Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004156.1 Hibiscus syriacus cultivar Beakdansim tig00009094_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: 80075
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:566 original size:59 final size:59
Alignment explanation
Indices: 488--660 Score: 231
Period size: 59 Copynumber: 2.9 Consensus size: 59
478 CTTTTTGTAG
* * *
488 CTTTTAATAGTTGACGGACTCAATAAAGCAACTCCCTATAGTGGGGGACTATTTCATAA
1 CTTTTAATAGTCGACGGACTCAATAAAGCAACACCCTATAGTGGGGGACCATTTCATAA
*** * *
547 CTTTTAATAGTCGGA-GGACTCAATAAAGCAACACCCTATAGTGATTGACGATTTTATAA
1 CTTTTAATAGTC-GACGGACTCAATAAAGCAACACCCTATAGTGGGGGACCATTTCATAA
* *
606 CTTTTAATAGTCGAGGGACTCAATAAAGTAACACCCTATAGTCGGGGGACCATTT
1 CTTTTAATAGTCGACGGACTCAATAAAGCAACACCCTATAGT-GGGGGACCATTT
661 GTGTATTTTA
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
58 2 0.02
59 87 0.88
60 10 0.10
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (59 bp):
CTTTTAATAGTCGACGGACTCAATAAAGCAACACCCTATAGTGGGGGACCATTTCATAA
Found at i:834 original size:13 final size:14
Alignment explanation
Indices: 807--835 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
797 CGGAGCTTGA
807 ATCTTGTGAGAAAC
1 ATCTTGTGAGAAAC
821 ATCTTGTG-GAAAC
1 ATCTTGTGAGAAAC
834 AT
1 AT
836 TAGCAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (14 bp):
ATCTTGTGAGAAAC
Found at i:2662 original size:30 final size:30
Alignment explanation
Indices: 2626--2683 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
2616 TCACTCAAAT
*
2626 ATCTCATGAGATCCAAGTTTAATTCCCTAC
1 ATCTCATGAGACCCAAGTTTAATTCCCTAC
2656 ATCTCATGAGACCCAAGTTTAATTCCCT
1 ATCTCATGAGACCCAAGTTTAATTCCCT
2684 CCATTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (30 bp):
ATCTCATGAGACCCAAGTTTAATTCCCTAC
Found at i:3564 original size:35 final size:35
Alignment explanation
Indices: 3525--3593 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
3515 ATATCTAACA
* *
3525 TAATTATTATCTTATTTAAAAGTTAAATTTTATAT
1 TAATTATTATATTATGTAAAAGTTAAATTTTATAT
* * *
3560 TAATTTTTGTATTATGTATAAGTTAAATTTTATA
1 TAATTATTATATTATGTAAAAGTTAAATTTTATA
3594 GTTTAATTCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (35 bp):
TAATTATTATATTATGTAAAAGTTAAATTTTATAT
Found at i:3836 original size:19 final size:21
Alignment explanation
Indices: 3807--3859 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 21
3797 TAAGAATCAA
*
3807 AAATT-AAATATTTTAAAAAT
1 AAATTAAAATATTATAAAAAT
3827 -AA-TAAAATA-TATAAAAAT
1 AAATTAAAATATTATAAAAAT
3845 CAAATTAAAATATTA
1 -AAATTAAAATATTA
3860 AAACTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 9 0.33
19 7 0.26
20 2 0.07
21 7 0.26
22 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATTAAAATATTATAAAAAT
Found at i:3869 original size:20 final size:21
Alignment explanation
Indices: 3806--3870 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 21
3796 ATAAGAATCA
*
3806 AAAATT-AAATATTTTAAAAAT
1 AAAATTAAAATA-TATAAAAAT
3827 --AA-TAAAATATATAAAAAT
1 AAAATTAAAATATATAAAAAT
* *
3845 CAAATTAAAATAT-TAAAACT
1 AAAATTAAAATATATAAAAAT
3865 AAAATT
1 AAAATT
3871 TCAATTTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 9 0.24
19 7 0.19
20 13 0.35
21 8 0.22
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTAAAATATATAAAAAT
Found at i:5835 original size:34 final size:35
Alignment explanation
Indices: 5763--5836 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
5753 ATTAATGTTC
* *
5763 AAATTCCAAAACACTTCAATTACATTTTGAACCCT
1 AAATTCCAAAACACTTCAATTACATTATAAACCCT
* * *
5798 AAATTCCAAAATACTTTAATTATA-TATAAACCCT
1 AAATTCCAAAACACTTCAATTACATTATAAACCCT
5832 AAATT
1 AAATT
5837 GAAGTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.34
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTATAAACCCT
Found at i:5900 original size:35 final size:35
Alignment explanation
Indices: 5831--5908 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
5821 ATATAAACCC
5831 TAAATTGAAGTATTTTAGAATTTAAGGTTCAGAAT
1 TAAATTGAAGTATTTTAGAATTTAAGGTTCAGAAT
* * * *
5866 GT-AATTGAATTATTTTGGAATTT-GGGATTTAGAAT
1 -TAAATTGAAGTATTTTAGAATTTAAGG-TTCAGAAT
