Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 14 of 325
Found at i:4321414 original size:38 final size:33
Alignment explanation
Indices: 4321320--4321406 Score: 165
Period size: 33 Copynumber: 2.6 Consensus size: 33
4321310 CCTTTCTAAG
4321320 TGGTATACACAAAGTATACCTTTCCTTTTCATA
1 TGGTATACACAAAGTATACCTTTCCTTTTCATA
4321353 TGGTATACACAAAGTATACCTTTCCTTTTCATA
1 TGGTATACACAAAGTATACCTTTCCTTTTCATA
*
4321386 TGTTATACACAAAGTATACCT
1 TGGTATACACAAAGTATACCT
4321407 AACCTTTCTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (33 bp):
TGGTATACACAAAGTATACCTTTCCTTTTCATA
Found at i:4322168 original size:20 final size:22
Alignment explanation
Indices: 4322126--4322173 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
4322116 TGTAAAAGTG
*
4322126 ATTTATCTATCAATAATCTTTC
1 ATTTATCTATCAATAAACTTTC
4322148 ATTT-TCTATCAA-AAACTTTC
1 ATTTATCTATCAATAAACTTTC
4322168 AATTTA
1 -ATTTA
4322174 CAGCATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTATCTATCAATAAACTTTC
Found at i:4324039 original size:23 final size:22
Alignment explanation
Indices: 4323996--4324052 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
4323986 AAACAAAGGG
*
4323996 AGAAATTAAAGGAAAAAAAAAA
1 AGAAATTAAAAGAAAAAAAAAA
4324018 AGAAAGTTAAAAGAACATAAAAGAAA
1 AGAAA-TTAAAAGAA-A-AAAA-AAA
4324044 A-AAATTAAA
1 AGAAATTAAA
4324053 TTGCTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 8 0.27
24 6 0.20
25 7 0.23
26 4 0.13
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (22 bp):
AGAAATTAAAAGAAAAAAAAAA
Found at i:4326801 original size:37 final size:37
Alignment explanation
Indices: 4326751--4326835 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
4326741 ATTAGTGACA
*
4326751 AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATT
1 AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
* * *
4326788 AGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATC
1 AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
*
4326825 AGTGACAAGTG
1 AGTGATAAGTG
4326836 ATAAGTGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
Found at i:4326870 original size:51 final size:51
Alignment explanation
Indices: 4326783--4326883 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
4326773 TACACTTATC
* *
4326783 TGATTAGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATCAGTGACAAG
1 TGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
* *
4326834 TGATAAGTGATAAGTGGTAGTTTTAGCTACGCTTATCTGATCAGTGACAA
1 TGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
4326884 ATGAGAAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.35
Consensus pattern (51 bp):
TGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
Found at i:4328786 original size:14 final size:13
Alignment explanation
Indices: 4328769--4328810 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 13
4328759 TATATATATA
4328769 AATTATATTTATTT
1 AATTA-ATTTATTT
4328783 AATTAA-TTATTT
1 AATTAATTTATTT
4328795 --TTAATTTATTT
1 AATTAATTTATTT
4328806 AATTA
1 AATTA
4328811 TATTCAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 4 0.16
11 6 0.24
12 6 0.24
13 4 0.16
14 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATTAATTTATTT
Found at i:4328800 original size:10 final size:10
Alignment explanation
Indices: 4328750--4328814 Score: 55
Period size: 9 Copynumber: 6.5 Consensus size: 10
4328740 ATTTATTATC
4328750 ATATTTATATAT
1 ATATTTA-AT-T
*
4328762 ATATATAAATT
1 ATAT-TTAATT
4328773 ATATTT-ATT
1 ATATTTAATT
*
4328782 -TAATTAATT
1 ATATTTAATT
*
4328791 ATTTTTAATT
1 ATATTTAATT
4328801 -TATTTAATT
1 ATATTTAATT
4328810 ATATT
1 ATATT
4328815 CAATGATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
8 4 0.09
9 14 0.33
10 12 0.28
11 5 0.12
12 6 0.14
13 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATTTAATT
Found at i:4328807 original size:19 final size:18
Alignment explanation
Indices: 4328769--4328814 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
4328759 TATATATATA
4328769 AATTATATTTATTTAATT
1 AATTATATTTATTTAATT
* *
4328787 AATTATTTTTAATTTATTT
1 AATTATATTT-ATTTAATT
4328806 AATTATATT
1 AATTATATT
4328815 CAATGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTATATTTATTTAATT
Found at i:4329726 original size:133 final size:133
Alignment explanation
Indices: 4329486--4329726 Score: 315
Period size: 133 Copynumber: 1.8 Consensus size: 133
4329476 GGAGTTGTAA
* * * * *
4329486 ATTTTATCTACACTCTTATTTAGGATTGTAAAATCTGAACTATTCGATGAATTTTATATTAATCC
1 ATTTTATCTACACTCTTATTTAAGATAGTAAAACCCGAACTATTCGATGAATTTTAAATTAATCC
* * * **
4329551 ATTTTAAATGAAATGATTTTTCTTTTTGAGAGGATTTTTTTTTATTGATAGTTGGTATTAAACAG
66 ATTTTAAATGAAATGAATTTTCTTTTTGAAAGGAATGATTTTTATTGATAGTTGGTATTAAACAG
4329616 TAG
131 TAG
* * *
4329619 ATTTTATCTACACTCTTATTTAAGATAGTAAAACCCGAATTATTCGATGGATTTTAAATTAATCT
1 ATTTTATCTACACTCTTATTTAAGATAGTAAAACCCGAACTATTCGATGAATTTTAAATTAATCC
* *
4329684 ATTTTCAATGAAGT-AATTTTC-TTTTGAAAAGTGAATGATTTTT
66 ATTTTAAATGAAATGAATTTTCTTTTTG-AAAG-GAATGATTTTT
4329727 TATTTATTTA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
131 5 0.05
132 9 0.10
133 77 0.85
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.46
Consensus pattern (133 bp):
ATTTTATCTACACTCTTATTTAAGATAGTAAAACCCGAACTATTCGATGAATTTTAAATTAATCC
ATTTTAAATGAAATGAATTTTCTTTTTGAAAGGAATGATTTTTATTGATAGTTGGTATTAAACAG
TAG
Found at i:4337631 original size:20 final size:22
Alignment explanation
Indices: 4337579--4337633 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
4337569 TTCGTTGAAC
4337579 AATATTAATAACTAATAAACAAA
1 AATATTAATAA-TAATAAACAAA
*
4337602 AATA--AA-AATAATAAAACATA
1 AATATTAATAATAAT-AAACAAA
4337622 AATATTAATAAT
1 AATATTAATAAT
4337634 TATTGGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
19 4 0.15
20 12 0.44
21 2 0.07
22 2 0.07
23 7 0.26
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AATATTAATAATAATAAACAAA
Found at i:4337887 original size:19 final size:19
Alignment explanation
Indices: 4337863--4337900 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4337853 TATTTTTCCA
4337863 AAAAATGAT-TAAAAATTAT
1 AAAAAT-ATATAAAAATTAT
*
4337882 AAAAATATATAAATATTAT
1 AAAAATATATAAAAATTAT
4337901 TGTAGCACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AAAAATATATAAAAATTAT
Found at i:4340442 original size:17 final size:18
Alignment explanation
Indices: 4340422--4340459 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4340412 TTTCACAATG
*
4340422 TAAAAAAT-ACAATAAAT
1 TAAAAAATAAAAATAAAT
*
4340439 TAAAATATAAAAATAAAT
1 TAAAAAATAAAAATAAAT
4340457 TAA
1 TAA
4340460 CAAGTTACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAATAAAAATAAAT
Found at i:4341381 original size:3 final size:3
Alignment explanation
Indices: 4341373--4341402 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4341363 GGTGTAACAA
4341373 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4341403 TTATGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4343157 original size:21 final size:20
Alignment explanation
Indices: 4343123--4343163 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
4343113 AAAACATCAA
* *
4343123 TAAATTTAATATATTATTTTT
1 TAAATATAAAATATT-TTTTT
4343144 TAAATATAAAATATTTTTTT
1 TAAATATAAAATATTTTTTT
4343164 ATATTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAAATATAAAATATTTTTTT
Found at i:4346950 original size:3 final size:3
Alignment explanation
Indices: 4346939--4346987 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
4346929 CAATAATACC
*
4346939 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4346987 A
1 A
4346988 GCAAAAGTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4348048 original size:31 final size:29
Alignment explanation
Indices: 4348013--4348081 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
4348003 TTGTTTGTAA
**
4348013 TTGGGCTGAGGGTCTATTTTGGGTCTTGGGT
1 TTGGGCTGAGGGT-TATTTT-GGTAATGGGT
* *
4348044 TTGGGCTGGTGGGTTGTTTTGGTAATGGGT
1 TTGGGCT-GAGGGTTATTTTGGTAATGGGT
4348074 TTGGGCTG
1 TTGGGCTG
4348082 GGTTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 15 0.45
31 12 0.36
32 5 0.15
ACGTcount: A:0.06, C:0.07, G:0.45, T:0.42
Consensus pattern (29 bp):
TTGGGCTGAGGGTTATTTTGGTAATGGGT
