Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008307.1 Hibiscus syriacus cultivar Beakdansim tig00110997_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: 148309
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:3847 original size:29 final size:29
Alignment explanation
Indices: 3783--3848 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
3773 TAAAGTTTAA
**
3783 AAAAGTTAAGGGACCAAAAATGTAATTTT
1 AAAAGTTAAGGGACCAAAAAAATAATTTT
* * *
3812 AATAGTTTAGGGA-CAAAAAAATATTTTT
1 AAAAGTTAAGGGACCAAAAAAATAATTTT
3840 GAAAAGTTA
1 -AAAAGTTA
3849 TGTATTTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (29 bp):
AAAAGTTAAGGGACCAAAAAAATAATTTT
Found at i:4993 original size:20 final size:21
Alignment explanation
Indices: 4964--5002 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4954 TTGATGTACT
4964 ACGTTGGAAATTAATGTTAGA
1 ACGTTGGAAATTAATGTTAGA
*
4985 ACGTT-GAAATTGATGTTA
1 ACGTTGGAAATTAATGTTA
5003 TGTTGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (21 bp):
ACGTTGGAAATTAATGTTAGA
Found at i:6250 original size:2 final size:2
Alignment explanation
Indices: 6245--6275 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6235 TATGATGTTT
6245 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
6276 GATTTATTTC
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:17867 original size:27 final size:27
Alignment explanation
Indices: 17829--17880 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
17819 GCGAAAAGAG
17829 TAAGGAGCTGAGCTTGACATCAATCAC
1 TAAGGAGCTGAGCTTGACATCAATCAC
17856 TAAGGAGCTGAGCTTGACATCAATC
1 TAAGGAGCTGAGCTTGACATCAATC
17881 CCCAAGGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (27 bp):
TAAGGAGCTGAGCTTGACATCAATCAC
Found at i:17887 original size:27 final size:27
Alignment explanation
Indices: 17830--17887 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
17820 CGAAAAGAGT
*
17830 AAGGAGCTGAGCTTGACATCAATCACT
1 AAGGAGCTGAGCTTGACATCAATCACC
*
17857 AAGGAGCTGAGCTTGACATCAATCCCC
1 AAGGAGCTGAGCTTGACATCAATCACC
17884 AAGG
1 AAGG
17888 CATATTTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
AAGGAGCTGAGCTTGACATCAATCACC
Found at i:28977 original size:29 final size:29
Alignment explanation
Indices: 28944--29043 Score: 73
Period size: 29 Copynumber: 3.4 Consensus size: 29
28934 AAAATTTTGG
*
28944 TTAGTGACCAAAATGTAAATTTTTAAAGT
1 TTAGGGACCAAAATGTAAATTTTTAAAGT
* * * **
28973 TTA--GTCCAAAGTATAAAGTTTAAAAAAGT
1 TTAGGGACCAAAATGTAAA-TTT-TTAAAGT
29002 TTAGGGACCAAAAATGT-AA-TTTTAATAGT
1 TTAGGGACC-AAAATGTAAATTTTTAA-AGT
*
29031 TTAGGGACAAAAA
1 TTAGGGACCAAAA
29044 AATATTTTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
27 11 0.20
28 9 0.17
29 24 0.44
31 5 0.09
32 5 0.09
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (29 bp):
TTAGGGACCAAAATGTAAATTTTTAAAGT
Found at i:29060 original size:29 final size:29
Alignment explanation
Indices: 28996--29060 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
28986 TAAAGTTTAA
**
28996 AAAAGTTTAGGGACCAAAAATGTAATTTT
1 AAAAGTTTAGGGACCAAAAAAATAATTTT
* *
29025 AATAGTTTAGGGA-CAAAAAAATATTTTT
1 AAAAGTTTAGGGACCAAAAAAATAATTTT
29053 GAAAAGTT
1 -AAAAGTT
29061 ATGTATTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (29 bp):
AAAAGTTTAGGGACCAAAAAAATAATTTT
Found at i:30217 original size:20 final size:21
Alignment explanation
Indices: 30188--30226 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
30178 TTGATGTACT
30188 ACGTTGGAAATTAATGTTAGA
1 ACGTTGGAAATTAATGTTAGA
*
30209 ACGTT-GAAATTGATGTTA
1 ACGTTGGAAATTAATGTTA
30227 TGTTGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (21 bp):
ACGTTGGAAATTAATGTTAGA
Found at i:42995 original size:27 final size:27
