Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold171
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: 2364178
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 278680 characters in sequence are not A, C, G, or T
File 4 of 13
Found at i:567064 original size:12 final size:11
Alignment explanation
Indices: 567038--567113 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
567028 TCTATTATCT
*
567038 CTCCTGTCTCTC
1 CTCCTATCTC-C
567050 CTCCTATCATCC
1 CTCCTATC-TCC
567062 CTCCTATCT--
1 CTCCTATCTCC
*
567071 CTACTATCT--
1 CTCCTATCTCC
*
567080 CTCCTGTCTCTC
1 CTCCTATCTC-C
567092 CTCCTATCATCC
1 CTCCTATC-TCC
*
567104 CTCCTCTCTC
1 CTCCTATCTC
567114 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:567065 original size:24 final size:24
Alignment explanation
Indices: 567029--567114 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
567019 TCTCCTCTCT
* *
567029 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
567053 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
567074 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
567095 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
567115 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:567089 original size:9 final size:9
Alignment explanation
Indices: 567016--567093 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
567006 TCCTCCTGTC
567016 ATCTCTCCT
1 ATCTCTCCT
* **
567025 CTCTCTATT
1 ATCTCTCCT
567034 ATCTCTCCT
1 ATCTCTCCT
*
567043 GTCTCTCCT
1 ATCTCTCCT
* *
567052 -CCTAT-C-
1 ATCTCTCCT
*
567058 ATCCCTCCT
1 ATCTCTCCT
*
567067 ATCTCTACT
1 ATCTCTCCT
567076 ATCTCTCCT
1 ATCTCTCCT
*
567085 GTCTCTCCT
1 ATCTCTCCT
567094 CCTATCATCC
Statistics
Matches: 50, Mismatches: 16, Indels: 6
0.69 0.22 0.08
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 43 0.86
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (9 bp):
ATCTCTCCT
Found at i:567089 original size:18 final size:18
Alignment explanation
Indices: 567016--567090 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 18
567006 TCCTCCTGTC
* *
567016 ATCTCTCCTCTCTCTATT
1 ATCTCTCCTGTCTCTACT
*
567034 ATCTCTCCTGTCTCTCCTCCT
1 ATCTCTCCTG--TCT-CTACT
*
567055 ATCATCCCTCCTATCTCTACT
1 ATC-T--CTCCTGTCTCTACT
567076 ATCTCTCCTGTCTCT
1 ATCTCTCCTGTCTCT
567091 CCTCCTATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
18 19 0.42
20 4 0.09
21 13 0.29
22 4 0.09
24 5 0.11
ACGTcount: A:0.11, C:0.43, G:0.03, T:0.44
Consensus pattern (18 bp):
ATCTCTCCTGTCTCTACT
Found at i:576040 original size:42 final size:42
Alignment explanation
Indices: 575985--576103 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
575975 TTCTTCTCTC
* *
575985 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
576027 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
576069 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
576104 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:576044 original size:12 final size:11
Alignment explanation
Indices: 576018--576093 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
576008 TCTATTATCT
*
576018 CTCCTGTCTCTC
1 CTCCTATCTC-C
576030 CTCCTATCATCC
1 CTCCTATC-TCC
576042 CTCCTATCT--
1 CTCCTATCTCC
*
576051 CTACTATCT--
1 CTCCTATCTCC
*
576060 CTCCTGTCTCTC
1 CTCCTATCTC-C
576072 CTCCTATCATCC
1 CTCCTATC-TCC
*
576084 CTCCTCTCTC
1 CTCCTATCTC
576094 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:576045 original size:24 final size:24
Alignment explanation
Indices: 576009--576094 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
575999 CCTCCTCTCT
* *
576009 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
576033 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
576054 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
576075 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
576095 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:576069 original size:18 final size:18
Alignment explanation
Indices: 576000--576070 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
575990 CCTGTCATCC
* *
576000 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
576018 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
576040 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
576060 CTCCTGTCTCT
1 CTCCTGTCTCT
576071 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:576794 original size:20 final size:20
Alignment explanation
Indices: 576769--576810 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
576759 AAATACTGGT
*
576769 TTTTTTCCTCTCTTTTTGTA
1 TTTTTTCATCTCTTTTTGTA
* *
576789 TTTTTTCATTTTTTTTTGTA
1 TTTTTTCATCTCTTTTTGTA
576809 TT
1 TT
576811 CTTGAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTTTCATCTCTTTTTGTA
Found at i:587150 original size:42 final size:42
Alignment explanation
Indices: 587095--587213 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
587085 TTCTTCTCTC
* *
587095 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
587137 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
587179 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
587214 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:587154 original size:12 final size:11
Alignment explanation
Indices: 587128--587203 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
587118 TCTATTATCT
*
587128 CTCCTGTCTCTC
1 CTCCTATCTC-C
587140 CTCCTATCATCC
1 CTCCTATC-TCC
587152 CTCCTATCT--
1 CTCCTATCTCC
*
587161 CTACTATCT--
1 CTCCTATCTCC
*
587170 CTCCTGTCTCTC
1 CTCCTATCTC-C
587182 CTCCTATCATCC
1 CTCCTATC-TCC
*
587194 CTCCTCTCTC
1 CTCCTATCTC
587204 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:587155 original size:24 final size:24
Alignment explanation
Indices: 587119--587204 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
587109 CCTCCTCTCT
* *
587119 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
587143 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
587164 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
587185 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
587205 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:587179 original size:18 final size:18
Alignment explanation
Indices: 587110--587180 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
587100 CCTGTCATCC
* *
587110 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
587128 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
587150 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
587170 CTCCTGTCTCT
1 CTCCTGTCTCT
587181 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:597555 original size:12 final size:11
Alignment explanation
Indices: 597533--597607 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 11
597523 AGAGAAAGAA
*
597533 GAGAGAGGAGG
1 GAGATAGGAGG
597544 GATGATAGGAGG
1 GA-GATAGGAGG
*
597556 AGAGACAGGA--
1 -GAGATAGGAGG
*
597566 GAGATAGTA--
1 GAGATAGGAGG
597575 GAGATAGGAGG
1 GAGATAGGAGG
597586 GATGATAGGAGG
1 GA-GATAGGAGG
*
597598 AGAGACAGGA
1 -GAGATAGGA
597608 CAGATAATAG
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
9 15 0.29
11 4 0.08
12 29 0.56
13 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.48, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:597584 original size:42 final size:42
Alignment explanation
Indices: 597523--597641 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
597513 TAGCCCTCAA
* *
597523 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
597565 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
597607 ACAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
597642 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:603821 original size:12 final size:11
Alignment explanation
Indices: 603799--603874 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
603789 AGAGAAAGAA
*
603799 GAGAGAGGAGG
1 GAGATAGGAGG
603810 GATGATAGGAGG
1 GA-GATAGGAGG
*
603822 AGAGACAGGA--
1 -GAGATAGGAGG
*
603832 GAGATAGTA--
1 GAGATAGGAGG
603841 GAGATAGGAGG
1 GAGATAGGAGG
603852 GATGATAGGAGG
1 GA-GATAGGAGG
*
603864 AGAGACAGGAG
1 -GAGATAGGAG
603875 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:603831 original size:24 final size:24
Alignment explanation
Indices: 603798--603883 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
603788 AAGAGAAAGA
*
603798 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
603822 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
603840 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
603864 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
603884 AGAGAGGAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:603833 original size:9 final size:9
Alignment explanation
Indices: 603819--603896 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
603809 GGATGATAGG
*
603819 AGGAGAGAC
1 AGGAGAGAT
603828 AGGAGAGAT
1 AGGAGAGAT
*
603837 AGTAGAGAT
1 AGGAGAGAT
*
603846 AGGAGGGAT
1 AGGAGAGAT
* *
603855 --GATAG-G
1 AGGAGAGAT
*
603861 AGGAGAGAC
1 AGGAGAGAT
603870 AGGAGAGAT
1 AGGAGAGAT
** *
603879 AATAGAGAG
1 AGGAGAGAT
603888 AGGAGAGAT
1 AGGAGAGAT
603897 GACAGGAGGA
Statistics
Matches: 50, Mismatches: 16, Indels: 6
0.69 0.22 0.08
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 43 0.86
ACGTcount: A:0.44, C:0.03, G:0.44, T:0.10
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:603849 original size:18 final size:18
Alignment explanation
Indices: 603822--603896 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 18
603812 TGATAGGAGG
603822 AGAGACAGGAGAGATAGT
1 AGAGACAGGAGAGATAGT
* *
603840 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGA--GA-GAT---AGT
*
603864 AGAGACAGGAGAGATAAT
1 AGAGACAGGAGAGATAGT
*
603882 AGAGAGAGGAGAGAT
1 AGAGACAGGAGAGAT
603897 GACAGGAGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
18 24 0.53
20 2 0.04
21 6 0.13
22 2 0.04
24 11 0.24
ACGTcount: A:0.44, C:0.03, G:0.43, T:0.11
Consensus pattern (18 bp):
AGAGACAGGAGAGATAGT
Found at i:603850 original size:42 final size:42
Alignment explanation
