Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002444.1 Hibiscus syriacus cultivar Beakdansim tig00005005_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: 50393
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:5398 original size:32 final size:32
Alignment explanation
Indices: 5335--5407 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
5325 TAAAAGTTTA
* * *
5335 AAAATTTAATAGTTATTTCGTAATAGTTTAAC
1 AAAATTTAATAATTATTTCATAATAGATTAAC
*
5367 AAAATTTAATAATTATTTTATAATCA-ATTAAC
1 AAAATTTAATAATTATTTCATAAT-AGATTAAC
5399 AAACATTTA
1 AAA-ATTTA
5408 TTGTCATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 29 0.83
33 6 0.17
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (32 bp):
AAAATTTAATAATTATTTCATAATAGATTAAC
Found at i:5786 original size:90 final size:91
Alignment explanation
Indices: 5661--5829 Score: 268
Period size: 91 Copynumber: 1.9 Consensus size: 91
5651 TAAATTACGT
* *
5661 TTTTAGTCCGTTTTAGTATCTAAACTTTT-ATTTTTTTCAAAAGTATACCTAAAGTTCAATTTTA
1 TTTTAATCCGTTTTAGTATCTAAACTTTTAATTTTTTTCAAAAGTATACCTAAACTTCAATTTTA
5725 GTTTCATTTTAGTAAATTACGGTTTA
66 GTTTCATTTTAGTAAATTACGGTTTA
* * * * *
5751 TTTTAATCTGTTTTAGTGTCTAAACTTTTAATTTTTTTCAAATGTATACCTAAACTTTAGTTTTA
1 TTTTAATCCGTTTTAGTATCTAAACTTTTAATTTTTTTCAAAAGTATACCTAAACTTCAATTTTA
5816 GTTTCATTTTAGTA
66 GTTTCATTTTAGTA
5830 TCTCATTGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 26 0.37
91 45 0.63
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (91 bp):
TTTTAATCCGTTTTAGTATCTAAACTTTTAATTTTTTTCAAAAGTATACCTAAACTTCAATTTTA
GTTTCATTTTAGTAAATTACGGTTTA
Found at i:12487 original size:248 final size:243
Alignment explanation
Indices: 12052--12779 Score: 1055
Period size: 248 Copynumber: 3.0 Consensus size: 243
12042 TTGTCAACGA
* * *
12052 AAAAAAGTTGTATTGAAATAATTTGGGTACAAATTACTCCCTCCGTCTCACTAAATGTGTTAATT
1 AAAAAAGTTGTATTGAAATAATTTGGGTACAAATTACTCCTTCCATCTCACTAAATGTGTTCATT
* * *
12117 ATTAACTTTCAAAAAGTCAAAAAAATAATAGAAAGTCGTTAGTTTTATTAAAAATATAAAATATC
66 ATTGACTTTCAAAAAGTAAAAAAAAT-ATAGAAAGTCATTAGTTTTATTAAAAATA-AAAATATC
*
12182 CAAAATTACAATGAAGATTTACAAGTATAACCGTAAACCTAAAATATAATTATGACATTTTTCTA
129 CAAAATTACAATGAAGATTTACAAGCATAACCGTAAACCTAAAATATAATTATGACATTTTTCTA
*
12247 TTACCATAGAGACAAAAATTAGCCACTTATATCACATAAGGACCAATAAG
194 TTACCATAGAGACAAAAATTAGCCACTTATATCACATAAGGACCAAGAAG
12297 AAAAAAGTTGTATTGAAATAATTTGGGTACAAATTACTCCTTCCATCTCACTAAATGTGTTCATT
1 AAAAAAGTTGTATTGAAATAATTTGGGTACAAATTACTCCTTCCATCTCACTAAATGTGTTCATT
12362 ATTGACTTTCAAAAAGTAAAAAAAAAAATGATAGAAAGTCATTAGTTTTATTAAAAATAAAAAAT
66 ATTGACTTTCAAAAAGT---AAAAAAAAT-ATAGAAAGTCATTAGTTTTATTAAAAAT-AAAAAT
* *
12427 ATCCAAAATTACAATGAAGAATTACAAGCAAAACCGTAAACCTAAAATATAATTATGACATTTTT
126 ATCCAAAATTACAATGAAGATTTACAAGCATAACCGTAAACCTAAAATATAATTATGACATTTTT
* *
12492 CTATTACCATAGAGACAAAAATTAG-CAATCTATATCAAATAAGGACCAAAGAAG
191 CTATTACCATAGAGACAAAAATTAGCCACT-TATATCACATAAGGACC-AAGAAG
*
12546 GAAAAAGTTGTATTGAAATAATTTGGGTACAAATTACTCCTTCCATCTCACTAAATGTGTTCATT
1 AAAAAAGTTGTATTGAAATAATTTGGGTACAAATTACTCCTTCCATCTCACTAAATGTGTTCATT
12611 ATTGACTTTCAAAAAGTCAAAAAAAAT-T-----G--A-TAG----A--AAAAAT----ATATCC
66 ATTGACTTTCAAAAAGT-AAAAAAAATATAGAAAGTCATTAGTTTTATTAAAAATAAAAATATCC
