Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007781.1 Hibiscus syriacus cultivar Beakdansim tig00110064_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: 78383
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:8815 original size:13 final size:15
Alignment explanation
Indices: 8793--8829 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
8783 TTTGACAGAA
8793 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
8805 AAATAAAATACTTGC
1 AAATAAAATACTTGC
8820 AAATAAAATA
1 AAATAAAATA
8830 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:11029 original size:3 final size:3
Alignment explanation
Indices: 11021--11106 Score: 154
Period size: 3 Copynumber: 28.7 Consensus size: 3
11011 AATATATATT
*
11021 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
11069 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
11107 TGGATAAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16184 original size:21 final size:21
Alignment explanation
Indices: 16158--16199 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16148 ATTTGAATAT
*
16158 TATGAACGGGTATCGATTCCC
1 TATGAACGGGTACCGATTCCC
*
16179 TATGAAGGGGTACCGATTCCC
1 TATGAACGGGTACCGATTCCC
16200 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAACGGGTACCGATTCCC
Found at i:16261 original size:21 final size:21
Alignment explanation
Indices: 16228--16267 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
16218 TTTTTGCAGA
*
16228 AAAAGCATTCCCAAACGGCTCC
1 AAAAGCA-TCCCCAACGGCTCC
16250 AAAA-CATCCCCAACGGCT
1 AAAAGCATCCCCAACGGCT
16268 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (21 bp):
AAAAGCATCCCCAACGGCTCC
Found at i:17081 original size:21 final size:19
Alignment explanation
Indices: 17039--17087 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
17029 AACGATTTTC
*
17039 TTTTGAAAACAAAAATATAT
1 TTTTGAAAACAAAAATA-AA
* *
17059 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAAT-AAA
17079 TTTTGAAAA
1 TTTTGAAAA
17088 ATGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (19 bp):
TTTTGAAAACAAAAATAAA
Found at i:17908 original size:26 final size:27
Alignment explanation
Indices: 17848--17922 Score: 107
Period size: 26 Copynumber: 2.7 Consensus size: 27
17838 AAATGCACTT
*
17848 AATTTTAACAATTGGTATTAATATATATCA
1 AATTTCAACAATTGGTA-T--TATATATCA
17878 AATTTCAACAATTGGTATTA-ATATCA
1 AATTTCAACAATTGGTATTATATATCA
17904 AATTTCAACAATTGGTATT
1 AATTTCAACAATTGGTATT
17923 GCATAAAGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 25 0.57
27 2 0.05
29 1 0.02
30 16 0.36
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (27 bp):
AATTTCAACAATTGGTATTATATATCA
Found at i:18402 original size:29 final size:28
Alignment explanation
Indices: 18370--18429 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 28
18360 AATTTAAGGC
*
18370 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTATTTGGACTT-AATTGAATTT-A
18401 AAAATGTATTTGGACTTAATTGAATTTA
1 AAAATGTATTTGGACTTAATTGAATTTA
18429 A
1 A
18430 TCAAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 2 0.07
29 10 0.36
30 11 0.39
31 5 0.18
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (28 bp):
AAAATGTATTTGGACTTAATTGAATTTA
Found at i:18415 original size:30 final size:30
Alignment explanation
Indices: 18370--18429 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
18360 AATTTAAGGC
*
18370 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAATGGTATTTGGACTT-AATTGAATTTAA
18401 AAAAT-GTATTTGGACTTAATTGAATTTAA
1 AAAATGGTATTTGGACTTAATTGAATTTAA
18430 TCAAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 12 0.43
30 11 0.39
31 5 0.18
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (30 bp):
AAAATGGTATTTGGACTTAATTGAATTTAA
Found at i:18520 original size:19 final size:19
Alignment explanation
Indices: 18493--18558 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
18483 AATGTTTTTA
* *
18493 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
18512 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* * *
18531 TGAACAATAAATCACTGTT
1 TGAACAGTAAATTACTATT
18550 TGAACAGTA
1 TGAACAGTA
18559 CCTCGAGGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:22233 original size:62 final size:64
Alignment explanation
Indices: 22135--22289 Score: 185
Period size: 67 Copynumber: 2.4 Consensus size: 64
22125 TATCAGTATC
*
22135 CTTTGAGTTGTTTTTCTTGAAACAAATTTTGTCTCTC-GAGACAATTTCTTTT-A-AAAAAAAT
1 CTTTGAGTTGTTTCTCTTGAAACAAATTTTGTCTCTCTGAGACAATTTCTTTTGAGAAAAAAAT
22196 CTTTGAGTATGTTTCT-TTGAAAACAAATTTT-TGCTCTCTTGAGACAATTTCTTTTGATGAAAA
1 CTTTGAGT-TGTTTCTCTTG-AAACAAATTTTGT-CTCTC-TGAGACAATTTCTTTTGA-GAAAA
22259 AAAT
61 AAAT
* * *
22263 ATTTGAGTTTGTTTCCCTTTAAACAAA
1 CTTTGAG-TTGTTTCTCTTGAAACAAA
22290 ACACCTATCT
Statistics
Matches: 80, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
61 12 0.15
62 22 0.28
64 15 0.19
65 1 0.01
67 27 0.34
68 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (64 bp):
CTTTGAGTTGTTTCTCTTGAAACAAATTTTGTCTCTCTGAGACAATTTCTTTTGAGAAAAAAAT
Found at i:24495 original size:32 final size:32
Alignment explanation
Indices: 24407--24495 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 32
