Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold81
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: 1151237
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 79344 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:116773 original size:17 final size:18
Alignment explanation
Indices: 116759--116792 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
116749 CAATTAAATG
116759 AATATAAAT-CATAAAAA
1 AATATAAATACATAAAAA
116776 AATATAAATACATAAAA
1 AATATAAATACATAAAA
116793 TTAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
AATATAAATACATAAAAA
Found at i:118304 original size:28 final size:28
Alignment explanation
Indices: 118272--118328 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
118262 GATAAAATTT
*
118272 CAACATCTTTTTAACCTTTTTGTTCATC
1 CAACATCTTTTGAACCTTTTTGTTCATC
118300 CAACATCTTTTGAACCTTTTTGTTCATC
1 CAACATCTTTTGAACCTTTTTGTTCATC
118328 C
1 C
118329 TTATAGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.47
Consensus pattern (28 bp):
CAACATCTTTTGAACCTTTTTGTTCATC
Found at i:120692 original size:33 final size:32
Alignment explanation
Indices: 120655--120728 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
120645 TGATATAAAA
*
120655 ATAATATAAAAAAATAATTATGTTAAAATTTAT
1 ATAATATAAAAAAATAA-TATATTAAAATTTAT
** *
120688 ATAATATAAATTATTAATATATTAAAATTTAT
1 ATAATATAAAAAAATAATATATTAAAATTTAT
120720 ATAAATATA
1 AT-AATATA
120729 TAATATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
ATAATATAAAAAAATAATATATTAAAATTTAT
Found at i:120708 original size:20 final size:20
Alignment explanation
Indices: 120685--120755 Score: 53
Period size: 20 Copynumber: 3.5 Consensus size: 20
120675 TGTTAAAATT
120685 TATATAATATAAATTATTAA
1 TATATAATATAAATTATTAA
120705 TATAT--TA-AAATTTATATAAA
1 TATATAATATAAA-TTAT-T-AA
*
120725 TATATAATATTTAAAATA-TAA
1 TATATAATA--TAAATTATTAA
120746 T-TATAATATA
1 TATATAATATA
120756 TAAAAATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 18
0.69 0.02 0.30
Matches are distributed among these distances:
17 3 0.07
18 8 0.19
19 1 0.02
20 19 0.45
21 3 0.07
22 3 0.07
24 2 0.05
25 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATAATATAAATTATTAA
Found at i:120725 original size:27 final size:26
Alignment explanation
Indices: 120658--120758 Score: 78
Period size: 32 Copynumber: 3.5 Consensus size: 26
120648 TATAAAAATA
* *
120658 ATATAAAAAAATAATTATGTTAAAATTT
1 ATATAAATATATAA-TAT-TTAAAATTT
120686 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAA-AT--A-TA-TAATAT-TTAAAATTT
*
120718 ATATAAATATATAATATTTAAAATAT
1 ATATAAATATATAATATTTAAAATTT
120744 A-ATTATAATATATAA
1 ATA-TA-AATATATAA
120759 AAATATATAA
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
25 1 0.02
26 11 0.18
27 15 0.24
28 8 0.13
29 2 0.03
31 3 0.05
32 19 0.31
33 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
ATATAAATATATAATATTTAAAATTT
Found at i:120743 original size:22 final size:22
Alignment explanation
Indices: 120690--120765 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 22
120680 AAATTTATAT
120690 AATATAAATTATTAATATATTAAA
1 AATATAAATTA-TAATATA-TAAA
*
120714 ATTTATATAAATATATAATAT-TTAA
1 A---ATATAAAT-TATAATATATAAA
120739 AATAT-AATTATAATATATAAA
1 AATATAAATTATAATATATAAA
120760 AATATA
1 AATATA
120766 TAAATATGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
20 8 0.18
21 11 0.25
22 4 0.09
24 1 0.02
25 4 0.09
27 14 0.32
28 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATATAAATTATAATATATAAA
Found at i:120752 original size:6 final size:7
Alignment explanation
Indices: 120685--120789 Score: 62
Period size: 7 Copynumber: 15.1 Consensus size: 7
120675 TGTTAAAATT
120685 TATATAA
1 TATATAA
120692 TATA-AA
1 TATATAA
120698 T-TATTAA
1 TATA-TAA
120705 TATATTAA
1 TATA-TAA
* *
120713 AAT-TTA
1 TATATAA
120719 TATA-AA
1 TATATAA
120725 TATATAA
1 TATATAA
*
120732 TATTTAA
1 TATATAA
*
120739 AATATAA
1 TATATAA
120746 T-TATAA
1 TATATAA
120752 TATATAAAAA
1 TATAT---AA
120762 TATATAA
1 TATATAA
*
120769 -ATATGA
1 TATATAA
120775 TATA-AA
1 TATATAA
120781 TATAATAA
1 TAT-ATAA
120789 T
1 T
120790 CGTCGGGTGA
Statistics
Matches: 76, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
5 2 0.03
6 27 0.36
7 29 0.38
8 11 0.14
10 7 0.09
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:120779 original size:11 final size:10
Alignment explanation
Indices: 120686--120788 Score: 59
Period size: 9 Copynumber: 11.0 Consensus size: 10
120676 GTTAAAATTT
120686 ATATAATATAA
1 ATAT-ATATAA
120697 AT-TAT-T-A
1 ATATATATAA
120704 ATATAT-TAA
1 ATATATATAA
*
120713 A-ATTTATATA
1 ATATATATA-A
120723 A-ATATAT-A
1 ATATATATAA
*
120731 ATATTTA-AA
1 ATATATATAA
120740 ATATA-ATTATA
1 ATATATA-TA-A
120751 ATATATA-AA
1 ATATATATAA
120760 A-ATATATAA
1 ATATATATAA
120769 ATATGATATAA
1 ATAT-ATATAA
120780 ATATA-ATAA
1 ATATATATAA
120789 TCGTCGGGTG
Statistics
Matches: 75, Mismatches: 4, Indels: 28
0.70 0.04 0.26
Matches are distributed among these distances:
7 3 0.04
8 16 0.21
9 24 0.32
10 13 0.17
11 18 0.24
12 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (10 bp):
ATATATATAA
Found at i:120915 original size:14 final size:14
Alignment explanation
Indices: 120896--120953 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
120886 CAAAAAAATA
120896 TATATATTATAATT
1 TATATATTATAATT
*
120910 TATATAATATAAATTAT
1 TATATATTAT-AA-T-T
*
120927 TAATATATTAAAATT
1 T-ATATATTATAATT
120942 TATATA-TATAAT
1 TATATATTATAAT
120954 ATTTTAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
13 5 0.14
14 14 0.39
15 4 0.11
16 2 0.06
17 4 0.11
18 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATTATAATT
Found at i:120932 original size:18 final size:17
Alignment explanation
Indices: 120892--120998 Score: 62
Period size: 18 Copynumber: 6.2 Consensus size: 17
120882 AACACAAAAA
* *
120892 AATATATATATTATAATT
1 AATATATATA-AATTATT
*
120910 TATATAATATAAATTATT
1 AATAT-ATATAAATTATT
120928 AATATAT-TAAA--ATT
1 AATATATATAAATTATT
*
120942 TATATATATAATATT-TT
1 AATATATATAA-ATTATT
*
120959 AA-ATATAATTATAATATATA
1 AATATAT-A-TA-AAT-TATT
*
120979 AAAATATATAAATTATT
1 AATATATATAAATTATT
120996 AAT
1 AAT
120999 TTTACATAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 23
0.68 0.09 0.23
Matches are distributed among these distances:
14 9 0.13
15 3 0.04
16 9 0.13
17 11 0.16
18 20 0.29
19 9 0.13
20 4 0.06
21 4 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATATATAAATTATT
Found at i:120933 original size:32 final size:32
Alignment explanation
Indices: 120897--120998 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 32
120887 AAAAAAATAT
120897 ATATATTATAATTTATATAATATAAATTATTA
1 ATATATTATAATTTATATAATATAAATTATTA
*
120929 ATATATTAAAATTTATAT-ATATAATATT-TTAA
1 ATATATTATAATTTATATAATATAA-ATTATT-A
* *
120961 ATATAATTATAATATATAAAAATATATAAATTATTA
1 ATAT-ATTATAAT-T-TATATA-ATATAAATTATTA
120997 AT
1 AT
120999 TTTACATAGT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
31 8 0.14
32 25 0.43
33 7 0.12
34 1 0.02
35 3 0.05
36 6 0.10
37 8 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATATATTATAATTTATATAATATAAATTATTA
Found at i:120954 original size:23 final size:22
Alignment explanation
Indices: 120895--120988 Score: 95
Period size: 21 Copynumber: 4.3 Consensus size: 22
120885 ACAAAAAAAT
* *
120895 ATATATATTATAATTTA-TATA
1 ATATATATTATAATATATTAAA
*
120916 ATATAAATTATTAATATATTAAA
1 ATATATATTA-TAATATATTAAA
* *
120939 ATTTATATATATAATAT-TTTAA
1 ATATATAT-TATAATATATTAAA
*
120961 ATATA-ATTATAATATATAAAA
1 ATATATATTATAATATATTAAA
120982 ATATATA
1 ATATATA
120989 AATTATTAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
20 8 0.14
21 19 0.32
22 15 0.25
23 15 0.25
24 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATATTATAATATATTAAA
Found at i:121571 original size:20 final size:18
Alignment explanation
Indices: 121540--121586 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
121530 TATTAAAAAT
121540 ATTAATAATTTAAATTA-A
1 ATTAATAATTT-AATTATA
121558 ATTAGATAATTTTAATTATA
1 ATTA-ATAA-TTTAATTATA
121578 ATTATATAA
1 ATTA-ATAA
121587 ATATAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTAATAATTTAATTATA
Found at i:121593 original size:20 final size:20
Alignment explanation
