Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001036.1 Hibiscus syriacus cultivar Beakdansim tig00002059_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: 69671
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Found at i:2286 original size:18 final size:18
Alignment explanation
Indices: 2263--2312 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
2253 TTATGATTAT
2263 ACAACTATTAGTTGCATG
1 ACAACTATTAGTTGCATG
* *
2281 ACAACTAATAATTTTGCATG
1 ACAACT-ATTA-GTTGCATG
*
2301 ACAACTAATAGT
1 ACAACTATTAGT
2313 GATGTTCTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 7 0.28
19 5 0.20
20 13 0.52
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (18 bp):
ACAACTATTAGTTGCATG
Found at i:9088 original size:26 final size:25
Alignment explanation
Indices: 9044--9098 Score: 92
Period size: 26 Copynumber: 2.2 Consensus size: 25
9034 GATAAACATA
9044 TAGGAACATAACATACAAGCTAAGG
1 TAGGAACATAACATACAAGCTAAGG
*
9069 TAGGAACATTAACATTCAAGCTAAGG
1 TAGGAACA-TAACATACAAGCTAAGG
9095 TAGG
1 TAGG
9099 CATCATGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (25 bp):
TAGGAACATAACATACAAGCTAAGG
Found at i:12217 original size:12 final size:12
Alignment explanation
Indices: 12202--12227 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12192 TCATCAGAGC
12202 AATAATCATGGA
1 AATAATCATGGA
12214 AATAATCATGGA
1 AATAATCATGGA
12226 AA
1 AA
12228 ACCCTTTTAC
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:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (12 bp):
AATAATCATGGA
Found at i:18596 original size:17 final size:17
Alignment explanation
Indices: 18570--18616 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
18560 TTACTTTCTA
*
18570 TTATTTTTATTCA-TTAT
1 TTATTCTTATT-ATTTAT
18587 TTATTCTTATTATTTAT
1 TTATTCTTATTATTTAT
18604 TTACTTCATTATT
1 TTA-TTC-TTATT
18617 TCTAAATCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 17 0.65
18 3 0.12
19 5 0.19
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTCTTATTATTTAT
Found at i:20124 original size:18 final size:17
Alignment explanation
Indices: 20101--20164 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 17
20091 CTTAAGTTTA
20101 AAATAATTTAAATTAAAT
1 AAATAATTTAAA-TAAAT
20119 AAATAATTT-AA-AAAT
1 AAATAATTTAAATAAAT
*
20134 AATATTATTTCAAATAAAT
1 AA-ATAATTT-AAATAAAT
20153 AAATAA-TTAAAT
1 AAATAATTTAAAT
20165 TATAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
15 6 0.15
16 10 0.25
17 4 0.10
18 14 0.35
19 6 0.15
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATTTAAATAAAT
Found at i:20198 original size:22 final size:23
Alignment explanation
Indices: 20164--20216 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
20154 AATAATTAAA
20164 TTATAAAAATAAATAA-ATA-TTT
1 TTATAAAAATAAA-AATATACTTT
* *
20186 TTATAATATTAAAAATATACCTTT
1 TTATAAAAATAAAAATATA-CTTT
20210 TTATAAA
1 TTATAAA
20217 TGTTTCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 2 0.08
22 14 0.56
24 9 0.36
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
TTATAAAAATAAAAATATACTTT
Found at i:24625 original size:21 final size:22
Alignment explanation
Indices: 24590--24643 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
24580 TGTTAATAGA
* *
24590 CTAAAAATTTTTAAACATATGAT
1 CTAAAAA-TTTTAAAAATAAGAT
24613 CTAAAAA-TTTAAAAATAAGAT
1 CTAAAAATTTTAAAAATAAGAT
*
24634 -TTAAAATTTT
1 CTAAAAATTTT
24644 GATAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.19
21 15 0.56
23 7 0.26
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (22 bp):
CTAAAAATTTTAAAAATAAGAT
Found at i:26609 original size:19 final size:19
Alignment explanation
Indices: 26585--26635 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
26575 AAATGACCAA
* *
26585 CAAATTTGCAACGTGATCT
