Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008715.1 Hibiscus syriacus cultivar Beakdansim tig00111768_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: 43943
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:1853 original size:33 final size:33
Alignment explanation
Indices: 1816--1878 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1806 ATCATTGACC
* *
1816 ATCGCAATGCGAAATGCAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAAACGCAACGATAGA
*
1849 ATCGCAATGCGAAATGAAAAAGGCAACGAT
1 ATCGCAATGCGAAATGAAAAACGCAACGAT
1879 GATTAACATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAAACGCAACGATAGA
Found at i:2127 original size:20 final size:21
Alignment explanation
Indices: 2089--2138 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
2079 ATTCATTTGA
2089 CTATCGCAACGCGGAAAATGG
1 CTATCGCAACGCGGAAAATGG
2110 CTATCGCAACGC-GAAAATGG
1 CTATCGCAACGCGGAAAATGG
*
2130 TTATCGCAA
1 CTATCGCAA
2139 TGAGAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (21 bp):
CTATCGCAACGCGGAAAATGG
Found at i:2145 original size:20 final size:20
Alignment explanation
Indices: 2089--2147 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
2079 ATTCATTTGA
*
2089 CTATCGCAACGCGGAAAATGG
1 CTATCGCAACG-AGAAAATGG
*
2110 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
* *
2130 TTATCGCAATGAGAAAAT
1 CTATCGCAACGAGAAAAT
2148 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 23 0.68
21 11 0.32
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:2238 original size:17 final size:18
Alignment explanation
Indices: 2185--2247 Score: 101
Period size: 19 Copynumber: 3.5 Consensus size: 18
2175 GATTTTCTCG
2185 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
2203 TTGCGCTTTTCATTTCGCA
1 TTGCG-ATTTCATTTCGCA
2222 TTGCGATTTCA-TTCGCA
1 TTGCGATTTCATTTCGCA
2239 TTGCGATTT
1 TTGCGATTT
2248 TCTCGTTGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
17 15 0.36
18 10 0.24
19 17 0.40
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:4257 original size:20 final size:19
Alignment explanation
Indices: 4222--4288 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
4212 GAAACTTAAA
*
4222 ATCGCAACACGAAATGACT
1 ATCGCAACGCGAAATGACT
*
4241 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
4261 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
4280 ATCGCAACG
1 ATCGCAACG
4289 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4296 original size:14 final size:14
Alignment explanation
Indices: 4277--4334 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4267 ATGCGAAATG
4277 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4291 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
4307 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
4323 AAAATCGCAACG
1 AAAATCGCAACG
4335 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4319 original size:32 final size:33
Alignment explanation
Indices: 4261--4339 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
4251 GGAAATGGCT
*
4261 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
4294 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
4326 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
4340 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:4395 original size:30 final size:31
Alignment explanation
Indices: 4351--4435 Score: 118
Period size: 30 Copynumber: 2.7 Consensus size: 31
4341 ACAAATCGCA
* *
4351 TTGCGATTTTCATTTCGCGTTGCAATTTTTCG
1 TTGCGA-TTTCATTTCGCATTGCAATTTGTCG
*
4383 TTGCGA-TTCATTTCGCATTGCGATTTGTCG
1 TTGCGATTTCATTTCGCATTGCAATTTGTCG
4413 TTGCGATTTTCATTTCGCATTGC
1 TTGCGA-TTTCATTTCGCATTGC
4436 GATAGCCATT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
30 27 0.56
32 21 0.44
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (31 bp):
TTGCGATTTCATTTCGCATTGCAATTTGTCG
Found at i:4416 original size:13 final size:13
Alignment explanation
Indices: 4368--4422 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 13
