Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 31 of 105
Found at i:6208910 original size:19 final size:18
Alignment explanation
Indices: 6208888--6208950 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
6208878 ATTTTACAAA
6208888 TTTTAAAATATTATAGTCT
1 TTTTAAAATATTATAGT-T
** *
6208907 TTTTAATTTATTATAATT
1 TTTTAAAATATTATAGTT
* *
6208925 TTTTAAAATATTTTAGAT
1 TTTTAAAATATTATAGTT
6208943 TTTTAAAA
1 TTTTAAAA
6208951 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
18 22 0.61
19 14 0.39
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTAAAATATTATAGTT
Found at i:6208951 original size:19 final size:19
Alignment explanation
Indices: 6208922--6208958 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6208912 ATTTATTATA
* *
6208922 ATTTTTTAAAATATTTTAG
1 ATTTTTAAAAAAATTTTAG
6208941 ATTTTTAAAAAAATTTTA
1 ATTTTTAAAAAAATTTTA
6208959 AAGAATTTTT
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTTTAAAAAAATTTTAG
Found at i:6210616 original size:19 final size:19
Alignment explanation
Indices: 6210569--6210622 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
6210559 CTTAAGTAAG
*
6210569 AATAATATTGTATTTATTA
1 AATAATATTATATTTATTA
*
6210588 AAT-ATAATTATATTTTTTA
1 AATAAT-ATTATATTTATTA
*
6210607 AGTAATATTAT-TTTAT
1 AATAATATTATATTTAT
6210623 AGTATTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 6 0.21
19 21 0.72
20 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
AATAATATTATATTTATTA
Found at i:6211204 original size:15 final size:15
Alignment explanation
Indices: 6211184--6211212 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6211174 ATATTAAAAA
6211184 AATTATTTAATTTTG
1 AATTATTTAATTTTG
6211199 AATTATTTAATTTT
1 AATTATTTAATTTT
6211213 TAAATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
AATTATTTAATTTTG
Found at i:6211218 original size:16 final size:15
Alignment explanation
Indices: 6211183--6211219 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
6211173 TATATTAAAA
6211183 AAATTATTTAATTTT
1 AAATTATTTAATTTT
*
6211198 GAATTATTTAATTTTT
1 AAATTATTTAA-TTTT
6211214 AAATTA
1 AAATTA
6211220 AATATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
AAATTATTTAATTTT
Found at i:6215475 original size:23 final size:23
Alignment explanation
Indices: 6215449--6215493 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6215439 ATGCTTATTT
6215449 AGTTATTT-TTAATTTCTTTTTAA
1 AGTT-TTTATTAATTTCTTTTTAA
*
6215472 AGTTTTTATTATTTTCTTTTTA
1 AGTTTTTATTAATTTCTTTTTA
6215494 CTTTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (23 bp):
AGTTTTTATTAATTTCTTTTTAA
Found at i:6215893 original size:68 final size:66
Alignment explanation
Indices: 6215712--6215893 Score: 167
Period size: 65 Copynumber: 2.7 Consensus size: 66
6215702 TTTAAAGATG
* * * * *
6215712 ATTTTTACACTAAAATGATTTTTTAAAACAGTTA-GAAAAAAG-TTAAAAAGGTCATTTTTCCTA
1 ATTTTTACAATAAAATGATTTTTTAAAATAATTAGGAAAAAAGTTTAAAAAGATCAATTTTCCTA
6215775 A
66 A
* * *
6215776 ATTTTTACAAAAAAAAAGTATTTTTT-AAATAATTAGG-AAAAATTATTAAAAA-ATCAAATTTT
1 ATTTTTAC-AATAAAATG-ATTTTTTAAAATAATTAGGAAAAAAGT-TTAAAAAGATC-AATTTT
* *
6215838 CTTGA
62 CCTAA
* *
6215843 TTTTTTACATTAAAATGATTTTTTAATATATAATTAGGAAAAAAGTTTAAA
1 ATTTTTACAATAAAATGATTTTTTAA-A-ATAATTAGGAAAAAAGTTTAAA
6215894 CATCAATTTT
Statistics
Matches: 93, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
64 8 0.09
65 25 0.27
66 17 0.18
67 23 0.25
68 14 0.15
69 6 0.06
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (66 bp):
ATTTTTACAATAAAATGATTTTTTAAAATAATTAGGAAAAAAGTTTAAAAAGATCAATTTTCCTA
A
Found at i:6230617 original size:15 final size:17
Alignment explanation
Indices: 6230597--6230628 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
6230587 ATAATTTATC
6230597 TATAATA-AT-TAAAAA
1 TATAATATATATAAAAA
6230612 TATAATATATATAAAAA
1 TATAATATATATAAAAA
6230629 CAAACAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TATAATATATATAAAAA
Found at i:6230951 original size:137 final size:136
Alignment explanation
Indices: 6230805--6231079 Score: 451
Period size: 137 Copynumber: 2.0 Consensus size: 136
6230795 AATATATGGA
* *
6230805 ATACCATATATATTAATTTTAATATTTTCATCAAAATATATAAAATATTATACATATCATAACAT
1 ATACCATATATATTAATTTTAATATTTTCATCAAAATATATAAAATACTATACATAACATAACAT
*
6230870 AAAAAATTAACAAAAAAAATATTTTTCTTCTTTTAATTGTTTAACATCTAAACGTTTATATATGT
66 AAAAAATTAACAAAAAAAATAGTTTTCTTCTTTTAATTGTTTAACATCTAAAC-TTTATATATGT
6230935 CTAATAT
130 CTAATAT
* **
6230942 ATACTATATATATTAATTTTAATATTTTTTTCAAAATATATAAAATACTATACATAACATAACAT
1 ATACCATATATATTAATTTTAATATTTTCATCAAAATATATAAAATACTATACATAACATAACAT
* * * *
6231007 AAAAATTTAACAAAAAAAATCGTTTTCTTCTTTTAATTGTTTAACATTTAAACTTTATATATGTT
66 AAAAAATTAACAAAAAAAATAGTTTTCTTCTTTTAATTGTTTAACATCTAAACTTTATATATGTC
6231072 TAATAT
131 TAATAT
6231078 AT
1 AT
6231080 TTTTATTATA
Statistics
Matches: 128, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
136 19 0.15
137 109 0.85
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (136 bp):
ATACCATATATATTAATTTTAATATTTTCATCAAAATATATAAAATACTATACATAACATAACAT
AAAAAATTAACAAAAAAAATAGTTTTCTTCTTTTAATTGTTTAACATCTAAACTTTATATATGTC
TAATAT
Found at i:6232338 original size:36 final size:33
Alignment explanation
Indices: 6232297--6232377 Score: 83
Period size: 36 Copynumber: 2.3 Consensus size: 33
6232287 TTATCATGGA
*
6232297 AATAATAT-CATGCAATAATAATATGATACATCATGC
1 AATAATATACATGCAAGAAT-A-AT-ATA-ATCATGC
6232333 AATAATAATAACCATGCAAGAATAATATAATCATGC
1 AATAAT-AT-A-CATGCAAGAATAATATAATCATGC
6232369 AATAATATA
1 AATAATATA
6232378 GATTATCATG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
34 1 0.03
35 2 0.05
36 19 0.47
37 5 0.12
38 2 0.05
39 1 0.03
40 10 0.25
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.28
Consensus pattern (33 bp):
AATAATATACATGCAAGAATAATATAATCATGC
Found at i:6232387 original size:20 final size:20
Alignment explanation
Indices: 6232303--6232387 Score: 79
Period size: 19 Copynumber: 4.3 Consensus size: 20
6232293 TGGAAATAAT
6232303 ATCATGCAATAATAATATGATA
1 ATCATGCAATAAT-ATA-GATA
6232325 CATCATGCAAT-A-ATA-ATA
1 -ATCATGCAATAATATAGATA
* * *
6232343 ACCATGCAAGAATA-ATATA
1 ATCATGCAATAATATAGATA
*
6232362 ATCATGCAATAATATAGATT
1 ATCATGCAATAATATAGATA
6232382 ATCATG
1 ATCATG
6232388 TAATTATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 8 0.15
18 5 0.10
19 16 0.31
20 12 0.23
22 1 0.02
23 10 0.19
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.29
Consensus pattern (20 bp):
ATCATGCAATAATATAGATA
Found at i:6232552 original size:13 final size:13
Alignment explanation
Indices: 6232513--6232569 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
6232503 ATCAACCATT
*
6232513 TAAAATAATAAATAT
1 TAAAAT-ATAAA-AA
*
6232528 TAAAACATAAAAA
1 TAAAATATAAAAA
*
6232541 TAATATATAAAAA
1 TAAAATATAAAAA
6232554 TAAAATA-AAAAA
1 TAAAATATAAAAA
6232566 TAAA
1 TAAA
6232570 TGAGAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
12 9 0.24
13 18 0.49
14 5 0.14
15 5 0.14
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAATATAAAAA
Found at i:6234186 original size:17 final size:17
Alignment explanation
Indices: 6234145--6234188 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
6234135 AAGGCCCTAG
6234145 ATTCACAAAGATTCTAA
1 ATTCACAAAGATTCTAA
* *
6234162 ATTTCACAGAGGTTCTAA
1 A-TTCACAAAGATTCTAA
6234180 ATTCACAAA
1 ATTCACAAA
6234189 AATTTTAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (17 bp):
ATTCACAAAGATTCTAA
Found at i:6234294 original size:17 final size:17
Alignment explanation
Indices: 6234272--6234322 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
6234262 TCCAAGTTTT
6234272 ACAAAGATTCTAAATTC
1 ACAAAGATTCTAAATTC
* *
6234289 ACAAAG-CTCTAAGTTTC
1 ACAAAGATTCTAA-ATTC
* *
6234306 ACAGAGATTCTAGATTC
1 ACAAAGATTCTAAATTC
6234323 GTAAAAGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 5 0.19
17 17 0.65
18 4 0.15
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (17 bp):
ACAAAGATTCTAAATTC
Found at i:6234357 original size:87 final size:87
Alignment explanation
Indices: 6234238--6234406 Score: 225
Period size: 86 Copynumber: 1.9 Consensus size: 87
6234228 CCAAAGTCAC
* * *
6234238 AAAGTTTCCAGATTAGTAATAGGTTCCAAGTTTTACAAAGATTCTAAATTCACAAAGCTCTAAGT
1 AAAGTTTCCAGATTAGTAAAAGGTTCCAAGTTTCACAAAGATT-TAAATTCACAAAGCTCCAAGT
6234303 TTCACAGAGATTCTAGATTCGTA
65 TTCACAGAGATTCTAGATTCGTA
** * *
6234326 AAAGTTT-CAGATTCA-TAAAAGGTTCCAAGTTTCACAAAGATTTTGATTCACAAGGTTCCAAGT
1 AAAGTTTCCAGATT-AGTAAAAGGTTCCAAGTTTCACAAAGATTTAAATTCACAAAGCTCCAAGT
* *
6234389 TTCGCAGAGGTTCTAGAT
65 TTCACAGAGATTCTAGAT
6234407 GTGGAATATT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
86 32 0.45
87 31 0.44
88 8 0.11
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (87 bp):
AAAGTTTCCAGATTAGTAAAAGGTTCCAAGTTTCACAAAGATTTAAATTCACAAAGCTCCAAGTT
TCACAGAGATTCTAGATTCGTA
Found at i:6234661 original size:17 final size:18
Alignment explanation
Indices: 6234616--6234661 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
6234606 AACTGAAAAA
6234616 TTCACAAGAA-TTCAGAT
1 TTCACAAGAATTTCAGAT
* *
