Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007544.1 Hibiscus syriacus cultivar Beakdansim tig00021135_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: 154132
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:5611 original size:29 final size:30
Alignment explanation
Indices: 5541--5604 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
5531 AATAATTACT
**
5541 AAAATAGCACCTTTTTCGAATTAAATTCCC
1 AAAATAGCACCCATTTCGAATTAAATTCCC
*
5571 ACAATAGCACCCATTTCGAATT-AATTCCC
1 AAAATAGCACCCATTTCGAATTAAATTCCC
5600 AAAAT
1 AAAAT
5605 GTCACCCGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.30
Consensus pattern (30 bp):
AAAATAGCACCCATTTCGAATTAAATTCCC
Found at i:5668 original size:17 final size:17
Alignment explanation
Indices: 5616--5668 Score: 90
Period size: 17 Copynumber: 3.1 Consensus size: 17
5606 TCACCCGTCA
5616 CGGTCAAC-GGTCGGGT
1 CGGTCAACGGGTCGGGT
5632 CAGGTCAACGGGTCGGGT
1 C-GGTCAACGGGTCGGGT
5650 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
5667 CG
1 CG
5669 TAACCGGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
16 1 0.03
17 25 0.71
18 9 0.26
ACGTcount: A:0.13, C:0.25, G:0.45, T:0.17
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:10557 original size:31 final size:31
Alignment explanation
Indices: 10521--10618 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
10511 TTAAAAAATA
*
10521 AAAATAAGTATTAAATTTATTAATTGATTAT
1 AAAATAATTATTAAATTTATTAATTGATTAT
* * * *
10552 AAAATAATTATCATACTTATTAAATT-ACTAT
1 AAAATAATTATTAAATTTATT-AATTGATTAT
* *
10583 AAAATAATTATTAAATTTATTCATTG-TCAT
1 AAAATAATTATTAAATTTATTAATTGATTAT
10613 AAAATA
1 AAAATA
10619 GTCATAATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
30 11 0.20
31 39 0.72
32 4 0.07
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (31 bp):
AAAATAATTATTAAATTTATTAATTGATTAT
Found at i:10725 original size:74 final size:74
Alignment explanation
Indices: 10584--10740 Score: 253
Period size: 74 Copynumber: 2.1 Consensus size: 74
10574 AATTACTATA
* *
10584 AAATAATTATTAAATTTATTCATTGTCATAAAATAGTCATAATATTATATTTTTCACGAAGCTTT
1 AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTATATTTTTCACGAAG-TTT
10649 TTTTATTGAG
65 TTTTATTGAG
10659 -AATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAGTT
1 AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATA-TTATATTTTTCACG-AAGTT
*
10723 TTTTTTTTGAG
64 TTTTTATTGAG
10734 AAATATT
1 AAATATT
10741 GCTTCCAACT
Statistics
Matches: 76, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
74 41 0.54
75 26 0.34
76 9 0.12
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (74 bp):
AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTATATTTTTCACGAAGTTTT
TTTATTGAG
Found at i:16355 original size:19 final size:19
Alignment explanation
Indices: 16308--16358 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
16298 ATATAATTAA
**
16308 TGTACCGATATACCCCTAG
1 TGTACCGATGCACCCCTAG
16327 TGTACCGATGCACCCCTAG
1 TGTACCGATGCACCCCTAG
*
16346 TGTACTGATGCAC
1 TGTACCGATGCAC
16359 TAAGTCTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (19 bp):
TGTACCGATGCACCCCTAG
Found at i:20752 original size:128 final size:128
Alignment explanation
Indices: 20522--20778 Score: 435
Period size: 128 Copynumber: 2.0 Consensus size: 128
20512 GATGATCGTC
*
20522 GTCTTCTTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCATTTGG
1 GTCTTCTTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCATTTGA
* **
20587 AATGATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATCTATCCGTCATAGCTTT
66 AATAATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATAAATCCGTCATAGCTTT
* *
20650 GTCTTCTTTGATTGCCAAGATTTTGGAAGA-AAGTAAACTAACTTCCTCACAAGCTTCTCGTTTG
1 GTCTTCTTTGATTGCCAAGATTTTGGAAGAGAA-TAAACTAACTTCCTCACAAGCTTCCCATTTG
*
20714 AAATAATCTCTCCATATGATTTGAGACCATTGATAATCGTGGAAAATAAATCCGTCATAGCTTT
65 AAATAATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATAAATCCGTCATAGCTTT
20778 G
1 G
20779 ATATCTTCAT
Statistics
Matches: 121, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
127 2 0.02
128 119 0.98
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (128 bp):
GTCTTCTTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCATTTGA
AATAATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATAAATCCGTCATAGCTTT
Found at i:34457 original size:25 final size:25
Alignment explanation
Indices: 34429--34477 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
34419 CAATGGTCAA
34429 CGGGTCGGGTCGAGTCAGGTCAAAC
1 CGGGTCGGGTCGAGTCAGGTCAAAC
* *
34454 CGGGTTGGGTCGGGTCAGGTCAAA
1 CGGGTCGGGTCGAGTCAGGTCAAA
34478 GAGTTGGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.18
Consensus pattern (25 bp):
CGGGTCGGGTCGAGTCAGGTCAAAC
Found at i:43937 original size:18 final size:19
Alignment explanation
Indices: 43907--43943 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
43897 TACTACTCCT
43907 AAGAAACAAAAGAAAAGAA
1 AAGAAACAAAAGAAAAGAA
*
43926 AAGAAA-AAAAGAAGAGAA
1 AAGAAACAAAAGAAAAGAA
43944 GAAATGAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (19 bp):
AAGAAACAAAAGAAAAGAA
Found at i:45216 original size:136 final size:136
Alignment explanation
Indices: 44954--45666 Score: 797
Period size: 136 Copynumber: 5.2 Consensus size: 136
44944 ATCAATCAAA
* * * *
44954 ATTTCCAATTGAGTGTTCATAATGAGAAGTACTCATCTGACAAAGGGAGAAGAAGCTCATAATGA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
* * * * *
45019 GAAAAACTTGTTCGACCTATTGCTCGATTCACGTCATTTTGAATCAGTAATGCCTCTCTTGAGGG
66 GAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTTGAATCAGCAAAGCCTCACTTGAGGG
45084 ATTAAC
131 ATTAAC
* * * * *
45090 ATTTTCAATGGAGAGTTCATAATGAGAAGAGCTCATCCGATAGAGGGAGAAGAAGTTCATAATGA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
* * * * * ** *
45155 GAAGAACTTGTTCGACCTATTGCACAATTCATGGCATATCAAATCAGCAAAGGCTCACTTGAGGG
66 GAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTTGAATCAGCAAAGCCTCACTTGAGGG
*
45220 ATCAAC
131 ATTAAC
* * * * *
45226 ATTTCC--TGTATGAATATCATGATGAGAAGAACTCATCCAACAAAGGGAGAAGACGCTCATAAT
1 ATTTCCAATGGA-GAGT-TCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAAT
** * * *
45289 GAGAAGAACTTGTTCGACCTATTGCTTTATTCACGACATTTCGAATCAGCAACGCCTCGCTTGAG
64 GAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTTGAATCAGCAAAGCCTCACTTGAG
45354 GGATTAAC
129 GGATTAAC
* * * * * *
45362 ATTTCCAATGGAGAGTTCATAATGAAAATAACTCATCCGATATAGTGATAAGAAGCTCATAATGA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
* * ** *
45427 GAAGAACTTGTTCGACCTATTGCTCGATTCACGATATTTTGAATTAG-AAATATCTCGCTTGA-G
66 GAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTTGAATCAGCAAA-GCCTCACTTGAGG
45490 GATTAAC
130 GATTAAC
* * * * *
