Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 98 of 279
Found at i:31616759 original size:46 final size:44
Alignment explanation
Indices: 31616570--31616938 Score: 209
Period size: 44 Copynumber: 8.5 Consensus size: 44
31616560 ATCTACTCTG
* *
31616570 CTGTAA-CTTCAGGGAGATAAGATC--CTTTATTTGAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCTGC-TTCTTT-AATCTGCTCCA
* * * *
31616614 CTGTAA-CTTCAGGGAGATAGGAT-AG-TGTCTTCAATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCTGCT-TCTTTAATCTGCTCCA
* * * *
31616657 CTGTAATCTCAGGGAGATAAGAT-TTCTGGCCTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTGCT-TCTTTAATCTGCTCCA
* * *
31616701 CTGTAACCTCAGGGAGATAAGATCTGACATTCTTTAGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCTG-C-TTCTTTAATCTGCTCCA
* * * * * * *
31616747 CTGTAATCTCAGGGAAATAAGACCTGGTGC---GATCCGCTCTA
1 CTGTAATCTCAGGGAGATAAGATCTGCTTCTTTAATCTGCTCCA
*
31616788 CTGTAA-CTTCAGAGAGATAAGA--T-C--CTTTAATCTGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCTGCTTCTTTAATCTGCTCCA
* * * * *
31616827 CTGTAA-CTTCAGGGAGATAGGAT-TACTATATTCAATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCTGCT-TCTTTAATCTGCTCCA
** *
31616871 CTGTAATCTCAGGGAGATAAGATCTGCAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCTGC--TTCTTTAATCTGCTCCA
*
31616917 CCGTAATCTCAGGG-GAATAAGA
1 CTGTAATCTCAGGGAG-ATAAGA
31616939 CCTTTTATAA
Statistics
Matches: 255, Mismatches: 48, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
36 1 0.00
39 29 0.11
40 2 0.01
41 25 0.10
43 30 0.12
44 97 0.38
45 5 0.02
46 64 0.25
47 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
CTGTAATCTCAGGGAGATAAGATCTGCTTCTTTAATCTGCTCCA
Found at i:31616834 original size:39 final size:42
Alignment explanation
Indices: 31616570--31616895 Score: 225
Period size: 44 Copynumber: 7.6 Consensus size: 42
31616560 ATCTACTCTG
* * *
31616570 CTGTAACTTCAGGGAGATAAGATCCTTTATTTGAATCCGCTCCA
1 CTGTAACTTCAGGGAGATAAGAT-CTATA-TTCAATCTGCTCCA
* * * * *
31616614 CTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCTGCTCCG
1 CTGTAACTTCAGGGAGATAAGAT-CTATATTCAATCTGCTCCA
****
31616657 CTGTAA-TCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCA
1 CTGTAACT-TCAGGGAGATAAGA--TCTATATTCAATCTGCTCCA
* * * *
31616701 CTGTAACCTCAGGGAGATAAGATCTGACATTCTTTAGTCTGTTCCA
1 CTGTAACTTCAGGGAGATAAGATCT-ATATTC---AATCTGCTCCA
* * ** * * * *
31616747 CTGTAA-TCTCAGGGAAATAAGACCT-GGTGCGATCCGCTCTA
1 CTGTAACT-TCAGGGAGATAAGATCTATATTCAATCTGCTCCA
* *
31616788 CTGTAACTTCAGAGAGATAAGATC-CT-TT-AATCTGCTCCA
1 CTGTAACTTCAGGGAGATAAGATCTATATTCAATCTGCTCCA
* *
31616827 CTGTAACTTCAGGGAGATAGGATTACTATATTCAATCTGCTCCG
1 CTGTAACTTCAGGGAGATAAGA-T-CTATATTCAATCTGCTCCA
31616871 CTGTAA-TCTCAGGGAGATAAGATCT
1 CTGTAACT-TCAGGGAGATAAGATCT
31616896 GCAATTCTTT
Statistics
Matches: 221, Mismatches: 44, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
39 28 0.13
40 2 0.01
41 26 0.12
42 8 0.04
43 36 0.16
44 90 0.41
45 1 0.00
46 30 0.14
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (42 bp):
CTGTAACTTCAGGGAGATAAGATCTATATTCAATCTGCTCCA
Found at i:31616845 original size:170 final size:173
Alignment explanation
Indices: 31616604--31616941 Score: 461
Period size: 170 Copynumber: 2.0 Consensus size: 173
31616594 CTTTATTTGA
* * * *
31616604 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCTGCTCCGCTGTAATCTCAG
1 ATCCGCTCCACTGTAACTTCAGAGAGATA-GAGAGTGCCTTCAATCTGCTCCACTGTAATCTCAG
* * *
31616669 GGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG-ACATTC
65 GGAGATAAGATTACTAGACTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGCA-ATTC
*
31616733 TTTAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCG
129 TTTAGTCTGTTCCACCGTAATCTCAGGGAAATAAGACCTGGTGCG
* *
31616778 ATCCGCTCTACTGTAACTTCAGAGAGATA-AGA-T-CCTTTAATCTGCTCCACTGTAA-CTTCAG
1 ATCCGCTCCACTGTAACTTCAGAGAGATAGAGAGTGCCTTCAATCTGCTCCACTGTAATC-TCAG
* * * * *
31616839 GGAGATAGGATTACTATATTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCT
65 GGAGATAAGATTACTAGACTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGCAATTCT
* *
31616904 TTGGTCTGTTCCACCGTAATCTCAGGGGAATAAGACCT
130 TTAGTCTGTTCCACCGTAATCTCAGGGAAATAAGACCT
31616942 TTTATAATGA
Statistics
Matches: 145, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
169 1 0.01
170 113 0.78
171 2 0.01
172 2 0.01
174 27 0.19
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (173 bp):
ATCCGCTCCACTGTAACTTCAGAGAGATAGAGAGTGCCTTCAATCTGCTCCACTGTAATCTCAGG
GAGATAAGATTACTAGACTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGCAATTCTT
TAGTCTGTTCCACCGTAATCTCAGGGAAATAAGACCTGGTGCG
Found at i:31629536 original size:9 final size:10
Alignment explanation
Indices: 31629525--31629586 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 10
31629515 GGTACAAATA
31629525 AATAAATAA-
1 AATAAATAAT
*
31629534 AATGCAATAAT
1 AAT-AAATAAT
31629545 AATGATAATAAT
1 AAT-A-AATAAT
31629557 AAT-AATAAT
1 AATAAATAAT
31629566 AATAAACTCAAT
1 AATAAA-T-AAT
31629578 AATAAATAA
1 AATAAATAA
31629587 AATGATAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
9 12 0.27
10 9 0.20
11 6 0.13
12 18 0.40
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (10 bp):
AATAAATAAT
Found at i:31629582 original size:3 final size:3
Alignment explanation
Indices: 31629539--31629570 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
31629529 AATAAAATGC
*
31629539 AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31629571 ACTCAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:31630260 original size:23 final size:23
Alignment explanation
Indices: 31630232--31630277 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
31630222 CCTTGGGTGT
31630232 TTTATTTGGGTTGGTTTTGGGTA
1 TTTATTTGGGTTGGTTTTGGGTA
31630255 TTTATTTGGGTTGGTTTTGGGTA
1 TTTATTTGGGTTGGTTTTGGGTA
31630278 GCGGGCCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.00, G:0.35, T:0.57
Consensus pattern (23 bp):
TTTATTTGGGTTGGTTTTGGGTA
Found at i:31635244 original size:24 final size:24
Alignment explanation
Indices: 31635212--31635261 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
31635202 CAAACCATGC
31635212 AAATGTTACCGAGAATTCAACTAG
1 AAATGTTACCGAGAATTCAACTAG
31635236 AAATGTTACCGAGAATTCAACTAG
1 AAATGTTACCGAGAATTCAACTAG
31635260 AA
1 AA
31635262 TGACTCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (24 bp):
AAATGTTACCGAGAATTCAACTAG
Found at i:31635313 original size:14 final size:14
Alignment explanation
Indices: 31635294--31635320 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31635284 GACGACAACA
31635294 ACCACCACCACCAC
1 ACCACCACCACCAC
31635308 ACCACCACCACCA
1 ACCACCACCACCA
31635321 TCATCCGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.63, G:0.00, T:0.00
Consensus pattern (14 bp):
ACCACCACCACCAC
Found at i:31640297 original size:14 final size:15
Alignment explanation
Indices: 31640233--31640299 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 15
31640223 TTATTAAAAA
*
31640233 ATAATAAAATATA-T
1 ATAATTAAATATATT
*
31640247 ATTA-TAACATA-ATT
1 ATAATTAA-ATATATT
*
31640261 ATTATTAAATATATT
1 ATAATTAAATATATT
31640276 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
31640289 ATAATTTAATA
1 ATAATTAAATA
31640300 AAATTCTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 12 0.27
14 18 0.41
15 14 0.32
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:31640299 original size:61 final size:60
Alignment explanation
Indices: 31640234--31640423 Score: 162
Period size: 61 Copynumber: 3.1 Consensus size: 60
31640224 TATTAAAAAA
31640234 TAATAAAATATATATTATAACATAATTATTATTAAATATATTATAATTAAAATATATAATT
1 TAATAAAATATATA-TATAACATAATTATTATTAAATATATTATAATTAAAATATATAATT
* * * * * * *
31640295 TAATAAAAT-TCT-TAATAA-TTAA-TATTCTTATATGA-ATTTACTCAAATCATAATATATGAT
1 TAATAAAATATATAT-ATAACATAATTATTATTAAAT-ATA-TTA-T--AATTAAAATATATAAT
*
31640355 AC
60 -T
*
31640357 T-GTAAAATATA-A-AGTAACATAATTATTATTAAATATATTATAATTAAAATATATAATT
1 TAATAAAATATATATA-TAACATAATTATTATTAAATATATTATAATTAAAATATATAATT
31640415 TAATAAAAT
1 TAATAAAAT
31640424 TCTTAATAAT
Statistics
Matches: 97, Mismatches: 18, Indels: 30
0.67 0.12 0.21
Matches are distributed among these distances:
57 10 0.10
58 9 0.09
59 24 0.25
60 3 0.03
61 32 0.33
62 9 0.09
63 10 0.10
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (60 bp):
TAATAAAATATATATATAACATAATTATTATTAAATATATTATAATTAAAATATATAATT
Found at i:31640417 original size:14 final size:15
Alignment explanation
Indices: 31640378--31640419 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31640368 AAGTAACATA
*
31640378 ATTATTATTAAATAT
1 ATTATAATTAAATAT
31640393 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
31640407 A-TATAATTTAATA
1 ATTATAATTAAATA
31640420 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:31640555 original size:120 final size:120
Alignment explanation
Indices: 31640251--31640544 Score: 502
Period size: 120 Copynumber: 2.5 Consensus size: 120
31640241 ATATATATTA
31640251 TAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
1 TAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
* *
31640316 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAAG
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAAG
31640371 TAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
1 TAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
*
31640436 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAATT
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAA-G
* * *
31640491 TGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 T-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
31640545 TAAAATAATT
Statistics
Matches: 166, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 3 0.02
120 161 0.97
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (120 bp):
TAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAAG
Found at i:31644090 original size:6 final size:6
Alignment explanation
Indices: 31644081--31644109 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31644071 TTGATGTTGG
31644081 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
31644110 TGGGGAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:31648710 original size:16 final size:16
Alignment explanation
Indices: 31648689--31648740 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
31648679 TTTGGTTCGC
31648689 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
31648705 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
31648721 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
31648737 TGTA
1 TGTA
31648741 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:31648787 original size:45 final size:44
Alignment explanation
Indices: 31648721--31648815 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
31648711 GGATTAGAGG
* *
31648721 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