24397 AGAGTCGAGG
*
24407 GTTACCTATG-TCTTTC-GAGATATATGGACAGT
1 GTTACCTATGTTC-TTCGGA-ATATATGAACAGT
* * *
24439 -TTACATATGTCCTTCAGG-ACATATGAACAGT
1 GTTACCTATGTTCTTC-GGAATATATGAACAGT
24470 GTTACCTATGTTCTTCGGAATATATG
1 GTTACCTATGTTCTTCGGAATATATG
24496 GATAGGTCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
31 24 0.53
32 20 0.44
33 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (32 bp):
GTTACCTATGTTCTTCGGAATATATGAACAGT
Found at i:25319 original size:9 final size:9
Alignment explanation
Indices: 25305--25330 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
25295 TATAAAAATA
25305 TTATTATTT
1 TTATTATTT
25314 TTATTATTT
1 TTATTATTT
25323 TTATTATT
1 TTATTATT
25331 ACTACTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTATTT
Found at i:28293 original size:35 final size:35
Alignment explanation
Indices: 28247--28322 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
28237 AAAACAGTCA
* *
28247 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
28282 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
28317 TCAATT
1 TCAATT
28323 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:28866 original size:130 final size:130
Alignment explanation
Indices: 28720--28967 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
28710 TATTTATATA
* **
28720 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
28785 TTAGCACATGATCATGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
28850 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
28915 TTAACGCATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTA
28968 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:28998 original size:130 final size:129
Alignment explanation
Indices: 28734--28998 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
28724 ATTTGGTCCT
* ** *
28734 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
28799 TGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
28864 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACGCATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *
28929 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
28993 -A
128 CA
28994 AAATT
1 AAATT
28999 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:29445 original size:16 final size:18
Alignment explanation
Indices: 29424--29457 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
29414 ATTTCTTATT
29424 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
29440 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
29458 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:31099 original size:31 final size:31
Alignment explanation
Indices: 31062--31178 Score: 78
Period size: 31 Copynumber: 3.7 Consensus size: 31
31052 TAATTTTTCG
31062 TAAGTTTAAGAACTATTTTATAATAATTTGA
1 TAAGTTTAAGAACTATTTTATAATAATTTGA
* * * **
31093 TAAGTTTATTG-ACTATGTTGTAATAGCTTGA
1 TAAGTTTA-AGAACTATTTTATAATAATTTGA
* ** * *
31124 TAAAGTGTAATTACTATTTTGTAATTATTTGA
1 T-AAGTTTAAGAACTATTTTATAATAATTTGA
*
31156 -AGAGTTTAAAGATC-ATTTTATAA
1 TA-AGTTT-AAGAACTATTTTATAA
31179 CTTTTAAAAT
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
30 1 0.02
31 37 0.58
32 26 0.41
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (31 bp):
TAAGTTTAAGAACTATTTTATAATAATTTGA
Found at i:31146 original size:32 final size:31
Alignment explanation
Indices: 31073--31148 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
31063 AAGTTTAAGA
* * *
31073 ACTATTTTATAATAATTTGATAAGTTTATTG
1 ACTATTTTGTAATAACTTGATAAGTTAATTG
* *
31104 ACTATGTTGTAATAGCTTGATAAAGTGTAATT-
1 ACTATTTTGTAATAACTTGAT-AAGT-TAATTG
31136 ACTATTTTGTAAT
1 ACTATTTTGTAAT
31149 TATTTGAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 17 0.46
32 16 0.43
33 4 0.11
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (31 bp):
ACTATTTTGTAATAACTTGATAAGTTAATTG
Found at i:32561 original size:56 final size:56
Alignment explanation
Indices: 32487--32599 Score: 136
Period size: 56 Copynumber: 2.0 Consensus size: 56
32477 TGAAATACAA
* * * * * *
32487 TGATGGATTTATGACATTTGATATCATCATTGTCGTAACTATTTTGACTTGTTTGC
1 TGATGAATTTATGACATTTGACATCATCATTATCGCAACTACTTCGACTTGTTTGC
* * * *
32543 TGATGAATTTATGTCATTTGACGTCATTATTATCGCAACTGCTTCGACTTGTTTGC
1 TGATGAATTTATGACATTTGACATCATCATTATCGCAACTACTTCGACTTGTTTGC
32599 T
1 T
32600 AGTTTGTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (56 bp):
TGATGAATTTATGACATTTGACATCATCATTATCGCAACTACTTCGACTTGTTTGC
Found at i:33024 original size:16 final size:17
Alignment explanation
Indices: 33005--33040 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
32995 TTTTACCATT
*
33005 TTTTCATCTAAATT-TA
1 TTTTAATCTAAATTATA
33021 TTTTAATCTAAATTATA
1 TTTTAATCTAAATTATA
33038 TTT
1 TTT
33041 CCTTATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAATCTAAATTATA
Found at i:35499 original size:20 final size:21
Alignment explanation
Indices: 35450--35502 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
35440 CAATTTTTTA
* *
35450 GAAAAATGATCGATCCCTTAT
1 GAAAAAGGATCGATCCCCTAT
*
35471 GAGAAAGGATCGATCCCCT-T
1 GAAAAAGGATCGATCCCCTAT
35491 GAAAAAGGATCG
