCGCACAACTTGCATTAACAGACTATTTCT
* *
30851050 CGGATATCCATATTATTACGTATTCTAGTTAAGCAAGGTTGACCCTTCAGTTTGCGACGCAATTC
66 CGGATATCCATATTATTACGTATTCTAGTTAAGCAAGGTCGACCATTCAGTTTGCGACGCAATTC
30851115 TCTAT
131 TCTAT
** ** * * ** *
30851120 ATGATCGGCTTGTATGACCTAGATTTTTACACCATCCGCACAACTTTTATTGACTGGTTGTTTCT
1 ATGATCGGCTTGTATGACCTAGATTCCTACACCATCCGCACAACTTGCATTAACAGACTATTTCT
* * **
30851185 CGGATATCCATATTGTTACGTATTCTAGTTGAGCAAGGTCGACCATTTGGTTTGCGACGCAATTC
66 CGGATATCCATATTATTACGTATTCTAGTTAAGCAAGGTCGACCATTCAGTTTGCGACGCAATTC
30851250 TCTAT
131 TCTAT
30851255 CCGGTAATAG
Statistics
Matches: 116, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
135 116 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (135 bp):
ATGATCGGCTTGTATGACCTAGATTCCTACACCATCCGCACAACTTGCATTAACAGACTATTTCT
CGGATATCCATATTATTACGTATTCTAGTTAAGCAAGGTCGACCATTCAGTTTGCGACGCAATTC
TCTAT
Found at i:30852400 original size:9 final size:9
Alignment explanation
Indices: 30852386--30852416 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30852376 GTTAAACGAA
30852386 TCGAGTTAT
1 TCGAGTTAT
*
30852395 TCGAGTTAA
1 TCGAGTTAT
30852404 TCGAGTTAT
1 TCGAGTTAT
30852413 TCGA
1 TCGA
30852417 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:30853208 original size:5 final size:5
Alignment explanation
Indices: 30853198--30853228 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
30853188 GAACAAATAT
30853198 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
30853229 ATTCCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:30853328 original size:5 final size:5
Alignment explanation
Indices: 30853318--30853343 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30853308 CTCGAAAATT
30853318 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
30853344 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:30855366 original size:124 final size:124
Alignment explanation
Indices: 30855103--30855513 Score: 642
Period size: 124 Copynumber: 3.3 Consensus size: 124
30855093 CCCAAACATG
* * *
30855103 CTACTGTAGCAAAAACGTGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAATATCCTGC
* *
30855168 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAATTCGAAATTATTTTTTCAGGAC
66 TTGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * * *
30855228 CTACTATAGCAAAAGCGCGTCCACGTGAGAGCGATTTCAGAAATTCTTCTAATAAAGTATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAATATCCTGC
*
30855293 TTGAAGCGTTTTTATACTATTTACTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * *
30855352 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAGAAATTTTTCTGATAAAATATCTTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAATATCCTGC
30855417 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * *
30855476 TTACTGTAGCAAACGCGAGTCCACGTGGGAGGGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
30855514 CTTAATAAAT
Statistics
Matches: 260, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
124 195 0.75
125 65 0.25
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAATATCCTGC
TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:30855725 original size:6 final size:6
Alignment explanation
Indices: 30855707--30855750 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
30855697 AAAAAGCCTA
* *
30855707 AACCCT AAACCT AACCCT AACCCT AACCCT AACCCT GACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA
30855751 AAACCCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.36, C:0.45, G:0.02, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:30868106 original size:64 final size:64
Alignment explanation
Indices: 30868028--30868285 Score: 507
Period size: 64 Copynumber: 4.0 Consensus size: 64
30868018 TTTCTTCCAT
30868028 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
1 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
