Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 113 of 206
Found at i:33771895 original size:21 final size:21
Alignment explanation
Indices: 33771865--33771905 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33771855 ATCTGTCAAA
*
33771865 TATGTGAATAATATATTTAGT
1 TATGTAAATAATATATTTAGT
*
33771886 TATGTAAATATTATATTTAG
1 TATGTAAATAATATATTTAG
33771906 GAAATTTATC
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:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
TATGTAAATAATATATTTAGT
Found at i:33777406 original size:92 final size:92
Alignment explanation
Indices: 33777255--33777426 Score: 213
Period size: 92 Copynumber: 1.9 Consensus size: 92
33777245 CTGAAATAAA
* *
33777255 TCTTATGAGCAATCTGAAGTGTTATCAGGGGAGAATATTTAGCCTACGGGCCTTACACTATGTGC
1 TCTTATGAGCAATCTGAAGTGTTATCAGGGGAGAAAATTTAGCCTACAGGCCTTACACTATGTGC
*
33777320 ACCTGGTGTCTTATCGGTTGGAATAGC
66 ACCTGGCGTCTTATCGGTTGGAATAGC
* * * * * *
33777347 TCTTATGAGCAATTTGACA-TGTTATC-GGGAGATAAAATTTAGCCTATAGGCTTTGCACTATTT
1 TCTTATGAGCAATCTGA-AGTGTTATCAGGG-GAGAAAATTTAGCCTACAGGCCTTACACTATGT
* *
33777410 GCATCTGGCGTGTTATC
64 GCACCTGGCGTCTTATC
33777427 AAATGGTCAC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
91 3 0.04
92 63 0.94
93 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (92 bp):
TCTTATGAGCAATCTGAAGTGTTATCAGGGGAGAAAATTTAGCCTACAGGCCTTACACTATGTGC
ACCTGGCGTCTTATCGGTTGGAATAGC
Found at i:33780882 original size:33 final size:33
Alignment explanation
Indices: 33780840--33781100 Score: 152
Period size: 33 Copynumber: 7.7 Consensus size: 33
33780830 AAGATATGGT
*
33780840 GGAATCAGCACTTAGCAACCACTAATGAATAGG
1 GGAATCAGCACTTAGCAACCCCTAATGAATAGG
33780873 GGAATCAGCACTTAGCAACCCCT--TG----GG
1 GGAATCAGCACTTAGCAACCCCTAATGAATAGG
*
33780900 GGAATCAGCACTTAGCAACCCCTTCACATTTAAAGATACGG
1 GGAATCAGCACTTAGCAACCCC-T-A-A--T-GA-ATA-GG
* * * *
33780941 TGGAATCAACACTTAGCAACCACAAATGAATTGG
1 -GGAATCAGCACTTAGCAACCCCTAATGAATAGG
*
33780975 GGAATCAACACTTAGCAACCCCT--TG---A-G
1 GGAATCAGCACTTAGCAACCCCTAATGAATAGG
*
33781002 GGAATCAGCACTTAGCAACCCCCTATATATTTAAAGATACGG
1 GGAATCAGCACTTAGCAA-CCCC--TA-A--T-GA-ATA-GG
* * *
33781044 TGGAATCAGCACATAGCAACCACC-AATGAGTTGG
1 -GGAATCAGCACTTAGCAACC-CCTAATGAATAGG
33781078 GGAATCAGCACTTAGCAACCCCT
1 GGAATCAGCACTTAGCAACCCCT
33781101 TCATATTCAA
Statistics
Matches: 178, Mismatches: 17, Indels: 66
0.68 0.07 0.25
Matches are distributed among these distances:
27 42 0.24
28 5 0.03
30 1 0.01
31 4 0.02
32 2 0.01
33 62 0.35
34 5 0.03
35 4 0.02
36 2 0.01
37 2 0.01
39 2 0.01
40 3 0.02
41 2 0.01
42 23 0.13
43 19 0.11
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCCCTAATGAATAGG
Found at i:33780905 original size:27 final size:27
Alignment explanation
Indices: 33780871--33780923 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
33780861 CTAATGAATA
33780871 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
33780898 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
33780924 CACATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.19
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTG
Found at i:33780954 original size:102 final size:102
Alignment explanation
Indices: 33780795--33781101 Score: 472
Period size: 103 Copynumber: 3.0 Consensus size: 102
33780785 CCAGTGATTC
* * *
33780795 GGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCC-TTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
* *
33780860 ACTAATGAATAGGGGAATCAGCACTTAGCAACCCCTTG
65 ACAAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
*
33780898 GGGGAATCAGCACTTAGCAACCCCTTCACATTTAAAGATACGGTGGAATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCA
*
33780963 CAAATGAATTGGGGAATCAACACTTAGCAACCCCTTG
66 CAAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
* * *
33781000 AGGGAATCAGCACTTAGCAACCCCCTAT-ATATTTAAAGATACGGTGGAATCAGCACATAGCAAC
1 GGGGAATCAGCACTTAGCAA-CCCCT-TCACATTTAAAGATACGGTGGAATCAGCACTTAGCAAC
* *
33781064 CACCAATGAGTTGGGGAATCAGCACTTAGCAACCCCTT
64 CACAAATGAATTGGGGAATCAGCACTTAGCAACCCCTT
33781102 CATATTCAAT
Statistics
Matches: 188, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
102 91 0.48
103 96 0.51
104 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACCA
CAAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:33787835 original size:27 final size:27
Alignment explanation
Indices: 33787797--33787872 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
33787787 AAGATATGGT
*
33787797 GGAATCAGCACTTAGCAACCCCTTGGG
1 GGAATCAGCACTTAGCAACCCCTTGAG
33787824 GGAATCAGCACTTAGCAACCCCTTGAG
1 GGAATCAGCACTTAGCAACCCCTTGAG
*
33787851 GGAATCAACACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
33787873 CTTTATATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (27 bp):
GGAATCAGCACTTAGCAACCCCTTGAG
Found at i:33787897 original size:97 final size:100
Alignment explanation
Indices: 33787753--33787950 Score: 269
Period size: 97 Copynumber: 2.0 Consensus size: 100
33787743 CAGTGATTCG
* ** *
33787753 GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC-
1 GGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATACAGTGGAATCAGAACTTAGCAACCA
*
33787817 CC-T-TGGGGGAATCAGCACTTAGCAACCCCTTGA
66 CCATGTCGGGGAATCAGCACTTAGCAACCCCTTGA
* *
33787850 GGGAATCAACACTTAGCAACCCCCTTT-ATATTTAAAGATACAGTGGAATCAGAACTTAGCAACC
1 GGGAATCAACACTTAGCAA-CCCCTTTCACATTCAAAGATACAGTGGAATCAGAACTTAGCAACC
33787914 ACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTT
65 ACC-AT--GTCGGGGAATCAGCACTTAGCAACCCCTT
33787951 CATATTCAAT
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
97 50 0.57
98 9 0.10
100 1 0.01
103 27 0.31
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (100 bp):
GGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATACAGTGGAATCAGAACTTAGCAACCA
CCATGTCGGGGAATCAGCACTTAGCAACCCCTTGA
Found at i:33801971 original size:5 final size:5
Alignment explanation
Indices: 33801961--33802014 Score: 81
Period size: 5 Copynumber: 10.8 Consensus size: 5
33801951 ATAAGGAAAA
* * *
33801961 ATATG ATATG ATATG ACATG ACATG ACATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
33802011 ATAT
1 ATAT
33802015 TGTGCTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.35
Consensus pattern (5 bp):
ATATG
Found at i:33802056 original size:5 final size:5
Alignment explanation
Indices: 33802046--33802077 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
33802036 AATAAGGAAA
*
33802046 GATAT GATAT GATAC GATAT GATAT GATAT GA
1 GATAT GATAT GATAT GATAT GATAT GATAT GA
33802078 ATTAATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (5 bp):
GATAT
Found at i:33802678 original size:65 final size:66
Alignment explanation
Indices: 33802596--33802728 Score: 189
Period size: 66 Copynumber: 2.0 Consensus size: 66
33802586 ATGAGAGCTT
* * * *
33802596 AGACTAGGCCCCCAAAA-GGGTTACTAAACCGAGAAG-AGGACATCCAAAAATAGAGCAAAACAA
1 AGACAAGGCCCCAAAAAGGGGTTACTAAACCGA-AAGAAAGACATCAAAAAATAGAGCAAAACAA
33802659 GG
65 GG
* *
33802661 AGACAAGGCCCCAAAAAGGGGTTATTAAACCGAAAGAAAGACATCAAAAAATAGAGCAGAACAAG
1 AGACAAGGCCCCAAAAAGGGGTTACTAAACCGAAAGAAAGACATCAAAAAATAGAGCAAAACAAG
33802726 G
66 G
33802727 AG
1 AG
33802729 GACGACAACC
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 18 0.30
66 42 0.70
ACGTcount: A:0.49, C:0.19, G:0.23, T:0.09
Consensus pattern (66 bp):
AGACAAGGCCCCAAAAAGGGGTTACTAAACCGAAAGAAAGACATCAAAAAATAGAGCAAAACAAG
G
Found at i:33807792 original size:51 final size:51
Alignment explanation
Indices: 33807731--33807841 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
33807721 TTTATTTCTC
*
33807731 ATTTT-CATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATTTCAT
1 ATTTTCCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATG-TTTCAT
** *
33807782 -TTTTCCATTTTCATTTTGGAGAAAACCTTAATCGTTTCCAAATGTTTCAT
1 ATTTTCCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTCAT
33807832 ATTTCTCCAT
1 ATTT-TCCAT
33807842 GTCACCATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
50 10 0.19
51 38 0.72
52 5 0.09
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (51 bp):
ATTTTCCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTCAT
Found at i:33809637 original size:41 final size:41
Alignment explanation
Indices: 33809535--33809640 Score: 167
Period size: 41 Copynumber: 2.6 Consensus size: 41
33809525 ACTGGCAATT
* * *
33809535 AGCCTGCTAGACGTATAGTCCGAAATATTTCACCGGCGTCA
1 AGCCTGCTAGACGTATAGTCTGAAACATTTCACCGGCATCA
33809576 AGCCTGCTAGACGTATAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTATAGTCTGAAACATTTCACCGGCATCA
* *
33809617 AGCCTGCTAGATGTAAAGTCTGAA
1 AGCCTGCTAGACGTATAGTCTGAA
33809641 TTATCTCACT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACGTATAGTCTGAAACATTTCACCGGCATCA
Found at i:33817110 original size:2 final size:2
Alignment explanation
Indices: 33817103--33817139 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
33817093 ATTATACATG
33817103 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
33817140 CGATCATAAA
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:33817534 original size:41 final size:41
Alignment explanation
Indices: 33817432--33817537 Score: 167
Period size: 41 Copynumber: 2.6 Consensus size: 41
33817422 ACTGGCAATT
* * * *
33817432 AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCGGCGTCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCA
*
33817473 AGCCTGCTAGACGTATAGTCTGAAACATTTCACCAGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCA
33817514 AGCCTGCTAGACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
33817538 TTATCTCATT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCA
Found at i:33822893 original size:13 final size:14
Alignment explanation
Indices: 33822875--33822904 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
33822865 AATTGTTATT
33822875 TGTTTTATG-TTTC
1 TGTTTTATGTTTTC
33822888 TGTTTTATGTTTTC
1 TGTTTTATGTTTTC
33822902 TGT
1 TGT
33822905 ATAGGAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.70
