Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006306.1 Hibiscus syriacus cultivar Beakdansim tig00015070_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: 65064
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1278 original size:8 final size:8
Alignment explanation
Indices: 1265--1305 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1255 CTCATTTTCA
1265 GAGAATTT
1 GAGAATTT
1273 GAGAATTT
1 GAGAATTT
*
1281 -AGAGTTT
1 GAGAATTT
*
1288 GGGAATTT
1 GAGAATTT
1296 GAGAATTT
1 GAGAATTT
1304 GA
1 GA
1306 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1710 original size:127 final size:127
Alignment explanation
Indices: 1377--2355 Score: 1471
Period size: 127 Copynumber: 7.9 Consensus size: 127
1367 ATCGGAGTAT
1377 TATTCACATGAAGGCGCGTTCCCGGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
1 TATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
1441 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAG--ATATCAGTACCTATTATTTCAC
66 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
1501 TATTCACATGAA-G-GCGTTCCGGGGGCG-GCCTTCCATTATTTCATCAGAGAATATGTTATCAT
1 TATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
*
1563 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
***
1625 -AGGGGACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TA-TTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1689 TTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTCAC
65 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
1751 TATTCACATGAAGGCGCATCCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1816 TTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTA-TTCAC
65 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
1877 TATTCACATGAAGGCACGTTCCCGGGG-GCGCGCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGCGCGC-CTTCCATTATTTCGTCAGAGAATATGTTATCA
* *
1941 TTGTCCTATTATGTCACTCA------T-----ACACTAGATATATCAGTACCTA-TATTTCTC
65 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** *
1992 -AAGGACATGAAGGCGCGTTCCTGGGGGGCGCGCCTTCCA-TATTTCGTCAGAGAATATGTTATC
1 TATTCACATGAAGGCGCGTTCC--CGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
2055 ATTGCCCTATTATGTCACTCATGT-CCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
64 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
2118 TATTCACATGAAGGCGCGTT-CCGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCAT
1 TATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
*
2182 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * *
2244 -AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
2308 ATTGCCCTATTA--TCACTCA-GTCCCTCGGGGACACTAGATATATCAGTA
64 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2356 AATCAGGTAA
Statistics
Matches: 784, Mismatches: 40, Indels: 61
0.89 0.05 0.07
Matches are distributed among these distances:
114 19 0.02
115 69 0.09
116 10 0.01
117 4 0.01
119 1 0.00
120 1 0.00
122 83 0.11
123 3 0.00
124 59 0.08
125 154 0.20
126 155 0.20
127 177 0.23
128 49 0.06
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (127 bp):
TATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:2049 original size:115 final size:119
Alignment explanation
Indices: 1846--2320 Score: 574
Period size: 115 Copynumber: 3.9 Consensus size: 119
1836 TGTCCCTCGG
* *
1846 GACACTAGATATATCAGTACCTATTA-TTCACTATTCACATGAAGGCACGTTCCCGGGGGCGCG-
1 GACACTAGATATATCAGTACCTATTATTTCACTATGCACATGAAGGCGCGTTCCCGGGGGCGCGC
*
1909 CTTCCATTATTTCATCAGAGAATATGTTATCATTGTCCTATTATGTCACTCA-T
66 CTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCACT
* * * *
1962 -ACACTAGATATATCAGTACCTA-TATTTCTC-AAGGACATGAAGGCGCGTTCCTGGGGGGCGCG
1 GACACTAGATATATCAGTACCTATTATTTCACTATGCACATGAAGGCGCGTTCC-CGGGGGCGCG
*
2024 CCTTCCA-TATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCT
65 CCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCA----CT
*
2082 CGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTT-CC-GGGGC
1 ----GACACTAGATATATCAGTACCTATTATTTCACTATGCACATGAAGGCGCGTTCCCGGGGGC
2145 GCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCT
62 GCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCA-----CT
* * *
2208 CGGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGGACATGAAGGCGCGTTCCCGGGGG
1 ----GACACTAGATATATCAGTACCTATTATTTCACTA-TGCACATGAAGGCGCGTTCCCGGGGG
** *
2272 CGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTAT
61 CGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTAT
2321 CACTCAGTCC
Statistics
Matches: 315, Mismatches: 24, Indels: 28
0.86 0.07 0.08
Matches are distributed among these distances:
114 19 0.06
115 78 0.25
116 6 0.02
120 1 0.00
124 15 0.05
125 67 0.21
126 61 0.19
127 18 0.06
128 50 0.16
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (119 bp):
GACACTAGATATATCAGTACCTATTATTTCACTATGCACATGAAGGCGCGTTCCCGGGGGCGCGC
CTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCACT
Found at i:2172 original size:125 final size:127
Alignment explanation
Indices: 1962--2355 Score: 581
Period size: 125 Copynumber: 3.1 Consensus size: 127
1952 TGTCACTCAT
* *** *
1962 ACACTAGATATATCAGTACCTA-TATTTCTC-AAGGACATGAAGGCGCGTTCCTGGGGGGCGCGC
1 ACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCC--CGGGGCGCGC
2025 CTTCCA-TATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT-CCTCGGGG
64 CTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
2087 ACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTT-CCGGGGCGCGCCT
1 ACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCT
*
2151 TCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
66 TCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* ***
