Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002948.1 Hibiscus syriacus cultivar Beakdansim tig00006084_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: 40900
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:7229 original size:22 final size:22
Alignment explanation
Indices: 7203--7245 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
7193 TATTTTAGAA
* *
7203 AAATATAAATCATATACTTTTG
1 AAATATAAATAATATAATTTTG
*
7225 AAATATATATAATATAATTTT
1 AAATATAAATAATATAATTTT
7246 AGTAACATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATATAAATAATATAATTTTG
Found at i:7319 original size:25 final size:25
Alignment explanation
Indices: 7281--7329 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
7271 ATTTAAAATA
* *
7281 TATATATAAGTTTGAAAGTATATAT
1 TATATACAAGTTTGAAAATATATAT
*
7306 TATATACAATTTTGAAAATATATA
1 TATATACAAGTTTGAAAATATATA
7330 ATTTTGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (25 bp):
TATATACAAGTTTGAAAATATATAT
Found at i:7346 original size:18 final size:18
Alignment explanation
Indices: 7304--7347 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 18
7294 GAAAGTATAT
*
7304 ATTATATACAATTTTGAA
1 ATTATATATAATTTTGAA
7322 A--ATATATAATTTTGAA
1 ATTATATATAATTTTGAA
7338 ATTATATATA
1 ATTATATATA
7348 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 15 0.65
18 8 0.35
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (18 bp):
ATTATATATAATTTTGAA
Found at i:7494 original size:14 final size:15
Alignment explanation
Indices: 7477--7509 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
7467 ATTTCCATTG
7477 TTTTATTTT-ATTAT
1 TTTTATTTTGATTAT
7491 TTTTATTTTGATTAT
1 TTTTATTTTGATTAT
7506 TTTT
1 TTTT
7510 TAGGTCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTATTTTGATTAT
Found at i:12694 original size:20 final size:23
Alignment explanation
Indices: 12632--12774 Score: 83
Period size: 22 Copynumber: 6.5 Consensus size: 23
12622 TTTTGTCCCC
*
12632 TATATATATAT--TTTTTATTTAT
1 TATATATATATCATTATT-TTTAT
* *
12654 T-TACTATAT-TCCTTTTTTTTAT
1 TATA-TATATATCATTATTTTTAT
12676 T-TATAT-TAT-ATTATTTTTAT
1 TATATATATATCATTATTTTTAT
* *
12696 TATATATATATCATTATATATA-
1 TATATATATATCATTATTTTTAT
* *
12718 TATATATATAT-A-TATATATAT
1 TATATATATATCATTATTTTTAT
* *
12739 ATATATATATAT-ATATATATATAT
1 -TATATATATATCAT-TATTTTTAT
12763 ATATATATATAT
1 -TATATATATAT
12775 ATATATGTAT
Statistics
Matches: 106, Mismatches: 4, Indels: 20
0.82 0.03 0.15
Matches are distributed among these distances:
20 19 0.18
21 13 0.12
22 40 0.38
23 13 0.12
24 21 0.20
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATATATATCATTATTTTTAT
Found at i:12696 original size:14 final size:14
Alignment explanation
Indices: 12672--12778 Score: 72
Period size: 16 Copynumber: 7.1 Consensus size: 14
12662 TTCCTTTTTT
12672 TTATTTATATTATA
1 TTATTTATATTATA
*
12686 TTATTTTTATTATA
1 TTATTTATATTATA
*
12700 -TATATATCATTATA
1 TTATTTAT-ATTATA
*
12714 TATATATATATATATA
1 T-TATTTATAT-TATA
*
12730 TATATATATATATATA
1 T-TATTTATAT-TATA
*
12746 TATATATATATATATA
1 T-TATTTATAT-TATA
*
12762 TATATATATATATATA
1 T-TATTTATAT-TATA
12778 T
1 T
12779 ATGTATGTCT
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
13 5 0.06
14 19 0.22
15 2 0.02
16 60 0.70
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:12703 original size:2 final size:2
Alignment explanation
Indices: 12696--12780 Score: 154
Period size: 2 Copynumber: 42.5 Consensus size: 2
12686 TTATTTTTAT
12696 TA TA TA TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12738 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
12780 T
1 T
12781 GTATGTCTGT
Statistics
