Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 93 of 202
Found at i:27976668 original size:225 final size:224
Alignment explanation
Indices: 27976281--27976735 Score: 745
Period size: 225 Copynumber: 2.0 Consensus size: 224
27976271 TAGGTTAGTG
**
27976281 AGAATTTTCTAACGGTAGTAACTAAATTACATTTATTTTATTTGAGGGATCAAAATGAAAGGGCT
1 AGAATTTTCTAACGGTAGTAACTAAATTACATTTATTTTATTTGAGGGATCAAAATGAAAGCACT
*
27976346 TAAAAAGTTGAGTAATCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCAATAT
66 TAAAAAGTTGAGTAACCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCAATAT
* * *
27976411 AGGAGGACATGGGTTCGATTGTACTGAATCTCATTATCCTCTTA-TT-TA-TGGAGAGGGACTAT
131 AAGAGGACATGGGTTCGAGTGTACTGAATCTCATTATCCTCTTATTTATAGTGGAGAGAGACTAT
27976473 GTATAGTTTTAAACATTGTCTTCTCAAAA
196 GTATAGTTTTAAACATTGTCTTCTCAAAA
* * *
27976502 AGAATTTTCTAACGGTAGTGACTAAATTACAAGTTTTTTTTTTATTTGAGGGATTAAAATGAAAG
1 AGAATTTTCTAACGGTAGTAACTAAATTAC-A---TTTATTTTATTTGAGGGATCAAAATGAAAG
*
27976567 CACTTAAAAAGTTGGGTAACCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCA
62 CACTTAAAAAGTTGAGTAACCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCA
27976632 ATATAAGAGGACATGGGTTCGAGTGTACTGAATCTCATTATCCTCTTATTTATAGGTTGGAGAGA
127 ATATAAGAGGACATGGGTTCGAGTGTACTGAATCTCATTATCCTCTTATTTATA-G-TGGAGAGA
27976697 GACTATGTATAGTTTTAAACATTGTCTTCTCAAAA
190 GACTATGTATAGTTTTAAACATTGTCTTCTCAAAA
27976732 AGAA
1 AGAA
27976736 CATATATGAA
Statistics
Matches: 215, Mismatches: 10, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
221 29 0.13
222 1 0.00
225 135 0.63
226 2 0.01
227 2 0.01
230 46 0.21
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (224 bp):
AGAATTTTCTAACGGTAGTAACTAAATTACATTTATTTTATTTGAGGGATCAAAATGAAAGCACT
TAAAAAGTTGAGTAACCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCAATAT
AAGAGGACATGGGTTCGAGTGTACTGAATCTCATTATCCTCTTATTTATAGTGGAGAGAGACTAT
GTATAGTTTTAAACATTGTCTTCTCAAAA
Found at i:27977197 original size:13 final size:13
Alignment explanation
Indices: 27977179--27977214 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27977169 CTACAGTATG
27977179 ATAAAAATTTCGT
1 ATAAAAATTTCGT
27977192 ATAAAAATTTCGT
1 ATAAAAATTTCGT
27977205 -TAAGAAATTT
1 ATAA-AAATTT
27977215 TACCGTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (13 bp):
ATAAAAATTTCGT
Found at i:27977988 original size:16 final size:17
Alignment explanation
Indices: 27977967--27978000 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27977957 GTTCCATGTT
27977967 GAATTAAATTG-AATGA
1 GAATTAAATTGAAATGA
*
27977983 GAATTATATTGAAATGA
1 GAATTAAATTGAAATGA
27978000 G
1 G
27978001 TTAAATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (17 bp):
GAATTAAATTGAAATGA
Found at i:27978383 original size:25 final size:25
Alignment explanation
Indices: 27978311--27978383 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
27978301 GACACACCAT
*
27978311 AGCTCGCATGAGCTTCCCGTTACTC
1 AGCTCGCATGAGCTTCCCGTTATTC
*
27978336 AGCTCGCATAAGCTTCCCGTTATTC
1 AGCTCGCATGAGCTTCCCGTTATTC
*
27978361 AGCTCGCATGAGCTTCCCATTAT
1 AGCTCGCATGAGCTTCCCGTTAT
27978384 ACAACTCGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.19, C:0.33, G:0.18, T:0.30
Consensus pattern (25 bp):
AGCTCGCATGAGCTTCCCGTTATTC
Found at i:27978398 original size:25 final size:25
Alignment explanation
Indices: 27978313--27978400 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 25
27978303 CACACCATAG
* * *
27978313 CTCGCATGAGCTTCCCGTTACT-CAG
1 CTCGCAGGAGCTTCCCATTA-TACAA
** * * *
27978338 CTCGCATAAGCTTCCCGTTATTCAG
1 CTCGCAGGAGCTTCCCATTATACAA
*
27978363 CTCGCATGAGCTTCCCATTATACAA
1 CTCGCAGGAGCTTCCCATTATACAA
*
27978388 CTCGGAGGAGCTT
1 CTCGCAGGAGCTT
27978401 ACTATTTACA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
24 1 0.02
25 54 0.98
ACGTcount: A:0.20, C:0.32, G:0.19, T:0.28
Consensus pattern (25 bp):
CTCGCAGGAGCTTCCCATTATACAA
Found at i:27990690 original size:11 final size:9
Alignment explanation
Indices: 27990650--27990683 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
27990640 TTTTATTGAA
*
27990650 TTTTGTCTT
1 TTTTGACTT
27990659 TTTTGA-TT
1 TTTTGACTT
27990667 TTTTGACTT
1 TTTTGACTT
27990676 TTTTGACT
1 TTTTGACT
27990684 GATTTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.09, G:0.12, T:0.71
Consensus pattern (9 bp):
TTTTGACTT
Found at i:28005732 original size:3 final size:3
Alignment explanation
Indices: 28005724--28005774 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
28005714 TCAGAAACAC
28005724 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28005772 ATT
1 ATT
28005775 CAGTACTAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28009603 original size:29 final size:29
Alignment explanation
Indices: 28009553--28009634 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 29
28009543 GGTGCCTTCG
* *
28009553 AACCAATAGCT-TAGATATCACTTGGTTCA
1 AACCAACAGCTCT-GATACCACTTGGTTCA
*
28009582 AACCAACAGCTC-GAATACCACTTGGTTCG
1 AACCAACAGCTCTG-ATACCACTTGGTTCA
28009611 AACCAACAGCTCTGATACCACTTG
1 AACCAACAGCTCTGATACCACTTG
28009635 TTACGGGACT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.02
29 45 0.96
30 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCAACAGCTCTGATACCACTTGGTTCA
Found at i:28011476 original size:7 final size:7
Alignment explanation
Indices: 28011464--28011488 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28011454 AAGGCCGAAA
28011464 TTAAATT
1 TTAAATT
28011471 TTAAATT
1 TTAAATT
28011478 TTAAATT
1 TTAAATT
28011485 TTAA
1 TTAA
28011489 TAGTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:28012382 original size:20 final size:20
Alignment explanation
Indices: 28012357--28012396 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28012347 CTTAGATGAG
*
28012357 TTGTAAGATATTTTGTTATT
1 TTGTAAGATATTTTATTATT
*
28012377 TTGTAAGGTATTTTATTATT
1 TTGTAAGATATTTTATTATT
28012397 AACTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (20 bp):
TTGTAAGATATTTTATTATT
Found at i:28013360 original size:4 final size:4
Alignment explanation
Indices: 28013353--28013383 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
28013343 TATATATATA
28013353 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
28013384 CAAAGCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:28019667 original size:2 final size:2
Alignment explanation
Indices: 28019660--28019686 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28019650 AGAATTCAGA
28019660 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
28019687 ATTTTCAACT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28028501 original size:13 final size:13
Alignment explanation
Indices: 28028483--28028513 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28028473 CACATGACTA
28028483 ATTTCATATAGCC
1 ATTTCATATAGCC
*
28028496 ATTTCATATATCC
1 ATTTCATATAGCC
28028509 ATTTC
1 ATTTC
28028514 CATTTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.45
Consensus pattern (13 bp):
ATTTCATATAGCC
Found at i:28031841 original size:25 final size:25
Alignment explanation
Indices: 28031775--28031854 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
28031765 GCTATATAAT
** *
28031775 GGGAAGCTCATAAGAGCCA-ATAAC
1 GGGAAGCTCCGAAGAGCCATATATC
* *
28031799 AGGTAGCTCCGAAGAGCCAT-TAATC
1 GGGAAGCTCCGAAGAGCCATAT-ATC
* *
28031824 GGGAAGCTCCGGATAGCCATATATC
1 GGGAAGCTCCGAAGAGCCATATATC
28031849 GGGAAG
1 GGGAAG
28031855 TTCAAGCGAG
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
24 16 0.36
25 27 0.61
26 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.29, T:0.16
Consensus pattern (25 bp):
GGGAAGCTCCGAAGAGCCATATATC
Found at i:28032043 original size:25 final size:25
Alignment explanation
Indices: 28032015--28032063 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28032005 GGAAGGTCGC
28032015 AAGAACCATATAACGAAAAGCTCGT
1 AAGAACCATATAACGAAAAGCTCGT
**
28032040 AAGAACCATATAACGGGAAGCTCG
1 AAGAACCATATAACGAAAAGCTCG
28032064 AGAGGGCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (25 bp):
AAGAACCATATAACGAAAAGCTCGT
Found at i:28033727 original size:16 final size:16
Alignment explanation
Indices: 28033687--28033727 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
28033677 AGTTTTAGTT
28033687 TGACCCAATCTGTTAA
1 TGACCCAATCTGTTAA
* *
28033703 TGGCTCAATCTGTTAA
1 TGACCCAATCTGTTAA
28033719 TGACCCAAT
1 TGACCCAAT
28033728 TAATAAGCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (16 bp):
TGACCCAATCTGTTAA
Found at i:28033787 original size:23 final size:22
Alignment explanation
Indices: 28033750--28033825 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
28033740 TCAAGTCAAG
*
28033750 TTGTCTTCCACAATTTTAGGGAT
1 TTGT-TTCCACAATTTTAGGAAT
* * *
