Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 13 of 16
Found at i:1664439 original size:14 final size:15
Alignment explanation
Indices: 1664414--1664444 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1664404 AATAAACATT
1664414 TTATATTTTTTAAAA
1 TTATATTTTTTAAAA
1664429 TTATA-TTTTTAAAA
1 TTATATTTTTTAAAA
1664443 TT
1 TT
1664445 TTAACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATTTTTTAAAA
Found at i:1666098 original size:6 final size:6
Alignment explanation
Indices: 1666087--1666129 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
1666077 ATTTTTCTTA
*
1666087 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTCC TCTTTC T
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC T
1666130 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (6 bp):
TCTTTC
Found at i:1667065 original size:21 final size:22
Alignment explanation
Indices: 1667040--1667083 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1667030 GATACTAATT
1667040 AAATTAATATTTAAT-AATTTA
1 AAATTAATATTTAATAAATTTA
* * *
1667061 AAATTTATTTTTATTAAATTTA
1 AAATTAATATTTAATAAATTTA
1667083 A
1 A
1667084 TTATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATTAATATTTAATAAATTTA
Found at i:1668943 original size:19 final size:19
Alignment explanation
Indices: 1668919--1668956 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1668909 ATTCAACTTT
1668919 ATCATTATTGAATAAATAA
1 ATCATTATTGAATAAATAA
*
1668938 ATCATTGTTGAATAAATAA
1 ATCATTATTGAATAAATAA
1668957 CGAGCAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (19 bp):
ATCATTATTGAATAAATAA
Found at i:1669139 original size:40 final size:40
Alignment explanation
Indices: 1669092--1669167 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
1669082 TAAACATAAA
* * *
1669092 AATTTATCTTATCTTTATTAGATAACAAACTTATTAAGTG
1 AATTTATCTTATCTTTATTAAAAAACAAACCTATTAAGTG
*
1669132 AATTTATCTTATCTTTGTTAAAAAACAAACCTATTA
1 AATTTATCTTATCTTTATTAAAAAACAAACCTATTA
1669168 GGCAAATTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.43
Consensus pattern (40 bp):
AATTTATCTTATCTTTATTAAAAAACAAACCTATTAAGTG
Found at i:1673200 original size:31 final size:31
Alignment explanation
Indices: 1673154--1673237 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
1673144 CCTTCTAACA
*
1673154 AAAACCCACCA-AGAATTCCAACTTAAAATAG
1 AAAACCCA-CATAGAATTTCAACTTAAAATAG
* *
1673185 AAATCCCACATAGAATTTCAACTTAAAATTG
1 AAAACCCACATAGAATTTCAACTTAAAATAG
*
1673216 AAAACCCACATTGAATTTCAAC
1 AAAACCCACATAGAATTTCAAC
1673238 AATTATTTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.04
31 45 0.96
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.23
Consensus pattern (31 bp):
AAAACCCACATAGAATTTCAACTTAAAATAG
Found at i:1673287 original size:20 final size:21
Alignment explanation
Indices: 1673262--1673300 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1673252 TATACTTGAA
1673262 AAACCAAAC-AAAAAACAATG
1 AAACCAAACTAAAAAACAATG
1673282 AAACCAAACTAAAAAACAA
1 AAACCAAACTAAAAAACAA
1673301 AAACCAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.72, C:0.21, G:0.03, T:0.05
Consensus pattern (21 bp):
AAACCAAACTAAAAAACAATG
Found at i:1673314 original size:18 final size:20
Alignment explanation
Indices: 1673262--1673306 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1673252 TATACTTGAA
1673262 AAACCAAAC-AAAAAACAATG
1 AAACCAAACTAAAAAACAA-G
1673282 AAACCAAACTAAAAAACAA-
1 AAACCAAACTAAAAAACAAG
1673301 AAACCA
1 AAACCA
1673307 GCTAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.71, C:0.22, G:0.02, T:0.04
Consensus pattern (20 bp):
AAACCAAACTAAAAAACAAG
Found at i:1674019 original size:2 final size:2
Alignment explanation
Indices: 1674010--1674039 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1674000 AGTAATAAAT
1674010 TA TA -A 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 T
1674040 GAAAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1674289 original size:44 final size:45
Alignment explanation
Indices: 1674200--1674320 Score: 110
Period size: 44 Copynumber: 2.7 Consensus size: 45
1674190 TTTTATTTTG
* *
1674200 ATTT-AATTTAATT-TAAATTAATAT-TTAATAATTAAATAAATTT
1 ATTTAAATTTAATTATAAA-AAATATATTAATAATAAAATAAATTT
1674243 ATTTAAATTTAATTATAAAAAATATATTAAT-ATAAAAATAAA-TT
1 ATTTAAATTTAATTATAAAAAATATATTAATAAT-AAAATAAATTT
* * *
1674287 A-TTAATTTTAAATAATATATAAATAATATTAATA
1 ATTTAAATTT-AATTATA-AAAAAT-ATATTAATA
1674321 GGTTAAGTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
43 11 0.17
44 25 0.38
45 21 0.32
46 8 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (45 bp):
ATTTAAATTTAATTATAAAAAATATATTAATAATAAAATAAATTT
Found at i:1675273 original size:5 final size:5
Alignment explanation
Indices: 1675265--1675300 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
1675255 TTTATTAAAT
*
1675265 ATTAA ATTAA ATTAA ATTAA ATTAA CTTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
1675301 AAAATACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:1675471 original size:1 final size:1
Alignment explanation
Indices: 1675465--1675489 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1675455 CCCAAAATAG
1675465 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1675490 GATAAGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1676060 original size:22 final size:22
Alignment explanation
Indices: 1676035--1676090 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1676025 AGTTTGAAAA
*
1676035 AAAAAGTAAATAAATACTTTCG
1 AAAAACTAAATAAATACTTTCG
*
1676057 AAAATCTAAATAAATACTTTTC-
1 AAAAACTAAATAAATAC-TTTCG
*
1676079 AAAATCTAAATA
1 AAAAACTAAATA
1676091 GGGGCAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAAACTAAATAAATACTTTCG
Found at i:1676281 original size:18 final size:19
Alignment explanation
Indices: 1676258--1676311 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
1676248 AATTTTAGAT
* *
1676258 ATATAATATGATATAA-AA
1 ATATAATATAATAAAATAA
1676276 ATATAAATATAATAAAATAA
1 ATAT-AATATAATAAAATAA
*
1676296 ATA-AATATATTAAAAT
1 ATATAATATAATAAAAT
1676312 TTATATAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 16 0.52
19 10 0.32
20 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATATAATATAATAAAATAA
Found at i:1676541 original size:13 final size:13
Alignment explanation
Indices: 1676523--1676559 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1676513 TAAACATAAT
1676523 TATAATATAAAAA
1 TATAATATAAAAA
1676536 TATAATAT--AAA
1 TATAATATAAAAA
*
1676547 TATAAGATAAAAA
1 TATAATATAAAAA
1676560 AAACTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
TATAATATAAAAA
Found at i:1678535 original size:20 final size:21
Alignment explanation
Indices: 1678507--1678546 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1678497 TTCTTGCTTC
*
1678507 CAAAGGTCAA-GAATTGGCTG
1 CAAAAGTCAAGGAATTGGCTG
1678527 CAAAAGTCAATGGAATTGGC
1 CAAAAGTCAA-GGAATTGGC
1678547 CCCCCAAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
CAAAAGTCAAGGAATTGGCTG
Found at i:1678815 original size:17 final size:18
Alignment explanation
Indices: 1678778--1678823 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1678768 TTAATAAATA
*
1678778 ATATATTTTTATCATATTT
1 ATATA-TTTTATCATAGTT
1678797 ATATATTTTATCAT-GTT
1 ATATATTTTATCATAGTT
1678814 ATA-ATTTTAT
1 ATATATTTTAT
1678824 TTAAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.27
17 5 0.19
18 9 0.35
19 5 0.19
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
ATATATTTTATCATAGTT
Found at i:1678840 original size:16 final size:17
Alignment explanation
Indices: 1678821--1678853 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1678811 GTTATAATTT
1678821 TATTTA-AAAAATTTTA
