Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006658.1 Hibiscus syriacus cultivar Beakdansim tig00016474_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: 63723
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:156 original size:14 final size:15
Alignment explanation
Indices: 134--175 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
124 GAAATAAAAA
*
134 AATAAATAAAATATT
1 AATAAATAAAATATG
*
149 AA-AAATAAAAAATG
1 AATAAATAAAATATG
163 AATAAATAAAATA
1 AATAAATAAAATA
176 AAATGTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AATAAATAAAATATG
Found at i:180 original size:18 final size:18
Alignment explanation
Indices: 133--180 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
123 AGAAATAAAA
*
133 AAAT-AAATAAAAT-ATT
1 AAATAAAATAAAATGAAT
149 AAA-AATAA-AAAATGAAT
1 AAATAA-AATAAAATGAAT
166 AAATAAAATAAAATG
1 AAATAAAATAAAATG
181 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
16 9 0.35
17 9 0.35
18 8 0.31
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
AAATAAAATAAAATGAAT
Found at i:1936 original size:15 final size:16
Alignment explanation
Indices: 1916--1945 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1906 AATGGTTCAC
1916 CAATTATAG-ATGATT
1 CAATTATAGAATGATT
1931 CAATTATAGAATGAT
1 CAATTATAGAATGAT
1946 AATTATTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (16 bp):
CAATTATAGAATGATT
Found at i:12244 original size:29 final size:29
Alignment explanation
Indices: 12143--12244 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 29
12133 AAAATTAAAG
*
12143 TTTAGGTGCTAAAACATATCAAACTAGTAA
1 TTTAGGTACTAAAACATATCAAACTA-TAA
** ** *
12173 TTTAGGTACTAAATGTATAGT-TTACTCA-AG
1 TTTAGGTACTAAA-ACATA-TCAAACT-ATAA
12203 TTTAGGTACTAAAACATATCAAACTATAA
1 TTTAGGTACTAAAACATATCAAACTATAA
12232 TTTAGGTACTAAA
1 TTTAGGTACTAAA
12245 TGCATAGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
28 2 0.04
29 20 0.36
30 26 0.46
31 6 0.11
32 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (29 bp):
TTTAGGTACTAAAACATATCAAACTATAA
Found at i:12257 original size:59 final size:60
Alignment explanation
Indices: 12140--12265 Score: 227
Period size: 59 Copynumber: 2.1 Consensus size: 60
12130 AAAAAAATTA
* *
12140 AAGTTTAGGTGCTAAAACATATCAAACTAGTAATTTAGGTACTAAATGTATAGTTTACTC
1 AAGTTTAGGTACTAAAACATATCAAACTAGTAATTTAGGTACTAAATGCATAGTTTACTC
12200 AAGTTTAGGTACTAAAACATATCAAACTA-TAATTTAGGTACTAAATGCATAGTTTACTC
1 AAGTTTAGGTACTAAAACATATCAAACTAGTAATTTAGGTACTAAATGCATAGTTTACTC
12259 AAGTTTA
1 AAGTTTA
12266 TAATATAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 36 0.56
60 28 0.44
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (60 bp):
AAGTTTAGGTACTAAAACATATCAAACTAGTAATTTAGGTACTAAATGCATAGTTTACTC
Found at i:12377 original size:28 final size:28
Alignment explanation
Indices: 12296--12377 Score: 64
Period size: 28 Copynumber: 3.0 Consensus size: 28
12286 ATGTAATATA
12296 TTTTTAAAAT--TA-GTTT-TTAAATTT
1 TTTTTAAAATAATATGTTTATTAAATTT
* * ** **
12320 TTATTTTAAATCAATATCTAAATTTGATTT
1 TT-TTTAAAAT-AATATGTTTATTAAATTT
12350 TTTTTAAAATAATATGTTTATTAAATTT
1 TTTTTAAAATAATATGTTTATTAAATTT
12378 AAATTTCAAT
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
24 2 0.05
25 7 0.17
28 15 0.38
29 8 0.20
30 8 0.20
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTTTAAAATAATATGTTTATTAAATTT
Found at i:16314 original size:19 final size:20
Alignment explanation
