Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 93 of 185
Found at i:29253025 original size:15 final size:15
Alignment explanation
Indices: 29252976--29253026 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
29252966 TTTATATATG
29252976 AATTGTAAAAATATATA
1 AATT-TAAAAATATA-A
*
29252993 AATTTAAAAAATCTAA
1 AATTT-AAAAATATAA
29253009 AATTATAAAAAT-TAA
1 AATT-TAAAAATATAA
29253024 AAT
1 AAT
29253027 AAAAAACAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 6 0.19
16 12 0.39
17 13 0.42
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AATTTAAAAATATAA
Found at i:29255458 original size:20 final size:21
Alignment explanation
Indices: 29255435--29255481 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
29255425 GGGTTAAGAT
*
29255435 TGAGCTGAA-TTGAGCTCGAA-
1 TGAGCTGAACTTAAGCTC-AAG
29255455 TGAGCT-AACTTAAGCTCAAG
1 TGAGCTGAACTTAAGCTCAAG
29255475 TGAGCTG
1 TGAGCTG
29255482 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (21 bp):
TGAGCTGAACTTAAGCTCAAG
Found at i:29257383 original size:12 final size:12
Alignment explanation
Indices: 29257350--29257430 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
29257340 TTTCCACTCG
29257350 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
29257361 AGCTCTCTTTCA
1 ATTTCTTTTTCA
29257373 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
29257386 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
29257399 --TTCTCTTTCA
1 ATTTCTTTTTCA
29257409 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
29257421 ATCTCTTTTT
1 ATTTCTTTTT
29257431 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:29257391 original size:21 final size:20
Alignment explanation
Indices: 29257365--29257420 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
29257355 TTTTCAAGCT
29257365 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
29257386 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
29257401 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
29257421 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:29257483 original size:15 final size:15
Alignment explanation
Indices: 29257460--29257506 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
29257450 TTTTGAAATA
29257460 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
29257475 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
29257490 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
29257506 T
1 T
29257507 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:29258563 original size:12 final size:11
Alignment explanation
Indices: 29258552--29258615 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
29258542 TTTTCACTTC
29258552 TTTTTTTTCTT
1 TTTTTTTTCTT
29258563 CTTTTTTTTACTT
1 -TTTTTTTT-CTT
29258576 TTTTTTTTCGTT
1 TTTTTTTTC-TT
** **
29258588 TTTGCTCACTT
1 TTTTTTTTCTT
29258599 CTTTTTTTTCTT
1 -TTTTTTTTCTT
29258611 TTTTT
1 TTTTT
29258616 CGAATTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
11 8 0.20
12 30 0.73
13 3 0.07
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:29258578 original size:23 final size:21
Alignment explanation
Indices: 29258551--29258627 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 21
29258541 CTTTTCACTT
*
29258551 CTTTTTTTTCTTCTTTTTTTTA
1 CTTTTTTTT-TTCTTTTTTTCA
*
29258573 CTTTTTTTTTTCGTTTTTGCTCA
1 CTTTTTTTTTTC-TTTTT-TTCA
29258596 CTTCTTTTTTTTCTTTTTTTCGA
1 CTT-TTTTTTTTCTTTTTTTC-A
*
29258619 ATTTTTTTT
1 CTTTTTTTT
29258628 AATTTCGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
21 3 0.06
22 22 0.47
23 13 0.28
24 9 0.19
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.77
Consensus pattern (21 bp):
CTTTTTTTTTTCTTTTTTTCA
Found at i:29258623 original size:16 final size:16
Alignment explanation
Indices: 29258603--29258643 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
29258593 TCACTTCTTT
*
29258603 TTTTTCTTTTTTTCGAA
1 TTTTT-TTTATTTCGAA
29258620 TTTTTTTTAATTTCGAA
1 TTTTTTTT-ATTTCGAA
29258637 TTTTTTT
1 TTTTTTT
29258644 GTGATACTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.73
Consensus pattern (16 bp):
TTTTTTTTATTTCGAA
Found at i:29260160 original size:20 final size:20
Alignment explanation
Indices: 29260137--29260183 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29260127 GGGTTAAGAT
*
29260137 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTAAGCTC-AAG
*
29260157 TGAGCTGACTTAAGCTCAAG
1 TGAGCTGAATTAAGCTCAAG
29260177 TGAGCTG
1 TGAGCTG
29260184 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTAAGCTCAAG
Found at i:29275584 original size:13 final size:14
Alignment explanation
Indices: 29275549--29275632 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 14
29275539 CTCACATTTT
29275549 TTTTCTTTT-TCATC
1 TTTTCTTTTCTCA-C
29275563 TTATTCTTTTCTCA-
1 TT-TTCTTTTCTCAC
*
29275577 TTTTCTTTTCACTTAC
1 TTTTCTTTT--CTCAC
*
29275593 TTTTACTATTTTTCA-
1 TTTT-CT-TTTCTCAC
*
29275608 -TTTCTTTTTCTCAT
1 TTTTC-TTTTCTCAC
29275622 TTTTCTTTTCT
1 TTTTCTTTTCT
29275633 TTTACATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
13 14 0.25
14 14 0.25
15 14 0.25
16 9 0.16
17 2 0.04
18 3 0.05
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTTCTCAC
Found at i:29275595 original size:24 final size:27
Alignment explanation
Indices: 29275549--29275604 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 27
29275539 CTCACATTTT
29275549 TTTTCTTTTTCATCTTATTCTTTT-CTCA
1 TTTTCTTTTTCATCTTA-TCTTTTACT-A
29275577 TTTTC-TTTTCA-CTTA-CTTTTACTA
1 TTTTCTTTTTCATCTTATCTTTTACTA
29275601 TTTT
1 TTTT
29275605 TCATTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 10 0.37
25 2 0.07
26 4 0.15
27 6 0.22
28 5 0.19
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTCTTTTTCATCTTATCTTTTACTA
Found at i:29275614 original size:19 final size:19
Alignment explanation
Indices: 29275582--29275642 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
29275572 TCTCATTTTC
*
29275582 TTTTCACTTACTTTTACTAT
1 TTTTCA-TTTCTTTTACTAT
*
29275602 TTTTCATTTCTTTTTCTCAT
1 TTTTCATTTCTTTTACT-AT
*
29275622 TTTTCTTTTCTTTTAC-AT
1 TTTTCATTTCTTTTACTAT
29275640 TTT
1 TTT
29275643 CACTCTGTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.14
19 9 0.25
20 22 0.61
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTCATTTCTTTTACTAT
Found at i:29275657 original size:45 final size:44
Alignment explanation
Indices: 29275569--29275657 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 44
29275559 CATCTTATTC
* *
29275569 TTTTCTCATTTTCTTTTCACTTACTTTTACTATTTTTCATTTCT
1 TTTTCTCATTTTCTTTTCACTTACTTTTACTACTGTTCATTTCT
**
29275613 TTTTCTCATTTTTCTTTTCTTTTACATTTTCACT-CTGTTC-TTTCT
1 TTTTCTCA-TTTTCTTTTCACTTAC-TTTT-ACTACTGTTCATTTCT
29275658 CTCTCATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
44 8 0.21
45 19 0.50
46 8 0.21
47 3 0.08
ACGTcount: A:0.11, C:0.21, G:0.01, T:0.66
Consensus pattern (44 bp):
TTTTCTCATTTTCTTTTCACTTACTTTTACTACTGTTCATTTCT
Found at i:29280608 original size:22 final size:22
Alignment explanation
Indices: 29280567--29280623 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
29280557 AAAGGGTATC
* *
29280567 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
29280588 TACAAATCATATCTTCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
29280610 TACATATCATATCT
1 TACAAATCATATCT
29280624 AAGATTACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.37
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:29280617 original size:17 final size:17
Alignment explanation
Indices: 29280595--29280647 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 17
29280585 GATTACAAAT
29280595 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
29280612 CATATCATATCTAAGATTA
1 CATATC-T-TCTAAGATTA
* *
29280631 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
29280648 TGTTTTCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
19 16 0.50
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:29280626 original size:19 final size:20
Alignment explanation
Indices: 29280580--29280636 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 20
29280570 AAATTAAATC
*
29280580 TCTAAGATTACAAATCATATCT
1 TCTAAGATTACATATCATA--T
29280602 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
29280621 TCTAAGATTACATATC
1 TCTAAGATTACATATC
29280637 CTCGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 16 0.47
22 18 0.53
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:29288370 original size:20 final size:20
Alignment explanation
Indices: 29288345--29288391 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
29288335 AATAAGAAAG
29288345 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
29288365 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
29288385 ATATAAA
1 ATATAAA
29288392 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:29289914 original size:28 final size:28
Alignment explanation
Indices: 29289868--29289941 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
29289858 ATTCAAATAA
* *
29289868 CTTCGTTCCAGTCCACTGTGTCTTGTTG
1 CTTCGATCCACTCCACTGTGTCTTGTTG
*
29289896 CTTCGATCCACTCCTCTGTGTCTTGTTG
1 CTTCGATCCACTCCACTGTGTCTTGTTG
29289924 CTTCGATCCACTCCACTG
1 CTTCGATCCACTCCACTG
29289942 CACTTCAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.09, C:0.34, G:0.18, T:0.39
Consensus pattern (28 bp):
CTTCGATCCACTCCACTGTGTCTTGTTG
Found at i:29290164 original size:44 final size:43
Alignment explanation
Indices: 29290019--29290331 Score: 215
Period size: 44 Copynumber: 7.3 Consensus size: 43
29290009 GTTTTTTCTG
* * * *
29290019 TCTGCTCCGCTACTGCTTAAGGAGATAAGACTTG--A--TACGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCGCCATCTTCGA
* *** **
29290059 TCTGCTCCACTACTGCTTAGGGAGATAGGACTCG-TGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCGCCATCTTCGA
* * *
29290102 TCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCGCCATCTTCGA
* * ** **
29290146 TCTGCTCCACTACTGCTTAGGGAAATAGGATCTAACATCTTTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC-GCCATCTTCGA
* * **** **
29290190 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC-GCCATCTTCGA
* * * *
29290233 TCTGCTTCACTACTGCTTAGGGAGATGAGATTTGCCATTTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCGCCATCTTCGA
* *
29290277 TCTACTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC-GCCATCTTCGA
*
29290321 CCTGCTCCACT
1 TCTGCTCCACT
29290332 GTAACCTCAG
Statistics
Matches: 211, Mismatches: 54, Indels: 12
0.76 0.19 0.04
Matches are distributed among these distances:
40 30 0.14
43 67 0.32
44 114 0.54
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCGCCATCTTCGA
Found at i:29290236 original size:87 final size:86
Alignment explanation
Indices: 29290058--29290306 Score: 236
Period size: 87 Copynumber: 2.8 Consensus size: 86
29290048 ACTTGATACG
* * *
29290058 ATCTGCTCCACTACTGCTTAGGGAGATAGGA-CTCGTGGCTTAAATCTGCTTCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTCAT--CTTTAATCTGCTCCACTACTGCTTAG
* * * **
29290122 GAAGATAAGATTCGCCGTCTTCG
64 GGAGATAAGACTCGCCGGCTTAA
* * *
29290145 ATCTGCTCCACTACTGCTTAGGGAAATAGGATCTAACATCTTTTACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCT--CATCTTTAATCTGCTCCACTACTGCTTAG
* **
29290210 GGAGATAGGACT-GGTGGCTTAA
64 GGAGATAAGACTCGCCGGCTTAA
* * * *
29290232 ATCTGCTTCACTACTGCTTAGGGAGAT-GAGATTTGCCAT-TTTCGATCTACTCCACTACTGCTT
1 ATCTGCTCCACTACTGCTTAGGGAGATAG-GATCT--CATCTTT-AATCTGCTCCACTACTGCTT
29290295 AGGGAGATAAGA
62 AGGGAGATAAGA
29290307 TCTACCATCT
Statistics
Matches: 134, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
86 4 0.03
87 95 0.71
88 33 0.25
90 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (86 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTCATCTTTAATCTGCTCCACTACTGCTTAGGG
AGATAAGACTCGCCGGCTTAA
Found at i:29290249 original size:131 final size:131
Alignment explanation
Indices: 29290060--29290331 Score: 436
Period size: 131 Copynumber: 2.1 Consensus size: 131
29290050 TTGATACGAT
29290060 CTGCTCCACTACTGCTTAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
* * * **
29290125 GATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAAATAGGATCTAACATCTTTTA
66 GATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGGAAATAAGATCTAACATCTTCGA
29290190 C
131 C
* *
29290191 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGGA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
