Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005309.1 Hibiscus syriacus cultivar Beakdansim tig00012015_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: 98533
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3248 original size:23 final size:22
Alignment explanation
Indices: 3210--3252 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3200 CAATTCCTTT
3210 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
3232 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
3253 CCAGCACCAA
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:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:13379 original size:37 final size:37
Alignment explanation
Indices: 13321--13423 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
13311 CCTTTTCGTC
*
13321 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
13358 TTGCTAGGATTCAAACTCCTAAAAATAAGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
13395 CTATTATGATTTAAACTCCTAAAGATAGG
1 CTACTAGGATTCAAACTCCTAAAAATAGG
13424 GTCCACAAGC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:14289 original size:4 final size:4
Alignment explanation
Indices: 14276--14305 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
14266 TATATATTAA
14276 TATT TCATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT T
14306 TTTCCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:14315 original size:25 final size:25
Alignment explanation
Indices: 14287--14364 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
14277 ATTTCATTTA
14287 TTTATTTATTTATTTATTTTTTCCT
1 TTTATTTATTTATTTATTTTTTCCT
* * *
14312 TTTATTTTTTTACTTATTTTTATTCT
1 TTTATTTATTTATTTATTTTT-TCCT
* *
14338 TCATTTTTTCATTTATTCATTTTTTCC
1 T--TTATTT-ATTTATTTATTTTTTCC
14365 CTCTAACACA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
25 19 0.46
26 4 0.10
28 7 0.17
29 11 0.27
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTATTTATTTATTTATTTTTTCCT
Found at i:17631 original size:15 final size:15
Alignment explanation
Indices: 17611--17641 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17601 GAACATTTCA
17611 TGCATTCTTGCATTT
1 TGCATTCTTGCATTT
*
17626 TGCATTTTTGCATTT
1 TGCATTCTTGCATTT
17641 T
1 T
17642 TACATCTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (15 bp):
TGCATTCTTGCATTT
Found at i:18820 original size:21 final size:20
Alignment explanation
Indices: 18796--18862 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
18786 AATCAAGAAC
*
18796 AAAAAAGAAAGAAGCAAAAGA
1 AAAAAAGAAAGAAAC-AAAGA
18817 AAAAAA-AAGAGAAACAAAGA
1 AAAAAAGAA-AGAAACAAAGA
* *
18837 AAAAAAGAAAAAAAGAAAGA
1 AAAAAAGAAAGAAACAAAGA
18857 ACAAAA
1 A-AAAA
18863 TCAAAAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAGAAACAAAGA
Found at i:18837 original size:8 final size:8
Alignment explanation
Indices: 18796--18854 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
18786 AATCAAGAAC
18796 AAAAAAG-
1 AAAAAAGA
*
18803 AAAGAAGCA
1 AAAAAAG-A
18812 AAAGAAA-A
1 AAA-AAAGA
18820 AAAAAGAGA
1 AAAAA-AGA
*
18829 AACAAAGA
1 AAAAAAGA
18837 AAAAAAGA
1 AAAAAAGA
18845 AAAAAAGA
1 AAAAAAGA
18853 AA
1 AA
18855 GAACAAAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
7 8 0.19
8 25 0.58
9 8 0.19
10 2 0.05
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:18857 original size:28 final size:27
Alignment explanation
Indices: 18811--18875 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
18801 AGAAAGAAGC
18811 AAAAGAAAAAAAAAGAGAAACAAAGA-AA
1 AAAAGAAAAAAAAAGAG-AACAAA-ATAA
*
18839 AAAAGAAAAAAAGAA-AGAACAAAATCA
1 AAAAGAAAAAAA-AAGAGAACAAAATAA
18866 AAAAGAAAAA
1 AAAAGAAAAA
18876 GGGACAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 1 0.03
27 17 0.50
28 14 0.41
29 2 0.06
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.02
Consensus pattern (27 bp):
AAAAGAAAAAAAAAGAGAACAAAATAA
Found at i:19720 original size:18 final size:18
Alignment explanation
Indices: 19697--19731 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19687 GAAAGGGACA
