Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 18 of 318
Found at i:4714212 original size:76 final size:76
Alignment explanation
Indices: 4714132--4714357 Score: 266
Period size: 76 Copynumber: 3.0 Consensus size: 76
4714122 GTTAAGTTTC
* *
4714132 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
4714197 CTGTCTTTCAA
66 CTGTCTTTCAA
* *
4714208 AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGA-A-GCTGAGG--TTTTCCATTT
1 AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
*
4714269 CTGTGTTTC--
66 CTGTCTTTCAA
* * * ** *
4714278 AAAAAATCAGCTCATATTGCGAGTGATGGAGTTGAGCCTTGACTCACACGCTAAGGTATTTTCAA
1 AAAAAATCAGCTCATATTGCGAGAGGT-GAGTTGAGCC-TCA-AGACACGCTGAGGTATTTTCAA
* *
4714343 ATTCTGTTTTTCAA
63 TTTCTGTCTTTCAA
4714357 A
1 A
4714358 TTTTGTTTTT
Statistics
Matches: 126, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
70 25 0.20
71 9 0.07
72 19 0.15
73 1 0.01
74 7 0.06
75 7 0.06
76 41 0.33
77 16 0.13
79 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (76 bp):
AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
CTGTCTTTCAA
Found at i:4714372 original size:15 final size:14
Alignment explanation
Indices: 4714336--4714368 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4714326 CGCTAAGGTA
4714336 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
4714350 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
4714364 TTTTC
1 TTTTC
4714369 CAAAAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:4714703 original size:13 final size:13
Alignment explanation
Indices: 4714685--4714735 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
4714675 TATATACATC
4714685 ATAATAAAAAAAT
1 ATAATAAAAAAAT
*
4714698 ATAATAAAAATAT
1 ATAATAAAAAAAT
*
4714711 ATATACAAAACAAAT
1 ATA-ATAAAA-AAAT
4714726 ATAA-AAAAAA
1 ATAATAAAAAA
4714736 TTACATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 2 0.06
13 19 0.58
14 6 0.18
15 6 0.18
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAATAAAAAAAT
Found at i:4719132 original size:25 final size:24
Alignment explanation
Indices: 4719092--4719161 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
4719082 TTTTGGGTTT
*
4719092 ACACAGTTTGGGACACAGG-CTGTC
1 ACACAGCTTGGGACAC-GGCCTGTC
4719116 ACACAGCTTGAGGACACGGCCTGTC
1 ACACAGCTTG-GGACACGGCCTGTC
* *
4719141 ACACAGCCTGGTGACATGGCC
1 ACACAGCTTGG-GACACGGCC
4719162 GTGTGTCATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
24 12 0.30
25 28 0.70
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.17
Consensus pattern (24 bp):
ACACAGCTTGGGACACGGCCTGTC
Found at i:4720806 original size:2 final size:2
Alignment explanation
Indices: 4720799--4720829 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4720789 GACCTCAAGG
4720799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4720830 GATAATAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4723696 original size:13 final size:13
Alignment explanation
Indices: 4723678--4723703 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4723668 ATACTTAGTA
4723678 CTGATAATGTGTT
1 CTGATAATGTGTT
4723691 CTGATAATGTGTT
1 CTGATAATGTGTT
4723704 AAATATAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
CTGATAATGTGTT
Found at i:4726849 original size:27 final size:27
Alignment explanation
Indices: 4726819--4726870 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
4726809 TTTGAGAGAT
4726819 AGACATTCCGAGAAATTATTTTTATTG
1 AGACATTCCGAGAAATTATTTTTATTG
*
4726846 AGACATTCTGAGAAATTATTTTTAT
1 AGACATTCCGAGAAATTATTTTTAT
4726871 CGCAACATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (27 bp):
AGACATTCCGAGAAATTATTTTTATTG
Found at i:4730720 original size:5 final size:5
Alignment explanation
Indices: 4730710--4730740 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
4730700 TACTAAAGGA
4730710 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
4730741 GAGGAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4735425 original size:2 final size:2
Alignment explanation
Indices: 4735418--4735466 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
4735408 TGTATCAAAT
4735418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4735460 TA TA TA T
1 TA TA TA T
4735467 TACATTAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4739402 original size:304 final size:303
Alignment explanation
Indices: 4738920--4739765 Score: 842
Period size: 308 Copynumber: 2.7 Consensus size: 303
4738910 CTCGGTGAGA
* * * *
4738920 AAATTACAGGAATGCACATCCATAATTAAAATAAAG-AATATTTTTTGATGGAATTTTAGTCTTT
1 AAATTACAGGAATGCACATCCTTAATTAAAAT-AAGTAATATTATTT-AGGGTATTTTAGTCTTT
* * * ** * *
4738984 TCACTTTAAAAATCAATAAAAATCAAGGATATAGT-AGGATTCAAACCCATGCCAAGTGCATTAG
64 TCACTTTAAAAAT-AATAAAAAT-ATGCATATGGTGA-GATTTGAACCCACGCCAATTGCATTA-
*
4739048 TAAAACCTTTAATTTACCACTCAACTAAAGCTTCGTTTTAATATTTTTATACATTTTATTTTTAT
125 TAAAACCTTTAATTTACCACTCAACTAAA-CTTC-TTTTAATATTTTTATACATTTTAATTTTAT
* * * *
4739113 TTTGCACACTTTATTA-T-CTCCA-TTA-A-ATGTATA-TT-TATATCTACCTATACTATTGTTT
188 TATGCACACTTTATTACTCCACCAGTTATATATCTATACTTGTATAT-TACCTATACTATTATTT
* * * *
4739171 AAACTCTTGACTGAGTT-AGTGTCGCAAGTCAACCGAGT-ACCAACT-AATTGGTTAGG
252 AAACTCCTG-CTGAGTTGA-CGTCAC-ACTCAACCGAGTCACCAACTCAA----TTAGG
4739227 AAATTACAGGAATGCACATCCTTAATTAAAATAAGTAATATTATTTAGGGTATTTTAGTCTTTTC
1 AAATTACAGGAATGCACATCCTTAATTAAAATAAGTAATATTATTTAGGGTATTTTAGTCTTTTC
* * * * * *
4739292 AATTTAAAAATGAATAAAAATATGTATATGGTGAGATTTGAATCTACACAAATTGCATTATAAAA
66 ACTTTAAAAAT-AATAAAAATATGCATATGGTGAGATTTGAACCCACGCCAATTGCATTATAAAA
*
4739357 CCTTTAATTTACCACTCAACTAAACATTCATTTTAATATTTTTATAAATTTTAATTTTATTATGC
130 CCTTTAATTTACCACTCAACTAAAC-TTC-TTTTAATATTTTTATACATTTTAATTTTATTATGC
** *
4739422 ACA-TTCTATTACTTCCACCAGTTATATATCTATACTTGTATATTATTTATACTATTATTTAAGC
193 ACACTT-TATTAC-TCCACCAGTTATATATCTATACTTGTATATTACCTATACTATTATTTAAAC
* * * *
4739486 TCCTGTTGTGTTGACGTCACCCTCAACCGGGTCACCAACTCAATTAGG
256 TCCTGCTGAGTTGACGTCACACTCAACCGAGTCACCAACTCAATTAGG
* * * ** * * *
4739534 AAGTTATAGGAATGC-CCTTTTGTAATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTT
1 AAATTACAGGAATGCACATCCT-TAATTAAAATAAGTAATATTATT-TAGGGTATTTTAGTCTTT
* * * *
4739598 TCACTTAAAAAACTAATAAAAATATACATATGGCGAAATTTGAACCCACGCCAATTGCATTAATA
64 TCACTTTAAAAA-TAATAAAAATATGCATATGGTGAGATTTGAACCCACGCCAATTGCATT-ATA
** *
4739663 AAATATTTAATTTACCA-TGCAACTAAAGTT-TTTATATATATTTTTATACATTTTAATTTTATT
127 AAACCTTTAATTTACCACT-CAACTAAACTTCTTT-TA-ATATTTTTATACATTTTAATTTTATT
* * * *
4739726 ATGCACACTTTATTACCTTCATCAGTTGTTTATCTATACT
189 ATGCACACTTTATTA-CTCCACCAGTTATATATCTATACT
4739766 ATTATTTAAA
Statistics
Matches: 454, Mismatches: 61, Indels: 47
0.81 0.11 0.08
Matches are distributed among these distances:
303 3 0.01
304 72 0.16
305 26 0.06
306 47 0.10
307 86 0.19
308 127 0.28
309 40 0.09
310 22 0.05
311 26 0.06
312 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (303 bp):
AAATTACAGGAATGCACATCCTTAATTAAAATAAGTAATATTATTTAGGGTATTTTAGTCTTTTC
ACTTTAAAAATAATAAAAATATGCATATGGTGAGATTTGAACCCACGCCAATTGCATTATAAAAC
CTTTAATTTACCACTCAACTAAACTTCTTTTAATATTTTTATACATTTTAATTTTATTATGCACA
CTTTATTACTCCACCAGTTATATATCTATACTTGTATATTACCTATACTATTATTTAAACTCCTG
CTGAGTTGACGTCACACTCAACCGAGTCACCAACTCAATTAGG
Found at i:4740817 original size:21 final size:21
Alignment explanation
Indices: 4740793--4740832 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4740783 GTCAACAACC
4740793 AAATGTTCACACAAACAGATA
1 AAATGTTCACACAAACAGATA
**
4740814 AAATGTTCTGACAAACAGA
1 AAATGTTCACACAAACAGA
4740833 CGTATATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.20
Consensus pattern (21 bp):
AAATGTTCACACAAACAGATA
Found at i:4742984 original size:22 final size:23
Alignment explanation
Indices: 4742952--4742996 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
4742942 ATTGTTGTGC
*
4742952 ATTTAGTATTGTTAATTTGATGT
1 ATTTAGTATTGTTAATTTCATGT
4742975 ATTTA-TATTGTTAATTTCATGT
1 ATTTAGTATTGTTAATTTCATGT
4742997 GTTATTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (23 bp):
ATTTAGTATTGTTAATTTCATGT
Found at i:4748511 original size:40 final size:39
Alignment explanation
Indices: 4748467--4748572 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 39
4748457 TACTAGCTCA
* *
4748467 AAGCCTGCGGAACTTTAAGCCCAGATAT-AGTACCAGCACT
1 AAGCCTGCGGGA-TTTAA-CCCAGATATAAGTACCAGCACG
* * *
4748507 AAGCCTGCGGGATTTAACTCGGATATACATTACCAGCACG
1 AAGCCTGCGGGATTTAACCCAGATATA-AGTACCAGCACG
*
4748547 AAGCCTGCGGGATTTAACCTAGATAT
1 AAGCCTGCGGGATTTAACCCAGATAT
4748573 TTAATATATC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 7 0.12
39 5 0.09
40 44 0.79
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (39 bp):
AAGCCTGCGGGATTTAACCCAGATATAAGTACCAGCACG
Found at i:4751682 original size:63 final size:63
Alignment explanation
Indices: 4751583--4751709 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 63
4751573 CATGAGGACT
* *
4751583 CGACAGTATCACCAGTCGAAGGACTATGCTCATGTGCACTAGTAAGACCAGCCGGAGACGATC
1 CGACAGTATCACCAGTAGAAGGACTATGCTCATGTGCACCAGTAAGACCAGCCGGAGACGATC
* * *
4751646 CGACAGTATCACTAGTTAG-AGGACTA-GACTCATGTGCACCATTAAGACCAGCTGGAGACGATC
1 CGACAGTATCACCAG-TAGAAGGACTATG-CTCATGTGCACCAGTAAGACCAGCCGGAGACGATC
4751709 C
1 C
4751710 TGAAGAAGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
62 1 0.02
63 54 0.95
64 2 0.04
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (63 bp):
CGACAGTATCACCAGTAGAAGGACTATGCTCATGTGCACCAGTAAGACCAGCCGGAGACGATC
Found at i:4754666 original size:17 final size:17
Alignment explanation
Indices: 4754635--4754678 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
4754625 TGATAGAGTT
4754635 GAAAGAAAA-TGGAGAG
1 GAAAGAAAATTGGAGAG
4754651 GAAAGAAAATTGGAGAG
1 GAAAGAAAATTGGAGAG
*
4754668 G-TAGAAAATTG
1 GAAAGAAAATTG
4754679 TTTTTTCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (17 bp):
GAAAGAAAATTGGAGAG
Found at i:4754995 original size:23 final size:24
Alignment explanation
Indices: 4754962--4755009 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4754952 TTCTCTTCTC
*
4754962 TTCTCTCCTCT-TTCATTCTCATT