Consensus pattern (14 bp):
TGTTTTATGTTTTC
Found at i:33825114 original size:11 final size:11
Alignment explanation
Indices: 33825090--33825120 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
33825080 TAAATTAGTT
33825090 AAAATAATAAAC
1 AAAATAA-AAAC
33825102 AAAATAAAAAC
1 AAAATAAAAAC
33825113 AAAATAAA
1 AAAATAAA
33825121 TGTTATCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAATAAAAAC
Found at i:33833566 original size:21 final size:21
Alignment explanation
Indices: 33833540--33833581 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
33833530 AGTACCATAG
33833540 GAAATTAAATCTTTTATACAT
1 GAAATTAAATCTTTTATACAT
33833561 GAAATTAAATCTTTTATACAT
1 GAAATTAAATCTTTTATACAT
33833582 TTATAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (21 bp):
GAAATTAAATCTTTTATACAT
Found at i:33835875 original size:26 final size:23
Alignment explanation
Indices: 33835805--33835876 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 23
33835795 TCGAGCTGAA
33835805 GAAA-GGTAAGCTC-TATCAAGCT
1 GAAACGGTAAGCTCATA-CAAGCT
*
33835827 GAAACGATAAGCTCATA-AGAGCT
1 GAAACGGTAAGCTCATACA-AGCT
33835850 GATATATCGGTAAGCTCATACAAGCT
1 GA-A-A-CGGTAAGCTCATACAAGCT
33835876 G
1 G
33835877 TGGTGAGTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
22 5 0.12
23 14 0.34
24 3 0.07
25 1 0.02
26 17 0.41
27 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (23 bp):
GAAACGGTAAGCTCATACAAGCT
Found at i:33837515 original size:19 final size:19
Alignment explanation
Indices: 33837491--33837565 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
33837481 AATTTTTGAG
33837491 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
33837510 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
33837529 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
33837550 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
33837566 AGATGTGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 34 0.64
21 19 0.36
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:33837537 original size:21 final size:21
Alignment explanation
Indices: 33837492--33837554 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
33837482 ATTTTTGAGG
33837492 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
33837511 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
33837532 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
33837553 AT
1 AT
33837555 GTAATCTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.45
21 23 0.55
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:33843897 original size:44 final size:45
Alignment explanation
Indices: 33843759--33844174 Score: 388
Period size: 44 Copynumber: 9.4 Consensus size: 45
33843749 ATCAGTGAAC
* * * * *
33843759 ATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCAAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAG
*
33843803 AT-GCAAATCTTGTCTT-CTCATATTGGT-G-GCAGAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCT-ATATTGGTCGTG-A-AGTAGATCGAAG
* * * *
33843847 AAAGCAGATCTTGTCTTCATTTATTGG-CGTGAAGTAGGTCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAG
* * * *
33843891 ATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAG
* * * * *
33843935 AT-GCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAG
* * * *
33843979 AAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAA
1 ATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAG
* * * *
33844023 ATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAG
* * * *
33844067 AT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAG
* * * * *
33844111 AAAGCAGATATTATCTTCATGTATTGG-CGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAG
*
33844155 ATAGCAGATCTTGCCTTCCT
1 ATAGCAGATCTTGTCTTCCT
33844175 GCACCGACAG
Statistics
Matches: 297, Mismatches: 62, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
42 4 0.01
43 63 0.21
44 168 0.57
45 60 0.20
46 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCTATATTGGTCGTGAAGTAGATCGAAG
Found at i:33844174 original size:132 final size:132
Alignment explanation
Indices: 33843759--33844161 Score: 700
Period size: 132 Copynumber: 3.1 Consensus size: 132
33843749 ATCAGTGAAC
* * *
33843759 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAAATCTTGTCTTCTCAT
1 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
* * *
33843824 ATTGGTGGC-AGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGGCGTGAAGTAGGTCG
66 ACTGGTGGCGA-AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
33843888 AAG
130 AAG
*
33843891 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCAT
1 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
33843956 ACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA
66 ACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA
*
33844021 AA
131 AG
33844023 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
1 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
* *
33844088 ACTGGTGGCGAAGTAGATCGAAGAAAGCAGATATTATCTTCATGTATTGGCGTGAAGTAGATCGA
66 ACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA
33844153 AG
131 AG
33844155 ATAGCAG
1 ATAGCAG
33844162 ATCTTGCCTT
Statistics
Matches: 258, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
132 257 1.00
133 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (132 bp):
ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
ACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA
AG
Found at i:33844254 original size:264 final size:262
Alignment explanation
Indices: 33843759--33844260 Score: 602
Period size: 264 Copynumber: 1.9 Consensus size: 262
33843749 ATCAGTGAAC
*
33843759 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAAATCTTGTCTTCTCAT
1 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAAATCTTGTCTTCCCAT
* * * * *
33843824 ATTGGTGGCAGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATTTATTGGCGTGAAGTAGGTCGA
66 ACTGGTGGCAGAGTAGATCGAAGAAAGCAGATATTATCTTCATGTATTGGCGTGAAGTAGATCGA
* * * ** ** ** ** * * *
33843889 AGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATCTTCCC
131 AGATAGCAGATCCTGCCTTCCTACACCGACAGGAAGCAGATCGAAGAACCAGACCTTAGCCTCCC
* * * *
33843954 ATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC
196 ATA-GGGTGGC-AAGTAGAGCGAAAAAAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATC
33844019 GAAA
259 GAAA
* *
33844023 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCAT
1 ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAAATCTTGTCTTCCCAT
33844088 ACTGGTGGC-GAAGTAGATCGAAGAAAGCAGATATTATCTTCATGTATTGGCGTGAAGTAGATCG
66 ACTGGTGGCAG-AGTAGATCGAAGAAAGCAGATATTATCTTCATGTATTGGCGTGAAGTAGATCG
* *
33844152 AAGATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAG-CCTT-GCCT
130 AAGATAGCAGATCCTGCCTTCCTACACCGACAG-GAAGCAGATCGAAGA-ACCAGACCTTAGCCT
* *
33844215 CCC-T-GGGTTGC-AGTAGAGCAGGCTAAAAATAGTAGATCTTGCCTTC
193 CCCATAGGGTGGCAAGTAGAGC--G--AAAAA-AGCAGATCTTGCCTTC
33844261 CTGCACCGAC
Statistics
Matches: 200, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
259 7 0.04
261 6 0.03
263 6 0.03
264 162 0.81
265 16 0.08
266 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (262 bp):
ATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAAATCTTGTCTTCCCAT
ACTGGTGGCAGAGTAGATCGAAGAAAGCAGATATTATCTTCATGTATTGGCGTGAAGTAGATCGA
AGATAGCAGATCCTGCCTTCCTACACCGACAGGAAGCAGATCGAAGAACCAGACCTTAGCCTCCC
ATAGGGTGGCAAGTAGAGCGAAAAAAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGA
AA
Found at i:33844417 original size:88 final size:88
Alignment explanation
Indices: 33844155--33844373 Score: 375
Period size: 88 Copynumber: 2.5 Consensus size: 88
33844145 TAGATCGAAG
33844155 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
* *
33844220 GGTTGCAGTAGAGCAGGCTAAAA
66 GGTTGCAGTGGAGCAGGTTAAAA
* * *
33844243 ATAGTAGATCTTGCCTTCCTGCACCGACACCGAAGCAGATCGAAGACACCGGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
* *
33844308 GGTTGCAGCGGAGCAGATTAAAA
66 GGTTGCAGTGGAGCAGGTTAAAA
33844331 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
33844374 TGACCTCAGC
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 122 1.00
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.19
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGTGGAGCAGGTTAAAA
Found at i:33844447 original size:44 final size:44
Alignment explanation
Indices: 33844384--33844589 Score: 283
Period size: 44 Copynumber: 4.7 Consensus size: 44
33844374 TGACCTCAGC
*
33844384 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
*
33844428 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
33844472 TCTATCTCCCTGGGCAGTAGTGGAAT-GGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGG-TTGAAGATTGTGA-AT
* *
33844516 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
*
33844560 CCTATCTCCCTGAGT-AGCAGTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
33844590 GGAAAATAGC
Statistics
Matches: 143, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
43 3 0.02
44 135 0.94
45 5 0.03
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:33844650 original size:132 final size:132
Alignment explanation
Indices: 33844328--33844650 Score: 338
Period size: 132 Copynumber: 2.4 Consensus size: 132
33844318 GAGCAGATTA
* * * * *
33844328 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGATGACCTCAGCCCTATCTCC
1 AAAATAGCAGATCTTGCCTTCCTGCACCGATAGTGAAGCAGATCGAAGACGTCAGTCCTATCTCC
* *
33844393 CTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGT
66 CTGGTCAGCAGTGGAATAGGTTAAAGATCGTGAACCCTATCTCCCTGGTCAGCAGTGGAATAGGT
*
33844458 TG
131 GG
* * * ** * * *
33844460 AAGATTG-AGAATTCTAT--CTCCCTGGGCAG-TAGTGGAATG--GATTGAAGATTGT-AGGTCC
1 AAAATAGCAG-A-TCT-TGCCTTCCTGCACCGATAGT-GAA-GCAGATCGAAGA-CGTCA-GTCC
*
33844518 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAACCCTATCTCCCTGAGT-AGCAGTG
59 TATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATCGTGAACCCTATCTCCCTG-GTCAGCAGTG
*
33844582 GAGTAGGTGG
123 GAATAGGTGG
* *