1 TATTTATAAAAATTTTA
*
1678837 TATTTATATAAATTTTA
1 TATTTATAAAAATTTTA
1678854 ATATGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTATAAAAATTTTA
Found at i:1679244 original size:27 final size:27
Alignment explanation
Indices: 1679204--1679257 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1679194 ATATATTTGA
1679204 TTATTTTATAAT-AATATTTAAAAAATT
1 TTATTTTATAATAAATA-TTAAAAAATT
*
1679231 TTATATTTAT-ATAAATATTAATAAATT
1 TTAT-TTTATAATAAATATTAAAAAATT
1679258 AATCATTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTATTTTATAATAAATATTAAAAAATT
Found at i:1679584 original size:22 final size:22
Alignment explanation
Indices: 1679559--1679611 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1679549 AAATTGTAAA
* *
1679559 TATTGAGATCGAATTTTAATTT
1 TATTGAAATCAAATTTTAATTT
1679581 TATTGAAATCAAATTTTAATTT
1 TATTGAAATCAAATTTTAATTT
*
1679603 TATTAAAAT
1 TATTGAAAT
1679612 TCAACTCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (22 bp):
TATTGAAATCAAATTTTAATTT
Found at i:1680156 original size:2 final size:2
Alignment explanation
Indices: 1680144--1680176 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1680134 GAATGAAGTA
1680144 AT AT AT CAT 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
1680177 TTTTATATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1681536 original size:13 final size:13
Alignment explanation
Indices: 1681518--1681543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1681508 TTATAATACC
1681518 TTCTAATTATATA
1 TTCTAATTATATA
1681531 TTCTAATTATATA
1 TTCTAATTATATA
1681544 CGTAAAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTCTAATTATATA
Found at i:1681596 original size:13 final size:13
Alignment explanation
Indices: 1681568--1681601 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1681558 TAACAATTCA
*
1681568 TAATTTAATTTAAT
1 TAATTT-ATATAAT
1681582 TAATTTATATAAT
1 TAATTTATATAAT
1681595 TAATTTA
1 TAATTTA
1681602 AAAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTTATATAAT
Found at i:1683430 original size:22 final size:20
Alignment explanation
Indices: 1683403--1683456 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 20
1683393 AATAGACGAT
1683403 AAAATATAAAAGTCATATTAA
1 AAAATATAAAAGTCATA-TAA
*
1683424 ATAAATAT-TAA-TCATATAA
1 A-AAATATAAAAGTCATATAA
1683443 AAAATTATAAAAGT
1 AAAA-TATAAAAGT
1683457 GTGTAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
18 3 0.11
19 7 0.26
20 7 0.26
21 4 0.15
22 6 0.22
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAATATAAAAGTCATATAA
Found at i:1683858 original size:19 final size:18
Alignment explanation
Indices: 1683825--1683873 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
1683815 TTTATAATTA
*
1683825 AATTTAAATAAAAATATT
1 AATTTAAATAAAAATAAT
*
1683843 AATTTAATTAATAAATAAT
1 AATTTAAATAA-AAATAAT
1683862 AATTTAAATAAA
1 AATTTAAATAAA
1683874 TTCAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTTAAATAAAAATAAT
Found at i:1684454 original size:8 final size:8
Alignment explanation
Indices: 1684441--1684557 Score: 62
Period size: 8 Copynumber: 13.5 Consensus size: 8
1684431 AATATAAATT
1684441 ATATATAA
1 ATATATAA
*
1684449 ATATATGA
1 ATATATAA
1684457 ATATATTAAA
1 ATATA-T-AA
*
1684467 ATTTATATA
1 ATATATA-A
1684476 ATATA-AA
1 ATATATAA
1684483 ATAT-TAA
1 ATATATAA
1684490 A-ATAATAAA
1 ATAT-AT-AA
1684499 ATTTATATAA
1 A--TATATAA
1684509 ATATAT-A
1 ATATATAA
*
1684516 ATACTTTAA
1 ATA-TATAA
1684525 ATATAATTATA
1 ATAT-A-TA-A
1684536 ATATATAAAA
1 ATATAT--AA
1684546 ATATATAA
1 ATATATAA
1684554 ATAT
1 ATAT
1684558 GATATAAATA
Statistics
Matches: 86, Mismatches: 6, Indels: 34
0.68 0.05 0.27
Matches are distributed among these distances:
6 2 0.02
7 12 0.14
8 29 0.34
9 15 0.17
10 18 0.21
11 8 0.09
12 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (8 bp):
ATATATAA
Found at i:1684482 original size:33 final size:34
Alignment explanation
Indices: 1684443--1684518 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 34
1684433 TATAAATTAT
* *
1684443 ATATAAATATATGAATATATTAAAATTTATAT-A
1 ATATAAATATATGAAAATAATAAAATTTATATAA
*
1684476 ATATAAA-ATATTAAAATAATAAAATTTATATAA
1 ATATAAATATATGAAAATAATAAAATTTATATAA
1684509 ATATATAATA
1 ATATA-AATA
1684519 CTTTAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 21 0.57
33 13 0.35
34 2 0.05
35 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (34 bp):
ATATAAATATATGAAAATAATAAAATTTATATAA
Found at i:1684536 original size:60 final size:63
Alignment explanation
Indices: 1684411--1684567 Score: 176
Period size: 55 Copynumber: 2.7 Consensus size: 63
1684401 AATTAAAATG
* *
1684411 TAATAAAAAATATAAAAAATAATATAAATTATATATAAATATATGAATATATTAAAATTTATA
1 TAATATAAAATATAAAAAATAATATAAATTATATATAAATATATGAATATATTAAAATATATA
*
1684474 TAATATAAAATAT-TAAAATAATA-AAATT-TATATAAATATAT-AATACT-TT-AAATATA-A
1 TAATATAAAATATAAAAAATAATATAAATTATATATAAATATATGAATA-TATTAAAATATATA
*
1684531 T--TATAATATAT-AAAAAT-ATATAAA-TATGATATAAATA
1 TAATATAAAATATAAAAAATAATATAAATTAT-ATATAAATA
1684568 CATAAATTAT
Statistics
Matches: 85, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
54 4 0.05
55 18 0.21
56 9 0.11
57 2 0.02
58 6 0.07
59 6 0.07
60 14 0.16
61 5 0.06
62 9 0.11
63 12 0.14
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (63 bp):
TAATATAAAATATAAAAAATAATATAAATTATATATAAATATATGAATATATTAAAATATATA
Found at i:1684537 original size:6 final size:7
Alignment explanation
Indices: 1684429--1684543 Score: 56
Period size: 6 Copynumber: 17.6 Consensus size: 7
1684419 AATATAAAAA
1684429 ATAATAT
1 ATAATAT
1684436 A-AAT-T
1 ATAATAT
1684441 AT-ATAT
1 ATAATAT
1684447 A-AATAT
1 ATAATAT
1684453 ATGAATAT
1 AT-AATAT
1684461 ATTAA-A-
1 A-TAATAT
*
1684467 AT-TTAT
1 ATAATAT
1684473 ATAATAT
1 ATAATAT
*
1684480 AAAATAT
1 ATAATAT
*
1684487 -TAAAAT
1 ATAATAT
*
1684493 AATAAAAT
1 -ATAATAT
*
1684501 -TTATAT
1 ATAATAT
1684507 A-AATAT
1 ATAATAT
1684513 ATAATACT
1 ATAATA-T
*
1684521 TTAA-AT
1 ATAATAT
1684527 ATAAT-T
1 ATAATAT
1684533 ATAATAT
1 ATAATAT
1684540 ATAA
1 ATAA
1684544 AAATATATAA
Statistics
Matches: 82, Mismatches: 10, Indels: 32
0.66 0.08 0.26
Matches are distributed among these distances:
5 6 0.07
6 36 0.44
7 21 0.26
8 18 0.22
9 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:1684567 original size:11 final size:10
Alignment explanation
Indices: 1684418--1684567 Score: 72
Period size: 9 Copynumber: 15.5 Consensus size: 10
1684408 ATGTAATAAA
*
1684418 AAATATA-AA
1 AAATATATAT
1684427 AAATA-ATAT
1 AAATATATAT
1684436 AAAT-TATAT
1 AAATATATAT
1684445 ATAA-ATATAT
1 A-AATATATAT
*
1684455 GAATATAT-T
1 AAATATATAT
*
1684464 AAA-ATTTAT
1 AAATATATAT
*
1684473 ATA-ATATA-
1 AAATATATAT
1684481 AAATAT-TA-
1 AAATATATAT
1684489 AAATA-ATA-
1 AAATATATAT
*
1684497 AAATTTATAT
1 AAATATATAT
1684507 AAATATATAAT
1 AAATATAT-AT
** *
1684518 ACTTTAAATAT
1 A-AATATATAT
1684529 AATTATAATATAT
1 AA--AT-ATATAT
*
1684542 AAAAATATAT
1 AAATATATAT
1684552 AAATATGATAT
1 AAATAT-ATAT
1684563 AAATA
1 AAATA
1684568 CATAAATTAT
Statistics
Matches: 108, Mismatches: 17, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
8 19 0.18
9 32 0.30
10 29 0.27
11 16 0.15
12 5 0.05
13 7 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (10 bp):
AAATATATAT
Found at i:1685684 original size:18 final size:18
Alignment explanation
Indices: 1685661--1685695 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1685651 CTTATGTTTG
1685661 CCAAACATGCCATGCTTC
1 CCAAACATGCCATGCTTC
*
1685679 CCAAACTTGCCATGCTT
1 CCAAACATGCCATGCTT
1685696 GAATTTCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.11, T:0.26
Consensus pattern (18 bp):
CCAAACATGCCATGCTTC