5901 TAAATTGA
1 TAAATTGA
5909 GGATTGTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 3 0.08
35 32 0.89
36 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.42
Consensus pattern (35 bp):
TAAATTGAAGTATTTTAGAATTTAAGGTTCAGAAT
Found at i:14174 original size:8 final size:8
Alignment explanation
Indices: 14161--14187 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
14151 ACGGCTCAAG
14161 GAAATGAA
1 GAAATGAA
14169 GAAATGAA
1 GAAATGAA
14177 GAAATGAA
1 GAAATGAA
14185 GAA
1 GAA
14188 TCATAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (8 bp):
GAAATGAA
Found at i:15963 original size:99 final size:99
Alignment explanation
Indices: 15849--16037 Score: 288
Period size: 99 Copynumber: 1.9 Consensus size: 99
15839 TTATAATATT
* * * * * **
15849 ATATGTATACAATAAAGCTTGAGTTGTCCCTTTAGAGCAATTTGTTAAACGCCATGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACGCCACAGCTTTATGG
* *
15914 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAACTAACCTGATAAAGGTGATTATA
*
15948 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACGCCCCAGCTTTATGG
1 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACGCCACAGCTTTATGG
16013 ATAAGATTCAACTAACCTGATAAAG
66 ATAAGATTCAACTAACCTGATAAAG
16038 ACAAATTACA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACGCCACAGCTTTATGG
ATAAGATTCAACTAACCTGATAAAGGTGATTATA
Found at i:18539 original size:37 final size:37
Alignment explanation
Indices: 18498--18722 Score: 138
Period size: 37 Copynumber: 6.0 Consensus size: 37
18488 TTGGGGAAAG
* *
18498 TCAATCTTAAGCCTTCACGGAAGAGCAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
* * **
18535 TCAATTTTAAGCCTTCACAGAAGAGTAGTAAATAAAA
1 TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
* *
18572 TCAATCTTAAGTCTTCA-TGATAGAGTAGTGAAGC-AA
1 TCAATCTTAAGCCTTCACAGA-AGAGTAGTGAAGCAAA
* * * * * ** **
18608 GCCATCAGTAAGGCTTC-CGAGTAAGATGATAAGTCATCCGGA
1 TCAATC-TTAAGCCTTCAC-AG-AAGA-G-T-AGTGAAGCAAA
**
18650 -CCGTCTTAAGCCTTCAC-GAAAGAGTAGT-AAGGCAAA
1 TCAATCTTAAGCCTTCACAG-AAGAGTAGTGAA-GCAAA
* *
18686 TTAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
18723 ATAATTTCGA
Statistics
Matches: 142, Mismatches: 32, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
35 1 0.01
36 13 0.09
37 93 0.65
38 8 0.06
39 7 0.05
40 9 0.06
41 10 0.07
42 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
Found at i:18804 original size:55 final size:55
Alignment explanation
Indices: 18728--19119 Score: 387
Period size: 55 Copynumber: 7.1 Consensus size: 55
18718 GCAAAATAAT
* * *
18728 TTCGAGTCCTATACTCTCTGAAAGAATAGGGCGCAAATACATTTGTTGAAGATTG
1 TTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCAAACACATTTGTTGAAGATTG
* * * *
18783 ATCGAGTCCTATACTCCCTGAAAGAATAGGGAGTAAAGACATTTGCTGAAGATTG
1 TTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCAAACACATTTGTTGAAGATTG
* * * * *
18838 CTCGAGTCCTATACTCCTTGAAAGAATAGGGAGCAAACACGTTTGCTAAAGATTG
1 TTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCAAACACATTTGTTGAAGATTG
* * * *** *
18893 TTTGAGTCCTGTACTCTCTGAAAGAATAGGGAGTGGACACGTTTGTTGAAGATTG
1 TTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCAAACACATTTGTTGAAGATTG
* * **** *
18948 TTTCGAGTCCTATACTCCATGAAAGAATAAGGAG--TGGGCATTTGTTGAATATTG
1 -TTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCAAACACATTTGTTGAAGATTG
* * * * ** *
19002 TTTGAGTCATATACTCCCTGAAAAAATAGGAAGCGGAC-CAATTTGCTGAAGATTG
1 TTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCAAACAC-ATTTGTTGAAGATTG
* * * *
19057 TTTGAGTCCTATATTCCCTGAAAGAATAGGGAGCAGACACATTT-TTCGAAGATTT
1 TTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCAAACACATTTGTT-GAAGATTG
*
19112 TTCAAGTC
1 TTCGAGTC
19120 TCACTTATCC
Statistics
Matches: 278, Mismatches: 53, Indels: 12
0.81 0.15 0.03
Matches are distributed among these distances:
53 27 0.10
54 16 0.06
55 206 0.74
56 29 0.10
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (55 bp):
TTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCAAACACATTTGTTGAAGATTG
Found at i:19501 original size:26 final size:26
Alignment explanation
