Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006150.1 Hibiscus syriacus cultivar Beakdansim tig00014609_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: 51276
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:8386 original size:1 final size:1
Alignment explanation
Indices: 8376--8449 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
8366 ATGCTTGAAG
* * * * * * * * *
8376 AAAAAGAAAAAAAAAAGAGAAAAGAAAAAGAAAAAAAAAAGAGAAAAAAAAGAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
8441 AAGAAAAAA
1 AAAAAAAAA
8450 GGGGGGTCAA
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:8392 original size:11 final size:11
Alignment explanation
Indices: 8376--8450 Score: 98
Period size: 11 Copynumber: 6.5 Consensus size: 11
8366 ATGCTTGAAG
8376 AAAAAGAAAAA
1 AAAAAGAAAAA
8387 AAAAAGAGAAAA
1 AAAAAGA-AAAA
8399 GAAAAAGAAAAA
1 -AAAAAGAAAAA
*
8411 AAAAAGAGAAA
1 AAAAAGAAAAA
8422 AAAAAGAAAAA
1 AAAAAGAAAAA
8433 AAGAAA-AAAAGA
1 AA-AAAGAAAA-A
8445 AAAAAG
1 AAAAAG
8451 GGGGGTCAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
11 36 0.63
12 14 0.25
13 7 0.12
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:8398 original size:8 final size:8
Alignment explanation
Indices: 8373--8449 Score: 77
Period size: 8 Copynumber: 9.1 Consensus size: 8
8363 ATTATGCTTG
8373 AAGAAAAA
1 AAGAAAAA
*
8381 GAAAAAAAA
1 -AAGAAAAA
8390 AAGAGAAAA
1 AAGA-AAAA
8399 GAA-AAAGAA
1 -AAGAAA-AA
8408 AA-AAAAA
1 AAGAAAAA
8415 AGAGAAAAAA
1 A-AG-AAAAA
8425 AAGAAAAA
1 AAGAAAAA
8433 AAGAAAAA
1 AAGAAAAA
8441 AAGAAAAA
1 AAGAAAAA
8449 A
1 A
8450 GGGGGGTCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
7 3 0.05
8 33 0.55
9 16 0.27
10 8 0.13
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:8398 original size:19 final size:19
Alignment explanation
Indices: 8374--8442 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 19
8364 TTATGCTTGA
8374 AGAAAAAGAAAAAAAAAAG
1 AGAAAAAGAAAAAAAAAAG
*
8393 AG-AAAAGAAAAAGAAAA-
1 AGAAAAAGAAAAAAAAAAG
*
8410 A-AAAAAGAGAAAAAAAAG
1 AGAAAAAGAAAAAAAAAAG
*
8428 AAAAAAAGAAAAAAA
1 AGAAAAAGAAAAAAA
8443 GAAAAAAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
17 14 0.33
18 15 0.35
19 14 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (19 bp):
AGAAAAAGAAAAAAAAAAG
Found at i:8402 original size:24 final size:24
Alignment explanation
Indices: 8373--8448 Score: 115
Period size: 24 Copynumber: 3.3 Consensus size: 24
8363 ATTATGCTTG
8373 AAGAAAAAGAAAAAAAAAAGAGAA
1 AAGAAAAAGAAAAAAAAAAGAGAA
8397 AAGAAAAAGAAAAAAAAAAGAG-A
1 AAGAAAAAGAAAAAAAAAAGAGAA
*
8420 AA-AAAAAGAAAAAAAGAA-A-AA
1 AAGAAAAAGAAAAAAAAAAGAGAA
8441 AAGAAAAA
1 AAGAAAAA
8449 AGGGGGGTCA
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
21 4 0.08
22 20 0.41
23 3 0.06
24 22 0.45
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (24 bp):
AAGAAAAAGAAAAAAAAAAGAGAA
Found at i:8415 original size:35 final size:35
Alignment explanation
Indices: 8376--8449 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
8366 ATGCTTGAAG
*
8376 AAAAAGAAAAAAAAAAG-AGAAAAGAAAAAGAAAAA
1 AAAAAGAAAAAAAAAAGAAAAAAAGAAAAA-AAAAA
* *
8411 AAAAAGAGAAAAAAAAGAAAAAAAGAAAAAAAGAA
1 AAAAAGAAAAAAAAAAGAAAAAAAGAAAAAAAAAA
8446 AAAA
1 AAAA
8450 GGGGGGTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 24 0.69
36 11 0.31
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (35 bp):
AAAAAGAAAAAAAAAAGAAAAAAAGAAAAAAAAAA
Found at i:9587 original size:83 final size:83
Alignment explanation
Indices: 9486--9858 Score: 695
Period size: 83 Copynumber: 4.6 Consensus size: 83
9476 AATAGAACAA
9486 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
9551 AAGCATTGAGTTTAGAAG
66 AAGCATTGAGTTTAGAAG
9569 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
9634 AAGCATTGAGTTTAGAAG
66 AAGCATTGAGTTTAGAAG
*
9652 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTTATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
9717 AAGCATTGAGTTTAGAAG
66 AAGCATTGAGTTTAGAAG
9735 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
9800 AAGCATT--G---A-AAG
66 AAGCATTGAGTTTAGAAG
9812 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
9859 GTTTGGTATG
Statistics
Matches: 288, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
77 50 0.17
78 1 0.00
81 1 0.00
83 236 0.82
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATC
AAGCATTGAGTTTAGAAG
Found at i:11226 original size:114 final size:113
Alignment explanation
Indices: 10691--11548 Score: 1291
Period size: 114 Copynumber: 7.6 Consensus size: 113
10681 GATTCAATCT
** * *
10691 ATCATTTGAAAGATCAGCTTTTCCAGAG--ATTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
