Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002577.1 Hibiscus syriacus cultivar Beakdansim tig00005222_pilon, whole genome shotgun sequence
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: 118497
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:664 original size:21 final size:23
Alignment explanation
Indices: 636--693 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
626 TTAACCTTTT
*
636 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGATACCTATTAC
659 ATTATATAAGCGATACCTATTAC
1 ATTATATAAGCGATACCTATTAC
682 ATTATATAAGCG
1 ATTATATAAGCG
694 GTACTAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (23 bp):
ATTATATAAGCGATACCTATTAC
Found at i:678 original size:106 final size:105
Alignment explanation
Indices: 545--773 Score: 304
Period size: 106 Copynumber: 2.2 Consensus size: 105
535 TAAGTAATTA
* *
545 ACCTATTTA-ATATATAAACGCTACCTATTAC-GTATATAAGCACTACCTAATATGTTATTGTG-
1 ACCTA-TTACATATATAAGCGATACCTATTACAGTATATAAGCACTA-CTAATATGTTATTGTGC
* *
607 ATGATAATGTTTCTAGTAATTAACCT-TTTATTATATAAGCGCT
64 ATAATAATGTTAC-AGTAATTAACCTATTTA-TATATAAGCGCT
* ** *
650 ACCTATTACATTATATAAGCGATACCTATTACATTATATAAGCGGTACTAATATGTTATTGTGCT
1 ACCTATTACA-TATATAAGCGATACCTATTACAGTATATAAGCACTACTAATATGTTATTGTGCA
715 TAATAATGTTACAGTAATTAACCTATTTATATATAAGCGCT
65 TAATAATGTTACAGTAATTAACCTATTTATATATAAGCGCT
*
756 ATCTATTACATATATAAG
1 ACCTATTACATATATAAG
774 TGGTATCTAA
Statistics
Matches: 110, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
104 3 0.03
105 14 0.13
106 68 0.62
107 25 0.23
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (105 bp):
ACCTATTACATATATAAGCGATACCTATTACAGTATATAAGCACTACTAATATGTTATTGTGCAT
AATAATGTTACAGTAATTAACCTATTTATATATAAGCGCT
Found at i:753 original size:83 final size:82
Alignment explanation
Indices: 660--865 Score: 306
Period size: 83 Copynumber: 2.5 Consensus size: 82
650 ACCTATTACA
* *
660 TTATATAAGCGATACCTATTACATTATATAAGCGGTACTAATATGTTATTGTGCTTAATAATGTT
1 TTATATAAGCGCTACCTATTACA-TATATAAGCGGTACTAATATGTTATTGTGATTAATAATGTT
725 AC-AGTAATTAACCTATT
65 ACTAGTAATTAACCTATT
* * *
742 TATATATAAGCGCTATCTATTACATATATAAGTGGTATCTAATATGTTATTGTGATTGATAATGT
1 T-TATATAAGCGCTACCTATTACATATATAAGCGGTA-CTAATATGTTATTGTGATTAATAATGT
*
807 TTCTAGTAATTAACCTATT
64 TACTAGTAATTAACCTATT
*
826 TTATTATAAGCGCTACCTATTACATATATAAGCGCTACTA
1 TTA-TATAAGCGCTACCTATTACATATATAAGCGGTACTA
866 TTACATTATA
Statistics
Matches: 111, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
82 13 0.12
83 52 0.47
84 46 0.41
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (82 bp):
TTATATAAGCGCTACCTATTACATATATAAGCGGTACTAATATGTTATTGTGATTAATAATGTTA
CTAGTAATTAACCTATT
Found at i:772 original size:189 final size:190
Alignment explanation
Indices: 537--910 Score: 594
Period size: 189 Copynumber: 2.0 Consensus size: 190
527 ATAACAAATA
*
537 AGTAATTAACCTATTTAATATATAAACGCTACCTATTACGTATATAAGCACTACCTAATATGTTA
1 AGTAATTAACCTATTTAATATATAAACGCTACCTATTACATATATAAGCACTACCTAATATGTTA
*
602 TTGTGA-TGATAATGTTTCTAGTAATTAACCTTTTATTA-TATAAGCGCTACCTATTACATTATA
66 TTGTGATTGATAATGTTTCTAGTAATTAACCTATT-TTATTATAAGCGCTACCTATTACA-TATA
*
665 TAAGCGATACCTATTACATTATATAAGCGGTA-CTAATATGTTATTGTGCTTAATAATGTTAC
129 TAAGCGATA-CTATTACATTATATAAGCGGTACCTAATATGTTATTGTACTTAATAATGTTAC
* * *** *
727 AGTAATTAACCTATTT-ATATATAAGCGCTATCTATTACATATATAAGTGGTATCTAATATGTTA
1 AGTAATTAACCTATTTAATATATAAACGCTACCTATTACATATATAAGCACTACCTAATATGTTA
791 TTGTGATTGATAATGTTTCTAGTAATTAACCTATTTTATTATAAGCGCTACCTATTACATATATA
66 TTGTGATTGATAATGTTTCTAGTAATTAACCTATTTTATTATAAGCGCTACCTATTACATATATA
* *
856 AGCGCTACTATTACATTATATAAGCGGTACCTAATATGTTATTGTACTTGATAAT
131 AGCGATACTATTACATTATATAAGCGGTACCTAATATGTTATTGTACTTAATAAT
911 ATTTCCGGTT
Statistics
Matches: 170, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
188 22 0.13
189 85 0.50
190 63 0.37
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (190 bp):
AGTAATTAACCTATTTAATATATAAACGCTACCTATTACATATATAAGCACTACCTAATATGTTA
TTGTGATTGATAATGTTTCTAGTAATTAACCTATTTTATTATAAGCGCTACCTATTACATATATA
AGCGATACTATTACATTATATAAGCGGTACCTAATATGTTATTGTACTTAATAATGTTAC
Found at i:858 original size:22 final size:23
Alignment explanation
Indices: 830--888 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 23
