Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008876.1 Hibiscus syriacus cultivar Beakdansim tig00112114_pilon, whole genome shotgun sequence
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: 1683876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:793939 original size:19 final size:19
Alignment explanation
Indices: 793900--793976 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
793890 AAATCGCAAC
*
793900 GCGAATTTAGTTTCGCATT
1 GCGATTTTAGTTTCGCATT
*
793919 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCATT
793938 GCGATTTT-G--TCG--TT
1 GCGATTTTAGTTTCGCATT
793952 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCATT
*
793971 ACGATT
1 GCGATT
793977 CTCTCGTTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
18 1 0.02
19 32 0.65
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCATT
Found at i:793959 original size:33 final size:33
Alignment explanation
Indices: 793917--794008 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
793907 TAGTTTCGCA
* * *
793917 TTGCGATTTT-AGTTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
*
793950 TTGCGATTTTCATTTCGCATTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
793983 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
794009 AGTCATTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
33 52 0.98
34 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:794007 original size:19 final size:19
Alignment explanation
Indices: 793910--794008 Score: 76
Period size: 19 Copynumber: 5.7 Consensus size: 19
793900 GCGAATTTAG
793910 TTTCGCATTGCGATTTT-A
1 TTTCGCATTGCGATTTTCA
*
793928 GTTTCGCGTTGCGA-TTT--
1 -TTTCGCATTGCGATTTTCA
*
793945 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
793962 TTTCGCATTACGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
793978 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
793995 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
794009 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 11 0.17
15 3 0.05
16 11 0.17
17 11 0.17
18 3 0.05
19 24 0.38
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:794134 original size:14 final size:14
Alignment explanation
Indices: 794115--794151 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
794105 CATCAATTAA
794115 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
794129 ACAAATCATCTTTT
1 ACAAATCAACTTTT
794143 ACAAATCAA
1 ACAAATCAA
794152 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:795568 original size:21 final size:21
Alignment explanation
Indices: 795502--795568 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
795492 GTGAATCGGG
*
795502 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
795522 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
795544 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
795565 CTCT
1 CTCT
795569 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:802776 original size:21 final size:21
Alignment explanation
Indices: 802750--802789 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
802740 CCCCCTTTGA
*
802750 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
802771 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
802790 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:807070 original size:19 final size:19
Alignment explanation
Indices: 807015--807088 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 19
807005 TGAAATGAAA
*
807015 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
*
807035 ATCGCAATGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
* **
807055 ATCGTAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
807074 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
807089 TTAAAAAGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
19 21 0.46
20 23 0.50
21 2 0.04
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:807160 original size:33 final size:33
Alignment explanation
Indices: 807073--807165 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
807063 GCGAAATGAA
*
807073 AATCGCAACGCGAAATTTAAAA-AGCAACGAGAG
1 AATCGCAACGCGAAA-TTAAAATCGCAACGAGAG
* *
807106 AATCGCAACGCAAAATTAAAATCGCATCGAGAG
1 AATCGCAACGCGAAATTAAAATCGCAACGAGAG
*
807139 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATTAAAATCGCAA
807166 TGCGATTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 6 0.11
33 47 0.89
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATTAAAATCGCAACGAGAG
Found at i:807163 original size:19 final size:19
Alignment explanation
Indices: 807006--807170 Score: 91
Period size: 19 Copynumber: 9.1 Consensus size: 19
806996 TCTTTTGGTT
*
807006 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
807025 GAGAATGACTATCGCAATGC
1 GA-AATGAAAATCGCAACGC
** *
807045 GGAAATGACTATCGTAACGC
1 -GAAATGAAAATCGCAACGC
807065 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
807084 GAAATTTAAAA-AGCAA--C
1 GAAA-TGAAAATCGCAACGC
*
807101 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* * *
807117 AAAATTAAAATCGC-A-TC
1 GAAATGAAAATCGCAACGC
*
807134 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
807150 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
807169 GA
1 GA
807171 TTTTGGTTTC
Statistics
Matches: 108, Mismatches: 24, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
13 3 0.03
14 11 0.10
15 3 0.03
16 3 0.03
17 3 0.03
18 3 0.03
19 47 0.44
20 33 0.31
21 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:807201 original size:14 final size:14
Alignment explanation
Indices: 807182--807237 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
807172 TTTGGTTTCG
807182 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
807196 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
807215 CGTTGCGATTATCT
1 CGTTGCGATTATCT
807229 CGTTGCGAT
1 CGTTGCGAT
807238 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:807214 original size:33 final size:33
Alignment explanation
Indices: 807166--807258 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
807156 AAAATCGCAA
**
807166 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
807199 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
** *
807232 TGCGATAGTCATTTTCGTGTTGCGATT
1 TGCGATTTTCA-TTTCGCGTTGCGATT
807259 TTCATTTTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 40 0.74
34 14 0.26
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:807278 original size:20 final size:20
Alignment explanation
Indices: 807230--807280 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
807220 CGATTATCTC
** *
807230 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
807250 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
807270 GTTGCGATTTT
1 GTTGCGATTTT
807281 AAGTTTAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:807829 original size:20 final size:20
Alignment explanation
Indices: 807804--807996 Score: 201
Period size: 20 Copynumber: 9.6 Consensus size: 20
807794 CTTTAAAAAT
807804 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
807824 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
807844 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
807865 CGCATTACGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* * *
807885 CTCGTTGTGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
807905 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
807925 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
807945 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
807965 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
807986 CTCGTTGCGAT
1 CGCGTTGCGAT
807997 AGTCAGAATC
Statistics
Matches: 138, Mismatches: 29, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
20 105 0.76
21 33 0.24
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:807890 original size:40 final size:41
Alignment explanation
Indices: 807806--807996 Score: 305
Period size: 40 Copynumber: 4.7 Consensus size: 41
807796 TTAAAAATCG
*
807806 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
807847 CGTTGCGATTTACGGATACGCATTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
807887 CGTTGTGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
807927 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
807968 CGTTGCGATTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
807997 AGTCAGAATC
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
40 73 0.53
