Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold112
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: 1714866
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 134939 characters in sequence are not A, C, G, or T
File 1 of 11
Found at i:5695 original size:18 final size:17
Alignment explanation
Indices: 5664--5699 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5654 AACAATGTTA
*
5664 TTTTTAAAATTTTTATT
1 TTTTTAAAAATTTTATT
5681 TTTTATAAAAATTTTATT
1 TTTT-TAAAAATTTTATT
5699 T
1 T
5700 CAACTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAAAAATTTTATT
Found at i:6194 original size:16 final size:16
Alignment explanation
Indices: 6152--6242 Score: 57
Period size: 16 Copynumber: 5.7 Consensus size: 16
6142 AATAATTAAA
* *
6152 ATATAGTAT-AAATAT
1 ATATAATATAAAATTT
* *
6167 ATATATTTTAAAATTT
1 ATATAATATAAAATTT
6183 ATATAATAT-AAA-TT
1 ATATAATATAAAATTT
6197 AT-TAATGTATCAAAATTT
1 ATATAA--TAT-AAAATTT
6215 ATATAAATATAAAATATT
1 ATAT-AATATAAAAT-TT
*
6233 TTA-AATATAA
1 ATATAATATAA
6243 TTAAAATATG
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
13 3 0.05
14 4 0.07
15 13 0.21
16 19 0.31
17 8 0.13
18 11 0.18
19 1 0.02
20 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (16 bp):
ATATAATATAAAATTT
Found at i:6266 original size:29 final size:27
Alignment explanation
Indices: 6219--6272 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 27
6209 AAATTTATAT
6219 AAATATAAAATATTTTAAATATAATTA
1 AAATATAAAATATTTTAAATATAATTA
6246 AAATATGAAAA-ATTATATAAATATAAT
1 AAATAT-AAAATATT-T-TAAATATAAT
6273 ATACGAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.38
28 5 0.21
29 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AAATATAAAATATTTTAAATATAATTA
Found at i:8175 original size:14 final size:13
Alignment explanation
Indices: 8159--8183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8149 AAAAGTAATA
8159 AAAAAACTCGAAG
1 AAAAAACTCGAAG
8172 AAAAAACTCGAA
1 AAAAAACTCGAA
8184 TATATTTTTG
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:0.64, C:0.16, G:0.12, T:0.08
Consensus pattern (13 bp):
AAAAAACTCGAAG
Found at i:9673 original size:10 final size:10
Alignment explanation
Indices: 9658--9701 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
9648 TTAATTTAAT
9658 TAAAAAATTA
1 TAAAAAATTA
9668 TAAAAAATTA
1 TAAAAAATTA
*
9678 TAATAAA--A
1 TAAAAAATTA
9686 T-AAAAA-TA
1 TAAAAAATTA
9694 TAAAAAAT
1 TAAAAAAT
9702 ATTTAGATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 4 0.14
8 4 0.14
9 5 0.17
10 16 0.55
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:9695 original size:16 final size:16
Alignment explanation
Indices: 9670--9702 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
9660 AAAAATTATA
9670 AAAAATTATAATAAAAT
1 AAAAATTATAA-AAAAT
9687 AAAAA-TATAAAAAAT
1 AAAAATTATAAAAAAT
9702 A
1 A
9703 TTTAGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATTATAAAAAAT
Found at i:11136 original size:194 final size:195
Alignment explanation
Indices: 10845--11205 Score: 548
Period size: 194 Copynumber: 1.9 Consensus size: 195
10835 TTAACTCCTT
* * *
10845 TTACTTTCCCTTGGATAAAAAAAATTATCCAAACAAGAGAAAGGAATCTCTTTTTCTTTGTTTTA
1 TTACTTTCCCTTGGATAAAAAAAATTACCCAAACAAAAGAAAGAAATCTCTTTTTCTTTGTTTTA
*
10910 CTTTACTTTTCCTTTCTTTACCTTAATCCAAACATAGAGTTAAACTTAAAGATATATGTTATTTT
66 CTTTACTTTTCCTTTCTTTACCTTAATCCAAACATAGAGTTAAACTTAAAGATATATGTTATCTT
* * *
10975 ACAAATTTTGTTTGTGAAATTTAATTATTTCATTGTCAATGAATACAAGAGATACTCAACTCTCC
131 ACAAAATTTATTTGTGAAATTTAATAATTTCATTGTCAATGAATACAAGAGATACTCAACTCTCC
* *
11040 TTACTTTCCCTTGGAT-AAAAAAATTACCCCAATAAAAGAAAGAAATC-CATTTTTCTTTGTTTT
1 TTACTTTCCCTTGGATAAAAAAAATTACCCAAACAAAAGAAAGAAATCTC-TTTTTCTTTGTTTT
* ** *
11103 ACTTTACTTTTTCTTT-TCTTATTTTAGTCCAAACATAGAGTTAAACTTAAAGATATATGTTATC
65 ACTTTACTTTTCCTTTCT-TTACCTTAATCCAAACATAGAGTTAAACTTAAAGATATATGTTATC
* *
11167 TTATAAAATTTATTTGTGAAATTTAATAATTTCTTTGTC
129 TTACAAAATTTATTTGTGAAATTTAATAATTTCATTGTC
11206 GATGTCAATG
Statistics
Matches: 149, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
193 2 0.01
194 131 0.88
195 16 0.11
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (195 bp):
TTACTTTCCCTTGGATAAAAAAAATTACCCAAACAAAAGAAAGAAATCTCTTTTTCTTTGTTTTA
CTTTACTTTTCCTTTCTTTACCTTAATCCAAACATAGAGTTAAACTTAAAGATATATGTTATCTT
ACAAAATTTATTTGTGAAATTTAATAATTTCATTGTCAATGAATACAAGAGATACTCAACTCTCC
Found at i:14121 original size:23 final size:23
Alignment explanation
Indices: 14086--14129 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
14076 AAAATTTAAA
14086 TATTAATATTTAAATTTTAAATT
1 TATTAATATTTAAATTTTAAATT
*
14109 TATTAGATA-TTAATTTTTAAA
1 TATTA-ATATTTAAATTTTAAA
14130 AATGATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATTAATATTTAAATTTTAAATT
Found at i:14404 original size:2 final size:2
Alignment explanation
Indices: 14399--14436 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14389 TTTTTTTAAT
14399 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
14437 ATTCTAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14524 original size:20 final size:20
Alignment explanation
Indices: 14476--14541 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
14466 TAAAAATTAA
* *
14476 ATTTATTTTATGTAATTTTAT
1 ATTTATTTTATATAA-TTCAT
*
14497 AATT-TTTTATATAATTCAT
1 ATTTATTTTATATAATTCAT
*
14516 ATTTATTTTATTTAATAATCAT
1 ATTTATTTTATATAAT--TCAT
14538 ATTT
1 ATTT
14542 TATTATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.19
20 19 0.51
21 3 0.08
22 8 0.22
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTATTTTATATAATTCAT
Found at i:14545 original size:27 final size:27
Alignment explanation
Indices: 14490--14566 Score: 94
Period size: 25 Copynumber: 3.1 Consensus size: 27
14480 ATTTTATGTA
* *
14490 ATTTTATAATTT-TTTATATAATTCAT
1 ATTTTATTATTTATTTATATAAATCAT
14516 A-TTTA-T-TTTATTTA-AT-AATCAT
1 ATTTTATTATTTATTTATATAAATCAT
14538 ATTTTATTATTTATTTATATAAATCAT
1 ATTTTATTATTTATTTATATAAATCAT
14565 AT
1 AT
14567 ATGTTAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
22 6 0.14
23 9 0.21
24 5 0.12
25 12 0.28
26 3 0.07
27 8 0.19
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTTATTATTTATTTATATAAATCAT
Found at i:15009 original size:2 final size:2
Alignment explanation
Indices: 15002--15042 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
14992 ATTTAGTCTC
15002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15043 CACACACACT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15689 original size:2 final size:2
Alignment explanation
Indices: 15682--15736 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
15672 GGACTTTATT
15682 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
15724 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
15737 GAACTGTAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15893 original size:14 final size:14
Alignment explanation
Indices: 15871--15927 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
15861 ATTACAAAAT
*
15871 AAATATATATATTA
1 AAATTTATATATTA
15885 AAATTTATATAATATA
1 AAATTTATAT-AT-TA
*
15901 AATTATTAATATATTA
1 AA--ATTTATATATTA
15917 AAATTTATATA
1 AAATTTATATA
15928 AAATATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 17 0.47
15 2 0.06
16 8 0.22
17 2 0.06
18 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATTTATATATTA
