Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 82 of 190
Found at i:23724388 original size:14 final size:14
Alignment explanation
Indices: 23724369--23724399 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23724359 TTTGGTTATA
*
23724369 ATTGGACTTTGGAC
1 ATTGGACATTGGAC
23724383 ATTGGACATTGGAC
1 ATTGGACATTGGAC
23724397 ATT
1 ATT
23724400 TTGATTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (14 bp):
ATTGGACATTGGAC
Found at i:23729165 original size:24 final size:21
Alignment explanation
Indices: 23729136--23729180 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 21
23729126 ACTTATTAAG
23729136 TTAAATATTAGATTAAATTTAATA
1 TTAAATATT--ATTAAA-TTAATA
23729160 TTAAATATTATTAAATTAATA
1 TTAAATATTATTAAATTAATA
23729181 GAATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
24 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAAATATTATTAAATTAATA
Found at i:23744140 original size:25 final size:24
Alignment explanation
Indices: 23744076--23744169 Score: 62
Period size: 25 Copynumber: 3.8 Consensus size: 24
23744066 ATGTAATCGG
* *
23744076 GAAGCTCTTTCGAGCCATATAATA
1 GAAGCTCTTACGAGCCATATAAAA
* * **
23744100 GAAAGCTCATATGAGCTGTATAACAA
1 G-AAGCTCTTACGAGCCATATAA-AA
* ***
23744126 GAAGCTCTTACGAGCCAAATATCGG
1 GAAGCTCTTACGAGCCATATA-AAA
*
23744151 GAAGCTCATACGAGCCATA
1 GAAGCTCTTACGAGCCATA
23744170 AACGAGAAGC
Statistics
Matches: 51, Mismatches: 16, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
24 1 0.02
25 48 0.94
26 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (24 bp):
GAAGCTCTTACGAGCCATATAAAA
Found at i:23746440 original size:41 final size:41
Alignment explanation
Indices: 23746383--23746492 Score: 184
Period size: 41 Copynumber: 2.7 Consensus size: 41
23746373 TAGCAACCCC
*
23746383 TCGGGAAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
* * *
23746424 TCGGGGAATTTGCACTTAGCAACCCTTTTTTTATCAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
23746465 TCGGGGAATCTGCACTTAGCAACCCCTT
1 TCGGGGAATCTGCACTTAGCAACCCCTT
23746493 ACATTCAATG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (41 bp):
TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
Found at i:23746583 original size:19 final size:20
Alignment explanation
Indices: 23746534--23746584 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
23746524 TTCAATCTGG
* *
23746534 AACCTTATTTTACAACATTT
1 AACCATATTTTTCAACATTT
*
23746554 TACCA-ACTTTTTCAA-ATTT
1 AACCATA-TTTTTCAACATTT
23746573 AACCATATTTTT
1 AACCATATTTTT
23746585 TGTAATTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (20 bp):
AACCATATTTTTCAACATTT
Found at i:23755087 original size:4 final size:4
Alignment explanation
Indices: 23755078--23755104 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
23755068 AAGTTTTATT
23755078 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
23755105 TTACTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:23755123 original size:26 final size:26
Alignment explanation
Indices: 23755072--23755124 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
23755062 GTTGTAAAGT
* *
23755072 TTTATTTTTATTTATTTATTTATTTA
1 TTTATTTTTACTTATTTAATTATTTA
23755098 TTTATTTTTACTTAGTTTAATT-TTTA
1 TTTATTTTTACTTA-TTTAATTATTTA
23755124 T
1 T
23755125 GTAAATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTATTTTTACTTATTTAATTATTTA
Found at i:23758843 original size:18 final size:19
Alignment explanation
Indices: 23758820--23758868 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
23758810 AAGTTTTATT
*
23758820 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
23758838 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
23758857 TTTAATTTTTAT
1 TTT-ATTTTTAT
23758869 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:23758848 original size:22 final size:22
Alignment explanation
Indices: 23758811--23758868 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
23758801 CAAGTTGTAA
* *
23758811 AGTTTTATTTTTATTTTTATTT
1 AGTTTAATTTTTATTTTTACTT
*
23758833 A-TTTATTTATTTATTTTTACTT
1 AGTTTAATT-TTTATTTTTACTT
23758855 AGTTTAATTTTTAT
1 AGTTTAATTTTTAT
23758869 GTAAATATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 19 0.63
23 6 0.20
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (22 bp):
AGTTTAATTTTTATTTTTACTT
Found at i:23759877 original size:16 final size:15
Alignment explanation
Indices: 23759856--23759895 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 15
23759846 TTGGTGCTTT
23759856 TGCTATATGTATATTA
1 TGCTATATGTATA-TA
23759872 TGCTATATGTATATA
1 TGCTATATGTATATA
23759887 TGCATATAT
1 TGC-TATAT
23759896 ATCAATCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (15 bp):
TGCTATATGTATATA
Found at i:23760554 original size:15 final size:15
Alignment explanation
Indices: 23760534--23760563 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23760524 TGTTGTCAAC
23760534 GTTTGATTGCTACAA
1 GTTTGATTGCTACAA
23760549 GTTTGATTGCTACAA
1 GTTTGATTGCTACAA
23760564 CAAGAGTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
GTTTGATTGCTACAA
Found at i:23762380 original size:61 final size:61
Alignment explanation
Indices: 23762283--23762405 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 61
23762273 TTAACAACTT
* *
23762283 ACTTAATTTCACGATCGGACAATCTAAATGATTCGAATCAACAATGAACCGAGTTCCTATC
1 ACTTAATTTCACGATCGGACAATCTAAACGACTCGAATCAACAATGAACCGAGTTCCTATC
* * * *
23762344 ACTTAATTTCATGATCGGGCAATCTAAACGACTCGAATCAACACTGAACCGAGTTCGTATC
1 ACTTAATTTCACGATCGGACAATCTAAACGACTCGAATCAACAATGAACCGAGTTCCTATC
23762405 A
1 A
23762406 TTTGGTATCA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (61 bp):
ACTTAATTTCACGATCGGACAATCTAAACGACTCGAATCAACAATGAACCGAGTTCCTATC
Found at i:23763000 original size:46 final size:49
Alignment explanation
Indices: 23762913--23763008 Score: 135
Period size: 51 Copynumber: 2.0 Consensus size: 49
23762903 GTTTAGTTAT
* *
23762913 ATTAGTTTAATTAATTAAGTTGTTTTTTAAGTTTCTTTAGTTGCTTAAATC
1 ATTAGGTTAATGAATTAAGTTGTTTTTTAA--TTCTTTAGTTGCTTAAATC
23762964 ATTAGGTTAATGAATTAAGTTG-TTTTTAA-T-TTTAGTTGCTTAAAT
1 ATTAGGTTAATGAATTAAGTTGTTTTTTAATTCTTTAGTTGCTTAAAT
23763009 AATTTTGGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
46 15 0.35
47 1 0.02
50 7 0.16
51 20 0.47
ACGTcount: A:0.29, C:0.04, G:0.14, T:0.53
Consensus pattern (49 bp):
ATTAGGTTAATGAATTAAGTTGTTTTTTAATTCTTTAGTTGCTTAAATC
Found at i:23765256 original size:43 final size:43
Alignment explanation
Indices: 23765207--23765290 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
23765197 AAGAAAGCAC
23765207 GCATGGGACGACATT-AAAGGAGCTGTTGATTTCTCCTTTTCAT
1 GCATGGGACGACATTAAAAGGAGCTGTTGATTTCT-CTTTTCAT
* *
23765250 GCATGGGGCGACATTAAAAGGAGCTGTTGTTTTCTCTTTTC
1 GCATGGGACGACATTAAAAGGAGCTGTTGATTTCTCTTTTC
23765291 CATGTGCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 20 0.53
44 18 0.47
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (43 bp):
GCATGGGACGACATTAAAAGGAGCTGTTGATTTCTCTTTTCAT
Found at i:23765563 original size:21 final size:21
Alignment explanation
Indices: 23765539--23765583 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
23765529 TTTCCAACCA
23765539 GCTATGAAAA-CATTCACATTT
1 GCTA-GAAAATCATTCACATTT
23765560 GCTAGAAAATTCCATTCACATTT
1 GCTAGAAAA-T-CATTCACATTT
23765583 G
1 G
23765584 TGCCCATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
23 12 0.57
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (21 bp):
GCTAGAAAATCATTCACATTT
Found at i:23771930 original size:21 final size:22
Alignment explanation
Indices: 23771901--23771951 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
23771891 TCTCTCTCGC
*
23771901 TTTCCTTTTCACCTTTTTCA-T
1 TTTCATTTTCACCTTTTTCACT
**
23771922 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCACCTTTTTCACT
23771944 TTT-ATTTT
1 TTTCATTTT
23771952 TCTCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCACCTTTTTCACT
Found at i:23777309 original size:561 final size:561
Alignment explanation
Indices: 23774480--23777540 Score: 5410
Period size: 560 Copynumber: 5.5 Consensus size: 561
23774470 TAAAAAAACA
* * * * *
23774480 ACCAAAATTGGTTCCTTAATGCTCGTAACTAAGATCCAATGCGCCTTAGCTACAATATTCGGTTT
1 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTGCAAGATTCGGTTT
*
23774545 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCACTCAAAACAG
66 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
* * *
23774610 CAAAATTGGACCAAGATTCAGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAGTATTGATTTTCT
131 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
23774675 TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
196 TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
*
23774740 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCCAAAAAAAAACCTAATTACTA
261 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
23774805 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAA---------TGGGCTGAATTTTTTTACATAGGA
