Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 174 of 210
Found at i:52005368 original size:23 final size:23
Alignment explanation
Indices: 52005326--52005369 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
52005316 CCTACTGAAG
*
52005326 AACGGTAAGCTCTATTGAGCTAA
1 AACGGTAAGCTCTATAGAGCTAA
52005349 AACGGTAAGCTC-ATAAGAGCT
1 AACGGTAAGCTCTAT-AGAGCT
52005370 GATATATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (23 bp):
AACGGTAAGCTCTATAGAGCTAA
Found at i:52017558 original size:18 final size:18
Alignment explanation
Indices: 52017521--52017582 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
52017511 TCTTTCTAGT
52017521 TTATTTTTATTT-ATTAAA
1 TTATTTTTATTTAATT-AA
52017539 TTATTTTTATTTAATTAA
1 TTATTTTTATTTAATTAA
*
52017557 TT-TTTATT-TTTAAATTTA
1 TTATTT-TTATTT-AATTAA
52017575 TTATTTTT
1 TTATTTTT
52017583 CATTATCTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 6 0.15
18 27 0.69
19 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTTATTTAATTAA
Found at i:52017559 original size:15 final size:14
Alignment explanation
Indices: 52017530--52017565 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
52017520 TTTATTTTTA
*
52017530 TTTATTAAATTATT
1 TTTATTTAATTATT
52017544 TTTATTTAATTAATT
1 TTTATTTAATT-ATT
52017559 TTTATTT
1 TTTATTT
52017566 TTAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATTTAATTATT
Found at i:52017578 original size:15 final size:14
Alignment explanation
Indices: 52017523--52017582 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 14
52017513 TTTCTAGTTT
52017523 ATTTTTATTTATTAA
1 ATTTTTATTT-TTAA
52017538 ATTATTT-TTATTTAATTA
1 ATT-TTTATT-TTT-A--A
52017556 ATTTTTATTTTTAA
1 ATTTTTATTTTTAA
52017570 ATTTATTATTTTT
1 ATTT-TTATTTTT
52017583 CATTATCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
14 5 0.13
15 15 0.39
16 6 0.16
17 6 0.16
18 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTTATTTTTAA
Found at i:52017582 original size:21 final size:21
Alignment explanation
Indices: 52017520--52017568 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 21
52017510 TTCTTTCTAG
52017520 TTTATTTTTATTT-ATTAA--
1 TTTATTTTTATTTAATTAATT
*
52017538 ATTATTTTTATTTAATTAATT
1 TTTATTTTTATTTAATTAATT
52017559 TTTATTTTTA
1 TTTATTTTTA
52017569 AATTTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 12 0.46
19 5 0.19
21 9 0.35
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATTTTTATTTAATTAATT
Found at i:52025330 original size:23 final size:23
Alignment explanation
Indices: 52025295--52025338 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
52025285 AGGCAAACCT
*
52025295 AAAACCTACATAAACT-CAATCC
1 AAAACATACATAAACTACAATCC
52025317 AAAACATACCATAAACTACAAT
1 AAAACATA-CATAAACTACAAT
52025339 TCACCATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAACATACATAAACTACAATCC
Found at i:52028485 original size:32 final size:32
Alignment explanation
Indices: 52028444--52028510 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
52028434 GATAAGTGGC
52028444 ACTGTAAGAACATTTACATTGCGAGAAAGATA
1 ACTGTAAGAACATTTACATTGCGAGAAAGATA
52028476 ACTGTAAGAACATTTACATTGCGAGAAAGATA
1 ACTGTAAGAACATTTACATTGCGAGAAAGATA
52028508 ACT
1 ACT
52028511 TACTTTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (32 bp):
ACTGTAAGAACATTTACATTGCGAGAAAGATA
Found at i:52030023 original size:37 final size:37
Alignment explanation
Indices: 52029927--52030025 Score: 96
Period size: 37 Copynumber: 2.7 Consensus size: 37
52029917 AAGAATTTAA
* *
52029927 TATTATATTAAATTAA-ATTTAATATTTATCTAGATAT
1 TATTTTATTAATTTAATA-TTAATATTTATCTAGATAT
* * * *
52029964 TAATATGA-GATATTTAAT-TTAATATTTATCTATATAT
1 T-ATTTTATTA-ATTTAATATTAATATTTATCTAGATAT
52030001 TATTTTATTAATTTAATATTAATAT
1 TATTTTATTAATTTAATATTAATAT
52030026 GATTAATTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
36 11 0.23
37 29 0.60
38 8 0.17
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (37 bp):
TATTTTATTAATTTAATATTAATATTTATCTAGATAT
Found at i:52037207 original size:22 final size:22
Alignment explanation
Indices: 52037179--52037231 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
52037169 AAACTTCCGT
52037179 AGCATGTCATGCATATATT-GG-A
1 AGCATGTCAT--ATATATTAGGTA
52037201 AGCATGTCATATATATTAGGTA
1 AGCATGTCATATATATTAGGTA
*
52037223 AGAATGTCA
1 AGCATGTCA
52037232 CTAGAACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 7 0.25
21 2 0.07
22 19 0.68
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (22 bp):
AGCATGTCATATATATTAGGTA
Found at i:52055580 original size:29 final size:29
Alignment explanation
Indices: 52055547--52055608 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
52055537 TATCATGAAA
*
52055547 ATAAAAG-CCC-AAATAAAATCATAAAGTCC
1 ATAAAAGTCCCAAAATAAAAT-AT-AAGCCC
52055576 ATAAAAGTCCCAAAATAAAATATAAGCCC
1 ATAAAAGTCCCAAAATAAAATATAAGCCC
52055605 ATAA
1 ATAA
52055609 TCATGAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 16 0.53
30 5 0.17
31 9 0.30
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.18
Consensus pattern (29 bp):
ATAAAAGTCCCAAAATAAAATATAAGCCC
Found at i:52056616 original size:5 final size:5
Alignment explanation
Indices: 52056606--52056632 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
52056596 GTAATTTGAT
52056606 AATTA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AA
52056633 ACCAAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:52068511 original size:9 final size:9
Alignment explanation
Indices: 52068497--52068521 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52068487 GTGTGGGAAA
52068497 ATTTTGTGT
1 ATTTTGTGT
52068506 ATTTTGTGT
1 ATTTTGTGT
52068515 ATTTTGT
1 ATTTTGT
52068522 ATTTTATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.20, T:0.68
Consensus pattern (9 bp):
ATTTTGTGT
Found at i:52069087 original size:2 final size:2
Alignment explanation
Indices: 52069080--52069110 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52069070 GTTATAATTG
52069080 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52069111 TCGAATAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52069764 original size:41 final size:41
Alignment explanation
Indices: 52069709--52069909 Score: 258
Period size: 41 Copynumber: 4.9 Consensus size: 41
52069699 GAAGGCTTAT
* * *
52069709 TGCCAGTGAGACAATTCAGACTCTATGTCTAGCAGGCTGGA
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
* * * *
52069750 TGCCGGTGAAACAATGCAGACTCTATGTCTAGAATGCTGGA
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
* *
52069791 TGCTGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTTGA
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
* * *
52069832 TGCCGGTGAAATAATTCAGAGTTTATGTCTAGCAGGCTTGA
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
* * * *
52069873 TGCCAGTGAAACATTTCGGACTTTAAGTCTAGCAGGC
1 TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGC
52069910 CAAAAGCCGG
Statistics
Matches: 140, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 140 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (41 bp):
TGCCGGTGAAACAATTCAGACTTTATGTCTAGCAGGCTGGA
Found at i:52070180 original size:2 final size:2
Alignment explanation
Indices: 52070173--52070199 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52070163 AGTGATAATC
52070173 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
52070200 GCATTTGGTA
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:52080094 original size:19 final size:19
Alignment explanation
Indices: 52080067--52080104 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
52080057 ATTTAGTATT
* *
52080067 TAATTGTAATCTAAAATGA
1 TAATCGTAATCCAAAATGA
52080086 TAATCGTAATCCAAAATGA
1 TAATCGTAATCCAAAATGA
52080105 CAATTACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
TAATCGTAATCCAAAATGA
Found at i:52080823 original size:23 final size:23
Alignment explanation
Indices: 52080796--52080844 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
52080786 AATCATTGTA
* *
52080796 TTGCACCGAAGTGTC-ACTTTTAT
1 TTGCACCAAAGTG-CAACTTTCAT
52080819 TTGCACCAAAGTGCAACTTTCAT
1 TTGCACCAAAGTGCAACTTTCAT
52080842 TTG
1 TTG
52080845 TGCGCATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (23 bp):
TTGCACCAAAGTGCAACTTTCAT
Found at i:52083942 original size:91 final size:90
Alignment explanation
Indices: 52083784--52083951 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 90
52083774 ACACTCCTGC
* * *
52083784 TTGTGGATGAACCACAAGTGTTGTAAGTTAATACGCTACCAGTAATTGTGAATACACAACGGGTT
1 TTGTGGATAAACCACAAGTGTTGTAAGTTAATACACTACCAGTAATTGTGAATACACAACGGATT
52083849 TGCAGATAAAAGCTGCCATTAAATG
66 TGCAGATAAAAGCTGCCATTAAATG
* * *
52083874 TTGTGGATAAACCACAATTGTTTGTAGGTTAATACACTACCAGTAATTGTGAATACACAATGGAT
1 TTGTGGATAAACCACAAGTG-TTGTAAGTTAATACACTACCAGTAATTGTGAATACACAACGGAT
52083939 TTGCAGATAAAAG
65 TTGCAGATAAAAG
52083952 TTACCAGTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 18 0.25
91 53 0.75
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (90 bp):
TTGTGGATAAACCACAAGTGTTGTAAGTTAATACACTACCAGTAATTGTGAATACACAACGGATT
TGCAGATAAAAGCTGCCATTAAATG
Found at i:52087371 original size:19 final size:20
