Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013471.1 Kokia drynarioides strain JFW-HI SEQ_128497, 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: 179377
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 624 characters in sequence are not A, C, G, or T
Found at i:90 original size:4 final size:4
Alignment explanation
Indices: 81--114 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
71 TTCTTCCTCC
*
81 TTCT TTCT TTCT TTCT TTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
115 CTTCAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTCT
Found at i:98 original size:12 final size:11
Alignment explanation
Indices: 48--114 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 11
38 ACATTACCTT
48 TTTTTTCTTTC
1 TTTTTTCTTTC
59 TCTTTCTTC-TTC
1 T-TTT-TTCTTTC
* *
71 TTCTTCCTCCTTC
1 TT-TT-TTCTTTC
84 TTTCTTTCTTTC
1 TTT-TTTCTTTC
96 TTTTTTTCTTTC
1 -TTTTTTCTTTC
108 TTTTTTC
1 TTTTTTC
115 CTTCAATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
11 9 0.19
12 26 0.55
13 12 0.26
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:759 original size:31 final size:31
Alignment explanation
Indices: 724--788 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
714 TACAAAAGGG
***
724 TCACTAAACTATTTTCAAGTTTTCATTTAAA
1 TCACTAAACTATTCAAAAGTTTTCATTTAAA
*
755 TCACTAAACTATTCAAAAGTTTTTATTTAAA
1 TCACTAAACTATTCAAAAGTTTTCATTTAAA
786 TCA
1 TCA
789 ATGGACTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.43
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGTTTTCATTTAAA
Found at i:2918 original size:3 final size:3
Alignment explanation
Indices: 2910--2941 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2900 TAAGTGTTCT
*
2910 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2942 TTGTATGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3887 original size:24 final size:24
Alignment explanation
Indices: 3826--3888 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
3816 TAGACTAATA
* *
3826 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
3850 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
3874 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
3889 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:5850 original size:24 final size:24
Alignment explanation
Indices: 5822--5896 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
5812 AATTTGACTC
* *
5822 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTA
5846 AAACAAATAAACATAA-TTTAATTA
1 AAACAAATAAACA-AAGTTTAATTA
* * *
5870 AAACAATTAAACAAAGTTCAACTA
1 AAACAAATAAACAAAGTTTAATTA
5894 AAA
1 AAA
5897 TATTATTTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 2 0.05
24 41 0.93
25 1 0.02
ACGTcount: A:0.60, C:0.11, G:0.05, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTA
Found at i:6823 original size:6 final size:6
Alignment explanation
Indices: 6812--6836 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6802 TGTACATAAT
6812 TATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG T
6837 TTTGAACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:7141 original size:13 final size:13
Alignment explanation
Indices: 7123--7147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7113 AGTTCAAGTG
7123 AAAAAATGATTTT
1 AAAAAATGATTTT
7136 AAAAAATGATTT
1 AAAAAATGATTT
7148 CAACATCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAAAAATGATTTT
Found at i:11950 original size:18 final size:17
Alignment explanation
Indices: 11929--11980 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
11919 GGTGAAGATT
11929 ACGATGACGATGAAGACG
1 ACGATGA-GATGAAGACG
* *
11947 ACGAT-A-TTGAAGAAG
1 ACGATGAGATGAAGACG
11962 ACGATGAAGATGAAGACG
1 ACGATG-AGATGAAGACG
11980 A
1 A
11981 AGAAGACGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 12 0.44
17 2 0.07
18 13 0.48
ACGTcount: A:0.44, C:0.12, G:0.31, T:0.13
Consensus pattern (17 bp):
ACGATGAGATGAAGACG
Found at i:11976 original size:15 final size:15
Alignment explanation
Indices: 11929--11992 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
11919 GGTGAAGATT
*
11929 ACGATGACGATGAAG
1 ACGATGAAGATGAAG
* *
11944 ACGACGATATTGAAGAAG
1 ACGATGA-A--GATGAAG
11962 ACGATGAAGATGAAG
1 ACGATGAAGATGAAG
* *
11977 ACGAAGAAGACGAAG
1 ACGATGAAGATGAAG
11992 A
1 A
11993 TGAAAACGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
15 26 0.67
17 1 0.03
18 12 0.31
ACGTcount: A:0.47, C:0.11, G:0.31, T:0.11
Consensus pattern (15 bp):
ACGATGAAGATGAAG
Found at i:13578 original size:28 final size:28
Alignment explanation
Indices: 13538--13592 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
13528 AGCATTAATG
*
13538 GTGCAATTGACTGCTAGATGGAAGTTTA
1 GTGCAATTGACTGCCAGATGGAAGTTTA
13566 GTGCAATTGACTGCCAGATGGAAGTTT
1 GTGCAATTGACTGCCAGATGGAAGTTT
13593 GGGTATTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (28 bp):
GTGCAATTGACTGCCAGATGGAAGTTTA
Found at i:18552 original size:5 final size:5
Alignment explanation
Indices: 18544--18568 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18534 ATTCTATTCT
18544 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
18569 AAATGTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:32277 original size:25 final size:25
Alignment explanation
Indices: 32249--32353 Score: 183
Period size: 25 Copynumber: 4.1 Consensus size: 25
32239 AACTTTCGAA
32249 TAATTCAATGACCAAAACAAAAACT
1 TAATTCAATGACCAAAACAAAAACT
32274 TAATTCAATGACCAAAACAAAAACTT
1 TAATTCAATGACCAAAACAAAAAC-T
32300 AATAATTCAATGACCAAAACAAAAACT
1 --TAATTCAATGACCAAAACAAAAACT
32327 TAATTCAATGACCAAAACAAAAACT
1 TAATTCAATGACCAAAACAAAAACT
32352 TA
1 TA
32354 CCTATAATTT
Statistics
Matches: 77, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
25 51 0.66
26 1 0.01
27 1 0.01
28 24 0.31
ACGTcount: A:0.56, C:0.19, G:0.04, T:0.21
Consensus pattern (25 bp):
TAATTCAATGACCAAAACAAAAACT
Found at i:32314 original size:53 final size:53
Alignment explanation
Indices: 32247--32353 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
32237 AAAACTTTCG
32247 AATAATTCAATGACCAAAACAAAAACTTAATTCAATGACCAAAACAAAAACTT
1 AATAATTCAATGACCAAAACAAAAACTTAATTCAATGACCAAAACAAAAACTT
32300 AATAATTCAATGACCAAAACAAAAACTTAATTCAATGACCAAAACAAAAACTT
1 AATAATTCAATGACCAAAACAAAAACTTAATTCAATGACCAAAACAAAAACTT
32353 A
1 A
32354 CCTATAATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.57, C:0.19, G:0.04, T:0.21
Consensus pattern (53 bp):