1 CAAATTTGCAACGCGAACT
*
26604 CAAATTCGCAACGCGAACT
1 CAAATTTGCAACGCGAACT
*
26623 CTAATTTCGCAAC
1 CAAATTT-GCAAC
26636 ATAGGTTCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.25
Consensus pattern (19 bp):
CAAATTTGCAACGCGAACT
Found at i:26735 original size:20 final size:20
Alignment explanation
Indices: 26670--26736 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
26660 TTTTCCAATT
*
26670 TCGCAACGCGAATAGGTAAA
1 TCGCAACGCGAATATGTAAA
* * **
26690 TCACAATGATAATATGTAAA
1 TCGCAACGCGAATATGTAAA
26710 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
26730 TTGCAAC
1 TCGCAAC
26737 ACAGAAGTTA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:26813 original size:20 final size:20
Alignment explanation
Indices: 26790--26833 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
26780 GAACTCTAAT
*
26790 TTCGCAACGCGATTTCCGAA
1 TTCGCAACGCGAATTCCGAA
* *
26810 TTCGCAACGCTAATTCCTAA
1 TTCGCAACGCGAATTCCGAA
26830 TTCG
1 TTCG
26834 TGATTCGCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.30
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCGAA
Found at i:26904 original size:40 final size:41
Alignment explanation
Indices: 26860--27024 Score: 163
Period size: 40 Copynumber: 3.9 Consensus size: 41
26850 TGTGAAATTT
26860 GCAACACGATTTTCTAATTCGCGACGCTAATT-CTAAAATC
1 GCAACACGATTTTCTAATTCGCGACGCTAATTCCTAAAATC
* * *
26900 GCAACGCGATTTTCTAATTTGCGACGCTAATTCCTAATA-C
1 GCAACACGATTTTCTAATTCGCGACGCTAATTCCTAAAATC
* * * * *
26940 GCGACGCCAATTTCGAATTCGCGACGCCTAATTCCTAATTCGCAATTC
1 GCAACACGATTTTCTAATTCGCGACG-CTAATTCCTAA-----AA-TC
**
26988 GCAACACGATTTTCTAATTCGCGACTTTAATTCCTAA
1 GCAACACGATTTTCTAATTCGCGACGCTAATTCCTAA
27025 TTTGCGACGC
Statistics
Matches: 100, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
40 52 0.52
41 16 0.16
46 1 0.01
47 10 0.10
48 21 0.21
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (41 bp):
GCAACACGATTTTCTAATTCGCGACGCTAATTCCTAAAATC
Found at i:26936 original size:20 final size:20
Alignment explanation
Indices: 26873--27071 Score: 139
Period size: 20 Copynumber: 9.6 Consensus size: 20
26863 ACACGATTTT
26873 CTAATTCGCGACGCTAATT-
1 CTAATTCGCGACGCTAATTC
* * * * *
26892 CTAAAATCGCAACGCGATTTT
1 CT-AATTCGCGACGCTAATTC
*
26913 CTAATTTGCGACGCTAATTC
1 CTAATTCGCGACGCTAATTC
* * *
26933 CTAATACGCGACGCCAATTT
1 CTAATTCGCGACGCTAATTC
*
26953 CGAATTCGCGACGCCTAATTC
1 CTAATTCGCGACG-CTAATTC
* * *
26974 CTAATTCGCAATTCGCAACACGATTTT
1 CTAATTCGCGA--CGC--TA--A-TTC
**
27001 CTAATTCGCGACTTTAATTC
1 CTAATTCGCGACGCTAATTC
*
27021 CTAATTTGCGACGCTAATTC
1 CTAATTCGCGACGCTAATTC
* *
27041 CTAATTCACGACGCTAATTT
1 CTAATTCGCGACGCTAATTC
*
27061 CGAATTCGCGA
1 CTAATTCGCGA
27072 TTCGCAACGC
Statistics
Matches: 135, Mismatches: 35, Indels: 19
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.01
20 97 0.72
21 17 0.13
22 1 0.01
23 3 0.02
24 1 0.01
25 1 0.01
26 1 0.01
27 12 0.09
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (20 bp):
CTAATTCGCGACGCTAATTC
Found at i:26998 original size:88 final size:87
Alignment explanation
Indices: 26898--27095 Score: 261
Period size: 88 Copynumber: 2.3 Consensus size: 87
26888 AATTCTAAAA
* * *
26898 TCGCAACGCGATTTTCTAATTTGCGACGCTAATTCCTAATACGCGACGCCAATTTCGAATTCGCG
1 TCGCAACGCGATTTTCTAATTCGCGACGCTAATTCCTAATACGCGACGCCAATTCCGAATTCACG
*
26963 ACGCCTAATTCCTAATTCGCAAT
66 ACG-CTAATTCCGAATTCGCAAT
* ** ** * *
26986 TCGCAACACGATTTTCTAATTCGCGACTTTAATTCCTAATTTGCGACGCTAATTCCTAATTCACG
1 TCGCAACGCGATTTTCTAATTCGCGACGCTAATTCCTAATACGCGACGCCAATTCCGAATTCACG
* *
27051 ACGCTAATTTCGAATTCGCGAT
66 ACGCTAATTCCGAATTCGCAAT
*
27073 TCGCAACGCGATTTTGTAATTCG
1 TCGCAACGCGATTTTCTAATTCG
27096 GAATTAGCGT
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
87 37 0.39
88 58 0.61