10754 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
*
10802 ATCATTTGAT-GATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
10865 GAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
66 G-AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
*
10914 ATCATTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
10978 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
*
11026 ATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
11091 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * *
11139 ATCAAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGA
1 ATC-ATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* **
11204 AGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTTTCTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * * *
11253 A--AATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * * *
11316 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * * *
11364 ATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGA
1 ATC-ATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
11429 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* ** *
11478 ATCATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-
1 ATCATTTGATGGATCATCTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
11542 AGAAGAA
65 AGAAGAA
11549 TTTATTCAAT
Statistics
Matches: 711, Mismatches: 27, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
110 17 0.02
111 148 0.21
112 132 0.19
113 164 0.23
114 250 0.35
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:11262 original size:225 final size:225
Alignment explanation
Indices: 10708--11548 Score: 1307
Period size: 225 Copynumber: 3.7 Consensus size: 225
10698 GAAAGATCAG
* *
10708 CTTTTCCAGAG-ATTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 CTTTTCCAGAGAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
10772 AAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAT-GATCAGCTTTTCCAGAG-AAGTTC
66 AAGAATTTGTTCAACCTTTTACCTGAATCCA-CATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
*
10835 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
130 ATAATGAGAAGAACTCATCTGAAGAAGGAAG-AAGAAGTTCATAATGAGAAGAACTTGTTCAACC
* * * *
10900 TTTTACCTGAATCCATC-ATTTGATGGATCAG
194 TTTTACCTGAATTCATCAAATTGATGGATTAT
*
10931 CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 CTTTTCCAGAGAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
10996 AAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
66 AAGAATTTGTTCAACCTTTTACCTGAATCCA-CATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
11061 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
130 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
11126 TTTACCTGAATTCATCAAATTGATGGATTAT
195 TTTACCTGAATTCATCAAATTGATGGATTAT
11157 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAG-AAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* ** * * * * *
11222 GAAGAATTTATTCAACCTTTTTTCTGAATTCA-AATTGATGGATTATCTTTTCCAGAGAAGGTTC
65 GAAGAATTTGTTCAACCTTTTACCTGAATCCACATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
* *
11286 ATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCT
130 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
* *
11351 TTTGCTTGAATTCATCAAATTGATGGATTAT
195 TTTACCTGAATTCATCAAATTGATGGATTAT
11382 CTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAA-GTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * * * * **
11447 GAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCATCCCCAGCAGAAAGT
65 GAAGAATTTGTTCAACCTTTTACCTGAATCCA-CATTTGATGGATCAGCTTTTCCAG-AGAAAGT
*
11512 TCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
128 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
11549 TTTATTCAAT
Statistics
Matches: 576, Mismatches: 33, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
223 11 0.02
224 94 0.16
225 273 0.47
226 59 0.10
227 105 0.18
228 34 0.06
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (225 bp):
CTTTTCCAGAGAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTTTACCTGAATCCACATTTGATGGATCAGCTTTTCCAGAGAAAGTTCA
TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
TTACCTGAATTCATCAAATTGATGGATTAT
Found at i:11426 original size:339 final size:336
Alignment explanation
Indices: 10702--11548 Score: 1308
Period size: 339 Copynumber: 2.5 Consensus size: 336
10692 TCATTTGAAA
*
10702 GATCAGCTTTTCCAGAG-ATTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 GATCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
10766 AATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAT-GATCAGCTTTTCCAGAG-
66 AATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCATCTTTTCCAGAGA
*
