Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 186 of 199
Found at i:54045836 original size:27 final size:26
Alignment explanation
Indices: 54045784--54045838 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
54045774 TTTAAAATAC
* *
54045784 TTTTAAAATATTTTTTTATTTTTTTA
1 TTTTAAAATATTTTTTTATATGTTTA
54045810 TTTTAAAAATATTTTTTT-TAATGTTTA
1 TTTT-AAAATATTTTTTTAT-ATGTTTA
54045837 TT
1 TT
54045839 AAAAAATGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTAAAATATTTTTTTATATGTTTA
Found at i:54045843 original size:26 final size:27
Alignment explanation
Indices: 54045788--54045845 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
54045778 AAATACTTTT
* * *
54045788 AAAATATTTTTTTATTTTTTTATTTTA
1 AAAATATTTTTTTATATGTTTATTTAA
54045815 AAAATATTTTTTT-TAATGTTTA-TTAA
1 AAAATATTTTTTTAT-ATGTTTATTTAA
54045841 AAAAT
1 AAAAT
54045846 GGGCCGGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
AAAATATTTTTTTATATGTTTATTTAA
Found at i:54047328 original size:18 final size:18
Alignment explanation
Indices: 54047305--54047339 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54047295 TCTGACAAAA
*
54047305 AAAACTGTTAAAATAAAT
1 AAAACTATTAAAATAAAT
54047323 AAAACTATTAAAATAAA
1 AAAACTATTAAAATAAA
54047340 CTGATGGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAACTATTAAAATAAAT
Found at i:54047453 original size:27 final size:27
Alignment explanation
Indices: 54047377--54047493 Score: 110
Period size: 27 Copynumber: 4.4 Consensus size: 27
54047367 CTTAGGGAAG
* * ***
54047377 AGGCGGCACCAGTCACGCCTTTTTCAT
1 AGGCAGCACCGGTCACGCCTTCCCCAT
*
54047404 AGGCGGCA-CGGTCACGCCTTCCCCAT
1 AGGCAGCACCGGTCACGCCTTCCCCAT
* * *
54047430 AGGCAGTACCGGTCACGCCATCCCCAA
1 AGGCAGCACCGGTCACGCCTTCCCCAT
* * *
54047457 AGGCGGCACCGGTTATGCCTTCCCCAT
1 AGGCAGCACCGGTCACGCCTTCCCCAT
*
54047484 AGGCGGCACC
1 AGGCAGCACC
54047494 CACTCCCCCA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
26 20 0.27
27 55 0.73
ACGTcount: A:0.19, C:0.38, G:0.26, T:0.17
Consensus pattern (27 bp):
AGGCAGCACCGGTCACGCCTTCCCCAT
Found at i:54047603 original size:19 final size:20
Alignment explanation
Indices: 54047568--54047619 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
54047558 GGAGAATAGA
54047568 AGAAAGAAAGAAAAGAAAAG
1 AGAAAGAAAGAAAAGAAAAG
* *
54047588 AGAAAGAAA-TAAAGAAAAT
1 AGAAAGAAAGAAAAGAAAAG
54047607 AG-AAGAAAGAAAA
1 AGAAAGAAAGAAAA
54047620 TGTATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 13 0.46
20 9 0.32
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (20 bp):
AGAAAGAAAGAAAAGAAAAG
Found at i:54047615 original size:14 final size:14
Alignment explanation
Indices: 54047562--54047620 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
54047552 AGAGAGGGAG
54047562 AATAGAAGAAAGAA
1 AATAGAAGAAAGAA
*
54047576 AGA-A-AAGAAAAGAG
1 A-ATAGAAG-AAAGAA
*
54047590 AA-AGAAATAAAGAA
1 AATAG-AAGAAAGAA
54047604 AATAGAAGAAAGAA
1 AATAGAAGAAAGAA
54047618 AAT
1 AAT
54047621 GTATTATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
13 5 0.14
14 26 0.72
15 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (14 bp):
AATAGAAGAAAGAA
Found at i:54051857 original size:16 final size:17
Alignment explanation
Indices: 54051836--54051867 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54051826 AAATATGCAA
54051836 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
54051852 TCACATAACTTCATAT
1 TCACATAACTTCATAT
54051868 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:54052166 original size:43 final size:41
Alignment explanation
Indices: 54052028--54052191 Score: 163
Period size: 43 Copynumber: 3.9 Consensus size: 41
54052018 GACTCGTACA
* * * * *
54052028 ATGCCAACGTCTCAGACGTGGTCTTACATGTAATCACATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAACACA-ATCG
* *
54052071 ATGCC-ACTGTCCCA-ACAGGGTCTTACACGAATCA-AATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAACACAAT-CG
*
54052111 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAACACAA-TCG
*
54052154 ATGCCAACGTCCCAGACGTGGTCTTACACGATAACACA
1 ATGCCAACGTCCCAGACATGGTCTTACACGA-AACACA
54052192 TATTGGAAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 2 0.02
40 13 0.13
41 20 0.19
42 19 0.18
43 48 0.47
44 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAACACAATCG
Found at i:54052167 original size:83 final size:84
Alignment explanation
Indices: 54052028--54052184 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 84
54052018 GACTCGTACA
* * * *
54052028 ATGCCAACGTCTCAGACGTGGTCTTACATGTAATCACATATCAATGCCACTGTCCCA-ACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAGAC-GTGG
54052091 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
* *
54052111 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCAATGCC-ACTGTCCCAGACGTG
54052174 GTCTTACACGA
64 GTCTTACACGA
54052185 TAACACATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
82 1 0.02
83 47 0.73
84 16 0.25
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCAATGCCACTGTCCCAGACGTGGT
CTTACACGAATCAAATACG
Found at i:54058752 original size:16 final size:17
Alignment explanation
Indices: 54058731--54058762 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54058721 AAATATGCAA
54058731 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
54058747 TCACATAACTTCATAT
1 TCACATAACTTCATAT
54058763 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:54059061 original size:43 final size:41
Alignment explanation
Indices: 54058923--54059086 Score: 163
Period size: 43 Copynumber: 3.9 Consensus size: 41
54058913 GACTCGTACA
* * * * *
54058923 ATGCCAACGTCCCAGACGTGGTCTTAAATGTAATCACATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAACACA-ATCG
* *
54058966 ATGCC-ACTGTCCCA-ACAGGGTCTTACACGAATCA-AATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAACACAAT-CG
*
54059006 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAACACAA-TCG
*
54059049 ATGCCAACGTCCCAGACGTGGTCTTACACGATAACACA
1 ATGCCAACGTCCCAGACATGGTCTTACACGA-AACACA
54059087 TATTGGAAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
39 2 0.02
40 13 0.13
41 20 0.19
42 18 0.17
43 49 0.48
44 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAACACAATCG
Found at i:54059062 original size:83 final size:84
Alignment explanation
Indices: 54058923--54059079 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 84
54058913 GACTCGTACA
* * *
54058923 ATGCCAACGTCCCAGACGTGGTCTTAAATGTAATCACATATCAATGCCACTGTCCCA-ACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTAAACGTAAACACATATCAATGCCACTGTCCCAGAC-GTGG
54058986 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
* * *
54059006 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTAAACGTAAACACATA-TCAATGCC-ACTGTCCCAGACGTG
54059069 GTCTTACACGA
64 GTCTTACACGA
54059080 TAACACATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
82 1 0.02
83 47 0.73
84 16 0.25
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTAAACGTAAACACATATCAATGCCACTGTCCCAGACGTGGT
CTTACACGAATCAAATACG
Found at i:54060691 original size:14 final size:14
Alignment explanation
Indices: 54060672--54060700 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54060662 TAATGTATTT
54060672 AATTTATATTACAA
1 AATTTATATTACAA
54060686 AATTTATATTACAA
1 AATTTATATTACAA
54060700 A
1 A
54060701 GTTGGTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATATTACAA
Found at i:54061934 original size:14 final size:14
Alignment explanation
Indices: 54061917--54061951 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
54061907 GAAATTACAT
54061917 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
54061931 GTTAGTATAGTATC
1 GTTAGAATAGTATC
*
54061945 ATTAGAA
1 GTTAGAA
54061952 AAAAAAAGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:54064018 original size:19 final size:19
Alignment explanation
Indices: 54063996--54064033 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
54063986 TTTCCTTCTC
54063996 CTTCTTC-TTCTCTTCTTTT
1 CTTCTTCTTTCTC-TCTTTT
54064015 CTTCTTCTTTCTCTCTTTT
1 CTTCTTCTTTCTCTCTTTT
54064034 GGCTGGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTCTTCTTTCTCTCTTTT
Found at i:54070727 original size:46 final size:44
Alignment explanation
Indices: 54070668--54070758 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 44
54070658 GAAATAAAAC
