Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002243.1 Hibiscus syriacus cultivar Beakdansim tig00004561_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: 60076
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:2345 original size:41 final size:43
Alignment explanation
Indices: 2273--2373 Score: 134
Period size: 41 Copynumber: 2.4 Consensus size: 43
2263 TTTTCATGCT
* * *
2273 TGATTAAATCCTTCGGGTTCATTAGTAAGTCTTTTGAGCATGA
1 TGATTAAATCATTCGGGTTCACTAGTAAGTCTTTCGAGCATGA
*
2316 TGATTAAATCATT-GGG-TCACTAGTAAGTCTTTCGAGCATGG
1 TGATTAAATCATTCGGGTTCACTAGTAAGTCTTTCGAGCATGA
* *
2357 TGATTAAGTTATTCGGG
1 TGATTAAATCATTCGGG
2374 CCATCCGTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 33 0.65
42 6 0.12
43 12 0.24
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (43 bp):
TGATTAAATCATTCGGGTTCACTAGTAAGTCTTTCGAGCATGA
Found at i:9211 original size:17 final size:17
Alignment explanation
Indices: 9189--9232 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
9179 ATGTAAAAAT
*
9189 AAATATTTAAATTTAAA
1 AAATATTTAAAATTAAA
* **
9206 AAATATATAAAATTATT
1 AAATATTTAAAATTAAA
9223 AAATATTTAA
1 AAATATTTAA
9233 TCAAGTAGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAAATTAAA
Found at i:17119 original size:17 final size:17
Alignment explanation
Indices: 17097--17132 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17087 AATTTAATCA
17097 TTTCAAGTTTAATTTGT
1 TTTCAAGTTTAATTTGT
* *
17114 TTTCAATTTTACTTTGT
1 TTTCAAGTTTAATTTGT
17131 TT
1 TT
17133 CGTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.64
Consensus pattern (17 bp):
TTTCAAGTTTAATTTGT
Found at i:21155 original size:14 final size:14
Alignment explanation
Indices: 21138--21233 Score: 58
Period size: 14 Copynumber: 6.9 Consensus size: 14
21128 TTGAATTGAA
21138 TAAATTTTAAACTT
1 TAAATTTTAAACTT
*
21152 TAAATTCTAAA--T
1 TAAATTTTAAACTT
* *
21164 TAAATTGAATAAATTT
1 TAAATT--TTAAACTT
* *
21180 TAAACTTTAAATTT
1 TAAATTTTAAACTT
21194 TAAA--TTAAA-TT
1 TAAATTTTAAACTT
21205 GAATAAATTTTAAACTT
1 ---TAAATTTTAAACTT
*
21222 TAAATTCTAAAC
1 TAAATTTTAAAC
21234 CTATCAAATG
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
11 2 0.03
12 12 0.18
14 40 0.60
16 11 0.16
17 2 0.03
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (14 bp):
TAAATTTTAAACTT
Found at i:21170 original size:35 final size:35
Alignment explanation
Indices: 21105--21232 Score: 201
Period size: 35 Copynumber: 3.7 Consensus size: 35
21095 AGATAAGATC
*
21105 ATAAA-TTTAAA-TTATAAA-T-TAAATTGAATTGA
1 ATAAATTTTAAACTT-TAAATTCTAAATTAAATTGA
21137 ATAAATTTTAAACTTTAAATTCTAAATTAAATTGA
1 ATAAATTTTAAACTTTAAATTCTAAATTAAATTGA
*
21172 ATAAATTTTAAACTTTAAATTTTAAATTAAATTGA
1 ATAAATTTTAAACTTTAAATTCTAAATTAAATTGA
21207 ATAAATTTTAAACTTTAAATTCTAAA
1 ATAAATTTTAAACTTTAAATTCTAAA
21233 CCTATCAAAT
Statistics
Matches: 89, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.06
33 10 0.11
34 3 0.03
35 71 0.80
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (35 bp):
ATAAATTTTAAACTTTAAATTCTAAATTAAATTGA
Found at i:21695 original size:13 final size:13
Alignment explanation
Indices: 21677--21714 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
21667 TGCTGTGTTA
21677 GGAGGGCCACAGT
1 GGAGGGCCACAGT
21690 GGAGGGCCACAGT
1 GGAGGGCCACAGT
*
21703 GGAGGGACACAG
1 GGAGGGCCACAG
21715 CTCCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.47, T:0.05
Consensus pattern (13 bp):
GGAGGGCCACAGT
Found at i:27043 original size:28 final size:27
Alignment explanation
Indices: 27012--27097 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 27
27002 GATTGGGATG
* *
27012 AATATAAATGAACGAACATAAGCGAACA