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (87 bp):
TCGCAACGCGATTTTCTAATTCGCGACGCTAATTCCTAATACGCGACGCCAATTCCGAATTCACG
ACGCTAATTCCGAATTCGCAAT
Found at i:27113 original size:20 final size:20
Alignment explanation
Indices: 27090--27129 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
27080 GCGATTTTGT
*
27090 AATTCGGAATTAGCGTCGCG
1 AATTCGAAATTAGCGTCGCG
27110 AATTCGAAATTAGCGTCGCG
1 AATTCGAAATTAGCGTCGCG
27130 CATTAGGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (20 bp):
AATTCGAAATTAGCGTCGCG
Found at i:27200 original size:21 final size:20
Alignment explanation
Indices: 27146--27400 Score: 105
Period size: 20 Copynumber: 12.2 Consensus size: 20
27136 GAACAACACG
*
27146 GAATTTCAAATTCGCAACGC
1 GAATTCCAAATTCGCAACGC
* *
27166 GAACTCCAATTTCGCAACGC
1 GAATTCCAAATTCGCAACGC
* *
27186 GATTTTCCAAATTCGCGACGC
1 GA-ATTCCAAATTCGCAACGC
* * *
27207 GAATTCCGAATTTGCGACGC
1 GAATTCCAAATTCGCAACGC
* * * *
27227 TAATTCCTAATTCGCGATGC
1 GAATTCCAAATTCGCAACGC
* *
27247 TAATTCCTAATTCGCGATTCGCAATGC
1 GAATTCC-AA------ATTCGCAACGC
* *
27274 GATTTTCCAAATTCGCAATGC
1 GA-ATTCCAAATTCGCAACGC
* *
27295 GATTTTCCAAATTCGCAATGC
1 GA-ATTCCAAATTCGCAACGC
* * * *
27316 GATTTTCTAATTCGCGACGC
1 GAATTCCAAATTCGCAACGC
* * ** *
27336 TAATTCCTAATTCGTGACAC
1 GAATTCCAAATTCGCAACGC
* * * *
27356 GATTTTCTAATTCGCGACGC
1 GAATTCCAAATTCGCAACGC
* * *
27376 TAATTCCTAATTCGCGACGC
1 GAATTCCAAATTCGCAACGC
*
27396 TAATT
1 GAATT
27401 TCTAGTTCGC
Statistics
Matches: 191, Mismatches: 35, Indels: 18
0.78 0.14 0.07
Matches are distributed among these distances:
20 123 0.64
21 51 0.27
27 13 0.07
28 4 0.02
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (20 bp):
GAATTCCAAATTCGCAACGC
Found at i:27242 original size:40 final size:40
Alignment explanation
Indices: 27154--27437 Score: 194
Period size: 40 Copynumber: 6.8 Consensus size: 40
27144 CGGAATTTCA
* * * * * *
27154 AATTCGCAACGCGAACTCC-AATTTCGCAACGCGATTTTCCA
1 AATTCGCGACGCTAATTCCTAA-TTCGCGACGCTA-TTTCCT
* * * *
27195 AATTCGCGACGCGAATTCCGAATTTGCGACGCTAATTCCT
1 AATTCGCGACGCTAATTCCTAATTCGCGACGCTATTTCCT
* *
27235 AATTCGCGATGCTAATTCCTAATTCGCGATTCGCAATGCGATTTTCCA
1 AATTCGCGACGCTAATTCCTAATTCGCGA--CGC--T---A-TTTCCT
* * * * * * * * *
27283 AATTCGCAATGCGATTTTCCAAATTCGCAATGCGATTTTCT
1 AATTCGCGACGCTA-ATTCCTAATTCGCGACGCTATTTCCT
* * * *
27324 AATTCGCGACGCTAATTCCTAATTCGTGACACGATTTTCT
1 AATTCGCGACGCTAATTCCTAATTCGCGACGCTATTTCCT
27364 AATTCGCGACGCTAATTCCTAATTCGCGACGCTAATTT-CT
1 AATTCGCGACGCTAATTCCTAATTCGCGACGCT-ATTTCCT
* * *
27404 AGTTCGCGACGATAATTCCTAATTTGCGACGCTA
1 AATTCGCGACGCTAATTCCTAATTCGCGACGCTA
27438 ATTCTGAATT
Statistics
Matches: 195, Mismatches: 37, Indels: 24
0.76 0.14 0.09
Matches are distributed among these distances:
39 1 0.01
40 111 0.57
41 45 0.23
42 6 0.03
44 1 0.01
47 3 0.02
48 16 0.08
49 12 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (40 bp):
AATTCGCGACGCTAATTCCTAATTCGCGACGCTATTTCCT
Found at i:27243 original size:20 final size:20
Alignment explanation
Indices: 27190--27441 Score: 189
Period size: 20 Copynumber: 12.2 Consensus size: 20
27180 CAACGCGATT
* *
27190 TTCCAAATTCGCGACGCGAA
1 TTCCTAATTCGCGACGCTAA
* *
27210 TTCCGAATTTGCGACGCTAA
1 TTCCTAATTCGCGACGCTAA
*
27230 TTCCTAATTCGCGATGCTAA
1 TTCCTAATTCGCGACGCTAA
*
27250 TTCCTAATTCGCGATTCGCAATGCGATT
1 TTCCTAATTCGCGA--CGC--T---A-A
* * * * *
27278 TTCCAAATTCGCAATGCGATT
1 TTCCTAATTCGCGACGCTA-A
* * * * *
27299 TTCCAAATTCGCAATGCGAT
1 TTCCTAATTCGCGACGCTAA
*
27319 TTTCTAATTCGCGACGCTAA
1 TTCCTAATTCGCGACGCTAA
* * * *
27339 TTCCTAATTCGTGACACGAT
1 TTCCTAATTCGCGACGCTAA
*
27359 TTTCTAATTCGCGACGCTAA
1 TTCCTAATTCGCGACGCTAA
27379 TTCCTAATTCGCGACGCTAA
1 TTCCTAATTCGCGACGCTAA
* * *
27399 TTTCTAGTTCGCGACGATAA
1 TTCCTAATTCGCGACGCTAA
*
