Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008709.1 Hibiscus syriacus cultivar Beakdansim tig00111758_pilon, whole genome shotgun sequence
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: 3030657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 15
Found at i:1143920 original size:21 final size:21
Alignment explanation
Indices: 1143899--1143937 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1143889 AAACTTTTAT
1143899 TTAAAATTAAAAAA-ATAATA
1 TTAAAATTAAAAAACATAATA
* *
1143919 TTATATTTAAAAAACATAA
1 TTAAAATTAAAAAACATAA
1143938 AAATTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAAATTAAAAAACATAATA
Found at i:1156012 original size:2 final size:2
Alignment explanation
Indices: 1156007--1156041 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1155997 TCTCTCTCTC
* *
1156007 TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1156042 TTGAGGTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1156286 original size:105 final size:105
Alignment explanation
Indices: 1156099--1156287 Score: 297
Period size: 105 Copynumber: 1.8 Consensus size: 105
1156089 TTTGATCAAG
* * * *
1156099 TATGAACACATTGAAAATTCAATAATCAACATATGGACTAATTTAATTAAGCTTTGGGTGGTTTT
1 TATGAACACATTGAAAATTAAATAATCAACATATGAACTAATTTAATTAAGCTTTGGATCGTTTT
* *
1156164 TGCATGTGAACACATTGAATATATATATATTTTTTAAACA
66 TGCATATGAACAAATTGAATATATATATATTTTTTAAACA
* *
1156204 TATGAACACATTGAAACTTAAATAATCAACATATGAACTAATTTAATTAAGTTTTGGATCGTTTT
1 TATGAACACATTGAAAATTAAATAATCAACATATGAACTAATTTAATTAAGCTTTGGATCGTTTT
*
1156269 TGCGTATGAACAAATTGAA
66 TGCATATGAACAAATTGAA
1156288 AAAATAAATA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 75 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (105 bp):
TATGAACACATTGAAAATTAAATAATCAACATATGAACTAATTTAATTAAGCTTTGGATCGTTTT
TGCATATGAACAAATTGAATATATATATATTTTTTAAACA
Found at i:1164171 original size:31 final size:34
Alignment explanation
Indices: 1164133--1164199 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
1164123 CGATGTCGAG
1164133 GGCTTTGATG-T-CCTTG-TGATGGACATCAAAC
1 GGCTTTGATGATACCTTGATGATGGACATCAAAC
*
1164164 GGCTTTGATGATATCTTGATGATGGACATCAAAC
1 GGCTTTGATGATACCTTGATGATGGACATCAAAC
1164198 GG
1 GG
1164200 GTTATAACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 10 0.31
32 1 0.03
33 4 0.12
34 17 0.53
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (34 bp):
GGCTTTGATGATACCTTGATGATGGACATCAAAC
Found at i:1164443 original size:3 final size:3
Alignment explanation
Indices: 1164435--1164479 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1164425 TTGTCCGGAT
1164435 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1164480 CTTTATTAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1169753 original size:29 final size:29
Alignment explanation
Indices: 1169717--1169774 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1169707 CAGAATTTGG
* *
1169717 GTCCCACTCCAAGTTGGTACCTAAAGATT
1 GTCCCACTCCAAGTTGGCACCAAAAGATT
1169746 GTCCCACTCCAAGTTGGCACCAAAAGATT
1 GTCCCACTCCAAGTTGGCACCAAAAGATT
1169775 TGGATACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (29 bp):
GTCCCACTCCAAGTTGGCACCAAAAGATT
Found at i:1170163 original size:2 final size:2
Alignment explanation
Indices: 1170156--1170187 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1170146 TACTCTTATA
1170156 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1170188 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1170192 original size:2 final size:2
Alignment explanation
Indices: 1170187--1170219 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1170177 TCTCTCTCTC
1170187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1170220 GAGAATGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1173952 original size:13 final size:13
Alignment explanation
Indices: 1173934--1173960 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1173924 TATAATATAT
1173934 AGTTTTTGAAAAC
1 AGTTTTTGAAAAC
1173947 AGTTTTTGAAAAC
1 AGTTTTTGAAAAC
1173960 A
1 A
1173961 TATAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
AGTTTTTGAAAAC
Found at i:1174019 original size:74 final size:71
Alignment explanation
Indices: 1173920--1174290 Score: 298
Period size: 74 Copynumber: 5.1 Consensus size: 71
1173910 ATTTTTTAAA
* * *
1173920 AAAATATA-ATATATAGTTTTTGAAAACAGTTTTTGAAAACATATAATATAAACTCTTTAAAAAA
1 AAAATATATATATATAG-TTTTGAAAACAATTTTTGAAAACATATAATATATAGT-TTTAAAAAA
1173984 TCGGTTTATG
64 TC-GTTT-TG
* * *
1173994 AAAATATATATATATAGTTTTGAAAACAATTTTTGAAAAAATATATTATATAGTTTT-GAAAA-C
1 AAAATATATATATATAGTTTTGAAAACAATTTTTGAAAACATATAATATATAGTTTTAAAAAATC
1174057 GATTTTTG
66 G--TTTTG
* * *
1174065 AAAATATATATATTATATAGTTTTGAAAACGATTTTTGAAAATATATATTATATAGTTTTGAAAA
1 -AAA-ATATATA-TATATAGTTTTGAAAACAATTTTTGAAAACATATAATATATAGTTTT-AAAA
1174130 CAAT--TTTTG
62 -AATCGTTTTG
* * * *
1174139 AAAATATAT-TATATAGTTTTGAAAAATAATTTGTGAAAACATATATATATATA-TATATATATA
1 AAAATATATATATATAGTTTTG-AAAACAATTTTTGAAAACATATA-ATATATAGT-TTTA-AAA
* * *
1174202 TAT--ATAT-
62 AATCGTTTTG
* * * * * *
1174209 ATATATATATATATTATAGTTTCGAAAATAA-TTTTGAAAATATATAATATATAGTTTT-TAAGA
1 A-AAATATATATA-TATAGTTTTGAAAACAATTTTTGAAAACATATAATATATAGTTTTAAAAAA
1174272 TCGGTTTTG
64 TC-GTTTTG
1174281 AAAATATATA
1 AAAATATATA
1174291 ATTTTTTATA
Statistics
Matches: 245, Mismatches: 30, Indels: 47
0.76 0.09 0.15
Matches are distributed among these distances:
68 3 0.01
70 23 0.09
71 59 0.24
72 36 0.15
73 22 0.09
74 90 0.37
75 8 0.03
76 2 0.01
77 2 0.01
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (71 bp):
AAAATATATATATATAGTTTTGAAAACAATTTTTGAAAACATATAATATATAGTTTTAAAAAATC
GTTTTG
Found at i:1174048 original size:36 final size:36
Alignment explanation
Indices: 1173894--1174191 Score: 318
Period size: 36 Copynumber: 8.1 Consensus size: 36
1173884 ATTAATATAG
* * * *
1173894 TATAGTTTTTGAAAATATTTTTTAAAAAAATATAATA
1 TATAG-TTTTGAAAACAATTTTTGAAAAAATATATTA
* * *
1173931 TATAGTTTTTGAAAACAGTTTTTGAAAACATATAATA
1 TATAG-TTTTGAAAACAATTTTTGAAAAAATATATTA
* * *
1173968 TAAACTCTTT-AAAA-AATCGGTTTATGAAAATATATA-TA
1 TATAGT-TTTGAAAACAAT---TTT-TGAAAAAATATATTA
1174006 TATAGTTTTGAAAACAATTTTTGAAAAAATATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAAAATATATTA
*
1174042 TATAGTTTTGAAAACGATTTTTGAAAATATATATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAA-A-ATATATTA
* *
1174080 TATAGTTTTGAAAACGATTTTTGAAAATATATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAAAATATATTA
1174116 TATAGTTTTGAAAACAATTTTTG--AAAATATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAAAATATATTA
* * *
1174150 TATAGTTTTGAAAAATAATTTGTGAAAACATATATATA
1 TATAGTTTTG-AAAACAATTTTTGAAAAAATATAT-TA
1174188 TATA
1 TATA
1174192 TATATATATA
Statistics
Matches: 229, Mismatches: 18, Indels: 27
0.84 0.07 0.10
Matches are distributed among these distances:
34 20 0.09
35 24 0.10
36 66 0.29
37 51 0.22
38 54 0.24
39 14 0.06
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (36 bp):
TATAGTTTTGAAAACAATTTTTGAAAAAATATATTA
Found at i:1174186 original size:2 final size:2
Alignment explanation
Indices: 1174179--1174226 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1174169 TTGTGAAAAC
1174179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1174221 AT -T AT A
1 AT AT AT A
1174227 GTTTCGAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1174287 original size:36 final size:35
Alignment explanation
Indices: 1174211--1174292 Score: 74
Period size: 36 Copynumber: 2.3 Consensus size: 35
1174201 ATATATATAT
* ***
1174211 ATATATATATATTATAGTTTCGAAAATAATTTTGAAA
1 ATATATA-ATA-TATAGTTTTGAAAACGTTTTTGAAA
* * *
1174248 ATATATAATATATAGTTTTTAAGATCGGTTTTGAAA
1 ATATATAATATATAGTTTTGAA-AACGTTTTTGAAA
1174284 ATATATAAT
1 ATATATAAT
1174293 TTTTTATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 10 0.26
36 21 0.55
37 7 0.18
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (35 bp):
ATATATAATATATAGTTTTGAAAACGTTTTTGAAA
Found at i:1174334 original size:16 final size:16
Alignment explanation
Indices: 1174294--1174342 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1174284 ATATATAATT
* *
1174294 TTTTATATAGTTAGTTA
1 TTTTAT-TATTTATTTA
1174311 TTTATATTATTTATTTA
1 TTT-TATTATTTATTTA
*
1174328 TTTTATTGTTTATTT
1 TTTTATTATTTATTT
1174343 TCGTTTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.39
17 14 0.50
18 3 0.11
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTATTATTTATTTA
Found at i:1175551 original size:12 final size:12
Alignment explanation
Indices: 1175534--1175569 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
1175524 TATTTCTCAA
1175534 TTTTATTTTATT
1 TTTTATTTTATT
1175546 TTTTATTTTATT
1 TTTTATTTTATT
1175558 TTTTATATTTAT
1 TTTTAT-TTTAT
1175570 ATATTTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:1179802 original size:109 final size:108
Alignment explanation
Indices: 1179676--1179881 Score: 324
Period size: 109 Copynumber: 1.9 Consensus size: 108
1179666 CCAGATTATA
* ** **
1179676 ATATTATATGATTACAATAAAGCTTGAGTAGCCCCTCTAGAGCAATTGGTTAATTGCCCTTGCTT
1 ATATTATATGATTACAATAAAGCTTGAGCAGCCCCTCTAGAGCAATTGGTTAATCACCCCGGCTT
1179741 TATGGATAAGATTCAGCTAGCCTGATAAAGGTGATTATAATAT
66 TATGGATAAGATTCAGCTAGCCTGATAAAGGTGATTATAATAT
* *
1179784 ATATATATAT-ATATACAATAAAGCTTGAGCCGTCCCTCTAGAGCAATTGGTTAATCACCCCGGC
1 ATAT-TATATGAT-TACAATAAAGCTTGAGCAGCCCCTCTAGAGCAATTGGTTAATCACCCCGGC
1179848 TTTATGGATAAGATTCAGCTAGCCTGATAAAGGT
64 TTTATGGATAAGATTCAGCTAGCCTGATAAAGGT
1179882 AAATTACAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 6 0.07
109 83 0.93
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (108 bp):
ATATTATATGATTACAATAAAGCTTGAGCAGCCCCTCTAGAGCAATTGGTTAATCACCCCGGCTT
TATGGATAAGATTCAGCTAGCCTGATAAAGGTGATTATAATAT
Found at i:1182143 original size:34 final size:34
Alignment explanation
Indices: 1182044--1182268 Score: 192
Period size: 35 Copynumber: 6.4 Consensus size: 34
1182034 ATTTTTGAAA
*
1182044 AAAATATAATATATAGTTTTTAGAAAA-CGGTTTTTG
1 AAAATAT-ATATATAG-TTTT-GAAAATCAGTTTTTG
* *
1182080 AAAACATATAATATATACTTTTAAAAAAATCAGTTTTTG
1 -AAA-ATAT-ATATATAGTTTT--GAAAATCAGTTTTTG
* * *
1182119 AAAATATATATATAGTTTTGAAAATAATTTTTTTA
1 AAAATATATATATAGTTTTGAAAATCA-GTTTTTG
*
1182154 AAAATATATTATATAGTTTTGAAAA-CGATTTTTTG
1 AAAATATA-TATATAGTTTTGAAAATC-AGTTTTTG
*
1182189 --AATATATATATAGTTTTGAAAATGA-TTTTTG
1 AAAATATATATATAGTTTTGAAAATCAGTTTTTG
* *
1182220 AAAATATATTATATAGTTTTGAAAAAT-AATTTGTG
1 AAAATATA-TATATAGTTTTG-AAAATCAGTTTTTG
*
1182255 AAAAAATATATATA
1 AAAATATATATATA
1182269 TATATTATAG
Statistics
Matches: 163, Mismatches: 13, Indels: 27
0.80 0.06 0.13
Matches are distributed among these distances:
31 6 0.04
32 17 0.10
33 12 0.07
34 25 0.15
35 36 0.22
36 28 0.17
37 11 0.07
38 20 0.12
39 8 0.05
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (34 bp):
AAAATATATATATAGTTTTGAAAATCAGTTTTTG
Found at i:1182167 original size:36 final size:36
Alignment explanation
Indices: 1182024--1182272 Score: 176
Period size: 37 Copynumber: 7.0 Consensus size: 36