Found at i:1685712 original size:15 final size:15
Alignment explanation
Indices: 1685688--1685722 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1685678 CCCAAACTTG
1685688 CCATGCTTGAATTTC
1 CCATGCTTGAATTTC
* *
1685703 CCATGTTTGAATTTT
1 CCATGCTTGAATTTC
1685718 CCATG
1 CCATG
1685723 ACCATGGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (15 bp):
CCATGCTTGAATTTC
Found at i:1685767 original size:21 final size:21
Alignment explanation
Indices: 1685740--1685787 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1685730 CCATGGTAAC
*
1685740 CCCCATGCGCAAGATGATGAG
1 CCCCATGCGCAACATGATGAG
* * *
1685761 CTCCATGTGCAACATGGTGAG
1 CCCCATGCGCAACATGATGAG
1685782 CCCCAT
1 CCCCAT
1685788 AAACAGCGGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (21 bp):
CCCCATGCGCAACATGATGAG
Found at i:1685856 original size:21 final size:21
Alignment explanation
Indices: 1685832--1685873 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1685822 TAGTCCTCCC
1685832 ACACCATGTCCATGTGAACTG
1 ACACCATGTCCATGTGAACTG
1685853 ACACCATGTCCATGTGAACTG
1 ACACCATGTCCATGTGAACTG
1685874 TGTCCTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
ACACCATGTCCATGTGAACTG
Found at i:1686367 original size:15 final size:15
Alignment explanation
Indices: 1686327--1686359 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1686317 ATATCCCCCT
1686327 GCTGGAGGATATCCA
1 GCTGGAGGATATCCA
1686342 GCTGGAGGATATCCA
1 GCTGGAGGATATCCA
1686357 GCT
1 GCT
1686360 TGTGGATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.21
Consensus pattern (15 bp):
GCTGGAGGATATCCA
Found at i:1688621 original size:11 final size:11
Alignment explanation
Indices: 1688598--1688663 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
1688588 GTTTTTAAAA
1688598 TATTTAA-ATT
1 TATTTAATATT
*
1688608 TATTTATTATT
1 TATTTAATATT
1688619 TATTTAATATT
1 TATTTAATATT
1688630 TAAATATTAATATT
1 T--AT-TTAATATT
* *
1688644 AAAATTAATATT
1 -TATTTAATATT
1688656 TGATTTAA
1 T-ATTTAA
1688664 ATAAAAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
10 6 0.14
11 14 0.32
12 13 0.30
13 3 0.07
14 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
TATTTAATATT
Found at i:1688639 original size:14 final size:13
Alignment explanation
Indices: 1688622--1688656 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
1688612 TATTATTTAT
1688622 TTAATATTTAAATA
1 TTAATATTTAAA-A
1688636 TTAATA-TTAAAA
1 TTAATATTTAAAA
1688648 TTAATATTT
1 TTAATATTT
1688657 GATTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 7 0.35
14 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAATATTTAAAA
Found at i:1689215 original size:14 final size:15
Alignment explanation
Indices: 1689184--1689236 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 15
1689174 TTTTTTTATT
1689184 AATTAAATAATAATTTA
1 AATTAAAT-AT-ATTTA
1689201 AATTAAAT-TATTTA
1 AATTAAATATATTTA
1689215 AATTAAATATATCTT-
1 AATTAAATATAT-TTA
1689230 AATTAAA
1 AATTAAA
1689237 ATCTAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.38
15 11 0.32
16 2 0.06
17 8 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTAAATATATTTA
Found at i:1689500 original size:6 final size:6
Alignment explanation
Indices: 1689489--1689520 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1689479 TATTTATAAT
1689489 TAAATA TAAATA TAAATA TAAATA TAAATA TA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TA
1689521 TAATTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TAAATA
Found at i:1689530 original size:12 final size:12
Alignment explanation
Indices: 1689483--1689530 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
1689473 TAAAAATATT
1689483 TATAATTAAATA
1 TATAATTAAATA
1689495 TA-AATATAAATA
1 TATAAT-TAAATA
1689507 TA-AATATAAATA
1 TATAAT-TAAATA
*
1689519 TATAATTTAATA
1 TATAATTAAATA
1689531 AATTTATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
11 3 0.09
12 27 0.82
13 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TATAATTAAATA
Found at i:1689530 original size:18 final size:18
Alignment explanation
Indices: 1689483--1689530 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1689473 TAAAAATATT
1689483 TATAATTAAATATAAATA
1 TATAATTAAATATAAATA
1689501 TA-AATATAAATATAAATA
1 TATAAT-TAAATATAAATA
*
1689519 TATAATTTAATA
1 TATAATTAAATA
1689531 AATTTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAATTAAATATAAATA
Found at i:1689624 original size:21 final size:21
Alignment explanation
Indices: 1689600--1689652 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1689590 ATGTCAGATA
**
1689600 TAAATATAAT-AATTTAATTTT
1 TAAAT-TAATAAATTTAAAATT
1689621 TAAATTAATAAATTTAAAATT
1 TAAATTAATAAATTTAAAATT
1689642 TAAATTGAATA
1 TAAATT-AATA
1689653 TTAATGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 20 0.71
22 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAATTAATAAATTTAAAATT
Found at i:1691194 original size:19 final size:19
Alignment explanation
Indices: 1691156--1691200 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1691146 TTGGGTCAAA
1691156 TAATT-ATTTTTGATTAAT
1 TAATTAATTTTTGATTAAT
1691174 TAATTAATTATTTGA-TAAT
1 TAATTAATT-TTTGATTAAT
*
1691193 TATTTAAT
1 TAATTAAT
1691201 AATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 14 0.58
20 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TAATTAATTTTTGATTAAT
Found at i:1691221 original size:29 final size:26
Alignment explanation
Indices: 1691188--1691251 Score: 85
Period size: 25 Copynumber: 2.4 Consensus size: 26
1691178 TAATTATTTG
1691188 ATAATTATTTAATAATATATATATGAAGT
1 ATAATTATTTAAT-AT-T-TATATGAAGT
1691217 ATAATTA-TTAATATTTATATGAAGT
1 ATAATTATTTAATATTTATATGAAGT
*
1691242 AAAATTATTT
1 ATAATTATTT
1691252 TACTTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 16 0.48
26 3 0.09
27 2 0.06
28 5 0.15
29 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (26 bp):
ATAATTATTTAATATTTATATGAAGT
Found at i:1691405 original size:15 final size:15
Alignment explanation
Indices: 1691385--1691413 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1691375 CGCAAACTTT
1691385 GGGGCTCCATCAATG
1 GGGGCTCCATCAATG
1691400 GGGGCTCCATCAAT
1 GGGGCTCCATCAAT
1691414 ATTAGATTAA
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:0.21, C:0.28, G:0.31, T:0.21
Consensus pattern (15 bp):
GGGGCTCCATCAATG
Found at i:1691470 original size:14 final size:14
Alignment explanation
Indices: 1691469--1691648 Score: 89
Period size: 15 Copynumber: 11.6 Consensus size: 14
1691459 TTGAATTTAA
1691469 TAAATTATAAT-A-T
1 TAAATT-TAATAATT
1691482 TAAATTTAATTAA-T
1 TAAATTTAA-TAATT
1691496 TAAATTTAAATAATT
1 TAAATTT-AATAATT
1691511 T-AATTTAAAATAATT
1 TAAATTT--AATAATT
1691526 TAAATTTAATTAATTT
1 TAAATTTAA-TAA-TT
1691542 TAATATTAAATCAATTAATT
1 TAA-ATT---T-AA-TAATT
* *
1691562 TAAAATTAAAATATT
1 TAAATTTAATA-ATT
1691577 TAAATTTTAAATAATTT
1 TAAA-TTT-AATAA-TT
*
1691594 TAAATCTAAATAATT
1 TAAAT-TTAATAATT
*
1691609 TAAATTTAAAATTATT
1 TAAATTT--AATAATT
*
1691625 TAAAATTAAAATAATT
1 T-AAATT-TAATAATT
1691641 TAAATTTA
1 TAAATTTA
1691649 TAAAAAACTT
Statistics
Matches: 135, Mismatches: 10, Indels: 43
0.72 0.05 0.23
Matches are distributed among these distances:
12 3 0.02
13 7 0.05
14 22 0.16
15 37 0.27
16 34 0.25
17 18 0.13
19 2 0.01
20 6 0.04
21 6 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATTTAATAATT
Found at i:1691493 original size:10 final size:10
Alignment explanation
Indices: 1691491--1691545 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
1691481 TTAAATTTAA
1691491 TTAATTAAAT
1 TTAATTAAAT
*
1691501 TTAAAT-AAT
1 TTAATTAAAT
1691510 TTAATTTAAA-
1 TTAA-TTAAAT
*
1691520 ATAATTTAAAT
1 TTAA-TTAAAT
*
1691531 TTAATTAATT
1 TTAATTAAAT