2213 ACACTAGATATATCAGTACCTATTATTTCTC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGC
1 ACACTAGATATATCAGTACCTATTATTTCACTA-TTCACATGAAGGCGCGTTCCC-GGGGCGCGC
* *
2277 CTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTA--TCACTCA-GTCCCTCGGGG
64 CTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
2338 ACACTAGATATATCAGTA
1 ACACTAGATATATCAGTA
2356 AATCAGGTAA
Statistics
Matches: 249, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
124 15 0.06
125 99 0.40
126 68 0.27
127 18 0.07
128 49 0.20
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (127 bp):
ACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCT
TCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
Found at i:2301 original size:493 final size:493
Alignment explanation
Indices: 1377--2355 Score: 1505
Period size: 493 Copynumber: 2.0 Consensus size: 493
1367 ATCGGAGTAT
* *
1377 TATTCACATGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATT
1 TATTCACATGAAGGCACGTTCCCGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
* * **
1442 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATCAGTACCTATTATTTCACTATTCA
66 GCCCTATTATGTCACTCATGACACT----GACACTA-ATATCAGTACCTATTATTTCACTAAGCA
1507 CATGAAGGCGTTCCGGGGGCGGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATT
126 CATGAAGGCGTTCCGGGGGCGGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATT
* *
1572 ATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACATGAA
191 ATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACAGGGCACATGAA
*
1637 GGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATG
256 GGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATG
**
1702 TCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCG
321 TCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCACATGAAGGCG
1767 CATCCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCA
386 CATCCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTA--TCA
1832 CTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTCAC
449 CTCA-GTCCCTCGGGGACACTAGATATATCAGTACCTATTATTCAC
1877 TATTCACATGAAGGCACGTTCCCGGGGGCGCGCTTCCATTATTTCATCAGAGAATATGTTATCAT
1 TATTCACATGAAGGCACGTTCCCGGGGGCGC-CTTCCATTATTTCATCAGAGAATATGTTATCAT
* * * *
1942 TGTCCTATTATGTCACTCAT-ACACT-AGA-T-ATATCAGTACCTA-TATTTCTC-AAGGACATG
65 TGCCCTATTATGTCACTCATGACACTGACACTAATATCAGTACCTATTATTTCACTAAGCACATG
*
2001 AAGGCGCGTTCCTGGGGGGCGCGCCTTCCA-TATTTCGTCAGAGAATATGTTATCATTGCCCTAT
130 AA-G-GCGTTCC--GGGGGCG-GCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTAT
**
2065 TATGTCACTCATGT-CCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-TTCACATG
190 TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC-AGGGCACATG
2128 AAGGCGCGTT-CCGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTA
254 AAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTA
* *
2192 TGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGGACATGAA
319 TGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTCACTA-GGCACATGAA
* * * *
2256 GGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTAT
382 GGCGCATCCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTAT
2321 CACTCAGTCCCTCGGGGACACTAGATATATCAGTA
447 CACTCAGTCCCTCGGGGACACTAGATATATCAGTA
2356 AATCAGGTAA
Statistics
Matches: 445, Mismatches: 24, Indels: 29
0.89 0.05 0.06
Matches are distributed among these distances:
490 15 0.03
491 36 0.08
492 91 0.20
493 153 0.34
494 56 0.13
495 10 0.02
500 33 0.07
501 51 0.11
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (493 bp):
TATTCACATGAAGGCACGTTCCCGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
GCCCTATTATGTCACTCATGACACTGACACTAATATCAGTACCTATTATTTCACTAAGCACATGA
AGGCGTTCCGGGGGCGGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTC
ACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACAGGGCACATGAAGGCGC
GTTCCCGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACT
CATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCACATGAAGGCGCATCC
CCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATCACTCAGTC
CCTCGGGGACACTAGATATATCAGTACCTATTATTCAC
Found at i:2785 original size:31 final size:30
Alignment explanation
Indices: 2747--2827 Score: 83
Period size: 33 Copynumber: 2.6 Consensus size: 30
2737 AAATTTAATG
2747 TTAAATTTCGAATACATAATTTATATTTAAA
1 TTAAATTTCGAATA-ATAATTTATATTTAAA
* **
2778 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATA--A--TTTATATTTAAA
2811 TTAAATTTCGAATAATA
1 TTAAATTTCGAATAATA
2828 TAATTTGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 3 0.07
30 5 0.12
31 9 0.21
33 17 0.40
34 8 0.19
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (30 bp):
TTAAATTTCGAATAATAATTTATATTTAAA
Found at i:2841 original size:33 final size:33
Alignment explanation
Indices: 2747--2843 Score: 110
Period size: 31 Copynumber: 3.0 Consensus size: 33
2737 AAATTTAATG
*
2747 TTAAATTTCGAAT-ACATAATTTATA-TTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
* * **
2778 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATA-TTTTAAA
*
2811 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
2844 AACATTTATC
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
30 4 0.08
31 17 0.32
33 17 0.32
34 15 0.28
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (33 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAA
Found at i:3406 original size:21 final size:21
Alignment explanation
Indices: 3354--3442 Score: 128
Period size: 21 Copynumber: 4.3 Consensus size: 21
3344 TATGGTATAA
*
3354 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
3375 AA-CCTGGGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