6234633 TT-ATAAGGATTTCAG-T
1 TTCACAAGAATTTCAGAT
6234649 TTCACAAGAATTT
1 TTCACAAGAATTT
6234662 TCAAGTTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (18 bp):
TTCACAAGAATTTCAGAT
Found at i:6234760 original size:23 final size:21
Alignment explanation
Indices: 6234754--6234804 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
6234744 GATTTGCATT
6234754 TAAAAGATTCAAAGTTTCATA
1 TAAAAGATTCAAAGTTTCATA
* ** *
6234775 TAAAAAATTCATGGATTCATA
1 TAAAAGATTCAAAGTTTCATA
*
6234796 TTAAAGATT
1 TAAAAGATT
6234805 TCAAGGCTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (21 bp):
TAAAAGATTCAAAGTTTCATA
Found at i:6234784 original size:21 final size:23
Alignment explanation
Indices: 6234737--6234785 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
6234727 TATAGACAAG
* *
6234737 ATTCAAAGATTTGCATTTAAAAG
1 ATTCAAAGATTTGCATATAAAAA
6234760 ATTCAAAG-TTT-CATATAAAAA
1 ATTCAAAGATTTGCATATAAAAA
6234781 ATTCA
1 ATTCA
6234786 TGGATTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 3 0.12
23 8 0.33
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (23 bp):
ATTCAAAGATTTGCATATAAAAA
Found at i:6234993 original size:46 final size:45
Alignment explanation
Indices: 6234921--6235174 Score: 160
Period size: 46 Copynumber: 5.5 Consensus size: 45
6234911 AATTTCATAA
* * * *
6234921 ATTCACATT-TAAAAACTTTA-ATATTTCACAACCAAATTTTGAAAG
1 ATTCACATTCAAAAAATTTTAGA-ATTTCACATCCAAAATTT-AAAG
* *
6234966 ATTCACATTCGAAAAATTTTAGAATTTCGCATCCAAAATTTCAACA-
1 ATTCACATTCAAAAAATTTTAGAATTTCACATCCAAAATTT-AA-AG
* * * *
6235012 ATTCTCATCCAAAAAAAAATTTAGGATTTCA-A-CCAAAATTTTAAAG
1 ATTCACATTC--AAAAAATTTTAGAATTTCACATCCAAAA-TTTAAAG
* * * * *
6235058 ATTGACATTTAAAACATTTTAGAGA-TTCACATCCAAAGTTTAAAA
1 ATTCACATTCAAAAAATTTTAGA-ATTTCACATCCAAAATTTAAAG
* * * * *
6235103 AGTTCTCATCCAAAAAAAAATTTAGGATTTCACATCCAAAATTTCAATG
1 A-TTCACATTC--AAAAAATTTTAGAATTTCACATCCAAAATTT-AAAG
* *
6235152 ATTTACATTCGAAAAATTTTAGA
1 ATTCACATTCAAAAAATTTTAGA
6235175 GATTCATAAC
Statistics
Matches: 157, Mismatches: 37, Indels: 29
0.70 0.17 0.13
Matches are distributed among these distances:
44 14 0.09
45 19 0.12
46 68 0.43
47 7 0.04
48 46 0.29
49 3 0.02
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (45 bp):
ATTCACATTCAAAAAATTTTAGAATTTCACATCCAAAATTTAAAG
Found at i:6235190 original size:94 final size:93
Alignment explanation
Indices: 6234943--6235202 Score: 321
Period size: 92 Copynumber: 2.8 Consensus size: 93
6234933 AAACTTTAAT
* * * *
6234943 ATTTCACAACCAAATTTTGAAAGATTCACATTCGAAAAATTTTAGA-ATTTCGCATCCAAAATTT
1 ATTTCAC-ACCAAAATTTCAAAGATTCACATTCGAAAAATTTTAGAGA-TTCACATCCAAAGTTT
*
6235007 CAACAA-TTCTCATCCAAAAAAAAATTTAGG
64 -AAAAAGTTCTCATCCAAAAAAAAATTTAGG
* * *
6235037 ATTTCA-ACCAAAATTTTAAAGATTGACATT-TAAAACATTTTAGAGATTCACATCCAAAGTTTA
1 ATTTCACACCAAAATTTCAAAGATTCACATTCGAAAA-ATTTTAGAGATTCACATCCAAAGTTTA
6235100 AAAAGTTCTCATCCAAAAAAAAATTTAGG
65 AAAAGTTCTCATCCAAAAAAAAATTTAGG
* * * * * *
6235129 ATTTCACATCCAAAATTTCAATGATTTACATTCGAAAAATTTTAGAGATTCATAACTAAAGTTTT
1 ATTTCACA-CCAAAATTTCAAAGATTCACATTCGAAAAATTTTAGAGATTCACATCCAAAGTTTA
6235194 AAAAGTTCT
65 AAAAGTTCT
6235203 GTTAGTCTTG
Statistics
Matches: 145, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
91 8 0.06
92 73 0.50
93 2 0.01
94 58 0.40
95 4 0.03
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.33
Consensus pattern (93 bp):
ATTTCACACCAAAATTTCAAAGATTCACATTCGAAAAATTTTAGAGATTCACATCCAAAGTTTAA
AAAGTTCTCATCCAAAAAAAAATTTAGG
Found at i:6243636 original size:3 final size:3
Alignment explanation
Indices: 6243628--6243656 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6243618 AAACACCATT
6243628 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6243657 TATTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6243689 original size:21 final size:21
Alignment explanation
Indices: 6243663--6243724 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 21
6243653 TATTTATTTA
6243663 ATTTTTTTTCTCTTTCTTTCC
1 ATTTTTTTTCTCTTTCTTTCC
* * *
6243684 A-TTTTTTACATTTTTC-TTCT
1 ATTTTTTTTC-TCTTTCTTTCC
* *
6243704 TTTTTTTTTTTCTTTCTTTCC
1 ATTTTTTTTCTCTTTCTTTCC
6243725 TCCTTTCTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (21 bp):
ATTTTTTTTCTCTTTCTTTCC
Found at i:6243915 original size:23 final size:23
Alignment explanation
Indices: 6243884--6243942 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
6243874 GAAAAAATGA
*
6243884 GATTCGAATCCCAGAAGATCTGG
1 GATTTGAATCCCAGAAGATCTGG
6243907 GATTTGAATCCCAGAAGATCTGG
1 GATTTGAATCCCAGAAGATCTGG
6243930 GATTTGAATCCCA
1 GATTTGAATCCCA
6243943 AAAAGCTCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (23 bp):
GATTTGAATCCCAGAAGATCTGG
Found at i:6245328 original size:13 final size:12
Alignment explanation
Indices: 6245309--6245339 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6245299 CAAAATTAAA
*
6245309 AATAAAAAATTT
1 AATAAAAAAATT
6245321 AATAAAAAAATT
1 AATAAAAAAATT
6245333 AATAAAA
1 AATAAAA
6245340 TTTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:6249357 original size:42 final size:42
Alignment explanation
Indices: 6249310--6249391 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
6249300 TTTATTCCCA
*
6249310 GTGGATATCTCAATCCTTATCCAGGAATGACATCTACACCCG
1 GTGGATATCCCAATCCTTATCCAGGAATGACATCTACACCCG
* *
6249352 GTGGATATCCCAATCCTTATTCAGGAATGACATTTACACC
1 GTGGATATCCCAATCCTTATCCAGGAATGACATCTACACC
6249392 TGCTCTGGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (42 bp):
GTGGATATCCCAATCCTTATCCAGGAATGACATCTACACCCG
Found at i:6250246 original size:47 final size:47
Alignment explanation
Indices: 6250177--6250271 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
6250167 TAAAGAAAGG
6250177 TGTAGCTCCCAAAAAGAAAGAGAATGCAGCCCAAGCAGTAAACTATA
1 TGTAGCTCCCAAAAAGAAAGAGAATGCAGCCCAAGCAGTAAACTATA
6250224 TGTAGCTCCCAAAAAGAAAGAGAATGCAGCCCAAGCAGTAAACTATA
1 TGTAGCTCCCAAAAAGAAAGAGAATGCAGCCCAAGCAGTAAACTATA
6250271 T
1 T
6250272 AGGGCAATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (47 bp):
TGTAGCTCCCAAAAAGAAAGAGAATGCAGCCCAAGCAGTAAACTATA
Found at i:6257249 original size:51 final size:50
Alignment explanation
Indices: 6257139--6257268 Score: 156
Period size: 51 Copynumber: 2.6 Consensus size: 50
6257129 AACAAAGAGA
** *
6257139 AATTTTAAAGTTGTTGAGTCTCTGTTGAG-AGAAACTTTTCCAAGATAAG
1 AATTTTAAAGTTGTTGAACCTCTGCTGAGAAGAAACTTTTCCAAGATAAG
** * *
6257188 AATTTTAAAGTTGTTGAACCTCTGCTGAGAAGAGCCCTTTT-CATGATATG
1 AATTTTAAAGTTGTTGAACCTCTGCTGAGAAGA-AACTTTTCCAAGATAAG
*
6257238 AGATTTTAAAGTTGTTGAACCTCTACTGAGA
1 A-ATTTTAAAGTTGTTGAACCTCTGCTGAGA
6257269 GGAGTTTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
49 26 0.37
50 11 0.16
51 33 0.47
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (50 bp):
AATTTTAAAGTTGTTGAACCTCTGCTGAGAAGAAACTTTTCCAAGATAAG
Found at i:6257534 original size:3 final size:3
Alignment explanation
Indices: 6257522--6257584 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
6257512 CTGTAAACAC
6257522 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6257569 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
6257585 TATTTAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6257663 original size:16 final size:14
Alignment explanation
Indices: 6257621--6257667 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
6257611 GTTTTCTGTA
*
6257621 TTTTTCTTCTTCTT-
1 TTTTTCCTCTT-TTC
6257635 TTTTTCCTCTTTTC
1 TTTTTCCTCTTTTC
6257649 TTTTTCCTTCATTTTC
1 TTTTTCC-TC-TTTTC
6257665 TTT
1 TTT
6257668 CTTATCCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 2 0.07
14 17 0.59
15 2 0.07
16 8 0.28
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTCCTCTTTTC
Found at i:6257917 original size:19 final size:20
Alignment explanation
Indices: 6257883--6257920 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6257873 AAGAAATGAG
6257883 AAAAAAGAGACCAAAAAAAT
1 AAAAAAGAGACCAAAAAAAT
*
6257903 AAAAAAGA-ACTAAAAAAA
1 AAAAAAGAGACCAAAAAAA
6257921 AGAGAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.79, C:0.08, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAAAAGAGACCAAAAAAAT
Found at i:6258760 original size:13 final size:13
Alignment explanation
Indices: 6258744--6258768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6258734 TTAAAAAATT
6258744 TTTAAAAATAAAC
1 TTTAAAAATAAAC
6258757 TTTAAAAATAAA
1 TTTAAAAATAAA
6258769 ATAATATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTAAAAATAAAC
Found at i:6258960 original size:22 final size:20
Alignment explanation
Indices: 6258934--6258980 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 20
6258924 GAGTATTTAT
6258934 AAAAATTTTCAATACAATAAAAA
1 AAAAATTTT-AAT--AATAAAAA
6258957 AAAAATTTTAATAATAAATAA
1 AAAAATTTTAATAATAAA-AA
6258978 AAA
1 AAA
6258981 TTGATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.26
21 5 0.22
22 3 0.13
23 9 0.39
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATTTTAATAATAAAAA
Found at i:6258997 original size:23 final size:19
Alignment explanation
Indices: 6258932--6258982 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
