Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005675.1 Hibiscus syriacus cultivar Beakdansim tig00013273_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: 68350
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7444 original size:39 final size:40
Alignment explanation
Indices: 7389--7505 Score: 150
Period size: 39 Copynumber: 3.0 Consensus size: 40
7379 ATGTACACTC
* *
7389 AGTAAGGGCTTACCCTGTGCACAAAG-CAGAGGAGCCTGCT
1 AGTAAGGACTTACCCTGAGCACAAAGCCA-AGGAGCCTGCT
* * * *
7429 -GTAAGGACTTACCCTGAGTATAAAGCCAATGAGCCT-TT
1 AGTAAGGACTTACCCTGAGCACAAAGCCAAGGAGCCTGCT
7467 AGTAAGGACTTACCCTGAGCACAAAGCCAAGGAGCCTGC
1 AGTAAGGACTTACCCTGAGCACAAAGCCAAGGAGCCTGC
7506 AGAAAGCATT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.02
39 61 0.95
40 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.19
Consensus pattern (40 bp):
AGTAAGGACTTACCCTGAGCACAAAGCCAAGGAGCCTGCT
Found at i:9625 original size:2 final size:2
Alignment explanation
Indices: 9618--9649 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9608 TGAACCATTG
9618 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
9650 GAACATAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10705 original size:23 final size:23
Alignment explanation
Indices: 10673--10734 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
10663 ACCTTATATA
10673 GCACTTCGGTGCATTTCTACATG
1 GCACTTCGGTGCATTTCTACATG
* * * **
10696 GCACTACGGTACAATTCTATGTG
1 GCACTTCGGTGCATTTCTACATG
10719 GCACTTCGGTGCATTT
1 GCACTTCGGTGCATTT
10735 ATACGAGCTG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACATG
Found at i:10907 original size:39 final size:37
Alignment explanation
Indices: 10847--10927 Score: 85
Period size: 39 Copynumber: 2.1 Consensus size: 37
10837 AATGTATGAA
*
10847 ATATATGTATATGATGTGTGATATGAAT-TGTATGACATG
1 ATATATGTATATGATGGGTGAT-TGAATCTGT-T-ACATG
* *
10886 ATATATGTGTGAT-ATGGGTGATTGCATCTGTTACATG
1 ATATATGTAT-ATGATGGGTGATTGAATCTGTTACATG
10923 ATATA
1 ATATA
10928 CATGAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
37 10 0.27
38 5 0.14
39 20 0.54
40 2 0.05
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (37 bp):
ATATATGTATATGATGGGTGATTGAATCTGTTACATG
Found at i:14956 original size:2 final size:2
Alignment explanation
Indices: 14951--14988 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14941 TATATATATA
14951 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
14989 AACATAAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17543 original size:35 final size:35
Alignment explanation
Indices: 17486--17565 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
17476 TAACACAGTC
*
17486 TTCAATTTAATTCTAAATCCTAAATTCTAAAATAA
1 TTCAATTTAATTCTAAACCCTAAATTCTAAAATAA
* *
17521 TTCAA-TTACATTTTAAACCCTAAATTCTAAAATAC
1 TTCAATTTA-ATTCTAAACCCTAAATTCTAAAATAA
*
17556 TTCAAATTAA
1 TTCAATTTAA
17566 GCTTTAGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 3 0.08
35 34 0.85
36 3 0.08
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (35 bp):
TTCAATTTAATTCTAAACCCTAAATTCTAAAATAA
Found at i:22727 original size:20 final size:21
Alignment explanation
Indices: 22681--22740 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
22671 TTCCCCTGTG
22681 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTT-AAA
22704 GGGGGAATCGGTTCCCTT-AA
1 GGGGGAATCGGTTCCCTTAAA
* *
22724 GGGGGGATCGATTCCCT
1 GGGGGAATCGGTTCCCT
22741 CTGCACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 17 0.49
22 5 0.14
23 13 0.37
ACGTcount: A:0.18, C:0.23, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTTAAA
Found at i:28526 original size:21 final size:21
Alignment explanation
Indices: 28498--28552 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
28488 CGTTATACAA
28498 GGGGGGAATCGGTA-CCCCCT
1 GGGGGGAATCGGTACCCCCCT
28518 GGGAGGGAATCGGTACCCCCCT
1 GGG-GGGAATCGGTACCCCCCT
28540 GGGGGGAATCGGT
1 GGGGGGAATCGGT
28553 TCCCTTCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 3 0.09
21 21 0.64
22 9 0.27
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.15
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCCT
Found at i:30674 original size:20 final size:20
Alignment explanation
Indices: 30624--30693 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
30614 CAAAATAAGG
* * *
30624 GTATTGATATTAAGCCCTTCA
1 GTATAGATACTAA-CCCTTGA
30645 GTATCA-ATACTAACCCTTGA
1 GTAT-AGATACTAACCCTTGA
* *
30665 GTATAGATACTCACACTTG-
1 GTATAGATACTAACCCTTGA
*
30684 GTATCGATAC
1 GTATAGATAC
30694 CAAAAATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 10 0.24
20 21 0.51
21 10 0.24
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
GTATAGATACTAACCCTTGA
Found at i:30692 original size:19 final size:20
Alignment explanation
Indices: 30644--30693 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
30634 TAAGCCCTTC
* *
30644 AGTATCAATACTAACCCTTG
1 AGTATCGATACTAACACTTG
* *
30664 AGTATAGATACTCACACTTG
1 AGTATCGATACTAACACTTG
30684 -GTATCGATAC
1 AGTATCGATAC
30694 CAAAAATTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTAACACTTG
Found at i:34032 original size:35 final size:36
Alignment explanation
Indices: 33946--34049 Score: 117
Period size: 35 Copynumber: 2.9 Consensus size: 36
33936 CTTAAAAGAC
* *
33946 ATAATAGATATTTTTTAATTTGAAATATTCAAAAAG
1 ATAATAGATATATTTTAATTTCAAATATTCAAAAAG
*
33982 AT-ATA-ATTATATTTTAATATTCAAA-ATT-AAATAG
1 ATAATAGA-TATATTTTAAT-TTCAAATATTCAAAAAG
* *
34016 ATAATAGATATCTTTTAATTTGAAATATTCAAAA
1 ATAATAGATATATTTTAATTTCAAATATTCAAAA
34050 GAATATTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 13 0.23
35 32 0.57
36 11 0.20
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (36 bp):
ATAATAGATATATTTTAATTTCAAATATTCAAAAAG
Found at i:35724 original size:23 final size:23
Alignment explanation
Indices: 35693--35764 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
35683 TGGTAGCTAG
* *
35693 TTTAGCGTAATATGCAGCG-CTTA
1 TTTAACGTAATAGGCAGCGTC-TA
*
35716 TTTAACGTAATAGGTAGCGTCTA
1 TTTAACGTAATAGGCAGCGTCTA
**
35739 TTTAACGTAATAGATAGCGTCTA
1 TTTAACGTAATAGGCAGCGTCTA
35762 TTT
1 TTT
35765 TATTTTACCG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (23 bp):
TTTAACGTAATAGGCAGCGTCTA
Found at i:35841 original size:75 final size:75
Alignment explanation
Indices: 35739--35914 Score: 264
Period size: 75 Copynumber: 2.3 Consensus size: 75
35729 GTAGCGTCTA
* *
35739 TTTAACGTAATAGATAGCGTCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACGTAATAGATAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAC
*
35804 CGGTAGG-TAT
66 CGGT-GGCTAG
* *
35814 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTATTAACATTTAAACAAAC
1 TTTAACGTAATAGATAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAC
35879 CGGTGGCTAG
66 CGGTGGCTAG
* * *
35889 TTTAACATAATAAATAGCGCTTATTT
1 TTTAACGTAATAGATAGCGCCTATTT
35915 AACATAATAG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 2 0.02
75 89 0.98
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (75 bp):
TTTAACGTAATAGATAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAC
CGGTGGCTAG
Found at i:35919 original size:23 final size:23
Alignment explanation
Indices: 35889--35960 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