41 65 0.47
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:808028 original size:20 final size:20
Alignment explanation
Indices: 808005--808057 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
807995 ATAGTCAGAA
*
808005 TCGCGTTGCGA-TTTATATGT
1 TCGCGTTGCGATTTTA-ATAT
808025 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAT
*
808045 TCGTGTTGCGATT
1 TCGCGTTGCGATT
808058 ATGTAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAT
Found at i:808030 original size:121 final size:121
Alignment explanation
Indices: 807806--808038 Score: 337
Period size: 121 Copynumber: 1.9 Consensus size: 121
807796 TTAAAAATCG
807806 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
* * * *
807871 ACGATTTACGTATTCTCGTTGTGATTTACAGATACGCGTTGCGATTTACGTATTCT
66 ACGATTCACGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
* *
807927 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACTCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
* * *
807992 GCGATAGTCA-G-AATCGCGTTGCGATTTATATG-TTCGCGTTGCGATTT
66 ACGAT--TCACGTAATCGCGTTGCGATTTACA-GATACGCGTTGCGATTT
808039 TAATATTCGT
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
121 96 0.96
122 2 0.02
123 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (121 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
ACGATTCACGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
Found at i:808083 original size:21 final size:22
Alignment explanation
Indices: 808051--808097 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
808041 ATATTCGTGT
808051 TGCG-ATTATGTAAAATCGCAA
1 TGCGAATTATGTAAAATCGCAA
** *
808072 TGCGAATT-TGTACTATCGCAT
1 TGCGAATTATGTAAAATCGCAA
808093 TGCGA
1 TGCGA
808098 TTCTTCATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (22 bp):
TGCGAATTATGTAAAATCGCAA
Found at i:808826 original size:2 final size:2
Alignment explanation
Indices: 808819--808857 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
808809 TACTCTAATC
808819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
808858 TTTTTAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:810580 original size:24 final size:24
Alignment explanation
Indices: 810548--810603 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
810538 TAATCATTTT
*
810548 TCTTGTGACA-TATTTTTTCACTGA
1 TCTTGTGACACT-TATTTTCACTGA
*
810572 TCTTGTGACACTTATTTTCTCTGA
1 TCTTGTGACACTTATTTTCACTGA
810596 TCTTGTGA
1 TCTTGTGA
810604 TACGTTCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (24 bp):
TCTTGTGACACTTATTTTCACTGA
Found at i:812002 original size:3 final size:3
Alignment explanation
Indices: 811996--812033 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
811986 ATAATTTATT
811996 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
812034 TATTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:815799 original size:23 final size:22
Alignment explanation
Indices: 815773--815855 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 22
815763 ATTTTATATT
815773 AGAGTATGGAACTTATAAAATTA
1 AGAGTAT-GAACTTATAAAATTA
*
815796 AGAGGTA--AACTT-TAATATT-
1 AGA-GTATGAACTTATAAAATTA
* *
815815 AGAGAATCGAACCTATAAAATTA
1 AGAGTAT-GAACTTATAAAATTA
*
815838 AGAG-A-GAATTTATAAAAT
1 AGAGTATGAACTTATAAAAT
815856 ATTAAGGAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
18 2 0.04
19 3 0.06
20 17 0.35
21 9 0.19
22 7 0.15
23 7 0.15
24 3 0.06
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (22 bp):
AGAGTATGAACTTATAAAATTA
Found at i:815807 original size:21 final size:23
Alignment explanation
Indices: 815782--815842 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 23
815772 TAGAGTATGG
*
815782 AACTTATAAAATTAAGAG-GT-A
1 AACTTATAAAATTAAGAGAATCA
* *
815803 AACTT-TAATATT-AGAGAATCG
1 AACTTATAAAATTAAGAGAATCA
*
815824 AACCTATAAAATTAAGAGA
1 AACTTATAAAATTAAGAGA
815843 GAATTTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.13
20 7 0.23
21 9 0.29
22 6 0.19
23 5 0.16
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (23 bp):
AACTTATAAAATTAAGAGAATCA
Found at i:815814 original size:42 final size:42
Alignment explanation
Indices: 815758--815841 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
815748 AGGGATAGAA
* * * *
815758 GTAAAATTTTATATTAGAGTATGGAACTTATAAAATTAAGAG
1 GTAAAATTTAATATTAGAGAATCGAACCTATAAAATTAAGAG
*
815800 GTAAACTTTAATATTAGAGAATCGAACCTATAAAATTAAGAG
1 GTAAAATTTAATATTAGAGAATCGAACCTATAAAATTAAGAG
815842 AGAATTTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.32
Consensus pattern (42 bp):
GTAAAATTTAATATTAGAGAATCGAACCTATAAAATTAAGAG
Found at i:816715 original size:2 final size:2
Alignment explanation
Indices: 816710--816747 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
816700 ATATATATAT
816710 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
816748 GGGCACTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:817100 original size:17 final size:17
Alignment explanation
Indices: 817064--817097 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
817054 CCTTGAAAAG
817064 TTTAAATTTTTATATAA
1 TTTAAATTTTTATATAA
*
817081 TTTAAATATTTTTTATA
1 TTTAAAT-TTTTATATA
817098 TTTTTATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAATTTTTATATAA
Found at i:817596 original size:101 final size:103
Alignment explanation
Indices: 817408--817611 Score: 304
Period size: 101 Copynumber: 2.0 Consensus size: 103
817398 ATCATTCTAA
* * * *
817408 ATTAGTCTATAAACTTTTGAATATTTTTATTTTATCTCTATATTATTAGCATATGCTAATCATGT
1 ATTAGTCTATAAACTTTTGAACATTTTTATTTTACCTCTACATTATCAGCATATGCTAATCATGT
* * *
817473 TCTCTATTGATAAAATCGTT-AAAAATTTAATTATCAT
66 TCTCTATTAACAAAATCATTAAAAAATTTAATTATCAT
* *
817510 ATTA-TCTCTAAACTTTTGAACATTTTTATTTTACCTCTACATTATCAGTATATGCTAATCATGT
1 ATTAGTCTATAAACTTTTGAACATTTTTATTTTACCTCTACATTATCAGCATATGCTAATCATGT
*
817574 TCTCTATTAACAAAATCATTAAAAAATTTAATTGTCAT
66 TCTCTATTAACAAAATCATTAAAAAATTTAATTATCAT
817612 GTAAATACTT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 71 0.78
102 20 0.22
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (103 bp):
ATTAGTCTATAAACTTTTGAACATTTTTATTTTACCTCTACATTATCAGCATATGCTAATCATGT
TCTCTATTAACAAAATCATTAAAAAATTTAATTATCAT
Found at i:818857 original size:28 final size:28
Alignment explanation
Indices: 818821--818875 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
818811 ATTTCATACT
* *
818821 CAGAAATCAGATACAAAAATATAGTAAC
1 CAGAAATCAGATAAAAAAATACAGTAAC
* *
818849 CAGAGATCATATAAAAAAATACAGTAA
1 CAGAAATCAGATAAAAAAATACAGTAA
818876 ATCAAGTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (28 bp):
CAGAAATCAGATAAAAAAATACAGTAAC
Found at i:818887 original size:29 final size:30
Alignment explanation
Indices: 818854--818915 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
818844 GTAACCAGAG
*
818854 ATCATATAAA-AAAATACAGTAAATCAAGT
1 ATCATATAAACAAAATACAGAAAATCAAGT
* * *
818883 ATCATATAAACAATATTCAGAAAATCAGGT
1 ATCATATAAACAAAATACAGAAAATCAAGT
818913 ATC
1 ATC
818916 GTGTCATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (30 bp):
ATCATATAAACAAAATACAGAAAATCAAGT
Found at i:824188 original size:19 final size:19
Alignment explanation
Indices: 824164--824203 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
824154 TAACATATTC
824164 TATTTAAAATTTAAATTAA
1 TATTTAAAATTTAAATTAA
*
824183 TATTTAATATTTAAATTAA
1 TATTTAAAATTTAAATTAA
824202 TA
1 TA
824204 ATTAGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTAAAATTTAAATTAA
Found at i:828949 original size:16 final size:16
Alignment explanation
Indices: 828928--828960 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
828918 AGTTATATAC
828928 ATGATTTTGCCTTTAA
1 ATGATTTTGCCTTTAA
828944 ATGATTTTGCCTTTAA
1 ATGATTTTGCCTTTAA
828960 A
1 A
828961 GCATATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (16 bp):
ATGATTTTGCCTTTAA
Found at i:831342 original size:59 final size:59
Alignment explanation
Indices: 831254--831380 Score: 175
Period size: 59 Copynumber: 2.2 Consensus size: 59
831244 ACTCCGAAGT
* **
831254 TTTTGAATATTCTAATTTCATCACTAATTATGACTCTAATTTTAAATTAATCTTTAAAC
1 TTTTGAATATTATAATTTCATCACTAATTATGACTCTAATTTTAAATTAATCTCCAAAC
* * *
831313 TTTTGAATATTAT-ATTTCATCCCTAAATTATGACTCTATTTTTAAATTGATCTCCAAAC
1 TTTTGAATATTATAATTTCATCACT-AATTATGACTCTAATTTTAAATTAATCTCCAAAC
*
831372 TTTTTAATA
1 TTTTGAATA
831381 ATCCAATTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 10 0.17
59 50 0.83
