Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397272.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.0, 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: 3572271
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 44823 characters in sequence are not A, C, G, or T
File 6 of 9
Found at i:2113128 original size:2 final size:2
Alignment explanation
Indices: 2113121--2113147 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2113111 AAAATCATGC
2113121 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 T
2113148 CCTACAGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2115227 original size:14 final size:14
Alignment explanation
Indices: 2115195--2115237 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2115185 TTAATTTAAA
2115195 AAAAACATAAAACTAT
1 AAAAA-ATAAAA-TAT
2115211 AAAAAATAAAATAT
1 AAAAAATAAAATAT
* *
2115225 AAATAATTAAATA
1 AAAAAATAAAATA
2115238 CGAAATACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 14 0.56
15 6 0.24
16 5 0.20
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAATAAAATAT
Found at i:2115471 original size:28 final size:27
Alignment explanation
Indices: 2115419--2115483 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 27
2115409 TGAGTTACTA
* *
2115419 GAAAAGAGAAATAAAAATAAAAAGACC
1 GAAAAGAGAAAGAAAAAGAAAAAGACC
2115446 GAAAAGAGAAGAGAAAAAGAAAAAGA--
1 GAAAAGAGAA-AGAAAAAGAAAAAGACC
2115472 -AAAAGAGAAAGA
1 GAAAAGAGAAAGA
2115484 GGCGTAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 3 0.09
25 9 0.26
27 10 0.29
28 13 0.37
ACGTcount: A:0.72, C:0.03, G:0.22, T:0.03
Consensus pattern (27 bp):
GAAAAGAGAAAGAAAAAGAAAAAGACC
Found at i:2118719 original size:2 final size:2
Alignment explanation
Indices: 2118712--2118739 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2118702 CCCCTAACTA
2118712 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2118740 CAAACTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2120272 original size:2 final size:2
Alignment explanation
Indices: 2120265--2120299 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2120255 CATGAAGTTT
2120265 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2120300 TTAAGTGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2141164 original size:18 final size:20
Alignment explanation
Indices: 2141138--2141186 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
2141128 TAATGGTGCC
*
2141138 ATAACTAAAATAATA-AT-A
1 ATAATTAAAATAATATATAA
2141156 ATAATTAAAA-AATATATAA
1 ATAATTAAAATAATATATAA
2141175 ATATATTAAAAT
1 ATA-ATTAAAAT
2141187 CTATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.15
18 11 0.42
19 4 0.15
20 7 0.27
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATTAAAATAATATATAA
Found at i:2141712 original size:15 final size:16
Alignment explanation
Indices: 2141687--2141716 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2141677 TAAATATTAA
2141687 TATATAATTTACTTTT
1 TATATAATTTACTTTT
2141703 TATA-AATTTACTTT
1 TATATAATTTACTTT
2141717 GACTTAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATAATTTACTTTT
Found at i:2148692 original size:20 final size:20
Alignment explanation
Indices: 2148656--2148693 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2148646 AAAAATATAC
**
2148656 AAATAATAAAATTTAAATTT
1 AAATAATAAAAAATAAATTT
2148676 AAATAATAAAAAATAAAT
1 AAATAATAAAAAATAAAT
2148694 ATCTCAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATAAAAAATAAATTT
Found at i:2148730 original size:15 final size:17
Alignment explanation
Indices: 2148710--2148742 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2148700 AATATAATTA
2148710 ATAA-TTTTGTAA-GTT
1 ATAATTTTTGTAATGTT
2148725 ATAATTTTTGTAATGTT
1 ATAATTTTTGTAATGTT
2148742 A
1 A
2148743 ACACAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (17 bp):
ATAATTTTTGTAATGTT
Found at i:2149487 original size:339 final size:336
Alignment explanation
Indices: 2148702--2149832 Score: 871
Period size: 357 Copynumber: 3.3 Consensus size: 336
2148692 ATATCTCAAA
* * * *
2148702 TATAATTAATAATTTTGTAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGAAAATATGT
1 TATAATTAATAATTTTATAAGCTATAATTTTTGTAATGTTAACACAAAATAGAAAGCAAATATAT
** * * * * * * *
2148767 TTATATTTAAAGCGTATATATACTA-AAAGT-ATTTTAATATATATATAATAGTAATTATATTTC
66 TTATA-TTAAA-TATATATATA-TATATA-TAAATGTAATTTATATATAATAG-AATGATACTTA
* * * * * *
2148830 TTCT-ACTTGAACCCAATGTATATAAAGTATATATATTAAAAGAAATTACAAGTTAATTAATAAT
126 ATATAAATT-AACACAA--TATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATAAT
* ** * * * * *
2148894 CATAGTTTCATTAATTAATTTAATTAACTATATAGGTTTGTCTTTAATTATATGAAATTAAAAAA
188 CATA-ATTCAAGAATCAATTTAATTAACTATACAGATTTGTCCTTAATTACATGAAATTAAAAAA
* * * * * * * * *
2148959 ATAATTAGGTTTTC-AAACTATTCTAATCTTACAA-CTTCTCCTTAGATTTA-AATATTATAAGT
252 A-AACTAAG-TTCCAAAACTATTCTAATCTCAAAAGC-TCTCTTTAAATATATTA-ATTATAAGT
* *
2149021 TTATATAAACAA-AGGTATATATAT
313 TTATAGAAACAATA-ATATATATAT
* * * * *
2149045 TGTAATTAATAATTTTATAAGTTA-AAATTTTGTAATGTTAACATAAAATAGAAAGTAAATATAT
1 TATAATTAATAATTTTATAAGCTATAATTTTTGTAATGTTAACACAAAATAGAAAGCAAATATAT
*
2149109 TTATATTTAAAGTACATATATAAAAGCATTTTAATATATATATATATAAATGTAATTCTAT-TCC
66 TTATA--T----T--A-A-AT------A---T-ATATATATATATATAAATGTAATT-TATAT-A
* * * * * *
2149173 TTATA-AATGA-ACTTAATATATA-TATATA-TATATATAAAGTATATGTATTAAAAGACATTAC
109 TAATAGAATGATACTTAATATAAATTA-ACACAATATATAAACTATATATATTAAAAGACATTAC
* * * * * *
2149234 AAGTTAATTAATGATTATAGTTTCATGAATCAATTTAATTAATTATA-TGAGTTTGTCCTTAATT
173 AAGTTAATTAATAATCATA-ATTCAAGAATCAATTTAATTAACTATACAGA-TTTGTCCTTAATT
* * * * *
2149298 ACATGAAATTTTAAAAAAAAAACTAAGTTTCAAAACTATTTTAATCTTACAA-CTTCTCTTTAGG
236 ACATGAAA--TT-AAAAAAAAACTAAGTTCCAAAACTATTCTAATCTCAAAAGC-TCTCTTTA-A
*
2149362 CT-TA-TATATTATAAGTTTATAGAAA-AA-AAGTATATATAT
296 ATATATTA-ATTATAAGTTTATAGAAACAATAA-TATATATAT
* * * *
2149401 TATAATTAATAATTTTATAAGTTATAATTTTTGTAGTGTTAACACAAAATAGAAAGCAAGTATGT
1 TATAATTAATAATTTTATAAGCTATAATTTTTGTAATGTTAACACAAAATAGAAAGCAAATATAT
* * * * * * * **
2149466 TTATATTTAAAGTATATATATACTAAAAAT-ATTTTAGTTTATATATAATAGTAATTATATTTCT
66 TTATA-TTAAA-TATATATATA-TATATATAAATGTAATTTATATATAATAG-AATGATACTTAA
* * *
2149530 TATAAATTAACACAATATATAAACTCTGTATATTTAAAGACATTACAAGTTAATTAATAATCATA
127 TATAAATTAACACAATATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATCATA
* * * **
2149595 ATTCAAGAATTAATTTAATTAACTATACAGATTTGTTCTTAATTTCATGAAATTAAAAAAAAGTT
192 ATTCAAGAATCAATTTAATTAACTATACAGATTTGTCCTTAATTACATGAAATTAAAAAAAAACT
* * * *
2149660 ATGTTCCTAAACTATTCTAATCTCAAAAGCTCTGTTTAAATATATTAATTATAAGTTTATATAAA
257 AAGTTCCAAAACTATTCTAATCTCAAAAGCTCTCTTTAAATATATTAATTATAAGTTTATAGAAA
2149725 CAATAATATATATAT
322 CAATAATATATATAT
*
2149740 TATAATTAATAATTTTATAAGCTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATAT
1 TATAATTAATAATTTTATAAGCTATAATTTTTGTAATGTTAACACAAAATAGAAAGCAAATATAT
*
2149805 TTATATTAAATTTATATATATATATATA
66 TTATATTAAATATATATATATATATATA
2149833 GTAGTAACTG
Statistics
Matches: 642, Mismatches: 98, Indels: 102
0.76 0.12 0.12
Matches are distributed among these distances:
336 5 0.01
337 10 0.02
338 69 0.11
339 95 0.15
340 12 0.02
341 52 0.08
342 89 0.14
343 25 0.04
347 1 0.00
348 1 0.00
349 3 0.00
350 2 0.00
351 1 0.00
352 1 0.00
354 1 0.00
355 90 0.14
356 41 0.06
357 97 0.15
358 16 0.02
359 8 0.01
360 16 0.02
361 7 0.01
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (336 bp):
TATAATTAATAATTTTATAAGCTATAATTTTTGTAATGTTAACACAAAATAGAAAGCAAATATAT
TTATATTAAATATATATATATATATATAAATGTAATTTATATATAATAGAATGATACTTAATATA
AATTAACACAATATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATCATAATTC
AAGAATCAATTTAATTAACTATACAGATTTGTCCTTAATTACATGAAATTAAAAAAAAACTAAGT
TCCAAAACTATTCTAATCTCAAAAGCTCTCTTTAAATATATTAATTATAAGTTTATAGAAACAAT
AATATATATAT
Found at i:2150337 original size:35 final size:35
Alignment explanation
Indices: 2150285--2150392 Score: 126
Period size: 35 Copynumber: 3.1 Consensus size: 35
2150275 ATTCTATGAG
** *
2150285 TTATTCTATATGGAGTAGTGTTTTATTTATTCTAA
1 TTATTCTATATAAAGTAGTGCTTTATTTATTCTAA
* * *
2150320 TTATTCTGTATAAAGTAGTGCTTTATTTGTTTTAA
1 TTATTCTATATAAAGTAGTGCTTTATTTATTCTAA
* * * *
2150355 TTGTTCTATGTGAAGTAGTGCTTTACTTATTCTAA
1 TTATTCTATATAAAGTAGTGCTTTATTTATTCTAA
2150390 TTA
1 TTA
2150393 GGCAGACCTC
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 59 1.00
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (35 bp):
TTATTCTATATAAAGTAGTGCTTTATTTATTCTAA
Found at i:2154743 original size:6 final size:6
Alignment explanation
Indices: 2154734--2154764 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2154724 ATCTAAAAGT
2154734 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
2154765 CATATATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:2175641 original size:6 final size:6
Alignment explanation
Indices: 2175632--2175665 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2175622 AGCGCCTGGG
2175632 CCTGTT CCTGTT CCTGTT CCTGTT CCTGTT CCTG
1 CCTGTT CCTGTT CCTGTT CCTGTT CCTGTT CCTG
2175666 AAGATGCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.18, T:0.47
Consensus pattern (6 bp):
CCTGTT
Found at i:2176110 original size:20 final size:20
Alignment explanation
Indices: 2176085--2176123 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2176075 AATGATATTA
* *
2176085 TTAATTTGACATTTGAATAT
1 TTAATTTCACATTTAAATAT
2176105 TTAATTTCACATTTAAATA
1 TTAATTTCACATTTAAATA
2176124 ATAATGTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAATTTCACATTTAAATAT
Found at i:2183658 original size:20 final size:20
Alignment explanation
Indices: 2183633--2183671 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2183623 ATATTTTAGA
*
2183633 TTAAA-TATTTTAAGAAAATT
1 TTAAATTATATTAA-AAAATT
2183653 TTAAATTATATTAAAAAAT
1 TTAAATTATATTAAAAAAT
2183672 CAATTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
TTAAATTATATTAAAAAATT
Found at i:2184307 original size:42 final size:41
Alignment explanation
Indices: 2184190--2184320 Score: 133
Period size: 42 Copynumber: 3.2 Consensus size: 41
2184180 TGTTCTATGA
* *
2184190 TAAAAGAAAGTCAAATTCTTCTCTTCTCTTTCCTAGAATTTG
1 TAAAAAAAAGTCAAATTCTT-TTTTCTCTTTCCTAGAATTTG
* * ** * **
2184232 TAAGAGAAA-TTTAA-T-GTTTTTCTCTTTTTTAGAATTTG
1 TAAAAAAAAGTCAAATTCTTTTTTCTCTTTCCTAGAATTTG
*
2184270 TAAAAAAAAGTCAAATTCTTTTATTCTCTTTCCTAGAAATTG
1 TAAAAAAAAGTCAAATTCTTTT-TTCTCTTTCCTAGAATTTG
2184312 TAAAAAAAA
1 TAAAAAAAA
2184321 TTCGATGTTC
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
38 25 0.36
39 4 0.06
40 2 0.03
41 6 0.09
42 33 0.47
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (41 bp):
TAAAAAAAAGTCAAATTCTTTTTTCTCTTTCCTAGAATTTG
Found at i:2184329 original size:80 final size:80
Alignment explanation
Indices: 2184190--2184338 Score: 217
Period size: 80 Copynumber: 1.9 Consensus size: 80
2184180 TGTTCTATGA
* * * * * * *
2184190 TAAAAGAAAGTCAAATTCTTCTCTTCTCTTTCCTAGAATTTGTAAGAGAAATTTAATGTTTTTCT