820 CCTATTTTAT
830 TATAAGCGCTACCTATTACA-TA
1 TATAAGCGCTACCTATTACATTA
852 TATAAGCGCTA-CTATTACATTA
1 TATAAGCGCTACCTATTACATTA
*
874 TATAAGCGGTACCTA
1 TATAAGCGCTACCTA
889 ATATGTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 8 0.24
22 23 0.68
23 3 0.09
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (23 bp):
TATAAGCGCTACCTATTACATTA
Found at i:4995 original size:20 final size:20
Alignment explanation
Indices: 4966--5014 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
4956 ATTTCTAATT
*
4966 TCAT-TATGCGAGGCATTCG
1 TCATGTATGCGAGGCACTCG
4985 TCATGTATGCGAGGCACTCG
1 TCATGTATGCGAGGCACTCG
5005 TCATGTATGC
1 TCATGTATGC
5015 TTTTATGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (20 bp):
TCATGTATGCGAGGCACTCG
Found at i:10853 original size:19 final size:19
Alignment explanation
Indices: 10826--10865 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
10816 AAAAATAGTC
*
10826 AATATCACAATTTACTATA
1 AATACCACAATTTACTATA
* *
10845 AATACCACAGTTTATTATA
1 AATACCACAATTTACTATA
10864 AA
1 AA
10866 AATCAAGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (19 bp):
AATACCACAATTTACTATA
Found at i:32202 original size:21 final size:24
Alignment explanation
Indices: 32166--32225 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
32156 ATATATATAT
* *
32166 ATAATAAATATAATAACG-AAAA-A
1 ATAAT-AATGTAATAAAGTAAAATA
*
32189 A-AATAATTTAATAAAGTAAAATA
1 ATAATAATGTAATAAAGTAAAATA
32212 ATAATAATGTAATA
1 ATAATAATGTAATA
32226 TAATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.32
22 7 0.23
23 3 0.10
24 11 0.35
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (24 bp):
ATAATAATGTAATAAAGTAAAATA
Found at i:32218 original size:16 final size:16
Alignment explanation
Indices: 32197--32234 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
32187 AAAAATAATT
32197 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
32213 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
32229 T-ATAAA
1 TAATAAA
32235 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:33006 original size:35 final size:37
Alignment explanation
Indices: 32944--33035 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 37
32934 GGATCATATC
* * *
32944 TTTAG-GAGTTTAAAACATAGCAAAATTCTATCCTAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCCTAT
* *
32980 TTTAG-GAG-TTGAATCCTAGCAGAATTCTATCTTAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCCTAT
*
33015 TTTTGAGAGTTTGAATCCTAG
1 TTTAGAGAGTTTGAATCCTAG
33036 TAGGACGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 26 0.54
36 11 0.23
37 11 0.23
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (37 bp):
TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCCTAT
Found at i:33804 original size:106 final size:103
Alignment explanation
Indices: 33496--33843 Score: 389
Period size: 106 Copynumber: 3.3 Consensus size: 103
33486 AATATTGTTC
* * ** * *
33496 CGAGTCCAATATTCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT-GAA-T-CGAAAATGTTTGTTGACA
* * * * *
33561 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
63 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
33602 CGAGTCTAATATCCTTCGCTGTGAAGATGAAATTGACTCTGAA-CG-AAAT-CTTGTTGACAATC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATCGAAAATGTTTGTTGACAATC
* *
33664 AGCCGTCCCTTTGTTGTGAAGTTGAACTTTTGTTGTCT
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
33702 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGACTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-TCG-AAAATGTTTGTTGACA
*
33767 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
63 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
33808 CGAGTGCCACGATATCCTCCGTTGTGGAA-TTGAAAT
1 CGAGT-CCA--ATATCCTTCGCTGT-GAAGTTGAAAT
33844 CGCGGATGGC
Statistics
Matches: 205, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
100 81 0.40
101 5 0.02
102 1 0.00
103 1 0.00
105 7 0.03
106 86 0.42
107 3 0.01
109 18 0.09
110 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (103 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATCGAAAATGTTTGTTGACAATC
AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:34442 original size:33 final size:33