Indices: 603789--603907 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
603779 TAGCCCTCAA
* *
603789 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
603831 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * *
603873 AGAGATAATAGAGAGAGGAGAGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
603908 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:610213 original size:28 final size:29
Alignment explanation
Indices: 610173--610244 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
610163 AAGAAAGATT
* *
610173 AAGGAAGTGAAATCAA-CAAGAAATATGA
1 AAGGAAATGAAATCAAGCAAGAAATATCA
* *
610201 AGGGAAATGAAAT-AAGCCAGAAATATCA
1 AAGGAAATGAAATCAAGCAAGAAATATCA
610229 AAGGAAGA-GAAATCAA
1 AAGGAA-ATGAAATCAA
610245 TGAAGAGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.06
28 31 0.86
29 3 0.08
ACGTcount: A:0.57, C:0.08, G:0.22, T:0.12
Consensus pattern (29 bp):
AAGGAAATGAAATCAAGCAAGAAATATCA
Found at i:617162 original size:21 final size:21
Alignment explanation
Indices: 617138--617183 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
617128 TAGAAATATG
*
617138 TATTGATACTTCATGAACTTA
1 TATTGACACTTCATGAACTTA
* * *
617159 TATTGGCACTTCATGAGCTTG
1 TATTGACACTTCATGAACTTA
617180 TATT
1 TATT
617184 AATATACAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (21 bp):
TATTGACACTTCATGAACTTA
Found at i:619803 original size:19 final size:19
Alignment explanation
Indices: 619757--619796 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
619747 TTTTTTTAGC
619757 ATACCCATGAAAAAAAATA
1 ATACCCATGAAAAAAAATA
619776 ATACCCATG-AAAAAAATA
1 ATACCCATGAAAAAAAATA
619794 ATA
1 ATA
619797 AGCCATGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.62, C:0.15, G:0.05, T:0.17
Consensus pattern (19 bp):
ATACCCATGAAAAAAAATA
Found at i:625949 original size:42 final size:42
Alignment explanation
Indices: 625894--626012 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
625884 TTCTTCTCTC
* *
625894 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
625936 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
625978 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
626013 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:625953 original size:12 final size:11
Alignment explanation
Indices: 625927--626002 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
625917 TCTATTATCT
*
625927 CTCCTGTCTCTC
1 CTCCTATCTC-C
625939 CTCCTATCATCC
1 CTCCTATC-TCC
625951 CTCCTATCT--
1 CTCCTATCTCC
*
625960 CTACTATCT--
1 CTCCTATCTCC
*
625969 CTCCTGTCTCTC
1 CTCCTATCTC-C
625981 CTCCTATCATCC
1 CTCCTATC-TCC
*
625993 CTCCTCTCTC
1 CTCCTATCTC
626003 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:625954 original size:24 final size:24
Alignment explanation
Indices: 625918--626003 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
625908 CCTCCTCTCT
* *
625918 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
625942 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
625963 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
625984 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
626004 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:625978 original size:18 final size:18
Alignment explanation
Indices: 625909--625979 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
625899 CCTGTCATCC
* *
625909 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
625927 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
625949 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
625969 CTCCTGTCTCT
1 CTCCTGTCTCT
625980 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:627841 original size:11 final size:11
Alignment explanation
Indices: 627825--627849 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
627815 GACTAAAAAG
627825 AACCAACAAGA
1 AACCAACAAGA
627836 AACCAACAAGA
1 AACCAACAAGA
627847 AAC
1 AAC
627850 ATAAAGAAAT
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:0.64, C:0.28, G:0.08, T:0.00
Consensus pattern (11 bp):
AACCAACAAGA
Found at i:634235 original size:18 final size:18
Alignment explanation
Indices: 634212--634319 Score: 58
Period size: 21 Copynumber: 5.3 Consensus size: 18
634202 ATCTTCTTCT
634212 CTCCTCCTCCTATCATCC
1 CTCCTCCTCCTATCATCC
*
634230 CTCCT-CTCTCTATTATCTCTC
1 CTCCTCCTC-CTATCA--TC-C
634251 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
*
634272 CTCCTATCTCTACTATC-TCTC
1 CTCC--TC-CTCCTATCATC-C
634293 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
634314 CTCCTC
1 CTCCTC
634320 TCTCTTCTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 32
0.66 0.04 0.30
Matches are distributed among these distances:
17 3 0.04
18 14 0.20
19 4 0.06
20 6 0.09
21 22 0.31
22 6 0.09
23 4 0.06
24 8 0.11
25 3 0.04
ACGTcount: A:0.10, C:0.48, G:0.02, T:0.40
Consensus pattern (18 bp):
CTCCTCCTCCTATCATCC
Found at i:634267 original size:42 final size:42
Alignment explanation
Indices: 634215--634333 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
634205 TTCTTCTCTC
*
634215 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
634257 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
634299 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
634334 TTGAGGGCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:634274 original size:12 final size:11
Alignment explanation
Indices: 634248--634323 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
634238 TCTATTATCT
*
634248 CTCCTGTCTCTC
1 CTCCTATCTC-C
634260 CTCCTATCATCC
1 CTCCTATC-TCC
634272 CTCCTATCT--
1 CTCCTATCTCC
*
634281 CTACTATCT--
1 CTCCTATCTCC
*
634290 CTCCTGTCTCTC
1 CTCCTATCTC-C
634302 CTCCTATCATCC
1 CTCCTATC-TCC
*
634314 CTCCTCTCTC
1 CTCCTATCTC
634324 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:636447 original size:21 final size:21
Alignment explanation
Indices: 636423--636463 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
636413 CGATGTGTTT
*
636423 GAAAAGA-AAGTAGATGAATTA
1 GAAAAGAGAA-TAAATGAATTA
636444 GAAAAGAGAATAAATGAATT
1 GAAAAGAGAATAAATGAATT
636464 GCAAGAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.20
Consensus pattern (21 bp):
GAAAAGAGAATAAATGAATTA
Found at i:643003 original size:23 final size:24
Alignment explanation
Indices: 642973--643017 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
642963 ATTTTTTTTC
642973 AAGAATACAAAAA-AAAGGAAAGA
1 AAGAATACAAAAAGAAAGGAAAGA
*
642996 AAGAATACAAAAAGAGAGGAAA
1 AAGAATACAAAAAGAAAGGAAA
643018 AAAACCAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.71, C:0.04, G:0.20, T:0.04
Consensus pattern (24 bp):
AAGAATACAAAAAGAAAGGAAAGA
Found at i:643786 original size:12 final size:11
Alignment explanation
Indices: 643767--643842 Score: 70
Period size: 12 Copynumber: 6.9 Consensus size: 11
643757 AGAGAAAGAA
643767 GAGATAGGAGG
1 GAGATAGGAGG
643778 GATGATAGGAGG
1 GA-GATAGGAGG
*
643790 AGAGATAGTA--
1 -GAGATAGGAGG
*
643800 GAGATAGGAAG
1 GAGATAGGAGG
643811 GATGATAGGAGG
1 GA-GATAGGAGG
643823 AGAGATAGGA--
1 -GAGATAGGAGG
643833 GAGATAGGAG
1 GAGATAGGAG
643843 AGATAATAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
9 17 0.31
11 4 0.07
12 30 0.55
13 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.46, T:0.13
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:643794 original size:33 final size:33
Alignment explanation
Indices: 643757--643851 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 33
643747 TAGCCCTCAA
*
643757 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAGGAGGGATGATAGGAGG
* *
643790 AGAGATAGTAGAGATAGGAAGGATGATAGGAGG
1 AGAGATAGAAGAGATAGGAGGGATGATAGGAGG
* * *
643823 AGAGATAGGAGAGATAGGAGAGATAATAG
1 AGAGATAGAAGAGATAGGAGGGATGATAG
643852 AGAAAGGAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (33 bp):
AGAGATAGAAGAGATAGGAGGGATGATAGGAGG
Found at i:643834 original size:9 final size:9
Alignment explanation
Indices: 643787--643847 Score: 59
Period size: 9 Copynumber: 6.1 Consensus size: 9
643777 GGATGATAGG
643787 AGGAGAGAT
1 AGGAGAGAT
*
643796 AGTAGAGAT
1 AGGAGAGAT
643805 AGGAAGGATGAT
1 AGG-A-GA-GAT
643817 AGGAGGAGAGAT
1 ---AGGAGAGAT
643829 AGGAGAGAT
1 AGGAGAGAT
643838 AGGAGAGAT
1 AGGAGAGAT
643847 A
1 A
643848 ATAGAGAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
9 29 0.66
10 1 0.02
11 2 0.05
12 6 0.14
13 2 0.05
14 1 0.02
15 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.43, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:648222 original size:42 final size:42
Alignment explanation
Indices: 648167--648246 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
648157 TTCTTCTCTC
* * *
648167 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
648209 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCT
648247 CCTATCCTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.10, C:0.46, G:0.03, T:0.41
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
Found at i:654648 original size:32 final size:33
Alignment explanation
Indices: 654588--654649 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
654578 TACAAGCCAA
** *
654588 TGTATCGATACAATTTTTTGTGTATCGATATAT
1 TGTATCGATACAATACTTGGTGTATCGATATAT
654621 TGTATCGATAC-ATACTTGGTGTATCGATA
1 TGTATCGATACAATACTTGGTGTATCGATA
654650 CAAGTTTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATATAT
Found at i:655408 original size:36 final size:36
Alignment explanation
Indices: 655359--655430 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
655349 TTTATTAATA
* *
655359 ATTCTCCCTCTTAATCAAGTAATTCATATGAAAAAT
1 ATTCTCCCCCTTAATCAAGTAATTCATATCAAAAAT
655395 ATTCTCCCCCTTAATCAAGTAATTCATATCAAAAAT
1 ATTCTCCCCCTTAATCAAGTAATTCATATCAAAAAT
655431 TTATTTGCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (36 bp):
ATTCTCCCCCTTAATCAAGTAATTCATATCAAAAAT
Found at i:657240 original size:13 final size:13
Alignment explanation
Indices: 657222--657247 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
657212 ATAATCACCC
657222 TGTATCGATACAA
1 TGTATCGATACAA
657235 TGTATCGATACAA
