Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006069.1 Hibiscus syriacus cultivar Beakdansim tig00014354_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: 99443
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:5765 original size:13 final size:13
Alignment explanation
Indices: 5744--5808 Score: 94
Period size: 13 Copynumber: 5.0 Consensus size: 13
5734 AATGACGCGC
5744 AATGCGCGTCATA
1 AATGCGCGTCATA
*
5757 AATGTGCGTCATA
1 AATGCGCGTCATA
*
5770 AATGCGTGTCATA
1 AATGCGCGTCATA
*
5783 AATGTGCGTCATA
1 AATGCGCGTCATA
*
5796 AATGCGTGTCATA
1 AATGCGCGTCATA
5809 GATTTATGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:5773 original size:26 final size:26
Alignment explanation
Indices: 5744--5808 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
5734 AATGACGCGC
*
5744 AATGCGCGTCATAAATGTGCGTCATA
1 AATGCGTGTCATAAATGTGCGTCATA
5770 AATGCGTGTCATAAATGTGCGTCATA
1 AATGCGTGTCATAAATGTGCGTCATA
5796 AATGCGTGTCATA
1 AATGCGTGTCATA
5809 GATTTATGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (26 bp):
AATGCGTGTCATAAATGTGCGTCATA
Found at i:9335 original size:27 final size:27
Alignment explanation
Indices: 9297--9358 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
9287 GATAATGGCT
9297 CTGAATCATTCAGAATGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
*
9324 CTGAATCATTCAGAATGTACTTTTATG
1 CTGAATCATTCAGAATGTACTTCTATG
9351 CTGAATCA
1 CTGAATCA
9359 GTCAACACTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTATG
Found at i:9447 original size:33 final size:33
Alignment explanation
Indices: 9409--9482 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
9399 CAGAGGTACA
*
9409 AAACAAACGCGCTGAATGGTTCCATTAAGAGGC
1 AAACAAACGCGCTGAATGATTCCATTAAGAGGC
*
9442 AAACAAACGTGCTGAATGATTCCATTAAGAGGC
1 AAACAAACGCGCTGAATGATTCCATTAAGAGGC
9475 AAACAAAC
1 AAACAAAC
9483 AACCCCTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (33 bp):
AAACAAACGCGCTGAATGATTCCATTAAGAGGC
Found at i:13231 original size:66 final size:66
Alignment explanation
Indices: 13145--13277 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
13135 ACTATAGTTA
13145 ATGTTCAGTCTTTTTTTGGGGAGGAAGAAAAAGTAGAGAGAATGTTGAGTGTTGAATATGTTGCT
1 ATGTTCAGTCTTTTTTTGGGGAGGAAGAAAAAGTAGAGAGAATGTTGAGTGTTGAATATGTTGCT
13210 G
66 G
* * *
13211 ATGTTCAGTCTTTTTTTGGGGAGGAAGAAAAGGTAGAGAGAATGTTGAGTGTTTAATATGTTTCT
1 ATGTTCAGTCTTTTTTTGGGGAGGAAGAAAAAGTAGAGAGAATGTTGAGTGTTGAATATGTTGCT
13276 G
66 G
13277 A
1 A
13278 CGTGTGTAGG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.29, C:0.05, G:0.31, T:0.36
Consensus pattern (66 bp):
ATGTTCAGTCTTTTTTTGGGGAGGAAGAAAAAGTAGAGAGAATGTTGAGTGTTGAATATGTTGCT
G
Found at i:17237 original size:26 final size:24
Alignment explanation
Indices: 17198--17245 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
17188 TAATCTATTT
17198 TTTATTATTCTAAAATTTTATAAA
1 TTTATTATTCTAAAATTTTATAAA
*
17222 TTTATATATTACTAAATTTTTATA
1 TTTAT-TATT-CTAAAATTTTATA
17246 TTTTTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 4 0.19
26 12 0.57
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTATTATTCTAAAATTTTATAAA
Found at i:26295 original size:22 final size:21
Alignment explanation
Indices: 26253--26292 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
26243 GAGTTTATTT
*
26253 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
26274 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
26293 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:28273 original size:18 final size:17
