Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001551.1 Hibiscus syriacus cultivar Beakdansim tig00003053_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: 62511
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1718 original size:60 final size:59
Alignment explanation
Indices: 1617--1788 Score: 174
Period size: 60 Copynumber: 2.9 Consensus size: 59
1607 AATTATGTAT
* *
1617 TTCATTTTAAATTAATCC-CTAAACTTTTAA-ATGTTCTAATTTCATCCCTAAACTATGA-C
1 TTCATTATAAATTAATCCTC-AAACTTTGAACAT-TTC-AATTTCATCCCTAAACTATGACC
1676 TATCATTATAAATTAATCCTCAAACTCTTGAACATTTCAATTTCATCCC-AAACTATGACC
1 T-TCATTATAAATTAATCCTCAAACT-TTGAACATTTCAATTTCATCCCTAAACTATGACC
* ** * * *
1736 TTCATTCTAAATTGGTCTTCAAACTTTTTGAGCATTCCAATTTCAT-CCTAAAC
1 TTCATTATAAATTAATCCTCAAAC--TTTGAACATTTCAATTTCATCCCTAAAC
1789 CATACGTATA
Statistics
Matches: 97, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
59 31 0.32
60 55 0.57
61 9 0.09
62 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.40
Consensus pattern (59 bp):
TTCATTATAAATTAATCCTCAAACTTTGAACATTTCAATTTCATCCCTAAACTATGACC
Found at i:2009 original size:60 final size:60
Alignment explanation
Indices: 1929--2093 Score: 199
Period size: 60 Copynumber: 2.8 Consensus size: 60
1919 ATGAAATTGA
* * *
1929 AATATTCAAAAGTTTGAGGACTAATTTAGAAA-GAGGGTCATAGTTTAGAGATAAAATTAT
1 AATATTCAAAAGTTTAAGGACTAATTTA-AAATGAGGGTCATAATTTAGAGATAAAATTAG
* * * * * *
1989 AATATTAAAAATTTTAAGGACTAATTTAAAATAAGAGTCATAATTTAGGGATGAAATTAG
1 AATATTCAAAAGTTTAAGGACTAATTTAAAATGAGGGTCATAATTTAGAGATAAAATTAG
* * *
2049 AATATTCAAAAGTTTAA-AACTAATTTAAAATGAGGATTATAATTT
1 AATATTCAAAAGTTTAAGGACTAATTTAAAATGAGGGTCATAATTT
2094 GGGGACATAC
Statistics
Matches: 88, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 26 0.30
60 62 0.70
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (60 bp):
AATATTCAAAAGTTTAAGGACTAATTTAAAATGAGGGTCATAATTTAGAGATAAAATTAG
Found at i:2889 original size:27 final size:27
Alignment explanation
Indices: 2858--3055 Score: 279
Period size: 27 Copynumber: 7.3 Consensus size: 27
2848 AGCGCCGTAT
* *
2858 GGAGCGCCGTACGGCTGAGGCGTAGTA
1 GGAGCGCCGTACGGCTGAGGCGGAGTC
* * * *
2885 TGAGCGCCGTACTGCTGAGGCGTAGTA
1 GGAGCGCCGTACGGCTGAGGCGGAGTC
*
2912 TGAGCGCCGTACGGCTGAGGCGGAGTC
1 GGAGCGCCGTACGGCTGAGGCGGAGTC
*
2939 GGAGAGCCGTACGGCTGAGGCGGAGTC
1 GGAGCGCCGTACGGCTGAGGCGGAGTC
*
2966 GGAGAGCCGTACGGCTGAGGCGGAGTC
1 GGAGCGCCGTACGGCTGAGGCGGAGTC
*
2993 GGAGAGCCGTACGGCTGAGGCGGAGTC
1 GGAGCGCCGTACGGCTGAGGCGGAGTC
* * *
3020 GAAGCGTCGTACGGATGAGGCGGAGTC
1 GGAGCGCCGTACGGCTGAGGCGGAGTC
3047 GGAGCGCCG
1 GGAGCGCCG
3056 GCGGTGTATG
Statistics
Matches: 158, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 158 1.00
ACGTcount: A:0.18, C:0.23, G:0.45, T:0.14
Consensus pattern (27 bp):
GGAGCGCCGTACGGCTGAGGCGGAGTC
Found at i:3786 original size:94 final size:95
Alignment explanation
Indices: 3624--3817 Score: 372
Period size: 94 Copynumber: 2.1 Consensus size: 95
3614 GGATGAATGG
3624 GACTCGAATATGAGGCCCTTTGTAAAGGGATTCAAAGCTTAACCATTAAGTAGGATTGTAAACTA
1 GACTCGAATATGAGGCCCTTTGTAAAGGGATTCAAAGCTTAACCATTAAGTAGGATTGTAAACTA
*
3689 GTCGAATCAAGTTTGAGTGTTATTTAATTT
66 GTCGAATCAAGTTTGAGTGTTATTTAACTT
3719 GACTCGAATATGAGG-CCTTTGTAAAGGGATTCAAAGCTTAACCATTAAGTAGGATTGTAAACTA
1 GACTCGAATATGAGGCCCTTTGTAAAGGGATTCAAAGCTTAACCATTAAGTAGGATTGTAAACTA
3783 GTCGAATCAAGTTTGAGTGTTATTTAACTT
66 GTCGAATCAAGTTTGAGTGTTATTTAACTT
3813 GACTC
1 GACTC
3818 AAAAAATTCA
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 83 0.85
95 15 0.15
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33
Consensus pattern (95 bp):
GACTCGAATATGAGGCCCTTTGTAAAGGGATTCAAAGCTTAACCATTAAGTAGGATTGTAAACTA