Indices: 19471--19524 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
19461 CAACAACCGA
*
19471 GCCCATAAGCCCGATGTTCAACCAGT
1 GCCCAAAAGCCCGATGTTCAACCAGT
*
19497 GCCCAAAAGCCCGATGTTCAACCCGT
1 GCCCAAAAGCCCGATGTTCAACCAGT
19523 GC
1 GC
19525 AACCGTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.37, G:0.20, T:0.17
Consensus pattern (26 bp):
GCCCAAAAGCCCGATGTTCAACCAGT
Found at i:21683 original size:15 final size:15
Alignment explanation
Indices: 21663--21694 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21653 AGCTAGGAGC
21663 AGCTCGTGAAGAACT
1 AGCTCGTGAAGAACT
21678 AGCTCGTGAAGAACT
1 AGCTCGTGAAGAACT
21693 AG
1 AG
21695 TTTCCAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (15 bp):
AGCTCGTGAAGAACT
Found at i:28653 original size:64 final size:63
Alignment explanation
Indices: 28576--28718 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 63
28566 TTGGACCCTT
*
28576 AGTGCATCGATGCA-CTAAGAGTGCATCGATGCATGAAATACATTCGATG-TTTCA-AAATAGC-
1 AGTGCATCGATGCAGCT--G-GTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-A-CT
28637 CAG
61 CAG
* *
28640 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTG
1 AGTGCATCGATGCA--GCTGGTGCATCGATGCATCAAATACATTCGATGTTTTCATAAAACTCAG
28705 AGTGCATCGATGCA
1 AGTGCATCGATGCA
28719 TAGTATATGC
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
64 42 0.60
65 23 0.33
66 3 0.04
67 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (63 bp):
AGTGCATCGATGCAGCTGGTGCATCGATGCATCAAATACATTCGATGTTTTCATAAAACTCAG
Found at i:28730 original size:65 final size:64
Alignment explanation
Indices: 28576--28755 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 64
28566 TTGGACCCTT
*
28576 AGTGCATCGATGCACTAAG-AGTGCATCGATGCATGAAATACATTCGATG-TTTCAAAATAGCCA
1 AGTGCATCGATGCA-T-AGTAGTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCA
28639 G
64 G
* * *
28640 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTC
1 AGTGCATCGATGCATAG-TAGTGCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGC-C
*
28703 TG
63 AG
* * * *
28705 AGTGCATCGATGCATAGTATATGCATCGGTGCGTGAAATGCATTTGATGTT
1 AGTGCATCGATGCATAGTA-GTGCATCGATGCATGAAATGCATTCGATGTT
28756 CAATTTATTC
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 43 0.44
65 50 0.51
66 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAGTAGTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAG
Found at i:32390 original size:64 final size:63
Alignment explanation
Indices: 32322--32531 Score: 194
Period size: 65 Copynumber: 3.3 Consensus size: 63
32312 TCCTTTATAA
*
32322 TGGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGT
1 TGGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-CCAGAGTGCATCGATGCATGGT
* * * * *
32386 TGGTGCATCGATGCATCAAATGCATTCGATGTTTCCATAAA-ACTCTGAGTGCATCAATACAT-A
1 TGGTGCATCGATGCATAAAATGCATTCGATGTTT-CA-AAATAC-CAGAGTGCATCGATGCATGG
32449 T
63 T
* * * * * *
32450 TATGTGCATCGGTGCATAAAATACATTCGAT-CTTCAATTTATTCCATG-GTGCATCGATGCATG
1 T-GGTGCATCGATGCATAAAATGCATTCGATGTTTCAA--AATACCA-GAGTGCATCGATGCATG
32513 GAT
62 G-T
*
32516 TGGTGCATCGGTGCAT
1 TGGTGCATCGATGCAT
32532 CACTCTGAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 52 0.44
65 59 0.50
66 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (63 bp):
TGGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCAGAGTGCATCGATGCATGGT
Found at i:34365 original size:65 final size:65
Alignment explanation
Indices: 34221--34382 Score: 197
Period size: 65 Copynumber: 2.5 Consensus size: 65
34211 TTCTTTATAA
* *
34221 TGGTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATGGATGCATGGC
1 TGGTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGC
* * * *
34285 TGGAGTATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATA
1 TGGTGCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATGCATA
34348 G-
64 GC
* *
34349 TATGTGCATCGGTGCATGAAATGCATTCGATGTT
1 T-GGTGCATCGATGCATGAAATGCATTCGATGTT
34383 CAATTTATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
64 30 0.36
65 50 0.60
66 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGGTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGC
Found at i:39120 original size:12 final size:12
Alignment explanation
Indices: 39103--39129 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39093 ACTAAAAATG
39103 ATTAATTTTAAT
1 ATTAATTTTAAT
39115 ATTAATTTTAAT
1 ATTAATTTTAAT
39127 ATT
1 ATT
39130 TGTTTAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTAATTTTAAT
Found at i:39222 original size:82 final size:82
Alignment explanation
Indices: 39061--39223 Score: 256
Period size: 82 Copynumber: 2.0 Consensus size: 82
39051 TTAGGATTGG
* * *
39061 ATTTGGTAACTTATAATTTTGGGTGTAGGTAAACTAAAAATGATTAATTTTAATATTAATTTTAA
1 ATTTGGTAACTCATAACTTTGGGTGTAGGTAAACTAAAAATGATTAATTTTAATATTAATTATAA
39126 TATTTGTTTAATGTTTA
66 TATTTGTTTAATGTTTA
* *
39143 ATTTGGTAACTCATAACTTTGGGTGTAGGTAAACTAAAAATTATTAATTTTAATATTAATTATCA
1 ATTTGGTAACTCATAACTTTGGGTGTAGGTAAACTAAAAATGATTAATTTTAATATTAATTATAA
*
39208 -ATTTGTCTTTATGTTT
66 TATTTGT-TTAATGTTT
39224 TGTGTAATTC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
81 6 0.08
82 68 0.92
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (82 bp):
ATTTGGTAACTCATAACTTTGGGTGTAGGTAAACTAAAAATGATTAATTTTAATATTAATTATAA
TATTTGTTTAATGTTTA
Found at i:42351 original size:2 final size:2
Alignment explanation
Indices: 42344--42369 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42334 CAATTTCAAT
42344 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
42370 ACTATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45318 original size:2 final size:2
Alignment explanation
Indices: 45311--45335 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45301 CATATACAAT
45311 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
45336 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:45340 original size:2 final size:2
Alignment explanation
Indices: 45335--45418 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
45325 ACACACACAC
45335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45419 CTTCATATTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47078 original size:15 final size:15
Alignment explanation
Indices: 47058--47086 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47048 GTTAGAATCT
47058 TAATATATATATATA
1 TAATATATATATATA
47073 TAATATATATATAT
1 TAATATATATATAT
47087 TGTTTTGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATATATATATA
Found at i:47080 original size:13 final size:13
Alignment explanation
Indices: 47062--47086 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47052 GAATCTTAAT
47062 ATATATATATATA
1 ATATATATATATA
47075 ATATATATATAT
1 ATATATATATAT
47087 TGTTTTGGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:48418 original size:20 final size:20
Alignment explanation
Indices: 48393--48482 Score: 162
Period size: 20 Copynumber: 4.5 Consensus size: 20
48383 ATGACCAACA
48393 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
48413 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
48433 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
*
48453 AAATCGCAACGCGAATCTGT
1 AAATCGCAACGCGAATATGT
*
48473 AATTCGCAAC
1 AAATCGCAAC
48483 ACAAAAGTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:48496 original size:20 final size:20
Alignment explanation
Indices: 48473--48517 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
48463 GCGAATCTGT
*
48473 AATTCGCAACACAAAAGTTA
1 AATTCGCAACACAAAAGTCA
48493 AATTCGCAACACAAAAGTCA
1 AATTCGCAACACAAAAGTCA
48513 AATTC
1 AATTC
48518 ACAAAGCGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACAAAAGTCA
Found at i:48500 original size:40 final size:40
Alignment explanation
Indices: 48393--48502 Score: 134
Period size: 40 Copynumber: 2.8 Consensus size: 40
48383 ATGACCAACA
* *
48393 AAATCGCAACGCGAATATGTAAATCGCAACGCGAATATGT
1 AAATCGCAACACGAAAATGTAAATCGCAACGCGAATATGT
* * *
48433 AAATCGCAACGCGAATATGTAAATCGCAACGCGAATCTGT
1 AAATCGCAACACGAAAATGTAAATCGCAACGCGAATATGT
*
48473 AATTCGCAACAC-AAAA-GTTAAATTCGCAAC
1 AAATCGCAACACGAAAATG-TAAA-TCGCAAC
48503 ACAAAAGTCA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
38 1 0.02
39 7 0.11
40 56 0.88