Alignment explanation
Indices: 28219--28267 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
28209 TTGGACCCTT
* *
28219 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
28237 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
28255 AGTGCATTCGATG
1 AGTGCA-TCGATG
28268 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:28369 original size:17 final size:19
Alignment explanation
Indices: 28331--28377 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
28321 AAATCCTTAG
*
28331 TGCATCGGTGCATGGTAAA
1 TGCATCGATGCATGGTAAA
28350 TGCATCGATGCAT-G-AAA
1 TGCATCGATGCATGGTAAA
28367 TGCATTCGATG
1 TGCA-TCGATG
28378 TTCAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.27
18 7 0.27
19 12 0.46
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (19 bp):
TGCATCGATGCATGGTAAA
Found at i:28390 original size:65 final size:63
Alignment explanation
Indices: 28285--28409 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 63
28275 ATAGCCAGAG
* *
28285 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGGTAAA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CATAGTGCATCGATGCATGGTAAA
* * *
28350 TGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAATCATGGTGCATCGATGCATGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTC-A-TAAAATCATAGTGCATCGATGCATGG
28410 ATTGGTGCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
63 3 0.06
64 18 0.34
65 32 0.60
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (63 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCATAGTGCATCGATGCATGGTAAA
Found at i:32098 original size:18 final size:18
Alignment explanation
Indices: 32060--32099 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
32050 TTAGGAAGCT
* **
32060 GTTAGTTTGTTAAGATTA
1 GTTAGCTTGTTAAGAGCA
32078 GTTAGCTTGTTAAGAGCA
1 GTTAGCTTGTTAAGAGCA
32096 GTTA
1 GTTA
32100 TGAGTTGCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (18 bp):
GTTAGCTTGTTAAGAGCA
Found at i:33022 original size:15 final size:16
Alignment explanation
Indices: 33002--33032 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
32992 AGAAAAATCC
33002 ACTATAATA-TTTAAA
1 ACTATAATAGTTTAAA
33017 ACTATAATAGTTTAAA
1 ACTATAATAGTTTAAA
33033 CGTACTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
ACTATAATAGTTTAAA
Found at i:34208 original size:111 final size:111
Alignment explanation
Indices: 34014--34235 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
34004 TGGAAATCAT
* *
34014 ATATCTCTACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
34079 TATTTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
34125 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
34190 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
34236 TTTTTGTAAT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:35771 original size:18 final size:18
Alignment explanation
Indices: 35748--35783 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35738 CAGCCACCAG
35748 AGCCATATATGATGCCGC
1 AGCCATATATGATGCCGC
35766 AGCCATATATGATGCCGC
1 AGCCATATATGATGCCGC
35784 CATCGCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (18 bp):
AGCCATATATGATGCCGC
Found at i:36134 original size:6 final size:6
Alignment explanation
Indices: 36119--36180 Score: 55
Period size: 6 Copynumber: 11.3 Consensus size: 6
36109 ACCTGCTCAA
*
36119 GACGAC GACGAT GACGAT GACGAT ---GAT GACGAT GACGAT G--G-T
1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT
* *
36161 GACGAC AACGAT GACGAT GA
1 GACGAT GACGAT GACGAT GA