3395 AACCCTGCGGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
*
3416 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
3437 AACCCT
1 AACCCT
3443 ACGGAGATGG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
20 18 0.30
21 42 0.69
22 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:5238 original size:17 final size:19
Alignment explanation
Indices: 5216--5259 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5206 ATAATTATAT
5216 AAATATTAT-TTTA-ATAA
1 AAATATTATATTTACATAA
*
5233 AAATATAATATTTACATAA
1 AAATATTATATTTACATAA
*
5252 ATATATTA
1 AAATATTA
5260 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTATATTTACATAA
Found at i:5251 original size:19 final size:18
Alignment explanation
Indices: 5203--5263 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
5193 TTCTAAATAA
* *
5203 ATAATAATT-ATATAAAT
1 ATAATATTTAATAAAAAT
*
5220 ATTAT-TTTAATAAAAAT
1 ATAATATTTAATAAAAAT
*
5237 ATAATATTTACATAAATAT
1 ATAATATTTA-ATAAAAAT
5256 ATTAATAT
1 A-TAATAT
5264 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.06
17 15 0.43
18 4 0.11
19 8 0.23
20 6 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATATTTAATAAAAAT
Found at i:5299 original size:33 final size:34
Alignment explanation
Indices: 5231--5300 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
5221 TTATTTTAAT
* *
5231 AAAAATATAATATTTACATAAATATATTAATATA
1 AAAAATATAATATTTACATAAATATACTAACATA
5265 AAAAATAATAACTATTTA-A-AAA-ATACTAACATA
1 AAAAAT-ATAA-TATTTACATAAATATACTAACATA
5298 AAA
1 AAA
5301 TAAATTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 12 0.38
34 9 0.28
35 5 0.16
36 6 0.19
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAAATATAATATTTACATAAATATACTAACATA
Found at i:6600 original size:23 final size:24
Alignment explanation
Indices: 6550--6600 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
6540 TATCAAGCAC
*
6550 AATAATATATTAGGTAGCGCTTAT
1 AATAATATAATAGGTAGCGCTTAT
*
6574 -ATAATGTAATAGGTAGCG-TTAT
1 AATAATATAATAGGTAGCGCTTAT
6596 AATAA
1 AATAA
6601 AATACGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (24 bp):
AATAATATAATAGGTAGCGCTTAT
Found at i:6664 original size:84 final size:85
Alignment explanation
Indices: 6523--6681 Score: 257
Period size: 84 Copynumber: 1.9 Consensus size: 85
6513 TATGTTATAT
* * * * *
6523 CATTTAACTGGAAATATTATCAAGCACAATAATATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTACCAAACACAATAACATATTAGGTAACGCTTATATAATGTAATAGGT
6588 AGCG-TTATAATAAAATACG
66 AGCGCTTATAATAAAATACG
*
6607 CATTTAACCGGAAATATTACCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTACCAAACACAATAACATATTAGGTAACGCTTATATAATGTAATAGGT
6672 AGCGCTTATA
66 AGCGCTTATA
6682 TTGACCTATT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 63 0.93
85 5 0.07
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (85 bp):
CATTTAACCGGAAATATTACCAAACACAATAACATATTAGGTAACGCTTATATAATGTAATAGGT
AGCGCTTATAATAAAATACG
Found at i:10555 original size:17 final size:17
Alignment explanation
Indices: 10535--10570 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
10525 TATAATTTTT
10535 GGTCTCGATATATTTGG
1 GGTCTCGATATATTTGG
10552 GG--TCGATATATTTGG
1 GGTCTCGATATATTTGG
10567 GGTC
1 GGTC
10571 GATACTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
15 15 0.88
17 2 0.12
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.39
Consensus pattern (17 bp):
GGTCTCGATATATTTGG
Found at i:10557 original size:15 final size:15
Alignment explanation
Indices: 10539--10574 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
10529 ATTTTTGGTC
10539 TCGATATATTTGGGG
1 TCGATATATTTGGGG
10554 TCGATATATTTGGGG
1 TCGATATATTTGGGG
10569 TCGATA
1 TCGATA
10575 CTTTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (15 bp):
TCGATATATTTGGGG
Found at i:10904 original size:201 final size:200
Alignment explanation
Indices: 10554--12022 Score: 1163
Period size: 200 Copynumber: 7.5 Consensus size: 200
10544 ATATTTGGGG
* * * * * * * *
10554 TCGATATATTTGGGGTCGATACTTTTTATAAATGTACCGACACTTTATGCGTGGACATTGTTTGG
1 TCGATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTAT-CGTGCACATGGTTTGG
* * * * * * * * *
10619 -TATTCATTATCGACATAAAGTATCGACAC-AAATGCAAAAAGTATCGATACATTACGTAGACCT
65 AAATACATTATGGACAAAAAGTATCGACACTAAATG-AATAAGTGTCGATACTTTATGTATACCT
* *
10682 ATTTGCTCATAAAATCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAAT-
129 ATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTAT-ATC
* *
10746 TTTCG-GTC
193 TAT-GTGTT
* * * *
10754 TCGATGTATTTGGGGTCGATACTT-TTAATAAATGTATCGACACTTTATGCGTGCACATAGTTTG
1 TCGATGTATTTAGGATCGACACTTGTT-ATAAATGTATCGACACTTTAT-CGTGCACATGGTTTG
* * * * *
10818 GGAATTCATTATGGATAAAAAGTATCGACAC-AAATAAATAAAGTGTCGATACTTTATATATACC
64 GAAATACATTATGGACAAAAAGTATCGACACTAAATGAAT-AAGTGTCGATACTTTATGTATACC
10882 TATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATATC
128 TATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATATC
10947 TATGTGTT
193 TATGTGTT
* * * * *
10955 TCGATGTTTTTAGTATCGACACTTGTTATAAATGTATCGATACTTTGTCGTGCACTTGGTTTGGA
1 TCGATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATCGTGCACATGGTTTGG-
*** * ** * *
11020 AAATACATTATGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACATG
65 AAATACATTATGGACAAAAAGTATCGACACTAAATGAATAAGTGTCGATACTTTATGTATACCTA
** ** * ** *
11085 TTTTCTCAT-AAACCGGTGCATTTAGGCCGGTTACATTGTTATTTTACCTATTACATTATATCTA
130 TTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATATCTA
11149 TGTGTT
195 TGTGTT
* * * * *
11155 TCGATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTGTCGTGCACTTGGTTTAGA
1 TCGATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATCGTGCACATGGTTT-GG
*** **
11220 AAATACATTATGGACAAAAAGTATCGACACTTGTTGAATTTGTGTCGATACTTTATGTATACCTA
65 AAATACATTATGGACAAAAAGTATCGACACTAAATGAATAAGTGTCGATACTTTATGTATACCTA
** ** * ** * *
11285 TTTTCTCA-AAAACCGGTGTATTTAGGCCGGTTACATTGTTATTTTATCTATTACATTATATC--
130 TTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATATCTA
11347 TGTGTT
195 TGTGTT
* * * * * * *
11353 TCGAT-TTTTTTGTATCGACAC-T-TTGT---CG--T-G-CAC----T--TG---AT--TTGGAA
1 TCGATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATCGTGCACATGGTTTGGA
* *** * ** *
11397 AATACATTATGTACAAAAAGTATCGACACTTGTTGCATTTGTGTCGATACTTTATGTATACATAT
66 AATACATTATGGACAAAAAGTATCGACACTAAATGAATAAGTGTCGATACTTTATGTATACCTAT
* * * *
11462 TTTCTCATAAAACTGGTAAATTTAAATCGGTTATATTGTAAAGTGACCTATTACATTTTAAT-TA
131 TTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTAT-ATCTA
11526 TAG-GTT
195 T-GTGTT
* * * * *
11532 TCGATGTATTTGGGATCGACACATGTTATAAATGTATCGACACTTTTTTGTGCA-TTGGTTTGGA
1 TCGATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATCGTGCACATGGTTTGGA
*** * ** * *
11596 AACTACATTATGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACTTG
66 AA-TACATTATGGACAAAAAGTATCGACACTAAATGAATAAGTGTCGATACTTTATGTATACCTA
** *** * ** *
11661 TTTTCTCAT-AAACCGGTGTATTTAGGTCGGTTACATTGTTATTTTACCTATTACATTATATCTA
130 TTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATATCTA
11725 TGTGTT
195 TGTGTT
* * *
11731 TCGATG-ATTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTGG
1 TCGATGTA-TTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATCGTGCACATGGTTTGG
* * ** * ** *
11795 AAAATACATTCTAGACAAAAAGTATCGACACT-TGTTAGATTTGTGTCGATACTTTATGTATACT
65 -AAATACATTATGGACAAAAAGTATCGACACTAAATGA-ATAAGTGTCGATACTTTATGTATACC
* * ** * ** * * * *
11859 TGTTTTCTCA-AAAACCAGTTTATTTAGATTGGTTACATTGTTAATTTACTTATTACATTATAAT
128 TATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTAT-AT
11923 -TATGTGTT
192 CTATGTGTT
* * *
11931 TCGATG---TT----T------TTGTTATAAATGTATCGACAATTTTCTCGTGCACTTGGTTTGG
1 TCGATGTATTTAGGATCGACACTTGTTATAAATGTATCGAC-ACTTTATCGTGCACATGGTTTGG
* * *
11983 AAATACATTATGGACAACATGTATCGACAC-GAATGAATAA
65 AAATACATTATGGACAAAAAGTATCGACACTAAATGAATAA
12023 AACAAATTCA
Statistics
Matches: 1096, Mismatches: 127, Indels: 106
0.82 0.10 0.08
Matches are distributed among these distances:
176 72 0.07
177 40 0.04
178 2 0.00
179 10 0.01
180 14 0.01
181 1 0.00
182 5 0.00
184 1 0.00
185 1 0.00
186 2 0.00
187 48 0.04
188 25 0.02
189 4 0.00
190 1 0.00
192 1 0.00
193 2 0.00
195 5 0.00
196 1 0.00
197 18 0.02
198 15 0.01
199 102 0.09
200 508 0.46
201 213 0.19
202 5 0.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (200 bp):
TCGATGTATTTAGGATCGACACTTGTTATAAATGTATCGACACTTTATCGTGCACATGGTTTGGA
AATACATTATGGACAAAAAGTATCGACACTAAATGAATAAGTGTCGATACTTTATGTATACCTAT
TTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATATCTAT
GTGTT
Found at i:11680 original size:376 final size:378
Alignment explanation
Indices: 10662--11937 Score: 1217
Period size: 376 Copynumber: 3.3 Consensus size: 378
10652 GCAAAAAGTA
* * * * * *
10662 TCGATACATTACGTAGACCTATTTGCTCATAAAATCGGTAAATTTAAACCGGTTACATTGTAAAG
1 TCGATACTTTATGTATACATATTTTCTCAT-AAACCGGTAAATTTAAACCGGTTACATTGTAAAG
* * * * * *
10727 TGACCTATTACATTATAAT-TTTCG-GTCTCGATGTATTTGGGGTCGATAC-TTTTAATAAATGT
65 TGACCTATTACATTAT-ATCTAT-GTGTTTCGATGTATTTAGGATCGACACATGTT-ATAAATGT
* * * ** * * ***
10789 ATCGACACTTTATGCGTGCACATAGTTT-GGGAATTCATTATGGATAAAAAGTATCGACAC-AAA
127 ATCGACACTTTGT-CGTGCACTTGGTTTAGAAAATACATTATGGACAAAAAGTATCGACACTTGT
* ** * ** **
10852 TAAATAAAGTGTCGATACTTTATATATACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTT
191 TGAAT-TTGTGTCGATACTTTATGTATACCTATTTTCTCA-AAAACCGGTGTATTTAGGCCGGTT
* ** *
10917 ACATTGTAAAGTGACCTATTACATTATATCTATGTGTTTCGATGTTTTTAGTATCGACACTTGTT
254 ACATTGTTATTTTACCTATTACATTATATC-ATGTGTTTC----------G-AT-G--A--T-TT
* *
10982 ATAAATGTATCGATACTTTGTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGA
301 -T---TGTATCGACACTTTGTCGTGCACTTGATTTGGAAAATACATTATGGACAAAAAGTATCGA
*
11047 CACTTGTTGGATTTGTG
362 CACTTGTTGCATTTGTG
* ** ** * **
11064 TCGATACTTTATGTATACATGTTTTCTCATAAACCGGTGCATTTAGGCCGGTTACATTGTTATTT
1 TCGATACTTTATGTATACATATTTTCTCATAAACCGGTAAATTTAAACCGGTTACATTGTAAAGT
* * * *
11129 TACCTATTACATTATATCTATGTGTTTCGATGTTTTTAGTATCGACACTTGTTATAAATGTATCG
66 GACCTATTACATTATATCTATGTGTTTCGATGTATTTAGGATCGACACATGTTATAAATGTATCG
11194 ACACTTTGTCGTGCACTTGGTTTAGAAAATACATTATGGACAAAAAGTATCGACACTTGTTGAAT
131 ACACTTTGTCGTGCACTTGGTTTAGAAAATACATTATGGACAAAAAGTATCGACACTTGTTGAAT
11259 TTGTGTCGATACTTTATGTATACCTATTTTCTCAAAAACCGGTGTATTTAGGCCGGTTACATTGT
196 TTGTGTCGATACTTTATGTATACCTATTTTCTCAAAAACCGGTGTATTTAGGCCGGTTACATTGT
* *
11324 TATTTTATCTATTACATTATATC-TGTGTTTCGAT-TTTTTTGTATCGACACTTTGTCGTGCACT
261 TATTTTACCTATTACATTATATCATGTGTTTCGATGATTTTTGTATCGACACTTTGTCGTGCACT
*
11387 TGATTTGGAAAATACATTATGTACAAAAAGTATCGACACTTGTTGCATTTGTG
326 TGATTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTTGCATTTGTG
* * *
11440 TCGATACTTTATGTATACATATTTTCTCATAAAACTGGTAAATTTAAATCGGTTATATTGTAAAG
1 TCGATACTTTATGTATACATATTTTCTCAT-AAACCGGTAAATTTAAACCGGTTACATTGTAAAG
* *
11505 TGACCTATTACATTTTAAT-TATAG-GTTTCGATGTATTTGGGATCGACACATGTTATAAATGTA
65 TGACCTATTACATTAT-ATCTAT-GTGTTTCGATGTATTTAGGATCGACACATGTTATAAATGTA
* * * *
11568 TCGACACTTTTTTGTGCA-TTGGTTTGGAAACTACATTATGGACAAAAAGTATCGACACTTGTTG
128 TCGACACTTTGTCGTGCACTTGGTTTAGAAAATACATTATGGACAAAAAGTATCGACACTTGTTG
* * * * *
11632 GATTTGTGTCGATACTTTATGTATACTTGTTTTCTCATAAACCGGTGTATTTAGGTCGGTTACAT
193 AATTTGTGTCGATACTTTATGTATACCTATTTTCTCAAAAACCGGTGTATTTAGGCCGGTTACAT
11697 TGTTATTTTACCTATTACATTATATCTATGTGTTTCGATGATTTTAGTATCGACACTTGTTATAA