19697 ATATTTTCAAAACTTTTG
1 ATATTTTCAAAACTTTTG
*
19715 ATATTTTCAGAACTTTT
1 ATATTTTCAAAACTTTT
19732 AAAATAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (18 bp):
ATATTTTCAAAACTTTTG
Found at i:20571 original size:106 final size:106
Alignment explanation
Indices: 20446--21389 Score: 1305
Period size: 106 Copynumber: 9.0 Consensus size: 106
20436 GCCACTCGAG
* * *
20446 ACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
20511 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
* * *
20552 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTTA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
* *
20617 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
* *
20658 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATATCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
* *
20723 GAGCCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
* * *
20764 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCATTTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
*
20829 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACT-CAA
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
* * * * * *
20869 GACAACACAAGTTCAACTTCACAACGAATGGACGGCTAGTTGTCAAC-AATAATTTCCCAATTTC
1 -ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
* * *
20933 AGAGCCAGTTTCAACTTCGCAGCGAAGGATATTGGACTCCAG
65 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
*
20975 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
*
21040 GATCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
* * *
21081 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAATAAACAACTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
* * *
21146 GAGTCAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAA
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
* ** * * *
21186 GACAACACAAGCCCAACTTCACGACGAAGGGACGGTTGATTGTCAAC-AA-AATTT--C-A-TTC
1 -ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
** ** *
21245 AGAGTTAATTTCAACTTCACAGCGAAGGATATTGGACTAGAG
65 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
* * * * * * ** *
21287 ACAACACAAGTTCAACTTTACAAAGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCTGTTCCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
*
21352 GAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
66 GAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
21390 GGAACAATGC
Statistics
Matches: 749, Mismatches: 77, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
100 76 0.10
101 4 0.01
102 6 0.01
104 5 0.01
105 97 0.13
106 561 0.75
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA
Found at i:21049 original size:317 final size:317
Alignment explanation
Indices: 20439--21389 Score: 1414
Period size: 317 Copynumber: 3.0 Consensus size: 317
20429 ATATCGTGCC
* * *
20439 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
20504 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAA-ACAACGCAAGTTCAAC
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT-CAAGACAACACAAGTTCAAC
* * * *
20568 TTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTTAGAGCCAATTTCAACTT
130 TTCACGACGAAGGGACGGCTAGTTGTCAA-CAATAATTTCCCAATTTCAGAGCCAATTTCAACTT
*
20633 CACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
194 CACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
* *
20698 GTCAATAAACAATATCCCAATTTCAGAGCCAATTTCAATTTCACAGCGAAGGATATTGG
259 GTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
20757 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
20822 ATTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* * * *
20887 TCACAACGAATGGACGGCTAGTTGTCAACAATAATTTCCCAATTTCAGAGCCAGTTTCAACTTCG
131 TCACGACGAAGGGACGGCTAGTTGTCAACAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
20952 CAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
196 CAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
21017 CAATAAACAATTTCCCAATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