36181 TGACGACAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
3 5 0.11
4 1 0.02
5 1 0.02
6 38 0.84
ACGTcount: A:0.34, C:0.18, G:0.34, T:0.15
Consensus pattern (6 bp):
GACGAT
Found at i:36146 original size:9 final size:9
Alignment explanation
Indices: 36134--36186 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
36124 CGACGATGAC
36134 GATGACGAT
1 GATGACGAT
36143 GATGACGAT
1 GATGACGAT
* * *
36152 GACGATGGT
1 GATGACGAT
* * *
36161 GACGACAAC
1 GATGACGAT
36170 GATGACGAT
1 GATGACGAT
36179 GATGACGA
1 GATGACGA
36187 CAACGAGGAG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.34, T:0.17
Consensus pattern (9 bp):
GATGACGAT
Found at i:36151 original size:21 final size:21
Alignment explanation
Indices: 36147--36192 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
36137 GACGATGATG
*
36147 ACGATGACGATGGTGACGACA
1 ACGATGACGATGATGACGACA
36168 ACGATGACGATGATGACGACA
1 ACGATGACGATGATGACGACA
36189 ACGA
1 ACGA
36193 GGAGTCAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (21 bp):
ACGATGACGATGATGACGACA
Found at i:36192 original size:15 final size:15
Alignment explanation
Indices: 36122--36186 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
36112 TGCTCAAGAC
*
36122 GACGACGATGACGAT
1 GACGATGATGACGAT
36137 GACGATGATGACGAT
1 GACGATGATGACGAT
* *
36152 GACGATGGTGACGAC
1 GACGATGATGACGAT
* * *
36167 AACGATGACGATGAT
1 GACGATGATGACGAT
36182 GACGA
1 GACGA
36187 CAACGAGGAG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.15
Consensus pattern (15 bp):
GACGATGATGACGAT
Found at i:41115 original size:201 final size:198
Alignment explanation
Indices: 40737--41245 Score: 524
Period size: 201 Copynumber: 2.6 Consensus size: 198
40727 TTGGCTTTGT
* * *
40737 GCATGAAGAACAAACTAAAATTGCTTGATAGGCATGCTCGAGGGTTATTTCCGAGAAGATAATCC
1 GCATGAAGAA-AAACTAAAATGGCTTGATAGGCATGTTCGAGGGGTATTTCCGAGAAGATAATCC
* * *
40802 ATTTTTTTCTAATTTTTAAGCTTGAAGGCGTAGTATTACAACTTATCTTTCAATTGAAGATAATA
65 ATTTTTTTATAATTTTAAAGCTTAAAGGCGTAGTATTACAACTTATCTTTCAATTGAAGATAATA
* * * *
40867 TCAACACATACAAGAAATTGTAAATGGGGTAAAAATTGCGTTGAAAATGGTTCCAAACCTGGGTT
130 TCAACACATACAAGAAATTGTAAATGAGGCAAAAATCGCGTTGAAAATGATTCCAAACCTGGGTT
40932 TTAC
195 TTAC
* * * * * **
40936 GCATGAAGAAATAACTAGACTGGCTTGGTAGTCATGTTCGAGGGGTATTTCTGAGAAGATAATTG
1 GCATGAAGAAA-AACTAAAATGGCTTGATAGGCATGTTCGAGGGGTATTTCCGAGAAGATAATCC
** * * * * * *
41001 ATTTTTTTTTATAATTTTAAAGCTTAAAGGTTTTGTATTACAACTTATGTTTTAGTTGAGGGTAA
65 A--TTTTTTTATAATTTTAAAGCTTAAAGGCGTAGTATTACAACTTATCTTTCAATTGAAGATAA
* * * * * *
41066 TATCAGCACATGCAAGACATTGTAAGTGAGGCAAAAATCGCGTTGAAAATGATTCCAAAGCTTGG
128 TATCAACACATACAAGAAATTGTAAATGAGGCAAAAATCGCGTTGAAAATGATTCCAAACCTGGG
**
41131 TTTTGT
193 TTTTAC
* * * *
41137 GCATGAA-AAACAAGTTAAAATGGCTTGTTAGGCATGTTGGAGGGGTATTTCC-AGGAAGTTAA-
1 GCATGAAGAAA-AA-CTAAAATGGCTTGATAGGCATGTTCGAGGGGTATTTCCGA-GAAGATAAT
* * ** *
41199 CCGGATTTTTTTAT--TTTTTAATCTTAGTGGTGTAGTATTACAACTTA
63 CC--ATTTTTTTATAATTTTAAAGCTTAAAGGCGTAGTATTACAACTTA
41246 CCTGTCAGTT
Statistics
Matches: 253, Mismatches: 50, Indels: 15
0.80 0.16 0.05
Matches are distributed among these distances:
198 28 0.11
199 54 0.21
200 15 0.06
201 155 0.61
202 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (198 bp):
GCATGAAGAAAAACTAAAATGGCTTGATAGGCATGTTCGAGGGGTATTTCCGAGAAGATAATCCA
TTTTTTTATAATTTTAAAGCTTAAAGGCGTAGTATTACAACTTATCTTTCAATTGAAGATAATAT
CAACACATACAAGAAATTGTAAATGAGGCAAAAATCGCGTTGAAAATGATTCCAAACCTGGGTTT
TAC
Found at i:43101 original size:70 final size:70
