Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004907.1 Hibiscus syriacus cultivar Beakdansim tig00011039_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: 273424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2567 original size:15 final size:15
Alignment explanation
Indices: 2547--2582 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2537 AAAAACAAAT
2547 TAAATAAAG-ATAAGA
1 TAAATAAAGCA-AAGA
2562 TAAATAAAGCAAAGA
1 TAAATAAAGCAAAGA
2577 TAAATA
1 TAAATA
2583 GTAAGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.67, C:0.03, G:0.11, T:0.19
Consensus pattern (15 bp):
TAAATAAAGCAAAGA
Found at i:2645 original size:4 final size:4
Alignment explanation
Indices: 2621--2708 Score: 63
Period size: 4 Copynumber: 21.2 Consensus size: 4
2611 AAGAAGAAAA
* * *
2621 AAAT ATAT AAAT AAAAC AAAT AAAT AAAAT AATAT AAA- AAGT AAA- AAAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT AA-AT AAAT AAAT AAAT AAAT
* * *
2670 AATAT ATAT ATAT ATAT ATAAT AAAT AAAT AAAT AAAT A
1 AA-AT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT A
2709 GTATATATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
3 5 0.07
4 47 0.68
5 17 0.25
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:2786 original size:2 final size:2
Alignment explanation
Indices: 2671--2770 Score: 54
Period size: 2 Copynumber: 52.5 Consensus size: 2
2661 GTAAAAAATA
* * * *
2671 AT AT AT AT AT AT AT AT AT A- AT AA AT AA AT AA AT AA AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
2713 AT AT AT -T AT A- AT A- AA ACT GAT A- AT A- AA AA AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT
2751 AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
2771 AAAAATAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
1 8 0.10
2 65 0.84
3 3 0.04
4 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (2 bp):
AT
Found at i:12681 original size:32 final size:32
Alignment explanation
Indices: 12640--12730 Score: 123
Period size: 30 Copynumber: 2.9 Consensus size: 32
12630 ACAATTACAT
12640 AAACTTTTCAGTGATATATCACTTCATTTCAG
1 AAACTTTTCAGTGATATATCACTTCATTTCAG
* * *
12672 AAACTTTTCAAT--TATATCACTTTATTTCAT
1 AAACTTTTCAGTGATATATCACTTCATTTCAG
* *
12702 AAACTTTTCAGTGATATATTATTTCATTT
1 AAACTTTTCAGTGATATATCACTTCATTT
12731 AAAAAATAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 27 0.54
32 23 0.46
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.47
Consensus pattern (32 bp):
AAACTTTTCAGTGATATATCACTTCATTTCAG
Found at i:12763 original size:18 final size:18
Alignment explanation
Indices: 12740--12776 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12730 TAAAAAATAA
12740 CGTCATTTTCTCATAGAC
1 CGTCATTTTCTCATAGAC
*
12758 CGTCATTTTCTTATAGAC
1 CGTCATTTTCTCATAGAC
12776 C
1 C
12777 ATTTAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.41
Consensus pattern (18 bp):
CGTCATTTTCTCATAGAC
Found at i:14124 original size:2 final size:2
Alignment explanation
Indices: 14117--14165 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
14107 TTTTTAAAAT
14117 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
14159 TA TA TA T
1 TA TA TA T
14166 GAATTTAAAA
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:15245 original size:29 final size:29
Alignment explanation
Indices: 15208--15267 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
15198 CACAACTAAT
* *
15208 CCATCATTCTTTTATTCAACAGTGTTTAA
1 CCATCATTCTTTTACTCAACAGTATTTAA
* *
15237 CCATTATTCTTTTACTCAACGGTATTTAA
1 CCATCATTCTTTTACTCAACAGTATTTAA
15266 CC
1 CC
15268 GTTCATCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (29 bp):
CCATCATTCTTTTACTCAACAGTATTTAA
Found at i:15468 original size:81 final size:81
Alignment explanation
Indices: 15239--15640 Score: 558
Period size: 81 Copynumber: 5.0 Consensus size: 81
15229 GTGTTTAACC
*
15239 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACT-GCATAATTGGTACCTTTCTACCA
1 ATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCA
* *
15303 ATTGCATAGTTAGGCC
66 ATTGCACAGTTAGGCT
* * * * *
15319 ATTATTATTTTACTCAACGATATTTAA-CTTTCATATAACTGGCGTAATTGGTACTTTTCTACCA
1 ATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCA
*
15383 ATTGCACAGTTAGACT
66 ATTGCACAGTTAGGCT
* * * *
15399 ATTATTATTTTACTCAACGATATTTAACCTTTCATCTAACTGGCATAATTGGAATCTTTCTACCA
1 ATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCA
15464 ATTGCACAGTTAGGCT
66 ATTGCACAGTTAGGCT
** * * *
15480 ATTATTGGTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGGTATCTTTCTACTA
1 ATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCA
* * *
15545 ATTGCACAATTATGTT
66 ATTGCACAGTTAGGCT
* * *
15561 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAGC-AGCATAATTGGTACCTTTTCTACC
1 ATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACC-TTTCTACC
15625 AATTGCACAGTTAGGC
65 AATTGCACAGTTAGGC
15641 CTCAAAGGCA
Statistics
Matches: 284, Mismatches: 35, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
79 11 0.04
80 99 0.35
81 174 0.61
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (81 bp):
ATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCA
ATTGCACAGTTAGGCT
Found at i:15689 original size:68 final size:68
Alignment explanation
Indices: 15602--15846 Score: 294
Period size: 68 Copynumber: 3.6 Consensus size: 68
15592 TCATCTAGCA
** *
15602 GCATAATTGGTACCTTTTCTACCAATTGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTA
1 GCATAATTGACACC-TTTCTATCAATTGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTA
15667 ACTG
65 ACTG
* * *
15671 GCATAATTGACACCTTTCTATCAAATGCAAAGTTAGGCCTCAAAGGCACGTAGCCTTTCATCTAA
1 GCATAATTGACACCTTTCTATCAATTGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAA
15736 CTG
66 CTG
* * * * *
15739 GCATAAATGACACCTTTCTGTC-ATATGCACAGTTAGGCCTCAGAGGTACTTAGCATTTCATCTA
1 GCATAATTGACACCTTTCTATCAAT-TGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTA
15803 ACTG
65 ACTG
* * * * * * * *
15807 ACATAAATGATATCTTTCTTTTAAATACACAGTTAGGCCT
1 GCATAATTGACACCTTTCTATCAATTGCACAGTTAGGCCT
15847 ATTAATCTTT
Statistics
Matches: 153, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 1 0.01
68 139 0.91
69 13 0.08
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (68 bp):
GCATAATTGACACCTTTCTATCAATTGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAA
CTG
Found at i:16141 original size:54 final size:56
Alignment explanation
Indices: 16054--16246 Score: 187
Period size: 59 Copynumber: 3.4 Consensus size: 56
16044 ACATGTATTT
** * * * **
16054 CCCATACGAAAATTTGTACAATT-GATATTAATTTCTTA-TTTCGCACACGTAGTG-
1 CCCATACGAAAATTCATACACTTAG-TATGAATTTCTTATTTTAGCACACAAAGTGA
*
16108 CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCATACAAAGTGA
1 CCCATACGAAAATTCATACACTTAGTATGAATTTC-T--TATTTTAGCACACAAAGTGA
*
16167 CCAATACGAAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAAAGTG-
1 CCCATACGAAAATTCATACACTTAGTATGAATTTC-T--TATTTTAGCACACAAAGTGA
* *
16225 CCCAATACGGAAATACATACAC
1 CCC-ATACGAAAATTCATACAC
16247 CACTTTTCTA
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
54 29 0.24
55 2 0.02
57 2 0.02
58 14 0.12
59 72 0.61
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (56 bp):
CCCATACGAAAATTCATACACTTAGTATGAATTTCTTATTTTAGCACACAAAGTGA
Found at i:16178 original size:59 final size:59
Alignment explanation
Indices: 16111--16246 Score: 236
Period size: 59 Copynumber: 2.3 Consensus size: 59
16101 CGTAGTGCCC
*
16111 ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCATACAAAGTGACCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAAAGTGACCA
*
16170 ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAAAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAAAGTGACCA
* *
16229 ATACGGAAATACATACAC
1 ATACGAAAATTCATACAC
16247 CACTTTTCTA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 73 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (59 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAAAGTGACCA
Found at i:16499 original size:81 final size:81
Alignment explanation
Indices: 16262--16656 Score: 567
Period size: 81 Copynumber: 4.9 Consensus size: 81
16252 TTCTAATGTG
* *
16262 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGATACTTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
* *
16327 AGTTAGGCCAATATTC
66 AGTTAGGCTATTATTC
* * * *
16343 TTTTAGTCAACGGTATTTAACCATTTATCTAACT-GCATAATTGGTACTTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
* *
16407 AGTTTGACTATTATTC
66 AGTTAGGCTATTATTC
*
16423 TTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGGTACCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
* *
16488 AGTTATGCTATTATTG
66 AGTTAGGCTATTATTC
* * * * * *
16504 TTTTACTCAAAGGCATTTAGCCATTCATCTAACTGGCATAATTGGTATCTTTCTACTAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
16569 AGTTAGGCTATTATTC
66 AGTTAGGCTATTATTC
* ** * *
16585 TCTTACTCAAATGTATTTAATCGTTCATCTAGCTGGCATAATTGGTACCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
16650 AGTTAGG
66 AGTTAGG
16657 TCTCAAAGGC
Statistics
Matches: 279, Mismatches: 34, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
80 72 0.26
81 207 0.74
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (81 bp):
TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
AGTTAGGCTATTATTC
Found at i:16706 original size:68 final size:67
Alignment explanation
Indices: 16608--16840 Score: 263
Period size: 68 Copynumber: 3.4 Consensus size: 67
16598 TATTTAATCG
* ** * * *
16608 TTCATCTAGCTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGTCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACATTTCTATCAATTG-ACAGTTAGGCCTCAAAGGCACTTAG
