Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006474.1 Hibiscus syriacus cultivar Beakdansim tig00015690_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: 104767
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1500 original size:20 final size:19
Alignment explanation
Indices: 1469--1588 Score: 100
Period size: 19 Copynumber: 6.8 Consensus size: 19
1459 GTCTTTGGTT
1469 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1488 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
**
1508 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1527 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1541 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1560 G--A-G---ATCGCAACGC
1 GAAATGAAAATCGCAACGA
1573 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1589 TGCGATTTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
13 10 0.12
14 10 0.12
15 1 0.01
16 4 0.05
17 3 0.04
19 35 0.44
20 17 0.21
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1536 original size:33 final size:33
Alignment explanation
Indices: 1494--1588 Score: 165
Period size: 33 Copynumber: 2.9 Consensus size: 33
1484 ACGAGATAAT
**
1494 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1527 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1560 GAG-ATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
1589 TGCGATTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 26 0.43
33 34 0.57
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1611 original size:19 final size:19
Alignment explanation
Indices: 1589--1636 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1579 AAAATCGCAA
1589 TGCGATTTTAATTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
1608 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
1628 TGCGATTTT
1 TGCGATTTT
1637 CATTCTCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:2192 original size:20 final size:20
Alignment explanation
Indices: 2151--2262 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
2141 GTTATGTAAA
* *
2151 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
*
2171 TCACATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
2191 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
2212 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
2232 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
2252 TCGCATTGCGA
1 TCGCATTGCGA
2263 ATTATGAAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 56 0.73
21 18 0.23
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:2226 original size:41 final size:40
Alignment explanation
Indices: 2169--2276 Score: 126
Period size: 41 Copynumber: 2.7 Consensus size: 40
2159 CGATAGTAAG
* * *
2169 ATTCACATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
2209 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
2250 ATTCGCATTGCGAATTATGAAATCGCA
1 ATTCGCATTGCGATTTACGTAATCGCA
2277 ACGCGAATAC
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
40 22 0.39
41 34 0.61
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:2274 original size:40 final size:40
Alignment explanation
Indices: 2142--2386 Score: 144
Period size: 40 Copynumber: 6.0 Consensus size: 40
2132 ATGAATGGCG
* * * *
2142 TTATGTAAATCGCATTGCGATAGTAAG-ATTCACATTGCGAT
1 TTATG-AAATCGCATTGCGAT-TTACGTATTCGCATTGCGAA
* * * * * *
2183 TTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGAT
1 TTATGAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAA
* *
2224 TTACT-TAATCGCGTTGCGATTTACGTATTCGCATTGCGAA
1 TTA-TGAAATCGCATTGCGATTTACGTATTCGCATTGCGAA
** * * *
2264 TTATGAAATCGCAACGCGA-ATACGTAAATCGCAATGCGAA
1 TTATGAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAA
* *
2304 TTAGGAAAAT-GCATTGCGATAGT-CAGTA-TCGCATTGCG-A
1 TTATG-AAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAA
* * * *
2343 TTTTCCAAATTCGCATTGCGATTTACTTATTCGTATTGCGAA
1 TTAT-GAAA-TCGCATTGCGATTTACGTATTCGCATTGCGAA
2385 TT
1 TT
2387 GGGAAAATCG
Statistics
Matches: 157, Mismatches: 32, Indels: 29
0.72 0.15 0.13
Matches are distributed among these distances:
39 13 0.08
40 75 0.48
41 63 0.40
42 6 0.04
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (40 bp):
TTATGAAATCGCATTGCGATTTACGTATTCGCATTGCGAA
Found at i:2275 original size:20 final size:20
Alignment explanation
Indices: 2174--2322 Score: 86
Period size: 20 Copynumber: 7.4 Consensus size: 20
2164 GTAAGATTCA
* * *
2174 CATTGCGATTTACGTATTCG
1 CATTGCGAATTACGAAATCG
* * * *
2194 CATTGCGATTTTCCTAATTCG
1 CATTGCGA-ATTACGAAATCG
* **
2215 CATTGCGATTTACTTAATCG
1 CATTGCGAATTACGAAATCG
* * * *
2235 CGTTGCGATTTACGTATTCG
1 CATTGCGAATTACGAAATCG
*
2255 CATTGCGAATTATGAAATCG
1 CATTGCGAATTACGAAATCG
**
2275 CAACGCGAA-TACGTAAATCG
1 CATTGCGAATTACG-AAATCG
* *
2295 CAATGCGAATTAGGAAAAT-G
1 CATTGCGAATTACG-AAATCG
2315 CATTGCGA
1 CATTGCGA
2323 TAGTCAGTAT
Statistics
Matches: 105, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
19 3 0.03
20 78 0.74
21 24 0.23