326 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTACATAGGA
23774861 ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
391 ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
* *
23774926 CAATTTGGCCTGATTTTCAACTAAGTTTAAATTAAATTTCCTGATTGGGCTTGGAACGTCTTATT
456 CAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAATTTCCTGATTGGGCTTGGAACGTCTTATT
* *
23774991 GGGCCTTGCCTTCAAGAACTTGGGCTTGTAATCCATTTTCT
521 GGGCCTTGCCTTCAAGAACTTGGGCTTGTAATTCGTTTTCT
* * * *
23775032 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGGTCCAATGCGCCTTAGCTACAGGACTCGGTTT
1 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTGCAAGATTCGGTTT
*
23775097 CTTGGACCAAGATTTCCAAGAATTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
66 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
* * *
23775162 AAAAAATGGACTAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
131 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
* * * *
23775227 TTTTCCTTCGTATACACAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCAATTTACTTTTGA
196 TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
23775292 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCT-AAAAAAAACCTAATTACTA
261 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
23775356 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTACATAGGA
326 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTACATAGGA
23775421 ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
391 ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
* * *
23775486 CAATTTGGCCTGATTTTCAACTAAGTCTAATTTATATTTCCTGATTGGGCTTGGAACATTTTATT
456 CAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAATTTCCTGATTGGGCTTGGAACGTCTTATT
*
23775551 GGGCCTTGCCTTCAAGAACTTAGGCTTGTAA-TCTGTTTTCT
521 GGGCCTTGCCTTCAAGAACTTGGGCTTGTAATTC-GTTTTCT
* *
23775592 ACCAAAATTGGTCCGTTGATGCTCGTAACTGAGATCCAATGTGCCTTAGCTGCAAGATTCGGTTT
1 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTGCAAGATTCGGTTT
*
23775657 CTTGGACCAAGAATTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
66 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
*
23775722 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCCTGATTTTCT
131 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
23775787 TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
196 TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
*
23775852 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAAACCTAATTAAT
261 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCT-AAAAAAAAACCTAATTACT
*
23775917 AATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGGATTTTTTTACATAGG
325 AATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTACATAGG
*
23775982 AATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACCTTG
390 AATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTG
23776047 ACAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAATTTCCTGATTGGGCTTGGAACGTCTTAT
455 ACAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAATTTCCTGATTGGGCTTGGAACGTCTTAT
23776112 TGGGCCTTGCCTTCAAGAACTTGGGCTTGTAATTCGTTTTCT
520 TGGGCCTTGCCTTCAAGAACTTGGGCTTGTAATTCGTTTTCT
*
23776154 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTGCAGGATTCGGTTT
1 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTGCAAGATTCGGTTT
* * *
23776219 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCACTAAAAATAG
66 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
* *
23776284 TAAAACTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
131 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
*
23776349 TTTTCCTTCGTTTACGCAACTAATGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
196 TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
*
23776414 ACGTATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCT-AAAAAAAACCTAATTACTA
261 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
*
23776478 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTGTTACATAGGA
326 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTACATAGGA
*
23776543 ATTAAATCATAAAGTTTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
391 ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
23776608 CAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAATTTCCTGATTGGGCTTGGAACGTCTTATT
456 CAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAATTTCCTGATTGGGCTTGGAACGTCTTATT
23776673 GGGCCTTGCCTTCAAGAACTTGGGCTTGTAA-TCTGTTTTCT
521 GGGCCTTGCCTTCAAGAACTTGGGCTTGTAATTC-GTTTTCT
* * *
23776714 ACAAAAATAGGTTCGTTGATGCTCGTAACTGAGATCGAATGCGCCTTAGCTGCAAGATTCGGTTT
1 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTGCAAGATTCGGTTT
* *
23776779 CTTGGACCAAGATTTCCAATATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAACCAG
66 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
* *
23776844 CAAAATTGGACCAAGATTCGATTTCTTGATTTTCTTGAATACAAGAAAGTGAATCTTGATTTTCT
131 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
* *
23776909 TTTTCCTTCGTTTAGGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCTATTTAGTTTTGA
196 TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
*
23776974 ACGTATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
261 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
*
23777039 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGAGCTGCTTGGGCTGAATTTTTTTACATAGGA
326 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTACATAGGA
23777104 ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
391 ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
* *
23777169 CAATTTGGCCTGATTTTCAACTAAGTTTAATTTAAGTTTCCTGATTGGGCTTGGAACGTCTTATT
456 CAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAATTTCCTGATTGGGCTTGGAACGTCTTATT
*
23777234 GGGCCTTGCCTTCAAAAACTTGGGCTTGTAATTCGTTTTCT
521 GGGCCTTGCCTTCAAGAACTTGGGCTTGTAATTCGTTTTCT
*
23777275 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCAGCAAGATTCGGTTT
1 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTGCAAGATTCGGTTT
*
23777340 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATTGCTCAAAACAG
66 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
23777405 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
131 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
** *
23777470 TTTTCCTTCGTACACGCAACTAAGGTCTTGCTAATAAATTCGTGAATGGTTCCATTTAGTTTTGA
196 TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
23777535 ACGCAT
261 ACGCAT
23777541 TTGCCTAGCC
Statistics
Matches: 2388, Mismatches: 105, Indels: 23
0.95 0.04 0.01
Matches are distributed among these distances:
551 51 0.02
552 285 0.12
559 3 0.00
560 1010 0.42
561 497 0.21
562 540 0.23
563 2 0.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (561 bp):
ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTGCAAGATTCGGTTT
CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTACATAGGA
ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
CAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAATTTCCTGATTGGGCTTGGAACGTCTTATT
GGGCCTTGCCTTCAAGAACTTGGGCTTGTAATTCGTTTTCT
Found at i:23788017 original size:6 final size:6
Alignment explanation
Indices: 23788006--23788045 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
23787996 AAAAAAGAAA
* * *
23788006 AAAATC ATAATC AAAATC ATAATC AAAATC AAAAAC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
23788046 AGAAGAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:23788045 original size:12 final size:12
Alignment explanation
Indices: 23788006--23788036 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
23787996 AAAAAAGAAA
23788006 AAAATCATAATC
1 AAAATCATAATC
23788018 AAAATCATAATC
1 AAAATCATAATC
23788030 AAAATCA
1 AAAATCA
23788037 AAAACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATCATAATC
Found at i:23790313 original size:6 final size:7
Alignment explanation
Indices: 23790287--23790336 Score: 59
Period size: 8 Copynumber: 7.0 Consensus size: 7
23790277 TGAGTCAGAA
23790287 AAAATATG
1 AAAA-ATG
23790295 AAAAATG
1 AAAAATG
23790302 AAAAAATG
1 -AAAAATG
23790310 AAAAA-G
1 AAAAATG
23790316 AAAAATG
1 AAAAATG
23790323 -AAAATG
1 AAAAATG
23790329 TAAAAATG
1 -AAAAATG
23790337 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 12 0.32
7 9 0.24
8 17 0.45
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (7 bp):
AAAAATG
Found at i:23790318 original size:14 final size:14
Alignment explanation
Indices: 23790286--23790336 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
23790276 TTGAGTCAGA
23790286 AAAAATATGAAAAATG
1 AAAAA-ATGAAAAA-G
23790302 AAAAAATGAAAAAG
1 AAAAAATGAAAAAG
*
23790316 -AAAAATGAAAATG
1 AAAAAATGAAAAAG
*
23790329 TAAAAATG
1 AAAAAATG
23790337 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 12 0.36
14 8 0.24
15 8 0.24
16 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.16
Consensus pattern (14 bp):
AAAAAATGAAAAAG
Found at i:23791842 original size:128 final size:127
Alignment explanation
Indices: 23791570--23791807 Score: 343