16673 CCT
65 CCT
* * *
16676 TTCATCTAACTAGCATAATTGACACATTTCTATCAAATGTACAGTTAGGCCTCAAAGGCACTAAG
1 TTCATCTAACTGGCATAATTGACACATTTCTATCAATTG-ACAGTTAGGCCTCAAAGGCACTTAG
16741 CCT
65 CCT
* * *
16744 TTCATCTAACTGGCATAAATT-ACACATTTCTGTCATATAT-ATAGTTAGGCCTCAAAGGAACTT
1 TTCATCTAACTGGCAT-AATTGACACATTTCTATCA-AT-TGACAGTTAGGCCTCAAAGGCACTT
*
16807 AGCAT
63 AGCCT
* * *
16812 TTCATCTATCTGGCATAAATGAGACATTT
1 TTCATCTAACTGGCATAATTGACACATTT
16841 ATGTTAAATT
Statistics
Matches: 141, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
67 3 0.02
68 132 0.94
69 5 0.04
70 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (67 bp):
TTCATCTAACTGGCATAATTGACACATTTCTATCAATTGACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:16856 original size:68 final size:68
Alignment explanation
Indices: 16650--16859 Score: 269
Period size: 68 Copynumber: 3.1 Consensus size: 68
16640 CCAATTGCAC
* * * * *
16650 AGTTAGGTCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACATTTCTATCAAATG
1 AGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATA
*
16715 TAC
66 TAT
* * *
16718 AGTTAGGCCTCAAAGGCACTAAGCCTTTCATCTAACTGGCATAAATTACACATTTCTGTCATATA
1 AGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATA
16783 TAT
66 TAT
* * * * * *
16786 AGTTAGGCCTCAAAGGAACTTAGCATTTCATCTATCTGGCATAAATGAGACATTTATGTTAAAT-
1 AGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATA
16850 TCAT
66 T-AT
16854 AGTTAG
1 AGTTAG
16860 ACCTATTAAT
Statistics
Matches: 123, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
67 1 0.01
68 122 0.99
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (68 bp):
AGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATA
TAT
Found at i:17206 original size:59 final size:59
Alignment explanation
Indices: 17121--17293 Score: 251
Period size: 59 Copynumber: 3.0 Consensus size: 59
17111 TCGCACACGT
* *
17121 AGTGCCC-ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACATAA
1 AGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAA
* *
17179 AGTGCCCAATATGGAAATTCATTCACTTAGTATGAATTTCTTAGTATTTTAGCACACAA
1 AGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAA
* * * **
17238 AGTGGCCAATACAGAAATTCATACACTTAGTTTGAATTTCTTAACATTTT-GCACAC
1 AGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACAC
17294 TTAGTGCCAT
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 13 0.13
59 90 0.87
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (59 bp):
AGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAA
Found at i:17873 original size:21 final size:20
Alignment explanation
Indices: 17816--17873 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
17806 CCTTATCATG
*
17816 GTATCAATACTACCT-AATC
1 GTATCAATACTACTTCAATC
*
17835 GATATCGATACTGA-TTCAATC
1 G-TATCAATACT-ACTTCAATC
17856 AGTATCAATACTACTTCA
1 -GTATCAATACTACTTCA
17874 TCTAATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 11 0.35
21 18 0.58
22 1 0.03
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (20 bp):
GTATCAATACTACTTCAATC
Found at i:22042 original size:29 final size:29
Alignment explanation
Indices: 22010--22071 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
22000 CACAACTAAT
* * *
22010 CCATCATTCTTTTATTCAACAG-TGTTTAA
1 CCATCATTCATTTACTCAAC-GTTATTTAA
*
22039 CCATTATTCATTTACTCAACGTTATTTAA
1 CCATCATTCATTTACTCAACGTTATTTAA
22068 CCAT
1 CCAT
22072 TCATCTAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.44
Consensus pattern (29 bp):
CCATCATTCATTTACTCAACGTTATTTAA
Found at i:22182 original size:81 final size:81
Alignment explanation
Indices: 22039--22283 Score: 357
Period size: 81 Copynumber: 3.0 Consensus size: 81
22029 CAGTGTTTAA
* * *
22039 CCATTATTCATTTACTCAACGTTATTTAACCATTCATCTAACTGGCATAATTGATA-TCTTTCTA
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGATACT-TTTCTA
*
22103 CCAATTACACAGTTAGG
65 CCAATTGCACAGTTAGG
* *
22120 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGTTACTTTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGATACTTTTCTAC
22185 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
** * * * * *
22201 GTATTATTCTTTTACTCAACGGCATTTAACCGTTCATCTAATTGGTATAATTGGTACCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGATACTTTTCTAC
22266 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
22282 CC
1 CC
22284 TCAAAGGCAT
Statistics
Matches: 147, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
81 146 0.99
82 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (81 bp):
CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGATACTTTTCTAC
CAATTGCACAGTTAGG
Found at i:22305 original size:68 final size:68
Alignment explanation
Indices: 22215--22488 Score: 318
Period size: 68 Copynumber: 4.0 Consensus size: 68
22205 TATTCTTTTA
* * * * * * * **
22215 CTCAACGGCATTTAACCGTTCATCTAATTGGTATAATTGGTACCTTTCTACCAATTGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGATACCTTTCTGTCAATTGCACAGTTA
22280 GGC
66 GGC
* * *
22283 CTCAAAGGCATTTAGCCTTTCATATAACTGGCATAATTGATACCTTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGATACCTTTCTGTCAATTGCACAGTTA
22348 GGC
66 GGC
* * *
22351 CTCAAAGGCACTCAGCCTTTCATCTAACTGACATAAATT-ACACCTTTCTGTC-ATATGCACAGT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCAT-AATTGATACCTTTCTGTCAAT-TGCACAGT
22414 TAGGC
64 TAGGC
* * * * * * *
22419 CTCAAAGGTACTTAGCATTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCATAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGATACCTTTCTGTCAATTGCACAGTTA
22484 GGC
66 GGC
22487 CT
1 CT
22489 ATTAATCTTT
Statistics
Matches: 178, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
67 4 0.02
68 169 0.95
69 5 0.03
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGATACCTTTCTGTCAATTGCACAGTTA
GGC
Found at i:22831 original size:59 final size:59
Alignment explanation
Indices: 22746--22918 Score: 269
Period size: 59 Copynumber: 3.0 Consensus size: 59
22736 TCGCACACGT
* *
22746 AGTGCCC-ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACATAA
1 AGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAA
* *
22804 AGTGCCCAATATGGAAATTCATTCACTTAGTATGAATTTCTTAGTATTTTAGCACACAA
1 AGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAA
* **
22863 AGTGCCCAATACGGAAATTCATACACTTAGTTTGAATTTCTTAACATTTT-GCACAC
1 AGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACAC
22919 TTAGTGCCAT
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
58 13 0.12
59 92 0.88
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (59 bp):
AGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAGTATTTTAGCACACAA
Found at i:25175 original size:21 final size:21
Alignment explanation
Indices: 25151--25190 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25141 AGGATTATTA
*
25151 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
25172 TAATTTTTTATAATAAATA
1 TAATATTTTAAAATAAATA
25191 TTATAAATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:29443 original size:6 final size:6
Alignment explanation
Indices: 29432--29468 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
29422 TCGACTCGTC
* *
29432 TCGTGA TCGTGA TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
29469 AATATGTATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.05, C:0.16, G:0.43, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:29609 original size:21 final size:20
Alignment explanation
Indices: 29585--29653 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
29575 ATTTGAATAA
29585 ATCGAAACGCGAACTTCGACT
1 ATCGAAA-GCGAACTTCGACT
* * *
29606 ATCGCAA-CGAACTTGGAAT
1 ATCGAAAGCGAACTTCGACT
*
29625 AAATCGCAATGCGAACTTCGACT
1 --ATCG-AAAGCGAACTTCGACT
29648 ATCGAA
1 ATCGAA
29654 TAAATCGCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
19 10 0.27
20 2 0.05
21 14 0.38
22 1 0.03
23 10 0.27
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGAAAGCGAACTTCGACT
Found at i:29639 original size:42 final size:42
Alignment explanation
Indices: 29561--29826 Score: 216
Period size: 42 Copynumber: 6.7 Consensus size: 42
29551 TGCGATTTTG
* * *
29561 GACTATCTCAACGAA-TTTGAATAAATCGAAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
29602 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
29644 GACTAT---------C---GAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
29674 GACTATCGCAACGCGAACTT-CAACT--ATCGCAA--TGAATTTG
1 GACTATCGCAA--CGAACTTGGAA-TAAATCGCAACGCGAACTTC
* *
29714 GAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
29758 GACTATCGCAACGAACTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
29798 GACTATCGCAACGAATTTGG-A-AAATCGCA
1 GACTATCGCAACGAACTTGGAATAAATCGCA
29827 TTGCTATAGT
Statistics
Matches: 180, Mismatches: 21, Indels: 49
0.72 0.08 0.20
Matches are distributed among these distances:
30 28 0.16
33 1 0.01
40 56 0.31
41 17 0.09
42 67 0.37
43 2 0.01
44 9 0.05
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:29657 original size:30 final size:30
Alignment explanation
Indices: 29621--29681 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
29611 AACGAACTTG
*
29621 GAATAAATCGCAATGCGAACTTCGACTATC
1 GAATAAATCGCAACGCGAACTTCGACTATC
29651 GAATAAATCGCAACGCGAACTTCGACTATC
1 GAATAAATCGCAACGCGAACTTCGACTATC
29681 G
1 G
29682 CAACGCGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (30 bp):
GAATAAATCGCAACGCGAACTTCGACTATC
Found at i:29681 original size:21 final size:21
Alignment explanation
Indices: 29657--29810 Score: 149
Period size: 21 Copynumber: 7.4 Consensus size: 21
29647 TATCGAATAA
*
29657 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
**
29678 ATCGCAACGCGAACTTCAACT
