Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005872.1 Hibiscus syriacus cultivar Beakdansim tig00013801_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: 130137
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5949 original size:6 final size:6
Alignment explanation
Indices: 5938--5969 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5928 CCATTGGGGC
5938 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
5970 CAAATATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:9084 original size:20 final size:20
Alignment explanation
Indices: 9044--9084 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9034 TTAGTTGACT
* * *
9044 TTTATTATTTTTATCATAAA
1 TTTAATATTTTTATAACAAA
9064 TTTAATATTTTTATAACAAA
1 TTTAATATTTTTATAACAAA
9084 T
1 T
9085 AATATAAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATATTTTTATAACAAA
Found at i:9200 original size:18 final size:18
Alignment explanation
Indices: 9152--9204 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
9142 ACTTTTTATT
9152 ATTTTATTATAAATCTAACA
1 ATTTTATT-TAAAT-TAACA
* * *
9172 TTTTTA-ATAAATTATCA
1 ATTTTATTTAAATTAACA
9189 ATTTTATTTAAATTAA
1 ATTTTATTTAAATTAA
9205 TTTATTATTG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
20 5 0.19
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTATTTAAATTAACA
Found at i:10215 original size:14 final size:14
Alignment explanation
Indices: 10196--10222 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10186 TTAATCAATG
10196 CAATTTTAAATATA
1 CAATTTTAAATATA
10210 CAATTTTAAATAT
1 CAATTTTAAATAT
10223 TTTAATTAAA
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
CAATTTTAAATATA
Found at i:11610 original size:2 final size:2
Alignment explanation
Indices: 11603--11652 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
11593 GCAAAGGGAA
11603 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
11645 AT AT AT AT
1 AT AT AT AT
11653 CTACAAATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11832 original size:68 final size:67
Alignment explanation
Indices: 11690--11832 Score: 170
Period size: 68 Copynumber: 2.1 Consensus size: 67
11680 ATATATGACA
* *
11690 AAATAAAAAAAGTTAGTAAAAAAGATAATATAAAATAATAAATAATAATAAAATAAAGTAAAATA
1 AAATAAAAAAAGTTAGTAAAAAAGATAATATAAAATAATAAATAAGAATAAAATAAAATAAAATA
11755 AT
66 AT
11757 AATATAAAAAAAGGTTAGCT-AAAAA-ATAA-AT-AAATAA-ACACATAAGAATAAAATGAAAAT
1 AA-ATAAAAAAA-GTTAG-TAAAAAAGATAATATAAAATAATA-A-ATAAGAATAAAAT-AAAAT
11817 AAAATAAAT
60 AAAAT-AAT
11826 AAATAAA
1 AAATAAA
11833 TAATAGTATA
Statistics
Matches: 67, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
65 1 0.01
66 7 0.10
67 16 0.24
68 27 0.40
69 15 0.22
70 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (67 bp):
AAATAAAAAAAGTTAGTAAAAAAGATAATATAAAATAATAAATAAGAATAAAATAAAATAAAATA
AT
Found at i:11921 original size:2 final size:2
Alignment explanation
Indices: 11914--11951 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
11904 TAACTATAAC
*
11914 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11952 AAAGAGATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:12053 original size:14 final size:15
Alignment explanation
Indices: 12015--12053 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
12005 TAATTATTAT
*
12015 AATAATAAATAAAAC
1 AATACTAAATAAAAC
12030 AATACTAAATAAAAC
1 AATACTAAATAAAAC
12045 AAT-CTAAAT
1 AATACTAAAT
12054 TAGGACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AATACTAAATAAAAC
Found at i:13808 original size:106 final size:106
Alignment explanation
Indices: 13620--14670 Score: 1721
Period size: 106 Copynumber: 9.9 Consensus size: 106
13610 GTGAAGTTGA
* * *
13620 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTTGAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
13685 ATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* *
13726 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
13791 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
13832 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
13897 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
13938 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
14003 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGAG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
