Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004765.1 Hibiscus syriacus cultivar Beakdansim tig00010748_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: 45622
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:6738 original size:9 final size:9
Alignment explanation
Indices: 6727--6777 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
6717 AAATAATGTT
*
6727 AATAATAAT
1 AATAATAAA
*
6736 AATAATATCA
1 AATAATA-AA
*
6746 AATTATAAA
1 AATAATAAA
*
6755 AAT-ATAAG
1 AATAATAAA
6763 AATAATAAA
1 AATAATAAA
6772 AATAAT
1 AATAAT
6778 TTTATATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 7 0.21
9 21 0.62
10 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
AATAATAAA
Found at i:7219 original size:2 final size:2
Alignment explanation
Indices: 7212--7261 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
7202 GTTTAAAACA
7212 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT -T 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 AT
7252 AT AT AT AT AT
1 AT AT AT AT AT
7262 CTCAGAGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8488 original size:11 final size:11
Alignment explanation
Indices: 8472--8498 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
8462 TTACTCTCTC
8472 TTTTTTTTCTT
1 TTTTTTTTCTT
8483 TTTTTTTTCTT
1 TTTTTTTTCTT
8494 TTTTT
1 TTTTT
8499 GATAACGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:11529 original size:13 final size:12
Alignment explanation
Indices: 11486--11517 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
11476 CTTAATCTTT
11486 AATTTACCTTGA
1 AATTTACCTTGA
11498 AATTTACCTTGA
1 AATTTACCTTGA
11510 AATTTACC
1 AATTTACC
11518 CTTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (12 bp):
AATTTACCTTGA
Found at i:11624 original size:14 final size:14
Alignment explanation
Indices: 11605--11644 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
11595 TGCCTCTTTT
11605 TTATTTATATTATA
1 TTATTTATATTATA
*
11619 TTATTTTTATTATA
1 TTATTTATATTATA
11633 TATATCTTATAT
1 T-TAT-TTATAT
11645 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:11777 original size:31 final size:32
Alignment explanation
Indices: 11703--11825 Score: 103
Period size: 31 Copynumber: 3.8 Consensus size: 32
11693 ACTATGTATA
*
11703 TATTT-TTTCTTAATATTATATTTTATACGTTTT
1 TATTTATTTTTTAATATTATATTTT-TA-GTTTT
*
11736 TATATATATTTTTTAATATTCTA-TTTTAGTTTT
1 TAT-T-TATTTTTTAATATTATATTTTTAGTTTT
* * *
11769 TATTTA-TTTATATATATTATATTTTTACTTTA
1 TATTTATTTTTTA-ATATTATATTTTTAGTTTT
*
11801 T-TTTATTTTTCTATTATT-TATTTTT
1 TATTTATTTTT-TAATATTATATTTTT
11826 CTTAATATCA
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
30 5 0.07
31 20 0.27
32 17 0.23
33 13 0.17
34 3 0.04
35 4 0.05
36 13 0.17
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (32 bp):
TATTTATTTTTTAATATTATATTTTTAGTTTT
Found at i:11807 original size:16 final size:16
Alignment explanation
Indices: 11783--11827 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
11773 TATTTATATA
*
11783 TATTATATTTTTACT-T
1 TATTTTATTTTT-CTAT
11799 TATTTTATTTTTCTAT
1 TATTTTATTTTTCTAT
11815 TA-TTTATTTTTCT
1 TATTTTATTTTTCT
11828 TAATATCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTATTTTTCTAT
Found at i:11825 original size:15 final size:15
Alignment explanation
Indices: 11768--11827 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
11758 ATTTTAGTTT
* *
11768 TTATTTATTTATATA
1 TTATTTATTTTTCTA
11783 -TATTATATTTTTACT-
1 TTATT-TATTTTT-CTA
11798 TTATTTTATTTTTCTA
1 TTA-TTTATTTTTCTA
11814 TTATTTATTTTTCT
1 TTATTTATTTTTCT
11828 TAATATCATG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 4 0.11
15 19 0.50
16 13 0.34
17 2 0.05
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTTATTTTTCTA
Found at i:11946 original size:17 final size:18
Alignment explanation
Indices: 11926--11972 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
11916 TTTTATTTCT
11926 TTTTAATTTTTTTTAC-C
1 TTTTAATTTTTTTTACTC
*
11943 TTTT-TTATTTTTTTACTC
1 TTTTAAT-TTTTTTTACTC
*
11961 TATTAATTTTTT
1 TTTTAATTTTTT