Alignment explanation
Indices: 43019--43163 Score: 245
Period size: 70 Copynumber: 2.1 Consensus size: 70
43009 AGTAAGCCAG
* **
43019 ATTCAGTAATAGCGAAAATCATGTGCTTCGAGAATATCAATGAACCGAGAACGTATAAGTTATTC
1 ATTCAGTAATAGCAAAAATCATGTGCTTCGAGAATATCAATGAACCGAGAACGTATAAGGCATTC
*
43084 CTTTA
66 CCTTA
*
43089 ATTCAGTAATAGCAAAAATCATGTTCTTCGAGAATATCAATGAACCGAGAACGTATAAGGCATTC
1 ATTCAGTAATAGCAAAAATCATGTGCTTCGAGAATATCAATGAACCGAGAACGTATAAGGCATTC
43154 CCTTA
66 CCTTA
43159 ATTCA
1 ATTCA
43164 AGGGTATTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (70 bp):
ATTCAGTAATAGCAAAAATCATGTGCTTCGAGAATATCAATGAACCGAGAACGTATAAGGCATTC
CCTTA
Found at i:46792 original size:22 final size:22
Alignment explanation
Indices: 46754--46795 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
46744 ATTCTTATTT
*
46754 TATTAATATATAGTTAAAATAA
1 TATTAATATATAATTAAAATAA
46776 TATT-ATATATAAATTAAAAT
1 TATTAATATAT-AATTAAAAT
46796 TTCAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAATATATAATTAAAATAA
Found at i:49237 original size:20 final size:20
Alignment explanation
Indices: 49209--49281 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
49199 ATTTTATAGT
49209 ATTTATATAAATTTATTAATA
1 ATTT-TATAAATTTATTAATA
*
49230 ATTTTATAATTTTA-TAATAA
1 ATTTTATAAATTTATTAAT-A
* *
49250 ATTTAATAAGTATT-TT-ATA
1 ATTTTATAAAT-TTATTAATA
*
49269 ATTTTTTAAATTT
1 ATTTTATAAATTT
49282 TTTTGACGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
18 2 0.05
19 13 0.30
20 21 0.49
21 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (20 bp):
ATTTTATAAATTTATTAATA
Found at i:49237 original size:31 final size:30
Alignment explanation
Indices: 49191--49273 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 30
49181 TTCGATAATA
*
49191 TAATAATTATTTTATAGTATTTAT-ATAAATT
1 TAATAA-TATTTTATAAT-TTTATAATAAATT
*
49222 TATTAATAATTTTATAATTTTATAATAAATT
1 TAATAAT-ATTTTATAATTTTATAATAAATT
49253 TAATAAGTATTTTATAATTTT
1 TAATAA-TATTTTATAATTTT
49274 TTAAATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.13
31 39 0.85
32 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTATAATAAATT
Found at i:49240 original size:19 final size:19
Alignment explanation
Indices: 49214--49254 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
49204 ATAGTATTTA
* *
49214 TATAAATTTATTAATAATTT
1 TATAATTTTA-TAATAAATT
49234 TATAATTTTATAATAAATT
1 TATAATTTTATAATAAATT
49253 TA
1 TA
49255 ATAAGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAATTTTATAATAAATT
Found at i:50041 original size:31 final size:29
Alignment explanation
Indices: 49997--50089 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 29
49987 CAATAAAATT
49997 TTAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAATTATAAAATA-TTATTAAATTTA
*
50027 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAA-ATTATAAAA-TATTATTAAATTTA
* * *
50058 TCTAAATACTATAAAATAATTATTATATTTA
1 T-TAAAAATTATAAAAT-ATTATTAAATTTA
50089 T
1 T
50090 CAAACTCTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
30 7 0.13
31 41 0.76
32 6 0.11
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
TTAAAAATTATAAAATATTATTAAATTTA
Found at i:50102 original size:31 final size:30
Alignment explanation
Indices: 50004--50102 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 30
49994 ATTTTAAAAA
* * **
50004 TTATAAAATACTTATTAAATTTATTAAAAGA
1 TTATAAAATAATTATTAAATTTA-TCAAATC
* *
50035 TTATAAAATTATTAATAAATTTATCTAAATAC
1 TTATAAAATAATTATTAAATTTATC-AAAT-C
*
50067 -TATAAAATAATTATTATATTTATCAAACTC