1 TAAAAAAAAGTCAAATTCTTCTATTCTCTTTCCTAGAAATTGTAAAAAAAATTCAATGTTCTTCT
2184255 CTTTTTTAGAATTTG
66 CTTTTTTAGAATTTG
* *
2184270 TAAAAAAAAGTCAAATTCTTTTATTCTCTTTCCTAGAAATTGTAAAAAAAATTCGATGTTCTTCT
1 TAAAAAAAAGTCAAATTCTTCTATTCTCTTTCCTAGAAATTGTAAAAAAAATTCAATGTTCTTCT
2184335 CTTT
66 CTTT
2184339 CTTAAAATCA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 60 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (80 bp):
TAAAAAAAAGTCAAATTCTTCTATTCTCTTTCCTAGAAATTGTAAAAAAAATTCAATGTTCTTCT
CTTTTTTAGAATTTG
Found at i:2185792 original size:26 final size:26
Alignment explanation
Indices: 2185761--2185810 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2185751 TTAATCATGA
*
2185761 TTCTCATGTAATTTTAGAGGTACGAT
1 TTCTCATGTAACTTTAGAGGTACGAT
*
2185787 TTCTCATGTAACTTTGGAGGTACG
1 TTCTCATGTAACTTTAGAGGTACG
2185811 GTTTATGTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (26 bp):
TTCTCATGTAACTTTAGAGGTACGAT
Found at i:2192413 original size:3 final size:3
Alignment explanation
Indices: 2192405--2192429 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2192395 AATTGTTCCT
2192405 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
2192430 TTGGTATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:2192855 original size:2 final size:2
Alignment explanation
Indices: 2192848--2192886 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2192838 ATTGAGATTT
* *
2192848 GA GA GA GA GA GA GA GA GA GA -A AA GA GA GA CA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2192887 AGGAAACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.54, C:0.03, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2192873 original size:19 final size:19
Alignment explanation
Indices: 2192851--2192887 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2192841 GAGATTTGAG
*
2192851 AGAGAGAGAGAGAGAGAAA
1 AGAGAGACAGAGAGAGAAA
2192870 AGAGAGACAGAGAGAGAA
1 AGAGAGACAGAGAGAGAA
2192888 GGAAACAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.41, T:0.00
Consensus pattern (19 bp):
AGAGAGACAGAGAGAGAAA
Found at i:2193361 original size:16 final size:16
Alignment explanation
Indices: 2193340--2193376 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2193330 AAAAAATTAA
* *
2193340 AAAAATTAATTTTTTT
1 AAAAATAAAATTTTTT
2193356 AAAAATAAAATTTTTT
1 AAAAATAAAATTTTTT
2193372 AAAAA
1 AAAAA
2193377 AGAGTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAAATAAAATTTTTT
Found at i:2193591 original size:20 final size:17
Alignment explanation
Indices: 2193555--2193607 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 17
2193545 TAAAAATTTA
2193555 CTAAACAACTTTAATTTAATT
1 CTAAA-AACTTT-ATTT--TT
2193576 CTAAAAACTATTATTTTT
1 CTAAAAACT-TTATTTTT
2193594 CATAAAAACTTTAT
1 C-TAAAAACTTTAT
2193608 AATAGCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.23
19 8 0.27
20 8 0.27
21 7 0.23
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (17 bp):
CTAAAAACTTTATTTTT
Found at i:2205601 original size:16 final size:17
Alignment explanation
Indices: 2205570--2205602 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2205560 AACCCAATTC
*
2205570 CAATTAAACTTTAGAAT
1 CAATTAAACTTAAGAAT
2205587 CAATT-AACTTAAGAAT
1 CAATTAAACTTAAGAAT
2205603 AAGAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (17 bp):
CAATTAAACTTAAGAAT
Found at i:2210801 original size:85 final size:85
Alignment explanation
Indices: 2210589--2210803 Score: 315
Period size: 85 Copynumber: 2.5 Consensus size: 85
2210579 NNNNNNNNNN
* * * *
2210589 AATGATTGGTAATATGTTAGAATAAAACATTAAGAATTATGTTTGGGAATTAATGTTTAGAATTA
1 AATGATTGGTAATATGCTAGAATTAAACATTAAGAATTATATTTGAGAATTAATGTTTAGAATTA
*
2210654 TTGTTTGGATTTTTAATTAA
66 TTATTTGGATTTTTAATTAA
* * *
2210674 AATGATTGGTAATATACTAGAATTAAATATTAAAAATTATATTTGAGAATTAATGTTTAGAATTA
1 AATGATTGGTAATATGCTAGAATTAAACATTAAGAATTATATTTGAGAATTAATGTTTAGAATTA
2210739 TTATTTGGATTTTTAATTAA
66 TTATTTGGATTTTTAATTAA
** *
2210759 AATGATTGACAATATGCTAGAATTAAACATT-GGAATTAATATTTG
1 AATGATTGGTAATATGCTAGAATTAAACATTAAGAATT-ATATTTG
2210804 GGTGTTACTT
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
84 4 0.03
85 111 0.97
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.42
Consensus pattern (85 bp):
AATGATTGGTAATATGCTAGAATTAAACATTAAGAATTATATTTGAGAATTAATGTTTAGAATTA
TTATTTGGATTTTTAATTAA
Found at i:2213943 original size:60 final size:60
Alignment explanation
Indices: 2213875--2213990 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
2213865 TCTACTTGTA
* * * *
2213875 TTAATTATTCCACATAG-AGTAATGCTTCACTTATTCTAGTTGTTCCGTGTGAAGTAGTGC
1 TTAATTATTCCACAT-GTAGTAATGCTCCACTTATTCTAATTATTCCGCGTGAAGTAGTGC
*
2213935 TTAATTATTCCACATGTAGTAATGCTCCACTTATTCTAATTATTCTGCGTGAAGTA
1 TTAATTATTCCACATGTAGTAATGCTCCACTTATTCTAATTATTCCGCGTGAAGTA
2213991 ATGTTTTACT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 49 0.98
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (60 bp):
TTAATTATTCCACATGTAGTAATGCTCCACTTATTCTAATTATTCCGCGTGAAGTAGTGC
Found at i:2218776 original size:21 final size:21
Alignment explanation
Indices: 2218750--2218789 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2218740 ACTTTAAGTG
2218750 ATTAAAATAATAA-ATAATAAC
1 ATTAAAA-AATAACATAATAAC
2218771 ATTAAAAAATAACATAATA
1 ATTAAAAAATAACATAATA
2218790 TTTTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTAAAAAATAACATAATAAC
Found at i:2223014 original size:169 final size:165
Alignment explanation
Indices: 2222730--2223046 Score: 447
Period size: 169 Copynumber: 1.9 Consensus size: 165
2222720 TTCAAAGACC
*
2222730 TTAATATTGAGAATTATTGTTTGGATAATTAATTAAAATGATTTGATGCTAGAATTAAACATTAA
1 TTAATATTGAGAATTATTGTTTGGATAATTAATTAAAATGATTTGATACTAGAATTAAACATTAA
* * * **
2222795 GAATAATGTTTGGGAATTAATATTTAAAATTATTGTTTGGATTTTTAATTAAAATGATTGGTAAT
66 AAATAATGTTTGAGAATTAATATTTAAAATTATTATTTGGATTTTTAATTAAAATGATTGACAAT
2222860 ATGTTAGAATTAAACATTAAGATTTATGTTGGGAA
131 ATGTTAGAATTAAACATTAAGATTTATGTTGGGAA
* * * * * *
2222895 TTAATGTTTAGAATTATTGTTTGGAT-CTGTAATTAAAATGATTGGTAATATACTATAATTAAAT
1 TTAATATTGAGAATTATTGTTTGGATAAT-TAATTAAAATGATT--T--GATACTAGAATTAAAC
* * *
2222959 ATTAAAAATTATGTTTGAGAATTAATGTTTAGAATTATTATTTGGATTTTTAATTAAAATGATTG
61 ATTAAAAATAATGTTTGAGAATTAATATTTAAAATTATTATTTGGATTTTTAATTAAAATGATTG
2223024 ACAATATGTTAGAATTAAACATT
126 ACAATATGTTAGAATTAAACATT
2223047 GGAATTAATA
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
164 1 0.01
165 38 0.29
167 1 0.01
169 92 0.70
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (165 bp):
TTAATATTGAGAATTATTGTTTGGATAATTAATTAAAATGATTTGATACTAGAATTAAACATTAA
AAATAATGTTTGAGAATTAATATTTAAAATTATTATTTGGATTTTTAATTAAAATGATTGACAAT
ATGTTAGAATTAAACATTAAGATTTATGTTGGGAA
Found at i:2223021 original size:85 final size:85
Alignment explanation
Indices: 2222730--2223046 Score: 410
Period size: 85 Copynumber: 3.8 Consensus size: 85
2222720 TTCAAAGACC
* ** *
2222730 TTAATATTGAGAATTATTGTTTGGATAATTAATTAAAATGATT--T--GATGCTAGAATTAAACA
1 TTAATATTTAGAATTATTGTTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAACA
*
2222791 TTAAGAATAATGTTTGGGAA
66 TTAAGAATTATGTTTGGGAA
* *
2222811 TTAATATTTAAAATTATTGTTTGGATTTTTAATTAAAATGATTGGTAATATGTTAGAATTAAACA
1 TTAATATTTAGAATTATTGTTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAACA
*
2222876 TTAAGATTTATG-TTGGGAA
66 TTAAGAATTATGTTTGGGAA
* * * * * *
2222895 TTAATGTTTAGAATTATTGTTTGGATCTGTAATTAAAATGATTGGTAATATACTATAATTAAATA
1 TTAATATTTAGAATTATTGTTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAACA
* *
2222960 TTAAAAATTATGTTTGAGAA
66 TTAAGAATTATGTTTGGGAA
* * ** *
2222980 TTAATGTTTAGAATTATTATTTGGATTTTTAATTAAAATGATTGACAATATGTTAGAATTAAACA
1 TTAATATTTAGAATTATTGTTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAACA
2223045 TT
66 TT
2223047 GGAATTAATA
Statistics
Matches: 203, Mismatches: 28, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
81 39 0.19
83 1 0.00
84 74 0.36
85 89 0.44
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (85 bp):
TTAATATTTAGAATTATTGTTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGAATTAAACA
TTAAGAATTATGTTTGGGAA
Found at i:2225705 original size:25 final size:25
Alignment explanation
Indices: 2225671--2225727 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
2225661 CTTTTGAAAC
*
2225671 TAATATTTATTTATTATATAAAGAT
1 TAATATTTATTTATTACATAAAGAT
* * *
2225696 TAATGTTTATTTATTGCATGAAGAT
1 TAATATTTATTTATTACATAAAGAT
2225721 TAATATT
1 TAATATT
2225728 ATTAATCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.51
Consensus pattern (25 bp):
TAATATTTATTTATTACATAAAGAT
Found at i:2231465 original size:17 final size:17
Alignment explanation
Indices: 2231445--2231477 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2231435 AAAATTACTT
*
2231445 TTCTTTTTTCATTAAAA
1 TTCTTCTTTCATTAAAA
2231462 TTCTTCTTTCATTAAA
1 TTCTTCTTTCATTAAA
2231478 CACCTACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCTTCTTTCATTAAAA
Found at i:2236261 original size:15 final size:15
Alignment explanation
Indices: 2236214--2236262 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
2236204 TTTGCACACC
*
2236214 TATTTTTTTTTCTAT
1 TATTTTTTTTACTAT
* * *
2236229 TATTATTTTTATTTT
1 TATTTTTTTTACTAT
*
2236244 TATTTTTTTTAGTAT
1 TATTTTTTTTACTAT
2236259 TATT
1 TATT
2236263 ATTATAAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (15 bp):
TATTTTTTTTACTAT
Found at i:2238724 original size:27 final size:25
Alignment explanation
Indices: 2238670--2238724 Score: 58
Period size: 27 Copynumber: 2.0 Consensus size: 25
2238660 TGTGAACGTA
2238670 AGAGAAAATAAATATTTATTAGGTATT
1 AGAGAAAATAAATATTTATTA-G-ATT
2238697 AGAGAATAAGTAAATATTTTATTA-ATT
1 AGAGAA-AA-TAAATA-TTTATTAGATT
2238724 A
1 A
2238725 CCTTAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
27 10 0.40
28 2 0.08
29 6 0.24
30 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (25 bp):
AGAGAAAATAAATATTTATTAGATT
Found at i:2244722 original size:21 final size:21
Alignment explanation
Indices: 2244698--2244739 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2244688 TCACTTCCTT
*
2244698 TATTATACAGTATCAATAATA
1 TATTACACAGTATCAATAATA
* *
2244719 TATTACATAGTATTAATAATA
1 TATTACACAGTATCAATAATA
2244740 AGATTAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (21 bp):
TATTACACAGTATCAATAATA
Found at i:2263430 original size:16 final size:16
Alignment explanation
Indices: 2263409--2263439 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2263399 TCCAAATTGG
2263409 AAGAAGGTAATGTCCC
1 AAGAAGGTAATGTCCC
2263425 AAGAAGGTAATGTCC
1 AAGAAGGTAATGTCC
2263440 TTTATTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (16 bp):
AAGAAGGTAATGTCCC
Found at i:2268477 original size:35 final size:35
Alignment explanation
Indices: 2268431--2268500 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2268421 ACCAGTTGTC
2268431 AGACATCTTTACTAAAAGACTCAGCAAAGATAAGT
1 AGACATCTTTACTAAAAGACTCAGCAAAGATAAGT
2268466 AGACATCTTTACTAAAAGACTCAGCAAAGATAAGT
