Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 118 of 125
Found at i:36925697 original size:29 final size:29
Alignment explanation
Indices: 36925455--36925831 Score: 218
Period size: 30 Copynumber: 12.8 Consensus size: 29
36925445 CCCTCGAACC
* * *
36925455 TTTCCAAAATTATATTTTGACCCTTAAAC-
1 TTTCTAAAATTACATTTT-ACCCCTAAACT
* *
36925484 TTTCTATAAATTACATTTTGATCCCTATACT
1 TTTCTA-AAATTACATTTT-ACCCCTAAACT
* * * *
36925515 TTTCCAAAATTATATTTTAACCCTAAATT
1 TTTCTAAAATTACATTTTACCCCTAAACT
*
36925544 TTTCTATAAATTACATTTTAACCCCTTGAACT
1 TTTCTA-AAATTACATTTT-ACCCC-TAAACT
* * *
36925576 TTTCTAAAATTATATTTTAACCTTAAAACT
1 TTTCTAAAATTACATTTTACCCCT-AAACT
* * *
36925606 TTT-TATATATTACATTTTGATCCCTAAACA
1 TTTCTA-AAATTACATTTT-ACCCCTAAACT
* * ***
36925636 TTTCCAAAATTATATTTTGACCTAAAAAC-
1 TTTCTAAAATTACATTTT-ACCCCTAAACT
36925665 TTTCTAAAATTACATGTTTACCCCT-AACT
1 TTTCTAAAATTACAT-TTTACCCCTAAACT
* * * * **
36925694 TTTCCATAATTCCATTTTA-ACCTCGA-T
1 TTTCTAAAATTACATTTTACCCCTAAACT
*
36925721 TTTACCAAAATTATCATTTTACCCCTAAAC-
1 TTT-CTAAAATTA-CATTTTACCCCTAAACT
* * *
36925751 TTTCTAAAATTCCATTTT-GCCCT-GA-T
1 TTTCTAAAATTACATTTTACCCCTAAACT
* *
36925777 TTCTCCAAAATTACCATTTTACCCCTCGAA-T
1 TT-TCTAAAATTA-CATTTTACCCCT-AAACT
*
36925808 TTTCTAAAATTCCATTTTTACCCC
1 TTTCTAAAATTACA-TTTTACCCC
36925832 CGATTTCACT
Statistics
Matches: 269, Mismatches: 56, Indels: 45
0.73 0.15 0.12
Matches are distributed among these distances:
26 3 0.01
27 19 0.07
28 27 0.10
29 69 0.26
30 112 0.42
31 29 0.11
32 10 0.04
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTCTAAAATTACATTTTACCCCTAAACT
Found at i:36925798 original size:56 final size:57
Alignment explanation
Indices: 36925670--36925915 Score: 245
Period size: 56 Copynumber: 4.3 Consensus size: 57
36925660 AAAACTTTCT
* * ** *
36925670 AAAATTA-CATGTTTACCCCT-AACTTTTCCATAATTCCATTTTAACCTCGATTT-TACC
1 AAAATTACCAT-TTTACCCCTGAAC-TTTCTAAAATTCCATTTTTGCCCCGATTTCT-CC
* * *
36925727 AAAATTATCATTTTACCCCTAAACTTTCTAAAATTCCA-TTTTGCCCTGATTTCTCC
1 AAAATTACCATTTTACCCCTGAACTTTCTAAAATTCCATTTTTGCCCCGATTTCTCC
* * * *
36925783 AAAATTACCATTTTACCCCTCGAATTTTCTAAAATTCCATTTTTACCCCCGATTTCACT
1 AAAATTACCATTTTACCCCT-GAACTTTCTAAAATTCCATTTTT-GCCCCGATTTCTCC
** *
36925842 AAAATTACCATTTT-CCCC-GAACTTTCTAAAATTTTATTTTTGACCCCAATTTCAT-C
1 AAAATTACCATTTTACCCCTGAACTTTCTAAAATTCCATTTTTG-CCCCGATTTC-TCC
36925898 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
36925916 GCGAGTATGT
Statistics
Matches: 160, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
56 74 0.46
57 48 0.30
58 14 0.09
59 24 0.15
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCTGAACTTTCTAAAATTCCATTTTTGCCCCGATTTCTCC
Found at i:36925804 original size:86 final size:86
Alignment explanation
Indices: 36925446--36925831 Score: 213
Period size: 86 Copynumber: 4.4 Consensus size: 86
36925436 ATACTTTGAC
* ** *
36925446 CCTCGAACCTTTCCAAAATTAT-ATTTTGACCCTTAAACTTTCTATAAATTACAT-TTTGATCCC
1 CCTCGAA-TTTTCCAAAATTATCATTTT-ACCCCAAAACTTTCTA-AAATTACATGTTT-ACCCC
**
36925509 TATACTTTTCCAAAATTATATTTTAA
62 TA-ACTTTTCCAAAATTCCATTTTAA
* * ** * *
36925535 CC-CTAAATTTTTCTATAAATTA-CATTTTAACCCCTTGAACTTTTCTAAAATTATAT-TTTAAC
1 CCTC-GAA-TTTTCCA-AAATTATCATTTT-ACCCC-AAAAC-TTTCTAAAATTACATGTTTACC
* * * * *
36925597 CTTAAAACTTTT-TATATATTACATTTTGAT
60 CCT--AACTTTTCCA-AAATTCCATTTT-AA
* * **
36925627 CC-CTAAACATTTCCAAAATTAT-ATTTTGACCTAAAAACTTTCTAAAATTACATGTTTACCCCT
1 CCTC-GAA-TTTTCCAAAATTATCATTTT-ACCCCAAAACTTTCTAAAATTACATGTTTACCCCT
*
36925690 AACTTTTCCATAATTCCATTTTAA
63 AACTTTTCCAAAATTCCATTTTAA
* * * *
36925714 CCTCG-ATTTTACCAAAATTATCATTTTACCCCTAAACTTTCTAAAATTCCAT-TTT-GCCCTGA
1 CCTCGAATTTT-CCAAAATTATCATTTTACCCCAAAACTTTCTAAAATTACATGTTTACCCCTAA
*
36925776 -TTTCTCCAAAATTACCATTTTACC
65 CTTT-TCCAAAATT-CCATTTTA-A
* *
36925800 CCTCGAATTTTCTAAAATT-CCATTTTTACCCC
1 CCTCGAATTTTCCAAAATTATCA-TTTTACCCC
36925832 CGATTTCACT
Statistics
Matches: 235, Mismatches: 42, Indels: 43
0.73 0.13 0.13
Matches are distributed among these distances:
83 3 0.01
84 13 0.06
85 16 0.07
86 53 0.23
87 13 0.06
88 18 0.08
89 24 0.10
90 30 0.13
91 45 0.19
92 20 0.09
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (86 bp):
CCTCGAATTTTCCAAAATTATCATTTTACCCCAAAACTTTCTAAAATTACATGTTTACCCCTAAC
TTTTCCAAAATTCCATTTTAA
Found at i:36925843 original size:29 final size:29
Alignment explanation
Indices: 36925667--36925915 Score: 123
Period size: 29 Copynumber: 8.7 Consensus size: 29
36925657 CTAAAAACTT
**
36925667 TCTAAAATTA-CATGTTTACCCCTAACTTT-
1 TCTAAAATTACCAT-TTTACCCCCGA-TTTC
* * * *
36925696 TCCATAATT-CCATTTTAACCTCGATTT-
1 TCTAAAATTACCATTTTACCCCCGATTTC
* * ** *
36925723 TACCAAAATTATCATTTTACCCCTAAACTT-
1 T-CTAAAATTACCATTTTACCCC-CGATTTC
* *
36925753 TCTAAAATT-CCATTTT-GCCCTGATTTC
1 TCTAAAATTACCATTTTACCCCCGATTTC
*
36925780 TCCAAAATTACCATTTTACCCCTCGAATTT-
1 TCTAAAATTACCATTTTACCCC-CG-ATTTC
36925810 TCTAAAATT-CCATTTTTACCCCCGATTTC
1 TCTAAAATTACCA-TTTTACCCCCGATTTC
* *
36925839 ACTAAAATTACCATTTT--CCCCGAACTT-
1 TCTAAAATTACCATTTTACCCCCG-ATTTC
** *
36925866 TCTAAAATT-TTATTTTTGA-CCCCAATTTC
1 TCTAAAATTACCA-TTTT-ACCCCCGATTTC
36925895 ATC-AAAATTACCATTTTACCC
1 -TCTAAAATTACCATTTTACCC
36925916 GCGAGTATGT
Statistics
Matches: 168, Mismatches: 32, Indels: 40
0.70 0.13 0.17
Matches are distributed among these distances:
26 4 0.02
27 32 0.19
28 38 0.23
29 62 0.37
30 28 0.17
31 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (29 bp):
TCTAAAATTACCATTTTACCCCCGATTTC
Found at i:36926953 original size:59 final size:57
Alignment explanation
Indices: 36926873--36927042 Score: 196
Period size: 59 Copynumber: 2.9 Consensus size: 57
36926863 TTTGAATCTA
* * * * *** **
36926873 AAAAAAACTTAGGTACCAAATTAGAAAAAAATATCAAGTTCGGGTATTAAATTGGATT
1 AAAAAAATTTAGATA-CAAATTAGAAAAAAGTGTCAAGTTCAAATACCAAATTGGATT
* *
36926931 AAAAAAAGTTTAGATACAAAATTAGGAAAAAGTGTCAAGTTCAAATACCAAATTGGATC
1 AAAAAAA-TTTAGATAC-AAATTAGAAAAAAGTGTCAAGTTCAAATACCAAATTGGATT
36926990 AAAAAATATTTAGATATCAAATTAGAAAAAAGTGTCAAGTTCAAATACCAAAT
1 AAAAAA-ATTTAGATA-CAAATTAGAAAAAAGTGTCAAGTTCAAATACCAAAT
36927043 GTTTATTATT
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
58 8 0.08
59 86 0.90
60 2 0.02
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (57 bp):
AAAAAAATTTAGATACAAATTAGAAAAAAGTGTCAAGTTCAAATACCAAATTGGATT
Found at i:36929298 original size:3 final size:3
Alignment explanation
Indices: 36929290--36929314 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36929280 TTAGTTTTAA
36929290 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
36929315 GGTAACCATA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:36929724 original size:14 final size:14
Alignment explanation
Indices: 36929705--36929737 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
36929695 ATAAGTCTAG
36929705 AATTAATTT-GTACA
1 AATTAATTTAG-ACA
36929719 AATTAATTTAGACA
1 AATTAATTTAGACA
36929733 AATTA
1 AATTA
36929738 TTGCATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (14 bp):
AATTAATTTAGACA
Found at i:36930326 original size:19 final size:19
Alignment explanation
Indices: 36930275--36930327 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
36930265 AACTCAACTC
36930275 AATAATTAAGTTT-AGGATT
1 AATAATTAA-TTTAAGGATT
*
36930294 AATAATATATTTTAAGGA-T
1 AATAAT-TAATTTAAGGATT
36930313 AATAATGTAATTTAA
1 AATAAT-TAATTTAA
36930328 TAACATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (19 bp):
AATAATTAATTTAAGGATT
Found at i:36931450 original size:30 final size:31
Alignment explanation
Indices: 36931416--36931473 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
36931406 TTTAGTTCAT
* * *
36931416 TTATATATTTATATAAT-TTTTTTAAAAATA
1 TTATAAATATATATAATATTTTGTAAAAATA
*
36931446 TTATAAATATATATTATATTTTGTAAAA
1 TTATAAATATATATAATATTTTGTAAAA
36931474 TTTTATGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 14 0.61
31 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (31 bp):
TTATAAATATATATAATATTTTGTAAAAATA
Found at i:36931761 original size:21 final size:21
Alignment explanation
Indices: 36931721--36931771 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
36931711 ATGCTTAAAT
*
36931721 CAAAAATT-ATAAAATTATAA
1 CAAAAATTGATAAAATCATAA
36931741 -AAAAATTGATAAAAATCATAA
1 CAAAAATTGAT-AAAATCATAA
36931762 GCAAAAATTG
1 -CAAAAATTG
36931772 GGAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.27
20 2 0.08
21 9 0.35
23 8 0.31
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (21 bp):
CAAAAATTGATAAAATCATAA
Found at i:36936506 original size:31 final size:31
Alignment explanation
Indices: 36936468--36936535 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
36936458 TTAAAAAAAT
* *
36936468 ATTGAACTATTCGAAAGTTTTTATTTAACTC
1 ATTGAACTATTCAAAAGTTGTTATTTAACTC
*
36936499 ATTGAACTATTCAAAAGTTGTTATTTAAGTC
1 ATTGAACTATTCAAAAGTTGTTATTTAACTC
36936530 ATTGAA
1 ATTGAA
36936536 TTGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (31 bp):
ATTGAACTATTCAAAAGTTGTTATTTAACTC
Found at i:36938481 original size:11 final size:11
Alignment explanation
Indices: 36938465--36938489 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
36938455 GGCTGGTTGT
36938465 TGAAGTAGTAA
1 TGAAGTAGTAA
36938476 TGAAGTAGTAA
1 TGAAGTAGTAA
36938487 TGA
1 TGA
36938490 CCTTTACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (11 bp):
TGAAGTAGTAA
Found at i:36957338 original size:13 final size:13
Alignment explanation
Indices: 36957320--36957344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36957310 ACCAAATGAT
36957320 ATTAATTGATTTG
1 ATTAATTGATTTG
36957333 ATTAATTGATTT
1 ATTAATTGATTT
36957345 AACCGACTGA
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:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
ATTAATTGATTTG