1 ATCGCAACGCGAACTTGGACT
* * *
29699 ATCGCAA--TGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
* *
29718 AAATCGCAA--CGAATTTGGAAT
1 --ATCGCAACGCGAACTTGGACT
*
29739 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
29762 ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
29781 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
29802 ATCGCAACG
1 ATCGCAACG
29811 AATTTGGAAA
Statistics
Matches: 116, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
19 25 0.22
21 82 0.71
23 9 0.08
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:29799 original size:63 final size:62
Alignment explanation
Indices: 29651--29810 Score: 191
Period size: 63 Copynumber: 2.6 Consensus size: 62
29641 TTCGACTATC
* * * *
29651 GAATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCAACTATCGCAATGAATTTG
1 GAAT-AATCGCAACGCGAACTTGGAATATCGCAACGCGAACTTCAACTATCGCAACGAACTTG
* *
29714 GAATAAATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTG
1 GAAT-AATCGCAACGCGAACTTGGAAT--ATCGCAACGCGAACTTCAACTATCGCAACGAACTTG
* *
29777 GACT-ATCGCAACGCGAACTTGGACTATCGCAACG
1 GAATAATCGCAACGCGAACTTGGAATATCGCAACG
29811 AATTTGGAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
61 25 0.30
63 59 0.70
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (62 bp):
GAATAATCGCAACGCGAACTTGGAATATCGCAACGCGAACTTCAACTATCGCAACGAACTTG
Found at i:29824 original size:19 final size:19
Alignment explanation
Indices: 29699--29826 Score: 85
Period size: 21 Copynumber: 6.3 Consensus size: 19
29689 AACTTCAACT
* *
29699 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAACTTGG-A-AA
*
29720 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGG-A-AA
* **
29741 ATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTGGAAA
**
29762 ATCGCAACGAACTTGGACT
1 ATCGCAACGAACTTGGAAA
**
29781 ATCGCAACGCGAACTTGGACT
1 ATCGCAA--CGAACTTGGAAA
*
29802 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAACTTGGAAA
29821 ATCGCA
1 ATCGCA
29827 TTGCTATAGT
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
19 33 0.35
21 53 0.56
22 1 0.01
23 7 0.07
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (19 bp):
ATCGCAACGAACTTGGAAA
Found at i:29825 original size:40 final size:40
Alignment explanation
Indices: 29655--29826 Score: 161
Period size: 40 Copynumber: 4.2 Consensus size: 40
29645 ACTATCGAAT
*
29655 AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTT-CA
1 AAATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTGGA
* * * * * *
29696 ACTATCGCAA--TGAATTTGGAATAAATCGCAACGAATTTGGAA
1 A-AATCGCAACGCGAACTTCGACT--ATCGCAACGAACTTGG-A
29738 TAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
1 -AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
** * *
29779 CTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGA
1 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
29819 AAATCGCA
1 AAATCGCA
29827 TTGCTATAGT
Statistics
Matches: 104, Mismatches: 19, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
40 56 0.54
41 2 0.02
42 37 0.36
43 1 0.01
44 8 0.08
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
Found at i:30780 original size:5 final size:5
Alignment explanation
Indices: 30770--30798 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
30760 TTAGGATGTT
30770 TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATA
30799 TATTATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:35349 original size:13 final size:13
Alignment explanation
Indices: 35331--35403 Score: 110
Period size: 13 Copynumber: 5.6 Consensus size: 13
35321 GGAATGAGCA
*
35331 TCATAAATACGCG
1 TCATAAATGCGCG
**
35344 TCATAAATGAACG
1 TCATAAATGCGCG
35357 TCATAAATGCGCG
1 TCATAAATGCGCG
*
35370 TCATAAATGCGTG
1 TCATAAATGCGCG
35383 TCATAAATGCGCG
1 TCATAAATGCGCG
35396 TCATAAAT
1 TCATAAAT
35404 TTATTACGCA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 53 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:43832 original size:2 final size:2
Alignment explanation
Indices: 43825--43858 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
43815 CAGCGGCTCA
43825 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
43859 GGCAATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56894 original size:17 final size:17
Alignment explanation
Indices: 56872--56910 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
56862 TGAATCAAAT
56872 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
56889 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
56906 -AATTA
1 TAATTA
56911 ATTGTAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:61958 original size:14 final size:13
Alignment explanation
Indices: 61936--61973 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
61926 ACTTTTTATA
61936 TTAATTATAATTC
1 TTAATTATAATTC
*
61949 TTATATTATAAATC
1 TTA-ATTATAATTC
61963 TTAATTATAAT
1 TTAATTATAAT
61974 CATTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATTATAATTC
Found at i:61979 original size:13 final size:12
Alignment explanation
Indices: 61936--61992 Score: 55
Period size: 13 Copynumber: 4.6 Consensus size: 12
61926 ACTTTTTATA
61936 TTAATTATAATTC
1 TTAATTATAA-TC
61949 TTATATTATAAATC
1 TTA-ATTAT-AATC
61963 TTAATTATAATC
1 TTAATTATAATC
*
61975 ATTAAAT-TAAT-
1 -TTAATTATAATC
61986 TTAATTA
1 TTAATTA
61993 AATAATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 5 0.13
12 8 0.21
13 13 0.34
14 10 0.26
15 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAATTATAATC
Found at i:62200 original size:2 final size:2
Alignment explanation
Indices: 62193--62217 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62183 TAGAATAAAC
62193 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
62218 TCATATGAGT
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
Found at i:65208 original size:19 final size:19
Alignment explanation
Indices: 65172--65210 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
65162 TTTAGGGGAT
65172 AAATTTTTTTTTAAATAAAA
1 AAATTTTTTTTT-AATAAAA
65192 AAATATTTTTTTT-ATAAAA
1 AAAT-TTTTTTTTAATAAAA
65211 TATATGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTTTTTTTTAATAAAA
Found at i:65659 original size:22 final size:21
Alignment explanation
Indices: 65611--65659 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
65601 TTTATTTTAT
* *
65611 AATTATATATAATATTAATTA
1 AATTATATATAATATAAAATA
65632 ATATTATATATAATTATAAAATA
1 A-ATTATATATAA-TATAAAATA
65655 AATTA
1 AATTA
65660 CAAAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTATATATAATATAAAATA
Found at i:65859 original size:21 final size:21
Alignment explanation
Indices: 65817--65859 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
65807 GGTAAAAAAA
* *
65817 TTACCTAAAATATTATTATTT
1 TTACCTAAAACATAATTATTT
65838 TTACCTAAAACATCAATT-TTT
1 TTACCTAAAACAT-AATTATTT
65859 T
1 T
65860 AACATTTCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (21 bp):
TTACCTAAAACATAATTATTT
Found at i:68124 original size:21 final size:21
Alignment explanation
Indices: 68098--68151 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
68088 CTTACAATTG
68098 ACTTGAACCAAATTTGATTCA
1 ACTTGAACCAAATTTGATTCA
*
68119 ACTTGAATCAAATTTGATTCA
1 ACTTGAACCAAATTTGATTCA
68140 ACTTGAATCCAA
1 ACTTGAA-CCAA
68152 CATGAATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (21 bp):
ACTTGAACCAAATTTGATTCA
Found at i:72507 original size:182 final size:178
Alignment explanation
Indices: 72205--72584 Score: 606
Period size: 182 Copynumber: 2.1 Consensus size: 178
72195 TTTTCTAATT
* * * *
72205 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTAAATAATATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTAAATAATATATATAA
*
72269 AATAAAAATTTTAGATAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTAGATCT
66 AATAAAAAATTTAGATAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTAGATCT
*
72334 TAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 TAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
72382 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAAATAA-TTAAAT-A-ATAT-A
*
72446 TTATAAAATAAAAAATTTATAT-AATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
61 -TATAAAATAAAAAATTTAGATAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
72510 AGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
125 AGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
72564 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
72585 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 7, Indels: 11
0.91 0.03 0.05
Matches are distributed among these distances:
177 13 0.07
178 29 0.15
179 6 0.03
180 1 0.01
181 6 0.03
182 114 0.61
183 19 0.10
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (178 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTAAATAATATATATAA
AATAAAAAATTTAGATAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTAGATCT
TAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:77430 original size:103 final size:103
Alignment explanation
Indices: 77205--77422 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
77195 GTCGAGGGTC
77205 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
77270 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
** *
77308 TATGTGGTTATTCGGGACATATATGTATTCTTTGGAACATGTTTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
77373 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
77411 TATGTGGTCCTT
1 TATGTGGTCCTT
77423 ATGGACATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:82660 original size:103 final size:103
Alignment explanation
Indices: 82435--82652 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