27419 TTCCTAATTTGCGACGCTAA
1 TTCCTAATTCGCGACGCTAA
27439 TTC
1 TTC
27442 TGAATTACAA
Statistics
Matches: 188, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
20 148 0.79
21 22 0.12
22 2 0.01
24 1 0.01
26 2 0.01
27 1 0.01
28 12 0.06
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (20 bp):
TTCCTAATTCGCGACGCTAA
Found at i:27333 original size:129 final size:129
Alignment explanation
Indices: 27152--27392 Score: 331
Period size: 129 Copynumber: 1.9 Consensus size: 129
27142 CACGGAATTT
*
27152 CAAATTCGCAACGCGAACTCCAATTTCGCAACGCGATTTTCCAAATTCGCGACGCGAATTCCGAA
1 CAAATTCGCAACGCGAACTCCAAATTCGCAACGCGATTTTCCAAATTCGCGACGCGAATTCCGAA
* * * *
27217 TTTGCGACGCTAATTCCTAATTCGCGATGCTAATTCCTAATTCGCGATTCGCAATGCGATTTTC
66 TTCGCGACACGAATTCCTAATTCGCGACGCTAATTCCTAATTCGCGATTCGCAATGCGATTTTC
* ** * * * *
27281 CAAATTCGCAATGCGATTTTCCAAATTCGCAATGCGATTTT-CTAATTCGCGACGCTAATTCCTA
1 CAAATTCGCAACGCGA-ACTCCAAATTCGCAACGCGATTTTCCAAATTCGCGACGCGAATTCCGA
* * *
27345 ATTCGTGACACGATTTTCTAATTCGCGACGCTAATTCCTAATTCGCGA
65 ATTCGCGACACGAATTCCTAATTCGCGACGCTAATTCCTAATTCGCGA
27393 CGCTAATTTC
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
129 76 0.79
130 20 0.21
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (129 bp):
CAAATTCGCAACGCGAACTCCAAATTCGCAACGCGATTTTCCAAATTCGCGACGCGAATTCCGAA
TTCGCGACACGAATTCCTAATTCGCGACGCTAATTCCTAATTCGCGATTCGCAATGCGATTTTC
Found at i:27366 original size:109 final size:109
Alignment explanation
Indices: 27170--27372 Score: 280
Period size: 109 Copynumber: 1.9 Consensus size: 109
27160 CAACGCGAAC
* * *
27170 TCCAATTTCGCAACGCGATTTTCCAAATTCGCGACGCGAATTCCGAATTTGCGACGCTAATTCCT
1 TCCAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGAATTCCGAATTCGCGACGCTAATTCCT
** *
27235 AATTCGCGATGCTAATTCCTAATTCGCGATTCGCAATGCGATTT
66 AATTCGCGACACGAATTCCTAATTCGCGATTCGCAATGCGATTT
* * * * *
27279 TCCAAATTCGCAATGCGATTTTCCAAATTCGCAATGCGATTTTCTAATTCGCGACGCTAATTCCT
1 TCCAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGAATTCCGAATTCGCGACGCTAATTCCT
* * *
27344 AATTCGTGACACGATTTTCTAATTCGCGA
66 AATTCGCGACACGAATTCCTAATTCGCGA
27373 CGCTAATTCC
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
109 80 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (109 bp):
TCCAAATTCGCAACGCGATTTTCCAAATTCGCAACGCGAATTCCGAATTCGCGACGCTAATTCCT
AATTCGCGACACGAATTCCTAATTCGCGATTCGCAATGCGATTT
Found at i:27561 original size:20 final size:20
Alignment explanation
Indices: 27465--27561 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 20
27455 CGCGTTGCGA
*
27465 ATCGCGAATTAGGAATTAGC
1 ATCGCGAATTAGAAATTAGC
* * *
27485 GTCGCGAATTAGAAAATCGC
1 ATCGCGAATTAGAAATTAGC
* *
27505 ATCGCGAATTAGAAAATCGC
1 ATCGCGAATTAGAAATTAGC
* *
27525 ATCGTGAATTAGTAATTAGC
1 ATCGCGAATTAGAAATTAGC
* *
27545 GTCGCGAATTTGAAATT
1 ATCGCGAATTAGAAATT
27562 TCGTGTTGCG
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
ATCGCGAATTAGAAATTAGC
Found at i:27609 original size:20 final size:20
Alignment explanation
Indices: 27586--27655 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
27576 TGACTTCTGT
27586 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
**
27606 GTTGCGATTTACATATTATC
1 GTTGCGATTTACATATTCGC
*
27626 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACATATTCGC
27646 GTTGCGATTT
1 GTTGCGATTT
27656 TGGAACCTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:27610 original size:40 final size:42
Alignment explanation
Indices: 27561--27657 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 42
27551 AATTTGAAAT
* *
27561 TTCGTGTTGCGAATTTGAC-T-TCTGT-GTTGCGATTTACATA
1 TTCGCGTTGCGAATTTGACATAT-TATCGTTGCGATTTACATA
*
27601 TTCGCGTTGCG-ATTT-ACATATTATCGTTGCGATTTACCTA
1 TTCGCGTTGCGAATTTGACATATTATCGTTGCGATTTACATA
*
27641 TTCGCGTTGCGATTTTG