1 TTCTCTCCTCTAATCATTCTCATT
* *
4754985 TTCTCTTCTCTAATCATTCTTATT
1 TTCTCTCCTCTAATCATTCTCATT
4755009 T
1 T
4755010 GAAATGATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.58
Consensus pattern (24 bp):
TTCTCTCCTCTAATCATTCTCATT
Found at i:4765120 original size:3 final size:3
Alignment explanation
Indices: 4765114--4765143 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4765104 CCCCTTTTTT
4765114 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4765144 GCACGAGTTT
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):
TAA
Found at i:4766152 original size:17 final size:17
Alignment explanation
Indices: 4766130--4766162 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4766120 GATATGATAC
4766130 TAAAAT-TATTAAAAAAT
1 TAAAATATA-TAAAAAAT
4766147 TAAAATATATAAAAAA
1 TAAAATATATAAAAAA
4766163 GGGAAACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATATATAAAAAAT
Found at i:4766449 original size:22 final size:21
Alignment explanation
Indices: 4766414--4766508 Score: 65
Period size: 18 Copynumber: 4.7 Consensus size: 21
4766404 AAAAGGTATC
* * *
4766414 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
4766435 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
4766458 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
4766477 TGC-AATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
4766495 TGCATATCATATCT
1 TACAAATCATATCT
4766509 AAGATTGCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
18 17 0.27
19 17 0.27
21 4 0.06
22 15 0.24
23 9 0.15
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:4766474 original size:19 final size:19
Alignment explanation
Indices: 4766450--4766523 Score: 141
Period size: 19 Copynumber: 3.9 Consensus size: 19
4766440 AATCATATCT
4766450 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
4766469 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
4766487 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
4766506 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
4766524 TGAAGATTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.33
19 36 0.67
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:4766496 original size:37 final size:38
Alignment explanation
Indices: 4766443--4766523 Score: 141
Period size: 37 Copynumber: 2.2 Consensus size: 38
4766433 ATTACAAAAT
4766443 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
4766479 CA-ATCATATCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
4766516 CATATCAT
1 CATATCAT
4766524 TGAAGATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
35 3 0.07
36 3 0.07
37 31 0.74
38 5 0.12
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGATTG
Found at i:4766543 original size:37 final size:37
Alignment explanation
Indices: 4766453--4766532 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
4766443 CATATCTTCT
* *
4766453 AAGATTGCATATCATATCTAAGATTGCAATCATATCT
1 AAGATTACATATCATATCTAAGATTGCAATCATATCG
*
4766490 AAGATTGCATATCATATCTAAGATTGCATATCAT-T-G
1 AAGATTACATATCATATCTAAGATTGCA-ATCATATCG
4766526 AAGATTA
1 AAGATTA
4766533 TATTTCCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 6 0.15
37 29 0.73
38 5 0.12
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (37 bp):
AAGATTACATATCATATCTAAGATTGCAATCATATCG
Found at i:4766680 original size:21 final size:20
Alignment explanation
Indices: 4766642--4766681 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4766632 TTGGATTTCG
* *
4766642 TTTTTTTTTTTGGTTTATTA
1 TTTTTGTTTTTGGCTTATTA
4766662 TTTTTGTTTTTGGACTTATT
1 TTTTTGTTTTTGG-CTTATT
4766682 TCTGGGCTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.10, C:0.03, G:0.12, T:0.75
Consensus pattern (20 bp):
TTTTTGTTTTTGGCTTATTA
Found at i:4766929 original size:45 final size:45
Alignment explanation
Indices: 4766874--4767064 Score: 231
Period size: 45 Copynumber: 4.3 Consensus size: 45
4766864 AGAAGGCTAT
* * *
4766874 ATCTGCTATCTTTAATCTGCTCCCTGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCAATCTGCTCCCCGTCTAATACAGAGACGCCAA
**
4766919 ATCTGTTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCAATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * *
4766964 ATCTGCT-TCTTCAATCTGCTCCTCGTCTAATATAGAGATGCCAA
1 ATCTGTTATCTTCAATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * * * *
4767008 ATCTGTTATCTCCGATTTGCTCCCCGTCTAATATAAAGATGCCAA
1 ATCTGTTATCTTCAATCTGCTCCCCGTCTAATACAGAGACGCCAA
*
4767053 ATCTGTCATCTT
1 ATCTGTTATCTT
4767065 GGATCTGATT
Statistics
Matches: 128, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
44 38 0.30
45 90 0.70
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.34
Consensus pattern (45 bp):
ATCTGTTATCTTCAATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:4767001 original size:89 final size:90
Alignment explanation
Indices: 4766874--4767057 Score: 264
Period size: 89 Copynumber: 2.1 Consensus size: 90
4766864 AGAAGGCTAT
* **
4766874 ATCTGCTATCTTTAATCTGCTCCCTGTCTAATACAGAGACGCCAAATCTGTTATCTTTGATCTGC
1 ATCTGCTATCTTCAATCTGCTCCCTGTCTAATACAGAGACGCCAAATCTGTTATCTCCGATCTGC
*
4766939 TCCCCGTCTAATACAGAGACGCCAA
66 TCCCCGTCTAATACAAAGACGCCAA
* * *
4766964 ATCTGCT-TCTTCAATCTGCT-CCTCGTCTAATATAGAGATGCCAAATCTGTTATCTCCGATTTG
1 ATCTGCTATCTTCAATCTGCTCCCT-GTCTAATACAGAGACGCCAAATCTGTTATCTCCGATCTG
* *
4767027 CTCCCCGTCTAATATAAAGATGCCAA
65 CTCCCCGTCTAATACAAAGACGCCAA
4767053 ATCTG
1 ATCTG
4767058 TCATCTTGGA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
88 3 0.04
89 74 0.88
90 7 0.08
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (90 bp):
ATCTGCTATCTTCAATCTGCTCCCTGTCTAATACAGAGACGCCAAATCTGTTATCTCCGATCTGC
TCCCCGTCTAATACAAAGACGCCAA
Found at i:4767216 original size:78 final size:78
Alignment explanation
Indices: 4767087--4767381 Score: 448
Period size: 78 Copynumber: 3.8 Consensus size: 78
4767077 ATGTAAACAC
* *
4767087 ATGAAGGTCAGATCTGCTATGTCTTCAATCTACTCCCCGTATAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCT
*
4767152 TGGATCTGGTTCA
66 TGGATCTGCTTCA
* *
4767165 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATC
*
4767229 TTGGATCTGCTTTA
65 TTGGATCTGCTTCA
*
4767243 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCT
*
4767308 TGGGTCTGCTTCA
66 TGGATCTGCTTCA
* * * ** *
4767321 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGTCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATC
4767382 TGTTTCTTCG
Statistics
Matches: 197, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
77 2 0.01
78 193 0.98
79 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:4767906 original size:220 final size:219
Alignment explanation
Indices: 4767323--4767910 Score: 908
Period size: 220 Copynumber: 2.7 Consensus size: 219
4767313 CTGCTTCAAT
* *
4767323 GAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGTCAAATCTGTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
*** *
4767388 TTCGATTTGTTCTCTGA-AAGTACAGAGATACCAAATCATCTTAGATCTGCTTCAGCATAAACAC
66 TTCGATTTGTTCTCTGACAA-TACAGAGATGTTAAATCATCTTAGATCTGCTTCAGCGTAAACAC
4767452 GTGAAAGCAAAATCTGCTATGTCCTCGATCTGCTCCTTGTCAACGCAAGGATGCCAAATCATCTT
130 GTGAAAGC-AAATCTGCTATGTCCTCGATCTGCTCCTTGTCAACGCAAGGATGCCAAATCATCTT
*
4767517 GGATCTACTTCGATGTGAAGACATCC
194 GGATCTACTTCGATGTGAAAACATCC
* * *
4767543 TAAGGTTAAATCTGCTATGTCTTCGATCTGCTCTTCGTCGAATATGGAGATGCCAAATCTGTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
* * *
4767608 TTCGATTTGTTCTCTGTCAATACAGAGATGTTAAATTATTTTAGATCTGCTTCAGCGTAAACACG
66 TTCGATTTGTTCTCTGACAATACAGAGATGTTAAATCATCTTAGATCTGCTTCAGCGTAAACACG
* *
4767673 TGAAAGCCAAATCTGTTATGTCTTCGATCTGCTCCTTGTCAACGCAAGGATGCCAAATCATCTTG
131 TGAAAG-CAAATCTGCTATGTCCTCGATCTGCTCCTTGTCAACGCAAGGATGCCAAATCATCTTG
*
4767738 GATCTACTTCGATTTGAAAACATCC
195 GATCTACTTCGATGTGAAAACATCC
* * *
4767763 GAAGGTTAGATCTGCTATGTCTTCGATATGCTCTCCTTCGAATATGGAGATGCCAAATCTATTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
* * * *
4767828 TTCGATTTGTTCTCTGACAATACAGAGATGTTAAATCATCTTGGATCCGCTTCAACGTAAACACC
66 TTCGATTTGTTCTCTGACAATACAGAGATGTTAAATCATCTTAGATCTGCTTCAGCGTAAACACG
* *
4767893 TGGAGGTCAAATCTGCTA
131 TGAAAG-CAAATCTGCTA
4767911 CGCTTTAGCC
Statistics
Matches: 333, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
220 330 0.99
221 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (219 bp):
GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
TTCGATTTGTTCTCTGACAATACAGAGATGTTAAATCATCTTAGATCTGCTTCAGCGTAAACACG
TGAAAGCAAATCTGCTATGTCCTCGATCTGCTCCTTGTCAACGCAAGGATGCCAAATCATCTTGG
ATCTACTTCGATGTGAAAACATCC
Found at i:4770619 original size:21 final size:20
Alignment explanation
Indices: 4770582--4770620 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4770572 CCCAATTCCA
**
4770582 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
4770602 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
4770621 TTTGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:4771017 original size:17 final size:17
Alignment explanation
Indices: 4770995--4771027 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4770985 TATTTAGAAG
*
4770995 ATTAAATTTTTTTTATA
1 ATTAAATTATTTTTATA
4771012 ATTAAATTATTTTTAT
1 ATTAAATTATTTTTAT
4771028 TAAATATGCT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTAAATTATTTTTATA
Found at i:4774336 original size:26 final size:26
Alignment explanation
Indices: 4774300--4774372 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
4774290 TGATACAAAT
*
4774300 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
4774326 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
4774352 TGATAATAGGTTAGGTAAATG
1 TGATAATAGGTTAGGTAAATG
4774373 GGTTAGGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:4774378 original size:13 final size:13
Alignment explanation
Indices: 4774360--4774385 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4774350 CATGATAATA
4774360 GGTTAGGTAAATG
1 GGTTAGGTAAATG
4774373 GGTTAGGTAAATG
1 GGTTAGGTAAATG
4774386 TTCCATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (13 bp):
GGTTAGGTAAATG
Found at i:4774382 original size:65 final size:65