10829 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAGAAGTTCATAATGAGAAGAATTTGT
131 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AAGAAGTTCATAATGAGAAGAATTTAT
*
10894 TCAACCTTTTACCTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATGAGAAG
195 TCAACCTTTTACCTGAATCCA-CAATTGATGGATCAGCTTTTCCAGAGAAGTTCATAATGAGAAG
* *
10959 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
259 AACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAAT
*
11024 CCATCATTTGATG
324 CCATCAATTGATG
11037 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
11102 TAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGA
65 TAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATC-ATTTGATGGATCATCTTTTCCAGA
*
11167 GAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTA
129 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTA
** * * *
11232 TTCAACCTTTTTTCTGAATTCA-AATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAA
194 TTCAACCTTTTACCTGAATCCACAATTGATGGATCAGCTTTTCCAGAGAA-GTTCATAATGAGAA
* * *
11296 GAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAA
258 GAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAA
*
11361 TTCATCAAATTGATG
323 TCCATC-AATTGATG
* * *
11376 GATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCAGCTTTTCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * * **
11441 TAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCATCCCCAGCA
65 TAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCATCTTTTCCAG-A
*
11506 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
129 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
11549 TTTATTCAAT
Statistics
Matches: 469, Mismatches: 34, Indels: 15
0.91 0.07 0.03
Matches are distributed among these distances:
335 17 0.04
337 107 0.23
338 112 0.24
339 197 0.42
340 36 0.08
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (336 bp):
GATCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCATCTTTTCCAGAGA
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATT
CAACCTTTTACCTGAATCCACAATTGATGGATCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAA
CCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATCC
ATCAATTGATG
Found at i:11700 original size:3 final size:3
Alignment explanation
Indices: 11685--11773 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
11675 TTTTTATCCA
* * *
11685 TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
11733 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
11774 AATATATATT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:18237 original size:22 final size:22
Alignment explanation
Indices: 18190--18239 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
18180 GGAACATTAT
*
18190 CGATCCAAGTCAGAAACAATAC
1 CGATCCAAGTCAGAAACAATAA
* *
18212 CGATCCAATTCAGTAAA-ACTAA
1 CGATCCAAGTCAG-AAACAATAA
18234 CGATCC
1 CGATCC
18240 CATTTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (22 bp):
CGATCCAAGTCAGAAACAATAA
Found at i:22596 original size:20 final size:20
Alignment explanation
Indices: 22552--22765 Score: 189
Period size: 20 Copynumber: 10.6 Consensus size: 20
22542 GATTCTGACT
* *
22552 ATCGCAACGAGTATCCATAAA
1 ATCGCAACGCGTATCCGT-AA
22573 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
22593 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
22614 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
22634 ATCGCAACGAGAATACATAA
1 ATCGCAACGCGTATCCGTAA
* **
22654 ATCGCAACGTGTATCTATAA
1 ATCGCAACGCGTATCCGTAA
* * * *
22674 ATCACAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
22694 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
22714 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
22735 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
22755 ATCACAACGCG
1 ATCGCAACGCG
22766 ATTTTTAAAG
Statistics
Matches: 154, Mismatches: 33, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
20 105 0.68
21 49 0.32
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:22597 original size:41 final size:41
Alignment explanation
Indices: 22552--22763 Score: 293
Period size: 41 Copynumber: 5.2 Consensus size: 41
22542 GATTCTGACT
* * *
22552 ATCGCAACGAGTATCCATAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
22593 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * **
22634 ATCGCAACGAGAATACAT-AAATCGCAACGTGTATCTATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
22674 ATCACAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
22714 ATCGCAACGACAATACGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
22755 ATCACAACG
1 ATCGCAACG
22764 CGATTTTTAA
Statistics
Matches: 150, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 69 0.46