6258922 TGGAGTATTT
6258932 ATAAAAATTTTCAATACAATAAA
1 ATAAAAATTTT-AAT--AAT-AA
*
6258955 AAAAAAATTTTAATAATAA
1 ATAAAAATTTTAATAATAA
6258974 ATAAAAATT
1 ATAAAAATT
6258983 GATTAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 10 0.38
20 3 0.12
22 3 0.12
23 10 0.38
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAAATTTTAATAATAA
Found at i:6263674 original size:62 final size:62
Alignment explanation
Indices: 6263607--6263735 Score: 170
Period size: 62 Copynumber: 2.1 Consensus size: 62
6263597 TTTAAGGCAT
* * *
6263607 TTTTTGGATAAAAATATCTTGATTAATC-TCCAACAAAAAATTGGAGGGGATTATTCAAGGCG
1 TTTTTGGATAAAAATACCTTGAATAATCTTCCAAC-AAAAATTGAAGGGGATTATTCAAGGCG
* * * * *
6263669 TTTTTGGCTGAAAATACCTTGAATAATCTTCTAACAAAAATTGAAGGTGATTATTGAAGGCG
1 TTTTTGGATAAAAATACCTTGAATAATCTTCCAACAAAAATTGAAGGGGATTATTCAAGGCG
6263731 TTTTT
1 TTTTT
6263736 AGCAAGAACA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 53 0.91
63 5 0.09
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (62 bp):
TTTTTGGATAAAAATACCTTGAATAATCTTCCAACAAAAATTGAAGGGGATTATTCAAGGCG
Found at i:6266725 original size:20 final size:21
Alignment explanation
Indices: 6266702--6266749 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
6266692 AAATTTGTCA
*
6266702 AAAATTTCTAAA-ATTTTTAT
1 AAAATTTCTAAATAATTTTAT
*
6266722 AAAAATTCTAAATAATTTTAT
1 AAAATTTCTAAATAATTTTAT
6266743 AAAATTT
1 AAAATTT
6266750 TTGAAAGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATTTCTAAATAATTTTAT
Found at i:6266740 original size:21 final size:21
Alignment explanation
Indices: 6266678--6266746 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
6266668 AAGGAAAAAG
*
6266678 TAAAAATTGTTTAAAAATTTGT-
1 TAAAAATT-TCTAAAAATTT-TA
* *
6266700 CAAAAATTTCTAAAATTTTTA
1 TAAAAATTTCTAAAAATTTTA
6266721 TAAAAA-TTCTAAATAATTTTA
1 TAAAAATTTCTAAA-AATTTTA
6266742 TAAAA
1 TAAAA
6266747 TTTTTGAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.20
21 25 0.62
22 7 0.17
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAAAATTTCTAAAAATTTTA
Found at i:6266748 original size:10 final size:9
Alignment explanation
Indices: 6266687--6267013 Score: 81
Period size: 9 Copynumber: 33.8 Consensus size: 9
6266677 GTAAAAATTG
6266687 TTTAAAAAT
1 TTTAAAAAT
6266696 TTGTCAAAAAT
1 TT-T-AAAAAT
*
6266707 TTCTAAAATTT
1 TT-TAAAA-AT
6266718 TTATAAAAAT
1 TT-TAAAAAT
*
6266728 TCTAAATAAT
1 TTTAAA-AAT
6266738 TTTATAAAATT
1 TTTA-AAAA-T
* *
6266749 TTTGAAAGT
1 TTTAAAAAT
* *
6266758 TCTAAAAAA
1 TTTAAAAAT
6266767 TTTAAAAAT
1 TTTAAAAAT
*
6266776 TTCTTAAAAT
1 TT-TAAAAAT
*
6266786 TTAAAAAAT
1 TTTAAAAAT
*
6266795 ATTCAAAACACT
1 -TTTAAAA-A-T
*
6266807 TCTAAAAGAT
1 TTTAAAA-AT
6266817 TATTAAAAAATT
1 T-TT-AAAAA-T
6266829 CTTTAAAAA-
1 -TTTAAAAAT
6266838 -TTAAAAAT
1 TTTAAAAAT
*
6266846 TTATAAAAAAA
1 TT-T-AAAAAT
6266857 TTT-AAAAT
1 TTTAAAAAT
* *
6266865 TTCAAAAAA
1 TTTAAAAAT
*** **
6266874 AACAAAGCT
1 TTTAAAAAT
6266883 TTT-AAAAT
1 TTTAAAAAT
*
6266891 TCTAAAAA-
1 TTTAAAAAT
* **
6266899 ATTATAACCT
1 TTTA-AAAAT
*
6266909 TTCCAAAAAGTT
1 TT-TAAAAA--T
6266921 TTTAAAAAT
1 TTTAAAAAT
*
6266930 TCTAAAAAT
1 TTTAAAAAT
**
6266939 TCAAAACAAT
1 TTTAAA-AAT
*
6266949 TGTAAAAAAT
1 T-TTAAAAAT
*
6266959 TCTAAAAAT
1 TTTAAAAAT
6266968 TTTAAAAAAT
1 TTT-AAAAAT
* *
6266978 TCTAAAAAAA
1 T-TTAAAAAT
6266988 TTT-AAAAT
1 TTTAAAAAT
6266996 TTATATAAAAT
1 TT-TA-AAAAT
6267007 TTTAAAA
1 TTTAAAA
6267014 TAAATGAAAT
Statistics
Matches: 230, Mismatches: 56, Indels: 64
0.66 0.16 0.18
Matches are distributed among these distances:
7 7 0.03
8 19 0.08
9 68 0.30
10 62 0.27
11 62 0.27
12 11 0.05
13 1 0.00
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:6266783 original size:20 final size:19
Alignment explanation
Indices: 6266687--6266792 Score: 65
Period size: 21 Copynumber: 5.4 Consensus size: 19
6266677 GTAAAAATTG
* *
6266687 TTTAAAAATTTGTCAAAAA
1 TTTAAAAATTTTTAAAAAA
*
6266706 TTTCTAAAATTTTTATAAAAA
1 TTT-AAAAATTTTTA-AAAAA
*
6266727 TTCTAAATAA-TTTTATAAAAT
1 TT-TAAA-AATTTTTA-AAAAA
** * *
6266748 TTTTGAAAGTTCTAAAAAA
1 TTTAAAAATTTTTAAAAAA
6266767 TTTAAAAATTTCTT--AAAA
1 TTTAAAAATTT-TTAAAAAA
6266785 TTTAAAAA
1 TTTAAAAA
6266793 ATATTCAAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
18 12 0.18
19 17 0.25
20 15 0.22
21 21 0.31
22 3 0.04
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (19 bp):
TTTAAAAATTTTTAAAAAA
Found at i:6266784 original size:11 final size:10
Alignment explanation
Indices: 6266678--6266839 Score: 66
Period size: 11 Copynumber: 15.8 Consensus size: 10
6266668 AAGGAAAAAG
6266678 TAAAAATTGTT
1 TAAAAATT-TT
6266689 TAAAAATTTGT
1 TAAAAATTT-T
* *
6266700 CAAAAATTTC
1 TAAAAATTTT
6266710 T-AAAATTTT
1 TAAAAATTTT
* *
6266719 TATAAAAATTC
1 TA-AAAATTTT
6266730 TAAATAA-TTT
1 TAAA-AATTTT
6266740 TATAAAATTTT
1 TA-AAAATTTT
* * *
6266751 T-GAAAGTTC
1 TAAAAATTTT
*
6266760 TAAAAA-ATT
1 TAAAAATTTT
6266769 TAAAAATTTCT
1 TAAAAATTT-T
6266780 T-AAAA-TTT
1 TAAAAATTTT
* *
6266788 AAAAAATATT
1 TAAAAATTTT
* * *
6266798 CAAAACACTTC
1 TAAAA-ATTTT
6266809 TAAAAGATTATT
1 TAAAA-ATT-TT
*
6266821 AAAAAATTCTT
1 TAAAAATT-TT
6266832 TAAAAATT
1 TAAAAATT
6266840 AAAAATTTAT
Statistics
Matches: 111, Mismatches: 27, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
8 1 0.01
9 27 0.24
10 23 0.21
11 55 0.50
12 5 0.05
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (10 bp):
TAAAAATTTT
Found at i:6266855 original size:19 final size:19
Alignment explanation
Indices: 6266833--6266875 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6266823 AAAATTCTTT
6266833 AAAAATTAAAAATTT-ATAA
1 AAAAATTAAAAATTTCA-AA
*
6266852 AAAAATTTAAAATTTCAAA
1 AAAAATTAAAAATTTCAAA
6266871 AAAAA
1 AAAAA
6266876 CAAAGCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATTAAAAATTTCAAA
Found at i:6266956 original size:20 final size:18
Alignment explanation
Indices: 6266924--6266994 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 18
6266914 AAAAGTTTTT
6266924 AAAAATTCT-AAAAATTCA
1 AAAAATT-TAAAAAATTCA
6266942 AAACAATTGTAAAAAATTCTA
1 AAA-AATT-TAAAAAATTC-A
*
6266963 AAAATTTTAAAAAATTCTAA
1 AAAAATTTAAAAAATTC--A
6266983 AAAAATTTAAAA
1 AAAAATTTAAAA
6266995 TTTATATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.07
19 15 0.33
20 23 0.51
21 4 0.09
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.30
Consensus pattern (18 bp):
AAAAATTTAAAAAATTCA
Found at i:6267005 original size:29 final size:30
Alignment explanation
Indices: 6266924--6267018 Score: 99
Period size: 29 Copynumber: 3.2 Consensus size: 30
6266914 AAAAGTTTTT
* *
6266924 AAAAATTCTAAAAA-TTCAAAACAATTGT-A
1 AAAAATTCTAAAAATTTTAAAA-AATTCTAA
6266953 AAAAATTCTAAAAATTTTAAAAAATTCTAA
1 AAAAATTCTAAAAATTTTAAAAAATTCTAA
* *
6266983 AAAAATT-T-AAAATTTATATAAAATTTTAA
1 AAAAATTCTAAAAATTT-TAAAAAATTCTAA
6267012 AATAAAT
1 AA-AAAT
6267019 GAAATAAGTT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.12
29 33 0.57
30 18 0.31
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAAATTCTAAAAATTTTAAAAAATTCTAA
Found at i:6267187 original size:15 final size:16
Alignment explanation
Indices: 6267162--6267196 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
6267152 AAAAATCACA
6267162 AAAACTTAAAAAATCT
1 AAAACTTAAAAAATCT
6267178 AAAA-TTAAAAAATCT
1 AAAACTTAAAAAATCT
6267193 AAAA
1 AAAA
6267197 ATTTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAACTTAAAAAATCT
Found at i:6267216 original size:19 final size:18
Alignment explanation
Indices: 6267182--6267262 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 18
6267172 AAATCTAAAA
* *
6267182 TTAAAAAATCTAAAAATT
1 TTAAAAAATATGAAAATT
*
6267200 TTAAAAAATTTTGAAAA-T
1 TTAAAAAA-TATGAAAATT
6267218 TTAAAAAATATGAAAATTT
1 TTAAAAAATATGAAAA-TT
*
6267237 TTGAAAAATATGAAAAAATT
1 TTAAAAAATATG--AAAATT
6267257 TTAAAA
1 TTAAAA
6267263 TATTCTAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.13
18 17 0.32
19 18 0.34
20 7 0.13
21 4 0.08
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (18 bp):
TTAAAAAATATGAAAATT
Found at i:6267223 original size:17 final size:17
Alignment explanation
Indices: 6267162--6267252 Score: 78
Period size: 19 Copynumber: 5.2 Consensus size: 17
6267152 AAAAATCACA
* *
6267162 AAAACTTAAAAAATCT-
1 AAAATTTAAAAAATATG
* *
6267178 AAAA-TTAAAAAATCTA
1 AAAATTTAAAAAATATG
*
6267194 AAAATTTTAAAAAATTTTG
1 AAAA-TTTAAAAAA-TATG
6267213 AAAATTTAAAAAATATG
1 AAAATTTAAAAAATATG
*
6267230 AAAATTTTTGAAAAATATG
1 AAAA--TTTAAAAAATATG
6267249 AAAA
1 AAAA
6267253 AATTTTAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
15 11 0.17
16 8 0.12
17 7 0.11
18 17 0.26
19 22 0.34
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (17 bp):
AAAATTTAAAAAATATG
Found at i:6267251 original size:36 final size:34
Alignment explanation
Indices: 6267167--6267252 Score: 93
Period size: 36 Copynumber: 2.5 Consensus size: 34
6267157 TCACAAAAAC
* *
6267167 TTAAAAAATCT-AAAATTAAAAAATCTAAAAATT
1 TTAAAAAATATGAAAATTAAAAAATATAAAAATT
* *
6267200 TTAAAAAATTTTGAAAATTTAAAAAATATGAAAATTT
1 TTAAAAAA-TATGAAAA-TTAAAAAATAT-AAAAATT
*
