Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 27
Found at i:3207083 original size:14 final size:14
Alignment explanation
Indices: 3207045--3207084 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3207035 ATAGTTAGAT
* *
3207045 TAAAAATTATATCA
1 TAAAAATTATTTAA
*
3207059 TACAAATTATTTAA
1 TAAAAATTATTTAA
3207073 TAAAAATTATTT
1 TAAAAATTATTT
3207085 TATATTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAAATTATTTAA
Found at i:3214665 original size:2 final size:2
Alignment explanation
Indices: 3214658--3214682 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3214648 AAAGAAGGAA
3214658 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
3214683 GAGAGAGAGA
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:3214687 original size:2 final size:2
Alignment explanation
Indices: 3214682--3214715 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3214672 ATATATATAT
3214682 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3214716 GGGGGATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3216255 original size:28 final size:28
Alignment explanation
Indices: 3216223--3216282 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
3216213 GTGATGATCT
3216223 GCGTCTTACCCCACGTAACGCCACATCA
1 GCGTCTTACCCCACGTAACGCCACATCA
*
3216251 GCGTCTTACCCCACGTGACGCCACATCA
1 GCGTCTTACCCCACGTAACGCCACATCA
3216279 GCGT
1 GCGT
3216283 AAAGCGCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.42, G:0.18, T:0.18
Consensus pattern (28 bp):
GCGTCTTACCCCACGTAACGCCACATCA
Found at i:3217956 original size:84 final size:87
Alignment explanation
Indices: 3217866--3218053 Score: 274
Period size: 84 Copynumber: 2.2 Consensus size: 87
3217856 ATATAATTTC
* * *
3217866 TAAAATAATATCATAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAGCAA
1 TAAAATAATATCCTAAATCATAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAA
*
3217931 ATATAAGAT-AAA-ATA-TATT
66 AGATAAGATAAAATATATTATT
* * * * *
3217950 TAAAATAATATCCTAAATCATAATTAAAATATTTAAAACTATTTAAACTAAAATATCTAAAATAG
1 TAAAATAATATCCTAAATCATAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAA
3218015 AGATAAGATAAAATATATTATT
66 AGATAAGATAAAATATATTATT
3218037 TAAAATAATATCCTAAA
1 TAAAATAATATCCTAAA
3218054 ACATGAGTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
84 65 0.71
85 3 0.03
86 3 0.03
87 21 0.23
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.32
Consensus pattern (87 bp):
TAAAATAATATCCTAAATCATAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAA
AGATAAGATAAAATATATTATT
Found at i:3219016 original size:18 final size:18
Alignment explanation
Indices: 3218993--3219034 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3218983 AACATCTTTG
*
3218993 TTTTTTTTAAACAATGGT
1 TTTTTTTTAAACAATGAT
*
3219011 TTTTTTTTAAACAGTGAT
1 TTTTTTTTAAACAATGAT
3219029 TTTTTT
1 TTTTTT
3219035 CATTTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.62
Consensus pattern (18 bp):
TTTTTTTTAAACAATGAT
Found at i:3221543 original size:21 final size:20
Alignment explanation
Indices: 3221495--3221543 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3221485 TTTTAAGATT
* *
3221495 TTTATATGTTAAAATTAATT
1 TTTATATTTTAAAATTAATA
* *
3221515 TTTTTATTTTATAAATTTATA
1 TTTATATTTTA-AAATTAATA
3221536 TTTATATT
1 TTTATATT
3221544 AATTATTAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTATATTTTAAAATTAATA
Found at i:3221610 original size:28 final size:28
Alignment explanation
Indices: 3221578--3221686 Score: 110
Period size: 29 Copynumber: 3.8 Consensus size: 28
3221568 TTAATTTATT
* * *
3221578 AAATATGTTTTATTTTTACTTTAACTGA
1 AAATATATTTTATTTTTATTTTAACTAA
* *
3221606 AAATATATTTTAGTATTATTTTAAACTAA
1 AAATATATTTTATTTTTATTTT-AACTAA
* * *
3221635 AAATATATTTGAATTTTATTTTAAGTCAA
1 AAATATATTTTATTTTTATTTTAACT-AA
* *
3221664 AAATATATTTTATTCTTAATTTA
1 AAATATATTTTATTTTTATTTTA
3221687 GCCTGTTAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
28 21 0.32
29 45 0.68
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (28 bp):
AAATATATTTTATTTTTATTTTAACTAA
Found at i:3222096 original size:15 final size:16
Alignment explanation
Indices: 3222065--3222100 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3222055 GCCACCATCT
3222065 AATAAAGTAAAAATAA
1 AATAAAGTAAAAATAA
*
3222081 AATAAA-TAAAATTAA
1 AATAAAGTAAAAATAA
3222096 AATAA
1 AATAA
3222101 CTTTCAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (16 bp):
AATAAAGTAAAAATAA
Found at i:3224289 original size:9 final size:10
Alignment explanation
Indices: 3224268--3224301 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
3224258 TTCTTGAATC
3224268 AAAATATTAA
1 AAAATATTAA
3224278 AAAATATTAA
1 AAAATATTAA
3224288 AAAATATTAA
1 AAAATATTAA
3224298 AAAA
1 AAAA
3224302 AAGAGACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATATTAA
Found at i:3225235 original size:17 final size:15
Alignment explanation
Indices: 3225198--3225248 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3225188 AAAAATATTG
* *
3225198 ATAATATATTTTTTA
1 ATAAAATATTTTGTA
3225213 ATAAAATATTTTGTA
1 ATAAAATATTTTGTA
*
3225228 TATAAAAATATTAT-TA
1 -AT-AAAATATTTTGTA
3225244 ATAAA
1 ATAAA
3225249 CTATCTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 3 0.10
15 15 0.48
16 4 0.13
17 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
ATAAAATATTTTGTA
Found at i:3228250 original size:2 final size:2
Alignment explanation
Indices: 3228245--3228269 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3228235 TCACACAATG
3228245 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3228270 TATCTATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3230657 original size:17 final size:17
Alignment explanation
Indices: 3230611--3230657 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
3230601 TTGAGATAGT
*
3230611 TTTTGGGATACACCGAA
1 TTTTGGGATACATCGAA
*
3230628 TTTTGGGATACATCGAG
1 TTTTGGGATACATCGAA
3230645 TTTTGGGATACAT
1 TTTTGGGATACAT
3230658 GTGATATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (17 bp):
TTTTGGGATACATCGAA
Found at i:3231367 original size:16 final size:17
Alignment explanation
Indices: 3231346--3231378 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3231336 TCCTATATAG
3231346 AATAT-AAAAATGATTA
1 AATATAAAAAATGATTA
3231362 AATATAAAAAATGATTA
1 AATATAAAAAATGATTA
3231379 TTTTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
AATATAAAAAATGATTA
Found at i:3231399 original size:16 final size:17
Alignment explanation
Indices: 3231378--3231419 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
3231368 AAAAATGATT
3231378 ATTTTTTAAT-TTTAAA
1 ATTTTTTAATATTTAAA
3231394 A-TTTTTAATATTTAAA
1 ATTTTTTAATATTTAAA
*
3231410 TTTATTTTAA
1 ATT-TTTTAA
3231420 GAAAAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 7 0.32
17 1 0.05
18 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTTAATATTTAAA
Found at i:3231400 original size:15 final size:16
Alignment explanation
Indices: 3231380--3231409 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3231370 AAATGATTAT
3231380 TTTTTAAT-TTTAAAA
1 TTTTTAATATTTAAAA
3231395 TTTTTAATATTTAAA
1 TTTTTAATATTTAAA
3231410 TTTATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTAATATTTAAAA
Found at i:3234121 original size:187 final size:188
Alignment explanation
Indices: 3233806--3234180 Score: 743
Period size: 187 Copynumber: 2.0 Consensus size: 188
3233796 GAAGCTGAGG
3233806 AAGAAAGCAGAGACGCTGAGCCAGTAGAATCAAGCACTGTTGGCTCAGCTGAAGCAGAATCTCTC
1 AAGAAAGCAGAGACGCTGAGCCAGTAGAATCAAGCACTGTTGGCTCAGCTGAAGCAGAATCTCTC
3233871 CAATGCAAATAACTCAAAATTCAGCAAATGCGATTCAGTTTTAACCCAAATCCTCCCGCTTCTAG
66 CAATGCAAATAACTCAAAATTCAGCAAATGCGATTCAGTTTTAACCCAAATCCTCCCGCTTCTAG
3233936 TAATTCCTCATCCGAATTGGCAAATTAAATTCATTTTGGGTTCTG-ATTTGTTTAAAA
131 TAATTCCTCATCCGAATTGGCAAATTAAATTCATTTTGGGTTCTGAATTTGTTTAAAA
3233993 AAGAAAGCAGAGACGCTGAGCCAGTAGAATCAAGCACTGTTGGCTCAGCTGAAGCAGAATCTCTC
1 AAGAAAGCAGAGACGCTGAGCCAGTAGAATCAAGCACTGTTGGCTCAGCTGAAGCAGAATCTCTC
3234058 CAATGCAAATAACTCAAAATTCAGCAAATGCGATTCAGTTTTAACCCAAATCCTCCCGCTTCTAG
66 CAATGCAAATAACTCAAAATTCAGCAAATGCGATTCAGTTTTAACCCAAATCCTCCCGCTTCTAG
3234123 TAATTCCTCATCCGAATTGGCAAATTAAATTCATTTTGGGTTCTGAATTTGTTTAAAA
131 TAATTCCTCATCCGAATTGGCAAATTAAATTCATTTTGGGTTCTGAATTTGTTTAAAA
3234181 TCTGTAGACA
Statistics
Matches: 187, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
187 175 0.94
188 12 0.06
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (188 bp):
AAGAAAGCAGAGACGCTGAGCCAGTAGAATCAAGCACTGTTGGCTCAGCTGAAGCAGAATCTCTC
CAATGCAAATAACTCAAAATTCAGCAAATGCGATTCAGTTTTAACCCAAATCCTCCCGCTTCTAG
TAATTCCTCATCCGAATTGGCAAATTAAATTCATTTTGGGTTCTGAATTTGTTTAAAA
Found at i:3234237 original size:2 final size:2
Alignment explanation
Indices: 3234230--3234263 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3234220 GTTTTCTTTC
3234230 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3234264 GTAGTAGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3234328 original size:37 final size:36
Alignment explanation
Indices: 3234277--3234522 Score: 115
Period size: 37 Copynumber: 6.4 Consensus size: 36
3234267 GTAGTACAGC
*
3234277 ATAATTTTTTGAAAATGCTTTTGAAATGATATAATAT
1 ATAA-TTTTTGAAAATGATTTTGAAATGATATAATAT
* * * *
3234314 ATAATTTTCAGAAAACGGTTTTTGAAAATGAATATATTAT
1 ATAATTTT-TGAAAA-TGATTTTG-AAATG-ATATAATAT
* *
3234354 ATAGTTTTTGAAAAT-ATTTTGGAAATATATATAATAT
1 ATAATTTTTGAAAATGATTTT-GAAAT-GATATAATAT
* * *
3234391 AT-AGTTTTAAAAACGATTTTTTGGAAAT-ATATAAATAT
1 ATAATTTTTGAAAATGA--TTTT-GAAATGATAT-AATAT
* *
3234429 ATTATATAGTTTTTAAAAT-ATTTTGAAAATAAATATATAATAT
1 A-TA-AT--TTTTGAAAATGATTTTG-AAAT---GATATAATAT
* ** *
3234472 ATAGTTTTTGAAAAACATTTTGAAAATATATATAATAT