Alignment explanation
Indices: 4774308--4774437 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
4774298 ATTGATAATA
*
4774308 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG
1 GGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG
*
4774373 GGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATG
1 GGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG
4774438 TTTCATGATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (65 bp):
GGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG
Found at i:4774388 original size:39 final size:39
Alignment explanation
Indices: 4774334--4774411 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
4774324 CATGATAATA
4774334 GGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG
1 GGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG
4774373 GGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG
1 GGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG
4774412 TTCCATGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (39 bp):
GGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG
Found at i:4774409 original size:26 final size:26
Alignment explanation
Indices: 4774369--4774474 Score: 185
Period size: 26 Copynumber: 4.1 Consensus size: 26
4774359 AGGTTAGGTA
4774369 AATGGGTTAGGTAAATGTTCCATGAT
1 AATGGGTTAGGTAAATGTTCCATGAT
*
4774395 AATAGGTTAGGTAAATGTTCCATGAT
1 AATGGGTTAGGTAAATGTTCCATGAT
*
4774421 AATGGGTTAGGTAAATGTTTCATGAT
1 AATGGGTTAGGTAAATGTTCCATGAT
*
4774447 AATGGGTTAGGTAAATGTTTCATGAT
1 AATGGGTTAGGTAAATGTTCCATGAT
4774473 AA
1 AA
4774475 GAATTTCATG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
AATGGGTTAGGTAAATGTTCCATGAT
Found at i:4776189 original size:27 final size:27
Alignment explanation
Indices: 4776091--4776194 Score: 122
Period size: 27 Copynumber: 3.8 Consensus size: 27
4776081 AAGCGTTCTG
* *
4776091 GTGGCTATGCCACAAATATCTG-ATCTA
1 GTGGCTCTGCCAC-ATTATCTGTATCTA
*
4776118 GTGGCTCTGCCACATATATCTGT-TCTG
1 GTGGCTCTGCCACAT-TATCTGTATCTA
4776145 GTGGCTCTGCCACGATTATCTGTATCTA
1 GTGGCTCTGCCAC-ATTATCTGTATCTA
* *
4776173 GTGACTCTGTCACATTATCTGT
1 GTGGCTCTGCCACATTATCTGT
4776195 TCTGGCAGCC
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.01
27 50 0.75
28 16 0.24
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACATTATCTGTATCTA
Found at i:4776192 original size:54 final size:54
Alignment explanation
Indices: 4776085--4776199 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
4776075 TGGAGGAAGC
*
4776085 GTTCTGGTGGCTATGCCACAAATATCTGATCTAGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCT
* * * *
4776139 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTAGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTAGTGACTCTGCCACATATATCT
4776193 GTTCTGG
1 GTTCTGG
4776200 CAGCCATACT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCT
Found at i:4780663 original size:3 final size:3
Alignment explanation
Indices: 4780645--4780693 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
4780635 TTTAATGAGA
*
4780645 TAT T-T TAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
4780690 TAT T
1 TAT T
4780694 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:4780665 original size:11 final size:11
Alignment explanation
Indices: 4780649--4780687 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
4780639 ATGAGATATT
4780649 TTATTATTTTA
1 TTATTATTTTA
*
4780660 TTATTATTTCA
1 TTATTATTTTA
4780671 TTATTATTTTA
1 TTATTATTTTA
4780682 TTATTA
1 TTATTA
4780688 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:4780673 original size:19 final size:19
Alignment explanation
Indices: 4780645--4780686 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
4780635 TTTAATGAGA
*
4780645 TATTTTATTATT-TTATTAT
1 TATTTCATTATTATT-TTAT
4780664 TATTTCATTATTATTTTAT
1 TATTTCATTATTATTTTAT
4780683 TATT
1 TATT
4780687 AATTATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTCATTATTATTTTAT
Found at i:4782884 original size:46 final size:46
Alignment explanation
Indices: 4782830--4783415 Score: 824
Period size: 46 Copynumber: 13.0 Consensus size: 46
4782820 GCTCTCTGAA
*
4782830 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
4782876 -TAGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 AT-GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
4782922 -TAGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 AT-GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
4782968 ATGAAATGTGCAAGACCATGGTTGAAAGATACTATGGAAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
4783014 ATGAAATGTGCAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
4783060 -TAGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 AT-GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
4783106 -TGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
4783151 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** *
4783197 ATGAAA-GAATAAGACCATGGTTGAAAGATACCATAGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
4783242 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCA-GAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-CATGAT
* *
4783288 ATGAAATGTGTAAGACCA----TG---CA-ACCATGGCAACGTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** *
4783326 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
4783372 A-GAAATTGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATGAAA-TGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
4783416 TCAAAGATAA
Statistics
Matches: 491, Mismatches: 33, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
37 1 0.00
38 28 0.06
39 1 0.00
42 4 0.01
45 90 0.18
46 364 0.74
47 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:4783341 original size:38 final size:38
Alignment explanation
Indices: 4783272--4783345 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
4783262 GTTGAAAGAT
***
4783272 ACCATGGCAACCAGATATGAAATGTGTAAGACCATGCA
1 ACCATGGCAACCAGATATGAAATGAACAAGACCATGCA
**
4783310 ACCATGGCAACGTGATATGAAATGAACAAGACCATG
1 ACCATGGCAACCAGATATGAAATGAACAAGACCATG
4783346 GTTGAAAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.18
Consensus pattern (38 bp):
ACCATGGCAACCAGATATGAAATGAACAAGACCATGCA
Found at i:4783385 original size:84 final size:84
Alignment explanation
Indices: 4783226--4783390 Score: 235
Period size: 84 Copynumber: 2.0 Consensus size: 84
4783216 GTTGAAAGAT
*** *
4783226 ACCATAGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCAGATATG
1 ACCATAGCAACATGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCAGACATG
*
4783291 AAATGTGTAAGACCATGCA
66 AAATGAGTAAGACCATGCA
* *
4783310 ACCATGGCAACGTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAA-CATGACA-
1 ACCATAGCAACATGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCA-GACAT
4783373 GAAATTGAGTAAGACCAT
65 GAAA-TGAGTAAGACCAT
4783391 AGTTGAAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
83 6 0.08
84 66 0.92
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (84 bp):
ACCATAGCAACATGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCAGACATG
AAATGAGTAAGACCATGCA
Found at i:4791445 original size:3 final size:3
Alignment explanation
Indices: 4791437--4791470 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4791427 GGAAAAAATA
4791437 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4791471 GTGACAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4792457 original size:475 final size:476
Alignment explanation
Indices: 4791728--4792682 Score: 1707
Period size: 475 Copynumber: 2.0 Consensus size: 476
4791718 AAAAAGAAAA
*
4791728 AAATAGATAAATGTATAAATATATAACTAAATACATACAAAGGAAAATAAAATATAAAAGATCGA
1 AAATAGATAAATGTAAAAATATATAACTAAATACATACAAAGGAAAATAAAATATAAAAGATCGA
* * *
4791793 AAGTAAGGGACTAAATTAGTATCTAAACAAAATTTAAAGTAAAAATCATAATAGAATAAACAAAT
66 AAGTAAAGGACTAAATCAGGATCTAAACAAAATTTAAAGTAAAAATCATAATAGAATAAACAAAT
* * *
4791858 TAAACAATAAAATAAGGTAAGGGATTAAAATCAAATGCGTGAAGGAAAGATAGGGATCAATTAGG
131 TAAACAATAAAATAAGGTAAGGGATTAAAATCAAATGCGCGAAGGAAAGACAGCGATCAATTAGG
4791923 CAATAATCCCCTTGTCCCTTAAACGCAGCTTTTCATGAAGGACCAAAATAAAACAAAACCAAATT
196 CAATAATCCCCTTGTCCCTTAAACGCAGCTTTTCATGAAGGACCAAAATAAAACAAAACCAAATT
*
4791988 TTGTGGCAAAATTACAAAAGAAAAAGAAATAAAAAGAAGGGATTGGATTGAAAAACAAATAAAAG
261 TTGTGGCAAAATTACAAAAGAAAAAGAAATAAAAAGAAGGGACTGGATTGAAAAACAAATAAAAG
*
4792053 GCGAAAGGCTAGGGATCGCAATAAACCTTTTTGTAGCGAAAACACGCAGATCTTGCCAGCTCTCG
326 GCAAAAGGCTAGGGATCGCAATAAACCTTTTTGTAGCGAAAACACGCAGATCTTGCCAGCTCTCG
* *
4792118 AGTCGAATCTCCGGTTGCTTCGAAATGATGCCATTTTGGTGCTTCTGAGCACCAGCCAAAACGAC
391 AGTCGAATCTCAGGTTGCTTCGAAACGATGCCATTTTGGTGCTTCTGAGCACCAGCCAAAACGAC
4792183 GCCGTTAAACTAT-TCCTATAT
456 GCCGTTAAACTATCT-CTATAT
4792204 AAATAGATAAATGTAAAAATATATAACTAAATACATACAAAGGAAAATAAAATATAAAAGATCGA
1 AAATAGATAAATGTAAAAATATATAACTAAATACATACAAAGGAAAATAAAATATAAAAGATCGA
4792269 AAGTAAAGGACTAAATCAGGATCTAAACAAAATTTAAAGTAAAAATCATAATAGAAT-AACAAAT
66 AAGTAAAGGACTAAATCAGGATCTAAACAAAATTTAAAGTAAAAATCATAATAGAATAAACAAAT
4792333 TAAACAATAAAATAAGGTAAGGGATTAAAATCAAATGCGCGAAGGAAAGACAGCGATCAATTAGG
131 TAAACAATAAAATAAGGTAAGGGATTAAAATCAAATGCGCGAAGGAAAGACAGCGATCAATTAGG
* *
4792398 CAATAATCCCCTTGTCTCTTAAACGCAGCTTTTCATGAAGGACCAAAATGAAACAAAACCAAATT
196 CAATAATCCCCTTGTCCCTTAAACGCAGCTTTTCATGAAGGACCAAAATAAAACAAAACCAAATT
*
4792463 TTGTGGCAAAATTACAAAATAAAAAGAAATAAAAAGAAGGGACTGGATTGAAAAACAAATAAAAG
261 TTGTGGCAAAATTACAAAAGAAAAAGAAATAAAAAGAAGGGACTGGATTGAAAAACAAATAAAAG
* * * *
4792528 GCAAAAGGCTAGGGATTGCAATAAACCTTTTTGTCGCGAAACCACGCAGATCTTGCTAGCTCTCG
326 GCAAAAGGCTAGGGATCGCAATAAACCTTTTTGTAGCGAAAACACGCAGATCTTGCCAGCTCTCG
*
4792593 AGTCGAATCTCAGGTTGCTTCGAAACGATGCCATTTTGGTGCTTCTGAGCACCAGCCAAAACGCC
391 AGTCGAATCTCAGGTTGCTTCGAAACGATGCCATTTTGGTGCTTCTGAGCACCAGCCAAAACGAC
*
4792658 GCCGTTTAACTATCTCTATAT
456 GCCGTTAAACTATCTCTATAT
4792679 AAAT
1 AAAT
4792683 CAATTTTTTT
Statistics
Matches: 458, Mismatches: 20, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
475 339 0.74
476 119 0.26
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (476 bp):