6267237 TTGAAAAATATGAAAA
1 TTAAAAAATATGAAAA
6267253 AATTTTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 8 0.18
34 2 0.05
35 4 0.09
36 17 0.39
37 13 0.30
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (34 bp):
TTAAAAAATATGAAAATTAAAAAATATAAAAATT
Found at i:6267351 original size:10 final size:9
Alignment explanation
Indices: 6267182--6267352 Score: 89
Period size: 10 Copynumber: 18.0 Consensus size: 9
6267172 AAATCTAAAA
*
6267182 TTAAAAAAT
1 TTAAAAATT
*
6267191 CTAAAAATT
1 TTAAAAATT
6267200 TTAAAAAATT
1 TT-AAAAATT
*
6267210 TTGAAAATT
1 TTAAAAATT
* *
6267219 TAAAAAATA
1 TTAAAAATT
* *
6267228 TGAAAATTT
1 TTAAAAATT
6267237 TTGAAAAATAT
1 TT-AAAAAT-T
**
6267248 GAAAAAATT
1 TTAAAAATT
6267257 TTAAAATATT
1 TTAAAA-ATT
*
6267267 CTAAAAACTT
1 TTAAAAA-TT
6267277 TT-AAAATT
1 TTAAAAATT
6267285 CTATGAAAAA--
1 -T-T-AAAAATT
6267295 TTAAATAATT
1 TTAAA-AATT
6267305 TTAAAAA-T
1 TTAAAAATT
*
6267313 CTAAAACATT
1 TTAAAA-ATT
*
6267323 TCAAAACAATT
1 T-TAAA-AATT
6267334 TTAAAAATT
1 TTAAAAATT
6267343 GTTAAAAATT
1 -TTAAAAATT
6267353 CAAATTTTAA
Statistics
Matches: 123, Mismatches: 22, Indels: 33
0.69 0.12 0.19
Matches are distributed among these distances:
7 3 0.02
8 11 0.09
9 46 0.37
10 50 0.41
11 8 0.07
12 5 0.04
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.36
Consensus pattern (9 bp):
TTAAAAATT
Found at i:6267663 original size:10 final size:10
Alignment explanation
Indices: 6267644--6267678 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
6267634 TTACTTAATT
6267644 TTTTAGAATC
1 TTTTAGAATC
*
6267654 TTTTAAAATC
1 TTTTAGAATC
*
6267664 TTTTAGAATG
1 TTTTAGAATC
6267674 TTTTA
1 TTTTA
6267679 TGATTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (10 bp):
TTTTAGAATC
Found at i:6267766 original size:20 final size:20
Alignment explanation
Indices: 6267640--6267768 Score: 75
Period size: 20 Copynumber: 6.4 Consensus size: 20
6267630 AAGTTTACTT
*
6267640 AATTTTTTAGAATCTTTTAA
1 AATTTTTTAGAATTTTTTAA
* * *
6267660 AATCTTTTAGAATGTTTTAT
1 AATTTTTTAGAATTTTTTAA
* * *
6267680 GATTTTTCTAGAAATTTTAAA
1 AATTTTT-TAGAATTTTTTAA
* *
6267701 AACTATTCTAGAATTATTTTATA
1 AA-TTTTTTAGAATT-TTTTA-A
** * *
6267724 TTTTTTTTAG---TCTTTGA
1 AATTTTTTAGAATTTTTTAA
*
6267741 ATTTTTTTAGAATTTTTTAA
1 AATTTTTTAGAATTTTTTAA
6267761 AATTTTTT
1 AATTTTTT
6267769 TTTTAATTAT
Statistics
Matches: 78, Mismatches: 24, Indels: 14
0.67 0.21 0.12
Matches are distributed among these distances:
17 10 0.13
18 3 0.04
19 1 0.01
20 34 0.44
21 16 0.21
22 13 0.17
23 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (20 bp):
AATTTTTTAGAATTTTTTAA
Found at i:6268111 original size:4 final size:4
Alignment explanation
Indices: 6268102--6268127 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6268092 TTTGTTATTA
6268102 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
6268128 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:6273111 original size:18 final size:17
Alignment explanation
Indices: 6273090--6273143 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 17
6273080 AAAAGGTCTC
6273090 AAAGATAAAAAAAAAAAA
1 AAAGA-AAAAAAAAAAAA
6273108 AAAGAAAGAAAAGGAAAAAA
1 AAAGAAA-AAAA--AAAAAA
6273128 AAAGAGAAAAGAAAAA
1 AAAGA-AAAA-AAAAA
6273144 TGAATGTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 2 0.06
18 9 0.29
19 3 0.10
20 13 0.42
21 4 0.13
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAAAAAAAAA
Found at i:6273115 original size:22 final size:22
Alignment explanation
Indices: 6273090--6273142 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
6273080 AAAAGGTCTC
6273090 AAAGATAAA-AAAAAAAAAAAAG
1 AAAGA-AAAGAAAAAAAAAAAAG
* *
6273112 AAAGAAAAGGAAAAAAAAAGAG
1 AAAGAAAAGAAAAAAAAAAAAG
6273134 AAAAGAAAA
1 -AAAGAAAA
6273143 ATGAATGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 16 0.59
23 8 0.30
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (22 bp):
AAAGAAAAGAAAAAAAAAAAAG
Found at i:6273125 original size:16 final size:17
Alignment explanation
Indices: 6273097--6273143 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
6273087 CTCAAAGATA
*
6273097 AAAAAAAAAAAAAAGAAAG
1 AAAAGAAAAAAAAAG--AG
6273116 AAAAGGAAAAAAAAAGAG
1 AAAA-GAAAAAAAAAGAG
6273134 AAAAGAAAAA
1 AAAAGAAAAA
6273144 TGAATGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 6 0.23
18 6 0.23
19 4 0.15
20 10 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAAGAG
Found at i:6273138 original size:23 final size:22
Alignment explanation
Indices: 6273100--6273142 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6273090 AAAGATAAAA
6273100 AAAAAAAAAAAGAAAGAAAAGG
1 AAAAAAAAAAAGAAAGAAAAGG
*
6273122 AAAAAAAAAGAGAAAAGAAAA
1 AAAAAAAAAAAG-AAAGAAAA
6273143 ATGAATGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAGAAAGAAAAGG
Found at i:6273511 original size:15 final size:15
Alignment explanation
Indices: 6273488--6273524 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
6273478 TCACTAATAG
6273488 ATAAAAAAAATTAAAA
1 ATAAAAAAAA-TAAAA
6273504 ATAAAAAAAATAAAA
1 ATAAAAAAAATAAAA
6273519 ATAAAA
1 ATAAAA
6273525 GAATGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
ATAAAAAAAATAAAA
Found at i:6273538 original size:18 final size:17
Alignment explanation
Indices: 6273500--6273554 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
6273490 AAAAAAAATT
*
6273500 AAAAATAAAAAA-A-AT
1 AAAAATAAAAAAGAGAA
6273515 AAAAATAAAAGAATG-GAA
1 AAAAATAAAA-AA-GAGAA
6273533 AAAAATAAAAAAGAGAA
1 AAAAATAAAAAAGAGAA
6273550 AAAAA
1 AAAAA
6273555 AGACTCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 10 0.29
16 3 0.09
17 10 0.29
18 11 0.32
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAAATAAAAAAGAGAA
Found at i:6274758 original size:22 final size:21
Alignment explanation
Indices: 6274730--6274840 Score: 91
Period size: 22 Copynumber: 5.1 Consensus size: 21
6274720 ATTTTTAAGT
6274730 TTTGAGTTTTCAAAGAAGAATC
1 TTTGAG-TTTCAAAGAAGAATC
*
6274752 TTTGAGTTTCAAATG-AGAATA
1 TTTGAGTTTCAAA-GAAGAATC
* *
6274773 TTTGAGATTTCAAATAGGAATC
1 TTTGAG-TTTCAAAGAAGAATC
* *
6274795 TTAGAGTTTTTAAATG-AGAATC
1 TTTGAG-TTTCAAA-GAAGAATC
* * *
6274817 TTCGAGTTTCAAATAAAAATC
1 TTTGAGTTTCAAAGAAGAATC
6274838 TTT
1 TTT
6274841 AAGATATGAA
Statistics
Matches: 70, Mismatches: 14, Indels: 11
0.74 0.15 0.12
Matches are distributed among these distances:
21 31 0.44
22 39 0.56
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (21 bp):
TTTGAGTTTCAAAGAAGAATC
Found at i:6274794 original size:43 final size:43
Alignment explanation
Indices: 6274730--6274840 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
6274720 ATTTTTAAGT
*
6274730 TTTGAGTTTTCAAAGAAGAATCTTTGAG-TTTCAAATGAGAATA
1 TTTGAG-TTTCAAATAAGAATCTTTGAGTTTTCAAATGAGAATA
* * * *
6274773 TTTGAGATTTCAAATAGGAATCTTAGAGTTTTTAAATGAGAATC
1 TTTGAG-TTTCAAATAAGAATCTTTGAGTTTTCAAATGAGAATA
* *
6274817 TTCGAGTTTCAAATAAAAATCTTT
1 TTTGAGTTTCAAATAAGAATCTTT
6274841 AAGATATGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 39 0.68
44 18 0.32
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (43 bp):
TTTGAGTTTCAAATAAGAATCTTTGAGTTTTCAAATGAGAATA
Found at i:6275040 original size:78 final size:78
Alignment explanation
Indices: 6274953--6275110 Score: 289
Period size: 78 Copynumber: 2.0 Consensus size: 78
6274943 GAACCTTTGG
6274953 ACTCGAATGAGAAGCTTTGAACTTTTGGATGTGACTTTCCAAAATTTGAATGAAAAGCTTTAAAC
1 ACTCGAATGAGAAGCTTTGAACTTTTGGATGTGACTTTCCAAAATTTGAATGAAAAGCTTTAAAC
6275018 TTTTTGGATGTGA
66 TTTTTGGATGTGA
* * *
6275031 ACTCGAATGAGAAGTTTTGAACTTTTGGATGTGACTTTCCAAATTTTGGATGAAAAGCTTTAAAC
1 ACTCGAATGAGAAGCTTTGAACTTTTGGATGTGACTTTCCAAAATTTGAATGAAAAGCTTTAAAC
6275096 TTTTTGGATGTGA
66 TTTTTGGATGTGA
6275109 AC
1 AC
6275111 CTCAAATTTA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (78 bp):
ACTCGAATGAGAAGCTTTGAACTTTTGGATGTGACTTTCCAAAATTTGAATGAAAAGCTTTAAAC
TTTTTGGATGTGA
Found at i:6275598 original size:4 final size:4
Alignment explanation
Indices: 6275589--6275614 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6275579 TAGAAGAGCA
6275589 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
6275615 CAAAGTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:6275633 original size:57 final size:59
Alignment explanation
Indices: 6275546--6275655 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 59
6275536 TAAAAAAGCA
* * *
6275546 TTATTTATTTCCTAAAGTTATGGAACCTCTATTTAGAAGAGCATTATTTATTTATTTAT
1 TTATTTATTTCCTAAAGTCATGGAACCTCTAATTAGAAGAGCAATATTTATTTATTTAT
* * *
6275605 TTATTTATTT-C-AAAGTCATTGAGCCTCTAATTAGATGAGCAATATTTATTT
1 TTATTTATTTCCTAAAGTCATGGAACCTCTAATTAGAAGAGCAATATTTATTT
6275656 TTCAAAGTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 34 0.76
58 1 0.02
59 10 0.22
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (59 bp):
TTATTTATTTCCTAAAGTCATGGAACCTCTAATTAGAAGAGCAATATTTATTTATTTAT
Found at i:6275670 original size:43 final size:43
Alignment explanation
Indices: 6275601--6275915 Score: 298
Period size: 43 Copynumber: 7.3 Consensus size: 43
6275591 ATTTATTTAT