Alignment explanation
Indices: 52087348--52087416 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 20
52087338 AAGTCAATTT
52087348 GTATCGATACCTTTATAAT-
1 GTATCGATACCTTTATAATA
*
52087367 GTATCGAT-CC-TTAGGAATAA
1 GTATCGATACCTTTA-TAAT-A
* *
52087387 GTATCGATA-CTTTATACTG
1 GTATCGATACCTTTATAATA
52087406 GTATCGATACC
1 GTATCGATACC
52087417 AAATTGGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
17 3 0.08
18 5 0.12
19 17 0.43
20 12 0.30
21 3 0.08
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (20 bp):
GTATCGATACCTTTATAATA
Found at i:52089442 original size:12 final size:12
Alignment explanation
Indices: 52089404--52089445 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
52089394 ATTGATCATA
52089404 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
52089416 GAGGGATATT-TG
1 GAGAGAT-TTGAG
52089428 GAGAGATTTGAG
1 GAGAGATTTGAG
52089440 GAGAGA
1 GAGAGA
52089446 ATATTGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:52089452 original size:24 final size:24
Alignment explanation
Indices: 52089404--52089450 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
52089394 ATTGATCATA
*
52089404 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
52089428 GAGAGATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
52089451 GGGATTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:52090330 original size:106 final size:107
Alignment explanation
Indices: 52090132--52090353 Score: 315
Period size: 106 Copynumber: 2.1 Consensus size: 107
52090122 CCCTAAAATA
** *
52090132 GGTAAAATAACTGAAATACCCCTATAGGAGAAAATAATTGAAATACCCTCATAGGGTAAAATAAC
1 GGTAAAATAACCAAAATACCCC-ATAGGAGAAAATAACTGAAATACCCTCATAGGGTAAAATAAC
* *
52090197 TGAAATACCCCTATAGAATAAATTGACCGAAATACCACCATAG
65 TGAAATACCCCCATAGAATAAAATGACCGAAATACCACCATAG
*
52090240 GGTAAAATAACCAAAATACCCC-TAGG-GTAAAATAACTGAAATATCCC-CATAGGGTAAAATGA
1 GGTAAAATAACCAAAATACCCCATAGGAG-AAAATAACTGAAATA-CCCTCATAGGGTAAAATAA
** *
52090302 CTGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAG
64 CTGAAATACCCCCATAGAATAAAATGACCGAAATACCACCATAG
52090346 GGTAAAAT
1 GGTAAAAT
52090354 GATTGTTATA
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
105 1 0.01
106 79 0.77
107 3 0.03
108 20 0.19
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (107 bp):
GGTAAAATAACCAAAATACCCCATAGGAGAAAATAACTGAAATACCCTCATAGGGTAAAATAACT
GAAATACCCCCATAGAATAAAATGACCGAAATACCACCATAG
Found at i:52090355 original size:27 final size:27
Alignment explanation
Indices: 52090132--52090353 Score: 270
Period size: 27 Copynumber: 8.3 Consensus size: 27
52090122 CCCTAAAATA
*
52090132 GGTAAAATAACTGAAATACCCCTATAG
1 GGTAAAATAACTGAAATACCCCCATAG
* *
52090159 GAG-AAAATAATTGAAATACCCTCATAG
1 G-GTAAAATAACTGAAATACCCCCATAG
*
52090186 GGTAAAATAACTGAAATACCCCTATAG
1 GGTAAAATAACTGAAATACCCCCATAG
** * * * *
52090213 AATAAATTGACCGAAATACCACCATAG
1 GGTAAAATAACTGAAATACCCCCATAG
**
52090240 GGTAAAATAACCAAAATA-CCCC-TAG
1 GGTAAAATAACTGAAATACCCCCATAG
*
52090265 GGTAAAATAACTGAAATATCCCCATAG
1 GGTAAAATAACTGAAATACCCCCATAG
*
52090292 GGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATAACTGAAATACCCCCATAG
* *
52090319 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATAACTGAAATACCCCCATAG
52090346 GGTAAAAT
1 GGTAAAAT
52090354 GATTGTTATA
Statistics
Matches: 167, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
25 19 0.11
26 8 0.05
27 139 0.83
28 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (27 bp):
GGTAAAATAACTGAAATACCCCCATAG
Found at i:52098467 original size:11 final size:11
Alignment explanation
Indices: 52098451--52098483 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
52098441 TAAAAAGTGT
52098451 AGAGAAAACTA
1 AGAGAAAACTA
*
52098462 AGAGAAACCT-
1 AGAGAAAACTA
52098472 AGAGAAAACTA
1 AGAGAAAACTA
52098483 A
1 A
52098484 ACCTAAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.61, C:0.12, G:0.18, T:0.09
Consensus pattern (11 bp):
AGAGAAAACTA
Found at i:52107266 original size:16 final size:16
Alignment explanation
Indices: 52107236--52107277 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
52107226 GATATTTATA
*
52107236 TTTTATTTTTATTAACT
1 TTTTATTATTATTAA-T
52107253 TTTTATTATT-TTAAT
1 TTTTATTATTATTAAT
52107268 TTTTAATTAT
1 TTTT-ATTAT
52107278 CATGGAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTATTATTAAT
Found at i:52107851 original size:12 final size:13
Alignment explanation
Indices: 52107834--52107862 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52107824 TGTTTTTACA
52107834 TTAAATTTAA-AT
1 TTAAATTTAATAT
52107846 TTAAATTTAATAT
1 TTAAATTTAATAT
52107859 TTAA
1 TTAA
52107863 TTTGATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAATTTAATAT
Found at i:52109318 original size:21 final size:21
Alignment explanation
Indices: 52109285--52109344 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
52109275 AACTTTTGAC
52109285 TTTTACAAT-TTATAATTA-TA
1 TTTTA-AATATTATAATTATTA
*
52109305 TTGTTAATTATTATAATTAATTA
1 TT-TTAAATATTATAATT-ATTA
52109328 TTTTAAATATT-TAATTA
1 TTTTAAATATTATAATTA
52109345 AATAATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 5 0.15
21 16 0.47
22 9 0.26
23 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTAAATATTATAATTATTA
Found at i:52111948 original size:15 final size:15
Alignment explanation
Indices: 52111912--52111940 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52111902 CCACCACCGG
52111912 CCACCACCACCACTT
1 CCACCACCACCACTT
52111927 CCACCACCACCACT
1 CCACCACCACCACT
52111941 ATCACCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.62, G:0.00, T:0.10
Consensus pattern (15 bp):
CCACCACCACCACTT
Found at i:52118362 original size:21 final size:21
Alignment explanation
Indices: 52118315--52118369 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
52118305 ACCATTATTT
* *
52118315 CTAATCTCACCACTAAAGTAT
1 CTAATCTCACCGCTAAAGTAA
* *
52118336 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTAAAGTAA
*
52118357 CTAATCTAACCGC
1 CTAATCTCACCGC
52118370 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.35, G:0.07, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTAAAGTAA
Found at i:52121772 original size:23 final size:23
Alignment explanation
Indices: 52121739--52121782 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
52121729 TAATTTCTAA
*
52121739 AAACAAATTTT-CTTTTTATTTC
1 AAACAAATTTTAATTTTTATTTC
52121761 AAACAAAATTTTAATTTTTATT
1 AAAC-AAATTTTAATTTTTATT
52121783 ATGATTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
AAACAAATTTTAATTTTTATTTC
Found at i:52123724 original size:30 final size:31
Alignment explanation
Indices: 52123685--52123744 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
52123675 AGAGGTGGGA
*
52123685 TGGGAAGGGAATAAAAGTTTT-AGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTGA-GGGAAAAG
*
52123716 TGGG-AGGGAGTAAAAATTTTGAGGGAAAA
1 TGGGAAGGGAATAAAAATTTTGAGGGAAAA
52123745 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGAGGGAAAAG
Found at i:52125402 original size:25 final size:24
Alignment explanation
Indices: 52125364--52125421 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
52125354 ATGTTCAAGC
* *
52125364 GAGCTATATTAGGAAGCTCAAAAA
1 GAGCTACATCAGGAAGCTCAAAAA
*
52125388 GAGCATACATCAGGAAGCTCATAAA
1 GAGC-TACATCAGGAAGCTCAAAAA
52125413 GAGCTACAT
1 GAGCTACAT
52125422 TTGTGTCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (24 bp):
GAGCTACATCAGGAAGCTCAAAAA
Found at i:52128103 original size:20 final size:21
Alignment explanation
Indices: 52128078--52128198 Score: 108
Period size: 20 Copynumber: 5.9 Consensus size: 21
52128068 ATTAAATGAT
52128078 AAAAAAG-TACAACTAAAAAG
1 AAAAAAGTTACAACTAAAAAG
*
52128098 AAAAAAGTTACAACT-AAATG
1 AAAAAAGTTACAACTAAAAAG
*
52128118 ATAAAAAG-TACAAGTAAAAA-
1 A-AAAAAGTTACAACTAAAAAG
* **
52128138 CAAAAAGTTACAACTAAATGACT
1 AAAAAAGTTACAACTAAA--AAG
* *
52128161 AAAAAAG-TACAAATAAAAAC
1 AAAAAAGTTACAACTAAAAAG
*
52128181 AAAAAAGTTATAACTAAA
1 AAAAAAGTTACAACTAAA
52128199 TGTTGAAAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
19 6 0.07
20 35 0.43
21 24 0.30
22 10 0.12
23 6 0.07
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.17
Consensus pattern (21 bp):
AAAAAAGTTACAACTAAAAAG
Found at i:52128103 original size:42 final size:42
Alignment explanation
Indices: 52128044--52128209 Score: 219
Period size: 42 Copynumber: 4.0 Consensus size: 42
52128034 ATAATAATAA
* ** *
52128044 ACAACTAAAAACCAAAAACATACAATTAAATGATAAAAAAGT
1 ACAACTAAAAACAAAAAAGTTACAACTAAATGATAAAAAAGT
*
52128086 ACAACTAAAAAGAAAAAAGTTACAACTAAATGAT-AAAAAGT
1 ACAACTAAAAACAAAAAAGTTACAACTAAATGATAAAAAAGT
*
52128127 ACAAGTAAAAAC-AAAAAGTTACAACTAAATGACTAAAAAAGT
1 ACAACTAAAAACAAAAAAGTTACAACTAAATGA-TAAAAAAGT
* * *
52128169 ACAAATAAAAACAAAAAAGTTATAACTAAATGTTGAAAAAA
1 ACAACTAAAAACAAAAAAGTTACAACTAAATGAT-AAAAAA
52128210 AATGCAACTC
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
40 20 0.18
41 18 0.16
42 48 0.44
43 24 0.22
ACGTcount: A:0.64, C:0.11, G:0.08, T:0.17
Consensus pattern (42 bp):
ACAACTAAAAACAAAAAAGTTACAACTAAATGATAAAAAAGT
Found at i:52128188 original size:83 final size:83