258 TGTTATTTTACCTATTACATTATATC-ATGTGTTTC----------G-AT-G--A--T-TT-T--
* * * *
11762 ATGTATCGACACTTTTTCGTGCACTTGGTTTGGAAAATACATTCTAGACAAAAAGTATCGACACT
302 -TGTATCGACACTTTGTCGTGCACTTGATTTGGAAAATACATTATGGACAAAAAGTATCGACACT
11827 TGTTAG-ATTTGTG
366 TGTT-GCATTTGTG
* * * * ** * ** * *
11840 TCGATACTTTATGTATACTTGTTTTCTCAAAAACCAGTTTATTTAGATTGGTTACATTGTTAATT
1 TCGATACTTTATGTATACATATTTTCTCATAAACCGGTAAATTTAAACCGGTTACATTGTAAAGT
* *
11905 TACTTATTACATTATAAT-TATGTGTTTCGATGT
66 GACCTATTACATTAT-ATCTATGTGTTTCGATGT
11938 TTTTGTTATA
Statistics
Matches: 741, Mismatches: 99, Indels: 71
0.81 0.11 0.08
Matches are distributed among these distances:
376 231 0.31
377 92 0.12
378 11 0.01
379 1 0.00
380 2 0.00
381 1 0.00
387 2 0.00
388 2 0.00
389 2 0.00
395 1 0.00
396 2 0.00
397 1 0.00
398 9 0.01
399 54 0.07
400 157 0.21
401 142 0.19
402 31 0.04
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (378 bp):
TCGATACTTTATGTATACATATTTTCTCATAAACCGGTAAATTTAAACCGGTTACATTGTAAAGT
GACCTATTACATTATATCTATGTGTTTCGATGTATTTAGGATCGACACATGTTATAAATGTATCG
ACACTTTGTCGTGCACTTGGTTTAGAAAATACATTATGGACAAAAAGTATCGACACTTGTTGAAT
TTGTGTCGATACTTTATGTATACCTATTTTCTCAAAAACCGGTGTATTTAGGCCGGTTACATTGT
TATTTTACCTATTACATTATATCATGTGTTTCGATGATTTTTGTATCGACACTTTGTCGTGCACT
TGATTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTTGCATTTGTG
Found at i:11885 original size:576 final size:579
Alignment explanation
Indices: 10860--11943 Score: 1795
Period size: 576 Copynumber: 1.9 Consensus size: 579
10850 AATAAATAAA
*
10860 GTGTCGATACTTTATATATACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTA
1 GTGTCGATACTTTATATATACATATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTA
* * *
10925 AAGTGACCTATTACATTATATCTATGTGTTTCGATGTTTTTAGTATCGACACTTGTTATAAATGT
66 AAGTGACCTATTACATTATATCTATGTGTTTCGATGTATTTAGGATCGACACATGTTATAAATGT
*
10990 ATCGATACTTTGTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTT
131 ATCGACACTTTGTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTT
11055 GGATTTGTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTGCATTTAGGCCGGTTACA
196 GGATTTGTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTGCATTTAGGCCGGTTACA
*
11120 TTGTTATTTTACCTATTACATTATATCTATGTGTTTCGATGTTTTTAGTATCGACACTTGTTATA
261 TTGTTATTTTACCTATTACATTATATCTATGTGTTTCGATGATTTTAGTATCGACACTTGTTATA
*
11185 AATGTATCGACACTTTGTCGTGCACTTGGTTTAGAAAATACATTATGGACAAAAAGTATCGACAC
326 AATGTATCGACACTTTGTCGTGCACTTGGTTTAGAAAATACATTATAGACAAAAAGTATCGACAC
* *
11250 TTGTTGAATTTGTGTCGATACTTTATGTATACCTATTTTCTCAAAAACCGGTGTATTTAGGCCGG
391 TTGTTGAATTTGTGTCGATACTTTATGTATACCTATTTTCTCAAAAACCAGTGTATTTAGACCGG
* * *
11315 TTACATTGTTATTTTA-TCTATTACATTAT-A-TCTGTGTTTCGATTTTTTTGTATCGACACTTT
456 TTACATTGTTAATTTACT-TATTACATTATAATTATGTGTTTCGATGTTTTTGTATCGACACTTT
11377 GTCGTGCACTTGATTTGGAAAATACATTATGTACAAAAAGTATCGACACTTGTTGCATTT
520 GTCGTGCACTTGATTTGGAAAATACATTATGTACAAAAAGTATCGACACTTGTTGCATTT
* * * *
11437 GTGTCGATACTTTATGTATACATATTTTCTCATAAAACTGGTAAATTTAAATCGGTTATATTGTA
1 GTGTCGATACTTTATATATACATATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTA
* *
11502 AAGTGACCTATTACATTTTAAT-TATAG-GTTTCGATGTATTTGGGATCGACACATGTTATAAAT
66 AAGTGACCTATTACATTAT-ATCTAT-GTGTTTCGATGTATTTAGGATCGACACATGTTATAAAT
* * *
11565 GTATCGACACTTTTTTGTGCA-TTGGTTTGGAAACTACATTATGGACAAAAAGTATCGACACTTG
129 GTATCGACACTTTGTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTG
* * *
11629 TTGGATTTGTGTCGATACTTTATGTATACTTGTTTTCTCATAAACCGGTGTATTTAGGTCGGTTA
194 TTGGATTTGTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTGCATTTAGGCCGGTTA
11694 CATTGTTATTTTACCTATTACATTATATCTATGTGTTTCGATGATTTTAGTATCGACACTTGTTA
259 CATTGTTATTTTACCTATTACATTATATCTATGTGTTTCGATGATTTTAGTATCGACACTTGTTA
* * *
11759 TAAATGTATCGACACTTTTTCGTGCACTTGGTTTGGAAAATACATTCTAGACAAAAAGTATCGAC
324 TAAATGTATCGACACTTTGTCGTGCACTTGGTTTAGAAAATACATTATAGACAAAAAGTATCGAC
* * * *
11824 ACTTGTT-AGATTTGTGTCGATACTTTATGTATACTTGTTTTCTCAAAAACCAGTTTATTTAGAT
389 ACTTGTTGA-ATTTGTGTCGATACTTTATGTATACCTATTTTCTCAAAAACCAGTGTATTTAGAC
*
11888 TGGTTACATTGTTAATTTACTTATTACATTATAATTATGTGTTTCGATGTTTTTGT
453 CGGTTACATTGTTAATTTACTTATTACATTATAATTATGTGTTTCGATGTTTTTGT
11944 TATAAATGTA
Statistics
Matches: 469, Mismatches: 32, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
575 1 0.00
576 313 0.67
577 133 0.28
578 22 0.05
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (579 bp):
GTGTCGATACTTTATATATACATATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACATTGTA
AAGTGACCTATTACATTATATCTATGTGTTTCGATGTATTTAGGATCGACACATGTTATAAATGT
ATCGACACTTTGTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTT
GGATTTGTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTGCATTTAGGCCGGTTACA
TTGTTATTTTACCTATTACATTATATCTATGTGTTTCGATGATTTTAGTATCGACACTTGTTATA
AATGTATCGACACTTTGTCGTGCACTTGGTTTAGAAAATACATTATAGACAAAAAGTATCGACAC
TTGTTGAATTTGTGTCGATACTTTATGTATACCTATTTTCTCAAAAACCAGTGTATTTAGACCGG
TTACATTGTTAATTTACTTATTACATTATAATTATGTGTTTCGATGTTTTTGTATCGACACTTTG
TCGTGCACTTGATTTGGAAAATACATTATGTACAAAAAGTATCGACACTTGTTGCATTT
Found at i:12197 original size:18 final size:18
Alignment explanation
Indices: 12148--12206 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
12138 TGGATGGATT
*
12148 AAATTTAAATTCAAACTC
1 AAATTCAAATTCAAACTC
* * * *
12166 AAACTCAAACTCAAATTG
1 AAATTCAAATTCAAACTC
*
12184 AAATTGAAATTCAAACTC
1 AAATTCAAATTCAAACTC
*
12202 TAATT
1 AAATT
12207 ATAAATGAAA
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATTCAAATTCAAACTC
Found at i:12206 original size:12 final size:12
Alignment explanation
Indices: 12154--12206 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
12144 GATTAAATTT
12154 AAATTCAAACTC
