Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002640.1 Hibiscus syriacus cultivar Beakdansim tig00005384_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: 138979
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5194 original size:23 final size:23
Alignment explanation
Indices: 5162--5205 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5152 CGTTTTATGA
*
5162 TATTTCTAAATAAATAAATATTT
1 TATTTATAAATAAATAAATATTT
*
5185 TATTTATAAATATATAAATAT
1 TATTTATAAATAAATAAATAT
5206 ATATATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATTT
Found at i:5220 original size:27 final size:26
Alignment explanation
Indices: 5171--5224 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
5161 ATATTTCTAA
*
5171 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTATTCAT-AATAT
*
5198 ATAAATATATATATTT-TTCATAATAT
1 ATAAATAAATAT-TTTATTCATAATAT
5224 A
1 A
5225 ATTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 15 0.62
28 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
ATAAATAAATATTTTATTCATAATAT
Found at i:5755 original size:26 final size:27
Alignment explanation
Indices: 5703--5760 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
5693 TAATTCTTTC
*
5703 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
5731 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
5757 TTTT
1 TTTT
5761 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:7379 original size:14 final size:14
Alignment explanation
Indices: 7359--7394 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
7349 ATTTTAAATA
7359 ATTTACATTTACAT
1 ATTTACATTTACAT
* *
7373 TTTTACATTTGCAT
1 ATTTACATTTACAT
7387 ATTTACAT
1 ATTTACAT
7395 CTGGCATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTTACATTTACAT
Found at i:11085 original size:14 final size:15
Alignment explanation
Indices: 11066--11094 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11056 ATCCAGCAAA
11066 GAAAGAAA-AAAAAG
1 GAAAGAAAGAAAAAG
11080 GAAAGAAAGAAAAAG
1 GAAAGAAAGAAAAAG
11095 ATAAAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAAG
Found at i:14396 original size:35 final size:35
Alignment explanation
Indices: 14345--14411 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
14335 TTCAACCAAA
*
14345 AATAGAATATTGGGGC-ATTTTGAAGGCTCATAAC
1 AATAGAATATTGGGGCAATCTTGAAGGCTCATAAC
* *
14379 AATATGAATATTTGGGCAATCTTGGAGGCTCAT
1 AATA-GAATATTGGGGCAATCTTGAAGGCTCAT
14412 CTCAACAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 4 0.14
35 11 0.39
36 13 0.46
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (35 bp):
AATAGAATATTGGGGCAATCTTGAAGGCTCATAAC
Found at i:17004 original size:113 final size:112
Alignment explanation
Indices: 16794--18451 Score: 2152
Period size: 113 Copynumber: 14.8 Consensus size: 112
16784 TCTTAAAACA
16794 TTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
16859 AGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAGCT
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
*
16907 TTTCCAGAGATAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * * *
16972 AGAATTTGTTCAACCTTTTGTTTGAATTCATCATTCGATGGATCATCA
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
* *
17020 TTACCAGGTAGAGTTCATAATGATAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
17085 AGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCT
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
*
17133 TTTCCAGAGATAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * * *
17198 AGAATTTGTTCAACCTTTTGTTTGAATTCATCATTCGATGGATCATCA
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
* * * *
17246 TTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATAAGA
1 TTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
17311 AGAGCTTGTTCAACCTTTTGCTCAAATCCATTACTTGATGGATCAG-T
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
*