1 AGACATCTTTACTAAAAGACTCAGCAAAGATAAGT
2268501 TTGAGTTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (35 bp):
AGACATCTTTACTAAAAGACTCAGCAAAGATAAGT
Found at i:2273956 original size:17 final size:18
Alignment explanation
Indices: 2273920--2273962 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2273910 CGTTTTTAAG
*
2273920 AATATATATCTTTATTATA
1 AATAT-TATCTTTATAATA
2273939 AATATTATCTTT-TAATA
1 AATATTATCTTTATAATA
*
2273956 AAAATTA
1 AATATTA
2273963 AAAGGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.45
18 7 0.32
19 5 0.23
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATTATCTTTATAATA
Found at i:2278687 original size:5 final size:5
Alignment explanation
Indices: 2278677--2278701 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2278667 TTTGCTTCTG
2278677 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
2278702 TTGTAGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:2290097 original size:71 final size:71
Alignment explanation
Indices: 2289999--2290136 Score: 190
Period size: 71 Copynumber: 1.9 Consensus size: 71
2289989 ACCCTGACAC
* * *
2289999 AACCTAAATTAATTTAACTAATTTTAAATTTTAT-TAAATTTAATCATTTAATTAATT-ACTTAA
1 AACCTAAATTAAGTTAAATAATTTTAAATTTT-TCTAAATTTAATAATTTAATTAATTGA-TTAA
2290062 TTACCCTA
64 TTACCCTA
* * *
2290070 AACCTTAATTAAGTTAAATAATTTTAAATTTTTCTAAATTTACTAATTTAATTTATTGATTAATT
1 AACCTAAATTAAGTTAAATAATTTTAAATTTTTCTAAATTTAATAATTTAATTAATTGATTAATT
2290135 AC
66 AC
2290137 TAATACATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
70 1 0.02
71 57 0.97
72 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.48
Consensus pattern (71 bp):
AACCTAAATTAAGTTAAATAATTTTAAATTTTTCTAAATTTAATAATTTAATTAATTGATTAATT
ACCCTA
Found at i:2290225 original size:37 final size:37
Alignment explanation
Indices: 2290183--2290369 Score: 347
Period size: 37 Copynumber: 5.1 Consensus size: 37
2290173 ACTAATTCCC
2290183 TAAACCCTAAACCCTAATTTAAATAAATAAAATATTA
1 TAAACCCTAAACCCTAATTTAAATAAATAAAATATTA
* *
2290220 TAAACCCTAAACGCTAATTTAAGTAAATAAAATATTA
1 TAAACCCTAAACCCTAATTTAAATAAATAAAATATTA
2290257 TAAACCCTAAACCCTAATTTAAATAAATAAAATATTA
1 TAAACCCTAAACCCTAATTTAAATAAATAAAATATTA
*
2290294 TAAACCCTAAACCCTAATTTAAATAAACAAAATATTA
1 TAAACCCTAAACCCTAATTTAAATAAATAAAATATTA
2290331 TAAACCCTAAACCCTAATTTAAATAAATAAAATATTA
1 TAAACCCTAAACCCTAATTTAAATAAATAAAATATTA
2290368 TA
1 TA
2290370 TAATATTACT
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 144 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (37 bp):
TAAACCCTAAACCCTAATTTAAATAAATAAAATATTA
Found at i:2290329 original size:429 final size:426
Alignment explanation
Indices: 2289467--2290329 Score: 1091
Period size: 429 Copynumber: 2.0 Consensus size: 426
2289457 TAATTAATTT
* *
2289467 AAATA-TTTTTAAATTAACTTATATTACTAATTTAATTCATTTGTAAATAACTAATTACAAAATT
1 AAATATTTTTTAAATTAACTAATATTACTAATTTAATTCATTTCTAAATAACTAATTACAAAATT
* *
2289531 TTTTCATTTGATTAGTTAAATTCTTTAATTACCCTAACATAACCTTAATTAATATAACTAATTTT
66 TTTTCATTTGATTAGTTAAATTCTTTAATTACCCTAACACAACCTAAATTAATATAACTAATTTT
* * * ** **
2289596 AAAATTTATTATATTTACTCATTTAATTATTTGTTTAATTACCCTAAACCTTAATTAAGTTAGGT
131 AAAATTTATTAAATTTAATCATTTAATTAATTACTTAATTACCCTAAACCTTAATTAAGTTAAAT
* *
2289661 AATTTTAATTTTTTCTAAATTTACTAATTTAATTTATTATTAATTGCTAATACATGATTATTTTT
196 AATTTTAAATTTTTCTAAATTTACTAATTTAATTTATTATTAATTACTAATACATGATTATTTTT
* *
2289726 ATTTACTTAAATTATTTAATTAATTCCCTAAACCCTAAACCCTAATTTAAATAAACAAAATAGTG
261 ATTCACTTAAATTATTTAACTAATTCCCTAAACCCTAAACCCTAATTTAAATAAACAAAATAGTG
*** ** * * *** * ** * * * *
2289791 TATAATGTTACTCATTTATTAATTTCTTATTTACTTATATAACACGTACCATTACTTAATTAACT
326 TATAACCCTAAACACTAATTAATAAATAAAATACTTATATAACACCTACCATAACTTAAATAAAT
* * * ***
2289856 AAATTATTTAATTCACTCATTAAACCTTTAATTAATTT
391 AAAATATTTAA-T-ACTCACTAAACCTTTAAATAAACA
*
2289894 AAATATTTTTTAAAATTAACTAATATTACTGATTTAATTCATTTCTAAATAACTAATTA-AAACA
1 AAATATTTTTT-AAATTAACTAATATTACTAATTTAATTCATTTCTAAATAACTAATTACAAA-A
* *
2289958 TTTTTT-ATTTGATTAGTTAAATTCTTTAATTACCCTGACACAACCTAAATTAATTTAACTAATT
64 TTTTTTCATTTGATTAGTTAAATTCTTTAATTACCCTAACACAACCTAAATTAATATAACTAATT
*
2290022 TTAAATTTTATTAAATTTAATCATTTAATTAATTACTTAATTACCCTAAACCTTAATTAAGTTAA
129 TTAAAATTTATTAAATTTAATCATTTAATTAATTACTTAATTACCCTAAACCTTAATTAAGTTAA
*
2290087 ATAATTTTAAATTTTTCTAAATTTACTAATTTAATTTATTGATTAATTACTAATACATTATTATT
194 ATAATTTTAAATTTTTCTAAATTTACTAATTTAATTTATT-ATTAATTACTAATACATGATTATT
*
2290152 TTTATTCACTTAAATTATTTAACTAATTCCCTAAACCCTAAACCCTAATTTAAATAAATAAAATA
258 TTTATTCACTTAAATTATTTAACTAATTCCCTAAACCCTAAACCCTAATTTAAATAAACAAAATA
* * *
2290217 -T-TATAAACCCTAAACGCTAATTTAAGTAAATAAAATA-TTATA-AAC-CCTAAACCCTAATTT
323 GTGTAT-AACCCTAAACACTAA-TTAA-TAAATAAAATACTTATATAACACCT--ACCATAACTT
2290277 AAATAAATAAAATATTATAA-AC-C-CTAAACCCTAATTTAAATAAACA
383 AAATAAATAAAATATT-TAATACTCACTAAA-CC---TTTAAATAAACA
2290323 AAATATT
1 AAATATT
2290330 ATAAACCCTA
Statistics
Matches: 375, Mismatches: 47, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
425 4 0.01
426 3 0.01
427 12 0.03
428 169 0.45
429 179 0.48
430 8 0.02
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (426 bp):
AAATATTTTTTAAATTAACTAATATTACTAATTTAATTCATTTCTAAATAACTAATTACAAAATT
TTTTCATTTGATTAGTTAAATTCTTTAATTACCCTAACACAACCTAAATTAATATAACTAATTTT
AAAATTTATTAAATTTAATCATTTAATTAATTACTTAATTACCCTAAACCTTAATTAAGTTAAAT
AATTTTAAATTTTTCTAAATTTACTAATTTAATTTATTATTAATTACTAATACATGATTATTTTT
ATTCACTTAAATTATTTAACTAATTCCCTAAACCCTAAACCCTAATTTAAATAAACAAAATAGTG
TATAACCCTAAACACTAATTAATAAATAAAATACTTATATAACACCTACCATAACTTAAATAAAT
AAAATATTTAATACTCACTAAACCTTTAAATAAACA
Found at i:2302014 original size:14 final size:13
Alignment explanation
Indices: 2301981--2302048 Score: 84
Period size: 13 Copynumber: 5.1 Consensus size: 13
2301971 GGTTCCCACC
2301981 ATTTCCCTCCAAA
1 ATTTCCCTCCAAA
2301994 ATTTCCCTCCAAA
1 ATTTCCCTCCAAA
2302007 ATTTTCCCTCCAAA
1 A-TTTCCCTCCAAA
* *
2302021 GGATTT-CTTCCAAG
1 --ATTTCCCTCCAAA
2302035 ATTTCCCTCCAAA
1 ATTTCCCTCCAAA
2302048 A
1 A
2302049 CCATTTGGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
12 4 0.09
13 21 0.45
14 18 0.38
15 3 0.06
16 1 0.02
ACGTcount: A:0.29, C:0.34, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTTCCCTCCAAA
Found at i:2302018 original size:27 final size:25
Alignment explanation
Indices: 2301981--2302048 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 25
2301971 GGTTCCCACC
2301981 ATTTCCCTCCAAAATTTCCCTCCAAA
1 ATTTCCCTCCAAAATTT-CCTCCAAA
* *
2302007 ATTTTCCCTCCAAAGGATTTCTTCCAAG
1 A-TTTCCCTCCAAA--ATTTCCTCCAAA
2302035 ATTTCCCTCCAAAA
1 ATTTCCCTCCAAAA
2302049 CCATTTGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 24 0.65
28 7 0.19
29 4 0.11
ACGTcount: A:0.29, C:0.34, G:0.04, T:0.32
Consensus pattern (25 bp):
ATTTCCCTCCAAAATTTCCTCCAAA
Found at i:2302158 original size:26 final size:26
Alignment explanation
Indices: 2302099--2302152 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2302089 AGGAAATCCC
* * *
2302099 TACATGGGTCTTGGTGGTTGGCACCC
1 TACATGGGTCTTGGGGGCTGGCACCA
2302125 TACATGGGTCTTGGAGGGCTGGCACCA
1 TACATGGGTCTTGG-GGGCTGGCACCA
2302152 T
1 T
2302153 CTTGGGCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.15, C:0.22, G:0.35, T:0.28
Consensus pattern (26 bp):
TACATGGGTCTTGGGGGCTGGCACCA
Found at i:2310768 original size:28 final size:28
Alignment explanation
Indices: 2310736--2310877 Score: 133
Period size: 28 Copynumber: 4.9 Consensus size: 28
2310726 TAACTTTAAC
*
2310736 ATGTTTGTCTAAATTTAGACAAGAAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAT
2310764 ATGTTTGTCTTAATTTAAGACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAG-AAAAT
* * *
2310794 ATTTTTTGTCTTAATCTAGACAAGAAAAC
1 A-TGTTTGTCTTAATTTAGACAAGAAAAT
* *
2310823 ATATTTGT-TTCAATTTAGACTAGATAAAAT
1 ATGTTTGTCTT-AATTTAGAC-A-AGAAAAT
* * *
2310853 ATTTTTATCTTAATTAAAGACAAGA
1 ATGTTTGTCTTAATT-TAGACAAGA
2310878 GTTGTCTTAA
Statistics
Matches: 94, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.02
28 29 0.31
29 15 0.16
30 29 0.31
31 19 0.20
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAT
Found at i:2310838 original size:59 final size:58
Alignment explanation
Indices: 2310739--2310866 Score: 161
Period size: 59 Copynumber: 2.2 Consensus size: 58
2310729 CTTTAACATG
* * * *
2310739 TTTGTCTAAATTTAGACAAGAAAATATGTTTGTCTTAATTTAAGACAAGA-AAAATATTT
1 TTTGTCTTAATCTAGACAAGAAAACATATTTGTCTTAATTT-AGACAAGATAAAATA-TT
*
2310798 TTTGTCTTAATCTAGACAAGAAAACATATTTGT-TTCAATTTAGACTAGATAAAATATT
1 TTTGTCTTAATCTAGACAAGAAAACATATTTGTCTT-AATTTAGACAAGATAAAATATT
*
2310856 TTTATCTTAAT
1 TTTGTCTTAAT
2310867 TAAAGACAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 21 0.34
59 40 0.66
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (58 bp):
TTTGTCTTAATCTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGATAAAATATT
Found at i:2311040 original size:17 final size:17
Alignment explanation
Indices: 2311018--2311050 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2311008 ATAATAATAA
2311018 AATAAA-AGTTATTATTC
1 AATAAAGAGTT-TTATTC
2311035 AATAAAGAGTTTTATT
1 AATAAAGAGTTTTATT
2311051 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (17 bp):
AATAAAGAGTTTTATTC
Found at i:2313823 original size:15 final size:15
Alignment explanation
Indices: 2313801--2313841 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2313791 AGCGAACATC
2313801 AAATACTTTTAATAT
1 AAATACTTTTAATAT
* *
2313816 ATATACTTTAAATAT
1 AAATACTTTTAATAT
*
2313831 AAATATTTTTA
1 AAATACTTTTA
2313842 CTTTTTATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATACTTTTAATAT
Found at i:2314089 original size:3 final size:3
Alignment explanation
Indices: 2314081--2314112 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2314071 TTTTATAATT
*
2314081 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2314113 TATTAAGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2314260 original size:40 final size:40
Alignment explanation
Indices: 2314215--2314370 Score: 152
Period size: 40 Copynumber: 3.9 Consensus size: 40
2314205 CACCCTCTCC
* *
2314215 TTCTTCTTTCTTTTCTTCCCCAACGACTGCTAG-TAGCTCA
1 TTCTTCTTTCTTTTCTTCCCCAACCACTGCTAGCCA-CTCA
* * * * * *
2314255 TTCTTCTTTTTTTTTCTTCCTCAGCCACTACCAGCCACTCC
1 TTCTTC-TTTCTTTTCTTCCCCAACCACTGCTAGCCACTCA
* * *
2314296 TTCTTCTTTCTTTTTTTCCCCAACCATTGCTAGCCACTCT
1 TTCTTCTTTCTTTTCTTCCCCAACCACTGCTAGCCACTCA
* * * *
2314336 TTCTTCTTTTTTTTCTTCCCTAGCCACTGGTAGCC
1 TTCTTCTTTCTTTTCTTCCCCAACCACTGCTAGCC
2314371 GCTCCTTATT
Statistics
Matches: 92, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 61 0.66
41 30 0.33
42 1 0.01
ACGTcount: A:0.12, C:0.35, G:0.08, T:0.46
Consensus pattern (40 bp):
TTCTTCTTTCTTTTCTTCCCCAACCACTGCTAGCCACTCA
Found at i:2314296 original size:81 final size:80
Alignment explanation
Indices: 2314211--2314363 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 80
2314201 TTTTCACCCT
* *
2314211 CTCCTTCTTCTTTCTTTTCTTCCCCAACGACTGCTAG-TAGCTCATTCTTCTTTTTTTTTCTT-C