**
54070668 TGTAATAGAATAGAGTTGTAATCAGTGATTCAAT-TGTTTGGTTGAA
1 TGTAATAGAATAGAACTGTAAT-AGT-ATT-AATGTGTTTGGTTGAA
* *
54070714 TGTAATGGAATAGAACTGTAATAGTATTATTGTGTTTGGTTGAA
1 TGTAATAGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAA
54070758 T
1 T
54070759 AGAATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 2 0.05
44 16 0.40
45 3 0.08
46 19 0.47
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (44 bp):
TGTAATAGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAA
Found at i:54072044 original size:16 final size:16
Alignment explanation
Indices: 54072023--54072066 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
54072013 CTTAGTCCCG
54072023 GAATGGCCATTCGATC
1 GAATGGCCATTCGATC
54072039 GAATGGCCATTCGATC
1 GAATGGCCATTCGATC
*
54072055 GAATGGCTATTC
1 GAATGGCCATTC
54072067 AGCCAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (16 bp):
GAATGGCCATTCGATC
Found at i:54084644 original size:59 final size:60
Alignment explanation
Indices: 54084511--54084664 Score: 229
Period size: 59 Copynumber: 2.6 Consensus size: 60
54084501 TGCACACCTC
** * ** *
54084511 TATCTAGATAGCATTTTATTAATTTAATATTAATATGAGATATTAAATTTAATTTCATATT
1 TATCTAGATAATATTTTATTAATTTAATATTAATATGAGA-ATTAAATTAAATTAAATAAT
54084572 TATCTAGATAATATTTTATTAATTTAATATTAATATGAG-ATTAAATTAAATTAAATAAT
1 TATCTAGATAATATTTTATTAATTTAATATTAATATGAGAATTAAATTAAATTAAATAAT
*
54084631 TATCTTGATAATATTTTATTAATTTAATATTAAT
1 TATCTAGATAATATTTTATTAATTTAATATTAAT
54084665 GTAATTAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 49 0.57
61 37 0.43
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (60 bp):
TATCTAGATAATATTTTATTAATTTAATATTAATATGAGAATTAAATTAAATTAAATAAT
Found at i:54092355 original size:45 final size:44
Alignment explanation
Indices: 54092280--54092366 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 44
54092270 GAATGAATAG
*
54092280 GAAATGAGAAATGAGAAATATTTAGGAATGATTATAGTTTTCTTC
1 GAAATGAGAAAT-AGAAATATTTAGGAATGATTATAGGTTTCTTC
*
54092325 GAAATGGAGAAAT-GAAATCATTT-GGAAATGATTGTAGGTTTC
1 GAAAT-GAGAAATAGAAAT-ATTTAGG-AATGATTATAGGTTTC
54092367 CAAAAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
44 7 0.19
45 23 0.62
46 7 0.19
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (44 bp):
GAAATGAGAAATAGAAATATTTAGGAATGATTATAGGTTTCTTC
Found at i:54092607 original size:26 final size:26
Alignment explanation
Indices: 54092549--54092607 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
54092539 TATTTTCTCG
54092549 AAATTTTACCAGGGGCAAAATCGATA
1 AAATTTTACCAGGGGCAAAATCGATA
* * *
54092575 AAGTTTTACCATGGGTAAAATCG-TCA
1 AAATTTTACCAGGGGCAAAATCGAT-A
54092601 AAATTTT
1 AAATTTT
54092608 GCTAGAGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 27 0.96
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (26 bp):
AAATTTTACCAGGGGCAAAATCGATA
Found at i:54097887 original size:4 final size:4
Alignment explanation
Indices: 54097878--54097905 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
54097868 GTGAAGCAAT
54097878 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
54097906 GAGTATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:54100272 original size:23 final size:22
Alignment explanation
Indices: 54100240--54100287 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
54100230 ATATATGAGT
* *
54100240 TTTATCCAATACATGTATTTATA
1 TTTATACAATACATATATTT-TA
54100263 TTTATACAATACATATATTTTA
1 TTTATACAATACATATATTTTA
54100285 TTT
1 TTT
54100288 GTAATGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTATACAATACATATATTTTA
Found at i:54102155 original size:84 final size:84
Alignment explanation
Indices: 54102012--54102245 Score: 269
Period size: 84 Copynumber: 2.8 Consensus size: 84
54102002 TTAAGGGCGT
* * * **
54102012 AAAAA-GCCCTCAAACGTTTTCAAAAAAAGTAATTAAGTCCTTACTTTTTTATACTCAATTGGGT
1 AAAAAGGCTCTCAAA-GCTTTCAAAAAAAGCAATTAAGTCCTT--TTTTTTGCACTCAATTGGGT
* **
54102076 ACTTGAACTTTCAAAATGCATC
63 ACTTAAACTGCCAAAATGCATC
*
54102098 AAAAAGGCTCTCAAA-CTTT-AAAAAAA-CAATTAAGCCCTGCTTTTTTTTGCACTCAATTGGGT
1 AAAAAGGCTCTCAAAGCTTTCAAAAAAAGCAATTAAG---TCCTTTTTTTTGCACTCAATTGGGT
*
54102160 ATTTAAACTGCCAAAATGCATC
63 ACTTAAACTGCCAAAATGCATC
* *
54102182 AAAAAGGCTCTCAAAGTTTTTCAAAAAAAGCGATTAAGTCCTTTTTTTTGCACTCAATTGGGTA
1 AAAAAGGCTCTCAAAG-CTTTCAAAAAAAGCAATTAAGTCCTTTTTTTTGCACTCAATTGGGTA
54102246 ATTTCACAAT
Statistics
Matches: 127, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
83 7 0.06
84 58 0.46
85 28 0.22
86 12 0.09
87 15 0.12
88 7 0.06
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (84 bp):
AAAAAGGCTCTCAAAGCTTTCAAAAAAAGCAATTAAGTCCTTTTTTTTGCACTCAATTGGGTACT
TAAACTGCCAAAATGCATC
Found at i:54102371 original size:10 final size:9
Alignment explanation
Indices: 54102332--54102475 Score: 55
Period size: 9 Copynumber: 15.4 Consensus size: 9
54102322 TGACATGCAA
*
54102332 AAAAAATAT
1 AAAAATTAT
54102341 AAAAA-T-T
1 AAAAATTAT
*
54102348 AAAAATCAAT
1 AAAAAT-TAT
*
54102358 AAAAGTTAT
1 AAAAATTAT
54102367 AAAAATTATT
1 AAAAATTA-T
***
54102377 AATTTTTAAT
1 AAAAATT-AT
54102387 AAAAA-TATT
1 AAAAATTA-T
*
54102396 AAAATTTTATT
1 AAAA-ATTA-T
* *
54102407 GAAAACTAT
1 AAAAATTAT
54102416 AAAAA-TAT
1 AAAAATTAT
*
54102424 AAAAATCAT
1 AAAAATTAT
54102433 AAAAA-TAT
1 AAAAATTAT
*
54102441 AAAATTTTAT
1 AAAA-ATTAT
*
54102451 AAAAATCATTAA
1 -AAAA--ATTAT
54102463 AAAAATTAT
1 AAAAATTAT
54102472 AAAA
1 AAAA
54102476 TGCATAAAAA
Statistics
Matches: 100, Mismatches: 22, Indels: 26
0.68 0.15 0.18
Matches are distributed among these distances:
7 6 0.06
8 16 0.16
9 40 0.40
10 19 0.19
11 16 0.16
12 3 0.03
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:54102403 original size:20 final size:20
Alignment explanation
Indices: 54102365--54102404 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54102355 AATAAAAGTT
*
54102365 ATAAAAATTATTAATTTTTA
1 ATAAAAATTATTAAATTTTA
54102385 ATAAAAA-TATTAAAATTTTA
1 ATAAAAATTATT-AAATTTTA
54102405 TTGAAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAAAATTATTAAATTTTA
Found at i:54102419 original size:8 final size:8
Alignment explanation
Indices: 54102408--54102444 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
54102398 AATTTTATTG
*
54102408 AAAACTAT
1 AAAAATAT
54102416 AAAAATAT
1 AAAAATAT
54102424 AAAAATCAT
1 AAAAAT-AT
54102433 AAAAATAT
1 AAAAATAT
54102441 AAAA
1 AAAA
54102445 TTTTATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:54106776 original size:21 final size:22
Alignment explanation
Indices: 54106752--54106803 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
54106742 TGGCCAGTAC
*
54106752 AAATAACAA-AAACAATAGC-AA
1 AAATAACAACAAA-AACAGCAAA
54106773 AAATAACAACAAAAACAGCAGAA
1 AAATAACAACAAAAACAGCA-AA
54106796 AAATAACA
1 AAATAACA
54106804 GCACCAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 14 0.52
22 3 0.11
23 10 0.37
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (22 bp):
AAATAACAACAAAAACAGCAAA
Found at i:54106797 original size:23 final size:24
Alignment explanation
Indices: 54106756--54106803 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
54106746 CAGTACAAAT
*
54106756 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
*
54106780 AACAAAAACAGCAG-AAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
54106803 A
1 A
54106804 GCACCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.06
Consensus pattern (24 bp):
AACAAAAACAACAGCAAAAATAAC
Found at i:54107454 original size:11 final size:11
Alignment explanation
Indices: 54107434--54107477 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
54107424 CTCAACACCA
54107434 AAATTGAGAGG
1 AAATTGAGAGG
*
54107445 AAATTTAGAGG
1 AAATTGAGAGG
*
54107456 AAACTGAGAGG
1 AAATTGAGAGG
54107467 AAATTTGAGAG
1 AAA-TTGAGAG
54107478 AGGATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.32, T:0.20
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:54109670 original size:3 final size:3
Alignment explanation
Indices: 54109662--54109686 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54109652 CTAACAATCA
54109662 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
54109687 GCATCTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54117973 original size:22 final size:23
Alignment explanation
Indices: 54117937--54117994 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