30868092 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
1 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
30868156 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
1 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
*
30868220 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTGCATAAATGTAAATATGC
1 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
30868284 TT
1 TT
30868286 AAAATTTATC
Statistics
Matches: 193, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 193 1.00
ACGTcount: A:0.20, C:0.12, G:0.13, T:0.55
Consensus pattern (64 bp):
TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
Found at i:30871660 original size:24 final size:23
Alignment explanation
Indices: 30871623--30871667 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
30871613 TTAAATCCAA
* *
30871623 AAAATAAAATGACTATATTTCTC
1 AAAATAAAAGGACTAAATTTCTC
30871646 AAAATAAAAGGGACTAAATTTC
1 AAAATAAAA-GGACTAAATTTC
30871668 AAATGTACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (23 bp):
AAAATAAAAGGACTAAATTTCTC
Found at i:30882037 original size:25 final size:26
Alignment explanation
Indices: 30881998--30882062 Score: 105
Period size: 25 Copynumber: 2.5 Consensus size: 26
30881988 ATTACTTAGG
30881998 AAGCCTTTGTGGCTAATCTTGT-GAA
1 AAGCCTTTGTGGCTAATCTTGTGGAA
**
30882023 AAGTTTTTGTGGCTAATCTTGTGGAA
1 AAGCCTTTGTGGCTAATCTTGTGGAA
30882049 AAGCCTTTGTGGCT
1 AAGCCTTTGTGGCT
30882063 TGTTATTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (26 bp):
AAGCCTTTGTGGCTAATCTTGTGGAA
Found at i:30895426 original size:41 final size:41
Alignment explanation
Indices: 30895381--30895660 Score: 488
Period size: 41 Copynumber: 6.8 Consensus size: 41
30895371 TTGTATATAA
* ** * * *
30895381 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* *
30895422 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
30895463 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
30895504 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
30895545 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
30895586 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
30895627 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
30895661 ACTTACAAAA
Statistics
Matches: 229, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 229 1.00
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.19
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:30904995 original size:9 final size:9
Alignment explanation
Indices: 30904965--30904989 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30904955 TTTATTATCC
30904965 TTATTATTG
1 TTATTATTG
30904974 TTATTATTG
1 TTATTATTG
30904983 TTATTAT
1 TTATTAT
30904990 GATTATCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:30908488 original size:29 final size:30
Alignment explanation
Indices: 30908456--30908515 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
30908446 AAAATTATAA
*
30908456 AAAAATTTGTAAAAATG-GTAAAAAA-TATT
1 AAAAATAT-TAAAAATGTGTAAAAAAGTATT
30908485 -AAAATATTAAAAATGTGTAAAAAAGTATT
1 AAAAATATTAAAAATGTGTAAAAAAGTATT
30908514 AA
1 AA
30908516 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 8 0.30
28 14 0.52
29 4 0.15
30 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (30 bp):
AAAAATATTAAAAATGTGTAAAAAAGTATT
Found at i:30911972 original size:1 final size:1
Alignment explanation
Indices: 30911961--30911991 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
30911951 TTGGTCCCAT
*
30911961 AAAAGAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30911992 GAATGCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:30912404 original size:4 final size:4
Alignment explanation
Indices: 30912395--30912425 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
30912385 TCAATGTAAA