1 TTCGCGTTGCGAATTTG
27658 GAACCTGTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
38 2 0.04
39 7 0.15
40 36 0.75
41 3 0.06
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (42 bp):
TTCGCGTTGCGAATTTGACATATTATCGTTGCGATTTACATA
Found at i:30431 original size:27 final size:28
Alignment explanation
Indices: 30387--30456 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
30377 AATAGGTGAG
* *
30387 ATGGAAATGTTATAGCAAG-GTAT-AAGT
1 ATGGAAATGTTGTGGCAAGTGT-TGAAGT
30414 ATGGAAATGTTGTGGCAAGTGTTGAAGT
1 ATGGAAATGTTGTGGCAAGTGTTGAAGT
30442 A---AAATGTTGTGGCAA
1 ATGGAAATGTTGTGGCAA
30457 CCAGTATAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 14 0.36
27 18 0.46
28 7 0.18
ACGTcount: A:0.36, C:0.04, G:0.30, T:0.30
Consensus pattern (28 bp):
ATGGAAATGTTGTGGCAAGTGTTGAAGT
Found at i:33227 original size:31 final size:31
Alignment explanation
Indices: 33205--33437 Score: 403
Period size: 31 Copynumber: 7.5 Consensus size: 31
33195 ATAGATTCCA
* *
33205 AAGAACCTAGGTAATCAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
* *
33236 AAGAACCTAGGTAATCAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
33267 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
33298 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
33329 AAGAACATAGGTAAACAGTCAATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
* *
33360 AAGAATATAGGTAAACAGTCCATATGTCCTG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
33391 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
33422 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
33438 CCTCGACCCT
Statistics
Matches: 194, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 194 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:36946 original size:12 final size:12
Alignment explanation
Indices: 36929--36953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36919 AAGACAGCAC
36929 ACTCCTTACCCT
1 ACTCCTTACCCT
36941 ACTCCTTACCCT
1 ACTCCTTACCCT
36953 A
1 A
36954 TCAGATCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.48, G:0.00, T:0.32
Consensus pattern (12 bp):
ACTCCTTACCCT
Found at i:37738 original size:31 final size:31
Alignment explanation
Indices: 37713--37948 Score: 436
Period size: 31 Copynumber: 7.6 Consensus size: 31
37703 TCCATAAATT
* *
37713 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
37744 CCGAAGAACATAGGAAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
37775 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
37806 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
37837 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
37868 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
37899 CCAAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
37930 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
37949 CCTCGACCCT
Statistics
Matches: 199, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 199 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:39809 original size:64 final size:63
Alignment explanation
Indices: 39708--39936 Score: 255
Period size: 64 Copynumber: 3.6 Consensus size: 63
39698 TCTTTTAATG
* * * * *
39708 AAAGTATGCATCGATGCACTACTTGTGCATCGGTGCATTAAATGCATTTGATGTT-TCCTTATTA
1 AAAG-ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTT-TTA
* * * *
39772 ATGAGATGCATCGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTA
1 A-AAGATGCATCGATGCACTACC-TATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTA
* * * * *
39836 AAAGGATGCATCGATGCATTAGCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTA
1 AAA-GATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTA
*
39900 AAAGAGTGCATCGATGCACTACCAATGCATCGATGCA
1 AAAGA-TGCATCGATGCACTACCTATGCATCGATGCA
39937 CATTCAAACA
Statistics