54117927 TGGGTATTCA
* *
54117937 TTATTTTT-TATAATTTTGTATG
1 TTATTTTTATAAAATTTTATATG
*
54117959 -TATTTTTATAAAATTTTATGTG
1 TTATTTTTATAAAATTTTATATG
*
54117981 TTTTTTTTATAAAA
1 TTATTTTTATAAAA
54117995 AATGAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 11 0.37
23 12 0.40
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (23 bp):
TTATTTTTATAAAATTTTATATG
Found at i:54117978 original size:20 final size:20
Alignment explanation
Indices: 54117941--54117985 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
54117931 TATTCATTAT
*
54117941 TTTTTATAATTTTGTATGTA
1 TTTTTATAAATTTGTATGTA
*
54117961 TTTTTATAAAATTT-TATGTG
1 TTTTTAT-AAATTTGTATGTA
54117981 TTTTT
1 TTTTT
54117986 TTTATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTTTATAAATTTGTATGTA
Found at i:54118249 original size:31 final size:29
Alignment explanation
Indices: 54118214--54118285 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
54118204 TAATAGATGT
*
54118214 GTGACCAAAATATTAAATTTTGATAACGTT-A
1 GTGACCAAAATATAAAATTTT-A-AAC-TTGA
*
54118245 GTGACTAAAATATAAAATTTTAAACTTGA
1 GTGACCAAAATATAAAATTTTAAACTTGA
*
54118274 GTAACCAAAATA
1 GTGACCAAAATA
54118286 GAAACACTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.06
29 14 0.39
30 1 0.03
31 19 0.53
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (29 bp):
GTGACCAAAATATAAAATTTTAAACTTGA
Found at i:54119204 original size:5 final size:5
Alignment explanation
Indices: 54119194--54119230 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
54119184 TAGTTACTTG
54119194 CATAC CATAC CATAC CATAC CATAC CATAC CATAC CA
1 CATAC CATAC CATAC CATAC CATAC CATAC CATAC CA
54119231 CTTTACAGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (5 bp):
CATAC
Found at i:54123262 original size:13 final size:13
Alignment explanation
Indices: 54123244--54123268 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54123234 GATATCAATA
54123244 GAGGTCAAAATCG
1 GAGGTCAAAATCG
54123257 GAGGTCAAAATC
1 GAGGTCAAAATC
54123269 AAGAGGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (13 bp):
GAGGTCAAAATCG
Found at i:54123837 original size:22 final size:23
Alignment explanation
Indices: 54123782--54123845 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 23
54123772 ACTTACGAAA
*
54123782 TTAAAATATAATAATATATAAGT
1 TTAAAATATAAAAATATATAAGT
* *
54123805 TT-AATTTTAAAAATAT-TGAA-T
1 TTAAAATATAAAAATATAT-AAGT
*
54123826 TTAAAATATAAATAT-TATAA
1 TTAAAATATAAAAATATATAA
54123846 TACTACATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
21 7 0.22
22 23 0.72
23 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
TTAAAATATAAAAATATATAAGT
Found at i:54123996 original size:21 final size:18
Alignment explanation
Indices: 54123965--54124023 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 18
54123955 AATTTATTGT
54123965 AATATTATTTAAATTTTTA
1 AATATTATTT-AATTTTTA
54123984 AATATCTATTTTAA-TTTT-
1 AATAT-TA-TTTAATTTTTA
*
54124002 AATAGTGTATTTAATTTATA
1 AATA-T-TATTTAATTTTTA
54124022 AA
1 AA
54124024 AGTATTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 9 0.27
19 15 0.45
20 6 0.18
21 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (18 bp):
AATATTATTTAATTTTTA
Found at i:54126176 original size:4 final size:4
Alignment explanation
Indices: 54126167--54126233 Score: 125
Period size: 4 Copynumber: 16.8 Consensus size: 4
54126157 GAAGAAGATA
54126167 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
54126215 TATG TATG TCTG TATG TAT
1 TATG TATG TATG TATG TAT
54126234 TAAAAAACAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.24, C:0.01, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:54151081 original size:19 final size:19
Alignment explanation
Indices: 54151057--54151096 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54151047 TAATTTGAAT
* *
54151057 TTTTTTAAATATAATATAA
1 TTTTTTAAATAAAATAAAA
*
54151076 TTTTTTTAATAAAATAAAA
1 TTTTTTAAATAAAATAAAA
54151095 TT
1 TT
54151097 AACTTAGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTTAAATAAAATAAAA
Found at i:54176178 original size:8 final size:8
Alignment explanation
Indices: 54176165--54176199 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
54176155 TTTAGACCCT
54176165 TTTATTTC
1 TTTATTTC
54176173 TTTATTTC
1 TTTATTTC
*
54176181 TTTCTTTC
1 TTTATTTC
*
54176189 TTTCTTTC
1 TTTATTTC
54176197 TTT
1 TTT
54176200 CATCATAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTATTTC
Found at i:54176186 original size:4 final size:4
Alignment explanation
Indices: 54176169--54176200 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
54176159 GACCCTTTTA
*
54176169 TTTC TTTA TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
54176201 ATCATAGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:54187913 original size:29 final size:29
Alignment explanation
Indices: 54187857--54187915 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
54187847 TGGGAAAGAC
* *
54187857 AGAACGTAAAACAAACCCTCGTCCTGACA
1 AGAACGTAAAACAAACCCTAGGCCTGACA
*
54187886 AGAACGTAAAACAAACCCTAGGCTTGACA
1 AGAACGTAAAACAAACCCTAGGCCTGACA
54187915 A
1 A
54187916 CCCTAAGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.14
Consensus pattern (29 bp):
AGAACGTAAAACAAACCCTAGGCCTGACA
Found at i:54190271 original size:37 final size:37
Alignment explanation
Indices: 54190213--54190359 Score: 129
Period size: 37 Copynumber: 3.9 Consensus size: 37
54190203 AGTGCGCTCT
54190213 ATCGAGCCAAATCTTACTGTTATACTGAATGAAG-TTCA
1 ATCGAG-CAAATCTTACTGTTATACTGAATGAAGCTT-A
* * * *
54190251 ATCGAGCAAATCATATTGTTATTCTGAATGGAGCTTA
1 ATCGAGCAAATCTTACTGTTATACTGAATGAAGCTTA
* * * * *
54190288 ATTGAGTAAATCTTACTGTTTTACT-AACTGATGTTTAA
1 ATCGAGCAAATCTTACTGTTATACTGAA-TGAAGCTT-A
* *
54190326 ATCGAACAAAT-TCTACTGTTATACTGAGTGAAGC
1 ATCGAGCAAATCT-TACTGTTATACTGAATGAAGC
54190360 CCAAATGAGT
Statistics
Matches: 84, Mismatches: 20, Indels: 10
0.74 0.18 0.09
Matches are distributed among these distances:
36 2 0.02
37 49 0.58
38 32 0.38
39 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (37 bp):
ATCGAGCAAATCTTACTGTTATACTGAATGAAGCTTA
Found at i:54190369 original size:75 final size:74
Alignment explanation
Indices: 54190221--54190370 Score: 160
Period size: 75 Copynumber: 2.0 Consensus size: 74
54190211 CTATCGAGCC
* * * * * *
54190221 AAATCTTACTGTTATACTGAATGAAGTTCAATCGAGCAAATCATATTGTTATTCTGAATGGAGCT
1 AAATCTTACTGTTATACTGAATGAAGTTAAATCGAACAAATCATACTGTTATACTGAATGAAGCC
* *
54190286 TAATTGAGT
66 CAAATGAGT
* * *
54190295 AAATCTTACTGTTTTACT-AACTGATGTTTAAATCGAACAAATTC-TACTGTTATACTGAGTGAA
1 AAATCTTACTGTTATACTGAA-TGAAG-TTAAATCGAACAAA-TCATACTGTTATACTGAATGAA
54190358 GCCCAAATGAGT
63 GCCCAAATGAGT
54190370 A
1 A
54190371 GAAATATATG
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
73 2 0.03
74 21 0.34
75 37 0.60
76 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (74 bp):
AAATCTTACTGTTATACTGAATGAAGTTAAATCGAACAAATCATACTGTTATACTGAATGAAGCC
CAAATGAGT
Found at i:54191177 original size:25 final size:25
Alignment explanation
Indices: 54191135--54191182 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
54191125 GAGTTACACG
*
54191135 GCCTGGCACACGGACGTGTGACATA
1 GCCTGGCACACAGACGTGTGACATA
54191160 GCCTGGCACACA-AGCGTGTGACA
1 GCCTGGCACACAGA-CGTGTGACA
54191183 CGACCGTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.15
Consensus pattern (25 bp):
GCCTGGCACACAGACGTGTGACATA
Found at i:54191814 original size:5 final size:5
Alignment explanation
Indices: 54191804--54191830 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
54191794 TCACAATTTC
54191804 ATCAT ATCAT ATCAT ATCAT ATCAT AT
1 ATCAT ATCAT ATCAT ATCAT ATCAT AT
54191831 ACATGTTTCA
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:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATCAT
Found at i:54197714 original size:45 final size:41
Alignment explanation
Indices: 54197640--54197721 Score: 94
Period size: 44 Copynumber: 1.9 Consensus size: 41
54197630 TTATATAATG
* *
54197640 AATATTTATATGTTTTGTGTTATTTATATAATATATGCAAAAC
1 AATATTTATATGTTTTGTGTCATATATAT-AT-TATGCAAAAC
54197683 AATATATTATATGATTTT-TGTACATATATATATTATGCA
1 AATAT-TTATATG-TTTTGTGT-CATATATATATTATGCA
54197722 CGAATAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