28033773 TTGTTTGGCTA-AATTGTAGGTAT
1 TTGTTT--CCACAATTTTAGGAAT
28033796 TTGTCTTCCACAATTTTAGGAAT
1 TTGT-TTCCACAATTTTAGGAAT
28033819 TTGTTTC
1 TTGTTTC
28033826 TCTTTTATCC
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
22 7 0.16
23 32 0.74
24 4 0.09
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.47
Consensus pattern (22 bp):
TTGTTTCCACAATTTTAGGAAT
Found at i:28036335 original size:27 final size:27
Alignment explanation
Indices: 28036280--28036354 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
28036270 AACATAGAAG
*
28036280 GTCTGCCAGGATAATAAACACGAGATA
1 GTCTGCCAGGACAATAAACACGAGATA
* * *
28036307 GTTTGCCAGGACACTAAACAC-ATGGTA
1 GTCTGCCAGGACAATAAACACGA-GATA
* * *
28036334 GTCTGCTATGACAGTAAACAC
1 GTCTGCCAGGACAATAAACAC
28036355 TGGGTGAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (27 bp):
GTCTGCCAGGACAATAAACACGAGATA
Found at i:28043914 original size:34 final size:34
Alignment explanation
Indices: 28043876--28043941 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
28043866 CAGTAAAATG
*
28043876 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTAC-AGAAAATATTTTAC
*
28043910 TTTTCTGTAAAATGATTTACAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACAGAAAATATTTT
28043942 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (34 bp):
TTTTCCGTAAAATGATTTACAGAAAATATTTTAC
Found at i:28052389 original size:16 final size:16
Alignment explanation
Indices: 28052364--28052409 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
28052354 CGCTGTTATG
*
28052364 GAATAGAGTTGTAATA
1 GAATAAAGTTGTAATA
*
28052380 GAATAAAGTT-TAATG
1 GAATAAAGTTGTAATA
28052395 GAATAAAGTTGTAAT
1 GAATAAAGTTGTAAT
28052410 CAGTAATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.33
Consensus pattern (16 bp):
GAATAAAGTTGTAATA
Found at i:28052398 original size:15 final size:16
Alignment explanation
Indices: 28052361--28052409 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
28052351 GTTCGCTGTT
*
28052361 ATGGAATAGAGTTGTA
1 ATGGAATAAAGTTGTA
*
28052377 ATAGAATAAAGTT-TA
1 ATGGAATAAAGTTGTA
28052392 ATGGAATAAAGTTGTA
1 ATGGAATAAAGTTGTA
28052408 AT
1 AT
28052410 CAGTAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.45, C:0.00, G:0.22, T:0.33
Consensus pattern (16 bp):
ATGGAATAAAGTTGTA
Found at i:28072971 original size:22 final size:22
Alignment explanation
Indices: 28072919--28072988 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
28072909 TGGACATGTC
* *
28072919 ACCACTAATTTATAGATAAACT
1 ACCACTGATTTGTAGATAAACT
** *
28072941 GTCATTGATTTGTAGATAAACT
1 ACCACTGATTTGTAGATAAACT
* *
28072963 ACCACTGATTTGCAAATAAACT
1 ACCACTGATTTGTAGATAAACT
28072985 ACCA
1 ACCA
28072989 TTCATAAAAC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (22 bp):
ACCACTGATTTGTAGATAAACT
Found at i:28076222 original size:20 final size:20
Alignment explanation
Indices: 28076199--28076237 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28076189 TTTGGAGAAA
*
28076199 AGAAAGAATGATGAATGATG
1 AGAAAGAATGAGGAATGATG
*
28076219 AGAATGAATGAGGAATGAT
1 AGAAAGAATGAGGAATGAT
28076238 TGAGGGATGC
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:0.49, C:0.00, G:0.31, T:0.21
Consensus pattern (20 bp):
AGAAAGAATGAGGAATGATG
Found at i:28084143 original size:46 final size:46
Alignment explanation
Indices: 28084076--28084169 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
28084066 AAAAGGTCCT
*
28084076 TAGTCAAGTATTATTGTTGGATACGACAACAATAATGCATTAAGAC
1 TAGTCAAGTATTATAGTTGGATACGACAACAATAATGCATTAAGAC
*
28084122 TAGTCAAGTATTATAGTTGGATACGACAATAATAATGCATTAAGAC
1 TAGTCAAGTATTATAGTTGGATACGACAACAATAATGCATTAAGAC
28084168 TA
1 TA
28084170 ACATGTAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (46 bp):
TAGTCAAGTATTATAGTTGGATACGACAACAATAATGCATTAAGAC
Found at i:28100074 original size:20 final size:20
Alignment explanation
Indices: 28099943--28100096 Score: 209
Period size: 20 Copynumber: 7.7 Consensus size: 20
28099933 AAGTGTAACA
*
28099943 GAGGCACCGAAGTGCGAACG
1 GAGGCACCGAAGTGCAAACG
*
28099963 GAGGCACCGAAGTGCGAACG
1 GAGGCACCGAAGTGCAAACG
*
28099983 GAGGCACCGAAGTGCGAACG
1 GAGGCACCGAAGTGCAAACG
28100003 GAGGCACCGAAGTGCAAACG
1 GAGGCACCGAAGTGCAAACG
*
28100023 GAGGCACCGAAGTGGAAACG
1 GAGGCACCGAAGTGCAAACG
*
28100043 GAGGCACCGAAGTGCAAACA
1 GAGGCACCGAAGTGCAAACG
** * *
28100063 GAGGCATTGAAGAGCAAATG
1 GAGGCACCGAAGTGCAAACG
* *
28100083 AAGGCACTGAAGTG
1 GAGGCACCGAAGTG
28100097 AAAAATCTTA
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 122 1.00
ACGTcount: A:0.34, C:0.21, G:0.37, T:0.07
Consensus pattern (20 bp):
GAGGCACCGAAGTGCAAACG
Found at i:28100131 original size:21 final size:21
Alignment explanation
Indices: 28100105--28100169 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
28100095 TGAAAAATCT
*
28100105 TACAAGTGCACGTTCAAACCC
1 TACAAGCGCACGTTCAAACCC
*
28100126 TACAAGCACACGTTCAAACCC
1 TACAAGCGCACGTTCAAACCC
*
28100147 TACAAGCGCACATTCAAACCC
1 TACAAGCGCACGTTCAAACCC
28100168 TA
1 TA
28100170 TTGGCATGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.37, C:0.35, G:0.11, T:0.17
Consensus pattern (21 bp):
TACAAGCGCACGTTCAAACCC
Found at i:28112000 original size:86 final size:86
Alignment explanation
Indices: 28111851--28112016 Score: 305
Period size: 86 Copynumber: 1.9 Consensus size: 86
28111841 ATTCGTTGTG
* *
28111851 TATTTTGGGAATTTAGAGGTATCCTAAACCCCTCCTCTAAATTCCAAGTGGAAGTGTTCTTTTAC
1 TATTTTAGGAATTTAGAGGTATCCTAAACCCCTCCTCTAAATTCCAAGTGGAAGTGTTATTTTAC
28111916 CTATGCTAAATATGTGATAAA
66 CTATGCTAAATATGTGATAAA
*
28111937 TATTTTAGGAATTTAGAGGTATCCTAAACCCCTCCTCTAAATTCCAAGTGTAAGTGTTATTTTAC
1 TATTTTAGGAATTTAGAGGTATCCTAAACCCCTCCTCTAAATTCCAAGTGGAAGTGTTATTTTAC
28112002 CTATGCTAAATATGT
66 CTATGCTAAATATGT
28112017 TTGTGAATTC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (86 bp):
TATTTTAGGAATTTAGAGGTATCCTAAACCCCTCCTCTAAATTCCAAGTGGAAGTGTTATTTTAC
CTATGCTAAATATGTGATAAA
Found at i:28113302 original size:17 final size:17
Alignment explanation
Indices: 28113280--28113322 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28113270 CTGTCACATG
*
28113280 AATTAAATTAATTAT-TC
1 AATTAAATTAATT-TGAC
*
28113297 AATTAATTTAATTTGAC
1 AATTAAATTAATTTGAC
28113314 AATTAAATT
1 AATTAAATT
28113323 TTAAACGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (17 bp):
AATTAAATTAATTTGAC
Found at i:28114916 original size:20 final size:20
Alignment explanation
Indices: 28114893--28114955 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
28114883 TGGGCCTTCA
*
28114893 TGGCATTCTATTAGCCTTTG
1 TGGCATTATATTAGCCTTTG
* * * *
28114913 TGGCATTTTGTTAGTCGTTG
1 TGGCATTATATTAGCCTTTG
28114933 TGGCATTATATT-GCCTTTG
1 TGGCATTATATTAGCCTTTG
28114952 TGGC
1 TGGC
28114956 GTACTTAGTA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 9 0.26
20 26 0.74
ACGTcount: A:0.13, C:0.16, G:0.25, T:0.46
Consensus pattern (20 bp):
TGGCATTATATTAGCCTTTG
Found at i:28126448 original size:29 final size:29
Alignment explanation
Indices: 28126415--28126571 Score: 131
Period size: 29 Copynumber: 5.4 Consensus size: 29
28126405 GTCGTAACAG
** *
28126415 TCCCTTTTCATATTCGATGGCCGAAACCA
1 TCCCTTTTCATATTCGATGGTTGACACCA
* * *
28126444 TCCCTTTTCATTAATCAATGGTTGTCACCA
1 TCCCTTTTCA-TATTCGATGGTTGACACCA
* *
28126474 TCCCTTTTTC-TATTTGATGGTTGTCACCA
1 TCCC-TTTTCATATTCGATGGTTGACACCA
* * * * *
28126503 TCCCGTTTCATAATCGATAGCTGA-AGCTA
1 TCCCTTTTCATATTCGATGGTTGACA-CCA
*
28126532 TCCCTTTTCATATTCGATGG-TCATCACCA
1 TCCCTTTTCATATTCGATGGTTGA-CACCA
28126561 TCCCTTTTCAT
1 TCCCTTTTCAT
28126572 TAATCAATGA
Statistics
Matches: 101, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
28 7 0.07
29 71 0.70
30 18 0.18
31 5 0.05
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.39
Consensus pattern (29 bp):
TCCCTTTTCATATTCGATGGTTGACACCA
Found at i:28126551 original size:58 final size:59
Alignment explanation
Indices: 28126415--28126579 Score: 183
Period size: 58 Copynumber: 2.8 Consensus size: 59
28126405 GTCGTAACAG
* ** * * *
28126415 TCCCTTTTCATATTCGATGGCCGAAACCATCCCTTTTCATTAATCAATGGTTGTCACCA
1 TCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATTAATCAATAGCTGTAACCA
* * * * *
28126474 TCCCTTTTTC-TATTTGATGGTTGTCACCATCCCGTTTCA-TAATCGATAGCTG-AAGCTA
1 TCCC-TTTTCATATTCGATGGTCGTCACCATCCCTTTTCATTAATCAATAGCTGTAA-CCA
*
28126532 TCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATTAATCAAT
1 TCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATTAATCAAT
28126580 GATTACCGAT
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
57 6 0.07
58 41 0.48
59 34 0.40
60 5 0.06
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (59 bp):
TCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATTAATCAATAGCTGTAACCA
Found at i:28132466 original size:33 final size:33
Alignment explanation
Indices: 28132429--28132494 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
28132419 AGCATCCTAG
28132429 ATCCTCTTATACTCACTATTGAGGTAACCTATC
1 ATCCTCTTATACTCACTATTGAGGTAACCTATC
*
28132462 ATCCTCTTATACTTACTATTGAGGTAACCTATC
1 ATCCTCTTATACTCACTATTGAGGTAACCTATC
28132495 GCCCACCTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (33 bp):
ATCCTCTTATACTCACTATTGAGGTAACCTATC
Found at i:28140139 original size:13 final size:13
Alignment explanation
Indices: 28140121--28140148 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28140111 AACATCACAT
28140121 GTTTTATGTAAAA
1 GTTTTATGTAAAA
28140134 GTTTTATGTAAAA
1 GTTTTATGTAAAA
28140147 GT
1 GT
28140149 GAGAGTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (13 bp):
GTTTTATGTAAAA
Found at i:28144174 original size:6 final size:6
Alignment explanation
Indices: 28144163--28144196 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
28144153 TAAGATATTT
28144163 CCCCAC CCCCAC CCCCAC CCCCACC CCCCAC CCC
1 CCCCAC CCCCAC CCCCAC CCCCA-C CCCCAC CCC
28144197 ACCTCATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.15, C:0.85, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCAC
Found at i:28154939 original size:33 final size:33
Alignment explanation
Indices: 28154884--28154964 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 33
28154874 TAGTCCAACT
* ** *
28154884 ATGGTCTTACACATGCATTGCCATGGCCCTGCC
1 ATGGTCTTACACATGCAGTGCCATAACCCAGCC
** * *
28154917 ATGGTCTTACATTTGTAGTGCCATAACCCAGCT
1 ATGGTCTTACACATGCAGTGCCATAACCCAGCC
*
28154950 ATGGTCTTATACATG
1 ATGGTCTTACACATG
28154965 TATTTATACT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (33 bp):
ATGGTCTTACACATGCAGTGCCATAACCCAGCC
Found at i:28155508 original size:38 final size:39
Alignment explanation
Indices: 28155466--28155575 Score: 116
Period size: 38 Copynumber: 2.8 Consensus size: 39
28155456 TCTGATAGTT
* *
28155466 CGAAGCAAAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
* * * *
28155504 CGAAGTAAAG-TGATACCCAGTATCTCATCGAATCTATC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
* *
28155542 TGAAGTAAAATAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAAAGT--TGACACCCAGTGTCTCATCGA
28155576 CTCGAGGTCG
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
37 18 0.31
38 21 0.36
41 19 0.33
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (39 bp):
CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:28164492 original size:16 final size:16
Alignment explanation
Indices: 28164439--28164494 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
28164429 TACATAATAG
*
28164439 TCCATTCCAA-TGATA
1 TCCATTTCAATTGATA
* * *
28164454 TCCTTTTCATTTGAAA
1 TCCATTTCAATTGATA
28164470 T-CATTTCAATTGATA
1 TCCATTTCAATTGATA
28164485 TCCATTTCAA
1 TCCATTTCAA
28164495 CCTTTTCATT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.43
Consensus pattern (16 bp):
TCCATTTCAATTGATA
Found at i:28167202 original size:27 final size:28
Alignment explanation
Indices: 28167172--28167227 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
28167162 ACTCAACTCT
28167172 TGTTCAAACAACCCATTTAGACAA-ACC
1 TGTTCAAACAACCCATTTAGACAAGACC
* * *
28167199 TGTTTAAACAATCTATTTAGACAAGACC
1 TGTTCAAACAACCCATTTAGACAAGACC
28167227 T
1 T
28167228 TTGAGACAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (28 bp):
TGTTCAAACAACCCATTTAGACAAGACC
Found at i:28168810 original size:16 final size:17
Alignment explanation
Indices: 28168789--28168825 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
28168779 AAGGGGATGA
28168789 AAATAAATTT-TTAATT
1 AAATAAATTTATTAATT
28168805 AAATAAATTTGATTAATT
1 AAATAAATTT-ATTAATT
28168823 AAA
1 AAA
28168826 ATTTTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATAAATTTATTAATT
Found at i:28175221 original size:14 final size:15
Alignment explanation
Indices: 28175194--28175222 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28175184 GACTGACTCC
28175194 TTTAATTCTTAAATT
1 TTTAATTCTTAAATT
28175209 TTTAATT-TTAAATT
1 TTTAATTCTTAAATT
28175223 AAATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATTCTTAAATT
Found at i:28175226 original size:19 final size:20
Alignment explanation
Indices: 28175202--28175248 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
28175192 CCTTTAATTC
28175202 TTAAATTTTT-AATTTTAAA
1 TTAAATTTTTAAATTTTAAA
28175221 TTAAATTTTTAAATTTTAAA
1 TTAAATTTTTAAATTTTAAA
28175241 TTAAATTT
1 TTAAATTT
28175249 AATACCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAAATTTTTAAATTTTAAA
Found at i:28175240 original size:7 final size:7
Alignment explanation
Indices: 28175197--28175242 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
28175187 TGACTCCTTT
28175197 AATTCTTA
1 AATT-TTA
*
28175205 AATTTTT
1 AATTTTA
28175212 AATTTTA
1 AATTTTA
28175219 AA--TTA
1 AATTTTA
28175224 AATTTTTA
1 AA-TTTTA
28175232 AATTTTA
1 AATTTTA
28175239 AATT
1 AATT
28175243 AAATTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 5 0.15
7 19 0.58
8 9 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTTA
Found at i:28176948 original size:23 final size:23
Alignment explanation
Indices: 28176920--28176969 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
28176910 AAGTATAAGT
28176920 ATATAATTAGTTATATATAACGC
1 ATATAATTAGTTATATATAACGC
* *
28176943 ATATAATTGGTTATATATAATGC
1 ATATAATTAGTTATATATAACGC
28176966 ATAT
1 ATAT
28176970 TTTCTTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (23 bp):
ATATAATTAGTTATATATAACGC
Found at i:28177014 original size:14 final size:14
Alignment explanation
Indices: 28176978--28177035 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
28176968 ATTTTCTTTC
28176978 TATATTATTATCTTA
1 TATATTATTAT-TTA
*
28176993 T-TAATATTATTTA
1 TATATTATTATTTA
28177006 TATATTATTA---A
1 TATATTATTATTTA
28177017 TATATT-TTAATTTA
1 TATATTATT-ATTTA
28177031 TATAT
1 TATAT
28177036 ATTTAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
10 2 0.06
11 8 0.22
13 4 0.11
14 21 0.58
15 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTATTATTTA
Found at i:28177046 original size:15 final size:14
Alignment explanation
Indices: 28177016--28177056 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
28177006 TATATTATTA
*
28177016 ATATATTTTAATTT
1 ATATATTTTAAATT
28177030 ATATATATTTAAATT
1 ATATAT-TTTAAATT
28177045 ATATA-TTTAAAT
1 ATATATTTTAAAT
28177057 GATAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATTTTAAATT
Found at i:28177052 original size:13 final size:13
Alignment explanation
Indices: 28177031--28177056 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28177021 TTTTAATTTA
28177031 TATATATTTAAAT
1 TATATATTTAAAT
28177044 TATATATTTAAAT
1 TATATATTTAAAT
28177057 GATAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATTTAAAT
Found at i:28177242 original size:21 final size:21
Alignment explanation
Indices: 28177202--28177240 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28177192 AAATCATGGA
28177202 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
28177223 TAAATCCAAGCGA-TCTTT
1 TAAATCCAAGCGACTCTTT
28177241 TCGTAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:28179785 original size:12 final size:12
Alignment explanation
Indices: 28179768--28179792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28179758 ATTTTATAAC
28179768 ATAAATATTGTT
1 ATAAATATTGTT
28179780 ATAAATATTGTT
1 ATAAATATTGTT
28179792 A
1 A
28179793 ATAGCCTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:28180582 original size:35 final size:35
Alignment explanation
Indices: 28180536--28180606 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
28180526 TTAAAGAAAG
28180536 ATAGTTTTGGCCCGTTTTCCTATAATCTATAATAT
1 ATAGTTTTGGCCCGTTTTCCTATAATCTATAATAT
28180571 ATAGTTTTGGCCCGTTTTCCTATAATCTATAATAT
1 ATAGTTTTGGCCCGTTTTCCTATAATCTATAATAT
28180606 A
1 A
28180607 GAAAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (35 bp):
ATAGTTTTGGCCCGTTTTCCTATAATCTATAATAT
Found at i:28185174 original size:305 final size:305
Alignment explanation
Indices: 28184497--28185420 Score: 1392
Period size: 305 Copynumber: 3.0 Consensus size: 305
28184487 AATTACAAAA
* * *
28184497 GAATAAAAAGGAAAGCCCTTTTCACCAGCAATAACATGCATAGCAAAGAAATAAAATGATTTTAG
1 GAATAAAAAGGAAGGCCCTTTTCACCAGCAATAACATGCAGAGCGAAGAAATAAAATGATTTTAG
* * * * *
28184562 ATCCAAATTTGAGTAAAACCAAGTTCTTAGCAAAAATTATGCAAAATCCACATCAAATTTACAAT
66 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGATATACAAT
* *
28184627 TAATCATGTAGAGTCTCCAAGTACCAA-CAGATAAAACTAATAACATAGAGATATAGTTTAAAGA
131 TAATAATGTA-AGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
* *