35879 CGGTGGCTAG
**
35889 TTTAACATAATAAATAGCGCTTA
1 TTTAACATAATAGGTAGCGCTTA
*
35912 TTTAACATAATAGGTAGAGCTTA
1 TTTAACATAATAGGTAGCGCTTA
*
35935 TTTAACATAATAGGTAGCGCCTA
1 TTTAACATAATAGGTAGCGCTTA
35958 TTT
1 TTT
35961 TATTTTACCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (23 bp):
TTTAACATAATAGGTAGCGCTTA
Found at i:35978 original size:196 final size:196
Alignment explanation
Indices: 35644--36096 Score: 676
Period size: 196 Copynumber: 2.3 Consensus size: 196
35634 AAGTTGTATA
* ** * * * * **
35644 TATTTTACCGTTTACATAATCGTTAACCTTTAAACAAACTGGTAGCTAGTTTAGCGTAATATGCA
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGTGGCTAGTTTAACATAATAAACA
* * * *
35709 GCGCTTATTTAACGTAATAGGTAGCGTCTATTTAACGTAATAGATAGCGTCTATTTTATTTTACC
66 GCGCTTATTTAACATAATAGGTAGAGTCTATTTAACATAATAGATAGCGCCTATTTTATTTTACC
* * *
35774 GTTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTATTTTAACGTAATAGGTAGCGCCTATT
131 GTTTACATTATTAGTAACCTTTAAACAAACAGGTAAGTATTTTAACGTAATAGGTAGCACCTATT
35839 T
196 T
* *
35840 TATTTTACCGTTTACATTATTATTAACATTTAAACAAACCGGTGGCTAGTTTAACATAATAAATA
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGTGGCTAGTTTAACATAATAAACA
*
35905 GCGCTTATTTAACATAATAGGTAGAG-CTTATTTAACATAATAGGTAGCGCCTATTTTATTTTAC
66 GCGCTTATTTAACATAATAGGTAGAGTC-TATTTAACATAATAGATAGCGCCTATTTTATTTTAC
*
35969 CGTTTACATTATTAGTAACCTTTAAACAAACATGTAAGTATTTTAACGTAATAGGTAGCACCTAT
130 CGTTTACATTATTAGTAACCTTTAAACAAACAGGTAAGTATTTTAACGTAATAGGTAGCACCTAT
36034 TT
195 TT
* *
36036 TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAACCGGTAGG-TAGTTTAACATAATA
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGT-GGCTAGTTTAACATAATA
36097 GGTAGCACCT
Statistics
Matches: 232, Mismatches: 23, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
195 1 0.00
196 229 0.99
197 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (196 bp):
TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGGTGGCTAGTTTAACATAATAAACA
GCGCTTATTTAACATAATAGGTAGAGTCTATTTAACATAATAGATAGCGCCTATTTTATTTTACC
GTTTACATTATTAGTAACCTTTAAACAAACAGGTAAGTATTTTAACGTAATAGGTAGCACCTATT
T
Found at i:36035 original size:121 final size:121
Alignment explanation
Indices: 35814--36035 Score: 320
Period size: 121 Copynumber: 1.8 Consensus size: 121
35804 CGGTAGGTAT
* *
35814 TTTAACGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTATTAACATTTAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAC
* * * *
35879 CGGTGGCTAGTTTAACATAATAAATAGCGCTTATTTAACATAATAGGTAGAGCTTA
66 AGGTAGCTAGTTTAACATAATAAATAGCACCTATTTAACATAATAGGTAGAGCTTA
*
35935 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAC
* * * **
36000 ATGTAAG-TATTTTAACGTAATAGGTAGCACCTATTT
66 AGGT-AGCTAGTTTAACATAATAAATAGCACCTATTT
36036 TATTTTACCG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
121 87 0.99
122 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (121 bp):
TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACATTTAAACAAAC
AGGTAGCTAGTTTAACATAATAAATAGCACCTATTTAACATAATAGGTAGAGCTTA
Found at i:36058 original size:75 final size:75
Alignment explanation
Indices: 35935--36117 Score: 294
Period size: 75 Copynumber: 2.4 Consensus size: 75
35925 GTAGAGCTTA
* *
35935 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAAC
* *
36000 ATGTAAGTAT
66 AGGTAAGTAG
*
36010 TTTAACGTAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAAC
1 TTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAAC
* *
36075 CGGTAGGTAG
66 AGGTAAGTAG
*
36085 TTTAACATAATAGGTAGCACCTATGTTATTTTA
1 TTTAACATAATAGGTAGCACCTATTTTATTTTA
36118 ACCGGTTAAG