AATAATTCAATGACCAAAACAAAAACTTAATTCAATGACCAAAACAAAAACTT
Found at i:32694 original size:6 final size:6
Alignment explanation
Indices: 32683--32716 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
32673 TTCGCTTTCC
32683 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCC
1 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCC
32717 TGCCTATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCA
Found at i:34357 original size:15 final size:15
Alignment explanation
Indices: 34339--34368 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34329 TTGACTTTCA
34339 TTTTTCTATTATTAT
1 TTTTTCTATTATTAT
*
34354 TTTTTTTATTATTAT
1 TTTTTCTATTATTAT
34369 ATTTCTACCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTATTATTAT
Found at i:59752 original size:17 final size:17
Alignment explanation
Indices: 59727--59790 Score: 92
Period size: 17 Copynumber: 3.7 Consensus size: 17
59717 GACCCAACAG
59727 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
*
59744 AAATTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
59761 AGTTTAAATTTATTATA
1 AATTTAAATTTATTTTA
59778 AATTTAAACTTTA
1 AATTTAAA-TTTA
59791 AATCTATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
17 37 0.90
18 4 0.10
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:59792 original size:7 final size:6
Alignment explanation
Indices: 59727--59793 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
59717 GACCCAACAG
* * * *
59727 AATTTA AATTT- ATTTTA AAATTA AATTT- ATTTTA AGTTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
59772 -ATTATA AATTTA AACTTTA AAT
1 AATT-TA AATTTA AA-TTTA AAT
59794 CTATTTAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 27 0.56
7 9 0.19
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:59801 original size:34 final size:33
Alignment explanation
Indices: 59727--59804 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 33
59717 GACCCAACAG
* * *
59727 AATTTAAATTTATTTTAAAATTAAATTTATTTT
1 AATTTAAATTTATTATAAAATTAAATTTAATCT
*
59760 AAGTTTAAATTTATTATAAATTTAAACTTTAAATCT
1 AA-TTTAAATTTATTATAAAATTAAA-TTT-AATCT
59796 -ATTTAAATT
1 AATTTAAATT
59805 AATGTCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 2 0.05
34 29 0.76
35 4 0.11
36 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (33 bp):
AATTTAAATTTATTATAAAATTAAATTTAATCT
Found at i:61624 original size:30 final size:30
Alignment explanation
Indices: 61588--61849 Score: 219
Period size: 30 Copynumber: 8.8 Consensus size: 30
61578 CCCCCCGAGT
61588 TTCCAAAAATCCCATTTTTAACCCCAAAAC
1 TTCCAAAAATCCCATTTTTAACCCCAAAAC
* * *
61618 TTCCAAAAATCTCATTTTT-ACCCAAAAAT
1 TTCCAAAAATCCCATTTTTAACCCCAAAAC
* * *
61647 TTCCAAAAATCTCATTTTT-ACCCAAAAAT
1 TTCCAAAAATCCCATTTTTAACCCCAAAAC
* **
61676 TTCCAAAAAGT-CCATTTTTACCCCCCTGAAC
1 TTCCAAAAA-TCCCATTTTTA-ACCCCAAAAC
* *
61707 TTCCAAAAAT-CCATTTTTGACCTCAAAAC
1 TTCCAAAAATCCCATTTTTAACCCCAAAAC
* ** * * * **
61736 TTCTAAAAATTACATTTTTATCCTC-GAGT
1 TTCCAAAAATCCCATTTTTAACCCCAAAAC
* ***
61765 TTCCAAAAATCCCATTTTTGACCTTGAAAC
1 TTCCAAAAATCCCATTTTTAACCCCAAAAC
* * *
61795 TTCCAAAAATTCCATTTTTGACCTCAAAAC
1 TTCCAAAAATCCCATTTTTAACCCCAAAAC
* *
61825 TTCCAAAAATTCCATTTTTACCCCC
1 TTCCAAAAATCCCATTTTTAACCCC
61850 GAACCTCTAA
Statistics
Matches: 191, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
29 88 0.46
30 89 0.47
31 14 0.07
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (30 bp):
TTCCAAAAATCCCATTTTTAACCCCAAAAC
Found at i:61872 original size:89 final size:89
Alignment explanation
Indices: 61562--61902 Score: 302
Period size: 89 Copynumber: 3.8 Consensus size: 89
61552 AAAATGTCTG
*** *
61562 AAAATTACATTTTTACCCCCCCGAGTTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAA
1 AAAATTACATTTTTA--CCCCCGAACCTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAA
*
61627 -TCTCATTTTT-ACC-CAAAAATTTCCA
64 TTC-CATTTTTGACCTC-AAAACTTCCA
*** ** *
61652 AAAATCT-CATTTTTACCCAAAAATTTCCAAAAAGT-CCATTTTTACCCCCCTG-AACTTCCAAA
1 AAAAT-TACATTTTTACCCCCGAACCTCCAAAAA-TCCCATTTTTA-ACCCC-GAAACTTCCAAA
*
61714 AA-TCCATTTTTGACCTCAAAACTTCTA
62 AATTCCATTTTTGACCTCAAAACTTCCA
* * *** * **
61741 AAAATTACATTTTTATCCTCGAGTTTCCAAAAATCCCATTTTTGACCTTGAAACTTCCAAAAATT
1 AAAATTACATTTTTACCCCCGAACCTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATT
61806 CCATTTTTGACCTCAAAACTTCCA
66 CCATTTTTGACCTCAAAACTTCCA
* * * * **
61830 AAAATTCCATTTTTACCCCCGAACCTCTAAAATTTNCC-TTTTTAACCCCGAAACTTTAAAAAAT
1 AAAATTACATTTTTACCCCCGAACCTCCAAAA-ATCCCATTTTTAACCCCGAAACTTCCAAAAAT
61894 TACCATTTT
65 T-CCATTTT
61903 CCCCCGAATG
Statistics
Matches: 207, Mismatches: 32, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
87 1 0.00
88 46 0.22
89 135 0.65
90 24 0.12
91 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (89 bp):
AAAATTACATTTTTACCCCCGAACCTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATT
CCATTTTTGACCTCAAAACTTCCA
Found at i:61909 original size:58 final size:58
Alignment explanation
Indices: 61799--61997 Score: 215
Period size: 58 Copynumber: 3.4 Consensus size: 58
61789 TGAAACTTCC
* * * * **
61799 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATT-CCATTTTTACCCCCGAACCTCT
1 AAAAATTCCATTTTTAACCCCGAAAC-TCTAAAAATTACCA-TTTTACCCCCGAATGTCT
* * *
61858 AAAATTTNCC-TTTTTAACCCCGAAACTTTAAAAAATTACCATTTT-CCCCCGAATGTCA
1 AAAAATT-CCATTTTTAACCCCGAAACTCT-AAAAATTACCATTTTACCCCCGAATGTCT
* * * * *
61916 AAAAACTCCATTTTTGACCTCGAAACTCTCAAAATTACCCTTTTACCCCCGAATGTCT
1 AAAAATTCCATTTTTAACCCCGAAACTCTAAAAATTACCATTTTACCCCCGAATGTCT
61974 AAAAATTCCATTTTTAACCCCGAA
1 AAAAATTCCATTTTTAACCCCGAA
61998 TTTTCCCAAG
Statistics
Matches: 115, Mismatches: 20, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
57 15 0.13
58 65 0.57
59 30 0.26
60 5 0.04
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (58 bp):
AAAAATTCCATTTTTAACCCCGAAACTCTAAAAATTACCATTTTACCCCCGAATGTCT
Found at i:61949 original size:29 final size:29
Alignment explanation
Indices: 61710--61951 Score: 106
Period size: 30 Copynumber: 8.2 Consensus size: 29
61700 CCTGAACTTC
* *
61710 CAAAAATCCATTTTTGACCTCAAAACTTCT
1 CAAAATTCCATTTTTGACCTCGAAAC-TCT
* * ***
61740 AAAAATTACATTTTT-ATCCTCGAGTTTC-
1 CAAAATTCCATTTTTGA-CCTCGAAACTCT
* *
61768 CAAAAATCCCATTTTTGACCTTGAAACT-T
1 C-AAAATTCCATTTTTGACCTCGAAACTCT
*
61797 CCAAAAATTCCATTTTTGACCTCAAAACT-T
1 -C-AAAATTCCATTTTTGACCTCGAAACTCT
* *
61827 CCAAAAATTCCATTTTT-ACCCCCGAACCTCT
1 -C-AAAATTCCATTTTTGA-CCTCGAAACTCT