28184691 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAATTTACCCAAGACCAGCAAAAGAAAAAAA
195 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCCAAGACCAGCAAAA-AAAAAGA
* * *
28184756 ATGCAAGGTAGTTTAACACAAAATCAACAGTAAGAAAGAATAATCTG
259 TTGCAAGGTAATTCAACACAAAATCAACAGTAAGAAAGAATAATCTG
* *
28184803 GAATAAAAAAGGAAGGCCCTTTTCACTAGCAATAACATGCAGAGCGAAAAAATAAAATGATTTTA
1 GAAT-AAAAAGGAAGGCCCTTTTCACCAGCAATAACATGCAGAGCGAAGAAATAAAATGATTTTA
*
28184868 GATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATACAAAACCCACATCAGATATACAA
65 GATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGATATACAA
* *
28184933 TTAATAATGT-AGTCTCAAAGTACCAAGTAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
130 TTAATAATGTAAGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
*
28184997 ATACAAAAGCTACTAACCAATTAGCT-TGAACCAAAACTTACCCAAGACCAGCAAAAAAGAAAGA
195 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCCAAGACCAGCAAAAAA-AAAGA
* * *
28185061 TTGTAAGGTAATTCAACACAAAAATCAACAATAAGAAAGAATAATTTG
259 TTGCAAGGTAATTCAACAC-AAAATCAACAGTAAGAAAGAATAATCTG
* * * *
28185109 GAATAAAAAGGAAGGCCCTTTTCACCAGCAGTAATATGCAGAGCGAAGAAATAAAACGGTTTTAG
1 GAATAAAAAGGAAGGCCCTTTTCACCAGCAATAACATGCAGAGCGAAGAAATAAAATGATTTTAG
*
28185174 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGAAATACAAT
66 ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGATATACAAT
* * *
28185239 TAATAATGTAGAGTCTCCAAGTACTAAGCAGATAAAAC---TAACATAGAAATATAATTTAAATA
131 TAATAATGTA-AGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGA
* * *
28185301 AAACACAAGCTACTAACCAATTAGCTCTAAACCAAAACTTACCCAAGACTAGCAAAAAAAAAAAA
195 AAACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCCAAGACCAGC----AAAAAAAA
*
28185366 AGATTGCAAGGTAATTCAACACAAAATCAGCAGTAAGAAAGAATAATCTG
256 AGATTGCAAGGTAATTCAACACAAAATCAACAGTAAGAAAGAATAATCTG
28185416 GAATA
1 GAATA
28185421 CCCACAAAGA
Statistics
Matches: 562, Mismatches: 45, Indels: 21
0.89 0.07 0.03
Matches are distributed among these distances:
304 48 0.09
305 214 0.38
306 94 0.17
307 177 0.31
308 23 0.04
309 6 0.01
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (305 bp):
GAATAAAAAGGAAGGCCCTTTTCACCAGCAATAACATGCAGAGCGAAGAAATAAAATGATTTTAG
ATCCAAATTTGAGTAAAACCAAGTTGTTAGCAGAAATTATGCAAAACCCACATCAGATATACAAT
TAATAATGTAAGTCTCCAAGTACCAAGCAGATAAAACTAATAACATAGAAATATAGTTTAAAGAA
AACAAAAGCTACTAACCAATTAGCTCTGAACCAAAACTTACCCAAGACCAGCAAAAAAAAAGATT
GCAAGGTAATTCAACACAAAATCAACAGTAAGAAAGAATAATCTG
Found at i:28193939 original size:27 final size:27
Alignment explanation
Indices: 28193884--28193941 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
28193874 ATTAATGGCC
* **
28193884 GCTTCCATCACTGCTTGTGTCATGGTT
1 GCTTCCATCACTGCTTGCGTCATCATT
*
28193911 GCTTCCATCATTGCTTGCGTCATCATT
1 GCTTCCATCACTGCTTGCGTCATCATT
28193938 GCTT
1 GCTT
28193942 TGATGATAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.41
Consensus pattern (27 bp):
GCTTCCATCACTGCTTGCGTCATCATT
Found at i:28198964 original size:21 final size:20
Alignment explanation
Indices: 28198940--28198984 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28198930 AAAACCCCAG
*
28198940 AAAAAT-GCAAAAAAATCAGA
1 AAAAATAGCAAAAAAAT-AAA
*
28198960 AAAAATAGCAAAATAATAAA
1 AAAAATAGCAAAAAAATAAA
28198980 AAAAA
1 AAAAA
28198985 ATCTCACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.11
Consensus pattern (20 bp):
AAAAATAGCAAAAAAATAAA
Found at i:28198985 original size:21 final size:20
Alignment explanation
Indices: 28198940--28198986 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
28198930 AAAACCCCAG
* *
28198940 AAAAATGCAAAAAAATCAGA
1 AAAAATGCAAAAAAATAAAA
*
28198960 AAAAATAGCAAAATAATAAAA
1 AAAAAT-GCAAAAAAATAAAA
28198981 AAAAAT
1 AAAAAT
28198987 CTCACTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (20 bp):
AAAAATGCAAAAAAATAAAA
Found at i:28200003 original size:24 final size:24
Alignment explanation
Indices: 28199963--28200029 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
28199953 ATTTTGTGTT
*
28199963 TTTTTTCTCTA-TA-TTTTAATGA
1 TTTTTTCTTTATTATTTTTAATGA
* *
28199985 TTTTTTCTTTATTATTTTTCATTGT
1 TTTTTTCTTTATTATTTTT-AATGA
*
28200010 TTTTTTCATT-TTATTTTTAA
1 TTTTTTCTTTATTATTTTTAA
28200030 AAAAGAAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.27
23 3 0.08
24 12 0.32
25 12 0.32
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.72
Consensus pattern (24 bp):
TTTTTTCTTTATTATTTTTAATGA
Found at i:28200026 original size:12 final size:13
Alignment explanation
Indices: 28199986--28200027 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
28199976 TTTTAATGAT
*
28199986 TTTTTCTTTATTA
1 TTTTTCATTATTA
*
28199999 TTTTTCATTGTT-
1 TTTTTCATTATTA
28200011 TTTTTCATT-TTA
1 TTTTTCATTATTA
28200023 TTTTT
1 TTTTT
28200028 AAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 2 0.08
12 14 0.54
13 10 0.38
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTTCATTATTA
Found at i:28203304 original size:7 final size:7
Alignment explanation
Indices: 28203292--28203317 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28203282 TGTATTGTTT
28203292 TTTTTTC
1 TTTTTTC
28203299 TTTTTTC
1 TTTTTTC
28203306 TTTTTTC
1 TTTTTTC
28203313 TTTTT
1 TTTTT
28203318 CCGAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:28206311 original size:188 final size:188
Alignment explanation
Indices: 28205994--28206373 Score: 697
Period size: 188 Copynumber: 2.0 Consensus size: 188
28205984 TATTCGCATA
*
28205994 ATTGGTCTACCAAAGATAGCGTTATATGCCATCGGGTGATTGACCACATAGAATTGGACACACTC
1 ATTGGTCTACCAAAGATAGCGTTATATGCCATCGGGTGATCGACCACATAGAATTGGACACACTC
*
28206059 TGTGGTTGTATGCTCGCTGTCACCTAGAGTGGCTGGCAACGTGATGTGCCCCTTACTTCGACAGG
66 CGTGGTTGTATGCTCGCTGTCACCTAGAGTGGCTGGCAACGTGATGTGCCCCTTACTTCGACAGG
28206124 ATGGTTCGCGAAGCCGTACAAAGGGCTGGCTACAAATAAGGATTTCTCTTTTAAGCCT
131 ATGGTTCGCGAAGCCGTACAAAGGGCTGGCTACAAATAAGGATTTCTCTTTTAAGCCT
28206182 ATTGGTCTACCAAAGATAGCGTTATATGCCATCGGGTGATCGACCACATAGAATTGGACACACTC
1 ATTGGTCTACCAAAGATAGCGTTATATGCCATCGGGTGATCGACCACATAGAATTGGACACACTC
* *
28206247 CGTGGTTGTATGCTCGCTGTCACTTAGAGTGGCTGGCAACGTGATGTGCCCTTTACTTCGACAGG
66 CGTGGTTGTATGCTCGCTGTCACCTAGAGTGGCTGGCAACGTGATGTGCCCCTTACTTCGACAGG
* * *
28206312 ATGGTTCGTGAAGCCGTACAAAGGGCTGGCTACGAATAATGATTTCTCTTTTAAGCCT
131 ATGGTTCGCGAAGCCGTACAAAGGGCTGGCTACAAATAAGGATTTCTCTTTTAAGCCT
28206370 ATTG
1 ATTG
28206374 TCTTATATGC
Statistics
Matches: 185, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
188 185 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (188 bp):
ATTGGTCTACCAAAGATAGCGTTATATGCCATCGGGTGATCGACCACATAGAATTGGACACACTC
CGTGGTTGTATGCTCGCTGTCACCTAGAGTGGCTGGCAACGTGATGTGCCCCTTACTTCGACAGG
ATGGTTCGCGAAGCCGTACAAAGGGCTGGCTACAAATAAGGATTTCTCTTTTAAGCCT
Found at i:28207948 original size:9 final size:9
Alignment explanation
Indices: 28207930--28207991 Score: 72
Period size: 9 Copynumber: 6.8 Consensus size: 9
28207920 TTTGGTTAAA
*
28207930 AATTATCCG
1 AATTACCCG
28207939 AATTACCCG
1 AATTACCCG
*
28207948 -ATTAACCG
1 AATTACCCG
*
28207956 AATTAACCG
1 AATTACCCG
28207965 AATTACCCG
1 AATTACCCG
28207974 AAAATTACCCG
1 --AATTACCCG
28207985 AATTACC
1 AATTACC
28207992 TGAAAATTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.15
9 31 0.66
11 9 0.19
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:28207951 original size:17 final size:17
Alignment explanation
Indices: 28207931--28207985 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
28207921 TTGGTTAAAA
*
28207931 ATTATCCGAATTACCCG
1 ATTAACCGAATTACCCG
*
28207948 ATTAACCGAATTAACCG
1 ATTAACCGAATTACCCG
*
28207965 AATTACCCGAAAATTACCCG
1 -ATTAACCG--AATTACCCG
28207985 A
1 A
28207986 ATTACCTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 15 0.48
18 7 0.23
19 1 0.03
20 8 0.26
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (17 bp):
ATTAACCGAATTACCCG
Found at i:28207985 original size:20 final size:20
Alignment explanation
Indices: 28207939--28208003 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
28207929 AAATTATCCG
*
28207939 AATTACCCG-ATTAACCG--
1 AATTACCCGAATTACCCGAA
*
28207956 AATTAACCGAATTACCCGAA
1 AATTACCCGAATTACCCGAA
*
28207976 AATTACCCGAATTACCTGAA
1 AATTACCCGAATTACCCGAA
28207996 AATTACCC
1 AATTACCC
28208004 AAAAAGTTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
17 8 0.20
18 7 0.17
20 26 0.63
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (20 bp):
AATTACCCGAATTACCCGAA
Found at i:28208008 original size:11 final size:11
Alignment explanation
Indices: 28207965--28208007 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
28207955 GAATTAACCG
28207965 AATTACCCGAA
1 AATTACCCGAA
28207976 AATTACCCG--
1 AATTACCCGAA
*
28207985 AATTACCTGAA
1 AATTACCCGAA
28207996 AATTACCC-AA
1 AATTACCCGAA
28208006 AA