1 TGTATCGATACAA
657248 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:659346 original size:15 final size:15
Alignment explanation
Indices: 659321--659356 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
659311 CATCAATTTC
*
659321 TTTTGGAGCTTCTTCA
1 TTTT-GAGCTTCCTCA
659337 TTTTGAGCTTCCTCA
1 TTTTGAGCTTCCTCA
659352 TTTTG
1 TTTTG
659357 GACATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.11, C:0.19, G:0.17, T:0.53
Consensus pattern (15 bp):
TTTTGAGCTTCCTCA
Found at i:661181 original size:21 final size:21
Alignment explanation
Indices: 661152--661196 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
661142 AAGTTTTCAT
*
661152 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
661172 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
661194 TTT
1 TTT
661197 CATCTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:663435 original size:13 final size:13
Alignment explanation
Indices: 663417--663442 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
663407 CAATTTTTTG
663417 TGTATCGATACAT
1 TGTATCGATACAT
663430 TGTATCGATACAT
1 TGTATCGATACAT
663443 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:663457 original size:32 final size:33
Alignment explanation
Indices: 663397--663460 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
663387 TACAAGCCAA
** *
663397 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
663430 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
663461 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:668981 original size:13 final size:13
Alignment explanation
Indices: 668963--668987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
668953 AGAATGCACA
668963 GTATCGATACATT
1 GTATCGATACATT
668976 GTATCGATACAT
1 GTATCGATACAT
668988 GACCAAATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:669000 original size:20 final size:21
Alignment explanation
Indices: 668975--669027 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
668965 ATCGATACAT
*
668975 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
668995 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
669016 TGTATCGATACA
1 TGTATCGATACA
669028 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:669113 original size:20 final size:21
Alignment explanation
Indices: 669068--669120 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
669058 CCTTAACTGT
669068 TTGTATCGATACA-CACAAGA
1 TTGTATCGATACATCACAAGA
*
669088 -TGTATCGATACATCCCAA-A
1 TTGTATCGATACATCACAAGA
669107 TTGTATCGATACAT
1 TTGTATCGATACAT
669121 TGGCTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (21 bp):
TTGTATCGATACATCACAAGA
Found at i:675271 original size:13 final size:13
Alignment explanation
Indices: 675252--675288 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
675242 ACAGCATTCT
675252 CTGTATCGATACA
1 CTGTATCGATACA
*
675265 TTGTATCGATACA
1 CTGTATCGATACA
*
675278 CTGTATTGATA
1 CTGTATCGATA
675289 AAAAGGGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:681207 original size:18 final size:18
Alignment explanation
Indices: 681180--681250 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
681170 CTTGTCATCC
*
681180 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTATTATCT
*
681198 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTGTCTCT-AT--TATC-T
* *
681220 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTATTATCT
681240 CTCCTGTCTCT
1 CTCCTGTCTCT
681251 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 20 0.49
19 1 0.02
20 1 0.02
21 8 0.20
22 1 0.02
24 10 0.24
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTATTATCT
Found at i:681211 original size:42 final size:42
Alignment explanation
Indices: 681164--681271 Score: 180
Period size: 42 Copynumber: 2.6 Consensus size: 42
681154 CTTCTTCTCT
* * *
681164 TCTCCTCTTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTC
1 TCTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTC
*
681206 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTC
1 TCTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTC
681248 TCTCCTCCTATCATCCCTCCTCTC
1 TCTCCTCCTATCATCCCTCCTCTC
681272 AATTCTTTCT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.09, C:0.46, G:0.03, T:0.42
Consensus pattern (42 bp):
TCTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTC
Found at i:681224 original size:12 final size:11
Alignment explanation
Indices: 681198--681268 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
681188 TCTATTATCT
*
681198 CTCCTGTCTCTC
1 CTCCTATCTC-C
681210 CTCCTATCATCC
1 CTCCTATC-TCC
681222 CTCCTATCT--
1 CTCCTATCTCC
*
681231 CTACTATCT--
1 CTCCTATCTCC
*
681240 CTCCTGTCTCTC
1 CTCCTATCTC-C
681252 CTCCTATCATCC
1 CTCCTATC-TCC
681264 CTCCT
1 CTCCT
681269 CTCAATTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
9 15 0.31
11 1 0.02
12 29 0.59
13 4 0.08
ACGTcount: A:0.10, C:0.48, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:682042 original size:15 final size:15
Alignment explanation
Indices: 682024--682057 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
682014 TGGTTTTTTT
682024 TTCTCTCTTTTTGTA
1 TTCTCTCTTTTTGTA
* *
682039 TTCTTTTTTTTTGTA
1 TTCTCTCTTTTTGTA
682054 TTCT
1 TTCT
682058 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (15 bp):
TTCTCTCTTTTTGTA
Found at i:682058 original size:15 final size:15
Alignment explanation
Indices: 682031--682059 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
682021 TTTTTCTCTC
682031 TTTTTGTATTCTTTT
1 TTTTTGTATTCTTTT
682046 TTTTTGTATTCTTT
1 TTTTTGTATTCTTT
682060 AAAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (15 bp):
TTTTTGTATTCTTTT
Found at i:683881 original size:21 final size:22
Alignment explanation
Indices: 683852--683895 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
683842 GATTAAAGAA
683852 AATTGTTTT-ATTAAGGGGGAG
1 AATTGTTTTGATTAAGGGGGAG
*
683873 AATTTTTTTGATTAAGGGGGAG
1 AATTGTTTTGATTAAGGGGGAG
683895 A
1 A
683896 GAAAAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.32, T:0.39
Consensus pattern (22 bp):
AATTGTTTTGATTAAGGGGGAG
Found at i:684467 original size:13 final size:13
Alignment explanation
Indices: 684449--684473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
684439 AGAATGCACA
684449 GTATCGATACATT
1 GTATCGATACATT
684462 GTATCGATACAT
1 GTATCGATACAT
684474 GACCAAATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:684486 original size:20 final size:21
Alignment explanation
Indices: 684461--684513 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
684451 ATCGATACAT
*
684461 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
684481 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
684502 TGTATCGATACA
1 TGTATCGATACA
684514 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:684599 original size:20 final size:21
Alignment explanation
Indices: 684554--684606 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
684544 CCTTAACTGT
684554 TTGTATCGATACA-CACAAGA
1 TTGTATCGATACATCACAAGA
*
684574 -TGTATCGATACATCCCAA-A
1 TTGTATCGATACATCACAAGA
684593 TTGTATCGATACAT
1 TTGTATCGATACAT
684607 TAGCTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (21 bp):
TTGTATCGATACATCACAAGA
Found at i:688493 original size:20 final size:17
Alignment explanation
Indices: 688433--688517 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 17
688423 TTTTAACTAG
* *
688433 ATGTATTGATACATTGA
1 ATGTATCGATACATTTA
* *
688450 ATGTATGGATACATTGAAGA
1 ATGTATCGATACATT---TA
688470 ATGTATCGATACATTTATA
1 ATGTATCGATACA-TT-TA
688489 TATGTATCGATACATTTA
1 -ATGTATCGATACATTTA
688507 ATGTATCGATA
1 ATGTATCGATA
688518 TATCTGGGTA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
17 25 0.42
18 2 0.03
19 4 0.07
20 27 0.45
21 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39
Consensus pattern (17 bp):
ATGTATCGATACATTTA
Found at i:689182 original size:17 final size:18
Alignment explanation
Indices: 689160--689193 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
689150 AACTTAGTTT
689160 ATAG-TTATCAATTTTGA
1 ATAGTTTATCAATTTTGA
*
689177 ATAGTTTATTAATTTTG
1 ATAGTTTATCAATTTTG
689194 TCTTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (18 bp):
ATAGTTTATCAATTTTGA
Found at i:693628 original size:21 final size:22
Alignment explanation
Indices: 693585--693628 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
693575 GGGAAATTCA
693585 TAAAATTTTTGAGAAAAATATT
1 TAAAATTTTTGAGAAAAATATT
693607 TAAAA-TTTTG-GAAAAATCATT
1 TAAAATTTTTGAGAAAAAT-ATT
693628 T
1 T
693629 GATAGGCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (22 bp):
TAAAATTTTTGAGAAAAATATT
Found at i:695563 original size:79 final size:78
Alignment explanation
Indices: 695433--695602 Score: 277
Period size: 79 Copynumber: 2.2 Consensus size: 78
695423 ACTGCTAGTA
* *
695433 TTTTGGAAATAAAACTGGGTTGGAGTATCCTCTCAAAAATAACAGGGTTGGAGTATCCATGATTG
1 TTTTGGAAATAAAACGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCATGATTG
695498 TGGAAAATCAATG
66 TGGAAAATCAATG
* *
695511 TTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTGATT
1 TTTTGGAAATAAAA-CGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCATGATT
**
695576 GTGGAAAATTGATG
65 GTGGAAAATCAATG
695590 TTTTGGAAATAAA
1 TTTTGGAAATAAA
695603 TATCCACCTA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
78 14 0.16
79 71 0.84
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (78 bp):
TTTTGGAAATAAAACGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCATGATTG
TGGAAAATCAATG
Found at i:698814 original size:132 final size:134
Alignment explanation
Indices: 698577--698840 Score: 437
Period size: 132 Copynumber: 2.0 Consensus size: 134
698567 AAAGGCTATT
698577 TAGTACTTTGTTCACATAGCTTAAATATATTTGAGGGAAGACTTTAACAAATTTCGTAAGGTTTG
1 TAGTACTTTGTTCACATAGCTTAAATATATTTGAGGGAAGACTTTAACAAATTTCGTAAGGTTTG
* *
698642 TCCTCCATACAAGGTTGAAGTAGATAGGTGCCACCAAC-T-TGTGGGCTTTAAGATGGAAAATGA
66 CCCTCCATACAAGGTTGAAGTAGATAGGTGCCACCAACTTGTGTGGGCTTTAAGATGGAAAAGGA
