Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008478.1 Hibiscus syriacus cultivar Beakdansim tig00111309_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: 1476524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:364733 original size:21 final size:21
Alignment explanation
Indices: 364690--364783 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
364680 TTTTCCCAAT
** *
364690 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
364710 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
364731 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
364752 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
364773 TCGCAACGCGA
1 TCGCAATGCGA
364784 TACTGACTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
20 12 0.17
21 57 0.83
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:364797 original size:20 final size:20
Alignment explanation
Indices: 364772--364886 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
364762 AATTTGGAAA
364772 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
364792 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
364813 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
364833 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* *
364853 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
364873 TTCGCAACGAGATA
1 ATCGCAACGCGATA
364887 ATACATAATC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.76
21 15 0.19
22 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:364814 original size:41 final size:41
Alignment explanation
Indices: 364769--364906 Score: 179
Period size: 41 Copynumber: 3.4 Consensus size: 41
364759 GCGAATTTGG
*
364769 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
364810 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
** * *
364850 AATTTCGCAACGCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
364891 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
364907 TTTCAAAGCG
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 33 0.41
41 47 0.59
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:365101 original size:22 final size:22
Alignment explanation
Indices: 365073--365116 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
365063 CACTCTCTCA
365073 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
365095 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
365117 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:365595 original size:25 final size:24
Alignment explanation
Indices: 365541--365595 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
365531 TGTTTATTAT
* *
365541 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
365565 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
365591 TGTTT
1 TGTTT
365596 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:367560 original size:19 final size:19
Alignment explanation
Indices: 367538--367673 Score: 166
Period size: 19 Copynumber: 7.1 Consensus size: 19
367528 TTGGGTCGGA
367538 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
367557 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
367576 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
367595 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
* *
367614 TCAAACCGGTTGAAACCGG-
1 TCAGACCGG-TCAAACCGGT
*
367633 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
367653 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
367673 T
1 T
367674 TCCAGCAGCC
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
18 2 0.02
19 77 0.74
20 16 0.15
21 9 0.09
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:367602 original size:29 final size:28
Alignment explanation
Indices: 367543--367673 Score: 122
Period size: 29 Copynumber: 4.5 Consensus size: 28
367533 TCGGATCAGA
*
367543 CCGGTCAAACCGGTTCAGACCGGTCAAA
1 CCGGTCAAACCGGTTCAAACCGGTCAAA
* * *
367571 CCGATTCAGACCGG-TCAAACCGGTTCAGA
1 CCG-GTCAAACCGGTTCAAACCGG-TCAAA
* *
367600 CCGGTCAAACTGGTTCAAACCGGTTGAAA
1 CCGGTCAAACCGGTTCAAACCGG-TCAAA
*
367629 CCGGTCAAACCGG-TCAGAACCGGTTGAAAA
1 CCGGTCAAACCGGTTCA-AACCGG-T-CAAA
*
367659 CCGGTTAAACCGGTT
1 CCGGTCAAACCGGTT
367674 TCCAGCAGCC
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
28 21 0.25
29 48 0.56
30 15 0.18
31 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (28 bp):
CCGGTCAAACCGGTTCAAACCGGTCAAA
Found at i:374914 original size:9 final size:9
Alignment explanation
Indices: 374896--374994 Score: 63
Period size: 9 Copynumber: 10.3 Consensus size: 9
374886 GGTCGGGTTG
*
374896 GGTCAGACC
1 GGTCAAACC
374905 GGTCAAACC
1 GGTCAAACC
*
374914 GGTTCAGACC
1 GG-TCAAACC
*
374924 GGTCAAACT
1 GGTCAAACC
* *
374933 GGTTCGAACT
1 GG-TCAAACC
*
374943 GGTTGAAACC
1 GG-TCAAACC
*
374953 AGTCAAACC
1 GGTCAAACC
374962 GGTCAGAACC
1 GGTCA-AACC
*
374972 GGTTGAAAACC
1 GG-T-CAAACC
*
374983 GGTTAAACC
1 GGTCAAACC
374992 GGT
1 GGT
374995 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
9 35 0.49
10 29 0.40
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:374920 original size:19 final size:19
Alignment explanation
Indices: 374898--374995 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
374888 TCGGGTTGGG
374898 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
374917 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
* * *
374936 TC-GAACTGGTTGAAACCAG-
1 TCAG-ACCGG-TCAAACCGGT
*
374955 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
374975 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
374995 T
1 T
374996 TCCAGCAGCC
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 15 0.24
21 9 0.15
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:374993 original size:20 final size:21
Alignment explanation
Indices: 374957--374995 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
374947 GAAACCAGTC
374957 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
374978 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
374996 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:376690 original size:20 final size:20
Alignment explanation
Indices: 376665--376710 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
376655 TAGTTTACTT
376665 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
376685 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
376705 TCGCAA
1 TCGCAA
376711 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:376719 original size:19 final size:20
Alignment explanation
Indices: 376676--376720 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
376666 CGCAACACGA
376676 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
376696 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
376715 AAATGA
1 AAATGA
376721 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:376726 original size:19 final size:19
Alignment explanation
Indices: 376684--376759 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 19
376674 GAAAATGACT
***
376684 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
376704 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
376723 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
376737 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
376756 ATCG
1 ATCG
376760 TAACGACAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.22
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.43
20 10 0.22
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:376746 original size:33 final size:33
Alignment explanation
Indices: 376704--376793 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
376694 GGAAATGGCT
376704 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
376737 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
376770 ATTGCAACGCGAAATGAAAATCGC
1 ATCGCAATGCGAAATGAAAATCGC
376794 GTTGCGATAG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:376816 original size:20 final size:20
Alignment explanation
Indices: 376791--376840 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
376781 AAATGAAAAT
376791 CGCGTTGCGATAGTCATTTC
1 CGCGTTGCGATAGTCATTTC