1182014 ATAGTCTAGT
** *
1182024 TTTTGAAAAT-ATTTTTGAAAAAAATATAATATATAG
1 TTTTGAAAATAATTTTT-TTAAAAATATATTATATAG
*** * * *
1182060 TTTTTAGAAAA-CGGTTTTTGAAAACATATAATATATAC
1 -TTTT-GAAAATAATTTTTTTAAAA-ATATATTATATAG
* * *
1182098 TTTT-AAAAAAATCAGTTTTTGAAAATATA-TATATAG
1 TTTTGAAAATAAT--TTTTTTAAAAATATATTATATAG
1182134 TTTTGAAAATAATTTTTTTAAAAATATATTATATAG
1 TTTTGAAAATAATTTTTTTAAAAATATATTATATAG
** *
1182170 TTTTGAAAACGA-TTTTTT--GAATATA-TATATAG
1 TTTTGAAAATAATTTTTTTAAAAATATATTATATAG
* *
1182202 TTTTGAAAATGA--TTTTTGAAAATATATTATATAG
1 TTTTGAAAATAATTTTTTTAAAAATATATTATATAG
* **
1182236 TTTTGAAAAATAATTTGTGAAAAAATATATATATATA
1 TTTTG-AAAATAATTTTTTTAAAAATATAT-TATATA
1182273 TTATAGTTTC
Statistics
Matches: 172, Mismatches: 25, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
31 5 0.03
32 18 0.10
33 12 0.07
34 12 0.07
35 29 0.17
36 27 0.16
37 35 0.20
38 34 0.20
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (36 bp):
TTTTGAAAATAATTTTTTTAAAAATATATTATATAG
Found at i:1182313 original size:35 final size:37
Alignment explanation
Indices: 1182262--1182343 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
1182252 GTGAAAAAAT
*
1182262 ATATATATATATTATAG-TTTCAAAAATAATTTTGAAA
1 ATATATA-ATATTATAGTTTTCAAAAACAATTTTGAAA
* * *
1182299 ATATATAATA-TATAGTTTTTAAAAGCAGTTTTGAAA
1 ATATATAATATTATAGTTTTCAAAAACAATTTTGAAA
*
1182335 ATGTATAAT
1 ATATATAAT
1182344 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.13
36 27 0.69
37 7 0.18
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (37 bp):
ATATATAATATTATAGTTTTCAAAAACAATTTTGAAA
Found at i:1182372 original size:4 final size:4
Alignment explanation
Indices: 1182345--1182417 Score: 60
Period size: 4 Copynumber: 17.8 Consensus size: 4
1182335 ATGTATAATT
* * * *
1182345 TTTA TTT- TTTA TATA GTTA GTTA TTTA TATTA TTTA TTTA TTTCA CTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTT-A TTTA
1182394 TTTA TTTTA TTTTA TTT- TTTA TTT
1 TTTA -TTTA -TTTA TTTA TTTA TTT
1182418 TCGTTTTTAG
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
3 6 0.10
4 36 0.62
5 16 0.28
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1182387 original size:17 final size:17
Alignment explanation
Indices: 1182345--1182417 Score: 64
Period size: 17 Copynumber: 4.4 Consensus size: 17
1182335 ATGTATAATT
1182345 TTTATTT-TTTATA-TA
1 TTTATTTATTTATATTA
* *
1182360 GTTAGTTATTTATATTA
1 TTTATTTATTTATATTA
*
1182377 TTTATTTATTTCA-CTTA
1 TTTATTTATTT-ATATTA
*
1182394 TTTATTTTATTT-TATTT
1 TTTA-TTTATTTATATTA
1182411 TTTATTT
1 TTTATTT
1182418 TCGTTTTTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
15 5 0.11
16 9 0.20
17 24 0.52
18 8 0.17
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTATTTATTTATATTA
Found at i:1182418 original size:17 final size:17
Alignment explanation
Indices: 1182365--1182418 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
1182355 ATATAGTTAG
1182365 TTATTTATATTATTTA-T
1 TTATTT-TATTATTTATT
*
1182382 TTATTTCACTTATTTATT
1 TTATTTTA-TTATTTATT
*
1182400 TTATTTTATTTTTTATT
1 TTATTTTATTATTTATT
1182417 TT
1 TT
1182419 CGTTTTTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 23 0.72
18 8 0.25
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTTTATTATTTATT
Found at i:1183567 original size:14 final size:14
Alignment explanation
Indices: 1183550--1183576 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1183540 TGTATGTTTA
1183550 TTAACATTTTTTCC
1 TTAACATTTTTTCC
1183564 TTAACATTTTTTC
1 TTAACATTTTTTC
1183577 TTTCAAAATT
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:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAACATTTTTTCC
Found at i:1183610 original size:17 final size:17
Alignment explanation
Indices: 1183584--1183626 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1183574 TTCTTTCAAA
*
1183584 ATTTAATTTAATTTCTTT
1 ATTT-ATTTTATTTCTTT
*
1183602 -TTTATTTTATTTTTTT
1 ATTTATTTTATTTCTTT
1183618 ATTTATTTT
1 ATTTATTTT
1183627 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTATTTTATTTCTTT
Found at i:1183634 original size:17 final size:17
Alignment explanation
Indices: 1183614--1183677 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
1183604 TATTTTATTT
*
1183614 TTTTATTTATTTTTTAA
1 TTTTATATATTTTTTAA
*
1183631 TTTTA-ATATTTTCTCAA
1 TTTTATATATTTT-TTAA
* *
1183648 TTTTATTTTATTTTTTAT
1 TTTTA-TATATTTTTTAA
1183666 TTTTATATATTT
1 TTTTATATATTT
1183678 ATATATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.16
17 19 0.50
18 7 0.18
19 6 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATATATTTTTTAA
Found at i:1183636 original size:42 final size:41
Alignment explanation
Indices: 1183605--1183686 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 41
1183595 TTTCTTTTTT
1183605 ATTTTATTTT-TTTATTTATTTTTTAATTTTAATATTTTCTCA
1 ATTTTATTTTATTT-TTTATTTTTTAA-TTTAATATTTTCTCA
1183647 ATTTTATTTTATTTTTTATTTTTATATATTTATATATTTT
1 ATTTTATTTTATTTTTTATTTTT-TA-ATTTA-ATATTTT
1183687 AAAATTTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
42 19 0.53
43 9 0.25
44 8 0.22
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (41 bp):
ATTTTATTTTATTTTTTATTTTTTAATTTAATATTTTCTCA
Found at i:1187784 original size:30 final size:30
Alignment explanation
Indices: 1187709--1187784 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
1187699 CCCTTAAGTT
* ** *
1187709 TCTACTTTTGCTATTCCAATCCTTTAAATG
1 TCTATTTTTGCTATTTTAGTCCTTTAAATG
* * *
1187739 TTTGTTTTTGTTATTTTAGTCCTTTAAATG
1 TCTATTTTTGCTATTTTAGTCCTTTAAATG
1187769 TCTATATTTT-CTATTT
1 TCTAT-TTTTGCTATTT
1187785 AGACCCTTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.58
Consensus pattern (30 bp):
TCTATTTTTGCTATTTTAGTCCTTTAAATG
Found at i:1187811 original size:29 final size:29
Alignment explanation
Indices: 1187775--1187836 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
1187765 AATGTCTATA
1187775 TTTTCTA-TTTAGACCC-TTAAGTTTAGGT
1 TTTTCTATTTTAG-CCCTTTAAGTTTAGGT
*
1187803 TTTTACTATTTTAGCCCTTTAAGTTTATGT
1 TTTT-CTATTTTAGCCCTTTAAGTTTAGGT
1187833 TTTT
1 TTTT
1187837 TCTAATTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 4 0.13
29 6 0.20
30 20 0.67
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.56
Consensus pattern (29 bp):
TTTTCTATTTTAGCCCTTTAAGTTTAGGT
Found at i:1189868 original size:17 final size:17
Alignment explanation
Indices: 1189846--1189881 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1189836 TTAGGCCTAG
1189846 TTACTACCTAGAACCCC
1 TTACTACCTAGAACCCC
1189863 TTACTACCTAGAACCCC
1 TTACTACCTAGAACCCC
1189880 TT
1 TT
1189882 GTTTATGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.39, G:0.06, T:0.28
Consensus pattern (17 bp):
TTACTACCTAGAACCCC
Found at i:1190662 original size:25 final size:25
Alignment explanation
Indices: 1190625--1190702 Score: 120
Period size: 25 Copynumber: 3.1 Consensus size: 25
1190615 GCAGGACCGA
1190625 CGGTTGCAGTGCCGATCCCTCCAGG
1 CGGTTGCAGTGCCGATCCCTCCAGG
* *
1190650 CGGTTGCAATGCCGTTCCCTCCAGG
1 CGGTTGCAGTGCCGATCCCTCCAGG
* *
1190675 CGGTTGCAGTGTCGATCCCTCCATG
1 CGGTTGCAGTGCCGATCCCTCCAGG
1190700 CGG
1 CGG
1190703 ATCTTCGAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.12, C:0.35, G:0.31, T:0.23
Consensus pattern (25 bp):
CGGTTGCAGTGCCGATCCCTCCAGG
Found at i:1192420 original size:18 final size:18
Alignment explanation
Indices: 1192375--1192420 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1192365 GGGATCAGGG
1192375 TCAGCGGGCTCTTCGGCT
1 TCAGCGGGCTCTTCGGCT
* * **
1192393 TTAGCTGGCTCTTCTTCT
1 TCAGCGGGCTCTTCGGCT
1192411 TCAGCGGGCT
1 TCAGCGGGCT
1192421 GAGGACTTTC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.07, C:0.30, G:0.28, T:0.35
Consensus pattern (18 bp):
TCAGCGGGCTCTTCGGCT
Found at i:1194347 original size:20 final size:20
Alignment explanation
Indices: 1194322--1194363 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1194312 ATTCTTGCGC
1194322 TCGAAAATCCTCAATTTCAT
1 TCGAAAATCCTCAATTTCAT
* *
1194342 TCGAAACTCCTCCATTTCAT
1 TCGAAAATCCTCAATTTCAT
1194362 TC
1 TC
1194364 AGATCGAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.05, T:0.36
Consensus pattern (20 bp):
TCGAAAATCCTCAATTTCAT
Found at i:1201613 original size:11 final size:11
Alignment explanation
Indices: 1201597--1201629 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1201587 TTTTTCTTTT
1201597 CTTGATATTTG
1 CTTGATATTTG
*
1201608 CTTGATATTGG
1 CTTGATATTTG
1201619 CTTGATATTTG
1 CTTGATATTTG
1201630 AATTCTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.52
Consensus pattern (11 bp):
CTTGATATTTG
Found at i:1205150 original size:16 final size:16
Alignment explanation
Indices: 1205129--1205202 Score: 130
Period size: 16 Copynumber: 4.6 Consensus size: 16
1205119 CAGGTCGAGA
1205129 AAACATACATCAATAC
1 AAACATACATCAATAC
1205145 AAACATACATCAATAC
1 AAACATACATCAATAC
1205161 AAACATACATCAATAC
1 AAACATACATCAATAC
*
1205177 AAACATACATCAACAC
1 AAACATACATCAATAC
*
1205193 ATACATACAT
1 AAACATACAT
1205203 GATACATGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 56 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (16 bp):
AAACATACATCAATAC
Found at i:1205588 original size:36 final size:36
Alignment explanation
Indices: 1205532--1205640 Score: 146
Period size: 38 Copynumber: 2.9 Consensus size: 36
1205522 TATCTTATTA
* * *
1205532 AAAAACAAAGTGTTGTCTCGCTAGAGACAGTTTTCTT
1 AAAAACAAA-TTTTGTCTCGCTTGAGACACTTTTCTT
1205569 AAAAACAAATTTTGTCTCGCTTGAGACAACTTTCTCTT
1 AAAAACAAATTTTGTCTCGCTTGAGAC-ACTTT-TCTT
* *
1205607 AAAAACAAATTATGTCTCGCTTGAGACATTTTTC
1 AAAAACAAATTTTGTCTCGCTTGAGACACTTTTC
1205641 CAGAAAGTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
36 18 0.28
37 17 0.26
38 30 0.46
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (36 bp):
AAAAACAAATTTTGTCTCGCTTGAGACACTTTTCTT
Found at i:1207604 original size:30 final size:30
Alignment explanation
Indices: 1207448--1207614 Score: 92
Period size: 30 Copynumber: 5.6 Consensus size: 30
1207438 GAAATTACTG
* * *
1207448 TTTAGTCCATTAACT-TTCTGTTTTAGTTAT
1 TTTAGTCCTTTAAATGTT-TGTTTTTGTTAT
* **
1207478 TTTAGTCCTTTAAATTTTTGTTTTTCCT-T
1 TTTAGTCCTTTAAATGTTTGTTTTTGTTAT
* *** ** * *
1207507 TTTAGCCCTTTTGGT-TTCTGTTAATATCAT
1 TTTAGTCCTTTAAATGTT-TGTTTTTGTTAT
* * *
1207537 TTTAGTCCCTT-AA-GTTTATACTTTTTTCTAT
1 TTTAGTCCTTTAAATGTTTGT--TTTTGT-TAT
*
1207568 TCTAGTCCTTTAAATGTTTGTTTTTGTTAT
1 TTTAGTCCTTTAAATGTTTGTTTTTGTTAT
1207598 TTTAGTCCTTTAAATGT
1 TTTAGTCCTTTAAATGT
1207615 CTATACTTGC
Statistics
Matches: 100, Mismatches: 28, Indels: 18
0.68 0.19 0.12
Matches are distributed among these distances:
28 4 0.04
29 19 0.19
30 52 0.52
31 18 0.18
32 2 0.02
33 5 0.05
ACGTcount: A:0.18, C:0.14, G:0.10, T:0.58
Consensus pattern (30 bp):
TTTAGTCCTTTAAATGTTTGTTTTTGTTAT
Found at i:1207629 original size:30 final size:30
Alignment explanation
Indices: 1207564--1207629 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1207554 ATACTTTTTT
* * * **
1207564 CTATTCTAGTCCTTTAAATGTTTGTTTTTG
1 CTATTTTAGTCCTTTAAATGTCTATACTTG
*