Matches: 81, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.01
2 78 0.96
3 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12936 original size:16 final size:17
Alignment explanation
Indices: 12900--12950 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
12890 TTTGTTTTTA
*
12900 TTTATTTATA-TA-TAT
1 TTTATTTTTACTATTAT
*
12915 TATATTTTTACT-TTAT
1 TTTATTTTTACTATTAT
*
12931 TTTATTTTTTCTATTAT
1 TTTATTTTTACTATTAT
12948 TTT
1 TTT
12951 TTTCTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.28
16 14 0.48
17 7 0.24
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTTACTATTAT
Found at i:12939 original size:17 final size:17
Alignment explanation
Indices: 12895--12950 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
12885 CTATTTTTGT
*
12895 TTTTATTTATTTA-TATA
1 TTTTATTT-TTTACTTTA
*
12912 TATTATATTTTTACTTTA
1 TTTTAT-TTTTTACTTTA
12930 TTTTATTTTTT-CTATTA
1 TTTTATTTTTTACT-TTA
12947 TTTT
1 TTTT
12951 TTTCTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 21 0.64
18 10 0.30
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTACTTTA
Found at i:13098 original size:16 final size:16
Alignment explanation
Indices: 13053--13098 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
13043 TATGTACACA
13053 TTATTTTTATT-CCTTT
1 TTATTTTT-TTACCTTT
13069 TTAATTTCTTTTACCTTT
1 TT-ATTT-TTTTACCTTT
13087 TTATTTTTTTAC
1 TTATTTTTTTAC
13099 TCCATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 8 0.30
17 10 0.37
18 9 0.33
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTTTTTTACCTTT
Found at i:13217 original size:27 final size:28
Alignment explanation
Indices: 13155--13218 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 28
13145 ATTCATTTAT
*
13155 TTTTATTT-TTTTATTATTTTTTACATG
1 TTTTATTTATTTTATCATTTTTTACATG
* * *
13182 TTTT-GTTATTTT-TCATTTTTTTCTTG
1 TTTTATTTATTTTATCATTTTTTACATG
13208 TTTTATTTATT
1 TTTTATTTATT
13219 ATTCTCACGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 17 0.57
27 13 0.43
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (28 bp):
TTTTATTTATTTTATCATTTTTTACATG
Found at i:16300 original size:14 final size:13
Alignment explanation
Indices: 16278--16331 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
16268 CAATCAGAAC
16278 AAAAA-AAAGAGA
1 AAAAACAAAGAGA
16290 AAAAAGCAAAGAGA
1 AAAAA-CAAAGAGA
16304 AAATAA-AAAGAGAA
1 AAA-AACAAAGAG-A
16318 AAAAACAAAG-GA
1 AAAAACAAAGAGA
16330 AA
1 AA
16332 CTTAAAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.22
13 9 0.24
14 18 0.49
15 2 0.05
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAACAAAGAGA
Found at i:16331 original size:13 final size:13
Alignment explanation
Indices: 16273--16331 Score: 66
Period size: 13 Copynumber: 4.4 Consensus size: 13
16263 AGATTCAATC
16273 AGAACAAAAAAAAG
1 AGAA-AAAAAAAAG
*
16287 AGAAAAAAGCAAAG
1 AGAAAAAA-AAAAG
*
16301 AGAAAATAAAAAG
1 AGAAAAAAAAAAG
16314 AGAAAAAAACAAAG
1 AGAAAAAAA-AAAG
16328 -GAAA
1 AGAAA
16332 CTTAAAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
13 20 0.51
14 19 0.49
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (13 bp):
AGAAAAAAAAAAG
Found at i:16344 original size:25 final size:27
Alignment explanation
Indices: 16281--16331 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
16271 TCAGAACAAA
*
16281 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAAACAAAGAGAAAAT
16308 AAAAAGAGAAAAAAACAAAG-GAAA
1 AAAAAGAGAAAAAAACAAAGAGAAA
16332 CTTAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (27 bp):
AAAAAGAGAAAAAAACAAAGAGAAAAT
Found at i:16523 original size:69 final size:69
Alignment explanation
Indices: 16406--16542 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 69