* *
376811 CGCGTTCCGATAGTCATTTT
1 CGCGTTGCGATAGTCATTTC
376831 CGCGTTGCGA
1 CGCGTTGCGA
376841 AAGTAAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.26, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATAGTCATTTC
Found at i:376851 original size:20 final size:19
Alignment explanation
Indices: 376790--376866 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
376780 GAAATGAAAA
* *
376790 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGAAAGTAATT
* * *
376809 TCCGCGTTCCGATAGTCATTT
1 T-CGCGTTGCGAAAGT-AATT
376830 TCGCGTTGCGAAAGTAAGTT
1 TCGCGTTGCGAAAGTAA-TT
*
376850 TCGTGTTGCGAAAGTAA
1 TCGCGTTGCGAAAGTAA
376867 ACTATTCTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 43 0.90
21 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (19 bp):
TCGCGTTGCGAAAGTAATT
Found at i:377241 original size:21 final size:20
Alignment explanation
Indices: 377209--377270 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
377199 ACTCACCTGT
377209 CATCCCTCAAGAGTCCCCTC
1 CATCCCTCAAGAGTCCCCTC
** * *
377229 CAATCGTTCAAGAGGCCCCTAT
1 C-ATCCCTCAAGAGTCCCCT-C
377251 CATCCCTCAAGAGTCCCCTC
1 CATCCCTCAAGAGTCCCCTC
377271 ACCATTCAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.44, G:0.13, T:0.21
Consensus pattern (20 bp):
CATCCCTCAAGAGTCCCCTC
Found at i:377294 original size:40 final size:42
Alignment explanation
Indices: 377205--377294 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
377195 CCCGACTCAC
* * *
377205 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
*
377247 CTATCATCCCTCAAGAGTCCCCT-C-ACCATTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
377287 CTGTCATC
1 CTGTCATC
377295 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 20 0.47
41 1 0.02
42 22 0.51
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCATTCAAGAGGCCA
Found at i:377310 original size:40 final size:41
Alignment explanation
Indices: 377208--377294 Score: 122
Period size: 40 Copynumber: 2.1 Consensus size: 41
377198 GACTCACCTG
* * *
377208 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCC-ACCATTCAAGAGGCCACTA
*
377250 TCATCCCTCAAGAGTCCCCT-CACCATTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCACCATTCAAGAGGCCACTA
377290 TCATC
1 TCATC
377295 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 20 0.49
41 1 0.02
42 20 0.49
ACGTcount: A:0.24, C:0.40, G:0.14, T:0.22
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCTCCACCATTCAAGAGGCCACTA
Found at i:378654 original size:14 final size:14
Alignment explanation
Indices: 378620--378658 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
378610 TTGATTGTTT
378620 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
378634 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
378648 TGTTGATTTGT
1 AATTGATTTGT
378659 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:378819 original size:19 final size:17
Alignment explanation
Indices: 378794--378843 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
378784 TATCGCAACT
378794 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
378812 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
378827 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
378844 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:378887 original size:20 final size:20
Alignment explanation
Indices: 378870--378917 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
378860 CGATTTTCTA
378870 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
378890 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
378910 GTTGCGAT
1 GTTGCGAT
378918 TTCCCCGTTG
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:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:379167 original size:20 final size:20
Alignment explanation
Indices: 379144--379256 Score: 172
Period size: 20 Copynumber: 5.7 Consensus size: 20
379134 CGATTTTCAA
*
379144 AATCTCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
379164 AATCTCGTTGCAAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
379184 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
379204 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
379224 TATCGTGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
379244 TATCGCGTTGCGA
1 AATCGCGTTGCGA
379257 TTTTGTATTA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:380130 original size:24 final size:24
Alignment explanation
Indices: 380103--380156 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
380093 GTATTTGAAA
*
380103 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
380127 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
380151 TTTGAT
1 TTTGAT
380157 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:380339 original size:3 final size:3
Alignment explanation
Indices: 380331--380375 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
380321 ATATAATCCT
* * *
380331 GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
380376 AAAGTCCCCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:380348 original size:12 final size:12
Alignment explanation
Indices: 380331--380379 Score: 98
Period size: 12 Copynumber: 4.1 Consensus size: 12
380321 ATATAATCCT
380331 GAAGAAGAAAAA
1 GAAGAAGAAAAA
380343 GAAGAAGAAAAA
1 GAAGAAGAAAAA
380355 GAAGAAGAAAAA
1 GAAGAAGAAAAA
380367 GAAGAAGAAAAA
1 GAAGAAGAAAAA
380379 G
1 G
380380 TCCCCGAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:382751 original size:33 final size:33
Alignment explanation
Indices: 382709--382835 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
382699 GGAAATTACT
* *
382709 ATCGCAATGCGAAATGAAAATCACAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
382742 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
382775 ATCACAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
382808 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
382836 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:382870 original size:19 final size:19
Alignment explanation
Indices: 382835--382911 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
382825 AAATCGCAAC
*
382835 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
382854 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
382873 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
382887 GCGATTTTTA-TTTCGCATT
1 GCGA-TTTTAGTTTCGCGTT
382906 GCGATT
1 GCGATT
382912 CCCTCGTTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
14 8 0.16
15 4 0.08
16 1 0.02
17 1 0.02
18 3 0.06
19 33 0.66
ACGTcount: A:0.13, C:0.16, G:0.25, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:382892 original size:33 final size:33
Alignment explanation
Indices: 382850--382976 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
382840 TTTAGTTTCG
* * *
382850 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
* *
382883 CGTTGCGATTTTTATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
382916 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
382949 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
382977 AGTAATTTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
33 86 0.99
34 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:382942 original size:19 final size:18
Alignment explanation
Indices: 382845--382976 Score: 74
Period size: 19 Copynumber: 7.7 Consensus size: 18
382835 GCGAATTTAG
382845 TTTCGCGTTGCGATTTT-A
1 TTTCGC-TTGCGATTTTCA
382863 GTTTCGCGTTGCGA-TTT--
1 -TTTCGC-TTGCGATTTTCA
* *
382880 TGTCG-TTGCGATTTTTA
1 TTTCGCTTGCGATTTTCA
382897 TTTCGCATTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
**
382913 CCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
382930 TTTCGCATTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
*
382946 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
382963 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
382977 AGTAATTTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 30
0.70 0.07 0.23
Matches are distributed among these distances:
14 18 0.20
15 3 0.03
16 17 0.19
17 16 0.18
18 3 0.03
19 32 0.36