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (20 bp):
CATTGCGAATTACGAAATCG
Found at i:2425 original size:21 final size:22
Alignment explanation
Indices: 2377--2425 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2367 ACTTATTCGT
2377 ATTGCG-AATTGGGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
**
2398 AACGCGAAATT-GGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
2419 ATTGCGA
1 ATTGCGA
2426 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (22 bp):
ATTGCGAAATTGGGAAAATCGC
Found at i:2755 original size:29 final size:28
Alignment explanation
Indices: 2701--2774 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
2691 AAGTACATTA
*
2701 TTTAAAATAAA-TATTAATTATATTATT
1 TTTAAAATAAATTATAAATTATATTATT
* *
2728 TTTAAAGATAAATTATAAATTTTCTTATT
1 TTTAAA-ATAAATTATAAATTATATTATT
*
2757 GTTAAAA-AATATTATAAA
1 TTTAAAATAA-ATTATAAA
2775 AATAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 8 0.20
28 14 0.35
29 18 0.45
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (28 bp):
TTTAAAATAAATTATAAATTATATTATT
Found at i:11200 original size:60 final size:60
Alignment explanation
Indices: 11077--11200 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
11067 TAAAATACAC
* * *
11077 AAATAATCCTTTGATTATAGGATATTACTTTATTAAGTCTCTCAGCTATTAAAAATTACA
1 AAATAATCCTTTGACTATAGAATATTACTTTATTAAGTCTCTCAGCTATTAAAAATTAAA
* * * *
11137 AAATAGTCCTTTGACTATAGAATATTACTTTTTTAAGTC-CATC-GACTATTAGAAGTTAAA
1 AAATAATCCTTTGACTATAGAATATTACTTTATTAAGTCTC-TCAG-CTATTAAAAATTAAA
11197 AAAT
1 AAAT
11201 GATCACCCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.04
60 53 0.96
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (60 bp):
AAATAATCCTTTGACTATAGAATATTACTTTATTAAGTCTCTCAGCTATTAAAAATTAAA
Found at i:11685 original size:41 final size:41
Alignment explanation
Indices: 11640--11768 Score: 152
Period size: 41 Copynumber: 3.1 Consensus size: 41
11630 TTTCCCAAAT
* * *
11640 TCGCATTGCGATTTTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTTTCGTAAATCGCAATGCGAATACGTAAA
* * * * *
11681 TCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTTTCGTAAATCGCAATGCGAATACGTAAA
* *
11722 TCTCAATGCGATTTACGTAAATCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGATTTTCGTAAATCGCAATGCGAATAC-GTAAA
11763 TCGCAA
1 TCGCAA
11769 CGAGATTCTG
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 1 0.01
41 70 0.99
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (41 bp):
TCGCAATGCGATTTTCGTAAATCGCAATGCGAATACGTAAA
Found at i:11686 original size:20 final size:20
Alignment explanation
Indices: 11661--11768 Score: 119
Period size: 20 Copynumber: 5.3 Consensus size: 20
11651 TTTTCCTAAT
11661 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
11681 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
11702 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
11722 TCTCAATGCGATTTACGTAAA
1 TCGCAATGCGA-ATACGTAAA
11743 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
11763 TCGCAA
1 TCGCAA
11769 CGAGATTCTG
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.52
21 34 0.47
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:11739 original size:21 final size:21
Alignment explanation
Indices: 11618--11753 Score: 118
Period size: 21 Copynumber: 6.6 Consensus size: 21
11608 GATTCTGACT
* **
11618 ATCGCATTGCGATTT-CCCAA
1 ATCGCAATGCGATTTACGTAA
* * *
11638 ATTCGCATTGCGATTTTCCTAA
1 A-TCGCAATGCGATTTACGTAA
* *
11660 TTCGCAATGCGA-ATACGTAA
1 ATCGCAATGCGATTTACGTAA
* * *
11680 ATCGCAACGCGAATTT-GGAAA
1 ATCGCAATGCG-ATTTACGTAA
11701 ATCGCAATGCGA-TTACGTAA
1 ATCGCAATGCGATTTACGTAA
*
11721 ATCTCAATGCGATTTACGTAA
1 ATCGCAATGCGATTTACGTAA
11742 ATCGCAATGCGA
1 ATCGCAATGCGA
11754 ATCTGTAAAT
Statistics
Matches: 94, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.02
20 30 0.32
21 57 0.61
22 5 0.05
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (21 bp):
ATCGCAATGCGATTTACGTAA
Found at i:11778 original size:20 final size:20
Alignment explanation
Indices: 11738--11778 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11728 TGCGATTTAC
* *
11738 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGAGAATCT
*
11758 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGAGAATCT
11778 G
1 G
11779 ACTATCGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
GTAAATCGCAACGAGAATCT
Found at i:11816 original size:82 final size:80
Alignment explanation
Indices: 11599--11817 Score: 221
Period size: 82 Copynumber: 2.7 Consensus size: 80
11589 GTTTCCAGAT
* * * *
11599 TCGCAACGCGATTCTGACTATCGCATTGCGATTTCCCAAATTCGCATTGCGATTTTCCTAATTCG
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTT--CAAATTCGCAATGCGATTTACCTAAATCG
11664 CAATGCGAATACGTAAA
64 CAATGCGAATACGTAAA
** * * *
11681 TCGCAACGCGAATT-TGGAAAATCGCAATGCGATTACGTAAA-TCTCAATGCGATTTACGTAAAT
1 TCGCAACGCG-ATTCT-GACTATCGCAATGCGATTTC--AAATTCGCAATGCGATTTACCTAAAT
11744 CGCAATGCGAAT-CTGTAAA
62 CGCAATGCGAATAC-GTAAA
