Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004296.1 Hibiscus syriacus cultivar Beakdansim tig00009427_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: 97412
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2617 original size:14 final size:14
Alignment explanation
Indices: 2598--2638 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
2588 TTTTTGTCTA
*
2598 TATGCAGAGATTAT
1 TATGCAGGGATTAT
2612 TATGCAGGGATTTAT
1 TATGCAGGGA-TTAT
2627 TA-GCAGGGATTA
1 TATGCAGGGATTA
2639 CTTCCTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.64
15 6 0.24
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (14 bp):
TATGCAGGGATTAT
Found at i:2702 original size:4 final size:4
Alignment explanation
Indices: 2693--2719 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2683 TTCAAATATG
2693 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
2720 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2858 original size:3 final size:3
Alignment explanation
Indices: 2850--2878 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2840 GAATAGGGTT
2850 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
2879 TTACCATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:8239 original size:22 final size:22
Alignment explanation
Indices: 8191--8244 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
8181 AAATTTTCCC
*
8191 TTATTTATTTTATTTAATGTAT
1 TTATTTTTTTTATTTAATGTAT
* *
8213 ATATTTTTTATTATTTATTGT-T
1 TTATTTTTT-TTATTTAATGTAT
8235 TTATTTTTTT
1 TTATTTTTTT
8245 GTTTCTATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 16 0.59
23 10 0.37
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (22 bp):
TTATTTTTTTTATTTAATGTAT
Found at i:9444 original size:21 final size:19
Alignment explanation
Indices: 9411--9454 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
9401 TACTTTTCAT
*
9411 TTTTCTTTCATCATTTATTTA
1 TTTTATTTCATCA-TT-TTTA
*
9432 TTTTATTTTATCATTTTTA
1 TTTTATTTCATCATTTTTA
9451 TTTT
1 TTTT
9455 GCTAACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTATTTCATCATTTTTA
Found at i:12609 original size:94 final size:95
Alignment explanation
Indices: 12431--12611 Score: 224
Period size: 94 Copynumber: 1.9 Consensus size: 95
12421 TAATATTTTA
* * * ** *
12431 TATACAATAAAGCTTGAGTTGTTCCTCTAGAGAAATTGGTTAAACTCCCCAGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGCTGTCCCTATAGAGAAATTGGTTAAAAGCCCCAGCTTTATGGATAAG
* **
12496 ATTCAGCTAGTCTGATAAAGGTGATTATAC
66 ATTCAACTAACCTGATAAAGGTGATTATAC
*
12526 TATA-AATAAAGCTTGAGCTGTCCCTATA-AGGCAATTGGTTAAAAGCCCC-GACTTTATGGATA
1 TATACAATAAAGCTTGAGCTGTCCCTATAGA-GAAATTGGTTAAAAGCCCCAG-CTTTATGGATA
*
12588 AGATTCAACTAACCTGGTAAAGGT
64 AGATTCAACTAACCTGATAAAGGT
12612 TTTTACATAT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
93 2 0.03
94 67 0.92
95 4 0.05
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGCTGTCCCTATAGAGAAATTGGTTAAAAGCCCCAGCTTTATGGATAAG
ATTCAACTAACCTGATAAAGGTGATTATAC
Found at i:14033 original size:36 final size:36
Alignment explanation
Indices: 13978--14181 Score: 187
Period size: 36 Copynumber: 5.9 Consensus size: 36
13968 TAATTTACTC
*
13978 AAAACAAAGTTTTGTCTCTCTCGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
* * * *
14015 AAAACAAATTCTGTCTCTCTTAAGACATTTTCTTTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
14051 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
14087 GAAACAAA------ATCT-TTGA-ATCTGTTT-TCCTT
1 AAAACAAATTTTGTCTCTCTTGAGA-CAGTTTCT-CTT
* * *
14116 AAAA-AAA-TTTGTCTCCCTTGAGACAGTTTATTTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
14150 AAAACAAATTTTTTCTCTCTTGAGACAGTTTC
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTC
14182 CCTCGAAACA
Statistics
Matches: 133, Mismatches: 22, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
28 4 0.03
29 15 0.11
30 3 0.02
33 2 0.02
34 15 0.11
35 5 0.04
36 81 0.61
37 8 0.06
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:14034 original size:21 final size:20
Alignment explanation
Indices: 14009--14071 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
13999 CGAGACAGTT
14009 TCTCTTAAAACAAATTCTGTC
1 TCTCTTAAAACAAATT-TGTC
*
14030 TCTCTTAAGAC--ATTT-TC
1 TCTCTTAAAACAAATTTGTC
14047 T-T-TTAAAACAAATTTTGTC
1 TCTCTTAAAACAAA-TTTGTC
14066 TCTCTT
1 TCTCTT
14072 GAGACAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 6 0.18
16 1 0.03
17 4 0.12
18 4 0.12
19 6 0.18
20 1 0.03
21 12 0.35
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.46