45497 ATTTCCAATGGAGAGTTCATAATGAGAAGAACACATCCGACAGAGGGAGAACAAGTTTATAATGA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
* * * ** *
45562 GAAGAACTTGTTCGACCTATTG-TACGATTCATGGCATTTTGAATCAGCAACGGATCACTTGAGA
66 GAAGAACTTGTTCGACCTATTGCT-CGATTCACGACATTTTGAATCAGCAAAGCCTCACTTGAGG
*
45626 GATCAAC
130 GATTAAC
** * * * *
45633 ATTTCCTGTAGAAAGATCATGATGAGAAGAACTC
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
45667 GTAGCTTTAA
Statistics
Matches: 479, Mismatches: 90, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
134 4 0.01
135 116 0.24
136 353 0.74
137 3 0.01
138 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (136 bp):
ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
GAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTTGAATCAGCAAAGCCTCACTTGAGGG
ATTAAC
Found at i:59135 original size:12 final size:12
Alignment explanation
Indices: 59118--59144 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
59108 CATCGAATGC
59118 AGTTGGATCAGG
1 AGTTGGATCAGG
59130 AGTTGGATCAGG
1 AGTTGGATCAGG
59142 AGT
1 AGT
59145 CACTCCTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.41, T:0.26
Consensus pattern (12 bp):
AGTTGGATCAGG
Found at i:62484 original size:97 final size:97
Alignment explanation
Indices: 62342--62622 Score: 456
Period size: 97 Copynumber: 2.9 Consensus size: 97
62332 GTAGATTTCG
* ** * * * * *
62342 TGATTCATAAATCAATAATGATAATATTTTCTAGTGAAAACAGGAAACCCGATAACATATTTCAG
1 TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
*
62407 GCAACCATAGTTCATAAAACCAGTACGTTCCA
66 GTAACCATAGTTCATAAAACCAGTACGTTCCA
62439 TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
1 TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
*
62504 GTAACCATAGTTCATAAAACCAATACGTTCCA
66 GTAACCATAGTTCATAAAACCAGTACGTTCCA
*
62536 TGATCCATAAACCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
1 TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
62601 GTAACCATAGTTCAT-AAACCAG
66 GTAACCATAGTTCATAAAACCAG
62623 GAAATCAGGA
Statistics
Matches: 172, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
96 6 0.03
97 166 0.97
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (97 bp):
TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
GTAACCATAGTTCATAAAACCAGTACGTTCCA
Found at i:64093 original size:22 final size:22
Alignment explanation
Indices: 64058--64261 Score: 143
Period size: 22 Copynumber: 9.2 Consensus size: 22
64048 AAATATGTAG
* **
64058 TATAG-TTTTAAAAACATATGG
1 TATAGTTTTTGAAAACATATAA
* *
64079 TGTAGTTTTTGAAAACATATTA
1 TATAGTTTTTGAAAACATATAA
* **
64101 TATTGTTTTAAAAAACATATAATA
1 TATAGTTTTTGAAAACATAT-A-A
* *
64125 TATAGTTTTTGAAAATATATAG
1 TATAGTTTTTGAAAACATATAA
*
64147 TATAGTTTTT-AAAACATATTAT
1 TATAGTTTTTGAAAACATA-TAA
*
64169 TATATGGTTTTGAAAACATAT-A
1 TATA-GTTTTTGAAAACATATAA
64191 TATAGTTTTTGAAAAACATATGTAA
1 TATAGTTTTTG-AAAACATA--TAA
*
64216 TATATATATTTTGAAAACATAT-A
1 TATA-GT-TTTTGAAAACATATAA
* *
64239 TAT-GATTTTG-ATA-ATATAA
1 TATAGTTTTTGAAAACATATAA
64258 TATA
1 TATA
64262 TATTATATAT
Statistics
Matches: 146, Mismatches: 23, Indels: 29
0.74 0.12 0.15
Matches are distributed among these distances:
18 4 0.03
19 6 0.04
20 5 0.03
21 17 0.12
22 57 0.39
23 11 0.08
24 27 0.18
25 5 0.03
26 9 0.06
27 5 0.03
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (22 bp):
TATAGTTTTTGAAAACATATAA
Found at i:64136 original size:46 final size:44
Alignment explanation
Indices: 64058--64241 Score: 187
Period size: 46 Copynumber: 4.1 Consensus size: 44
64048 AAATATGTAG
** *
64058 TATAGTTTTAAAAACATAT--GGTGTAGTTTTTGAAAACATATTA
1 TATAGTTTTAAAAACATATAATATATAGTTTTTGAAAACATA-TA
* *
64101 TATTGTTTTAAAAAACATATAATATATAGTTTTTGAAAATATATA
1 TATAGTTTT-AAAAACATATAATATATAGTTTTTGAAAACATATA
* * *
64146 GTATAGTTTTTAAAACATATTAT-TATATGGTTTTGAAAACATATA
1 -TATAGTTTTAAAAACATATAATATATA-GTTTTTGAAAACATATA
64191 TATAGTTTTTGAAAAACATATGTAATATATA-TATTTTGAAAACATATA
1 TATAG-TTTT-AAAAACATA--TAATATATAGT-TTTTGAAAACATATA
64239 TAT
1 TAT
64242 GATTTTGATA
Statistics
Matches: 117, Mismatches: 13, Indels: 17
0.80 0.09 0.12
Matches are distributed among these distances:
43 8 0.07
44 19 0.16
45 32 0.27
46 33 0.28
48 21 0.18
49 4 0.03
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (44 bp):
TATAGTTTTAAAAACATATAATATATAGTTTTTGAAAACATATA
Found at i:64239 original size:19 final size:19
Alignment explanation
Indices: 64215--64265 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
64205 AACATATGTA
64215 ATATATATATTTTGAAAAC
1 ATATATATATTTTGAAAAC
* *
64234 ATATATATGATTTTGATAAT
1 ATATATAT-ATTTTGAAAAC
64254 ATAATATATATT
1 AT-ATATATATT
64266 ATATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 8 0.29
20 14 0.50
21 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (19 bp):
ATATATATATTTTGAAAAC
Found at i:64271 original size:47 final size:45
Alignment explanation
Indices: 64085--64274 Score: 167
Period size: 46 Copynumber: 4.1 Consensus size: 45
64075 ATGGTGTAGT
* * *
64085 TTTTGAAAACATATTATATTG-TTTTAAAAAACATA-TAATATATA
1 TTTTGAAAACATA-TATATAGATTTTGAAAAACATATTATTATATA
* * *
64129 GTTTTTGAAAATATATAGTATAG-TTTT-TAAAACATATTATTATATGG
1 --TTTTGAAAACATATA-TATAGATTTTGAAAAACATATTATTATAT-A
*
64176 TTTTGAAAACATATATATAGTTTTTGAAAAACATATGTAATATATATA
1 TTTTGAAAACATATATATAGATTTTGAAAAACATAT-T-AT-TATATA
64224 TTTTGAAAACATATATAT-GATTTTGATAATATA-ATATATATTATATA
1 TTTTGAAAACATATATATAGATTTTGA-AA-A-ACATAT-TATTATATA
64271 TTTT
1 TTTT
64275 TTAAAAGTAT
Statistics
Matches: 123, Mismatches: 10, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
44 5 0.04
45 28 0.23
46 36 0.29
47 18 0.15
48 24 0.20
49 11 0.09
50 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (45 bp):
TTTTGAAAACATATATATAGATTTTGAAAAACATATTATTATATA
Found at i:64275 original size:28 final size:28
Alignment explanation
Indices: 64235--64302 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
64225 TTTGAAAACA
*
64235 TATATATGATTTTGATAA-TATAATATATAT
1 TATATAT--TTTTGAAAAGTATAATAT-TAT
* *
64265 TATATATTTTTTAAAAGTATATTATTAT
1 TATATATTTTTGAAAAGTATAATATTAT
*
64293 TATTTATTTT
1 TATATATTTT
64303 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 19 0.58
29 7 0.21
30 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
TATATATTTTTGAAAAGTATAATATTAT
Found at i:64305 original size:5 final size:5
Alignment explanation
Indices: 64286--64337 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
64276 TAAAAGTATA
* *
64286 TTATT ATTA-T TTATT TTATT TTATT TTATT ATATCA TTA-T TTATT TTATT
1 TTATT -TTATT TTATT TTATT TTATT TTATT TTAT-T TTATT TTATT TTATT
64336 TT
1 TT
64338 TGGTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
4 6 0.15
5 28 0.72
6 5 0.13
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:64314 original size:25 final size:24
Alignment explanation