31648766 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
31648810 TGTAAT
1 TGTAAT
31648816 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:31648985 original size:25 final size:25
Alignment explanation
Indices: 31648953--31649007 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
31648943 TAATTTAATC
*
31648953 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
31648977 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
31649002 ATATAT
1 ATATAT
31649008 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:31649005 original size:16 final size:16
Alignment explanation
Indices: 31648984--31649033 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
31648974 TAAATATATT
31648984 AAATATATTATAATTA
1 AAATATATTATAATTA
*
31649000 AAATATATAATTTAA-TA
1 AAATATAT--TATAATTA
31649017 AAAT-TATTAATAATTA
1 AAATATATT-ATAATTA
31649033 A
1 A
31649034 TATTCTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.04
15 3 0.11
16 14 0.50
17 6 0.21
18 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATATTATAATTA
Found at i:31649007 original size:18 final size:18
Alignment explanation
Indices: 31648986--31649033 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
31648976 AATATATTAA
31648986 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
31649004 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
31649021 -TAT-TAATAATTAA
1 ATATATTATAATTAA
31649034 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:31657435 original size:30 final size:29
Alignment explanation
Indices: 31657379--31657457 Score: 70
Period size: 30 Copynumber: 2.7 Consensus size: 29
31657369 TTTAGGATTG
*
31657379 AAATTTTTAAATGTGAAAATTTTAAGTATT
1 AAATTTTT-ATTGTGAAAATTTTAAGTATT
* * *
31657409 AAATTTTTATTGTTAAATTTTATAAGTGTT
1 AAATTTTTATTGTGAAAATTT-TAAGTATT
* * *
31657439 GAATTTGTATT-AGAAAATT
1 AAATTTTTATTGTGAAAATT
31657458 ATTTGAAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (29 bp):
AAATTTTTATTGTGAAAATTTTAAGTATT
Found at i:31669518 original size:32 final size:33
Alignment explanation
Indices: 31669474--31669535 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
31669464 ATAGATGGAG
*
31669474 AAGCATAAAAGAATAGAAAAT-AAAAAAAAAGGA
1 AAGCATAAAAGAACA-AAAATGAAAAAAAAAGGA
*
31669507 AAGC-TAAAAGAACATAAATGAAAAAAAAA
1 AAGCATAAAAGAACAAAAATGAAAAAAAAA
31669536 ATTAAATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 4 0.15
32 18 0.69
33 4 0.15
ACGTcount: A:0.73, C:0.05, G:0.13, T:0.10
Consensus pattern (33 bp):
AAGCATAAAAGAACAAAAATGAAAAAAAAAGGA
Found at i:31670552 original size:24 final size:24
Alignment explanation
Indices: 31670504--31670552 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
31670494 TTCTAAAAAA
*
31670504 TTCAAAAAAATATACATAAATATT
1 TTCAAAAAAATATACATAAAAATT
*
31670528 TTCAAATAAATATA-ATAATAAATT
1 TTCAAAAAAATATACATAA-AAATT
31670552 T
1 T
31670553 AAATTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (24 bp):
TTCAAAAAAATATACATAAAAATT
Found at i:31670566 original size:6 final size:6
Alignment explanation
Indices: 31670557--31670603 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
31670547 AAATTTAAAT
** *
31670557 TTAATA TTAATA TTAATA TTAAATA AAAATA TTTATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TT-AATA TTAATA TTAATA TTAATA TTAA
31670604 ATAAAATAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TTAATA
Found at i:31670566 original size:12 final size:13
Alignment explanation
Indices: 31670551--31670606 Score: 64
Period size: 12 Copynumber: 4.5 Consensus size: 13
31670541 AATAATAAAT
31670551 TTAAAT-TTAATA
1 TTAAATATTAATA
31670563 TT-AATATTAATA
1 TTAAATATTAATA
**
31670575 TTAAATAAAAATA
1 TTAAATATTAATA
*
31670588 TT-TATATTAATA
1 TTAAATATTAATA
31670600 TTAAATA
1 TTAAATA
31670607 AAATAAGCCC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 3 0.09
12 19 0.54
13 13 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAATATTAATA
Found at i:31670594 original size:25 final size:25
Alignment explanation
Indices: 31670559--31670609 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
31670549 ATTTAAATTT
31670559 AATATTAATATTAATATTAAATAAA
1 AATATTAATATTAATATTAAATAAA
*
31670584 AATATTTATATTAATATTAAATAAA
1 AATATTAATATTAATATTAAATAAA
31670609 A
1 A
31670610 TAAGCCCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATTAATATTAATATTAAATAAA
Found at i:31670605 original size:19 final size:19
Alignment explanation
Indices: 31670536--31670606 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
31670526 TTTTCAAATA
*
31670536 AATA-TAATAATAAAT-TT
1 AATATTAATATTAAATATT
31670553 AA-ATTTAATATT-AATATT
1 AATA-TTAATATTAAATATT
*
31670571 AATATTAA-ATAAAAATATT
1 AATATTAATAT-TAAATATT
*
31670590 TATATTAATATTAAATA
1 AATATTAATATTAAATA
31670607 AAATAAGCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
16 1 0.02
17 7 0.16
18 14 0.33
19 19 0.44
20 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTAATATTAAATATT
Found at i:31670671 original size:18 final size:19
Alignment explanation
Indices: 31670644--31670687 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
31670634 CCCATCCTCC
31670644 CACCCCCACCCTC-ACCCT
1 CACCCCCACCCTCGACCCT
*
31670662 CACCCTCACCCTCGACCCT
1 CACCCCCACCCTCGACCCT
*
31670681 CTCCCCC
1 CACCCCC
31670688 TCAAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.14, C:0.70, G:0.02, T:0.14
Consensus pattern (19 bp):
CACCCCCACCCTCGACCCT
Found at i:31670681 original size:7 final size:6
Alignment explanation
Indices: 31670644--31670681 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
31670634 CCCATCCTCC
*
31670644 CACCCC CACCCT CACCCT CACCCT CACCCT CGACCCT C
1 CACCCT CACCCT CACCCT CACCCT CACCCT C-ACCCT C
31670682 TCCCCCTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.16, C:0.68, G:0.03, T:0.13
Consensus pattern (6 bp):
CACCCT
Found at i:31684507 original size:41 final size:41
Alignment explanation
Indices: 31684462--31684546 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
31684452 AGTTTGCTCA
*
31684462 CTATCTTCCGGTCAGGACTGATTATTCACTTCAGAAATTGG
1 CTATCTTCCGGTCAGGACTAATTATTCACTTCAGAAATTGG
*
31684503 CTATCTTCCGGTCAGGACTAATTATTCGCTTCAGAAATTGG
1 CTATCTTCCGGTCAGGACTAATTATTCACTTCAGAAATTGG
31684544 CTA
1 CTA
31684547 AGTTGTATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (41 bp):
CTATCTTCCGGTCAGGACTAATTATTCACTTCAGAAATTGG
Found at i:31688627 original size:21 final size:21
Alignment explanation
Indices: 31688561--31688655 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
31688551 CAAACACGCC
*
31688561 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCAAAAGAGCTA
* * * *
31688582 AGCAAAAGCTTAAAAGAGCTG
1 AACAGAAGCTCAAAAGAGCTA
31688603 AACAGAAGCTCAAAAGAGCTA
1 AACAGAAGCTCAAAAGAGCTA
* *** *
31688624 AACAGAAACTCGTGAGAGCTG
1 AACAGAAGCTCAAAAGAGCTA
31688645 AACAGAAGCTC
1 AACAGAAGCTC
31688656 GTAAGAGTTG
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (21 bp):
AACAGAAGCTCAAAAGAGCTA
Found at i:31688662 original size:42 final size:42
Alignment explanation
Indices: 31688561--31688662 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 42
31688551 CAAACACGCC
* *
31688561 AACAGAAGCTCATAAGAGCTAAGCAAAAGCTTAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTAAACAAAAGCTCAAAAGAGCTG
* ***
31688603 AACAGAAGCTCAAAAGAGCTAAACAGAAA-CTCGTGAGAGCTG
1 AACAGAAGCTCATAAGAGCTAAACA-AAAGCTCAAAAGAGCTG
*
31688645 AACAGAAGCTCGTAAGAG
1 AACAGAAGCTCATAAGAG
31688663 TTGATCAACC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 48 0.94
43 3 0.06
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAAAAGCTCAAAAGAGCTG
Found at i:31688871 original size:17 final size:17
Alignment explanation
Indices: 31688851--31688887 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
31688841 ATTAAATTCG
*
31688851 ATAATATATTTCCAACA
1 ATAATATAATTCCAACA
*
31688868 ATAATTTAATTCCAACA
1 ATAATATAATTCCAACA
31688885 ATA
1 ATA
31688888 GAAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATATAATTCCAACA
Found at i:31694677 original size:21 final size:21
Alignment explanation
Indices: 31694649--31694719 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
31694639 ACACACCAAT
*
31694649 AGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCAAAAGAGCTGAAC
* *
31694670 AAAAGCTCAAAAGAGCTTAAC
1 AGAAGCTCAAAAGAGCTGAAC
* *
31694691 AGAAGCTCAAAAAAGCTGAAT
1 AGAAGCTCAAAAGAGCTGAAC
31694712 AGAAGCTC
1 AGAAGCTC
31694720 GTAAGAGTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (21 bp):
AGAAGCTCAAAAGAGCTGAAC
Found at i:31707979 original size:18 final size:17
Alignment explanation
Indices: 31707949--31707983 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31707939 TTCCTTTTGG
31707949 CCTTAGTTGTTCTATAT
1 CCTTAGTTGTTCTATAT
*
31707966 CCTTAAGTTTTTCTATAT
1 CCTT-AGTTGTTCTATAT
31707984 TTGGGGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (17 bp):
CCTTAGTTGTTCTATAT
Found at i:31711763 original size:31 final size:30
Alignment explanation
Indices: 31711698--31711764 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
31711688 TCTTTATTTT
* *
31711698 CCCCCAAAATTTTTACTCCTTCCCACTTTC
1 CCCCCAAAACTTTTACTCCTTCCCACTCTC
* *
31711728 CCCCCAAAGCTTTTACTCCTCTCCCATCTCAC
1 CCCCCAAAACTTTTACTCCT-TCCCA-CTCTC
31711760 CCCCC
1 CCCCC
31711765 TTCTACCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 18 0.58
31 5 0.16
32 8 0.26
ACGTcount: A:0.18, C:0.51, G:0.01, T:0.30
Consensus pattern (30 bp):
CCCCCAAAACTTTTACTCCTTCCCACTCTC
Found at i:31712211 original size:17 final size:18
Alignment explanation
Indices: 31712177--31712211 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31712167 TTTATTAAAA
31712177 AATACATTTTTTACATTT
1 AATACATTTTTTACATTT
*
31712195 AATATATTTTTTA-ATTT
1 AATACATTTTTTACATTT
31712212 CAAAATACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
AATACATTTTTTACATTT
Found at i:31717799 original size:14 final size:15
Alignment explanation
Indices: 31717762--31717803 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
31717752 AAGCAATATC
31717762 CATTCAAAATCTAAAG
1 CATTCAAAATC-AAAG
31717778 -ATTCAAAATCAAAG
1 CATTCAAAATCAAAG
31717792 CATT-AAAA-CAAA
1 CATTCAAAATCAAA
31717804 AACACTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.21
Consensus pattern (15 bp):
CATTCAAAATCAAAG
Found at i:31724197 original size:28 final size:28
Alignment explanation
Indices: 31724157--31724219 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
31724147 ATGAACCATA
* *
31724157 AAAAATTATGAAAAATGGAAATAAAATAT
1 AAAAA-TAAGAAAAATAGAAATAAAATAT
* * *
31724186 AAAAATAAGAAAAATATATATAAAATCT
1 AAAAATAAGAAAAATAGAAATAAAATAT
31724214 AAAAAT
1 AAAAAT
31724220 TTTATATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (28 bp):
AAAAATAAGAAAAATAGAAATAAAATAT
Found at i:31727558 original size:51 final size:51
Alignment explanation
Indices: 31727468--31727575 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 51