Found at i:36958096 original size:21 final size:20
Alignment explanation
Indices: 36958071--36958111 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
36958061 TTTTAACAAT
*
36958071 TTTAACATTAAAATAAAATAA
1 TTTAACAAT-AAATAAAATAA
*
36958092 TTTAACAATATATAAAATAA
1 TTTAACAATAAATAAAATAA
36958112 ATAACCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTAACAATAAATAAAATAA
Found at i:36958157 original size:16 final size:18
Alignment explanation
Indices: 36958136--36958168 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
36958126 ATTATTGATA
36958136 ATATTAT-TTAA-ATTAT
1 ATATTATATTAATATTAT
36958152 ATATTATATTAATATTA
1 ATATTATATTAATATTA
36958169 ACATTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTATATTAATATTAT
Found at i:36958714 original size:4 final size:4
Alignment explanation
Indices: 36958652--36958688 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
36958642 GCTATATCAT
*
36958652 TTTA TCTA TTTA TTTA TTT- TTTA TTT- TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
36958689 TCCTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:36959894 original size:2 final size:2
Alignment explanation
Indices: 36959887--36959916 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36959877 GTTTTGATGA
36959887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36959917 GAAATTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36960042 original size:15 final size:16
Alignment explanation
Indices: 36960004--36960049 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
36959994 TCACTTTTAA
*
36960004 TATTAAATTAAT-TTT
1 TATTAAAATAATATTT
36960019 TATTAAAAATAATATTT
1 TATT-AAAATAATATTT
36960036 T-TTAAAATAATATT
1 TATTAAAATAATATT
36960050 GGTTAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 15 0.54
16 9 0.32
17 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTAAAATAATATTT
Found at i:36964429 original size:15 final size:16
Alignment explanation
Indices: 36964391--36964436 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
36964381 TCCCTTTTAA
*
36964391 TATTAAATTAAT-TTT
1 TATTAAAATAATATTT
36964406 TATTAAAAATAATATTT
1 TATT-AAAATAATATTT
36964423 T-TTAAAATAATATT
1 TATTAAAATAATATT
36964437 GGTTAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 15 0.54
16 9 0.32
17 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTAAAATAATATTT
Found at i:36966062 original size:9 final size:10
Alignment explanation
Indices: 36966041--36966066 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
36966031 TTATTAATTT
36966041 AAAATTTTAA
1 AAAATTTTAA
36966051 AAAATTTTAA
1 AAAATTTTAA
36966061 AAAATT
1 AAAATT
36966067 AAATGAAAAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:36970064 original size:116 final size:114
Alignment explanation
Indices: 36969859--36970086 Score: 305
Period size: 116 Copynumber: 2.0 Consensus size: 114
36969849 ACAACTCTAC
*
36969859 ATTGAGTCCATTCTGGCTCTTCAGGAAGCTAGCAGTCGGCTCACACAAGGTATGCATGGTATCTC
1 ATTGAGTCCATTCTGGCTCATCAGGAAGCTAGCAGTCGGCTCACACAAGGTATGCATGGTATCTC
* *
36969924 AGTTTTTAGGAGGCGTTCCACATTAAATAGCCTTTTTGAACTTTTTGTAT
66 AGTTTTTAGAAGGCCTTCCACATTAAATAGCC-TTTTGAACTTTTTGTAT
* * ** * * **
36969974 ATTGAGTCTATTCTGGTTCATCAGGAAAGCTAGTTGTTGGCTCACACAAGGTTTGTGTGGTATCT
1 ATTGAGTCCATTCTGGCTCATCAGG-AAGCTAGCAGTCGGCTCACACAAGGTATGCATGGTATCT
* *
36970039 CA-TTTGTTAGAAGGCCTTCCGCATTAAATAGCCTTTTGAGCTTTTTGT
65 CAGTTT-TTAGAAGGCCTTCCACATTAAATAGCCTTTTGAACTTTTTGT
36970087 CCTTGACTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
115 39 0.40
116 59 0.60
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (114 bp):
ATTGAGTCCATTCTGGCTCATCAGGAAGCTAGCAGTCGGCTCACACAAGGTATGCATGGTATCTC
AGTTTTTAGAAGGCCTTCCACATTAAATAGCCTTTTGAACTTTTTGTAT
Found at i:36971150 original size:6 final size:6
Alignment explanation
Indices: 36971139--36971165 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
36971129 CCTTTTATGA
36971139 TGCCCT TGCCCT TGCCCT TGCCCT TGC
1 TGCCCT TGCCCT TGCCCT TGCCCT TGC
36971166 ATCTCTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.19, T:0.33
Consensus pattern (6 bp):
TGCCCT
Found at i:36978713 original size:8 final size:8
Alignment explanation
Indices: 36978700--36978728 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
36978690 CTCATATCGA
36978700 TGAAACTT
1 TGAAACTT
36978708 TGAAACTT
1 TGAAACTT
36978716 TGAAACTT
1 TGAAACTT
36978724 TGAAA
1 TGAAA
36978729 AGATTAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (8 bp):
TGAAACTT
Found at i:36989285 original size:29 final size:29
Alignment explanation
Indices: 36989253--36989314 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
36989243 AAAATGAGAC
36989253 TTTGGA-TGCCCGG-GGGCCAAAATGGTAAT
1 TTTGGACT-CCCGGAGGG-CAAAATGGTAAT
* *
36989282 TTTGGACTCTCGGAGGGTAAAATGGTAAT
1 TTTGGACTCCCGGAGGGCAAAATGGTAAT
36989311 TTTG
1 TTTG
36989315 AAAAAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.31
Consensus pattern (29 bp):
TTTGGACTCCCGGAGGGCAAAATGGTAAT
Found at i:36989580 original size:28 final size:29
Alignment explanation
Indices: 36989416--36989695 Score: 207
Period size: 30 Copynumber: 9.5 Consensus size: 29
36989406 ATTCGGGGAT
* *
36989416 AAAATGGTAATTTTTGAATTTTTTGGGGTCA
1 AAAATGG-AATTTTTGAA-GTTTTGGGGTTA
**
36989447 AAAATGGAATTTTTGAAGTTTCAAGGG-TA
1 AAAATGGAATTTTTGAAGTTT-TGGGGTTA
* * *
36989476 AAAATGTAATTTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAA-TTTTT-GAAGTTTTGGGGTTA
*
36989507 AAAATGGAATTTTTGAAAGTTTTGGGGGGTA
1 AAAATGGAATTTTTG-AAGTTTT-GGGGTTA
* * *
36989538 AAAAAGTAATTTTTGGA-TTTTGGGGTTA
1 AAAATGGAATTTTTGAAGTTTTGGGGTTA
*
36989566 AAAATGGAATCTTTGGAA-TTTTGAGGG-T-
1 AAAATGGAAT-TTTTGAAGTTTTG-GGGTTA
* *
36989594 AAAATGTAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTT-GAAGTTTTGGGGTTA
36989624 AAAATGGAATTTTTGAAAG-TTTGAGGG-T-
1 AAAATGGAATTTTTG-AAGTTTTG-GGGTTA
* * **
36989652 AAAATGTAATTTTGGGAAGTTTTAAGGTTA
1 AAAATGGAATTTT-TGAAGTTTTGGGGTTA
* *
36989682 AAAGTGAAATTTTT
1 AAAATGGAATTTTT
36989696 TAAAGTTCAG
Statistics
Matches: 199, Mismatches: 32, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
27 3 0.02
28 46 0.23
29 43 0.22
30 65 0.33
31 42 0.21
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (29 bp):
AAAATGGAATTTTTGAAGTTTTGGGGTTA
Found at i:36989617 original size:58 final size:57
Alignment explanation
Indices: 36989271--36989732 Score: 272
Period size: 58 Copynumber: 7.9 Consensus size: 57
36989261 CCCGGGGGCC
* ** * * **
36989271 AAAATGGTAATTTTGGACTCTCGGAGGGTAAAATGGTAATTTTGAAAAAATTTGGGGTTA
1 AAAATGG-AATTTTGGAAT-TTTGAGGGTAAAAT-GTAATTTTTAGAAGTTTTGGGGTTA
* * * *** * * * *
36989331 AAAAT-AACATTTTAG-ATGTTTGAGGGTAAAACGGTAATTTTTAGAAAAATCGAGATAA
1 AAAATGGA-ATTTTGGAAT-TTTGAGGGTAAAA-TGTAATTTTTAGAAGTTTTGGGGTTA
* * * *
36989389 AAAATGGGATTTTGGACA-TTCG-GGGATAAAATGGTAATTTTT-GAATTTTTTGGGGTCA
1 AAAATGGAATTTTGGA-ATTTTGAGGG-TAAAAT-GTAATTTTTAGAA-GTTTTGGGGTTA
* ** * * *
36989447 AAAATGGAATTTTTGAAGTTTCAAGGGTAAAAATGTAATTTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTGGAA-TTTTGAGGGT-AAAATGTAA-TTTTTAGAAGTTTTGGGGTTA
* * * *
36989507 AAAATGGAATTTTTGAAAGTTTTGGGGGGTAAAAAAGTAATTTTT-GGA-TTTTGGGGTTA
1 AAAATGGAA-TTTTGGAA-TTTT-GAGGGT-AAAATGTAATTTTTAGAAGTTTTGGGGTTA
*
36989566 AAAATGGAATCTTTGGAATTTTGAGGGTAAAATGTAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAAT-TTTGGAATTTTGAGGGTAAAATGTAATTTTTAGAAGTTTTGGGGTTA
* * ** **
36989624 AAAATGGAATTTTTGAAAGTTTGAGGGTAAAATGTAATTTTGGGAAGTTTTAAGGTTA
1 AAAATGGAA-TTTTGGAATTTTGAGGGTAAAATGTAATTTTTAGAAGTTTTGGGGTTA
* * ** ** * *
36989682 AAAGTGAAATTTTTTAAAGTTCAGGGGTAAAATGTAATTTTTGGACAGTTT
1 AAAATGGAATTTTGGAATTTTGA-GGGTAAAATGTAATTTTTAGA-AGTTT
36989733 AGGGACCTTT
Statistics
Matches: 318, Mismatches: 62, Indels: 45
0.75 0.15 0.11
Matches are distributed among these distances:
56 13 0.04
57 23 0.07
58 169 0.53
59 44 0.14
60 38 0.12
61 18 0.06
62 13 0.04
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (57 bp):
AAAATGGAATTTTGGAATTTTGAGGGTAAAATGTAATTTTTAGAAGTTTTGGGGTTA
Found at i:36991729 original size:16 final size:16
Alignment explanation
Indices: 36991708--36991808 Score: 69
Period size: 17 Copynumber: 6.0 Consensus size: 16
36991698 TATTTTTTGG
36991708 AATTTTAATGTT-AAAT
1 AATTTTAAT-TTAAAAT
36991724 AATTTTTAATTTAAAAT
1 AA-TTTTAATTTAAAAT
*
36991741 AAATTTAAATTTAAAAT
1 -AATTTTAATTTAAAAT
* * *
36991758 AAATTTAAACTCAAAAT
1 -AATTTTAATTTAAAAT
**
36991775 AAATTCGAATTTAAAAT
1 -AATTTTAATTTAAAAT
**
36991792 AAATTAAAATTTAAAAT
1 -AATTTTAATTTAAAAT
36991809 TAAAAATTGG
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
16 4 0.05
17 67 0.92
18 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (16 bp):
AATTTTAATTTAAAAT
Found at i:36991740 original size:17 final size:17
Alignment explanation
Indices: 36991720--36991808 Score: 115
Period size: 17 Copynumber: 5.2 Consensus size: 17
36991710 TTTTAATGTT
* *
36991720 AAATAATTTTTAATTTA
1 AAATAAATTTAAATTTA
36991737 AAATAAATTTAAATTTA
1 AAATAAATTTAAATTTA
* *
36991754 AAATAAATTTAAACTCA
1 AAATAAATTTAAATTTA
**
36991771 AAATAAATTCGAATTTA
1 AAATAAATTTAAATTTA
*
36991788 AAATAAATTAAAATTTA
1 AAATAAATTTAAATTTA
36991805 AAAT
1 AAAT
36991809 TAAAAATTGG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 62 1.00
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
AAATAAATTTAAATTTA
Found at i:36993654 original size:15 final size:15
Alignment explanation
Indices: 36993634--36993663 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36993624 TAATCACTAA
36993634 TAGAAAATCCTTGTC
1 TAGAAAATCCTTGTC
36993649 TAGAAAATCCTTGTC
1 TAGAAAATCCTTGTC
36993664 CCAACAACGT
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:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
TAGAAAATCCTTGTC
Found at i:36995677 original size:60 final size:58