Found at i:4348619 original size:46 final size:45
Alignment explanation
Indices: 4348514--4348799 Score: 201
Period size: 46 Copynumber: 6.6 Consensus size: 45
4348504 TTTTAATCCA
* * *
4348514 CTCCACTGTAA-CTTCAGGGAGATAGGA--T-AGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTGAAT-TCTTTGATCTG
* * *
4348557 CTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGATCTG
* * * *
4348603 TTCCACTGTAATCTCAGGGAGATAAGACCTG-A---TGTGATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGATCTG
* * * * *
4348644 CTCTACTGTAA-CTTTAGAGAGATAAGATC------CTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTTGATCTG
* * * *
4348683 CTCCATTGTAATCTCAAGGAGATAGGAT-T-ACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTTGATCTG
* *
4348727 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTTGATCTG
*
4348773 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
4348800 CCTGTATTAT
Statistics
Matches: 189, Mismatches: 37, Indels: 31
0.74 0.14 0.12
Matches are distributed among these distances:
39 25 0.13
40 2 0.01
41 28 0.15
43 23 0.12
44 34 0.18
45 2 0.01
46 71 0.38
47 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (45 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTTGATCTG
Found at i:4348769 original size:170 final size:170
Alignment explanation
Indices: 4348429--4348803 Score: 513
Period size: 170 Copynumber: 2.2 Consensus size: 170
4348419 TTTCAATCCA
* * * * *
4348429 TTCCACTG-CATCTTCAGGGAAATAAGACTTAATGCGACCTACTCTGCTGTAACCTCAGAGAGAT
1 TTCCACTGTAATC-TCAGGGAGATAAGACCTGATGCGACCTACTCTACTGTAACCTCAGAGAGAT
* * *
4348493 AAGATCCTTTATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGC
65 AAGATCC----TTTTAATCCACTCCACTGTAACTTCAAGGAGATAGGATACTATCTTCGATCTGC
4348558 TCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
126 TCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
* * * * *
4348603 TTCCACTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTTAGAGAGATA
1 TTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGACCTACTCTACTGTAACCTCAGAGAGATA
* * *
4348668 AGATCC-TTTAATCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCC
66 AGATCCTTTTAATCCACTCCACTGTAACT-TCAAGGAGATAGGA-TACTATCTTCGATCTGCTCC
*
4348731 GCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
129 GCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
4348773 TTCCACTGTAATCTCAGGGAGATAAGACCTG
1 TTCCACTGTAATCTCAGGGAGATAAGACCTG
4348804 TATTATAAAC
Statistics
Matches: 181, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
168 1 0.01
169 31 0.17
170 89 0.49
174 57 0.31
175 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (170 bp):
TTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGACCTACTCTACTGTAACCTCAGAGAGATA
AGATCCTTTTAATCCACTCCACTGTAACTTCAAGGAGATAGGATACTATCTTCGATCTGCTCCGC
TGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
Found at i:4350773 original size:31 final size:29
Alignment explanation
Indices: 4350738--4350806 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
4350728 TTGTTTGTAA
**
4350738 TTGGGCTGAGGGTCTATTTTGGGTCTTGGGT
1 TTGGGCTGAGGGT-TATTTT-GGTAATGGGT
* *
4350769 TTGGGCTGGTGGGTTGTTTTGGTAATGGGT
1 TTGGGCT-GAGGGTTATTTTGGTAATGGGT
4350799 TTGGGCTG
1 TTGGGCTG
4350807 GGTTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 15 0.45
31 12 0.36
32 5 0.15
ACGTcount: A:0.06, C:0.07, G:0.45, T:0.42
Consensus pattern (29 bp):
TTGGGCTGAGGGTTATTTTGGTAATGGGT
Found at i:4352406 original size:3 final size:3
Alignment explanation
Indices: 4352395--4352440 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
4352385 CAATAATACC
*
4352395 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4352441 GCAAAAGTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4353514 original size:31 final size:29
Alignment explanation
Indices: 4353479--4353547 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
4353469 TTGTTTGTAA
**
4353479 TTGGGCTGAGGGTCTATTTTGGGTCTTGGGT
1 TTGGGCTGAGGGT-TATTTT-GGTAATGGGT
* *
4353510 TTGGGCTGGTGGGTTGTTTTGGTAATGGGT
1 TTGGGCT-GAGGGTTATTTTGGTAATGGGT
4353540 TTGGGCTG
1 TTGGGCTG
4353548 GGTTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 15 0.45
31 12 0.36
32 5 0.15
ACGTcount: A:0.06, C:0.07, G:0.45, T:0.42
Consensus pattern (29 bp):
TTGGGCTGAGGGTTATTTTGGTAATGGGT
Found at i:4354020 original size:6 final size:6
Alignment explanation
Indices: 4354009--4354037 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4353999 TAAACAGCTC
4354009 ACACTA ACACTA ACACTA ACACTA ACACT
1 ACACTA ACACTA ACACTA ACACTA ACACT
4354038 CCCCCATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.17
Consensus pattern (6 bp):
ACACTA
Found at i:4359069 original size:87 final size:87
Alignment explanation
Indices: 4358923--4359099 Score: 345
Period size: 87 Copynumber: 2.0 Consensus size: 87
4358913 AACATATTGC
4358923 ACACCTTTATTAATCATGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
1 ACACCTTTATTAATCATGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
4358988 GACTAGAATGACTTACTAATTA
66 GACTAGAATGACTTACTAATTA
*
4359010 ACACCTTTATTAATCGTGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
1 ACACCTTTATTAATCATGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
4359075 GACTAGAATGACTTACTAATTA
66 GACTAGAATGACTTACTAATTA
4359097 ACA
1 ACA
4359100 TTCGAACTCA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (87 bp):
ACACCTTTATTAATCATGAATTGATAGATCTATTCTCTCATTTCAATTTCATTGGATCTTTAAAA
GACTAGAATGACTTACTAATTA
Found at i:4366678 original size:16 final size:16
Alignment explanation
Indices: 4366657--4366689 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4366647 GAACACTAAG
4366657 GCAGGAAAAAACGAAA
1 GCAGGAAAAAACGAAA
4366673 GCAGGAAAAAACGAAA
1 GCAGGAAAAAACGAAA
4366689 G
1 G
4366690 TGAAACTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.12, G:0.27, T:0.00
Consensus pattern (16 bp):
GCAGGAAAAAACGAAA
Found at i:4367547 original size:26 final size:26
Alignment explanation
Indices: 4367511--4367560 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
4367501 ATTTGTCCTC
4367511 AACAGATTCTTACACGCAAATAAATT
1 AACAGATTCTTACACGCAAATAAATT
4367537 AACAGATTCTTACACGCAAATAAA
1 AACAGATTCTTACACGCAAATAAA
4367561 AATATAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (26 bp):
AACAGATTCTTACACGCAAATAAATT
Found at i:4374011 original size:18 final size:17
Alignment explanation
Indices: 4373982--4374015 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
4373972 ACAATTTATA
4373982 TTAAATTATAATTATTT
1 TTAAATTATAATTATTT
4373999 TTAAATATATAATTATT
1 TTAAAT-TATAATTATT
4374016 ACCATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATTATAATTATTT
Found at i:4377026 original size:2 final size:2
Alignment explanation
Indices: 4377019--4377049 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4377009 GTAGAAATTA
*
4377019 CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4377050 ACACATATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4380970 original size:38 final size:38
Alignment explanation
Indices: 4380919--4380994 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
4380909 ACTGAAAATG
4380919 GACCTTCAATCCTTTAAAGAAATGCAAACATTTATCAA
1 GACCTTCAATCCTTTAAAGAAATGCAAACATTTATCAA
4380957 GACCTTCAATCCTTTAAAGAAATGCAAACATTTATCAA
1 GACCTTCAATCCTTTAAAGAAATGCAAACATTTATCAA
4380995 CCATATTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (38 bp):
GACCTTCAATCCTTTAAAGAAATGCAAACATTTATCAA
Found at i:4380972 original size:20 final size:18
Alignment explanation
Indices: 4380919--4380976 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
4380909 ACTGAAAATG
4380919 GACCTTCAATCCTTTAAA
1 GACCTTCAATCCTTTAAA
** * * *
4380937 GAAATGCAAACATTTATCAA
1 GACCTTCAATCCTTTA--AA
4380957 GACCTTCAATCCTTTAAA
1 GACCTTCAATCCTTTAAA
4380975 GA
1 GA
4380977 AATGCAAACA
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
18 15 0.54
20 13 0.46
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (18 bp):
GACCTTCAATCCTTTAAA
Found at i:4380990 original size:18 final size:18
Alignment explanation
Indices: 4380931--4380990 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
4380921 CCTTCAATCC
4380931 TTTAAAGAAATGCAAACA
1 TTTAAAGAAATGCAAACA
** * * *
4380949 TTTATCAAGACCTTCAATCC