82425 GTCGAGGGTC
82435 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
82500 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
82538 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
82603 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
82641 TATGTGGTCCTT
1 TATGTGGTCCTT
82653 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:82695 original size:23 final size:22
Alignment explanation
Indices: 82662--82736 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
82652 TATGGACATT
82662 ATTATAT--GGCATTACGGTGCA
1 ATTATATGCGGCATT-CGGTGCA
* *
82683 ATTCTATGCGGCACTCCGGTGCA
1 ATTATATGCGGCA-TTCGGTGCA
* *
82706 ATTATATGTGGCACTTCGGTGGA
1 ATTATATGCGGCA-TTCGGTGCA
82729 ATTATATG
1 ATTATATG
82737 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.13
23 38 0.84
24 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (22 bp):
ATTATATGCGGCATTCGGTGCA
Found at i:85914 original size:18 final size:18
Alignment explanation
Indices: 85906--85970 Score: 130
Period size: 18 Copynumber: 3.6 Consensus size: 18
85896 AATGCATTTT
85906 ATGCATCGATGCACTTCC
1 ATGCATCGATGCACTTCC
85924 ATGCATCGATGCACTTCC
1 ATGCATCGATGCACTTCC
85942 ATGCATCGATGCACTTCC
1 ATGCATCGATGCACTTCC
85960 ATGCATCGATG
1 ATGCATCGATG
85971 TACTCATGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (18 bp):
ATGCATCGATGCACTTCC
Found at i:85945 original size:10 final size:10
Alignment explanation
Indices: 85914--85964 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
85904 TTATGCATCG
85914 ATGCACTTCC
1 ATGCACTTCC
*
85924 ATGCA--TCG
1 ATGCACTTCC
85932 ATGCACTTCC
1 ATGCACTTCC
*
85942 ATGCA--TCG
1 ATGCACTTCC
85950 ATGCACTTCC
1 ATGCACTTCC
85960 ATGCA
1 ATGCA
85965 TCGATGTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
8 14 0.42
10 19 0.58
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (10 bp):
ATGCACTTCC
Found at i:86009 original size:63 final size:64
Alignment explanation
Indices: 85942--86082 Score: 207
Period size: 64 Copynumber: 2.2 Consensus size: 64
85932 ATGCACTTCC
** * *
85942 ATGCATCGATGCAC-TTCCATGCATCGATGTACTCATG-TTTTTATGAAAACATCGAATGCA-TT
1 ATGCATCGATGCACAAACCATGCATCGATGTACTCAGGCTTGTT-TG-AAACATCGAATGCATTT
86004 T
64 T
86005 ATGCATCGATGCACAAACCATGCATCGATGTACTCAGGCTTGTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAACCATGCATCGATGTACTCAGGCTTGTTTGAAACATCGAATGCATTTT
86069 ATGCATCGATGCAC
1 ATGCATCGATGCAC
86083 CCTTAGTGCG
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
63 28 0.39
64 39 0.55
65 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACAAACCATGCATCGATGTACTCAGGCTTGTTTGAAACATCGAATGCATTTT
Found at i:88034 original size:21 final size:21
Alignment explanation
Indices: 88009--88048 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
87999 AAGACTTTAT
88009 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
88030 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
88049 AAACAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:91884 original size:21 final size:22
Alignment explanation
Indices: 91860--91933 Score: 82
Period size: 21 Copynumber: 3.4 Consensus size: 22
91850 TTGTGCATAA
91860 TGCATCGATACACT-ATGAATG
1 TGCATCGATACACTCATGAATG
91881 TGCATCGATACA-TCATGAA-G
1 TGCATCGATACACTCATGAATG
* * *
91901 ATGCACCGATGCACTCCTTGAATG
1 -TGCATCGATACACT-CATGAATG
91925 TGCATCGAT
1 TGCATCGAT
91934 GCATCCGTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.05
21 27 0.61
22 1 0.02
23 13 0.30
24 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (22 bp):
TGCATCGATACACTCATGAATG
Found at i:93503 original size:27 final size:27
Alignment explanation
Indices: 93459--93513 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
93449 ACTCCAGGAG
*
93459 CTAGTTCTTCACGAGCTCCTCCTACAC
1 CTAGTTCTTCACGAGCTCCACCTACAC
* *
93486 CTAGTTCTTCTC-ATGCTCCACCTCCAC
1 CTAGTTCTTCACGA-GCTCCACCTACAC
93513 C
1 C
93514 GGCACCAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.16, C:0.44, G:0.09, T:0.31
Consensus pattern (27 bp):
CTAGTTCTTCACGAGCTCCACCTACAC
Found at i:94650 original size:65 final size:64
Alignment explanation
Indices: 94528--94683 Score: 226
Period size: 64 Copynumber: 2.4 Consensus size: 64
94518 CACCATTTCG
** * *
94528 AATGCATTTTATGCATCGATGCAC-TGCCATGCATCGATGCACTCAGGTTTTTATGAAAACATCA
1 AATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGCTTGTTATG-AAACATCA
* *
94592 AATGCATTTTATGCATCAATGCACACACCATGCATCGATGCACTCAGACTTGTT-TGAAACATCG
1 AATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAG-CTTGTTATGAAACATCA
94656 AATGCATTTTATGCATCGATGCACACAC
1 AATGCATTTTATGCATCGATGCACACAC
94684 GCTCCCAACT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
64 57 0.69
65 22 0.27
66 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
AATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGCTTGTTATGAAACATCA
Found at i:98177 original size:2 final size:2
Alignment explanation
Indices: 98170--98200 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
98160 TCGTTTGTTT
*
98170 AC AC AC AC AC AC AG AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
98201 ATTATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:98208 original size:2 final size:2
Alignment explanation
Indices: 98203--98239 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
98193 CACACACAAT
98203 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
98240 TATTGTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:101266 original size:25 final size:25
Alignment explanation
Indices: 101238--101294 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
101228 TCATTCGTTG
101238 AAATTTTTCCTCTTAAGCTTCCATA
1 AAATTTTTCCTCTTAAGCTTCCATA
101263 AAATTTTTCCTCTTAAGCTTCCATA
1 AAATTTTTCCTCTTAAGCTTCCATA
101288 AAATTTT
1 AAATTTT
101295 AATTACCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.46
Consensus pattern (25 bp):
AAATTTTTCCTCTTAAGCTTCCATA
Found at i:102607 original size:23 final size:23
Alignment explanation
Indices: 102577--102622 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
102567 TTAAGTCGAT
102577 GACACTTTTCTGTATGGGCTCTA
1 GACACTTTTCTGTATGGGCTCTA
102600 GACACTTTTCTGTATGGGCTCTA
1 GACACTTTTCTGTATGGGCTCTA
102623 CAGATACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (23 bp):
GACACTTTTCTGTATGGGCTCTA
Found at i:107451 original size:3 final size:3
Alignment explanation
Indices: 107430--107525 Score: 59
Period size: 3 Copynumber: 30.3 Consensus size: 3
107420 TTAATATTAG
* * * * * *
107430 TAA TAT TAA TAA GTAA TAA TAA T-A TTA TAAA TAA CAT TAA CAA TAT
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* *
107476 TAA TTAA TTAA TAA TAA TTAA TAA TAA AAA TAA TATT TAA TAA TAA TAA
1 TAA -TAA -TAA TAA TAA -TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
107525 T
1 T
107526 CCGGATGAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
2 2 0.03
3 53 0.74
4 17 0.24
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:107454 original size:19 final size:18
Alignment explanation
Indices: 107430--107525 Score: 81
Period size: 19 Copynumber: 5.1 Consensus size: 18
107420 TTAATATTAG
107430 TAATATTAATAAGTAATAA
1 TAATATTAATAA-TAATAA
107449 TAATATT-ATAAATAACATTAA
1 TAATATTAAT-AAT-A-A-TAA
*
107470 CAATATTAAT--TAATTAA
1 TAATATTAATAATAA-TAA
*
107487 TAATAATTAATAATAAAAA
1 TAAT-ATTAATAATAATAA
107506 TAATATTTAATAATAATAA
1 TAATA-TTAATAATAATAA
107525 T
1 T
107526 CCGGATGAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
17 8 0.12
18 11 0.17
19 30 0.47
20 4 0.06
21 9 0.14
22 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (18 bp):
TAATATTAATAATAATAA
Found at i:107904 original size:70 final size:71
Alignment explanation
Indices: 107813--108001 Score: 218
Period size: 70 Copynumber: 2.7 Consensus size: 71
107803 GCGTTCAACT
* * * **
107813 TCCTCCATGGCTGAGTGTTCATTTACTAGTGGGGTGTCCTCCATGACTGAGGCTTGAGGATGTGC
1 TCCTCCATGGCTGAGGGTTCATATACTAATGGGGTGTCCTCCATGACTGAGGCTCAAGGATGTGC
107878 TCAATG
66 TCAATG
* * * * * *
107884 TCC-CCATGGCTAAGGGTTCATCTACTAACGGGGTGTCCTCCATGAATGAGGCTCAAGGTTGTGT
1 TCCTCCATGGCTGAGGGTTCATATACTAATGGGGTGTCCTCCATGACTGAGGCTCAAGGATGTGC
* *
107948 TCGATT
66 TCAATG
* * * *
107954 TCCTCCATGACCGAGGGTTCACATACTAATGAGGTGTCCTCCATGACT
1 TCCTCCATGGCTGAGGGTTCATATACTAATGGGGTGTCCTCCATGACT
108002 AAGTCTCTTG
Statistics
Matches: 97, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
70 58 0.60
71 39 0.40
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (71 bp):
TCCTCCATGGCTGAGGGTTCATATACTAATGGGGTGTCCTCCATGACTGAGGCTCAAGGATGTGC
TCAATG
Found at i:108060 original size:67 final size:67
Alignment explanation
Indices: 107966--108116 Score: 167
Period size: 67 Copynumber: 2.3 Consensus size: 67
107956 CTCCATGACC
* * * * * * *
107966 GAGGGTTCACATACTAATGAGGTGTCCTCCATGACTAAGTCTCTTGAGTATGGCTTCCTCTATGG
1 GAGGGTTCACCTACTGATAAGGAGTCCTCCATGACTAAGGCTCTTGAGTATGGCTTCCGCCATGG
108031 TT
66 TT
** * * * ** *
108033 GAGGGTTTGCCTACTGATAAGGAGTCCTCTATGACTGAGGCTTTTGAGTATTTCTTTCGCCATGG
1 GAGGGTTCACCTACTGATAAGGAGTCCTCCATGACTAAGGCTCTTGAGTATGGCTTCCGCCATGG
108098 TT
66 TT
108100 GAGGGTTCACCTACTGA
1 GAGGGTTCACCTACTGA
108117 ATATTGATGT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (67 bp):
GAGGGTTCACCTACTGATAAGGAGTCCTCCATGACTAAGGCTCTTGAGTATGGCTTCCGCCATGG
TT
Found at i:122324 original size:34 final size:30
Alignment explanation
Indices: 122286--122354 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
122276 TTGATATAAC
*
122286 AATTTAAGGCAAAATGGTTTTTGGAGTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
122320 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