Alignment explanation
Indices: 36995479--36995677 Score: 170
Period size: 60 Copynumber: 3.4 Consensus size: 58
36995469 TGGGTTTTTA
*
36995479 GGGGT-AAAATGGTAATTTTT-GTGAAATCGGGGCTAAAAATGGAATTTGGAAAGTTT
1 GGGGTAAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTGGAAAGTTT
* * ** * ** * * *
36995535 GGGGAATAAAATGGTAAATTTTGGCAAAAACAAGGTCAAAAAATGAAATTTTGGAAAGTTC
1 GGGGTA-AAAATGGTAATTTTTGGTGAAATCGGGGT-TAAAAATGGAA-TTTGGAAAGTTT
* * * * * *
36995596 GGAGG-CAAAACGATAAGTTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTT
1 GG-GGTAAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTT-GGAAAGTTT
36995655 GAGGGTAAAAATGGTAATTTTTG
1 G-GGGTAAAAATGGTAATTTTTG
36995678 AAAGTTTTGG
Statistics
Matches: 105, Mismatches: 29, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
56 4 0.04
58 17 0.16
59 25 0.24
60 44 0.42
61 13 0.12
62 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.29, T:0.29
Consensus pattern (58 bp):
GGGGTAAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTGGAAAGTTT
Found at i:36995712 original size:30 final size:30
Alignment explanation
Indices: 36995652--36995942 Score: 340
Period size: 30 Copynumber: 9.7 Consensus size: 30
36995642 TTTAGGGAAG
* *
36995652 TTTGAGGGTAAAAATGGTAATTTTTG-AAAGT
1 TTTG-GGGTCAAAAT-GTAATTTTGGAAAAGT
* **
36995683 TTTGGGGTCAAAGTAAAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
*
36995713 TTTGGAGTCAAAATGTAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
36995743 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* *
36995773 TTTGGGATCAAAATGTAATTTT-TAGAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGA-AAAGT
* *
36995803 TCTGGGGTCAAAATGTAATTTT-TAGAAAG-
1 TTTGGGGTCAAAATGTAATTTTGGA-AAAGT
* * *
36995832 TTTAGGGTCAAAATATAATTTT-TAGAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGA-AAAGT
*
36995862 TTTGGGGTCAAAATGTAATTTTAGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* *
36995892 TTTAGGGTCAAAATATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGT
* *
36995922 TTAGGGGTCAAAATGAAATTT
1 TTTGGGGTCAAAATGTAATTT
36995943 CTAGACAATT
Statistics
Matches: 229, Mismatches: 27, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
29 34 0.15
30 190 0.83
31 5 0.02
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTGGGGTCAAAATGTAATTTTGGAAAAGT
Found at i:36995726 original size:89 final size:86
Alignment explanation
Indices: 36995641--36995942 Score: 301
Period size: 89 Copynumber: 3.4 Consensus size: 86
36995631 TAAAAATGGG
* * *
36995641 ATTTAGGGAAGTTTGAGGGTAAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAGTAAAATTTTG
1 ATTTAGGAAAGTTTGAGGGTCAAAAT-GTAATTTTTGAAAGTTTTGGGGTCAAAGT-AAATTTTA
36995706 GAAAAGTTTTGGAGTCAAAATGTA
64 GAAAAGTTTTGG-GTCAAAATGTA
* * * *
36995730 ATTTTGGAAAAGTTTTG-GGGTCAAAATGTAATTTTGGAAAAGTTTTGGGATCAAAATGTAATTT
1 ATTTAGG-AAAG-TTTGAGGGTCAAAATGTAATTTTTG-AAAGTTTTGGGGTC-AAA-GTAAATT
*
36995794 TTAG-AAAGTTCTGGGGTCAAAATGTA
61 TTAGAAAAGTT-TTGGGTCAAAATGTA
*
36995820 ATTTTTA-GAAAGTTT-AGGGTCAAAATATAATTTTTAGAAAGTTTTGGGGTCAAAATGT-AATT
1 A--TTTAGGAAAGTTTGAGGGTCAAAATGTAATTTTT-GAAAGTTTTGGGGTC-AAA-GTAAATT
*
36995882 TTAGAAAAGTTTTAGGGTCAAAATATA
61 TTAGAAAAGTTTT-GGGTCAAAATGTA
* *
36995909 ATTTTGGAAAAGTTT-AGGGGTCAAAATGAAATTT
1 ATTTAGG-AAAGTTTGA-GGGTCAAAATGTAATTT
36995943 CTAGACAATT
Statistics
Matches: 180, Mismatches: 18, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
87 3 0.02
88 9 0.05
89 82 0.46
90 63 0.35
91 18 0.10
92 5 0.03
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (86 bp):
ATTTAGGAAAGTTTGAGGGTCAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAGTAAATTTTAGA
AAAGTTTTGGGTCAAAATGTA
Found at i:36995870 original size:119 final size:117
Alignment explanation
Indices: 36995649--36995957 Score: 367
Period size: 119 Copynumber: 2.6 Consensus size: 117
36995639 GGATTTAGGG
* * * *
36995649 AAGTTTGAGGGTAAAAATGGTAATTTTTGAAAGTTTTGGGGTC-AAA-GTAAAATTTTGGAAAAG
1 AAGTTTTAGGGTCAAAAT-GTAATTTTTGAAAG-TTTGGGGTCAAAATGT-AATTTTTAG-AAAG
* * * *
36995712 TTTTGGAGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAA
62 TTTAGG-GTCAAAATATAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATTTTAGAA
36995769 AAGTTTT-GGGATCAAAATGTAATTTTTAGAAAGTTCTGGGGTCAAAATGTAATTTTTAGAAAGT
1 AAGTTTTAGGG-TCAAAATGTAATTTTT-GAAAGTT-TGGGGTCAAAATGTAATTTTTAGAAAGT
36995833 TTAGGGTCAAAATATAATTTTTAG-AAAGTTTTGGGGTCAAAATGTAATTTTAGAA
63 TTAGGGTCAAAATATAA-TTTTAGAAAAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * * *
36995888 AAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATGAAATTTCTAGACAA-T
1 AAGTTTTAGGGTCAAAATGTAATTTTTG-AAAGTTT-GGGGTCAAAATGTAATTTTTAGA-AAGT
36995952 TTAGGG
63 TTAGGG
36995958 ACTTACAAAG
Statistics
Matches: 167, Mismatches: 12, Indels: 21
0.83 0.06 0.10
Matches are distributed among these distances:
118 2 0.01
119 110 0.66
120 43 0.26
121 10 0.06
122 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (117 bp):
AAGTTTTAGGGTCAAAATGTAATTTTTGAAAGTTTGGGGTCAAAATGTAATTTTTAGAAAGTTTA
GGGTCAAAATATAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATTTTAGAA
Found at i:36997867 original size:6 final size:6
Alignment explanation
Indices: 36997850--36997928 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
36997840 TTTAGACTTT
* * * * * *
36997850 AATTTA AA-TTA ATTTTA AATTTA AA-ATA AATTTA GACTCA AATTCA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
36997896 AATTTA AAGTTT- AATTTA AATATA AATTTA AAT
1 AATTTA AA-TTTA AATTTA AATTTA AATTTA AAT
36997929 AAATCTAAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
5 11 0.19
6 43 0.75
7 3 0.05
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:37001025 original size:13 final size:13
Alignment explanation
Indices: 37001004--37001089 Score: 53
Period size: 11 Copynumber: 7.1 Consensus size: 13
37000994 TTTATGGACT
37001004 TTTAATATTTAAA
1 TTTAATATTTAAA
* *
37001017 TTTAGTATTTTAAT
1 TTTAATA-TTTAAA
37001031 TTTAAT-TTT-AA
1 TTTAATATTTAAA
37001042 TTTAA-ATTT-AA
1 TTTAATATTTAAA
**
37001053 GGTAA-ATTTAAAA
1 TTTAATATTT-AAA
*
37001066 TTTAAGA--TAAA
1 TTTAATATTTAAA
37001077 TTTAA-ATTTAAA
1 TTTAATATTTAAA
37001089 T
1 T
37001090 AAATTTAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
10 1 0.02
11 26 0.45
12 9 0.16
13 11 0.19
14 11 0.19
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (13 bp):
TTTAATATTTAAA
Found at i:37001051 original size:6 final size:6
Alignment explanation
Indices: 37001004--37001103 Score: 66
Period size: 6 Copynumber: 16.8 Consensus size: 6
37000994 TTTATGGACT
* * * *
37001004 TTTAATA TTTAAA TTTAGTA TTTTAA TTTTAA TTTTAA TTTAAA TTT-AA
1 TTTAA-A TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
37001053 GGTAAA TTTAAAA TTTAAGA --TAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTT-AAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
37001099 ATTAA
1 TTTAA
37001104 TTTGACTCTA
Statistics
Matches: 76, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
4 5 0.07
5 6 0.08
6 49 0.64
7 16 0.21
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:37001051 original size:11 final size:11
Alignment explanation
Indices: 37001025--37001097 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
37001015 AATTTAGTAT
*
37001025 TTTAATTTTAAT
1 TTTAA-TTTAAA
37001037 TTTAATTTAAA
1 TTTAATTTAAA
**
37001048 TTTAAGGTAAA
1 TTTAATTTAAA
37001059 TTTAAAATTTAAGA
1 TTT--AATTTAA-A
*
37001073 -TAAATTTAAA
1 TTTAATTTAAA
*
37001083 TTTAA-ATAAA
1 TTTAATTTAAA
37001093 TTTAA
1 TTTAA
37001098 AATTAATTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
10 10 0.20
11 27 0.55
12 5 0.10
13 6 0.12
14 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:37001066 original size:18 final size:17
Alignment explanation
Indices: 37001040--37001103 Score: 94
Period size: 18 Copynumber: 3.8 Consensus size: 17
37001030 TTTTAATTTT
*
37001040 AATTTAAATTTAAGGTA
1 AATTTAAATTTAAGATA
37001057 AATTTAAAATTTAAGATA
1 AATTT-AAATTTAAGATA
37001075 AATTTAAATTTAA-ATA
1 AATTTAAATTTAAGATA
*
37001091 AATTTAAAATTAA
1 AATTTAAATTTAA
37001104 TTTGACTCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
16 15 0.34
17 13 0.30
18 16 0.36
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AATTTAAATTTAAGATA
Found at i:37007181 original size:11 final size:11
Alignment explanation
Indices: 37007165--37007189 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
37007155 TAATTAAAAC
37007165 AAAATAATATG
1 AAAATAATATG
37007176 AAAATAATATG
1 AAAATAATATG
37007187 AAA
1 AAA
37007190 TTTTCAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (11 bp):
AAAATAATATG
Found at i:37024111 original size:20 final size:21
Alignment explanation
Indices: 37024086--37024125 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
37024076 TGTCCTTCAA
*
37024086 TATCAGCTCCCTTTT-TTTCT
1 TATCAGCACCCTTTTATTTCT
37024106 TATCAGCACCCTTTTATTTC
1 TATCAGCACCCTTTTATTTC
37024126 CCCTATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.30, G:0.05, T:0.50
Consensus pattern (21 bp):
TATCAGCACCCTTTTATTTCT
Found at i:37038402 original size:13 final size:13
Alignment explanation
Indices: 37038380--37038415 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
37038370 TTATACAAAA
37038380 AAATTTAT-ATA-
1 AAATTTATAATAT
37038391 AAATTTA-AATAT
1 AAATTTATAATAT
37038403 AAATTTATAATAT
1 AAATTTATAATAT
37038416 TCTGAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.45
12 7 0.32
13 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTTATAATAT
Found at i:37044594 original size:9 final size:9
Alignment explanation
Indices: 37044580--37044609 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
37044570 TCAATTGTAC
37044580 ATTATTTTG
1 ATTATTTTG
37044589 ATTATTTTG
1 ATTATTTTG
37044598 ATTATTTTG
1 ATTATTTTG
37044607 ATT