11973 CCTTTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.04
17 13 0.54
18 9 0.38
19 1 0.04
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTAATTTTTTTTACTC
Found at i:15148 original size:11 final size:11
Alignment explanation
Indices: 15129--15158 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
15119 AGATTCAATC
*
15129 AGAACAAAAAG
1 AGAAAAAAAAG
15140 AGAAAAAAAAG
1 AGAAAAAAAAG
15151 AGAAAAAA
1 AGAAAAAA
15159 GCAAAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:15401 original size:69 final size:69
Alignment explanation
Indices: 15257--15394 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
15247 GATTCAAACT
* * *
15257 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCATTCGAAGATTATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
15322 TCAA
66 TCAA
* *
15326 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAATATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
15391 TCAA
66 TCAA
15395 GAGAGATACA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:16977 original size:36 final size:36
Alignment explanation
Indices: 16930--17155 Score: 207
Period size: 36 Copynumber: 6.4 Consensus size: 36
16920 ATTGAAAACA
*
16930 TTTCCCTTGAAATAAATTTCATCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
**
16966 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
* *
17002 TTTCCCTTGAAATAAA-TT-A----T-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACA-G
*** *
17031 TTTTATTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
** * * * *
17067 TTTCTTTTGGAACTAAGTTTTATCTCTCTTTAGACAG
1 TTTCCCTTGAAAC-AAATTTCATCTCTCTTGAGACAG
* * *
17104 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
*
17140 TTTCCCTTTAAACAAA
1 TTTCCCTTGAAACAAA
17156 ATCTTTGAAT
Statistics
Matches: 152, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.01
29 17 0.11
30 3 0.02
31 1 0.01
35 2 0.01
36 95 0.62
37 32 0.21
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
Found at i:17026 original size:101 final size:101
Alignment explanation
Indices: 16843--17121 Score: 301
Period size: 101 Copynumber: 2.8 Consensus size: 101
16833 TAAAAAGAAG
* * * * * *
16843 ATTTTATCTCGCTTTAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCT
1 ATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* * *
16908 TGAAACATAAA-CATTGAAAACATTTCCCTTGAAATAA
66 TG-AA-ATAAATTATTGAAAACATTTCACTTGAAACAA
* *
16945 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 ATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* ** * *
17009 TGAAATAAATTATTTGAATATGTTTTATTTGAAACAA
66 TGAAATAAATTA-TTGAAAACATTTCACTTGAAACAA
** * * * * *
17046 ATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTATCTCTCTTTAGACAGTTTCTCT
1 ATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
*
17111 TGAAACAAATT
66 TGAAATAAATT
17122 TCGTCTCTCT
Statistics
Matches: 150, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
99 5 0.03
100 3 0.02
101 76 0.51
102 66 0.44
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (101 bp):
ATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
TGAAATAAATTATTGAAAACATTTCACTTGAAACAA
Found at i:17198 original size:138 final size:138
Alignment explanation
Indices: 16950--17209 Score: 358
Period size: 138 Copynumber: 1.9 Consensus size: 138
16940 AATAAATTTC
* *
16950 ATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAT
1 ATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * ** *
17015 AAATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC
17080 TAAGTTTT
131 TAAGTTTT
* * * *
17088 ATCTCTCTTTAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGATAGTTTCCCTTTAAAC
1 ATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * ** *
17153 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTTCCTTGAGACAGTTTCT
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCT
17210 CTTGAAACAC
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
138 104 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (138 bp):
ATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:17248 original size:67 final size:67