14044 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
14109 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* * * * *
14150 AAGTT-ATTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGAGTTGTCCGAAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
14214 ATATCCTTCGCTATGAAGTTGAAATTGGCGCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* * *
14255 AAATTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
14320 ATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
14361 AAGTTG-TTGTTGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
14425 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
14466 AAGTTG-TTGTTTACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
14530 ATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* * * * * *
14571 AAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCA
1 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
14636 ATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAA
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
14671 TGAAACTGAA
Statistics
Matches: 887, Mismatches: 56, Indels: 4
0.94 0.06 0.00
Matches are distributed among these distances:
105 295 0.33
106 592 0.67
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
Found at i:13991 original size:212 final size:212
Alignment explanation
Indices: 13611--14670 Score: 1723
Period size: 211 Copynumber: 5.0 Consensus size: 212
13601 TCCTCCGTCG
* * *
13611 TGAAGTTGA-AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * * * *
13675 CTTGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGA
*
13740 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
13805 GAAGTTGAAATTGGCTC
196 GAAGTTGAAATTGGCTC
*
13822 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
13887 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGA
*
13952 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
14017 GAAGTTGAAATTGGCTC
196 GAAGTTGAAATTGGCTC
* *
14034 TGATATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
14099 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTT-ATTGTTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGA
* * * * *
14163 CAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGAGTTGTCCGAAGTCCAATATCCTTCGCTAT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
*
14228 GAAGTTGAAATTGGCGC
196 GAAGTTGAAATTGGCTC
* * * *
14245 TGAAATTGGGAAATTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
14310 CTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGA
* *
14374 CAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
14439 GAAGTTGAAATTGGCTC
196 GAAGTTGAAATTGGCTC
* *
14456 TGAAATTGGGAAGTTG-TTGTTTACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
14520 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGTTGA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGA
* * * *
14585 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
*
14650 GAAGTTGAAATTGACTC
196 GAAGTTGAAATTGGCTC
14667 TGAA
1 TGAA
14671 TGAAACTGAA
Statistics
Matches: 786, Mismatches: 60, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
210 97 0.12
211 384 0.49
212 305 0.39
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (212 bp):
TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGA
CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGT
GAAGTTGAAATTGGCTC
Found at i:18456 original size:24 final size:22
Alignment explanation
Indices: 18429--18486 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 22
18419 AGTAAAAAAG
18429 ATAATAGAAAATAATAAAATAATA
1 ATAATA-AAAA-AATAAAATAATA
* *
18453 ATAA-AATAAAGTAAAATAATA
1 ATAATAAAAAAATAAAATAATA
18474 ATAATATAAAAAA
1 ATAATA-AAAAAA
18487 AGGTTAGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 15 0.54
22 4 0.14
23 5 0.18
24 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (22 bp):
ATAATAAAAAAATAAAATAATA
Found at i:18467 original size:21 final size:20
Alignment explanation
Indices: 18436--18487 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
18426 AAGATAATAG
18436 AAAAT-AATAAAATAATAAT
1 AAAATAAATAAAATAATAAT
18455 AAAATAAAGTAAAATAATAAT
1 AAAATAAA-TAAAATAATAAT
*
18476 AATATAAA-AAAA
1 AAAATAAATAAAA