261 CAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
21074 ACTCCAAACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * **
21139 AATTTCAGAGTCAATTTCAACTTCTCAGCGAAGGATCTTGGACCCAAGACAACACAAGCCCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* **
21204 TCACGACGAAGGGACGG-TTGATTGTCAACAA-AATTT--C-A-TTCAGAGTTAATTTCAACTTC
131 TCACGACGAAGGGACGGCTAG-TTGTCAACAATAATTTCCCAATTTCAGAGCCAATTTCAACTTC
** * * * * *
21263 ACAGCGAAGGATATTGGACTAGAGACAACACAAGTTCAACTTTACAAAGAAGGGACGGCTGGTTG
195 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* * ** * *
21328 TCAACAAATAATTTCCCTGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
260 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
21386 ACTC
1 ACTC
21390 GGAACAATGC
Statistics
Matches: 578, Mismatches: 52, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
311 1 0.00
312 128 0.22
313 1 0.00
314 1 0.00
316 7 0.01
317 297 0.51
318 143 0.25
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (317 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
TCACGACGAAGGGACGGCTAGTTGTCAACAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
CAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
CAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:22146 original size:37 final size:37
Alignment explanation
Indices: 22088--22192 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
22078 CCTTTTCGTC
*
22088 CTACTAGAATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGTATTCAAACTCCTAAAAATATGATAGAATT
* * *
22125 TTTCTAGTATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGTATTCAAACTCCTAAAAATATGATAGAATT
* *
22162 CTACTA-TGATTTAAACTCCTAAAGATATGAT
1 CTACTAGT-ATTCAAACTCCTAAAAATATGAT
22193 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 1 0.02
37 58 0.98
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (37 bp):
CTACTAGTATTCAAACTCCTAAAAATATGATAGAATT
Found at i:22801 original size:2 final size:2
Alignment explanation
Indices: 22794--22836 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
22784 GTATTATTAC
22794 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
22836 T
1 T
22837 TGTAATTATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23050 original size:2 final size:2
Alignment explanation
Indices: 23043--23079 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23033 TTTACTCATT
23043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23080 TCATTTATTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23089 original size:4 final size:4
Alignment explanation
Indices: 23077--23113 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
23067 TATATATATA
*
23077 TATT CATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
23114 TTCCTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:23122 original size:16 final size:16
Alignment explanation
Indices: 23103--23143 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
23093 TATTTATTTA
*
23103 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
23119 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
23134 TATT-TTTATT
1 T-TTATTTATT
23144 CTTCAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:23139 original size:12 final size:12
Alignment explanation
Indices: 23082--23140 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
23072 ATATATATTC
*
23082 ATTTATTTATTT
1 ATTTATTTTTTT
*
23094 ATTTATTTATTT
1 ATTTATTTTTTT
*
23106 ATTTATTTTTCCT
1 ATTTATTTTT-TT
23119 -TTTATTTTTTTT
1 ATTTA-TTTTTTT
*
23131 ACTTATTTTT
1 ATTTATTTTT
23141 ATTCTTCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 31 0.77
13 9 0.22
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:33689 original size:70 final size:68
Alignment explanation
Indices: 33556--33690 Score: 198
Period size: 70 Copynumber: 2.0 Consensus size: 68
33546 CTCTAAAAAT
* * * *
33556 CTTAGATTGATTACCTAAAAGAAAATGAAAAATGATAAAATTTAATAAATATATCTTTGATCAAA
1 CTTAGATTGATTACCTAAAAGAAAATAAAAAATGATAAAATTTAAGAAAGATATCTTTCATCAAA
33621 CAC
66 CAC
* *
