Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009377.1 Hibiscus syriacus cultivar Beakdansim tig00113249_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: 55386
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2163 original size:6 final size:6
Alignment explanation
Indices: 2152--2254 Score: 179
Period size: 6 Copynumber: 17.2 Consensus size: 6
2142 GACACGTATT
*
2152 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG AACACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
2200 ACCACG ACCACG ACCTCG ACCACG ACCTCG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2248 ACCACG A
1 ACCACG A
2255 GCCGAGCCGA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 91 1.00
ACGTcount: A:0.33, C:0.49, G:0.17, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:2262 original size:5 final size:5
Alignment explanation
Indices: 2252--2300 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
2242 ACCACGACCA
* * *
2252 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
2301 ACGGACGGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.14, C:0.39, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:18703 original size:2 final size:2
Alignment explanation
Indices: 18696--18726 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18686 ATGGTACAAC
18696 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18727 TGATATGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20889 original size:12 final size:12
Alignment explanation
Indices: 20867--20898 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
20857 TTTTAAACTT
20867 ATAAT-AATTAA
1 ATAATAAATTAA
20878 ATAATAAATTAA
1 ATAATAAATTAA
20890 ATAATAAAT
1 ATAATAAAT
20899 GGATGACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAATAAATTAA
Found at i:29128 original size:30 final size:29
Alignment explanation
Indices: 29061--29135 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 29
29051 TATGGTCAAA
** * *
29061 AATCAATGTGACCACCGAACTTTCAATTT
1 AATCAATCAGACCACCCAACTTTCAATTG
*
29090 AATCAATCAGACCACCCAACTATTTAATTG
1 AATCAATCAGACCACCCAACT-TTCAATTG
* *
29120 ATTCAATCAAACCACC
1 AATCAATCAGACCACC
29136 GACCGTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 18 0.47
30 20 0.53
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.27
Consensus pattern (29 bp):
AATCAATCAGACCACCCAACTTTCAATTG
Found at i:31888 original size:29 final size:29
Alignment explanation
Indices: 31799--31917 Score: 114
Period size: 29 Copynumber: 4.1 Consensus size: 29
31789 CCGAAATTTG
31799 TTCGGTTCGGTTAATAATTTTCAAATAAA
1 TTCGGTTCGGTTAATAATTTTCAAATAAA
* * *** ** *
31828 TTTTGGTTCGATTAA-CGGTTAAAGAAAAAA
1 -TTCGGTTCGGTTAATAATTTTCA-AATAAA
* *
31858 TTCGGTTTGGTTAATAATTTTCAAATTAA
1 TTCGGTTCGGTTAATAATTTTCAAATAAA
*
31887 TTTGGTTCGGTTAATAATTTTCAAATAAA
1 TTCGGTTCGGTTAATAATTTTCAAATAAA
31916 TT
1 TT
31918 AACCGAACAG
Statistics
Matches: 66, Mismatches: 21, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
29 46 0.70
30 20 0.30
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (29 bp):
TTCGGTTCGGTTAATAATTTTCAAATAAA
Found at i:32031 original size:17 final size:17
Alignment explanation
Indices: 31980--32031 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
31970 AAAAATCTGT
*
31980 TAATTCGGTTCAGTTAA
1 TAATTTGGTTCAGTTAA
*
31997 TAA-TT--TTCA--AAA
1 TAATTTGGTTCAGTTAA
32009 TAATTTGGTTCAGTTAA
1 TAATTTGGTTCAGTTAA
32026 TAATTT
1 TAATTT
32032 TCAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
12 5 0.19
13 2 0.07
14 4 0.15
15 4 0.15
16 1 0.04
17 11 0.41
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.46