30912395 ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACT
1 ACTC ACTC ACTC ACTC ACTC ACTC ACTC ACT
30912426 TTTTTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
ACTC
Found at i:30915287 original size:25 final size:25
Alignment explanation
Indices: 30915252--30915335 Score: 125
Period size: 25 Copynumber: 3.4 Consensus size: 25
30915242 TATATATTAA
30915252 ATATATATTTTATTTTTAATCAAAT
1 ATATATATTTTATTTTTAATCAAAT
*
30915277 ATATATTTTTTATTTTTAATCAAAT
1 ATATATATTTTATTTTTAATCAAAT
* * *
30915302 ATATATATTTTATATAT-ATTAAAT
1 ATATATATTTTATTTTTAATCAAAT
30915326 ATATATATTT
1 ATATATATTT
30915336 AATATGGGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 16 0.30
25 38 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATATATATTTTATTTTTAATCAAAT
Found at i:30915328 original size:13 final size:13
Alignment explanation
Indices: 30915298--30915340 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
30915288 ATTTTTAATC
30915298 AAATATATATATT
1 AAATATATATATT
*
30915311 --TTATATATATT
1 AAATATATATATT
30915322 AAATATATATATT
1 AAATATATATATT
*
30915335 TAATAT
1 AAATAT
30915341 GGGCTGGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 10 0.40
13 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AAATATATATATT
Found at i:30920391 original size:27 final size:28
Alignment explanation
Indices: 30920360--30920416 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
30920350 TTTTTTTTCA
* *
30920360 TTGTTTTGCTATTA-TATTGTTACTATT
1 TTGTTTTACTATTAGTATTGCTACTATT
* *
30920387 TTGTTTTATTATTAGTTTTGCTACTATT
1 TTGTTTTACTATTAGTATTGCTACTATT
30920415 TT
1 TT
30920417 AGAGATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.65
Consensus pattern (28 bp):
TTGTTTTACTATTAGTATTGCTACTATT
Found at i:30922861 original size:21 final size:20
Alignment explanation
Indices: 30922836--30922901 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
30922826 TGAAATATTT
30922836 TTTTTCAAAGTTTAATTAAAA
1 TTTTTCAAAG-TTAATTAAAA
*
30922857 TTTTT-ATGAAGTAAATGT-AAA
1 TTTTTCA--AAGTTAAT-TAAAA
30922878 -TTTTCAAAGATTAATT-AAA
1 TTTTTCAAAG-TTAATTAAAA
30922897 TTTTT
1 TTTTT
30922902 TTTTAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
19 7 0.19
20 13 0.35
21 13 0.35
22 4 0.11
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (20 bp):
TTTTTCAAAGTTAATTAAAA
Found at i:30926560 original size:18 final size:19
Alignment explanation
Indices: 30926532--30926571 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
30926522 ATGAAAGTAA
*
30926532 GATTGTGTTTGAAATGGAT
1 GATTGTGTTTGAAATGAAT
*
30926551 GATTGT-TTTGATATGAAT
1 GATTGTGTTTGAAATGAAT
30926569 GAT
1 GAT
30926572 ATTTATGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (19 bp):
GATTGTGTTTGAAATGAAT
Found at i:30930622 original size:2 final size:2
Alignment explanation
Indices: 30930615--30930651 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
30930605 GTCCTACCAT
30930615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30930652 TTTTGTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30931571 original size:17 final size:19
Alignment explanation
Indices: 30931535--30931579 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
30931525 GTTTAACTAA
30931535 TATTTTATATTTAATATAT
1 TATTTTATATTTAATATAT
*
30931554 TATTTT-TA-TTAATTTA-
1 TATTTTATATTTAATATAT
30931570 T-TTTTATATT
1 TATTTTATATT
30931580 GCTTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 4 0.17
16 3 0.13
17 8 0.35
18 2 0.09
19 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTATATTTAATATAT
Found at i:30931929 original size:208 final size:209
Alignment explanation
Indices: 30931562--30931980 Score: 831
Period size: 208 Copynumber: 2.0 Consensus size: 209
30931552 ATTATTTTTA
30931562 TTAATTTATTTTTATATTGCTTATAATACTTTGTTTTATATACAGCAACTTAATCAATAGAGCTA