31727458 CCAAACATTT
* * *
31727468 GTTCATATAAAATAATAGTTCTTACCAAATGACAGTTCATGCAAAATAATA
1 GTTCATATAAAATAATAGTTCATACCAAATAACAATTCATGCAAAATAATA
* *
31727519 GTTCATATGAAAT-ATCAGTTCATACCGAATAACAATTCATGCAAAATAATA
1 GTTCATATAAAATAAT-AGTTCATACCAAATAACAATTCATGCAAAATAATA
31727570 GTTCAT
1 GTTCAT
31727576 GCTCCATCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 2 0.04
51 49 0.96
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (51 bp):
GTTCATATAAAATAATAGTTCATACCAAATAACAATTCATGCAAAATAATA
Found at i:31727577 original size:17 final size:17
Alignment explanation
Indices: 31727468--31727575 Score: 83
Period size: 17 Copynumber: 6.4 Consensus size: 17
31727458 CCAAACATTT
*
31727468 GTTCATATAAAATAATA
1 GTTCATACAAAATAATA
* * * *
31727485 GTTCTTACCAAATGACA
1 GTTCATACAAAATAATA
*
31727502 GTTCATGCAAAATAATA
1 GTTCATACAAAATAATA
**
31727519 GTTCATATGAAAT-ATCA
1 GTTCATACAAAATAAT-A
** *
31727536 GTTCATACCGAATAACA
1 GTTCATACAAAATAATA
* *
31727553 ATTCATGCAAAATAATA
1 GTTCATACAAAATAATA
31727570 GTTCAT
1 GTTCAT
31727576 GCTCCATCAT
Statistics
Matches: 66, Mismatches: 23, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
16 2 0.03
17 63 0.95
18 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (17 bp):
GTTCATACAAAATAATA
Found at i:31728671 original size:33 final size:31
Alignment explanation
Indices: 31728617--31728724 Score: 89
Period size: 33 Copynumber: 3.5 Consensus size: 31
31728607 ATATACATTT
* * *
31728617 TATATATTAGATA-ATACAAAACCTATAAACTCA
1 TATATATTATATATA-ATAAAACC-A-AAACACA
*
31728650 TATATATTATATATAATAAAACC--CACACA
1 TATATATTATATATAATAAAACCAAAACACA
* * * *
31728679 CATATATTATATAT-TTAACACCAAAACCCA
1 TATATATTATATATAATAAAACCAAAACACA
31728709 TATATATTATATATAA
1 TATATATTATATATAA
31728725 ATAACAAAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
28 6 0.10
29 17 0.28
30 17 0.28
33 19 0.32
34 1 0.02
ACGTcount: A:0.50, C:0.16, G:0.01, T:0.33
Consensus pattern (31 bp):
TATATATTATATATAATAAAACCAAAACACA
Found at i:31730207 original size:32 final size:31
Alignment explanation
Indices: 31730142--31730208 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
31730132 ACCTAAAATT
* * *
31730142 ATTAATTCTAATTATTTTAATATTTTATTTA
1 ATTAATTCTAATTATTTTAATATCTAATCTA
31730173 ATTAATTTCTAATTA-TTTAATTATCTAATCTA
1 ATTAA-TTCTAATTATTTTAA-TATCTAATCTA
31730205 ATTA
1 ATTA
31730209 CGATTTTCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTAATTCTAATTATTTTAATATCTAATCTA
Found at i:31735335 original size:19 final size:18
Alignment explanation
Indices: 31735311--31735347 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
31735301 TAATTGAATT
*
31735311 AAAATAAATTTAAATTTTA
1 AAAATAAAATT-AATTTTA
31735330 AAAATAAAATTAATTTTA
1 AAAATAAAATTAATTTTA
31735348 TAATTCGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATAAAATTAATTTTA
Found at i:31737554 original size:25 final size:26
Alignment explanation
Indices: 31737503--31737559 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
31737493 CTTGTTATCT
*
31737503 TTTTTTCAAATTTCAGCTTCTCATAC
1 TTTTTCCAAATTTCAGCTTCTCATAC
*
31737529 TTTTTCCAAATTTCGGCCTT-TC-TAC
1 TTTTTCCAAATTTCAG-CTTCTCATAC
31737554 TTTTTC
1 TTTTTC
31737560 TTTGAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.32
26 16 0.57
27 3 0.11
ACGTcount: A:0.18, C:0.25, G:0.05, T:0.53
Consensus pattern (26 bp):
TTTTTCCAAATTTCAGCTTCTCATAC
Found at i:31744953 original size:39 final size:39
Alignment explanation
Indices: 31744899--31744977 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
31744889 TCGAGTCTTT
31744899 GTGCAAACGAAGGAGTCATTTTGCTGCTTGTGTCGTGTA
1 GTGCAAACGAAGGAGTCATTTTGCTGCTTGTGTCGTGTA
* *
31744938 GTGCAAACGAAGGAGTCATTTTGCTTCTTGTTTCGTGTA
1 GTGCAAACGAAGGAGTCATTTTGCTGCTTGTGTCGTGTA
31744977 G
1 G
31744978 GTGTTTTCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.35
Consensus pattern (39 bp):
GTGCAAACGAAGGAGTCATTTTGCTGCTTGTGTCGTGTA
Found at i:31748421 original size:43 final size:44
Alignment explanation
Indices: 31748346--31748477 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 44
31748336 CAAAAAGCTC
* *
31748346 ATACGATGCCAAC-GTCCTAGAC-GTGGTCTTACATGTAATCAAAT
1 ATACGATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAATCAAAT
* * *
31748390 A-ACGATGCCACTGTCCCAGACAGGGTTTTACACGAAATCATAT
1 ATACGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAAT
* * *
31748433 ATA--ATGCCAATGTCCCAGACATGGTCTTACACGTGAATCACAT
1 ATACGATGCCACTGTCCCAGACAGGGTCTTACACGT-AATCAAAT
31748476 AT
1 AT
31748478 CGGAAACCTA
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
42 29 0.39
43 42 0.57
44 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (44 bp):
ATACGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAAT
Found at i:31752137 original size:18 final size:18
Alignment explanation
Indices: 31752114--31752172 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
31752104 AAGACTTAAA
31752114 CACATCTAAACATCCTAT
1 CACATCTAAACATCCTAT
31752132 CACATCTAAACA---TA-
1 CACATCTAAACATCCTAT
*
31752146 C-CATTTCAAACATCCTAT
1 CACATCT-AAACATCCTAT
31752164 CACATCTAA
1 CACATCTAA
31752173 CCAACATGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 4 0.12
14 6 0.18
15 2 0.06
17 2 0.06
18 15 0.45
19 4 0.12
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (18 bp):
CACATCTAAACATCCTAT
Found at i:31755493 original size:22 final size:22
Alignment explanation
Indices: 31755465--31755535 Score: 83
Period size: 21 Copynumber: 3.2 Consensus size: 22
31755455 GGGAAAAAAT
*
31755465 AAAAAAAT-GAATTATAGGGACA
1 AAAAAAATCGAATTACA-GGACA
*
31755487 AAAAAAATCAAATTACAGGA-A
1 AAAAAAATCGAATTACAGGACA
*
31755508 AAAAAAGTCGAATTACAAGGACA
1 AAAAAAATCGAATTAC-AGGACA
31755531 AAAAA
1 AAAAA
31755536 GGGTTGAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 15 0.36
22 15 0.36
23 12 0.29
ACGTcount: A:0.63, C:0.08, G:0.14, T:0.14
Consensus pattern (22 bp):
AAAAAAATCGAATTACAGGACA
Found at i:31755536 original size:22 final size:22
Alignment explanation
Indices: 31755465--31755535 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
31755455 GGGAAAAAAT
* *
31755465 AAAAAAAT-GAATTATAGGGAC
1 AAAAAAATCGAATTACAAGGAC
*
31755486 AAAAAAAATCAAATTAC-AGGA-
1 -AAAAAAATCGAATTACAAGGAC
31755507 AAAAAAAGTCGAATTACAAGGAC
1 AAAAAAA-TCGAATTACAAGGAC
31755530 AAAAAA
1 AAAAAA
31755536 GGGTTGAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 7 0.17
21 8 0.20
22 15 0.37
23 11 0.27
ACGTcount: A:0.63, C:0.08, G:0.14, T:0.14
Consensus pattern (22 bp):
AAAAAAATCGAATTACAAGGAC
Found at i:31755617 original size:22 final size:23
Alignment explanation
Indices: 31755592--31755653 Score: 83
Period size: 22 Copynumber: 2.7 Consensus size: 23
31755582 TACATGAACT
31755592 AAAAATTTGAATTATAGAGACAA
1 AAAAATTTGAATTATAGAGACAA
* *
31755615 AAAAA--TCAATTTACAGAGACAA
1 AAAAATTTGAA-TTATAGAGACAA
31755637 AAAAATTTGAATTATAG
1 AAAAATTTGAATTATAG
31755654 GGGGAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.09
22 16 0.50
23 10 0.31
24 3 0.09
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.26
Consensus pattern (23 bp):
AAAAATTTGAATTATAGAGACAA
Found at i:31755702 original size:40 final size:43
Alignment explanation
Indices: 31755592--31755708 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 43
31755582 TACATGAACT
*
31755592 AAAAATTTGAATTATAGAGACAAAAAAATCAATTTACAGAGACAA
1 AAAAATTTGAATTATAGGGACAAAAAAATCAA--TACAGAGACAA
** *
31755637 AAAAATTTGAATTATAGGGGGAAAAAAA-C-A-ACAGGGACAA
1 AAAAATTTGAATTATAGGGACAAAAAAATCAATACAGAGACAA
* * *
31755677 ACAAATTAGAATTATAGGGACAAAAAATTCAA
1 AAAAATTTGAATTATAGGGACAAAAAAATCAA
31755709 ATTACAAGGA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 32 0.52
41 1 0.02
42 1 0.02
43 1 0.02
44 1 0.02
45 25 0.41
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.20
Consensus pattern (43 bp):
AAAAATTTGAATTATAGGGACAAAAAAATCAATACAGAGACAA
Found at i:31759771 original size:86 final size:88
Alignment explanation
Indices: 31759674--31759849 Score: 248
Period size: 91 Copynumber: 2.0 Consensus size: 88
31759664 AGTGTAAAAA
* *
31759674 GCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCC-C-TTTTTTTGCACTCAATTGGGTACTTGA
1 GCCCTCAAACTTTTTCAAAAAAAGAAATTAAGCCCTCTTTTTTTTACACTCAATTGGGTACTTGA
** *
31759737 ACTTTCAAAATGTATAAAAAAGT
66 ACTGCCAAAATGCATAAAAAAGT
*
31759760 GCCCTTAAACTTTTTCAAAAAAAGAAATTAAGCCCTGTCTTTTTTTTTACACTCAATTGGGTACT
1 GCCCTCAAACTTTTTCAAAAAAAGAAATTAAGCCC--TC-TTTTTTTTACACTCAATTGGGTACT
*
31759825 TGAACTGCCAAAATGCATCAAAAAG
63 TGAACTGCCAAAATGCATAAAAAAG
31759850 GCTCTTTGAC
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
86 33 0.42
89 1 0.01
91 44 0.56
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (88 bp):
GCCCTCAAACTTTTTCAAAAAAAGAAATTAAGCCCTCTTTTTTTTACACTCAATTGGGTACTTGA
ACTGCCAAAATGCATAAAAAAGT
Found at i:31759991 original size:10 final size:10
Alignment explanation
Indices: 31759978--31760039 Score: 81
Period size: 10 Copynumber: 6.3 Consensus size: 10
31759968 AAAAATAAAT
31759978 AAAAATTATA
1 AAAAATTATA
*
31759988 AAAAATTGTA
1 AAAAATTATA
31759998 AAAAATTATA
1 AAAAATTATA
**
31760008 AAATTTTAT-
1 AAAAATTATA
*
31760017 AAAAATCATA
1 AAAAATTATA
31760027 AAAAATTATA
1 AAAAATTATA
31760037 AAA
1 AAA
31760040 TGCATCAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
9 6 0.14
10 37 0.86
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:31759999 original size:19 final size:19
Alignment explanation
Indices: 31759976--31760039 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
31759966 ATAAAAATAA
31759976 ATAAAAATTATAAAAAATT
1 ATAAAAATTATAAAAAATT
* **
31759995 GTAAAAAATTATAAAATTTT
1 AT-AAAAATTATAAAAAATT
*
31760015 ATAAAAATCATAAAAAATT
1 ATAAAAATTATAAAAAATT
31760034 ATAAAA
1 ATAAAA
31760040 TGCATCAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAATTATAAAAAATT
Found at i:31760040 original size:29 final size:28
Alignment explanation
Indices: 31759979--31760040 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
31759969 AAAATAAATA
**
31759979 AAAATTATAAAAAATTGTAAAAAATTAT
1 AAAATTATAAAAAATCATAAAAAATTAT
*
31760007 AAAATTTTATAAAAATCATAAAAAATTAT
1 AAAATTATA-AAAAATCATAAAAAATTAT
31760036 AAAAT
1 AAAAT
31760041 GCATCAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAATTATAAAAAATCATAAAAAATTAT
Found at i:31761101 original size:19 final size:19
Alignment explanation
Indices: 31761077--31761187 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
31761067 AATCTTTAGG
31761077 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
31761096 GATATGCAATATTAGTTAT
1 GATATGCAATCTTAGATAT
**
31761115 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31761134 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
31761153 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31761172 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
31761188 AGATATGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:31761128 original size:38 final size:38