1 AAATTCAAACTC
*
12166 AAACTCAAACTC
1 AAATTCAAACTC
* * *
12178 AAATTGAAATTG
1 AAATTCAAACTC
12190 AAATTCAAACTC
1 AAATTCAAACTC
*
12202 TAATT
1 AAATT
12207 ATAAATGAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (12 bp):
AAATTCAAACTC
Found at i:12215 original size:24 final size:24
Alignment explanation
Indices: 12170--12217 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12160 AAACTCAAAC
*
12170 TCAAACTCAAATTGAAATTGAAAT
1 TCAAACTCAAATTGAAAATGAAAT
*
12194 TCAAACTCTAATT-ATAAATGAAAT
1 TCAAACTCAAATTGA-AAATGAAAT
12218 GAAAATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (24 bp):
TCAAACTCAAATTGAAAATGAAAT
Found at i:13484 original size:6 final size:6
Alignment explanation
Indices: 13474--13507 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13464 CTTGTTTGGA
* *
13474 TCATCA TCATCT TCATCT TCATCG TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
13508 TGACCGCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:14319 original size:2 final size:2
Alignment explanation
Indices: 14312--14363 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
14302 GTTTCCGGAG
14312 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
*
14354 AT AT GT AT AT
1 AT AT AT AT AT
14364 CCTTCTCCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14723 original size:15 final size:15
Alignment explanation
Indices: 14699--14742 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
14689 AGGAGGTTGT
14699 GGTTGAGAAGAGATG
1 GGTTGAGAAGAGATG
* *
14714 GGTTGGGAAGAGGTG
1 GGTTGAGAAGAGATG
14729 GGTTGAGAAGAGAT
1 GGTTGAGAAGAGAT
14743 TTGAGAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.50, T:0.20
Consensus pattern (15 bp):
GGTTGAGAAGAGATG
Found at i:15426 original size:198 final size:199
Alignment explanation
Indices: 15108--16366 Score: 1972
Period size: 198 Copynumber: 6.3 Consensus size: 199
15098 TTGCAAAATG
* * * * *
15108 ACCTATTACATTAAAATTTTGGGTTTCGATGTTCTTAGGATCGATACTTGTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
*
15173 CACTTTTTCGTGCACTTGGTTTAGAAATGCATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
66 CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
* * * *
15238 GTGTCGATACTTTTT-TACACTTGTTTTCTAAAAAACTAGTATATTTAGACCGATTACATTGTTA
131 GTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTCGTATATTTAGACCGGTTACATTGTTA
15302 ATTT
196 ATTT
* *
15306 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATAGACACTTGTTATAAATGTATAGA
1 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
* * * *
15371 TACTTATTCGTGCACTTGGTTTAGAAATACATTATGGACAAAAAGTATCGACACTTGTTTTATTT
66 CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
* * * *
15436 TTGTTGATACTTTTTGTACACCTGTTTTCTCAAAAATTTGTATATTTAGACCGGTTACATTGTTA
131 GTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTCGTATATTTAGACCGGTTACATTGTTA
15501 ATTT
196 ATTT
* * *
15505 ACCTATTACATTAAAATTTTGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
*
15570 CACTTTTTCGTGCACTTGGTTTAGAAATACATTATGGACCAAAAGTATCGACACTTGTTTTATTT
66 CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
* * * *
15635 TTGTTGATA-TTTTTGTACACATGTTTTCTCAAAAAC-CGATATATTTAGACTGGTTACATTGTT
131 GTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTCG-TATATTTAGACCGGTTACATTGTT
15698 AATTT
195 AATTT
* *
15703 ACCTATTACATTATAATTATGAGTTTCGATATTTTTGGGATCGACACTTGTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
* * *
15768 CACTTTTTCGTGCACTAGGTTTAGAAATACATTTTGGATCAAAAGTATCGACACTTGTTTTATTT
66 CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
* * *
15833 GTGTCGATAATTTTTGTACACCTGTTTTCTCAAAAAC-CGATATATTTAGACTGGTTACACTGTT
131 GTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTCG-TATATTTAGACCGGTTACATTGTT
15897 AATTT
195 AATTT
15902 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
* * * *
15967 CACTTTTTCATGTACTAGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGCTTTATTT
66 CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
16032 GTGTCGATACTTTTTGTACACCTGTTTTCTC-AAAAC-CGGTATATTTAGACCGGTTACATTGTT
131 GTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTC-GTATATTTAGACCGGTTACATTGTT
*
16095 AACTT
195 AATTT
*
16100 ACCTATTATATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
* *
16165 CACCTTTTCGTACACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
66 CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
* * * * **
16230 GTGTCGATATTTTTTGTACACCTGTTTTCTCAAAAATTGGTATATTTAGACTGACTACATTGTTA
131 GTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTCGTATATTTAGACCGGTTACATTGTTA
16295 ATTT
196 ATTT
* * *
16299 ACCTATTACATTATAATTATGGGTTTCAATGTTTTTGGGATCGATATTTGTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
16364 CAC
66 CAC
16367 ATAAGTTTAT
Statistics
Matches: 983, Mismatches: 72, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
197 1 0.00
198 498 0.51
199 484 0.49
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (199 bp):
ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
GTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTCGTATATTTAGACCGGTTACATTGTTA
ATTT
Found at i:15826 original size:397 final size:397
Alignment explanation
Indices: 15108--16366 Score: 1988
Period size: 397 Copynumber: 3.2 Consensus size: 397
15098 TTGCAAAATG
* * * *
15108 ACCTATTACATTAAAATTTTGGGTTTCGATGTTCTTAGGATCGATACTTGTTATAAATGTATCGA
1 ACCTATTACATTAAAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
*
15173 CACTTTTTCGTGCACTTGGTTTAGAAATGCATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
66 CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
* * * *
15238 GTGTCGATACTTTTT-TACACTTGTTTTCT-AAAAAACTAGTATATTTAGACCGATTACATTGTT