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 99 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (75 bp):
TTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAAC
AGGTAAGTAG
Found at i:37401 original size:18 final size:17
Alignment explanation
Indices: 37378--37420 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
37368 ATATATACAT
37378 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
37396 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
37413 ATAA-AATA
1 ATAATAATA
37421 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:37406 original size:51 final size:51
Alignment explanation
Indices: 37313--37432 Score: 117
Period size: 51 Copynumber: 2.5 Consensus size: 51
37303 GAATATATAT
* * * * *
37313 ATATATATATATA-ATAAAAT-ATAGTAAAAAAATAAATGAAAATAATTTA
1 ATATATATATATACATATAATAATAATAAAAAAATAAATAAAAATAAATGA
**
37362 ATATATATATATACATATAATAATAATAACATGAAT-AATAAAAATAAATGA
1 ATATATATATATACATATAATAATAATAA-AAAAATAAATAAAAATAAATGA
*
37413 ATA-A-A-ATATCCATATAATAA
1 ATATATATATATACATATAATAA
37433 ATAAAGGGAC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
48 14 0.23
49 14 0.23
50 7 0.12
51 21 0.35
52 4 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (51 bp):
ATATATATATATACATATAATAATAATAAAAAAATAAATAAAAATAAATGA
Found at i:37843 original size:37 final size:37
Alignment explanation
Indices: 37777--37881 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
37767 GTGCTTGTGG
* * * * *
37777 ATCCTATGTTTAAGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
37814 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
37851 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
37882 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:38728 original size:105 final size:105
Alignment explanation
Indices: 38424--38980 Score: 732
Period size: 105 Copynumber: 5.3 Consensus size: 105
38414 GCATTGTTCC
* * * *
38424 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * * *
38488 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
38530 GAGTCCAATATCCTTCCCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
38590 CAGA-GGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CA-ACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
38630 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * *
38695 TAACGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
38735 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
38800 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGACTG
66 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
38840 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
38905 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 GCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
* * * *
38947 AGTGTCACGATATCCTCCGTTGTGGAGTTGAAAT
1 -GAGTC-CAATATCCTTCGTTGTGAAGTTGAAAT
38981 CGCGGATGTT
Statistics
Matches: 402, Mismatches: 37, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
100 81 0.20
101 1 0.00
102 7 0.02
104 6 0.01
105 199 0.50
106 79 0.20
107 1 0.00
108 4 0.01
109 24 0.06
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:39208 original size:36 final size:36
Alignment explanation
Indices: 39153--39222 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
39143 GGAGAGAAAT
* *
39153 TGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAGC
1 TGTCTCAAGCGAGACAAAATTCATTTCAAGGGAAGC
*
39189 TGTCTCAAGCGAGATAAAATTCATTTCAAGGGAA
1 TGTCTCAAGCGAGACAAAATTCATTTCAAGGGAA
39223 ATGTTTATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTCATTTCAAGGGAAGC
Found at i:39283 original size:39 final size:40