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (18 bp):
TTTCGCTTGCGATTTTCA
Found at i:383102 original size:14 final size:15
Alignment explanation
Indices: 383083--383119 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
383073 CATCAATTAA
383083 ACAAATCAAC-TTTT
1 ACAAATCAACATTTT
383097 ACAAATC-ACATTTT
1 ACAAATCAACATTTT
383111 ACAAATCAA
1 ACAAATCAA
383120 TTAAACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACATTTT
Found at i:384537 original size:21 final size:21
Alignment explanation
Indices: 384471--384537 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
384461 GTGAATCGGG
*
384471 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
384491 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
384513 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
384534 CTCT
1 CTCT
384538 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:384556 original size:42 final size:41
Alignment explanation
Indices: 384471--384593 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
384461 GTGAATCGGG
* * * *
384471 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
384513 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
384555 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
384594 TGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:384983 original size:91 final size:90
Alignment explanation
Indices: 384811--384995 Score: 264
Period size: 91 Copynumber: 2.0 Consensus size: 90
384801 ATTTCAAACT
* *
384811 TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTG---AAGAATAAACAGTTTAGC
*
384876 AGAATTGGCAGCAACCGGATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
384904 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTG-ATAATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGAAGAATAAACAGTTTAGCA
* *
384968 GTATTGGCAGTAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
384995 T
1 T
384996 AAGCAATCTA
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
91 41 0.49
93 18 0.21
95 25 0.30
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGAAGAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:386749 original size:14 final size:14
Alignment explanation
Indices: 386730--386818 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
386720 GGAAATGACT
386730 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
386744 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
*
386761 CTATCGCAACGATAGA
1 --ATCGCAACGAGAGA
*
386777 ATCGCAACGTGAAATGAAA
1 ATCGCAAC--G--A-GAGA
*
386796 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
386810 ATCGCAACG
1 ATCGCAACG
386819 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 26 0.45
15 1 0.02
16 7 0.12
17 7 0.12
18 1 0.02
19 16 0.28
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:386763 original size:33 final size:33
Alignment explanation
Indices: 386681--386835 Score: 184
Period size: 33 Copynumber: 4.5 Consensus size: 33
386671 TCTTTTGGTT
386681 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAG---A-G--AATCGCAACGC
**
386720 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
** * *
386754 GAAATGACTATCGCAACGATAGAATCGCAACGT
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
386787 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
386820 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
386836 AGCGAAATGA
Statistics
Matches: 106, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
33 75 0.71
34 11 0.10
36 1 0.01
37 1 0.01
40 18 0.17
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:386800 original size:19 final size:19
Alignment explanation
Indices: 386681--386859 Score: 127
Period size: 19 Copynumber: 10.1 Consensus size: 19
386671 TCTTTTGGTT
*
386681 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
386700 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
386720 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
386738 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
386754 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
386771 G--AT-AGAATCGCAACGT
1 GAAATGAAAATCGCAACGC
*
386787 GAAATGAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
*
386804 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
386820 GAAATGAAAATCGCAAAGC
1 GAAATGAAAATCGCAACGC
*
386839 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
386858 GA
1 GA
386860 TTTTGGTTTC
Statistics
Matches: 127, Mismatches: 16, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
14 27 0.21
15 4 0.03
16 4 0.03
17 5 0.04
18 5 0.04
19 52 0.41
20 28 0.22
21 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:386903 original size:33 final size:32
Alignment explanation
Indices: 386855--386947 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 32
386845 AAAATCGCAA
* *
386855 TGCGATTTTGGTTTCGCGTTGCGATTATCTTGT
1 TGCGATTTT-ATTTCGCGTTGCGATTATCTCGT
*
386888 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTT-ATTTCGCGTTGCGATTATCTCGT
*
386921 TGCGATAGTTATTTCCGCGTTGCGATT
1 TGCGAT-TTTATTT-CGCGTTGCGATT
386948 TTCATTCTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (32 bp):
TGCGATTTTATTTCGCGTTGCGATTATCTCGT
Found at i:386910 original size:19 final size:19
Alignment explanation
Indices: 386886--386953 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 19
386876 CGATTATCTT
386886 GTTGCGATTTTCATTTCGC
1 GTTGCGATTTTCATTTCGC
*
386905 GTTGCGA--TTC---TCTC
1 GTTGCGATTTTCATTTCGC
*
386919 GTTGCGATAGTT-ATTTCCGC
1 GTTGCGAT-TTTCATTT-CGC
386939 GTTGCGATTTTCATT
1 GTTGCGATTTTCATT
386954 CTCGAAACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 15
0.68 0.05 0.27
Matches are distributed among these distances:
14 10 0.26
17 5 0.13
19 10 0.26
20 13 0.34
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.46
Consensus pattern (19 bp):
GTTGCGATTTTCATTTCGC
Found at i:387496 original size:20 final size:20
Alignment explanation
Indices: 387471--387582 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
387461 GCTATGTAAA
387471 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
387491 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
387511 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* **
387532 TCGCATTGCGATTTACTTAAT
1 TCGCATTGCGATGTAAGT-AT
* * *
387553 T-GCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
387572 TCGCATTGCGA
1 TCGCATTGCGA
387583 ATTATGAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.08
20 52 0.65
21 22 0.28
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:387541 original size:41 final size:40
Alignment explanation
Indices: 387489--387582 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 40
387479 CGATAGTAAG
*
387489 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATT-GCATTGCGATTTACCT
* * *
387529 AATTCGCATTGCGATTTACTTAATTGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATTGCATTGCGATTTACCT
387570 ATTCGCATTGCGA
1 ATTCGCATTGCGA
387583 ATTATGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
40 13 0.27
41 32 0.67
42 3 0.06
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATTGCATTGCGATTTACCT
Found at i:387603 original size:21 final size:21
Alignment explanation
Indices: 387572--387644 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
387562 ATTTACGTAT
* *
387572 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
387593 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
387613 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
387634 TTGCAATGCGA
1 TCGCAATGCGA
387645 TAGTCAGTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:387657 original size:41 final size:41
Alignment explanation
Indices: 387572--387747 Score: 115
Period size: 41 Copynumber: 4.3 Consensus size: 41
387562 ATTTACGTAT
*
387572 TCGCATTGCGAATTATGAAAATCGCAACGCGAATACGTAAA
1 TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGTAAA
* * * *
387613 TCGCAATGCGAATTAGGAAAATTGCAATGCG-ATA-GTCAGTA
1 TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGT-A-AA
* *** * ** * * *
387654 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTAC-TTAT