* * *
61858 -AAAATTTNCC-TTTTTAACCCCGAAACTTT
1 CAAAA-TT-CCATTTTTGACCTCGAAACTCT
* * * ** *
61887 AAAAAATTACCA-TTTT-CCCCCGAATGTCA
1 -CAAAATT-CCATTTTTGACCTCGAAACTCT
* *
61916 AAAAACTCCATTTTTGACCTCGAAACTCT
1 CAAAATTCCATTTTTGACCTCGAAACTCT
61945 CAAAATT
1 CAAAATT
61952 ACCCTTTTAC
Statistics
Matches: 161, Mismatches: 36, Indels: 31
0.71 0.16 0.14
Matches are distributed among these distances:
27 3 0.02
28 14 0.09
29 60 0.37
30 79 0.49
31 5 0.03
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (29 bp):
CAAAATTCCATTTTTGACCTCGAAACTCT
Found at i:61977 original size:87 final size:85
Alignment explanation
Indices: 61829--61987 Score: 187
Period size: 87 Copynumber: 1.8 Consensus size: 85
61819 CAAAACTTCC
* * * * *
61829 AAAAATTCCATTTTTACCCCCGAACCTCTAAAATTTNCCTTTTTAACCCCGAAACTTTAAAAAAT
1 AAAAACTCCATTTTTACCCCCGAAACTCTAAAATTTACCCTTTTAACCCCGAAACTCT-AAAAAT
61894 TACCATTTTCCCCCGAATGTCA
65 T-CCATTTTCCCCCGAATGTCA
* * **
61916 AAAAACTCCATTTTTGA-CCTCGAAACTCTCAAAA-TTACCCTTTTACCCCCGAATGTCTAAAAA
1 AAAAACTCCATTTTT-ACCCCCGAAACTCT-AAAATTTACCCTTTTAACCCCGAAACTCTAAAAA
61979 TTCCATTTT
64 TTCCATTTT
61988 TAACCCCGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
85 7 0.11
86 7 0.11
87 42 0.69
88 5 0.08
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (85 bp):
AAAAACTCCATTTTTACCCCCGAAACTCTAAAATTTACCCTTTTAACCCCGAAACTCTAAAAATT
CCATTTTCCCCCGAATGTCA
Found at i:61978 original size:29 final size:28
Alignment explanation
Indices: 61829--61998 Score: 119
Period size: 29 Copynumber: 5.9 Consensus size: 28
61819 CAAAACTTCC
*
61829 AAAAATTCCATTTTTACCCCCGAACCTCT
1 AAAAATTCC-TTTTTACCCCCGAATCTCT
* * * *
61858 AAAATTTNCCTTTTTAACCCCGAAACTTT
1 AAAAATT-CCTTTTTACCCCCGAATCTCT
* * *
61887 AAAAAATTACCATTTT-CCCCCGAATGTCA
1 -AAAAATT-CCTTTTTACCCCCGAATCTCT
* * *
61916 AAAAACTCCATTTTTGA-CCTCGAAACTCT
1 AAAAATTCC-TTTTT-ACCCCCGAATCTCT
* * *
61945 CAAAATTACCCTTTTACCCCCGAATGTCT
1 AAAAATT-CCTTTTTACCCCCGAATCTCT
*
61974 AAAAATTCCATTTTTAACCCCGAAT
1 AAAAATTCC-TTTTTACCCCCGAAT
61999 TTTCCCAAGA
Statistics
Matches: 106, Mismatches: 27, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
27 2 0.02
28 13 0.12
29 75 0.71
30 16 0.15
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAAATTCCTTTTTACCCCCGAATCTCT
Found at i:63634 original size:6 final size:6
Alignment explanation
Indices: 63625--63653 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
63615 AGCACCTAAC
63625 GATGTT GATGTT GATGTT GATGTT GATGT
1 GATGTT GATGTT GATGTT GATGTT GATGT
63654 GTTTGTTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.48
Consensus pattern (6 bp):
GATGTT
Found at i:66992 original size:6 final size:6
Alignment explanation
Indices: 66981--67053 Score: 53
Period size: 6 Copynumber: 12.7 Consensus size: 6
66971 GGCCCAACAG
* * * * *
66981 AATTTA AATTT- ATTTTA AAATT- AATTTT ATTTTA AGTTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
67026 ACTTAA AATTTA AATTTA AAATTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
67054 AATGTCCAAA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
5 11 0.22
6 39 0.78
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:67020 original size:23 final size:23
Alignment explanation
Indices: 66981--67055 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
66971 GGCCCAACAG
* *
66981 AATTTAAATTT-ATTTTAAAATT
1 AATTAAAATTTAAATTTAAAATT
** * * *
67003 AATTTTATTTTAAGTTTAAATTT
1 AATTAAAATTTAAATTTAAAATT
*
67026 ACTTAAAATTTAAATTTAAAATT
1 AATTAAAATTTAAATTTAAAATT
67049 AAATTAA
1 -AATTAA
67056 TGTCCAAATA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 9 0.22
23 26 0.65
24 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
AATTAAAATTTAAATTTAAAATT
Found at i:67021 original size:17 final size:17
Alignment explanation
Indices: 66981--67043 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
66971 GGCCCAACAG
66981 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
66998 AAATTAATTTTATTTTA
1 AATTTAAATTTATTTTA
* * *
67015 AGTTTAAATTTACTTAA
1 AATTTAAATTTATTTTA
67032 AATTTAAATTTA
1 AATTTAAATTTA
67044 AAATTAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:67797 original size:22 final size:22
Alignment explanation
Indices: 67754--67797 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
67744 TTAATGGCAT
** *
67754 TAATTAATAATAGTAATTATAA
1 TAATTAATAATAACAATAATAA
67776 TAATTAATAATAACAATAATAA
1 TAATTAATAATAACAATAATAA
67798 CTTTTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAATTAATAATAACAATAATAA
Found at i:68842 original size:29 final size:29
Alignment explanation
Indices: 68810--68990 Score: 136
Period size: 29 Copynumber: 6.2 Consensus size: 29
68800 AAAATTATAT
*
68810 TTTTAACCCTAAAACTTCTAAAAATTCCA
1 TTTTAACCCCAAAACTTCTAAAAATTCCA
* *
68839 TTTTTAAACCCAAAACTT-TCAAAAATTACA
1 -TTTTAACCCCAAAACTTCT-AAAAATTCCA
* * * *
68869 TTTTTACCCCTAAACTTCCAAAAAATCCA
1 TTTTAACCCCAAAACTTCTAAAAATTCCA
* * * *
68898 TTTTGACCCCAAAAATTTTAAAATTTACCA
1 TTTTAACCCCAAAACTTCTAAAAATT-CCA
** *
68928 TTTT-ACCCCCGAA-TGTCCAAAAATTCCA
1 TTTTAACCCCAAAACT-TCTAAAAATTCCA
*
68956 TTTTGACCCCAAAACATTC-AAAAATTACCA
1 TTTTAACCCCAAAAC-TTCTAAAAATT-CCA
*
68986 ATTTA
1 TTTTA
68991 CCCTAGATGT
Statistics
Matches: 118, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
28 8 0.07
29 70 0.59
30 39 0.33
31 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (29 bp):
TTTTAACCCCAAAACTTCTAAAAATTCCA
Found at i:68842 original size:30 final size:31
Alignment explanation
Indices: 68790--68901 Score: 126
Period size: 30 Copynumber: 3.7 Consensus size: 31
68780 GGAGGTCCTC
* *
68790 AAACTTCTCCAAAATTATATTTTTAACCCTA
1 AAACTTCTCAAAAATTACATTTTTAACCCTA
*
68821 AAACTTCT-AAAAATTCCATTTTTAAACCC-A
1 AAACTTCTCAAAAATTACATTTTT-AACCCTA
*
68851 AAACTT-TCAAAAATTACATTTTTACCCCT-
1 AAACTTCTCAAAAATTACATTTTTAACCCTA
* *
68880 AAACTTC-CAAAAAATCCATTTT
1 AAACTTCTCAAAAATTACATTTT
68902 GACCCCAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
29 24 0.34
30 33 0.47
31 13 0.19
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (31 bp):
AAACTTCTCAAAAATTACATTTTTAACCCTA
Found at i:68947 original size:58 final size:58
Alignment explanation
Indices: 68829--69124 Score: 195
Period size: 58 Copynumber: 5.1 Consensus size: 58
68819 TAAAACTTCT
* * * * * **
68829 AAAAATTCCATTTTTAAACCCAAAACTTTCAAAAATTA-CATTTTTACCCCTAAACT-TCC
1 AAAAAATCCA-TTTTGACCCCAAAAATTTTAAAAATTACCA-TTTTACCCCCGAA-TGTCC