Alignment explanation
Indices: 52128044--52128200 Score: 235
Period size: 83 Copynumber: 1.9 Consensus size: 83
52128034 ATAATAATAA
* * *
52128044 ACAACTAAAAACCAAAAACATACAATTAAATGATAAAAAAGTACAACTAAAAAGAAAAAAGTTAC
1 ACAACTAAAAACCAAAAACATACAACTAAATGATAAAAAAGTACAAATAAAAACAAAAAAGTTAC
52128109 AACTAAATGATAAAAAGT
66 AACTAAATGATAAAAAGT
* **
52128127 ACAAGTAAAAA-CAAAAAGTTACAACTAAATGACTAAAAAAGTACAAATAAAAACAAAAAAGTTA
1 ACAACTAAAAACCAAAAACATACAACTAAATGA-TAAAAAAGTACAAATAAAAACAAAAAAGTTA
*
52128191 TAACTAAATG
65 CAACTAAATG
52128201 TTGAAAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
82 18 0.27
83 48 0.73
ACGTcount: A:0.64, C:0.11, G:0.08, T:0.17
Consensus pattern (83 bp):
ACAACTAAAAACCAAAAACATACAACTAAATGATAAAAAAGTACAAATAAAAACAAAAAAGTTAC
AACTAAATGATAAAAAGT
Found at i:52128198 original size:21 final size:20
Alignment explanation
Indices: 52128044--52128198 Score: 118
Period size: 21 Copynumber: 7.5 Consensus size: 20
52128034 ATAATAATAA
52128044 ACAACTAAAAACCAAAAACA-T
1 ACAACTAAAAA-CAAAAA-AGT
* * *
52128065 ACAATTAAATGATAAAAAAGT
1 ACAACTAAA-AACAAAAAAGT
*
52128086 ACAACTAAAAAGAAAAAAGTT
1 ACAACTAAAAACAAAAAAG-T
* *
52128107 ACAACTAAATGA-TAAAAAGT
1 ACAACTAAA-AACAAAAAAGT
*
52128127 ACAAGTAAAAAC-AAAAAGTT
1 ACAACTAAAAACAAAAAAG-T
*
52128147 ACAACTAAATGACTAAAAAAGT
1 ACAACTAAA-AAC-AAAAAAGT
*
52128169 ACAAATAAAAACAAAAAAGTT
1 ACAACTAAAAACAAAAAAG-T
*
52128190 ATAACTAAA
1 ACAACTAAA
52128199 TGTTGAAAAA
Statistics
Matches: 108, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
19 7 0.06
20 34 0.31
21 50 0.46
22 11 0.10
23 6 0.06
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.17
Consensus pattern (20 bp):
ACAACTAAAAACAAAAAAGT
Found at i:52141004 original size:3 final size:3
Alignment explanation
Indices: 52140992--52141030 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
52140982 AAAGAGGAGG
* *
52140992 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
52141031 GGAAAAATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52141004 original size:9 final size:9
Alignment explanation
Indices: 52140986--52141030 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
52140976 AAAGAAAAAG
*
52140986 AGGAGGAGA
1 AGGAGAAGA
52140995 AGGAGAAGA
1 AGGAGAAGA
*
52141004 AGAAGAAGA
1 AGGAGAAGA
*
52141013 AGAAGAAGA
1 AGGAGAAGA
52141022 AGGAGAAGA
1 AGGAGAAGA
52141031 GGAAAAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (9 bp):
AGGAGAAGA
Found at i:52141440 original size:16 final size:16
Alignment explanation
Indices: 52141419--52141449 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52141409 TTACTTATGT
52141419 TGGTATACATGGCTAC
1 TGGTATACATGGCTAC
*
52141435 TGGTATACATTGCTA
1 TGGTATACATGGCTA
52141450 ACCAGCTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (16 bp):
TGGTATACATGGCTAC
Found at i:52144628 original size:6 final size:6
Alignment explanation
Indices: 52144613--52144742 Score: 107
Period size: 6 Copynumber: 20.7 Consensus size: 6
52144603 AACCAAACTG
* * * * **
52144613 AAATCA AAATCT AAATCA AAATCT AAATCG AGATCA AAATTG AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* **
52144661 AAATCA AAATCA GAATCA GTGAGTGTTTCA AAATCA AAATCA AAATCA
1 AAATCA AAATCA AAATCA ---A---AATCA AAATCA AAATCA AAATCA
* *
52144709 AAATCA AAATCA AAATCA GAATCG AAATCA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
52144743 TGAAATCGAA
Statistics
Matches: 97, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
6 93 0.96
9 1 0.01
12 3 0.03
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.22
Consensus pattern (6 bp):
AAATCA
Found at i:52144749 original size:18 final size:18
Alignment explanation
Indices: 52144690--52144754 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
52144680 TGAGTGTTTC
*
52144690 AAAATCAAAATCAAAATC
1 AAAATCAAAATCAAAATT
*
52144708 AAAATCAAAATCAAAATC
1 AAAATCAAAATCAAAATT
* *
52144726 AGAATCGAAATCAAAATT
1 AAAATCAAAATCAAAATT
* *
52144744 GAAATCGAAAT
1 AAAATCAAAAT
52144755 AACCCTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.62, C:0.14, G:0.06, T:0.18
Consensus pattern (18 bp):
AAAATCAAAATCAAAATT
Found at i:52144754 original size:12 final size:12
Alignment explanation
Indices: 52144697--52144754 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
52144687 TTCAAAATCA
**
52144697 AAATCAAAATCA
1 AAATCAAAATTG
**
52144709 AAATCAAAATCA
1 AAATCAAAATTG
* *
52144721 AAATCAGAATCG
1 AAATCAAAATTG
52144733 AAATCAAAATTG
1 AAATCAAAATTG
*
52144745 AAATCGAAAT
1 AAATCAAAAT
52144755 AACCCTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.60, C:0.14, G:0.07, T:0.19
Consensus pattern (12 bp):
AAATCAAAATTG
Found at i:52145247 original size:21 final size:21
Alignment explanation
Indices: 52145221--52145260 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52145211 AACGTGGCAA
52145221 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCCACATCAGCTG
*
52145242 GTTAACTTGCCACGTCAGC
1 GTTAACTTGCCACATCAGC
52145261 GGTCCAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTG
Found at i:52146897 original size:6 final size:6
Alignment explanation
Indices: 52146888--52146939 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
52146878 ATAGGAATAG
*
52146888 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GCATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
52146936 GTAT
1 GTAT
52146940 CCATATACAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (6 bp):
GTATAT
Found at i:52148105 original size:28 final size:28
Alignment explanation
Indices: 52148073--52148133 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
52148063 GTCTGGATGC
*
52148073 GGTACTTACCAAAATAGATTAATCTCGT
1 GGTACTTACCAAAATAGATTAATCTCAT
*
52148101 GGTACTTACCAAAATAGATTAATTTCAT
1 GGTACTTACCAAAATAGATTAATCTCAT
52148129 GGTAC
1 GGTAC
52148134 GGGTTATCGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (28 bp):
GGTACTTACCAAAATAGATTAATCTCAT
Found at i:52148340 original size:63 final size:63
Alignment explanation
Indices: 52148261--52148386 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
52148251 GCAAGTCCAT
52148261 AACCTGAAACTTCCAGATATTTAGTTGGACTCATGTTATTGAAGTAGTTCCGTGAAATAGGAC
1 AACCTGAAACTTCCAGATATTTAGTTGGACTCATGTTATTGAAGTAGTTCCGTGAAATAGGAC
52148324 AACCTGAAACTTCCAGATATTTAGTTGGACTCATGTTATTGAAGTAGTTCCGTGAAATAGGAC
1 AACCTGAAACTTCCAGATATTTAGTTGGACTCATGTTATTGAAGTAGTTCCGTGAAATAGGAC
52148387 TAGTATGGGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (63 bp):
AACCTGAAACTTCCAGATATTTAGTTGGACTCATGTTATTGAAGTAGTTCCGTGAAATAGGAC
Found at i:52150766 original size:29 final size:29
Alignment explanation
Indices: 52150734--52150800 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
52150724 TACCATTAAA
52150734 GGCCCTTTTTTTTAAAATTTACCAAAATG
1 GGCCCTTTTTTTTAAAATTTACCAAAATG
** * ** *
52150763 GGCCCGATATTTTATTATTTACCAGAATG
1 GGCCCTTTTTTTTAAAATTTACCAAAATG
52150792 GGCCCTTTT
1 GGCCCTTTT
52150801 CCCCGAAAAC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (29 bp):
GGCCCTTTTTTTTAAAATTTACCAAAATG
Found at i:52151125 original size:11 final size:11
Alignment explanation
Indices: 52151095--52151158 Score: 67
Period size: 11 Copynumber: 5.7 Consensus size: 11
52151085 AAACTAATCC
52151095 TCTCTCAATTAT
1 TCTCTCAATT-T
*
52151107 TTTCTCAATTT
1 TCTCTCAATTT
52151118 TCTCTCAATTT
1 TCTCTCAATTT
*
52151129 GCTCTCAATTT
1 TCTCTCAATTT
* *
52151140 CCT-TCCAAATT
1 TCTCT-CAATTT
52151151 TCTCTCAA
1 TCTCTCAA
52151159 ATCCATATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 1 0.02
11 33 0.75
12 10 0.23
ACGTcount: A:0.22, C:0.28, G:0.02, T:0.48
Consensus pattern (11 bp):
TCTCTCAATTT
Found at i:52152349 original size:7 final size:7
Alignment explanation
Indices: 52152337--52152362 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52152327 TAGCCGATTG
52152337 GTATTTA
1 GTATTTA
52152344 GTATTTA
1 GTATTTA
52152351 GTATTTA
1 GTATTTA
52152358 GTATT
1 GTATT
52152363 ATGTATATAA
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:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:52153018 original size:18 final size:18
Alignment explanation
Indices: 52152976--52153018 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
52152966 TGCCTGGTGC
* *
52152976 GTTTCCTAGCCCTTTTAT
1 GTTTCCTAACCCTTATAT
* *
52152994 GTATCCTAACCCTTATCT
1 GTTTCCTAACCCTTATAT
52153012 GTTTCCT
1 GTTTCCT
52153019 TTTTCGAGTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.14, C:0.30, G:0.09, T:0.47
Consensus pattern (18 bp):
GTTTCCTAACCCTTATAT
Found at i:52153558 original size:21 final size:21
Alignment explanation
Indices: 52153532--52153581 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
52153522 CAAAAACCCT
**
52153532 AACCCTAACTTTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
52153553 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
52153574 AACCCTAA
1 AACCCTAA
52153582 ACTAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:52153616 original size:7 final size:7
Alignment explanation
Indices: 52153596--52153636 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
52153586 ATTTATTAAA
52153596 AATTTAT
1 AATTTAT
