Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002075.1 Hibiscus syriacus cultivar Beakdansim tig00004238_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: 86929
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4505 original size:22 final size:22
Alignment explanation
Indices: 4463--4507 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4453 TAAATTACTC
*
4463 ATTATTTTATAACTTTATAATA
1 ATTATTTTATAACATTATAATA
*
4485 ATTATTTTATGACAATT-TAATA
1 ATTATTTTATAAC-ATTATAATA
4507 A
1 A
4508 ATTTAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTATTTTATAACATTATAATA
Found at i:9628 original size:44 final size:46
Alignment explanation
Indices: 9564--9653 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
9554 TTAACACAAA
*
9564 GGAAAGAACTCCAAATGAGTTTCT-AAAGACATTGCAGATAGTTAT
1 GGAAACAACTCCAAATGAGTTTCTAAAAGACATTGCAGATAGTTAT
*
9609 GGAAACAAC-CCATATGAGTTTCTAAAAGACATTGCAGATAGTTAT
1 GGAAACAACTCCAAATGAGTTTCTAAAAGACATTGCAGATAGTTAT
9654 TTAAGATACA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 13 0.31
45 29 0.69
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (46 bp):
GGAAACAACTCCAAATGAGTTTCTAAAAGACATTGCAGATAGTTAT
Found at i:25563 original size:56 final size:56
Alignment explanation
Indices: 25436--25887 Score: 305
Period size: 51 Copynumber: 8.6 Consensus size: 56
25426 TGACGAGCCT
* *
25436 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTC-ATAAAACGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * * *
25491 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * *
25547 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAAT-AAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAAACGGGTCC
* * * ** **
25602 GCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCAA-CGAACTAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* ** **
25653 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** ***
25704 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAATTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
25755 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* * ** **
25806 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAA-CGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
* *
25857 GCTCCCTATTCTTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
25888 AATCTTCAAC
Statistics
Matches: 365, Mismatches: 26, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
51 243 0.67
55 71 0.19
56 51 0.14
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (56 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
Found at i:25658 original size:51 final size:51
Alignment explanation
Indices: 25543--25897 Score: 557
Period size: 51 Copynumber: 6.9 Consensus size: 51
25533 AATAAAACGG
* * * ** **
25543 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
25598 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
25649 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
25700 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAATTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
25751 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
25802 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
25853 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
25898 AAACGAATTT
Statistics
Matches: 285, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
51 254 0.89
55 31 0.11
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:25726 original size:102 final size:102
Alignment explanation
Indices: 25436--25901 Score: 576
Period size: 102 Copynumber: 4.4 Consensus size: 102
25426 TGACGAGCCT
* * * *
25436 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAACGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACAAACTTGTCCGCTCCCTA
* * ** **