Alignment explanation
Indices: 34405--34470 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
34395 GTCTTGAAAG
*
34405 AGATAT-AATTCGTTTCAAGGGAAACGATCTCAA
1 AGATATCAATT-GTTTCAAGAGAAACGATCTCAA
* * *
34438 AGATATCTATTGTTTCATGAGAAACGGTCTCAA
1 AGATATCAATTGTTTCAAGAGAAACGATCTCAA
34471 GGGAAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (33 bp):
AGATATCAATTGTTTCAAGAGAAACGATCTCAA
Found at i:34620 original size:65 final size:65
Alignment explanation
Indices: 34447--34899 Score: 293
Period size: 65 Copynumber: 6.7 Consensus size: 65
34437 AAGATATCTA
* * * **
34447 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
34512 TT
64 TT
* * *
34514 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
34579 T
65 T
* ** * * *
34580 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
* *
34645 ACAAA-ACT
57 TCAAAGATT
* * * * * * * * * *
34653 TTGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * * *
34718 TTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA-TTATTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
*
34782 ACAAA-ATT
57 TCAAAGATT
* * * * * * *** *
34790 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
34854 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
34900 AAAAGCAATC
Statistics
Matches: 300, Mismatches: 63, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
64 23 0.08
65 110 0.37
66 4 0.01
67 24 0.08
68 32 0.11
70 1 0.00
71 1 0.00
72 36 0.12
73 64 0.21
74 5 0.02
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:34631 original size:36 final size:36
Alignment explanation
Indices: 34579--34840 Score: 254
Period size: 36 Copynumber: 7.4 Consensus size: 36
34569 ATTCAAAGAT
*
34579 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * *
34615 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* ** * *
34651 CTTTGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * * * *
34688 TTTGTTTCAAAGAAAACATAT-TC---A-A-A--TAT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACGAAA
*
34717 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGAC-AAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * *
34752 ATTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
34788 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
34825 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
34841 TGTTTTCAAT
Statistics
Matches: 183, Mismatches: 32, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 30 0.16
36 65 0.36
37 64 0.35
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
Found at i:34670 original size:37 final size:36
Alignment explanation
Indices: 34579--34834 Score: 190
Period size: 37 Copynumber: 7.3 Consensus size: 36
34569 ATTCAAAGAT
** *
34579 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACGAAA
* * *
34615 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACGAAA
* * *
34651 CTTTGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACGAAA
* * *
34688 TTTGTTTC-AAAGAAAACATAT-TC---A-A-A--TAT
1 TTTGTTTCAAAAG-AAAC-TGTCTCAAGAGAGACGAAA
** *
34717 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGAC-AAA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACGAAA
* * ** *
34752 ATTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACGAAA
** *
34788 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACGAAA
*
34825 TTTATTTCAA
1 TTTGTTTCAA
34835 GGGAAATGTT
Statistics
Matches: 177, Mismatches: 30, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
28 2 0.01
29 14 0.08
30 2 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 34 0.19
36 56 0.32
37 64 0.36
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACGAAA
Found at i:34711 original size:138 final size:137
Alignment explanation
Indices: 34531--34899 Score: 461
Period size: 137 Copynumber: 2.7 Consensus size: 137
34521 CAAGAGTAAT
* * * *
34531 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAC
*
34596 TGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCA
66 TGTCTCAAGAGAGAC-AAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCA
*
34661 AAAGCAAC
130 AAAGAAAC
* * * * *
34669 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAAT
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAC
* * * * * *
