Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_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: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:659017 original size:4 final size:5
Alignment explanation
Indices: 658989--659014 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
658979 CTCAAAAAAG
658989 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
659015 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:672974 original size:35 final size:36
Alignment explanation
Indices: 672863--672974 Score: 181
Period size: 36 Copynumber: 3.1 Consensus size: 36
672853 ATACAATCTG
*
672863 TCCATCACCATTATCACGCCTATATCATCACCATCT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
672899 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
* *
672935 TCCATCACCA-TATCACTCCTATATCATCACCAAAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
672970 TCCAT
1 TCCAT
672975 TTTTCATTCC
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 27 0.38
36 44 0.62
ACGTcount: A:0.30, C:0.38, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:673135 original size:25 final size:22
Alignment explanation
Indices: 673107--673157 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
673097 TCTTTGATAA
673107 CTTTTTTATCCATTTCAATTCTTTC
1 CTTTTTT-TCCATTT--ATTCTTTC
673132 C--TTTTTCCATTTATTCTTTC
1 CTTTTTTTCCATTTATTCTTTC
673152 CTTTTT
1 CTTTTT
673158 CCATTTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
20 9 0.38
22 10 0.42
23 4 0.17
25 1 0.04
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (22 bp):
CTTTTTTTCCATTTATTCTTTC
Found at i:673147 original size:20 final size:21
Alignment explanation
Indices: 673110--673163 Score: 83
Period size: 20 Copynumber: 2.5 Consensus size: 21
673100 TTGATAACTT
673110 TTTTATCCATTTCAATTCTTTCC
1 TTTT-TCCATTT-AATTCTTTCC
673133 TTTTTCCATTT-ATTCTTTCC
1 TTTTTCCATTTAATTCTTTCC
673153 TTTTTCCATTT
1 TTTTTCCATTT
673164 CTATTTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.65
22 7 0.23
23 4 0.13
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTCCATTTAATTCTTTCC
Found at i:673878 original size:15 final size:15
Alignment explanation
Indices: 673858--673914 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
673848 ATATATTATA
673858 AGAAGAAGAAAAAAC
1 AGAAGAAGAAAAAAC
673873 AGAAGAAGAAAAAA-
1 AGAAGAAGAAAAAAC
*
673887 A-ATAGAAAAAGAAAAC
1 AGA-AGAAGAA-AAAAC
673903 -GAAGAA-AAAAAA
1 AGAAGAAGAAAAAA
673915 TGAAAATGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 5 0.14
14 9 0.24
15 22 0.59
16 1 0.03
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (15 bp):
AGAAGAAGAAAAAAC
Found at i:673893 original size:26 final size:26
Alignment explanation
Indices: 673877--673946 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
673867 AAAAACAGAA
673877 GAAGAAAAAAAATAGAAAAAGAAAAC
1 GAAGAAAAAAAATAGAAAAAGAAAAC
*
673903 GAAGAAAAAAAAT-GAAAATGAGAAA-
1 GAAGAAAAAAAATAGAAAAAGA-AAAC
* *
673928 GAA-AAGAAAAAGAGAAAAA
1 GAAGAAAAAAAATAGAAAAA
673947 AATGAGAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 7 0.18
25 15 0.39
26 16 0.42
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (26 bp):
GAAGAAAAAAAATAGAAAAAGAAAAC
Found at i:673912 original size:17 final size:16
Alignment explanation
Indices: 673892--673948 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 16
673882 AAAAAAATAG
*
673892 AAAAAGAAAACGAAGAAA
1 AAAAAGAAAAAG-AG-AA
*
673910 AAAAATGAAAATGAGAA
1 AAAAA-GAAAAAGAGAA
673927 AGAAAAGAAAAAGAGAA
1 A-AAAAGAAAAAGAGAA
673944 AAAAA
1 AAAAA
673949 TGAGAGATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 4 0.11
17 14 0.40
18 11 0.31
19 6 0.17
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAAAGAGAA
Found at i:673926 original size:18 final size:18
Alignment explanation
Indices: 673892--673967 Score: 70
Period size: 18 Copynumber: 4.3 Consensus size: 18
673882 AAAAAAATAG
*
673892 AAAAA-GAAAACGAAGAAA
1 AAAAATGAAAATG-AGAAA
673910 AAAAATGAAAATGAGAAA
1 AAAAATGAAAATGAGAAA
* *
673928 GAAAA-GAAAAAGAG-AA
1 AAAAATGAAAATGAGAAA
*
673944 AAAAATGAGAGATGA-AAA
1 AAAAATGA-AAATGAGAAA
673962 AAAAAT
1 AAAAAT
673968 ATTTCACTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.12
17 10 0.21
18 26 0.54
19 6 0.12
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAATGAAAATGAGAAA
Found at i:678054 original size:49 final size:46
Alignment explanation
Indices: 677943--678064 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 46
677933 GTAACCATGC
*
677943 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
* * * **
677989 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTG-GTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAAA
*
678038 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
678065 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
45 2 0.03
46 23 0.36
49 25 0.39
50 14 0.22
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
Found at i:681082 original size:23 final size:23
Alignment explanation
Indices: 681052--681132 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 23
681042 CTCTATCCCT
681052 TCTTTATTTCATTTCATTTCTTA
1 TCTTTATTTCATTTCATTTCTTA
* *
681075 TCTTTA-TT-ATTTCATTTATTCT
1 TCTTTATTTCATTTCATTTCTT-A
*
681097 TCCTTTATTAACCATCTTCATTTTCTTA
1 T-CTTTATT--TCAT-TTCA-TTTCTTA
681125 TCTTTATT
1 TCTTTATT
681133 GCAGTCAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 11 0.24
22 3 0.07
23 11 0.24
24 1 0.02
27 9 0.20
28 5 0.11
29 5 0.11
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.63
Consensus pattern (23 bp):
TCTTTATTTCATTTCATTTCTTA
Found at i:681088 original size:26 final size:26
Alignment explanation
Indices: 681055--681132 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
681045 TATCCCTTCT
681055 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
*
681081 TTATTTCATTT-A-TTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
**
681104 TTA-ACCATCTTCATTTTCTTATCTTTA
1 TTATTTCAT-TTCA-TTTCTTATCTTTA
681131 TT
1 TT
681133 GCAGTCAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 3 0.07
23 10 0.23
24 6 0.14
25 1 0.02
26 16 0.37
27 7 0.16
ACGTcount: A:0.19, C:0.18, G:0.00, T:0.63
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTATCTTTA
Found at i:682921 original size:18 final size:18
Alignment explanation
Indices: 682898--682939 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
682888 TTGAAAGTGC
682898 AAAAAAATTCCGAAAATT
1 AAAAAAATTCCGAAAATT
*
682916 AAAAAAATTCTGAAAATT
1 AAAAAAATTCCGAAAATT
682934 AAAAAA
1 AAAAAA
682940 GAAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAAAAATTCCGAAAATT
Found at i:689898 original size:13 final size:13
Alignment explanation
Indices: 689880--689925 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
689870 GTGATGGTCT
689880 TGATGAAGGATGA
1 TGATGAAGGATGA
*
689893 TGATGATGGATGA
1 TGATGAAGGATGA
* *
689906 TGATGATGGTTGA
1 TGATGAAGGATGA
689919 TGATGAA
1 TGATGAA
689926 ATGGCAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (13 bp):
TGATGAAGGATGA
Found at i:689899 original size:16 final size:16
Alignment explanation
Indices: 689880--689913 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
689870 GTGATGGTCT
689880 TGATGAAGGATGATGA
1 TGATGAAGGATGATGA
* *
689896 TGATGGATGATGATGA
1 TGATGAAGGATGATGA
689912 TG
1 TG
689914 GTTGATGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (16 bp):
TGATGAAGGATGATGA
Found at i:689920 original size:16 final size:16
Alignment explanation
Indices: 689888--689924 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
689878 CTTGATGAAG
689888 GATGATGATGATGGAT
1 GATGATGATGATGGAT
* *
689904 GATGATGATGGTTGAT
1 GATGATGATGATGGAT
689920 GATGA
1 GATGA
689925 AATGGCAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (16 bp):
GATGATGATGATGGAT
Found at i:693662 original size:16 final size:15
Alignment explanation
Indices: 693643--693681 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
693633 GTTGATAATT
693643 AAGAAATGAAAATGAA
1 AAGAAATG-AAATGAA
* *
693659 AAGAATTGAAATGGA
1 AAGAAATGAAATGAA
693674 AAGAAATG
1 AAGAAATG
693682 TTATCAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (15 bp):
AAGAAATGAAATGAA
Found at i:693915 original size:36 final size:35
Alignment explanation
Indices: 693818--693926 Score: 130
Period size: 35 Copynumber: 3.1 Consensus size: 35
693808 GGTGGTTATT
* * * *
693818 TAGGCGTGAAATGGTGATAGAAGATGGTAAGGATA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
* * * *
693853 TAGGCATGCAATGATAATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
693888 TAGGCGTGAAAATGGTGATGGAAGATGGTGATGTT-
1 TAGGCGTG-AAATGGTGATGGAAGATGGTGATGTTA
693923 TAGG
1 TAGG
693927 TAGTATCTCA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 38 0.62
36 23 0.38
ACGTcount: A:0.33, C:0.04, G:0.37, T:0.27
Consensus pattern (35 bp):
TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
Found at i:694642 original size:16 final size:15
Alignment explanation
Indices: 694605--694643 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
694595 TCTTTGATAA
694605 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
*
694620 CAATTCTTTCCATTTT
1 CATTTCTTTCCA-TTT
694636 CATTTCTT
1 CATTTCTT
694644 AATTATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (15 bp):
CATTTCTTTCCATTT
Found at i:695686 original size:2 final size:2
Alignment explanation
Indices: 695669--695718 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
695659 TCATAATAAC
*
695669 TA TA GA TA TA -A 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
695710 TA TA TA TA T
1 TA TA TA TA T
695719 GAAAATAGCT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:696997 original size:20 final size:19
Alignment explanation
Indices: 696955--696997 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
696945 ATCAACCACT
* *
696955 TCCATTTGATACTTGTGGT
1 TCCATTTGATACTAGTGGG
696974 TCCATTTGATATCTAGTGGG
1 TCCATTTGATA-CTAGTGGG
696994 TCCA
1 TCCA
696998 AGTCCTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (19 bp):
TCCATTTGATACTAGTGGG
Found at i:701219 original size:34 final size:35
Alignment explanation
Indices: 701181--701256 Score: 136
Period size: 34 Copynumber: 2.2 Consensus size: 35
701171 GGTCACATCA
701181 TTATATTATAAGTTATTTACTTCAAATAC-TTAGC
1 TTATATTATAAGTTATTTACTTCAAATACTTTAGC
*
701215 TTATATTATAAGTTATTTACTTCAAATACTTTATC
1 TTATATTATAAGTTATTTACTTCAAATACTTTAGC
701250 TTATATT
1 TTATATT
701257 TTGGGAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 29 0.73
35 11 0.28
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (35 bp):
TTATATTATAAGTTATTTACTTCAAATACTTTAGC
Found at i:702756 original size:6 final size:6
Alignment explanation
Indices: 702745--702784 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
702735 TGCTGCAATA
*
702745 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
702785 GTCTCCTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:702997 original size:16 final size:16
Alignment explanation
Indices: 702968--703027 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
702958 GAGTTGTAAG
*
702968 TTATCTTCACTTTCTTA
1 TTAT-TTCATTTTCTTA
*
702985 TTATTTCATTTTCCTTT
1 TTATTTCATTTT-CTTA
* * *
703002 TTCTTTCATTTTTTTC
1 TTATTTCATTTTCTTA
703018 TTATTTCATT
1 TTATTTCATT
703028 ACCTTATCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 18 0.50
17 18 0.50
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTCATTTTCTTA
Found at i:709970 original size:34 final size:35
Alignment explanation
Indices: 709923--709994 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 35
709913 ACATCATTAC
709923 ATTATAAGATATTTACTTCAAATAC-TTAGCTTAT
1 ATTATAAGATATTTACTTCAAATACTTTAGCTTAT
* * *
709957 ATTATAAGTTATTTACTTCAAATGCTTTATCTTAT
1 ATTATAAGATATTTACTTCAAATACTTTAGCTTAT
709992 ATT
1 ATT
709995 TTGGGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 23 0.68
35 11 0.32
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.49
Consensus pattern (35 bp):
ATTATAAGATATTTACTTCAAATACTTTAGCTTAT
Found at i:711493 original size:6 final size:6
Alignment explanation
Indices: 711482--711521 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
711472 TGCTGCAATA
*
711482 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
711522 GTTTCCTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:711734 original size:16 final size:16
Alignment explanation
Indices: 711705--711764 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
711695 GAGTTGTAAG
*
711705 TTATCTTCACTTTCTTA
1 TTAT-TTCATTTTCTTA
*
711722 TTATTTCATTTTCCTTT
1 TTATTTCATTTT-CTTA
* * *
711739 TTCTTTCATTTTTTTC
1 TTATTTCATTTTCTTA
711755 TTATTTCATT
1 TTATTTCATT
711765 ACCTTATCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 18 0.50
17 18 0.50
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTCATTTTCTTA
Found at i:722593 original size:20 final size:19
Alignment explanation
Indices: 722554--722592 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
722544 TTTTTTGGAG
*
722554 TGTTTGGTGAGTTTATTTT
1 TGTTTGGTGAGGTTATTTT
*
722573 TGTTTTGTGAGGTTATTTT
1 TGTTTGGTGAGGTTATTTT
722592 T
1 T
722593 TATTACTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.26, T:0.64
Consensus pattern (19 bp):
TGTTTGGTGAGGTTATTTT
Found at i:742113 original size:26 final size:26
Alignment explanation
Indices: 742074--742126 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
742064 CTAGAACACA
* *
742074 CCCATGTGCTTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
742100 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
742126 C
1 C
742127 GTTCCTTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:746336 original size:24 final size:24
Alignment explanation
Indices: 746309--746369 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
746299 TTTTCATGAT
* *
746309 CCAATGGACAT-AACTTTTGGGATG
1 CCAAGGGACATGAA-TTTTGGGATA
*
746333 CCAAGGGTCATGAATTTTGGGATA
1 CCAAGGGACATGAATTTTGGGATA
746357 CCAAGGGACATGA
1 CCAAGGGACATGA
746370 TCATTCAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (24 bp):
CCAAGGGACATGAATTTTGGGATA
Found at i:748119 original size:35 final size:35
Alignment explanation
Indices: 748068--748154 Score: 140
Period size: 35 Copynumber: 2.5 Consensus size: 35
748058 TAGTGATACT
748068 ACCTATATCATCACCATCTTCCATCACCATATCAC
1 ACCTATATCATCACCATCTTCCATCACCATATCAC
* *
748103 ACCTATATCATTACCATCTTCCATCACCATTTCAC
1 ACCTATATCATCACCATCTTCCATCACCATATCAC
*
748138 -CCTAAATCATCACCATC
1 ACCTATATCATCACCATC
748155 CCTTAACCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
34 15 0.31
35 33 0.69
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.30
Consensus pattern (35 bp):
ACCTATATCATCACCATCTTCCATCACCATATCAC
Found at i:748562 original size:2 final size:2
Alignment explanation
Indices: 748555--748595 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
748545 TTATCACCAT
748555 TA TA TA 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 TA TA TA T
748596 TCCGCTGCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:749187 original size:18 final size:18
Alignment explanation
Indices: 749160--749199 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
749150 GAGTGCATGG
*
749160 CATGTGTGACATTGTTCA
1 CATGTATGACATTGTTCA
749178 CATGTATGACATTGTTCA
1 CATGTATGACATTGTTCA
749196 CATG
1 CATG
749200 CATAGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (18 bp):
CATGTATGACATTGTTCA
Found at i:751369 original size:2 final size:2
Alignment explanation
Indices: 751362--751406 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
751352 AGTTATTTTC
751362 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
751404 AT A
1 AT A
751407 GTTATTATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:753010 original size:17 final size:17
Alignment explanation
Indices: 752990--753028 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
752980 GAAAAAAAAG
752990 AAGAAAA-AAATTCAGAA
1 AAGAAAACAAATTCA-AA
753007 AAGAAAAACAAATTCAAA
1 AAG-AAAACAAATTCAAA
753025 AAGA
1 AAGA
753029 GAAAGCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.72, C:0.08, G:0.10, T:0.10
Consensus pattern (17 bp):
AAGAAAACAAATTCAAA
Found at i:753021 original size:19 final size:19
Alignment explanation
Indices: 752984--753032 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
752974 AGAAAAGAAA
752984 AAAAAGAAGAAAAAAATTC
1 AAAAAGAAGAAAAAAATTC
*
753003 AGAAAAGAA-AAACAAATTC
1 A-AAAAGAAGAAAAAAATTC
753022 AAAAAG-AGAAA
1 AAAAAGAAGAAA
753033 GCAAGCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.04
18 8 0.30
19 11 0.41
20 7 0.26
ACGTcount: A:0.73, C:0.06, G:0.12, T:0.08
Consensus pattern (19 bp):
AAAAAGAAGAAAAAAATTC
Found at i:759051 original size:11 final size:13
Alignment explanation
Indices: 759019--759048 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
759009 TGGCTAAAGA
759019 TGAAAAGGTATGT
1 TGAAAAGGTATGT
759032 TGAAAAGGTATG-
1 TGAAAAGGTATGT
759044 TGAAA
1 TGAAA
759049 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:762347 original size:24 final size:25