AAATAGATAAATGTAAAAATATATAACTAAATACATACAAAGGAAAATAAAATATAAAAGATCGA
AAGTAAAGGACTAAATCAGGATCTAAACAAAATTTAAAGTAAAAATCATAATAGAATAAACAAAT
TAAACAATAAAATAAGGTAAGGGATTAAAATCAAATGCGCGAAGGAAAGACAGCGATCAATTAGG
CAATAATCCCCTTGTCCCTTAAACGCAGCTTTTCATGAAGGACCAAAATAAAACAAAACCAAATT
TTGTGGCAAAATTACAAAAGAAAAAGAAATAAAAAGAAGGGACTGGATTGAAAAACAAATAAAAG
GCAAAAGGCTAGGGATCGCAATAAACCTTTTTGTAGCGAAAACACGCAGATCTTGCCAGCTCTCG
AGTCGAATCTCAGGTTGCTTCGAAACGATGCCATTTTGGTGCTTCTGAGCACCAGCCAAAACGAC
GCCGTTAAACTATCTCTATAT
Found at i:4793931 original size:51 final size:51
Alignment explanation
Indices: 4793855--4793981 Score: 184
Period size: 51 Copynumber: 2.5 Consensus size: 51
4793845 TTCAATTTGC
* *
4793855 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTA-GCTTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCAACTT-TAGGCTTTAATCTAT
* ** *
4793906 TCCACTACAACTTCAGGGAGATAAGATTTGCGGCTTTAGGCTTTAGTCTAT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCAACTTTAGGCTTTAATCTAT
4793957 TCCACTGCAACTTCAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAG
4793982 GCTTGCTATG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 2 0.03
51 66 0.97
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (51 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGCAACTTTAGGCTTTAATCTAT
Found at i:4794152 original size:89 final size:88
Alignment explanation
Indices: 4794040--4794597 Score: 515
Period size: 89 Copynumber: 6.3 Consensus size: 88
4794030 GGGCTTGTCA
* * **
4794040 CTTCAATCTACTCCACTGTAACTTCAAGGAGATAAGATTAGTGGCTTCAATCTGCTCCACTACAA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT-GTAACTTCAATCTGCTCCACTACAA
4794105 CTTCAGGGAGATAAGATTTGCTAT
65 CTTCAGGGAGATAAGATTTGCTAT
* * * * * * **
4794129 CTTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATCTTTAACTTCAATTTGTTCCACTGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGAT-TGTAACTTCAATCTGCTCCACTACAA
* *
4794194 CTTCAGGGAAATAAGATTCGCTAT
65 CTTCAGGGAGATAAGATTTGCTAT
* * * * * * * *
4794218 CTTCATTCTGCTCCATTGTAACATCAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTGCAA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TTGTAACTTCAATCTGCTCCACTACAA
* *
4794283 CTTTAGGGAGATAA-AGTTT-ATAAT
65 CTTCAGGGAGATAAGA-TTTGCT-AT
* * *
4794307 -TTTAATCTGCTCTACTGCAACTTC-AGAGAGATAAGATTTGATATCTTCAATCTGCTCCACTAC
1 CTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGA-TTG-TAACTTCAATCTGCTCCACTAC
* * * *
4794370 AACTTCAAGAAGATAAGACTTG-TAA
63 AACTTCAGGGAGATAAGATTTGCTAT
* * * * * * *
4794395 CTTCAACCTGCTCCACTACAACTTTAAGGAGATAAGGTT-TATAGCTTTAATCTGCTCTATTGA-
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTGTA-A-CTTCAATCTGCTCCACT-AC
**
4794458 AACTTCAGATAGATAAGATTTGCTAT
63 AACTTCAGGGAGATAAGATTTGCTAT
* * *
4794484 CTTCAATCTGCTCCACTGCCACTTCAGGGAGATAAGACTTGTAACTTCAA-CTTGCTCCACTGCA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TTGTAACTTCAATC-TGCTCCACTACA
*
4794548 ACTTCAGGGAAATAAGATTTGC-AT
64 ACTTCAGGGAGATAAGATTTGCTAT
*
4794572 CTTCAATCTG-TCCCACTGTAACTTCA
1 CTTCAATCTGCT-CCACTGCAACTTCA
4794598 CAAGTATAAG
Statistics
Matches: 375, Mismatches: 75, Indels: 39
0.77 0.15 0.08
Matches are distributed among these distances:
86 2 0.01
87 2 0.01
88 92 0.25
89 269 0.72
90 8 0.02
91 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (88 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTGTAACTTCAATCTGCTCCACTACAAC
TTCAGGGAGATAAGATTTGCTAT
Found at i:4794198 original size:133 final size:133
Alignment explanation
Indices: 4793718--4794597 Score: 668
Period size: 133 Copynumber: 6.5 Consensus size: 133
4793708 GTAGCCTCGT
* * * * *
4793718 TCTAATCCACTGCAACTTCAGGG-G-TATAGAAATTGTCACTTCAATCTGTTCCACTATAACTTC
1 TCTACTCCACTGCAACTTTAGGGAGATA-AG-ATTTGTAACTTCAATCTGTTCCACTGTAACTTC
* * * * * * *
4793781 AGGGAGATAAGATTAG-TAGCTTTAATATGTTCCACTGCAACTTTAGGGAAATAAGA-TTCGTAT
64 AAGGAGATAAGATTAGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTAA
4793844 CTTCAA
128 CTTCAA
* * * **
4793850 TTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTACA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAAC-T-T--C---AATCTGTTCCACTGTA
* * * * **
4793915 ACTTCAGGGAGATAAGATTTGCGGCTTTAGGCTTTAGTCTATTCCACTGCAACTTCAGGGAGATA
59 ACTTCAAGGAGATAAGA-TT--AGC--TA-GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
* **
4793980 AGGCTTGCTATGGTAGATCTAA
118 AGACTTG-TA----ACTTC-AA
* * * ** * **
4794002 TCTGAC-CTACTGCAACTTTAGAGG-TATAGGGCTTGTCACTTCAATCTACTCCACTGTAACTTC
1 TCT-ACTCCACTGCAACTTTAG-GGAGATAAGATTTGTAACTTCAATCTGTTCCACTGTAACTTC
* * * *
4794065 AAGGAGATAAGATTAG-TGGCTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGCTAT
64 AAGGAGATAAGATTAGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAA
4794129 CTTCAA
128 CTTCAA
*
4794135 TCTACTCCACTGCAACTTTAGGGAGATAAGATCTT-TAACTTCAATTTGTTCCACTGTAACTTCA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGAT-TTGTAACTTCAATCTGTTCCACTGTAACTTCA
* * * * * * * *
4794199 GGGAAATAAGATTCGCTATCTTCATTCTGCTCCATTGTAACATCAGGGAGATAAGACTTGTAACT
65 AGGAGATAAGATTAGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACT
4794264 TCAA
130 TCAA
* * * * * * *
4794268 CCTACTCCACTGCAACTTTAGGGAGATAA-AGTTTATAATTTTAATCTGCTCTACTGCAACTTC-
1 TCTACTCCACTGCAACTTTAGGGAGATAAGA-TTTGTAACTTCAATCTGTTCCACTGTAACTTCA
* * * * * *
4794331 AGAGAGATAAGATTTGATATCTTCAATCTGCTCCACTACAACTTCAAGAAGATAAGACTTGTAAC
65 AG-GAGATAAGATTAGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAC
4794396 TTCAA
129 TTCAA
* * * * * * * * * * * *
4794401 CCTGCTCCACTACAACTTTAAGGAGATAAGGTTTATAGCTTTAATCTGCTCTATTGAAACTTC-A
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAATCTGTTCCACTGTAACTTCAA
* * * *
4794465 GATAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCCACTTCAGGGAGATAAGACTTGTAACT
66 G-GAGATAAGATTAGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACT
4794530 TCAA
130 TCAA
* * * * * *
4794534 -CTTGCTCCACTGCAACTTCAGGGAAATAAGATTTGCATCTTCAATCTGTCCCACTGTAACTTCA
1 TC-TACTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAATCTGTTCCACTGTAACTTCA
4794598 CAAGTATAAG
Statistics
Matches: 604, Mismatches: 109, Indels: 68
0.77 0.14 0.09
Matches are distributed among these distances:
132 36 0.06
133 345 0.57
134 43 0.07
136 1 0.00
138 38 0.06
139 33 0.05
140 2 0.00
142 2 0.00
144 2 0.00
145 30 0.05
146 33 0.05
147 4 0.01
148 1 0.00
150 1 0.00
151 3 0.00
152 27 0.04
153 3 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (133 bp):
TCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAATCTGTTCCACTGTAACTTCAA
GGAGATAAGATTAGCTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTT
CAA
Found at i:4794576 original size:44 final size:44
Alignment explanation
Indices: 4793723--4794597 Score: 620
Period size: 44 Copynumber: 19.3 Consensus size: 44
4793713 CTCGTTCTAA
* *
4793723 TCCACTGCAACTTCAGGG-G-TATAGAAATTGTCA-CTTCAATCTGT
1 TCCACTGCAACTTCAGGGAGATA-AG-ATTTGT-ATCTTCAATCTGC
** * * * * *
4793767 TCCACTATAACTTCAGGGAGATAAGATTAGTAGCTTTAATATGT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * * *
4793811 TCCACTGCAACTTTAGGGAAATAAGATTCGTATCTTCAATTTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* *
4793855 TCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGT-A----T--CTTCAATCTGC
* * * * **
4793906 TCCACTACAACTTCAGGGAGATAAGATTTGCGGCTTTAGGCTTTAGTCTAT
1 TCCACTGCAACTTCAGGGAGATAAGATTT---G---TA-TCTTCAATCTGC
** *
4793957 TCCACTGCAACTTCAGGGAGATAAGGCTTGCTATGGTAGATCTAATCTGAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TAT-CT---TC-AATCTG-C
* * * * ** *
4794008 -CTACTGCAACTTTAGAGG-TATAGGGCTTGTCA-CTTCAATCTAC
1 TCCACTGCAACTTCAG-GGAGATAAGATTTGT-ATCTTCAATCTGC
* * * **
4794051 TCCACTGTAACTTCAAGGAGATAAGATTAGTGGCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* *
4794095 TCCACTACAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTGC
* * * *
4794140 TCCACTGCAACTTTAGGGAGATAAGATCTT-TAACTTCAATTTGT
1 TCCACTGCAACTTCAGGGAGATAAGAT-TTGTATCTTCAATCTGC
* * * *
4794184 TCCACTGTAACTTCAGGGAAATAAGATTCGCTATCTTCATTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTGC
* * * * * * *
4794229 TCCATTGTAACATCAGGGAGATAAGACTTGTAACTTCAACCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * *
4794273 TCCACTGCAACTTTAGGGAGATAA-AGTTTATAAT-TTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTTGT-ATCTTCAATCTGC
* *
4794317 TCTACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTGC
* * * * * *
4794362 TCCACTACAACTTCAAGAAGATAAGACTTGTAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * * * * * *
4794406 TCCACTACAACTTTAAGGAGATAAGGTTTATAGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
* * * **
4794450 TCTATTGAAACTTCAGATAGATAAGATTTGCTATCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTGC
* * *
4794495 TCCACTGCCACTTCAGGGAGATAAGACTTGTAACTTCAA-CTTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATC-TGC
* *
4794539 TCCACTGCAACTTCAGGGAAATAAGATTTGCATCTTCAATCTG-
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
*
4794582 TCCCACTGTAACTTCA
1 T-CCACTGCAACTTCA
4794598 CAAGTATAAG
Statistics
Matches: 652, Mismatches: 139, Indels: 80
0.75 0.16 0.09
Matches are distributed among these distances:
43 8 0.01
44 379 0.58
45 149 0.23
46 7 0.01
48 2 0.00
49 3 0.00
50 27 0.04
51 73 0.11
53 1 0.00
54 1 0.00
56 1 0.00
57 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTGC
Found at i:4801324 original size:3 final size:3
Alignment explanation
Indices: 4801318--4801375 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
4801308 GAAAAAAATA
** *
4801318 AAT AAT AA- AAT AAAT AAT AGC AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4801363 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
4801376 GTGACAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4801561 original size:18 final size:19
Alignment explanation
Indices: 4801523--4801570 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
4801513 GTGCAATTTG
*
4801523 TAATAA-AATAGATAATGA
1 TAATAATAATAGATAATAA
4801541 TAATAATAATAGATAA-AA
1 TAATAATAATAGATAATAA
*
4801559 TAATTATAATAG
1 TAATAATAATAG