* *
11763 TCGCAACGAGATTCTGACTATCGCAATACTGAATTTCAAATTCGCAACT-CGATTT
1 TCGCAACGCGATTCTGACTATCGCAATGC-G-ATTTCAAATTCGCAA-TGCGATTT
11818 CTGAATTCGC
Statistics
Matches: 112, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
81 19 0.17
82 67 0.60
83 26 0.23
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (80 bp):
TCGCAACGCGATTCTGACTATCGCAATGCGATTTCAAATTCGCAATGCGATTTACCTAAATCGCA
ATGCGAATACGTAAA
Found at i:12655 original size:24 final size:24
Alignment explanation
Indices: 12628--12681 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
12618 GTATTCGAAA
12628 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
12652 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
12676 TTTGAT
1 TTTGAT
12682 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:15112 original size:20 final size:20
Alignment explanation
Indices: 15087--15180 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
15077 GACATTCATT
15087 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
15107 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* * *
15127 TGACTATCGCAATGCAGAAT
1 TGACTATCGCAACGCGGAAA
15147 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
15167 TGACTATCGCAACG
1 TGACTATCGCAACG
15181 AGAGAATCGC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 62 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:15151 original size:40 final size:40
Alignment explanation
Indices: 15087--15180 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
15077 GACATTCATT
15087 TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
* *
15127 TGACTATCGCAATGCAGAAT-TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGC-GAATATGACTATCGCAACACGGAAA
15167 TGACTATCGCAACG
1 TGACTATCGCAACG
15181 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 46 0.92
41 4 0.08
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (40 bp):
TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
Found at i:15209 original size:19 final size:19
Alignment explanation
Indices: 15185--15272 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
15175 GCAACGAGAG
15185 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
15204 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
15223 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
15237 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
15257 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
15273 TAGTTTCGCG
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
14 8 0.13
16 5 0.08
17 2 0.03
18 3 0.05
19 31 0.52
20 11 0.18
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:15228 original size:52 final size:52
Alignment explanation
Indices: 15132--15272 Score: 192
Period size: 53 Copynumber: 2.7 Consensus size: 52
15122 GGAAATGACT
* ** **
15132 ATCGCAATGCAGAATTGACTATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAGA
* *
15186 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGA
15238 ATCGCAATGCGAAAATGAAAATCGCAACGCGAAAT
1 ATCGCAATGCG-AAATGAAAATCGCAACGCGAAAT
15273 TAGTTTCGCG
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
52 31 0.40
53 37 0.47
54 10 0.13
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.16
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:15349 original size:33 final size:33
Alignment explanation
Indices: 15282--15350 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
15272 TTAGTTTCGC
** * *
15282 GTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 GTTGCGATAGTCATTTCCGCATTGCGATACTCT
* *
15315 GTTGCGATAGTCATTTCCGCGTTGCGATAGTCT
1 GTTGCGATAGTCATTTCCGCATTGCGATACTCT
15348 GTT
1 GTT
15351 TTGCATTCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.43
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCCGCATTGCGATACTCT
Found at i:15463 original size:14 final size:14
Alignment explanation
Indices: 15444--15480 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
15434 CATCAATTAA
15444 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
15458 ACAAATCATCTTTT
1 ACAAATCAACATTT
15472 ACAAATCAA
1 ACAAATCAA
15481 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:16891 original size:21 final size:21
Alignment explanation
Indices: 16867--16936 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
16857 TGACAGTGGC
16867 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** *
16888 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGA
16909 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
16930 CTCTTGA
1 CTCTTGA
16937 GGGATGATAG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.08
21 33 0.85
22 3 0.08
ACGTcount: A:0.19, C:0.16, G:0.43, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:16901 original size:42 final size:42
Alignment explanation
Indices: 16855--16960 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
16845 CCTCTTCAAC
* *
16855 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