43 11 0.32
44 12 0.35
45 11 0.32
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.49
Consensus pattern (41 bp):
AATATTTATATGTTTTGTGTCATATATATATTATGCAAAAC
Found at i:54198191 original size:49 final size:49
Alignment explanation
Indices: 54198086--54198201 Score: 119
Period size: 49 Copynumber: 2.4 Consensus size: 49
54198076 CCAATTCACG
** *
54198086 GTGGTTATACGGTCATAGGTTGAAGTATAACCAGGGCTCCTAGTTGATA
1 GTGGTTATACGGTCACGGGTTGAAGTATAACCAGGGCTCCTAGTTGAGA
** * * *
54198135 GCAGTTATGCGGTCACGGGTTGGAGTATAACTCAGGAGC-CC-ATTTGAGA
1 GTGGTTATACGGTCACGGGTTGAAGTATAAC-CAGG-GCTCCTAGTTGAGA
*
54198184 GTGGTTATATGGTCACGG
1 GTGGTTATACGGTCACGG
54198202 TTTTAAGTTT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
49 45 0.85
50 6 0.11
51 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (49 bp):
GTGGTTATACGGTCACGGGTTGAAGTATAACCAGGGCTCCTAGTTGAGA
Found at i:54198845 original size:49 final size:49
Alignment explanation
Indices: 54198725--54198847 Score: 142
Period size: 49 Copynumber: 2.5 Consensus size: 49
54198715 ATGGTATTAA
* * * *
54198725 ACTTGAACCCGTGACTATATAATCACCGTCAACTAGGGACCCGAGTTAT
1 ACTTCAACCCATGACTGTATAACCACCGTCAACTAGGGACCCGAGTTAT
* * *
54198774 ACTTCAACCTATGACTGCATAACCACCGTCAACTA-GGAGCCCTAGTTAT
1 ACTTCAACCCATGACTGTATAACCACCGTCAACTAGGGA-CCCGAGTTAT
*
54198823 ACTTCAACCCCTGA-TCGTATAACCA
1 ACTTCAACCCATGACT-GTATAACCA
54198848 TTGTGAACTG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
48 4 0.06
49 58 0.94
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (49 bp):
ACTTCAACCCATGACTGTATAACCACCGTCAACTAGGGACCCGAGTTAT
Found at i:54199129 original size:52 final size:52
Alignment explanation
Indices: 54199063--54199166 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
54199053 ATATAGAAGA
54199063 TAATTTTTTATTTTGTAAGGGATAGTGGCTGAGAGAATTCATAGATTAGAGG
1 TAATTTTTTATTTTGTAAGGGATAGTGGCTGAGAGAATTCATAGATTAGAGG
54199115 TAATTTTTTATTTTGTAAGGGATAGTGGCTGAGAGAATTCATAGATTAGAGG
1 TAATTTTTTATTTTGTAAGGGATAGTGGCTGAGAGAATTCATAGATTAGAGG
54199167 GGAGCAAAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (52 bp):
TAATTTTTTATTTTGTAAGGGATAGTGGCTGAGAGAATTCATAGATTAGAGG
Found at i:54201799 original size:50 final size:50
Alignment explanation
Indices: 54201692--54201938 Score: 219
Period size: 50 Copynumber: 4.8 Consensus size: 50
54201682 ATTTGGGTAA
* * *
54201692 AGAGATCCCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTAAGACTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGAC-ATG
* * * *
54201748 AGAGGTCTCATGTAAGACCATGTCTGGCACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** * * * *
54201798 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** * * *
54201848 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ACATG
* ** *
54201897 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
54201939 TGTTATTATC
Statistics
Matches: 157, Mismatches: 33, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
49 39 0.25
50 78 0.50
51 2 0.01
55 1 0.01
56 37 0.24
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:54204422 original size:19 final size:18
Alignment explanation
Indices: 54204400--54204442 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54204390 TTTTTCAGGC
*
54204400 CATTTTTATTTTCCTTTTT
1 CATTTTTA-TTTCCATTTT
* *
54204419 CATTTATATTTGCATTTT
1 CATTTTTATTTCCATTTT
54204437 CATTTT
1 CATTTT
54204443 GGAGAAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.16, C:0.14, G:0.02, T:0.67
Consensus pattern (18 bp):
CATTTTTATTTCCATTTT
Found at i:54205246 original size:17 final size:18
Alignment explanation
Indices: 54205224--54205276 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
54205214 ACTTAATCAC
*
54205224 TTTAATATTAA-ATTTAA
1 TTTAATATTAATATTAAA
* *
54205241 TTTAATGTAAATATTAAA
1 TTTAATATTAATATTAAA
*
54205259 TTAAAT-TTAATATTAAA
1 TTTAATATTAATATTAAA
54205276 T
1 T
54205277 CTTATTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 20 0.67
18 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTAATATTAATATTAAA
Found at i:54205325 original size:62 final size:62
Alignment explanation
Indices: 54205248--54205398 Score: 275
Period size: 62 Copynumber: 2.4 Consensus size: 62
54205238 TAATTTAATG
* *
54205248 TAAATATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAGAATGTTTATCTACAAGA
1 TAAACATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAGAATATTTATCTACAAGA
*
54205310 TAAACATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAGATTATTTATCTACAAGA
1 TAAACATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAGAATATTTATCTACAAGA
54205372 TAAACATTAAATTAAATTTAATATTAA
1 TAAACATTAAATTAAATTTAATATTAA
54205399 GATAATCACT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 86 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.40
Consensus pattern (62 bp):
TAAACATTAAATTAAATTTAATATTAAATCTTATTAAAATAATAGAATATTTATCTACAAGA
Found at i:54205424 original size:20 final size:18
Alignment explanation
Indices: 54205377--54205425 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
54205367 CAAGATAAAC
54205377 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
54205394 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
54205414 ATTAAATTAATA
1 ATTAAATTAATA
54205426 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:54205472 original size:38 final size:37
Alignment explanation
Indices: 54205409--54205480 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
54205399 GATAATCACT
54205409 TTAATATTAAATTAATAAAATACTATTAACAATAAGTC
1 TTAATATTAAATTAATAAAATACTATTAA-AATAAGTC
*
54205447 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAA
54205481 TATTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
37 11 0.35
38 18 0.58
39 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (37 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAAGTC
Found at i:54205922 original size:9 final size:9
Alignment explanation
Indices: 54205898--54205937 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
54205888 AAAATATCAT
54205898 ATTAATTTTA
1 ATTAA-TTTA
*
54205908 ATTAATTTG
1 ATTAATTTA
54205917 ATTAATTTA
1 ATTAATTTA
54205926 ATTAATTTA
1 ATTAATTTA
54205935 ATT
1 ATT
54205938 TTACTTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
9 23 0.82
10 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:54235243 original size:4 final size:4
Alignment explanation
Indices: 54235234--54235301 Score: 104
Period size: 4 Copynumber: 17.5 Consensus size: 4
54235224 TTTGAGTTCA
* *
54235234 ATAC ATAC ATAC ATAC --AC ACAC ACAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
54235280 ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC AT
54235302 GATTTGTTAC
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
2 2 0.03
4 59 0.97
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:54237613 original size:4 final size:4
Alignment explanation
Indices: 54237604--54237639 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
54237594 GAAAATAAAC
54237604 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
54237640 TCATTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:54241388 original size:39 final size:39
Alignment explanation
Indices: 54241334--54241412 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
54241324 GGTGAATTAG
*
54241334 ACAAATTAGGCAATTGGGTAGTCTTTGGACAATCTCACC
1 ACAAATTAGGCAATTGGGTAGCCTTTGGACAATCTCACC
54241373 ACAAATTAGGCAATTGGGTAGCCTTTGGACAATCTCACC
1 ACAAATTAGGCAATTGGGTAGCCTTTGGACAATCTCACC
54241412 A
1 A
54241413 ATATATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (39 bp):
ACAAATTAGGCAATTGGGTAGCCTTTGGACAATCTCACC
Found at i:54243276 original size:24 final size:24
Alignment explanation
Indices: 54243249--54243294 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
54243239 AAATAATTAC
54243249 AAATATCAAATA-ATGAGATTAAAT
1 AAATATCAAATATAT-AGATTAAAT
* *
54243273 AAATCTTAAATATATAGATTAA
1 AAATATCAAATATATAGATTAA
54243295 GTCTTAGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (24 bp):
AAATATCAAATATATAGATTAAAT
Found at i:54243763 original size:23 final size:24
Alignment explanation
Indices: 54243715--54243776 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
54243705 AAATTCTTTT
*
54243715 TGTTTTGA-TTAATT-ATGTCATG
1 TGTTTTGATTTAATTAATGTCATA
*