1 ATT
37044610 GGTATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (9 bp):
ATTATTTTG
Found at i:37047171 original size:20 final size:18
Alignment explanation
Indices: 37047146--37047180 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
37047136 ATTCTTTATT
37047146 TATTTTTTAAAATTATAA
1 TATTTTTTAAAATTATAA
*
37047164 TTTTTTTTAAAATTATA
1 TATTTTTTAAAATTATA
37047181 GTCAAGTAAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTTTAAAATTATAA
Found at i:37053665 original size:19 final size:21
Alignment explanation
Indices: 37053643--37053681 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
37053633 AAAAATCTTA
37053643 TAAAA-TATAAA-ATATTATT
1 TAAAATTATAAATATATTATT
*
37053662 TAAAATTCTAAATATATTAT
1 TAAAATTATAAATATATTAT
37053682 AAAAGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATTATAAATATATTATT
Found at i:37059905 original size:14 final size:14
Alignment explanation
Indices: 37059886--37059938 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
37059876 TAAATTAGTA
37059886 AAATCACATGCACC
1 AAATCACATGCACC
37059900 AAATCACATGCACC
1 AAATCACATGCACC
37059914 -AA-CAC---CACC
1 AAATCACATGCACC
37059923 AAATCACATGCACC
1 AAATCACATGCACC
37059937 AA
1 AA
37059939 CACCTTAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 4 0.12
10 2 0.06
11 3 0.09
12 3 0.09
13 2 0.06
14 20 0.59
ACGTcount: A:0.45, C:0.38, G:0.06, T:0.11
Consensus pattern (14 bp):
AAATCACATGCACC
Found at i:37059922 original size:23 final size:23
Alignment explanation
Indices: 37059896--37059942 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
37059886 AAATCACATG
37059896 CACCAAATCACATGCACCAACAC
1 CACCAAATCACATGCACCAACAC
37059919 CACCAAATCACATGCACCAACAC
1 CACCAAATCACATGCACCAACAC
37059942 C
1 C
37059943 TTAACTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.45, G:0.04, T:0.09
Consensus pattern (23 bp):
CACCAAATCACATGCACCAACAC
Found at i:37062853 original size:18 final size:19
Alignment explanation
Indices: 37062827--37062869 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
37062817 TAATATCCCA
37062827 ATAAATTA-TTAAAAAATT
1 ATAAATTATTTAAAAAATT
* *
37062845 ATAATTTATTTTTAAAAATT
1 ATAAATTA-TTTAAAAAATT
37062865 ATAAA
1 ATAAA
37062870 CCATATTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 7 0.35
20 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAATTATTTAAAAAATT
Found at i:37065322 original size:61 final size:61
Alignment explanation
Indices: 37065227--37065354 Score: 188
Period size: 61 Copynumber: 2.1 Consensus size: 61
37065217 TGGGTATTTT
* * *
37065227 TCGAGAAAAATATTTTAAATTTTTTTGATGTTGGCCATCAAATGGCCGATA-CCTCCTGTTC
1 TCGAGAAAAAAAATTTAAATTTTTTTGATGTTGGCCATCAAATGGCCGACATCC-CCTGTTC
*
37065288 TCGAGAAAAAAAATTTAAATTTTTTTTG-TGTTGGCCATCAAATTGCCGACATCCCCTGTTC
1 TCGAGAAAAAAAATTTAAA-TTTTTTTGATGTTGGCCATCAAATGGCCGACATCCCCTGTTC
37065349 TCGAGA
1 TCGAGA
37065355 GTCATCAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
61 51 0.84
62 10 0.16
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (61 bp):
TCGAGAAAAAAAATTTAAATTTTTTTGATGTTGGCCATCAAATGGCCGACATCCCCTGTTC
Found at i:37065361 original size:95 final size:96
Alignment explanation
Indices: 37065262--37065446 Score: 275
Period size: 97 Copynumber: 1.9 Consensus size: 96
37065252 TGATGTTGGC
* * **
37065262 CATCAAATGGCCGATACCTCCTGTTCTCGAG-AAAAAAAATT-TAAATTTTTTTTGTGTTGGCCA
1 CATCAAATGGCCGACACCTCCTGTTCTCGAGAAAAAAAAATTCAAAATTTTTTGAGTGTTGGCCA
*
37065325 TCAAATTGCCGACATCCCCTGTTCTCGAGAGT
66 TCAAATGGCCGACA-CCCCTGTTCTCGAGAGT
*
37065357 CATCAAATGGCCGACACCTCCTGTTCTGGAGAAAAAAAAATTCAAAATTTTTTGAGTGTTGGCCA
1 CATCAAATGGCCGACACCTCCTGTTCTCGAGAAAAAAAAATTCAAAATTTTTTGAGTGTTGGCCA
* *
37065422 TCAAATGGTCGACACCCCTTTTCTC
66 TCAAATGGCCGACACCCCTGTTCTC
37065447 AAATAAAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
95 29 0.36
96 20 0.25
97 31 0.39
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (96 bp):
CATCAAATGGCCGACACCTCCTGTTCTCGAGAAAAAAAAATTCAAAATTTTTTGAGTGTTGGCCA
TCAAATGGCCGACACCCCTGTTCTCGAGAGT
Found at i:37065370 original size:34 final size:34
Alignment explanation
Indices: 37065323--37065388 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
37065313 TTGTGTTGGC
*
37065323 CATCAAATTGCCGACATCC-CCTGTTCTCGAGAGT
1 CATCAAATGGCCGACA-CCTCCTGTTCTCGAGAGT
*
37065357 CATCAAATGGCCGACACCTCCTGTTCTGGAGA
1 CATCAAATGGCCGACACCTCCTGTTCTCGAGA
37065389 AAAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (34 bp):
CATCAAATGGCCGACACCTCCTGTTCTCGAGAGT
Found at i:37065477 original size:60 final size:63
Alignment explanation
Indices: 37065357--37065497 Score: 191
Period size: 60 Copynumber: 2.3 Consensus size: 63
37065347 TCTCGAGAGT
*
37065357 CATCAAATGGCCGACACCTCCTGTTCTGGAGAAAAAAAAATTCAAAATTTTTTGAGTGTTGGC
1 CATCAAATGGCCGACACCTCCTGTTCTGCAGAAAAAAAAATTCAAAATTTTTTGAGTGTTGGC
* * * *
37065420 CATCAAATGGTCGACACC-CCTTTTCT-CA-AATAAAAAATTCTAAATTTTTTTGA-TGTTGGC
1 CATCAAATGGCCGACACCTCCTGTTCTGCAGAAAAAAAAATTC-AAAATTTTTTGAGTGTTGGC
*
37065480 CATCAAATGACCGACACC
1 CATCAAATGGCCGACACC
37065498 AACTTCTTCT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
60 34 0.49
61 12 0.17
62 7 0.10
63 17 0.24
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (63 bp):
CATCAAATGGCCGACACCTCCTGTTCTGCAGAAAAAAAAATTCAAAATTTTTTGAGTGTTGGC
Found at i:37065967 original size:83 final size:83
Alignment explanation
Indices: 37065826--37066123 Score: 515
Period size: 83 Copynumber: 3.6 Consensus size: 83
37065816 GTATAAAAAA
** *
37065826 TTTATATCTTTAAATAAAATTTTTTATTATATTACAATTTTTATAATATAATGTGTTGATTTGAC
1 TTTATATCTTTAAATAAAAAATTTTATTATATTACAATTTTTATCATATAATGTGTTGATTTGAC
37065891 AATACAATATTTATTAAT
66 AATACAATATTTATTAAT
* *
37065909 TCTATATTTTTAAATAAAAAATTTTATTATATTACAATTTTTATCATATAATGTGTTGATTTGAC
1 TTTATATCTTTAAATAAAAAATTTTATTATATTACAATTTTTATCATATAATGTGTTGATTTGAC
37065974 AATACAATATTTATTAAT
66 AATACAATATTTATTAAT
*
37065992 TTTATATCTTTAAATAAAAAATTTTATTATATTACAATTTTTATCATATAATGTGTTAATTTGAC
1 TTTATATCTTTAAATAAAAAATTTTATTATATTACAATTTTTATCATATAATGTGTTGATTTGAC
37066057 AATACAATATTTATTAAT
66 AATACAATATTTATTAAT
** *
37066075 TTTATATCTTTAAATAAAATTTTTTATTATATTACAAATTTTATCATAT
1 TTTATATCTTTAAATAAAAAATTTTATTATATTACAATTTTTATCATAT
37066124 TTTATATTTA
Statistics
Matches: 204, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 204 1.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.51
Consensus pattern (83 bp):
TTTATATCTTTAAATAAAAAATTTTATTATATTACAATTTTTATCATATAATGTGTTGATTTGAC
AATACAATATTTATTAAT
Found at i:37066249 original size:20 final size:20
Alignment explanation
Indices: 37066220--37066272 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
37066210 ACCACCCACT
* *
37066220 TTCCACCTCACTTAAACC-TA
1 TTCCAGCTCAC-TAAACCAAA
37066240 TTCCAGCTCAGCTAAACCAAAA
1 TTCCAGCTCA-CTAAACC-AAA
37066262 TTCCAGCTCAC
1 TTCCAGCTCAC
37066273 CAACATCCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 15 0.54
21 2 0.07
22 11 0.39
ACGTcount: A:0.32, C:0.38, G:0.06, T:0.25
Consensus pattern (20 bp):
TTCCAGCTCACTAAACCAAA
Found at i:37066314 original size:20 final size:20
Alignment explanation
Indices: 37066289--37066326 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37066279 CCCGAGACCG
37066289 CCGTTGACCGACTTTGTCTA
1 CCGTTGACCGACTTTGTCTA
* *
37066309 CCGTTGATCGATTTTGTC
1 CCGTTGACCGACTTTGTC
37066327 CGTCGTTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.39
Consensus pattern (20 bp):
CCGTTGACCGACTTTGTCTA
Found at i:37068089 original size:12 final size:12
Alignment explanation
Indices: 37068072--37068105 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37068062 GAGCCTCAAG
*
37068072 ACCAACCCGAGT
1 ACCAACCCGAGC
*
37068084 ACCAACCGGAGC
1 ACCAACCCGAGC
37068096 ACCAACCCGA
1 ACCAACCCGA
37068106 TCCCCAGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.44, G:0.18, T:0.03
Consensus pattern (12 bp):
ACCAACCCGAGC
Found at i:37068577 original size:30 final size:30
Alignment explanation
Indices: 37068543--37068634 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
37068533 TCCCTTTACT
*
37068543 TTTTAAATTTAATTT-GTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTCG-AATTTC-TTGTATA
37068573 TTTTAAATTTAATTTCGAATTTCTTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
* ** *
37068603 TTTTAATTTTTCTTTCTAATTTCATT-TATA
1 TTTTAAATTTAATTTCGAATTTC-TTGTATA
37068633 TT
1 TT
37068635 CTAATTATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
29 2 0.04
30 49 0.91
31 3 0.06
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTAATTTCGAATTTCTTGTATA
Found at i:37069532 original size:62 final size:61
Alignment explanation
Indices: 37069429--37069704 Score: 380
Period size: 62 Copynumber: 4.5 Consensus size: 61
37069419 TCCGAGGAAA
*
37069429 ATGGACAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTTG
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTTG
* *
37069490 ATGGCCAACACCAAAAAAATTTGAAATTGTTTTCTCGAGAAAAGGGAGGTGTCGGCCATTTG
1 ATGGCCAACACCAAAAAAATTTG-AATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTTG
37069552 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCA-TTG
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTTG
* * * * ***
37069612 CATGACCAACATCAAAAAAATTTAAATTTTTTTTCTCGAGAAATA-GGGGATGTCGGCCATGCA
1 -ATGGCCAACACCAAAAAAATTTGAA-TTTTTTTCTCGAGAAA-AGGGGGGTGTCGGCCATTTG
* *
37069675 ATGGCCAACACC-CAAAAATGT-AATTTTTTT
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTT
37069705 TTGTAATAGA
Statistics
Matches: 194, Mismatches: 16, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
59 7 0.04
60 5 0.03
61 83 0.43
62 98 0.51
63 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (61 bp):
ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTTG
Found at i:37069580 original size:123 final size:123