1 TTAATTTATTTTTATATTGCTTATAATACTTTGTTTTATATACAGCAACTTAATCAATAGAGCTA
30931627 ACTGACATTGGAATATTGAAAAATTTCAAAACAAATTAAATTAAATTAAGAATTTTTAAAGATAT
66 ACTGACATTGGAATATTGAAAAATTTCAAAACAAATTAAATTAAATTAAGAATTTTTAAAGATAT
30931692 AAAGTTTCTAATAGTTTAAATAAATTAAGAAAATATAAGAAAAATAACAAAAACTTTTAGAAGAT
131 AAAGTTTCTAATAGTTTAAATAAATTAAGAAAATATAAGAAAAATAACAAAAACTTTTAGAAGAT
30931757 TAAAAAGTGATATT
196 TAAAAAGTGATATT
30931771 TTAATTTA-TTTTATATTGCTTATAATACTTTGTTTTATATACAGCAACTTAATCAATAGAGCTA
1 TTAATTTATTTTTATATTGCTTATAATACTTTGTTTTATATACAGCAACTTAATCAATAGAGCTA
30931835 ACTGACATTGGAATATTGAAAAATTTCAAAACAAATTAAATTAAATTAAGAATTTTTAAAGATAT
66 ACTGACATTGGAATATTGAAAAATTTCAAAACAAATTAAATTAAATTAAGAATTTTTAAAGATAT
30931900 AAAGTTTCTAATAGTTTAAATAAATTAAGAAAATATAAGAAAAATAACAAAAACTTTTAGAAGAT
131 AAAGTTTCTAATAGTTTAAATAAATTAAGAAAATATAAGAAAAATAACAAAAACTTTTAGAAGAT
30931965 TAAAAAGTGATATT
196 TAAAAAGTGATATT
30931979 TT
1 TT
30931981 GTTTCTTCTT
Statistics
Matches: 210, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
208 202 0.96
209 8 0.04
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (209 bp):
TTAATTTATTTTTATATTGCTTATAATACTTTGTTTTATATACAGCAACTTAATCAATAGAGCTA
ACTGACATTGGAATATTGAAAAATTTCAAAACAAATTAAATTAAATTAAGAATTTTTAAAGATAT
AAAGTTTCTAATAGTTTAAATAAATTAAGAAAATATAAGAAAAATAACAAAAACTTTTAGAAGAT
TAAAAAGTGATATT
Found at i:30932382 original size:83 final size:81
Alignment explanation
Indices: 30932295--30932554 Score: 290
Period size: 80 Copynumber: 3.2 Consensus size: 81
30932285 AAATAAATTC
* * *
30932295 ATTTTAAAGGGACTAAAGTGTAATTTTACTATATATTAAATTATGATTTCTTTATTTATAAGAGG
1 ATTTT-AAGGGAC-AAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGG
* *
30932360 ACTGAATTGAAAATTTTT
64 ATTAAATTGAAAATTTTT
* * * * **
30932378 ATTTTAAGAGGTCAAAGTGCAATTTTATTATAATATTAATTTGTAATTTATCCATTTATAAGAGG
1 ATTTTAAG-GGACAAAGTGCAATTTTACTAT-ATATTAATTTATAATTTCTTTATTTATAAGAGG
*
30932443 ATTAAATTG-AAATTATT
64 ATTAAATTGAAAATTTTT
* * * * *
30932460 ATTGTGAGGGACAAAATACAAATTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGAT
1 ATTTTAAGGGACAAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGAT
* *
30932525 TAAATTTAAAATTTTC
66 TAAATTGAAAATTTTT
*
30932541 ATTTT-CGGGACAAA
1 ATTTTAAGGGACAAA
30932555 TCGTTTGTGT
Statistics
Matches: 146, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
80 45 0.31
81 27 0.18
82 32 0.22
83 42 0.29
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (81 bp):
ATTTTAAGGGACAAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGAT
TAAATTGAAAATTTTT
Found at i:30933485 original size:12 final size:12
Alignment explanation
Indices: 30933468--30933499 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
30933458 ATTTCCTCTT
30933468 ATCATCATCACC
1 ATCATCATCACC
30933480 ATCATCATCACC
1 ATCATCATCACC
*
30933492 ACCATCAT
1 ATCATCAT
30933500 GACTCAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (12 bp):
ATCATCATCACC
Found at i:30933488 original size:15 final size:15
Alignment explanation
Indices: 30933468--30933499 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30933458 ATTTCCTCTT
*
30933468 ATCATCATCACCATC
1 ATCATCACCACCATC
30933483 ATCATCACCACCATC
1 ATCATCACCACCATC
30933498 AT
1 AT
30933500 GACTCAACTA
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:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (15 bp):
ATCATCACCACCATC
Found at i:30936338 original size:16 final size:17
Alignment explanation
Indices: 30936308--30936340 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30936298 TCGGAAAATT
*
30936308 TTTTAAAATTTATAAAG
1 TTTTAAAATTAATAAAG
30936325 TTTT-AAATTAATAAAG
1 TTTTAAAATTAATAAAG
30936341 GTAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TTTTAAAATTAATAAAG
Found at i:30936440 original size:55 final size:54