33624 CTTAGATTGATTATCTAAAATAAAATCAAAAAAATGATAAAATTTAAGAAAGATATCTTTCATCA
1 CTTAGATTGATTACCTAAAAGAAAAT--AAAAAATGATAAAATTTAAGAAAGATATCTTTCATCA
33689 AA
64 AA
33691 TACATCCATT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
68 24 0.41
70 35 0.59
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (68 bp):
CTTAGATTGATTACCTAAAAGAAAATAAAAAATGATAAAATTTAAGAAAGATATCTTTCATCAAA
CAC
Found at i:53169 original size:14 final size:16
Alignment explanation
Indices: 53133--53177 Score: 67
Period size: 14 Copynumber: 2.9 Consensus size: 16
53123 GACTTTTGAC
53133 TGTAGAAAAACAGACTG
1 TGTAG-AAAACAGACTG
53150 TGTAGAAAACAGA-T-
1 TGTAGAAAACAGACTG
53164 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
53178 AAGTCTGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 13 0.48
15 1 0.04
16 8 0.30
17 5 0.19
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.18
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:55472 original size:51 final size:51
Alignment explanation
Indices: 55396--55496 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
55386 TAAGGAAAGG
*
55396 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
55447 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
55497 CTCCCCCTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:58348 original size:14 final size:14
Alignment explanation
Indices: 58323--58396 Score: 103
Period size: 14 Copynumber: 5.0 Consensus size: 14
58313 CCTGATACCA
*
58323 TGTAGAAAAACAGAT
1 TGTAG-AAAACAGAC
58338 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
58352 TGTAGAAAAACAGAC
1 TGTAG-AAAACAGAC
58367 TGTGTAGAAAACAGAC
1 --TGTAGAAAACAGAC
58383 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
58397 AAGTCTGTTA
Statistics
Matches: 55, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
14 27 0.49
15 14 0.25
16 9 0.16
17 5 0.09
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:58376 original size:31 final size:30
Alignment explanation
Indices: 58323--58396 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 30
58313 CCTGATACCA
58323 TGTAGAAAAACAGA-TTGTAGAAAACAGAC
1 TGTAGAAAAACAGACTTGTAGAAAACAGAC
58352 TGTAGAAAAACAGACTGTGTAGAAAACAGAC
1 TGTAGAAAAACAGACT-TGTAGAAAACAGAC
58383 TGTAG-AAAACAGAC
1 TGTAGAAAAACAGAC
58397 AAGTCTGTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
29 14 0.33
30 10 0.23
31 19 0.44
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (30 bp):
TGTAGAAAAACAGACTTGTAGAAAACAGAC
Found at i:65769 original size:59 final size:57
Alignment explanation
Indices: 65679--65790 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 57
65669 TAAATAGTTC
*
65679 ACCCTTAAGTGGGGTTTCGTGGGAATCATATTTTGGATCCAAAATTTATGTTATTTT
1 ACCCTTAAGTGGGGTTTCATGGGAATCATATTTTGGATCCAAAATTTATGTTATTTT
*
65736 ACCCTTAAGTGTGGGGTTTCATGGTAATCATATTTTGGATCCAAAATTTATGTTA
1 ACCCTTAA--GTGGGGTTTCATGGGAATCATATTTTGGATCCAAAATTTATGTTA
65791 AAAGCTATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
57 8 0.16
59 43 0.84
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (57 bp):
ACCCTTAAGTGGGGTTTCATGGGAATCATATTTTGGATCCAAAATTTATGTTATTTT
Found at i:66143 original size:15 final size:17
Alignment explanation
Indices: 66105--66166 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
66095 AAATGTATAT
*
66105 AATATATGATTTTTGAA
1 AATATATAATTTTTGAA
*
66122 AATATATAATTTTTAAA
1 AATATATAATTTTTGAA
*
66139 AATATATATAGTTTTGAA
1 AATATATA-ATTTTTGAA
*
66157 AACATATAAT
1 AATATATAAT
66167 ATATATGGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 24 0.63
18 14 0.37
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (17 bp):
AATATATAATTTTTGAA
Found at i:66145 original size:19 final size:19
Alignment explanation
Indices: 66106--66169 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
66096 AATGTATATA
* *
66106 ATATATGATTTTT-GAAA-
1 ATATATAATTTTTAAAAAT
66123 ATATATAATTTTTAAAAAT
1 ATATATAATTTTTAAAAAT
* *
66142 ATATATAGTTTTGAAAACAT
1 ATATATAATTTTTAAAA-AT
66162 ATAATATA
1 AT-ATATA
66170 TATGGTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 12 0.31