* * * * *
29290256 GATGAGATTTGCCATTTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
66 GATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGGAAATAAGATCTAACATCTTCGA
29290321 C
131 C
29290322 CTGCTCCACT
1 CTGCTCCACT
29290332 GTAACCTCAG
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 129 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (131 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGACTCGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
GATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGGAAATAAGATCTAACATCTTCGA
C
Found at i:29290556 original size:46 final size:46
Alignment explanation
Indices: 29290295--29290572 Score: 197
Period size: 46 Copynumber: 6.3 Consensus size: 46
29290285 ACTACTGCTT
* * *
29290295 AGGGAGATAAGATCT-ACCA-TCTTCGACCTGCTCCACTGTAACCTC
1 AGGGAGATAAGATCTGA-AATTCTTCGATCTACTCCACTGTAACCTC
* * * *
29290340 AGGGAGATAAGATCTGAAATTCTTCGGTTTACTCCGCTGTAACCTT
1 AGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
* * * * *
29290386 AGGGAGATAAGATTTG----T-TGCGATCTACTCTACTGTAACTTG
1 AGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
* * ** * * *
29290427 AGAGAGATGAGATCCT-TTATT-TT-AATCCACTCCACTGTAACTTC
1 AGGGAGATAAGAT-CTGAAATTCTTCGATCTACTCCACTGTAACCTC
* * * *
29290471 AGGGAGATAGGAT-T-ACTAGTTC--CAATCTGCTCCACTGTAACCTC
1 AGGGAGATAAGATCTGA--AATTCTTCGATCTACTCCACTGTAACCTC
* *
29290515 AGGGAGATAAGATCTGAAATTCTTCGGTCCACTCCACTGTAACCTC
1 AGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
29290561 AGGGAGATAAGA
1 AGGGAGATAAGA
29290573 CTTGCACCCA
Statistics
Matches: 180, Mismatches: 38, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
41 28 0.16
42 3 0.02
44 63 0.35
45 19 0.11
46 67 0.37
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (46 bp):
AGGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTC
Found at i:29290646 original size:44 final size:44
Alignment explanation
Indices: 29290580--29290843 Score: 194
Period size: 44 Copynumber: 5.9 Consensus size: 44
29290570 AGACTTGCAC
*
29290580 CCACTGTAA-CTTCAGGGAGATAAGGTTTGTGGCTTCGATCTGCT
1 CCACTGTAATC-TCAGGGAGATAAGATTTGTGGCTTCGATCTGCT
* * * *
29290624 CCTCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCT
1 CCACTGTAATCTCAGGGAGATAAGATTTGTGGCTTCGATCTGCT
* * * * *
29290668 CCACTGTAACCTCAGGGAGATAAGAATTGAAAT-TCTTCGGTCTACT
1 CCACTGTAATCTCAGGGAGATAAGATTTG---TGGCTTCGATCTGCT
*** * * *
29290714 CCACTGTAATCTCAGGGAGATAAGACCTAAAAT-TCTTCGGTCTACT
1 CCACTGTAATCTCAGGGAGATAAGA--T-TTGTGGCTTCGATCTGCT
* * **** * * *
29290760 CCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCC
1 CCACTGTAATCTCAGGGAGATAAGATTTGTGGCTTCGATCTGCT
*
29290804 CCACTGTAA-CTTCAGGGAGATAAGGTTTGTGGCTTCGATC
1 CCACTGTAATC-TCAGGGAGATAAGATTTGTGGCTTCGATC
29290844 AACTCTTCTG
Statistics
Matches: 172, Mismatches: 39, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
43 1 0.01
44 98 0.57
45 1 0.01
46 71 0.41
47 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (44 bp):
CCACTGTAATCTCAGGGAGATAAGATTTGTGGCTTCGATCTGCT
Found at i:29290690 original size:166 final size:171
Alignment explanation
Indices: 29290295--29290739 Score: 516
Period size: 166 Copynumber: 2.6 Consensus size: 171
29290285 ACTACTGCTT
* * * *
29290295 AGGGAGATAAGATCTACCATCTTCGACCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 AGGGAGATAAGATCTACTAGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
* * * *
29290360 TCTTCGGTTTACTCCGCTGTAACCTTAGGGAGATAAGATTTGTTGCGATCTACTCTACTGTAACT
66 TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA---CTTGCGATC-ACTCTACTGTAACT
* * * *
29290425 TGAGAGAGATGAGATCCTTTATTTTAATCCACTCCACTGTAACTTC
127 TCAGAGAGATAAGAT-CTTTACTTCAATCCACTCCACTGTAACTTC
*
29290471 AGGGAGATAGGAT-TACTAG-TTCCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAA
1 AGGGAGATAAGATCTACTAGCTT-CAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAA
*
29290534 TTCTTCGGTCCACTCCACTGTAACCTCAGGGAGATAAGACTTGC-A-C-C-C-ACTGTAACTTCA
65 TTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCGATCACTCTACTGTAACTTCA
* * * * ** *
29290594 GGGAGATAAGGT-TTGTGGCTTCGATCTGCTCCTCTGTAA-TCTC
130 GAGAGATAAGATCTT-T-ACTTCAATCCACTCCACTGTAACT-TC
*
29290637 AGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGAAT-TGAAA
1 AGGGAGATAAGATCTACTAGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAG-ATCTGAAA
*
29290700 TTCTTCGGTCTACTCCACTGTAATCTCAGGGAGATAAGAC
65 TTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
29290740 CTAAAATTCT
Statistics
Matches: 237, Mismatches: 25, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
164 2 0.01
165 2 0.01
166 128 0.54
167 6 0.03
168 1 0.00
170 1 0.00
171 1 0.00
172 4 0.02
174 2 0.01
175 78 0.33
176 12 0.05
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (171 bp):
AGGGAGATAAGATCTACTAGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCGATCACTCTACTGTAACTTCAG
AGAGATAAGATCTTTACTTCAATCCACTCCACTGTAACTTC
Found at i:29290785 original size:46 final size:46
Alignment explanation
Indices: 29290666--29290785 Score: 204
Period size: 46 Copynumber: 2.6 Consensus size: 46
29290656 CTTCAATCTG
** *
29290666 CTCCACTGTAACCTCAGGGAGATAAGAATTGAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTAAAATTCTTCGGTCTA
*
29290712 CTCCACTGTAATCTCAGGGAGATAAGACCTAAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTAAAATTCTTCGGTCTA
29290758 CTCCACTGTAACCTCAGGGAGATAAGAC
1 CTCCACTGTAACCTCAGGGAGATAAGAC
29290786 TTGCATATTC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (46 bp):
CTCCACTGTAACCTCAGGGAGATAAGACCTAAAATTCTTCGGTCTA
Found at i:29292204 original size:7 final size:7
Alignment explanation
Indices: 29292192--29292243 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
29292182 GCCTCTCCAT
29292192 TTTTTCA
1 TTTTTCA
29292199 TTTTTCA
1 TTTTTCA
*
29292206 -TTTTCT
1 TTTTTCA
29292212 TTTTTCCA
1 TTTTT-CA
29292220 -TTTTCA
1 TTTTTCA
*
29292226 -TTCTCA
1 TTTTTCA
29292232 TTTTTCA
1 TTTTTCA
29292239 TTTTT
1 TTTTT
29292244 TCTGAGTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 12 0.32
7 25 0.66
8 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTCA
Found at i:29292215 original size:13 final size:14
Alignment explanation
Indices: 29292193--29292227 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
29292183 CCTCTCCATT
29292193 TTTTCATTTTT-CA
1 TTTTCATTTTTCCA
*
29292206 TTTTCTTTTTTCCA
1 TTTTCATTTTTCCA
29292220 TTTTCATT
1 TTTTCATT
29292228 CTCATTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCATTTTTCCA
Found at i:29292216 original size:20 final size:20
Alignment explanation
Indices: 29292191--29292243 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
29292181 AGCCTCTCCA
*
29292191 TTTTTTCATTTTTCATTTTC
1 TTTTTTCATTTTTCATTCTC
29292211 TTTTTTCCA-TTTTCATTCTC
1 TTTTTT-CATTTTTCATTCTC
*
29292231 ATTTTTCATTTTT
1 TTTTTTCATTTTT
29292244 TCTGAGTGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTCATTTTTCATTCTC
Found at i:29293241 original size:16 final size:16
Alignment explanation
Indices: 29293206--29293241 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29293196 GATTTTGATT
*
29293206 TTTTTCTTTTTTCTTC
1 TTTTTCTTTTTTCTTA
*
29293222 TTTTTCTTTTTTTTTA
1 TTTTTCTTTTTTCTTA
29293238 TTTT
1 TTTT
29293242 GATTTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTCTTTTTTCTTA
Found at i:29297930 original size:20 final size:20
Alignment explanation
Indices: 29297905--29297951 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
29297895 AATAAGAAAG
29297905 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
29297925 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
29297945 ATATAAA
1 ATATAAA
29297952 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:29318316 original size:17 final size:16
Alignment explanation
Indices: 29318294--29318336 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
29318284 AAGGTGGTCT
29318294 TTTTATTTTTCACTTCA
1 TTTTATTTTTCACTT-A
*
29318311 TTTTATTTATTTACTTA
1 TTTTATTT-TTCACTTA
29318328 -TTTATTTTT
1 TTTTATTTTT
29318337 TTAGAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 7 0.29
17 9 0.38
18 6 0.25
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTTTTCACTTA
Found at i:29322646 original size:58 final size:59
Alignment explanation
Indices: 29322564--29322677 Score: 169
Period size: 58 Copynumber: 1.9 Consensus size: 59
29322554 TTTAAAAAGG
* *
29322564 AAAAGATAAAAACAACATATATTAAATACTTT-ATTTTATTTATTTTTCAAATAAAACCC
1 AAAAGATAAAAACAACATATATTAAATA-TTTGATTTTATTTATTTTTAAAACAAAACCC
* *
29322623 AAAAGAT-AAAACATCATATATTAATTATTTGATTTTATTTATTTTTAAAACAAAA
1 AAAAGATAAAAACAACATATATTAAATATTTGATTTTATTTATTTTTAAAACAAAA
29322678 TTCATTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 3 0.06
58 40 0.80
59 7 0.14
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (59 bp):
AAAAGATAAAAACAACATATATTAAATATTTGATTTTATTTATTTTTAAAACAAAACCC
Found at i:29323175 original size:18 final size:19
Alignment explanation
Indices: 29323152--29323189 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
29323142 TTTTAATATT
29323152 ATATATATTAAT-TTTTTA
1 ATATATATTAATATTTTTA
* *
29323170 ATATATTTTTATATTTTTA
1 ATATATATTAATATTTTTA
29323189 A
1 A
29323190 AAATTGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATATATTAATATTTTTA
Found at i:29326273 original size:22 final size:22
Alignment explanation
Indices: 29326230--29326273 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29326220 TAATCTCATG
* ** *
29326230 TAATACTATATTCTTTTCATTA
1 TAATACTATATTATCATAATTA
29326252 TAATACTATATTATCATAATTA
1 TAATACTATATTATCATAATTA
29326274 CATATAATAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATACTATATTATCATAATTA
Found at i:29326773 original size:27 final size:29
Alignment explanation
Indices: 29326722--29326776 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
29326712 TATGTTATAA
29326722 TAATAGTTATATATGTAATAATATTTTAG
1 TAATAGTTATATATGTAATAATATTTTAG
*
29326751 TAATAGTTATATAT-T-ATATTATTTTA
1 TAATAGTTATATATGTAATAATATTTTA
29326777 TGTATTAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.40
28 1 0.04
29 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (29 bp):
TAATAGTTATATATGTAATAATATTTTAG
Found at i:29327826 original size:161 final size:161
Alignment explanation
Indices: 29327557--29327887 Score: 637
Period size: 161 Copynumber: 2.1 Consensus size: 161
29327547 GTTCAAAACA
29327557 ATAT-AACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTCCCTATT
1 ATATGAACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTCCCTATT
29327621 ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTGACTGTCT
66 ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTGACTGTCT
29327686 CAATCAAAACTATATAAAAAAACCATTGAAT
131 CAATCAAAACTATATAAAAAAACCATTGAAT
*
29327717 ATATGAACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTTCCTATT
1 ATATGAACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTCCCTATT
*
29327782 ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTGATTGTCT
66 ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTGACTGTCT
29327847 CAATCAAAACTATATAAAAAAACCATTGAAT
131 CAATCAAAACTATATAAAAAAACCATTGAAT
29327878 ATATGAACTT
1 ATATGAACTT
29327888 TTACATTATA
Statistics
Matches: 168, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
160 4 0.02
161 164 0.98
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (161 bp):
ATATGAACTTACCTTAATTCCCACATTTACATAATAAAACAATTAACTAAACAATTTTCCCTATT
ACCACAATTCATATCATCAGGTGAGTTCATCATATAAAAATTGTAAAACATTCCATTGACTGTCT
CAATCAAAACTATATAAAAAAACCATTGAAT
Found at i:29328324 original size:131 final size:131
Alignment explanation
Indices: 29328090--29328354 Score: 449
Period size: 131 Copynumber: 2.0 Consensus size: 131
29328080 GGAGGCTACA
* *
29328090 CATCCTCCTCTAGAAACACACCTGAATCACTATAAAGATAGCTCGGTAATCCGCAACAAATGCTA
1 CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCGCAACAAATGCTA
* ** *
29328155 GATTCCAATAAGTTTAGTGAATAAATAGTACGTCATCATCTTGTCTTATATCAAACCCATACAAC
66 GATTCCAATAAGTTTAGTGAATAAACAACAAGTCATCATCTTGTCTTATATCAAACCCATACAAC
29328220 G
131 G
*
29328221 CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCGCAACAAATGCTG
1 CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCGCAACAAATGCTA
* *
29328286 GATTCCAATAAGTTTAGTGAATAAACAACAAGTCATCATCTTGTGTTATATCAAACCCGTACAAC
66 GATTCCAATAAGTTTAGTGAATAAACAACAAGTCATCATCTTGTCTTATATCAAACCCATACAAC