17358 ATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAG
1 -TTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * * * *
17423 AAGAGCTTGTTCAACCTTTTGCTCAAATCCATTACTTGATGGATCAGCA
64 AAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
* *
17472 TTTCCATAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCA-GGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
17537 AGATCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCT
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
*
17585 TTTCCAGAGATAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
** * * * * * * *
17650 AGATTTTGTTCAACCTTTTGTTTGAATTCATCATTCAATAGATCATCA
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
* *
17698 TTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGA
1 TTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
17763 AAAACTTGTTCAACTTTTTGCTCGAATTCATCACTTGATGGATCAACT
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
* * *
17811 TTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGA
1 TTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * * * *
17876 AGAGCTTGTTCAACTTTTTTCTCAAATCCATCACTCAATGGATCAGAT
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
*
17924 TTTCCAGAGATAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * * * *
17989 AGAATTTGTTCAACCTTTTGTTTGAATTCATCATTCAATGGATCATCA
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
* *
18037 TTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGA
1 TTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
18102 AAAACTTGTTCAACTTTTTGCTCGAATTCATCACTTGATGGATCAACT
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
* * * *
18150 ATACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGTAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
18215 AGAACTTGTTCAA-CTTTTCGCTTGAATTTATCATTCGATGGACCAGCA
65 AGAACTTGTTCAACCTTTT-GCTCGAATTCATCACTCGATGGATCAGCT
* * * * *
18263 TTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGA
1 TTTCCA-GGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
18328 AGAACTTG---------TTGCTCGAATT-ATCACTCGATGGATCAACT
65 AGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
* * *
18366 TTTCCAAAGAGAGTTCATAATGAGAAGAATTCATCTGAGGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCC-AGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
18431 AGAACTTGTTCAATCTTTTGC
65 AGAACTTGTTCAACCTTTTGC
18452 ATGATTCTAT
Statistics
Matches: 1360, Mismatches: 162, Indels: 47
0.87 0.10 0.03
Matches are distributed among these distances:
103 78 0.06
104 9 0.01
105 2 0.00
112 12 0.01
113 1253 0.92
114 6 0.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (112 bp):
TTTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCT
Found at i:18356 original size:103 final size:103
Alignment explanation
Indices: 18242--18440 Score: 281
Period size: 103 Copynumber: 1.9 Consensus size: 103
18232 TCGCTTGAAT
* * ** *
18242 TTATCATTCGATGGACCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAAG
1 TTATCACTCGATGGACCAACATTGCCAAAGAGAGTTCATAATAAGAAGAACTCATCTGAAGAAAG
18307 AAGAAGAAATTCATAATGAGAAGAACTTGTTGCTCGAA
66 AAGAAGAAATTCATAATGAGAAGAACTTGTTGCTCGAA
* * * * * * *
18345 TTATCACTCGATGGATCAACTTTTCCAAAGAGAGTTCATAATGAGAAGAATTCATCTGAGGAAGG
1 TTATCACTCGATGGACCAACATTGCCAAAGAGAGTTCATAATAAGAAGAACTCATCTGAAGAAAG
*
18410 AAGAAGAAGTTCATAATGAGAAGAACTTGTT
66 AAGAAGAAATTCATAATGAGAAGAACTTGTT
18441 CAATCTTTTG
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
103 83 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (103 bp):
TTATCACTCGATGGACCAACATTGCCAAAGAGAGTTCATAATAAGAAGAACTCATCTGAAGAAAG
AAGAAGAAATTCATAATGAGAAGAACTTGTTGCTCGAA
Found at i:18825 original size:19 final size:19
Alignment explanation
Indices: 18793--18866 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 19
18783 ATTTCATTTG
18793 TTTTA-TTTATTATTATTA
1 TTTTATTTTATTATTATTA
* *
18811 TTTTGTTTTAATATTATTA
