Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006355.1 Hibiscus syriacus cultivar Beakdansim tig00015233_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: 67323
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1354 original size:20 final size:19
Alignment explanation
Indices: 1327--1365 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1317 TCGATACTAA
1327 ACCTTTGGTATCGATAACC
1 ACCTTTGGTATCGATAACC
1346 ACCTATTGGTATCGATAACC
1 ACCT-TTGGTATCGATAACC
1366 CCTGACAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (19 bp):
ACCTTTGGTATCGATAACC
Found at i:11380 original size:4 final size:5
Alignment explanation
Indices: 11348--11377 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
11338 GATAAAGATG
*
11348 ATAAG ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
11378 TAATTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:11496 original size:12 final size:12
Alignment explanation
Indices: 11479--11503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11469 AAAGATAAAG
11479 ATTAAATAAATA
1 ATTAAATAAATA
11491 ATTAAATAAATA
1 ATTAAATAAATA
11503 A
1 A
11504 AATTGATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAATAAATA
Found at i:12368 original size:85 final size:83
Alignment explanation
Indices: 12253--12449 Score: 220
Period size: 85 Copynumber: 2.3 Consensus size: 83
12243 AAAAACAAGC
* * * * *
12253 TAAAGATAAT-TTCTAATATAATACCTTAAATCATAATTAAAACACTTAA-AACTATTTAAACTG
1 TAAA-ATAATATT-TAAAATAATATCCTAAATCACAATTAAAACAC-TAACAACTATTTAAACTA
12316 AAATACCTAAAACAAAGATAAAA
63 AAATACCTAAAAC-AA-ATAAAA
* * * *
12339 TAAAATAATATTTAAAATAATATCCTAAATCCCAATTGAAATACTAACATCTATTTAAACTAAAA
1 TAAAATAATATTTAAAATAATATCCTAAATCACAATTAAAACACTAACAACTATTTAAACTAAAA
*
12404 TACCTAAAACAAATATAA
66 TACCTAAAACAAATAAAA
* *
12422 T-ATATAATATTTAAAATATTATCCTAAA
1 TAAAATAATATTTAAAATAATATCCTAAA
12450 ACTTGAGTTT
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
82 25 0.26
83 6 0.06
84 5 0.05
85 55 0.57
86 6 0.06
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (83 bp):
TAAAATAATATTTAAAATAATATCCTAAATCACAATTAAAACACTAACAACTATTTAAACTAAAA
TACCTAAAACAAATAAAA
Found at i:13801 original size:19 final size:20
Alignment explanation
Indices: 13779--13820 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
13769 ACTCAAGAAC
13779 ATTTCTTCT-CTTCA-AAAAT
1 ATTTCTTCTCCTT-AGAAAAT
*
13798 ATTTTTTCTCCTTAGAAAAT
1 ATTTCTTCTCCTTAGAAAAT
13818 ATT
1 ATT
13821 CTTTTTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTTCTTCTCCTTAGAAAAT
Found at i:15854 original size:19 final size:19
Alignment explanation
Indices: 15830--15866 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15820 AGTTTCAGAG
15830 AGTGAAACAGATCCAAGAA
1 AGTGAAACAGATCCAAGAA
* *
15849 AGTGAATCAGATTCAAGA
1 AGTGAAACAGATCCAAGA
15867 GATAGAGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.16
Consensus pattern (19 bp):
AGTGAAACAGATCCAAGAA
Found at i:18081 original size:7 final size:7
Alignment explanation
Indices: 18069--18093 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18059 GTATGAAAAT
18069 GAGGGAA
1 GAGGGAA
18076 GAGGGAA
1 GAGGGAA
18083 GAGGGAA
1 GAGGGAA
18090 GAGG
1 GAGG
18094 TATCCGCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (7 bp):
GAGGGAA
Found at i:19088 original size:32 final size:32
Alignment explanation
Indices: 19043--19190 Score: 109
Period size: 32 Copynumber: 4.6 Consensus size: 32
