Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008096.1 Hibiscus syriacus cultivar Beakdansim tig00110616_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: 303958
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8238 original size:91 final size:92
Alignment explanation
Indices: 7891--8440 Score: 907
Period size: 92 Copynumber: 6.1 Consensus size: 92
7881 TAAGGAGACC
7891 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
7956 TTATTGAATTTGGAAGAGGAATGTGCT
66 TTATTGAATTTGGAAGAGGAATGTGCT
7983 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
*
8048 TTATTGAATTTGGAAGAGGAATATGCT
66 TTATTGAATTTGGAAGAGGAATGTGCT
*
8075 CATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
8140 TTA-TGAATTTGGAAGAGGAATGTGCT
66 TTATTGAATTTGGAAGAGGAATGTGCT
8166 CATAGCATCTTCTGGAAGTGTTCTTTGAG-TATCTGATCTGGTTTGGTATGAACCACAGAACCAG
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
8230 TTATTGAATTTGGAAGAGGAATGTGCT
66 TTATTGAATTTGGAAGAGGAATGTGCT
*
8257 CATAGCA---TCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGTATGAACCACAGAACCAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
* *
8318 TCATTGAATTTGGAAGA-CAATGTGCT
66 TTATTGAATTTGGAAGAGGAATGTGCT
* * * * * *
8344 CATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCCCAAAACCAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
* ** * *
8409 TCATTGAATTTAAAAGATGAATTTGCT
66 TTATTGAATTTGGAAGAGGAATGTGCT
8436 CATAG
1 CATAG
8441 TAGAAATAAG
Statistics
Matches: 435, Mismatches: 16, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
87 15 0.03
88 56 0.13
89 12 0.03
90 67 0.15
91 115 0.26
92 170 0.39
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (92 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
TTATTGAATTTGGAAGAGGAATGTGCT
Found at i:8392 original size:179 final size:182
Alignment explanation
Indices: 7901--8441 Score: 876
Period size: 179 Copynumber: 3.0 Consensus size: 182
7891 CATAGCATCT
7901 TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATT
1 TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATT
*
7966 TGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
66 TGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGT
*
8031 ATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATATGCTCATAGTATCT
131 ATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATATGCTCATAG--TCA
8085 TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTA-TGAATT
1 TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATT
*
8149 TGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTG-AGTATCTGATCTGGTTTGGT
66 TGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGT
*
8213 ATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATGTGCTCATAG-CA
131 ATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATATGCTCATAGTCA
* *
8264 TCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGTATGAACCACAGAACCAATCATTGAATT
1 TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATT
* * *
8328 TGGAAGA-CAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGT
66 TGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGT
* * * * ** * *
8392 ATGAACCCCAAAACCAATCATTGAATTTAAAAGATGAATTTGCTCATAGT
131 ATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATATGCTCATAGT
8442 AGAAATAAGG
Statistics
Matches: 336, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
178 58 0.17
179 104 0.31
182 66 0.20
183 50 0.15
184 58 0.17
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (182 bp):
TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATT
TGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGT
ATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATATGCTCATAGTCA
Found at i:11028 original size:21 final size:22
Alignment explanation
Indices: 10975--11028 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
10965 ATCTACACTC
*
10975 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
10997 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
11019 TTCAAA-ATGA
1 TTCAAAGATGA
11029 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:11828 original size:76 final size:76
Alignment explanation
Indices: 11702--12115 Score: 785
Period size: 76 Copynumber: 5.5 Consensus size: 76
11692 CTATTTCCCA
11702 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
11767 ATCCTTCGGGT
66 AGCCTTCGGGT
*
11778 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
11843 AGCCTTCGGGT
66 AGCCTTCGGGT
11854 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
11919 AGCCTTCGGGT
66 AGCCTTCGGGT
11930 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
11994 AGCCTTCGGGT
66 AGCCTTCGGGT
12005 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
12070 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
12081 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
12116 CATTTCCATC
Statistics
Matches: 332, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
75 75 0.23
76 257 0.77
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:12071 original size:151 final size:151
Alignment explanation
Indices: 11702--12115 Score: 783
Period size: 151 Copynumber: 2.7 Consensus size: 151
11692 CTATTTCCCA
11702 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
11767 ATCCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTT
11832 GATGTTTTCAAAGCCTTCGGGT
130 GATGTTTTCAAAGCCTTCGGGT
11854 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
11919 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTTTG
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTTTG
11984 ATGTTTTCAAAGCCTTCGGGT
131 ATGTTTTCAAAGCCTTCGGGT
12005 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
12070 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
12116 CATTTCCATC
Statistics
Matches: 258, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
151 152 0.59
152 106 0.41
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (151 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTTTG
ATGTTTTCAAAGCCTTCGGGT
Found at i:12098 original size:227 final size:228
Alignment explanation
Indices: 11702--12115 Score: 785
Period size: 227 Copynumber: 1.8 Consensus size: 228
11692 CTATTTCCCA
11702 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
11767 ATCCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
11832 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
11897 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
11930 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
11994 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