29328351 G
131 G
29328352 CAT
1 CAT
29328355 GAAATAACTC
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
131 125 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (131 bp):
CATCCTCCCCTAGAAACACACCTGAATCACTATAAAGATAGCTCAGTAATCCGCAACAAATGCTA
GATTCCAATAAGTTTAGTGAATAAACAACAAGTCATCATCTTGTCTTATATCAAACCCATACAAC
G
Found at i:29332403 original size:11 final size:11
Alignment explanation
Indices: 29332389--29332414 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29332379 TTGATAATTA
29332389 TTTTTTATATT
1 TTTTTTATATT
29332400 TTTTTTATATT
1 TTTTTTATATT
29332411 TTTT
1 TTTT
29332415 AATTGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTATATT
Found at i:29339447 original size:19 final size:19
Alignment explanation
Indices: 29339425--29339489 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
29339415 AGTGTAACAT
29339425 AATTTAATAAAATCTAAAC
1 AATTTAATAAAATCTAAAC
* * *
29339444 AATTTAA-ATAAGTGTAACAT
1 AATTTAATA-AAATCTAA-AC
* *
29339464 AATCTAATAAAACCTAAAC
1 AATTTAATAAAATCTAAAC
29339483 AATTTAA
1 AATTTAA
29339490 ATTGATTAAG
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
20 12 0.35
21 1 0.03
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (19 bp):
AATTTAATAAAATCTAAAC
Found at i:29339455 original size:39 final size:39
Alignment explanation
Indices: 29339412--29339491 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
29339402 CATCCACATC
* *
29339412 ATAAGTGTAACATAATTTAATAAAATCTAAACAATTTAA
1 ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
29339451 ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
1 ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
29339490 AT
1 AT
29339492 TGATTAAGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (39 bp):
ATAAGTGTAACATAATCTAATAAAACCTAAACAATTTAA
Found at i:29342328 original size:113 final size:114
Alignment explanation
Indices: 29342113--29342581 Score: 547
Period size: 113 Copynumber: 4.1 Consensus size: 114
29342103 TAAAGAAAGT
** * * * * ** *
29342113 ATTAGTGGCGCTTATTTAAAATCGCCACTAAAGCATAGAATTAGCGGCGAGTCGCAAAAAGCACC
1 ATTAGTGGCGCTTATACAAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCGCC
* * *
29342178 GCAATACATCTTAACGAAAACGCAGAGTTTGGTCTTGAGGTACACTAGC
66 GCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGC
* *
29342227 ATTAGTGGCGCTTATACAAAAACGCCGCTAAAGAATAGTATTGGCGGCGAGTAGTGAAAAGCG-C
1 ATTAGTGGCGCTTATACAAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCGCC
* * *
29342291 GCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGG
66 GCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGC
* ** * *
29342340 ATTAGTGGCGCTTAT-CGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTATTGTAAAGCGC
1 ATTAGTGGCGCTTATAC-AAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCGC
* *
29342404 CGCAA-A-ATATTAACCAAAACGCA-ACGCTTTGGTCTTGATGTATACTAGC
65 CGCAATATATCTTAACCAAAACGCAGA-G-TTTGGTCTTGAGGTATACTAGC
* * * * *
29342453 AGTAGTGACGCTTATATC-AAAACGCCGCTAAATCATAGTATTAGCGGTGAGTAGTGAAAAGTGC
1 ATTAGTGGCGCTTATA-CAAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCGC
* * * *
29342517 CGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGC
65 CGCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTA-GC
29342568 -TTAGTGGCGCTTAT
1 ATTAGTGGCGCTTAT
29342582 TGGAAAATGC
Statistics
Matches: 300, Mismatches: 45, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
111 1 0.00
112 17 0.06
113 175 0.58
114 87 0.29
115 19 0.06
116 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (114 bp):
ATTAGTGGCGCTTATACAAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCGCC
GCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGC
Found at i:29342508 original size:226 final size:228
Alignment explanation
Indices: 29342170--29342599 Score: 636
Period size: 227 Copynumber: 1.9 Consensus size: 228
29342160 CGAGTCGCAA
* * * *
29342170 AAAGCACCGCAATACATCTTAACGAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCATTAGTGG
1 AAAGCACCGCAATACATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCAGTAGTGA
* *
29342235 CGCTTATACAAAAACGCCGCTAAAGAATAGTATTGGCGGCGAGTAGTGAAAAGCG-CGCAATATT
66 CGCTTATACAAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCGCCGCAAGATT
29342299 TCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACG
131 TCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACG
*
29342364 CCGCTAAAGCATAGTATTAGCGGCGCTTATTGT
196 CCGCAAAAGCATAGTATTAGCGGCGCTTATTGT
* * *
29342397 AAAGCGCCGCAA-A-ATATTAACCAAAACGCA-ACGCTTTGGTCTTGATGTATACTAGCAGTAGT
1 AAAGCACCGCAATACATATTAACCAAAACGCAGA-G-TTTGGTCTTGAGGTACACTAGCAGTAGT
** * *
29342459 GACGCTTATATC-AAAACGCCGCTAAATCATAGTATTAGCGGTGAGTAGTGAAAAGTGCCGCAAG
64 GACGCTTATA-CAAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCGCCGCAAG
* * *
29342523 ATTTCTTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGCTTAGTGGCGCTTATTGGAAA
128 ATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAA
*
29342588 ATGCCGCAAAAG
193 ACGCCGCAAAAG
29342600 ATTAACCAAA
Statistics
Matches: 181, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
224 1 0.01
225 16 0.09
226 75 0.41
227 89 0.49
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (228 bp):
AAAGCACCGCAATACATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCAGTAGTGA
CGCTTATACAAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCGCCGCAAGATT
TCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACG
CCGCAAAAGCATAGTATTAGCGGCGCTTATTGT
Found at i:29342709 original size:188 final size:186
Alignment explanation
Indices: 29342379--29342877 Score: 730
Period size: 188 Copynumber: 2.7 Consensus size: 186
29342369 AAAGCATAGT
* *
29342379 ATTAGCGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAACGCTTTGGTCTTGATG
1 ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* * * * *
29342444 TATACTAGCAGTAGTGACGCTTATATCAAAACGCCGCTAAATCATAGTATTAGCGGTGAGTAGTG
66 TATACTAGCATTAGTGGCGCTTATAT-AAAACGCCGCTAAAT-ATAGTATTAGCGGCGAGTACTA
* * *
29342509 AAAAGTGCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGG
129 AAAAGCGCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGG
* * ** * *
29342567 CTTAGTGGCGCTTATTGGAAAATGCCGCAAAAGATTAACCAAAACGCAGCGCTTTGATCTTGATG
1 ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* *
29342632 TATAGTAGCATTAGTGGCGCTTATACTAAAACGCCGTTAAAGTATAGTATTAGCGGCGAGTACTA
66 TATACTAGCATTAGTGGCGCTTATA-TAAAACGCCGCTAAA-TATAGTATTAGCGGCGAGTACTA
*
29342697 AAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGG
129 AAAAGCGCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGG
29342755 ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* * *
29342820 TATACTAGCAGTT-GTGGCGCTTATGGTAAAACGCCGCTAAAACATATTATTAGCGGCG
66 TATACTAGCA-TTAGTGGCGCTTAT-ATAAAACGCCGCT-AAATATAGTATTAGCGGCG
29342878 CGTTGTAGGA
Statistics
Matches: 276, Mismatches: 30, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
188 269 0.97
189 7 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (186 bp):
ATTAGTGGCGCTTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
TATACTAGCATTAGTGGCGCTTATATAAAACGCCGCTAAATATAGTATTAGCGGCGAGTACTAAA
AAGCGCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGG
Found at i:29342837 original size:74 final size:73
Alignment explanation
Indices: 29342698--29342861 Score: 195
Period size: 74 Copynumber: 2.2 Consensus size: 73
29342688 CGAGTACTAA
* * * *
29342698 AAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAGGATTAGTGG
1 AAAGCGCCGCAA-A-ATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCATTAGTGG
*
29342763 CGCTTATTGT
64 CGCTTATGGT
* * *
29342773 AAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCAGTT-GTGG
1 AAAGCGCCGCAAAATATTAACCAAAACGCAGAG-TTTGGTCTTGAGGTACACTAGCA-TTAGTGG
29342837 CGCTTATGGT
64 CGCTTATGGT
*
29342847 AAAACGCCGCTAAAA
1 AAAGCGCCGC-AAAA
29342862 CATATTATTA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
73 17 0.22
74 42 0.55
75 18 0.23
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (73 bp):
AAAGCGCCGCAAAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCATTAGTGGCG
CTTATGGT
Found at i:29342936 original size:17 final size:17
Alignment explanation
Indices: 29342900--29342944 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
29342890 CGCCACTAGA
29342900 TTATTATAT-ATTTAGT
1 TTATTATATAATTTAGT
29342916 TTATTATATAATTTA-T
1 TTATTATATAATTTAGT
29342932 GTTATTATATAAT
1 -TTATTATATAAT
29342945 GTAGGAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
TTATTATATAATTTAGT
Found at i:29343689 original size:15 final size:16
Alignment explanation
Indices: 29343669--29343699 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
29343659 TATTTATGTT
29343669 TATTAAAAATA-AAAA
1 TATTAAAAATATAAAA
29343684 TATTAAAAATATAAAA
1 TATTAAAAATATAAAA
29343700 AAATATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TATTAAAAATATAAAA
Found at i:29346526 original size:18 final size:18
Alignment explanation
Indices: 29346505--29347279 Score: 710
Period size: 18 Copynumber: 43.7 Consensus size: 18
29346495 CACAAATTAA
29346505 ATAACTTACATTAA-TTAC
1 ATAACTTACA-TAACTTAC
* * * *
29346523 ATAACTTATAAAAATTAA
1 ATAACTTACATAACTTAC
29346541 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
* *
29346559 ATAAATTA-AGAACCTTAC
1 ATAACTTACATAA-CTTAC
29346577 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
* *
29346595 ATAAATTAAATAACTTAC
1 ATAACTTACATAACTTAC
*
29346613 ATAACTTACATAAATTA-
1 ATAACTTACATAACTTAC
29346630 AGTAACTTACATTAA-TTAC
1 A-TAACTTACA-TAACTTAC
* * *
29346649 ATAACTTACAAAAATTAA
1 ATAACTTACATAACTTAC
29346667 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
*
29346685 ATAACTTACATAAATTA-
1 ATAACTTACATAACTTAC
29346702 AGTAACTTACATAACTTAC
1 A-TAACTTACATAACTTAC
* *
29346721 ATAAATTAAATAACTTAC
1 ATAACTTACATAACTTAC
* *
29346739 GTAACTTACATAAATTA-
1 ATAACTTACATAACTTAC
*
29346756 AGTAACTTACATAAATTA-
1 A-TAACTTACATAACTTAC
29346774 AGTAACTTACATAACTTAC
1 A-TAACTTACATAACTTAC
* *
29346793 ATAAATTAAATAACTTAC
1 ATAACTTACATAACTTAC
*
29346811 ATAACTTACATAAATTA-
1 ATAACTTACATAACTTAC
29346828 AGTAACTTACATTAA-TTAC
1 A-TAACTTACA-TAACTTAC
* * *
29346847 ATAACTTACAAAAATTAA
1 ATAACTTACATAACTTAC
29346865 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
*
29346883 ATAAATTA-AGTAACTTAC
1 ATAACTTACA-TAACTTAC
* *
29346901 ATAACTTACATAAATTAA
1 ATAACTTACATAACTTAC
*
29346919 ATAACTTACGTAACTTAC
1 ATAACTTACATAACTTAC
*
29346937 ATAAATTA-AGTAACTTAC
1 ATAACTTACA-TAACTTAC
* *
29346955 ATAACTTACATAAATTAA
1 ATAACTTACATAACTTAC
29346973 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
*
29346991 ATAAATTA-AGTAACTTAC
1 ATAACTTACA-TAACTTAC
*
29347009 ATTAA-TTACATAAATTA-
1 A-TAACTTACATAACTTAC
29347026 AGTAACTTACATAACTTAC
1 A-TAACTTACATAACTTAC
*
29347045 ATAACTTACATAAATTA-
1 ATAACTTACATAACTTAC
* * *
29347062 AGTAACTTACAAAAATTAA
1 A-TAACTTACATAACTTAC
29347081 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
* *
29347099 ATAAATTAAATAACTTAC
1 ATAACTTACATAACTTAC
* * **
29347117 ATAAATTAAATAACTGGC
1 ATAACTTACATAACTTAC
*
29347135 ATAACTTACATTA--TAC
1 ATAACTTACATAACTTAC
* *
29347151 ATAACCTT-CTTAACTGAC
1 ATAA-CTTACATAACTTAC
* * *
29347169 ATTA--TACACAACTCAC
1 ATAACTTACATAACTTAC
*
29347185 ATAA-TTA-AT-ATTATAC
1 ATAACTTACATAACT-TAC
*
29347201 ACAACTTACATAA--TAC
1 ATAACTTACATAACTTAC
*
29347217 ATTACTTACATAACTTAC
1 ATAACTTACATAACTTAC
29347235 AGT-ACTTACATAA--TAC
1 A-TAACTTACATAACTTAC
29347251 ATAA--TACATAACTTAC
1 ATAACTTACATAACTTAC
29347267 ATAACTTACATAA
1 ATAACTTACATAA
29347280 TACATAAAAA
Statistics
Matches: 627, Mismatches: 87, Indels: 86
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.01
15 4 0.01
16 50 0.08
17 27 0.04
18 516 0.82
19 23 0.04
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:29346549 original size:27 final size:27
Alignment explanation
Indices: 29346519--29347129 Score: 728
Period size: 27 Copynumber: 22.6 Consensus size: 27
29346509 CTTACATTAA
* *
29346519 TTACATAACTTATAAAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
29346546 TTACATAACTTACATAAATTAAGA-ACC
1 TTACATAACTTACATAAATTAA-ATAAC
* * *
29346573 TTACATAACTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
* * * *
29346600 TTAAATAACTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
** * *
29346627 TTAAGTAACTTACATTAATTACATAAC
1 TTACATAACTTACATAAATTAAATAAC