33844592 AAAATAGCAGATCTTGCCTTCCTACACCGATAGTGAAGCAGATCGAGGACGTCAGTCCT
1 AAAATAGCAGATCTTGCCTTCCTGCACCGATAGTGAAGCAGATCGAAGACGTCAGTCCT
33844651 TTCGCCTTGA
Statistics
Matches: 148, Mismatches: 28, Indels: 30
0.72 0.14 0.15
Matches are distributed among these distances:
130 1 0.01
131 16 0.11
132 110 0.74
133 20 0.14
134 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (132 bp):
AAAATAGCAGATCTTGCCTTCCTGCACCGATAGTGAAGCAGATCGAAGACGTCAGTCCTATCTCC
CTGGTCAGCAGTGGAATAGGTTAAAGATCGTGAACCCTATCTCCCTGGTCAGCAGTGGAATAGGT
GG
Found at i:33844951 original size:11 final size:11
Alignment explanation
Indices: 33844935--33844959 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33844925 CAAAACAGGC
33844935 TTTTAGCGGCG
1 TTTTAGCGGCG
33844946 TTTTAGCGGCG
1 TTTTAGCGGCG
33844957 TTT
1 TTT
33844960 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.32, T:0.44
Consensus pattern (11 bp):
TTTTAGCGGCG
Found at i:33845009 original size:40 final size:40
Alignment explanation
Indices: 33844948--33845100 Score: 150
Period size: 40 Copynumber: 3.8 Consensus size: 40
33844938 TAGCGGCGTT
* *
33844948 TTAGCGGCGTTTGGATAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGTTT-TATAAAAAACGCCGCTAAAAATCAAGCA
** *
33844989 TTAGCGGCGCTTTTAT-AAAAACGCCGCTAAAGGTCGAGCA
1 TTAGCGGCG-TTTTATAAAAAACGCCGCTAAAAATCAAGCA
**
33845029 TTAGCGGCGCTTTT-TGGAAAACGCCGCTAAAAAT-AAGCA
1 TTAGCGGCG-TTTTATAAAAAACGCCGCTAAAAATCAAGCA
* ** * *
33845068 TTACCGGCGTTTTCCAAAAAGCGCCGCAAAAAA
1 TTAGCGGCGTTTTATAAAAAACGCCGCTAAAAA
33845101 CCTAAGCCAA
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
38 4 0.04
39 27 0.29
40 49 0.52
41 11 0.12
42 3 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGTTTTATAAAAAACGCCGCTAAAAATCAAGCA
Found at i:33845195 original size:41 final size:41
Alignment explanation
Indices: 33845135--33845255 Score: 197
Period size: 41 Copynumber: 3.0 Consensus size: 41
33845125 TGAGTTTTTG
* * *
33845135 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCTGCTAATTCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
33845176 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
33845217 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
33845256 CCGCTTTTGA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:33845640 original size:14 final size:14
Alignment explanation
Indices: 33845623--33845657 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
33845613 GTTTAATATG
33845623 TATGGTTTAGGGTA
1 TATGGTTTAGGGTA
* *
33845637 TATGATTTAGGTTA
1 TATGGTTTAGGGTA
33845651 TATGGTT
1 TATGGTT
33845658 AATTTAGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (14 bp):
TATGGTTTAGGGTA
Found at i:33845734 original size:14 final size:15
Alignment explanation
Indices: 33845706--33845738 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
33845696 AAGGTTTATA
33845706 GATTATGGAATTAGG
1 GATTATGGAATTAGG
33845721 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
33845735 GATT
1 GATT
33845739 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:33845979 original size:7 final size:7
Alignment explanation
Indices: 33845956--33846014 Score: 55
Period size: 7 Copynumber: 8.4 Consensus size: 7
33845946 TAAATAAGAT
33845956 TTAGGGG
1 TTAGGGG
**
33845963 TTAGTAG
1 TTAGGGG
33845970 TTAGGGG
1 TTAGGGG
*
33845977 TTAGGGA
1 TTAGGGG
33845984 TTAGGGG
1 TTAGGGG
*
33845991 TTAGAGG
1 TTAGGGG
**
33845998 TTAAAGG
1 TTAGGGG
*
33846005 TTAGAGG
1 TTAGGGG
33846012 TTA
1 TTA
33846015 AGAGTTAGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:33850498 original size:43 final size:43
Alignment explanation
Indices: 33850438--33850528 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
33850428 CTTTGAGTTC
* * * *
33850438 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
33850480 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
33850523 ATTACC
1 ATTACC
33850529 TTGCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:33850868 original size:43 final size:43
Alignment explanation
Indices: 33850803--33851028 Score: 280
Period size: 42 Copynumber: 5.3 Consensus size: 43
33850793 AAGATATATT
** *
33850803 TTTAGCGGCGTTTGTGTTAAAAGCGCCGCTAAAGCTCAAT-ATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-ATGATC
* * * *
33850846 TTTAGCGGTGTTCGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
* * *
33850889 TTTAGCGGCGTTTGTGGG-GAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
* * *
33850931 TTTAGTGGCGTTTGTGGG-GAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
*
33850973 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TTAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGA-TC
33851016 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
33851029 ATTTATAAAA
Statistics
Matches: 164, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
42 82 0.50
43 82 0.50
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
Found at i:33850922 original size:42 final size:42
Alignment explanation
Indices: 33850803--33851028 Score: 301
Period size: 43 Copynumber: 5.3 Consensus size: 42
33850793 AAGATATATT
** * * *
33850803 TTTAGCGGCGTTTGTGTTAAAAGCGCCGCTAAAGCTCAAT-ATC
1 TTTAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTC-TTGGTC
* *
33850846 TTTAGCGGTGTTCGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
*
33850889 TTTAGCGGCGTTTGTGGGGAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGGTC
* * *
33850931 TTTAGTGGCGTTTGTGGGGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGGTC
*
33850973 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTAGTC
1 TTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
33851016 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
33851029 ATTTATAAAA
Statistics
Matches: 164, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
42 81 0.49
43 83 0.51
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:33851153 original size:22 final size:21
Alignment explanation
Indices: 33851120--33851164 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
33851110 TTTAGTGGCG
*
33851120 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
33851141 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
33851163 CT
1 CT
33851165 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:33851236 original size:44 final size:44
Alignment explanation
Indices: 33851179--33851276 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
33851169 TGGTGTAGTG
* *
33851179 AGTGGAGCAGATTAAAGCCGAT-AATCCTATCTCTCTGAAGTTGC
1 AGTGAAGCAGATTAAAACC-ATGAATCCTATCTCTCTGAAGTTGC
* * * *
33851223 AGTGAAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGC
1 AGTGAAGCAGATTAAAACCATGAATCCTATCTCTCTGAAGTTGC
*
33851267 AG-AAAGCAGA
1 AGTGAAGCAGA
33851277 ACGCATCTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
43 7 0.16
44 38 0.84
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
AGTGAAGCAGATTAAAACCATGAATCCTATCTCTCTGAAGTTGC
Found at i:33851720 original size:19 final size:19
Alignment explanation
Indices: 33851696--33851770 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
33851686 AATCTTCGAG
33851696 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
33851715 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
33851734 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
33851755 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
33851771 AGATGTGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:33851746 original size:21 final size:21
Alignment explanation
Indices: 33851697--33851759 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
33851687 ATCTTCGAGG
33851697 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
*
33851716 ATATGTAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
33851737 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
33851758 AT
1 AT
33851760 GTAATCTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 18 0.45
21 22 0.55
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:33852253 original size:27 final size:27
Alignment explanation
Indices: 33852215--33852267 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
33852205 GAGGAGAAGG
33852215 GAAAATTGCCCTTCCAGCCCCTCTATA
1 GAAAATTGCCCTTCCAGCCCCTCTATA
33852242 GAAAATTGCCCTTCCAGCCCCTCTAT
1 GAAAATTGCCCTTCCAGCCCCTCTAT
33852268 GTAATTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.38, G:0.11, T:0.26
Consensus pattern (27 bp):
GAAAATTGCCCTTCCAGCCCCTCTATA
Found at i:33855532 original size:14 final size:15
Alignment explanation
Indices: 33855507--33855535 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33855497 TTATTTTGTG
33855507 TTTACTATGTGTGAA
1 TTTACTATGTGTGAA
33855522 TTTAC-ATGTGTGAA
1 TTTACTATGTGTGAA
33855536 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (15 bp):
TTTACTATGTGTGAA
Found at i:33856742 original size:43 final size:43
Alignment explanation
Indices: 33856681--33856804 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
33856671 ATTTTCGATA
* *
33856681 TGTGTTCTCGTGTAAGACCACGTCTGGGACGTTGGCATCGA-C
1 TGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAATC
33856723 TTGTGTTTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCAATC
1 -TGTGTTTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCAATC
** * * * *
33856767 TGTAATTACATGTAAGACCACGTTTGGGACATTGGCAT
1 TGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
33856805 TGTACAAGCT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
42 1 0.01
43 64 0.94
44 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (43 bp):
TGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAATC
Found at i:33865193 original size:45 final size:45
Alignment explanation
Indices: 33865107--33865193 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
33865097 TGAACCGAAA
* *
33865107 ATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTACACCGGAC
1 ATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATACACCGGAC
* * *
33865152 ATCATTGATTAATGAGGTGGTTGCTGTGTGCTGAATCCACCG