1 TTATAAAATAATTATTAAATTTATCAAA-TC
50097 TTATAA
1 TTATAA
50103 TTTATTACAA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
30 5 0.09
31 50 0.91
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (30 bp):
TTATAAAATAATTATTAAATTTATCAAATC
Found at i:51026 original size:5 final size:5
Alignment explanation
Indices: 51018--51043 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
51008 AAAAAAAAAA
51018 AAAGC AAAGC AAAGC AAAGC AAAGC A
1 AAAGC AAAGC AAAGC AAAGC AAAGC A
51044 GCTTATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGC
Found at i:52868 original size:22 final size:24
Alignment explanation
Indices: 52839--52882 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
52829 TGAAATGAGG
52839 TAAATGA-TAA-A-ATTATTTTTT
1 TAAATGATTAATAGATTATTTTTT
52860 TAAAGTGATTAATAGATTATTTT
1 TAAA-TGATTAATAGATTATTTT
52883 GATAGGTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 3 0.16
24 1 0.05
25 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (24 bp):
TAAATGATTAATAGATTATTTTTT
Found at i:56973 original size:30 final size:29
Alignment explanation
Indices: 56937--57011 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
56927 AAATAATGAC
56937 TAAAATAAATAAAATTAAAACTATAGTA-TT
1 TAAAATAAATAAAATTAAAACT-T-GTAGTT
*
56967 TAAAATATAAAAAATATTAAAACTTGTAGTT
1 TAAAATA-AATAAA-ATTAAAACTTGTAGTT
*
56998 AAAAATAAATAAAA
1 TAAAATAAATAAAA
57012 GTATTAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 1 0.03
30 15 0.38
31 14 0.36
32 9 0.23
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.31
Consensus pattern (29 bp):
TAAAATAAATAAAATTAAAACTTGTAGTT
Found at i:57017 original size:32 final size:32
Alignment explanation
Indices: 56938--57019 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 32
56928 AATAATGACT
*
56938 AAAATAAAT-AAA-ATTAAAACTATAGTATTT
1 AAAATAAATAAAATATTAAAACTATAGTATTA
56968 AAAATATAA-AAAATATTAAAACT-T-GTAGTTA
1 AAAATA-AATAAAATATTAAAACTATAGTA-TTA
56999 AAAATAAATAAAAGTATTAAA
1 AAAATAAATAAAA-TATTAAA
57020 TTTAGTGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
30 11 0.24
31 18 0.40
32 16 0.36
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (32 bp):
AAAATAAATAAAATATTAAAACTATAGTATTA
Found at i:58191 original size:3 final size:3
Alignment explanation
Indices: 58183--58239 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
58173 ATTTTTTATT
** * *
58183 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA AAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
58231 TAA AAA TAA
1 TAA TAA TAA
58240 AATGAAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:58452 original size:45 final size:45
Alignment explanation
Indices: 58358--58978 Score: 1030
Period size: 45 Copynumber: 13.8 Consensus size: 45
58348 AAGATGAAAA
* *
58358 TTTTGAAAACATCATGAACTGAATGACTTA-AGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
* *
58402 TTTTGAAAATATCATGCATTGAAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
58447 TTTTGAAAACATCATGCACTGAAGGACTTACAGATG-CCTCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC-CGAAGG
*
58492 TTTTGAAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
* *
58537 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
**
58582 TTTTGAAAACATCATGCACTGAAGGGTTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
58627 TTTTGAAAACATTATGCACTGAAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
* * *
58672 TTTTGAAAACATCATGTACTGAAGGGCATACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
