Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015279.1 Kokia drynarioides strain JFW-HI SEQ_130324, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 271778
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 417 characters in sequence are not A, C, G, or T
Found at i:1855 original size:14 final size:14
Alignment explanation
Indices: 1836--1870 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1826 AACCAAAAAG
*
1836 AAAAGATTACTCAT
1 AAAAGAATACTCAT
1850 AAAAGAATACTCAT
1 AAAAGAATACTCAT
1864 AAAAGAA
1 AAAAGAA
1871 AAAAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (14 bp):
AAAAGAATACTCAT
Found at i:2277 original size:16 final size:17
Alignment explanation
Indices: 2234--2266 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
2224 AGATAACCTC
2234 AAAAGATAAAAACGAAAG
1 AAAA-ATAAAAACGAAAG
2252 AAAAAT-AAAACGAAA
1 AAAAATAAAAACGAAA
2267 AAATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.60
17 2 0.13
18 4 0.27
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAATAAAAACGAAAG
Found at i:2752 original size:12 final size:12
Alignment explanation
Indices: 2735--2804 Score: 74
Period size: 12 Copynumber: 6.0 Consensus size: 12
2725 AATGGGTCTA
2735 ATAAACGAGCTT
1 ATAAACGAGCTT
2747 ATAAACGAGCTT
1 ATAAACGAGCTT
*
2759 -TATACGAGC-T
1 ATAAACGAGCTT
*
2769 ATTAAACGAGCTA
1 A-TAAACGAGCTT
* *
2782 ATAAACGAAC-C
1 ATAAACGAGCTT
2793 ATAAACGAGCTT
1 ATAAACGAGCTT
2805 GTTCGTTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
10 1 0.02
11 17 0.36
12 28 0.60
13 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.23
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:2801 original size:35 final size:35
Alignment explanation
Indices: 2736--2803 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
2726 ATGGGTCTAA
* * ** *
2736 TAAACGAGCTTATAAACGAGCTTTATACGAGCTAT
1 TAAACGAGCTAATAAACGAACCATAAACGAGCTAT
2771 TAAACGAGCTAATAAACGAACCATAAACGAGCT
1 TAAACGAGCTAATAAACGAACCATAAACGAGCT
2804 TGTTCGTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (35 bp):
TAAACGAGCTAATAAACGAACCATAAACGAGCTAT
Found at i:3520 original size:15 final size:15
Alignment explanation
Indices: 3502--3535 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3492 AAATATATAT
3502 ATATAAAACAAACCA
1 ATATAAAACAAACCA
*
3517 ATATAAAACAAGCCA
1 ATATAAAACAAACCA
3532 ATAT
1 ATAT
3536 TTGGTAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.62, C:0.18, G:0.03, T:0.18
Consensus pattern (15 bp):
ATATAAAACAAACCA
Found at i:3617 original size:20 final size:19
Alignment explanation
Indices: 3594--3668 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 19
3584 AATTCATACC
*
3594 TTTTTATACTTCCTCGTGTT
1 TTTTTATA-TTCCTAGTGTT
*
3614 TTTTTGGTATTCCTTA-TAGTT
1 TTTTT-ATATTCC-TAGT-GTT
3635 TTTTTATATTTCCTAGTGTGT
1 TTTTTATA-TTCCTAGTGT-T
3656 TTTGTTAT-TTCCT
1 TTT-TTATATTCCT
3669 CAAAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
20 21 0.47
21 20 0.44
22 4 0.09
ACGTcount: A:0.12, C:0.13, G:0.12, T:0.63
Consensus pattern (19 bp):
TTTTTATATTCCTAGTGTT
Found at i:3668 original size:41 final size:40
Alignment explanation
Indices: 3594--3685 Score: 96
Period size: 41 Copynumber: 2.3 Consensus size: 40
3584 AATTCATACC
* * * * **
3594 TTTTTATACTTCCTCGTGTTTTTTTGGTATTCCTTATAGTT
1 TTTTTATATTTCCTAGTGTTGTTTTGGTATTCCTCA-AAAT
*
3635 TTTTTATATTTCCTAGTG-TGTTTTGTTATTTCCTCAAAAT
1 TTTTTATATTTCCTAGTGTTGTTTTGGTA-TTCCTCAAAAT
3675 TTTTTATATTT
1 TTTTTATATTT
3686 TCTCATATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 21 0.49
41 22 0.51
ACGTcount: A:0.16, C:0.12, G:0.10, T:0.62
Consensus pattern (40 bp):
TTTTTATATTTCCTAGTGTTGTTTTGGTATTCCTCAAAAT
Found at i:17267 original size:31 final size:31
Alignment explanation
Indices: 17227--17285 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
17217 AAAAGATCAT
17227 TAAAATATTTGAA-AGTTTTCATTTAAGTCAC
1 TAAAATATTTGAATA-TTTTCATTTAAGTCAC
* *
17258 TAAACTATTTGAATATTTTTATTTAAGT