GTCGAATCAAGTTTGAGTGTTATTTAACTT
Found at i:4415 original size:15 final size:16
Alignment explanation
Indices: 4392--4424 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4382 TAATTTATAC
4392 ATAAATTTT-AATTTT
1 ATAAATTTTAAATTTT
*
4407 ATAACTTTTAAATTTT
1 ATAAATTTTAAATTTT
4423 AT
1 AT
4425 TTTTTATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATTTTAAATTTT
Found at i:4631 original size:30 final size:30
Alignment explanation
Indices: 4597--4655 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
4587 GAATAAGTCA
*
4597 TTGAACT-TTAAAAAAAACTCAATTTAACTC
1 TTGAACTCATAAAAAAAAC-CAATTTAACTC
*
4627 TTGAACTCGATCAAAAAAACCAATTTAAC
1 TTGAACTC-ATAAAAAAAACCAATTTAAC
4656 CCATCTACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 9 0.36
32 9 0.36
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.29
Consensus pattern (30 bp):
TTGAACTCATAAAAAAAACCAATTTAACTC
Found at i:6724 original size:6 final size:6
Alignment explanation
Indices: 6708--6738 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6698 ATCTAATCTC
*
6708 ATCATT GTCATT ATCATT ATCATT ATCATT A
1 ATCATT ATCATT ATCATT ATCATT ATCATT A
6739 ATCCATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.48
Consensus pattern (6 bp):
ATCATT
Found at i:7116 original size:21 final size:21
Alignment explanation
Indices: 7061--7117 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
7051 AATAAGTGTA
* * *
7061 CCGAAGTACCGCATATATGTT
1 CCGAAGGACCACATATATGTC
* **
7082 CCAAAGGATTACATATATGTC
1 CCGAAGGACCACATATATGTC
7103 CCGAAGGACCACATA
1 CCGAAGGACCACATA
7118 GAACCCTTAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (21 bp):
CCGAAGGACCACATATATGTC
Found at i:11438 original size:6 final size:6
Alignment explanation
Indices: 11422--11469 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
11412 ATATAATCCC
*
11422 ATCATT GTCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
11470 TAATCCCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (6 bp):
ATCATT
Found at i:13009 original size:331 final size:331
Alignment explanation
Indices: 12407--13071 Score: 1141
Period size: 331 Copynumber: 2.0 Consensus size: 331
12397 ATGTATCGAT
*
12407 ACCAATATTAGATTCGATGTTGTCTGGTATCGATACCCTTAACATGGTATCGATACTACTATACT
1 ACCAATATTAGATTCGATGTTGTCTGGTATCGATACCCTTAACATGCTATCGATACTACTATACT
12472 ATGGTACCGATACCTACTCATTGATATCGATACTCTATGAACAATTATATGAATTTTTGCCTTAG
66 ATGGTACCGATACCTACTCATTGATATCGATACTCTATGAACAATTATATGAATTTTTGCCTTAG
* *
12537 GGTATCGATACTTATTCAACCAGTATAGATACCCATACCCCAATTATTACTTCTTTTCTCTTTCA
131 GGTATCGATACTCATTCAACCAGTATAGATACCCATACCCCAATTACTACTTCTTTTCTCTTTCA
* * * * *
12602 AGTATCGGTACTGAATGAACAATACCGATACCCCTTACCCATAATTTACTTGTTTCACTTGAAAA
196 AATATCGATACTGAATGAACAATACCGATAACCCTTACCCAGAATTTACTTGTTTCACTCGAAAA
*
12667 TTTTCCATAACTTACTAAATTTCCACTCTATTACTTCTTTTACTTTATCAAACTCAAATATACTT
261 TTTTCCATAACTTACTAAATTTCCACTCTATTACTTCTTTTACTTCATCAAACTCAAATATACTT
12732 ACTCAA
326 ACTCAA
* *
12738 ACCAATATTAGATTTGTTGTTGTCTGGTATCGATACCCTTAACATGCTATCGATACTACTATACT
1 ACCAATATTAGATTCGATGTTGTCTGGTATCGATACCCTTAACATGCTATCGATACTACTATACT
*
12803 ATGGTATCGATACCTACTCATTGATATCGATACTCTATGAACAATTATATGAATTTTTGCCTTAG
66 ATGGTACCGATACCTACTCATTGATATCGATACTCTATGAACAATTATATGAATTTTTGCCTTAG
* * * *
12868 GGTATTGATACTCATTCAACCAGTATCGATAGCCATACCCCAATTACTACTTCTTTTCTCTTTGA
131 GGTATCGATACTCATTCAACCAGTATAGATACCCATACCCCAATTACTACTTCTTTTCTCTTTCA
* * * *
12933 AATATCGATATTGAATGAACAATACCGATAACTCTTGCCTAGAATTTACTTGTTTCACTCGAAAA
196 AATATCGATACTGAATGAACAATACCGATAACCCTTACCCAGAATTTACTTGTTTCACTCGAAAA
*
12998 TTTTCCATAACTTATTAAATTTCCACTCTATTACTTCTTTTACTTCATCAAACTCAAATATACTT
261 TTTTCCATAACTTACTAAATTTCCACTCTATTACTTCTTTTACTTCATCAAACTCAAATATACTT