Alignment explanation
Indices: 31761084--31761187 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
31761074 AGGGATATGC
* *
31761084 AATCTTAGATATGATATGCAATATTAGTTATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
31761122 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
31761160 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
31761188 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATGATATAT
Found at i:31761213 original size:22 final size:21
Alignment explanation
Indices: 31761077--31761213 Score: 105
Period size: 19 Copynumber: 6.9 Consensus size: 21
31761067 AATCTTTAGG
*
31761077 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* * *
31761096 GATATGCAATATT--AGTTAT
1 GATATGTAATCTTAGAGATAT
*
31761115 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
31761134 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
31761153 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
31761172 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
31761194 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
31761214 TTAATTTGTA
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
19 77 0.77
22 12 0.12
23 11 0.11
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:31771555 original size:6 final size:6
Alignment explanation
Indices: 31771546--31771572 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31771536 ACTTAAAGAC
31771546 AAAGGA AAAGGA AAAGGA AAAGGA AAA
1 AAAGGA AAAGGA AAAGGA AAAGGA AAA
31771573 ATAGATGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:31782681 original size:22 final size:22
Alignment explanation
Indices: 31782656--31782698 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31782646 CCAGAAAAAG
31782656 TAAGATCCAATTTCAAAGTTTC
1 TAAGATCCAATTTCAAAGTTTC
*
31782678 TAAGATCCACTTTCAAAGTTT
1 TAAGATCCAATTTCAAAGTTT
31782699 TCTATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (22 bp):
TAAGATCCAATTTCAAAGTTTC
Found at i:31785964 original size:17 final size:17
Alignment explanation
Indices: 31785942--31785981 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
31785932 GGCCAATTTG
31785942 GGGCATGTGGACCACAC
1 GGGCATGTGGACCACAC
* *
31785959 GGGCATGTGGGCCACAT
1 GGGCATGTGGACCACAC
31785976 GGGCAT
1 GGGCAT
31785982 ATGAGCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (17 bp):
GGGCATGTGGACCACAC
Found at i:31787394 original size:36 final size:35
Alignment explanation
Indices: 31787353--31787431 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 35
31787343 TACTTTCTAT
* *
31787353 TTGGTGTGTTTTGGTGGGACTAGCTCTGT-TGAGCA
1 TTGGTGTGTTCTAGTGGGACTAGCTCT-TATGAGCA
*
31787388 TCTGGTGTGTTCTAGTTGGACTAGCTCTTATGAGCA
1 T-TGGTGTGTTCTAGTGGGACTAGCTCTTATGAGCA
31787424 TTGGTGTG
1 TTGGTGTG
31787432 ATTGGCTCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 9 0.23
36 30 0.77
ACGTcount: A:0.13, C:0.13, G:0.34, T:0.41
Consensus pattern (35 bp):
TTGGTGTGTTCTAGTGGGACTAGCTCTTATGAGCA
Found at i:31790656 original size:27 final size:28
Alignment explanation
Indices: 31790624--31790695 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
31790614 CGACTTTATA
31790624 AAATTTTATAATTTTTTATA-T-TTCTAT
1 AAATTTTATAATTTTTTATATTGTTC-AT
* *
31790651 ATATTTTATAATTTTTTATGTTGTTCAT
1 AAATTTTATAATTTTTTATATTGTTCAT
*
31790679 AAATTTTACAATTTTTT
1 AAATTTTATAATTTTTT
31790696 TTATATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 18 0.46
28 18 0.46
29 3 0.08
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (28 bp):
AAATTTTATAATTTTTTATATTGTTCAT
Found at i:31791077 original size:93 final size:91
Alignment explanation
Indices: 31790912--31791086 Score: 208
Period size: 93 Copynumber: 1.9 Consensus size: 91
31790902 ACGATCAAAG
* * *
31790912 GGCCTTTTTAATACATTTGGCAATTCAAGTACCTAATTGAGTGTAAAAAAAACGTAGGGGTTTAA
1 GGCCTTTTTAATACATTTGGAAATTCAAGTACCTAATTGAGTGTAAAAAAAACG-AGGAGCTTAA
*
31790977 TAGTTTTTTTTAAAAAAAAAATTTGAA
65 TAGTTTTTTTGAAAAAAAAAATTTGAA
* ** * * *
31791004 GGCCTTTTTGATATTTTTGGAAAGTTTAAGTATCTAATTGAGTGTAAAAGAAAAC-ATGAGCTTA
1 GGCCTTTTTAATACATTTGGAAA-TTCAAGTACCTAATTGAGTGTAAAA-AAAACGAGGAGCTTA
*
31791068 ATTATTTTTTTTGAAAAAA
64 A-TAGTTTTTTTGAAAAAA
31791087 TTTGAAGAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
92 26 0.38
93 38 0.55
94 5 0.07
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (91 bp):
GGCCTTTTTAATACATTTGGAAATTCAAGTACCTAATTGAGTGTAAAAAAAACGAGGAGCTTAAT
AGTTTTTTTGAAAAAAAAAATTTGAA
Found at i:31791085 original size:92 final size:91
Alignment explanation
Indices: 31790912--31791086 Score: 210
Period size: 92 Copynumber: 1.9 Consensus size: 91
31790902 ACGATCAAAG
* * *
31790912 GGCCTTTTTAATACATTTGGCAATTCAAGTACCTAATTGAGTGTAAAAAAAACGTAGGGGTTTAA
1 GGCCTTTTTAATACATTTGGAAATTCAAGTACCTAATTGAGTGTAAAAAAAACG-AGGAGCTTAA
31790977 TAGTTTTTTTTAAAAAAAAAATTTGAA
65 TAGTTTTTTTTAAAAAAAAAATTTGAA
* ** * * *
31791004 GGCCTTTTTGATATTTTTGGAAAGTTTAAGTATCTAATTGAGTGTAAAAGAAAAC-ATGAGCTTA
1 GGCCTTTTTAATACATTTGGAAA-TTCAAGTACCTAATTGAGTGTAAAA-AAAACGAGGAGCTTA
*
31791068 ATTA-TTTTTTTTGAAAAAA
64 A-TAGTTTTTTTTAAAAAAA
31791087 TTTGAAGAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
92 40 0.57
93 25 0.36
94 5 0.07
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (91 bp):
GGCCTTTTTAATACATTTGGAAATTCAAGTACCTAATTGAGTGTAAAAAAAACGAGGAGCTTAAT
AGTTTTTTTTAAAAAAAAAATTTGAA
Found at i:31791403 original size:7 final size:7
Alignment explanation
Indices: 31791381--31791425 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 7
31791371 GTTTAGTGAC
31791381 TAGGGTT
1 TAGGGTT
31791388 TATGGGTT
1 TA-GGGTT
31791396 TAGGGTTT
1 TAGGG-TT
31791404 TAGTGGTT
1 TAG-GGTT
31791412 TAGGG-T
1 TAGGGTT
31791418 TAGGGTT
1 TAGGGTT
31791425 T
1 T
31791426 TGTTAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 6 0.18
7 9 0.26
8 17 0.50
9 2 0.06
ACGTcount: A:0.13, C:0.00, G:0.40, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:31791534 original size:34 final size:34
Alignment explanation
Indices: 31791495--31791611 Score: 146
Period size: 34 Copynumber: 3.4 Consensus size: 34
31791485 AGGTTTAAAA
*
31791495 TTTTTAAAAAAATTAATTAAATTAGGTTTTAGGG
1 TTTTTAAAAAAATTAATTAAATTAGGATTTAGGG
* ** * *
31791529 GTTTTAAGTAAATTAATTAAATTAGGGTCTAGGG
1 TTTTTAAAAAAATTAATTAAATTAGGATTTAGGG
*
31791563 TTTTTAAGAAAAA-TAATTAAATTAAGATTTAGGG
1 TTTTTAA-AAAAATTAATTAAATTAGGATTTAGGG
31791597 TTTTTAAAAATAATT
1 TTTTTAAAAA-AATT
31791612 TTGTGTTTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
33 3 0.04
34 62 0.90
35 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (34 bp):
TTTTTAAAAAAATTAATTAAATTAGGATTTAGGG
Found at i:31791898 original size:125 final size:125
Alignment explanation
Indices: 31791688--31792957 Score: 1467
Period size: 125 Copynumber: 10.2 Consensus size: 125
31791678 ATTTTGTTTT
* * * * * * * *
31791688 TTTTTCTACAGCAGTTTCTAAAAAAATTAATTTTGAGAATATGATTCTAAAAAAATAGTGAC-AA
1 TTTTTCTACAGTAGTTCCTGAAAAAA-TAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAA
* *
31791752 AATGCTTCAAGCAGGATGCACTGTCAGAAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTC
65 AATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACGTGGACGCTC
* ** * * *
31791814 TTTTTCTATAGTAGTTTTTG-AAAAATAATTTTGAAAAGACGGTTCTGAAAAAATAATGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * * * * *
31791878 ATGCTTTAAGTAGTACGCACTGTTAGCAAAAGTACTAAAAAAAC-CCCACGTGGACACTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGGACGCTC
* * * *
31791937 TTTTTGTACAGTAGTTCCTG-AAAAATAATTTTGAGAAGATGGTTTTGAAAAAATAGTGTGAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * * *
31792001 CTGCTTCAAGCAGCATGCACTATTAGCAAAATTACTAAAAAAAGCTCTCACGTGGACACTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACGTGGACGCTC
* * * * **
31792062 TTTTTTTACAGTAGTTCTTG-AAAAGTAATTTTGAAAAGACAATTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * *
31792126 ACGCTTAAAGTAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACGTGGACGCTC
* **
31792187 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGATAGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * * * * *
31792252 ACGCTTCAAGCAGGATACATTGTCAGCAAAATTACTAAAAAATCTCCCATGCGGATGCTA
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGGACGCTC
** ** * * *
31792312 TTTTTCTATTGTAGTTTTTGAAAAAATAATTTTGAGAAGACGGTTAT-AAAAAATAATGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* ** * * * * *
31792376 ACGCTTCAATTAGTATGTACTGTCAGCAAAAGTACTAAAAAAGCTCCTACATGGACGCTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGGACGCTC
* * *
31792436 TTTTTCTACAGTAGCTCCTGAAAAAATAATTTTTAGAAGACGGTTCTGAAAAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * *
31792501 ATTCTTCAAGCAGGATGCACTGTAAGCAAAATTACTAAAAAAAGCTCCCACATGGATGCTT
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACGTGGACGCTC
* **
31792562 TTTTTCTATAACAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTG-AAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * * *
31792626 ACGCTTCAAGCAGGATGCACTGTCAACAAAATTACTAACAAAAGCTTCCATGTAGACACTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAA-AAAAGCTCCCACGTGGACGCTC
* * * *
31792687 TTTTTTTATAGTAGTTCCTGAAAAAATAATTCT-AAAAGACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * **
31792751 ATGCTTCAAGCAAGATGCACTGTCAACAAAATTACTGAAACAAGCTCCCGTGTGGACGCTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACGTGGACGCTC
** * *
31792812 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATAGTTCTGAAAATATAGTTTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* ** *
31792877 ATGCTTCAAGCAGAATGCACTGTCAGCAAAATTACTGAAAAAAGCTCATACGTGGACGTTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACGTGGACGCTC
*
31792938 TTTTTCTATAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
31792958 CTTGGCTTTA
Statistics
Matches: 975, Mismatches: 159, Indels: 20
0.84 0.14 0.02
Matches are distributed among these distances:
123 98 0.10
124 157 0.16
125 469 0.48
126 251 0.26
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGGACGCTC
Found at i:31792903 original size:625 final size:625
Alignment explanation
Indices: 31791708--31792919 Score: 1684
Period size: 625 Copynumber: 1.9 Consensus size: 625
31791698 GCAGTTTCTA
* * * * * *
31791708 AAAAAATTAATTTTGAGAATATGATTCTAAAAAAATAGTGACAAAATGCTTCAAGCAGGATGCAC
1 AAAAAATTAATTTTGAGAAGACGATTATAAAAAAATAATGAAAAAACGCTTCAAGCAGGATGCAC
* * * **
31791773 TGTCAGAAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAGTAGTTTTTGAAAA
66 TGTCAGAAAAAGTACTGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGCTCCTGAAAA
* * * *
31791838 ATAATTTTGAAAAGACGGTTCTGAAAAAATAATGTAAAAAATGCTTTAAGTAGTACGCACTGTTA
131 ATAATTTTGAAAAGACGGTTCTGAAAAAATAATGTAAAAAATGCTTCAAGCAGGACGCACTGTAA
* * **
31791903 GCAAAAGTACTAAAAAAACCCCACGTGGACACTCTTTTTGTACAGTAGTTCCTGAAAAATAATTT
196 GCAAAAGTACTAAAAAAACCCCACATGGACACTCTTTTTCTACAACAGTTCCTGAAAAATAATTT
* * * * *