54243737 TGTTTTGATTTAATTAAT-TTATA
1 TGTTTTGATTTAATTAATGTCATA
* *
54243760 TGTTTTTATTTACTTAA
1 TGTTTTGATTTAATTAA
54243777 AGTAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 8 0.24
23 24 0.71
24 2 0.06
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.60
Consensus pattern (24 bp):
TGTTTTGATTTAATTAATGTCATA
Found at i:54244228 original size:21 final size:19
Alignment explanation
Indices: 54244189--54244228 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
54244179 ATTTACTTTT
*
54244189 AATATAATAATTCAAAATA
1 AATATAATAATTAAAAATA
54244208 AATATAATAATATTAAAAATA
1 AATATAAT-A-ATTAAAAATA
54244229 CATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AATATAATAATTAAAAATA
Found at i:54245772 original size:21 final size:21
Alignment explanation
Indices: 54245746--54245788 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
54245736 GGTTCGCTGT
*
54245746 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
54245767 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
54245788 A
1 A
54245789 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:54245788 original size:16 final size:16
Alignment explanation
Indices: 54245769--54245801 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54245759 TGTATTGGAT
*
54245769 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
54245785 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
54245801 T
1 T
54245802 AGCAAATCAA
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:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:54245846 original size:45 final size:44
Alignment explanation
Indices: 54245780--54245874 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
54245770 GGATTAGAGG
* *
54245780 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
54245825 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
54245869 TGTAAT
1 TGTAAT
54245875 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:54246056 original size:18 final size:17
Alignment explanation
Indices: 54246035--54246069 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54246025 TTATTATTAA
*
54246035 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54246053 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54246070 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54253319 original size:4 final size:4
Alignment explanation
Indices: 54253310--54253385 Score: 71
Period size: 4 Copynumber: 19.0 Consensus size: 4
54253300 GCCGGTAAAT
* * * * * * *
54253310 TCTC TCTC TCTC TCTC TCTC TCTC CCCC TCCC TCCC TCCC TCCC TCCC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
* *
54253358 TCCC TCTC TCCC TCTC TCTC TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC
54253386 ATTTTTTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 66 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (4 bp):
TCTC
Found at i:54253327 original size:12 final size:12
Alignment explanation
Indices: 54253311--54253385 Score: 82
Period size: 12 Copynumber: 6.4 Consensus size: 12
54253301 CCGGTAAATT
*
54253311 CTCTCTCTCTCT
1 CTCTCTCTCTCC
54253323 CTCTCTCTCTCC
1 CTCTCTCTCTCC
*
54253335 C-C-CTCCCTCC
1 CTCTCTCTCTCC
* *
54253345 CTCCCTCCCTCC
1 CTCTCTCTCTCC
*
54253357 CTCCCTCTCTCC
1 CTCTCTCTCTCC
*
54253369 CTCTCTCTCTCT
1 CTCTCTCTCTCC
54253381 CTCTC
1 CTCTC
54253386 ATTTTTTTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
10 8 0.14
11 2 0.04
12 46 0.82
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (12 bp):
CTCTCTCTCTCC
Found at i:54253385 original size:8 final size:8
Alignment explanation
Indices: 54253313--54253383 Score: 79
Period size: 8 Copynumber: 8.9 Consensus size: 8
54253303 GGTAAATTCT
*
54253313 CTCTCTCT
1 CTCTCTCC
*
54253321 CTCTCTCT
1 CTCTCTCC
*
54253329 CTCTCCCC
1 CTCTCTCC
*
54253337 CTCCCTCC
1 CTCTCTCC
*
54253345 CTCCCTCC
1 CTCTCTCC
*
54253353 CTCCCTCC
1 CTCTCTCC
54253361 CTCTCTCC
1 CTCTCTCC
*
54253369 CTCTCTCT
1 CTCTCTCC
54253377 CTCTCTC
1 CTCTCTC
54253384 TCATTTTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 57 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (8 bp):
CTCTCTCC
Found at i:54256420 original size:50 final size:50
Alignment explanation
Indices: 54256345--54256443 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
54256335 TGAATTTTTA
54256345 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATATT
1 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATATT
54256395 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATAT
1 TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATAT
54256444 CATAGTTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.45
Consensus pattern (50 bp):
TACTTATAATATGTAGTAGGTTTATTCATTAGCTTCAATAATTAGATATT
Found at i:54256765 original size:12 final size:12
Alignment explanation
Indices: 54256748--54256772 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54256738 AGTAGTAATG
54256748 ATTAATTCTGCT
1 ATTAATTCTGCT
54256760 ATTAATTCTGCT
1 ATTAATTCTGCT
54256772 A
1 A
54256773 CTGTGAAAAT
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
ATTAATTCTGCT
Found at i:54257069 original size:40 final size:40
Alignment explanation
Indices: 54257014--54257095 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
54257004 GCGACTCTAT
54257014 CCTTATTATTCCTAGTAGCTTCGTACATATTGACTTTAAC
1 CCTTATTATTCCTAGTAGCTTCGTACATATTGACTTTAAC
54257054 CCTTATTATTCCTAGTAGCTTCGTACATATTGACTTTAAC
1 CCTTATTATTCCTAGTAGCTTCGTACATATTGACTTTAAC
54257094 CC
1 CC
54257096 GACCACTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (40 bp):
CCTTATTATTCCTAGTAGCTTCGTACATATTGACTTTAAC
Found at i:54261454 original size:10 final size:10
Alignment explanation
Indices: 54261439--54261464 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
54261429 TGGTTATTAA
54261439 GGATGGGTTT
1 GGATGGGTTT
54261449 GGATGGGTTT
1 GGATGGGTTT
54261459 GGATGG
1 GGATGG
54261465 AGGTGGAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.54, T:0.35
Consensus pattern (10 bp):
GGATGGGTTT
Found at i:54268109 original size:18 final size:18
Alignment explanation
Indices: 54268086--54268124 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
54268076 GGATAGATTT
54268086 ATATTTTGTAGATCAAAC
1 ATATTTTGTAGATCAAAC
54268104 ATATTTTGTAGATCAAAC
1 ATATTTTGTAGATCAAAC
54268122 ATA
1 ATA
54268125 ATATTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (18 bp):
ATATTTTGTAGATCAAAC
Found at i:54268353 original size:18 final size:19
Alignment explanation
Indices: 54268316--54268357 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54268306 TATATATAAG
*
54268316 ATATATATTTTTAATATTT
1 ATATATATTTTAAATATTT
54268335 ACTATATA-TTTAAAT-TTT
1 A-TATATATTTTAAATATTT
54268353 ATATA
1 ATATA
54268358 ATATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 4 0.19
19 7 0.33
20 6 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATATTTTAAATATTT
Found at i:54269748 original size:29 final size:27
Alignment explanation
Indices: 54269684--54269748 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 27
54269674 CTTATTTGAC
* *
54269684 CTAATTTGATTCCTATTAATAATAGGA
1 CTAATTTGATTCCAATTAATAAGAGGA
54269711 CTACA-TTGA-TCCAATTAATAGTAGAGGGA
1 CTA-ATTTGATTCCAATTAATA--AGA-GGA
54269740 CTAATTTGA
1 CTAATTTGA
54269749 CAAGTTCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
26 10 0.32
27 7 0.23
28 4 0.13
29 10 0.32
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (27 bp):
CTAATTTGATTCCAATTAATAAGAGGA
Found at i:54270038 original size:17 final size:17
Alignment explanation
Indices: 54270016--54270071 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
54270006 TTAGATTAAT
54270016 TTATATTTTATATATTA
1 TTATATTTTATATATTA
54270033 TTATA--TTA-A-ATTA
1 TTATATTTTATATATTA
* *
54270046 TTTATATCTTATTTATTA
1 -TTATATTTTATATATTA
54270064 TTATATTT
1 TTATATTT
54270072 ATTTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 4 0.12
14 6 0.19
15 3 0.09
16 3 0.09
17 12 0.38
18 4 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATATTTTATATATTA
Found at i:54270052 original size:31 final size:32
Alignment explanation
Indices: 54270005--54270070 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
54269995 ATATAAAAAA
* *
54270005 ATTAGATTAATTTATATTTTATATATTATTAT
1 ATTAAATTAATTTATATCTTATATATTATTAT
*