1 AA
28208008 AGTTCGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 8 0.29
10 4 0.14
11 16 0.57
ACGTcount: A:0.47, C:0.26, G:0.07, T:0.21
Consensus pattern (11 bp):
AATTACCCGAA
Found at i:28209285 original size:17 final size:17
Alignment explanation
Indices: 28209260--28209296 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28209250 TCTCATGAGG
*
28209260 CTTATGCGAGCTCTCCT
1 CTTACGCGAGCTCTCCT
28209277 CTTACGCGAGCTCTCCT
1 CTTACGCGAGCTCTCCT
28209294 CTT
1 CTT
28209297 GTGACCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.38, G:0.16, T:0.35
Consensus pattern (17 bp):
CTTACGCGAGCTCTCCT
Found at i:28220858 original size:24 final size:24
Alignment explanation
Indices: 28220831--28220878 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28220821 AAAAGTTTGT
*
28220831 TTAGGGTTTACAAAATTTCAAATA
1 TTAGGCTTTACAAAATTTCAAATA
* * *
28220855 TTAGTCTTTCCAAATTTTCAAATA
1 TTAGGCTTTACAAAATTTCAAATA
28220879 CTCTATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (24 bp):
TTAGGCTTTACAAAATTTCAAATA
Found at i:28221108 original size:3 final size:3
Alignment explanation
Indices: 28221100--28221143 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
28221090 TCGTGAACTC
28221100 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28221144 ATCATATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28221564 original size:20 final size:20
Alignment explanation
Indices: 28221539--28221603 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
28221529 TCATTTTGCA
**
28221539 ATAAAAATACATAAGATTTT
1 ATAAAAATACATAAGAAATT
* **
28221559 ATAAAAATATATATTAAATT
1 ATAAAAATACATAAGAAATT
28221579 ATAAAAATACATACA-AAATT
1 ATAAAAATACATA-AGAAATT
28221599 ATAAA
1 ATAAA
28221604 TAAATGAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (20 bp):
ATAAAAATACATAAGAAATT
Found at i:28225368 original size:2 final size:2
Alignment explanation
Indices: 28225361--28225408 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
28225351 TAATTTACTA
*
28225361 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC CC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
28225403 AC AC AC
1 AC AC AC
28225409 GCACTCTCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:28228261 original size:10 final size:10
Alignment explanation
Indices: 28228248--28228307 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 10
28228238 ATATTCTATT
*
28228248 AAAATGATTA
1 AAAATCATTA
28228258 AAAATCA-TA
1 AAAATCATTA
28228267 AAAAGTCATTA
1 AAAA-TCATTA
*
28228278 AAAATTA-TA
1 AAAATCATTA
*
28228287 AAAATCATAA
1 AAAATCATTA
28228297 AAAAT-ATTA
1 AAAATCATTA
28228306 AA
1 AA
28228308 GATTATAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 19 0.45
10 17 0.40
11 6 0.14
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAATCATTA
Found at i:28228278 original size:29 final size:27
Alignment explanation
Indices: 28228244--28228319 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 27
28228234 TAATATATTC
*
28228244 TATTAAAATGATTAAAAATCATAAAAAG
1 TATTAAAATGA-TAAAAATCATAAAAAA
*
28228272 TCATTAAAAATTATAAAAATCATAAAAAA
1 T-ATT-AAAATGATAAAAATCATAAAAAA
*
28228301 TATTAAAGATTATAAAAAT
1 TATTAAA-ATGATAAAAAT
28228320 AAGGAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 3 0.07
28 15 0.35
29 19 0.44
30 6 0.14
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (27 bp):
TATTAAAATGATAAAAATCATAAAAAA
Found at i:28228279 original size:20 final size:19
Alignment explanation
Indices: 28228248--28228301 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
28228238 ATATTCTATT
*
28228248 AAAATGATTAAAAATCATA
1 AAAATCATTAAAAATCATA
*
28228267 AAAAGTCATTAAAAATTATA
1 AAAA-TCATTAAAAATCATA
*
28228287 AAAATCATAAAAAAT
1 AAAATCATTAAAAAT
28228302 ATTAAAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAATCATTAAAAATCATA
Found at i:28228307 original size:19 final size:19
Alignment explanation
Indices: 28228244--28228318 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
28228234 TAATATATTC
* *
28228244 TATT-AAAATGATTAAAAA
1 TATTAAAAATCATAAAAAA
*
28228262 TCA-TAAAAAGTCATTAAAAA
1 T-ATTAAAAA-TCATAAAAAA
28228282 T-TATAAAAATCATAAAAAA
1 TAT-TAAAAATCATAAAAAA
* *
28228301 TATTAAAGATTATAAAAA
1 TATTAAAAATCATAAAAA
28228319 TAAGGAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.04
19 28 0.60
20 17 0.36
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
TATTAAAAATCATAAAAAA
Found at i:28228316 original size:9 final size:9
Alignment explanation
Indices: 28228256--28228655 Score: 95
Period size: 10 Copynumber: 41.7 Consensus size: 9
28228246 TTAAAATGAT
*
28228256 TAAAAATCA
1 TAAAAATTA
*
28228265 TAAAAAGTCA
1 TAAAAA-TTA
28228275 TTAAAAATTA
1 -TAAAAATTA
*
28228285 TAAAAATCA
1 TAAAAATTA
*
28228294 TAAAAAATA
1 TAAAAATTA
*
28228303 TTAAAGATTA
1 -TAAAAATTA
*
28228313 TAAAAATAA
1 TAAAAATTA
*
28228322 GGAAAAAATTA
1 --TAAAAATTA
28228333 T-AAAA-TA
1 TAAAAATTA
*
28228340 TTAAAATTAA
1 TAAAAATT-A
*
28228350 TATAAACTTA
1 TA-AAAATTA
* *
28228360 TAATACTTA
1 TAAAAATTA
*
28228369 TAAAAGCTTA
1 TAAAA-ATTA
*
28228379 TAAATATTA
1 TAAAAATTA
*
28228388 TAAAAAAATA
1 T-AAAAATTA
28228398 TAATAAATCTA
1 TAA-AAAT-TA
**
28228409 -ATTAATTA
1 TAAAAATTA
28228417 TAAAAATATA
1 TAAAAAT-TA
28228427 TAAAAAAATTAA
1 T--AAAAATT-A
28228439 TAAACATATTA
1 TAAA-A-ATTA
*
28228450 -AAATATT-
1 TAAAAATTA
*
28228457 TAAAATTTTA
1 TAAAA-ATTA
*
28228467 TAAAAACCTA
1 TAAAAA-TTA
*
28228477 T-AAAATTCT
1 TAAAAATT-A
*
28228486 TAAAAATTC
1 TAAAAATTA
*
28228495 T-TAAA-TA
1 TAAAAATTA
* *
28228502 TTAAAACTA
1 TAAAAATTA
*
28228511 TTAAAATTGA
1 TAAAAATT-A
*
28228521 TATAAATTA
1 TAAAAATTA
*
28228530 TAATAA-TA
1 TAAAAATTA
28228538 TAATAAATTA
1 TAA-AAATTA
28228548 TAAATAGATT-
1 TAAA-A-ATTA
28228558 TATAAAATTAA
1 TA-AAAATT-A
*
28228569 TAAAATATATT
1 TAAAA-AT-TA
28228580 TAAAATATT-
1 TAAAA-ATTA
*
28228589 TAATAATTTA
1 TAA-AAATTA
* *
28228599 TAACAAGTAA
1 TAA-AAATTA
28228609 TAAAAATTCA
1 TAAAAATT-A
28228619 TAAAAAAACTTA
1 T--AAAAA-TTA
28228631 TAAATAA-TA
1 TAAA-AATTA
*
28228640 TAATAAATTG
1 TAA-AAATTA
28228650 TAAAAA
1 TAAAAA
28228656 AAATTATAAA
Statistics
Matches: 295, Mismatches: 49, Indels: 94
0.67 0.11 0.21
Matches are distributed among these distances:
7 5 0.02
8 28 0.09
9 98 0.33
10 101 0.34
11 42 0.14
12 19 0.06
13 2 0.01
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:28228327 original size:28 final size:27
Alignment explanation
Indices: 28228274--28228346 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
28228264 ATAAAAAGTC
* *
28228274 ATTAAAAATTATAAAAATCATAAAAAA
1 ATTAAAAATTATAAAAATAAGAAAAAA
* *
28228301 TATTAAAGATTATAAAAATAAGGAAAAA
1 -ATTAAAAATTATAAAAATAAGAAAAAA
*
28228329 ATTATAAAA-TATTAAAAT
1 ATTA-AAAATTATAAAAAT
28228347 TAATATAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 12 0.32
28 26 0.68
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (27 bp):
ATTAAAAATTATAAAAATAAGAAAAAA
Found at i:28228380 original size:19 final size:19
Alignment explanation
Indices: 28228356--28228392 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28228346 TTAATATAAA
28228356 CTTAT-AATACTTATAAAAG
1 CTTATAAATA-TTATAAAAG
28228375 CTTATAAATATTATAAAA
1 CTTATAAATATTATAAAA
28228393 AAATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (19 bp):
CTTATAAATATTATAAAAG
Found at i:28228398 original size:13 final size:13
Alignment explanation
Indices: 28228380--28228442 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
28228370 AAAAGCTTAT
*
28228380 AAATATTATAAAA
1 AAATATAATAAAA
*
28228393 AAATATAATAAATC
1 AAATATAATAAA-A
* *
28228407 TAAT-TAATTATAA
1 AAATATAA-TAAAA
28228420 AAATAT-ATAAAA
1 AAATATAATAAAA
28228432 AAAT-TAATAAA
1 AAATATAATAAA
28228443 CATATTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
11 1 0.03
12 13 0.33
13 18 0.46
14 7 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATAAAA
Found at i:28228436 original size:25 final size:27
Alignment explanation
Indices: 28228384--28228439 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
28228374 GCTTATAAAT
28228384 ATTATAAAAAAATATAATAAATCTAATTA
1 ATTATAAAAAAATATAATAAA--TAATTA
*
28228413 ATTATAAAAATATATAA-AAA-AATTA
1 ATTATAAAAAAATATAATAAATAATTA
28228438 AT
1 AT
28228440 AAACATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 7 0.27
28 3 0.12
29 16 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
ATTATAAAAAAATATAATAAATAATTA
Found at i:28228437 original size:21 final size:21
Alignment explanation
Indices: 28228412--28228452 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28228402 AAATCTAATT
28228412 AATT-ATAAAAATATATAAAAA
1 AATTAATAAAAATAT-TAAAAA
*
28228433 AATTAATAAACATATTAAAA
1 AATTAATAAAAATATTAAAA