1 AATATAAATAAACGAACATAA-TGAACA
* *
27040 AATATAAATAAACAAACATGAATAAACA
1 AATATAAATAAACGAACAT-AATGAACA
*
27068 AACATAAATAAACGAACATAAATGAACA
1 AATATAAATAAACGAACAT-AATGAACA
27096 AA
1 AA
27098 GTACCAAACG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 47 0.96
29 2 0.04
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (27 bp):
AATATAAATAAACGAACATAATGAACA
Found at i:27053 original size:14 final size:14
Alignment explanation
Indices: 27036--27097 Score: 88
Period size: 14 Copynumber: 4.4 Consensus size: 14
27026 AACATAAGCG
*
27036 AACAAATATAAATA
1 AACAAACATAAATA
*
27050 AACAAACATGAATA
1 AACAAACATAAATA
27064 AACAAACATAAATA
1 AACAAACATAAATA
* *
27078 AACGAACATAAATG
1 AACAAACATAAATA
27092 AACAAA
1 AACAAA
27098 GTACCAAACG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.68, C:0.13, G:0.05, T:0.15
Consensus pattern (14 bp):
AACAAACATAAATA
Found at i:28289 original size:23 final size:23
Alignment explanation
Indices: 28263--28348 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
28253 TACGCGTTCT
*
28263 TTCGGGACAATTCTATGTGATCA
1 TTCGGGACAATTCTATGTGGTCA
* ** * *
28286 TTCGAGACCTTTCTACGTGGTCC
1 TTCGGGACAATTCTATGTGGTCA
* *
28309 TTCGGGACAATACTATGTGGTCT
1 TTCGGGACAATTCTATGTGGTCA
*
28332 TTCGGGACATTTCTATG
1 TTCGGGACAATTCTATG
28349 CGCAGTTTAT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (23 bp):
TTCGGGACAATTCTATGTGGTCA
Found at i:28567 original size:2 final size:2
Alignment explanation
Indices: 28515--28552 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28505 TATATATATA
28515 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28553 CGCGCGTGCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:34115 original size:35 final size:35
Alignment explanation
Indices: 34069--34313 Score: 312
Period size: 35 Copynumber: 7.0 Consensus size: 35
34059 GTTAATAAGA
*
34069 AGAACGAAAGGAAGCATCACACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
*
34104 CGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
* * * * **
34139 CGAACAGAA-TAAGATATTGCACTTTCGATTCAAGT
1 AGAACGGAAGGAAG-CATCACACTTTCGATTCAAGT
* ** *
34174 AGAACGAAAGGAAAAATCATACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
34209 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
* * *
34244 AGAATGAAAGGAAGCATCACACTTTTGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
* **
34279 CGAACGGAAGGAAGCATTGCACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
34314 GTTTATCTTT
Statistics
Matches: 179, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
34 3 0.02
35 174 0.97
36 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (35 bp):
AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
Found at i:34901 original size:20 final size:19
Alignment explanation
Indices: 34876--34922 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
34866 TTCGTCCTCT
*
34876 TATATTATAATATTATATAA
1 TATATTATAACATTATA-AA
34896 TATATT-T-ACATTATAAA
1 TATATTATAACATTATAAA
34913 TCATATTATA
1 T-ATATTATA
34923 TAATATATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 2 0.09
20 6 0.26
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATTATAACATTATAAA
Found at i:36081 original size:5 final size:5
Alignment explanation
Indices: 36071--36102 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
36061 TAATATTCAT
36071 TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
36103 CATCTAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:36091 original size:14 final size:14
Alignment explanation
Indices: 36072--36102 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
36062 AATATTCATT
36072 TTTATTTTATTTTA
1 TTTATTTTATTTTA