*
68888 AAAAAATCCATTTTGACCCCAAAAATTTTAAAATTTACCATTTTACCCCCGAATGTCC
1 AAAAAATCCATTTTGACCCCAAAAATTTTAAAAATTACCATTTTACCCCCGAATGTCC
* * * ** *
68946 AAAAATTCCATTTTGACCCCAAAACA-TTCAAAAATTACCAATTTACCCTAG-ATGTCT
1 AAAAAATCCATTTTGACCCCAAAA-ATTTTAAAAATTACCATTTTACCCCCGAATGTCC
** * * * ** * *
69003 AAAACCTCCATTATTGACCTCGAAACTCCTAAAAATTATCATTTTACTCCCCGAATGTCT
1 AAAAAATCCATT-TTGACCCCAAAAATTTTAAAAATTACCATTTTAC-CCCCGAATGTCC
* ** * * * ** * * * *
69063 AAAAATTCTGTTTTTATCCCGAATTTTTTGAAAATTACCATTTTACCCTCGGATGTCT
1 AAAAAATCCATTTTGACCCCAAAAATTTTAAAAATTACCATTTTACCCCCGAATGTCC
69121 AAAA
1 AAAA
69125 TTTCATTTTA
Statistics
Matches: 188, Mismatches: 42, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
57 16 0.09
58 118 0.63
59 40 0.21
60 14 0.07
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.33
Consensus pattern (58 bp):
AAAAAATCCATTTTGACCCCAAAAATTTTAAAAATTACCATTTTACCCCCGAATGTCC
Found at i:69146 original size:58 final size:59
Alignment explanation
Indices: 69034--69147 Score: 133
Period size: 58 Copynumber: 1.9 Consensus size: 59
69024 GAAACTCCTA
* * * * *
69034 AAAATTATCATTTTACTCCCCGAATGTCTAAAAATTCTGTTTTTATCCCGAATTTTTTG
1 AAAATTACCATTTTACTCCCCGAATGTCTAAAAATTCTATTTTAAACCCAAATTTTTTG
* * *
69093 AAAATTACCATTTTAC-CCTCGGATGTCTAAAATTTC-ATTTTAAACTCCAAATTTT
1 AAAATTACCATTTTACTCCCCGAATGTCTAAAAATTCTATTTTAAAC-CCAAATTTT
69148 CCCAAAATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
57 6 0.13
58 25 0.54
59 15 0.33
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (59 bp):
AAAATTACCATTTTACTCCCCGAATGTCTAAAAATTCTATTTTAAACCCAAATTTTTTG
Found at i:78981 original size:19 final size:20
Alignment explanation
Indices: 78952--78990 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
78942 AATATTTATA
*
78952 TATTTTATCAATTTAATTTT
1 TATTTTATCAATTAAATTTT
78972 TATTTT-TCAATTAAATTTT
1 TATTTTATCAATTAAATTTT
78991 ATCATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTATCAATTAAATTTT
Found at i:80407 original size:37 final size:39
Alignment explanation
Indices: 80311--80410 Score: 104
Period size: 37 Copynumber: 2.7 Consensus size: 39
80301 TAGATCTTTG
* *
80311 AATCTTATCATGTATAAGATTTTTAGTTTAGTTAGTTTT
1 AATCTTATCATGTATAAGATTTTTAGATTAGTTAGTTAT
* *
80350 AAT-TTGA--ATTGTATAA-ATTTTTA-ATTCGTTTG-TAT
1 AATCTT-ATCA-TGTATAAGATTTTTAGATTAGTTAGTTAT
80385 AATCTTATCATGTATAAGATTTTTAG
1 AATCTTATCATGTATAAGATTTTTAG
80411 CTTTAATCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
35 6 0.12
36 15 0.30
37 16 0.32
38 9 0.18
39 4 0.08
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (39 bp):
AATCTTATCATGTATAAGATTTTTAGATTAGTTAGTTAT
Found at i:86676 original size:17 final size:17
Alignment explanation
Indices: 86633--86729 Score: 50
Period size: 17 Copynumber: 5.6 Consensus size: 17
86623 TCCAATTTTT
* *
86633 AATTTTAATTTACTTTA
1 AATTTAAATTTACTCTA
* * *
86650 AGTTTGAATTTGCTCTA
1 AATTTAAATTTACTCTA
** * *
86667 AATTTAAATTCATTTTTTG
1 AATTTAAATT--TACTCTA
* *
86686 AGTTTAAATTTACTTTA
1 AATTTAAATTTACTCTA
* *
86703 AATTTAAATTTATTGTA
1 AATTTAAATTTACTCTA
*
86720 AATTAAAATT
1 AATTTAAATT
86730 AATTAAAAAG
Statistics
Matches: 60, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
17 48 0.80
19 12 0.20
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTACTCTA
Found at i:87447 original size:3 final size:3
Alignment explanation
Indices: 87439--87514 Score: 57
Period size: 3 Copynumber: 25.0 Consensus size: 3
87429 TCTAATACAT
* * * * *
87439 TAA TAA TAA TAA TAT TAA TAA TAA CAG TAA TAA TGAA T-T TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
87484 TAA TAA TAAA TAA T-A TAA TAAA TAA GAA TAA
1 TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA
87515 AATTTGAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
2 3 0.05
3 46 0.79
4 9 0.16
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:87501 original size:12 final size:13
Alignment explanation
Indices: 87439--87514 Score: 66
Period size: 12 Copynumber: 5.7 Consensus size: 13
87429 TCTAATACAT
87439 TAATAATAAT-AA
1 TAATAATAATAAA
*
87451 TATTAATAATAACA
1 TAATAATAATAA-A
* *
87465 GTAATAATGAATTTAT
1 -TAATAAT-AA-TAAA
87481 TAATAATAATAAA
1 TAATAATAATAAA
87494 TAAT-ATAATAAA
1 TAATAATAATAAA
*
87506 TAAGAATAA
1 TAATAATAA
87515 AATTTGAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
12 20 0.39
13 11 0.22
14 3 0.06
15 13 0.25
16 2 0.04
17 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:88612 original size:29 final size:28
Alignment explanation
Indices: 88558--88743 Score: 105
Period size: 28 Copynumber: 6.5 Consensus size: 28
88548 AAAATATCCA
* * **
88558 AAAATTATATTTTGACCCTTAAACTTCC
1 AAAATTACATTTTTACCCTCGAACTTCC
*
88586 TAAAAATTACATTTTTCCCCT-GAACTTTCC
1 --AAAATTACATTTTTACCCTCGAAC-TTCC
88616 AAAATTACATTTTTACCCTCGAACCTTCC
1 AAAATTACATTTTTACCCTCGAA-CTTCC
* * * *
88645 AAAATTCCA-TTTGA-CCTTG-ATTTCACC
1 AAAATTACATTTTTACCCTCGAACTT--CC
** **
88672 AAAATTATCA-TTTTACCCTC-ATTTTTAA
1 AAAATTA-CATTTTTACCCTCGA-ACTTCC
*
88700 AAAATTACATTTTTACCCCCCGAACTTTCC
1 AAAATTACATTTTTA-CCCTCGAAC-TTCC
*
88730 AAAATTCCATTTTT
1 AAAATTACATTTTT
88744 TGACCTCGAT
Statistics
Matches: 122, Mismatches: 21, Indels: 26
0.72 0.12 0.15
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 14 0.11
28 40 0.33
29 25 0.20
30 40 0.33
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATTACATTTTTACCCTCGAACTTCC
Found at i:88624 original size:28 final size:28
Alignment explanation
Indices: 88588--88743 Score: 122
Period size: 28 Copynumber: 5.5 Consensus size: 28
88578 AAACTTCCTA
*
88588 AAAATTACATTTTTCCCCTGAACTTTCC
1 AAAATTACATTTTTACCCTGAACTTTCC
*
88616 AAAATTACATTTTTACCCTCGAACCTTCC
1 AAAATTACATTTTTACCCT-GAACTTTCC
* * *
88645 AAAATTCCA-TTTGACCTTG-A-TTTCACC
1 AAAATTACATTTTTACCCTGAACTTT--CC
* ** **
88672 AAAATTATCA-TTTTACCCTCATTTTTAA
1 AAAATTA-CATTTTTACCCTGAACTTTCC
*
88700 AAAATTACATTTTTACCCCCCGAACTTTCC
1 AAAATTACATTTTTA--CCCTGAACTTTCC
*
88730 AAAATTCCATTTTT
1 AAAATTACATTTTT
88744 TGACCTCGAT
Statistics
Matches: 99, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 11 0.11
28 46 0.46
29 16 0.16
30 23 0.23
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATTACATTTTTACCCTGAACTTTCC
Found at i:91724 original size:12 final size:12
Alignment explanation
Indices: 91701--91734 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
91691 GATAATTTAT
91701 AAAAAAGAAAAAG
1 AAAAAAG-AAAAG
91714 AAAAAAGAAAAG