16897 GATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
16939 GATGATAGGGGCCTCTTGAACG
1 GATGATAGGGGCCTCTTGAACG
16961 ATAAGGGAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.20, C:0.16, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
Found at i:16948 original size:21 final size:21
Alignment explanation
Indices: 16882--16957 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
16872 GAACGGTGGG
16882 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGAGGGATGAT
* * **
16903 AGGGGCCTCTTGAACGG-TGGG
1 AGGGGACTCTTG-AGGGATGAT
16924 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGAGGGATGAT
*
16945 AGGGGCCTCTTGA
1 AGGGGACTCTTGA
16958 ACGATAAGGG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.20, C:0.14, G:0.43, T:0.22
Consensus pattern (21 bp):
AGGGGACTCTTGAGGGATGAT
Found at i:16985 original size:42 final size:41
Alignment explanation
Indices: 16836--16960 Score: 169
Period size: 42 Copynumber: 3.0 Consensus size: 41
16826 TCTAGAATAT
* * * *
16836 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGGA-CTCTTGAAGGATGATAGGGGCCTCTTGAACGG
*
16878 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGG
1 TGGGA-GGGACTCTTGAAGGATGATAGGGGCCTCTTGAACGG
*
16920 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACG
1 TGGGA-GGGACTCTTGAAGGATGATAGGGGCCTCTTGAACG
16961 ATAAGGGAGG
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
42 73 0.95
43 4 0.05
ACGTcount: A:0.20, C:0.18, G:0.41, T:0.22
Consensus pattern (41 bp):
TGGGAGGGACTCTTGAAGGATGATAGGGGCCTCTTGAACGG
Found at i:17493 original size:20 final size:20
Alignment explanation
Indices: 17469--17535 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
17459 GAAACTTAAA
17469 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
17489 TTCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
17509 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
17529 ATCGCAA
1 ATCGCAA
17536 CGAGAGAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:17607 original size:20 final size:20
Alignment explanation
Indices: 17582--17691 Score: 202
Period size: 20 Copynumber: 5.5 Consensus size: 20
17572 GATTCTTTCG
**
17582 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
17602 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
17622 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
17642 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
17662 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
17682 TTGCGATAGT
1 TTGCGATAGT
17692 AAACTATTCT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:17630 original size:40 final size:40
Alignment explanation
Indices: 17544--17691 Score: 202
Period size: 40 Copynumber: 3.9 Consensus size: 40
17534 AACGAGAGAA
* **
17544 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
**
17579 TCG--TTGCGATAGTCAAATTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
17617 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
17657 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
17692 AAACTATTCT
Statistics
Matches: 100, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
33 9 0.09
34 13 0.13
35 3 0.03
36 2 0.02
38 5 0.05
40 68 0.68
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:17649 original size:60 final size:56
Alignment explanation
Indices: 17544--17691 Score: 194
Period size: 60 Copynumber: 2.6 Consensus size: 56
17534 AACGAGAGAA
* **
17544 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCTTTCGTTGCGATAGTCAAAT
**
17597 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTC--TTTCG--TTGCGATAGTCAAAT
17657 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
17692 AAACTATTCT
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
53 14 0.17
54 14 0.17
56 2 0.02
58 5 0.06
60 48 0.58
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (56 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCTTTCGTTGCGATAGTCAAAT
Found at i:19616 original size:20 final size:20
Alignment explanation
Indices: 19564--19631 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
19554 GAAACTTTAA
* **
19564 ATCGCAACACAAAAATGAAA
1 ATCGCAACACGAAAATGACT
19584 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
19604 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
19624 ATCGCAAC
1 ATCGCAAC
19632 GCAAGAATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.44, C:0.25, G:0.15, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:19721 original size:21 final size:20
Alignment explanation
Indices: 19675--19724 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
19665 GCGATTCTCT
19675 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
19695 CATTGCGATAGTCATTTTTCG
1 CGTTGCGATAGTCA-AATTCG
19716 CGTTGCGAT
1 CGTTGCGAT
19725 TCACTCGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:20341 original size:20 final size:20
Alignment explanation
Indices: 20314--20407 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