34734 TGTCTCAAGAGAGACAAAATTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAA
66 TGTCTCAAGAGAGACAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAA
**
34799 GGGAAAC
131 AAGAAAC
* * * * * * *
34806 TATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAA
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAAGGGAAA
*
34870 CTGTCTCAAGGGAGACAAAATTTGTTTTAA
65 CTGTCTCAAGAGAGAC-AAATTTGTTTTAA
34900 AAAAGCAATC
Statistics
Matches: 194, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
136 3 0.02
137 111 0.57
138 80 0.41
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (137 bp):
TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAA
AAGAAAC
Found at i:34767 original size:35 final size:35
Alignment explanation
Indices: 34721--34840 Score: 177
Period size: 35 Copynumber: 3.3 Consensus size: 35
34711 AAATATTTTG
*
34721 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTA
*
34756 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TTA
* *
34793 TTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTA
34829 TTTCAAGGGAAA
1 TTTCAAGGGAAA
34841 TGTTTTCAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
35 31 0.40
36 14 0.18
37 29 0.38
38 3 0.04
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (35 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTA
Found at i:35289 original size:18 final size:18
Alignment explanation
Indices: 35262--35297 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35252 TGTTGAATCC
* *
35262 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
35280 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
35298 TTGATGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:36396 original size:10 final size:10
Alignment explanation
Indices: 36383--36469 Score: 54
Period size: 10 Copynumber: 8.2 Consensus size: 10
36373 TTGATTCTTG
36383 TTTTTTTTTC
1 TTTTTTTTTC
*
36393 -TTTTTTTCC
1 TTTTTTTTTC
36402 TTTTGTTCGTGTT-
1 TTTT-TT--T-TTC
36415 TTTCTTTTTTC
1 TTT-TTTTTTC
*
36426 TTTGTTTTTC
1 TTTTTTTTTC
36436 TTTGTTTTTT-
1 TTT-TTTTTTC
36446 TTTCTTCTTTTC
1 TTT-TT-TTTTC
*
36458 TTTTTTCTTC
1 TTTTTTTTTC
36468 TT
1 TT
36470 GATTGGATCT
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
9 8 0.13
10 25 0.41
11 17 0.28
12 3 0.05
13 6 0.10
14 2 0.03
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:36405 original size:17 final size:16
Alignment explanation
Indices: 36385--36463 Score: 65
Period size: 16 Copynumber: 4.9 Consensus size: 16
36375 GATTCTTGTT
36385 TTTTTTTCTTTTTTTCC
1 TTTTTTTCTTTTTTT-C
* *
36402 TTTTGTTCGTGTTTTTC
1 TTTTTTTC-TTTTTTTC
36419 -TTTTTTCTTTGTTTT-
1 TTTTTTTCTTT-TTTTC
*
36434 TCTTTGTT-TTTTTTTC
1 T-TTTTTTCTTTTTTTC
*
36450 TTCTTTTCTTTTTT
1 TTTTTTTCTTTTTT
36464 CTTCTTGATT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
15 10 0.20
16 20 0.41
17 13 0.27
18 6 0.12
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTTTTTC
Found at i:37591 original size:8 final size:8
Alignment explanation
Indices: 37575--37613 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
37565 AATGTAGATG
37575 AAAATGCA
1 AAAATGCA
*
37583 AAAAGGCA
1 AAAATGCA
37591 AAAATGC-
1 AAAATGCA
37598 AAAATGCA
1 AAAATGCA
*
37606 AGAATGCA
1 AAAATGCA
37614 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:37601 original size:15 final size:15
Alignment explanation
Indices: 37575--37613 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
37565 AATGTAGATG
37575 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
37591 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
37606 AGAATGCA
1 AAAATGCA
37614 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:38951 original size:5 final size:5
Alignment explanation
Indices: 38941--38968 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
38931 GCAAGTGATG
38941 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
38969 GATGAAAAGA
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:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:40781 original size:22 final size:22
Alignment explanation
Indices: 40756--40810 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
40746 GCTATCCCAT
40756 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