4801571 TGAGGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.31
Consensus pattern (19 bp):
TAATAATAATAGATAATAA
Found at i:4804386 original size:25 final size:25
Alignment explanation
Indices: 4804335--4804388 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
4804325 TCTTGCTGGG
*
4804335 TTGTCAATGTCATTGCCTTGTCTGC
1 TTGTCAATGTCATTGCCTTATCTGC
4804360 TTGTCAATGTCATTGCCTTAT-TGGC
1 TTGTCAATGTCATTGCCTTATCT-GC
4804385 TTGT
1 TTGT
4804389 TTTGTATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (25 bp):
TTGTCAATGTCATTGCCTTATCTGC
Found at i:4812676 original size:17 final size:17
Alignment explanation
Indices: 4812653--4812696 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4812643 CTTAAAATTT
4812653 ACTAATTAAACTAAAT-A
1 ACTAATTAAAC-AAATCA
* *
4812670 TCTAATTTAACAAATCA
1 ACTAATTAAACAAATCA
4812687 ACTAATTAAA
1 ACTAATTAAA
4812697 TAGCTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (17 bp):
ACTAATTAAACAAATCA
Found at i:4817115 original size:46 final size:46
Alignment explanation
Indices: 4817043--4817313 Score: 425
Period size: 46 Copynumber: 5.9 Consensus size: 46
4817033 TTCTGAAATG
*
4817043 AAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATA
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATA
*
4817089 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATA
* *
4817135 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATAGGATATA
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATA
*
4817181 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATA
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATA
* * *
4817227 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACAGA
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATA
* * * * *
4817273 AAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
4817314 TCAAAGATAA
Statistics
Matches: 209, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 209 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATA
Found at i:4817615 original size:16 final size:17
Alignment explanation
Indices: 4817594--4817626 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4817584 ATGATGGAGC
4817594 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
4817610 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
4817627 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:4822006 original size:18 final size:18
Alignment explanation
Indices: 4821985--4822029 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
4821975 GCAAAAATGA
4821985 GAAATGAATATGAAA-TAT
1 GAAATGAATATGAAACT-T
*
4822003 GAAATGAATGTGAAACTT
1 GAAATGAATATGAAACTT
4822021 GAAATGAAT
1 GAAATGAAT
4822030 TCAAGTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.20, T:0.27
Consensus pattern (18 bp):
GAAATGAATATGAAACTT
Found at i:4824101 original size:12 final size:12
Alignment explanation
Indices: 4824084--4824116 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4824074 TTGCTTGCCC
4824084 ATATTAATTTTT
1 ATATTAATTTTT
4824096 ATATT-ATTTTT
1 ATATTAATTTTT
4824107 ATA-TAATTTT
1 ATATTAATTTT
4824117 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:4824277 original size:30 final size:30
Alignment explanation
Indices: 4824243--4824302 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4824233 ATTTAACAAG
*
4824243 CAAATGTCGCTAAAATAATAACAAAATTAA
1 CAAATGTCGCTAAAATAACAACAAAATTAA
** *
4824273 CAAATGTCTTTAAAATTACAACAAAATTAA
1 CAAATGTCGCTAAAATAACAACAAAATTAA
4824303 TAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGTCGCTAAAATAACAACAAAATTAA
Found at i:4824359 original size:22 final size:22
Alignment explanation
Indices: 4824334--4824376 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4824324 TATCCAAATA
4824334 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
4824356 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
4824377 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:4824380 original size:11 final size:11
Alignment explanation
Indices: 4824341--4824381 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
4824331 ATAATAACAA
4824341 CAAAATAGTAG
1 CAAAATAGTAG
* *
4824352 CAACATAATAG
1 CAAAATAGTAG
*
4824363 TAAAATAGTAG
1 CAAAATAGTAG
4824374 CAAAATAG
1 CAAAATAG
4824382 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:4824791 original size:5 final size:6
Alignment explanation
Indices: 4824781--4824852 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 6
4824771 AATAGTATTT
* *
4824781 TATTAA T-TTAA TATTAAA GTGATT-A TTTTAA TATTAA AATTAA T-TTAA
1 TATTAA TATTAA TATT-AA -T-ATTAA TATTAA TATTAA TATTAA TATTAA
* *
4824829 TATT-A TTTTAA TATTAA AATTAA T
1 TATTAA TATTAA TATTAA TATTAA T
4824853 GTAATATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
5 16 0.31
6 28 0.55
7 3 0.06
8 1 0.02
9 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
TATTAA
Found at i:4824797 original size:11 final size:11
Alignment explanation
Indices: 4824781--4824845 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 11
4824771 AATAGTATTT
4824781 TATTAATTTAA
1 TATTAATTTAA
4824792 TATTAAAGTGATT-A
1 TATT-AA-T--TTAA
*
4824806 TTTTAATATTAA
1 TATTAAT-TTAA
*
4824818 AATTAATTTAA
1 TATTAATTTAA
*
4824829 TATTATTTTAA
1 TATTAATTTAA
4824840 TATTAA
1 TATTAA
4824846 AATTAATGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 25 0.58
12 9 0.21
13 3 0.07
14 4 0.09
15 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
TATTAATTTAA
Found at i:4824827 original size:17 final size:17
Alignment explanation
Indices: 4824782--4824860 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 17
4824772 ATAGTATTTT
4824782 ATTAATTTAATATTAAA
1 ATTAATTTAATATTAAA
*
4824799 GTGATTATTTTAATATTAAA
1 ---ATTAATTTAATATTAAA
4824819 ATTAATTTAATATT---
1 ATTAATTTAATATTAAA
4824833 A-T--TTTAATATTAAA
1 ATTAATTTAATATTAAA
*
4824847 ATTAATGTAATATT
1 ATTAATTTAATATT
4824861 TATCTTGTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
11 9 0.18
13 1 0.02
14 2 0.04
15 1 0.02
17 21 0.42
20 16 0.32
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
ATTAATTTAATATTAAA
Found at i:4824833 original size:28 final size:28
Alignment explanation
Indices: 4824802--4824860 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
4824792 TATTAAAGTG
*
4824802 ATTATTTTAATATTAAAATTAATTTAAT
1 ATTATTTTAATATTAAAATTAATGTAAT
4824830 ATTATTTTAATATTAAAATTAATGTAAT
1 ATTATTTTAATATTAAAATTAATGTAAT
4824858 ATT
1 ATT
4824861 TATCTTGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTATTTTAATATTAAAATTAATGTAAT
Found at i:4834447 original size:9 final size:9
Alignment explanation
Indices: 4834421--4834463 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
4834411 TGCCAACAAA
*
4834421 AATTAAATA
1 AATTAAATT
4834430 AATTAAATT
1 AATTAAATT
4834439 AATTAAATT
1 AATTAAATT
*
4834448 -TTCTAAATT
1 AAT-TAAATT
4834457 AATTAAA
1 AATTAAA
4834464 GGAAAATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 1 0.03
9 27 0.93
10 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:4835250 original size:11 final size:11
Alignment explanation
Indices: 4835234--4835265 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4835224 TATATTAAAC
4835234 ATAAGTAACTA
1 ATAAGTAACTA
4835245 ATAAGTAACTA
1 ATAAGTAACTA
*
4835256 AAAAGTAACT
1 ATAAGTAACT
4835266 TAAAGTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.25
Consensus pattern (11 bp):
ATAAGTAACTA
Found at i:4835273 original size:21 final size:22
Alignment explanation
Indices: 4835236--4835286 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
4835226 TATTAAACAT
4835236 AAGTAACTAATAAGT-AACTAAA
1 AAGTAACTAATAAGTAAAC-AAA
*
4835258 AAGTAACTTA-AAGTAAACAAA
1 AAGTAACTAATAAGTAAACAAA
4835279 AA-TAACTA
1 AAGTAACTA
4835287 TTTCAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 12 0.46
ACGTcount: A:0.61, C:0.10, G:0.08, T:0.22
Consensus pattern (22 bp):
AAGTAACTAATAAGTAAACAAA
Found at i:4835398 original size:2 final size:2
Alignment explanation
Indices: 4835391--4835428 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4835381 CCCGCATTAG
4835391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4835429 AGGTTATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4836130 original size:23 final size:23
Alignment explanation
Indices: 4836081--4836137 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
4836071 TTAAATATAA
*
4836081 ATTTTATA-ATTATTAATTAATT
1 ATTTTATATATTTTTAATTAATT
* *
4836103 CTTTTTATATATTTTTAA-TATTT
1 -ATTTTATATATTTTTAATTAATT
4836126 ATTTTAT-TATTT
1 ATTTTATATATTT
4836138 ATATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 6 0.21
23 11 0.38
24 7 0.24
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTTATATATTTTTAATTAATT
Found at i:4836200 original size:19 final size:19
Alignment explanation
Indices: 4836176--4836215 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4836166 ACAATAAAAA
4836176 AAATAATTCAAAATGATTG
1 AAATAATTCAAAATGATTG
4836195 AAATAATTCAAAATGATTG
1 AAATAATTCAAAATGATTG
4836214 AA
1 AA
4836216 GCCTAATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (19 bp):
AAATAATTCAAAATGATTG
Found at i:4837318 original size:20 final size:20
Alignment explanation
Indices: 4837293--4837334 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4837283 TCTTTCGTTT
4837293 GTTTCTTATTTTTACGTGCA
1 GTTTCTTATTTTTACGTGCA
4837313 GTTTCTTATTTTTACGTGCA
1 GTTTCTTATTTTTACGTGCA
4837333 GT
1 GT
4837335 CATTTTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (20 bp):
GTTTCTTATTTTTACGTGCA
Found at i:4841767 original size:26 final size:26
Alignment explanation
Indices: 4841731--4841891 Score: 288
Period size: 26 Copynumber: 6.2 Consensus size: 26
4841721 CATGAAATTC
*
4841731 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
4841757 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
4841783 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
4841809 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
4841835 TTATCATGAAACATTTACCTAACC-A
1 TTATCATGAAACATTTACCTAACCTA
*