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (40 bp):
AAATCGCAACACGAAAATGTAAATCGCAACGCGAATATGT
Found at i:49066 original size:20 final size:20
Alignment explanation
Indices: 49043--49088 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
49033 AAACTTAAAT
49043 TCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
49063 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
49083 TCGCAA
1 TCGCAA
49089 ATTGAAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:49094 original size:14 final size:14
Alignment explanation
Indices: 49077--49103 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49067 AACGCGAAAA
49077 TGAAAATCGCAAAT
1 TGAAAATCGCAAAT
49091 TGAAAATCGCAAA
1 TGAAAATCGCAAA
49104 GCGATTTTAG
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:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (14 bp):
TGAAAATCGCAAAT
Found at i:49126 original size:19 final size:20
Alignment explanation
Indices: 49104--49157 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
49094 AAATCGCAAA
49104 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
* *
49123 GCGATTTTCATTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
49143 GCGATTTTAAGTTTC
1 GCGATTTTAAGTTTC
49158 AGAAACTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:51266 original size:21 final size:21
Alignment explanation
Indices: 51236--51332 Score: 142
Period size: 21 Copynumber: 4.6 Consensus size: 21
51226 GATTCACCTG
*
51236 TCATCGTTCAAGAGGCCCCTA
1 TCATCCTTCAAGAGGCCCCTA
51257 TCATCCTTCAAGAGGCCCCTA
1 TCATCCTTCAAGAGGCCCCTA
*
51278 TCATCCTTCAAGAGGCCCCTC
1 TCATCCTTCAAGAGGCCCCTA
*
51299 CCA-CCGTTCAAGAGGCCCCTA
1 TCATCC-TTCAAGAGGCCCCTA
*
51320 TCATCGTTCAAGA
1 TCATCCTTCAAGA
51333 TGTCTCTCCC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.96
22 1 0.01
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.23
Consensus pattern (21 bp):
TCATCCTTCAAGAGGCCCCTA
Found at i:51354 original size:42 final size:42
Alignment explanation
Indices: 51266--51354 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
51256 ATCATCCTTC
* *
51266 AAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCGTTC
1 AAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACAGTTA
* * * * *
51308 AAGAGGCCCCTATCATCGTTCAAGATGTCTCTCCCATAGTTA
1 AAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACAGTTA
51350 AAGAG
1 AAGAG
51355 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.22
Consensus pattern (42 bp):
AAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACAGTTA
Found at i:51696 original size:30 final size:29
Alignment explanation
Indices: 51635--51696 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
51625 GGTGTGTTAT
*
51635 TAGGGGTTGAAGACAATGAATATTTTAAA
1 TAGGGGTTGAAGACAATGAATATTTCAAA
* *
51664 TAGGGTGTTGAAGACAATGATTATTTCGAA
1 TAGGG-GTTGAAGACAATGAATATTTCAAA
51694 TAG
1 TAG
51697 TGCCAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (29 bp):
TAGGGGTTGAAGACAATGAATATTTCAAA
Found at i:52748 original size:14 final size:15
Alignment explanation
Indices: 52728--52761 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
52718 TTTGCTTGTT
*
52728 TAATTGATTTGTAAA
1 TAATTGATGTGTAAA
52743 -AATTGATGTGTAAA
1 TAATTGATGTGTAAA
52757 TAATT
1 TAATT
52762 CTTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (15 bp):
TAATTGATGTGTAAA
Found at i:52980 original size:20 final size:20
Alignment explanation
Indices: 52955--53003 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
52945 ACGTTACGAT
52955 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAA
*
52975 AGTCAAATTCGCAACGTGAA
1 AGTCAAATTCGCAACGCGAA
52995 AGTCAAATT
1 AGTCAAATT
53004 TGCGCTGCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAA
Found at i:53086 original size:49 final size:49
Alignment explanation
Indices: 53014--53127 Score: 174
Period size: 49 Copynumber: 2.3 Consensus size: 49
53004 TGCGCTGCGA
* *
53014 TTTCGTGTTTCGAATTTGACTTTCGTAACAATCGCAACGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGACTTTCGTAACAATCGCAACGCGAATTTGAC
* *
53063 TTTCGCGTTGCGAATTTGACTTTCGTAATAATCGCAACGTGAATTTGAC