1 ATAATTTTTGAAAATGATTTTG-AAAT-GATATAATAT
*
3234510 ATAGTTTTT-AAAA
1 ATAATTTTTGAAAA
3234523 CATTTTTGAA
Statistics
Matches: 168, Mismatches: 20, Indels: 42
0.73 0.09 0.18
Matches are distributed among these distances:
36 12 0.07
37 36 0.21
38 33 0.20
39 30 0.18
40 34 0.20
41 2 0.01
42 3 0.02
43 14 0.08
44 4 0.02
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (36 bp):
ATAATTTTTGAAAATGATTTTGAAATGATATAATAT
Found at i:3234467 original size:38 final size:36
Alignment explanation
Indices: 3234333--3234534 Score: 208
Period size: 38 Copynumber: 5.2 Consensus size: 36
3234323 AGAAAACGGT
*
3234333 TTTTGAAAATGA-ATATATTATATAGTTTTTGAAAATA
1 TTTTGAAAAT-ATATATAATATATAGTTTTT-AAAATA
* * *
3234370 TTTTGGAAATATATATAATATATAGTTTTAAAAACGATT
1 TTTTGAAAATATATATAATATATAGTTTT-TAAA--ATA
*
3234409 TTTTGGAAATATATAAATATATTATATAGTTTTTAAAATA
1 TTTT-GAAA-ATAT--ATATAATATATAGTTTTTAAAATA
*
3234449 TTTTGAAAATAAATATATAATATATAGTTTTTGAAAAACA
1 TTTTGAAAAT--ATATATAATATATAGTTTTT--AAAATA
*
3234489 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAATA
3234525 TTTTTGAAAA
1 -TTTTGAAAA
3234535 CGTAGTTTGT
Statistics
Matches: 142, Mismatches: 10, Indels: 26
0.80 0.06 0.15
Matches are distributed among these distances:
36 7 0.05
37 37 0.26
38 39 0.27
39 10 0.07
40 26 0.18
41 4 0.03
42 3 0.02
43 16 0.11
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAATA
Found at i:3235331 original size:21 final size:20
Alignment explanation
Indices: 3235297--3235335 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3235287 TATTTTTAAA
3235297 AACATTTTTGAAAACTCATAT
1 AACATTTTTGAAAA-TCATAT
3235318 AACA-TTTTGTAAAATCAT
1 AACATTTTTG-AAAATCAT
3235336 TTTGAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (20 bp):
AACATTTTTGAAAATCATAT
Found at i:3235344 original size:155 final size:155
Alignment explanation
Indices: 3235036--3235310 Score: 352
Period size: 155 Copynumber: 1.8 Consensus size: 155
3235026 AGAAAACGGT
* *
3235036 TTTTGAAAATGAATATATTATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTTT
1 TTTTGAAAATGAATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTT
* *
3235101 TAAAAACGATTTTTTGGAAATATATAAATATATTATATAGTTTTAAAATATTTTGAAAATAAATA
66 TAAAAACGATTTTTTGGAAATATATAAATATAATATATAGTTTTAAAACATTTTGAAAATAAATA
* * *
3235166 TATAATATATAGTTTTTGAAAAACA
131 CATAATATAAAATTTTTGAAAAACA
3235191 TTTTGAAAAT-ATATATAATATATAGTTTTTAAAACAT-TTTTGAAAACT-TATATAATATATAG
1 TTTTGAAAATGA-ATATAATATATAGTTTTTAAAA-ATATTTTGAAAA-TATATATAATATATAG
* * *
3235253 TTTTAAAAA-TA-TTTTT-GAAA-A-AT-TATATAATATATATTTTTAAAAACATTTTTGAAAA
63 TTTTAAAAACGATTTTTTGGAAATATATAAATATAATATATAGTTTT-AAAACA-TTTTGAAAA
3235311 CTCATATAAC
Statistics
Matches: 108, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
149 15 0.14
150 7 0.06
151 10 0.09
152 4 0.04
153 5 0.05
154 2 0.02
155 62 0.57
156 3 0.03
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (155 bp):
TTTTGAAAATGAATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTT
TAAAAACGATTTTTTGGAAATATATAAATATAATATATAGTTTTAAAACATTTTGAAAATAAATA
CATAATATAAAATTTTTGAAAAACA
Found at i:3235387 original size:37 final size:36
Alignment explanation
Indices: 3235003--3235388 Score: 295
Period size: 37 Copynumber: 10.3 Consensus size: 36
3234993 AATGCTTTTG
* * *
3235003 AAATGATATAATATATAATTTTCAGAAAACGGTTTTTG-A
1 AAATAATATAATATATAGTTTT-A-AAAAC--ATTTTGAA
* * *
3235042 AAATGAATATATTATATAGTTTTTGAAAATATTTTG-A
1 AAAT-AATATAATATATAG-TTTTAAAAACATTTTGAA
3235079 AAATATATATAATATATAGTTTTAAAAACGATTTTTTGGAA
1 AAATA-ATATAATATATAGTTTTAAAAAC-A--TTTT-GAA
* *
3235120 ATATATAAATATATTATATAGTTTT-AAAATATTTTGAA
1 A-A-AT-AATATAATATATAGTTTTAAAAACATTTTGAA
*
3235158 AATAAATATATAATATATAGTTTTTGAAAAACATTTTG-A
1 AA-ATA-ATATAATATATAG-TTTT-AAAAACATTTTGAA
*
3235197 AAATATATATAATATATAGTTTTTAAAACATTTTTGAA
1 AAATA-ATATAATATATAGTTTTAAAAACA-TTTTGAA
* * *
3235235 AACTTATATAATATATAGTTTTAAAAATATTTTTGAA
1 AAATAATATAATATATAGTTTTAAAAACA-TTTTGAA
* *
3235272 AAATTATATAATATATATTTTTAAAAACATTTTTGAA
1 AAATAATATAATATATAGTTTTAAAAACA-TTTTGAA
* * * * *
3235309 AACTCATATAACAT-T--TTGTAAAATCATTTTGAA
1 AAATAATATAATATATAGTTTTAAAAACATTTTGAA
* *
3235342 AACT-ATATAATATATAGTTTTGGAAAA-ATTTTAGAA
1 AAATAATATAATATATAGTTTT-AAAAACATTTT-GAA
3235378 AAATAATATAA
1 AAATAATATAA
3235389 AGTTTAAAAA
Statistics
Matches: 291, Mismatches: 33, Indels: 48
0.78 0.09 0.13
Matches are distributed among these distances:
32 8 0.03
33 12 0.04
34 9 0.03
35 8 0.03
36 26 0.09
37 128 0.44
38 28 0.10
39 19 0.07
40 22 0.08
41 7 0.02
42 5 0.02
43 18 0.06
44 1 0.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (36 bp):
AAATAATATAATATATAGTTTTAAAAACATTTTGAA
Found at i:3235401 original size:69 final size:68
Alignment explanation
Indices: 3235184--3235425 Score: 204
Period size: 69 Copynumber: 3.4 Consensus size: 68
3235174 ATAGTTTTTG
* *
3235184 AAAAA-CATTTTGAAAATATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATAATA
1 AAAAATCATTTTGAAAA-CTATATAATATATAGTTTTAAAAACATTTTTG-AAA---A-ATAATA
* *
3235248 TATAGTTTT
60 TAAAGTTTA
* * * *
3235257 AAAAAT-ATTTTTGAAAAATTATATAATATATATTTTTAAAAACATTTTTGAAAACTCATATAAC
1 AAAAATCA-TTTTG-AAAACTATATAATATATAGTTTTAAAAACATTTTTGAAAAATAATATAA-
* *
3235321 ATTTTG
63 AGTTTA
* * *
3235327 TAAAATCATTTTGAAAACTATATAATATATAGTTTTGGAAAA-ATTTTAGAAAAATAATATAAAG
1 AAAAATCATTTTGAAAACTATATAATATATAGTTTT-AAAAACATTTTTGAAAAATAATATAAAG
3235391 TTTAA
65 TTT-A
** *
3235396 AAAAATGTTTTTG-AAACATATATATTATAT
1 AAAAATCATTTTGAAAAC-TATATAATATAT
3235426 TATTATTATT
Statistics
Matches: 140, Mismatches: 21, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
68 8 0.06
69 65 0.46
70 19 0.14
71 1 0.01
73 9 0.06
74 34 0.24
75 4 0.03
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (68 bp):
AAAAATCATTTTGAAAACTATATAATATATAGTTTTAAAAACATTTTTGAAAAATAATATAAAGT
TTA
Found at i:3235458 original size:16 final size:16
Alignment explanation
Indices: 3235418--3235461 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
3235408 GAAACATATA
3235418 TATTATATTATTATTAT
1 TATTAT-TTATTATTAT
**
3235435 TAGCATTTATTATTAT
1 TATTATTTATTATTAT
3235451 TATTATTTATT
1 TATTATTTATT
3235462 TACTTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTATTTATTATTAT
Found at i:3236653 original size:24 final size:25
Alignment explanation
Indices: 3236614--3236660 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3236604 TCTTTAATTT
3236614 ATTTTTATTCTATTTTCATTTATCA
1 ATTTTTATTCTATTTTCATTTATCA
3236639 ATTTTTATTCCT-TTTT-ATTTAT
1 ATTTTTATT-CTATTTTCATTTAT
3236661 TTTTTTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.29
25 13 0.62
26 2 0.10
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (25 bp):
ATTTTTATTCTATTTTCATTTATCA
Found at i:3236733 original size:12 final size:14
Alignment explanation
Indices: 3236718--3236798 Score: 85
Period size: 15 Copynumber: 5.6 Consensus size: 14
3236708 TTTTGATTTG
3236718 TTATT-TTATT-TT
1 TTATTATTATTATT
* *
3236730 TTATTTAATACTTGTT
1 TTA-TTATTA-TTATT
3236746 TTATTATTATTATT
1 TTATTATTATTATT
3236760 ATTATTATTATTATT
1 -TTATTATTATTATT
3236775 ATTATTATTATTATT
1 -TTATTATTATTATT
3236790 TCTATTATT
1 T-TATTATT
3236799 TATCTAACAT
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
12 3 0.05
13 2 0.03
14 7 0.12
15 43 0.72
16 5 0.08
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.69
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:3236754 original size:3 final size:3
Alignment explanation
Indices: 3236746--3236798 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
3236736 AATACTTGTT
3236746 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
3236794 TTA TT
1 TTA TT
3236799 TATCTAACAT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.02
3 46 0.96
4 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3242918 original size:29 final size:29
Alignment explanation
Indices: 3242842--3242921 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
3242832 ATATATAACT
* *
3242842 TTTTAAAA-TTACATTTTTAGTCCCTCACC
1 TTTTAAAACTTACA-TTTTAGTCCATCAAC
* * * *
3242871 TTTCAAAGCTTATACTTTAG-CCATCAAAC
1 TTTTAAAACTTACATTTTAGTCCATC-AAC
3242900 TTTTAAAACTTACATTTTAGTC
1 TTTTAAAACTTACATTTTAGTC
3242922 ACTAACCAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
28 4 0.11
29 29 0.76
30 5 0.13
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.42
Consensus pattern (29 bp):
TTTTAAAACTTACATTTTAGTCCATCAAC
Found at i:3243171 original size:14 final size:15
Alignment explanation
Indices: 3243154--3243189 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3243144 TTATTAAAAA
3243154 TATTTTT-ATTCTTT
1 TATTTTTAATTCTTT
*
3243168 TATTTTTAATTTTTT
1 TATTTTTAATTCTTT
3243183 TATTTTT
1 TATTTTT
3243190 TTAAAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (15 bp):
TATTTTTAATTCTTT
Found at i:3264507 original size:67 final size:67
Alignment explanation
Indices: 3264394--3264535 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 67
3264384 GGAGAGGTAA
* * * * * *
3264394 GATAATTGTAACTGCATACAGAATTGTGTTAGATGAAACACGATAATTGAGGTAGAATATGACGA
1 GATAATTGTAACTACATACAGAATTGCGTTAAATGAAACACAATAATTGAAGTAGAACATGACGA
3264459 TT
66 TT
* * *
3264461 GATAATTGTAATTATATACGGAATTGCGTTAAATGAAACACAATAATTGAAGTAGAACATGACGA
1 GATAATTGTAACTACATACAGAATTGCGTTAAATGAAACACAATAATTGAAGTAGAACATGACGA
3264526 TT
66 TT
3264528 GATAATTG
1 GATAATTG
3264536 GAAGCATGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.30
Consensus pattern (67 bp):
GATAATTGTAACTACATACAGAATTGCGTTAAATGAAACACAATAATTGAAGTAGAACATGACGA
TT
Found at i:3277976 original size:64 final size:65
Alignment explanation
Indices: 3277865--3277987 Score: 153
Period size: 64 Copynumber: 1.9 Consensus size: 65
3277855 GATTGTGGAT
* * *