1 ATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATACACCG
33865194 AGTATCTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (45 bp):
ATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATACACCGGAC
Found at i:33867869 original size:29 final size:29
Alignment explanation
Indices: 33867826--33867881 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
33867816 ATTTTAAAAA
* * *
33867826 AATTATATACGAAAATGGTATGTCAGCCC
1 AATTATATACCAAAATAGTATGCCAGCCC
*
33867855 AATTATGTACCAAAATAGTATGCCAGC
1 AATTATATACCAAAATAGTATGCCAGC
33867882 TGCAGTGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (29 bp):
AATTATATACCAAAATAGTATGCCAGCCC
Found at i:33868570 original size:3 final size:3
Alignment explanation
Indices: 33868562--33868587 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33868552 TGAATGTAAT
33868562 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
33868588 TTAAGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33868610 original size:113 final size:110
Alignment explanation
Indices: 33868405--33868785 Score: 484
Period size: 113 Copynumber: 3.5 Consensus size: 110
33868395 TTACTAATTA
* *
33868405 TTATAAATT-ATTTTTGTTTAGTTTA--GTTT-TTGTAATTTTTTTATGAATGTAA----T-TT-
1 TTATAAATTGA-TTGTGTTTAGTTTAGTGTTTATTGTGA-TTTTTTATGAATGTAATTTTTATTA
*
33868460 TTTTTAAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
64 TTTTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
*
33868507 TTATAAATTGCTTGTGTTTAGTTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTATTATTAT
1 TTATAAATTGATTGTGTTTAGTTTAGTGTTTATTGTGATTTTTTATGAATGTAATTT-TTATTAT
*
33868572 TATTATTATTATTATTTT-AAGTTATTTTGTTAGTAATTTATGATTAGG
65 T-TT-TTA-AATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
* * *
33868620 TTATAAATTGTTTGTGCTTAGTTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTTTTTTATT
1 TTATAAATTGATTGTGTTTAGTTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTTTATTATT
*
33868685 TTTTAAATTATTTTAAAGTTATTTTTTTAGTAATTTATGATTAGG
66 TTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
* * * * *
33868730 TTATAAATT-ATT-TGTTTAGTTTAATGTGTATTTTGATTTATTATG-ATGTAGTTTTT
1 TTATAAATTGATTGTGTTTAGTTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTTT
33868786 TTTTTATTTC
Statistics
Matches: 247, Mismatches: 17, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
102 22 0.09
104 20 0.08
105 5 0.02
107 10 0.04
108 28 0.11
109 11 0.04
110 43 0.17
111 4 0.02
112 9 0.04
113 87 0.35
114 8 0.03
ACGTcount: A:0.27, C:0.01, G:0.13, T:0.60
Consensus pattern (110 bp):
TTATAAATTGATTGTGTTTAGTTTAGTGTTTATTGTGATTTTTTATGAATGTAATTTTTATTATT
TTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
Found at i:33869075 original size:21 final size:22
Alignment explanation
Indices: 33869024--33869076 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
33869014 TTATTGTAAT
* *
33869024 TATATTATTATTGTACTATATT
1 TATAATATTATTGTACTATATG
** *
33869046 TATCGTATTATT-TACTGTATG
1 TATAATATTATTGTACTATATG
33869067 TATAATATTA
1 TATAATATTA
33869077 ATGTGTTTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.55
Consensus pattern (22 bp):
TATAATATTATTGTACTATATG
Found at i:33871386 original size:48 final size:48
Alignment explanation
Indices: 33871325--33871433 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
33871315 CTTTATATTT
* ***
33871325 ATTT-AATTGAGATTTATTACAACATTAAAACTTGGAAC-AAATTTTGTA
1 ATTTAAATT-AGATTAATTACAACATTAAAAAAAGGAACTAAA-TTTGTA
*
33871373 ATTTAAATTAGATTAATTGCAACATTAAAAAAAGGAACTAAATTTGTA
1 ATTTAAATTAGATTAATTACAACATTAAAAAAAGGAACTAAATTTGTA
*
33871421 ATATAAATTAGAT
1 ATTTAAATTAGAT
33871434 ACATTGGAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 46 0.87
49 7 0.13
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (48 bp):
ATTTAAATTAGATTAATTACAACATTAAAAAAAGGAACTAAATTTGTA
Found at i:33878377 original size:32 final size:33
Alignment explanation
Indices: 33878310--33878377 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
33878300 TCTTGTTGGG
* * *
33878310 TTTGATTTTCCTTTGTGGTAGGTCTATGTCGGA
1 TTTGATTTTCCTTTGTGGTAGATCTATGCCAGA
33878343 TTTGA-TTTCCTTTGTGGTAGCATCTAT-CCAGA
1 TTTGATTTTCCTTTGTGGTAG-ATCTATGCCAGA
33878375 TTT
1 TTT
33878378 CATCAGCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (33 bp):
TTTGATTTTCCTTTGTGGTAGATCTATGCCAGA
Found at i:33880018 original size:29 final size:28
Alignment explanation
Indices: 33879985--33880047 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
33879975 AAAAGCCATT
*
33879985 TTTTTTAAAAAATTACCGAAATGGGCCGA
1 TTTTTTAAAAAATTACCGAAATGAGCC-A
** * *
33880014 TTTTTTAATTATTTACCGGAATGAGCCA
1 TTTTTTAAAAAATTACCGAAATGAGCCA
33880042 TTTTTT
1 TTTTTT
33880048 CCGAAATCGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (28 bp):
TTTTTTAAAAAATTACCGAAATGAGCCA
Found at i:33880345 original size:22 final size:22
Alignment explanation
Indices: 33880320--33880389 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
33880310 AAATTCAATA
33880320 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
33880342 TCAATTCCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
33880364 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
33880386 TCAA
1 TCAA
33880390 ACTCTCAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.31, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:33880395 original size:30 final size:30
Alignment explanation
Indices: 33880361--33880419 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
33880351 TTCAAAAATT
* *
33880361 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
33880391 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
33880420 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:33880405 original size:52 final size:51
Alignment explanation
Indices: 33880339--33880441 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
33880329 TTCAAAAATT
* * *
33880339 CTCTCAATTCCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
*
33880391 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
33880442 TCCATATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 4 0.09
52 38 0.83
53 4 0.09
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (51 bp):
CTCTCAATTCCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:33880430 original size:21 final size:22
Alignment explanation
Indices: 33880391--33880432 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
33880381 TTCTCTCAAA
33880391 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
33880413 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
33880433 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:33880538 original size:29 final size:29
Alignment explanation
Indices: 33880477--33880538 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
33880467 CAATTTCATT
* * *
33880477 TTTTAAGAAAATTTTAAAATTTATTATTT
1 TTTTAAAAAAATTTTAAAATTTATTAATA
*
33880506 TTTTAAAAATAATTTT-AAATTTTTTAATA
1 TTTTAAAAA-AATTTTAAAATTTATTAATA
33880535 TTTT
1 TTTT
33880539 CAACAATGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTTAAAAAAATTTTAAAATTTATTAATA
Found at i:33880658 original size:14 final size:15
Alignment explanation
Indices: 33880629--33880662 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33880619 TAATTTTAAA
33880629 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
33880644 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
33880658 TTTTA
1 TTTTA
33880663 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:33883032 original size:23 final size:23
Alignment explanation
Indices: 33883004--33883069 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
33882994 TGAAAACCCT
**
33883004 AACCCTAACATATTTTAATTAAA
1 AACCCTAACATAACTTAATTAAA
* *
33883027 ATCCCTAACCTAACTTAATTAAA
1 AACCCTAACATAACTTAATTAAA
*
33883050 AACCCTAACCTAACTTAATT
1 AACCCTAACATAACTTAATT
33883070 TAATTAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (23 bp):
AACCCTAACATAACTTAATTAAA
Found at i:33883039 original size:28 final size:28
Alignment explanation
Indices: 33882959--33883085 Score: 142
Period size: 29 Copynumber: 4.6 Consensus size: 28
33882949 NNTAATTTAA
33882959 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAA-CTAT
*
33882988 TTTACA-TGAAAACCCTAACCCTAACATAT
1 TTTA-ATTAAAAACCCTAACCCTAAC-TAT
*
33883017 TTTAATTAAAATCCCTAA-CCTAAC---
1 TTTAATTAAAAACCCTAACCCTAACTAT
*
33883041 -TTAATTAAAAACCCTAA-CCTAACTTAA
1 TTTAATTAAAAACCCTAACCCTAAC-TAT
33883068 TTTAATTAAAAACCCTAA
1 TTTAATTAAAAACCCTAA
33883086 TTTAATTAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
23 22 0.26
28 25 0.29
29 38 0.44
30 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (28 bp):
TTTAATTAAAAACCCTAACCCTAACTAT
Found at i:33883084 original size:23 final size:23
Alignment explanation
Indices: 33883004--33883092 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
33882994 TGAAAACCCT
* *
33883004 AACCCTAACATATTTTAATTAAA
1 AACCCTAACTTAATTTAATTAAA
* * *
33883027 ATCCCTAACCTAACTTAATTAAA
1 AACCCTAACTTAATTTAATTAAA
33883050 AACCCTAACCTAACTTAATTTAATTAAA
1 AA--C---CCTAACTTAATTTAATTAAA
*
33883078 AACCCTAATTTAATT
1 AACCCTAACTTAATT
33883093 AAAAGTTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
23 31 0.58
25 1 0.02
26 1 0.02
28 20 0.38
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (23 bp):
AACCCTAACTTAATTTAATTAAA
Found at i:33889970 original size:16 final size:17
Alignment explanation
Indices: 33889944--33889975 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
33889934 ATCAAAATCA
33889944 AAAACAAAAAGAAAAAG
1 AAAACAAAAAGAAAAAG
33889961 AAAA-AAAAAGAAAAA
1 AAAACAAAAAGAAAAA
33889976 TCAAAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAACAAAAAGAAAAAG
Found at i:33889976 original size:35 final size:36
Alignment explanation
Indices: 33889926--33890001 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
33889916 AGTTCAGAGT
** *
33889926 AAAAAAAAATCAAAATCAAAAACAAAA-AGAAAAAG
1 AAAAAAAAAGAAAAATCAAAAACAAAAGAAAAAAAG