Indices: 64286--64337 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
64276 TAAAAGTATA
64286 TTATTAT-TATTTATTTTATTTTATT
1 TTATTATATA-TTA-TTTATTTTATT
64311 TTATTATATCATTATTTATTTTATT
1 TTATTATAT-ATTATTTATTTTATT
64336 TT
1 TT
64338 TGGTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 20 0.80
26 4 0.16
27 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (24 bp):
TTATTATATATTATTTATTTTATT
Found at i:65650 original size:15 final size:15
Alignment explanation
Indices: 65630--65702 Score: 69
Period size: 15 Copynumber: 4.8 Consensus size: 15
65620 ATTCTTGACT
*
65630 TTTAATTATTTCCAA
1 TTTAATTATTTTCAA
*
65645 TTTAATT-TTTTTAA
1 TTTAATTATTTTCAA
* *
65659 TTTAATTTTTTTCTA
1 TTTAATTATTTTCAA
65674 TTTAATTATGATTT-AA
1 TTTAATTAT--TTTCAA
65690 TTTAATTTATTTT
1 TTTAA-TTATTTT
65703 TTTACTTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
14 12 0.25
15 23 0.48
16 6 0.12
17 7 0.15
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (15 bp):
TTTAATTATTTTCAA
Found at i:66371 original size:20 final size:19
Alignment explanation
Indices: 66346--66393 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
66336 TTCGAGAATG
*
66346 AAAATCGCAACGCAGAAATA
1 AAAATCGCAACGC-GAAACA
*
66366 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACA
66385 AAAATCGCA
1 AAAATCGCA
66394 TTGCGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.52, C:0.25, G:0.15, T:0.08
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:66411 original size:19 final size:19
Alignment explanation
Indices: 66389--66553 Score: 125
Period size: 19 Copynumber: 9.1 Consensus size: 19
66379 GAAACCAAAA
*
66389 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
66408 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
66427 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
66446 TCACGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
66460 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
66479 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
66493 TCTCGTTGAGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
66512 TCCGCGTTACGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
66532 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
66552 TC
1 TC
66554 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
14 19 0.16
16 4 0.03
17 5 0.04
19 59 0.51
20 28 0.24
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:66478 original size:33 final size:33
Alignment explanation
Indices: 66394--66528 Score: 135
Period size: 33 Copynumber: 3.9 Consensus size: 33
66384 CAAAATCGCA
** *
66394 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATAGTCATTTCGCGTTGCGA--TTC---TCTCG
** *
66432 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
*
66465 TTGCGATAGTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
* *
66498 TTGAGATAGTCATTTCCGCGTTACGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
66529 ATTATCTCGT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
33 47 0.54
34 13 0.15
36 3 0.03
38 24 0.28
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:66530 original size:20 final size:20
Alignment explanation
Indices: 66507--66553 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
66497 GTTGAGATAG
66507 TCATTTCCGCGTTACGATTC
1 TCATTTCCGCGTTACGATTC
* * *
66527 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTACGATTC
66547 TCATTTC
1 TCATTTC
66554 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTACGATTC
Found at i:68606 original size:21 final size:21
Alignment explanation
Indices: 68582--68648 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
68572 TCATTCCTCG
68582 AGAGTCCCCTCTCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * * *
68603 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCTCACCGTTCA
* *
68624 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCTCACCGTTCA
68645 AGAG
1 AGAG
68649 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCTCACCGTTCA
Found at i:70024 original size:14 final size:14
Alignment explanation
Indices: 70005--70040 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
69995 ATTGTTTAAT
70005 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
70019 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
70033 TGATTTGT
1 TGATTTGT
70041 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:70198 original size:38 final size:38
Alignment explanation
Indices: 70147--70227 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
70137 AAAAAGTACT
* *
70147 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAATGAAA
*
70185 ATCGCAACGCGAAATGAAAATCGCAACGAGAAATTAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAATGAAA
*
70223 TTCGC
1 ATCGC
70228 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAAATGAAA
Found at i:70227 original size:19 final size:19
Alignment explanation
Indices: 70147--70218 Score: 126
Period size: 19 Copynumber: 3.8 Consensus size: 19
70137 AAAAAGTACT
*
70147 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
70166 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
70185 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
70204 ATCGCAACGAGAAAT
1 ATCGCAACGCGAAAT
70219 TAAATTCGCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:70245 original size:19 final size:19
Alignment explanation
Indices: 70223--70353 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
70213 AGAAATTAAA
*
70223 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
70242 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
* *
70258 CTCG--TTGCAATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
70275 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
70289 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
70308 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
* *
70323 -TCTCATTGCAATTTTCAT
1 TTCGCATTGCGATTTTCAT
70341 TTCGCATTGCGAT
1 TTCGCATTGCGAT
70354 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
16 9 0.11
17 9 0.11
19 38 0.46
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:70271 original size:33 final size:32
Alignment explanation
Indices: 70227--70353 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
70217 ATTAAATTCG
*
70227 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCAATTTTCATTTCGCATTGCGATT-CCT
*
70260 CGTTGCAATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCAATTTTCATTTCGCATTGCG--ATTCCT
*
70293 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCAATTTTCATTTCGCATTGCGATTC-CT
*
70326 CATTGCAATTTTCATTTCGCATTGCGAT
1 CGTTGCAATTTTCATTTCGCATTGCGAT
70354 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (32 bp):
CGTTGCAATTTTCATTTCGCATTGCGATTCCT
Found at i:70316 original size:66 final size:66
