Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 172 of 433
Found at i:53586385 original size:12 final size:13
Alignment explanation
Indices: 53586349--53586386 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
53586339 AAATATTTGA
53586349 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
53586362 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
53586376 CTTG-TCTTAAT
1 CTTGTTCTTAAT
53586387 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:53597555 original size:21 final size:20
Alignment explanation
Indices: 53597523--53597571 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
53597513 TTCTTCAAAT
*
53597523 TTGTTTACCTATTATTATTA
1 TTGTTTATCTATTATTATTA
53597543 TTCGTTTATCTATTATTATTA
1 TT-GTTTATCTATTATTATTA
53597564 TTGTTTAT
1 TTGTTTAT
53597572 ATTACAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.63
Consensus pattern (20 bp):
TTGTTTATCTATTATTATTA
Found at i:53605691 original size:15 final size:15
Alignment explanation
Indices: 53605671--53605714 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
53605661 CCGTAATAGT
53605671 CACATATCATATAAA
1 CACATATCATATAAA
*
53605686 CACATATCATAATATA
1 CACATATCAT-ATAAA
53605702 CACATATTCATAT
1 CACATA-TCATAT
53605715 TTTAAGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 10 0.38
16 12 0.46
17 4 0.15
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (15 bp):
CACATATCATATAAA
Found at i:53605706 original size:16 final size:16
Alignment explanation
Indices: 53605671--53605713 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
53605661 CCGTAATAGT
53605671 CACATATCAT-ATAAA
1 CACATATCATAATAAA
*
53605686 CACATATCATAATATA
1 CACATATCATAATAAA
53605702 CACATATTCATA
1 CACATA-TCATA
53605714 TTTTAAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.40
16 10 0.40
17 5 0.20
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (16 bp):
CACATATCATAATAAA
Found at i:53615797 original size:21 final size:20
Alignment explanation
Indices: 53615768--53615813 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
53615758 TATAAACTAT
53615768 ATTTATTAATTAGTTTTGTAAA
1 ATTTATTAATTA-TTTT-TAAA
*
53615790 ATTT-TTAATTATTTTTCAA
1 ATTTATTAATTATTTTTAAA
53615809 ATTTA
1 ATTTA
53615814 GAAGAGGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 7 0.32
22 4 0.18
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTTATTAATTATTTTTAAA
Found at i:53621281 original size:21 final size:21
Alignment explanation
Indices: 53621257--53621299 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
53621247 TAACTCTTGC
53621257 AACTGAGCCTTCAATTCTTTT
1 AACTGAGCCTTCAATTCTTTT
53621278 AACTGAGCCTTCAATTCTTTT
1 AACTGAGCCTTCAATTCTTTT
53621299 A
1 A
53621300 TTCAGTCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (21 bp):
AACTGAGCCTTCAATTCTTTT
Found at i:53634617 original size:13 final size:13
Alignment explanation
Indices: 53634595--53634627 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
53634585 AAGGGTTTGT
53634595 TTAT-TAAACTAA
1 TTATCTAAACTAA
53634607 TTATCTAAACTAA
1 TTATCTAAACTAA
*
53634620 TTAACTAA
1 TTATCTAA
53634628 TTTAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:53635927 original size:28 final size:29
Alignment explanation
Indices: 53635895--53636009 Score: 119
Period size: 29 Copynumber: 4.0 Consensus size: 29
53635885 TACGTGCATC
*
53635895 TGACCCATTAAGCCC-AATCATATTCATA
1 TGACCCATTAAGCCCAAATCACATTCATA
* *
53635923 TGACCCATTAAGCCCAAACCACCTGT-ATA
1 TGACCCATTAAGCCCAAATCACAT-TCATA
* * *
53635952 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGACCCATTAAGCCCAAATCACATTCATA
* * *
53635981 TGGCCCATTAGGCCC-AGTCACATTCATA
1 TGACCCATTAAGCCCAAATCACATTCATA
53636009 T
1 T
53636010 TCATGCTCAC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 28 0.37
29 46 0.61
30 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.26
Consensus pattern (29 bp):
TGACCCATTAAGCCCAAATCACATTCATA
Found at i:53638057 original size:13 final size:13
Alignment explanation
Indices: 53638041--53638068 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53638031 TGGCCCTAGC
53638041 CCTAGGCCTCTAT
1 CCTAGGCCTCTAT
53638054 CCTAGGCCTCTAT
1 CCTAGGCCTCTAT
53638067 CC
1 CC
53638069 AACACCCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.43, G:0.14, T:0.29
Consensus pattern (13 bp):
CCTAGGCCTCTAT
Found at i:53639117 original size:29 final size:29
Alignment explanation
Indices: 53639082--53639158 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
53639072 AATCATATTC
* *
53639082 ATATGGCCTATTAAGCCCAAACCACCTAT
1 ATATGGCCTATTAGGCCCAAACCACATAT
* * * *
53639111 ATATGGCCCATTAGGCCCAAATCATATTT
1 ATATGGCCTATTAGGCCCAAACCACATAT
*
53639140 ATATGGCCTGTTAGGCCCA
1 ATATGGCCTATTAGGCCCA
53639159 GTAACATTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (29 bp):
ATATGGCCTATTAGGCCCAAACCACATAT
Found at i:53639146 original size:58 final size:57
Alignment explanation
Indices: 53639048--53639158 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 57
53639038 AAATTCACAT
* * *
53639048 ACCTGTATCTGGCCCATTACGCGCAATCATATTCATATGGCCTATTAAGCCCAAACC
1 ACCTATATATGGCCCATTACGCCCAATCATATTCATATGGCCTATTAAGCCCAAACC
* * * *
53639105 ACCTATATATGGCCCATTAGGCCCAAATCATATTTATATGGCCTGTTAGGCCCA
1 ACCTATATATGGCCCATTACGCCC-AATCATATTCATATGGCCTATTAAGCCCA
53639159 GTAACATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 20 0.43
58 26 0.57
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (57 bp):
ACCTATATATGGCCCATTACGCCCAATCATATTCATATGGCCTATTAAGCCCAAACC
Found at i:53639407 original size:16 final size:16
Alignment explanation
Indices: 53639382--53639440 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
53639372 GTAGCCAAAC
53639382 TTTCGGCTTTTTGGCA
1 TTTCGGCTTTTTGGCA
*
53639398 TTTTGGCTTTTTGGCA
1 TTTCGGCTTTTTGGCA
* * *
53639414 TATCGACATTTTGGCA
1 TTTCGGCTTTTTGGCA
53639430 TTTCGGCTTTT
1 TTTCGGCTTTT
53639441 GCCGATTCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.51
Consensus pattern (16 bp):
TTTCGGCTTTTTGGCA
Found at i:53639408 original size:7 final size:8
Alignment explanation
Indices: 53639390--53639441 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
53639380 ACTTTCGGCT
53639390 TTTTGGCA
1 TTTTGGCA
*
53639398 TTTTGGCT
1 TTTTGGCA
53639406 TTTTGGCA
1 TTTTGGCA
* * *
53639414 TATCGACA
1 TTTTGGCA
53639422 TTTTGGCA
1 TTTTGGCA
*
53639430 TTTCGGC-
1 TTTTGGCA
53639437 TTTTG
1 TTTTG
53639442 CCGATTCATA
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
7 4 0.12
8 30 0.88
ACGTcount: A:0.12, C:0.15, G:0.23, T:0.50
Consensus pattern (8 bp):
TTTTGGCA
Found at i:53642442 original size:64 final size:64
Alignment explanation
Indices: 53642339--53642463 Score: 153
Period size: 64 Copynumber: 2.0 Consensus size: 64
53642329 TAGTTGATGG
* * * * * *
53642339 TCATCACCATCACTTTTCCTAATCAATAGCTAAAGCTATCTCTTTTCATATTCGATGGTCGTCA
1 TCATCACCATCACTTTTCATAATCAATAGCCAAACCTATCCCATTTCATATTCGATAGTCGTCA
* * *
53642403 TCATCCACCATCCCTTTTCATAAT-GATAGCCGAACCTATCCCATTTCATATTCGATAGTCG
1 TCAT-CACCATCACTTTTCATAATCAATAGCCAAACCTATCCCATTTCATATTCGATAGTCG
53642464 AAGCTATCCC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 34 0.67
65 17 0.33
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.35
Consensus pattern (64 bp):
TCATCACCATCACTTTTCATAATCAATAGCCAAACCTATCCCATTTCATATTCGATAGTCGTCA
Found at i:53642452 original size:28 final size:29
Alignment explanation
Indices: 53642412--53642480 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
53642402 ATCATCCACC
53642412 ATCCCTTTTCATAAT-GATAGCCGAACCT
1 ATCCCTTTTCATAATCGATAGCCGAACCT
* * * *
53642440 ATCCCATTTCATATTCGATAGTCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAACCT
53642469 ATCCCTTTTCAT
1 ATCCCTTTTCAT
53642481 CGGTCGATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 13 0.37
29 22 0.63
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAACCT
Found at i:53646117 original size:42 final size:42
Alignment explanation
Indices: 53646060--53646181 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 42
53646050 TCAGGGTTAT
53646060 TGAGATTAC-GTGTAAGACCATATCTGGGATATGGCATCAATA
1 TGAGATTACAG-GTAAGACCATATCTGGGATATGGCATCAATA
* * *
53646102 TGAGACTT-CAGGTAAGACCATATCTCGGCTATTGGCATCGATA
1 TGAGA-TTACAGGTAAGACCATATCTGGGATA-TGGCATCAATA
**
53646145 TGAGATTACCTGTAAGACCATATCTGGGATATGGCAT
1 TGAGATTACAGGTAAGACCATATCTGGGATATGGCAT
53646182 TGGTACGGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
42 32 0.46
43 37 0.54
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (42 bp):
TGAGATTACAGGTAAGACCATATCTGGGATATGGCATCAATA
Found at i:53646699 original size:18 final size:18
Alignment explanation
Indices: 53646632--53646810 Score: 265
Period size: 18 Copynumber: 9.9 Consensus size: 18
53646622 ATAATCTTCA
53646632 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
53646651 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
53646670 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
53646687 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
53646705 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
53646723 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
53646740 ATGATTGCAATCTTAGTT
1 ATGATTGCAATCTTAGAT
*
53646758 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
53646775 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
53646793 ATGATATACAATCTTAGA
1 ATGAT-TGCAATCTTAGA
53646811 AGATATGATT
Statistics
Matches: 147, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
17 47 0.32
18 66 0.45
19 34 0.23
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:53646703 original size:35 final size:36
Alignment explanation
Indices: 53646632--53646810 Score: 274
Period size: 35 Copynumber: 5.0 Consensus size: 36
53646622 ATAATCTTCA
*
53646632 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGAT-TACAATCTTAGAT
* *
53646670 ATGA-TACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATTACAATCTTAGAT
53646705 ATGATTGCAATCTTAGATATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATTACAATCTTAGAT
*
53646740 ATGATTGCAATCTTAGTTATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATTACAATCTTAGAT
53646775 ATGATTGCAATCTTAGATATGATATACAATCTTAGA
1 ATGATTGCAATCTTAGATATGAT-TACAATCTTAGA
53646811 AGATATGATT
Statistics
Matches: 133, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
35 84 0.63
36 33 0.25
37 12 0.09
38 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (36 bp):
ATGATTGCAATCTTAGATATGATTACAATCTTAGAT
Found at i:53646719 original size:53 final size:54
Alignment explanation
Indices: 53646632--53646810 Score: 283
Period size: 53 Copynumber: 3.3 Consensus size: 54
53646622 ATAATCTTCA
53646632 ATGATATGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
53646687 ATGAT-TGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT
* * *
53646740 ATGAT-TGCAATCTTAGTTATGA-TACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATTGCAATCTTAGATATGA-TACAATCTTAGAT
*
53646793 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
53646811 AGATATGATT
Statistics
Matches: 117, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
52 16 0.14
53 68 0.58