13063 ACTCAA
326 ACTCAA
13069 ACC
1 ACC
13072 TTCTTATATT
Statistics
Matches: 313, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
331 313 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (331 bp):
ACCAATATTAGATTCGATGTTGTCTGGTATCGATACCCTTAACATGCTATCGATACTACTATACT
ATGGTACCGATACCTACTCATTGATATCGATACTCTATGAACAATTATATGAATTTTTGCCTTAG
GGTATCGATACTCATTCAACCAGTATAGATACCCATACCCCAATTACTACTTCTTTTCTCTTTCA
AATATCGATACTGAATGAACAATACCGATAACCCTTACCCAGAATTTACTTGTTTCACTCGAAAA
TTTTCCATAACTTACTAAATTTCCACTCTATTACTTCTTTTACTTCATCAAACTCAAATATACTT
ACTCAA
Found at i:14587 original size:15 final size:16
Alignment explanation
Indices: 14569--14602 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
14559 AAGAAAATAA
*
14569 AAAAG-GCATAAATTT
1 AAAAGTGCATAAAGTT
14584 AAAAGTGCATAAAGTT
1 AAAAGTGCATAAAGTT
14600 AAA
1 AAA
14603 TAGCGGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (16 bp):
AAAAGTGCATAAAGTT
Found at i:14795 original size:16 final size:16
Alignment explanation
Indices: 14770--14818 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
14760 CAATTAGTAA
*
14770 TTAGTGGTTAGAAAGG
1 TTAGTGGTTAGAAAAG
*
14786 TTAGTTGTTAGAAAAG
1 TTAGTGGTTAGAAAAG
* *
14802 TTAGCGGTTAGCAAAG
1 TTAGTGGTTAGAAAAG
14818 T
1 T
14819 CCGAACCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (16 bp):
TTAGTGGTTAGAAAAG
Found at i:15023 original size:4 final size:4
Alignment explanation
Indices: 15014--15043 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
15004 TATTAGAAAC
15014 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
15044 AAACAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:15190 original size:146 final size:146
Alignment explanation
Indices: 14881--15169 Score: 422
Period size: 146 Copynumber: 2.0 Consensus size: 146
14871 ATCAAATATT
* * *
14881 ATAAAT-AATAAATAAACAAACAATGGTTAGAATGCAATAAAATAAAAATCAGTAGCTAGTAGAG
1 ATAAATAAATAAATAAA-AAACAATGATTAGAATGCAATAAAATAAAAATCAGTAACTAGCAGAG
* *
14945 TCCAAACCATAATAATGCGGATCATACCCCGAATTGGGTCACTACAAGGCCAAATCAAATATTAG
65 TCCAAACCATAATAATGCGGATCATACCCCGAATCGGGTCACCACAAGGCCAAATCAAATATTAG
15010 AAACAATAAATAAATAA
130 AAACAATAAATAAATAA
* * *
15027 ATAAATAAATAAATAAAAAACAATGATTA-AAGTGCAATAAAATAAAAGTTAGTAATTAGCAGAG
1 ATAAATAAATAAATAAAAAACAATGATTAGAA-TGCAATAAAATAAAAATCAGTAACTAGCAGAG
* * *
15091 -CACGAACCATAATAATGCGGATCATACCCCGAATCGGGTCACCACAAGGCCGAATCGAATATTA
65 TC-CAAACCATAATAATGCGGATCATACCCCGAATCGGGTCACCACAAGGCCAAATCAAATATTA
*
15155 TAAACAATAAATAAA
129 GAAACAATAAATAAA
15170 AATGATTAAA
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
145 3 0.02
146 115 0.90
147 10 0.08
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (146 bp):
ATAAATAAATAAATAAAAAACAATGATTAGAATGCAATAAAATAAAAATCAGTAACTAGCAGAGT
CCAAACCATAATAATGCGGATCATACCCCGAATCGGGTCACCACAAGGCCAAATCAAATATTAGA
AACAATAAATAAATAA
Found at i:15255 original size:122 final size:123
Alignment explanation
Indices: 15038--15291 Score: 422
Period size: 122 Copynumber: 2.1 Consensus size: 123
15028 TAAATAAATA
15038 AATAAA-AAACAATGATTAAAGTGCAATAAAATAAAAGTTAGTAATTAGCAGAGCACGAACCATA
1 AATAAATAAACAATGATTAAAGTGCAATAAAATAAAAGTTAGTAATTAGCAGAGCACGAACCATA
* * * *
15102 ATAATGCGGATCATACCCCGAATCGGGTCACCACAAGGCCGAATCGAATATTATAAAC
66 ATAATGCGGATCATAACCCGAATCAGGTCACCACAAGGCCGAATCGAATAATAGAAAC
**
15160 AATAAATAAA-AATGATTAAAGTGCAATAAAATAAAAGTTAGTAATTAGCAGAGTTCGAACCATA
1 AATAAATAAACAATGATTAAAGTGCAATAAAATAAAAGTTAGTAATTAGCAGAGCACGAACCATA
* *
15224 ATAATGTGGATCATAACCCGGATCAGGTCACCACAAGGCCGAATCGAATAATAGAAAC
66 ATAATGCGGATCATAACCCGAATCAGGTCACCACAAGGCCGAATCGAATAATAGAAAC
15282 AATAAATAAA
1 AATAAATAAA
15292 TAAATAAATA
Statistics