Alignment explanation
Indices: 762301--762355 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
762291 ACAGTTATGC
*
762301 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
762325 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
762350 CA-TTGA
1 CACTTGA
762356 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:764493 original size:30 final size:31
Alignment explanation
Indices: 764454--764513 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
764444 ACATGCTGCC
***
764454 ATGATATCTAAGTGATATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
*
764485 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGAAAACATAATA
764514 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:766989 original size:32 final size:33
Alignment explanation
Indices: 766928--766994 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
766918 ACAAAATTAA
* *
766928 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
766960 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGATAG
766993 AA
1 AA
766995 ATATTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:767565 original size:19 final size:20
Alignment explanation
Indices: 767527--767569 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
767517 GAAACCCCTT
*
767527 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
767547 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
767566 TGAA
1 TGAA
767570 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:771349 original size:25 final size:25
Alignment explanation
Indices: 771321--771375 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
771311 AAGTCGATAA
771321 GGAATCGCTAAATTCAGATCGAATT
1 GGAATCGCTAAATTCAGATCGAATT
*
771346 GGAATCGGTAAATTCAGATCGAATT
1 GGAATCGCTAAATTCAGATCGAATT
771371 GGAAT
1 GGAAT
771376 TTTACAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (25 bp):
GGAATCGCTAAATTCAGATCGAATT
Found at i:773169 original size:59 final size:59
Alignment explanation
Indices: 773087--773208 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 59
773077 CAGCAGGCTG
** * *
773087 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGACATGACCTTATGTGC
1 CATATTCGGGAATACACTAAAGGATACCTAGTCCAGATGGTGGACACGACCTTATGTGC
* ** * *
773146 CATATTCGGGACTGTACTTAAGGATACCTAGTCCAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTCCAGATGGTGGACACGACCTTATGTGC
773205 CATA
1 CATA
773209 CTAGGGATAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTCCAGATGGTGGACACGACCTTATGTGC
Found at i:773347 original size:24 final size:25
Alignment explanation
Indices: 773319--773397 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
773309 GCAAGTGTAT
773319 TGGTA-AAATAAGCTTACGAGCTTA
1 TGGTACAAATAAGCTTACGAGCTTA
*
773343 TGGTACAAAT--G-GTA--AG-TATA
1 TGGTACAAATAAGCTTACGAGCT-TA
773363 TTGGTA-AAATAAGCTTACGAGCTTA
1 -TGGTACAAATAAGCTTACGAGCTTA
773388 TGGTACAAAT
1 TGGTACAAAT
773398 GGTAAGTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 19
0.67 0.03 0.30
Matches are distributed among these distances:
19 1 0.02
20 8 0.19
21 5 0.12
22 3 0.07
23 3 0.07
24 10 0.23
25 12 0.28
26 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (25 bp):
TGGTACAAATAAGCTTACGAGCTTA
Found at i:773365 original size:45 final size:45
Alignment explanation
Indices: 773305--773436 Score: 221
Period size: 45 Copynumber: 2.9 Consensus size: 45
773295 GTTATGGAAT
* *
773305 AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTACA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
773350 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
*
773395 AATGGTAAGTA-ATTTGGTAAACTAAGCTTACGAGCTTATGGT
1 AATGGTAAGTATA-TTGGTAAAATAAGCTTACGAGCTTATGGT
773437 TAATAAATGG
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
44 1 0.01
45 82 0.99
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (45 bp):
AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
Found at i:773392 original size:36 final size:36
Alignment explanation
Indices: 773351--773453 Score: 84
Period size: 45 Copynumber: 2.6 Consensus size: 36
773341 TATGGTACAA
773351 ATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTT
1 ATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTT
*
773387 ATGGTACAAATGGTAAGTAATTTGGTAAACTAAGCTTACGAGCTT
1 ATGGT---AA--GT-A-T-A-TTGGTAAAATAAGCTTACGAGCTT
*
773432 ATGGTTAA-TA-AATGGTAAAATA
1 ATGG-TAAGTATATTGGTAAAATA
773454 GTGAATATGC
Statistics
Matches: 54, Mismatches: 3, Indels: 21
0.69 0.04 0.27
Matches are distributed among these distances:
35 9 0.17
36 6 0.11
39 3 0.06
40 1 0.02
41 2 0.04
42 1 0.02
43 3 0.06
44 1 0.02
45 27 0.50
46 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (36 bp):
ATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTT
Found at i:782064 original size:24 final size:23
Alignment explanation
Indices: 782037--782097 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
782027 AACTTTCTTT
782037 CTTTTCTTTTCTTCTTTTTGAGTG
1 CTTTTCTTTTCTTC-TTTTGAGTG
*
782061 C-TTTCAATTTTTTTCTTTTGAGTG
1 CTTTTC--TTTTCTTCTTTTGAGTG
**
782085 CTTTGATTTTCTT
1 CTTTTCTTTTCTT
782098 TGCTGGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
23 10 0.33
24 11 0.37
25 9 0.30
ACGTcount: A:0.08, C:0.15, G:0.11, T:0.66
Consensus pattern (23 bp):
CTTTTCTTTTCTTCTTTTGAGTG
Found at i:794433 original size:59 final size:59
Alignment explanation
Indices: 794358--794495 Score: 213
Period size: 59 Copynumber: 2.3 Consensus size: 59
794348 TCGACTCAGA
* *
794358 TCAGGTTGGATTCATGTCAAATCAGTTTGGGTCATTTTCAGAATGATTTGACATCATAT
1 TCAGGTTGGGTTCATGTCAAATCAGTTCGGGTCATTTTCAGAATGATTTGACATCATAT
* * *
794417 TCAGGTTGGGTCCATGTCAAATCAGTTCGGGTCATTTTCATAATGATTTGATATCATAT
1 TCAGGTTGGGTTCATGTCAAATCAGTTCGGGTCATTTTCAGAATGATTTGACATCATAT
* *
794476 TCAGTTTGGGTTCAGGTCAA
1 TCAGGTTGGGTTCATGTCAA
794496 GTTAATTTCA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 71 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (59 bp):
TCAGGTTGGGTTCATGTCAAATCAGTTCGGGTCATTTTCAGAATGATTTGACATCATAT
Found at i:795150 original size:2 final size:2
Alignment explanation
Indices: 795143--795205 Score: 51
Period size: 2 Copynumber: 31.0 Consensus size: 2
795133 AAGTATGGGC
*
795143 TA TA TA TA TA TA TA TA TA TA -A CTA TA TA TA TA -A GTA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
*
795185 TA -A GTA TA AA GTA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA
795206 CACACACATA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
1 3 0.06
2 43 0.86
3 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (2 bp):
TA
Found at i:795160 original size:12 final size:12
Alignment explanation
Indices: 795143--795192 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
795133 AAGTATGGGC
795143 TATATATAT-A-
1 TATATATATAAG
*
795153 TATATATATAAC
1 TATATATATAAG
795165 TATATATATAAG
1 TATATATATAAG
*
795177 TATATACATAAG
1 TATATATATAAG
795189 TATA
1 TATA
795193 AAGTATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
12 26 0.72
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (12 bp):
TATATATATAAG
Found at i:796048 original size:24 final size:26
Alignment explanation
Indices: 796011--796059 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
796001 GTGCGGTTCC
*
796011 TTTTAAAATAAAATT-ATGTTAAATA
1 TTTTAAAATAAAATTGATATTAAATA
*
796036 TTTT-AAATCAAATTGATATTAAAT
1 TTTTAAAATAAAATTGATATTAAAT
796060 TGACTCATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (26 bp):
TTTTAAAATAAAATTGATATTAAATA
Found at i:799181 original size:14 final size:14
Alignment explanation
Indices: 799164--799190 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
799154 TGAATAAAAA
799164 AATAAAATTAAAGT
1 AATAAAATTAAAGT
799178 AATAAAATTAAAG
1 AATAAAATTAAAG
799191 GATTGAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (14 bp):
AATAAAATTAAAGT
Found at i:799199 original size:14 final size:14
Alignment explanation
Indices: 799164--799203 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
799154 TGAATAAAAA
*
799164 AATAAAATTAAAGT
1 AATAAAATTAAAGG
799178 AATAAAATTAAAGG
1 AATAAAATTAAAGG
* *
799192 ATTGAAATTAAA
1 AATAAAATTAAA
799204 CTAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (14 bp):
AATAAAATTAAAGG
Found at i:799231 original size:21 final size:21
Alignment explanation
Indices: 799196--799239 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
799186 TAAAGGATTG
*
799196 AAATTAAACTAAATTAAAAGGC
1 AAATCAAACTAAATT-AAAGGC
799218 AAATCAAA-TAAATTAAAGGC
1 AAATCAAACTAAATTAAAGGC