41 81 0.54
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:23338 original size:19 final size:19
Alignment explanation
Indices: 23314--23433 Score: 97
Period size: 19 Copynumber: 6.5 Consensus size: 19
23304 TTCTAAACTT
*
23314 AAAATCGCAACATGAAATG
1 AAAATCGCAACACGAAATG
23333 AAAATCGCAACACGAAATG
1 AAAATCGCAACACGAAATG
** *
23352 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-A-CGAAATG
**
23373 ACTATCGC-A-ACG--A-G
1 AAAATCGCAACACGAAATG
*
23387 AGAATCGCAACACGAAATG
1 AAAATCGCAACACGAAATG
* **
23406 AAAATCGCAACGCGAAACC
1 AAAATCGCAACACGAAATG
23425 AAAATCGCA
1 AAAATCGCA
23434 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
14 7 0.08
15 2 0.02
16 3 0.04
17 1 0.01
18 2 0.02
19 52 0.63
20 2 0.02
21 14 0.17
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:23372 original size:21 final size:21
Alignment explanation
Indices: 23346--23390 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
23336 ATCGCAACAC
23346 GAAATGACTATCGCAACGAGA
1 GAAATGACTATCGCAACGAGA
23367 GAAATGACTATCGCAACGAGA
1 GAAATGACTATCGCAACGAGA
23388 GAA
1 GAA
23391 TCGCAACACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (21 bp):
GAAATGACTATCGCAACGAGA
Found at i:23520 original size:20 final size:20
Alignment explanation
Indices: 23458--23513 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
23448 TCGCGTTGCG
23458 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
* *
23478 ATT-TACGCATTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
23498 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
23514 TTTCATTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:25540 original size:94 final size:92
Alignment explanation
Indices: 25212--25587 Score: 594
Period size: 93 Copynumber: 4.1 Consensus size: 92
25202 TAGATTGCTT
* *
25212 AGTAAATTTATTCGGTTGCTACCAATAT-TGCTAAACTGTTTATTC-TTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAAT-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
25275 TATTTGTCTTTGTTTTGTCTTTTGGTTGA
65 TATTTGTCTTTGTTTTGTC-TTTGGTTGA
* *
25304 AGTAAATTTATTTGGTTGCTGCCAATTCGGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* * *
25369 ATTTGTCTTTGTTTTATCTTTGGTGGGG
66 ATTTGTCTTTGTTTTGTCTTTGGT-TGA
*
25397 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
25462 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTC-TTTGGTTG-A
* * *
25491 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
25556 ATTTGTCTTTGTTTTGTCTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTGGTTGA
25583 AGTAA
1 AGTAA
25588 TGCAATCCAT
Statistics
Matches: 264, Mismatches: 15, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
91 1 0.00
92 51 0.19
93 125 0.47
94 87 0.33
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.47
Consensus pattern (92 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTGGTTGA
Found at i:25552 original size:187 final size:185
Alignment explanation
Indices: 25212--25579 Score: 621
Period size: 187 Copynumber: 2.0 Consensus size: 185
25202 TAGATTGCTT
*
25212 AGTAAATTTATTCGGTTGCTACCAATATTGCTAAACTGTTTATTCTTAACACTGTGAAGTTAGTA
1 AGTAAATTTATTCGGTTGCTACCAATATTGCTAAACTGTGTATTCTTAACACTGTGAAGTTAGTA
*
25277 TTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTTGGTTGCTGCCAATTCGGCTAAACTG
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCGGCTAAACTG
*
25342 TGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTATCTTTGGTGGGG
131 TGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTATCTTTGGTGGGG
* *
25397 AGTAAATTTGTTCGGTTGCTGCCAAT-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTACCAATAT-TGCTAAACTGTGTATTC-TTAACACTGTGAAGTTAG
* *
25461 TATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAA
64 TATTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTCGGCTAAA
* *
25526 CTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTGGT
128 CTGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTATCTTTGGT
25580 TGAAGTAATG
Statistics
Matches: 171, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
184 1 0.01
185 40 0.23
186 46 0.27
187 84 0.49
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.47
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTACCAATATTGCTAAACTGTGTATTCTTAACACTGTGAAGTTAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCGGCTAAACTG
TGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTATCTTTGGTGGGG
Found at i:25718 original size:19 final size:20
Alignment explanation
Indices: 25696--25742 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
25686 AAATGAATTG
25696 CGCAACGAGAAAT-GAAAAT
1 CGCAACGAGAAATCGAAAAT
25715 CGCAACGAGAAATGCGAAAAT
1 CGCAACGAGAAAT-CGAAAAT