1 CTCCTTCTTCTTTCTTTTCTTCCCCAACCACTGCTAGCCA-CTCATTCTTC-TTTTTTTTCTTCC
2314274 CTCAGCCACTACCAGCCA
64 CT-AGCCACTACCAGCCA
* * *
2314292 CTCCTTCTTCTTTCTTTTTTTCCCCAACCATTGCTAGCCACTCTTTCTTCTTTTTTTTCTTCCCT
1 CTCCTTCTTCTTTCTTTTCTTCCCCAACCACTGCTAGCCACTCATTCTTCTTTTTTTTCTTCCCT
2314357 AGCCACT
66 AGCCACT
2314364 GGTAGCCGCT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
80 18 0.28
81 46 0.71
82 1 0.02
ACGTcount: A:0.12, C:0.36, G:0.06, T:0.46
Consensus pattern (80 bp):
CTCCTTCTTCTTTCTTTTCTTCCCCAACCACTGCTAGCCACTCATTCTTCTTTTTTTTCTTCCCT
AGCCACTACCAGCCA
Found at i:2317498 original size:40 final size:41
Alignment explanation
Indices: 2317389--2317498 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 41
2317379 TGTTGTTTGA
* * **
2317389 ATATTTATTTTTTAGTTATTTAAGTTTATGTTGTTTGTTTGG
1 ATATTTA-TTTTTAGTTATTTAAGTTTATATCGTTTGCATGG
* * * *
2317431 ATCTTTATGTTTAGTTATCTACGTTTATATCG-TTGCATGG
1 ATATTTATTTTTAGTTATTTAAGTTTATATCGTTTGCATGG
* *
2317471 ATATTTGTTTTTAGTTATTTAAATTTAT
1 ATATTTATTTTTAGTTATTTAAGTTTAT
2317499 GTTTAAGATC
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
40 28 0.52
41 20 0.37
42 6 0.11
ACGTcount: A:0.22, C:0.05, G:0.15, T:0.59
Consensus pattern (41 bp):
ATATTTATTTTTAGTTATTTAAGTTTATATCGTTTGCATGG
Found at i:2318191 original size:49 final size:49
Alignment explanation
Indices: 2318119--2318214 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 49
2318109 TCTGAAACCG
* *
2318119 TGACATACTCTCCTACTCCAACAAA-AGCACACCATCCTCAATGGCACCA
1 TGACATACTCTCCTACTCCAACAAAGA-CACACCATCCTAAATAGCACCA
* ** *
2318168 TGACATACTCTCCTATTTTAACAAAGACACACTATCCTAAATAGCAC
1 TGACATACTCTCCTACTCCAACAAAGACACACCATCCTAAATAGCAC
2318215 ATTACAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
49 39 0.98
50 1 0.03
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.23
Consensus pattern (49 bp):
TGACATACTCTCCTACTCCAACAAAGACACACCATCCTAAATAGCACCA
Found at i:2323835 original size:20 final size:20
Alignment explanation
Indices: 2323806--2323843 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2323796 AATCAAGGAG
*
2323806 AACCAGTTTTAGGGTTTCAA
1 AACCAATTTTAGGGTTTCAA
*
2323826 AACCAATTTTTGGGTTTC
1 AACCAATTTTAGGGTTTC
2323844 GTGGAAAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (20 bp):
AACCAATTTTAGGGTTTCAA
Found at i:2325323 original size:15 final size:15
Alignment explanation
Indices: 2325303--2325356 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
2325293 ATTACAATGC
2325303 AATGTGATTGCAAGT
1 AATGTGATTGCAAGT
*
2325318 AATGTGATTACAAGT
1 AATGTGATTGCAAGT
* *
2325333 AATGTGATTGTAAAT
1 AATGTGATTGCAAGT
2325348 AATGTGATT
1 AATGTGATT
2325357 ACAGGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:2325339 original size:30 final size:31
Alignment explanation
Indices: 2325293--2325359 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
2325283 CGTTTGATAC
*
2325293 ATTACAATGCAATGTGATTGCAAGTAATGTG
1 ATTACAATGCAATGTGATTGCAAATAATGTG
* *
2325324 ATTACAA-GTAATGTGATTGTAAATAATGTG
1 ATTACAATGCAATGTGATTGCAAATAATGTG
2325354 ATTACA
1 ATTACA
2325360 GGAAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.34
Consensus pattern (31 bp):
ATTACAATGCAATGTGATTGCAAATAATGTG
Found at i:2325570 original size:21 final size:21
Alignment explanation
Indices: 2325544--2325684 Score: 67
Period size: 21 Copynumber: 6.4 Consensus size: 21
2325534 TTCTTAAATA
2325544 TATTTTTAATATCATATATTT
1 TATTTTTAATATCATATATTT
*
2325565 TATTTTTATTTATTATTATAATATTT
1 TATTTTTA---A-TATCAT-ATATTT
* * *
2325591 TATATTTTATTTTTA-ATATATT
1 TAT-TTTTAATATCATATAT-TT
* *
2325613 TATATTT-ATATTAT-TAATTT
1 TATTTTTAATATCATAT-ATTT
* *
2325633 TA--TATAATATCATATTTTAAAT
1 TATTTTTAATATCATATATT---T
2325655 ATATTTTTAATATCATATATTT
1 -TATTTTTAATATCATATATTT
2325677 TATTTTTA
1 TATTTTTA
2325685 TTTATTATTA
Statistics
Matches: 92, Mismatches: 11, Indels: 34
0.67 0.08 0.25
Matches are distributed among these distances:
18 2 0.02
19 8 0.09
20 10 0.11
21 25 0.27
22 7 0.08
23 6 0.07
24 1 0.01
25 19 0.21
26 9 0.10
27 5 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTAATATCATATATTT
Found at i:2325598 original size:49 final size:51
Alignment explanation
Indices: 2325541--2325921 Score: 221
Period size: 54 Copynumber: 7.0 Consensus size: 51
2325531 CATTTCTTAA
2325541 ATATATTTTTAATATCATATATTT-TATTTTTATTTATTATTATAATATTTT
1 ATATATTTTTAATATCATATATTTATATTTTTATTTATTATTAT-ATATTTT
* *
2325592 ATATTTTATTTTTAATAT-ATTTATATTTATATTATTAATTTTATATAATATCATATTTT
1 ATA---TATTTTTAATATCA--TATATTTATATT-TTTA-TTTAT-TATTAT-ATATTTT
2325651 AAATATATTTTTAATATCATATATTT-TATTTTTATTTATTATTATA-ATTTT
1 --ATATATTTTTAATATCATATATTTATATTTTTATTTATTATTATATATTTT
* * *
2325702 ATATA-TTTTATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTT
1 ATATATTTTTA-ATATCATATATTTATATTTTTA-T-TT-A---TTAT-T-ATAT-A-TT-TT
*
2325764 AAATATATTTTTAATGTCATATATTT-TA-TTTTATTTATTATTATTATATTTT
1 --ATATATTTTTAATATCATATATTTATATTTTTATTTATTATTA-TATATTTT
* * * * **
2325816 ATAT-TTTATT--TTTAATATATTTATATTTATA-TTATTAATTTTTATATAAT
1 ATATATTT-TTAATATCATATATTTATATTTTTATTTATT-A-TTATATATTTT
* * *
2325866 ATCATATTTTAAATAT-ATTTTATTTTTATTTATTATTATAATT-TTATATATTTT
1 AT-ATATTTTTAATATCA-TATATTTATATTT-TTATT-T-ATTATTATATATTTT
2325920 AT
1 AT
2325922 TTTCATTTCT
Statistics
Matches: 261, Mismatches: 25, Indels: 85
0.70 0.07 0.23
Matches are distributed among these distances:
48 15 0.06
49 25 0.10
50 27 0.10
51 14 0.05
52 9 0.03
53 22 0.08
54 31 0.12
55 15 0.06
56 17 0.07
57 14 0.05
58 20 0.08
59 14 0.05
60 3 0.01
61 6 0.02
62 7 0.03
63 2 0.01
64 15 0.06
65 5 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (51 bp):
ATATATTTTTAATATCATATATTTATATTTTTATTTATTATTATATATTTT
Found at i:2325616 original size:6 final size:6
Alignment explanation
Indices: 2325558--2325624 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
2325548 TTTAATATCA
* * *
2325558 TATATT T-TATT TTTATT TATTATT ATAATATTT TATATT T-TATT TTTA-A
1 TATATT TATATT TATATT TA-TATT -T-ATA-TT TATATT TATATT TATATT
2325607 TATATT TATATT TATATT
1 TATATT TATATT TATATT
2325625 ATTAATTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 23 0.46
7 7 0.14
8 4 0.08
9 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATATT
Found at i:2325661 original size:63 final size:61
Alignment explanation
Indices: 2325591--2325924 Score: 173
Period size: 64 Copynumber: 5.4 Consensus size: 61
2325581 TATAATATTT
*
2325591 TATATTTTATTTTTAATATATTTATATTTATATTA-T-TAATTTTATATAATATCATATTTTAAA
1 TATATTTTATTTTT-ATATATTTATTTTTATATTATTATAATTTTATAT-AT-T-ATATTTTAAA
* * * * *
2325654 TATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTAA
1 TATA-TTTTATTTTTATATA-TTTATTTTTA--TATTATTATAATTTTATATATTATATTTTAAA
* * * * *
2325719 TATATTTATATTTTTAT-TATTAATTTTTATA-TAATATCATTTCT-TA-AATATATTTTTAA
1 TATATTT-TATTTTTATATATTTATTTTTATATTATTATAATTT-TATATATTATATTTTAAA
* * * *
2325778 TGTCA---TATATTT-TAT-TTTATTTAT-TATTATTAT-ATTTTATAT-TT-TATTTTTAA
1 TAT-ATTTTATTTTTATATATTTATTTTTATATTATTATAATTTTATATATTATATTTTAAA
* * * * *
2325831 TATA-TTTATATTTATATTATTAATTTTTATA-TAATATCATATTTTAAATATATTTTATTTT-T
1 TATATTTTATTTTTATA-TATTTATTTTTATATTATTAT-A-ATTTT--ATATATTATATTTTAA
2325893 A
61 A
*
2325894 TTTATTATTATAATTTTATATATTTTATTTT
1 TATATT-TTAT--TTTTATATA-TTTATTTT
2325925 CATTTCTTTA
Statistics
Matches: 212, Mismatches: 28, Indels: 58
0.71 0.09 0.19
Matches are distributed among these distances:
52 1 0.00
53 12 0.06
54 16 0.08
55 15 0.07
56 8 0.04
57 12 0.06
58 2 0.01
59 13 0.06
60 17 0.08
61 3 0.01
62 4 0.02
63 24 0.11
64 28 0.13
65 22 0.10
66 8 0.04
67 16 0.08
68 11 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (61 bp):
TATATTTTATTTTTATATATTTATTTTTATATTATTATAATTTTATATATTATATTTTAAA
Found at i:2325682 original size:112 final size:113
Alignment explanation
Indices: 2325537--2325886 Score: 627
Period size: 112 Copynumber: 3.1 Consensus size: 113
2325527 ATTTCATTTC
2325537 TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
1 TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
2325602 TTTAATATATTTATATTTATATTATTAA-TTTTATATAATATCATATT
66 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT
2325649 TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTAT
1 TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTAT
*
2325713 TTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TT
65 TTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT
* *
2325761 CTTAAATATATTTTTAATGTCATATATTTTA-TTTTATTTATTATTATTATATTTTATATTTTAT
1 -TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTAT
2325825 TTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT
65 TTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT
2325874 TTAAATATATTTT
1 TTAAATATATTTT
2325887 ATTTTTATTT
Statistics
Matches: 229, Mismatches: 4, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
111 3 0.01
112 176 0.77
113 50 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (113 bp):
TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT
Found at i:2325685 original size:6 final size:6
Alignment explanation
Indices: 2325674--2325748 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
2325664 ATATCATATA
* * * *
2325674 TTTTAT TTTTAT TTATTAT TATAAT TTTATAT ATTTTAT TTTTA- ATATAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTT-TAT -TTTTAT TTTTAT TTTTAT
* *
2325724 TTATAT TTTTAT TATTAAT TTTTAT
1 TTTTAT TTTTAT T-TTTAT TTTTAT
2325749 ATAATATCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
5 3 0.06
6 33 0.61
7 15 0.28
8 3 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAT
Found at i:2325795 original size:5 final size:5
Alignment explanation
Indices: 2325785--2326065 Score: 60
Period size: 5 Copynumber: 54.4 Consensus size: 5
2325775 TAATGTCATA
* * *
2325785 TATTT TATTT TA-TT TATTAT TATTA TATTTT ATATTT TATTTT TAATA
1 TATTT TATTT TATTT TATT-T TATTT TA-TTT -TATTT TA-TTT TATTT
* * ** ** * *
2325833 TATTT ATATTT ATATTAT TAATT T-TTA TATAA TATCA TATTT TAAATA
1 TATTT -TATTT -TATT-T TATTT TATTT TATTT TATTT TATTT T-ATTT
* *
2325881 TATTT TATTTT TATTTAT TATTAT AATTT TA-TA TATTT TATTT TCATTT
1 TATTT TA-TTT TA-TT-T TATT-T TATTT TATTT TATTT TATTT T-ATTT
* * * * * * *
2325930 CT-TTAA TATAT T-TTT TATAT TA-TA TATTT TATTT TAATT TGTTT TA-CT
1 -TATT-T TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
* * * * *
2325978 TATAT TATATA AATGT TAATT T-TTT TATTT TATTT TATTT TAATTTT
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TATTT TATTT T-A-TTT
* * * *
2326025 TATTCT TATAT TA-TA TATTT TATTT TAATA T-TTT TATTT TA
1 TATT-T TATTT TATTT TATTT TATTT TATTT TATTT TATTT TA
2326066 ATTATAATAT
Statistics
Matches: 198, Mismatches: 52, Indels: 52
0.66 0.17 0.17
Matches are distributed among these distances:
4 24 0.12
5 104 0.53
6 59 0.30
7 11 0.06
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (5 bp):
TATTT
Found at i:2325819 original size:48 final size:47