Consensus pattern (20 bp):
TCTCTTAAAACAAATTTGTC
Found at i:14197 original size:99 final size:100
Alignment explanation
Indices: 14007--14343 Score: 487
Period size: 99 Copynumber: 3.3 Consensus size: 100
13997 CTCGAGACAG
* * * *
14007 TTTCTCTTAAAACAAATTCTGTCTCTCTTAAGACATTTTCTTTTAAAACAAATTTTGTCTCTCTT
1 TTTC-CTTAAAACAAATT-TGTCTCCCTTGAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTT
14072 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
64 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
*
14109 TTTCCTTAAAA-AAATTTGTCTCCCTTGAGACAGTTTATTTTAAAACAAATTTTTTCTCTCTTGA
1 TTTCCTTAAAACAAATTTGTCTCCCTTGAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTGA
* *
14173 GACAGTTTCCCTCGAAACAAAATCTATGAATCTGT
66 GACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
* *
14208 TTTCCTTAAAACAAGTTTCATCTCCCTTGAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTG
1 TTTCCTTAAAACAAATTT-GTCTCCCTTGAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTG
* *
14273 AGACGGTTTCCCTTGAAACAAAAATCTTTGAATCTAT
65 AGACAGTTTCCCTTGAAAC-AAAATCTTTGAATCTGT
* * **
14310 TTCCCTTGAAACAAATTTTGTCTCTTTTGAGACA
1 TTTCCTTAAAACAAA-TTTGTCTCCCTTGAGACA
14344 TTTTCCCTTG
Statistics
Matches: 211, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
99 87 0.41
100 10 0.05
101 68 0.32
102 43 0.20
103 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (100 bp):
TTTCCTTAAAACAAATTTGTCTCCCTTGAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTGA
GACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
Found at i:14273 original size:36 final size:36
Alignment explanation
Indices: 14213--14281 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
14203 TCTGTTTTCC
*
14213 TTAAAACAAGTTTCATCTCCCTTGAGACAGTTTATT
1 TTAAAACAAATTTCATCTCCCTTGAGACAGTTTATT
** * *
14249 TTAAAACAAATTTTGTCTCTCTTGAGACGGTTT
1 TTAAAACAAATTTCATCTCCCTTGAGACAGTTT
14282 CCCTTGAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (36 bp):
TTAAAACAAATTTCATCTCCCTTGAGACAGTTTATT
Found at i:14359 original size:167 final size:166
Alignment explanation
Indices: 14148--14497 Score: 477
Period size: 167 Copynumber: 2.1 Consensus size: 166
14138 ACAGTTTATT
*
14148 TTAAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATCTATGAATCTGTTTTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATCTATGAATCTGTTTTCC
* * * * *
14213 TTAAAACAAGTTTCATCTCCCTTGAGACAGTTTATTTTAAAACAAATTTTGTCTCTCTTGAGACG
66 TTAAAACAAATTTCATCTCCCTCGAGACAATTTATCTT-AAA-AAATTTTGTCTCCCTTGAGACG
*
14278 GTTTCCCTTGAAACA-AAAATCTTTGAATCTATTTCCC
129 ATTTCCCTTGAAACACAAAATCTTTGAATCTATTTCCC
* * * * * *
14315 TTGAAACAAATTTTGTCTCTTTTGAGACATTTTCCCTTGAAACAAAATCTTTTAATCTGTTTTCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATCTATGAATCTGTTTTCC
* * * * *
14380 TTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTCTTGAAAAATTTTGTCTCCCTTGAGACGAT
66 TTAAAACAAATTTCATCTCCCTCGAGACAATTTATCTTAAAAAATTTTGTCTCCCTTGAGACGAT
** *
14445 TTCTTTTGAAACACAAAATCTTTGAATTTATTTCCC
131 TTCCCTTGAAACACAAAATCTTTGAATCTATTTCCC
14481 TTAAAACAAAATTTTGT
1 TTAAAAC-AAATTTTGT
14498 TTACCTTGAT
Statistics
Matches: 159, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
165 33 0.21
166 29 0.18
167 97 0.61
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (166 bp):
TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATCTATGAATCTGTTTTCC
TTAAAACAAATTTCATCTCCCTCGAGACAATTTATCTTAAAAAATTTTGTCTCCCTTGAGACGAT
TTCCCTTGAAACACAAAATCTTTGAATCTATTTCCC
Found at i:14398 original size:65 final size:66
Alignment explanation
Indices: 14252--14421 Score: 234
Period size: 65 Copynumber: 2.6 Consensus size: 66
14242 GTTTATTTTA
**
14252 AAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAATCTTTGAATCTATTTCCCTT
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAAATCTTTGAATCTATTTCCCTT
14317 G
66 G
* * * * *
14318 AAACAAATTTTGTCTCTTTTGAGACATTTTCCCTTGAAAC-AAAATCTTTTAATCTGTTTTCCTT
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAAATCTTTGAATCTATTTCCCTT
*
14382 T
66 G
* * *
14383 AAACAAATTTCGTCTCTCTCGAGACAATTTCTCTTGAAA
1 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAA
14422 AATTTTGTCT
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
65 55 0.60
66 37 0.40
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (66 bp):
AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAAATCTTTGAATCTATTTCCCTT
G
Found at i:14432 original size:34 final size:34
Alignment explanation
Indices: 14387--14455 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