Alignment explanation
Indices: 37069428--37069704 Score: 402
Period size: 123 Copynumber: 2.3 Consensus size: 123
37069418 ATCCGAGGAA
*
37069428 AATGGACAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTTG-AT
1 AATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCA-TTGCAT
* * **
37069492 GGCCAACACCAAAAAAATTTGAAA-TTGTTTTCTCGAGAAA-AGGGAGGTGTCGGCCATTT
65 GACCAACACCAAAAAAATTT-AAATTTGTTTTCTCGAGAAATAGGG-GATGTCGGCCATGC
*
37069551 GATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTGCATG
1 AATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTGCATG
* *
37069616 ACCAACATCAAAAAAATTTAAATTTTTTTTCTCGAGAAATAGGGGATGTCGGCCATGC
66 ACCAACACCAAAAAAATTTAAATTTGTTTTCTCGAGAAATAGGGGATGTCGGCCATGC
* *
37069674 AATGGCCAACACC-CAAAAATGT-AATTTTTTT
1 AATGGCCAACACCAAAAAAATTTGAATTTTTTT
37069705 TTGTAATAGA
Statistics
Matches: 140, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
121 9 0.06
122 13 0.09
123 114 0.81
124 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (123 bp):
AATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGGCCATTGCATG
ACCAACACCAAAAAAATTTAAATTTGTTTTCTCGAGAAATAGGGGATGTCGGCCATGC
Found at i:37071108 original size:36 final size:35
Alignment explanation
Indices: 37071035--37071108 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
37071025 CATTGAGACT
* *
37071035 TAAATTTTTTTGTCTAAATTAGTCCTTTAATTTGG
1 TAAATTTTTTTGTCTAAATTAGTCCTTTAACTGGG
*
37071070 TAAACTTTTTTTTTCTAAATTAGT-CTTTAAACTGGG
1 TAAA-TTTTTTTGTCTAAATTAGTCCTTT-AACTGGG
37071106 TAA
1 TAA
37071109 TTATTCTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 8 0.24
36 26 0.76
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.51
Consensus pattern (35 bp):
TAAATTTTTTTGTCTAAATTAGTCCTTTAACTGGG
Found at i:37071477 original size:153 final size:153
Alignment explanation
Indices: 37070994--37071600 Score: 837
Period size: 153 Copynumber: 4.0 Consensus size: 153
37070984 GGTTAACGCA
* * *
37070994 TTTTTGGGTCTCAACTTAATAATTATTTTCACATTGAGACTTAAA---TTTTTTTGTCTAAATTA
1 TTTTGGGGTCTCAACTTAACAATTATTTTCACATTGAAACTTAAATCCTTTTTTTGTCTAAATTA
* * *
37071056 GTCCTTTAATTTGGTAAACTTTTTTTTTCTAAATTAGTCTTTAAACTGGGTAATTATTCTCAAA-
66 GTCCTTTAATTTGGTAAAC-TTTTTTTTCCAAATTAGTCTTTAAACTAGGCAATTATTCTCAAAG
*
37071120 TGAAGTCT-ATATTTTTGTGCAAG
130 TGAAGTCTGATTTTTTTGTGCAAG
* * *
37071143 TTTTGGGGGCTCAACTTAACAATTATTTTCACATTAAAACTCAAATCCTTTTTTTTGTCTAAATT
1 TTTTGGGGTCTCAACTTAACAATTATTTTCACATTGAAACTTAAATCC-TTTTTTTGTCTAAATT
*
37071208 AGTCCTTTAATTTGGTAAACTTTTTTTTTCC-------TCTTTAAACTAGACAATTATTCTCAAA
65 AGTCCTTTAATTTGGTAAAC-TTTTTTTTCCAAATTAGTCTTTAAACTAGGCAATTATTCTCAAA
* *
37071266 GTGAAGTTTGATTTTGTGTGTGCAAG
129 GTGAAGTCTGATTTT-TTTGTGCAAG
*
37071292 TTTTGGGGTCTCAACTTAACAATTATTTTCACATTGAAACTTGAATCCTTTTTTTGTCTAAATTA
1 TTTTGGGGTCTCAACTTAACAATTATTTTCACATTGAAACTTAAATCCTTTTTTTGTCTAAATTA
* * * *
37071357 GTCCTTTAAATTAGTAAACTTTTTTTCCCAAATTAGTCTTTAAGCTAGGCAATTATTCTCAAAGT
66 GTCCTTTAATTTGGTAAACTTTTTTTTCCAAATTAGTCTTTAAACTAGGCAATTATTCTCAAAGT
*
37071422 GAAGTCTGGTTTTTTTGTGCAAG
131 GAAGTCTGATTTTTTTGTGCAAG
* * * *
37071445 TTTTGGGATCTCAACTTAACAGTTATTTTCACATTGCGAA-TTAAATCC-TTTTTGGTCTAAATT
1 TTTTGGGGTCTCAACTTAACAATTATTTTCACATTG-AAACTTAAATCCTTTTTTTGTCTAAATT
*
37071508 AGTCCTTTAATTTGGTAAATTTTTTTTTTCCAAATTAGTCTTTAAACTAGGCAATTATTCTCAAA
65 AGTCCTTTAATTTGGTAAA-CTTTTTTTTCCAAATTAGTCTTTAAACTAGGCAATTATTCTCAAA
37071573 GTGAAGTCTGATTTTTTTTGTGCAAG
129 GTGAAGTCTGA-TTTTTTTGTGCAAG
37071599 TT
1 TT
37071601 AGTCCTTAAT
Statistics
Matches: 405, Mismatches: 36, Indels: 29
0.86 0.08 0.06
Matches are distributed among these distances:
146 24 0.06
147 16 0.04
148 38 0.09
149 92 0.23
152 31 0.08
153 148 0.37
154 56 0.14
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.46
Consensus pattern (153 bp):
TTTTGGGGTCTCAACTTAACAATTATTTTCACATTGAAACTTAAATCCTTTTTTTGTCTAAATTA
GTCCTTTAATTTGGTAAACTTTTTTTTCCAAATTAGTCTTTAAACTAGGCAATTATTCTCAAAGT
GAAGTCTGATTTTTTTGTGCAAG
Found at i:37078292 original size:26 final size:27
Alignment explanation
Indices: 37078263--37078319 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
37078253 CTAACGCTTG
37078263 TTTTAGCTTTATTTT-TCCC-TTTTTATT
1 TTTTAG-TTT-TTTTCTCCCTTTTTTATT
*
37078290 TTTTTGTTTTTTTCTCCCTTTTTTATT
1 TTTTAGTTTTTTTCTCCCTTTTTTATT
37078317 TTT
1 TTT
37078320 CATATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 4 0.15
26 7 0.26
27 16 0.59
ACGTcount: A:0.07, C:0.14, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTAGTTTTTTTCTCCCTTTTTTATT
Found at i:37082818 original size:222 final size:221
Alignment explanation
Indices: 37082250--37082915 Score: 1190
Period size: 221 Copynumber: 3.0 Consensus size: 221
37082240 GTAGGTTGCT
* * * *
37082250 TTGTTATGCAGTATACTATTGTATAATTCCTTGCTATGTTATTCGGACTCGAGTGCGAGTATCAA
1 TTGTTATGCTGTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCGAGTATCAA
* *
37082315 ACATGGGTATATGCCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAAGC
66 ACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGGC
* *
37082380 TCTTTTGAAAATTATATCTCCACACCTAAGGTCAAATACGTGTCGGACATGGTACTTAAAGCCAA
131 TCTTTTGAAAATTATATCTCCACACCTATGGTCAAATACGTGTCGGACACGGTACTTAAAGCCAA
*
37082445 ATGAAGAGTCGAAGCAATTTCTGATC
196 ATGAAGAGTCGAAGCAATTTCCGATC
37082471 TTGTTATG-TGGTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCGAGTATCA
1 TTGTTATGCT-GTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCGAGTATCA
37082535 AACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGG
65 AACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGG
37082600 CTCTTTTGAAAATTATATCTCCACACCTATGGTCAAATACGTGTCGGACACGGTACTTAAAGCCA
130 CTCTTTTGAAAATTATATCTCCACACCTATGGTCAAATACGTGTCGGACACGGTACTTAAAGCCA
37082665 AATGAAGAGTCGAAGCAATTTCCGATC
195 AATGAAGAGTCGAAGCAATTTCCGATC
37082692 TTGTTAATGCTGTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCGAGTATCA
1 TTGTT-ATGCTGTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCGAGTATCA
*
37082757 AACATGGGTATATAACCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGG
65 AACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGG
* *
37082822 CACTTTTGAAAATTATATCTCCACACCTATGGTCAAATACGTGTAGGACACGGTACTTAAAGCCA
130 CTCTTTTGAAAATTATATCTCCACACCTATGGTCAAATACGTGTCGGACACGGTACTTAAAGCCA
*
37082887 AATGAAGAGTCCAAGCAATTTCCGATC
195 AATGAAGAGTCGAAGCAATTTCCGATC
37082914 TT
1 TT
37082916 AAATAGTCAT
Statistics
Matches: 429, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
221 216 0.50
222 212 0.49
223 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (221 bp):
TTGTTATGCTGTATACTATCGTATAATTCCTTGCTATGTTGTTCTGACTCGAGTGCGAGTATCAA
ACATGGGTATATACCCGACTCGGCTATGTTCAATTTGTTTCAAGTTTTTTCATGTATTTAGAGGC
TCTTTTGAAAATTATATCTCCACACCTATGGTCAAATACGTGTCGGACACGGTACTTAAAGCCAA
ATGAAGAGTCGAAGCAATTTCCGATC
Found at i:37087309 original size:25 final size:25
Alignment explanation
Indices: 37087281--37087334 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
37087271 TTTTCCATTA
*
37087281 TAATTTA-AATTTTTATATTATTGTT
1 TAATTTATAATTTGTA-ATTATTGTT
* *
37087306 TAATTTATAGTTTGTAATTATTTTT
1 TAATTTATAATTTGTAATTATTGTT
37087331 TAAT
1 TAAT
37087335 AATTTTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (25 bp):
TAATTTATAATTTGTAATTATTGTT
Found at i:37088011 original size:22 final size:23
Alignment explanation
Indices: 37087986--37088045 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
37087976 TAAAAATGAT
* *
37087986 AAAATTTTAATTTAATTCTT-TA
1 AAAATTATAATTTAATTATTGTA
* * *
37088008 AAAATTACACTTTTATTATTGTA
1 AAAATTATAATTTAATTATTGTA
37088031 AAAATTATAATTTAA
1 AAAATTATAATTTAA
37088046 CTTTGACCGC
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (23 bp):
AAAATTATAATTTAATTATTGTA
Found at i:37088126 original size:17 final size:18
Alignment explanation
Indices: 37088086--37088125 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
37088076 TTCACCCCTG
37088086 TAAAAATGCAAAAAAATA
1 TAAAAATGCAAAAAAATA
*
37088104 TAAAAAT-CAATAAAAT-
1 TAAAAATGCAAAAAAATA
37088120 TAAAAA
1 TAAAAA
37088126 AAATTCATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (18 bp):
TAAAAATGCAAAAAAATA
Found at i:37089033 original size:7 final size:7
Alignment explanation
Indices: 37089016--37089053 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
37089006 AAAAAAGTGC
37089016 AAATA-A
1 AAATATA
*
37089022 AAATACA
1 AAATATA
37089029 AAATATA
1 AAATATA
37089036 AAATATA
1 AAATATA
*
37089043 AAATATT
1 AAATATA
37089050 AAAT
1 AAAT
37089054 TTAGGGTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATATA
Found at i:37090266 original size:41 final size:42
Alignment explanation
Indices: 37090177--37090268 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 42
37090167 AACAATTAAA
**
37090177 TATATATT-TTAATTTTAATATTTCATATATTTATATGTAGT
1 TATATATTATTAATTTTAATATCACATATATTTATATGTAGT
*
37090218 TAT-TATTAATTAATTTTAA-ATCACATAT-TTTATTATTTA-T
1 TATATATT-ATTAATTTTAATATCACATATATTTA-TATGTAGT
37090258 TATATATTATT
1 TATATATTATT
37090269 TTAAGTTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
40 15 0.34
41 19 0.43
42 10 0.23
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (42 bp):
TATATATTATTAATTTTAATATCACATATATTTATATGTAGT
Found at i:37111687 original size:29 final size:29
Alignment explanation
Indices: 37111655--37111710 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
37111645 ATAATTTTTG
37111655 AAATCTAAAAAATAAAAAAATTAAATTTA
1 AAATCTAAAAAATAAAAAAATTAAATTTA
* *
37111684 AAATTTAAAAAATAGAAAAATTAAATT
1 AAATCTAAAAAATAAAAAAATTAAATT
37111711 CTTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (29 bp):
AAATCTAAAAAATAAAAAAATTAAATTTA
Found at i:37111723 original size:29 final size:29
Alignment explanation
Indices: 37111655--37111724 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