Alignment explanation
Indices: 30936392--30936508 Score: 198
Period size: 55 Copynumber: 2.1 Consensus size: 54
30936382 TTTAATCATT
*
30936392 TAAAAGTTATTAAGATATAGTCTATTAAAATAGTAAAATTATATATTTATTATCA
1 TAAAAATTATTAAGATATAGTCTATTAAAATAGTAAAATTATATATTTA-TATCA
*
30936447 TAAAAATTATTAAGATATAGTCTATTAAAATAGTAAAATTATATTTTTATTATCA
1 TAAAAATTATTAAGATATAGTCTATTAAAATAGTAAAATTATATATTTA-TATCA
30936502 TAAAAAT
1 TAAAAAT
30936509 AGTAGGGTGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (54 bp):
TAAAAATTATTAAGATATAGTCTATTAAAATAGTAAAATTATATATTTATATCA
Found at i:30936442 original size:25 final size:25
Alignment explanation
Indices: 30936414--30936498 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 25
30936404 AGATATAGTC
30936414 TATTAAAATAGTAAAATTATATATT
1 TATTAAAATAGTAAAATTATATATT
**
30936439 TATTATCATA--AAAATTATTAAGATATAGT
1 TATTAAAATAGTAAAATTA-T---ATAT--T
*
30936468 CTATTAAAATAGTAAAATTATATTTT
1 -TATTAAAATAGTAAAATTATATATT
30936494 TATTA
1 TATTA
30936499 TCATAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 18
0.67 0.07 0.26
Matches are distributed among these distances:
23 7 0.15
24 1 0.02
25 13 0.28
26 1 0.02
27 4 0.09
28 3 0.07
29 1 0.02
30 8 0.17
31 1 0.02
32 7 0.15
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (25 bp):
TATTAAAATAGTAAAATTATATATT
Found at i:30936453 original size:31 final size:31
Alignment explanation
Indices: 30936418--30936512 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 31
30936408 ATAGTCTATT
30936418 AAAATAGTAAAATTATATATTTATTATCATA
1 AAAATAGTAAAATTATATATTTATTATCATA
* * * * *
30936449 AAAAT--T---ATTA-AGATATAGTCT-ATT
1 AAAATAGTAAAATTATATATTTATTATCATA
*
30936473 AAAATAGTAAAATTATATTTTTATTATCATA
1 AAAATAGTAAAATTATATATTTATTATCATA
30936504 AAAATAGTA
1 AAAATAGTA
30936513 GGGTGTGAGT
Statistics
Matches: 46, Mismatches: 11, Indels: 14
0.65 0.15 0.20
Matches are distributed among these distances:
24 7 0.15
25 7 0.15
26 5 0.11
29 5 0.11
30 6 0.13
31 16 0.35
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
AAAATAGTAAAATTATATATTTATTATCATA
Found at i:30936485 original size:32 final size:32
Alignment explanation
Indices: 30936392--30936488 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 32
30936382 TTTAATCATT
30936392 TAAAAGTTATTAAGATATAGTCTATTAAAATAG
1 TAAAA-TTATTAAGATATAGTCTATTAAAATAG
**
30936425 TAAAATTA-T---ATAT--T-TATTATCATA-
1 TAAAATTATTAAGATATAGTCTATTAAAATAG
30936449 -AAAATTATTAAGATATAGTCTATTAAAATAG
1 TAAAATTATTAAGATATAGTCTATTAAAATAG
30936480 TAAAATTAT
1 TAAAATTAT
30936489 ATTTTTATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
23 7 0.14
24 1 0.02
25 8 0.16
26 1 0.02
27 4 0.08
28 4 0.08
29 1 0.02
30 8 0.16
31 1 0.02
32 11 0.22
33 5 0.10
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.40
Consensus pattern (32 bp):
TAAAATTATTAAGATATAGTCTATTAAAATAG
Found at i:30937348 original size:17 final size:19
Alignment explanation
Indices: 30937312--30937356 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
30937302 GTTTAACTAA
30937312 TATTTTATATTTAATATAT
1 TATTTTATATTTAATATAT
*
30937331 TATTTT-TA-TTAATTTA-
1 TATTTTATATTTAATATAT
30937347 T-TTTTATATT
1 TATTTTATATT
30937357 GCTTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 4 0.17
16 3 0.13
17 8 0.35
18 2 0.09
19 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTATATTTAATATAT
Found at i:30937951 original size:83 final size:81
Alignment explanation
Indices: 30937864--30938123 Score: 290
Period size: 80 Copynumber: 3.2 Consensus size: 81
30937854 AAATAAATTC
* * *
30937864 ATTTTAAAGGGACTAAAGTGTAATTTTACTATATATTAAATTATGATTTCTTTATTTATAAGAGG
1 ATTTT-AAGGGAC-AAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGG
* *
30937929 ACTGAATTGAAAATTTTT
64 ATTAAATTGAAAATTTTT
* * * * **