3277865 CCGAACTCGACCTGCATCCGACCTGAGAACGACCTGAACCCGAATTGAACTGA-AAATATGATAC
1 CCGAACCCGAACTGCATCCGACCTGAGAACGACCCGAACCCGAATTGAACTGATAAATATGATAC
* * *
3277929 CCGAACCCGAACTGCATCCGA-CTGA-TATGAACCCGAACCCGAGATTGACCTGATAAATA
1 CCGAACCCGAACTGCATCCGACCTGAGAACG-ACCCGAACCCGA-ATTGAACTGATAAATA
3277988 ACTGGTATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
62 2 0.04
63 15 0.30
64 28 0.56
65 5 0.10
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (65 bp):
CCGAACCCGAACTGCATCCGACCTGAGAACGACCCGAACCCGAATTGAACTGATAAATATGATAC
Found at i:3278022 original size:16 final size:16
Alignment explanation
Indices: 3278001--3278087 Score: 102
Period size: 16 Copynumber: 5.4 Consensus size: 16
3277991 GGTATTACCC
3278001 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
3278017 GACCTGTTTTCAACAT
1 GACCTGTTTTCAACCT
* * *
3278033 GACTTGTTTTTAACAT
1 GACCTGTTTTCAACCT
* *
3278049 GACTTGTTTTCAATCT
1 GACCTGTTTTCAACCT
* *
3278065 GACATGTTTTTAACCT
1 GACCTGTTTTCAACCT
3278081 GACCTGT
1 GACCTGT
3278088 AAATGATCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 61 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:3278057 original size:32 final size:32
Alignment explanation
Indices: 3278005--3278087 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
3277995 TTACCCGACC
* *
3278005 TGTTTTCAACCTGACCTGTTTTCAA-CATGACT
1 TGTTTTTAACCTGACCTGTTTTCAATC-TGACA
* *
3278037 TGTTTTTAACATGACTTGTTTTCAATCTGACA
1 TGTTTTTAACCTGACCTGTTTTCAATCTGACA
3278069 TGTTTTTAACCTGACCTGT
1 TGTTTTTAACCTGACCTGT
3278088 AAATGATCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
32 43 0.98
33 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (32 bp):
TGTTTTTAACCTGACCTGTTTTCAATCTGACA
Found at i:3278371 original size:14 final size:14
Alignment explanation
Indices: 3278349--3278395 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
3278339 TGCAAAGGAA
*
3278349 AATTAATATAGTTT
1 AATTTATATAGTTT
3278363 AATTTATATA----
1 AATTTATATAGTTT
3278373 AA-TTATATAGTTT
1 AATTTATATAGTTT
3278386 AATTTATATA
1 AATTTATATA
3278396 ATGACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:3278382 original size:23 final size:24
Alignment explanation
Indices: 3278348--3278396 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
3278338 ATGCAAAGGA
3278348 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
3278372 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
3278395 AA
1 AA
3278397 TGACAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:3278711 original size:15 final size:15
Alignment explanation
Indices: 3278691--3278727 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
3278681 TAATTTACTT
3278691 TATATAGTTTATATA
1 TATATAGTTTATATA
3278706 TATATAGTTTATATA
1 TATATAGTTTATATA
3278721 TACTATA
1 TA-TATA
3278728 CATGGTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:3278763 original size:13 final size:13
Alignment explanation
Indices: 3278747--3278773 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3278737 TACATATTAT
3278747 ATAAAATTATTTA
1 ATAAAATTATTTA
3278760 ATAAAATTATTTA
1 ATAAAATTATTTA
3278773 A
1 A
3278774 ATGTAAATTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:3278783 original size:15 final size:14
Alignment explanation
Indices: 3278747--3278789 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
3278737 TACATATTAT
3278747 ATAAAATTATTT-A
1 ATAAAATTATTTAA
3278760 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
3278774 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
3278789 A
1 A
3278790 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:3279292 original size:14 final size:13
Alignment explanation
Indices: 3279276--3279300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3279266 ACATATTATA
3279276 AAAATTATTTAAT
1 AAAATTATTTAAT
3279289 AAAATTATTTAA
1 AAAATTATTTAA
3279301 ATGTAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTATTTAAT
Found at i:3279637 original size:21 final size:20
Alignment explanation
Indices: 3279608--3279687 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 20
3279598 TCCATTTACA
3279608 TTAGGGTTTATGATTTAGTAT
1 TTAGGGTTTATGATTTA-TAT
* * * *
3279629 TTAGTGTTTGTGGTTTAAAGT
1 TTAGGGTTTATGATTTATA-T
*
3279650 TTAGGGTTTATGGTTTATGAT
1 TTAGGGTTTATGATTTAT-AT
*
3279671 TTAAGGTTTATGATTTA
1 TTAGGGTTTATGATTTA
3279688 AGGTTTATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (20 bp):
TTAGGGTTTATGATTTATAT
Found at i:3279665 original size:14 final size:14
Alignment explanation
Indices: 3279642--3279695 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
3279632 GTGTTTGTGG
* * *
3279642 TTTAAAGTTTAGGG
1 TTTAAGGTTTATGA
*
3279656 TTTATGGTTTATGA
1 TTTAAGGTTTATGA
3279670 TTTAAGGTTTATGA
1 TTTAAGGTTTATGA
3279684 TTTAAGGTTTAT
1 TTTAAGGTTTAT
3279696 ATAAACTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (14 bp):
TTTAAGGTTTATGA
Found at i:3279780 original size:2 final size:2
Alignment explanation
Indices: 3279775--3279859 Score: 136
Period size: 2 Copynumber: 42.0 Consensus size: 2
3279765 TTATATAGTT
3279775 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3279816 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
3279860 CATGGTTTAT
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 1 0.01
2 74 0.95
3 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3280169 original size:610 final size:592
Alignment explanation
Indices: 3279227--3280384 Score: 1853
Period size: 610 Copynumber: 1.9 Consensus size: 592
3279217 CTTTATAGTT
3279227 TATATATATAGTTTTATATACTATACATGGTTTATACATACATATTATAAAAATTATTTAATAAA
1 TATATATATAGTTTTATATACTATACATGGTTTATACATACATATTATAAAAATTATTTAATAAA
3279292 ATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATT
66 ATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATT
* *
3279357 GCATATTATATGGTTCATAAATAGTAGTTCATGTCATATTAATTTAAATTGCATAATTTGTATTT
131 GCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAAATT-CACAATTTGTATTT
*
3279422 TAGTTGCATGTTAGGTTAATTCACATTAATGTCTCATTTATTTTGTTGTTATGAATAAGTAATAA
195 TAGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAA
* *
3279487 TAAAACCAAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACATTAGTTTACATAGGCCTA
260 TAAAACCAAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACATTAGGTTACATAGGCCCA
* *
3279552 GTGCAAGCCCACTCTTTTATTACAAATATATATGCAATAGTGCTAGTCCATTTACATTAGGGTTT
325 ATGCAAGCCCACTCTTTTATTACAAATATATATGCAATAGTGCTAGTCCATTTAAATTAGGGTTT
* * ** *
3279617 ATGATTTAGTATTTAGTGTTTGTGGTTTAAAGTTTAGGGTTTATGGTTTATGATTTAAGGTTTAT
390 ATG-GTT--TA--T-G-GTTTATGGTTTAAAGTTTA-GAATTAGGGTTTATGATTT-A-G-----
* *
3279682 GATTTAAGGTTTATATAAACTATATATTTTACTACTTTATATAGTTTATGTATAGTGTTTCTATA
440 GATTTAAGGTTTATATAAACTATATATTTTACTACTTTATATAGTTTATGCATAGTATTTCTATA
3279747 AAC-TATAAGTAATTTACTTTATATAGTTTATATATATATATATATAATATATATATATATATAT
505 AACATATAAGTAATTTACTTTATATAGTTTATATATATATATATATAATATATATATATATATAT
3279811 ATATATATATATATATATATATA
570 ATATATATATATATATATATATA
3279834 TATATATATAGTTTATATATACTATACATGGTTTATACATACATATATATAAAATTATTTAATAA
1 TATATATATAGTTT-TATATACTATACATGGTTTATACATACATAT-TATAAAA--A-TT-AT--
3279899 AATTAATAAAATTATTTAAATGTAAATTATAT-AAACATGATTAATTAGGTGTTAAAT-ATTAGT
58 --TTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGT
3279962 ATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAAATT-ACAA
121 ATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAAATTCACAA
3280026 TTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAAT
186 TTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAAT
*
3280091 AAGTAAT-A-AAAACC-CAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACATTAGGTTAC
251 AAGTAATAATAAAACCAAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACATTAGGTTAC
*
3280153 ATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTAAA
316 ATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCAATAGTGCTAGTCCATTTAAA
3280218 TTAGGGTTTATGGTTTATGGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATGATTTAGGATTTA
381 TTAGGGTTTATGGTTTATGGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATGATTTAGGATTTA
* * *
3280283 GGGTTTTTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTATTTCTATAAACTAT
446 AGGTTTATATAAACTATATATTTTACTACTTTATATAGTTTATGCATAGTATTTCTATAAAC-AT
3280348 ATAAGTAATTTACTTTATATAGTTTATATATATATAT
510 ATAAGTAATTTACTTTATATAGTTTATATATATATAT
3280385 GTTAGTTTAT
Statistics
Matches: 520, Mismatches: 19, Indels: 34
0.91 0.03 0.06
Matches are distributed among these distances:
595 63 0.12
597 38 0.07
600 1 0.00
601 1 0.00
602 16 0.03
603 18 0.03
604 1 0.00
605 1 0.00
607 16 0.03
608 31 0.06
609 9 0.02
610 119 0.23
611 7 0.01
612 3 0.01
613 76 0.15
615 65 0.12
616 25 0.05
617 30 0.06
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (592 bp):
TATATATATAGTTTTATATACTATACATGGTTTATACATACATATTATAAAAATTATTTAATAAA
ATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATT
GCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAAATTCACAATTTGTATTTT
AGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAAT
AAAACCAAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACATTAGGTTACATAGGCCCAA
TGCAAGCCCACTCTTTTATTACAAATATATATGCAATAGTGCTAGTCCATTTAAATTAGGGTTTA
TGGTTTATGGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATGATTTAGGATTTAAGGTTTATAT
AAACTATATATTTTACTACTTTATATAGTTTATGCATAGTATTTCTATAAACATATAAGTAATTT
ACTTTATATAGTTTATATATATATATATATAATATATATATATATATATATATATATATATATAT
ATATATA
Found at i:3280234 original size:7 final size:7
Alignment explanation
Indices: 3280222--3280248 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3280212 TTTAAATTAG
3280222 GGTTTAT
1 GGTTTAT
3280229 GGTTTAT
1 GGTTTAT
3280236 GGTTTAT
1 GGTTTAT
3280243 GGTTTA
1 GGTTTA