40778 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
40800 CAAACCTTTGA
1 CAAACCTTTGA
40811 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:41238 original size:18 final size:18
Alignment explanation
Indices: 41215--41250 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41205 TTAACATCAA
* *
41215 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
41233 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
41251 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:41733 original size:37 final size:37
Alignment explanation
Indices: 41672--41802 Score: 178
Period size: 37 Copynumber: 3.6 Consensus size: 37
41662 ATTGAAAACA
* * *
41672 TTTCCCTTGAAA-TAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
*
41708 TTTCACTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
* *
41745 TTTCCCTTG-AA-ATAATTTTGTCTCTCTTGAGACAA
1 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
41780 TTTCCCTTGAAACAAAATATTTG
1 TTTCCCTTGAAACAAAAT-TTTG
41803 AATATGTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
35 31 0.37
36 15 0.18
37 33 0.40
38 4 0.05
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
Found at i:41762 original size:35 final size:35
Alignment explanation
Indices: 41672--41791 Score: 168
Period size: 35 Copynumber: 3.3 Consensus size: 35
41662 ATTGAAAACA
* *
41672 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAAT-AATTTTGTCTCTCTTGAGACAG
* *
41708 TTTCACTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTG-AA-ATAATTTTGTCTCTCTTGAGACAG
*
41745 TTTCCCTTGAAATAATTTTGTCTCTCTTGAGACAA
1 TTTCCCTTGAAATAATTTTGTCTCTCTTGAGACAG
41780 TTTCCCTTGAAA
1 TTTCCCTTGAAA
41792 CAAAATATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 34 0.45
36 10 0.13
37 30 0.40
38 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (35 bp):
TTTCCCTTGAAATAATTTTGTCTCTCTTGAGACAG
Found at i:41781 original size:20 final size:20
Alignment explanation
Indices: 41723--41782 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
41713 CTTGAAACAA
41723 AATTTTGTCTCTCTTGAGAC
1 AATTTTGTCTCTCTTGAGAC
* * *
41743 -A-GTT-TC-C-CTTGAAAT
1 AATTTTGTCTCTCTTGAGAC
41758 AATTTTGTCTCTCTTGAGAC
1 AATTTTGTCTCTCTTGAGAC
41778 AATTT
1 AATTT
41783 CCCTTGAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
15 6 0.21
16 2 0.07
17 4 0.14
18 4 0.14
19 2 0.07
20 11 0.38
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.45
Consensus pattern (20 bp):
AATTTTGTCTCTCTTGAGAC
Found at i:41918 original size:36 final size:36
Alignment explanation
Indices: 41810--41933 Score: 144
Period size: 36 Copynumber: 3.4 Consensus size: 36
41800 TTGAATATGT
*
41810 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * *
41845 TTGT-TTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TT-TCTCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
41882 TTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
41918 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
41934 ATCTTTGAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
35 3 0.04
36 42 0.58
37 28 0.38
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:41960 original size:138 final size:138
Alignment explanation
Indices: 41613--41996 Score: 459
Period size: 137 Copynumber: 2.8 Consensus size: 138
41603 GATTGCTTTT
* * * * *
41613 TTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAACATTTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATATATTTCC
* * *
41677 CTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCACTTGAAACAAAATTTTGTCTCTCTTGAGA
65 CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCACTTGAAACAAAATTTTGTCTCTCTTGAGA
41742 CAGTTTCCC
130 CAGTTTCCC
* * * * * * *
41751 TTGAAA-TAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTCCC
** * * *
41815 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTGT-TTTTGGAACTAAGTTTTGTCTCTCTTGAGA
66 TTGAAACAAATTTCGTCTCCCTTGAGACAGTT-TCACTTGAAACAAAATTTTGTCTCTCTTGAGA
*
41879 CAGTTTCTC
130 CAGTTTCCC
* * *
41888 TTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTCCC
* * * * * *
41953 CTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACA
66 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCACTTGAAACA
41997 CAAAATCTTC