31791968 TGAGAAGATGGTTTTGAAAAAATAGTGTGAAAACTGCTTCAAGCAGCATGCACTATTAGCAAAAT
261 TGAGAAGACGGTTCTGAAAAAATAGTGTAAAAACTGCTTCAAGCAGCATGCACTATCAACAAAAT
* * * *
31792033 TACTAAAAAAAGCTCTCACGTGGACACTCTTTTTTTACAGTAGTTCTTGAAAAGTAATTTTGAAA
326 TACTAAAAAAAGCTCTCACGTAGACACTCTTTTTTTACAGTAGTTCCTGAAAAATAATTCTGAAA
* * *
31792098 AGACAATTCTGAAAAAATAGTGTCAAAAACGCTTAAAGTAGGATGCACTGTCAGCAAAATTACTG
391 AGACAATTCTGAAAAAATAGTGTCAAAAACGCTTAAAGCAAGATGCACTGTCAACAAAATTACTG
*
31792163 AAAAAAGCTCCCACGTGGACACTCTTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGAT
456 AAAAAAGCTCCCACGTGGACACTCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGAT
* *
31792228 AGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATACATTGTCAGCAAAATTACT-AAAA
521 AGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGAATACACTGTCAGCAAAATTACTGAAAA
31792292 AATCTCCCATGCGGATGCTATTTTTCTATTGTAGTTTTTG
586 AATCTCCCATGCGGATGCTATTTTTCTATTGTAGTTTTTG
* ** * *
31792332 AAAAAA-TAATTTTGAGAAGACGGTTAT-AAAAAATAATGTAAAAAACGCTTCAATTAGTATGTA
1 AAAAAATTAATTTTGAGAAGACGATTATAAAAAAATAATG-AAAAAACGCTTCAAGCAGGATGCA
* *
31792395 CTGTCAGCAAAAGTACT-AAAAAAGCTCCTACATGGACGCTCTTTTTCTACAGTAGCTCCTGAAA
65 CTGTCAGAAAAAGTACTGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGCTCCTG-AA
* * * * *
31792459 AAATAATTTTTAGAAGACGGTTCTGAAAAAATAGTGTAAAAAATTCTTCAAGCAGGATGCACTGT
129 AAATAATTTTGAAAAGACGGTTCTGAAAAAATAATGTAAAAAATGCTTCAAGCAGGACGCACTGT
* ** * *
31792524 AAGCAAAATTACTAAAAAAAGCTCCCACATGGATGCTTTTTTTCTATAACAGTTCCTGAAAAAAT
194 AAGCAAAAGTACTAAAAAAA-C-CCCACATGGACACTCTTTTTCTACAACAGTTCCTG-AAAAAT
* *
31792589 AATTTTGAGAAGACGGTTCTG-AAAAATAGTGTCAAAAAC-GCTTCAAGCAGGATGCACTGTCAA
256 AATTTTGAGAAGACGGTTCTGAAAAAATAGTGT-AAAAACTGCTTCAAGCAGCATGCACTATCAA
* * *
31792652 CAAAATTACTAACAAAAGCT-TCCATGTAGACACTCTTTTTTTATAGTAGTTCCTGAAAAAATAA
320 CAAAATTACTAAAAAAAGCTCT-CACGTAGACACTCTTTTTTTACAGTAGTTCCTG-AAAAATAA
** * *
31792716 TTCT-AAAAGACGGTTCTGAAAAAATAGTGTCAAAAATGCTTCAAGCAAGATGCACTGTCAACAA
383 TTCTGAAAAGACAATTCTGAAAAAATAGTGTCAAAAACGCTTAAAGCAAGATGCACTGTCAACAA
* ** *
31792780 AATTACTGAAACAAGCTCCCGTGTGGACGCTCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTT
448 AATTACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTT
* * * *
31792845 GAGAAGATAGTTCTGAAAATATAGTTTCAAAAATGCTTCAAGCAGAATGCACTGTCAGCAAAATT
513 GAGAAGATAGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGAATACACTGTCAGCAAAATT
31792910 ACTGAAAAAA
578 ACTGAAAAAA
31792920 GCTCATACGT
Statistics
Matches: 511, Mismatches: 68, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
622 48 0.09
623 128 0.25
624 8 0.02
625 281 0.55
626 46 0.09
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (625 bp):
AAAAAATTAATTTTGAGAAGACGATTATAAAAAAATAATGAAAAAACGCTTCAAGCAGGATGCAC
TGTCAGAAAAAGTACTGAAAAAAGCTCCCACATGGACGCTCTTTTTCTACAGTAGCTCCTGAAAA
ATAATTTTGAAAAGACGGTTCTGAAAAAATAATGTAAAAAATGCTTCAAGCAGGACGCACTGTAA
GCAAAAGTACTAAAAAAACCCCACATGGACACTCTTTTTCTACAACAGTTCCTGAAAAATAATTT
TGAGAAGACGGTTCTGAAAAAATAGTGTAAAAACTGCTTCAAGCAGCATGCACTATCAACAAAAT
TACTAAAAAAAGCTCTCACGTAGACACTCTTTTTTTACAGTAGTTCCTGAAAAATAATTCTGAAA
AGACAATTCTGAAAAAATAGTGTCAAAAACGCTTAAAGCAAGATGCACTGTCAACAAAATTACTG
AAAAAAGCTCCCACGTGGACACTCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGAT
AGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGAATACACTGTCAGCAAAATTACTGAAAA
AATCTCCCATGCGGATGCTATTTTTCTATTGTAGTTTTTG
Found at i:31797972 original size:18 final size:18
Alignment explanation
Indices: 31797949--31797987 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
31797939 GGAAAATGAA
*
31797949 ACATATAAGAGTTAGGAT
1 ACATATAAGAGTTAGAAT
*
31797967 ACATATAAGGGTTAGAAT
1 ACATATAAGAGTTAGAAT
31797985 ACA
1 ACA
31797988 CACCTGGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.26
Consensus pattern (18 bp):
ACATATAAGAGTTAGAAT
Found at i:31798182 original size:31 final size:31
Alignment explanation
Indices: 31798144--31798208 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
31798134 ATTTACCGAC
* * * *
31798144 GCCTCTGCTCTTCTGATAGCAAATATGGTTT
1 GCCTCTGCTCCTCCGAGAGCAAATATGGCTT
*
31798175 GCCTCTGCTCCTCCGAGAGTAAATATGGCTT
1 GCCTCTGCTCCTCCGAGAGCAAATATGGCTT
31798206 GCC
1 GCC
31798209 ATGGCATGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.18, C:0.28, G:0.22, T:0.32
Consensus pattern (31 bp):
GCCTCTGCTCCTCCGAGAGCAAATATGGCTT
Found at i:31799589 original size:20 final size:21
Alignment explanation
Indices: 31799561--31799599 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
31799551 ATTAATTAAA
*
31799561 ATTACATAA-ATGAAAAAAAT
1 ATTAAATAATATGAAAAAAAT
*
31799581 ATTAAATAATATTAAAAAA
1 ATTAAATAATATGAAAAAA
31799600 TTGAAACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
ATTAAATAATATGAAAAAAAT
Found at i:31801041 original size:6 final size:6
Alignment explanation
Indices: 31801030--31801069 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
31801020 TAATGCTCAT
31801030 CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG CCAT
1 CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG CCAT
31801070 CAATATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.35, G:0.15, T:0.33
Consensus pattern (6 bp):
CCATTG
Found at i:31802602 original size:28 final size:28
Alignment explanation
Indices: 31802570--31802626 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
31802560 GATAATAAAG
*
31802570 ATAGAATTTTGTTTTTCTCTCAAATGGA
1 ATAGAATTTTGCTTTTCTCTCAAATGGA
31802598 ATAGAATTTTGCTTTTCTCTCAAATGGA
1 ATAGAATTTTGCTTTTCTCTCAAATGGA
31802626 A
1 A
31802627 ACGTATAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (28 bp):
ATAGAATTTTGCTTTTCTCTCAAATGGA
Found at i:31803925 original size:7 final size:7
Alignment explanation
Indices: 31803913--31803945 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
31803903 TCTGAAATTG
31803913 ATATACT
1 ATATACT
31803920 ATATACT
1 ATATACT
31803927 ATATACT
1 ATATACT
31803934 ATATACT
1 ATATACT
31803941 ATATA
1 ATATA
31803946 ATGTTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATACT
Found at i:31808666 original size:86 final size:86
Alignment explanation
Indices: 31808546--31808708 Score: 222
Period size: 86 Copynumber: 1.9 Consensus size: 86
31808536 AAATTTAGAT
* * *
31808546 TCGGTGAATTCATCAAGTACGTCTCAATAAGACCATCCACACTCTCGAATATGAACTCATTAAAA
1 TCGGTGAATTCATCAAGTACATCTCAATAAGACCACCCAAACTCTCGAATATGAACTCATTAAAA
31808611 GTATA-AACTCAACATCTCAAG
66 GTA-AGAACTCAACATCTCAAG
* * ** *
31808632 TCGGTGAATTCATCAAGT-CTATCTCAATAGGACCACCCAAACTCTTGGCTATGAACTCATTAAG
1 TCGGTGAATTCATCAAGTAC-ATCTCAATAAGACCACCCAAACTCTCGAATATGAACTCATTAAA
31808696 AGTAAGAACTCAA
65 AGTAAGAACTCAA
31808709 ACTTATGCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
85 2 0.03
86 65 0.97
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (86 bp):
TCGGTGAATTCATCAAGTACATCTCAATAAGACCACCCAAACTCTCGAATATGAACTCATTAAAA
GTAAGAACTCAACATCTCAAG
Found at i:31816830 original size:12 final size:12
Alignment explanation
Indices: 31816813--31816847 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
31816803 TCACTCTCAC
31816813 TTTCTTTTTCAA
1 TTTCTTTTTCAA
**
31816825 TTTCTTTTTCGT
1 TTTCTTTTTCAA
31816837 TTTCTTTTTCA
1 TTTCTTTTTCA
31816848 CAATCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.17, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:31816840 original size:24 final size:24
Alignment explanation
Indices: 31816813--31816914 Score: 79
Period size: 24 Copynumber: 4.2 Consensus size: 24
31816803 TCACTCTCAC
31816813 TTTCTTTTTCAATTTCTTTTTCGT
1 TTTCTTTTTCAATTTCTTTTTCGT
*
31816837 TTTCTTTTTCACA-ATCTTTTTCGATTCT
1 TTTCTTTTTCA-ATTTCTTTTTCG----T
31816865 TTTCTCTCTTTCAATTT-TTTTTC--
1 TTTCT-T-TTTCAATTTCTTTTTCGT
* *
31816888 -TTCTTTTTCAATCTCTTTTTCTT
1 TTTCTTTTTCAATTTCTTTTTCGT
31816911 TTTC
1 TTTC
31816915 ATTACAACAT
Statistics
Matches: 63, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
20 8 0.13
21 7 0.11
22 4 0.06
24 23 0.37
25 1 0.02
28 6 0.10
29 8 0.13
30 6 0.10
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTCTTTTTCAATTTCTTTTTCGT
Found at i:31816898 original size:20 final size:20
Alignment explanation
Indices: 31816851--31816910 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
31816841 TTTTTCACAA
* *
31816851 TCTTTTTCGA-TTCTTTTC-
1 TCTTTTTCAATTTTTTTTCT
*
31816869 TCTCTTTCAATTTTTTTTCT
1 TCTTTTTCAATTTTTTTTCT
*
31816889 TCTTTTTCAATCTCTTTTTCT
1 TCTTTTTCAAT-TTTTTTTCT
31816910 T
1 T
31816911 TTTCATTACA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 8 0.24
19 7 0.21
20 10 0.29
21 9 0.26
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.68
Consensus pattern (20 bp):
TCTTTTTCAATTTTTTTTCT
Found at i:31816910 original size:18 final size:17
Alignment explanation
Indices: 31816851--31816915 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
31816841 TTTTTCACAA
*
31816851 TCTTTTTCGATTCTTTT
1 TCTTTTTCAATTCTTTT
* *
31816868 CTCTCTTTCAATTTTTTTTCT
1 -TCTTTTTCAA--TTCTTT-T
31816889 TCTTTTTCAATCTCTTTT
1 TCTTTTTCAAT-TCTTTT
31816907 TCTTTTTCA
1 TCTTTTTCA
31816916 TTACAACATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
18 19 0.50
19 4 0.11
20 14 0.37
21 1 0.03
ACGTcount: A:0.09, C:0.22, G:0.02, T:0.68
Consensus pattern (17 bp):
TCTTTTTCAATTCTTTT
Found at i:31818833 original size:40 final size:40
Alignment explanation
Indices: 31818773--31818849 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
31818763 TCTGCCTTGG
* *
31818773 GAAGCTGAACATGCAGCAACATTTTAATGGGAGTTTTTTA
1 GAAGCTGAACATGCAACAACATTTTAATAGGAGTTTTTTA
*
31818813 GAAGCTGAACGTGCAACAACATTTTAATAGGAGTTTT
1 GAAGCTGAACATGCAACAACATTTTAATAGGAGTTTT
31818850 GGAGCACGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (40 bp):
GAAGCTGAACATGCAACAACATTTTAATAGGAGTTTTTTA
Found at i:31821563 original size:18 final size:17
Alignment explanation
Indices: 31821534--31821569 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
31821524 ATCTCTCCCG
*
31821534 TTTTGAAATATTATAAA
1 TTTTGAAATATTAGAAA
31821551 TTTTGATAATATTAGAAA
1 TTTTGA-AATATTAGAAA
31821569 T
1 T
31821570 CAACTACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (17 bp):
TTTTGAAATATTAGAAA
Found at i:31822216 original size:16 final size:16
Alignment explanation
Indices: 31822188--31822230 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
31822178 AGTTAAAATG
31822188 TAATTTCATAATTGTAT
1 TAATTT-ATAATTGTAT
*
31822205 TAATTTATAATTTTAT
1 TAATTTATAATTGTAT
* *
31822221 AAATATATAA
1 TAATTTATAA
31822231 ATATATTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TAATTTATAATTGTAT
Found at i:31827315 original size:6 final size:7
Alignment explanation
Indices: 31827294--31827325 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
31827284 GAAAATCCTG
31827294 AAATAAA
1 AAATAAA
31827301 AAATAAA
1 AAATAAA
31827308 AAATAAA
1 AAATAAA
31827315 AAATGAAA
1 AAAT-AAA
31827323 AAA
1 AAA