Alignment explanation
Indices: 2325766--2326079 Score: 140
Period size: 44 Copynumber: 6.9 Consensus size: 47
2325756 CATTTCTTAA
2325766 ATATATTTTTAATGTCATATATTTTATTTTATTTATTATTATTATA-TTT
1 ATATA-TTTTAAT-T-ATATATTTTATTTTATTTATTATTATTATATTTT
* * * **
2325815 -TATATTTTATTTTTAATATATTTATATTTATATTATTAATTTTTATATAAT
1 ATATATTTTAATTAT-ATAT-TTTAT-TTTAT-TTATT-ATTATTATATTTT
2325866 ATCATATTTTAA--ATATATTTTATTTTTATTTATTATTA-TA-ATTTT
1 AT-ATATTTTAATTATATATTTTA-TTTTATTTATTATTATTATATTTT
* * *
2325911 ATATATTTT-ATT-T-TCA-TTTCTTTAATATATT-TT-TTATA--TT
1 ATATATTTTAATTATAT-ATTTTATTTTATTTATTATTATTATATTTT
* * * * *
2325951 ATATATTTT-ATT-T-TAATTTGTTTTACTTA-TATTATATAAATGTT
1 ATATATTTTAATTATATATTTTATTTTATTTATTATTAT-TATATTTT
* * *
2325995 A-ATTTTTTTATT-T-TATTTTATTTTAATTT-TTATTCTTATA--TT
1 ATATATTTTAATTATATATTTTATTTT-ATTTATTATTATTATATTTT
* * *
2326037 ATATATTTT-ATTTTAATATTTTTATTTTAATTA-TAATATTATA
1 ATATATTTTAATTAT-ATA-TTTTATTTTATTTATTATTATTATA
2326080 AAATATTTTT
Statistics
Matches: 208, Mismatches: 28, Indels: 62
0.70 0.09 0.21
Matches are distributed among these distances:
39 2 0.01
40 27 0.13
41 5 0.02
42 19 0.09
43 18 0.09
44 28 0.13
45 27 0.13
46 16 0.08
47 14 0.07
48 14 0.07
49 14 0.07
50 13 0.06
51 2 0.01
52 1 0.00
53 8 0.04
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (47 bp):
ATATATTTTAATTATATATTTTATTTTATTTATTATTATTATATTTT
Found at i:2325891 original size:34 final size:32
Alignment explanation
Indices: 2325557--2325924 Score: 130
Period size: 33 Copynumber: 11.4 Consensus size: 32
2325547 TTTTAATATC
* *
2325557 ATATATTTTATTTTTATTTATTATTATAATATTT-
1 ATATATTTTATTTTTATATAATA-TAT-AT-TTTA
*
2325591 -TATATTTTATTTTTA-AT-ATATTTATATTT-
1 ATATATTTTATTTTTATATAATATATAT-TTTA
* *
2325620 ATAT-TATTAATTTTATATAATATCATATTTTAA
1 ATATATTTTATTTTTATATAATAT-ATATTTT-A
* * * * *
2325653 ATATATTTTTAATATCATAT-AT-TTTATTTTT
1 ATATA-TTTTATTTTTATATAATATATATTTTA
* * *
2325684 ATTTATTATTATAATTTTATATATTTTAT-TTTTA
1 ATATATT-TTAT--TTTTATATAATATATATTTTA
*
2325718 ATATATTTATATTTTTAT-T-AT-TA-ATTTTT
1 ATATATTT-TATTTTTATATAATATATATTTTA
* * * * * * * *
2325747 ATATAATATCATTTCTTAAATATATTTTTAATGTC
1 ATAT-ATTTTATTT-TTATATA-ATATATATTTTA
* *
2325782 ATATATTTTA-TTTTATTTATTATTATTATATTT-
1 ATATATTTTATTTTTATATAATA-TA-TAT-TTTA
*
2325815 -TATATTTTATTTTTA-AT-ATATTTATATTT-
1 ATATATTTTATTTTTATATAATATATAT-TTTA
*
2325844 ATAT-TATTAATTTTTATATAATATCATATTTTAA
1 ATATAT-TTTATTTTTATATAATAT-ATATTTT-A
* *
2325878 ATATATTTTATTTTTATTTATTATTATAATTTT-
1 ATATATTTTATTTTTATATAATA-TAT-ATTTTA
2325911 ATATATTTTATTTT
1 ATATATTTTATTTT
2325925 CATTTCTTTA
Statistics
Matches: 253, Mismatches: 45, Indels: 73
0.68 0.12 0.20
Matches are distributed among these distances:
29 37 0.15
30 29 0.11
31 23 0.09
32 39 0.15
33 55 0.22
34 43 0.17
35 27 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (32 bp):
ATATATTTTATTTTTATATAATATATATTTTA
Found at i:2325915 original size:10 final size:9
Alignment explanation
Indices: 2325557--2325921 Score: 91
Period size: 9 Copynumber: 42.2 Consensus size: 9
2325547 TTTTAATATC
2325557 ATATA-TTT
1 ATATATTTT
2325565 -TAT-TTTT
1 ATATATTTT
*
2325572 ATTTATTATT
1 ATATATT-TT
2325582 ATA-ATATTT
1 ATATAT-TTT
2325591 -TATATTTT
1 ATATATTTT
*
2325599 AT-T-TTTA
1 ATATATTTT
2325606 ATATATTTAT
1 ATATATTT-T
* *
2325616 ATTTATATT
1 ATATATTTT
2325625 AT-TAATTTT
1 ATAT-ATTTT
*
2325634 ATATA--AT
1 ATATATTTT
2325641 ATCATATTTT
1 AT-ATATTTT
2325651 AAATATATTTT
1 --ATATATTTT
* *
2325662 -TA-ATATC
1 ATATATTTT
2325669 ATATA-TTT
1 ATATATTTT
2325677 -TAT-TTTT
1 ATATATTTT
*
2325684 ATTTATTATT
1 ATATATT-TT
2325694 ATA-ATTTT
1 ATATATTTT
2325702 ATATATTTT
1 ATATATTTT
*
2325711 AT-T-TTTA
1 ATATATTTT
2325718 ATATA-TTT
1 ATATATTTT
2325726 ATAT-TTTT
1 ATATATTTT
2325734 ATTATTAATTTT
1 A-TA-T-ATTTT
**
2325746 -TATATAAT
1 ATATATTTT
2325754 ATCAT-TTCTT
1 AT-ATATT-TT
2325764 AAATATATTTT
1 --ATATATTTT
* *
2325775 -TA-ATGTC
1 ATATATTTT
2325782 ATATATTTT
1 ATATATTTT
*
2325791 AT-TTTATTT
1 ATATAT-TTT
*
2325800 AT-TATTAT
1 ATATATTTT
2325808 -TATA-TTT
1 ATATATTTT
2325815 -TATATTTT
1 ATATATTTT
*
2325823 AT-T-TTTA
1 ATATATTTT
2325830 ATATATTTAT
1 ATATATTT-T
* *
2325840 ATTTATATT
1 ATATATTTT
2325849 AT-TAATTTT
1 ATAT-ATTTT
**
2325858 -TATATAAT
1 ATATATTTT
2325866 ATCATATTTT
1 AT-ATATTTT
*
2325876 AAATATATTT
1 ATATAT-TTT
2325886 -TAT-TTTT
1 ATATATTTT
*
2325893 ATTTATTATT
1 ATATATT-TT
2325903 ATA-ATTTT
1 ATATATTTT
2325911 ATATATTTT
1 ATATATTTT
2325920 AT
1 AT
2325922 TTTCATTTCT
Statistics
Matches: 260, Mismatches: 42, Indels: 109
0.63 0.10 0.27
Matches are distributed among these distances:
7 46 0.18
8 68 0.26
9 83 0.32
10 42 0.16
11 11 0.04
12 10 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
ATATATTTT
Found at i:2325937 original size:71 final size:71
Alignment explanation
Indices: 2325808--2325969 Score: 172
Period size: 73 Copynumber: 2.3 Consensus size: 71
2325798 TTATTATTAT
*
2325808 TATATTTTATATTTTATTTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATAT
1 TATATTTTAT-TTTTATTTTTAATATATTTATATTTATATTATTAATTTCTATATAATAT-ATAT
2325873 TTTA-A-A
64 TTTATATA
* * *
2325879 TATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT-TTCATTTCT-T-TAATATAT
1 TATATTTTATTTTTATTT-TTAATAT-A-TTTATAT-TTATATTATTAATTTCTATATAATATAT
*
2325941 TTTTTATATTA
62 ATTTTATA-TA
*
2325952 TATATTTTATTTTAATTT
1 TATATTTTATTTTTATTT
2325970 GTTTTACTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
70 15 0.19
71 23 0.29
72 2 0.03
73 32 0.41
74 6 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (71 bp):
TATATTTTATTTTTATTTTTAATATATTTATATTTATATTATTAATTTCTATATAATATATATTT
TATATA
Found at i:2325943 original size:33 final size:31
Alignment explanation
Indices: 2325782--2325963 Score: 126
Period size: 33 Copynumber: 5.6 Consensus size: 31
2325772 TTTTAATGTC
2325782 ATATATTTTATTTTATTTATT-AT-TA--TT
1 ATATATTTTATTTTATTTATTAATATATTTT
2325809 ATAT-TTTATATTTTATTT-TTAATATATTTAT
1 ATATATTT-TATTTTATTTATTAATATATTT-T
* *
2325840 ATTTATATTATTAATTTT-TATATAATATCATATTTT
1 A--TATATT-TT-ATTTTATTTATTA-AT-ATATTTT
*
2325876 AAATATATTTTATTTTTATTTATTATTATAATTTT
1 --ATATATTTTA-TTTTATTTATTAATAT-ATTTT
*
2325911 ATATATTTTATTTTCATTTCTTTAATATATTTT
1 ATATATTTTATTTT-ATTT-ATTAATATATTTT
*
2325944 TTATATTATATATTTTATTT
1 ATATATT-T-TATTTTATTT
2325964 TAATTTGTTT
Statistics
Matches: 124, Mismatches: 8, Indels: 39
0.73 0.05 0.23
Matches are distributed among these distances:
26 5 0.04
27 16 0.13
28 2 0.02
30 1 0.01
31 2 0.02
32 4 0.03
33 28 0.23
34 19 0.15
35 26 0.21
36 14 0.11
37 6 0.05
38 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (31 bp):
ATATATTTTATTTTATTTATTAATATATTTT
Found at i:2326045 original size:20 final size:19
Alignment explanation
Indices: 2325547--2326079 Score: 102
Period size: 20 Copynumber: 28.6 Consensus size: 19
2325537 TTAAATATAT
*
2325547 TTTTAATATCATATATTTTA
1 TTTT-ATATTATATATTTTA
2325567 TTTT-TATT-TATTATTATAATA
1 TTTTATATTATA-TATT-T--TA
* *
2325588 TTTTATATTTTATTTTTAATA
1 TTTTATATTATATATTT--TA
2325609 TATTTATATT-TATATTATTAA
1 T-TTTATATTATATATT-TT-A
**
2325630 TTTTATA-TA-ATATCATA
1 TTTTATATTATATATTTTA
2325647 TTTTA-A--ATATA--TT-
1 TTTTATATTATATATTTTA
* *
2325660 TTTAATATCATATATTTTA
1 TTTTATATTATATATTTTA
*
2325679 TTTT-TATT-TAT-TATTA
1 TTTTATATTATATATTTTA
* *
2325695 --TAATTTTATATATTTTA
1 TTTTATATTATATATTTTA
2325712 TTTT-TA--ATATATTTATA
1 TTTTATATTATATATTT-TA
*
2325729 TTTT-TATTAT-TAATTT-
1 TTTTATATTATATATTTTA
* * *
2325745 TTATATAATATCATTTCTTAAATA
1 TTTTATATTAT-ATAT-TT---TA
*
2325769 TATTTTTAATGTCATATATTTTA
1 T-TTTAT-AT-T-ATATATTTTA
*
2325792 TTTTAT-TTATTATTATTATA
1 TTTTATATTA-TA-TATTTTA
* *
2325812 TTTTATATTTTATTTTTAATA
1 TTTTATATTATATATTT--TA
2325833 TATTTATATT-TATATTATTAA
1 T-TTTATATTATATATT-TT-A
**
2325854 TTTT-TA-TATAATATCATA
1 TTTTATATTAT-ATATTTTA
2325872 TTTTA-A--ATATATTTTA
1 TTTTATATTATATATTTTA
*
2325888 TTTT-TATT-TATTATTATAA
1 TTTTATATTATA-TATT-TTA
*
2325907 TTTTATA-TATTTTATTTTCA
1 TTTTATATTA-TATATTTT-A
* *
2325927 -TTTCT-TTA-ATATATT-
1 TTTTATATTATATATTTTA
2325942 TTTTATATTATATATTTTA
1 TTTTATATTATATATTTTA
*
2325961 TTTTA-A-T-T-TGTTTTA
1 TTTTATATTATATATTTTA
* *
2325976 -CTTATATTATATAAATGTTA
1 TTTTATATTATAT--ATTTTA
*
2325996 -ATT-T-TT-T-TATTTTA
1 TTTTATATTATATATTTTA
*
2326010 TTTTATTTTA-AT-TTTTA
1 TTTTATATTATATATTTTA
2326027 TTCTTATATTATATATTTTA
1 TT-TTATATTATATATTTTA
*
2326047 TTTTAATATT-TTTATTTTAA
1 TTTT-ATATTATATATTTT-A
*
2326067 TTATAATATTATA
1 TT-TTATATTATA
2326080 AAATATTTTT
Statistics
Matches: 380, Mismatches: 53, Indels: 159
0.64 0.09 0.27
Matches are distributed among these distances:
13 4 0.01
14 11 0.03
15 13 0.03
16 46 0.12
17 53 0.14
18 48 0.13
19 54 0.14
20 69 0.18
21 34 0.09
22 29 0.08
23 6 0.02
24 1 0.00
25 3 0.01
26 3 0.01
27 4 0.01
28 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTATATTATATATTTTA
Found at i:2326065 original size:51 final size:53
Alignment explanation
Indices: 2325954--2326065 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 53
2325944 TTATATTATA
**
2325954 TATTTTATTTTAATTTGTTTTACTTATATTATATAAATGTTAATTTTTTTATTT
1 TATTTTATTTTAATTTGTTTTACTTATATTATAT-AATGTTAATTTTAATATTT
*
2326008 TATTTTATTTTAATTT-TTATT-CTTATATTATAT-AT-TTTATTTTAATATTTT
1 TATTTTATTTTAATTTGTT-TTACTTATATTATATAATGTTAATTTTAATA-TTT
2326059 TATTTTA
1 TATTTTA
2326066 ATTATAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
50 9 0.17
51 12 0.23
53 14 0.26
54 18 0.34
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (53 bp):
TATTTTATTTTAATTTGTTTTACTTATATTATATAATGTTAATTTTAATATTT
Found at i:2329572 original size:21 final size:21
Alignment explanation
Indices: 2329548--2329587 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2329538 ACCCAAGCTT
*
2329548 TAAGACTCGATACGTAAGACC
1 TAAGACTCGAGACGTAAGACC
* *
2329569 TAAGCCTCGAGACTTAAGA
1 TAAGACTCGAGACGTAAGA
2329588 TTAAAGAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
TAAGACTCGAGACGTAAGACC
Found at i:2330085 original size:14 final size:14
Alignment explanation
Indices: 2330064--2330097 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2330054 CTCGAGTTTT
*
2330064 GAGTCTCAATTCTC
1 GAGTCTCAAGTCTC
*
2330078 GTGTCTCAAGTCTC
1 GAGTCTCAAGTCTC
2330092 GAGTCT
1 GAGTCT
2330098 TAAGGCTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (14 bp):
GAGTCTCAAGTCTC
Found at i:2330176 original size:21 final size:21
Alignment explanation
Indices: 2330151--2330201 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2330141 GAATTTAAGG
*
2330151 CTTGAGTCTTAAGTCTCGA-GT
1 CTTGAGTCTTAAGTCAC-ATGT
* *
2330172 CTTGAGGCTTGAGTCACATGT
1 CTTGAGTCTTAAGTCACATGT
2330193 CTTGAGTCT
1 CTTGAGTCT
2330202 CGAGTCCCGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (21 bp):
CTTGAGTCTTAAGTCACATGT
Found at i:2330185 original size:14 final size:14
Alignment explanation
Indices: 2330145--2330186 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