Period size: 128 Copynumber: 1.9 Consensus size: 127
23791560 AACAGATCAG
* *
23791570 TGAATATAACAGATCTGGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACGACGAATCTTATCT
1 TGAA-ATAATAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACGACGAATCTTATCT
* * * *
23791635 TCAAGTTTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGTCAGTAGTGGAGTAGGT
65 TCAAGTGTAAGGAAGCAGATTGAAGCCACAAGTCCTATCTCCCTAGTCAGTAGTGGAGTAGGT
* * **
23791698 TGGAAATTATAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGTGAATCTTATCT
1 T-GAAATAATAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACGACGAATCTTATCT
*
23791763 TCAAGTGTAAGGAAGCAGATTGAAGCCGATAA-TCCTATCTCCCTA
65 TCAAGTGTAAGGAAGCAGATTGAAGCC-ACAAGTCCTATCTCCCTA
23791808 AAGTTGTAGT
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
128 91 0.94
129 6 0.06
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (127 bp):
TGAAATAATAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACGACGAATCTTATCTT
CAAGTGTAAGGAAGCAGATTGAAGCCACAAGTCCTATCTCCCTAGTCAGTAGTGGAGTAGGT
Found at i:23792036 original size:44 final size:44
Alignment explanation
Indices: 23791776--23792305 Score: 266
Period size: 44 Copynumber: 12.2 Consensus size: 44
23791766 AGTGTAAGGA
* * * *
23791776 AGCAGATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * **
23791820 AGCGGATTAAAGTA--ATAGATCTTATCTCTCTGATGTTGCAGCAG
1 AGCAGATTGAAG-ACGATA-ATCTTATCTCCCTGAAGTTGCAGTGG
** * * * ** * *
23791864 AGTGGATCGCA-TC-A-GGTCTTTTCTCCCTGAAGTTGCAGCGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
* * ** *
23791905 AGCAGACTG-AGTAAGCA-GGTCTTATCCCCCTGAAGTTGCAGTGG
1 AGCAGATTGAAG-ACG-ATAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * **
23791949 GGCAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTATAGTGG
1 AGCAGATTGAAGACGA-TAATCTTATCTCCCTGAAGTTGCAGTGG
* * *
23791994 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
23792038 AG-AGGATTAAAGTA--ATAGATCTTATCTCTCTGAAGTTCCAGTAG
1 AGCA-GATTGAAG-ACGATA-ATCTTATCTCCCTGAAGTTGCAGTGG
** * * * ** * *
23792082 AGTGGATCGCA-TC-A-GGTCTTATCTCCCTGAGGTTGTAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
** * * **
23792123 AGCAGATTG-AGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGG
1 AGCAGATTGAAGACGATAA-TCTTATCTCCCTGAAGTTGCAGTGG
* * * *
23792167 GGCAGACTGAAGAAGCA-AATCTTATCTCCCTGAGGTTGCAGTGG
1 AGCAGATTGAAGACG-ATAATCTTATCTCCCTGAAGTTGCAGTGG
* * *
23792211 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAGGTTGCAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
23792255 AGCGGATTAAAGTA--ATAGATCTTATCTCTCTGAAGTTGCAGTAG
1 AGCAGATTGAAG-ACGATA-ATCTTATCTCCCTGAAGTTGCAGTGG
23792299 AGCAGAT
1 AGCAGAT
23792306 CGCATCAAGT
Statistics
Matches: 365, Mismatches: 97, Indels: 48
0.72 0.19 0.09
Matches are distributed among these distances:
40 2 0.01
41 52 0.14
42 1 0.00
43 14 0.04
44 253 0.69
45 42 0.12
46 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (44 bp):
AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
Found at i:23792288 original size:217 final size:218
Alignment explanation
Indices: 23791776--23792318 Score: 838
Period size: 218 Copynumber: 2.5 Consensus size: 218
23791766 AGTGTAAGGA
*
23791776 AGCAGATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
* * *
23791841 TTATCTCTCTGATGTTGCAGCAGAGTGGATCGCATCAGGTCTTTTCTCCCTGAAGTTGCAGCGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGA
* * * ** *
23791906 GCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATGACAAATC
131 GCAGACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGATCGAAGAAGACAAATC
*
23791971 TTATCTCCCTGAAGTTATAGTGG
196 TTATCTCCCTGAAGTTACAGTGG
*
23791994 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGAGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
* * * *
23792059 TTATCTCTCTGAAGTTCCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGTAGTGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGA
*
23792124 GCAGATTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGA-CTGAAGAAG-CAAAT
131 GCAGACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGATC-GAAGAAGACAAAT
* *
23792187 CTTATCTCCCTGAGGTTGCAGTGG
195 CTTATCTCCCTGAAGTTACAGTGG
* * *
23792211 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
** *
23792276 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTT
66 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTT
23792319 GCGGACTAGA
Statistics
Matches: 297, Mismatches: 27, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
217 127 0.43
218 170 0.57
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (218 bp):
AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGA
GCAGACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGATCGAAGAAGACAAATC
TTATCTCCCTGAAGTTACAGTGG
Found at i:23796935 original size:7 final size:6
Alignment explanation
Indices: 23796888--23796931 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
23796878 AAGAGACTGT
* *
23796888 AGAAAA AGAAAA AGAACA AGAAAA A-AAGAG AGAAAA AGAAAA AG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA AG
23796932 GAAAGATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 2 0.06
6 28 0.88
7 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:23801567 original size:49 final size:47
Alignment explanation
Indices: 23801510--23801604 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 47
23801500 TTTAATGTGT
* *
23801510 TTAGTTTAATTAATTCAATTGTTTTAATTTTCTTTAGTTGCTTAAATAC
1 TTAGTTTAATTAATTAAATTGTTTTAA-ATT-TTTAGTTGCTTAAATAC
23801559 TTAGTTTAATTAATTAAATTGTTTTAAATTTTTAGTTGCTTAAATA
1 TTAGTTTAATTAATTAAATTGTTTTAAATTTTTAGTTGCTTAAATA
23801605 ATTTCGACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 16 0.36
48 2 0.05
49 26 0.59
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (47 bp):
TTAGTTTAATTAATTAAATTGTTTTAAATTTTTAGTTGCTTAAATAC
Found at i:23802696 original size:61 final size:61
Alignment explanation
Indices: 23802601--23802723 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 61
23802591 TTAGCAACTT
* * * * *
23802601 ACTTAATTTTACGATCGGGCAATCTAAACGACTCGAATTAACACTGAACTGAGTTTGTATC
1 ACTTAATTTCACGATCAGGCAATCTAAACGACTCGAATAAACACCGAACTGAGTTCGTATC
23802662 ACTTAATTTCACGATCAGGCAATCTAAACGACTCGAATAAACACCGAACTGAGTTCGTATC
1 ACTTAATTTCACGATCAGGCAATCTAAACGACTCGAATAAACACCGAACTGAGTTCGTATC
23802723 A
1 A
23802724 TAGCATTTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (61 bp):
ACTTAATTTCACGATCAGGCAATCTAAACGACTCGAATAAACACCGAACTGAGTTCGTATC
Found at i:23805481 original size:30 final size:30
Alignment explanation
Indices: 23805445--23805506 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
23805435 CCCTTTAAAG
*
23805445 TAAAAAAAATTAGGTTTTTTTTAGTTTTCC
1 TAAAAAAAAATAGGTTTTTTTTAGTTTTCC
23805475 TAAAAAAAAATAGGTTTTTTTTAGTTTTCC
1 TAAAAAAAAATAGGTTTTTTTTAGTTTTCC
23805505 TA
1 TA
23805507 TTAGGACTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (30 bp):
TAAAAAAAAATAGGTTTTTTTTAGTTTTCC
Found at i:23808912 original size:24 final size:26
Alignment explanation
Indices: 23808863--23808926 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
23808853 AAGAAGGGTT
*
23808863 GAAATTGGCTAAGTGAAATGATGATG
1 GAAATTGGCTAAGTGAAATGAGGATG
*
23808889 GAAA-TGGCTAGGTG-AATGAGGATG
1 GAAATTGGCTAAGTGAAATGAGGATG
*
23808913 GAGATTTGGCTAAG
1 GA-AATTGGCTAAG
23808927 GTTTTGAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 11 0.34
25 10 0.31
26 11 0.34
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (26 bp):
GAAATTGGCTAAGTGAAATGAGGATG
Found at i:23810457 original size:36 final size:36
Alignment explanation
Indices: 23810411--23810513 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 36
23810401 ATCAGGCACC
*
23810411 CCACCACCACCAGCAATATTCCTTTCGGGACACACA
1 CCACCACCACCAGCATTATTCCTTTCGGGACACACA
** *
23810447 CCACCACCACCAGCATTATTCCTTTCGGGACGTACG
1 CCACCACCACCAGCATTATTCCTTTCGGGACACACA
*
23810483 CCACCACCACCAACATTACTTCCTTT-GGGAC
1 CCACCACCACCAGCATTA-TTCCTTTCGGGAC
23810514 TTCGAGACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 54 0.89
37 7 0.11
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (36 bp):
CCACCACCACCAGCATTATTCCTTTCGGGACACACA
Found at i:23810850 original size:20 final size:20
Alignment explanation
Indices: 23810825--23810865 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
23810815 CAAGCTGAAC
*
23810825 TAAGCTCAAACTTAGCTCAA
1 TAAGCTCAAACCTAGCTCAA
23810845 TAAGCTCAAACCTAGCTCAA
1 TAAGCTCAAACCTAGCTCAA
23810865 T
1 T
23810866 TTAATTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (20 bp):
TAAGCTCAAACCTAGCTCAA
Found at i:23811038 original size:27 final size:28
Alignment explanation
Indices: 23811002--23811078 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 28
23810992 GTGTTTTAAT
*
23811002 TTAATGCATGTTTTTAATATGTCCTAG-
1 TTAATACATGTTTTTAATATGTCCTAGC
* * *
23811029 TTAATACATGTTATTAATTTGTCTTAGC
1 TTAATACATGTTTTTAATATGTCCTAGC
* * **
23811057 CTATTACATAATTTTAATATGT