122349 AATTTA
1 AATTTA
122355 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:122365 original size:29 final size:30
Alignment explanation
Indices: 122295--122354 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
122285 CAATTTAAGG
*
122295 CAAAATGGTTTTTGGAGTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
122326 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
122355 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:122460 original size:21 final size:21
Alignment explanation
Indices: 122434--122491 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
122424 AGGGTGTCAA
*
122434 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
* *
122455 AGTGCATCTATGCATCCCTAC
1 AGTGCATCCATGCACCCCTAC
122476 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
122492 TGCACTAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:122504 original size:22 final size:23
Alignment explanation
Indices: 122476--122518 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
122466 GCATCCCTAC
122476 AGTGCATCCATGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
**
122498 AGTGCATTGATGCACCATGCA
1 AGTGCATCCATGCACCATGCA
122519 GTGTATCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:122521 original size:42 final size:41
Alignment explanation
Indices: 122434--122532 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 41
122424 AGGGTGTCAA
*
122434 AGTGCATCCATGCACCCCTGCAGTGCATCTATGCATCCCTAC
1 AGTGCATCCATGCACCCCT-CAGTGCATCTATGCATCCATAC
*
122476 AGTGCATCCATGCACCTGCACT-AGTGCAT-TGATGCA-CCATGC
1 AGTGCATCCATGCACC--C-CTCAGTGCATCT-ATGCATCCATAC
*
122518 AGTGTATCCATGCAC
1 AGTGCATCCATGCAC
122533 TCAAACACTG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
42 35 0.70
43 12 0.24
44 1 0.02
45 2 0.04
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (41 bp):
AGTGCATCCATGCACCCCTCAGTGCATCTATGCATCCATAC
Found at i:122578 original size:20 final size:20
Alignment explanation
Indices: 122553--122626 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
122543 AATGCAATTA
*
122553 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTACT
*
122573 GTGCATCGATGCAT-CAAGGCT
1 GTGCATCGATGCATCCTA--CT
122594 GTGCATCGATGCATCCTACT
1 GTGCATCGATGCATCCTACT
*
122614 GTGCATCCATGCA
1 GTGCATCGATGCA
122627 CGAAGGCTGC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.02
20 28 0.60
21 16 0.34
22 2 0.04
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCATCCTACT
Found at i:122597 original size:21 final size:20
Alignment explanation
Indices: 122553--122608 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
122543 AATGCAATTA
***
122553 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCAGGCT
122573 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-AGGCT
122594 GTGCATCGATGCATC
1 GTGCATCGATGCATC
122609 CTACTGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGCT
Found at i:122598 original size:41 final size:41
Alignment explanation
Indices: 122553--122635 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
122543 AATGCAATTA
* *
122553 GTGCATCGATGCATCCTTCTGTGCATCGATGCATC-AAGGCT
1 GTGCATCGATGCATCCTACTGTGCATCCATGCA-CGAAGGCT
122594 GTGCATCGATGCATCCTACTGTGCATCCATGCACGAAGGCT
1 GTGCATCGATGCATCCTACTGTGCATCCATGCACGAAGGCT
122635 G
1 G
122636 CAACGGCTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.27
Consensus pattern (41 bp):
GTGCATCGATGCATCCTACTGTGCATCCATGCACGAAGGCT
Found at i:131045 original size:56 final size:56
Alignment explanation
Indices: 130981--131097 Score: 216
Period size: 56 Copynumber: 2.1 Consensus size: 56
130971 CTATGGTGTT
* *
130981 GAATAAAAAATTCTATGATATATTATTAAGGATGTGTTAGATCTATTATAGCATTA
1 GAATAAAAAATTATATGATATATTATTAAGAATGTGTTAGATCTATTATAGCATTA
131037 GAATAAAAAATTATATGATATATTATTAAGAATGTGTTAGATCTATTATAGCATTA
1 GAATAAAAAATTATATGATATATTATTAAGAATGTGTTAGATCTATTATAGCATTA
131093 GAATA
1 GAATA
131098 TCAATTATGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (56 bp):
GAATAAAAAATTATATGATATATTATTAAGAATGTGTTAGATCTATTATAGCATTA
Found at i:132903 original size:45 final size:44
Alignment explanation
Indices: 132813--132983 Score: 182
Period size: 45 Copynumber: 3.8 Consensus size: 44
132803 ATAAACTGGA
* * *
132813 AAAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAACTTATGGAAAAATGGTAAGTATATTGGT
* * *
132857 AAAATAAGCTTATGAACTTATGAAACAAATGGTAAGTATAATGGT
1 AAAATAAGCTTACGAACTTATGGAA-AAATGGTAAGTATATTGGT
* * *
132902 AAGATAAGCTTAC-AAGCTTATGGGATAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAA-CTTAT-GGAAAAATGGTAAGTATATTGGT
* *
132947 AAAATAAACTTACGAGCTTATGGTTAATAAATGGTAA
1 AAAATAAGCTTACGAACTTATGG--AA-AAATGGTAA
132984 AATATTAAAT
Statistics
Matches: 104, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
44 26 0.25
45 65 0.62
46 4 0.04
47 9 0.09
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (44 bp):
AAAATAAGCTTACGAACTTATGGAAAAATGGTAAGTATATTGGT
Found at i:136393 original size:24 final size:24
Alignment explanation
Indices: 136361--136420 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
136351 GAGTGCCCTG
136361 GTGCATTGGCATGATATTCGCATT
1 GTGCATTGGCATGATATTCGCATT
136385 GTGCATTGGCATGATATTCGCATT
1 GTGCATTGGCATGATATTCGCATT
136409 GTGCATTGGCAT
1 GTGCATTGGCAT
136421 CATACCATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (24 bp):
GTGCATTGGCATGATATTCGCATT
Found at i:141792 original size:14 final size:14
Alignment explanation
Indices: 141773--141802 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
141763 CGTTTTCTTT
141773 ACCCGTTTTCGTCA
1 ACCCGTTTTCGTCA
141787 ACCCGTTTTCGTCA
1 ACCCGTTTTCGTCA
141801 AC
1 AC
141803 AACAACCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.17, C:0.37, G:0.13, T:0.33
Consensus pattern (14 bp):
ACCCGTTTTCGTCA
Found at i:145994 original size:22 final size:22
Alignment explanation
Indices: 145966--146010 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
145956 AAAAGGGTTC
*
145966 ACTAACCTTTCTAGATTCTAAA
1 ACTAACCATTCTAGATTCTAAA
145988 ACTAACCATTCTAGATTCTAAA
1 ACTAACCATTCTAGATTCTAAA
146010 A
1 A
146011 ATATTAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (22 bp):
ACTAACCATTCTAGATTCTAAA
Found at i:147103 original size:23 final size:19
Alignment explanation
Indices: 147049--147105 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 19
147039 TTGAAATATG
147049 AATAAATGAAAATGTAAATA
1 AATAAAT-AAAATGTAAATA
147069 AATAAGATTAAAATGCTGAAATGA
1 AATAA-A-TAAAATG-T-AAAT-A
147093 AATAACATAAAAT
1 AATAA-ATAAAAT
147106 AATGGGAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.16
21 7 0.23
22 2 0.06
23 10 0.32
24 7 0.23
ACGTcount: A:0.61, C:0.04, G:0.11, T:0.25
Consensus pattern (19 bp):
AATAAATAAAATGTAAATA
Found at i:148990 original size:12 final size:12
Alignment explanation
Indices: 148973--148999 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
148963 TTTTTAACTC
148973 TTTTTACTCTCT
1 TTTTTACTCTCT
148985 TTTTTACTCTCT
1 TTTTTACTCTCT
148997 TTT
1 TTT
149000 CAAAACCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTACTCTCT
Found at i:149702 original size:23 final size:23
Alignment explanation
Indices: 149676--149721 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
149666 ATATAGTTAT
*
149676 AAATAATA-TTAATTAATAATAAC
1 AAATAACATTTAA-TAATAATAAC
*
149699 AAATAACATTTGATAATAATAAC
1 AAATAACATTTAATAATAATAAC
149722 CCTGACTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAACATTTAATAATAATAAC
Found at i:153552 original size:17 final size:17
Alignment explanation
Indices: 153518--153559 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
153508 CCATTCCCTT
* *
153518 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAAAAACTC
153534 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
*
153551 TCGTTCGAG
1 TCTTTCGAG
153560 CAACAAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:161118 original size:16 final size:16
Alignment explanation
Indices: 161097--161155 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
161087 CCAACGTTTA
*
161097 TGTTCGTTTATGATCG
1 TGTTCGTTTATGTTCG
*
161113 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGTTCG
161129 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
161145 TGTTCGTTTAT
1 TGTTCGTTTAT
161156 TTATTCCTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:162330 original size:24 final size:22
Alignment explanation
Indices: 162296--162339 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
162286 TATATTTGAT
162296 ACGAAATTTATAAAATTTTAAG
1 ACGAAATTTATAAAATTTTAAG
162318 ACGATAATATTATAAAATTTTA
1 ACGA-AAT-TTATAAAATTTTA
162340 GTAGACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 3 0.15
24 13 0.65
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (22 bp):
ACGAAATTTATAAAATTTTAAG
Found at i:164002 original size:14 final size:13
Alignment explanation
Indices: 163965--164003 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
163955 TTAAAATTTA
* *
163965 TAAAATATATATT
1 TAAAATATTTAAT
163978 TAAAATATTTAAT
1 TAAAATATTTAAT
163991 TAAAATTATTTAA
1 TAAAA-TATTTAA
164004 AATACATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAAATATTTAAT
Found at i:166499 original size:32 final size:32
Alignment explanation
Indices: 166463--166526 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
166453 GAATATGTGA
*
166463 AGGAATTGAAATATGT-TGAAATTGAAATCTAT
1 AGGAATTGAAATATGTAAG-AATTGAAATCTAT
*
166495 AGGAATTGAAATCTGTAAGAATTGAAATCTAT
1 AGGAATTGAAATATGTAAGAATTGAAATCTAT
166527 TTTCATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.33
Consensus pattern (32 bp):