4841860 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
4841886 TTATCA
1 TTATCA
4841892 ATTTGTATCA
Statistics
Matches: 130, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
25 24 0.18
26 106 0.82
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:4842363 original size:10 final size:10
Alignment explanation
Indices: 4842348--4842385 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
4842338 GTTTTAGCTT
4842348 TTATCTTTAA
1 TTATCTTTAA
4842358 TTATCTTTAA
1 TTATCTTTAA
*
4842368 TTAT-TTGTAT
1 TTATCTT-TAA
4842378 TTATCTTT
1 TTATCTTT
4842386 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:4857641 original size:33 final size:33
Alignment explanation
Indices: 4857602--4857820 Score: 357
Period size: 33 Copynumber: 6.6 Consensus size: 33
4857592 TGGAAATGTT
*
4857602 AGGTATACTTTGTGTATACCATATGAAAAGGGA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
* *
4857635 AGGTATACTTTCTGTATACTATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
*
4857668 AGGTATACTTTGTGTATACCATATGAAAAGGGA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
*
4857701 AGGTATATTTTGTGTATACCATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
* *
4857734 ATGTATATTTTGTGTATACCATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
*
4857767 ATGTATACTTTGTGTATACCATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
*
4857800 AGGTATACTTTGTGTGTACCA
1 AGGTATACTTTGTGTATACCA
4857821 CTTGGAAATG
Statistics
Matches: 174, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 174 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (33 bp):
AGGTATACTTTGTGTATACCATATGAAAAGGAA
Found at i:4858812 original size:18 final size:17
Alignment explanation
Indices: 4858789--4858826 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 17
4858779 ACATATATAT
4858789 TAAAAATACATATAAAAA
1 TAAAAATA-ATATAAAAA
4858807 TAAAAAATAATATAAAAA
1 T-AAAAATAATATAAAAA
4858825 TA
1 TA
4858827 CCATTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 11 0.58
19 7 0.37
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAATAATATAAAAA
Found at i:4859451 original size:3 final size:3
Alignment explanation
Indices: 4859443--4859901 Score: 194
Period size: 3 Copynumber: 150.7 Consensus size: 3
4859433 TTCTAATACC
* * *
4859443 ATT ATT ATT ACT ACTT A-T ATT ATT ATT ACTT ATT ATT GTT A-C ATTT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT A-TT ATT ATT ATT ATT A-TT
* * ** *
4859489 ATT ATT CATGT ATAT ATT ATG ATT ATT GTT ATT ATT AAC ATT CTT ATT
1 ATT ATT -AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
4859537 GTT ACT ATT ATT TTT ATTT ATT ATT ATC AAT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
4859582 ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ACT ATT ATT ATT A-T CTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
4859629 AGT ATT A-A ACTA ATT GATT -TC A-T ATT ATT ATT ATT A-T ATAT ATAT
1 ATT ATT ATT A-TT ATT -ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T
** * * *
4859674 ATT -TT GCGT -TT ATTT ACTT ATT ACT -TT ATT ATT AATT AAT -TT AGT
1 ATT ATT -ATT ATT A-TT A-TT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
* * * ** * *
4859719 ATT ATT AATC ATT AATT ATT ATT ATC CTT ATT AAC ATGT CATC GTT -TT
1 ATT ATT -ATT ATT -ATT ATT ATT ATT ATT ATT ATT AT-T -ATT ATT ATT
* * ** * * *
4859767 ATT ATT AAT ATAT ATG ATT ATT GCT CTT GTT AAT A-T ATT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
4859812 TTCT ACTT -TG ACTT GTT -GT GTT ATT ATT ATG ATT ATT ATT ATT ATT
1 AT-T A-TT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4859858 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4859902 ACTATCTTTC
Statistics
Matches: 339, Mismatches: 81, Indels: 72
0.69 0.16 0.15
Matches are distributed among these distances:
2 22 0.06
3 264 0.78
4 49 0.14
5 4 0.01
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:4860836 original size:10 final size:9
Alignment explanation
Indices: 4860810--4860840 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
4860800 TTATGTGTTC
4860810 TTTATTTTA
1 TTTATTTTA
4860819 TTTATTTTA
1 TTTATTTTA
4860828 TTCTATTTTA
1 TT-TATTTTA
4860838 TTT
1 TTT
4860841 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4869197 original size:38 final size:38
Alignment explanation
Indices: 4869155--4869231 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
4869145 CCCTTATCTC
4869155 CTTCCATCATCTCTTTAATGAGAACTTCCACATCGTCA
1 CTTCCATCATCTCTTTAATGAGAACTTCCACATCGTCA
4869193 CTTCCATCATCTCTTTAATGAGAACTTCCACATCGTCA
1 CTTCCATCATCTCTTTAATGAGAACTTCCACATCGTCA
4869231 C
1 C
4869232 GCTTTACATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.32, G:0.08, T:0.34
Consensus pattern (38 bp):
CTTCCATCATCTCTTTAATGAGAACTTCCACATCGTCA
Found at i:4871327 original size:15 final size:15
Alignment explanation
Indices: 4871307--4871335 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4871297 ATTTCATTTT
4871307 ATTTTTAAAAAAATC
1 ATTTTTAAAAAAATC
4871322 ATTTTTAAAAAAAT
1 ATTTTTAAAAAAAT
4871336 TACGTCAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTTAAAAAAATC
Found at i:4874018 original size:12 final size:13
Alignment explanation
Indices: 4874001--4874033 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4873991 TTGCGAGCGC
*
4874001 TCTTTTTGTTG-T
1 TCTTTTGGTTGCT
4874013 TCTTTTGGTTGCT
1 TCTTTTGGTTGCT
4874026 TCTTTTGG
1 TCTTTTGG
4874034 CATAAATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.00, C:0.12, G:0.21, T:0.67
Consensus pattern (13 bp):
TCTTTTGGTTGCT
Found at i:4880308 original size:13 final size:13
Alignment explanation
Indices: 4880290--4880314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4880280 TGCCTATGAA
4880290 TTTATAGAGGAGT
1 TTTATAGAGGAGT
4880303 TTTATAGAGGAG
1 TTTATAGAGGAG
4880315 ATGTCATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (13 bp):
TTTATAGAGGAGT
Found at i:4886364 original size:17 final size:17
Alignment explanation
Indices: 4886342--4886377 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4886332 CCCCTTTGCT
*
4886342 TTAGTTTAATTAGTTAA
1 TTAGTTTAATTAATTAA
*
4886359 TTAGTTTAGTTAATTAA
1 TTAGTTTAATTAATTAA
4886376 TT
1 TT
4886378 TAATAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (17 bp):
TTAGTTTAATTAATTAA
Found at i:4886369 original size:13 final size:13
Alignment explanation
Indices: 4886347--4886379 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4886337 TTGCTTTAGT
4886347 TTAA-TTAGTTAA
1 TTAATTTAGTTAA
*
4886359 TTAGTTTAGTTAA
1 TTAATTTAGTTAA
4886372 TTAATTTA
1 TTAATTTA
4886380 ATAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 3 0.17
13 15 0.83
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (13 bp):
TTAATTTAGTTAA
Found at i:4887074 original size:96 final size:96
Alignment explanation
Indices: 4886940--4887129 Score: 299
Period size: 96 Copynumber: 2.0 Consensus size: 96
4886930 GTGTCCGAGG
* * *
4886940 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGAG
1 AAGTCTATCATCGAAGGGAACGATGGAGAAGACAAGGAGCCCAAGAAGCTTGGTTCGACCAAGAG
* *
4887005 AAAAGCCAAAGCCAATAGGGCAAAAAGGAAC
66 AAAAGCCAAAACCAAGAGGGCAAAAAGGAAC
* * *
4887036 AAGTCTATCATGGAAGGGAACGATGGAGAAGACGAGGAGTCCAAGAAGCTTGGTTCGACCAAGAG
1 AAGTCTATCATCGAAGGGAACGATGGAGAAGACAAGGAGCCCAAGAAGCTTGGTTCGACCAAGAG
*
4887101 AAAAGCCAAAACCAAGAGGGCAAAGAGGA
66 AAAAGCCAAAACCAAGAGGGCAAAAAGGA
4887130 GCAAAAAGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.41, C:0.17, G:0.31, T:0.11
Consensus pattern (96 bp):
AAGTCTATCATCGAAGGGAACGATGGAGAAGACAAGGAGCCCAAGAAGCTTGGTTCGACCAAGAG
AAAAGCCAAAACCAAGAGGGCAAAAAGGAAC
Found at i:4899271 original size:47 final size:46
Alignment explanation
Indices: 4899220--4899352 Score: 133
Period size: 46 Copynumber: 2.9 Consensus size: 46
4899210 GAATTATGAG
* *
4899220 GCATCTAAACTCATTGAGTTGCGTTCTGAATTCACTTATGGATGCAA
1 GCATCCAAACTCATTGAGTTGCGTTCCGAATTCA-TTATGGATGCAA
* * * *
4899267 GCATCCAAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGTGAA
1 GCATCCAAACTCATTGAGTTGCGTTCCGAATTCATTATGGATG-CAA
* * * * * *
4899314 -CACCCGAGCTCGTTGAGTTGCGTTTCGAGTTCATTATGG
1 GCATCCAAACTCATTGAGTTGCGTTCCGAATTCATTATGG
4899353 GTGAAATTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
46 43 0.58
47 31 0.42
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (46 bp):
GCATCCAAACTCATTGAGTTGCGTTCCGAATTCATTATGGATGCAA
Found at i:4903817 original size:55 final size:54
Alignment explanation
Indices: 4903723--4903847 Score: 144
Period size: 55 Copynumber: 2.3 Consensus size: 54
4903713 GAACATGCCA
** *
4903723 AAACAACACGGGCGTACGACACGCCCGTGTCTAGAACCCGTGACT-GAACCTGTC
1 AAACAACACGGGCGTACGACACGCCCGTACCAAGAACCCGTG-CTCGAACCTGTC
* * * * *
4903777 AAATCAACACGGGCGTTCGACACTCCCGTACCAAGCACCCGTGGTCGAACCTGTT
1 AAA-CAACACGGGCGTACGACACGCCCGTACCAAGAACCCGTGCTCGAACCTGTC
4903832 AAACTAACACGGGCGT
1 AAAC-AACACGGGCGT
4903848 GGGCCTACAT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
54 5 0.08
55 55 0.92
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (54 bp):
AAACAACACGGGCGTACGACACGCCCGTACCAAGAACCCGTGCTCGAACCTGTC
Found at i:4907114 original size:13 final size:13
Alignment explanation
Indices: 4907046--4907112 Score: 89
Period size: 13 Copynumber: 5.2 Consensus size: 13
4907036 GAAGCATCAC
*
4907046 TCACACGAGCATG
1 TCACACGAGCGTG
*
4907059 TCACTCGAGCGTG
1 TCACACGAGCGTG
*
4907072 TCACTCGAGCGTG
1 TCACACGAGCGTG
*
4907085 TCACACGGGCGTG
1 TCACACGAGCGTG
*
4907098 TCCCACGAGCGTG
1 TCACACGAGCGTG
4907111 TC
1 TC
4907113 CCTGCCGAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.19
Consensus pattern (13 bp):
TCACACGAGCGTG
Found at i:4915845 original size:41 final size:41
Alignment explanation
Indices: 4915788--4915869 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
4915778 GTTTACTGAT
* ** *
4915788 TAATGTATATCTGATACTGTTACT-ATGATGGGCTTAGGCCC
1 TAATGCATATCTGATACTGAAACTGA-AATGGGCTTAGGCCC
*
4915829 TAATGCATATTTGATACTGAAACTGAAATGGGCTTAGGCCC
1 TAATGCATATCTGATACTGAAACTGAAATGGGCTTAGGCCC
4915870 AGACTACATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 34 0.97
