Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009394.1 Hibiscus syriacus cultivar Beakdansim tig00113295_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: 57025
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1124 original size:2 final size:2
Alignment explanation
Indices: 1119--1192 Score: 127
Period size: 2 Copynumber: 38.5 Consensus size: 2
1109 CTCATTATCT
1119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1159 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1193 TTTATTTTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 66 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1165 original size:36 final size:36
Alignment explanation
Indices: 1119--1197 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
1109 CTCATTATCT
1119 TATA-TATATATATATATATATATATATATAATATA
1 TATATTATATATATATATATATATATATATAATATA
1154 TATATTATATATATATATATATATATATATAATATA
1 TATATTATATATATATATATATATATATATAATATA
*
1190 TATTTTAT
1 TATATTAT
1198 TTTTAATAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 4 0.10
36 38 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TATATTATATATATATATATATATATATATAATATA
Found at i:4252 original size:21 final size:20
Alignment explanation
Indices: 4226--4284 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
4216 ACATATGTAA
4226 TCCTTTGGAACATATATGCGG
1 TCCTTTGGAACATATAT-CGG
* *
4247 TTCTTTGAGACACATAT-TTGG
1 TCCTTTG-GA-ACATATATCGG
*
4268 TCCTTTGGAATATATAT
1 TCCTTTGGAACATATAT
4285 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 5 0.16
20 3 0.10
21 14 0.45
22 3 0.10
23 6 0.19
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (20 bp):
TCCTTTGGAACATATATCGG
Found at i:4284 original size:2 final size:2
Alignment explanation
Indices: 4277--4316 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4267 GTCCTTTGGA
4277 AT AT AT AT 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 AT AT AT AT
4317 GATCCTTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4393 original size:23 final size:23
Alignment explanation
Indices: 4366--4446 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
4356 TTATTGACAT
4366 TTCAGTGCATTTCTATGCGGCAC
1 TTCAGTGCATTTCTATGCGGCAC
*
4389 TTCAGTGCATTTCTACGCGGCAC
1 TTCAGTGCATTTCTATGCGGCAC
* * *
4412 TTTAGTGCATTTCTATGTGGTAC
1 TTCAGTGCATTTCTATGCGGCAC
*
4435 TTTAGTGCATTT
1 TTCAGTGCATTT
4447 TATACGAGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (23 bp):
TTCAGTGCATTTCTATGCGGCAC
Found at i:11458 original size:2 final size:2
Alignment explanation
Indices: 11449--11481 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
11439 ATTTTTTAAA
11449 AT AT -T 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 AT
11482 TCTATAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:15354 original size:29 final size:29
Alignment explanation
Indices: 15312--15379 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
15302 CCCTCTCTGG
*
15312 AATTTTATAAGTTC-AGATTCACCCCCTAA
1 AATTTTAAAAGTTCAAGATTC-CCCCCTAA
* *
15341 AATTTTAAAAGTTCAAGTTTCCCCCTTAA
1 AATTTTAAAAGTTCAAGATTCCCCCCTAA
15370 AATTTTAAAA
1 AATTTTAAAA
15380 ATTTAAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 30 0.86
30 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (29 bp):
AATTTTAAAAGTTCAAGATTCCCCCCTAA
Found at i:15387 original size:29 final size:28
Alignment explanation
Indices: 15333--15389 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
15323 TTCAGATTCA
*
15333 CCCCCTAAAATTTTAAAAGTTCAAGTTT
1 CCCCCTAAAATTTTAAAAATTCAAGTTT
*
15361 CCCCCTTAAAATTTTAAAAATTTAAGTTT
1 CCCCC-TAAAATTTTAAAAATTCAAGTTT
15390 GTTCTCCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (28 bp):