AGGAATTGAAATATGTAAGAATTGAAATCTAT
Found at i:166501 original size:16 final size:16
Alignment explanation
Indices: 166463--166526 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 16
166453 GAATATGTGA
* *
166463 AGGAATTGAAATATGT
1 AGGAATTGAAATCTAT
* *
166479 TGAAATTGAAATCTAT
1 AGGAATTGAAATCTAT
*
166495 AGGAATTGAAATCTGT
1 AGGAATTGAAATCTAT
*
166511 AAGAATTGAAATCTAT
1 AGGAATTGAAATCTAT
166527 TTTCATATTC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.33
Consensus pattern (16 bp):
AGGAATTGAAATCTAT
Found at i:167182 original size:37 final size:38
Alignment explanation
Indices: 167098--167186 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
167088 CCTAAACTCG
*
167098 AACCCGATCCGACCTGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
167136 AACCCGACCCGA-CTCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGACCT-GACCCGAATATCACACTTAAAAA
167173 AACCCGACCCGACC
1 AACCCGACCCGACC
167187 CGAATAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
37 18 0.38
38 30 0.62
ACGTcount: A:0.37, C:0.39, G:0.11, T:0.12
Consensus pattern (38 bp):
AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
Found at i:167441 original size:37 final size:38
Alignment explanation
Indices: 167355--167445 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 38
167345 TTTTCACCCT
*
167355 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAACATCACACTTAAAA
** *
167394 AAACCCGACCCGACTTGACCTGAACATCACACTT-AAA
1 AAACCCGACCCGACCCGACCCGAACATCACACTTAAAA
167431 AAACCCGACCCGACC
1 AAACCCGACCCGACC
167446 TGAACAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 17 0.36
38 23 0.49
39 7 0.15
ACGTcount: A:0.38, C:0.40, G:0.11, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACCCGAACATCACACTTAAAA
Found at i:167602 original size:254 final size:257
Alignment explanation
Indices: 167049--167633 Score: 901
Period size: 259 Copynumber: 2.3 Consensus size: 257
167039 TATAAGGTAA
* *
167049 AATTATATATTTTTTTCGGGCCGGTCCGGTTTTTTTCACCCTAAACTCGAACCCGATCCGACCTG
1 AATTATATA-TATTTTCGGGCCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGA-CC--CC-G
*
167114 ACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCG
61 ACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAACATCACACTTAAAAAACCCG
* *
167179 ACCCGACCCGAATAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAAATAGAAATCCGACC
126 ACCCGACCCGAACAAAATAAAGGTTCATCCGACCCGACCCGAATATATGAAATAGAAATCCGA-C
*
167244 TGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCG
190 --ACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCG
167309 ACCCG
253 ACCCG
*
167314 AATTATATATATTTTCGGGCCGGTCAGGTTTTTTTCACCCTAAACCCGAACCCGA-CCCGACCCG
1 AATTATATATATTTTCGGGCCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCCGACCCG
* *
167378 AATATCACACTTAAAAAAACCCGACCCGACTTGACCTGAACATCACACTTAAAAAACCCGACCCG
66 AATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAACATCACACTTAAAAAACCCGACCCG
* *
167443 ACCTGAACAAAAT-AAGGTTCATCCGACCCGACCCGAATATATGAATTAGAAATCC-A-ACCCGA
131 ACCCGAACAAAATAAAGGTTCATCCGACCCGACCCGAATATATGAAATAGAAATCCGACACCCGA
*
167505 CCCGAAATAAT-AAAAAATCATTTTTATTTAATAAAAAAAAGTGACTTAATCCGACCCGACCTG
196 CCCGAAATAATAAAAAAAT-ATTTTTATTTAAT-AAAAAAAGTGACTTAATCCGACCCGACCCG
* * * *
167568 AATTATATATATTTTCGGGTCGATCCGATTTTTTTCACCCTAAACCCGACCCCGACCCCGACCCG
1 AATTATATATATTTTCGGGCCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCCGACCCG
167633 A
66 A
167634 CCCGACCGAC
Statistics
Matches: 300, Mismatches: 17, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
252 7 0.02
253 30 0.10
254 78 0.26
255 10 0.03
257 1 0.00
258 40 0.13
259 79 0.26
260 2 0.01
262 1 0.00
264 43 0.14
265 9 0.03
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (257 bp):
AATTATATATATTTTCGGGCCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCCGACCCG
AATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAACATCACACTTAAAAAACCCGACCCG
ACCCGAACAAAATAAAGGTTCATCCGACCCGACCCGAATATATGAAATAGAAATCCGACACCCGA
CCCGAAATAATAAAAAAATATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCGACCCG
Found at i:167827 original size:27 final size:24
Alignment explanation
Indices: 167797--167865 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 24
167787 TCCTCCAACA
167797 ATGGAATTGAATTCCATCCATTTTTGG
1 ATGGAATTGAATTCCATCCA--TTT-G
* * *
167824 ATGGAATTCACTTTCCCT-CATTTG
1 ATGGAATTGA-ATTCCATCCATTTG
167848 ATGGAATTGAATTCCATC
1 ATGGAATTGAATTCCATC
167866 ACAGATTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
23 5 0.15
24 10 0.29
25 3 0.09
27 11 0.32
28 5 0.15
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (24 bp):
ATGGAATTGAATTCCATCCATTTG
Found at i:168305 original size:50 final size:50
Alignment explanation
Indices: 168246--168371 Score: 189
Period size: 50 Copynumber: 2.5 Consensus size: 50
168236 GTAGTAGTAA
* *
168246 AGCGCGCCCCCTGAACCGCGCTATATGCTGATTTGGCGTCACATGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGGCGTCACATGGGTAT
** * *
168296 AGCGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCGTCACATGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGGCGTCACATGGGTAT
*
168346 AGCGCGCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTGAACCGCGCTATAC
168372 CTGGGTATCT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.17, C:0.35, G:0.28, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGCTATACGCTGATCTGGCGTCACATGGGTAT
Found at i:168394 original size:50 final size:48
Alignment explanation
Indices: 168246--168401 Score: 136
Period size: 50 Copynumber: 3.1 Consensus size: 48
168236 GTAGTAGTAA
* * * * * *
168246 AGCGCGCCCCCTGAACCGCGCTATATGCTGATTTGGCGTCACATGGGTAT
1 AGCGCGCCCCCTGACCCGCGATATACGGTGATCT-G-GACACATGGGTAT
* *
168296 AGCGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCGTCACATGGGTAT
1 AGCGCGCCCCCTGACCCGCGATATACGGTGATCT-G-GACACATGGGTAT
* *
168346 AGCGCGCCCCCTGATCCGCGCTATACCTGG-GTATCT-GACACATGGGGTAT
1 AGCGCGCCCCCTGACCCGCGATATA-C-GGTG-ATCTGGACACAT-GGGTAT
168396 AGCGCG
1 AGCGCG
168402 GTGCAGGGGG
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
49 6 0.07
50 78 0.85
51 2 0.02
52 6 0.07
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.21
Consensus pattern (48 bp):
AGCGCGCCCCCTGACCCGCGATATACGGTGATCTGGACACATGGGTAT
Found at i:168509 original size:10 final size:10
Alignment explanation
Indices: 168494--168533 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
168484 TTTATCACAC
168494 CAAATTCTCT
1 CAAATTCTCT
168504 CAAATTCTCT
1 CAAATTCTCT
168514 -AAATTTCTCT
1 CAAA-TTCTCT
*
168524 CAAATACTCT
1 CAAATTCTCT
168534 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:168854 original size:111 final size:111
Alignment explanation
Indices: 168660--168881 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
168650 TGGAAATCAT
* *
168660 ATATCTCTATACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
168725 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
168771 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
168836 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
168882 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:170157 original size:15 final size:15
Alignment explanation
Indices: 170137--170192 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 15
170127 ACCTGCTCAG
170137 GACGACGACGACGAT
1 GACGACGACGACGAT
170152 GACGACGACGACGATGGT
1 GACGACGACGACGA---T
*
170170 GACGACGACAACGAT
1 GACGACGACGACGAT
*
170185 GACAACGA
1 GACGACGA
170193 TGAGTCAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 22 0.61
18 14 0.39
ACGTcount: A:0.36, C:0.25, G:0.32, T:0.07
Consensus pattern (15 bp):
GACGACGACGACGAT
Found at i:170184 original size:18 final size:18
Alignment explanation
Indices: 170137--170186 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
170127 ACCTGCTCAG
*
170137 GACGACGACGACGATGAC
1 GACGACGACGATGATGAC
*
170155 GACGACGACGATGGTGAC
1 GACGACGACGATGATGAC
*
170173 GACGACAACGATGA
1 GACGACGACGATGA
170187 CAACGATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.34, C:0.24, G:0.34, T:0.08
Consensus pattern (18 bp):
GACGACGACGATGATGAC
Found at i:174607 original size:16 final size:16
Alignment explanation
Indices: 174588--174622 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
174578 TTGTTTATTT
*
174588 TTTTCGTCGTTGATCA
1 TTTTCGCCGTTGATCA
174604 TTTTCGCCGTTGATCA
1 TTTTCGCCGTTGATCA
174620 TTT
1 TTT
174623 CTATGCGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.51
Consensus pattern (16 bp):
TTTTCGCCGTTGATCA
Found at i:175555 original size:3 final size:3
Alignment explanation
Indices: 175549--175598 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
175539 TTTACTCATT
*
175549 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA TTTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA
175596 TTA
1 TTA
175599 CAAACATGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:188266 original size:16 final size:16
Alignment explanation
Indices: 188245--188300 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
188235 GCTTGAAGAT
188245 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
*
188261 AAAAAGAAAAAAAAAA
1 AAAAAGAAAAGAAAAA
* *
188277 GAAAAAAAAAAGAGAAGA
1 -AAAAAGAAAAGA-AAAA
188295 AAAAAG
1 AAAAAG
188301 GGGGTCAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 15 0.45
17 15 0.45
18 3 0.09
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:188299 original size:1 final size:1
Alignment explanation
Indices: 188245--188287 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
188235 GCTTGAAGAT
* * * *
188245 AAAAAGAAAAGAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