1207594 TTATTTTAGTCCTTTAAATGTCTATACTTG
1 CTATTTTAGTCCTTTAAATGTCTATACTTG
1207624 CTATTT
1 CTATTT
1207630 AGACCCTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.56
Consensus pattern (30 bp):
CTATTTTAGTCCTTTAAATGTCTATACTTG
Found at i:1210308 original size:12 final size:12
Alignment explanation
Indices: 1210279--1210323 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
1210269 CTCGAGACTC
1210279 GAGCTCGA--TT
1 GAGCTCGATTTT
1210289 GAAGCTCGATTTT
1 G-AGCTCGATTTT
1210302 GAGCTCGATTTT
1 GAGCTCGATTTT
1210314 GAGCTCGATT
1 GAGCTCGATT
1210324 CAAGCTCGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 1 0.03
11 7 0.22
12 21 0.66
13 3 0.09
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (12 bp):
GAGCTCGATTTT
Found at i:1210339 original size:17 final size:17
Alignment explanation
Indices: 1210317--1210353 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1210307 CGATTTTGAG
*
1210317 CTCGATTCAAGCTCGAA
1 CTCGATTAAAGCTCGAA
1210334 CTCGATTAAAGCTCGAA
1 CTCGATTAAAGCTCGAA
1210351 CTC
1 CTC
1210354 AAACTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTAAAGCTCGAA
Found at i:1210349 original size:11 final size:12
Alignment explanation
Indices: 1210280--1210332 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
1210270 TCGAGACTCG
*
1210280 AGCTCGA-TTGA
1 AGCTCGATTTTA
*
1210291 AGCTCGATTTTG
1 AGCTCGATTTTA
*
1210303 AGCTCGATTTTG
1 AGCTCGATTTTA
*
1210315 AGCTCGA-TTCA
1 AGCTCGATTTTA
1210326 AGCTCGA
1 AGCTCGA
1210333 ACTCGATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 16 0.43
12 21 0.57
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (12 bp):
AGCTCGATTTTA
Found at i:1210657 original size:21 final size:21
Alignment explanation
Indices: 1210632--1210725 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
1210622 TGGCATAACT
1210632 TAAACCCTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
* *
1210653 TAAACCCTAACACATAAATCT
1 TAAACCCTAACACATAAACCC
* * *
1210674 TAAACTCTAA-ACTCTAAACCT
1 TAAACCCTAACAC-ATAAACCC
* * *
1210695 TAAATCCTATCACATAAACTC
1 TAAACCCTAACACATAAACCC
*
1210716 TAAATCCTAA
1 TAAACCCTAA
1210726 AACCCTAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.03
21 55 0.93
22 2 0.03
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACCCTAACACATAAACCC
Found at i:1210676 original size:42 final size:41
Alignment explanation
Indices: 1210628--1210726 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 41
1210618 TTCATGGCAT
1210628 AACTTAAACCCTAACAC-ATAAACCCTAAACCCTAACACATA
1 AACTTAAACCCTAA-ACTATAAACCCTAAACCCTAACACATA
* * * * *
1210669 AATCTTAAACTCTAAACTCTAAACCTTAAATCCTATCACATA
1 AA-CTTAAACCCTAAACTATAAACCCTAAACCCTAACACATA
*
1210711 AACTCTAAATCCTAAA
1 AACT-TAAACCCTAAA
1210727 ACCCTAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
41 6 0.12
42 42 0.88
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (41 bp):
AACTTAAACCCTAAACTATAAACCCTAAACCCTAACACATA
Found at i:1211027 original size:15 final size:14
Alignment explanation
Indices: 1211001--1211030 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1210991 TTTATTCATC
1211001 AATAATGTATTTTT
1 AATAATGTATTTTT
*
1211015 AATAATGTAATTTT
1 AATAATGTATTTTT
1211029 AA
1 AA
1211031 AAAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:1219691 original size:8 final size:8
Alignment explanation
Indices: 1219662--1219699 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1219652 GTCATGTGAC
1219662 AAATAAATA
1 AAAT-AATA
1219671 AAA-AATA
1 AAATAATA
*
1219678 AAATAATG
1 AAATAATA
1219686 AAATAATA
1 AAATAATA
1219694 AAATAA
1 AAATAA
1219700 CAAGCAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 7 0.27
8 16 0.62
9 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (8 bp):
AAATAATA
Found at i:1221576 original size:45 final size:45
Alignment explanation
Indices: 1221512--1221783 Score: 391
Period size: 45 Copynumber: 6.0 Consensus size: 45
1221502 AGTCAAGTTG
* *
1221512 AGAATAACATCACTAAAAGATTGACTCCTCTTCACAAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
*
1221557 AGAATGACATCACTGAAAGATTGACTCCTCTTCACGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* ***
1221602 AGAATGACATCACTAAAAGATTGACTTCTCTTTGTGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * *
1221647 AGAATGACATCACTAAAAGATTGACTTCTCTTCGCGATAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* *
1221692 AGAAAGACATCACTAAAAGATTGACTCCTCTTCACGAGAACGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
* * * * *
1221737 AGAAAGACATCACTAACATATTGAATCCTCTTCGCGAGAAAGTCA
1 AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
1221782 AG
1 AG
1221784 TTGAGGTTTC
Statistics
Matches: 206, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 206 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (45 bp):
AGAATGACATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCA
Found at i:1221868 original size:39 final size:37
Alignment explanation
Indices: 1221790--1221998 Score: 203
Period size: 37 Copynumber: 5.7 Consensus size: 37
1221780 CAAGTTGAGG
* *
1221790 TTTCTAGGGAAACAATCCTGAGAA-TGACTAAAACGAA
1 TTTCTAGAGAAACAATCCTAAGAAGTGACTAAAAC-AA
*
1221827 TTTCTAGAGAAACAATCCTAAGAATGTGACTCAAACGAA
1 TTTCTAGAGAAACAATCCTAAGAA-GTGACTAAAAC-AA
**
1221866 TTTCTAGAGAAACAATCCTAAGAAG-GACTCTAACAAA
1 TTTCTAGAGAAACAATCCTAAGAAGTGACTAAAAC-AA
* ** * * *
1221903 TTTCTAAAGAAATGATGCTAAGGA-TGACTAAAA-AC
1 TTTCTAGAGAAACAATCCTAAGAAGTGACTAAAACAA
** * *
1221938 TTTCTAGAGAAATGATCCTAAAAAG-GAATAAAACAA
1 TTTCTAGAGAAACAATCCTAAGAAGTGACTAAAACAA
*
1221974 TTTCTAGAGAAATAATCCTAAGAAG
1 TTTCTAGAGAAACAATCCTAAGAAG
1221999 GATTAGAGTG
Statistics
Matches: 146, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
35 28 0.19
36 24 0.16
37 57 0.39
38 1 0.01
39 36 0.25
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (37 bp):
TTTCTAGAGAAACAATCCTAAGAAGTGACTAAAACAA
Found at i:1221882 original size:76 final size:71
Alignment explanation
Indices: 1221790--1221997 Score: 220
Period size: 76 Copynumber: 2.8 Consensus size: 71
1221780 CAAGTTGAGG
* * * *
1221790 TTTCTAGGGAAACAATCCTGAGAATGACTAAAACGAATTTCTAGAGAAACAATCCTAAGAATGTG
1 TTTCTAGAGAAACAATCCTAAGAAGGACTAAAAC-AATTTCTAGAGAAATAATCCTAAGAA--TG
1221855 ACTCAAACGAA-
63 ACT-AAA--AAC
** * * * *
1221866 TTTCTAGAGAAACAATCCTAAGAAGGACTCTAACAAATTTCTAAAGAAATGATGCTAAGGATGAC
1 TTTCTAGAGAAACAATCCTAAGAAGGACTAAAAC-AATTTCTAGAGAAATAATCCTAAGAATGAC
1221931 TAAAAAC
65 TAAAAAC
** * *
1221938 TTTCTAGAGAAATGATCCTAAAAAGGAATAAAACAATTTCTAGAGAAATAATCCTAAGAA
1 TTTCTAGAGAAACAATCCTAAGAAGGACTAAAACAATTTCTAGAGAAATAATCCTAAGAA
1221998 GGATTAGAGT
Statistics
Matches: 110, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
71 24 0.22
72 28 0.25
73 3 0.03
74 5 0.05
76 50 0.45
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (71 bp):
TTTCTAGAGAAACAATCCTAAGAAGGACTAAAACAATTTCTAGAGAAATAATCCTAAGAATGACT
AAAAAC
Found at i:1221949 original size:35 final size:34
Alignment explanation
Indices: 1221825--1222000 Score: 154
Period size: 39 Copynumber: 4.9 Consensus size: 34
1221815 GACTAAAACG
**
1221825 AATTTCTAGAGAAACAATCCTAAGAATGTGACTCAAA
1 AATTTCTAGAGAAATGATCCTAAGAA-G-GACT-AAA
**
1221862 CGAATTTCTAGAGAAACAATCCTAAGAAGGACTCTAACA
1 --AATTTCTAGAGAAATGATCCTAAGAAGGA--CTAA-A
* * * *
1221901 AATTTCTAAAGAAATGATGCTAAGGATGACTAAA
1 AATTTCTAGAGAAATGATCCTAAGAAGGACTAAA
* *
1221935 AACTTTCTAGAGAAATGATCCTAAAAAGGAATAAAA
1 AA-TTTCTAGAGAAATGATCCTAAGAAGGACT-AAA
*
1221971 CAATTTCTAGAGAAATAATCCTAAGAAGGA
1 -AATTTCTAGAGAAATGATCCTAAGAAGGA
1222001 TTAGAGTGTG
Statistics
Matches: 117, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
34 3 0.03
35 27 0.23
36 28 0.24
37 27 0.23
38 3 0.03
39 29 0.25
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.23
Consensus pattern (34 bp):
AATTTCTAGAGAAATGATCCTAAGAAGGACTAAA
Found at i:1231343 original size:14 final size:14
Alignment explanation
Indices: 1231335--1231368 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1231325 TGGTTTAAGG
1231335 TTTAGGGTTTATAA
1 TTTAGGGTTTATAA
1231349 TTTAGGGTTT-TAA
1 TTTAGGGTTTATAA
*
1231362 GTTAGGG
1 TTTAGGG
1231369 GTAGCGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTATAA
Found at i:1231370 original size:14 final size:14
Alignment explanation
Indices: 1231336--1231368 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1231326 GGTTTAAGGT
*
1231336 TTAGGGTTTATAAT
1 TTAGGGTTTATAAG
1231350 TTAGGGTTT-TAAG
1 TTAGGGTTTATAAG
1231363 TTAGGG
1 TTAGGG
1231369 GTAGCGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTATAAG
Found at i:1241777 original size:65 final size:65
Alignment explanation
Indices: 1241661--1242239 Score: 802
Period size: 65 Copynumber: 9.0 Consensus size: 65
1241651 GGTAGGGTGA
* *
1241661 ACAAGTACAAATCACTCATATGACTCATGTACCTTTGCGGTGCATGAGGTGGAGTGATAATTGAA
1 ACAA-TACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAA
1241726 T
65 T
* * * *
1241727 ACAGTATATATCACTCATATGACTCATGTACCTTTGTGGTGCATGGGGTGGAGTGATAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* *
1241792 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGTTGCATGGGGTGGAGTGATAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
*
1241857 ACAATACAGATCACTCATATGACTCATGTACCTTTGTAGTGCATGAGGTGGAGTGATAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* * * *
1241922 ATAGTACAGATCACTCATATGACTCATATACCTTTGTGGTGCATGAGGTGAAGTGATAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* *
1241987 ACAATATAGATCACTCATATGACTAATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATT-ATA
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGA-A
1242051 T
65 T
* * *
1242052 ACAATACATATCACTCATATGACTCATGTACCTTTGTGGTG-GTTATGGTGGAGTGATAATTGAA
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGA-GGTGGAGTGATAATTGAA
*
1242116 C
65 T
* * * * *
1242117 ACATTACAG---A-TC-----ACTCATGTACCTTTGTGGTGCATGAAGCGGAGTTATAATTGAAC
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* * * *
1242173 ACATTATAGATCACTCATATGACTCATGTACCTTTGTGGAGCATGAGGCGGAGTGATAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
1242238 AC
1 AC
1242240 TGCAAAGATC
Statistics
Matches: 459, Mismatches: 41, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
56 44 0.10
57 2 0.00
59 1 0.00
60 2 0.00
61 2 0.00
62 1 0.00
64 3 0.01
65 400 0.87
66 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (65 bp):
ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
Found at i:1242140 original size:56 final size:55
Alignment explanation
Indices: 1242073--1242190 Score: 166
Period size: 56 Copynumber: 2.1 Consensus size: 55
1242063 CACTCATATG
* *
1242073 ACTCATGTACCTTTGTGGTGGTTATG-GTGGAGTGATAATTGAACACATTACAGATC
1 ACTCATGTACCTTTGTGGT-G-CATGAGCGGAGTGATAATTGAACACATTACAGATC
* *
1242129 ACTCATGTACCTTTGTGGTGCATGAAGCGGAGTTATAATTGAACACATTATAGATC
1 ACTCATGTACCTTTGTGGTGCATG-AGCGGAGTGATAATTGAACACATTACAGATC
1242185 ACTCAT
1 ACTCAT
1242191 ATGACTCATG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
54 3 0.05
55 1 0.02
56 52 0.93
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (55 bp):