Indices: 121552--121598 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
121542 TAATAATTTA
* *
121552 AATTA-AATTAGATAATTTT
1 AATTATAATTAGATAAATAT
*
121571 AATTATAATTATATAAATAT
1 AATTATAATTAGATAAATAT
121591 AATATATA
1 AAT-TATA
121599 TAAAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 5 0.22
20 14 0.61
21 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATTATAATTAGATAAATAT
Found at i:121606 original size:31 final size:30
Alignment explanation
Indices: 121571--121671 Score: 73
Period size: 32 Copynumber: 3.1 Consensus size: 30
121561 AGATAATTTT
121571 AATTATAATTATATAAATATAATATATATAA
1 AATTATAATTATATAAATATAATATAT-TAA
*
121602 AATTATTAAAATTTGATATGAATAT-ATA-ATTTAA
1 AATTA-T--AA-TT-ATATAAATATAATATA-TTAA
*
121636 AATT-TATATTATATAAATTATTAATGTATTAA
1 AATTATA-ATTATATAAA-TA-TAATATATTAA
121668 AATT
1 AATT
121672 GATATAAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 21
0.70 0.04 0.26
Matches are distributed among these distances:
29 6 0.11
30 5 0.09
31 7 0.12
32 12 0.21
33 1 0.02
34 10 0.18
35 6 0.11
36 9 0.16
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (30 bp):
AATTATAATTATATAAATATAATATATTAA
Found at i:121613 original size:25 final size:24
Alignment explanation
Indices: 121577--121659 Score: 57
Period size: 25 Copynumber: 3.4 Consensus size: 24
121567 TTTTAATTAT
121577 AATTA-TATAAATATAATATATATAA
1 AATTATTA-AAAT-TAATATATATAA
* *
121602 AATTATTAAAATTTGATATGAATATAT
1 AATTATTAAAA-TTAATAT--ATATAA
*
121629 AA-T-TTAAAATTTATAT-TATATA
1 AATTATTAAAATTAATATATATA-A
121651 AATTATTAA
1 AATTATTAA
121660 TGTATTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
21 4 0.09
22 2 0.04
23 1 0.02
24 10 0.21
25 19 0.40
26 4 0.09
27 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AATTATTAAAATTAATATATATAA
Found at i:121965 original size:30 final size:31
Alignment explanation
Indices: 121909--121966 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
121899 TTAATGTTAA
*
121909 TTAAAATTTTTATTTTTTAAAAATATTTGTG
1 TTAAAATTTTTATCTTTTAAAAATATTTGTG
*
121940 TTAAAA-TTTTA-CTTTTAATATATATTT
1 TTAAAATTTTTATCTTTTAA-AAATATTT
121967 AAATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 12 0.50
31 6 0.25
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (31 bp):
TTAAAATTTTTATCTTTTAAAAATATTTGTG
Found at i:121996 original size:21 final size:20
Alignment explanation
Indices: 121972--122025 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 20
121962 TATTTAAATA
121972 TAAATATAAAATATAATTTTT
1 TAAATATAAAATATAA-TTTT
*
121993 TAAATATATAA-A-AATTTT
1 TAAATATAAAATATAATTTT
* *
122011 TAAAAATTAAATATA
1 TAAATATAAAATATA
122026 TTTATCGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 12 0.44
19 3 0.11
20 2 0.07
21 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATATAAAATATAATTTT
Found at i:123593 original size:18 final size:19
Alignment explanation
Indices: 123553--123594 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
123543 TTGAATCGAA
* *
123553 TTTTATTTAGTTTTTTTAT
1 TTTTAATTAGTTTTTATAT
123572 TTTTAATTAGTTTTTAT-T
1 TTTTAATTAGTTTTTATAT
123590 TTTTA
1 TTTTA
123595 TAGTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTAATTAGTTTTTATAT
Found at i:125346 original size:2 final size:2
Alignment explanation
Indices: 125339--125386 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
125329 AAGATCTTGA
125339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
125381 AT AT AT
1 AT AT AT
125387 TAATGCAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:126182 original size:15 final size:15
Alignment explanation
Indices: 126162--126190 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
126152 AAATAATCGA
126162 AAAATTACAAACGTT
1 AAAATTACAAACGTT
126177 AAAATTACAAACGT
1 AAAATTACAAACGT
126191 AATTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (15 bp):
AAAATTACAAACGTT
Found at i:127194 original size:11 final size:11
Alignment explanation
Indices: 127178--127208 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
127168 TTATAATATA
127178 TTAATATTATT
1 TTAATATTATT
127189 TTAATATTATT
1 TTAATATTATT
*
127200 TTAAAATTA
1 TTAATATTA
127209 ATTTGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTAATATTATT
Found at i:127342 original size:21 final size:21
Alignment explanation
Indices: 127316--127368 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
127306 AAAAGTTTAT
*
127316 TTTTATATTAATATTTATAT-A
1 TTTTATATTAA-ATTTAAATAA
127337 TTTTATAATTAAATTTAAATAA
1 TTTTAT-ATTAAATTTAAATAA
*
127359 TTTTTTATTA
1 TTTTATATTA
127369 TTTTAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATATTAAATTTAAATAA
Found at i:127842 original size:16 final size:16
Alignment explanation
Indices: 127821--127868 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
127811 TCGAAATAGT
*
127821 CCGAACCCAAGACAGC
1 CCGAACCCAAGAAAGC
*
127837 CCGAACCTAAGAAAGC
1 CCGAACCCAAGAAAGC
* *
127853 CTGAACCCAAAAAAGC
1 CCGAACCCAAGAAAGC
127869 TCGAGCTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.44, C:0.35, G:0.17, T:0.04
Consensus pattern (16 bp):
CCGAACCCAAGAAAGC
Found at i:127932 original size:16 final size:16
Alignment explanation
Indices: 127913--127944 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
127903 GAAAGAACCC
127913 GAACCCGAACCCGAGA
1 GAACCCGAACCCGAGA
*
127929 GAACCTGAACCCGAGA
1 GAACCCGAACCCGAGA
127945 CTGATCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.34, G:0.25, T:0.03
Consensus pattern (16 bp):
GAACCCGAACCCGAGA
Found at i:129332 original size:16 final size:16
Alignment explanation
Indices: 129311--129378 Score: 79
Period size: 16 Copynumber: 4.3 Consensus size: 16
129301 AAACTGATCC
129311 AAACTTAAATAAATCT
1 AAACTTAAATAAATCT
129327 AAACTTAAA-AAAT-T
1 AAACTTAAATAAATCT
* *
129341 CAAACCTAAATAAATTT
1 -AAACTTAAATAAATCT
129358 AAA-TATAAATAAATCT
1 AAACT-TAAATAAATCT
129374 AAACT
1 AAACT
129379 CAATCTAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
14 1 0.02
15 12 0.27
16 29 0.66
17 2 0.05
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (16 bp):
AAACTTAAATAAATCT
Found at i:129780 original size:6 final size:6
Alignment explanation
Indices: 129771--129832 Score: 70
Period size: 6 Copynumber: 10.0 Consensus size: 6
129761 AAATTTTTAT
* *
129771 TTTAAA TTTAAA TTTAAA TTTAAT TTTAAA TATAAA TAATTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA TTTAAA
* *
129821 ATTAAA TATAAA
1 TTTAAA TTTAAA
129833 AATTAATTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
6 42 0.89
8 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:133028 original size:18 final size:16
Alignment explanation
Indices: 133005--133048 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
132995 AAATTATATA
133005 ATATTTATATTATTTATT
1 ATATTTATATTA-TT-TT
* *
133023 ATATTTAAAATATTTT
1 ATATTTATATTATTTT
133039 ATATTTATAT
1 ATATTTATAT
133049 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.45
17 2 0.09
18 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTATATTATTTT
Found at i:133106 original size:33 final size:32
Alignment explanation
Indices: 133037--133112 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
133027 TTAAAATATT
133037 TTATATTTATATAAATTTAAATAAATTAATAAA
1 TTATATTT-TATAAATTTAAATAAATTAATAAA
* * *
133070 TTATATTTTATAAATTTTTAA-AAATATATTATA
1 TTATATTTTATAAA-TTTAAATAAAT-TAATAAA
133103 TTATATTTTA
1 TTATATTTTA
133113 ATTATTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 10 0.26
33 28 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTATATTTTATAAATTTAAATAAATTAATAAA
Found at i:134092 original size:15 final size:16
Alignment explanation
Indices: 134072--134108 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
134062 AGTTATATAT
*
134072 TCTTTTAATT-TTTTC
1 TCTTTTAATTGTTTTA
134087 TCTTTTAATTGTTTTA
1 TCTTTTAATTGTTTTA
134103 TCTTTT
1 TCTTTT
134109 CGTGTTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.14, C:0.11, G:0.03, T:0.73
Consensus pattern (16 bp):
TCTTTTAATTGTTTTA
Found at i:134471 original size:22 final size:22
Alignment explanation
Indices: 134446--134496 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
134436 CTAATAAGAA
134446 TTTAATTAATT-TTAAAATTAT-T
1 TTTAATT-ATTATT-AAATTATAT
134468 TTTAATTATTATTAAATTATAT
1 TTTAATTATTATTAAATTATAT
134490 TTTAATT