18 3 0.08
19 15 0.38
20 4 0.10
21 5 0.13
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATATAATTTTTAAAAAT
Found at i:66168 original size:42 final size:42
Alignment explanation
Indices: 66122--66254 Score: 102
Period size: 42 Copynumber: 3.2 Consensus size: 42
66112 GATTTTTGAA
66122 AATATATAATTTTTAAAAATATATATAGTTTTGAAAACATAT
1 AATATATAATTTTTAAAAATATATATAGTTTTGAAAACATAT
** * *
66164 AATATAT-ATGGTTTTTGAAA-ATA-GTA--TTTAAAACACATATAT
1 AATATATAAT--TTTTAAAAATATATATAGTTTTGAAA-AC--ATAT
66206 AATATATAATTTTTGAAAACATAT-TATAGTTTTTG-AAA-ATAT
1 AATATATAATTTTT-AAAA-ATATATATAG-TTTTGAAAACATAT
66248 AATATAT
1 AATATAT
66255 GTTATATAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
39 6 0.09
40 2 0.03
41 8 0.11
42 34 0.49
43 10 0.14
44 4 0.06
45 1 0.01
46 2 0.03
47 3 0.04
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (42 bp):
AATATATAATTTTTAAAAATATATATAGTTTTGAAAACATAT
Found at i:66197 original size:38 final size:40
Alignment explanation
Indices: 66146--66224 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
66136 AAAAATATAT
* **
66146 ATAGTTTTGAAAACATATA-AT-ATATATGGTTTTTGAAA
1 ATAGTTTTGAAAACACATATATAATATATAATTTTTGAAA
66184 ATAGTATTT-AAAACACATATATAATATATAATTTTTGAAA
1 ATAGT-TTTGAAAACACATATATAATATATAATTTTTGAAA
66224 A
1 A
66225 CATATTATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 14 0.40
39 5 0.14
40 16 0.46
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.41
Consensus pattern (40 bp):
ATAGTTTTGAAAACACATATATAATATATAATTTTTGAAA
Found at i:66253 original size:20 final size:20
Alignment explanation
Indices: 66209--66253 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
66199 CATATATAAT
66209 ATATAATTTTTGAAAACATA
1 ATATAATTTTTGAAAACATA
* * *
66229 TTATAGTTTTTGAAAATATA
1 ATATAATTTTTGAAAACATA
66249 ATATA
1 ATATA
66254 TGTTATATAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATAATTTTTGAAAACATA
Found at i:66281 original size:2 final size:2
Alignment explanation
Indices: 66276--66372 Score: 50
Period size: 2 Copynumber: 52.0 Consensus size: 2
66266 TTTAAAATAA
*
66276 AT AT AT CAT AT AT AT AT AT AT AT AT -T AT AT -T AT TT AT A- AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
66316 AT -T GT TT AT -T AT TT AT AT -T AT AT -T AT TT CAT AT AT GT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
*
66354 AT AT AT AT AT CT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT
66373 CTATTTATTT
Statistics
Matches: 73, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
1 9 0.12
2 61 0.84
3 3 0.04
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (2 bp):
AT
Found at i:66287 original size:27 final size:29
Alignment explanation
Indices: 66225--66289 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
66215 TTTTTGAAAA
*
66225 CATATTATAGTTTTTGAAAATATAATATAT
1 CATA-TATAGATTTTGAAAATATAATATAT
**
66255 GTTATATAGATTTT-AAAATA-AATATAT
1 CATATATAGATTTTGAAAATATAATATAT
66282 CATATATA
1 CATATATA
66290 TATATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 13 0.43
28 6 0.20
29 9 0.30
30 2 0.07
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (29 bp):
CATATATAGATTTTGAAAATATAATATAT
Found at i:66289 original size:29 final size:31
Alignment explanation
Indices: 66225--66291 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
66215 TTTTTGAAAA
*
66225 CATAT-TATAGTTTTTGAAAATATAATATAT
1 CATATATATAGATTTTGAAAATATAATATAT
*
66255 -GT-TATATAGATTTT-AAAATA-AATATAT
1 CATATATATAGATTTTGAAAATATAATATAT
66282 CATATATATA
1 CATATATATA
66292 TATATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 7 0.23
28 8 0.26
29 16 0.52
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (31 bp):
CATATATATAGATTTTGAAAATATAATATAT
Found at i:66304 original size:9 final size:9
Alignment explanation
Indices: 66276--66377 Score: 67
Period size: 9 Copynumber: 11.8 Consensus size: 9
66266 TTTAAAATAA
*
66276 ATATATCAT
1 ATATATTAT
66285 ATATATATAT
1 ATATAT-TAT
66295 ATATATTAT
1 ATATATTAT
66304 AT-TATT-T