Alignment explanation
Indices: 39221--39302 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 40
39211 ATTTCAAGGG
* * *
39221 AAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACA
1 AAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAA
* * *
39261 AAAT-TTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAAA
1 AAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAA
39300 AAA
1 AAA
39303 AATCATTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 32 0.89
40 4 0.11
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (40 bp):
AAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAA
Found at i:39338 original size:105 final size:104
Alignment explanation
Indices: 39222--39432 Score: 377
Period size: 105 Copynumber: 2.0 Consensus size: 104
39212 TTTCAAGGGA
*
39222 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTAT
1 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGAGAAACTAT
*
39287 CTCAAGAGAGAAAAAAAATCATTTCAAGGGAAATGTTTTC
66 CTCAAGAGAG-AAAAAAATAATTTCAAGGGAAATGTTTTC
39327 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGAGAAACTAT
1 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGAGAAACTAT
* *
39392 CTCAGGAGAGAAAAAATTAATTTCAAGGGAAATGTTTTC
66 CTCAAGAGAGAAAAAAATAATTTCAAGGGAAATGTTTTC
39431 AA
1 AA
39433 GAGAAACTGT
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 29 0.28
105 73 0.72
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (104 bp):
AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGAGAAACTAT
CTCAAGAGAGAAAAAAATAATTTCAAGGGAAATGTTTTC
Found at i:39389 original size:39 final size:39
Alignment explanation
Indices: 39335--39409 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
39325 TCAATGTTTA
* *
39335 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
*
39374 TGTTTCGAGAGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
39410 AATTTCAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 3 0.09
39 29 0.91
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:39467 original size:195 final size:194
Alignment explanation
Indices: 39126--39486 Score: 537
Period size: 195 Copynumber: 1.8 Consensus size: 194
39116 CGTTAAATTG
** * * * *
39126 TTTCAAAGTTTATGTTTGGAGAGAAATTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAGCTG
1 TTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGAGAAACTA
* * *
39191 TCTCAAGCGAGATAAAATTCATTTCAAGGGAAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGG
66 TCTCAAGAGAGAAAAAATTAATTTCAAGGGAAATG--T-TGTTTCAAGAGAAACTGTCTCAAGGG
*
39256 AGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAAT
128 AGACAAAATTTTCTGTTTCGAGGGAAAATATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAAT
39321 GT
193 GT
* *
39323 TTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGAGAAA
1 TTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGAGAAA
*
39388 CTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAATG-T-TTTCAAGAGAAACTGTCTCAAGGG
63 CTATCTCAAGAGAGAAAAAATTAATTTCAAGGGAAATGTTGTTTCAAGAGAAACTGTCTCAAGGG
39451 AGACAAAATTTTCTGTTTCGAGGGAAAATATCTCAA
128 AGACAAAATTTTCTGTTTCGAGGGAAAATATCTCAA
39487 TCAAGATAAA
Statistics
Matches: 148, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
195 59 0.40
196 1 0.01
197 42 0.28
199 3 0.02
200 43 0.29
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (194 bp):
TTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGAGAAACTA
TCTCAAGAGAGAAAAAATTAATTTCAAGGGAAATGTTGTTTCAAGAGAAACTGTCTCAAGGGAGA
CAAAATTTTCTGTTTCGAGGGAAAATATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAATGT
Found at i:39650 original size:72 final size:75
Alignment explanation
Indices: 39503--39662 Score: 213
Period size: 72 Copynumber: 2.2 Consensus size: 75
39493 TAAAATCTTC
* * * *
39503 TTAA-AAAAACAGTCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAATGAAATGAAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
39567 CAAATCTTGTT
65 CAAATCATGTT
*
39578 TTAAGAAAAACAATCTTGAATGAAATG-AAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGAC
1 TTAAGAAAAACAATCTTGAATGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
39640 AAAGT-ATGTT
66 AAA-TCATGTT
39650 TTAAGAAAAACAA
1 TTAAGAAAAACAA
39663 ATTTGAGTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
72 38 0.49
73 12 0.16
75 7 0.09
76 20 0.26
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (75 bp):
TTAAGAAAAACAATCTTGAATGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
AAATCATGTT
Found at i:41130 original size:183 final size:183
Alignment explanation
Indices: 40816--41352 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
40806 ATCAGGTTTA
*
40816 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* ** *
40881 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGATTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
40945 TTCCTCTATAACCAATTGCCTTAGTGGGATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
40999 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * *
41064 ACCAAGTGTCCGAACAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTTGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
41129 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
41182 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGTAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
41247 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
* *
41312 TCCTCTATAATCAATTGCCTTAGTGGAATAGCTCAACTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
41353 CGGATTTAAT
Statistics
Matches: 336, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
183 335 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:44872 original size:19 final size:20
Alignment explanation
Indices: 44844--44881 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
44834 TGCAAATGAT
*
44844 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
44863 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
44882 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:46598 original size:18 final size:17
Alignment explanation
Indices: 46575--46617 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
46565 ATATACACAT
46575 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
46593 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
46610 ATAA-AATA
1 ATAATAATA
46618 TTCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:46618 original size:56 final size:55
Alignment explanation
Indices: 46500--46618 Score: 134
Period size: 58 Copynumber: 2.1 Consensus size: 55
46490 AATATTAAAG
* * * *
46500 AATATATATATATATATATATAATAATAATATAGTAAAAAAATAAATGAAAATAATTT
1 AATATATATATACACATATATAATAATAACATAATAAAAAAATAAATG-AAATAA--T
46558 AATATATATATACACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-
1 AATATATATATACACATAT-ATAATAATAACAT-AATAA-AAAAATAAATGAAATAAT
46614 AATAT
1 AATAT
46619 TCATATAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 5 0.09
58 17 0.31
59 17 0.31
60 4 0.07
61 11 0.20
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (55 bp):
AATATATATATACACATATATAATAATAACATAATAAAAAAATAAATGAAATAAT
Found at i:46625 original size:56 final size:57
Alignment explanation
Indices: 46501--46618 Score: 134