**
33889961 AAAAAAAAAGAAAAATCAAAGTCAAAAGAAAAAAAG
1 AAAAAAAAAGAAAAATCAAAAACAAAAGAAAAAAAG
33889997 AAAAA
1 AAAAA
33890002 TTAATCAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.80, C:0.07, G:0.08, T:0.05
Consensus pattern (36 bp):
AAAAAAAAAGAAAAATCAAAAACAAAAGAAAAAAAG
Found at i:33890008 original size:30 final size:28
Alignment explanation
Indices: 33889956--33890022 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 28
33889946 AACAAAAAGA
33889956 AAAAGAAAAAAAAAGAAAAATCAAAGTC
1 AAAAGAAAAAAAAAGAAAAATCAAAGTC
33889984 AAAAGAAAAAAAGAA-AAATTAATCAAAGTC
1 AAAAGAAAAAAA-AAGAAA--AATCAAAGTC
*
33890014 AAAATAAAA
1 AAAAGAAAA
33890023 GTATGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 15 0.43
29 2 0.06
30 18 0.51
ACGTcount: A:0.75, C:0.06, G:0.09, T:0.10
Consensus pattern (28 bp):
AAAAGAAAAAAAAAGAAAAATCAAAGTC
Found at i:33890900 original size:7 final size:7
Alignment explanation
Indices: 33890882--33890912 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
33890872 TTTTAGTCAA
33890882 AAAAATG
1 AAAAATG
33890889 AAAAAATG
1 -AAAAATG
33890897 AAAAATG
1 AAAAATG
33890904 AAAAATG
1 AAAAATG
33890911 AA
1 AA
33890913 CAAGTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:33891667 original size:14 final size:14
Alignment explanation
Indices: 33891648--33891679 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
33891638 AAACAAGCAA
33891648 GCAATTATCATCAG
1 GCAATTATCATCAG
*
33891662 GCAATTATTATCAG
1 GCAATTATCATCAG
33891676 GCAA
1 GCAA
33891680 GAGGAATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (14 bp):
GCAATTATCATCAG
Found at i:33892438 original size:128 final size:128
Alignment explanation
Indices: 33892174--33892446 Score: 354
Period size: 128 Copynumber: 2.1 Consensus size: 128
33892164 AGTGAATATA
* ** * **
33892174 ACAGATCTTGTCTCTCTAAGCAGTAGTGGAGTAGATCAAAGACGGCGAATCTTATCTTCAAGTGT
1 ACAGATCTTGTCTCCCTAAGCAGTAGCAGAGCAGATCAAAGACGGCGAATCTTAAATTCAAGTGT
* * *
33892239 AAGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATT
66 AAGGAAACAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGATTGGAAATG
**
33892302 ACAGATCTTGTCTCCCTAAGCAGTAGCAGAGCAGATTGAAGACGGCGAATCTTAAATTCAAGTGT
1 ACAGATCTTGTCTCCCTAAGCAGTAGCAGAGCAGATCAAAGACGGCGAATCTTAAATTCAAGTGT
* * *
33892367 AAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGAGGTTA-CAGTGGAGTAGATT-GAAGAT
66 AAGGAAACAGATTTAAGCCACAAGTCCTATCTCCCT--GGTCAGCAGTGGAATAGATTGGAA-AT
33892430 G
128 G
* *
33892431 ATA-ATCTTATCTCCCT
1 ACAGATCTTGTCTCCCT
33892447 GAAGTTGCAG
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
128 106 0.84
129 16 0.13
130 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (128 bp):
ACAGATCTTGTCTCCCTAAGCAGTAGCAGAGCAGATCAAAGACGGCGAATCTTAAATTCAAGTGT
AAGGAAACAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGATTGGAAATG
Found at i:33892444 original size:44 final size:44
Alignment explanation
Indices: 33892394--33892597 Score: 218
Period size: 44 Copynumber: 4.6 Consensus size: 44
33892384 CCACAAGTCC
* * *
33892394 TATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGATGATAATCT
1 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGAAGATAATCT
* * *
33892438 TATCTCCCTGAAGTTGCAGTGGAGCAGATTG-AGAAAACAAGTCT
1 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGAAGATAA-TCT
* * ***
33892482 TATC-CTCCTGAAGTCGCAGT-GAGGCAGACCAAAGAAGCA-AATCT
1 TATCTC-CCTGAGGTTGCAGTGGA-GCAGATTGAAGAAG-ATAATCT
* *
33892526 TATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGACGATAATCT
1 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGAAGATAATCT
*
33892570 TATCTCCCTGAGGTTGCAGTGAAGCAGA
1 TATCTCCCTGAGGTTGCAGTGGAGCAGA
33892598 CTGAGAATAG
Statistics
Matches: 132, Mismatches: 20, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
43 10 0.08
44 112 0.85
45 9 0.07
46 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGAAGATAATCT
Found at i:33892764 original size:100 final size:100
Alignment explanation
Indices: 33892610--33893222 Score: 821
Period size: 100 Copynumber: 6.1 Consensus size: 100
33892600 GAGAATAGCA
* * ** * *
33892610 AATCTTACTTTCCTGGCAATGCAATGGAACAAGATTAACGCCACAACAGCGAACCTTGCTTCCCC
1 AATCTTACTTCCCAGGCGGTGCAGTGGAAC-AGATTAACGCCACAACGGCGAACCTTGCTTCCCC
* * * *
33892675 GATATTGCAGTTAAAAAGATTAAACCTACCACAACG
65 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
* * * *
33892711 AATCGTACTTCTCAAGCGGTGCAGTGGAACAGATTAACGCCACAACGGTGAACCTTGCTTCCCCG
1 AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAACGCCACAACGGCGAACCTTGCTTCCCCG
33892776 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
* * ** *
33892811 AATCTTACTTCTCTGGTAGTGCAGTGGAACAGATTAACGCCACAACGGCAAACCTTGCTTCCCCG
1 AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAACGCCACAACGGCGAACCTTGCTTCCCCG
* *
33892876 ACATTGCAGTTAAAAAGATTAAAGCTACAACAACA
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
* * *
33892911 AATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTAACGCCACAATGGCGAACCTTGCTTCCCCG
1 AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAACGCCACAACGGCGAACCTTGCTTCCCCG
33892976 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
* * * ** *
33893011 AATCTTACTTCCCAGGCGGTGTAGTGGAACAGATTAACGCCACAACAGTGAATTTTACTTCCCCG
1 AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAACGCCACAACGGCGAACCTTGCTTCCCCG
* * *
33893076 ACATTGTAGTTAAAAATATTAAAGCTACAACAGTG
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
* * * ** * * *
33893111 AATCTTACTTCCCAGGCGGTGTAGTGGAACAGATTAAAGCCACATCGAAGTATCTTACTTCCCCG
1 AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAACGCCACAACGGCGAACCTTGCTTCCCCG
* *
33893176 ACATTGCAATTAAAAGGATTAAAGCTACAACAGCG
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
*
33893211 AATCTTGCTTCC
1 AATCTTACTTCC
33893223 TCGACATCAT
Statistics
Matches: 458, Mismatches: 54, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
100 436 0.95
101 22 0.05
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (100 bp):
AATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAACGCCACAACGGCGAACCTTGCTTCCCCG
ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
Found at i:33892784 original size:50 final size:50
Alignment explanation
Indices: 33892610--33893229 Score: 384
Period size: 50 Copynumber: 12.4 Consensus size: 50
33892600 GAGAATAGCA
* * * * * *
33892610 AATCTTACTTTCCTGGCAATGCAATGGAACAAGATTAACGCCACAACAGCG
1 AATCTTACTTCCCCGACATTGCAGTGGAAC-AGATTAAAGCCACAACAGCG
* * * ** * * *
33892661 AACCTTGCTTCCCCGATATTGCAGTTAAAAAGATTAAA-CCTACCACAACG
1 AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCC-ACAACAGCG
* * * ** * * *
33892711 AATCGTACTT-CTCAAGCGGTGCAGTGGAACAGATTAACGCCACAACGGTG
1 AATCTTACTTCCCCGA-CATTGCAGTGGAACAGATTAAAGCCACAACAGCG
* * ** * *
33892761 AACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
1 AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCCACAACAGCG
* * ** * * * *
33892811 AATCTTACTTCTCTGGTAGTGCAGTGGAACAGATTAACGCCACAACGGCA
1 AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCCACAACAGCG
* * ** * * * *
33892861 AACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAACA
1 AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCCACAACAGCG
* **** * **
33892911 AATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTAACGCCACAATGGCG
1 AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCCACAACAGCG
* * ** * *
33892961 AACCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
1 AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCCACAACAGCG
* * ** * * *
33893011 AATCTTACTTCCCAGGCGGTGTAGTGGAACAGATTAACGCCACAACAGTG
1 AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCCACAACAGCG
* * ** * * * *
33893061 AATTTTACTTCCCCGACATTGTAGTTAAAAATATTAAAGCTACAACAGTG
1 AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCCACAACAGCG
* * ** * * *
33893111 AATCTTACTTCCCAGGCGGTGTAGTGGAACAGATTAAAGCCACATC-GAAG
1 AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCCACAACAG-CG
* * * * *
33893161 TATCTTACTTCCCCGACATTGCAAT-TAAAAGGATTAAAGCTACAACAGCG
1 AATCTTACTTCCCCGACATTGCAGTGGAACA-GATTAAAGCCACAACAGCG
* *
33893211 AATCTTGCTTCCTCGACAT
1 AATCTTACTTCCCCGACAT
33893230 CATAGTTAAA
Statistics
Matches: 409, Mismatches: 153, Indels: 15
0.71 0.27 0.03
Matches are distributed among these distances:
49 9 0.02
50 375 0.92
51 25 0.06
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (50 bp):
AATCTTACTTCCCCGACATTGCAGTGGAACAGATTAAAGCCACAACAGCG
Found at i:33893843 original size:16 final size:16
Alignment explanation
Indices: 33893822--33893855 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33893812 AGAAAATAAA
33893822 AAAATAGCACAAAGAG
1 AAAATAGCACAAAGAG
* *
33893838 AAAATAGGAGAAAGAG
1 AAAATAGCACAAAGAG
33893854 AA
1 AA
33893856 GAAAGATGTA
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:0.65, C:0.06, G:0.24, T:0.06
Consensus pattern (16 bp):
AAAATAGCACAAAGAG
Found at i:33894841 original size:4 final size:4
Alignment explanation
Indices: 33894834--33894858 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
33894824 GTTTAATTAA
33894834 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
33894859 CATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:33899227 original size:18 final size:19
Alignment explanation
Indices: 33899194--33899230 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33899184 TGCTTATTTG
33899194 AATTATTAAATATATTTAA
1 AATTATTAAATATATTTAA
*
33899213 AATTATTAACT-TATTTAA
1 AATTATTAAATATATTTAA
33899231 CATTCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTATTAAATATATTTAA
Found at i:33903416 original size:20 final size:20
Alignment explanation
Indices: 33903380--33903421 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
33903370 AAATTGATTT
* *
33903380 TTAAATTATTTTGAACT-AA
1 TTAAAATATTTTAAACTCAA
33903399 TTAAAATATTTATAAACTCAA
1 TTAAAATATTT-TAAACTCAA
33903420 TT
1 TT
33903422 TTATGGATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.53
20 5 0.26
21 4 0.21