3280249 AAGTTTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (7 bp):
GGTTTAT
Found at i:3280288 original size:41 final size:40
Alignment explanation
Indices: 3280212--3280288 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
3280202 TGCTAGTCCA
* *
3280212 TTTAAATTAGGGTTTATGGTTTATGGTTTATGGTTTAAAG
1 TTTAAATTAGGGTTTATGATTTATGGTTTAGGGTTTAAAG
3280252 TTTAGAATTAGGGTTTATGATTTA-GGATTTAGGGTTT
1 TTTA-AATTAGGGTTTATGATTTATGG-TTTAGGGTTT
3280289 TTATAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 6 0.18
41 27 0.82
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (40 bp):
TTTAAATTAGGGTTTATGATTTATGGTTTAGGGTTTAAAG
Found at i:3280793 original size:26 final size:26
Alignment explanation
Indices: 3280760--3280814 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
3280750 TGCTAGTCCA
*
3280760 TTTAAATTAGGGTTTATGGTTTAAAG
1 TTTAAATTAGGGTTTATGATTTAAAG
*
3280786 TTTAAATTAGGGTTTATGATTTAAGG
1 TTTAAATTAGGGTTTATGATTTAAAG
3280812 TTT
1 TTT
3280815 CTATAACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (26 bp):
TTTAAATTAGGGTTTATGATTTAAAG
Found at i:3280830 original size:525 final size:537
Alignment explanation
Indices: 3279818--3281309 Score: 2155
Period size: 548 Copynumber: 2.7 Consensus size: 537
3279808 TATATATATA
*
3279818 TATATA-TATATATATATATATATATAGTTTATATATACTATACATGGTTTATACATACATA-TA
1 TATATAGTTTATATATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTA
3279881 TATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATAT-AAACATGATTAATT
66 TATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATT
3279945 AGGTGTTAAAT-ATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAT
131 AGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAT
*
3280009 ATTAATTTAAATT--ACAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCAT
196 ATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCAT
*
3280072 TTATTTTGTTGTTATGAATAAGTAAT-A-AAAACCCAAAATAAGTCCATTTGCAATAGTGCTAGT
261 TTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAATAAGTCCATTTGCAATAGTGCTAGT
*
3280135 CCATTAACATTAGGTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATT
326 CCATTAACATTAGTTTACATAGGCCCAATGC-AGCCCACTCTTTTATTACAAATATATAT--ATT
3280200 AGTGCTAGTCCATTTAAATTAGGGTTTATGGTTTATGGTTTATGGTTTAAAGTTTAGAATTAGGG
388 AGTGCTAGTCCATTTAAA-TA--G-TTA-GG----TGGTTTATGGTTTAAAGTTTAGAATTAGGG
* *
3280265 TTTATGATTTAGGATTTAGGGTTTTTATAAACTATATATTTTATTACTTTATATAGTTTATGCAT
444 TTTATGATTT--GA--TAGGGTTTCTATAAACTATATATTTTACTACTTTATATAGTTTATGCAT
3280330 AGTATTTCTATAAACTATATAAGTAATTTACTT
505 AGTATTTCTATAAACTATATAAGTAATTTACTT
*
3280363 TATATAGTTTATATATATATATGT-TAGTTTATATATACTATACATGGTTTATACATACATATTA
1 TATATAGTTTATATATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTA
*
3280427 TATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATGATATAAAACATGATTAATT
66 TATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATT
*
3280492 AGGTGTTAAATAATCAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAT
131 AGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAT
3280557 ATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCAT
196 ATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCAT
*
3280622 TTATTTTGTTGTTACGAATAAGTAATAATAAAACCAAAAAATAAGTCCA-TTGCAATAGTGCTAG
261 TTATTTTGTTGTTATGAATAAGTAATAATAAAACC-AAAAATAAGTCCATTTGCAATAGTGCTAG
3280686 TCCATTAACATTAGTTTACATAGGCCCAATGCAGCCCACTCTTTTATTACAAATATATAT-TTAG
325 TCCATTAACATTAGTTTACATAGGCCCAATGCAGCCCACTCTTTTATTACAAATATATATATTAG
3280750 TGCTAGTCCATTT-AA-A-TTA-G-GGTTTATGGTTTAAAGTTTA-AATTAGGGTTTATGATTT-
390 TGCTAGTCCATTTAAATAGTTAGGTGGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATGATTTG
* *
3280808 A-A-GGTTTCTAT-AACTATATATTTTACTACTTTATATAGTTTATGTATAGTGTTTCTATAAAC
455 ATAGGGTTTCTATAAACTATATATTTTACTACTTTATATAGTTTATGCATAGTATTTCTATAAAC
3280870 TATATAAGTAATTTACTT
520 TATATAAGTAATTTACTT
* *
3280888 TATATAGTTTATATATATATATATATATATATATATATATATATATATATAGTTTATATACTATG
1 TATATAG--------------T-T-TATATATATATATATATA-GT-T-TA---TATATACTATA
3280953 CATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAA
44 CATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAA
* *
3281018 ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCTTATTATATGGTT
109 ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTT
* * * * * *
3281083 CAT-AATAGTAGTACGTGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTACACGTTAGG
174 CATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGG
* * *
3281147 TTAATTCACATTAATAGCCCATTTATTTTATTGTTATGAATAAGTAATAATAAAACCCAAAAATA
239 TTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAA-CCAAAAATA
** * * * *
3281212 AGTCCATTTGCAATTTTGCTAGTCCATTAACATTAATTTAGATAGACCCAATGTAAGCCCACTCT
303 AGTCCATTTGCAATAGTGCTAGTCCATTAACATTAGTTTACATAGGCCCAATG-CAGCCCACTCT
*
3281277 TTTATTACAAATATATATACATTAGTGATAGTC
367 TTTATTACAAATATATAT--ATTAGTGCTAGTC
3281310 TTTTTACATT
Statistics
Matches: 873, Mismatches: 36, Indels: 69
0.89 0.04 0.07
Matches are distributed among these distances:
525 73 0.08
526 8 0.01
527 1 0.00
530 1 0.00
533 18 0.02
534 20 0.02
539 2 0.00
540 1 0.00
541 17 0.02
542 2 0.00
543 1 0.00
544 1 0.00
545 46 0.05
546 66 0.08
547 146 0.17
548 264 0.30
549 28 0.03
550 74 0.08
551 29 0.03
552 63 0.07
553 12 0.01
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.42
Consensus pattern (537 bp):
TATATAGTTTATATATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTA
TATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATT
AGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAT
ATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCAT
TTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAATAAGTCCATTTGCAATAGTGCTAGT
CCATTAACATTAGTTTACATAGGCCCAATGCAGCCCACTCTTTTATTACAAATATATATATTAGT
GCTAGTCCATTTAAATAGTTAGGTGGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATGATTTGA
TAGGGTTTCTATAAACTATATATTTTACTACTTTATATAGTTTATGCATAGTATTTCTATAAACT
ATATAAGTAATTTACTT
Found at i:3280947 original size:2 final size:2
Alignment explanation
Indices: 3280897--3280938 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3280887 TTATATAGTT
3280897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3280939 GTTTATATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3281860 original size:64 final size:64
Alignment explanation
Indices: 3281732--3281871 Score: 192
Period size: 64 Copynumber: 2.2 Consensus size: 64
3281722 GAACTGAAAA
* *
3281732 TGACCCGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCCGAACTGATT
1 TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCCGAACCGATT
* * * * *
3281796 TGACCTGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCT-AAATTGACCTGTATCCGATT
1 TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCCG-AACCGATT
*
3281860 TTACCCGACCTG
1 TGACCCGACCTG
3281872 TCAAGATCCG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 8 0.12
64 58 0.88
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (64 bp):
TGACCCGACCTGAACCCGATCTGGATCTGATGTCAAATCAACCTGAAAATAACCCGAACCGATT
Found at i:3292357 original size:33 final size:33
Alignment explanation
Indices: 3292320--3292382 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
3292310 ACCAGATGTT
* **
3292320 GCCGCCGCCTTCACCTAGTTTTATGACCCCGCA
1 GCCGCCACCTTCACAGAGTTTTATGACCCCGCA
3292353 GCCGCCACCTTCACAGAGTTTTATGACCCC
1 GCCGCCACCTTCACAGAGTTTTATGACCCC
3292383 TCCTGGAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.17, C:0.41, G:0.17, T:0.24
Consensus pattern (33 bp):
GCCGCCACCTTCACAGAGTTTTATGACCCCGCA
Found at i:3292831 original size:13 final size:12
Alignment explanation
Indices: 3292813--3292858 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
3292803 GTATTTAGTA
*
3292813 TTTTTATTGTAA
1 TTTTTATTGTAC
*
3292825 TTGTTTATTGGAC
1 TT-TTTATTGTAC
3292838 TTTTTTATTGTAC
1 -TTTTTATTGTAC
3292851 TTTTTATT
1 TTTTTATT
3292859 ATTATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 10 0.34
13 17 0.59
14 2 0.07
ACGTcount: A:0.17, C:0.04, G:0.11, T:0.67
Consensus pattern (12 bp):
TTTTTATTGTAC
Found at i:3298545 original size:15 final size:15
Alignment explanation
Indices: 3298512--3298547 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3298502 ATTATTTTAA
* *
3298512 TAAAAATTAAAATAT
1 TAAAAATTAAAACAC
3298527 TAAAAATTAAAACAC
1 TAAAAATTAAAACAC
3298542 TAAAAA
1 TAAAAA
3298548 AATAATCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAAATTAAAACAC
Found at i:3312833 original size:19 final size:17
Alignment explanation
Indices: 3312801--3312836 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
3312791 TTGTGCATCT
3312801 TTATTTATTTGTTTGAA
1 TTATTTATTTGTTTGAA
3312818 TTATTTGATATTGTTTGAA
1 TTATTT-AT-TTGTTTGAA
3312837 GATGACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (17 bp):
TTATTTATTTGTTTGAA
Found at i:3316514 original size:17 final size:16
Alignment explanation
Indices: 3316491--3316528 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
3316481 ATATTCTATT
*
3316491 ATATTTAATTTATTTA
1 ATATTTAAATTATTTA
3316507 AGTATTTAAATTATTTA
1 A-TATTTAAATTATTTA
3316524 ATATT
1 ATATT
3316529 GTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
ATATTTAAATTATTTA
Found at i:3319460 original size:11 final size:10
Alignment explanation
Indices: 3319438--3319479 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
3319428 AATTAATTAA
*
3319438 TATATTTTTT
1 TATATTTATT
3319448 TACTATTTATT
1 TA-TATTTATT
3319459 TATTATTTATT
1 TA-TATTTATT
3319470 TA-ATTTATT
1 TATATTTATT
3319479 T
1 T
3319480 GTTTTGGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 8 0.28
10 2 0.07
11 19 0.66
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TATATTTATT
Found at i:3320691 original size:16 final size:16
Alignment explanation