Found at i:15947 original size:27 final size:27
Alignment explanation
Indices: 15877--15946 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 27
15867 AAATAAATAT
15877 ATATATTAAAATTTATATAATATAAATTATTA
1 ATATATTAAAA-TT-TAT-ATA-AAA-TATTA
15909 ATATATTAAAATTTATATAAAATATATA
1 ATATATTAAAATTTATATAAAATAT-TA
*
15937 ATATTTTAAA
1 ATATATTAAA
15947 TATAATTACG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 3 0.08
28 14 0.39
29 3 0.08
30 3 0.08
31 2 0.06
32 11 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATATTAAAATTTATATAAAATATTA
Found at i:16966 original size:17 final size:18
Alignment explanation
Indices: 16944--16978 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16934 TTTAGTTTGT
16944 ACTTAAA-TAAGCTTTTA
1 ACTTAAATTAAGCTTTTA
*
16961 ACTTAAATTAATCTTTTA
1 ACTTAAATTAAGCTTTTA
16979 TTTGGTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (18 bp):
ACTTAAATTAAGCTTTTA
Found at i:17318 original size:28 final size:29
Alignment explanation
Indices: 17287--17346 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
17277 AAATTTTTTT
*
17287 TATTTTCAT-AAATAGGTTTTTTATA-AAA
1 TATTTT-ATAAAATAGATTTTTTATACAAA
* *
17315 TATTTTTTAAAATAGATTTTTTTTACAAA
1 TATTTTATAAAATAGATTTTTTATACAAA
17344 TAT
1 TAT
17347 ATTGAGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 20 0.74
29 6 0.22
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
TATTTTATAAAATAGATTTTTTATACAAA
Found at i:17637 original size:19 final size:18
Alignment explanation
Indices: 17605--17642 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17595 TATTATTATT
17605 TTTAATAAAATTAATTAAA
1 TTTAATAAAATTAA-TAAA
17624 TTTAA-AAAATTTAATAAA
1 TTTAATAAAA-TTAATAAA
17642 T
1 T
17643 AATATATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTAATAAAATTAATAAA
Found at i:18031 original size:23 final size:23
Alignment explanation
Indices: 17996--18039 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
17986 AAAATTTTTT
*
17996 AAAATCTAATTTATTTTTATTTAA
1 AAAATCTAATTTA-ATTTATTTAA
*
18020 AAAAT-TAGTTTAATTTATTT
1 AAAATCTAATTTAATTTATTT
18040 TTATTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 6 0.33
24 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
AAAATCTAATTTAATTTATTTAA
Found at i:21511 original size:23 final size:21
Alignment explanation
Indices: 21462--21511 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 21
21452 AAATTTCATA
*
21462 AAAATAAATTAAATTAATTTT
1 AAAATAAAATAAATTAATTTT
21483 ATAAATAAAAATAAATTAGATTTT
1 A-AAAT-AAAATAAATTA-ATTTT
21507 AAAAT
1 AAAAT
21512 TTTTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 1 0.04
22 4 0.16
23 14 0.56
24 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATAAAATAAATTAATTTT
Found at i:21677 original size:15 final size:15
Alignment explanation
Indices: 21659--21689 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21649 ATAATGCATG
21659 TAAAAATAAATTAAA
1 TAAAAATAAATTAAA
21674 TAAAAATAAATTAAA
1 TAAAAATAAATTAAA
21689 T
1 T
21690 TAATTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAATAAATTAAA
Found at i:21887 original size:9 final size:9
Alignment explanation
Indices: 21870--21900 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
21860 TTGATATATT
*
21870 ATTTATTAA
1 ATTTTTTAA
21879 ATTTTTTAA
1 ATTTTTTAA
21888 ATTTTTTAA
1 ATTTTTTAA
21897 ATTT
1 ATTT
21901 AATTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:26608 original size:24 final size:23
Alignment explanation
Indices: 26575--26640 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
26565 TCGAAGTAAA
26575 AAAATA-AAAATAATAATGATAAT
1 AAAATATAAAATAATAAT-ATAAT
26598 AAAATATAAAAT-ATAATATAAT
1 AAAATATAAAATAATAATATAAT
** *
26620 ATGACATAAAA-AATAATATAA
1 AAAATATAAAATAATAATATAA
26641 ATACGATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 22 0.58
23 11 0.29
24 5 0.13
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (23 bp):
AAAATATAAAATAATAATATAAT
Found at i:26613 original size:17 final size:17
Alignment explanation
Indices: 26577--26733 Score: 72
Period size: 18 Copynumber: 9.1 Consensus size: 17
26567 GAAGTAAAAA
26577 AATAAAA-ATAATAATGAT
1 AATAAAATATAA-AAT-AT
26595 AATAAAATATAAAATAT
1 AATAAAATATAAAATAT
* * *
26612 AATATAATATGACATA-
1 AATAAAATATAAAATAT
* *
26628 AAAAATAATAT-AAATAC
1 AATAA-AATATAAAATAT
* *
26645 GATATAAATATATAAATGT
1 AATA-AAATATA-AAATAT
* *
26664 ATTAAAATATATAAATGT
1 AATAAAATATA-AAATAT
* * *
26682 ATTAAAAT-TTATATAT
1 AATAAAATATAAAATAT
* *
26698 TATAAATTATAAAA-AT
1 AATAAAATATAAAATAT
*
26714 AAAAAAATTATAAAAATAT
1 AATAAAA-TAT-AAAATAT
26733 A
1 A
26734 TAATATTTTA
Statistics
Matches: 106, Mismatches: 23, Indels: 19
0.72 0.16 0.13
Matches are distributed among these distances:
16 22 0.21
17 34 0.32
18 37 0.35
19 13 0.12
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (17 bp):
AATAAAATATAAAATAT
Found at i:26628 original size:22 final size:23
Alignment explanation
Indices: 26603--26659 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
26593 ATAATAAAAT
*
26603 ATAAAATATAATAT-AATATGAC
1 ATAAAATATAATATAAATACGAC
* *
26625 ATAAAAAATAATATAAATACGAT
1 ATAAAATATAATATAAATACGAC
26648 ATAAATATATAA
1 ATAAA-ATATAA
26660 ATGTATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.45
23 11 0.38
24 5 0.17
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (23 bp):
ATAAAATATAATATAAATACGAC
Found at i:26659 original size:8 final size:8
Alignment explanation
Indices: 26646--26776 Score: 58
Period size: 8 Copynumber: 16.2 Consensus size: 8
26636 TATAAATACG
26646 ATATAAAT
1 ATATAAAT
26654 ATATAAAT
1 ATATAAAT
*
26662 GTATTAAAAT
1 ATA-T-AAAT
26672 ATATAAAT
1 ATATAAAT
*
26680 GTATTAAA-
1 ATA-TAAAT
* *
26688 ATTTATAT
1 ATATAAAT
26696 ATTATAAAT
1 A-TATAAAT
*
26705 -TATAAAA
1 ATATAAAT
* *
26712 ATAAAAAA
1 ATATAAAT
*
26720 ATTATAAAA
1 A-TATAAAT
26729 ATATATAAT
1 ATATA-AAT
* *
26738 ATTTTAA-
1 ATATAAAT
26745 A-A-AAAT
1 ATATAAAT
26751 -TATAACAT
1 ATATAA-AT
*
26759 ATAAAAAT
1 ATATAAAT
26767 ATATAAAT
1 ATATAAAT
26775 AT
1 AT
26777 GAAAACGATA
Statistics
Matches: 92, Mismatches: 18, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
5 2 0.02
6 1 0.01
7 12 0.13
8 44 0.48
9 27 0.29
10 6 0.07
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (8 bp):
ATATAAAT
Found at i:26696 original size:20 final size:18
Alignment explanation
Indices: 26650--26694 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
26640 AATACGATAT
26650 AAATATATAAATGTATTA
1 AAATATATAAATGTATTA
26668 AAATATATAAATGTATTA
1 AAATATATAAATGTATTA
*
26686 AAATTTATA
1 AAATATATA
26695 TATTATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
AAATATATAAATGTATTA
Found at i:26740 original size:42 final size:44
Alignment explanation
Indices: 26646--26745 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 44
26636 TATAAATACG
* * * *
26646 ATATA-AATA-TATAAATGTATTAAAATATATAAATGTATTAAA
1 ATATATAATATTATAAATGTATAAAAATAAAAAAATGTATAAAA
*
26688 ATTTAT-ATATTATAAAT-TATAAAAATAAAAAAAT-TATAAAA
1 ATATATAATATTATAAATGTATAAAAATAAAAAAATGTATAAAA
*
26729 ATATATAATATTTTAAA
1 ATATATAATATTATAAA
26746 AAAATTATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
41 11 0.23
42 30 0.62
43 7 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (44 bp):
ATATATAATATTATAAATGTATAAAAATAAAAAAATGTATAAAA