18488 GGTTAGCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 9 0.30
20 2 0.07
21 19 0.63
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATAAATAAAATAATAAT
Found at i:18508 original size:4 final size:4
Alignment explanation
Indices: 18495--18562 Score: 52
Period size: 4 Copynumber: 16.5 Consensus size: 4
18485 AAAGGTTAGC
* *
18495 TAAA -AAA TAAA TAAA TAAA CACA TAAGA -ATAA -AAA TGAAAA TAAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA-A TA-AA TAAA T--AAA T-AAA
18541 TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TA
18563 GTATAATATG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
3 5 0.09
4 38 0.70
5 7 0.13
6 4 0.07
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (4 bp):
TAAA
Found at i:18755 original size:14 final size:15
Alignment explanation
Indices: 18717--18755 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
18707 TAATTATTAT
*
18717 AATAATAAATAAAAC
1 AATACTAAATAAAAC
18732 AATACTAAATAAAAC
1 AATACTAAATAAAAC
18747 AAT-CTAAAT
1 AATACTAAAT
18756 TAGGACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AATACTAAATAAAAC
Found at i:20314 original size:86 final size:87
Alignment explanation
Indices: 20185--20358 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
20175 TCCTCACCTT
20185 TGAGAATAGTCATATAGTTGAATCTCTGCATCATTAATTTA-TTTTTTTTCATTTAATAATCGAT
1 TGAGAATAGTCATATAGTTGAATCTCTGCATCATTAATTTATTTTTTTTTCATTTAATAATCGAT
20249 ATTTGATTTATTGAGTTTAGGG
66 ATTTGATTTATTGAGTTTAGGG
20271 TGAGAATAGTCATATAGTTGAATCTCTGCATCATTAATTTATTTTTTTTTCATTTAATAATCGAT
1 TGAGAATAGTCATATAGTTGAATCTCTGCATCATTAATTTATTTTTTTTTCATTTAATAATCGAT
20336 ATTTGATTTATTGAGTTTAGGG
66 ATTTGATTTATTGAGTTTAGGG
20358 T
1 T
20359 TAATTAGTGA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 41 0.47
87 46 0.53
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (87 bp):
TGAGAATAGTCATATAGTTGAATCTCTGCATCATTAATTTATTTTTTTTTCATTTAATAATCGAT
ATTTGATTTATTGAGTTTAGGG
Found at i:23682 original size:14 final size:14
Alignment explanation
Indices: 23663--23692 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23653 TTTATATTTT
*
23663 TTAAAATTACATTA
1 TTAAAAATACATTA
23677 TTAAAAATACATTA
1 TTAAAAATACATTA
23691 TT
1 TT
23693 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:23784 original size:11 final size:11
Alignment explanation
Indices: 23768--23808 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
23758 TAGTTTGAGT
23768 TCGAGCTTGAA
1 TCGAGCTTGAA
**
23779 TCGAGCTCAAAA
1 TCGAGCT-TGAA
23791 TCGAGCTTGAA
1 TCGAGCTTGAA
23802 TCGAGCT
1 TCGAGCT
23809 CCTGAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:26641 original size:20 final size:20
Alignment explanation
Indices: 26616--26655 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
26606 ACCTGAAAAA
26616 CTTGACATAACTTTTAGTTT
1 CTTGACATAACTTTTAGTTT
26636 CTTGACATAACTTTTAGTTT
1 CTTGACATAACTTTTAGTTT
26656 TGTGGATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (20 bp):
CTTGACATAACTTTTAGTTT
Found at i:30864 original size:19 final size:19
Alignment explanation
Indices: 30840--30878 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
30830 TCGAATGCAT
*
30840 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGAACTC
*
30859 TCCATGCATCGATGAACTC
1 TCCATGCACCGATGAACTC
30878 T
1 T
30879 GAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGAACTC
Found at i:31003 original size:64 final size:65
Alignment explanation
Indices: 30826--30988 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
30816 GAATTAATTG
* * * * *
30826 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGAACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
30891 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
30954 A
65 A
30955 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
30989 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:36802 original size:20 final size:21
Alignment explanation
Indices: 36777--36826 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
36767 CTTCATAAAC
36777 CGATGCAT-TT-AACAATGCAT
1 CGATGCATCTTGAA-AATGCAT
*
36797 CGATGCATCCTTGAATATGCAT
1 CGATGCAT-CTTGAAAATGCAT
36819 CGATGCAT
1 CGATGCAT
36827 AAGACCATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (21 bp):