ACTCATGTACCTTTGTGGTGCATGAGCGGAGTGATAATTGAACACATTACAGATC
Found at i:1242226 original size:121 final size:121
Alignment explanation
Indices: 1242012--1242236 Score: 319
Period size: 121 Copynumber: 1.9 Consensus size: 121
1242002 CATATGACTA
* * * *
1242012 ATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTATATACAATACATATCACTCATATGACTC
1 ATGTACCTTTGTGGTGCATGAAGCGGAGTGATAATTATACACAATACAGATCACTCATATGACTC
* * * *
1242077 ATGTACCTTTGTGGTGGTTATGGTGGAGTGATAATTGAACACATTACAGATCACTC
66 ATGTACCTTTGTGGAGATGATGGCGGAGTGATAATTGAACACATTACAGATCACTC
* * *
1242133 ATGTACCTTTGTGGTGCATGAAGCGGAGTTATAATTGA-ACACATTATAGATCACTCATATGACT
1 ATGTACCTTTGTGGTGCATGAAGCGGAGTGATAATT-ATACACAATACAGATCACTCATATGACT
1242197 CATGTACCTTTGTGGAGCATGA-GGCGGAGTGATAATTGAA
65 CATGTACCTTTGTGGAG-ATGATGGCGGAGTGATAATTGAA
1242237 TACTGCAAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
121 88 0.97
122 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (121 bp):
ATGTACCTTTGTGGTGCATGAAGCGGAGTGATAATTATACACAATACAGATCACTCATATGACTC
ATGTACCTTTGTGGAGATGATGGCGGAGTGATAATTGAACACATTACAGATCACTC
Found at i:1242249 original size:65 final size:64
Alignment explanation
Indices: 1242129--1242258 Score: 181
Period size: 65 Copynumber: 2.0 Consensus size: 64
1242119 ATTACAGATC
* * * *
1242129 ACTCATGTACCTTTGTGGTGCATGAAGCGGAGTTATAATTGAACACATTATAGATCACTCATATG
1 ACTCATGTACCTTTGTGGAGCATGAAGCGGAGTGATAATTGAACACATCAAAGATCACTCA-ATG
* *
1242194 ACTCATGTACCTTTGTGGAGCATGAGGCGGAGTGATAATTGAATAC-TGCAAAGATCACTCAATG
1 ACTCATGTACCTTTGTGGAGCATGAAGCGGAGTGATAATTGAACACAT-CAAAGATCACTCAATG
1242258 A
1 A
1242259 GACTAGAGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 5 0.09
65 53 0.91
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (64 bp):
ACTCATGTACCTTTGTGGAGCATGAAGCGGAGTGATAATTGAACACATCAAAGATCACTCAATG
Found at i:1242498 original size:34 final size:34
Alignment explanation
Indices: 1242460--1242535 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
1242450 CAGTGCAGTT
1242460 AAAGGAAAGATACAGGAAAAAGAATAA-TATAGTG
1 AAAGGAAAGATACAGGAAAAAGAATAAGTATA-TG
** *
1242494 AAAGGATTGATACAGGAAAAAGAGTAAGTATATG
1 AAAGGAAAGATACAGGAAAAAGAATAAGTATATG
1242528 ATAAGGAA
1 A-AAGGAA
1242536 CAATACAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 27 0.75
35 9 0.25
ACGTcount: A:0.55, C:0.03, G:0.25, T:0.17
Consensus pattern (34 bp):
AAAGGAAAGATACAGGAAAAAGAATAAGTATATG
Found at i:1246231 original size:65 final size:65
Alignment explanation
Indices: 1246115--1246589 Score: 686
Period size: 65 Copynumber: 7.3 Consensus size: 65
1246105 GGTAGGGTGA
1246115 ACAAGTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAA
1 ACAA-TACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAA
1246180 T
65 T
* * * *
1246181 ACAACACATATCACTCAAATGACTCATGTACCTTTGTGGTGCATGGGGTGGAGTGATAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
*
1246246 ACATTACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* *
1246311 ACAATAAAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* * * * * *
1246376 ATAGTATATATCACTCATATGACTCATGTACTTTTGTGGAGCATGAGGTGGAGTGATAATTG--T
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* * * * *
1246439 ACAATACAGATCACTTATATGACTCATGTACCTTTGTGGTGCATAATGTGGAATGGTAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* * * * *
1246504 ACAGTACATATCACTTATATGACTCAAGTACCTTTGTGGTGTATGAGGTGGAGTGATAATTGAAT
1 ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* * *
1246569 ACTACAAAGATCACTCA-ATGA
1 ACAATACAGATCACTCATATGA
1246590 GACTAGAGTA
Statistics
Matches: 364, Mismatches: 43, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
63 52 0.14
64 4 0.01
65 304 0.84
66 4 0.01
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (65 bp):
ACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
Found at i:1246783 original size:17 final size:17
Alignment explanation
Indices: 1246763--1246797 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1246753 GTAAAGAAAT
1246763 CAGTACAGAAAAAGGAA
1 CAGTACAGAAAAAGGAA
* *
1246780 CAGTACAGTAAAATGAA
1 CAGTACAGAAAAAGGAA
1246797 C
1 C
1246798 GACATAGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.20, T:0.11
Consensus pattern (17 bp):
CAGTACAGAAAAAGGAA
Found at i:1248025 original size:59 final size:59
Alignment explanation
Indices: 1247899--1248174 Score: 426
Period size: 59 Copynumber: 4.7 Consensus size: 59
1247889 AAATGGGTTT
* **
1247899 TAAAATGATAAGGAAATCATACTAAGTGTATGAAATTTCCTGATATAGCACTAAGTGTGC
1 TAAAATGATAAGGAAATCATACTAAGTGTATG-AATTTCCAGATAGGGCACTAAGTGTGC
1247959 TAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGC
1 TAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGC
* * * *
1248018 TAGAATGATAAGGAAATCATGCTAAGTGTATGAATTTTCATATAGGGCACTAAGTGTGC
1 TAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGC
* *
1248077 TAAAATGATAAGAAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTATGTGTGC
1 TAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGC
* * * *
1248136 TAAAAAGACAAGGAAATCGTACTAATTGTATGAATTTCC
1 TAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCC
1248175 TATTGAATTT
Statistics
Matches: 198, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
59 166 0.84
60 32 0.16
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (59 bp):
TAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGC
Found at i:1253995 original size:31 final size:31
Alignment explanation
Indices: 1253957--1254054 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
1253947 AGATAGGGCG
1253957 CTAAGTGTGCTAAAATGATAAGGAAATCATA
1 CTAAGTGTGCTAAAATGATAAGGAAATCATA
* ** * *
1253988 CTAAGTGT-ATGAATTTCTATATAGG---GC--A
1 CTAAGTGTGCT-AAAAT-GATA-AGGAAATCATA
1254016 CTAAGTGTGCTAAAATGATAAGGAAATCATA
1 CTAAGTGTGCTAAAATGATAAGGAAATCATA
1254047 CTAAGTGT
1 CTAAGTGT
1254055 ATGAATTTCC
Statistics
Matches: 48, Mismatches: 10, Indels: 18
0.63 0.13 0.24
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 12 0.25
29 2 0.04
30 2 0.04
31 20 0.42
32 3 0.06
33 3 0.06
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (31 bp):
CTAAGTGTGCTAAAATGATAAGGAAATCATA
Found at i:1254001 original size:59 final size:59
Alignment explanation
Indices: 1253909--1254358 Score: 749
Period size: 59 Copynumber: 7.6 Consensus size: 59
1253899 AATGGGTTTC
* *
1253909 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCGCTAAGTGTGCT
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
* *
1253968 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTATATAGGGCACTAAGTGTGCT
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
* * *
1254027 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAAATAGGGCACCAAGTGTGTT
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
*
1254086 AAAATGATAAGGAAAGCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
*
1254145 AAAATTATAA-GAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
*
1254203 AAAATGATAAGGAAATCATATTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
* * *
1254262 AAAATGGTAAGGAAATCATGCTAAGTGTATGAATTTCCAGATACGGCACTAAGTGTGCT
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
* * *
1254321 AAAAAGACAAGGAAATCATACTAATTGTATGAATTTCC
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCC
1254359 TATTGAATTT
Statistics
Matches: 367, Mismatches: 23, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
58 56 0.15
59 311 0.85
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (59 bp):
AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
Found at i:1254138 original size:28 final size:28
Alignment explanation
Indices: 1254105--1254199 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
1254095 AGGAAAGCAT
1254105 ACTAAGTGTATGAATTTCCAGATAGGGC
1 ACTAAGTGTATGAATTTCCAGATAGGGC
* * * * ****
1254133 ACTAAGTGTGCTAAAATTAT-AAGAAATCAT
1 ACTAAGTGT-AT-GAATT-TCCAGATAGGGC
1254163 ACTAAGTGTATGAATTTCCAGATAGGGC
1 ACTAAGTGTATGAATTTCCAGATAGGGC
1254191 ACTAAGTGT
1 ACTAAGTGT
1254200 GCTAAAATGA
Statistics
Matches: 47, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
27 1 0.02
28 26 0.55
29 2 0.04
30 17 0.36
31 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (28 bp):
ACTAAGTGTATGAATTTCCAGATAGGGC
Found at i:1254335 original size:235 final size:236
Alignment explanation
Indices: 1253909--1254358 Score: 749
Period size: 235 Copynumber: 1.9 Consensus size: 236
1253899 AATGGGTTTC
* *
1253909 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCGCTAAGTGTGCTAAAATG
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCTAAAATG
* *
1253974 ATAAGGAAATCATACTAAGTGTATGAATTTCTATATAGGGCACTAAGTGTGCTAAAATGATAAGG
66 ATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCTAAAATGATAAGG
* * * *
1254039 AAATCATACTAAGTGTATGAATTTCCAAATAGGGCACCAAGTGTGTTAAAATGATAAGGAAAGCA
131 AAATCATACTAAGTGTATGAATTTCCAAATACGGCACCAAGTGTGCTAAAAAGACAAGGAAAGCA
1254104 TACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
196 TACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
*
1254145 AAAATTATAA-GAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCTAAAATG
1 AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCTAAAATG
* *
1254209 ATAAGGAAATCATATTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCTAAAATGGTAAGG
66 ATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCTAAAATGATAAGG
* * * *
1254274 AAATCATGCTAAGTGTATGAATTTCCAGATACGGCACTAAGTGTGCTAAAAAGACAAGGAAATCA
131 AAATCATACTAAGTGTATGAATTTCCAAATACGGCACCAAGTGTGCTAAAAAGACAAGGAAAGCA
*
1254339 TACTAATTGTATGAATTTCC
196 TACTAAGTGTATGAATTTCC
1254359 TATTGAATTT
Statistics
Matches: 198, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
235 189 0.95
236 9 0.05
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (236 bp):
AAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCTAAAATG
ATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCTAAAATGATAAGG
AAATCATACTAAGTGTATGAATTTCCAAATACGGCACCAAGTGTGCTAAAAAGACAAGGAAAGCA
TACTAAGTGTATGAATTTCCAGATAGGGCACTAAGTGTGCT
Found at i:1262467 original size:23 final size:23
Alignment explanation
Indices: 1262441--1262490 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1262431 ATCAAATACA
*
1262441 ATAACATAATAGGTAACGCTTAT
1 ATAACATAATAAGTAACGCTTAT
** **
1262464 ATAATGTAATAAGTAGTGCTTAT
1 ATAACATAATAAGTAACGCTTAT
1262487 ATAA
1 ATAA
1262491 TAAAATATGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (23 bp):
ATAACATAATAAGTAACGCTTAT
Found at i:1262625 original size:23 final size:23
Alignment explanation
Indices: 1262599--1262671 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1262589 ATCAAGAATA
* *
1262599 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAAGTAGCGCTTAT
*
1262622 ATAACATAATAAGTAGCACTTAT
1 ATAACATAATAAGTAGCGCTTAT
*
1262645 ATAACATAATAAGTAACGCTTAT
1 ATAACATAATAAGTAGCGCTTAT
1262668 ATAA
1 ATAA
1262672 TAAAATAGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (23 bp):
ATAACATAATAAGTAGCGCTTAT
Found at i:1262745 original size:181 final size:181
Alignment explanation
Indices: 1262441--1262829 Score: 591