Found at i:26766 original size:16 final size:17
Alignment explanation
Indices: 26745--26781 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
26735 AATATTTTAA
26745 AAAAAT-TATAACATAT-
1 AAAAATATATAA-ATATG
26761 AAAAATATATAAATATG
1 AAAAATATATAAATATG
26778 AAAA
1 AAAA
26782 CGATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATATATAAATATG
Found at i:27153 original size:29 final size:28
Alignment explanation
Indices: 27115--27177 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 28
27105 AAAAATAAAT
27115 TTAAAATTTAT-TTTAATTTAAGTTTTTTA
1 TTAAAATTTATATTTAA-TTAA-TTTTTTA
*
27144 TTAAATTTTATCGATTTAATTAATTTTTTA
1 TTAAAATTTAT--ATTTAATTAATTTTTTA
27174 TTAA
1 TTAA
27178 CTCGTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 10 0.33
30 11 0.37
31 4 0.13
32 5 0.17
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (28 bp):
TTAAAATTTATATTTAATTAATTTTTTA
Found at i:28259 original size:2 final size:2
Alignment explanation
Indices: 28254--28301 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
28244 GTAATGTGTG
* * * *
28254 TA TA TA TA TA TA TA TA TG TG TG TG 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
28296 TA TA TA
1 TA TA TA
28302 CATACCATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28275 original size:22 final size:22
Alignment explanation
Indices: 28247--28292 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
28237 ATAAATTGTA
28247 ATGTGTGTATATATATATATAT
1 ATGTGTGTATATATATATATAT
*
28269 ATGTGTGTGTATATATATATAT
1 ATGTGTGTATATATATATATAT
28291 AT
1 AT
28293 ATATATATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (22 bp):
ATGTGTGTATATATATATATAT
Found at i:28279 original size:24 final size:24
Alignment explanation
Indices: 28248--28294 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
28238 TAAATTGTAA
28248 TGTGTGTATATATATATATATATG
1 TGTGTGTATATATATATATATATG
28272 TGTGTGTATATATATATATATAT
1 TGTGTGTATATATATATATATAT
28295 ATATATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
TGTGTGTATATATATATATATATG
Found at i:28929 original size:28 final size:26
Alignment explanation
Indices: 28863--28929 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
28853 ATTTGAAGGT
*
28863 TTATATATT-TATATTTATATAATAA
1 TTATATATTATATATTGATATAATAA
*
28888 TTATATTTTATATATTGATAAGTAAATAA
1 TTATATATTATATATTGAT-A-T-AATAA
28917 -TATATATTATATA
1 TTATATATTATATA
28930 AAATTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 8 0.23
26 8 0.23
27 1 0.03
28 13 0.37
29 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
TTATATATTATATATTGATATAATAA
Found at i:28933 original size:19 final size:21
Alignment explanation
Indices: 28911--28956 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
28901 ATTGATAAGT
*
28911 AAATAATATA-TATTATA-TA
1 AAATAATATATTAATATATTA
28930 AAATTTAATATATTAATATATTA
1 AAA--TAATATATTAATATATTA
28953 AAAT
1 AAAT
28957 TATTTTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
19 3 0.14
21 8 0.36
22 6 0.27
23 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATAATATATTAATATATTA
Found at i:29115 original size:2 final size:2
Alignment explanation
Indices: 29097--29136 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
29087 TGTTATTGTA
* *
29097 CT CT TT CT CT CT AT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29137 TTGTGTGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:30617 original size:3 final size:3
Alignment explanation
Indices: 30611--30647 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
30601 GAACCAACTT
30611 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30648 ATTTTTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30922 original size:13 final size:13
Alignment explanation
Indices: 30904--30933 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30894 TCTGAATATG
*
30904 TATTAAATATTAA
1 TATTAAATATAAA
30917 TATTAAATATAAA
1 TATTAAATATAAA
30930 TATT
1 TATT
30934 TAAAAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:32029 original size:17 final size:17
Alignment explanation
Indices: 31998--32042 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
31988 ATAGAGCTTC
*
31998 TTATTCATT-AAAATAT
1 TTATTTATTAAAAATAT
*
32014 TTTTTTATTAAAAATAT
1 TTATTTATTAAAAATAT
32031 TTATTTATTAAA
1 TTATTTATTAAA
32043 TAAATTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTTATTAAAAATAT
Found at i:32049 original size:17 final size:16
Alignment explanation
Indices: 31998--32050 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
31988 ATAGAGCTTC
* *
31998 TTATTCATTAAAATAT
1 TTATTTATTAAAAAAT
*
32014 TTTTTTATTAAAAATAT
1 TTATTTATTAAAAA-AT
32031 TTATTTATTAAATAAAT
1 TTATTTATTAAA-AAAT
32048 TTA
1 TTA
32051 ACTATTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 11 0.35
17 18 0.58
18 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTATTAAAAAAT
Found at i:33484 original size:5 final size:5
Alignment explanation
Indices: 33474--33502 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
33464 AAAGATGAAA
33474 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
33503 AGAAAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:34291 original size:11 final size:11
Alignment explanation
Indices: 34262--34291 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
34252 TCTTTATCTG
*
34262 AAAAAAACAAA
1 AAAAAAATAAA
34273 AAAAAAATAAA
1 AAAAAAATAAA
34284 AAAAAAAT
1 AAAAAAAT
34292 CTTTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:34773 original size:21 final size:24
Alignment explanation
Indices: 34738--34780 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
34728 TATTTTTAAT
34738 TATTTCTTAAATTTT-AATATAAA
1 TATTTCTTAAATTTTAAATATAAA
34761 TATTT-TT-AATTTTAAATATA
1 TATTTCTTAAATTTTAAATATA
34781 TCGTGTTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTCTTAAATTTTAAATATAAA
Found at i:35254 original size:15 final size:16
Alignment explanation
Indices: 35234--35289 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
35224 TTATTTTATG
35234 TATTTAATATAATA-A
1 TATTTAATATAATATA
* *
35249 TATTTAAAATATTATA
1 TATTTAATATAATATA
* *
35265 TATTT-ATATATTTTA
1 TATTTAATATAATATA
35280 TATATTAATA
1 TAT-TTAATA
35290 ATTTATATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 23 0.68
16 8 0.24
17 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTTAATATAATATA
Found at i:35273 original size:8 final size:8
Alignment explanation
Indices: 35214--35328 Score: 62
Period size: 8 Copynumber: 14.1 Consensus size: 8
35204 TTTTTATTCG
35214 TATATTTA
1 TATATTTA
35222 TATTATTTTA
1 TA-TA-TTTA
*
35232 TGTATTTA
1 TATATTTA
*
35240 -ATA-TAA
1 TATATTTA
35246 TAATATTTA
1 T-ATATTTA
*
35255 -AAATATTA
1 TATAT-TTA
35263 TATATTTA
1 TATATTTA
35271 TATATTTTA
1 TATA-TTTA
*
35280 TATATTAA
1 TATATTTA
35288 TA-ATTTA
1 TATATTTA
*
35295 TAT-TATA
1 TATATTTA
35302 TCA-ATTTTAA
1 T-ATA-TTT-A
*
35312 AATATTTA
1 TATATTTA
35320 TATATTTA
1 TATATTTA
35328 T
1 T
35329 GTTATGTTCG
Statistics
Matches: 81, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
6 2 0.02
7 15 0.19
8 34 0.42
9 23 0.28
10 7 0.09
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (8 bp):
TATATTTA
Found at i:35294 original size:15 final size:15
Alignment explanation
Indices: 35248--35297 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