1 TCGCATTGCGAATTAGGAAAATCGCAACGCGA-ATACGTAAA
* * ** *
387695 TCGCATTGCGAATTGGGAAAATCGTAACGCGAAATTGGAAAA
1 TCGCATTGCGAATTAGGAAAATCGCAACGCG-AATACGTAAA
387737 TCGCATTGCGA
1 TCGCATTGCGA
387748 TAGTCATAAT
Statistics
Matches: 97, Mismatches: 31, Indels: 13
0.69 0.22 0.09
Matches are distributed among these distances:
39 2 0.02
40 4 0.04
41 75 0.77
42 13 0.13
43 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (41 bp):
TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGTAAA
Found at i:387698 original size:20 final size:21
Alignment explanation
Indices: 387654--387705 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
387644 ATAGTCAGTA
*
387654 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
387675 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
387695 TCGCATTGCGA
1 TCGCATTGCGA
387706 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:387747 original size:21 final size:22
Alignment explanation
Indices: 387695--387747 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
387685 ATTTACTTAT
387695 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* **
387716 TCGTAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
387737 TCGCATTGCGA
1 TCGCATTGCGA
387748 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:389477 original size:17 final size:18
Alignment explanation
Indices: 389457--389491 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
389447 ATACAAACTC
*
389457 AAAAGAAGA-AAAGGAAA
1 AAAAAAAGACAAAGGAAA
389474 AAAAAAAGACAAAGGAAA
1 AAAAAAAGACAAAGGAAA
389492 GTGCGGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAAAGACAAAGGAAA
Found at i:389770 original size:39 final size:39
Alignment explanation
Indices: 389727--389867 Score: 140
Period size: 39 Copynumber: 3.4 Consensus size: 39
389717 TCTCTCTTTT
389727 TTTCCTAATCTAAAATTTCTCTCAATATTTTTTGTGCTG
1 TTTCCTAATCTAAAATTTCTCTCAATATTTTTTGTGCTG
* * * * *
389766 TTTCCTAATCTAAAAGTAAATTCTAT-AAGATTTGGGTTTCTCTCTTTT
1 TTTCCTAATCTAAAA-T---TTCTCTCAATATTT---TTTGT-GC--TG
389814 TTTCCTAATCTAAAATTTCTCTCAATATTTTTTGTGCTG
1 TTTCCTAATCTAAAATTTCTCTCAATATTTTTTGTGCTG
389853 TTTCCTAATCTAAAA
1 TTTCCTAATCTAAAA
389868 GTAAACATAC
Statistics
Matches: 81, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
39 31 0.38
40 1 0.01
41 1 0.01
42 10 0.12
43 5 0.06
44 5 0.06
45 10 0.12
46 1 0.01
47 1 0.01
48 16 0.20
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (39 bp):
TTTCCTAATCTAAAATTTCTCTCAATATTTTTTGTGCTG
Found at i:389815 original size:87 final size:87
Alignment explanation
Indices: 389689--389872 Score: 368
Period size: 87 Copynumber: 2.1 Consensus size: 87
389679 TATGTCTATT
389689 TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATCTAAAATTTCTCTCAATA
1 TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATCTAAAATTTCTCTCAATA
389754 TTTTTTGTGCTGTTTCCTAATC
66 TTTTTTGTGCTGTTTCCTAATC
389776 TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATCTAAAATTTCTCTCAATA
1 TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATCTAAAATTTCTCTCAATA
389841 TTTTTTGTGCTGTTTCCTAATC
66 TTTTTTGTGCTGTTTCCTAATC
389863 TAAAAGTAAA
1 TAAAAGTAAA
389873 CATACAATAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 97 1.00
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (87 bp):
TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATCTAAAATTTCTCTCAATA
TTTTTTGTGCTGTTTCCTAATC
Found at i:389822 original size:48 final size:48
Alignment explanation
Indices: 389689--389828 Score: 156
Period size: 48 Copynumber: 3.1 Consensus size: 48
389679 TATGTCTATT
389689 TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATC
1 TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATC
* * * * *
389737 TAAAA-T---TTCTCTCAATATTT---TTTGT-GC--TGTTTCCTAATC
1 TAAAAGTAAATTCTAT-AAGATTTGGGTTTCTCTCTTTTTTTCCTAATC
389776 TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATC
1 TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATC
389824 TAAAA
1 TAAAA
389829 TTTCTCTCAA
Statistics
Matches: 71, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
39 16 0.23
40 1 0.01
41 1 0.01
42 10 0.14
43 5 0.07
44 5 0.07
45 10 0.14
46 1 0.01
47 1 0.01
48 21 0.30
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (48 bp):
TAAAAGTAAATTCTATAAGATTTGGGTTTCTCTCTTTTTTTCCTAATC
Found at i:391344 original size:21 final size:21
Alignment explanation
Indices: 391318--391376 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
391308 ATTATCCAAT
*
391318 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
391339 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
391360 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
391377 TAATAAATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:392156 original size:164 final size:164
Alignment explanation
Indices: 391885--392212 Score: 656
Period size: 164 Copynumber: 2.0 Consensus size: 164
391875 TTTGTACAAC
391885 TTCTTCAACAGTACTCAGAACTTCTGAAGATCCAACAACACTCGATTCATCATTATTTGTTTCTT
1 TTCTTCAACAGTACTCAGAACTTCTGAAGATCCAACAACACTCGATTCATCATTATTTGTTTCTT
391950 CCTCCTCTTGAGAAGCTCGAACAAATTTAAATCACTATAATATCTGTAATAAACGAACAACAATT
66 CCTCCTCTTGAGAAGCTCGAACAAATTTAAATCACTATAATATCTGTAATAAACGAACAACAATT
392015 TTTGTGAAAATATTACTATTAATGAATATATTGA
131 TTTGTGAAAATATTACTATTAATGAATATATTGA
392049 TTCTTCAACAGTACTCAGAACTTCTGAAGATCCAACAACACTCGATTCATCATTATTTGTTTCTT
1 TTCTTCAACAGTACTCAGAACTTCTGAAGATCCAACAACACTCGATTCATCATTATTTGTTTCTT
392114 CCTCCTCTTGAGAAGCTCGAACAAATTTAAATCACTATAATATCTGTAATAAACGAACAACAATT
66 CCTCCTCTTGAGAAGCTCGAACAAATTTAAATCACTATAATATCTGTAATAAACGAACAACAATT
392179 TTTGTGAAAATATTACTATTAATGAATATATTGA
131 TTTGTGAAAATATTACTATTAATGAATATATTGA
392213 ACGATAACAT
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (164 bp):
TTCTTCAACAGTACTCAGAACTTCTGAAGATCCAACAACACTCGATTCATCATTATTTGTTTCTT
CCTCCTCTTGAGAAGCTCGAACAAATTTAAATCACTATAATATCTGTAATAAACGAACAACAATT
TTTGTGAAAATATTACTATTAATGAATATATTGA
Found at i:394851 original size:2 final size:2
Alignment explanation
Indices: 394844--394891 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
394834 TAGTTTTTGG
394844 TA TA TA TA TA TA 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 TA TA TA TA TA TA
394886 TA TA TA
1 TA TA TA
394892 ATTACTCACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:402753 original size:24 final size:20
Alignment explanation
Indices: 402719--402763 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 20
402709 TTAATTATTT
402719 AAAAAAATTAAATAAAAATATA
1 AAAAAAATT-AATAAAAA-ATA
402741 AAAAAACATTTAATAAAAAATA
1 AAAAAA-A-TTAATAAAAAATA
402763 A
1 A
402764 TTTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 10 0.48
23 9 0.43
24 2 0.10
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAAAATTAATAAAAAATA
Found at i:402755 original size:23 final size:21
Alignment explanation
Indices: 402719--402763 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
402709 TTAATTATTT
402719 AAAAAAATTAAATAAAAATATA
1 AAAAAAATTAAATAAAAA-ATA
*
402741 AAAAAACATTTAATAAAAAATA
1 AAAAAA-ATTAAATAAAAAATA
402763 A
1 A
402764 TTTTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAAATTAAATAAAAAATA
Found at i:407637 original size:25 final size:24
Alignment explanation
Indices: 407594--407648 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
407584 AAGAGGAATA
*
407594 AAAAT-ATATAATTATTAAGT-GC
1 AAAATAATATAATTAATAAGTAGC
*
407616 AAAATAATATAATGATAATAAGTAGT
1 AAAATAATATAAT--TAATAAGTAGC
407642 AAAATAA
1 AAAATAA
407649 AAAAAAACGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
23 7 0.26
25 7 0.26
26 8 0.30
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (24 bp):
AAAATAATATAATTAATAAGTAGC
Found at i:408072 original size:51 final size:50
Alignment explanation
Indices: 408015--408124 Score: 211
Period size: 51 Copynumber: 2.2 Consensus size: 50
408005 ACATATAATG
408015 ATAATAATAGTAGCAAAAGAGAAAAATATATTTATATACGTTAATAGTAAA
1 ATAATAATAGTAGCAAAAGAGAAAAATATATTTATATACG-TAATAGTAAA
408066 ATAATAATAGTAGCAAAAGAGAAAAATATATTTATATACGTAATAGTAAA