1691541 TTAAT
1 TTAAT
1691546 ATTAAATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
9 7 0.19
10 25 0.68
11 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TTAATTAAAT
Found at i:1691517 original size:66 final size:66
Alignment explanation
Indices: 1691444--1691648 Score: 219
Period size: 66 Copynumber: 3.1 Consensus size: 66
1691434 AAGTAGGTAA
* * *
1691444 TTAATTTAAAATAATTTGAATTTAATAAATTATAATATTAAATTTAATTAA-TT-AAATTTAAAT
1 TTAATTTAAAATAATTTAAATTTAATAAATTATAATATTAAA-TCAATTAATTTAAAATTAAAAT
1691507 AAT
65 -AT
* *
1691510 TTAATTTAAAATAATTTAAATTTAATTAATTTTAATATTAAATCAATTAATTTAAAATTAAAATA
1 TTAATTTAAAATAATTTAAATTTAATAAATTATAATATTAAATCAATTAATTTAAAATTAAAATA
1691575 T
66 T
* * *
1691576 TTAAATTTTAAATAATTTTAAATCTAA-ATAATT-TAA-ATTTAA--AATT-ATTTAAAATTAAA
1 TT-AATTTAAAATAA-TTTAAATTTAATA-AATTATAATATTAAATCAATTAATTTAAAATTAAA
1691635 ATAAT
63 AT-AT
1691640 TTAAATTTA
1 TT-AATTTA
1691649 TAAAAAACTT
Statistics
Matches: 123, Mismatches: 10, Indels: 14
0.84 0.07 0.10
Matches are distributed among these distances:
63 15 0.12
64 14 0.11
65 7 0.06
66 50 0.41
67 23 0.19
68 14 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (66 bp):
TTAATTTAAAATAATTTAAATTTAATAAATTATAATATTAAATCAATTAATTTAAAATTAAAATA
T
Found at i:1691521 original size:15 final size:16
Alignment explanation
Indices: 1691446--1691648 Score: 168
Period size: 16 Copynumber: 12.4 Consensus size: 16
1691436 GTAGGTAATT
1691446 AATTTAAAATAATTTGA
1 AATTTAAAATAATTT-A
*
1691463 ATTTAATAAATTATAATATTA
1 AATT--TAAA--ATAAT-TTA
*
1691484 AATTT-AATTAA-TTA
1 AATTTAAAATAATTTA
1691498 AATTT-AAATAATTT-
1 AATTTAAAATAATTTA
1691512 AATTTAAAATAATTTA
1 AATTTAAAATAATTTA
*
1691528 AATTT-AATTAATTTTA
1 AATTTAAAATAA-TTTA
*
1691544 ATATTAAATCAATTAATTTA
1 A-ATTTAA--AA-TAATTTA
*
1691564 AAATTAAAAT-ATTTA
1 AATTTAAAATAATTTA
*
1691579 AATTTTAAATAATTTTA
1 AATTTAAAATAA-TTTA
*
1691596 AATCT-AAATAATTTA
1 AATTTAAAATAATTTA
*
1691611 AATTTAAAATTATTTA
1 AATTTAAAATAATTTA
*
1691627 AAATTAAAATAATTTA
1 AATTTAAAATAATTTA
1691643 AATTTA
1 AATTTA
1691649 TAAAAAACTT
Statistics
Matches: 152, Mismatches: 17, Indels: 35
0.75 0.08 0.17
Matches are distributed among these distances:
14 18 0.12
15 37 0.24
16 49 0.32
17 16 0.11
18 3 0.02
19 9 0.06
20 6 0.04
21 12 0.08
22 2 0.01
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTAAAATAATTTA
Found at i:1691573 original size:21 final size:21
Alignment explanation
Indices: 1691533--1691571 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1691523 ATTTAAATTT
*
1691533 AATTAATTTTAATATTAAATC
1 AATTAATTTTAAAATTAAATC
1691554 AATTAA-TTTAAAATTAAA
1 AATTAATTTTAAAATTAAA
1691572 ATATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTAATTTTAAAATTAAATC
Found at i:1691596 original size:32 final size:31
Alignment explanation
Indices: 1691557--1691674 Score: 130
Period size: 32 Copynumber: 3.7 Consensus size: 31
1691547 TTAAATCAAT
1691557 TAATTTAAAATTAAAATATTTAAATTTTAAA
1 TAATTTAAAATTAAAATATTTAAATTTTAAA
* *
1691588 TAATTTTAAATCT-AAATAATTTAAATTTAAAA
1 TAATTTAAAAT-TAAAAT-ATTTAAATTTTAAA
*
1691620 TTATTTAAAATTAAAATAATTTAAATTTATAAA
1 TAATTTAAAATTAAAAT-ATTTAAATTT-TAAA
* * *
1691653 AAACTTAAAAATTAAAAAATTT
1 TAA-TTTAAAATTAAAATATTT
1691675 TAAACTAATC
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
31 15 0.21
32 38 0.52
33 8 0.11
34 12 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
TAATTTAAAATTAAAATATTTAAATTTTAAA
Found at i:1691655 original size:26 final size:27
Alignment explanation
Indices: 1691611--1691662 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
1691601 AAATAATTTA
**
1691611 AATTTAAAATTATTTAAAA-TTAAAAT
1 AATTTAAAATTATAAAAAACTTAAAAT
*
1691637 AATTTAAATTTATAAAAAACTTAAAA
1 AATTTAAAATTATAAAAAACTTAAAA
1691663 ATTAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
AATTTAAAATTATAAAAAACTTAAAAT
Found at i:1695341 original size:21 final size:22
Alignment explanation
Indices: 1695317--1695368 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1695307 ATATATTTAA
1695317 TAAATATAAAAAATAATATA-T
1 TAAATATAAAAAATAATATATT
* * * *
1695338 TAAATGTGATATATAATATATT
1 TAAATATAAAAAATAATATATT
1695360 TAAATATAA
1 TAAATATAA
1695369 TTAAATTATG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
TAAATATAAAAAATAATATATT
Found at i:1697866 original size:29 final size:29
Alignment explanation
Indices: 1697834--1697897 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
1697824 AACTTCTATA
1697834 ATATTTAAA-ACTTATATTTATATATAAAT
1 ATATTTAAATACTTATATTTATATAT-AAT
* * * * *
1697863 ATATGTAAATATTTATTTTTATGTATTAT
1 ATATTTAAATACTTATATTTATATATAAT
1697892 ATATTT
1 ATATTT
1697898 TATAAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (29 bp):
ATATTTAAATACTTATATTTATATATAAT
Found at i:1704007 original size:2 final size:2
Alignment explanation
Indices: 1703995--1704031 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1703985 AGAAGTTTGA
1703995 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1704032 CAACAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1704277 original size:2 final size:2
Alignment explanation
Indices: 1704264--1704309 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1704254 ACAAACCAAA
* *
1704264 AT AT AC AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1704306 AT AT
1 AT AT
1704310 CAATAAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1705558 original size:16 final size:17
Alignment explanation
Indices: 1705514--1705559 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1705504 ATATTAATAT
*
1705514 TTATATTATTATAAATAA
1 TTATATTATTA-AAAAAA
*
1705532 TTAAATT-TTAAAAAAA
1 TTATATTATTAAAAAAA
1705548 TT-TATTATTAAA
1 TTATATTATTAAA
1705560 TAATAAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 3 0.12
18 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATATTATTAAAAAAA
Found at i:1708489 original size:20 final size:20
Alignment explanation
Indices: 1708444--1708491 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1708434 TAAACAAAAG
*
1708444 AATTTTTTTTACAAAATGAT
1 AATTTTTTTTACAAAATAAT
* *
1708464 AGTTTTTTTTA-AGAATAAAT
1 AATTTTTTTTACAAAAT-AAT
1708484 AATTTTTT
1 AATTTTTT
1708492 GAAATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (20 bp):
AATTTTTTTTACAAAATAAT
Found at i:1717191 original size:24 final size:23
Alignment explanation
Indices: 1717117--1717194 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 23
1717107 ACTAGTGTAT
**
1717117 TTTATAAATA-TTATAATATCATA
1 TTTATAAATATTTA-AATATTTTA
1717140 TTTA-AAATATGTTAAATA-TTTA
1 TTTATAAATAT-TTAAATATTTTA
1717162 TATTATATAATATTTAAATATTTTA
1 T-TTATA-AATATTTAAATATTTTA
1717187 TTTATAAA
1 TTTATAAA
1717195 ATTATATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
22 8 0.17
23 13 0.28
24 16 0.34
25 10 0.21
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
TTTATAAATATTTAAATATTTTA
Found at i:1717213 original size:14 final size:14
Alignment explanation
Indices: 1717171--1717215 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 14
1717161 ATATTATATA
1717171 ATATTTAAATATTTT
1 ATATTTAAA-ATTTT
1717186 AT-TTATAAAA--TT
1 ATATT-TAAAATTTT
1717198 ATATTTAAAATTTT
1 ATATTTAAAATTTT
1717212 ATAT
1 ATAT
1717216 AATTATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
12 9 0.35
13 2 0.08
14 9 0.35
15 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTTAAAATTTT
Found at i:1717579 original size:17 final size:17
Alignment explanation
Indices: 1717557--1717594 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1717547 ATTATTATAT
1717557 ATTTTATTTTTAATTAA
1 ATTTTATTTTTAATTAA
*
1717574 ATTTTATTTTTAATTAT
1 ATTTTATTTTTAATTAA
1717591 ATTT
1 ATTT