28228453 TATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTAATAAAAATATTAAAAA
Found at i:28228574 original size:22 final size:21
Alignment explanation
Indices: 28228542--28228594 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
28228532 ATAATATAAT
28228542 AAATT-AT-AAATAGATTTATA
1 AAATTAATAAAATAGATTTA-A
*
28228562 AAATTAATAAAATATATTTAA
1 AAATTAATAAAATAGATTTAA
28228583 AATATTTAATAA
1 AA-A-TTAATAA
28228595 TTTATAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 5 0.18
22 11 0.39
23 7 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAATTAATAAAATAGATTTAA
Found at i:28229408 original size:28 final size:26
Alignment explanation
Indices: 28229360--28229419 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
28229350 TTTCATATTT
**
28229360 TTTTTATAATTTATTAGATTTTTTTA
1 TTTTTATAATTTATTAGATTTTAATA
28229386 TTTTTATAAGTTTGTATTA-ATTTTAATA
1 TTTTTATAA--TT-TATTAGATTTTAATA
28229414 TTTTTA
1 TTTTTA
28229420 ATTTTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 9 0.31
28 15 0.52
29 5 0.17
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (26 bp):
TTTTTATAATTTATTAGATTTTAATA
Found at i:28229436 original size:18 final size:16
Alignment explanation
Indices: 28229402--28229453 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 16
28229392 TAAGTTTGTA
28229402 TTAA-TTTTAATATTT
1 TTAATTTTTAATATTT
28229417 TTAATTTTTAATAAATTT
1 TTAATTTTTAAT--ATTT
*
28229435 TTAATTTTTTATGATTT
1 TTAATTTTTAAT-ATTT
28229452 TT
1 TT
28229454 TTATATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 4 0.12
16 7 0.22
17 6 0.19
18 15 0.47
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTAATTTTTAATATTT
Found at i:28229456 original size:19 final size:18
Alignment explanation
Indices: 28229402--28229443 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
28229392 TAAGTTTGTA
28229402 TTAA-TTTTAAT--ATTT
1 TTAATTTTTAATAAATTT
28229417 TTAATTTTTAATAAATTT
1 TTAATTTTTAATAAATTT
28229435 TTAATTTTT
1 TTAATTTTT
28229444 TATGATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.17
16 7 0.29
18 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAATTTTTAATAAATTT
Found at i:28229462 original size:18 final size:18
Alignment explanation
Indices: 28229358--28229463 Score: 60
Period size: 18 Copynumber: 5.8 Consensus size: 18
28229348 AATTTCATAT
*
28229358 TTTTTTTATAATTTATTAGA
1 TTTTTTTATATTTTA-TA-A
28229378 TTTTTTTAT-TTTTATAA
1 TTTTTTTATATTTTATAA
*
28229395 GTTTGTATTA-A-TTT-TAA
1 -TTT-TTTTATATTTTATAA
*
28229412 TATTTTTA-ATTTTTAATAA
1 TTTTTTTATA-TTTT-ATAA
* * * *
28229431 ATTTTTAATTTTTTATGA
1 TTTTTTTATATTTTATAA
28229449 TTTTTTTATATTTTA
1 TTTTTTTATATTTTA
28229464 AAAAAAAGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
15 5 0.08
16 2 0.03
17 7 0.11
18 23 0.35
19 20 0.30
20 9 0.14
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (18 bp):
TTTTTTTATATTTTATAA
Found at i:28229678 original size:37 final size:37
Alignment explanation
Indices: 28229628--28229699 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
28229618 ATGCATGGGC
*
28229628 TGTTAAAATTAAGTGACCCGAATCCTTATTTAAATAT
1 TGTTAAAATTAAGTGACCCAAATCCTTATTTAAATAT
* *
28229665 TGTTAGAATTAAGTGACCCAAATTCTTATTTAAAT
1 TGTTAAAATTAAGTGACCCAAATCCTTATTTAAAT
28229700 CAAATACAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (37 bp):
TGTTAAAATTAAGTGACCCAAATCCTTATTTAAATAT
Found at i:28236535 original size:33 final size:34
Alignment explanation
Indices: 28236463--28236547 Score: 127
Period size: 33 Copynumber: 2.5 Consensus size: 34
28236453 AATTTTTTTT
*
28236463 AAAATTAATTAAATTAGGTTTTAGGGGTTTTAAG
1 AAAATTAATTAAATTAGGGTTTAGGGGTTTTAAG
* *
28236497 TAAATTAATTAAATTAGGGTTTA-GTGTTTTAAG
1 AAAATTAATTAAATTAGGGTTTAGGGGTTTTAAG
*
28236530 AAAATTAACTAAATTAGG
1 AAAATTAATTAAATTAGG
28236548 TTTTTGTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 25 0.54
34 21 0.46
ACGTcount: A:0.41, C:0.01, G:0.18, T:0.40
Consensus pattern (34 bp):
AAAATTAATTAAATTAGGGTTTAGGGGTTTTAAG
Found at i:28236861 original size:124 final size:125
Alignment explanation
Indices: 28236610--28236874 Score: 367
Period size: 124 Copynumber: 2.1 Consensus size: 125
28236600 GATTTTGTGT
* *
28236610 TTTTTCTACTGTAGTTTCTGAAAAAATAAATTTGAGAAGACGGTTTTGAAAAAATAGTGACAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAAATTTGAGAAGACGGTTCTGAAAAAATAGTGACAAAA
* * * * *
28236675 ATGCTTCAAGCAGGATGCACTGTCAGCTAAAGTACTAAAAAAGCTCCTACATTGACGCTC
66 ACGCTTCAAACAGGATGCACTGTCAACAAAAGTACTAAAAAAGCTCCTACATGGACGCTC
*
28236735 TTTTTCTACAGTAGTTTCTG-AAAAATAATTTTGAGAAGACGGTTCT-AAAAAATAGTGTA-AAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAAATTTGAGAAGACGGTTCTGAAAAAATAGTG-ACAAA
* * *
28236797 AACGCTTCAAACAGGATGCACTGTCAACAAAATTATTGAAAAAAGCTCGC-ACGTGGACGCTC
65 AACGCTTCAAACAGGATGCACTGTCAACAAAAGTACT-AAAAAAGCTC-CTACATGGACGCTC
*
28236859 TTTTTCTATAGTAGTT
1 TTTTTCTACAGTAGTT
28236875 CTTGCTTCGC
Statistics
Matches: 125, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
123 45 0.36
124 60 0.48
125 20 0.16
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTTCTGAAAAAATAAATTTGAGAAGACGGTTCTGAAAAAATAGTGACAAAA
ACGCTTCAAACAGGATGCACTGTCAACAAAAGTACTAAAAAAGCTCCTACATGGACGCTC
Found at i:28242486 original size:51 final size:51
Alignment explanation
Indices: 28242413--28242631 Score: 192
Period size: 51 Copynumber: 4.3 Consensus size: 51
28242403 TATGAACATG
* * * *
28242413 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATAGATAATGGTCACA
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAT-GACAATGGTCACA
* * ** *
28242464 TGTGTAGTACTATGTGTAGGCTACCATGTGTACCGGATGACCTTGGTCACG
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
* * * * * * *
28242515 TGTGTAGTACTATGCGTAGGCTACTACGTGAACCAGA-AAGC-TTGATCACG
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGA-CAATGGTCACA
* * ** *
28242565 TGTGTAGTACTATATGTAGGCTACTGCGTGTTTCGGATGACAATAGTCACA
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
* *
28242616 TGGGTGGTACTATGTG
1 TGTGTAGTACTATGTG
28242632 CAAACCACTG
Statistics
Matches: 133, Mismatches: 31, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
50 40 0.30
51 90 0.68
52 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATGACAATGGTCACA
Found at i:28245270 original size:25 final size:24
Alignment explanation
Indices: 28245233--28245284 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
28245223 ATTGTTATAA
* *
28245233 AAAATTATAAAAT-AAAAATTAATT
1 AAAATTACAAAATGAAAAAAT-ATT
28245257 AAAATTACATAAATGAAAAAATATT
1 AAAATTACA-AAATGAAAAAATATT
28245282 AAA
1 AAA
28245285 TAATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATTACAAAATGAAAAAATATT
Found at i:28248432 original size:3 final size:3
Alignment explanation
Indices: 28248424--28248474 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
28248414 AAGAAAAAAT
28248424 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28248472 ATA
1 ATA
28248475 TATCTTGAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28249849 original size:19 final size:21
Alignment explanation
Indices: 28249825--28249869 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
28249815 ACATCGTTTC
28249825 CAGAAGC-C-TGAAAGCTAAA
1 CAGAAGCTCATGAAAGCTAAA
*
28249844 CAGAAGCTCATGAGAGCTAAA
1 CAGAAGCTCATGAAAGCTAAA
28249865 CAGAA
1 CAGAA
28249870 ACCCATATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 1 0.04
21 15 0.65
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (21 bp):
CAGAAGCTCATGAAAGCTAAA
Found at i:28249894 original size:42 final size:42
Alignment explanation
Indices: 28249842--28249942 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
28249832 CTGAAAGCTA
* * * *
28249842 AACAGAAGCTCATGAGAGCTAAACAGAAACCCATATGGGTTG
1 AACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTG
* * *
28249884 AACAAAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
1 AACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTG
*
28249926 AACAAAAGCTCAAAAGA
1 AACAAAAGCTCATAAGA
28249943 ACTGGGCAGA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (42 bp):
AACAAAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTG
Found at i:28249906 original size:21 final size:21
Alignment explanation
Indices: 28249837--28249942 Score: 81
Period size: 21 Copynumber: 5.0 Consensus size: 21
28249827 GAAGCCTGAA
* * *
28249837 AGCTAAACAGAAGCTCATGAG
1 AGCTGAACAAAAGCTCATAAG
* * *
28249858 AGCTAAACAGAAA-CCCATATG
1 AGCTGAACA-AAAGCTCATAAG
* * *
28249879 GGTTGAACAAAAGCTCGTAAG
1 AGCTGAACAAAAGCTCATAAG
28249900 AGCTGAACAGAAA-CTCATAAG
1 AGCTGAACA-AAAGCTCATAAG
* *
28249921 AGTTGAACAAAAGCTCAAAAG
1 AGCTGAACAAAAGCTCATAAG
28249942 A
1 A
28249943 ACTGGGCAGA
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
20 6 0.09