14377 TCCTTTAAAC
*
14387 AAATTTCGTCTCTCTCGAGACAATTTCTCTTGAA
1 AAATTTCGTCTCCCTCGAGACAATTTCTCTTGAA
* * * *
14421 AAATTTTGTCTCCCTTGAGACGATTTCTTTTGAA
1 AAATTTCGTCTCCCTCGAGACAATTTCTCTTGAA
14455 A
1 A
14456 CACAAAATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (34 bp):
AAATTTCGTCTCCCTCGAGACAATTTCTCTTGAA
Found at i:14439 original size:99 final size:103
Alignment explanation
Indices: 14308--14490 Score: 232
Period size: 101 Copynumber: 1.8 Consensus size: 103
14298 CTTTGAATCT
** *
14308 ATTTCCCTTGAAACAAATTTTGTCTCTTTTGAGAC-ATTTTCCCTTG-AA-ACAAAATCTTTTAA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACGA-TTTCCCTTGAAACACAAAATCTTTGAA
* * *
14370 TCTGTTTTCCTTTAAACAAATTTCGTCTCTCTCGAGACA
65 TCTATTTCCCTTAAAACAAATTTCGTCTCTCTCGAGACA
* **
14409 ATTTCTCTTG-AA-AAATTTTGTCTCCCTTGAGACGATTTCTTTTGAAACACAAAATCTTTGAAT
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACGATTTCCCTTGAAACACAAAATCTTTGAAT
*
14472 TTATTTCCCTTAAAACAAA
66 CTATTTCCCTTAAAACAAA
14491 ATTTTGTTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
99 26 0.38
100 5 0.07
101 38 0.55
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (103 bp):
ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACGATTTCCCTTGAAACACAAAATCTTTGAAT
CTATTTCCCTTAAAACAAATTTCGTCTCTCTCGAGACA
Found at i:14550 original size:266 final size:265
Alignment explanation
Indices: 14052--14557 Score: 574
Period size: 266 Copynumber: 1.9 Consensus size: 265
14042 TTTTCTTTTA
14052 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTA
* * * * *
14117 AAAAAATTTGTCTCCCTTGAGACAGTTTATTTTAAAACAAATTTTTTCTCTCTTGAGACAGTTTC
66 AAAAAATTTGTCTCCCTCGAGACAATTTATCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTC
* * * *
14182 CCTCGAAACAAAATCTATGAATCTGTTTTCCTTAAAACAAGTTTCATCTCCCTTGAGACAGTTTA
131 CCTCGAAACAAAATCTATGAATCTATTTCCCTTAAAACAAATTTCATCTACCTTGAGACAGTTTA
** * ** *
14247 TTTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAATCTTTGAATCTATTT
196 TCATAAAACAAA-TATGAATATCTTGAGACGGTTTCCCTTGAAACAAAAATCTTTGAATCTATTT
14312 CCCTTG
260 CCCTTG
* * *
14318 AAACAAATTTTGTCTCTTTTGAGACATTTTCCCTTGAAACAAAATCTTTTAATCTGTTTTCCTTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCC-TT
* * * *
14383 AAACAAATTTCGTCTCTCTCGAGACAATTTCTCTT-GAA-AAATTTTGTCTCCCTTGAGAC-GAT
65 AAAAAAATTT-GTCTCCCTCGAGACAATTTATCTTAAAACAAATTTTGTCTCCCTTGAGACAG-T
** * * * ** * *
14445 TTCTTTTGAAACACAAAATCTTTGAATTTATTTCCCTTAAAACAAAATTTTGTTTACCTTGATAC
128 TTCCCTCG-AA-ACAAAATCTATGAATCTATTTCCCTTAAAAC-AAATTTCATCTACCTTGAGAC
* * * **
14510 TGTTTCTCATGAAACAACA-AT-AATAT-TTGAGATTGTTTCCCTTGAAAC
190 AGTTTATCATAAAACAA-ATATGAATATCTTGAGACGGTTTCCCTTGAAAC
14558 GAATTCTGTC
Statistics
Matches: 197, Mismatches: 36, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
265 1 0.01
266 104 0.53
267 17 0.09
268 47 0.24
269 27 0.14
270 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.40
Consensus pattern (265 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTA
AAAAAATTTGTCTCCCTCGAGACAATTTATCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTC
CCTCGAAACAAAATCTATGAATCTATTTCCCTTAAAACAAATTTCATCTACCTTGAGACAGTTTA
TCATAAAACAAATATGAATATCTTGAGACGGTTTCCCTTGAAACAAAAATCTTTGAATCTATTTC
CCTTG
Found at i:15043 original size:50 final size:50
Alignment explanation
Indices: 14973--15071 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
14963 GCAGTGCCCA
*
14973 ACCCGAACCAGTAAGCTAGGGTTTCCAGAACCCTAGCCCTTTCTCACCCG
1 ACCCGAACCAGTAAGCTAGGGTTTCAAGAACCCTAGCCCTTTCTCACCCG
*
15023 ACCCGAACTAGTAAGCTAGGGTTTCAAGAACCCTAGCCCTTTCTCACCC
1 ACCCGAACCAGTAAGCTAGGGTTTCAAGAACCCTAGCCCTTTCTCACCC
15072 ATCAGTGCCG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.21
Consensus pattern (50 bp):
ACCCGAACCAGTAAGCTAGGGTTTCAAGAACCCTAGCCCTTTCTCACCCG
Found at i:16094 original size:23 final size:22
Alignment explanation
Indices: 16058--16100 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
16048 TTTTTTCGTT
16058 TATATTATAGTTATTATTTTCA
1 TATATTATAGTTATTATTTTCA
*
16080 TATATGTATATTTATTATTTT
1 TATAT-TATAGTTATTATTTT
16101 TTATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (22 bp):
TATATTATAGTTATTATTTTCA
Found at i:16119 original size:20 final size:21
Alignment explanation
Indices: 16094--16136 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16084 TGTATATTTA
*
16094 TTATTTTTTA-TTTTATTTCT
1 TTATTTATTATTTTTATTTCT
16114 TTATTTATTATTTTTATTTCT
1 TTATTTATTATTTTTATTTCT
16135 TT
1 TT
16137 TTATTCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (21 bp):