* *
12657 AAAATTACAATGAAGATTTACAAGCATAACTGTAAACCTAAAATAAAATTATGACATTTTTCTAT
130 AAAATTACAATGAAGATTTACAAGCATAACCGTAAACCTAAAATATAATTATGACATTTTTCTAT
* *
12722 TACCATAAAGACAAAAATTAGCCACCTATATCACATAAGGACCAAAGAAG
195 TACCATAGAGACAAAAATTAGCCACTTATATCACATAAGGACC-AAGAAG
*
12772 GAAAAAGT
1 AAAAAAGT
12780 AAAAATAACT
Statistics
Matches: 453, Mismatches: 23, Indels: 33
0.89 0.05 0.06
Matches are distributed among these distances:
226 118 0.26
227 2 0.00
231 6 0.01
233 1 0.00
237 3 0.01
238 1 0.00
240 1 0.00
245 79 0.17
247 12 0.03
248 143 0.32
249 87 0.19
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (243 bp):
AAAAAAGTTGTATTGAAATAATTTGGGTACAAATTACTCCTTCCATCTCACTAAATGTGTTCATT
ATTGACTTTCAAAAAGTAAAAAAAATATAGAAAGTCATTAGTTTTATTAAAAATAAAAATATCCA
AAATTACAATGAAGATTTACAAGCATAACCGTAAACCTAAAATATAATTATGACATTTTTCTATT
ACCATAGAGACAAAAATTAGCCACTTATATCACATAAGGACCAAGAAG
Found at i:13277 original size:41 final size:41
Alignment explanation
Indices: 13191--13391 Score: 133
Period size: 41 Copynumber: 4.9 Consensus size: 41
13181 CGTTTTTTGA
* * * ** * *
13191 ACAAACGCCGCAAAAGACTC-TGACTTTCGTGGTGTTTGTAA
1 ACAAACGCCACTAAAGACTCAT-ACTTTAGTGGCATTTTTAT
* *
13232 ACAAACGCCCCTAAAGACTCATA-TTATAGTGGGGA-TTTTAT
1 ACAAACGCCACTAAAGACTCATACTT-TAGT-GGCATTTTTAT
* *
13273 ACAAACGCCGCTATAA-ACTCGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCACTA-AAGACTCATACTTTAGTGGCATTTTTAT
* * ** *
13314 ACAAACGTCACTAAAGACTCGTACTTTAGTGGTGTTTTTGT
1 ACAAACGCCACTAAAGACTCATACTTTAGTGGCATTTTTAT
* * * * *
13355 AAAAATGCCGCTATAA-ACTCGTATTTTAGTGGCATTT
1 ACAAACGCCACTA-AAGACTCATACTTTAGTGGCATTT
13392 GTGTTTACAA
Statistics
Matches: 130, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
40 7 0.05
41 114 0.88
42 9 0.07
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (41 bp):
ACAAACGCCACTAAAGACTCATACTTTAGTGGCATTTTTAT
Found at i:13330 original size:82 final size:84
Alignment explanation
Indices: 13227--13406 Score: 231
Period size: 82 Copynumber: 2.2 Consensus size: 84
13217 TCGTGGTGTT
* * * *
13227 TGTAAACAAACGCCCCTAAAGACTCATA-TTATAGTGGGGATTTTATACAAACGCCGCTATAAAC
1 TGTATACAAACGTCACTAAAGACTCATACTT-TAGTGGGGATTTTATAAAAACGCCGCTATAAAC
13291 TCGTACTTTAGTGGCATTT-
65 TCGTACTTTAGTGGCATTTG
* * * * *
13310 T-TATACAAACGTCACTAAAGACTCGTACTTTAGTGGTGTTTTTGTAAAAATGCCGCTATAAACT
1 TGTATACAAACGTCACTAAAGACTCATACTTTAGTGGGGATTTTATAAAAACGCCGCTATAAACT
*
13374 CGTATTTTAGTGGCATTTG
66 CGTACTTTAGTGGCATTTG
*
13393 TGTTTACAAACGTC
1 TGTATACAAACGTC
13407 GTAAGTTTAC
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
82 68 0.82
83 4 0.05
84 11 0.13
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (84 bp):
TGTATACAAACGTCACTAAAGACTCATACTTTAGTGGGGATTTTATAAAAACGCCGCTATAAACT
CGTACTTTAGTGGCATTTG
Found at i:13940 original size:21 final size:21
Alignment explanation
Indices: 13914--13972 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
13904 TGATATATTA
*
13914 TTATGGATTTCAATTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
13935 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
**
13956 TTATGGATGGCAAGTTT
1 TTATGGATTTCAAGTTT