Matches: 138, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
63 4 0.03
64 128 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (63 bp):
AAAGATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTA
Found at i:44624 original size:64 final size:63
Alignment explanation
Indices: 44523--44751 Score: 264
Period size: 64 Copynumber: 3.6 Consensus size: 63
44513 TCTTTTAATG
* * * *
44523 AAAGTATGCATCGATGCACTACTTGTGCATCGGTGCATTAAATGCATTCGATGTT-TCCTTATTA
1 AAAG-ATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTT-TTA
* * * *
44587 ATGAGATGCATCGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTA
1 A-AAGATGCATCGATGCACTACC-TATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTA
* * * * *
44651 AAAGGATGCATCGATGCATTAGCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTA
1 AAA-GATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTA
*
44715 AAAGAGTGCATCGATGCACTACCAATGCATCGATGCA
1 AAAGA-TGCATCGATGCACTACCTATGCATCGATGCA
44752 CATTCAAACA
Statistics
Matches: 139, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
63 4 0.03
64 129 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (63 bp):
AAAGATGCATCGATGCACTACCTATGCATCGATGCATTAAATGCATTCGATGTTATTCTTTTA
Found at i:57237 original size:19 final size:19
Alignment explanation
Indices: 57215--57251 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
57205 TTGGCTTGAA
57215 AGAAAT-ATTTTGACACATG
1 AGAAATAATTTTGA-ACATG
57234 AGAAATAATTTTGAACAT
1 AGAAATAATTTTGAACAT
57252 CTACTAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (19 bp):
AGAAATAATTTTGAACATG
Found at i:62889 original size:55 final size:55
Alignment explanation
Indices: 62798--63282 Score: 476
Period size: 55 Copynumber: 8.8 Consensus size: 55
62788 ATACTTGAAA
* * * * * *
62798 AATCTTCAA-ATAACGAGTCTGTTCCCTATTCTTTCAGGGAGTATAAAACTCAAAC
1 AATCTTCAACA-AACGGGTCCGCTCCCTATTCATTCAGAGAGTATAAAACTCGAAC
* * ** * * * *
62853 AATCTTTAACAAACGTGTTTGATCCCTATTCATTCAGGGAGTATAAGACTCAAAC
1 AATCTTCAACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAAAACTCGAAC
* * * * *
62908 AATCTTCAATAAACGGGTCCACTCCCTATCCATTCAGGGAGTATAGAACTCGAAC
1 AATCTTCAACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAAAACTCGAAC
* * *
62963 GATCTTCATA-AAACGGGTCCGCTCTCTATTCATTTAGAGAGTATAGAAA-TCGAAC
1 AATCTTCA-ACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATA-AAACTCGAAC
* * * *
63018 AATCTTCAACAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCAACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAAAACTCGAAC
* *
63073 AATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAAACTCGAAC
1 AATCTTCA-ACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAAAACTCGAAC
* * * * * *
63128 AATCTTCAACAAATGGGTCCCCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAT
1 AATCTTCAACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAAAACTCGAAC
* * * * * *
63183 AATCTTCATA-AAACGGGCCCGTTCTCTATTCCTTCAGAGAGTATAGAACTCGAAT
1 AATCTTCA-ACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAAAACTCGAAC
* ** * * *
63238 AATCTTCAACGAACTTGTTCACTCCCTATTCCTTCAGAGAGTATA
1 AATCTTCAACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATA
63283 TGACTCAATC
Statistics
Matches: 374, Mismatches: 47, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
54 5 0.01
55 363 0.97
56 6 0.02
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (55 bp):
AATCTTCAACAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAAAACTCGAAC
Found at i:62992 original size:110 final size:110
Alignment explanation
Indices: 62820--63282 Score: 572
Period size: 110 Copynumber: 4.2 Consensus size: 110
62810 ACGAGTCTGT
* * * * * * ** * *
62820 TCCCTATTCTTTCAGGGAGTATAAAACTCAAACAATCTTTA-ACAAACGTGTTTGATCCCTATTC