1 TTTAATT
134497 TAAATACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTAATTATTATTAAATTATAT
Found at i:134807 original size:19 final size:19
Alignment explanation
Indices: 134770--134809 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
134760 AAATAATTAC
**
134770 TTTTTTATTTTTATCAATT
1 TTTTTTATTTTTAAAAATT
134789 TTTTTTATTTTTAAAAATT
1 TTTTTTATTTTTAAAAATT
134808 TT
1 TT
134810 AAAATAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTTATTTTTAAAAATT
Found at i:134848 original size:25 final size:26
Alignment explanation
Indices: 134805--134858 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
134795 ATTTTTAAAA
* * *
134805 ATTTTAAAATAATAGTAAT-TAATTT
1 ATTTTAAAATAAAAATAATATAATAT
*
134830 ATTTTTAAATAAAAATAATATAATAT
1 ATTTTAAAATAAAAATAATATAATAT
134856 ATT
1 ATT
134859 AATATCAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTTTAAAATAAAAATAATATAATAT
Found at i:135305 original size:28 final size:31
Alignment explanation
Indices: 135238--135310 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 31
135228 TTTATGAAAA
135238 AAAATTA--TTTAAATCTTAAAATAGTAAAT
1 AAAATTATTTTTAAATCTTAAAATAGTAAAT
*
135267 AAAATTATTTTTAAATTTTAAAA-A-T-AAT
1 AAAATTATTTTTAAATCTTAAAATAGTAAAT
* *
135295 AATATTTTTTTTAAAT
1 AAAATTATTTTTAAAT
135311 AATTTAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 17 0.44
29 8 0.21
30 1 0.03
31 13 0.33
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
AAAATTATTTTTAAATCTTAAAATAGTAAAT
Found at i:135697 original size:19 final size:18
Alignment explanation
Indices: 135675--135716 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
135665 AATTTAGATT
135675 TAATTCAATT-ATTTGAATA
1 TAATTCAATTAATTT--ATA
*
135694 TAATTTAATTAATTTATA
1 TAATTCAATTAATTTATA
135712 TAATT
1 TAATT
135717 ATTTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTCAATTAATTTATA
Found at i:135781 original size:12 final size:12
Alignment explanation
Indices: 135742--135789 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
135732 TAGTAATTTT
*
135742 AAATATGATATA
1 AAATATAATATA
*
135754 AAAAATAATA-A
1 AAATATAATATA
135765 AAATATAATATA
1 AAATATAATATA
*
135777 AAATATGATATA
1 AAATATAATATA
135789 A
1 A
135790 TATAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAATATAATATA
Found at i:135808 original size:17 final size:17
Alignment explanation
Indices: 135766--135808 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
135756 AAATAATAAA
135766 AATATAATATAAAATAT
1 AATATAATATAAAATAT
*
135783 GATATAATATAAAA-AT
1 AATATAATATAAAATAT
135799 AATATGAATA
1 AATAT-AATA
135809 CGACATGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:136070 original size:2 final size:2
Alignment explanation
Indices: 136063--136090 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
136053 CAAATTGGTA
136063 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
136091 TTAATCTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:136377 original size:28 final size:30
Alignment explanation
Indices: 136346--136402 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
136336 ATGTATTATT
**
136346 ATTTTTAATTTATAAAT-A-AATTTAAATA
1 ATTTTTAATGAATAAATAATAATTTAAATA
*
136374 ATTTTTTATGAATAAATAATAATTTAAAT
1 ATTTTTAATGAATAAATAATAATTTAAAT
136403 TGAATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.58
29 1 0.04
30 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (30 bp):
ATTTTTAATGAATAAATAATAATTTAAATA
Found at i:136422 original size:20 final size:21
Alignment explanation
Indices: 136382--136422 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
136372 TAATTTTTTA
*
136382 TGAATAAATAATAATTTAAAT
1 TGAATAAATAATAATTCAAAT
*
136403 TGAATAAA-AATAGTTCAAAT
1 TGAATAAATAATAATTCAAAT
136423 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (21 bp):
TGAATAAATAATAATTCAAAT
Found at i:136734 original size:22 final size:22
Alignment explanation
Indices: 136706--136773 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
136696 AATAATTAAA
136706 ATAAAATAATTTAAATTTAATT
1 ATAAAATAATTTAAATTTAATT
*
136728 ATAAAAT-ATATAAATATTAA-T
1 ATAAAATAATTTAAAT-TTAATT
* *
136749 ATAAAAATATTTTTAAATTTTATT
1 AT-AAAATA-ATTTAAATTTAATT
136773 A
1 A
136774 ATTATGAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 10 0.27
22 16 0.43
23 3 0.08
24 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAAATAATTTAAATTTAATT
Found at i:137414 original size:2 final size:2
Alignment explanation
Indices: 137402--137460 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
137392 ATCTTTATTT
*
137402 TA TA CA 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
137444 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
137461 GCTAGAAGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:138795 original size:2 final size:2
Alignment explanation
Indices: 138788--138813 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
138778 TTATACATAC
138788 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
138814 TATGGTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:140011 original size:105 final size:106
Alignment explanation
Indices: 139808--140012 Score: 254
Period size: 105 Copynumber: 1.9 Consensus size: 106
139798 TGATATTCAA
* * *
139808 TAGATTTAGATTCAAATGTCAGTATCTGAGATTGAGCTAAAAAAGAAAAAGCAATTCGAACCGTA
1 TAGATTTAGATTCAAATCTCAGCATCTGAGATTGAGCAAAAAAAGAAAAAGCAATTCGAACCGTA
* * *
139873 ATTTTCACTTCTAGTTCACTTCAGTTTATTATGATATCTAC
66 ATTTTCACTTCTAGTCCACTTCAATTTAGTATGATATCTAC
* * * *
139914 TAGATTTAGATTCGAATCTC-GACATTTGAGATTGAG-AAAAAAATAAAAATCAATTCGAACCGT
1 TAGATTTAGATTCAAATCTCAG-CATCTGAGATTGAGCAAAAAAAGAAAAAGCAATTCGAACCGT
* * *
139977 -ATTGTTCACTTCTAGTCCAGTTTAATTTGGTATGAT
65 AATT-TTCACTTCTAGTCCACTTCAATTTAGTATGAT
140013 TTTCGATTCA
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
104 3 0.04
105 51 0.61
106 30 0.36
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (106 bp):
TAGATTTAGATTCAAATCTCAGCATCTGAGATTGAGCAAAAAAAGAAAAAGCAATTCGAACCGTA
ATTTTCACTTCTAGTCCACTTCAATTTAGTATGATATCTAC
Found at i:141296 original size:14 final size:14
Alignment explanation
Indices: 141277--141304 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
141267 ACCTAAGAAG
141277 CATGGACATAGATA
1 CATGGACATAGATA
141291 CATGGACATAGATA
1 CATGGACATAGATA
141305 TATGATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
CATGGACATAGATA
Found at i:141908 original size:2 final size:2
Alignment explanation
Indices: 141901--141935 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
141891 GTATGAGATT
141901 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
141936 CCGTAATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:144309 original size:28 final size:25
Alignment explanation
Indices: 144275--144328 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
144265 CTCTTCCATT
*
144275 ATTTT-ATTATT-TATTATAATTATA
1 ATTTTAATTATTAT-TTATAAATATA
144299 ATTTTAATTATTATTTATAAATATA
1 ATTTTAATTATTATTTATAAATATA
144324 ATTTT
1 ATTTT
144329 TGTAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 21 0.78
26 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTTAATTATTATTTATAAATATA
Found at i:144335 original size:28 final size:28
Alignment explanation
Indices: 144278--144328 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
144268 TTCCATTATT
144278 TTATTATTTATTATAATTATAATTTTAA
1 TTATTATTTATTATAATTATAATTTTAA
144306 TTATTATTTA-TA-AA-TATAATTTT
1 TTATTATTTATTATAATTATAATTTT
144329 TGTAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.39
26 2 0.09
27 2 0.09
28 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTATTATTTATTATAATTATAATTTTAA
Found at i:145362 original size:2 final size:2
Alignment explanation
Indices: 145349--145397 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
145339 TTTACTAAGA
*
145349 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
145391 AT AT AT A
1 AT AT AT A
145398 AAGTACATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:145855 original size:17 final size:19
Alignment explanation
Indices: 145835--145883 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 19
145825 TATATCAATT
145835 ATATAAA-TA-TAAATATA
1 ATATAAATTATTAAATATA
145852 ATATAAATTATTAAATAT-
1 ATATAAATTATTAAATATA
*
145870 ATTTAAATT-TTAAA