131 GTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGA-TATATTTAGACCGGTTACATTGTT
*
15301 AATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATAGACACTTGTTATAAATGT
195 AATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGT
* * *
15366 ATAGATACTTATTCGTGCACTTGGTTTAGAAATACATTATGGACAAAAAGTATCGACACTTGTTT
260 ATCGACACTTTTTCGTGCACTTGGTTTAGAAATACATTATGGAC-AAAAGTATCGACACTTGTTT
* * * * *
15431 TATTTTTGTTGATACTTTTTGTACACCTGTTTTCTCAAAAATTTGTATATTTAGACCGGTTACAT
324 TATTTGTGTCGATAATTTTTGTACACCTGTTTTCTCAAAAATTCGTATATTTAGACTGGTTACAT
15496 TGTTAATTT
389 TGTTAATTT
* *
15505 ACCTATTACATTAAAATTTTGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCGA
1 ACCTATTACATTAAAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
*
15570 CACTTTTTCGTGCACTTGGTTTAGAAATACATTATGGACCAAAAGTATCGACACTTGTTTTATTT
66 CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
* * *
15635 TTGTTGATA-TTTTTGTACACATGTTTTCTCAAAAACCGATATATTTAGACTGGTTACATTGTTA
131 GTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGATATATTTAGACCGGTTACATTGTTA
* *
15699 ATTTACCTATTACATTATAATTATGAGTTTCGATATTTTTGGGATCGACACTTGTTATAAATGTA
196 ATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTA
* *
15764 TCGACACTTTTTCGTGCACTAGGTTTAGAAATACATTTTGGATCAAAAGTATCGACACTTGTTTT
261 TCGACACTTTTTCGTGCACTTGGTTTAGAAATACATTATGGA-CAAAAGTATCGACACTTGTTTT
* *
15829 ATTTGTGTCGATAATTTTTGTACACCTGTTTTCTCAAAAA-CCGATATATTTAGACTGGTTACAC
325 ATTTGTGTCGATAATTTTTGTACACCTGTTTTCTCAAAAATTCG-TATATTTAGACTGGTTACAT
15893 TGTTAATTT
389 TGTTAATTT
*
15902 ACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
1 ACCTATTACATTAAAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
* * * *
15967 CACTTTTTCATGTACTAGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGCTTTATTT
66 CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
* *
16032 GTGTCGATACTTTTTGTACACCTGTTTTCTC-AAAACCGGTATATTTAGACCGGTTACATTGTTA
131 GTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGATATATTTAGACCGGTTACATTGTTA
* *
16096 ACTTACCTATTATATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTA
196 ATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTA
* * *
16161 TCGACACCTTTTCGTACACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTT
261 TCGACACTTTTTCGTGCACTTGGTTTAGAAATACATTATGGA-CAAAAGTATCGACACTTGTTTT
* * **
16226 ATTTGTGTCGATATTTTTTGTACACCTGTTTTCTCAAAAATTGGTATATTTAGACTGACTACATT
325 ATTTGTGTCGATAATTTTTGTACACCTGTTTTCTCAAAAATTCGTATATTTAGACTGGTTACATT
16291 GTTAATTT
390 GTTAATTT
* * * *
16299 ACCTATTACATTATAATTATGGGTTTCAATGTTTTTGGGATCGATATTTGTTATAAATGTATCGA
1 ACCTATTACATTAAAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
16364 CAC
66 CAC
16367 ATAAGTTTAT
Statistics
Matches: 797, Mismatches: 59, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
396 6 0.01
397 762 0.96
398 29 0.04
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (397 bp):
ACCTATTACATTAAAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGA
CACTTTTTCGTGCACTTGGTTTAGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTT
GTGTCGATACTTTTTGTACACATGTTTTCTCAAAAACCGATATATTTAGACCGGTTACATTGTTA
ATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTA
TCGACACTTTTTCGTGCACTTGGTTTAGAAATACATTATGGACAAAAGTATCGACACTTGTTTTA
TTTGTGTCGATAATTTTTGTACACCTGTTTTCTCAAAAATTCGTATATTTAGACTGGTTACATTG
TTAATTT
Found at i:16762 original size:19 final size:19
Alignment explanation
Indices: 16738--16786 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
16728 TTACATTCAC
16738 ATACAAAATTATAAACCGT
1 ATACAAAATTATAAACCGT
* *
16757 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAACCGT
16776 ATACAAAATTA
1 ATACAAAATTA
16787 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAACCGT
Found at i:20394 original size:19 final size:19
Alignment explanation
Indices: 20372--20415 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
20362 TTTCTATATG
*
20372 TAATATCATGTTTTACCTA
1 TAATATAATGTTTTACCTA
* *
20391 TAATATAATTTTTTGCCTA
1 TAATATAATGTTTTACCTA
20410 TAATAT
1 TAATAT
20416 TAAATAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (19 bp):
TAATATAATGTTTTACCTA
Found at i:21424 original size:183 final size:182
Alignment explanation
Indices: 20881--21632 Score: 944
Period size: 182 Copynumber: 4.1 Consensus size: 182
20871 GTAGCGCTTT
* * * *
20881 ACCGGTTTTGTCATATTTTTACCTGTTATATTATTATCGATCGATACATTTTTTTAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTAGCTATTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
* * * *
20946 CACTTTATAGGTGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGT
66 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGTCAATACTTATATTAAATT
* * *
21011 ATCGACACTCTCAACATAT-CCGATAGTTCTTTATCGGTTTTGTCATTTTGAG
131 ATCGACACTTTCAACATATCCCG-TAGTGCTTTACCGGTTTTGTCATTTTGAG
* * ** * *
21063 ACCAGTTTTGTCATATTTTTAGCTATTATATTGTTATGGATCGATATATTTTCATAAAATATCTA
1 ACCGGTTTTGTCATATTTTTAGCTATTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
* * *
21128 CACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGAA-ACTTATTTTAAA
66 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAATGTC-AATACTTATATTAAA
* * * * *
21191 TTGTCGACACTTTCAACATATCCAGTAGCGCTTTACCGGATTTGTCATTTTGGG
129 TTATCGACACTTTCAACATATCCCGTAGTGCTTTACCGGTTTTGTCATTTTGAG
*
21245 ACTGGTTTTGTCATATTTTTAGCTATTATATTGTTATGGATCGATACATTTTTTTTAAAGTATCG
1 ACCGGTTTTGTCATATTTTTAGCTATTATATTGTTATGGATCGATACA-TTTTTTTAAAGTATCG
*
21310 ACACTTTATAGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAAAAT-TCAATACTTATATTAA
65 ACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCC--AAAAATGTCAATACTTATATTAA
* **
21374 ATTATCGACATTTTCAACATATCCCGTA-TTTTTTACCGGTTTTGTCATTTTTGAG