16396 ATTCAAACTG
* *
16406 TGAGATTGATCAAGCACAATCATTTACGAATCACTGACCCACTTCACTCGAAGATCATAGAGCAT
1 TGAGATTGATCAAGCACAATCATTTACGAATCACTGAACCACTCCACTCGAAGATCATAGAGCAT
16471 CAAA
66 CAAA
* *
16475 TGAGATTGATCAAGCACAATCATTT-CTGAATTACTGAATCACTCCACTCGAAGATCATAGAGCA
1 TGAGATTGATCAAGCACAATCATTTAC-GAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
16539 TCAA
65 TCAA
16543 GAGAGACACA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 1 0.02
69 62 0.98
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (69 bp):
TGAGATTGATCAAGCACAATCATTTACGAATCACTGAACCACTCCACTCGAAGATCATAGAGCAT
CAAA
Found at i:18059 original size:37 final size:37
Alignment explanation
Indices: 18007--18078 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
17997 TAAAAAGAAG
* *
18007 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAA
* *
18044 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
18079 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:18141 original size:36 final size:37
Alignment explanation
Indices: 18094--18178 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
18084 ATTGAAAACA
* * *
18094 TTTCCCTTGAAAT-GAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAAATTTTGCCTCCCTTGAGATAG
18130 TTTCCCTTGAAATAAAATTTTGCCTCCCTTGAGATAG
1 TTTCCCTTGAAATAAAATTTTGCCTCCCTTGAGATAG
*
18167 TTTCTCTTGAAA
1 TTTCCCTTGAAA
18179 CATAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 13 0.30
37 31 0.70
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTCCCTTGAAATAAAATTTTGCCTCCCTTGAGATAG
Found at i:18183 original size:102 final size:101
Alignment explanation
Indices: 18007--18383 Score: 441
Period size: 102 Copynumber: 3.7 Consensus size: 101
17997 TAAAAAGAAG
* *
18007 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA-AAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
18072 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
65 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
* *
18109 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAATAAAATTTTGCCTCCCTTGAGATAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA-AAAATTTTGTCTCCCTTGAGACAGTTTCTCT
18174 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
65 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
* * * * * *
18211 ATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTATCTT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
* * ** *** * *
18276 GAAACA-AAATATTTGAATATGTTTTATTTGAAACAT
66 GAAACATAAACA-TTGAAAACATTTCCCTTGAAATAA
** * * ** ** * *
18312 ATTTAATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTT-GAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
18377 TGAAACA
65 TGAAACA
18384 AATTTCGTCT
Statistics
Matches: 240, Mismatches: 33, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
100 4 0.02
101 72 0.30
102 164 0.68
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (101 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
GAAACATAAACATTGAAAACATTTCCCTTGAAATAA
Found at i:18243 original size:36 final size:36
Alignment explanation
Indices: 18196--18453 Score: 255
Period size: 36 Copynumber: 7.3 Consensus size: 36
18186 ATTGAAAACA
* *
18196 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
18232 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * *
18268 TTTATCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* * ** *
18297 TTT-TATTTGAAACATATTTAATCTCCCTTGAGACAG
1 TTTCT-CTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * *
18333 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
18370 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
18406 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