58717 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA-CCCGAAGG
*
58763 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
58808 TTTTGAAAACATCATGCACCGAAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
* *
58853 TTTTGAAAACATCATGCACTAAAGGACTTATAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
*
58898 TTTTGAAAACATCATGCACTGAATGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
* *
58943 TTTTGAAAACATTATGCACTGAAGGGCTTACAGATG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATG
58979 TGGGAAATAG
Statistics
Matches: 539, Mismatches: 34, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
44 28 0.05
45 465 0.86
46 46 0.09
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
Found at i:61072 original size:75 final size:75
Alignment explanation
Indices: 60944--61116 Score: 265
Period size: 75 Copynumber: 2.3 Consensus size: 75
60934 GATATAGGCC
* * * *
60944 TTCAGCATGCCCCAACATTTGCCAATACAAGCATTCAAAATGCGTCAACATTCCTCATTTTGATT
1 TTCAGCATGCCCCAGCATTTGCTAATACAAACATTCAAAATGCGTCAACATTCCTCATTATGATT
61009 GAAATGGGCT
66 GAAATGGGCT
* * * *
61019 TTCAGCATTCCCCAGCATTTGCTGATACAAACATTCAAAATGCGTCAATATTCCTGATTATGATT
1 TTCAGCATGCCCCAGCATTTGCTAATACAAACATTCAAAATGCGTCAACATTCCTCATTATGATT
61084 GAAATGGGCT
66 GAAATGGGCT
*
61094 TTCAGCATGCCTCAGCATTTGCT
1 TTCAGCATGCCCCAGCATTTGCT
61117 TATTGTTGAT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (75 bp):
TTCAGCATGCCCCAGCATTTGCTAATACAAACATTCAAAATGCGTCAACATTCCTCATTATGATT
GAAATGGGCT
Found at i:63577 original size:32 final size:32
Alignment explanation
Indices: 63541--63601 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
63531 TGAAGAAATA
*
63541 GTTGTTATGCTCATATTGTAGAGATACTTTTC
1 GTTGTTATGCTCATATCGTAGAGATACTTTTC
*
63573 GTTGTTATGCTCATCTCGTAGAGATACTT
1 GTTGTTATGCTCATATCGTAGAGATACTT
63602 CTTGTTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (32 bp):
GTTGTTATGCTCATATCGTAGAGATACTTTTC
Found at i:63997 original size:28 final size:28
Alignment explanation
Indices: 63946--64001 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
63936 TCCATAATCT
63946 GGATCTCTCTAGACTGCCAATTTTTTTG
1 GGATCTCTCTAGACTGCCAATTTTTTTG
63974 GGATC-CTCTAGACTGCCAATTTTTTTG
1 GGATCTCTCTAGACTGCCAATTTTTTTG
64001 G
1 G
64002 TTCATTTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (28 bp):
GGATCTCTCTAGACTGCCAATTTTTTTG
Found at i:64154 original size:9 final size:9
Alignment explanation
Indices: 64126--64166 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
64116 CTTGGTTAAA
64126 TTTTTCCTT
1 TTTTTCCTT
* *
64135 TTCTTCTTT
1 TTTTTCCTT
64144 TTTTTCCTT
1 TTTTTCCTT
64153 TTTTTCCTT
1 TTTTTCCTT
64162 TTTTT
1 TTTTT
64167 GACTGTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCCTT
Found at i:65292 original size:26 final size:27
Alignment explanation
Indices: 65240--65292 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
65230 TAGTTCTTTG
* *
65240 CCCTCTATTTTTTTTCTTCGTTGTTCT
1 CCCTCTATTCTTTTTCTTCATTGTTCT
65267 CCCTCT-TTCTTTTTCTGTCATT-TTCT
1 CCCTCTATTCTTTTTCT-TCATTGTTCT
65293 GTTCTTGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.04, C:0.28, G:0.06, T:0.62
Consensus pattern (27 bp):
CCCTCTATTCTTTTTCTTCATTGTTCT
Found at i:65560 original size:26 final size:26
Alignment explanation
Indices: 65531--65597 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
65521 GCGTCGACAG
*
65531 AGGCAGCTGCTGGGAACTCTTGGATA
1 AGGCGGCTGCTGGGAACTCTTGGATA
*
65557 AGGCGGCTGCTGAGAACTCTTGGATA
1 AGGCGGCTGCTGGGAACTCTTGGATA
*
65583 AGGCGGCAGCTGGGA