12059 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAA
12116 CATTTCCATC
Statistics
Matches: 182, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
227 150 0.82
228 32 0.18
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (228 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
Found at i:12247 original size:3 final size:3
Alignment explanation
Indices: 12241--12368 Score: 159
Period size: 3 Copynumber: 41.7 Consensus size: 3
12231 TCATTTAAAT
* *
12241 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* * *
12287 TTA GTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
12336 TTA TTA TTA TTA ATA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
12369 TAATAAATAA
Statistics
Matches: 110, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
2 1 0.01
3 100 0.91
4 9 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:33250 original size:19 final size:19
Alignment explanation
Indices: 33226--33265 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
33216 CTAAATTGAA
33226 TAGACTCGGTTTAAGTTAT
1 TAGACTCGGTTTAAGTTAT
33245 TAGACTCGGTTTAAGTTAT
1 TAGACTCGGTTTAAGTTAT
33264 TA
1 TA
33266 ACGAATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (19 bp):
TAGACTCGGTTTAAGTTAT
Found at i:35553 original size:12 final size:12
Alignment explanation
Indices: 35536--35568 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35526 GCTTAGGTGG
35536 TCCTATAAAATA
1 TCCTATAAAATA
35548 TCCTATAAAATA
1 TCCTATAAAATA
35560 T--TATAAAAT
1 TCCTATAAAAT
35569 GGCATCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
12 13 0.62
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (12 bp):
TCCTATAAAATA
Found at i:46500 original size:29 final size:31
Alignment explanation
Indices: 46463--46522 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
46453 TTGTAATTAT
*
46463 TTAGTCATTAAATTT-TTAAA-TATTATAAA
1 TTAGACATTAAATTTATTAAATTATTATAAA
46492 TTAGACATTAAATTTATTAAATTATTATAAA
1 TTAGACATTAAATTTATTAAATTATTATAAA
46523 ATATTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 14 0.50
30 5 0.18
31 9 0.32
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
TTAGACATTAAATTTATTAAATTATTATAAA
Found at i:46529 original size:21 final size:20
Alignment explanation
Indices: 46469--46531 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
46459 TTATTTAGTC
46469 ATTAAATT-TT-TAAATATT
1 ATTAAATTATTATAAATATT
**
46487 A-TAAATTAGACATTAAAT-TT
1 ATTAAATTA-TTA-TAAATATT
46507 ATTAAATTATTATAAAATATT
1 ATTAAATTATTAT-AAATATT
46528 ATTA
1 ATTA
46532 TGTATAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
17 6 0.18
18 1 0.03
19 1 0.03
20 8 0.24
21 18 0.53
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTAAATTATTATAAATATT
Found at i:49904 original size:29 final size:27
Alignment explanation
Indices: 49841--49904 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 27
49831 TTATTTTCAC
* **
49841 ATTATAATATTATTTAATATATCAAAT
1 ATTATAAAATTATAAAATATATCAAAT
49868 ATAATATAAAATTATAAAATATATTCACAAT
1 AT--TATAAAATTATAAAATATA-TCA-AAT
49899 ATTATA
1 ATTATA
49905 CTTTAAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.07
29 20 0.67
30 3 0.10
31 5 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (27 bp):
ATTATAAAATTATAAAATATATCAAAT
Found at i:63591 original size:21 final size:21
Alignment explanation
Indices: 63567--63614 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
63557 GAAAATATTT
* *
63567 ATTTTAGATAGAGAAATTAAC
1 ATTTTAGATAGAAAAAATAAC
** *
63588 ATTTCCGATATAAAAAATAAC
1 ATTTTAGATAGAAAAAATAAC
63609 ATTTTA
1 ATTTTA
63615 AGTAATACTC
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (21 bp):
ATTTTAGATAGAAAAAATAAC
Found at i:71501 original size:14 final size:14
Alignment explanation
Indices: 71482--71510 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
71472 TGCGCCTCGC
71482 GCCTCAAGGCTCCA
1 GCCTCAAGGCTCCA
71496 GCCTCAAGGCTCCA
1 GCCTCAAGGCTCCA
71510 G
1 G
71511 GACACTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.41, G:0.24, T:0.14
Consensus pattern (14 bp):
GCCTCAAGGCTCCA
Found at i:74540 original size:23 final size:22
Alignment explanation
Indices: 74500--74551 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
74490 CATAATTATT
74500 AAAAAAATTAAATAAAAATACC
1 AAAAAAATTAAATAAAAATACC
* * *
74522 AAAAACATTTAATAAAAA-A-T
1 AAAAAAATTAAATAAAAATACC
74542 AAAAAAATTA
1 AAAAAAATTA
74552 GGTTGAACCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 8 0.32
21 1 0.04
22 16 0.64
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAAAATTAAATAAAAATACC
Found at i:75112 original size:25 final size:22
Alignment explanation
Indices: 75067--75110 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
75057 TAAATAATTT
*
75067 AATTATATTATATTTTAAAATA
1 AATTATATTACATTTTAAAATA
75089 AATTATTATTACATTATTAAAA
1 AATTA-TATTACATT-TTAAAA
75111 ATGATCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 8 0.42
24 6 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTATATTACATTTTAAAATA
Found at i:82171 original size:28 final size:28
Alignment explanation
Indices: 82118--82177 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
82108 TTATTTCACT
* *
82118 AATTTTTTTATAAAATTGAATTAAA-TG
1 AATTTTTTTATAAAATTCAATGAAATTG
82145 AATTTTTTTATAAAATTTCAATGAAATTG
1 AATTTTTTTATAAAA-TTCAATGAAATTG
82174 AATT
1 AATT
82178 AGAAAGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 15 0.52
28 8 0.28
29 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (28 bp):
AATTTTTTTATAAAATTCAATGAAATTG
Found at i:82369 original size:24 final size:24
Alignment explanation
Indices: 82342--82392 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
82332 TTTGATATTT
*
82342 AATT-TTTTAATATTTTTTATTATA
1 AATTATTTTAAT-TTTTTTATTAAA
* *
82366 AATTATTTTTATTTTTTTCTTAAA
1 AATTATTTTAATTTTTTTATTAAA
82390 AAT
1 AAT
82393 CAAATAAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
AATTATTTTAATTTTTTTATTAAA
Found at i:91504 original size:24 final size:24
Alignment explanation
Indices: 91475--91543 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 24
91465 GCTTCTTTTC
91475 CTTTTCCTTTTCCTTCTTGTCTTT
1 CTTTTCCTTTTCCTTCTTGTCTTT
* *
91499 CTTTTCTTTCTTCTCCTTGTTGTCTTT
1 CTTTTC---CTTTTCCTTCTTGTCTTT
*
91526 CATCTT-CTTTTCCTTCTT
1 C-TTTTCCTTTTCCTTCTT
91544 TCCGTGGTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
24 16 0.44
27 17 0.47
28 3 0.08
ACGTcount: A:0.01, C:0.29, G:0.04, T:0.65
Consensus pattern (24 bp):
CTTTTCCTTTTCCTTCTTGTCTTT
Found at i:100122 original size:15 final size:16