18442 TTTCCCTTGAAA
1 TTTCTCTTGAAA
18454 AAAAATCTTT
Statistics
Matches: 184, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
28 3 0.02
29 16 0.09
30 2 0.01
35 1 0.01
36 130 0.71
37 32 0.17
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:18397 original size:21 final size:21
Alignment explanation
Indices: 18372--18436 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
18362 TGAGACAGTT
18372 TCTCTTGAAACAAATTTCGTC
1 TCTCTTGAAACAAATTTCGTC
* *
18393 TCTCTTGAGAC--A----GTT
1 TCTCTTGAAACAAATTTCGTC
18408 TCTCTTGAAACAAATTTCGTC
1 TCTCTTGAAACAAATTTCGTC
18429 TCTCTTGA
1 TCTCTTGA
18437 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 12 0.35
17 1 0.03
19 1 0.03
21 20 0.59
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTCGTC
Found at i:18451 original size:72 final size:73
Alignment explanation
Indices: 18303--18453 Score: 214
Period size: 73 Copynumber: 2.1 Consensus size: 73
18293 TATGTTTTAT
* * * * *
18303 TTGAAACATATTTAATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTAATCTCCCTTGAGACAGTTTCTCTTGAAACTAAATTTCGTCTCTCTTGAGAC
*
18368 AGTTTCTC
66 AGTTTCCC
** *
18376 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTCTCTTGAGAC
1 TTGAAACAAATTTAATCTCCCTTGAGACAGTTTCTCTTGAAACTAAATTTCGTCTCTCTTGAGAC
18440 AGTTTCCC
66 AGTTTCCC
18448 TTGAAA
1 TTGAAA
18454 AAAAATCTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
72 32 0.46
73 37 0.54
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (73 bp):
TTGAAACAAATTTAATCTCCCTTGAGACAGTTTCTCTTGAAACTAAATTTCGTCTCTCTTGAGAC
AGTTTCCC
Found at i:18498 original size:174 final size:174
Alignment explanation
Indices: 18196--18511 Score: 458
Period size: 174 Copynumber: 1.8 Consensus size: 174
18186 ATTGAAAACA
* *
18196 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTT
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTT
* * * *
18261 GAGACAATTTATCTTGAAACAAAATATTTGAATATGTTTTATTTGAAACATATTTAATCTCCCTT
66 GAGACAATTTACCTTGAAAAAAAATATTTGAATATGTTTTATCTGAAACAAATTTAATCTCCCTT
18326 GAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
131 GAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
* *
18370 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTT
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTT
* * * * **
18435 GAGACAGTTTCCCTTGAAAAAAAATCTTTGAAT-T-TATTTCTCCT-AATACAAATTTTGTCTCC
66 GAGACAATTTACCTTGAAAAAAAATATTTGAATATGT-TTTAT-CTGAA-ACAAATTTAATCTCC
18497 CTTGAGACAGTTTCT
128 CTTGAGACAGTTTCT
18512 CTTGAAACAC
Statistics
Matches: 125, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
172 1 0.01
173 7 0.06
174 117 0.94
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (174 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTT
GAGACAATTTACCTTGAAAAAAAATATTTGAATATGTTTTATCTGAAACAAATTTAATCTCCCTT
GAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
Found at i:18510 original size:65 final size:67
Alignment explanation
Indices: 18406--18577 Score: 208
Period size: 65 Copynumber: 2.6 Consensus size: 67
18396 CTTGAGACAG
* * * * **
18406 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAA-A-AAAATCTTTGAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATT
18469 TA
66 TA
* *
18471 TTTCTCC-TAATACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
1 TTTC-CCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAAT
18535 TTA
65 TTA
*
18538 TTTCCCTTAAAACAAAATTTTG-CTTCCCTTGAGACCGTTT
1 TTTCCCTTAAAAC-AAATTTTGTC-TCCCTTGAGACAGTTT
18578 TTCATGAAAC
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
65 40 0.44
66 4 0.04
67 24 0.26
68 23 0.25
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.40
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATT
TA
Found at i:19464 original size:111 final size:111
Alignment explanation
Indices: 19265--19469 Score: 304
Period size: 111 Copynumber: 1.8 Consensus size: 111
19255 TTCCAGTTTC
* * *
19265 AGAGCCAATTTCAACTTCATAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAA
**
19330 TGAAGGGGCGACTGGTTGTCAACAAACAACTTTTCAGTTTCATTTT
66 CAAAGGGGCGACTGGTTGTCAACAAACAACTTTTCAGTTTCATTTT
* * *
19376 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAA
* *
19441 CAAAGGGGCG-GTTGTCTGTCAACAAACAA
66 CAAAGGGGCGACTGGT-TGTCAACAAACAA
19470 TTTCCCAGTT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
110 3 0.04
111 80 0.96
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (111 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAA
CAAAGGGGCGACTGGTTGTCAACAAACAACTTTTCAGTTTCATTTT
Found at i:20909 original size:14 final size:14
Alignment explanation
Indices: 20890--20929 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
20880 TATTCCTTTT
20890 TTATTTATATTATA
1 TTATTTATATTATA
*
20904 TTATTTTTATTATA
1 TTATTTATATTATA
20918 TATATCTTATAT
1 T-TAT-TTATAT
20930 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:20958 original size:25 final size:22
Alignment explanation
Indices: 20910--20959 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
20900 TATATTATTT
* *
20910 TTATTATATATATCTTATATCA
1 TTATTATATATATATTAGATCA
20932 TTATATATATATATATATAGATGCA
1 TTAT-TATATATATAT-TAGAT-CA
20957 TTA
1 TTA
20960 ATTTTTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 10 0.43
24 4 0.17
25 5 0.22
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (22 bp):
TTATTATATATATATTAGATCA
Found at i:21007 original size:18 final size:18
Alignment explanation
Indices: 20984--21120 Score: 87
Period size: 18 Copynumber: 8.0 Consensus size: 18
20974 ACTATGTATA
20984 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
* *
21002 TATATTTTATACGTTTATAT
1 TATATTTT-TTC-TTAATAT
*
21022 ATATATATTTTCTTAATAT
1 -TATATTTTTTCTTAATAT
*
21041 TCTATTTTTT-TT--TAT
1 TATATTTTTTCTTAATAT
* *
21056 T-TA-TTTAT-AT-ATAT
1 TATATTTTTTCTTAATAT
* * *
21070 TATATTTTTACTTTATTT
1 TATATTTTTTCTTAATAT
*
21088 TAT-TTTTTTC-TATTAT
1 TATATTTTTTCTTAATAT
21104 TAT-TTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
21121 CATGTATATC
Statistics
Matches: 92, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
13 5 0.05
14 6 0.07
15 6 0.07
16 16 0.17
17 14 0.15
18 22 0.24
19 8 0.09
20 8 0.09
21 7 0.08
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:21009 original size:45 final size:43
Alignment explanation
Indices: 20956--21120 Score: 122
Period size: 39 Copynumber: 4.0 Consensus size: 43
20946 ATATAGATGC
*
20956 ATTA-ATTTTTCTCTATTTACTATGTATATATATTTTTTCTTAAT
1 ATTATATTTTTTTCTATTTA-TAT-TATATATATTTTTTCTTAAT
* * *
21000 ATTATATTTTATAC-GTTTATA-TATATATA--TTTTCTTAAT
1 ATTATATTTTTTTCTATTTATATTATATATATTTTTTCTTAAT
* * *
21039 ATTCTATTTTTTTTTATTTAT-TTATATATATTATATTT-TTACT
1 ATTATATTTTTTTCTATTTATATTATATATATT-T-TTTCTTAAT
* *
21082 -TTAT-TTTATTT-T-TTTCTATTAT-TAT-TTTTTTCTTAAT
1 ATTATATTTTTTTCTATTTATATTATATATATTTTTTCTTAAT
21119 AT
1 AT
21121 CATGTATATC
Statistics
Matches: 97, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
36 3 0.03
37 5 0.05
38 3 0.03
39 27 0.28
40 18 0.19
41 14 0.14
42 3 0.03
43 7 0.07
44 11 0.11
45 6 0.06
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (43 bp):
ATTATATTTTTTTCTATTTATATTATATATATTTTTTCTTAAT
Found at i:21104 original size:44 final size:43
Alignment explanation
Indices: 21015--21101 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 43
21005 ATTTTATACG
*
21015 TTTATATATATATATTTTCTTAATATTCTATTTTTTTTTATTTA