Indices: 3320667--3320742 Score: 79
Period size: 16 Copynumber: 4.9 Consensus size: 16
3320657 TAACAAACTT
3320667 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
*
3320683 GTTTGTTTTCTACA-A
1 GTCTGTTTTCTACACA
*
3320698 TTGTCTG-TTTCT--ATA
1 --GTCTGTTTTCTACACA
3320713 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
*
3320729 GTCAGTTTTCTACA
1 GTCTGTTTTCTACA
3320743 TGGTATCAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
13 5 0.10
14 6 0.12
15 2 0.04
16 33 0.66
17 4 0.08
ACGTcount: A:0.18, C:0.20, G:0.13, T:0.49
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:3327944 original size:2 final size:2
Alignment explanation
Indices: 3327937--3327994 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
3327927 CAACACATAC
3327937 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
3327979 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3327995 CAACAAAGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3333673 original size:144 final size:143
Alignment explanation
Indices: 3333414--3333694 Score: 397
Period size: 144 Copynumber: 2.0 Consensus size: 143
3333404 TGCCTTACAT
* *
3333414 TATCGATACCAACCCTTGGAGGGTATCGATACAAAAAAATAGCTTCGATATTTTGGGAAAACACT
1 TATCGACACCAACCCTTGGAGGGTATCGATACAAAAAAATAACTTCGATATTTTGGGAAAACACT
* * * *
3333479 CGTAACCGATATTATGCTTTAGAGTACCGATACTTTTATAGGAGGCTATTGATACTA-CCTCGAG
66 CGTAACCAATACTATGCTTTAGAGTACCGATACTTTTATACGAGGATATTGATACTATCC-CGAG
*
3333543 TATGGATATCACAG
130 TATCGATATCACAG
*
3333557 TATCGACACCAACCCTTGGGGAGGGTATCGATAC-CAAAAATAACTTCGATATTTTGGGAAAACA
1 TATCGACACCAACCCTT--GGAGGGTATCGATACAAAAAAATAACTTCGATATTTTGGGAAAACA
* * * *
3333621 CTAGGT-ACCAATACTATTCTTTAGAGTACTGATGCTTTTATACGAGGATATTGATACTATCCCG
64 CT-CGTAACCAATACTATGCTTTAGAGTACCGATACTTTTATACGAGGATATTGATACTATCCCG
3333685 AGTATCGATA
128 AGTATCGATA
3333695 CCAAAAATGG
Statistics
Matches: 122, Mismatches: 12, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
143 16 0.13
144 87 0.71
145 19 0.16
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (143 bp):
TATCGACACCAACCCTTGGAGGGTATCGATACAAAAAAATAACTTCGATATTTTGGGAAAACACT
CGTAACCAATACTATGCTTTAGAGTACCGATACTTTTATACGAGGATATTGATACTATCCCGAGT
ATCGATATCACAG
Found at i:3335655 original size:41 final size:41
Alignment explanation
Indices: 3335454--3335688 Score: 283
Period size: 41 Copynumber: 5.7 Consensus size: 41
3335444 ATTCAATTAA
* ** * * * *
3335454 ATTCGATCATGAAAATATGCAATAGTTCACCATTCGA-TTCA
1 ATTCGATCATGATAGCATACAATAATTCACCATTCAACTT-G
* * * * *
3335495 ATTCAATCATGACAACATGCAATACTTCACCATTCAACTTG
1 ATTCGATCATGATAGCATACAATAATTCACCATTCAACTTG
* *
3335536 ATTCGGTCATGGTAGCATACAATAATTCACCATTCAACTTG
1 ATTCGATCATGATAGCATACAATAATTCACCATTCAACTTG
* * *
3335577 ATTCAATCATGATAACATACAATAATTCATCATTCAACTTG
1 ATTCGATCATGATAGCATACAATAATTCACCATTCAACTTG
*
3335618 ATTCGATCATGATAGCATACATTAATTCACCATTCAACTTG
1 ATTCGATCATGATAGCATACAATAATTCACCATTCAACTTG
*
3335659 ATTCGATCATGGTAGCATACAATAATTCAC
1 ATTCGATCATGATAGCATACAATAATTCAC
3335689 ACAAAAAATC
Statistics
Matches: 169, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 167 0.99
42 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (41 bp):
ATTCGATCATGATAGCATACAATAATTCACCATTCAACTTG
Found at i:3335724 original size:82 final size:82
Alignment explanation
Indices: 3335542--3335709 Score: 212
Period size: 82 Copynumber: 2.0 Consensus size: 82
3335532 CTTGATTCGG
* *
3335542 TCATGGTAGCATACAATAATTCACCATTCAACTTGATTCAATCATGATAACATACAATAATTCAT
1 TCATGATAGCATACATTAATTCACCATTCAACTTGATTCAATCATGATAACATACAATAATTCAT
*** * ** *
3335607 CATTCAACTTGATTCGA
66 CAAAAAAATCAATTAGA
* * *
3335624 TCATGATAGCATACATTAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCA-
1 TCATGATAGCATACATTAATTCACCATTCAACTTGATTCAATCATGATAACATACAATAATTCAT
3335688 CACAAAAAATCAATTAGA
66 CA-AAAAAATCAATTAGA
3335706 TCAT
1 TCAT
3335710 AGCAACATGT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 2 0.03
82 71 0.97
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (82 bp):
TCATGATAGCATACATTAATTCACCATTCAACTTGATTCAATCATGATAACATACAATAATTCAT
CAAAAAAATCAATTAGA
Found at i:3338531 original size:21 final size:20
Alignment explanation
Indices: 3338502--3338540 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3338492 TCCAAAAAAA
*
3338502 TAAATATAATTCAATTTTTAT
1 TAAAAATAA-TCAATTTTTAT
*
3338523 TAAAAATAATCTATTTTT
1 TAAAAATAATCAATTTTT
3338541 TCTTACTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAATAATCAATTTTTAT
Found at i:3338709 original size:20 final size:19
Alignment explanation
Indices: 3338664--3338710 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
3338654 AAGTCAGGTG
*
3338664 AAAATATATTTAATATTAA
1 AAAATATATATAATATTAA
3338683 AATAATATATAT-ATATATAA
1 AA-AATATATATAATAT-TAA
3338703 TAAAATAT
1 -AAAATAT
3338711 TATCTTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 6 0.25
20 16 0.67
21 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATATATATAATATTAA
Found at i:3339011 original size:6 final size:6
Alignment explanation
Indices: 3339000--3339026 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3338990 GCAAGGATAA
3339000 AAATAT AAATAT AAATAT AAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT AAA
3339027 ACAAAGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:3339156 original size:14 final size:14
Alignment explanation
Indices: 3339148--3339190 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
3339138 GTAAATGTTA
3339148 AAAATTAAAAGTCT
1 AAAATTAAAAGTCT
3339162 AAAATTAAAA-TACT
1 AAAATTAAAAGT-CT
3339176 AAAAAATTAAAAGTC
1 --AAAATTAAAAGTC
3339191 AATGGCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.04
14 12 0.48
16 11 0.44
17 1 0.04
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.26
Consensus pattern (14 bp):
AAAATTAAAAGTCT
Found at i:3341958 original size:39 final size:40
Alignment explanation
Indices: 3341904--3341979 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
3341894 CCCTAAAATG
3341904 TAAAGACGAGGCTATAG-CAGCTAACCCACCCACACTATA
1 TAAAGACGAGGCTATAGCCAGCTAACCCACCCACACTATA
3341943 TAAAGACGAGGCTATAGCCAGCTAACCCACCCACACT
1 TAAAGACGAGGCTATAGCCAGCTAACCCACCCACACT
3341980 CCATTTCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 17 0.47
40 19 0.53
ACGTcount: A:0.37, C:0.33, G:0.16, T:0.14
Consensus pattern (40 bp):
TAAAGACGAGGCTATAGCCAGCTAACCCACCCACACTATA
Found at i:3344463 original size:30 final size:31
Alignment explanation
Indices: 3344388--3344528 Score: 107
Period size: 30 Copynumber: 4.7 Consensus size: 31
3344378 TTATAATATT
* *
3344388 TTAAATTAAG-ATAAAATATATATTTTATAT
1 TTAAAATAAGAATAAAATATATATTTTATAA
* * *
3344418 TTAAGATAAAAATAAAACATAT-TTCTTA-AA
1 TTAAAATAAGAATAAAATATATATT-TTATAA
3344448 TTAAAATAAGAATAAAATATATA--TTATAA
1 TTAAAATAAGAATAAAATATATATTTTATAA
* * * * *
3344477 GTTAAGATATGATTAAAATATAT-CTTT-TAG
1 -TTAAAATAAGAATAAAATATATATTTTATAA
* *
3344507 GTAATATAAGAATAAAATATAT
1 TTAAAATAAGAATAAAATATAT
3344529 TTGATAAATT
Statistics
Matches: 88, Mismatches: 16, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
28 3 0.03
29 20 0.23
30 50 0.57
31 15 0.17
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (31 bp):
TTAAAATAAGAATAAAATATATATTTTATAA
Found at i:3352255 original size:23 final size:24
Alignment explanation
Indices: 3352216--3352267 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
3352206 CACTAGAGGT
3352216 TATGAAATTTGTCCCGAAGGACCAC
1 TATGAAA-TTGTCCCGAAGGACCAC
*
3352241 TATGAAA-TGTCCCGAAGGACCGC
1 TATGAAATTGTCCCGAAGGACCAC
3352264 TATG
1 TATG
3352268 TCCCGAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 19 0.73
25 7 0.27
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
TATGAAATTGTCCCGAAGGACCAC
Found at i:3352270 original size:18 final size:18
Alignment explanation
Indices: 3352247--3352281 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3352237 CCACTATGAA
3352247 ATGTCCCGAAGGACCGCT
1 ATGTCCCGAAGGACCGCT
3352265 ATGTCCCGAAGGACCGC
1 ATGTCCCGAAGGACCGC
3352282 GTAGACCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.34, G:0.29, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGGACCGCT
Found at i:3352591 original size:2 final size:2
Alignment explanation
Indices: 3352586--3352643 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
3352576 TATCTTATTC
3352586 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
3352628 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3352644 CCACAAATAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3353781 original size:21 final size:21
Alignment explanation
Indices: 3353756--3353798 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
3353746 CTTCCACGTG
3353756 AAGAAGAAAAAAAGAG-AGAAG
1 AAGAA-AAAAAAAGAGAAGAAG
3353777 AAGAAAAAAAAAGAGAAGAAG
1 AAGAAAAAAAAAGAGAAGAAG
3353798 A
1 A
3353799 GAACTCTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAAAAGAGAAGAAG
Found at i:3353793 original size:15 final size:18
Alignment explanation
Indices: 3353755--3353798 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
3353745 GCTTCCACGT
3353755 GAAGAAGAAAAAAAGAGA
1 GAAGAAGAAAAAAAGAGA
*
3353773 GAAGAAGAAAAAAAAAGA
1 GAAGAAGAAAAAAAGAGA
3353791 GAAGAAGA
1 GAAGAAGA
3353799 GAACTCTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAAAAAAGAGA
Found at i:3355782 original size:23 final size:23
Alignment explanation
Indices: 3355756--3355819 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
3355746 CAGCTCGTAT
3355756 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* ***
3355779 AATTGCACCGGAGTGCCGTGTAG
1 AATTGCACCGAAGTGCCACATAG
*
3355802 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
3355820 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:3356006 original size:103 final size:103