* * * * *
29346654 TTACAAAAATTAAATAACTTACATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
29346681 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
29346708 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
29346735 TTACGTAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
* * *
29346762 TTACATAAATTA-AGTAACTTACATAAC
1 TTACATAACTTACA-TAAATTAAATAAC
* * * *
29346789 TTACATAAATTAAATAACTTACATAAC
1 TTACATAACTTACATAAATTAAATAAC
* * * * *
29346816 TTACATAAATTA-AGTAACTTACATTAA
1 TTACATAACTTACA-TAAATTAAATAAC
*
29346843 TTACATAACTTACAAAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
29346870 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
29346897 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
29346924 TTACGTAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
29346951 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
*
29346978 TTACATAACTTACATAAATTAAGTAAC
1 TTACATAACTTACATAAATTAAATAAC
*
29347005 TTACATTAA-TTACATAAATTAAGTAAC
1 TTACA-TAACTTACATAAATTAAATAAC
* * *
29347032 TTACATAACTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
*
29347059 TTA-AGTAACTTACAAAAATTAAATAAC
1 TTACA-TAACTTACATAAATTAAATAAC
29347086 TTACATAACTTACATAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
29347113 TTACATAAATTAAATAA
1 TTACATAACTTACATAA
29347130 CTGGCATAAC
Statistics
Matches: 514, Mismatches: 60, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
26 7 0.01
27 500 0.97
28 7 0.01
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.33
Consensus pattern (27 bp):
TTACATAACTTACATAAATTAAATAAC
Found at i:29347112 original size:63 final size:63
Alignment explanation
Indices: 29346505--29347287 Score: 665
Period size: 63 Copynumber: 12.5 Consensus size: 63
29346495 CACAAATTAA
* * * *
29346505 ATAACTTACATTAA-TTACATAACTTATAAAAATTAAATAACTTACATAACTTACATAAATTA-
1 ATAACTTACA-TAACTTACATAACTTACATAAATTAAATAACTTACATAAATTACATAACTTAC
* * *
29346567 AGAACCTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAAATTA-
1 ATAA-CTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAAATTACATAACTTAC
* *
29346630 AGTAACTTACATTAA-TTACATAACTTACAAAAATTAAATAACTTACATAACTTACATAACTTAC
1 A-TAACTTACA-TAACTTACATAACTTACATAAATTAAATAACTTACATAAATTACATAACTTAC
* * * *
29346694 ATAAATTA-AGTAACTTACATAACTTACATAAATTAAATAACTTACGTAACTTACATAAATTA-
1 ATAACTTACA-TAACTTACATAACTTACATAAATTAAATAACTTACATAAATTACATAACTTAC
* * * * * *
29346756 AGTAACTTACATAAATTA-AGTAACTTACATAACTTACATAAATTAAATAACTTACATAACTTAC
1 A-TAACTTACATAACTTACA-TAACTTACATAAATTAAATAACTTACATAAATTACATAACTTAC
* * * * *
29346820 ATAAATTA-AGTAACTTACATTAA-TTACATAACTTACAA-AAATTAAATAACTTACATAACTTA
1 ATAACTTACA-TAACTTACA-TAACTTACATAAATTA-AATAACTTACATAAATTACATAACTTA
29346882 C
63 C
* * * *
29346883 ATAAATTA-AGTAACTTACATAACTTACATAAATTAAATAACTTACGTAACTTACATAAATTA-
1 ATAACTTACA-TAACTTACATAACTTACATAAATTAAATAACTTACATAAATTACATAACTTAC
* * * *
29346945 AGTAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAAATTA-AGTAACTTAC
1 A-TAACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAAATTACA-TAACTTAC
* * *
29347009 ATTAA-TTACATAAATTA-AGTAACTTACATAACTTACATAACTTACATAAATTA-AGTAACTTA
1 A-TAACTTACATAACTTACA-TAACTTACATAAATTAAATAACTTACATAAATTACA-TAACTTA
29347071 C
63 C
* * * * **
29347072 AAAAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAAATTAAATAACTGGC
1 ATAACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAAATTACATAACTTAC
* * * *
29347135 ATAACTTACATTA--TACATAACCTT-CTTAACTGACATTATACACAACTCACAT-AATTA-AT-
1 ATAACTTACATAACTTACATAA-CTTAC---A-T-AAATTA-A-ATAACTTACATAAATTACATA
*
29347194 ATTATAC
58 ACT-TAC
* * * *
29347201 ACAACTTACATAA--TACATTACTTACATAACTTACAGT-ACTTACAT-AA-TACATAA--TAC
1 ATAACTTACATAACTTACATAACTTACATAAATTA-AATAACTTACATAAATTACATAACTTAC
29347258 ATAACTTACATAACTTACATAA--TACATAAA
1 ATAACTTACATAACTTACATAACTTACATAAA
29347288 AATATATCAT
Statistics
Matches: 615, Mismatches: 69, Indels: 79
0.81 0.09 0.10
Matches are distributed among these distances:
57 22 0.04
58 2 0.00
59 17 0.03
60 1 0.00
61 13 0.02
62 27 0.04
63 465 0.76
64 21 0.03
65 6 0.01
66 26 0.04
67 6 0.01
68 9 0.01
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (63 bp):
ATAACTTACATAACTTACATAACTTACATAAATTAAATAACTTACATAAATTACATAACTTAC
Found at i:29347226 original size:25 final size:25
Alignment explanation
Indices: 29347171--29347235 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
29347161 TAACTGACAT
* *
29347171 TATACACAACTCACATAATTAATAT
1 TATACACAACTTACATAATTAATAC
29347196 TATACACAACTTACATAA-TACATTAC
1 TATACACAACTTACATAATTA-A-TAC
*
29347222 T-TACATAACTTACA
1 TATACACAACTTACA
29347236 GTACTTACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.06
25 30 0.86
26 3 0.09
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (25 bp):
TATACACAACTTACATAATTAATAC
Found at i:29347253 original size:7 final size:7
Alignment explanation
Indices: 29347241--29347286 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
29347231 TTACAGTACT
29347241 TACATAA
1 TACATAA
29347248 TACATAA
1 TACATAA
29347255 TACATAA
1 TACATAA
29347262 CTTACATAA
1 --TACATAA
29347271 CTTACATAA
1 --TACATAA
29347280 TACATAA
1 TACATAA
29347287 AAATATATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 21 0.57
9 16 0.43
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:29352649 original size:21 final size:21
Alignment explanation
Indices: 29352623--29352688 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
29352613 CAACTTAAAA
*
29352623 CAGAGGCTGCAGCGAGGGAAG
1 CAGAGGCTGCAGCGAGAGAAG
*
29352644 CAGAGGCTACAGCGAGAGAAG
1 CAGAGGCTGCAGCGAGAGAAG
* * *
29352665 CAAAGGCCGTAGCGAGAGAAG
1 CAGAGGCTGCAGCGAGAGAAG
29352686 CAG
1 CAG
29352689 CGAGAGAAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.35, C:0.20, G:0.41, T:0.05
Consensus pattern (21 bp):
CAGAGGCTGCAGCGAGAGAAG
Found at i:29352692 original size:12 final size:12
Alignment explanation
Indices: 29352675--29352700 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29352665 CAAAGGCCGT
29352675 AGCGAGAGAAGC
1 AGCGAGAGAAGC
29352687 AGCGAGAGAAGC
1 AGCGAGAGAAGC
29352699 AG
1 AG
29352701 AGGTTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.42, T:0.00
Consensus pattern (12 bp):
AGCGAGAGAAGC
Found at i:29353166 original size:43 final size:43
Alignment explanation
Indices: 29353119--29353207 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
29353109 TCATATCATA
*
29353119 TAGTGGCATTTGTGAAAT-AAGCGCCG-TGAAAGAACACTACTTT
1 TAGTGGCATTTGT-AAATGAAGCACCGCT-AAAGAACACTACTTT
* * *
29353162 TAGTGGCGTTTGTAGATGAAGCACCGCTAAAGAACATTACTTT
1 TAGTGGCATTTGTAAATGAAGCACCGCTAAAGAACACTACTTT
29353205 TAG
1 TAG
29353208 CGGCGTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
42 3 0.08
43 36 0.90
44 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (43 bp):
TAGTGGCATTTGTAAATGAAGCACCGCTAAAGAACACTACTTT
Found at i:29353243 original size:42 final size:42
Alignment explanation
Indices: 29353137--29353430 Score: 272
Period size: 42 Copynumber: 6.9 Consensus size: 42
29353127 TTTGTGAAAT
* ** **
29353137 AAGCGCCG-TGAAAGAACACT-ACTTTTAGTGGCGTTTGTAGATG
1 AAGCGCCGCT-AAAGAACA-TGACTTTTAGCGGCGTTT-TTTACC
* * *
29353180 AAGCACCGCTAAAGAACATTACTTTTAGCGGCGTTTTCTACC
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTACC
* *
29353222 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTACC
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTACC
* * ** * *
29353264 AACCGCCACTATTGAACATTACTTTTAGCGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTACC
* * *
29353306 TAAGCGCTGCTAAAGAACATGA-TCTTTAGCGGTGTTTTTTCCC
1 -AAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTTTTACC
* * * *
29353349 AAGCGCTGCTAAAGAACATGA-TCATTAACGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTTTTACC
* *
29353391 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCCTTTTTT
1 -AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTT
29353431 TCTGTAAGCG
Statistics
Matches: 215, Mismatches: 30, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
42 119 0.55
43 95 0.44
44 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTACC
Found at i:29353246 original size:85 final size:85
Alignment explanation
Indices: 29353136--29353428 Score: 234
Period size: 85 Copynumber: 3.4 Consensus size: 85
29353126 ATTTGTGAAA
* * ** * *
29353136 TAAGCGCCG-TGAAAGAACACTACTTTTAGTGGCGTTTGTAGATGAAGCACCGCTAAAGAACATT
1 TAAGCGCCGCT-AAAGAACATTACTTTTAGCGGCGTTT-TAGACCAACCACCACTAAAGAACATT
29353200 ACTTTTAGCGGCGTTTTCTACC
64 ACTTTTAGCGGCGTTTTCTACC
* ** * **
29353222 -AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTACCAACCGCCACTATTGAACATTAC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTAGACCAACCACCACTAAAGAACATTAC
* *
29353286 TTTTAGCGGCGTTTTTTTCC
66 TTTTAGCGGCGTTTTCTACC
* * * *** * * ** *
29353306 TAAGCGCTGCTAAAGAACATGA-TCTTTAGCGGTGTTTTTTCCCAAGCGCTGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTAGACCAACCACCACTAAAGAACATTA
* * * *
29353370 -TCATTAACGGCGTTTTTTTCC
65 CT-TTTAGCGGCGTTTTCTACC
* * *
29353391 TAAGCGCCGCTAAAGAACATGACCTTTAGCGGCCTTTT
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTT
29353429 TTTCTGTAAG
Statistics
Matches: 171, Mismatches: 31, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
84 39 0.23
85 131 0.77
86 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (85 bp):
TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTAGACCAACCACCACTAAAGAACATTAC
TTTTAGCGGCGTTTTCTACC
Found at i:29353429 original size:85 final size:85
Alignment explanation
Indices: 29353188--29353430 Score: 274
Period size: 85 Copynumber: 2.9 Consensus size: 85
29353178 TGAAGCACCG
* * * * * * * *
29353188 CTAAAGAACATTACTTTTAGCGGCGTTTTCTACC-AAGCGCCGCTATAGAACATTACTTTTAGCG
1 CTAAAGAACATGACTATTAACGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGACCTTTAGCG
29353252 GCGTTTTTTACCAACCGCCA
66 GCGTTTTTTACCAACCGCCA
** * * * * *
29353272 CTATTGAACATTACTTTTAGCGGCGTTTTTTTCCTAAGCGCTGCTAAAGAACATGATCTTTAGCG
1 CTAAAGAACATGACTATTAACGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGACCTTTAGCG
* * * **
29353337 GTGTTTTTTCCCAAGCGCTG
66 GCGTTTTTTACCAACCGCCA
29353357 CTAAAGAACATGA-TCATTAACGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGACCTTTAGC
1 CTAAAGAACATGACT-ATTAACGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGACCTTTAGC
*
29353421 GGCCTTTTTT
65 GGCGTTTTTT
29353431 TCTGTAAGCG
Statistics
Matches: 134, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
84 31 0.23
85 103 0.77
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (85 bp):
CTAAAGAACATGACTATTAACGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGACCTTTAGCG
GCGTTTTTTACCAACCGCCA
Found at i:29354488 original size:436 final size:435
Alignment explanation
Indices: 29353578--29354595 Score: 1768
Period size: 436 Copynumber: 2.3 Consensus size: 435
29353568 TGGTGTAGTG
* *
29353578 GTTCCAGATGTTTACAGTCTTTGCGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCC
1 GTTCCAGATGTTAACAGTCTTTCCGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCC
*
29353643 TTGCACCCTATATACTTCTCCAAGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
66 TTGCACCCTATATAGTTCTCCAAGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
* *
29353708 CCATGTGGGTAGTAGACTTTCATTTCCCAGCAAATTTAAATCTTCAGTAATACACCACTTGTATC
131 CCATGTGGGTAGTAGATTTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATC
* *
29353773 CACTCTTCTACGTGTATTTGCTAGTATTGTCTCCTCGCCAGACCTAGTGTCTGGCTGCAAAGTTT
196 CACTCTTCTACGTGTATTTGCTAGTATTGTCTCCTCGCCAGACCTAGTGTCTGGCTACAAAGTGT
* *
29353838 TCCACAGAGGGATGGATCGAATCCTTTCTATTTGGTCTTCAGAAAAAAGATTTCTTAACCCATCT
261 TCCACAGAGGGATGGATCAAATCCTTTCTATTTGGTCTTCAGAAAAAAGATTTCTTAACACATCT
29353903 TCCTTCCAGGTATTTAAATTTGTTTAAATTAATTCTTCCACCATGGTATATCTCCTATCAATATT
326 TCCTTCCAGGTATTTAAATTTGTTTAAATTAATTCTTCCACCATGGTATATCTCCTATCAATATT
* *
29353968 CTAATTTTGTAGTTTTCCATTCCTAGGATATAGAAGCCATGTGTC
391 CTAATTTTGTAGTTTTCCATTCCCAGGATATAGAAGCCATGTGTA
* *
29354013 GTTCCAGATGTTAACAGTCTTTCTGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCT
1 GTTCCAGATGTTAACAGTCTTTCCGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCC
* *
29354078 TTGCACCCTATATAGTTCTCCATGTAAAAGAAGGGTGAGTTCCTAACTCGGCATTTAAAAAATCA
66 TTGCACCCTATATAGTTCTCCAAGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
*
29354143 CCACGTGGGTAGTAGATTTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATC
131 CCATGTGGGTAGTAGATTTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATC
*
29354208 CACTCTTCTCCGTGTATTTGCTAGTATTGTCTCCTCGCCAGACCTTAGTGTCTGGCTACAAAGTG
196 CACTCTTCTACGTGTATTTGCTAGTATTGTCTCCTCGCCAGACC-TAGTGTCTGGCTACAAAGTG
*
29354273 TTCCACAGAGGGATGGATCAAATCCTTTCTATTTGGTCTTCATAAAAAAGATTTCTTAACACATC
260 TTCCACAGAGGGATGGATCAAATCCTTTCTATTTGGTCTTCAGAAAAAAGATTTCTTAACACATC
* * * *
29354338 TTCTTTCCAGGTATTTAAATTT-TTATTAATTAATTCTTCTACCATGGTATATCTCCTATCCATA
325 TTCCTTCCAGGTATTTAAATTTGTT-TAAATTAATTCTTCCACCATGGTATATCTCCTATCAATA
*
29354402 TTCTAATTTTGTAGTTTTCCATTCCCAGGATATTGAAGCCATGTGTA
389 TTCTAATTTTGTAGTTTTCCATTCCCAGGATATAGAAGCCATGTGTA
* *
29354449 GTTCCAGATGTTAACAGTTTTTCCGTCGCCTATTCTTCAATCAACCCCTGATTCTAATAAGTCCC
1 GTTCCAGATGTTAACAGTCTTTCCGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCC
*
29354514 TTGCACCCTATATAGTTCTCCAGGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
66 TTGCACCCTATATAGTTCTCCAAGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
*
29354579 TCATGTGGGTAGTAGAT
131 CCATGTGGGTAGTAGAT
29354596 AGCTTTCATG
Statistics
Matches: 550, Mismatches: 31, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
435 230 0.42
436 320 0.58
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (435 bp):
GTTCCAGATGTTAACAGTCTTTCCGTCGCCTATTCTTCAACCAACCCCTGATTCTAATAAGTCCC
TTGCACCCTATATAGTTCTCCAAGTAAAAGAAGGGTGAGTTCCTAACTCAGCATTTAAAAAATCA
CCATGTGGGTAGTAGATTTTCATTTCCCAGCAAATTTAAATCTTCAGTAAGACACCACTTGTATC
CACTCTTCTACGTGTATTTGCTAGTATTGTCTCCTCGCCAGACCTAGTGTCTGGCTACAAAGTGT
TCCACAGAGGGATGGATCAAATCCTTTCTATTTGGTCTTCAGAAAAAAGATTTCTTAACACATCT
TCCTTCCAGGTATTTAAATTTGTTTAAATTAATTCTTCCACCATGGTATATCTCCTATCAATATT
CTAATTTTGTAGTTTTCCATTCCCAGGATATAGAAGCCATGTGTA
Found at i:29358435 original size:5 final size:6
Alignment explanation
Indices: 29358390--29358442 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
29358380 TTAGTTCATC
** * *
29358390 TTTATT TTTCCT TTTATT TCTATT TGTAGTGT TTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTA-T-T TTTATT TTTATT TTTATT
29358440 TTT
1 TTT
29358443 TTAATTTCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
6 32 0.84
7 2 0.05
8 4 0.11
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:29358477 original size:3 final size:3
Alignment explanation
Indices: 29358469--29358496 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29358459 TTTTTAATCC
29358469 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29358497 TCTCCTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:29358600 original size:15 final size:14
Alignment explanation
Indices: 29358574--29358604 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
29358564 AATTTTGTAC
29358574 TTATTTTAATATAT
1 TTATTTTAATATAT
29358588 TTATTTATAATATAT
1 TTATTT-TAATATAT
29358603 TT
1 TT
29358605 TAATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTTAATATAT
Found at i:29363432 original size:87 final size:87
Alignment explanation
Indices: 29363274--29363802 Score: 691
Period size: 87 Copynumber: 6.1 Consensus size: 87
29363264 ACTTGTAATC
* ** * * *
29363274 TTCGATCTGCTTCACTGTCGACGCAGGAGGGCAAGATCTACTATCTTTAACCAGCTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
29363339 CCGATAGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
29363361 TTCAATCTGCTTCGCTGTTAACGCAGGAGGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
* * * *
29363426 CTGATAGATGCAAGGCATTGTT
66 CCGATGGAGGCAAGGCTTTGTT
** * * *
29363448 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTATTATCTTCAACCAACTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
29363513 CCGATGGAGACAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
** * * *
29363535 TTCGATCTTATTCGCTATTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAACTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
29363600 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * *
29363622 TTCGATCTGCTTTGCTGTTAACGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCATTGAAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
* * *
29363687 CCGATGAAGACAAGGCTTTATT
66 CCGATGGAGGCAAGGCTTTGTT
** * ** * * *
29363709 TTCGATCTGCTTCGCTGTTATTGTACAAAGGCAAAATTTGCT-TCTTTAGCCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
29363773 CCGATGGAGGCAAGGTTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
29363795 TTCGATCT
1 TTCGATCT
29363803 TCACTGATCT
Statistics
Matches: 384, Mismatches: 58, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
86 45 0.12
87 339 0.88
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:29365504 original size:16 final size:17
Alignment explanation
Indices: 29365471--29365514 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
29365461 GATTTCTCTT
29365471 TTTTTCTTTTGACTTTTA
1 TTTTTCTTTT-ACTTTTA
29365489 TTTTTCTTTT-CTTTTA
1 TTTTTCTTTTACTTTTA
*
29365505 TTTTTGTTTT
1 TTTTTCTTTT
29365515 TGATTTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.60
18 10 0.40
ACGTcount: A:0.07, C:0.09, G:0.05, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTACTTTTA
Found at i:29373556 original size:17 final size:18
Alignment explanation
Indices: 29373534--29373567 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29373524 ATAATTGTAA
29373534 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
29373551 TTTAAATGTTTAATTAT
1 TTTAAATGTCTAATTAT
29373568 CACAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:29373575 original size:24 final size:24
Alignment explanation
Indices: 29373548--29373616 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 24
29373538 AATTCTAATT
29373548 ATTTTTAAATGTTTAATTATCACA
1 ATTTTTAAATGTTTAATTATCACA
* * * **
29373572 ATTTCT--A--TTAAATTATAATT
1 ATTTTTAAATGTTTAATTATCACA
*
29373592 ATTTTTAAATGTATAATTATCACA
1 ATTTTTAAATGTTTAATTATCACA
29373616 A
1 A
29373617 CTTTATTTTA
Statistics
Matches: 30, Mismatches: 11, Indels: 8
0.61 0.22 0.16
Matches are distributed among these distances:
20 14 0.47
22 2 0.07
24 14 0.47
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (24 bp):
ATTTTTAAATGTTTAATTATCACA
Found at i:29383830 original size:20 final size:20
Alignment explanation
Indices: 29383807--29383940 Score: 69
Period size: 20 Copynumber: 6.7 Consensus size: 20
29383797 ACTTCGGTAT
*
29383807 CCCTGATTGCACATATGTGC
1 CCCTGATTGCACATATGTAC
* *
29383827 CCCT-ATTTGTACCT-TGATAC
1 CCCTGA-TTGCACATATG-TAC
*
29383847 CCCTGATTGCACATACT-TTC
1 CCCTGATTGCACATA-TGTAC
* * * *
29383867 CCCTGTTTGTAC-TTTAGTAT
1 CCCTGATTGCACATAT-GTAC
* *
29383887 CCCTGATTGCACATACGTGC
1 CCCTGATTGCACATATGTAC
* * * **
29383907 CCCTGTTTGTACTTCGGTAC
1 CCCTGATTGCACATATGTAC
29383927 CCCTGATTGCACAT
1 CCCTGATTGCACAT
29383941 GTGTGCCTTT
Statistics
Matches: 80, Mismatches: 26, Indels: 16
0.66 0.21 0.13
Matches are distributed among these distances:
18 1 0.01
19 4 0.05
20 72 0.90
21 2 0.03
22 1 0.01
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.36
Consensus pattern (20 bp):
CCCTGATTGCACATATGTAC
Found at i:29383851 original size:40 final size:40
Alignment explanation
Indices: 29383728--29383999 Score: 255
Period size: 40 Copynumber: 6.8 Consensus size: 40
29383718 AGATAATTAT
* * *
29383728 CCCTGATTGAACATACGTGCCCCTATTTGTATTTCGGTAC
1 CCCTGATTGCACATATGTGCCCCTATTTGTACTTCGGTAC
** * * ** * *
29383768 CATTAATTACACATACAT-CCCCTGTTTGTACTTCGGTAT
1 CCCTGATTGCACATATGTGCCCCTATTTGTACTTCGGTAC
*
29383807 CCCTGATTGCACATATGTGCCCCTATTTGTACCTT-GATAC
1 CCCTGATTGCACATATGTGCCCCTATTTGTA-CTTCGGTAC
* * ** *
29383847 CCCTGATTGCACATACT-TTCCCCTGTTTGTACTTTAGTAT
1 CCCTGATTGCACATA-TGTGCCCCTATTTGTACTTCGGTAC
* *
29383887 CCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTAC
1 CCCTGATTGCACATATGTGCCCCTATTTGTACTTCGGTAC
* **
29383927 CCCTGATTGCACATGTGTGCCTTTATTTGTACTTCGGTAC
1 CCCTGATTGCACATATGTGCCCCTATTTGTACTTCGGTAC
* * * *
29383967 CCCTGAATGCA-ATTATATTCCCCTATTTATACT
1 CCCTGATTGCACA-TATGTGCCCCTATTTGTACT
29384000 CTAGTAACCC
Statistics
Matches: 186, Mismatches: 40, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
39 34 0.18
40 148 0.80
41 4 0.02
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (40 bp):
CCCTGATTGCACATATGTGCCCCTATTTGTACTTCGGTAC
Found at i:29383894 original size:80 final size:79
Alignment explanation
Indices: 29383725--29383940 Score: 299
Period size: 80 Copynumber: 2.7 Consensus size: 79
29383715 TATAGATAAT
* * ** * *
29383725 TATCCCTGATTGAACATACGTGCCCCTATTTGTATTTCGGTACCATTAATTACACATACATCCCC
1 TATCCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATACATCCCC
*
29383790 TGTTTGTACTTCGG
66 TGTTTGTACTTCAG
* * *
29383804 TATCCCTGATTGCACATATGTGCCCCTATTTGTACCTT-GATACCCCTGATTGCACATACTTTCC
1 TATCCCTGATTGCACATACGTGCCCCTATTTGTA-CTTCGGTACCCCTGATTGCACATAC-ATCC
*
29383868 CCTGTTTGTACTTTAG
64 CCTGTTTGTACTTCAG
*
29383884 TATCCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTGCACAT
1 TATCCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACAT
29383941 GTGTGCCTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
79 51 0.43
80 69 0.57
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.37
Consensus pattern (79 bp):
TATCCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATACATCCCC
TGTTTGTACTTCAG
Found at i:29383940 original size:120 final size:119
Alignment explanation
Indices: 29383777--29384012 Score: 316
Period size: 120 Copynumber: 2.0 Consensus size: 119
29383767 CCATTAATTA
*
29383777 CACATACATCCCCTGTTTGTACTTCGGTATCCCTGATTGCACATATGTGCCCCTATTTGTACCTT
1 CACATACATCCCCTGTTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTTGTA-CTT
* * * * *
29383842 -GATACCCCTGATTGCACA-TACT-TTCCCCTGTTTGTACTTTAGTATCCCTGATTG
65 CGATACCCCTGAATGCA-ATTA-TATTCCCCTATTTATACTCTAGTAACCCTGATTG
* * **
29383896 CACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTGCACATGTGTGCCTTTATTTGTACTT
1 CACATACAT-CCCCTGTTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTTGTACTT
*
29383961 CGGTACCCCTGAATGCAATTATATTCCCCTATTTATACTCTAGTAACCCTGA
65 CGATACCCCTGAATGCAATTATATTCCCCTATTTATACTCTAGTAACCCTGA
29384013 ATCAAACAGT
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
119 13 0.13
120 89 0.87
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (119 bp):
CACATACATCCCCTGTTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTTGTACTTC
GATACCCCTGAATGCAATTATATTCCCCTATTTATACTCTAGTAACCCTGATTG
Found at i:29383971 original size:80 final size:78
Alignment explanation
Indices: 29383725--29383977 Score: 283
Period size: 80 Copynumber: 3.2 Consensus size: 78
29383715 TATAGATAAT
* * ** * * *
29383725 TATCCCTGATTGAACATACGTGCCCCTATTTGTATTTCGGTACCATTAATTACACATACATCCCC
1 TATCCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATA-TTCCCC
29383790 TGTTTGTACTTCGG
65 TGTTTGTACTTCGG
* *
29383804 TATCCCTGATTGCACATATGTGCCCCTATTTGTACCTT-GATACCCCTGATTGCACATACTTTCC
1 TATCCCTGATTGCACATACGTGCCCCTATTTGTA-CTTCGGTACCCCTGATTGCACATA--TTCC
**
29383868 CCTGTTTGTACTTTAG
63 CCTGTTTGTACTTCGG
* * *
29383884 TATCCCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTGCACATGTGTGCCT
1 TATCCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATAT-T-CCC
* *
29383949 TTATTTGTACTTCGG
64 CTGTTTGTACTTCGG
* *
29383964 TACCCCTGAATGCA
1 TATCCCTGATTGCA
29383978 ATTATATTCC
Statistics
Matches: 146, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
78 1 0.01
79 51 0.35
80 94 0.64
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (78 bp):
TATCCCTGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATTCCCCT
GTTTGTACTTCGG
Found at i:29395930 original size:25 final size:26
Alignment explanation
Indices: 29395901--29395956 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
29395891 TTAATTAGTA
*
29395901 TAAAATATT-AATAATTCAAT-AAAT
1 TAAAATATTAAATAATTAAATAAAAT
29395925 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATTAAATAATTAAATAAAAT
29395951 TAAAAT
1 TAAAAT
29395957 TTAGGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATATTAAATAATTAAATAAAAT
Found at i:29396661 original size:22 final size:19
Alignment explanation
Indices: 29396622--29396663 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
29396612 TGCAAAGTTG
29396622 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
29396641 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
29396663 A
1 A