1 TTAATACATGTTTTTAATATGT
23811079 TTTAGCTCCA
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.49
Consensus pattern (28 bp):
TTAATACATGTTTTTAATATGTCCTAGC
Found at i:23813817 original size:43 final size:42
Alignment explanation
Indices: 23813754--23813839 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
23813744 AAGGCACCTA
** * *
23813754 GAAAAGAGAAATCAGTAGCTCTTTTAATGTCGTCCCTTGCAT
1 GAAAAGAGAAATCAACAGCTCCTTTAATGTCGTCCCATGCAT
23813796 GAAAAGGAGAAATCAACAGCTCCTTTAATGTCGTCCCATGCAT
1 GAAAA-GAGAAATCAACAGCTCCTTTAATGTCGTCCCATGCAT
23813839 G
1 G
23813840 CTTTCTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 5 0.13
43 34 0.87
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
GAAAAGAGAAATCAACAGCTCCTTTAATGTCGTCCCATGCAT
Found at i:23815059 original size:19 final size:21
Alignment explanation
Indices: 23815027--23815070 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
23815017 TCAAAACAAA
23815027 AAAAATCAAGAAAAAGAAAGG
1 AAAAATCAAGAAAAAGAAAGG
*
23815048 AAAAAT-AA-AAAAAGAAAGT
1 AAAAATCAAGAAAAAGAAAGG
23815067 AAAA
1 AAAA
23815071 TAATTATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (21 bp):
AAAAATCAAGAAAAAGAAAGG
Found at i:23824490 original size:12 final size:12
Alignment explanation
Indices: 23824473--23824497 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23824463 AAAATCTGAT
23824473 TTCAATGTGTAA
1 TTCAATGTGTAA
23824485 TTCAATGTGTAA
1 TTCAATGTGTAA
23824497 T
1 T
23824498 GTGTATAAGG
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:23824686 original size:16 final size:16
Alignment explanation
Indices: 23824665--23824696 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
23824655 ATTATAAAGT
23824665 CTAAAAAATTAAAATA
1 CTAAAAAATTAAAATA
23824681 CTAAAAAATTAAAATA
1 CTAAAAAATTAAAATA
23824697 AGTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
CTAAAAAATTAAAATA
Found at i:23827830 original size:19 final size:18
Alignment explanation
Indices: 23827794--23827833 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23827784 TTTCCACTCG
*
23827794 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
23827812 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
23827831 TTT
1 TTT
23827834 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:23827942 original size:17 final size:18
Alignment explanation
Indices: 23827917--23827970 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
23827907 TTTCTTTCTC
23827917 CAATCTTTT-TCTCTTTTT
1 CAAT-TTTTCTCTCTTTTT
* *
23827935 CAATTTTTGTTTCTTTTT
1 CAATTTTTCTCTCTTTTT
23827953 C--TTTTGTCTCTCTTTTT
1 CAATTTT-TCTCTCTTTTT
23827970 C
1 C
23827971 TTCTCTCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 14 0.45
18 13 0.42
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.69
Consensus pattern (18 bp):
CAATTTTTCTCTCTTTTT
Found at i:23828861 original size:12 final size:11
Alignment explanation
Indices: 23828844--23828889 Score: 65
Period size: 11 Copynumber: 3.9 Consensus size: 11
23828834 GCTCTCTTTC
23828844 TTTTTTTTCAA
1 TTTTTTTTCAA
23828855 TTTTTTTTCAA
1 TTTTTTTTCAA
23828866 TTTTTTTTTCAACA
1 -TTTTTTTTC-A-A
23828880 TTTTTTTTCA
1 TTTTTTTTCA
23828890 CAACTTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.34
12 10 0.31
13 10 0.31
14 1 0.03
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:23828948 original size:11 final size:11
Alignment explanation
Indices: 23828932--23828972 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
23828922 GAAACTAGTT
23828932 TTTTTTTCGAA
1 TTTTTTTCGAA
*
23828943 TTTTTTTTTGAA
1 -TTTTTTTCGAA
*
23828955 TTTTTTTCGAG
1 TTTTTTTCGAA
23828966 TTTTTTT
1 TTTTTTT
23828973 TTGAGAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.73
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:23828948 original size:12 final size:12
Alignment explanation
Indices: 23828931--23828973 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
23828921 GGAAACTAGT
23828931 TTTTTTTTCGAA
1 TTTTTTTTCGAA
*
23828943 TTTTTTTTTGAA
1 TTTTTTTTCGAA
*
23828955 -TTTTTTTCGAG
1 TTTTTTTTCGAA
23828966 TTTTTTTT
1 TTTTTTTT
23828974 TGAGAAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:23828958 original size:23 final size:23
Alignment explanation
Indices: 23828932--23828976 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
23828922 GAAACTAGTT
23828932 TTTTTTTCGAATTTTTTTTTGAA
1 TTTTTTTCGAATTTTTTTTTGAA
*
23828955 TTTTTTTCGAGTTTTTTTTTGA
1 TTTTTTTCGAATTTTTTTTTGA
23828977 GAAACTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.04, G:0.11, T:0.71
Consensus pattern (23 bp):
TTTTTTTCGAATTTTTTTTTGAA
Found at i:23844547 original size:12 final size:12
Alignment explanation
Indices: 23844476--23844521 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
23844466 GACTAGAAGA
*
23844476 GAAAAATGAAAGT
1 GAAAAA-GAAATT
*
23844489 GAAAAAGAGATT
1 GAAAAAGAAATT
23844501 GAAAAAGAAATT
1 GAAAAAGAAATT
*
23844513 GCAAAAGAA
1 GAAAAAGAA
23844522 GAAAAAGCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 23 0.79
13 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.22, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:23856018 original size:18 final size:17
Alignment explanation
Indices: 23855987--23856021 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23855977 TAAAAATAAA
23855987 ACTTTACAACTTGGGCC
1 ACTTTACAACTTGGGCC
*
23856004 ACTTTGACAATTTGGGCC
1 ACTTT-ACAACTTGGGCC
23856022 TGATTTTTCA
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:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (17 bp):
ACTTTACAACTTGGGCC
Found at i:23870588 original size:10 final size:10
Alignment explanation
Indices: 23870573--23870622 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
23870563 ATTGGGTTAA
23870573 AATTGAGCTG
1 AATTGAGCTG
*
23870583 AATTGATCTCG
1 AATTGAGCT-G
23870594 AA-TGAGCTG
1 AATTGAGCTG
*
23870603 AATTGAGCTC
1 AATTGAGCTG
*
23870613 AAGTGAGCTG
1 AATTGAGCTG
23870623 GAAACGAGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 27 0.82
11 3 0.09
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (10 bp):
AATTGAGCTG
Found at i:23870599 original size:20 final size:20
Alignment explanation
Indices: 23870576--23870622 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
23870566 GGGTTAAAAT
*
23870576 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
23870596 TGAGCTGAATTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
23870616 TGAGCTG
1 TGAGCTG
23870623 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:23875149 original size:18 final size:18
Alignment explanation
Indices: 23875126--23875162 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23875116 CTCTTTTTGC
23875126 TCTTTTTC-ATTCTCTTTT
1 TCTTTTTCGATT-TCTTTT
23875144 TCTTTTTCGATTTCTTTT
1 TCTTTTTCGATTTCTTTT
23875162 T
1 T
23875163 TTTGTCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.05, C:0.19, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTCGATTTCTTTT
Found at i:23879302 original size:19 final size:18
Alignment explanation
Indices: 23879266--23879305 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23879256 TTTCCACTCG
*
23879266 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
23879284 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
23879303 TTT
1 TTT
23879306 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:23879433 original size:18 final size:17
Alignment explanation
Indices: 23879385--23879434 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
23879375 CTTCTTTCTC
*
23879385 CAATCTTTTTCTCTTTTT
1 CAAT-TTTTTTTCTTTTT
23879403 CAATTTTTGTTTCTTTTT
1 CAATTTTT-TTTCTTTTT
*
23879421 CAGTTTCTTTTTCT
1 CAATTT-TTTTTCT
23879435 CTCGTCACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 22 0.79
19 2 0.07
ACGTcount: A:0.10, C:0.18, G:0.04, T:0.68
Consensus pattern (17 bp):
CAATTTTTTTTCTTTTT
Found at i:23884754 original size:219 final size:218
Alignment explanation
Indices: 23884375--23884817 Score: 681
Period size: 219 Copynumber: 2.0 Consensus size: 218
23884365 GAAACACTTA
* * *
23884375 ATGTCCCTCATTCGGTTGGAAGAAGACTCGGTTACCTTGCCTTTGTTGGTGTCGCCCAAAGGCTT
1 ATGTCCCTCATTCGGTTGGAAGAAGACTCGATCACCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
* *
23884440 GCTTGTTTTGGACGGCACTATTTGCTTCTTGGCATGGATCAGTGGATTGTTTTTACTCGTGCTTT
66 GCTTGTTTTAGACGGCACTATTTGCTTCTTGGCATGGATCAGTGGATTGTTTTTACTCATGCTTT
* * *
23884505 GGCCCCATTTTGTTGTGCCTACAGTGGTATAACCTCGAACGGCACCTTTTCGCTTGAGCTTCTTT
131 GGCCCCATTTTGTTATGCCTACAGTGGTATAACCTCGAACAG-ACCTTTTCGCTTGAGCTGCTTT
*
23884570 TCCACCTTGATGGTCATGTGCACC
195 TCCACCTTGATGGCCATGTGCACC
* * *
23884594 ATGTCCCTCGTTCGGTTGGAAGAAGACTCTATCGCCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
1 ATGTCCCTCATTCGGTTGGAAGAAGACTCGATCACCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
* * * *
23884659 GTTTGTTTTAGATGGCACTATTTGC-TCATTGGCATGGATCGGTGGATTGTTTTTAGTCATGCTT
66 GCTTGTTTTAGACGGCACTATTTGCTTC-TTGGCATGGATCAGTGGATTGTTTTTACTCATGCTT