1 TCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCTCTATTC
* * *
62884 ATTCAGGGAGTATA-AGACTCAAACAATCTTCAATAAACGGGTCCAC
65 ATTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCAC
* *
62930 TCCCTA-TCCATTCAGGGAGTATAGAACTCGAACGATCTTCATAAAACGGGTCCGCTCTCTATTC
1 TCCCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTC
* * **
62994 ATTTAGAGAGTATAGAAATCGAACAATCTTCAACAAACGGGTCTGC
65 ATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCAC
* *
63040 TCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCC
1 TCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCA
* * *
63105 TTCAGAGAGTATAAAACTCGAACAATCTTCAACAAATGGGTCCCC
66 TTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCAC
* * * * *
63150 TCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCATAAAACGGGCCCGTTCTCTATTCC
1 TCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCA
* * ** *
63215 TTCAGAGAGTATAGAACTCGAATAATCTTCAACGAACTTGTTCAC
66 TTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCAC
63260 TCCCTATTCCTTCAGAGAGTATA
1 TCCCTATTCCTTCAGAGAGTATA
63283 TGACTCAATC
Statistics
Matches: 310, Mismatches: 39, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
109 2 0.01
110 303 0.98
111 5 0.02
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (110 bp):
TCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCA
TTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCAC
Found at i:63076 original size:165 final size:164
Alignment explanation
Indices: 62823--63282 Score: 536
Period size: 165 Copynumber: 2.8 Consensus size: 164
62813 AGTCTGTTCC
* * * * * * *
62823 CTATTCTTTCAGGGAGTATA-AAACTCAAACAATCTTTAACAAACGTGTTTGATCCCTATTCATT
1 CTATTCTTT-AGAGAGTATAGAAA-TCGAACAATCTTCAACAAACGGGTCTGATCTCTATTCCTT
* * *
62887 CAGGGAGTATA-AGACTCAAACAATCTTCAATAAACGGGTCCACTCCCTA-TCCATTCAGGGAGT
64 CAGAGAGTATAGA-ACTCGAACAATCTTCAATAAACGGGTCCACTCCCTATTCC-TTCAGAGAGT
* * *
62950 ATAGAACTCGAACGATCTTCATA-AAACGGGTCCGCTCT
127 ATAAAACTCGAACAATCTTCA-ACAAACGGGTCCCCTCT
*
62988 CTATTCATTTAGAGAGTATAGAAATCGAACAATCTTCAACAAACGGGTCTGCTCTCTATTCCTTC
1 CTATTC-TTTAGAGAGTATAGAAATCGAACAATCTTCAACAAACGGGTCTGATCTCTATTCCTTC
* *
63053 AGAGAGTATAGAACTCGAACAATCTTC-ATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT
65 AGAGAGTATAGAACTCGAACAATCTTCAAT-AAACGGGTCCACTCCCTATTCCTTCAGAGAGTAT
*
63117 AAAACTCGAACAATCTTCAACAAATGGGTCCCCTCT
129 AAAACTCGAACAATCTTCAACAAACGGGTCCCCTCT
* * * * * *
63153 CTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCATA-AAACGGGCCCGTTCTCTATTCCTT
1 CTATT-CTTTAGAGAGTATAGAAATCGAACAATCTTCA-ACAAACGGGTCTGATCTCTATTCCTT
* ** ** *
63217 CAGAGAGTATAGAACTCGAATAATCTTCAACGAACTTGTTCACTCCCTATTCCTTCAGAGAGTAT
64 CAGAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCCACTCCCTATTCCTTCAGAGAGTAT
63282 A
129 A
63283 TGACTCAATC
Statistics
Matches: 255, Mismatches: 31, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
164 3 0.01
165 239 0.94
166 13 0.05
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (164 bp):
CTATTCTTTAGAGAGTATAGAAATCGAACAATCTTCAACAAACGGGTCTGATCTCTATTCCTTCA
GAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCCACTCCCTATTCCTTCAGAGAGTATAA
AACTCGAACAATCTTCAACAAACGGGTCCCCTCT
Found at i:64707 original size:14 final size:14
Alignment explanation
Indices: 64672--64867 Score: 76
Period size: 14 Copynumber: 14.2 Consensus size: 14
64662 TTTTATTTTA
*
64672 TTTTATTTTTCATT
1 TTTTCTTTTTCATT
64686 TTTCTCTTTCTTC-TT
1 TTT-TCTTT-TTCATT
64701 TTTTCTTTTTCATT
1 TTTTCTTTTTCATT
*
64715 TTTTC--TTCCATT
1 TTTTCTTTTTCATT
** *
64727 TTCCCATTTTTTATT
1 TTTTC-TTTTTCATT
*
64742 TCTT-TTTTTC-TT
1 TTTTCTTTTTCATT
* *
64754 TTCAT-TTTTTCATCA
1 TT-TTCTTTTTCAT-T
**
64769 TTTT-TTCATCATTT
1 TTTTCTTTTTCA-TT
*
64783 TTTCTCATTTTTCCTT
1 TTT-TC-TTTTTCATT
*
64799 TCTTCTTTTTC-TT