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (59 bp):
TTTTGAATATTATAATTTCATCACTAATTATGACTCTAATTTTAAATTAATCTCCAAAC
Found at i:831400 original size:59 final size:59
Alignment explanation
Indices: 831253--831400 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 59
831243 GACTCCGAAG
* * **
831253 TTTTTGAATATTCTAATTTCATCACTAATTATGACTCTAATTTTAAATTAATCTTTAAAC
1 TTTTT-AATAATCTAATTTCATCACAAATTATGACTCTAATTTTAAATTAATCTCCAAAC
* * * *
831313 TTTTGAAT-AT-TATATTTCATCCCTAAATTATGACTCTATTTTTAAATTGATCTCCAAAC
1 TTTTTAATAATCTA-ATTTCATCAC-AAATTATGACTCTAATTTTAAATTAATCTCCAAAC
* *
831372 TTTTTAATAATCCAATTTCATCTCAAATT
1 TTTTTAATAATCTAATTTCATCACAAATT
831401 TTTCTAAATA
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
57 2 0.03
58 10 0.14
59 45 0.62
60 15 0.21
61 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (59 bp):
TTTTTAATAATCTAATTTCATCACAAATTATGACTCTAATTTTAAATTAATCTCCAAAC
Found at i:831609 original size:60 final size:60
Alignment explanation
Indices: 831516--831647 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
831506 CTATATACAT
* * * *
831516 ATAATTTTGGATGAAATTGGAATATTCAAAAAGTTTTA-GGACCAATTTAGAATG-ATAGTC
1 ATAATTTAGGATAAAATTGGAATATTCAAAAAG-TTTAGGGACCAATTTAAAAAGAATA-TC
* *
831576 ATAATTTAAGGATAAAATTGGAATATT-TAAAAGTTTAGGGTCCAATTTAAAAAGAATATC
1 ATAATTT-AGGATAAAATTGGAATATTCAAAAAGTTTAGGGACCAATTTAAAAAGAATATC
831636 ATAATTTGAGGA
1 ATAATTT-AGGA
831648 CATATGATGC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 4 0.06
60 38 0.61
61 20 0.32
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.34
Consensus pattern (60 bp):
ATAATTTAGGATAAAATTGGAATATTCAAAAAGTTTAGGGACCAATTTAAAAAGAATATC
Found at i:831752 original size:21 final size:21
Alignment explanation
Indices: 831716--831761 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
831706 TTATATAAAT
831716 AATAAAATAATAATTTTAGTAA
1 AATAAAATAATAATTTTA-TAA
*
831738 AATAAATTAAT-ATTTTATAA
1 AATAAAATAATAATTTTATAA
831758 AATA
1 AATA
831762 TTTTTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 10 0.43
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAAAATAATAATTTTATAA
Found at i:835285 original size:16 final size:19
Alignment explanation
Indices: 835264--835299 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
835254 AATTAATAAA
835264 TTTT-AATTT-ATA-TATT
1 TTTTAAATTTCATATTATT
835280 TTTTAAATTTCATATTATT
1 TTTTAAATTTCATATTATT
835299 T
1 T
835300 AAATACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 3 0.18
19 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTAAATTTCATATTATT
Found at i:850112 original size:62 final size:62
Alignment explanation
Indices: 850037--850164 Score: 193
Period size: 62 Copynumber: 2.1 Consensus size: 62
850027 ATCTATTCCC
* * *
850037 TCCATTCCAGAATGTGCATCTCAATGTTTATAGACATTTACGAGTGAGTTATGAATACCTTT
1 TCCATTCCAGAATGTGCATCTCAACGTTTATAGACATGTACGAATGAGTTATGAATACCTTT
* * * *
850099 TCCATTCCGGAATGTGCATCTCGACGTTTATCGACATGTATGAATGAGTTATGAATACCTTT
1 TCCATTCCAGAATGTGCATCTCAACGTTTATAGACATGTACGAATGAGTTATGAATACCTTT
850161 TCCA
1 TCCA
850165 AGTAGGTTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (62 bp):
TCCATTCCAGAATGTGCATCTCAACGTTTATAGACATGTACGAATGAGTTATGAATACCTTT
Found at i:853422 original size:37 final size:36
Alignment explanation
Indices: 853347--853422 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
853337 TTTTTATATT
*
853347 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
853383 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
853420 TTT
1 TTT
853423 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:853604 original size:20 final size:20
Alignment explanation
Indices: 853568--853605 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
853558 ATCCTATTCC
**
853568 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
853588 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
853606 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:855253 original size:18 final size:17
Alignment explanation
Indices: 855227--855260 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
855217 TATTCAATCA
855227 ATTAGATATGTTTTTATC
1 ATTAGATAT-TTTTTATC
*
855245 ATTATATATTTTTTAT
1 ATTAGATATTTTTTAT
855261 GCGTTAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (17 bp):
ATTAGATATTTTTTATC
Found at i:857068 original size:14 final size:12
Alignment explanation
Indices: 857035--857074 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
857025 GACCTTACCT
857035 TTTAAATTATTA
1 TTTAAATTATTA
*
857047 TTTAAATTCATTT
1 TTTAAATT-ATTA
857060 TTCTAAATTATTA
1 TT-TAAATTATTA
857073 TT
1 TT
857075 AAAAAATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 10 0.42
14 6 0.25
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAAATTATTA
Found at i:870938 original size:171 final size:173
Alignment explanation
Indices: 870653--870996 Score: 674
Period size: 171 Copynumber: 2.0 Consensus size: 173
870643 AATAAATTAA
870653 CCATGAATCTATGATTCCAGAGGCTGCCCTACAAGGAAAGCCAATAATAATGCAAAAGCAAGAGA
1 CCATGAATCTATGATTCCAGAGGCTGCCCTACAAGGAAAGCCAATAATAATGCAAAAGCAAGAGA
870718 AGTGCTGCAGGATCAACTTAGTTATGATAAAACCATGAATCATACTAGGAACCAGAAAGT-AACA
66 AGTGCTGCAGGATCAACTTAGTTATGATAAAACCATGAATCATACTAGGAACCAGAAAGTAAACA
870782 TGCTTCGACAATTTACAAC-ACATGAAAAAAGCCTTGTGAATT
131 TGCTTCGACAATTTACAACAACATGAAAAAAGCCTTGTGAATT
870824 CCATGAATCTATGATTCCAGAGGCTGCCCTACAAGGAAAGCCAATAATAATGCAAAAGCAAGAGA
1 CCATGAATCTATGATTCCAGAGGCTGCCCTACAAGGAAAGCCAATAATAATGCAAAAGCAAGAGA
870889 AGTGCTGCAGGATCAACTTAGTTATGATAAAACCATGAATCATACTAGGAACCAGAAAGTAAACA
66 AGTGCTGCAGGATCAACTTAGTTATGATAAAACCATGAATCATACTAGGAACCAGAAAGTAAACA
870954 TGCTTCGACAATTTACAACAACATGAAAAAAGCCTTGTGAATT
131 TGCTTCGACAATTTACAACAACATGAAAAAAGCCTTGTGAATT
870997 TGTTGATAGA
Statistics
Matches: 171, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
171 125 0.73
172 23 0.13
173 23 0.13
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (173 bp):
CCATGAATCTATGATTCCAGAGGCTGCCCTACAAGGAAAGCCAATAATAATGCAAAAGCAAGAGA
AGTGCTGCAGGATCAACTTAGTTATGATAAAACCATGAATCATACTAGGAACCAGAAAGTAAACA
TGCTTCGACAATTTACAACAACATGAAAAAAGCCTTGTGAATT
Found at i:873641 original size:19 final size:18
Alignment explanation
Indices: 873612--873656 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
873602 GGTCAATCAT
*
873612 ATTTT-TATAATTTTTAA
1 ATTTTATATAATTTATAA
*
873629 ATTTTCATATAATTTATAT
1 ATTTT-ATATAATTTATAA
873648 ATTTTATAT
1 ATTTTATAT
873657 TTTATCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 4 0.17
19 15 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTATATAATTTATAA
Found at i:878167 original size:19 final size:19
Alignment explanation
Indices: 878143--878186 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
878133 CACCTGAGTA
* *
878143 TAATTTTTTTTATTAATTT
1 TAATTTTTTTAATTAAATT
*
878162 TAATTTATTTAATTAAATT
1 TAATTTTTTTAATTAAATT
878181 T-ATTTT
1 TAATTTT
878187 CAATCCAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TAATTTTTTTAATTAAATT
Found at i:887466 original size:92 final size:92
Alignment explanation
Indices: 887294--887467 Score: 217
Period size: 92 Copynumber: 1.9 Consensus size: 92
887284 TGCTTCTAAC
* * *
887294 ATTCGACTAAGTAGTCATTTTGCCCCATATTCTTTTTTCTTTTTGGAGCATTTTAGCCCCGATAT
1 ATTCGACTAAATAGTCATTTAGCCCCATATTCTATTTTCTTTTTGGAGCATTTTAGCCCCGATAT
* **
887359 TTTATTTTAGGGCAAAAGACCCATAAT
66 TTCATTTTAAAGCAAAAGACCCATAAT
* ** *
887386 ATTCGACTAAATAGTCACTTTAG-CCCTTATTC-ATTTTCTTTTTGGAGCATTTTGATTCTCGAT
1 ATTCGACTAAATAGTCA-TTTAGCCCCATATTCTATTTTCTTTTTGGAGCATTTT-AGCCCCGAT
*
887449 GTTTCATTTTAAAGCAAAA
64 ATTTCATTTTAAAGCAAAA
887468 AAGACTCTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
91 20 0.29
92 45 0.65
93 4 0.06
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (92 bp):
ATTCGACTAAATAGTCATTTAGCCCCATATTCTATTTTCTTTTTGGAGCATTTTAGCCCCGATAT
TTCATTTTAAAGCAAAAGACCCATAAT
Found at i:889939 original size:14 final size:16
Alignment explanation
Indices: 889915--889946 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
889905 GAAGTATTTT
889915 TTAATTATAAAA-ACA
1 TTAATTATAAAATACA
889930 TTAA-TATAAAATACA
1 TTAATTATAAAATACA
889945 TT
1 TT
889947 TTATTATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAATTATAAAATACA
Found at i:893170 original size:32 final size:32
Alignment explanation
Indices: 893134--893229 Score: 156
Period size: 32 Copynumber: 3.0 Consensus size: 32
893124 TATCAAACTC
893134 TTTATAGCACAATATTCGAATATTCAACAACA