25499 TTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
60 TTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACTTGTCC
* * * **
25547 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACAAACTTGTCCGCTCCCTATT
* * *
25612 CTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTAGTCC
62 CATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
*
25653 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATT
*
25718 CAGAGAGTATAGGACTCAATCTTCAACGAATTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
* *
25755 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATT
25820 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
*
25857 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAAC
25902 GAATTTGCTT
Statistics
Matches: 320, Mismatches: 29, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
102 206 0.64
106 36 0.11
107 10 0.03
110 2 0.01
111 65 0.20
112 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATT
CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
Found at i:27268 original size:19 final size:19
Alignment explanation
Indices: 27246--27288 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
27236 TTTCATTTTT
27246 ATTTTTTCTTCCCTTTTCC
1 ATTTTTTCTTCCCTTTTCC
**
27265 ATTTTTTCTTCTTTTTTCC
1 ATTTTTTCTTCCCTTTTCC
27284 -TTTTT
1 ATTTTT
27289 GTTTTTTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTTCTTCCCTTTTCC
Found at i:27329 original size:18 final size:16
Alignment explanation
Indices: 27273--27338 Score: 66
Period size: 18 Copynumber: 4.1 Consensus size: 16
27263 CCATTTTTTC
27273 TTCTTTTTTC-C-TTT
1 TTCTTTTTTCTCATTT
*
27287 TTGTTTTTTCCATCATTT
1 TTCTTTTTT-C-TCATTT
27305 TTCTTTTTTCTCATTT
1 TTCTTTTTTCTCATTT
27321 TCTCATTTTTTCTC-TTT
1 T-TC-TTTTTTCTCATTT
27338 T
1 T
27339 ATTTCTTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
14 8 0.18
15 1 0.02
16 7 0.16
17 8 0.18
18 20 0.45
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.73
Consensus pattern (16 bp):
TTCTTTTTTCTCATTT
Found at i:47132 original size:56 final size:55
Alignment explanation
Indices: 47027--47159 Score: 221
Period size: 56 Copynumber: 2.4 Consensus size: 55
47017 TCCACTAGAA
**
47027 AGCATGCACCAAATCTAATCTTTTTTATATTTTATTTTAATAACTTTATTACTCC
1 AGCATGCACCAAATCTAATCTTTTTTATATTTTATTTTAATAAAATTATTACTCC
*
47082 AGCATGCACCAAATCTAAGTTTTTTTTATATTTTATTTTAATAAAATTATTACTCC
1 AGCATGCACCAAATCTAA-TCTTTTTTATATTTTATTTTAATAAAATTATTACTCC
*
47138 GGCATGCACCAAATCTAATCTT
1 AGCATGCACCAAATCTAATCTT
47160 AATTCAGATT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
55 21 0.29
56 51 0.71
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (55 bp):
AGCATGCACCAAATCTAATCTTTTTTATATTTTATTTTAATAAAATTATTACTCC
Found at i:48227 original size:52 final size:52
Alignment explanation
Indices: 48147--48267 Score: 170
Period size: 52 Copynumber: 2.3 Consensus size: 52
48137 AGATGCATCA
* **
48147 TGTAGATTTCACCTTTCGACTCGAATTTTATGTGCCTAAACGGAGGGAGAGG
1 TGTAGTTTTCACCTTTCGACTCGAATTTTATGTGCCTAAACGGAGAAAGAGG
* * * *
48199 TGTAGTTTTCTCCTTTCGGCTCGTATTTTATGTGCCTAAACGGAGAAAGATG
1 TGTAGTTTTCACCTTTCGACTCGAATTTTATGTGCCTAAACGGAGAAAGAGG
*
48251 TGTAGTTTCCACCTTTC
1 TGTAGTTTTCACCTTTC
48268 ACTTATGGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (52 bp):
TGTAGTTTTCACCTTTCGACTCGAATTTTATGTGCCTAAACGGAGAAAGAGG
Found at i:52202 original size:55 final size:55
Alignment explanation
Indices: 52176--52753 Score: 547
Period size: 55 Copynumber: 10.8 Consensus size: 55
52166 AATCCTTGGC
*
52176 AAACGGGTCCGCTCTCTATCCCTTCAAAGAGTATAGAACTCGAACAATCTTCATA
1 AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
* *
52231 AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCATA
1 AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
* * *
52286 AAATGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-A