698705 GAGA
131 GAGA
*
698709 TAGTACTTTGTTCACATAGGC-TAAATATATTTGAGGGAAGACTTTAACAAATTTCGTAGGGTTT
1 TAGTACTTTGTTCACATA-GCTTAAATATATTTGAGGGAAGACTTTAACAAATTTCGTAAGGTTT
* *
698773 GCCCTTCC-TATAGGGTTGAAGTAGATAGGTGCCACCAACTTGTGTGGGCTTTAAGATGGAAAAG
65 GCCC-TCCATACAAGGTTGAAGTAGATAGGTGCCACCAACTTGTGTGGGCTTTAAGATGGAAAAG
698837 GAGA
129 GAGA
698841 AAGGCGTTCT
Statistics
Matches: 123, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
132 92 0.75
133 6 0.05
134 25 0.20
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (134 bp):
TAGTACTTTGTTCACATAGCTTAAATATATTTGAGGGAAGACTTTAACAAATTTCGTAAGGTTTG
CCCTCCATACAAGGTTGAAGTAGATAGGTGCCACCAACTTGTGTGGGCTTTAAGATGGAAAAGGA
GAGA
Found at i:699052 original size:61 final size:60
Alignment explanation
Indices: 698854--699294 Score: 416
Period size: 61 Copynumber: 7.3 Consensus size: 60
698844 GCGTTCTGCG
* * * * * * *
698854 CTTTGAGGACT-AGAAGGTGCTAGCAGCTAGTGTGGGCTTTGCAAA-GAGAAAGCATCCTGCT
1 CTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA-AAAGCATTCTACT
* * *
698915 CTTTGAGGACTGGAAA-GTGCCA-CAACTTGTGTGGGCTTTGAAAGG-AAATCA-TCTTGCT
1 CTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCATTC-TACT
* * *
698973 CTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTGAAAAAGAAAA-CAAGTTCTATT
1 CTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGC-A-TTCTACT
* *
699034 CTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACT
1 CTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCATTCTACT
* * * * *
699095 CTTTAAGGACTGAAAGGTGTCACCAATTTATGTGGGCTTTAAAAGGAAAAGGCATTCTGCT
1 CTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCATTCTACT
* * * *
699156 CCTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-GTGTCTTGCT
1 CTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCAT-TC-TACT
* ** * * *
699217 CTTTGTGGACT-AGAAGGTGCCACCAACTTGCATGAGCTTTAAAAGGAAAAGACGTCCTACT
1 CTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-CATTCTACT
699278 CTTTGAGGACTGAAAGG
1 CTTTGAGGACTGAAAGG
699295 ATAAAAGGTT
Statistics
Matches: 321, Mismatches: 39, Indels: 40
0.80 0.10 0.10
Matches are distributed among these distances:
56 1 0.00
57 3 0.01
58 26 0.08
59 25 0.08
60 24 0.07
61 230 0.72
62 8 0.02
63 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (60 bp):
CTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCATTCTACT
Found at i:699130 original size:122 final size:121
Alignment explanation
Indices: 698799--699294 Score: 405
Period size: 122 Copynumber: 4.0 Consensus size: 121
698789 TGAAGTAGAT
* * * * *
698799 AGGTGCCACCAACTTGTGTGGGCTTTAAGATGGAAAAGGAGAAAGGCGTTCTGCGCTTTGAGGAC
1 AGGTGCCACCAACTTGTGTGGGC-TT----T--AAAAGGA-AAAGGCATCCTACTCTTTAAGGAC
* * * * * * *
698864 TAGAAGGTGCTAGCAGC-TAGTGTGGGCTTTG-CAAAGAGAAAGCATCCTGCTCTTTGAGGACTG
58 TAGAAGGTGCCACCAACTTA-TGTGGGC-TTGAAAAAGA-AAAGCATTCTACTCTTTGAGGA-TT
698927 GAA
119 GAA
* * * * *
698930 A-GTGCCA-CAACTTGTGTGGGCTTTGAAAGG-AAA-TCATCTTGCTCTTTGAGGACTAGAAGGT
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTAAGGACTAGAAGGT
* *
698991 GCCACCAACTTGTGTGGGCTTGAAAAAGAAAA-CAAGTTCTATTCTTTGAGGATTGAA
66 GCCACCAACTTATGTGGGCTTGAAAAAGAAAAGC-A-TTCTACTCTTTGAGGATTGAA
699048 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTAAGGACT-GAAAGG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTAAGGACTAG-AAGG
* * * * * * *
699112 TGTCACCAATTTATGTGGGCTTTAAAAGGAAAAGGCATTCTGCTCCTTGAGGACTGAA
65 TGCCACCAACTTATGTGGGCTTGAAAAAGAAAA-GCATTCTACTCTTTGAGGATTGAA
* ** * * **
699170 AGGTACCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCTTGCTCTTTGTGGACTAGAAGGT
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTAAGGACTAGAAGGT
*** * * * * * *
699235 GCCACCAACTTGCATGAGCTTTAAAAGGAAAAGACGTCCTACTCTTTGAGGACTGAA
66 GCCACCAACTTATGTGGGCTTGAAAAAGAAAAG-CATTCTACTCTTTGAGGATTGAA
699292 AGG
1 AGG
699295 ATAAAAGGTT
Statistics
Matches: 306, Mismatches: 46, Indels: 35
0.79 0.12 0.09
Matches are distributed among these distances:
117 1 0.00
118 12 0.04
119 60 0.20
120 26 0.08
121 5 0.02
122 175 0.57
123 2 0.01
124 2 0.01
128 2 0.01
129 14 0.05
130 6 0.02
131 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (121 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTAAGGACTAGAAGGT
GCCACCAACTTATGTGGGCTTGAAAAAGAAAAGCATTCTACTCTTTGAGGATTGAA
Found at i:699236 original size:183 final size:182
Alignment explanation
Indices: 698794--699294 Score: 504
Period size: 183 Copynumber: 2.7 Consensus size: 182
698784 AGGGTTGAAG
* * * *
698794 TAGATAGGTGCCACCAACTTGTGTGGGCTTTAAGATGGAAAAGGAGAAAGGCGT-TCTGCGCTTT
1 TAGA-AGGTACCACCAACTTGTGTGGGC-TT--GA---AAAAGGA-AAAGGTGTCTATGCTCTTT
* * * * * *
698858 GAGGACTAGAAGGTGCTAGCAGCTAGTGTGGGCTTTGCAAA-GAGAAA-GCATCCTGCTCTTTGA
58 GAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA-AAAGGCATCCTACTCTTTGA
* * * *
698921 GGACTGGAAA-GTGCCACAACTTGTGTGGGCTTTGAAAGGAAATCATCTTGCTCTTTGAGGAC
121 GGACT-GAAAGGTGCCACAACTTATGTGGGCTTTAAAAGGAAAGCATCTTGCTCCTTGAGGAC
* * *
698983 TAGAAGGTGCCACCAACTTGTGTGGGCTTGAAAAAGAAAACAAGT-TCTAT--TCTTTGAGGA-T
1 TAGAAGGTACCACCAACTTGTGTGGGCTTGAAAAAGGAAA-AGGTGTCTATGCTCTTTGAGGACT
* *
699044 TGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTAAGGACTGAA
65 AG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAA
* *
699109 AGGTGTCACCAATTTATGTGGGCTTTAAAAGGAAAAGGCAT-TCTGCTCCTTGAGGAC
129 AGGTGCCA-CAACTTATGTGGGCTTTAAAAGG-AAA-GCATCT-TGCTCCTTGAGGAC
* *
699166 T-GAAAGGTACCACCAACTTGTGTGGGCTT-TAAAAGGAAAAGGTGTCT-TGCTCTTTGTGGACT
1 TAG-AAGGTACCACCAACTTGTGTGGGCTTGAAAAAGGAAAAGGTGTCTATGCTCTTTGAGGACT
** * * *
699228 AGAAGGTGCCACCAACTTGCATGAGCTTTAAAAGGAAAAGACGTCCTACTCTTTGAGGACTGAAA
65 AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAA
699293 GG
130 GG
699295 ATAAAAGGTT
Statistics
Matches: 266, Mismatches: 31, Indels: 36
0.80 0.09 0.11
Matches are distributed among these distances:
179 12 0.05
180 58 0.22
181 27 0.10
182 26 0.10
183 110 0.41
184 2 0.01
185 2 0.01
187 2 0.01
188 23 0.09
189 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (182 bp):
TAGAAGGTACCACCAACTTGTGTGGGCTTGAAAAAGGAAAAGGTGTCTATGCTCTTTGAGGACTA
GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACTGAAAG
GTGCCACAACTTATGTGGGCTTTAAAAGGAAAGCATCTTGCTCCTTGAGGAC
Found at i:700274 original size:10 final size:9
Alignment explanation
Indices: 700259--700296 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
700249 CTTAAGTAGG
700259 TTCTTTTATT
1 TTCTTTT-TT
700269 TTCTTTTTT
1 TTCTTTTTT
*
700278 CT-TTTTTT
1 TTCTTTTTT
700286 TTCTTTTTT
1 TTCTTTTTT
700295 TT
1 TT
700297 TGAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 11 0.44
10 7 0.28
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:700281 original size:17 final size:17
Alignment explanation
Indices: 700259--700294 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
700249 CTTAAGTAGG
700259 TTCTTTTATTTTCTTTT
1 TTCTTTTATTTTCTTTT
*
700276 TTCTTTTTTTTTCTTTT
1 TTCTTTTATTTTCTTTT
700293 TT
1 TT
700295 TTTGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (17 bp):
TTCTTTTATTTTCTTTT
Found at i:700297 original size:10 final size:10
Alignment explanation
Indices: 700272--700297 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
700262 TTTTATTTTC
700272 TTTTTTCTTT
1 TTTTTTCTTT
700282 TTTTTTCTTT
1 TTTTTTCTTT
700292 TTTTTT
1 TTTTTT
700298 GAAAAAAAGG
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:702396 original size:13 final size:13
Alignment explanation
Indices: 702378--702403 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
702368 TACACCAAGT
702378 ATGTATCGATACA
1 ATGTATCGATACA
702391 ATGTATCGATACA
1 ATGTATCGATACA
702404 CAAATAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:702401 original size:32 final size:33
Alignment explanation
Indices: 702360--702423 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
702350 TAGCCAAACT
*
702360 TGTATCGATACACCAAGT-A-TGTATCGATACAA
1 TGTATCGATACA-CAAATAATTGTATCGATACAA
702392 TGTATCGATACACAAATAATTGTATCGATACA
1 TGTATCGATACACAAATAATTGTATCGATACA
702424 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 13 0.45
33 12 0.41
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAATAATTGTATCGATACAA
Found at i:703822 original size:18 final size:17
Alignment explanation
Indices: 703790--703824 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
703780 GTTTGTTAAT
703790 TTAAAGATATTCTATGC
1 TTAAAGATATTCTATGC
*
703807 TTAAATGATTTTCTATGC
1 TTAAA-GATATTCTATGC
703825 AATTTTTGAT
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:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (17 bp):
TTAAAGATATTCTATGC
Found at i:706194 original size:13 final size:13
Alignment explanation
Indices: 706176--706201 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
706166 TACACCAAGT
706176 ATGTATCGATACA
1 ATGTATCGATACA
706189 ATGTATCGATACA
1 ATGTATCGATACA
706202 CAAATAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:706199 original size:32 final size:33
Alignment explanation
Indices: 706158--706221 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
706148 TAGCCAAACT
*
706158 TGTATCGATACACCAAGT-A-TGTATCGATACAA
1 TGTATCGATACA-CAAATAATTGTATCGATACAA
706190 TGTATCGATACACAAATAATTGTATCGATACA
1 TGTATCGATACACAAATAATTGTATCGATACA
706222 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 13 0.45
33 12 0.41
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAATAATTGTATCGATACAA
Found at i:708089 original size:21 final size:21
Alignment explanation
Indices: 708063--708102 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
708053 TGACTTTTTG
708063 TTATGCATGAAAATGGTTTCC
1 TTATGCATGAAAATGGTTTCC
708084 TTATGCATGAAAATGGTTT
1 TTATGCATGAAAATGGTTT
708103 TTTAGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (21 bp):
TTATGCATGAAAATGGTTTCC
Found at i:708295 original size:19 final size:19
Alignment explanation
Indices: 708271--708332 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
708261 TTTTGAATTT
708271 CAAACAGTTTGTATCGATA
1 CAAACAGTTTGTATCGATA