20304 CGATAGTCAG
20314 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
20334 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
20354 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
20375 ATTCGCGTTGCGATTTGCGT
1 ATTCGCATTGCGATTTACGT
20395 ATTCGCATTGCGA
1 ATTCGCATTGCGA
20408 ATTATGAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 46 0.75
21 15 0.25
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:20401 original size:41 final size:40
Alignment explanation
Indices: 20314--20407 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 40
20304 CGATAGTCAG
** *
20314 ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAAATTCGCATTGCGATTTACGT
* * * *
20354 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTGCGT
1 ATTCGCATTGCGA-TTTACAAATTCGCATTGCGATTTACGT
20395 ATTCGCATTGCGA
1 ATTCGCATTGCGA
20408 ATTATGAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 12 0.27
41 33 0.73
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACAAATTCGCATTGCGATTTACGT
Found at i:20888 original size:2 final size:2
Alignment explanation
Indices: 20881--20929 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
20871 GAGATTTAAG
20881 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20923 TA TA TA T
1 TA TA TA T
20930 GGGTTTCTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22833 original size:19 final size:18
Alignment explanation
Indices: 22809--22877 Score: 84
Period size: 19 Copynumber: 3.7 Consensus size: 18
22799 CCGGTTTTCA
*
22809 ACCGGTTCTGACCAGTTTG
1 ACCGG-TCTGACCGGTTTG
* *
22828 ACCGGTTTCAACCGGTTTG
1 ACCGGTCT-GACCGGTTTG
22847 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTG-ACCGGTTTG
22866 ACCGGTCTGACC
1 ACCGGTCTGACC
22878 CGACCCGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.12
19 38 0.88
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.28
Consensus pattern (18 bp):
ACCGGTCTGACCGGTTTG
Found at i:22835 original size:9 final size:9
Alignment explanation
Indices: 22809--22877 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
22799 CCGGTTTTCA
22809 ACCGGTTCTG
1 ACCGGTT-TG
*
22819 ACCAGTTTG
1 ACCGGTTTG
*
22828 ACCGGTTTCA
1 ACCGGTTT-G
22838 ACCGGTTTG
1 ACCGGTTTG
*
22847 ACCGGTCTG
1 ACCGGTTTG
22856 AACCGGTTTG
1 -ACCGGTTTG
*
22866 ACCGGTCTG
1 ACCGGTTTG
22875 ACC
1 ACC
22878 CGACCCGACC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
9 28 0.56
10 22 0.44
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:22895 original size:17 final size:17
Alignment explanation
Indices: 22873--22911 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
22863 TTGACCGGTC
22873 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
22890 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
22907 TGACC
1 TGACC
22912 GTTGACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:29265 original size:59 final size:60
Alignment explanation
Indices: 29195--29315 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
29185 GCCTTCCTCC
29195 GTACAATCTCTTTGAA-CGTCTCTCTTTCCCTACATAGTATCTTTGTATTAAGCAAGTTT
1 GTACAATCTCTTTGAACCGTCTCTCTTTCCCTACATAGTATCTTTGTATTAAGCAAGTTT
**
29254 GTACAATCTCTTTGAACCGTCTCTCTTTCTGTACATAGTATCTTTGTATTAAGCAAGTTT
1 GTACAATCTCTTTGAACCGTCTCTCTTTCCCTACATAGTATCTTTGTATTAAGCAAGTTT
29314 GT
1 GT
29316 CATGTATCTG
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 16 0.27
60 43 0.73
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (60 bp):
GTACAATCTCTTTGAACCGTCTCTCTTTCCCTACATAGTATCTTTGTATTAAGCAAGTTT
Found at i:31821 original size:14 final size:15
Alignment explanation
Indices: 31796--31828 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
31786 TAAATGCAAT
*
31796 AATTTGCTTTTAATA
1 AATTTGCTTTTAAAA
31811 AATTTGC-TTTAAAA
1 AATTTGCTTTTAAAA
31825 AATT
1 AATT
31829 AGTAGTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (15 bp):
AATTTGCTTTTAAAA
Found at i:33201 original size:30 final size:29
Alignment explanation
Indices: 33162--33222 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
33152 CAATTTTGAA
*
33162 AAAAATAATAGTTCAGATACTAAAATAGAT
1 AAAAATAATAGTTCAGATA-TAAAATACAT
* *
33192 AAAACTAATAGTTTAGATATAAAATACAT
1 AAAAATAATAGTTCAGATATAAAATACAT
33221 AA
1 AA
33223 TTTAGCCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (29 bp):
AAAAATAATAGTTCAGATATAAAATACAT
Found at i:33226 original size:20 final size:20
Alignment explanation
Indices: 33190--33227 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33180 ACTAAAATAG
*
33190 ATAAAACTAATAGTTTAGAT
1 ATAAAACTAATAATTTAGAT
33210 ATAAAA-TACATAATTTAG
1 ATAAAACTA-ATAATTTAG
33228 CCATAATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (20 bp):
ATAAAACTAATAATTTAGAT
Found at i:33329 original size:2 final size:2
Alignment explanation
Indices: 33322--33348 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33312 TATCTATCAG
33322 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