1 TTTA--AAGAAATGCAAACA
4380969 TTTAAAGAAATGCAAACA
1 TTTAAAGAAATGCAAACA
4380987 TTTA
1 TTTA
4380991 TCAACCATAT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (18 bp):
TTTAAAGAAATGCAAACA
Found at i:4382416 original size:21 final size:21
Alignment explanation
Indices: 4382392--4382439 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4382382 ACACGAGGTG
4382392 CCTGATACAACACATACAGTA
1 CCTGATACAACACATACAGTA
** * *
4382413 CCTGATATGACACATATAGTG
1 CCTGATACAACACATACAGTA
4382434 CCTGAT
1 CCTGAT
4382440 CGGCAAAGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (21 bp):
CCTGATACAACACATACAGTA
Found at i:4383376 original size:15 final size:16
Alignment explanation
Indices: 4383314--4383376 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 16
4383304 ATTTATTTAC
4383314 TTTATATTATAATA--A
1 TTTA-ATTATAATATTA
*
4383329 TATAATTTATAATAATTA
1 TTTAA-TTATAAT-ATTA
4383347 TTTAATTAATAAATATT-
1 TTTAATT-AT-AATATTA
4383364 TTTAATTATAATA
1 TTTAATTATAATA
4383377 CAAGTGTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.03
15 14 0.35
16 3 0.08
17 9 0.22
18 10 0.25
19 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAATTATAATATTA
Found at i:4387132 original size:12 final size:12
Alignment explanation
Indices: 4387102--4387134 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4387092 ATATTCTTTT
4387102 AAAATT-ATATA
1 AAAATTAATATA
4387113 AAAA-TAATATA
1 AAAATTAATATA
4387124 AAAATTAATAT
1 AAAATTAATAT
4387135 GGGCGGGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:4395440 original size:6 final size:6
Alignment explanation
Indices: 4395429--4395463 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4395419 CTCACTGATG
4395429 TTTATA TTTATA TTTATA TTTATA TTTATA TTTAT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTAT
4395464 TCTGCTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:4407067 original size:40 final size:40
Alignment explanation
Indices: 4406997--4407214 Score: 359
Period size: 40 Copynumber: 5.5 Consensus size: 40
4406987 AAACCAAGTA
* * *
4406997 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
4407036 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
4407076 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
4407116 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
4407156 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
4407196 CCTTCGAGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
4407215 TTATTATCCG
Statistics
Matches: 169, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 14 0.08
40 155 0.92
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:4412213 original size:26 final size:27
Alignment explanation
Indices: 4412166--4412217 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
4412156 CAAGTTTCTA
*
4412166 TTTGATTTGTTTTTTTTAAATTTAGTT
1 TTTGATTTGTTTTGTTTAAATTTAGTT
4412193 TTTGATTT-TTTTGGTTT-AATTTAGT
1 TTTGATTTGTTTT-GTTTAAATTTAGT
4412218 CTCATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.69
Consensus pattern (27 bp):
TTTGATTTGTTTTGTTTAAATTTAGTT
Found at i:4412369 original size:23 final size:25
Alignment explanation
Indices: 4412343--4412402 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
4412333 TATAACATAT
*
4412343 AAAATTAAAAAAAATGT-A-TTTGA
1 AAAATTAAAAAAAATGTAATTTTAA
* * *
4412366 AAAAGT-ATAAAAATTTAATTTTAA
1 AAAATTAAAAAAAATGTAATTTTAA
4412390 AAAATTAAAAAAA
1 AAAATTAAAAAAA
4412403 TAAAGTTATG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 8 0.29
23 6 0.21
24 9 0.32
25 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (25 bp):
AAAATTAAAAAAAATGTAATTTTAA
Found at i:4414611 original size:19 final size:18
Alignment explanation
Indices: 4414587--4414622 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4414577 CCTCATAATT
*
4414587 TTTTTTTTGTATTTCCTTG
1 TTTTTTTGGTA-TTCCTTG
4414606 TTTTTTTGGTATTCCTT
1 TTTTTTTGGTATTCCTT
4414623 TATAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (18 bp):
TTTTTTTGGTATTCCTTG
Found at i:4415077 original size:20 final size:20
Alignment explanation
Indices: 4415054--4415119 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
4415044 TTTCCTAAGA
*
4415054 ATTTTTTGTACTCTCTCATG
1 ATTTTTGGTACTCTCTCATG
* * *
4415074 ATTTTTGGTTCTCTCTCGTA
1 ATTTTTGGTACTCTCTCATG
* *
4415094 ATTTTTGGTATTTTCTCATG
1 ATTTTTGGTACTCTCTCATG
4415114 ATTTTT
1 ATTTTT
4415120 TTTTGGTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.14, C:0.15, G:0.12, T:0.59
Consensus pattern (20 bp):
ATTTTTGGTACTCTCTCATG
Found at i:4415142 original size:24 final size:24
Alignment explanation
Indices: 4415095--4415152 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
4415085 TCTCTCGTAA
*
4415095 TTTTTGGTATTTTCTCATGATTTT
1 TTTTTGGTATTTTCTCATCATTTT
*
4415119 TTTTTGGTATTTTCTCTTC-TTTT
1 TTTTTGGTATTTTCTCATCATTTT
4415142 TTTCTT-GTATT
1 TTT-TTGGTATT
4415153 CCTCGTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.09, C:0.10, G:0.10, T:0.71
Consensus pattern (24 bp):
TTTTTGGTATTTTCTCATCATTTT
Found at i:4415350 original size:20 final size:20
Alignment explanation
Indices: 4415327--4415369 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4415317 TGTTTTTTTA
*
4415327 ACTCTCTCAGAATTTTTGGT
1 ACTCCCTCAGAATTTTTGGT
*
4415347 ACTCCCTCATAATTTTTGGT
1 ACTCCCTCAGAATTTTTGGT
4415367 ACT
1 ACT
4415370 TCATCATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (20 bp):
ACTCCCTCAGAATTTTTGGT
Found at i:4415383 original size:20 final size:20
Alignment explanation
Indices: 4415337--4415382 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4415327 ACTCTCTCAG
*
4415337 AATTTTTGGTACTCCCTCAT
1 AATTTTTGGTACTCCATCAT
*
4415357 AATTTTTGGTACTTCATCAT
1 AATTTTTGGTACTCCATCAT
4415377 -ATTTTT
1 AATTTTT
4415383 TAGTTTGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (20 bp):
AATTTTTGGTACTCCATCAT
Found at i:4416945 original size:20 final size:20
Alignment explanation
Indices: 4416893--4416935 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
4416883 ATCAGTATTC
4416893 TTATCCTGAATTTCAGGATT
1 TTATCCTGAATTTCAGGATT
4416913 TTATCCTGAATTTCAGGATT
1 TTATCCTGAATTTCAGGATT
4416933 TTA
1 TTA
4416936 ATTTGGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (20 bp):
TTATCCTGAATTTCAGGATT
Found at i:4418890 original size:16 final size:17
Alignment explanation
Indices: 4418869--4418903 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4418859 TTTCTTCACT
4418869 AAAGACAAA-GAGGAAA
1 AAAGACAAAGGAGGAAA
4418885 AAAGACAAATGGAGGAAA
1 AAAGACAAA-GGAGGAAA
4418903 A
1 A
4418904 TTTTATGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.66, C:0.06, G:0.26, T:0.03
Consensus pattern (17 bp):
AAAGACAAAGGAGGAAA
Found at i:4421128 original size:60 final size:60
Alignment explanation
Indices: 4421033--4421154 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 60
4421023 TTTGCAGATG
* *
4421033 ATTGCATTTTATTCGCAGAAGCTACTGAAAAAGGAGTGCATTCCTTAAAACGGATTTTGA
1 ATTGCATTTTATTCGCAAAAGCTACTGAAAAAGGAGTACATTCCTTAAAACGGATTTTGA
* *
4421093 ATTGCATTTTATTCGCAAAAGCTACTGAAAGAGGAGTACATTCCTTAAAATGGATTTTGA
1 ATTGCATTTTATTCGCAAAAGCTACTGAAAAAGGAGTACATTCCTTAAAACGGATTTTGA
4421153 AT
1 AT
4421155 GAATATGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (60 bp):
ATTGCATTTTATTCGCAAAAGCTACTGAAAAAGGAGTACATTCCTTAAAACGGATTTTGA
Found at i:4424931 original size:22 final size:22
Alignment explanation
Indices: 4424900--4424941 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4424890 AATACATGAT
*
4424900 AAAATCTATAATTCACATTTCA
1 AAAATCTATAATTCAAATTTCA
*
4424922 AAAATTTATAATTCAAATTT
1 AAAATCTATAATTCAAATTT
4424942 GGCCCCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATCTATAATTCAAATTTCA
Found at i:4428127 original size:27 final size:27
Alignment explanation
Indices: 4428093--4428151 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
4428083 AAACAAAGCC
* *
4428093 AAAT-TATATATGAATAATTTTA-AAGA
1 AAATATATATAT-AATAAATTTAGAAAA
4428119 AAATATATATATAATAAATTTAGAAAA
1 AAATATATATATAATAAATTTAGAAAA
4428146 AAATAT
1 AAATAT
4428152 TTACATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (27 bp):
AAATATATATATAATAAATTTAGAAAA
Found at i:4428151 original size:23 final size:25