1 TTTTCTTTTTCATT
*
64812 CTTTTCATTTTTTA-T
1 -TTTTC-TTTTTCATT
*
64827 TATT-TTTTTCA--
1 TTTTCTTTTTCATT
*
64838 TTAT-TTTTTCATT
1 TTTTCTTTTTCATT
64851 TTTTCTTTTTCATT
1 TTTTCTTTTTCATT
64865 TTT
1 TTT
64868 ATTTCTTCTT
Statistics
Matches: 135, Mismatches: 28, Indels: 38
0.67 0.14 0.19
Matches are distributed among these distances:
11 9 0.07
12 18 0.13
13 20 0.15
14 50 0.37
15 27 0.20
16 7 0.05
17 4 0.03
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTCTTTTTCATT
Found at i:64755 original size:53 final size:53
Alignment explanation
Indices: 64676--64832 Score: 129
Period size: 57 Copynumber: 2.8 Consensus size: 53
64666 ATTTTATTTT
* *
64676 ATTTTTCATTTTTCTCTTTCTTCTTTTTTCTTTTTCATTTTTTCTTCCA-TTTTCCC
1 ATTTTTCA--TTTCT-TTTTTTCTTTTTTCTTTTTCATTTTTTCAT-CATTTTTCCC
* *
64732 ATTTTTTATTTCTTTTTTTCTTTTCATT-TTTTCATCATTTTTTCATCATTTTTTCTC
1 ATTTTTCATTTCTTTTTTTCTTTT--TTCTTTT--TCATTTTTTCATCA-TTTTTCCC
* *
64789 ATTTTTCCTTTCTTCTTTTTCTTCTTTTCATTTTTTATTATTTT
1 ATTTTTCATTTCTT-TTTTTCTT-TTTTC-TTTTTCATT-TTTT
64833 TTTCATTATT
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
53 10 0.12
54 9 0.11
55 4 0.05
56 18 0.22
57 24 0.29
58 12 0.14
59 6 0.07
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (53 bp):
ATTTTTCATTTCTTTTTTTCTTTTTTCTTTTTCATTTTTTCATCATTTTTCCC
Found at i:64761 original size:11 final size:10
Alignment explanation
Indices: 64747--64854 Score: 73
Period size: 11 Copynumber: 10.6 Consensus size: 10
64737 TTATTTCTTT
64747 TTTTCTTTTCA
1 TTTT-TTTTCA
*
64758 TTTTTTCATCA
1 TTTTTT-TTCA
*
64769 TTTTTTCATCA
1 TTTTTT-TTCA
*
64780 TTTTTTCTCA
1 TTTTTTTTCA
64790 TTTTTCCTTTC-
1 TTTTT--TTTCA
*
64801 TTCTTTTTC-
1 TTTTTTTTCA
*
64810 -TTCTTTTCA
1 TTTTTTTTCA
64819 TTTTTTATT-A
1 TTTTTT-TTCA
64829 -TTTTTTTCA
1 TTTTTTTTCA
64838 TTATTTTTTCA
1 TT-TTTTTTCA
64849 TTTTTT
1 TTTTTT
64855 CTTTTTCATT
Statistics
Matches: 81, Mismatches: 7, Indels: 19
0.76 0.07 0.18
Matches are distributed among these distances:
8 8 0.10
9 10 0.12
10 20 0.25
11 40 0.49
12 3 0.04
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:64836 original size:61 final size:57
Alignment explanation
Indices: 64740--64867 Score: 168
Period size: 61 Copynumber: 2.2 Consensus size: 57
64730 CCATTTTTTA
64740 TTTCTTTTTTTCTTTTCATTTTTTCATCATTTTTTCATCATTTTTTCTCATTTTTCCTT
1 TTTCTTTTTTTCTTTTCATTTTTTCATCATTTTTTCATCA-TTTTT-TCATTTTTCCTT
* * *
64799 TCTTCTTTTTCTTCTTTTCATTTTTT-ATTATTTTTTTCATTATTTTTTCATTTTTTCTT
1 T-TTCTTTTT-TTCTTTTCATTTTTTCATCA-TTTTTTCATCATTTTTTCATTTTTCCTT
*
64858 TTTCATTTTT
1 TTTCTTTTTT
64868 ATTTCTTCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
57 1 0.02
58 7 0.11
59 13 0.21
60 16 0.26
61 25 0.40
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (57 bp):
TTTCTTTTTTTCTTTTCATTTTTTCATCATTTTTTCATCATTTTTTCATTTTTCCTT
Found at i:64862 original size:105 final size:104
Alignment explanation
Indices: 64677--64867 Score: 255
Period size: 105 Copynumber: 1.8 Consensus size: 104
64667 TTTTATTTTA
* *
64677 TTTTTCATTTTTCTCTTTCTTCTTTTTTCTTTTTCATTTTTTCTTCCATTTTCCCATTTTTTATT
1 TTTTTCATTTTTCTCTTTCTTCTTTTTTCTTTTTCATTTTTTATT-CATTTTCCCATTATTTATT
*
64742 TCTTTTTTTCTTTTCATTTTTTCATCATTTTTTCATCATT
65 TCATTTTTTCTTTTCATTTTTTCATCATTTTTTCATCATT
**
64782 TTTTCTCATTTTTC-CTTTCTTC-TTTTTCTTCTTTTCATTTTTTATT-ATTTTTTTCATTATTT
1 TTTT-TCATTTTTCTCTTTCTTCTTTTTTC-T-TTTTCATTTTTTATTCA-TTTTCCCATTATTT
64844 -TTTCATTTTTTCTTTTTCATTTTT
62 ATTTCATTTTTTC-TTTTCATTTTT
64868 ATTTCTTCTT
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
104 18 0.24
105 35 0.46
106 23 0.30
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.73
Consensus pattern (104 bp):
TTTTTCATTTTTCTCTTTCTTCTTTTTTCTTTTTCATTTTTTATTCATTTTCCCATTATTTATTT
CATTTTTTCTTTTCATTTTTTCATCATTTTTTCATCATT
Done.