1 TTTATATATATATATTTTCTT-ATATTCTATTTTTTTCTATTTA
*
21059 TTTATATATATTATATTTTTACTT-TATTTTATTTTTTTCTATT
1 TTTATATATA-TATA-TTTT-CTTATATTCTATTTTTTTCTATT
21102 ATTATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
44 10 0.26
45 21 0.55
46 4 0.11
47 3 0.08
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (43 bp):
TTTATATATATATATTTTCTTATATTCTATTTTTTTCTATTTA
Found at i:21106 original size:16 final size:15
Alignment explanation
Indices: 21038--21114 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 15
21028 ATTTTCTTAA
* *
21038 TATTCTATTTTTTTT
1 TATTTTATTTTTTTC
* * *
21053 TA-TTTATTTATATA
1 TATTTTATTTTTTTC
*
21067 TATTATATTTTTACTT-
1 TATTTTATTTTT--TTC
21083 TATTTTATTTTTTTC
1 TATTTTATTTTTTTC
21098 TATTATTATTTTTTTC
1 TATT-TTATTTTTTTC
21114 T
1 T
21115 TAATATCATG
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
14 12 0.24
15 13 0.27
16 23 0.47
17 1 0.02
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTATTTTTTTC
Found at i:21246 original size:18 final size:17
Alignment explanation
Indices: 21214--21257 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
21204 TGTACATATT
21214 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
21231 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
21249 ATTTTTTTA
1 ATTTTTTTA
21258 ATCCATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:21365 original size:26 final size:25
Alignment explanation
Indices: 21311--21366 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
21301 CATTTTATTC
21311 ATTT-TTTTTATTTTTACGTGTTTT
1 ATTTATTTTTATTTTTACGTGTTTT
* * *
21335 -GTTATTTTTCATTTTTTCTTGTTTT
1 ATTTATTTTT-ATTTTTACGTGTTTT
21360 ATTTATT
1 ATTTATT
21367 ATTCTCACGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.08
24 5 0.20
25 13 0.52
26 5 0.20
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (25 bp):
ATTTATTTTTATTTTTACGTGTTTT
Found at i:23055 original size:41 final size:41
Alignment explanation
Indices: 22969--23058 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
22959 AATATATTTT
* * **
22969 AATTTGAAATATTAAAATATATAGACATCATTTACTATTTT
1 AATTTAAAATATTAAAATATATAGACATCATTTAATATTCA
*
23010 AATTTAAAATATTCAAAATATATA-ATTATC-TTTAATATTCA
1 AATTTAAAATATT-AAAATATATAGA-CATCATTTAATATTCA
23051 AATTTAAA
1 AATTTAAA
23059 TAGATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 29 0.69
42 13 0.31
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (41 bp):
AATTTAAAATATTAAAATATATAGACATCATTTAATATTCA
Found at i:26596 original size:27 final size:27
Alignment explanation
Indices: 26560--26612 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
26550 TTTTTGAAAT
* *
26560 ATATTTTATTCTTATCTTAAGTTAAAA
1 ATATTTTATTCTTACCTTAACTTAAAA
*
26587 ATATTTTATTTTTACCTTAACTTAAA
1 ATATTTTATTCTTACCTTAACTTAAA
26613 TATTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (27 bp):
ATATTTTATTCTTACCTTAACTTAAAA
Found at i:26624 original size:25 final size:27
Alignment explanation
Indices: 26583--26652 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
26573 ATCTTAAGTT
26583 AAAAATATTT-TATTTTTACCT-TAAC-
1 AAAAATATTTATA-TTTTACCTATAACA
** **
26608 TTAAATATTTATATTTTATTTATAACA
1 AAAAATATTTATATTTTACCTATAACA
26635 AAAAATATTTATATTTTA
1 AAAAATATTTATATTTTA
26653 TTCTTTTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 14 0.39
26 6 0.17
27 16 0.44
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
AAAAATATTTATATTTTACCTATAACA
Found at i:26698 original size:30 final size:31
Alignment explanation
Indices: 26662--26965 Score: 104
Period size: 31 Copynumber: 10.0 Consensus size: 31
26652 ATTCTTTTAA
* *
26662 TATTTTAAAATTAATATTAAAATAAAATAT-T
1 TATTTT-AAATTAAGATAAAAATAAAATATAT
*