29396664 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:29397516 original size:16 final size:16
Alignment explanation
Indices: 29397496--29397548 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
29397486 TTGGTTCGCT
*
29397496 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
*
29397512 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
29397528 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
29397544 GTAAT
1 GTAAT
29397549 AGGTAATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.04, G:0.34, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:29397617 original size:44 final size:46
Alignment explanation
Indices: 29397530--29397622 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
29397520 ATAGATGCGT
* *
29397530 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTGAATGG
29397576 AATGGAATAGAGGCGTAAT-GGT-ATTCTTCTATTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTGAATGG
29397620 AAT
1 AAT
29397623 AGCGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 3 0.07
46 19 0.42
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTGAATGG
Found at i:29397618 original size:39 final size:44
Alignment explanation
Indices: 29397530--29397635 Score: 123
Period size: 46 Copynumber: 2.5 Consensus size: 44
29397520 ATAGATGCGT
* *
29397530 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTT--ATGG
29397576 AATGGAATAGAGGCGTAAT-GGT-ATTCTTCTATTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTATGG
* *
29397615 AATGGAATAGCGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
29397636 CATAAGGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 18 0.33
40 2 0.04
43 1 0.02
44 12 0.22
45 3 0.05
46 19 0.35
ACGTcount: A:0.29, C:0.06, G:0.30, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTCTATTTGGTTATGG
Found at i:29397833 original size:18 final size:17
Alignment explanation
Indices: 29397781--29397833 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
29397771 TTATTATTAA
29397781 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
29397799 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
29397816 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
29397834 CATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29407541 original size:26 final size:24
Alignment explanation
Indices: 29407504--29407553 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
29407494 TGTCGAGCCG
* *
29407504 AATTAATTAAAATGTGATATAAAATT
1 AATTAATCAAAA-GTAAT-TAAAATT
29407530 AATTAATCAAAAGTAATTAAAATT
1 AATTAATCAAAAGTAATTAAAATT
29407554 CAAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 11 0.50
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (24 bp):
AATTAATCAAAAGTAATTAAAATT
Found at i:29407546 original size:14 final size:14
Alignment explanation
Indices: 29407524--29407573 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
29407514 AATGTGATAT
29407524 AAAATTAATTAATC
1 AAAATTAATTAATC
*
29407538 AAAAGTAATTAAAATTC
1 AAAATTAATT--AA-TC
*
29407555 AAAATTAATTAACC
1 AAAATTAATTAATC
29407569 AAAAT
1 AAAAT
29407574 AATCAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 15 0.50
15 2 0.07
16 2 0.07
17 11 0.37
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAATTAATTAATC
Found at i:29407562 original size:31 final size:30
Alignment explanation
Indices: 29407524--29407583 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
29407514 AATGTGATAT
* *
29407524 AAAATTAATTAATCAAAAGTAATTAAAATTC
1 AAAATTAATTAACCAAAA-TAATCAAAATTC
29407555 AAAATTAATTAACCAAAATAATCAAAATT
1 AAAATTAATTAACCAAAATAATCAAAATT
29407584 TATCAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (30 bp):
AAAATTAATTAACCAAAATAATCAAAATTC
Found at i:29409619 original size:39 final size:39
Alignment explanation
Indices: 29409523--29409621 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
29409513 ATTCACTTTT
* * * * * *
29409523 AAGCATGTATCACATTACACATATAATCACATAGCATTT
1 AAGCATATATCACAATACTCATATAACCACATAACATTC
* * *
29409562 AAGCATATATTACAATACTCATATTACCACATAACGTTC
1 AAGCATATATCACAATACTCATATAACCACATAACATTC
29409601 AAGCATATATCACAATACTCA
1 AAGCATATATCACAATACTCA
29409622 AAAACATGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAACCACATAACATTC
Found at i:29419918 original size:12 final size:13
Alignment explanation
Indices: 29419894--29419922 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29419884 GGGCTATAAC
29419894 TATTGCATTTATT
1 TATTGCATTTATT
29419907 TATTGC-TTTATT
1 TATTGCATTTATT
29419919 TATT
1 TATT
29419923 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:29427401 original size:48 final size:48
Alignment explanation
Indices: 29427228--29427405 Score: 259
Period size: 48 Copynumber: 3.7 Consensus size: 48
29427218 CTTTGTGTAA
* * *
29427228 TAACAG-ATTTTGGTAGCCTGCACATAGTCCGTGCCACCCTTGTGTCT
1 TAACAGAATATTGGTAGCCTGCACACAGTCCGTGCCACCCTTGTATCT
* * * *
29427275 TAACAGAATATTGGTGGTCTGCACACAATCCATGCCACCCTTGTATCT
1 TAACAGAATATTGGTAGCCTGCACACAGTCCGTGCCACCCTTGTATCT
* * *
29427323 TAACAGAAAATTGGTGGCCTGCACAAAGTCCGTGCCACCCTTGTATCT
1 TAACAGAATATTGGTAGCCTGCACACAGTCCGTGCCACCCTTGTATCT
29427371 TAACAGAATATTGGTAGCCTGCACACAGTCCGTGC
1 TAACAGAATATTGGTAGCCTGCACACAGTCCGTGC
29427406 TACATACGCG
Statistics
Matches: 115, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 6 0.05
48 109 0.95
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (48 bp):
TAACAGAATATTGGTAGCCTGCACACAGTCCGTGCCACCCTTGTATCT
Found at i:29430419 original size:18 final size:16
Alignment explanation
Indices: 29430394--29430470 Score: 59
Period size: 18 Copynumber: 4.5 Consensus size: 16
29430384 ACCTCAAACC
29430394 CCTAAACCTAGTAAAAA
1 CCTAAACCTA-TAAAAA
29430411 CCATAAACC-ATAAAAA
1 CC-TAAACCTATAAAAA
*
29430427 TTCCTAAACCCATAAAAA
1 --CCTAAACCTATAAAAA
29430445 CCCTCAAACCTA-AATAAA
1 -CCT-AAACCTATAA-AAA
*
29430463 CATAAACC
1 CCTAAACC
29430471 CTCAAGCCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
16 11 0.22
17 16 0.31
18 24 0.47
ACGTcount: A:0.53, C:0.29, G:0.01, T:0.17
Consensus pattern (16 bp):
CCTAAACCTATAAAAA
Found at i:29431995 original size:23 final size:24
Alignment explanation
Indices: 29431969--29432017 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
29431959 AAAGAATGGC
* **
29431969 TAAAAT-ATTTAATTTTGAAAAAT
1 TAAAATGATTAAATTTAAAAAAAT
29431992 T-AAATGATTAAATTTAAAAAAAT
1 TAAAATGATTAAATTTAAAAAAAT
29432015 TAA
1 TAA
29432018 TAATTGAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
22 4 0.19
23 16 0.76
24 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
TAAAATGATTAAATTTAAAAAAAT
Found at i:29433529 original size:39 final size:39
Alignment explanation
Indices: 29433477--29433553 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
29433467 GCTAAGATAG
*
29433477 AGCAATAGTGGCGTTTTT-ATGAAAACATCGCAAAAAAGA
1 AGCAATAGCGGCGTTTTTCA-GAAAACATCGCAAAAAAGA
* *
29433516 AGCATTAGCGGCGTTTTTCGAGAAAACGTCGCAAAAAA
1 AGCAATAGCGGCGTTTTTC-AGAAAACATCGCAAAAAA
29433554 CCAAAACCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 16 0.48
40 16 0.48
41 1 0.03
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (39 bp):
AGCAATAGCGGCGTTTTTCAGAAAACATCGCAAAAAAGA
Found at i:29433670 original size:41 final size:41
Alignment explanation
Indices: 29433611--29433817 Score: 236
Period size: 41 Copynumber: 5.0 Consensus size: 41
29433601 CGTTTATGAG
* * *
29433611 AAAGTGTCGGTAACGCTCTGGGTTTTAGCGGCGTTTTTTTA
1 AAAGCGTCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTTA
*
29433652 AAAGCGTCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTAA
1 AAAGCGTCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTTA
* * * *
29433693 AAAGTGTCGCTAATGCTCTAGGTTTTACCGGCGTTTTTTAA
1 AAAGCGTCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTTA
* * * * ***
29433734 AAAGCGCCGGTAATGGTCTGGGTTTTACCTATGTTTTTTT-
1 AAAGCGTCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTTA
* * *
29433774 AAAGCGCCGCTAATGGTCTTGGTTTTAGCGGCGTTTTTGTTA
1 AAAGCGTCGCTAATGCTCTGGGTTTTAGCGGCGTTTTT-TTA
29433816 AA
1 AA
29433818 GCGCCGCAAA
Statistics
Matches: 142, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
40 32 0.23
41 108 0.76
42 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (41 bp):
AAAGCGTCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTTTA
Found at i:29434221 original size:14 final size:14
Alignment explanation
Indices: 29434202--29434229 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29434192 ATATGGATTA
29434202 ATTAGGGATTATGG
1 ATTAGGGATTATGG
29434216 ATTAGGGATTATGG
1 ATTAGGGATTATGG
29434230 TTTAATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.36, T:0.36
Consensus pattern (14 bp):
ATTAGGGATTATGG
Found at i:29434266 original size:7 final size:7
Alignment explanation
Indices: 29434256--29434294 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
29434246 GATTTAATGT
29434256 TTAGGGG
1 TTAGGGG
29434263 TTAGGGG
1 TTAGGGG
29434270 TTTAGGGG
1 -TTAGGGG
**
29434278 TTAGACG
1 TTAGGGG
29434285 TTAGGGG
1 TTAGGGG
29434292 TTA
1 TTA
29434295 ATAGTTAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.18, C:0.03, G:0.46, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:29434274 original size:15 final size:15
Alignment explanation
Indices: 29434254--29434294 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
29434244 GGGATTTAAT
**
29434254 GTTTAGGGGTTAGGG
1 GTTTAGGGGTTAGAC
29434269 GTTTAGGGGTTAGAC
1 GTTTAGGGGTTAGAC
29434284 G-TTAGGGGTTA
1 GTTTAGGGGTTA
29434295 ATAGTTAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.17, C:0.02, G:0.46, T:0.34
Consensus pattern (15 bp):
GTTTAGGGGTTAGAC
Found at i:29434808 original size:326 final size:314
Alignment explanation
Indices: 29434104--29435038 Score: 1086
Period size: 326 Copynumber: 2.9 Consensus size: 314
29434094 TATCACTACA
** * *
29434104 GTTTAGGGTTTTT-A--A-TTTAGGGTATATGATTTTATTTAAAGATTTAAGGTCAGTTTAAGAG
1 GTTTAGGGTTTTTAATTAGTTTAGGGTATATGA-TAAATTT-AAGATTTAAGGCCAGTTTAGGAG
29434165 TTCATATTTTAAGGTTTTAGGGAGTATATATGGATTAATTAGGGATTATGGATTAGGGATTATGG
64 TTCATATTTTAAGG-TTTAGGGAGTATATATGGATTAATTAGGGATTATGGATTAGGGATTATGG
*
29434230 TTTAATTAAGGGTTGGGATTTAATGTTTAGGGGTTAGGGGTTTAGGGGTTAGACGTTAGGGGTTA
128 TTTAATTAAGGGTTGGGATTTAATGTTTAGGGGTTAGGGGTTTAGAGGTTAGACGTTAGGGGTTA
* **
29434295 ATAGTTAGGGATTTGGGGTTTATGAATTTAGGGGTCGGGTTAGGGTTTTGGGATTAGATTGTTTT
193 AGAGTTAGGGATTTGGGGTTTACAAATTTAGGGGTCGGGTTAGGGTTTTGGGATTAGATTGTTTT
*
29434360 TTATTTATATTTTAAATATGTTATTATATATGTAATTGTAATTTAACATAATAATAAAATT
258 TTATTTATATTTTAAATATG-T-TTATATATGTAATTGTAA--TAACATAATAATAAAAAT
*
29434421 GTTTAGGGTTTTTAGTTAGTTTAGGGTATATGATAAATTTAAGATTTAAGGCCAGTTTAGGAGTT
1 GTTTAGGGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAGATTTAAGGCCAGTTTAGGAGTT
* * *
29434486 CATATTTTAAGGTTTAGGTAGTATATATGGATTTAGCTATAGGGATTGTGGATTAGGGATTATGG
66 CATATTTTAAGGTTTAGGGAGTATATATGGA-TTA-AT-TAGGGATTATGGATTAGGGATTATGG
29434551 TTTAAAATTTAAGGGTTGGGATTTAAGGTTTAGGTGTTAGGGGTTTAGGGGTTTAGAGGTTAGAC
128 TTT--AA-TTAAGGGTTGGGATTTAA----T--GT-TTAGGGG-TTAGGGGTTTAGAGGTTAGAC
* *
29434616 G-TAGGGGTTAAGAGTTAGGGATTTGGGGTTTACAAATTTAGGGGTCGTGTTAGGGTTTTGGGTT
182 GTTAGGGGTTAAGAGTTAGGGATTTGGGGTTTACAAATTTAGGGGTCGGGTTAGGGTTTTGGGAT
* * * *
29434680 TAGATTATTATTTTTCTTTATATTTTAAATATG-TTAT-TATGTAGTTGTAA-AAGATAATAATA
247 TAGATT-GT-TTTTTATTTATATTTTAAATATGTTTATATATGTAATTGTAATAACATAATAATA
29434742 AAAAT
310 AAAAT
*
29434747 GTTTAGGGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAGATTTAAGGCCGGTTTAGGAGTT
1 GTTTAGGGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAGATTTAAGGCCAGTTTAGGAGTT
*
29434812 CATATTTTAAGGTTTAGGGAGTACTATATATATATGGGGATTAATTAGGGATTATAGATTAGGGA
66 CATATTTTAAGGTTTAGGGAG-------TATATAT--GGATTAATTAGGGATTATGGATTAGGGA
* ** *
29434877 TTATGTTTTAATTAAGGGTT-GG-CCTGA--TTTA------A--GGTTTAGAGGTTAGACGTTAG
122 TTATGGTTTAATTAAGGGTTGGGATTTAATGTTTAGGGGTTAGGGGTTTAGAGGTTAGACGTTAG
* * * **** ** *
29434930 TGGTTAAGAGTTAGAGATTTAGGGTTTAGGGTTTTAAAGGTCGGGTTAGGGTTTTGGGTTTAGAT
187 GGGTTAAGAGTTAGGGATTTGGGGTTTACAAATTTAGGGGTCGGGTTAGGGTTTTGGGATTAGAT
* *
29434995 TAATTTTTTATTTATATTTTAAATATG-TTCT-TATGTAATTGTAA
252 T-GTTTTTTATTTATATTTTAAATATGTTTATATATGTAATTGTAA
29435039 AAGATGTATA
Statistics
Matches: 545, Mismatches: 43, Indels: 68
0.83 0.07 0.10
Matches are distributed among these distances:
309 54 0.10
310 61 0.11
311 1 0.00
317 13 0.02
318 21 0.04
319 39 0.07