1 TTTTATTTTATTATTATTA
* *
18830 TATTATATTATTATTATTA
1 TTTTATTTTATTATTATTA
18849 TTATTATTATTATTATTA
1 TT-TTATT-TTATTATTA
18867 AATAAATAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
18 4 0.09
19 28 0.62
20 4 0.09
21 9 0.20
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (19 bp):
TTTTATTTTATTATTATTA
Found at i:18887 original size:3 final size:3
Alignment explanation
Indices: 18799--18866 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
18789 TTTGTTTTAT
* *
18799 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA -TA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18843 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
18867 AATAAATAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
2 8 0.14
3 51 0.86
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:20528 original size:20 final size:19
Alignment explanation
Indices: 20503--20544 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
20493 CTATTTTATA
20503 AATTATATATTAATTATTTT
1 AATTATATATTAATT-TTTT
* *
20523 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
20542 AAT
1 AAT
20545 ATCGAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:38274 original size:2 final size:2
Alignment explanation
Indices: 38267--38299 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38257 CGTTAAACAA
38267 AT AT AT 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 AT AT AT A
38300 ACTGAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39757 original size:18 final size:18
Alignment explanation
Indices: 39730--39803 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
39720 GGTCACAACC
39730 CGACCCGACCCGTTGACT
1 CGACCCGACCCGTTGACT
*
39748 CGATCCGACCCGTT---T
1 CGACCCGACCCGTTGACT
*
39763 --ACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACT
*
39779 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACT
39797 CGACCCG
1 CGACCCG
39804 TTGACCGTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 11 0.23
15 1 0.02
18 36 0.75
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (18 bp):
CGACCCGACCCGTTGACT
Found at i:39770 original size:13 final size:13
Alignment explanation
Indices: 39752--39824 Score: 65
Period size: 13 Copynumber: 5.1 Consensus size: 13
39742 TTGACTCGAT
*
39752 CCGACCCGTTTAC
1 CCGACCCGTTGAC
39765 CCGACCCGTTGACCCGAC
1 CCGACCCGTT-----GAC
39783 CCGACCCGTTGAC
1 CCGACCCGTTGAC
39796 CCGACCCGTTGAC
1 CCGACCCGTTGAC
*
39809 CGTTGACCCGTTGAC
1 C--CGACCCGTTGAC
39824 C
1 C
39825 ATTGACCGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
13 27 0.53
15 12 0.24
18 12 0.24
ACGTcount: A:0.15, C:0.45, G:0.22, T:0.18
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:39770 original size:31 final size:31
Alignment explanation
Indices: 39731--39809 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
39721 GTCACAACCC
* *
39731 GACCCGACCCGTTGACTCGATCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
39762 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
39793 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
39810 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:39796 original size:8 final size:8
Alignment explanation
Indices: 39785--39824 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
39775 GACCCGACCC
39785 GACCCGTT
1 GACCCGTT
39793 GACCC---
1 GACCCGTT
39798 GACCCGTT
1 GACCCGTT
39806 GA-CCGTT
1 GACCCGTT
39813 GACCCGTT
1 GACCCGTT
39821 GACC
1 GACC
39825 ATTGACCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:39818 original size:15 final size:14
Alignment explanation
Indices: 39785--39831 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
39775 GACCCGACCC
*
39785 GACCCGTTGACC-C
1 GACCCGTTGACCTT
39798 GACCCGTTGACCGTT
1 GACCCGTTGACC-TT
39813 GACCCGTTGACCATT
1 GACCCGTTGACC-TT
39828 GACC
1 GACC
39832 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.21
Consensus pattern (14 bp):