1 ATATAAATTATTAAA
145884 CACTAATACT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 12 0.41
18 10 0.34
19 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAAATTATTAAATATA
Found at i:146089 original size:78 final size:78
Alignment explanation
Indices: 146006--146161 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
145996 AAGAGAGTCG
146006 ATTAGTATATATTAATTTATCTAAAGTTTGAAATTTACATGTATCTCACTACTTTATAAAAGTAG
1 ATTAGTATATATTAATTTATCTAAAGTTTGAAATTTACATGTATCTCACTACTTTATAAAAGTAG
146071 GTTAAAATATTCT
66 GTTAAAATATTCT
*
146084 ATTAGTATATATTAATTTATCTAAAGTTTGAAATTTACATGTATCTCACTACTTTATAAAAGTGG
1 ATTAGTATATATTAATTTATCTAAAGTTTGAAATTTACATGTATCTCACTACTTTATAAAAGTAG
146149 GTTAAAATATTCT
66 GTTAAAATATTCT
146162 CTTACCCCAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.44
Consensus pattern (78 bp):
ATTAGTATATATTAATTTATCTAAAGTTTGAAATTTACATGTATCTCACTACTTTATAAAAGTAG
GTTAAAATATTCT
Found at i:146140 original size:37 final size:37
Alignment explanation
Indices: 146021--146140 Score: 111
Period size: 37 Copynumber: 3.1 Consensus size: 37
146011 TATATATTAA
146021 TTTATCTAAAGTTTGAAATTTACATGTATCTCACTAC
1 TTTATCTAAAGTTTGAAATTTACATGTATCTCACTAC
* * * * *
146058 TTTAT-AAAAGTAGGTTAAAATATT-CTATTAGTATAT-ATTAA
1 TTTATCTAAAGT---TTGAAAT-TTAC-A-T-GTATCTCACTAC
146099 TTTATCTAAAGTTTGAAATTTACATGTATCTCACTAC
1 TTTATCTAAAGTTTGAAATTTACATGTATCTCACTAC
146136 TTTAT
1 TTTAT
146141 AAAAGTGGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 20
0.68 0.11 0.22
Matches are distributed among these distances:
36 10 0.16
37 14 0.22
38 3 0.05
39 14 0.22
40 3 0.05
41 9 0.14
42 10 0.16
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (37 bp):
TTTATCTAAAGTTTGAAATTTACATGTATCTCACTAC
Found at i:146287 original size:35 final size:32
Alignment explanation
Indices: 146197--146298 Score: 91
Period size: 35 Copynumber: 3.0 Consensus size: 32
146187 CATATGTTTG
146197 GATAT-AATAATTTTAAATATAATTAAATAAATAT
1 GATATAAATAATTTTAAATAT-A-TAAAT-AATAT
* * *
146231 AATATATATAAAGTATTAAATATATGAAATAATAT
1 GATATAAAT-AA-TTTTAAATATAT-AAATAATAT
146266 GATATAAATATATTTTAAAATATATAAA-AATAT
1 GATATAAATA-ATTTT-AAATATATAAATAATAT
146299 AAATTATTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
33 5 0.09
34 11 0.20
35 24 0.43
36 7 0.12
37 9 0.16
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (32 bp):
GATATAAATAATTTTAAATATATAAATAATAT
Found at i:146300 original size:8 final size:9
Alignment explanation
Indices: 146227--146389 Score: 58
Period size: 9 Copynumber: 18.4 Consensus size: 9
146217 AATTAAATAA
*
146227 ATATAATAT
1 ATATAAAAT
*
146236 ATATAAAGT
1 ATATAAAAT
146245 AT-T-AAAT
1 ATATAAAAT
*
146252 ATATGAAAT
1 ATATAAAAT
**
146261 A-ATATGAT
1 ATATAAAAT
*
146269 ATA-AATAT
1 ATATAAAAT
*
146277 ATTTTAAAAT
1 A-TATAAAAT
146287 ATATAAAA-
1 ATATAAAAT
*
146295 ATATAAATT
1 ATATAAAAT
*
146304 AT-TAATAT
1 ATATAAAAT
*
146312 AT-TAAATT
1 ATATAAAAT
* *
146320 TTATATAA-
1 ATATAAAAT
146328 ATATAAAAT
1 ATATAAAAT
*
146337 ACATTAAAA-
1 ATA-TAAAAT
**
146346 ATAATTATGAT
1 AT-A-TAAAAT
146357 ATAATAAAAT
1 AT-ATAAAAT
146367 ATATAAACAT
1 ATATAAA-AT
146377 A-ATATAAAT
1 ATATA-AAAT
146386 ATAT
1 ATAT
146390 GAATTATCAA
Statistics
Matches: 113, Mismatches: 27, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
7 5 0.04
8 35 0.31
9 41 0.36
10 28 0.25
11 4 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (9 bp):
ATATAAAAT
Found at i:146661 original size:2 final size:2
Alignment explanation
Indices: 146654--146685 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
146644 TTAGAATTGA
146654 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
146686 GTTATATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146912 original size:22 final size:22
Alignment explanation
Indices: 146887--146928 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
146877 ATATTTTTTA
146887 AAAT-TTAATTATAAAAATATAT
1 AAATATTAA-TATAAAAATATAT
146909 AAATATTAATATAAAAATAT
1 AAATATTAATATAAAAATAT
146929 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATTAATATAAAAATATAT
Found at i:147010 original size:25 final size:27
Alignment explanation
Indices: 146946--147010 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 27
146936 ATTATTTAAT
146946 ATTTTAACAATAATTCAAACCTAAAATA
1 ATTTTAA-AATAATTCAAACCTAAAATA
**
146974 A-TTT-AAGCAATT-AAACCTAAAA-A
1 ATTTTAAAATAATTCAAACCTAAAATA
146997 ATTTTAAAATAATT
1 ATTTTAAAATAATT
147011 TCAGACAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
23 2 0.06
24 13 0.42
25 11 0.35
26 1 0.03
27 3 0.10
28 1 0.03
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.34
Consensus pattern (27 bp):
ATTTTAAAATAATTCAAACCTAAAATA
Found at i:149400 original size:3 final size:3
Alignment explanation
Indices: 149392--149426 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
149382 GTTTGCATGC
149392 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
149427 TACATCCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:151793 original size:15 final size:16
Alignment explanation
Indices: 151775--151815 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
151765 TTAATTTAAT
*
151775 TTAAATAAATA-TTTA
1 TTAAATAAAAATTTTA
151790 TT-AATAAAAATTTTA
1 TTAAATAAAAATTTTA
151805 TTAATATAAAA
1 TTAA-ATAAAA
151816 TAATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 7 0.32
15 8 0.36
16 1 0.05
17 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATAAAAATTTTA
Found at i:151815 original size:16 final size:16
Alignment explanation
Indices: 151781--151827 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
151771 TAATTTAAAT
151781 AAATATTTATTAATAA
1 AAATATTTATTAATAA
151797 AAAT-TTTATTAATATA
1 AAATATTTATTAATA-A
151813 AAATAATTT-TTAATA
1 AAAT-ATTTATTAATA
151828 TTTTAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.36
16 9 0.32
17 6 0.21
18 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTTATTAATAA
Found at i:151850 original size:16 final size:18
Alignment explanation
Indices: 151791--151850 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 18
151781 AAATATTTAT
*
151791 TAATAAAAATTTTATTAATA
1 TAATAATAA-TTT-TTAATA
151811 TAA-AATAATTTTTAATA
1 TAATAATAATTTTTAATA
**
151828 TTTTAAT-A-TTTTAATA
1 TAATAATAATTTTTAATA
151844 TAATAAT
1 TAATAAT
151851 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 13 0.38
17 8 0.24
18 6 0.18
19 4 0.12
20 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATAATTTTTAATA
Found at i:151853 original size:21 final size:21
Alignment explanation
Indices: 151823--151862 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
151813 AAATAATTTT
* *
151823 TAATATTTTAATATTTTAATA
1 TAATAATTTAAAATTTTAATA
151844 TAATAATTTAAAATTTTAA
1 TAATAATTTAAAATTTTAA
151863 CTTAAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATAATTTAAAATTTTAATA
Found at i:151861 original size:8 final size:8
Alignment explanation
Indices: 151816--151844 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
151806 TAATATAAAA
151816 TAAT-TTT
1 TAATATTT
151823 TAATATTT
1 TAATATTT
151831 TAATATTT
1 TAATATTT
151839 TAATAT
1 TAATAT
151845 AATAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TAATATTT
Found at i:153261 original size:29 final size:28
Alignment explanation
Indices: 153241--153298 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
153231 TATGATTTAT
153241 ATAAATAAAATATA-AAATATAATAATTAA
1 ATAAA-AAAATATATAAATAT-ATAATTAA
*
153270 ATAAAAAATTATATAAATATATAAATTAA
1 ATAAAAAAATATATAAATATAT-AATTAA
153299 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAAAAAAATATATAAATATATAATTAA
Found at i:153264 original size:12 final size:13
Alignment explanation
Indices: 153238--153295 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
153228 TTATATGATT
153238 TATATAAATAAAA
1 TATATAAATAAAA
*
153251 TATA-AAATATAA
1 TATATAAATAAAA
153263 TA-ATTAAATAAAA
1 TATA-TAAATAAAA
* *
153276 AAT-TATAT-AAA
1 TATATAAATAAAA
153287 TATATAAAT
1 TATATAAAT
153296 TAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
11 6 0.17
12 17 0.49
13 12 0.34
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TATATAAATAAAA
Found at i:153293 original size:20 final size:20
Alignment explanation
Indices: 153237--153294 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