1717595 CAGGAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATTTTTAATTAA
Found at i:1718468 original size:14 final size:14
Alignment explanation
Indices: 1718449--1718475 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1718439 GGGTATTTTA
1718449 TTTTTAATTTTATT
1 TTTTTAATTTTATT
1718463 TTTTTAATTTTAT
1 TTTTTAATTTTAT
1718476 AATAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTAATTTTATT
Found at i:1718653 original size:19 final size:20
Alignment explanation
Indices: 1718618--1718672 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1718608 AAAATTTGTA
1718618 TATATATATATATATTA-ATT
1 TATATAT-TATATATTATATT
1718638 TATTATATTATA-ATTATATT
1 TA-TATATTATATATTATATT
*
1718658 TAAATATTATATATT
1 TATATATTATATATT
1718673 TAAATAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATATTATATATTATATT
Found at i:1718839 original size:18 final size:19
Alignment explanation
Indices: 1718803--1718840 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1718793 AAATTAATTA
* *
1718803 AAATATATTTAAATTTAAT
1 AAATATATTCAAATATAAT
1718822 AAATA-ATTCAAATATAAT
1 AAATATATTCAAATATAAT
1718840 A
1 A
1718841 TTATATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATATTCAAATATAAT
Found at i:1718933 original size:26 final size:26
Alignment explanation
Indices: 1718881--1718931 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1718871 AAATATATCA
1718881 AAATTAAATATAAAATATAATATTTT
1 AAATTAAATATAAAATATAATATTTT
* * *
1718907 AAATTAATTCTAATATATAA-ATTTT
1 AAATTAAATATAAAATATAATATTTT
1718932 TATAAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATTAAATATAAAATATAATATTTT
Found at i:1718966 original size:12 final size:13
Alignment explanation
Indices: 1718948--1718985 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
1718938 TTACATAAAT
1718948 TTATAAAATATAA
1 TTATAAAATATAA
1718961 -TATAAAATATAA
1 TTATAAAATATAA
1718973 TTATATAAATATA
1 TTATA-AAATATA
1718986 TTAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
13 4 0.17
14 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATAAAATATAA
Found at i:1719747 original size:3 final size:3
Alignment explanation
Indices: 1719741--1719766 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1719731 TTCTTTTTTT
1719741 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1719767 CATTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1719856 original size:17 final size:17
Alignment explanation
Indices: 1719830--1719907 Score: 70
Period size: 17 Copynumber: 4.5 Consensus size: 17
1719820 AAAATTTATT
1719830 TAATATAATTATTAAAA
1 TAATATAATTATTAAAA
* *
1719847 TAATAAAATTTATTTAAA
1 TAATATAA-TTATTAAAA
*
1719865 T-ATATAATCTTTTAAATA
1 TAATATAAT-TATTAAA-A
*
1719883 TAATTATAA-TATAAAAA
1 TAA-TATAATTATTAAAA
1719900 TAATATAA
1 TAATATAA
1719908 ATATATTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
16 6 0.12
17 21 0.43
18 16 0.33
19 1 0.02
20 5 0.10
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATATAATTATTAAAA
Found at i:1720118 original size:17 final size:17
Alignment explanation
Indices: 1720092--1720126 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1720082 TGCATGCTAT
1720092 GCTAGGGCTAGAGCCTA
1 GCTAGGGCTAGAGCCTA
* *
1720109 GCTAGTGCTAGGGCCTA
1 GCTAGGGCTAGAGCCTA
1720126 G
1 G
1720127 ATGCCCTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.37, T:0.20
Consensus pattern (17 bp):
GCTAGGGCTAGAGCCTA
Found at i:1720281 original size:13 final size:13
Alignment explanation
Indices: 1720263--1720288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1720253 ATATTAATTA
1720263 ATTTATTTATTTT
1 ATTTATTTATTTT
1720276 ATTTATTTATTTT
1 ATTTATTTATTTT
1720289 CCTGCATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:1720353 original size:4 final size:4
Alignment explanation
Indices: 1720325--1720376 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
1720315 CCAATAATAC
* * * * *
1720325 ATTT ATTC ATCT ATTT ATCT ATTT ATTT ATTT ATTC ATTT ATTT ATCT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1720373 ATTT
1 ATTT
1720377 GACTGATTGG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:1722036 original size:13 final size:13
Alignment explanation
Indices: 1722018--1722044 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1722008 TACTGAAGTC
1722018 AGAATAAAACCGA
1 AGAATAAAACCGA
1722031 AGAATAAAACCGA
1 AGAATAAAACCGA
1722044 A
1 A
1722045 CTCAACACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.15, G:0.15, T:0.07
Consensus pattern (13 bp):
AGAATAAAACCGA
Found at i:1726898 original size:12 final size:11
Alignment explanation
Indices: 1726873--1726911 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1726863 GTTCTGCAAA
1726873 AAACAAAAAAAT
1 AAAC-AAAAAAT
*
1726885 AAATAAATAAAT
1 AAACAAA-AAAT
1726897 AAACAAAAAAT
1 AAACAAAAAAT
1726908 AAAC
1 AAAC
1726912 TTTTTCAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (11 bp):
AAACAAAAAAT
Found at i:1731944 original size:40 final size:37
Alignment explanation
Indices: 1731884--1731963 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 37
1731874 AATAAAAAAG
*
1731884 AAAAGAAAAAAAAAGAGAAGCAAGTTCACC-AAGGTGAA
1 AAAAAAAAAAAAAAGAGAAGCAAG-TCACCTAAGGT-AA
1731922 AAAAAAAAAAAAGGAAGAGAAGCAAGTCACCTAAGGTAA
1 AAAAAAAAAAAA--AAGAGAAGCAAGTCACCTAAGGTAA
1731961 AAA
1 AAA
1731964 GGAAAAGTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
38 11 0.29
39 10 0.26
40 17 0.45
ACGTcount: A:0.62, C:0.10, G:0.20, T:0.07
Consensus pattern (37 bp):
AAAAAAAAAAAAAAGAGAAGCAAGTCACCTAAGGTAA
Found at i:1744371 original size:21 final size:20
Alignment explanation
Indices: 1744333--1744372 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1744323 ATTTAAAAAA
*
1744333 TTAAATTTATTTATTTAAAT
1 TTAAATTTATTTAATTAAAT
1744353 TTAAATTTAATTTAATTAAA
1 TTAAATTT-ATTTAATTAAA
1744373 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATTTATTTAATTAAAT
Found at i:1744532 original size:22 final size:22
Alignment explanation
Indices: 1744490--1744532 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1744480 ATGACTTATG
* *
1744490 TGATTAATTGAAATATTAAATT
1 TGATTAATCGAAATATAAAATT
1744512 TGATTAATCCGAAATA-AAAAT
1 TGATTAAT-CGAAATATAAAAT
1744533 AATTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (22 bp):
TGATTAATCGAAATATAAAATT
Found at i:1744819 original size:15 final size:14
Alignment explanation
Indices: 1744786--1744831 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
1744776 TATATTTTTT
*
1744786 ATAATTAAATTTAA
1 ATAAATAAATTTAA
*
1744800 ATAAATAAATTATTA
1 ATAAATAAATT-TAA
1744815 ATAAATAATATTTAA
1 ATAAATAA-ATTTAA
1744830 AT
1 AT
1744832 CAAGCTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 10 0.37
15 14 0.52
16 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATAAATTTAA
Found at i:1745352 original size:20 final size:21
Alignment explanation
Indices: 1745315--1745356 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1745305 AAAAAAGTTA
*
1745315 ATTTTTCGTTAATCCAAATTT
1 ATTTTTCATTAATCCAAATTT
1745336 ATTTTTCATTAAT-CAAATTT
1 ATTTTTCATTAATCCAAATTT
1745356 A
1 A
1745357 AATTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTTCATTAATCCAAATTT
Found at i:1745446 original size:22 final size:21
Alignment explanation
Indices: 1745408--1745460 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1745398 GAGTCAAAAA
*
1745408 TAATTTAAAATTAAATTGATT
1 TAATTTAAAATTAAATTAATT
1745429 TAATATTAAAATGT-AATTAATT
1 TAAT-TTAAAAT-TAAATTAATT
* *
1745451 TCATTAAAAA
1 TAATTTAAAA
1745461 AATTGAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.33
22 17 0.63
23 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTAAATTAATT
Found at i:1746682 original size:28 final size:25
Alignment explanation
Indices: 1746639--1746696 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 25
1746629 ACTTAAATTT
1746639 ATTTTATAATTATATA-ATATATATTA
1 ATTTTATAATTATATATAT-TATA-TA
*
1746665 ATTTTATATATTTTTATATATTATATA
1 ATTTTATA-A-TTATATATATTATATA
1746692 ATTTT
1 ATTTT
1746697 GATCATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 8 0.29
27 8 0.29
28 10 0.36
29 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTATAATTATATATATTATATA
Found at i:1746784 original size:17 final size:17
Alignment explanation
Indices: 1746762--1746794 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1746752 TATTTATATT
1746762 TTAAATT-TTAATAAAAA
1 TTAAATTATTAA-AAAAA
1746779 TTAAATTATTAAAAAA
1 TTAAATTATTAAAAAA
1746795 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAATTATTAAAAAAA
Found at i:1746797 original size:22 final size:22
Alignment explanation
Indices: 1746771--1746820 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1746761 TTTAAATTTT
*
1746771 AATAAAAATTAAATTATTAAAA
1 AATAAAAATTAAAATATTAAAA
***
1746793 AATAATTTTTAAAATATTAAAA
1 AATAAAAATTAAAATATTAAAA
1746815 ATATAA
1 A-ATAA
1746821 TATAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAAAATTAAAATATTAAAA
Found at i:1746815 original size:23 final size:22
Alignment explanation
Indices: 1746779--1746821 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1746769 TTAATAAAAA
*
1746779 TTAAATTATTAAAAAATAATTT
1 TTAAAATATTAAAAAATAATTT
1746801 TTAAAATATTAAAAATATAAT
1 TTAAAATATTAAAAA-ATAAT
1746822 ATAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAATATTAAAAAATAATTT
Found at i:1746836 original size:31 final size:31
Alignment explanation
Indices: 1746800--1746862 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
1746790 AAAAATAATT
1746800 TTTAAAATA-TTAAAAATATAATATAAATAAA
1 TTTAAAATACTTAAAAATA-AATATAAATAAA
* ***
1746831 TTTAAATTACTTATTTATAAATATAAATAAA
1 TTTAAAATACTTAAAAATAAATATAAATAAA
1746862 T
1 T
1746863 AACCTCATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
TTTAAAATACTTAAAAATAAATATAAATAAA
Found at i:1750580 original size:2 final size:2
Alignment explanation
Indices: 1750573--1750600 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1750563 CCGATAACAA
1750573 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
1750601 TACCATGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1750951 original size:48 final size:48
Alignment explanation
Indices: 1750876--1750969 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
1750866 AAACTATGAC
*
1750876 CTAATACCATAGTTTTAGGGTCAAATCAGATTTCTCTCCTTTTCAACA
1 CTAATACCATAATTTTAGGGTCAAATCAGATTTCTCTCCTTTTCAACA
* ** *
1750924 CTAATAGCATAATTTTAGGGTTGAATCAGATTTGTCTCCTTTTCAA
1 CTAATACCATAATTTTAGGGTCAAATCAGATTTCTCTCCTTTTCAA
1750970 AACTCTACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (48 bp):
CTAATACCATAATTTTAGGGTCAAATCAGATTTCTCTCCTTTTCAACA
Found at i:1753360 original size:21 final size:21
Alignment explanation
Indices: 1753334--1753376 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1753324 ATTTGGGTAA
1753334 ATTTTAAATATTATATATTTT
1 ATTTTAAATATTATATATTTT
* *
1753355 ATTTTATATTTTATATATTTT
1 ATTTTAAATATTATATATTTT
1753376 A
1 A
1753377 AAAAATCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTAAATATTATATATTTT
Found at i:1753765 original size:57 final size:53
Alignment explanation
Indices: 1753663--1753798 Score: 148
Period size: 57 Copynumber: 2.5 Consensus size: 53
1753653 AAAATTTTAA
* * *
1753663 ATTAAATTTTAAATTTATTGAATTTCATATTTTAATATAAGAAAAAAAGTTATAAAT
1 ATTAAATTTTAAATTTATTAAATTTCATATCTCAATAT--GAAAAAAA--TATAAAT
* **
1753720 ATTAAATTTTAAATTTATTAAATTTCGTAATCTCGTTAT-AAAAAAATATAAAT
1 ATTAAATTTTAAATTTATTAAATTTCAT-ATCTCAATATGAAAAAAATATAAAT
*
1753773 ATTAAATTTTAAGCTTTATTAAATTT
1 ATTAAATTTTAA-ATTTATTAAATTT
1753799 TAAGCTTTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
53 19 0.27
54 12 0.17
55 7 0.10
57 26 0.37
58 6 0.09
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (53 bp):
ATTAAATTTTAAATTTATTAAATTTCATATCTCAATATGAAAAAAATATAAAT
Found at i:1753792 original size:17 final size:17
Alignment explanation
Indices: 1753772--1753806 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1753762 AAAATATAAA
1753772 TATTAAATTTTAAGCTT
1 TATTAAATTTTAAGCTT
1753789 TATTAAATTTTAAGCTT
1 TATTAAATTTTAAGCTT
1753806 T
1 T
1753807 TAATTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (17 bp):
TATTAAATTTTAAGCTT
Found at i:1755811 original size:15 final size:16
Alignment explanation
Indices: 1755784--1755815 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1755774 AAATTTATTT
1755784 TATTTTAATAATTATA
1 TATTTTAATAATTATA
1755800 TATTTT-ATAATTATA
1 TATTTTAATAATTATA
1755815 T
1 T
1755816 TTAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTAATAATTATA
Found at i:1755849 original size:16 final size:16
Alignment explanation
Indices: 1755819--1755868 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1755809 ATTATATTTA
**
1755819 AATAAAAATTTTAATT
1 AATAAAAATAATAATT
* *
1755835 ATTAAATATAATAATT
1 AATAAAAATAATAATT
*
1755851 AATAAAAATAATATTT
1 AATAAAAATAATAATT
1755867 AA
1 AA
1755869 AATTTAATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAAAAATAATAATT
Found at i:1756244 original size:15 final size:16
Alignment explanation
Indices: 1756220--1756260 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
1756210 ATTTTTTTTA
1756220 ATTTATTTAAATT-G-
1 ATTTATTTAAATTAGT
1756234 ATTTGATTTAAATTAGT
1 ATTT-ATTTAAATTAGT
1756251 ATTTATTTAA
1 ATTTATTTAA
1756261 TAAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.17
15 9 0.38
16 7 0.29
17 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTTATTTAAATTAGT
Found at i:1757201 original size:17 final size:18
Alignment explanation
Indices: 1757169--1757206 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1757159 TTATAAGCTT
1757169 TAAATATTTTATTTTA-A
1 TAAATATTTTATTTTATA
1757186 TAAATA-TTTATATTTATA
1 TAAATATTTTAT-TTTATA
1757204 TAA
1 TAA
1757207 TTAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAATATTTTATTTTATA
Found at i:1758432 original size:26 final size:27
Alignment explanation
Indices: 1758398--1758453 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
1758388 AATAAAAGGG
1758398 AAATGATAT-T-TAAAATAAATTTTTATA
1 AAATGATATATATAAAAT-AA-TTTTATA
*
1758425 AAAT-ATATATATTAAATAATTTTATA
1 AAATGATATATATAAAATAATTTTATA
1758451 AAA
1 AAA
1758454 AATCAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 14 0.54
27 7 0.27
28 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
AAATGATATATATAAAATAATTTTATA
Found at i:1760306 original size:18 final size:18
Alignment explanation
Indices: 1760278--1760320 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
1760268 AAATTATTTA
*
1760278 TAAAAAATAAT-TTTTTT
1 TAAAAAATAATATTTCTT
1760295 TAAAAAATTAATAATTTCTT
1 TAAAAAA-TAAT-ATTTCTT
1760315 TAAAAA
1 TAAAAA
1760321 CTATTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 4 0.18
20 11 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAAAATAATATTTCTT
Found at i:1761293 original size:18 final size:20
Alignment explanation
Indices: 1761249--1761295 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1761239 TTGTTGTTTT
1761249 CTGTTTTGGTTACTGCATCTC
1 CTGTTTTGGTTA-TGCATCTC
*
1761270 CTGTTTTGGTT-TGCA-CTG
1 CTGTTTTGGTTATGCATCTC
1761288 CTGTTTTG
1 CTGTTTTG
1761296 CTTGGTACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 10 0.40
19 4 0.16
21 11 0.44
ACGTcount: A:0.06, C:0.19, G:0.23, T:0.51
Consensus pattern (20 bp):
CTGTTTTGGTTATGCATCTC
Found at i:1766172 original size:258 final size:258