1 AAAAAAGAAAAG
*
91726 AAAAGAGAA
1 AAAAAAGAA
91735 TTATGGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:93504 original size:16 final size:17
Alignment explanation
Indices: 93472--93504 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
93462 ATGCTTGGTA
93472 GAAAATAAAAGTGAGAG
1 GAAAATAAAAGTGAGAG
93489 GAAAATAAAA-TGAGAG
1 GAAAATAAAAGTGAGAG
93505 ATTAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (17 bp):
GAAAATAAAAGTGAGAG
Found at i:95139 original size:13 final size:14
Alignment explanation
Indices: 95116--95145 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
95106 GGATCTCACC
95116 TTTTTATTTTTTTT
1 TTTTTATTTTTTTT
95130 TTTTTATTTTTTTT
1 TTTTTATTTTTTTT
95144 TT
1 TT
95146 ATACATGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTATTTTTTTT
Found at i:97934 original size:18 final size:19
Alignment explanation
Indices: 97900--97940 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
97890 AATTACACAA
*
97900 AAAAATCAAAATTATTT-T
1 AAAAATCAAAATAATTTAT
97918 AAAAATACAAAA-AATTTAT
1 AAAAAT-CAAAATAATTTAT
97937 AAAA
1 AAAA
97941 TATTTTGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:99027 original size:96 final size:96
Alignment explanation
Indices: 98850--99034 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 96
98840 GAAAATGATG
* *
98850 TTCGATTAGCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAAGCGCAAATTTTCAGAATCGA
1 TTCGATTAGCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAAATTTTCAGAATCGA
*
98915 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAGAAACATTGCCTCGATTAAGGGTA
** * *
98946 TTCGATTATTTCGATTTGCAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTC-GAAACTC
1 TTCGATTAGCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAAATTTTCAG-AA-TC
*
99010 GAA-ATAAA-AGAATATTGCCTCGATT
64 GAAGATAAAGA-AACATTGCCTCGATT
99035 TTAAAGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
95 2 0.03
96 71 0.91
97 5 0.06
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (96 bp):
TTCGATTAGCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCACAAATTTTCAGAATCGA
AGATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:99416 original size:29 final size:29
Alignment explanation
Indices: 99296--99604 Score: 286
Period size: 30 Copynumber: 10.5 Consensus size: 29
99286 TATCGAAGAC
* * *
99296 AAAATGGTAATTTTGGGAAAGTTCGGGGTTA
1 AAAATGG-AATTTTTGG-AAGTTTGGGGGTA
* * *
99327 AAAATGGAAATTTTAGACA--TTCGGGGT-
1 AAAATGGAATTTTTGGA-AGTTTGGGGGTA
* * *
99354 AAAATGGTAA-TTTT-GAGAGTTTCGAGGTCG
1 AAAATGG-AATTTTTGGA-AGTTTGGGGGT-A
99384 AAAATGGAATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGGGGGTA
* ***
99413 AAAATAGAATTTTTGGAAGTTTTAAGGTAA
1 AAAATGGAATTTTTGGAAGTTTGGGGGT-A
* *
99443 AAAATGAAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGGGGGTA
* *
99472 AAAATGGAGTTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAG-TTTGGGGGTA
* * *
99502 AAAATGGAATTTTTGGAAGTTAGTGGGCA
1 AAAATGGAATTTTTGGAAGTTTGGGGGTA
* *
99531 AAAATGGAGTTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTGGGGGT-A
**
99561 AAAATGGAATTTTTGGAAGTTTGATGGTA
1 AAAATGGAATTTTTGGAAGTTTGGGGGTA
99590 AAAATGGAATTTTTG
1 AAAATGGAATTTTTG
99605 AATAGTTTAG
Statistics
Matches: 228, Mismatches: 39, Indels: 24
0.78 0.13 0.08
Matches are distributed among these distances:
26 3 0.01
27 11 0.05
28 14 0.06
29 90 0.39
30 101 0.44
31 9 0.04
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTGGGGGTA
Found at i:99434 original size:59 final size:59
Alignment explanation
Indices: 99296--99604 Score: 315
Period size: 59 Copynumber: 5.3 Consensus size: 59
99286 TATCGAAGAC
* * * * * *
99296 AAAATGGTAATTTTGGGAAAG-TTCGGGGTTAAAAATGGAAATTTTAGACA--TTCGGGGT-
1 AAAATGG-AATTTTTGG-AAGTTTCGAGGTCAAAAATGGAATTTTTGGA-AGTTTGGGGGTA
*
99354 AAAATGGTAA-TTTT-GAGAGTTTCGAGGTCGAAAATGGAATTTTTGGAAGTTTGGGGGTA
1 AAAATGG-AATTTTTGGA-AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTA
* ** * * *
99413 AAAATAGAATTTTTGGAAGTTTTAAGGTAAAAAATGAAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTA
* * * * * * *
99472 AAAATGGAGTTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTAGTGGGCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTA
* * **
99531 AAAATGGAGTTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTGATGGTA
1 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTA
99590 AAAATGGAATTTTTG
1 AAAATGGAATTTTTG
99605 AATAGTTTAG
Statistics
Matches: 214, Mismatches: 30, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
55 1 0.00
56 4 0.02
57 25 0.12
58 19 0.09
59 163 0.76
60 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTA
Found at i:100196 original size:22 final size:21
Alignment explanation
Indices: 100161--100221 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
100151 ATTAAAGCCT
*
100161 TATTAATATCATTAATAAAAA
1 TATTAATATTATTAATAAAAA
*
100182 TATTAAATATTATTAATAAAAT
1 TATT-AATATTATTAATAAAAA
100204 TATTTAATATGT-TTAATA
1 TA-TTAATAT-TATTAATA
100222 TGTATTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 4 0.11
22 28 0.80
23 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
TATTAATATTATTAATAAAAA
Found at i:101027 original size:24 final size:23
Alignment explanation
Indices: 100990--101036 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
100980 TTGGACTTTG
*
100990 ATTTAAATAGATTTAAACTTTAA
1 ATTTAAATAAATTTAAACTTTAA
*
101013 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAACTTTAA
101037 GTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATAAATTTAAACTTTAA
Found at i:101028 original size:17 final size:17
Alignment explanation
Indices: 101003--101082 Score: 106
Period size: 17 Copynumber: 4.6 Consensus size: 17
100993 TAAATAGATT
*
101003 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
101021 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
*
101038 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
101055 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
101072 TAAATTTAAAT
1 TAAATTTAAAT
101083 CCTGTTGGAC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
17 49 0.92
18 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:101030 original size:6 final size:6
Alignment explanation
Indices: 101000--101082 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
100990 ATTTAAATAG
* *
101000 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
101047 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