35238 TAATATAATA
35248 ATAT-TTAA-AATATT
1 ATATATTAATAAT-TT
*
35262 ATATATTTATATATTTT
1 ATATA-TTA-ATAATTT
35279 ATATATTAATAATTT
1 ATATATTAATAATTT
35294 ATAT
1 ATAT
35298 TATATCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 4 0.13
15 10 0.33
16 6 0.20
17 8 0.27
18 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATATTAATAATTT
Found at i:35651 original size:22 final size:22
Alignment explanation
Indices: 35621--35681 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
35611 TTTAAAATAA
35621 AAATAATTTTTATATTAATATTT
1 AAATAATTTTTATATTAA-ATTT
*
35644 ATAT-A-TTTTATAATTAAATTT
1 AAATAATTTTTAT-ATTAAATTT
*
35665 AAATAATTTTTTTATTA
1 AAATAATTTTTATATTA
35682 TTAAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 13 0.41
22 11 0.34
23 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AAATAATTTTTATATTAAATTT
Found at i:35652 original size:21 final size:22
Alignment explanation
Indices: 35621--35674 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
35611 TTTAAAATAA
35621 AAATAATTTT-TATATTAATATTT
1 AAATAATTTTATA-ATTAA-ATTT
*
35644 ATAT-ATTTTATAATTAAATTT
1 AAATAATTTTATAATTAAATTT
35665 AAATAATTTT
1 AAATAATTTT
35675 TTTATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.26
22 15 0.56
23 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATAATTTTATAATTAAATTT
Found at i:36469 original size:28 final size:28
Alignment explanation
Indices: 36425--36499 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
36415 AATAATTATT
36425 TATTTTATAATTAAATTT-AAATAATAATAA
1 TATTTT-T-ATTAAATTTAAAAT-ATAATAA
*
36455 TATTTTTATTAAATTTAAAATATATTAA
1 TATTTTTATTAAATTTAAAATATAATAA
* *
36483 AATTTTT-TAAAATTTAA
1 TATTTTTATTAAATTTAA
36500 TTTGAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.22
28 21 0.51
29 5 0.12
30 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TATTTTTATTAAATTTAAAATATAATAA
Found at i:36940 original size:2 final size:2
Alignment explanation
Indices: 36933--36961 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
36923 AGTTAAAGTT
36933 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36962 AGTTCTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36942 original size:32 final size:31
Alignment explanation
Indices: 36884--36943 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
36874 TAAAAAATCA
* *
36884 AAATATTAGTTATAATTTTTTAATATATGGC
1 AAATATTAGTTATAAGTTTATAATATATGGC
36915 AAATATTAAGTTA-AAGTTTATATATATAT
1 AAATATT-AGTTATAAGTTTATA-ATATAT
36944 ATATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (31 bp):
AAATATTAGTTATAAGTTTATAATATATGGC
Found at i:37129 original size:3 final size:3
Alignment explanation
Indices: 37123--37173 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
37113 GCAGCAGCAG
* *
37123 CAA CAA CAA CAAA CAA CAA CAA CAA CAG CAA CAA CAA CAA CAA CGA
1 CAA CAA CAA C-AA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
37169 CAA CA
1 CAA CA
37174 TTAACAGGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.33, G:0.04, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:42383 original size:23 final size:23
Alignment explanation
Indices: 42357--42436 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
42347 TTAAATCACA
42357 TAATTATTTTAAATATAATATTT
1 TAATTATTTTAAATATAATATTT
* * *
42380 TAATAAATTTAAATTTAATA-TT
1 TAATTATTTTAAATATAATATTT
*
42402 TAA--ATTTTAAAATTTATAATTTTT
1 TAATTATTTT-AAA--TATAATATTT
*
42426 TTATTATTTTA
1 TAATTATTTTA
42437 CTATGCTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
20 4 0.09
21 3 0.07
22 5 0.11
23 22 0.50
24 4 0.09
25 1 0.02
26 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TAATTATTTTAAATATAATATTT
Found at i:42398 original size:15 final size:15
Alignment explanation
Indices: 42378--42423 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 15
42368 AATATAATAT
42378 TTTAATAAATTTAAA
1 TTTAATAAATTTAAA
42393 TTTAAT--ATTTAAA
1 TTTAATAAATTTAAA
*
42406 TTTTA-AAATTTATAA
1 TTTAATAAATTTA-AA
42421 TTT
1 TTT
42424 TTTTATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.41
14 5 0.19
15 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAATAAATTTAAA
Found at i:42416 original size:14 final size:14
Alignment explanation
Indices: 42362--42424 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
42352 TCACATAATT
*
42362 ATTTT-AAATATAA
1 ATTTTAAAATTTAA
42375 TATTTTAATAAATTTAA
1 -ATTTT-A-AAATTTAA
*
42392 A-TTTAATATTTAA
1 ATTTTAAAATTTAA
42405 ATTTTAAAATTTATA
1 ATTTTAAAATTTA-A
42420 ATTTT
1 ATTTT
42425 TTTATTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
13 8 0.20
14 16 0.39
15 9 0.22
16 1 0.02
17 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTTAAAATTTAA
Found at i:42754 original size:18 final size:19
Alignment explanation
Indices: 42721--42756 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42711 GAATTGATTC
*
42721 AATTTAAAAATTATATTAT
1 AATTTAAAAATAATATTAT
42740 AATTT-AAAATAATATTA
1 AATTTAAAAATAATATTA
42757 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTTAAAAATAATATTAT
Found at i:42866 original size:2 final size:2
Alignment explanation
Indices: 42842--42883 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
42832 TTGTTAACTA
* *
42842 AT AT AT GAT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42884 ACTCAAATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:43042 original size:16 final size:16
Alignment explanation
Indices: 42997--43042 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
42987 GATCAAATAA
42997 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
* * **
43013 TACTTAAACATAAAAT
1 AATTTAAATTTAAAAT
43029 AATTTAAATTTAAA
1 AATTTAAATTTAAA
43043 TTTAAATTGA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:43370 original size:22 final size:22
Alignment explanation
Indices: 43332--43386 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
43322 AATAAAATAA
* *
43332 TTAATAATTTTATATTAATAT-T
1 TTAAT-ATTTTAAATTAAAATCT
43354 TTAATATTTTAAAATTAAAATCT
1 TTAATATTTT-AAATTAAAATCT
*
43377 TAAATATTTT
1 TTAATATTTT
43387 TATTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.18
22 13 0.46
23 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAATATTTTAAATTAAAATCT
Found at i:45578 original size:30 final size:30
Alignment explanation
Indices: 45538--45605 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
45528 CGAAAAAAAT
*
45538 ATAAATTTATAATTAAAAT-T-TAATTATTATG
1 ATAAA-TTAT-ATTAAAATATCTAATT-TCATG
45569 ATAAATTATATTAAAATATCTAATTTCATG
1 ATAAATTATATTAAAATATCTAATTTCATG
45599 ATAAATT
1 ATAAATT
45606 TTAAAATAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.24
30 16 0.47
31 10 0.29
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
ATAAATTATATTAAAATATCTAATTTCATG
Found at i:45971 original size:15 final size:16
Alignment explanation
Indices: 45941--45974 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
45931 TTTTATTGAC
45941 AATTTATTAATACAAT
1 AATTTATTAATACAAT
*
45957 AATTT-TTAATTCAAT
1 AATTTATTAATACAAT
45972 AAT
1 AAT
45975 ATAAGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTATTAATACAAT
Found at i:46786 original size:14 final size:14
Alignment explanation
Indices: 46766--46809 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
46756 ATAATTTTTA
46766 TTTTCTTTTTCTT-
1 TTTTCTTTTTCTTC