6275601 TTATTTATTTATTTCAAAGTCATTGAGCCTCTAATTAGATGAGCA
1 TTATTTA-TT-TTTCAAAGTCATTGAGCCTCTAATTAGATGAGCA
* ** * ** * *
6275646 ATATTTATTTTTCAAAGTTGTTGAGCCTTTGTTTAGAAGAGCT
1 TTATTTATTTTTCAAAGTCATTGAGCCTCTAATTAGATGAGCA
** * * * *
6275689 TTATTTATTTTTCAAAGTTGTTAAGTCTCTATTTAGAAGAGCA
1 TTATTTATTTTTCAAAGTCATTGAGCCTCTAATTAGATGAGCA
* * ** *
6275732 TTA-TTATTTTTCAAAATCATTGAACCT-TTGTTAAAATGAGCA
1 TTATTTATTTTTCAAAGTCATTGAGCCTCTAATT-AGATGAGCA
*
6275774 TTATTTATTTTTCAAAGTCATTGAGCCTCTATTTAGATGAGCA
1 TTATTTATTTTTCAAAGTCATTGAGCCTCTAATTAGATGAGCA
* *
6275817 TTATTTATTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAG--
1 TTATTTATTTTTCAAAGTCATTGAGCCTCTAATTAGATGAGCA
* * * * *
6275858 TCTATTTACTTTTCTAAAGTCGTTGAGCCTTTGATTAGAGGAGTC-
1 T-TATTTATTTTTC-AAAGTCATTGAGCCTCTAATTAGATGAG-CA
6275903 TTATTTATTTTTC
1 TTATTTATTTTTC
6275916 CAAAAGTTGT
Statistics
Matches: 227, Mismatches: 36, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.02
42 39 0.17
43 161 0.71
44 16 0.07
45 7 0.03
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (43 bp):
TTATTTATTTTTCAAAGTCATTGAGCCTCTAATTAGATGAGCA
Found at i:6275871 original size:128 final size:129
Alignment explanation
Indices: 6275612--6275915 Score: 307
Period size: 128 Copynumber: 2.4 Consensus size: 129
6275602 TATTTATTTA
* * * * * * ** *
6275612 TTTC-AAAGTCATTGAGCCTCTAATTAGATGAGCAATATTTATTTTTCAAAGTTGTTGAGCCTTT
1 TTTCTAAAATCATTGAACCTTTGATTAAATGAGCATTATTTATTTTTCAAAGTCATTGAGCCTCT
* * ** * *
6275676 GTTTAGAAGAGCTTTATTTATTTTTCAAAGTTGTTAAGTCTCTATTTAGAAGAGCATTATTATT
66 ATTTAGAAGAGCATTATTTATTTTTCAAAGTCATTAAGCCTCTATTTAGAAGAGCATTATTACT
6275740 TTTC-AAAATCATTGAACCTTTG-TTAAAATGAGCATTATTTATTTTTCAAAGTCATTGAGCCTC
1 TTTCTAAAATCATTGAACCTTTGATT-AAATGAGCATTATTTATTTTTCAAAGTCATTGAGCCTC
* * *
6275803 TATTTAGATGAGCATTATTTATTTTTCAAAGTCATTGAGCCTCTGA-TTAGAGGAG--TCTATTT
65 TATTTAGAAGAGCATTATTTATTTTTCAAAGTCATTAAGCCTCT-ATTTAGAAGAGCAT-TA-TT
6275865 ACT
127 ACT
* * * * *
6275868 TTTCTAAAGTCGTTGAGCCTTTGATTAGAGGAGTC-TTATTTATTTTTC
1 TTTCTAAAATCATTGAACCTTTGATTAAATGAG-CATTATTTATTTTTC
6275916 CAAAAGTTGT
Statistics
Matches: 146, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
126 1 0.01
127 4 0.03
128 104 0.71
129 34 0.23
130 3 0.02
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.44
Consensus pattern (129 bp):
TTTCTAAAATCATTGAACCTTTGATTAAATGAGCATTATTTATTTTTCAAAGTCATTGAGCCTCT
ATTTAGAAGAGCATTATTTATTTTTCAAAGTCATTAAGCCTCTATTTAGAAGAGCATTATTACT
Found at i:6276215 original size:8 final size:7
Alignment explanation
Indices: 6276170--6276236 Score: 54
Period size: 6 Copynumber: 9.9 Consensus size: 7
6276160 TTATTTTATT
6276170 TTATTT-
1 TTATTTA
6276176 TTATTTA
1 TTATTTA
*
6276183 TCTATTTG
1 T-TATTTA
6276191 TTA-TTA
1 TTATTTA
*
6276197 TTA-AT-
1 TTATTTA
6276202 TTATTTA
1 TTATTTA
6276209 TTCATTTAA
1 TT-ATTT-A
6276218 TTATTTA
1 TTATTTA
6276225 TTA-TTA
1 TTATTTA
6276231 TTATTT
1 TTATTT
6276237 TGGGTTAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
5 3 0.06
6 19 0.38
7 11 0.22
8 14 0.28
9 3 0.06
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (7 bp):
TTATTTA
Found at i:6276216 original size:34 final size:32
Alignment explanation
Indices: 6276157--6276233 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 32
6276147 TCTAGCCCAA
*
6276157 TTATTATT-TTATTTTATTTTTATTT-ATCTAT
1 TTATTATTATTAATTTATTTTTATTTAAT-TAT
*
6276188 TTGTTATTATTAATTTATTTATTCATTTAATTAT
1 TTATTATTATTAATTTATTT-TT-ATTTAATTAT
6276222 TTATTATTATTA
1 TTATTATTATTA
6276234 TTTTGGGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 7 0.18
32 10 0.26
33 2 0.05
34 18 0.46
35 2 0.05
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (32 bp):
TTATTATTATTAATTTATTTTTATTTAATTAT
Found at i:6276231 original size:26 final size:25
Alignment explanation
Indices: 6276169--6276232 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
6276159 ATTATTTTAT
* *
6276169 TTTATTTTTATTTATCTATTTGTTA
1 TTTATTATTATTTATCTATTTATTA
6276194 -TTATTAATTTATTTAT-TCATTTAATTA
1 TTTATT-A-TTATTTATCT-ATTT-ATTA
6276221 TTTATTATTATT
1 TTTATTATTATT
6276233 ATTTTGGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
26 17 0.53
27 4 0.12
28 5 0.16
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTATTATTATTTATCTATTTATTA
Found at i:6276232 original size:37 final size:37
Alignment explanation
Indices: 6276156--6276235 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
6276146 GTCTAGCCCA
* * *
6276156 ATTATTATTTTATTTTATTTTTATTTATCTATTTGTT
1 ATTATTAATTTATTTTATTTTTAATTATCTATTTATT
*
6276193 ATTATTAATTTA-TTTATTCATTTAATTATTTA-TTATT
1 ATTATTAATTTATTTTATT--TTTAATTATCTATTTATT
6276230 ATTATT
1 ATTATT
6276236 TTGGGTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 6 0.16
37 21 0.57
38 10 0.27
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.69
Consensus pattern (37 bp):
ATTATTAATTTATTTTATTTTTAATTATCTATTTATT
Found at i:6276756 original size:19 final size:19
Alignment explanation
Indices: 6276732--6276770 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6276722 CTAGGTTGAT
6276732 AAAGAAAGAGG-GAGAGAAA
1 AAAGAAA-AGGAGAGAGAAA
6276751 AAAGAAAAGGAGAGAGAAA
1 AAAGAAAAGGAGAGAGAAA
6276770 A
1 A
6276771 TGAGGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
AAAGAAAAGGAGAGAGAAA
Found at i:6276764 original size:17 final size:20
Alignment explanation
Indices: 6276732--6276770 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
6276722 CTAGGTTGAT
6276732 AAAGAAAGAGGGAGAGA-AA
1 AAAGAAAGAGGGAGAGAGAA
6276751 AAAGAAA-A-GGAGAGAGAA
1 AAAGAAAGAGGGAGAGAGAA
6276769 AA
1 AA
6276771 TGAGGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAGGGAGAGAGAA
Found at i:6277562 original size:55 final size:55
Alignment explanation
Indices: 6277503--6277613 Score: 125
Period size: 55 Copynumber: 2.0 Consensus size: 55
6277493 TTTTTTCCAA
* * * *
6277503 AAAAAAAGAAAAAAATAGAAAGAATTTCTAAATAG-GCCCGAATGGTTAAAAATTT
1 AAAAAAAGAAAAAAAGAAAAAGAATTTCTAAATAGAG-CCAAATGGTAAAAAATTT
**** *
6277558 AAAAATTTCAAAAAAGAAAAAGAATTTCTAAATTGAGCCAAATGGTAAAAAATTT
1 AAAAAAAGAAAAAAAGAAAAAGAATTTCTAAATAGAGCCAAATGGTAAAAAATTT
6277613 A
1 A
6277614 GAGATTCCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
55 45 0.98
56 1 0.02
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (55 bp):
AAAAAAAGAAAAAAAGAAAAAGAATTTCTAAATAGAGCCAAATGGTAAAAAATTT
Found at i:6277625 original size:55 final size:54
Alignment explanation
Indices: 6277511--6277693 Score: 178
Period size: 53 Copynumber: 3.4 Consensus size: 54
6277501 AAAAAAAAAG
* * * * *
6277511 AAAAAAATAGAAAGAATTTCTAAATAG-GCCCGAATGGTTAAAAATTTAAAAATTTC
1 AAAAAAA-A-AAAGAATTTCTAAATTGAG-CCAAATGGTAAAAAATTTAGAAATTCC
*
6277567 AAAAAAGAAAAAGAATTTCTAAATTGAGCCAAATGGTAAAAAATTTAGAGATTCC
1 AAAAAA-AAAAAGAATTTCTAAATTGAGCCAAATGGTAAAAAATTTAGAAATTCC
* * * *
6277622 --AAAAAATAAGATATTTCTAAATTAACCCAAATGGTAAAAAATTTAGAAATT-T
1 AAAAAAAAAAAGA-ATTTCTAAATTGAGCCAAATGGTAAAAAATTTAGAAATTCC
* *
6277674 AAAATAAAAAA-TATTTCTAA
1 AAAAAAAAAAAGAATTTCTAA
6277694 TTTGGCCCAA
Statistics
Matches: 108, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
52 14 0.13
53 40 0.37
54 7 0.06
55 38 0.35
56 8 0.07
57 1 0.01
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (54 bp):
AAAAAAAAAAAGAATTTCTAAATTGAGCCAAATGGTAAAAAATTTAGAAATTCC
Found at i:6280831 original size:19 final size:19
Alignment explanation
Indices: 6280790--6280840 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
6280780 TTTAGGGGGT
* *
6280790 TTTTAGGTTTCACTAAGGG
1 TTTTAGTTTTCACTAAGGA
6280809 TTTTAGTTTTCATCT-AGGA
1 TTTTAGTTTTCA-CTAAGGA
*
6280828 TTTTGGTTTTCAC
1 TTTTAGTTTTCAC
6280841 CTTAATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 25 0.89
20 2 0.07
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.51
Consensus pattern (19 bp):
TTTTAGTTTTCACTAAGGA
Found at i:6282569 original size:13 final size:12
Alignment explanation
Indices: 6282546--6282608 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 12
6282536 GTTTCTTTCT
6282546 ATTTAATTTTAA
1 ATTTAATTTTAA
6282558 ATTTAGATTTTAA
1 ATTTA-ATTTTAA
*
6282571 ATTCTTGATTTTTAA
1 A-T-TT-AATTTTAA
* *
6282586 GTTTTAATTTTAT
1 -ATTTAATTTTAA
6282599 ATTTAATTTT
1 ATTTAATTTT
6282609 TATATGCTCG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
12 14 0.34
13 14 0.34
14 3 0.07
15 9 0.22
16 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (12 bp):
ATTTAATTTTAA
Found at i:6282582 original size:14 final size:13
Alignment explanation
Indices: 6282546--6282608 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
6282536 GTTTCTTTCT
6282546 ATTTA-ATTTTAA
1 ATTTAGATTTTAA
6282558 ATTTAGATTTTAA
1 ATTTAGATTTTAA
*
6282571 ATTCTTGATTTTTAA
1 ATT-TAGA-TTTTAA
* *
6282586 GTTTTA-ATTTTAT
1 -ATTTAGATTTTAA
6282599 ATTTA-ATTTT
1 ATTTAGATTTT
6282609 TATATGCTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 14 0.33
13 15 0.36
14 4 0.10
15 7 0.17
16 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (13 bp):
ATTTAGATTTTAA
Found at i:6290785 original size:10 final size:11
Alignment explanation
Indices: 6290771--6290807 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