54 28 0.24
55 5 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (54 bp):
ATGATATGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT
Found at i:53650299 original size:33 final size:33
Alignment explanation
Indices: 53650257--53650322 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
53650247 TTAAGGTAGC
*
53650257 ATGTTAAGCAGGAATGCCCACTTGTTTGCCAAT
1 ATGTTAAGCAAGAATGCCCACTTGTTTGCCAAT
*
53650290 ATGTTAAGCAAGAATGCGCACTTGTTTGCCAAT
1 ATGTTAAGCAAGAATGCCCACTTGTTTGCCAAT
53650323 CTTTCTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (33 bp):
ATGTTAAGCAAGAATGCCCACTTGTTTGCCAAT
Found at i:53653256 original size:7 final size:7
Alignment explanation
Indices: 53653246--53653317 Score: 72
Period size: 7 Copynumber: 9.9 Consensus size: 7
53653236 AAAAAAAAGG
53653246 GAAAAAA
1 GAAAAAA
53653253 GAAAAAAA
1 G-AAAAAA
*
53653261 AAGAAAAA
1 GA-AAAAA
*
53653269 GGAAAAA
1 GAAAAAA
*
53653276 GAAAAAG
1 GAAAAAA
53653283 GAAAAAGA
1 GAAAAA-A
*
53653291 AAAAAAA
1 GAAAAAA
*
53653298 GAAAAAG
1 GAAAAAA
53653305 GAAAAAA
1 GAAAAAA
53653312 GAAAAA
1 GAAAAA
53653318 TGGAGAGGCC
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
7 36 0.69
8 16 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:53653267 original size:6 final size:6
Alignment explanation
Indices: 53653248--53653317 Score: 69
Period size: 6 Copynumber: 11.8 Consensus size: 6
53653238 AAAAAAGGGA
53653248 AAAAAG -AAAA- AAAAAG AAAAAGG AAAAAG AAAAAGG AAAAAG --AAA-
1 AAAAAG AAAAAG AAAAAG AAAAA-G AAAAAG AAAAA-G AAAAAG AAAAAG
53653293 AAAAAG AAAAAGG AAAAAAG AAAAA
1 AAAAAG AAAAA-G -AAAAAG AAAAA
53653318 TGGAGAGGCC
Statistics
Matches: 55, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
4 3 0.05
5 11 0.20
6 22 0.40
7 14 0.25
8 5 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:53653276 original size:13 final size:13
Alignment explanation
Indices: 53653258--53653317 Score: 83
Period size: 13 Copynumber: 4.8 Consensus size: 13
53653248 AAAAAGAAAA
53653258 AAAAAGAAAAAGG
1 AAAAAGAAAAAGG
53653271 AAAAAGAAAAAGG
1 AAAAAGAAAAAGG
53653284 AAAAAG--AAA--
1 AAAAAGAAAAAGG
53653293 AAAAAGAAAAAGG
1 AAAAAGAAAAAGG
53653306 AAAAAAGAAAAA
1 -AAAAAGAAAAA
53653318 TGGAGAGGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.14
11 6 0.14
13 19 0.45
14 11 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGG
Found at i:53653288 original size:36 final size:37
Alignment explanation
Indices: 53653235--53653317 Score: 127
Period size: 36 Copynumber: 2.3 Consensus size: 37
53653225 CTTCTATTTC
*
53653235 AAAAA-AAAAGGGAAAAAAGAAAAAAAAAGAAAAAGG-
1 AAAAAGAAAAAGGAAAAAAG-AAAAAAAAGAAAAAGGA
53653271 AAAAAGAAAAAGG-AAAAAGAAAAAAAAGAAAAAGGA
1 AAAAAGAAAAAGGAAAAAAGAAAAAAAAGAAAAAGGA
53653307 AAAAAGAAAAA
1 AAAAAGAAAAA
53653318 TGGAGAGGCC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 16 0.36
36 22 0.50
37 6 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (37 bp):
AAAAAGAAAAAGGAAAAAAGAAAAAAAAGAAAAAGGA
Found at i:53653317 original size:22 final size:22
Alignment explanation
Indices: 53653246--53653317 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 22
53653236 AAAAAAAAGG
* *
53653246 GAAAAAAGAAAAAAAAAGAAAAA
1 GAAAAAA-AAGAAAAAGGAAAAA
*
53653269 G--GAAAAAGAAAAAGGAAAAA
1 GAAAAAAAAGAAAAAGGAAAAA
53653289 GAAAAAAAAGAAAAAGGAAAAAA
1 GAAAAAAAAGAAAAAGG-AAAAA
53653312 GAAAAA
1 GAAAAA
53653318 TGGAGAGGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
20 14 0.33
21 3 0.07
22 13 0.31
23 12 0.29
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
GAAAAAAAAGAAAAAGGAAAAA
Found at i:53655072 original size:93 final size:93
Alignment explanation
Indices: 53654960--53655131 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
53654950 GCCCATAAGT
* *
53654960 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53655025 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
53655053 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53655118 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
53655132 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:53655127 original size:46 final size:46
Alignment explanation
Indices: 53654952--53655127 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
53654942 TGTAACCCGC
* * *
53654952 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
53654998 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
53655048 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
53655091 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
53655128 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:53657151 original size:44 final size:44
Alignment explanation
Indices: 53657010--53657189 Score: 195
Period size: 44 Copynumber: 4.1 Consensus size: 44
53657000 CAAAGAAACA
* *
53657010 AGATTTGGCATCCTTGTGTTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATTGAAGATAGC
* * * * * * * **
53657054 AGATCTGACATTCCTGTGCTTACAGCGAAGTAGATTGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAGATTGAAGATAGC
*
53657099 AGCA--TGGCATCCCTGTGTTCATAGGGAAC-GAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TTGAAGATAGC
*
53657142 AGATTTGGCATCCTTGTGTTTATAGGGAACAGATTGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATTGAAGATAGC
53657186 AGAT
1 AGAT
53657190 CTAACCTTCA
Statistics
Matches: 108, Mismatches: 22, Indels: 12
0.76 0.15 0.08
Matches are distributed among these distances:
42 3 0.03
43 11 0.10
44 78 0.72
45 15 0.14
46 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATTGAAGATAGC
Found at i:53657310 original size:34 final size:34
Alignment explanation
Indices: 53657266--53657344 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
53657256 CAAATCGAGG
* *
53657266 ACATAACAGATTTGACTCTTAGATGTTCTTAGAC
1 ACATAGCAGATTTGACTCTCAGATGTTCTTAGAC
53657300 ACATAGCAGATTTGACTCTCAGATGTTCTTAGAC
1 ACATAGCAGATTTGACTCTCAGATGTTCTTAGAC
53657334 ACATAGCAGAT
1 ACATAGCAGAT
53657345 CTAACCTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (34 bp):
ACATAGCAGATTTGACTCTCAGATGTTCTTAGAC
Found at i:53657356 original size:34 final size:34
Alignment explanation
Indices: 53657266--53657358 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 34
53657256 CAAATCGAGG
* * * *
53657266 ACATAACAGATTTGACTCTTAGATGTTCTTAGAC
1 ACATAGCAGATCTAACTCTCAGATGTTCTTAGAC
* *
53657300 ACATAGCAGATTTGACTCTCAGATGTTCTTAGAC
1 ACATAGCAGATCTAACTCTCAGATGTTCTTAGAC
53657334 ACATAGCAGATCTAAC-CTTCAGATG
1 ACATAGCAGATCTAACTC-TCAGATG
53657359 ATTAGACTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 1 0.02
34 53 0.98
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (34 bp):
ACATAGCAGATCTAACTCTCAGATGTTCTTAGAC
Found at i:53657675 original size:83 final size:83
Alignment explanation
Indices: 53657583--53658467 Score: 1421
Period size: 83 Copynumber: 10.7 Consensus size: 83
53657573 GAAGTAGATC
* * **
53657583 CAAGATGGTTTGGCATCCTTGTGCTTACAAGAAACAAATCGAGGACATAGCAGATTAGACTTTTG
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
*
53657648 GATGTTCTCAAGCAGACT
66 GATGTTCTCAAACAGACT
*
53657666 CAAGATGGTTTGGCTTCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
*
53657731 GATGTTCTCAAATAGACT
66 GATGTTCTCAAACAGACT
*
53657749 CAAGATGGTTTGGCGTCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
*
53657814 GATGTCCTCAAACAGACT
66 GATGTTCTCAAACAGACT
* * * *
53657832 CAAGATGGTTTGGCATTCTTGTGCTTACAAGAAACAAATCGACGACATAACAGATTAGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
*
53657897 AATGTTCTCAAACAGACT
66 GATGTTCTCAAACAGACT
* *
53657915 CAAGATGGTTTGGCATCCTTGTTCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTTA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
53657980 GATGTTCTCAAACAGACT
66 GATGTTCTCAAACAGACT
* * *
53657998 TAAGATGGTTTGGCATCCTTTTGCTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
53658063 GATGTTCTCAAACAGACT
66 GATGTTCTCAAACAGACT
* * * * * *
53658081 CAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCATATTTGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
* *
53658146 GATGTTCTCATATAGACT
66 GATGTTCTCAAACAGACT
* *
53658164 CAAGATGATTTGGCATCCTTGTGCTTATAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
53658229 GATGTTCTCAAACAGACT
66 GATGTTCTCAAACAGACT
* *
53658247 TAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
53658312 GATGTTCTCAAACAGACT
66 GATGTTCTCAAACAGACT
* * * * * *
53658330 CAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAAATTTGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
53658395 GATGTTCTCAAACAGACT
66 GATGTTCTCAAACAGACT
*
53658413 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGA-GACATAGCAGATT
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATT
53658468 TGGCTTTCAC
Statistics
Matches: 742, Mismatches: 60, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
82 12 0.02
83 730 0.98
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (83 bp):
CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATAGCAGATTAGACTCTCA
GATGTTCTCAAACAGACT
Found at i:53659247 original size:17 final size:19
Alignment explanation
Indices: 53659225--53659408 Score: 169
Period size: 17 Copynumber: 10.4 Consensus size: 19
53659215 ATGGAAATAT
53659225 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
53659242 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
*
53659261 AATCTTAGATATGATA--C
1 AATCTTACATATGATATGC
* **
53659278 AATCTTAGATAT-A-ACAC
1 AATCTTACATATGATATGC
*
53659295 AATCTTAGATATGAT-TGC
1 AATCTTACATATGATATGC
*
53659313 AATCTTAGATATGATA--C
1 AATCTTACATATGATATGC
*
53659330 AATCTTAGATATGAT-TGC
1 AATCTTACATATGATATGC
*
53659348 AATCTTAGATATGATA--C
1 AATCTTACATATGATATGC
*
53659365 AATCTTAGATATGAT-TGC
1 AATCTTACATATGATATGC
* *
53659383 AATCTTAAATATGATATAC
1 AATCTTACATATGATATGC
53659402 AATCTTA
1 AATCTTA
53659409 GAAGATATGA
Statistics
Matches: 149, Mismatches: 5, Indels: 24
0.84 0.03 0.13
Matches are distributed among these distances:
15 1 0.01
16 1 0.01
17 64 0.43
18 49 0.33
19 34 0.23
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:53659323 original size:35 final size:35
Alignment explanation
Indices: 53659233--53659410 Score: 250
Period size: 35 Copynumber: 5.0 Consensus size: 35
53659223 ATAATCTTCA
*
53659233 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGATAT-A-ATACAATCTTAGAT
* *
53659271 ATGA-TACAATCTTAGATATAACACAATCTTAGAT
1 ATGATTGCAATCTTAGATATAATACAATCTTAGAT
*
53659305 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATAATACAATCTTAGAT
*
53659340 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATAATACAATCTTAGAT
*
53659375 ATGATTGCAATCTTAAATATGATATACAATCTTAGA
1 ATGATTGCAATCTTAGATAT-A-ATACAATCTTAGA
53659411 AGATATGATT
Statistics
Matches: 129, Mismatches: 8, Indels: 7
0.90 0.06 0.05
Matches are distributed among these distances:
34 16 0.12
35 82 0.64
36 14 0.11
37 13 0.10
38 4 0.03
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (35 bp):
ATGATTGCAATCTTAGATATAATACAATCTTAGAT
Found at i:53659895 original size:25 final size:25
Alignment explanation
Indices: 53659862--53659915 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
53659852 CATATTATAT
*
53659862 TTTACTATATATCATAATACT-TTTC