Consensus pattern (17 bp):
TAATTTGGTTCAGTTAA
Found at i:32056 original size:30 final size:29
Alignment explanation
Indices: 31980--32049 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
31970 AAAAATCTGT
*
31980 TAATTCGGTTCAGTTAATAATTTTCAAAA
1 TAATTTGGTTCAGTTAATAATTTTCAAAA
32009 TAATTTGGTTCAGTTAATAATTTTC-AAA
1 TAATTTGGTTCAGTTAATAATTTTCAAAA
32037 TAAATTTTGGTTC
1 T-AA-TTTGGTTC
32050 GATTAATCGA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 4 0.11
29 26 0.68
30 8 0.21
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (29 bp):
TAATTTGGTTCAGTTAATAATTTTCAAAA
Found at i:32157 original size:29 final size:29
Alignment explanation
Indices: 32117--32180 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
32107 AAAAAATCAG
*
32117 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTAGGTTCGGTTAATAATTTTCAAA
32146 TTAATTAGGTTCGGTTAATAATTTTCAAA
1 TTAATTAGGTTCGGTTAATAATTTTCAAA
*
32175 TAAATT
1 TTAATT
32181 TTGGTTCGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.45
Consensus pattern (29 bp):
TTAATTAGGTTCGGTTAATAATTTTCAAA
Found at i:32157 original size:138 final size:135
Alignment explanation
Indices: 31929--32355 Score: 581
Period size: 137 Copynumber: 3.1 Consensus size: 135
31919 ACCGAACAGG
* * * * *
31929 TTAACCAAATTTTTTCTTCGATTAATTCGATTAATAATTT-AAAAAATCTGTTAATTCGGTTCAG
1 TTAACCGAATTTTTGCTTCGATTAATTCGGTTAAT-ATTTAAAAAAATCAGTTAATTCGGTTCGG
*
31993 TTAATAATTTTCAAAATAATTTGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAATC
65 TTAATAATTTTCAAATTAATTTGGTTC-GTTAATAATTTTCAAATAAATTTTGGTTCGATTAA-C
32058 GAACCGAA
128 GAACCGAA
*
32066 TTAACCGAATTTTTGCTTCGTTTAATTCGGTTAATAGTTTAAAAAAATCAGTTAATTCGGTTCGG
1 TTAACCGAATTTTTGCTTCGATTAATTCGGTTAATA-TTTAAAAAAATCAGTTAATTCGGTTCGG
*
32131 TTAATAATTTTCAAATTAATTAGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACC
65 TTAATAATTTTCAAATTAATTTGGTTC-GTTAATAATTTTCAAATAAATTTTGGTTCGATTAA-C
* *
32196 AAACCAAA
128 GAACCGAA
** * * *
32204 TTAACCG-ATTTTTGCTTCGATTAATTTAGTTAAT-TTTCAAAAATATTCGGTTAGTTCGGTTCG
1 TTAACCGAATTTTTGCTTCGATTAATTCGGTTAATATTT-AAAAA-AATCAGTTAATTCGGTTCG
32267 GTTAATAATTTTCAAATTAATTTGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAAC
64 GTTAATAATTTTCAAATTAATTTGGTTCG-TTAATAATTTTCAAATAAATTTTGGTTCGATTAAC
*
32332 TGAACTGAA
128 -GAACCGAA
*
32341 TTAACTGAATATTTT
1 TTAACCGAAT-TTTT
32356 TTCTTTAACC
Statistics
Matches: 259, Mismatches: 23, Indels: 14
0.88 0.08 0.05
Matches are distributed among these distances:
135 3 0.01
136 8 0.03
137 146 0.56
138 98 0.38
139 4 0.02
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (135 bp):
TTAACCGAATTTTTGCTTCGATTAATTCGGTTAATATTTAAAAAAATCAGTTAATTCGGTTCGGT
TAATAATTTTCAAATTAATTTGGTTCGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGAA
CCGAA
Found at i:32303 original size:29 final size:30
Alignment explanation
Indices: 32261--32330 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 30
32251 CGGTTAGTTC
* *
32261 GGTTCGGTTAATAATTTTCAAATTAA-TTT
1 GGTTCGATTAATAATTTTCAAATAAATTTT
32290 GGTTCGATTAATAATTTTCAAATAAATTTT
1 GGTTCGATTAATAATTTTCAAATAAATTTT
32320 GGTTCGATTAA
1 GGTTCGATTAA
32331 CTGAACTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (30 bp):
GGTTCGATTAATAATTTTCAAATAAATTTT
Found at i:32344 original size:275 final size:263
Alignment explanation
Indices: 31856--32355 Score: 661
Period size: 275 Copynumber: 1.9 Consensus size: 263
31846 TTAAAGAAAA
* *
31856 AATTCGGTTTGGTTAATAATTTTCAAATTAATTTGGTTCGGTTAATAATTTTCAAATAAATTAAC
1 AATTCGGTTCGGTTAATAATTTTCAAATTAATTAGGTTCGGTTAATAATTTTCAAATAAATTAAC
* ** * * *