*
46779 TCTTTCTTTTACTTC
1 T-TTTCTTTTTCTTC
46794 TTTTCTTTTT-TTC
1 TTTTCTTTTTCTTC
46807 TTT
1 TTT
46810 GTGGCAAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.26
14 19 0.70
15 1 0.04
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTTTTTCTTC
Found at i:47474 original size:20 final size:20
Alignment explanation
Indices: 47449--47504 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
47439 TTTTTACCCA
* *
47449 AATGTATCGATACATTTTTT
1 AATGTATCGATACATTCTTC
*
47469 AATGTATCGATATATTCTTC
1 AATGTATCGATACATTCTTC
47489 AATGTATCGATACATT
1 AATGTATCGATACATT
47505 ATGTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:51628 original size:24 final size:24
Alignment explanation
Indices: 51601--51673 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 24
51591 ATTTTTTGTA
51601 TTATATATTATTTTATTTATAAAT
1 TTATATATTATTTTATTTATAAAT
* ** *
51625 TTAT-TAATATGATACTTACTAAAT
1 TTATATATTATTTTATTTA-TAAAT
*
51649 TTATTCATTTATATTTTATTTATAA
1 TTA-T-ATAT-TATTTTATTTATAA
51674 TTATATTTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
23 10 0.29
24 12 0.34
25 1 0.03
27 4 0.11
28 8 0.23
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (24 bp):
TTATATATTATTTTATTTATAAAT
Found at i:53199 original size:37 final size:39
Alignment explanation
Indices: 53114--53199 Score: 90
Period size: 37 Copynumber: 2.3 Consensus size: 39
53104 TAAATGATTC
* *
53114 AAACTTGA-TAAACTCAAATGTTAAACTTAATTTACTCG
1 AAACTTGATTAAACTCAAATATTAAACTTAATTTAATCG
** * *
53152 AAA-TCAATTAATCT-AAATATTAAACTTAA-TTAATCT
1 AAACTTGATTAAACTCAAATATTAAACTTAATTTAATCG
53188 AAACTTGATTAA
1 AAACTTGATTAA
53200 CTTGAGTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
36 8 0.21
37 22 0.58
38 8 0.21
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.36
Consensus pattern (39 bp):
AAACTTGATTAAACTCAAATATTAAACTTAATTTAATCG
Found at i:56989 original size:20 final size:22
Alignment explanation
Indices: 56955--57003 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
56945 TATTTAAATT
56955 TATTATTTTATATTTATATTAA
1 TATTATTTTATATTTATATTAA
* *
56977 TATT-TTTTA-ATTTTTATTAT
1 TATTATTTTATATTTATATTAA
56997 TATTATT
1 TATTATT
57004 AATTTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.54
21 7 0.29
22 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTATTTTATATTTATATTAA
Found at i:57007 original size:19 final size:18
Alignment explanation
Indices: 56954--57010 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
56944 ATATTTAAAT
*
56954 TTATTATTTTATATTTATA
1 TTATTATTTTA-ATTTTTA
*
56973 TTAATATTTTTTAATTTTTA
1 TT-AT-TATTTTAATTTTTA
56993 TTATTATTATTAATTTTT
1 TTATTATT-TTAATTTTT
57011 TTGTTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 3 0.09
19 13 0.41
20 10 0.31
21 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTATTTTAATTTTTA
Found at i:57010 original size:20 final size:19
Alignment explanation
Indices: 56954--57011 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 19
56944 ATATTTAAAT
56954 TTATTATTTTATATTTATATTA
1 TTATTATTTTA-ATTT-T-TTA
*
56976 ATATT-TTTTAA-TTTTTA
1 TTATTATTTTAATTTTTTA
56993 TTATTATTATTAATTTTTT
1 TTATTATT-TTAATTTTTT
57012 TGTTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 7 0.23
18 3 0.10
19 6 0.19
20 6 0.19
21 5 0.16
22 4 0.13
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTATTTTAATTTTTTA
Found at i:57050 original size:21 final size:20
Alignment explanation
Indices: 57019--57066 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
57009 TTTTGTTTAA
**
57019 AATTAAAAAAATTTATGATT
1 AATTAAAAAAATTTACCATT
57039 AATTATAAAAAATTTACCATT
1 AATTA-AAAAAATTTACCATT
57060 AATTAAA
1 AATTAAA
57067 TTTATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTAAAAAAATTTACCATT
Found at i:57078 original size:16 final size:16
Alignment explanation
Indices: 57059--57135 Score: 61
Period size: 16 Copynumber: 4.7 Consensus size: 16
57049 AATTTACCAT
*
57059 TAATTAAATTTATTTA
1 TAATTAAATTTAATTA
*
57075 TAATTAAATTAAATTA
1 TAATTAAATTTAATTA
57091 -AATTATAATTTAAAAATT-
1 TAATTA-AATTT---AATTA
57109 TAATATAAATTTAATT-
1 TAAT-TAAATTTAATTA
*
57125 TAATTTAATTT
1 TAATTAAATTT
57136 TAAGATTTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
15 11 0.22
16 26 0.51
19 12 0.24
20 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTAAATTTAATTA
Found at i:57084 original size:21 final size:21
Alignment explanation
Indices: 57060--57100 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57050 ATTTACCATT
* *
57060 AATTAAATTTATTTATAATTA
1 AATTAAATTAAATTATAATTA
57081 AATTAAATTAAATTATAATT
1 AATTAAATTAAATTATAATT
57101 TAAAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTAAATTAAATTATAATTA
Found at i:57118 original size:11 final size:10
Alignment explanation
Indices: 57058--57134 Score: 77
Period size: 10 Copynumber: 7.6 Consensus size: 10
57048 AAATTTACCA
57058 TTAATTAAAT
1 TTAATTAAAT
*
57068 TTATTTATAAT
1 TTAATTA-AAT
*
57079 TAAATTAAAT
1 TTAATTAAAT
*
57089 TAAATTATAAT
1 TTAATTA-AAT
57100 TTAA--AAAT
1 TTAATTAAAT
57108 TTAATATAAAT
1 TTAAT-TAAAT
*
57119 TTAATTTAAT
1 TTAATTAAAT
57129 TTAATT
1 TTAATT
57135 TTAAGATTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.12
9 1 0.02
10 26 0.46
11 23 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TTAATTAAAT
Found at i:57126 original size:5 final size:5
Alignment explanation
Indices: 57058--57135 Score: 52
Period size: 5 Copynumber: 15.4 Consensus size: 5
57048 AAATTTACCA
* * * * * *
57058 TTAAT TAAAT TTATT TATAAT TAAAT TAAAT TAAAT TATAAT TTAA- -AAAT
1 TTAAT TTAAT TTAAT T-TAAT TTAAT TTAAT TTAAT T-TAAT TTAAT TTAAT
*
57108 TTAAT ATAAAT TTAAT TTAAT TTAAT TT
1 TTAAT -TTAAT TTAAT TTAAT TTAAT TT
57136 TAAGATTTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
3 2 0.03
5 44 0.76
6 12 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (5 bp):
TTAAT
Found at i:59418 original size:18 final size:20
Alignment explanation
Indices: 59395--59435 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
59385 CATTTTGATT
59395 TTTATATC-A-TCGTATCAA
1 TTTATATCAAGTCGTATCAA
*
59413 TTTATATCAAGTTGTATCAA
1 TTTATATCAAGTCGTATCAA
59433 TTT
1 TTT
59436 GTATTGGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTATATCAAGTCGTATCAA
Found at i:59437 original size:10 final size:10
Alignment explanation
Indices: 59406--59439 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
59396 TTATATCATC
59406 GTATCAATTT
1 GTATCAATTT
* *
59416 ATATCAAGTT
1 GTATCAATTT
59426 GTATCAATTT
1 GTATCAATTT
59436 GTAT
1 GTAT
59440 TGGACTTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (10 bp):
GTATCAATTT
Found at i:61096 original size:15 final size:17
Alignment explanation
Indices: 61076--61112 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
61066 ATTTTAAAAT
*
61076 AAAAAAT-T-AAGCTAA
1 AAAAAATCTGAAGATAA
61091 AAAAAATCTGAAGATAA
1 AAAAAATCTGAAGATAA
61108 AAAAA
1 AAAAA
61113 CTATAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 11 0.58
ACGTcount: A:0.70, C:0.05, G:0.08, T:0.16
Consensus pattern (17 bp):
AAAAAATCTGAAGATAA
Found at i:62776 original size:23 final size:23
Alignment explanation
Indices: 62750--62802 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
62740 AATCAGACAT
62750 TTTTAAAAAATAATATTCATATG
1 TTTTAAAAAATAATATTCATATG
*
62773 TTTTAAAAAATAATATTGATATG