Alignment explanation
Indices: 17104--17285 Score: 203
Period size: 67 Copynumber: 2.7 Consensus size: 67
17094 CTTTAGACAG
* * * * * * **
17104 TTTCTCTTGAAACAAATTTCGTC-TCTCTTGAGATAGTTTCCCTT-TAA-ACAAAATCTTTGAAT
1 TTTCCCTTAAAACAAATTTTGTCTTC-CTTGAGACAGTTTCTCTTGAAACACAAAATCTTAAAAT
17166 TTA
65 TTA
*
17169 TTTCCCCTAAAACAAATTTTGTCTTCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTAAAATT
1 TTTCCCTTAAAACAAATTTTGTCTTCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTAAAATT
17234 TA
66 TA
* *
17236 TTTCCCTTAAAACAAAATTTTGT-TTCCCTTGAGACCGTTT-TCATGAAACA
1 TTTCCCTTAAAAC-AAATTTTGTCTT-CCTTGAGACAGTTTCTCTTGAAACA
17286 ACAGATATCT
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
65 35 0.35
66 4 0.04
67 39 0.39
68 22 0.22
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTTCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTAAAATT
TA
Found at i:18219 original size:110 final size:107
Alignment explanation
Indices: 18003--18261 Score: 283
Period size: 110 Copynumber: 2.4 Consensus size: 107
17993 GCTTCCCAGT
* * *
18003 TTCAGAGCTAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGC-AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* *
18068 CAACGAAGGGGCGACTGATTATCAACAAACAACTTTTCAGTTTC
65 CAACGAAGGGGCGACTGACTATCAACAAACAACTTTCCAG-TTC
*
18112 ATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTC
1 -TTCAGAG-CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* * * * * * * *
18177 GCAGCGATGGGGTGGCTGGCTGTCAACAAATAA-TTTCCCAGTTC
64 ACAACGAAGGGGCGACTGACTATCAACAAACAACTTT-CCAGTTC
* *
18221 --CAGAGCCAATTTCAAC-TCTACGACGGAGGATATTGGACTCG
1 TTCAGAG-CAATTTCAACTTC-ACAACGAAGGATATTGGACTCG
18262 GAACAATACT
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
105 2 0.02
106 34 0.27
109 6 0.05
110 85 0.66
111 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (107 bp):
TTCAGAGCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCAC
AACGAAGGGGCGACTGACTATCAACAAACAACTTTCCAGTTC
Found at i:19653 original size:14 final size:14
Alignment explanation
Indices: 19634--19673 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
19624 ATTCCTTTTT
19634 TTATTTATATTATA
1 TTATTTATATTATA
*
19648 TTATTTTTATTATA
1 TTATTTATATTATA
19662 TATATCTTATAT
1 T-TAT-TTATAT
19674 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:19768 original size:38 final size:36
Alignment explanation
Indices: 19715--19856 Score: 129
Period size: 33 Copynumber: 4.1 Consensus size: 36
19705 TTTTTTTCCA
* *
19715 TTTACTATGTATATATTTTTTTCTTAATATTATATT
1 TTTACTTTTTATATATTTTTTTCTTAATATTATATT
*
19751 TTATACGTTTTTATATA-TTTTTTCTTAATATTCTATT
1 TT-TAC-TTTTTATATATTTTTTTCTTAATATTATATT
* * * *
19788 TTTA-TTTTTATTTATTTATAT-AT-ATATTATATT
1 TTTACTTTTTATATATTTTTTTCTTAATATTATATT
*
19821 TTTACTTTATT-T-TATTTTTTTC-TATTATT-TATT
1 TTTACTTT-TTATATATTTTTTTCTTAATATTATATT
19854 TTT
1 TTT
19857 CTTAATATCA
Statistics
Matches: 88, Mismatches: 11, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
33 28 0.32
34 18 0.20
35 6 0.07
36 4 0.05
37 24 0.27
38 8 0.09
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.69
Consensus pattern (36 bp):
TTTACTTTTTATATATTTTTTTCTTAATATTATATT
Found at i:19840 original size:18 final size:17
Alignment explanation
Indices: 19786--19856 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 17
19776 TAATATTCTA
19786 TTTT-TATT-TTTATTT
1 TTTTCTATTATTTATTT
* *
19801 ATTTATATATATATTATATT
1 TTTTCTAT-TAT-TTAT-TT
*
19821 TTTACT-TTATTTTATTT
1 TTTTCTATTA-TTTATTT
19838 TTTTCTATTATTTATTT
1 TTTTCTATTATTTATTT
19855 TT
1 TT
19857 CTTAATATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
15 3 0.07
16 3 0.07
17 17 0.39
18 10 0.23
19 6 0.14
20 5 0.11
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTATTATTTATTT
Found at i:19928 original size:87 final size:83
Alignment explanation
Indices: 19769--19927 Score: 207
Period size: 87 Copynumber: 1.9 Consensus size: 83
19759 TTTTATATAT
*
19769 TTTTTCTTAATATTCTATTTTTATTTTTATTTATTTATATATATATTATATTTTTACTTTATTTT
1 TTTTTCTTAATATTCTATTTTTATTTTTATTTATTTATATATATATTATATATTTACTTTATTTT