Statistics
Matches: 203, Mismatches: 39, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
136 3 0.01
137 110 0.54
138 90 0.44
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (138 bp):
TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTCCC
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCACTTGAAACAAAATTTTGTCTCTCTTGAGAC
AGTTTCCC
Found at i:41993 original size:65 final size:67
Alignment explanation
Indices: 41889--42048 Score: 207
Period size: 65 Copynumber: 2.4 Consensus size: 67
41879 CAGTTTCTCT
* ** * * **
41889 TAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
41952 CC
66 CC
*
41954 TAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
*
42019 CT
66 CC
*
42021 TAAAACATAATTTTGTTTCCCTTGAGAC
1 TAAAACA-AATTTTGTCTCCCTTGAGAC
42049 CGTTTCTCAT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 32 0.39
66 2 0.02
67 29 0.35
68 19 0.23
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (67 bp):
TAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCC
CC
Found at i:42824 original size:106 final size:103
Alignment explanation
Indices: 42669--43016 Score: 387
Period size: 106 Copynumber: 3.3 Consensus size: 103
42659 GCCATCCGCG
* * *
42669 ATTTCAACTCCACAACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAGCGAAGGATAT--TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGAA
* *
42734 GTGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGTCA
63 GGGACGGCTGATTGTCAACAAACA-TTTTC--ATTTCAGAGTCA
* * *
42778 ATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGACAACAAAAGTTCAACTTCACAACAAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
42843 ACGGCTGATTGTCAAC-AAGA-TTTC-GTTCAGAGTCA
66 ACGGCTGATTGTCAACAAACATTTTCATTTCAGAGTCA
* * * * *
42878 ATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * **
42943 GCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCA
66 ACGGCTGATTGTCAACAAAC-ATTT-TCA-TTTCAGAGTCA
* *
42984 ATTTCAACTTCACAGCGGAGAATATTGGACTCG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCG
43017 GAACAATATT
Statistics
Matches: 203, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
100 81 0.40
101 2 0.01
102 1 0.00
103 6 0.03
104 1 0.00
105 3 0.01
106 85 0.42
107 3 0.01
109 21 0.10
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (103 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGATTGTCAACAAACATTTTCATTTCAGAGTCA
Found at i:43541 original size:35 final size:35
Alignment explanation
Indices: 43477--43576 Score: 110
Period size: 35 Copynumber: 2.7 Consensus size: 35
43467 TTTCGTCCTA
* *
43477 CTAGGATTCAAACTCTCAAAAATAAGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
43514 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
43549 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
43577 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.38
36 18 0.33
37 16 0.29
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:44095 original size:15 final size:15
Alignment explanation
Indices: 44053--44095 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
44043 GTTTTTAAAG
44053 TTATTATATATATATAT
1 TTATTAT-TAT-TATAT
* *
44070 TTATAACTATTATAT
1 TTATTATTATTATAT
44085 TTATTATTATT
1 TTATTATTATT
44096 TTACTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:44304 original size:24 final size:25
Alignment explanation
Indices: 44277--44329 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
44267 TGTTTTCATG
*
44277 TATTTA-TATTATA-TTATATTACAT
1 TATTTATTATTATACTT-TATTAAAT
*
44301 TA-TTATTATTTTACTTTATTAAAT
1 TATTTATTATTATACTTTATTAAAT
44325 TATTT
1 TATTT
44330 TTTTTCGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 3 0.12
24 17 0.71
25 4 0.17
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTATTATTATACTTTATTAAAT
Found at i:44307 original size:16 final size:16
Alignment explanation
Indices: 44284--44321 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
44274 ATGTATTTAT
44284 ATTA-TATTATATTAC
1 ATTATTATTATATTAC
*
44299 ATTATTATTATTTTAC
1 ATTATTATTATATTAC
*
44315 TTTATTA
1 ATTATTA
44322 AATTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTATTATATTAC
Found at i:44326 original size:21 final size:22
Alignment explanation