Alignment explanation
Indices: 42957--43008 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
42947 GCGAAAAGAG
42957 TAAGGAGCTGAGCTTGACATCAATCAC
1 TAAGGAGCTGAGCTTGACATCAATCAC
42984 TAAGGAGCTGAGCTTGACATCAATC
1 TAAGGAGCTGAGCTTGACATCAATC
43009 CCCAAGGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (27 bp):
TAAGGAGCTGAGCTTGACATCAATCAC
Found at i:43015 original size:27 final size:27
Alignment explanation
Indices: 42958--43015 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
42948 CGAAAAGAGT
*
42958 AAGGAGCTGAGCTTGACATCAATCACT
1 AAGGAGCTGAGCTTGACATCAATCACC
*
42985 AAGGAGCTGAGCTTGACATCAATCCCC
1 AAGGAGCTGAGCTTGACATCAATCACC
43012 AAGG
1 AAGG
43016 GATATTTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
AAGGAGCTGAGCTTGACATCAATCACC
Found at i:53845 original size:28 final size:27
Alignment explanation
Indices: 53802--53876 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 27
53792 ATGCTCCATC
*
53802 AAAAAAAAAAAAAAAATAGCA-GTTCGA
1 AAAAAAAAAAAAAAAAAAG-ATGTTCGA
53829 AAAAAAAAAAAAGAAAAAAGATGTTCGA
1 AAAAAAAAAAAA-AAAAAAGATGTTCGA
53857 AAAAAAGAGAAAAAAAAAAA
1 AAAAAA-A-AAAAAAAAAAA
53877 AAATGGAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
27 13 0.30
28 18 0.42
29 7 0.16
30 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.12, T:0.08
Consensus pattern (27 bp):
AAAAAAAAAAAAAAAAAAGATGTTCGA
Found at i:56071 original size:47 final size:47
Alignment explanation
Indices: 56014--56212 Score: 175
Period size: 47 Copynumber: 4.3 Consensus size: 47
56004 TATGTACGAT
*
56014 CTATTACTGGCAGTTTGTACTACATAATGGGCACTGAATGTGCCATA
1 CTATTACTGGCAGTTTATACTACATAATGGGCACTGAATGTGCCATA
* * * * *
56061 CTATTGCTGGCAGTTTATA-TACATACTAGACACTGAATGTGCCTTA
1 CTATTACTGGCAGTTTATACTACATAATGGGCACTGAATGTGCCATA
* * * * * * ** *
56107 CAATTATTGGCAATTTATACTAAAGATTGGGCACCAAATGTGACATA
1 CTATTACTGGCAGTTTATACTACATAATGGGCACTGAATGTGCCATA
* ** * * * * *
56154 CTGTTACTGGCAGTTTATACTGTATACTGGGTACTAAATGTGACGTA
1 CTATTACTGGCAGTTTATACTACATAATGGGCACTGAATGTGCCATA
*
56201 CTGTTACTGGCA
1 CTATTACTGGCA
56213 ACTATGTTGC
Statistics
Matches: 121, Mismatches: 30, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
46 38 0.31
47 83 0.69
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (47 bp):
CTATTACTGGCAGTTTATACTACATAATGGGCACTGAATGTGCCATA
Found at i:76084 original size:36 final size:36
Alignment explanation
Indices: 76037--76109 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
76027 AGAGAAACTG
76037 AAGTACGAAATAGGCTCAAGAACTTACCTTTGTGCT
1 AAGTACGAAATAGGCTCAAGAACTTACCTTTGTGCT
*
76073 AAGTACGAAATAGGCTCAAGAACTTATCTTTGTGCT
1 AAGTACGAAATAGGCTCAAGAACTTACCTTTGTGCT
76109 A
1 A
76110 TGGAACATGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (36 bp):
AAGTACGAAATAGGCTCAAGAACTTACCTTTGTGCT
Found at i:88131 original size:17 final size:17
Alignment explanation
Indices: 88111--88143 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
88101 TTTTGGAAAG
88111 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
88128 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
88144 TTAACTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:95320 original size:18 final size:18
Alignment explanation
Indices: 95297--95331 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
95287 CGATACTCTC
*
95297 CCCTTGGGTATCGATACA
1 CCCTTGAGTATCGATACA
95315 CCCTTGAGTATCGATAC
1 CCCTTGAGTATCGATAC
95332 CGAAATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (18 bp):
CCCTTGAGTATCGATACA
Found at i:104323 original size:21 final size:21
Alignment explanation
Indices: 104299--104339 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