Matches: 123, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
122 120 0.98
123 3 0.02
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (123 bp):
AATAAATAAACAATGATTAAAGTGCAATAAAATAAAAGTTAGTAATTAGCAGAGCACGAACCATA
ATAATGCGGATCATAACCCGAATCAGGTCACCACAAGGCCGAATCGAATAATAGAAAC
Found at i:20590 original size:30 final size:29
Alignment explanation
Indices: 20549--20607 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
20539 CAATTTAAGG
* * *
20549 CAAAATGTTTTTGTACTTGAATTGAATTTA
1 CAAAATATTTTTGGACTT-AATTAAATTTA
20579 CAAAATATTTTTGGACTTAATTAAATTTA
1 CAAAATATTTTTGGACTTAATTAAATTTA
20608 TTCCAAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (29 bp):
CAAAATATTTTTGGACTTAATTAAATTTA
Found at i:20968 original size:20 final size:21
Alignment explanation
Indices: 20931--20969 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20921 TTGAGTAGAA
20931 AAAACATCCCCAAACGGCTCT
1 AAAACATCCCCAAACGGCTCT
20952 AAAACATCCCC-AACGGCT
1 AAAACATCCCCAAACGGCT
20970 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.13
Consensus pattern (21 bp):
AAAACATCCCCAAACGGCTCT
Found at i:22136 original size:19 final size:20
Alignment explanation
Indices: 22112--22159 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
22102 AACGATTTTC
*
22112 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
22131 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
22151 TTTTGAAAA
1 TTTTGAAAA
22160 AGAATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:23470 original size:29 final size:30
Alignment explanation
Indices: 23401--23459 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
23391 CAATTTAAGG
23401 CAAAATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
*
23431 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
23460 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:23565 original size:21 final size:21
Alignment explanation
Indices: 23539--23594 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
23529 AGGGTGTCAA
23539 AGTGCATCCATGCATCCCTAC
1 AGTGCATCCATGCATCCCTAC
**
23560 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCATCCCTAC
23581 AGTGCATCCATGCA
1 AGTGCATCCATGCA
23595 CCTGCACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTAC
Found at i:25011 original size:19 final size:20
Alignment explanation
Indices: 24987--25034 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
24977 AACGATTTTC
*
24987 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
25006 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
25026 TTTTGAAAA
1 TTTTGAAAA
25035 AGAATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:26346 original size:29 final size:30
Alignment explanation
Indices: 26277--26335 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
26267 CAATTTAAGG
26277 CAAAATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
*
26307 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
26336 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:26704 original size:20 final size:22
Alignment explanation
Indices: 26666--26705 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
26656 TTTGAGTAGA
26666 AAAATCATCCCCAAATGGCTCC
1 AAAATCATCCCCAAATGGCTCC
26688 AAAA-CATCCCC-AATGGCT
1 AAAATCATCCCCAAATGGCT
26706 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAATCATCCCCAAATGGCTCC
Found at i:30073 original size:91 final size:91
Alignment explanation
Indices: 29914--30622 Score: 811
Period size: 91 Copynumber: 7.8 Consensus size: 91
29904 TATAAACCAG
* * * * * *
29914 TCAACATTTACAGCAGG-GAGTTCATAATGAGAAGAACTCATTCGACGAGGGAGAAGAAGTTTAA
1 TCAACATTTCCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
* *