Indices: 44302--44352 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
44292 ATATTACATT
*
44302 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
44323 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
44345 TTTATTAT
1 ATTATTAT
44353 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:60505 original size:19 final size:19
Alignment explanation
Indices: 60481--60527 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
60471 GCAGGTAAGG
60481 AATGTCTCTTCTTAATATA
1 AATGTCTCTTCTTAATATA
60500 AATGTCTCTTCTTAATATA
1 AATGTCTCTTCTTAATATA
60519 AATGTCTCT
1 AATGTCTCT
60528 GTCCTGCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (19 bp):
AATGTCTCTTCTTAATATA
Found at i:63052 original size:25 final size:24
Alignment explanation
Indices: 63021--63095 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 24
63011 AAACCCAGAC
63021 AATGAATGAAAATATCAAACTTTGA
1 AATGAATGAAAA-ATCAAACTTTGA
* *
63046 AATGAATGAAAAACCAAA--ATGCA
1 AATGAATGAAAAATCAAACTTTG-A
63069 AATGCAATGAAAAGATCAAACTTTGA
1 AATG-AATGAAAA-ATCAAACTTTGA
63095 A
1 A
63096 GATCTTCCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
22 2 0.05
23 5 0.12
24 13 0.32
25 17 0.41
26 2 0.05
27 2 0.05
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (24 bp):
AATGAATGAAAAATCAAACTTTGA
Found at i:64048 original size:17 final size:16
Alignment explanation
Indices: 64026--64074 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
64016 GTTAGGGTTA
64026 AGATTTGGGGATTTTAG
1 AGATTTGGGG-TTTTAG
*
64043 AGATTTTGGGGCTTTAG
1 AGA-TTTGGGGTTTTAG
64060 AGATTTGGGGCTTTT
1 AGATTTGGGG-TTTT
64075 GTAATTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.25
17 14 0.50
18 7 0.25
ACGTcount: A:0.18, C:0.04, G:0.35, T:0.43
Consensus pattern (16 bp):
AGATTTGGGGTTTTAG
Found at i:64081 original size:16 final size:16
Alignment explanation
Indices: 64026--64073 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
64016 GTTAGGGTTA
*
64026 AGATTTGGGGATTTTAG
1 AGATTTGGGG-CTTTAG
64043 AGATTTTGGGGCTTTAG
1 AGA-TTTGGGGCTTTAG
64060 AGATTTGGGGCTTT
1 AGATTTGGGGCTTT
64074 TGTAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 11 0.38
17 11 0.38
18 7 0.24
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.42
Consensus pattern (16 bp):
AGATTTGGGGCTTTAG
Found at i:64862 original size:17 final size:17
Alignment explanation
Indices: 64840--64885 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
64830 TCCTAAAATT
64840 TTATAAATTCATTTATC
1 TTATAAATTCATTTATC
64857 TTATAAATTCATTTATC
1 TTATAAATTCATTTATC
64874 TTATAAATTCAT
1 TTATAAATTCAT
64886 CCCTCTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATAAATTCATTTATC
Found at i:66767 original size:48 final size:45
Alignment explanation
Indices: 66705--66796 Score: 132
Period size: 48 Copynumber: 2.0 Consensus size: 45
66695 ACCAAACATA
66705 AATTTAAGTACATATCATGATTGAAAAATAATTAAAATAATTCATCAT
1 AATTTAAGTACATATCATGATT-AAAAATAATTAAAA-AATT-ATCAT
*
66753 AATTTAATGT-CATATCATTATTAAAAATAATTAAAAAATTATCA
1 AATTTAA-GTACATATCATGATTAAAAATAATTAAAAAATTATCA
66797 CGTAACATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 4 0.10
46 4 0.10
47 14 0.33
48 18 0.43
49 2 0.05
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (45 bp):
AATTTAAGTACATATCATGATTAAAAATAATTAAAAAATTATCAT
Found at i:69209 original size:38 final size:38
Alignment explanation
Indices: 69158--69235 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
69148 AATATTGGCT
69158 AAGTGGACACTTTCATTCCCTCTATTATTTGCAACTTC
1 AAGTGGACACTTTCATTCCCTCTATTATTTGCAACTTC
69196 AAGTGGACACTTTCATTCCCTCTATTATTTGCAACTTC
1 AAGTGGACACTTTCATTCCCTCTATTATTTGCAACTTC
69234 AA
1 AA
69236 TTCCTTTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (38 bp):
AAGTGGACACTTTCATTCCCTCTATTATTTGCAACTTC
Found at i:71644 original size:88 final size:89
Alignment explanation
Indices: 71494--71670 Score: 331
Period size: 88 Copynumber: 2.0 Consensus size: 89
71484 GACTCCTCGC
71494 ACATCACTCAATCTTTATTAAAACCCATCACTTGTTTTGTTTTTTGTCGCTCTCTGTTGGTGTGT
1 ACATCACTCAATCTTTATTAAAACCCATCACTTGTTTTGTTTTTTGTCGCTCTCTGTTGGTGTG-
71559 TTGTT-GCCCCCTTTATCTTTACGT
65 TTGTTGGCCCCCTTTATCTTTACGT
71583 ACATCACTCAAT-TTTATTAAAACCCATCACTTGTTTTGTTTTTTGTCGCTCTCTGTTGGTGTGT