Period size: 181 Copynumber: 2.1 Consensus size: 181
1262431 ATCAAATACA
* * ** ** *
1262441 ATAACATAATAGGTAACGCTTATATAATGTAATAAGTAGTGCTTATATAATAAAATATGTTAATT
1 ATAACATAATAGGTAGCACTTATATAACATAATAAGTAACGCTTATATAATAAAATAGGTTAATT
* * * *
1262506 ATTTAATTTGTTATTATAACATATTAGGTAAACGCCTAAAATGTTATCAATGATAACATAATCGG
66 ATTTAATTTGTTATTACAACATATTAGGTAAACACCTAAAATGTTACCAATGATAACATAACCGG
* * * *
1262571 TTATTTATTGGAAACATTATCAAGAATAATAACATATTAGGTAGCGCTTAT
131 TTAATTACTAGAAACATTATCAAGAACAATAACATATTAGGTAGCGCTTAT
*
1262622 ATAACATAATAAGTAGCACTTATATAACATAATAAGTAACGCTTATATAATAAAATAGGTTAATT
1 ATAACATAATAGGTAGCACTTATATAACATAATAAGTAACGCTTATATAATAAAATAGGTTAATT
1262687 ATTTAATTTGTTATTACAACATATTAGGTAAACACCTAAAATGTTACCAATGATAACATAACCGG
66 ATTTAATTTGTTATTACAACATATTAGGTAAACACCTAAAATGTTACCAATGATAACATAACCGG
* *
1262752 TTAATTACTAGAAACATTATCAAGCACAATAACATATTAGGTAGTGCTTAT
131 TTAATTACTAGAAACATTATCAAGAACAATAACATATTAGGTAGCGCTTAT
*
1262803 ATAACGTAATAGGTAG-AGCTTATATAA
1 ATAACATAATAGGTAGCA-CTTATATAA
1262830 TAAAATAGGT
Statistics
Matches: 187, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 1 0.01
181 186 0.99
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (181 bp):
ATAACATAATAGGTAGCACTTATATAACATAATAAGTAACGCTTATATAATAAAATAGGTTAATT
ATTTAATTTGTTATTACAACATATTAGGTAAACACCTAAAATGTTACCAATGATAACATAACCGG
TTAATTACTAGAAACATTATCAAGAACAATAACATATTAGGTAGCGCTTAT
Found at i:1262806 original size:23 final size:23
Alignment explanation
Indices: 1262780--1262839 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1262770 ATCAAGCACA
* *
1262780 ATAACATATTAGGTAGTGCTTAT
1 ATAACATAATAGGTAGAGCTTAT
*
1262803 ATAACGTAATAGGTAGAGCTTAT
1 ATAACATAATAGGTAGAGCTTAT
* *
1262826 ATAATAAAATAGGT
1 ATAACATAATAGGT
1262840 TAATTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGAGCTTAT
Found at i:1262911 original size:158 final size:158
Alignment explanation
Indices: 1262622--1262977 Score: 489
Period size: 158 Copynumber: 2.3 Consensus size: 158
1262612 TAGCGCTTAT
*
1262622 ATAACATAATAAGTAGCACTTATATAACATAATAAGTAACGCTTATATAATAAAATAGGTTAATT
1 ATAACATATTAAGTAGCACTTATATAACATAATAAGTAACGCTTATATAATAAAATAGGTTAATT
*
1262687 ATTTAATTTGTTATTACAACATATTAGGTAAACACCTAAAATGTTACCAATGATAACATAACCGG
66 ACTTAATTTGTTATTACAACATATTAGGTAAACACCTAAAATGTTACCAATGATAACATAACCGG
* *
1262752 TTAATTACTAGAAACATTATCAAGCACA
131 TTAATTACTAGAAACAATATCAAACACA
* ** * *
1262780 ATAACATATTAGGTAGTGCTTATATAACGTAATAGGTAGA-GCTTATATAATAAAATAGGTTAAT
1 ATAACATATTAAGTAGCACTTATATAACATAATAAGTA-ACGCTTATATAATAAAATAGGTTAAT
* * * *
1262844 TACTTAATTTGTTATTGCAACATATTAGGTAAACGCTTAAAATGTTACCAATGATAACATAATCG
65 TACTTAATTTGTTATTACAACATATTAGGTAAACACCTAAAATGTTACCAATGATAACATAACCG
* * * *
1262909 GTTAATTATTTGAAACAATATTAAACATA
130 GTTAATTACTAGAAACAATATCAAACACA
* ** * * *
1262938 ATAACATATTATGTAGCGTTTATGTAACAAAATAGGTAAC
1 ATAACATATTAAGTAGCACTTATATAACATAATAAGTAAC
1262978 TACTTAATTT
Statistics
Matches: 173, Mismatches: 23, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
157 1 0.01
158 171 0.99
159 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (158 bp):
ATAACATATTAAGTAGCACTTATATAACATAATAAGTAACGCTTATATAATAAAATAGGTTAATT
ACTTAATTTGTTATTACAACATATTAGGTAAACACCTAAAATGTTACCAATGATAACATAACCGG
TTAATTACTAGAAACAATATCAAACACA
Found at i:1263281 original size:73 final size:71
Alignment explanation
Indices: 1263040--1263282 Score: 344
Period size: 73 Copynumber: 3.4 Consensus size: 71
1263030 AAAATTTAAA
* *
1263040 CTACCTATTACATTAAAATACCTACTGGTTTTTTAAGGTTGTTAATAATGTAAACGGTAAAAAAA
1 CTACCTATTACATTAAAATACCTACCGTTTTTTTAAGGTTGTTAATAATGTAAACGGTAAAAAAA
1263105 -AGGCG
66 TAGGCG
* * *
1263110 CTACCTATTATATTAAAATACCTATCGATTTTTTTGAAAGTTGTTAATAATGTAAACGGTAAAAA
1 CTACCTATTACATTAAAATACCTACCG-TTTTTTT-AAGGTTGTTAATAATGTAAACGGTAAAAA
1263175 AATAGGCG
64 AATAGGCG
* * * *
1263183 TTACCTATTACATTAAAATAGCTACCAGTTTTTTTAAGGTTGCTAATAATGTAAACAGTAAAAAA
1 CTACCTATTACATTAAAATACCTACC-GTTTTTTTAAGGTTGTTAATAATGTAAACGGT-AAAAA
1263248 AATAGGCG
64 AATAGGCG
* *
1263256 CTACCTATTACATTTAACTACCTACCG
1 CTACCTATTACATTAAAATACCTACCG
1263283 GATATGTTGA
Statistics
Matches: 152, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
70 24 0.16
71 6 0.04
72 52 0.34
73 69 0.45
74 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (71 bp):
CTACCTATTACATTAAAATACCTACCGTTTTTTTAAGGTTGTTAATAATGTAAACGGTAAAAAAA
TAGGCG
Found at i:1263829 original size:114 final size:111
Alignment explanation
Indices: 1263370--1263818 Score: 621
Period size: 112 Copynumber: 4.0 Consensus size: 111
1263360 ATAAAATATA
* * *
1263370 GATACTTTATAAAAATGTATCAATACTTTT-CAATATAGCAGGTGAAAATATGACAAAACCAGTT
1 GATACTTTATAAAAATGTATCGATA-TTTTACAATATAACAGGTAAAAATATGACAAAACCAGTT
* * *
1263434 TTATTATGACAAAACCGGTAAAGAACTACCTGATATGTTGAAAATAT
65 TCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTGAAAGTAT
* *
1263481 CAATACTTTATAAAAATGTATCGATATTTTACAACATAACAGGTAAAAATATGACAAAACCAGTT
1 -GATACTTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATATGACAAAACCAGTT
* * * * * * *
1263546 TCATTAAGACAAAACCGATAAAAAGCTACTTAATATGTTAAAAGTTT
65 TCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTGAAAGTAT
* * *
1263593 CGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAATCAATT
1 -GATACTTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATATGACAAAACCAGTT
*
1263658 TCATTATAACAAAACCGGTAAAGAGCTACCTGATATGTTGAAAGTATT
65 TCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTGAAAGTA-T
* * *
1263706 GATCCTTTTTATAAAAATGTATCGATATTTTATAATATAACAGGTAAAAACATGACAAAACCAGT
1 GATAC--TTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATATGACAAAACCAGT
* *
1263771 TTCATTATGATAAAATCGGTAAAGAGCTACCTGATATGTTGAAAGTAT
64 TTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTGAAAGTAT
1263819 AGAATTTTTT
Statistics
Matches: 296, Mismatches: 37, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
111 4 0.01
112 193 0.65
113 2 0.01
114 97 0.33
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (111 bp):
GATACTTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTT
CATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTGAAAGTAT
Found at i:1267816 original size:31 final size:32
Alignment explanation
Indices: 1267780--1267856 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 32
1267770 TCAAAAAACA
1267780 TAAGATATGGTCACTTTT-GTTTTTATCTAAT
1 TAAGATATGGTCACTTTTCGTTTTTATCTAAT
* *
1267811 TAAGATATGGT-AATTTTCGTTTTTATTTAAT
1 TAAGATATGGTCACTTTTCGTTTTTATCTAAT
* *
1267842 TAAGATGTGTTCACT
1 TAAGATATGGTCACT
1267857 CCGAGTTAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.13
31 32 0.82
32 2 0.05
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (32 bp):
TAAGATATGGTCACTTTTCGTTTTTATCTAAT
Found at i:1268255 original size:18 final size:17
Alignment explanation
Indices: 1268214--1268251 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1268204 CTATTTATTA
*
1268214 TTTATTTTTATTTTAAAT
1 TTTA-TTTTATATTAAAT
1268232 TTTATTTTATATTAAAT
1 TTTATTTTATATTAAAT
1268249 TTT
1 TTT
1268252 TATTCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTATATTAAAT
Found at i:1268697 original size:30 final size:28
Alignment explanation
Indices: 1268623--1268693 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 28
1268613 TCTATATATA
1268623 TTAATTTAAAATA-TTTTTA-TATTAAC
1 TTAATTTAAAATATTTTTTATTATTAAC
*
1268649 TT-A-TT-AAATATATTTTATTATTAAC
1 TTAATTTAAAATATTTTTTATTATTAAC
1268674 TTAATTTAGAAATATTTTTT
1 TTAATTTA-AAATATTTTTT
1268694 TATTTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
23 5 0.14
24 7 0.19
25 10 0.27
26 3 0.08
27 2 0.05
29 10 0.27
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (28 bp):
TTAATTTAAAATATTTTTTATTATTAAC
Found at i:1269820 original size:21 final size:21
Alignment explanation
Indices: 1269794--1269836 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1269784 ATTTGAGTTT
1269794 AATCCTTATGTGCATAAGAAA
1 AATCCTTATGTGCATAAGAAA
1269815 AATCCTTATGTGCATAAGAAA
1 AATCCTTATGTGCATAAGAAA
1269836 A
1 A
1269837 GTACGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
AATCCTTATGTGCATAAGAAA
Found at i:1270768 original size:14 final size:14
Alignment explanation
Indices: 1270749--1270778 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1270739 GAGAAGCTTG
1270749 TACAATTCTAAAGA
1 TACAATTCTAAAGA
1270763 TACAATTCTAAAGA
1 TACAATTCTAAAGA
1270777 TA
1 TA
1270779 ACATAAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (14 bp):
TACAATTCTAAAGA
Found at i:1276922 original size:27 final size:29
Alignment explanation
Indices: 1276883--1276936 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
1276873 TCGAATACCT
1276883 AAAAATATATTTTAA-A-AAAAATTTAAG
1 AAAAATATATTTTAAGACAAAAATTTAAG
1276910 AAAAATCAT-TTTTAAGACAAAAATTTA
1 AAAAAT-ATATTTTAAGACAAAAATTTA
1276937 TTTGCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 12 0.50
28 3 0.12
29 9 0.38
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATATATTTTAAGACAAAAATTTAAG
Found at i:1277788 original size:8 final size:8
Alignment explanation
Indices: 1277772--1277818 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
1277762 TCATGAGCAA
1277772 AAATATAT
1 AAATATAT
*
1277780 AAGTATAT
1 AAATATAT
1277788 AAATATAT
1 AAATATAT
*
1277796 -AATACAT
1 AAATATAT
*
1277803 AATACATAT
1 AA-ATATAT
1277812 AAATATA
1 AAATATA
1277819 ATGTAGTAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
7 6 0.19
8 19 0.61
9 6 0.19
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (8 bp):
AAATATAT
Found at i:1290806 original size:21 final size:21
Alignment explanation
Indices: 1290780--1290824 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1290770 GATTTCTGGG
* *
1290780 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1290801 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1290822 CAA
1 CAA
1290825 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1291791 original size:31 final size:31
Alignment explanation
Indices: 1291753--1291908 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
1291743 AGGGTCGAGG
1291753 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1291784 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1291815 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1291846 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1291877 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1291908 G
1 G
1291909 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1295086 original size:21 final size:21
Alignment explanation
Indices: 1295060--1295104 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1295050 GATTTCTGGG
*
1295060 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
1295081 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1295102 CAA
1 CAA
1295105 ACGAACAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1296073 original size:31 final size:31
Alignment explanation
Indices: 1296035--1296190 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
1296025 AGGGTCGAGG