1 GAAAAAGGATCG
35503 TTTCATTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (21 bp):
GAAAAAGGATCGATCCCCTAT
Found at i:48227 original size:29 final size:30
Alignment explanation
Indices: 48193--48260 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
48183 ATTTAGTTTA
* *
48193 TAAAGTTTAATAAACAAATTAAAAAAATTG
1 TAAAGTTTAATAAACAAAATAAAAAAATAG
**
48223 -AAAGTACAATAAACAAAATAAAAAAATAG
1 TAAAGTTTAATAAACAAAATAAAAAAATAG
48252 TAAAGTTTA
1 TAAAGTTTA
48261 GTGATAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.25
Consensus pattern (30 bp):
TAAAGTTTAATAAACAAAATAAAAAAATAG
Found at i:56224 original size:20 final size:20
Alignment explanation
Indices: 56199--56265 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
56189 AATTCACAAT
56199 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
56219 GCGAATTGGAAAATTCGCAAT
1 GCGAATAAGTAAA-TCGCAAC
56240 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
56260 GCGAAT
1 GCGAAT
56266 TGGGAAAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:56234 original size:41 final size:42
Alignment explanation
Indices: 56189--56302 Score: 171
Period size: 41 Copynumber: 2.7 Consensus size: 42
56179 CGATTTTCCC
*
56189 AATTCACAATGCGAATAAGTAAATCGCAACGCGAATT-GGAA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
56230 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
*
56272 AA-TCGCAATGCGATAATAA-AAAATCGCAACG
1 AATTCGCAATGCG--AATAAGTAAATCGCAACG
56303 AGATACTTAC
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
41 46 0.68
42 17 0.25
43 5 0.07
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (42 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
Found at i:56238 original size:21 final size:20
Alignment explanation
Indices: 56209--56284 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 20
56199 GCGAATAAGT
56209 AAATCGCAACGCGAATTGGA
1 AAATCGCAACGCGAATTGGA
* ** *
56229 AAATTCGCAATGCGAATAAGT
1 AAA-TCGCAACGCGAATTGGA
56250 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATT-GGA
*
56271 AAATCGCAATGCGA
1 AAATCGCAACGCGA
56285 TAATAAAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGA
Found at i:56343 original size:20 final size:20
Alignment explanation
Indices: 56295--56346 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
56285 TAATAAAAAA
* *
56295 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
56315 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
56335 TCGCAACGCGAT
1 TCGCAACGCGAT
56347 TTACATAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:56926 original size:19 final size:19
Alignment explanation
Indices: 56866--56935 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 19
56856 TTCGAGAATG
56866 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
56886 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
56902 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
56919 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
56936 CCAAAATCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 7 0.17
16 5 0.12
17 4 0.10
18 1 0.03
19 15 0.38
20 8 0.20
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:56941 original size:19 final size:19
Alignment explanation
Indices: 56902--56943 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
56892 GCAACGAGAT
*
56902 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
56921 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
56940 AATC
1 AATC
56944 ACATTGCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.26, G:0.14, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:56969 original size:19 final size:19
Alignment explanation
Indices: 56947--57107 Score: 126
Period size: 20 Copynumber: 8.8 Consensus size: 19
56937 CAAAATCACA
56947 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
56966 TTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGC-G
56986 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
57005 TTGTGATTGTC---T-G-G
1 TTGCGATTTTCATTTCGCG
* **
57019 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
57038 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
57052 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
57072 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
57092 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
57108 AACCAAAAGA
Statistics
Matches: 113, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 36 0.32
20 49 0.43
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:57023 original size:39 final size:39
Alignment explanation
Indices: 56947--57023 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
56937 CAAAATCACA
* **
56947 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
*
56986 TTGCGATTTTCATTTCGCGTTGTGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
57024 ATAGTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:57032 original size:33 final size:33
Alignment explanation
Indices: 56995--57082 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
56985 GTTGCGATTT
* * *
56995 TCATTTCGCGTTGTGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