1 ATAATAATAGTAGCAAAAGAGAAAAATATATTTATATACGTAATAGTAAA
408116 ATAATAATA
1 ATAATAATA
408125 AATATAATAG
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 19 0.32
51 40 0.68
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (50 bp):
ATAATAATAGTAGCAAAAGAGAAAAATATATTTATATACGTAATAGTAAA
Found at i:408148 original size:2 final size:2
Alignment explanation
Indices: 408136--408166 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
408126 ATATAATAGT
*
408136 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
408167 GATAACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:412279 original size:3 final size:3
Alignment explanation
Indices: 412271--412295 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
412261 TTAAATGCAA
412271 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
412296 GGGATCACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:416110 original size:22 final size:22
Alignment explanation
Indices: 416067--416111 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
416057 ATGCAGCTCC
* *
416067 CAGCTCCCTTTGTTGAATTTTT
1 CAGCCCCCTTTGTTGAACTTTT
416089 CAGCCCCCTTTGTTTG-ACTTTT
1 CAGCCCCCTTTG-TTGAACTTTT
416111 C
1 C
416112 CAACAATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.11, C:0.29, G:0.13, T:0.47
Consensus pattern (22 bp):
CAGCCCCCTTTGTTGAACTTTT
Found at i:420175 original size:17 final size:16
Alignment explanation
Indices: 420138--420169 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
420128 ATCTCCAAAA
420138 AAAATTTACTATTCAT
1 AAAATTTACTATTCAT
420154 AAAATTTACTATTCAT
1 AAAATTTACTATTCAT
420170 GTAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATTTACTATTCAT
Found at i:428891 original size:21 final size:21
Alignment explanation
Indices: 428865--428913 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
428855 CCCACAAGCG
428865 ATACCCCTTTACTCCATCAGC
1 ATACCCCTTTACTCCATCAGC
428886 ATACCCCTTTACTCCATCAGC
1 ATACCCCTTTACTCCATCAGC
428907 ATACCCC
1 ATACCCC
428914 AAGAATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.45, G:0.04, T:0.27
Consensus pattern (21 bp):
ATACCCCTTTACTCCATCAGC
Found at i:436174 original size:15 final size:15
Alignment explanation
Indices: 436156--436191 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
436146 AATTTAAAGA
436156 ACCTCATGTGTCACC
1 ACCTCATGTGTCACC
436171 ACCTCATGTGTCACC
1 ACCTCATGTGTCACC
436186 ACCTCA
1 ACCTCA
436192 ATAGTAGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.42, G:0.11, T:0.25
Consensus pattern (15 bp):
ACCTCATGTGTCACC
Found at i:438159 original size:31 final size:31
Alignment explanation
Indices: 438087--438159 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
438077 GTTAACCCAT
*
438087 GGTGACCACATCTTAAATAAATAAAAACAAA
1 GGTGACCATATCTTAAATAAATAAAAACAAA
* * * * *
438118 AGTAATCATATCTTAATTAAATAAAAACGAA
1 GGTGACCATATCTTAAATAAATAAAAACAAA
*
438149 GGTGGCCATAT
1 GGTGACCATAT
438160 ATAATGTATT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (31 bp):
GGTGACCATATCTTAAATAAATAAAAACAAA
Found at i:441903 original size:2 final size:2
Alignment explanation
Indices: 441896--441920 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
441886 TTTGGGATTT
441896 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
441921 AGATTACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:442083 original size:5 final size:5
Alignment explanation
Indices: 442063--442113 Score: 77
Period size: 5 Copynumber: 10.2 Consensus size: 5
442053 GAATTGAAGT
*
442063 AGTGA AGTGTA A-TGA AGTGA AGTGA AGTGA AGTGA AGTGA GGTGA AGTGA
1 AGTGA AGTG-A AGTGA AGTGA AGTGA AGTGA AGTGA AGTGA AGTGA AGTGA
442113 A
1 A
442114 ATAGGGAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
4 2 0.05
5 38 0.90
6 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.22
Consensus pattern (5 bp):
AGTGA
Found at i:442201 original size:12 final size:12
Alignment explanation
Indices: 442169--442202 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
442159 AGAAAGAAAA
*
442169 ATATATATATAT
1 ATATATATTTAT
442181 ATATATATTTAT
1 ATATATATTTAT
*
442193 ATTTATATTT
1 ATATATATTT
442203 CCCGATTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATATATATTTAT
Found at i:450492 original size:19 final size:21
Alignment explanation
Indices: 450459--450502 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
450449 TTGTTCTCTA
**
450459 TTAATTTTTTGTCAA-ATT-T
1 TTAATTTTTACTCAATATTAT
450478 TTAATTTTTACTCAATATTAT
1 TTAATTTTTACTCAATATTAT
450499 TTAA
1 TTAA
450503 ATATATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 3 0.14
21 5 0.24
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAATTTTTACTCAATATTAT
Found at i:467077 original size:20 final size:20
Alignment explanation
Indices: 467052--467092 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
467042 ATCTTACATA
*
467052 GGGGTATCGGTACCCTATGG
1 GGGGTATCAGTACCCTATGG
*
467072 GGGGTATCAGTACCCTCTGG
1 GGGGTATCAGTACCCTATGG
467092 G
1 G
467093 TAATATCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.22, G:0.39, T:0.24
Consensus pattern (20 bp):
GGGGTATCAGTACCCTATGG
Found at i:467447 original size:14 final size:14
Alignment explanation
Indices: 467416--467463 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
467406 TTTTCTTATT
*
467416 GAAAATCATTTT-A
1 GAAAATAATTTTGA
467429 GAAAATAATTTTGA
1 GAAAATAATTTTGA
* *
467443 GAAAATTATTACTGA
1 GAAAATAATT-TTGA
467458 GAAAAT
1 GAAAAT
467464 TATTACTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 11 0.37
14 10 0.33
15 9 0.30
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.33
Consensus pattern (14 bp):
GAAAATAATTTTGA
Found at i:467460 original size:15 final size:15
Alignment explanation
Indices: 467440--467470 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
467430 AAAATAATTT
467440 TGAGAAAATTATTAC
1 TGAGAAAATTATTAC
467455 TGAGAAAATTATTAC
1 TGAGAAAATTATTAC
467470 T
1 T
467471 CTCCCTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (15 bp):
TGAGAAAATTATTAC
Found at i:467767 original size:16 final size:16
Alignment explanation
Indices: 467732--467782 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 16
467722 AACATTTAAG
467732 TTCAAACATCCAAAACAAA
1 TTCAAACATCC---ACAAA
467751 TTCAAACATCCACAAA
1 TTCAAACATCCACAAA
*
467767 TTCAAACATTCACAAA
1 TTCAAACATCCACAAA
467783 CATCTAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 20 0.65
19 11 0.35
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (16 bp):
TTCAAACATCCACAAA
Found at i:469737 original size:23 final size:23
Alignment explanation
Indices: 469677--469730 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
469667 ACCCTCATGT
*
469677 GGGGGTATTGGTACCCATTCAAA
1 GGGGGTATTGGTACCCATGCAAA
*
469700 GAGGGTATTGGTACCCATGCAAA
1 GGGGGTATTGGTACCCATGCAAA
469723 GGGGGTAT
1 GGGGGTAT
469731 CGATACCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (23 bp):
GGGGGTATTGGTACCCATGCAAA
Found at i:473576 original size:22 final size:21
Alignment explanation
Indices: 473534--473573 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
473524 TAAGAATATT
473534 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
473555 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
473574 ATAAACTCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:475491 original size:19 final size:20
Alignment explanation
Indices: 475467--475505 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
475457 GTTATAAGAT
475467 TGGGGGTATCGGTA-CCTCC
1 TGGGGGTATCGGTATCCTCC
475486 TGGGGGTATCGGTATCCTCC
1 TGGGGGTATCGGTATCCTCC
475506 GAGCATTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.10, C:0.26, G:0.36, T:0.28
Consensus pattern (20 bp):
TGGGGGTATCGGTATCCTCC
Found at i:477799 original size:38 final size:38
Alignment explanation
Indices: 477704--477790 Score: 107
Period size: 35 Copynumber: 2.5 Consensus size: 38
477694 AATATAATTA
*
477704 TAAAT-ATAACAAACTTACAAT-A--AATATTAAATGG
1 TAAATAATAACAAAATTACAATAACTAATATTAAATGG
*
477738 TAAATAATAACCAAATTACAATAACTAATATTAAATGG