33349 CTCAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35884 original size:11 final size:11
Alignment explanation
Indices: 35868--35898 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
35858 GTTTATAATC
35868 TTTATCTTTCG
1 TTTATCTTTCG
35879 TTTATCTTTCG
1 TTTATCTTTCG
35890 TTTATCTTT
1 TTTATCTTT
35899 GTTGTCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.10, C:0.16, G:0.06, T:0.68
Consensus pattern (11 bp):
TTTATCTTTCG
Found at i:35923 original size:15 final size:15
Alignment explanation
Indices: 35905--35935 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35895 CTTTGTTGTC
*
35905 TTAATCTTCATCTTG
1 TTAATCTTAATCTTG
35920 TTAATCTTAATCTTG
1 TTAATCTTAATCTTG
35935 T
1 T
35936 GTTATTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.16, G:0.06, T:0.55
Consensus pattern (15 bp):
TTAATCTTAATCTTG
Found at i:44049 original size:282 final size:282
Alignment explanation
Indices: 43327--44433 Score: 1503
Period size: 282 Copynumber: 3.9 Consensus size: 282
43317 ATCTAACGAT
* * * * *
43327 TTTAGTACTTAAACTATTAATTTTGGTCCGTTTTAGTA-CTAAAACTTTTAATTTTTCCAATA-C
1 TTTAGTACCTAAACTATCAATTTTGATCCGTTTTAGTACCT-AAACTTTTATTTTTTTCAA-AGC
* * * * *
43390 CATACCTAAAATTTAGGTACTAAAACGGACCAATATTGATATTTTAGGTACTAAACACATTAAGT
64 CATACCTAAAGTTTAGGTACTAAAACGGACCAAAACTGATAGTTTAGGTACTAAACACGTTAAGT
* * *
43455 TTTTAATGGTGGGATACTAAAATGAATTGAAAACTAAACGTT-TGGTATGTTTTTGAAAAAAAAT
129 TTTTAACGGT-GGATACTAAAATGAAATGAAAACTAAACGTTAT-GTATGTTTTTG-AAAAAATT
* *
43519 GAAAGTTTAGGTGCTAAGACGGACCAAAACTGATAGTTTGGGTACCAAATGTGTAGTTTACCTAA
191 GAAAGTTTAGGTGCTAAGACGGACCAAAACTAATAGTTTAGGTACCAAATGTGTAGTTTACCTAA
*
43584 ATATAAA-TTTTTGGGTAAACTACACA
256 ATATAAATTTTTTGGGTAAACTACGCA
* *
43610 TTTAGTACCTAAACTATCAATTTTGATACGTTTTAGTACCTAAAC-TTAATTTTTTTTCAAAGCC
1 TTTAGTACCTAAACTATCAATTTTGATCCGTTTTAGTACCTAAACTTTTA-TTTTTTTCAAAGCC
* *
43674 ATACCTAAAGTTTAGGTACTAAAACGGACCAAAAGTGATAGTTTAGGTACTAAACATGTTAAGTT
65 ATACCTAAAGTTTAGGTACTAAAACGGACCAAAACTGATAGTTTAGGTACTAAACACGTTAAGTT
* * *
43739 TTTAATGGTGTAATACTAAAATGAAATGAAAACTAAACGTTATGTATGCTTTTGAAAAAATTGAA
130 TTTAACGGTG-GATACTAAAATGAAATGAAAACTAAACGTTATGTATGTTTTTGAAAAAATTGAA
* * * * *
43804 AGTTTAGGTGTTAAAATGGACCAGAACTAATAGTTTGGGTACCAAATGTGTAGTTTACCTAAATA
194 AGTTTAGGTGCTAAGACGGACCAAAACTAATAGTTTAGGTACCAAATGTGTAGTTTACCTAAATA
*
43869 TAAATTTTTTGGATAAACTACGCA
259 TAAATTTTTTGGGTAAACTACGCA
* * * *
43893 TTTAGTACCTAAGCTATCAGTTTTAATCCGTTTTAGTACCTAAACTTTATTATTTTTTTCAAAGT
1 TTTAGTACCTAAACTATCAATTTTGATCCGTTTTAGTACCTAAAC-TT-TTATTTTTTTCAAAGC
* * *
43958 CATACCTAAAGTTTAGGTACTAAAACGGAACAAAACTGATAGTTTAGGCACTAAACACGTTAAGA
64 CATACCTAAAGTTTAGGTACTAAAACGGACCAAAACTGATAGTTTAGGTACTAAACACGTTAAGT
* *
44023 TTTTAACGGT-G-CACTAAAATGAAATGAAAACTAAACGTTATGCATGTTTTTGAAAAAATTGAA
129 TTTTAACGGTGGATACTAAAATGAAATGAAAACTAAACGTTATGTATGTTTTTGAAAAAATTGAA
* * *
44086 AGTTTAGATGATAAGACAGACCAAAACTAATAGTTTAGGTACCAAATGTGTAG-TTACCTAAATA
194 AGTTTAGGTGCTAAGACGGACCAAAACTAATAGTTTAGGTACCAAATGTGTAGTTTACCTAAATA
*
44150 T-ATTTTTTTGGGTAAACTACGCA
259 TAAATTTTTTGGGTAAACTACGCA
*
44173 TTTAGTACCTAAACTATCAATTTTGATCCGTTTTAGTACCTAAACTTTTAATTTTTTTCAAAACC
1 TTTAGTACCTAAACTATCAATTTTGATCCGTTTTAGTACCTAAACTTTT-ATTTTTTTCAAAGCC
* * *
44238 ATACTTAAAGTTTAGGTACTAAAACAGACCAAAACTGATAGTTTATGTACTAAACACGTTAAGTT
65 ATACCTAAAGTTTAGGTACTAAAACGGACCAAAACTGATAGTTTAGGTACTAAACACGTTAAGTT
* * * * * * * * *
44303 TTTAACGGTGGGTAGTAAAATGGAATAAAAATTAAATGTTAGGTAAGTTTTTTAAAAAAATTGAA
130 TTTAACGGTGGATACTAAAATGAAATGAAAACTAAACGTTATGTATG-TTTTTGAAAAAATTGAA
* * * ***
44368 AGTTTAGGTGCTAAGACGGACCAAAACTGATAGTCTAGGTATCAAATGCACAGTTTACCTAAATA
194 AGTTTAGGTGCTAAGACGGACCAAAACTAATAGTTTAGGTACCAAATGTGTAGTTTACCTAAATA
44433 T
259 T
44434 CAAACCAAAA
Statistics
Matches: 731, Mismatches: 79, Indels: 28
0.87 0.09 0.03
Matches are distributed among these distances:
278 2 0.00
279 83 0.11
280 63 0.09
281 38 0.05
282 234 0.32
283 224 0.31
284 3 0.00
285 82 0.11
286 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (282 bp):
TTTAGTACCTAAACTATCAATTTTGATCCGTTTTAGTACCTAAACTTTTATTTTTTTCAAAGCCA
TACCTAAAGTTTAGGTACTAAAACGGACCAAAACTGATAGTTTAGGTACTAAACACGTTAAGTTT
TTAACGGTGGATACTAAAATGAAATGAAAACTAAACGTTATGTATGTTTTTGAAAAAATTGAAAG
TTTAGGTGCTAAGACGGACCAAAACTAATAGTTTAGGTACCAAATGTGTAGTTTACCTAAATATA
AATTTTTTGGGTAAACTACGCA
Found at i:44557 original size:172 final size:172
Alignment explanation
Indices: 44265--44608 Score: 679
Period size: 172 Copynumber: 2.0 Consensus size: 172
44255 ACTAAAACAG
44265 ACCAAAACTGATAGTTTATGTACTAAACACGTTAAGTTTTTAACGGTGGGTAGTAAAATGGAATA
1 ACCAAAACTGATAGTTTATGTACTAAACACGTTAAGTTTTTAACGGTGGGTAGTAAAATGGAATA
44330 AAAATTAAATGTTAGGTAAGTTTTTTAAAAAAATTGAAAGTTTAGGTGCTAAGACGGACCAAAAC
66 AAAATTAAATGTTAGGTAAGTTTTTTAAAAAAATTGAAAGTTTAGGTGCTAAGACGGACCAAAAC
44395 TGATAGTCTAGGTATCAAATGCACAGTTTACCTAAATATCAA
131 TGATAGTCTAGGTATCAAATGCACAGTTTACCTAAATATCAA
44437 ACCAAAACTGATAGTTTATGTACTAAACACGTTAAGTTTTTAACGGTGGGTAGTAAAATGGAATA