1 TTTTAAAAAATAATATTCATATG
62796 TTTTAAA
1 TTTTAAA
62803 TTTATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (23 bp):
TTTTAAAAAATAATATTCATATG
Found at i:62979 original size:1 final size:1
Alignment explanation
Indices: 62973--63001 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
62963 AACTAAAGAT
62973 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
63002 GCTGAATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:66061 original size:20 final size:22
Alignment explanation
Indices: 66038--66087 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
66028 AATTTTTATT
66038 TAAATTTAAT-TATAAA-AATA
1 TAAATTTAATATATAAATAATA
* *
66058 TAAAATTAATATTTAAATAATA
1 TAAATTTAATATATAAATAATA
66080 -AAATTTAA
1 TAAATTTAA
66088 AACTGATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.36
21 12 0.48
22 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATATATAAATAATA
Found at i:66650 original size:15 final size:15
Alignment explanation
Indices: 66628--66666 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
66618 ATTAAATTAA
66628 TTAAATTTT-AATTGT
1 TTAAATTTTAAATT-T
*
66643 TTATATTTTAAATTT
1 TTAAATTTTAAATTT
66658 TTAAATTTT
1 TTAAATTTT
66667 TATAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TTAAATTTTAAATTT
Found at i:66668 original size:23 final size:23
Alignment explanation
Indices: 66628--66678 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
66618 ATTAAATTAA
*
66628 TTAAA-TTTTAATTGTTTATATT
1 TTAAATTTTTAATTGTTTATAAT
66650 TTAAATTTTTAAATT-TTTATAAT
1 TTAAATTTTT-AATTGTTTATAAT
66673 TTAAAT
1 TTAAAT
66679 AAATATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 17 0.65
24 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTAAATTTTTAATTGTTTATAAT
Found at i:66758 original size:20 final size:22
Alignment explanation
Indices: 66715--66759 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
66705 AATGTCAAAT
*
66715 ATAAGTAAAAAATATATTTATA
1 ATAAGTAAAAAATATATTAATA
66737 ATAAGTAAAAAAT-T-TTAATA
1 ATAAGTAAAAAATATATTAATA
66757 ATA
1 ATA
66760 TAGAACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 1 0.05
22 13 0.59
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (22 bp):
ATAAGTAAAAAATATATTAATA
Found at i:66949 original size:13 final size:13
Alignment explanation
Indices: 66931--66956 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
66921 AAACCAAATT
66931 TTATTTTAATTAA
1 TTATTTTAATTAA
66944 TTATTTTAATTAA
1 TTATTTTAATTAA
66957 ATCGAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTTTAATTAA
Found at i:67670 original size:2 final size:2
Alignment explanation
Indices: 67663--67691 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
67653 GGATATTTGC
67663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
67692 AATAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68236 original size:2 final size:2
Alignment explanation
Indices: 68229--68261 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
68219 ATTATGCATA
68229 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
68262 TTCAACTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:69279 original size:21 final size:22
Alignment explanation
Indices: 69244--69285 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
69234 TATCATTTTC
69244 TAAAAATCTTTAAAA-TAAATT
1 TAAAAATCTTTAAAATTAAATT
69265 TAAAAAT-TTTAAAAATTAAAT
1 TAAAAATCTTT-AAAATTAAAT
69286 ATATCTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 11 0.58
22 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAATCTTTAAAATTAAATT
Found at i:71785 original size:20 final size:20
Alignment explanation
Indices: 71746--71785 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
71736 AAATTTTAAT
*
71746 TATTTTTAATATATATATAA
1 TATTTTTAATATATAAATAA
71766 TATTTTTAA-ATATGAAATAA
1 TATTTTTAATATAT-AAATAA
71786 ATAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTTTAATATATAAATAA
Found at i:71788 original size:21 final size:20
Alignment explanation
Indices: 71746--71788 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
71736 AAATTTTAAT
*
71746 TATTTTTAATATATATATAA
1 TATTTTTAATATAAATATAA
71766 TATTTTTAAATATGAAATA-AA
1 TATTTTT-AATAT-AAATATAA
71787 TA
1 TA
71789 AAATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTTTTAATATAAATATAA
Found at i:71942 original size:32 final size:30
Alignment explanation
Indices: 71906--71972 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 30
71896 AATAACAGTT
**
71906 AAATTAATGAGTAATTATATTTACCATTCATC
1 AAATTAACAAGTAATTATATTTA--ATTCATC
* *
71938 AAATTTACAAGTAATTATTTTTAATTCATC
1 AAATTAACAAGTAATTATATTTAATTCATC
71968 AAATT
1 AAATT
71973 TATAATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 12 0.39
32 19 0.61
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (30 bp):
AAATTAACAAGTAATTATATTTAATTCATC
Found at i:71965 original size:30 final size:31
Alignment explanation
Indices: 71915--71974 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 31
71905 TAAATTAATG
71915 AGTAATTATATTTACCATTCATCAAATTTACA
1 AGTAATTATATTTA-CATTCATCAAATTTACA
*
71947 AGTAATTATTTTTA-ATTCATCAAATTTA
1 AGTAATTATATTTACATTCATCAAATTTA
71975 TAATTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 14 0.52
32 13 0.48
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (31 bp):
AGTAATTATATTTACATTCATCAAATTTACA
Found at i:72939 original size:53 final size:52
Alignment explanation
Indices: 72849--72949 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 52
72839 TATTTTTAAA
* *
72849 TTTATACATTGATAATCTTTTACGTATTAGTGACATAAATAAACGTTAATGG
1 TTTATACATCGATAATCTTTTACGTATTAATGACATAAATAAACGTTAATGG
72901 TTTATACATCGATAATCTTTTTACGTATTAATGACATAAATAAACGTTA
1 TTTATACATCGATAATC-TTTTACGTATTAATGACATAAATAAACGTTA
72950 GTGGAGAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 16 0.35
53 30 0.65
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (52 bp):
TTTATACATCGATAATCTTTTACGTATTAATGACATAAATAAACGTTAATGG
Found at i:80790 original size:19 final size:17
Alignment explanation
Indices: 80768--80809 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
80758 TTAAATTTAT
80768 TATTTATAATATAATAAAA
1 TATTTATAA-A-AATAAAA
80787 TATTTA-AAAAATAAAA
1 TATTTATAAAAATAAAA
80803 T-TTTATA
1 TATTTATA
80810 TTAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 1 0.05
18 2 0.09
19 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATTTATAAAAATAAAA
Found at i:81061 original size:19 final size:19
Alignment explanation
Indices: 80999--81061 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
80989 AATAAAAATA
*
80999 TTGAATTT-AAAAAATAAA
1 TTGAATTTAAAAAAATAAG
* *
81017 TTTAA-ATAAAAAAATAAG
1 TTGAATTTAAAAAAATAAG
* *
81035 ACT-CATTTAAAAAAATAAG
1 -TTGAATTTAAAAAAATAAG
81054 TTGAATTT
1 TTGAATTT
81062 TGACACTAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
17 1 0.03
18 15 0.45
19 17 0.52
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.33
Consensus pattern (19 bp):
TTGAATTTAAAAAAATAAG
Found at i:85910 original size:97 final size:99
Alignment explanation
Indices: 85751--85946 Score: 335
Period size: 97 Copynumber: 2.0 Consensus size: 99
85741 CCTAATTTTC
85751 CTGACTTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTCAGTTCCAGGGCAATGCACCAAA
1 CTGACTTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTCAGTTCCAGGGCAATGCACCAAA