CCCCCTAAAATTTTAAAAATTCAAGTTT
Found at i:17298 original size:17 final size:17
Alignment explanation
Indices: 17278--17324 Score: 78
Period size: 16 Copynumber: 2.8 Consensus size: 17
17268 CTTTCTTTCA
17278 TTTTTCATTTTTTTGTC
1 TTTTTCATTTTTTTGTC
*
17295 TTTTTCA-TTTTTAGTC
1 TTTTTCATTTTTTTGTC
17311 TTTTTCATTTTTTT
1 TTTTTCATTTTTTT
17325 TCAGGCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTCATTTTTTTGTC
Found at i:22042 original size:3 final size:3
Alignment explanation
Indices: 22020--22075 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
22010 ATATTATAAA
* *
22020 TAT TAAT TA- TAT TGT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22064 TATT TAT TAT TA
1 TA-T TAT TAT TA
22076 CATTTGCAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 36 0.80
4 5 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:22047 original size:17 final size:16
Alignment explanation
Indices: 22020--22075 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 16
22010 ATATTATAAA
22020 TATTAATTATATTGTTAT
1 TATT-ATTATATT-TTAT
22038 TATTATTATATTATTAT
1 TATTATTATATT-TTAT
22055 TATTATTA-ATATTTAT
1 TATTATTATAT-TTTAT
22071 TATTA
1 TATTA
22076 CATTTGCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 11 0.31
17 21 0.58
18 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATTATTATATTTTAT
Found at i:23626 original size:15 final size:15
Alignment explanation
Indices: 23595--23625 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23585 TTTTAACTTG
23595 TTATTTATTTTATTT
1 TTATTTATTTTATTT
23610 TTATTTATTTT-TTT
1 TTATTTATTTTATTT
23624 TT
1 TT
23626 TTGCATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTATTTATTTTATTT
Found at i:23889 original size:2 final size:2
Alignment explanation
Indices: 23882--23944 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
23872 TATATGTGCG
23882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23924 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
23945 TTAAAGTATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36973 original size:55 final size:55
Alignment explanation
Indices: 36907--37366 Score: 387
Period size: 55 Copynumber: 8.6 Consensus size: 55
36897 GTGAAGCAAA
* *
36907 TGAAGATTGTTCGAGTCTTATACTCTCTGAACAAATAGAGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * * *
36962 TGAAGATTGTTCAAGTCTCATACTCTCTTAAGCAATAGGGAGCAGACATGAATAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
37017 TGAAAATTGTTCGAGTCTAATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * *
37072 TGAAAATTATTCGAGTCTTATACTCTCTGAAGGAATAGGGGGCAGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
* * * * *
37127 TGAAGA----TCAAGTCCTATACTTTCTGAAGGAATAGGGAG-AGGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCA-GACACGATTGT
* * ** *
37178 TGAAGGTTTTTTAAGTCATATACTCTCTGAAGAAATAGGGAGCAGACACG-TTGAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG-T
* * * *
37233 TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
* * * * * ** *
37284 TGAAGA-T-TT--AGTCATATACTCTCTGAAGGAATAGAGAACAAACTTG-TTTT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
37334 ATGAAGATTGTTTGAGTTTTATACTCCCTGAAG
1 -TGAAGATTGTTCGAGTCTTATACTCTCTGAAG
37367 CAAAAAAGAG
Statistics
Matches: 337, Mismatches: 50, Indels: 36
0.80 0.12 0.09
Matches are distributed among these distances:
50 4 0.01
51 115 0.34
52 8 0.02
53 2 0.01
54 4 0.01
55 203 0.60
56 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
Found at i:37171 original size:51 final size:51
Alignment explanation
Indices: 37036--37317 Score: 291
Period size: 51 Copynumber: 5.4 Consensus size: 51
37026 TTCGAGTCTA