Alignment explanation
Indices: 70220--70352 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
70210 ACGAGAAATT
*
70220 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCAATTTTCATTTCGCATTGC
70285 G
66 G
*
70286 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCAATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCAATTTTCATTTCGCATTGC
70351 G
66 G
70352 A
1 A
70353 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCAATTTTCATTTCGCATTGC
G
Found at i:72880 original size:24 final size:24
Alignment explanation
Indices: 72846--72899 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
72836 CTGAAATATC
*
72846 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
72870 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
72894 ATCAAA
1 ATCAAA
72900 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:73473 original size:12 final size:12
Alignment explanation
Indices: 73454--73487 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
73444 TGCCGGATAG
73454 GGAA-GGATGTA
1 GGAACGGATGTA
*
73465 GGAACGGATATA
1 GGAACGGATGTA
73477 GGAACGGATGT
1 GGAACGGATGT
73488 CGCCGGAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.35, C:0.06, G:0.41, T:0.18
Consensus pattern (12 bp):
GGAACGGATGTA
Found at i:73709 original size:20 final size:21
Alignment explanation
Indices: 73684--73735 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
73674 TTTTCCTAAT
*
73684 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
73704 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
73725 TCGCAATGCGA
1 TCGCAATGCGA
73736 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:73809 original size:20 final size:20
Alignment explanation
Indices: 73720--73811 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
73710 TGCGAATTTG
* *
73720 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
73740 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
73760 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
73781 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
73801 GAAAATCGCAA
1 GAAAATCGCAA
73812 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:74100 original size:20 final size:20
Alignment explanation
Indices: 74025--74092 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
74015 CAACGGGGAA
74025 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
74045 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
74065 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
74085 ATCGCAAC
1 ATCGCAAC
74093 TAGAAAATAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:74160 original size:19 final size:19
Alignment explanation
Indices: 74119--74205 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
74109 GAAATGAAAA
74119 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
74135 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
74152 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
74171 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
74190 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
74206 TCGTTGCGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 49 0.74
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:74189 original size:38 final size:33
Alignment explanation
Indices: 74119--74215 Score: 149
Period size: 38 Copynumber: 2.8 Consensus size: 33
74109 GAAATGAAAA
74119 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
74152 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
74190 TCGCATTGCGATTTTCTCGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
74216 AGTCAGTTTC
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
33 23 0.39
35 3 0.05
36 3 0.05
38 30 0.51
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:76270 original size:20 final size:20
Alignment explanation
Indices: 76244--76290 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
76234 GAAACTTAAA
76244 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
76264 ATTGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
76284 ATCGCAA
1 ATCGCAA
76291 TGTGAAATGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:76320 original size:14 final size:14
Alignment explanation
Indices: 76301--76390 Score: 63
Period size: 14 Copynumber: 5.8 Consensus size: 14
76291 TGTGAAATGC
76301 AAATCGCAACGACA
1 AAATCGCAACGACA
* *
76315 AAATCGCAATATGAAATGA
1 AAATCGC-A-ACG--A-CA
76334 AAATCGCAACGACA
1 AAATCGCAACGACA
*
76348 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
*
76364 TGAAATCGCAATGACA
1 --AAATCGCAACGACA
76380 AAATCGCAACG
1 AAATCGCAACG
76391 CGAAACACAA
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
14 27 0.46
15 2 0.03
16 9 0.15
17 2 0.03
18 11 0.19
19 8 0.14
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:76321 original size:33 final size:32
Alignment explanation
Indices: 76284--76388 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 32
76274 GGAAATGGCT
76284 ATCGCAATGTGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGTGAAATG-AAATCGCAACGACAAA
*
76317 ATCGCAATATGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGTGAAATG-AAATCGCAACGACAAA
* *
76350 ATCGCAATGCGAAATGAAATCGCAATGACAAA
1 ATCGCAATGTGAAATGAAATCGCAACGACAAA
76382 ATCGCAA
1 ATCGCAA
76389 CGCGAAACAC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 22 0.33
33 45 0.67
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.15
Consensus pattern (32 bp):
ATCGCAATGTGAAATGAAATCGCAACGACAAA
Found at i:76427 original size:19 final size:19
Alignment explanation
Indices: 76405--76498 Score: 100
Period size: 19 Copynumber: 5.5 Consensus size: 19
76395 ACACAAATCA
76405 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
76424 CATTGCGA-TTT--TGTCG
1 CATTGCGATTTTCATTTCG
76440 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
76457 CATTGCGA-TTT--TGTCG
1 CATTGCGATTTTCATTTCG
76473 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
76490 CATTGCGAT
1 CATTGCGAT
76499 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 12 0.20
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 21 0.34
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:76445 original size:14 final size:14
Alignment explanation
Indices: 76426--76482 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
76416 TCATTTCGCA
76426 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
76440 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
76457 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
76473 TTGCGATTTT
1 TTGCGATTTT
76483 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:76449 original size:33 final size:33
Alignment explanation
Indices: 76407--76498 Score: 184
Period size: 33 Copynumber: 2.8 Consensus size: 33
76397 ACAAATCACA