26693 T-TTTT-ATTTAAGATAAAAATAAAATATAT
1 TATTTTAAATTAAGATAAAAATAAAATATAT
* * *
26722 TATTTT-AGTTTA-AT--ATA-AAAATATA-
1 TATTTTAAATTAAGATAAAAATAAAATATAT
* **
26747 T-TTTTAAATTGAA-ATTAAAATAATGTATA-
1 TATTTTAAATT-AAGATAAAAATAAAATATAT
* * *
26776 TATATATAAGTTAAGATAAGAATAAAATATA-
1 TAT-TTTAAATTAAGATAAAAATAAAATATAT
* * *
26807 TATTTTAATTTAATA-AAATAATAATAA-ATAA
1 TATTTTAAATTAAGATAAA-AATAA-AATATAT
* * ** **
26838 TAATTGAAGGTAAGAATATAATATATTTAATA-AT
1 TATTTTAAATTAAG-ATA-AA-A-ATAAAATATAT
* * *
26872 CTAATTTAAGTTAAGATAAAAATAAAATGTAT
1 -TATTTTAAATTAAGATAAAAATAAAATATAT
* ** ** *
26904 T-TTTAAAAGTTACTATATGAATAAAATATAA
1 TATTTTAAA-TTAAGATAAAAATAAAATATAT
*
26935 T-TTTTAAATTAAGTTAAAAATAAAATATAT
1 TATTTTAAATTAAGATAAAAATAAAATATAT
26965 T
1 T
26966 TTATGTTAAT
Statistics
Matches: 202, Mismatches: 50, Indels: 43
0.68 0.17 0.15
Matches are distributed among these distances:
24 4 0.02
25 4 0.02
26 11 0.05
27 2 0.01
28 21 0.10
29 13 0.06
30 53 0.26
31 62 0.31
32 4 0.02
33 3 0.01
34 10 0.05
35 15 0.07
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.41
Consensus pattern (31 bp):
TATTTTAAATTAAGATAAAAATAAAATATAT
Found at i:26764 original size:83 final size:84
Alignment explanation
Indices: 26661--26829 Score: 202
Period size: 86 Copynumber: 2.0 Consensus size: 84
26651 TATTCTTTTA
* * * *
26661 ATATTTTAAAATTAATATTAAAATAA-AATAT-TTTTTTATTTAAGATAAAAATAAAATATATTA
1 ATATTTTAAAATTAATATTAAAATAAGAATATATATATAAGTTAAGATAAAAATAAAATATA-TA
*
26724 TTTTAGTTTAATATAAA-AAT
65 TTTTAATTTAATA-AAATAAT
* * *
26744 ATATTTTTAAATTGAA-ATTAAAATAATGTATATATATATAAGTTAAGATAAGAATAAAATATAT
1 ATATTTTAAAATT-AATATTAAAATAA-GAATATATATATAAGTTAAGATAAAAATAAAATATAT
26808 ATTTTAATTTAATAAAATAAT
64 ATTTTAATTTAATAAAATAAT
26829 A
1 A
26830 ATAAATAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
83 22 0.30
84 5 0.07
85 22 0.30
86 24 0.33
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (84 bp):
ATATTTTAAAATTAATATTAAAATAAGAATATATATATAAGTTAAGATAAAAATAAAATATATAT
TTTAATTTAATAAAATAAT
Found at i:26766 original size:24 final size:26
Alignment explanation
Indices: 26712--26768 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
26702 AAGATAAAAA
* * *
26712 TAAAATATATTATTTTAGTTTAATAT
1 TAAAATATATTATTTAAATTGAATAT
*
26738 AAAAATATATT-TTTAAATTGAA-AT
1 TAAAATATATTATTTAAATTGAATAT
26762 TAAAATA
1 TAAAATA
26769 ATGTATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 8 0.31
25 8 0.31
26 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
TAAAATATATTATTTAAATTGAATAT
Found at i:26813 original size:61 final size:55
Alignment explanation
Indices: 26739--26865 Score: 139
Period size: 56 Copynumber: 2.2 Consensus size: 55
26729 GTTTAATATA
* *
26739 AAAATATATTTTTAAATTGAAATTAAAATAATGTATATATATATAAGTT-AAGATAAGAAT
1 AAAATATATTTTT-AATT-AAA-TAAAATAAT-AATAAATA-ATAA-TTGAAGATAAGAAT
* *
26799 AAAATATATATTTTAATTTAATAAAATAATAATAAATAATAATTGAAGGTAAGAAT
1 AAAATATAT-TTTTAATTAAATAAAATAATAATAAATAATAATTGAAGATAAGAAT
*
26855 ATAATATATTT
1 AAAATATATTT
26866 AATAATCTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
55 4 0.07
56 22 0.37
57 6 0.10
58 9 0.15
59 2 0.03
60 13 0.22
61 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (55 bp):
AAAATATATTTTTAATTAAATAAAATAATAATAAATAATAATTGAAGATAAGAAT
Found at i:26914 original size:31 final size:30
Alignment explanation
Indices: 26879--27036 Score: 112
Period size: 31 Copynumber: 5.3 Consensus size: 30
26869 AATCTAATTT
*
26879 AAGTTAAGATAAAAATAAAATGTATTTTTAA
1 AAGTTAAGATAAAAATAAAATATATTTTT-A
** **
26910 AAGTTACTATATGAATAAAATATAATTTTTA
1 AAGTTAAGATAAAAATAAAATAT-ATTTTTA
*
26941 AA-TTAAGTTAAAAATAAAATATA-TTTT-
1 AAGTTAAGATAAAAATAAAATATATTTTTA
* * ** *