1 ACCAAAACTGATAGTTTATGTACTAAACACGTTAAGTTTTTAACGGTGGGTAGTAAAATGGAATA
*
44502 AAAATTAAATGTTAGGTAAGTTTTTTAAAAAAATTGAAAGTTTAGGTGTTAAGACGGACCAAAAC
66 AAAATTAAATGTTAGGTAAGTTTTTTAAAAAAATTGAAAGTTTAGGTGCTAAGACGGACCAAAAC
44567 TGATAGTCTAGGTATCAAATGCACAGTTTACCTAAATATCAA
131 TGATAGTCTAGGTATCAAATGCACAGTTTACCTAAATATCAA
44609 TTTTTTTTAG
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 171 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.31
Consensus pattern (172 bp):
ACCAAAACTGATAGTTTATGTACTAAACACGTTAAGTTTTTAACGGTGGGTAGTAAAATGGAATA
AAAATTAAATGTTAGGTAAGTTTTTTAAAAAAATTGAAAGTTTAGGTGCTAAGACGGACCAAAAC
TGATAGTCTAGGTATCAAATGCACAGTTTACCTAAATATCAA
Found at i:51362 original size:11 final size:11
Alignment explanation
Indices: 51348--51377 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
51338 TCCTCATTCG
51348 TCCCTCCCTCC
1 TCCCTCCCTCC
51359 TCCCTCCCTCC
1 TCCCTCCCTCC
*
51370 TCCTTCCC
1 TCCCTCCC
51378 CTTCCCCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (11 bp):
TCCCTCCCTCC
Found at i:51382 original size:6 final size:6
Alignment explanation
Indices: 51371--51432 Score: 82
Period size: 6 Copynumber: 11.3 Consensus size: 6
51361 CCTCCCTCCT
51371 CCTTCC CCTTCC CCTTCC CCTT-- -CTTCC CCTTCC CCTTCC CCTTCC
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC
51416 CCTT-- -CTTCC CCTTCC CC
1 CCTTCC CCTTCC CCTTCC CC
51433 AAGAAATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
3 6 0.12
6 44 0.88
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CCTTCC
Found at i:51389 original size:27 final size:26
Alignment explanation
Indices: 51359--51432 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 26
51349 CCCTCCCTCC
51359 TCCCTCCCTCCTCCTTCCCCTTCCCCT
1 TCCCTCCCTCC-CCTTCCCCTTCCCCT
* *
51386 TCCCCTTCTTCCCCTTCCCCTTCCCCT
1 T-CCCTCCCTCCCCTTCCCCTTCCCCT
* *
51413 TCCCCTTCTTCCCCTTCCCC
1 T-CCCTCCCTCCCCTTCCCC
51433 AAGAAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 36 0.82
28 8 0.18
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (26 bp):
TCCCTCCCTCCCCTTCCCCTTCCCCT
Found at i:51396 original size:21 final size:21
Alignment explanation
Indices: 51372--51432 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 21
51362 CTCCCTCCTC
51372 CTTCCCCTTCCCCTTCCCCTT
1 CTTCCCCTTCCCCTTCCCCTT
51393 CTTCCCCTTCCCCTTCCCCTT
1 CTTCCCCTTCCCCTTCCCCTT
51414 C--CCCTTCTTCCCCTTCCCC
1 CTTCCC--CTTCCCCTTCCCC
51433 AAGAAATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.08
21 35 0.92
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (21 bp):
CTTCCCCTTCCCCTTCCCCTT
Found at i:73954 original size:21 final size:21
Alignment explanation
Indices: 73891--73956 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
73881 CCCTAACTTA
** *
73891 AAACCCTAAATTATAAACTAT
1 AAACCCTAAACCATAAACTCT
* *
73912 AAATCCTAAACCATAACCTCT
1 AAACCCTAAACCATAAACTCT
* *
73933 AAACCCTAAACCCTAAATTCT
1 AAACCCTAAACCATAAACTCT
73954 AAA
1 AAA
73957 TTCTAACTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (21 bp):
AAACCCTAAACCATAAACTCT
Found at i:74965 original size:2 final size:2
Alignment explanation
Indices: 74958--74985 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
74948 TTAAAATTTA
74958 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
74986 TTAAAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75347 original size:2 final size:2
Alignment explanation
Indices: 75342--75377 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
75332 AATTATGGTT
75342 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
75378 TTTTAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84419 original size:29 final size:29
Alignment explanation
Indices: 84377--84454 Score: 156
Period size: 29 Copynumber: 2.7 Consensus size: 29
84367 CTGTTTATAT
84377 ACTTGAAGCTGAATTCAACTAATATGTGC
1 ACTTGAAGCTGAATTCAACTAATATGTGC
84406 ACTTGAAGCTGAATTCAACTAATATGTGC
1 ACTTGAAGCTGAATTCAACTAATATGTGC
84435 ACTTGAAGCTGAATTCAACT
1 ACTTGAAGCTGAATTCAACT
84455 TTTAGAATCG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (29 bp):
ACTTGAAGCTGAATTCAACTAATATGTGC
Found at i:88713 original size:3 final size:3
Alignment explanation
Indices: 88705--88746 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
88695 AGGATAAATG
*
88705 TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT T-T TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
88747 GATTCATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:90236 original size:7 final size:7
Alignment explanation
Indices: 90226--90311 Score: 52
Period size: 7 Copynumber: 12.3 Consensus size: 7
90216 CCAAACCCTA
90226 AAACTCT
1 AAACTCT
*
90233 AAACCCT
1 AAACTCT
90240 AAAC-CTT
1 AAACTC-T
*
90247 AAACCCT
1 AAACTCT
* *
90254 AAATTTT
1 AAACTCT
90261 AAACTCT
1 AAACTCT
* *
90268 AAACCCC
1 AAACTCT
*
90275 AAATTCT
1 AAACTCT
90282 AAA-TCTT
1 AAACTC-T
90289 AAACTCT
1 AAACTCT
*
90296 -AATTCCT
1 AAACT-CT
90303 AAACTCT
1 AAACTCT
90310 AA
1 AA