76407 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
76440 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
76473 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
76499 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:76535 original size:20 final size:20
Alignment explanation
Indices: 76483--76526 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
76473 TTGCGATTTT
*
76483 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
76502 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
76522 CATTT
1 CATTT
76527 TCGTGTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:77061 original size:18 final size:18
Alignment explanation
Indices: 77019--77061 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
77009 CGATCAGATG
* *
77019 ATGGCTCTCGGTGAGGTG
1 ATGGCTCTCGGCGAGGTA
* *
77037 ATAGCTCTGGGCGAGGTA
1 ATGGCTCTCGGCGAGGTA
77055 ATGGCTC
1 ATGGCTC
77062 CCGAAGTGGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.40, T:0.26
Consensus pattern (18 bp):
ATGGCTCTCGGCGAGGTA
Found at i:78406 original size:20 final size:20
Alignment explanation
Indices: 78381--78454 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
78371 AATAGTTTCT
*
78381 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
78401 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
78421 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
78441 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
78455 GTTACGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:78706 original size:20 final size:21
Alignment explanation
Indices: 78681--78726 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
78671 TCTGAGAGAT
78681 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
78701 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
78723 GGAG
1 GGAG
78727 GTGGGTGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
22 16 0.73
ACGTcount: A:0.22, C:0.15, G:0.43, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:78715 original size:22 final size:22
Alignment explanation
Indices: 78688--78731 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
78678 GATGGAGATA
78688 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
78710 GACGGATTTCGTCGGAGGTGGG
1 GACGGATTTCGCCGGAGATGGG
78732 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.48, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:78945 original size:20 final size:20
Alignment explanation
Indices: 78920--78971 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
78910 ATTATGTATT
78920 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
* *
78940 ATCGCGTTGCGAATGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
78960 ATCTCGTTGCGA
1 ATCGCGTTGCGA
78972 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:79005 original size:20 final size:20
Alignment explanation
Indices: 78980--79033 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
78970 GATTTTGTAT
78980 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
79000 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
79020 TATCGCATTGCGAT
1 TATCGCATTGCGAT
79034 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:79005 original size:61 final size:61
Alignment explanation
Indices: 78902--79036 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 61
78892 TTTGAAAATT
* * * *
78902 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGA-ATGTCAGTATC
1 GCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGATA-GTCAGTATC
* * * *
78963 TCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATC
1 GCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGATAGTCAGTATC
79024 GCATTGCGATTTT
1 GCATTGCGATTTT
79037 CCCAATTCGC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 62 0.98
62 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (61 bp):
GCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGATAGTCAGTATC
Found at i:79052 original size:61 final size:61
Alignment explanation
Indices: 78919--79054 Score: 150
Period size: 61 Copynumber: 2.2 Consensus size: 61
78909 GATTATGTAT
* * * * * ** *
78919 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAATGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAATGTCAGTATCGCATTGCGATTTTCCAA
* *
78980 TATCGCATTGCGATAGTAAGTATCGCATTGCG-ATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAT-GTCAGTATCGCATTGCGATTTT-CCAA
79042 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
79055 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 2 0.03
61 58 0.94
62 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTAAGAATCGCATTGCGAATGTCAGTATCGCATTGCGATTTTCCAA
Found at i:79293 original size:19 final size:19
Alignment explanation
Indices: 79271--79325 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 19
79261 GGTCACTGAG
**
79271 ATTATTTTCTCTTTATTTT
1 ATTATTTTAACTTTATTTT
79290 ATTA-TTTAACTTTATTTT
1 ATTATTTTAACTTTATTTT
79308 ATTA-TTTAACTTTATTTT
1 ATTATTTTAACTTTATTTT
79326 TGACTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
18 30 0.88
19 4 0.12
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTATTTTAACTTTATTTT
Found at i:79304 original size:18 final size:18
Alignment explanation
Indices: 79281--79325 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
79271 ATTATTTTCT
79281 CTTTATTTTATTATTTAA
1 CTTTATTTTATTATTTAA
79299 CTTTATTTTATTATTTAA
1 CTTTATTTTATTATTTAA
79317 CTTTATTTT
1 CTTTATTTT
79326 TGACTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
CTTTATTTTATTATTTAA
Found at i:83145 original size:12 final size:12
Alignment explanation
Indices: 83130--83163 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
83120 CTCCTCGGCA
83130 TCCTTGGCAAGC
1 TCCTTGGCAAGC
83142 TCCTTGGCAAGC
1 TCCTTGGCAAGC
83154 TCCTTGGCAA
1 TCCTTGGCAA
83164 CGTTGGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.24, T:0.26
Consensus pattern (12 bp):
TCCTTGGCAAGC
Found at i:87162 original size:16 final size:16
Alignment explanation
Indices: 87141--87201 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
87131 TAATAAATAA
87141 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
87157 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
87173 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
87189 ACGAACATAAACG
1 ACGAACATAAACG
87202 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:88292 original size:14 final size:14
Alignment explanation
Indices: 88275--88325 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
88265 GATTGGGTTA
*
88275 AACATAAATGAACG
1 AACATAAACGAACG
88289 AACATAAACG-A-G
1 AACATAAACGAACG
88301 --CATAAACGAACG
1 AACATAAACGAACG
88313 AACATAAACGAAC
1 AACATAAACGAAC
88326 ATAACCGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