1 TTTATAGCACAATATTCGAATATTCAACAACA
* * *
893166 TTTATAGCTCAATGTTCCAATATTCAACAACA
1 TTTATAGCACAATATTCGAATATTCAACAACA
*
893198 TTTATAGCCCAATATTCGAATATTCAACAACA
1 TTTATAGCACAATATTCGAATATTCAACAACA
893230 GAGATGGACC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (32 bp):
TTTATAGCACAATATTCGAATATTCAACAACA
Found at i:894237 original size:12 final size:12
Alignment explanation
Indices: 894220--894244 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
894210 ACCGTTAAAG
894220 AAAAATATTATT
1 AAAAATATTATT
894232 AAAAATATTATT
1 AAAAATATTATT
894244 A
1 A
894245 TTTTTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATATTATT
Found at i:894338 original size:21 final size:21
Alignment explanation
Indices: 894314--894383 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
894304 TAAAAAATTA
*
894314 GTAGAGAAAATAATATTTTAG
1 GTAGAAAAAATAATATTTTAG
* * * * *
894335 GTAGTCTTAATATTAACATTTTCG
1 GTAG---AAAAAATAATATTTTAG
*
894359 GTACAAAAAATAATATTTTAG
1 GTAGAAAAAATAATATTTTAG
894380 GTAG
1 GTAG
894384 TATTTTACCA
Statistics
Matches: 33, Mismatches: 13, Indels: 6
0.63 0.25 0.12
Matches are distributed among these distances:
21 19 0.58
24 14 0.42
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (21 bp):
GTAGAAAAAATAATATTTTAG
Found at i:895257 original size:21 final size:21
Alignment explanation
Indices: 895233--895275 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
895223 GTTACTTTTC
895233 GATTTAAT-TGATTATATTATT
1 GATTTAATATGATTA-ATTATT
895254 GATTTAATAATGATTAATTATT
1 GATTTAAT-ATGATTAATTATT
895276 TTTTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
GATTTAATATGATTAATTATT
Found at i:895882 original size:4 final size:4
Alignment explanation
Indices: 895873--895930 Score: 75
Period size: 4 Copynumber: 14.8 Consensus size: 4
895863 AATGTTAGAC
**
895873 AATA AATA AATA AATA AATA AATA AATA AAT- GTTA AATA AATAA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT-A AATA
895921 AAT- AATA AAT
1 AATA AATA AAT
895931 GAAAAGGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 4 0.09
4 39 0.83
5 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:895912 original size:27 final size:27
Alignment explanation
Indices: 895879--895931 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
895869 AGACAATAAA
895879 TAAATAAAT-AAATAAATAAATAAATGT
1 TAAATAAATAAAATAAAT-AATAAATGT
895906 TAAATAAATAAAATAAATAATAAATG
1 TAAATAAATAAAATAAATAATAAATG
895932 AAAAGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (27 bp):
TAAATAAATAAAATAAATAATAAATGT
Found at i:895946 original size:31 final size:32
Alignment explanation
Indices: 895880--895953 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 32
895870 GACAATAAAT
* * *
895880 AAAT-AAATAAATAAATAAATAAATGTTAAAT
1 AAATAAAATAAATAAATAAATAAAAGTGAAAA
895911 AAATAAAATAAAT-AATAAATGAAAAG-GAAAA
1 AAATAAAATAAATAAATAAAT-AAAAGTGAAAA
895942 AAATAATAATAA
1 AAATAA-AATAA
895954 TTTAAAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 20 0.54
32 17 0.46
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (32 bp):
AAATAAAATAAATAAATAAATAAAAGTGAAAA
Found at i:896022 original size:15 final size:15
Alignment explanation
Indices: 895991--896023 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
895981 TTTTAAAAGC
895991 AATAGAATAAAGAAA
1 AATAGAATAAAGAAA
896006 AATATGAATAAAGAAA
1 AATA-GAATAAAGAAA
896022 AA
1 AA
896024 AAATAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (15 bp):
AATAGAATAAAGAAA
Found at i:896039 original size:16 final size:17
Alignment explanation
Indices: 895991--896060 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
895981 TTTTAAAAGC
895991 AATAGAATAAAG-AAAAA
1 AATA-AATAAAGAAAAAA
* *
896008 TATGAATAAAGAAAAAA
1 AATAAATAAAGAAAAAA
* *
896025 AATAATTAAAG-AAAAT
1 AATAAATAAAGAAAAAA
896041 AATAAAATAAAGTAAAAAA
1 AAT-AAATAAAG-AAAAAA
896060 A
1 A
896061 CTTAGAACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
16 14 0.34
17 22 0.54
19 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
AATAAATAAAGAAAAAA
Found at i:897878 original size:65 final size:66
Alignment explanation
Indices: 897751--897910 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 66
897741 AGGCCAATAT
* * * * *
897751 CCTTCGCTGTGAAGTTGAAATTG-AC--TCTGAAACTGGGAAGTTGTTTGTTGACAGCCAGCGGC
1 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAGTTGTTTGTTGACAACCAGCGGC
897813 C
66 C
*
897814 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGGAA-TT-TTTGTTGACAATCAGCGG
1 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACT-GGGAAGTTGTTTGTTGACAACCAGCGG
897877 CC
65 CC
*
897879 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
1 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTT
897911 GAGTCCAATA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 21 0.24
64 1 0.01
65 49 0.57
66 10 0.12
67 5 0.06
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (66 bp):
CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAGTTGTTTGTTGACAACCAGCGGC
C
Found at i:897981 original size:106 final size:107
Alignment explanation
Indices: 897814--898015 Score: 302
Period size: 106 Copynumber: 1.9 Consensus size: 107
897804 GCCAGCGGCC
* * * *
897814 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGGAATTTTTGTTGACAATCAGCGGCC
1 CCTTCGCTGTGAAGTTGAAATTGTGC-GTCTGAAACTGGGGAATTTTTGTTGACAACCAGCGGCC
897879 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATAT
65 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATAT
* *
897922 CCTTCGCTGTGAAGTTGAAATTG-GC-TCTGAAA-TTGGGAAGTTGTTTGTTGACAGCCAGCGGC
1 CCTTCGCTGTGAAGTTGAAATTGTGCGTCTGAAACTGGGGAA-TT-TTTGTTGACAACCAGCGGC
897984 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
898016 GATACTGGGA
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
104 6 0.07
105 8 0.09
106 49 0.57
107 2 0.02
108 21 0.24
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.37
Consensus pattern (107 bp):
CCTTCGCTGTGAAGTTGAAATTGTGCGTCTGAAACTGGGGAATTTTTGTTGACAACCAGCGGCCC
CTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATAT
Found at i:898032 original size:171 final size:171
Alignment explanation
Indices: 897744--898080 Score: 602
Period size: 171 Copynumber: 2.0 Consensus size: 171
897734 TGTTTCGAGG
897744 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAGCCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAGCCAG
* * * *
897809 CGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGGAATTTTTGTTGACAATCAG
66 CGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAACTGGGAAATTTTTGTTAACAACCAG
897874 CGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
131 CGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
* *
897915 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAGCCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAGCCAG
* *
897980 CGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAACCAG
66 CGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAACTGGGAAATTTTTGTTAACAACCAG
898045 CGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
131 CGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
898081 GATACTGGGA
Statistics
Matches: 158, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
171 158 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (171 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAGCCAG
CGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAACTGGGAAATTTTTGTTAACAACCAG
CGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
Found at i:898052 original size:65 final size:65
Alignment explanation
Indices: 897922--898138 Score: 283
Period size: 65 Copynumber: 3.5 Consensus size: 65
897912 AGTCCAATAT
* * * * * * * *
897922 CCTTCGCTGTGAAGTTGAAATTG-G--CTCTGAAATTGGGAAGTTGTTTGTTGACAGCCAGCGGC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATT-TTTGTTAACAACCAGCGGC
897984 C
65 C
897985 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAACCAGCGGCC
898050 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGG--A-----GTTAACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAACCAGCGGCC
898108 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
898139 TGAGTTCCAA
Statistics
Matches: 143, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
58 48 0.34
63 22 0.15
64 1 0.01
65 58 0.41
66 14 0.10
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (65 bp):