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAAAATATTTTAAACTCAA
Found at i:33906587 original size:8 final size:8
Alignment explanation
Indices: 33906574--33906598 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
33906564 TATACTAAAC
33906574 AATAAAAT
1 AATAAAAT
33906582 AATAAAAT
1 AATAAAAT
33906590 AATAAAAT
1 AATAAAAT
33906598 A
1 A
33906599 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:33910207 original size:26 final size:26
Alignment explanation
Indices: 33910178--33910269 Score: 87
Period size: 26 Copynumber: 3.3 Consensus size: 26
33910168 AAGGGATGCT
33910178 TTTGTGGCGTATTTGAAAGGAAAGCC
1 TTTGTGGCGTATTTGAAAGGAAAGCC
* *
33910204 TTTGTGGCGAGAATTGATTGAAAATGG-ATGCC
1 TTTGTGGC--GTA-T--TTG-AAA-GGAAAGCC
*
33910236 TTTGTGGCGTATTTGAAAGGAAAGCT
1 TTTGTGGCGTATTTGAAAGGAAAGCC
33910262 TTTGTGGC
1 TTTGTGGC
33910270 AAGTATAGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
25 2 0.04
26 22 0.42
27 3 0.06
28 2 0.04
29 2 0.04
30 2 0.04
31 3 0.06
32 15 0.28
33 2 0.04
ACGTcount: A:0.25, C:0.10, G:0.32, T:0.34
Consensus pattern (26 bp):
TTTGTGGCGTATTTGAAAGGAAAGCC
Found at i:33910266 original size:58 final size:57
Alignment explanation
Indices: 33910166--33910300 Score: 207
Period size: 58 Copynumber: 2.3 Consensus size: 57
33910156 ACACGTTAGA
* *
33910166 AAAAGGGATGCTTTTGTGGCGTATTTGAAAGGAAAGCCTTTGTGGCGAGAATTGATTG
1 AAAA-GGATGCTTTTGTGGCGTATTTGAAAGGAAAGCCTTTGTGGCAAGAATAGATTG
* * *
33910224 AAAATGGATGCCTTTGTGGCGTATTTGAAAGGAAAGCTTTTGTGGCAAGTATAGATTG
1 AAAA-GGATGCTTTTGTGGCGTATTTGAAAGGAAAGCCTTTGTGGCAAGAATAGATTG
33910282 AAAAGGATGCTTTTGTGGC
1 AAAAGGATGCTTTTGTGGC
33910301 AAATCTCTGA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
57 14 0.20
58 56 0.80
ACGTcount: A:0.28, C:0.09, G:0.31, T:0.32
Consensus pattern (57 bp):
AAAAGGATGCTTTTGTGGCGTATTTGAAAGGAAAGCCTTTGTGGCAAGAATAGATTG
Found at i:33910288 original size:32 final size:30
Alignment explanation
Indices: 33910193--33910392 Score: 94
Period size: 31 Copynumber: 6.7 Consensus size: 30
33910183 GGCGTATTTG
* *
33910193 AAAGGAAAGCCTTTGTGGCGAGAATTGATTGA
1 AAAGG-AAGCCTTTGTGGCAAGTA-TGATTGA
*
33910225 AAATGGATGCCTTTGTGGC--GTAT--TTG-
1 AAA-GGAAGCCTTTGTGGCAAGTATGATTGA
*
33910251 AAAGGAAAGCTTTTGTGGCAAGTATAGATTGA
1 AAAGG-AAGCCTTTGTGGCAAGTAT-GATTGA
* * *
33910283 AAAGGATGCTTTTGTGGCAA--AT-CTCTGA
1 AAAGGAAGCCTTTGTGGCAAGTATGAT-TGA
* ** * *
33910311 ATA-GAAGGCCTTCATGGCAGGTACTGACTGA
1 AAAGGAA-GCCTTTGTGGCAAGTA-TGATTGA
* * * *
33910342 AAAGGATGCCTTTTTGGCGAGTACTAATTGA
1 AAAGGAAGCCTTTGTGGCAAGTA-TGATTGA
**
33910373 AAAGGGTGCCTTTGTGGCAA
1 AAAGGAAGCCTTTGTGGCAA
33910393 ACTTTTGAAA
Statistics
Matches: 128, Mismatches: 25, Indels: 31
0.70 0.14 0.17
Matches are distributed among these distances:
25 2 0.02
26 14 0.11
27 6 0.05
28 18 0.14
29 3 0.02
30 3 0.02
31 58 0.45
32 22 0.17
33 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (30 bp):
AAAGGAAGCCTTTGTGGCAAGTATGATTGA
Found at i:33914657 original size:51 final size:52
Alignment explanation
Indices: 33914575--33914686 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 52
33914565 ATAAAAATGG
*
33914575 TGAAAATGAAGAAATGGAAAACATTTGGAAAT-GATTATGATTTTCTCCAAAA
1 TGAAAATGAAGAAATGGAAAACATTTGGAAATGGA-TACGATTTTCTCCAAAA
* * * * * *
33914627 TGAATATGGAGAAATGG-AATCATTTTGAAATGGATGCGTTTTTCTCCAAAA
1 TGAAAATGAAGAAATGGAAAACATTTGGAAATGGATACGATTTTCTCCAAAA
33914678 TGAAAATGA
1 TGAAAATGA
33914687 CTTGAAAATG
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
51 33 0.66
52 17 0.34
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (52 bp):
TGAAAATGAAGAAATGGAAAACATTTGGAAATGGATACGATTTTCTCCAAAA
Found at i:33915784 original size:85 final size:85
Alignment explanation
Indices: 33915641--33915810 Score: 304
Period size: 85 Copynumber: 2.0 Consensus size: 85
33915631 TTATAGGGTA
33915641 GGTCTCTCCCTCTCAGCACACACCTTTTACTTCCTCATTTTCAAGGTGGTTTATCTGGTACAAAT
1 GGTCTCTCCCTCTCAGCACACACCTTTTACTTCCTCATTTTCAAGGTGGTTTATCTGGTACAAAT
33915706 ATAGCTGGCTGAGAGTGACG
66 ATAGCTGGCTGAGAGTGACG
* * * *
33915726 GGTCTCTCCCTCTCAGCACACACCTTTTACTTCTTCTTTTTCAGGGTGGTTTATCTGGTACAAGT
1 GGTCTCTCCCTCTCAGCACACACCTTTTACTTCCTCATTTTCAAGGTGGTTTATCTGGTACAAAT
33915791 ATAGCTGGCTGAGAGTGACG
66 ATAGCTGGCTGAGAGTGACG
33915811 TGGACTGAGT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (85 bp):
GGTCTCTCCCTCTCAGCACACACCTTTTACTTCCTCATTTTCAAGGTGGTTTATCTGGTACAAAT
ATAGCTGGCTGAGAGTGACG
Found at i:33919040 original size:18 final size:17
Alignment explanation
Indices: 33919011--33919049 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 17
33919001 AATACAGAAA
33919011 AAAAGAAAAAATTAGTGAG
1 AAAAGAAAAAA-TAGT-AG
33919030 AAAAG-AAAAATAGTAG
1 AAAAGAAAAAATAGTAG
33919046 AAAA
1 AAAA
33919050 ATTAGGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 5 0.25
19 5 0.25
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (17 bp):
AAAAGAAAAAATAGTAG
Found at i:33922618 original size:4 final size:4
Alignment explanation
Indices: 33922609--33922634 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
33922599 TTAATAAACT
33922609 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
33922635 ATCACCAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:33922891 original size:30 final size:31
Alignment explanation
Indices: 33922835--33922892 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
33922825 CACCCTTAAA
** *
33922835 ATATTTACACTATTGGTCCTTCAAATTTTTT
1 ATATTTACACTATTAATCCCTCAAATTTTTT
33922866 ATATTTACACT-TTAATCCCTCAAATTT
1 ATATTTACACTATTAATCCCTCAAATTT
33922893 CAAGTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.48
Consensus pattern (31 bp):
ATATTTACACTATTAATCCCTCAAATTTTTT
Found at i:33923066 original size:23 final size:23
Alignment explanation
Indices: 33923035--33923083 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
33923025 ACCTACTTTC
* *
33923035 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
*
33923058 TTACAGTAGTAATTTTTGGGATA
1 TTACAGTAGTAATTTTCGGGATA
33923081 TTA
1 TTA
33923084 GATCAGCCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:33943046 original size:104 final size:102
Alignment explanation
Indices: 33942849--33943212 Score: 563
Period size: 104 Copynumber: 3.6 Consensus size: 102
33942839 TATATAAAAG
** * * * *
33942849 GGGTTGCTGTGTGTTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGAT-CACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTTT
**
33942912 G-AATGTGAAGGGGGTTGCTATGTGCTGATTCCCCCGA
65 GAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGA
33942949 GGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
33943014 GAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCGA
65 GAAATGAAAA-GGGGGTTGCTATGTGCTGATTCCCCCGA
33943053 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
1 -GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
*
33943118 GAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCGA
65 GAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGA
* **
33943156 GGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
33943213 ATAACGGCTA
Statistics
Matches: 246, Mismatches: 12, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
100 22 0.09
101 21 0.09
102 68 0.28
103 34 0.14
104 76 0.31
105 25 0.10
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (102 bp):
GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTG
AAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGA
Found at i:33961230 original size:31 final size:31
Alignment explanation
Indices: 33961194--33961252 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
33961184 TTGCCAAATA
*
33961194 ACTTAAATAAAAACTTTTT-AATAGTTCAATG
1 ACTTAAATAAAAA-TTTTTGAATAATTCAATG
33961225 ACTTAAATAAAAATTTTTGAATAATTCA
1 ACTTAAATAAAAATTTTTGAATAATTCA
33961253 GTGATCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (31 bp):
ACTTAAATAAAAATTTTTGAATAATTCAATG
Found at i:33966010 original size:41 final size:41
Alignment explanation
Indices: 33965897--33966013 Score: 182
Period size: 41 Copynumber: 2.9 Consensus size: 41
33965887 AGTAAGATGA
* * *
33965897 TTCAGACTTTACGTCTAGCAGGCTTGATACCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
33965938 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
33965979 TTCGGACTTTACGTCTAGCAGGC-TAATTGCCGGTG
1 TTCAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTG
33966014 TACTGAATTA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 3 0.04
41 68 0.96
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
Found at i:33976583 original size:20 final size:21
Alignment explanation
Indices: 33976551--33976594 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
33976541 TCCTTTTACG
33976551 TTCCTCTCTTTTTTTTCTT-T
1 TTCCTCTCTTTTTTTTCTTCT
33976571 TTCCT-TCTATTTTTTTCTTCT
1 TTCCTCTCT-TTTTTTTCTTCT
33976592 TTC
1 TTC
33976595 TGCTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCCTCTCTTTTTTTTCTTCT
Found at i:33976606 original size:20 final size:19
Alignment explanation
Indices: 33976558--33976606 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
33976548 ACGTTCCTCT
*
33976558 CTTTTTTTTCTTTTTCCTT
1 CTTTTTTTTCTTTTTCCTG
33976577 CTATTTTTTTCTTCTTT-CTG
1 CT-TTTTTTTCTT-TTTCCTG
33976597 CTTTTCTTTT
1 CTTTT-TTTT
33976607 TTTATCTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 18 0.69
21 3 0.12
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (19 bp):
CTTTTTTTTCTTTTTCCTG
Found at i:33977276 original size:63 final size:63
Alignment explanation
Indices: 33977152--33977276 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 63
33977142 GTAGGTCGTG
* * * * * *
33977152 TAACTCACTATTTTGGAATTAGAGTCATATGGGCCAGAGACACGGGCGTGTGTCCAGGCCATA
1 TAACTCACTATTTTGGAATCAAAATCATACGGGCCAAAGACACGGGCGTGTGTCCAAGCCATA
*
33977215 TAACTCACTATTTTGGAATCAAAATCATACGGGCCAAAGACACGGGCGTGTGTCTAAGCCAT
1 TAACTCACTATTTTGGAATCAAAATCATACGGGCCAAAGACACGGGCGTGTGTCCAAGCCAT
33977277 GTTAGAGGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (63 bp):