*
25736 CGAAACG
1 CGCAACG
25743 CAACGCGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 13 0.52
21 12 0.48
ACGTcount: A:0.49, C:0.19, G:0.23, T:0.09
Consensus pattern (20 bp):
CGCAACGAGAAATCGAAAAT
Found at i:25752 original size:19 final size:20
Alignment explanation
Indices: 25728--25771 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
25718 AACGAGAAAT
25728 GCGAAAATCG-AAA-CGCAAC
1 GCGAAAA-CGAAAATCGCAAC
25747 GCG-AAACGAAAATCGCAAC
1 GCGAAAACGAAAATCGCAAC
25766 GCGAAA
1 GCGAAA
25772 CTATAATCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 6 0.27
19 12 0.55
20 2 0.09
ACGTcount: A:0.48, C:0.25, G:0.23, T:0.05
Consensus pattern (20 bp):
GCGAAAACGAAAATCGCAAC
Found at i:25868 original size:20 final size:20
Alignment explanation
Indices: 25816--25874 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
25806 GATTCTCTCG
**
25816 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
25836 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
25856 TTGCGATAGTCATTTTCGC
1 TTGCGATAGTCATTTTCGC
25875 GTTGTGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:26456 original size:21 final size:21
Alignment explanation
Indices: 26365--26469 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
26355 GACTCACCTG
* *
26365 TCATCGTTTAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
26387 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
26407 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
26428 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
26449 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
26470 CCAACATTCT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:26462 original size:42 final size:42
Alignment explanation
Indices: 26362--26472 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
26352 CCCGACTCAC
* * * * *
26362 CTGTCATCGTTTAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
26404 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
26446 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
26473 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:27869 original size:13 final size:13
Alignment explanation
Indices: 27822--27874 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
27812 TTGATTGTTT
27822 AATTGATTTGTAA
1 AATTGATTTGTAA
*
27835 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
27849 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
27863 AATTGATGTGTA
1 AATTGATTTGTA
27875 CATAATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:28050 original size:34 final size:33
Alignment explanation
Indices: 27962--28057 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
27952 AAAACAGACT
* ** *
27962 ATCGCAACGCGGAAATGACTATCGCAACAAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
27996 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
28029 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
28058 CAGGGTCTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:28120 original size:24 final size:24
Alignment explanation
Indices: 28086--28163 Score: 122
Period size: 24 Copynumber: 3.2 Consensus size: 24
28076 CTGAAAAATA
*
28086 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
*
28110 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
28134 ATCAAAGTCC-AGGTATTGACCAAG
1 ATCAAAGTCCGA-GTATTGACCAAG
28158 ATCAAA
1 ATCAAA
28164 TTTCGAATAC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
ATCAAAGTCCGAGTATTGACCAAG
Found at i:29052 original size:20 final size:19
Alignment explanation
Indices: 29023--29317 Score: 218
Period size: 20 Copynumber: 14.6 Consensus size: 19
29013 GTCAGAATCT
*
29023 CGTTGTGATTTACAGATTCG
1 CGTTGCGATTTAC-GATTCG
*
29043 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACG-ATTCG
* *
29063 CATTGCGATTTACGTAATCG
1 CGTTGCGATTTACG-ATTCG
* *
29083 CATTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCG
29103 CGTTGCGATTTTACGTATT-G
1 CGTTGCGA-TTTACG-ATTCG
*
29123 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTAC-GATTCG
* *
29144 CGTTGCGATTTACATATTCT
1 CGTTGCGATTTAC-GATTCG
*
29164 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTAC-GATTCG
* *
29184 CGTTACGATTTACGTATTCT
1 CGTTGCGATTTACG-ATTCG
*
29204 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCG
29224 CGTTGCGATTTTACGTATT-G
1 CGTTGCGA-TTTACG-ATTCG
* *
29244 TCGTTACGATTTACGGATACG
1 -CGTTGCGATTTAC-GATTCG
* *
29265 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTAC-GATTCG
* *
29286 CGTTGCGATAGT-CAGAATCG
1 CGTTGCGAT-TTAC-GATTCG
29306 CGTTGCGATTTA
1 CGTTGCGATTTA
29318 TATGTTCGCG
Statistics
Matches: 226, Mismatches: 32, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