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAACCAGCGGCC
Found at i:899224 original size:19 final size:19
Alignment explanation
Indices: 899200--899246 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 19
899190 GGTTATTGTG
899200 TTTGATCAAAGGTTTGGCA
1 TTTGATCAAAGGTTTGGCA
899219 TTTGATGCTCAAAGGTTTGGCA
1 TTTGA---TCAAAGGTTTGGCA
899241 TTTGAT
1 TTTGAT
899247 GCTCAAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.24
22 19 0.76
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (19 bp):
TTTGATCAAAGGTTTGGCA
Found at i:899232 original size:22 final size:22
Alignment explanation
Indices: 899205--899259 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
899195 TTGTGTTTGA
899205 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
899227 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
899249 TCAAAGGTTTG
1 TCAAAGGTTTG
899260 ATGGGGTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:902980 original size:4 final size:4
Alignment explanation
Indices: 902971--903028 Score: 75
Period size: 4 Copynumber: 14.8 Consensus size: 4
902961 AATGTTAGAC
**
902971 AATA AATA AATA AATA AATA AATA AATA AAT- GTTA AATA AATAA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT-A AATA
903019 AAT- AATA AAT
1 AATA AATA AAT
903029 GAAAAGGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 4 0.09
4 39 0.83
5 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:903010 original size:27 final size:27
Alignment explanation
Indices: 902977--903029 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
902967 AGACAATAAA
902977 TAAATAAAT-AAATAAATAAATAAATGT
1 TAAATAAATAAAATAAAT-AATAAATGT
903004 TAAATAAATAAAATAAATAATAAATG
1 TAAATAAATAAAATAAATAATAAATG
903030 AAAAGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (27 bp):
TAAATAAATAAAATAAATAATAAATGT
Found at i:903043 original size:27 final size:27
Alignment explanation
Indices: 902986--903052 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
902976 ATAAATAAAT
* * *
902986 AAATAAATAAATAAATGTTAAATAAATA
1 AAATAAAT-AATAAATGTAAAAGAAAAA
903014 AAATAAATAATAAATG-AAAAGGAAAAA
1 AAATAAATAATAAATGTAAAA-GAAAAA
903041 AAAT-AATAATAA
1 AAATAAATAATAA
903053 TTTAAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.31
27 16 0.46
28 8 0.23
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (27 bp):
AAATAAATAATAAATGTAAAAGAAAAA
Found at i:903121 original size:15 final size:15
Alignment explanation
Indices: 903090--903122 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
903080 TTTTAAAAGC
903090 AATAGAATAAAGAAA
1 AATAGAATAAAGAAA
903105 AATATGAATAAAGAAA
1 AATA-GAATAAAGAAA
903121 AA
1 AA
903123 AAATAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (15 bp):
AATAGAATAAAGAAA
Found at i:903138 original size:16 final size:17
Alignment explanation
Indices: 903090--903159 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
903080 TTTTAAAAGC
903090 AATAGAATAAAG-AAAAA
1 AATA-AATAAAGAAAAAA
* *
903107 TATGAATAAAGAAAAAA
1 AATAAATAAAGAAAAAA
* *
903124 AATAATTAAAG-AAAAT
1 AATAAATAAAGAAAAAA
903140 AATAAAATAAAGTAAAAAA
1 AAT-AAATAAAG-AAAAAA
903159 A
1 A
903160 CTTAGAACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
16 14 0.34
17 22 0.54
19 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
AATAAATAAAGAAAAAA
Found at i:910714 original size:20 final size:19
Alignment explanation
Indices: 910691--910781 Score: 65
Period size: 20 Copynumber: 4.6 Consensus size: 19
910681 GTTTCCATAT
*
910691 TCGCATTGCGGTTTACGTAA
1 TCGCATTGC-GATTACGTAA
910711 TCGCATTGCGATTACGTAAA
1 TCGCATTGCGATTACGT-AA
* * **
910731 TAGCAATGCGAAGACGTAAA
1 TCGCATTGCGATTACGT-AA
* * *
910751 TCGCAATGTGAATACGTAAA
1 TCGCATTGCGATTACGT-AA
*
910771 TCGCAATGCGA
1 TCGCATTGCGA
910782 ATCTGACTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 7 0.11
20 54 0.89
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (19 bp):
TCGCATTGCGATTACGTAA
Found at i:910767 original size:40 final size:39
Alignment explanation
Indices: 910705--910803 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 39
910695 ATTGCGGTTT
* *
910705 ACGTAATCGCATTGCGATTACGTAAATAGCAATGCGAAG
1 ACGTAATCGCAATGCGAATACGTAAATAGCAATGCGAAG
* *
910744 ACGTAAATCGCAATGTGAATACGTAAATCGCAATGCGAATCTG
1 ACGT-AATCGCAATGCGAATACGTAAATAGCAATGCGAA---G
910787 AC-T-ATCGCAATGCGAAT
1 ACGTAATCGCAATGCGAAT
910804 CTGACTATCG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 4 0.08
40 43 0.84
42 1 0.02
43 3 0.06
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (39 bp):
ACGTAATCGCAATGCGAATACGTAAATAGCAATGCGAAG
Found at i:910783 original size:20 final size:20
Alignment explanation
Indices: 910704--910783 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
910694 CATTGCGGTT
* *
910704 TACGT-AATCGCATTGCGAT
1 TACGTAAATCGCAATGCGAA
*
910723 TACGTAAATAGCAATGCGAA
1 TACGTAAATCGCAATGCGAA
* *
910743 GACGTAAATCGCAATGTGAA
1 TACGTAAATCGCAATGCGAA
910763 TACGTAAATCGCAATGCGAA
1 TACGTAAATCGCAATGCGAA
910783 T
1 T
910784 CTGACTATCG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 5 0.10
20 47 0.90
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (20 bp):
TACGTAAATCGCAATGCGAA
Found at i:910793 original size:20 final size:20
Alignment explanation
Indices: 910770--910817 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
910760 GAATACGTAA
910770 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
910790 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
910810 ATCGCAAT
1 ATCGCAAT
910818 ACGATTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:910834 original size:20 final size:20
Alignment explanation
Indices: 910811--910855 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
910801 AATCTGACTA
910811 TCGCAATACGATTTACATAT
1 TCGCAATACGATTTACATAT
* * *
910831 TCGCATTGCGATTTACGTAT
1 TCGCAATACGATTTACATAT
910851 TCGCA
1 TCGCA
910856 TTGTCTAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (20 bp):
TCGCAATACGATTTACATAT
Found at i:910856 original size:20 final size:20
Alignment explanation
Indices: 910819--910858 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
910809 TATCGCAATA
910819 CGATTTACATATTCGCATTG
1 CGATTTACATATTCGCATTG
*
910839 CGATTTACGTATTCGCATTG
1 CGATTTACATATTCGCATTG
910859 TCTAACTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (20 bp):
CGATTTACATATTCGCATTG
Found at i:911492 original size:22 final size:22
Alignment explanation
Indices: 911467--911520 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
911457 TGGGGAAGGG
*
911467 TGTCGTTGGATATAGGAACGGA
1 TGTCGTTGGATATAGAAACGGA
911489 TGTCGTTGGATATAGAAACGGA
1 TGTCGTTGGATATAGAAACGGA
*
911511 TGTCGCTGGA
1 TGTCGTTGGA
911521 GAGAGTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.35, T:0.28
Consensus pattern (22 bp):
TGTCGTTGGATATAGAAACGGA
Found at i:911716 original size:20 final size:20
Alignment explanation
Indices: 911678--911798 Score: 58
Period size: 20 Copynumber: 6.0 Consensus size: 20
911668 CAGTATTGAC
* * *
911678 ATAGTCAGAATCTCGTTGCG
1 ATAGTCAGATTCGCATTGCG
911698 ATAGTCAGATTCGCATTGCG
1 ATAGTCAGATTCGCATTGCG
*
911718 AT--TTACGTATTCGCATTGCG
1 ATAGTCA-G-ATTCGCATTGCG
*
911738 AT--TTACGTATTCGCATTGCG
1 ATAGTCA-G-ATTCGCATTGCG
*
911758 ATTTACGT-A-A-TCGCAATGCG
1 A--TA-GTCAGATTCGCATTGCG
* *
911778 ATAGTCAGAATCGCGTTGCG
1 ATAGTCAGATTCGCATTGCG
911798 A
1 A
911799 ATCTGGAAAC
Statistics
Matches: 84, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
17 2 0.02
18 5 0.06
19 2 0.02
20 71 0.85
21 1 0.01
22 1 0.01
24 1 0.01
25 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (20 bp):
ATAGTCAGATTCGCATTGCG
Found at i:911797 original size:40 final size:40
Alignment explanation
Indices: 911694--911798 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 40
911684 AGAATCTCGT
* *
911694 TGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCAT
1 TGCGATAGTCAGATTCGCATTGCGATTTACGTAATCGCAA
*
911734 TGCGAT--TTACGTATTCGCATTGCGATTTACGTAATCGCAA
1 TGCGATAGTCA-G-ATTCGCATTGCGATTTACGTAATCGCAA
* *
911774 TGCGATAGTCAGAATCGCGTTGCGA
1 TGCGATAGTCAGATTCGCATTGCGA
911799 ATCTGGAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 49 0.89
41 1 0.02
42 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (40 bp):
TGCGATAGTCAGATTCGCATTGCGATTTACGTAATCGCAA
Found at i:915674 original size:30 final size:30
Alignment explanation
Indices: 915571--915674 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 30
915561 TTGCGAACAC