TTATTTATTATTTTTATTTCT
Found at i:16147 original size:26 final size:27
Alignment explanation
Indices: 16089--16145 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
16079 ATATATGTAT
* *
16089 ATTTATTATTTTTTATTTTATTTCTTT
1 ATTTATTATTTTTTATTTTATTTATTC
*
16116 ATTTATTA-TTTTTATTTCTTTTTATTC
1 ATTTATTATTTTTTATTT-TATTTATTC
16143 ATT
1 ATT
16146 ATATCATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.75
Consensus pattern (27 bp):
ATTTATTATTTTTTATTTTATTTATTC
Found at i:22832 original size:34 final size:35
Alignment explanation
Indices: 22767--22833 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
22757 AAGATATTTA
* * *
22767 TATATTTTCTTTAAAAAATTTAAATTCATAAAATT
1 TATATTTTCTTAAAAAAATTAAAAATCATAAAATT
22802 TATATTTT-TTAAAAAAATTGAAAAAT-ATAAAA
1 TATATTTTCTTAAAAAAATT-AAAAATCATAAAA
22834 AACGTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (35 bp):
TATATTTTCTTAAAAAAATTAAAAATCATAAAATT
Found at i:23712 original size:60 final size:60
Alignment explanation
Indices: 23599--23714 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
23589 AAAGGTAGGC
* * * *
23599 TATTGATTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATTCTCTGACTATAGCA
1 TATTGATTTATTAAATCCATCGACAATTAAAAGTTACAAAATGATACTCTGACTATAGCA
* * * *
23659 TATTGTTTTGTTAAATCCTTCGACAATTAAAATTTACAAAATGATCACT-TGACTAT
1 TATTGATTTATTAAATCCATCGACAATTAAAAGTTACAAAATGAT-ACTCTGACTAT
23715 TCATTATGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 45 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (60 bp):
TATTGATTTATTAAATCCATCGACAATTAAAAGTTACAAAATGATACTCTGACTATAGCA
Found at i:24362 original size:18 final size:19
Alignment explanation
Indices: 24318--24364 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
24308 ATTTATATAG
24318 TAATTTAA-TTAATCAAAT
1 TAATTTAATTTAATCAAAT
*
24336 T-ATTCTAATTTAATC-ATT
1 TAATT-TAATTTAATCAAAT
24354 TAATTTAATTT
1 TAATTTAATTT
24365 CATGAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 13 0.52
19 9 0.36
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATTTAATTTAATCAAAT
Found at i:31011 original size:41 final size:41
Alignment explanation
Indices: 30954--31062 Score: 179
Period size: 39 Copynumber: 2.7 Consensus size: 41
30944 TTATCTTTTC
*
30954 AATTTTGTAAA-AAAATATATATATAAATTTTATGAATTTA
1 AATTTTTTAAAGAAAATATATATATAAATTTTATGAATTTA
30994 AATTTTTTAAAG-AAA-ATATATATAAATTTTATGAATTTA
1 AATTTTTTAAAGAAAATATATATATAAATTTTATGAATTTA
*
31033 AATTTTTTAAAGAAAATATATAAATAAATT
1 AATTTTTTAAAGAAAATATATATATAAATT
31063 GTAGTAATAT
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
39 36 0.56
40 16 0.25
41 12 0.19
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (41 bp):
AATTTTTTAAAGAAAATATATATATAAATTTTATGAATTTA
Found at i:32698 original size:19 final size:19
Alignment explanation
Indices: 32674--32727 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
32664 AAAATATCAT
32674 AATTATATTTTAAAT-TTAC
1 AATTATATTTTAAATCTT-C
*
32693 AATTATACTTGTAAATCTTC
1 AATTATA-TTTTAAATCTTC
32713 -ATTATAATTTTAAAT
1 AATTAT-ATTTTAAAT
32728 ATTTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 19 0.63
20 9 0.30
21 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (19 bp):
AATTATATTTTAAATCTTC
Found at i:37733 original size:21 final size:21
Alignment explanation
Indices: 37707--37769 Score: 126
Period size: 21 Copynumber: 3.0 Consensus size: 21
37697 TCTGAGTTAC
37707 CCGCGACGGTCGCAATAGCGT
1 CCGCGACGGTCGCAATAGCGT
37728 CCGCGACGGTCGCAATAGCGT
1 CCGCGACGGTCGCAATAGCGT
37749 CCGCGACGGTCGCAATAGCGT
1 CCGCGACGGTCGCAATAGCGT
37770 TCGCCGCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.14
Consensus pattern (21 bp):
CCGCGACGGTCGCAATAGCGT
Found at i:37788 original size:12 final size:12
Alignment explanation
Indices: 37773--37803 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
37763 ATAGCGTTCG
*
37773 CCGCAATAACGC
1 CCGCAACAACGC
37785 CCGCAACAACGC
1 CCGCAACAACGC
37797 CCGCAAC
1 CCGCAAC
37804 GACCGCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.48, G:0.16, T:0.03
Consensus pattern (12 bp):
CCGCAACAACGC
Found at i:38548 original size:20 final size:20
Alignment explanation
Indices: 38523--38583 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
38513 GTTTGTGATT
38523 AATCCTTTGGAGAAGGGATC
1 AATCCTTTGGAGAAGGGATC
***
38543 AATCCTTTGCTTAAGGGATC
1 AATCCTTTGGAGAAGGGATC
*
38563 AATCCTTTTGAGCAAGGGATC
1 AATCCTTTGGAG-AAGGGATC
38584 GATAGTTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