54270037 ATTAAATT-ATTTATATCTTATTTATTATTAT
1 ATTAAATTAATTTATATCTTATATATTATTAT
54270068 ATT
1 ATT
54270071 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 24 0.77
32 7 0.23
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (32 bp):
ATTAAATTAATTTATATCTTATATATTATTAT
Found at i:54270197 original size:25 final size:24
Alignment explanation
Indices: 54270151--54270197 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
54270141 TATATTTCAT
*
54270151 ATATCATTATATTAAATTATTTAA
1 ATATCATTATATTAAATGATTTAA
* *
54270175 ATATCATATATCTTAACTGATTT
1 ATATCAT-TATATTAAATGATTT
54270198 TTTACTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATCATTATATTAAATGATTTAA
Found at i:54270991 original size:98 final size:98
Alignment explanation
Indices: 54270822--54271013 Score: 384
Period size: 98 Copynumber: 2.0 Consensus size: 98
54270812 GTGTCTTTAG
54270822 TGTAGTTACATTGTCCGTATACTTGTAATTTTTTCAACAAATTGGTCTAATAAAATTCCATCATT
1 TGTAGTTACATTGTCCGTATACTTGTAATTTTTTCAACAAATTGGTCTAATAAAATTCCATCATT
54270887 ATCATTAAATATCTTTTGAATAATGTCTTGAAC
66 ATCATTAAATATCTTTTGAATAATGTCTTGAAC
54270920 TGTAGTTACATTGTCCGTATACTTGTAATTTTTTCAACAAATTGGTCTAATAAAATTCCATCATT
1 TGTAGTTACATTGTCCGTATACTTGTAATTTTTTCAACAAATTGGTCTAATAAAATTCCATCATT
54270985 ATCATTAAATATCTTTTGAATAATGTCTT
66 ATCATTAAATATCTTTTGAATAATGTCTT
54271014 AAACGGTTTT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (98 bp):
TGTAGTTACATTGTCCGTATACTTGTAATTTTTTCAACAAATTGGTCTAATAAAATTCCATCATT
ATCATTAAATATCTTTTGAATAATGTCTTGAAC
Found at i:54277612 original size:2 final size:2
Alignment explanation
Indices: 54277605--54277639 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54277595 CTGATGCTGG
54277605 TC TC TC TC 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 TC TC TC TC T
54277640 TTTACATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:54284724 original size:25 final size:25
Alignment explanation
Indices: 54284645--54284726 Score: 67
Period size: 31 Copynumber: 3.0 Consensus size: 25
54284635 CGTCCTATGT
* * *
54284645 ATCAATTTAACCCTTATACTATTAA
1 ATCAAATTAATCCTTTTACTATTAA
54284670 ATCAAATTAATCTCTCTATTA-TAAAAATTAA
1 ATCAAATTAATC-CT-T-TTACT----ATTAA
54284701 ATCAAATTAATCCTTTTACTATTAA
1 ATCAAATTAATCCTTTTACTATTAA
54284726 A
1 A
54284727 AAAATCAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
25 16 0.35
26 2 0.04
27 2 0.04
28 5 0.11
29 2 0.04
30 2 0.04
31 17 0.37
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (25 bp):
ATCAAATTAATCCTTTTACTATTAA
Found at i:54284730 original size:34 final size:31
Alignment explanation
Indices: 54284665--54284741 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 31
54284655 CCCTTATACT
*
54284665 ATTAAATCAAATTAATCTCTCTATTATAAAA
1 ATTAAATCAAATTAATCTCTCTATTAAAAAA
*
54284696 ATTAAATCAAATTAATCCTTTTACTATTAAAAAA
1 ATTAAATCAAATTAAT-C-TCT-CTATTAAAAAA
* *
54284730 ATCAAATAAAAT
1 ATTAAATCAAAT
54284742 AAAATTGCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 16 0.41
32 1 0.03
33 2 0.05
34 20 0.51
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (31 bp):
ATTAAATCAAATTAATCTCTCTATTAAAAAA
Found at i:54284993 original size:14 final size:14
Alignment explanation
Indices: 54284972--54285013 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
54284962 GTTTGATTGC
54284972 CAGTAAAATATTTT
1 CAGTAAAATATTTT
*
54284986 CCGTAAAATGA-TTT
1 CAGTAAAAT-ATTTT
*
54285000 CAGGAAAATATTTT
1 CAGTAAAATATTTT
54285014 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (14 bp):
CAGTAAAATATTTT
Found at i:54285026 original size:34 final size:35
Alignment explanation
Indices: 54284982--54285048 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54284972 CAGTAAAATA
*
54284982 TTTTCCGTAAAATGATTT-CAGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACAGAAAAATATTTTAC
* *
54285016 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACAGAAAAATATTTT
54285049 CTGTTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACAGAAAAATATTTTAC
Found at i:54285862 original size:2 final size:2
Alignment explanation
Indices: 54285855--54285896 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
54285845 CATAAAACCC
54285855 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
54285897 GGCTCGCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54296980 original size:21 final size:21
Alignment explanation
Indices: 54296941--54296980 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54296931 GCATGTATAT
** *
54296941 ATAATATATTTTTTTATAAAA
1 ATAATATATAATTTAATAAAA
54296962 ATAATATATAATTTAATAA
1 ATAATATATAATTTAATAA
54296981 GAAACTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATATATAATTTAATAAAA
Found at i:54314842 original size:5 final size:5
Alignment explanation
Indices: 54314834--54314869 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
54314824 GTAAACTAAA
54314834 CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC C
1 CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC C
54314870 CAATCGCCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.61, G:0.19, T:0.00
Consensus pattern (5 bp):
CGCAC
Found at i:54315933 original size:25 final size:25
Alignment explanation
Indices: 54315903--54315958 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
54315893 TTTCTAAAAT
54315903 TAAAAT-ATATTAGATA-TATTATTTC
1 TAAAATGAT-TTAGA-ACTATTATTTC
* *
54315928 TAAAATGATTTATAACTTTTATTTC
1 TAAAATGATTTAGAACTATTATTTC
54315953 TAAAAT
1 TAAAAT
54315959 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 24 0.89
26 2 0.07
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (25 bp):
TAAAATGATTTAGAACTATTATTTC
Found at i:54321544 original size:27 final size:26
Alignment explanation
Indices: 54321506--54321563 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
54321496 ACTCTAGTAC
*
54321506 AATTTTAACGATTCTACCCCTCAATAA
1 AATTTTAACGATTATACCCCT-AATAA
* *
54321533 AATTTTGACGATTATACCCCTAGTAA
1 AATTTTAACGATTATACCCCTAATAA
54321559 AATTT
1 AATTT
54321564 CGAGAAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (26 bp):
AATTTTAACGATTATACCCCTAATAA
Found at i:54324231 original size:15 final size:15
Alignment explanation
Indices: 54324213--54324241 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54324203 CAATCAAATC
54324213 CTCTATAATCTCATT
1 CTCTATAATCTCATT
54324228 CTCTATAATCTCAT
1 CTCTATAATCTCAT
54324242 ATGTTCAGTC
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:0.28, G:0.00, T:0.45
Consensus pattern (15 bp):
CTCTATAATCTCATT
Found at i:54325387 original size:30 final size:30
Alignment explanation
Indices: 54325351--54325410 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
54325341 GGGTCCTTGT
54325351 AACCACTGTCACCCATCATAATAAAATTTG
1 AACCACTGTCACCCATCATAATAAAATTTG
*
54325381 AACCACTTTCACCCATCATAATAAAATTTG
1 AACCACTGTCACCCATCATAATAAAATTTG
54325411 TCCACCTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.28
Consensus pattern (30 bp):
AACCACTGTCACCCATCATAATAAAATTTG
Found at i:54326015 original size:31 final size:30
Alignment explanation
Indices: 54325980--54326039 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
54325970 AGAGGTGGGA
*
54325980 TGGGAAAGGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AAGGAATAAAAATTTTAGGGGAAAAG
* * *
54326011 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGAATAAAAATTTTAGGGGAAAA
54326040 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAAGGAATAAAAATTTTAGGGGAAAAG
Found at i:54326267 original size:9 final size:9
Alignment explanation
Indices: 54326253--54326289 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54326243 TATAGTTTGA
54326253 TATTCGAAT
1 TATTCGAAT
54326262 TATTCGAAT
1 TATTCGAAT
*
54326271 TATTCGAGT
1 TATTCGAAT
54326280 TATTCGAAT
1 TATTCGAAT
54326289 T
1 T
54326290 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54335216 original size:38 final size:39
Alignment explanation
Indices: 54335154--54335257 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 39
54335144 TTTTTCTATA
* *
54335154 TTTATGTATATTTTATAAATTTTTTTACGATTTTTATAAAAT
1 TTTATCTATATTTTA-ATA-TTTTTTACGATTTTTAT-AAAT
*
54335196 TTTA-C-AT-TTTTAATAATTTTTTACGATTTTTATAAGT
1 TTTATCTATATTTTAAT-ATTTTTTACGATTTTTATAAAT
54335233 TTTATCTATATTTTAATATTTTTTA
1 TTTATCTATATTTTAATATTTTTTA