* * * *
37036 ATACTCTCTGAAGAAATAGGGAGCAGACACGA-ATGTTGAAAATTATTCGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCAGACAC-ATTTGTTGAAGATTA----AGTCAT
* * *
37091 ATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTAAGTCAT
* * *
37142 ATACTTTCTGAAGGAATAGGGAG-AGGACACGTTTGTTGAAGGTTTTTTAAGTCAT
1 ATACTCTCTGAAGGAATAGGGAGCA-GACACATTTGTTGAA-G---ATTAAGTCAT
* * * *
37197 ATACTCTCTGAAGAAATAGGGAGCAGACAC-GTTGATTGAAGATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTG-TTGAAGATTAAGTCAT
* * *
37248 ATACTCTCTGAAGGAATGGGGAGCGGACACATTTGTTGAAGATTTAGTCAT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTAAGTCAT
37299 ATACTCTCTGAAGGAATAG
1 ATACTCTCTGAAGGAATAG
37318 AGAACAAACT
Statistics
Matches: 193, Mismatches: 25, Indels: 22
0.80 0.10 0.09
Matches are distributed among these distances:
50 1 0.01
51 106 0.55
52 4 0.02
54 5 0.03
55 76 0.39
56 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (51 bp):
ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTAAGTCAT
Found at i:37200 original size:106 final size:104
Alignment explanation
Indices: 37036--37317 Score: 338
Period size: 106 Copynumber: 2.7 Consensus size: 104
37026 TTCGAGTCTA
* ** * * *
37036 ATACTCTCTGAAGAAATAGGGAGCA-GACACGAATGTTGAAAATTATTCGAGTCTTATACTCTCT
1 ATACTCTCTGAAGGAATAGGGAG-AGGACACGTTTGTTG-AAGTTATT-TAGTCATATACTCTCT
* *
37100 GAAGGAATAGGGGGCAGACACATTTG-TTGAAGATCAAGTCCT
63 GAAGGAATAGGGAGCAGACAC-GTTGATTGAAGATCAAGTCCT
* *
37142 ATACTTTCTGAAGGAATAGGGAGAGGACACGTTTGTTGAAGGTTTTTTAAGTCATATACTCTCTG
1 ATACTCTCTGAAGGAATAGGGAGAGGACACGTTTGTTGAA-GTTATTT-AGTCATATACTCTCTG
* **
37207 AAGAAATAGGGAGCAGACACGTTGATTGAAGATTGAGTCCT
64 AAGGAATAGGGAGCAGACACGTTGATTGAAGATCAAGTCCT
* * *
37248 ATACTCTCTGAAGGAATGGGGAGCGGACACATTTGTTGAAG--ATTTAGTCATATACTCTCTGAA
1 ATACTCTCTGAAGGAATAGGGAGAGGACACGTTTGTTGAAGTTATTTAGTCATATACTCTCTGAA
37311 GGAATAG
66 GGAATAG
37318 AGAACAAACT
Statistics
Matches: 153, Mismatches: 19, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
102 24 0.16
103 3 0.02
105 7 0.05
106 119 0.78
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (104 bp):
ATACTCTCTGAAGGAATAGGGAGAGGACACGTTTGTTGAAGTTATTTAGTCATATACTCTCTGAA
GGAATAGGGAGCAGACACGTTGATTGAAGATCAAGTCCT
Found at i:37339 original size:157 final size:159
Alignment explanation
Indices: 37036--37366 Score: 397
Period size: 157 Copynumber: 2.1 Consensus size: 159
37026 TTCGAGTCTA
* *
37036 ATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAAATTATTCGAGTCTTATACTCTCTG
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTG-AAATGATTCGAGTCCTATACTCTCTG
* *
37101 AAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCCTATACTTTCTGAAGGAATAGGGAGA
65 AAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCATATACTCTCTGAAGGAATA-GGAGA
** * * *
37166 GGACACGTTTGTTGAAGGTTTTTTAAGTCAT
129 ACAAACGTTTGTTGAAGATTGTTTAAGTCAT
*
37197 ATACTCTCTGAAGAAATAGGGAGCAGACACG-TTGATTG-AA-GATT-GAGTCCTATACTCTCTG
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGAATG-TTGAAATGATTCGAGTCCTATACTCTCTG
* **
37258 AAGGAAT-GGGGAGCGGACACATTTGTTGAAGATTTAGTCATATACTCTCTGAAGGAATA-GAGA
65 AAGGAATAGGGG-GCAGACACATTTGTTGAAGATCAAGTCATATACTCTCTGAAGGAATAGGAGA
* **
37321 ACAAACTTGTTT-TATGAAGATTGTTTGAGTTTT
129 ACAAAC--GTTTGT-TGAAGATTGTTTAAGTCAT
*
37354 ATACTCCCTGAAG
1 ATACTCTCTGAAG
37367 CAAAAAAGAG
Statistics
Matches: 148, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
155 7 0.05
156 5 0.03
157 95 0.64
158 3 0.02
159 2 0.01
160 2 0.01
161 34 0.23
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (159 bp):
ATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAATGATTCGAGTCCTATACTCTCTGA
AGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCATATACTCTCTGAAGGAATAGGAGAAC
AAACGTTTGTTGAAGATTGTTTAAGTCAT
Found at i:37395 original size:157 final size:156
Alignment explanation
Indices: 37084--37398 Score: 341
Period size: 157 Copynumber: 2.0 Consensus size: 156
37074 AAAATTATTC
* * *
37084 GAGTCTTATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCCTATACTTT
1 GAGTCCTATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCATATACTCT
** * * * *
37149 CTGAAGGAATAGGGAGAGGACACGTTTGTTGAAGGTTTTTTAAGTCATATACTCTCTGAAGAAAT
66 CTGAAGGAATA-GGAGAACAAACGTTTGTTGAAGATTGTTTAAGTCATATACTCCCTGAAGAAAT
** * ** *
37214 AGGGAGCAGACACGTTGATTGAAGATT
130 AAAGAGCAAACACAATGATCGAAGATT
* **
37241 GAGTCCTATACTCTCTGAAGGAAT-GGGGAGCGGACACATTTGTTGAAGATTTAGTCATATACTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGG-GCAGACACATTTGTTGAAGATCAAGTCATATACTC
* **
37305 TCTGAAGGAATA-GAGAACAAACTTGTTT-TATGAAGATTGTTTGAGTTTTATACTCCCTGAAGC
65 TCTGAAGGAATAGGAGAACAAAC--GTTTGT-TGAAGATTGTTTAAGTCATATACTCCCTGAAG-
* *
37368 AAA-AAAGAGCAAACCCAATGGTCGAAGATT
126 AAATAAAGAGCAAACACAATGATCGAAGATT
37398 G
1 G
37399 TTCAAAGAAG
Statistics
Matches: 130, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
155 7 0.05
156 5 0.04
157 115 0.88
158 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (156 bp):
GAGTCCTATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCATATACTCT
CTGAAGGAATAGGAGAACAAACGTTTGTTGAAGATTGTTTAAGTCATATACTCCCTGAAGAAATA
AAGAGCAAACACAATGATCGAAGATT
Found at i:37588 original size:3 final size:3
Alignment explanation
Indices: 37566--37619 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
37556 AATATTATAA
* *
37566 TAT TAAT TA- TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAA TATT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
37612 TAT TAT TA
1 TAT TAT TA
37620 CATTTGCAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 2 0.05
3 37 0.84
4 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:39429 original size:2 final size:2
Alignment explanation
Indices: 39424--39462 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
39414 TATTGGTGTG
*
39424 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39463 TTAAAGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49271 original size:3 final size:3
Alignment explanation
Indices: 49257--49296 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
49247 CCAATATGTA
*
49257 AAT AAT ATT AAT AAT AAT AAT AAT ACAT AAAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AA
49297 GAAAGAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 28 0.85
4 4 0.12
5 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:49872 original size:27 final size:28
Alignment explanation
Indices: 49834--49908 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 28
49824 CCCTCTCTGG
*
49834 AATTTTATAAGTTC-A-TTCACCCCCTAA
1 AATTTTAAAAGTTCAAGTTC-CCCCCTAA
*
49861 AATTTTAAAAGTTCAAGTTTCCCCCTTAA
1 AATTTTAAAAGTTCAAG-TTCCCCCCTAA
* *
49890 AATTTTAAAAATTTAAGTT
1 AATTTTAAAAGTTCAAGTT
49909 TGTTCTCCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 13 0.32
28 3 0.07
29 22 0.54
30 3 0.07
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.40
Consensus pattern (28 bp):
AATTTTAAAAGTTCAAGTTCCCCCCTAA
Found at i:49894 original size:29 final size:28
Alignment explanation
Indices: 49853--49909 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
49843 AGTTCATTCA
*
49853 CCCCCTAAAATTTTAAAAGTTCAAGTTT
1 CCCCCTAAAATTTTAAAAATTCAAGTTT
*
49881 CCCCCTTAAAATTTTAAAAATTTAAGTTT
1 CCCCC-TAAAATTTTAAAAATTCAAGTTT
49910 GTTCTCCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (28 bp):
CCCCCTAAAATTTTAAAAATTCAAGTTT
Done.