104289 TTCTATGTTG
* *
104299 TCCTTTGGGACATATATGTAA
1 TCCTTTAGAACATATATGTAA
*
104320 TCCTTTAGAACGTATATGTA
1 TCCTTTAGAACATATATGTA
104340 GTTTGTTGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (21 bp):
TCCTTTAGAACATATATGTAA
Found at i:104403 original size:23 final size:21
Alignment explanation
Indices: 104376--104523 Score: 147
Period size: 21 Copynumber: 6.9 Consensus size: 21
104366 TTATATTATG
*
104376 TATGTGGTCCTTAAGGAGAAATA
1 TATGTGGTCCTT-AGG-GACATA
*
104399 TATGTGGTTCTTCA-GGACATA
1 TATGTGGTCCTT-AGGGACATA
*
104420 TATGTGGTCCTTAAGGAGAAATA
1 TATGTGGTCCTT-AGG-GACATA
*
104443 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTAGGGACATA
* *
104464 TATGTTGTCCTTCGGGACATA
1 TATGTGGTCCTTAGGGACATA
* * *
104485 TATGTGGTCCTTCGAGACAGA
1 TATGTGGTCCTTAGGGACATA
*
104506 TATGTGGT-CTTTGGGACA
1 TATGTGGTCCTTAGGGACA
104524 AATTCTATGT
Statistics
Matches: 109, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.07
21 68 0.62
22 4 0.04
23 29 0.27
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (21 bp):
TATGTGGTCCTTAGGGACATA
Found at i:104439 original size:44 final size:43
Alignment explanation
Indices: 104376--104514 Score: 192
Period size: 44 Copynumber: 3.2 Consensus size: 43
104366 TTATATTATG
*
104376 TATGTGGTCCTTAAGGAGAAATATATGTGGTTCTTCAGGACATA
1 TATGTGGTCCTTAAGGAGAAATATATGTGGTCCTTC-GGACATA
104420 TATGTGGTCCTTAAGGAGAAATATATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTAAGGAGAAATATATGTGGTCCTTC-GGACATA
* * * *
104464 TATGTTGTCCTT-CGG-GACATATATGTGGTCCTTCGAGACAGA
1 TATGTGGTCCTTAAGGAGAAATATATGTGGTCCTTCG-GACATA
104506 TATGTGGTC
1 TATGTGGTC
104515 TTTGGGACAA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.01
42 31 0.36
43 2 0.02
44 53 0.61
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (43 bp):
TATGTGGTCCTTAAGGAGAAATATATGTGGTCCTTCGGACATA
Found at i:115083 original size:23 final size:23
Alignment explanation
Indices: 115053--115099 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
115043 TACTCCCCCT
115053 TACTTTAACACTTCTTCAATTTA
1 TACTTTAACACTTCTTCAATTTA
115076 TACTTTAACACTTCTTCAATTTA
1 TACTTTAACACTTCTTCAATTTA
115099 T
1 T
115100 CATGTAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.49
Consensus pattern (23 bp):
TACTTTAACACTTCTTCAATTTA
Found at i:125572 original size:60 final size:59
Alignment explanation
Indices: 125461--125587 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 59
125451 CAGCATGCTG
* * *
125461 CATATTCGGGAATACACTAAAGAATACCTAGTTTATATGATGGCCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGAATACCTAGTATAGATGATGGACACGACCTTATGTGT
** * * * *
125520 CATATTCGGGAACTGTACTTAAGGATACCTAGTATAGATGGTGGACATGACCTTATGTGT
1 CATATTCGGGAA-TACACTAAAGAATACCTAGTATAGATGATGGACACGACCTTATGTGT
125580 CATATTCG
1 CATATTCG
125588 AGATTGCACT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
59 12 0.21
60 46 0.79
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGAATACCTAGTATAGATGATGGACACGACCTTATGTGT
Found at i:125676 original size:20 final size:20
Alignment explanation
Indices: 125641--125693 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
125631 CCTCAGGGTT
* *
125641 GTATATGGGCTATTGTCTATT
1 GTATAT-GGTTATTGTCTATG
*
125662 GTTTATGGTTATTGTCTATG
1 GTATATGGTTATTGTCTATG
125682 GTATATGGTTAT
1 GTATATGGTTAT
125694 GGAATAATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.51
Consensus pattern (20 bp):
GTATATGGTTATTGTCTATG
Found at i:125759 original size:45 final size:45
Alignment explanation
Indices: 125690--125842 Score: 213
Period size: 45 Copynumber: 3.4 Consensus size: 45
125680 TGGTATATGG
* * *
125690 TTATGGAAT-AATGGCAAGTGTATTGGTAAAATAAGTTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