37111645 ATAATTTTTG
*
37111655 AAATCTAAAAAATAAAAAAATTAAATTTA
1 AAATATAAAAAATAAAAAAATTAAATTTA
* *
37111684 AAATTTAAAAAATAGAAAAATTAAATTCTTA
1 AAATATAAAAAATAAAAAAATTAAA-T-TTA
37111715 AAA-ATAAAAA
1 AAATATAAAAA
37111725 TATATTAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.64
30 7 0.19
31 6 0.17
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (29 bp):
AAATATAAAAAATAAAAAAATTAAATTTA
Found at i:37116698 original size:8 final size:8
Alignment explanation
Indices: 37116685--37116710 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
37116675 ATTAAAACAC
37116685 TCCATCCT
1 TCCATCCT
37116693 TCCATCCT
1 TCCATCCT
37116701 TCCATCCT
1 TCCATCCT
37116709 TC
1 TC
37116711 TTCCGTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (8 bp):
TCCATCCT
Found at i:37118561 original size:31 final size:31
Alignment explanation
Indices: 37118523--37118584 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
37118513 TGTCTGTTTC
37118523 CATAAAAGCTTTGCTAGATTGGTTGTATTCT
1 CATAAAAGCTTTGCTAGATTGGTTGTATTCT
37118554 CATAAAAGCTTTGCTAGATTGGTTGTATTCT
1 CATAAAAGCTTTGCTAGATTGGTTGTATTCT
37118585 TAGTGTCGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (31 bp):
CATAAAAGCTTTGCTAGATTGGTTGTATTCT
Found at i:37135887 original size:132 final size:132
Alignment explanation
Indices: 37135650--37135913 Score: 447
Period size: 132 Copynumber: 2.0 Consensus size: 132
37135640 ACCCGACACC
37135650 AAGCTGAAAACACACAAAACCACAACTCACGGACATGACCAGGAAACAAAAGGTCCCTTCATTTT
1 AAGCTGAAAACACACAAAACCACAACTCACGGACATGACCAGGAAACAAAAGGTCCCTTCATTTT
* * *
37135715 GTAGTTATTATACCCTTCCTTACATCATTAGAAAACTTCAAAGAAAACTATGTAACAGCTTTCCA
66 ATAGCTATTATACCCTTCCTTACATCATTAGAAAACTTCAAAGAAAACTATGTAACAGCTTGCCA
37135780 AT
131 AT
* * *
37135782 AAGCTGAAAACACACAAAACCGCAACTCGCGGACATGACCGGGAAACAAAAGGTCCCTTCATTTT
1 AAGCTGAAAACACACAAAACCACAACTCACGGACATGACCAGGAAACAAAAGGTCCCTTCATTTT
* * *
37135847 ATAGCTATTATGCCCTTCTTTACATCATTAGAAAACTTCAAATAAAACTATGTAACAGCTTGCCA
66 ATAGCTATTATACCCTTCCTTACATCATTAGAAAACTTCAAAGAAAACTATGTAACAGCTTGCCA
37135912 AT
131 AT
37135914 TACAACATTA
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 123 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (132 bp):
AAGCTGAAAACACACAAAACCACAACTCACGGACATGACCAGGAAACAAAAGGTCCCTTCATTTT
ATAGCTATTATACCCTTCCTTACATCATTAGAAAACTTCAAAGAAAACTATGTAACAGCTTGCCA
AT
Found at i:37138051 original size:22 final size:21
Alignment explanation
Indices: 37138020--37138061 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
37138010 CACTCGCTGA
37138020 TCTTCAAACCCATATTTCTTT
1 TCTTCAAACCCATATTTCTTT
* *
37138041 TCTTCGAAACCCCTTTTTCTT
1 TCTTC-AAACCCATATTTCTT
37138062 GTTTTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.19, C:0.31, G:0.02, T:0.48
Consensus pattern (21 bp):
TCTTCAAACCCATATTTCTTT
Found at i:37142726 original size:16 final size:15
Alignment explanation
Indices: 37142705--37142739 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
37142695 AATTGTTAAG
37142705 ATTATTAATATATAAA
1 ATTATTAA-ATATAAA
*
37142721 ATTATTAAATATTAA
1 ATTATTAAATATAAA
37142736 ATTA
1 ATTA
37142740 AAAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTATTAAATATAAA
Found at i:37142728 original size:25 final size:21
Alignment explanation
Indices: 37142693--37142742 Score: 55
Period size: 25 Copynumber: 2.2 Consensus size: 21
37142683 TAAACATTAA
*
37142693 AAAATTGTTAAGATTATTAATATAT
1 AAAATTATTAA-A-TATTAA-AT-T
37142718 AAAATTATTAAATATTAAATT
1 AAAATTATTAAATATTAAATT
37142739 AAAA
1 AAAA
37142743 ATAATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 2 0.08
23 6 0.25
24 1 0.04
25 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAATTATTAAATATTAAATT
Found at i:37142752 original size:23 final size:25
Alignment explanation
Indices: 37142718--37142773 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
37142708 ATTAATATAT
*
37142718 AAAATTAT-TAAATAT-TAAAT-TA
1 AAAATAATATAAATATATAAATCTA
**
37142740 AAAATAATATAAATATATATTTCTA
1 AAAATAATATAAATATATAAATCTA
37142765 AAAATAATA
1 AAAATAATA
37142774 CGGACGGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.25
23 7 0.25
24 3 0.11
25 11 0.39
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAATAATATAAATATATAAATCTA
Found at i:37152270 original size:31 final size:31
Alignment explanation
Indices: 37152232--37152293 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
37152222 GCTATGATTC
*
37152232 TATTGAGAGAGTAATTGTGTTTCTCAGTAGA
1 TATTGAGAGAGTAATTGTGCTTCTCAGTAGA
*
37152263 TATTGAGAGAGTAATTGTGCTTCTCATTAGA
1 TATTGAGAGAGTAATTGTGCTTCTCAGTAGA
37152294 GTCATCTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (31 bp):
TATTGAGAGAGTAATTGTGCTTCTCAGTAGA
Found at i:37155857 original size:3 final size:3
Alignment explanation
Indices: 37155849--37155882 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
37155839 CCTAAAACTC
* *
37155849 AAT AAT AAT AAT AAT AAT AAT AGT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
37155883 GTGGTTGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:37167552 original size:27 final size:26
Alignment explanation
Indices: 37167498--37167551 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 26
37167488 CTGCCCACAT
37167498 TATTTTTTTTAATTAATAATTTTATA
1 TATTTTTTTTAATTAATAATTTTATA
37167524 TATTTTTATTT-ATTAA-AATTTTATA
1 TATTTTT-TTTAATTAATAATTTTATA
37167549 TAT
1 TAT
37167552 AGTCACCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 12 0.44
26 12 0.44
27 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TATTTTTTTTAATTAATAATTTTATA
Found at i:37173871 original size:17 final size:17
Alignment explanation
Indices: 37173837--37173878 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
37173827 AAATAATATA
37173837 TTTCTTATTTATTCACT
1 TTTCTTATTTATTCACT
*
37173854 TTTCATTATTT-TTTACT
1 TTTC-TTATTTATTCACT
37173871 TTT-TTATT
1 TTTCTTATT
37173879 ATAAATATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCTTATTTATTCACT
Found at i:37179555 original size:30 final size:30
Alignment explanation
Indices: 37179495--37179573 Score: 78
Period size: 32 Copynumber: 2.7 Consensus size: 30
37179485 AATCGTAAAC
*
37179495 AATTAT-AAAATATATAGAAATATAGAAAAA
1 AATTATAAAAATATAAAGAAATATAG-AAAA
*
37179525 AATTATAAAAATTATAAAGAAGTA-AG-AAA
1 AATTATAAAAA-TATAAAGAAATATAGAAAA
37179554 AA-TATAAAAA-ATTAAAGAAA
1 AATTATAAAAATA-TAAAGAAA
37179574 GATAAATTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
26 1 0.02
27 7 0.16
28 8 0.19
29 5 0.12
30 6 0.14
31 6 0.14
32 10 0.23
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (30 bp):
AATTATAAAAATATAAAGAAATATAGAAAA
Found at i:37179565 original size:9 final size:9
Alignment explanation
Indices: 37179464--37179579 Score: 51
Period size: 10 Copynumber: 12.4 Consensus size: 9
37179454 TGACATGTGG
37179464 TAAAAAAT-
1 TAAAAAATA
37179472 TAAAAAA-A
1 TAAAAAATA
* *
37179480 TATAAAATCG
1 TAAAAAAT-A
*
37179490 TAAACAATTA
1 TAAA-AAATA
*
37179500 TAAAATATA
1 TAAAAAATA
*
37179509 TAGAAATATA
1 TA-AAAAATA
*
37179519 GAAAAAAATTA
1 -TAAAAAA-TA
*
37179530 TAAAAATTA
1 TAAAAAATA
*
37179539 TAAAGAAGTA
1 TAAA-AAATA
37179549 -AGAAAAATA
1 TA-AAAAATA
37179558 TAAAAAAT-
1 TAAAAAATA
*
37179566 TAAAGAAAGA
1 TAAA-AAATA
37179576 TAAA
1 TAAA
37179580 TTTGTAAAAG
Statistics
Matches: 82, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
8 17 0.21
9 25 0.30
10 34 0.41
11 6 0.07
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (9 bp):
TAAAAAATA
Found at i:37179797 original size:10 final size:10
Alignment explanation
Indices: 37179776--37179833 Score: 59
Period size: 10 Copynumber: 6.1 Consensus size: 10
37179766 TTTTTATGCA
37179776 TTTTATAA-T
1 TTTTATAATT
*
37179785 TTTTATGATT
1 TTTTATAATT
**
37179795 TTTTATAAAA
1 TTTTATAATT
37179805 TTTTATAATT
1 TTTTATAATT
37179815 TTTT-T-ATT
1 TTTTATAATT
*
37179823 TTTTACAATT
1 TTTTATAATT
37179833 T
1 T
37179834 ATATATATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 7 0.18
9 8 0.21
10 24 0.62
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:37179807 original size:29 final size:27
Alignment explanation
Indices: 37179775--37179904 Score: 111
Period size: 28 Copynumber: 4.5 Consensus size: 27
37179765 TTTTTTATGC
*
37179775 ATTTTATAATTTTTATGATTTTTTATAAA
1 ATTTTATAATTTTT-TTA-TTTTTATAAA
*
37179804 ATTTTATAATTTTTTTATTTTT-TACA
1 ATTTTATAATTTTTTTATTTTTATAAA
*
37179830 ATTTATATATATATATTTCTAATTTTTAATAAA
1 ATTT-TATA-AT-T-TTT-TTATTTTT-ATAAA
37179863 ATTTTA-ATATTTTTTTATTTTTATTAAA
1 ATTTTATA-ATTTTTTTATTTTTA-TAAA
* *
37179891 ATTTGATCATTTTT
1 ATTTTATAATTTTT
37179905 ATAAATTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
26 7 0.08
27 10 0.12
28 26 0.31
29 18 0.21
30 4 0.05
31 11 0.13
32 2 0.02
33 7 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
ATTTTATAATTTTTTTATTTTTATAAA
Found at i:37179819 original size:21 final size:19
Alignment explanation
Indices: 37179776--37179880 Score: 68
Period size: 20 Copynumber: 5.3 Consensus size: 19
37179766 TTTTTATGCA
* *
37179776 TTTTATAATTTTTATGATT
1 TTTTATAAATTTTATAATT
37179795 TTTTATAAAATTTTATAATT
1 TTTTAT-AAATTTTATAATT
** *
37179815 TTTT-TATTTTTTACAATT
1 TTTTATAAATTTTATAATT
* * *
37179833 TATATATATATATTTCTAATT
1 T-TTTATAAAT-TTTATAATT
* *
37179854 TTTAATAAAATTTTAATATTT
1 TTTTAT-AAATTTT-ATAATT
37179875 TTTTAT
1 TTTTAT
37179881 TTTTATTAAA
Statistics
Matches: 65, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
18 11 0.17
19 9 0.14
20 25 0.38
21 20 0.31
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTATAAATTTTATAATT
Found at i:37179889 original size:20 final size:19
Alignment explanation
Indices: 37179866--37179926 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
37179856 TAATAAAATT
*