2330135 GGTCTTGAAT
2330145 TTAAGGCTTGAGTC
1 TTAAGGCTTGAGTC
* *
2330159 TTAAGTCTCGAGTC
1 TTAAGGCTTGAGTC
*
2330173 TTGAGGCTTGAGTC
1 TTAAGGCTTGAGTC
2330187 ACATGTCTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.36
Consensus pattern (14 bp):
TTAAGGCTTGAGTC
Found at i:2339632 original size:66 final size:66
Alignment explanation
Indices: 2339526--2339707 Score: 188
Period size: 66 Copynumber: 2.8 Consensus size: 66
2339516 CTTATTCTCC
* ** * * *
2339526 TAACATCAAATAAGTCATTCCTTAATGTACTTTTCCATGAT-CGACACGTTCTCCCATTATTAAG
1 TAACATCAAATAAATCATTCCTTAACATGCTTTTCCATGATAAG-CACGTTCTCCCATGATTAAG
2339590 CT
65 CT
* * * * *
2339592 TAACATCAAATAAATCATTCCTTAACATGCTCTTCCATGATAAGTATGTTCTCCTATGATTGAGC
1 TAACATCAAATAAATCATTCCTTAACATGCTTTTCCATGATAAGCACGTTCTCCCATGATTAAGC
2339657 T
66 T
* * * * *
2339658 TAACATCCAATAACT-ATTCTTTAACATGTTTTTCCATGGTAAAGCACGTT
1 TAACATCAAATAAATCATTCCTTAACATGCTTTTCCATGAT-AAGCACGTT
2339708 TTCTCATAAT
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
65 21 0.22
66 73 0.77
67 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (66 bp):
TAACATCAAATAAATCATTCCTTAACATGCTTTTCCATGATAAGCACGTTCTCCCATGATTAAGC
T
Found at i:2351608 original size:19 final size:18
Alignment explanation
Indices: 2351586--2351693 Score: 56
Period size: 19 Copynumber: 5.3 Consensus size: 18
2351576 TTAATATTTT
2351586 ATAATTCAATTAAATATTA
1 ATAATT-AATTAAATATTA
2351605 ATAAATAATAATTTAAATATTA
1 AT-AAT--TAA-TTAAATATTA
* *
2351627 TTAATTAATTTAATTATTA
1 ATAATTAA-TTAAATATTA
* *
2351646 ATATTTTATTTATAAT-TTA
1 ATA-ATTAATTA-AATATTA
2351665 ATATTATTAAGATTAAAATATTA
1 ATA--ATT-A-ATT-AAATATTA
2351688 ATAATT
1 ATAATT
2351694 TTAATTAATT
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
19 26 0.37
20 11 0.16
21 9 0.13
22 17 0.24
23 7 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
ATAATTAATTAAATATTA
Found at i:2351622 original size:22 final size:20
Alignment explanation
Indices: 2351595--2351648 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
2351585 TATAATTCAA
2351595 TTAAATATTAATAAATAATAAT
1 TTAAATATTAATAAAT--TAAT
*
2351617 TTAAATATT-ATTAATTAAT
1 TTAAATATTAATAAATTAAT
*
2351636 TTAATTATTAATA
1 TTAAATATTAATA
2351649 TTTTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.43
20 2 0.07
21 5 0.18
22 9 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATATTAATAAATTAAT
Found at i:2351900 original size:15 final size:16
Alignment explanation
Indices: 2351869--2351902 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2351859 AATTTTTTTA
2351869 TTAAAATTTTAAAAAT
1 TTAAAATTTTAAAAAT
*
2351885 TTAAAA-TTTAATAAT
1 TTAAAATTTTAAAAAT
2351900 TTA
1 TTA
2351903 TTATGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATTTTAAAAAT
Found at i:2352038 original size:25 final size:25
Alignment explanation
Indices: 2352010--2352083 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 25
2352000 AACATTAAAA
2352010 ATATTAAAATATTAATATTTTAATC
1 ATATTAAAATATTAATATTTTAATC
* *
2352035 ATATT--ACTATTAATAATGTTTAAATT
1 ATATTAAAATATTAAT-AT-TTT-AATC
2352061 ATATATAAAATATTAAT-TTTTAA
1 ATAT-TAAAATATTAATATTTTAA
2352084 AATTTATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
23 8 0.20
24 2 0.05
25 10 0.25
26 10 0.25
27 2 0.05
29 8 0.20
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (25 bp):
ATATTAAAATATTAATATTTTAATC
Found at i:2352047 original size:40 final size:40
Alignment explanation
Indices: 2351958--2352047 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 40
2351948 TTTTTTATTT
* *
2351958 ATACTCATTAAAAATTTAATATATTGATAATTTAATAAATA
1 ATACT-ATTAAAAATTTAAAATATTAATAATTTAATAAATA
* * *
2351999 AAAC-ATTAAAAATATTAAAATATTAATATTTTAAT-CATA
1 ATACTATTAAAAAT-TTAAAATATTAATAATTTAATAAATA
*
2352038 TTACTATTAA
1 ATACTATTAA
2352048 TAATGTTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
39 14 0.35
40 23 0.57
41 3 0.08
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (40 bp):
ATACTATTAAAAATTTAAAATATTAATAATTTAATAAATA
Found at i:2363950 original size:18 final size:18
Alignment explanation
Indices: 2363927--2363992 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
2363917 ATTTTCATTA
2363927 ATTCAGAGGCATTTGAAG
1 ATTCAGAGGCATTTGAAG
* *
2363945 ATTCAGAAGC-TTTCAAAG
1 ATTCAGAGGCATTT-GAAG
*
2363963 ATT-GGAAGGCATTTGAAG
1 ATTCAG-AGGCATTTGAAG
*
2363981 ATTGAGA-GCATT
1 ATTCAGAGGCATT
2363993 ACGGAGATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
17 9 0.24
18 25 0.66
19 4 0.11
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.29
Consensus pattern (18 bp):
ATTCAGAGGCATTTGAAG
Found at i:2364255 original size:51 final size:50
Alignment explanation
Indices: 2364199--2364316 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 50
2364189 CCTCAAGTGA
*
2364199 AGTTCGTGATCAAGATCAAGTTGTCAAGACCCTTGAAGTGAAGATATCAAGT
1 AGTTCGTGATCAAGATCAAGTTGTCAAGACCCTTGAAGTAAAGAT-T-AAGT
* * * *
2364251 -GTTCGTGATCAAGATTACGTTTTTAAGACCCTTGAAGTAAAGATTAAGT
1 AGTTCGTGATCAAGATCAAGTTGTCAAGACCCTTGAAGTAAAGATTAAGT
2364300 GAAGTTCGTGATCAAGA
1 --AGTTCGTGATCAAGA
2364317 CTAAGTCCGA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
49 4 0.07
50 1 0.02
51 39 0.67
52 14 0.24
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (50 bp):
AGTTCGTGATCAAGATCAAGTTGTCAAGACCCTTGAAGTAAAGATTAAGT
Found at i:2372501 original size:40 final size:40
Alignment explanation
Indices: 2372453--2372673 Score: 175
Period size: 36 Copynumber: 5.8 Consensus size: 40
2372443 GAATCAACAA
* *
2372453 GTGCTATTATAAAGAGTACCCTTAAAGGATAACAAATTGT
1 GTGCTATTATAAAGAGCACCCTTCAAGGATAACAAATTGT
* * *
2372493 GTGATATTACAAAGAGCA-CCTCCCAAGGATCAAC-AA--GT
1 GTGCTATTATAAAGAGCACCCT-TCAAGGAT-AACAAATTGT
* *
2372531 GT--TTTTATAAAGAGCA-CCTTCCAAGGATAATAAATTGT
1 GTGCTATTATAAAGAGCACCCTT-CAAGGATAACAAATTGT
* *
2372569 GTGCTATTACAAATAGCACCCTAT-AAGGATTAAC-AA----
1 GTGCTATTATAAAGAGCACCCT-TCAAGGA-TAACAAATTGT
*
2372605 GTGCTATTATAAAGAGTACCC--CAAGGATTAACAAATTGT
1 GTGCTATTATAAAGAGCACCCTTCAAGGA-TAACAAATTGT
* *
2372644 GTGCTATTATAAAGTGCACCCTTCATGGAT
1 GTGCTATTATAAAGAGCACCCTTCAAGGAT
2372674 TAACTAGTGC
Statistics
Matches: 143, Mismatches: 19, Indels: 38
0.71 0.09 0.19
Matches are distributed among these distances:
34 10 0.07
35 4 0.03
36 42 0.29
38 8 0.06
39 22 0.15
40 42 0.29
41 14 0.10
42 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (40 bp):
GTGCTATTATAAAGAGCACCCTTCAAGGATAACAAATTGT
Found at i:2372539 original size:76 final size:76
Alignment explanation
Indices: 2372410--2372692 Score: 299
Period size: 76 Copynumber: 3.7 Consensus size: 76
2372400 TAATGATTCT
* * *
2372410 AAATTATGTGCTATTATAAA-AGGCACCCT-CTAAGAATCAACAAGTGCTATTATAAAGAGTACC
1 AAATTGTGTGCTATTACAAAGA-GCACCCTAC-AAGGATCAACAAGTGCTATTATAAAGAGTACC
*
2372473 CTTAAAGGATAAC
64 CTTCAAGGATAAC
* * * * *
2372486 AAATTGTGTGATATTACAAAGAGCA-CCTCCCAAGGATCAACAAGTGTTTTTATAAAGAGCA-CC
1 AAATTGTGTGCTATTACAAAGAGCACCCT-ACAAGGATCAACAAGTGCTATTATAAAGAGTACCC
*
2372549 TTCCAAGGATAAT
65 TT-CAAGGATAAC
* * *
2372562 AAATTGTGTGCTATTACAAATAGCACCCTATAAGGATTAACAAGTGCTATTATAAAGAGTACCC-
1 AAATTGTGTGCTATTACAAAGAGCACCCTACAAGGATCAACAAGTGCTATTATAAAGAGTACCCT
2372626 -CAAGGATTAAC
66 TCAAGGA-TAAC
* * * * * * *
2372637 AAATTGTGTGCTATTATAAAGTGCACCCTTCATGGATTAACTAGTGCTATTTTAAA
1 AAATTGTGTGCTATTACAAAGAGCACCCTACAAGGATCAACAAGTGCTATTATAAA
2372693 AAACACCCTT
Statistics
Matches: 174, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
74 6 0.03
75 58 0.33
76 103 0.59
77 7 0.04
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (76 bp):
AAATTGTGTGCTATTACAAAGAGCACCCTACAAGGATCAACAAGTGCTATTATAAAGAGTACCCT
TCAAGGATAAC
Found at i:2372635 original size:34 final size:35
Alignment explanation
Indices: 2372417--2372701 Score: 146
Period size: 36 Copynumber: 7.6 Consensus size: 35
2372407 TCTAAATTAT
* *
2372417 GTGCTATTATAAA-AGGCACCCTCTAAGAATCAACAA
1 GTGCTATTATAAAGA-GCACCCTC-AAGGATTAACAA
* *
2372453 GTGCTATTATAAAGAGTACCCTTAAAGGA-TAACAAA
1 GTGCTATTATAAAGAGCACCC-TCAAGGATTAAC-AA
* * * *
2372489 TTGTGTGATATTACAAAGAGCACCTCCCAAGGATCAACAA
1 ----GTGCTATTATAAAGAGCACC-CTCAAGGATTAACAA
* * * *
2372529 GTGTTTTTATAAAGAGCACCTTCCAAGGATAATAA-ATTGT
1 GTGCTATTATAAAGAGCACCCT-CAAGGAT--TAACA---A
* * *
2372569 GTGCTATTACAAATAGCACCCTATAAGGATTAACAA
1 GTGCTATTATAAAGAGCACCCT-CAAGGATTAACAA
*
2372605 GTGCTATTATAAAGAGTACCC-CAAGGATTAACAAA
1 GTGCTATTATAAAGAGCACCCTCAAGGATTAAC-AA
* * *
2372640 TTGTGTGCTATTATAAAGTGCACCCTTCATGGATTAACTA
1 ----GTGCTATTATAAAGAGCACCC-TCAAGGATTAACAA
* * *
2372680 GTGCTATTTTAAAAAACACCCT
1 GTGCTATTATAAAGAGCACCCT
2372702 TTAAATTGCT
Statistics
Matches: 189, Mismatches: 37, Indels: 47
0.69 0.14 0.17
Matches are distributed among these distances:
34 10 0.05
35 6 0.03
36 83 0.44
37 3 0.02
38 5 0.03
39 20 0.11
40 48 0.25
41 14 0.07
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (35 bp):
GTGCTATTATAAAGAGCACCCTCAAGGATTAACAA
Found at i:2373523 original size:28 final size:28
Alignment explanation
Indices: 2373417--2373523 Score: 115
Period size: 28 Copynumber: 3.6 Consensus size: 28
2373407 TGTAATAGTA
*
2373417 ATTGCAATATACTTCTTTAAATAGTTTT
1 ATTGCAATATACTTCTTCAAATAGTTTT
* *
2373445 ATTCCAATATACTTTTTTCAAGATTTTAGTTTT
1 ATTGCAATATAC-TTCTTCAA-A---TAGTTTT
* *
2373478 ATTGCAATATACTGCTTCAAATACTTTT
1 ATTGCAATATACTTCTTCAAATAGTTTT
*
2373506 ATTGCAATATACATCTTC
1 ATTGCAATATACTTCTTC
2373524 CAAAATCATA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
28 33 0.51
29 6 0.09
30 1 0.02
31 1 0.02
32 6 0.09
33 18 0.28
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.48
Consensus pattern (28 bp):
ATTGCAATATACTTCTTCAAATAGTTTT
Found at i:2373969 original size:81 final size:81
Alignment explanation
Indices: 2373876--2374161 Score: 446
Period size: 81 Copynumber: 3.5 Consensus size: 81
2373866 ATTTAAATTA
* * * *
2373876 GACTAATCAAAATTTAATTACTGGCCATCCAATTTATCTCTAAATAAATTAAGGTAATTGAGAGA
1 GACTAATCAAAATTTAATTATTGGCCATCCAATTTATCTCTAAATAAATCAAGATAATTAAGAGA
2373941 TAATATTCATATTTTT
66 TAATATTCATATTTTT
* * * *
2373957 GATTAATCAAAATTTAATTATTGACCATCCAATTTATCTCTAAATAAATCAAGATAGTTTAGAGA
1 GACTAATCAAAATTTAATTATTGGCCATCCAATTTATCTCTAAATAAATCAAGATAATTAAGAGA
2374022 TAATATTCATATTTTT
66 TAATATTCATATTTTT
* *
2374038 GACTAATCAAAATTTAATTATTGGTCATCCAATTTATCTATAAATAAATCAAGATAATTAAGAGA
1 GACTAATCAAAATTTAATTATTGGCCATCCAATTTATCTCTAAATAAATCAAGATAATTAAGAGA
2374103 TAATATTCATATTTTT
66 TAATATTCATATTTTT
* * **
2374119 GACCAATCAAAATTTAAGTATTGGCCATTTAATTTATCTCTAA
1 GACTAATCAAAATTTAATTATTGGCCATCCAATTTATCTCTAA
2374162 TAATTATATT
Statistics
Matches: 186, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 186 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (81 bp):
GACTAATCAAAATTTAATTATTGGCCATCCAATTTATCTCTAAATAAATCAAGATAATTAAGAGA
TAATATTCATATTTTT
Found at i:2374798 original size:255 final size:255
Alignment explanation
Indices: 2374347--2374854 Score: 809
Period size: 255 Copynumber: 2.0 Consensus size: 255
2374337 AATAATTTAA
* * ***