Period size: 60 Copynumber: 2.0 Consensus size: 57
46491 ATATTAAAGA
* * * *
46501 ATATATATATATATATATATAATAATAATATAGTAAAAAAATAAATGAAAATAATTTAAT
1 ATATATATACACATATATATAATAATAACATAATAAAAAAATAAATG-AAATAA--TAAT
46561 ATATATATACACATATA-ATAATAATAACATGAATAATAAAAATAAATG-AATAA-AAT
1 ATATATATACACATATATATAATAATAACAT-AATAA-AAAAATAAATGAAATAATAAT
46617 AT
1 AT
46619 TCATATAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
56 5 0.10
59 17 0.33
60 19 0.37
61 11 0.21
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (57 bp):
ATATATATACACATATATATAATAATAACATAATAAAAAAATAAATGAAATAATAAT
Found at i:47040 original size:37 final size:37
Alignment explanation
Indices: 46974--47078 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
46964 GTGCTTGTGG
* * * * *
46974 ATCCTATCTTTAAGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
47011 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
47048 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
47079 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:47692 original size:60 final size:59
Alignment explanation
Indices: 47622--47899 Score: 188
Period size: 60 Copynumber: 4.6 Consensus size: 59
47612 TCTTAAATCT
* * **
47622 TTTAATTATTAAAAGTTATAAAATGGTTCCTTGACTATAGGATCTTACTTTGTTGAGTTC
1 TTTAACTATTAAAAGTTACAAAATGGTTCCTCAACTATA-GATCTTACTTTGTTGAGTTC
* * * * * **
47682 TTTAACTATTAAAAGTTATAAAATGGTTGCTCGATTATAG-TGCGTTGCTACGTTGAGTTC
1 TTTAACTATTAAAAGTTACAAAATGGTTCCTCAACTATAGAT-C-TTACTTTGTTGAGTTC
* ** * *
47742 ATCGACTATTAAAATTTACAAAATGGTT-ATCTAACTATAGGAT-TTCACTTTGTTGAGTTC
1 TTTAACTATTAAAAGTTACAAAATGGTTCCTC-AACTATA-GATCTT-ACTTTGTTGAGTTC
** ** ** * * * *
47802 CCTGGCTATTAAAAGTTACAAAATAATCCCTCAACTATAGAGTGTTGCTTTGTTGAATTC
1 TTTAACTATTAAAAGTTACAAAATGGTTCCTCAACTATAGA-TCTTACTTTGTTGAGTTC
* *
47862 TCCT-ACTATTAAAAGTTACAAAAT-GATCACTCAACTAT
1 T-TTAACTATTAAAAGTTACAAAATGGTTC-CTCAACTAT
47900 TTATTATGTT
Statistics
Matches: 173, Mismatches: 34, Indels: 22
0.76 0.15 0.10
Matches are distributed among these distances:
58 1 0.01
59 9 0.05
60 155 0.90
61 7 0.04
62 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (59 bp):
TTTAACTATTAAAAGTTACAAAATGGTTCCTCAACTATAGATCTTACTTTGTTGAGTTC
Found at i:47841 original size:120 final size:120
Alignment explanation
Indices: 47628--47886 Score: 281
Period size: 120 Copynumber: 2.2 Consensus size: 120
47618 ATCTTTTAAT
* * **
47628 TATTAAAAGTTATAAAATGGTTCCTTGACTATAGGATCTTACTTTGTTGAGTTCTTTAACTATTA
1 TATTAAAAGTTACAAAATGGTTCCTTAACTATAGGATCTTACTTTGTTGAGTTCCCTAACTATTA
* ** ** * * * *
47693 AAAGTTATAAAATGGTTGCTCGATTATAGTGCGTTGCTACGTTGAGTTCAT-CGAC
66 AAAGTTACAAAATAATCCCTCAACTATAGAGCGTTGCTACGTTGAATTC-TCCGAC
* * **
47748 TATTAAAATTTACAAAATGGTT-ATCTAACTATAGGAT-TTCACTTTGTTGAGTTCCCTGGCTAT
1 TATTAAAAGTTACAAAATGGTTCCT-TAACTATAGGATCTT-ACTTTGTTGAGTTCCCTAACTAT
* ** *
47811 TAAAAGTTACAAAATAATCCCTCAACTATAGAGTGTTGCTTTGTTGAATTCTCCTAC
64 TAAAAGTTACAAAATAATCCCTCAACTATAGAGCGTTGCTACGTTGAATTCTCCGAC
47868 TATTAAAAGTTACAAAATG
1 TATTAAAAGTTACAAAATG
47887 ATCACTCAAC
Statistics
Matches: 114, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
119 4 0.04
120 110 0.96
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (120 bp):
TATTAAAAGTTACAAAATGGTTCCTTAACTATAGGATCTTACTTTGTTGAGTTCCCTAACTATTA
AAAGTTACAAAATAATCCCTCAACTATAGAGCGTTGCTACGTTGAATTCTCCGAC
Found at i:50387 original size:3 final size:3
Alignment explanation
Indices: 50344--50372 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
50334 ACCACCTTAC
50344 ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