20 25 0.76
21 8 0.24
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (20 bp):
AATCCTTTGGAGAAGGGATC
Found at i:40110 original size:20 final size:20
Alignment explanation
Indices: 40085--40133 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
40075 TGCTATGGCA
40085 AAATGGAATAGCTGATGTGG
1 AAATGGAATAGCTGATGTGG
40105 AAATGGAATAGCTGATGTGG
1 AAATGGAATAGCTGATGTGG
40125 AAATGGAAT
1 AAATGGAAT
40134 GATGGTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.33, T:0.24
Consensus pattern (20 bp):
AAATGGAATAGCTGATGTGG
Found at i:41663 original size:10 final size:10
Alignment explanation
Indices: 41650--41688 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
41640 AATCCACCAC
*
41650 ATGCAACTAA
1 ATGCATCTAA
*
41660 ATGCTTCTAA
1 ATGCATCTAA
*
41670 ATACATCTAA
1 ATGCATCTAA
41680 ATGCATCTA
1 ATGCATCTA
41689 TATTATTCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (10 bp):
ATGCATCTAA
Found at i:44342 original size:21 final size:21
Alignment explanation
Indices: 44313--44353 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44303 AATGGAGAAG
*
44313 AAAATGATAGAAAGTAAAAGT
1 AAAAAGATAGAAAGTAAAAGT
*
44334 AAAAAGATAGAAAGTGAAAG
1 AAAAAGATAGAAAGTAAAAG
44354 GTGAAAACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (21 bp):
AAAAAGATAGAAAGTAAAAGT
Found at i:52082 original size:21 final size:21
Alignment explanation
Indices: 52058--52099 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52048 AATCCACCAC
52058 ATGCAACTAAATGCTTCTAAA
1 ATGCAACTAAATGCTTCTAAA
* * *
52079 ATGCATCTATATGGTTCTAAA
1 ATGCAACTAAATGCTTCTAAA
52100 TGGGCCTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGCAACTAAATGCTTCTAAA
Found at i:59585 original size:59 final size:59
Alignment explanation
Indices: 59477--59617 Score: 142
Period size: 59 Copynumber: 2.4 Consensus size: 59
59467 AGTTGGGTGT
* * * * * **
59477 CCATTTTGTAACTTTTAATGGTTGAGGGACTAAACAAAATAACTTCCTA-TAGTCTGA-GA
1 CCATTTTATAACTTTTAATAGTCGAAGGACTAAACAAAACAACACCCTATTA-TC-GAGGA
* * *
59536 CCATTTTTTAACTTTTAATAGTCGAAGGACTTAACAAAGCAACACCCTATTATCGAGGGA
1 CCATTTTATAACTTTTAATAGTCGAAGGACTAAACAAAACAACACCCTATTATCGA-GGA
*
59596 TCATTTTATAACTTTTAATAGT
1 CCATTTTATAACTTTTAATAGT
59618 TGGGAAACTC
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 2 0.03
59 42 0.62
60 24 0.35
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (59 bp):
CCATTTTATAACTTTTAATAGTCGAAGGACTAAACAAAACAACACCCTATTATCGAGGA
Found at i:63613 original size:19 final size:20
Alignment explanation
Indices: 63586--63627 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
63576 TCTTTATCAG
*
63586 TTCTTTATCTTT-GTTTATC
1 TTCTCTATCTTTCGTTTATC
63605 TTCTCTATCTTTCGTTTATC
1 TTCTCTATCTTTCGTTTATC
63625 TTC
1 TTC
63628 ATTGCTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.10, C:0.21, G:0.05, T:0.64
Consensus pattern (20 bp):
TTCTCTATCTTTCGTTTATC
Found at i:65480 original size:26 final size:26
Alignment explanation
Indices: 65448--65499 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
65438 CCTTCTCGGG
65448 TTAGATCTG-CTTCAGGTCAACTGGGT
1 TTAGATCTGTC-TCAGGTCAACTGGGT
65474 TTAGATCTGTCTCAGGTCAACTGGGT
1 TTAGATCTGTCTCAGGTCAACTGGGT
65500 CAAACCTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (26 bp):
TTAGATCTGTCTCAGGTCAACTGGGT
Found at i:65580 original size:3 final size:3
Alignment explanation
Indices: 65574--65644 Score: 94
Period size: 3 Copynumber: 24.7 Consensus size: 3
65564 GTATTATTTG
* *
65574 TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA TAG TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
65620 TAG TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
65645 TAAATACGTA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
2 6 0.10
3 53 0.90
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:66638 original size:23 final size:23
Alignment explanation
Indices: 66612--66656 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
66602 ATATATGGTT
66612 ATATCTATTCATCATGAATAGTC
1 ATATCTATTCATCATGAATAGTC
* *
66635 ATATTTATTCATGATGAATAGT
1 ATATCTATTCATCATGAATAGT
66657 TACATACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (23 bp):
ATATCTATTCATCATGAATAGTC
Found at i:66667 original size:23 final size:23
Alignment explanation
Indices: 66618--66670 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
66608 GGTTATATCT
* **
66618 ATTCATCATGAATAGTCATATTT
1 ATTCATCATGAATAGTCACATAC
* *
66641 ATTCATGATGAATAGTTACATAC
1 ATTCATCATGAATAGTCACATAC
66664 ATTCATC
1 ATTCATC