36086 TTTATTTTATTTTA
1 TTTATTTTATTTTA
36100 TTT
1 TTT
36103 CATCTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:37795 original size:19 final size:19
Alignment explanation
Indices: 37771--37816 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
37761 CATCATGCAT
37771 TTTGCATTTCGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
37790 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCGTTATTTTC
37809 TTTGCATT
1 TTTGCATT
37817 CATATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTGCATTTCGTTATTTTC
Found at i:41600 original size:165 final size:165
Alignment explanation
Indices: 41271--41999 Score: 926
Period size: 164 Copynumber: 4.4 Consensus size: 165
41261 AAAGACCCCC
* * * * * *
41271 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTA
1 GAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
** * * * * * *
41336 TCTGTCACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCATATCATTTGCAGCACAA
65 TCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAA
* * *
41400 CTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTT
127 CTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTT
*
41439 GAGTTCGACTACGCTCAGCT-CAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
1 GAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
*
41503 TCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAGCTC
65 TCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTC
* *
41568 AAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTT
130 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTT
* *
41604 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTAG
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
* * * *
41669 CTACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAATATAACTCA
66 CTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTCA
* * ** * *
41734 AGGGTAGAAGGGTTATATATC-ACCAAAGACCTTC
131 AGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTT
* *
41768 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGTTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
* * * *
41833 CTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGACACATCATTTGCAGCATAACTTA
66 CTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTCA
* * *
41898 AGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTT
131 AGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTT
* * ** * ** * *
41933 GATTTTGACTAC-CTCAGCTCCAAGGCACATCATTTATAACATAGCCCAAGGCAAGAAGGGCTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
41997 CTG
66 CTG
42000 TCAAGAAGAT
Statistics
Matches: 493, Mismatches: 64, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
164 220 0.45
165 210 0.43
166 4 0.01
167 42 0.09
168 17 0.03
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
CTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTCA
AGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTT
Found at i:41818 original size:329 final size:330
Alignment explanation
Indices: 41271--41967 Score: 943
Period size: 329 Copynumber: 2.1 Consensus size: 330
41261 AAAGACCCCC
* * * *
41271 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTA
1 GAGTTCGACTAC-CTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTA
* ** * * *
41336 TCTGTCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGCACAAC
64 GC-GTCACCAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACACAAC
* * * * * *
41401 TTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGAC
128 TCAAGGCTAGAAGGGTTATATACCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGAC
41466 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