153227 TTTATATGAT
*
153237 TTATATAAATAAAATATAAAA
1 TTATATAAAT-AAATAAAAAA
*
153258 -TATAATAATTAAATAAAAAA
1 TTAT-ATAAATAAATAAAAAA
*
153278 TTATATAAATATATAAA
1 TTATATAAATAAATAAA
153295 TTAATTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 23 0.74
21 8 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TTATATAAATAAATAAAAAA
Found at i:153589 original size:21 final size:21
Alignment explanation
Indices: 153555--153595 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
153545 ATATGTTATA
*
153555 TTTTTAATTAATTTTTAAAAT
1 TTTTTAATTAATTTTAAAAAT
153576 TTTTTAA-TATATTTTAAAAA
1 TTTTTAATTA-ATTTTAAAAA
153596 ATATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTAATTAATTTTAAAAAT
Found at i:153664 original size:2 final size:2
Alignment explanation
Indices: 153657--153686 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
153647 ATAATTTTTC
153657 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
153687 TACATTCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:154803 original size:21 final size:20
Alignment explanation
Indices: 154769--154807 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
154759 CTTTTTTATA
154769 TGATTAATAATTTAATAAAT
1 TGATTAATAATTTAATAAAT
*
154789 TGATTATTGAATTTAATAA
1 TGATTAAT-AATTTAATAA
154808 TACATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
TGATTAATAATTTAATAAAT
Found at i:155161 original size:19 final size:20
Alignment explanation
Indices: 155137--155177 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
155127 AATATTTTTA
*
155137 TTAAAAT-ATTAAATTAATT
1 TTAAAATAAATAAATTAATT
155156 TTAAAATAAATAAATTAATT
1 TTAAAATAAATAAATTAATT
155176 TT
1 TT
155178 TTTTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAATAAATAAATTAATT
Found at i:157418 original size:24 final size:24
Alignment explanation
Indices: 157391--157440 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
157381 TATATAAAAG
157391 TGGTTTTAGCTTGTAAAAAATAAT
1 TGGTTTTAGCTTGTAAAAAATAAT
157415 TGGTTTTAGCTTGTAAAAAATAAT
1 TGGTTTTAGCTTGTAAAAAATAAT
157439 TG
1 TG
157441 TAAATGTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (24 bp):
TGGTTTTAGCTTGTAAAAAATAAT
Found at i:159813 original size:45 final size:45
Alignment explanation
Indices: 159762--159850 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
159752 AGGAAAAAGT
* * *
159762 TGGAGAGAGGCGCGTCAAGCTCGGGCAAGGCGGCAAAGAAGAAGG
1 TGGAGAGAGGCGAGTCAAGATCGAGCAAGGCGGCAAAGAAGAAGG
* *
159807 TGGAGAGGGGCGAGTCAAGATCTAGCAAGGCGGCAAAGAAGAAG
1 TGGAGAGAGGCGAGTCAAGATCGAGCAAGGCGGCAAAGAAGAAG
159851 AAGGAGGCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.16, G:0.43, T:0.08
Consensus pattern (45 bp):
TGGAGAGAGGCGAGTCAAGATCGAGCAAGGCGGCAAAGAAGAAGG
Found at i:160205 original size:4 final size:4
Alignment explanation
Indices: 160182--160233 Score: 59
Period size: 4 Copynumber: 12.5 Consensus size: 4
160172 TCCTCTATCC
* * *
160182 TACA TACA TGCA TATGCA TACA TACT TACA TACA TACA TACA TATA TACA
1 TACA TACA TACA TA--CA TACA TACA TACA TACA TACA TACA TACA TACA
160232 TA
1 TA
160234 TATTTACATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 36 0.90
6 4 0.10
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (4 bp):
TACA
Found at i:160771 original size:2 final size:2
Alignment explanation
Indices: 160764--160789 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
160754 CACTAATTCC
160764 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
160790 GTTTTATACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:161967 original size:2 final size:2
Alignment explanation
Indices: 161960--161986 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
161950 TATTACTAAC
161960 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 A
161987 ATTTAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:162122 original size:29 final size:28
Alignment explanation
Indices: 162059--162122 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
162049 TTATCAATTG
* * *
162059 AATTTTTTTTAATATATTTAATATTTAA
1 AATTTTTTTTAATATAATAAATAATTAA
*
162087 AAGTTTTTTATAATA-AATAAATAATTAA
1 AA-TTTTTTTTAATATAATAAATAATTAA
162115 ATATTTTT
1 A-ATTTTT
162123 AATTTTTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
AATTTTTTTTAATATAATAAATAATTAA
Found at i:167190 original size:31 final size:31
Alignment explanation
Indices: 167144--167202 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
167134 CGATAATTGA
*
167144 AAAATGCATCGATACATCTAGGTAAAAAGAC
1 AAAATGCATCAATACATCTAGGTAAAAAGAC
* *
167175 AAAATGTATCAATACATTTAGGTAAAAA
1 AAAATGCATCAATACATCTAGGTAAAAA
167203 TGTGACTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (31 bp):
AAAATGCATCAATACATCTAGGTAAAAAGAC
Found at i:168168 original size:32 final size:31
Alignment explanation
Indices: 168111--168199 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 31
168101 CGACATTGGG
* *
168111 TTTAGAAAGGTTGCCACCAATTTGTGTAGGC
1 TTTAGAAAGATTGCCACCAACTTGTGTAGGC
*
168142 TTTAGAGAAGATTGCTACCAACTTGTGTAGGC
1 TTTAGA-AAGATTGCCACCAACTTGTGTAGGC
* * **
168174 TTTAGAAGGGTTGCCACTGACTTGTG
1 TTTAGAAAGATTGCCACCAACTTGTG
168200 GGTTTTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 21 0.43
32 28 0.57
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (31 bp):
TTTAGAAAGATTGCCACCAACTTGTGTAGGC
Found at i:168354 original size:30 final size:31
Alignment explanation
Indices: 168307--168407 Score: 145
Period size: 30 Copynumber: 3.3 Consensus size: 31
168297 TCCACTGACT
*
168307 TGTGGGCTTTGAGAGAGGTTGCCACCGATTTG
1 TGTGGGCTTTGAGAGAGGTTGCCACC-AATTG
*
168339 TGTGGGCTTT-A-AGAGGTTGCCACCAACT-
1 TGTGGGCTTTGAGAGAGGTTGCCACCAATTG
168367 TGTGGGCTTTGAGAGAGGTTGCCACCAACTTG
1 TGTGGGCTTTGAGAGAGGTTGCCACCAA-TTG
168399 TGTGGGCTT
1 TGTGGGCTT
168408 CGAAAGGGTG
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
28 10 0.16
29 3 0.05
30 28 0.45
31 2 0.03
32 19 0.31
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.31
Consensus pattern (31 bp):
TGTGGGCTTTGAGAGAGGTTGCCACCAATTG
Found at i:168680 original size:29 final size:29
Alignment explanation
Indices: 168162--168671 Score: 370
Period size: 28 Copynumber: 17.8 Consensus size: 29
168152 ATTGCTACCA
*
168162 ACTTGTGTAGGCTTT-AGAAGGGTTGCCACTG
1 ACTTGTG--GGCTTTGAAAAGGG-TGCCACTG
* * * *
168193 ACTTGTGGG-TTTTAAAAAGATGCCATTG
1 ACTTGTGGGCTTTGAAAAGGGTGCCACTG
* * * *
168221 ATTTGTGGACTTCG-AAAGGGTACCACT-
1 ACTTGTGGGCTTTGAAAAGGGTGCCACTG
* **
168248 AGCTTGTGGGCTTCGAAAA-GGTATCACT-
1 A-CTTGTGGGCTTTGAAAAGGGTGCCACTG
168276 AGCTTGTGGGCTTTG-AAAGGGT-CCACTG
1 A-CTTGTGGGCTTTGAAAAGGGTGCCACTG
* * *
168304 ACTTGTGGGCTTTGAGAGAGGTTGCCACCG
1 ACTTGTGGGCTTTGA-AAAGGGTGCCACTG
* * * **
168334 ATTTGTGTGGGCTTT-AAGAGGTTGCCACCA
1 A-CT-TGTGGGCTTTGAAAAGGGTGCCACTG
* * **
168364 ACTTGTGGGCTTTGAGAGAGGTTGCCACCA
1 ACTTGTGGGCTTTGA-AAAGGGTGCCACTG
* *
168394 ACTTGTGTGGGCTTCG-AAAGGGTGCCGCTG
1 AC-T-TGTGGGCTTTGAAAAGGGTGCCACTG
*
168424 ACTTGTGGGCTTT-TAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAAGGGTGCCACTG
** *
168452 ACTCCTGGGCTTTG-GAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAAGGGTGCCACTG
** * *
168480 ACTCATGGGCTTTGAGAA-GGTGCCATTG
1 ACTTGTGGGCTTTGAAAAGGGTGCCACTG
* *
168508 ACTCGTGGGCTTTG-AAAGGGTGCCACTA
1 ACTTGTGGGCTTTGAAAAGGGTGCCACTG
* * **
168536 ACTTATGGGCTTTG-AAACGGTGTAACTG
1 ACTTGTGGGCTTTGAAAAGGGTGCCACTG
* *
168564 ACTTGTGGGCTTTTAAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAAGGGTGCCACTG
* * * *
168593 ACTTGTGGGTTTTGGAAA-GATGCCATTG
1 ACTTGTGGGCTTTGAAAAGGGTGCCACTG
*
168621 ACTCGTGGGCTTT-AAAAGAGGTGCCACTG
1 ACTTGTGGGCTTTGAAAAG-GGTGCCACTG
168650 ACTTGTGGGCTTTGAAAAGGGT
1 ACTTGTGGGCTTTGAAAAGGGT
168672 CATATTGACG
Statistics
Matches: 394, Mismatches: 62, Indels: 48
0.78 0.12 0.10
Matches are distributed among these distances:
27 26 0.07
28 216 0.55
29 70 0.18
30 52 0.13
31 10 0.03
32 20 0.05
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (29 bp):
ACTTGTGGGCTTTGAAAAGGGTGCCACTG
Found at i:173427 original size:21 final size:21
Alignment explanation
Indices: 173380--173435 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
173370 AAAAATTTTT
*
173380 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
173401 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