* * * *
23884723 TGGCTCCATTTTGTTATGCCTGCGGTGGTATAACCTCGAACAGTCCTTTTCGCTTGAGCTGCTTT
130 TGGCCCCATTTTGTTATGCCTACAGTGGTATAACCTCGAACAGACCTTTTCGCTTGAGCTGCTTT
23884788 TCCACCTTGATGGCCATGTGCACC
195 TCCACCTTGATGGCCATGTGCACC
23884812 ATGTCC
1 ATGTCC
23884818 ATGATTTCAA
Statistics
Matches: 203, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
218 51 0.25
219 152 0.75
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (218 bp):
ATGTCCCTCATTCGGTTGGAAGAAGACTCGATCACCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
GCTTGTTTTAGACGGCACTATTTGCTTCTTGGCATGGATCAGTGGATTGTTTTTACTCATGCTTT
GGCCCCATTTTGTTATGCCTACAGTGGTATAACCTCGAACAGACCTTTTCGCTTGAGCTGCTTTT
CCACCTTGATGGCCATGTGCACC
Found at i:23887849 original size:20 final size:20
Alignment explanation
Indices: 23887819--23887856 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
23887809 AAAAATATGC
23887819 AAACTTATT-AATTTAAATA
1 AAACTTATTAAATTTAAATA
23887838 AAACTATATTAAATTTAAA
1 AAACT-TATTAAATTTAAA
23887857 AAGTCCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
AAACTTATTAAATTTAAATA
Found at i:23888498 original size:33 final size:33
Alignment explanation
Indices: 23888461--23888556 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 33
23888451 TAAGTTAATG
23888461 CATGACTTAATTTAATGATGCAAACTTAACTAA
1 CATGACTTAATTTAATGATGCAAACTTAACTAA
* *
23888494 CATGA---AAGTT-A-CAT---AA-TTAAACTAA
1 CATGACTTAATTTAATGATGCAAACTT-AACTAA
*
23888519 CATGACTTTATTTAATGATGCAAACTTAACTAA
1 CATGACTTAATTTAATGATGCAAACTTAACTAA
23888552 CATGA
1 CATGA
23888557 AAGTTACATA
Statistics
Matches: 48, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
24 2 0.04
25 13 0.27
28 5 0.10
29 2 0.04
30 6 0.12
33 18 0.38
34 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (33 bp):
CATGACTTAATTTAATGATGCAAACTTAACTAA
Found at i:23889194 original size:25 final size:28
Alignment explanation
Indices: 23889165--23889250 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
23889155 GGTCAAACAA
23889165 TAATTAG-ATA-T-TATTAAATATGTCC
1 TAATTAGTATAGTGTATTAAATATGTCC
* *
23889190 TAATTAGTTTAGGTGTTTTAAATATGTCC
1 TAATTAGTATA-GTGTATTAAATATGTCC
*
23889219 TAATTAGT-TCAAGTGTTTTAAATATGTCC
1 TAATTAGTAT--AGTGTATTAAATATGTCC
23889248 TAA
1 TAA
23889251 ACTAATACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
25 7 0.13
26 2 0.04
28 2 0.04
29 41 0.77
30 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (28 bp):
TAATTAGTATAGTGTATTAAATATGTCC
Found at i:23889220 original size:29 final size:29
Alignment explanation
Indices: 23889178--23889250 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
23889168 TTAGATATTA
* *
23889178 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
23889207 TTAAATATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
23889236 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
23889251 ACTAATACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:23896135 original size:25 final size:28
Alignment explanation
Indices: 23896106--23896191 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
23896096 GGTCAAACAA
23896106 TAATTAG-ATA-T-TATTAAATATGTCC
1 TAATTAGTATAGTGTATTAAATATGTCC
* *
23896131 TAATTAGTTTAGGTGTTTTAAATATGTCC
1 TAATTAGTATA-GTGTATTAAATATGTCC
*
23896160 TAATTAGT-TCAAGTGTTTTAAATATGTCC
1 TAATTAGTAT--AGTGTATTAAATATGTCC
23896189 TAA
1 TAA
23896192 ACTAATACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
25 7 0.13
26 2 0.04
28 2 0.04
29 41 0.77
30 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (28 bp):
TAATTAGTATAGTGTATTAAATATGTCC
Found at i:23896161 original size:29 final size:29
Alignment explanation
Indices: 23896119--23896191 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
23896109 TTAGATATTA
* *
23896119 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
23896148 TTAAATATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
23896177 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
23896192 ACTAATACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:23901990 original size:12 final size:12
Alignment explanation
Indices: 23901962--23902001 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
23901952 ACTCGATTTC
*
23901962 TTTTCAAGCTCT
1 TTTTCAATCTCT
* *
23901974 CTTTCAATTTCT
1 TTTTCAATCTCT
23901986 TTTTCAATCTCT
1 TTTTCAATCTCT
23901998 TTTT
1 TTTT
23902002 GCTTTTCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTTCAATCTCT
Found at i:23902054 original size:15 final size:15
Alignment explanation
Indices: 23902031--23902077 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
23902021 TTTTGAAATC
23902031 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
23902046 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
23902061 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
23902077 T
1 T
23902078 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:23902247 original size:35 final size:35
Alignment explanation
Indices: 23902201--23902274 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
23902191 AGGAATACCT
23902201 ATTGGTACGTTCATCGTGAGTGACCTTGTGATCCA
1 ATTGGTACGTTCATCGTGAGTGACCTTGTGATCCA
23902236 ATTGGTACGTTCATCGTGAGTGACCTTGTGATCCA
1 ATTGGTACGTTCATCGTGAGTGACCTTGTGATCCA
23902271 ATTG
1 ATTG
23902275 CCATGGTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (35 bp):
ATTGGTACGTTCATCGTGAGTGACCTTGTGATCCA
Found at i:23903176 original size:14 final size:14
Alignment explanation
Indices: 23903159--23903220 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
23903149 ATTTCACTTC
23903159 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
*
23903173 TTTTTTTAC-TCTT
1 TTTTTTTTCTTCTT
* *
23903186 TTCTTTTTGCTCACTT
1 TT-TTTTTTCT-TCTT
*
23903202 CTTTTTTTCTT-TT
1 TTTTTTTTCTTCTT
23903215 TTTTTT
1 TTTTTT
23903221 CAAATTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
13 13 0.34
14 14 0.37
15 7 0.18
16 4 0.11
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:23907637 original size:15 final size:13
Alignment explanation
Indices: 23907617--23907665 Score: 71
Period size: 13 Copynumber: 3.6 Consensus size: 13
23907607 ACTAGCTCTC
*
23907617 TTTTTTTTTCACA
1 TTTTTTTTTCAAA
23907630 TTTTTTTTTCAAAAA
1 TTTTTTTTTC--AAA
23907645 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
23907658 TTTTTTTT
1 TTTTTTTT
23907666 CACAACTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 21 0.64
15 12 0.36
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:23911921 original size:49 final size:49
Alignment explanation
Indices: 23911865--23912018 Score: 152
Period size: 49 Copynumber: 3.1 Consensus size: 49
23911855 GAGCTCGTAT
23911865 CATTATGTAACTCTTATGTTAGTTAAGTTTGCATCATAAATATGACATG
1 CATTATGTAACTCTTATGTTAGTTAAGTTTGCATCATAAATATGACATG
** * * *
23911914 CATTATGTAACTCCCATGTTAGTTTAAGTCTGCATCATTAAATTAAGTCATG
1 CATTATGTAACTCTTATGTTAG-TTAAGTTTGCATCA-TAAA-TATGACATG
* * * *
23911966 CATTAAGTAACTCATT-TGTTCA-TTTAGTTTGCATCTTAATTAT-ATCATG
1 CATTATGTAACTC-TTATGTT-AGTTAAGTTTGCATCATAAATATGA-CATG
23912015 CATT
1 CATT
23912019 TAAGCATCAT
Statistics
Matches: 85, Mismatches: 14, Indels: 12
0.77 0.13 0.11
Matches are distributed among these distances:
49 30 0.35
50 16 0.19
51 15 0.18
52 23 0.27
53 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (49 bp):
CATTATGTAACTCTTATGTTAGTTAAGTTTGCATCATAAATATGACATG
Found at i:23924514 original size:21 final size:22
Alignment explanation
Indices: 23924485--23924535 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
23924475 TCTCTCTCGC
*
23924485 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
23924506 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
23924528 TTT-ATTTT
1 TTTCATTTT
23924536 TATCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:23924534 original size:27 final size:28
Alignment explanation
Indices: 23924499--23924551 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
23924489 CTTTTCGCCT
* *
23924499 TTTTCATTTTCATTTTCTTCTTTTTCAC
1 TTTTCATTTTCATCTTCTCCTTTTTCAC
*
23924527 TTTT-ATTTTTATCTTCTCCTTTTTC
1 TTTTCATTTTCATCTTCTCCTTTTTC
23924552 TTTTTCCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTCATTTTCATCTTCTCCTTTTTCAC
Found at i:23928649 original size:42 final size:42
Alignment explanation
Indices: 23928602--23928681 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
23928592 ACATCTTTTT
23928602 CTTTTTCAATTT-TTTTCTCAATCT-CAATTTCTTTTTCTCTCA
1 CTTTTTCAATTTCTTTT-TC-ATCTGCAATTTCTTTTTCTCTCA
* * *
23928644 CTTTTTCGATTTCTTTTTCTTTTGCAATTTCTTTTTCT
1 CTTTTTCAATTTCTTTTTCATCTGCAATTTCTTTTTCT
23928682 TTTTCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 2 0.06
42 27 0.82
43 4 0.12
ACGTcount: A:0.12, C:0.21, G:0.03, T:0.64
Consensus pattern (42 bp):
CTTTTTCAATTTCTTTTTCATCTGCAATTTCTTTTTCTCTCA
Found at i:23928665 original size:18 final size:18
Alignment explanation
Indices: 23928644--23928722 Score: 106
Period size: 18 Copynumber: 4.4 Consensus size: 18