6290761 ATTCAATTAT
*
6290771 TTTTTGCTTTT
1 TTTTTGCTTTA
6290782 TTTTTG-TTTA
1 TTTTTGCTTTA
6290792 TTTTTGCTTTA
1 TTTTTGCTTTA
6290803 TTTTT
1 TTTTT
6290808 TTCTTGCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.05, C:0.05, G:0.08, T:0.81
Consensus pattern (11 bp):
TTTTTGCTTTA
Found at i:6291217 original size:19 final size:19
Alignment explanation
Indices: 6291195--6291231 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6291185 GTTTTTAAAA
*
6291195 TTTTTCTTCTTTTTTCTTC
1 TTTTTCTTCATTTTTCTTC
*
6291214 TTTTTCTTGATTTTTCTT
1 TTTTTCTTCATTTTTCTT
6291232 TTCATCTTGA
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:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTTCTTCATTTTTCTTC
Found at i:6291230 original size:16 final size:18
Alignment explanation
Indices: 6291211--6291247 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
6291201 TTCTTTTTTC
6291211 TTCTTTT-TCTTGA-TTT
1 TTCTTTTATCTTGAGTTT
6291227 TTCTTTTCATCTTGAGTTT
1 TTCTTTT-ATCTTGAGTTT
6291246 TT
1 TT
6291248 TATCTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.08, C:0.14, G:0.08, T:0.70
Consensus pattern (18 bp):
TTCTTTTATCTTGAGTTT
Found at i:6291368 original size:15 final size:15
Alignment explanation
Indices: 6291348--6291379 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6291338 GTCACAACCA
*
6291348 TTCTTTGTTTTTTTT
1 TTCTTTCTTTTTTTT
6291363 TTCTTTCTTTTTTTT
1 TTCTTTCTTTTTTTT
6291378 TT
1 TT
6291380 TCATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (15 bp):
TTCTTTCTTTTTTTT
Found at i:6291375 original size:11 final size:11
Alignment explanation
Indices: 6291372--6291411 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
6291362 TTTCTTTCTT
6291372 TTTTTTTTTCA
1 TTTTTTTTTCA
*
6291383 TTTTTTTCTC-
1 TTTTTTTTTCA
6291393 TTTTTTTCTTCA
1 TTTTTTT-TTCA
6291405 TTTTTTT
1 TTTTTTT
6291412 ACATGCCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 7 0.28
11 11 0.44
12 7 0.28
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:6291375 original size:12 final size:12
Alignment explanation
Indices: 6291358--6291411 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
6291348 TTCTTTGTTT
*
6291358 TTTTTTTCTTTCT
1 TTTTTTTC-TTCA
*
6291371 TTTTTTTTTTCA
1 TTTTTTTCTTCA
6291383 TTTTTTTC-TC-
1 TTTTTTTCTTCA
6291393 TTTTTTTCTTCA
1 TTTTTTTCTTCA
6291405 TTTTTTT
1 TTTTTTT
6291412 ACATGCCTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 8 0.22
11 4 0.11
12 17 0.47
13 7 0.19
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTCTTCA
Found at i:6291386 original size:22 final size:22
Alignment explanation
Indices: 6291361--6291411 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
6291351 TTTGTTTTTT
*
6291361 TTTTCTTTCT-TTTTTTTTTTCA
1 TTTT-TTTCTCTTTTTTTCTTCA
6291383 TTTTTTTCTCTTTTTTTCTTCA
1 TTTTTTTCTCTTTTTTTCTTCA
6291405 TTTTTTT
1 TTTTTTT
6291412 ACATGCCTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTTCTCTTTTTTTCTTCA
Found at i:6296655 original size:16 final size:16
Alignment explanation
Indices: 6296634--6296666 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6296624 TATATGTAAC
*
6296634 TTTATTACTTTTTTAT
1 TTTATTACATTTTTAT
6296650 TTTATTACATTTTTAT
1 TTTATTACATTTTTAT
6296666 T
1 T
6296667 ATTTTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTACATTTTTAT
Found at i:6297769 original size:28 final size:26
Alignment explanation
Indices: 6297719--6297771 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
6297709 TAAACTCTGT
* *
6297719 AATTTTTGTTACATTAGTGCCTAAAG
1 AATTTTTGTTACATTAATACCTAAAG
6297745 AATTTTTGTGTCACATTAATACCTAAA
1 AATTTTTGT-T-ACATTAATACCTAAA
6297772 CTTTAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 1 0.04
28 13 0.57
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (26 bp):
AATTTTTGTTACATTAATACCTAAAG
Found at i:6298057 original size:29 final size:30
Alignment explanation
Indices: 6297995--6298067 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 30
6297985 ATCTCAAAAG
* * *
6297995 ATTTTAAAACTTCTAAAAAAATTATATA-A
1 ATTTTAAAAATTTTCAAAAAATTATATATA
* * *
6298024 ATTTTCAAAATTTTCAAAAAATTCTATATT
1 ATTTTAAAAATTTTCAAAAAATTATATATA
*
6298054 TTTTTAAAAATTTT
1 ATTTTAAAAATTTT
6298068 TTAACATTTC
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTTTAAAAATTTTCAAAAAATTATATATA
Found at i:6298101 original size:18 final size:18
Alignment explanation
Indices: 6298066--6298131 Score: 51
Period size: 20 Copynumber: 3.4 Consensus size: 18
6298056 TTTAAAAATT
*
6298066 TTTTAACATTTCTAAAAA
1 TTTTAAAATTTCTAAAAA
*
6298084 TTTTAAAATTTTTTAAAATA
1 TTTTAAAA-TTTCTAAAA-A
* **
6298104 TATTAAAAACTCTAAAAAAA
1 TTTTAAAATTTCT--AAAAA
6298124 TTTTAAAA
1 TTTTAAAA
6298132 ATATATAGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
18 7 0.19
19 10 0.27
20 16 0.43
21 4 0.11
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAATTTCTAAAAA
Found at i:6298102 original size:10 final size:10
Alignment explanation
Indices: 6298053--6298102 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
6298043 AATTCTATAT
6298053 TTTTTTAAAAA
1 TTTTTT-AAAA
*
6298064 TTTTTTAACA
1 TTTTTTAAAA
*
6298074 -TTTCTAAAA
1 TTTTTTAAAA
*
6298083 -ATTTTAAAA
1 TTTTTTAAAA
6298092 TTTTTTAAAA
1 TTTTTTAAAA
6298102 T
1 T
6298103 ATATTAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:6298233 original size:24 final size:21
Alignment explanation
Indices: 6298190--6298241 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 21
6298180 AAACAATTTC
*
6298190 AAAAAATTTATAAAATTTATA
1 AAAAAATTTATAAAAATTATA
*
6298211 AAAAAATTTCATTCAAAAATTATT
1 AAAAAATTT-A-T-AAAAATTATA
6298235 AAAAAAT
1 AAAAAAT
6298242 AACCAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 9 0.35
22 1 0.04
23 1 0.04
24 15 0.58
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAATTTATAAAAATTATA
Found at i:6298315 original size:20 final size:18
Alignment explanation
Indices: 6298292--6298369 Score: 68
Period size: 20 Copynumber: 4.1 Consensus size: 18
6298282 TTTTTAAGAT
6298292 TTCTTAAAAATTTTCAACAA
1 TTCTTAAAAATTTT-AA-AA
*
6298312 TTCTAAAAAATTTTAAAA
1 TTCTTAAAAATTTTAAAA
*
6298330 TT-TTATAAATTTTATAAAAA
1 TTCTTA-AAAATTT-T-AAAA
* *
6298350 TTTTTAAAAAATTTAAAA
1 TTCTTAAAAATTTTAAAA
6298368 TT
1 TT
6298370 TATAACAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
17 2 0.04
18 16 0.33
19 4 0.08
20 24 0.49
21 3 0.06
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TTCTTAAAAATTTTAAAA
Found at i:6298339 original size:9 final size:9
Alignment explanation
Indices: 6298319--6298347 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
6298309 CAATTCTAAA
6298319 AAATTTTA-
1 AAATTTTAT
6298327 AAATTTTAT
1 AAATTTTAT
6298336 AAATTTTAT
1 AAATTTTAT
6298345 AAA
1 AAA
6298348 AATTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AAATTTTAT
Found at i:6298348 original size:28 final size:27
Alignment explanation
Indices: 6298295--6298447 Score: 75
Period size: 28 Copynumber: 5.6 Consensus size: 27
6298285 TTAAGATTTC
*
6298295 TTAAAAATTTTCAACAATTCTA-AAAAATT
1 TTAAAAAATTT-AA-AATT-TATAAAAATT
*
6298324 TT-AAAATTTTATAAATTTTATAAAAATTT
1 TTAAAAAATTTA-AAA-TTTATAAAAA-TT
*
6298353 TTAAAAAATTTAAAATTTATAACAA--
1 TTAAAAAATTTAAAATTTATAAAAATT
* *
6298378 TT-AAAAATATGAAATATTTATATAAATT
1 TTAAAAAAT-TTAAA-ATTTATAAAAATT
* * * * *
6298406 ATAAAAATTATTATAATTT-GAAAATTT
1 TTAAAAAAT-TTAAAATTTATAAAAATT
* *
6298433 TTCAAAAATCTAAAA
1 TTAAAAAATTTAAAA
6298448 ATTCTTCATA
Statistics
Matches: 97, Mismatches: 17, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
24 6 0.06
25 6 0.06
26 13 0.13
27 16 0.16
28 30 0.31
29 18 0.19
30 8 0.08
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (27 bp):
TTAAAAAATTTAAAATTTATAAAAATT
Found at i:6298384 original size:17 final size:18
Alignment explanation
Indices: 6298344--6298385 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
6298334 ATAAATTTTA
*
6298344 TAAAAATTTTTAAAAAAT
1 TAAAAATTTATAAAAAAT
* *
6298362 TTAAAATTTAT-AACAAT
1 TAAAAATTTATAAAAAAT
6298379 TAAAAAT
1 TAAAAAT
6298386 ATGAAATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATTTATAAAAAAT
Found at i:6298450 original size:19 final size:19
Alignment explanation
Indices: 6298426--6298477 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
6298416 TTATAATTTG
*
6298426 AAAATTTTTCAAAAATCTA
1 AAAATTTTTCAAAAATCAA
*
6298445 AAAATTCTTCATAAAATCAA
1 AAAATTTTTCA-AAAATCAA
6298465 AAAATTTTT-AAAA
1 AAAATTTTTCAAAA
6298478 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 3 0.10
19 11 0.38
20 15 0.52
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTTTTCAAAAATCAA
Found at i:6298485 original size:15 final size:16
Alignment explanation
Indices: 6298465--6298514 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
6298455 ATAAAATCAA
6298465 AAAATTT-TTAAAATT
1 AAAATTTATTAAAATT
*
6298480 AAAATTTATAAAAATT
1 AAAATTTATTAAAATT
* *
6298496 -AAATTTCTTAAAGTT
1 AAAATTTATTAAAATT
6298511 AAAA
1 AAAA
6298515 AAAAAAAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 19 0.66
16 10 0.34