1296035 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1296066 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1296097 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1296128 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1296159 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1296190 G
1 G
1296191 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1298991 original size:31 final size:30
Alignment explanation
Indices: 1298927--1298993 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
1298917 GTAAATTTTT
* *
1298927 AAAGTTTAGAGACTAAAGTGTAAAGTTGTA
1 AAAGTTTAGAGACTAAAGTATAAAATTGTA
1298957 AAAGTTTA-AGGACTAAAAGTATAAAATT-TCA
1 AAAGTTTAGA-GACT-AAAGTATAAAATTGT-A
1298988 AAAGTT
1 AAAGTT
1298994 AAATTTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 1 0.03
30 13 0.41
31 18 0.56
ACGTcount: A:0.48, C:0.04, G:0.18, T:0.30
Consensus pattern (30 bp):
AAAGTTTAGAGACTAAAGTATAAAATTGTA
Found at i:1301512 original size:18 final size:18
Alignment explanation
Indices: 1301450--1301519 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
1301440 ATTCTAAATG
* *
1301450 TTTACAATTATTAGATGA
1 TTTACAGTTATCAGATGA
* * *
1301468 TTTTCAGTGATCATATGA
1 TTTACAGTTATCAGATGA
*
1301486 TTTTCAGTTATCAGATGA
1 TTTACAGTTATCAGATGA
*
1301504 TTTACAGTTATTAGAT
1 TTTACAGTTATCAGAT
1301520 AATTATAAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (18 bp):
TTTACAGTTATCAGATGA
Found at i:1305530 original size:16 final size:16
Alignment explanation
Indices: 1305506--1305601 Score: 71
Period size: 16 Copynumber: 6.1 Consensus size: 16
1305496 ATCTATTTTA
*
1305506 ATTACTATATTTATAT
1 ATTATTATATTTATAT
1305522 ATTATTATATTT-TAATT
1 ATTATTATATTTAT-A-T
1305539 ATTTATTATATTTA-AT
1 A-TTATTATATTTATAT
* *
1305555 ATT-TAATA-TTATAA
1 ATTATTATATTTATAT
1305569 ATTATTAGTA-TTAT-T
1 ATTATTA-TATTTATAT
1305584 ATTATATATATTTA-AT
1 ATTAT-TATATTTATAT
1305600 AT
1 AT
1305602 AATTTAAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
13 3 0.05
14 8 0.12
15 12 0.18
16 28 0.43
17 3 0.05
18 11 0.17
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:1305548 original size:26 final size:27
Alignment explanation
Indices: 1305513--1305585 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 27
1305503 TTAATTACTA
*
1305513 TATTTA-TATATTATTATATTTTA-AT
1 TATTTATTATATTATTATATTTAATAT
*
1305538 TATTTATTATATT-TAATATTTAATAT
1 TATTTATTATATTATTATATTTAATAT
1305564 TATAAATTATTAGTATTATTAT
1 TAT---TTATTA-TATTATTAT
1305586 TATATATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 14 0.37
26 11 0.29
29 6 0.16
30 4 0.11
31 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
TATTTATTATATTATTATATTTAATAT
Found at i:1305978 original size:51 final size:52
Alignment explanation
Indices: 1305901--1306034 Score: 141
Period size: 51 Copynumber: 2.7 Consensus size: 52
1305891 CACCTGTAGC
* * * * * *
1305901 AGTAAAGCGC-CCCCCTGAAAT-GCGCTATATGCTGATTTGGCGCCACGTGG
1 AGTATAGCGCGCCCCCTGATATCGCGCTATACGCTGACTGGGCGACACGTGG
**
1305951 AGTATAGCGCGCCCCCTG-TATCGCGCTATACGCTGACTGGGTTACACGTGG
1 AGTATAGCGCGCCCCCTGATATCGCGCTATACGCTGACTGGGCGACACGTGG
* * *
1306002 GGTATAACGCGCCCCCTGCTA-CGCGCTATACGC
1 AGTATAGCGCGCCCCCTGATATCGCGCTATACGC
1306035 CATGTAGGGG
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
50 11 0.15
51 58 0.82
52 2 0.03
ACGTcount: A:0.19, C:0.31, G:0.28, T:0.22
Consensus pattern (52 bp):
AGTATAGCGCGCCCCCTGATATCGCGCTATACGCTGACTGGGCGACACGTGG
Found at i:1309770 original size:9 final size:9
Alignment explanation
Indices: 1309756--1309787 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1309746 GCTGTCATCA
1309756 TCATCGTCG
1 TCATCGTCG
1309765 TCATCGTCG
1 TCATCGTCG
*
1309774 TCGTCGTCG
1 TCATCGTCG
1309783 TCATC
1 TCATC
1309788 ATCCTGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.09, C:0.34, G:0.22, T:0.34
Consensus pattern (9 bp):
TCATCGTCG
Found at i:1311832 original size:111 final size:111
Alignment explanation
Indices: 1311638--1311859 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
1311628 ATTACAAAAA
* * *
1311638 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTGTTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
1311703 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
*
1311749 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAATACTTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1311814 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
1311860 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:1311981 original size:17 final size:17
Alignment explanation
Indices: 1311921--1311978 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
1311911 GAATTATATT
1311921 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
1311938 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
1311955 AGTAAAATACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
1311973 ATTAAA
1 AGTAAA
1311979 TACATAATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
17 26 0.67
18 13 0.33
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:1314494 original size:2 final size:2
Alignment explanation
Indices: 1314487--1314511 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1314477 AAGTAAAAAC
1314487 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1314512 ACACAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1315827 original size:21 final size:20
Alignment explanation
Indices: 1315778--1315827 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1315768 TAATGTTATT
* *
1315778 TAATA-TATCAAATGCATTC
1 TAATATTATAAAATACATTC
*
1315797 TAAAATTATAAAATACATTC
1 TAATATTATAAAATACATTC
1315817 ATAATATTATA
1 -TAATATTATA
1315828 TTTTAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATATTATAAAATACATTC
Found at i:1320092 original size:3 final size:3
Alignment explanation
Indices: 1320086--1320153 Score: 61
Period size: 3 Copynumber: 22.3 Consensus size: 3
1320076 ATAAGAAAAA
*
1320086 AAT AAT AATT AA- AAG AAT AAT AAT AAT AAT AAT AA- AAT -AT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1320129 AAAT AAT ATAT AAT ATAT AAA AAT A
1 -AAT AAT A-AT AAT A-AT AAT AAT A
1320154 TTTTCAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
2 6 0.11
3 37 0.67
4 12 0.22
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1320099 original size:12 final size:11
Alignment explanation
Indices: 1320074--1320141 Score: 68
Period size: 12 Copynumber: 6.1 Consensus size: 11
1320064 AGTAAAAAAT
* *
1320074 AAATAAGAAAA
1 AAATAATAATA
1320085 AAATAATAATTA
1 AAATAATAA-TA
*
1320097 AAAGAATAATA
1 AAATAATAATA
1320108 ATAATAATAATA
1 A-AATAATAATA
1320120 AAAT-ATAAT-
1 AAATAATAATA
1320129 AAATAATATATA
1 AAATAATA-ATA
1320141 A
1 A
1320142 TATATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
9 4 0.08
10 8 0.17
11 16 0.33
12 20 0.42
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AAATAATAATA
Found at i:1320200 original size:37 final size:37
Alignment explanation
Indices: 1320131--1320380 Score: 160
Period size: 38 Copynumber: 6.8 Consensus size: 37
1320121 AATATAATAA
* *
1320131 ATAATATATAATATATAAAAATATTTTCAAAAAAATTAT
1 ATAATATAT-ATTTTTAAAAATATTTT-AAAAAAATTAT
* *
1320170 ATAATATATATTTTTAAAAATACTTTAAAAAAAACTAT
1 ATAATATATATTTTTAAAAATA-TTTTAAAAAAATTAT
* *
1320208 AT-AT-TATATATTTAAAAATATTTT--CAAAATTAT
1 ATAATATATATTTTTAAAAATATTTTAAAAAAATTAT
* * * **
1320241 ATATTATATAATTTTCAAAAATGTTTTAAAATTA-TAT
1 ATAATATAT-ATTTTTAAAAATATTTTAAAAAAATTAT
* * *
1320278 ATTATATAAATGTTTTAAAAATGTTTTTAAAAAAA--AT
1 ATAATATATAT-TTTTAAAAAT-ATTTTAAAAAAATTAT
* * * **
1320315 AT-ATAT-TATATTCAAAAATGTTTTAAAACTA-TAT
1 ATAATATATATTTTTAAAAATATTTTAAAAAAATTAT
* * *
1320349 ATTATATAAATGTTTTAAAAATGATTTCAAAA
1 ATAATATATAT-TTTTAAAAAT-ATTTTAAAA
1320381 CTATATATTA
Statistics
Matches: 165, Mismatches: 33, Indels: 27
0.73 0.15 0.12
Matches are distributed among these distances:
33 18 0.11
34 13 0.08
35 12 0.07
36 37 0.22
37 32 0.19
38 41 0.25
39 12 0.07
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (37 bp):
ATAATATATATTTTTAAAAATATTTTAAAAAAATTAT
Found at i:1320241 original size:24 final size:24
Alignment explanation
Indices: 1320210--1320260 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
1320200 AAAACTATAT
1320210 ATTATATATTTAAAAATATTTTCAAA
1 ATTATATA-TTAAAAA-ATTTTCAAA
* *
1320236 ATTATATATTATATAATTTTCAAA
1 ATTATATATTAAAAAATTTTCAAA
1320260 A
1 A
1320261 ATGTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 5 0.22
26 8 0.35
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTATATATTAAAAAATTTTCAAA
Found at i:1320288 original size:26 final size:25
Alignment explanation
Indices: 1320259--1320368 Score: 77
Period size: 26 Copynumber: 4.5 Consensus size: 25
1320249 TAATTTTCAA
1320259 AAATGTTTTAAAATTATATATTATAT
1 AAATGTTTTAAAATTATAT-TTATAT
* * *
1320285 AAATGTTTTAAAA--ATGTTTTTAA
1 AAATGTTTTAAAATTATATTTATAT
*** * * *
1320308 AAAAAATAT-ATATTATATTCA-A-
1 AAATGTTTTAAAATTATATTTATAT
*
1320330 AAATGTTTTAAAACTATATATTATAT
1 AAATGTTTTAAAATTATAT-TTATAT
1320356 AAATGTTTTAAAA
1 AAATGTTTTAAAA
1320369 ATGATTTCAA
Statistics
Matches: 60, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
22 7 0.12
23 17 0.28
24 9 0.15
25 1 0.02
26 26 0.43
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (25 bp):
AAATGTTTTAAAATTATATTTATAT
Found at i:1320333 original size:71 final size:73
Alignment explanation
Indices: 1320200--1320556 Score: 279
Period size: 71 Copynumber: 4.8 Consensus size: 73
1320190 TACTTTAAAA
* * * *
1320200 AAAACTATATATTATAT--A---TTTAAAAATATTTTCAAAATTATATATTATATAATTTTCAAA
1 AAAACTATATATTATATAAATGTTTTAAAAATGTTTTCAAAACTATATATTATATTATATTCAAA
1320260 AATGTTTT
66 AATGTTTT
* * * *
1320268 AAAATTATATATTATATAAATGTTTTAAAAATGTTTTTAAAA-AAAATA-TATATTATATTCAAA
1 AAAACTATATATTATATAAATGTTTTAAAAATGTTTTCAAAACTATATATTATATTATATTCAAA
1320331 AATGTTTT
66 AATGTTTT
* *
1320339 AAAACTATATATTATATAAATGTTTTAAAAATGATTTCAAAACTATATATTATATATGTATTC-A
1 AAAACTATATATTATATAAATGTTTTAAAAATGTTTTCAAAACTATATATTATAT-TATATTCAA
1320403 AAATGTTTT
65 AAATGTTTT
* *
1320412 CAAAAACTACTACATAATATATATATATATATATATT-AAAATGTTTTCAAAAATAATATATTAT
1 --AAAACTA-T--AT-AT-TATATA-A-ATGT-T-TTAAAAATGTTTTCAAAACT-ATATATTAT
* * *
1320476 ATATGTTTTCAAAAAAGTTTT
54 AT-TATATTCAAAAATGTTTT
* * * ** * *
1320497 CCAAAAAT-TATATAATATATAT-TTCCAAAAACCGTTTTCAAAATTATATA-TATATTATAT
1 --AAAACTATATATTATATAAATGTTTTAAAAA-TGTTTTCAAAACTATATATTATATTATAT
1320557 GTATTTTAAA
Statistics
Matches: 238, Mismatches: 28, Indels: 41
0.78 0.09 0.13
Matches are distributed among these distances:
68 16 0.07
70 1 0.00
71 60 0.25
72 8 0.03
73 35 0.15
74 11 0.05
75 17 0.07
76 13 0.05
77 2 0.01
78 2 0.01
79 7 0.03
80 8 0.03
81 3 0.01
82 3 0.01
83 17 0.07
84 20 0.08
85 15 0.06
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (73 bp):
AAAACTATATATTATATAAATGTTTTAAAAATGTTTTCAAAACTATATATTATATTATATTCAAA
AATGTTTT
Found at i:1320407 original size:47 final size:46
Alignment explanation
Indices: 1320344--1320466 Score: 139
Period size: 47 Copynumber: 2.7 Consensus size: 46