1 AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
*
52340 CAAACGGGTCCACTCTCTATCCCTTCAGAGAGTATAGAACTCG---AA----C---
1 -AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
* *
52386 -AACGGGTCCTCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
1 AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
* * * * * * *
52440 AAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTCA-A
1 AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA
* * * * * *
52494 CAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTC-AACCAATCTTCA-A
1 -AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGA-ACTCGAA-CAATCTTCATA
* * * * *
52549 TAAACGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCA-A
1 -AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
* * * * * *
52604 CAAACGGGTTCGCTCCCTATTCATTCAGGGAGTATAGAACTCAAACAATCTTCATA
1 -AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
* * *
52660 AAATGTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCG----ATCTTCA-A
1 AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
* * * *
52710 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAATATA-AGACTCGA
1 -AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGA-ACTCGA
52754 TCTTCATAAA
Statistics
Matches: 461, Mismatches: 41, Indels: 45
0.84 0.07 0.08
Matches are distributed among these distances:
44 39 0.08
47 2 0.00
48 1 0.00
50 2 0.00
51 45 0.10
52 2 0.00
54 5 0.01
55 362 0.79
56 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (55 bp):
AAACGGGTCCGCTCTCTATCCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA
Found at i:52294 original size:110 final size:110
Alignment explanation
Indices: 52149--52753 Score: 655
Period size: 110 Copynumber: 5.6 Consensus size: 110
52139 TTCTTTCAAG
** * *
52149 GAGTATA-AGACTCGAACAATCCTT-GGCAAACGGGTCCGCTCTCTATCCCTTCAAAGAGTATAG
1 GAGTATAGA-ACTCGAACAAT-CTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAG
*
52212 AACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGA
64 AACTCGAACAATCTTCATAAAACGTGTCCGCTCTCTATTCCTTCAGA
* * *
52259 GAGTATAGAACTCGAATAATCTTCATA-AAATGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGA
1 GAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA
* * *
52323 ACTCGAACAATCTTCA-ACAAACGGGTCCACTCTCTATCCCTTCAGA
65 ACTCGAACAATCTTCATA-AAACGTGTCCGCTCTCTATTCCTTCAGA
*
52369 GAGTATAGAACTCG----------AAC-AACGGGTCCTCTCTCTATTCCTTCAGAGAGTATAGAA
1 GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAA
* * * *
52423 CTCGAACAATCTTCATAAAACGTGTCTGCTCCCTATTCATTCAGG
66 CTCGAACAATCTTCATAAAACGTGTCCGCTCTCTATTCCTTCAGA
* * * * * *
52468 GAGTATA-AGACTCAAACAATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-A
1 GAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA
* *
52531 GACTC-AACCAATCTTCA-ATAAACGTGTTCGCTCCCTATTCCTTCAGA
65 -ACTCGAA-CAATCTTCATA-AAACGTGTCCGCTCTCTATTCCTTCAGA
* * * * *
52578 GAGTATAGGACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTCATTCAGGGAGTATAGAA
1 GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAA
* *
52643 CTCAAACAATCTTCATAAAATGTGTCCGCTCTCTATTCCTTCAGA
66 CTCGAACAATCTTCATAAAACGTGTCCGCTCTCTATTCCTTCAGA
* * *
52688 GAGTATAGAACTCG----ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAATATA-AG
1 GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-
52748 ACTCGA
65 ACTCGA
52754 TCTTCATAAA
Statistics
Matches: 424, Mismatches: 45, Indels: 56
0.81 0.09 0.11
Matches are distributed among these distances:
98 1 0.00
99 82 0.19
100 2 0.00
105 1 0.00
106 44 0.10
109 11 0.03
110 278 0.66
111 5 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (110 bp):
GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAA
CTCGAACAATCTTCATAAAACGTGTCCGCTCTCTATTCCTTCAGA
Found at i:52402 original size:44 final size:44