Alignment explanation
Indices: 4428098--4428160 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 25
4428088 AAGCCAAATT
* *
4428098 ATATATGAATAATTTTAAAGAAAATAT
1 ATATAT-AATAAATTT-AAGAAAATAA
4428125 ATATATAATAAATTT-AGAAAA-AA
1 ATATATAATAAATTTAAGAAAATAA
*
4428148 ATATTTACATAAA
1 ATATATA-ATAAA
4428161 ATATTATGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 7 0.22
24 11 0.34
26 8 0.25
27 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (25 bp):
ATATATAATAAATTTAAGAAAATAA
Found at i:4428159 original size:27 final size:26
Alignment explanation
Indices: 4428105--4428159 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
4428095 ATTATATATG
* * *
4428105 AATAATTTTAAAGAAAATATATATAT
1 AATAAATTTAAAAAAAATATATACAT
*
4428131 AATAAATTTAGAAAAAAATATTTACAT
1 AATAAATTTA-AAAAAAATATATACAT
4428158 AA
1 AA
4428160 AATATTATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (26 bp):
AATAAATTTAAAAAAAATATATACAT
Found at i:4428171 original size:27 final size:28
Alignment explanation
Indices: 4428134--4428194 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
4428124 TATATATAAT
*
4428134 AAAT-TTA-GAAAAAAAT-ATTTACATA
1 AAATATTATGAAAAAAATAATGTACATA
* *
4428159 AAATATTATGAAAACAATAATGTATATA
1 AAATATTATGAAAAAAATAATGTACATA
4428187 AAA-ATTAT
1 AAATATTAT
4428195 ATGTGTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 4 0.13
26 3 0.10
27 13 0.43
28 10 0.33
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATATTATGAAAAAAATAATGTACATA
Found at i:4429016 original size:6 final size:6
Alignment explanation
Indices: 4429005--4429038 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
4428995 TCGTGGACTC
4429005 AAATAA AAATAA AAATAA AAATAACA AAATAA AA
1 AAATAA AAATAA AAATAA AAAT-A-A AAATAA AA
4429039 TAATGATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.73
7 2 0.08
8 5 0.19
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:4429744 original size:14 final size:14
Alignment explanation
Indices: 4429725--4429752 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4429715 ATTGATTTTT
4429725 ATAATATTATAAAA
1 ATAATATTATAAAA
4429739 ATAATATTATAAAA
1 ATAATATTATAAAA
4429753 TCTTATAAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAATATTATAAAA
Found at i:4439588 original size:11 final size:11
Alignment explanation
Indices: 4439574--4439599 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4439564 AGAAAAATTA
4439574 AAAAAAAAAAG
1 AAAAAAAAAAG
4439585 AAAAAAAAAAG
1 AAAAAAAAAAG
4439596 AAAA
1 AAAA
4439600 GGAGAATGAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:4440423 original size:20 final size:18
Alignment explanation
Indices: 4440398--4440434 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
4440388 TTGCATGCAT
4440398 TTTCTTTTTCTTTTCTTTTC
1 TTTCTTTTT-TTTT-TTTTC
4440418 TTTCTTTTTTTTTTTTT
1 TTTCTTTTTTTTTTTTT
4440435 GAATTTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTCTTTTTTTTTTTTTC
Found at i:4444431 original size:15 final size:15
Alignment explanation
Indices: 4444408--4444441 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4444398 AGCATCTGAT
* *
4444408 CAGCTACAGCTGCAG
1 CAGCAACAGCTCCAG
4444423 CAGCAACAGCTCCAG
1 CAGCAACAGCTCCAG
4444438 CAGC
1 CAGC
4444442 TGCTGGCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.38, G:0.24, T:0.09
Consensus pattern (15 bp):
CAGCAACAGCTCCAG
Found at i:4447286 original size:20 final size:20
Alignment explanation
Indices: 4447261--4447298 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4447251 TAAATTTTTA
*
4447261 TATATAAAATTTTAAAAAAT
1 TATATAAAATATTAAAAAAT
*
4447281 TATATAATATATTAAAAA
1 TATATAAAATATTAAAAA
4447299 TACTAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATATAAAATATTAAAAAAT
Found at i:4451107 original size:20 final size:20
Alignment explanation
Indices: 4451075--4451112 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4451065 ATTTTTATAT
4451075 ATTTTCTTATTAAAATTTAC
1 ATTTTCTTATTAAAATTTAC
*
4451095 ATTTT-TTAGTTAATATTT
1 ATTTTCTTA-TTAAAATTT
4451113 TTATATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (20 bp):
ATTTTCTTATTAAAATTTAC
Found at i:4479559 original size:16 final size:17
Alignment explanation
Indices: 4479538--4479590 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
4479528 TAGAGTGAAA
4479538 AAAAATTGAAAAGAT-G
1 AAAAATTGAAAAGATGG
* *
4479554 AAAAATT-AAATGGCTGG
1 AAAAATTGAAA-AGATGG
4479571 AAAAA-TGAAAAGATGG
1 AAAAATTGAAAAGATGG
4479587 AAAA
1 AAAA
4479591 CATAATTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 3 0.10
16 18 0.60
17 9 0.30
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.17
Consensus pattern (17 bp):
AAAAATTGAAAAGATGG
Found at i:4483204 original size:60 final size:59
Alignment explanation
Indices: 4483138--4483251 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 59
4483128 ACTAGGTGAT
* *
4483138 AAAAAAGACACAATT-TAATAGTTGGGTGACCATTTTGTAACTTTTCATAGTTGGATGACC
1 AAAAAAGA-A-AATTATAATAGTTGGGTGAACACTTTGTAACTTTTCATAGTTGGATGACC
* *
4483198 AAAAAAGAAATTTACTAATAGTTGGGTGAACACTTTGTAACTTTTTATAGTTGG
1 AAAAAAGAAAATTA-TAATAGTTGGGTGAACACTTTGTAACTTTTCATAGTTGG
4483252 GTGATTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 3 0.06
59 1 0.02
60 44 0.92
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (59 bp):
AAAAAAGAAAATTATAATAGTTGGGTGAACACTTTGTAACTTTTCATAGTTGGATGACC
Found at i:4485056 original size:16 final size:16
Alignment explanation
Indices: 4485017--4485065 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
4485007 ATTTTATGAA
*
4485017 CTTTTTTTTTATAATT
1 CTTTTTTTTGATAATT
* *
4485033 TTTATTTTTTGATTATT
1 CTT-TTTTTTGATAATT
*
4485050 CTTTTTTTTGAAAATT
1 CTTTTTTTTGATAATT
4485066 ATTTGTTGAC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (16 bp):
CTTTTTTTTGATAATT
Found at i:4492373 original size:25 final size:21
Alignment explanation
Indices: 4492312--4492373 Score: 52
Period size: 25 Copynumber: 2.6 Consensus size: 21
4492302 TTAAAAGGAT
4492312 AAATATATAATATAGTATGAAA
1 AAATATATAATA-AGTATGAAA
*
4492334 AACATATGTACATAAGATAATGTAAA
1 AA-ATATATA-ATAAG-T-ATG-AAA
4492360 AAATATATATATAA
1 AAATATATA-ATAA
4492374 CTAATAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 2 0.06
23 8 0.25
24 4 0.12
25 13 0.41
26 5 0.16
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (21 bp):
AAATATATAATAAGTATGAAA
Found at i:4492593 original size:24 final size:26
Alignment explanation
Indices: 4492564--4492626 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
4492554 ATATACGAAG
*
4492564 CAATTTAAAGTAGA-TAATATA-AA-A
1 CAATTTAAAATA-ATTAATATATAACA
4492588 CAATTTAAAATAATTAATATATAACA
1 CAATTTAAAATAATTAATATATAACA
*
4492614 TAATTTAAAATAA
1 CAATTTAAAATAA
4492627 AATAAAGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 1 0.03
24 18 0.53
25 2 0.06
26 13 0.38
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (26 bp):
CAATTTAAAATAATTAATATATAACA
Found at i:4492899 original size:28 final size:28
Alignment explanation
Indices: 4492853--4492940 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
4492843 AAAATAACAG
*
4492853 TATGTAAAGACTTAAAAAATAAATAATGTA
1 TATG-AAAGA-TTTAAAAATAAATAATGTA
* *
4492883 TATGAAAGATTTAAAAATGATAGTAA-ATA
1 TATGAAAGATTTAAAAAT-A-AATAATGTA
* *
4492912 TAT-AAAAATTT-AAAACAAATAATGTA
1 TATGAAAGATTTAAAAATAAATAATGTA
4492938 TAT
1 TAT
4492941 ATGTATAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
25 4 0.08
26 6 0.12
27 4 0.08
28 15 0.31
29 11 0.23
30 8 0.17
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (28 bp):
TATGAAAGATTTAAAAATAAATAATGTA
Found at i:4495406 original size:7 final size:7
Alignment explanation
Indices: 4495394--4495424 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4495384 ATGAATTTTT
4495394 TTTATAA
1 TTTATAA
4495401 TTTATAA
1 TTTATAA
*
4495408 TTTATCA
1 TTTATAA
4495415 TTTATAA
1 TTTATAA
4495422 TTT
1 TTT
4495425 TCTATTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTATAA
Found at i:4501272 original size:375 final size:375
Alignment explanation
Indices: 4500582--4501334 Score: 1506
Period size: 375 Copynumber: 2.0 Consensus size: 375
4500572 TAGTGATTGA
4500582 AATCTAATGAATATTCATAATTAAAATTACAAGTATTATTGAAATTGTGTAAATGAGGACTAGTT