31921 CGAACAGGTTAACCAAATTTTTTCTTCGATTAATTCGATTAATAATTTAAAAAATCTGTTAATTC
66 CAAACAAATTAACCAAATTTTTGCTTCGATTAATTAGATTAAT-ATTTAAAAAATCGGTTAATTC
31986 GGTTCAGTTAATAATTTTCAAAATAATTTGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCG
130 GGTTCAGTTAATAATTTTCAAAATAATTTGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCG
32051 ATTAATCGAACCGAATTAACCGAAT-TTTTGCTTCGTTTAATTCGGTTAATAGTTTAAAAAAATC
195 ATTAATCGAACCGAATTAACCGAATATTTTGCTTCGTTTAATTCGGTTAATAGTTTAAAAAAATC
32115 AGTT
260 AGTT
32119 AATTCGGTTCGGTTAATAATTTTCAAATTAATTAGGTTCGGTTAATAATTTTCAAATAAATTTTG
1 AATTCGGTTCGGTTAATAATTTTCAAATTAATTAGGTTCGGTTAATAATTTTCAAAT-AA-----
*
32184 GTTCGATTAACCAAACCAAATTAACC-GATTTTTGCTTCGATTAATTTAG-TTAAT-TTTCAAAA
60 -----ATTAACCAAA-CAAATTAACCAAATTTTTGCTTCGATTAA-TTAGATTAATATTT-AAAA
* * *
32246 ATATTCGGTTAGTTCGGTTCGGTTAATAATTTTCAAATTAATTTGGTTC-GATTAATAATTTTCA
117 A-A-TCGGTTAATTCGGTTCAGTTAATAATTTTCAAAATAATTTGGTTCAG-TTAATAATTTTCA
* *
32310 AATAAATTTTGGTTCGATTAA-CTGAACTGAATTAACTGAATATTTT
179 AATAAATTTTGGTTCGATTAATC-GAACCGAATTAACCGAATATTTT
32356 TTCTTTAACC
Statistics
Matches: 204, Mismatches: 14, Indels: 25
0.84 0.06 0.10
Matches are distributed among these distances:
263 55 0.27
264 2 0.01
272 3 0.01
273 5 0.02
274 33 0.16
275 102 0.50
276 4 0.02
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (263 bp):
AATTCGGTTCGGTTAATAATTTTCAAATTAATTAGGTTCGGTTAATAATTTTCAAATAAATTAAC
CAAACAAATTAACCAAATTTTTGCTTCGATTAATTAGATTAATATTTAAAAAATCGGTTAATTCG
GTTCAGTTAATAATTTTCAAAATAATTTGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGA
TTAATCGAACCGAATTAACCGAATATTTTGCTTCGTTTAATTCGGTTAATAGTTTAAAAAAATCA
GTT
Found at i:45817 original size:60 final size:60
Alignment explanation
Indices: 45708--45878 Score: 159
Period size: 60 Copynumber: 2.8 Consensus size: 60
45698 ATATATATAA
* * * * * **
45708 TTTGGGATGAAATTGAGATGTACAAAAAGTTTGGGGATCGATTTAGAATGA-AGATTATAGT
1 TTTGGGATGAAATTGAAATGTTC-AAAAGTTTGAGGATCAATCTAGAATGATAG-CCATAGT
*
45769 TTTGGGATGAACTTGAAATGTTCAAAAGTTTGAGGA-CTAATCTAGAATGATAGCCATAGT
1 TTTGGGATGAAATTGAAATGTTCAAAAGTTTGAGGATC-AATCTAGAATGATAGCCATAGT
* * * * * *
45829 TTAGGTATGAAATTGAAAGGTTTAAAAGTTT-AGGGATCAATTTAAAATGA
1 TTTGGGATGAAATTGAAATGTTCAAAAGTTTGA-GGATCAATCTAGAATGA
45879 GAATCATAAT
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
59 2 0.02
60 66 0.73
61 23 0.25
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (60 bp):
TTTGGGATGAAATTGAAATGTTCAAAAGTTTGAGGATCAATCTAGAATGATAGCCATAGT
Found at i:50475 original size:18 final size:18
Alignment explanation
Indices: 50452--50489 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
50442 TTACGGCAAA
50452 TTCTCTAGCAGGGAACGT
1 TTCTCTAGCAGGGAACGT
*
50470 TTCTCTAGCAGGGATCGT
1 TTCTCTAGCAGGGAACGT
50488 TT
1 TT
50490 TTCACGAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (18 bp):
TTCTCTAGCAGGGAACGT
Found at i:52874 original size:60 final size:59
Alignment explanation
Indices: 52731--52891 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 59
52721 CATATGTCCC
52731 CAAACTATAAC-CTTCATTTTAAATTAATCCTTAAACTTTTGAATATTCAATTTCATCCT
1 CAAACTATAACTC-TCATTTTAAATTAATCCTTAAACTTTTGAATATTCAATTTCATCCT
* * * * *
52790 CAAACTATAATTCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTATAATTTTATCCT
1 CAAACTATAACTCTCATTTTAAATTAATCCTTAAACTTTTGAATATT-CAATTTCATCCT
* * *
52850 CAAACTATAACTCTCATTTCAAATTATTCCTTAAAATTTTGA
1 CAAACTATAACTCTCATTTTAAATTAATCCTTAAACTTTTGA
52892 TCATTTTAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
59 42 0.47
60 48 0.53
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (59 bp):