GACCCGTTGACCTT
Found at i:41147 original size:18 final size:18
Alignment explanation
Indices: 41121--41155 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41111 TCGAAAGGAA
*
41121 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
41139 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
41156 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:44946 original size:18 final size:18
Alignment explanation
Indices: 44919--44992 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
44909 GGTCACAACC
44919 CGACCCGACCCGTTGACT
1 CGACCCGACCCGTTGACT
*
44937 CGATCCGACCCGTT---T
1 CGACCCGACCCGTTGACT
*
44952 --ACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACT
*
44968 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACT
44986 CGACCCG
1 CGACCCG
44993 TTGACCGTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 11 0.23
15 1 0.02
18 36 0.75
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (18 bp):
CGACCCGACCCGTTGACT
Found at i:44959 original size:13 final size:13
Alignment explanation
Indices: 44941--45013 Score: 65
Period size: 13 Copynumber: 5.1 Consensus size: 13
44931 TTGACTCGAT
*
44941 CCGACCCGTTTAC
1 CCGACCCGTTGAC
44954 CCGACCCGTTGACCCGAC
1 CCGACCCGTT-----GAC
44972 CCGACCCGTTGAC
1 CCGACCCGTTGAC
44985 CCGACCCGTTGAC
1 CCGACCCGTTGAC
*
44998 CGTTGACCCGTTGAC
1 C--CGACCCGTTGAC
45013 C
1 C
45014 ATTGACCGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
13 27 0.53
15 12 0.24
18 12 0.24
ACGTcount: A:0.15, C:0.45, G:0.22, T:0.18
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:44959 original size:31 final size:31
Alignment explanation
Indices: 44920--44998 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
44910 GTCACAACCC
* *
44920 GACCCGACCCGTTGACTCGATCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
44951 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
44982 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
44999 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:44985 original size:8 final size:8
Alignment explanation
Indices: 44974--45013 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
44964 GACCCGACCC
44974 GACCCGTT
1 GACCCGTT
44982 GACCC---
1 GACCCGTT
44987 GACCCGTT
1 GACCCGTT
44995 GA-CCGTT
1 GACCCGTT
45002 GACCCGTT
1 GACCCGTT
45010 GACC
1 GACC
45014 ATTGACCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:45007 original size:15 final size:14
Alignment explanation
Indices: 44974--45020 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
44964 GACCCGACCC
*
44974 GACCCGTTGACC-C
1 GACCCGTTGACCTT
44987 GACCCGTTGACCGTT
1 GACCCGTTGACC-TT
45002 GACCCGTTGACCATT
1 GACCCGTTGACC-TT
45017 GACC
1 GACC
45021 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.21
Consensus pattern (14 bp):
GACCCGTTGACCTT
Found at i:46332 original size:18 final size:18
Alignment explanation
Indices: 46306--46340 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46296 TCGAAAGGAA
*
46306 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
46324 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
46341 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:56074 original size:55 final size:54
Alignment explanation
Indices: 55815--56104 Score: 235
Period size: 55 Copynumber: 5.3 Consensus size: 54
55805 CTGCTCCCTT
* * * *
55815 TTCTTTTAGGGAGTATAGGACTCAAACAATCTTCAAAAATGGGTAT-GCTCCTTC
1 TTCTTTCAGGGAGTATAGGACTCAAACAATCTTCAAAAATAGGTCTGGTTCC-TC
** ** * * * *
55869 TTCTTTCAAAGAGTATAGGACTCAAACAATCTTCAGTAATCGTGT-TCGCTCCGTT
1 TTCTTTCAGGGAGTATAGGACTCAAACAATCTTCAAAAATAG-GTCTGGTTCC-TC
* * * * * * *
55924 TTCTTTCAGGGAGTACAGGACTCAAACAATCTTTAGCAAACATGTCTGATCCCTC
1 TTCTTTCAGGGAGTATAGGACTCAAACAATCTTCA-AAAATAGGTCTGGTTCCTC
* * * *
55979 TTCTTTCAGGAAGTATAAGACTCGAACAATCTTCAGAAAATAGGTCAT-TTTCCTC
1 TTCTTTCAGGGAGTATAGGACTCAAACAATCTTCA-AAAATAGGTC-TGGTTCCTC
* * * * *