54335258 TTAAAATTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
37 7 0.13
38 19 0.35
39 16 0.29
40 9 0.16
42 4 0.07
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (39 bp):
TTTATCTATATTTTAATATTTTTTACGATTTTTATAAAT
Found at i:54335235 original size:19 final size:19
Alignment explanation
Indices: 54335164--54335235 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
54335154 TTTATGTATA
54335164 TTTTATAAATTTTTTTACGAT
1 TTTTATAAA--TTTTTACGAT
*
54335185 TTTTATAAAATTTTAC-AT
1 TTTTATAAATTTTTACGAT
*
54335203 TTTTAATAATTTTTTACGAT
1 TTTT-ATAAATTTTTACGAT
*
54335223 TTTTATAAGTTTT
1 TTTTATAAATTTT
54335236 ATCTATATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.13
19 24 0.53
20 6 0.13
21 9 0.20
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTATAAATTTTTACGAT
Found at i:54340894 original size:21 final size:21
Alignment explanation
Indices: 54340854--54340910 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
54340844 ATTTTGACTT
54340854 TTTTCTCTT-GTTCGGTTTTTTC
1 TTTTCTCTTGGTT--GTTTTTTC
54340876 TTTTCTCTTGGTTGTTTTTTC
1 TTTTCTCTTGGTTGTTTTTTC
54340897 TTTTCTCTTGGTTG
1 TTTTCTCTTGGTTG
54340911 GAAAAACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.65
22 9 0.26
23 3 0.09
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (21 bp):
TTTTCTCTTGGTTGTTTTTTC
Found at i:54341503 original size:29 final size:30
Alignment explanation
Indices: 54341444--54341501 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
54341434 TTCGAGTCTT
*
54341444 GGGGCAAAAATGTAATTATGCAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
54341474 GGGGC-AAAATCGTAAATT-TGAAAAAGTT
1 GGGGCAAAAAT-GT-AATTATGAAAAAGTT
54341502 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 5 0.20
30 16 0.64
31 4 0.16
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:54341730 original size:13 final size:13
Alignment explanation
Indices: 54341712--54341743 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54341702 TTTCCAGCAA
54341712 TTATGAATTTATT
1 TTATGAATTTATT
54341725 TTATGAATTTATT
1 TTATGAATTTATT
*
54341738 TGATGA
1 TTATGA
54341744 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:54341951 original size:50 final size:50
Alignment explanation
Indices: 54341838--54342079 Score: 295
Period size: 50 Copynumber: 4.7 Consensus size: 50
54341828 ATTCGGGTAA
* * * *
54341838 AGAGATCCCATGTAAGACCATGTCTGGGACGTGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
54341894 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
54341944 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
54341994 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
**
54342044 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
54342080 TTTAGCATGT
Statistics
Matches: 167, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
50 94 0.56
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 38 0.23
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:54342022 original size:100 final size:103
Alignment explanation
Indices: 54341838--54342079 Score: 355
Period size: 100 Copynumber: 2.3 Consensus size: 103
54341828 ATTCGGGTAA
*
54341838 AGAGATCCCATGTAAGACCATGTCTGGGACGTGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
54341903 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
* * *
54341944 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
*
54342006 TAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
*
54342044 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGC
54342080 TTTAGCATGT
Statistics
Matches: 126, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
100 52 0.41
101 33 0.26
105 2 0.02
106 39 0.31
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
Found at i:54347433 original size:25 final size:25
Alignment explanation
Indices: 54347405--54347485 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
54347395 ATTCAGGAAT
54347405 GCTCATACGAGCACATA-AACGAGAA
1 GCTCATACGAGC-CATATAACGAGAA
* *
54347430 GCTCTTTCGAGCCATATAACGAGAA
1 GCTCATACGAGCCATATAACGAGAA
**
54347455 GCTCCGGA-GAGCCAT-TAATCGAGAA
1 GCT-CATACGAGCCATATAA-CGAGAA
54347480 GCTCAT
1 GCTCAT
54347486 GAAAGAGCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
24 8 0.17
25 37 0.80
26 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (25 bp):
GCTCATACGAGCCATATAACGAGAA
Found at i:54347499 original size:27 final size:27
Alignment explanation
Indices: 54347462--54347564 Score: 179
Period size: 27 Copynumber: 3.8 Consensus size: 27
54347452 GAAGCTCCGG
* *
54347462 AGAGCCATTAATCGAGAAGCTCATGAA
1 AGAGCCTTTAATCGGGAAGCTCATGAA
54347489 AGAGCCTTTAATCGGGAAGCTCATGAA
1 AGAGCCTTTAATCGGGAAGCTCATGAA
54347516 AGAGCCTTTAATCGGGAAGCTCATGAA
1 AGAGCCTTTAATCGGGAAGCTCATGAA
*
54347543 GGAGCCTTTAATCGGGAAGCTC
1 AGAGCCTTTAATCGGGAAGCTC
54347565 CGAAGAGCCA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (27 bp):
AGAGCCTTTAATCGGGAAGCTCATGAA
Found at i:54354863 original size:30 final size:29
Alignment explanation
Indices: 54354815--54354904 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
54354805 AACTATGTTG
* *
54354815 CTCACATAAGTTGAATTTATATCAAGGTTA
1 CTCACACAAGCTGAATTTATAT-AAGGTTA
* * *
54354845 CTCACACAAGCTGGATTTATGTTAAGGTTT
1 CTCACACAAGCTGAATTTAT-ATAAGGTTA
* *
54354875 CTCACACAAGCTTAATTTATATTAGGTTA
1 CTCACACAAGCTGAATTTATATAAGGTTA
54354904 C
1 C
54354905 CCGTCTAAGT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 7 0.14
30 41 0.84
31 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (29 bp):
CTCACACAAGCTGAATTTATATAAGGTTA
Found at i:54357355 original size:51 final size:49
Alignment explanation
Indices: 54357291--54357386 Score: 120
Period size: 51 Copynumber: 1.9 Consensus size: 49
54357281 ATTTTTCAGG
* *
54357291 TCATTTTCATTTTCATTTTGGAAAAAATCACATTCATTTCCAAATGACT
1 TCATTTTCATTTTCATTTTGGAAAAAACCACAATCATTTCCAAATGACT
* * **
54357340 TCATTTATCCATTTTCGTTTTGGAGAAAACCTTAATCATTTCCAAAT
1 TCATTT-T-CATTTTCATTTTGGAAAAAACCACAATCATTTCCAAAT
54357387 ATTTTATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 6 0.15
50 1 0.03
51 32 0.82
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (49 bp):
TCATTTTCATTTTCATTTTGGAAAAAACCACAATCATTTCCAAATGACT
Found at i:54375942 original size:417 final size:416
Alignment explanation
Indices: 54375168--54376002 Score: 1483
Period size: 417 Copynumber: 2.0 Consensus size: 416
54375158 GCAGTCCAAC
* *
54375168 TAGATTTTAAGTGCCTATTTGGATTTCTAAATGGGATGAAAATAGATTTTAAATTAAATAAATTT
1 TAGATTTTAAGTGCCAATTTGGATTTCTAAATAGGATGAAAATAGATTTTAAATTAAATAAATTT
*
54375233 AATTAATTAAAATTTTTAAACCTAAACCTTAACTGAAAAAATTGTTCATCTCCTCTTTTTAATTT
66 AATTAATTAAAATTTTTAAACCTAAACCTTAACTGAAAAAACTGTTCATCTCCTCTTTTTAATTT
*
54375298 TTCTCCGTCTCTTCTTTTTTTAGGTTTTTTTTTCATTTGACTGGAAAAACTATTATTAAGATCAA
131 TTCTCCGTCTCTTCTTTTTTTAGGTTTTTTTTTCATTTGACTGAAAAAACTATTATTAAGATCAA
* *
54375363 AATAGTTGAAATCAAATTGACTGCTTCATAAAGTTGGATTCAATGGAGAGTTCAGGTATGTCTTC
196 AATAGTTGAAATCAAATTGACTGCTTCATAAAGATGGATTCAATAGAGAGTTCAGGTATGTCTTC
54375428 TTTGCATTCCTCTGTCTCTTTTATTCAATACTGAAAAACAAAAGATTGAATTTTTTATTGTTTAA
261 TTTGCATTCCTCTGTCTCTTTTATTCAATACTGAAAAACAAAAGATTGAATTTTTTATTGTTTAA
* * *
54375493 TGAAAACCCTAAATTAAAATTCTTGATATTTTCTTCAACTTTTTGAAATTGTTTGTGAACATGTA
326 AGAAAACCCTAAATTAAAATTCTTAATATTTTCTTCAACTTTTT-AAATTGTTCGTGAACATGTA
*
54375558 TTTTATTTTGCGTCGGTAGACATCCCA
390 TTTTATTTTGCGTCAGTAGACATCCCA
*
54375585 TAGATTTTAAGTGTCAATTTGGATTTCTAAATAGGATGAAAATAGATTTTAAATTAAATAAATTT
1 TAGATTTTAAGTGCCAATTTGGATTTCTAAATAGGATGAAAATAGATTTTAAATTAAATAAATTT
*
54375650 AATTAATTAAAATTTTTAAACCTAAACCTTAACTGAAAAAACTGTTTATCTCCTCTTTTTAATTT
66 AATTAATTAAAATTTTTAAACCTAAACCTTAACTGAAAAAACTGTTCATCTCCTCTTTTTAATTT
* *
54375715 TTCTTCGTCTCTTC-TTTTTTAGGTTTTTTTTTTCATTTGACTGAAAAAATTATTATTAAGATCA
131 TTCTCCGTCTCTTCTTTTTTTAGG-TTTTTTTTTCATTTGACTGAAAAAACTATTATTAAGATCA
*
54375779 AAATAGTTGAAATCAAATTGACTGCTTCATAAAGATGGGTTCAATAGAGAGTTCAGGTATGTCTT
195 AAATAGTTGAAATCAAATTGACTGCTTCATAAAGATGGATTCAATAGAGAGTTCAGGTATGTCTT
* *
54375844 CTTTGTATTCCTCTGTCTTTTTTATTCAATACTGAAAAACAAAAGATTGAATTTTTTATTGTTTA
260 CTTTGCATTCCTCTGTCTCTTTTATTCAATACTGAAAAACAAAAGATTGAATTTTTTATTGTTTA
*
54375909 AAGAAAACCCTAAATTAAAATTCTTAATATTTTCTTCGACTTTTTAAATTGTTCGTGAACATGTA
325 AAGAAAACCCTAAATTAAAATTCTTAATATTTTCTTCAACTTTTTAAATTGTTCGTGAACATGTA
54375974 TTTTATTTTGCGTCAGTAGACATCCCA