1 TAAAATATTTGAATATTTTCATTTAAGT
17286 TGTTACACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.47
Consensus pattern (31 bp):
TAAAATATTTGAATATTTTCATTTAAGTCAC
Found at i:28682 original size:5 final size:6
Alignment explanation
Indices: 28667--28701 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
28657 ATATTCCTAG
*
28667 TTTTTC TTTTTC TTTTTC TTTTTC TTATT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
28702 GTTTGGATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:38571 original size:31 final size:31
Alignment explanation
Indices: 38513--38574 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
38503 TTAATAACCC
*
38513 AGTGACTTAAATAAAAACTTCTTAATAGTTT
1 AGTGACTTAAATAAAAACTTCTGAATAGTTT
* *
38544 AGTGACTTACATGAAAACTT-TCGAATAGTTT
1 AGTGACTTAAATAAAAACTTCT-GAATAGTTT
38575 GTGGACCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTCTGAATAGTTT
Found at i:45219 original size:23 final size:23
Alignment explanation
Indices: 45193--45240 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
45183 AATTTAACTT
*
45193 TTTTTAGTACCTAAACTTGACAC
1 TTTTTAGTACCTAAACTCGACAC
* *
45216 TTTTTGGTATCTAAACTCGACAC
1 TTTTTAGTACCTAAACTCGACAC
45239 TT
1 TT
45241 ATCCCTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTTTAGTACCTAAACTCGACAC
Found at i:45380 original size:31 final size:31
Alignment explanation
Indices: 45339--45413 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
45329 TTAATATAAC
*
45339 ATTTGGTACCTAAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTGTTCCTA
* * *
45370 ATTTGATACCTAAATTTGACTCTTGTTCCTA
1 ATTTGGTACCTAAACTTGACACTTGTTCCTA
45401 ATTTGGTACCTAA
1 ATTTGGTACCTAA
45414 TCTTTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.43
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTGTTCCTA
Found at i:45693 original size:31 final size:29
Alignment explanation
Indices: 45599--45727 Score: 96
Period size: 26 Copynumber: 4.5 Consensus size: 29
45589 AAACATAGGA
45599 ACCAAATTAGGAAAAAAGTCAAGTTCAAGT
1 ACCAAATTAGGAAAAAA-TCAAGTTCAAGT
* *
45629 ACCAAATTGAGTCG-AAAAA--AA-TTTAGGT
1 ACCAAATT-AG--GAAAAAATCAAGTTCAAGT
45657 ACCAAATTAGGAAAAGATATCAAGTTCAAGT
1 ACCAAATTAGGAAAA-A-ATCAAGTTCAAGT
*
45688 ACCAAATT-GGATAAAAA--AA-TTTAAGT
1 ACCAAATTAGGA-AAAAATCAAGTTCAAGT
*
45714 ACTAAATTA-GAAAA
1 ACCAAATTAGGAAAA
45728 TATTTTTAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 27
0.71 0.05 0.23
Matches are distributed among these distances:
25 4 0.05
26 18 0.22
27 5 0.06
28 14 0.17
29 3 0.04
30 14 0.17
31 18 0.22
32 5 0.06
33 1 0.01
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (29 bp):
ACCAAATTAGGAAAAAATCAAGTTCAAGT
Found at i:45705 original size:58 final size:57
Alignment explanation
Indices: 45585--45727 Score: 177
Period size: 58 Copynumber: 2.5 Consensus size: 57
45575 ATCTAAAAAA
** *
45585 AAAAAAACATAGGAACCAAATTAGGAAAAAAGTCAAGTTCAAGTACCAAATTGAGTC
1 AAAAAAATTTAGGTACCAAATTAGGAAAAAAGTCAAGTTCAAGTACCAAATTGAGTC
45642 GAAAAAAATTTAGGTACCAAATTAGGAAAAGATA-TCAAGTTCAAGTACCAAATTG-GAT-
1 -AAAAAAATTTAGGTACCAAATTAGGAAAA-A-AGTCAAGTTCAAGTACCAAATTGAG-TC
* *
45700 AAAAAAATTTAAGTACTAAATTA-GAAAA
1 AAAAAAATTTAGGTACCAAATTAGGAAAA
45728 TATTTTTAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
56 5 0.06
57 21 0.27
58 27 0.35
59 23 0.30
60 1 0.01
ACGTcount: A:0.53, C:0.10, G:0.15, T:0.22
Consensus pattern (57 bp):
AAAAAAATTTAGGTACCAAATTAGGAAAAAAGTCAAGTTCAAGTACCAAATTGAGTC
Found at i:51813 original size:5 final size:5
Alignment explanation
Indices: 51803--51840 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
51793 AATTGGGTCA
* *
51803 TTTTC TTTTC TTTTC TTTT- TTTTC TTTTT TTTTA TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
51841 GTTAATCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (5 bp):
TTTTC
Found at i:51827 original size:9 final size:9
Alignment explanation
Indices: 51803--51834 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
51793 AATTGGGTCA
51803 TTTTCTTTT