*
915571 TAAATAAACGAACATGAACAC-CTTACAAAA
1 TAAATAAACGAACATGAACACTTTTA-AAAA
*
915601 TAAATAAACGAACATAAACA-TGATATTAAAAA
1 TAAATAAACGAACATGAACACT--T-TTAAAAA
* *
915633 T--TTAAATGAACATGAACACTTTTAAAAA
1 TAAATAAACGAACATGAACACTTTTAAAAA
*
915661 TAAACAAACGAACA
1 TAAATAAACGAACA
915675 CGAGCATACT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
28 8 0.14
29 1 0.02
30 41 0.69
31 1 0.02
32 5 0.08
33 3 0.05
ACGTcount: A:0.58, C:0.14, G:0.07, T:0.21
Consensus pattern (30 bp):
TAAATAAACGAACATGAACACTTTTAAAAA
Found at i:920394 original size:15 final size:17
Alignment explanation
Indices: 920374--920406 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
920364 TAGTATCATT
920374 TTAATAA-A-ATATTAA
1 TTAATAATATATATTAA
920389 TTAATAATATATATTAA
1 TTAATAATATATATTAA
920406 T
1 T
920407 AATTTTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATAATATATATTAA
Found at i:920419 original size:22 final size:22
Alignment explanation
Indices: 920389--920446 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
920379 AAAATATTAA
*
920389 TTAATAATAT-ATATTAATAATT
1 TTAACAATATAATA-TAATAATT
*
920411 TTAACAATATAATATAATATTT
1 TTAACAATATAATATAATAATT
* *
920433 TTAATATTATAATA
1 TTAACAATATAATA
920447 ATATATGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAACAATATAATATAATAATT
Found at i:920450 original size:30 final size:32
Alignment explanation
Indices: 920392--920451 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
920382 ATATTAATTA
*
920392 ATAATATATATTAATAATTTTAACAATATAAT
1 ATAATATATATTAATAATTATAACAATATAAT
* *
920424 ATAATAT-TTTTAAT-ATTATAATAATATA
1 ATAATATATATTAATAATTATAACAATATA
920452 TGATAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.48
31 6 0.24
32 7 0.28
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (32 bp):
ATAATATATATTAATAATTATAACAATATAAT
Found at i:920804 original size:20 final size:23
Alignment explanation
Indices: 920777--920819 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
920767 TTATTCTAAT
*
920777 TTTTTTTAA-AAATAATATTAAC
1 TTTTTATAATAAATAATATTAAC
920799 TTTTTATAATAAATAATATTA
1 TTTTTATAATAAATAATATTA
920820 TTTCTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTTATAATAAATAATATTAAC
Found at i:920879 original size:21 final size:22
Alignment explanation
Indices: 920855--920898 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
920845 AATAATTTTT
920855 AAAAA-AAATTATCAACTAATG
1 AAAAATAAATTATCAACTAATG
* *
920876 AAAAATAATTTATGAACTAATG
1 AAAAATAAATTATCAACTAATG
920898 A
1 A
920899 CGATGACGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (22 bp):
AAAAATAAATTATCAACTAATG
Found at i:922231 original size:31 final size:30
Alignment explanation
Indices: 922196--922296 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 30
922186 TGTTCAAAAG
*
922196 TTTAAGGACTAATTTAGAATGATAGTCATAA
1 TTTAAGGACTAATTTAGAATGAT-GTAATAA
* * * *
922227 TTTAA-GAATGAAATTAGAAT-ATTTAAAAA
1 TTTAAGGACT-AATTTAGAATGATGTAATAA
* * *
922256 TTTAGGGACTAATTTAAAATGAGGATAATAA
1 TTTAAGGACTAATTTAGAATGATG-TAATAA
922287 TTTAAGGACT
1 TTTAAGGACT
922297 CTCTTTATAC
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
29 16 0.30
30 9 0.17
31 28 0.53
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.35
Consensus pattern (30 bp):
TTTAAGGACTAATTTAGAATGATGTAATAA
Found at i:926429 original size:23 final size:22
Alignment explanation
Indices: 926403--926466 Score: 56
Period size: 25 Copynumber: 2.7 Consensus size: 22
926393 TCAAACTATT
*
926403 ATAAAGATAGACAAAATCGTGTC
1 ATAAAG-TAGACAAAATCGTGCC
926426 ATAAATGTAGACGAACAATCGTGCC
1 ATAAA-GTAGAC-AA-AATCGTGCC
* *
926451 GTAAAGGCAGACAAAA
1 ATAAA-GTAGACAAAA
926467 ATAAATACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 12 0.35
24 5 0.15
25 17 0.50
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (22 bp):
ATAAAGTAGACAAAATCGTGCC
Found at i:926455 original size:25 final size:23
Alignment explanation
Indices: 926410--926466 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 23
926400 ATTATAAAGA
*
926410 TAGACAAAATCGTGTCATAAATG
1 TAGACAAAATCGTGCCATAAATG
* *
926433 TAGACGAACAATCGTGCCGTAAAGG
1 TAGAC-AA-AATCGTGCCATAAATG
*
926458 CAGACAAAA
1 TAGACAAAA
926467 ATAAATACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 7 0.25
24 4 0.14
25 17 0.61
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (23 bp):
TAGACAAAATCGTGCCATAAATG
Found at i:928067 original size:2 final size:2
Alignment explanation
Indices: 928060--928096 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
928050 TAGATTGTTA
928060 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
928097 TTCAAGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:930372 original size:35 final size:33
Alignment explanation
Indices: 930333--930398 Score: 114
Period size: 35 Copynumber: 1.9 Consensus size: 33
930323 TTAGACACAC
930333 AAGTTTAAACGCTTTGTCTCTTTCAAAAAAAAAAA
1 AAGTTTAAACGCTTTGTC-C-TTCAAAAAAAAAAA
930368 AAGTTTAAACGCTTTGTCCTTCAAAAAAAAA
1 AAGTTTAAACGCTTTGTCCTTCAAAAAAAAA
930399 TTTAAACGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 12 0.39
34 1 0.03
35 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (33 bp):
AAGTTTAAACGCTTTGTCCTTCAAAAAAAAAAA
Found at i:931292 original size:33 final size:33
Alignment explanation
Indices: 931255--931326 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
931245 GTTAAATTTG
931255 ATTTTATCGC-CCTCACTTTCTATG-GTTAATTAT
1 ATTTTATC-CTCCTCACTTTCTATGAG-TAATTAT
*
931288 ATTTTTTCCTCCTCACTTTCTATGAGTAATTAT
1 ATTTTATCCTCCTCACTTTCTATGAGTAATTAT
931321 ACTTTT
1 A-TTTT
931327 TCTCCTTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
32 1 0.03
33 29 0.83
34 5 0.14
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (33 bp):
ATTTTATCCTCCTCACTTTCTATGAGTAATTAT
Found at i:931327 original size:33 final size:32
Alignment explanation
Indices: 931265--931332 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
931255 ATTTTATCGC
*
931265 CCTCACTTTCTATGGTTAATTATATTTTTTCCT
1 CCTCACTTTCTATGGTTAATTATACTTTTT-CT
931298 CCTCACTTTCTATGAG-TAATTATACTTTTTCT
1 CCTCACTTTCTATG-GTTAATTATACTTTTTCT
931330 CCT
1 CCT
931333 TAAGCTGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 5 0.15
33 27 0.82
34 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.06, T:0.51
Consensus pattern (32 bp):
CCTCACTTTCTATGGTTAATTATACTTTTTCT
Found at i:935229 original size:18 final size:18
Alignment explanation
Indices: 935208--935242 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
935198 TAATGATTTA
935208 ATTAT-TAAGTATAAATTC
1 ATTATCTAA-TATAAATTC
935226 ATTATCTAATATAAATT
1 ATTATCTAATATAAATT
935243 AAAGTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTATCTAATATAAATTC
Found at i:937576 original size:12 final size:12
Alignment explanation
Indices: 937559--937599 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
937549 AGCATTGTAC
* *
937559 GCATGCATGCAT
1 GCATGCAAGCTT
937571 GCATGCAAGCTT
1 GCATGCAAGCTT
937583 GCATGCAAGCTT
1 GCATGCAAGCTT
937595 GCATG
1 GCATG
937600 TGATAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (12 bp):
GCATGCAAGCTT
Found at i:950484 original size:23 final size:25
Alignment explanation
Indices: 950440--950487 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
950430 TTTAATCTCA
950440 TCATTTGGACAATGATGAGAATAATT
1 TCATTTGGACAA-GATGAGAATAATT
950466 TCATTTGGAC-A-ATGAGAATAAT
1 TCATTTGGACAAGATGAGAATAAT
950488 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.50
25 1 0.05
26 10 0.45
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (25 bp):
TCATTTGGACAAGATGAGAATAATT
Found at i:953541 original size:23 final size:25
Alignment explanation
Indices: 953497--953544 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
953487 TTTAATCTCA
953497 TCATTTGGACAATGATGAGAATAATT
1 TCATTTGGACAA-GATGAGAATAATT
953523 TCATTTGGAC-A-ATGAGAATAAT
1 TCATTTGGACAAGATGAGAATAAT
953545 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.50
25 1 0.05
26 10 0.45
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (25 bp):
TCATTTGGACAAGATGAGAATAATT
Found at i:956605 original size:23 final size:25
Alignment explanation
Indices: 956561--956608 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
956551 TTTAATCTCA
956561 TCATTTGGACAATGATGAGAATAATT
1 TCATTTGGACAA-GATGAGAATAATT
956587 TCATTTGGAC-A-ATGAGAATAAT
1 TCATTTGGACAAGATGAGAATAAT
956609 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.50