30937947 ATTTTAAGAGGTCAAAGTGCAATTTTATTATAATATTAATTTGTAATTTATCCATTTATAAGAGG
1 ATTTTAAG-GGACAAAGTGCAATTTTACTAT-ATATTAATTTATAATTTCTTTATTTATAAGAGG
*
30938012 ATTAAATTG-AAATTATT
64 ATTAAATTGAAAATTTTT
* * * * *
30938029 ATTGTGAGGGACAAAATACAAATTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGAT
1 ATTTTAAGGGACAAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGAT
* *
30938094 TAAATTTAAAATTTTC
66 TAAATTGAAAATTTTT
*
30938110 ATTTT-CGGGACAAA
1 ATTTTAAGGGACAAA
30938124 TCGTTTGTGT
Statistics
Matches: 146, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
80 45 0.31
81 27 0.18
82 32 0.22
83 42 0.29
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (81 bp):
ATTTTAAGGGACAAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGAT
TAAATTGAAAATTTTT
Found at i:30942777 original size:5 final size:5
Alignment explanation
Indices: 30942767--30942794 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
30942757 AAACCCACCC
30942767 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
30942795 TTCAAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:30943857 original size:34 final size:34
Alignment explanation
Indices: 30943819--30943886 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
30943809 CTAAGAAAGA
30943819 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
1 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
30943853 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
1 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
30943887 TCATTGCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (34 bp):
GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
Found at i:30953154 original size:19 final size:18
Alignment explanation
Indices: 30953130--30953183 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
30953120 TGCCAGAAGT
30953130 AAATAAAAGAAAAATTAGA
1 AAATAAAAGAAAAATTA-A
** *
30953149 AAATAAAAGTTAAACTAA
1 AAATAAAAGAAAAATTAA
*
30953167 AAATAAAATAAAAATTA
1 AAATAAAAGAAAAATTA
30953184 TAATAGAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (18 bp):
AAATAAAAGAAAAATTAA
Found at i:30953174 original size:23 final size:23
Alignment explanation
Indices: 30953148--30953197 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
30953138 GAAAAATTAG
*
30953148 AAAATAAAAGTTA-AACTAAAAAT
1 AAAATAAAAATTATAA-TAAAAAT
*
30953171 AAAATAAAAATTATAATAGAAAT
1 AAAATAAAAATTATAATAAAAAT
30953194 AAAA
1 AAAA
30953198 ATGGCTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAATAAAAATTATAATAAAAAT
Found at i:30953677 original size:25 final size:25
Alignment explanation
Indices: 30953640--30953688 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
30953630 TTGCTTAGGG
30953640 ATTTTATTGTATTCAATATTAATAT
1 ATTTTATTGTATTCAATATTAATAT
*
30953665 ATTTATATT-TATTTAATATTAATA
1 ATTT-TATTGTATTCAATATTAATA
30953689 CAAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTATTGTATTCAATATTAATAT
Found at i:30956451 original size:3 final size:3
Alignment explanation
Indices: 30956443--30956477 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
30956433 TCAGTCCCAG
30956443 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
30956478 TGAAGAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:30957579 original size:12 final size:12
Alignment explanation
Indices: 30957559--30957604 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
30957549 NNNNNNNNNG
30957559 TCTCCCTCTCTC
1 TCTCCCTCTCTC
30957571 TCT--CTCTCTC
1 TCTCCCTCTCTC
30957581 TC-CCCGTCTCTC
1 TCTCCC-TCTCTC
30957593 TCTCCCTCTCTC
1 TCTCCCTCTCTC
30957605 CATATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.30
11 1 0.03
12 17 0.57
13 3 0.10
ACGTcount: A:0.00, C:0.57, G:0.02, T:0.41
Consensus pattern (12 bp):
TCTCCCTCTCTC
Found at i:30961864 original size:27 final size:27
Alignment explanation