128 ATTATCGACACTTTCAACATATCCCGTAGTGCTTTACCGGTTTTGTCA-TTTTGAG
** *
21429 ACATGTTTTGTCATATTTTTA-C-ATGTCATATTGTTATGGATCGATATATTTTTTTTAAAGTAT
1 ACCGGTTTTGTCATATTTTTAGCTAT-T-ATATTGTTATGGATCGATACA-TTTTTTTAAAGTAT
* * * *
21492 CGACATTTTATAGCCGCTATAACTTCTTCTCTTTTAAATTTCAAAAATGTCGATACTTATATTAA
63 CGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGTCAATACTTATATTAA
* ** * * *
21557 ATTATCGACACTTTCAATATATCTGGTA-TCGTTTTACCGATTTTGTCATTTCGAG
128 ATTATCGACACTTTCAACATATCCCGTAGT-GCTTTACCGGTTTTGTCATTTTGAG
* *
21612 ACCGGTTTTATCATATATTTA
1 ACCGGTTTTGTCATATTTTTA
21633 CATGTAATAT
Statistics
Matches: 497, Mismatches: 60, Indels: 25
0.85 0.10 0.04
Matches are distributed among these distances:
181 2 0.00
182 204 0.41
183 133 0.27
184 153 0.31
185 4 0.01
186 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (182 bp):
ACCGGTTTTGTCATATTTTTAGCTATTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAATGTCAATACTTATATTAAATT
ATCGACACTTTCAACATATCCCGTAGTGCTTTACCGGTTTTGTCATTTTGAG
Found at i:23018 original size:15 final size:16
Alignment explanation
Indices: 22998--23031 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
22988 TGCCAAGTTT
*
22998 TTTGTTTC-TTTCTTA
1 TTTGTTTCGTTTCTCA
23013 TTTGTTTCGTTTCTCA
1 TTTGTTTCGTTTCTCA
23029 TTT
1 TTT
23032 TAAATGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.06, C:0.15, G:0.09, T:0.71
Consensus pattern (16 bp):
TTTGTTTCGTTTCTCA
Found at i:26061 original size:2 final size:2
Alignment explanation
Indices: 26054--26088 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
26044 AGATAAAAAT
26054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26089 AACACTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36663 original size:22 final size:20
Alignment explanation
Indices: 36628--36667 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
36618 CAGTTAGCTC
36628 TAACAACCCTAACAACCAAG
1 TAACAACCCTAACAACCAAG
36648 TAACAACCTCCTAACAACCA
1 TAACAA-C-CCTAACAACCA
36668 GTCACACATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.47, C:0.38, G:0.03, T:0.12
Consensus pattern (20 bp):
TAACAACCCTAACAACCAAG
Found at i:43758 original size:23 final size:23
Alignment explanation
Indices: 43686--43768 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
43676 ATAATTTGCA
43686 CCGAAGTG-CCACATA--TTTGTC
1 CCGAA-TGACCACATAGTTTTGTC
* * *
43707 TCGAATGACCACATAGTTTTATT
1 CCGAATGACCACATAGTTTTGTC
**
43730 TTGAATGACCACATAGTTTTGTC
1 CCGAATGACCACATAGTTTTGTC
*
43753 CCGAATGACCGCATAG
1 CCGAATGACCACATAG
43769 AACCCTCGAC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
20 2 0.04
21 11 0.22
23 37 0.74
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (23 bp):
CCGAATGACCACATAGTTTTGTC
Found at i:55572 original size:17 final size:16
Alignment explanation
Indices: 55550--55583 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
55540 TAAAAATAGT
55550 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
55567 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
55583 A
1 A
55584 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:57381 original size:43 final size:44
Alignment explanation
Indices: 57334--57470 Score: 133
Period size: 43 Copynumber: 3.2 Consensus size: 44
57324 TTACAACATA
* * *
57334 TAGCGGCGATTGT-TCA-ACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATT-TAGCATACAAACGCCGCAATAGGTGTTGATATT
57377 TAGCGGCG-TTTAGCATTA-AAACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGATTTAGCA-TACAAACGCCGCAATAGGTGTTGATATT
* * * * *
57420 TAACGGC-ATTTGGCAGACAAACACCGCAATA-GTCGTTGATGTT
1 TAGCGGCGATTTAGCATACAAACGCCGCAATAGGT-GTTGATATT
57463 TAGCGGCG
1 TAGCGGCG
57471 TTTTCTTCAC
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
41 1 0.01
42 7 0.09
43 69 0.88
44 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
TAGCGGCGATTTAGCATACAAACGCCGCAATAGGTGTTGATATT
Found at i:57447 original size:86 final size:86
Alignment explanation
Indices: 57350--57516 Score: 196
Period size: 86 Copynumber: 1.9 Consensus size: 86
57340 CGATTGTTCA
* *
57350 ACAAACGCCGCAAAAGGT-ATTGATATTTAGCGGCGTTTAGCATT-A-AAACGCCGCAATAGGTG
1 ACAAACACCGCAAAA-GTCATTGATATTTAGCGGCGTTT-GC-TTCACAAACGCCGCAATAGATG
57412 TTGATATTTAACGGCATTTGGCAG
63 TTGATATTTAACGGCATTTGGCAG
* * * * * *
57436 ACAAACACCGCAATAGTCGTTGATGTTTAGCGGCGTTTTCTTCACAAACGCCGCAGTAGATGTTT
1 ACAAACACCGCAAAAGTCATTGATATTTAGCGGCGTTTGCTTCACAAACGCCGCAATAGATGTTG
* *
57501 ATTTTTACCGGCATTT
66 ATATTTAACGGCATTT
57517 TATTACAAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 2 0.03
85 4 0.06
86 62 0.91
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (86 bp):
ACAAACACCGCAAAAGTCATTGATATTTAGCGGCGTTTGCTTCACAAACGCCGCAATAGATGTTG
ATATTTAACGGCATTTGGCAG
Found at i:57865 original size:20 final size:20
Alignment explanation
Indices: 57840--57877 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
57830 CTCTCTGTTC
57840 TGCCGCTGCCTCTCTCTGGG
1 TGCCGCTGCCTCTCTCTGGG
*
57860 TGCCGCTGCTTCTCTCTG
1 TGCCGCTGCCTCTCTCTG
57878 CTTCTGCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.39, G:0.26, T:0.34
Consensus pattern (20 bp):
TGCCGCTGCCTCTCTCTGGG
Found at i:58280 original size:21 final size:20
Alignment explanation
Indices: 58239--58289 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
58229 AATAATTAAT
*
58239 TAAA-ATAAAAAATTCATGG
1 TAAATATAAAAAAGTCATGG
58258 TACAATATAAATAAAGTCA-GG
1 TA-AATATAAA-AAAGTCATGG
*
58279 TAAATTTAAAA
1 TAAATATAAAA
58290 CATCTACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 9 0.33
21 9 0.33
22 6 0.22
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (20 bp):
TAAATATAAAAAAGTCATGG
Done.