Indices: 16290--16327 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
16280 AATTTAATCG
*
16290 AATATATAAT-TTAAAATTT
1 AATATAAAATCTTAAAATTT
16309 AATATAAAATCTTAAAATT
1 AATATAAAATCTTAAAATT
16328 CATCAACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTT
Found at i:21222 original size:23 final size:23
Alignment explanation
Indices: 21192--21236 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
21182 ACTACGATGC
21192 AATTCTACGCGGCACTTCGGTGA
1 AATTCTACGCGGCACTTCGGTGA
*
21215 AATTCTACGTGGCACTTCGGTG
1 AATTCTACGCGGCACTTCGGTG
21237 CATTTATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
AATTCTACGCGGCACTTCGGTGA
Found at i:27998 original size:23 final size:23
Alignment explanation
Indices: 27965--28021 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
27955 CATTTTATAT
* *
27965 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACAC
*
27988 GGCACTTCGGTGCAATTCTATAC
1 GGCACTTCGGTGCAATTCTACAC
*
28011 TGCACTTCGGT
1 GGCACTTCGGT
28022 ACATTTATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:31220 original size:15 final size:15
Alignment explanation
Indices: 31200--31243 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
31190 TACCCACCCT
31200 GCATCCGCCCGCCCC
1 GCATCCGCCCGCCCC
*
31215 GCATCCGCCCACCCC
1 GCATCCGCCCGCCCC
*
31230 ACATCCGCCCGCCC
1 GCATCCGCCCGCCC
31244 AGCTAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.11, C:0.66, G:0.16, T:0.07
Consensus pattern (15 bp):
GCATCCGCCCGCCCC
Found at i:41508 original size:229 final size:229
Alignment explanation
Indices: 40988--42146 Score: 2022
Period size: 229 Copynumber: 5.1 Consensus size: 229
40978 ATTTCACAAC
40988 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAATTACCTAGAGCTGC
1 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAATTACCTAGAGCTGC
* * *
41053 TTCCCTTGAATTGGTGCATGTAATCATCTAGTTTATTGAAGTCAATAGGTCTACTGTTCCAGCAT
66 TTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTTCCTGCAT
41118 GCATGGATGGAT-AAAAAAAAGATCGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTCATG
131 GCATGGATGGATAAAAAAAAAGATCGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTCATG
41182 TGCGTATATATATAGAGAAAGAGAGACCTGATCA
196 TGCGTATATATATAGAGAAAGAGAGACCTGATCA
41216 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAATTACCTAGAGCTGC
1 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAATTACCTAGAGCTGC
* * *
41281 TTCCCTTGAATTGGTGCATGTAATCATCTAGTTTATTGAAGTCAATAGGTCTACTGTTCCAGCAT
66 TTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTTCCTGCAT
41346 GCATGGATGGATAAAAAAAAAGATCGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTCATG
131 GCATGGATGGATAAAAAAAAAGATCGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTCATG
41411 TGCGTATATATATAGAGAAAGAGAGACCTGATCA
196 TGCGTATATATATAGAGAAAGAGAGACCTGATCA
41445 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAATTACCTAGAGCTGC
1 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAATTACCTAGAGCTGC
41510 TTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTTCCTGCAT
66 TTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTTCCTGCAT
41575 GCATGGATGGATAAAAAAAAAGATCGATAGGAATCGC-TGCAACGCCAAGTAATTAGAATTCATG
131 GCATGGATGGATAAAAAAAAAGATCGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTCATG
41639 TGCGTATATATATAGAGAAAGAGAGACCTGATCA
196 TGCGTATATATATAGAGAAAGAGAGACCTGATCA
41673 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGC-------T-ATTACCTAGAGCTGC