390 TTTTATTTTGCGTCAGTAGACATCCCA
54376001 TA
1 TA
54376003 AAATGCAACT
Statistics
Matches: 399, Mismatches: 18, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
416 56 0.14
417 343 0.86
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (416 bp):
TAGATTTTAAGTGCCAATTTGGATTTCTAAATAGGATGAAAATAGATTTTAAATTAAATAAATTT
AATTAATTAAAATTTTTAAACCTAAACCTTAACTGAAAAAACTGTTCATCTCCTCTTTTTAATTT
TTCTCCGTCTCTTCTTTTTTTAGGTTTTTTTTTCATTTGACTGAAAAAACTATTATTAAGATCAA
AATAGTTGAAATCAAATTGACTGCTTCATAAAGATGGATTCAATAGAGAGTTCAGGTATGTCTTC
TTTGCATTCCTCTGTCTCTTTTATTCAATACTGAAAAACAAAAGATTGAATTTTTTATTGTTTAA
AGAAAACCCTAAATTAAAATTCTTAATATTTTCTTCAACTTTTTAAATTGTTCGTGAACATGTAT
TTTATTTTGCGTCAGTAGACATCCCA
Found at i:54381637 original size:21 final size:22
Alignment explanation
Indices: 54381613--54381663 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
54381603 ATTTATCATG
54381613 AAATTAAAT-AAATT-ATACAAT
1 AAATTAAATAAAATTAATA-AAT
*
54381634 AAATCAAATAAAATTAATAAAT
1 AAATTAAATAAAATTAATAAAT
54381656 -AATTAAAT
1 AAATTAAAT
54381664 TATATAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 15 0.58
22 8 0.31
23 3 0.12
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATTAAATAAAATTAATAAAT
Found at i:54382739 original size:28 final size:28
Alignment explanation
Indices: 54382674--54382741 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
54382664 ACGTTCAAAC
* *
54382674 TTACATTTTT-GTCATTTTCGTCTACCAT
1 TTAC-TTTTTGGTCATTTTCATCCACCAT
*
54382702 TTTCTTTTTGGTCATTTTCATCCACCA-
1 TTACTTTTTGGTCATTTTCATCCACCAT
54382729 TTACTTGTTTGGT
1 TTACTT-TTTGGT
54382742 TTTCATCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 10 0.29
28 24 0.71
ACGTcount: A:0.15, C:0.21, G:0.10, T:0.54
Consensus pattern (28 bp):
TTACTTTTTGGTCATTTTCATCCACCAT
Found at i:54382880 original size:37 final size:38
Alignment explanation
Indices: 54382839--54382957 Score: 132
Period size: 37 Copynumber: 3.1 Consensus size: 38
54382829 ATTTCTTTTG
*
54382839 TTAGAGAAAAGCCCCTCTATTTTTAAATA-ATATTATT
1 TTAGAGAAAAGCCCCTCTATTTTAAAATATATATTATT
* ** * *
54382876 TTAGAGAAAAACCATTCTATTTAAAAAATATATTATTTTTT
1 TTAGAGAAAAGCCCCTCTATTT-TAAAATATA-TA-TTATT
*
54382917 GTTAGAGAAAAGCCCCTCTATTTTAAAATATATATTGTT
1 -TTAGAGAAAAGCCCCTCTATTTTAAAATATATATTATT
54382956 TT
1 TT
54382958 TTTATTTGAG
Statistics
Matches: 66, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
37 19 0.29
38 7 0.11
39 5 0.08
40 4 0.06
41 12 0.18
42 19 0.29
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (38 bp):
TTAGAGAAAAGCCCCTCTATTTTAAAATATATATTATT
Found at i:54382977 original size:44 final size:43
Alignment explanation
Indices: 54382797--54383001 Score: 190
Period size: 44 Copynumber: 4.8 Consensus size: 43
54382787 TAAAAAGTAT
* * * *
54382797 GAGAAAACCCCCTCTATTTAAAAAAAAATATTATTTCTTTTGTTA
1 GAGAAAAACCCCTCTATTTTAAAAAATATATTA-TT-TTTTATTA
* * *
54382842 GAGAAAAGCCCCTCTATTTT--TAAATA-A-TA-TTATT-TTA
1 GAGAAAAACCCCTCTATTTTAAAAAATATATTATTTTTTATTA
** *
54382879 GAGAAAAACCATTCTA-TTTAAAAAATATATTATTTTTTGTTA
1 GAGAAAAACCCCTCTATTTTAAAAAATATATTATTTTTTATTA
* * * *
54382921 GAGAAAAGCCCCTCTATTTTAAAATATATATTGTTTTTTTATTT
1 GAGAAAAACCCCTCTATTTTAAAAAATATATT-ATTTTTTATTA
54382965 GAGAAAAACCCCTCTATTTTAAAAAATGTATATTATT
1 GAGAAAAACCCCTCTATTTTAAAAAA--TATATTATT
54383002 ATGAGTCAAC
Statistics
Matches: 130, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
36 3 0.02
37 16 0.12
38 8 0.06
39 2 0.02
40 2 0.02
41 6 0.05
42 17 0.13
43 18 0.14
44 32 0.25
45 20 0.15
46 6 0.05
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (43 bp):
GAGAAAAACCCCTCTATTTTAAAAAATATATTATTTTTTATTA
Found at i:54384795 original size:20 final size:20
Alignment explanation
Indices: 54384772--54384815 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
54384762 AATAAAGTAG
54384772 AAGCAACTCAAAG-ACAAAAA
1 AAGCAA-TCAAAGAACAAAAA
* *
54384792 AAGCAATGAGAGAACAAAAA
1 AAGCAATCAAAGAACAAAAA
54384812 AAGC
1 AAGC
54384816 CACAAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.64, C:0.16, G:0.16, T:0.05
Consensus pattern (20 bp):
AAGCAATCAAAGAACAAAAA
Found at i:54398568 original size:15 final size:15
Alignment explanation
Indices: 54398544--54398595 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
54398534 TATTTACAAA
*
54398544 ATAAAAATAAGGTAT
1 ATAAAAATAAAGTAT
*
54398559 ATAAAGATAAAGTAT
1 ATAAAAATAAAGTAT
*
54398574 ATATAAAA-AAA-TAA
1 ATA-AAAATAAAGTAT
54398588 ATAAAAAT
1 ATAAAAAT
54398596 GTTTGCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 5 0.16
15 19 0.61
16 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (15 bp):
ATAAAAATAAAGTAT
Found at i:54400060 original size:24 final size:25
Alignment explanation
Indices: 54400033--54400091 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
54400023 CTTTGGTAGT
54400033 TTGGG-TTGATGGGGCT-TTTGGGTA
1 TTGGGTTTG-TGGGGCTGTTTGGGTA
*
54400057 TTGGGTTTGTTGGGCTGTTTGGGTA
1 TTGGGTTTGTGGGGCTGTTTGGGTA
*
54400082 TTGAGTTTGT
1 TTGGGTTTGT
54400092 AAAAAATTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.07, C:0.03, G:0.42, T:0.47
Consensus pattern (25 bp):
TTGGGTTTGTGGGGCTGTTTGGGTA
Found at i:54400070 original size:25 final size:25
Alignment explanation
Indices: 54400044--54400091 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
54400034 TGGGTTGATG
54400044 GGGCT-TTTGGGTATTGGGTTTGTT
1 GGGCTGTTTGGGTATTGGGTTTGTT
*
54400068 GGGCTGTTTGGGTATTGAGTTTGT
1 GGGCTGTTTGGGTATTGGGTTTGT
54400092 AAAAAATTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.06, C:0.04, G:0.42, T:0.48
Consensus pattern (25 bp):
GGGCTGTTTGGGTATTGGGTTTGTT
Found at i:54402776 original size:7 final size:7
Alignment explanation
Indices: 54402766--54402790 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54402756 TCGCTCCGGG
54402766 CTCCTCT
1 CTCCTCT
54402773 CTCCTCT
1 CTCCTCT
54402780 CTCCTCT
1 CTCCTCT
54402787 CTCC
1 CTCC
54402791 CTTTTCTTTT
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:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (7 bp):
CTCCTCT
Found at i:54403439 original size:3 final size:3
Alignment explanation
Indices: 54403431--54403463 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
54403421 TATTCCAATG
54403431 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54403464 GTTTGTGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54403569 original size:19 final size:20
Alignment explanation
Indices: 54403523--54403574 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
54403513 ACTTATACAT
* *
54403523 ACTTAAATATATTTTTTTAC
1 ACTTACATATATTTTTATAC
*
54403543 A-TTTCATA-ATTTTTATAC
1 ACTTACATATATTTTTATAC
54403561 ACTTACATATATTT
1 ACTTACATATATTT
54403575 ATGCATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 10 0.38
19 11 0.42
20 5 0.19
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.54
Consensus pattern (20 bp):
ACTTACATATATTTTTATAC
Found at i:54404249 original size:106 final size:106
Alignment explanation
Indices: 54404057--54404257 Score: 348
Period size: 106 Copynumber: 1.9 Consensus size: 106
54404047 AAAATTTTTC
54404057 TAAATAAGGCAATATTTCACGTTTAGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCACGTTTAGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
* *
54404122 TTCTTGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
66 TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
* * *
54404163 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCACGTTTAGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
54404228 TTCTCGTTCGACTAAACAGCCAAATATCCT
66 TTCTCGTTCGACCAAACAGCCAAATATCCT
54404258 CTTAAAGCTT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 89 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (106 bp):
TAAATAAGGCAATATTTCACGTTTAGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
Found at i:54405193 original size:19 final size:19
Alignment explanation
Indices: 54405171--54405214 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
54405161 AAATATCTTA
*
54405171 AATTTTCAAAGTTATTTTG
1 AATTTTCAAAATTATTTTG
*
54405190 AATTTTTGAAAATTATTTTG
1 AA-TTTTCAAAATTATTTTG
54405210 -ATTTT
1 AATTTT
54405215 TTTTGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 3 0.14
20 15 0.68
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
AATTTTCAAAATTATTTTG
Done.