31827326 AGTTTATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (7 bp):
AAATAAA
Found at i:31832798 original size:21 final size:23
Alignment explanation
Indices: 31832759--31832801 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
31832749 ATTCAAAATA
31832759 AAATAATACAGTCTAAAAATATC
1 AAATAATACAGTCTAAAAATATC
*
31832782 AAATAATA-A-TCTTAAAATAT
1 AAATAATACAGTCTAAAAATAT
31832802 TTTTAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATAATACAGTCTAAAAATATC
Found at i:31833631 original size:34 final size:33
Alignment explanation
Indices: 31833526--31833623 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 33
31833516 GAGCAATACG
*
31833526 GTAGCAATCAATATGCTTATAACAGTTCAATATA
1 GTAGCAAT-AATATGCTTATAACAGTTCAATAAA
*
31833560 GTAGCAAATAATATGCTTATAACGGTTCAATAAA
1 GTAGC-AATAATATGCTTATAACAGTTCAATAAA
*
31833594 GTAGCAAGTAATATGCTTATAACAGATCAA
1 GTAGCAA-TAATATGCTTATAACAGTTCAA
31833624 CTCAGTAGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 2 0.03
34 53 0.91
35 3 0.05
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (33 bp):
GTAGCAATAATATGCTTATAACAGTTCAATAAA
Found at i:31834906 original size:11 final size:11
Alignment explanation
Indices: 31834890--31834914 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31834880 AACTTGTTCA
31834890 AATTAATCATC
1 AATTAATCATC
31834901 AATTAATCATC
1 AATTAATCATC
31834912 AAT
1 AAT
31834915 ACACAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTAATCATC
Found at i:31843430 original size:26 final size:28
Alignment explanation
Indices: 31843401--31843452 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
31843391 TTTTTTCTTT
*
31843401 TAAAAAAACATAAATT-T-AAAAAAATG
1 TAAAAAAACAAAAATTGTCAAAAAAATG
*
31843427 TAAAAATACAAAAATTGTCAAAAAAA
1 TAAAAAAACAAAAATTGTCAAAAAAA
31843453 AACCTCTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 1 0.05
28 7 0.32
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (28 bp):
TAAAAAAACAAAAATTGTCAAAAAAATG
Found at i:31843878 original size:18 final size:17
Alignment explanation
Indices: 31843838--31843884 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
31843828 TTTAAAAAAA
*
31843838 ATATTTTTTTAATTTCT
1 ATATTTTTTTAAATTCT
31843855 -TGATTTTTTTATAATTCT
1 AT-ATTTTTTTA-AATTCT
*
31843873 ATATTTCTTTAA
1 ATATTTTTTTAA
31843885 TTTTTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.04
17 10 0.40
18 13 0.52
19 1 0.04
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (17 bp):
ATATTTTTTTAAATTCT
Found at i:31844854 original size:12 final size:12
Alignment explanation
Indices: 31844839--31844881 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
31844829 TGATAAATAA
*
31844839 TAAAATAATATT
1 TAAAATAAAATT
*
31844851 TAAAATAAAATG
1 TAAAATAAAATT
*
31844863 CAATAATAAAATT
1 TAA-AATAAAATT
31844876 TAAAAT
1 TAAAAT
31844882 TAACATCATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (12 bp):
TAAAATAAAATT
Found at i:31848403 original size:29 final size:29
Alignment explanation
Indices: 31848355--31848410 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
31848345 GTCGTACATA
** *
31848355 GTCTGGCACACGACTGTGTGTCACACACG
1 GTCTGGCACACGACCATGTGCCACACACG
31848384 GTCTGGCACACGACCATGTGCCACACA
1 GTCTGGCACACGACCATGTGCCACACA
31848411 TGGCCTACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.18
Consensus pattern (29 bp):
GTCTGGCACACGACCATGTGCCACACACG
Found at i:31848780 original size:16 final size:16
Alignment explanation
Indices: 31848759--31848789 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31848749 AATTTCATAA
*
31848759 AACCAATTACAACAAG
1 AACCAATTAAAACAAG
31848775 AACCAATTAAAACAA
1 AACCAATTAAAACAA
31848790 CCTCTTTACA
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:0.61, C:0.23, G:0.03, T:0.13
Consensus pattern (16 bp):
AACCAATTAAAACAAG
Found at i:31853190 original size:6 final size:6
Alignment explanation
Indices: 31853179--31853205 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31853169 ATGTGCAACT
31853179 CAATAC CAATAC CAATAC CAATAC CAA
1 CAATAC CAATAC CAATAC CAATAC CAA
31853206 GCAGACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (6 bp):
CAATAC
Found at i:31853481 original size:23 final size:23
Alignment explanation
Indices: 31853455--31853499 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31853445 TGATTTTGAA
*
31853455 TATTATTTGACAAA-ATTTCTAAG
1 TATT-TTTCACAAATATTTCTAAG
*
31853478 TATTTTTCATAAATATTTCTAA
1 TATTTTTCACAAATATTTCTAA
31853500 AAAATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (23 bp):
TATTTTTCACAAATATTTCTAAG
Found at i:31875889 original size:232 final size:232
Alignment explanation
Indices: 31875479--31875938 Score: 722
Period size: 232 Copynumber: 2.0 Consensus size: 232
31875469 GCTGCCTATC
* ** *
31875479 GAGAAAGACTCAGTTTGAGCCCACAAAACCCAAATCCATGACTACCATATGAACTCATTTCAATA
1 GAGAAAGACTCAGCTTGAGCCCACAAAACCCAAATCCACAACTACCATATGAACTCATTTCAACA
*
31875544 AAGTATCTACAATGTCAGAAATACACAGATCAGTTTAGAGTCTTCACCACAGTTCTCATGTCAAT
66 AAGTATCTACAATGTCAGAAATACACAGATCAGTTCAGAGTCTTCACCACAGTTCTCATGTCAAT
*
31875609 TCATATTAGAATGTTTGACCAAACCACAGTTTCAATCACTACTATGTCTCAACAAATCATAATAA
131 TCATATTAGAATGTTTGACCAAACCACAGTTTCAATCACTACTATGTCTCAACAAATCACAATAA
* *
31875674 CTAAACAGGAATACTTATAGGTTTAGTGTCAGACATT
196 CTAAACAGGAATACTTACAAGTTTAGTGTCAGACATT
* * ** *
31875711 GAGAAAGACTCAGCTTGAGCCCATAAAACTCACGTCCACAACTACCATGTGAACTCATTTCAACA
1 GAGAAAGACTCAGCTTGAGCCCACAAAACCCAAATCCACAACTACCATATGAACTCATTTCAACA
* * * * *
31875776 AATTATCTACAATGTCAGAAATGCATAGATCAGTTCAGAGTCTTTACCACAGTTCTTATGTCAAT
66 AAGTATCTACAATGTCAGAAATACACAGATCAGTTCAGAGTCTTCACCACAGTTCTCATGTCAAT
* * *
31875841 TCATTTTAGAATGTTTGACCAAGCCACAGTTTCAATCACTATTATGTCTCAACAAATCACAATAA
131 TCATATTAGAATGTTTGACCAAACCACAGTTTCAATCACTACTATGTCTCAACAAATCACAATAA
*
31875906 CTGAACAGGAATACTTACAAGTTTAGTGTCAGA
196 CTAAACAGGAATACTTACAAGTTTAGTGTCAGA
31875939 AACTCGATCC
Statistics
Matches: 206, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
232 206 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (232 bp):
GAGAAAGACTCAGCTTGAGCCCACAAAACCCAAATCCACAACTACCATATGAACTCATTTCAACA
AAGTATCTACAATGTCAGAAATACACAGATCAGTTCAGAGTCTTCACCACAGTTCTCATGTCAAT
TCATATTAGAATGTTTGACCAAACCACAGTTTCAATCACTACTATGTCTCAACAAATCACAATAA
CTAAACAGGAATACTTACAAGTTTAGTGTCAGACATT
Found at i:31876496 original size:22 final size:22
Alignment explanation
Indices: 31876471--31876531 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
31876461 ACATAGTATG
* *
31876471 TCAGATACAGATGCAGAACATA
1 TCAGATTCAGATGCAGAACAAA
* * * *
31876493 TCAGATTTATATGTAGAATAAA
1 TCAGATTCAGATGCAGAACAAA
31876515 TCAGATTCAGATGCAGA
1 TCAGATTCAGATGCAGA
31876532 TTTCTAACCC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (22 bp):
TCAGATTCAGATGCAGAACAAA
Found at i:31877835 original size:749 final size:749
Alignment explanation
Indices: 31876367--31879136 Score: 4888
Period size: 749 Copynumber: 3.7 Consensus size: 749
31876357 ATTTAGTACT
* * *
31876367 AATTAGTAAACTACAATTGTTATCTCATTTACCGTAGATCATCTGTTACTCAGAATTAGATACAG
1 AATTAGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCCGTTACTCAGAATTAGATACAA
* *
31876432 AATAGAAACAAAGAAAGTCGGATATAGTTACATAGTATGTCAGATACAGATGCAGAACATATCAG
66 AATAGAAACAAAGAAAGTCGGATACAGTTACATGGTATGTCAGATACAGATGCAGAACATATCAG
* * *
31876497 ATTTATATGTAGAATAAATCAGATTCAGATGCAGATTTCTAACCCTATCTATTACACACCATCTT
131 ATTTATATGTAGAATAAATCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTC
* *
31876562 TATCCATCTCAACACACCATATAGGGCATCAAGTACTCGTCCATCCATACACTGC-TAATGACTA
196 TATCCATCCCAACACACCATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTA
* * * * *
31876626 TATCTCACGTTTCAGAATAATCAAAGCGTAATTGTCAAATCAGAATGCGATAAATCGCCACAGAT
261 TATCTCACATTTCAGAATAATCACAGCGTAGTTGCCAGATCAGAATGCGATAAATCGCCACAGAT
* * * *
31876691 TTAATAGATAATTAAACAGTCACACTTCCTTC-TTAAACAACACCAATCTCAATACGAATGCAAT
326 TCAATAGATAATTAAACAGTCACACTTCCTTCTTTATACAGCACCAATCTCAATGCGAATGCAAT
*
31876755 CCAACGGATGCAGATATAAGTATGCGGAGTAACAAATTCGGATCATACTCAATGTTATGTGTATA
391 CCAACGGATGCAGATATAAGTATGCGGAGTAACAGATTCGGATCATACTCAATGTTATGTGTATA
* * *
31876820 ATAATAGTTTATACAAAAAC-----ACCCACTAATGGATTTCATAGCCAAAATTAGATCATACTA
456 ATAATAGTTTATACAAAAACAAATTACCCACTAATAGATTTCATAGCCCAAATTAGATCATACTG
* *
31876880 GCTCTACTGTTACATGGTATGTCAGATACAGATGTAGAACATATCAGATTTATATGTAGAATAAA
521 GCTCTACTGTTACATGGTATGTTAGATATAGATGTAGAACATATCAGATTTATATGTAGAATAAA
* *
31876945 TTAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTCCATCCATCCCAACACACC
586 TCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTCTATCCATCCCAACACACC
31877010 ATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTATATGTCACGTTTCAGAAT
651 ATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTATATGTCACGTTTCAGAAT
31877075 AATCGCAGCGTAGCTGCCAGATCAGAATGCAATA
716 AATCGCAGCGTAGCTGCCAGATCAGAATGCAATA
* * *
31877109 AATTAGTAAACTACAATTGTAATATCATTTATCGTAGATCATCTGTTACTCAGAATTAGATACAA
1 AATTAGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCCGTTACTCAGAATTAGATACAA
* *
31877174 AATATAAACAAAGAAAGTCGGATACAGTTACATGGTATGTCAGACACAGATGCAGAACATATCAG
66 AATAGAAACAAAGAAAGTCGGATACAGTTACATGGTATGTCAGATACAGATGCAGAACATATCAG
*
31877239 ATTTATATGTAGAATAAATCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTT
131 ATTTATATGTAGAATAAATCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTC
*
31877304 TATCCATCTCAACACACCATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTA
196 TATCCATCCCAACACACCATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTA
* * * *
31877369 TATATCACATTTTAGAATAATCACAGCGTCGTTGCCAGATCAGAATGCGATAAATCGCCATAGAT
261 TATCTCACATTTCAGAATAATCACAGCGTAGTTGCCAGATCAGAATGCGATAAATCGCCACAGAT
*
31877434 TCAATAGATAATTAAACAGTCACACTTCCTTCTTTATACAGCACCAATCCCAATGCGAATGCAAT
326 TCAATAGATAATTAAACAGTCACACTTCCTTCTTTATACAGCACCAATCTCAATGCGAATGCAAT
* *
31877499 CCAACGGATGCATATTTAAGTATGCGGAGTAACAGATTCGGATCATACTCAATGTTATGTGTATA
391 CCAACGGATGCAGATATAAGTATGCGGAGTAACAGATTCGGATCATACTCAATGTTATGTGTATA
*
31877564 ATAATAGTTTATACAAAAACAAATTATCCACTAATAGATTTCATAGCCCAAATTAGATCATACTG
456 ATAATAGTTTATACAAAAACAAATTACCCACTAATAGATTTCATAGCCCAAATTAGATCATACTG
*
31877629 GCTCTACTGTTACATGGTATGTTAGATATAGATGTAGAACATATCATATTTATATGTAGAATAAA
521 GCTCTACTGTTACATGGTATGTTAGATATAGATGTAGAACATATCAGATTTATATGTAGAATAAA
*
31877694 TCAGATTCAGATGCAGATTTTTAACCCCATCCATTACACACCATCTCTATCCATCCCAACACACC
586 TCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTCTATCCATCCCAACACACC
*
31877759 ATATAGGGTATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTATATGTCACGTTTCAGAAT
651 ATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTATATGTCACGTTTCAGAAT
31877824 AATCGCAGCGTAGCTGCCAGATCAGAATGCAATA
716 AATCGCAGCGTAGCTGCCAGATCAGAATGCAATA
*
31877858 AATTAGGAAACTACAATTGTAATCTCATTTACCGTAGATCATCCGTTACTCAGAATTAGATACAA
1 AATTAGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCCGTTACTCAGAATTAGATACAA
31877923 AATAGAAACAAAGAAAGTCGGATACAGTTACATGGTATGTCAGATACAGATGCAGAACATATCAG