25 1 0.05
26 10 0.45
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (25 bp):
TCATTTGGACAAGATGAGAATAATT
Found at i:957259 original size:23 final size:23
Alignment explanation
Indices: 957199--957259 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
957189 ATACATATAT
*
957199 ATTTAATTTTTAAAAAAATTAAA
1 ATTTAATTTTAAAAAAAATTAAA
*
957222 ATTATAATTTGAAAAAAAATCT-AA
1 ATT-TAATTTTAAAAAAAAT-TAAA
*
957246 ATTTTATTTTAAAA
1 ATTTAATTTTAAAA
957260 CCCCTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 12 0.38
24 19 0.59
25 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTAATTTTAAAAAAAATTAAA
Found at i:962659 original size:14 final size:13
Alignment explanation
Indices: 962632--962699 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 13
962622 ATGAAAAAAC
962632 ATAATATATAATT
1 ATAATATATAATT
962645 ATAATATATTAATT
1 ATAATATA-TAATT
*
962659 ATAATAT-GAATT
1 ATAATATATAATT
962671 ATATATATATATATAT
1 ATA-ATATATA-AT-T
962687 ATATATATATAAT
1 ATA-ATATATAAT
962700 AATATTTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
12 7 0.15
13 12 0.25
14 13 0.27
15 4 0.08
16 12 0.25
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (13 bp):
ATAATATATAATT
Found at i:962677 original size:2 final size:2
Alignment explanation
Indices: 962670--962697 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
962660 TAATATGAAT
962670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
962698 ATAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:962704 original size:14 final size:14
Alignment explanation
Indices: 962635--962704 Score: 58
Period size: 16 Copynumber: 5.0 Consensus size: 14
962625 AAAAAACATA
962635 ATATATAAT--TAT
1 ATATATAATAATAT
*
962647 A-ATATATTAAT-T
1 ATATATAATAATAT
*
962659 ATAATATGAATTATAT
1 AT-ATAT-AATAATAT
962675 ATATATATATATATAT
1 ATATATA-ATA-ATAT
962691 ATATATAATAATAT
1 ATATATAATAATAT
962705 TTTATAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
11 6 0.13
12 3 0.07
13 1 0.02
14 9 0.20
15 13 0.28
16 14 0.30
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (14 bp):
ATATATAATAATAT
Found at i:969073 original size:22 final size:22
Alignment explanation
Indices: 969048--969101 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
969038 ATCATATGTC
969048 GAAACAATTAAACAAAAAAATT
1 GAAACAATTAAACAAAAAAATT
*
969070 GAAACAATTAAACAAAAATATT
1 GAAACAATTAAACAAAAAAATT
969092 -ATAACAATTA
1 GA-AACAATTA
969102 TATCTAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.65, C:0.09, G:0.04, T:0.22
Consensus pattern (22 bp):
GAAACAATTAAACAAAAAAATT
Found at i:970983 original size:24 final size:24
Alignment explanation
Indices: 970956--971001 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
970946 GTTTACATGT
* *
970956 TTTTTTCTTTTCTTGTGGCACGTA
1 TTTTTTCTGTTATTGTGGCACGTA
970980 TTTTTTCTGTTATTGTGGCACG
1 TTTTTTCTGTTATTGTGGCACG
971002 ATCCTTGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.15, G:0.20, T:0.57
Consensus pattern (24 bp):
TTTTTTCTGTTATTGTGGCACGTA
Found at i:971871 original size:20 final size:21
Alignment explanation
Indices: 971846--971892 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
971836 TCCCAAAAAC
971846 TCTAAA-CTCAAATATCT-AAT
1 TCTAAACCT-AAATATCTAAAT
*
971866 TCTAAACCTAAATCTCTAAAT
1 TCTAAACCTAAATATCTAAAT
971887 TCTAAA
1 TCTAAA
971893 ACACACATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (21 bp):
TCTAAACCTAAATATCTAAAT
Found at i:973290 original size:60 final size:59
Alignment explanation
Indices: 973166--973302 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 59
973156 TAAAGTTTAG
* ** * * *
973166 AGACTAATTTAAAATGAGGGTCATAGTTTGAAGATTAAATTAGAATATTTAAATTTTCTT
1 AGACCAATTTAAAATGAAAGTCATAGTTTGAAGATGAAATTAGAATATTCAAA-TATCTT
*
973226 AGACCAATTTAAAATGAAAGTCATAGTTTGAAGATGAAATTAGAATGTTCAAA-ATCTT
1 AGACCAATTTAAAATGAAAGTCATAGTTTGAAGATGAAATTAGAATATTCAAATATCTT
*
973284 AAAGACCATTTTAAAATGA
1 --AGACCAATTTAAAATGA
973303 TGATCATGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 4 0.06
60 63 0.94
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (59 bp):
AGACCAATTTAAAATGAAAGTCATAGTTTGAAGATGAAATTAGAATATTCAAATATCTT
Found at i:973712 original size:23 final size:23
Alignment explanation
Indices: 973682--973729 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
973672 TAGGATTTAG
*
973682 TTCTAATAC-TTATTTTATAATAT
1 TTCTAATACTTTAATTTATAA-AT
973705 TTCTAATACTTTAATTTATAAAT
1 TTCTAATACTTTAATTTATAAAT
973728 TT
1 TT
973730 TTGTATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (23 bp):
TTCTAATACTTTAATTTATAAAT
Found at i:974158 original size:19 final size:19
Alignment explanation
Indices: 974134--974171 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
974124 AAACCTTCAT
974134 ATTTTGATTATATATATAA
1 ATTTTGATTATATATATAA
* *
974153 ATTTTGGTTCTATATATAA
1 ATTTTGATTATATATATAA
974172 TAAAATACAT
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:0.03, G:0.08, T:0.53
Consensus pattern (19 bp):
ATTTTGATTATATATATAA
Found at i:974434 original size:2 final size:2
Alignment explanation
Indices: 974427--974456 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
974417 TATTTCACCG
974427 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
974457 ATTTGTTGTA
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):
TA
Found at i:978235 original size:30 final size:30
Alignment explanation
Indices: 978199--978260 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
978189 TTATTACGCC
978199 TTCTTTAGGTACATGAAGCCCTTAAACTCG
1 TTCTTTAGGTACATGAAGCCCTTAAACTCG
978229 TTCTTTAGGTACATGAAGCCCTTAAACTCG
1 TTCTTTAGGTACATGAAGCCCTTAAACTCG
978259 TT
1 TT
978261 TACATCCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (30 bp):
TTCTTTAGGTACATGAAGCCCTTAAACTCG
Found at i:988690 original size:25 final size:24
Alignment explanation
Indices: 988642--988701 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
988632 GGGTTATGAG
*
988642 GTTTAAGGTTTGATTGAGACTTGA
1 GTTTAGGGTTTGATTGAGACTTGA
*
988666 TGTTTAGGGTTTGATT-AGGATTTGA
1 -GTTTAGGGTTTGATTGA-GACTTGA
*
988691 GGTTAGGGTTT
1 GTTTAGGGTTT
988702 ACTTGAGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.45
Consensus pattern (24 bp):
GTTTAGGGTTTGATTGAGACTTGA
Found at i:989559 original size:46 final size:46
Alignment explanation
Indices: 989453--989625 Score: 204
Period size: 46 Copynumber: 3.8 Consensus size: 46
989443 TCCAAACTGA
*** *
989453 TATTGAATATTATCATTTTATAAGGATGAACTAGTCGATTATTTGG
1 TATTGAATATTATCATCCAATAAGGATGAACTAGTCAATTATTTGG
* * * * *
989499 TATTGGACACTATCATCCGATAAGGATGAACGAGTCAATTATTTGG
1 TATTGAATATTATCATCCAATAAGGATGAACTAGTCAATTATTTGG
* *
989545 TATTGAATATTATCATCCAATAAAGATG-ATTAGTCAATTATTTGG
1 TATTGAATATTATCATCCAATAAGGATGAACTAGTCAATTATTTGG
* ** *
989590 AACCGGATATTATCATCCAATAAGGATGAACTAGTC
1 TATTGAATATTATCATCCAATAAGGATGAACTAGTC
989626 GGTAATTATA
Statistics
Matches: 105, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
45 38 0.36
46 67 0.64
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (46 bp):
TATTGAATATTATCATCCAATAAGGATGAACTAGTCAATTATTTGG
Found at i:989600 original size:45 final size:45
Alignment explanation
Indices: 989531--989618 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
989521 AGGATGAACG
* **
989531 AGTCAATTATTTGGTATTGAATATTATCATCCAATAAAGATGATT
1 AGTCAATTATTTGGAACCGAATATTATCATCCAATAAAGATGATT
* *
989576 AGTCAATTATTTGGAACCGGATATTATCATCCAATAAGGATGA
1 AGTCAATTATTTGGAACCGAATATTATCATCCAATAAAGATGA
989619 ACTAGTCGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (45 bp):
AGTCAATTATTTGGAACCGAATATTATCATCCAATAAAGATGATT
Found at i:989613 original size:91 final size:92
Alignment explanation
Indices: 989453--989625 Score: 222
Period size: 91 Copynumber: 1.9 Consensus size: 92
989443 TCCAAACTGA
*** * * * ** *
989453 TATTGAATATTATCATTTTATAAGGATGAACTAGTCGATTATTTGGTATTGGACACTATCATCCG
1 TATTGAATATTATCATCCAATAAAGATGAACTAGTCAATTATTTGGAACCGGACACTATCATCCA
989518 ATAAGGATGAACGAGTCAATTATTTGG
66 ATAAGGATGAACGAGTCAATTATTTGG
* * *
989545 TATTGAATATTATCATCCAATAAAGATG-ATTAGTCAATTATTTGGAACCGGATATTATCATCCA
1 TATTGAATATTATCATCCAATAAAGATGAACTAGTCAATTATTTGGAACCGGACACTATCATCCA
*
989609 ATAAGGATGAACTAGTC
66 ATAAGGATGAACGAGTC
989626 GGTAATTATA
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
91 44 0.65
92 24 0.35
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (92 bp):