29978 AATGAAAAGAACTTGTTGAACCTTGCA
65 AATGAGAAGAACTTGTTCAACCTTGCA
* * * *
30005 TCAACGTTTCCAGCAGG-GAGTTCATAATGAGAAGAACTCATCCAATGAGGGATAAGAAGTTCAT
1 TCAACATTTCCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
*
30069 AATGAGAAGAACTTGTTCAACCTTGGA
65 AATGAGAAGAACTTGTTCAACCTTGCA
*
30096 TCAACATTTCCAGT-GAGGAGTTCATAATGAGAA-AACTCATCCAAGGAGGGAGAAGAAGTTCAT
1 TCAACATTTCCAGTGGA-GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
* *
30159 AATGAGAAGAACTTATTCAATCTTGGC-
65 AATGAGAAGAACTTGTTCAACCTT-GCA
* * * * *
30186 TCAACAGTTCCAGTGGAGAGATCATAATGAGAAGAACTTATCCGACGAGGGAGAAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
30251 ATGAGAAGAACTTGTTCGACCTTGGC-
66 ATGAGAAGAACTTGTTCAACCTT-GCA
* *
30277 TCAATAATTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
* *
30342 ATGAGAAGAACTTGTTTAACCTT-CGG
66 ATGAGAAGAACTTGTTCAACCTTGC-A
**
30368 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
30433 ATGAGAAGAACTTGTTCAATCTTG-A
66 ATGAGAAGAACTTGTTCAACCTTGCA
* * * * *
30458 CTCAACATTTCCAATAAGAGAGATCAT-A--AG-A-AA-TCATGCGAA-AAGGGAGAAGAAGTTC
1 -TCAACATTTCCAGT-GGAGAGTTCATAATGAGAAGAACTCAT-CCAACGAGGGAGAAGAAGTTC
*
30516 ATAATGAGATGAACTTGTTCAACCTTG-A
63 ATAATGAGAAGAACTTGTTCAACCTTGCA
* * * * ** * *
30544 CTCAATATTTCTAATAGGAGAGTTCATAATGAGAAAAACTCATCTGACGAGTGAGAAAAAGTTCA
1 -TCAACATTTCCAGT-GGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
*
30609 TAATGAGAAAAACT
64 TAATGAGAAGAACT
30623 CATACGACGA
Statistics
Matches: 539, Mismatches: 61, Indels: 35
0.85 0.10 0.06
Matches are distributed among these distances:
86 68 0.13
87 5 0.01
88 1 0.00
89 6 0.01
90 79 0.15
91 341 0.63
92 39 0.07
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (91 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGCA
Found at i:30607 original size:39 final size:39
Alignment explanation
Indices: 30564--30656 Score: 152
Period size: 39 Copynumber: 2.4 Consensus size: 39
30554 CTAATAGGAG
*
30564 AGTTCATAATGAGAAAAACTCAT-CTGACGAGTGAGAAAA
1 AGTTCATAATGAGAAAAACTCATAC-GACGAGAGAGAAAA
30603 AGTTCATAATGAGAAAAACTCATACGACGAGAGAGAAAA
1 AGTTCATAATGAGAAAAACTCATACGACGAGAGAGAAAA
*
30642 AGTTCATAATAAGAA
1 AGTTCATAATGAGAA
30657 CTTGTTCAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
39 50 0.98
40 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.19
Consensus pattern (39 bp):
AGTTCATAATGAGAAAAACTCATACGACGAGAGAGAAAA
Found at i:32441 original size:91 final size:91
Alignment explanation
Indices: 32271--32979 Score: 827
Period size: 91 Copynumber: 7.8 Consensus size: 91
32261 TATAAACCAG
* * * * * *
32271 TCAACATTTACAGCAGG-GAGTTCATAATGAGAAGAACTCATTCGACGAGGGAGAAGAAGTTTAA
1 TCAACATTTCCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
* *
32335 AATGAAAAGAACTTGTTGAACCTTGCA
65 AATGAGAAGAACTTGTTCAACCTTGCA
* * * * * *
32362 TTAACGTTTCCAGCGGGGAGTTCATAATGAGAAGAACTCATCCAATGAGGGATAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
32427 ATGAGAAGAACTTGTTCAACCTTGGA
66 ATGAGAAGAACTTGTTCAACCTTGCA
*
32453 TCAACATTTCCAGT-GAGGAGTTCATAATGAGAA-AACTCATCCAAGGAGGGAGAAGAAGTTCAT
1 TCAACATTTCCAGTGGA-GAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
*
32516 AATGAGAAGAACTTATTCAACCTTGGC-
65 AATGAGAAGAACTTGTTCAACCTT-GCA
* * * *
32543 TCAACAGTTCCAGTGGAGAGTTCATAATGAGAAGAACTTATCCGACGAGGGAGAAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
32608 ATGAGAAGAACTTGTTCGACCTTGGC-
66 ATGAGAAGAACTTGTTCAACCTT-GCA
* * *
32634 TCAATAATTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAATTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
32699 ATGAGAAGAACTTGTTCAACCTT-CGG
66 ATGAGAAGAACTTGTTCAACCTTGC-A
* * **
32725 TCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAACGCATCTGACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