23928634 TTTTCTCTCA
23928644 CTTTTTCGA-TTTCTTTTT
1 CTTTTTC-ACTTTCTTTTT
* *
23928662 CTTTTGCAATTTCTTTTT
1 CTTTTTCACTTTCTTTTT
*
23928680 CTTTTTCATTTTCTTTTT
1 CTTTTTCACTTTCTTTTT
*
23928698 CTTCTTCACTTTCTTTTT
1 CTTTTTCACTTTCTTTTT
23928716 CTTTTTC
1 CTTTTTC
23928723 TTCTTTTTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
17 1 0.02
18 53 0.98
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (18 bp):
CTTTTTCACTTTCTTTTT
Found at i:23928684 original size:36 final size:36
Alignment explanation
Indices: 23928644--23928722 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
23928634 TTTTCTCTCA
23928644 CTTTTTCGA-TTTCTTTTTCTT-TTGCAATTTCTTTTT
1 CTTTTTC-ATTTTCTTTTTCTTCTT-CAATTTCTTTTT
*
23928680 CTTTTTCATTTTCTTTTTCTTCTTCACTTTCTTTTT
1 CTTTTTCATTTTCTTTTTCTTCTTCAATTTCTTTTT
23928716 CTTTTTC
1 CTTTTTC
23928723 TTCTTTTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 1 0.03
36 37 0.93
37 2 0.05
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (36 bp):
CTTTTTCATTTTCTTTTTCTTCTTCAATTTCTTTTT
Found at i:23928736 original size:6 final size:6
Alignment explanation
Indices: 23928629--23928724 Score: 84
Period size: 6 Copynumber: 16.0 Consensus size: 6
23928619 TCAATCTCAA
* ** ** * **
23928629 TTTCTT TTTCTC TCACTT TTTCGA TTTCTT TTTCTT TTGCAA TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* * **
23928677 TTTCTT TTTCAT TTTCTT TTTCTT CTTCAC TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
23928725 CTTTTTCATT
Statistics
Matches: 66, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:23937021 original size:10 final size:11
Alignment explanation
Indices: 23937003--23937029 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
23936993 ATATACTTCA
23937003 AATTTTTTTTG
1 AATTTTTTTTG
23937014 AATTTTTTTTG
1 AATTTTTTTTG
23937025 AATTT
1 AATTT
23937030 CCTCTTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:23937104 original size:5 final size:5
Alignment explanation
Indices: 23937094--23937123 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
23937084 AAGGGAAGAG
23937094 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
23937124 TACAACCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:23947592 original size:20 final size:19
Alignment explanation
Indices: 23947528--23947592 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
23947518 TATAAATGCA
*
23947528 AATGAGCTTAAAATGAGTTG
1 AATGAGC-TAAAATGAGCTG
* *
23947548 ATTGAGCTAAGAGTGAGCTCG
1 AATGAGCTAA-AATGAGCT-G
23947569 -ATGAGCTAAAATTGAGCTG
1 AATGAGCTAAAA-TGAGCTG
23947588 AATGA
1 AATGA
23947593 ACTTGAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 5 0.14
20 30 0.83
21 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (19 bp):
AATGAGCTAAAATGAGCTG
Found at i:23947890 original size:12 final size:12
Alignment explanation
Indices: 23947873--23947937 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
23947863 TCACACTCTT
23947873 TTTTTTTTTGAA
1 TTTTTTTTTGAA
23947885 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
23947897 TTTCCTTTTTTTCAA
1 -TT--TTTTTTTGAA
* *
23947912 -ATTTTTTTAAA
1 TTTTTTTTTGAA
*
23947923 TTTTTTTTCGAA
1 TTTTTTTTTGAA
23947935 TTT
1 TTT
23947938 CCTCTTCTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 9 0.21
12 23 0.53
13 2 0.05
15 9 0.21
ACGTcount: A:0.18, C:0.06, G:0.05, T:0.71
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:23952321 original size:29 final size:29
Alignment explanation
Indices: 23952287--23952359 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
23952277 ATGTATTAGT
* *
23952287 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
23952316 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
23952345 TTAGGACATATTTAA
1 TTAGGACATATTTAA
23952360 TAATATCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:23962635 original size:14 final size:13
Alignment explanation
Indices: 23962606--23962631 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23962596 TGTGTTTTGC
23962606 TGCTGTTGTTTAA
1 TGCTGTTGTTTAA
23962619 TGCTGTTGTTTAA
1 TGCTGTTGTTTAA
23962632 ATGCAGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (13 bp):
TGCTGTTGTTTAA
Found at i:23975389 original size:18 final size:19
Alignment explanation
Indices: 23975366--23975414 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
23975356 GTTGTAAAGT
*
23975366 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
23975384 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
23975403 TTTAATTTTTAT
1 TTT-ATTTTTAT
23975415 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:23975394 original size:22 final size:22
Alignment explanation
Indices: 23975365--23975414 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
23975355 AGTTGTAAAG
* *
23975365 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
23975386 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
23975409 TTTTAT
1 TTTTAT
23975415 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:23976834 original size:17 final size:18
Alignment explanation
Indices: 23976802--23976854 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
23976792 TCAAATTAGG
* *
23976802 TTCGTGAATTAAAAAAAA
1 TTCGTGCATAAAAAAAAA
**
23976820 TTCGTGCA-AAAAAAATT
1 TTCGTGCATAAAAAAAAA
23976837 TTCGTGCATAAAAAAAAA
1 TTCGTGCATAAAAAAAAA
23976855 AAGGTTGTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.26
Consensus pattern (18 bp):
TTCGTGCATAAAAAAAAA
Found at i:23977160 original size:12 final size:12
Alignment explanation
Indices: 23977145--23977189 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
23977135 TAAAAAAAAG
23977145 GAAAAAAAATTC
1 GAAAAAAAATTC
23977157 GAAAAAAAAATT-
1 G-AAAAAAAATTC
*
23977169 TAAAAAAAATTC
1 GAAAAAAAATTC
23977181 GAAAAAAAA
1 GAAAAAAAA
23977190 ATTTTGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
12 9 0.31
13 10 0.34
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (12 bp):
GAAAAAAAATTC
Found at i:23977162 original size:13 final size:13
Alignment explanation
Indices: 23977146--23977192 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
23977136 AAAAAAAAGG
23977146 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
23977159 AAAAAAAATT--T
1 AAAAAAAATTCGA
23977170 AAAAAAAATTCGA
1 AAAAAAAATTCGA
23977183 AAAAAAAATT
1 AAAAAAAATT
23977193 TTGTATTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.33
13 20 0.67
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:23977173 original size:24 final size:24
Alignment explanation
Indices: 23977146--23977193 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
23977136 AAAAAAAAGG
23977146 AAAAAAAATTCGAAAAAAAAATTT
1 AAAAAAAATTCGAAAAAAAAATTT
23977170 AAAAAAAATTCGAAAAAAAAATTT
1 AAAAAAAATTCGAAAAAAAAATTT
23977194 TGTATTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAAAAAATTCGAAAAAAAAATTT
Found at i:23978165 original size:5 final size:6
Alignment explanation
Indices: 23978149--23978174 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23978139 AATAGCATGT
23978149 GAAAAA GAAAAA GAAAAA GAAAAA GA
1 GAAAAA GAAAAA GAAAAA GAAAAA GA
23978175 GCGCGAGNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:23980162 original size:82 final size:82
Alignment explanation
Indices: 23980003--23980165 Score: 229
Period size: 82 Copynumber: 2.0 Consensus size: 82
23979993 TTGTGTCTGC
* * * * *
23980003 AGGTTATTGAATTCGGCTACTTAATGGCTAAGGAGACATGCATTTAAGGTGCTGTTAACATGCAA
1 AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
23980068 GGAACGGCATTTAAAGA
66 GGAACGGCATTTAAAGA
**
23980085 AGGTCATTGAAATTCGGCTACTTAATGGCAAAGGAAACATGCA-TTAAGGAGATGTTCCCATGCA
1 AGGTCATTG-AATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCA
* *
23980149 TGGAACGGTATTTAAAG
65 AGGAACGGCATTTAAAG
23980166 GGAAGTAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 40 0.56
83 31 0.44
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (82 bp):
AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
GGAACGGCATTTAAAGA
Found at i:23982536 original size:19 final size:18
Alignment explanation
Indices: 23982514--23982551 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
23982504 ACGATGAAGT
*
23982514 TTCGTTCTTCTTGAGTCAA
1 TTCGTTCTACTTGA-TCAA
23982533 TTCGTTCTACTTGATCAA
1 TTCGTTCTACTTGATCAA
23982551 T
1 T
23982552 GAAGTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.47
Consensus pattern (18 bp):
TTCGTTCTACTTGATCAA
Found at i:23988225 original size:10 final size:10
Alignment explanation
Indices: 23988210--23988271 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
23988200 TTTGAACCAT
*
23988210 TACCAATTCG
1 TACCAATTCA
*
23988220 TACCAAATACCA
1 TACC-AAT-TCA
*
23988232 TACCATTTCA
1 TACCAATTCA
23988242 TACCAATTCCA
1 TACCAATT-CA
* *
23988253 TACCATTTCG
1 TACCAATTCA
23988263 TACCAATTC
1 TACCAATTC
23988272 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:23988255 original size:21 final size:21
Alignment explanation