101083 CCTGTTGGAC
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
4 2 0.03
5 13 0.22
6 36 0.61
7 8 0.14
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:103109 original size:27 final size:27
Alignment explanation
Indices: 103071--103124 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
103061 CATTAGGTTT
*
103071 TAAAGTGAAGGGAACTATCATGAATTA
1 TAAAGTGAAGGGAACTATCACGAATTA
*
103098 TAAAGTGAAGGGAGCTATCACGAATTA
1 TAAAGTGAAGGGAACTATCACGAATTA
103125 AATTGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (27 bp):
TAAAGTGAAGGGAACTATCACGAATTA
Found at i:107393 original size:33 final size:33
Alignment explanation
Indices: 107350--107537 Score: 214
Period size: 33 Copynumber: 5.6 Consensus size: 33
107340 GAACTCCTTC
* *
107350 GGCATGTGCGAGCTGAGACTGTGAGCTCCCCTT
1 GGCATGTGCGAGCTGATACTGTGAGCTCCCATT
* *
107383 AGCATGTGCGAGCTGATATTGTGAGCTCCCATT
1 GGCATGTGCGAGCTGATACTGTGAGCTCCCATT
* *
107416 GGCATGTGCAAGCTAATACTNATTGTGAGCTCCCATT
1 GGCATGTGCGAGCTGATAC----TGTGAGCTCCCATT
* *
107453 GGCATGTGCGAGCTAATACTGTGAGCTCCTATT
1 GGCATGTGCGAGCTGATACTGTGAGCTCCCATT
* * * *
107486 GGCATGTGCGAGTTGATATTGTGAACTCCCCTT
1 GGCATGTGCGAGCTGATACTGTGAGCTCCCATT
* *
107519 GGCATGTACGAGTTGATAC
1 GGCATGTGCGAGCTGATAC
107538 CTCGAGCCCC
Statistics
Matches: 133, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
33 101 0.76
37 32 0.24
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (33 bp):
GGCATGTGCGAGCTGATACTGTGAGCTCCCATT
Found at i:108946 original size:20 final size:21
Alignment explanation
Indices: 108913--108958 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
108903 GGTTACAGAC
* *
108913 GTTCTTTTTATTTTCTTTTT-
1 GTTCTTTTCATTTTATTTTTG
*
108933 GTTCTTTTCGTTTTATTTTTG
1 GTTCTTTTCATTTTATTTTTG
108954 GTTCT
1 GTTCT
108959 CGAAAATTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.04, C:0.11, G:0.11, T:0.74
Consensus pattern (21 bp):
GTTCTTTTCATTTTATTTTTG
Found at i:110394 original size:20 final size:20
Alignment explanation
Indices: 110369--110407 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
110359 TCTTTGTCAT
*
110369 GCTCTGTTATGTTCTGCTCC
1 GCTCTGTTAGGTTCTGCTCC
*
110389 GCTCTGTTCGGTTCTGCTC
1 GCTCTGTTAGGTTCTGCTC
110408 TGTTTTGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.23, T:0.44
Consensus pattern (20 bp):
GCTCTGTTAGGTTCTGCTCC
Found at i:112362 original size:19 final size:19
Alignment explanation
Indices: 112322--112360 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
112312 AAAACCTCTC
*
112322 TTAAAATTATTCAAATATT
1 TTAAAATAATTCAAATATT
112341 TTAAAATAATTC-AATATT
1 TTAAAATAATTCAAATATT
112359 TT
1 TT
112361 TACCAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAATAATTCAAATATT
Found at i:112389 original size:21 final size:19
Alignment explanation
Indices: 112334--112389 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
112324 AAAATTATTC
*
112334 AAATA-TTTTAAAATAATT
1 AAATATTTTTAAAATAAAT
*
112352 CAATATTTTTACCAAATAAAT
1 AAATATTTTTA--AAATAAAT
112373 AAATTTATTTTTAAAAT
1 AAA--TATTTTTAAAAT
112390 TAAAAAACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 4 0.13
19 5 0.17
21 13 0.43
23 8 0.27
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATATTTTTAAAATAAAT
Found at i:114964 original size:31 final size:31
Alignment explanation
Indices: 114920--114983 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
114910 TTTTTGTCAC
* * *
114920 AAGTGGTAGTTAAATTATACTT-CATTACCTA
1 AAGTGATAGTTAAACTATA-TTCCATAACCTA
*
114951 AAGTGATATTTAAACTATATTCCATAACCTA
1 AAGTGATAGTTAAACTATATTCCATAACCTA
114982 AA
1 AA
114984 TCTAGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (31 bp):
AAGTGATAGTTAAACTATATTCCATAACCTA
Found at i:115822 original size:4 final size:5
Alignment explanation
Indices: 115811--115840 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
115801 AATATAATAT
115811 TAAAA T-AAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
115841 TTACTAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:118301 original size:16 final size:18
Alignment explanation
Indices: 118262--118295 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
118252 TAAGTTTATA
118262 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
118279 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
118296 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:118449 original size:20 final size:19
Alignment explanation
Indices: 118421--118461 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
118411 TAAAATTATT
118421 AAATATTAAAATAAAATAAA
1 AAATATTAAAA-AAAATAAA
* *
118441 AAATTTTAAAAAAATTAAA
1 AAATATTAAAAAAAATAAA
118460 AA
1 AA
118462 TAATATGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATATTAAAAAAAATAAA
Found at i:118460 original size:18 final size:18
Alignment explanation
Indices: 118383--118462 Score: 54
Period size: 18 Copynumber: 4.4 Consensus size: 18
118373 GATGACTATA
* *
118383 TAAAAATTTTCAATAAAT
1 TAAAAATTTTAAAAAAAT
* * **
118401 AAAAAAATTATAAAATTAT
1 -TAAAAATTTTAAAAAAAT
* *
118420 TAAATA-TTAAAATAAAAT
1 TAAAAATTTTAAA-AAAAT
*
118438 AAAAAATTTTAAAAAAAT
1 TAAAAATTTTAAAAAAAT
118456 TAAAAAT
1 TAAAAAT
118463 AATATGGGCG
Statistics
Matches: 43, Mismatches: 16, Indels: 5
0.67 0.25 0.08
Matches are distributed among these distances:
17 4 0.09
18 22 0.51
19 17 0.40
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATTTTAAAAAAAT
Found at i:121077 original size:4 final size:4
Alignment explanation
Indices: 121068--121098 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
121058 TATAGATTGT
*
121068 ATAC ATAC ATAC ATAC ATTC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
121099 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:122277 original size:10 final size:10
Alignment explanation
Indices: 122262--122286 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
122252 TATAATTAAA
122262 TTTTTATATT
1 TTTTTATATT
122272 TTTTTATATT
1 TTTTTATATT
122282 TTTTT
1 TTTTT
122287 CCTATGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATATT
Found at i:126920 original size:18 final size:17
Alignment explanation
Indices: 126899--126958 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
126889 GAATTGATAA
126899 TTTATGTGATCTGCTTAT
1 TTTATGTGA-CTGCTTAT
*
126917 TTTATGTGAAATGCTTAT
1 TTTATGTG-ACTGCTTAT
*
126935 TATATGTGCACTGCTTAT
1 TTTATGTG-ACTGCTTAT
126953 TTTATG