37179866 TTAATATTTTTTTATTTTTA
1 TTAA-ATTTTTTCATTTTTA
**
37179886 TTAAAATTTGATCATTTTTA
1 TT-AAATTTTTTCATTTTTA
*
37179906 -TAAATTTTTCTGATTTTTA
1 TTAAATTTTT-TCATTTTTA
37179925 TT
1 TT
37179927 TTTTATAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 6 0.19
19 9 0.28
20 15 0.47
21 2 0.06
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (19 bp):
TTAAATTTTTTCATTTTTA
Found at i:37183041 original size:15 final size:17
Alignment explanation
Indices: 37183023--37183055 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
37183013 TTCGACTTAA
37183023 ATAAATA-TA-AAATAT
1 ATAAATATTATAAATAT
37183038 ATAAATATTATAAATAT
1 ATAAATATTATAAATAT
37183055 A
1 A
37183056 ATCAGTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAATATTATAAATAT
Found at i:37190737 original size:15 final size:15
Alignment explanation
Indices: 37190719--37190748 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37190709 TATTCTCCTT
37190719 TCAAAACTTCTACTG
1 TCAAAACTTCTACTG
*
37190734 TCAAAATTTCTACTG
1 TCAAAACTTCTACTG
37190749 ACTTCCCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (15 bp):
TCAAAACTTCTACTG
Found at i:37204640 original size:42 final size:43
Alignment explanation
Indices: 37204581--37204665 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 43
37204571 CTTTTAACAT
37204581 TATTATTTTAAATTGACATCATTCAAGCTAAG-ACCCTTTTAG
1 TATTATTTTAAATTGACATCATTCAAGCTAAGAACCCTTTTAG
* * * *
37204623 TATTATTTTGATTTGACATCATTTAAGCTAAGAATCCTTTTAG
1 TATTATTTTAAATTGACATCATTCAAGCTAAGAACCCTTTTAG
37204666 CATTGTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 29 0.76
43 9 0.24
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (43 bp):
TATTATTTTAAATTGACATCATTCAAGCTAAGAACCCTTTTAG
Found at i:37209226 original size:16 final size:16
Alignment explanation
Indices: 37209207--37209242 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
37209197 ATCGTGAGAA
37209207 TCGAGACATCAGAGTG
1 TCGAGACATCAGAGTG
*
37209223 TCGAGGCATCAGAGTG
1 TCGAGACATCAGAGTG
37209239 TCGA
1 TCGA
37209243 CCAACTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.19
Consensus pattern (16 bp):
TCGAGACATCAGAGTG
Found at i:37223963 original size:22 final size:22
Alignment explanation
Indices: 37223915--37223964 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
37223905 CACGTATTAA
37223915 AAAAATTATAATATTTTTTACT
1 AAAAATTATAATATTTTTTACT
* *
37223937 TAAAATTATATTATTTTTATA-T
1 AAAAATTATAATATTTTT-TACT
37223959 AAAAAT
1 AAAAAT
37223965 AAATTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAAATTATAATATTTTTTACT
Found at i:37224627 original size:21 final size:20
Alignment explanation
Indices: 37224592--37224647 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
37224582 GGTATTTTTG
37224592 TTTT-AATTAGGTTTAGGAT
1 TTTTAAATTAGGTTTAGGAT
*
37224611 TTTTAAATTAGGGTTTAGGCT
1 TTTTAAATTA-GGTTTAGGAT
*
37224632 TTTAAAATTAAGGTTT
1 TTTTAAATT-AGGTTT
37224648 TAGTATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.12
20 5 0.16
21 22 0.69
22 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTTAAATTAGGTTTAGGAT
Found at i:37236274 original size:23 final size:24
Alignment explanation
Indices: 37236229--37236275 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
37236219 TATTCGTTTA
*
37236229 ATGTTCGCAAACATATAAATGAAC
1 ATGTTCACAAACATATAAATGAAC
37236253 ATGTTCACAAACAT-TAAATGAAC
1 ATGTTCACAAACATATAAATGAAC
37236276 TAAGCCTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
ATGTTCACAAACATATAAATGAAC
Found at i:37238228 original size:11 final size:11
Alignment explanation
Indices: 37238212--37238236 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
37238202 ACAGCATTAC
37238212 TCCCCGTTAAA
1 TCCCCGTTAAA
37238223 TCCCCGTTAAA
1 TCCCCGTTAAA
37238234 TCC
1 TCC
37238237 TAGAAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.40, G:0.08, T:0.28
Consensus pattern (11 bp):
TCCCCGTTAAA
Found at i:37241061 original size:20 final size:18
Alignment explanation
Indices: 37241015--37241062 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
37241005 CTAAATGAAA
37241015 AAAAAAATT-AAAAATTT
1 AAAAAAATTAAAAAATTT
37241032 AAAAATAATTAAAAAATATT
1 AAAAA-AATTAAAAAAT-TT
37241052 AAATAAAATTA
1 AAA-AAAATTA
37241063 TATTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 6 0.22
20 10 0.37
21 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAAATTAAAAAATTT
Found at i:37241062 original size:10 final size:9
Alignment explanation
Indices: 37241015--37241062 Score: 53
Period size: 10 Copynumber: 5.1 Consensus size: 9
37241005 CTAAATGAAA
37241015 AAAAAAATT
1 AAAAAAATT
*
37241024 -AAAAATTT
1 AAAAAAATT
37241032 AAAAATAATT
1 AAAAA-AATT
37241042 AAAAAATATT
1 AAAAAA-ATT
37241052 AAATAAAATT
1 AAA-AAAATT
37241062 A
1 A
37241063 TATTTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 7 0.21
9 5 0.15
10 18 0.55
11 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAAAATT
Found at i:37268660 original size:14 final size:14
Alignment explanation
Indices: 37268641--37268670 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
37268631 CTTATTTTTC
*
37268641 TTTTTCCTTTTCCT
1 TTTTTCCTTTACCT
37268655 TTTTTCCTTTACCT
1 TTTTTCCTTTACCT
37268669 TT
1 TT
37268671 AATCTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTCCTTTACCT
Found at i:37268968 original size:3 final size:3
Alignment explanation
Indices: 37268960--37269032 Score: 92
Period size: 3 Copynumber: 24.3 Consensus size: 3
37268950 CAATCTTCAG
* * * * * *
37268960 CTT CTT CTT CTT CTC CTT CCT CCT CCT CCT CCT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
37269008 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
37269033 CACTATCTGC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (3 bp):
CTT
Found at i:37269349 original size:27 final size:27
Alignment explanation
Indices: 37269298--37269349 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
37269288 TTTTAATATT
* *
37269298 TAATTTGATATTTAAGTTTTTTTTTCC
1 TAATTTAATATTTAAGTTTTATTTTCC
37269325 TAATTTAATATTTAA-TTTTGATTTT
1 TAATTTAATATTTAAGTTTT-ATTTT
37269350 AATTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (27 bp):
TAATTTAATATTTAAGTTTTATTTTCC
Found at i:37269489 original size:53 final size:53
Alignment explanation
Indices: 37269426--37269534 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
37269416 ATTTCAATAT
37269426 TTAATTAAGTGTTTTAATTTTTTTATTCCAAATAAATACTTTCGATTTTTTTA
1 TTAATTAAGTGTTTTAATTTTTTTATTCCAAATAAATACTTTCGATTTTTTTA
37269479 TTAATTAAGTGTTTTAATTTTTTTATTCCAAATAAATACTTTCGATTTTTTTA
1 TTAATTAAGTGTTTTAATTTTTTTATTCCAAATAAATACTTTCGATTTTTTTA
37269532 TTA
1 TTA
37269535 GAATATGCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.57
Consensus pattern (53 bp):
TTAATTAAGTGTTTTAATTTTTTTATTCCAAATAAATACTTTCGATTTTTTTA
Found at i:37269498 original size:25 final size:25
Alignment explanation
Indices: 37269426--37269505 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
37269416 ATTTCAATAT
37269426 TTAATTAAGTGTTTTAATTTTTTTA
1 TTAATTAAGTGTTTTAATTTTTTTA
* * * **
37269451 TTCCAAATAAATACTTTCGATTTTTTTA
1 TT--AATTAAGT-GTTTTAATTTTTTTA
37269479 TTAATTAAGTGTTTTAATTTTTTTA
1 TTAATTAAGTGTTTTAATTTTTTTA
37269504 TT
1 TT
37269506 CCAAATAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
25 16 0.38
26 6 0.14
27 6 0.14
28 14 0.33
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (25 bp):
TTAATTAAGTGTTTTAATTTTTTTA
Found at i:37269527 original size:28 final size:28
Alignment explanation
Indices: 37269442--37269533 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 28
37269432 AAGTGTTTTA
37269442 ATTTTTTTATTCCAAATAAATACTTTCG
1 ATTTTTTTATTCCAAATAAATACTTTCG
* * * **
37269470 ATTTTTTTATT--AATTAAGT-GTTTTA
1 ATTTTTTTATTCCAAATAAATACTTTCG
37269495 ATTTTTTTATTCCAAATAAATACTTTCG
1 ATTTTTTTATTCCAAATAAATACTTTCG
37269523 ATTTTTTTATT
1 ATTTTTTTATT
37269534 AGAATATGCA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
25 14 0.27
26 6 0.12
27 6 0.12
28 25 0.49
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.58
Consensus pattern (28 bp):
ATTTTTTTATTCCAAATAAATACTTTCG
Found at i:37272173 original size:20 final size:20
Alignment explanation
Indices: 37272144--37272252 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
37272134 ACTTACGTAT
* *
37272144 TCAGGATTTATGCCGGTAAA
1 TCAGGCTTTATGCCGGTGAA
*
37272164 TCAGGCTTTATGCCGGTGAT
1 TCAGGCTTTATGCCGGTGAA
** *
37272184 TCAGGCTTTATGAAGGTGAT
1 TCAGGCTTTATGCCGGTGAA
* *
37272204 TCAGGCTTTATGTCGGTGTA
1 TCAGGCTTTATGCCGGTGAA
* * *
37272224 TCAGGCTTTGTGTCGGTGTA
1 TCAGGCTTTATGCCGGTGAA
37272244 TCAGGCTTT
1 TCAGGCTTT
37272253 GTGCTGGTGT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (20 bp):
TCAGGCTTTATGCCGGTGAA
Found at i:37272261 original size:20 final size:20
Alignment explanation
Indices: 37272144--37272268 Score: 96
Period size: 20 Copynumber: 6.2 Consensus size: 20
37272134 ACTTACGTAT
* * **
37272144 TCAGGATTTATGCCGGTAAA
1 TCAGGCTTTATGCTGGTGTA
*
37272164 TCAGGCTTTATGCCGGTG-A
1 TCAGGCTTTATGCTGGTGTA
**
37272183 TTCAGGCTTTATGAAGGTG-A
1 -TCAGGCTTTATGCTGGTGTA
37272203 TTCAGGCTTTATG-TCGGTGTA
1 -TCAGGCTTTATGCT-GGTGTA
*
37272224 TCAGGCTTTGTG-TCGGTGTA
1 TCAGGCTTTATGCT-GGTGTA
*
37272244 TCAGGCTTTGTGCTGGTGTA
1 TCAGGCTTTATGCTGGTGTA
*
37272264 ACAGG
1 TCAGG
37272269 TTTTGTGCAG
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
19 1 0.01
20 91 0.97
21 2 0.02
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.35
Consensus pattern (20 bp):
TCAGGCTTTATGCTGGTGTA
Found at i:37272262 original size:40 final size:39
Alignment explanation
Indices: 37272163--37272275 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 39
37272153 ATGCCGGTAA
* *
37272163 ATCAGGCTTTATGCCGGTG-ATTCAGGCTTTATGAAGGTG
1 ATCAGGCTTTATGCTGGTGTA-TCAGGCTTTGTGAAGGTG