4358 TTTCATTTCG
*
4368 CGTTGCAATTTTT
1 CGTTGCGATTTTT
4381 CGTTGCGATTCATTT
1 CGTTGCGATT--TTT
*
4396 CGCATTGCGATTTGT
1 CG--TTGCGATTTTT
4411 CGTTGCGATTTT
1 CGTTGCGATTTT
4423 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 18 0.51
15 9 0.26
17 8 0.23
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (13 bp):
CGTTGCGATTTTT
Found at i:4445 original size:19 final size:20
Alignment explanation
Indices: 4423--4466 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4413 TTGCGATTTT
*
4423 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTACGATAGC
* *
4442 CATTTCCGCGTTACGATAGT
1 CATTTCCGCATTACGATAGC
4462 CATTT
1 CATTT
4467 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTACGATAGC
Found at i:6634 original size:22 final size:22
Alignment explanation
Indices: 6609--6652 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6599 GATTTAGATA
6609 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
6631 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
6653 TGAGAGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:6865 original size:20 final size:20
Alignment explanation
Indices: 6840--6892 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
6830 GATTATGTAT
6840 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6860 TATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6880 TATCTCGTTGCGA
1 TATCGCGTTGCGA
6893 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:6905 original size:41 final size:41
Alignment explanation
Indices: 6860--6937 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
6850 CGAAAGTCAG
* * * *
6860 TATCGCGTTGCAAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCAAAAGTAAGTATCGCATTGCGATTTTGTAT
* *
6901 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCAAAAGTAAGTATCGCATTGCGATTTT
6938 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCAAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:6926 original size:20 final size:19
Alignment explanation
Indices: 6820--6934 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
6810 CGCTTTGAAA
*
6820 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* *
6841 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* * *
6861 ATCGCGTTGCAAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
6881 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
6902 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
6922 ATCGCATTGCGAT
1 ATCGCATTGCGAT
6935 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.06
20 47 0.61
21 23 0.30
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:6952 original size:21 final size:21
Alignment explanation
Indices: 6923--7015 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
6913 ATAGTAAGTA
6923 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
6944 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
6964 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
6985 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
7005 TCGCATTGCGA
1 TCGCATTGCGA
7016 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:6953 original size:41 final size:41
Alignment explanation
Indices: 6903--7015 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 41
6893 TTTTGTATTA
*
6903 TCGCATTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGAT-GTAAGTATTCGCATTGCGATTTTCCCAAT
* **
6944 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
* **
6985 TCGCGTTGCGATTTACTTATTCGCATTGCGA
1 TCGCGTTGCGATGTAAGTATTCGCATTGCGA
7016 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 4 0.06
41 63 0.94
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
Found at i:9279 original size:43 final size:43
Alignment explanation
Indices: 9210--9301 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
9200 TTAAGAATAC
* *
9210 TTTTAATATGTTAGTTTGTTGTATTTGCGGATTGTTAC-TCTAG
1 TTTTAATATGTTAGTTTGGTGAATTTGCGGATTGTTACAT-TAG
* * *
9253 TTTTAATTTGTTGGTTTGGTGAATTTGTGGATTGTTACATTAG
1 TTTTAATATGTTAGTTTGGTGAATTTGCGGATTGTTACATTAG