1 TTTAATATATATCATAATA-TATTTC
* *
53659887 TTTAATATATATTATATTATATTTC
1 TTTAATATATATCATAATATATTTC
53659912 TTTA
1 TTTA
53659916 TATTACCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTAATATATATCATAATATATTTC
Found at i:53667578 original size:42 final size:42
Alignment explanation
Indices: 53667511--53667630 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 42
53667501 AGGATTACTG
*
53667511 AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATA
1 AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATACA
* * * * *
53667553 AGGCTT-TGTGTAAGACCATAGCTGGGTTATTGACATCGATACA
1 A-GATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATACA
* *
53667596 AGATTACATGTAAGACCATATATGGGATATGGCAT
1 AGATTACGTGTAAGACCATATCTGGGATATGGCAT
53667631 TGGTGCAGAA
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
42 29 0.47
43 33 0.53
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATACA
Found at i:53676270 original size:25 final size:24
Alignment explanation
Indices: 53676206--53676273 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
53676196 AGGAAGTGCT
* *
53676206 AAAAGGGCTATGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACA
* *
53676230 GAAAGGGTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTA-CA
*
53676255 AAAAGGGCTTTACCCCAGT
1 AAAAGGGCTTTGCCCCAGT
53676274 ATTAAAAGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 19 0.53
25 17 0.47
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACA
Found at i:53680974 original size:21 final size:21
Alignment explanation
Indices: 53680944--53680991 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
53680934 TATTTATCTA
53680944 ATTAAATAATTATAAAATATC
1 ATTAAATAATTATAAAATATC
*
53680965 ATTAATTAATTATAAAATATC
1 ATTAAATAATTATAAAATATC
53680986 ATTAAA
1 ATTAAA
53680992 ATATCACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAAATAATTATAAAATATC
Found at i:53687000 original size:17 final size:16
Alignment explanation
Indices: 53686978--53687012 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
53686968 CAAGATGGGG
53686978 TGGAAAATTGAGAAAAA
1 TGGAAAATT-AGAAAAA
*
53686995 TGGAAAATTATAAAAA
1 TGGAAAATTAGAAAAA
53687011 TG
1 TG
53687013 CCCCTAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (16 bp):
TGGAAAATTAGAAAAA
Found at i:53689376 original size:43 final size:43
Alignment explanation
Indices: 53689329--53689415 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
53689319 CACGGCCGTT
53689329 TGTCCCTATTTCGAATGCCTACAC-GACCTAAGAAATGGGCGTG
1 TGTCCCTATTTCGAATGCCTACACAG-CCTAAGAAATGGGCGTG
* * *
53689372 TGTCCCTATTTTGAATGCCTACACAGCCTAAGACATGGGTGTG
1 TGTCCCTATTTCGAATGCCTACACAGCCTAAGAAATGGGCGTG
53689415 T
1 T
53689416 CTCTTAGCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 39 0.98
44 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (43 bp):
TGTCCCTATTTCGAATGCCTACACAGCCTAAGAAATGGGCGTG
Found at i:53691747 original size:40 final size:40
Alignment explanation
Indices: 53691581--53691748 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
53691571 CATTTGAATG
* * * *
53691581 ATATCCGGGCTAAGTCCCAAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCAAAGGCAATTGTGCTAGTGGTT
* * *
53691621 ATATTCGGGCTAAGACCCAAAGGC-ATTCGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCAAAGGCAATT-GTGCTAGTGGTT
* * ****
53691661 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCC
1 ATATCCGGGCTAAGACCCAAAGGCAATTGTGCTAG-TGGTT
* *
53691702 A-ATCCGGGTTAAGACCCAAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCAAAGGCAATTGTGCTAGTGGTT
53691741 ATATCCGG
1 ATATCCGG
53691749 TTAAATCCCG
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
39 4 0.04
40 93 0.91
41 5 0.05
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCAAAGGCAATTGTGCTAGTGGTT
Found at i:53696991 original size:25 final size:25
Alignment explanation
Indices: 53696961--53697010 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
53696951 ATGATGGTAC
*
53696961 ATGATATAT-TGATATATTGAAATGG
1 ATGATATATGT-ATATAATGAAATGG
53696986 ATGATATATGTATATAATGAAATGG
1 ATGATATATGTATATAATGAAATGG
53697011 TAAGATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (25 bp):
ATGATATATGTATATAATGAAATGG
Found at i:53697745 original size:51 final size:51
Alignment explanation
Indices: 53697686--53697785 Score: 191
Period size: 51 Copynumber: 2.0 Consensus size: 51
53697676 GAATTGAGTA
53697686 AATTTCATATTTGAAATGGATAGATATGATTAAAGTTTATACGAGCTTACT
1 AATTTCATATTTGAAATGGATAGATATGATTAAAGTTTATACGAGCTTACT
*
53697737 AATTTCATATTTGAAATGGATAGATATGATTAAAGTTTATGCGAGCTTA
1 AATTTCATATTTGAAATGGATAGATATGATTAAAGTTTATACGAGCTTA
53697786 TTAAGCATTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (51 bp):
AATTTCATATTTGAAATGGATAGATATGATTAAAGTTTATACGAGCTTACT
Found at i:53700216 original size:40 final size:40
Alignment explanation
Indices: 53700155--53700378 Score: 335
Period size: 40 Copynumber: 5.6 Consensus size: 40
53700145 AGCTACTGCT
* *
53700155 CAAATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
53700195 CAATTGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
53700235 CAATTGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
53700275 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
** * * *
53700315 CAAATGCCTTCGGGACTT-GCCCGGAACTAGTCACTAGCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
53700354 CAGATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
53700379 TTATCATCCA
Statistics
Matches: 172, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
39 33 0.19
40 137 0.80
41 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:53708307 original size:40 final size:40
Alignment explanation
Indices: 53708252--53708482 Score: 349
Period size: 40 Copynumber: 5.8 Consensus size: 40
53708242 GGATATAGCT
* * *
53708252 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
53708292 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
53708332 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
53708372 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
53708412 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
53708451 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
53708483 TTATCATCCA
Statistics
Matches: 178, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 33 0.19
40 143 0.80
41 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:53711024 original size:46 final size:45
Alignment explanation
Indices: 53710974--53711140 Score: 198
Period size: 46 Copynumber: 3.6 Consensus size: 45
53710964 TGTTTGGGCA
53710974 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATG
*
53711020 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA--A-GAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATG-GATGCGAA-T--G
* *
53711065 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
* *
53711112 CCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
53711141 GCTTATGGGC
Statistics
Matches: 106, Mismatches: 5, Indels: 21
0.80 0.04 0.16
Matches are distributed among these distances:
42 3 0.03
43 6 0.06
45 29 0.27
46 30 0.28
47 30 0.28
49 5 0.05
50 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
Found at i:53711089 original size:47 final size:45
Alignment explanation
Indices: 53710974--53711140 Score: 191
Period size: 47 Copynumber: 3.6 Consensus size: 45
53710964 TGTTTGGGCA
* *
53710974 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCAC--ATGGATGCGAACGC
* *
53711020 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-A-GAGATG-TAACTAGGC
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACATG-GATGCGAAC---GC
53711066 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAACGC
1 -TCCGAGCTCGTTGAGTTGAGTCCGAGTTCAC-ATGGATGCGAACGC
53711113 -CCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC
53711141 GCTTATGGGC
Statistics
Matches: 107, Mismatches: 4, Indels: 21
0.81 0.03 0.16
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
45 29 0.27
46 30 0.28
47 31 0.29
49 5 0.05
50 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACATGGATGCGAACGC
Found at i:53711140 original size:92 final size:93
Alignment explanation
Indices: 53710970--53711140 Score: 299
Period size: 92 Copynumber: 1.8 Consensus size: 93
53710960 AGGATGTTTG
* *
53710970 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
53711035 TTGAGTCCGAGTTCAAGAGATGTAACTA
66 TTGAGTCCGAGTTCAAGAGATGTAACTA
* *
53711063 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
53711127 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
53711141 GCTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 40 0.54
93 34 0.46
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCAAGAGATGTAACTA
Found at i:53714515 original size:39 final size:39
Alignment explanation
Indices: 53714384--53714574 Score: 172
Period size: 40 Copynumber: 4.8 Consensus size: 39
53714374 GGATATAACG
* ** **
53714384 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGCG
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
53714424 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
53714464 ACTTGCACAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
53714502 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
53714542 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAATGCCTTCGGGACTTAGCCCGGA
53714575 CATCGTTCGA
Statistics
Matches: 124, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 24 0.19
39 21 0.17
40 69 0.56
41 10 0.08
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:53714519 original size:78 final size:80
Alignment explanation
Indices: 53714424--53714574 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 80
53714414 GGTTATAGCG
* * * *
53714424 ACTCGCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAATGCCTTCGGG-CT
1 ACTCGCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACT
53714486 TAGCCCGGATTTATTA
65 TAGCCCGGATTTATTA
** *
53714502 ACTCGCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
53714567 AGCCCGGA
66 AGCCCGGA
53714575 CATCGTTCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
77 3 0.05
78 34 0.54
79 15 0.24
80 11 0.17
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
AGCCCGGATTTATTA
Found at i:53721648 original size:29 final size:29
Alignment explanation
Indices: 53721613--53721687 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
53721603 GGTTGTGAGA
* *
53721613 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
53721642 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
53721671 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
53721688 TGGTTGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:53729527 original size:29 final size:29
Alignment explanation
Indices: 53729492--53729565 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
53729482 GTTGTGAGAT
* *
53729492 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
53729521 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
53729550 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
53729566 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:53731206 original size:31 final size:31