Alignment explanation
Indices: 100093--100125 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
100083 ATAAGTTATT
100093 TTTTCAATTTATATAA
1 TTTTCAATTTATATAA
*
100109 TTTT-AATTTGTATAA
1 TTTTCAATTTATATAA
100124 TT
1 TT
100126 ATAAATTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTCAATTTATATAA
Found at i:107759 original size:2 final size:2
Alignment explanation
Indices: 107752--107819 Score: 86
Period size: 2 Copynumber: 35.0 Consensus size: 2
107742 TAATTTTAAT
* * * *
107752 TA TA TA TA TA TA TA TA TA TA -A TT TA TA TA TT TA -A TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
107792 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
107820 CGGCCCGATA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:107835 original size:12 final size:12
Alignment explanation
Indices: 107820--107845 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
107810 TATATATATA
107820 CGGCCCGATACC
1 CGGCCCGATACC
107832 CGGCCCGATACC
1 CGGCCCGATACC
107844 CG
1 CG
107846 TTTAAATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.50, G:0.27, T:0.08
Consensus pattern (12 bp):
CGGCCCGATACC
Found at i:110381 original size:16 final size:15
Alignment explanation
Indices: 110360--110391 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
110350 ATTGGAATAC
110360 AACTTGAACTCTAAAA
1 AACTTGAACT-TAAAA
110376 AACTTGAACTTAAAA
1 AACTTGAACTTAAAA
110391 A
1 A
110392 TATTCTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25
Consensus pattern (15 bp):
AACTTGAACTTAAAA
Found at i:111401 original size:32 final size:32
Alignment explanation
Indices: 111365--111426 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
111355 ATCAGTGAAA
111365 TTATCGAACTATTGCAAAATAATCATCAAATT
1 TTATCGAACTATTGCAAAATAATCATCAAATT
111397 TTATCGAACTATTGCAAAATAATCATCAAA
1 TTATCGAACTATTGCAAAATAATCATCAAA
111427 ATCTATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (32 bp):
TTATCGAACTATTGCAAAATAATCATCAAATT
Found at i:111452 original size:32 final size:32
Alignment explanation
Indices: 111362--111454 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
111352 ATGATCAGTG
* *
111362 AAAT-TATCGAACTATTGCAAAATAATCATCA
1 AAATCTATCAAACTATTACAAAATAATCATCA
* * * *
111393 AATTTTATCGAACTATTGCAAAATAATCATCA
1 AAATCTATCAAACTATTACAAAATAATCATCA
* * *
111425 AAATCTATCAAATTATTATAAATTAATCAT
1 AAATCTATCAAACTATTACAAAATAATCAT
111455 TATACTTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 3 0.06
32 50 0.94
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.34
Consensus pattern (32 bp):
AAATCTATCAAACTATTACAAAATAATCATCA
Found at i:126859 original size:62 final size:62
Alignment explanation
Indices: 126763--126884 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 62
126753 TTCCGGTCAT
* * *
126763 TTATATTATCGATTTGTTATAATTTAACTATTAAGTTGTTAA-TTTCCTTATTCTAATGATG
1 TTATATTATCGATTTGGTATAATTTAACAATTAAGTTGTTAACTTTCCTTATCCTAATGATG
* *
126824 TTATATTGTCGATTTTGGTATAATTTAACAATTAAGTTGTTAACTTTCTTTATCCTAATGA
1 TTATATTATCGA-TTTGGTATAATTTAACAATTAAGTTGTTAACTTTCCTTATCCTAATGA
126885 CGTGACATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 11 0.20
62 28 0.52
63 15 0.28
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (62 bp):
TTATATTATCGATTTGGTATAATTTAACAATTAAGTTGTTAACTTTCCTTATCCTAATGATG
Found at i:128337 original size:20 final size:21
Alignment explanation
Indices: 128312--128353 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
128302 CCGGAAAATG
*
128312 TTAAT-ATTTTAATAACAAAA
1 TTAATAATTTTAATAAAAAAA
128332 TTAATAATTTTAATAAAAAAA
1 TTAATAATTTTAATAAAAAAA
128353 T
1 T
128354 AGCATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAATAATTTTAATAAAAAAA
Found at i:131367 original size:75 final size:75
Alignment explanation
Indices: 131244--131540 Score: 441
Period size: 75 Copynumber: 4.0 Consensus size: 75
131234 TTCGCGGGGC
* * * *
131244 CTAACCGGATTCTTCTCGGGAATTTCAGGCTTCCCCGTGGCCGATTGTCCCGAACCAACACCTCT
1 CTAACCGGCTTCTTCTCGGGAATTTCAGGCTTCCCCGTGGCTGGTTGTCCCGAACCAACACCTTT
*
131309 AACAGAAGGG
66 GACAGAAGGG
* ** *
131319 CTAACTGGCTTCTTCTCGGGAATTTCAGGCTTTTCCGTGGTTGGTTGTCCCGAACCAACACCTTT
1 CTAACCGGCTTCTTCTCGGGAATTTCAGGCTTCCCCGTGGCTGGTTGTCCCGAACCAACACCTTT
131384 GACAGAAGGG
66 GACAGAAGGG
*
131394 CTAACCGGCTTCTTCTCGGGAATTTCAGGCTTCCCCGTGGCTGGTTGTCCCGAACCAACACATTT
1 CTAACCGGCTTCTTCTCGGGAATTTCAGGCTTCCCCGTGGCTGGTTGTCCCGAACCAACACCTTT
131459 GACAGAAGGG
66 GACAGAAGGG
* * * * **
131469 CTAACCGGCTTCTTCTCGGGAATTTCAGGCTTACCCTTGGTTGGTTGTCCCAAACCAAGTCCTTT
1 CTAACCGGCTTCTTCTCGGGAATTTCAGGCTTCCCCGTGGCTGGTTGTCCCGAACCAACACCTTT
*
131534 GGCAGAA
66 GACAGAA
131541 CTTGATGATG
Statistics
Matches: 200, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 200 1.00
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (75 bp):
CTAACCGGCTTCTTCTCGGGAATTTCAGGCTTCCCCGTGGCTGGTTGTCCCGAACCAACACCTTT
GACAGAAGGG
Found at i:136418 original size:21 final size:19
Alignment explanation
Indices: 136394--136441 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
136384 TAACCGGTGT
136394 AACCGGTTTCGGTTTTAAAAA
1 AACCGGTTT--GTTTTAAAAA
*
136415 AACCGGTTTTTTTTAAAAA
1 AACCGGTTTGTTTTAAAAA
136434 AACCGGTT
1 AACCGGTT
136442 ATAAAAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 17 0.65
21 9 0.35
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (19 bp):
AACCGGTTTGTTTTAAAAA
Found at i:136421 original size:15 final size:15
Alignment explanation
Indices: 136403--136460 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 15
136393 TAACCGGTTT
136403 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
136418 CGGTTTTTTTTAAAAAAAC
1 CGG----TTTTAAAAAAAC
*
136437 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
136452 CGATTTTAA
1 CGGTTTTAA
136461 TATTCCAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 21 0.58
19 15 0.42
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:136679 original size:21 final size:21
Alignment explanation
Indices: 136627--136683 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
136617 TTTTACACTT
136627 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
* *
136648 AGGAAATCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
*
136669 AGGGTACCGATTCCC
1 AGGGAACCGATTCCC
136684 CCACGCTCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (21 bp):
AGGGAACCGATTCCCTATGAG
Found at i:136900 original size:13 final size:13
Alignment explanation
Indices: 136879--136933 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
136869 AAGTTCGATA
*
136879 AATTCAAATACTT