1 ATATATTAT
*
66311 ATAATATTGT
1 AT-ATATTAT
66321 -T-TATTAT
1 ATATATTAT
*
66328 TTATATTAT
1 ATATATTAT
66337 AT-TATT-T
1 ATATATTAT
66344 CATATATGT-T
1 -ATATAT-TAT
66354 ATATA-TAT
1 ATATATTAT
*
66362 ATCTATTAT
1 ATATATTAT
*
66371 ATCTATT
1 ATATATT
66378 TATTTATTTA
Statistics
Matches: 78, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
7 10 0.13
8 16 0.21
9 41 0.53
10 11 0.14
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (9 bp):
ATATATTAT
Found at i:66357 original size:19 final size:18
Alignment explanation
Indices: 66292--66394 Score: 64
Period size: 19 Copynumber: 6.1 Consensus size: 18
66282 CATATATATA
*
66292 TATATATATTATATTATT
1 TATATATGTTATATTATT
66310 TATAATATTGTT-TATTA-T
1 TAT-ATA-TGTTATATTATT
66328 T-TATA--TTATATTATT
1 TATATATGTTATATTATT
66343 TCATATATGTTATA-TA--
1 T-ATATATGTTATATTATT
* *
66359 TATATCTATTATATCTATT
1 TATATATGTTATAT-TATT
*
66378 TATTTAT-TTAT-TTATT
1 TATATATGTTATATTATT
66394 T
1 T
66395 TCAAGTCCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 26
0.69 0.05 0.26
Matches are distributed among these distances:
13 2 0.03
14 5 0.07
15 12 0.18
16 9 0.13
17 8 0.12
18 11 0.16
19 18 0.26
20 3 0.04
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (18 bp):
TATATATGTTATATTATT
Found at i:66381 original size:4 final size:4
Alignment explanation
Indices: 66320--66394 Score: 53
Period size: 4 Copynumber: 17.8 Consensus size: 4
66310 TATAATATTG
* * * *
66320 TTTA -TTA TTTA TATTA TATTA TTTCA TATA TGTTA TATA TATA TCTA
1 TTTA TTTA TTTA T-TTA T-TTA TTT-A TTTA T-TTA TTTA TTTA TTTA
*
66367 TTATA TCTA TTTA TTTA TTTA TTTA TTT
1 TT-TA TTTA TTTA TTTA TTTA TTTA TTT
66395 TCAAGTCCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.05
4 38 0.64
5 18 0.31
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (4 bp):
TTTA
Found at i:66895 original size:19 final size:19
Alignment explanation
Indices: 66871--66936 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
66861 ATACAGTAGA
66871 AAACAATCGAAATAGGCAG
1 AAACAATCGAAATAGGCAG
* * *
66890 AAACAA-GGCAATATACAGTAG
1 AAACAATCG-AA-ATA-GGCAG
66911 AAAACAATCGAAATAGGCAG
1 -AAACAATCGAAATAGGCAG
66931 AAACAA
1 AAACAA
66937 GGCAATATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
18 1 0.03
19 14 0.39
20 6 0.17
21 6 0.17
22 8 0.22
23 1 0.03
ACGTcount: A:0.56, C:0.15, G:0.18, T:0.11
Consensus pattern (19 bp):
AAACAATCGAAATAGGCAG
Found at i:66901 original size:41 final size:41
Alignment explanation
Indices: 66856--66947 Score: 184
Period size: 41 Copynumber: 2.2 Consensus size: 41
66846 AATCTACCAA
66856 GCAATATACAGTAGAAAACAATCGAAATAGGCAGAAACAAG
1 GCAATATACAGTAGAAAACAATCGAAATAGGCAGAAACAAG
66897 GCAATATACAGTAGAAAACAATCGAAATAGGCAGAAACAAG
1 GCAATATACAGTAGAAAACAATCGAAATAGGCAGAAACAAG
66938 GCAATATACA
1 GCAATATACA
66948 AACAAAAATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.13
Consensus pattern (41 bp):
GCAATATACAGTAGAAAACAATCGAAATAGGCAGAAACAAG
Found at i:66916 original size:22 final size:21
Alignment explanation
Indices: 66853--66917 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
66843 AGAAATCTAC
66853 CAAGCAATATACAGTAGAAAA
1 CAAGCAATATACAGTAGAAAA
* * *
66874 CAATCGAA-ATA-GGCAG-AAA
1 CAAGC-AATATACAGTAGAAAA
66893 CAAGGCAATATACAGTAGAAAA
1 CAA-GCAATATACAGTAGAAAA
66915 CAA
1 CAA
66918 TCGAAATAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
19 8 0.24
20 7 0.21
21 10 0.30
22 8 0.24
ACGTcount: A:0.55, C:0.15, G:0.17, T:0.12
Consensus pattern (21 bp):
CAAGCAATATACAGTAGAAAA
Found at i:68476 original size:27 final size:27
Alignment explanation
Indices: 68446--68511 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
68436 CTTTAGATAG
68446 AATAAGATAAGACTTATTTAAACTTTA
1 AATAAGATAAGACTTATTTAAACTTTA
68473 AATAAGATAAGACTTATTTAAACTTTA
1 AATAAGATAAGACTTATTTAAACTTTA
68500 AATAAGATAAGA
1 AATAAGATAAGA
68512 ATAAGAGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (27 bp):
AATAAGATAAGACTTATTTAAACTTTA
Found at i:75084 original size:19 final size:19