125734 TTATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
125779 TTAT-GATATTAAATGGTAATTAT-TTGGTAAAATAAGCTTACGAGC
1 TTATGGA-A-TAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
125824 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
125843 AGATTTTATA
Statistics
Matches: 97, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
44 20 0.21
45 64 0.66
46 13 0.13
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:126581 original size:32 final size:32
Alignment explanation
Indices: 126515--126581 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
126505 AATAACTATA
* ** *
126515 ACTAATATGCATTAACTGAATGTGACTTTTAC
1 ACTAATATGAATTAACTGAATGTGACAATGAC
* *
126547 ACTATTATGAATTATCTGAATGTGACAATGAC
1 ACTAATATGAATTAACTGAATGTGACAATGAC
126579 ACT
1 ACT
126582 GTTGTATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (32 bp):
ACTAATATGAATTAACTGAATGTGACAATGAC
Found at i:127606 original size:6 final size:6
Alignment explanation
Indices: 127583--127659 Score: 75
Period size: 6 Copynumber: 12.8 Consensus size: 6
127573 TATTGGATAT
* * ** * *
127583 TATTGA TATGGG TATTGA TATTGA TATTGA TACGGG TATTGA TAATGA
1 TATTGA TATTGA TATTGA TATTGA TATTGA TATTGA TATTGA TATTGA
*
127631 TATTGA T-CTGA GTATTGA TATTGA TATTG
1 TATTGA TATTGA -TATTGA TATTGA TATTG
127660 GTACTAGTAT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
5 3 0.05
6 49 0.89
7 3 0.05
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.44
Consensus pattern (6 bp):
TATTGA
Found at i:127613 original size:24 final size:24
Alignment explanation
Indices: 127583--127659 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 24
127573 TATTGGATAT
127583 TATTGATATGGGTATTGATATTGA
1 TATTGATATGGGTATTGATATTGA
* *
127607 TATTGATACGGGTATTGATAATGA
1 TATTGATATGGGTATTGATATTGA
* *
127631 TATTGATCTGAGTATTGATATTGA
1 TATTGATATGGGTATTGATATTGA
127655 TATTG
1 TATTG
127660 GTACTAGTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.44
Consensus pattern (24 bp):
TATTGATATGGGTATTGATATTGA
Found at i:127668 original size:24 final size:24
Alignment explanation
Indices: 127594--127693 Score: 112
Period size: 24 Copynumber: 4.2 Consensus size: 24
127584 ATTGATATGG
**
127594 GTATTGATATTGATATTGATACGG
1 GTATTGATATTGATATTGATACTA
*
127618 GTATTGATAATGATATTGAT-CTGA
1 GTATTGATATTGATATTGATACT-A
*
127642 GTATTGATATTGATATTGGTACTA
1 GTATTGATATTGATATTGATACTA
* * * *
127666 GTATTGATACTGGTATTTATACCA
1 GTATTGATATTGATATTGATACTA
127690 GTAT
1 GTAT
127694 CAATACCAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.95
25 2 0.03
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (24 bp):
GTATTGATATTGATATTGATACTA
Found at i:127670 original size:12 final size:12
Alignment explanation
Indices: 127594--127693 Score: 55
Period size: 12 Copynumber: 8.3 Consensus size: 12
127584 ATTGATATGG
*
127594 GTATTGATA-TT
1 GTATTGATACTA
**
127605 GATATTGATACGG
1 G-TATTGATACTA
*
127618 GTATTGATAAT-
1 GTATTGATACTA
127629 GATATTGAT-CTGA
1 G-TATTGATACT-A
*
127642 GTATTGATA-TT
1 GTATTGATACTA
*
127653 GATATTGGTACTA
1 G-TATTGATACTA
*
127666 GTATTGATACTG
1 GTATTGATACTA
* *
127678 GTATTTATACCA
1 GTATTGATACTA
127690 GTAT
1 GTAT
127694 CAATACCAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
11 4 0.06
12 60 0.88
13 4 0.06
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (12 bp):
GTATTGATACTA
Found at i:136944 original size:60 final size:59
Alignment explanation
Indices: 136844--136969 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 59
136834 CAGCATGCTG
** * * *
136844 CATATTCGGGAATACACTAAAGGATACCTACTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTACTACAGATGGTGGACACGACCTTATGCGT