TAACTCACTATTTTGGAATCAAAATCATACGGGCCAAAGACACGGGCGTGTGTCCAAGCCATA
Found at i:33978999 original size:43 final size:43
Alignment explanation
Indices: 33978944--33979026 Score: 141
Period size: 43 Copynumber: 1.9 Consensus size: 43
33978934 TAGTACAACA
33978944 ATTAAATGAATGATATTCTAGGATCTTTAGCTATATTAGTGCG
1 ATTAAATGAATGATATTCTAGGATCTTTAGCTATATTAGTGCG
*
33978987 ATTAAA-GTAATGATATTCTAGGATTTTTAGCTATATTAGT
1 ATTAAATG-AATGATATTCTAGGATCTTTAGCTATATTAGT
33979027 AGATGTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (43 bp):
ATTAAATGAATGATATTCTAGGATCTTTAGCTATATTAGTGCG
Found at i:33986279 original size:54 final size:54
Alignment explanation
Indices: 33986221--33986335 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
33986211 CACATGGTCG
* *
33986221 TGTCGCAGGCCGTATGCTAGACCGTGTAACACTCTGAC-TAGTGACACACGACCA
1 TGTCGCAGGCCGTATGCTAGACCGTGTAACACACTGACTTAAT-ACACACGACCA
* * * ** *
33986275 TGTCGTAGGTCGTGTGCTAGGTCGTGTAACACACTGACTTAATACACACGGCCA
1 TGTCGCAGGCCGTATGCTAGACCGTGTAACACACTGACTTAATACACACGACCA
33986329 TGTCGCA
1 TGTCGCA
33986336 AGCCATCTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 48 0.94
55 3 0.06
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.23
Consensus pattern (54 bp):
TGTCGCAGGCCGTATGCTAGACCGTGTAACACACTGACTTAATACACACGACCA
Found at i:33987307 original size:37 final size:37
Alignment explanation
Indices: 33987252--33987334 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
33987242 ATACAACCGA
* *
33987252 AACACGCCAAACGCTCATAAGAGTTAATCCAACTGAT
1 AACACGCCAAACACTCATAAGAGCTAATCCAACTGAT
* * *
33987289 AACATGCCAAACACTCATAATAGCTAATCCCACTGAT
1 AACACGCCAAACACTCATAAGAGCTAATCCAACTGAT
33987326 AACACGCCA
1 AACACGCCA
33987335 CGACACTAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.18
Consensus pattern (37 bp):
AACACGCCAAACACTCATAAGAGCTAATCCAACTGAT
Found at i:33989945 original size:6 final size:6
Alignment explanation
Indices: 33989934--33989972 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
33989924 CCCACCCCAA
*
33989934 ATACAG ATACAG AATACAG GTACAG AATACAG ATACAG A
1 ATACAG ATACAG -ATACAG ATACAG -ATACAG ATACAG A
33989973 AATTATAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (6 bp):
ATACAG
Found at i:33989951 original size:13 final size:13
Alignment explanation
Indices: 33989933--33989973 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
33989923 TCCCACCCCA
33989933 AATACAGATACAG
1 AATACAGATACAG
*
33989946 AATACAGGTACAG
1 AATACAGATACAG
33989959 AATACAGATACAG
1 AATACAGATACAG
33989972 AA
1 AA
33989974 ATTATAGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.15
Consensus pattern (13 bp):
AATACAGATACAG
Found at i:33990285 original size:12 final size:12
Alignment explanation
Indices: 33990268--33990297 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33990258 CCGTGTCTCG
33990268 CACACGGCCAAC
1 CACACGGCCAAC
*
33990280 CACACGGCCAAG
1 CACACGGCCAAC
33990292 CACACG
1 CACACG
33990298 CCCATGTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.47, G:0.20, T:0.00
Consensus pattern (12 bp):
CACACGGCCAAC
Found at i:33994203 original size:23 final size:22
Alignment explanation
Indices: 33994160--33994203 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
33994150 TTCTAAGTCG
33994160 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
33994183 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
33994204 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:33994312 original size:45 final size:45
Alignment explanation
Indices: 33994248--33994336 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
33994238 AATAGATACT
* * *
33994248 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTC
33994293 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGT
33994337 TCATTTCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTC
Found at i:33994407 original size:51 final size:50
Alignment explanation
Indices: 33994347--33994533 Score: 232
Period size: 51 Copynumber: 3.7 Consensus size: 50
33994337 TCATTTCACA
* * * *
33994347 TAGTAGCCTGCGCATAGTACTGCACATGTGACCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCCGGTACACG
* * * *
33994398 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATCCGGTACACG
* * * *
33994449 TAGTAGCCTGCACATACTACTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCCGGTACACG
33994499 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
33994534 CACTTTCACT
Statistics
Matches: 114, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 41 0.36
51 69 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCCGGTACACG
Found at i:33994513 original size:101 final size:101
Alignment explanation
Indices: 33994343--33994529 Score: 295
Period size: 101 Copynumber: 1.8 Consensus size: 101
33994333 ATGTTCATTT
* * * *
33994343 CACATAGTAGCCTGCGCATAGTACTGCACATGTGACCATTACCATCCGATACACGTAGTAGCCTG
1 CACATAGTAGCCTGCACATACTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTG
33994408 CACATAGTACTACACACGTGATCGAAACTATCCGGTA
65 CACATAGTACTACACACGTGATCGAAACTATCCGGTA
* *
33994445 CACATAGTAGCCTGCACATACTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTG
1 CACATAGTAGCCTGCACATACTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTG
33994509 CACATAGTACTACACACGTGA
65 CACATAGTACTACACACGTGA
33994530 CCATCACTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 4 0.05
101 41 0.53
102 33 0.42
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.22
Consensus pattern (101 bp):
CACATAGTAGCCTGCACATACTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGC
ACATAGTACTACACACGTGATCGAAACTATCCGGTA
Found at i:33994551 original size:101 final size:101
Alignment explanation
Indices: 33994336--33994563 Score: 266
Period size: 101 Copynumber: 2.3 Consensus size: 101
33994326 ATCAATAATG
* * * *
33994336 TTCA-TTTCACATAGTAGCCTGCGCATAGTACTGCACATGTGACCATTACCATCCGATACACGTA
1 TTCACTTTCACATAGTAGCCTGCACATACTACTACACATGCGACCA-TACCATCCGATACACGTA
*
33994400 GTAGCCTGCACATAGTACTACACACGTGATCGAAACT
65 GTAGCCTGCACATAGTACTACACACGTGATCCAAACT
* * * * *
33994437 ATC-CGGTACACATAGTAGCCTGCACATACTACTACACATGCGACC-TATCATTCCGGTACACGT
1 TTCAC-TTTCACATAGTAGCCTGCACATACTACTACACATGCGACCATACCA-TCCGATACACGT
*
33994500 AGTAGCCTGCACATAGTACTACACACGTGA-CCATCACT
64 AGTAGCCTGCACATAGTACTACACACGTGATCCA-AACT
* * *
33994538 TTCACTTTTACATAGTGGCCTACACA
1 TTCACTTTCACATAGTAGCCTGCACA
33994564 CAATCCGTGC
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
100 6 0.06
101 64 0.61
102 35 0.33
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (101 bp):
TTCACTTTCACATAGTAGCCTGCACATACTACTACACATGCGACCATACCATCCGATACACGTAG
TAGCCTGCACATAGTACTACACACGTGATCCAAACT
Found at i:34006242 original size:15 final size:16
Alignment explanation
Indices: 34006216--34006246 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
34006206 CAAATACTAG
34006216 AATTTTTCTTTATTTA
1 AATTTTTCTTTATTTA
34006232 AATTTTT-TTTATTTA
1 AATTTTTCTTTATTTA
34006247 TTTCTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
AATTTTTCTTTATTTA
Found at i:34013802 original size:13 final size:13
Alignment explanation
Indices: 34013784--34013813 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
34013774 AGCCCAAACT
34013784 CAATTACCCAACC
1 CAATTACCCAACC
34013797 CAATTACCCAACC
1 CAATTACCCAACC
34013810 CAAT
1 CAAT
34013814 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:34013960 original size:9 final size:9
Alignment explanation
Indices: 34013948--34014015 Score: 93
Period size: 9 Copynumber: 7.4 Consensus size: 9
34013938 AATAAAAAAA
34013948 AATTCGGGT
1 AATTCGGGT
34013957 AATTCGGGT
1 AATTCGGGT
*
34013966 ATTTTTC-GGT
1 A--ATTCGGGT
*
34013976 AATTCGGTT
1 AATTCGGGT
34013985 AATTCGGGT
1 AATTCGGGT
34013994 AATTCGGGT
1 AATTCGGGT
34014003 AATTCGGGT
1 AATTCGGGT
34014012 AATT
1 AATT
34014016 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
8 3 0.06
9 42 0.81
10 4 0.08
11 3 0.06
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:34022777 original size:26 final size:27
Alignment explanation
Indices: 34022748--34022882 Score: 97
Period size: 27 Copynumber: 5.1 Consensus size: 27
34022738 TCTATTGTAG
*
34022748 TTAAATA-ACTAG-TTTATTATACTGTT
1 TTAAATATA-TAGTTTTAATATACTGTT
*
34022774 TT-AATATATTGTTTTAATATACTGTT
1 TTAAATATATAGTTTTAATATACTGTT
* * *
34022800 TT-AGTATACT-GTTATAAATATATTGTT
1 TTAAATATA-TAGTT-TTAATATACTGTT
*
34022827 TT-AATATA-ATGTTTTAATATATTGTT
1 TTAAATATATA-GTTTTAATATACTGTT
* *
34022853 ATAAATATACT-GTTTTAATATAATGTT
1 TTAAATATA-TAGTTTTAATATACTGTT
34022880 TTA
1 TTA
34022883 GTATACTGTT
Statistics
Matches: 90, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
25 6 0.07
26 39 0.43
27 45 0.50
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (27 bp):
TTAAATATATAGTTTTAATATACTGTT
Found at i:34022781 original size:13 final size:13
Alignment explanation
Indices: 34022760--34022901 Score: 160
Period size: 13 Copynumber: 10.8 Consensus size: 13
34022750 AAATAACTAG
*
34022760 TTTATTATACTGT
1 TTTAATATACTGT
*
34022773 TTTAATATATTGT
1 TTTAATATACTGT
34022786 TTTAATATACTGT
1 TTTAATATACTGT
*
34022799 TTTAGTATACTGT
1 TTTAATATACTGT
* *
34022812 TATAAATATATTGT
1 T-TTAATATACTGT
*
34022826 TTTAATATAATGT
1 TTTAATATACTGT
*
34022839 TTTAATATATTGT
1 TTTAATATACTGT
*
34022852 TATAAATATACTGT
1 T-TTAATATACTGT
*
34022866 TTTAATATAATGT
1 TTTAATATACTGT
*
34022879 TTTAGTATACTGT
1 TTTAATATACTGT
*
34022892 TATAA-ATACT
1 TTTAATATACT
34022902 ACACCTTAAT
Statistics
Matches: 109, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
12 5 0.05
13 83 0.76
14 21 0.19
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTAATATACTGT
Found at i:34022826 original size:40 final size:40
Alignment explanation
Indices: 34022760--34022899 Score: 219
Period size: 40 Copynumber: 3.5 Consensus size: 40
34022750 AAATAACTAG
* * *
34022760 TTTATTATACTGTT-TTAATATATTGTTTTAATATACTGT
1 TTTAGTATACTGTTATAAATATATTGTTTTAATATAATGT
34022799 TTTAGTATACTGTTATAAATATATTGTTTTAATATAATGT