19834 ATTTTTTTCTATTATTTA
66 ATTTTTTTCTATTATTTA
* *
19852 TTTTTCTTAATATCATGTATATCTTTATTTTTATTTGTTT-TACT-TAGTATTATATATTTA-TT
1 TTTTTCTTAATAT--TCTAT-T-TTTATTTTTATTTATTTATA-TATA-TATTATATATTTACTT
*
19914 TTTTTTATTTTTTT
60 TATTTTATTTTTTT
19928 TAATAAATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
83 13 0.20
85 4 0.06
86 20 0.30
87 29 0.44
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (83 bp):
TTTTTCTTAATATTCTATTTTTATTTTTATTTATTTATATATATATTATATATTTACTTTATTTT
ATTTTTTTCTATTATTTA
Found at i:20091 original size:19 final size:17
Alignment explanation
Indices: 20047--20099 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
20037 TGTTTTTTTA
20047 ATATTTTATTCATTTTGT
1 ATATTTTATT-ATTTTGT
*
20065 ATATTTTTATTATTTTTT
1 ATA-TTTTATTATTTTGT
*
20083 ACGTATTTTGTTATTTT
1 A--TATTTTATTATTTT
20100 CTATTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 10 0.33
19 18 0.60
20 2 0.07
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.70
Consensus pattern (17 bp):
ATATTTTATTATTTTGT
Found at i:23473 original size:3 final size:3
Alignment explanation
Indices: 23465--23520 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
23455 GTGATACATT
23465 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23513 TTA TTA TT
1 TTA TTA TT
23521 TTTGCCACGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:23660 original size:21 final size:20
Alignment explanation
Indices: 23622--23695 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
23612 AATAACCTAA
* **
23622 AAAACTCTAAATTGCAATCT
1 AAAACTCCAAATCACAATCT
*
23642 AAAAGCTCCAAATCACAATCC
1 AAAA-CTCCAAATCACAATCT
*
23663 AAAA-TCCTAAATCACATTACT
1 AAAACTCC-AAATCACAAT-CT
*
23684 CAAACTCCAAAT
1 AAAACTCCAAAT
23696 TGTAACCCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 3 0.07
20 13 0.30
21 24 0.56
22 3 0.07
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAACTCCAAATCACAATCT
Found at i:29239 original size:15 final size:15
Alignment explanation
Indices: 29219--29249 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29209 ACGGGTATCT
29219 GGTAATCGCGTACCC
1 GGTAATCGCGTACCC
*
29234 GGTAATCGGGTACCC
1 GGTAATCGCGTACCC
29249 G
1 G
29250 ATACCCGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.29, G:0.32, T:0.19
Consensus pattern (15 bp):
GGTAATCGCGTACCC
Found at i:29937 original size:14 final size:15
Alignment explanation
Indices: 29908--29937 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29898 ACAAAATTTA
29908 TATATTTTTTACATT
1 TATATTTTTTACATT
29923 TATATTTTTTA-ATT
1 TATATTTTTTACATT
29937 T
1 T
29938 TTTCCTGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATATTTTTTACATT
Found at i:36678 original size:31 final size:31
Alignment explanation
Indices: 36643--36714 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
36633 GGATTACTGG
* *
36643 TGTCATTGTTTGGCATTGTTCCTATCATCAT
1 TGTCATTGTTTGGCATTCTTCCGATCATCAT
* *
36674 TGTCACTGTTTGGCATTCTTCCGATCGTCAT
1 TGTCATTGTTTGGCATTCTTCCGATCATCAT
* *
36705 TCTTATTGTT
1 TGTCATTGTT
36715 CATCTTCTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.49
Consensus pattern (31 bp):
TGTCATTGTTTGGCATTCTTCCGATCATCAT
Found at i:37773 original size:44 final size:42
Alignment explanation
Indices: 37724--37811 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 42
37714 TCATATAGGT
*
37724 TACGACTTTCAAAACATCAACAAATTTATGATCATCTAAATTCG
1 TACGACTTTCAAAACATCAACAAATTT-GGATCATCT-AATTCG
***
37768 TACGACTTTCAAAACATCGTGAAATTTGGATCATCTAATTCG
1 TACGACTTTCAAAACATCAACAAATTTGGATCATCTAATTCG
37810 TA
1 TA
37812 TAACAAAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 8 0.20
43 8 0.20
44 24 0.60
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (42 bp):
TACGACTTTCAAAACATCAACAAATTTGGATCATCTAATTCG
Found at i:44590 original size:2 final size:2
Alignment explanation
Indices: 44583--44607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44573 TTCTTGATTC
44583 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
44608 GCTTCATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.