Alignment explanation
Indices: 53731171--53731350 Score: 306
Period size: 31 Copynumber: 5.8 Consensus size: 31
53731161 ACAAATGACA
*
53731171 AGTGAAAAGTGGTAGCTTCGGCTACCTGATT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
53731202 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
53731233 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
53731264 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
53731295 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
53731326 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
53731351 AAGTGACAAG
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 139 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:53731486 original size:46 final size:47
Alignment explanation
Indices: 53731370--53731491 Score: 174
Period size: 47 Copynumber: 2.6 Consensus size: 47
53731360 GTGATTTTCA
* *
53731370 TATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGATACTG
1 TATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACTG
* *
53731417 TATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATTC-G
1 TATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACTG
* * *
53731463 TGTAAGACCATAGCTGGGCTATGGCATCA
1 TATAAGACCATATCTGGGATATGGCATCA
53731492 TTATGTGAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
46 27 0.40
47 41 0.60
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (47 bp):
TATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACTG
Found at i:53733206 original size:34 final size:34
Alignment explanation
Indices: 53733163--53733229 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
53733153 TTGTGGATCC
*
53733163 GAAGCTGCTTTCAAACTATCTCGAATTACTTTCT
1 GAAGCTGCTTTCAAACTATCGCGAATTACTTTCT
53733197 GAAGCTGCTTTCAAACTATCGCGAATTACTTTC
1 GAAGCTGCTTTCAAACTATCGCGAATTACTTTC
53733230 ACTTTATCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (34 bp):
GAAGCTGCTTTCAAACTATCGCGAATTACTTTCT
Found at i:53746334 original size:18 final size:18
Alignment explanation
Indices: 53746311--53746345 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53746301 TTCCCGGATG
*
53746311 ATAATCTATCACTAACTT
1 ATAATCTATCAATAACTT
*
53746329 ATAATCTTTCAATAACT
1 ATAATCTATCAATAACT
53746346 CGAGCCATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATCTATCAATAACTT
Found at i:53750092 original size:19 final size:19
Alignment explanation
Indices: 53750068--53750125 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
53750058 GAACGGTTGA
*
53750068 GACACACGTCCGTGTCTCT
1 GACACACGCCCGTGTCTCT
53750087 GACACACGCCCGTGTCTCT
1 GACACACGCCCGTGTCTCT
53750106 GACACACGCCCGTGTCTCT
1 GACACACGCCCGTGTCTCT
53750125 G
1 G
53750126 CACGTGTGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.16, C:0.40, G:0.22, T:0.22
Consensus pattern (19 bp):
GACACACGCCCGTGTCTCT
Found at i:53750295 original size:27 final size:27
Alignment explanation
Indices: 53750257--53750311 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
53750247 CATACATTTC
*
53750257 ATATACATTTTTCCATTTTAAATATAA
1 ATATACATTTTTCCATTTCAAATATAA
53750284 ATATACATTTTTCCATTTCAAATATAA
1 ATATACATTTTTCCATTTCAAATATAA
53750311 A
1 A
53750312 ACATTCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATACATTTTTCCATTTCAAATATAA
Found at i:53760844 original size:31 final size:29
Alignment explanation
Indices: 53760809--53760876 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 29
53760799 AATATCAAAA
* *
53760809 TTATATATGAATTTTGATTTAATATGCAATG
1 TTATATATGAACTTTAATTT--TATGCAATG
* * *
53760840 TTATACATGAACTTTAATTTTGTGCAATT
1 TTATATATGAACTTTAATTTTATGCAATG
53760869 TTATATAT
1 TTATATAT
53760877 AAAAATTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 14 0.45
31 17 0.55
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (29 bp):
TTATATATGAACTTTAATTTTATGCAATG
Found at i:53761093 original size:16 final size:16
Alignment explanation
Indices: 53761074--53761108 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53761064 TGTATAATCA
*
53761074 TAACAAATTATAAATT
1 TAACAAAGTATAAATT
*
53761090 TAACCAAGTATAAATT
1 TAACAAAGTATAAATT
53761106 TAA
1 TAA
53761109 GATTTTCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (16 bp):
TAACAAAGTATAAATT
Found at i:53780542 original size:308 final size:306
Alignment explanation
Indices: 53779906--53780836 Score: 1346
Period size: 308 Copynumber: 3.0 Consensus size: 306
53779896 AATTACAAAA
* * * * *
53779906 GAATAAAAAAGAAAGCCTTTTTCACTAGCAGTAACATGCAGAGCGAAGAAATAAAATAATTTTAA
1 GAATAAAAAAGAAAGCCCTTTTCACCAGCAGTAACATGCAGAGCAAAGAAATAAAATGATTTTAG
*
53779971 ATCCAAATTTGAGTAAAACCAAGTTCTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
66 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
* * * * *
53780036 TAATCATGTAGAGTCTCCAAGTACCAATCAGATAAAACTAATAACATATATATATAGTTTAAAGA
131 TAATAATGTAGAGTCTCAAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAG-
* * * * *
53780101 AAACAAAAACTATTAACCAATTAGCTCTAAACCAAAATTTACCTAAGACCAGCAAAAAAAAAAAA
195 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCTAAGACCAGCAAAAAAAAAAAG
* * * *
53780166 ATTTGCAAGGTAGTTCAACACAAAATCACAGTAAAAAAGAATAATCTG
260 A-TTGCAAGGTAATTCAGCACAAAATCACAATAAGAAAGAATAATCTG
* * * *
53780214 GAATAAAAAGGAAAGCCCTTTTCACCAGCAATAACATGCAGAGCAAAAAAATAAAACGATTTTAG
1 GAATAAAAAAGAAAGCCCTTTTCACCAGCAGTAACATGCAGAGCAAAGAAATAAAATGATTTTAG
* * * * *
53780279 ATCCAAATTTGTGTAAAACCAAGTTGTTAGTAGAAATTATGCAAAACTCACAACAGATATACAAT
66 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
53780344 TAATAATGTAGAGTCTCAAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
131 TAATAATGTAGAGTCTCAAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
* * *
53780409 ATACAAAAGCTACTAACCAATTAGCT-TGAACCAAAACTTACCTAAGACTAGC-AAAAAAGAATG
196 A-ACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCTAAGACCAGCAAAAAAAAAAAG
*
53780472 ATTGCAAGGTAATTCAGCACAAAATCAGCAATAAGAAAGAATAATTTG
260 ATTGCAAGGTAATTCAGCACAAAATCA-CAATAAGAAAGAATAATCTG
* * * *
53780520 GAATAAAAAAAGAAAGGCCCTTTTCACCATCAGTAATATGCAAAACAAAGAAATAAAATGATTTT
1 GAAT-AAAAAAGAAA-GCCCTTTTCACCAGCAGTAACATGCAGAGCAAAGAAATAAAATGATTTT
* *
53780585 AGATCCAAATTTGAGTAAAACCAAGTTGTTAGCATAAATTATGCAAAACCCACATCACAAATACA
64 AGATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACA
* * *
53780650 ATTAATGATGTAGAGTCTTCAAA-TACTAAGCAGATAAAACTAATAACATAGAAATATAATTTAA
129 ATTAATAATGTAGAGTC-TCAAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAA
* *
53780714 AGAAACACAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCCAAGACCAGCAAAAATAAAA
193 AGAAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCTAAGACCAGC--AAA-AAAA
53780779 AAAAGATTGCAAGGTAATTCAGCACAAAATCAACAATAAGAAAGAATAATCTG
255 AAAAGATTGCAAGGTAATTCAGCACAAAATC-ACAATAAGAAAGAATAATCTG
53780832 GAATA
1 GAATA
53780837 CCCTCAAAGA
Statistics
Matches: 555, Mismatches: 57, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
305 24 0.04
306 30 0.05
307 57 0.10
308 379 0.68
309 5 0.01
311 3 0.01
312 56 0.10
313 1 0.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.22
Consensus pattern (306 bp):
GAATAAAAAAGAAAGCCCTTTTCACCAGCAGTAACATGCAGAGCAAAGAAATAAAATGATTTTAG
ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
TAATAATGTAGAGTCTCAAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
AACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCTAAGACCAGCAAAAAAAAAAAGA
TTGCAAGGTAATTCAGCACAAAATCACAATAAGAAAGAATAATCTG
Found at i:53781415 original size:16 final size:16
Alignment explanation
Indices: 53781375--53781419 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
53781365 AGGTTTAGGT
*
53781375 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
53781392 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
53781406 TTAAAAATTTATTT
1 TTAAAAATTTATTT
53781420 TCATATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 10 0.40
17 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:53788335 original size:15 final size:16
Alignment explanation
Indices: 53788315--53788347 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53788305 GAGATTATTT
53788315 TTCA-TTTGAATAACA
1 TTCATTTTGAATAACA
*
53788330 TTCATTTTGAATTACA
1 TTCATTTTGAATAACA
53788346 TT
1 TT
53788348 TACAATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (16 bp):
TTCATTTTGAATAACA
Found at i:53791710 original size:12 final size:12
Alignment explanation
Indices: 53791695--53791732 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
53791685 CTTTCGAATC
53791695 TTTTTTCTTTCT
1 TTTTTTCTTTCT
*
53791707 TTTTTT-TGTTGT
1 TTTTTTCT-TTCT
53791719 TTTTTTCTTTCT
1 TTTTTTCTTTCT
53791731 TT
1 TT
53791733 ATATATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (12 bp):
TTTTTTCTTTCT
Found at i:53792287 original size:3 final size:3
Alignment explanation
Indices: 53792279--53792307 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53792269 CTACTTTAAT
53792279 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53792308 CTTACTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:53797090 original size:21 final size:21
Alignment explanation
Indices: 53797064--53797104 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
53797054 AAAAGAGAAA
53797064 AAAACAAAAAAAATAAAAAAC
1 AAAACAAAAAAAATAAAAAAC
53797085 AAAACAAAAAAAATAAAAAA
1 AAAACAAAAAAAATAAAAAA
53797105 AGAGAGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (21 bp):
AAAACAAAAAAAATAAAAAAC
Found at i:53797104 original size:16 final size:16
Alignment explanation
Indices: 53797061--53797097 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
53797051 ATGAAAAGAG
53797061 AAAAAAACAAAA-AAA
1 AAAAAAACAAAACAAA
53797076 ATAAAAAACAAAACAAA
1 A-AAAAAACAAAACAAA
53797093 AAAAA
1 AAAAA
53797098 TAAAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 15 0.75
17 4 0.20
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAAAAACAAAACAAA
Found at i:53797707 original size:11 final size:12
Alignment explanation
Indices: 53797687--53797712 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53797677 TCATTCATTC
53797687 AAAAGAAAAAAA
1 AAAAGAAAAAAA
53797699 AAAAGAAAAAAA
1 AAAAGAAAAAAA
53797711 AA
1 AA
53797713 TGGAGAGGTC
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:53799206 original size:77 final size:77
Alignment explanation
Indices: 53799064--53799927 Score: 608
Period size: 77 Copynumber: 11.0 Consensus size: 77
53799054 TTTCTGTTTC
* * **
53799064 AAAATTCAACTCATATTACGAGAAATGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
53799127 TCTGTTTTTCAA
66 TCTGTTTTTCAA
* * *
53799139 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTATTTTTAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCACACGCTGAGGTATTTTCAAT
**
53799203 TTCTGTTTTTTTA
65 TTCTGTTTTTCAA
* ** * *
53799216 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGG-GGCGCGCTGAGGTATTGTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
* *
53799279 TTTGTGTTTTAATTCA
66 TCTGT-TTTTCA---A
* * * *
53799295 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAACCTCAAGTCACA--TTGAGGTATTTTCAA-T
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
* **
53799357 T-T-ATCATC--
66 TCTGTTTTTCAA
* * *