Alignment explanation
Indices: 1765706--1766187 Score: 707
Period size: 258 Copynumber: 1.9 Consensus size: 258
1765696 GACGAAGGAA
* *
1765706 CTGCCTCTTCTTGAAGCAAGATCACTTGACGACATTGATTTGGCTTTCAAGCAACTTCAAGAAGG
1 CTGCCTCTTCTTGAAGCAAGATCACTTGAAGACAGTGATTTGGCTTTCAAGCAACTTCAAGAAGG
* *
1765771 AGTAGATGTTAAGGAAGTGATTCTTCCAAGTATGATTGAGAACCAGCAGGATCATGCAGATACCA
66 AGTAGATGTCAAGGAAGTAATTCTTCCAAGTATGATTGAGAACCAGCAGGATCATGCAGATACCA
* *
1765836 ATTCAAAGTTACCTGTCGTCGAGGCAAGATCTCCGGAGGATATAAATAATGCTTTCCAACATGGC
131 ATTCAAAATTACCTGTCGTCGAGGCAAGATCTCCGGAGGATATAAATAATGCTTTCCAACAAGGC
* *
1765901 CCTGAACCTAATCCAGCTGAGCTGCCACAAATGGAAGAAATAAAGACAGACACCAATGTGGAG
196 CCGGAACCTAATCCAGCCGAGCTGCCACAAATGGAAGAAATAAAGACAGACACCAATGTGGAG
* ** * * * *
1765964 CTGCCTGTTCTTGAAGCAAGATCGGTTGAAGATAGTGATTTGGCTTTTAAGCAACTTCATGTAGG
1 CTGCCTCTTCTTGAAGCAAGATCACTTGAAGACAGTGATTTGGCTTTCAAGCAACTTCAAGAAGG
** *
1766029 AGTAGATGTCGTGGAAGTAATTCTTCCAAGTATGATTGAGAATCCA-CAGGATGATGCAGATACC
66 AGTAGATGTCAAGGAAGTAATTCTTCCAAGTATGATTGAGAA-CCAGCAGGATCATGCAGATACC
* * * **
1766093 AATTCAAAATTACCTGTTGTCGAGTCTAGATC-CCTGGAGGATATATGTAATGCTTTCCAACAAG
130 AATTCAAAATTACCTGTCGTCGAGGCAAGATCTCC-GGAGGATATAAATAATGCTTTCCAACAAG
* *
1766157 GCCCGGGATCTAATCCAGCCGAGCTGCCACA
194 GCCCGGAACCTAATCCAGCCGAGCTGCCACA
1766188 TTCCACAGAC
Statistics
Matches: 197, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
257 2 0.01
258 192 0.97
259 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (258 bp):
CTGCCTCTTCTTGAAGCAAGATCACTTGAAGACAGTGATTTGGCTTTCAAGCAACTTCAAGAAGG
AGTAGATGTCAAGGAAGTAATTCTTCCAAGTATGATTGAGAACCAGCAGGATCATGCAGATACCA
ATTCAAAATTACCTGTCGTCGAGGCAAGATCTCCGGAGGATATAAATAATGCTTTCCAACAAGGC
CCGGAACCTAATCCAGCCGAGCTGCCACAAATGGAAGAAATAAAGACAGACACCAATGTGGAG
Found at i:1767257 original size:402 final size:398
Alignment explanation
Indices: 1766500--1767499 Score: 1146
Period size: 402 Copynumber: 2.5 Consensus size: 398
1766490 AAGCAGGCTA
* * * *
1766500 TCTGGAAGATATAGATAAACCTTTCCAACAGGGCCCAGAATCTAATCCAGCTGGGCTGCCACATT
1 TCTGGAAGATATACATAAAGCTTTCCAACAGGG-CCAGAATCTAATCCAGCTGAGCTGCTACA-T
* * * * * *
1766565 CCTTGGACTTAAGGATTGGATCATCAGAAGTAGAGCAGCACGAAGTGGTTTCTGCTAAAGAGATT
64 CCTTTGACTTGAGGATTGAATCATCAGAAGTAGAG-AGCATGATGTGGTTTCTACTAAAGAGATT
* * *
1766630 GAAGTTAGTAATGCCATCTTTGGTATTCAAGAAAGTAGTGAGAATGCTGCT-G-G---------T
128 GAAGTTAGTAATGCCGTCTCTGGTATTCAAGAAAATAGTGAGAATGCTGCTGGTGAACCAAAAAT
* * * * **
1766684 GAATATGAAGAAGTGGAAGAAATGAAGACAGAGACTAATGTGGAGCTGCCGATTCTTGAAGCAAG
193 GAATATGAAGAAATGGAAGAAATAAAGACAGAGACGAATGTGGAGCTGCCGACTCTCAAAGCAAG
** * * *
1766749 ATTGGTACAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTAGTTGTTGAGGATGTAA
258 ATCAGTACAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTAGATGTCGAGGAAGTAA
* * * * * ** * *
1766814 TTCTTCCAAGTATGATTGAGAACCATCTGGATCATGCAGATACCAATTCAAAGTTAGCTGTTGTC
323 TTCTTCCAAGTATGATAGAGAACCAGCAGGATCAAGCAGATAACAACACAAAGTTACCTATTGTC
*
1766879 GAGGCAAGATC
388 GAAGCAAGATC
* * * * * *
1766890 TCTGGAGGATATACATAATGCTTTCCAACAAGGCCTAGAACCTAATCCAGCCGAGCTGCTGCATC
1 TCTGGAAGATATACATAAAGCTTTCCAACAGGGCC-AGAATCTAATCCAGCTGAGCTGCTACATC
* *
1766955 CTTTAGACTTGAGGATTGAATCATCAGAAGTAGAGAGCCATGATTTGGTTTCTACTAAAGATATT
65 CTTT-GACTTGAGGATTGAATCATCAGAAGTAGAGAG-CATGATGTGGTTTCTACTAAAGAGATT
* *
1767020 GAAGTTGGTAATGCCGTCTCTGTTATTCAAGAAAATAGTGAGAATGCTGCTGGTGAACCAAAAAA
128 GAAGTTAGTAATGCCGTCTCTGGTATTCAAGAAAATAGTGAGAATGCTGCTGGTGAACC-AAAAA
* * *
1767085 TGAATATGAAGAAATGGAAGAAATAAAGACGGAGAGGGATGTGGAGCTGCCTG-CTCTCAAAGCA
192 TGAATATGAAGAAATGGAAGAAATAAAGACAGAGACGAATGTGGAGCTGCC-GACTCTCAAAGCA
* *
1767149 AGATCAGTACAAGATATTGATTTGGCTTTTAGGCAACTTCATGAAGGAGTGGATG-CGAAGGAAG
256 AGATCAGTACAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTAGATGTCG-AGGAAG
1767213 TAATTCTTCCAAGTATGATAGAGAACCAGCAGGATCAAGCAGATAACAACACAAAGTTACCTATT
320 TAATTCTTCCAAGTATGATAGAGAACCAGCAGGATCAAGCAGATAACAACACAAAGTTACCTATT
*
1767278 GTCGAAGCTAGATC
385 GTCGAAGCAAGATC
** *
1767292 TCTGGAAGATATACATAACAG-TTTCCAATGGGGCCAGTAATCTAATCCAGCTGAGATGCTACAT
1 TCTGGAAGATATACATAA-AGCTTTCCAACAGGGCCAG-AATCTAATCCAGCTGAGCTGCTACAT
* * ** * * **
1767356 TCTTCTGACTTGAGGATTGAATCATCAGGAGTAGAGAGGTGTGATGTGGTTTCAACTGAAGAGGC
64 CCTT-TGACTTGAGGATTGAATCATCAGAAGTAGAGA-GCATGATGTGGTTTCTACTAAAGAGAT
* * * ** * *
1767421 TAAAGTCACTAATGTAGTCTCTGGTATTCAAGAACATAGTCAGAATGCTGCTGGTGAACCAAGAA
127 TGAAGTTAGTAATGCCGTCTCTGGTATTCAAGAAAATAGTGAGAATGCTGCTGGTGAACCAA-AA
* *
1767486 ATAAACATGAAGAA
191 ATGAATATGAAGAA
1767500 GAACCTGAAA
Statistics
Matches: 508, Mismatches: 80, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
389 9 0.02
390 146 0.29
391 1 0.00
392 1 0.00
401 5 0.01
402 342 0.67
403 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (398 bp):
TCTGGAAGATATACATAAAGCTTTCCAACAGGGCCAGAATCTAATCCAGCTGAGCTGCTACATCC
TTTGACTTGAGGATTGAATCATCAGAAGTAGAGAGCATGATGTGGTTTCTACTAAAGAGATTGAA
GTTAGTAATGCCGTCTCTGGTATTCAAGAAAATAGTGAGAATGCTGCTGGTGAACCAAAAATGAA
TATGAAGAAATGGAAGAAATAAAGACAGAGACGAATGTGGAGCTGCCGACTCTCAAAGCAAGATC
AGTACAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTAGATGTCGAGGAAGTAATTC
TTCCAAGTATGATAGAGAACCAGCAGGATCAAGCAGATAACAACACAAAGTTACCTATTGTCGAA
GCAAGATC
Found at i:1769713 original size:47 final size:47
Alignment explanation
Indices: 1769644--1769739 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
1769634 GATCCCTTTG
*
1769644 ACTTTGTTTGTATCCATTAGCTAGCATTACTTTTGCAAATCTACCAA
1 ACTTTGTTTGCATCCATTAGCTAGCATTACTTTTGCAAATCTACCAA
1769691 ACTTTGTTTGCATCCATTAGCTAGCATTACTTTTGCAAATCTACCAA
1 ACTTTGTTTGCATCCATTAGCTAGCATTACTTTTGCAAATCTACCAA
1769738 AC
1 AC
1769740 CAGGCCCTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (47 bp):
ACTTTGTTTGCATCCATTAGCTAGCATTACTTTTGCAAATCTACCAA
Found at i:1772553 original size:13 final size:13
Alignment explanation
Indices: 1772535--1772560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1772525 TACACCAAGT
1772535 ATGTATCGATACA
1 ATGTATCGATACA
1772548 ATGTATCGATACA
1 ATGTATCGATACA
1772561 CAAAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1774324 original size:16 final size:17
Alignment explanation
Indices: 1774292--1774324 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1774282 ATCTTTGTTC
*
1774292 AAAGGAGAATCGAGCAA
1 AAAGGACAATCGAGCAA
1774309 AAAGGACAAT-GAGCAA
1 AAAGGACAATCGAGCAA
1774325 GTAATATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.12, G:0.27, T:0.06
Consensus pattern (17 bp):
AAAGGACAATCGAGCAA
Found at i:1776652 original size:15 final size:15
Alignment explanation
Indices: 1776632--1776662 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1776622 TAAAAATGTC
*
1776632 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1776647 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1776662 C
1 C
1776663 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1778765 original size:13 final size:13
Alignment explanation
Indices: 1778747--1778771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1778737 CATTTTTCTT
1778747 TGTATCGATACAC
1 TGTATCGATACAC
1778760 TGTATCGATACA
1 TGTATCGATACA
1778772 TGGGGATTAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1778926 original size:20 final size:20
Alignment explanation
Indices: 1778883--1778928 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1778873 AAATCTTTTG
1778883 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1778904 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1778924 CAAAA
1 CAAAA
1778929 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1781361 original size:13 final size:13
Alignment explanation
Indices: 1781343--1781368 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1781333 TACACCAAGT