56034 TTCTTTCAGGGAGTATAGGACTCGAACAATCTTTTAAAAATGGGTCTGCTCCCTC
1 TTCTTTCAGGGAGTATAGGACTCAAACAATC-TTCAAAAATAGGTCTGGTTCCTC
*
56089 TTCTTTCAAGGAGTAT
1 TTCTTTCAGGGAGTAT
56105 GTTGAGTTAA
Statistics
Matches: 190, Mismatches: 39, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
54 38 0.20
55 143 0.75
56 9 0.05
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (54 bp):
TTCTTTCAGGGAGTATAGGACTCAAACAATCTTCAAAAATAGGTCTGGTTCCTC
Found at i:59047 original size:13 final size:13
Alignment explanation
Indices: 59019--59054 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
59009 TAATGGGCAA
*
59019 TTTTGAAAGACTAT
1 TTTTGAAA-ACAAT
59033 TTTTGAAAACAAT
1 TTTTGAAAACAAT
59046 TTTTGAAAA
1 TTTTGAAAA
59055 AATCAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (13 bp):
TTTTGAAAACAAT
Found at i:64093 original size:30 final size:30
Alignment explanation
Indices: 64031--64094 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
64021 TAAATATTAA
* *
64031 ATATGTATATAAACTTTGATTCAATGTGCG
1 ATATGTATATAAACTTTGATTCAATATACG
*
64061 ATATGATATATAAAC-TTGATTTAATATACG
1 ATATG-TATATAAACTTTGATTCAATATACG
64091 ATAT
1 ATAT
64095 ATGAACTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 21 0.70
31 9 0.30
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (30 bp):
ATATGTATATAAACTTTGATTCAATATACG
Found at i:65664 original size:21 final size:21
Alignment explanation
Indices: 65622--65665 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
65612 TTTATATTAT
*
65622 TATTTTTTAAATGAATACAAAA
1 TATTTTTTAAAT-AATAAAAAA
65644 TATTTTTTAAGAT-ATAAAAAA
1 TATTTTTTAA-ATAATAAAAAA
65665 T
1 T
65666 TAAGTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 10 0.50
23 2 0.10
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
TATTTTTTAAATAATAAAAAA
Found at i:66134 original size:21 final size:21
Alignment explanation
Indices: 66104--66143 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
66094 AATTAGTTGA
*
66104 AAAATTAAAGGTAAATTATTT
1 AAAATAAAAGGTAAATTATTT
66125 AAAATAAAAGGTAAATTAT
1 AAAATAAAAGGTAAATTAT
66144 ATCAATGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAATAAAAGGTAAATTATTT
Found at i:67260 original size:22 final size:22
Alignment explanation
Indices: 67226--67273 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
67216 ATTGGTATAT
*
67226 TTTATCTTTTATTTT-AAATAA
1 TTTACCTTTTATTTTCAAATAA
*
67247 TTTACCTTTATATTTTCAACTAA
1 TTTACCTTT-TATTTTCAAATAA
67270 TTTA
1 TTTA
67274 TAATGTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 6 0.26
23 9 0.39
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTACCTTTTATTTTCAAATAA
Found at i:67758 original size:15 final size:15
Alignment explanation
Indices: 67738--67767 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
67728 TGACTATGAA
*
67738 ATATTTTAATGGAAG
1 ATATTTCAATGGAAG
67753 ATATTTCAATGGAAG
1 ATATTTCAATGGAAG
67768 TTGGTAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (15 bp):
ATATTTCAATGGAAG
Found at i:75590 original size:18 final size:18
Alignment explanation
Indices: 75563--75597 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
75553 GATAACAATA
*
75563 TGACAGATGAAAATGTTG
1 TGACAAATGAAAATGTTG
75581 TGACAAATGAAAATGTT
1 TGACAAATGAAAATGTT
75598 TAGAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.29
Consensus pattern (18 bp):
TGACAAATGAAAATGTTG
Found at i:77138 original size:11 final size:13
Alignment explanation
Indices: 77110--77140 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
77100 AAGAATAATA
77110 ATATAATTTAAAT
1 ATATAATTTAAAT
*
77123 ATATAATTTAATT
1 ATATAATTTAAAT
77136 ATATA
1 ATATA
77141 TCATTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATAATTTAAAT
Found at i:78023 original size:31 final size:31
Alignment explanation
Indices: 77952--78026 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
77942 GGGGCCTGTA
* *