66671 CTAATACATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTCATCATGAATAGTCACATAC
Found at i:69723 original size:23 final size:22
Alignment explanation
Indices: 69680--69730 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
69670 AAAAAACCGG
*
69680 AAAC-TACCAAAAGGCAAAGAT
1 AAACATACCAAAAGACAAAGAT
*
69701 AAACATACCACAAAGACAGAGAT
1 AAACATACCA-AAAGACAAAGAT
69724 AAACATA
1 AAACATA
69731 TCAGAAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 4 0.15
22 5 0.19
23 17 0.65
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (22 bp):
AAACATACCAAAAGACAAAGAT
Found at i:74073 original size:3 final size:3
Alignment explanation
Indices: 74065--74112 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
74055 AAAATATATA
74065 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
74113 GTAAAAGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:74355 original size:20 final size:20
Alignment explanation
Indices: 74330--74378 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
74320 TTTCACATCC
*
74330 TCCCTCAGCTTATTTATAGT
1 TCCCTCAGCTTATTTACAGT
74350 TCCCTCAGCTTATTTACAGT
1 TCCCTCAGCTTATTTACAGT
*
74370 TACCTCAGC
1 TCCCTCAGC
74379 CGAACAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.31, G:0.10, T:0.39
Consensus pattern (20 bp):
TCCCTCAGCTTATTTACAGT
Found at i:81023 original size:33 final size:33
Alignment explanation
Indices: 80981--81081 Score: 193
Period size: 33 Copynumber: 3.1 Consensus size: 33
80971 ACCTAGTGTA
80981 TATGGTGGACACGACCTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
*
81014 TATGGTGGACACGACCTTATGTGTCATACGAAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
81047 TATGGTGGACACGACCTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTGTCATACGGAT
81080 TA
1 TA
81082 GCACTACGGT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (33 bp):
TATGGTGGACACGACCTTATGTGTCATACGGAT
Found at i:81044 original size:17 final size:17
Alignment explanation
Indices: 80991--81076 Score: 65
Period size: 17 Copynumber: 5.2 Consensus size: 17
80981 TATGGTGGAC
80991 ACGACCTTATGTGTCAT
1 ACGACCTTATGTGTCAT
* *
81008 ACGGA--TTATG-GTGGAC
1 AC-GACCTTATGTGT-CAT
81024 ACGACCTTATGTGTCAT
1 ACGACCTTATGTGTCAT
* * *
81041 ACGA-ATTATG-GTGGAC
1 ACGACCTTATGTGT-CAT
81057 ACGACCTTATGTGTCAT
1 ACGACCTTATGTGTCAT
81074 ACG
1 ACG
81077 GATTAGCACT
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
15 6 0.12
16 18 0.35
17 21 0.41
18 6 0.12
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (17 bp):
ACGACCTTATGTGTCAT
Found at i:81060 original size:16 final size:17
Alignment explanation
Indices: 80981--81067 Score: 56
Period size: 17 Copynumber: 5.2 Consensus size: 17
80971 ACCTAGTGTA
*
80981 TATGGTGGACACGACCT
1 TATGGTGGACACGACAT
* * *
80998 TAT-GTGTCATACG-GAT
1 TATGGTG-GACACGACAT
*
81014 TATGGTGGACACGACCT
1 TATGGTGGACACGACAT
* *
81031 TAT-GTGTCATACGA-AT
1 TATGGTG-GACACGACAT
*
81047 TATGGTGGACACGACCT
1 TATGGTGGACACGACAT
81064 TATG
1 TATG
81068 TGTCATACGG
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
16 23 0.46
17 27 0.54
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (17 bp):
TATGGTGGACACGACAT
Found at i:86144 original size:17 final size:17
Alignment explanation
Indices: 86122--86175 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
86112 AATGTTAATA
86122 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
86139 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
86156 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
86173 TTT
1 TTT
86176 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:87778 original size:21 final size:21
Alignment explanation
Indices: 87748--87818 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
87738 TATGCCATCT
* *
87748 CCGCATGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
87769 CCGCAGGGTT--ATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
87788 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
87809 CCGCAGGGTT
1 CCGCAGGGTT
87819 TTATACCATA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
19 15 0.35
20 4 0.09
21 24 0.56
ACGTcount: A:0.17, C:0.34, G:0.27, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:88370 original size:34 final size:34
Alignment explanation
Indices: 88320--88417 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
88310 AAATGTTTTT
*
88320 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
88354 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