57028 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
57061 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
57083 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:59189 original size:21 final size:21
Alignment explanation
Indices: 59165--59231 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
59155 TCATTCCTCG
59165 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
59186 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
59207 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
59228 AGAG
1 AGAG
59232 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:59189 original size:42 final size:42
Alignment explanation
Indices: 59109--59231 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
59099 GCCCGACTCG
* * * * * * *
59109 CCTATCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
59151 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
59193 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
59232 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:61593 original size:12 final size:12
Alignment explanation
Indices: 61576--61600 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61566 TCTTCAGGGA
61576 CTTTTTCTTCTT
1 CTTTTTCTTCTT
61588 CTTTTTCTTCTT
1 CTTTTTCTTCTT
61600 C
1 C
61601 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:61809 original size:24 final size:24
Alignment explanation
Indices: 61775--61828 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
61765 CTGAAACATC
* *
61775 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
61799 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
61823 ATCAAA
1 ATCAAA
61829 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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:62913 original size:20 final size:20
Alignment explanation
Indices: 62888--62945 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
62878 ATTCATTTGA
62888 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
62908 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
62928 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
62946 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:63005 original size:19 final size:19
Alignment explanation
Indices: 62964--63050 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
62954 GAAATGAAAA
62964 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
62980 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
62997 TCGCATTGCGATTATCATT
1 TCGCATTGCGATTTTCATT
63016 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
63035 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
63051 TCGTTGCGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 47 0.73
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:65088 original size:20 final size:19
Alignment explanation
Indices: 65053--65118 Score: 98
Period size: 20 Copynumber: 3.5 Consensus size: 19
65043 GAAACTTAAA
65053 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
65072 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
65092 ATCGCAACGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
65110 ATCGCAACG
1 ATCGCAACG
65119 ACAAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 9 0.21
19 16 0.37
20 18 0.42
ACGTcount: A:0.36, C:0.26, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:65166 original size:19 final size:18
Alignment explanation
Indices: 65144--65207 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
65134 GAAACACAAA
65144 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* *
65163 TCGCGTTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
65179 TCG--TTGCGATTTTTATT
1 TCGCATTGCGA-TTTTATT
65196 TCGCATTGCGAT
1 TCGCATTGCGAT
65208 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
14 6 0.16
16 7 0.19
17 4 0.11
18 4 0.11
19 16 0.43
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:65215 original size:19 final size:20
Alignment explanation
Indices: 65193--65235 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
65183 TGCGATTTTT
65193 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
65212 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
65232 ATTT
1 ATTT
65236 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:65226 original size:20 final size:20
Alignment explanation
Indices: 65201--65246 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
65191 TTATTTCGCA
65201 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
65221 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
65241 TTGCGA
1 TTGCGA
65247 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:65745 original size:18 final size:18
Alignment explanation
Indices: 65719--65763 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
65709 GTCGATCAGA
*
65719 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
65737 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
65755 TGATGGCTC
1 TGATGGCTC
65764 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:67108 original size:20 final size:20
Alignment explanation
Indices: 67083--67120 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
67073 AATAGTTTCT