Alignment explanation
Indices: 75060--75108 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
75050 AGAGGTAAGG
75060 CTATCTAAAATAAAGCCAT
1 CTATCTAAAATAAAGCCAT
*
75079 CTATCTCAAATAAAGCCAT
1 CTATCTAAAATAAAGCCAT
*
75098 CTATCTGAAAT
1 CTATCTAAAAT
75109 CCCCATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (19 bp):
CTATCTAAAATAAAGCCAT
Found at i:75803 original size:18 final size:18
Alignment explanation
Indices: 75766--75803 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
75756 TTTTAAGATT
*
75766 TTATATTCGATTTAAATA
1 TTATATTCGATTCAAATA
*
75784 TTATATTCGATTCAATTA
1 TTATATTCGATTCAAATA
75802 TT
1 TT
75804 CGAATATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATATTCGATTCAAATA
Found at i:83762 original size:16 final size:15
Alignment explanation
Indices: 83732--83777 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
83722 GGGGAGTGGG
83732 AGTAATTTTTCAAAA
1 AGTAATTTTTCAAAA
83747 AGTAATTTTTCGAAAA
1 AGTAATTTTTC-AAAA
* * *
83763 AATGATTTTTTAAAA
1 AGTAATTTTTCAAAA
83778 GAAAATCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (15 bp):
AGTAATTTTTCAAAA
Found at i:83910 original size:18 final size:18
Alignment explanation
Indices: 83887--83924 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
83877 TTTTAAGATT
83887 TTATATTCAATTTAAATA
1 TTATATTCAATTTAAATA
*
83905 TTATATTCAATTTAATTA
1 TTATATTCAATTTAAATA
83923 TT
1 TT
83925 TGAATATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATTCAATTTAAATA
Found at i:85307 original size:22 final size:19
Alignment explanation
Indices: 85264--85318 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 19
85254 ATTGGCATGT
85264 TTTTGAAACCCCTTTCTGG
1 TTTTGAAACCCCTTTCTGG
*
85283 TTTTGAAACCCTTATATACTGG
1 TTTTGAAACCCCT-T-T-CTGG
85305 TTTTGAAACCCCTT
1 TTTTGAAACCCCTT
85319 GATTGGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 12 0.39
20 1 0.03
21 2 0.06
22 16 0.52
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.42
Consensus pattern (19 bp):
TTTTGAAACCCCTTTCTGG
Found at i:91618 original size:31 final size:31
Alignment explanation
Indices: 91580--91699 Score: 153
Period size: 31 Copynumber: 4.0 Consensus size: 31
91570 CCCGAAGGAC
* * *
91580 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
91611 CAGTCCATA--T-CCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
91639 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
91670 CAGTCCATATGTCCCGAAGAAC--AGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
91699 C
1 C
91700 CCTCGACCCT
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
28 24 0.29
29 9 0.11
30 1 0.01
31 48 0.59
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:92639 original size:21 final size:21
Alignment explanation
Indices: 92615--92659 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
92605 TGTTGTTCGT
* *
92615 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
92636 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
92657 TTG
1 TTG
92660 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:95815 original size:31 final size:31
Alignment explanation
Indices: 95740--95850 Score: 179
Period size: 31 Copynumber: 3.6 Consensus size: 31
95730 CCAGTCCATT
* *
95740 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* *
95771 CAG-AGGACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
95801 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
95832 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
95851 CCTCGACCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
30 26 0.36
31 47 0.64
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:96786 original size:20 final size:20
Alignment explanation
Indices: 96763--96803 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
96753 GTTGTTCGTT
* *
96763 TGAAGGGGTATCGGTTCCCC
1 TGAAGGGGTACCGATTCCCC
*
96783 TGAATGGGTACCGATTCCCC
1 TGAAGGGGTACCGATTCCCC
96803 T
1 T
96804 TGCCCAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (20 bp):
TGAAGGGGTACCGATTCCCC
Done.