21 55 0.83
22 5 0.08
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (21 bp):
AGCTGAACAAAAGCTCATAAG
Found at i:28257507 original size:21 final size:21
Alignment explanation
Indices: 28257483--28257581 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
28257473 AAAGCTGAAC
*
28257483 AGAAGCTCATGAGAGCTAAAA
1 AGAAGCTCATAAGAGCTAAAA
*
28257504 AGAAGCTCATAAGAGCTAAAC
1 AGAAGCTCATAAGAGCTAAAA
* * * * *
28257525 AGAAACCCATAAGGGTTGAACA
1 AGAAGCTCATAAGAGCT-AAAA
* * * *
28257547 A-AAGCTCGTACGAGCTGAAC
1 AGAAGCTCATAAGAGCTAAAA
*
28257567 AGAAACTCATAAGAG
1 AGAAGCTCATAAGAG
28257582 TTCTCAACAA
Statistics
Matches: 56, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
20 2 0.04
21 51 0.91
22 3 0.05
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTAAAA
Found at i:28260354 original size:57 final size:58
Alignment explanation
Indices: 28260287--28260401 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 58
28260277 ATTTTTACAT
**
28260287 TTTTCATTTTGGAGAAAACCACCTTCACTTCCAAATGAGTC-CATTTCTCCATTTTCA
1 TTTTCATTTTGGAGAAAACCACAATCACTTCCAAATGAGTCTCATTTCTCCATTTTCA
* * * **
28260344 TTTTCATTTTGGAGAAAATCATAATCATTTCCAAATGTTTCTCATTTCTCCATTTTCA
1 TTTTCATTTTGGAGAAAACCACAATCACTTCCAAATGAGTCTCATTTCTCCATTTTCA
28260402 CTATTTTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 34 0.68
58 16 0.32
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.43
Consensus pattern (58 bp):
TTTTCATTTTGGAGAAAACCACAATCACTTCCAAATGAGTCTCATTTCTCCATTTTCA
Found at i:28263523 original size:34 final size:34
Alignment explanation
Indices: 28263479--28263555 Score: 127
Period size: 34 Copynumber: 2.3 Consensus size: 34
28263469 TATTGGGCCA
28263479 GGCTGTGTGATCCACACGACCAAGGCCATTTTAG
1 GGCTGTGTGATCCACACGACCAAGGCCATTTTAG
* * *
28263513 TGCTGTGTGATCTACACGGCCAAGGCCATTTTAG
1 GGCTGTGTGATCCACACGACCAAGGCCATTTTAG
28263547 GGCTGTGTG
1 GGCTGTGTG
28263556 GGCCACACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.27
Consensus pattern (34 bp):
GGCTGTGTGATCCACACGACCAAGGCCATTTTAG
Found at i:28264930 original size:25 final size:25
Alignment explanation
Indices: 28264891--28264980 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
28264881 AATTGTTTTT
* *
28264891 GATAGTATATCCTGAAACTGCTATA
1 GATAGTATATACTGAAACTACTATA
* *
28264916 GGTAGTATATACTGAGACTACTATA
1 GATAGTATATACTGAAACTACTATA
*
28264941 GATAG-ACTATACTGAAAATACTCA-A
1 GATAGTA-TATACTGAAACTACT-ATA
* *
28264966 GTTAGTGTATACTGA
1 GATAGTATATACTGA
28264981 TACTGTAGTA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
24 1 0.02
25 51 0.96
26 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (25 bp):
GATAGTATATACTGAAACTACTATA
Found at i:28272050 original size:73 final size:73
Alignment explanation
Indices: 28271926--28272067 Score: 221
Period size: 73 Copynumber: 1.9 Consensus size: 73
28271916 AGAGAATATT
* * *
28271926 TACTATTCATGCGTCTTTTCGTGCAGGGAATATTTACTGTTTACGCCAGAGAATTTTTCCTGTTC
1 TACTATTCATGCGTCTTTTCGTGCAGGGAATATCTACTGTTTACGCCAGAGAATATTTCATGTTC
28271991 ACTTTTCA
66 ACTTTTCA
* * **
28271999 TACTATTCATGCGTCTTTTCTTGTAGGGAATATCTACTGTTTACGTTAGAGAATATTTCATGTTC
1 TACTATTCATGCGTCTTTTCGTGCAGGGAATATCTACTGTTTACGCCAGAGAATATTTCATGTTC
28272064 ACTT
66 ACTT
28272068 GTCTTTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (73 bp):
TACTATTCATGCGTCTTTTCGTGCAGGGAATATCTACTGTTTACGCCAGAGAATATTTCATGTTC
ACTTTTCA
Found at i:28277428 original size:100 final size:100
Alignment explanation
Indices: 28277255--28277461 Score: 396
Period size: 100 Copynumber: 2.1 Consensus size: 100
28277245 CATCTTTTGA
28277255 TGAGATTTGTTCTCTTGCATCAAGAGCTCTCATTCTTAAAAGATTTACTTTTATTCCAGTATTTT
1 TGAGATTTGTTCTCTTGCATCAAGAGCTCTCATTCTTAAAAGATTTACTTTTATTCCAGTATTTT
*
28277320 TGTGAAGATATTGAATCTCCATTAAAGGGGCATGT
66 TGTGAAGATATTGAACCTCCATTAAAGGGGCATGT
*
28277355 TGAGATTTGTTCTCTTGCATCAGGAGCTCTCATTCTTAAAAGATTTACTTTTATTCCAGTATTTT
1 TGAGATTTGTTCTCTTGCATCAAGAGCTCTCATTCTTAAAAGATTTACTTTTATTCCAGTATTTT
28277420 TGTGAAGATATTGAACCTCCATTAAAGGGGCATGT
66 TGTGAAGATATTGAACCTCCATTAAAGGGGCATGT
28277455 TGAGATT
1 TGAGATT
28277462 CAACTTCTCC
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 105 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.41
Consensus pattern (100 bp):
TGAGATTTGTTCTCTTGCATCAAGAGCTCTCATTCTTAAAAGATTTACTTTTATTCCAGTATTTT
TGTGAAGATATTGAACCTCCATTAAAGGGGCATGT
Found at i:28280962 original size:11 final size:11
Alignment explanation
Indices: 28280889--28280963 Score: 50
Period size: 11 Copynumber: 6.7 Consensus size: 11
28280879 ATTCCAAAAA
28280889 TAATATTATTT
1 TAATATTATTT
*
28280900 TAATAGTTTAATAT
1 TAATA--TT-ATTT
*
28280914 TAA-ATTAAATT
1 TAATATT-ATTT
28280925 TAATACTTATTT
1 TAATA-TTATTT
*
28280937 TAATAGTA-TT
1 TAATATTATTT
28280947 T--TATTATTT
1 TAATATTATTT
28280956 TAATATTA
1 TAATATTA
28280964 AAGTGATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 20 0.40
12 9 0.18
13 5 0.10
14 6 0.12
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (11 bp):
TAATATTATTT
Found at i:28281901 original size:5 final size:5
Alignment explanation
Indices: 28281891--28281936 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
28281881 CATTTTTTTA
* *
28281891 TCTTT TCTTT TCTCT TCTTT TCTTT TCTTT CCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
28281937 TTGTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:28283735 original size:26 final size:26
Alignment explanation
Indices: 28283706--28283782 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
28283696 TTTTTGATGT
*
28283706 AATATGAAAGAAAGCCTTTGTGGTGG
1 AATATGAAAGAAAGCCTTTGTGGCGG
*
28283732 AATATGAAAGAAAACCTTTGTGGCGG
1 AATATGAAAGAAAGCCTTTGTGGCGG
* *
28283758 AATATGAAAGGAATGTCTTTGTGGC
1 AATATGAAA-GAAAGCCTTTGTGGC
28283783 AAACTCCGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 33 0.73
27 12 0.27
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.27
Consensus pattern (26 bp):
AATATGAAAGAAAGCCTTTGTGGCGG
Found at i:28297843 original size:3 final size:3
Alignment explanation
Indices: 28297835--28297873 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
28297825 GTCGAGAAAG
* * *
28297835 TGA TGA TGA TGA CGA TGA CGA TGA TGA TGG TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
28297874 CGGTGAATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.28
Consensus pattern (3 bp):
TGA
Found at i:28298531 original size:13 final size:13
Alignment explanation
Indices: 28298468--28298529 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
28298458 ACACTCAAAT
28298468 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
**
28298481 TCCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
28298494 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
*
28298507 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
28298520 TTTTCAAAAG
1 TTTTCAAAAG
28298530 TAATGAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
12 5 0.12
13 32 0.80
14 3 0.08
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:28299782 original size:59 final size:59
Alignment explanation
Indices: 28299709--28299826 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
28299699 CAAAAGATAC
28299709 CCAACACATTCCTAACTTATACCAACATGATATCAATTCATCATTCATCAAATTAACCT
1 CCAACACATTCCTAACTTATACCAACATGATATCAATTCATCATTCATCAAATTAACCT
28299768 CCAACACATTCCTAACTTATACCAACATGATATCAATTCATCATTCATCAAATTAACCT
1 CCAACACATTCCTAACTTATACCAACATGATATCAATTCATCATTCATCAAATTAACCT
28299827 TCCTAAACAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.31
Consensus pattern (59 bp):
CCAACACATTCCTAACTTATACCAACATGATATCAATTCATCATTCATCAAATTAACCT
Found at i:28303679 original size:38 final size:40
Alignment explanation
Indices: 28303610--28303698 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 40
28303600 TTAAAATTAT
* *
28303610 TTATATTAAAAAACACTACCATAAATATAATAAATG-TTTTG
1 TTATATT-AAAAACACTACAATAAATATAATAAA-GATTTTA
28303651 TTATATTAAAAACAC-A-AATAAATATAATAAAGATTTTA
1 TTATATTAAAAACACTACAATAAATATAATAAAGATTTTA
*
28303689 TTGTATTAAA
1 TTATATTAAA
28303699 TATAAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
37 1 0.02
38 27 0.61
39 1 0.02
40 8 0.18
41 7 0.16
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (40 bp):
TTATATTAAAAACACTACAATAAATATAATAAAGATTTTA
Found at i:28303805 original size:6 final size:6
Alignment explanation
Indices: 28303794--28303849 Score: 112
Period size: 6 Copynumber: 9.3 Consensus size: 6
28303784 AGTTAGTGAT
28303794 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
28303842 TAAATA TA
1 TAAATA TA
28303850 TATAATTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TAAATA
Found at i:28307286 original size:7 final size:7
Alignment explanation