CGATGCATCTTGAAAATGCAT
Found at i:38397 original size:21 final size:21
Alignment explanation
Indices: 38359--38398 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38349 CGGGAGCTAA
*
38359 TTCTTCACGAGCTGCTCCTAG
1 TTCTTCACGAGCTCCTCCTAG
* *
38380 TTCTTCTCGTGCTCCTCCT
1 TTCTTCACGAGCTCCTCCT
38399 CCTCCTCCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.38, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTTCACGAGCTCCTCCTAG
Found at i:38748 original size:8 final size:8
Alignment explanation
Indices: 38737--38767 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
38727 GTTTGAATAT
38737 TTGGATGC
1 TTGGATGC
38745 TTGGATGC
1 TTGGATGC
38753 TTGGATGC
1 TTGGATGC
38761 TTGGATG
1 TTGGATG
38768 TTTGAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.10, G:0.39, T:0.39
Consensus pattern (8 bp):
TTGGATGC
Found at i:39462 original size:19 final size:19
Alignment explanation
Indices: 39438--39476 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39428 TCGAATGCAT
39438 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
39457 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
39476 T
1 T
39477 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:39493 original size:65 final size:64
Alignment explanation
Indices: 39375--39583 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
39365 TATTCAAAGG
* *
39375 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
39436 ATTC
61 ATTT
39440 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
39505 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
39569 CATGCATCGATGCAC
1 CATGCACCGATGCAC
39584 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.41
65 65 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:39601 original size:64 final size:65
Alignment explanation
Indices: 39424--39586 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
39414 GAATTAATTG
* * * *
39424 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
39489 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
39552 A
65 A
39553 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
39587 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:47849 original size:22 final size:23
Alignment explanation
Indices: 47824--47872 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
47814 AATTGAAATG
* *
47824 TTTTAATTTTTTATTA-TTTTTA
1 TTTTAATATTTGATTATTTTTTA
*
47846 TTTTTATATTTGATTATTTTTTA
1 TTTTAATATTTGATTATTTTTTA
47869 TTTT
1 TTTT
47873 TATTACATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTTAATATTTGATTATTTTTTA
Found at i:47866 original size:17 final size:15
Alignment explanation
Indices: 47824--47873 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
47814 AATTGAAATG
*
47824 TTTTAATTTTTTATTA
1 TTTTTATTTTTTA-TA
47840 TTTTTA-TTTTTATA
1 TTTTTATTTTTTATA
47854 TTTGATTATTTTTTAT-
1 TTT--TTATTTTTTATA
47870 TTTT
1 TTTT
47874 ATTACATGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 6 0.20
15 6 0.20
16 11 0.37
17 7 0.23
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTTATTTTTTATA
Found at i:50518 original size:18 final size:20
Alignment explanation
Indices: 50480--50523 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
50470 TGTATAATCT
*
50480 TATAATCCCTTAAATTGATA
1 TATAATCCCCTAAATTGATA
50500 TATAATCCCCTAAATAT-ATA
1 TATAATCCCCTAAAT-TGATA
50520 TATA
1 TATA
50524 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (20 bp):
TATAATCCCCTAAATTGATA
Found at i:54209 original size:12 final size:12
Alignment explanation
Indices: 54192--54217 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54182 GACTATAGTC
54192 AGTTGTCCCAGA
1 AGTTGTCCCAGA
54204 AGTTGTCCCAGA
1 AGTTGTCCCAGA
54216 AG
1 AG
54218 ACTCGAGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (12 bp):
AGTTGTCCCAGA
Found at i:74539 original size:2 final size:2
Alignment explanation
Indices: 74534--74560 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
74524 TATATAATTA
74534 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
74561 CACACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74548 original size:230 final size:229
Alignment explanation
Indices: 74099--74546 Score: 616
Period size: 230 Copynumber: 1.9 Consensus size: 229