* *
32790 ATGAGAATAACTTGTTCAATCTTG-A
66 ATGAGAAGAACTTGTTCAACCTTGCA
* * * *
32815 CTCAACATTTCCAATAAGAGAGATCAT-A--AG-A-AA-TCATCCGAA-AAGGGAGAAGAAGTTC
1 -TCAACATTTCCAGT-GGAGAGTTCATAATGAGAAGAACTCATCC-AACGAGGGAGAAGAAGTTC
32873 ATAATGAGAAGAACTTGTTCAACCTTG-A
63 ATAATGAGAAGAACTTGTTCAACCTTGCA
* * * * ** *
32901 CTCAATATTTCTAATAGGAGAGTTCATAATGAGAAAAACTCATCTGACGAGGGAGAAAAAGTTCA
1 -TCAACATTTCCAGT-GGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
*
32966 TAATGAGAAAAACT
64 TAATGAGAAGAACT
32980 CATACGACGA
Statistics
Matches: 538, Mismatches: 62, Indels: 35
0.85 0.10 0.06
Matches are distributed among these distances:
86 68 0.13
87 4 0.01
88 1 0.00
89 5 0.01
90 84 0.16
91 334 0.62
92 42 0.08
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (91 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGCA
Found at i:32964 original size:39 final size:39
Alignment explanation
Indices: 32921--33013 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
32911 CTAATAGGAG
*
32921 AGTTCATAATGAGAAAAACTCAT-CTGACGAGGGAGAAAA
1 AGTTCATAATGAGAAAAACTCATAC-GACGAGAGAGAAAA
*
32960 AGTTCATAATGAGAAAAACTCATACGACGAGAGAGATAA
1 AGTTCATAATGAGAAAAACTCATACGACGAGAGAGAAAA
*
32999 AGTTCATAATAAGAA
1 AGTTCATAATGAGAA
33014 CTTGTTCAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 49 0.98
40 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.19
Consensus pattern (39 bp):
AGTTCATAATGAGAAAAACTCATACGACGAGAGAGAAAA
Found at i:35087 original size:26 final size:26
Alignment explanation
Indices: 35056--35113 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
35046 TAACTCCTAA
35056 AATTTGGCATAATTTCATATCCTGAC
1 AATTTGGCATAATTTCATATCCTGAC
35082 AATTTGGCATAATTTCATATCCTGAC
1 AATTTGGCATAATTTCATATCCTGAC
35108 AATTTG
1 AATTTG
35114 CACTACCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (26 bp):
AATTTGGCATAATTTCATATCCTGAC
Found at i:42263 original size:30 final size:29
Alignment explanation
Indices: 42221--42278 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
42211 CCCTAAACTT
* * *
42221 TTCAAAGTTTATACTTTGGTCACCAAACA
1 TTCAAAATTTATAATTTGATCACCAAACA
*
42250 TTCAAAATCTTATAATTTGATCACTAAAC
1 TTCAAAAT-TTATAATTTGATCACCAAAC
42279 TAAATCCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (29 bp):
TTCAAAATTTATAATTTGATCACCAAACA
Found at i:48990 original size:11 final size:11
Alignment explanation
Indices: 48982--49012 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
48972 GAAGAAAAGT
48982 TATAGAAAAAA
1 TATAGAAAAAA
48993 TATAGAAAAAA
1 TATAGAAAAAA
49004 TATAGAAAA
1 TATAGAAAA
49013 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (11 bp):
TATAGAAAAAA
Found at i:49019 original size:20 final size:21
Alignment explanation
Indices: 48967--49043 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 21
48957 CGACACAGAG
48967 AGAAAGAAGAAAAGTTATAGAAA
1 AGAAAGAA-AAAAG-TATAGAAA
*
48990 AAATATAGAAAAAA-TATAGAAA
1 AGA-A-AGAAAAAAGTATAGAAA
49012 AGAAAGAAAAAAG---AGAAA
1 AGAAAGAAAAAAGTATAGAAA
49030 ATGAAA-AAAAAAGT
1 A-GAAAGAAAAAAGT
49044 GAGAAAGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
18 13 0.28
19 4 0.09
20 8 0.17
21 1 0.02
22 10 0.21
23 2 0.04
24 5 0.11
25 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (21 bp):
AGAAAGAAAAAAGTATAGAAA
Found at i:49023 original size:22 final size:22
Alignment explanation
Indices: 48967--49023 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
48957 CGACACAGAG
**
48967 AGAAAGAAGAAAAGTTATAGAAA
1 AGAAAGAA-AAAAAATATAGAAA
* *
48990 A-AATATAGAAAAAATATAGAAA
1 AGAA-AGAAAAAAAATATAGAAA
49012 AGAAAGAAAAAA
1 AGAAAGAAAAAA