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAATTTATTAAAATT
Found at i:6298493 original size:16 final size:15
Alignment explanation
Indices: 6298465--6298498 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
6298455 ATAAAATCAA
*
6298465 AAAATTTTTAAAATT
1 AAAATTTTAAAAATT
6298480 AAAATTTATAAAAATT
1 AAAATTT-TAAAAATT
6298496 AAA
1 AAA
6298499 TTTCTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTTTAAAAATT
Found at i:6298749 original size:29 final size:29
Alignment explanation
Indices: 6298700--6298821 Score: 95
Period size: 29 Copynumber: 4.2 Consensus size: 29
6298690 TTTTTGAATT
* *
6298700 TTTTTTAATTTTTCTAGAATTTCTA-AAG
1 TTTTTTAATTTTTTTAAAATTTCTAGAAG
* * *
6298728 TTTTTTAATTTTTTTAAAAATTTTTATAAA
1 TTTTTTAATTTTTTT-AAAATTTCTAGAAG
* * *
6298758 TTTTTAAGAATTTTTTAAATTTTTCTAGAA-
1 TTTTTTA-ATTTTTTTAAA-ATTTCTAGAAG
* * * *
6298788 TTTTTTTATTATTTTAAAATTTTTAAAAG
1 TTTTTTAATTTTTTTAAAATTTCTAGAAG
6298817 TTTTT
1 TTTTT
6298822 AGAATTATTT
Statistics
Matches: 73, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
28 21 0.29
29 22 0.30
30 16 0.22
31 14 0.19
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.61
Consensus pattern (29 bp):
TTTTTTAATTTTTTTAAAATTTCTAGAAG
Found at i:6298821 original size:11 final size:10
Alignment explanation
Indices: 6298696--6299131 Score: 142
Period size: 10 Copynumber: 43.8 Consensus size: 10
6298686 GCTTTTTTTG
**
6298696 AATTTTTTTT
1 AATTTTTTAA
*
6298706 AATTTTTCTAG
1 AATTTTT-TAA
*
6298717 AA-TTTCTAA
1 AATTTTTTAA
*
6298726 AGTTTTTT-A
1 AATTTTTTAA
*
6298735 ATTTTTTTAA
1 AATTTTTTAA
*
6298745 AAATTTTTATA
1 AATTTTTTA-A
6298756 AA-TTTTTAA
1 AATTTTTTAA
6298765 GAATTTTTT-A
1 -AATTTTTTAA
*
6298775 AATTTTTCTAG
1 AATTTTT-TAA
6298786 AATTTTTT--
1 AATTTTTTAA
*
6298794 TATTATTTTAA
1 AATT-TTTTAA
6298805 AA-TTTTTAA
1 AATTTTTTAA
* *
6298814 AAGTTTTTAG
1 AATTTTTTAA
*
6298824 AATTATTT-A
1 AATTTTTTAA
6298833 AATTTTTTACAA
1 AATTTTTT--AA
6298845 AATTTTTTTTAA
1 AA--TTTTTTAA
**
6298857 GTTTTTTTAA
1 AATTTTTTAA
*
6298867 ATTTTTTTGAA
1 AATTTTTT-AA
* *
6298878 ATTTTTTTAT
1 AATTTTTTAA
*
6298888 AA-TTTTTAG
1 AATTTTTTAA
*
6298897 AATTTTTAAA
1 AATTTTTTAA
* * *
6298907 AATATTTCAT
1 AATTTTTTAA
*
6298917 AATTTTTTAG
1 AATTTTTTAA
* **
6298927 ATTTTTTTTG
1 AATTTTTTAA
*
6298937 AATTTTTAAA
1 AATTTTTTAA
* *
6298947 AATGTTTTAT
1 AATTTTTTAA
*
6298957 AA-TTTGT-A
1 AATTTTTTAA
*
6298965 GATTTTTTATTA
1 AATTTTTTA--A
* * *
6298977 GAAATATCT-A
1 -AATTTTTTAA
6298987 AATTTTTTACAA
1 AATTTTTT--AA
6298999 AATTTTTT--
1 AATTTTTTAA
6299007 AATTTTTTAAAA
1 AATTTTTT--AA
6299019 AATTTATTTTAA
1 AA-TT-TTTTAA
*
6299031 AATTTTTTGA
1 AATTTTTTAA
6299041 AATTTTTTAA
1 AATTTTTTAA
*
6299051 AATTTCTT--
1 AATTTTTTAA
6299059 AA-TTTTT-A
1 AATTTTTTAA
*
6299067 AATTTTTT-T
1 AATTTTTTAA
* *
6299076 AGTTTTTT-T
1 AATTTTTTAA
* *
6299085 AACTTTTGAA
1 AATTTTTTAA
* *
6299095 AATATTTT-G
1 AATTTTTTAA
*
6299104 AATTTTTTAT
1 AATTTTTTAA
6299114 AA-TTTTTAA
1 AATTTTTTAA
6299123 AATTGTTTT
1 AATT-TTTT
6299132 GAATTTATCT
Statistics
Matches: 318, Mismatches: 69, Indels: 77
0.69 0.15 0.17
Matches are distributed among these distances:
7 4 0.01
8 16 0.05
9 91 0.29
10 135 0.42
11 35 0.11
12 21 0.07
13 6 0.02
14 10 0.03
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:6298833 original size:69 final size:67
Alignment explanation
Indices: 6298690--6298841 Score: 164
Period size: 69 Copynumber: 2.2 Consensus size: 67
6298680 TCCTTAGCTT
* * **
6298690 TTTTTGAATTTTTTTTAATTTTTCTAGAATTTCTAAAGTTTTTTAATTTTTTTAAAAATTTTTAT
1 TTTTT-AAATTTTTTAAATTTTTCTAGAATTTCTAAAGTTTTTTAAAATTTTTAAAAATTTTTAT
6298755 AAA
65 AAA
* ** *
6298758 TTTTTAAGAATTTTTTAAATTTTTCTAGAATTTTTTTA-TTATTTTAAAATTTTTAAAAGTTTTT
1 TTTTT-A-AATTTTTTAAATTTTTCTAGAATTTCTAAAGTT-TTTTAAAATTTTTAAAAATTTTT
*
6298822 A-GAA
63 ATAAA
6298826 TTATTTAAATTTTTTA
1 TT-TTTAAATTTTTTA
6298842 CAAAATTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
67 9 0.13
68 13 0.18
69 49 0.69
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (67 bp):
TTTTTAAATTTTTTAAATTTTTCTAGAATTTCTAAAGTTTTTTAAAATTTTTAAAAATTTTTATA
AA
Found at i:6298854 original size:33 final size:29
Alignment explanation
Indices: 6298769--6298903 Score: 89
Period size: 29 Copynumber: 4.4 Consensus size: 29
6298759 TTTTAAGAAT
* *
6298769 TTTTTAAA-TTTTTCTAGAATTTTTTT-AT
1 TTTTTAAATTTTTTC-AAAATTTTTTTAAA
* *
6298797 TATTTTAAAATTTTT-AAAA-GTTTTTAGAA
1 T-TTTTAAATTTTTTCAAAATTTTTTTA-AA
*
6298826 TTATTTAAATTTTTTACAAAATTTTTTTTAAGTT
1 TT-TTTAAATTTTTT-CAAAA-TTTTTTTAA--A
**
6298860 TTTTTAAATTTTTTTGAAATTTTTTTATAA
1 TTTTTAAATTTTTTCAAAATTTTTTTA-AA
6298890 TTTTTAGAATTTTT
1 TTTTTA-AATTTTT
6298904 AAAAATATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 23
0.73 0.08 0.20
Matches are distributed among these distances:
27 5 0.06
28 5 0.06
29 20 0.24
30 11 0.13
31 19 0.22
32 5 0.06
33 18 0.21
34 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (29 bp):
TTTTTAAATTTTTTCAAAATTTTTTTAAA
Found at i:6299022 original size:12 final size:10
Alignment explanation
Indices: 6298986--6299131 Score: 69
Period size: 9 Copynumber: 14.9 Consensus size: 10
6298976 AGAAATATCT
6298986 AAATTTTTTACA
1 AAATTTTTT--A
6298998 AAATTTTTT-
1 AAATTTTTTA
6299007 -AATTTTTTAAA
1 AAATTTTTT--A
6299018 AAATTTATTTTA
1 AAA-TT-TTTTA
*
6299030 AAATTTTTTG
1 AAATTTTTTA
6299040 AAATTTTTTA
1 AAATTTTTTA
*
6299050 AAATTTCTT-
1 AAATTTTTTA
6299059 -AA-TTTTT-
1 AAATTTTTTA
6299066 AAATTTTTT-
1 AAATTTTTTA
* *
6299075 TAGTTTTTT-
1 AAATTTTTTA
* * *
6299084 TAACTTTTGA
1 AAATTTTTTA
*
6299094 AAATATTTT-
1 AAATTTTTTA
*
6299103 GAATTTTTTA
1 AAATTTTTTA
*
6299113 TAA-TTTTTA
1 AAATTTTTTA
6299122 AAATTGTTTT
1 AAATT-TTTT
6299132 GAATTTATCT
Statistics
Matches: 105, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
7 4 0.04
8 12 0.11
9 33 0.31
10 29 0.28
11 6 0.06
12 15 0.14
13 2 0.02
14 4 0.04
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (10 bp):
AAATTTTTTA
Found at i:6299097 original size:28 final size:28
Alignment explanation
Indices: 6299035--6299137 Score: 79
Period size: 28 Copynumber: 3.8 Consensus size: 28
6299025 TTTTAAAATT
* * *
6299035 TTTTG-AAATTTTTTAAAATTTCT-TAA
1 TTTTGAAAATTTTTTTAATTTTTTATAA
* *
6299061 TTTT-TAAATTTTTTTAGTTTTTT-TAA
1 TTTTGAAAATTTTTTTAATTTTTTATAA
* *
6299087 CTTTTGAAAATATTTTGAATTTTTTATAA
1 -TTTTGAAAATTTTTTTAATTTTTTATAA
* *
6299116 TTTTTAAAATTGTTTTGAATTT
1 TTTTGAAAATT-TTTTTAATTT
6299138 ATCTTTTAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
26 21 0.34
27 4 0.06
28 24 0.39
29 13 0.21
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (28 bp):
TTTTGAAAATTTTTTTAATTTTTTATAA
Found at i:6300040 original size:19 final size:19
Alignment explanation
Indices: 6300008--6300071 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 19
6299998 TTAATTCTAA
*
6300008 TAAAA-TGAAATTGGGCTT
1 TAAAATTGAATTTGGGCTT
6300026 TAAAATTGAATTT-GGC-T
1 TAAAATTGAATTTGGGCTT
* * *
6300043 TACAATTAGATTTTGGACTT
1 TAAAATT-GAATTTGGGCTT
6300063 TAAAATTGA
1 TAAAATTGA
6300072 CATGAACTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 7 0.19
18 13 0.35
19 10 0.27
20 7 0.19
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (19 bp):
TAAAATTGAATTTGGGCTT
Found at i:6304415 original size:16 final size:16
Alignment explanation
Indices: 6304394--6304426 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6304384 TTTAACACTA
6304394 TATATTGATACATAAT
1 TATATTGATACATAAT
6304410 TATATTGATACATAAT
1 TATATTGATACATAAT
6304426 T
1 T
6304427 TCCTTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TATATTGATACATAAT
Found at i:6305991 original size:63 final size:63
Alignment explanation
Indices: 6305922--6306121 Score: 174
Period size: 63 Copynumber: 3.2 Consensus size: 63
6305912 TAAAAAAAAA
* * *
6305922 CCTTAAATAATCTCCTTTAAAATATATTAGTGAATTTTTTAAAGTGTTTTTACTCTAAAAATG
1 CCTTAAATAATCTCCTTTAAAATATATTAATGAATTTTTTAAAGTATTTTTAATCTAAAAATG
* * ** * * * * *
6305985 TCTTAAATAATAC-CCTTCAATTTTTTTTATTTGGATTATTT-AAGATATTTTTAGA-C-AAAAA
1 CCTTAAATAAT-CTCCTTTAAAATATATTA-ATGAATTTTTTAAAG-TATTTTTA-ATCTAAAAA
*
6306046 TA
62 TG
* * * * *
6306048 CCTTAAATAATCTCTTTTAAAATATATCAACGAATTTTTTAAGGCATTTTTAATCTAAAAATG
1 CCTTAAATAATCTCCTTTAAAATATATTAATGAATTTTTTAAAGTATTTTTAATCTAAAAATG
6306111 CCTTAAATAAT
1 CCTTAAATAAT
6306122 ACATTTCAAT
Statistics
Matches: 102, Mismatches: 27, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
61 1 0.01
62 16 0.16
63 68 0.67
64 17 0.17
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.44
Consensus pattern (63 bp):
CCTTAAATAATCTCCTTTAAAATATATTAATGAATTTTTTAAAGTATTTTTAATCTAAAAATG
Found at i:6306071 original size:126 final size:127
Alignment explanation
Indices: 6305892--6306134 Score: 335
Period size: 126 Copynumber: 1.9 Consensus size: 127
6305882 TTGAAAGGGC
* * **
6305892 TTATTTAAGGCATTTTTAGATAAAAAAAAACCTTAAATAATCTCCTTTAAAATATATTAGTGAAT
1 TTATTTAAGACATTTTTAGA-AAAAAAAAACCTTAAATAATCTCCTTTAAAATATATCAACGAAT
** * * *
6305957 TTTTTAAAGTGTTTTTACTCTAAAAATGTCTTAAATAATACCCTTCAATTTTTTTTATTTGGA
65 TTTTTAAAGCATTTTTAATCTAAAAATGCCTTAAATAATACACTTCAATTTTTTTTATTTGGA