1 AATCTAATGAATATTCATAATTAAAATTACAAGTATTATTGAAATTGTGTAAATGAGGACTAGTT
4500647 TGAAAGAGGTGTAAAAGTGTAGTGAAATCATAGAAATTGTGAAACTTTACATTTGAGAATAAATA
66 TGAAAGAGGTGTAAAAGTGTAGTGAAATCATAGAAATTGTGAAACTTTACATTTGAGAATAAATA
4500712 ATGTGAATCCAGTGACATTTGAATGCCCACGTAGATTAGCGTGGAACTTCATGGCATGCCATAGG
131 ATGTGAATCCAGTGACATTTGAATGCCCACGTAGATTAGCGTGGAACTTCATGGCATGCCATAGG
4500777 AACCCAAGCACTCCCGTGTTAATCATGATATTCATGATGTTGCACTTTGGTGCCTCCTATTCTGT
196 AACCCAAGCACTCCCGTGTTAATCATGATATTCATGATGTTGCACTTTGGTGCCTCCTATTCTGT
4500842 TATTCACTTTGGTGCCTGTGTTTCCAACACTTTTGTGCTTTGTGTAATGTGATATTTTCCATGTA
261 TATTCACTTTGGTGCCTGTGTTTCCAACACTTTTGTGCTTTGTGTAATGTGATATTTTCCATGTA
4500907 CCCATCTCGTTCAAATGTGATTAGCATGGGCTAAAAAGTCGTGGTAAGTG
326 CCCATCTCGTTCAAATGTGATTAGCATGGGCTAAAAAGTCGTGGTAAGTG
4500957 AATCTAATGAATATTCATAATTAAAATTACAAGTATTATTGAAATTGTGTAAATGAGGACTAGTT
1 AATCTAATGAATATTCATAATTAAAATTACAAGTATTATTGAAATTGTGTAAATGAGGACTAGTT
4501022 TGAAAGAGGTGTAAAAGTGTAGTGAAATCATAGAAATTGTGAAACTTTACATTTGAGAATAAATA
66 TGAAAGAGGTGTAAAAGTGTAGTGAAATCATAGAAATTGTGAAACTTTACATTTGAGAATAAATA
4501087 ATGTGAATCCAGTGACATTTGAATGCCCACGTAGATTAGCGTGGAACTTCATGGCATGCCATAGG
131 ATGTGAATCCAGTGACATTTGAATGCCCACGTAGATTAGCGTGGAACTTCATGGCATGCCATAGG
4501152 AACCCAAGCACTCCCGTGTTAATCATGATATTCATGATGTTGCACTTTGGTGCCTCCTATTCTGT
196 AACCCAAGCACTCCCGTGTTAATCATGATATTCATGATGTTGCACTTTGGTGCCTCCTATTCTGT
4501217 TATTCACTTTGGTGCCTGTGTTTCCAACACTTTTGTGCTTTGTGTAATGTGATATTTTCCATGTA
261 TATTCACTTTGGTGCCTGTGTTTCCAACACTTTTGTGCTTTGTGTAATGTGATATTTTCCATGTA
4501282 CCCATCTCGTTCAAATGTGATTAGCATGGGCTAAAAAGTCGTGGTAAGTG
326 CCCATCTCGTTCAAATGTGATTAGCATGGGCTAAAAAGTCGTGGTAAGTG
4501332 AAT
1 AAT
4501335 TCTGATAACA
Statistics
Matches: 378, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
375 378 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (375 bp):
AATCTAATGAATATTCATAATTAAAATTACAAGTATTATTGAAATTGTGTAAATGAGGACTAGTT
TGAAAGAGGTGTAAAAGTGTAGTGAAATCATAGAAATTGTGAAACTTTACATTTGAGAATAAATA
ATGTGAATCCAGTGACATTTGAATGCCCACGTAGATTAGCGTGGAACTTCATGGCATGCCATAGG
AACCCAAGCACTCCCGTGTTAATCATGATATTCATGATGTTGCACTTTGGTGCCTCCTATTCTGT
TATTCACTTTGGTGCCTGTGTTTCCAACACTTTTGTGCTTTGTGTAATGTGATATTTTCCATGTA
CCCATCTCGTTCAAATGTGATTAGCATGGGCTAAAAAGTCGTGGTAAGTG
Found at i:4509332 original size:27 final size:27
Alignment explanation
Indices: 4509302--4509356 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
4509292 ACAATATTGG
*
4509302 TAATTAAAGCAT-TATATACTATTAGAA
1 TAATT-AAGCATATATATACTAGTAGAA
*
4509329 TAATTAATCATATATATACTAGTAGAA
1 TAATTAAGCATATATATACTAGTAGAA
4509356 T
1 T
4509357 GCGAGTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (27 bp):
TAATTAAGCATATATATACTAGTAGAA
Found at i:4513102 original size:135 final size:135
Alignment explanation
Indices: 4512912--4513278 Score: 441
Period size: 135 Copynumber: 2.7 Consensus size: 135
4512902 TGTATCTGAC
* * * * *
4512912 CTGCTCCACTCTTGTTCAGCGGAGACAATATCTGATATATTTAGCCTGCTTCACTCCTGCTCAGT
1 CTGCTCCACTCCTGCTCAGCGAAGAAAAGATCTGATATATTTAGCCTGCTTCACTCCTGCTCAGT
* * *
4512977 GAAGATAAGTCTGATGATTGAAATCTGCTCCATCGCTAG-TACAGGGAGATAAGATTCACCAAAA
66 GAAGATAAGGCTGATGATTGAAATCTGCTCCATCG-TAGATACAGGGAGATAAAACTCACCAAAA
4513041 TTCGAT
130 TTCGAT
* * * * *
4513047 CTGCTCCGCTCCTGCTCAGCGAAGATAAGATCTGCTATACTTAGCCTGCTTCACTCCTACTCAGT
1 CTGCTCCACTCCTGCTCAGCGAAGAAAAGATCTGATATATTTAGCCTGCTTCACTCCTGCTCAGT
* * * *
4513112 GAAGATAAGGCTGATGATT-AGAATCTGCTCCATTGTCGATACATGGAGATAAAACTCGCCAAAA
66 GAAGATAAGGCTGATGATTGA-AATCTGCTCCATCGTAGATACAGGGAGATAAAACTCACCAAAA
*
4513176 TTTGAT
130 TTCGAT
* * * * * * * *
4513182 CTGCTTCACTCCTACTCAGTGAAGAAAAGATCAGGTATGTTTAGCCTGCTCCACTTCTGCTCAGT
1 CTGCTCCACTCCTGCTCAGCGAAGAAAAGATCTGATATATTTAGCCTGCTTCACTCCTGCTCAGT
* **
4513247 GAAGATAAGGCTGGTGGCTGAAATCTGCTCCA
66 GAAGATAAGGCTGATGATTGAAATCTGCTCCA
4513279 CTCCTATTCA
Statistics
Matches: 197, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
134 3 0.02
135 193 0.98
136 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (135 bp):
CTGCTCCACTCCTGCTCAGCGAAGAAAAGATCTGATATATTTAGCCTGCTTCACTCCTGCTCAGT
GAAGATAAGGCTGATGATTGAAATCTGCTCCATCGTAGATACAGGGAGATAAAACTCACCAAAAT
TCGAT
Found at i:4513290 original size:44 final size:44
Alignment explanation
Indices: 4513227--4513346 Score: 186
Period size: 44 Copynumber: 2.7 Consensus size: 44
4513217 TATGTTTAGC
* * *
4513227 CTGCTCCACTTCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAAT
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGACTGGTGGCTGAAAG
**
4513271 CTGCTCCACTCCTATTCAGTGAAGATAAGACTGGTGGCTGAAAG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGACTGGTGGCTGAAAG
*
4513315 CTGCTCCACCCCTGCTCAGTGAAGATAAGACT
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGACT
4513347 TCGCCAAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (44 bp):
CTGCTCCACTCCTGCTCAGTGAAGATAAGACTGGTGGCTGAAAG
Found at i:4521148 original size:21 final size:21
Alignment explanation
Indices: 4521124--4521168 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4521114 GCTAGCTCAT
*
4521124 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
* *
4521145 CATGTTTTTCTGGGACTCTAG
1 CATGTTGTTCTGGGACTCCAG
4521166 CAT
1 CAT
4521169 TTGATCCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:4528147 original size:26 final size:26
Alignment explanation
Indices: 4528111--4528214 Score: 172
Period size: 26 Copynumber: 4.0 Consensus size: 26
4528101 ACAAATTGAC
*
4528111 AATGGGTTAGGTAAATGTTCCATGAT
1 AATGGGTTAGGTAAATATTCCATGAT
*
4528137 AATGGATTAGGTAAATATTCCATGAT
1 AATGGGTTAGGTAAATATTCCATGAT
4528163 AATGGGTTAGGTAAATATTCCATGAT
1 AATGGGTTAGGTAAATATTCCATGAT
* *
4528189 AATGGTTTAGGTAAATGTTCCATGAT
1 AATGGGTTAGGTAAATATTCCATGAT
4528215 GGGCATTTCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.36
Consensus pattern (26 bp):
AATGGGTTAGGTAAATATTCCATGAT
Found at i:4534150 original size:46 final size:45
Alignment explanation
Indices: 4534101--4534315 Score: 197
Period size: 46 Copynumber: 4.7 Consensus size: 45
4534091 GGGCATCGAA
*
4534101 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGA-T-GCGAATGTCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGACTAG-GAA--TCCGAG
*** * *
4534147 CTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GACTAGGAATCCGAG
*** * *
4534194 CTCG-TGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GACTAGGAATCCGAG
* *
4534240 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGA-T-GCGAACGCCCAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGACTAG-GAA-TCCGAG
4534285 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4534316 GCGGGTTACA
Statistics
Matches: 149, Mismatches: 13, Indels: 15
0.84 0.07 0.08
Matches are distributed among these distances:
43 1 0.01
44 3 0.02
45 36 0.24
46 73 0.49
47 31 0.21
48 1 0.01
49 3 0.02
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (45 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGACTAGGAATCCGAG
Found at i:4537327 original size:29 final size:29
Alignment explanation
Indices: 4537259--4537342 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
4537249 CATAGTATCA
* * * * *
4537259 TATCTTGGGTTTATTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGG-TTTCTC
4537289 TAT-TCTGGATTTCTTTATTCTGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGTTTCTC
4537318 TATCTTGGATTTCTTTATTC-GGTTT
1 TATCTTGGATTTCTTTATTCTGGTTT
4537343 TCTTGTTATC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 5 0.11
29 23 0.49
30 19 0.40
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.57
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCTGGTTTCTC
Found at i:4537346 original size:14 final size:15
Alignment explanation
Indices: 4537272--4537346 Score: 84
Period size: 15 Copynumber: 5.1 Consensus size: 15
4537262 CTTGGGTTTA
* *
4537272 TTTATCCTGGATCTC
1 TTTATTCTGGATTTC
4537287 TTTATTCTGGATTTC
1 TTTATTCTGGATTTC
4537302 TTTATTCTGG-TTTC
1 TTTATTCTGGATTTC
*
4537316 TCTA-TCTTGGATTTC
1 TTTATTC-TGGATTTC
*
4537331 TTTATTC-GGTTTTC
1 TTTATTCTGGATTTC
4537345 TT
1 TT
4537347 GTTATCTTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
13 2 0.04
14 18 0.35
15 30 0.58
16 2 0.04
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.59
Consensus pattern (15 bp):
TTTATTCTGGATTTC