1 AGGCGGCTGCTGGGA
65598 GCTAGGTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.19
Consensus pattern (26 bp):
AGGCGGCTGCTGGGAACTCTTGGATA
Found at i:65733 original size:3 final size:3
Alignment explanation
Indices: 65725--65812 Score: 131
Period size: 3 Copynumber: 28.7 Consensus size: 3
65715 ATTTTTTATT
**
65725 TAA TAA TAA TAA TATA TATA TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
65772 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
65813 TGAAAAAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
3 71 0.91
4 7 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:69850 original size:17 final size:18
Alignment explanation
Indices: 69828--69877 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 18
69818 ATATAACACA
*
69828 TATGTCACGAAGGACC-C
1 TATGTCCCGAAGGACCAC
69845 TATGTCCCGAAGG-CCAC
1 TATGTCCCGAAGGACCAC
69862 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
69878 TCGTAGACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:70552 original size:18 final size:18
Alignment explanation
Indices: 70509--70554 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
70499 TTTAAGTTGG
**
70509 TGCATCGATGCACTCCTA
1 TGCATCGATGCACTAATA
70527 TGCATCGATGCACTAAT-
1 TGCATCGATGCACTAATA
70544 TGCATTCGATG
1 TGCA-TCGATG
70555 TTCATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (18 bp):
TGCATCGATGCACTAATA
Found at i:70982 original size:196 final size:192
Alignment explanation
Indices: 70680--71069 Score: 719
Period size: 196 Copynumber: 2.0 Consensus size: 192
70670 TAATATTCCT
70680 AACTTTCATACACATATTTACACTCATTCTTACTCAATAATCATTCTTTAACCTCAAATATCCTT
1 AACTTTCATACACATATTTACACTCATTCTTACTCAATAATCATTCTTTAACCTCAAATATCCTT
70745 TATATGGCATTGAAGAATCATACACAAATATCAACATGTTCTAAATCTCATCCTAACACTTCCAA
66 TATATGGCATTGAAGAATCATACACAAATATCAACATGTTCTAAATCTCATCCTAACACTTCCAA
70810 TTCCTTATTTAGATTGATGACAAGTCAAATCCAACTTCTAATTCTAATTATTAACTATAACA
131 TTCCTTATTTAGATTGATGACAAGTCAAATCCAACTTCTAATTCTAATTATTAACTATAACA
70872 AACTTTCATACACATATTTACACTCATTCTTACTCAATAATCACTTCTTT-ACCTCCAAATCATA
1 AACTTTCATACACATATTTACACTCATTCTTACTCAATAATCA-TTCTTTAACCT-C-AA--ATA
70936 TCCTTTATATGGCATTGAAGAATCATACACAAATATCAACATGTTCTAAATCTCATCCTAACACT
61 TCCTTTATATGGCATTGAAGAATCATACACAAATATCAACATGTTCTAAATCTCATCCTAACACT
*
71001 TCCAATTCCTTATTTAGATTGATGACAAGTCAAATCCAACTTCTAATTCTAATTATTAACTCTAA
126 TCCAATTCCTTATTTAGATTGATGACAAGTCAAATCCAACTTCTAATTCTAATTATTAACTATAA
71066 CA
191 CA
71068 AA
1 AA
71070 ATTTTATTCA
Statistics
Matches: 192, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
192 47 0.24
193 7 0.04
194 2 0.01
196 136 0.71
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.36
Consensus pattern (192 bp):
AACTTTCATACACATATTTACACTCATTCTTACTCAATAATCATTCTTTAACCTCAAATATCCTT
TATATGGCATTGAAGAATCATACACAAATATCAACATGTTCTAAATCTCATCCTAACACTTCCAA
TTCCTTATTTAGATTGATGACAAGTCAAATCCAACTTCTAATTCTAATTATTAACTATAACA
Found at i:74028 original size:18 final size:18
Alignment explanation
Indices: 74001--74036 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
73991 ATATAACACA
*
74001 TATGTTCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
74019 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
74037 GTAGACTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:78297 original size:18 final size:18
Alignment explanation
Indices: 78270--78305 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
78260 ATATAACACA
*
78270 TATGTTCCGAAGAACCAC
1 TATGTCCCGAAGAACCAC
*