52153603 AAATTTAT
1 -AATTTAT
52153611 AATTTAT
1 AATTTAT
52153618 AA-TTA-
1 AATTTAT
52153623 AATTTAT
1 AATTTAT
52153630 AATTTAT
1 AATTTAT
52153637 TTGACAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.06
6 6 0.19
7 16 0.52
8 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATTTAT
Found at i:52153617 original size:26 final size:25
Alignment explanation
Indices: 52153584--52153636 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 25
52153574 AACCCTAAAC
52153584 TAATTTATTAA-AAATTTATAAATTTA
1 TAATTTA-TAATAAATTTAT-AATTTA
52153610 TAATTTATAATTAAATTTATAATTTA
1 TAATTTATAA-TAAATTTATAATTTA
52153636 T
1 T
52153637 TTGACAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 3 0.12
26 14 0.56
27 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TAATTTATAATAAATTTATAATTTA
Found at i:52153668 original size:129 final size:130
Alignment explanation
Indices: 52153466--52153711 Score: 424
Period size: 129 Copynumber: 1.9 Consensus size: 130
52153456 AATAAAATAG
*
52153466 AAATTTATAAATTTATAATTTATAATTAAATTTTGATATTAATTGACAAACCCTAACAAAAACCC
1 AAATTTATAAATTTATAATTTATAATTAAATTTTAATATTAATTGACAAACCCTAACAAAAACCC
** *
52153531 TAACCCTAACTTTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACTAATTTATTAA
66 TAACCCTAACCGTTAACTTAAAAACACTAAACCCTTAACTTAAAAACCCTAAACTAATTTATTAA
*
52153595 AAATTTATAAATTTATAATTTATAATTAAATTTATAAT-TTATTTGACAAACCCTAACAAAAACC
1 AAATTTATAAATTTATAATTTATAATTAAATTT-TAATATTAATTGACAAACCCTAACAAAAACC
52153659 CTAACCCTAACCGTTAACTTAAAAACACTAAACCCTTAACTTAAAAACCCTAA
65 CTAACCCTAACCGTTAACTTAAAAACACTAAACCCTTAACTTAAAAACCCTAA
52153712 CCCTTAACTT
Statistics
Matches: 110, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
129 84 0.76
130 26 0.24
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (130 bp):
AAATTTATAAATTTATAATTTATAATTAAATTTTAATATTAATTGACAAACCCTAACAAAAACCC
TAACCCTAACCGTTAACTTAAAAACACTAAACCCTTAACTTAAAAACCCTAAACTAATTTATTAA
Found at i:52153692 original size:22 final size:21
Alignment explanation
Indices: 52153661--52153788 Score: 177
Period size: 21 Copynumber: 6.0 Consensus size: 21
52153651 CAAAAACCCT
*
52153661 AACCCTAACCGTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
52153682 AACACTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
52153704 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
52153725 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
52153746 AACCCCAACCCTTAACATAAA
1 AACCCTAACCCTTAACTTAAA
52153767 AACCCCATAACCC-TAATCTTAA
1 AA-CCC-TAACCCTTAA-CTTAA
52153789 CAAAAATTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
21 62 0.65
22 25 0.26
23 9 0.09
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.22
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:52159920 original size:22 final size:25
Alignment explanation
Indices: 52159866--52159923 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
52159856 GCTACATGTT
52159866 TAGAGACATTGATCAATATATTTACA
1 TAGAGACATTGATCAATATA-TTACA
*
52159892 TAAAGACATTGATCAATATA-T-C-
1 TAGAGACATTGATCAATATATTACA
52159914 TAGAGACATT
1 TAGAGACATT
52159924 TGAATGTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 9 0.30
23 1 0.03
24 1 0.03
26 19 0.63
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (25 bp):
TAGAGACATTGATCAATATATTACA
Found at i:52169014 original size:2 final size:2
Alignment explanation
Indices: 52169007--52169034 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52168997 AAACATGTGA
52169007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52169035 TTGTATAAGA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52169939 original size:27 final size:27
Alignment explanation
Indices: 52169903--52169971 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
52169893 GGAGGGCCTG
* * *
52169903 CCACAGGCGGCACCAATGGTGGCAGTA
1 CCACAGGCGGCACCAAAGGTGCCACTA
* *
52169930 GCAGAGGCGGCACCAAAGGTGCCACTA
1 CCACAGGCGGCACCAAAGGTGCCACTA
52169957 CCACAGGCGGCACCA
1 CCACAGGCGGCACCA
52169972 GCCCTTATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.28, C:0.33, G:0.32, T:0.07
Consensus pattern (27 bp):
CCACAGGCGGCACCAAAGGTGCCACTA
Found at i:52170025 original size:13 final size:13
Alignment explanation
Indices: 52170007--52170033 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52169997 ATTCGACTGG
52170007 AGGAGAAGAAAGA
1 AGGAGAAGAAAGA
52170020 AGGAGAAGAAAGA
1 AGGAGAAGAAAGA
52170033 A
1 A
52170034 AAAGAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
AGGAGAAGAAAGA
Found at i:52170038 original size:10 final size:10
Alignment explanation
Indices: 52170025--52170081 Score: 78
Period size: 10 Copynumber: 5.7 Consensus size: 10
52170015 AAAGAAGGAG
52170025 AAGAAAGAAA
1 AAGAAAGAAA
52170035 AAGAAAGAAA
1 AAGAAAGAAA
* *
52170045 AGGAAAGGAA
1 AAGAAAGAAA
*
52170055 AAGAAAGGAA
1 AAGAAAGAAA
52170065 AAGAAAGAAA
1 AAGAAAGAAA
*
52170075 AGGAAAG
1 AAGAAAG
52170082 GAGAAGAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:52170051 original size:5 final size:5
Alignment explanation
Indices: 52170027--52170083 Score: 60
Period size: 5 Copynumber: 11.4 Consensus size: 5
52170017 AGAAGGAGAA
* * * * * *
52170027 GAAAG AAAAA GAAAG AAAAG GAAAG GAAAA GAAAG GAAAA GAAAG AAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
52170077 GAAAG GA
1 GAAAG GA
52170084 GAAGAAGAAG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:52170059 original size:30 final size:30
Alignment explanation
Indices: 52170019--52170089 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
52170009 GAGAAGAAAG
52170019 AAGGAGAAGAAAGAAAAAGAAAGAAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGAAAAGGA
* *
52170049 AAGGAAAAGAAAGGAAAAGAAAGAAAAGGA
1 AAGGAGAAGAAAGAAAAAGAAAGAAAAGGA
52170079 AAGGAGAAGAA
1 AAGGAGAAGAA
52170090 GAAGAGGGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (30 bp):
AAGGAGAAGAAAGAAAAAGAAAGAAAAGGA
Found at i:52170082 original size:20 final size:19
Alignment explanation
Indices: 52170015--52170089 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 19
52170005 GGAGGAGAAG
*
52170015 AAAG-AAGGAGAAGAAAGAA
1 AAAGAAAGGAAAAGAAAG-A
52170034 AAAGAAA-GAAAAGGAAAGGA
1 AAAGAAAGGAAAA-GAAA-GA
52170054 AAAGAAAGGAAAAGAAAGA
1 AAAGAAAGGAAAAGAAAGA
*
52170073 AAAGGAAAGGAGAAGAA
1 AAA-GAAAGGAAAAGAA
52170090 GAAGAGGGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
19 13 0.27
20 30 0.61
21 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (19 bp):
AAAGAAAGGAAAAGAAAGA
Found at i:52177752 original size:39 final size:39
Alignment explanation
Indices: 52177709--52177829 Score: 154
Period size: 39 Copynumber: 3.1 Consensus size: 39
52177699 ATATTATTTG
* * * *
52177709 ATTTAGGGTTATCAAAGTACAAACGGAGCACGAATGTGT
1 ATTTAGGGGTATCGAAGTACAAACGGAGCACGTATGTGC
* *
52177748 ATTTAGGGGTATTGAAGTACAAAAGGAGCACGTATGTGC
1 ATTTAGGGGTATCGAAGTACAAACGGAGCACGTATGTGC
*
52177787 ATTCAGGGGTA-CTGAAGTACAAACAGGAGCACGTATGTGC
1 ATTTAGGGGTATC-GAAGTACAAAC-GGAGCACGTATGTGC
52177827 ATT
1 ATT
52177830 CATACAATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
39 53 0.75
40 18 0.25
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (39 bp):
ATTTAGGGGTATCGAAGTACAAACGGAGCACGTATGTGC
Found at i:52177826 original size:40 final size:40
Alignment explanation
Indices: 52177723--52177831 Score: 168
Period size: 39 Copynumber: 2.8 Consensus size: 40
52177713 AGGGTTATCA
* * * *
52177723 AAGTACAAAC-GGAGCACGAATGTGTATTTAGGGGTATTG
1 AAGTACAAACAGGAGCACGTATGTGCATTCAGGGGTACTG
52177762 AAGTACAAA-AGGAGCACGTATGTGCATTCAGGGGTACTG
1 AAGTACAAACAGGAGCACGTATGTGCATTCAGGGGTACTG
52177801 AAGTACAAACAGGAGCACGTATGTGCATTCA
1 AAGTACAAACAGGAGCACGTATGTGCATTCA
52177832 TACAATAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
39 43 0.67
40 21 0.33
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (40 bp):
AAGTACAAACAGGAGCACGTATGTGCATTCAGGGGTACTG
Found at i:52183080 original size:9 final size:9
Alignment explanation
Indices: 52183062--52183096 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
52183052 TCCACTCTTC
52183062 TAAA-TTTT
1 TAAATTTTT
52183070 TAAATTTTT
1 TAAATTTTT
52183079 TAAATTTTT
1 TAAATTTTT
52183088 TAAATTTTT
1 TAAATTTTT
52183097 GTTGTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.15
9 22 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TAAATTTTT
Found at i:52186221 original size:20 final size:20
Alignment explanation
Indices: 52186196--52186235 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52186186 AAATCAAATG
* * *
52186196 ATCGTTTTCTTTAGTTTACC
1 ATCGTTCTCTCTAGTCTACC
52186216 ATCGTTCTCTCTAGTCTACC
1 ATCGTTCTCTCTAGTCTACC
52186236 CTTCAGTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.10, T:0.47
Consensus pattern (20 bp):
ATCGTTCTCTCTAGTCTACC
Found at i:52186458 original size:29 final size:28
Alignment explanation
Indices: 52186426--52186512 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
52186416 TCATAAGAAC
52186426 ATTTTATGAAATTATATTTAATAATAATT
1 ATTTTAT-AAATTATATTTAATAATAATT
* * *
52186455 A-TTT-TAAATTGTATTAAATCAT-A-T
1 ATTTTATAAATTATATTTAATAATAATT
* *
52186479 ATTTTAATTAAAATATATTTAATATTAATT
1 ATTTT-A-TAAATTATATTTAATAATAATT