Indices: 30961834--30961889 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
30961824 CCCAGAAAGA
30961834 GATGTTACTTGCAAGGCATGAGTGTGG
1 GATGTTACTTGCAAGGCATGAGTGTGG
30961861 GATGTTACTTGCAAGGCATGAGTGTGG
1 GATGTTACTTGCAAGGCATGAGTGTGG
30961888 GA
1 GA
30961890 CAATTATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.38, T:0.29
Consensus pattern (27 bp):
GATGTTACTTGCAAGGCATGAGTGTGG
Found at i:30965699 original size:41 final size:41
Alignment explanation
Indices: 30965651--30965732 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
30965641 ATAGCAAAAT
30965651 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
1 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
30965692 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
1 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
30965733 TAAAGCTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (41 bp):
CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
Found at i:30966358 original size:7 final size:7
Alignment explanation
Indices: 30966340--30966373 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
30966330 ATATTTGTAA
30966340 GTGTGT-
1 GTGTGTG
30966346 GTGTGTG
1 GTGTGTG
30966353 GTGTGTG
1 GTGTGTG
30966360 GTGTGTG
1 GTGTGTG
30966367 GTGTGTG
1 GTGTGTG
30966374 CATCATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.00, C:0.00, G:0.56, T:0.44
Consensus pattern (7 bp):
GTGTGTG
Found at i:30967996 original size:365 final size:365
Alignment explanation
Indices: 30967326--30968044 Score: 1332
Period size: 365 Copynumber: 2.0 Consensus size: 365
30967316 ATGAGTTTCC
30967326 ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATCTCA
1 ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATCTCA
* * *
30967391 GCAAGCATATTTTGGAAGAAGAAATTTAAAATCATACCATATATTATACTAGTTTTAGTCAACAG
66 GCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAGTCAACAG
30967456 CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
131 CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
*
30967521 AAGAAAAAGATAACAGGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTACTCAGCTC
196 AAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTACTCAGCTC
30967586 TGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACTG
261 TGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACTG
30967651 TATACACAGACAGTCAGAGGCGAATCTAGTGAGTTTATCG
326 TATACACAGACAGTCAGAGGCGAATCTAGTGAGTTTATCG
*
30967691 ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTTTTAACAATTTAAGAAACCAACATCTCA
1 ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATCTCA
30967756 GCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAGTCAACAG
66 GCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAGTCAACAG
30967821 CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
131 CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
* * *
30967886 AGGAAAAAGATAACACGCATGACAGAAAATATTAAATAGGAAGTTTGTTTGATGTTA-TCCTGCT
196 AAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTACT-CAGCT
*
30967950 TTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACT
260 CTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACT
*
30968015 GTATTCACAGACAGTCAGAGGCGAATCTAG
325 GTATACACAGACAGTCAGAGGCGAATCTAG
30968045 GGGGCAGGCA
Statistics
Matches: 343, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
364 1 0.00
365 342 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (365 bp):
ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATCTCA
GCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAGTCAACAG
CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
AAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTACTCAGCTC
TGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACTG
TATACACAGACAGTCAGAGGCGAATCTAGTGAGTTTATCG
Done.