Alignment explanation
Indices: 52342--52431 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
52332 ATCTTCAACA
52342 AACGGGTCCACTCTCTATCCCTTCAGAGAGTATAGAACTCGAAC
1 AACGGGTCCACTCTCTATCCCTTCAGAGAGTATAGAACTCGAAC
* *
52386 AACGGGTCCTCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AACGGGTCCACTCTCTATCCCTTCAGAGAGTATAGAACTCGAAC
52430 AA
1 AA
52432 TCTTCATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (44 bp):
AACGGGTCCACTCTCTATCCCTTCAGAGAGTATAGAACTCGAAC
Found at i:52521 original size:154 final size:155
Alignment explanation
Indices: 52231--52702 Score: 585
Period size: 154 Copynumber: 3.0 Consensus size: 155
52221 AATCTTCATA
* *
52231 AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCATAAAATGGGTCT
1 AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCT
* * * * * * *
52296 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCACTCTCTATC
66 GCTCCCTATTCATTCAGGGAGTATAGAACTCAAACAATCTTCAACAAACGTGTCCGCTCTCTATT
52361 CCTTCAGAGAGTATAGAACTCGAA-
131 CCTTCAGAGAGTATAGAACTCGAAT
* * *
52385 CAACGGGTCCTCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCT
1 AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCT
* *
52450 GCTCCCTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTCAACAAACGTGTCTGCTCCCTAT
66 GCTCCCTATTCATTCAGGGAGTATAGA-ACTCAAACAATCTTCAACAAACGTGTCCGCTCTCTAT
* * *
52514 TCATTCAGGGAGTATAAGACTCAACCAATCTTCAAT
130 TCCTTCAGAGAGTAT-AG----AA-C--TC--GAAT
* * * *
52550 AAACGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCA-ACAAACGGGT-
1 AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTC
*
52613 TCGCTCCCTATTCATTCAGGGAGTATAGAACTCAAACAATCTTCATA-AAATGTGTCCGCTCTCT
65 T-GCTCCCTATTCATTCAGGGAGTATAGAACTCAAACAATCTTCA-ACAAACGTGTCCGCTCTCT
52677 ATTCCTTCAGAGAGTATAGAACTCGA
128 ATTCCTTCAGAGAGTATAGAACTCGA
52703 TCTTCAACAA
Statistics
Matches: 272, Mismatches: 30, Indels: 31
0.82 0.09 0.09
Matches are distributed among these distances:
153 1 0.00
154 126 0.46
155 3 0.01
157 2 0.01
159 3 0.01
160 3 0.01
162 2 0.01
164 6 0.02
165 124 0.46
166 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (155 bp):
AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCT
GCTCCCTATTCATTCAGGGAGTATAGAACTCAAACAATCTTCAACAAACGTGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTCGAAT
Found at i:52545 original size:209 final size:213
Alignment explanation
Indices: 52175--52753 Score: 696
Period size: 209 Copynumber: 2.7 Consensus size: 213
52165 CAATCCTTGG
* * *
52175 CAAACGGGTCCGCTCTCTATCCCTTCAAAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTC
1 CAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTC
* * * *
52240 CGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCATA-AAATGGGTCTGCTCTCTA
66 CGCTCTCTATTCCTTCAGAGAGTATAGAACTC-AACAATCTTCA-ACAAACGTGTCTGCTCCCTA
*
52304 TTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAACGGGTCCACTCTCTATCCCTTCAG
129 TTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCCACTCCCTATCCCTTCAG
*
52368 AGAGTAT-A-GAAC-TC-GAA
193 AGAGTATGACGAACATCTCAA
*
52385 C-AACGGGTCCTCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTC
1 CAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTC
* * * *
52449 TGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTCAACAAACGTGTCTGCTCCCTA
66 CGCTCTCTATTCCTTCAGAGAGTATAGA-ACTC-AACAATCTTCAACAAACGTGTCTGCTCCCTA
* * * * * * *
52513 TTCATTCAGGGAGTATAAGACTC-AACCAATCTTCAATAAACGTGTTCGCTCCCTATTCCTTCAG
129 TTCCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAACAAACGGGTCCACTCCCTATCCCTTCAG
52577 AGAGTATAGGACTCGAACAATCTTCAA
193 AGAGTAT--GA--CGAAC-ATC-TCAA
* * * * * *
52604 CAAACGGGTTCGCTCCCTATTCATTCAGGGAGTATAGAACTCAAACAATCTTCATAAAATGTGTC
1 CAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTC
* *