1 AATTGAAATACTT
136892 AATTGAAATACTT
1 AATTGAAATACTT
* *
136905 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
136919 AATTGAAATACTT
1 AATTGAAATACTT
136932 AA
1 AA
136934 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:137013 original size:32 final size:32
Alignment explanation
Indices: 136919--137017 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
136909 AACTCAACAT
* * *
136919 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
136952 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
1 AATTCAAATACTTAAAAAC-TTCAAGTTCGATA
136985 AATTCAAATACTTAAAAACTTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCAAGTTCGATA
137017 A
1 A
137018 TTGAAGCAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 14 0.23
33 46 0.74
34 2 0.03
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (32 bp):
AATTCAAATACTTAAAAACTTCAAGTTCGATA
Found at i:137049 original size:21 final size:21
Alignment explanation
Indices: 137012--137051 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
137002 ACTTCAAGTT
*
137012 CGATAATTGAAGCAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
137033 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
137052 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:139371 original size:24 final size:23
Alignment explanation
Indices: 139321--139364 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
139311 AAACCCAGAA
*
139321 CGGTTTTTTTTCCGGATAAAAAC
1 CGGTTTTTTATCCGGATAAAAAC
*
139344 CGGTTTTTTATCTGG-TAAAAA
1 CGGTTTTTTATCCGGATAAAAA
139365 ACCCGGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (23 bp):
CGGTTTTTTATCCGGATAAAAAC
Found at i:140659 original size:23 final size:25
Alignment explanation
Indices: 140633--140678 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
140623 CAAAAATAAA
140633 TAGATAAATAAT-GAAT-TATAATG
1 TAGATAAATAATGGAATCTATAATG
*
140656 TAGATATATAATGGAATCTATAA
1 TAGATAAATAATGGAATCTATAA
140679 CTAAGGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 4 0.20
25 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (25 bp):
TAGATAAATAATGGAATCTATAATG
Found at i:144906 original size:20 final size:20
Alignment explanation
Indices: 144871--144910 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
144861 TTATCATCCA
144871 ATTTCATCTGAATTTAGAAAT
1 ATTTCATCTGAATTTA-AAAT
144892 ATTTCATCT-AATTTAAAAT
1 ATTTCATCTGAATTTAAAAT
144911 TCAATCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTCATCTGAATTTAAAAT
Found at i:155671 original size:31 final size:31
Alignment explanation
Indices: 155596--155678 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
155586 TGATAATGAA
* **
155596 TTTTAGATAAAATATTAATTTGATTTATAAAC
1 TTTT-GATAAAATATTAATTTAACCTATAAAC
* *
155628 -TTTAATTGAAATATTAATTTAACCTATAAAC
1 TTTTGA-TAAAATATTAATTTAACCTATAAAC
*
155659 TTTTGATAAAATATAAATTT
1 TTTTGATAAAATATTAATTT
155679 GATTCATGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
30 1 0.02
31 36 0.88
32 4 0.10
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTTGATAAAATATTAATTTAACCTATAAAC
Found at i:156150 original size:17 final size:17
Alignment explanation
Indices: 156124--156156 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
156114 TGGGCTCGGC
*
156124 CTGGCTTGTTTAAAAGT
1 CTGGCATGTTTAAAAGT
156141 CTGGCATGTTTAAAAG
1 CTGGCATGTTTAAAAG
156157 CATGTTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (17 bp):
CTGGCATGTTTAAAAGT
Found at i:158210 original size:5 final size:5
Alignment explanation
Indices: 158198--158391 Score: 253
Period size: 5 Copynumber: 38.4 Consensus size: 5
158188 TAGATCTGTG
* * * * *
158198 ATAAT ACAAT ACAAT ACAAT ACAAT ATAAT ACAAT ATAATAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT
* * *
158250 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ACAAT ACAAT ACAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * * *
158300 ACAAT ATAAT ACAAT ACAAT ACAAT ACAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
158350 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
158392 GTTTGGTTTA
Statistics
Matches: 179, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
5 173 0.97
6 2 0.01
7 4 0.02
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:175203 original size:12 final size:12
Alignment explanation
Indices: 175188--175212 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
175178 TTATTATTAA
175188 AAATAACATTTT
1 AAATAACATTTT
175200 AAATAACATTTT
1 AAATAACATTTT
175212 A
1 A
175213 CCAAAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAACATTTT
Found at i:177709 original size:20 final size:22
Alignment explanation
Indices: 177664--177721 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
177654 ACATGGATAG
177664 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
177688 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
177708 TGCATCGATGCACT
1 TGCATCGATGCACT
177722 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:178518 original size:18 final size:18
Alignment explanation
Indices: 178495--178546 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
178485 GGGTCTACGC
178495 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
178513 GGTCCTTTGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
178531 GGTCATTCGGGACATA
1 GGTCCTTCGGGACATA
178547 TGTGTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:186368 original size:2 final size:2
Alignment explanation
Indices: 186345--186388 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
186335 ACAGTATTAA
* * *
186345 AT AT AT AA AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
186387 AT
1 AT
186389 GGGCAGACGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:196828 original size:2 final size:2
Alignment explanation
Indices: 196809--196854 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
196799 GCTTCATAAA
*
196809 AT AT A- AT AT AT TT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
196849 AT AT AT
1 AT AT AT
196855 TTAAATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:211665 original size:68 final size:68
Alignment explanation
Indices: 211556--211690 Score: 261
Period size: 68 Copynumber: 2.0 Consensus size: 68
211546 TACGCCGAAC
*
211556 AGTTTGTGTGCGTTCTGGAAAATTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
1 AGTTTGTGTGCGTTCTGGAAAACTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
211621 GGG
66 GGG
211624 AGTTTGTGTGCGTTCTGGAAAACTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