52186509 ATTT
1 ATTT
52186513 CAAATTTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 14 0.32
27 1 0.02
28 16 0.36
29 2 0.05
30 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTATAAATTATATTTAATAATAATT
Found at i:52186688 original size:67 final size:66
Alignment explanation
Indices: 52186613--52186825 Score: 150
Period size: 67 Copynumber: 3.2 Consensus size: 66
52186603 ATTATAATGT
52186613 ATTT-AATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTA
1 ATTTAAATAATAATTATGTTTAAATATGATTAAA-TATTTATTATTGATATTAATAATCTTATTA
52186677 AA
65 AA
* * ** * * * * * * *
52186679 ATTTAAATAACAATAACAAATTT--CTGCTAATTATAAGAATT-TTATT-AAATT-ATATATTTT
1 ATTTAAATAATAAT--TATGTTTAAAT-ATGATTA-AATATTTATTATTGATATTAATA-ATCTT
52186739 AATTAAAA
61 -ATT-AAA
* * * *
52186747 TATATTTAGTAATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTAT
1 -AT-TTAAATAATAATTATGTTTAAATATGATT-AAATATTTATTATTGATATTAATAATCTTAT
52186812 TAAA
63 TAAA
52186816 ATTTAAATAA
1 ATTTAAATAA
52186826 CATTAACAAT
Statistics
Matches: 103, Mismatches: 28, Indels: 31
0.64 0.17 0.19
Matches are distributed among these distances:
65 3 0.03
66 12 0.12
67 23 0.22
68 17 0.17
69 20 0.19
70 18 0.17
71 7 0.07
72 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (66 bp):
ATTTAAATAATAATTATGTTTAAATATGATTAAATATTTATTATTGATATTAATAATCTTATTAA
A
Found at i:52186723 original size:137 final size:138
Alignment explanation
Indices: 52186569--52186990 Score: 427
Period size: 137 Copynumber: 2.9 Consensus size: 138
52186559 TAAGAATATG
* *
52186569 AATTATTAAGAATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
* * *
52186634 AATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAAA
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
52186699 TTTCTGCT
131 TTTCTGCT
**** *
52186707 AATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAGTAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
*
52186771 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTAACAAT
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAAC-A-
* *
52186836 AATCATT-TACCAAAAC
129 AAT--TTCT-GC----T
** * ** * * ** * *
52186852 AATT-TTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTAT
1 AATTATTAAG--AATTTTATTAA-ATTA-TATACCA-A-A-ATT-A---AAATATATTTAATAAT
52186916 AATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATA
55 AATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATA
52186981 ACAATAACAA
120 ACAATAACAA
52186991 TAATCATTTA
Statistics
Matches: 237, Mismatches: 26, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
137 110 0.46
138 6 0.03
139 3 0.01
140 1 0.00
141 3 0.01
145 6 0.03
147 8 0.03
148 3 0.01
149 5 0.02
151 1 0.00
152 2 0.01
153 1 0.00
154 1 0.00
155 1 0.00
156 86 0.36
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (138 bp):
AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
TTTCTGCT
Found at i:52186745 original size:18 final size:17
Alignment explanation
Indices: 52186717--52186751 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52186707 AATTATAAGA
*
52186717 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52186734 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52186752 TTAGTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52186870 original size:156 final size:156
Alignment explanation
Indices: 52186693--52187020 Score: 611
Period size: 156 Copynumber: 2.1 Consensus size: 156
52186683 AAATAACAAT
* *
52186693 AACAAATTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAGTA
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
52186758 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
*
52186823 TAACATTAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
*
52186849 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATT
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
52186914 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
52186979 TAACAATAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
*
52187005 AACAATTTTATGCTAA
1 AACAATTTTCTGCTAA
52187021 GGGTATTCTA
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 167 1.00
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (156 bp):
AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
TAACAATAACAATAATCATTTACCAA
Found at i:52186901 original size:18 final size:18
Alignment explanation
Indices: 52186873--52186921 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
52186863 AATTATAAGA
52186873 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
52186890 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
52186906 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
52186922 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:52186907 original size:16 final size:16
Alignment explanation
Indices: 52186873--52186927 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
52186863 AATTATAAGA
52186873 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
52186890 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
52186906 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
52186920 ATGTTTAA
1 AT-TTTAA
52186928 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:52187164 original size:16 final size:16
Alignment explanation
Indices: 52187143--52187194 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
52187133 GATTAGCTAT
52187143 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52187159 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52187175 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52187191 TACA
1 TACA
52187195 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.37, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:52188318 original size:22 final size:23
Alignment explanation
Indices: 52188277--52188322 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
52188267 TGTCCAAAAA
52188277 TATAATATAATTTTAGTTAATTT
1 TATAATATAATTTTAGTTAATTT
52188300 TATAATA-AATTTT-GATTAATTT
1 TATAATATAATTTTAG-TTAATTT
52188322 T
1 T
52188323 GATTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 14 0.64
23 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TATAATATAATTTTAGTTAATTT
Found at i:52193319 original size:31 final size:31
Alignment explanation
Indices: 52193276--52193347 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
52193266 ATGGTGGGTG
*
52193276 GCCGGCGGCAACAAGAAGGTAGCAAATAGTT
1 GCCGACGGCAACAAGAAGGTAGCAAATAGTT
52193307 GCCGACGGCAACAAGAAGGTAGCAAATAGTT
1 GCCGACGGCAACAAGAAGGTAGCAAATAGTT
52193338 GCCGACGGCA
1 GCCGACGGCA
52193348 GTGGAGCAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.35, C:0.22, G:0.32, T:0.11
Consensus pattern (31 bp):
GCCGACGGCAACAAGAAGGTAGCAAATAGTT
Found at i:52197155 original size:20 final size:22
Alignment explanation
Indices: 52197113--52197155 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
52197103 CTTGGAAAAT
*
52197113 TTATTGTGTTGAATAGTAGTGG
1 TTATTGTGTTGAATAATAGTGG
*
52197135 TTATTGT-TTTAATAATA-TGG
1 TTATTGTGTTGAATAATAGTGG
52197155 T
1 T
52197156 ATGATGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (22 bp):
TTATTGTGTTGAATAATAGTGG
Found at i:52201446 original size:16 final size:16
Alignment explanation
Indices: 52201425--52201457 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52201415 TTCGCTGTAT
52201425 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
52201441 TGGAATAGAGTCGTAA
1 TGGAATAGAGGCGTAA
52201457 T
1 T
52201458 AGTAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:52201708 original size:16 final size:16
Alignment explanation
Indices: 52201671--52201712 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52201661 TTAATCATAT
*
52201671 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
52201687 TT-AAATATATTATAA
1 TTAAAATATATTATAA
52201702 TTAAAATATAT
1 TTAAAATATAT
52201713 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:52201719 original size:14 final size:15
Alignment explanation
Indices: 52201680--52201721 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52201670 TTTAAACATA
*
52201680 ATTATTATTAAATAT
1 ATTATAATTAAATAT
52201695 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
52201709 A-TATAATTTAATA
1 ATTATAATTAAATA
52201722 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:52201887 original size:120 final size:121
Alignment explanation
Indices: 52201669--52201945 Score: 459
Period size: 120 Copynumber: 2.3 Consensus size: 121
52201659 ATTTAATCAT
52201669 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
52201734 ATTAATATTCTTATATGAATTTACTCAAATCATAATTTATGATACTATAAAAGATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATA
* *
52201790 ATTT-AACATAACTATTATTAAATCTATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
52201854 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATA
* * *
52201910 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAA
52201946 TATTAAATAA
Statistics
Matches: 145, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
120 139 0.96
121 6 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATA
Found at i:52201892 original size:59 final size:58