173422 CAAATGTATCGATA
1 CAAATGTATCGATA
173436 TAGGGTCCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:173497 original size:19 final size:19
Alignment explanation
Indices: 173473--173540 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
173463 AATTCAACAA
173473 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
173492 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
173507 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
173524 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
173541 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:173512 original size:13 final size:13
Alignment explanation
Indices: 173494--173518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173484 ACATAAGTTT
173494 TGTATCGATACAA
1 TGTATCGATACAA
173507 TGTATCGATACA
1 TGTATCGATACA
173519 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:173516 original size:32 final size:32
Alignment explanation
Indices: 173475--173537 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
173465 TTCAACAATT
*
173475 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
173507 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
173538 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:173598 original size:13 final size:13
Alignment explanation
Indices: 173580--173605 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
173570 CATTTTTCTG
173580 TGTATCGATACAT
1 TGTATCGATACAT
173593 TGTATCGATACAT
1 TGTATCGATACAT
173606 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:173602 original size:33 final size:33
Alignment explanation
Indices: 173560--173626 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
173550 GCCAAGGAAA
***
173560 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
173593 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
173626 T
1 T
173627 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:176033 original size:51 final size:53
Alignment explanation
Indices: 175977--176095 Score: 147
Period size: 51 Copynumber: 2.3 Consensus size: 53
175967 AATTCTCCAC
* * *
175977 AATCGGGGATA-TTTCAACTCCGATTTTATTTTC-AAAACACTAA-TT-TTCTAT
1 AATCGGGGATACTCT-AACTCCGATTTTATTTCCAAAAACACCAATTTCTTC-AT
*
176028 AATCGGGAATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAT
1 AATCGGGGATACTCTAACTCCGATTTTATTTCC-AAAAACACCAATTTCTTCAT
176082 AATCGGGGATACTC
1 AATCGGGGATACTC
176096 CAACCCCGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
51 27 0.47
52 2 0.03
53 9 0.16
54 17 0.29
55 3 0.05
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (53 bp):
AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCAT
Found at i:176154 original size:28 final size:27
Alignment explanation
Indices: 176086--176155 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
176076 CTTCATAATC
176086 GGGGATACTCCAACCCCGTTAATCATCA
1 GGGGATACTCCAACCCCGTTAATCA-CA
*
176114 -GGGATACTCCAACCCCGTTATTTC-CGA
1 GGGGATACTCCAACCCCGTTA-ATCAC-A
176141 GGGGATACTCCAACC
1 GGGGATACTCCAACC
176156 TCGGTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 1 0.03
27 21 0.55
28 16 0.42
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCACA
Found at i:176207 original size:52 final size:51
Alignment explanation
Indices: 176141--176314 Score: 183
Period size: 52 Copynumber: 3.4 Consensus size: 51
176131 TTATTTCCGA
* *
176141 GGGGATACTCCAACCTCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCTCGGTTTTATT-CTAAAATACCAATTTTTCCACAATC
* * * **
176193 GGGGATACTCCAACCCCGGTTTTATTTTCAAAATGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACCTCGGTTTTATTCT-AAAATACCAATTTTTCC-ACAATC
* *
176245 GGGGATACTCCAA-CTCTGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACCTC-GGTTTTA-TT-CTAAAATACCAATTTTTCCACAATC
*
176297 GAGGATACTCCAACCTCG
1 GGGGATACTCCAACCTCG
176315 TTATTTCATC
Statistics
Matches: 100, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
51 9 0.09
52 72 0.72
53 15 0.15
54 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGGTTTTATTCTAAAATACCAATTTTTCCACAATC
Found at i:176294 original size:104 final size:103
Alignment explanation
Indices: 175974--176311 Score: 278
Period size: 105 Copynumber: 3.2 Consensus size: 103
175964 CTCAATTCTC
* * * * * *
175974 CACAATCGGGGATATTTCAACTCCGATTTTATTTTCAAAA-CACTAATTTT-CTATAATCGGGAA
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAATC-C-AATTTTCCTTTAATCGGGGA
* *
176037 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
64 TACTCCAACTCTGATTTTATTTCC-AAAAACACCAATTT-TT
* * ** * ** * *
176079 CATAATCGGGGATACTCCAACCCC-G-TTAATCATCAGGGATACTCCAA--CCCCGTTATTTCCG
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCA---A-AATCCAATTTTCCTTTA-AT-C-
* * * *
176140 AGGGGATACTCCAAC-CTCGGTTTTA-TTGCTAAAACACTAATTTTT
59 -GGGGATACTCCAACTCT-GATTTTATTTCCAAAAACACCAATTTTT
176185 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAATGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAAT-CCAATTTTCCTTTAATCGGGGA
*
176250 TACTCCAACTCTGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTT
*
176290 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
176312 TCGTTATTTC
Statistics
Matches: 178, Mismatches: 36, Indels: 39
0.70 0.14 0.15
Matches are distributed among these distances:
103 7 0.04
104 41 0.23
105 43 0.24
106 12 0.07
107 39 0.22
108 11 0.06
109 25 0.14
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (103 bp):
CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAATCCAATTTTCCTTTAATCGGGGATA
CTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTT
Found at i:176330 original size:28 final size:28
Alignment explanation
Indices: 176294--176370 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
176284 ATTTTTCACA
* * *
176294 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
176322 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
176350 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
176371 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:176339 original size:212 final size:212
Alignment explanation
Indices: 175969--176421 Score: 615
Period size: 212 Copynumber: 2.1 Consensus size: 212
175959 AGTTTCTCAA
* * * *
175969 TTCTCCACAATCGGGGATATTTCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
* * *
176034 GAATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCATAATCGGGGATACTCCAA
66 GAATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* * *
176099 CCCCGTTAATCATCAGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTCGGTTTT
131 CCCCGTTAATCATCAGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
* *
176164 ATTGCTAAAACACTAAT
196 ATTCCCAAAACACTAAT
* * ** *
176181 TTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAATGCCAATTTTCCTTTAATCG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCG
* * *
176246 GGGATACTCCAACTCTGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCA
65 GGAATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCA
* * *
176309 ACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCT
130 ACCCCGTTA-ATCATCAGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCT
* * *
176374 TTATTCCCAAAATATTGAT
194 TTATTCCCAAAACACTAAT
* *
176393 TTCT-CATAATTGGGGATACTCCAACCCCG
1 TTCTCCACAATCGGGGATACTCCAACCCCG
176422 TTATTTTCGA
Statistics
Matches: 210, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
211 50 0.24
212 127 0.60
213 33 0.16
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (212 bp):
TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
GAATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
CCCCGTTAATCATCAGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
ATTCCCAAAACACTAAT
Found at i:176436 original size:107 final size:104
Alignment explanation
Indices: 176036--176449 Score: 320
Period size: 107 Copynumber: 3.9 Consensus size: 104
176026 ATAATCGGGA
* * * * * *
176036 ATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCATAATCGGGGATACTCCAACC
1 ATACTCCAACCCCGGTTTTA-TTCC-AAAAATACTAATTTC-TCACAATCGGGGATACTCCAACC
**
176101 CCGTTAATCATCAGGGATACTCCAACCCCGTTATTTCCGAGGGG
63 CCGTT-ATTTTCAGGGATACTCCAACCCCGTTA-TTCCGAGGGG
* * * * *
176145 ATACTCCAACCTCGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCAACCCC
1 ATACTCCAACCCCGGTTTTATTCCAAAAATACTAATTTCT-CACAATCGGGGATACTCCAACCCC