**
37272202 ATTCAGGCTTTATG-TCGGTGTATCAGGCTTTGTGTCGGTG
1 A-TCAGGCTTTATGCT-GGTGTATCAGGCTTTGTGAAGGTG
* * *
37272242 TATCAGGCTTTGTGCTGGTGTAACAGGTTTTGTG
1 -ATCAGGCTTTATGCTGGTGTATCAGGCTTTGTG
37272276 CAGGATATAC
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
39 1 0.02
40 58 0.94
41 3 0.05
ACGTcount: A:0.16, C:0.14, G:0.32, T:0.38
Consensus pattern (39 bp):
ATCAGGCTTTATGCTGGTGTATCAGGCTTTGTGAAGGTG
Found at i:37272273 original size:20 final size:21
Alignment explanation
Indices: 37272163--37272276 Score: 98
Period size: 20 Copynumber: 5.7 Consensus size: 21
37272153 ATGCCGGTAA
*
37272163 ATCAGGCTTTATGC-CGGTG-
1 ATCAGGCTTTGTGCTCGGTGT
* **
37272182 ATTCAGGCTTTATG-AAGGTG-
1 A-TCAGGCTTTGTGCTCGGTGT
*
37272202 ATTCAGGCTTTATG-TCGGTGT
1 A-TCAGGCTTTGTGCTCGGTGT
37272223 ATCAGGCTTTGTG-TCGGTGT
1 ATCAGGCTTTGTGCTCGGTGT
37272243 ATCAGGCTTTGTGCT-GGTGT
1 ATCAGGCTTTGTGCTCGGTGT
* *
37272263 AACAGGTTTTGTGC
1 ATCAGGCTTTGTGC
37272277 AGGATATACA
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
19 1 0.01
20 82 0.96
21 2 0.02
ACGTcount: A:0.16, C:0.15, G:0.32, T:0.38
Consensus pattern (21 bp):
ATCAGGCTTTGTGCTCGGTGT
Found at i:37274862 original size:52 final size:52
Alignment explanation
Indices: 37274800--37274913 Score: 201
Period size: 52 Copynumber: 2.2 Consensus size: 52
37274790 GTATCACTTG
*
37274800 CTGTTATGTGGCTTTCCTAATTCAGAGACAGACAGATTTGCTTCTTTTGATC
1 CTGTTATGTGGCTTTCCTAATTCAGAGACAGACAAATTTGCTTCTTTTGATC
*
37274852 CTGTTATGTGGTTTTCCTAATTCAGAGACAGACAAATTTGCTTCTTTTGATC
1 CTGTTATGTGGCTTTCCTAATTCAGAGACAGACAAATTTGCTTCTTTTGATC
*
37274904 TTGTTATGTG
1 CTGTTATGTG
37274914 TCAGTGTTAC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (52 bp):
CTGTTATGTGGCTTTCCTAATTCAGAGACAGACAAATTTGCTTCTTTTGATC
Found at i:37277008 original size:31 final size:31
Alignment explanation
Indices: 37276968--37277027 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
37276958 TTATAAAATG
37276968 TTCAATGAATTATTCAAAAGTTTTTATTTAA
1 TTCAATGAATTATTCAAAAGTTTTTATTTAA
* * *
37276999 TTCATTGAATTTTTCGAAAGTTTTTATTT
1 TTCAATGAATTATTCAAAAGTTTTTATTT
37277028 TAGTTATCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (31 bp):
TTCAATGAATTATTCAAAAGTTTTTATTTAA
Found at i:37277687 original size:18 final size:18
Alignment explanation
Indices: 37277666--37277714 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
37277656 TGTTATAAAA
*
37277666 ATTATATTAATTATATAT
1 ATTATATTAAATATATAT
*
37277684 ATTAAATGATAAATATATAT
1 ATTATAT--TAAATATATAT
37277704 -TTATATTAAAT
1 ATTATATTAAAT
37277715 CATTAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 5 0.19
18 6 0.23
19 5 0.19
20 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATTATATTAAATATATAT
Found at i:37281101 original size:20 final size:20
Alignment explanation
Indices: 37281076--37281113 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37281066 TTAAATTAAA
*
37281076 ATAAAAAATAATTTTCAATT
1 ATAAAAAATAAATTTCAATT
*
37281096 ATAAAATATAAATTTCAA
1 ATAAAAAATAAATTTCAA
37281114 CCAAGTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAAAAATAAATTTCAATT
Found at i:37281971 original size:14 final size:14
Alignment explanation
Indices: 37281952--37281979 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37281942 TGAGACATAA
37281952 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
37281966 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
37281980 TCCAACAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:37291928 original size:226 final size:226
Alignment explanation
Indices: 37291534--37291993 Score: 911
Period size: 226 Copynumber: 2.0 Consensus size: 226
37291524 TTTGAATCCC
37291534 TTCATCATCATCATCACATGCTTGTTTCAGTTTTGCTTCTCTGCTTCTTCATTGTTCATACAATT
1 TTCATCATCATCATCACATGCTTGTTTCAGTTTTGCTTCTCTGCTTCTTCATTGTTCATACAATT
37291599 CTGTGGCAATGATTGCAAGGCTGGTCTGCTCTTCCCAAATGGCTGCTGCACTCATAAAAAAAAAA
66 CTGTGGCAATGATTGCAAGGCTGGTCTGCTCTTCCCAAATGGCTGCTGCACTCATAAAAAAAAAA
37291664 ACCGAATTACCATCACTGAACCATTTCAAAGCACTATTTCTATGTTACTAGGAGAGTGAAAGTAA
131 ACCGAATTACCATCACTGAACCATTTCAAAGCACTATTTCTATGTTACTAGGAGAGTGAAAGTAA
37291729 CCTCACCTTATTGAGATTATCATCTTCTTTG
196 CCTCACCTTATTGAGATTATCATCTTCTTTG
37291760 TTCATCATCATCATCACATGCTTGTTTCAGTTTTGCTTCTCTGCTTCTTCATTGTTCATACAATT
1 TTCATCATCATCATCACATGCTTGTTTCAGTTTTGCTTCTCTGCTTCTTCATTGTTCATACAATT
37291825 CTGTGGCAATGATTGCAAGGCTGGTCTGCTCTTCCCAAATGGCTGCTGCACTCATAAAAAAAAAA
66 CTGTGGCAATGATTGCAAGGCTGGTCTGCTCTTCCCAAATGGCTGCTGCACTCATAAAAAAAAAA
37291890 ACCGAATTACCATCACTGAACCATTTCAAAGCACTATTTCTATGTTACTAGGAGAGTGAAAGTAA
131 ACCGAATTACCATCACTGAACCATTTCAAAGCACTATTTCTATGTTACTAGGAGAGTGAAAGTAA
37291955 CCTCACCTTATTGAGATTATCATCTTCTTTG
196 CCTCACCTTATTGAGATTATCATCTTCTTTG
*
37291986 TTCTTCAT
1 TTCATCAT
37291994 ATTGTCATTG
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
226 233 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (226 bp):
TTCATCATCATCATCACATGCTTGTTTCAGTTTTGCTTCTCTGCTTCTTCATTGTTCATACAATT
CTGTGGCAATGATTGCAAGGCTGGTCTGCTCTTCCCAAATGGCTGCTGCACTCATAAAAAAAAAA
ACCGAATTACCATCACTGAACCATTTCAAAGCACTATTTCTATGTTACTAGGAGAGTGAAAGTAA
CCTCACCTTATTGAGATTATCATCTTCTTTG
Found at i:37292966 original size:42 final size:42
Alignment explanation
Indices: 37292907--37292997 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
37292897 CTCAAGTGCA
*
37292907 TCTTCGGAAACAGCAGCATCATTGGTCCCATCAGCTACCAAT
1 TCTTCAGAAACAGCAGCATCATTGGTCCCATCAGCTACCAAT
*
37292949 TCTTCAGAAACAGCAGCATCATTGGTCTCATCAGCTACCAAT
1 TCTTCAGAAACAGCAGCATCATTGGTCCCATCAGCTACCAAT
37292991 TCTTCAG
1 TCTTCAG
37292998 CCACCAATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (42 bp):
TCTTCAGAAACAGCAGCATCATTGGTCCCATCAGCTACCAAT
Found at i:37293003 original size:15 final size:15
Alignment explanation
Indices: 37292979--37293012 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
37292969 ATTGGTCTCA
*
37292979 TCAGCTACCAATTCT
1 TCAGCCACCAATTCT
37292994 TCAGCCACCAATTCT
1 TCAGCCACCAATTCT
37293009 TCAG
1 TCAG
37293013 AAACAACAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.35, G:0.09, T:0.29
Consensus pattern (15 bp):
TCAGCCACCAATTCT
Found at i:37293007 original size:57 final size:57
Alignment explanation
Indices: 37292937--37293054 Score: 209
Period size: 57 Copynumber: 2.1 Consensus size: 57
37292927 ATTGGTCCCA
* * *
37292937 TCAGCTACCAATTCTTCAGAAACAGCAGCATCATTGGTCTCATCAGCTACCAATTCT
1 TCAGCCACCAATTCTTCAGAAACAACAGCATCATTGGTCTCATCAGCCACCAATTCT
37292994 TCAGCCACCAATTCTTCAGAAACAACAGCATCATTGGTCTCATCAGCCACCAATTCT
1 TCAGCCACCAATTCTTCAGAAACAACAGCATCATTGGTCTCATCAGCCACCAATTCT
37293051 TCAG
1 TCAG
37293055 AAACAACAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.26
Consensus pattern (57 bp):
TCAGCCACCAATTCTTCAGAAACAACAGCATCATTGGTCTCATCAGCCACCAATTCT
Found at i:37293038 original size:99 final size:99
Alignment explanation
Indices: 37292907--37293096 Score: 317
Period size: 99 Copynumber: 1.9 Consensus size: 99
37292897 CTCAAGTGCA
* * * * *
37292907 TCTTCGGAAACAGCAGCATCATTGGTCCCATCAGCTACCAATTCTTCAGAAACAGCAGCATCATT
1 TCTTCAGAAACAACAGCATCATTGGTCCCATCAGCCACCAATTCTTCAGAAACAACAACATCATT
*
37292972 GGTCTCATCAGCTACCAATTCTTCAGCCACCAAT
66 GGTCTCATCAGCCACCAATTCTTCAGCCACCAAT
*
37293006 TCTTCAGAAACAACAGCATCATTGGTCTCATCAGCCACCAATTCTTCAGAAACAACAACATCATT
1 TCTTCAGAAACAACAGCATCATTGGTCCCATCAGCCACCAATTCTTCAGAAACAACAACATCATT
37293071 GGTCTCATCAGCCACCAATTCTTCAG
66 GGTCTCATCAGCCACCAATTCTTCAG
37293097 ATACAGCAGC
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 84 1.00
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.25
Consensus pattern (99 bp):
TCTTCAGAAACAACAGCATCATTGGTCCCATCAGCCACCAATTCTTCAGAAACAACAACATCATT
GGTCTCATCAGCCACCAATTCTTCAGCCACCAAT
Found at i:37293041 original size:42 final size:42
Alignment explanation
Indices: 37292994--37293175 Score: 274
Period size: 42 Copynumber: 4.3 Consensus size: 42
37292984 TACCAATTCT
*
37292994 TCAGCCACCAATTCTTCAGAAACAACAGCATCATTGGTCTCA
1 TCAGCCACCAATTCTTCAGAAACAACAGCAACATTGGTCTCA
* *
37293036 TCAGCCACCAATTCTTCAGAAACAACAACATCATTGGTCTCA
1 TCAGCCACCAATTCTTCAGAAACAACAGCAACATTGGTCTCA
* * *
37293078 TCAGCCACCAATTCTTCAGATACAGCAGCAACATTGGTATCA
1 TCAGCCACCAATTCTTCAGAAACAACAGCAACATTGGTCTCA
* * *
37293120 TCAGCTACCAATTCTTCAGATACAGCAGCAACATTGGTCTCA
1 TCAGCCACCAATTCTTCAGAAACAACAGCAACATTGGTCTCA
*
37293162 TCAGCTACCAATTC
1 TCAGCCACCAATTC
37293176 CTCATTTGGT
Statistics
Matches: 132, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 132 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (42 bp):
TCAGCCACCAATTCTTCAGAAACAACAGCAACATTGGTCTCA
Found at i:37298069 original size:26 final size:26
Alignment explanation
Indices: 37298033--37298086 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
37298023 GTTGCACATT
37298033 AACCACAATCTTTTCTTCTCAAAATC
1 AACCACAATCTTTTCTTCTCAAAATC
37298059 AACCACAATCTTTTCTTCTCAAAATC
1 AACCACAATCTTTTCTTCTCAAAATC
37298085 AA
1 AA
37298087 TCTTTCTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (26 bp):
AACCACAATCTTTTCTTCTCAAAATC
Found at i:37301773 original size:16 final size:16
Alignment explanation
Indices: 37301752--37301797 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
37301742 TTAATTTTGA
* *
37301752 ATTTAATTTTTAACTT
1 ATTTAAATTTAAACTT
*
37301768 ATTTAAATTTAAATTT
1 ATTTAAATTTAAACTT
37301784 ATTTTAAATTTAAA
1 A-TTTAAATTTAAA
37301798 TTTAAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTAAATTTAAACTT
Found at i:37301779 original size:6 final size:6
Alignment explanation
Indices: 37301768--37301804 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
37301758 TTTTTAACTT
*
37301768 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
37301805 CAAATGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTAA
Done.