CAAACTATAACTCTCATTTTAAATTAATCCTTAAACTTTTGAATATTCAATTTCATCCT
Found at i:52902 original size:60 final size:59
Alignment explanation
Indices: 52731--52917 Score: 218
Period size: 60 Copynumber: 3.1 Consensus size: 59
52721 CATATGTCCC
*
52731 CAAACTATAAC-CTTCATTTTAAATTAATCCTTAAACTTTTGA-ATATTCAATTTCATCCT
1 CAAACTATAACTC-TCATTTTAAATTAATCCTTAAACTTTTGATAT-TTTAATTTCATCCT
* * * * *
52790 CAAACTATAATTCTCATTTTAAATTAGTCCCTAAACTTTTGAATATTATAATTTTATCCT
1 CAAACTATAACTCTCATTTTAAATTAATCCTTAAACTTTTG-ATATTTTAATTTCATCCT
* * * *
52850 CAAACTATAACTCTCATTTCAAATTATTCCTTAAAATTTTGATCATTTTAATTCCATCCGT
1 CAAACTATAACTCTCATTTTAAATTAATCCTTAAACTTTTGAT-ATTTTAATTTCATCC-T
52911 -AAACTAT
1 CAAACTAT
52918 TTTTTATTAA
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
59 38 0.35
60 68 0.62
61 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (59 bp):
CAAACTATAACTCTCATTTTAAATTAATCCTTAAACTTTTGATATTTTAATTTCATCCT
Found at i:53132 original size:59 final size:59
Alignment explanation
Indices: 52987--53133 Score: 174
Period size: 59 Copynumber: 2.5 Consensus size: 59
52977 AATAGCCTGG
* ** * *
52987 GGACCAATTTAGAATAAAGGTCATAG-TTGGGGATGAAATTGAAATGTTAAAAAGTTTAA
1 GGACTAATTTAGAATAAAGGT-ATAGTTTAAGGATGAAATTAAAATATTAAAAAGTTTAA
*
53046 GGACTAATTTAGAATAATA-GTATAGTTTAAGGATGAAATTAAAATATTTAAAAGTTTATA
1 GGACTAATTTAGAATAA-AGGTATAGTTTAAGGATGAAATTAAAATATTAAAAAGTTTA-A
* *
53106 -GACTATTTTAAAATAAAGGTATAGTTTA
1 GGACTAATTTAGAATAAAGGTATAGTTTA
53134 GGGACATGTG
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
58 5 0.07
59 69 0.91
60 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.34
Consensus pattern (59 bp):
GGACTAATTTAGAATAAAGGTATAGTTTAAGGATGAAATTAAAATATTAAAAAGTTTAA
Found at i:53344 original size:20 final size:19
Alignment explanation
Indices: 53319--53372 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
53309 GCGAAATAAA
53319 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
53339 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
53359 AATCGCAACGCGAT
1 AATCGCAACGCGAT
53373 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:53451 original size:20 final size:20
Alignment explanation
Indices: 53422--53469 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
53412 GATTTTCCAT
* *
53422 AATCGCAACGCGAATATAAA
1 AATCGCAACGCAAACATAAA
* *
53442 AATCGTAACGCAAACATATA
1 AATCGCAACGCAAACATAAA
53462 AATCGCAA
1 AATCGCAA
53470 AGCGATTCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.21, G:0.12, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCAAACATAAA
Found at i:53510 original size:20 final size:20
Alignment explanation
Indices: 53463--53511 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
53453 AAACATATAA
*
53463 ATCGCAAAGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
53483 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
53503 ATCGCAACG
1 ATCGCAACG
53512 AGTATCCGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:53547 original size:20 final size:20
Alignment explanation
Indices: 53503--53655 Score: 155
Period size: 20 Copynumber: 7.5 Consensus size: 20
53493 GATTCTGACT
* *
53503 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATACGT-AA
*
53524 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
* *
53544 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATACGTAA
* **
53564 ATCGCAACGGGTATTTGTAA
1 ATCGCAACGCGTATACGTAA
* *
53584 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATACGTAA
* *
53604 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
*
53624 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATACGT-AA