88388 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
88418 CATTAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:89102 original size:128 final size:128
Alignment explanation
Indices: 88817--89435 Score: 1028
Period size: 128 Copynumber: 4.9 Consensus size: 128
88807 TTACCTGATT
*
88817 TACTGATATATCTAGTGT-CCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* * *** *
88881 TGACAAAATAATGGAA-G-GCG-CCCCGGGAACGTGCCTTCAAGTCCCCT-GAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
88941 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
*
89005 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCTCCTTCATGTGAATAGTGAAATAATAGG
65 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
89069 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
89134 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
89197 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
89262 TGACAAAATAATGGAAGGCGCG--CCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
89323 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATA-GGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
89387 TG---AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
89436 ACTCCGATTA
Statistics
Matches: 471, Mismatches: 15, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
122 17 0.04
124 42 0.09
125 83 0.18
126 83 0.18
127 5 0.01
128 241 0.51
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:89519 original size:8 final size:8
Alignment explanation
Indices: 89506--89546 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
89496 TCACAAGCTT
89506 TCAAATTC
1 TCAAATTC
89514 TCAAATTC
1 TCAAATTC
* *
89522 CCAAACTC
1 TCAAATTC
89530 T-AAATTC
1 TCAAATTC
89537 TCAAATTC
1 TCAAATTC
89545 TC
1 TC
89547 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:92538 original size:12 final size:12
Alignment explanation
Indices: 92520--92554 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
92510 ATACATAAAT
92520 ATATTTAATATA
1 ATATTTAATATA
*
92532 TTATTTAATATA
1 ATATTTAATATA
*
92544 ATAATTAATAT
1 ATATTTAATAT
92555 TAGTTATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATTTAATATA
Found at i:94313 original size:27 final size:26
Alignment explanation
Indices: 94267--94363 Score: 81
Period size: 26 Copynumber: 3.6 Consensus size: 26
94257 AAATATTTTA
94267 TTTTTA-CTTCAACTTT-AAAATGTAT
1 TTTTTATCTT-AACTTTAAAAATGTAT
*
94292 TTGTTTATCTTAACTTTAAAAATATAT
1 TT-TTTATCTTAACTTTAAAAATGTAT
* * **
94319 TTATTATTTTATTAAATTAAAAATGTAGT
1 TTTTTATCTTA--ACTTTAAAAATGTA-T
94348 TTTTATATCTTAACTT
1 TTTT-TATCTTAACTT
94364 CATAAAAGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
25 2 0.04
26 17 0.31
27 13 0.24
28 13 0.24
29 4 0.07
30 6 0.11
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (26 bp):
TTTTTATCTTAACTTTAAAAATGTAT
Found at i:94440 original size:57 final size:58
Alignment explanation
Indices: 94377--94490 Score: 146
Period size: 57 Copynumber: 2.0 Consensus size: 58
94367 AAAAGAATTT
* * *
94377 AAGTTAATA-AAAGATTAGAATATTTTTAA-A-ATTAAGAT-AAACATAAAATATATTTTA
1 AAGTTAATATAAA-AATAAAATATATTTAATACATTAA-ATGAAA-ATAAAATATATTTTA
94434 AAGTTAATATAAAAATAAAATATATTTAATACATTAAATGAAAATAAAATATATTTT
1 AAGTTAATATAAAAATAAAATATATTTAATACATTAAATGAAAATAAAATATATTTT
94491 CTTAAAATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
57 22 0.44
58 20 0.40
59 8 0.16
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (58 bp):
AAGTTAATATAAAAATAAAATATATTTAATACATTAAATGAAAATAAAATATATTTTA
Found at i:94445 original size:29 final size:28
Alignment explanation
Indices: 94395--94490 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 28
94385 AAAAGATTAG
*
94395 AATAT-TTTTAAAATTAAGATAAACATAA
1 AATATATTTTAAAATTAATATAAA-ATAA
*
94423 AATATATTTTAAAGTTAATATAAAAATAA
1 AATATATTTTAAAATTAATAT-AAAATAA
94452 AATATA-TTTAATACATTAA-ATGAAAATAA
1 AATATATTTTAA-A-ATTAATAT-AAAATAA
94481 AATATATTTT
1 AATATATTTT
94491 CTTAAAATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.17
29 39 0.66
30 10 0.17
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (28 bp):
AATATATTTTAAAATTAATATAAAATAA
Found at i:94826 original size:17 final size:16
Alignment explanation
Indices: 94784--94839 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
94774 AGTTTAACCA
94784 AAATCAACCCGAACTG
1 AAATCAACCCGAACTG
* *
94800 AAAGCAACCCAAACTG
1 AAATCAACCCGAACTG
*
94816 AAAATCAACCCGAACCG
1 -AAATCAACCCGAACTG
94833 AAATCAA
1 AAATCAA
94840 TTAGAACTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 21 0.62