1 TTTCGCGTTGCGAATTTGACTTTCGTAACAATCGCAACGCGAATTTGAC
* *
53112 TTTCGCATTGCAAATT
1 TTTCGCGTTGCGAATT
53128 CAAGGAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (49 bp):
TTTCGCGTTGCGAATTTGACTTTCGTAACAATCGCAACGCGAATTTGAC
Found at i:61161 original size:23 final size:21
Alignment explanation
Indices: 61109--61170 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
61099 TTTTGGTGCA
*
61109 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
61129 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
61150 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
61171 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:61177 original size:22 final size:22
Alignment explanation
Indices: 61152--61193 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
61142 CCCCCTTTGA
*
61152 AGGGGAACCGATTCCCCCCCAC
1 AGGGGAACCGATACCCCCCCAC
*
61174 AGGGGAATCGATACCCCCCC
1 AGGGGAACCGATACCCCCCC
61194 TGGGGTTCTG
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:0.24, C:0.43, G:0.24, T:0.10
Consensus pattern (22 bp):
AGGGGAACCGATACCCCCCCAC
Found at i:61693 original size:11 final size:11
Alignment explanation
Indices: 61677--61708 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
61667 CAAAACCATA
61677 TTTTTCAAAAG
1 TTTTTCAAAAG
61688 TTTTTCAAAAG
1 TTTTTCAAAAG
61699 TTTTTCAAAA
1 TTTTTCAAAA
61709 ACTTTGCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TTTTTCAAAAG
Found at i:65368 original size:24 final size:24
Alignment explanation
Indices: 65291--65354 Score: 128
Period size: 24 Copynumber: 2.7 Consensus size: 24
65281 AAAATCTGAG
65291 ATTGACCAAGATCAAAGTCCGGGT
1 ATTGACCAAGATCAAAGTCCGGGT
65315 ATTGACCAAGATCAAAGTCCGGGT
1 ATTGACCAAGATCAAAGTCCGGGT
65339 ATTGACCAAGATCAAA
1 ATTGACCAAGATCAAA
65355 TTTCGAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (24 bp):
ATTGACCAAGATCAAAGTCCGGGT
Found at i:65501 original size:12 final size:12
Alignment explanation
Indices: 65480--65513 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
65470 GGTTGTGGGT
*
65480 TTTGAGATTGTG
1 TTTGATATTGTG
65492 TTTGATATTGTG
1 TTTGATATTGTG
*
65504 TTTGGTATTG
1 TTTGATATTG
65514 GATATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:66144 original size:14 final size:15
Alignment explanation
Indices: 66108--66145 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
66098 GAAATCATTG
66108 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
66123 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
66138 AAAAATTA
1 AAAAATTA
66146 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:66326 original size:20 final size:19
Alignment explanation
Indices: 66283--66410 Score: 73
Period size: 20 Copynumber: 6.5 Consensus size: 19
66273 AAAACATTTT
* *
66283 TGTTGCGAAACTAAAA-CC
1 TGTTGCGAAATTAAAATCG
66301 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAA-TCG
66321 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT--AAAATCG
* **
66341 AGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAA-TCG
*
66361 CGTTGCG-AATTCAGAAATCG
1 TGTTGCGAAATT-A-AAATCG
* * * *
66381 AGTTACGAATTTGAAATTCAG
1 TGTTGCGAAATT-AAAATC-G
66402 TGTTGCGAA
1 TGTTGCGAA
66411 TTTGGAAACT
Statistics
Matches: 85, Mismatches: 15, Indels: 17
0.73 0.13 0.15
Matches are distributed among these distances:
18 15 0.18
19 10 0.12
20 39 0.46
21 21 0.25
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (19 bp):
TGTTGCGAAATTAAAATCG
Found at i:66350 original size:40 final size:40
Alignment explanation
Indices: 66302--66455 Score: 150
Period size: 40 Copynumber: 3.8 Consensus size: 40
66292 ACTAAAACCT
*
66302 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATTAAAATTCGCGTTGCGAATTCGAAAATCGA
**
66342 GTTGCGAAAACAAAATTCGCGTTGCGAATTC-AGAAATCGA
1 GTTGCGAAATTAAAATTCGCGTTGCGAATTCGA-AAATCGA
* * * * * *
66382 GTTACGAATTTGAAATTCAGTGTTGCGAATTTGGAAA-CTGA
1 GTTGCGAAATTAAAATTC-GCGTTGCGAATTCGAAAATC-GA
* ** *
66423 GTTGCGATATTGGAGTTCGCGTTGCGAATTCGA
1 GTTGCGAAATTAAAATTCGCGTTGCGAATTCGA
66456 GATCGCGTTG
Statistics
Matches: 91, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