1 TTTTCTTTT
51812 CTTTTCTTTT
1 -TTTTCTTTT
51822 TTTTCTTTT
1 TTTTCTTTT
51831 TTTT
1 TTTT
51835 TATTTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:51827 original size:19 final size:19
Alignment explanation
Indices: 51803--51840 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
51793 AATTGGGTCA
*
51803 TTTTCTTTTCTTTTCTTTT
1 TTTTCTTTTCTTTTATTTT
*
51822 TTTTCTTTTTTTTTATTTT
1 TTTTCTTTTCTTTTATTTT
51841 GTTAATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (19 bp):
TTTTCTTTTCTTTTATTTT
Found at i:64586 original size:16 final size:16
Alignment explanation
Indices: 64567--64611 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
64557 CTCAAGTCCG
64567 AAATAATTCAAATACA
1 AAATAATTCAAATACA
*
64583 AAATATTTCAAACT-CA
1 AAATAATTCAAA-TACA
64599 AAATAA-TCAAATA
1 AAATAATTCAAATA
64612 ATTTGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 5 0.20
16 18 0.72
17 1 0.04
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAATTCAAATACA
Found at i:68705 original size:17 final size:19
Alignment explanation
Indices: 68678--68715 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
68668 TTTATATTTC
*
68678 ATAATTCAACCTAA-ACAA
1 ATAATTCAACCCAATACAA
68696 ATAA-TCAACCCAATACAA
1 ATAATTCAACCCAATACAA
68714 AT
1 AT
68716 CGTGGGACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (19 bp):
ATAATTCAACCCAATACAA
Found at i:73876 original size:26 final size:26
Alignment explanation
Indices: 73827--73876 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
73817 CAACAACTTT
* *
73827 AAAATAATAATAATTTAAATAATTTA
1 AAAATAATAATAAATTAAAAAATTTA
73853 AAAATAATAA-AAATTAATAAAATT
1 AAAATAATAATAAATTAA-AAAATT
73877 ATATTTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAATAATAATAAATTAAAAAATTTA
Found at i:75726 original size:46 final size:46
Alignment explanation
Indices: 75655--75760 Score: 142
Period size: 46 Copynumber: 2.3 Consensus size: 46
75645 GTTACATAAC
* *
75655 ATTTTTAATACTTTAATATTTTATTAATTATTAAATTAAATTTATA
1 ATTTTTAATATTTTAATATTTTATTAATGATTAAATTAAATTTATA
* * * *
75701 ATTTTGAATATTTTTATCTTTTATTAATGATTGAATTAAATTTATA
1 ATTTTTAATATTTTAATATTTTATTAATGATTAAATTAAATTTATA
*
75747 GTTTTTAA-ATTTTA
1 ATTTTTAATATTTTA
75761 CTGTGAGTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
45 5 0.10
46 46 0.90
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (46 bp):
ATTTTTAATATTTTAATATTTTATTAATGATTAAATTAAATTTATA
Found at i:85462 original size:6 final size:6
Alignment explanation
Indices: 85448--85478 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
85438 TTAATGTGAG
*
85448 AGACAC AGACTC AGACTC AGACTC AGACTC A
1 AGACTC AGACTC AGACTC AGACTC AGACTC A
85479 TTCGAACGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.39, C:0.32, G:0.16, T:0.13
Consensus pattern (6 bp):
AGACTC
Found at i:86036 original size:18 final size:18
Alignment explanation
Indices: 85989--86036 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
85979 ATTTATACGC
85989 AAATTTTATATCTCAAAT
1 AAATTTTATATCTCAAAT
86007 ATAATTTATATAT-TCAAATT
1 A-AATTT-TATATCTCAAA-T
86027 AAATTTTATA
1 AAATTTTATA
86037 AACAAGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.19
19 15 0.56
20 7 0.26
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATTTTATATCTCAAAT
Found at i:94304 original size:27 final size:29
Alignment explanation
Indices: 94246--94305 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
94236 AAGAACCCAT
94246 AAAA-CATTAGAAATTATAAAAACAATAG
1 AAAATCATTAGAAATTATAAAAACAATAG
* *
94274 AAAATCATTA-AAATTTTATAAA-AATAG
1 AAAATCATTAGAAATTATAAAAACAATAG
94301 AAAAT
1 AAAAT
94306 TTTTCATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.34
28 14 0.48
29 5 0.17
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (29 bp):
AAAATCATTAGAAATTATAAAAACAATAG
Found at i:100796 original size:29 final size:30
Alignment explanation
Indices: 100735--100801 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
100725 GTCTAAACTA
* * *