799238 AA
1 AA
799240 TTAATAGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 6 0.29
22 7 0.33
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20
Consensus pattern (21 bp):
AAATCAAACTAAATTAAAGGC
Found at i:805112 original size:24 final size:24
Alignment explanation
Indices: 805043--805112 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
805033 TAAATATTAA
* * * *
805043 TAAAATATTTATCTAATT-ACAAT
1 TAAAATATTTATTTATTTAAAAAG
* *
805066 TAAAATATATA-TAATTTATAAAAG
1 TAAAATATTTATTTATTTA-AAAAG
805090 TAAAATATTTATTTATTTAAAAA
1 TAAAATATTTATTTATTTAAAAA
805113 TATCAGAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
22 3 0.08
23 10 0.28
24 17 0.47
25 6 0.17
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (24 bp):
TAAAATATTTATTTATTTAAAAAG
Found at i:805215 original size:31 final size:33
Alignment explanation
Indices: 805170--805231 Score: 85
Period size: 31 Copynumber: 1.9 Consensus size: 33
805160 ATTTAAAAAT
*
805170 AAATAAATATTATTAAT-TTAC-AAAATTAATC
1 AAATAAATATTATTAATATGACTAAAATTAATC
805201 AAAT-AATATATATTAATATGACTAAAATTAA
1 AAATAAATAT-TATTAATATGACTAAAATTAA
805232 AGAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 5 0.19
31 11 0.41
32 3 0.11
33 8 0.30
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (33 bp):
AAATAAATATTATTAATATGACTAAAATTAATC
Found at i:805238 original size:33 final size:31
Alignment explanation
Indices: 805170--805238 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 31
805160 ATTTAAAAAT
* *
805170 AAATAAATATTATTAATTTACAAAATTAATC
1 AAATAAATATTATTAATTGACAAAATTAAAC
*
805201 AAAT-AATATATATTAATATGACTAAAATTAAAG
1 AAATAAATAT-TATTAAT-TGAC-AAAATTAAAC
805234 AAATA
1 AAATA
805239 TAAAATAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 5 0.16
31 11 0.35
32 3 0.10
33 12 0.39
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (31 bp):
AAATAAATATTATTAATTGACAAAATTAAAC
Found at i:805247 original size:15 final size:15
Alignment explanation
Indices: 805223--805261 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
805213 TTAATATGAC
*
805223 TAAAATTAAAGAAATA
1 TAAAA-TAAAGAAAAA
805239 TAAAATAAAGAAAAA
1 TAAAATAAAGAAAAA
*
805254 TATAATAA
1 TAAAATAA
805262 TATGAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (15 bp):
TAAAATAAAGAAAAA
Found at i:805659 original size:10 final size:10
Alignment explanation
Indices: 805644--805675 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
805634 TTCGAATACC
805644 AAATTAAAAT
1 AAATTAAAAT
805654 AAATTAAAAT
1 AAATTAAAAT
805664 AAATTAAAAT
1 AAATTAAAAT
805674 AA
1 AA
805676 CTTGTAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:806717 original size:6 final size:6
Alignment explanation
Indices: 806687--806754 Score: 64
Period size: 6 Copynumber: 10.7 Consensus size: 6
806677 TTTTTTATTA
* **
806687 AATAAT ATATATAT ATATATAT AATACT AATTTT AATAAT AATAAT AATAAT
1 AATAAT A-ATA-AT A-ATA-AT AATAAT AATAAT AATAAT AATAAT AATAAT
*
806739 AATAAT AAAAAT AATA
1 AATAAT AATAAT AATA
806755 TGAAAAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
6 36 0.68
7 6 0.11
8 11 0.21
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (6 bp):
AATAAT
Found at i:806732 original size:9 final size:9
Alignment explanation
Indices: 806687--806754 Score: 64
Period size: 9 Copynumber: 7.1 Consensus size: 9
806677 TTTTTTATTA
806687 AATAATATAT
1 AATAATA-AT
806697 ATATATATATAT
1 A-ATA-ATA-AT
*
806709 AATACTAAT
1 AATAATAAT
**
806718 TTTAATAAT
1 AATAATAAT
806727 AATAATAAT
1 AATAATAAT
806736 AATAATAAT
1 AATAATAAT
*
806745 AAAAATAAT
1 AATAATAAT
806754 A
1 A
806755 TGAAAAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
9 33 0.67
10 3 0.06
11 6 0.12
12 7 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (9 bp):
AATAATAAT
Found at i:809999 original size:28 final size:30
Alignment explanation
Indices: 809941--810000 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
809931 TGCCAACCCA
* *
809941 GCCAACCTTTGAAATTATGCACCATTCGGT
1 GCCAACCTTTGAAATCATGCACCAATCGGT
809971 GCCAACCTTTG-AA-CATGCACCGAAT-GGT
1 GCCAACCTTTGAAATCATGCACC-AATCGGT
809999 GC
1 GC
810001 AGCCTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.44
29 4 0.15
30 11 0.41
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (30 bp):
GCCAACCTTTGAAATCATGCACCAATCGGT
Found at i:810904 original size:21 final size:21
Alignment explanation
Indices: 810864--810905 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
810854 CAAAATATTT
*
810864 AATAATATTTATGATCATTAA
1 AATAATATTTATGATAATTAA
* *
810885 AATATTATTTATGCTAATTAA
1 AATAATATTTATGATAATTAA
810906 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
AATAATATTTATGATAATTAA
Found at i:813273 original size:25 final size:25
Alignment explanation
Indices: 813240--813307 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
813230 TAGGGTTGGT
*
813240 TAATCGGTTTAGGGTTTTTTATGTTA
1 TAAT-GGTTTAGGGTTTTTTAGGTTA
* *
813266 TAATGGTTTAAGGTATTTTAGGTTA
1 TAATGGTTTAGGGTTTTTTAGGTTA
*
813291 -AAGTGATTTAGGGTTTT
1 TAA-TGGTTTAGGGTTTT
813308 AATGGTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
24 2 0.06
25 29 0.83
26 4 0.11
ACGTcount: A:0.24, C:0.01, G:0.25, T:0.50
Consensus pattern (25 bp):
TAATGGTTTAGGGTTTTTTAGGTTA
Found at i:814892 original size:2 final size:2
Alignment explanation
Indices: 814887--814917 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
814877 TCTCTCTCTC
814887 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 T
814918 TGGGAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:820857 original size:44 final size:44
Alignment explanation
Indices: 820772--820902 Score: 192
Period size: 44 Copynumber: 3.0 Consensus size: 44
820762 CTGGAGCAAT
* * *
820772 AAATGATAAATGTT-GGGCATTTTTTAAGGCCCATGTCATCCAG
1 AAATGATAAATGTTGGGGCATTTTTGAAGGCCCATATCATCCAA
* *
820815 AAATGATAAATGTTGGGGCATTTTTGAAGGCCCGTATTATCCAA
1 AAATGATAAATGTTGGGGCATTTTTGAAGGCCCATATCATCCAA
* *
820859 AAATGATAAATGTTGGGGCATTTTCGAAGGCTCATATCATCCAA
1 AAATGATAAATGTTGGGGCATTTTTGAAGGCCCATATCATCCAA
820903 GAATACAATA
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 14 0.18
44 64 0.82
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (44 bp):
AAATGATAAATGTTGGGGCATTTTTGAAGGCCCATATCATCCAA
Found at i:823238 original size:133 final size:131
Alignment explanation
Indices: 823031--823498 Score: 445
Period size: 133 Copynumber: 3.5 Consensus size: 131
823021 ATAAATCTAC
* * * * * * * * *
823031 CTCGATTCAATCTTTCCTGAGGAACAATGGAAAGAATCAATGTTTCGATATATTATCTATCCTGA
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACGTTTCTAGATATTATCTACCCTGA
* *
823096 AGAAACAGCGGAGCAGATCCCCTCTTTCTATATTTGATATTCCCTGAGGAATAATGGAACAAATC
66 AGAAGCAGCGGAGCAGATCCCCT-TTTC-ATATTTGATATTCCCTGAGGAATAGTGGAACAAATC
823161 T-T
129 TGT
* * * * *
823163 CCTCGATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAACGTTTCTCGATATGATTTACCCTG
1 -CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACGTTTCTAGATATTATCTACCCTG
* * * **
823228 AAGAAGCAGCGGAGCAGATCTCCTTATTCCAAATTTGATCA-TCCCTGAGGAACAGTGGAATGAA
65 AAGAAGCAGCGGAGCAGATCCCCTT-TT-CATATTTGAT-ATTCCCTGAGGAATAGTGGAACAAA
*
823292 TATGT
127 TCTGT
* * * * *
823297 CTCGATTCAATATTCCCTGAAGAATAGTGGAATAAATCAATGTTTTTAGATCTTATCTACCCTGA
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACGTTTCTAGATATTATCTACCCTGA
** * * * * * * * *
823362 AGAAGCAGCAAAACATATCCCATTTTTGCATATCTGATCTTTCCTAAGGAATAGTAGAACAAATC
66 AGAAGCAGCGGAGCAGATCCC-CTTTT-CATATTTGATATTCCCTGAGGAATAGTGGAACAAATC
823427 TGT
129 TGT
* * * * * * * *
823430 CTCGATTTAATATTCCCTAAAGAACAGTGAAATGAATCAACATTTCCATATATAATTTACCCTGA
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACGTTTCTAGATATTATCTACCCTGA
823495 AGAA
66 AGAA
823499 ACATCGAAGC
Statistics
Matches: 271, Mismatches: 58, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
132 1 0.00
133 265 0.98
134 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (131 bp):
CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACGTTTCTAGATATTATCTACCCTGA
AGAAGCAGCGGAGCAGATCCCCTTTTCATATTTGATATTCCCTGAGGAATAGTGGAACAAATCTG
T
Found at i:824059 original size:2 final size:2
Alignment explanation
Indices: 824052--824090 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
824042 TTCAAAAAGC
824052 TA TA 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 TA TA T
824091 TGGGAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:827982 original size:10 final size:8
Alignment explanation
Indices: 827952--827999 Score: 59