1 TAAATAATAACAAAATTACAATAACTAATATTAAATGG
477776 T-AAT-A-AACAAAATTA
1 TAAATAATAACAAAATTA
477791 ACAAAATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
34 5 0.11
35 23 0.50
36 2 0.04
37 3 0.07
38 13 0.28
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.29
Consensus pattern (38 bp):
TAAATAATAACAAAATTACAATAACTAATATTAAATGG
Found at i:477820 original size:34 final size:34
Alignment explanation
Indices: 477780--477868 Score: 126
Period size: 34 Copynumber: 2.6 Consensus size: 34
477770 AAATGGTAAT
* *
477780 AAACAAAATTAACAAAATAAA-TTAACAAAAAGTC
1 AAACAAAATTAACAAAATAAATTTAA-AAAAAATA
*
477814 CAACAAAATTAACAAAATAAATTTAAAAAAAATA
1 AAACAAAATTAACAAAATAAATTTAAAAAAAATA
*
477848 AAACTAAATTAACAAAATAAA
1 AAACAAAATTAACAAAATAAA
477869 GTAAGTATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 45 0.92
35 4 0.08
ACGTcount: A:0.70, C:0.10, G:0.01, T:0.19
Consensus pattern (34 bp):
AAACAAAATTAACAAAATAAATTTAAAAAAAATA
Found at i:477859 original size:20 final size:19
Alignment explanation
Indices: 477827--477868 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
477817 CAAAATTAAC
477827 AAAATAAATTTAAAAAAAAT
1 AAAATAAATTT-AAAAAAAT
*
477847 AAAACTAAA-TTAACAAAAT
1 AAAA-TAAATTTAAAAAAAT
477866 AAA
1 AAA
477869 GTAAGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 10 0.50
20 6 0.30
21 4 0.20
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAATAAATTTAAAAAAAT
Found at i:477909 original size:15 final size:15
Alignment explanation
Indices: 477889--477923 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
477879 AATTATAAAT
477889 AATAAAAAAAATTAC
1 AATAAAAAAAATTAC
*
477904 AAT-AAAAAAATTCC
1 AATAAAAAAAATTAC
477918 AATAAA
1 AATAAA
477924 CAACTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAAAAAATTAC
Found at i:479022 original size:30 final size:30
Alignment explanation
Indices: 478988--479090 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
478978 CCCGAAGGAC
478988 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
479018 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
*
479048 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
* *
479078 CTGTCCATAGGTC
1 CTATCCAGAGGTC
479091 CCGAAGAACC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAA
Found at i:479114 original size:31 final size:31
Alignment explanation
Indices: 479076--479203 Score: 123
Period size: 31 Copynumber: 4.1 Consensus size: 31
479066 GATCCTCGGT
* *
479076 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
479107 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
479138 TACCGTCCATATGTCTCGAATG-ACATAGGTAA
1 AACTGTCCATATGTCCCGAA-GAACATAGGT-A
* * * *
479170 AACTATCCATATGTTCAGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
479201 AAC
1 AAC
479204 CCTCGACTCT
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
31 53 0.70
32 23 0.30
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:480555 original size:21 final size:21
Alignment explanation
Indices: 480529--480574 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
480519 ATTTTATTCG
* *
480529 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
480550 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
480571 CTTG
1 CTTG
480575 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:481514 original size:19 final size:19
Alignment explanation
Indices: 481492--481529 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
481482 TTGTGACGGT
*
481492 GCACGTCTCTGTCGACGTC
1 GCACGTCTCTATCGACGTC
481511 GCACGTCTCTATCGACGTC
1 GCACGTCTCTATCGACGTC
481530 ACTGAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.37, G:0.24, T:0.26
Consensus pattern (19 bp):
GCACGTCTCTATCGACGTC
Found at i:483113 original size:17 final size:18
Alignment explanation
Indices: 483095--483127 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
483085 TAATTAAATA
483095 AAATA-TTAAA-AAATTT
1 AAATAGTTAAATAAATTT
483111 AAATAGTTAAATAAATT
1 AAATAGTTAAATAAATT
483128 ACTAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAATAGTTAAATAAATTT
Found at i:484173 original size:177 final size:177
Alignment explanation
Indices: 483877--484234 Score: 716
Period size: 177 Copynumber: 2.0 Consensus size: 177
483867 AAATACCCTC
483877 TTTTCCCGTTTACCTCCGCTTCTTCTCCCAAGCGTTCTTTGTTCTTGATTTTGATTTCACAATCT
1 TTTTCCCGTTTACCTCCGCTTCTTCTCCCAAGCGTTCTTTGTTCTTGATTTTGATTTCACAATCT
483942 TATCTCCAATCCAATCTCTTTGATTTTCCACCGTTAATTCTTCCATTCTTGTATCTTCCACGATT
66 TATCTCCAATCCAATCTCTTTGATTTTCCACCGTTAATTCTTCCATTCTTGTATCTTCCACGATT
484007 CCAAGCTCTCTCTCTTATCTTCTCTTAAATCCCATATTTTCCCCAGA
131 CCAAGCTCTCTCTCTTATCTTCTCTTAAATCCCATATTTTCCCCAGA
484054 TTTTCCCGTTTACCTCCGCTTCTTCTCCCAAGCGTTCTTTGTTCTTGATTTTGATTTCACAATCT
1 TTTTCCCGTTTACCTCCGCTTCTTCTCCCAAGCGTTCTTTGTTCTTGATTTTGATTTCACAATCT
484119 TATCTCCAATCCAATCTCTTTGATTTTCCACCGTTAATTCTTCCATTCTTGTATCTTCCACGATT
66 TATCTCCAATCCAATCTCTTTGATTTTCCACCGTTAATTCTTCCATTCTTGTATCTTCCACGATT
484184 CCAAGCTCTCTCTCTTATCTTCTCTTAAATCCCATATTTTCCCCAGA
131 CCAAGCTCTCTCTCTTATCTTCTCTTAAATCCCATATTTTCCCCAGA
484231 TTTT
1 TTTT
484235 TTTCTTTTCC
Statistics
Matches: 181, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 181 1.00
ACGTcount: A:0.17, C:0.31, G:0.07, T:0.45
Consensus pattern (177 bp):
TTTTCCCGTTTACCTCCGCTTCTTCTCCCAAGCGTTCTTTGTTCTTGATTTTGATTTCACAATCT
TATCTCCAATCCAATCTCTTTGATTTTCCACCGTTAATTCTTCCATTCTTGTATCTTCCACGATT
CCAAGCTCTCTCTCTTATCTTCTCTTAAATCCCATATTTTCCCCAGA
Found at i:487141 original size:15 final size:15
Alignment explanation
Indices: 487121--487151 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
487111 CAACAAATAG
487121 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
487136 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
487151 A
1 A
487152 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:488184 original size:30 final size:30
Alignment explanation
Indices: 488149--488240 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 30
488139 CACAGTCCAG
**
488149 GACTTAGTTCCATCACCACCGTTCAAAGTA
1 GACTTAGTTCCATCACCACCCATCAAAGTA
* *
488179 GACTTAGTTCCATCACCGCCCATCAAATTA
1 GACTTAGTTCCATCACCACCCATCAAAGTA
* * * * *
488209 AACTTAGATCCATCACCGCCAATCAAATTA
1 GACTTAGTTCCATCACCACCCATCAAAGTA
488239 GA
1 GA
488241 TTCTCCTCTC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (30 bp):
GACTTAGTTCCATCACCACCCATCAAAGTA
Found at i:492164 original size:22 final size:22
Alignment explanation
Indices: 492139--492186 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
492129 CCCATTCCAC
*
492139 TGTTTGGTACCTGTTCCGCCGT
1 TGTTTGGTACCTATTCCGCCGT
492161 TGTTTGGTACCTATTCCGCCGT
1 TGTTTGGTACCTATTCCGCCGT
492183 TGTT
1 TGTT
492187 GATAACTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.06, C:0.25, G:0.25, T:0.44
Consensus pattern (22 bp):
TGTTTGGTACCTATTCCGCCGT
Found at i:493564 original size:2 final size:2
Alignment explanation
Indices: 493524--493548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
493514 TCCTTGAGGT
493524 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
493549 TACACACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:504639 original size:11 final size:11
Alignment explanation
Indices: 504623--504647 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
504613 GTCGGTTCCT
504623 TCAAATATGAA
1 TCAAATATGAA
504634 TCAAATATGAA
1 TCAAATATGAA
504645 TCA
1 TCA
504648 GTCTCTTCCG
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:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (11 bp):
TCAAATATGAA
Found at i:507890 original size:2 final size:2
Alignment explanation
Indices: 507883--507930 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
507873 TTATGAAAGA
507883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
507925 AT AT AT
1 AT AT AT
507931 GACTACATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:508482 original size:23 final size:23
Alignment explanation
Indices: 508452--508519 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
508442 CATCTTATAT
508452 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