42 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (41 bp):
TAATGCATATCTGATACTGAAACTGAAATGGGCTTAGGCCC
Found at i:4923894 original size:18 final size:18
Alignment explanation
Indices: 4923871--4923926 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
4923861 TATGAGAAAA
4923871 GTGATTGTATATATGTAT
1 GTGATTGTATATATGTAT
4923889 GTGATTTGT-TA-A---AT
1 GTGA-TTGTATATATGTAT
* *
4923903 GTGGTTGTATATGTGTAT
1 GTGATTGTATATATGTAT
4923921 GTGATT
1 GTGATT
4923927 TGTTAAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 12
0.66 0.07 0.27
Matches are distributed among these distances:
13 4 0.14
14 7 0.24
17 1 0.03
18 13 0.45
19 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (18 bp):
GTGATTGTATATATGTAT
Found at i:4923911 original size:32 final size:32
Alignment explanation
Indices: 4923875--4923938 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
4923865 AGAAAAGTGA
4923875 TTGTATATATGTATGTGATTTGTTAAATGTGG
1 TTGTATATATGTATGTGATTTGTTAAATGTGG
*
4923907 TTGTATATGTGTATGTGATTTGTTAAATGTGG
1 TTGTATATATGTATGTGATTTGTTAAATGTGG
4923939 CCTATTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (32 bp):
TTGTATATATGTATGTGATTTGTTAAATGTGG
Found at i:4924694 original size:2 final size:2
Alignment explanation
Indices: 4924687--4924722 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4924677 ATGGTATGCG
4924687 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4924723 GTTATAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4926092 original size:30 final size:30
Alignment explanation
Indices: 4926056--4926112 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4926046 AAGGCTATGA
4926056 CACACGGGCATGTGG-TCTACCCGTGTGTCT
1 CACACGGGCATGTGGAT-TACCCGTGTGTCT
*
4926086 CACACGGGCGTGTGGATTACCCGTGTG
1 CACACGGGCATGTGGATTACCCGTGTG
4926113 GAAGTGTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (30 bp):
CACACGGGCATGTGGATTACCCGTGTGTCT
Found at i:4929582 original size:3 final size:3
Alignment explanation
Indices: 4929574--4929602 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4929564 AAATCAGTAA
4929574 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4929603 ACAATATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4929950 original size:52 final size:52
Alignment explanation
Indices: 4929890--4929993 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
4929880 AAGGAAAGAA
* * *
4929890 AGAGGATGAGGGGAAAGGGGATAGGGGGCGACTAGCGGTGGGTGATGGAGGC
1 AGAGGATGAGGGGAAAGGAGATAGGGGGCGACTAGCAGTGGGTGACGGAGGC
*
4929942 AGAGGATGAGGGGAAAGGAGATAGGGGGCGACTGGCAGTGGGTGACGGAGGC
1 AGAGGATGAGGGGAAAGGAGATAGGGGGCGACTAGCAGTGGGTGACGGAGGC
4929994 TGGAGTAGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.26, C:0.09, G:0.55, T:0.11
Consensus pattern (52 bp):
AGAGGATGAGGGGAAAGGAGATAGGGGGCGACTAGCAGTGGGTGACGGAGGC
Found at i:4934275 original size:31 final size:31
Alignment explanation
Indices: 4934240--4934340 Score: 156
Period size: 31 Copynumber: 3.4 Consensus size: 31
4934230 ATTAAAACTC
4934240 ATAATT-AAGAATAACAACAAGTATTTATCAT
1 ATAATTCAA-AATAACAACAAGTATTTATCAT
4934271 ATAATTCAAAAT---AACAAGTATTTATCAT
1 ATAATTCAAAATAACAACAAGTATTTATCAT
4934299 ATAATTCAAAATAACAACAAGTATTTATCAT
1 ATAATTCAAAATAACAACAAGTATTTATCAT
*
4934330 ATAATTTAAAA
1 ATAATTCAAAA
4934341 GATAATAAGA
Statistics
Matches: 65, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
28 28 0.43
31 35 0.54
32 2 0.03
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.34
Consensus pattern (31 bp):
ATAATTCAAAATAACAACAAGTATTTATCAT
Found at i:4934295 original size:28 final size:29
Alignment explanation
Indices: 4934255--4934340 Score: 138
Period size: 28 Copynumber: 2.9 Consensus size: 29
4934245 TAAGAATAAC
4934255 AACAAGTATTTATCATATAATTCAAAAT-
1 AACAAGTATTTATCATATAATTCAAAATA
4934283 AACAAGTATTTATCATATAATTCAAAATAA
1 AACAAGTATTTATCATATAATTCAAAAT-A
*
4934313 CAACAAGTATTTATCATATAATTTAAAA
1 -AACAAGTATTTATCATATAATTCAAAA
4934341 GATAATAAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
28 28 0.52
31 26 0.48
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.35
Consensus pattern (29 bp):
AACAAGTATTTATCATATAATTCAAAATA
Found at i:4934804 original size:30 final size:30
Alignment explanation
Indices: 4934748--4934804 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
4934738 ACAGCCATGA
* *
4934748 CACACGGGCATGTGGTCTGCCTGTGTGTCT
1 CACACGGGCATGTGGTCTACCCGTGTGTCT
*
4934778 CACACGGGCGTGTGGAT-TACCCGTGTG
1 CACACGGGCATGTGG-TCTACCCGTGTG
4934805 GAAGAGTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 22 0.96
31 1 0.04
ACGTcount: A:0.12, C:0.26, G:0.35, T:0.26
Consensus pattern (30 bp):
CACACGGGCATGTGGTCTACCCGTGTGTCT
Found at i:4948729 original size:16 final size:16
Alignment explanation
Indices: 4948708--4948750 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
4948698 AAATTAGGGT
4948708 AATAAATAAAA-AATAA
1 AATAAATAAAATAA-AA
4948724 AATAAATGAAAATAAAA
1 AATAAAT-AAAATAAAA
4948741 AA-AAATAAAA
1 AATAAATAAAA
4948751 CATGTTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.16
16 11 0.44
17 8 0.32
18 2 0.08
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (16 bp):
AATAAATAAAATAAAA
Found at i:4949319 original size:19 final size:19
Alignment explanation
Indices: 4949295--4949332 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4949285 AATTAAAAAG
4949295 ATAAAAAAATCAGAAGGGC
1 ATAAAAAAATCAGAAGGGC
*
4949314 ATAAAAAAATCGGAAGGGC
1 ATAAAAAAATCAGAAGGGC
4949333 CAAAGATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.11, G:0.24, T:0.11
Consensus pattern (19 bp):
ATAAAAAAATCAGAAGGGC
Found at i:4954636 original size:17 final size:17
Alignment explanation
Indices: 4954614--4954659 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
4954604 AGTGGGGCTC
4954614 GTTACTTTTTTTTATTT
1 GTTACTTTTTTTTATTT
4954631 GTTACTTTTTTATTTATTT
1 GTTAC-TTTTT-TTTATTT
*
4954650 TTTA-TTTTTT
1 GTTACTTTTTT
4954660 GAAAGTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
18 5 0.19
19 10 0.38
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (17 bp):
GTTACTTTTTTTTATTT
Found at i:4954646 original size:19 final size:18
Alignment explanation
Indices: 4954614--4954659 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
4954604 AGTGGGGCTC
4954614 GTTAC-TTTTTTTTATTT
1 GTTACTTTTTTTTTATTT
4954631 GTTACTTTTTTATTTATTT
1 GTTACTTTTTT-TTTATTT
*
4954650 TTTA-TTTTTT
1 GTTACTTTTTT
4954660 GAAAGTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 11 0.42
19 10 0.38
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (18 bp):
GTTACTTTTTTTTTATTT
Found at i:4955451 original size:9 final size:9
Alignment explanation
Indices: 4955439--4955471 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4955429 GAATTATTCG
4955439 AATCGAGTT
1 AATCGAGTT
4955448 AATCGAGTT
1 AATCGAGTT
*
4955457 AATCGAATT
1 AATCGAGTT
4955466 AATCGA
1 AATCGA
4955472 ATCAACTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (9 bp):
AATCGAGTT
Found at i:4955472 original size:9 final size:9
Alignment explanation
Indices: 4955439--4955484 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
4955429 GAATTATTCG
*
4955439 AATCGAGTT
1 AATCGAATT
*
4955448 AATCGAGTT
1 AATCGAATT
4955457 AATCGAATT
1 AATCGAATT
*
4955466 AATCGAATC
1 AATCGAATT
4955475 AACTCGAATT
1 AA-TCGAATT
4955485 TTTTTTTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (9 bp):
AATCGAATT
Found at i:4955875 original size:23 final size:24
Alignment explanation
Indices: 4955847--4955893 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
4955837 TTATTCAAAC
4955847 CCCTTA-CCCCCATTTCAACGAAA
1 CCCTTACCCCCCATTTCAACGAAA
*
4955870 CCCTTACCCCCCATTTCTACGAAA
1 CCCTTACCCCCCATTTCAACGAAA
4955894 GACGAAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.28, C:0.45, G:0.04, T:0.23
Consensus pattern (24 bp):
CCCTTACCCCCCATTTCAACGAAA
Found at i:4960759 original size:19 final size:19
Alignment explanation
Indices: 4960737--4960774 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4960727 ATGACTTAGG
4960737 GCCTCATTTATCATTCTAT
1 GCCTCATTTATCATTCTAT
4960756 GCCTCATTTATCATTCTAT
1 GCCTCATTTATCATTCTAT
4960775 CAACATTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.47
Consensus pattern (19 bp):
GCCTCATTTATCATTCTAT
Found at i:4966324 original size:18 final size:18
Alignment explanation
Indices: 4966282--4966325 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
4966272 AGGGAACGGG
* *
4966282 GTAAGCACTTCGTGCTTA
1 GTAAGCTCTTCGTACTTA
4966300 GTAAGCTCTTCGTACTTA
1 GTAAGCTCTTCGTACTTA
4966318 GTAAGCTC
1 GTAAGCTC
4966326 ATGTAACAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (18 bp):
GTAAGCTCTTCGTACTTA
Found at i:4969364 original size:21 final size:22
Alignment explanation
Indices: 4969329--4969384 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
4969319 CTTACTTTTA
4969329 TATTATATATTATATAATTATT
1 TATTATATATTATATAATTATT
* *
4969351 TATTTTAT-TTATATTATTATT
1 TATTATATATTATATAATTATT
*
4969372 TATTATACATTAT
1 TATTATATATTAT
4969385 TCATATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTATATATTATATAATTATT
Found at i:4969370 original size:17 final size:17
Alignment explanation
Indices: 4969325--4969385 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
4969315 AAACCTTACT
*
4969325 TTTATATTA-TATATTA
1 TTTATATTATTATTTTA
*
4969341 TATA-ATTATTTATTTTA
1 TTTATATTA-TTATTTTA
4969358 TTTATATTATTA-TTTA
1 TTTATATTATTATTTTA
*
4969374 TTATACATTATT
1 TT-TATATTATT
4969386 CATATATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.11
16 9 0.24
17 20 0.54
18 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATATTATTATTTTA
Found at i:4969440 original size:18 final size:18
Alignment explanation
Indices: 4969425--4969537 Score: 58
Period size: 18 Copynumber: 6.3 Consensus size: 18
4969415 ATACTTATTA
4969425 ATTATTTATACATTATAT
1 ATTATTTATACATTATAT
*
4969443 ATTATTTTTACA-TATAT
1 ATTATTTATACATTATAT
* *
4969460 ACTTTATATTATATATCATA-
1 A--TTAT-TTATACATTATAT
* * * *
4969480 CTCATTT-TATATTATGT
1 ATTATTTATACATTATAT
*
4969497 CATTTTTTATACTATTATAT