**
708290 CAAACAGAAAATGTATCGATA
1 CAAACAG--TTTGTATCGATA
*
708311 CATA-AGTGTTGTATCGATA
1 CAAACAGT-TTGTATCGATA
708330 CAA
1 CAA
708333 TGTATCGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (19 bp):
CAAACAGTTTGTATCGATA
Found at i:708338 original size:13 final size:13
Alignment explanation
Indices: 708320--708344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
708310 ACATAAGTGT
708320 TGTATCGATACAA
1 TGTATCGATACAA
708333 TGTATCGATACA
1 TGTATCGATACA
708345 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:708340 original size:32 final size:32
Alignment explanation
Indices: 708299--708371 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
708289 ACAAACAGAA
708299 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
708331 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
708363 AATGTATCG
1 AATGTATCG
708372 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:708357 original size:19 final size:18
Alignment explanation
Indices: 708301--708363 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
708291 AAACAGAAAA
708301 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
708320 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
708333 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
708352 TGTATCGATACA
1 TGTATCGATACA
708364 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:708414 original size:21 final size:21
Alignment explanation
Indices: 708388--708429 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
708378 AGCTACTGCC
708388 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
708409 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
708430 GTATCGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:708434 original size:13 final size:13
Alignment explanation
Indices: 708416--708443 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
708406 ATTAAGGAAA
708416 TGTATCGATACAT
1 TGTATCGATACAT
708429 TGTATCGATACAT
1 TGTATCGATACAT
708442 TG
1 TG
708444 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:710923 original size:52 final size:52
Alignment explanation
Indices: 710798--711189 Score: 212
Period size: 52 Copynumber: 7.5 Consensus size: 52
710788 TTAAGTTTCT
* * * * *
710798 CAATTATTCATAATTGAGGATACTCCAACCCCGATTTTGTTTTC-AAAACAC
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* ** * *
710849 CAATTTTCCTTTAATC-AGGGATAGTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ACAATCGA-GGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * * * *
710902 CAATTTTTCACAATCGAGGATACTCTAACCTCG---TTATTTCATCAGGGATACTC
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTATTTC--CA--AAAACAC
*** * ** * * *
710955 CAACCACATT-AC-CTCCGAAGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATAT
1 CAA--TTTTTCACAAT-CG-A-GGATACTCCAACCCCGATTTTATTTCCAAAAACAC
** * * * *
711009 TGATTTCTCATAATCGGGGATACTCCAACCCC-AGTTTTATTT-CTAAAACAC
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGA-TTTTATTTCCAAAAACAC
* * * *
711060 TAATTTTTCACAATCGGGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACAC
1 CAATTTTTCACAATC--GAGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* ** * * *
711113 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAT
1 CAATTTTTC-ACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
711166 CAATTTTTCACAATCGAGGATACT
1 CAATTTTTCACAATCGAGGATACT
711190 GCAATCTCGT
Statistics
Matches: 255, Mismatches: 60, Indels: 51
0.70 0.16 0.14
Matches are distributed among these distances:
49 7 0.03
51 47 0.18
52 84 0.33
53 80 0.31
54 13 0.05
55 3 0.01
56 15 0.06
58 3 0.01
59 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (52 bp):
CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
Found at i:711032 original size:51 final size:52
Alignment explanation
Indices: 710974--711189 Score: 183
Period size: 51 Copynumber: 4.2 Consensus size: 52
710964 TACCTCCGAA
* * * * *
710974 GGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATC-G
1 GGGATACTCCAACCCCGGTTTTATTCCCAAAACACTAATTTCTCACAATCGG
* * * *
711025 GGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTTCACAATCGGG
1 GGGATACTCCAACCCCGGTTTTATTCCCAAAACACTAATTTCTCACAATC-GG
** *
711078 GGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-TC-CTTTAATC-G
1 GGGATACTCCAACCCCGGTTTTATTCCCAAAACACTAATTTCTCAC---AATCGG
* * * *
711130 GGGATACTCCAACTCCGATTTTATTTCCAAAA-ACATCAATTTTTCACAATC-G
1 GGGATACTCCAACCCCGGTTTTATTCCCAAAACAC-T-AATTTCTCACAATCGG
*
711182 AGGATACT
1 GGGATACT
711190 GCAATCTCGT
Statistics
Matches: 138, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
51 44 0.32
52 44 0.32
53 43 0.31
54 6 0.04
55 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (52 bp):
GGGATACTCCAACCCCGGTTTTATTCCCAAAACACTAATTTCTCACAATCGG
Found at i:711091 original size:53 final size:51
Alignment explanation
Indices: 710974--711189 Score: 227
Period size: 53 Copynumber: 4.2 Consensus size: 51
710964 TACCTCCGAA
* * * * * * *
710974 GGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCG
* *
711025 GGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTTCACAATCGGG
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATC--G
* * * **
711078 GGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTC-ACAATCG
* *
711130 GGGATACTCCAACTCCGATTTTATTTCCAAAA-ACATCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACAC-T-AATTTTTCACAATCG
*
711182 AGGATACT
1 GGGATACT
711190 GCAATCTCGT
Statistics
Matches: 136, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
51 43 0.32
52 42 0.31
53 47 0.35
54 4 0.03
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCG
Found at i:711285 original size:264 final size:264
Alignment explanation
Indices: 710815--711304 Score: 820
Period size: 264 Copynumber: 1.9 Consensus size: 264
710805 TCATAATTGA
* *
710815 GGATACTCCAACCCCGATTTTGTTTTCAAAACACCAATTTTCCTTTAATCAGGGATAGTCCAACT
1 GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAACT
710880 CCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCTAACCTCGTTATTTCATC
66 CCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCTAACCTCGTTATTTCATC
* * *
710945 AGGGATACTCCAACCACATTACCTCCGAAGGGATACTCCAACCCCGGCTTTATTCCCAAAATATT
131 AGGGATACGCCAACCACATTACCTCCGAAGGGAAACTCCAACCCCAGCTTTATTCCCAAAATATT
711010 GATTTCTCATAATCGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTTCACAATC
196 GATTTCTCATAATCGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTTCACAATC
711075 GGGG
261 GGGG
* *
711079 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACT
1 GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAACT
* *
711144 CCGATTTTATTTCCAAAAACATCAATTTTTCACAATCGAGGATACTGC-AATCTCGTTATTTCAT
66 CCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACT-CTAACCTCGTTATTTCAT
* * * * * *
711208 CGGGGATACGCCAACCCCGTTACCTCCGAGGGGAAACTCCTACCCCAGCTTTATTTCCAAAATAT
130 CAGGGATACGCCAACCACATTACCTCCGAAGGGAAACTCCAACCCCAGCTTTATTCCCAAAATAT
*
711273 TGATTTCTCATAATTGGGGATACTCCAACCCC
195 TGATTTCTCATAATCGGGGATACTCCAACCCC
711305 GTTATTTCCG
Statistics
Matches: 209, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
264 208 1.00
265 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (264 bp):
GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCAACT
CCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCTAACCTCGTTATTTCATC
AGGGATACGCCAACCACATTACCTCCGAAGGGAAACTCCAACCCCAGCTTTATTCCCAAAATATT
GATTTCTCATAATCGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTTCACAATC
GGGG
Found at i:711340 original size:79 final size:78
Alignment explanation
Indices: 711208--711442 Score: 231
Period size: 79 Copynumber: 3.0 Consensus size: 78
711198 GTTATTTCAT
* ** * * * *
711208 CGGGGATACGCCAACCCCGTTACCTCCGAGGGGAAACTCCTACCCCAGCTTTATTTCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCGA-TTTTATTTCCAAAATAT
*
711273 TGATTTCTCATAAT
65 TGATTTCTCATAAC
* * *
711287 TGGGGATACTCCAACCCCGTTATTTCCGAGGGGATATTCCAATCCCGATTTTATTTCC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCGATTTTATTTCCAAAAT-A
* * *
711351 TCGATTTGTCAGAAC
64 TTGATTTCTCATAAC
* * * *
711366 CAGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCG-TTATTATCTCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCGATT-TTATTTCCAAAATA
*
711430 TTAAATTTCTCAT
64 TT-GATTTCTCAT
711443 CGGGAAATAT
Statistics
Matches: 125, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
78 5 0.04
79 106 0.85
80 14 0.11
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCGATTTTATTTCCAAAATATT
GATTTCTCATAAC
Found at i:723726 original size:1 final size:1
Alignment explanation
Indices: 723720--723800 Score: 72
Period size: 1 Copynumber: 81.0 Consensus size: 1
723710 CCTTCTTTTC
* ** * * * * *
723720 AAAAAAAAAAACAAAAGCAAAAAAAAAACAACAAAAAAACAAAAAAAAAAACAAAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
723785 ACAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAA
723801 GAAGAATCTG
Statistics
Matches: 61, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:723741 original size:11 final size:11
Alignment explanation
Indices: 723720--723800 Score: 101
Period size: 11 Copynumber: 7.4 Consensus size: 11
723710 CCTTCTTTTC
723720 AAAAAAA-AAA
1 AAAAAAACAAA
* *
723730 ACAAAAGCAAA
1 AAAAAAACAAA
*
723741 AAAAAAACAAC
1 AAAAAAACAAA
723752 AAAAAAACAAAA
1 AAAAAAAC-AAA
723764 AAAAAAACAAA
1 AAAAAAACAAA
723775 AAAAAAACAAA
1 AAAAAAACAAA
* *
723786 CAAAAAAGAAA
1 AAAAAAACAAA
723797 AAAA
1 AAAA
723801 GAAGAATCTG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
10 5 0.08
11 45 0.75
12 10 0.17
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:723758 original size:23 final size:21
Alignment explanation
Indices: 723720--723800 Score: 92
Period size: 23 Copynumber: 3.8 Consensus size: 21
723710 CCTTCTTTTC
* *
723720 AAAAAAAA-AAACAAAAGCAA
1 AAAAAAAACAAAAAAAAACAA
723740 AAAAAAAACAACAAAAAAACAAA
1 AAAAAAAACAA-AAAAAAAC-AA
723763 AAAAAAAACAAAAAAAAAACAA
1 AAAAAAAAC-AAAAAAAAACAA
* *
723785 ACAAAAAAGAAAAAAA
1 AAAAAAAACAAAAAAA
723801 GAAGAATCTG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