508475 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* * *
508498 GGTACTTCGATGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
508520 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:511703 original size:25 final size:26
Alignment explanation
Indices: 511675--511725 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
511665 TTAATAATTG
* *
511675 AAAATTAGTTATGAAAAAATAAAAAA
1 AAAATTAATTATAAAAAAATAAAAAA
*
511701 AAAATTAATTTTAAAAAAATAAAAA
1 AAAATTAATTATAAAAAAATAAAAA
511726 CTTTTTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAATTAATTATAAAAAAATAAAAAA
Found at i:516573 original size:29 final size:29
Alignment explanation
Indices: 516535--516608 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 29
516525 AACAAAATAA
516535 TATATATTTGATTTTTTAGTAATTTAA-TTTT
1 TATAT-TTTGATTTTTTA-T-ATTTAATTTTT
*
516566 TAT-TTTTGGTATTTTTATATTTAATTTTT
1 TATATTTTGAT-TTTTTATATTTAATTTTT
516595 TATATTTTGTATTT
1 TATATTTTG-ATTT
516609 AAACTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
28 6 0.16
29 13 0.35
30 14 0.38
31 4 0.11
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (29 bp):
TATATTTTGATTTTTTATATTTAATTTTT
Found at i:516592 original size:22 final size:21
Alignment explanation
Indices: 516537--516610 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
516527 CAAAATAATA
* *
516537 TATATTTGATTTTTTAGTAATT
1 TATATTTAATTTTTTA-TATTT
*
516559 TA-ATTTTTATTTTTGGTAT-TTT
1 TATA-TTTAATTTTT--TATATTT
516581 TATATTTAATTTTTTATATTT
1 TATATTTAATTTTTTATATTT
*
516602 TGTATTTAA
1 TATATTTAA
516611 ACTATTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
20 3 0.07
21 12 0.28
22 24 0.56
23 2 0.05
24 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TATATTTAATTTTTTATATTT
Found at i:516623 original size:29 final size:28
Alignment explanation
Indices: 516556--516625 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
516546 TTTTTTAGTA
**
516556 ATTTAATTTTTATTTTTGGTATTTTTAT
1 ATTTAATTTTTATTTTTGGTATTTAAAT
516584 ATTTAATTTTTTATATTTT-GTATTTAAACT
1 ATTTAA-TTTTTAT-TTTTGGTATTTAAA-T
*
516614 ATTTTATTTTTA
1 ATTTAATTTTTA
516626 AAAATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.17
29 20 0.56
30 10 0.28
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (28 bp):
ATTTAATTTTTATTTTTGGTATTTAAAT
Found at i:516780 original size:21 final size:21
Alignment explanation
Indices: 516747--516792 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
516737 ATCGCTAATT
*
516747 AACACCGTAAAGTGCCACATC
1 AACAACGTAAAGTGCCACATC
* *
516768 AACAACGTGAAGTGTCACATC
1 AACAACGTAAAGTGCCACATC
516789 AACA
1 AACA
516793 TAATAACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.15
Consensus pattern (21 bp):
AACAACGTAAAGTGCCACATC
Found at i:518916 original size:21 final size:21
Alignment explanation
Indices: 518875--518917 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
518865 GAATGGAAAG
* *
518875 ATAGAGGAATAGGAGAGTGGA
1 ATAGAGAAATAGGAGAATGGA
518896 ATAGAGAAACTAGG-GAATGGA
1 ATAGAGAAA-TAGGAGAATGGA
518917 A
1 A
518918 ATCTTCACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.47, C:0.02, G:0.37, T:0.14
Consensus pattern (21 bp):
ATAGAGAAATAGGAGAATGGA
Found at i:519271 original size:21 final size:21
Alignment explanation
Indices: 519230--519272 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
519220 GAATGGAAAG
* *
519230 ATAGAGGAATAGGAGAGTGGA
1 ATAGAGAAATAGGAGAATGGA
519251 ATAGAGAAACTAGG-GAATGGA
1 ATAGAGAAA-TAGGAGAATGGA
519272 A
1 A
519273 ATCTTCACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.47, C:0.02, G:0.37, T:0.14
Consensus pattern (21 bp):
ATAGAGAAATAGGAGAATGGA
Found at i:519410 original size:355 final size:355
Alignment explanation
Indices: 518752--519450 Score: 1362
Period size: 355 Copynumber: 2.0 Consensus size: 355
518742 TTGAGATTAT
*
518752 ATTGTTTTTGCTTACTCTTTGCACATCTGGCAATTGTTCTTCTTTACAAGCAAGGGAAAGAATAC
1 ATTGTTCTTGCTTACTCTTTGCACATCTGGCAATTGTTCTTCTTTACAAGCAAGGGAAAGAATAC
*
518817 TTGAAGAGTAGATAATATAGAAATTTTCAGGAAAAGGGAGAGGAAATAGAATGGAAAGATAGAGG
66 TTGAAGAGTAGATAATAGAGAAATTTTCAGGAAAAGGGAGAGGAAATAGAATGGAAAGATAGAGG
518882 AATAGGAGAGTGGAATAGAGAAACTAGGGAATGGAAATCTTCACACTTGAGGTCAAATGTCAATT
131 AATAGGAGAGTGGAATAGAGAAACTAGGGAATGGAAATCTTCACACTTGAGGTCAAATGTCAATT
*
518947 CAATATATGTCAATAACTGAAAGTTACTAGAAACTGAAAGGACATACGTCCACATAAGCTACTTC
196 CAATATATGTCAATAACTGAAAGCTACTAGAAACTGAAAGGACATACGTCCACATAAGCTACTTC
519012 CTAAACACCCGAGTTCATATGAAATGCCACATTTAACCTTAAATGCCCTTATAGTTTCCTAAATA
261 CTAAACACCCGAGTTCATATGAAATGCCACATTTAACCTTAAATGCCCTTATAGTTTCCTAAATA
519077 CTACAAGTTACATCGAGAAATTTTCAGGAA
326 CTACAAGTTACATCGAGAAATTTTCAGGAA
*
519107 ATTGTTCTTGCTTACTCTTTGCACATCTGGCAATTGTTCTTCTTTGCAAGCAAGGGAAAGAATAC
1 ATTGTTCTTGCTTACTCTTTGCACATCTGGCAATTGTTCTTCTTTACAAGCAAGGGAAAGAATAC
519172 TTGAAGAGTAGATAATAGAGAAATTTTCAGGAAAAGGGAGAGGAAATAGAATGGAAAGATAGAGG
66 TTGAAGAGTAGATAATAGAGAAATTTTCAGGAAAAGGGAGAGGAAATAGAATGGAAAGATAGAGG
519237 AATAGGAGAGTGGAATAGAGAAACTAGGGAATGGAAATCTTCACACTTGAGGTCAAATGTCAATT
131 AATAGGAGAGTGGAATAGAGAAACTAGGGAATGGAAATCTTCACACTTGAGGTCAAATGTCAATT
519302 CAATATATGTCAATAACTGAAAGCTACTAGAAACTGAAAGGACATACGTCCACATAAGCTACTTC
196 CAATATATGTCAATAACTGAAAGCTACTAGAAACTGAAAGGACATACGTCCACATAAGCTACTTC
519367 CTAAACACCCGAGTTCATATGAAATGCCACATTTAACCTTAAATGCCCTTATAGTTTCCTAAATA
261 CTAAACACCCGAGTTCATATGAAATGCCACATTTAACCTTAAATGCCCTTATAGTTTCCTAAATA
519432 CTACAAGTTACATCGAGAA
326 CTACAAGTTACATCGAGAA
519451 TCTAAAATAC
Statistics
Matches: 340, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
355 340 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (355 bp):
ATTGTTCTTGCTTACTCTTTGCACATCTGGCAATTGTTCTTCTTTACAAGCAAGGGAAAGAATAC
TTGAAGAGTAGATAATAGAGAAATTTTCAGGAAAAGGGAGAGGAAATAGAATGGAAAGATAGAGG
AATAGGAGAGTGGAATAGAGAAACTAGGGAATGGAAATCTTCACACTTGAGGTCAAATGTCAATT
CAATATATGTCAATAACTGAAAGCTACTAGAAACTGAAAGGACATACGTCCACATAAGCTACTTC
CTAAACACCCGAGTTCATATGAAATGCCACATTTAACCTTAAATGCCCTTATAGTTTCCTAAATA
CTACAAGTTACATCGAGAAATTTTCAGGAA
Found at i:523216 original size:15 final size:15
Alignment explanation
Indices: 523196--523226 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
523186 GGTTCCTTCA
523196 GATGCTACCAATGAG
1 GATGCTACCAATGAG
523211 GATGCTACCAATGAG
1 GATGCTACCAATGAG
523226 G
1 G
523227 CTCCTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (15 bp):
GATGCTACCAATGAG
Found at i:523233 original size:15 final size:15
Alignment explanation
Indices: 523200--523233 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
523190 CCTTCAGATG
*
523200 CTACCAATGAGGATG
1 CTACCAATGAGGATC
*
523215 CTACCAATGAGGCTC
1 CTACCAATGAGGATC
523230 CTAC
1 CTAC
523234 AAAAAGTGAA
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:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (15 bp):
CTACCAATGAGGATC
Found at i:523805 original size:39 final size:39
Alignment explanation
Indices: 523751--523828 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
523741 TTGGAAGACG
*
523751 TGAATAAAATTCCCATTCCGAGATCTGTACATGGCTTCA
1 TGAATAAAACTCCCATTCCGAGATCTGTACATGGCTTCA
523790 TGAATAAAACTCCCATTCCGAGATCTGTACATGGCTTCA
1 TGAATAAAACTCCCATTCCGAGATCTGTACATGGCTTCA
523829 ATGTACCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (39 bp):
TGAATAAAACTCCCATTCCGAGATCTGTACATGGCTTCA
Found at i:524826 original size:2 final size:2
Alignment explanation
Indices: 524819--524853 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
524809 AATGGGTTGT
524819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
524854 GTATTGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:527265 original size:17 final size:17
Alignment explanation
Indices: 527233--527266 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
527223 ACATAAATAA
527233 AATAAATAAGTAAAAAC
1 AATAAATAAGTAAAAAC
527250 AATAACATAAGTAAAAA
1 AATAA-ATAAGTAAAAA
527267 TAAATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (17 bp):
AATAAATAAGTAAAAAC
Found at i:529266 original size:141 final size:141
Alignment explanation
Indices: 529074--529344 Score: 393