Period size: 7 Copynumber: 6.4 Consensus size: 8
827942 CCCTAAATTG
827952 AAAA-AGA
1 AAAAGAGA
827959 AAAAGAGA
1 AAAAGAGA
827967 AAAAGAGA
1 AAAAGAGA
827975 ACAAA-AGA
1 A-AAAGAGA
827983 AAAAG-GA
1 AAAAGAGA
827990 AAAAGA-A
1 AAAAGAGA
827997 AAA
1 AAA
828000 TAAGGTGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
7 18 0.49
8 16 0.43
9 3 0.08
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAGAGA
Found at i:829862 original size:2 final size:2
Alignment explanation
Indices: 829855--829899 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
829845 ATTTATATGT
829855 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
829897 TA T
1 TA T
829900 TTACATATCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:830986 original size:23 final size:24
Alignment explanation
Indices: 830954--830999 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
830944 TTTAATCCTT
*
830954 TTTATATTATTTTTATT-TATTTA
1 TTTATATTATTCTTATTATATTTA
*
830977 TTTATTTTATTCTTATTATATTT
1 TTTATATTATTCTTATTATATTT
831000 CTTATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTATATTATTCTTATTATATTTA
Found at i:831004 original size:23 final size:23
Alignment explanation
Indices: 830955--831005 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
830945 TTAATCCTTT
* * *
830955 TTATATTATTTTTATTTATTTAT
1 TTATTTTATTCTTATTTATTTAC
830978 TTATTTTATTCTTATTATATTT-C
1 TTATTTTATTCTTATT-TATTTAC
831001 TTATT
1 TTATT
831006 ATTTTGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (23 bp):
TTATTTTATTCTTATTTATTTAC
Found at i:831277 original size:20 final size:21
Alignment explanation
Indices: 831252--831299 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
831242 TTATCCTTAT
831252 TATTATTACTAT-TATATACA
1 TATTATTACTATATATATACA
* *
831272 TATTA-TATTATATATATATA
1 TATTATTACTATATATATACA
831292 TATTATTA
1 TATTATTA
831300 ACCTAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 17 0.71
21 2 0.08
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTACTATATATATACA
Found at i:831299 original size:18 final size:16
Alignment explanation
Indices: 831255--831297 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
831245 TCCTTATTAT
831255 TATTACTATTATATACA
1 TATTA-TATTATATACA
*
831272 TATTATATTATATATA
1 TATTATATTATATACA
831288 TA-TATATTAT
1 TATTATATTAT
831298 TAACCTAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.32
16 12 0.48
17 5 0.20
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATATTATATACA
Found at i:831648 original size:9 final size:9
Alignment explanation
Indices: 831570--831648 Score: 52
Period size: 9 Copynumber: 8.2 Consensus size: 9
831560 TTCTAATTTA
*
831570 TTTATTTAT
1 TTTATTTTT
831579 TTTATTTATT
1 TTTATTT-TT
*
831589 GTTTATTTGT
1 -TTTATTTTT
*
831599 TTAATTTTGT
1 TTTATTTT-T
831609 TTTATTCGTTT
1 TTTATT--TTT
*
831620 ATTATCTTTT
1 TTTAT-TTTT
*
831630 TTT-TTGTT
1 TTTATTTTT
831638 TTTATTTTT
1 TTTATTTTT
831647 TT
1 TT
831649 ACTTCCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
8 6 0.11
9 20 0.37
10 13 0.24
11 12 0.22
12 3 0.06
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (9 bp):
TTTATTTTT
Found at i:835388 original size:21 final size:20
Alignment explanation
Indices: 835356--835394 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
835346 GGATTTGGGA
*
835356 TTTTTTTGAATTTGAGAGGG
1 TTTTTTTGAATTTAAGAGGG
*
835376 TTTTTTTATAATTTAAGAG
1 TTTTTTT-GAATTTAAGAG
835395 AAACTAAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.54
Consensus pattern (20 bp):
TTTTTTTGAATTTAAGAGGG
Found at i:844004 original size:6 final size:6
Alignment explanation
Indices: 843988--844022 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
843978 CTTAATTGCG
* *
843988 AAAATT GAAATT AAAATT AAAATT AAAATT TAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
844023 ACTCTATTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (6 bp):
AAAATT
Found at i:844179 original size:22 final size:22
Alignment explanation
Indices: 844153--844212 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
844143 ACAACAATAT
844153 TAAAAGTAAAAATAAAATA-GAA
1 TAAAA-TAAAAATAAAATAGGAA
844175 TAAAACT--AAATAAAATTAGGAA
1 TAAAA-TAAAAATAAAA-TAGGAA
844197 -AAAATAAAAATAAAAT
1 TAAAATAAAAATAAAAT
844213 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
20 9 0.27
21 7 0.21
22 17 0.52
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (22 bp):
TAAAATAAAAATAAAATAGGAA
Found at i:844199 original size:20 final size:20
Alignment explanation
Indices: 844162--844204 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
844152 TTAAAAGTAA
*
844162 AAATAAAATAGAATAAAACT
1 AAATAAAATAGAATAAAAAT
*
844182 AAATAAAATTAGGA-AAAAAT
1 AAATAAAA-TAGAATAAAAAT
844202 AAA
1 AAA
844205 AATAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (20 bp):
AAATAAAATAGAATAAAAAT
Found at i:845386 original size:20 final size:18
Alignment explanation
Indices: 845358--845397 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
845348 ACCTAAACAC
845358 AAAAGAAAATAAATAAATA
1 AAAAGAAAATAAAT-AATA
*
845377 AAAAGAAAAATGAATAATA
1 AAAAG-AAAATAAATAATA
845396 AA
1 AA
845398 TAAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAAGAAAATAAATAATA
Found at i:845419 original size:14 final size:15
Alignment explanation
Indices: 845394--845423 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
845384 AAATGAATAA
845394 TAAATAAATATATAG
1 TAAATAAATATATAG
845409 TAAATAATATATATA
1 TAAATAA-ATATATA
845424 ATACTACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TAAATAAATATATAG
Found at i:846037 original size:30 final size:30
Alignment explanation
Indices: 845979--846063 Score: 124
Period size: 28 Copynumber: 2.9 Consensus size: 30
845969 ACTTTTCAAA
845979 ATGTTTTCAAAAAACTATATATAT-TATAT
1 ATGTTTTCAAAAAACTATATATATATATAT
846008 ATGTTTTC-AAAAACTATATAT-TATATAT
1 ATGTTTTCAAAAAACTATATATATATATAT
*
846036 ATGGTTTCAAAAAAACTATATAT-TATAT
1 ATGTTTTC-AAAAAACTATATATATATAT
846064 TGTTGAAAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
27 1 0.02
28 25 0.48
29 8 0.15
30 18 0.35
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (30 bp):
ATGTTTTCAAAAAACTATATATATATATAT
Found at i:850269 original size:39 final size:39
Alignment explanation
Indices: 850140--850442 Score: 350
Period size: 39 Copynumber: 8.2 Consensus size: 39
850130 TTAACTCAAC
* *
850140 ATATATATATTTTCAAAATGTTTTCAAAAACAATATATT
1 ATATATATGTTTTCAAAATGTTTTCAAAAACTATATATT
850179 ATATATA--TTTTCAAAATGTTTTCAAAAACTATATATTT
1 ATATATATGTTTTCAAAATGTTTTCAAAAACTATATA-TT
*
850217 ATATATATGTTTTCAAAATGTTTTCGAAAACTATATATT
1 ATATATATGTTTTCAAAATGTTTTCAAAAACTATATATT
* *
850256 ATATATATGTTTTCAAAATGTTTTCTAAAACTATATACT
1 ATATATATGTTTTCAAAATGTTTTCAAAAACTATATATT
*
850295 AAATATATGTTTTCAAAATGTTTTCAAAAAC-------T
1 ATATATATGTTTTCAAAATGTTTTCAAAAACTATATATT
* *
850327 ATATACATGCTTTCAAAATGTTTTCAAAAAC-------T
1 ATATATATGTTTTCAAAATGTTTTCAAAAACTATATATT
* * ** *
850359 ATATATATGCTTTCAAAATGTTTTCAAGAACTATGCACT
1 ATATATATGTTTTCAAAATGTTTTCAAAAACTATATATT
* *
850398 ATATATATGTTTTCAAAATGTTTTTAAAAATTATATATT
1 ATATATATGTTTTCAAAATGTTTTCAAAAACTATATATT
850437 ATATAT
1 ATATAT
850443 TTTTCAAAAA
Statistics
Matches: 236, Mismatches: 18, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
32 59 0.25
37 27 0.11
38 9 0.04
39 114 0.48
40 27 0.11
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (39 bp):
ATATATATGTTTTCAAAATGTTTTCAAAAACTATATATT
Found at i:850341 original size:32 final size:32
Alignment explanation
Indices: 850305--850392 Score: 158
Period size: 32 Copynumber: 2.8 Consensus size: 32
850295 AAATATATGT
850305 TTTCAAAATGTTTTCAAAAACTATATACATGC
1 TTTCAAAATGTTTTCAAAAACTATATACATGC
*
850337 TTTCAAAATGTTTTCAAAAACTATATATATGC
1 TTTCAAAATGTTTTCAAAAACTATATACATGC
*
850369 TTTCAAAATGTTTTCAAGAACTAT
1 TTTCAAAATGTTTTCAAAAACTAT
850393 GCACTATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (32 bp):
TTTCAAAATGTTTTCAAAAACTATATACATGC
Found at i:856350 original size:20 final size:19
Alignment explanation
Indices: 856313--856354 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
856303 TTAAAAGTAA
856313 AAATAAAATAGAATAAAACT
1 AAATAAAATAGAATAAAA-T
*
856333 AAATAAAATTAGGA-AAAAT
1 AAATAAAA-TAGAATAAAAT
856352 AAA
1 AAA
856355 AAATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (19 bp):
AAATAAAATAGAATAAAAT
Found at i:857497 original size:14 final size:15
Alignment explanation
Indices: 857472--857501 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
857462 AAATAAGTAA