1 TTTAGTATACTGTTATAAATATATTGTTTTAATATAATGT
* * *
34022839 TTTAATATATTGTTATAAATATACTGTTTTAATATAATGT
1 TTTAGTATACTGTTATAAATATATTGTTTTAATATAATGT
34022879 TTTAGTATACTGTTATAAATA
1 TTTAGTATACTGTTATAAATA
34022900 CTACACCTTA
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 13 0.14
40 79 0.86
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.54
Consensus pattern (40 bp):
TTTAGTATACTGTTATAAATATATTGTTTTAATATAATGT
Found at i:34022873 original size:53 final size:52
Alignment explanation
Indices: 34022765--34022892 Score: 148
Period size: 53 Copynumber: 2.4 Consensus size: 52
34022755 ACTAGTTTAT
* * *
34022765 TATACTGTTTTAATATATTGTTTTAATATACTGTTTTAGTATACTGTTATAAA
1 TATACTGTTTTAATATAATGTTTTAATATAATGTTTTAATATACTGTT-TAAA
* * * *
34022818 TATATTGTTTTAATATAATGTTTTAATATATTGTTATAAATATACTGTTTTAA
1 TATACTGTTTTAATATAATGTTTTAATATAATGTT-TTAATATACTGTTTAAA
* * *
34022871 TATAATGTTTTAGTATACTGTT
1 TATACTGTTTTAATATAATGTT
34022893 ATAAATACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
53 54 0.83
54 11 0.17
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (52 bp):
TATACTGTTTTAATATAATGTTTTAATATAATGTTTTAATATACTGTTTAAA
Found at i:34022963 original size:35 final size:35
Alignment explanation
Indices: 34022918--34022987 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
34022908 TAATTATTAA
*
34022918 TGTAACATACTGGTTTAATATACTGTTATAAAATT
1 TGTAACATACTAGTTTAATATACTGTTATAAAATT
* *
34022953 TGTAATATACTATTTTAATATACTGTTATAAAATT
1 TGTAACATACTAGTTTAATATACTGTTATAAAATT
34022988 ACTCAATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (35 bp):
TGTAACATACTAGTTTAATATACTGTTATAAAATT
Found at i:34025751 original size:142 final size:142
Alignment explanation
Indices: 34025594--34025880 Score: 538
Period size: 142 Copynumber: 2.0 Consensus size: 142
34025584 TAAAGTAAGA
*
34025594 ATACAAATGATGTATATTGAAATAGTGATGACATAAAAAGTGATTGGCTGATAAAAAATTTACCA
1 ATACAAATGATGTATATTGAAATAGTGATGACATAAAAAGTGATTGGCTGATAAAAAAATTACCA
* *
34025659 AGATACATCAAATTTATGATAAAGGGGACTAAATTATAAAGTGTATAGAATTTTATGATTTAAAT
66 AGATACATCAAATTTATGATAAAGAGGACTAAATTATAAAGTGTATAGAAGTTTATGATTTAAAT
34025724 AAAAGTATTAGG
131 AAAAGTATTAGG
34025736 ATACAAATGATGTATATTGAAATAGTGATGACATAAAAAGTGATTGGCTGATAAAAAAATTACCA
1 ATACAAATGATGTATATTGAAATAGTGATGACATAAAAAGTGATTGGCTGATAAAAAAATTACCA
*
34025801 AGATACATCAAATTTATGATAAAGAGGACTAAATTGTAAAGTGTATAGAAGTTTATGATTTAAAT
66 AGATACATCAAATTTATGATAAAGAGGACTAAATTATAAAGTGTATAGAAGTTTATGATTTAAAT
34025866 AAAAGTATTAGG
131 AAAAGTATTAGG
34025878 ATA
1 ATA
34025881 AAGAGTTTAA
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (142 bp):
ATACAAATGATGTATATTGAAATAGTGATGACATAAAAAGTGATTGGCTGATAAAAAAATTACCA
AGATACATCAAATTTATGATAAAGAGGACTAAATTATAAAGTGTATAGAAGTTTATGATTTAAAT
AAAAGTATTAGG
Found at i:34028375 original size:9 final size:9
Alignment explanation
Indices: 34028361--34028392 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
34028351 GATCAAGTAA
34028361 AATAAAATT
1 AATAAAATT
34028370 AATAAAATT
1 AATAAAATT
34028379 AATTAAAATT
1 AA-TAAAATT
34028389 AATA
1 AATA
34028393 TGATATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AATAAAATT
Found at i:34028387 original size:10 final size:10
Alignment explanation
Indices: 34028363--34028391 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
34028353 TCAAGTAAAA
34028363 TAAAATTAA-
1 TAAAATTAAT
34028372 TAAAATTAAT
1 TAAAATTAAT
34028382 TAAAATTAAT
1 TAAAATTAAT
34028392 ATGATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAATTAAT
Found at i:34030075 original size:102 final size:100
Alignment explanation
Indices: 34029896--34030239 Score: 431
Period size: 102 Copynumber: 3.4 Consensus size: 100
34029886 TATCGATGAA
* * *
34029896 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGATAAATGATGGTCACATGTGTAGTAC
* * *
34029961 TAAATGAAGGCTACAATGTGCACCGAGAAGCTCTGGT
66 TAAGTGAAGGCTACTATGTGAACCGA-AAGCT-TGGT
* * *
34029998 CATGTGTGTAGTACTGTGTGAATGCTACTACATGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGATAAATGATGGTCACATGTGTAGTAC
34030063 TAAGTGAAGGCTACTATGT-ATACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGA-ACCG-AAAGC-TTGGT
* *** * *
34030100 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGATAAATGATGGTCACATGTGTAGTAC
* * * *
34030164 TATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
66 TAAGTGAAGGCTACTATGTGAACCG-AAAGCTTGGT
* *
34030200 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGA
34030240 ATGATAAAAG
Statistics
Matches: 213, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
100 40 0.19
101 45 0.21
102 126 0.59
103 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (100 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGAACCGAAAGCTTGGT
Found at i:34030231 original size:50 final size:50
Alignment explanation
Indices: 34029896--34030233 Score: 349
Period size: 51 Copynumber: 6.7 Consensus size: 50
34029886 TATCGATGAA
* * * ***
34029896 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* ** * * * *
34029947 CACATGTGTAGTACTAAATGAAGGCTACAATGTGCACCG-AGAAGCTCTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAACT-TGGT
* * * * * ***
34029998 CATGTGTGTAGTACTGTGTGAATGCTACTACATGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * *
34030049 CACATGTGTAGTACTAAGTGAAGGCTACTATGT-ATACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGA-ACCGTAAAA-C-TTGGT
* *
34030100 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
*
34030150 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
34030200 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
34030234 TATCGAATGA
Statistics
Matches: 236, Mismatches: 42, Indels: 19
0.79 0.14 0.06
Matches are distributed among these distances:
49 4 0.02
50 90 0.38
51 134 0.57
52 7 0.03
53 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:34035221 original size:31 final size:31
Alignment explanation
Indices: 34035183--34035246 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
34035173 AGTTTATCAA
34035183 AAGAAACTTACTATGGATAAATTGTAATTGG
1 AAGAAACTTACTATGGATAAATTGTAATTGG
34035214 AAGAAACTTACTATGGATAAATTGTAATTGG
1 AAGAAACTTACTATGGATAAATTGTAATTGG
34035245 AA
1 AA
34035247 TTAGGACATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (31 bp):
AAGAAACTTACTATGGATAAATTGTAATTGG
Found at i:34036109 original size:18 final size:17
Alignment explanation
Indices: 34036086--34036119 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
34036076 TTCATTCAAT
34036086 AACATAAACATATCATAA
1 AACATAAACATA-CATAA
*
34036104 AACATACACATACATA
1 AACATAAACATACATA
34036120 TCATCTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (17 bp):
AACATAAACATACATAA
Found at i:34036440 original size:55 final size:55
Alignment explanation
Indices: 34036338--34036442 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
34036328 TCCTCACCCG
* * *
34036338 TGTAACTCTTTAAGTAGGGTCACACGGCCATGTCACACGCCCGTGTGCCAAGCCA
1 TGTAACTCTCTAAGTAGGGTCACACGGCCATGTCACAAGCCCATGTGCCAAGCCA
* ** *
34036393 TGTAACTCTCTAAGTAGGGTCTCACGGCCATGTTGCAAGTCCATGTGCCA
1 TGTAACTCTCTAAGTAGGGTCACACGGCCATGTCACAAGCCCATGTGCCA
34036443 GGCTGTGCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.25
Consensus pattern (55 bp):
TGTAACTCTCTAAGTAGGGTCACACGGCCATGTCACAAGCCCATGTGCCAAGCCA
Found at i:34036455 original size:55 final size:55
Alignment explanation
Indices: 34036341--34036458 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 55
34036331 TCACCCGTGT
* * * *
34036341 AACTCTTTAAGTAGGGTCACACGGCCATGTCACACGCCCGTGTGCCAAGCCATGT
1 AACTCTCTAAGTAGGGTCACACGGCCATGTCACAAGCCCATGTGCCAAGCCATGC
* ** * * **
34036396 AACTCTCTAAGTAGGGTCTCACGGCCATGTTGCAAGTCCATGTGCCAGGCTGTGC
1 AACTCTCTAAGTAGGGTCACACGGCCATGTCACAAGCCCATGTGCCAAGCCATGC
34036451 AACTCTCT
1 AACTCTCT
34036459 GAGTTGCCCC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.25
Consensus pattern (55 bp):
AACTCTCTAAGTAGGGTCACACGGCCATGTCACAAGCCCATGTGCCAAGCCATGC
Found at i:34038668 original size:9 final size:9
Alignment explanation
Indices: 34038654--34038679 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
34038644 TTTTCATAAT
34038654 CTTTTAGCC
1 CTTTTAGCC
34038663 CTTTTAGCC
1 CTTTTAGCC
34038672 CTTTTAGC
1 CTTTTAGC
34038680 TAATAGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.31, G:0.12, T:0.46
Consensus pattern (9 bp):
CTTTTAGCC
Found at i:34043958 original size:21 final size:21
Alignment explanation
Indices: 34043934--34043980 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
34043924 GAAAGAAAAA
34043934 ACAAACACATTCTTAAAGTAG
1 ACAAACACATTCTTAAAGTAG
*
34043955 ACAAACACTTTCTTAAAGTAG
1 ACAAACACATTCTTAAAGTAG
*
34043976 CCAAA
1 ACAAA
34043981 GCCCTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (21 bp):
ACAAACACATTCTTAAAGTAG
Found at i:34043988 original size:21 final size:21
Alignment explanation
Indices: 34043934--34043989 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
34043924 GAAAGAAAAA
*
34043934 ACAAACACATTCTTAAAGTAG
1 ACAAACACCTTCTTAAAGTAG
*
34043955 ACAAACACTTTCTTAAAGTAG
1 ACAAACACCTTCTTAAAGTAG
*
34043976 CCAAAGC-CCTTCTT
1 ACAAA-CACCTTCTT
34043990 TTTCAATTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (21 bp):
ACAAACACCTTCTTAAAGTAG
Found at i:34045190 original size:39 final size:41
Alignment explanation
Indices: 34045104--34045230 Score: 118
Period size: 39 Copynumber: 3.1 Consensus size: 41
34045094 ATTTTTCCTG
* * *
34045104 AAATCGCGTCCACGTCAGCGCGATGTCAGGGGACGTGTCAGC
1 AAATCGCGTCCACGTCAGCGCGAT-TCAGCGGACGTGGCAAC
* **
34045146 AAATCGCGTCCACGTCAGTGCGATT-A-CTTACGTGGCAAC
1 AAATCGCGTCCACGTCAGCGCGATTCAGCGGACGTGGCAAC
* * * *
34045185 AAATCGTGTCCACGTAAGCGCGATT-TGCTGACGTGG-AAGC
1 AAATCGCGTCCACGTCAGCGCGATTCAGCGGACGTGGCAA-C
34045225 AAATCG
1 AAATCG
34045231 TGCTTACGTG
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
39 32 0.44
40 16 0.22
41 1 0.01
42 23 0.32
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.20
Consensus pattern (41 bp):
AAATCGCGTCCACGTCAGCGCGATTCAGCGGACGTGGCAAC
Done.