39 1 0.01
40 61 0.67
41 29 0.32
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGCGTTGCGAATTCGAAAATCGA
Found at i:66463 original size:19 final size:19
Alignment explanation
Indices: 66423--66471 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
66413 TGGAAACTGA
* *
66423 GTTGCGATATTGGAGTTCGC
1 GTTGCGA-ATTCGAGATCGC
66443 GTTGCGAATTCGAGATCGC
1 GTTGCGAATTCGAGATCGC
*
66462 GTTGTGAATT
1 GTTGCGAATT
66472 TGTTGGTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.18, C:0.14, G:0.33, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTCGAGATCGC
Found at i:66833 original size:31 final size:31
Alignment explanation
Indices: 66795--66886 Score: 157
Period size: 31 Copynumber: 3.0 Consensus size: 31
66785 AGTTACGTCG
* *
66795 GGGACCATATTACAAACGGACTAAATGTTGA
1 GGGACCATATAACAAATGGACTAAATGTTGA
*
66826 GGGACCATATAACAAATGAACTAAATGTTGA
1 GGGACCATATAACAAATGGACTAAATGTTGA
66857 GGGACCATATAACAAATGGACTAAATGTTG
1 GGGACCATATAACAAATGGACTAAATGTTG
66887 GGAAATTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (31 bp):
GGGACCATATAACAAATGGACTAAATGTTGA
Found at i:70467 original size:16 final size:17
Alignment explanation
Indices: 70429--70469 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
70419 TGTTTATAAT
70429 TAGATTATTTAGACAAA
1 TAGATTATTTAGACAAA
70446 TA-ATTATTTA-A-AAA
1 TAGATTATTTAGACAAA
70460 TCAGATTATT
1 T-AGATTATT
70470 AGAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.18
15 2 0.09
16 14 0.64
17 2 0.09
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (17 bp):
TAGATTATTTAGACAAA
Found at i:71977 original size:61 final size:61
Alignment explanation
Indices: 71884--72021 Score: 190
Period size: 61 Copynumber: 2.3 Consensus size: 61
71874 AAGTTTTAAA
* * * * *
71884 TATTAAAAGTTA-CAAAATAGTTTTCTCACTATA-AAATATTATTTTATTAAGTCTCTTGAC
1 TATTAAAAGTTATAAAAATAATTTTCTAACTATATAAA-ATTATTTGATTAAGTCTCTCGAC
* *
71944 TATTAAAAGTTATAAAAATAATTTTTTAACTATATAAAATTATTTGATTAAGTTTCTCGAC
1 TATTAAAAGTTATAAAAATAATTTTCTAACTATATAAAATTATTTGATTAAGTCTCTCGAC
72005 TATTAAAAGTTATAAAA
1 TATTAAAAGTTATAAAA
72022 TGGTTACTCA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 12 0.17
61 54 0.78
62 3 0.04
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (61 bp):
TATTAAAAGTTATAAAAATAATTTTCTAACTATATAAAATTATTTGATTAAGTCTCTCGAC
Found at i:74445 original size:3 final size:3
Alignment explanation
Indices: 74439--74464 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
74429 TCAACGTTAT
74439 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
74465 TTAATAATTT
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:78878 original size:23 final size:23
Alignment explanation
Indices: 78852--78923 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
78842 GCTCGTAAGC
78852 TTATTTTACCAATATACTTACCA
1 TTATTTTACCAATATACTTACCA
*
78875 TTA--TTA-C-ATA-AGCTCGTAAGC-
1 TTATTTTACCAATATA-CT--T-ACCA
78896 TTATTTTACCAATATACTTACCA
1 TTATTTTACCAATATACTTACCA
78919 TTATT
1 TTATT
78924 CCATAAACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 20
0.63 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 1 0.03
21 7 0.19
22 4 0.11
23 12 0.32
24 1 0.03
25 5 0.14
26 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.43
Consensus pattern (23 bp):
TTATTTTACCAATATACTTACCA
Found at i:79049 original size:44 final size:44
Alignment explanation
Indices: 78837--79060 Score: 297
Period size: 44 Copynumber: 5.1 Consensus size: 44
78827 CCATTTAATC
* *
78837 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTA
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTA
* * *
78881 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTA
* *
78925 CATAAACTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTA
* ** * *
78969 CATAAGCTCGTAAGCTCATGCTATCAATCTACTTACTATAACTT-
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAA-TTA
* *
79013 CATAAGCTCGTAAGCTTATGTTATCAATATACTTACTATAATTTA
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAA-TTA
79058 CAT
1 CAT
79061 CACTGATGCC
Statistics
Matches: 163, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 158 0.97