193 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
* * *
41531 ACTCAGCTTCGAGGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAA
258 ACTCAGCTTCGAGGACACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAA
41596 AGACCTTT
323 AGACCTTT
* *
41604 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTAG
1 GAGTTCGACTAC-CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAG
* * * * * *
41669 C-T-ACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAATATAACT
65 CGTCACCAAAGACCCCCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAACACAACT
* * * *
41732 CAAGGGTAGAAGGGTTATATATC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGC
129 CAAGGCTAGAAGGGTTATATACCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAACGAC
* * *
41795 ACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTAC
193 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
* * * * *
41860 ACTCAGCTTCGAGGACACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAA
258 ACTCAGCTTCGAGGACACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAA
41925 AGACCTTT
323 AGACCTTT
* *
41933 GATTTTGACTACCTCAGCTCCAAGGCACATCATTT
1 GAGTTCGACTACCTCAGCTCCAAGGCACATCATTT
41968 ATAACATAGC
Statistics
Matches: 320, Mismatches: 42, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
328 23 0.07
329 199 0.62
330 40 0.12
332 41 0.13
333 17 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (330 bp):
GAGTTCGACTACCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAGC
GTCACCAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACACAACTCA
AGGCTAGAAGGGTTATATACCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGACACA
TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACT
CAGCTTCGAGGACACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGA
CCTTT
Found at i:42563 original size:20 final size:19
Alignment explanation
Indices: 42538--42584 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
42528 TTCGTCCTCT
*
42538 TATATTATAATATTATATAA
1 TATATTATAACATTATA-AA
42558 TATATT-T-ACATTATAAA
1 TATATTATAACATTATAAA
42575 TCATATTATA
1 T-ATATTATA
42585 TAATATATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 2 0.09
20 6 0.26
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATTATAACATTATAAA
Found at i:43753 original size:14 final size:14
Alignment explanation
Indices: 43734--43760 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43724 TAATATTCAT
43734 TTTTATTTTATTTA
1 TTTTATTTTATTTA
43748 TTTTATTTTATTT
1 TTTTATTTTATTT
43761 CATCTAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:44680 original size:15 final size:16
Alignment explanation
Indices: 44656--44698 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
44646 ATTTTAACTC
44656 AAAA-TAAAATAA-TA
1 AAAATTAAAATAATTA
*
44670 ACAATTAAAATAATTA
1 AAAATTAAAATAATTA
44686 AAAATTAAAATAA
1 AAAATTAAAATAA
44699 ATATTAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.12
15 8 0.32
16 14 0.56
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATTAAAATAATTA
Found at i:46171 original size:182 final size:183
Alignment explanation
Indices: 45789--46389 Score: 899
Period size: 182 Copynumber: 3.3 Consensus size: 183
45779 CGATACAAAT
* * *
45789 AAAATGTATCGATCCATAATAGTATAACAGGTAAAAATATGATC-AAACCGGT-T-TAATTATGA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-CAAAACCGGTCTCGAA--ATGA
* * * *
45851 TAAAACCGGTAAAACACTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATTGACAC
63 CAAAACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATCGACAC
45916 TTATGGAATTTAAAAGAGAAGCAA-TAATAGCGCCTATAAAGTGTCGATACTTTATA
128 TTATGGAATTTAAAAGAGAAG-AAGTAATAGCGCCTATAAAGTGTCGATACTTTATA