13973 ATTGGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:14773 original size:41 final size:41
Alignment explanation
Indices: 14728--14829 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 41
14718 ATTCGTAATG
*
14728 TAGTGGCGTTTTTATACAAACGTC-ACTAAAAACTCA-TACTT
1 TAGTGGCGTTTTTATACAAACGCCGA-TAAAAACT-AGTACTT
* * * *
14769 TAGTGGTGTTTTTGTACAAATGCCGATATAAACTAGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGATAAAAACTAGTACTT
* *
14810 TTGTGGCATTTTTATACAAA
1 TAGTGGCGTTTTTATACAAA
14830 TGTTGCTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
40 1 0.02
41 48 0.96
42 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGATAAAAACTAGTACTT
Found at i:25753 original size:44 final size:44
Alignment explanation
Indices: 25702--25810 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
25692 ACGTAGTCAA
* *
25702 TAGCGGTGTTTTTAGGAACAAACACCACTATATGACATAACATT
1 TAGCGGTGTTTTTAGGAACAAACACAACTATATGACAGAACATT
* * *
25746 TAGCGGTGTTTTTGGGAATAAACACAACTATATGTCAGAACATT
1 TAGCGGTGTTTTTAGGAACAAACACAACTATATGACAGAACATT
* *
25790 TAGCGGCGTTTTTTGG-ACAAA
1 TAGCGGTGTTTTTAGGAACAAA
25811 ATGCTACAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 4 0.07
44 53 0.93
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (44 bp):
TAGCGGTGTTTTTAGGAACAAACACAACTATATGACAGAACATT
Found at i:26478 original size:2 final size:2
Alignment explanation
Indices: 26471--26578 Score: 216
Period size: 2 Copynumber: 54.0 Consensus size: 2
26461 TGATGTTTTA
26471 AT 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 AT
26513 AT 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 AT
26555 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
26579 TTTTTAATTT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 106 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27048 original size:17 final size:18
Alignment explanation
Indices: 27015--27049 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27005 TGCAAAAACA
27015 AATACCTAAAAATATTTT
1 AATACCTAAAAATATTTT
*
27033 AATATCTAAAAA-ATTTT
1 AATACCTAAAAATATTTT
27050 CATTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
AATACCTAAAAATATTTT
Found at i:32298 original size:25 final size:24
Alignment explanation
Indices: 32270--32316 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
32260 ATAAAAATTT
* *
32270 ATTTTTATTTCCTTAAGATTTTAAA
1 ATTTATATTTACTT-AGATTTTAAA
*
32295 ATTTATCTTTACTTAGATTTTA
1 ATTTATATTTACTTAGATTTTA
32317 TAATATCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTTATATTTACTTAGATTTTAAA
Found at i:32751 original size:41 final size:42
Alignment explanation
Indices: 32686--32764 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 42
32676 ATAGATAATT
** * *
32686 AATATAATTTAATTTTTTTAATTAATAAAATTTTATTTGGTC
1 AATATAATTTAATTTTTCCAATTAACAAAAATTTATTTGGTC
*
32728 AATATAATTT-ATTTTTCCGATTAACAAAAATTTATTT
1 AATATAATTTAATTTTTCCAATTAACAAAAATTTATTT
32765 ATACCTTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 22 0.69
42 10 0.31
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (42 bp):
AATATAATTTAATTTTTCCAATTAACAAAAATTTATTTGGTC
Found at i:33132 original size:29 final size:31
Alignment explanation