74089 TTTAGTACCT
*
74099 AAAATATCATATTTGGTCTGTTTTAGTATCTAAACTTTTAATTTTTTTCCAAACATAATGTTAAG
1 AAAATATCATATTTGATCTGTTTTAGTATCTAAAC---T--TTTTTTTCCAAACATAATGTTAAG
* * * *
74164 TTTTTAACAGGGTACTAAAATGAAGCTAAAACTAAATATTAAGTATGATTTTTAAAAAAATTGAA
61 TTTTTAACAAGATACTAAAATGAAGCAAAAACTAAATATTAAGTATGATTTGT--AAAAATTGAA
* * * *
74229 AGTTTATGTACTAGAACAGACCAAAACTGATAATTTAGTAATAAACATGTAATTTACCCTAAAGT
124 AGTTTATATACAAGAACAAACCAAAACTGATAATTTAATAATAAACATGTAATTTACCCTAAAGT
*
74294 TTTATATGATTAATATTTATATATACACGTGTCTAACGTAA
189 TTTATATAATTAATATTTATATATACACGTGTCTAACGTAA
* *
74335 AAAATATCATATTTGATCTGTTTTAGTA-CATAAAC-TTTTTTTCTAAACCTAACT-TTAAGTTT
1 AAAATATCATATTTGATCTGTTTTAGTATC-TAAACTTTTTTTTCCAAACATAA-TGTTAAGTTT
* * *
74397 TTAATAAGATATTAAAATGAAGGAAAAACTAAATATTAAGTATGATTTGT-AAAATTGAAAGTTT
64 TTAACAAGATACTAAAATGAAGCAAAAACTAAATATTAAGTATGATTTGTAAAAATTGAAAGTTT
* *
74461 ATATACAATAACAAAGCAAAACTGATAATTTAATAATAAACATGTAATTTTACCCTAAAGTTTTA
129 ATATACAAGAACAAACCAAAACTGATAATTTAATAATAAACATGTAA-TTTACCCTAAAGTTTTA
*
74526 TATAATTAATATATATATATA
193 TATAATTAATATTTATATATA
74547 TATATATATA
Statistics
Matches: 191, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
227 55 0.29
228 36 0.19
230 66 0.35
231 1 0.01
235 1 0.01
236 32 0.17
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (229 bp):
AAAATATCATATTTGATCTGTTTTAGTATCTAAACTTTTTTTTCCAAACATAATGTTAAGTTTTT
AACAAGATACTAAAATGAAGCAAAAACTAAATATTAAGTATGATTTGTAAAAATTGAAAGTTTAT
ATACAAGAACAAACCAAAACTGATAATTTAATAATAAACATGTAATTTACCCTAAAGTTTTATAT
AATTAATATTTATATATACACGTGTCTAACGTAA
Found at i:75784 original size:2 final size:2
Alignment explanation
Indices: 75777--75810 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
75767 GACATTTTTA
75777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75811 AAATATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75870 original size:26 final size:26
Alignment explanation
Indices: 75841--75913 Score: 146
Period size: 26 Copynumber: 2.8 Consensus size: 26
75831 AATCTAATTA
75841 TATATATGAGACAATACATCTGCCGT
1 TATATATGAGACAATACATCTGCCGT
75867 TATATATGAGACAATACATCTGCCGT
1 TATATATGAGACAATACATCTGCCGT
75893 TATATATGAGACAATACATCT
1 TATATATGAGACAATACATCT
75914 ACCATTTCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (26 bp):
TATATATGAGACAATACATCTGCCGT
Found at i:80089 original size:2 final size:2
Alignment explanation
Indices: 80078--80119 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
80068 CCTAAAATTT
80078 TA TA TA -A TA TA TA TA TA TA TA TA TA -A T- TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80116 TA TA
1 TA TA
80120 CACACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:80102 original size:19 final size:17
Alignment explanation
Indices: 80078--80119 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
80068 CCTAAAATTT
80078 TATATAATATATATATATA
1 TATATAAT-TA-ATATATA
80097 TATATAATTAATATATA
1 TATATAATTAATATATA
80114 TATATA
1 TATATA
80120 CACACGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATAATTAATATATA
Found at i:91377 original size:2 final size:2
Alignment explanation
Indices: 91370--91394 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91360 CATTTATTAC
91370 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
91395 CATAAATGGC
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95062 original size:2 final size:2
Alignment explanation
Indices: 95055--95083 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
95045 TTTATTTAAT
95055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
95084 TAATAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:96270 original size:23 final size:23
Alignment explanation
Indices: 96244--96288 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
96234 CACCACAGCT
*
96244 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
96267 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
96289 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:96638 original size:149 final size:149
Alignment explanation
Indices: 96256--96719 Score: 853
Period size: 149 Copynumber: 3.1 Consensus size: 149
96246 TATAATTGCA
*
96256 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCTATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