52669 CGCTCTCTATTCCTTCAGAGAGTATAGAACT---CGATCTTCAACAAACGTGTCCGCTCCCTATT
66 CGCTCTCTATTCCTTCAGAGAGTATAGAACTCAACAATCTTCAACAAACGTGTCTGCTCCCTATT
*
52731 CCTTCAGAGAATATAAGACTCGA
131 CCTTCAGAGAGTATAAGACTCGA
52754 TCTTCATAAA
Statistics
Matches: 314, Mismatches: 38, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
208 4 0.01
209 167 0.53
210 3 0.01
212 1 0.00
215 4 0.01
216 47 0.15
217 3 0.01
219 3 0.01
220 81 0.26
221 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (213 bp):
CAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTC
CGCTCTCTATTCCTTCAGAGAGTATAGAACTCAACAATCTTCAACAAACGTGTCTGCTCCCTATT
CCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCACTCCCTATCCCTTCAGAGA
GTATGACGAACATCTCAA
Found at i:52811 original size:37 final size:37
Alignment explanation
Indices: 52770--52850 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
52760 TAAAATAAGT
*
52770 TTGCTTCACTACTCTTCCGTGAAGGTTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
*
52807 TTGCTTCACTACTCTTCCGTTAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
52844 TTGCTTC
1 TTGCTTC
52851 GAAGGTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
Found at i:54130 original size:7 final size:7
Alignment explanation
Indices: 54115--54188 Score: 51
Period size: 8 Copynumber: 9.7 Consensus size: 7
54105 TGAACTCTCC
*
54115 TTTTATT
1 TTTTCTT
54122 TTTTCTTT
1 TTTTC-TT
54130 TTTTCATT
1 TTTTC-TT
54138 TTTCTCTT
1 TTT-TCTT
*
54146 TTTTCAT
1 TTTTCTT
*
54153 TTTCCATT
1 TTTTC-TT
54161 TTTTCTT
1 TTTTCTT
54168 CTTTT-TT
1 -TTTTCTT
54175 CTTTTCGTT
1 -TTTTC-TT
54184 TTTTC
1 TTTTC
54189 CATCATTTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
7 20 0.36
8 31 0.56
9 4 0.07
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTCTT
Found at i:54139 original size:15 final size:15
Alignment explanation
Indices: 54121--54179 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
54111 CTCCTTTTAT
54121 TTTTTCTTTTTTTCA
1 TTTTTCTTTTTTTCA
54136 TTTTTCTCTTTTTTCA
1 TTTTTCT-TTTTTTCA
* *
54152 TTTTCCATTTTTTCTTCT
1 TTTTTC--TTTTT-TTCA
54170 TTTTTCTTTT
1 TTTTTCTTTT
54180 CGTTTTTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.19
16 17 0.46
17 4 0.11
18 9 0.24
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTTTTCA
Found at i:54155 original size:24 final size:25
Alignment explanation
Indices: 54120--54179 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
54110 TCTCCTTTTA
*
54120 TTTTTTCTTTTTTTCA-TTTTTC-TC
1 TTTTTTC-TTTTTCCATTTTTTCTTC
*
54144 TTTTTTCATTTTCCATTTTTTCTTC
1 TTTTTTCTTTTTCCATTTTTTCTTC
54169 TTTTTTCTTTT
1 TTTTTTCTTTT
54180 CGTTTTTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.19
24 13 0.42
25 12 0.39
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTTCTTTTTCCATTTTTTCTTC
Found at i:54170 original size:42 final size:40
Alignment explanation
Indices: 54120--54263 Score: 127
Period size: 42 Copynumber: 3.5 Consensus size: 40
54110 TCTCCTTTTA
*
54120 TTTT-TTCTTTTTTTCATTTTTCTCTTTTTTCATTTTCCATT
1 TTTTCTTCATTTTTTC-TTTTTCT-TTTTTTCATTTTCCATT
*
54161 TTTTCTTC-TTTTTTC-TTTTCGTTTTTTCCATCATTTTCCTTT
1 TTTTCTTCATTTTTTCTTTTTC-TTTTTT---TCATTTTCCATT
* * *
54203 TTTTC-TCATTTTTTCTTTTTCTTCTTCTCATTTT-TATT
1 TTTTCTTCATTTTTTCTTTTTCTTTTTTTCATTTTCCATT
*
54241 ATTATTTTTCATTTTTTCTTTTT
1 -TT-TTCTTCATTTTTTCTTTTT
54264 TCTCTTTTAT
Statistics
Matches: 87, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
38 2 0.02
39 19 0.22
40 3 0.03
41 28 0.32
42 30 0.34
43 5 0.06
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.74
Consensus pattern (40 bp):
TTTTCTTCATTTTTTCTTTTTCTTTTTTTCATTTTCCATT
Found at i:54173 original size:41 final size:39
Alignment explanation
Indices: 54119--54263 Score: 120
Period size: 41 Copynumber: 3.6 Consensus size: 39
54109 CTCTCCTTTT