1 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAATTACCTAGAGCTGC
41730 TTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTTCCTGCAT
66 TTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTTCCTGCAT
*
41795 GCATGGATGGATAGAAAAAACAAGGATGGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTC
131 GCATGGATGGATA-AAAAAA-AA-GATCGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTC
41860 ATGTGCG--TATATATAGAG--AGAGAGACCTGATCA
193 ATGTGCGTATATATATAGAGAAAGAGAGACCTGATCA
41893 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCT-A--AG----TACCTAGAGCTGC
1 AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAATTACCTAGAGCTGC
41951 TTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTTCCTGCAT
66 TTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTTCCTGCAT
*
42016 GCATGGATGGATAGAAAAAACAAGGATGGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTC
131 GCATGGATGGATA-AAAAAA-AA-GATCGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTC
*
42081 ATGTGCGTGTATATATAGAG--AGAGAGACCTGATCA
193 ATGTGCGTATATATATAGAGAAAGAGAGACCTGATCA
42116 AAGAGGGACCTTCTCATGCAGGCAACTTGGT
1 AAGAGGGACCTTCTCATGCAGGCAACTTGGT
42147 GTTGCAAGCG
Statistics
Matches: 916, Mismatches: 4, Indels: 27
0.97 0.00 0.03
Matches are distributed among these distances:
220 149 0.16
221 157 0.17
222 13 0.01
223 72 0.08
224 31 0.03
228 244 0.27
229 250 0.27
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (229 bp):
AAGAGGGACCTTCTCATGCAGGCAACTTGGTTTCTTAGAGCTAATTAGTAATTACCTAGAGCTGC
TTCCCTTGAATTGGTGCATGTAATCATCCAGTTTATTGAAGTCAATAGGCCTACTGTTCCTGCAT
GCATGGATGGATAAAAAAAAAGATCGATAGGAATCGCTTGCAACGCCAAGTAATTAGAATTCATG
TGCGTATATATATAGAGAAAGAGAGACCTGATCA
Found at i:48859 original size:19 final size:19
Alignment explanation
Indices: 48835--48898 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 19
48825 GTCGGGTCAG
48835 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCGA
48854 ACCGGTCAAACCGG-TCAGA
1 ACCGGTCAAACCGGTTC-GA
*
48873 ACCGGTTGAAAACCGGTT-GA
1 ACCGG-T-CAAACCGGTTCGA
48893 ACCGGT
1 ACCGGT
48899 TTCCAGCAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 2 0.05
19 22 0.55
20 8 0.20
21 7 0.17
22 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:48897 original size:9 final size:9
Alignment explanation
Indices: 48843--48899 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
48833 AGACCGGTCA
48843 AACCGGTTCG
1 AACCGGTT-G
**
48853 AACCGGTCA
1 AACCGGTTG
*
48862 AACCGGTCAG
1 AACCGGT-TG
48872 AACCGGTTG
1 AACCGGTTG
48881 AAAACCGGTTG
1 --AACCGGTTG
48892 AACCGGTT
1 AACCGGTT
48900 TCCAGCAGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 16 0.41
10 14 0.36
11 9 0.23
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (9 bp):
AACCGGTTG
Found at i:52311 original size:17 final size:16
Alignment explanation
Indices: 52284--52323 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
52274 TAAACAATAA
52284 ATAAATAAAAAGAAAT
1 ATAAATAAAAAGAAAT
*
52300 ATGAAATGAAAAGAAAT
1 AT-AAATAAAAAGAAAT
52317 ATAAATA
1 ATAAATA
52324 TATAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (16 bp):
ATAAATAAAAAGAAAT
Found at i:54464 original size:3 final size:3
Alignment explanation
Indices: 54451--54509 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
54441 ATGTAAACAA
*
54451 AAT AAT AAAT AAT AAT AAC AAT AAT AAT AAT -AT AAAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
54497 AAT AAT -AT AAT AA
1 AAT AAT AAT AAT AA