9296 TTTTAA
1 TTTTAA
9302 GGGTAAAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.54
Consensus pattern (43 bp):
TTTTAATATGTTAGTTTGGTGAATTTGCGGATTGTTACATTAG
Found at i:9503 original size:31 final size:31
Alignment explanation
Indices: 9430--9507 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
9420 CAGTTACGTT
9430 GGGGATCATATTGCAAACAGACTAAATGTTA
1 GGGGATCATATTGCAAACAGACTAAATGTTA
* * * *
9461 GGGTACCATATTGCAAACGGACTAAATGTTG
1 GGGGATCATATTGCAAACAGACTAAATGTTA
*
9492 GGGGATTATATTGCAA
1 GGGGATCATATTGCAA
9508 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGGATCATATTGCAAACAGACTAAATGTTA
Found at i:10141 original size:56 final size:56
Alignment explanation
Indices: 10071--10185 Score: 167
Period size: 56 Copynumber: 2.1 Consensus size: 56
10061 ATTTTACCTA
* ** * * *
10071 ACATGCCAGGATCCGACTGAATTCTGACTGATTACCTGATTTTATAGCTTTAACTG
1 ACATGCCAGAATCCGACTGAAACCTGACCGATTACCTGATTTGACAGCTTTAACTG
*
10127 ACATGTCAGAATCCGACTGAAACCTGACCGATTACCTGATTTGACAGCTTTAACTG
1 ACATGCCAGAATCCGACTGAAACCTGACCGATTACCTGATTTGACAGCTTTAACTG
10183 ACA
1 ACA
10186 CCTTCTTGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (56 bp):
ACATGCCAGAATCCGACTGAAACCTGACCGATTACCTGATTTGACAGCTTTAACTG
Found at i:10626 original size:31 final size:31
Alignment explanation
Indices: 10591--10654 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
10581 AATACATTCC
10591 CCCAACATTTAGT-TCGTTTACAATATGGTCT
1 CCCAACATTTAGTCT-GTTTACAATATGGTCT
*
10622 CCCAACATTTAGTCTGTTTGCAATATGGTCT
1 CCCAACATTTAGTCTGTTTACAATATGGTCT
10653 CC
1 CC
10655 AATGTAACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (31 bp):
CCCAACATTTAGTCTGTTTACAATATGGTCT
Found at i:13739 original size:32 final size:32
Alignment explanation
Indices: 13682--13745 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
13672 GATACTCAGC
*
13682 ATTCCTACTTCATTTTTGACTTCATATAATGT
1 ATTCCTACTTCATTTTTGACTTCATACAATGT
* *
13714 ATTCCTACTTGATTTTTTA-TGTCATACAATGT
1 ATTCCTACTTCATTTTTGACT-TCATACAATGT
13746 TCTGTAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (32 bp):
ATTCCTACTTCATTTTTGACTTCATACAATGT
Found at i:16108 original size:3 final size:3
Alignment explanation
Indices: 16100--16138 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
16090 GCCCCCCTCC
16100 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
16139 ATTGCCACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:19252 original size:104 final size:105
Alignment explanation
Indices: 19112--19313 Score: 325
Period size: 104 Copynumber: 1.9 Consensus size: 105
19102 TTGATACAAT
* * *
19112 TATCAATATAAATTGTGATGAATTTGTTTGACACTAAAAATATATTTTGTGACCACCAATATTAT
1 TATCAATAAAAATTATGATAAATTTGTTTGACACTAAAAATATATTTTGTGACCACCAATATTAT
*
19177 CACACTAAGTA-ATATTTAGTGACCAACTGTTCGATACTA
66 CACACTAAGTATATATTTAGTGACCAAATGTTCGATACTA
* *
19216 TATCAATAAAAATTATGATAAATTTGTTTGACACTAAAAATATATTTTGTGATCACCAATGTTAT
1 TATCAATAAAAATTATGATAAATTTGTTTGACACTAAAAATATATTTTGTGACCACCAATATTAT
* *
19281 CACACTAAGTATTTTTTTAGTGACCAAATGTTC
66 CACACTAAGTATATATTTAGTGACCAAATGTTC
19314 AACACACTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
104 71 0.80
105 18 0.20
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (105 bp):
TATCAATAAAAATTATGATAAATTTGTTTGACACTAAAAATATATTTTGTGACCACCAATATTAT
CACACTAAGTATATATTTAGTGACCAAATGTTCGATACTA
Found at i:20069 original size:21 final size:21
Alignment explanation
Indices: 20043--20088 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
20033 AATTTTTGGG
*
20043 CAAGGGGAATCAATACCCATT
1 CAAGGGGAACCAATACCCATT
* *
20064 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCAATACCCATT
20085 CAAG
1 CAAG
20089 CGAACAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCAATACCCATT
Found at i:21800 original size:23 final size:23
Alignment explanation
Indices: 21770--21829 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
21760 ATTATTATAT
21770 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