45 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (44 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTA
Found at i:79678 original size:233 final size:234
Alignment explanation
Indices: 79244--79747 Score: 834
Period size: 233 Copynumber: 2.2 Consensus size: 234
79234 CCATACCATT
* *
79244 AGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTAGAAATCCATATATTCAATATG
1 AGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTAGAAATCCATATATTCAATATG
*
79309 ATTTCCTTATCACTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAATATGATTCCC
66 ATTTCCTTATCACTTTAGCACACTCAGTGCTCCA-ATGAAAATCCATACACTCAATATGATTCCC
* *
79374 TTACCATTTTAGCACACTCAACGCTCCATATGGAAATTCATACACTCAGTATGATTTCTTTACCA
130 TTACCATTTTAGAACACTCAACGCTCCATATGGAAATTCATACACTCAGTATGATTTCCTTACCA
79439 TTTTAGCACACTCAGTGCTCCATATGGAAATTCATATACTC
195 TTTTAGCACACTC-GTGCTCCATATGGAAATTCATATACTC
* * * *
79480 ATTATGATTTCCTTATCATTTTAGGACATATAGTGCCCTATCTGGAAATCCATATATTCAATATG
1 AGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTAGAAATCCATATATTCAATATG
* *
79545 ATTTCCTTATCACTTTAGCACACTC-GTGTTCC-ATGAAAATCCATACACTCAGTATGATTCCCT
66 ATTTCCTTATCACTTTAGCACACTCAGTGCTCCAATGAAAATCCATACACTCAATATGATTCCCT
* ** *
79608 TACCATTTTATAACACTCAGTGCTCCATATGGATATTCATACACTCAGTATGATTTCCTTACCAT
131 TACCATTTTAGAACACTCAACGCTCCATATGGAAATTCATACACTCAGTATGATTTCCTTACCAT
79673 TTTAGCACACTCGTGCTCCATATGGAAATTCATATACTC
196 TTTAGCACACTCGTGCTCCATATGGAAATTCATATACTC
79712 AGTATGATTTCCTTATCATTTTAGCA-ATATAATGCC
1 AGTATGATTTCCTTATCATTTTAGCACATATAATGCC
79748 ATTTGGTAAT
Statistics
Matches: 250, Mismatches: 18, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
231 9 0.04
232 51 0.20
233 100 0.40
235 6 0.02
236 84 0.34
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (234 bp):
AGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTAGAAATCCATATATTCAATATG
ATTTCCTTATCACTTTAGCACACTCAGTGCTCCAATGAAAATCCATACACTCAATATGATTCCCT
TACCATTTTAGAACACTCAACGCTCCATATGGAAATTCATACACTCAGTATGATTTCCTTACCAT
TTTAGCACACTCGTGCTCCATATGGAAATTCATATACTC
Found at i:79684 original size:59 final size:59
Alignment explanation
Indices: 79146--79737 Score: 564
Period size: 59 Copynumber: 10.1 Consensus size: 59
79136 TTCCCTATAA
* * * * * * *
79146 TTTAGCACTCTCAGTGCTCTATATGGAATAT-C-TATACTTAATATGATTTTC-TCCTCAT
1 TTTAGCACACTCAGTGCTCCATATGGAA-ATCCATACACTCAGTATGATTTCCTTAC-CAT
** * * *
79204 TTTAGCACACGAAGTGC-CC-TATGCAAGAATCCATAC-CATTAGTATGATTCCCTTACCAT
1 TTTAGCACACTCAGTGCTCCATATG-GA-AATCCATACAC-TCAGTATGATTTCCTTACCAT
* * * * * * * * *
79263 TTTAGCACA-TATAATGC-CCTATCTAGAAATCCATATATTCAATATGATTTCCTTATCAC
1 TTTAGCACACT-CAGTGCTCC-ATATGGAAATCCATACACTCAGTATGATTTCCTTACCAT
* *
79322 TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAATATGATTCCCTTACCAT
1 TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCCTTACCAT
** * *
79381 TTTAGCACACTCAACGCTCCATATGGAAATTCATACACTCAGTATGATTTCTTTACCAT
1 TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCCTTACCAT
* * * *
79440 TTTAGCACACTCAGTGCTCCATATGGAAATTCATATACTCATTATGATTTCCTTATCAT
1 TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCCTTACCAT
* * * * * * * *
79499 TTTAGGACA-TATAGTGC-CCTATCTGGAAATCCATATATTCAATATGATTTCCTTATCAC
1 TTTAGCACACT-CAGTGCTCC-ATATGGAAATCCATACACTCAGTATGATTTCCTTACCAT
* * *
79558 TTTAGCACACTC-GTGTTCC--ATGAAAATCCATACACTCAGTATGATTCCCTTACCAT
1 TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCCTTACCAT
** * *
79614 TTTATAACACTCAGTGCTCCATATGGATATTCATACACTCAGTATGATTTCCTTACCAT
1 TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCCTTACCAT
* * *
79673 TTTAGCACACTC-GTGCTCCATATGGAAATTCATATACTCAGTATGATTTCCTTATCAT
1 TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCCTTACCAT
79731 TTTAGCA
1 TTTAGCA
79738 ATATAATGCC
Statistics
Matches: 441, Mismatches: 74, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
56 43 0.10
57 10 0.02
58 73 0.17
59 306 0.69
60 7 0.02
61 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.36
Consensus pattern (59 bp):
TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCCTTACCAT
Done.