1 ACATCACTCAATCTTTATTAAAACCCATCACTTGTTTTGTTTTTTGTCGCTCTCTGTTGGTGTGT
71647 TGTTGGCCCCCTTTATCTTTACGT
66 TGTTGGCCCCCTTTATCTTTACGT
71671 TGTGTCATTT
Statistics
Matches: 87, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
87 5 0.06
88 70 0.80
89 12 0.14
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.47
Consensus pattern (89 bp):
ACATCACTCAATCTTTATTAAAACCCATCACTTGTTTTGTTTTTTGTCGCTCTCTGTTGGTGTGT
TGTTGGCCCCCTTTATCTTTACGT
Found at i:74024 original size:46 final size:45
Alignment explanation
Indices: 73958--74048 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 45
73948 TGGACAATGG
73958 CTGTATTAGTGTGGCAATGGGCTGGAAACACGTGACCACCTATTT
1 CTGTATTAGTGTGGCAATGGGCTGGAAACACGTGACCACCTATTT
74003 CTGTATTATGTGTGGCAATGGGCTGGAAACACGTGACCACCTATTT
1 CTGTATTA-GTGTGGCAATGGGCTGGAAACACGTGACCACCTATTT
74049 GCTAACTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 8 0.18
46 37 0.82
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (45 bp):
CTGTATTAGTGTGGCAATGGGCTGGAAACACGTGACCACCTATTT
Found at i:82320 original size:71 final size:70
Alignment explanation
Indices: 82205--82346 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 70
82195 GACGAACCAA
82205 TGTCGATAACCTTAGATGCCTCTTGGCCTCCTCGGCGAACTTGGGCACAGTGATCTTCAAAACCC
1 TGTCGATAACCTTAGATGCCTCTTGGCCTCCTCGGCGAACTTGGGCACAGTGATCTTCAAAACCC
82270 CATCT
66 CATCT
82275 TGTCGATAACCTTAGATTGCCTCTTGGCCTCCTCGGCGAACTTGGGCACAGTGATCTTCAAAACC
1 TGTCGATAACCTTAGA-TGCCTCTTGGCCTCCTCGGCGAACTTGGGCACAGTGATCTTCAAAACC
82340 CCATCT
65 CCATCT
82346 T
1 T
82347 CCAAATGAGC
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 16 0.23
71 55 0.77
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (70 bp):
TGTCGATAACCTTAGATGCCTCTTGGCCTCCTCGGCGAACTTGGGCACAGTGATCTTCAAAACCC
CATCT
Found at i:89485 original size:20 final size:19
Alignment explanation
Indices: 89445--89485 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
89435 TGTTTTCAAT
*
89445 ATGAAGCATAATTTTTAGA
1 ATGAAGCATAATTTATAGA
89464 ATGAAGCATAATTTAATAGA
1 ATGAAGCATAATTT-ATAGA
89484 AT
1 AT
89486 ATTATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (19 bp):
ATGAAGCATAATTTATAGA
Found at i:99752 original size:12 final size:13
Alignment explanation
Indices: 99723--99771 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
99713 CTTAAATTGT
99723 ATATTTTATTAAA
1 ATATTTTATTAAA
*
99736 TTATTTT-TTAAA
1 ATATTTTATTAAA
**
99748 ATATTTTATTTTTA
1 ATATTTTA-TTAAA
99762 ATATTTTATT
1 ATATTTTATT
99772 TTGTTATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 11 0.37
13 8 0.27
14 11 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATATTTTATTAAA
Found at i:99766 original size:14 final size:14
Alignment explanation
Indices: 99747--99773 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
99737 TATTTTTTAA
99747 AATATTTTATTTTT
1 AATATTTTATTTTT
99761 AATATTTTATTTT
1 AATATTTTATTTT
99774 GTTATTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AATATTTTATTTTT
Found at i:100620 original size:20 final size:21
Alignment explanation
Indices: 100595--100639 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
100585 TATTGAAATA
100595 TTAATAACATATTTT-ATTAT
1 TTAATAACATATTTTAATTAT
**
100615 TTAATAATTTATTTTAATTAT
1 TTAATAACATATTTTAATTAT
100636 TTAA
1 TTAA
100640 AATTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATAACATATTTTAATTAT
Found at i:100621 original size:80 final size:80
Alignment explanation
Indices: 100516--100691 Score: 291
Period size: 80 Copynumber: 2.2 Consensus size: 80
100506 ATTATCCTCG
* * * *
100516 TTAA-AAAATAATTTAATACTTAATAATTTATTTTAATTATTTAAAAGTAAATAAAATTCATGGT
1 TTAATAAAATATTTTATTATTTAATAATTTATTTTAATTATTTAAAAGTAAATAAAATTCATGAT
100580 TTATATATTGAAATA
66 TTATATATTGAAATA
* *
100595 TTAATAACATATTTTATTATTTAATAATTTATTTTAATTATTTAAAATTAAATAAAATTCATGAT
1 TTAATAAAATATTTTATTATTTAATAATTTATTTTAATTATTTAAAAGTAAATAAAATTCATGAT
100660 TTATATATTGAAATA
66 TTATATATTGAAATA
100675 TTAATAAAATATTTTAT
1 TTAATAAAATATTTTAT
100692 ATCCAAGTGT
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 4 0.04
80 85 0.96
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (80 bp):
TTAATAAAATATTTTATTATTTAATAATTTATTTTAATTATTTAAAAGTAAATAAAATTCATGAT
TTATATATTGAAATA
Done.