53799365 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACCCGTTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
***
53799428 TCTGCTCAATTTATGTTTTTC
66 TCTG-------T-T-TTTCAA
53799449 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
*
53799512 TCTATTTTTC-A
66 TCTGTTTTTCAA
** *
53799523 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GGCACGCTGAGGTATTGTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
* *
53799586 TTTGTGTTTTAATTTA
66 TCTGT-TTTTCA---A
* *
53799602 TGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACA--TTGAGGTATTT
1 ------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTT
*
53799665 T--A--TC-----ATC-A
60 TCAATTTCTGTTTTTCAA
* *
53799673 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--GCACGCTAAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
*
53799736 TCTATTTTAATTTCCGTGTTTCAA
66 TC----------T--GTTTTTCAA
* *
53799760 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTATCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
53799825 TCTGTTTTTTCAATTTA
66 TCTG-TTTTTC-A---A
** *
53799842 TGCTTTTCAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTA
1 --------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCACACGCTGAGGTA
* *
53799906 GTTTCAATTTCTGCTTTTCAA
57 TTTTCAATTTCTGTTTTTCAA
53799927 A
1 A
53799928 TTCTATTTTT
Statistics
Matches: 636, Mismatches: 74, Indels: 156
0.73 0.09 0.18
Matches are distributed among these distances:
63 2 0.00
65 50 0.08
67 1 0.00
68 2 0.00
69 2 0.00
70 54 0.08
71 3 0.00
72 1 0.00
73 2 0.00
74 63 0.10
75 64 0.10
76 5 0.01
77 74 0.12
78 7 0.01
79 52 0.08
80 1 0.00
81 3 0.00
82 2 0.00
83 1 0.00
84 63 0.10
85 49 0.08
86 3 0.00
87 44 0.07
88 1 0.00
89 27 0.04
90 60 0.09
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (77 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
TCTGTTTTTCAA
Found at i:53799371 original size:70 final size:70
Alignment explanation
Indices: 53799295--53799428 Score: 223
Period size: 70 Copynumber: 1.9 Consensus size: 70
53799285 TTTTAATTCA
*
53799295 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAACCTCAAGTCACATTGAGGTATTTTCAATTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAACCTCAAGACACATTGAGGTATTTTCAATTTA
53799360 TCATC
66 TCATC
* * * *
53799365 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACCCGTTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAACCTCAAGACACATTGAGGTATTTTCAATTT
53799429 CTGCTCAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (70 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGCTGAACCTCAAGACACATTGAGGTATTTTCAATTTA
TCATC
Found at i:53799500 original size:154 final size:153
Alignment explanation
Indices: 53799216--53799825 Score: 693
Period size: 154 Copynumber: 4.0 Consensus size: 153
53799206 TGTTTTTTTA
** * * *
53799216 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGGCGCGCTGAGGTATTGTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTC
* * * * *
53799281 TGTGT--TTTA---ATTCAAAAAATCAACTCATATTGCGAGAGGTGAGCTGAACCTCAAGTCACA
66 TGTTTAATTTATGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
*
53799341 TTGAGGTATTTTCAATTTATCATC
130 CTGAGGTATTTTCAATTTATCATC
* * * *
53799365 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACCCGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTC
* * * *
53799430 TGCTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
66 TGTTTAATTTATG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
**
53799495 CTGAGGTATTTTCAATTTCTATTTTTC
130 CTGAGGTATTTTCAA-TT-TA-TCATC
* *
53799522 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAA--T
* *
53799587 TTGTGTTTTAATTTATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTC
63 TTCTG-TTTAATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
* *
53799651 ACATTGAGGTATTTT--A-TCATCA--
127 ACACTGAGGTATTTTCAATTTATCATC
*
53799673 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTAAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTC
* ** *
53799738 TATTTTAATTTCCGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
66 T-GTTTAATTTATGT-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--
* * *
53799803 ACACGCCGAGGTATTATCAATTT
125 ACACACTGAGGTATTTTCAATTT
53799826 CTGTTTTTTC
Statistics
Matches: 388, Mismatches: 50, Indels: 38
0.82 0.11 0.08
Matches are distributed among these distances:
148 13 0.03
149 59 0.15
150 62 0.16
151 4 0.01
152 40 0.10
153 1 0.00
154 68 0.18
155 6 0.02
156 3 0.01
157 5 0.01
158 55 0.14
159 58 0.15
160 5 0.01
161 9 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (153 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTC
TGTTTAATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACAC
TGAGGTATTTTCAATTTATCATC
Found at i:53799669 original size:307 final size:307
Alignment explanation
Indices: 53799121--53799833 Score: 1017
Period size: 307 Copynumber: 2.3 Consensus size: 307
53799111 TGAGGTATTT
* *
53799121 TCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT-TGGCTCACA
1 TCAATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--CACA
* * *
53799185 CGCTGAGGTATTTTTAATTTCTGTTTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
63 CGCTGAGGTATTTTCAATTTCT-ATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* *
53799250 CCTTGGGGCGCGCTGAGGTATTGTCAATTTTTGTGTTTTAATTCAAAAAATCAACTCATATTGCG
127 CCTCGGGGCACGCTGAGGTATTGTCAATTTTTGTGTTTTAATTCAAAAAATCAACTCATATTGCG
53799315 AGAGGTGAGCTGAACCTCAAGTCACATTGAGGTATTTTCAATTTATCATC-AAAAATCAACTCAT
192 AGAGGTGAGCTGAACCTCAAGTCACATTGAGGTA--TT--ATTTATCATCAAAAAATCAACTCAT
* * *
53799379 ATTGCGAGAGGTGAGTTGAGCCTCAAGACCCGTTGAGGTATTTTCAATTTCT-GC
253 ATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTATTTTCAATTTCTAGC
*
53799433 TCAATTTATGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGC
1 TCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACACGC
53799496 TGAGGTATTTTCAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
66 TGAGGTATTTTCAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
*
53799561 GGGGCACGCTGAGGTATTGTCAATTTTTGTGTTTTAATTTATGTTTCAAAAATCAACTCATATTG
131 GGGGCACGCTGAGGTATTGTCAATTTTTGTGTTTTAATTCA------AAAAATCAACTCATATTG
* *
53799626 CGAGAGGTGAGTTGAGCCTCAAGTCACATTGAGGTA-T-TTTATCATCAAAAAATCAACTCATAT
190 CGAGAGGTGAGCTGAACCTCAAGTCACATTGAGGTATTATTTATCATCAAAAAATCAACTCATAT
* * **
53799689 TGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTAAGGTATTTTCAATTTCTATT
255 TGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTATTTTCAATTTCTAGC
* * *
53799742 TTAATTTCCGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACAC
1 TCAATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACAC
* * *
53799807 GCCGAGGTATTATCAATTTCTGTTTTT
64 GCTGAGGTATTTTCAATTTCTATTTTT
53799834 TCAATTTATG
Statistics
Matches: 363, Mismatches: 25, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
307 91 0.25
308 85 0.23
309 12 0.03
310 37 0.10
311 43 0.12
312 15 0.04
313 80 0.22
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (307 bp):
TCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACACGC
TGAGGTATTTTCAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
GGGGCACGCTGAGGTATTGTCAATTTTTGTGTTTTAATTCAAAAAATCAACTCATATTGCGAGAG
GTGAGCTGAACCTCAAGTCACATTGAGGTATTATTTATCATCAAAAAATCAACTCATATTGCGAG
AGGTGAGTTGAGCCTCAAGACACGCTAAGGTATTTTCAATTTCTAGC
Found at i:53799718 original size:150 final size:150
Alignment explanation
Indices: 53799215--53799805 Score: 712
Period size: 150 Copynumber: 3.9 Consensus size: 150
53799205 CTGTTTTTTT
** *
53799215 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGGCGCGCTGAGGTATTGTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTGTCAATTT
* * * * *
53799280 TTG-TGT--TTTA--ATTCAAAAAATCAACTCATATTGCGAGAGGTGAGCTGAACCTCAAGTCAC
66 CTGTTTTAATTTATGTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCAC
*
53799340 ATTGAGGTATTTTCAATTTATC
130 ATTGAGGTATTTT-AATTCATC
* * * * *
53799362 ATCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACCCGTTGAGGTATTTTCAAT
1 A--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTGTCAAT
* * * *
53799427 TTCTG-CTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
64 TTCTGTTTTAATTTATG--TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGT
**
53799491 CACGCTGAGGTATTTTCAATTTCTATTTTTC
127 CACATTGAGGTATTTT-AA-TTC-A----TC
*
53799522 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTGTCAA--T
*
53799587 TTGTGTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCA
64 TTCTGTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCA
53799652 CATTGAGGTATTTT-A-TCATC
129 CATTGAGGTATTTTAATTCATC
* *
53799672 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTAAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTGTCAATTT
* * *
53799737 CTATTTTAATTTCCGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
66 CTGTTTTAATTT--ATGTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGT
53799802 CACA
127 CACA
53799806 CGCCGAGGTA
Statistics
Matches: 384, Mismatches: 39, Indels: 37
0.83 0.08 0.08
Matches are distributed among these distances:
147 1 0.00
148 13 0.03
149 59 0.15
150 67 0.17
151 4 0.01
152 45 0.12
154 56 0.15
155 7 0.02
156 1 0.00
157 1 0.00
158 55 0.14
159 58 0.15
160 8 0.02
161 9 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (150 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTGTCAATTT
CTGTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACA
TTGAGGTATTTTAATTCATC
Found at i:53799726 original size:65 final size:65
Alignment explanation
Indices: 53799608--53799730 Score: 201
Period size: 65 Copynumber: 1.9 Consensus size: 65
53799598 TTTATGTTTC
* * *
53799608 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACATTGAGGTATTTTATCATCA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACACTAAGGTATTTTATCATCA
* *
53799673 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTAAGGTATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACACTAAGGTATTTT
53799731 CAATTTCTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (65 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACACTAAGGTATTTTATCATCA
Found at i:53799729 original size:224 final size:234
Alignment explanation
Indices: 53799449--53799886 Score: 644
Period size: 224 Copynumber: 1.9 Consensus size: 234
53799439 TATGTTTTTC
*
53799449 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTC
** *
53799514 -T-A-T-T-TTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GGCACGCT
66 TTAATTCTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCC
* * *
53799571 GAGGTATTGTCAATTTTTGTGTTTT-AATTTATG-TTTCAAAAATCAACTCATATTGCGAGAGGT
131 GAGGTATTATCAATTTCTGTGTTTTCAATTTATGCTTTCAAAAATCAACTCATATTGCAAGAGGT
53799634 GAGTTGAGCCTCAAGTCACATTGAGGTATTTTATCATCA
196 GAGTTGAGCCTCAAGTCACATTGAGGTATTTTATCATCA
*
53799673 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTAAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTC
53799738 TATTTTAATTTCCGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
66 ----TTAA-TT-C-TGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
*
53799803 ACACGCCGAGGTATTATCAATTTCTGTTTTTTCAATTTATGCTTTTCAAAAATCAACTCATATTG