Alignment explanation
Indices: 3355835--3356150 Score: 587
Period size: 103 Copynumber: 3.1 Consensus size: 103
3355825 TAATGTCCAT
* * * *
3355835 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
3355900 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
3355938 AAAGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
3356003 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3356041 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
3356106 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3356144 AAGGACC
1 AAGGACC
3356151 GCGTAGACCC
Statistics
Matches: 207, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3359604 original size:23 final size:23
Alignment explanation
Indices: 3359568--3359613 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3359558 CATCACACAT
*
3359568 TATTTCCATCATTAATCTTATTC
1 TATTTCCATCATTAATATTATTC
*
3359591 TATTATCCAT-ATTATTATTATTC
1 TATT-TCCATCATTAATATTATTC
3359614 ATATCCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTCCATCATTAATATTATTC
Found at i:3360193 original size:2 final size:2
Alignment explanation
Indices: 3360188--3360264 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
3360178 TATCTTATTC
3360188 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
3360230 AT AT AT AT AT AT AT AT AT AT AT A- 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
3360265 CCGCAAATAC
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3366088 original size:22 final size:21
Alignment explanation
Indices: 3366057--3366097 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3366047 TATTAGTATA
*
3366057 TATATGTATATTAATTTTTTAT
1 TATATCTATATT-ATTTTTTAT
3366079 TATATCTATATTATTTTTT
1 TATATCTATATTATTTTTT
3366098 CCTAGCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TATATCTATATTATTTTTTAT
Found at i:3366149 original size:10 final size:10
Alignment explanation
Indices: 3366134--3366165 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3366124 TGTATATTAC
3366134 TTTTATTATA
1 TTTTATTATA
3366144 TTTTATTATA
1 TTTTATTATA
3366154 TTTTATT-TA
1 TTTTATTATA
3366163 TTT
1 TTT
3366166 CATTTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTATTATA
Found at i:3367386 original size:39 final size:38
Alignment explanation
Indices: 3367333--3367469 Score: 202
Period size: 39 Copynumber: 3.5 Consensus size: 38
3367323 GGATTTTTTT
3367333 ATAATAAGCATGTGGGGTAGAGATCATGTCTAGGTAGGA
1 ATAATAAGCATGTGGGGTAGAGATCATGTCT-GGTAGGA
* * *
3367372 ATAATAAGCATGTGGGGTAGATATCGTGTCTGGATATGA
1 ATAATAAGCATGTGGGGTAGAGATCATGTCTGG-TAGGA
*
3367411 ATAATAAGCATGTGGGGTAGAGATCATGTCCGGGTAGGA
1 ATAATAAGCATGTGGGGTAGAGATCATGT-CTGGTAGGA
*
3367450 ATAATAAGTATGTGGGGTAG
1 ATAATAAGCATGTGGGGTAG
3367470 GACTCTTATT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
38 2 0.02
39 83 0.94
40 3 0.03
ACGTcount: A:0.32, C:0.07, G:0.34, T:0.27
Consensus pattern (38 bp):
ATAATAAGCATGTGGGGTAGAGATCATGTCTGGTAGGA
Found at i:3369071 original size:95 final size:96
Alignment explanation
Indices: 3368958--3369222 Score: 356
Period size: 95 Copynumber: 2.7 Consensus size: 96
3368948 ACAAATTATA
* * *
3368958 ATTATATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTAGTTAAATGCCCCGGCTT
1 ATTATA-ATATATACAATAAA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTT
*
3369023 TATGGATAAGATTCAGCTAGCCTGATAAAGGCG
64 TATGGATAAGATTCAACTAGCCTGATAAAGGCG
*
3369056 ATTA-AA-ATATACAATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCAGCTTT
1 ATTATAATATATACAAT-AAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTT
* * *
3369119 ATGGATAATATTCAACTAGCCTGGTAAAGGTG
65 ATGGATAAGATTCAACTAGCCTGATAAAGGCG
* **
3369151 ATTATAATACTTATACAATGATA-TTGAACTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCT
1 ATTATAATA--TATACAAT-AAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCT
3369215 TTATGGAT
63 TTATGGAT
3369223 CCAGCTAGCC
Statistics
Matches: 149, Mismatches: 13, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
95 81 0.54
96 6 0.04
97 2 0.01
98 50 0.34
99 10 0.07
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (96 bp):
ATTATAATATATACAATAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTA
TGGATAAGATTCAACTAGCCTGATAAAGGCG
Found at i:3370461 original size:84 final size:84
Alignment explanation
Indices: 3370320--3371210 Score: 1106
Period size: 84 Copynumber: 10.6 Consensus size: 84
3370310 TTCTATTGGT
* **
3370320 AGCATAACTCAAGGATAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
*
3370385 TCCAAGGCATATCATTTGC
66 TCCAAGGCACATCATTTGC
*
3370404 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* *
3370469 TCCAAGGCATATCATTTGT
66 TCCAAGGCACATCATTTGC
* *
3370488 AGCAAAACTCAAGGCT-GTAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTCGACTACGCTCAG
1 AGCATAACTCAAGGCTAG-AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
*
3370552 CTCCAAGGCACATTATTTGC
65 CTCCAAGGCACATCATTTGC
* * * * **** *
3370572 AGTATAACTTAAGTCGAGAAAAACTATCTGCCAACCAAAGACCTTCGAGTTCGACTTCGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
3370637 TCCAAGGCACATCATTTGC
66 TCCAAGGCACATCATTTGC
* * *
3370656 AGTATAACTCAAGGCTATAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* *
3370721 TCCAAGGCATATCATTTAC
66 TCCAAGGCACATCATTTGC
* * *
3370740 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTACACTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
*
3370804 TCAAAGGCACATCATTTGC
66 TCCAAGGCACATCATTTGC
* * * * * * * * * *
3370823 AGTATAGCTTAAGTCGAAAAGAGCTATCTACCAACCAAAGACCTTCGAGTTTGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
**
3370888 TCCAAGGCACATCATTTAT
66 TCCAAGGCACATCATTTGC
* * * * * *
3370907 ATCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTTGAGTTCGATTACACTTAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* *
3370971 TCAAAGACACAATCATTTGC
66 TCCAAGGCAC-ATCATTTGC
* * * * * * *
3370991 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTATGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
*
3371056 TCTAAGGCACATCATTTGC
66 TCCAAGGCACATCATTTGC
* * * * ** *
3371075 AGCATAACTCAAGGCTAAAAGGGTTATCAGCCAACAAAAGACCTTTGAGTTCGACTACATTCAGT
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
** *
3371140 TTAAAGACACATCATTTGC
66 TCCAAGGCACATCATTTGC
* * *
3371159 AGCATAGCTCAAGGCAAGAAGGGTTATCTGCC-ACCAAAAGACCTTAGAGTTC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTC
3371211 AACGCATAAC
Statistics
Matches: 685, Mismatches: 116, Indels: 12
0.84 0.14 0.01
Matches are distributed among these distances:
83 103 0.15
84 549 0.80
85 33 0.05
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (84 bp):
AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
TCCAAGGCACATCATTTGC
Found at i:3371156 original size:419 final size:419
Alignment explanation
Indices: 3370320--3371210 Score: 1232
Period size: 419 Copynumber: 2.1 Consensus size: 419
3370310 TTCTATTGGT
* * *
3370320 AGCATAACTCAAGGATAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACACTCAGC
* * * * * * **
3370385 TCCAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACCTTC
65 TCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAAAAGAGCTATCTACCAACCAAAGACCTTC
* *
3370450 GAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCAAAACTCAAGGCTGTAAGGGTTAT
130 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTATAGCAAAACTCAAGGCTGTAAGGGTTAT
* * * * *
3370515 CTGCTAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTGCAGTATAAC
195 CTGCTAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGACACATCATTTGCAGCATAAC
*
3370580 TTAAGTCGAGAAAAACTATCTGCCAACCAAAGACCTTCGAGTTCGACTTCGCTCAGCTCCAAGGC
260 TTAAGTCGAGAAAAACTATCTGCCAACAAAAGACCTTCGAGTTCGACTTCGCTCAGCTCCAAGGC
* * *
3370645 ACATCATTTGCAGTATAACTCAAGGCTATAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
325 ACATCATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCAGCCAACAAAAGACCTTCGAGTTCGA
* * * *
3370710 CTACGCTCAGCTCCAAGGCATATCATTTAC
390 CTACACTCAGCTCAAAGACACATCATTTAC
* *
3370740 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCT
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGCT
* * * *
3370805 CAAAGGCACATCATTTGCAGTATAGCTTAAGTCGAAAAGAGCTATCTACCAACCAAAGACCTTCG
66 CAAAGGCACATCATTTGCAGCATAACTCAAGGCGAAAAGAGCTATCTACCAACCAAAGACCTTCG
* * *
3370870 AGTTTGACTACGCTCAGCTCCAAGGCACATCATTTATATCATAACTCAAGGCTAG-AAGGGTTAT
131 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTATAGCAAAACTCAAGGCT-GTAAGGGTTAT
* * *
3370934 CTG-TCAA-CAAAGACCTTTGAGTTCGATTACACTTAGCTCAAAGACACAATCATTTGCAGCATA
195 CTGCT-AACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGACAC-ATCATTTGCAGCATA
* *** *
3370997 GCTTAAGTCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTAT-GCTCAGCTCTAA
258 ACTTAAGTCGAGAAAAACTATCTGCCAACAAAAGACCTTCGAGTTCGACT-TCGCTCAGCTCCAA
*
3371061 GGCACATCATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCAGCCAACAAAAGACCTTTGAGTT
322 GGCACATCATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCAGCCAACAAAAGACCTTCGAGTT
* * * *
3371126 CGACTACATTCAGTTTAAAGACACATCATTTGC
387 CGACTACACTCAGCTCAAAGACACATCATTTAC
* * * *
3371159 AGCATAGCTCAAGGCAAGAAGGGTTATCTGCCACCAAAAGACCTTAGAGTTC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTC
3371211 AACGCATAAC
Statistics
Matches: 413, Mismatches: 53, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
418 35 0.08
419 329 0.80
420 49 0.12
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (419 bp):
AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACACTCAGCT
CAAAGGCACATCATTTGCAGCATAACTCAAGGCGAAAAGAGCTATCTACCAACCAAAGACCTTCG
AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTATAGCAAAACTCAAGGCTGTAAGGGTTATC
TGCTAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGACACATCATTTGCAGCATAACT
TAAGTCGAGAAAAACTATCTGCCAACAAAAGACCTTCGAGTTCGACTTCGCTCAGCTCCAAGGCA
CATCATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCAGCCAACAAAAGACCTTCGAGTTCGAC
TACACTCAGCTCAAAGACACATCATTTAC
Found at i:3373978 original size:18 final size:18
Alignment explanation
Indices: 3373952--3373986 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3373942 TCAAAAGGAC
*
3373952 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3373970 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3373987 CCGGCTGACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3376321 original size:8 final size:8
Alignment explanation
Indices: 3376310--3376356 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
3376300 CCGTTTACCC
3376310 GACCCGTT
1 GACCCGTT
3376318 GACCC---
1 GACCCGTT
3376323 GACCCGTT
1 GACCCGTT
*
3376331 GA-CCGCT
1 GACCCGTT
3376338 GACCCGTT
1 GACCCGTT
3376346 GA-CCGTT
1 GACCCGTT
3376353 GACC
1 GACC
3376357 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
5 5 0.16
7 13 0.41
8 14 0.44
ACGTcount: A:0.15, C:0.40, G:0.26, T:0.19
Consensus pattern (8 bp):
GACCCGTT
Found at i:3376350 original size:15 final size:13
Alignment explanation
Indices: 3376292--3376349 Score: 89
Period size: 13 Copynumber: 4.3 Consensus size: 13
3376282 AACCCGACAC
3376292 GACCCGACCCGTT
1 GACCCGACCCGTT
*
3376305 TACCCGACCCGTT
1 GACCCGACCCGTT
3376318 GACCCGACCCGTT
1 GACCCGACCCGTT
3376331 GACCGCTGACCCGTT
1 GACC-C-GACCCGTT
3376346 GACC
1 GACC
3376350 GTTGACCGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
13 28 0.68
14 1 0.02
15 12 0.29
ACGTcount: A:0.16, C:0.45, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3376355 original size:15 final size:14
Alignment explanation
Indices: 3376297--3376356 Score: 61
Period size: 13 Copynumber: 4.3 Consensus size: 14
3376287 GACACGACCC
* *
3376297 GACCCGTTTACC-C
1 GACCCGTTGACCGT
*
3376310 GACCCGTTGACC-C
1 GACCCGTTGACCGT
3376323 GACCCGTTGACCGCT
1 GACCCGTTGACCG-T
3376338 GACCCGTTGACCGTT
1 GACCCGTTGACCG-T
3376353 GACC
1 GACC
3376357 GGAGTTGACC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
13 24 0.57
15 18 0.43
ACGTcount: A:0.15, C:0.42, G:0.23, T:0.20
Consensus pattern (14 bp):
GACCCGTTGACCGT
Found at i:3377691 original size:18 final size:18
Alignment explanation
Indices: 3377665--3377699 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3377655 TTAAAAGGAC
*
3377665 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3377683 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3377700 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3378841 original size:47 final size:49
Alignment explanation
Indices: 3378786--3378895 Score: 129
Period size: 47 Copynumber: 2.3 Consensus size: 49
3378776 ATATTTTATT
* *
3378786 TGATTTCTGAAT-TGAATTCTGTTCTGATA-CGTTACATGAATTCTGTTC
1 TGATTTCTGAATCTGAATTATGTTCTGATATC-TGACATGAATTCTGTTC
* * *
3378834 TGA-TTCTG-ATCTGGATTATGTTCTGATATCTGATATGAATTCTGTTT
1 TGATTTCTGAATCTGAATTATGTTCTGATATCTGACATGAATTCTGTTC
3378881 TGATTTCTGATATCT
1 TGATTTCTGA-ATCT
3378896 CCGTTTACCG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
46 2 0.04
47 37 0.71
48 9 0.17
50 4 0.08
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (49 bp):
TGATTTCTGAATCTGAATTATGTTCTGATATCTGACATGAATTCTGTTC
Found at i:3378879 original size:24 final size:24
Alignment explanation
Indices: 3378798--3378893 Score: 106
Period size: 24 Copynumber: 4.0 Consensus size: 24
3378788 ATTTCTGAAT
* *
3378798 TGAATTCTGTTCTGATA-CGTTACA
1 TGAATTCTGTTCTGATATC-TGATA
*
3378822 TGAATTCTGTTCTGAT-TCTGATC
1 TGAATTCTGTTCTGATATCTGATA
* *
3378845 TGGATTATGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATATCTGATA
* *
3378869 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATA
3378893 T
1 T
3378894 CTCCGTTTAC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 16 0.27
24 44 0.73
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:3379063 original size:2 final size:2
Alignment explanation
Indices: 3379056--3379114 Score: 75
Period size: 2 Copynumber: 29.5 Consensus size: 2
3379046 GATGGGGGTG
* *
3379056 TA TA TA TA TA TA TGC T- TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3379098 TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA T
3379115 CTTTTTACTG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3381082 original size:13 final size:13
Alignment explanation
Indices: 3381063--3381120 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
3381053 AACTTGACAC
3381063 GACCCGACCCGTT
1 GACCCGACCCGTT
*
3381076 TACCCGACCCGTT
1 GACCCGACCCGTT
*
3381089 GACTCGACCCGTT
1 GACCCGACCCGTT
3381102 GACCGCTGACCCGTT
1 GACC-C-GACCCGTT
3381117 GACC
1 GACC
3381121 GTTGACCGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
13 26 0.67
14 1 0.03
15 12 0.31
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3381126 original size:15 final size:15
Alignment explanation
Indices: 3381081--3381127 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
3381071 CCGTTTACCC
*
3381081 GACCCGTTGA-C-TC
1 GACCCGTTGACCGTT
*
3381094 GACCCGTTGACCGCT
1 GACCCGTTGACCGTT
3381109 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
3381124 GACC
1 GACC
3381128 GGAGTTGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 10 0.34
14 1 0.03
15 18 0.62
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:3382461 original size:18 final size:18
Alignment explanation
Indices: 3382435--3382469 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3382425 TTAAAAGGAC
*
3382435 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3382453 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3382470 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3383610 original size:47 final size:47
Alignment explanation
Indices: 3383559--3383654 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 47
3383549 TTTATTTGAT
* *
3383559 TTCTGAAT-TGAATTCTGTTCTGATA-CGTTACCTGAATTCTGTTCTGA
1 TTCTG-ATCTGAATTATGTTCTGATATC-TTACATGAATTCTGTTCTGA
* * *
3383606 TTCTGATCTGGATTATGTTCTGATATCTTATATGAATTCTGTTTTGA
1 TTCTGATCTGAATTATGTTCTGATATCTTACATGAATTCTGTTCTGA
3383653 TT
1 TT
3383655 TCTTATATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
46 2 0.05
47 39 0.93
48 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (47 bp):
TTCTGATCTGAATTATGTTCTGATATCTTACATGAATTCTGTTCTGA
Found at i:3383653 original size:24 final size:24
Alignment explanation
Indices: 3383567--3383662 Score: 97
Period size: 24 Copynumber: 4.0 Consensus size: 24
3383557 ATTTCTGAAT
**
3383567 TGAATTCTGTTCTGATA-CGTTACC
1 TGAATTCTGTTCTGATATC-TTATA
* *
3383591 TGAATTCTGTTCTGAT-TCTGATC
1 TGAATTCTGTTCTGATATCTTATA
* *
3383614 TGGATTATGTTCTGATATCTTATA
1 TGAATTCTGTTCTGATATCTTATA
* *
3383638 TGAATTCTGTTTTGATTTCTTATA
1 TGAATTCTGTTCTGATATCTTATA
3383662 T
1 T
3383663 CTCCGTTTAC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 17 0.28
24 43 0.72
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTTATA
Found at i:3383832 original size:2 final size:2
Alignment explanation
Indices: 3383825--3383867 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
3383815 GATGTGGGTG
* *
3383825 TA TA TA TA TA TA TA TGC T- TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
3383867 T
1 T
3383868 CTTTTTACTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3385328 original size:23 final size:22
Alignment explanation
Indices: 3385284--3385328 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3385274 CAACCCTCAT
* **
3385284 TCCAACTCCGATCTACTCGCCG
1 TCCAACTCCGATCGACGAGCCG
3385306 TCCAACCTCCGATCGACGAGCCG
1 TCCAA-CTCCGATCGACGAGCCG
3385329 AAACCACCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.20, C:0.44, G:0.18, T:0.18
Consensus pattern (22 bp):
TCCAACTCCGATCGACGAGCCG
Found at i:3387193 original size:18 final size:18
Alignment explanation
Indices: 3387167--3387201 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3387157 TCAAAAGGAC
*
3387167 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3387185 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3387202 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3388371 original size:24 final size:23
Alignment explanation
Indices: 3388323--3388394 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
3388313 ATACGTTACC
*
3388323 TGAATTCTGTTCTGATTCTGATA
1 TGAATTATGTTCTGATTCTGATA
*
3388346 TGGATTATGTTCTGATATCTGATA
1 TGAATTATGTTCTGAT-TCTGATA
* *
3388370 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTATGTTCTGA-TTCTGATA
3388394 T
1 T
3388395 CTCCGTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 14 0.33
24 27 0.64
25 1 0.02
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.50
Consensus pattern (23 bp):
TGAATTATGTTCTGATTCTGATA
Found at i:3388579 original size:2 final size:2
Alignment explanation
Indices: 3388574--3388609 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3388564 ATATGCTTAA
3388574 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
3388610 CTTTTTACTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3391856 original size:18 final size:18
Alignment explanation
Indices: 3391830--3391864 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3391820 TCAAAAGGAC
*
3391830 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3391848 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3391865 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3393000 original size:12 final size:12
Alignment explanation
Indices: 3392962--3393053 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
3392952 ATTTCCGAAT
3392962 TGAATTCTGTTC
1 TGAATTCTGTTC
*
3392974 TG-ATAC-GTTACC
1 TGAATTCTGTT--C
3392986 TGAATTCTGTTC
1 TGAATTCTGTTC
*