54510 AAAAAATGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 41 0.82
4 5 0.10
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54470 original size:21 final size:22
Alignment explanation
Indices: 54446--54509 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 22
54436 ACAAAATGTA
54446 AACAA-AATAATAAATAATAAT
1 AACAATAATAATAAATAATAAT
54467 AACAATAATAATAATATAAATAAT
1 AACAATAATAATAA-AT-AATAAT
*
54491 AATAATAATAATATAATAA
1 AACAATAATAATA-AATAA
54510 AAAAAATGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
21 5 0.13
22 8 0.21
23 4 0.11
24 20 0.53
25 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (22 bp):
AACAATAATAATAAATAATAAT
Found at i:55219 original size:38 final size:38
Alignment explanation
Indices: 55171--55277 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 38
55161 TCAAAGATGT
* ***
55171 TTTTATTTCAAGAAAAACATACTCAAAGATTTTGTTTG
1 TTTTGTTTCAAGAAAAACATACTCAAAGATTTTGTAAA
** *
55209 TTTTGTTTCAAGGGAAACATACTCAAAGA--TGGTAAA
1 TTTTGTTTCAAGAAAAACATACTCAAAGATTTTGTAAA
*
55245 TTTTGTTTCAA-AATAAACAGACTCAAAGATTTT
1 TTTTGTTTCAAGAA-AAACATACTCAAAGATTTT
55278 TCTTAAAAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
36 28 0.51
38 27 0.49
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37
Consensus pattern (38 bp):
TTTTGTTTCAAGAAAAACATACTCAAAGATTTTGTAAA
Found at i:55276 original size:74 final size:70
Alignment explanation
Indices: 55142--55277 Score: 175
Period size: 74 Copynumber: 1.9 Consensus size: 70
55132 CAAAGATCGG
* *
55142 TGTTTCGAGAGAAACAAACTCAAAGATGTTTTTATTTCAAGAAAAACATACTCAAAGATTTTGTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTTTTTATTTCAAGAAAAACAGACTCAAAGATTTTGTT
55207 TGTTT
66 TGTTT
* * *
55212 TGTTTCAAGGGAAACATACTCAAAGATGGTAAATTTTGTTTCAA-AATAAACAGACTCAAAGATT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT---TTTTATTTCAAGAA-AAACAGACTCAAAGATT
55276 TT
61 TT
55278 TCTTAAAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
70 24 0.43
71 2 0.04
73 2 0.04
74 28 0.50
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (70 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTTTTTATTTCAAGAAAAACAGACTCAAAGATTTTGTT
TGTTT
Found at i:55486 original size:31 final size:30
Alignment explanation
Indices: 55422--55495 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
55412 TCAAAATTCG
* *
55422 TTTCAAGGGAAACTACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAACTCAAAGAT-GTTTTA
55453 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAAC-AACTCAAAGATGTTT-TA
*
55484 TTTCTAGAGAAA
1 TTTCAAGAGAAA
55496 TTGCCTCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 25 0.66
32 10 0.26
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATGTTTTA
Found at i:55561 original size:30 final size:29
Alignment explanation
Indices: 55527--55600 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 29
55517 TTTCTTTAAT
* ** *
55527 AGAAACGATCTCAAAGGTGGGTGTTTCAAG
1 AGAAACGA-CTCAAAGATAAGTGTTTCAAA
*
55557 AGAAACTAACTCAAAGATAAGTGTTTCAAA
1 AGAAAC-GACTCAAAGATAAGTGTTTCAAA
*
55587 AGAAAGGACTCAAA
1 AGAAACGACTCAAA
55601 TATTTTTTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 7 0.19
30 28 0.78
31 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.20
Consensus pattern (29 bp):
AGAAACGACTCAAAGATAAGTGTTTCAAA
Found at i:55840 original size:31 final size:32
Alignment explanation
Indices: 55802--55882 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 32