Indices: 23988210--23988272 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
23988200 TTTGAACCAT
* *
23988210 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
23988232 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
23988253 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
23988273 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:23988625 original size:15 final size:15
Alignment explanation
Indices: 23988581--23988634 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
23988571 AAAAGTTCGA
**
23988581 AAAAAAAATTTGAA-
1 AAAAAAAATTAAAAG
*
23988595 AAAAAAAATTCGAAAG
1 AAAAAAAATT-AAAAG
23988611 AAAAAAAATTAAAAG
1 AAAAAAAATTAAAAG
23988626 AAAAAAAAT
1 AAAAAAAAT
23988635 GTATACGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.29
15 15 0.43
16 10 0.29
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (15 bp):
AAAAAAAATTAAAAG
Found at i:23988629 original size:14 final size:14
Alignment explanation
Indices: 23988568--23988632 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 14
23988558 ATAGGTACGT
23988568 AAAAAAAGTTCGAAA-
1 AAAAAAA-TT-GAAAG
*
23988583 AAAAAATTTGAAA-
1 AAAAAAATTGAAAG
23988596 AAAAAAATTCGAAAG
1 AAAAAAATT-GAAAG
*
23988611 AAAAAAAATTAAAAG
1 -AAAAAAATTGAAAG
23988626 AAAAAAA
1 AAAAAAA
23988633 ATGTATACGG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.27
14 13 0.30
15 10 0.23
16 9 0.20
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (14 bp):
AAAAAAATTGAAAG
Found at i:23991252 original size:21 final size:22
Alignment explanation
Indices: 23991207--23991256 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
23991197 AGAGAAAAAT
*
23991207 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
23991229 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
23991250 -AAAGTGA
1 AAAAGTGA
23991257 GAGAGAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.26, T:0.08
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:23991351 original size:36 final size:33
Alignment explanation
Indices: 23991286--23991352 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
23991276 GTGAATGAAG
*
23991286 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
* *
23991319 TGAGTGAAGAAGAAGAGAGTGCTCAAACACAAGG
1 TGAGTGAAAAAG-AGAGAGAGCT-AAA-ACAAGG
23991353 GAGGAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 9 0.32
35 2 0.07
36 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.31, T:0.12
Consensus pattern (33 bp):
TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
Found at i:23998546 original size:43 final size:42
Alignment explanation
Indices: 23998458--23998678 Score: 225
Period size: 43 Copynumber: 5.4 Consensus size: 42
23998448 CTCGATGGAT
*
23998458 TCAGCACTTAGCAACCACC-TT-ATATTCAATA-ATACGGGGAA
1 TCAGCACTTAGCAACC-CCTTTCACATTCAA-AGATACGGGGAA
* *
23998499 TCAGCACATAGCAACCCCTTTCACAATCAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCCCTTTCACATTCAAAGATACGG-GGAA
*
23998542 TCAGCACTTAGCAACCCCTTTCATATTCAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCCCTTTCACATTCAAAGATACGG-GGAA
* *
23998585 TCAGCACTT-GACAA---C---CAC---CAATGATTCGGGGAA
1 TCAGCACTTAG-CAACCCCTTTCACATTCAAAGATACGGGGAA
* *
23998618 TTAGCACTTAGCAACCCCTTTCACATTCAAAGATACGGCAGAA
1 TCAGCACTTAGCAACCCCTTTCACATTCAAAGATACGG-GGAA
23998661 TCAGCACTTAGCAACCCC
1 TCAGCACTTAGCAACCCC
23998679 CTTTATATTC
Statistics
Matches: 150, Mismatches: 14, Indels: 30
0.77 0.07 0.15
Matches are distributed among these distances:
33 15 0.10
34 10 0.07
36 1 0.01
37 2 0.01
39 3 0.02
40 3 0.02
41 18 0.12
42 22 0.15
43 76 0.51
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (42 bp):
TCAGCACTTAGCAACCCCTTTCACATTCAAAGATACGGGGAA
Found at i:24000800 original size:20 final size:19
Alignment explanation
Indices: 24000777--24000841 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
24000767 AAGCTCAAAC
24000777 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
24000797 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
24000817 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
24000837 GAGCT
1 GAGCT
24000842 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:24014145 original size:15 final size:14
Alignment explanation
Indices: 24014125--24014172 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
24014115 CTCATTTTCA
24014125 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
24014140 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
24014154 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
24014169 TCTT
1 TCTT
24014173 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:24014177 original size:22 final size:21
Alignment explanation
Indices: 24014125--24014183 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
24014115 CTCATTTTCA
* *
24014125 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
24014146 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
24014167 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
24014184 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:24015200 original size:11 final size:11
Alignment explanation
Indices: 24015175--24015229 Score: 53
Period size: 10 Copynumber: 5.1 Consensus size: 11
24015165 GAATACAAAC
*
24015175 TTTTTTTTCGGA
1 TTTTTTTTC-AA
24015187 TTTTTTTTCAA
1 TTTTTTTTCAA
24015198 -TTTTTTT-AA
1 TTTTTTTTCAA
*
24015207 ATTTTTTTC-A
1 TTTTTTTTCAA
24015217 TTTTTTTTACAA
1 TTTTTTTT-CAA
24015229 T
1 T
24015230 ACCGTAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 2 0.05
10 22 0.59
11 2 0.05
12 11 0.30
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:24015201 original size:10 final size:10
Alignment explanation
Indices: 24015188--24015229 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
24015178 TTTTTCGGAT
24015188 TTTTTTTCAA
1 TTTTTTTCAA
*
24015198 TTTTTTTAAA
1 TTTTTTTCAA
*
24015208 TTTTTTTCAT
1 TTTTTTTCAA
24015218 TTTTTTTACAA
1 TTTTTTT-CAA
24015229 T
1 T
24015230 ACCGTAATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 24 0.89
11 3 0.11
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:24015211 original size:20 final size:20
Alignment explanation
Indices: 24015188--24015225 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24015178 TTTTTCGGAT
24015188 TTTTTTTCAATTTTTTTAAA
1 TTTTTTTCAATTTTTTTAAA
*
24015208 TTTTTTTCATTTTTTTTA
1 TTTTTTTCAATTTTTTTA
24015226 CAATACCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTCAATTTTTTTAAA
Found at i:24025429 original size:41 final size:41
Alignment explanation
Indices: 24025384--24025461 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
24025374 AAGTGTTAGT
24025384 ATATGCCTGGACGAATTTAATGCTGCCACTACATGTTATAA
1 ATATGCCTGGACGAATTTAATGCTGCCACTACATGTTATAA
*
24025425 ATATGCCTGGACGAATTTAATGCTGCTACTACATGTT
1 ATATGCCTGGACGAATTTAATGCTGCCACTACATGTT
24025462 TGGCCGAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (41 bp):
ATATGCCTGGACGAATTTAATGCTGCCACTACATGTTATAA
Found at i:24029128 original size:29 final size:29
Alignment explanation
Indices: 24029091--24029163 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
24029081 TTAGATATTA
* *
24029091 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
24029120 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
24029149 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
24029164 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:24033835 original size:52 final size:53
Alignment explanation
Indices: 24033766--24033866 Score: 177
Period size: 52 Copynumber: 1.9 Consensus size: 53
24033756 CATGCACATA
* *
24033766 TTGAGGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTGT
1 TTGAGGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTGT
24033819 TTGA-GCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TTGAGGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
24033867 CGTTTCCTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 42 0.91
53 4 0.09
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (53 bp):
TTGAGGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTGT
Found at i:24052426 original size:16 final size:15
Alignment explanation
Indices: 24052404--24052440 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
24052394 AAAAATTCAA
24052404 TTTTTTTTTCAAATT
1 TTTTTTTTTCAAATT
*
24052419 TCTTTTTTTTCGAATT
1 T-TTTTTTTTCAAATT
24052435 TTTTTT
1 TTTTTT
24052441 AAAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTCAAATT
Found at i:24066100 original size:52 final size:52
Alignment explanation
Indices: 24066017--24066117 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
24066007 TAAGGAAACG
* *
24066017 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
24066069 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
24066118 TATGTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:24087733 original size:52 final size:52
Alignment explanation
Indices: 24087672--24087772 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