10 8 0.25
11 1 0.03
12 2 0.06
13 1 0.03
14 20 0.62
ACGTcount: A:0.57, C:0.20, G:0.14, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:88311 original size:24 final size:24
Alignment explanation
Indices: 88275--88336 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
88265 GATTGGGTTA
*
88275 AACATAAATGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
88299 AGCATAAACGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
88323 AACATAACCGAACG
1 AACATAAACGAACG
88337 TTCACGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.55, C:0.21, G:0.15, T:0.10
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:88544 original size:17 final size:17
Alignment explanation
Indices: 88524--88559 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
88514 CAGGACAGTT
88524 TAATATCAATAAAAATA
1 TAATATCAATAAAAATA
88541 TAATATCAATAAAAATA
1 TAATATCAATAAAAATA
88558 TA
1 TA
88560 TGATAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATATCAATAAAAATA
Found at i:89874 original size:12 final size:12
Alignment explanation
Indices: 89859--89884 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
89849 TATATAAATT
89859 TTCAAAAAAAAA
1 TTCAAAAAAAAA
89871 TTCAAAAAAAAA
1 TTCAAAAAAAAA
89883 TT
1 TT
89885 TGGGGGTCAC
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:90269 original size:42 final size:43
Alignment explanation
Indices: 90217--90306 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
90207 TAGATATTTT
* *
90217 GCGGCATTTTT-CATACAAACGCTGCAAATGGTCTGGTATATA
1 GCGGCATTTTTGCATACAAACGCCGCAAAAGGTCTGGTATATA
* * * *
90259 GCGGCTTTTTTGGATGCAAACGCCGCAAAAGGTTTGGTATATA
1 GCGGCATTTTTGCATACAAACGCCGCAAAAGGTCTGGTATATA
90302 GCGGC
1 GCGGC
90307 GCAAATGGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 10 0.24
43 31 0.76
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (43 bp):
GCGGCATTTTTGCATACAAACGCCGCAAAAGGTCTGGTATATA
Found at i:92824 original size:9 final size:9
Alignment explanation
Indices: 92810--92893 Score: 60
Period size: 9 Copynumber: 8.8 Consensus size: 9
92800 GGCTGCTGGA
92810 AACCGGTTT
1 AACCGGTTT
92819 AACCGGTTTT
1 AACCGG-TTT
92829 CAACCGGTTCT
1 -AACCGGTT-T
*
92840 GACCGGTTT
1 AACCGGTTT
* *
92849 GACCGGTTCG
1 AACCGGTT-T
92859 AACCGGTTT
1 AACCGGTTT
* *
92868 GACCGGTCTG
1 AACCGGT-TT
*
92878 AACTGGTTT
1 AACCGGTTT
*
92887 GACCGGT
1 AACCGGT
92894 CTGACCTGAC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
9 27 0.46
10 25 0.42
11 7 0.12
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:92835 original size:20 final size:21
Alignment explanation
Indices: 92810--92867 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
92800 GGCTGCTGGA
92810 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
92830 AACCGGTTCTGACCGG-TTT-
1 AACCGGTTCTAACCGGTTTTC
* *
92849 GACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
92868 GACCGGTCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.41
20 13 0.41
21 6 0.19
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:92855 original size:19 final size:19
Alignment explanation
Indices: 92831--92897 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 19
92821 CCGGTTTTCA
92831 ACCGGTTCTG-ACCGGTTTG
1 ACCGG-TCTGAACCGGTTTG
92850 ACCGGT-TCGAACCGGTTTG
1 ACCGGTCT-GAACCGGTTTG
*
92869 ACCGGTCTGAACTGGTTTG
1 ACCGGTCTGAACCGGTTTG
92888 ACCGGTCTGA
1 ACCGGTCTGA
92898 CCTGACCCGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
17 1 0.02
18 2 0.05
19 40 0.91
20 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.31, T:0.28
Consensus pattern (19 bp):
ACCGGTCTGAACCGGTTTG
Found at i:92917 original size:12 final size:12
Alignment explanation
Indices: 92900--92928 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
92890 CGGTCTGACC
92900 TGACCCGACCGT
1 TGACCCGACCGT
92912 TGACCCGACCGT
1 TGACCCGACCGT
92924 TGACC
1 TGACC
92929 GTTGACTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:100076 original size:9 final size:9
Alignment explanation
Indices: 100062--100127 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 9
100052 GGCTGCTGGA
100062 AACCGGTTT
1 AACCGGTTT
100071 AACCGGTTTT
1 AACCGG-TTT
100081 CAACCGGTTCT
1 -AACCGGTT-T
*
100092 GACCGGTTT
1 AACCGGTTT
* *
100101 CGACCGGTTCG
1 -AACCGGTT-T
100112 AACCGGTTT
1 AACCGGTTT
*
100121 GACCGGT
1 AACCGGT
100128 CTGACCCGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 13 0.28
10 27 0.57
11 7 0.15
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:100087 original size:20 final size:21
Alignment explanation
Indices: 100062--100120 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
100052 GGCTGCTGGA
100062 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
100082 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
* *
100102 GACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
100121 GACCGGTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 25 0.76
21 8 0.24
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:100098 original size:10 final size:10
Alignment explanation
Indices: 100083--100133 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
100073 CCGGTTTTCA
100083 ACCGGTTCTG
1 ACCGGTTCTG
100093 ACCGGTT-TCG
1 ACCGGTTCT-G
100103 ACCGGTTC-G
1 ACCGGTTCTG
100112 AACCGGTT-TG
1 -ACCGGTTCTG
100122 ACCGG-TCTG
1 ACCGGTTCTG
100131 ACC
1 ACC
100134 CGACCCGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
8 1 0.03
9 12 0.33
10 23 0.64
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.25
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:100158 original size:22 final size:22
Alignment explanation
Indices: 100130--100202 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
100120 TGACCGGTCT
100130 GACCCGACCCGAAGGTTGACCC
1 GACCCGACCCGAAGGTTGACCC
100152 GACCCGACCCGAAGGTTGACCC
1 GACCCGACCCGAAGGTTGACCC
* **
100174 GACCTGACCCGACCGTTGACCC
1 GACCCGACCCGAAGGTTGACCC
100196 GACCCGA
1 GACCCGA
100203 TTGTTGACCG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.22, C:0.42, G:0.26, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGAAGGTTGACCC
Found at i:100217 original size:7 final size:7
Alignment explanation
Indices: 100205--100245 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
100195 CGACCCGATT
100205 GTTGACC
1 GTTGACC
100212 GTTGACC
1 GTTGACC
100219 GTTGACC
1 GTTGACC
100226 GTTGACC
1 GTTGACC
100233 GTTGACC
1 GTTGACC
*
100240 ATTGAC
1 GTTGAC
100246 TTTCTTTGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (7 bp):
GTTGACC
Found at i:107198 original size:16 final size:16
Alignment explanation
Indices: 107177--107207 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
107167 AAGCTATCAG
107177 GCAAAGTAAAATGTGT
1 GCAAAGTAAAATGTGT
107193 GCAAAGTAAAATGTG
1 GCAAAGTAAAATGTG