124 ACACGCCGAGGTATTATCAATTTCTGTGTTTTCAATTTATGC-TTTCAAAAATCAACTCATATTG
*
53799868 TAAGAGGTGAGTTGAGCCT
188 CAAGAGGTGAGTTGAGCCT
53799887 TGGCTCACAC
Statistics
Matches: 186, Mismatches: 10, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
224 63 0.34
229 1 0.01
230 1 0.01
232 1 0.01
235 1 0.01
236 4 0.02
237 39 0.21
238 2 0.01
239 27 0.15
240 8 0.04
242 39 0.21
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (234 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTTC
TTAATTCTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCC
GAGGTATTATCAATTTCTGTGTTTTCAATTTATGCTTTCAAAAATCAACTCATATTGCAAGAGGT
GAGTTGAGCCTCAAGTCACATTGAGGTATTTTATCATCA
Found at i:53799895 original size:90 final size:89
Alignment explanation
Indices: 53799670--53799983 Score: 302
Period size: 90 Copynumber: 3.5 Consensus size: 89
53799660 TATTTTATCA
* * * ** *
53799670 TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--GCACGCTAAGGTATTTTCA
1 TCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT-TGGTCACACGCCGAGGTAGTTTCA
* * ** *
53799733 ATTTCT-ATTTT-AATTTCCGTGTT
65 ATTTCTGCTTTTCAAATTCTATTTT
* *
53799756 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTA-TTAT
1 TC-AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT-TGGTCACACGCCGAGGTAGTT-T
*
53799820 CAATTTCTGTTTTTTC-AATT-TATGCTTT
63 CAATTTCTG-CTTTTCAAATTCTAT--TTT
* *
53799848 TC-AAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTAGTTTCA
1 TCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGG-TCACACGCCGAGGTAGTTTCA
53799912 ATTTCTGCTTTTCAAATTCTATTTT
65 ATTTCTGCTTTTCAAATTCTATTTT
53799937 TCAAAAAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTT
1 TC------AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTT
53799984 CTGCTTTTCG
Statistics
Matches: 194, Mismatches: 14, Indels: 30
0.82 0.06 0.13
Matches are distributed among these distances:
86 2 0.01
87 42 0.22
88 2 0.01
89 31 0.16
90 64 0.33
91 12 0.06
92 4 0.02
96 37 0.19
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (89 bp):
TCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGTCACACGCCGAGGTAGTTTCAA
TTTCTGCTTTTCAAATTCTATTTT
Found at i:53800099 original size:16 final size:16
Alignment explanation
Indices: 53800078--53800108 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53800068 CTGAAGTAAT
*
53800078 TTCAATTTCTGTTTTC
1 TTCAATTTATGTTTTC
53800094 TTCAATTTATGTTTT
1 TTCAATTTATGTTTT
53800109 TCAAAAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.13, G:0.06, T:0.65
Consensus pattern (16 bp):
TTCAATTTATGTTTTC
Found at i:53800188 original size:89 final size:88
Alignment explanation
Indices: 53800005--53800251 Score: 320
Period size: 89 Copynumber: 2.8 Consensus size: 88
53799995 TTTTTGCTTT
* * *
53800005 TCAATTTATATTTGTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCT
1 TCAATTTAT-TTTTTC-AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
* * * *
53800070 GAAGTAATTTCAATTTCTGTTTTCT
64 GAGGTAATCTCAATTTCCGTTTTCG
* * *
53800095 TCAATTTATGTTTTTCAAAAACCAGCTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCACACGC
1 TCAATTTAT-TTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGC
53800160 TGAGGTAATCTCAATTTCCG-TTT-G
63 TGAGGTAATCTCAATTTCCGTTTTCG
* *
53800184 TCAATTTA-TTTTTCAAAAACCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAA
1 TCAATTTATTTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
53800248 GGTA
66 GGTA
53800252 TTTTAATTTC
Statistics
Matches: 139, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
85 12 0.09
87 43 0.31
89 45 0.32
90 17 0.12
91 22 0.16
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (88 bp):
TCAATTTATTTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
GGTAATCTCAATTTCCGTTTTCG
Found at i:53800224 original size:87 final size:85
Alignment explanation
Indices: 53799673--53800908 Score: 517
Period size: 87 Copynumber: 15.1 Consensus size: 85
53799663 TTTATCATCA
* * * *
53799673 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTAAGGTATTTTCAATTTC
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
** * *
53799738 TATTT-T-AATTTCCGTGTTTC
66 CGTTTGTCAATTT--ATTTTTC
* *
53799758 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGT-ATTATCA
1 --AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTAATT-TCA
* *
53799822 ATTTCTGTTTTTTCAATTTATGCTTTTC
61 ATTTCCG-TTTGTCAATTTAT--TTTTC
* ** * *
53799850 AAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTAGTTTCAAT
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAAT
*
53799914 TTCTGCTTT-TCAAATTCTATTTTTC
63 TTCCG-TTTGTC-AATT-TATTTTTC
* * * *
53799939 AAAAAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT--------TCT--GCT--TTT
1 -------AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
* ** * *
53799992 CGATTTTTGCTTT-TCAATTTATATTTGTC
59 CAATTTCCG-TTTGTCAA--TTTATTTTTC
* * *
53800021 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAAGTAATTTCAATTT
1 -AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
* *
53800086 CTGTTTTCTTCAATTTATGTTTTTC
65 CCG-TTT-GTCAATTTA--TTTTTC
* * * * * *
53800111 AAAAACCAGCTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTAATCTCAATT
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTAATTTCAATT
53800176 TCCGTTTGTCAATTTATTTTTC
64 TCCGTTTGTCAATTTATTTTTC
* * *
53800198 AAAAACCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGT-ATTTTAATTT-
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
53800261 C---TG--------TTTTTC
66 CGTTTGTCAATTTATTTTTC
* * * * *
53800270 AAAAATCAACTCT-TATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGTTGAGGT-ATTGTAAATT
1 AAAAATCAACT-TATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT-TCAATT
**
53800333 TTTGTGTT-TCAATTTATGTTTTTC
64 TCCGT-TTGTCAATTTA--TTTTTC
* *
53800357 AAAAATCAACTTATATTGCGAGA---G-G-T--G----A-GACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-ATTTCAATTT
53800410 -C---TG--------TTTTTC
65 CCGTTTGTCAATTTATTTTTC
* * * *
53800419 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACTGAGGT-ATTGTCAATTT
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT-TCAATTT
** *
53800483 TTGTGTT-TCAATTTATGTTTTTT
65 CCGT-TTGTCAATTTA--TTTTTC
* * * * *
53800506 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCGGGACATGCTGAGGTAATTGCAATTT-
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
53800570 C-TATTGTC-A---A------
66 CGT-TTGTCAATTTATTTTTC
* * * * *
53800580 AAAAATCAA-TTCATATTGCAAGAAGTGAGTTGAGCTTC-GGCTCACGTGCTGAGGTATTTTCAA
1 AAAAATCAACTT-ATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC--GCTGAGGTAATTTCAA
*
53800643 TTT-C-TATT-TC----TATTTGTC
62 TTTCCGT-TTGTCAATTTATTTTTC
* *
53800661 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTT-
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
53800724 C---TG--------TTTTTC
66 CGTTTGTCAATTTATTTTTC
* * ** *
53800733 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGGCACGCTGAGG-AATTGTCAATTT
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT-TCAATTT
** * ****
53800797 TTGTGTT-TTAATTTCA--AAAA
65 CCGT-TTGTCAATTT-ATTTTTC
* * * *
53800817 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAGACGCTGAGGTACTTTCGATTTC
1 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
53800882 CGTTTTTCAATTTATGTTTTTC
66 CGTTTGTCAATTTA--TTTTTC
53800904 AAAAA
1 AAAAA
53800909 AAAATTAAAA
Statistics
Matches: 908, Mismatches: 115, Indels: 252
0.71 0.09 0.20
Matches are distributed among these distances:
62 28 0.03
65 1 0.00
66 1 0.00
67 1 0.00
69 1 0.00
71 1 0.00
72 65 0.07
73 69 0.08
74 44 0.05
75 15 0.02
76 66 0.07
77 2 0.00
78 22 0.02
80 36 0.04
81 5 0.01
82 25 0.03
83 6 0.01
84 74 0.08
85 18 0.02
86 6 0.01
87 175 0.19
88 21 0.02
89 72 0.08
90 81 0.09
91 28 0.03
92 9 0.01
96 36 0.04
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (85 bp):
AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
CGTTTGTCAATTTATTTTTC
Found at i:53800323 original size:72 final size:73
Alignment explanation
Indices: 53800192--53800344 Score: 202
Period size: 72 Copynumber: 2.1 Consensus size: 73
53800182 TGTCAATTTA
*
53800192 TTTTTCAAAAACCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATT-TT
1 TTTTTCAAAAACCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTGTA
53800256 AATTTCTG
66 AATTTCTG
* * * * * *
53800264 TTTTTCAAAAATCAACTCT-TATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGTTGAGGTATTGT
1 TTTTTCAAAAACCAACT-TATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTGT
*
53800328 AAATTTTTG
65 AAATTTCTG
*
53800337 TGTTTCAA
1 TTTTTCAA
53800345 TTTATGTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
72 54 0.77
73 16 0.23
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (73 bp):
TTTTTCAAAAACCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTGTA
AATTTCTG
Found at i:53800442 original size:149 final size:147
Alignment explanation
Indices: 53800238--53800530 Score: 496
Period size: 149 Copynumber: 2.0 Consensus size: 147
53800228 TGAGCCTCAG
* *
53800238 GACACGCTAAGGTATTTTAATTTCTGTTTTTCAAAAATCAACTCTTATTGTGAGAGGTGAGTTGA
1 GACACGCTAAGGTATTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
**
53800303 GCCTCGGGGCACGTTGAGGTATTGTAAATTTTTGTGTTTCAATTTATGTTTTTCAAAAATCAACT
66 GCCTCGGGGCACACTGAGGTATTGTAAATTTTTGTGTTTCAATTTATGTTTTTCAAAAATCAACT
*
53800368 TATATTGCGAGAGGTGA
131 CATATTGCGAGAGGTGA
*
53800385 GACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
1 GACACGCTAAGGTA-TTTT-AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
* *
53800450 GAGCCTCGGGGCACACTGAGGTATTGTCAATTTTTGTGTTTCAATTTATGTTTTTTAAAAATCAA
64 GAGCCTCGGGGCACACTGAGGTATTGTAAATTTTTGTGTTTCAATTTATGTTTTTCAAAAATCAA
53800515 CTCATATTGCGAGAGG
129 CTCATATTGCGAGAGG
53800531 CGAGTTGAGC
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
147 13 0.10
148 4 0.03
149 119 0.88
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (147 bp):
GACACGCTAAGGTATTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
GCCTCGGGGCACACTGAGGTATTGTAAATTTTTGTGTTTCAATTTATGTTTTTCAAAAATCAACT
CATATTGCGAGAGGTGA
Found at i:53800688 original size:80 final size:73
Alignment explanation
Indices: 53800488--53800891 Score: 314
Period size: 73 Copynumber: 5.3 Consensus size: 73
53800478 AATTTTTGTG
* * * * * *
53800488 TTTCAATTTATGTTTTTTAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCGGGACATGC
1 TTTCAATTTCTCTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACATGC
53800553 TGAGGTAA
66 TGAGGTAA
* * * * * *
53800561 TTGCAATTTCT-ATTGTCAAAAAAATCAATTCATATTGCAAGAAGTGAGTTGAGCTTC-GGCTCA
1 TTTCAATTTCTCTTTTTC--AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG---A
* *
53800624 CGTGCTGAGGTAT
61 CATGCTGAGGTAA
*
53800637 TTTCAATTTCTATTTCTATTTGTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TTTCAATTTC----TCT-TTT-TCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG
53800701 ACATGCTGAGGTAA
60 ACATGCTGAGGTAA
* ** * *
53800715 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGGCACGC
1 TTTCAATTTCTCTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACATGC
53800780 TGAGG-AA
66 TGAGGTAA
* * *