1 AGTTTGTGTGCGTTCTGGAAAACTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
211689 GG
66 GG
211691 AGATGCACTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.27
Consensus pattern (68 bp):
AGTTTGTGTGCGTTCTGGAAAACTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
GGG
Found at i:227447 original size:20 final size:20
Alignment explanation
Indices: 227430--227471 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
227420 TTTAATATAG
*
227430 AACAAATGGGTTCCATATGA
1 AACAAATGGATTCCATATGA
227450 AACAAATGGATTCCATATGA
1 AACAAATGGATTCCATATGA
227470 AA
1 AA
227472 AACCCAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (20 bp):
AACAAATGGATTCCATATGA
Found at i:232621 original size:2 final size:2
Alignment explanation
Indices: 232614--232649 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
232604 GATTATTATC
232614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
232650 AAATGATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:233720 original size:4 final size:4
Alignment explanation
Indices: 233711--233874 Score: 157
Period size: 4 Copynumber: 41.0 Consensus size: 4
233701 GTTATGCATC
*
233711 GTGT GTGT GTGT GTAT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * *
233759 GTGT GTGT GTGT GTCT CTGT GTGT GTGT GTGT GTGT GTGT CTGT ATGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * * * * * * * * *
233807 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT GTGT ATGT ATGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * *
233855 GTGT ATGT ATGT ATGT GTGT
1 GTGT GTGT GTGT GTGT GTGT
233875 ATGTATGTAT
Statistics
Matches: 147, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 147 1.00
ACGTcount: A:0.10, C:0.02, G:0.38, T:0.50
Consensus pattern (4 bp):
GTGT
Found at i:233879 original size:4 final size:4
Alignment explanation
Indices: 233800--234124 Score: 614
Period size: 4 Copynumber: 81.2 Consensus size: 4
233790 TGTGTGTGTC
*
233800 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTG TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
233848 TGTA TGTG TGTA TGTA TGTA TGTG TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
233896 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
233944 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
233992 TGTA TGTA TGTA TGTG TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
234040 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
234088 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
234125 TCTGCTTGCT
Statistics
Matches: 313, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 313 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:243586 original size:87 final size:87
Alignment explanation
Indices: 243481--243656 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
243471 AACTAAAAAA
243481 TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
1 TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
243546 GTTTTTATAATAAATCTGAATT
66 GTTTTTATAATAAATCTGAATT
*
243568 TATTATTACAATTGTTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
1 TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
243633 GTTTTTATAATAAATCTGAATT
66 GTTTTTATAATAAATCTGAATT
243655 TA
1 TA
243657 ACTCAACTAC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (87 bp):
TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
GTTTTTATAATAAATCTGAATT
Found at i:243869 original size:16 final size:17
Alignment explanation
Indices: 243840--243881 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
243830 CGATTATATA
*
243840 TATATATATAATATT-T
1 TATATATTTAATATTAT
*
243856 TATATATTTTATATTAAT
1 TATATATTTAATATT-AT
243874 TATATATT
1 TATATATT
243882 ACAAACCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 13 0.59
18 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATATTTAATATTAT
Found at i:246689 original size:18 final size:16
Alignment explanation
Indices: 246662--246695 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
246652 TATATTCATC
246662 TTTTTTTTATATTATAT
1 TTTTTTTTATA-TATAT
246679 TTTTTTATTATATATAT
1 TTTTTT-TTATATATAT
246696 CTTATATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTTATATATAT
Found at i:246715 original size:14 final size:14
Alignment explanation
Indices: 246706--246741 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
246696 CTTATATCAT
246706 TGTATATATATATA
1 TGTATATATATATA
246720 TGTATAGATATATATA
1 TGTAT--ATATATATA
246736 TGTATA
1 TGTATA
246742 GATGTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
16 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (14 bp):
TGTATATATATATA
Found at i:246730 original size:16 final size:16
Alignment explanation
Indices: 246711--246744 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
246701 ATCATTGTAT
246711 ATATATATATGTATAG
1 ATATATATATGTATAG
246727 ATATATATATGTATAG
1 ATATATATATGTATAG
246743 AT
1 AT
246745 GTATTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
ATATATATATGTATAG
Found at i:248832 original size:27 final size:27
Alignment explanation
Indices: 248793--248854 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
248783 ATCAGAACAA
*
248793 AAAGAGAAAA-AAAAAGA-AAAAAAGC
1 AAAGAGAAAATAAAAAGATAAAAAAAC
248818 AAAGAGAAAATAAAAAGATAAAAAAAC
1 AAAGAGAAAATAAAAAGATAAAAAAAC
248845 AAAG-GAAAAT
1 AAAGAGAAAAT
248855 TGAAGAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 10 0.29
26 13 0.38
27 11 0.32
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (27 bp):
AAAGAGAAAATAAAAAGATAAAAAAAC
Found at i:249992 original size:164 final size:164
Alignment explanation
Indices: 249721--250051 Score: 653
Period size: 164 Copynumber: 2.0 Consensus size: 164
249711 TTATGATTCG
*
249721 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTCTGATTAAACATTTTTCGAAAC
1 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
249786 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
66 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
249851 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
131 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
249885 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
1 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
249950 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
66 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
250015 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
131 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
250049 TCT
1 TCT
250052 TAGACAGTAA
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 166 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (164 bp):
TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
Found at i:250580 original size:37 final size:37
Alignment explanation
Indices: 250528--250908 Score: 185
Period size: 37 Copynumber: 11.1 Consensus size: 37
250518 TAAAAAGAAT
*
250528 ATTTTATCTCACTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * * *
250565 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* **
250602 A----A---CA-TTGAAAACA-TTTCCCTTGAAA-TGA
1 ATTTTATCTCACTTG-AGACAGTTTCCCTTGAAACAAA
* * *
250630 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * * ** *
250667 ATTTTACCTCCCTTGAGATAGTTTTTCTTGAAACATA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
*
250704 A----A---CA-TTGAAAACA-TTTCCCTTGAAAC-AA
1 ATTTTATCTCACTTG-AGACAGTTTCCCTTGAAACAAA
* *
250732 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* ***
250768 A--TTA--T---TTGA-ATATGTTTTATTTGAAAC-AA
1 ATTTTATCTCACTTGAGACA-GTTTCCCTTGAAACAAA
* * * ** * *
250797 ATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACTAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * *
250834 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
** *
250870 ATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
250907 AT
1 AT
250909 CTTTGAATTT
Statistics
Matches: 261, Mismatches: 51, Indels: 64
0.69 0.14 0.17
Matches are distributed among these distances:
28 6 0.02
29 46 0.18
30 9 0.03
31 2 0.01
32 1 0.00
33 2 0.01
34 2 0.01
35 9 0.03
36 82 0.31
37 102 0.39
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (37 bp):
ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
Found at i:250656 original size:102 final size:102
Alignment explanation
Indices: 250528--250768 Score: 401
Period size: 102 Copynumber: 2.4 Consensus size: 102
250518 TAAAAAGAAT
* * **
250528 ATTTTATCTCACTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGACAGTTTCTCT
**
250593 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
* *
250630 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGATAGTTTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGACAGTTTCTCT
250695 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
*
250732 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
250769 TTATTTGAAT
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 130 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
Found at i:250762 original size:65 final size:64
Alignment explanation
Indices: 250651--251035 Score: 236
Period size: 65 Copynumber: 5.8 Consensus size: 64
250641 CTTGAGATAG
** * * *
250651 TTTCCCTTGAAACAAAATTTTACCTCCCTTGAGATAGTTTTTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAACATTGAAAAT
250716 A
64 A
* * ** * *
250717 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTATTTGAATATG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACA-TTGAAAATA
*** ** * * * * *
250782 TTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAA-------AC-AT
* *
250847 TGAGACA-G
57 TGA-AAATA
* * * * * **
250855 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAA-CATTGAAAATA
* * * * * *
250920 TTTCCCCTAAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAATC-TTCAAATTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAACATTGAAA-AT
250984 A
64 A
* * * *
250985 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACAA
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
251036 CAAGATTGTT
Statistics
Matches: 250, Mismatches: 53, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
64 9 0.04
65 147 0.59
66 43 0.17
72 3 0.01
73 46 0.18
74 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (64 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACATTGAAAATA
Found at i:250764 original size:36 final size:36
Alignment explanation
Indices: 250717--250906 Score: 180
Period size: 36 Copynumber: 5.4 Consensus size: 36
250707 ATTGAAAACA
*
250717 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
250753 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * * *
250782 TTTTATTTGAAACAAATTTCATCTCCCTTAAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * *
250818 TTTCTTTTGGAACTAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
*
250855 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
250891 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
250907 ATCTTTGAAT
Statistics
Matches: 124, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.02
29 18 0.15
30 2 0.02
31 1 0.01
34 1 0.01
35 1 0.01
36 67 0.54
37 32 0.26
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:250838 original size:167 final size:168
Alignment explanation
Indices: 250549--250868 Score: 383
Period size: 167 Copynumber: 1.9 Consensus size: 168
250539 CTTGAGATAG
*
250549 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAAC
* ** ** * * *
250614 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCC
66 ATTTCACTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTACCTCCC
* *
250679 TTGAGATAGTTTTTCTTGAAACATAAACATTGAAAACA
131 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* ** *
250717 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AATTATTTGAATA
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACA-TTGAAAA
** * * ** * * ** *
250780 TGTTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACTAAATTTTGTCTCT
65 CATTTCACTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTACCTCC
250845 CTTGAGACAGTTTCTCTTGAAACA
130 CTTGAGACAGTTTCTCTTGAAACA
250869 AATTTCGTCT
Statistics
Matches: 125, Mismatches: 26, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
166 3 0.02
167 109 0.87
168 13 0.10
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (168 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAAC
ATTTCACTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTACCTCCC
TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:251000 original size:203 final size:204
Alignment explanation
Indices: 250629--251000 Score: 462
Period size: 203 Copynumber: 1.8 Consensus size: 204
250619 CCTTGAAATG
* * * **
250629 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGATAGTTTTTC
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTCACCTCCCTTGAGACAGTTTCCC
* * *
250694 TTGAAACATAAACATTGAAAACATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
66 TTGAAACATAAACATTGAAAACATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCC
** * * * *
250759 TTGAAACAAATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTT
131 TTGAAACAAATTATTCAAATATATTTCACTTAAAACAAATTTCATCTCCCTTAAGACAGTTTCTT