1 TTTATG
126959 AGTTCTGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
18 35 0.97
19 1 0.03
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.52
Consensus pattern (17 bp):
TTTATGTGACTGCTTAT
Found at i:132027 original size:18 final size:18
Alignment explanation
Indices: 132004--132038 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
131994 TGAAGAAATG
132004 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
132022 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
132039 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:132252 original size:20 final size:21
Alignment explanation
Indices: 132209--132253 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
132199 TAATTTATTT
132209 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
132230 TAATTTTATTTTGTTAG-TAG
1 TAATTTAATTTTGTTAGTTAG
132250 TAAT
1 TAAT
132254 AAGTAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:133039 original size:16 final size:16
Alignment explanation
Indices: 132993--133041 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
132983 TAAATCTAAC
*
132993 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
133009 T-A-TAA-TATAAAAA
1 TAATTAATTATCAAAA
133022 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
133038 TAAT
1 TAAT
133042 ATTCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:134433 original size:43 final size:43
Alignment explanation
Indices: 134351--134435 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
134341 ATTTACATGT
* *
134351 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
134394 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
134436 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:134753 original size:14 final size:16
Alignment explanation
Indices: 134729--134760 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
134719 ACAACCGGAT
134729 GATGTGAGTAC-CTCC
1 GATGTGAGTACACTCC
134744 GATG-GAGTACACTCC
1 GATGTGAGTACACTCC
134759 GA
1 GA
134761 ATTTGCAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (16 bp):
GATGTGAGTACACTCC
Found at i:135083 original size:45 final size:45
Alignment explanation
Indices: 135003--135094 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
134993 CCCTAGCTCA
* *
135003 TCAAGCCAAGGATGTCAGCCTCAATTTGACAAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTAACAAGCCACCGCAATAC
* * *
135048 TCAAGCCAAGGATATCAGGCTCAGTTTAACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTAACAAGCCACCGCAATAC
135093 TC
1 TC
135095 TACTCCTCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAATTTAACAAGCCACCGCAATAC
Found at i:135363 original size:21 final size:21
Alignment explanation
Indices: 135346--135400 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
135336 CCTTAAATCT
135346 TAAACCCTAAATTTTAAAACA
1 TAAACCCTAAATTTTAAAACA
** *
135367 CTAAACCCT-AATCATAAACCA
1 -TAAACCCTAAATTTTAAAACA
135388 TAAACCCTAAATT
1 TAAACCCTAAATT
135401 CGATACTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
21 12 0.43
22 8 0.29
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAATTTTAAAACA
Found at i:138492 original size:4 final size:4
Alignment explanation
Indices: 138469--138557 Score: 67
Period size: 4 Copynumber: 22.5 Consensus size: 4
138459 AAACACATTA
* * * * * *
138469 TCTT TCTC TCCT TC-T TCTT TCTT TCCTC TCCT TC-T TCCT TC-T TCCT
1 TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TCTT TCTT
* *
138515 TCCT TCTT TCTT CCTT TCTT TCTT TCTTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT TCTT TC
138558 CCGTTTATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
3 9 0.13
4 55 0.77
5 7 0.10
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (4 bp):
TCTT
Found at i:138507 original size:7 final size:7
Alignment explanation
Indices: 138472--138530 Score: 59
Period size: 7 Copynumber: 8.3 Consensus size: 7
138462 CACATTATCT
138472 TTCTCTCC
1 TTCT-TCC
*
138480 TTCTTCT
1 TTCTTCC
138487 TTCTTTCC
1 TTC-TTCC
138495 -TC-TCC
1 TTCTTCC
138500 TTCTTCC
1 TTCTTCC
138507 TTCTTCC
1 TTCTTCC
*
138514 TTCCTTCT
1 TT-CTTCC
138522 TTCTTCC
1 TTCTTCC
138529 TT
1 TT
138531 TCTTTCTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
5 3 0.07
6 2 0.05
7 25 0.58
8 13 0.30
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
TTCTTCC
Found at i:138518 original size:11 final size:11
Alignment explanation
Indices: 138472--138530 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
138462 CACATTATCT
138472 TTCTCTCCTT-C
1 TTCT-TCCTTCC
*
138483 TTCTTTCTTTCC
1 TTC-TTCCTTCC
138495 TCTCCTT-CTTCC
1 T-T-CTTCCTTCC
138507 TTCTTCCTTCC
1 TTCTTCCTTCC
*
138518 TTCTTTCTTCC
1 TTCTTCCTTCC
138529 TT
1 TT
138531 TCTTTCTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.08
11 25 0.62
12 8 0.20
13 3 0.08
14 1 0.03
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (11 bp):
TTCTTCCTTCC
Found at i:138543 original size:20 final size:20
Alignment explanation
Indices: 138469--138554 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 20
138459 AAACACATTA
138469 TCTTTCTCTCCTTCTT-CTT
1 TCTTTCTCTCCTTCTTCCTT
138488 TCTTTCCTCTCCTTCTTCC-T
1 TCTTT-CTCTCCTTCTTCCTT
* *
138508 TCTTCCT-TCCTTCTTTCTT
1 TCTTTCTCTCCTTCTTCCTT
* * * *
138527 CCTTTCTTTCTTTCTTTTCTT
1 TCTTTCTCTCCTTC-TTCCTT
138548 TCTTTCT
1 TCTTTCT
138555 TTCCCGTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.16
19 13 0.23
20 21 0.38
21 13 0.23
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
TCTTTCTCTCCTTCTTCCTT
Found at i:138547 original size:13 final size:13
Alignment explanation
Indices: 138518--138556 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
138508 TCTTCCTTCC
*
138518 TTCTTTC-TTCCT
1 TTCTTTCTTTCTT
138530 TTCTTTCTTTCTT
1 TTCTTTCTTTCTT
138543 TTCTTTCTTTCTT
1 TTCTTTCTTTCTT
138556 T
1 T
138557 CCCGTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTCTTTCTTTCTT
Found at i:138670 original size:19 final size:19
Alignment explanation
Indices: 138646--138684 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
138636 TTTACAATCA
*
138646 AAATAAAATTAACACACAC
1 AAATAAAATAAACACACAC
*
138665 AAATAAAATAAATACACAC
1 AAATAAAATAAACACACAC
138684 A
1 A
138685 CACACAGTCC
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:0.67, C:0.18, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATAAAATAAACACACAC
Found at i:139249 original size:16 final size:15
Alignment explanation