53800787 TTGTCAATTTTTGTGTTTTAATTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TT-TCAA---TT-TCTCTT--TTTC-----AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGC
* * *
53800852 CTCAGGAGACGCTGAGGTAC
54 CTCAGGACATGCTGAGGTAA
*
53800872 TTTCGATTTC-CGTTTTTCAA
1 TTTCAATTTCTC-TTTTTCAA
53800892 TTTATGTTTT
Statistics
Matches: 265, Mismatches: 38, Indels: 56
0.74 0.11 0.16
Matches are distributed among these distances:
72 9 0.03
73 66 0.25
74 35 0.13
76 23 0.09
77 4 0.02
78 26 0.10
79 4 0.02
80 37 0.14
81 4 0.02
82 2 0.01
83 2 0.01
84 50 0.19
85 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (73 bp):
TTTCAATTTCTCTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACATGC
TGAGGTAA
Found at i:53800703 original size:154 final size:152
Alignment explanation
Indices: 53800506--53800870 Score: 450
Period size: 154 Copynumber: 2.4 Consensus size: 152
53800496 TATGTTTTTT
* *
53800506 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCGGGACATGCTGAGGTAATTGCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTGCAATTTC
* *
53800571 T-ATTGTCAAAAAAATCAATTCATATTGCAAGAAGTGAGTTGAG-CTTCGGCTCACGTGCTGAGG
66 TGATTGTC--AAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTT-GGCGCAC--GCTGAGG
* * *
53800634 TATTTTCAATTTCTAT-TTCTATTTGTC
126 AATTGTCAATTTCTATGTTCTAATT-TC
*
53800661 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTGCAATTTC
* * * *
53800725 TGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGGGCACGCTGAGGAATTG
66 TGATTGTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTTGGCGCACGCTGAGGAATTG
* * *
53800790 TCAATTTTTGTGTTTTAATTTC
131 TCAATTTCTATGTTCTAATTTC
* *
53800812 AAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAGACGCTGAGGTA
1 -----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTA
53800871 CTTTCGATTT
Statistics
Matches: 184, Mismatches: 17, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
151 21 0.11
152 6 0.03
153 37 0.20
154 65 0.35
155 4 0.02
157 51 0.28
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (152 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTGCAATTTC
TGATTGTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTTGGCGCACGCTGAGGAATTG
TCAATTTCTATGTTCTAATTTC
Found at i:53801063 original size:86 final size:87
Alignment explanation
Indices: 53800918--53801128 Score: 280
Period size: 86 Copynumber: 2.4 Consensus size: 87
53800908 AAAAATTAAA
* * * * * * *
53800918 AAAAATCAATTCATGTTACTAGAGATGAGTTGAGCTTCGGGTCACATGCCGAGGTATTTTGAAAT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAA
* * *
53800983 TATATTT-TAATTTCTGTTTTC
66 TATATTTGCAAATTCTATTTTC
*
53801004 AAAAATCGACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAA
*
53801069 TCTATTTGGCAAATTCTATTTTC
66 TATATTT-GCAAATTCTATTTTC
* *
53801092 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT
53801129 TTGCTCACGT
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 63 0.58
88 45 0.42
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (87 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAAA
TATATTTGCAAATTCTATTTTC
Found at i:53802158 original size:11 final size:11
Alignment explanation
Indices: 53802142--53802179 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
53802132 TTCTTTCGAA
53802142 TCTTTTTTCTT
1 TCTTTTTTCTT
53802153 TCTTTTTT-TT
1 TCTTTTTTCTT
*
53802163 TGTTTTTTTCTT
1 T-CTTTTTTCTT
53802175 TCTTT
1 TCTTT
53802180 ATATATACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:53802332 original size:11 final size:11
Alignment explanation
Indices: 53802316--53802359 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
53802306 TCCCCCCCTC
53802316 CTTTCTCTCTT
1 CTTTCTCTCTT
*
53802327 CTTTCTCCCTT
1 CTTTCTCTCTT
* *
53802338 CTTT-TTTTTT
1 CTTTCTCTCTT
53802348 CTTTCTCTCTT
1 CTTTCTCTCTT
53802359 C
1 C
53802360 AAAATGATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (11 bp):
CTTTCTCTCTT
Found at i:53802802 original size:3 final size:3
Alignment explanation
Indices: 53802794--53802840 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
53802784 CTACTTTAAT
53802794 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53802841 CTTACTTCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53807229 original size:60 final size:60
Alignment explanation
Indices: 53807136--53807252 Score: 216
Period size: 60 Copynumber: 1.9 Consensus size: 60
53807126 CATTTTGGAG
*
53807136 ATAAATCTATTCAACTCTACCACCTTGCCCGTAAGGCGCTAGATTTCTTTTATAGTTCGC
1 ATAAATCTATTCAACTCCACCACCTTGCCCGTAAGGCGCTAGATTTCTTTTATAGTTCGC
*
53807196 ATAAATCTATTCAACTCCACCACCTTGCCCGTAAGGCGCTGGATTTCTTTTATAGTT
1 ATAAATCTATTCAACTCCACCACCTTGCCCGTAAGGCGCTAGATTTCTTTTATAGTT
53807253 TGCGGTGGAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (60 bp):
ATAAATCTATTCAACTCCACCACCTTGCCCGTAAGGCGCTAGATTTCTTTTATAGTTCGC
Found at i:53810243 original size:2 final size:2
Alignment explanation
Indices: 53810236--53810271 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
53810226 TAATATACAA
53810236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53810272 GTATGTGTAA
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):
AT
Found at i:53815245 original size:20 final size:21
Alignment explanation
Indices: 53815212--53815255 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
53815202 TATTTCTTTT
53815212 ATTTTAGTGGTTA-TATTGTA
1 ATTTTAGTGGTTATTATTGTA
* * *
53815232 ATTTTGGTGTTTATTTTTGTA
1 ATTTTAGTGGTTATTATTGTA
53815253 ATT
1 ATT
53815256 ATGAACTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.61
Consensus pattern (21 bp):
ATTTTAGTGGTTATTATTGTA
Found at i:53818297 original size:25 final size:26
Alignment explanation
Indices: 53818171--53818330 Score: 270
Period size: 26 Copynumber: 6.2 Consensus size: 26
53818161 CATGAAATTC
* *
53818171 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
* *
53818197 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
53818223 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
53818249 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
53818275 TTATCATGGAACA-TTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
53818300 TTATCAT-GAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
53818325 TTATCA
1 TTATCA
53818331 ATTTGTATCA
Statistics
Matches: 131, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
24 5 0.04
25 37 0.28
26 89 0.68
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:53825534 original size:26 final size:26
Alignment explanation
Indices: 53825498--53825659 Score: 261
Period size: 26 Copynumber: 6.2 Consensus size: 26
53825488 CATGAAATTC
*
53825498 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
53825524 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
* *
53825550 TTATCATGGAACATTTACCTAACTTA
1 TTATCATGAAACATTTACCTAACCTA
*
53825576 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
* *
53825602 TTATCATGGAACACTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
53825628 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
53825654 TTATCA
1 TTATCA
53825660 ATTTGTATCA
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 129 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:53827805 original size:20 final size:21
Alignment explanation
Indices: 53827782--53827839 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
53827772 GTCTCTAATC
*
53827782 GCACTATAATGCCTCTGTT-T
1 GCACTATGATGCCTCTGTTAT
*
53827802 GCACT-TCGGTGCCTCTGTTAT
1 GCACTAT-GATGCCTCTGTTAT
53827823 GCATCTATGATGCCTCT
1 GCA-CTATGATGCCTCT
53827840 AGTGTAGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 15 0.48
21 4 0.13
22 10 0.32
23 1 0.03
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.38
Consensus pattern (21 bp):
GCACTATGATGCCTCTGTTAT
Found at i:53832224 original size:54 final size:54
Alignment explanation
Indices: 53832161--53832266 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
53832151 ATTTTTGTGT
53832161 CAATTAAAGATTTTGTTATTCGATATTATTTTCTAAAATGTTATAGGAGTAACC
1 CAATTAAAGATTTTGTTATTCGATATTATTTTCTAAAATGTTATAGGAGTAACC
* * * *
53832215 CAATTAAAGATTTTGTTATTCGTTATTATTTTTTGAAATGTTATGGGAGTAA
1 CAATTAAAGATTTTGTTATTCGATATTATTTTCTAAAATGTTATAGGAGTAA
53832267 TCAATTCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (54 bp):
CAATTAAAGATTTTGTTATTCGATATTATTTTCTAAAATGTTATAGGAGTAACC
Found at i:53833297 original size:12 final size:12
Alignment explanation
Indices: 53833278--53833307 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53833268 AGCCACACGC
53833278 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
53833290 CTGTGTGCTAGG
1 CCGTGTGCTAGG
53833302 CCGTGT
1 CCGTGT
53833308 AACTGCCTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.23, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:53839884 original size:30 final size:30
Alignment explanation
Indices: 53839829--53839988 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
53839819 ATAGTGAATC
53839829 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
53839858 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
53839888 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* *
53839917 CGCACACTTAGTGCTGTATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
53839945 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
53839975 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53839989 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 47 0.39
30 47 0.39
31 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:53839921 original size:59 final size:57
Alignment explanation
Indices: 53839829--53839988 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
53839819 ATAGTGAATC
*
53839829 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
*
53839888 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTGTATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
53839945 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
53839989 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 49 0.53
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:53846762 original size:25 final size:25
Alignment explanation
Indices: 53846728--53846775 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
53846718 GCACTCTCTC
*
53846728 GAGCCATGTAACAGGATGCTTATGT
1 GAGCCATGTAACAGGAAGCTTATGT
*
53846753 GAGCCATGTATCAGGAAGCTTAT
1 GAGCCATGTAACAGGAAGCTTAT
53846776 CCGGGCTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (25 bp):
GAGCCATGTAACAGGAAGCTTATGT
Found at i:53849200 original size:16 final size:15
Alignment explanation
Indices: 53849181--53849226 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
53849171 TATTTTTAAA
53849181 AATTTTAATTCAAAAT
1 AATTTTAATT-AAAAT
53849197 AATTTATATATTAAAAT
1 AATTT-TA-ATTAAAAT
*
53849214 ATTTTTAATTAAA
1 AATTTTAATTAAA
53849227 TTTAGTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.22
16 7 0.26
17 11 0.41
18 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTTAATTAAAAT
Found at i:53849214 original size:17 final size:15
Alignment explanation
Indices: 53849158--53849226 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 15
53849148 ATATTAAATC
*
53849158 ATAATT-AAATAATT
1 ATAATTAAAATATTT
**
53849172 ATTTTTAAAA-ATTT