Alignment explanation
Indices: 52201709--52201892 Score: 137
Period size: 57 Copynumber: 3.1 Consensus size: 58
52201699 TAATTAAAAT
*
52201709 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAA-TAATATTCTTATATGAATTTACTAAAATCATA
* * * * * ** * *
52201768 ATTTATGATACTATAA-AAGATAAT-TTAA-CATAACTATTATTAAATCTATTATAATTAAA--A
1 A--TAT-A-A-TTTAATAA-A-ATTCTTAATAATAA-TATTCTTATATGAATT-TACTAAAATCA
52201828 T-
57 TA
52201829 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAT-AATATTCTTATATGAATTTACTAAAATCATA
52201888 ATATA
1 ATATA
52201893 TGATACTATA
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
55 2 0.02
56 15 0.16
57 17 0.19
58 5 0.05
59 9 0.10
61 4 0.04
62 6 0.07
63 16 0.18
64 15 0.16
65 2 0.02
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (58 bp):
ATATAATTTAATAAAATTCTTAATAATAATATTCTTATATGAATTTACTAAAATCATA
Found at i:52201904 original size:61 final size:61
Alignment explanation
Indices: 52201719--52201906 Score: 163
Period size: 61 Copynumber: 3.1 Consensus size: 61
52201709 ATATAATTTA
* * *
52201719 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATTTATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
** * * * * * * * * * *
52201780 ATAAAA--GATAATTTAA-C-ATAACTATTAT-TAAATCTATTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
52201838 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
52201900 ATAAAAT
1 ATAAAAT
52201907 ATAATTTGAA
Statistics
Matches: 90, Mismatches: 27, Indels: 20
0.66 0.20 0.15
Matches are distributed among these distances:
58 1 0.01
59 33 0.37
60 13 0.14
61 42 0.47
62 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:52206488 original size:32 final size:32
Alignment explanation
Indices: 52206452--52206515 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
52206442 TATTACATAG
52206452 ATTTAAAATATAATTTTATGCTAAAAATTTAT
1 ATTTAAAATATAATTTTATGCTAAAAATTTAT
52206484 ATTTAAAATATAATTTTATGCTAAAAATTTAT
1 ATTTAAAATATAATTTTATGCTAAAAATTTAT
52206516 TTAATTAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (32 bp):
ATTTAAAATATAATTTTATGCTAAAAATTTAT
Found at i:52206511 original size:19 final size:18
Alignment explanation
Indices: 52206455--52206509 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
52206445 TACATAGATT
52206455 TAAAATATAATTTTATGC
1 TAAAATATAATTTTATGC
* *
52206473 TAAAA-AT--TTATAT-T
1 TAAAATATAATTTTATGC
52206487 TAAAATATAATTTTATGC
1 TAAAATATAATTTTATGC
52206505 TAAAA
1 TAAAA
52206510 ATTTATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 5 0.17
15 7 0.24
17 7 0.24
18 10 0.34
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (18 bp):
TAAAATATAATTTTATGC
Found at i:52207217 original size:16 final size:18
Alignment explanation
Indices: 52207183--52207225 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
52207173 TGCCAGGTGC
*
52207183 ATATCCTAGCCCTTATAT
1 ATATCCTAACCCTTATAT
52207201 ATATCCTAACCCTTATAT
1 ATATCCTAACCCTTATAT
*
52207219 ATTTCCT
1 ATATCCT
52207226 TTTCCCAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.42
Consensus pattern (18 bp):
ATATCCTAACCCTTATAT
Found at i:52209961 original size:36 final size:36
Alignment explanation
Indices: 52209909--52209992 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
52209899 ATATATAATT
* * * * * *
52209909 ATCACTTTTAAATATTACAATTATATCATTATGCCGA
1 ATCACTTAT-AATATTACAAATACATCAATAGGCCAA
52209946 ATCACTTATAATATTACAAATACATCAATAGGCCAA
1 ATCACTTATAATATTACAAATACATCAATAGGCCAA
52209982 ATCACTTATAA
1 ATCACTTATAA
52209993 GTTCAATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 33 0.80
37 8 0.20
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.35
Consensus pattern (36 bp):
ATCACTTATAATATTACAAATACATCAATAGGCCAA
Found at i:52210262 original size:43 final size:43
Alignment explanation
Indices: 52210196--52210319 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
52210186 GGCTTGTACA
* * * * *
52210196 ATGCCAACGTCCCGGACGTGGTCTTACATGTAATCATATA-TTG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCG
52210239 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCG
*
52210282 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA
52210320 TATCGAAATC
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 4 0.06
43 63 0.90
44 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:52214311 original size:125 final size:126
Alignment explanation
Indices: 52213996--52214767 Score: 1025
Period size: 126 Copynumber: 6.2 Consensus size: 126
52213986 TAAGGCTAAG
** * * *
52213996 CAGGAACTACTGTAGAAAAAGAGCACCCACGTGTGACCATTTTTCAGTAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCTTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * * *
52214061 ATCCTGTTTGAAGCATTTTTGACACTATTTTTTCAAAAACGTCTTCTGAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
* ** * * *
52214122 CAGGAACTACGGTAGAAAAAGAGCACCCACGTGTGACCATTTTTCAGTAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCTTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* ** *
52214187 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAAAAATGTCTTCTGAAAATTA-TTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
* * * * * *
52214247 CAAGAACTACTGTAGAAAAAGAGCTTTCACGTGGGAACTTTTTTTAGTAATTTTGTTGATAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCTTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * *
52214312 ATTCTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACCGTCTTTTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
52214373 CAGGAACTACTGTAGAAAAAGAG-TGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
1 CAGGAACTACTGTAGAAAAAGAGCT-TCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
* * * *
52214437 CATCTTGCTTGAAGCGTTTTTTACACTATTTTTT-AGAACCGTCTTTTCGAAATTA-TTTTT
65 CATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
* * * *
52214497 CAGGAACTACTGTAGAAAAAGAG-TATCGACATGGGAGCTTTTTTCAATAATTTTGCTGATAGTG
1 CAGGAACTACTGTAGAAAAAGAGCT-TCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
* * *
52214561 CATCCTGCTTGAAACGTTTTTGACACTA-TTTTTCAGAACTGTCTTCTCTAAATTATTTTTT
65 CATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
* * * *
52214622 CATGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTACTGACAGTAC
1 CAGGAACTACTGTAGAAAAAGAGCTTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * * *
52214687 ATCCTGCTTGAAGCGTTTTTGACATTATCTTTTCCGAACCGTTTTCTCAAAATTAATTTTT
66 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
* *
52214748 CTGAAACTACTGTAGAAAAA
1 CAGGAACTACTGTAGAAAAA
52214768 AAACAAAATT
Statistics
Matches: 578, Mismatches: 62, Indels: 12
0.89 0.10 0.02
Matches are distributed among these distances:
123 5 0.01
124 107 0.19
125 214 0.37
126 252 0.44
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (126 bp):
CAGGAACTACTGTAGAAAAAGAGCTTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
Found at i:52214448 original size:251 final size:251
Alignment explanation
Indices: 52213999--52214767 Score: 1046
Period size: 251 Copynumber: 3.1 Consensus size: 251
52213989 GGCTAAGCAG
* * * * *
52213999 GAACTACTGTAGAAAAAGAGC-ACCCACGTGTGACCATTTTTCAGTAATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCTA-TCACGTGGGAACTTTTTTCAGTAATTTTGCTGATAGTGCAT
* * * * *
52214063 CCTGTTTGAAGCATTTTTGACACTATTTTTTCAAAAACGTCTTCTGAAAATTATTTTTTCAGGAA
65 CCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAA
* ** * * *
52214128 CTACGGTAGAAAAAGAGCACCCACGTGTGACCATTTTTCAGTAATTTTGCTGACAGTGCATCCTG
130 CTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTG
* **
52214193 CTTGAAGCGTTTTTGACACTATTTTTTCAAAAATGTCTTCTGAAAATTATTTTTCAA
195 CTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTGAAAATTATTTTTCAA
* * * *
52214250 GAACTACTGTAGAAAAAGAGCTTTCACGTGGGAACTTTTTTTAGTAATTTTGTTGATAGTGCATT
1 GAACTACTGTAGAAAAAGAGCTATCACGTGGGAACTTTTTTCAGTAATTTTGCTGATAGTGCATC
* *
52214315 CTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACCGTCTTTTCAAAATTATTTTTTCAGGAAC
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAAC
* *
52214380 TACTGTAGAAAAAGAGTGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCTTGC
131 TACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGC
* * *
52214445 TTGAAGCGTTTTTTACACTATTTTTT-AGAACCGTCTTTTCG-AAATTATTTTTCAG
196 TTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCT-GAAAATTATTTTTCAA
* * *
52214500 GAACTACTGTAGAAAAAGAG-TATCGACATGGGAGCTTTTTTCAATAATTTTGCTGATAGTGCAT
1 GAACTACTGTAGAAAAAGAGCTATC-ACGTGGGAACTTTTTTCAGTAATTTTGCTGATAGTGCAT
* * * *
52214564 CCTGCTTGAAACGTTTTTGACACTA-TTTTTCAGAACTGTCTTCTCTAAATTATTTTTTCATGAA
65 CCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAA
* *
52214628 CTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTACTGACAGTACATCCTG
130 CTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTG
* * * * * *
52214693 CTTGAAGCGTTTTTGACATTATCTTTTCCGAACCGTTTTCTCAAAATTAATTTTTC-T
195 CTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTGAAAATT-ATTTTTCAA
52214750 GAAACTACTGTAGAAAAA
1 G-AACTACTGTAGAAAAA
52214768 AAACAAAATT
Statistics
Matches: 456, Mismatches: 55, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
249 122 0.27
250 115 0.25
251 219 0.48