21793 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
21816 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
21830 TTTATATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:27295 original size:76 final size:75
Alignment explanation
Indices: 27205--27352 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 75
27195 TAAACTCAAA
27205 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
27269 TTTTAATTAATT
64 TTTTAATTAATT
* * * *
27281 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
27346 TTAATTA
66 TTAATTA
27353 GGATTTAGAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 24 0.36
76 43 0.64
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAATT
Found at i:27354 original size:19 final size:19
Alignment explanation
Indices: 27326--27387 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
27316 TGTATTTTAG
*
27326 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
27345 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
27364 ATTATATTATTTTTTAGTAT
1 TTTA-ATTAGGTTTTAGTAT
27384 TTTA
1 TTTA
27388 GTTTAAATTG
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:35775 original size:73 final size:74
Alignment explanation
Indices: 35633--35794 Score: 222
Period size: 73 Copynumber: 2.2 Consensus size: 74
35623 TTAAACTCAA
*
35633 ATTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 ATTTAGGATATTATTTT-AACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
35698 TTTAATTAAG
65 TTTAATTAAG
* * *
35708 TTTTAGGATATTATTTT-ATATTTTATCTTTATCTTTGTA-TTTAGTTTAAATAGG-TTTTAGTA
1 ATTTAGGATATTATTTTAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
*
35770 TTTTAATTAGG
65 -TTTAATTAAG
*
35781 ATTTAGAATATTAT
1 ATTTAGGATATTAT
35795 ATTTTTTTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
72 8 0.10
73 43 0.55
74 12 0.15
75 15 0.19
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (74 bp):
ATTTAGGATATTATTTTAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTAT
TTAATTAAG
Found at i:36440 original size:22 final size:20
Alignment explanation
Indices: 36408--36477 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 20
36398 TAAGTTTCTC
36408 TTTATCTTAATCTCTTTAATTTG
1 TTTAT-TTAAT-TCTTT-ATTTG
* *
36431 TTTATTTAATTATTTTTTTTG
1 TTTATTTAATT-CTTTATTTG
36452 TTTTATTTAATTC-TTATTT-
1 -TTTATTTAATTCTTTATTTG
36471 TTTATTT
1 TTTATTT
36478 TAACCACAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.17
20 5 0.12
21 5 0.12
22 19 0.46
23 5 0.12
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTATTTAATTCTTTATTTG
Found at i:36565 original size:20 final size:20
Alignment explanation
Indices: 36505--36565 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 20
36495 AAAATCTCCC
*
36505 TTTTATATTTAATA-CTATTAA
1 TTTTAT-TTTAATATCT-TTTA
*
36526 TATTTATTTTTTATAT-TTTTA
1 T-TTTA-TTTTAATATCTTTTA
36547 TTTTATTTTAATATCTTTT
1 TTTTATTTTAATATCTTTT
36566 CAACTTCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 8 0.24
20 8 0.24
21 5 0.15
22 11 0.33
23 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATTTTAATATCTTTTA
Found at i:42125 original size:11 final size:12
Alignment explanation
Indices: 42109--42137 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42099 ACTAATTCTC
42109 TTTTTTC-TTTA
1 TTTTTTCTTTTA
42120 TTTTTTCTTTTA
1 TTTTTTCTTTTA
42132 TTTTTT
1 TTTTTT
42138 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTCTTTTA
Found at i:42959 original size:37 final size:39
Alignment explanation
Indices: 42918--42997 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 39
42908 ATAATTCCAC
*
42918 TGAAGC-CGATTTTCATTTAACAATATGCCATT-AAATA
1 TGAAGCACGATTTCCATTTAACAATATGCCATTAAAATA
**
42955 TGAAGCACGATTTCCATTTAACAATATGGTATTAAAATA
1 TGAAGCACGATTTCCATTTAACAATATGCCATTAAAATA
42994 TGAA
1 TGAA
42998 TTAGACCACC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 6 0.16
38 23 0.61
39 9 0.24
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (39 bp):
TGAAGCACGATTTCCATTTAACAATATGCCATTAAAATA
Done.