20 8 0.15
21 9 0.17
22 15 0.28
23 19 0.36
24 2 0.04
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAAAAAAACAA
Found at i:723764 original size:34 final size:34
Alignment explanation
Indices: 723720--723800 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 34
723710 CCTTCTTTTC
* *
723720 AAAAAAAAAAACAAAAGCAAAAAAAAAAC-AACA
1 AAAAAAAAAAAAAAAAACAAAAAAAAAACAAACA
723753 AAAAAACAAAAAAAAAAACAAAAAAAAAACAAACA
1 AAAAAA-AAAAAAAAAAACAAAAAAAAAACAAACA
*
723788 AAAAAGAAAAAAA
1 AAAAAAAAAAAAA
723801 GAAGAATCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 6 0.14
34 28 0.65
35 9 0.21
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAAAAAAAAACAAAAAAAAAACAAACA
Found at i:723806 original size:11 final size:10
Alignment explanation
Indices: 723722--723800 Score: 81
Period size: 10 Copynumber: 7.7 Consensus size: 10
723712 TTCTTTTCAA
723722 AAAAAAAAAC
1 AAAAAAAAAC
*
723732 AAAAGCAAAA-
1 AAAA-AAAAAC
*
723742 AAAAAACAAC
1 AAAAAAAAAC
723752 AAAAAAACAA-
1 AAAAAAA-AAC
723762 AAAAAAAAAC
1 AAAAAAAAAC
723772 AAAAAAAAAAC
1 -AAAAAAAAAC
*
723783 AAACAAAAAAG
1 AAA-AAAAAAC
723794 AAAAAAA
1 AAAAAAA
723801 GAAGAATCTG
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.09
10 28 0.48
11 25 0.43
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:724972 original size:19 final size:19
Alignment explanation
Indices: 724950--724987 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
724940 TTGGCAGTAG
*
724950 CCAAATTTGTATCGATACA
1 CCAAATATGTATCGATACA
*
724969 CCAAGTATGTATCGATACA
1 CCAAATATGTATCGATACA
724988 ATGTATCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (19 bp):
CCAAATATGTATCGATACA
Found at i:724993 original size:13 final size:13
Alignment explanation
Indices: 724975--725000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
724965 TACACCAAGT
724975 ATGTATCGATACA
1 ATGTATCGATACA
724988 ATGTATCGATACA
1 ATGTATCGATACA
725001 CCAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:725019 original size:34 final size:32
Alignment explanation
Indices: 724957--725021 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
724947 TAGCCAAATT
**
724957 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
724989 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
725022 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:727256 original size:22 final size:21
Alignment explanation
Indices: 727231--727282 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
727221 TTGCAAGTTG
727231 AAATAAAAAATTTAGCTAATG-A
1 AAATAAAAAA-TTAGCTAA-GAA
**
727253 AAATAATGAATTAGCTAAGAA
1 AAATAAAAAATTAGCTAAGAA
727274 AAATAAAAA
1 AAATAAAAA
727283 CTTGCATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23
Consensus pattern (21 bp):
AAATAAAAAATTAGCTAAGAA
Found at i:731173 original size:13 final size:13
Alignment explanation
Indices: 731155--731192 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
731145 CATCTTTCAT
731155 TGTATCGATACAC
1 TGTATCGATACAC
731168 TGTATCGATACAC
1 TGTATCGATACAC
*
731181 TGTATTGATACA
1 TGTATCGATACA
731193 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:732884 original size:19 final size:19
Alignment explanation
Indices: 732860--732896 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
732850 TTTTTTTTTC
732860 AAGAATACAAAAAAAGAGA
1 AAGAATACAAAAAAAGAGA
*
732879 AAGAATACAAAAAGAGAG
1 AAGAATACAAAAAAAGAG
732897 GAAAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.70, C:0.05, G:0.19, T:0.05
Consensus pattern (19 bp):
AAGAATACAAAAAAAGAGA
Found at i:732892 original size:17 final size:18
Alignment explanation
Indices: 732860--732895 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
732850 TTTTTTTTTC
732860 AAGAATACAAAAAAAGAGA
1 AAGAATAC-AAAAAAGAGA
732879 AAGAATAC-AAAAAGAGA
1 AAGAATACAAAAAAGAGA
732896 GGAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.72, C:0.06, G:0.17, T:0.06
Consensus pattern (18 bp):
AAGAATACAAAAAAGAGA
Found at i:733673 original size:12 final size:11
Alignment explanation
Indices: 733656--733726 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
733646 AAGAAAAGAG
733656 AGGAGGGATGAT
1 AGGAGGGA-GAT
*
733668 AGGAGGAGAGAC
1 AGGAGG-GAGAT
733680 AGGA--GAGAT
1 AGGAGGGAGAT
*
733689 AGTA--GAGAT
1 AGGAGGGAGAT
733698 AGGAGGGATGAT
1 AGGAGGGA-GAT
*
733710 AGGAGGAGAGAC
1 AGGAGG-GAGAT
733722 AGGAG
1 AGGAG
733727 AGATAATAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
9 15 0.31
11 2 0.04
12 28 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.48, T:0.10
Consensus pattern (11 bp):
AGGAGGGAGAT
Found at i:733702 original size:42 final size:42
Alignment explanation
Indices: 733652--733759 Score: 180
Period size: 42 Copynumber: 2.6 Consensus size: 42
733642 GAGAAAGAAA
*
733652 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAG
1 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
*
733694 AGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
1 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
* *
733736 AGAGAGGAAGGATGACAGGAGGAG
1 AGAGAGGAGGGATGATAGGAGGAG
733760 GAGAGAAGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.42, C:0.03, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
Found at i:740420 original size:13 final size:13
Alignment explanation
Indices: 740402--740427 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
740392 TACACCAAGT
740402 ATGTATCGATACA
1 ATGTATCGATACA
740415 ATGTATCGATACA
1 ATGTATCGATACA
740428 CCAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:740446 original size:34 final size:32
Alignment explanation
Indices: 740384--740448 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
740374 TAGCCAAACT
**
740384 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
740416 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
740449 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:741183 original size:60 final size:60
Alignment explanation
Indices: 740955--741569 Score: 664
Period size: 55 Copynumber: 10.7 Consensus size: 60
740945 GAGTTGGTGG
* * * *
740955 CACATAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGTAGGACG-----TCTTTTAAATCC
1 CACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
* * * *
741010 CACACAAGTTGGTGGCAC-CTTCAATCCTCAAAGAGTAGGACGCCTTTTCTTTTAAAGCC
1 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
* * *
741069 CACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCC
1 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC-TTTCAAAGCC
* *
741129 CACACAAGTTGGTGGCATTTTTCAGTCCTCAAAAAGCAGGACGCCTTTTCTTTCAAAGCC
1 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
* * *
741189 CACACAAGTTGGTGGCAGTTTTTAGTCCTCAAAGAGTAGGACG-C----CTTTCAAAGCC
1 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
* * * *
741244 CACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTCAAAGCC
1 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
* * *
741304 CACACAAGTTGGTGGGACCTTTT-AGTCCTCAAAGAGTAGGACG-C----CGTTCAAAG-C
1 CACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
* **
741358 CACACAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGCAGGATGATTTTTCTTTTCAAAGCC
1 CACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC-TTTCAAAGCC
* * *
741419 CACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACC--TTC---CAAAGCC
1 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
* *
741474 CACACAAGTTGATGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACC---TC-TT-AAAGCC
1 CACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
*
741529 CACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 CACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
741570 TGCACCTTAT
Statistics
Matches: 489, Mismatches: 45, Indels: 52
0.83 0.08 0.09
Matches are distributed among these distances:
53 2 0.00
54 66 0.13
55 158 0.32
56 5 0.01
59 62 0.13
60 130 0.27
61 66 0.13
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (60 bp):
CACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
Found at i:741276 original size:115 final size:115
Alignment explanation
Indices: 740955--741569 Score: 789
Period size: 115 Copynumber: 5.4 Consensus size: 115
740945 GAGTTGGTGG
* * * * *
740955 CACATAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGTCTTTTAAATCCCACACAAGTT
1 CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTT
* * *
741020 GGTGGCACC-TTCAATCCTCAAAGAGTAGGACGCCTTTTCTTTTAAAGCC
66 GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
* *
741069 CACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACA
1 CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGC-----C-TTTCAAAGCCCACA
** *
741133 CAAGTTGGTGGCATTTTTCAGTCCTCAAAAAGCAGGACGCCTTTTCTTTCAAAGCC
60 CAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
** *
741189 CACACAAGTTGGTGGCAGTTTTTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTT
1 CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTT
* * *
741254 GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTCTCCTTCAAAGCC
66 GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
* * *
741304 CACACAAGTTGGTGGGACCTTTTAGTCCTCAAAGAGTAGGACGCCGTTCAAAG-CCACACAAGTT
1 CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTT
* * **
741368 GGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGATTTTTCTTTTCAAAGCC
66 GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC-TTTCAAAGCC
* * * *
741419 CACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTCCAAAGCCCACACAAGTT
1 CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTT
* * *
741484 GATGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACC---TC-TT-AAAGCC
66 GGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
*
741529 CACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGA
741570 TGCACCTTAT
Statistics
Matches: 438, Mismatches: 52, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
110 44 0.10
111 2 0.00
113 22 0.05
114 63 0.14
115 171 0.39
116 36 0.08
118 1 0.00
119 25 0.06
120 53 0.12