* ** * *
176210 GGTTTTATTTTCA---A-AATGCCAATTTTCCTTTAAT-C--GGGG
65 -G--TTATTTTCAGGGATACT-CCAA--CCCCGTTATTCCGAGGGG
* * * * * * *
176249 ATACTCCAACTCTGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAACCTC
1 ATACTCCAACCCCGGTTTTA-TTCCAAAAATACTAATTTCTCACAATCGGGGATACTCCAACCCC
*
176314 GTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGG
65 GTTATTT--TCAGGGATACTCCAACCCCGTTA-TTCCGAGGGG
* * * * * *
176357 ATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
1 ATACTCCAACCCCGGTTTTATTCCAAAAATACTAATTTCTCACAATCGGGGATACTCCAACCCCG
*
176422 TTATTTTCGAGGGGATACTCCAATCCCG
66 TTATTTTC-A-GGGATACTCCAACCCCG
176450 ATTTTTTTTT
Statistics
Matches: 238, Mismatches: 47, Indels: 42
0.73 0.14 0.13
Matches are distributed among these distances:
101 6 0.03
103 3 0.01
104 47 0.20
105 21 0.09
106 13 0.05
107 96 0.40
108 29 0.12
109 21 0.09
110 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (104 bp):
ATACTCCAACCCCGGTTTTATTCCAAAAATACTAATTTCTCACAATCGGGGATACTCCAACCCCG
TTATTTTCAGGGATACTCCAACCCCGTTATTCCGAGGGG
Found at i:176473 original size:79 final size:79
Alignment explanation
Indices: 176324--176528 Score: 232
Period size: 79 Copynumber: 2.6 Consensus size: 79
176314 GTTATTTCAT
* * *
176324 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
176389 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
176403 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
176467 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * * *
176482 CGGGGATACTCGAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
176529 TTATTATCTC
Statistics
Matches: 105, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
78 3 0.03
79 102 0.97
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:177572 original size:51 final size:50
Alignment explanation
Indices: 177496--177609 Score: 165
Period size: 51 Copynumber: 2.3 Consensus size: 50
177486 CGTCGCGACA
* * *
177496 GTATCTATACATTTTTCAATGTATCGATACATTTTGCCTTTTTACCCAGAT
1 GTATCGATACATTTTTCAATGTATCGATACATTCTACC-TTTTACCCAGAT
* * *
177547 GTATCGATACATTTTTTAATGTATCGATACATTCTATCTTTTACCTAGAT
1 GTATCGATACATTTTTCAATGTATCGATACATTCTACCTTTTACCCAGAT
177597 GTATCGATACATT
1 GTATCGATACATT
177610 CTGGCTTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 24 0.42
51 33 0.58
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.45
Consensus pattern (50 bp):
GTATCGATACATTTTTCAATGTATCGATACATTCTACCTTTTACCCAGAT
Found at i:177588 original size:26 final size:27
Alignment explanation
Indices: 177559--177640 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 27
177549 ATCGATACAT
*
177559 TTTTTA-ATGTATCGATACATTCTATC
1 TTTTTAGATGTATCGATACATTCTAGC
*
177585 TTTTACCTAGATGTATCGATACATTCTGGC
1 TTTT---TAGATGTATCGATACATTCTAGC
177615 TTTTTACCCAGATGTATCGATACATT
1 TTTTT----AGATGTATCGATACATT
177641 TTTAAATGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
29 2 0.04
30 22 0.48
31 17 0.37
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (27 bp):
TTTTTAGATGTATCGATACATTCTAGC
Found at i:177599 original size:30 final size:31
Alignment explanation
Indices: 177565--177640 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
177555 ACATTTTTTA
* *
177565 ATGTATCGATACATTCTATC-TTTTACCTAG
1 ATGTATCGATACATTCTAGCTTTTTACCCAG
*
177595 ATGTATCGATACATTCTGGCTTTTTACCCAG
1 ATGTATCGATACATTCTAGCTTTTTACCCAG
177626 ATGTATCGATACATT
1 ATGTATCGATACATT
177641 TTTAAATGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 18 0.43
31 24 0.57
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (31 bp):
ATGTATCGATACATTCTAGCTTTTTACCCAG
Found at i:189234 original size:160 final size:160
Alignment explanation
Indices: 189050--189375 Score: 616
Period size: 160 Copynumber: 2.0 Consensus size: 160
189040 CATCATAATG
189050 TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
1 TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
* *
189115 ATTTTGGCTATAAATAGACTAATGCAATCATAGCAAAAGATCCCTTTTTCAACCACATTTTCTAG
66 ATTTTGGCTATAAATAGACCAATGCAATCATAGCAAAAGATCCCTTCTTCAACCACATTTTCTAG
189180 CCTCATTACCATCCATATCTTAGCAAAACA
131 CCTCATTACCATCCATATCTTAGCAAAACA
189210 TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
1 TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
*
189275 ATTTTGGCTATAAATAGACCAATGCAATCCTAGCAAAAGATCCCTTCTTCAACCACATTTTCTAG
66 ATTTTGGCTATAAATAGACCAATGCAATCATAGCAAAAGATCCCTTCTTCAACCACATTTTCTAG
*
189340 CCTCATTACCATCCATATCTTAGCGAAACA
131 CCTCATTACCATCCATATCTTAGCAAAACA
189370 TCAACA
1 TCAACA
189376 TAAAAACTCA
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.27
Consensus pattern (160 bp):
TCAACACCTTATCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACCTCACCTTTCACCCCAAA
ATTTTGGCTATAAATAGACCAATGCAATCATAGCAAAAGATCCCTTCTTCAACCACATTTTCTAG
CCTCATTACCATCCATATCTTAGCAAAACA
Found at i:194718 original size:20 final size:20
Alignment explanation
Indices: 194693--194769 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
194683 GTAAAAAGAT
194693 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
194713 AGAATGTATCGATATATTCA
1 AGAATGTATCGATACATTGA
* *
194733 TA-CATGTATCGATACATTGT
1 -AGAATGTATCGATACATTGA
*
194753 CGAATGTATCGATACAT
1 AGAATGTATCGATACAT
194770 CTGGATAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 46 0.98
21 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:195020 original size:13 final size:13
Alignment explanation
Indices: 195002--195028 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
194992 TTTGTAGTTT
195002 GTTATTGCAACAA
1 GTTATTGCAACAA
195015 GTTATTGCAACAA
1 GTTATTGCAACAA
195028 G
1 G
195029 GGATGGGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (13 bp):
GTTATTGCAACAA
Found at i:198210 original size:2 final size:2
Alignment explanation
Indices: 198205--198230 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
198195 AAAAAAGACC
198205 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
198231 GAGTTTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:199803 original size:37 final size:37
Alignment explanation
Indices: 199762--199859 Score: 108
Period size: 37 Copynumber: 2.6 Consensus size: 37
199752 TGACAAGTAA
* * *
199762 TATTTGGGTGGC-TTGGTCAATCCACTATGATTGTTAG
1 TATTTGGGTGGCAGT-GCCAATCCACTATAATTGTTAG
*
199799 TATTTGGGTGGCAGTGCCAATTCACTATAATTGTTAG
1 TATTTGGGTGGCAGTGCCAATCCACTATAATTGTTAG
* * **
199836 AATTTAGGTGGCAGCACCAATCCA
1 TATTTGGGTGGCAGTGCCAATCCA
199860 AAAAAATAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 50 0.98
38 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (37 bp):
TATTTGGGTGGCAGTGCCAATCCACTATAATTGTTAG
Found at i:204559 original size:37 final size:36
Alignment explanation
Indices: 204503--204600 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 36
204493 CAACAAGTAC
*
204503 TATTTGGGTGGCTTGGCCAATCCACTATGATTGTTAG
1 TATTTGGGTGG-TAGGCCAATCCACTATGATTGTTAG
204540 TATTTGGGTGGTAGTGCCAATCCACTATGATTGTTAG
1 TATTTGGGTGGTAG-GCCAATCCACTATGATTGTTAG
* * *
204577 AATTTAGGTGGCAGCGCCAATCCA
1 TATTTGGGTGGTAG-GCCAATCCA
204601 AAAAAAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 2 0.04
37 53 0.96
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (36 bp):
TATTTGGGTGGTAGGCCAATCCACTATGATTGTTAG
Found at i:209025 original size:20 final size:20
Alignment explanation
Indices: 208988--209025 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
208978 CAACACTTAC
* *
208988 AATTCATACTTAGGAATTCA
1 AATTCATACTCAGAAATTCA
209008 AATTCATACTCAGAAATT
1 AATTCATACTCAGAAATT
209026 TAACTAACGA
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:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (20 bp):
AATTCATACTCAGAAATTCA
Found at i:209295 original size:28 final size:28
Alignment explanation
Indices: 209216--209298 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
209206 CAAATGCCAC
*
209216 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
209244 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
*
209272 CCTTTATATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
209299 ATTTTTGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:209306 original size:56 final size:54
Alignment explanation
Indices: 209216--209322 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 54
209206 CAAATGCCAC
*