Found at i:4539767 original size:46 final size:45
Alignment explanation
Indices: 4539714--4539982 Score: 253
Period size: 46 Copynumber: 5.8 Consensus size: 45
4539704 TATTTGGGCA
4539714 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
4539760 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *** * *
4539807 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
4539854 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*
4539900 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*
4539946 -CCTAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4539983 GCGGGTTACA
Statistics
Matches: 201, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
43 1 0.00
44 3 0.01
45 4 0.02
46 109 0.54
47 79 0.39
48 1 0.00
49 3 0.01
50 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:4539829 original size:47 final size:47
Alignment explanation
Indices: 4539760--4539882 Score: 237
Period size: 47 Copynumber: 2.6 Consensus size: 47
4539750 GATGCGAATG
*
4539760 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
4539807 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
4539854 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC
4539883 ACTTATGGAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (47 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
Found at i:4541673 original size:23 final size:24
Alignment explanation
Indices: 4541642--4541686 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
4541632 TAATTGTATA
*
4541642 TATTAATTAAAATA-TATTTTATT
1 TATTAATTAAAAAATTATTTTATT
*
4541665 TATTTATTAAAAAATTATTTTA
1 TATTAATTAAAAAATTATTTTA
4541687 AATTTTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTAATTAAAAAATTATTTTATT
Found at i:4552989 original size:62 final size:62
Alignment explanation
Indices: 4552921--4553090 Score: 286
Period size: 62 Copynumber: 2.7 Consensus size: 62
4552911 TTAAATTTAA
* * * *
4552921 TATTTATCTAGATTTTAATATGAGATATTAAATTAAATTTAATATTTATCTAGATAGTATTT
1 TATTTATTTAGATATTAATATGAGATATTAAATTAAATTTAATATTTATCTAGACAATATTT
*
4552983 TATTTATTTAGATATTAATATGAGATATTAAATTAAATTAAATATTTATCTAGACAATATTT
1 TATTTATTTAGATATTAATATGAGATATTAAATTAAATTTAATATTTATCTAGACAATATTT
*
4553045 TATTTATTTAGATATTAATATGAGATATTAAATTTAATTTAATATT
1 TATTTATTTAGATATTAATATGAGATATTAAATTAAATTTAATATT
4553091 AATGTGATTA
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 101 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (62 bp):
TATTTATTTAGATATTAATATGAGATATTAAATTAAATTTAATATTTATCTAGACAATATTT
Found at i:4556157 original size:21 final size:22
Alignment explanation
Indices: 4556128--4556168 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4556118 TTCATATATT
*
4556128 ATAACTAAAAT-TTTTTAACTA
1 ATAACTAAAATATGTTTAACTA
*
4556149 ATAATTAAAATATGTTTAAC
1 ATAACTAAAATATGTTTAAC
4556169 ATATTCTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (22 bp):
ATAACTAAAATATGTTTAACTA
Found at i:4559547 original size:46 final size:46
Alignment explanation
Indices: 4559441--4559708 Score: 349
Period size: 52 Copynumber: 5.6 Consensus size: 46
4559431 TTTGAGTACT
* *
4559441 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTC-GCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
4559486 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
4559532 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
4559584 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
4559636 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
4559682 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
4559709 GCTACACTTA
Statistics
Matches: 207, Mismatches: 9, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
45 34 0.16
46 79 0.38
52 94 0.45
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:4559666 original size:98 final size:97
Alignment explanation
Indices: 4559441--4559708 Score: 341
Period size: 98 Copynumber: 2.7 Consensus size: 97
4559431 TTTGAGTACT
* *
4559441 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGCTATACTTATCTGATCAAGTGAC------
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGCTACACTTATCTGATCAAGTGACAAGTGA
4559500 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
4559532 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTC-GCTACACTTATCTGATCAAGTGA
* *
4559597 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
59 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * *
4559636 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGC-TTCGCTACACTTATCTGATCAAGTGAC-AAGT
*
4559701 GATAAGTG
64 GAAAAGTG
4559709 GCTACACTTA
Statistics
Matches: 154, Mismatches: 8, Indels: 22
0.84 0.04 0.12
Matches are distributed among these distances:
91 13 0.08
97 21 0.14
98 64 0.42
99 13 0.08
104 43 0.28
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (97 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGCTACACTTATCTGATCAAGTGACAAGTGA
AAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:4559716 original size:37 final size:37
Alignment explanation
Indices: 4559672--4559817 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
4559662 GATAGCTTTA
*
4559672 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
4559709 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
4559746 GCTACACTTATCTGATTAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
4559783 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
4559818 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:4564466 original size:16 final size:15
Alignment explanation
Indices: 4564445--4564474 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4564435 AATGAGTCAG
4564445 AAATTAATAAGTAAAA
1 AAATTAATAA-TAAAA
4564461 AAATTAATAATAAA
1 AAATTAATAATAAA
4564475 TTTTGGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAATTAATAATAAAA
Found at i:4569180 original size:47 final size:47
Alignment explanation
Indices: 4569119--4569225 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 47
4569109 TTTAATATGA
* *
4569119 TCTATTTTCCATATATGT-TATTATCTTTCC-TTTCTCATTTTTTATTC
1 TCTATTTTCCATATAT-TCTATTATCTTTCCTTTTCT-ATATTTGATTC
** *
4569166 TCTATTTTTTATATATTCTATTTTCTTTCCTTTTCTATATTTGATTC
1 TCTATTTTCCATATATTCTATTATCTTTCCTTTTCTATATTTGATTC
*
4569213 TCTATTTCCCATA
1 TCTATTTTCCATA
4569226 AAGTATTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
46 1 0.02
47 44 0.88
48 5 0.10
ACGTcount: A:0.18, C:0.19, G:0.02, T:0.62
Consensus pattern (47 bp):
TCTATTTTCCATATATTCTATTATCTTTCCTTTTCTATATTTGATTC
Found at i:4569415 original size:19 final size:19
Alignment explanation
Indices: 4569393--4569459 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 19
4569383 CTCTCTCTCG
4569393 TCTCTATCTTTCTCTCATA
1 TCTCTATCTTTCTCTCATA
*
4569412 TCTCT-T-TTTTTCTCAT-
1 TCTCTATCTTTCTCTCATA
* * *
4569428 CCTTATATTTTTCTCTCATA
1 TC-TCTATCTTTCTCTCATA
* *
4569448 TTTCTTTCTTTC
1 TCTCTATCTTTC
4569460 GTACTCTTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
16 1 0.03
17 11 0.31
18 2 0.06
19 21 0.60
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (19 bp):
TCTCTATCTTTCTCTCATA
Found at i:4572307 original size:55 final size:55
Alignment explanation
Indices: 4572223--4572334 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
4572213 TATCTGCTAG
4572223 TGCGACATGATAAGTCGTTGCAGAGAGGTTGCCATTAGGGAGAAAATATAGAACA
1 TGCGACATGATAAGTCGTTGCAGAGAGGTTGCCATTAGGGAGAAAATATAGAACA
*
4572278 TGCGACATGATAAGTCGTTGCAGAGAGGTTGTCATTAGGGAGAAAATATAGAACA
1 TGCGACATGATAAGTCGTTGCAGAGAGGTTGCCATTAGGGAGAAAATATAGAACA
4572333 TG
1 TG
4572335 TAGGATGTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (55 bp):
TGCGACATGATAAGTCGTTGCAGAGAGGTTGCCATTAGGGAGAAAATATAGAACA
Found at i:4579848 original size:5 final size:5
Alignment explanation
Indices: 4579838--4579874 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
4579828 TATAAGTAAT
4579838 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
4579875 ATAATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:4580168 original size:21 final size:20
Alignment explanation
Indices: 4580127--4580171 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
4580117 TCATGTTGAA
**
4580127 TAAATTGAAGAATTAGGAGT
1 TAAATTGAAGAATTACAAGT
*
4580147 TAAATTGATAGAATTTCAAGT