Period size: 141 Copynumber: 1.9 Consensus size: 141
529064 CTGGTCAAGG
* ** *
529074 GATGACACGGCTCATACGCGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTCGGTTCC
1 GATGACACGGCTCATACACGATGAAGAACTCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCC
529139 TACGTGATGAGGACGGCTGATTAT-CTAAGGTTGACACGGCTCCTACGTGATGAGGA-AGTCTGG
66 TACGTGATGAGGACGGCTGATTATCCTAAGGTTGACAC-GCTCCTACGTGATGAGGAGA-TCTGG
529202 TCGTCTAAGGGTA
129 TCGTCTAAGGGTA
* * * *
529215 GATGACATGGTTCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
1 GATGACACGGCTCATACACGATGAAGAACTCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCC
* * * * *
529280 TACGTGATGATGACGGCTGGTTATCCTAATGTTGACACTCTCCTATGTGATGAGGAGATCTGGTC
66 TACGTGATGAGGACGGCTGATTATCCTAAGGTTGACACGCTCCTACGTGATGAGGAGATCTGGTC
529345 AGTTGATGTT
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
141 102 0.89
142 13 0.11
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (141 bp):
GATGACACGGCTCATACACGATGAAGAACTCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCC
TACGTGATGAGGACGGCTGATTATCCTAAGGTTGACACGCTCCTACGTGATGAGGAGATCTGGTC
GTCTAAGGGTA
Found at i:542060 original size:14 final size:14
Alignment explanation
Indices: 542041--542071 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
542031 ATAATATAAT
542041 AATGATTATTAACC
1 AATGATTATTAACC
542055 AATGATTATTAACC
1 AATGATTATTAACC
542069 AAT
1 AAT
542072 ATATATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (14 bp):
AATGATTATTAACC
Found at i:542167 original size:17 final size:17
Alignment explanation
Indices: 542135--542168 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
542125 ACATAAATAA
542135 AATAAATAAGTAAAAAC
1 AATAAATAAGTAAAAAC
542152 AATAACATAAGTAAAAA
1 AATAA-ATAAGTAAAAA
542169 TAAATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (17 bp):
AATAAATAAGTAAAAAC
Found at i:543706 original size:3 final size:3
Alignment explanation
Indices: 543698--543737 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
543688 TGTAATTAAT
**
543698 TAA TAA TAA TAAA TAA CGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
543738 AAAAAGACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:550789 original size:29 final size:28
Alignment explanation
Indices: 550739--550798 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
550729 TTTTAAAATA
550739 TTTAAAACATTTAATATAATATCTATATT
1 TTTAAAACATTTAATATAATATCTA-ATT
* * * *
550768 TTTAAAATATTTAATTTCATATTTAATT
1 TTTAAAACATTTAATATAATATCTAATT
550796 TTT
1 TTT
550799 TATTTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTAAAACATTTAATATAATATCTAATT
Found at i:553070 original size:31 final size:31
Alignment explanation
Indices: 553032--553114 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
553022 CTTTTAAAAC
*
553032 TTGCAATATAGTCCCTTAACATTTAGTCCGT
1 TTGCAATATAGTCCCTCAACATTTAGTCCGT
*
553063 TTGCAATATTGTCCCTCAACATTTAGTCCGT
1 TTGCAATATAGTCCCTCAACATTTAGTCCGT
*
553094 TTGCAATATGGTCCC-CAACAT
1 TTGCAATATAGTCCCTCAACAT
553115 AACTGTTGGG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 6 0.12
31 43 0.88
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (31 bp):
TTGCAATATAGTCCCTCAACATTTAGTCCGT
Found at i:553388 original size:13 final size:12
Alignment explanation
Indices: 553371--553395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
553361 AAATATATGA
553371 TAAAAAGATAAT
1 TAAAAAGATAAT
553383 TAAAAAGATAAT
1 TAAAAAGATAAT
553395 T
1 T
553396 TTATCTATTT
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:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (12 bp):
TAAAAAGATAAT
Found at i:554415 original size:27 final size:27
Alignment explanation
Indices: 554365--554417 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
554355 GTCGTTTTTA
* *
554365 TTTTTCTTTAATTAAGATATAGTCATT
1 TTTTTATTTAATTAAGATACAGTCATT
*
554392 TTTTTATTTAATTAAGATGCAGTCAT
1 TTTTTATTTAATTAAGATACAGTCAT
554418 CCCGAGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (27 bp):
TTTTTATTTAATTAAGATACAGTCATT
Found at i:555234 original size:24 final size:26
Alignment explanation
Indices: 555184--555263 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 26
555174 TATAATGTAA
* *
555184 TTATATATA-TTAACTTAAAT-TATT
1 TTATATAAACTTAATTTAAATATATT
555208 TT-TATAACAACTT-A-TTAAATATATT
1 TTATAT-A-AACTTAATTTAAATATATT
*
555233 TTATTATAAACTTAATTTAAAAATATT
1 TTA-TATAAACTTAATTTAAATATATT
555260 TTAT
1 TTAT
555264 TTTTATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
23 3 0.07
24 9 0.20
25 13 0.28
26 5 0.11
27 16 0.35
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (26 bp):
TTATATAAACTTAATTTAAATATATT
Found at i:559456 original size:19 final size:19
Alignment explanation
Indices: 559432--559469 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
559422 TTTTCCATAG
559432 CCTTTACTTCATCAAATAT
1 CCTTTACTTCATCAAATAT
559451 CCTTTACTTCATCAAATAT
1 CCTTTACTTCATCAAATAT
559470 TCTGCGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (19 bp):
CCTTTACTTCATCAAATAT
Found at i:560652 original size:10 final size:10
Alignment explanation
Indices: 560627--560662 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
560617 GATCCGACCT
560627 GTTGACCG-C
1 GTTGACCGTC
*
560636 ATTGACCGTC
1 GTTGACCGTC
560646 GTTGACCGTC
1 GTTGACCGTC
560656 GTTGACC
1 GTTGACC
560663 AGAACTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.14, C:0.31, G:0.28, T:0.28
Consensus pattern (10 bp):
GTTGACCGTC
Found at i:562800 original size:24 final size:24
Alignment explanation
Indices: 562766--562848 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
562756 AATTCTGTTA
*
562766 TGATACCTGACATGGATTTTGATC
1 TGATACTTGACATGGATTTTGATC
* *
562790 TGATACTTGACCTGGATTCTGATC
1 TGATACTTGACATGGATTTTGATC
* *
562814 TGATACTTGACATGAATTTTGATT
1 TGATACTTGACATGGATTTTGATC
*
562838 TGATTCTTGAC
1 TGATACTTGAC
562849 TTGAATTATG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
TGATACTTGACATGGATTTTGATC
Found at i:562809 original size:48 final size:48
Alignment explanation
Indices: 562757--562848 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
562747 TTCTATTTGA
* *
562757 ATTCTGTTATGATACCTGACATGGATTTTGATCTGATACTTGACCTGG
1 ATTCTGATATGATACCTGACATGAATTTTGATCTGATACTTGACCTGG
* * * *
562805 ATTCTGATCTGATACTTGACATGAATTTTGATTTGATTCTTGAC
1 ATTCTGATATGATACCTGACATGAATTTTGATCTGATACTTGAC
562849 TTGAATTATG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (48 bp):
ATTCTGATATGATACCTGACATGAATTTTGATCTGATACTTGACCTGG
Found at i:562863 original size:24 final size:24
Alignment explanation
Indices: 562773--562870 Score: 81
Period size: 24 Copynumber: 4.1 Consensus size: 24
562763 TTATGATACC
* * * *
562773 TGACATGGATTTTGATCTGATACT
1 TGACATGAATTATGATTTGATTCT
* * * * *
562797 TGACCTGGATTCTGATCTGATACT
1 TGACATGAATTATGATTTGATTCT
*
562821 TGACATGAATTTTGATTTGATTCT
1 TGACATGAATTATGATTTGATTCT
* *
562845 TGACTTGAATTATGTTTTGATT-T
1 TGACATGAATTATGATTTGATTCT
562868 TGA
1 TGA
562871 TATATCCATT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
23 4 0.06
24 60 0.94
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.46
Consensus pattern (24 bp):
TGACATGAATTATGATTTGATTCT
Found at i:565766 original size:31 final size:31
Alignment explanation
Indices: 565743--565852 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
565733 CATAGATTCT
* *
565743 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
565774 GAAGGACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
565805 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
565836 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
565853 CCTCGACCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:566680 original size:21 final size:21
Alignment explanation
Indices: 566656--566700 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
566646 TGTTGTTCGT
* *
566656 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
566677 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
566698 TTG
1 TTG
566701 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.