54119 ATTTTTTCT--TTTTTTCATTTTTCTCTTTTTTCATTTTCC
1 ATTTTTTCTCATTTTTTC-TTTTTCT-TTTTTTCATTTTCC
54158 ATTTTTTCTTC-TTTTTTC-TTTTCGTTTTTTCCATCATTTTCC
1 ATTTTTTC-TCATTTTTTCTTTTTC-TTTTTT---TCATTTTCC
* * * *
54200 TTTTTTTCTCATTTTTTCTTTTTCTTCTTCTCATTTT-T
1 ATTTTTTCTCATTTTTTCTTTTTCTTTTTTTCATTTTCC
*
54238 ATTATTATTTTTCATTTTTTCTTTTT
1 A-T-TT-TTTCTCATTTTTTCTTTTT
54264 TCTCTTTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 20
0.77 0.05 0.17
Matches are distributed among these distances:
39 26 0.29
40 4 0.04
41 27 0.30
42 27 0.30
43 5 0.06
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.74
Consensus pattern (39 bp):
ATTTTTTCTCATTTTTTCTTTTTCTTTTTTTCATTTTCC
Found at i:54180 original size:24 final size:23
Alignment explanation
Indices: 54130--54282 Score: 81
Period size: 21 Copynumber: 6.7 Consensus size: 23
54120 TTTTTTCTTT
54130 TTTTCA-TTTTTC-TCTTTTTTC
1 TTTTCATTTTTTCTTCTTTTTTC
54151 ATTTTCCATTTTTTCTTCTTTTTTC
1 -TTTT-CATTTTTTCTTCTTTTTTC
* * *
54176 TTTTCGTTTTTTCCATCATTTTCCTTTT
1 TTTTCATTTTTT-CTTC--TTT--TTTC
*
54204 TTTCTCATTTTTTCTT-TTTCTTC
1 TTT-TCATTTTTTCTTCTTTTTTC
* * * *
54227 TTCTCA-TTTTT-AT-TATTAT-
1 TTTTCATTTTTTCTTCTTTTTTC
*
54246 TTTTCATTTTTTCTT-TTTTCTC
1 TTTTCATTTTTTCTTCTTTTTTC
*
54268 TTTT-ATTTCTTCTTC
1 TTTTCATTTTTTCTTC
54283 AAGCGAAATA
Statistics
Matches: 101, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
19 5 0.05
20 9 0.09
21 19 0.19
22 11 0.11
23 13 0.13
24 13 0.13
25 12 0.12
26 3 0.03
28 8 0.08
29 8 0.08
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.73
Consensus pattern (23 bp):
TTTTCATTTTTTCTTCTTTTTTC
Found at i:54203 original size:18 final size:17
Alignment explanation
Indices: 54176--54214 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
54166 TTCTTTTTTC
*
54176 TTTTCGTTTTTTCCATCA
1 TTTTCCTTTTTTCC-TCA
*
54194 TTTTCCTTTTTTTCTCA
1 TTTTCCTTTTTTCCTCA
54211 TTTT
1 TTTT
54215 TTCTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCCTTTTTTCCTCA
Found at i:65570 original size:11 final size:11
Alignment explanation
Indices: 65554--65587 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
65544 CAATAGTGTT
*
65554 TCCTTTGGCAC
1 TCCTTTTGCAC
65565 TCCTTTTGCAC
1 TCCTTTTGCAC
65576 TCCTTTTGCAC
1 TCCTTTTGCAC
65587 T
1 T
65588 TGTAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.09, C:0.35, G:0.12, T:0.44
Consensus pattern (11 bp):
TCCTTTTGCAC
Found at i:71688 original size:40 final size:40
Alignment explanation
Indices: 71634--71741 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 40
71624 AAACATACCT
** *
71634 AAAATTTAATTTTTGTTTCATTTTAGTAGCCCGCCATTAA
1 AAAATTTAGCTTTTGTTTCATTTTAGTAGCACGCCATTAA
* * *
71674 AAAATTTAGCTTTTGTTTCATTTTAGTATCATGTCATTAA
1 AAAATTTAGCTTTTGTTTCATTTTAGTAGCACGCCATTAA
* *
71714 AAAAATTAGCTTTTGTTTCATTTCAGTA
1 AAAATTTAGCTTTTGTTTCATTTTAGTA
71742 CCTCGTTCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (40 bp):
AAAATTTAGCTTTTGTTTCATTTTAGTAGCACGCCATTAA
Found at i:72022 original size:25 final size:25
Alignment explanation
Indices: 71968--72031 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
71958 AGTTTACCTA
*
71968 ATTATTTTATTTTTGTTAAAATTTT
1 ATTATTTTATTTTTGTTAAAATATT
*
71993 A-TATTTTGTTTTTGTTAAAATATT
1 ATTATTTTATTTTTGTTAAAATATT
72017 ATTATTTTAATTTTT
1 ATTATTTT-ATTTTT
72032 ATTCAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 22 0.65
25 7 0.21
26 5 0.15
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (25 bp):
ATTATTTTATTTTTGTTAAAATATT
Found at i:72371 original size:19 final size:18
Alignment explanation
Indices: 72316--72367 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
72306 TTTGGGCCAC
72316 ATTGTAAAAT-TATGATAA
1 ATTGTAAAATATAT-ATAA
* * *
72334 CTTGTAAGACAGTATATAA
1 ATTGTAAAATA-TATATAA
72353 ATTGTAAAATATATA
1 ATTGTAAAATATATA