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (251 bp):
GAACTACTGTAGAAAAAGAGCTATCACGTGGGAACTTTTTTCAGTAATTTTGCTGATAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGGAAC
TACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGC
TTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTGAAAATTATTTTTCAA
Found at i:52214891 original size:33 final size:32
Alignment explanation
Indices: 52214853--52214957 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 32
52214843 TAACACAAAA
*
52214853 TTATTTTTTTAAAAACATAAACCCTAATTTTAT
1 TTATTTTTTTAAAAACCTAAACCCTAA-TTTAT
* * ** *
52214886 TTATTTATTTAAAACCCCTAAAATCTAATTTAA
1 TTATTTTTTTAAAA-ACCTAAACCCTAATTTAT
*
52214919 TTAATTTTTTAAAAACTCTAAACCCTAATTTAT
1 TTATTTTTTTAAAAAC-CTAAACCCTAATTTAT
52214952 TT-TTTT
1 TTATTTT
52214958 AAAATTCCTA
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
32 4 0.07
33 44 0.77
34 9 0.16
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (32 bp):
TTATTTTTTTAAAAACCTAAACCCTAATTTAT
Found at i:52227393 original size:6 final size:6
Alignment explanation
Indices: 52227382--52227425 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
52227372 GGAAACAATC
52227382 TTTCTT TTTCTT TTTCTT TTTCTTT TTTCTT TTTCTT TTT-TT TT
1 TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT TT
52227426 GGGGGGGGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
5 4 0.11
6 27 0.73
7 6 0.16
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTCTT
Found at i:52227408 original size:13 final size:13
Alignment explanation
Indices: 52227382--52227422 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
52227372 GGAAACAATC
52227382 TTTCTTTTTC-TT
1 TTTCTTTTTCTTT
52227394 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
52227407 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
52227420 TTT
1 TTT
52227423 TTTGGGGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTCTTTTTCTTT
Found at i:52240899 original size:21 final size:21
Alignment explanation
Indices: 52240875--52240915 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52240865 TCCAATTCAT
52240875 TATCA-ATACACATATATCTAA
1 TATCATATA-ACATATATCTAA
*
52240896 TATCATATAACATATTTCTA
1 TATCATATAACATATATCTA
52240916 TCCATTGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (21 bp):
TATCATATAACATATATCTAA
Found at i:52243829 original size:55 final size:55
Alignment explanation
Indices: 52243769--52243880 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
52243759 TTAGTTAATC
* *
52243769 TTAAATTTATCATTAATAGAAATCATCATCAAAATCTACTAAATACTATTCTAAA
1 TTAAATTTATCATTAATAGAAATCATCACCAAAATATACTAAATACTATTCTAAA
52243824 TTAAATTTATCATTAATAGAAATCATCACCAAAATATACTAAATACTATTCTAAA
1 TTAAATTTATCATTAATAGAAATCATCACCAAAATATACTAAATACTATTCTAAA
52243879 TT
1 TT
52243881 GGTTTATTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (55 bp):
TTAAATTTATCATTAATAGAAATCATCACCAAAATATACTAAATACTATTCTAAA
Found at i:52247591 original size:28 final size:28
Alignment explanation
Indices: 52247538--52247591 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
52247528 GAGAAAATAA
* * *
52247538 TTTAATTAAGTGAATTAATTAAATTTAT
1 TTTAATTAAGTCAAATAAATAAATTTAT
52247566 TTTAATTAA-TCAAATAAATAATATTT
1 TTTAATTAAGTCAAATAAATAA-ATTT
52247592 TGAGAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (28 bp):
TTTAATTAAGTCAAATAAATAAATTTAT
Found at i:52247696 original size:44 final size:44
Alignment explanation
Indices: 52247633--52247762 Score: 242
Period size: 44 Copynumber: 3.0 Consensus size: 44
52247623 AAATTATATG
* *
52247633 AATTAATTTAAAGACTAGATAACACATATTAATACATAATACTA
1 AATTAGTTTAAAGACTAGATAACACATATTAATACACAATACTA
52247677 AATTAGTTTAAAGACTAGATAACACATATTAATACACAATACTA
1 AATTAGTTTAAAGACTAGATAACACATATTAATACACAATACTA
52247721 AATTAGTTTAAAGACTAGATAACACATATTAATACACAATAC
1 AATTAGTTTAAAGACTAGATAACACATATTAATACACAATAC
52247763 ATGAAAGATC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 84 1.00
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (44 bp):
AATTAGTTTAAAGACTAGATAACACATATTAATACACAATACTA
Found at i:52252359 original size:23 final size:21
Alignment explanation
Indices: 52252320--52252364 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
52252310 CCAAAAAAAA
*
52252320 TATTAATGTAAAATTATATAT
1 TATTAATATAAAATTATATAT
52252341 TATTAATATATAAATT-TAT-T
1 TATTAATATA-AAATTATATAT
52252361 TATT
1 TATT
52252365 CATTCTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTAATATAAAATTATATAT
Found at i:52254342 original size:43 final size:43
Alignment explanation
Indices: 52254295--52254399 Score: 115
Period size: 43 Copynumber: 2.4 Consensus size: 43
52254285 CATTTATTTG
* *
52254295 AAAAAATGCCGCTATAGAACAT-AGCCTTTAGCAGCGCTTTTAT
1 AAAAAACGCCGCTAAAGAACATGA-CCTTTAGCAGCGCTTTTAT
* * *
52254338 AAAAAACGCTGCTAAAGAACATGACCTTTAGCGGCGC-TTTACC
1 AAAAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTA-T
* *
52254381 CACAAACGCCGCTAAAGAA
1 AAAAAACGCCGCTAAAGAA
52254400 ACGGTTCTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
42 4 0.08
43 47 0.90
44 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (43 bp):
AAAAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTAT
Found at i:52254598 original size:21 final size:20
Alignment explanation
Indices: 52254574--52254636 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 20
52254564 TAACTGAAGT
52254574 ATAATTCAAAATATTCTTACA
1 ATAATT-AAAATATTCTTACA
*
52254595 ATAATGTTAAA-A-T-TTACA
1 ATAAT-TAAAATATTCTTACA
*
52254613 AT-GTTAAAAATATTCTTACA
1 ATAATT-AAAATATTCTTACA
52254633 ATAA
1 ATAA
52254637 GAAAACAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 1 0.03
17 4 0.12
18 8 0.25
19 2 0.06
20 8 0.25
21 8 0.25
22 1 0.03
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (20 bp):
ATAATTAAAATATTCTTACA
Found at i:52260685 original size:14 final size:14
Alignment explanation
Indices: 52260655--52260702 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
52260645 AACCCGAGCC
*
52260655 CTAAATTCCTAAACT
1 CTAAATCCCT-AACT
52260670 CTAAATCCCTAACT
1 CTAAATCCCTAACT
* *
52260684 CTTAACCCCTAACAT
1 CTAAATCCCTAAC-T
52260699 CTAA
1 CTAA
52260703 CCCCTAAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (14 bp):
CTAAATCCCTAACT
Found at i:52260703 original size:14 final size:14
Alignment explanation
Indices: 52260666--52260709 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
52260656 TAAATTCCTA
* *
52260666 AACTCTAAATCCCT
1 AACTCTTAACCCCT
52260680 AACTCTTAACCCCT
1 AACTCTTAACCCCT
52260694 AACATC-TAACCCCT
1 AAC-TCTTAACCCCT
52260708 AA
1 AA
52260710 ACCCCTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 25 0.93
15 2 0.07
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.25
Consensus pattern (14 bp):
AACTCTTAACCCCT
Found at i:52260739 original size:21 final size:20
Alignment explanation
Indices: 52260709--52260749 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
52260699 CTAACCCCTA
*
52260709 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
52260730 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
52260750 TAATCCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:52261021 original size:22 final size:22
Alignment explanation
Indices: 52260976--52261037 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
52260966 TCTAACTCTT
** *
52260976 AACCCCTAATGTCTAACCCCTA
1 AACCCCTAACCTCTAAACCCTA
*
52260998 AACCCCTAACCTCTAAACCTTA
1 AACCCCTAACCTCTAAACCCTA
*
52261020 AATCCC-AACC-CTTAAACC
1 AACCCCTAACCTC-TAAACC
52261038 ATAATCCCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.03
21 10 0.29
22 23 0.68
ACGTcount: A:0.35, C:0.42, G:0.02, T:0.21
Consensus pattern (22 bp):
AACCCCTAACCTCTAAACCCTA
Found at i:52261047 original size:296 final size:296
Alignment explanation
Indices: 52260561--52261151 Score: 884
Period size: 296 Copynumber: 2.0 Consensus size: 296
52260551 CAATATATTT
*
52260561 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATT
1 AATTTATTATTATCTCCTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATT
* * * *
52260626 AATCTAAACCCAAAACCTTAACCCGAGCCCTAAATTCCTAAACTCTAAATCCCTAACTCTTAACC
66 AATCTAAACCCAAAACCCTAACCCGACCCCTAAATTCCTAAACTCTAAATCCCTAACCCCTAACC
* *
52260691 CCTAACATCTAACCCCTAAACCCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAATCC
131 CCTAACACCTAACCCCTAAACCCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAATCA
* * **
52260756 ATAATCTCTAAATCTATACTCCCTAAACCTTAAAATA-TGAACTCCTAAACCGGTCTTAAATATT
196 ATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGT-AACTCCTAAACCGACCTTAAATATT
* *
52260820 AAATTAATCATATACCCTAAACTAAAAACCCTAAACA
260 AAATAAATCATATACCCTAAACCAAAAACCCTAAACA
52260857 AATTTATTATTATCTCCTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
1 AATTTATTATTATCTCCTTTACAATTATATAAGAACATATTTAAAATATAAATT-AAAAAATAAT
** * *
52260922 TAATCTAAACCCAAAACCCTAACTTGACCCCTAAA-TCCTAAATCTCTAACT-CTTAACCCCTAA
65 TAATCTAAACCCAAAACCCTAACCCGACCCCTAAATTCCTAAA-CTCTAAATCCCTAACCCCTAA
*** * *
52260985 TGTCTAACCCCTAAACCCCT-AACCTCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAA
129 CCCCTAACACCT-AACCCCTAAACCCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAA
*
52261049 TCAATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGACCTTAAATC
193 TCAATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGACCTTAAATA
* * *
52261114 TTAAATAAATTATATACCTTAAACCAAAAATCCTAAAC
258 TTAAATAAATCATATACCCTAAACCAAAAACCCTAAAC
52261152 TATAGTGATA
Statistics
Matches: 265, Mismatches: 26, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
296 209 0.79
297 56 0.21
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.29
Consensus pattern (296 bp):
AATTTATTATTATCTCCTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATT
AATCTAAACCCAAAACCCTAACCCGACCCCTAAATTCCTAAACTCTAAATCCCTAACCCCTAACC
CCTAACACCTAACCCCTAAACCCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAATCA
ATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGACCTTAAATATTA
AATAAATCATATACCCTAAACCAAAAACCCTAAACA
Found at i:52261065 original size:15 final size:15
Alignment explanation
Indices: 52261038--52261078 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
52261028 CCCTTAAACC
52261038 ATAATCCCT-AATCA
1 ATAATCCCTAAATCA
*
52261052 ATAATCCCTAAATCC
1 ATAATCCCTAAATCA
*
52261067 ATACTCCCTAAA
1 ATAATCCCTAAA
52261079 CCTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAATCCCTAAATCA
Found at i:52261526 original size:41 final size:41
Alignment explanation
Indices: 52261425--52261624 Score: 192
Period size: 41 Copynumber: 4.9 Consensus size: 41
52261415 TAAAATGTTT
* * *
52261425 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGCCCCCAG--
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * *
52261464 TTAGCGACGCTTTTT-ATAAAACGCCGCTAAAACACCAAGCA
1 TTAGCGGCGCTTTTTCA-AAAACGCCGCTAAAACCCCGAGCA
* * *
52261505 TTAGTGGCGCTTTTTCAAAAACGCCGCGAAAACCCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * * *
52261546 TTAGCGTCGCATTTTCAAAAATGCCGCAAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
** * * *
52261587 TTAGCAACGCTTTCTT-GAAACCGCCGCTAAAGCCCCGA
1 TTAGCGGCGCTTT-TTCAAAAACGCCGCTAAAACCCCGA
52261625 AAGGTAAGCA
Statistics
Matches: 131, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.01
39 32 0.24
41 95 0.73
42 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
Found at i:52261587 original size:82 final size:80
Alignment explanation
Indices: 52261425--52261591 Score: 192
Period size: 80 Copynumber: 2.1 Consensus size: 80
52261415 TAAAATGTTT
* * * *
52261425 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGCCCCCAGTTAGCGACGCTTTTTATAAAACGCCG
1 TTAGCGGCGCTTTTTCAAAAACGCCGCGAAAACCCCCAGTTAGCGACGCTTTTCATAAAACGCCG
*
52261490 CTAAAACACCAAGCA
66 CAAAAACACCAAGCA
* ** * *
52261505 TTAGTGGCGCTTTTTCAAAAACGCCGCGAAAACCCTGAGCATTAGCGTCGCATTTTCA-AAAATG
1 TTAGCGGCGCTTTTTCAAAAACGCCGCGAAAACCCCCAG--TTAGCGACGC-TTTTCATAAAACG
* *
52261569 CCGCAAAAACCCCGAGCA
63 CCGCAAAAACACCAAGCA
52261587 TTAGC
1 TTAGC
52261592 AACGCTTTCT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
80 33 0.46
82 33 0.46
83 5 0.07
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (80 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCGAAAACCCCCAGTTAGCGACGCTTTTCATAAAACGCCG
CAAAAACACCAAGCA
Found at i:52262590 original size:20 final size:18
Alignment explanation
Indices: 52262549--52262590 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
52262539 GTATGATTTA
*
52262549 AAATTTTTGTATTATAAT
1 AAATTTTTGAATTATAAT
52262567 -AATTTTTGAATTATTAAAT
1 AAATTTTTGAATTA-T-AAT
52262586 AAATT
1 AAATT
52262591 AATATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 12 0.60
18 1 0.05
19 3 0.15
20 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
AAATTTTTGAATTATAAT
Found at i:52262664 original size:14 final size:15
Alignment explanation
Indices: 52262636--52262665 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52262626 GATATTATTT
52262636 TATATTAATTAAAAA
1 TATATTAATTAAAAA
*
52262651 TATATTATTTAAAAA
1 TATATTAATTAAAAA
52262666 ATTAATTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATATTAATTAAAAA
Found at i:52266025 original size:25 final size:25
Alignment explanation
Indices: 52265988--52266045 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
52265978 TATATATATA
52265988 TATTTA-GTTAGGTTCGAATAAGTG
1 TATTTAGGTTAGGTTCGAATAAGTG
52266012 TATTTAGGTTAGGTTCGAATAAGTG
1 TATTTAGGTTAGGTTCGAATAAGTG
52266037 TATTTAGGT
1 TATTTAGGT
52266046 ATGTAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 6 0.18
25 27 0.82
ACGTcount: A:0.28, C:0.03, G:0.26, T:0.43
Consensus pattern (25 bp):
TATTTAGGTTAGGTTCGAATAAGTG
Found at i:52266308 original size:41 final size:41
Alignment explanation
Indices: 52266257--52266360 Score: 165
Period size: 41 Copynumber: 2.5 Consensus size: 41
52266247 GGTTTAAAAC
* *
52266257 CTAGCTGGCTTAAGGCTGGTGAAATAATTCGAACTTTAAGT
1 CTAGCAGGCTTAAGGCCGGTGAAATAATTCGAACTTTAAGT
*
52266298 CTAGCAGGCTTAAGGCCGGTGAAATAATTCGGACTTTAAGT
1 CTAGCAGGCTTAAGGCCGGTGAAATAATTCGAACTTTAAGT
52266339 CTAGCAGGC-TAAGTGCCGGTGA
1 CTAGCAGGCTTAAG-GCCGGTGA
52266361 TCTGAATCAG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 4 0.07
41 55 0.93
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (41 bp):
CTAGCAGGCTTAAGGCCGGTGAAATAATTCGAACTTTAAGT
Found at i:52266384 original size:41 final size:41
Alignment explanation
Indices: 52266339--52266483 Score: 263
Period size: 41 Copynumber: 3.5 Consensus size: 41
52266329 GACTTTAAGT
52266339 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
52266380 CTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
52266421 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
52266462 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
52266484 ACATGTTAAA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:52266384 original size:82 final size:82
Alignment explanation
Indices: 52266298--52266484 Score: 247
Period size: 82 Copynumber: 2.3 Consensus size: 82
52266288 AACTTTAAGT
**
52266298 CTAGCAGGCTTAAG-GCCGGTGAAAT-AATTC-GGACTT-TAAGTCTAGCAGGCTAAGTGCCGGT
1 CTAGCAGGC-TAAGTGCCGGTGAAATGAA-TCAGG--TTATAAACCTAGCAGGCTAAGTGCCGGT
*
52266359 GATCTGAATCAGGTTATAAAC
62 GATCTGAATCAGGCTATAAAC
* **
52266380 CTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
1 CTAGCAGGCTAAGTGCCGGTGAAATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
*
52266445 TGAATCAGGCTATAAGC
66 TGAATCAGGCTATAAAC
52266462 CTAGCAGGCTAAGTGCCGGTGAA
1 CTAGCAGGCTAAGTGCCGGTGAA
52266485 CATGTTAAAT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
81 6 0.07
82 82 0.89
83 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (82 bp):
CTAGCAGGCTAAGTGCCGGTGAAATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
TGAATCAGGCTATAAAC
Found at i:52276383 original size:11 final size:11
Alignment explanation
Indices: 52276367--52276404 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
52276357 TTATAAAATG
52276367 ACAATATCTCA
1 ACAATATCTCA
52276378 ACAATATCTCA
1 ACAATATCTCA
52276389 ACAATATCTCA
1 ACAATATCTCA
52276400 ACAAT
1 ACAAT
52276405 TGATAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (11 bp):
ACAATATCTCA
Found at i:52280149 original size:19 final size:18
Alignment explanation
Indices: 52280125--52280190 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 18
52280115 AGTGCAAAAC
*
52280125 TAAAAAAAATTAAAATTT
1 TAAAAAAATTTAAAATTT
*
52280143 ATAAAAAATATTTATAATTGT
1 -TAAAAAA-ATTTAAAATT-T
52280164 TAAAAAAATTCTAAAATATT
1 TAAAAAAATT-TAAAAT-TT
*
52280184 TTAAAAA
1 TAAAAAA
52280191 TAACATATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 10 0.26
20 27 0.69
21 2 0.05
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAAAAAATTTAAAATTT
Found at i:52280328 original size:19 final size:18
Alignment explanation
Indices: 52280303--52280355 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
52280293 GGATGACTTC
52280303 AAAATTATAAAAAAAATT
1 AAAATTATAAAAAAAATT
*
52280321 AGAAATTA-AAAAATATATT
1 A-AAATTATAAAAA-AAATT
52280340 AATAATTATTAAAAAA
1 AA-AATTA-TAAAAAA
52280356 TTATAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 1 0.03
21 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAATTATAAAAAAAATT
Found at i:52280359 original size:11 final size:11
Alignment explanation
Indices: 52280325--52280378 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
52280315 AAAATTAGAA
52280325 ATTAAAAAATAT
1 ATTAAAAAAT-T
*
52280337 ATT-AATAATT
1 ATTAAAAAATT
52280347 ATTAAAAAATT
1 ATTAAAAAATT
52280358 A-T-AAAAATT
1 ATTAAAAAATT
**
52280367 CCTAAAAAATT
1 ATTAAAAAATT
52280378 A
1 A
52280379 AAATGTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 7 0.20
10 6 0.17
11 19 0.54
12 3 0.09
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:52280366 original size:20 final size:21
Alignment explanation
Indices: 52280325--52280378 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
52280315 AAAATTAGAA
*
52280325 ATTAAAAAATATATTAATAATT
1 ATTAAAAAAT-TATTAAAAATT
52280347 ATTAAAAAATTA-TAAAAATT
1 ATTAAAAAATTATTAAAAATT
**
52280367 CCTAAAAAATTA
1 ATTAAAAAATTA
52280379 AAATGTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.59
21 2 0.07
22 10 0.34
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAATTATTAAAAATT
Done.