TATTGAATATTATCATCCAATAAAGATGAACTAGTCAATTATTTGGAACCGGACACTATCATCCA
ATAAGGATGAACGAGTCAATTATTTGG
Found at i:990425 original size:27 final size:28
Alignment explanation
Indices: 990360--990425 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
990350 GTTCAATAGA
990360 TCAAAGTCGATAAGTAAGTTATAAAAAG
1 TCAAAGTCGATAAGTAAGTTATAAAAAG
*
990388 TCAAAGTCGATAAGTTAAG-T-TAGAAAG
1 TCAAAGTCGATAAG-TAAGTTATAAAAAG
*
990415 TCAAAGCCGAT
1 TCAAAGTCGAT
990426 CGAGTTAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 16 0.46
28 15 0.43
29 4 0.11
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (28 bp):
TCAAAGTCGATAAGTAAGTTATAAAAAG
Found at i:991363 original size:31 final size:31
Alignment explanation
Indices: 991291--991378 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 31
991281 AAATATTTAT
* *
991291 TTTACTCCTTAATTTTTAGATA-ATATACTAA
1 TTTAATCCTTAAATTTTAGATACA-ATACTAA
* *
991322 TTTAAT-CTTAAATTTTAGGTACAATACTGA
1 TTTAATCCTTAAATTTTAGATACAATACTAA
* * *
991352 TTTAGTCCTTAAAGTTAAGATACAATA
1 TTTAATCCTTAAATTTTAGATACAATA
991379 TCAATATGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
30 24 0.51
31 23 0.49
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (31 bp):
TTTAATCCTTAAATTTTAGATACAATACTAA
Found at i:993490 original size:18 final size:20
Alignment explanation
Indices: 993469--993505 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
993459 ATTCAAAAAT
993469 AAAATAAAA-TT-TTATTAA
1 AAAATAAAACTTGTTATTAA
993487 AAAATAAAACTTGTTATTA
1 AAAATAAAACTTGTTATTA
993506 GATTGTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAATAAAACTTGTTATTAA
Found at i:1000557 original size:6 final size:6
Alignment explanation
Indices: 1000548--1000737 Score: 380
Period size: 6 Copynumber: 31.7 Consensus size: 6
1000538 TGAACAAATA
1000548 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1000596 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1000644 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1000692 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATA
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATA
1000738 GGGTATAGGG
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 184 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:1000745 original size:7 final size:7
Alignment explanation
Indices: 1000733--1001275 Score: 962
Period size: 7 Copynumber: 77.7 Consensus size: 7
1000723 ATATGTATAT
1000733 GTATAGG
1 GTATAGG
1000740 GTATAGG
1 GTATAGG
1000747 GTATAGG
1 GTATAGG
1000754 GTATAGG
1 GTATAGG
1000761 GTATAGG
1 GTATAGG
1000768 GTATAGG
1 GTATAGG
1000775 GTATAGG
1 GTATAGG
1000782 GTATAGG
1 GTATAGG
1000789 GTATAGG
1 GTATAGG
1000796 GTATAGG
1 GTATAGG
1000803 GTATAGG
1 GTATAGG
1000810 GTATAGG
1 GTATAGG
1000817 GTATAGG
1 GTATAGG
1000824 GTATAGG
1 GTATAGG
1000831 GTATAGG
1 GTATAGG
1000838 GTATAGG
1 GTATAGG
1000845 GTATAGG
1 GTATAGG
1000852 GTATAGG
1 GTATAGG
1000859 GTATAGG
1 GTATAGG
1000866 GTATAGG
1 GTATAGG
1000873 GTATAGG
1 GTATAGG
1000880 GTATAGG
1 GTATAGG
1000887 GTATAGG
1 GTATAGG
1000894 GTATAGG
1 GTATAGG
1000901 GTATAGG
1 GTATAGG
1000908 GTATAGG
1 GTATAGG
1000915 GTATAGG
1 GTATAGG
1000922 GTATAGG
1 GTATAGG
1000929 GTATAGG
1 GTATAGG
1000936 GTATAGG
1 GTATAGG
1000943 GTATAGG
1 GTATAGG
1000950 GTATAGG
1 GTATAGG
1000957 GTATAGG
1 GTATAGG
1000964 GTATA-G
1 GTATAGG
1000970 GTATAGG
1 GTATAGG
1000977 GTATAGG
1 GTATAGG
1000984 GTATAGG
1 GTATAGG
1000991 GTATAGG
1 GTATAGG
1000998 GTATAGG
1 GTATAGG
1001005 GTATAGG
1 GTATAGG
1001012 GTATAGG
1 GTATAGG
1001019 GTATAGG
1 GTATAGG
1001026 GTATAGG
1 GTATAGG
1001033 GTATAGG
1 GTATAGG
1001040 GTATAGG
1 GTATAGG
1001047 GTATAGG
1 GTATAGG
1001054 GTATAGG
1 GTATAGG
1001061 GTATAGG
1 GTATAGG
1001068 GTATAGG
1 GTATAGG
1001075 GTATAGG
1 GTATAGG
1001082 GTATAGG
1 GTATAGG
*
1001089 GTATATG
1 GTATAGG
*
1001096 GTATATG
1 GTATAGG
*
1001103 GTATATG
1 GTATAGG
1001110 GTATAGG
1 GTATAGG
1001117 GTATAGG
1 GTATAGG
1001124 GTATAGG
1 GTATAGG
1001131 GTATAGG
1 GTATAGG
1001138 GTATAGG
1 GTATAGG
1001145 GTATAGG
1 GTATAGG
1001152 GTATAGG
1 GTATAGG
1001159 GTATAGG
1 GTATAGG
1001166 GTATAGG
1 GTATAGG
1001173 GTATAGG
1 GTATAGG
1001180 GTATAGG
1 GTATAGG
1001187 GTATAGG
1 GTATAGG
1001194 GTATAGG
1 GTATAGG
*
1001201 GTATATG
1 GTATAGG
*
1001208 GTATATG
1 GTATAGG
*
1001215 GTATATG
1 GTATAGG
*
1001222 GTATATG
1 GTATAGG
*
1001229 GTATATG
1 GTATAGG
*
1001236 GTATATG
1 GTATAGG
*
1001243 GTATATG
1 GTATAGG
*
1001250 GTATATG
1 GTATAGG
*
1001257 GTATATG
1 GTATAGG
*
1001264 GTATATG
1 GTATAGG
1001271 GTATA
1 GTATA
1001276 TGGAATAATT
Statistics
Matches: 532, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
6 6 0.01
7 526 0.99
ACGTcount: A:0.29, C:0.00, G:0.40, T:0.31
Consensus pattern (7 bp):
GTATAGG
Found at i:1004472 original size:44 final size:44
Alignment explanation
Indices: 1004404--1004538 Score: 168
Period size: 44 Copynumber: 3.1 Consensus size: 44
1004394 CAGCTACAGA
* * *
1004404 ATAGTTATTTCGAA-CTAAAACACACAGATCATAAGTACTCAACC
1 ATAGCTATTTC-AATCTAGAACACACGGATCATAAGTACTCAACC
* *
1004448 ATAGCTATTTTGAA-C-AGGAACACACGGATCATAAGTGCTCAACC
1 ATAGCTA-TTTCAATCTA-GAACACACGGATCATAAGTACTCAACC
*
1004492 ATAGTTATTTCAATCTAGAACACACGGATCATAAGTACTCAACC
1 ATAGCTATTTCAATCTAGAACACACGGATCATAAGTACTCAACC
1004536 ATA
1 ATA
1004539 ATCAGAAAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
43 6 0.08
44 69 0.87
45 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (44 bp):
ATAGCTATTTCAATCTAGAACACACGGATCATAAGTACTCAACC
Found at i:1021500 original size:2 final size:2
Alignment explanation
Indices: 1021493--1021518 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1021483 TGGATATGTA
1021493 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
1021519 TCTTCACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1031811 original size:2 final size:2
Alignment explanation
Indices: 1031804--1031834 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1031794 CTGCAGCTAT
1031804 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1031835 CATGCATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1032023 original size:97 final size:97
Alignment explanation
Indices: 1031857--1032050 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
1031847 TATGTGTGTA
1031857 TGAAATATTCTATATTTCAGATCTTTTAAGCAACTGGAAGTAACCAAAGATTAGGTTTAAGTTTT
1 TGAAATATTCTATATTTCAGATCTTTTAAGCAACTGGAAGTAACCAAAGATTAGGTTTAAGTTTT
1031922 GAGTTTATGAATAATGGTAGCTGATGAGATTG
66 GAGTTTATGAATAATGGTAGCTGATGAGATTG
1031954 TGAAATATTCTATATTTCAGATCTTTTAAGCAACTGGAAGTAACCAAAGATTAGGTTTAAGTTTT
1 TGAAATATTCTATATTTCAGATCTTTTAAGCAACTGGAAGTAACCAAAGATTAGGTTTAAGTTTT
1032019 GAGTTTATGAATAATGGTAGCTGATGAGATTG
66 GAGTTTATGAATAATGGTAGCTGATGAGATTG
1032051 ATTTTACAAA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (97 bp):
TGAAATATTCTATATTTCAGATCTTTTAAGCAACTGGAAGTAACCAAAGATTAGGTTTAAGTTTT
GAGTTTATGAATAATGGTAGCTGATGAGATTG
Found at i:1033986 original size:15 final size:15
Alignment explanation
Indices: 1033966--1034047 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
1033956 TTCCATAAAA
1033966 TGAATTACTGGAATT
1 TGAATTACTGGAATT
1033981 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1033996 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
1034011 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1034026 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
1034040 TGAATTAC
1 TGAATTAC
1034048 ATTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:1034000 original size:30 final size:30
Alignment explanation
Indices: 1033966--1034047 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
1033956 TTCCATAAAA
**
1033966 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
1033996 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
1034026 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
1034048 ATTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:1034026 original size:45 final size:44
Alignment explanation
Indices: 1033962--1034047 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 44
1033952 GGTTTTCCAT
**
1033962 AAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTGG
1 AAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTGG
1034007 AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1034048 ATTTCTGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (44 bp):
AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTGG
Done.