Indices: 33086--33148 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
33076 CAAATTATTG
** *
33086 TAACATTATAATTTTTAA-TATTATT-TTAA
1 TAACATTATAATAATTAATTAATATTATTAA
*
33115 TAACATTTTAATAATTAATTAATATTATTAA
1 TAACATTATAATAATTAATTAATATTATTAA
33146 TAA
1 TAA
33149 TATATTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.54
30 6 0.21
31 7 0.25
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (31 bp):
TAACATTATAATAATTAATTAATATTATTAA
Found at i:33166 original size:19 final size:19
Alignment explanation
Indices: 33119--33205 Score: 78
Period size: 20 Copynumber: 4.8 Consensus size: 19
33109 TTTTAATAAC
*
33119 ATTTTAATAAT-TAATTAAT
1 ATTTTAATAATAT-ATTATT
33138 ATTATTAATAATATATTATT
1 ATT-TTAATAATATATTATT
*
33158 ATTTTAATAAT-TAGTA-T
1 ATTTTAATAATATATTATT
*
33175 AATTT-ATAATA-ATT-TT
1 ATTTTAATAATATATTATT
*
33191 ATTTTAATAAAATAT
1 ATTTTAATAATATAT
33206 AACAATATCA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
16 12 0.21
17 10 0.18
18 6 0.11
19 11 0.20
20 16 0.29
21 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (19 bp):
ATTTTAATAATATATTATT
Found at i:33184 original size:35 final size:33
Alignment explanation
Indices: 33130--33207 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 33
33120 TTTTAATAAT
*
33130 TAATTAATATTATTAATAATATATTATTATTTTAA
1 TAATTAATATAATTAATAATA-ATT-TTATTTTAA
* *
33165 TAATTAGTATAATTTATAATAATTTTATTTTAA
1 TAATTAATATAATTAATAATAATTTTATTTTAA
33198 TAA--AATATAA
1 TAATTAATATAA
33208 CAATATCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 6 0.15
33 12 0.31
34 3 0.08
35 18 0.46
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
TAATTAATATAATTAATAATAATTTTATTTTAA
Found at i:35932 original size:21 final size:20
Alignment explanation
Indices: 35908--35956 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
35898 TAGCTATTTT
* *
35908 GTTAAAAGTTATTTATGAATA
1 GTTAAAA-TTATATATGAAAA
*
35929 GTTAGCAATTATATATGAAAA
1 GTTA-AAATTATATATGAAAA
35950 GTTAAAA
1 GTTAAAA
35957 ATAAAGATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (20 bp):
GTTAAAATTATATATGAAAA
Found at i:37920 original size:64 final size:63
Alignment explanation
Indices: 37831--37981 Score: 187
Period size: 64 Copynumber: 2.3 Consensus size: 63
37821 ATGCACATTC
* * * *
37831 ATAAGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATA
1 ATAA-TGCATCGATGCA-TCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCACA
* *
37895 GATAATGCATCGATGCATCCTTTTAAAATAAAAACATCGAATGCATTTTATGCACCGATGCACA
1 -ATAATGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCACA
*
37959 AGTAGTGCATCGATGCATACCTT
1 A-TAATGCATCGATGCAT-CCTT
37982 CATTGAAAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
63 4 0.05
64 64 0.84
65 8 0.11
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (63 bp):
ATAATGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCACA
Found at i:38462 original size:14 final size:14
Alignment explanation
Indices: 38440--38481 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
38430 TATATGTGAT
*
38440 ATGAATTACATGAA
1 ATGATTTACATGAA
38454 ATGATTTACATGAA
1 ATGATTTACATGAA
38468 ATGATTTACATGAA
1 ATGATTTACATGAA
38482 TACATGTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (14 bp):