26968 ATGTTAATAT-AAAATTGAAT-T-TTTTTCT
1 AAGTTAAGATAAAAATAAAATATATTTTT-A
* *
26996 TAGTTTAGATAAAAATAAAATATATTTTTTA
1 AAGTTAAGATAAAAATAAAATATA-TTTTTA
*
27027 ATGTTAAGAT
1 AAGTTAAGAT
27037 GTTAATTAAA
Statistics
Matches: 93, Mismatches: 25, Indels: 18
0.68 0.18 0.13
Matches are distributed among these distances:
26 5 0.05
27 9 0.10
28 15 0.16
29 9 0.10
30 16 0.17
31 28 0.30
32 11 0.12
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (30 bp):
AAGTTAAGATAAAAATAAAATATATTTTTA
Found at i:26974 original size:28 final size:27
Alignment explanation
Indices: 26923--27023 Score: 69
Period size: 28 Copynumber: 3.6 Consensus size: 27
26913 TTACTATATG
*
26923 AATAAAATATAATTTTTAAATTAAGTTAAA
1 AATAAAATAT-A-TTTT-AGTTAAGTTAAA
26953 AATAAAATATATTTTATGTTAA-TATAAA
1 AATAAAATATATTTTA-GTTAAGT-TAAA
* * * * * * *
26981 ATTGAATTTTTTTCTTAGTTTAGATAAA
1 AATAAAATATATT-TTAGTTAAGTTAAA
27009 AATAAAATATATTTT
1 AATAAAATATATTTT
27024 TTAATGTTAA
Statistics
Matches: 54, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
27 4 0.07
28 36 0.67
29 4 0.07
30 10 0.19
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.46
Consensus pattern (27 bp):
AATAAAATATATTTTAGTTAAGTTAAA
Found at i:27591 original size:2 final size:2
Alignment explanation
Indices: 27584--27644 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
27574 AAATAATTTC
27584 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
27626 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
27645 ACTTACTTTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38161 original size:37 final size:34
Alignment explanation
Indices: 38120--38203 Score: 87
Period size: 37 Copynumber: 2.4 Consensus size: 34
38110 TAGATTACAC
38120 ATATATATATATGTTATTATATGTTTTATTAATTTAT
1 ATATATATATAT-TTATTATATG-TTT-TTAATTTAT
* * * *
38157 ATATATTTACTATTTTTTTTATGTTTTTATTTTAT
1 ATATATATA-TATTTATTATATGTTTTTAATTTAT
*
38192 ATATACATATAT
1 ATATATATATAT
38204 CATTTCGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
34 3 0.08
35 15 0.38
36 3 0.08
37 16 0.40
38 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (34 bp):
ATATATATATATTTATTATATGTTTTTAATTTAT
Found at i:38236 original size:4 final size:5
Alignment explanation
Indices: 38224--38253 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
38214 ATCTTATATC
38224 TATTT TA-TT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT T
38254 CCCTCTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:38383 original size:22 final size:21
Alignment explanation
Indices: 38342--38396 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 21
38332 TTTATGGACA
38342 TTATTTTTTTATGTCTTTTAT
1 TTATTTTTTTATGTCTTTTAT
38363 TTATTATTTATTAT-TCTTTTAT
1 TTATT-TTT-TTATGTCTTTTAT
38385 TTATTTTATTTA
1 TTATTTT-TTTA
38397 ATTTACTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.32
22 17 0.55
23 4 0.13
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (21 bp):
TTATTTTTTTATGTCTTTTAT
Found at i:38393 original size:9 final size:9
Alignment explanation
Indices: 38311--38401 Score: 50
Period size: 9 Copynumber: 10.8 Consensus size: 9
38301 TATTTTCTAG
38311 TATTTTATT
1 TATTTTATT
*
38320 TATTTCATT
1 TATTTTATT
* *
38329 TCTTTTATG
1 TATTTTATT
* **
38338 GACATTATT
1 TATTTTATT
*
38347 T-TTTTATG
1 TATTTTATT
*
38355 TCTTTTATT
1 TATTTTATT
38364 TA--TTATT
1 TATTTTATT
38371 TA--TTA-T
1 TATTTTATT
*
38377 TCTTTTATT
1 TATTTTATT
38386 TATTTTATT
1 TATTTTATT
*
38395 TAATTTA
1 TATTTTA
38402 CTTGTTATCG
Statistics
Matches: 60, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
6 2 0.03
7 10 0.17
8 8 0.13
9 40 0.67
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (9 bp):
TATTTTATT
Done.