320 7 0.01
321 42 0.08
323 2 0.00
324 18 0.03
326 98 0.18
327 2 0.00
328 3 0.01
329 21 0.04
330 8 0.01
331 71 0.13
332 48 0.09
333 30 0.06
334 3 0.01
335 3 0.01
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.43
Consensus pattern (314 bp):
GTTTAGGGTTTTTAATTAGTTTAGGGTATATGATAAATTTAAGATTTAAGGCCAGTTTAGGAGTT
CATATTTTAAGGTTTAGGGAGTATATATGGATTAATTAGGGATTATGGATTAGGGATTATGGTTT
AATTAAGGGTTGGGATTTAATGTTTAGGGGTTAGGGGTTTAGAGGTTAGACGTTAGGGGTTAAGA
GTTAGGGATTTGGGGTTTACAAATTTAGGGGTCGGGTTAGGGTTTTGGGATTAGATTGTTTTTTA
TTTATATTTTAAATATGTTTATATATGTAATTGTAATAACATAATAATAAAAAT
Found at i:29435360 original size:19 final size:18
Alignment explanation
Indices: 29435336--29435384 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
29435326 AAATTATACG
29435336 AAATAAAATTAAAATACAA
1 AAATAAAATTAAAATA-AA
* *
29435355 AAATAAAAATGAAATAAA
1 AAATAAAATTAAAATAAA
29435373 AACACTAAAATT
1 AA-A-TAAAATT
29435385 TTTAATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 15 0.60
20 6 0.24
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATAAAATTAAAATAAA
Found at i:29435369 original size:25 final size:25
Alignment explanation
Indices: 29435336--29435383 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29435326 AAATTATACG
* *
29435336 AAATAAAATTAAAATACAAAAATAA
1 AAATAAAATAAAAACACAAAAATAA
* *
29435361 AAATGAAATAAAAACACTAAAAT
1 AAATAAAATAAAAACACAAAAAT
29435384 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (25 bp):
AAATAAAATAAAAACACAAAAATAA
Found at i:29435438 original size:47 final size:48
Alignment explanation
Indices: 29435369--29435467 Score: 155
Period size: 47 Copynumber: 2.1 Consensus size: 48
29435359 AAAAATGAAA
** * *
29435369 TAAAAACACTAAAATTTTTAATTTTGTCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTGATAATTTTATCTAATTTTTATAAATATTACC
29435417 TAAAAA-ACTAAAATTGATAATTTTATCTAATTTTTATAAATATTACC
1 TAAAAACACTAAAATTGATAATTTTATCTAATTTTTATAAATATTACC
29435464 TAAA
1 TAAA
29435468 CAAAAGTATG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 41 0.87
48 6 0.13
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (48 bp):
TAAAAACACTAAAATTGATAATTTTATCTAATTTTTATAAATATTACC
Found at i:29437188 original size:14 final size:14
Alignment explanation
Indices: 29437169--29437195 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29437159 TAAAAGGTTT
29437169 TTTAGTTAATCATC
1 TTTAGTTAATCATC
29437183 TTTAGTTAATCAT
1 TTTAGTTAATCAT
29437196 GTTGTTGTTC
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:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTAGTTAATCATC
Found at i:29437408 original size:22 final size:22
Alignment explanation
Indices: 29437382--29437458 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
29437372 CAAGTTGTAT
29437382 CCAATGCAAATTGTTGTTTTAG
1 CCAATGCAAATTGTTGTTTTAG
* *
29437404 CCAATTGAACAATTGTTG---TAT
1 CCAA-TGCA-AATTGTTGTTTTAG
29437425 CCAATGCAAATTGTTGTTTTAG
1 CCAATGCAAATTGTTGTTTTAG
**
29437447 TGAATGCAAATT
1 CCAATGCAAATT
29437459 TTATTATTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 8 0.18
20 3 0.07
21 6 0.14
22 16 0.36
23 3 0.07
24 8 0.18
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (22 bp):
CCAATGCAAATTGTTGTTTTAG
Found at i:29437438 original size:19 final size:19
Alignment explanation
Indices: 29437375--29437441 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
29437365 ATTTATGCAA
29437375 GTTGTATCCAATGCAAATT
1 GTTGTATCCAATGCAAATT
* *
29437394 GTTGTTTTAGCCAATTGAACAATT
1 GTTG---TATCCAA-TGCA-AATT
29437418 GTTGTATCCAATGCAAATT
1 GTTGTATCCAATGCAAATT
29437437 GTTGT
1 GTTGT
29437442 TTTAGTGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 13 0.33
20 3 0.08
21 6 0.15
22 6 0.15
23 3 0.08
24 8 0.21
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (19 bp):
GTTGTATCCAATGCAAATT
Found at i:29437775 original size:23 final size:24
Alignment explanation
Indices: 29437746--29437819 Score: 93
Period size: 23 Copynumber: 3.2 Consensus size: 24
29437736 ATTATTAATG
29437746 TATAACATATA-TTAATATGTATA
1 TATAACATATATTTAATATGTATA
*
29437769 TATAACATATATTTAA-AT-T-TG
1 TATAACATATATTTAATATGTATA
29437790 TATAACATATATTTTTAATATGTATA
1 TATAACATATA--TTTAATATGTATA
29437816 TATA
1 TATA
29437820 TTTATTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
21 12 0.28
22 1 0.02
23 18 0.42
24 6 0.14
25 1 0.02
26 5 0.12
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
TATAACATATATTTAATATGTATA
Found at i:29437793 original size:21 final size:21
Alignment explanation
Indices: 29437744--29437836 Score: 82
Period size: 22 Copynumber: 4.3 Consensus size: 21
29437734 ATATTATTAA
29437744 TGTATAACATATA-TTAATATGT
1 TGTATAACATATATTTAA-AT-T
*
29437766 ATATATAACATATATTTAAATT
1 -TGTATAACATATATTTAAATT
* *
29437788 TGTATAACATATATTTTTAATA
1 TGTATAACATATA-TTTAAATT
* *
29437810 TGTATATATATTTATTTAAATT
1 TGTATA-ACATATATTTAAATT
29437832 T-TATA
1 TGTATA
29437837 TATTTTTTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
21 16 0.27
22 20 0.34
23 19 0.32
24 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (21 bp):
TGTATAACATATATTTAAATT
Found at i:29437818 original size:19 final size:17
Alignment explanation
Indices: 29437796--29437843 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
29437786 TTTGTATAAC
29437796 ATATATTTTTAATATGTAT
1 ATATATTTTTAA-AT-TAT
*
29437815 ATATATTTATTTAAATTTT
1 ATATA-TT-TTTAAATTAT
29437834 ATATATTTTT
1 ATATATTTTT
29437844 TCAAAACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.12
18 2 0.08
19 12 0.46
20 4 0.15
21 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATATATTTTTAAATTAT
Found at i:29437826 original size:44 final size:42
Alignment explanation
Indices: 29437744--29437836 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 42
29437734 ATATTATTAA
29437744 TGTATAACATATATTAATATGTATATATAACATATATTTAAATT
1 TGTATAACATATATTAATATGTATATAT-A-ATATATTTAAATT
*
29437788 TGTATAACATATATTTTTAATATGTATATAT-ATTTATTTAAATT
1 TGTATAACATATA---TTAATATGTATATATAATATATTTAAATT
29437832 T-TATA
1 TGTATA
29437837 TATTTTTTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
43 4 0.09
44 26 0.58
47 15 0.33
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (42 bp):
TGTATAACATATATTAATATGTATATATAATATATTTAAATT
Found at i:29437837 original size:21 final size:22
Alignment explanation
Indices: 29437778--29437839 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 22
29437768 ATATAACATA
*
29437778 TATTTAAATTTGTATAACATATAT
1 TATTTAAATTT-TAT-ATATATAT
*
29437802 T-TTT-AATATGTATATATAT-T
1 TATTTAAAT-TTTATATATATAT
29437822 TATTTAAATTTTATATAT
1 TATTTAAATTTTATATAT
29437840 TTTTTCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 2 0.06
21 16 0.50
22 9 0.28
23 4 0.12
24 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (22 bp):
TATTTAAATTTTATATATATAT
Found at i:29437854 original size:19 final size:19
Alignment explanation
Indices: 29437814--29437855 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
29437804 TTAATATGTA
**
29437814 TATATATTTATTTAAATTT
1 TATATATTTATTTAAAACT
29437833 TATATATTT-TTTCAAAACT
1 TATATATTTATTT-AAAACT
29437852 TATA
1 TATA
29437856 AATCATATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATATTTATTTAAAACT
Found at i:29437983 original size:12 final size:12
Alignment explanation
Indices: 29437966--29437990 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29437956 TACATAATAC
29437966 ATAACTTACATA
1 ATAACTTACATA
29437978 ATAACTTACATA
1 ATAACTTACATA
29437990 A
1 A
29437991 CTTCTGTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:29438031 original size:9 final size:9
Alignment explanation
Indices: 29438013--29438228 Score: 113
Period size: 9 Copynumber: 25.3 Consensus size: 9
29438003 CTTATATATA
*
29438013 AACTTGCAT
1 AACTTACAT
29438022 AACTTACAT
1 AACTTACAT
*
29438031 AACAATATA-AC
1 AAC--T-TACAT
*
29438042 AACTTAGAT
1 AACTTACAT
29438051 AA--TACAT
1 AACTTACAT
* *
29438058 AGCCTACAT
1 AACTTACAT
*
29438067 AACTTAGAT
1 AACTTACAT
29438076 AACTTACAT
1 AACTTACAT
*
29438085 AA--TACAC
1 AACTTACAT
*
29438092 CACTTACAT
1 AACTTACAT
* *
29438101 AAATAAC-T
1 AACTTACAT
** *
29438109 TGCATA-AT
1 AACTTACAT
29438117 AACTTACAT
1 AACTTACAT
*
29438126 AA--TACAC
1 AACTTACAT
*
29438133 CACTTACAT
1 AACTTACAT
*
29438142 AACTTAAAT
1 AACTTACAT
29438151 AACTTACAT
1 AACTTACAT
29438160 AA--TACAT
1 AACTTACAT
29438167 AACTTACAT
1 AACTTACAT
29438176 AACTTACAT
1 AACTTACAT
29438185 AA--TACAT
1 AACTTACAT
* *
29438192 TACCTACAT
1 AACTTACAT
29438201 AACTTAC--
1 AACTTACAT
*
29438208 -ACTATACAC
1 AACT-TACAT
29438217 AACTTACAT
1 AACTTACAT
29438226 AAC
1 AAC
29438229 ATAATTAATA
Statistics
Matches: 154, Mismatches: 33, Indels: 40
0.68 0.15 0.18
Matches are distributed among these distances:
6 3 0.02
7 31 0.20
8 8 0.05
9 102 0.66
10 3 0.02
11 5 0.03
12 2 0.01
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.29
Consensus pattern (9 bp):
AACTTACAT
Found at i:29438087 original size:34 final size:33
Alignment explanation
Indices: 29438042--29438208 Score: 121
Period size: 34 Copynumber: 5.0 Consensus size: 33
29438032 ACAATATAAC
* *
29438042 AACTTAGATAATACATAGCCTACATAACTTAGAT
1 AACTTACATAATACATA-CCTACATAACTTACAT
* * *
29438076 AACTTACATAATAC--ACC-AC-TTACATAAAT
1 AACTTACATAATACATACCTACATAACTTACAT
* * *
29438105 AACTTGCATAATAACTTACATA-ATACACCACTTACAT
1 AACTTACATAAT-ACATACCTACAT--A--ACTTACAT
* *
29438142 AACTTAAATAACTTACATA-ATACATAACTTACAT
1 AACTTACATAA--TACATACCTACATAACTTACAT
29438176 AACTTACATAATACATTACCTACATAACTTACA
1 AACTTACATAATACA-TACCTACATAACTTACA
29438209 CTATACACAA
Statistics
Matches: 105, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
29 18 0.17
30 4 0.04
31 2 0.02
32 7 0.07
33 4 0.04
34 44 0.42
36 1 0.01
37 18 0.17
38 6 0.06
39 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (33 bp):
AACTTACATAATACATACCTACATAACTTACAT
Found at i:29438090 original size:25 final size:25
Alignment explanation
Indices: 29438062--29438228 Score: 153
Period size: 25 Copynumber: 6.7 Consensus size: 25
29438052 ATACATAGCC
*
29438062 TACATAACTTAGATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
** * * * *
29438087 TACACCACTTACATAAATAACTTGCA
1 TACATAACTTACATAACTTACAT-AA
* *
29438113 TA-ATAACTTACATAA--TACACCACT
1 TACATAACTTACATAACTTACA-TA-A
*
29438137 TACATAACTTAAATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
29438162 TACATAACTTACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
29438187 TACATTACCTACATAACTTACACT-A
1 TACATAACTTACATAACTTACA-TAA
*
29438212 TACACAACTTACATAAC
1 TACATAACTTACATAAC
29438229 ATAATTAATA
Statistics
Matches: 112, Mismatches: 23, Indels: 14
0.75 0.15 0.09
Matches are distributed among these distances:
23 2 0.02
24 2 0.02
25 99 0.88
26 5 0.04
27 4 0.04
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:29438098 original size:16 final size:14
Alignment explanation
Indices: 29438076--29438177 Score: 66
Period size: 16 Copynumber: 6.8 Consensus size: 14
29438066 TAACTTAGAT
29438076 AACTTACATAATAC
1 AACTTACATAATAC
*
29438090 ACCACTTACATAA-AT
1 A--ACTTACATAATAC
*
29438105 AACTTGCATAAT--
1 AACTTACATAATAC
29438117 AACTTACATAATAC
1 AACTTACATAATAC
*
29438131 ACCACTTACATAACTTAAAT
1 A--ACTTACATAA--T--AC
29438151 AACTTACATAATAC
1 AACTTACATAATAC
29438165 ATAACTTACATAA
1 --AACTTACATAA
29438178 CTTACATAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
12 11 0.16
13 9 0.13
14 3 0.04
15 2 0.03
16 32 0.46
18 11 0.16
20 2 0.03
ACGTcount: A:0.48, C:0.22, G:0.01, T:0.29
Consensus pattern (14 bp):
AACTTACATAATAC
Found at i:29438119 original size:12 final size:12
Alignment explanation
Indices: 29438074--29438208 Score: 75
Period size: 12 Copynumber: 10.8 Consensus size: 12
29438064 CATAACTTAG
29438074 ATAACTTACATA
1 ATAACTTACATA
29438086 ATACACCACTTACATAA
1 AT--A--ACTTACAT-A
*
29438103 ATAACTTGCATA
1 ATAACTTACATA
29438115 ATAACTTACATA
1 ATAACTTACATA
* *
29438127 ATACAC-CACTTA
1 ATA-ACTTACATA
29438139 CATAACTT--A-A
1 -ATAACTTACATA
29438149 ATAACTTACATA
1 ATAACTTACATA
* *
29438161 AT-ACATAACTTA
1 ATAAC-TTACATA
29438173 CATAACTTACATA
1 -ATAACTTACATA
*
29438186 AT-ACATTACCTA
1 ATAAC-TTACATA
29438198 CATAACTTACA
1 -ATAACTTACA
29438209 CTATACACAA
Statistics
Matches: 94, Mismatches: 12, Indels: 33
0.68 0.09 0.24
Matches are distributed among these distances:
9 7 0.07
10 1 0.01
11 5 0.05
12 39 0.41