*
45972 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAAACCGGTCTCGAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
* * * * * *
46037 AACCTGTAAAGCGTTACCTAATATGTTGAAAGTATCGA-TAC-TTTAATATAAGTATCGAAACTT
66 AACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAA-ATAAGTATCGACACTT
* * *
46100 TTGGAATTTAAAAGAAAAGAAGTAATAGCGCCTATAAAGTATCGATACTTTATA
130 ATGGAATTTAAAAGAGAAGAAGTAATAGCGCCTATAAAGTGTCGATACTTTATA
*
46154 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
46219 AACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATCGACACTTA
66 AACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATCGACACTTA
* * *
46284 TGAAATTTAAAAGAGAAGCAGTAATAGCGCCAATAAAGTGTCGATACTTTATAA
131 TGGAATTTAAAAGAGAAGAAGTAATAGCGCCTATAAAGTGTCGATACTTTAT-A
* *
46338 AAAATGTATCGATCCATAACAATGTAACAGGTAAAAATATGACAAAATCGGT
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
46390 AAAGCGCTAC
Statistics
Matches: 376, Mismatches: 34, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
181 6 0.02
182 162 0.43
183 151 0.40
184 55 0.15
185 2 0.01
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (183 bp):
AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
AACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATCGACACTTA
TGGAATTTAAAAGAGAAGAAGTAATAGCGCCTATAAAGTGTCGATACTTTATA
Found at i:48427 original size:22 final size:23
Alignment explanation
Indices: 48376--48429 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
48366 ATGTTTTTGT
48376 TTTA-TATATAAAATGATAGTATA
1 TTTATTATATAAAATGATAG-ATA
48399 TTTATTATATAAAATGATA-A-A
1 TTTATTATATAAAATGATAGATA
48420 TTTAATTATA
1 TTT-ATTATA
48430 AATTTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
22 7 0.24
23 4 0.14
24 14 0.48
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (23 bp):
TTTATTATATAAAATGATAGATA
Found at i:48432 original size:12 final size:12
Alignment explanation
Indices: 48415--48444 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
48405 ATATAAAATG
48415 ATAAATTTAATT
1 ATAAATTTAATT
48427 ATAAATTTAATT
1 ATAAATTTAATT
48439 ATAAAT
1 ATAAAT
48445 ACAGGTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATAAATTTAATT
Found at i:48702 original size:18 final size:17
Alignment explanation
Indices: 48670--48705 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
48660 GAAGTTTATT
*
48670 GGCAAGGAGGTAGAGGA
1 GGCAAGGAGGCAGAGGA
48687 GGCAATGGAGGCAGAGGA
1 GGCAA-GGAGGCAGAGGA
48705 G
1 G
48706 AATGAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.33, C:0.08, G:0.53, T:0.06
Consensus pattern (17 bp):
GGCAAGGAGGCAGAGGA
Found at i:49010 original size:66 final size:66
Alignment explanation
Indices: 48884--49010 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 66
48874 GGAAGTAGGA
* ** *
48884 GGAAAAATAGATGGAGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAACTTAAGATGGTGACGGG
1 GGAAAAATAGATGGAGTGGTCAAAGAAGTTGAGGAATTGAGGGGTGAACTTAAGAGGGTGACGGG
48949 T
66 T
* * * * * *
48950 GGAAAAATTGATGGAGTGGTCAAGGAAGTT-ATGGAATTGAGGTGTGTACTTACGGGGGTGA
1 GGAAAAATAGATGGAGTGGTCAAAGAAGTTGA-GGAATTGAGGGGTGAACTTAAGAGGGTGA
49011 AGGGGGTGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 1 0.02
66 49 0.98
ACGTcount: A:0.31, C:0.04, G:0.41, T:0.24
Consensus pattern (66 bp):
GGAAAAATAGATGGAGTGGTCAAAGAAGTTGAGGAATTGAGGGGTGAACTTAAGAGGGTGACGGG
T
Found at i:50819 original size:66 final size:66
Alignment explanation
Indices: 50731--50965 Score: 425
Period size: 66 Copynumber: 3.6 Consensus size: 66
50721 TTGTATCTGA
* *
50731 ATGTAATTATGTTTGAGGTGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
50796 G
66 G
*