24087662 CATGCACATA
* *
24087672 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
24087724 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
24087773 CGTTTCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:24102392 original size:7 final size:6
Alignment explanation
Indices: 24102366--24102408 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
24102356 CATTGTAGTG
* * *
24102366 AAAA-A AAAAGA AAATGA AAACGA AAAAGA AAAAGA AAAGGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
24102409 TCAAAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:24102393 original size:18 final size:17
Alignment explanation
Indices: 24102364--24102437 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 17
24102354 CACATTGTAG
24102364 TGAAAA-AAAAAGAAAA
1 TGAAAAGAAAAAGAAAA
24102380 TGAAAACGAAAAAGAAAA
1 TGAAAA-GAAAAAGAAAA
*
24102398 AGAAAAGGAAATCAA-AAAA
1 TGAAAA-GAAA--AAGAAAA
*
24102417 GTG-AGAGAAAAAGAAAA
1 -TGAAAAGAAAAAGAAAA
24102434 TGAA
1 TGAA
24102438 GAAAAGAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
16 10 0.21
17 5 0.11
18 23 0.49
19 6 0.13
20 3 0.06
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.07
Consensus pattern (17 bp):
TGAAAAGAAAAAGAAAA
Found at i:24102401 original size:24 final size:24
Alignment explanation
Indices: 24102366--24102417 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
24102356 CATTGTAGTG
* *
24102366 AAAA-AAAAAGAAAATGAAAACGA
1 AAAAGAAAAAGAAAAGGAAAACAA
*
24102389 AAAAGAAAAAGAAAAGGAAATCAA
1 AAAAGAAAAAGAAAAGGAAAACAA
24102413 AAAAG
1 AAAAG
24102418 TGAGAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (24 bp):
AAAAGAAAAAGAAAAGGAAAACAA
Found at i:24110487 original size:20 final size:20
Alignment explanation
Indices: 24110462--24110508 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24110452 AGCTCATTTC
*
24110462 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
24110482 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
24110502 CAGCTCA
1 CAGCTCA
24110509 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:24110511 original size:10 final size:10
Alignment explanation
Indices: 24110452--24110511 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
24110442 AGCTCTGTTT
*
24110452 AGCTCATTTCC
1 AGCTCAATT-C
* *
24110463 AGCTCACTTG
1 AGCTCAATTC
*
24110473 AGCTCAAGTC
1 AGCTCAATTC
24110483 AGCTC-ATTC
1 AGCTCAATTC
*
24110492 GAGATCAATTC
1 -AGCTCAATTC
24110503 AGCTCAATT
1 AGCTCAATT
24110512 TTAACCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 12 0.31
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:24114302 original size:21 final size:21
Alignment explanation
Indices: 24114268--24114309 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24114258 ACATTTCTAG
**
24114268 CTTTTTCTCGCTCAATTTCTT
1 CTTTTTCTAACTCAATTTCTT
*
24114289 CTTTTTCTAACTCATTTTCTT
1 CTTTTTCTAACTCAATTTCTT
24114310 TTTCAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.26, G:0.02, T:0.60
Consensus pattern (21 bp):
CTTTTTCTAACTCAATTTCTT
Found at i:24132767 original size:19 final size:18
Alignment explanation
Indices: 24132731--24132770 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24132721 TTTCCACTCG
*
24132731 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
24132749 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
24132768 TTT
1 TTT
24132771 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:24134250 original size:20 final size:19
Alignment explanation
Indices: 24134212--24134251 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
24134202 TTCATGTTAG
* *
24134212 TTAAGTTTGCATCATTAAA
1 TTAAGTTTGCATAAGTAAA
24134231 TTAAGTCTTGCATAAGTAAA
1 TTAAGT-TTGCATAAGTAAA
24134251 T
1 T
24134252 CATTTAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (19 bp):
TTAAGTTTGCATAAGTAAA
Found at i:24136329 original size:10 final size:10
Alignment explanation
Indices: 24136314--24136361 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
24136304 AATATATCTC
*
24136314 TTTTTTTCGA
1 TTTTTTTCAA
24136324 TTTTTTT-AA
1 TTTTTTTCAA
24136333 TTTTTTTCAAA
1 TTTTTTTC-AA
24136344 TTTTTTTTCAA
1 -TTTTTTTCAA
24136355 TTTTTTT
1 TTTTTTT
24136362 ACGAACCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
9 8 0.24
10 14 0.41
11 4 0.12
12 8 0.24
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:24136339 original size:12 final size:11
Alignment explanation
Indices: 24136314--24136361 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
24136304 AATATATCTC
*
24136314 TTTTTTTCGA-
1 TTTTTTTCAAT
24136324 TTTTTTT-AA-
1 TTTTTTTCAAT
24136333 TTTTTTTCAAAT
1 TTTTTTTC-AAT
24136345 TTTTTTTCAAT
1 TTTTTTTCAAT
24136356 TTTTTT
1 TTTTTT
24136362 ACGAACCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 8 0.24
10 7 0.21
11 11 0.32
12 8 0.24
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:24142633 original size:12 final size:12
Alignment explanation
Indices: 24142615--24142663 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 12
24142605 CTAGCTCTCT
24142615 TTTTTTTTCACAA
1 TTTTTTTTCA-AA
24142628 TTTTTTTTTCAAA
1 -TTTTTTTTCAAA
24142641 TTTTTTTTTCAAAA
1 -TTTTTTTTC-AAA
24142655 CTTTTTTTT
1 -TTTTTTTT
24142664 TCACAACTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 12 0.36
14 21 0.64
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:24142633 original size:14 final size:14
Alignment explanation
Indices: 24142614--24142669 Score: 87
Period size: 13 Copynumber: 4.0 Consensus size: 14
24142604 ACTAGCTCTC
24142614 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
24142628 TTTTTTTTTCA-AA
1 TTTTTTTTTCACAA
*
24142641 TTTTTTTTTCAAAA
1 TTTTTTTTTCACAA
24142655 CTTTTTTTTTCACAA
1 -TTTTTTTTTCACAA
24142670 CTTGATATCC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
13 13 0.33
14 13 0.33
15 13 0.33
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:24142671 original size:15 final size:15
Alignment explanation
Indices: 24142613--24142672 Score: 90
Period size: 15 Copynumber: 4.2 Consensus size: 15
24142603 AACTAGCTCT
24142613 CTTTTTTTTTCACAA
1 CTTTTTTTTTCACAA
24142628 -TTTTTTTTTCA-AA
1 CTTTTTTTTTCACAA
*
24142641 -TTTTTTTTTCAAAA
1 CTTTTTTTTTCACAA
24142655 CTTTTTTTTTCACAA
1 CTTTTTTTTTCACAA
24142670 CTT
1 CTT
24142673 GATATCCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
13 13 0.31
14 13 0.31
15 16 0.38
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (15 bp):
CTTTTTTTTTCACAA
Found at i:24147437 original size:22 final size:22
Alignment explanation
Indices: 24147409--24147452 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
24147399 TTTTGAACCA
24147409 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
24147431 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
24147453 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:24165049 original size:6 final size:6
Alignment explanation
Indices: 24165040--24165088 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
24165030 AACAGCATGT
* ** *
24165040 GAAAAA GAAAAA CAAAAA GAAAGT G-AAAA GAAATA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
24165087 GA
1 GA
24165089 GTGCGAGCGA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
5 3 0.09
6 31 0.91
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:24165591 original size:16 final size:15
Alignment explanation
Indices: 24165572--24165601 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
24165562 AGTATCAATT
24165572 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
24165588 TTTGATTGGGATGA
1 TTTGATTGGGATGA
24165602 TGGTTTGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:24171301 original size:29 final size:30
Alignment explanation
Indices: 24171205--24171311 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 30
24171195 ATTGGAGGAT
*
24171205 AAAAAAATTCGAAATTATAAAAAAAATTGAAA
1 AAAAAAATTCGAAGTT-TAAAAAAAATT-AAA
** * **
24171237 AAAAAAGA-GAGAGAGAATTTGAAAAAAATTTGA
1 AAAAAA-ATTCGA-AG--TTTAAAAAAAATTAAA
24171270 AAAAAAATTCGAAGTTT-AAAAAAATTAAA
1 AAAAAAATTCGAAGTTTAAAAAAAATTAAA
*
24171299 AAAGAAATTCGAA
1 AAAAAAATTCGAA
24171312 AAAAAAGGTC
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
29 22 0.37
30 3 0.05
32 11 0.19
33 11 0.19
34 10 0.17
35 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.12, T:0.21
Consensus pattern (30 bp):
AAAAAAATTCGAAGTTTAAAAAAAATTAAA
Found at i:24172321 original size:6 final size:6
Alignment explanation
Indices: 24172300--24172364 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
24172290 AAAATGAGTT
* *
24172300 AGAAAA AG--AA ACAAAA AGAAAA AGAAAA AGAAAA CGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
* * *
24172346 AGAAAT TGCAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA A
24172365 AATCGAAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
4 3 0.06
6 44 0.94
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (6 bp):
AGAAAA
Done.