250824 TTGGAACTA
196 TTGGAACTA
* ** *
250833 AATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTCTCTTGAGACAGTTTCCC
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTCACCTCCCTTGAGACAGTTTCCC
* *** * *
250897 TTGAAACA-AAATCTTTGAATTTATTTCCCCTAAAATAAATTTTGTCTCCCTTGAGACAGTTTCT
66 TTGAAACATAAA-CATTGAAAACATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCC
* * *
250961 CTTGAAACACAA-TCTTCAAATTTATTTCCCTTAAAACAAA
130 CTTGAAACA-AATTATTCAAATATATTTCACTTAAAACAAA
251001 ATTTTGTTTC
Statistics
Matches: 139, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
202 3 0.02
203 101 0.73
204 35 0.25
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (204 bp):
AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTCACCTCCCTTGAGACAGTTTCCC
TTGAAACATAAACATTGAAAACATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCC
TTGAAACAAATTATTCAAATATATTTCACTTAAAACAAATTTCATCTCCCTTAAGACAGTTTCTT
TTGGAACTA
Found at i:260310 original size:3 final size:3
Alignment explanation
Indices: 260302--260328 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
260292 ATCATAATTA
260302 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
260329 TACCTAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:265060 original size:43 final size:43
Alignment explanation
Indices: 264927--265080 Score: 167
Period size: 44 Copynumber: 3.6 Consensus size: 43
264917 ACAGTAAATA
* *
264927 GCTCAGCAGAGAAGATGAAGAAAGAGATTGCTGTGAAAGTGAA-G
1 GCTCAGCTGAGAAGATGGA-AAAGAGATTGCTGTG-AAGTGAATG
* * *
264971 GCTTAGCTGAGAAGAT-G-AAAGAGATGGCAT-TGACAGTGAATA
1 GCTCAGCTGAGAAGATGGAAAAGAGATTGC-TGTGA-AGTGAATG
* *
265013 GCTCAGCGGAGAAGGTGGAAAAGAGATTGCTGTGAAGTGAATG
1 GCTCAGCTGAGAAGATGGAAAAGAGATTGCTGTGAAGTGAATG
265056 GCTCAGCTGAGAAGAT-G-AAAGAGAT
1 GCTCAGCTGAGAAGATGGAAAAGAGAT
265081 AGCATTGACA
Statistics
Matches: 92, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
40 1 0.01
41 26 0.28
42 15 0.16
43 23 0.25
44 27 0.29
ACGTcount: A:0.38, C:0.10, G:0.34, T:0.18
Consensus pattern (43 bp):
GCTCAGCTGAGAAGATGGAAAAGAGATTGCTGTGAAGTGAATG
Found at i:265067 original size:85 final size:86
Alignment explanation
Indices: 264895--265095 Score: 295
Period size: 85 Copynumber: 2.4 Consensus size: 86
264885 ATAGCACAGT
*
264895 TGAGAAGATG-AAGAG--GGCGTTGACAGTAAATAGCTCAGCAGAGAAGATGAAGAAAGAGATTG
1 TGAGAAGATGAAAGAGATGGCATTGACAGTAAATAGCTCAGCAGAGAAGATGAAGAAAGAGATTG
*
264957 CTGTGAAAGTGAAGGCTTAGC
66 CTGTGAAAGTGAAGGCTCAGC
* * * *
264978 TGAGAAGATGAAAGAGATGGCATTGACAGTGAATAGCTCAGCGGAGAAGGTGGA-AAAGAGATTG
1 TGAGAAGATGAAAGAGATGGCATTGACAGTAAATAGCTCAGCAGAGAAGATGAAGAAAGAGATTG
265042 CTGTG-AAGTGAATGGCTCAGC
66 CTGTGAAAGTGAA-GGCTCAGC
*
265063 TGAGAAGATGAAAGAGATAGCATTGACAGTAAA
1 TGAGAAGATGAAAGAGATGGCATTGACAGTAAA
265096 GAGCAAGAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
83 10 0.09
84 12 0.11
85 53 0.50
86 31 0.29
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.18
Consensus pattern (86 bp):
TGAGAAGATGAAAGAGATGGCATTGACAGTAAATAGCTCAGCAGAGAAGATGAAGAAAGAGATTG
CTGTGAAAGTGAAGGCTCAGC
Found at i:265181 original size:72 final size:71
Alignment explanation
Indices: 265032--265167 Score: 263
Period size: 72 Copynumber: 1.9 Consensus size: 71
265022 AGAAGGTGGA
265032 AAAGAGATTGCTGTGAAGTGAATGGCTCAGCTGAGAAGATGAAAGAGATAGCATTGACAGTAAAG
1 AAAGAGATTGCTGTGAAGTGAATGGCTCAGCTGAGAAGATGAAAGAGATAGCATTGACAGTAAAG
265097 AGCAAG
66 AGCAAG
265103 AAAGAGATTGCTGTGAAAGTGAATGGCTCAGCTGAGAAGATGAAAGAGATAGCATTGACAGTAAA
1 AAAGAGATTGCTGTG-AAGTGAATGGCTCAGCTGAGAAGATGAAAGAGATAGCATTGACAGTAAA
265168 TAGCTCAGCA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
71 15 0.23
72 49 0.77
ACGTcount: A:0.41, C:0.10, G:0.30, T:0.19
Consensus pattern (71 bp):
AAAGAGATTGCTGTGAAGTGAATGGCTCAGCTGAGAAGATGAAAGAGATAGCATTGACAGTAAAG
AGCAAG
Found at i:265219 original size:45 final size:45
Alignment explanation
Indices: 265100--265286 Score: 238
Period size: 45 Copynumber: 4.2 Consensus size: 45
265090 AGTAAAGAGC
*
265100 AAGAAAGAGATTGCTGTGAAAGTGAATGGCTCAGCTGAGAA---G
1 AAGAAAGAGATAGCTGTGAAAGTGAATGGCTCAGCTGAGAAGGTG
* * * * *
265142 ATGAAAGAGATAGCAT-TGACAGTAAATAGCTCAGCAGAGAAGGTG
1 AAGAAAGAGATAGC-TGTGAAAGTGAATGGCTCAGCTGAGAAGGTG
* *
265187 AAGAAAGAGATTGCTGTGAAAGTGAATGGCTCAGCTGAGAAGGGG
1 AAGAAAGAGATAGCTGTGAAAGTGAATGGCTCAGCTGAGAAGGTG
* *
265232 AAGAAAGAGATAGCTGTGGAAGTGAATGGCTCAGCTGAGAAGATG
1 AAGAAAGAGATAGCTGTGAAAGTGAATGGCTCAGCTGAGAAGGTG
*
265277 AAAAAAGAGA
1 AAGAAAGAGA
265287 CAACTTGGCA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.27
43 1 0.01
44 1 0.01
45 87 0.71
ACGTcount: A:0.41, C:0.09, G:0.33, T:0.17
Consensus pattern (45 bp):
AAGAAAGAGATAGCTGTGAAAGTGAATGGCTCAGCTGAGAAGGTG
Found at i:270099 original size:55 final size:55
Alignment explanation
Indices: 270003--270200 Score: 272
Period size: 56 Copynumber: 3.6 Consensus size: 55
269993 CCCTATGTTC
* * * * *
270003 TAGATATATTCGATTACGAGACTCTTATTTTTATGCTTCTTATTGGCAACAACTGA
1 TAGATATATTCGATTTCG-GGCTCCTATTTTTATGCTTCTTAATGACAACAACTGA
*
270059 TAGATATATTCGATTTCGGGCTCCTATTTTTATGCCTCTTAATGACAACAACTGA
1 TAGATATATTCGATTTCGGGCTCCTATTTTTATGCTTCTTAATGACAACAACTGA
* * *
270114 TAGATATACTCGATTTCGGGATCCCTATTTTTATGCTTATTAATGACAACAACTGA
1 TAGATATATTCGATTTCGGGCT-CCTATTTTTATGCTTCTTAATGACAACAACTGA
*
270170 TAAATATATTCGATTTCGGGC-CTCTATTTTT
1 TAGATATATTCGATTTCGGGCTC-CTATTTTT
270201 TGAGGCCCTG
Statistics
Matches: 127, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
54 1 0.01
55 60 0.47
56 66 0.52
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (55 bp):
TAGATATATTCGATTTCGGGCTCCTATTTTTATGCTTCTTAATGACAACAACTGA
Found at i:285900 original size:12 final size:12
Alignment explanation
Indices: 285885--285939 Score: 101
Period size: 12 Copynumber: 4.6 Consensus size: 12
285875 GTTATTTAAA
285885 CGGGTATTGGGC
1 CGGGTATTGGGC
285897 CGGGTATTGGGC
1 CGGGTATTGGGC
285909 CGGGTATTGGGC
1 CGGGTATTGGGC
*
285921 CGGGAATTGGGC
1 CGGGTATTGGGC
285933 CGGGTAT
1 CGGGTAT
285940 ATATATATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.11, C:0.16, G:0.49, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:285991 original size:37 final size:38
Alignment explanation
Indices: 285937--286008 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
285927 TTGGGCCGGG
* *
285937 TATATATATATTATATTTATTTA-TTTATTTAAATTAAA
1 TATATAAATATTATATTT-TTTATTTTAATTAAATTAAA
285975 TATATAAATA-TATATTTTTTATTTTAATTAAATT
1 TATATAAATATTATATTTTTTATTTTAATTAAATT
286009 TATTAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 4 0.13
37 18 0.58