19 3 0.01
20 168 0.74
21 55 0.24
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATTTACGATTCG
Found at i:29193 original size:121 final size:121
Alignment explanation
Indices: 29023--29294 Score: 402
Period size: 121 Copynumber: 2.2 Consensus size: 121
29013 GTCAGAATCT
* * * * *
29023 CGTTGTGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTG
1 CGTTGCGATTTACAGATTCTCGTTGCGATTTACGTATACGCATTACGATTTACGTAATCGCATTG
*
29088 CGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
66 CGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTACGATTTACGGATACG
* * * * *
29144 CGTTGCGATTTACATATTCTCGTTGCGATTTACAG-ATACGCGTTACGATTTACGTATTCTCGTT
1 CGTTGCGATTTACAGATTCTCGTTGCGATTTAC-GTATACGCATTACGATTTACGTAATCGCATT
29208 GCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTACGATTTACGGATACG
65 GCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTACGATTTACGGATACG
* *
29265 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGA-TTTACAGATTCTCGTTGCGAT
29295 AGTCAGAATC
Statistics
Matches: 135, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
121 116 0.86
122 19 0.14
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (121 bp):
CGTTGCGATTTACAGATTCTCGTTGCGATTTACGTATACGCATTACGATTTACGTAATCGCATTG
CGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTACGATTTACGGATACG
Found at i:29316 original size:41 final size:41
Alignment explanation
Indices: 29045--29294 Score: 353
Period size: 40 Copynumber: 6.2 Consensus size: 41
29035 CAGATTCGCA
* * * * * *
29045 TTGCGATTTACGTATTCGCATTGCGA-TTTACGTAATCGCA
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
*
29085 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
*
29126 TTGCGATTTACGGATACGCGTTGCGA-TTTACATATTCTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
* *
29166 TTGCGATTTACAGATACGCGTTACGA-TTTACGTATTCTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
*
29206 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
* * *
29247 TTACGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
29288 TTGCGAT
1 TTGCGAT
29295 AGTCAGAATC
Statistics
Matches: 188, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
40 96 0.51
41 92 0.49
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCG
Found at i:29326 original size:20 final size:20
Alignment explanation
Indices: 29303--29355 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
29293 ATAGTCAGAA
*
29303 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
*
29323 TCGCGATGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
29343 TCGCGTTACGATT
1 TCGCGTTGCGATT
29356 CTGGAAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:36127 original size:2 final size:2
Alignment explanation
Indices: 36120--36169 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
36110 AATCAAACTT
36120 TA TA 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 TA TA TA
36161 TA TA T- TA TA
1 TA TA TA TA TA
36170 CCTACAAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37162 original size:33 final size:32
Alignment explanation
Indices: 37123--37233 Score: 151
Period size: 33 Copynumber: 3.6 Consensus size: 32
37113 CCTAAACCCG
*
37123 AACCCGACCCAACCCGAATATCACACTAAAAA
1 AACCCGACCCGACCCGAATATCACACTAAAAA
37155 AACCCCGACCCGACCCGAATATCACACTTAAAAA
1 AA-CCCGACCCGACCCGAATATCACAC-TAAAAA
*
37189 AACCCGACCCGA----AA-ATCACACTTAAAA
1 AACCCGACCCGACCCGAATATCACACTAAAAA
37216 AACCCGACCCGACCCGAA
1 AACCCGACCCGACCCGAA
37234 CAAAATAAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
27 17 0.24
28 7 0.10
29 2 0.03
31 2 0.03
32 2 0.03
33 33 0.46
34 8 0.11
ACGTcount: A:0.43, C:0.39, G:0.09, T:0.09
Consensus pattern (32 bp):
AACCCGACCCGACCCGAATATCACACTAAAAA
Found at i:37223 original size:27 final size:28
Alignment explanation
Indices: 37162--37227 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
37152 AAAAACCCCG
*
37162 ACCCGACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGAAAATCACACTTAAAAAA
37190 ACCCGACCCGAAAATCACACTT-AAAAA
1 ACCCGACCCGAAAATCACACTTAAAAAA
37217 ACCCGACCCGA
1 ACCCGACCCGA
37228 CCCGAACAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 16 0.43
28 21 0.57
ACGTcount: A:0.44, C:0.36, G:0.09, T:0.11
Consensus pattern (28 bp):
ACCCGACCCGAAAATCACACTTAAAAAA
Found at i:44227 original size:24 final size:24
Alignment explanation
Indices: 44181--44227 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
44171 GCCTATTCAT
* * *
44181 AGTTTTTATTTTTATTTTTAAATA
1 AGTTATTATTTTTATATTCAAATA
*
44205 AGTTATTATTTTTGTATTCAAAT
1 AGTTATTATTTTTATATTCAAAT
44228 TAAAATGGTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (24 bp):
AGTTATTATTTTTATATTCAAATA
Done.