Indices: 139227--139269 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
139217 CATTACTAAT
*
139227 TTAAAAATTTATAAA
1 TTAAAAAATTATAAA
*
139242 TTATAAAAATTCTAAA
1 TTA-AAAAATTATAAA
*
139258 TTAAAAACTTAT
1 TTAAAAAATTAT
139270 CATTTTAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAAATTATAAA
Found at i:140747 original size:18 final size:18
Alignment explanation
Indices: 140724--140759 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
140714 GTTTATAATA
*
140724 TTTTATATTATGTTATTT
1 TTTTATATTATGTAATTT
140742 TTTTATATTATGTAATTT
1 TTTTATATTATGTAATTT
140760 AGAATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTATATTATGTAATTT
Found at i:140997 original size:13 final size:13
Alignment explanation
Indices: 140979--141003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
140969 AATTTAAATA
140979 AAATTTTATATCT
1 AAATTTTATATCT
140992 AAATTTTATATC
1 AAATTTTATATC
141004 GAATCGAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTTTATATCT
Found at i:141648 original size:3 final size:3
Alignment explanation
Indices: 141640--141667 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
141630 AGTTATATGG
141640 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
141668 GGGACGTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:156274 original size:15 final size:14
Alignment explanation
Indices: 156224--156275 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
156214 TTTATCTCAA
* *
156224 ATTATATTTTAGTCA
1 ATTATATTTTAAT-T
* *
156239 ATTATATTTGAAAT
1 ATTATATTTTAATT
156253 ATTATATTTTAATT
1 ATTATATTTTAATT
156267 ATTTATATT
1 A-TTATATT
156276 ATTATTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (14 bp):
ATTATATTTTAATT
Found at i:156276 original size:20 final size:20
Alignment explanation
Indices: 156251--156288 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
156241 TATATTTGAA
156251 ATATTA-TATTTTAATTATTT
1 ATATTATTATTTT-ATTATTT
156271 ATATTATTATTTTATTAT
1 ATATTATTATTTTATTAT
156289 GAAATAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATTATTATTTTATTATTT
Found at i:156399 original size:16 final size:16
Alignment explanation
Indices: 156378--156437 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
156368 AACGGTGCGG
156378 TTAAAATTATTTTAAT
1 TTAAAATTATTTTAAT
*
156394 TTAAAATTTTTAATTAA-
1 TTAAAATTATT--TTAAT
*
156411 TTAAATTTA-TTTAAT
1 TTAAAATTATTTTAAT
*
156426 TAAAAATCTATT
1 TTAAAAT-TATT
156438 ATTATTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.12
15 5 0.15
16 13 0.38
17 8 0.24
18 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAATTATTTTAAT
Found at i:156412 original size:18 final size:18
Alignment explanation
Indices: 156378--156428 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
156368 AACGGTGCGG
156378 TTAAAATTA-TT--TTAA
1 TTAAAATTATTTAATTAA
156393 TTTAAAATT-TTTAATTAA
1 -TTAAAATTATTTAATTAA
*
156411 TTAAATTTATTTAATTAA
1 TTAAAATTATTTAATTAA
156429 AAATCTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.33
17 7 0.23
18 13 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAAATTATTTAATTAA
Found at i:165636 original size:4 final size:4
Alignment explanation
Indices: 165627--165657 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
165617 AAAAGGGAGC
165627 GAGT GAGT GAGT GAGT GAGT GAGT GAGT GAG
1 GAGT GAGT GAGT GAGT GAGT GAGT GAGT GAG
165658 AGAGATTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.52, T:0.23
Consensus pattern (4 bp):
GAGT
Found at i:165973 original size:16 final size:16
Alignment explanation
Indices: 165949--165979 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
165939 TACATATTTG
*
165949 TAATTTTTTAATTTTC
1 TAATATTTTAATTTTC
165965 TAATATTTTAATTTT
1 TAATATTTTAATTTT
165980 TAAATTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TAATATTTTAATTTTC
Found at i:166307 original size:27 final size:27
Alignment explanation
Indices: 166239--166310 Score: 101
Period size: 28 Copynumber: 2.7 Consensus size: 27
166229 AGTTTAAAGT
*
166239 TTTA-GTTTGAGGTTTAATGTTTATGA
1 TTTAGGTTTGAGGTTCAATGTTTATGA
*
166265 TTTGAGGTTTGAGGTTCAATGTTTATGG
1 TTT-AGGTTTGAGGTTCAATGTTTATGA
*
166293 TTTAGGTTCGAGGTTCAA
1 TTTAGGTTTGAGGTTCAA
166311 AGTAAAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 3 0.07
27 15 0.37
28 23 0.56
ACGTcount: A:0.21, C:0.04, G:0.28, T:0.47
Consensus pattern (27 bp):
TTTAGGTTTGAGGTTCAATGTTTATGA
Found at i:171838 original size:29 final size:28
Alignment explanation
Indices: 171800--171863 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 28
171790 TTTAAGAAAA
171800 TTGT-TAATATAACACTTGTAC-TTTTAAT
1 TTGTCTAATATAACACTTG-ACATTTT-AT
171828 TTGTCTAATATAACACTTGACATTTTAT
1 TTGTCTAATATAACACTTGACATTTTAT
171856 TTCGTCTA
1 TT-GTCTA
171864 TCAATTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 10 0.30
29 23 0.70
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (28 bp):
TTGTCTAATATAACACTTGACATTTTAT
Found at i:175087 original size:22 final size:24
Alignment explanation
Indices: 175060--175113 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
175050 AGTAAGTGAT
175060 TTAATATAAATATAA-ATATATAA
1 TTAATATAAATATAACATATATAA
* *
175083 -TAATA-ATATTTAACATATATAA
1 TTAATATAAATATAACATATATAA
175105 TTAATATAA
1 TTAATATAA
175114 TTATTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 6 0.24
22 13 0.52
23 5 0.20
24 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TTAATATAAATATAACATATATAA
Found at i:177147 original size:23 final size:23
Alignment explanation
Indices: 177121--177173 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
177111 CAAACTGTGT
177121 TAGCATCTATGCAAAAAAGCTAG
1 TAGCATCTATGCAAAAAAGCTAG
177144 TAGCATCTATGCAAAAAAGCTAG
1 TAGCATCTATGCAAAAAAGCTAG
177167 TAGCATC
1 TAGCATC
177174 ATCTCAGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (23 bp):
TAGCATCTATGCAAAAAAGCTAG
Found at i:179329 original size:27 final size:28
Alignment explanation
Indices: 179290--179358 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 28
179280 TTTAAAAAAC
179290 TTTTTATATTTTTATATTA-ATTTATATA
1 TTTTTATATTTTTA-ATTATATTTATATA
*
179318 TTTTTAT-TTTTTAATTATTTTTATATAA
1 TTTTTATATTTTTAATTATATTTATAT-A
179346 TTTTCTATCATTT
1 TTTT-TAT-ATTT
179359 CTCATTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
26 4 0.11
27 13 0.37
28 12 0.34
29 3 0.09
31 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTTATATTTTTAATTATATTTATATA
Done.