2374347 AGATAATTCAAAGAGACTATATTCTCATCCAAGTCCCCCACCCAACATTATAAATAGGGGCTCCT
1 AGATAATTCAAAGAGACTACATTCTCATCAAAGTCCCCCACCCAACATTATAAATAAAAGCTCCT
* * *
2374412 CCAAGACATTTTTATTCATTCGGAGGCATTTGAAGATTTGAAAGCATTTAAAGATTGAGAGGTAC
66 CCAAGACATTTTTATTCATTCAGAGGCATTTGAAGATTCGAAAGCATTTAAAGATTGAGAGGCAC
*
2374477 TTGAAGATTGAGAGCATCACAGAGATCGAGAAGAGTAAAAGATTTCTGAAGTGAAAATCAAGTAG
131 TCGAAGATTGAGAGCATCACAGAGATCGAGAAGAGTAAAAGATTTCTGAAGTGAAAATCAAGTAG
* *
2374542 TAGAAAAGTTCGTGATCAAGATCAAGCGGCAGTGAAATTCGTGATCGAGATATCAAGTAG
196 TAGAAAAGTTCGTGATCAAGATCAAGCGACAGTGAAATTCGTGATCAAGATATCAAGTAG
* * *
2374602 AGATAATTCAAAGAGATTACATTCTCATCAAAGTCTCCCACCCAGCATTATAAATAAAAGCTCCT
1 AGATAATTCAAAGAGACTACATTCTCATCAAAGTCCCCCACCCAACATTATAAATAAAAGCTCCT
* *
2374667 CCAAGACATTTTTATTCATTCAGAGGCATTTGAAGATTCGGAAGCATTTGAAGATTGAGAGGCAC
66 CCAAGACATTTTTATTCATTCAGAGGCATTTGAAGATTCGAAAGCATTTAAAGATTGAGAGGCAC
* * *
2374732 TCGAAGATTGAGAGCATTACAGAGATCGAGAAGAGTCAAAGATTTCTGAAGTGAAGATCAAGTAG
131 TCGAAGATTGAGAGCATCACAGAGATCGAGAAGAGTAAAAGATTTCTGAAGTGAAAATCAAGTAG
** * *
2374797 TAGCGAAGTTCGTGATCAAGATCAAGTGACAGTGAAGTTCGTGATCAAGATATCAAGT
196 TAGAAAAGTTCGTGATCAAGATCAAGCGACAGTGAAATTCGTGATCAAGATATCAAGT
2374855 GTTCGTGATT
Statistics
Matches: 230, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
255 230 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (255 bp):
AGATAATTCAAAGAGACTACATTCTCATCAAAGTCCCCCACCCAACATTATAAATAAAAGCTCCT
CCAAGACATTTTTATTCATTCAGAGGCATTTGAAGATTCGAAAGCATTTAAAGATTGAGAGGCAC
TCGAAGATTGAGAGCATCACAGAGATCGAGAAGAGTAAAAGATTTCTGAAGTGAAAATCAAGTAG
TAGAAAAGTTCGTGATCAAGATCAAGCGACAGTGAAATTCGTGATCAAGATATCAAGTAG
Found at i:2374818 original size:29 final size:29
Alignment explanation
Indices: 2374785--2374847 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
2374775 TTCTGAAGTG
*
2374785 AAGATCAAGT-AGTAGCGAAGTTCGTGATC
1 AAGATCAAGTGA-CAGCGAAGTTCGTGATC
*
2374814 AAGATCAAGTGACAGTGAAGTTCGTGATC
1 AAGATCAAGTGACAGCGAAGTTCGTGATC
2374843 AAGAT
1 AAGAT
2374848 ATCAAGTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.24
Consensus pattern (29 bp):
AAGATCAAGTGACAGCGAAGTTCGTGATC
Found at i:2374898 original size:51 final size:51
Alignment explanation
Indices: 2374843--2375052 Score: 215
Period size: 51 Copynumber: 4.1 Consensus size: 51
2374833 GTTCGTGATC
* * * * * *
2374843 AAGATATCAAGTGTTCGTGATTAGGATCAAGTTGTCAAAACCCTTGAAGTG
1 AAGATATCAAGTGTTCATGATCAAGATCAAGTCGTCAAGACCCTTGAAGCG
* * * *
2374894 AAGATATCAAGTGTTCATGATCAAGATTAAGTTGTTAAGACCCTTGAAACG
1 AAGATATCAAGTGTTCATGATCAAGATCAAGTCGTCAAGACCCTTGAAGCG
* * * * * * *
2374945 AAGATCAAGCAA-AGTTCGTGATCAAGATCAAGTCATCAAGATCTTTGAAGCA
1 AAGAT--ATCAAGTGTTCATGATCAAGATCAAGTCGTCAAGACCCTTGAAGCG
* * *
2374997 AAAATATCAAGTGTTCATGATCAAGATTAAGTCGTCAAGACCCTTGAAGTG
1 AAGATATCAAGTGTTCATGATCAAGATCAAGTCGTCAAGACCCTTGAAGCG
2375048 AAGAT
1 AAGAT
2375053 CAAGTGAAGT
Statistics
Matches: 126, Mismatches: 30, Indels: 6
0.78 0.19 0.04
Matches are distributed among these distances:
50 4 0.03
51 84 0.67
52 34 0.27
53 4 0.03
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (51 bp):
AAGATATCAAGTGTTCATGATCAAGATCAAGTCGTCAAGACCCTTGAAGCG
Found at i:2374975 original size:103 final size:103
Alignment explanation
Indices: 2374855--2375074 Score: 278
Period size: 103 Copynumber: 2.1 Consensus size: 103
2374845 GATATCAAGT
* * ** ** *
2374855 GTTCGTGATTAGGATCAAGTTGTCAAAACCCTTGAAGTGAAGATATCAAGTGTTCATGATCAAGA
1 GTTCGTGATCAAGATCAAGTCATCAAAACCCTTGAAGCAAAAATATCAAGTGTTCATGATCAAGA
* *
2374920 TTAAGTTGTTAAGACCCTTGAAACGAAGATCAAGCAAA
66 TTAAGTCGTCAAGACCCTTGAAACGAAGATCAAGCAAA
* * *
2374958 GTTCGTGATCAAGATCAAGTCATCAAGATCTTTGAAGCAAAAATATCAAGTGTTCATGATCAAGA
1 GTTCGTGATCAAGATCAAGTCATCAAAACCCTTGAAGCAAAAATATCAAGTGTTCATGATCAAGA
** **
2375023 TTAAGTCGTCAAGACCCTTGAAGTGAAGATCAAGTGAA
66 TTAAGTCGTCAAGACCCTTGAAACGAAGATCAAGCAAA
* *
2375061 GTTCATGACCAAGA
1 GTTCGTGATCAAGA
2375075 ATAAGTTTGC
Statistics
Matches: 99, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.26
Consensus pattern (103 bp):
GTTCGTGATCAAGATCAAGTCATCAAAACCCTTGAAGCAAAAATATCAAGTGTTCATGATCAAGA
TTAAGTCGTCAAGACCCTTGAAACGAAGATCAAGCAAA
Found at i:2375080 original size:52 final size:49
Alignment explanation
Indices: 2374848--2375080 Score: 164
Period size: 51 Copynumber: 4.6 Consensus size: 49
2374838 TGATCAAGAT
* * * * *
2374848 ATCAAGTGTTCGTGAT-TAGGATCAAGTTGTCAAAACCCTTGAAGTGAAG
1 ATCAAGTGTTCATGATCAAGAAT-AAGTCGTCAAGACCCTTGAAGTGAAG
* * * **
2374897 ATATCAAGTGTTCATGATCAAGATTAAGTTGTTAAGACCCTTGAAACGAAG
1 --ATCAAGTGTTCATGATCAAGAATAAGTCGTCAAGACCCTTGAAGTGAAG
* * * * * ** *
2374948 ATCAAGCAAAGTTCGTGATCAAG-ATCAAGTCATCAAGATCTTTGAAGCAAAAAT
1 ATCAAG---TGTTCATGATCAAGAAT-AAGTCGTCAAGACCCTTGAAG--TGAAG
*
2375002 ATCAAGTGTTCATGATCAAGATTAAGTCGTCAAGACCCTTGAAGTGAAG
1 ATCAAGTGTTCATGATCAAGAATAAGTCGTCAAGACCCTTGAAGTGAAG
*
2375051 ATCAAGTGAAGTTCATGACCAAGAATAAGT
1 ATCAAGT---GTTCATGATCAAGAATAAGT
2375081 TTGCATTTGT
Statistics
Matches: 140, Mismatches: 31, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
49 15 0.11
51 68 0.49
52 49 0.35
54 8 0.06
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (49 bp):
ATCAAGTGTTCATGATCAAGAATAAGTCGTCAAGACCCTTGAAGTGAAG
Found at i:2381054 original size:166 final size:166
Alignment explanation
Indices: 2380780--2381276 Score: 771
Period size: 166 Copynumber: 3.0 Consensus size: 166
2380770 TATCTAGTTG
* * * **
2380780 TTAAGGTACTATGATTCTATTGAGATATTAAAACACGTATGTATGAAGAGTCATAAATAAAAGAC
1 TTAAGGTACCATGATTCTATTGAGATATTAAAACACATATGTATGAAGAGTCATACATAGGAGAC
* *
2380845 ATATATTTTAATTGAATAC-AAAAATTGTTCACAGCCATATAATAAAGCTGGTTACTTTATTGTG
66 ATGTATTTTAATTGAAT-CTAAAAATTGTTCACAGCCATATAATAAAGCTGGTCACTTTATTGTG
2380909 TTAAAGTTGTAGTATCCAGATTACTTCCAACAAAATA
130 TTAAAGTTGTAGTATCCAGATTACTTCCAACAAAATA
2380946 TTAAGGTACCATGATTCTATTGAGATATTAAAACACATATGTATGAAGAGTCATACATAGGAGAC
1 TTAAGGTACCATGATTCTATTGAGATATTAAAACACATATGTATGAAGAGTCATACATAGGAGAC
* * *
2381011 ATGCATTTCAATTGAATCTAAAAATTGTTCACAGCTATATAATAAAGCTGGTCACTTTATTGTGT
66 ATGTATTTTAATTGAATCTAAAAATTGTTCACAGCCATATAATAAAGCTGGTCACTTTATTGTGT
* *
2381076 TAAAGTTGTAGTATCCACATTACTTCCAGCAAAATA
131 TAAAGTTGTAGTATCCAGATTACTTCCAACAAAATA
* * *
2381112 TTAAGGTACCAAGATTCTATTGAGATATTAAAACACAAATGTATGAAGAGTCATACATAGGAGAA
1 TTAAGGTACCATGATTCTATTGAGATATTAAAACACATATGTATGAAGAGTCATACATAGGAGAC
* *
2381177 ATGTATTTTAATTGAACCTAAAAATTGTTCACAGCCATATAATAAAGCTAGTCACTTTATTGTGT
66 ATGTATTTTAATTGAATCTAAAAATTGTTCACAGCCATATAATAAAGCTGGTCACTTTATTGTGT
* * * ** *
2381242 TAAGGCTGTAGTGTTGAGATTACTTCCAACGAAAT
131 TAAAGTTGTAGTATCCAGATTACTTCCAACAAAAT
2381277 GAATGTGATT
Statistics
Matches: 302, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
165 1 0.00
166 301 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (166 bp):
TTAAGGTACCATGATTCTATTGAGATATTAAAACACATATGTATGAAGAGTCATACATAGGAGAC
ATGTATTTTAATTGAATCTAAAAATTGTTCACAGCCATATAATAAAGCTGGTCACTTTATTGTGT
TAAAGTTGTAGTATCCAGATTACTTCCAACAAAATA
Found at i:2382171 original size:29 final size:28
Alignment explanation
Indices: 2382137--2382220 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
2382127 TCTTAATTTA
2382137 AGACAAGAAAAATATTTTTGGTCTTATCC
1 AGACAAGAAAAATATTTTT-GTCTTATCC
* * * * **
2382166 AGACAAAAAAAACATATTTGTCTCAATTT
1 AGACAAGAAAAATATTTTTGTCT-TATCC
*
2382195 AGATAAGATAAAATATTTTTGTCTTA
1 AGACAAGA-AAAATATTTTTGTCTTA
2382221 ATTAAAAATA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
28 4 0.10
29 25 0.60
30 13 0.31
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (28 bp):
AGACAAGAAAAATATTTTTGTCTTATCC
Found at i:2382394 original size:17 final size:17
Alignment explanation
Indices: 2382374--2382406 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2382364 ATAATTATAA
2382374 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
2382391 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
2382407 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:2384141 original size:3 final size:3
Alignment explanation
Indices: 2384133--2384173 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2384123 TAGGATGGAC
2384133 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2384174 GAATGATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2390193 original size:28 final size:30
Alignment explanation
Indices: 2390162--2390233 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
2390152 ACTTGTTTGG
*
2390162 TCTTAATTTAGACAA-AAATATA-TATTTA
1 TCTTAATTTAGACAAGAAAAATATTATTTA
* *
2390190 TCTTAATTTTAGACAAGAAAAATATTTTTTG
1 TCTTAA-TTTAGACAAGAAAAATATTATTTA
*
2390221 TCTCAATTTAGAC
1 TCTTAATTTAGAC
2390234 GAGTTAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.16
29 9 0.24
30 13 0.35
31 9 0.24
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (30 bp):
TCTTAATTTAGACAAGAAAAATATTATTTA
Found at i:2394893 original size:59 final size:59
Alignment explanation
Indices: 2394801--2394918 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
2394791 TTTTGCGGAT
2394801 ATGTATGCTCGATGGTTTCGCTTATCGAGAAGTGGTTTCAACCGATTTCCTTTATATAG
1 ATGTATGCTCGATGGTTTCGCTTATCGAGAAGTGGTTTCAACCGATTTCCTTTATATAG
* *
2394860 ATGTATGCTCGATGGTTTCGCTTATCGAGAAGTGGTTTCAACTGATTTCCTTTGTATAG
1 ATGTATGCTCGATGGTTTCGCTTATCGAGAAGTGGTTTCAACCGATTTCCTTTATATAG
2394919 TCTGATACAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (59 bp):
ATGTATGCTCGATGGTTTCGCTTATCGAGAAGTGGTTTCAACCGATTTCCTTTATATAG
Found at i:2395187 original size:97 final size:97
Alignment explanation
Indices: 2395021--2395214 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
2395011 CTCAATTTTG
2395021 TCAATTTGGGTGAGAGATTATTTTTGGCTCTTTTTTTGTTTTTGCAGATATGTATGCTCGATGGT
1 TCAATTTGGGTGAGAGATTATTTTTGGCTCTTTTTTTGTTTTTGCAGATATGTATGCTCGATGGT
2395086 TTCGCTTATCGAGAAGTGGTTTCAACCGATTT
66 TTCGCTTATCGAGAAGTGGTTTCAACCGATTT
2395118 TCAATTTGGGTGAGAGATTATTTTTGGCTCTTTTTTTGTTTTTGCAGATATGTATGCTCGATGGT
1 TCAATTTGGGTGAGAGATTATTTTTGGCTCTTTTTTTGTTTTTGCAGATATGTATGCTCGATGGT
2395183 TTCGCTTATCGAGAAGTGGTTTCAACCGATTT
66 TTCGCTTATCGAGAAGTGGTTTCAACCGATTT
2395215 CCTTTGTATA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (97 bp):
TCAATTTGGGTGAGAGATTATTTTTGGCTCTTTTTTTGTTTTTGCAGATATGTATGCTCGATGGT
TTCGCTTATCGAGAAGTGGTTTCAACCGATTT
Found at i:2399225 original size:2 final size:2
Alignment explanation
Indices: 2399218--2399242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2399208 AACCTTAAAA
2399218 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
2399243 AATTCTTGAC
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:2400868 original size:120 final size:123
Alignment explanation
Indices: 2400624--2400849 Score: 323
Period size: 125 Copynumber: 1.8 Consensus size: 123
2400614 GCAAATGACA
*
2400624 AAAGAAGAATTCAAAAGTAGATATTATAAATTGAAAAAAAATTAGTCTTATATATAGGAAAAAAA
1 AAAGAAGAATTCAAAAATAGATATTATAAATT--AAAAAAATTAGTCTTATATATAGGAAAAAAA
* * * *
2400689 TAGCTATTAACAATATTAAATATATATTACCGTTAGTTAATCGAAAAAAGAAAAAATAGG