50373 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:50835 original size:2 final size:2
Alignment explanation
Indices: 50823--50866 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
50813 TCATTTTAGA
*
50823 AT AT A- AT AT AT AT AC 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
50864 AT A
1 AT A
50867 CACGAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:60995 original size:23 final size:23
Alignment explanation
Indices: 60966--61056 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
60956 CATTATTATA
60966 TGGCACTATGGTGCAATTATACG
1 TGGCACTATGGTGCAATTATACG
* * *
60989 CGGCACTACGGTGCAATTCTACG
1 TGGCACTATGGTGCAATTATACG
* *
61012 TGGCACT-TCAGTGCAATTCTACG
1 TGGCACTAT-GGTGCAATTATACG
* *
61035 TGGCACTTTGGTGCATTTATAC
1 TGGCACTATGGTGCAATTATAC
61057 TAGCTGTGGT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 56 0.98
24 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (23 bp):
TGGCACTATGGTGCAATTATACG
Found at i:61377 original size:2 final size:2
Alignment explanation
Indices: 61365--61394 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
61355 TGATAAGGAC
*
61365 AT AT AT GT 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
61395 TTATTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64215 original size:20 final size:20
Alignment explanation
Indices: 64186--64228 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
64176 AGAAAGAGAC
*
64186 ATTTATTACCTGAGCAATAA
1 ATTTACTACCTGAGCAATAA
64206 ATTTACTACCTGAGCAATAA
1 ATTTACTACCTGAGCAATAA
64226 ATT
1 ATT
64229 CACTGATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (20 bp):
ATTTACTACCTGAGCAATAA
Found at i:67518 original size:110 final size:113
Alignment explanation
Indices: 67337--67549 Score: 252
Period size: 110 Copynumber: 1.9 Consensus size: 113
67327 GATAAACCAT
* * *
67337 TCAACATTTCCAATGGAGGGGTTCATAATGAGAAGAACTCGTCTGAAGAAAGAAAGAAATTCATA
1 TCAACATTTCCAATGGAGGAGTTCATAATAAGAAGAACTCATC--AAGAAAGAAAGAAATTCATA
* * * * *
67402 ATGAGAATAACTTGTTCAACCTTGGTTCGATTCTATCATAAAAAGGTGGA
64 ATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCATAAAAAGGTGGA
* * ** * *
67452 TCAACATTTTCAGTGGA-GAGTTCATAATAAGAAG-ACTCATC-AGAAAGGGAGAAGTTCGTAAT
1 TCAACATTTCCAATGGAGGAGTTCATAATAAGAAGAACTCATCAAGAAAGAAAGAAATTCATAAT
*
67514 GAGAAGAACTTATTTAACCTTAGCTCGATTCCATCA
66 GAGAAGAACTTATTCAACCTTAGCTCGATTCCATCA
67550 CATAAAGAGT
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
110 47 0.57
113 6 0.07
114 15 0.18
115 15 0.18
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
TCAACATTTCCAATGGAGGAGTTCATAATAAGAAGAACTCATCAAGAAAGAAAGAAATTCATAAT
GAGAAGAACTTATTCAACCTTAGCTCGATTCCATCATAAAAAGGTGGA
Found at i:68153 original size:17 final size:17
Alignment explanation
Indices: 68131--68165 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
68121 CACCTTACAT
68131 TATTATTATTATTATTA
1 TATTATTATTATTATTA
68148 TATTATTATTATTATTA
1 TATTATTATTATTATTA
68165 T
1 T
68166 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:68154 original size:20 final size:20
Alignment explanation
Indices: 68129--68166 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
68119 ACCACCTTAC
68129 ATTATTATTATTATTATTAT
1 ATTATTATTATTATTATTAT
68149 ATTATTATTATTATTATT
1 ATTATTATTATTATTATT
68167 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTATTATTATTATTATTAT
Found at i:68181 original size:3 final size:3
Alignment explanation
Indices: 68129--68166 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
68119 ACCACCTTAC
68129 ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
68167 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.