1781343 ATGTATCGATACA
1 ATGTATCGATACA
1781356 ATGTATCGATACA
1 ATGTATCGATACA
1781369 CAAAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1783972 original size:16 final size:16
Alignment explanation
Indices: 1783951--1783983 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1783941 AAAATTTAAA
1783951 ATATATATTAAT-ATTT
1 ATATAT-TTAATAATTT
1783967 ATATATTTAATAATTT
1 ATATATTTAATAATTT
1783983 A
1 A
1783984 ATTTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATTTAATAATTT
Found at i:1784899 original size:17 final size:17
Alignment explanation
Indices: 1784860--1784899 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
1784850 AGTAAAAAAT
1784860 AAATAAAA--AAAGGAG
1 AAATAAAATTAAAGGAG
1784875 -AA-AAAATTAAAGGAG
1 AAATAAAATTAAAGGAG
1784890 AAATAAAATT
1 AAATAAAATT
1784900 TTAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 4 0.19
14 2 0.10
15 7 0.33
16 2 0.10
17 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (17 bp):
AAATAAAATTAAAGGAG
Found at i:1784992 original size:20 final size:24
Alignment explanation
Indices: 1784942--1784987 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1784932 TTTAGTATTA
1784942 ATATTCATAAGTAAATAAAAATAT
1 ATATTCATAAGTAAATAAAAATAT
1784966 ATATTCATAAGTAAATAAAAAT
1 ATATTCATAAGTAAATAAAAAT
1784988 TTTCAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (24 bp):
ATATTCATAAGTAAATAAAAATAT
Found at i:1785360 original size:16 final size:15
Alignment explanation
Indices: 1785339--1785376 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1785329 AAATATATTA
1785339 AATAAATATTTTATAT
1 AATAAATATTTTA-AT
1785355 AATAAATA-TTTAAT
1 AATAAATATTTTAAT
1785369 AA-AAATAT
1 AATAAATAT
1785377 AAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.24
14 4 0.19
15 4 0.19
16 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAAATATTTTAAT
Found at i:1786511 original size:18 final size:18
Alignment explanation
Indices: 1786478--1786527 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1786468 TATTCATGTC
1786478 ATATTTA-TATTATTTTT-
1 ATATTTATTA-TATTTTTA
1786495 ATATTATATTATATTTTTA
1 ATATT-TATTATATTTTTA
*
1786514 ATATTTTTTATATT
1 ATATTTATTATATT
1786528 GTATTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 17 0.59
19 7 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATATTTATTATATTTTTA
Found at i:1786859 original size:43 final size:41
Alignment explanation
Indices: 1786779--1786874 Score: 113
Period size: 43 Copynumber: 2.3 Consensus size: 41
1786769 ATTATTTTTA
** * *
1786779 TTTTTAATTAA-AAATTTAAATTATTTAAAAATTTAAAATTT
1 TTTTTAATTAATTTATTTAAATTATATAAAAATATAAAA-TT
**
1786820 TTTATTAATTAATTTATTTAAATTATATAATGATATAAAATT
1 TTT-TTAATTAATTTATTTAAATTATATAAAAATATAAAATT
1786862 TTTTTAATTAATT
1 TTTTTAATTAATT
1786875 ACAATATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 13 0.28
42 13 0.28
43 21 0.45
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (41 bp):
TTTTTAATTAATTTATTTAAATTATATAAAAATATAAAATT
Found at i:1787013 original size:27 final size:28
Alignment explanation
Indices: 1786959--1787013 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1786949 GATAATTTAT
* *
1786959 TAATATATTTTTATATTTATGTCTTTAA
1 TAATATATTTTTATATTTATCTCGTTAA
*
1786987 TAAT-TATTTTTATTTTTATCTCGTTAA
1 TAATATATTTTTATATTTATCTCGTTAA
1787014 GATTATTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (28 bp):
TAATATATTTTTATATTTATCTCGTTAA
Found at i:1787525 original size:23 final size:23
Alignment explanation
Indices: 1787496--1787566 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
1787486 ATATAAATTT
*
1787496 TAAAATTATAAATATTTAATATA
1 TAAAATTATAAATATTTAATAAA
* *
1787519 TAAAATTTTAAAATATTAAATAAA
1 TAAAATTAT-AAATATTTAATAAA
*
1787543 T-AAATATAAAAATATTTAA-AAA
1 TAAAAT-TATAAATATTTAATAAA
1787565 TA
1 TA
1787567 TAATAAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.10
23 21 0.54
24 14 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAATTATAAATATTTAATAAA
Found at i:1787527 original size:31 final size:29
Alignment explanation
Indices: 1787483--1787574 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 29
1787473 TATTTACATG
**
1787483 TAAATAT-AAATTTTAAAATTATAAATATT
1 TAAATATAAAATTTTAAAA-TATAAATAAA
1787512 TAATATATAAAATTTTAAAATATTAAATAAA
1 TAA-ATATAAAATTTTAAAATA-TAAATAAA
1787543 TAAATATAAAAATATTTAAAA-ATATAATAAA
1 TAAATAT-AAAAT-TTTAAAATATA-AATAAA
1787574 T
1 T
1787575 TATTATTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
29 3 0.05
30 12 0.22
31 33 0.60
32 7 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TAAATATAAAATTTTAAAATATAAATAAA
Found at i:1787534 original size:15 final size:15
Alignment explanation
Indices: 1787484--1787539 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
1787474 ATTTACATGT
1787484 AAATAT-AAATTTTA
1 AAATATAAAATTTTA
1787498 AAAT-TATAAATATTTA
1 AAATATA-AAAT-TTTA
*
1787514 ATATATAAAATTTTA
1 AAATATAAAATTTTA
*
1787529 AAATATTAAAT
1 AAATATAAAAT
1787540 AAATAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 1 0.03
14 4 0.11
15 17 0.49
16 11 0.31
17 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATATAAAATTTTA
Found at i:1794400 original size:8 final size:8
Alignment explanation
Indices: 1794387--1794411 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1794377 AGCCAGCAGC
1794387 TTATAGAA
1 TTATAGAA
1794395 TTATAGAA
1 TTATAGAA
1794403 TTATAGAA
1 TTATAGAA
1794411 T
1 T
1794412 GCTAGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (8 bp):
TTATAGAA
Found at i:1795621 original size:10 final size:10
Alignment explanation
Indices: 1795603--1795631 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1795593 TCTTCCCCTC
1795603 TTTTT-TTTT
1 TTTTTATTTT
1795612 TTTTTATTTT
1 TTTTTATTTT
1795622 TTTTTATTTT
1 TTTTTATTTT
1795632 GGTGGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:1796729 original size:35 final size:35
Alignment explanation
Indices: 1796673--1796741 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
1796663 ATTAGAACCA
*
1796673 GATATCCTATCACGTCCAAGACCCTACTTAGGACG
1 GATATCCAATCACGTCCAAGACCCTACTTAGGACG
*
1796708 GATATCCAATCGA-GTCTAAGACCCTACTTAGGAC
1 GATATCCAATC-ACGTCCAAGACCCTACTTAGGAC
1796742 ATCTTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (35 bp):
GATATCCAATCACGTCCAAGACCCTACTTAGGACG
Found at i:1798520 original size:27 final size:26
Alignment explanation
Indices: 1798490--1798585 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 26
1798480 TTTCTAGAAT
*
1798490 AGCACCTAGCTGTACACAACTTCTCAC
1 AGCACATAGCTGTACACAAC-TCTCAC
* *
1798517 AGCACATAGCTATACACAAC-CT-AGT
1 AGCACATAGCTGTACACAACTCTCA-C
*
1798542 TGTACACATAGCTGTACACAA--CTCAC
1 AG--CACATAGCTGTACACAACTCTCAC
*
1798568 AGCACCTAGCTGTACACA
1 AGCACATAGCTGTACACA
1798586 TAGCTGTACA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
24 16 0.28
25 3 0.05
26 3 0.05
27 35 0.61
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.21
Consensus pattern (26 bp):
AGCACATAGCTGTACACAACTCTCAC
Found at i:1798559 original size:12 final size:12
Alignment explanation
Indices: 1798519--1798597 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 12
1798509 CTTCTCACAG
*
1798519 CACATAGCTATA
1 CACATAGCTGTA
*
1798531 CACAACCTAGTTGTA
1 CAC-A--TAGCTGTA
1798546 CACATAGCTGTA
1 CACATAGCTGTA
*
1798558 CACA-A-CT-CA
1 CACATAGCTGTA
1798567 CAGCACCTAGCTGTA
1 CA-CA--TAGCTGTA
1798582 CACATAGCTGTA
1 CACATAGCTGTA
1798594 CACA
1 CACA
1798598 ACTCCTTACA
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
9 3 0.06
10 4 0.08
11 1 0.02
12 26 0.49
13 2 0.04
14 5 0.09
15 12 0.23
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (12 bp):
CACATAGCTGTA
Done.