77952 AGCCTACCCAAGAAAATTCTCGGGACCACGG
1 AGCCTACCCAAGAAAAATCTCGGGACCACAG
*
77983 AGGCCTACCCAAGAAAAATCTCAGGG-CCGCAG
1 A-GCCTACCCAAGAAAAATCTC-GGGACCACAG
78015 AGCCTACCCAAG
1 AGCCTACCCAAG
78027 GGTCGTCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 12 0.31
32 24 0.62
33 3 0.08
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.11
Consensus pattern (31 bp):
AGCCTACCCAAGAAAAATCTCGGGACCACAG
Found at i:83950 original size:21 final size:19
Alignment explanation
Indices: 83912--83957 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
83902 AATTAATCCT
83912 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
83932 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
83953 A-TAAT
1 ACTAAT
83958 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:95847 original size:31 final size:31
Alignment explanation
Indices: 95812--95876 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
95802 TAACCTTACA
95812 ACTCTA-TCTTTTC-AATGGCTAAGA-TAGAACC
1 ACTCTAGT-TTTTCTAA-GGCTAA-ACTAGAACC
95843 ACTCTAGTTTTTCTAAGGCTAAACTAGAACC
1 ACTCTAGTTTTTCTAAGGCTAAACTAGAACC
95874 ACT
1 ACT
95877 TCCATTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
30 1 0.03
31 27 0.87
32 3 0.10
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (31 bp):
ACTCTAGTTTTTCTAAGGCTAAACTAGAACC
Found at i:99534 original size:2 final size:2
Alignment explanation
Indices: 99527--99568 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
99517 TAAAATGTTT
99527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
99569 AACACTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107634 original size:18 final size:18
Alignment explanation
Indices: 107611--107645 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
107601 ATATATGACT
107611 TACACATTTTAGTACATG
1 TACACATTTTAGTACATG
107629 TACACATTTTAGTACAT
1 TACACATTTTAGTACAT
107646 ACCAACAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (18 bp):
TACACATTTTAGTACATG
Found at i:108224 original size:23 final size:23
Alignment explanation
Indices: 108103--108225 Score: 115
Period size: 23 Copynumber: 5.3 Consensus size: 23
108093 CACCACTGCT
*
108103 CACATA-ATTTG-CACCGAAGTAC
1 CACATAGATTTGTC-CCGAAGGAC
* *
108125 CACATATAATTTGTCCCAAAGGAC
1 CACATA-GATTTGTCCCGAAGGAC
* * * * *
108149 TACATAAATATGTCCCAAAGAAC
1 CACATAGATTTGTCCCGAAGGAC
*
108172 CACATAGATTTGTCCCGAATGAC
1 CACATAGATTTGTCCCGAAGGAC
* *
108195 CATATAGATTTGTCTCGAAGGAC
1 CACATAGATTTGTCCCGAAGGAC
108218 CACATAGA
1 CACATAGA
108226 ACCCTCGACT
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
22 6 0.07
23 59 0.71
24 17 0.20
25 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (23 bp):
CACATAGATTTGTCCCGAAGGAC
Found at i:108625 original size:2 final size:2
Alignment explanation
Indices: 108618--108643 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
108608 TGTAATATTT
108618 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
108644 TATTCATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:113856 original size:24 final size:24
Alignment explanation
Indices: 113829--113924 Score: 119
Period size: 23 Copynumber: 4.1 Consensus size: 24
113819 CTGCTCAAAT
113829 AATTTG-CACCGAAGTG-CCACATAG
1 AATTTGTC-CCGAAG-GACCACATAG
*
113853 AATTTGTCCCGAAGTACCACATA-
1 AATTTGTCCCGAAGGACCACATAG
* *
113876 AATTTGTGCCAAAGGACCACATAG
1 AATTTGTCCCGAAGGACCACATAG
113900 -ATTTGTCCCGAAGGACCACATAG
1 AATTTGTCCCGAAGGACCACATAG
113923 AA
1 AA
113925 CCCTCGACTC
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
23 41 0.66
24 20 0.32
25 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCACATAG
Found at i:114373 original size:2 final size:2
Alignment explanation
Indices: 114366--114421 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
114356 TGTAATATTT
114366 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
114408 CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA
114422 TATATATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:114426 original size:2 final size:2
Alignment explanation
Indices: 114421--114497 Score: 145
Period size: 2 Copynumber: 38.0 Consensus size: 2
114411 ACACACACAC
114421 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
114463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
114498 GAAATCAAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 72 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:115001 original size:21 final size:20
Alignment explanation
Indices: 114959--115008 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
114949 ATTACTCTTG
114959 GTATCGATACCTCCACATCA
1 GTATCGATACCTCCACATCA
*
114979 GTATCGATACTACTTCA-ATCA
1 GTATCGATAC--CTCCACATCA
115000 GTATCGATA
1 GTATCGATA
115009 TTGCTTATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (20 bp):
GTATCGATACCTCCACATCA
Found at i:120167 original size:11 final size:11
Alignment explanation
Indices: 120151--120190 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
120141 TAACAATAAT
120151 AATAATAAATA
1 AATAATAAATA
120162 AATAATAAATA
1 AATAATAAATA
*
120173 AAGAA-AAATA
1 AATAATAAATA
120183 AA-AATAAA
1 AATAATAAA
120191 AATAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 2 0.07
10 10 0.37
11 15 0.56
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (11 bp):
AATAATAAATA
Found at i:120183 original size:31 final size:30
Alignment explanation
Indices: 120142--120218 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 30
120132 ATAAAATAAT
*
120142 AACAATAATAATAATAAATAAATAATAAATA
1 AACAAAAATAATAATAAATAAATAA-AAATA
* * *
120173 AAGAAAAATAAAAAT-AA-AAATAAAAATT
1 AACAAAAATAATAATAAATAAATAAAAATA
*
120201 GACAAAAATAATAA-AAAT
1 AACAAAAATAATAATAAAT
120219 GTGTTGCCTC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
28 17 0.46
29 6 0.16
30 2 0.05
31 12 0.32
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (30 bp):
AACAAAAATAATAATAAATAAATAAAAATA
Found at i:120187 original size:6 final size:6
Alignment explanation
Indices: 120129--120199 Score: 61
Period size: 6 Copynumber: 10.8 Consensus size: 6
120119 ATGGGTACCT
* * *
120129 AAAATAA AATAATA ACAATA ATAATA ATAAATA AATAATAA ATAAAGA
1 AAAAT-A AA-AATA AAAATA AAAATA A-AAATA AA-AAT-A A-AAATA
120177 AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAAT
120200 TGACAAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
6 32 0.59
7 14 0.26
8 7 0.13
9 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:121847 original size:27 final size:27
Alignment explanation
Indices: 121803--121870 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
121793 AACTGTAATT
*
121803 TTCGCCACAACATTTATTATTTTAACC
1 TTCGCTACAACATTTATTATTTTAACC
*
121830 TTTGCTACAACATTTATTATTTTAACC
1 TTCGCTACAACATTTATTATTTTAACC
121857 TTCGCTACAACATT
1 TTCGCTACAACATT
121871 CAATCAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.43
Consensus pattern (27 bp):
TTCGCTACAACATTTATTATTTTAACC
Found at i:122489 original size:31 final size:31
Alignment explanation
Indices: 122454--122521 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
122444 CAAAAATTGG
*
122454 AAAAGTTTAAG-GACTAAAAGGGTAATTTTCC
1 AAAAGTTTAAGAGACCAAAAGGGTAATTTT-C
* * *
122485 AAAAG-TTCAGAGACCAAAAGTGTAATTTTT
1 AAAAGTTTAAGAGACCAAAAGGGTAATTTTC
122515 AAAAGTT
1 AAAAGTT
122522 ATGTCTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (31 bp):
AAAAGTTTAAGAGACCAAAAGGGTAATTTTC
Found at i:123724 original size:19 final size:20
Alignment explanation
Indices: 123681--123726 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
123671 TTCTATGCTA
* *
123681 GAAATTTATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
*
123701 GAAATTGATGTTTGAATG-T
1 GAAATTGATGTTAGAATGTT
123720 GAAATTG
1 GAAATTG
123727 GATCATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Done.