188288 GAGAAGAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:188300 original size:12 final size:11
Alignment explanation
Indices: 188240--188300 Score: 86
Period size: 11 Copynumber: 5.3 Consensus size: 11
188230 ATTATGCTTG
188240 AAGATAAAAAGAA
1 AAGA-AAAAA-AA
188253 AAGAAAAAAAA
1 AAGAAAAAAAA
188264 AAGAAAAAAAA
1 AAGAAAAAAAA
188275 AAGAAAAAAAA
1 AAGAAAAAAAA
*
188286 AAGAGAAGAAAA
1 AAGA-AAAAAAA
188298 AAG
1 AAG
188301 GGGGTCAAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
11 28 0.61
12 14 0.30
13 4 0.09
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:189588 original size:83 final size:83
Alignment explanation
Indices: 189446--189997 Score: 915
Period size: 83 Copynumber: 6.7 Consensus size: 83
189436 GAACAAATGC
* * * *
189446 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTTTCTGATCTGGTTTGTTAAAACAAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
189511 CATTAAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
*
189529 AATGTGCTCATAGCATCTTCTGGAATTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
189594 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
* *
189612 AATGTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
* * *
189677 TATTGAATTTGGAAGAGG
66 CATTGAATTTGAAAGATG
* *
189695 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
189760 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
189778 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
189843 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
* *
189861 AATGTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
* * *
189926 TATTGAATTTGGAAGAGG
66 CATTGAATTTGAAAGATG
* * *
189944 AATGTGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
189998 ATATGAAACC
Statistics
Matches: 441, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 441 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
CATTGAATTTGAAAGATG
Found at i:189893 original size:249 final size:249
Alignment explanation
Indices: 189446--189997 Score: 1014
Period size: 249 Copynumber: 2.2 Consensus size: 249
189436 GAACAAATGC
* * * *
189446 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTTTCTGATCTGGTTTGTTAAAACAAAT
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACAAAT
*
189511 CATTAAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAATTGTTCTTTGAGTTATCTGATC
66 CATTAAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
189576 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGCATCTTCTGGAAGTGT
131 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGCATCTTCTGGAAGTGT
189641 TCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAGAGG
196 TCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAGAGG
* *
189695 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACAAAT
*
189760 CATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
66 CATTAAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
189825 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGCATCTTCTGGAAGTGT
131 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGCATCTTCTGGAAGTGT
189890 TCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAGAGG
196 TCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAGAGG
* *
189944 AATGTGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTG
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
189998 ATATGAAACC
Statistics
Matches: 293, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
249 293 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (249 bp):
AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACAAAT
CATTAAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATGAATGTGATCATAGCATCTTCTGGAAGTGT
TCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAGAGG
Found at i:190162 original size:114 final size:114
Alignment explanation
Indices: 189952--190391 Score: 754
Period size: 114 Copynumber: 3.9 Consensus size: 114
189942 GGAATGTGCT
* * * *
189952 AATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGATATGAAACCACAGAACCA
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATG-AACCACAGAACCA
190017 ATCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
65 ATCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
190067 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
190132 TCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
66 TCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
*
190181 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATATGATCTGGTTTGGTATGAACCACAGAACCAA
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
*
190246 TCATTAAATTAGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
66 TCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
*
190295 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
* * * * * *
190360 TTATTGAATTTGGAAGAGGAATGTGCTAATAG
66 TCATTAAATTTGAAAGATGAATTTGCTCATAG
190392 CATCTTCTGA
Statistics
Matches: 310, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 263 0.85
115 47 0.15
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (114 bp):
AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
TCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
Found at i:191357 original size:113 final size:113
Alignment explanation
Indices: 191159--191904 Score: 1399
Period size: 113 Copynumber: 6.6 Consensus size: 113
191149 GCAAAGATTT
*
191159 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
191224 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
191272 AAATCCATCA-TTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
191336 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
65 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
191385 AAATCCATCA-TTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
191449 GGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
65 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
191498 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
191563 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
191611 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
191676 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTAGGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
191724 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
191789 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
*
191837 AAATCCATCA-TTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCAGAA
1 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
191901 GAAG
65 GAAG
191905 AAGTTCATAA
Statistics
Matches: 622, Mismatches: 8, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
112 4 0.01
113 616 0.99
114 2 0.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
Found at i:191914 original size:33 final size:34
Alignment explanation
Indices: 191872--191957 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 34
191862 TTTCCAGAGA
191872 AAGTTCATAATGAGAAGAACTCATCAG-AAGAAG
1 AAGTTCATAATGAGAAGAACTCATCAGAAAGAAG
*
191905 AAGTTCATAATGAGAAGAACTCATCTGAAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCAGAAAGAAG
191939 -AGATTCATAATGAGAAGAA
1 AAG-TTCATAATGAGAAGAA
191958 TTTGTTCAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
33 28 0.56
34 22 0.44
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.20
Consensus pattern (34 bp):
AAGTTCATAATGAGAAGAACTCATCAGAAAGAAG
Found at i:192071 original size:146 final size:144
Alignment explanation
Indices: 191759--192045 Score: 388
Period size: 139 Copynumber: 2.0 Consensus size: 144
191749 TTTCCAGAGA
191759 AAGTTCATAATGAGAAGAACTCATCTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAA-GAGGAAGAAG-AATTCATAATGAGAAGAATTTGTT
* * * * * *
191824 CAACCTTATGCTCAAATCCATCATTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
64 CAACCTTATGCTCAAATCCATCATTCAATAGATCAACCTTTACAGAGAAAATTCATAATGAGAAG
191889 AACTCATCAGAAGAAG
129 AACTCATCAGAAGAAG
191905 AAGTTCATAATGAGAAGAACTCATCTGAA-A-GAAG-AG-ATTCATAATGAGAAGAATTTGTTCA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
* ** *
191966 A-CTTTTGCTTGAATTCATCACTT-AATAGATCAACCTTTACAGAGAAAATTCATAATGAGAAGA
66 ACCTTATGCTCAAATCCATCA-TTCAATAGATCAACCTTTACAGAGAAAATTCATAATGAGAAGA
* * *
192029 ATTCATCTGAAAAAG
130 ACTCATCAGAAGAAG
192044 AA
1 AA
192046 AGAAGAAGTT
Statistics
Matches: 127, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
139 63 0.50
140 28 0.22
142 2 0.02
143 4 0.03
144 1 0.01
146 29 0.23
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (144 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
ACCTTATGCTCAAATCCATCATTCAATAGATCAACCTTTACAGAGAAAATTCATAATGAGAAGAA
CTCATCAGAAGAAG
Found at i:192316 original size:3 final size:3
Alignment explanation
Indices: 192310--192386 Score: 100
Period size: 3 Copynumber: 25.0 Consensus size: 3
192300 TTTACTCATT
* *
192310 TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
192358 TTA TTA ATA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
192387 CAAACATGCC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 58 0.91
4 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:201813 original size:30 final size:31
Alignment explanation
Indices: 201746--201830 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
201736 GAGTCGAGGA
* * * *
201746 TTACCTATGTCTTTCGAGATATATGGATAGT
1 TTACCTATGTCCTTCGAGACATATGAACAGT
*
201777 TTACCTATGTCCTTCGGGACATATGAACAG-
1 TTACCTATGTCCTTCGAGACATATGAACAGT
* *
201807 TTACCTATGTTCTTCGAAACATAT
1 TTACCTATGTCCTTCGAGACATAT
201831 AGATAGGTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
30 21 0.46
31 25 0.54