50797 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
50862 G
66 G
*
50863 ATGTAATTATGTATGAGATGAGAAAAGTTAGCATTAGGTTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
50928 G
66 G
*
50929 ATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAG
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAG
50966 ATTGCTGTTG
Statistics
Matches: 162, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 162 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (66 bp):
ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
G
Found at i:50994 original size:48 final size:48
Alignment explanation
Indices: 50924--51061 Score: 233
Period size: 48 Copynumber: 2.9 Consensus size: 48
50914 TTCTTATACA
50924 TGTTG-ATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGC
1 TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGC
*
50971 TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGT
1 TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGC
* * *
51019 TGCTGAATGTAATTATGTGTGAGATGAGAAAAGTTAGCAATAG
1 TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAG
51062 GTGTTCTACA
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
47 5 0.06
48 81 0.94
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (48 bp):
TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGC
Found at i:51929 original size:201 final size:200
Alignment explanation
Indices: 51582--52951 Score: 1754
Period size: 201 Copynumber: 6.8 Consensus size: 200
51572 AATACGTAAA
* * *
51582 CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCTC-AAAATATCGAAACCAATAATTATAA
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCC-CAAAAACATCGAAACCCATAATTATAA
* * * * * * * *
51646 TGTAATAGGTAAATTTT-CAATGTAACCGGTAGAAATATATCGGTTTTATGAGAGAATAGGTCTA
65 TGTAATAGGT-AATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAA
* * *
51710 CATAATGTATCGACACTTTTGAAATTTGTGTCGATATTTTTTGTCCATAATGAATGCCTAAACGA
129 CATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCC-AAACGA
51775 GGTGCACG
193 GGTGCACG
*
51783 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATACT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * *
51848 GTAATAGGTAATTTTGCAATGTAACCGATAAAAATATATCGGTTTAATTAGAAAACATGTCAACA
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
* * * * *
51913 TAATGTATCAACACTTTTTAAATTTGTGTCGATACATTTTGCCCAGAATGAATGTCAAACTAGGT
131 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGT
51978 GCACG
196 GCACG
* ** * * * * *
51983 CATAAAGTGTTGATACATTTA-AAATTGTATCGATCCTAAAAACATTGAAACCGATACTTACAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * * * * * * * * * *
52047 GTAATAGGTAAATTTACAATGTTACCGATAGAAATATACCAGTTTTATGAGAGAATATGTCTACA
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
* * *
52112 TAATGTATCGATACTTTTTAAATTTGTGTCGATACTTTTTGCCCAGAATGAATGCCCAAATGAGG
131 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGAGG
52177 TGCACG
195 TGCACG
* *
52183 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCGAAACTCATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* *
52248 GTAATAGGCAATTTTGCAATGTAACCGGTATAAATATACCAGTTTAATTAGAAAACA-GTTCAAC
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATG-TCAAC
* * * * *
52312 ATAATGTATCGATACTTTTTAAATTTGTGTCGATACTTGTTGTCCAAAAATGAATGACAAACTAG
130 ATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCC-AGAATGAATGCCAAACGAG
*
52377 CTGCACG
194 GTGCACG
*
52384 CATAAAGTGTCGATACATTTA-AAATTA-TATCGATCCCAAAAACATCGAAACCCATAATTATAA
1 CATAAAGTGTCGATACATTTATAAA-AAGTATCGATCCCAAAAACATCGAAACCCATAATTATAA
* * * *
52447 TGTAAAAGGTAATTTTTGCAATGTAACTGGTATAAATATATCTGG-TTAATTAGAAAACATGTTA
65 TGTAATAGGTAA-TTTTGCAATGTAACCGGTATAAATATA-CCGGTTTAATTAGAAAACATGTCA