1 TAAATTGA-AGAATTACAAGT
4580168 TAAA
1 TAAA
4580172 AGTGAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (20 bp):
TAAATTGAAGAATTACAAGT
Found at i:4588467 original size:17 final size:18
Alignment explanation
Indices: 4588434--4588467 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4588424 ATCAATAATT
*
4588434 CCACAATATTCAACACAA
1 CCACAATATTAAACACAA
4588452 CCACAAT-TTAAACACA
1 CCACAATATTAAACACA
4588468 CGGTTTCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (18 bp):
CCACAATATTAAACACAA
Found at i:4592584 original size:3 final size:3
Alignment explanation
Indices: 4592574--4592611 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
4592564 AACAATGATG
4592574 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4592612 TATGACAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4592893 original size:3 final size:3
Alignment explanation
Indices: 4592885--4593054 Score: 118
Period size: 3 Copynumber: 56.7 Consensus size: 3
4592875 ATAGTATGAC
* * * *
4592885 AAT AAT AAT AAT AGT AAC AAA AAT AAT AAT AAC AA- ATAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * * *
4592929 ATAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT GAC AGT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
4592975 AAT AAT ACA- AAT AAA AAC AAT AGT AAC AAC AAT AAT AGA- AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
*
4593020 AAT ACT CAA- AAT AAT AAT AA- ACAT AAT AAT AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
4593055 ATATAAGACT
Statistics
Matches: 132, Mismatches: 23, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
2 7 0.05
3 119 0.90
4 6 0.05
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:4594520 original size:47 final size:47
Alignment explanation
Indices: 4594411--4594521 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
4594401 TCGGGATAAG
* *
4594411 CACATAGTGCTTCATCGGAACAAATCCGGGACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
4594458 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
4594505 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
4594522 ACTCAAGGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:4597364 original size:62 final size:62
Alignment explanation
Indices: 4597279--4597421 Score: 205
Period size: 62 Copynumber: 2.3 Consensus size: 62
4597269 TTATGCGATG
* * * * * *
4597279 AACAGTAAGTTACACGGCCTGGGCACACGCCTGTGTCTCTGGCCGTATGGTTTTATACCATA
1 AACAGTGAGTTACACGGCTTGGGCACACACCCGTGTCCCTGACCGTATGGTTTTATACCATA
*
4597341 AACAGTGAGTTACACGGCTTGGGCACACACCCGTGTCCCTGACCGTGTGGTTTTATACCATA
1 AACAGTGAGTTACACGGCTTGGGCACACACCCGTGTCCCTGACCGTATGGTTTTATACCATA
* *
4597403 AACAATGAGTTACAAGGCT
1 AACAGTGAGTTACACGGCT
4597422 GTTCGCACTG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (62 bp):
AACAGTGAGTTACACGGCTTGGGCACACACCCGTGTCCCTGACCGTATGGTTTTATACCATA
Found at i:4598019 original size:15 final size:14
Alignment explanation
Indices: 4598001--4598042 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
4597991 TAGAAGGAAT
4598001 AAAGGAAGAAAGAAA
1 AAAGGAA-AAAGAAA
*
4598016 AAAGAAAAAAGAAA
1 AAAGGAAAAAGAAA
4598030 AAATGGAAAAAGA
1 AAA-GGAAAAAGA
4598043 GGAAAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (14 bp):
AAAGGAAAAAGAAA
Found at i:4598030 original size:6 final size:7
Alignment explanation
Indices: 4598009--4598042 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
4597999 ATAAAGGAAG
4598009 AAAGAAA
1 AAAGAAA
4598016 AAAGAAA
1 AAAGAAA
4598023 AAAGAAA
1 AAAGAAA
*
4598030 AAATGGAA
1 AAA-GAAA
4598038 AAAGA
1 AAAGA
4598043 GGAAAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:4598717 original size:18 final size:18
Alignment explanation
Indices: 4598686--4598733 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
4598676 ATATATAAAG
*
4598686 AATATTATATAAAATT-T
1 AATATTAAATAAAATTGT
*
4598703 ATTATTGAAATAAAATTGT
1 AATATT-AAATAAAATTGT
4598722 AATATTAAATAA
1 AATATTAAATAA
4598734 TTTATCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 5 0.19
18 15 0.58
19 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATAAAATTGT
Found at i:4605918 original size:16 final size:17
Alignment explanation
Indices: 4605892--4605924 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4605882 GGTCTGTCTG
*
4605892 TATTAATTTTTTTATAA
1 TATTAATTTTTATATAA
4605909 TATT-ATTTTTATATAA
1 TATTAATTTTTATATAA
4605925 AAACAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTAATTTTTATATAA
Found at i:4607893 original size:31 final size:32
Alignment explanation
Indices: 4607858--4607917 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
4607848 TATTTTGTAC
*
4607858 TTAATTGAGCCA-TTGAACATTAAAATTATAA
1 TTAATTAAGCCATTTGAACATTAAAATTATAA
* * *
4607889 TTAATTAAGTCATTTGACCTTTAAAATTA
1 TTAATTAAGCCATTTGAACATTAAAATTA
4607918 AAGATCAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.42
32 14 0.58
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (32 bp):
TTAATTAAGCCATTTGAACATTAAAATTATAA
Found at i:4608733 original size:9 final size:8
Alignment explanation
Indices: 4608709--4608765 Score: 51
Period size: 9 Copynumber: 6.6 Consensus size: 8
4608699 CAATTTTCTA
4608709 TATATTTT
1 TATATTTT
*
4608717 AATAATTTT
1 TAT-ATTTT
4608726 CTATATTTT
1 -TATATTTT
4608735 TAATATTTT
1 T-ATATTTT
*
4608744 TATTTTTT
1 TATATTTT
*
4608752 TATAATTTA
1 TAT-ATTTT
4608761 TATAT
1 TATAT
4608766 CATGTTAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
8 14 0.35
9 24 0.60
10 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (8 bp):
TATATTTT
Found at i:4608799 original size:21 final size:21
Alignment explanation
Indices: 4608775--4608831 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
4608765 TCATGTTAAT
*
4608775 AATTTTTAATATTTTTTCTCC
1 AATTTTTAATATATTTTCTCC
*
4608796 AATTTTTTATATATTTTCT-C
1 AATTTTTAATATATTTTCTCC
* *
4608816 -ATTTTAAATAAATTTT
1 AATTTTTAATATATTTT
4608832 GTAGTTTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 13 0.42
20 1 0.03
21 17 0.55
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (21 bp):
AATTTTTAATATATTTTCTCC
Found at i:4608913 original size:29 final size:28
Alignment explanation
Indices: 4608880--4608960 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
4608870 TTTCTTCTAT
*
4608880 TTTTTATAATCTTTAATATGTTTAATATG-
1 TTTTTATAAT-TTTAATATATTT-ATATGA
* *
4608909 TTTTTAATAATTTTTATATATTTGTATGAA
1 TTTTT-ATAATTTTAATATATTTATATG-A
*
4608939 TTTTTATAATTTTAATAAATTT
1 TTTTTATAATTTTAATATATTT
4608961 TCAATAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.09
29 30 0.68
30 10 0.23
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.60
Consensus pattern (28 bp):
TTTTTATAATTTTAATATATTTATATGA
Found at i:4608927 original size:20 final size:20
Alignment explanation
Indices: 4608880--4608961 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
4608870 TTTCTTCTAT
*
4608880 TTTTTATA-ATCTTTAAT-A
1 TTTTTATATATTTTTAATAA
* *
4608898 TGTTTAATATGTTTTTAATAA
1 T-TTTTATATATTTTTAATAA
*
4608919 TTTTTATATATTTGT-ATGAA
1 TTTTTATATATTTTTAAT-AA
4608939 TTTTTATA-A-TTTTAATAAA
1 TTTTTATATATTTTTAAT-AA
4608958 TTTT
1 TTTT
4608962 CAATAATTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
18 4 0.08
19 17 0.33
20 28 0.55
21 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTTATATATTTTTAATAA
Found at i:4609629 original size:15 final size:15
Alignment explanation
Indices: 4609603--4609640 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
4609593 TTTGATGAAA
*
4609603 TTAATA-TTATTTTT
1 TTAATATTTATTTTC
4609617 TTAATATTTATTTTC
1 TTAATATTTATTTTC
4609632 TTAA-ATTTA
1 TTAATATTTA
4609641 GTCTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTAATATTTATTTTC
Found at i:4623305 original size:7 final size:7
Alignment explanation
Indices: 4623294--4623337 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
4623284 ATGCATCCCT
*
4623294 CAACATT
1 CAACATG
*
4623301 CAACATT
1 CAACATG
4623308 CAACATG
1 CAACATG
4623315 CAACATG
1 CAACATG
4623322 CAACATG
1 CAACATG
4623329 CAACATG
1 CAACATG
4623336 CA
1 CA
4623338 TGCATGCATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.43, C:0.30, G:0.09, T:0.18
Consensus pattern (7 bp):
CAACATG
Found at i:4626230 original size:23 final size:25