19033 CACTAGTGCA
* * *
19043 CATTATTTAAATGCGACACTGATACTATTATG
1 CATTATCTGAATGCGACACTGACACTATTATG
* * *
19075 CATTATCTGAATGCGACCCTGAAACTGA-TATT
1 CATTATCTGAATGCGACACTGACACT-ATTATG
* * * * * *
19107 CATTATCTTAATACGATATTGACATTATTGTG
1 CATTATCTGAATGCGACACTGACACTATTATG
* * * * *
19139 CATTATTTGAATACGACGCTAACACTACTATG
1 CATTATCTGAATGCGACACTGACACTATTATG
* *
19171 CATTATATGAATGTGACACT
1 CATTATCTGAATGCGACACT
19191 TTGCTAGTAT
Statistics
Matches: 87, Mismatches: 27, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
31 1 0.01
32 85 0.98
33 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36
Consensus pattern (32 bp):
CATTATCTGAATGCGACACTGACACTATTATG
Found at i:22447 original size:23 final size:23
Alignment explanation
Indices: 22421--22477 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
22411 TGTGACATGT
22421 TCTCTTCCTTTAATG-CACATTTA
1 TCTCTTCCTTT-ATGTCACATTTA
* *
22444 TCTCTGCCTTTATGTCACATTTT
1 TCTCTTCCTTTATGTCACATTTA
22467 TCTCTTCCTTT
1 TCTCTTCCTTT
22478 TGGTAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.14, C:0.28, G:0.05, T:0.53
Consensus pattern (23 bp):
TCTCTTCCTTTATGTCACATTTA
Found at i:23030 original size:15 final size:16
Alignment explanation
Indices: 22998--23050 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
22988 ATACCACATC
22998 AAAATATTAAAATTAAA
1 AAAATATTAAAA-TAAA
23015 AAAATATTAAGAA-AAA
1 AAAATATTAA-AATAAA
* *
23031 ATTAATATAAAAATAAA
1 A-AAATATTAAAATAAA
23048 AAA
1 AAA
23051 TTTATTCTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
16 7 0.23
17 21 0.70
18 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
AAAATATTAAAATAAA
Found at i:24371 original size:66 final size:66
Alignment explanation
Indices: 24233--24371 Score: 156
Period size: 66 Copynumber: 2.1 Consensus size: 66
24223 CTGGGAGAAG
* * * *
24233 AATTAA-AAAATATATTCTGAAAAGTAATGTCATTAACAAGAATCCGAATAAATTTGGAAGTAAT
1 AATTAATAAAATATATCCCGAAAAGTAATGTCATTAACAAGAATCCGAATAAATTCGAAAGTAAT
24297 C
66 C
* *** * *
24298 AAATAATAAAATATATCCCGAAAAGTAGA-GTCATTAATGTGTATCTGAATAAATTCGAAAGTAA
1 AATTAATAAAATATATCCCGAAAAGTA-ATGTCATTAACAAGAATCCGAATAAATTCGAAAGTAA
24362 TC
65 TC
*
24364 AGTTAATA
1 AATTAATA
24372 CCGCATTTAA
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
65 5 0.08
66 54 0.90
67 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.29
Consensus pattern (66 bp):
AATTAATAAAATATATCCCGAAAAGTAATGTCATTAACAAGAATCCGAATAAATTCGAAAGTAAT
C
Found at i:25165 original size:2 final size:2
Alignment explanation
Indices: 25158--25188 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25148 CTCTTGTCAT
25158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25189 TTGAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27530 original size:19 final size:19
Alignment explanation
Indices: 27508--27582 Score: 51
Period size: 19 Copynumber: 3.9 Consensus size: 19
27498 ATTGAAGTAA
27508 TTATTAAATAATTTAAATT
1 TTATTAAATAATTTAAATT
* * * *
27527 TTATTTATTTATTTAATAAT
1 TTATTAAATAATTTAA-ATT
* ** * *
27547 ATATTATTTATTTTATATT
1 TTATTAAATAATTTAAATT
*
27566 CTATTAAATAATTTAAA
1 TTATTAAATAATTTAAA
27583 ATATTTTATT
Statistics
Matches: 39, Mismatches: 16, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
19 27 0.69
20 12 0.31
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTAAATAATTTAAATT
Found at i:27538 original size:27 final size:29
Alignment explanation
Indices: 27508--27582 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 29