55792 TTTTTTTCAT
*
55802 TTTGTTTCAAGTGAAACAGAGTCAAAGAT-CC
1 TTTGTTTCAAGTGAAACAGACTCAAAGATACC
** **
55833 TTTGTTTCAAAAGAAAC-GACTCAAAGATGATG
1 TTTGTTTCAAGTGAAACAGACTCAAAGAT-ACC
55865 TTTGTTTCAAGTGAAACA
1 TTTGTTTCAAGTGAAACA
55883 AATTCGTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 10 0.25
31 15 0.38
32 15 0.38
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (32 bp):
TTTGTTTCAAGTGAAACAGACTCAAAGATACC
Found at i:55910 original size:35 final size:35
Alignment explanation
Indices: 55866--55991 Score: 103
Period size: 36 Copynumber: 3.5 Consensus size: 35
55856 AAGATGATGT
* *
55866 TTGTTTCAAGTGAAACAAATTCGTAATTTGGA-AAA
1 TTGTCTCAAGTGAAACAAATTCGT-ATTTAGAGAAA
* * *
55901 TTGTCTCAAGTGAGACAACATTTGTTTTTAGAGAAA
1 TTGTCTCAAGTGAAACAA-ATTCGTATTTAGAGAAA
** *
55937 TTGTCTCAAACGAAACAAAAATT-GTTTTTAGAGAAA
1 TTGTCTCAAGTGAAAC--AAATTCGTATTTAGAGAAA
* * *
55973 TTTTCTCAAGCGAGACAAA
1 TTGTCTCAAGTGAAACAAA
55992 GTTTGATTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
34 3 0.04
35 21 0.28
36 47 0.62
37 3 0.04
38 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (35 bp):
TTGTCTCAAGTGAAACAAATTCGTATTTAGAGAAA
Found at i:55941 original size:36 final size:36
Alignment explanation
Indices: 55898--55991 Score: 134
Period size: 36 Copynumber: 2.6 Consensus size: 36
55888 GTAATTTGGA
* * *
55898 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAAAAATTGTTTTTAGAG
* *
55934 AAATTGTCTCAAACGAAACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAAAAATTGTTTTTAGAG
*
55970 AAATTTTCTCAAGCGAGACAAA
1 AAATTGTCTCAAGCGAGACAAA
55992 GTTTGATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAAAAATTGTTTTTAGAG
Found at i:56183 original size:106 final size:105
Alignment explanation
Indices: 56012--56217 Score: 240
Period size: 106 Copynumber: 2.0 Consensus size: 105
56002 GATAAAACGT
* * **
56012 TCTCAAGTGAGATCAACTTTTTTTAATGTGAACAAATTCGAAATTTTTATTCTCAAAGGGCAAAT
1 TCTCAAGTGAGATCAACTTTTTTTAATGTGAACAAATTCGAAATTTGTATTATCAAAGGAAAAAT
**
56077 GCCTCAAATGAGACGAAATTTGTTTTGAA-AGAAATAACAA
66 GCCTCAAACAAGACGAAATTTGTTTT-AAGAGAAATAACAA
* *
56117 TCTCAAGTGAGATTAATTTTTGTTTCAA-GTGAATC-AATTCGAAATTTGTA-TATCAAAGGAAA
1 TCTCAAGTGAGATCAACTTTT-TTT-AATGTGAA-CAAATTCGAAATTTGTATTATCAAAGG-AA
* * *
56179 AAATGTCTCAAGCAAGACGAAGTTTGTTTTAAGAGAAAT
62 AAATGCCTCAAACAAGACGAAATTTGTTTTAAGAGAAAT
56218 TGTCTTAAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
105 29 0.34
106 53 0.62
107 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (105 bp):
TCTCAAGTGAGATCAACTTTTTTTAATGTGAACAAATTCGAAATTTGTATTATCAAAGGAAAAAT
GCCTCAAACAAGACGAAATTTGTTTTAAGAGAAATAACAA
Found at i:56402 original size:153 final size:154
Alignment explanation
Indices: 56175--56453 Score: 389
Period size: 153 Copynumber: 1.8 Consensus size: 154
56165 TATATCAAAG
* * * * * *
56175 GAAAAAATGTCTCAAGCAAGACGAAGTTTGTTTTAAGAGAAATTGTCTTAAATGAGGCAAAATTT
1 GAAAAAATCTCTCAAGCAAGACGAAATTTGCTTTAAGAGAAATTGTCTTAAACGAGACAAAATTA
* * *
56240 GTTTTAAAATTCTCAAAATTTATGG-GAAATGTCTCAAGCGAGAAAGAATTTTTTTTCAAGTACA
66 GTTTAAAAATTCTCAAAATTTATGGAAAAATGTCTCAAGCGAGAAAGAATTTTGTTTCAAGTACA
56304 ACAAATTTAAATTTGTATCTTAGA
131 ACAAATTTAAATTTGTATCTTAGA
* * * * * *
56328 GAAAAAATCTCTTAAGCGAGACGAAATTTGCTTTGATAGAAATTGTCTTGAGCGAGACAAAATTA
1 GAAAAAATCTCTCAAGCAAGACGAAATTTGCTTTAAGAGAAATTGTCTTAAACGAGACAAAATTA
* * *
56393 GTTTAAAAATTCTCAAAATTTGTGGAAAAATGTTTCAAGCGAGACAGAATTTTGTTTCAAG