* * * *
136903 CATATTCGGGAACTATAGTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGCGT
1 CATATTCGGGAA-TACACTAAAGGATACCTACTACAGATGGTGGACACGACCTTATGCGT
136963 CATATTC
1 CATATTC
136970 TGGATTGCAC
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
59 12 0.21
60 45 0.79
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTACTACAGATGGTGGACACGACCTTATGCGT
Found at i:137062 original size:20 final size:20
Alignment explanation
Indices: 137037--137075 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
137027 TATTGGGCTA
* *
137037 TTGTCTATTGTTTATGGTTG
1 TTGTCTATGGTATATGGTTG
137057 TTGTCTATGGTATATGGTT
1 TTGTCTATGGTATATGGTT
137076 ATGGAATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.05, G:0.26, T:0.56
Consensus pattern (20 bp):
TTGTCTATGGTATATGGTTG
Found at i:137146 original size:45 final size:45
Alignment explanation
Indices: 137074--137227 Score: 222
Period size: 45 Copynumber: 3.4 Consensus size: 45
137064 TGGTATATGG
* * *
137074 TTATGGAAT-AAGGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
137118 TTATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
137163 TTAT-GATATTAAATGGTGAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGA-A-TAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
137209 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
137228 AGATTTTATA
Statistics
Matches: 98, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
44 10 0.10
45 47 0.48
46 40 0.41
47 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.31
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:137538 original size:22 final size:22
Alignment explanation
Indices: 137512--137560 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
137502 GGCATGTAAT
137512 TTGAAAATATTCAATTTATTTG
1 TTGAAAATATTCAATTTATTTG
137534 TTGAAAATATTCAATTTATTTG
1 TTGAAAATATTCAATTTATTTG
137556 TTGAA
1 TTGAA
137561 TAAATTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (22 bp):
TTGAAAATATTCAATTTATTTG
Found at i:145384 original size:14 final size:14
Alignment explanation
Indices: 145352--145387 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
145342 ATTTTTTACG
*
145352 CAGGGATTTATTTG
1 CAGGGATTTATTTA
*
145366 TAGGGATTTATTTA
1 CAGGGATTTATTTA
145380 CAGGGATT
1 CAGGGATT
145388 ACTTATCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.42
Consensus pattern (14 bp):
CAGGGATTTATTTA
Found at i:145895 original size:60 final size:59
Alignment explanation
Indices: 145795--145924 Score: 197
Period size: 60 Copynumber: 2.2 Consensus size: 59
145785 CAGCAGGCTG
** * *
145795 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* *
145854 CATATTCGGGAACTATACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAA-TACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
145914 CATATTCGGGA
1 CATATTCGGGA
145925 TTGCACTACG
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
59 12 0.19
60 52 0.81
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:146093 original size:45 final size:45
Alignment explanation
Indices: 146024--146177 Score: 229
Period size: 45 Copynumber: 3.4 Consensus size: 45
146014 TGGTATATGG
*
146024 TTATGGAAT-AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
* * *
146068 ATATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
* *
146113 TTATGGTATTAAATGGTAAGTGTATTGGTAAAATAAGCTTACAAGC
1 TTATGG-AATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
*
146159 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
146178 AGATTTTATA
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
44 7 0.07
45 49 0.51
46 41 0.42
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
Done.