27498 ATTGAAGTAA
27508 TTATTAAATAATTTAAATTT-TATT-TAT
1 TTATTAAATAATTTAAATTTATATTATAT
* * * *
27535 TTATTTAATAATATATTATTTATTTTATAT
1 TTATTAAATAATTTA-AATTTATATTATAT
27565 TCTATTAAATAATTTAAA
1 T-TATTAAATAATTTAAA
27583 ATATTTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 13 0.35
28 4 0.11
29 3 0.08
30 5 0.14
31 12 0.32
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATTAAATAATTTAAATTTATATTATAT
Found at i:41161 original size:18 final size:18
Alignment explanation
Indices: 41138--41172 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41128 TCAACAGGTC
41138 GGGTCAACGGGTTGGGTT
1 GGGTCAACGGGTTGGGTT
* *
41156 GGGTCAATGGTTTGGGT
1 GGGTCAACGGGTTGGGT
41173 CAGGTTGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.09, G:0.49, T:0.31
Consensus pattern (18 bp):
GGGTCAACGGGTTGGGTT
Found at i:53091 original size:113 final size:115
Alignment explanation
Indices: 52820--53114 Score: 366
Period size: 119 Copynumber: 2.5 Consensus size: 115
52810 CCTGAAGGTG
* *
52820 CACTAGTATATATTCTGATGTGATTGCACTTTGTGTGCACATTAC-GATTCTGATATGATAGCAC
1 CACTAGTATATTTTCTGATGTGATTGCACTTTGTGTGCATATT-CTGATTCTGATATGATAGCAC
* * * * *
52884 TGTGTGTGCTTATATGTTCCGATTTTGATAATTGTGGTGTACCGGTGGGTA
65 TATGTGTGCTTACATGTTCCGATTGTGATAATTGTGGTGTACCAGTGGGAA
* * *
52935 CACTAGTATATATACATTTTGATGTGATTGCACTTTGTTTGCATATTCTGATTCTGATGTGATAG
1 CACTAGTATAT-T---TTCTGATGTGATTGCACTTTGTGTGCATATTCTGATTCTGATATGATAG
*
53000 CACTATGTGTG-TT-CAT-TTCTGA-TGTGATATATTGTGGTGTTACCAGTGGGAA
62 CACTATGTGTGCTTACATGTTCCGATTGTGATA-ATTGTGGTG-TACCAGTGGGAA
* * *
53052 CACTAGTATATTTTCAGATGTGATTGCACTTTGTGTGCATATTATGACTCTGATATGATAGCA
1 CACTAGTATATTTTCTGATGTGATTGCACTTTGTGTGCATATTCTGATTCTGATATGATAGCA
53115 GTCGTCTAAC
Statistics
Matches: 156, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
113 45 0.29
115 17 0.11
116 15 0.10
117 23 0.15
118 3 0.02
119 53 0.34
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.41
Consensus pattern (115 bp):
CACTAGTATATTTTCTGATGTGATTGCACTTTGTGTGCATATTCTGATTCTGATATGATAGCACT
ATGTGTGCTTACATGTTCCGATTGTGATAATTGTGGTGTACCAGTGGGAA
Found at i:57824 original size:13 final size:13
Alignment explanation
Indices: 57795--57836 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
57785 ATGTTACGTC
*
57795 TATTTATTTTAATT
1 TATTTA-TTTAAAT
57809 TATTTATTTAAAT
1 TATTTATTTAAAT
*
57822 TATTTATTTAGAT
1 TATTTATTTAAAT
57835 TA
1 TA
57837 GGTTATTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (13 bp):
TATTTATTTAAAT
Found at i:64312 original size:54 final size:54
Alignment explanation
Indices: 64076--64489 Score: 410
Period size: 54 Copynumber: 7.6 Consensus size: 54
64066 TGTGATTTTT
* * **
64076 AGAAACTAAGCCTGATTTTCA-GGGTTTCTTGATATTTTCAAATGAATTTGGAA
1 AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAA
* ** * *
64129 AGAAGCTAAGTCTGATTTTCAGAAGTTTCTTAATGATTTTCAAATGAATTTTGAA
1 AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTTTCAA
* * * * *
64184 AGAAGTTAAGTCCT-ATTTTC-GGAAGTTTCTTGATGATTTTTAAATGAGTTCTCAA
1 AGAAGCTAAG-CCTGATTTTCAGG-GGTTTCTTGATG-TTTTCAAATGAATTTTCAA
* *
64239 AGAAGCTAAGCCTGA-TTTCAGGGGTTTCTTGATGTTTTAAAAAGAATTTTCAA
1 AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAA
* *** *
64292 AGGAA-CTAAGTCTGATTTTCAAAAGTTTCTTGATGATTTAT-AAATGAGTTTTCAA
1 A-GAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATG-TTT-TCAAATGAATTTTCAA
* * * * *