17 13 0.38
ACGTcount: A:0.50, C:0.30, G:0.11, T:0.09
Consensus pattern (16 bp):
AAATCAACCCGAACTG
Found at i:95552 original size:45 final size:46
Alignment explanation
Indices: 95463--95552 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 46
95453 TAAACAAAAA
* * * *
95463 CAACCTGAATTGACCCGAAAATCTAAAGGTTAATCTCAATCGAAAT
1 CAACCCGAATTGACCCGAAAATCTAAAGCTTAATCCCAACCGAAAT
*
95509 CAACCCGAATTGA-CCGAAAATCTAAAGCTTGA-CCCGAACCGAAA
1 CAACCCGAATTGACCCGAAAATCTAAAGCTTAATCCC-AACCGAAA
95553 CTAACTGATC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
44 2 0.05
45 24 0.63
46 12 0.32
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (46 bp):
CAACCCGAATTGACCCGAAAATCTAAAGCTTAATCCCAACCGAAAT
Found at i:95581 original size:30 final size:31
Alignment explanation
Indices: 95540--95606 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
95530 CTAAAGCTTG
*
95540 ACCCGAACCGAA-ACTAACTGATCCGAGATTA
1 ACCCGAACCGAACACCAACTGATCCGA-ATTA
*
95571 ACCC-AACCGAACACCAACTGATCCGATTTA
1 ACCCGAACCGAACACCAACTGATCCGAATTA
95601 ACCCGA
1 ACCCGA
95607 CTCGATACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.37, C:0.34, G:0.13, T:0.15
Consensus pattern (31 bp):
ACCCGAACCGAACACCAACTGATCCGAATTA
Found at i:96771 original size:20 final size:20
Alignment explanation
Indices: 96726--96771 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
96716 GACCAACAAA
*
96726 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
96746 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
96765 ATCGCAA
1 ATCGCAA
96772 ATCAGTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:96851 original size:22 final size:23
Alignment explanation
Indices: 96806--96858 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
96796 ATTATGACTA
*
96806 TCGCAAT--GCGATTTTCCAATT
1 TCGCAATGCGCGATTTCCCAATT
*
96827 TCGCATTGCGCGATTTCCCAA-T
1 TCGCAATGCGCGATTTCCCAATT
96849 TCGCAATGCG
1 TCGCAATGCG
96859 AATAAGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.22
22 10 0.37
23 11 0.41
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (23 bp):
TCGCAATGCGCGATTTCCCAATT
Found at i:96875 original size:21 final size:21
Alignment explanation
Indices: 96849--96917 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
96839 ATTTCCCAAT
** *
96849 TCGCAATGCGAATAAGTAAAA
1 TCGCAATGCGAATTTGGAAAA
96870 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
96891 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
96912 TCGCAA
1 TCGCAA
96918 CGCGTATGAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:96951 original size:39 final size:40
Alignment explanation
Indices: 96908--97036 Score: 147
Period size: 39 Copynumber: 3.2 Consensus size: 40
96898 GCGAATTTGG
*
96908 AAAATCGCAACGCGTA-TGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGTACTGACTTTCGCAACGCGATAATAC
* *
96947 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT--
1 AAAATCGCAACGCG-TACTGACTTTCGCAACGCGATAATAC
** * *
96986 AATTTCGCAACGCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGC-GTACTGACTTTCGCAACGCGATAATAC
*
97027 ATAATCGCAA
1 AAAATCGCAA
97037 TGCGATTTTC
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
39 46 0.63
40 2 0.03
41 25 0.34
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.22
Consensus pattern (40 bp):
AAAATCGCAACGCGTACTGACTTTCGCAACGCGATAATAC
Found at i:96993 original size:19 final size:20
Alignment explanation
Indices: 96912--97022 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
96902 ATTTGGAAAA
*
96912 TCGCAACGCG-TA-TGACTA
1 TCGCAACGCGATACTGACTT
* **
96930 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
96951 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
96971 TCGCAACTCGATACT-AATT
1 TCGCAACGCGATACTGACTT
*
96990 TCGCAACGCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
97010 TCGCAACGAGATA
1 TCGCAACGCGATA
97023 ATACATAATC
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
18 10 0.13
19 20 0.26
20 29 0.38
21 15 0.20
22 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:97235 original size:21 final size:21
Alignment explanation
Indices: 97209--97251 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
97199 CACTCTCTCA
97209 CCCATCTCCGACGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
*
97230 CCCATCTCCGGCGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
97251 C
1 C
97252 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.44, G:0.16, T:0.19
Consensus pattern (21 bp):
CCCATCTCCGACGAAATCCGT
Done.