49024 GAGAAAATGA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (22 bp):
AGAAAGAAAAAAAATATAGAAA
Found at i:49028 original size:18 final size:18
Alignment explanation
Indices: 49007--49073 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
48997 GAAAAAATAT
49007 AGAAAAGAAAGAAAAAAG
1 AGAAAAGAAAGAAAAAAG
49025 AGAAAATGAAA-AAAAAAG
1 AGAAAA-GAAAGAAAAAAG
*
49043 TG---AGAAAGAAAAAA-
1 AGAAAAGAAAGAAAAAAG
49057 AGAAAA-AATAGAAAAAA
1 AGAAAAGAA-AGAAAAAA
49074 AATAGAAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
16 2 0.05
17 9 0.22
18 14 0.34
19 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (18 bp):
AGAAAAGAAAGAAAAAAG
Found at i:49035 original size:19 final size:18
Alignment explanation
Indices: 49007--49103 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 18
48997 GAAAAAATAT
49007 AGAAAA-GAAAGAAAAAAG
1 AGAAAATGAAA-AAAAAAG
49025 AGAAAATGAAAAAAAAAG
1 AGAAAATGAAAAAAAAAG
*
49043 TGAGAAA-G--AAAAAAAG
1 AGA-AAATGAAAAAAAAAG
*
49059 AAAAAATAGAAAAAAAATAG
1 AGAAAAT-GAAAAAAAA-AG
*
49079 A-AGAATGAGAAAAAAATAG
1 AGAAAATGA-AAAAAAA-AG
49098 AGAAAA
1 AGAAAA
49104 AAGAAGAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
15 3 0.05
16 9 0.14
17 1 0.02
18 18 0.28
19 28 0.43
20 6 0.09
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (18 bp):
AGAAAATGAAAAAAAAAG
Found at i:49074 original size:20 final size:20
Alignment explanation
Indices: 48983--49124 Score: 90
Period size: 20 Copynumber: 7.0 Consensus size: 20
48973 AAGAAAAGTT
* *
48983 ATAGAAAAAATATAGAAAAA
1 ATAGAAAAAAAAAAGAAAAA
* * *
49003 ATATAGAAAAGAAAGAAAAA
1 ATAGAAAAAAAAAAGAAAAA
* **
49023 AGAGAAAATGAAAA-AAAAA
1 ATAGAAAAAAAAAAGAAAAA
*
49042 GTGAGAAAGAAAAAAAGAAAAA
1 AT-AGAAA-AAAAAAAGAAAAA
* *
49064 ATAGAAAAAAAATAG-AAGA
1 ATAGAAAAAAAAAAGAAAAA
*
49083 ATGAGAAAAAAATAGAGAAAAA
1 AT-AGAAAAAAA-AAAGAAAAA
* * *
49105 AGAAGAAATAAGAAAGAAAA
1 A-TAGAAAAAAAAAAGAAAA
49125 CCGATCAAAT
Statistics
Matches: 92, Mismatches: 23, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
19 10 0.11
20 45 0.49
21 20 0.22
22 17 0.18
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (20 bp):
ATAGAAAAAAAAAAGAAAAA
Found at i:49088 original size:41 final size:41
Alignment explanation
Indices: 49007--49112 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
48997 GAAAAAATAT
49007 AGAAAAGAAAGAAAAAAGAGAAAATGAAAAAAAAAGTGAGAA
1 AGAAAAGAAAGAAAAAAGAGAAAA-GAAAAAAAAAGTGAGAA
*
49049 AGAAAA-AAAGAAAAAATAGAAAA-AAAATAGAAGAA-TGAGAA
1 AGAAAAGAAAGAAAAAAGAGAAAAGAAAA-A-AA-AAGTGAGAA
* *
49090 A-AAAATAGAGAAAAAAGAAGAAA
1 AGAAAAGAAAGAAAAAAG-AGAAA
49113 TAAGAAAGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
39 4 0.07
40 5 0.09
41 34 0.61
42 13 0.23
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (41 bp):
AGAAAAGAAAGAAAAAAGAGAAAAGAAAAAAAAAGTGAGAA
Found at i:49119 original size:70 final size:70
Alignment explanation
Indices: 48988--49124 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 70
48978 AAGTTATAGA
* *
48988 AAAAATATAGAAAAAATATAGAAAAGAAAGAAAAAAGAGAAAATGAAAAAAAAAGTGAGAAAGAA
1 AAAAATATAGAAAAAAAATAGAAAAGAAAGAAAAAAGAGAAAA-GAAAAAAAAAGTAAGAAAGAA
49053 AAAAAG
65 AAAAAG
* *
49059 AAAAA-ATAGAAAAAAAATAGAAGAATGAGAA-AAAAATAGAGAAAA-AAGAAGAAA-TAAGAAA
1 AAAAATATAGAAAAAAAATAGAA-AA-GA-AAGAAAAA-AGAGAAAAGAAAAAAAAAGTAAGAAA
49120 GAAAA
62 GAAAA
49125 CCGATCAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
70 27 0.47
71 14 0.24
72 7 0.12
73 10 0.17
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (70 bp):
AAAAATATAGAAAAAAAATAGAAAAGAAAGAAAAAAGAGAAAAGAAAAAAAAAGTAAGAAAGAAA
AAAAG
Found at i:50643 original size:16 final size:15
Alignment explanation
Indices: 50619--50652 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