53645 ATCGCAACGCG
1 ATCGCAACGCG
53656 ATTTTTAAAG
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
20 81 0.74
21 29 0.26
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATACGTAA
Found at i:53584 original size:40 final size:41
Alignment explanation
Indices: 53503--53655 Score: 229
Period size: 40 Copynumber: 3.8 Consensus size: 41
53493 GATTCTGACT
* *
53503 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* **
53544 ATCGCAACGAGAATACGT-AAATCGCAACGGGTATTTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
53584 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
53624 ATCGCAACGACAATACGTAAAATCGCAACGCG
1 ATCGCAACGAGAATACGTAAAATCGCAACGCG
53656 ATTTTTAAAG
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 72 0.72
41 28 0.28
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:53610 original size:60 final size:61
Alignment explanation
Indices: 53503--53653 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 61
53493 GATTCTGACT
* * *
53503 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAAAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAA
* ** * * * *
53564 ATCGCAACGGGTATTTGT-AAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAAAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAA
** *
53624 ATCGCAACGACAATACGTAAAATCGCAACG
1 ATCGCAACGAGTATCCGTAAAATCGCAACG
53654 CGATTTTTAA
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
60 48 0.65
61 26 0.35
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (61 bp):
ATCGCAACGAGTATCCGTAAAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAA
Found at i:54242 original size:20 final size:20
Alignment explanation
Indices: 54217--54307 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
54207 TTCTAAACTT
*
54217 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
54237 AAAATCGCAACAAGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
54257 ACTATCGCAACGCGAGAAGTG
1 AAAATCGCAACACGA-AAATG
*
54278 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
54297 AAAATCGCAAC
1 AAAATCGCAAC
54308 GAGAAACCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.25
20 30 0.49
21 16 0.26
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:54300 original size:19 final size:19
Alignment explanation
Indices: 54217--54324 Score: 101
Period size: 19 Copynumber: 5.5 Consensus size: 19
54207 TTCTAAACTT
54217 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-G-AAATG
*
54237 AAAATCGCAACAAGAAAATG
1 AAAATCGCAACGAG-AAATG
** *
54257 ACTATCGCAACGCGAGAAGTG
1 AAAATCGCAA--CGAGAAATG
*
54278 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAAATG
**
54297 AAAATCGCAACGAGAAACC
1 AAAATCGCAACGAGAAATG
54316 AAAATCGCA
1 AAAATCGCA
54325 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
19 32 0.43
20 26 0.35
21 13 0.18
22 3 0.04
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGAGAAATG
Found at i:54418 original size:20 final size:19
Alignment explanation
Indices: 54320--54431 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
54310 GAAACCAAAA
* *
54320 TCGCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
54339 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
54358 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
54372 TCTCGTTGCGATAGTT-ATT
1 TCGCGTTGCGAT-TTTCATT
54391 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
* *
54411 CTCTCGTTGTGA-TTTCATT
1 -TCGCGTTGCGATTTTCATT
54430 TC
1 TC
54432 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
14 10 0.13
17 5 0.06
18 2 0.03
19 38 0.49
20 21 0.27
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Done.