857472 TAAATAAATATATAG
1 TAAATAAATATATAG
857487 TAAATAATATATATA
1 TAAATAA-ATATATA
857502 ATACTACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TAAATAAATATATAG
Found at i:857565 original size:37 final size:39
Alignment explanation
Indices: 857525--857986 Score: 585
Period size: 39 Copynumber: 12.4 Consensus size: 39
857515 ATATATGTAA
* *
857525 AAAAACTATA-A-AATATATA-CTTTTCAAAATGTTTTC
1 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
*
857561 AAAAAACTATATA-T-TATATATGTTTTCAAAATGTTTTT
1 -AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
857599 AAAAACTATATATTATATATA--TTTT-AAAATGTTTTC
1 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
*
857635 AAAAACTATATCTTATATATA--TTTTCAAAATGTTTTC
1 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
857672 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
1 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
*
857711 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTTA
1 AAAAACTATATATTATATATATGTTTTCAAAATG-TTTTC
* *
857751 AAAAACTATATATTATATAAATTTTTTCAAAATGTTTTC
1 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
857790 AAAAACTATATATTATATATA--TTTTC---A-------
1 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
*
857817 AAA-ACTATATATTATATATATGTTTTCAAAATATTTTC
1 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
*
857855 AAAAACTATATACTATATATATAG-TTTCAAAATGTTTTC
1 AAAAACTATATATTATATATAT-GTTTTCAAAATGTTTTC
* *
857894 AAAAATTATATACTATATATATGTTTTCAAAATGTTTTC
1 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
* * * *
857933 AAAAACTCTATACTATATATATGTTTTTAAAATATTTTC
1 AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
*
857972 AAAAATTATATATTA
1 AAAAACTATATATTA
857987 AATAATTTTC
Statistics
Matches: 381, Mismatches: 21, Indels: 44
0.85 0.05 0.10
Matches are distributed among these distances:
26 17 0.04
27 3 0.01
28 5 0.01
31 1 0.00
34 1 0.00
36 34 0.09
37 68 0.18
38 21 0.06
39 194 0.51
40 37 0.10
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (39 bp):
AAAAACTATATATTATATATATGTTTTCAAAATGTTTTC
Found at i:857644 original size:25 final size:26
Alignment explanation
Indices: 857616--857664 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
857606 ATATATTATA
* *
857616 TATATTTTA-AAATGTTTTCAAAAAC
1 TATATCTTATAAATATTTTCAAAAAC
*
857641 TATATCTTATATATATTTTCAAAA
1 TATATCTTATAAATATTTTCAAAA
857665 TGTTTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (26 bp):
TATATCTTATAAATATTTTCAAAAAC
Found at i:857821 original size:26 final size:27
Alignment explanation
Indices: 857784--857847 Score: 112
Period size: 26 Copynumber: 2.4 Consensus size: 27
857774 TTTTCAAAAT
857784 GTTTTCAAAAACTATATATTATATATA
1 GTTTTCAAAAACTATATATTATATATA
857811 -TTTTCAAAAACTATATATTATATATA
1 GTTTTCAAAAACTATATATTATATATA
857837 TGTTTTCAAAA
1 -GTTTTCAAAA
857848 TATTTTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 26 0.74
28 9 0.26
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (27 bp):
GTTTTCAAAAACTATATATTATATATA
Found at i:857904 original size:104 final size:107
Alignment explanation
Indices: 857706--857925 Score: 347
Period size: 104 Copynumber: 2.1 Consensus size: 107
857696 TTTCAAAATG
* *
857706 TTTTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTTAAAAAACTATATATTATATAA
1 TTTTCAAAAACTATATATTATATATATGTTTTCAAAATGATTTTAAAAAACTATATACTATATAA
**
857771 ATTTTTTCAAAATGTTTTCAAAAACTATATA-T-TATATATA
66 ATAGTTTCAAAATGTTTTCAAAAACTATATACTATATATATA
* *
857811 TTTTCAAAAACTATATATTATATATATGTTTTCAAAAT-ATTTTCAAAAACTATATACTATATAT
1 TTTTCAAAAACTATATATTATATATATGTTTTCAAAATGATTTTAAAAAACTATATACTATATAA
* *
857875 ATAGTTTCAAAATGTTTTCAAAAATTATATACTATATATATG
66 ATAGTTTCAAAATGTTTTCAAAAACTATATACTATATATATA
857917 TTTTCAAAA
1 TTTTCAAAA
857926 TGTTTTCAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
104 50 0.48
105 39 0.37
106 16 0.15
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (107 bp):
TTTTCAAAAACTATATATTATATATATGTTTTCAAAATGATTTTAAAAAACTATATACTATATAA
ATAGTTTCAAAATGTTTTCAAAAACTATATACTATATATATA
Found at i:860454 original size:9 final size:8
Alignment explanation
Indices: 860424--860465 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
860414 AGTTATTTAA
860424 TATTTTTT
1 TATTTTTT
860432 TATTTTGTTT
1 TA-TTT-TTT
860442 TATTTTATT
1 TATTTT-TT
860451 TA-TTTTT
1 TATTTTTT
860458 TATTTTTT
1 TATTTTTT
860466 CTCTTTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 4 0.13
8 11 0.37
9 10 0.33
10 5 0.17
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.83
Consensus pattern (8 bp):
TATTTTTT
Found at i:860456 original size:25 final size:25
Alignment explanation
Indices: 860427--860480 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
860417 TATTTAATAT
* *
860427 TTTTTTATTTTGTTTTATTTTATTTA
1 TTTTTTATTTT-TTCTATTTGATTTA
*
860453 TTTTTTATTTTTTCTCTTTGATTTA
1 TTTTTTATTTTTTCTATTTGATTTA
860478 TTT
1 TTT
860481 AACATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.80
Consensus pattern (25 bp):
TTTTTTATTTTTTCTATTTGATTTA
Found at i:863943 original size:11 final size:11
Alignment explanation
Indices: 863929--863961 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
863919 TGGTGAGAAA
863929 GAATGAGAGAT
1 GAATGAGAGAT
863940 GAATGAGAGAT
1 GAATGAGAGAT
863951 GAATGAGAGAT
1 GAATGAGAGAT
863962 ACTTACTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (11 bp):
GAATGAGAGAT
Found at i:868592 original size:21 final size:21
Alignment explanation
Indices: 868547--868592 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
868537 ATTTCACAAG
*
868547 AAAAGCTGGTTACATCCCAGG
1 AAAAGCTGGTTACATCCCAGC
* **
868568 AAAAGCTGGTTGCATCTGAGC
1 AAAAGCTGGTTACATCCCAGC
868589 AAAA
1 AAAA
868593 ATTCCAAAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (21 bp):
AAAAGCTGGTTACATCCCAGC
Found at i:873500 original size:15 final size:15
Alignment explanation
Indices: 873482--873515 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
873472 ATTTAATTTA
873482 ATTTGCATGATGGTG
1 ATTTGCATGATGGTG
* *
873497 ATTTGTATGCTGGTG
1 ATTTGCATGATGGTG
873512 ATTT
1 ATTT
873516 TCAACTAAAT
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:0.18, C:0.06, G:0.29, T:0.47
Consensus pattern (15 bp):
ATTTGCATGATGGTG
Found at i:890705 original size:16 final size:16
Alignment explanation
Indices: 890684--890732 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
890674 AGCAATGAGT
890684 AATGAGATTAACGAGC
1 AATGAGATTAACGAGC
*
890700 AATGAGATTAACGAGT
1 AATGAGATTAACGAGC
*
890716 AATGAGCTTAACGAGC
1 AATGAGATTAACGAGC
890732 A
1 A
890733 GCGAGTGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (16 bp):
AATGAGATTAACGAGC
Found at i:891053 original size:16 final size:16
Alignment explanation
Indices: 891019--891057 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
891009 ATTATTAAAT
*
891019 TATTAA-ATTCTGTTA
1 TATTAATATTCTGATA
*
891034 TATTAATATTGTGATA
1 TATTAATATTCTGATA
891050 TATTAATA
1 TATTAATA
891058 AAAATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (16 bp):
TATTAATATTCTGATA
Found at i:896247 original size:6 final size:6
Alignment explanation
Indices: 896211--896240 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
896201 GTAAGATCGC
896211 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
896241 TTCTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:902384 original size:11 final size:11
Alignment explanation
Indices: 902370--902420 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
902360 GTACAAAAAC
902370 AAAAGAAAAGA
1 AAAAGAAAAGA
902381 AAAA-AAGAAGA
1 AAAAGAA-AAGA
**
902392 AAAATTTAAA-A
1 AAAA-GAAAAGA
902403 AAAAGAAAAGA
1 AAAAGAAAAGA
902414 AAAAGAA
1 AAAAGAA
902421 GAAAAGTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 5 0.15
11 25 0.76
12 2 0.06
13 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:902407 original size:28 final size:29
Alignment explanation
Indices: 902365--902435 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 29
902355 TTGGAGTACA
*
902365 AAAACAAAAGAAAAGAAAAAAAGAAGAAAAATTT
1 AAAA-AAAAGAAAAG--AAAAAGAAG-AAAA-GT
902399 AAAAAAAAGAAAAGAAAAAGAAGAAAAGT
1 AAAAAAAAGAAAAGAAAAAGAAGAAAAGT
902428 AAAAAAAA
1 AAAAAAAA
902436 AAGCAAGCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 9 0.25
30 4 0.11
31 9 0.25
33 10 0.28
34 4 0.11
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.06
Consensus pattern (29 bp):
AAAAAAAAGAAAAGAAAAAGAAGAAAAGT
Found at i:902422 original size:14 final size:15
Alignment explanation