*
52511 ACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC---TTGTCTAGAATGAATGCCCAAACG
128 ACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACG
* *
52573 AAGTGCATG
192 AGGTGCACG
* * * *
52582 CATAAAGTCTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCAAAACCCAAAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * * * *
52647 ATAATAGGTAACTTTGTAATGTAACCGATATAAATATACCAGTTTAATTAGAAAACATGTCAACA
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
* * * * * *
52712 TAATGTATCGACATTTTTTATATTTGTGTCGATACTTGTTGTCCAGAAATGAATGACAAACTAGC
131 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAG-AATGAATGCCAAACGAGG
52777 TGCACG
195 TGCACG
* ** * *
52783 CATAAAGTGTCGATACATTT-GAAATTGTATAGATCCCAAAAACATCGAAATCCATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * * * *
52847 GTAATAGGTAATTTTGCAATATAACCGGTAAAAATATACCGGATTAATTAGAAAACGTGTTAACA
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
* *
52912 TAATGTATCAACACTTTTTAAATTTGTTTCGATACTTTTT
131 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTT
52952 TAAAATTACG
Statistics
Matches: 1014, Mismatches: 137, Indels: 37
0.85 0.12 0.03
Matches are distributed among these distances:
197 11 0.01
198 114 0.11
199 186 0.18
200 247 0.24
201 436 0.43
202 20 0.02
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (200 bp):
CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGT
GCACG
Found at i:52670 original size:399 final size:398
Alignment explanation
Indices: 51582--52948 Score: 1863
Period size: 400 Copynumber: 3.4 Consensus size: 398
51572 AATACGTAAA
* *
51582 CATAAAGTGTCGATACATTTATTAAA--AGTATCGATCCTC-AAAATATCGAAACCAATAATTAT
1 CATAAAGTGTCGATACATTTA--AAATTA-TATCGATCC-CAAAAACATCGAAACCCATAATTAT
* * * * *
51644 AATGTAATAGGTAAATTTT-CAATGTAACCGGTAGAAATATATCGGTTTTATGAGAGAATAGGTC
62 AATGTAATAGGT-AATTTTGCAATGTAACCGGTAGAAATATATCGGATTAATGAGAAAACATGTC
* * * *
51708 TACATAATGTATCGACACTTTTGAAATTTGTGTCGATATTTTTTGTCCATAATGAATGCCTAAAC
126 TACATAATGTATCGACACTTTTTAAATTTGTGTCGATA---CTTGTCCAGAATGAATGCCCAAAC
*
51773 GAGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCA
188 GAGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCGAAACCCA
* * * *
51838 TAATTATACTGTAATAGGTAATTTTGCAATGTAACCGATAAAAATATATCGGTTTAATTAGAAAA
253 TAATTATAATGTAATAGGTAATTTTGCAATGTAACCGATATAAATATACCAGTTTAATTAGAAAA
* * *
51903 CATGTCAACATAATGTATCAACACTTTTTAAATTTGTGTCGATACATT-TTG-CCCAGAATGAAT
318 CATGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC-TTGTTGTCCAAAAATGAAT
* *
51966 GTCAAACTAGGTGCACG
382 GACAAACTAGCTGCACG
* * * * * * *
51983 CATAAAGTGTTGATACATTTAAAATTGTATCGATCCTAAAAACATTGAAACCGATACTTACAATG
1 CATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCGAAACCCATAATTATAATG
* * * * * * * * * *
52048 TAATAGGTAAATTTACAATGTTACCGATAGAAATATACCAGTTTTATGAGAGAATATGTCTACAT
66 TAATAGGTAATTTTGCAATGTAACCGGTAGAAATATATCGGATTAATGAGAAAACATGTCTACAT
* * *
52113 AATGTATCGATACTTTTTAAATTTGTGTCGATACTTTTTGCCCAGAATGAATGCCCAAATGAGGT
131 AATGTATCGACACTTTTTAAATTTGTGTCGATAC---TTGTCCAGAATGAATGCCCAAACGAGGT
*
52178 GCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCGAAACTCATAATT
193 GCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCGAAACCCATAATT
* *
52243 ATAATGTAATAGGCAATTTTGCAATGTAACCGGTATAAATATACCAGTTTAATTAGAAAACA-GT
258 ATAATGTAATAGGTAATTTTGCAATGTAACCGATATAAATATACCAGTTTAATTAGAAAACATG-
*
52307 TCAACATAATGTATCGATACTTTTTAAATTTGTGTCGATACTTGTTGTCCAAAAATGAATGACAA
322 TCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTTGTCCAAAAATGAATGACAA
52372 ACTAGCTGCACG
387 ACTAGCTGCACG
52384 CATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCGAAACCCATAATTATAATG
1 CATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCGAAACCCATAATTATAATG
* * * *
52449 TAAAAGGTAATTTTTGCAATGTAACTGGTATAAATATATCTGG-TTAATTAGAAAACATGT-TAA
66 TAATAGGTAA-TTTTGCAATGTAACCGGTAGAAATATATC-GGATTAATGAGAAAACATGTCT-A
* *
52512 CATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTCTAGAATGAATGCCCAAACGAAGT
128 CATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTCCAGAATGAATGCCCAAACGAGGT
* * * *
52577 GCATGCATAAAGTCTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCAAAACCCAAAATT
193 GCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCGAAACCCATAATT
* * *
52642 ATAATATAATAGGTAACTTTGTAATGTAACCGATATAAATATACCAGTTTAATTAGAAAACATGT
258 ATAATGTAATAGGTAATTTTGCAATGTAACCGATATAAATATACCAGTTTAATTAGAAAACATGT
* * *
52707 CAACATAATGTATCGACATTTTTTATATTTGTGTCGATACTTGTTGTCCAGAAATGAATGACAAA
323 CAACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTTGTCCAAAAATGAATGACAAA
52772 CTAGCTGCACG
388 CTAGCTGCACG
* * * *
52783 CATAAAGTGTCGATACATTTGAAATTGTATAGATCCCAAAAACATCGAAATCCATAATTATAATG
1 CATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCGAAACCCATAATTATAATG
* * * * *
52848 TAATAGGTAATTTTGCAATATAACCGGTAAAAATATACCGGATTAATTAGAAAACGTGT-TAACA
66 TAATAGGTAATTTTGCAATGTAACCGGTAGAAATATATCGGATTAATGAGAAAACATGTCT-ACA
* *
52912 TAATGTATCAACACTTTTTAAATTTGTTTCGATACTT
130 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTT
52949 TTTTAAAATT
Statistics
Matches: 865, Mismatches: 86, Indels: 33
0.88 0.09 0.03
Matches are distributed among these distances:
397 2 0.00
398 81 0.09
399 295 0.34
400 301 0.35
401 113 0.13
402 72 0.08
403 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (398 bp):
CATAAAGTGTCGATACATTTAAAATTATATCGATCCCAAAAACATCGAAACCCATAATTATAATG
TAATAGGTAATTTTGCAATGTAACCGGTAGAAATATATCGGATTAATGAGAAAACATGTCTACAT
AATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTCCAGAATGAATGCCCAAACGAGGTGCA
CGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCGAAACCCATAATTATA
ATGTAATAGGTAATTTTGCAATGTAACCGATATAAATATACCAGTTTAATTAGAAAACATGTCAA
CATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTGTTGTCCAAAAATGAATGACAAACTA
GCTGCACG
Found at i:53276 original size:15 final size:16
Alignment explanation
Indices: 53251--53281 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
53241 CAGTCTTTCT
53251 CAAAGCTCTTCTCAAC
1 CAAAGCTCTTCTCAAC
53267 CAAA-CTCTTCTCAAC
1 CAAAGCTCTTCTCAAC
53282 GACAACCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.39, G:0.03, T:0.26
Consensus pattern (16 bp):
CAAAGCTCTTCTCAAC
Found at i:53331 original size:18 final size:17
Alignment explanation
Indices: 53271--53322 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
53261 CTCAACCAAA
* *
53271 CTCTTCTCAACGACAACC
1 CTCTTCTCAACTA-ATCC
*
53289 TTCTTCTCAACTAATCC
1 CTCTTCTCAACTAATCC
53306 CTCATTCTCAACTAATC
1 CTC-TTCTCAACTAATC
53323 GCTACTTCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.27, C:0.38, G:0.02, T:0.33
Consensus pattern (17 bp):
CTCTTCTCAACTAATCC
Found at i:56257 original size:3 final size:3
Alignment explanation
Indices: 56249--56279 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
56239 TTAATTCGAG
*
56249 ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
56280 ATATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:56268 original size:15 final size:15
Alignment explanation
Indices: 56248--56277 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56238 GTTAATTCGA
56248 GATAATAATAATAAT
1 GATAATAATAATAAT
56263 GATAATAATAATAAT
1 GATAATAATAATAAT
56278 AAATATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (15 bp):
GATAATAATAATAAT
Done.