Alignment explanation
Indices: 4626181--4626230 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
4626171 CTTCTAATAG
* *
4626181 TATATATTTTTATAAATTTATATTT
1 TATATATTTTTATAAATTAATAATT
4626206 TATATATTTTTA-AAA-TAATAATT
1 TATATATTTTTATAAATTAATAATT
4626229 TA
1 TA
4626231 AAATATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 3 0.13
25 12 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATATATTTTTATAAATTAATAATT
Found at i:4628693 original size:20 final size:20
Alignment explanation
Indices: 4628635--4628697 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 20
4628625 TCCATTAAAT
* * *
4628635 TATTAAATGTCATAAAATAT
1 TATTAAATATTATAAAATAC
* *
4628655 TA-AAAAAATT-TAAAA-AC
1 TATTAAATATTATAAAATAC
4628672 TATTAAATATTATAAAATAC
1 TATTAAATATTATAAAATAC
4628692 TATTAA
1 TATTAA
4628698 TAATTTATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 3 0.09
18 11 0.33
19 9 0.27
20 10 0.30
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (20 bp):
TATTAAATATTATAAAATAC
Found at i:4635469 original size:16 final size:16
Alignment explanation
Indices: 4635445--4635491 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
4635435 GCAAAATAGT
*
4635445 TGTTATTCAGAACAAC
1 TGTTGTTCAGAACAAC
*
4635461 TGTTGTTCAAGAATAAC
1 TGTTGTTC-AGAACAAC
*
4635478 T-ATGTTCAGAACAA
1 TGTTGTTCAGAACAA
4635492 GACTTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 6 0.23
16 12 0.46
17 8 0.31
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (16 bp):
TGTTGTTCAGAACAAC
Found at i:4636890 original size:26 final size:25
Alignment explanation
Indices: 4636842--4636897 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
4636832 ATTAAAAAAG
*
4636842 AAAAAAAATTATGAAAGATAAGGGAA
1 AAAAAAAATTATGAAAAATAA-GGAA
4636868 ATAAAAAAA-TA-GAAAAATTAAGGAA
1 A-AAAAAAATTATGAAAAA-TAAGGAA
4636893 AAAAA
1 AAAAA
4636898 TTAAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 10 0.37
26 6 0.22
27 7 0.26
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (25 bp):
AAAAAAAATTATGAAAAATAAGGAA
Found at i:4643836 original size:3 final size:3
Alignment explanation
Indices: 4643828--4643854 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4643818 TAAGGAAAAT
4643828 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
4643855 CAAACCCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4644155 original size:17 final size:17
Alignment explanation
Indices: 4644133--4644170 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
4644123 TTAGTCTATG
4644133 TAATTTA-TTTTTATTT
1 TAATTTAGTTTTTATTT
4644149 ATAATTTAGTTTTTATTT
1 -TAATTTAGTTTTTATTT
4644167 TAAT
1 TAAT
4644171 AATATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TAATTTAGTTTTTATTT
Found at i:4644769 original size:17 final size:17
Alignment explanation
Indices: 4644747--4644779 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4644737 GTTTACTTTC
4644747 TTATATAATT-TTTAAAT
1 TTATAT-ATTATTTAAAT
4644764 TTATATATTATTTAAA
1 TTATATATTATTTAAA
4644780 AATTAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATATTATTTAAAT
Found at i:4651366 original size:31 final size:32
Alignment explanation
Indices: 4651297--4651367 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
4651287 AAGTTTAAGT
4651297 TTAAAAAA-TTATTAAAATTATACATTAATAA
1 TTAAAAAATTTATTAAAATTATACATTAATAA
* *
4651328 -CATAAAAATTTATTAAAA-TAT-TATTAAATAA
1 TTA-AAAAATTTATTAAAATTATACATT-AATAA
4651359 TTAAAAAAT
1 TTAAAAAAT
4651368 AATATATGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
30 4 0.12
31 19 0.58
32 10 0.30
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (32 bp):
TTAAAAAATTTATTAAAATTATACATTAATAA
Found at i:4653765 original size:21 final size:21
Alignment explanation
Indices: 4653740--4653799 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
4653730 AAAAATAGCG
*
4653740 GTAGCGGTGAGATCAG-TTATT
1 GTAGCGGTGAGAT-AGAATATT
*
4653761 GTAGCGGTGAGATTGAATATT
1 GTAGCGGTGAGATAGAATATT
4653782 GTAGCGGTGAGATTAGAA
1 GTAGCGGTGAGA-TAGAA
4653800 ACAATGGTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.85
22 4 0.12
ACGTcount: A:0.28, C:0.07, G:0.35, T:0.30
Consensus pattern (21 bp):
GTAGCGGTGAGATAGAATATT
Found at i:4655867 original size:32 final size:33
Alignment explanation
Indices: 4655799--4655928 Score: 183
Period size: 33 Copynumber: 4.0 Consensus size: 33
4655789 CATAAAAAAT
*
4655799 ATCATACATTAGTTTTACATATAAAAAAAGTCG
1 ATCATACATTAGTTTTACATATAAAAAAAGTAG
* * *
4655832 ATCATACATTAGGTTTACATAT-AACAAAGTTG
1 ATCATACATTAGTTTTACATATAAAAAAAGTAG
**
4655864 ATCATACATTAGTTTTGTATATAAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAAGTAG
*
4655897 ATAATACATTAGTTTTACATAT-AAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAAGTAG
4655929 TATAGTTATA
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
32 37 0.44
33 48 0.56
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (33 bp):
ATCATACATTAGTTTTACATATAAAAAAAGTAG
Found at i:4655873 original size:65 final size:65
Alignment explanation
Indices: 4655799--4655926 Score: 202
Period size: 65 Copynumber: 2.0 Consensus size: 65
4655789 CATAAAAAAT
* * *
4655799 ATCATACATTAGTTTTACATATAAAAAAAGTCGATCATACATTAGGTTTACATATAACAAAGTTG
1 ATCATACATTAGTTTTACATATAAAAAAAGTAGATAATACATTAGGTTTACATATAAAAAAGTTG
** *
4655864 ATCATACATTAGTTTTGTATATAAAAAAAGTAGATAATACATTAGTTTTACATATAAAAAAGT
1 ATCATACATTAGTTTTACATATAAAAAAAGTAGATAATACATTAGGTTTACATATAAAAAAGT
4655927 AGTATAGTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.35
Consensus pattern (65 bp):
ATCATACATTAGTTTTACATATAAAAAAAGTAGATAATACATTAGGTTTACATATAAAAAAGTTG
Found at i:4657289 original size:30 final size:30
Alignment explanation
Indices: 4657255--4657317 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
4657245 ATTTATTTTA
4657255 TTGTTAATTTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTCTTATTATTTTAGAA-GCAT
*
4657285 TTGTTAATTTTTTTATTATTTTAGAAGCAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAT
4657315 TTG
1 TTG
4657318 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAGAAGCAT
Found at i:4659156 original size:22 final size:22
Alignment explanation
Indices: 4659117--4659165 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
4659107 ACTTTTTTTC
*
4659117 ATTATTTTGCTATAATTTCACT
1 ATTATATTGCTATAATTTCACT
* * * *
4659139 ATTATATTGTTATTATTTTATT
1 ATTATATTGCTATAATTTCACT
4659161 ATTAT
1 ATTAT
4659166 TGTTTGAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (22 bp):
ATTATATTGCTATAATTTCACT
Found at i:4660178 original size:12 final size:12
Alignment explanation
Indices: 4660161--4660186 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4660151 ACCACGTGGA
4660161 AATTACGTGGCC
1 AATTACGTGGCC
4660173 AATTACGTGGCC
1 AATTACGTGGCC
4660185 AA
1 AA
4660187 AATATATTAT
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:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (12 bp):
AATTACGTGGCC
Found at i:4664926 original size:17 final size:17
Alignment explanation
Indices: 4664904--4664936 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4664894 TTTGGGAAAC
*
4664904 ATTTTAGGTTTGGGTTG
1 ATTTTAGGTTCGGGTTG
4664921 ATTTTAGGTTCGGGTT
1 ATTTTAGGTTCGGGTT
4664937 CAAGTTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.33, T:0.52
Consensus pattern (17 bp):
ATTTTAGGTTCGGGTTG
Found at i:4665133 original size:16 final size:16
Alignment explanation
Indices: 4665114--4665154 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4665104 GTAATTTCAA
4665114 GTTCATGTTAACGTGG
1 GTTCATGTTAACGTGG
* *
4665130 GTTCATGTCAACTTGG
1 GTTCATGTTAACGTGG
4665146 GTT-ATGTTA
1 GTTCATGTTA
4665155 GAGGTTTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (16 bp):
GTTCATGTTAACGTGG
Found at i:4668341 original size:35 final size:35
Alignment explanation
Indices: 4668301--4668371 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
4668291 GCAAAGTTGG
4668301 TTCTGGGATTTAGTTCTTAGTATTGATTCAAAAGT
1 TTCTGGGATTTAGTTCTTAGTATTGATTCAAAAGT
4668336 TTCTGGGATTTAGTTCTTAGTATTGATTCAAAAGT
1 TTCTGGGATTTAGTTCTTAGTATTGATTCAAAAGT
4668371 T
1 T
4668372 CAACAATCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.46
Consensus pattern (35 bp):
TTCTGGGATTTAGTTCTTAGTATTGATTCAAAAGT
Done.