85816 GCAGAGTTTCTAAGCA-A-TTGCTACATACATTT
66 GCAGAGTTTCTAAGCAGATTTGCTACATACATTT
* *
85848 CTGAC-TAAGAATTTGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAA
1 CTGACTTAAGAATTGGGATGGTTTGGTACATTGTTTTGA-TTTCAGTTCCAGGGCAATGCACCAA
*
85912 AGCAGAGTTTCTAAGCAGATTTGCTTCATACATTT
65 AGCAGAGTTTCTAAGCAGATTTGCTACATACATTT
85947 TCTAAAGAAA
Statistics
Matches: 93, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
96 32 0.34
97 46 0.49
98 1 0.01
99 14 0.15
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (99 bp):
CTGACTTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTCAGTTCCAGGGCAATGCACCAAA
GCAGAGTTTCTAAGCAGATTTGCTACATACATTT
Found at i:86234 original size:136 final size:136
Alignment explanation
Indices: 85848--86851 Score: 1972
Period size: 136 Copynumber: 7.4 Consensus size: 136
85838 ACATACATTT
*
85848 CTGACTAAGAATTTGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
1 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
85913 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
66 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
85978 ATTTTC
131 ATTTTC
85984 CTGACTTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAA
1 CTGAC-TAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAA
86049 AGCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCT
65 AGCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCT
86114 AATTTTC
130 AATTTTC
86121 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
1 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
86186 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
66 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
86251 ATTTTC
131 ATTTTC
*
86257 CTGACTAAGAATTTGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
1 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
86322 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
66 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
86387 ATTTTC
131 ATTTTC
86393 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
1 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
86458 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
66 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
86523 ATTTTC
131 ATTTTC
*
86529 CTGACTAAGAATTTGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
1 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
86594 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
66 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
86659 ATTTTC
131 ATTTTC
86665 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
1 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
86730 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
66 GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
86795 ATTTTC
131 ATTTTC
86801 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAG
1 CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAG
86852 CTATAGAAGT
Statistics
Matches: 862, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
136 727 0.84
137 135 0.16
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (136 bp):
CTGACTAAGAATTGGGATGGTTTGGTACATTGTTTTGATTTTCAGTTCCAGGGCAATTCACCAAA
GCAGAGTTTCTAAGCAGATTTGCTTCATACATTTTCTAAAGAAACTAGAGGAGCAATAAGGCCTA
ATTTTC
Found at i:88927 original size:29 final size:28
Alignment explanation
Indices: 88894--89014 Score: 88
Period size: 30 Copynumber: 4.2 Consensus size: 28
88884 AACCTTGGTT
*
88894 TTTAATATAAATTAAAAGTTAAAAGTTTA
1 TTTAATATAAATTAAAAATTAAAA-TTTA
* *
88923 TTTAAGTTTATATTAAAAATTAAAATTTA
1 TTTAA-TATAAATTAAAAATTAAAATTTA
*
88952 TTTAA-ATATAA-TAAAAATATAAAA-ATA
1 TTTAATATA-AATTAAAAAT-TAAAATTTA
* *
88979 TTCTAA-ATAAAATTATAAAATTTAAGATTTT
1 TT-TAATAT-AAATTA-AAAA-TTAAAATTTA
89010 TTTAA
1 TTTAA
89015 CTTACTAATA
Statistics
Matches: 74, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
27 13 0.18
28 13 0.18
29 17 0.23
30 27 0.36
31 4 0.05
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
TTTAATATAAATTAAAAATTAAAATTTA
Found at i:88985 original size:28 final size:27
Alignment explanation
Indices: 88931--88987 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
88921 TATTTAAGTT
* *
88931 TATATTAAAAATTAAAATTTATTTAAA
1 TATAATAAAAATTAAAATATATTTAAA
88958 TATAATAAAAATATAAAA-ATATTCTAAA
1 TATAATAAAAAT-TAAAATATATT-TAAA
88986 TA
1 TA
88988 AAATTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
TATAATAAAAATTAAAATATATTTAAA
Found at i:92343 original size:5 final size:5
Alignment explanation
Indices: 92333--92375 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
92323 TATTTTTATG
* *
92333 AATAT AATAT AA-AT AAAAT AATTAA AATAT AATAT AATAT AAT
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AAT
92376 TTTATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 4 0.12
5 26 0.79
6 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:92428 original size:20 final size:19
Alignment explanation
Indices: 92405--92446 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 19
92395 ATGATACGAA
92405 TTATTAATATATTAAAAT-TT
1 TTATTAA-ATA-TAAAATATT
92425 TTA-TAAATATAAAATATT
1 TTATTAAATATAAAATATT
92443 TTAT
1 TTAT
92447 ACACAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 3 0.15
20 3 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAAATATAAAATATT
Found at i:92720 original size:22 final size:22
Alignment explanation
Indices: 92695--92739 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
92685 AATATTTTAT
92695 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
92717 TAAATATTAATATAAAAATATA
1 TAAATATTAATATAAAAATATA
92739 T
1 T
92740 TTTAACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:93548 original size:11 final size:11
Alignment explanation
Indices: 93532--93558 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
93522 ATTGTTCTCA
93532 CATTTGATTTG
1 CATTTGATTTG
93543 CATTTGATTTG
1 CATTTGATTTG
93554 CATTT
1 CATTT
93559 ATATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.11, G:0.15, T:0.56
Consensus pattern (11 bp):
CATTTGATTTG
Found at i:96200 original size:2 final size:2
Alignment explanation
Indices: 96193--96239 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
96183 AATATTCCAC
96193 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
96235 TA TA T
1 TA TA T
96240 TAAATAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:96372 original size:29 final size:30
Alignment explanation
Indices: 96339--96404 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
96329 ATCTAAATAT
*
96339 TTAAAATAATC-AGAGTTTAAAT-ATTTAAA
1 TTAAAATAATCGAAAG-TTAAATGATTTAAA
96368 TTAAAA-AATCGAAAGTTAAATGATTTAAA
1 TTAAAATAATCGAAAGTTAAATGATTTAAA
*
96397 TGAAAATA
1 TTAAAATA
96405 TGAGAACTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 10 0.31
29 21 0.66
30 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (30 bp):
TTAAAATAATCGAAAGTTAAATGATTTAAA
Found at i:97520 original size:42 final size:43
Alignment explanation
Indices: 97472--97552 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
97462 AAATTGACAG
* *
97472 AGCTATTGACGATGAGCTTCAACAGGGAA-AAACAAAAACTAA
1 AGCTATTGAAGATGAGCTTCAAAAGGGAAGAAACAAAAACTAA
*
97514 AGCTATTGAAGATGAGCTTCAAAAGGGAAGAAAGAAAAA
1 AGCTATTGAAGATGAGCTTCAAAAGGGAAGAAACAAAAA