209216 CCTTTGTATTTGTCAAATATGGTAGTTTCCTTTGTATTTGT-CAAATATGGTGGTTT
1 CCTTTATATTTGTCAAATATGGTAGTTTCCTTTG--TTTGTACAAAT-TGGTGGTTT
* *
209272 CCTTTATATTTGTCAAATATGGTGGTTAT-TTTTGTTTGTACAAATTGGTGG
1 CCTTTATATTTGTCAAATATGGTAGTT-TCCTTTGTTTGTACAAATTGGTGG
209323 CTTGTTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
54 11 0.24
55 5 0.11
56 29 0.63
57 1 0.02
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (54 bp):
CCTTTATATTTGTCAAATATGGTAGTTTCCTTTGTTTGTACAAATTGGTGGTTT
Found at i:209340 original size:24 final size:24
Alignment explanation
Indices: 209303--209348 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
209293 GTGGTTATTT
209303 TTGTTTGTACAAATTGGTGGCTTG
1 TTGTTTGTACAAATTGGTGGCTTG
209327 TTGTTTGT-CAAAATTGGTGGCT
1 TTGTTTGTAC-AAATTGGTGGCT
209349 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTACAAATTGGTGGCTTG
Found at i:213921 original size:28 final size:28
Alignment explanation
Indices: 213842--213924 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
213832 CAAATGCCAC
*
213842 CCTTTGTATTTGTCAAATATGGTAGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
213870 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
*
213898 CCTTTATATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
213925 ATTTTTGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:213932 original size:56 final size:54
Alignment explanation
Indices: 213842--213948 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 54
213832 CAAATGCCAC
*
213842 CCTTTGTATTTGTCAAATATGGTAGTTTCCTTTGTATTTGT-CAAATATGGTGGTTT
1 CCTTTATATTTGTCAAATATGGTAGTTTCCTTTG--TTTGTACAAAT-TGGTGGTTT
* *
213898 CCTTTATATTTGTCAAATATGGTGGTTAT-TTTTGTTTGTACAAATTGGTGG
1 CCTTTATATTTGTCAAATATGGTAGTT-TCCTTTGTTTGTACAAATTGGTGG
213949 CTTATTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
54 11 0.24
55 5 0.11
56 29 0.63
57 1 0.02
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (54 bp):
CCTTTATATTTGTCAAATATGGTAGTTTCCTTTGTTTGTACAAATTGGTGGTTT
Found at i:213946 original size:26 final size:28
Alignment explanation
Indices: 213878--213960 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
213868 TTCCTTTGTA
* * * *
213878 TTTGTCAAATATGGTGGTTTCCTT-TATA
1 TTTGTCAAATATGGTGGCTT-ATTGTTTG
213906 TTTGTCAAATATGGTGG-TTATT-TTTG
1 TTTGTCAAATATGGTGGCTTATTGTTTG
213932 TTTGTACAAAT-TGGTGGCTTATTGTTTG
1 TTTGT-CAAATATGGTGGCTTATTGTTTG
213960 T
1 T
213961 CAAAATTGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
26 15 0.31
27 12 0.24
28 22 0.45
ACGTcount: A:0.19, C:0.07, G:0.22, T:0.52
Consensus pattern (28 bp):
TTTGTCAAATATGGTGGCTTATTGTTTG
Found at i:213953 original size:27 final size:26
Alignment explanation
Indices: 213878--213981 Score: 90
Period size: 24 Copynumber: 4.0 Consensus size: 26
213868 TTCCTTTGTA
* * * *
213878 TTTGTCAAATATGGTGGTTTCCTTTATA
1 TTTGTCAAAT-TGGTGGCTT-ATTTTTG
213906 TTTGTCAAATATGGTGG-TTATTTTTG
1 TTTGTCAAAT-TGGTGGCTTATTTTTG
213932 TTTGTACAAATTGGTGGCTTA---TTG
1 TTTGT-CAAATTGGTGGCTTATTTTTG
*
213956 TTTGTCAAAATTGGTGGCTAATTTTT
1 TTTGTC-AAATTGGTGGCTTATTTTT
213982 ATTAGAAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
23 1 0.02
24 21 0.32
26 15 0.23
27 12 0.18
28 17 0.26
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (26 bp):
TTTGTCAAATTGGTGGCTTATTTTTG
Found at i:214675 original size:18 final size:17
Alignment explanation
Indices: 214652--214703 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
214642 AATTATTATT
214652 ATATAATAATTAATATAA
1 ATATAATAA-TAATATAA
214670 ATATAA-AA-AATATTAA
1 ATATAATAATAATA-TAA
*
214686 ATATAATTATAATATAA
1 ATATAATAATAATATAA
214703 A
1 A
214704 ATACACAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 9 0.30
17 7 0.23
18 10 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATAATAATAATATAA
Found at i:214682 original size:27 final size:27
Alignment explanation
Indices: 214652--214704 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
214642 AATTATTATT
214652 ATATAATAAT-TAA-TATAAATATAAAAA
1 ATATAA-AATATAATTAT-AATATAAAAA
*
214679 ATATTAAATATAATTATAATATAAAA
1 ATATAAAATATAATTATAATATAAAA
214705 TACACAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.13
27 17 0.74
28 3 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
ATATAAAATATAATTATAATATAAAAA
Found at i:214706 original size:18 final size:16
Alignment explanation
Indices: 214657--214703 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
214647 TTATTATATA
214657 ATAAT-TAATATAAAT
1 ATAATATAATATAAAT
*
214672 ATAA-AAAATATTAAAT
1 ATAATATAATA-TAAAT
214688 ATAATTATAATATAAA
1 ATAA-TATAATATAAA
214704 ATACACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.31
16 9 0.35
17 4 0.15
18 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATATAATATAAAT
Found at i:215721 original size:94 final size:93
Alignment explanation
Indices: 215600--215792 Score: 332
Period size: 94 Copynumber: 2.1 Consensus size: 93
215590 AAGTTAAAAG
*
215600 CAACATGTCTTTGGACTATTAATAGTAAACCTTCCCTCGTATTTATGTTATAATTATTTTTTTCT
1 CAACATGTCTTCGGACTATTAATAGTAAACCTTCCCTCGTATTTATGTTATAATTATTTTTTTCT
*
215665 AAAGTACTTAATCTCCAACATCTATATT
66 AAAATACTTAATCTCCAACATCTATATT
*
215693 CAACATGTCCTTCGGACTATTAATAGTAAACCTTTCCTCGTATTTATGTTATAATTATTTTTTTC
1 CAACATGT-CTTCGGACTATTAATAGTAAACCTTCCCTCGTATTTATGTTATAATTATTTTTTTC
* *
215758 TAAAATACTTAATCTTCAACATTTATATT
65 TAAAATACTTAATCTCCAACATCTATATT
215787 CAACAT
1 CAACAT
215793 ATACCGACTT
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 8 0.09
94 86 0.91
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (93 bp):
CAACATGTCTTCGGACTATTAATAGTAAACCTTCCCTCGTATTTATGTTATAATTATTTTTTTCT
AAAATACTTAATCTCCAACATCTATATT
Found at i:216044 original size:11 final size:11
Alignment explanation
Indices: 216014--216047 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
216004 TTAAATAAGT
216014 TATAATATAAA
1 TATAATATAAA
*
216025 AAT-ATATAAA
1 TATAATATAAA
216035 TATAATATAAA
1 TATAATATAAA
216046 TA
1 TA
216048 CTCGGATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAATATAAA
Found at i:216247 original size:2 final size:2
Alignment explanation
Indices: 216242--216299 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
216232 TCTCTCTCTC
*
216242 TA TA TA TA TA TA TA TA TA TA TA TA CA 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
216284 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
216300 ACTCAAAAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:218108 original size:3 final size:3
Alignment explanation
Indices: 218093--218147 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
218083 AAACATTTAC
* *
218093 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -TT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
218140 ATT AAT AA
1 AAT AAT AA
218148 AAGACCATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:221052 original size:81 final size:79
Alignment explanation
Indices: 220953--221141 Score: 211
Period size: 79 Copynumber: 2.4 Consensus size: 79
220943 GTGTTCCTTT
* * * * *
220953 GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TCAGAAGAAAAAAAATCG-
1 GAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTCAG--GAAAAAAAACCGA
221016 GGATTGGAGTATCCCCTC
63 GG-TTGGAGTATCCCCTC
* ** * * *
221034 GAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGAGGT
1 GAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTCAGGAAAAAAAACCGAGGT
221099 TGGAGTATCCCCTC
66 TGGAGTATCCCCTC
* *
221113 GGAAGTAACGGGGTTGGAGTATCCCCGAT
1 GAAAATAACGGGGTTGGAGTATCCCCGAT
221142 GAAATAACGA
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
79 49 0.53
80 3 0.03
81 40 0.43
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (79 bp):
GAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTCAGGAAAAAAAACCGAGGT
TGGAGTATCCCCTC
Found at i:221136 original size:28 final size:28
Alignment explanation
Indices: 221093--221164 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
221083 GGAATAAAGC
** *
221093 CGAGGTTGGAGTATCCCCTCGGAAGTAA
1 CGAGGTTGGAGTATCCCCGAGGAAATAA
* *
221121 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGAGGTTGGAGTATCCCCGAGGAAATAA
221149 CGAGGTTGGAGTATCC
1 CGAGGTTGGAGTATCC
221165 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGAGGTTGGAGTATCCCCGAGGAAATAA
Done.