96320 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
96385 CCACAG-A-ATATATATATC
130 CCACAGAATATATATATATC
96403 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
*
96468 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGGGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
96533 CACAGAATATATATATATC
131 CACAGAATATATATATATC
96552 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
96617 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
96682 CACAGAATATATATATATATC
131 CACAG-A-ATATATATATATC
*
96703 CCGAAGGACTGCGTAGA
1 CCGAAGGACCGCGTAGA
96720 CCCTCGACTC
Statistics
Matches: 308, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
146 1 0.00
147 131 0.43
148 1 0.00
149 145 0.47
150 1 0.00
151 29 0.09
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:98222 original size:63 final size:63
Alignment explanation
Indices: 98116--98274 Score: 210
Period size: 63 Copynumber: 2.5 Consensus size: 63
98106 TAATGGAGGC
* * * * **
98116 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGCATTCGATGTTCATTTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
** **
98179 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTAAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
* *
98242 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTCCTTATGCATCGATGCAC
98275 CTTCAACAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 84 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
Found at i:98266 original size:19 final size:20
Alignment explanation
Indices: 98242--98279 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
98232 ATTAAAATTA
98242 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
98261 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
98280 ACAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:104458 original size:32 final size:32
Alignment explanation
Indices: 104410--104471 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
104400 ACATTAAACC
104410 TTAATAATTAATCTTTAAAACAAAAATAGATA
1 TTAATAATTAATCTTTAAAACAAAAATAGATA
*
104442 TTAATAATTCAA-CTTTAAAACAAAAGTAGA
1 TTAATAATT-AATCTTTAAAACAAAAATAGA
104472 ATAAAACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (32 bp):
TTAATAATTAATCTTTAAAACAAAAATAGATA
Found at i:104755 original size:21 final size:21
Alignment explanation
Indices: 104729--104772 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
104719 AGAACGATCA
*
104729 CATTAATTTCCGACAAATACC
1 CATTAATTTACGACAAATACC
104750 CATTAATTTACGACAAATACC
1 CATTAATTTACGACAAATACC
104771 CA
1 CA
104773 AAAAAGTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.27
Consensus pattern (21 bp):
CATTAATTTACGACAAATACC
Found at i:113192 original size:27 final size:27
Alignment explanation
Indices: 113139--113193 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
113129 TTAATTTATT
*
113139 TATATAATACAAAATAAATTAAAAATA
1 TATATAATACAAAATAAAATAAAAATA
* *
113166 TATATAATA-AATATAAAAATAACAATA
1 TATATAATACAAAAT-AAAATAAAAATA
113193 T
1 T
113194 CAAATTAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
TATATAATACAAAATAAAATAAAAATA
Found at i:115820 original size:23 final size:22
Alignment explanation
Indices: 115794--115857 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
115784 CAACTCATAT
115794 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
115817 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
115840 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
115858 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:116002 original size:102 final size:103
Alignment explanation
Indices: 115873--116089 Score: 391
Period size: 102 Copynumber: 2.1 Consensus size: 103
115863 TAATGTCCAT
115873 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
*
115938 GACCTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
115976 AATGACCACA-ATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
*
116040 GATCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
116078 AAGGACCACATA
1 AAGGACCACATA
116090 GACCCTCTAC
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 98 0.91
103 10 0.09
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:116580 original size:19 final size:20