ATGATTTACATGAA
Found at i:42103 original size:64 final size:63
Alignment explanation
Indices: 42014--42164 Score: 187
Period size: 64 Copynumber: 2.3 Consensus size: 63
42004 ATGCACATTC
* * * *
42014 ATAAGTGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATA
1 ATAA-TGCATCGATGCA-TCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCACA
* *
42078 GATAATGCATCGATGCATCCTTTTAAAATAAAAACATCGAATGCATTTTATGCACCGATGCACA
1 -ATAATGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCACA
*
42142 AGTAGTGCATCGATGCATACCTT
1 A-TAATGCATCGATGCAT-CCTT
42165 CATTGAAAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
63 4 0.05
64 64 0.84
65 8 0.11
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (63 bp):
ATAATGCATCGATGCATCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCACA
Found at i:45296 original size:55 final size:55
Alignment explanation
Indices: 45208--45326 Score: 211
Period size: 55 Copynumber: 2.2 Consensus size: 55
45198 ATTGTATGAG
*
45208 TGTGTATCGGTACACTGAGGAGTGTATCGATACACTCAAAACATCAAATACCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCAATACACTCAAAACATCAAATACCATT
* *
45263 TGTGTATCGGTACACTGAGGAGTGTATCAATACACTCAAAACATCGAATGCCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCAATACACTCAAAACATCAAATACCATT
45318 TGTGTATCG
1 TGTGTATCG
45327 ATGCCCTCAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCAATACACTCAAAACATCAAATACCATT
Found at i:45323 original size:35 final size:34
Alignment explanation
Indices: 45284--45367 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
45274 ACACTGAGGA
45284 GTGTATCAATACACTCAAAACATCGAATGCCATTT
1 GTGTATCAATACACTC-AAACATCGAATGCCATTT
* * * * **
45319 GTGTATCGATGCCCTCAAACATCGAGTGTTATTT
1 GTGTATCAATACACTCAAACATCGAATGCCATTT
*
45353 GTGTATCAGTACACT
1 GTGTATCAATACACT
45368 GAGGAGTGTT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
34 26 0.67
35 13 0.33
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (34 bp):
GTGTATCAATACACTCAAACATCGAATGCCATTT
Found at i:45753 original size:21 final size:21
Alignment explanation
Indices: 45725--45773 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
45715 TGTGTTAGGA
*
45725 AATA-GAACTTTGAA-CATGTG
1 AATATGAACTTCGAATCA-GTG
45745 AATATGAACTTCGAATCAGTG
1 AATATGAACTTCGAATCAGTG
*
45766 AATGTGAA
1 AATATGAA
45774 TATACTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 19 0.76
22 2 0.08
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (21 bp):
AATATGAACTTCGAATCAGTG
Found at i:46011 original size:22 final size:22
Alignment explanation
Indices: 45903--46012 Score: 70
Period size: 22 Copynumber: 5.1 Consensus size: 22
45893 GTCGAGGGTC
45903 TATGTGGTC-CTTCGG-GACAAAT
1 TATGTGG-CACTTCGGTG-CAAAT
**
45925 T-TGTGGCACTTCGGTGCAACC
1 TATGTGGCACTTCGGTGCAAAT
** *
45946 TATGTGGCACTTTAGTGCAACT
1 TATGTGGCACTTCGGTGCAAAT
* * *
45968 TATATGATC-CTT--GTGGACAAT
1 TATGTG-GCACTTCGGTGCA-AAT
45989 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
46011 TA
1 TA
46013 CGAGCTGTGG
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
20 6 0.09
21 25 0.37
22 32 0.47
23 5 0.07
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAT
Done.