13 25 0.27
14 5 0.05
15 1 0.01
16 8 0.09
17 3 0.03
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.30
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:29438121 original size:41 final size:38
Alignment explanation
Indices: 29438065--29438177 Score: 144
Period size: 41 Copynumber: 3.0 Consensus size: 38
29438055 CATAGCCTAC
*
29438065 ATAACTTAGATAACTTACATAATACACCACTTACATAA
1 ATAACTTAAATAACTTACATAATACACCACTTACATAA
29438103 ATAACTTGCATAATAACTTACATAATACACCACTTAC----
1 ATAACTT--A-AATAACTTACATAATACACCACTTACATAA
**
29438140 ATAACTTAAATAACTTACATAATACATAACTTACATAA
1 ATAACTTAAATAACTTACATAATACACCACTTACATAA
29438178 CTTACATAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
34 24 0.37
35 1 0.02
37 7 0.11
38 7 0.11
40 1 0.02
41 25 0.38
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (38 bp):
ATAACTTAAATAACTTACATAATACACCACTTACATAA
Found at i:29438128 original size:75 final size:75
Alignment explanation
Indices: 29438037--29438177 Score: 203
Period size: 75 Copynumber: 1.9 Consensus size: 75
29438027 ACATAACAAT
* * * *
29438037 ATAACAACTTAGATAATACA-TAGCCTACATAACTTAGATAACTTACATAATACACCACTTACAT
1 ATAACAACTTACATAATACACCA-CCTACATAACTTAAATAACTTACATAATACACAACTTACAT
29438101 AAATAACTTGC
65 AAATAACTTGC
* * *
29438112 ATAATAACTTACATAATACACCACTTACATAACTTAAATAACTTACATAATACATAACTTACATA
1 ATAACAACTTACATAATACACCACCTACATAACTTAAATAACTTACATAATACACAACTTACATA
29438177 A
66 A
29438178 CTTACATAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 57 0.98
76 1 0.02
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.29
Consensus pattern (75 bp):
ATAACAACTTACATAATACACCACCTACATAACTTAAATAACTTACATAATACACAACTTACATA
AATAACTTGC
Found at i:29438200 original size:75 final size:75
Alignment explanation
Indices: 29438062--29438202 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 75
29438052 ATACATAGCC
* * * * *
29438062 TACATAACTTAGATAACTTACATAATACACCACTTACATAAATAACTTGCATAATAACTTACATA
1 TACATAACTTAAATAACTTACATAATACACAACTTACATAAATAACATGAATAATAACCTACATA
29438127 ATACACCACT
66 ATACACCACT
* * * *
29438137 TACATAACTTAAATAACTTACATAATACATAACTTACATAACTTACAT-AATACATTACCTACAT
1 TACATAACTTAAATAACTTACATAATACACAACTTACATAAATAACATGAATA-ATAACCTACAT
29438201 AA
65 AA
29438203 CTTACACTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
74 3 0.05
75 53 0.95
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.30
Consensus pattern (75 bp):
TACATAACTTAAATAACTTACATAATACACAACTTACATAAATAACATGAATAATAACCTACATA
ATACACCACT
Found at i:29438231 original size:30 final size:29
Alignment explanation
Indices: 29438105--29438301 Score: 112
Period size: 30 Copynumber: 6.8 Consensus size: 29
29438095 TTACATAAAT
* *
29438105 AACTTGCATA-ATAACTTACATAATACAC
1 AACTTACATACATAACTTACATTATACAC
* * *
29438133 CACTTACATAACTTAAATAACTTACATAATACAT
1 AACTTACAT-AC----ATAACTTACATTATACAC
*
29438167 AAC-T---TACATAACTTACA-TA-ATAC
1 AACTTACATACATAACTTACATTATACAC
* *
29438190 -A-TTACCTACATAACTTACACTATACAC
1 AACTTACATACATAACTTACATTATACAC
*
29438217 AACTTACATAACATAA-TTAATATTATACAC
1 AACTTACAT-ACATAACTT-ACATTATACAC
*
29438247 AACTTACAGCCTATATAACTTACATTATACAC
1 AACTTACA---TACATAACTTACATTATACAC
*
29438279 AACTTA-ATTACATAATTTA-ATTA
1 AACTTACA-TACATAACTTACATTA
29438302 AAACTTTACA
Statistics
Matches: 133, Mismatches: 16, Indels: 40
0.70 0.08 0.21
Matches are distributed among these distances:
22 2 0.02
23 2 0.02
24 1 0.01
25 23 0.17
26 2 0.02
27 3 0.02
28 12 0.09
29 19 0.14
30 24 0.18
31 1 0.01
32 21 0.16
33 4 0.03
34 19 0.14
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (29 bp):
AACTTACATACATAACTTACATTATACAC
Found at i:29438331 original size:66 final size:62
Alignment explanation
Indices: 29438196--29438355 Score: 164
Period size: 66 Copynumber: 2.5 Consensus size: 62
29438186 ATACATTACC
* **
29438196 TACATAACTTACACTATACACAACTTACATAACATAATTAATATTATACACAACTTACAGCC
1 TACATAACTTACATTATACACAACTTACATAACATAATTAATATTATACACAACTTACAGAA
* * *
29438258 TATATAACTTACATTATACACAACTTA-ATTACATAATTTAATTAAAACTT-TACATAACTTACA
1 TACATAACTTACATTATACACAACTTACATAACATAA-TTAA-T---A-TTATACACAACTTACA
*
29438321 TAA
60 GAA
*
29438324 TACATAACTTTA-ATAATACACAACTTACATAA
1 TACATAAC-TTACATTATACACAACTTACATAA
29438356 TTACATTGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
61 8 0.10
62 29 0.36
63 1 0.01
66 34 0.43
67 8 0.10
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (62 bp):
TACATAACTTACATTATACACAACTTACATAACATAATTAATATTATACACAACTTACAGAA
Found at i:29440249 original size:66 final size:66
Alignment explanation
Indices: 29440109--29440254 Score: 188
Period size: 66 Copynumber: 2.2 Consensus size: 66
29440099 AGCCAGCATC
* *
29440109 GAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGTAGATGCACCAG
1 GAGAGAAGTTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGTAGATGCACCAA
29440174 T
66 T
* * * *
29440175 GAGAGAAGTTGAGGTTCAAAGGAAG-TATGAAGAACTCCAGCTGCAGCTTAAAGTAGCAT-CAGC
1 GAGAGAAGTTGAGGTTCAAA-AAAGATATGAAGAACTCCAGCTACAACTTAAAGTAG-ATGCACC
29440238 AAT
64 AAT
* *
29440241 GAGGGAAGTAGAGG
1 GAGAGAAGTTGAGG
29440255 CAGTAGCGAG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
66 65 0.93
67 5 0.07
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.18
Consensus pattern (66 bp):
GAGAGAAGTTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGTAGATGCACCAA
T
Found at i:29440760 original size:150 final size:150
Alignment explanation
Indices: 29440488--29440776 Score: 533
Period size: 150 Copynumber: 1.9 Consensus size: 150
29440478 TAGATTATTG
*
29440488 CTTTCGGTTGGTTTAGATTTGGTTTCTTTTGATTTGTTGTTACAGGAGGGCTGAAAATATGAAAA
1 CTTTCAGTTGGTTTAGATTTGGTTTCTTTTGATTTGTTGTTACAGGAGGGCTGAAAATATGAAAA
*
29440553 AATTTCTTTTACAAATCTGCCAAAATTAGTGGCGTTTTTTAAAAAAGTGCCGTTAAAAGTCACGG
66 AATTTCTTTTACAAATCTGCCAAAATTAGTGGCGTTTTTTAAAAAAGTGCCGCTAAAAGTCACGG
29440618 CCTTTAGCGAAAGTCATGGC
131 CCTTTAGCGAAAGTCATGGC
*
29440638 CTTTCAGTTGGTTTAGATTTGGTTTCTTTTGATTTGTTGTTACAGGAGGGCTGAAAATATGGAAA
1 CTTTCAGTTGGTTTAGATTTGGTTTCTTTTGATTTGTTGTTACAGGAGGGCTGAAAATATGAAAA
* *
29440703 ATTTTCTTTTACAAATCTGCCAAAATTAGTGGCGTTTTTTAAAAAAGTGCCGCTAAAAGTCATGG
66 AATTTCTTTTACAAATCTGCCAAAATTAGTGGCGTTTTTTAAAAAAGTGCCGCTAAAAGTCACGG
29440768 CCTTTAGCG
131 CCTTTAGCG
29440777 GTGTTTTTGG
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 134 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (150 bp):
CTTTCAGTTGGTTTAGATTTGGTTTCTTTTGATTTGTTGTTACAGGAGGGCTGAAAATATGAAAA
AATTTCTTTTACAAATCTGCCAAAATTAGTGGCGTTTTTTAAAAAAGTGCCGCTAAAAGTCACGG
CCTTTAGCGAAAGTCATGGC
Found at i:29440834 original size:45 final size:43
Alignment explanation
Indices: 29440745--29440998 Score: 312
Period size: 43 Copynumber: 5.9 Consensus size: 43
29440735 CGTTTTTTAA
* * * * * *
29440745 AAAAGTGCCGCTAAAAGTCATGGCCTTTAGCGGTGTTTTTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGG
* * *
29440788 AAAAGCGCCACTAAAGGTCATGGTATATATAGCGGTGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGG--TCTATAGCGGCGTTTGTGGG
* * *
29440833 AAAAGCGCTGCTAAAGGTCAAGGTCTATAGCGGCGATTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGG
*
29440876 AAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGA
1 AAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGG
*
29440919 AAAAGCACCGCTAAAGGTCATGGTCTATAGCGGCGTTTGT-GG
1 AAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGG
* * ** *
29440961 AGAAGCGCCTCTAAAGGTCATGACCTTTAGCGGCGTTT
1 AAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTT
29440999 ATTTCTAAAA
Statistics
Matches: 184, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
42 33 0.18
43 115 0.62
45 36 0.20
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGG
Found at i:29442316 original size:17 final size:17
Alignment explanation
Indices: 29442258--29442318 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 17
29442248 GCTCTCCTAC
*
29442258 TATATTAAATAATGTTATA
1 TATATT-AATAGT-TTATA
* *
29442277 TCATATCATATAGTATATAA
1 T-ATATTA-ATAGTTTAT-A
29442297 TATATTAATAGTTTATA
1 TATATTAATAGTTTATA
29442314 TATAT
1 TATAT
29442319 GTATCAATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 6 0.18
18 8 0.24
19 10 0.29
20 10 0.29
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (17 bp):
TATATTAATAGTTTATA
Found at i:29442621 original size:232 final size:233
Alignment explanation
Indices: 29442179--29442621 Score: 611
Period size: 232 Copynumber: 1.9 Consensus size: 233
29442169 ATATTATTGT
* * * * *
29442179 TTATTATTATATATTATATTGGTTGAAATATGTTATAAATCCCTATATTTTTCATATATTTGAAA
1 TTATTATTATATATTATACTAGTTGAAATATGATATAAATCCCTATACTTTTCATACATTTGAAA
*
29442244 GTTAGCTCTCCTACTATATTAAATAATGTTATATCATATCATATAGTATATAATATATTAATAGT
66 GTTAGCCCTCCTACTATATTAAATAATGTTATATCATATC----A--ATATAATATATTAATAGT
* ** * * *
29442309 TTATATATATGTATCAATGATTAAACATTATAATATCATGTAATATTATATAATTTATTATAATC
125 TTACATATATACATCAATGATTAAACATTATAATATCATGTAATACTATATAATTTATGATAATA
29442374 TATATTATAATAATAGTACATTATATATTACTTATTATCATATA
190 TATATTATAATAATAGTACATTATATATTACTTATTATCATATA
* * * *
29442418 TTATTATT-TATTATTATACTAGTTGAAATATGATCTAATTCTCTATACTTTTCGTACATTTGAA
1 TTATTATTATA-TATTATACTAGTTGAAATATGATATAAATCCCTATACTTTTCATACATTTGAA
* * *
29442482 AGTTAGCCCTCCTATTATATTATATAATGTTGTATCATATC-ATATAATATATTAATAGTTTACA
65 AGTTAGCCCTCCTACTATATTAAATAATGTTATATCATATCAATATAATATATTAATAGTTTACA
* **
29442546 TATATACATCAATGATTAAATATTATAATATCATGTAATACTATATCTTTTATGATAATATATAT
130 TATATACATCAATGATTAAACATTATAATATCATGTAATACTATATAATTTATGATAATATATAT
29442611 TATAATAATAG
195 TATAATAATAG
29442622 GTATATATGT
Statistics
Matches: 181, Mismatches: 22, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
232 90 0.50
238 2 0.01
239 89 0.49
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (233 bp):
TTATTATTATATATTATACTAGTTGAAATATGATATAAATCCCTATACTTTTCATACATTTGAAA
GTTAGCCCTCCTACTATATTAAATAATGTTATATCATATCAATATAATATATTAATAGTTTACAT
ATATACATCAATGATTAAACATTATAATATCATGTAATACTATATAATTTATGATAATATATATT
ATAATAATAGTACATTATATATTACTTATTATCATATA
Found at i:29442670 original size:239 final size:234
Alignment explanation
Indices: 29442179--29442671 Score: 589
Period size: 232 Copynumber: 2.1 Consensus size: 234
29442169 ATATTATTGT
* * * * * *
29442179 TTATTATTATA-TATTATATTGGTTGAAATATGTTATAAATCCCTATATTTTTCATATATTTGAA
1 TTATTATTTTATTATTATACTAGTTGAAATATGATATAAATCCCTATACTTTTCATACATTTGAA
*
29442243 AGTTAGCTCTCCTACTATATTAAATAATGTTATATCATATCATATAGTATATAATATATTAATAG
66 AGTTAGCCCTCCTACTATATTAAATAATGTTATATCATATC----A--ATATAATATATTAATAG
* ** * *
29442308 TTTATATATATGTATCAATGATTAAACATTATAATATCATGTAATATTATATAATTTATTATAAT
125 TTTACATATATACATCAATGATTAAACATTATAATATCATGTAATACTATATAATTTATGATAAT
* * *
29442373 CTATATTATAATAATAGTACATTATATATTACTTATTATCATATA
190 ATATATTATAATAATAGTACATTATATATTAATTATTATAATATA
* * * *
29442418 TTATTA-TTTATTATTATACTAGTTGAAATATGATCTAATTCTCTATACTTTTCGTACATTTGAA
1 TTATTATTTTATTATTATACTAGTTGAAATATGATATAAATCCCTATACTTTTCATACATTTGAA
* * *
29442482 AGTTAGCCCTCCTATTATATTATATAATGTTGTATCATATC-ATATAATATATTAATAGTTTACA
66 AGTTAGCCCTCCTACTATATTAAATAATGTTATATCATATCAATATAATATATTAATAGTTTACA
* **
29442546 TATATACATCAATGATTAAATATTATAATATCATGTAATACTATATCTTTTATGATAATATATAT
131 TATATACATCAATGATTAAACATTATAATATCATGTAATACTATATAATTTATGATAATATATAT
* * *
29442611 TATAATAATAGGTATA-TATGTATTAATATTTTTAGTAATATTTA
196 TATAATAATA-GTACATTATATATT-A-ATTATTA-TAATA--TA
29442655 TATATTATTTTATTATT
1 T-TATTATTTTATTATT
29442672 TTATGTATTA
Statistics
Matches: 217, Mismatches: 28, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
232 96 0.44
233 5 0.02
234 5 0.02
235 4 0.02
237 3 0.01
238 8 0.04
239 96 0.44
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (234 bp):
TTATTATTTTATTATTATACTAGTTGAAATATGATATAAATCCCTATACTTTTCATACATTTGAA
AGTTAGCCCTCCTACTATATTAAATAATGTTATATCATATCAATATAATATATTAATAGTTTACA
TATATACATCAATGATTAAACATTATAATATCATGTAATACTATATAATTTATGATAATATATAT
TATAATAATAGTACATTATATATTAATTATTATAATATA
Found at i:29449972 original size:17 final size:17
Alignment explanation
Indices: 29449947--29449983 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29449937 AATTTAAAAT
*
29449947 AACTATTATTCAAGAAC
1 AACTATTATCCAAGAAC
*
29449964 AACTGTTATCCAAGAAC
1 AACTATTATCCAAGAAC
29449981 AAC
1 AAC
29449984 CATCGTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.24
Consensus pattern (17 bp):
AACTATTATCCAAGAAC
Done.