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (31 bp):
TTACCTATGTCCTTCGAGACATATGAACAGT
Found at i:216561 original size:20 final size:20
Alignment explanation
Indices: 216536--216604 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
216526 AATAAGTCAG
*
216536 TAGTATCGATACTTAGAGGT
1 TAGTATCGATACTCAGAGGT
* * *
216556 TAGTATCGCTACCCAAAGGT
1 TAGTATCGATACTCAGAGGT
* * * *
216576 TAGTACCAATACTGAGGGGCT
1 TAGTATCGATACTCAGAGG-T
216597 TAGTATCG
1 TAGTATCG
216605 GTACCCAAGA
Statistics
Matches: 35, Mismatches: 13, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 28 0.80
21 7 0.20
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (20 bp):
TAGTATCGATACTCAGAGGT
Found at i:221164 original size:14 final size:14
Alignment explanation
Indices: 221145--221186 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
221135 GCGAGAGCAT
221145 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
**
221159 CCGAGGCCATCTAA
1 CCGAGGCCATCCGA
221173 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
221187 GGGGTAGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.24, C:0.40, G:0.26, T:0.10
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:223025 original size:42 final size:42
Alignment explanation
Indices: 222951--223030 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
222941 CGAAATCTAA
* * * *
222951 TGTTTGTTTCACGTAATTTATTTTTTGGAAAATATTTTTTCG
1 TGTTTGTTTCACATAATTCATTTTTCGAAAAATATTTTTTCG
* *
222993 TGTTTGTTTCACATAATTCGTTTTTCGAAAAATGTTTT
1 TGTTTGTTTCACATAATTCATTTTTCGAAAAATATTTT
223031 CAAGTGTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (42 bp):
TGTTTGTTTCACATAATTCATTTTTCGAAAAATATTTTTTCG
Found at i:223038 original size:42 final size:42
Alignment explanation
Indices: 222951--223040 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 42
222941 CGAAATCTAA
* * * *
222951 TGTTTGTTTCACGTAATTTATTTTTTGGAAAATATTTTTTCG
1 TGTTTGTTTCACATAATTTAGTTTTTCGAAAATATGTTTTCG
*
222993 TGTTTGTTTCACATAA-TTCGTTTTTCGAAAA-ATGTTTTCAAG
1 TGTTTGTTTCACATAATTTAGTTTTTCGAAAATATGTTTTC--G
223035 TGTTTG
1 TGTTTG
223041 GTTGGAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 7 0.17
41 12 0.29
42 22 0.54
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (42 bp):
TGTTTGTTTCACATAATTTAGTTTTTCGAAAATATGTTTTCG
Found at i:223284 original size:12 final size:12
Alignment explanation
Indices: 223255--223292 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
223245 AATTATTAAA
223255 ATATTTAA-AAT
1 ATATTTAATAAT
*
223266 ATATTTATTAAT
1 ATATTTAATAAT
*
223278 ATTTTTAATAAT
1 ATATTTAATAAT
223290 ATA
1 ATA
223293 ATATTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:223301 original size:22 final size:23
Alignment explanation
Indices: 223239--223317 Score: 81
Period size: 22 Copynumber: 3.4 Consensus size: 23
223229 TTTTAATCAA
* *
223239 AATATTAATTATTAAAATATTTAA-
1 AATA-TAA-TATTAATATTTTTAAT
*
223263 AATATATTTATTAATATTTTTAAT
1 AATATA-ATATTAATATTTTTAAT
223287 AATATAATATT-ATATTTTTAAT
1 AATATAATATTAATATTTTTAAT
*
223309 ATTATAATA
1 AATATAATA
223318 AAATAATCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
22 19 0.40
23 19 0.40
24 10 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATAATATTAATATTTTTAAT
Found at i:223356 original size:23 final size:23
Alignment explanation
Indices: 223307--223360 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
223297 TATATTTTTA
**
223307 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAAAG
*
223330 ATATTATAATAATATAAT-ATAAG
1 ATATTATAATAAAATAATCA-AAG
223353 ATATTATA
1 ATATTATA
223361 TTTTATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAAAG
Found at i:223499 original size:35 final size:34
Alignment explanation
Indices: 223456--223529 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 34
223446 AATATTATTT
*
223456 ATATATTTAATAT-TAATCTAAT-AATATTTTAATAA
1 ATATATTTAAAATAT-A-CTAATGAATATTTTAA-AA
*
223491 ATATATTTAAAATATACTAATGAATATTTTTAAA
1 ATATATTTAAAATATACTAATGAATATTTTAAAA
223525 ATATA
1 ATATA
223530 ATATAACACT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 12 0.34
35 22 0.63
36 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (34 bp):
ATATATTTAAAATATACTAATGAATATTTTAAAA
Found at i:223504 original size:23 final size:23
Alignment explanation
Indices: 223485--223529 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
223475 AATAATATTT
223485 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
223508 TAATGAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
223530 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:223923 original size:14 final size:14
Alignment explanation
Indices: 223867--223925 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
223857 CCAGAAATTT
* *
223867 AATTCATTTTCCAT
1 AATTCAATTTCCAG
* *
223881 AATTCAAATTCTAG
1 AATTCAATTTCCAG
*
223895 TAATTCATTTTCCAG
1 -AATTCAATTTCCAG
223910 AATTCAATTTCCAG
1 AATTCAATTTCCAG
223924 AA
1 AA
223926 AACTAATTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:224249 original size:59 final size:57
Alignment explanation
Indices: 224166--224311 Score: 177
Period size: 60 Copynumber: 2.4 Consensus size: 57
224156 TGTTAAGGGT
* * *
224166 AAAGTATACAAATTGTCCCTCGACTAT-AGTGTATTATTTATTAAGTCTCTCGACTATTA
1 AAAGTA-ACAAATGGTCCC-CGACTATAAGTGT-TGATTTATTAAGTCCCTCGACTATTA
*
224225 AAAGTTAACAAATGGTCCTCCGACTATAAAGTGTTGCTTTATTAAGTCCCTCGACTATTA
1 AAAG-TAACAAATGGTCC-CCGACTAT-AAGTGTTGATTTATTAAGTCCCTCGACTATTA
224285 AAAGTAACAAAATGGTCACCCGACTAT
1 AAAGTAAC-AAATGGTC-CCCGACTAT
224312 TCATTATGTT
Statistics
Matches: 77, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
59 25 0.32
60 46 0.60
61 6 0.08
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (57 bp):
AAAGTAACAAATGGTCCCCGACTATAAGTGTTGATTTATTAAGTCCCTCGACTATTA
Found at i:226979 original size:118 final size:118
Alignment explanation
Indices: 226771--227006 Score: 463
Period size: 118 Copynumber: 2.0 Consensus size: 118
226761 GATATCTTTG
226771 GAGATTTATTTTTAAATTTTAAAGTCTGAATTTAGAAAATATTTGGAATTATCTTTAGGATTATT
1 GAGATTTATTTTTAAATTTTAAAGTCTGAATTTAGAAAATATTTGGAATTATCTTTAGGATTATT
226836 TTTCTTTTAATTTCTATGTTTATCTCTAGGATTTTAGAGGCTATAAATACCCT
66 TTTCTTTTAATTTCTATGTTTATCTCTAGGATTTTAGAGGCTATAAATACCCT
*
226889 GAGATTTATTTTTAAATTTTAAAGTCTGAATTTAGAAAATATTTGGAATTGTCTTTAGGATTATT
1 GAGATTTATTTTTAAATTTTAAAGTCTGAATTTAGAAAATATTTGGAATTATCTTTAGGATTATT
226954 TTTCTTTTAATTTCTATGTTTATCTCTAGGATTTTAGAGGCTATAAATACCCT
66 TTTCTTTTAATTTCTATGTTTATCTCTAGGATTTTAGAGGCTATAAATACCCT
227007 CTAGGGTAAG
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.48
Consensus pattern (118 bp):
GAGATTTATTTTTAAATTTTAAAGTCTGAATTTAGAAAATATTTGGAATTATCTTTAGGATTATT
TTTCTTTTAATTTCTATGTTTATCTCTAGGATTTTAGAGGCTATAAATACCCT
Found at i:227039 original size:118 final size:118
Alignment explanation
Indices: 226799--227040 Score: 344
Period size: 118 Copynumber: 2.1 Consensus size: 118
226789 TTAAAGTCTG
226799 AATTTAGAAAATATTTGGAATTATCTTTAGGATTATTTTTCTTTTAATTTCTATGTTTATCTCTA
1 AATTTAGAAAATATTTGGAATTATCTTTAGGATTATTTTTCTTTTAATTTCTATGTTTATCTCTA
** **** * * **
226864 GGATTTTAGAGGCTATAAATACCCTGAGATTTATTTTTAAATTTTAAAGTCTG
66 GGATTTTAGAGGCTATAAATACCCTGAGAGGTAAGCCTAAATTTGAAACTCAA
*
226917 AATTTAGAAAATATTTGGAATTGTCTTTAGGATTATTTTTCTTTTAATTTCTATGTTTATCTCTA
1 AATTTAGAAAATATTTGGAATTATCTTTAGGATTATTTTTCTTTTAATTTCTATGTTTATCTCTA
*
226982 GGATTTTAGAGGCTATAAATACCCTCTAG-GGTAAGCCTAAA-TTGACAACTCAA
66 GGATTTTAGAGGCTATAAATACCCT-GAGAGGTAAGCCTAAATTTGA-AACTCAA
227035 AATTTA
1 AATTTA
227041 CCCTTTTTCT
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
117 3 0.03
118 105 0.95
119 2 0.02
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (118 bp):
AATTTAGAAAATATTTGGAATTATCTTTAGGATTATTTTTCTTTTAATTTCTATGTTTATCTCTA
GGATTTTAGAGGCTATAAATACCCTGAGAGGTAAGCCTAAATTTGAAACTCAA
Found at i:238615 original size:29 final size:29
Alignment explanation
Indices: 238580--238661 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
238570 AAACTAAATT
*
238580 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
238609 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
238638 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
238662 GTTAGGTGGG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:243384 original size:29 final size:29
Alignment explanation
Indices: 243349--243430 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
243339 AAACTAAATT
*
243349 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
243378 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
243407 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
243431 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:246212 original size:18 final size:18
Alignment explanation
Indices: 246185--246339 Score: 111
Period size: 18 Copynumber: 8.2 Consensus size: 18
246175 AATATAAAAT
*
246185 TATA-TATAAACTATATG
1 TATATTATAAACTATATA
246202 TATATTATAAACTATATA
1 TATATTATAAACTATATA
*
246220 -ATTATTATAAATTATATA
1 TA-TATTATAAACTATATA
** *
246238 TATAAATTAT-ATTTATGTGAA
1 TAT--ATTATAAACTATAT--A
246259 CTATATATATAAACTATGTATA
1 -TATAT-TATAAACTA--TATA
* *
246281 TAAAATTATAAACTATATT
1 T-ATATTATAAACTATATA
246300 TATATTATAAACTATATA
1 TATATTATAAACTATATA
*
246318 -ATTATTATAAGCTATATA
1 TA-TATTATAAACTATATA
246336 TATA
1 TATA
246340 AATTATGTTT
Statistics
Matches: 111, Mismatches: 12, Indels: 29
0.73 0.08 0.19
Matches are distributed among these distances:
17 6 0.05
18 60 0.54
19 12 0.11
20 7 0.06
21 14 0.13
22 10 0.09
24 2 0.02
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (18 bp):
TATATTATAAACTATATA
Done.