107208 GAAGATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
GCAAAGTAAAATGTGT
Found at i:108748 original size:13 final size:13
Alignment explanation
Indices: 108730--108755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
108720 CAATTTAATA
108730 CAAGGAACCGACG
1 CAAGGAACCGACG
108743 CAAGGAACCGACG
1 CAAGGAACCGACG
108756 GAGTGAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.31, T:0.00
Consensus pattern (13 bp):
CAAGGAACCGACG
Found at i:108804 original size:43 final size:43
Alignment explanation
Indices: 108738--108917 Score: 252
Period size: 43 Copynumber: 4.1 Consensus size: 43
108728 TACAAGGAAC
*
108738 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
* *
108781 CGACGCAAGGAACCAACGCAGTGAATGGTGGCGACTGAAGGCGCAACG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAA-G-G---CG
* * *
108829 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAAGAG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
*
108872 CGACGCAAGGAACCGACAGAGTGAATGGTGGCGACTGAAGGCG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
108915 CGA
1 CGA
108918 TTTACTGAAG
Statistics
Matches: 120, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
43 79 0.66
44 1 0.01
45 1 0.01
46 1 0.01
48 38 0.32
ACGTcount: A:0.31, C:0.21, G:0.39, T:0.10
Consensus pattern (43 bp):
CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
Found at i:108866 original size:91 final size:91
Alignment explanation
Indices: 108738--108915 Score: 313
Period size: 91 Copynumber: 2.0 Consensus size: 91
108728 TACAAGGAAC
* *
108738 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCGCGACGCAAGGAACCAAC-GCAG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAAGAGCGACGCAAGGAACCAACAG-AG
108802 TGAATGGTGGCGACTGAAGGCGCAACG
65 TGAATGGTGGCGACTGAAGGCGCAACG
*
108829 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAAGAGCGACGCAAGGAACCGACAGAGT
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAAGAGCGACGCAAGGAACCAACAGAGT
108894 GAATGGTGGCGACTGAAGGCGC
66 GAATGGTGGCGACTGAAGGCGC
108916 GATTTACTGA
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
91 82 0.99
92 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.39, T:0.10
Consensus pattern (91 bp):
CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAAGAGCGACGCAAGGAACCAACAGAGT
GAATGGTGGCGACTGAAGGCGCAACG
Found at i:110466 original size:22 final size:22
Alignment explanation
Indices: 110438--110486 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
110428 CACGTTTTCA
110438 AAAGCTATTAT-TTTCCTATTCG
1 AAAGCTATTATATTT-CTATTCG
*
110460 AAAGCTATTATATTTCTATTGG
1 AAAGCTATTATATTTCTATTCG
110482 AAAGC
1 AAAGC
110487 AAAAAAACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (22 bp):
AAAGCTATTATATTTCTATTCG
Found at i:111360 original size:20 final size:18
Alignment explanation
Indices: 111319--111355 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
111309 GTGGATTTTT
* *
111319 TTAAAAAATTAATATAAA
1 TTAAAAAAATAAAATAAA
111337 TTAAAAAAATAAAATAAA
1 TTAAAAAAATAAAATAAA
111355 T
1 T
111356 ATTAACCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TTAAAAAAATAAAATAAA
Found at i:115425 original size:136 final size:136
Alignment explanation
Indices: 115181--115801 Score: 938
Period size: 136 Copynumber: 4.6 Consensus size: 136
115171 GCTTAAAATG
* * * *
115181 AGAACTTGTTCGACCTATTACTCGATTCACGGCATTTCGAATCAACAATGCCTCGCTCGAGGGAT
1 AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTTGAGGGAT
* * *
115246 AAAAATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
66 TAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAAGTTCATA
115311 ATGAGA
131 ATGAGA
* *
115317 AGAACTTGTTTGACCTATTTCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTTGAGGGAT
1 AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTTGAGGGAT
* *
115382 TAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGAGAAAAAGTTCATA
66 TAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAAGTTCATA
115447 ATGAGA
131 ATGAGA
* * * *
115453 AGAACTTGTTCAACCTATTGCTCGATTCACGACATTTCGAATTATCAACGCCTCGCTTGAGGGAT
1 AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTTGAGGGAT
* * * **
115518 TAACATTTCCAATTGAGAGTTCATAATAAGAA-AACTCATCCGACAGAGGAAGAAGAAACTCATA
66 TAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAAGTTCATA
115582 ATGAGA
131 ATGAGA
* * ** *
115588 AGAACTTGTTCGACCTATTGCTCGATTCACGGTATTTCGAATCAGAAACATCTAGCTTGAGGGAT
1 AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTTGAGGGAT
115653 TAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAAGTTCATA
66 TAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAAGTTCATA
115718 ATGAGA
131 ATGAGA
* * * * * * *
115724 AGAACTTGTTCGACCTATTGCACGATTCATGGCTTTTCGAATCAGCAACACCTCACTTCAAGGAT
1 AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTTGAGGGAT
*
115789 CAACATTTCCAAT
66 TAACATTTCCAAT
115802 AGGAAGATCA
Statistics
Matches: 436, Mismatches: 48, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
135 119 0.27
136 317 0.73
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (136 bp):
AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTTGAGGGAT
TAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAAGTTCATA
ATGAGA
Found at i:115627 original size:271 final size:272
Alignment explanation
Indices: 115181--115801 Score: 947
Period size: 271 Copynumber: 2.3 Consensus size: 272
115171 GCTTAAAATG
* * *
115181 AGAACTTGTTCGACCTATTACTCGATTCACGGCATTTCGAATCAACAATGCCTCGCTCGAGGGAT
1 AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAACGCCTCGCTTGAGGGAT
* * * **
115246 AAAAATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
66 AAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGAAGAAGAAACTCATA
* * * * *
115311 ATGAGAAGAACTTGTTTGACCTATTTCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTTG
131 ATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGAAACACCTAGCTTG
115376 AGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGAGAAAAAG
196 AGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGAGAAAAAG
115441 TTCATAATGAGA
261 TTCATAATGAGA
* * * *
115453 AGAACTTGTTCAACCTATTGCTCGATTCACGACATTTCGAATTATCAACGCCTCGCTTGAGGGAT
1 AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAACGCCTCGCTTGAGGGAT
* *
115518 TAACATTTCCAATTGAGAGTTCATAATAAGAA-AACTCATCCGACAGAGGAAGAAGAAACTCATA
66 AAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGAAGAAGAAACTCATA
* *
115582 ATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGTATTTCGAATCAGAAACATCTAGCTTG
131 ATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGAAACACCTAGCTTG
* *
115647 AGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAAG
196 AGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGAGAAAAAG
115712 TTCATAATGAGA