38 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (38 bp):
TATATAAATATTATATTTTTTATTTTAATTAAATTAAA
Found at i:286017 original size:28 final size:33
Alignment explanation
Indices: 285940--286061 Score: 104
Period size: 32 Copynumber: 3.7 Consensus size: 33
285930 GGCCGGGTAT
* *
285940 ATATATATTATATTTATTTATTTATTTAAATTAA
1 ATATATA-AATATATATTTATTTATTTAAATTAA
*
285974 ATATATAAATATATATTT-TTTATTTTAATTAA
1 ATATATAAATATATATTTATTTATTTAAATTAA
* * * * * * *
286006 ATTTATTAATAT-TATATATATATATATATATAT
1 ATATATAAATATATATTTATTTATTTAAAT-TAA
*
286039 ATATATATATATATATATTATTT
1 ATATATAAATATATAT-TTATTT
286062 TTAATATTTA
Statistics
Matches: 68, Mismatches: 16, Indels: 7
0.75 0.18 0.08
Matches are distributed among these distances:
31 4 0.06
32 30 0.44
33 20 0.29
34 10 0.15
35 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
ATATATAAATATATATTTATTTATTTAAATTAA
Found at i:286018 original size:6 final size:7
Alignment explanation
Indices: 286009--286059 Score: 59
Period size: 8 Copynumber: 6.9 Consensus size: 7
285999 TAATTAAATT
286009 TATTA-A
1 TATTATA
286015 TATTATA
1 TATTATA
286022 TATATATA
1 TAT-TATA
286030 TATATATA
1 TAT-TATA
286038 TATATATA
1 TAT-TATA
286046 TATATATA
1 TAT-TATA
286054 TATTAT
1 TATTAT
286060 TTTTAATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.12
7 7 0.16
8 31 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TATTATA
Found at i:286025 original size:2 final size:2
Alignment explanation
Indices: 286014--286056 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
286004 AAATTTATTA
286014 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
286055 AT
1 AT
286057 TATTTTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:287693 original size:23 final size:22
Alignment explanation
Indices: 287660--287706 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
287650 GTAAATTAAT
*
287660 TTATATTTTTATCTAATTTATAA
1 TTATATGTTTA-CTAATTTATAA
* *
287683 TTATATGTTTAGTACTTTATAA
1 TTATATGTTTACTAATTTATAA
287705 TT
1 TT
287707 TAATATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (22 bp):
TTATATGTTTACTAATTTATAA
Found at i:289448 original size:22 final size:20
Alignment explanation
Indices: 289410--289456 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
289400 TCAAGTATTT
*
289410 TTTTTAATATTTGAATTAATA
1 TTTTTAAAATTTGAATTAA-A
*
289431 TTTTTAAAATTTGAAATTTAA
1 TTTTTAAAATTTG-AATTAAA
289452 TTTTT
1 TTTTT
289457 CTTTTTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTTAAAATTTGAATTAAA
Found at i:293788 original size:18 final size:20
Alignment explanation
Indices: 293756--293792 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
293746 ATTCATTTTA
293756 GATAACAAAATTAATATTTC
1 GATAACAAAATTAATATTTC
293776 GATAA-AAAA-TAATATTT
1 GATAACAAAATTAATATTT
293793 TAATTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
GATAACAAAATTAATATTTC
Found at i:299482 original size:14 final size:15
Alignment explanation
Indices: 299458--299492 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
299448 TTCACATGCC
*
299458 ATATTTTAAGAAAAT
1 ATATATTAAGAAAAT
299473 -TATATTAAGAAAAT
1 ATATATTAAGAAAAT
299487 ATATAT
1 ATATAT
299493 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (15 bp):
ATATATTAAGAAAAT
Found at i:302076 original size:3 final size:3
Alignment explanation
Indices: 302068--302148 Score: 56
Period size: 3 Copynumber: 25.7 Consensus size: 3
302058 TTTTAATTGT
* * * *
302068 TTA TTA TTAA TTA TTAA TTA CTA -TA TTA GTA TTA TTA TCAA TAA TTA
1 TTA TTA TT-A TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
302115 TTA TTA TTA TTAA TTT TTA TTAA TAA TTA TTA TT
1 TTA TTA TTA TT-A TTA TTA TT-A TTA TTA TTA TT
302149 TATTTATGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 2 0.03
3 48 0.76
4 13 0.21
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:302082 original size:7 final size:7
Alignment explanation
Indices: 302060--302152 Score: 57
Period size: 7 Copynumber: 13.3 Consensus size: 7
302050 TGTCCGAGTT
*
302060 TTAATTG
1 TTAATTA
*
302067 TTTATTA
1 TTAATTA
302074 TTAATTA
1 TTAATTA
302081 TTAATTA
1 TTAATTA
*
302088 CTATATTA
1 TTA-ATTA
*
302096 GT-ATTA
1 TTAATTA
*
302102 TT-ATCA
1 TTAATTA
*
302108 ATAATTA
1 TTAATTA
302115 TTATTATTA
1 TTA--ATTA
302124 TTAATT-
1 TTAATTA
*
302130 TTTATTA
1 TTAATTA
*
302137 ATAATTA
1 TTAATTA
*
302144 TTATTTA
1 TTAATTA
302151 TT
1 TT
302153 TATGGGTAGA
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
6 14 0.21
7 40 0.61
8 5 0.08
9 7 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (7 bp):
TTAATTA
Found at i:302083 original size:10 final size:10
Alignment explanation
Indices: 302068--302152 Score: 75
Period size: 10 Copynumber: 8.5 Consensus size: 10
302058 TTTTAATTGT
302068 TTATTATTAA
1 TTATTATTAA
*
302078 TTATTAATTAC
1 TTATT-ATTAA
*
302089 TATATTAGT-A
1 T-TATTATTAA
*
302099 TTATTATCAA
1 TTATTATTAA
*
302109 TAATTATT-A
1 TTATTATTAA
302118 TTATTATTAA
1 TTATTATTAA
*
302128 TTTTTATTAA
1 TTATTATTAA
* *
302138 TAATTATTAT
1 TTATTATTAA
302148 TTATT
1 TTATT
302153 TATGGGTAGA
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
9 13 0.22
10 34 0.59
11 7 0.12
12 4 0.07
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (10 bp):
TTATTATTAA
Found at i:302116 original size:13 final size:13
Alignment explanation
Indices: 302070--302148 Score: 61
Period size: 13 Copynumber: 5.7 Consensus size: 13
302060 TTAATTGTTT
*
302070 ATTATTAATTATTA
1 ATTATT-ATTAATA
*
302084 ATTACTATATTAGT-
1 ATTA-T-TATTAATA
*
302098 ATTATTATCAATA
1 ATTATTATTAATA
302111 ATTATTATTATTATTA
1 ATTATTATTA--A-TA
*
302127 ATTTTTATTAATA
1 ATTATTATTAATA
302140 ATTATTATT
1 ATTATTATT
302149 TATTTATGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
12 5 0.09
13 20 0.38
14 9 0.17
15 7 0.13
16 12 0.23
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (13 bp):
ATTATTATTAATA
Found at i:302118 original size:16 final size:16
Alignment explanation
Indices: 302068--302148 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 16
302058 TTTTAATTGT
*
302068 TTATTATTAATTATTAA
1 TTATTAATAATTATT-A
* * *
302085 TTACTATATTAGTATTA
1 TTATTA-ATAATTATTA
*
302102 TTATCAATAATTATTA
1 TTATTAATAATTATTA
*
302118 TTATTATTAA-T-TT-
1 TTATTAATAATTATTA
302131 TTATTAATAATTATTA
1 TTATTAATAATTATTA
302147 TT
1 TT
302149 TATTTATGGG
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
13 9 0.18
14 3 0.06
15 3 0.06
16 18 0.37
17 10 0.20
18 6 0.12
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (16 bp):
TTATTAATAATTATTA
Done.