1320334 GTTTTAAAAC
* *
1320344 TATATAT-TATA-T-AAATGTTTT-AAAAATGATTTCAAAACTATATA
1 TATATATATATATTAAAATGTTTTCAAAAAT-ACTACAAAA-TATATA
* *
1320388 T-TATATATGTATTCAAAATGTTTTCAAAAACTACTACATAATATATA
1 TATATATATATATT-AAAATGTTTTCAAAAA-TACTACAAAATATATA
1320435 TATATATATATATTAAAATGTTTTCAAAAATA
1 TATATATATATATTAAAATGTTTTCAAAAATA
1320467 ATATATTATA
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
43 5 0.07
44 4 0.06
45 1 0.01
46 2 0.03
47 32 0.48
48 22 0.33
49 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (46 bp):
TATATATATATATTAAAATGTTTTCAAAAATACTACAAAATATATA
Found at i:1320408 original size:107 final size:109
Alignment explanation
Indices: 1320193--1320435 Score: 298
Period size: 107 Copynumber: 2.2 Consensus size: 109
1320183 TTAAAAATAC
* *
1320193 TTTAAAAAAAACTATATATTATATATTTAAAAATATTTTCAAAATTATATATTATATAATTTTCA
1 TTTAAAAAAAACTATATATTATATATTCAAAAATATTTTCAAAACTATATATTATATAATTTTCA
* * *
1320258 AAAATGTTTTAAAATTATATATTATATAAATGTTTTAAAAATGTT
66 AAAATGTTTCAAAACTATATATTATAT-AATGTATTAAAAATGTT
*
1320303 TTTAAAAAAAA-TATATA-T-TATATTCAAAAATGTTTT-AAAACTATATATTATATAAATGTTT
1 TTTAAAAAAAACTATATATTATATATTCAAAAATATTTTCAAAACTATATATTATAT-AAT-TTT
* *
1320364 TAAAAATGATTTCAAAACTATATATTATAT-ATGTATTCAAAATGTT
64 CAAAAATG-TTTCAAAACTATATATTATATAATGTATTAAAAATGTT
* ** * *
1320410 TTCAAAAACTACTACATAATATATAT
1 TTTAAAAAAAACTATATATTATATAT
1320436 ATATATATAT
Statistics
Matches: 115, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
106 16 0.14
107 41 0.36
108 16 0.14
109 26 0.23
110 16 0.14
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (109 bp):
TTTAAAAAAAACTATATATTATATATTCAAAAATATTTTCAAAACTATATATTATATAATTTTCA
AAAATGTTTCAAAACTATATATTATATAATGTATTAAAAATGTT
Found at i:1320474 original size:84 final size:82
Alignment explanation
Indices: 1320366--1320518 Score: 211
Period size: 83 Copynumber: 1.8 Consensus size: 82
1320356 AAATGTTTTA
* *
1320366 AAAATGATTTCAAAACTATATATTATATATGTATTC-AAAATGTTTT-CAAAAACTACTACATAA
1 AAAATGATTTCAAAAATATATATTATATATGTATTCAAAAAAGTTTTCCAAAAA-T--TACATAA
1320429 TATATATATATATATATATT
63 TATATATATATATATATATT
* * *
1320449 AAAATGTTTTCAAAAATAATATATTATATATGTTTTCAAAAAAGTTTTCCAAAAATTATATAATA
1 AAAATGATTTCAAAAAT-ATATATTATATATGTATTCAAAAAAGTTTTCCAAAAATTACATAATA
1320514 TATAT
65 TATAT
1320519 TTCCAAAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
83 28 0.45
84 18 0.29
85 10 0.16
86 6 0.10
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (82 bp):
AAAATGATTTCAAAAATATATATTATATATGTATTCAAAAAAGTTTTCCAAAAATTACATAATAT
ATATATATATATATATT
Found at i:1320479 original size:46 final size:47
Alignment explanation
Indices: 1320382--1320479 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 47
1320372 ATTTCAAAAC
* *
1320382 TATATATTATATATGTATTCAAAATGTTTTCAAAAACTACTACATAA
1 TATATATTATATATATATTCAAAATGTTTTCAAAAACTAATACATAA
* *
1320429 TATATATATATATATATATT-AAAATGTTTTCAAAAA-TAATATATTA
1 TATATAT-TATATATATATTCAAAATGTTTTCAAAAACTAATACATAA
1320475 TATAT
1 TATAT
1320480 GTTTTCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
46 12 0.26
47 23 0.50
48 11 0.24
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (47 bp):
TATATATTATATATATATTCAAAATGTTTTCAAAAACTAATACATAA
Found at i:1320489 original size:25 final size:25
Alignment explanation
Indices: 1320442--1320490 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
1320432 ATATATATAT
1320442 ATATATTAAAATGTTTTCAAAAATA
1 ATATATTAAAATGTTTTCAAAAATA
*
1320467 ATATATTATATATGTTTTCAAAAA
1 ATATATTA-AAATGTTTTCAAAAA
1320491 AGTTTTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (25 bp):
ATATATTAAAATGTTTTCAAAAATA
Found at i:1320496 original size:38 final size:38
Alignment explanation
Indices: 1320425--1320562 Score: 118
Period size: 37 Copynumber: 3.5 Consensus size: 38
1320415 AAACTACTAC
* *** *
1320425 ATAATATATATATATATATATATTAAAATGTTTTCAAAA
1 ATAATATAT-TATATATATTTCCAAAAAAGTTTTCAAAA
* *
1320464 ATAATATATTATATATGTTTTCAAAAAAGTTTTCCAAAA
1 ATAATATATTATATATATTTCCAAAAAAGTTTT-CAAAA
* *
1320503 AT--TATATAATATATATTTCCAAAAACCGTTTTCAAAA
1 ATAATATATTATATATATTTCCAAAAA-AGTTTTCAAAA
*
1320540 TTATATATATATTATATGTATTT
1 --ATA-ATATATTATATATATTT
1320563 TAAAAACATT
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
37 25 0.31
38 23 0.29
39 18 0.22
42 14 0.17
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (38 bp):
ATAATATATTATATATATTTCCAAAAAAGTTTTCAAAA
Found at i:1320591 original size:2 final size:2
Alignment explanation
Indices: 1320580--1320628 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
1320570 ATTCGCAAAC
* * * *
1320580 TA TA TA -A TA TA TA TA TA TA GA TT TA TA TG TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1320621 TA TA TA TA
1 TA TA TA TA
1320629 AAATATGGAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1321316 original size:84 final size:83
Alignment explanation
Indices: 1321215--1322258 Score: 886
Period size: 84 Copynumber: 12.6 Consensus size: 83
1321205 GTTTGCCTCT
* * * * * * * *
1321215 GAGCTGAACGTAATCGAACCCGGAGGTCTTCAGTTAGCAGATAACCCTTCTCAACTTAAGCTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTT-TGTTGGCAGATAACCCTTCTCAACTTAAGTTATG
*
1321280 CTGCAAATGATGTGCCTTG
65 CTGCAAATGATATGCCTTG
* * * * *
1321299 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTT-TTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCA-ACTTAAGTTATG
* * *
1321363 CTGTAAATGATGTGCCCTCG
65 CTGCAAATGATATG-CCTTG
* * * * ** * * *
1321383 AAGCTGAGTGTAATTGAACTCGGGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
*
1321445 TGCAAATGATGTGCCGTT-
66 TGCAAATGATATGCC-TTG
* *
1321463 GAGCTGAGCATAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATG
* * * *
1321528 CTGCAAATGGTGTTCCCTCG
65 CTGCAAATGAT-ATGCCTTG
* * * ** * * * * *
1321548 AAGCTGAGTGTAATCGAACTCGGGGGTC--T-TTGGCAGATAGCTCTTCTCGACTTAAGCTATAC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
1321610 TGCAAATGATATGCCTTG
66 TGCAAATGATATGCCTTG
* * ** *
1321628 GAGCTGAGCCTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCT-AACCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCAA-CTTAAGTTAT
* * *
1321692 GTTGTAAATGATATGCTTTG
64 GCTGCAAATGATATGCCTTG
* * ** * * * *
1321712 GAGCTGAGCGTAGTCGAACTAGAAGGTCTTTTGGTCACATATAACTCTTCT-AGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCA-ACTTAAGTTAT
* * * *
1321776 GATGTAAATGATGTGCCCTCG
64 GCTGCAAATGATATG-CCTTG
* * * * ** * * * *
1321797 AAGCTGAGTGTAATCGAGCTCGGGGGTC--T-TTGGCAGATAGCCCTTCTCGATTTAAGCTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
*
1321859 TGCAAATGGTATGCCGTT-
66 TGCAAATGATATGCC-TTG
* *
1321877 GAGCTGAGCGTAGTCGAACTC-AAGGGTCTTTTGTTGGCAGACAACCCTTCT-AGACTTAAGTTG
1 GAGCTGAGCGTAGTCGAACTCGAA-GGTC-TTTGTTGGCAGATAACCCTTCTCA-ACTTAAGTTA
*
1321940 TGCTGCAAATGATATGCCTTA
63 TGCTGCAAATGATATGCCTTG
* ** * *
1321961 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGATAGATAACCCTTCT-AGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCA-ACTTAAGTTATG
* * * **
1322025 TTGTAAATAATATGCCCTCA
65 CTGCAAATGATATG-CCTTG
* * * ** * *
1322045 AAGCTGAGTGTAATCGAACTCGGGGGTC--T-TTGGCAGATAACCCTTCTCGACTTAAGCTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
1322107 TGCAAATGATATGCCTTG
66 TGCAAATGATATGCCTTG
* * *
1322125 GAGCTGAGCATAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGATTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCAACTTAAGTTATG
1322190 CTGCAAATGATATGCCTTG
65 CTGCAAATGATATGCCTTG
* * *
1322209 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
1322259 TGCCTTGAGC
Statistics
Matches: 766, Mismatches: 161, Indels: 67
0.77 0.16 0.07
Matches are distributed among these distances:
80 98 0.13
81 140 0.18
82 8 0.01
83 97 0.13
84 372 0.49
85 51 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (83 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
TGCAAATGATATGCCTTG
Found at i:1321585 original size:165 final size:164
Alignment explanation
Indices: 1321251--1322281 Score: 1052
Period size: 165 Copynumber: 6.2 Consensus size: 164
1321241 TCTTCAGTTA
* * *
1321251 GCAGATAACCCTTCTCAACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
* * * * * *
1321316 ACTCGAAGGTCTTTGGTGACAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGATGTGCCCT
66 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCCT
*
1321381 CGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTG
131 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
* * *
1321415 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCATAGTCG
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCG
* * * * *
1321479 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGGTGTTCC
65 AACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
1321544 CTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
129 CTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
* * * *
1321580 GCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCCTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
* * * * *
1321645 ACTCGAAGGTCTTTTGGTCACAGATAACCCTTCT-AACCTTGAGTTATGTTGTAAATGATATG-C
66 ACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTCGA-CTTAAGTTATGCTGCAAATGATATGCC
* * * * * * **
1321708 TTTGGAGCTGAGCGTAGTCGAACTAGAAGGTCTTTTG
129 CTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTG
* * * * * * * * * * * * *
1321745 GTCACATATAACTCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 G---CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
* ** * * * *
1321810 TCGAGCTCGGGGGTCTTT-G-G-CAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATGGTATG
62 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
* * * * **
1321872 CCGTTG-AGCTGAGCGTAGTCGAACTCAAGGGTCTTTTGTTG
127 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC---T-TTG
* * * * *
1321913 GCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
* * * * * * *
1321978 ACTCGAAGGTCTTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATATGCCCT
66 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCCT
*
1322043 CAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
131 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
*
1322077 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
* * *
1322142 ACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATG-CC
66 ACTCGAAGGTCTTT-GGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCC
* * * * **
1322206 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
130 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G
* * * * *
1322242 TGACAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATG
1 -G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
1322282 TTAAAAAAAT
Statistics
Matches: 715, Mismatches: 130, Indels: 41
0.81 0.15 0.05
Matches are distributed among these distances:
164 230 0.32
165 322 0.45
166 7 0.01
167 69 0.10
168 62 0.09
169 25 0.03
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (164 bp):
GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCCT
CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