66 GTTTAAAAATTCTCAAAATTTATGGAAAAATGTCTCAAGCGAGAAAGAATTTTGTTTCAAG
56454 GAAAAAACAC
Statistics
Matches: 107, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
153 76 0.71
154 31 0.29
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (154 bp):
GAAAAAATCTCTCAAGCAAGACGAAATTTGCTTTAAGAGAAATTGTCTTAAACGAGACAAAATTA
GTTTAAAAATTCTCAAAATTTATGGAAAAATGTCTCAAGCGAGAAAGAATTTTGTTTCAAGTACA
ACAAATTTAAATTTGTATCTTAGA
Found at i:56750 original size:4 final size:4
Alignment explanation
Indices: 56741--56786 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
56731 ATTATGTATC
* *
56741 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATAT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
56787 GTTGATGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:56794 original size:16 final size:17
Alignment explanation
Indices: 56735--56797 Score: 76
Period size: 16 Copynumber: 3.8 Consensus size: 17
56725 CAAATTATTA
*
56735 TGTATCATGTATGTATG
1 TGTATGATGTATGTATG
56752 TGTATGTATGTATGTATG
1 TGTATG-ATGTATGTATG
* *
56770 TATAT-ATGTATATATG
1 TGTATGATGTATGTATG
56786 TGT-TGATGTATG
1 TGTATGATGTATG
56798 CTTTTCTCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 18 0.46
17 5 0.13
18 15 0.38
ACGTcount: A:0.25, C:0.02, G:0.24, T:0.49
Consensus pattern (17 bp):
TGTATGATGTATGTATG
Found at i:56960 original size:22 final size:25
Alignment explanation
Indices: 56920--56975 Score: 91
Period size: 22 Copynumber: 2.4 Consensus size: 25
56910 ATTTGTTTTC
56920 CTTGCCCCATCAAAATTTGCCTT-T
1 CTTGCCCCATCAAAATTTGCCTTCT
56944 -TTGCCCCATC-AAATTTGCCTTCT
1 CTTGCCCCATCAAAATTTGCCTTCT
56967 CTTGCCCCA
1 CTTGCCCCA
56976 ACTTCAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.37
23 11 0.37
24 8 0.27
ACGTcount: A:0.18, C:0.38, G:0.09, T:0.36
Consensus pattern (25 bp):
CTTGCCCCATCAAAATTTGCCTTCT
Found at i:58038 original size:13 final size:13
Alignment explanation
Indices: 58005--58087 Score: 51
Period size: 14 Copynumber: 5.9 Consensus size: 13
57995 TGTTCTTTGC
58005 TCTTTTCTTTGTTTT
1 TCTTTTC-TT-TTTT
58020 TGCTTTTCTTTTTT
1 T-CTTTTCTTTTTT
58034 TCTTTT-TTTTCTT
1 TCTTTTCTTTT-TT
* *
58047 GCTCTTTGTTATTTT
1 TCT-TTTCTT-TTTT
* *
58062 TCTTTGCTTCTTT
1 TCTTTTCTTTTTT
*
58075 TCTCTTTGTTTTT
1 TCT-TTTCTTTTT
58088 CTGTTCTCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
12 4 0.07
13 15 0.28
14 18 0.33
15 9 0.17
16 8 0.15
ACGTcount: A:0.01, C:0.16, G:0.07, T:0.76
Consensus pattern (13 bp):
TCTTTTCTTTTTT
Found at i:58052 original size:23 final size:24
Alignment explanation
Indices: 58007--58053 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
57997 TTCTTTGCTC
*
58007 TTTTCTTTGTTTTTGCTTTTCTTT
1 TTTTCTTTGTTTTTGCTTCTCTTT
58031 TTTTCTTT-TTTTT-CTTGCTCTTT
1 TTTTCTTTGTTTTTGCTT-CTCTTT
58054 GTTATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 10 0.48
24 8 0.38
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (24 bp):
TTTTCTTTGTTTTTGCTTCTCTTT
Found at i:59411 original size:14 final size:13
Alignment explanation
Indices: 59366--59408 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
59356 CTTAAAAATG
*
59366 AAATGTAGATGCA
1 AAATGCAGATGCA
59379 AAATGCAAAGATGC-
1 AAATGC--AGATGCA
59393 AAATGCAGATGCA
1 AAATGCAGATGCA
59406 AAA
1 AAA
59409 ATGTTGATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 6 0.23
15 6 0.23
ACGTcount: A:0.51, C:0.12, G:0.21, T:0.16
Consensus pattern (13 bp):
AAATGCAGATGCA
Done.