50609 AAAGAAAATA
50619 AAAAGGCATAAATTT
1 AAAAGGCATAAATTT
50634 AAAAGTGCATAAATTT
1 AAAAG-GCATAAATTT
50650 AAA
1 AAA
50653 TAACGGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (15 bp):
AAAAGGCATAAATTT
Found at i:50861 original size:16 final size:16
Alignment explanation
Indices: 50820--50861 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
50810 CAATTAGTAA
50820 TTAGCAGTTAAAAAGG
1 TTAGCAGTTAAAAAGG
**
50836 TTAGTTGTTAGAAAA-G
1 TTAGCAGTTA-AAAAGG
50852 TTAGCAGTTA
1 TTAGCAGTTA
50862 TCAGAGGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (16 bp):
TTAGCAGTTAAAAAGG
Found at i:51593 original size:2 final size:2
Alignment explanation
Indices: 51586--51612 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51576 AATAGAGTAT
51586 AC 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 AC A
51613 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:56720 original size:22 final size:22
Alignment explanation
Indices: 56671--56714 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
56661 TAATAACTAC
56671 GTCTTTATGACACATTTCCTCT
1 GTCTTTATGACACATTTCCTCT
56693 GTCTTTATGGA-ACATTTCCTCT
1 GTCTTTAT-GACACATTTCCTCT
56715 TCCTTTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.18, C:0.25, G:0.11, T:0.45
Consensus pattern (22 bp):
GTCTTTATGACACATTTCCTCT
Found at i:57277 original size:34 final size:35
Alignment explanation
Indices: 57208--57288 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 35
57198 TTTTTAAATA
* *
57208 ATTTTATATTTTATTTCTTTAAATATTTTACTAATT
1 ATTTTATATTTTATATCTTTAAATATATTA-TAATT
57244 -TTTTATATTTTATAT-TTTAAATAAATATT-TAATT
1 ATTTTATATTTTATATCTTTAAAT--ATATTATAATT
57278 ATTTT-TATTTT
1 ATTTTATATTTT
57289 TTAAAAAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
34 18 0.45
35 18 0.45
36 4 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.65
Consensus pattern (35 bp):
ATTTTATATTTTATATCTTTAAATATATTATAATT
Found at i:57300 original size:27 final size:30
Alignment explanation
Indices: 57246--57300 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 30
57236 TACTAATTTT
*
57246 TTATATTTTATATTTTAAATAAATATTTAA
1 TTATATTTTATATTTTAAATAAAGATTTAA
*
57276 TTAT-TTTTAT-TTTTTAA-AAAGATTT
1 TTATATTTTATATTTTAAATAAAGATTT
57301 CAAACTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 6 0.26
29 6 0.26
30 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
TTATATTTTATATTTTAAATAAAGATTTAA
Found at i:59341 original size:2 final size:2
Alignment explanation
Indices: 59334--59361 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59324 AAAATATACA
59334 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
59362 GCTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61594 original size:61 final size:60
Alignment explanation
Indices: 61411--61608 Score: 310
Period size: 60 Copynumber: 3.2 Consensus size: 60
61401 CCTAAGAAAA
*
61411 CATAACAGTTTACGAAAGATCTCATCTTAAAGTCTCAGAAGTCAAATCCTTGTATCGAAACAC
1 CATAACAGTTTACGGAAGATCTCATCTTAAAGTCTCAGAA-TCAAAT-CTTGTATC-AAACAC
*
61474 CATAATAGTTTACGGAAGATCT-ATCTTAAAGTCTCAGAAATCAAATCATTGTATC-AACAC
1 CATAACAGTTTACGGAAGATCTCATCTTAAAGTCTCAG-AATCAAATC-TTGTATCAAACAC
61534 CATAACAGTTTACGGAAGATCTCATCTTAAAGTCTCAGAATCAAATCTTGTATCAAAACAC
1 CATAACAGTTTACGGAAGATCTCATCTTAAAGTCTCAGAATCAAATCTTGTATC-AAACAC
61595 CATAACAGTTTACG
1 CATAACAGTTTACG
61609 AACATCCAGA
Statistics
Matches: 127, Mismatches: 3, Indels: 12
0.89 0.02 0.08
Matches are distributed among these distances:
59 7 0.06
60 35 0.28
61 35 0.28
62 28 0.22
63 22 0.17
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (60 bp):
CATAACAGTTTACGGAAGATCTCATCTTAAAGTCTCAGAATCAAATCTTGTATCAAACAC
Done.