121 21 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (115 bp):
CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTT
GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCC
Found at i:742213 original size:21 final size:21
Alignment explanation
Indices: 742187--742226 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
742177 TGACTTTTTG
742187 TTATGCATGAAAATGGTTTCC
1 TTATGCATGAAAATGGTTTCC
742208 TTATGCATGAAAATGGTTT
1 TTATGCATGAAAATGGTTT
742227 TTTAGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (21 bp):
TTATGCATGAAAATGGTTTCC
Found at i:742446 original size:14 final size:14
Alignment explanation
Indices: 742427--742453 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
742417 AGAAAATGTA
742427 TCGATACATAAGTG
1 TCGATACATAAGTG
742441 TCGATACATAAGT
1 TCGATACATAAGT
742454 TTTGTATCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
TCGATACATAAGTG
Found at i:742518 original size:21 final size:21
Alignment explanation
Indices: 742492--742533 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
742482 AGCTACTGCC
742492 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
742513 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
742534 GATCTTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:744918 original size:52 final size:51
Alignment explanation
Indices: 744792--744926 Score: 180
Period size: 52 Copynumber: 2.6 Consensus size: 51
744782 AAAGTTAAGC
*
744792 CCAATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACA
1 CCAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACA
** * * *
744843 CCAATTTTCCTTTAGTCGGGGATACTCCAACTCTGATTTTATTTTCAAAAACA
1 CCAATTTTCC-ACAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACA
* *
744896 CCAATTTTTCACAATCGAGGATACTCCAACC
1 CCAATTTTCCACAATCGGGGATACTCCAACC
744927 TCATTATTTC
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
51 10 0.14
52 45 0.64
53 15 0.21
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
CCAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACA
Found at i:745071 original size:79 final size:79
Alignment explanation
Indices: 744939--745120 Score: 206
Period size: 79 Copynumber: 2.3 Consensus size: 79
744929 ATTATTTCAT
* ** *
744939 CAGGGATACTCCAACCCCTTTACCTCCGAGGGGATACTCCTACCCCAGCTTTATTTCCAAAAT-A
1 CAGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTTCC-AAATCA
* * *
745003 TTGATTTCTCATAAT
65 TCGATTTCTCACAAC
* * * * *
745018 TAGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCCC-GATTTTATTTCCTAATCA
1 CAGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAG-CTTTATTTCCAAATCA
*
745082 TCGATTTGTCACAAC
65 TCGATTTCTCACAAC
*
745097 CGGGGATACTCCAACCCCGTTATT
1 CAGGGATACTCCAACCCCGTTATT
745121 ATCTCCAAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 4 0.05
79 82 0.95
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (79 bp):
CAGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAATCAT
CGATTTCTCACAAC
Found at i:756546 original size:79 final size:77
Alignment explanation
Indices: 756463--756710 Score: 282
Period size: 79 Copynumber: 3.1 Consensus size: 77
756453 AAAAACGGGA
*
756463 TTGGAGTGTCTCCTCAAAAATAACGGGGTTGGAGTATCCCCA-TAGGTGGAAAATCGATGTTTTG
1 TTGGAGTATC-CCTCAAAAATAACGGGGTTGGAGTATCCCCATTA--TGGAAAATCGATGTTTTG
*
756527 GAAATAAAATTGAGG
63 GAAATAAAATCGAGG
* * * * *
756542 TTGGAGTATCCCTTCGAAAATAACGGGGTTAGAGTATTCCCGATTATGGAAAATCAATGTTTTAG
1 TTGGAGTATCCC-TCAAAAATAACGGGGTTGGAGTA-TCCCCATTATGGAAAATCGATGTTTTGG
* *
756607 AAATAAAGTCGGGG
64 AAATAAAATCGAGG
* * * *
756621 TTGGAGTATCCCCTGAAAAATAATGAGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGG
1 TTGGAGTAT-CCCTCAAAAATAACGGGGTTGGAGTATCCCC-ATTATGGAAAATCGATGTTTTGG
* *
756686 AAATAAAACCGGGG
64 AAATAAAATCGAGG
*
756700 TTAGAGTATCC
1 TTGGAGTATCC
756711 TCGATTGTGA
Statistics
Matches: 143, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
78 8 0.06
79 125 0.87
80 8 0.06
81 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (77 bp):
TTGGAGTATCCCTCAAAAATAACGGGGTTGGAGTATCCCCATTATGGAAAATCGATGTTTTGGAA
ATAAAATCGAGG
Found at i:756722 original size:51 final size:51
Alignment explanation
Indices: 756647--756762 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
756637 AAAATAATGA
*
756647 GGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAACCGG
1 GGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGAAAATAAAACCGG
* * * * * * *
756698 GGTTAGAGTATCCTCGATTGTGAAAATTTGATGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGAAAATAAAACCGG
756749 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
756763 TTCAAAAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGAAAATAAAACCGG
Found at i:756779 original size:79 final size:78
Alignment explanation
Indices: 756696--756931 Score: 330
Period size: 79 Copynumber: 3.0 Consensus size: 78
756686 AAATAAAACC
*
756696 GGGGTTAGAGTATCCTCGATTGTGAAAATTTGATGTTTTGAAAATAAAATCGGGGTTGGAGTATC
1 GGGGTTAGAGTATCCTCGATTGTGAAAA-TTGATGTTTTAAAAATAAAATCGGGGTTGGAGTATC
756761 CCTTCAAAAATAAT
65 CCTTCAAAAATAAT
* * * * *
756775 GGGGTTAGAATATCCCCGATTGTAGAAAATTGATATTTTAAAAATAAAATCGAGGTTGAAGTATT
1 GGGGTTAGAGTATCCTCGATTGT-GAAAATTGATGTTTTAAAAATAAAATCGGGGTTGGAGTA-T
756840 CCC-TCAAAAATAAT
64 CCCTTCAAAAATAAT
** * *
756854 GGGGTTAGAGTATCCTCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCTGGGTTGGAGTGTC
1 GGGGTTAGAGTATCCTCGATTGTG-AAAATTGATGTTTTAAAAATAAAATCGGGGTTGGAGTATC
*
756919 CCTTCATAAATAA
65 CCTTCAAAAATAA
756932 CAAGGTTGGA
Statistics
Matches: 137, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
78 5 0.04
79 123 0.90
80 9 0.07
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (78 bp):
GGGGTTAGAGTATCCTCGATTGTGAAAATTGATGTTTTAAAAATAAAATCGGGGTTGGAGTATCC
CTTCAAAAATAAT
Found at i:756804 original size:130 final size:130
Alignment explanation
Indices: 756565--756842 Score: 323
Period size: 130 Copynumber: 2.1 Consensus size: 130
756555 TCGAAAATAA
*
756565 CGGGGTTAGAGTATTCCCGATTATGGAAAATCAATGTTTTAGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTAGAGTATTCCCGATTATGGAAAATCAATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
* * * * **
756630 CCCCTGAAAAATAATGAGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAAC
66 CCCCTCAAAAATAATGAGGTTAGAATATCCCCAATTATGAAAAATCGATATTTTAAAAATAAAAC
* **
756695 CGGGGTTAGAGTA-TCCTCGATTGT-GAAAATTTGATGTTTT-GAAAATAAAATCGGGGTTGGAG
1 CGGGGTTAGAGTATTCC-CGATTATGGAAAA-TCAATGTTTTAG-AAATAAAATCGGGGTTGGAG
* * * * *
756757 TATCCCTTCAAAAATAATGGGGTTAGAATATCCCCGATTGT-AGAAAATTGATATTTTAAAAATA
63 TATCCCCTCAAAAATAATGAGGTTAGAATATCCCCAATTATGA-AAAATCGATATTTTAAAAATA
*
756821 AAAT
127 AAAC
*
756825 CGAGGTT-GAAGTATTCCC
1 CGGGGTTAG-AGTATTCCC
756843 TCAAAAATAA
Statistics
Matches: 125, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
129 11 0.09
130 111 0.89
131 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (130 bp):
CGGGGTTAGAGTATTCCCGATTATGGAAAATCAATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
CCCCTCAAAAATAATGAGGTTAGAATATCCCCAATTATGAAAAATCGATATTTTAAAAATAAAAC
Found at i:756851 original size:209 final size:209
Alignment explanation
Indices: 756518--756902 Score: 536
Period size: 209 Copynumber: 1.8 Consensus size: 209
756508 GTGGAAAATC
* * * * *
756518 GATGTTTTGGAAATAAAATTGAGGTTGGAGTATCCCTTCGAAAATAACGGGGTTAGAGTATTCCC
1 GATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCTTCAAAAATAACGGGGTTAGAATATCCCC
* * * * * * *
756583 GATTATGGAAAATCAATGTTTTAGAAATAAAGTCGGGGTTGGAGTATCCCCTGAAAAATAATGAG
66 GATTATAGAAAATCAATATTTTAAAAATAAAATCGAGGTTGAAGTATCCCCTCAAAAATAATGAG
* * **
756648 GTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAACCGGGGTTAGAGTATCCTC
131 GTTAGAGTATCCCCAATTATGAAAAATCAATGTTTTAAAAATAAAACCGGGGTTAGAGTATCCTC
756713 GATTGTGAAAATTT
196 GATTGTGAAAATTT
* *
756727 GATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCTTCAAAAATAATGGGGTTAGAATATCCCC
1 GATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCTTCAAAAATAACGGGGTTAGAATATCCCC
* ** * *
756792 GATTGTAGAAAATTGATATTTTAAAAATAAAATCGAGGTTGAAGTATTCCCTCAAAAATAATGGG
66 GATTATAGAAAATCAATATTTTAAAAATAAAATCGAGGTTGAAGTATCCCCTCAAAAATAATGAG
* * *
756857 GTTAGAGTATCCTCGATTGTGAAAAATCAATGTTTTAAAAATAAAA
131 GTTAGAGTATCCCCAATTATGAAAAATCAATGTTTTAAAAATAAAA
756903 TCTGGGTTGG
Statistics
Matches: 150, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
209 150 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (209 bp):
GATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCTTCAAAAATAACGGGGTTAGAATATCCCC
GATTATAGAAAATCAATATTTTAAAAATAAAATCGAGGTTGAAGTATCCCCTCAAAAATAATGAG
GTTAGAGTATCCCCAATTATGAAAAATCAATGTTTTAAAAATAAAACCGGGGTTAGAGTATCCTC
GATTGTGAAAATTT
Found at i:756910 original size:158 final size:158
Alignment explanation
Indices: 756696--756981 Score: 410
Period size: 158 Copynumber: 1.8 Consensus size: 158
756686 AAATAAAACC
* ** *
756696 GGGGTTAGAGTATCCTCGATTGTGAAAATTTGATGTTTTGAAAATAAAATCGGGGTTGGAGTATC
1 GGGGTTAGAGTATCCTCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCGGGGTTGGAGTATC
*** * *
756761 CCTTCAAAAATAATGGGGTTAGAATATCCCCGATTGTAGAAAATTGATATTTTAAAAATAAAATC
66 CCTTCAAAAATAACAAGGTTAGAATATCCCCGATGGTAGAAAATCGATATTTTAAAAATAAAATC
756826 GAGGTTGAAGTATTCCCTCAAAAATAAT
131 GAGGTTGAAGTATTCCCTCAAAAATAAT
* *
756854 GGGGTTAGAGTATCCTCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCTGGGTTGGAGTGTC
1 GGGGTTAGAGTATCCTCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCGGGGTTGGAGTATC
* * * * * * *
756919 CCTTCATAAATAACAAGGTTGGAGTATCTCCGATGGTGGAAAATCGGTATTTTAGAAATAAAA
66 CCTTCAAAAATAACAAGGTTAGAATATCCCCGATGGTAGAAAATCGATATTTTAAAAATAAAA
756982 ACATGAATGA
Statistics
Matches: 110, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
158 110 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (158 bp):
GGGGTTAGAGTATCCTCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCGGGGTTGGAGTATC
CCTTCAAAAATAACAAGGTTAGAATATCCCCGATGGTAGAAAATCGATATTTTAAAAATAAAATC
GAGGTTGAAGTATTCCCTCAAAAATAAT
Found at i:756944 original size:79 final size:78