66 AATAGAAACAAAGAAAGTCGGATACAGTTACATGGTATGTCAGATACAGATGCAGAACATATCAG
* * *
31877988 ATTTATATGTAGAATAAATCAGATTCAAATGCAAATTTCTAACCCTATCCATTACACACCATCTC
131 ATTTATATGTAGAATAAATCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTC
* *
31878053 CATCCATCCCAACACACCATATAGGGCATCAAGTACTCGTCCATCCTTACACTGCGTAATGACTA
196 TATCCATCCCAACACACCATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTA
* * * *
31878118 TATCTCATATTTTAGAATAATCACAGCGTAGCTGCCAGATCAGAATGCGATAAATCCCCACAGAT
261 TATCTCACATTTCAGAATAATCACAGCGTAGTTGCCAGATCAGAATGCGATAAATCGCCACAGAT
31878183 TCAATAGATAATTAAACAGTCACACTTCCTTCTTTATACAGCACCAATCTCAATGCGAATGCAAT
326 TCAATAGATAATTAAACAGTCACACTTCCTTCTTTATACAGCACCAATCTCAATGCGAATGCAAT
*
31878248 CCAACGGATGCAGATATAAGTTTGCGGAGTAACAGATTCGGATCATACTCAATGTTATGTGTATA
391 CCAACGGATGCAGATATAAGTATGCGGAGTAACAGATTCGGATCATACTCAATGTTATGTGTATA
*
31878313 ATAATAGTTTATACAAAAACCAATTACCCACTAATAGATTTCATAGCCCAAATTAGATCATACTG
456 ATAATAGTTTATACAAAAACAAATTACCCACTAATAGATTTCATAGCCCAAATTAGATCATACTG
31878378 GCTCTACTGTTACATGGTATGTTAGATATAGATGTAGAACATATCAGATTTATATGTAGAATAAA
521 GCTCTACTGTTACATGGTATGTTAGATATAGATGTAGAACATATCAGATTTATATGTAGAATAAA
31878443 TCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTCTATCCATCCCAACACACC
586 TCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTCTATCCATCCCAACACACC
31878508 ATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTATATGTCACGTTTCAGAAT
651 ATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTATATGTCACGTTTCAGAAT
*
31878573 AATCGCAGCGTAGCTGCCAGATCAGAATGTAATA
716 AATCGCAGCGTAGCTGCCAGATCAGAATGCAATA
31878607 AATTAGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCCGTTACTCAGAATTAGATACAA
1 AATTAGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCCGTTACTCAGAATTAGATACAA
31878672 AATAGAAACAAAGAAAGTCGGATACAGTTACATGGTATGTCAGATACAGATGCAGAACATATCAG
66 AATAGAAACAAAGAAAGTCGGATACAGTTACATGGTATGTCAGATACAGATGCAGAACATATCAG
31878737 ATTTATATGTAGAATAAATCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTC
131 ATTTATATGTAGAATAAATCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTC
31878802 TATCCATCCCAACACACCATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTA
196 TATCCATCCCAACACACCATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTA
* * * *
31878867 TATGTCACATTTCAGAATAATCGCAGCGTAGTTGCCAGATCAGAATGTGATAAATCACCACAGAT
261 TATCTCACATTTCAGAATAATCACAGCGTAGTTGCCAGATCAGAATGCGATAAATCGCCACAGAT
* *
31878932 TTAATAGATAATTAAATAGTCACACTTCCTTCTTTATACAGCACCAATCTCAATGCGAATGCAAT
326 TCAATAGATAATTAAACAGTCACACTTCCTTCTTTATACAGCACCAATCTCAATGCGAATGCAAT
* *
31878997 CCAACGGATGCAAATATAAGTATGCGGAGTAACAGATTCGGATCATACTCAATTTTATGTGTATA
391 CCAACGGATGCAGATATAAGTATGCGGAGTAACAGATTCGGATCATACTCAATGTTATGTGTATA
*
31879062 ATAATAGTTTATACAAAAACAAATTACCCACTAATGGATTTCATAGCCCAAATTAGATCATACTG
456 ATAATAGTTTATACAAAAACAAATTACCCACTAATAGATTTCATAGCCCAAATTAGATCATACTG
31879127 GCTCTACTGT
521 GCTCTACTGT
31879137 AGGCCTATGT
Statistics
Matches: 1933, Mismatches: 88, Indels: 7
0.95 0.04 0.00
Matches are distributed among these distances:
742 239 0.12
743 96 0.05
744 110 0.06
749 1488 0.77
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.28
Consensus pattern (749 bp):
AATTAGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCCGTTACTCAGAATTAGATACAA
AATAGAAACAAAGAAAGTCGGATACAGTTACATGGTATGTCAGATACAGATGCAGAACATATCAG
ATTTATATGTAGAATAAATCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTC
TATCCATCCCAACACACCATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTA
TATCTCACATTTCAGAATAATCACAGCGTAGTTGCCAGATCAGAATGCGATAAATCGCCACAGAT
TCAATAGATAATTAAACAGTCACACTTCCTTCTTTATACAGCACCAATCTCAATGCGAATGCAAT
CCAACGGATGCAGATATAAGTATGCGGAGTAACAGATTCGGATCATACTCAATGTTATGTGTATA
ATAATAGTTTATACAAAAACAAATTACCCACTAATAGATTTCATAGCCCAAATTAGATCATACTG
GCTCTACTGTTACATGGTATGTTAGATATAGATGTAGAACATATCAGATTTATATGTAGAATAAA
TCAGATTCAGATGCAGATTTCTAACCCCATCCATTACACACCATCTCTATCCATCCCAACACACC
ATATAGGGCATCAAGTACTCGTCCATCCCTACACTGCGTAATGACTATATGTCACGTTTCAGAAT
AATCGCAGCGTAGCTGCCAGATCAGAATGCAATA
Found at i:31878736 original size:22 final size:22
Alignment explanation
Indices: 31878711--31878771 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
31878701 ACATGGTATG
* *
31878711 TCAGATACAGATGCAGAACATA
1 TCAGATTCAGATGCAGAACAAA
* * * *
31878733 TCAGATTTATATGTAGAATAAA
1 TCAGATTCAGATGCAGAACAAA
31878755 TCAGATTCAGATGCAGA
1 TCAGATTCAGATGCAGA
31878772 TTTCTAACCC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (22 bp):
TCAGATTCAGATGCAGAACAAA
Found at i:31879690 original size:24 final size:24
Alignment explanation
Indices: 31879663--31879710 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
31879653 AAAAACTTCG
31879663 ACACTAACCTAAAAAGTAAAGTAA
1 ACACTAACCTAAAAAGTAAAGTAA
31879687 ACACTAACCTAAAAAGTAAAGTAA
1 ACACTAACCTAAAAAGTAAAGTAA
31879711 CTCTTACCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.17
Consensus pattern (24 bp):
ACACTAACCTAAAAAGTAAAGTAA
Found at i:31882305 original size:68 final size:68
Alignment explanation
Indices: 31882196--31882351 Score: 213
Period size: 68 Copynumber: 2.3 Consensus size: 68
31882186 CAGTTATGAT
* * * * * * *
31882196 CTTACACAAATTAAACTCATGTTTACTGTCCTAACGGACTCCATATGTTGCCATAGTCTAGCTAT
1 CTTACACATATTAAACCCATGTTCACTATCCTAACGAACTCCATATGTTGCCATAGACTAACTAT
31882261 GGG
66 GGG
** *
31882264 CTTACACATATTAAACCCATGTTCACTATCCTGGCGAACTCCTTATGTTGCCATAGACTAACTAT
1 CTTACACATATTAAACCCATGTTCACTATCCTAACGAACTCCATATGTTGCCATAGACTAACTAT
*
31882329 GGT
66 GGG
31882332 CTTACACATATTAAACCCAT
1 CTTACACATATTAAACCCAT
31882352 ATTTAACTGG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (68 bp):
CTTACACATATTAAACCCATGTTCACTATCCTAACGAACTCCATATGTTGCCATAGACTAACTAT
GGG
Found at i:31884245 original size:25 final size:25
Alignment explanation
Indices: 31884202--31884258 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
31884192 TGTAACTAAA
*
31884202 TATTAGG-CTTGTGCAAGTGTTATC
1 TATTAGGCCTTGTGCAAGTGTCATC
*
31884226 TATTAGGCCTTGTGCTAGTGTCATC
1 TATTAGGCCTTGTGCAAGTGTCATC
*
31884251 TATCAGGC
1 TATTAGGC
31884259 TTTGAGCCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (25 bp):
TATTAGGCCTTGTGCAAGTGTCATC
Found at i:31884499 original size:28 final size:28
Alignment explanation
Indices: 31884459--31884514 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
31884449 TATCGTGAGC
31884459 TAGTCAAAATTCTGAAGTTAACTCGAAT
1 TAGTCAAAATTCTGAAGTTAACTCGAAT
31884487 TAGTCAAAATTCTGAAGTTAACTCGAAT
1 TAGTCAAAATTCTGAAGTTAACTCGAAT
31884515 GAGTGATACC
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:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (28 bp):
TAGTCAAAATTCTGAAGTTAACTCGAAT
Found at i:31885415 original size:12 final size:12
Alignment explanation
Indices: 31885398--31885424 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31885388 AAGTTTCACT
31885398 GTTTGTCACACG
1 GTTTGTCACACG
31885410 GTTTGTCACACG
1 GTTTGTCACACG
31885422 GTT
1 GTT
31885425 GACCACACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (12 bp):
GTTTGTCACACG
Found at i:31890212 original size:16 final size:17
Alignment explanation
Indices: 31890191--31890222 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31890181 AAATATGCAA
31890191 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
31890207 TCACATAACTTCATAT
1 TCACATAACTTCATAT
31890223 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:31890537 original size:43 final size:42
Alignment explanation
Indices: 31890382--31890537 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 42
31890372 CGCTCGTACA
*
31890382 ATGCCAACGTCCCAGACGTGGTCTTACATGTA-ATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATA-CACA-ATCG
* **
31890425 ATGCC-ACTGTCCCAGACAG-GGTCTTAGACAAAT-CA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTATACACAAT-CG
* * * *
31890466 ATGCTAATGTCCTAGACATGGTCTTACACGTATACACAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAA-TCG
31890509 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
31890538 AAAAATACAT
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
40 2 0.02
41 26 0.29
42 7 0.08
43 52 0.58
44 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTATACACAATCG
Found at i:31893255 original size:22 final size:21
Alignment explanation
Indices: 31893204--31893255 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
31893194 AATTGATCCT
31893204 AATTTT-AAAAACATTAAAGA
1 AATTTTAAAAAACATTAAAGA
*
31893224 AATATATAAAAATACA-TAAAGAA
1 AAT-TTTAAAAA-ACATTAAAG-A
31893247 AATTTTAAA
1 AATTTTAAA
31893256 TTTTATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.12
21 2 0.08
22 14 0.54
23 7 0.27
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (21 bp):
AATTTTAAAAAACATTAAAGA
Found at i:31893287 original size:19 final size:20
Alignment explanation
Indices: 31893246--31893287 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
31893236 TACATAAAGA
*
31893246 AAAT-TTTAAATTTTATATT
1 AAATATTTAAATTTCATATT
31893265 -AATATTTAAA-TTCATATT
1 AAATATTTAAATTTCATATT
31893283 AAATA
1 AAATA
31893288 AATATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTTAAATTTCATATT
Found at i:31899295 original size:20 final size:21
Alignment explanation
Indices: 31899259--31899298 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
31899249 TTTGTCCGGG
*
31899259 CTCAAAATTAAATAAATAAAA
1 CTCAAAATTAAAAAAATAAAA
31899280 CTCAAAA-TAAAAAAATAAA
1 CTCAAAATTAAAAAAATAAA
31899299 TAGTCCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (21 bp):
CTCAAAATTAAAAAAATAAAA
Found at i:31907261 original size:83 final size:83
Alignment explanation
Indices: 31907112--31908126 Score: 1888
Period size: 83 Copynumber: 12.2 Consensus size: 83
31907102 CGATTTGTGG
* * * * ** *
31907112 GGATGCCAAATCCGT-TTAAGTCTGTTTTGAGAACATTCGAGAGTCATATCTGCTACGTCCTCGA
1 GGATGCCAAAT-CATCTTGAGTCTG-TTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGA
*
31907176 TTTGCTCCTTGTAAGCACAA
64 TTTGTTCCTTGTAAGCACAA
*
31907196 AGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31907261 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
31907279 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31907344 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
31907362 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31907427 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
31907445 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31907510 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
31907528 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31907593 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
31907611 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31907676 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
31907694 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31907759 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