Indices: 902365--902435 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 15
902355 TTGGAGTACA
*
902365 AAAACAAAAGAAAAGA
1 AAAA-AAAAGAAAAGT
*
902381 AAAAAAGAAGAAAAATTT
1 AAAAAA-AAG-AAAA-GT
902399 AAAAAAAAGAAAAG-
1 AAAAAAAAGAAAAGT
*
902413 AAAAAGAAGAAAAGT
1 AAAAAAAAGAAAAGT
902428 AAAAAAAA
1 AAAAAAAA
902436 AAGCAAGCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
14 13 0.28
15 9 0.20
16 11 0.24
17 7 0.15
18 6 0.13
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.06
Consensus pattern (15 bp):
AAAAAAAAGAAAAGT
Found at i:902434 original size:31 final size:32
Alignment explanation
Indices: 902359--902438 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 32
902349 ACAAAATTGG
902359 AGTACAAAAACAAAAGAAAAGAAAAAAAGAAGAAA
1 AGTA-AAAAA-AAAAGAAAAG-AAAAAAGAAGAAA
* **
902394 AATTTAAAAAAAAGAAAAG-AAAAAGAAGAAA
1 AGTAAAAAAAAAAGAAAAGAAAAAAGAAGAAA
902425 AGTAAAAAAAAAAG
1 AGTAAAAAAAAAAG
902439 CAAGCCAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 23 0.59
33 10 0.26
34 4 0.10
35 2 0.05
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.06
Consensus pattern (32 bp):
AGTAAAAAAAAAAGAAAAGAAAAAAGAAGAAA
Found at i:903168 original size:29 final size:30
Alignment explanation
Indices: 903109--903169 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
903099 AATGGATTTA
* * *
903109 TTTAGTGACCAAAGTATAAATTTTGAAAAG
1 TTTAGGGACCAAAATATAAATTTTAAAAAG
*
903139 TTTAGGGACCAAAATGT-AATTTTAAAAAG
1 TTTAGGGACCAAAATATAAATTTTAAAAAG
903168 TT
1 TT
903170 ACATATGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (30 bp):
TTTAGGGACCAAAATATAAATTTTAAAAAG
Found at i:904825 original size:40 final size:40
Alignment explanation
Indices: 904770--904928 Score: 275
Period size: 40 Copynumber: 4.0 Consensus size: 40
904760 AGGTTTATAG
*
904770 TACACTTCGGTGTATATGG-GGGCCACGACCTTATGTGTCA
1 TACACTTCGGTGTATATGGTGGG-CACGACCTTATGTGTAA
*
904810 TACACTTCGGTGTATATGGTGGGCACGACCTTATATGTAA
1 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
*
904850 TACACTTCGGTGTATATGGTGGGCACAACCTTATGTGTAA
1 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
904890 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTA
1 TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTA
904929 GCACTACGGT
Statistics
Matches: 113, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 110 0.97
41 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (40 bp):
TACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
Found at i:905126 original size:128 final size:128
Alignment explanation
Indices: 904898--905149 Score: 477
Period size: 128 Copynumber: 2.0 Consensus size: 128
904888 AATACACTTC
*
904898 GGTGTATATGGTGGGCACGACCTTATGTGTAGCACTACGGTGCAAATATTACTCGGATACCCAGG
1 GGTGTATATGGTGGGCACGACCTTATGTGTAGCACTACGGTGCAAATATTACTCGAATACCCAGG
*
904963 GTCCTCAGGGTTGTATATTGGGCTATAGGCTATGGTTTATGGTTTATTGCTTAATAAATCTTA
66 GTCCTCAGGGTTGTATATTGAGCTATAGGCTATGGTTTATGGTTTATTGCTTAATAAATCTTA
905026 GGTGTATATGGTGGGCACGACCTTATGTGTAGCACTACGGTGCAAATATTACTCGAATACCCAGG
1 GGTGTATATGGTGGGCACGACCTTATGTGTAGCACTACGGTGCAAATATTACTCGAATACCCAGG
*
905091 GTCCTCAGGGTTGTATATTGAGCTATAGGCTATGGTTTATGGTTTATTTCTTAATAAAT
66 GTCCTCAGGGTTGTATATTGAGCTATAGGCTATGGTTTATGGTTTATTGCTTAATAAAT
905150 GGTAAGCATG
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 121 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (128 bp):
GGTGTATATGGTGGGCACGACCTTATGTGTAGCACTACGGTGCAAATATTACTCGAATACCCAGG
GTCCTCAGGGTTGTATATTGAGCTATAGGCTATGGTTTATGGTTTATTGCTTAATAAATCTTA
Found at i:905388 original size:46 final size:45
Alignment explanation
Indices: 905161--905603 Score: 622
Period size: 46 Copynumber: 9.8 Consensus size: 45
905151 GTAAGCATGC
** * **
905161 AAATAAGCTTATAAGCTTATGGAAT-AATGACAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
*
905205 AAATAAGCTTAAGAGCTTATGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
*
905250 AAATAAGCTTATGAGCTTATGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
* * * ** * *
905295 AATTAAGATTACGAGCTTATGGAAT-AATAATAAGCATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
*
905339 AAATAAGCTTATGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGG-ATTAAATGGTAAGTATATTGGTA
905385 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGG-ATTAAATGGTAAGTATATTGGTA
*
905431 AAATAAGCTTACGAGCTTATGAAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATG-GATTAAATGGTAAGTATATTGGTA
* * *
905477 AAATAAGCTTATGAGCTTATAGAATTAAATGGTAAATATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGATTAAATGGTAAGTATATTGGTA
* *
905523 AAATAAGCTTACGAGCTTATGGGATTAAATGGTATGTATTTTGGTA
1 AAATAAGCTTACGAGCTTAT-GGATTAAATGGTAAGTATATTGGTA
905569 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTAT-GGATTAAATGGTAAG
905604 AGATTTATTT
Statistics
Matches: 360, Mismatches: 34, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
44 56 0.16
45 94 0.26
46 209 0.58
47 1 0.00
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.34
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
Found at i:911049 original size:19 final size:17
Alignment explanation
Indices: 911006--911057 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
910996 CATTTCTATA
*
911006 ATTATTT-CATTTCTTT
1 ATTATTTCCATTTTTTT
*
911022 -CTATTTCCATTATTTTT
1 ATTATTTCCATT-TTTTT
911039 ATTATTATCCATTTTTTT
1 ATTATT-TCCATTTTTTT
911057 A
1 A
911058 ATTCCACCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.17
16 4 0.14
17 4 0.14
18 10 0.34
19 6 0.21
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTATTTCCATTTTTTT
Found at i:915798 original size:76 final size:76
Alignment explanation
Indices: 915672--915826 Score: 283
Period size: 76 Copynumber: 2.0 Consensus size: 76
915662 GGATTAGGGT
915672 TTGTTATTTTATTTTGATTAACAATATCTTGGCAGATGATGGTTCCCTTTGGGTGGCATGGGTGA
1 TTGTTATTTTATTTTGATTAACAATATCTTGGCAGATGATGGTTCCCTTTGGGTGGCATGGGTGA
915737 AGGAGTATGTC
66 AGGAGTATGTC
* * *
915748 TTGTTGTTTTATTTTGATTAACGATATCTTGGCAGGTGATGGTTCCCTTTGGGTGGCATGGGTGA
1 TTGTTATTTTATTTTGATTAACAATATCTTGGCAGATGATGGTTCCCTTTGGGTGGCATGGGTGA
915813 AGGAGTATGTC
66 AGGAGTATGTC
915824 TTG
1 TTG
915827 AAGGGGGATG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.19, C:0.10, G:0.30, T:0.41
Consensus pattern (76 bp):
TTGTTATTTTATTTTGATTAACAATATCTTGGCAGATGATGGTTCCCTTTGGGTGGCATGGGTGA
AGGAGTATGTC
Found at i:917809 original size:54 final size:54
Alignment explanation
Indices: 917286--917790 Score: 654
Period size: 54 Copynumber: 9.3 Consensus size: 54
917276 CTATGTGTAC
* * * *
917286 TATCGACACTACGTGTGCAACCCACAGAATTCATAAAAAGTTTATGAACGACTG
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * * * *
917340 TATCGGCACTAAGTGTGTAACCCATATAATTCATAATATGTTTATGAAAGACTG
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * *
917394 TATCAACACTAAGTATGCAACCCATAGAATTCATAATATGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * *
917448 TATCGACACTAAGTGTGCAACCCACATAATCCATAATATGTTTATGAACCACCG
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * *
917502 TATCGACACTAAGTGTACAATCCATAAAATTCATAATATGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
*
917556 TATCCACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * **
917610 TATCCACACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAATGATTG
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* * * *
917664 GATCGGCACTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAACGAAACG
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACG-ACCG
* *
917719 TATTTG-C-CTTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAACGACCG
1 TA-TCGACAC-TAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
* *
917773 TATCGTCACTACGTGTGC
1 TATCGACACTAAGTGTGC
917791 TCCCCAAAGA
Statistics
Matches: 396, Mismatches: 50, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
53 2 0.01
54 346 0.87
55 46 0.12
56 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCG
Found at i:923880 original size:24 final size:26
Alignment explanation
Indices: 923852--923908 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 26
923842 TCTTTCTTTC
*
923852 TTATTTCTGTTTTCAT-TAT-TAT-TA
1 TTATTT-TATTTTCATATATATATATA
923876 TTATTATTATTTTCATATATATATATA
1 TTATT-TTATTTTCATATATATATATA
923903 TTATTT
1 TTATTT
923909 ATTATTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 13 0.46
25 4 0.14
26 4 0.14
27 7 0.25
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (26 bp):
TTATTTTATTTTCATATATATATATA
Found at i:923933 original size:17 final size:16