78288 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGAACCAC
78306 GTAGACCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (18 bp):
TATGTCCCGAAGAACCAC
Found at i:79182 original size:19 final size:19
Alignment explanation
Indices: 79154--79205 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
79144 TTTAAGTAGT
*
79154 TGCATTGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
79173 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
79192 TGCATCGATGCACT
1 TGCATCGATGCACT
79206 AATTGCATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:80412 original size:17 final size:17
Alignment explanation
Indices: 80372--80412 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
80362 TCATATTTAC
*
80372 CCCTTTAATTTCCTTTT
1 CCCTTTAATTTCCTTAT
* *
80389 TCATTTAATTTCCTTAT
1 CCCTTTAATTTCCTTAT
80406 CCCTTTA
1 CCCTTTA
80413 CTCATTCACA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.56
Consensus pattern (17 bp):
CCCTTTAATTTCCTTAT
Found at i:83104 original size:13 final size:13
Alignment explanation
Indices: 83086--83111 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
83076 TTAATTTCCA
83086 TATAATCATATAC
1 TATAATCATATAC
83099 TATAATCATATAC
1 TATAATCATATAC
83112 ACTCACCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TATAATCATATAC
Found at i:83413 original size:19 final size:19
Alignment explanation
Indices: 83387--83476 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
83377 TTTAGGCAGG
83387 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
* * *
83406 TACATCGATGGACTTCTTA
1 TGCATCGATGCACTCCTTA
83425 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
83444 TGCATCGATGTACTCCTTA
1 TGCATCGATGCACTCCTTA
83463 TGCATCGATGCACT
1 TGCATCGATGCACT
83477 AATTGCTTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:88902 original size:52 final size:52
Alignment explanation
Indices: 88824--88926 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
88814 TTATAATATT
*
88824 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGTTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
88876 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
88927 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:93475 original size:52 final size:52
Alignment explanation
Indices: 93397--93499 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
93387 TTATAATATT
93397 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
93449 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
93500 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:94315 original size:2 final size:2
Alignment explanation
Indices: 94308--94375 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
94298 ATCATAGTAC
94308 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
94350 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
94376 GCTATTAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99425 original size:70 final size:70
Alignment explanation
Indices: 99312--99443 Score: 264
Period size: 70 Copynumber: 1.9 Consensus size: 70
99302 TCGATCAACA
99312 ATCATTCTGGCACATTGATTATTCACTGTTTGATTCTTTGACTCATCATTGTTTTAAAGAATAGT
1 ATCATTCTGGCACATTGATTATTCACTGTTTGATTCTTTGACTCATCATTGTTTTAAAGAATAGT
99377 CAGGT
66 CAGGT
99382 ATCATTCTGGCACATTGATTATTCACTGTTTGATTCTTTGACTCATCATTGTTTTAAAGAAT
1 ATCATTCTGGCACATTGATTATTCACTGTTTGATTCTTTGACTCATCATTGTTTTAAAGAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (70 bp):
ATCATTCTGGCACATTGATTATTCACTGTTTGATTCTTTGACTCATCATTGTTTTAAAGAATAGT
CAGGT
Done.