64347 AGAAGCTAAGCAT-ATTTTCAAGGGTTTTTTGATGTTTTCAAATGAATGTTGAA
1 AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAA
* * *
64400 AGAAGCTAAGCCTGATTTTCATGGGTTTCTTGATGTATTCAAATGAATTTTTAA
1 AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAA
* ** *
64454 AGAAACTAAGCCCAATGTTTTAGGGGTTTCTTGATG
1 AGAAGCTAAGCCTGAT-TTTCAGGGGTTTCTTGATG
64490 ATAATGTAAA
Statistics
Matches: 301, Mismatches: 46, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
52 1 0.00
53 70 0.23
54 116 0.39
55 111 0.37
56 3 0.01
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (54 bp):
AGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAA
Found at i:64324 original size:108 final size:109
Alignment explanation
Indices: 64076--64546 Score: 431
Period size: 108 Copynumber: 4.3 Consensus size: 109
64066 TGTGATTTTT
* ** **
64076 AGAAACTAAGCCTGATTTTC-AGGGTTTCTTGAT-ATTTTCAAATGAATTTGGAAAGAAGCTAAG
1 AGAAGCTAAGCCTGATTTTCAAAAGTTTCTTGATGATTTTCAAATGAATTTTCAAAGAAGCTAAG
* ** *
64139 TCTGATTTTCAGAAGTTTCTTAATGATTTTCAAATGAATTTTGAA
66 CCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTTTGAA
* ** * * *
64184 AGAAGTTAAGTCCT-ATTTTCGGAAGTTTCTTGATGATTTTTAAATGAGTTCTCAAAGAAGCTAA
1 AGAAGCTAAG-CCTGATTTTCAAAAGTTTCTTGATGATTTTCAAATGAATTTTCAAAGAAGCTAA
* * *
64248 GCCTGA-TTTCAGGGGTTTCTTGATGTTTTAAAAAGAATTTTCAA
65 GCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTGAA
* *
64292 AGGAA-CTAAGTCTGATTTTCAAAAGTTTCTTGATGATTTAT-AAATGAGTTTTCAAAGAAGCTA
1 A-GAAGCTAAGCCTGATTTTCAAAAGTTTCTTGATGATTT-TCAAATGAATTTTCAAAGAAGCTA
* * * *
64355 AGCAT-ATTTTCAAGGGTTTTTTGATGTTTTCAAATGAATGTTGAA
64 AGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTGAA
*** * * *
64400 AGAAGCTAAGCCTGATTTTCATGGGTTTCTTGATG-TATTCAAATGAATTTTTAAAGAAACTAAG
1 AGAAGCTAAGCCTGATTTTCAAAAGTTTCTTGATGATTTTCAAATGAATTTTCAAAGAAGCTAAG
** * * * *
64464 CCCAATGTTTTAGGGGTTTCTTGATGATAATGT-AAATAAATTTTTAA
66 CCTGAT-TTTCAGGGGTTTCTTGATG-T--TTTCAAATGAATTTTGAA
* * * * *
64511 A-AAGCCAAGTCTGGTTTTCAAATGTTTCTCGATGAT
1 AGAAGCTAAGCCTGATTTTCAAAAGTTTCTTGATGAT
64547 AAGTCCTTCG
Statistics
Matches: 295, Mismatches: 53, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
106 1 0.00
107 30 0.10
108 144 0.49
109 49 0.17
110 56 0.19
111 13 0.04
112 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (109 bp):
AGAAGCTAAGCCTGATTTTCAAAAGTTTCTTGATGATTTTCAAATGAATTTTCAAAGAAGCTAAG
CCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTGAA
Found at i:64351 original size:163 final size:160
Alignment explanation
Indices: 64076--64463 Score: 480
Period size: 163 Copynumber: 2.4 Consensus size: 160
64066 TGTGATTTTT
* * **
64076 AGAAACTAAGCCTGATTTTCAGGGTTTCTTGATATTTTCAAATGAATTTGGAAA-GAAGCTAAGT
1 AGAAGCTAAGCCTGATTTTCAGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAGGAA-CTAAGT
* * * *
64140 CTGATTTTCAGAAGTTTCTTAATGATTTTCAAATGAATTTTGAAAGAAGTTAAGTCCTATTTTCG
65 CTGATTTTCAAAAGTTTCTTAATGATTTTCAAATGAATTTTCAAAGAAGCTAAG-CATATTTTC-
* *
64205 GAA-GTTTCTTGATGATTTTTAAATGAGT-TCTCAA
128 -AAGGTTTCTTGATG-TTTTCAAATGAATGT-TCAA
* *
64239 AGAAGCTAAGCCTGA-TTTCAGGGGTTTCTTGATGTTTTAAAAAGAATTTTCAAAGGAACTAAGT
1 AGAAGCTAAGCCTGATTTTCA-GGGTTTCTTGATGTTTTCAAATGAATTTTCAAAGGAACTAAGT
* *
64303 CTGATTTTCAAAAGTTTCTTGATGATTTAT-AAATGAGTTTTCAAAGAAGCTAAGCATATTTTCA
65 CTGATTTTCAAAAGTTTCTTAATGATTT-TCAAATGAATTTTCAAAGAAGCTAAGCATATTTTCA
* *
64367 AGGGTTTTTTGATGTTTTCAAATGAATGTTGAA
129 A-GGTTTCTTGATGTTTTCAAATGAATGTTCAA
* * *
64400 AGAAGCTAAGCCTGATTTTCATGGGTTTCTTGATGTATTCAAATGAATTTTTAAAGAAACTAAG