Found at i:1322105 original size:248 final size:249
Alignment explanation
Indices: 1321412--1322281 Score: 1230
Period size: 249 Copynumber: 3.5 Consensus size: 249
1321402 TCGGGGGTCT
* * * * *
1321412 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCATAG
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAG
* * * * * * *
1321476 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGGTGT
65 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGT
* *
1321541 TCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCT
130 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* *
1321606 ATACTGCAAATGATATGCCTTGGAGCTGAGCCTAGTCGAACTCGAAGGTCTTTTG
195 ATGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTG
* ** * * * *
1321661 GTCACAGATAACCCTTCTA-ACCTTGAGTTATGTTGTAAATGATATGCTTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTAGA-CTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* * * * * *
1321725 TCGAACTAGAAGGTCTTTTGGTCACATATAACTCTTCTAGCCTTGAGTTATGATGTAAATGATGT
65 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGT
* *
1321790 GCCCTCGAAGCTGAGTGTAATCGAGCTCGGGGGTCTTTGGCAGATAGCCCTTCTCGATTTAAGCT
130 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* *
1321855 ATGCTGCAAATGGTATGCCGTT-GAGCTGAGCGTAGTCGAACTC-AAGGGTCTTTTG
195 ATGCTGCAAATGATATGCC-TTGGAGCTGAGCATAGTCGAACTCGAA-GGTCTTTTG
* * *
1321910 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * * *
1321975 CGAACTCGAAGGTC-TTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATATG
66 CGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTG
* *
1322039 CCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
*
1322104 TGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTAG
196 TGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTG
* *
1322158 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * *
1322223 CGAACTCGAAGGTC-TTTGGTGACAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATG
66 CGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATG
1322282 TTAAAAAAAT
Statistics
Matches: 547, Mismatches: 67, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
247 2 0.00
248 267 0.49
249 275 0.50
250 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (249 bp):
TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTG
CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
TGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTG
Found at i:1325250 original size:21 final size:21
Alignment explanation
Indices: 1325224--1325268 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1325214 GATTTCTGGG
* *
1325224 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1325245 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1325266 CAA
1 CAA
1325269 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1327014 original size:23 final size:22
Alignment explanation
Indices: 1326955--1327021 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1326945 TATGGACATC
*
1326955 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1326977 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1326999 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
1327022 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:1327229 original size:16 final size:17
Alignment explanation
Indices: 1327210--1327242 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1327200 TATATGATAC
1327210 ATGTGAATG-ATGAATT
1 ATGTGAATGTATGAATT
*
1327226 ATGTGTATGTATGAATT
1 ATGTGAATGTATGAATT
1327243 TACTGCGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (17 bp):
ATGTGAATGTATGAATT
Found at i:1330056 original size:21 final size:21
Alignment explanation
Indices: 1330030--1330074 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1330020 TATTTCTGGG
* *
1330030 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1330051 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1330072 CAA
1 CAA
1330075 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1331797 original size:23 final size:22
Alignment explanation
Indices: 1331738--1331804 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1331728 TATGGACATC
*
1331738 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1331760 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1331782 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
1331805 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:1336796 original size:3 final size:3
Alignment explanation
Indices: 1336790--1336860 Score: 67
Period size: 3 Copynumber: 23.3 Consensus size: 3
1336780 AAATAAGAAA
*
1336790 AAT AAT AATT AA- AAG AAT AAT AAT AAT AAT AAT AAT AA- AAT -AT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1336833 AAT AAAT AAT ATAT AAT ATAT AAA AAT A
1 AAT -AAT AAT A-AT AAT A-AT AAT AAT A
1336861 TTTTCAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.10
3 40 0.69
4 12 0.21
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1336796 original size:12 final size:12
Alignment explanation
Indices: 1336758--1336837 Score: 52
Period size: 12 Copynumber: 6.1 Consensus size: 12
1336748 ACCCTAGACC
*
1336758 AGAAAAATAAAA
1 AGAAAAATAATA
1336770 AGAAAAAAATAAATA
1 AG--AAAAAT-AATA
1336785 AGAAAAATAATA
1 AGAAAAATAATA
*
1336797 ATTAAAAGAATAATA
1 A--GAAA-AATAATA
* *
1336812 ATAATAATAATA
1 AGAAAAATAATA
*
1336824 ATAAAATATAATA
1 AGAAAA-ATAATA
1336837 A
1 A
1336838 ATAATATATA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
12 19 0.34
13 15 0.27
14 9 0.16
15 13 0.23
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (12 bp):
AGAAAAATAATA
Found at i:1336858 original size:29 final size:29
Alignment explanation
Indices: 1336806--1336885 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
1336796 AATTAAAAGA
1336806 ATAAT-AATAATA-ATAATA-AT-AAAAT
1 ATAATAAATAATATATAATATATAAAAAT
1336831 ATAATAAATAATATATAATATATAAAAAT
1 ATAATAAATAATATATAATATATAAAAAT
** *
1336860 ATTTTCAAAAAACTATATAATATATA
1 ATAAT-AAATAA-TATATAATATATA
1336886 TTTTTTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 5 0.11
26 7 0.15
27 6 0.13
28 2 0.04
29 8 0.17
30 5 0.11
31 13 0.28
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
ATAATAAATAATATATAATATATAAAAAT
Found at i:1336883 original size:36 final size:36
Alignment explanation
Indices: 1336843--1337141 Score: 142
Period size: 36 Copynumber: 8.2 Consensus size: 36
1336833 AATAAATAAT
*
1336843 ATATAATATATAAAAATATTTTCAAAAAACTATATA
1 ATATAATATTTAAAAATATTTTCAAAAAACTATATA
* * *
1336879 ATATATATTTTTTAAAATA-TTTAAAAAAACTATATA
1 ATATA-ATATTTAAAAATATTTTCAAAAAACTATATA
* * *
1336915 TTAT-ATATTTAAAAATATTTTCAAAATTA-TATATT
1 ATATAATATTTAAAAATATTTTCAAAA-AACTATATA
* * *
1336950 ATATAAT-TTTCAAAAATGTTTT-AAAATTA-TATATT
1 ATATAATATTT-AAAAATATTTTCAAAA-AACTATATA
* * ***
1336985 ATATAAATGTTTTAAAAATGTTTT-TTTAAA-TATAT-
1 ATAT-AAT-ATTTAAAAATATTTTCAAAAAACTATATA
* * *
1337020 ATATTATATTCAAAAATGTTTT---AAAACTATATA
1 ATATAATATTTAAAAATATTTTCAAAAAACTATATA
* *
1337053 TTATATAAATGTTTTAAAAATGA-TTTCAAAACTA-TATATTA
1 --ATAT-AAT-ATTTAAAAAT-ATTTTCAAAA-AACTATA-TA
* *
1337094 TATATATATATATTCAAAATGTTTTC-AAAAACTATATA
1 -ATATA-ATAT-TTAAAAATATTTTCAAAAAACTATATA
1337132 ATATATATAT
1 ATATA-ATAT
1337142 ATATATATAT
Statistics
Matches: 210, Mismatches: 29, Indels: 47
0.73 0.10 0.16
Matches are distributed among these distances:
31 3 0.01
32 5 0.02
33 13 0.06
34 13 0.06
35 43 0.20
36 48 0.23
37 43 0.20
38 6 0.03
39 9 0.04
40 24 0.11
41 3 0.01
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.45
Consensus pattern (36 bp):
ATATAATATTTAAAAATATTTTCAAAAAACTATATA
Found at i:1336945 original size:24 final size:24
Alignment explanation
Indices: 1336914--1336964 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
1336904 AAAACTATAT
1336914 ATTATATATTTAAAAATATTTTCAAA
1 ATTATATA-TTAAAAA-ATTTTCAAA
* *
1336940 ATTATATATTATATAATTTTCAAA
1 ATTATATATTAAAAAATTTTCAAA
1336964 A
1 A
1336965 ATGTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 5 0.22
26 8 0.35
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTATATATTAAAAAATTTTCAAA
Found at i:1336948 original size:71 final size:68
Alignment explanation
Indices: 1336841--1336989 Score: 169
Period size: 71 Copynumber: 2.2 Consensus size: 68
1336831 ATAATAAATA
**
1336841 ATATA-TA-ATATATAAAAATATTTTCAAAAAACTATATAATATATATTTTTTAAAATATTTAAA
1 ATATATTATATATATAAAAATATTTTCAAAAAACTATATAATATA-ATTTTCAAAAATATTT--A
1336904 AAAACT
63 AAAACT
* * * * *
1336910 ATATATTATATATTTAAAAATATTTTCAAAATTA-TATATTATATAATTTTCAAAAATGTTTTAA
1 ATATATTATATATATAAAAATATTTTCAAAA-AACTATATAATATAATTTTCAAAAATATTTAAA
*
1336974 AATT
65 AACT
1336978 ATATATTATATA
1 ATATATTATATA
1336990 AATGTTTTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
68 17 0.25
69 5 0.07
70 15 0.22
71 31 0.45
72 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (68 bp):
ATATATTATATATATAAAAATATTTTCAAAAAACTATATAATATAATTTTCAAAAATATTTAAAA
ACT
Found at i:1336992 original size:26 final size:25
Alignment explanation
Indices: 1336963--1337071 Score: 86
Period size: 26 Copynumber: 4.5 Consensus size: 25
1336953 TAATTTTCAA
1336963 AAATGTTTTAAAATTATATATTATAT
1 AAATGTTTTAAAATTATAT-TTATAT
* * *
1336989 AAATGTTTTAAAA--ATGTTTTTTT
1 AAATGTTTTAAAATTATATTTATAT
* * * *
1337012 AAAT-ATAT-ATATTATATTCA-A-
1 AAATGTTTTAAAATTATATTTATAT
*
1337033 AAATGTTTTAAAACTATATATTATAT
1 AAATGTTTTAAAATTATAT-TTATAT
1337059 AAATGTTTTAAAA
1 AAATGTTTTAAAA
1337072 ATGATTTCAA
Statistics
Matches: 61, Mismatches: 15, Indels: 14
0.68 0.17 0.16
Matches are distributed among these distances:
21 6 0.10
22 4 0.07
23 19 0.31
24 5 0.08
25 1 0.02
26 26 0.43
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
AAATGTTTTAAAATTATATTTATAT
Found at i:1337089 original size:70 final size:71
Alignment explanation
Indices: 1336904--1337100 Score: 248
Period size: 70 Copynumber: 2.8 Consensus size: 71
1336894 AATATTTAAA
*
1336904 AAAACTATATATTATAT--A---TTTAAAAAT-ATTTTCAAAATTATATATTATATAATTTTCAA
1 AAAACTATATATTATATAAATGTTTTAAAAATGA-TTTCAAAA-TATATATTATAT-ATATTCAA
1336963 AAATGTTTT
63 AAATGTTTT
* * **
1336972 AAAATTATATATTATATAAATGTTTTAAAAATGTTTTTTTAAATATATA-TAT-TATATTCAAAA
1 AAAACTATATATTATATAAATGTTTTAAAAATG-ATTTCAAAATATATATTATATATATTCAAAA
1337035 ATGTTTT
65 ATGTTTT
1337042 AAAACTATATATTATATAAATGTTTTAAAAATGATTTCAAAACTATATATTATATATAT
1 AAAACTATATATTATATAAATGTTTTAAAAATGATTTCAAAA-TATATATTATATATAT
1337101 ATATATTCAA
Statistics
Matches: 110, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
68 16 0.15
69 6 0.05
70 55 0.50
71 4 0.04
72 8 0.07
73 15 0.14
74 6 0.05
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (71 bp):
AAAACTATATATTATATAAATGTTTTAAAAATGATTTCAAAATATATATTATATATATTCAAAAA
TGTTTT
Found at i:1337137 original size:2 final size:2
Alignment explanation
Indices: 1337126--1337157 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1337116 TTTCAAAAAC
1337126 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1337158 TTTAAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.