261 TTCATAATGAGA
* * * * * * * *
115724 AGAACTTGTTCGACCTATTGCACGATTCATGGCTTTTCGAATCAGCAACACCTCACTTCAAGGAT
1 AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAACGCCTCGCTTGAGGGAT
*
115789 CAACATTTCCAAT
66 AAACATTTCCAAT
115802 AGGAAGATCA
Statistics
Matches: 314, Mismatches: 35, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
271 228 0.73
272 86 0.27
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (272 bp):
AGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAACGCCTCGCTTGAGGGAT
AAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGAAGAAGAAACTCATA
ATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGAAACACCTAGCTTG
AGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGAGAAAAAG
TTCATAATGAGA
Found at i:117101 original size:44 final size:45
Alignment explanation
Indices: 117053--117181 Score: 156
Period size: 44 Copynumber: 2.9 Consensus size: 45
117043 TAAATTGAGG
117053 CATTTTTCGGATACAAACGCTGCAAAAGGTCTAGTATATAGC-GA
1 CATTTTTCGGATACAAACGCTGCAAAAGGTCTAGTATATAGCGGA
* * *
117097 CATTTTTCGAATACAAACG-TCGTAAAAGGTCTAGTATATAGCGGT
1 CATTTTTCGGATACAAACGCT-GCAAAAGGTCTAGTATATAGCGGA
* * ** *
117142 GA-TTTTCGGATACAAATGCCACAAAAGGTCTGGTATATAG
1 CATTTTTCGGATACAAACGCTGCAAAAGGTCTAGTATATAG
117182 TGGCGTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.01
44 69 0.96
45 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (45 bp):
CATTTTTCGGATACAAACGCTGCAAAAGGTCTAGTATATAGCGGA
Found at i:123390 original size:32 final size:32
Alignment explanation
Indices: 123349--123417 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
123339 TCATGTTTCA
123349 TAGTTAAAGAGAGGAAGGAAGAACTTAAAACC
1 TAGTTAAAGAGAGGAAGGAAGAACTTAAAACC
*
123381 TAGTTAAAGAGAGGGAGGAAGAACTTAAAACC
1 TAGTTAAAGAGAGGAAGGAAGAACTTAAAACC
*
123413 AAGTT
1 TAGTT
123418 CATTACCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.09, G:0.26, T:0.17
Consensus pattern (32 bp):
TAGTTAAAGAGAGGAAGGAAGAACTTAAAACC
Found at i:124972 original size:11 final size:11
Alignment explanation
Indices: 124956--124980 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
124946 CATACCAAAT
124956 TCACCAATTGA
1 TCACCAATTGA
124967 TCACCAATTGA
1 TCACCAATTGA
124978 TCA
1 TCA
124981 AATTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (11 bp):
TCACCAATTGA
Found at i:126495 original size:41 final size:43
Alignment explanation
Indices: 126450--126672 Score: 162
Period size: 41 Copynumber: 5.4 Consensus size: 43
126440 ATAAGTTTGA
* * *
126450 GGCGTTT-GTAAAAAAACGCCTCTATAGTGCTAA-TATATCGC
1 GGCGTTTACTAAAAAAACGCCTCTATAGTGCCAACTCTATCGC
* * * * *
126491 GGCGTTTACTTAAAAAACACCACTACT-GT-CCAACTGTATAGC
1 GGCGTTTACTAAAAAAACGCCTCTA-TAGTGCCAACTCTATCGC
* *
126533 GGCGTTT-GTACGAAAAA-GCCTCTATAGTG-CAACTCTATCGC
1 GGCGTTTACTA-AAAAAACGCCTCTATAGTGCCAACTCTATCGC
** * * *
126574 AACGTTTACTTAAAAAACGCCACTACT-GT-CCAACTCTATAGC
1 GGCGTTTACTAAAAAAACGCCTCTA-TAGTGCCAACTCTATCGC
* ** * *
126616 GGCGTTT-GTACGAAAACGCCTCTATAGTG-TAACTCTATCGT
1 GGCGTTTACTAAAAAAACGCCTCTATAGTGCCAACTCTATCGC
126657 GGCGTTTACTAAAAAA
1 GGCGTTTACTAAAAAA
126673 TGCCACAAAT
Statistics
Matches: 135, Mismatches: 34, Indels: 25
0.70 0.18 0.13
Matches are distributed among these distances:
40 2 0.01
41 68 0.50
42 63 0.47
43 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (43 bp):
GGCGTTTACTAAAAAAACGCCTCTATAGTGCCAACTCTATCGC
Found at i:126535 original size:42 final size:42
Alignment explanation
Indices: 126489--126704 Score: 160
Period size: 41 Copynumber: 5.2 Consensus size: 42
126479 CTAATATATC
* *
126489 GCGGCGTTTACTTAAAAAACACCACTACTGTCCAACTGTATA
1 GCGGCGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
* * * *
126531 GCGGCGTTTGTAC--GAAAAA-GCCTCTA-TAGTGCAACTCTATC
1 GCGGCG-TT-TACTTAAAAAACGCCACTACT-GTCCAACTCTATA
**
126572 GCAACGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
1 GCGGCGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
* * * ** *
126614 GCGGCGTTT--GTACGAAAACGCCTCTA-TAGTGTAACTCTATC
1 GCGGCGTTTACTTA-AAAAACGCCACTACT-GTCCAACTCTATA
* * * * *
126655 GTGGCGTTTAC-TAAAAAATGCCACAAATGTTCAACTCTATA
1 GCGGCGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
126696 GCGGCGTTT
1 GCGGCGTTT
126705 GTACAAAAAA
Statistics
Matches: 133, Mismatches: 29, Indels: 25
0.71 0.16 0.13
Matches are distributed among these distances:
39 3 0.02
40 6 0.05
41 80 0.60
42 38 0.29
43 3 0.02
44 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
Found at i:126589 original size:83 final size:83
Alignment explanation
Indices: 126450--126744 Score: 373
Period size: 83 Copynumber: 3.6 Consensus size: 83
126440 ATAAGTTTGA
* * *
126450 GGCGTTTGTA-AAAAAACGCCTCTATAGTGCTAA-TATATCGCGGCGTTTACTTAAAAAACACCA
1 GGCGTTTGTACGAAAAA-GCCTCTATAGTGC-AACTCTATCGCGGCGTTTACTTAAAAAACGCCA
*
126513 CTACTGTCCAACTGTATAGC
64 CTACTGTCCAACTCTATAGC
**
126533 GGCGTTTGTACGAAAAAGCCTCTATAGTGCAACTCTATCGCAACGTTTACTTAAAAAACGCCACT
1 GGCGTTTGTACGAAAAAGCCTCTATAGTGCAACTCTATCGCGGCGTTTACTTAAAAAACGCCACT
126598 ACTGTCCAACTCTATAGC
66 ACTGTCCAACTCTATAGC
* * * * *
126616 GGCGTTTGTACGAAAACGCCTCTATAGTGTAACTCTATCGTGGCGTTTAC-TAAAAAATGCCACA
1 GGCGTTTGTACGAAAAAGCCTCTATAGTGCAACTCTATCGCGGCGTTTACTTAAAAAACGCCACT
* *
126680 AATGTTCAACTCTATAGC
66 ACTGTCCAACTCTATAGC
** * * * *
126698 GGCGTTTGTAC-AAAAAAACTCTATAGTTCAACTATGTTGCGGCGTTT
1 GGCGTTTGTACGAAAAAGCCTCTATAGTGCAACTCTATCGCGGCGTTT
126745 GTTGAAGAAA
Statistics
Matches: 186, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
81 27 0.15
82 41 0.22
83 113 0.61
84 5 0.03
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (83 bp):
GGCGTTTGTACGAAAAAGCCTCTATAGTGCAACTCTATCGCGGCGTTTACTTAAAAAACGCCACT
ACTGTCCAACTCTATAGC
Found at i:136298 original size:32 final size:31
Alignment explanation
Indices: 136262--136338 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
136252 CGGGGCCACG
*
136262 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** ** *
136294 GGGCCTACCCGAGAATGATCTCAGGGCCGTA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
136325 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
136339 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:150215 original size:20 final size:21
Alignment explanation
Indices: 150187--150269 Score: 53
Period size: 20 Copynumber: 4.0 Consensus size: 21
150177 GAACCCCATG
*
150187 GGGGTATCGATTCCC-CTACA
1 GGGGAATCGATTCCCACTACA
* * *
150207 GGGGAATCGGTTCCCATTCAAA
1 GGGGAATCGATTCCCACT-ACA
* * **
150229 GGGGAATCGGTTCCC-TTATG
1 GGGGAATCGATTCCCACTACA
* *
150249 GGGGTATCGATTCCCTCTACA
1 GGGGAATCGATTCCCACTACA
150270 CCAAAATGCT
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 27 0.55
21 5 0.10
22 17 0.35
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (21 bp):
GGGGAATCGATTCCCACTACA
Done.