1 AGAAGCTAAGCCTGATTTTCA-GGGTTTCTTGATGTTTTCAAATGAATTTTCAAAGGAACTAAG
64464 CCCAATGTTT
Statistics
Matches: 196, Mismatches: 22, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
160 2 0.01
161 29 0.15
162 66 0.34
163 95 0.48
164 4 0.02
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (160 bp):
AGAAGCTAAGCCTGATTTTCAGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAGGAACTAAGTC
TGATTTTCAAAAGTTTCTTAATGATTTTCAAATGAATTTTCAAAGAAGCTAAGCATATTTTCAAG
GTTTCTTGATGTTTTCAAATGAATGTTCAA
Found at i:65462 original size:117 final size:116
Alignment explanation
Indices: 65207--65476 Score: 314
Period size: 117 Copynumber: 2.3 Consensus size: 116
65197 GGATAAATCA
* * *
65207 ATCAACATTTCCAATGGAAGAGTTTATAA--AGAAAACTCATCTATGAGGGATAAGAAGTTCATA
1 ATCAACATTTCCAATGGAAGAGTTCATAATGAGAAAACTCATCTATGAGGGAGAAGAAATTCATA
* * * * * *
65270 ATAAGAAGAACATGTTTAGCCTTTGTTTGATTCTATCACAGAATAAGGTGG
66 ATAAGAAGAACATGTTCAACCTTTGCTCGATTCCATCACAGAAGAAGGTGG
** * *
65321 ATCAACATTTTTAATGGAATAGTTCATAATGAGAAGAACTCGTCTGATGAGGGAGAAGAAATTCA
1 ATCAACATTTCCAATGGAAGAGTTCATAATGAGAA-AACTCATCT-ATGAGGGAGAAGAAATTCA
* * * * *
65386 TAATGAGAATAACTTGTTCAACTTTTGCTCGA-TCCATCACAGAAGGAGGTGG
64 TAATAAGAAGAACATGTTCAACCTTTGCTCGATTCCATCACAGAAGAAGGTGG
*
65438 ATCAATATTTCCAAT-GAAGAAGTTCATAATGAGAAAACT
1 ATCAACATTTCCAATGGAAG-AGTTCATAATGAGAAAACT
65477 TGTTCAAACA
Statistics
Matches: 129, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
114 25 0.19
116 11 0.09
117 52 0.40
118 41 0.32
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (116 bp):
ATCAACATTTCCAATGGAAGAGTTCATAATGAGAAAACTCATCTATGAGGGAGAAGAAATTCATA
ATAAGAAGAACATGTTCAACCTTTGCTCGATTCCATCACAGAAGAAGGTGG
Found at i:66443 original size:24 final size:24
Alignment explanation
Indices: 66416--66464 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
66406 TATATCAAAA
* *
66416 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATAAGGTCAAGT
* *
66440 ATCATATCAGAAATAAGGTCAAGT
1 ATCAAAACAGAAATAAGGTCAAGT
66464 A
1 A
66465 ACAGATCAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAAATAAGGTCAAGT
Found at i:66557 original size:24 final size:24
Alignment explanation
Indices: 66433--66547 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
66423 CATAAATCAG
*
66433 GTCAAGTATCATATCAGAAAT--AA
1 GTCAAGTATCAGATCAG-AATCCAA
*
66456 GGTCAAGTAACAGATCAGAATCCAA
1 -GTCAAGTATCAGATCAGAATCCAA
*
66481 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
66505 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
66529 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
66548 ATCAAATCAA
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
23 5 0.06
24 74 0.89
25 4 0.05
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:66564 original size:48 final size:48
Alignment explanation
Indices: 66433--66564 Score: 153
Period size: 48 Copynumber: 2.8 Consensus size: 48
66423 CATAAATCAG
* *
66433 GTCAAGTATCATATCAGAAAT-AAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAA-GTCAA-AAATCAGATCAGAATCCAA
* * * *
66481 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCAAAAATCAGATCAGAATCCAA
*
66529 GTCAAGTATCAGATCAGAAATCAAATCAAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTCAAAAATCAG
66565 GTAAAATATT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
47 4 0.06
48 62 0.89
49 4 0.06
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAAATCAGATCAGAATCCAA
Done.