* * * *
6306020 TTATTTAAGATATTTTTAG-ACAAAAATACCTTAAATAATCTCTTTTAAAATATATCAACGAATT
1 TTATTTAAGACATTTTTAGAAAAAAAAAACCTTAAATAATCTCCTTTAAAATATATCAACGAATT
* *
6306084 TTTTAAGGCATTTTTAATCTAAAAATGCCTTAAATAATACATTTCAATTTT
66 TTTTAAAGCATTTTTAATCTAAAAATGCCTTAAATAATACACTTCAATTTT
6306135 GAAAGGGCTT
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
126 83 0.83
128 17 0.17
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.44
Consensus pattern (127 bp):
TTATTTAAGACATTTTTAGAAAAAAAAAACCTTAAATAATCTCCTTTAAAATATATCAACGAATT
TTTTAAAGCATTTTTAATCTAAAAATGCCTTAAATAATACACTTCAATTTTTTTTATTTGGA
Found at i:6306772 original size:157 final size:156
Alignment explanation
Indices: 6306484--6306788 Score: 463
Period size: 157 Copynumber: 1.9 Consensus size: 156
6306474 CTCTAACCGA
* * * *
6306484 TTGAGCTATCCAATTTCTTTTTATTTTATCTCTTAAATCTTATAAGTAATGAAAGAGTTTATCTA
1 TTGAGCTATCCAAATTCTTTTTATTTTATCTCTTAAATCTTATAAGTAATAAAAAAGATTATCTA
* * * *
6306549 AGGTATTTTTAGACAAAAAAATGTCTTAAATAACTAAAAATGCCTTAAATAATCTCTTTCAATTT
66 AGGCATTTTTAGACAAAAAAATGCCTTAAATAACTAAAAATACCTCAAATAATCTCTTTCAATTT
*
6306614 TTTGAAAGGTATTATTTAAGGCATTTT
131 TTT-AAAGGCATTATTTAAGGCATTTT
*
6306641 TTGAGCTACTCCAAATT-TTTTTATTTTATCTCTTAAATCTTATAAGTAATAAAAAAGATTATTT
1 TTGAGCTA-TCCAAATTCTTTTTATTTTATCTCTTAAATCTTATAAGTAATAAAAAAGATTATCT
6306705 AAGGCATTTTTAGAC-AAAAAATGCCTTAAATAACTAAAAATACCTCAAATAATCT-TCTTCAAT
65 AAGGCATTTTTAGACAAAAAAATGCCTTAAATAACTAAAAATACCTCAAATAATCTCT-TTCAA-
6306768 TTTTTTAAAGGCATTATTTAA
128 TTTTTTAAAGGCATTATTTAA
6306789 AAAAATCCAC
Statistics
Matches: 135, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
155 1 0.01
156 56 0.41
157 71 0.53
158 7 0.05
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (156 bp):
TTGAGCTATCCAAATTCTTTTTATTTTATCTCTTAAATCTTATAAGTAATAAAAAAGATTATCTA
AGGCATTTTTAGACAAAAAAATGCCTTAAATAACTAAAAATACCTCAAATAATCTCTTTCAATTT
TTTAAAGGCATTATTTAAGGCATTTT
Found at i:6306822 original size:157 final size:156
Alignment explanation
Indices: 6306504--6306823 Score: 367
Period size: 157 Copynumber: 2.0 Consensus size: 156
6306494 CAATTTCTTT
* * * *
6306504 TTATTTTATCTCTTAAATCTTATAAGTAATGAAAGAGTTTATCTAAGGTATTTTTAGACAAAAAA
1 TTATTTTATCTCTTAAATCTTATAAGTAATAAAAAAGATTATCTAAGGCATTTTTAGACAAAAAA
* * * * *
6306569 ATGTCTTAAATAACTAAAAATGCCTTAAATAATCTCTTTCAATTTTTTGAAAGGTATTATTTAAG
66 ATGCCTTAAATAACTAAAAATACCTCAAATAATCTCTTTCAATTTTTTGAAAGGCATTATTTAAA
** **** ** **
6306634 GCATTTTTTGAGCTACTCCAAATTTTT
131 AAATCCACTGA-CTACTCCAAAAGTGA
*
6306661 TTATTTTATCTCTTAAATCTTATAAGTAATAAAAAAGATTATTTAAGGCATTTTTAGAC-AAAAA
1 TTATTTTATCTCTTAAATCTTATAAGTAATAAAAAAGATTATCTAAGGCATTTTTAGACAAAAAA
*
6306725 ATGCCTTAAATAACTAAAAATACCTCAAATAATCT-TCTTCAATTTTTTTAAAGGCATTATTTAA
66 ATGCCTTAAATAACTAAAAATACCTCAAATAATCTCT-TTCAATTTTTTGAAAGGCATTATTT-A
**
6306789 AAAAATCCACTGA-TACATTTTAAAAGTGA
129 AAAAATCCACTGACTAC--TCCAAAAGTGA
6306818 TTATTT
1 TTATTT
6306824 AAGGCGTTTT
Statistics
Matches: 136, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
155 4 0.03
156 60 0.44
157 72 0.53
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (156 bp):
TTATTTTATCTCTTAAATCTTATAAGTAATAAAAAAGATTATCTAAGGCATTTTTAGACAAAAAA
ATGCCTTAAATAACTAAAAATACCTCAAATAATCTCTTTCAATTTTTTGAAAGGCATTATTTAAA
AAATCCACTGACTACTCCAAAAGTGA
Found at i:6308873 original size:2 final size:2
Alignment explanation
Indices: 6308866--6308897 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6308856 AGCAATTGTA
6308866 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
6308898 GAGAATGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6309218 original size:2 final size:2
Alignment explanation
Indices: 6309213--6309253 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
6309203 CTCTCCTTTT
* *
6309213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6309254 GTATGTATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6309450 original size:58 final size:57
Alignment explanation
Indices: 6309333--6309450 Score: 125
Period size: 58 Copynumber: 2.0 Consensus size: 57
6309323 TTATATATAG
* *
6309333 AATTTAAATTTCATTTATATATAAAAATTTAGGAAAATTTAGGAAATTGACCCATTGA
1 AATTTAAATTTCATTTATATATAAAAATTTAGGAAAATTTA-GAAATTGACACACTGA
* * *
6309391 AATTTATATTTCATTTATTATATATAAAA-TT-GGGAAATGTTA-AAATTGATGACACTGA
1 AATTTAAATTTCATTTA-TATATA-AAAATTTAGGAAAAT-TTAGAAATTGA-CACACTGA
6309449 AA
1 AA
6309451 AATAGATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
57 7 0.14
58 29 0.57
59 11 0.22
60 4 0.08
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (57 bp):
AATTTAAATTTCATTTATATATAAAAATTTAGGAAAATTTAGAAATTGACACACTGA
Found at i:6309570 original size:20 final size:20
Alignment explanation
Indices: 6309545--6309584 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6309535 CAAACTTAAG
6309545 TAAAAA-AATAGTAATAATAA
1 TAAAAACAATAGTAA-AATAA
*
6309565 TAAAAACAATGGTAAAATAA
1 TAAAAACAATAGTAAAATAA
6309585 AACCAGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (20 bp):
TAAAAACAATAGTAAAATAA
Found at i:6311698 original size:20 final size:20
Alignment explanation
Indices: 6311673--6311711 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
6311663 TGATCGTAAG
*
6311673 TTTTTTTTTT-TTATTTTAA
1 TTTTTTTTTTCTTTTTTTAA
6311692 TTTTTTTTTTCTTTTTTTAA
1 TTTTTTTTTTCTTTTTTTAA
6311712 CTTGTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTTCTTTTTTTAA
Found at i:6311722 original size:3 final size:3
Alignment explanation
Indices: 6311716--6311746 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6311706 TTTTAACTTG
6311716 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6311747 CTTATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6311954 original size:18 final size:20
Alignment explanation
Indices: 6311931--6311974 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
6311921 TTGCATGGTA
*
6311931 TTATTTGCA-TGATTTT-TT
1 TTATTTGAATTGATTTTCTT
*
6311949 TTATTTTAATTGATTTTCTT
1 TTATTTGAATTGATTTTCTT
6311969 TTATTT
1 TTATTT
6311975 CAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (20 bp):
TTATTTGAATTGATTTTCTT
Found at i:6314645 original size:30 final size:29
Alignment explanation
Indices: 6314598--6314665 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
6314588 TTCAATTCAT
6314598 ATATATATAAATTAAAATTAAAATTAA-AA
1 ATATATA-AAATTAAAATTAAAATTAATAA
*
6314627 ATTATATAAAATTAAAAATTAAATTTAATAA
1 A-TATATAAAATT-AAAATTAAAATTAATAA
6314658 ATATATAA
1 ATATATAA
6314666 TTTATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
29 6 0.17
30 26 0.74
31 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
ATATATAAAATTAAAATTAAAATTAATAA
Found at i:6315798 original size:19 final size:19
Alignment explanation
Indices: 6315776--6315823 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
6315766 AATAATAAGA
6315776 TAATATATATTTAATTTTT
1 TAATATATATTTAATTTTT
* *
6315795 TAAT-TAATTTTTTATTTTT
1 TAATAT-ATATTTAATTTTT
6315814 TAA-ATATATT
1 TAATATATATT
6315824 CTAAATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATATATATTTAATTTTT
Found at i:6318061 original size:12 final size:12
Alignment explanation
Indices: 6318044--6318070 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6318034 ATAGTCAGTG
6318044 ATAACCACATAA
1 ATAACCACATAA
6318056 ATAACCACATAA
1 ATAACCACATAA
6318068 ATA
1 ATA
6318071 TAAGAGCCTG
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:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAACCACATAA
Found at i:6318521 original size:2 final size:2
Alignment explanation
Indices: 6318514--6318552 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6318504 AGGAAAAGAT
6318514 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6318553 CTTCAGACAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6322294 original size:39 final size:40
Alignment explanation
Indices: 6322232--6322311 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
6322222 CTTATACTAA
*
6322232 GATTGTTCAAAAGATTCATCAAAACCCTCCAAATACATTT
1 GATTGTTCAAAACATTCATCAAAACCCTCCAAATACATTT
*
6322272 GATTGTTC-AAACATTCATCAAAACCCTCCAAATGCATTT
1 GATTGTTCAAAACATTCATCAAAACCCTCCAAATACATTT
6322311 G
1 G
6322312 TTTAGTTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.30
Consensus pattern (40 bp):
GATTGTTCAAAACATTCATCAAAACCCTCCAAATACATTT
Found at i:6322851 original size:24 final size:24
Alignment explanation
Indices: 6322811--6322856 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6322801 TTTATGTTTA
*
6322811 ATATATATGATTTTATTCTAATAT
1 ATATATATGATTATATTCTAATAT
*
6322835 ATATATAT-ATATATATTTTAAT
1 ATATATATGAT-TATATTCTAAT
6322857 TTGCTTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATATATGATTATATTCTAATAT
Found at i:6324106 original size:2 final size:2
Alignment explanation
Indices: 6324093--6324141 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
6324083 ACATACTTAC
* * * *
6324093 AT AT AT AC AT AT AT AC AT AT AT AC AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6324135 AT AT AT A
1 AT AT AT A
6324142 CCACCCATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Done.