1 -ATTATTTATAC-ATTATAT
*
4969517 GTT-TTT-TAC-TTATAT
1 ATTATTTATACATTATAT
4969532 ATTATT
1 ATTATT
4969538 ATTATTAAAG
Statistics
Matches: 71, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
15 8 0.11
16 9 0.13
17 11 0.15
18 21 0.30
19 8 0.11
20 11 0.15
21 3 0.04
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTATTTATACATTATAT
Found at i:4969819 original size:17 final size:15
Alignment explanation
Indices: 4969797--4969851 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
4969787 CAATATATTT
4969797 TATATTTTTATATAA
1 TATATTTTTATATAA
*
4969812 GTATTATTCTTATA-AA
1 -TA-TATTTTTATATAA
*
4969828 TATATTTTTTATATAT
1 TATA-TTTTTATATAA
4969844 TATATTTT
1 TATATTTT
4969852 AAATCTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 2 0.06
15 13 0.39
16 9 0.27
17 9 0.27
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
TATATTTTTATATAA
Found at i:4971273 original size:18 final size:18
Alignment explanation
Indices: 4971250--4971285 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4971240 AGATACTACC
4971250 CTTATAAATTATTGTTGA
1 CTTATAAATTATTGTTGA
4971268 CTTATAAATTATTGTTGA
1 CTTATAAATTATTGTTGA
4971286 GATTTATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
CTTATAAATTATTGTTGA
Found at i:4981952 original size:205 final size:206
Alignment explanation
Indices: 4981592--4982140 Score: 919
Period size: 205 Copynumber: 2.7 Consensus size: 206
4981582 GCAGATCTGG
*
4981592 CTGAAGCAAGATCCAAGATGATTTAGCATCCTTGTGTTTACAAGGAGCAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTAGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCT
* *
4981657 GATTTGGCTTTAACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTATGTATTGTCAG
66 GATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
*
4981722 AGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGGGAGCAGATACATAGCAGATCTCACCTTC
131 AGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGGGAGCAGATACATAACAGATCTCACCTTC
4981787 AGATGTTTAT-A
196 AGATGTTT-TCA
* *
4981798 CTGAAGC-AGATCCAAGATGATTTAGCATCCTTGTGCTTACAAGGAGCAAATCGAGGACATAGTT
1 CTGAAGCAAGATCCAAGATGATTTAGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCT
*
4981862 GATTTAGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
*
4981927 AGAGCAAATCGAAGTCTGGCATCTCCACTTCAATGGGGAGCAGATACATAACAGATCTCACCTTC
131 AGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGGGAGCAGATACATAACAGATCTCACCTTC
4981992 AGATGTTTTCA
196 AGATGTTTTCA
* * * *
4982003 CTGAAGCAAGATCCAAGAAGATTT-GACATTCTTATGCTTACAAGGA--ACATCGAAGACATAGC
1 CTGAAGCAAGATCCAAGATGATTTAG-CATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGC
*
4982065 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
65 TGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
*
4982130 GAGAACAAATC
130 GAGAGCAAATC
4982141 AAAGAAGCAG
Statistics
Matches: 323, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
204 87 0.27
205 196 0.61
206 40 0.12
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (206 bp):
CTGAAGCAAGATCCAAGATGATTTAGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCT
GATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
AGAGCAAATCGAAGTCTGGCATCTCCACTTCAACGGGGAGCAGATACATAACAGATCTCACCTTC
AGATGTTTTCA
Found at i:4983842 original size:28 final size:27
Alignment explanation
Indices: 4983804--4983919 Score: 94
Period size: 28 Copynumber: 4.0 Consensus size: 27
4983794 TAAACCTTAC
4983804 TTTTATATTATATATTATATAATTATTTA
1 TTTTAT-TTATATATTAT-TAATTATTTA
*
4983833 TTTTATTTATATTATTATTTATTATACATTA
1 TTTTATTTATA-TATTATTAATTAT---TTA
*
4983864 TTCATATATTAT-TATTATT-ATTATTTA
1 TT-TTAT-TTATATATTATTAATTATTTA
*
4983891 CTTGTA-TTATATACTTATTAATTATTTA
1 -TTTTATTTATATA-TTATTAATTATTTA
4983919 T
1 T
4983920 ACATTATATA
Statistics
Matches: 74, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
25 4 0.05
26 2 0.03
27 11 0.15
28 21 0.28
29 12 0.16
30 5 0.07
31 12 0.16
32 3 0.04
33 4 0.05
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTTATTTATATATTATTAATTATTTA
Found at i:4983844 original size:21 final size:22
Alignment explanation
Indices: 4983809--4983919 Score: 99
Period size: 21 Copynumber: 5.1 Consensus size: 22
4983799 CTTACTTTTA
4983809 TATTATATATTATATAATTATT
1 TATTATATATTATATAATTATT
* *
4983831 TATTTTAT-TTATATTATTATT
1 TATTATATATTATATAATTATT
* *
4983852 TATTATACATTAT-TCA-TATAT
1 TATTATATATTATATAATTAT-T
*
4983873 TATTAT-TATTAT-TATTTACTT
1 TATTATATATTATATAATTA-TT
4983894 GTATTATATACTTAT-TAATTATT
1 -TATTATATA-TTATATAATTATT
4983917 TAT
1 TAT
4983920 ACATTATATA
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
20 9 0.12
21 30 0.41
22 21 0.29
23 4 0.05
24 9 0.12
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (22 bp):
TATTATATATTATATAATTATT
Found at i:4983850 original size:3 final size:3
Alignment explanation
Indices: 4983809--4983888 Score: 58
Period size: 3 Copynumber: 25.3 Consensus size: 3
4983799 CTTACTTTTA
*
4983809 TAT TAT ATAT TA- TAT AAT TATT TAT T-T TAT T-T ATAT TAT TATT TAT
1 TAT TAT -TAT TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TA-T TAT
*
4983855 TAT ACAT TAT TCAT ATAT TAT TAT TAT TAT TAT T
1 TAT -TAT TAT T-AT -TAT TAT TAT TAT TAT TAT T
4983889 TACTTGTATT
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
2 5 0.08
3 41 0.65
4 16 0.25
5 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:4983885 original size:34 final size:34
Alignment explanation
Indices: 4983842--4983919 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
4983832 ATTTTATTTA
4983842 TATTATTATTTATTATACAT-TATTCATATA-TTAT
1 TATTATTATTTATT-TACATGTATT-ATATACTTAT
*
4983876 TATTATTA-TTATTTACTTGTATTATATACTTAT
1 TATTATTATTTATTTACATGTATTATATACTTAT
4983909 TA--ATTATTTAT
1 TATTATTATTTAT
4983920 ACATTATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
31 4 0.10
32 13 0.32
33 15 0.38
34 8 0.20
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (34 bp):
TATTATTATTTATTTACATGTATTATATACTTAT
Found at i:4983929 original size:58 final size:58
Alignment explanation
Indices: 4983807--4983934 Score: 147
Period size: 58 Copynumber: 2.2 Consensus size: 58
4983797 ACCTTACTTT
* *
4983807 TATATTATATATTATATAATTATTTATTTTATTTATATTATTATTTATTATACATTATTCA
1 TATATTAT-TATTATATAATTATTTATTGTATTTATATTATTAATTATTATAC--TATTCA
4983868 TATATTATTATTAT-T-ATTATTTACTTGTATTATATACTTATTAATTATTTATAC-ATT-A
1 TATATTATTATTATATAATTATTTA-TTGTATT-TATA-TTATTAATTA-TTATACTATTCA
4983926 TATATTATT
1 TATATTATT
4983935 TTTACATATA
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
58 18 0.30
59 10 0.16
60 10 0.16
61 17 0.28
62 6 0.10
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (58 bp):
TATATTATTATTATATAATTATTTATTGTATTTATATTATTAATTATTATACTATTCA
Found at i:4983999 original size:143 final size:145
Alignment explanation
Indices: 4983805--4984068 Score: 317
Period size: 143 Copynumber: 1.8 Consensus size: 145
4983795 AAACCTTACT
* * *
4983805 TTTATATTATATATTATATAATTATTTATTTTATTTATATTATTATTTATTATACATTATT-C-A
1 TTTATATTATATATTATATAATTATTTATATTATTCATATTATTATCTATTATACATTATTACTA
*
4983868 TATATTATTATTATT-A-TTATTTACTTGTATTATATACTTATTAATTATTTATACATTATATAT
66 TATATTATTATTATTAAGTT-TTAACTTGTATTATATACTTATT-ATTATTTATACATTATATAT
4983931 TATTTTTACATATATAC
129 TATTTTTACATATATAC
* * ** *
4983948 TTTATATTATATATTATACTCA-T-TTTATATTATGTCAT-TTTTTATACTATTATATGTTTTTA
1 TTTATATTATATATTATA-TAATTATTTATATTAT-TCATATTATTAT-CTATTATACATTATTA
*
4984010 CTTATATATTATTATTATTAAAGGTTTTAACTTGTATTATATACTTATTTTTATTTATA
63 C-TATATATTATTATTATT-AA-GTTTTAACTTGTATTATATACTTATTATTATTTATA
4984069 TGTTAATAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
142 15 0.15
143 33 0.33
144 3 0.03
146 16 0.16
148 10 0.10
149 22 0.22
150 2 0.02
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.59
Consensus pattern (145 bp):
TTTATATTATATATTATATAATTATTTATATTATTCATATTATTATCTATTATACATTATTACTA
TATATTATTATTATTAAGTTTTAACTTGTATTATATACTTATTATTATTTATACATTATATATTA
TTTTTACATATATAC
Found at i:4984029 original size:73 final size:75
Alignment explanation
Indices: 4983867--4984068 Score: 172
Period size: 73 Copynumber: 2.7 Consensus size: 75
4983857 TACATTATTC
*
4983867 ATATATTATTATTATTATTATTTACTTGTATTATATACTTATTAATTATTTATACATTATATATT
1 ATATATTATTATTATTATTATTTACTTGCATTATATACTTATTAATTATTTATACATTATATATT
4983932 ATTTTTACAT
66 ATTTTTACAT
* * * *
4983942 ATATACT-TTA-TATTATATATTATAC-T-CATTTTATA-TTATGTCATTTTTTATAC--TAT-T
1 ATATATTATTATTATTAT-TATT-TACTTGCATTATATACTTAT-TAATTATTTATACATTATAT
* *
4983999 ATATGTTTTTACTT
63 AT-TATTTTTACAT
* * *
4984013 ATATATTATTATTATTAAAGGTT-TTAACTTGTATTATATACTTATT-TTTATTTATA
1 ATATATTATTATTATT--A--TTATTTACTTGCATTATATACTTATTAATTATTTATA
4984069 TGTTAATAAT
Statistics
Matches: 101, Mismatches: 13, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
70 3 0.03
71 18 0.18
72 7 0.07
73 28 0.28
74 10 0.10
75 21 0.21
76 9 0.09
77 5 0.05
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (75 bp):
ATATATTATTATTATTATTATTTACTTGCATTATATACTTATTAATTATTTATACATTATATATT
ATTTTTACAT
Found at i:4984324 original size:15 final size:16
Alignment explanation
Indices: 4984287--4984336 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
4984277 TATTTTATAA
4984287 TTTTATATAAGTAT-TAT
1 TTTTATATAA-TATAT-T
*
4984304 TCTTATA-AATATATT
1 TTTTATATAATATATT
*
4984319 TTTTATATATTATATT
1 TTTTATATAATATATT
4984335 TT
1 TT
4984337 AAATCTATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 10 0.36
16 12 0.43
17 6 0.21
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTATATAATATATT
Found at i:4987750 original size:6 final size:6
Alignment explanation
Indices: 4987732--4987782 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
4987722 ATGCAAAAAA
*
4987732 ATAAAT A-AAAT ATAAAT ATAAAT ATAAAAT AAAAAT ATAAA- ATAAA-
1 ATAAAT ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT ATAAAT
4987778 ATAAA
1 ATAAA
4987783 ACAAAATTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
5 15 0.37
6 21 0.51
7 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (6 bp):
ATAAAT
Done.