Alignment explanation
Indices: 756696--756981 Score: 317
Period size: 79 Copynumber: 3.6 Consensus size: 78
756686 AAATAAAACC
* * * *
756696 GGGGTTAGAGTATCCTCGATTGTGAAAATTTGATGTTTTGAAAATAAAATCGGGGTTGGAGTATC
1 GGGGTTAGAGTATCCTCGATTGTGAAAAATCGATATTTTAAAAATAAAATC-GGGTTGGAGTATC
756761 CCTTCAAAAATAAT
65 CCTTCAAAAATAAT
* * * *
756775 GGGGTTAGAATATCCCCGATTGT-AGAAAATTGATATTTTAAAAATAAAATCGAGGTTGAAGTAT
1 GGGGTTAGAGTATCCTCGATTGTGA-AAAATCGATATTTTAAAAATAAAATCG-GGTTGGAGTA-
756839 TCCC-TCAAAAATAAT
63 TCCCTTCAAAAATAAT
* * *
756854 GGGGTTAGAGTATCCTCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCTGGGTTGGAGTGTC
1 GGGGTTAGAGTATCCTCGATTGTGAAAAATCGATATTTTAAAAATAAAATC-GGGTTGGAGTATC
* *
756919 CCTTCATAAATAAC
65 CCTTCAAAAATAAT
** * * * * *
756933 AAGGTTGGAGTAT-CTCCGATGGTGGAAAATCGGTATTTTAGAAATAAAA
1 GGGGTTAGAGTATCCT-CGATTGTGAAAAATCGATATTTTAAAAATAAAA
756982 ACATGAATGA
Statistics
Matches: 176, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
78 8 0.05
79 162 0.92
80 6 0.03
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (78 bp):
GGGGTTAGAGTATCCTCGATTGTGAAAAATCGATATTTTAAAAATAAAATCGGGTTGGAGTATCC
CTTCAAAAATAAT
Found at i:756964 original size:288 final size:288
Alignment explanation
Indices: 756452--756981 Score: 681
Period size: 288 Copynumber: 1.8 Consensus size: 288
756442 ATTTTGGATG
* * * *
756452 TAAAAACGGGATTGGAGTGTCTCCTCAAAAATAACGGGGTTGGAGTATCCCCATAGGTGGAAAAT
1 TAAAAACGGGATTGGAGTATCTCCTCAAAAATAACGGGGTTAGAATATCCCCATAGGTAGAAAAT
* ** * * *
756517 CGATGTTTTGGAAATAAAATTGAGGTTGGAGTATCCCTTCGAAAATAACGGGGTTAGAGTATTCC
66 CGATATTTTAAAAATAAAATCGAGGTTGAAGTATCCCTTCAAAAATAACGGGGTTAGAGTATTCC
* * * * **
756582 CGATTATGGAAAATCAATGTTTTAGAAATAAAGTCGGGGTTGGAGTATCCCCTGAAAAATAATGA
131 CGATTATGAAAAATCAATGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAA
* * *
756647 GGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAACCGGGGTTAGAGTATCCT
196 GGTTGGAGTATCCCCAATGATGAAAAATCGATATTTTAGAAATAAAACCGGGGTTAGAGTATCCT
756712 CGATTGTGAAAATTTGATGTTTTGAAAA
261 CGATTGTGAAAATTTGATGTTTTGAAAA
* * * *
756740 TAAAATCGGGGTTGGAGTATC-CCTTCAAAAATAATGGGGTTAGAATATCCCCGAT-TGTAGAAA
1 TAAAAACGGGATTGGAGTATCTCC-TCAAAAATAACGGGGTTAGAATATCCCC-ATAGGTAGAAA
* *
756803 ATTGATATTTTAAAAATAAAATCGAGGTTGAAGTATTCCC-TCAAAAATAATGGGGTTAGAGTA-
64 ATCGATATTTTAAAAATAAAATCGAGGTTGAAGTA-TCCCTTCAAAAATAACGGGGTTAGAGTAT
* * * * *
756866 TCCTCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCTGGGTTGGAGTGTCCCTTCATAAATA
128 TCC-CGATTATGAAAAATCAATGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATA
* * * * *
756931 ACAAGGTTGGAGTATCTCCGATGGTGGAAAATCGGTATTTTAGAAATAAAA
192 ACAAGGTTGGAGTATCCCCAATGATGAAAAATCGATATTTTAGAAATAAAA
756982 ACATGAATGA
Statistics
Matches: 203, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
287 5 0.02
288 192 0.95
289 6 0.03
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (288 bp):
TAAAAACGGGATTGGAGTATCTCCTCAAAAATAACGGGGTTAGAATATCCCCATAGGTAGAAAAT
CGATATTTTAAAAATAAAATCGAGGTTGAAGTATCCCTTCAAAAATAACGGGGTTAGAGTATTCC
CGATTATGAAAAATCAATGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAA
GGTTGGAGTATCCCCAATGATGAAAAATCGATATTTTAGAAATAAAACCGGGGTTAGAGTATCCT
CGATTGTGAAAATTTGATGTTTTGAAAA
Found at i:759856 original size:74 final size:74
Alignment explanation
Indices: 759722--760555 Score: 602
Period size: 74 Copynumber: 11.4 Consensus size: 74
759712 GGAATAAGCA
* * ** * *
759722 TCCTACTCTTTGAGGACTG-AAAA-A-AAATGACGCAACCAGCTAGTGTGGGCTTTGAAGAAAAA
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
759784 GAAAAGATG
66 GAAAAGATG
* * * *
759793 TCCTGCTCTTTAAGGACTGAAAAAGATAGAGGGTGCCACCAACTTATGTGGGCTTTGAAG-AAAA
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
*
759857 -AAAACAT-
66 GAAAAGATG
* * * * *
759864 T-CTACACTTTTAGGACTGAAAAAGATAAAGGATGCCACCAGCTTGTGTGGGCTTTAAAGAAAAA
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
*
759928 GAAGAAG-TA
66 GAA-AAGATG
* * * * * * * *
759937 TCCTGCTCTTTGAGTATTGAAAAAGATAAAAGGTACCGCCAACTTGTGTAGGCTTT-AAAAAAAA
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
*
760001 GAAAAAGCATA
66 G-AAAAG-ATG
** * * ** * *
760012 T--TTTTCTTTGAGGACTAAAAAAGATAAAGAGCACCACCAGCTTGTGTAGGCTTTTAAGAAAAA
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
760075 GAAAA-AGTG
66 GAAAAGA-TG
* * *
760084 TCCTGCTCCTTGAGGACTGAAAAAGGTAAAGGGTGCCACCAGCTTGTGTGGCCTTTGAAGAAAAA
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAG--AAA
* * *
760149 AAAAAAAAAGG
64 AAGAAAAGATG
* *
760160 TCCTACTCTTTGAGGACTAAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
760225 GAAAA-A-G
66 GAAAAGATG
* * * ** * *
760232 -CATATGTTCATTGAGGACT-AAAAA-A-AAAGGGTGCCATTAGCTTATGTGTGCTTTTGAAGAA
1 TC--CTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGC-TTTGAAGAA
**
760293 AAAGAAAA-ACA
63 AAAGAAAAGATG
* * * * * ** * *
760304 TCCTACTTTTTAAGGACTGGAAAAGATAAAGGGTGTCACTTGCTTATGTAGGCTTTGAA-AAAAA
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
760368 TGAAAAAGTAT-
66 -G-AAAAG-ATG
* * * * * * **
760379 T-TTGCTCTTTGTGGACT-AAAATA-ATAAAAGGTGCCACTAGCTTATATAGGTTTTTGAAGAAA
1 TCCTGCTCTTTGAGGACTGAAAA-AGATAAAGGGTGCCACCAGCTTGTGT-GGGCTTTGAAGAAA
* ***
760441 AAGGAAAGGCA
64 AAGAAAAGATG
* * * ** * * * *
760452 TCTTGCTCTTTAAGGATTGAAAAAGATAAAATGTGCCACTAGCTTGTGTAGGCTTTAAAGTAAAA
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
*
760517 -AAAAGGTG
66 GAAAAGATG
* * *
760525 TCCTACTCTTTGAGGATTGAAAAAGGTAAAG
1 TCCTGCTCTTTGAGGACTGAAAAAGATAAAG
760556 TTTAGATAGT
Statistics
Matches: 606, Mismatches: 120, Indels: 72
0.76 0.15 0.09
Matches are distributed among these distances:
70 72 0.12
71 53 0.09
72 30 0.05
73 147 0.24
74 203 0.33
75 34 0.06
76 66 0.11
77 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (74 bp):
TCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA
GAAAAGATG
Found at i:760047 original size:144 final size:143
Alignment explanation
Indices: 759725--760555 Score: 542
Period size: 147 Copynumber: 5.7 Consensus size: 143
759715 ATAAGCATCC
* * * *
759725 TACTCTTTGAGGACT-GAAAA-A-AAATGACGCAACCAGCTAGTGTGGGCTTTGAAGAAAAAGAA
1 TACTCTTTGAGGACTAAAAAAGATAAAGGACGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAA
* * * *
759787 AAGATGTCCTGCTCTTTAAGGACTGAAAAAGATAGAGGGTGCCACCAACTTATGTGGGCTTT-GA
66 AAG-TGTCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAACTTGTGT-GGCTTTAAA
*
759851 AGAAAAAAAA-CATT
129 AAAAAAAAAAGCATT
* * * * *
759865 CTACACTTTTAGGACTGAAAAAGATAAAGGATGCCACCAGCTTGTGTGGGCTTTAAAGAAAAAGA
1 -TACTCTTTGAGGACTAAAAAAGATAAAGGACGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGA
* * * * * *
759930 AGAAGTATCCTGCTCTTTGAGTATTGAAAAAGATAAAAGGTACCGCCAACTTGTGTAGGCTTTAA
65 A-AAGTGTCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAACTTGTGT-GGCTTTAA
759995 AAAAAAGAAAAAGCATAT
128 AAAAAA-AAAAAGCAT-T
** * * *
760013 TTTTCTTTGAGGACTAAAAAAGATAAA-GAGCACCACCAGCTTGTGTAGGCTTTTAAGAAAAAGA
1 TACTCTTTGAGGACTAAAAAAGATAAAGGA-CGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAG-
* * *
760077 AAAAGTGTCCTGCTCCTTGAGGACTGAAAAAGGTAAAGGGTGCCACCAGCTTGTGTGGCCTTTGA
64 AAAAGTGTCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAACTTGTGTGG-CTTT-A
** *
760142 AGAAAAAAAAAAAAAAGGTCC
127 A-AAAAAAAAAAAGCA--T-T
**
760163 TACTCTTTGAGGACTAAAAAAGATAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAA
1 TACTCTTTGAGGACTAAAAAAGATAAAGGACGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAG-A
** * * * ** * *
760228 AAAGCAT-ATGTTCATTGAGGACT-AAAAA-A-AAAGGGTGCCATTAGCTTATGTGTGCTTTTGA
65 AAAGTGTCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAACTTGTGTG-GC-TTT-A
* *
760289 AGAAAAAGAAAAA-CATCC
127 A-AAAAAAAAAAAGCAT-T
* * ** ** * ** * *
760307 TACTTTTTAAGGACTGGAAAAGATAAAGGGTGTCACTTGCTTATGTAGGCTTTGAA-AAAAATGA
1 TACTCTTTGAGGACTAAAAAAGATAAAGGACGCCACCAGCTTGTGTGGGCTTTGAAGAAAAA-G-
* ** * * * * * * *
760371 AAAAGTATTTTGCTCTTTGTGGACT-AAAATA-ATAAAAGGTGCCACTAGCTTATATAGGTTTTT
64 AAAAGTGTCCTGCTCTTTGAGGACTGAAAA-AGATAAAGGGTGCCACCAACTTGTGT-GG-CTTT
** *
760434 GAAGAAAAAGGAAAGGCATCT
126 -AA-AAAAAAAAAAAGCAT-T
* * * * * * * * *
760455 TGCTCTTTAAGGATTGAAAAAGATAAAATG-TGCCACTAGCTTGTGTAGGCTTTAAAGTAAAAA-
1 TACTCTTTGAGGACTAAAAAAGAT-AAAGGACGCCACCAGCTTGTGTGGGCTTTGAAG-AAAAAG
* * * *
760518 AAAGGTGTCCTACTCTTTGAGGATTGAAAAAGGTAAAG
64 AAAAGTGTCCTGCTCTTTGAGGACTGAAAAAGATAAAG
760556 TTTAGATAGT
Statistics
Matches: 561, Mismatches: 99, Indels: 53
0.79 0.14 0.07
Matches are distributed among these distances:
141 13 0.02
142 4 0.01
143 6 0.01
144 143 0.25
145 24 0.04
146 33 0.06
147 176 0.31
148 71 0.13
149 23 0.04
150 67 0.12
151 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (143 bp):
TACTCTTTGAGGACTAAAAAAGATAAAGGACGCCACCAGCTTGTGTGGGCTTTGAAGAAAAAGAA
AAGTGTCCTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAACTTGTGTGGCTTTAAAAA
AAAAAAAAGCATT
Found at i:767630 original size:20 final size:20
Alignment explanation
Indices: 767605--767748 Score: 105
Period size: 20 Copynumber: 6.8 Consensus size: 20
767595 TTTTCACAAT
* *
767605 TTGTATTGATACATTGT-TTA
1 TTGTATCGATACATT-TCTCA
767625 TTGTATCGATACATTTCTCA
1 TTGTATCGATACATTTCTCA
*
767645 TTGTATCGATACATTCTGGGTTTACCCA
1 TTGTATCGATACA-------TTT-CTCA
*
767673 GATGTATCGATACATTT-TGCA
1 -TTGTATCGATACATTTCT-CA
*
767694 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTTCTCA
767714 TTGTATCGATACATTT-TGCA
1 TTGTATCGATACATTTCT-CA
*
767734 ATGTATCGATACATT
1 TTGTATCGATACATT
767749 CAAGCATTTT
Statistics
Matches: 102, Mismatches: 9, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.02
20 76 0.75
21 3 0.03
22 3 0.03
27 3 0.03
28 3 0.03
29 12 0.12
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTTCTCA
Found at i:770205 original size:17 final size:17
Alignment explanation
Indices: 770183--770215 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
770173 ATTTGCCTGT
770183 ATGTATCGATACATTTA
1 ATGTATCGATACATTTA
770200 ATGTATCGATACATTT
1 ATGTATCGATACATTT
770216 GGGTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (17 bp):
ATGTATCGATACATTTA
Done.