1 ATAATTAAAATATTT
53849186 -TAATTCAAAATAATTT
1 ATAATT-AAAAT-ATTT
53849202 ATATATTAAAATATTT
1 ATA-ATTAAAATATTT
*
53849218 TTAATTAAA
1 ATAATTAAA
53849227 TTTAGTTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 9 0.21
16 10 0.23
17 7 0.16
18 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATTAAAATATTT
Found at i:53849223 original size:33 final size:29
Alignment explanation
Indices: 53849164--53849223 Score: 75
Period size: 33 Copynumber: 1.9 Consensus size: 29
53849154 AATCATAATT
*
53849164 AAATAATTATTTTTAAAAATTTTAATTCA
1 AAATAATTATTATTAAAAATTTTAATTCA
53849193 AAATAATTTATATATTAAAATATTTTTAATT
1 AAATAA-TTAT-TATTAAAA-A-TTTTAATT
53849224 AAATTTAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 4 0.15
31 7 0.27
32 1 0.04
33 8 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
AAATAATTATTATTAAAAATTTTAATTCA
Found at i:53850078 original size:14 final size:15
Alignment explanation
Indices: 53850047--53850083 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
53850037 ATAATTCTAG
53850047 TTTTTATTATCATAA
1 TTTTTATTATCATAA
53850062 TTTTTATGT-TCAT-A
1 TTTTTAT-TATCATAA
53850076 TTTTTATT
1 TTTTTATT
53850084 TTTTAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 8 0.38
15 11 0.52
16 1 0.05
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTTATTATCATAA
Found at i:53851326 original size:20 final size:20
Alignment explanation
Indices: 53851301--53851365 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
53851291 TTATTTTGCA
**
53851301 ATAAAAATACATA-AGATTTT
1 ATAAAAATACATATA-AAATT
*
53851321 ATAAAAATATATATAAAATT
1 ATAAAAATACATATAAAATT
*
53851341 ATAAAAATACATACAAAATT
1 ATAAAAATACATATAAAATT
53851361 ATAAA
1 ATAAA
53851366 TAAATGAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 38 0.97
21 1 0.03
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
ATAAAAATACATATAAAATT
Found at i:53851333 original size:10 final size:10
Alignment explanation
Indices: 53851301--53851365 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
53851291 TTATTTTGCA
*
53851301 ATAAAAATAC
1 ATAAAAATAT
* * *
53851311 ATAAGATTTT
1 ATAAAAATAT
53851321 ATAAAAATAT
1 ATAAAAATAT
53851331 ATATAAAAT-T
1 ATA-AAAATAT
*
53851341 ATAAAAATAC
1 ATAAAAATAT
53851351 ATACAAAAT-T
1 ATA-AAAATAT
53851361 ATAAA
1 ATAAA
53851366 TAAATGAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
9 7 0.16
10 26 0.60
11 10 0.23
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:53851444 original size:17 final size:17
Alignment explanation
Indices: 53851424--53851458 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
53851414 AAAATAATAA
*
53851424 TTTTATAAATAAACCAT
1 TTTTATAAAAAAACCAT
*
53851441 TTTTTTAAAAAAACCAT
1 TTTTATAAAAAAACCAT
53851458 T
1 T
53851459 GATAAGACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTTATAAAAAAACCAT
Found at i:53854272 original size:25 final size:26
Alignment explanation
Indices: 53854226--53854274 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
53854216 ATGTTTTATT
* *
53854226 AATTTGGTAAATAGTATCTAAATATA
1 AATTTGATAAATAGAATCTAAATATA
*
53854252 AATTTGAT-AATAGAATTTAAATA
1 AATTTGATAAATAGAATCTAAATA
53854275 ATCGCATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (26 bp):
AATTTGATAAATAGAATCTAAATATA
Found at i:53858090 original size:9 final size:10
Alignment explanation
Indices: 53858058--53858082 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53858048 ATTTTTTATT
53858058 AAAATAATTA
1 AAAATAATTA
53858068 AAAATAATTA
1 AAAATAATTA
53858078 AAAAT
1 AAAAT
53858083 CATAAAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATAATTA
Found at i:53858192 original size:19 final size:19
Alignment explanation
Indices: 53858168--53858204 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
53858158 TTAATATAAA
53858168 CTTAT-AATACTTATAAAAG
1 CTTATAAATA-TTATAAAAG
53858187 CTTATAAATATTATAAAA
1 CTTATAAATATTATAAAA
53858205 ACAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (19 bp):
CTTATAAATATTATAAAAG
Found at i:53858244 original size:27 final size:28
Alignment explanation
Indices: 53858196--53858248 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
53858186 GCTTATAAAT
*
53858196 ATTATAAAAACAAATAATAAATCTAATTA
1 ATTATAAAAACAAATAAAAAAT-TAATTA
53858225 ATTAT-AAAA-AAATAAAAAATTAAT
1 ATTATAAAAACAAATAAAAAATTAAT
53858249 AAACATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 10 0.43
28 4 0.17
29 5 0.22
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (28 bp):
ATTATAAAAACAAATAAAAAATTAATTA
Found at i:53858327 original size:10 final size:10
Alignment explanation
Indices: 53858314--53858351 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
53858304 TAAATAATCA
53858314 TAAATATTAT
1 TAAATATTAT
*
53858324 TAAATATTGT
1 TAAATATTAT
53858334 TAAATATTA-
1 TAAATATTAT
*
53858343 AAAATATTA
1 TAAATATTA
53858352 AAATTGATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (10 bp):
TAAATATTAT
Found at i:53858466 original size:10 final size:10
Alignment explanation
Indices: 53858431--53858496 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
53858421 ATTTAATATT
* *
53858431 TTATAACAAG
1 TTATAAAAAA
53858441 TTAT-AAAAA
1 TTATAAAAAA
53858450 TTCATAAAAAA
1 TT-ATAAAAAA
*
53858461 TTATAAATAA
1 TTATAAAAAA
*
53858471 -TATAATAAA
1 TTATAAAAAA
*
53858480 TTGTAAAAAA
1 TTATAAAAAA
*
53858490 ATATAAA
1 TTATAAA
53858497 TTATACCCTT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
9 12 0.27
10 25 0.57
11 7 0.16
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:53858474 original size:29 final size:29
Alignment explanation
Indices: 53858442--53858497 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
53858432 TATAACAAGT
*
53858442 TATAA-AAATTCATAAAAAATTATAAATAA
1 TATAATAAATT-ATAAAAAAATATAAATAA
*
53858471 TATAATAAATTGTAAAAAAATATAAAT
1 TATAATAAATTATAAAAAAATATAAAT
53858498 TATACCCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (29 bp):
TATAATAAATTATAAAAAAATATAAATAA
Found at i:53860310 original size:2 final size:2
Alignment explanation
Indices: 53860303--53860334 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
53860293 AAATGAGGGG
53860303 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53860335 TTTAACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53861007 original size:34 final size:33
Alignment explanation
Indices: 53860977--53861060 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
53860967 AATTTAGAAT
*
53860977 TTTTTTTAAAATTAATTAAATTAGGTTTTAGG-
1 TTTTTTTAAAATTAATTAAATTAGGGTTTAGGA
*** *
53861009 GGGTTTAAGTAAATTAATTAAATTAGGGTTTAGGA
1 TTTTTTTA--AAATTAATTAAATTAGGGTTTAGGA
*
53861044 TTTTTTTAAAAATAATT
1 TTTTTTTAAAATTAATT
53861061 TTATGTTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
32 4 0.10
33 8 0.21
34 23 0.59
35 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (33 bp):
TTTTTTTAAAATTAATTAAATTAGGGTTTAGGA
Found at i:53861377 original size:125 final size:125
Alignment explanation
Indices: 53861150--53861376 Score: 325
Period size: 125 Copynumber: 1.8 Consensus size: 125
53861140 TCTTTTCTTT
* *
53861150 CTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGACAAAAATGCT
1 CTACAGTAGTTTCTAAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGAAAAAAATGCT
53861215 TCAAGCAGATGCACTATCAGCAAAAATACTGAAAAAAGCTCCCACGTGGACGCTCTTTTA
66 TCAAGCAGATGCACTATCAGCAAAAATACTGAAAAAAGCTCCCACGTGGACGCTCTTTTA
*
53861275 CTACAGTAGTTTCTAAAAAAATAATTTTGAGAATACGGTTCTT-AAAAAATAGT-ATAAAAAATG
1 CTACAGTAGTTTCTAAAAAAATAATTTTGAGAAGACGGTT-TTGAAAAAATAGTGA-AAAAAATG
* * * * *
53861338 CTTGAA-CTAAGATGCATTGTTAGCAAAATTACTGAAAAA
64 CTTCAAGC--AGATGCACTATCAGCAAAAATACTGAAAAA
53861377 GGACGCTCTT
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
124 2 0.02
125 60 0.67
126 28 0.31
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (125 bp):
CTACAGTAGTTTCTAAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGAAAAAAATGCT
TCAAGCAGATGCACTATCAGCAAAAATACTGAAAAAAGCTCCCACGTGGACGCTCTTTTA
Found at i:53868455 original size:18 final size:18
Alignment explanation
Indices: 53868420--53868455 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53868410 AAAAATGAAT
*
53868420 ATATAAGGGTTAGGATAC
1 ATATAAGGGCTAGGATAC
*
53868438 ATATAAGGGCTAGTATAC
1 ATATAAGGGCTAGGATAC
53868456 GTACCTGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAC
Found at i:53869056 original size:7 final size:7
Alignment explanation
Indices: 53869044--53869075 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
53869034 AGTTATATAT
53869044 AATACTA
1 AATACTA
53869051 AATACTA
1 AATACTA
53869058 AATACTA
1 AATACTA
53869065 AATACTA
1 AATACTA
53869072 AATA
1 AATA
53869076 AAAAAACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:53870010 original size:26 final size:24
Alignment explanation
Indices: 53869963--53870020 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
53869953 CTACAGACTG
* *
53869963 TTATAAAAATTATAAAAT-AAAAA
1 TTATTAAAATTACAAAATAAAAAA
53869986 TTAATTAAAATTACATAAATGAAAAAA
1 TT-ATTAAAATTACA-AAAT-AAAAAA
53870013 TTATTAAA
1 TTATTAAA
53870021 TAATATTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 10 0.34
25 4 0.14
26 6 0.21
27 7 0.24
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TTATTAAAATTACAAAATAAAAAA
Found at i:53874076 original size:28 final size:28
Alignment explanation
Indices: 53874044--53874099 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
53874034 TATGTTTAAT
53874044 TCCATACCAATGTCTACATGTTGGAGAA
1 TCCATACCAATGTCTACATGTTGGAGAA
53874072 TCCATACCAATGTCTACATGTTGGAGAA
1 TCCATACCAATGTCTACATGTTGGAGAA
53874100 GAACTAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (28 bp):
TCCATACCAATGTCTACATGTTGGAGAA
Found at i:53884074 original size:6 final size:6
Alignment explanation
Indices: 53884052--53884092 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
53884042 TTTTAAACGA
*
53884052 TTTCAT TTCTCCAT TTTCAT TTTTAT TTTCAT TTTCAT TTT
1 TTTCAT TT-T-CAT TTTCAT TTTCAT TTTCAT TTTCAT TTT
53884093 GGAGAAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 24 0.77
7 2 0.06
8 5 0.16
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCAT
Found at i:53888142 original size:78 final size:79
Alignment explanation
Indices: 53888005--53888220 Score: 251
Period size: 78 Copynumber: 2.7 Consensus size: 79
53887995 AATGATGTCT
* * * * * *
53888005 GGGCTAAGTCCCGACGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCAAAGGCATTCG
1 GGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCATTCG
* *
53888068 TGCGAGTTACTAATTTC
63 TGCGAGTTACTAAATCC
* *
53888085 GGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATTCGTG
53888148 CGAGTTACTAAATCC
65 CGAGTTACTAAATCC
* *
53888163 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGC
1 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGC
53888221 GTTTGAACGA
Statistics
Matches: 117, Mismatches: 13, Indels: 12
0.82 0.09 0.08
Matches are distributed among these distances:
77 2 0.02
78 55 0.47
79 7 0.06
80 51 0.44
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
GGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTCGTGC
GAGTTACTAAATCC
Done.