Alignment explanation
Indices: 116541--116579 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
116531 TTTTTTATTA
*
116541 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
116561 TGGGGGTATCGATTCCCCC
1 TGGGGGAATCGATTCCCCC
116580 TCTAGCATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.33, G:0.33, T:0.23
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:116631 original size:21 final size:21
Alignment explanation
Indices: 116607--116649 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
116597 TCATATTCGT
* *
116607 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
116628 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
116649 T
1 T
116650 AGCCCATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:119329 original size:87 final size:87
Alignment explanation
Indices: 119182--119356 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
119172 TGGTTTCAAC
119182 TGTCTCGATGCATACGCTACCACCTTCCCTTCTTGCATTAATACACACCCCAACCAGTTATGGGA
1 TGTCTCGATGCATACGCTACCACCTTCCCTTCTTGCATTAATACACACCCCAACCAGTTATGGGA
119247 TGCGTCACTGTATACTACAAAA
66 TGCGTCACTGTATACTACAAAA
*
119269 TGTCTCGATGCATACGCTACCACCTTCCCTTCTTGCATTAATACACACCCCAACCCGTTATGGGA
1 TGTCTCGATGCATACGCTACCACCTTCCCTTCTTGCATTAATACACACCCCAACCAGTTATGGGA
119334 TGCGTCACTGTATACTACAAAA
66 TGCGTCACTGTATACTACAAAA
119356 T
1 T
119357 TCTTACCAGA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (87 bp):
TGTCTCGATGCATACGCTACCACCTTCCCTTCTTGCATTAATACACACCCCAACCAGTTATGGGA
TGCGTCACTGTATACTACAAAA
Found at i:122806 original size:23 final size:22
Alignment explanation
Indices: 122780--122843 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
122770 CAGCTCATAT
122780 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
** *
122803 AATTGCACCGGCGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
122826 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
122844 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:123030 original size:103 final size:103
Alignment explanation
Indices: 122859--123076 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
122849 TAATGTCCAT
*
122859 AAGGTCCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
122924 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
122962 AATGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
*
123027 GACCTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
123065 AAGGACCACATA
1 AAGGACCACATA
123077 GACCCTCTAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGAATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:128576 original size:16 final size:15
Alignment explanation
Indices: 128555--128605 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
128545 CCCGATTACC
128555 GGTACCCGCAAATCCG
1 GGTACCCG-AAATCCG
*
128571 GGTACCCG-ATTACCG
1 GGTACCCGAAAT-CCG
128586 GGTACCCGTAACATCCG
1 GGTACCCG-AA-ATCCG
128603 GGT
1 GGT
128606 CGGGACACGG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 2 0.07
15 11 0.38
16 8 0.28
17 7 0.24
18 1 0.03
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (15 bp):
GGTACCCGAAATCCG
Found at i:128577 original size:30 final size:32
Alignment explanation
Indices: 128543--128605 Score: 103
Period size: 30 Copynumber: 2.0 Consensus size: 32
128533 GGGTATCGGA
128543 TACCCGATTACC-GGTACCCGCAA-ATCCGGG
1 TACCCGATTACCGGGTACCCGCAACATCCGGG
*
128573 TACCCGATTACCGGGTACCCGTAACATCCGGG
1 TACCCGATTACCGGGTACCCGCAACATCCGGG
128605 T
1 T
128606 CGGGACACGG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 12 0.40
31 10 0.33
32 8 0.27
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.19
Consensus pattern (32 bp):
TACCCGATTACCGGGTACCCGCAACATCCGGG
Found at i:128586 original size:15 final size:15
Alignment explanation
Indices: 128543--128593 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
128533 GGGTATCGGA
128543 TACCCGATTACC-GG
1 TACCCGATTACCGGG
*
128557 TACCCGCA-AATCCGGG
1 TACCCG-ATTA-CCGGG
128573 TACCCGATTACCGGG
1 TACCCGATTACCGGG
128588 TACCCG
1 TACCCG
128594 TAACATCCGG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 7 0.23
15 15 0.48
16 9 0.29
ACGTcount: A:0.22, C:0.37, G:0.24, T:0.18
Consensus pattern (15 bp):
TACCCGATTACCGGG
Done.