64 TAGCTATGAACAAGATTAAATACATATTACCATTAGTTAATCGAAAAAAGAAAAAATAGG
* * *
2400749 AAAGAAGAATTCAAAAATGGATATTATAAATT-AAAAAATTAGTTTTATATATA-GAAAAATATA
1 AAAGAAGAATTCAAAAATAGATATTATAAATTAAAAAAATTAGTCTTATATATAGGAAAAAAATA
* *
2400812 GCTATGGA-AAGATTAAATACATATTACTATTAGTTAAT
66 GCTATGAACAAGATTAAATACATATTACCATTAGTTAAT
2400850 TGCAAATAGG
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
120 26 0.29
121 15 0.16
122 20 0.22
125 30 0.33
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.31
Consensus pattern (123 bp):
AAAGAAGAATTCAAAAATAGATATTATAAATTAAAAAAATTAGTCTTATATATAGGAAAAAAATA
GCTATGAACAAGATTAAATACATATTACCATTAGTTAATCGAAAAAAGAAAAAATAGG
Found at i:2400896 original size:69 final size:69
Alignment explanation
Indices: 2400816--2401014 Score: 238
Period size: 69 Copynumber: 2.9 Consensus size: 69
2400806 AATATAGCTA
* *
2400816 TGGAAAGATTAAATACATATTACTATTAGTTAATTGCAAATAGGAGAAATAGGTGAGAAAAAAAA
1 TGGAAATATTAAATACATATTACTATTAGTTAATTGAAAATAGGAGAAATAGGTGAGAAAAAAAA
2400881 CTAT
66 CTAT
* * * * *
2400885 TGGAAATATTAAATACATATTACTGTTAGTTGATTGAAAATAAGAAAAATAGGTAAGAAAAAAAA
1 TGGAAATATTAAATACATATTACTATTAGTTAATTGAAAATAGGAGAAATAGGTGAG-AAAAAAA
2400950 ACTAT
65 ACTAT
* * * * * * *
2400955 T-GAAGATCATTAGATAAATATTACCATTAGTTTATTGGAAATAGGTGAAATAGTTGAGAA
1 TGGAA-AT-ATTAAATACATATTACTATTAGTTAATTGAAAATAGGAGAAATAGGTGAGAA
2401015 TTAATAAATA
Statistics
Matches: 109, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
69 53 0.49
70 17 0.16
71 39 0.36
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (69 bp):
TGGAAATATTAAATACATATTACTATTAGTTAATTGAAAATAGGAGAAATAGGTGAGAAAAAAAA
CTAT
Found at i:2406382 original size:26 final size:26
Alignment explanation
Indices: 2406353--2406407 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2406343 ATTTAAAATC
* *
2406353 AATAATTATAAAAACAATTATAATAA
1 AATAATAATAAAAACAAATATAATAA
* *
2406379 AATAATAATAACATCAAATATAATAA
1 AATAATAATAAAAACAAATATAATAA
2406405 AAT
1 AAT
2406408 TTAACATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (26 bp):
AATAATAATAAAAACAAATATAATAA
Found at i:2406398 original size:21 final size:20
Alignment explanation
Indices: 2406374--2406420 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
2406364 AAACAATTAT
2406374 AATAAAATAATAA-TAACATCA
1 AATAAAATAA-AATTAACAT-A
*
2406395 AATATAATAAAATTTAACATA
1 AATAAAATAAAA-TTAACATA
2406416 AATAA
1 AATAA
2406421 CATACGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 14 0.64
22 6 0.27
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAAAATAAAATTAACATA
Found at i:2407319 original size:23 final size:23
Alignment explanation
Indices: 2407289--2407333 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2407279 CTTACCCTTT
2407289 AGCTTTAGTAAGTACGGTCATGC
1 AGCTTTAGTAAGTACGGTCATGC
2407312 AGCTTTAGTAAGTACGGTCATG
1 AGCTTTAGTAAGTACGGTCATG
2407334 TTGCACCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (23 bp):
AGCTTTAGTAAGTACGGTCATGC
Found at i:2407363 original size:38 final size:38
Alignment explanation
Indices: 2407312--2407414 Score: 206
Period size: 38 Copynumber: 2.7 Consensus size: 38
2407302 ACGGTCATGC
2407312 AGCTTTAGTAAGTACGGTCATGTTGCACCTTGCCCTTT
1 AGCTTTAGTAAGTACGGTCATGTTGCACCTTGCCCTTT
2407350 AGCTTTAGTAAGTACGGTCATGTTGCACCTTGCCCTTT
1 AGCTTTAGTAAGTACGGTCATGTTGCACCTTGCCCTTT
2407388 AGCTTTAGTAAGTACGGTCATGTTGCA
1 AGCTTTAGTAAGTACGGTCATGTTGCA
2407415 TAGAACAACA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (38 bp):
AGCTTTAGTAAGTACGGTCATGTTGCACCTTGCCCTTT
Found at i:2418218 original size:9 final size:9
Alignment explanation
Indices: 2418163--2418220 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
2418153 TTGTCCTTTT
*
2418163 TTTATTTTA
1 TTTATTTCA
2418172 TTTATTTCA
1 TTTATTTCA
2418181 -TTA-TTCA
1 TTTATTTCA
2418188 TTTTATTTC-
1 -TTTATTTCA
*
2418197 TCTT-TTCCA
1 T-TTATTTCA
2418206 TTTATTTCA
1 TTTATTTCA
2418215 TTTATT
1 TTTATT
2418221 ATTATTGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
7 4 0.10
8 9 0.22
9 24 0.60
10 3 0.08
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATTTCA
Found at i:2422528 original size:4 final size:4
Alignment explanation
Indices: 2422519--2422545 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2422509 TGATAAATCT
2422519 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
2422546 GGAAGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:2422995 original size:27 final size:30
Alignment explanation
Indices: 2422928--2422996 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 30
2422918 TATTACTAAT
*
2422928 AATTTATTTAATTCAAAATAAAAATATAAA
1 AATTTATTTAAATCAAAATAAAAATATAAA
*
2422958 AATTTGA-TTAAAT-ATAAT-AAAA-ATAAA
1 AATTT-ATTTAAATCAAAATAAAAATATAAA
2422985 AATTTATTTAAA
1 AATTTATTTAAA
2422997 ACTTTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 1 0.03
27 15 0.43
28 4 0.11
29 4 0.11
30 10 0.29
31 1 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
AATTTATTTAAATCAAAATAAAAATATAAA
Found at i:2428858 original size:2 final size:2
Alignment explanation
Indices: 2428851--2428878 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2428841 TAGTTAGCAA
2428851 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
2428879 GGATTATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2431658 original size:30 final size:31
Alignment explanation
Indices: 2431602--2431660 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
2431592 ATTAAATTTA
*
2431602 AAATCATTTTTTTTAATCACTTAAATTTTTT
1 AAATCATTTTTTTTAATCACTCAAATTTTTT
*
2431633 AAAT-ATTTTATTTTGATCA-TCAAATTTT
1 AAATCATTTT-TTTTAATCACTCAAATTTT
2431661 AAAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (31 bp):
AAATCATTTTTTTTAATCACTCAAATTTTTT
Found at i:2432621 original size:15 final size:15
Alignment explanation
Indices: 2432601--2432663 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
2432591 GATAATTAAA
2432601 TTTATATATTATAAG
1 TTTATATATTATAAG
* *
2432616 TTTATATAAATAAAAG
1 TTTATAT-ATTATAAG
*
2432632 TATATATATTATAA-
1 TTTATATATTATAAG
* *
2432646 TTAATAATTTTATAAG
1 TTTAT-ATATTATAAG
2432662 TT
1 TT
2432664 ATTTTTTTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
14 3 0.08
15 20 0.54
16 14 0.38
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TTTATATATTATAAG
Found at i:2432629 original size:29 final size:31
Alignment explanation
Indices: 2432587--2432645 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
2432577 ACAACTTCTT
* *
2432587 TTTAGAT-AATTAAA-TTTATATATTATAAG
1 TTTAGATAAATAAAAGTATATATATTATAAG
*
2432616 TTTATATAAATAAAAGTATATATATTATAA
1 TTTAGATAAATAAAAGTATATATATTATAA
2432646 TTAATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 6 0.24
31 13 0.52
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTAGATAAATAAAAGTATATATATTATAAG
Found at i:2436282 original size:81 final size:80
Alignment explanation
Indices: 2436067--2436319 Score: 249
Period size: 81 Copynumber: 3.1 Consensus size: 80
2436057 ATATAATATA
* * * *
2436067 TTTTTGTATATGGCATGTAACAACAATATTTTTTTTTTCAACATGGTGTGTAACAACCTTTTTTA
1 TTTTTGTACATGACATATAATAACAATA--TTTTTTTTCAACATGGTGTGTAACAACC-TTTTTA
**
2436132 ACCAT-GATGTGTTTCATG
63 ACCATAG-TGTGTAACATG
* * * * * * ***
2436150 TTTTTGTACGTGACATGTAATAAGAAAAATTTTGTTCAACATGGCACGTAACAACCTTTTTCAAC
1 TTTTTGTACATGACATATAATAACAATATTTTTTTTCAACATGGTGTGTAACAACCTTTTT-AAC
* *
2436215 CATAGCGTGTAACATA
65 CATAGTGTGTAACATG
* * *
2436231 TATTTGTACATGACGTATAATAACAATATTTTTTTTCAACATAGTGTGTAACAACCTTTCTTAAC
1 TTTTTGTACATGACATATAATAACAATATTTTTTTTCAACATGGTGTGTAACAACCTTT-TTAAC
2436296 CA-AGGTGTGTAACATG
65 CATA-GTGTGTAACATG
2436312 TTTTTGTA
1 TTTTTGTA
2436320 TATGGCATGT
Statistics
Matches: 136, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
80 6 0.04
81 105 0.77
82 3 0.02
83 22 0.16
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (80 bp):
TTTTTGTACATGACATATAATAACAATATTTTTTTTCAACATGGTGTGTAACAACCTTTTTAACC
ATAGTGTGTAACATG
Found at i:2436331 original size:50 final size:50
Alignment explanation
Indices: 2436277--2436373 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 50
2436267 CAACATAGTG
*
2436277 TGTAACAACCTTTCTTAACCA-AGGTGTGTAACATGTTTTTGTATATGGCA
1 TGTAACAACCTTTCTTAACCATA-GTATGTAACATGTTTTTGTATATGGCA
* ** *
2436327 TGTAACAACCTTTTTTAATTATAGTATGTAATATGTTTTTGTATATG
1 TGTAACAACCTTTCTTAACCATAGTATGTAACATGTTTTTGTATATG
2436374 ATATATAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
50 40 0.98
51 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.44
Consensus pattern (50 bp):
TGTAACAACCTTTCTTAACCATAGTATGTAACATGTTTTTGTATATGGCA
Found at i:2436787 original size:27 final size:27
Alignment explanation
Indices: 2436742--2436793 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2436732 TTAACTAATT
**
2436742 AATTAATATTTTTGCAAAA-TAATTTA
1 AATTAATATTTTTAAAAAATTAATTTA
2436768 AATTAATTATTTTTAAAAAATTAATT
1 AATTAA-TATTTTTAAAAAATTAATT
2436794 AATTTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 11 0.50
28 5 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
AATTAATATTTTTAAAAAATTAATTTA
Found at i:2436790 original size:18 final size:20
Alignment explanation
Indices: 2436767--2436806 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
2436757 AAAATAATTT
2436767 AAATTAATT-ATTT-TTAAA
1 AAATTAATTAATTTATTAAA
2436785 AAATTAATTAATTTATTAAA
1 AAATTAATTAATTTATTAAA
2436805 AA
1 AA
2436807 TAAATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTAATTAATTTATTAAA
Found at i:2436795 original size:27 final size:25
Alignment explanation
Indices: 2436737--2436795 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
2436727 CCAACTTAAC
**
2436737 TAATT-AATTAATATTTTTGCAAAA
1 TAATTAAATTAATATTTTTAAAAAA
2436761 TAATTTAAATTAATTATTTTTAAAAAA
1 TAA-TTAAATTAA-TATTTTTAAAAAA
2436788 TTAATTAA
1 -TAATTAA
2436796 TTTATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 3 0.10
25 2 0.07
26 6 0.21
27 15 0.52
28 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TAATTAAATTAATATTTTTAAAAAA
Found at i:2436797 original size:26 final size:25
Alignment explanation
Indices: 2436737--2436802 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
2436727 CCAACTTAAC
**
2436737 TAATTAATTAA-TATTTTTGCAAAA
1 TAATTAATTAATTATTTTTAAAAAA
2436761 TAATTTAAATTAATTATTTTTAAAAAA
1 TAA-TT-AATTAATTATTTTTAAAAAA
*
2436788 TTAATTAATTTATTA
1 -TAATTAATTAATTA
2436803 AAAATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 3 0.09
25 2 0.06
26 14 0.40
27 13 0.37
28 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TAATTAATTAATTATTTTTAAAAAA
Found at i:2442179 original size:29 final size:29
Alignment explanation
Indices: 2442133--2442189 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
2442123 GTAGTGTTGT
*
2442133 CAAGAGGTTACGCTTGATCCTTAAAAGGG
1 CAAGAGGTTACGCCTGATCCTTAAAAGGG
* *
2442162 CAAGAGGTTGCGCCTGATCCTTGAAAGG
1 CAAGAGGTTACGCCTGATCCTTAAAAGG
2442190 CAAAGGGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (29 bp):
CAAGAGGTTACGCCTGATCCTTAAAAGGG
Done.