72368 ATAATTAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 11 0.42
19 12 0.46
20 3 0.12
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.37
Consensus pattern (18 bp):
ATTGTAAAATATATATAA
Found at i:73421 original size:123 final size:121
Alignment explanation
Indices: 73202--73601 Score: 425
Period size: 122 Copynumber: 3.3 Consensus size: 121
73192 AGTTTTAGTT
** * * *
73202 CGTTTTAGTATTTAAACTTT-TATTTCTTTAAAATTATATCTAACATTTAGTTTTTGTTTCATTT
1 CGTTTTAGTACCTAAACTTTCAATTTTTTTAAAATCATA-CTAACATTTAGTTTTTGTTTCATTT
* * *
73266 TAGTACTCCCAACTGTTAAAACT-TTAACGCGTTTAGTACCTAAACTATATATTTTTGTC
65 TA--ACACCCCACTGTTAAAAATCTTAACGCGTTTAGTACCTAAACTATA-ATTTTTGTC
*
73325 CGTTTTAGTACTTAAACTTTCAATTTTTTTAAAATCATACATAACATTTAGTTTTTGTTTCATTT
1 CGTTTTAGTACCTAAACTTTCAATTTTTTTAAAATCATAC-TAACATTTAGTTTTTGTTTCATTT
*
73390 TAACACCCCACTGTTAAAAATCTTAACGCGTTT-GTACCTAAACTATAATTTTTTATC
65 TAACACCCCACTGTTAAAAATCTTAACGCGTTTAGTACCTAAACTATAA-TTTTTGTC
** * * * **
73447 TATTTTAGTACCTAAACTTCCAA-TTTTTTAAAACCATGCCTAACATTTAGTTTTAATTTCATTT
1 CGTTTTAGTACCTAAACTTTCAATTTTTTTAAAATCAT-ACTAACATTTAGTTTTTGTTTCATTT
** * * * * * * *
73511 TAGTACCCCACT-ATGAAAACCTTAACGTGTTTAGTACTTAAACTATCAATTTTGGTT
65 TAACACCCCACTGTTAAAAATCTTAACGCGTTTAGTACCTAAACTAT-AATTTTTGTC
* *
73568 CG-GTTAGTACCTAAGCTTTCAATTTTTTTTAAAA
1 CGTTTTAGTACCTAAACTTTCAA-TTTTTTTAAAA
73602 AATTTAATGC
Statistics
Matches: 237, Mismatches: 31, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
120 33 0.14
121 63 0.27
122 69 0.29
123 31 0.13
124 41 0.17
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (121 bp):
CGTTTTAGTACCTAAACTTTCAATTTTTTTAAAATCATACTAACATTTAGTTTTTGTTTCATTTT
AACACCCCACTGTTAAAAATCTTAACGCGTTTAGTACCTAAACTATAATTTTTGTC
Found at i:73595 original size:121 final size:119
Alignment explanation
Indices: 73194--73601 Score: 408
Period size: 121 Copynumber: 3.3 Consensus size: 119
73184 AAATTATCAG
** * * ** *
73194 TTTTAGTTCGTTTTAGTATTTAAACTTT-TATTTCTTTAAAATTATATCTAACATTTAGTTTTTG
1 TTTT-GTTCG-TTTAGTACCTAAACTTTCAATTTTTTTAAAACCATACCTAACATTTAGTTTTTG
* * *
73258 TTTCATTTTAGTACTCCCAACTGTTAAAACTTTAACGCGTTTAGTACCTAAACTATATA
64 TTTCATTTTAGTAC-CCC-ACTATAAAAACCTTAACGCGTTTAGTACCTAAACTATA-A
* * * *
73317 TTTTTGTCCGTTTTAGTACTTAAACTTTCAATTTTTTTAAAATCATACATAACATTTAGTTTTTG
1 -TTTTGTTCG-TTTAGTACCTAAACTTTCAATTTTTTTAAAACCATACCTAACATTTAGTTTTTG
** * *
73382 TTTCATTTTAACACCCCACTGTTAAAAATCTTAACGCGTTT-GTACCTAAACTATAA
64 TTTCATTTTAGTACCCCACT-ATAAAAACCTTAACGCGTTTAGTACCTAAACTATAA
* * * * *
73438 TTTTTTATCTATTTTAGTACCTAAACTTCCAA-TTTTTTAAAACCATGCCTAACATTTAGTTTTA
1 TTTTGT-TC--GTTTAGTACCTAAACTTTCAATTTTTTTAAAACCATACCTAACATTTAGTTTTT
* * * *
73502 ATTTCATTTTAGTACCCCACTATGAAAACCTTAACGTGTTTAGTACTTAAACTATCAA
63 GTTTCATTTTAGTACCCCACTATAAAAACCTTAACGCGTTTAGTACCTAAACTAT-AA
* *
73560 TTTTGGTTCGGTTAGTACCTAAGCTTTCAATTTTTTTTAAAA
1 TTTT-GTTCGTTTAGTACCTAAACTTTCAA-TTTTTTTAAAA
73602 AATTTAATGC
Statistics
Matches: 239, Mismatches: 35, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
120 38 0.16
121 60 0.25
122 53 0.22
123 41 0.17
124 47 0.20
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (119 bp):
TTTTGTTCGTTTAGTACCTAAACTTTCAATTTTTTTAAAACCATACCTAACATTTAGTTTTTGTT
TCATTTTAGTACCCCACTATAAAAACCTTAACGCGTTTAGTACCTAAACTATAA
Found at i:81075 original size:41 final size:41
Alignment explanation
Indices: 81030--81130 Score: 157
Period size: 41 Copynumber: 2.5 Consensus size: 41
81020 ATTCACGTTG
* *
81030 CATTTCGCATTGCGATAGTTGAAAATCGCGTTACGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTC
**
81071 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTC
*
81112 TATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
81131 CTACAGTTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.40
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTC
Found at i:81101 original size:21 final size:21
Alignment explanation
Indices: 81034--81103 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
81024 ACGTTGCATT
*
81034 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** ** **
81055 TCGCGTTACG-TTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
81075 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
81096 TCGCGTTG
1 TCGCGTTG
81104 TGATTTTCTA
Statistics
Matches: 33, Mismatches: 15, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:81133 original size:20 final size:20
Alignment explanation
Indices: 81072--81133 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
81062 ACGTTTTTCC
81072 ATTTCGCGTTGCGATAGT-T
1 ATTTCGCGTTGCGATAGTCT
** * **
81091 GAAAATCGCGTTGTGATTTTCT
1 --ATTTCGCGTTGCGATAGTCT
81113 ATTTCGCGTTGCGATAGTCT
1 ATTTCGCGTTGCGATAGTCT
81133 A
1 A
81134 CAGTTGTCGT
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
20 16 0.53
21 13 0.43
22 1 0.03
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTCGCGTTGCGATAGTCT
Found at i:81250 original size:6 final size:6
Alignment explanation
Indices: 81239--81281 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
81229 AGACACGTAT
81239 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC G
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC G
81282 GACGGCGGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.49, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:81842 original size:6 final size:6
Alignment explanation
Indices: 81767--81845 Score: 108
Period size: 6 Copynumber: 13.5 Consensus size: 6
81757 TCTCGTCTAG
* * * *
81767 GGTCG- GGTCG- GGTCGG GGTCGG GGTCGG GGTCGG GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
81813 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
81846 AATACGTGTC
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
5 10 0.14
6 62 0.86
ACGTcount: A:0.00, C:0.16, G:0.57, T:0.27
Consensus pattern (6 bp):
GGTCGT
Found at i:82369 original size:2 final size:2
Alignment explanation
Indices: 82362--82398 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
82352 TCAAAACACA
82362 AT AT 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 AT AT A
82399 GCAACCCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82587 original size:44 final size:44
Alignment explanation
Indices: 82539--82627 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
82529 AAGCACGAAC
82539 CAAACAACCTTTGTGATAAAGAAATTATTAATATTCTCTAAGGA
1 CAAACAACCTTTGTGATAAAGAAATTATTAATATTCTCTAAGGA
82583 CAAACAACCTTTGTGATAAAGAAATTATTAATATTCTCTAAGGA
1 CAAACAACCTTTGTGATAAAGAAATTATTAATATTCTCTAAGGA
82627 C
1 C
82628 TTGAGTTCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (44 bp):
CAAACAACCTTTGTGATAAAGAAATTATTAATATTCTCTAAGGA
Found at i:82763 original size:31 final size:30
Alignment explanation
Indices: 82653--82773 Score: 188
Period size: 30 Copynumber: 4.0 Consensus size: 30
82643 AAAGGTATGA
82653 GCCTTTAATGTCAAAAGATTGAAAGTTATC
1 GCCTTTAATGTCAAAAGATTGAAAGTTATC
* *
82683 GCCTTTAATATCAAAAGATTGAAAATTATC
1 GCCTTTAATGTCAAAAGATTGAAAGTTATC
* *
82713 ACCTTTAATGTTAAAAGATTGAAAGTTATC
1 GCCTTTAATGTCAAAAGATTGAAAGTTATC
*
82743 GCCTTTAATGTCAAAAAGATTAAAAGTTATC
1 GCCTTTAATGTC-AAAAGATTGAAAGTTATC
82774 TTTGAACAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 64 0.79
31 17 0.21
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (30 bp):
GCCTTTAATGTCAAAAGATTGAAAGTTATC
Found at i:83575 original size:4 final size:4
Alignment explanation
Indices: 83566--83590 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
83556 GGGTAGGGTA
83566 GGAG GGAG GGAG GGAG GGAG GGAG G
1 GGAG GGAG GGAG GGAG GGAG GGAG G
83591 TAGCATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GGAG
Done.