3392998 TG-ATTCTGATC
1 TGAATTCTGTTC
* *
3393009 TGGATTATGTTC
1 TGAATTCTGTTC
* *
3393021 TG-ATATCTGATA
1 TGAAT-TCTGTTC
*
3393033 TGAATTCTGTTT
1 TGAATTCTGTTC
*
3393045 TGATTTCTG
1 TGAATTCTG
3393054 ATATCTCCGT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 15 0.24
12 36 0.58
13 5 0.08
14 3 0.05
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:3393043 original size:24 final size:24
Alignment explanation
Indices: 3392962--3393057 Score: 99
Period size: 24 Copynumber: 4.0 Consensus size: 24
3392952 ATTTCCGAAT
*
3392962 TGAATTCTGTTCTGATA-C-GTTA
1 TGAATTCTGTTCTGATATCTGATA
*
3392984 CCTGAATTCTGTTCTGAT-TCTGATC
1 --TGAATTCTGTTCTGATATCTGATA
* *
3393009 TGGATTATGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATATCTGATA
* *
3393033 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATA
3393057 T
1 T
3393058 CTCCGTTTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
23 14 0.23
24 44 0.73
25 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:3396494 original size:12 final size:12
Alignment explanation
Indices: 3396477--3396503 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3396467 GAACCCAGCA
3396477 CATTTGATAGTT
1 CATTTGATAGTT
3396489 CATTTGATAGTT
1 CATTTGATAGTT
3396501 CAT
1 CAT
3396504 CCTGCTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (12 bp):
CATTTGATAGTT
Found at i:3406093 original size:21 final size:20
Alignment explanation
Indices: 3406055--3406093 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3406045 CAACCCTTTA
* *
3406055 ATTTAACTAAGTTTTATTTG
1 ATTTAACTAACTTCTATTTG
3406075 ATTTCAACTAACTTCTATT
1 ATTT-AACTAACTTCTATT
3406094 CTCCGCGCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (20 bp):
ATTTAACTAACTTCTATTTG
Found at i:3407122 original size:16 final size:16
Alignment explanation
Indices: 3407101--3407134 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3407091 TTACTATTCA
*
3407101 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
3407117 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
3407133 CG
1 CG
3407135 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:3407902 original size:15 final size:16
Alignment explanation
Indices: 3407884--3407916 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3407874 GTGGCAGATC
3407884 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
3407899 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
3407915 AA
1 AA
3407917 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:3415964 original size:21 final size:20
Alignment explanation
Indices: 3415931--3415970 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3415921 TTCCTTTTAC
3415931 TATTTAAACTTAAACATATAT
1 TATTTAAACTTAAA-ATATAT
* *
3415952 TATTTTAATTTAAAATATA
1 TATTTAAACTTAAAATATA
3415971 CAAAAGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTAAACTTAAAATATAT
Found at i:3417932 original size:25 final size:26
Alignment explanation
Indices: 3417882--3417934 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
3417872 ATATATATAT
*
3417882 AAATAAAAAGTCAAAGAAAGAGAAAA
1 AAATAAAAAGTCAAAGAAACAGAAAA
*
3417908 AAATAAAAA-TTAAAGAGAACA-AAAA
1 AAATAAAAAGTCAAAGA-AACAGAAAA
3417933 AA
1 AA
3417935 TGAGTTAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.75, C:0.04, G:0.11, T:0.09
Consensus pattern (26 bp):
AAATAAAAAGTCAAAGAAACAGAAAA
Found at i:3417933 original size:26 final size:26
Alignment explanation
Indices: 3417882--3417934 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
3417872 ATATATATAT
* *
3417882 AAATAAAAAGTCAAAGAAAGAGAAAA
1 AAATAAAAAGTCAAAGAAACAAAAAA
*
3417908 AAATAAAAA-TTAAAGAGAACAAAAAA
1 AAATAAAAAGTCAAAGA-AACAAAAAA
3417934 A
1 A
3417935 TGAGTTAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.75, C:0.04, G:0.11, T:0.09
Consensus pattern (26 bp):
AAATAAAAAGTCAAAGAAACAAAAAA
Found at i:3417994 original size:19 final size:19
Alignment explanation
Indices: 3417944--3417998 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
3417934 ATGAGTTAGG
* ** *
3417944 AAAAAATATAAAAACAATT
1 AAAAAATAAAAAAAGGATA
3417963 AAAAAATAAAAAAAGGATA
1 AAAAAATAAAAAAAGGATA
3417982 AAAAAAT-AAAAAAGGAT
1 AAAAAATAAAAAAAGGAT
3417999 CAAATTGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 10 0.31
19 22 0.69
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (19 bp):
AAAAAATAAAAAAAGGATA
Found at i:3420210 original size:17 final size:17
Alignment explanation
Indices: 3420188--3420225 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
3420178 AATCCTAACT
3420188 GCATATTTGTCTAGTTC
1 GCATATTTGTCTAGTTC
3420205 GCATATTTGTCTAGTTC
1 GCATATTTGTCTAGTTC
3420222 GCAT
1 GCAT
3420226 GCTTTGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (17 bp):
GCATATTTGTCTAGTTC
Found at i:3421028 original size:6 final size:6
Alignment explanation
Indices: 3421017--3421045 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3421007 CAAAAATTAG
3421017 AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
3421046 ATCCAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:3421326 original size:20 final size:21
Alignment explanation
Indices: 3421303--3421342 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3421293 GGATCAAATT
3421303 GAATGAAAAT-AAAATAATAC
1 GAATGAAAATAAAAATAATAC
*
3421323 GAATTAAAATAAAAATAATA
1 GAATGAAAATAAAAATAATA
3421343 AAAAACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (21 bp):
GAATGAAAATAAAAATAATAC
Found at i:3422624 original size:3 final size:3
Alignment explanation
Indices: 3422616--3422658 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
3422606 GGAAATAGGA
*
3422616 AAT AAT AAT AAT AAT AAT AAT AAT AAAC AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A-AT AA
3422659 AAAGTTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 31 0.86
4 5 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3422637 original size:25 final size:26
Alignment explanation
Indices: 3422609--3422658 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
3422599 ATAAATAGGA
* *
3422609 AATAGGAAATAATAATAATA-ATAAT
1 AATAAGAAACAATAATAATATATAAT
*
3422634 AATAATAAACAATAATAATATATAA
1 AATAAGAAACAATAATAATATATAA
3422659 AAAGTTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (26 bp):
AATAAGAAACAATAATAATATATAAT
Found at i:3422723 original size:39 final size:37
Alignment explanation
Indices: 3422657--3422993 Score: 285
Period size: 39 Copynumber: 8.9 Consensus size: 37
3422647 AATAATATAT
* *
3422657 AAAAAGTTTTCAAAAAC-ATATAATATATAAATTTTC
1 AAAAATTTTTTAAAAACTATATAATATATAAATTTTC
* * **
3422693 AAAATATTTTTTTTAAAACTATATATTATATGTATTTTC
1 AAAA-A-TTTTTTAAAAACTATATAATATATAAATTTTC
* * * *
3422732 AGAAATGTTTTAAAAAATTATTTAATATATATAA-TTTC
1 AAAAAT-TTTTTAAAAACTATATAATATATA-AATTTTC
*
3422770 AAAAATGTTTTTTAAAAACTATATATTATATATAA-TTTC
1 AAAAA--TTTTTTAAAAACTATATAATATATA-AATTTTC
3422809 -AAAATGTCTTTTAAAAAACTATATAATATATAAATGTTTTC
1 AAAAAT-T-TTTT-AAAAACTATATAATATATAAA--TTTTC
* *
3422850 AAAAATGTTTTCAAAACTATATAATATAT-AATTTTC
1 AAAAATTTTTTAAAAACTATATAATATATAAATTTTC
* * *
3422886 -AAAATGTTTTCAAAACTATATACTATATATAATTTTC
1 AAAAATTTTTTAAAAACTATATAATATATA-AATTTTC
* * * *
3422923 -AAAATGTTTTAAAAACTATACATTATATATATATTTC
1 AAAAATTTTTTAAAAACTATATAATATATAAAT-TTTC
*
3422960 -AAAATGACTTTTAAAAACTATATAATATATAAAT
1 AAAAAT--TTTTTAAAAACTATATAATATATAAAT
3422994 GTTTTTGAAA
Statistics
Matches: 251, Mismatches: 31, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
35 27 0.11
36 12 0.05
37 45 0.18
38 48 0.19
39 105 0.42
40 5 0.02
41 4 0.02
42 5 0.02
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (37 bp):
AAAAATTTTTTAAAAACTATATAATATATAAATTTTC
Found at i:3422832 original size:37 final size:35
Alignment explanation
Indices: 3422657--3422991 Score: 257
Period size: 37 Copynumber: 8.9 Consensus size: 35
3422647 AATAATATAT
* *
3422657 AAAAAGTTTTCAAAAAC-ATATAATATATAAATTTTC
1 AAAATGTTTT-AAAAACTATATTATATAT-AATTTTC
* * *
3422693 AAAATATTTTTTTTAAAACTATA-TATTATATGTATTTTC
1 -AAA-A-TGTTTTAAAAACTATATTA-TATAT-AATTTTC
* *
3422732 AGAAATGTTTTAAAAAAT-TATTTAATATATATAATTTC
1 A-AAATGTTTTAAAAACTATA-TT-ATATATA-ATTTTC
3422770 AAAAATGTTTTTTAAAAACTATATATTATATATAA-TTTC
1 -AAAATG--TTTTAAAAAC--TATATTATATATAATTTTC
*
3422809 AAAATGTCTTTTAAAAAACTATATAATATATAAATGTTTTC
1 AAAATG--TTTT-AAAAACTATATTATATAT-AA--TTTTC
* *
3422850 AAAAATGTTTTCAAAACTATATAATATATAATTTTC
1 -AAAATGTTTTAAAAACTATATTATATATAATTTTC
*
3422886 AAAATGTTTTCAAAACTATATACTATATATAATTTTC
1 AAAATGTTTTAAAAACTATAT--TATATATAATTTTC
3422923 AAAATGTTTTAAAAACTATACATTATATAT-ATATTTC
1 AAAATGTTTTAAAAACTAT--ATTATATATAAT-TTTC
*
3422960 AAAATGACTTTTAAAAACTATATAATATATAA
1 AAAATG--TTTTAAAAACTATATTATATATAA
3422992 ATGTTTTTGA
Statistics
Matches: 251, Mismatches: 18, Indels: 57
0.77 0.06 0.17
Matches are distributed among these distances:
35 21 0.08
36 9 0.04
37 80 0.32
38 41 0.16
39 64 0.25
40 14 0.06
41 11 0.04
42 9 0.04
43 2 0.01
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (35 bp):
AAAATGTTTTAAAAACTATATTATATATAATTTTC
Found at i:3422857 original size:12 final size:12
Alignment explanation
Indices: 3422840--3422865 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3422830 TATAATATAT
3422840 AAATGTTTTCAA
1 AAATGTTTTCAA
3422852 AAATGTTTTCAA
1 AAATGTTTTCAA
3422864 AA
1 AA
3422866 CTATATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
AAATGTTTTCAA
Found at i:3441563 original size:12 final size:12
Alignment explanation
Indices: 3441545--3441580 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3441535 TATATATGTT
3441545 CATGTGATATGA
1 CATGTGATATGA
*
3441557 TATGTGATATGA
1 CATGTGATATGA
*
3441569 CCTGTGATATGA
1 CATGTGATATGA
3441581 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Done.