Alignment explanation
Indices: 923893--923962 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
923883 TATTTTCATA
* *
923893 TATATATATATTA-TT
1 TATATTTATTTTATTT
*
923908 TATTATTTATATTTCTTT
1 TA-TATTTAT-TTTATTT
*
923926 TATATTTATTTTTTTT
1 TATATTTATTTTATTT
*
923942 CTTTATTTATTTTTATTT
1 -TATATTTA-TTTTATTT
923960 TAT
1 TAT
923963 TCTTGTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.05
16 12 0.28
17 18 0.42
18 11 0.26
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TATATTTATTTTATTT
Found at i:923972 original size:34 final size:35
Alignment explanation
Indices: 923876--924274 Score: 100
Period size: 34 Copynumber: 10.9 Consensus size: 35
923866 ATTATTATTA
* *
923876 TTATTATTATTTTCATATATATATATATTATTTA-TTAT
1 TTATTTTTATTTT-ATAT-T-TAT-TTTTATTTATTTAT
* * *
923914 TTATATTTCTTTTATATTTATTTTT-TTTCTTTAT
1 TTATTTTTATTTTATATTTATTTTTATTTATTTAT
* *
923948 TTATTTTTATTTTAT-TCTTGTTTTTATTTATTTAC
1 TTATTTTTATTTTATAT-TTATTTTTATTTATTTAT
* * *
923983 TTATTATATGTATATTATTATTT-TCTTTATTT-TCTAT
1 TTATT-T-T-TATTTTA-TATTTATTTTTATTTATTTAT
* * * *
924020 ATT-TTTATATCTTTATCTTTATTTTTAGTT-TTTAC
1 -TTATTTTTAT-TTTATATTTATTTTTATTTATTTAT
* *
924055 CT-TTTTTA-TTT-TCTTTATCTTTGGTGATATGCTATTTACT
1 TTATTTTTATTTTATATTTAT-TTT--T-AT-T--TATTTA-T
* *
924095 TATATTTGTT-TTGTT-TCTTTATTTTT-TTTATTTTTT
1 T-TATTT-TTATT-TTATATTTATTTTTATTTA-TTTAT
* *
924131 TTATTTTTTTTATTATATTATATTATTATTATGTTCTTTAT
1 TTATTTTTATT-TTATATT-TA-T-TT-TTAT-TTATTTAT
* *
924172 TT-TATTTATTTTATTACCTTTTTTATCATTATTTTATTT-T
1 TTATTTTTATTTTA-TA--TTTATT-T--TTA-TTTATTTAT
*
924212 TTATTTTTTATTTT-TATCTCA-TTTTATTTATTTAT
1 TTA-TTTTTATTTTATAT-TTATTTTTATTTATTTAT
924247 TTATCTTTTA-TTT-TATTTA-TTTTATTTA
1 TTAT-TTTTATTTTATATTTATTTTTATTTA
924275 CTTTTATTAC
Statistics
Matches: 277, Mismatches: 39, Indels: 95
0.67 0.09 0.23
Matches are distributed among these distances:
31 7 0.03
32 6 0.02
33 15 0.05
34 57 0.21
35 50 0.18
36 11 0.04
37 16 0.06
38 31 0.11
39 15 0.05
40 18 0.06
41 19 0.07
42 17 0.06
43 6 0.02
44 9 0.03
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (35 bp):
TTATTTTTATTTTATATTTATTTTTATTTATTTAT
Found at i:923973 original size:23 final size:23
Alignment explanation
Indices: 923901--923976 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
923891 TATATATATA
*
923901 TATTATTTATTATTTATAT-TTCTTT
1 TATT-TTTATT-TTTAT-TCTTTTTT
* * *
923926 TATATTTATTTTTTTTCTTTATT
1 TATTTTTATTTTTATTCTTTTTT
923949 TATTTTTA-TTTTATTCTTGTTTT
1 TATTTTTATTTTTATTCTT-TTTT
923972 TATTT
1 TATTT
923977 ATTTACTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 10 0.24
23 23 0.55
24 6 0.14
25 3 0.07
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (23 bp):
TATTTTTATTTTTATTCTTTTTT
Found at i:923973 original size:27 final size:29
Alignment explanation
Indices: 923923--923980 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
923913 TTTATATTTC
* *
923923 TTTTATATTTATTTTTTTTCTTTATTTAT
1 TTTTATATTTATTCTTGTTCTTTATTTAT
923952 TTTTAT-TTTATTCTTGTT-TTTATTTAT
1 TTTTATATTTATTCTTGTTCTTTATTTAT
923979 TT
1 TT
923981 ACTTATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 11 0.41
28 10 0.37
29 6 0.22
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (29 bp):
TTTTATATTTATTCTTGTTCTTTATTTAT
Found at i:924123 original size:17 final size:18
Alignment explanation
Indices: 924097--924142 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
924087 TATTTACTTA
*
924097 TATTTGTTTT-GTTTCTT
1 TATTTTTTTTAGTTTCTT
* *
924114 TATTTTTTTTATTTTTTT
1 TATTTTTTTTAGTTTCTT
924132 TATTTTTTTTA
1 TATTTTTTTTA
924143 TTATATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.11, C:0.02, G:0.04, T:0.83
Consensus pattern (18 bp):
TATTTTTTTTAGTTTCTT
Found at i:924126 original size:9 final size:9
Alignment explanation
Indices: 924112--924279 Score: 88
Period size: 9 Copynumber: 17.9 Consensus size: 9
924102 GTTTTGTTTC
924112 TTTATTTTT
1 TTTATTTTT
924121 TTTATTTTT
1 TTTATTTTT
924130 TTTATTTTT
1 TTTATTTTT
*
924139 TTTATTATAT
1 TTTATT-TTT
* *
924149 TATATTATT
1 TTTATTTTT
* * *
924158 ATTATGTTC
1 TTTATTTTT
*
924167 TTTATTTTA
1 TTTATTTTT
924176 TTTA-TTTT
1 TTTATTTTT
* **
924184 ATTACCTTT
1 TTTATTTTT
*
924193 TTTATCATTAT
1 TTTAT--TTTT
924204 TTTATTTTT
1 TTTATTTTT
*
924213 TATTTTTTATT
1 T-TTATTT-TT
**
924224 TTTATCTCAT
1 TTTAT-TTTT
*
924234 TTTA-TTTA
1 TTTATTTTT
924242 TTTATTTATCT
1 TTTATTT-T-T
*
924253 TTTATTTTA
1 TTTATTTTT
*
924262 TTTATTTTA
1 TTTATTTTT
924271 TTTACTTTT
1 TTTA-TTTT
924280 ATTACCTTTA
Statistics
Matches: 119, Mismatches: 29, Indels: 21
0.70 0.17 0.12
Matches are distributed among these distances:
8 11 0.09
9 64 0.54
10 26 0.22
11 18 0.15
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTATTTTT
Found at i:924128 original size:5 final size:5
Alignment explanation
Indices: 924112--924282 Score: 96
Period size: 5 Copynumber: 34.2 Consensus size: 5
924102 GTTTTGTTTC
* *
924112 TTTAT TTT-T TTTAT TTT-T TTTAT TTT-T TTTAT TATAT TATAT TATTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT
*
924160 TATGT-T CTTTAT TTTA- TTTAT TTTAT TACCTT-T TTTAT CATTAT TTTAT
1 T-T-TAT -TTTAT TTTAT TTTAT TTTAT T---TTAT TTTAT -TTTAT TTTAT
* * *
924209 TTT-T TATT-T TTTATT TTTAT CTCAT TTTA- TTTA- TTTAT TTATCT
1 TTTAT T-TTAT TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT
924253 TTTAT TTTA- TTTAT TTTA- TTTACT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT T
924283 ACCTTTATTC
Statistics
Matches: 135, Mismatches: 10, Indels: 42
0.72 0.05 0.22
Matches are distributed among these distances:
4 38 0.28
5 65 0.48
6 26 0.19
7 4 0.03
8 2 0.01
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:924243 original size:4 final size:4
Alignment explanation
Indices: 924204--924274 Score: 53
Period size: 4 Copynumber: 18.0 Consensus size: 4
924194 TTATCATTAT
*
924204 TTTA TTT- TTTA TTT- TTTA -TT- TTTA TCTCA TTTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA -TTTA TTTA TTTA TTTA
*
924250 TCT- TTTA TTTTA TTTA TTTTA TTTA
1 TTTA TTTA -TTTA TTTA -TTTA TTTA
924275 CTTTTATTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
3 12 0.22
4 29 0.54
5 12 0.22
6 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:924259 original size:24 final size:24
Alignment explanation
Indices: 924210--924282 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
924200 TTATTTTATT
* * * *
924210 TTTTATTT-TTTATTTTTATCTCA
1 TTTTATTTATTTATTTATCTTTTA
924233 TTTTATTTATTTATTTATCTTTTA
1 TTTTATTTATTTATTTATCTTTTA
924257 TTTTATTTATTTTATTTA-CTTTTA
1 TTTTATTTA-TTTATTTATCTTTTA
924281 TT
1 TT
924283 ACCTTTATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 8 0.18
24 28 0.64
25 8 0.18
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTATTTATTTATTTATCTTTTA
Found at i:924289 original size:24 final size:25
Alignment explanation
Indices: 924237--924291 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
924227 ATCTCATTTT
**
924237 ATTTA-TTTATTTATCTTTTATTTT
1 ATTTATTTTATTTATCTTTTATTAC
924261 ATTTATTTTATTTA-CTTTTATTAC
1 ATTTATTTTATTTATCTTTTATTAC
*
924285 CTTTATT
1 ATTTATT
924292 CCTCTAACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (25 bp):
ATTTATTTTATTTATCTTTTATTAC
Found at i:927384 original size:150 final size:150
Alignment explanation
Indices: 927098--927393 Score: 337
Period size: 150 Copynumber: 2.0 Consensus size: 150
927088 AAGTCGTCGA
* ** *
927098 TTCAACAGAGAATACCTGTGAAGAACATAAGAGGCAAAAGGATGAAAAAGGAAATTTAAGCAGAA
1 TTCAACAGAGAATACCTGTGAAAAACATAAGAGGCAAAAGGATGAAAAAGGAAATCCAAGCAAAA
* * * ** * * ** *
927163 GGGCCTCCATGAATGTAATCCGAGACTGGCCCGTAGGTTTGAGAATGGATGGGGCATATGTAGCC
66 AGGCCTCAATGAATGTAATCCGAGACTGGCCCGTAGGTTTAAGAATCAATGGGACAGATACAACC
927228 AAGAAGACACCTCAAACTGC
131 AAGAAGACACCTCAAACTGC
* * *
927248 TTCAACAGAGAATTCTTGTGAAAAACATAAG-GCGCAAGAA-GATCG-GAAAGGAAATCCAAGCA
1 TTCAACAGAGAATACCTGTGAAAAACATAAGAG-GCAA-AAGGAT-GAAAAAGGAAATCCAAGCA
* * *
927310 AAAAGGCTTCAATGAATGTAGTCCGAGACTGGCCCGTGGGTTTAAGAATCAATGGGACAGATACA
63 AAAAGGCCTCAATGAATGTAATCCGAGACTGGCCCGTAGGTTTAAGAATCAATGGGACAGATACA
***
927375 ACTTTGAAGACACCTCAAA
128 ACCAAGAAGACACCTCAAA
927394 TAACTATATC
Statistics
Matches: 120, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
149 1 0.01
150 116 0.97
151 3 0.03
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.19
Consensus pattern (150 bp):
TTCAACAGAGAATACCTGTGAAAAACATAAGAGGCAAAAGGATGAAAAAGGAAATCCAAGCAAAA
AGGCCTCAATGAATGTAATCCGAGACTGGCCCGTAGGTTTAAGAATCAATGGGACAGATACAACC
AAGAAGACACCTCAAACTGC
Done.