97553 AACACCTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 27 0.77
43 8 0.23
ACGTcount: A:0.49, C:0.12, G:0.22, T:0.16
Consensus pattern (43 bp):
AGCTATTGAAGATGAGCTTCAAAAGGGAAGAAACAAAAACTAA
Found at i:101526 original size:30 final size:30
Alignment explanation
Indices: 101492--101549 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
101482 TCTAAATCCA
*
101492 ACTCAAAAACAAGAAAAAGCTTCGATTTTT
1 ACTCAAAAACAAGAAAAAGCTTCAATTTTT
*
101522 ACTCAGAAACAAGAAAAAGCTTCAATTT
1 ACTCAAAAACAAGAAAAAGCTTCAATTT
101550 AGGGTCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.24
Consensus pattern (30 bp):
ACTCAAAAACAAGAAAAAGCTTCAATTTTT
Found at i:103813 original size:18 final size:18
Alignment explanation
Indices: 103790--103825 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
103780 GTCGAACTAC
103790 GTCCTTAGAATGAAGCAT
1 GTCCTTAGAATGAAGCAT
*
103808 GTCCTTGGAATGAAGCAT
1 GTCCTTAGAATGAAGCAT
103826 CTGGTGTAGG
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:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (18 bp):
GTCCTTAGAATGAAGCAT
Found at i:108318 original size:2 final size:2
Alignment explanation
Indices: 108311--108353 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
108301 GGTAAACGCT
*
108311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT 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
108353 T
1 T
108354 CAAATCACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:111955 original size:21 final size:20
Alignment explanation
Indices: 111886--111957 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 20
111876 TTAGATAAAA
*
111886 TAAAAAAATTATTTACTTATT
1 TAAAAAATTTATTTA-TTATT
*
111907 TAAAATTTAATTTAATTTATTAAGT
1 TAAAA---AATTT-ATTTATT-ATT
111932 TAAAAAATTTATTTTATTATT
1 TAAAAAATTTA-TTTATTATT
111953 TAAAA
1 TAAAA
111958 TATTAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
21 13 0.31
22 11 0.26
24 6 0.14
25 12 0.29
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (20 bp):
TAAAAAATTTATTTATTATT
Found at i:111963 original size:29 final size:34
Alignment explanation
Indices: 111931--111993 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 34
111921 ATTTATTAAG
111931 TTAAAAA-AT-TTAT-TTTAT-TAT-TTAAAATA
1 TTAAAAATATATTATATTTATATATCTTAAAATA
111960 TTAAAAATTATATTATATTTATATATCTTAAAAT
1 TTAAAAA-TATATTATATTTATATATCTTAAAAT
111994 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 7 0.25
31 2 0.07
32 4 0.14
33 5 0.18
34 3 0.11
35 7 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (34 bp):
TTAAAAATATATTATATTTATATATCTTAAAATA
Found at i:111965 original size:27 final size:27
Alignment explanation
Indices: 111935--111994 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
111925 ATTAAGTTAA
*
111935 AAAATTTATTTTATTATTTA-AAATATT
1 AAAATTTATATTA-TATTTATAAATATT
* * *
111962 AAAAATTATATTATATTTATATATCTT
1 AAAATTTATATTATATTTATAAATATT
111989 AAAATT
1 AAAATT
111995 AAATTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
AAAATTTATATTATATTTATAAATATT
Found at i:111974 original size:46 final size:45
Alignment explanation
Indices: 111886--111974 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 45
111876 TTAGATAAAA
*
111886 TAAAAAAATTATTTACTTATTTAAAATTTAATTTAATTTATTAAGT
1 TAAAAAAATTATTTACTTATTTAAAATTTAA-TAAATTTATTAAGT
*
111932 TAAAAAATTTATTTTA-TTATTTAAAATATTAA-AAATTATATTA
1 TAAAAAAATTA-TTTACTTATTTAAAAT-TTAATAAATT-TATTA
111975 TATTTATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 4 0.11
46 26 0.68
47 8 0.21
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (45 bp):
TAAAAAAATTATTTACTTATTTAAAATTTAATAAATTTATTAAGT
Found at i:116433 original size:5 final size:5
Alignment explanation
Indices: 116412--116447 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
116402 AATAATTTTT
* *
116412 TTTAA TTTGA GTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
116448 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (5 bp):
TTTAA
Found at i:116474 original size:34 final size:34
Alignment explanation
Indices: 116431--116495 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
116421 AGTTAATTTA
116431 ATTTAATTT-AATTTAATAATAAAAAATATTTGT
1 ATTTAATTTAAATTTAATAATAAAAAATATTTGT
*
116464 ATTTAAATTTAAATTTAATTATAAAAAATATT
1 ATTT-AATTTAAATTTAATAATAAAAAATATT
116496 ACTATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 4 0.14
34 5 0.17
35 20 0.69
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (34 bp):
ATTTAATTTAAATTTAATAATAAAAAATATTTGT
Found at i:117048 original size:32 final size:33
Alignment explanation
Indices: 116984--117050 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 33
116974 CGTATCATAA
116984 TTAATATTTAAGGTATTATATATTTATATAATTT
1 TTAATATTTAA-GTATTATATATTTATATAATTT
117018 TTAATATTTAA-TAATT-TATA-TTATATTAATTT
1 TTAATATTTAAGT-ATTATATATTTATA-TAATTT
117050 T
1 T
117051 GATACGTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
31 5 0.16
32 12 0.39
33 3 0.10
34 11 0.35
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (33 bp):
TTAATATTTAAGTATTATATATTTATATAATTT
Found at i:117283 original size:20 final size:20
Alignment explanation
Indices: 117258--117295 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
117248 TTTATCTGAC
117258 TTAAATTATTATTTAAATAG
1 TTAAATTATTATTTAAATAG
* *
117278 TTAAATTTTTCTTTAAAT
1 TTAAATTATTATTTAAAT
117296 CTAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
TTAAATTATTATTTAAATAG
Found at i:118120 original size:9 final size:9
Alignment explanation
Indices: 118108--118132 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
118098 GTTTATGTTA
118108 TTTAAATTT
1 TTTAAATTT
118117 TTTAAATTT
1 TTTAAATTT
118126 TTTAAAT
1 TTTAAAT
118133 ATCTTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTAAATTT
Found at i:118579 original size:3 final size:3
Alignment explanation
Indices: 118571--118600 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
118561 ACTTTACAAC
118571 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
118601 CACACTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:121500 original size:2 final size:2
Alignment explanation
Indices: 121493--121530 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
121483 CCATTCCCAT
121493 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
121531 GATTTAGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:121776 original size:2 final size:2
Alignment explanation
Indices: 121769--121800 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
121759 AGATCTCCTC
121769 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
121801 GTACATAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130559 original size:35 final size:36
Alignment explanation
Indices: 130519--130625 Score: 108
Period size: 35 Copynumber: 2.9 Consensus size: 36
130509 ATAGTATAAA
*
130519 TATTAAAAGATATATTAAGTTATTAAATATTAAAAC
1 TATTAAAAGATATATTAAATTATTAAATATTAAAAC
* * *
130555 -ATTAAAAGATACATTAAATTATTTATATTTTAAAAC
1 TATTAAAAGATATATTAAATTA-TTAAATATTAAAAC
* * * * *
130591 TTAATAAAAAATTTATTAACTTATTAAATAATAAA
1 -TATTAAAAGATATATTAAATTATTAAATATTAAA
130626 TTAAAAAACA
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
35 19 0.34
36 12 0.21
37 9 0.16
38 16 0.29
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (36 bp):
TATTAAAAGATATATTAAATTATTAAATATTAAAAC
Done.