90312 CCCTAATAAG
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
6 6 0.10
7 48 0.80
8 6 0.10
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.29
Consensus pattern (7 bp):
AAACTCT
Found at i:90296 original size:14 final size:14
Alignment explanation
Indices: 90218--90311 Score: 71
Period size: 14 Copynumber: 6.6 Consensus size: 14
90208 ATCAAATTCC
* *
90218 AAACCCTAAAACTCT
1 AAACTCTAAATCT-T
* *
90233 AAACCCTAAACCTT
1 AAACTCTAAATCTT
* *
90247 AAACCCTAAATTTT
1 AAACTCTAAATCTT
* **
90261 AAACTCTAAACCCC
1 AAACTCTAAATCTT
*
90275 AAATTCTAAATCTT
1 AAACTCTAAATCTT
* *
90289 AAACTCTAATTCCT
1 AAACTCTAAATCTT
90303 AAACTCTAA
1 AAACTCTAA
90312 CCCTAATAAG
Statistics
Matches: 64, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
14 52 0.81
15 12 0.19
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.28
Consensus pattern (14 bp):
AAACTCTAAATCTT
Found at i:90531 original size:26 final size:24
Alignment explanation
Indices: 90498--90596 Score: 102
Period size: 25 Copynumber: 4.2 Consensus size: 24
90488 TTACATTCAT
90498 AATATTTTATATATTAACTTTAGTA
1 AATATTTTATATATTAACTTTA-TA
90523 AATATTTT-TATATTAAC-TTATTA
1 AATATTTTATATATTAACTTTA-TA
*
90546 AATATTTTATTAAACTTAA-TTTATA
1 AATATTTTA-TATA-TTAACTTTATA
*
90571 AATATTTTAT-T-TTTA-TTTATA
1 AATATTTTATATATTAACTTTATA
90592 AATAT
1 AATAT
90597 ATATTTTATG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
21 14 0.21
23 13 0.20
24 10 0.15
25 22 0.33
26 7 0.11
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (24 bp):
AATATTTTATATATTAACTTTATA
Found at i:90557 original size:12 final size:12
Alignment explanation
Indices: 90540--90581 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
90530 TTATATTAAC
90540 TTATTAAATATT
1 TTATTAAATATT
*
90552 TTATTAAACTTAAT
1 TTATTAAA--TATT
90566 TTA-TAAATATT
1 TTATTAAATATT
90577 TTATT
1 TTATT
90582 TTTATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 9 0.36
13 4 0.16
14 6 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:94115 original size:118 final size:120
Alignment explanation
Indices: 93849--94135 Score: 375
Period size: 118 Copynumber: 2.4 Consensus size: 120
93839 ATTTGTTTTG
* * * *
93849 AAAG-TTATGTATTAAAACAAACCAAAACTGATAGTTTAGGTACTAAATATGTCAAGTTTTGAAA
1 AAAGTTTATGTACTAAAACAAACCAAAATTGATAGTTTATGTACTAAACATGTCAAGTTTTGAAA
* *
93913 GGTGAGTTACTAAAATGAAATAAAAACTAAACGTTAGGTATGGTTTTAAAAAAATTA
66 GGTGAGGTACTAAAATGAAACAAAAACTAAAC--TAGGTATGGTTTTAAAAAAATTA
* ** * *
93970 AAAGTTTAGGTACTAAAACGGACCAAAATTGATAGTTTATGTACTAAACGTGAT-AAGTTTTTAA
1 AAAGTTTATGTACTAAAACAAACCAAAATTGATAGTTTATGTACTAAACATG-TCAAGTTTTGAA
* *
94034 AGGTG-GGTACTAAAATGAAACAAAAACTAAAC-ATGTATGGTTTTGAAAAAATTA
65 AGGTGAGGTACTAAAATGAAACAAAAACTAAACTAGGTATGGTTTTAAAAAAATTA
* * *
94088 AAAGTTTATGTACTAAAACATATCAAAATTGATAGTTTATGTATTAAA
1 AAAGTTTATGTACTAAAACAAACCAAAATTGATAGTTTATGTACTAAA
94136 TGCGTAGTTT
Statistics
Matches: 146, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
118 63 0.43
121 29 0.20
122 53 0.36
123 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (120 bp):
AAAGTTTATGTACTAAAACAAACCAAAATTGATAGTTTATGTACTAAACATGTCAAGTTTTGAAA
GGTGAGGTACTAAAATGAAACAAAAACTAAACTAGGTATGGTTTTAAAAAAATTA
Found at i:94835 original size:20 final size:20
Alignment explanation
Indices: 94798--94836 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
94788 TAAAATCCTA
** *
94798 AGGGGGCGAACTTGAATTTC
1 AGGGGGCGAAAATAAATTTC
94818 AGGGGGCGAAAATAAATTT
1 AGGGGGCGAAAATAAATTT
94837 TCAATATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.23
Consensus pattern (20 bp):
AGGGGGCGAAAATAAATTTC
Found at i:96966 original size:19 final size:19
Alignment explanation
Indices: 96942--96978 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
96932 CTGCAAGAGA
*
96942 AAGAAGGATTAGAAAAAAC
1 AAGAAGGAATAGAAAAAAC
*
96961 AAGAAGGAATCGAAAAAA
1 AAGAAGGAATAGAAAAAA
96979 AGGAGCAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.05, G:0.22, T:0.08
Consensus pattern (19 bp):
AAGAAGGAATAGAAAAAAC
Found at i:99360 original size:16 final size:17
Alignment explanation
Indices: 99329--99362 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
99319 AAATATTATT
*
99329 TTATTATTTATTTTAAA
1 TTATTATTTATATTAAA
99346 TTATT-TTTATATTAAA
1 TTATTATTTATATTAAA
99362 T
1 T
99363 AATAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTATATTAAA
Found at i:103079 original size:2 final size:2
Alignment explanation
Indices: 103072--103101 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
103062 GAAGCAGGTA
103072 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
103102 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:103106 original size:2 final size:2
Alignment explanation
Indices: 103101--103125 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
103091 TCTCTCTCTC
103101 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
103126 CAACAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.