31907777 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31907842 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
31907860 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31907925 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
31907943 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
31908008 TGTTCCTTGTAAGCACAA
66 TGTTCCTTGTAAGCACAA
*
31908026 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTCGATT
1 GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
*
31908091 TGTTCCTTGTAAACACAA
66 TGTTCCTTGTAAGCACAA
* *
31908109 GAATACCAAATCATCTTG
1 GGATGCCAAATCATCTTG
31908127 GATCCGCTTC
Statistics
Matches: 916, Mismatches: 14, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
83 898 0.98
84 18 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (83 bp):
GGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATATCCTAGATT
TGTTCCTTGTAAGCACAA
Found at i:31908382 original size:119 final size:119
Alignment explanation
Indices: 31908050--31908401 Score: 535
Period size: 119 Copynumber: 3.0 Consensus size: 119
31908040 CTTGAGTCTG
* * * * *
31908050 TTTGAGAACATTTGAGAGTCATATCTGCAATATCCTCGATTTGTTCCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
* *
31908115 CAAATCATCTTGGATCCGCTTCAGTATAAACATCTGAAGGTTAGACCTGATATC
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGATATC
*
31908169 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTATTCCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
* *
31908234 CAAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTTAGATCTGTTATC
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGATATC
* * *
31908288 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGACTTGTTTCTTGTAAACACAAAAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
** **
31908353 CAAATCATCTTGGATCTGCTTCAACATAAATGTCTGAA-GTCTAGATCTG
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGT-TAGATCTG
31908402 CTGTCTTCAA
Statistics
Matches: 213, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
118 2 0.01
119 211 0.99
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (119 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGATATC
Found at i:31919852 original size:3 final size:3
Alignment explanation
Indices: 31919846--31919905 Score: 50
Period size: 3 Copynumber: 19.0 Consensus size: 3
31919836 ATTTAAGAAA
* * *
31919846 AAT AAT ATAT AAT AAGT AAT AAT AAT ATAT AATT AAA AAT AAT ACT TAT
1 AAT AAT A-AT AAT AA-T AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT
31919895 AAT AA- AAT AAT
1 AAT AAT AAT AAT
31919906 TTTATAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 2 0.04
3 32 0.70
4 12 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:31919877 original size:17 final size:16
Alignment explanation
Indices: 31919712--31919921 Score: 62
Period size: 17 Copynumber: 12.5 Consensus size: 16
31919702 TAATAAAATG
31919712 TAAT-ATAATCATATAA
1 TAATAATAAT-ATATAA
* *
31919728 GAAAAATAATAGATATAA
1 TAATAATAAT--ATATAA
*
31919746 T-ATAAAGTAACATATAA
1 TAAT-AA-TAATATATAA
*
31919763 -AACAAT-ATATAT-A
1 TAATAATAATATATAA
31919776 TAATTAATAA-ATATAA
1 TAA-TAATAATATATAA
31919792 TATATGAA-AATATAATAA
1 TA-AT-AATAATAT-ATAA
* * *
31919810 TATATATAAAGAGATGTAA
1 TA-ATA-ATA-ATATATAA
* *
31919829 -AATAATAATTTAAGAA
1 TAATAATAATAT-ATAA
*
31919845 AAATAAT-ATATAATAA
1 TAATAATAATAT-ATAA
31919861 GTAATAATAATATATAA
1 -TAATAATAATATATAA
*
31919878 TTAAAAATAATACTTATAA
1 -TAATAATAATA--TATAA
*
31919897 TAA-AATAATTTTATAA
1 TAATAATAA-TATATAA
31919913 TATATAATA
1 TA-ATAATA
31919922 TAAAAGTAAA
Statistics
Matches: 147, Mismatches: 22, Indels: 48
0.68 0.10 0.22
Matches are distributed among these distances:
13 1 0.01
14 7 0.05
15 10 0.07
16 29 0.20
17 54 0.37
18 31 0.21
19 12 0.08
20 3 0.02
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (16 bp):
TAATAATAATATATAA
Found at i:31919887 original size:20 final size:20
Alignment explanation
Indices: 31919761--31919926 Score: 82
Period size: 20 Copynumber: 8.2 Consensus size: 20
31919751 AGTAACATAT
*
31919761 AAAACAATATATATATAATTA
1 AAAATAATA-ATATATAATTA
*
31919782 ATAAAT-ATAATATATGA--A
1 A-AAATAATAATATATAATTA
*
31919800 AATATAATAATATAT-A-TA
1 AAAATAATAATATATAATTA
31919818 AAGAGATGTAA-AATA-ATAATTTA
1 AA-A-A--TAATAATATATAA-TTA
31919841 AGAAA-AATAATATATAA-TA
1 A-AAATAATAATATATAATTA
*
31919860 AGTAATAATAATATATAATTA
1 A-AAATAATAATATATAATTA
* *
31919881 AAAATAATACT-TATAATAA
1 AAAATAATAATATATAATTA
*
31919900 AATAATTTTATAATATATAATATA
1 AA-AA--TAATAATATATAAT-TA
31919924 AAA
1 AAA
31919927 GTAAAATTAA
Statistics
Matches: 114, Mismatches: 11, Indels: 38
0.70 0.07 0.23
Matches are distributed among these distances:
17 4 0.04
18 14 0.12
19 17 0.15
20 36 0.32
21 16 0.14
22 12 0.11
23 11 0.10
24 4 0.04
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAATAATAATATATAATTA
Found at i:31919905 original size:54 final size:53
Alignment explanation
Indices: 31919826--31919965 Score: 133
Period size: 54 Copynumber: 2.6 Consensus size: 53
31919816 TAAAGAGATG
* * * *
31919826 TAAAATAATAATT-TAAGAAAAATAATATATAATA-AGTAATAATAATA-TATAAT
1 TAAAATAATACTTATAA-TAAAATAATATATAATATA-TAAT-ATAAAAGTAAAAT
*
31919879 TAAAAATAATACTTATAATAAAATAATTTTATAATATATAATATAAAAGTAAAAT
1 T-AAAATAATACTTATAATAAAATAA-TATATAATATATAATATAAAAGTAAAAT
* **
31919934 TAAAATAAAACAAATAATAAAATATATATATA
1 TAAAATAATACTTATAATAAAATA-ATATATA
31919966 GAATAATATA
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
53 1 0.01
54 48 0.67
55 22 0.31
56 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (53 bp):
TAAAATAATACTTATAATAAAATAATATATAATATATAATATAAAAGTAAAAT
Found at i:31921962 original size:54 final size:54
Alignment explanation
Indices: 31921880--31922035 Score: 225
Period size: 54 Copynumber: 3.0 Consensus size: 54
31921870 TATATTGTGG
**
31921880 GGACAATAAATAAAAAGAAAAGGAAAAGGACAAATTTTTTTTAGTTACAACGCT
1 GGACAATAAATTGAAAGAAAAGGAAAAGGACAAATTTTTTTTAGTTACAACGCT
31921934 GGACAATAAATTGAAAGAAAAGGAAAAGGACAAATTTTTTTTAGTTACAACGCT
1 GGACAATAAATTGAAAGAAAAGGAAAAGGACAAATTTTTTTTAGTTACAACGCT
* * *
31921988 --A-TA-AAATTGAAAGAAAAGGAAAAGGAC-GA-GTTTTTTAGTTACAACGCT
1 GGACAATAAATTGAAAGAAAAGGAAAAGGACAAATTTTTTTTAGTTACAACGCT
31922036 ATAAATATAG
Statistics
Matches: 97, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
48 18 0.19
49 1 0.01
50 24 0.25
51 1 0.01
52 1 0.01
54 52 0.54
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (54 bp):
GGACAATAAATTGAAAGAAAAGGAAAAGGACAAATTTTTTTTAGTTACAACGCT
Found at i:31925192 original size:43 final size:43
Alignment explanation
Indices: 31925128--31925232 Score: 174
Period size: 43 Copynumber: 2.4 Consensus size: 43
31925118 TTCAACGAAC
* *
31925128 TCGCACACTTAGTGCCGATTAATTAGCTGAAGCTATAATTGTA
1 TCGCACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTA
* *
31925171 TCGCACACTTAGTGCCAATTAATTAGCCGAGGCTGTAATTGTA
1 TCGCACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTA
31925214 TCGCACACTTAGTGCCAAT
1 TCGCACACTTAGTGCCAAT
31925233 ACATTAAACC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
TCGCACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTA
Found at i:31926878 original size:12 final size:11
Alignment explanation
Indices: 31926842--31926972 Score: 94
Period size: 12 Copynumber: 12.0 Consensus size: 11
31926832 AATACGATTT
31926842 TATAAAA-ATA
1 TATAAAATATA
*
31926852 TATAAAGAAATA
1 TATAAA-ATATA
31926864 TATAAAATATAA
1 TATAAAATAT-A
*
31926876 TATATAATATAA
1 TATAAAATAT-A
**
31926888 TATAATTTATA
1 TATAAAATATA
*
31926899 GATAAAATATA
1 TATAAAATATA
31926910 TAATAAAATATA
1 T-ATAAAATATA
* *
31926922 TA-ACTAATATT
1 TATA-AAATATA
31926933 TATAAAA-ATA
1 TATAAAATATA
*
31926943 TATAAAGTAT-
1 TATAAAATATA
*
31926953 T-TAAAATAAA
1 TATAAAATATA
31926963 T-TAAAATATA
1 TATAAAATATA
31926973 AAAAGGATTA
Statistics
Matches: 96, Mismatches: 17, Indels: 16
0.74 0.13 0.12
Matches are distributed among these distances:
9 6 0.06
10 25 0.26
11 25 0.26
12 40 0.42
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (11 bp):
TATAAAATATA
Found at i:31926930 original size:23 final size:23
Alignment explanation
Indices: 31926904--31926947 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
31926894 TTATAGATAA
31926904 AATATATAAT-AAAATATATAACT
1 AATAT-TAATAAAAATATATAACT
*
31926927 AATATTTATAAAAATATATAA
1 AATATTAATAAAAATATATAA
31926948 AGTATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AATATTAATAAAAATATATAACT
Found at i:31926953 original size:21 final size:22
Alignment explanation
Indices: 31926914--31926955 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
31926904 AATATATAAT
31926914 AAAATATATAACTAATATTTATA
1 AAAATATATAAC-AATATTTATA
*
31926937 AAAATATATAA-AGTATTTA
1 AAAATATATAACAATATTTA
31926956 AAATAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATATATAACAATATTTATA
Found at i:31931151 original size:44 final size:43
Alignment explanation
Indices: 31931101--31931183 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
31931091 CATGTTGATA
*
31931101 TCTTCGATCTGCTCTCCGCCGAACACAGAGACGCCAAATCTGCT
1 TCTTCGATCTGCTCTCCGAC-AACACAGAGACGCCAAATCTGCT
* * * * *
31931145 TCTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATC
1 TCTTCGATCTGCTCTCCGACAACACAGAGACGCCAAATC
31931184 ATCTTAGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 17 0.52
44 16 0.48
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (43 bp):
TCTTCGATCTGCTCTCCGACAACACAGAGACGCCAAATCTGCT
Found at i:31931507 original size:206 final size:206
Alignment explanation
Indices: 31931146--31931693 Score: 839
Period size: 206 Copynumber: 2.7 Consensus size: 206
31931136 AAATCTGCTT
*
31931146 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
** * *
31931211 GCAAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * ** * *
31931276 GGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTACAATGTGTCTGCCCTCCGTCGAATATA
131 GGATCTACTTCAGTATAAACATCTGAAGGCCAGATCTACAATGTATCCGCCCTCCGTCGAATATA
**
31931341 G-AGATGCCAAA
196 GTA-ACACCAAA
*
31931352 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
* * *
31931417 GTGAAAGCTAAATCAGCTATGAT-TTCGATTTGCTCCTTGTAAACACAAGGATGCCAAATCATCT
66 GTGAAAGCCAAATCAGCTATG-TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCT
* * *
31931481 TGGATCTACTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCCGCTCTCCGTCGAATAT
130 TGGATCTACTTCAGTATAAACATCTGAAGGCCAGATCTACAATGTATCCGCCCTCCGTCGAATAT
*
31931546 GGTAACACCAAA
195 AGTAACACCAAA
* *
31931558 CTTCGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
*
31931623 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
31931688 GGATCT
131 GGATCT
31931694 TGCTTCAGCG
Statistics
Matches: 310, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
205 1 0.00
206 307 0.99
207 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTACTTCAGTATAAACATCTGAAGGCCAGATCTACAATGTATCCGCCCTCCGTCGAATATA
GTAACACCAAA
Done.