67083 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
67103 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
67121 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:67680 original size:41 final size:41
Alignment explanation
Indices: 67635--67712 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
67625 CGAAAGTCAG
* *
67635 TATCGCATTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
67676 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
67713 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:67709 original size:20 final size:20
Alignment explanation
Indices: 67595--67709 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
67585 CGCTTTGAAA
*
67595 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
67616 ACCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* *
67636 ATCGCATTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
67656 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
67677 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
67697 ATCGCATTGCGAT
1 ATCGCATTGCGAT
67710 TTTCCCAATT
Statistics
Matches: 72, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
19 2 0.03
20 47 0.65
21 23 0.32
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:67727 original size:21 final size:21
Alignment explanation
Indices: 67698--67794 Score: 133
Period size: 21 Copynumber: 4.7 Consensus size: 21
67688 ATAGTCAGTA
*
67698 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
67719 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
67740 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
* *
67760 TCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
67781 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
67795 ACTTATTCGC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.25
21 49 0.75
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:67751 original size:62 final size:62
Alignment explanation
Indices: 67678--67811 Score: 166
Period size: 62 Copynumber: 2.2 Consensus size: 62
67668 TTTTTTATTA
*
67678 TCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
1 TCGCATTGCGAT--TCACGTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTTCCCAAT
* * * * **
67740 TCGCGTTGCGATTTACTTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTCACGTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTTCCCAAT
67801 TCGCATTGCGA
1 TCGCATTGCGA
67812 ATTGGGAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
60 2 0.03
61 18 0.29
62 42 0.68
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (62 bp):
TCGCATTGCGATTCACGTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTTCCCAAT
Found at i:67762 original size:41 final size:41
Alignment explanation
Indices: 67717--67814 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
67707 GATTTTCCCA
* *
67717 ATTCGCGTTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTT
67758 ATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTT
67799 ATTCGCATTGCGAATT
1 ATTCGCATTGCGAATT
67815 GGGAAAATCG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.40
Consensus pattern (41 bp):
ATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTT
Found at i:67763 original size:20 final size:20
Alignment explanation
Indices: 67698--67811 Score: 111
Period size: 21 Copynumber: 5.5 Consensus size: 20
67688 ATAGTCAGTA
* *
67698 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGA-TTTACCAAT
*
67719 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGA-TTTACCAAT
**
67740 TCGCGTTGCGATTTACTTAT
1 TCGCGTTGCGATTTACCAAT
* *
67760 TCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCG-ATTTACCAAT
**
67781 TCGCGTTGCGATTTACTTAT
1 TCGCGTTGCGATTTACCAAT
*
67801 TCGCATTGCGA
1 TCGCGTTGCGA
67812 ATTGGGAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
20 32 0.41
21 47 0.59
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTACCAAT
Found at i:73887 original size:20 final size:20
Alignment explanation
Indices: 73831--73888 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
73821 GCCGTTTTGG
* * *
73831 GTTAACTCATATCGGTCCGA
1 GTTAACTCAAACCGGTTCGA
*
73851 GTTGACTCAAACCGGTTCGA
1 GTTAACTCAAACCGGTTCGA
*
73871 GTTAACTCAAACTGGTTC
1 GTTAACTCAAACCGGTTC
73889 TAAGATGTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
GTTAACTCAAACCGGTTCGA
Found at i:77045 original size:2 final size:2
Alignment explanation
Indices: 77038--77069 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
77028 TCATTCTTTC
77038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77070 CATAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77355 original size:27 final size:26
Alignment explanation
Indices: 77292--77355 Score: 89
Period size: 25 Copynumber: 2.5 Consensus size: 26
77282 AAATTCTTAT
77292 TTAAA-TAATATC-AAATTACTTAAAC
1 TTAAACTAAT-TCAAAATTACTTAAAC
77317 TT-AACTAATTCAAAATTACTTATAAC
1 TTAAACTAATTCAAAATTACTTA-AAC
77343 TTAAACTAATTCA
1 TTAAACTAATTCA
77356 GTTGTTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.11
25 16 0.46
26 5 0.14
27 10 0.29
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (26 bp):
TTAAACTAATTCAAAATTACTTAAAC
Done.