Indices: 28307276--28307301 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28307266 TCCTTGCAAA
28307276 AAAAAAG
1 AAAAAAG
28307283 AAAAAAG
1 AAAAAAG
28307290 AAAAAAG
1 AAAAAAG
28307297 AAAAA
1 AAAAA
28307302 TAATGACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:28310216 original size:20 final size:21
Alignment explanation
Indices: 28310174--28310217 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
28310164 TGAATTGATT
*
28310174 ATTAATCGGATAGAAATTGTA
1 ATTAATCGGATAGAAATTCTA
28310195 ATTAAT-GGATA-AAATATCTA
1 ATTAATCGGATAGAAAT-TCTA
28310215 ATT
1 ATT
28310218 GGTGCATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 11 0.52
21 6 0.29
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (21 bp):
ATTAATCGGATAGAAATTCTA
Found at i:28317586 original size:37 final size:37
Alignment explanation
Indices: 28317536--28317612 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
28317526 TAATAGAAAG
* *
28317536 TATGGTGATGAATTTCTGGCAGTGGCCAACTGAATGA
1 TATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGA
28317573 TATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGA
1 TATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGA
28317610 TAT
1 TAT
28317613 TCATATAGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (37 bp):
TATGGTGATGAATTCCTGCCAGTGGCCAACTGAATGA
Found at i:28318723 original size:33 final size:33
Alignment explanation
Indices: 28318681--28318744 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
28318671 CTTACCGAAC
28318681 TTTGAATGTTAATTTACAAATATGTAATTCAAA
1 TTTGAATGTTAATTTACAAATATGTAATTCAAA
28318714 TTTGAATGTTAATTTACAAATATGTAATTCA
1 TTTGAATGTTAATTTACAAATATGTAATTCA
28318745 CTAACACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (33 bp):
TTTGAATGTTAATTTACAAATATGTAATTCAAA
Found at i:28320400 original size:45 final size:44
Alignment explanation
Indices: 28320333--28320419 Score: 129
Period size: 45 Copynumber: 2.0 Consensus size: 44
28320323 TAATAGATAC
* * * *
28320333 TCGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGT
1 TCGGTGGAATCAACACAGAGCAACCACCTTA-TAATAAATGATGT
28320378 TCGGTGGAATCAACACAGAGCAACCACCTTATAATAAATGAT
1 TCGGTGGAATCAACACAGAGCAACCACCTTATAATAAATGAT
28320420 ACCCGATTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
44 10 0.26
45 28 0.74
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (44 bp):
TCGGTGGAATCAACACAGAGCAACCACCTTATAATAAATGATGT
Found at i:28320508 original size:51 final size:50
Alignment explanation
Indices: 28320422--28320566 Score: 164
Period size: 51 Copynumber: 2.9 Consensus size: 50
28320412 TAAATGATAC
* * * ***
28320422 CCGATTCACATAGTAGCCTGGACATAGTACTACACATGTGACCATTTTCAT
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGCT-AT
* * * *
28320473 CTGATACACGTAGTAGCCTGCACATAATACTACACACGTGATCGAAGCTAT
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGA-CCAAGCTAT
* *
28320524 CCGGTACGCATAGTAGCCTGCACATAGTACTACACACGTGACC
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACC
28320567 TAGCAACTTC
Statistics
Matches: 77, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
50 1 0.01
51 73 0.95
52 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGCTAT
Found at i:28324384 original size:21 final size:21
Alignment explanation
Indices: 28324350--28324390 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28324340 GCGTGAAAGC
* *
28324350 AAAGAGGAAGGAGAGGATGAT
1 AAAGAAGAAAGAGAGGATGAT
*
28324371 AAAGAAGAAAGAGATGATGA
1 AAAGAAGAAAGAGAGGATGA
28324391 AATGGATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.10
Consensus pattern (21 bp):
AAAGAAGAAAGAGAGGATGAT
Found at i:28329231 original size:5 final size:5
Alignment explanation
Indices: 28329221--28329249 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28329211 TTACTAACAG
28329221 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
28329250 TCACAACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:28329747 original size:18 final size:19
Alignment explanation
Indices: 28329726--28329766 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
28329716 ATTAAATGTT
*
28329726 ATAAGTTATAAT-TAATAA
1 ATAAGTTATAATATAAAAA
*
28329744 ATAATTTATAATATAAAAA
1 ATAAGTTATAATATAAAAA
28329763 ATAA
1 ATAA
28329767 AAAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAAGTTATAATATAAAAA
Found at i:28332047 original size:54 final size:54
Alignment explanation
Indices: 28331978--28332116 Score: 181
Period size: 54 Copynumber: 2.6 Consensus size: 54
28331968 ACGGTTTGGC
* *
28331978 ACACGGCCTGCGACACGGCTGTGTGACCCAAGTTAGTAAGTTACAC-AGGTAGAG
1 ACACGGCCTGGGACACGGCTGTGTGTCCCAAGTTAGTAAGTTACACTA-GTAGAG
* * * * *
28332032 ACACGGGCTGGGACACGACTGTGTGTCTCAAGTTTGTGAGTTACACTAGTAGAG
1 ACACGGCCTGGGACACGGCTGTGTGTCCCAAGTTAGTAAGTTACACTAGTAGAG
* *
28332086 ACGCGGCCTGGGACACGGCCGTGTGTCCCAA
1 ACACGGCCTGGGACACGGCTGTGTGTCCCAA
28332117 CTTCGAAAGC
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 71 0.99
55 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (54 bp):
ACACGGCCTGGGACACGGCTGTGTGTCCCAAGTTAGTAAGTTACACTAGTAGAG
Found at i:28335493 original size:50 final size:50
Alignment explanation
Indices: 28335386--28335626 Score: 211
Period size: 50 Copynumber: 4.7 Consensus size: 50
28335376 GGTAAATAGA
* *
28335386 TCCCATGTAAGATCATGTCTGGGACATGGCATTGGCATCATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATGAGAGG
*
28335442 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
28335492 TCCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * **
28335542 TCCCATGTAAGACCATATCTGGGATATGGGATTGGTA--GTACA-GAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
*
28335590 TCTCATGTAAGACCATGTCTGGGACATGG-ATTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCA
28335627 TGTTATTATC
Statistics
Matches: 158, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
47 1 0.01
48 35 0.22
49 2 0.01
50 81 0.51
52 1 0.01
53 2 0.01
55 1 0.01
56 35 0.22
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:28337853 original size:16 final size:17
Alignment explanation
Indices: 28337828--28337861 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28337818 ATAAATTAAC
*
28337828 TAAAATAAAT-AAAAAA
1 TAAAAAAAATGAAAAAA
28337844 TAAAAAAAATGAAAAAA
1 TAAAAAAAATGAAAAAA
28337861 T
1 T
28337862 CGACAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAAAAAATGAAAAAA
Found at i:28338886 original size:8 final size:8
Alignment explanation
Indices: 28338873--28338917 Score: 81
Period size: 8 Copynumber: 5.6 Consensus size: 8
28338863 TCACAATAGT
28338873 TATCGAGA
1 TATCGAGA
28338881 TATCGAGA
1 TATCGAGA
28338889 TATCGAGA
1 TATCGAGA
28338897 TATCGAGA
1 TATCGAGA
*
28338905 TATCAAGA
1 TATCGAGA
28338913 TATCG
1 TATCG
28338918 TCGTTTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (8 bp):
TATCGAGA
Found at i:28343672 original size:24 final size:24
Alignment explanation
Indices: 28343636--28343773 Score: 168
Period size: 24 Copynumber: 5.8 Consensus size: 24
28343626 TAACACACCA
*
28343636 CGTTGTGGACAAGCCACTGTATAT
1 CGTTGTGGTCAAGCCACTGTATAT
* * *
28343660 CGTTGTAGTCAAGCCACTGGATAA
1 CGTTGTGGTCAAGCCACTGTATAT
* *
28343684 CGTTGTGGTTAAGCCATTGTATAT
1 CGTTGTGGTCAAGCCACTGTATAT
* *
28343708 CATTGTGGTCAAGCCACTATATAT
1 CGTTGTGGTCAAGCCACTGTATAT
* * * *
28343732 CATTGTGGTCAAGTCACTGAATAA
1 CGTTGTGGTCAAGCCACTGTATAT
28343756 CGTTGTGGTCAAGCCACT
1 CGTTGTGGTCAAGCCACT
28343774 TTCTATTGCA
Statistics
Matches: 95, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 95 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (24 bp):
CGTTGTGGTCAAGCCACTGTATAT
Found at i:28343756 original size:72 final size:72
Alignment explanation
Indices: 28343638--28343771 Score: 205
Period size: 72 Copynumber: 1.9 Consensus size: 72
28343628 ACACACCACG
* * * *
28343638 TTGTGGACAAGCCACTGTATATCGTTGTAGTCAAGCCACTGGATAACGTTGTGGTTAAGCCATTG
1 TTGTGGACAAGCCACTATATATCATTGTAGTCAAGCCACTGAATAACGTTGTGGTCAAGCCATTG
28343703 TATATCA
66 TATATCA
* * *
28343710 TTGTGGTCAAGCCACTATATATCATTGTGGTCAAGTCACTGAATAACGTTGTGGTCAAGCCA
1 TTGTGGACAAGCCACTATATATCATTGTAGTCAAGCCACTGAATAACGTTGTGGTCAAGCCA
28343772 CTTTCTATTG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (72 bp):
TTGTGGACAAGCCACTATATATCATTGTAGTCAAGCCACTGAATAACGTTGTGGTCAAGCCATTG
TATATCA
Found at i:28352018 original size:16 final size:15
Alignment explanation
Indices: 28351997--28352039 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
28351987 TTATTTCTTT
28351997 TTATTTTATATTTTGA
1 TTATTTTAT-TTTTGA
*
28352013 TTATTTTATTTTTGG
1 TTATTTTATTTTTGA
28352028 TT-TGTTTATTTT
1 TTAT-TTTATTTT
28352040 GTTTTTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 15 0.60
16 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (15 bp):
TTATTTTATTTTTGA
Done.