100735 AAAAAAAGTCATCTTATTTGATTCAAAATT
1 AAAAAATGTAATCTTATTTGATACAAAATT
*
100765 AAAAAATGTAATCTTATTTGCTACAAAA-T
1 AAAAAATGTAATCTTATTTGATACAAAATT
100794 AAATAAAT
1 AAA-AAAT
100802 TAAATTAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (30 bp):
AAAAAATGTAATCTTATTTGATACAAAATT
Found at i:112036 original size:10 final size:10
Alignment explanation
Indices: 111988--112036 Score: 50
Period size: 9 Copynumber: 5.2 Consensus size: 10
111978 ATTAAGTGTC
111988 ATAAAATATT
1 ATAAAATATT
*
111998 A-AAAA-AGT
1 ATAAAATATT
*
112006 ATAAAA-ACT
1 ATAAAATATT
*
112015 ATTAAATATT
1 ATAAAATATT
112025 ATAAAATATT
1 ATAAAATATT
112035 AT
1 AT
112037 TAATAAGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 3 0.09
9 15 0.47
10 14 0.44
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
ATAAAATATT
Found at i:112037 original size:20 final size:20
Alignment explanation
Indices: 111988--112044 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
111978 ATTAAGTGTC
111988 ATAAAATATTA--AAAAAGT
1 ATAAAATATTATTAAAAAGT
* * *
112006 ATAAAA-ACTATTAAATATT
1 ATAAAATATTATTAAAAAGT
*
112025 ATAAAATATTATTAATAAGT
1 ATAAAATATTATTAAAAAGT
112045 TATGAAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 3 0.10
18 6 0.21
19 11 0.38
20 9 0.31
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
ATAAAATATTATTAAAAAGT
Found at i:112471 original size:22 final size:22
Alignment explanation
Indices: 112423--112464 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
112413 AATATAATAA
112423 CAAAATGACAACAAAACAACAT
1 CAAAATGACAACAAAACAACAT
*
112445 CAAAATGGCAACAAAACAAC
1 CAAAATGACAACAAAACAAC
112465 GGTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.24, G:0.07, T:0.07
Consensus pattern (22 bp):
CAAAATGACAACAAAACAACAT
Found at i:113625 original size:21 final size:23
Alignment explanation
Indices: 113601--113647 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
113591 CAATATCGTT
113601 AATGAATTTTA-ATT-ATATTCA
1 AATGAATTTTATATTAATATTCA
* *
113622 AATGCATTTTATTTTAATATTCA
1 AATGAATTTTATATTAATATTCA
113645 AAT
1 AAT
113648 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 2 0.09
23 10 0.45
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (23 bp):
AATGAATTTTATATTAATATTCA
Found at i:129550 original size:30 final size:31
Alignment explanation
Indices: 129516--129579 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
129506 TTAATAAGAA
129516 TTTACAAAAAAAAGG-G-TTTAATTAATTTTT
1 TTTAC-AAAAAAAGGAGTTTTAATTAATTTTT
* **
129546 TTTACAGAAAGTGGAGTTTTAATTAATTTTT
1 TTTACAAAAAAAGGAGTTTTAATTAATTTTT
129577 TTT
1 TTT
129580 TTAAAATGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 6 0.21
31 17 0.59
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (31 bp):
TTTACAAAAAAAGGAGTTTTAATTAATTTTT
Found at i:136004 original size:26 final size:25
Alignment explanation
Indices: 135962--136021 Score: 59
Period size: 26 Copynumber: 2.3 Consensus size: 25
135952 TTAAGATGAT
135962 TATATAAAAACTTTTAATAAATAAAAA
1 TATAT-AAAACTTTTAA-AAATAAAAA
* *
135989 TATATAAAA-TTATTAAATATTAAAA
1 TATATAAAACTT-TTAAAAATAAAAA
136014 TAATATAA
1 T-ATATAA
136022 TATAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 10 0.34
26 14 0.48
27 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TATATAAAACTTTTAAAAATAAAAA
Found at i:137447 original size:21 final size:21
Alignment explanation
Indices: 137396--137447 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
137386 TATGATTCTA
* *
137396 AAAATTAAGAAAATATAAATAT
1 AAAA-TAAAAAAATATAAAAAT
137418 AAAATAAAAAAATATAAAAAT
1 AAAATAAAAAAATATAAAAAT
*
137439 -ACATAAAAA
1 AAAATAAAAA
137448 TTAAAAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 8 0.30
21 15 0.56
22 4 0.15
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAATAAAAAAATATAAAAAT
Found at i:137454 original size:26 final size:24
Alignment explanation
Indices: 137394--137473 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 24
137384 ATTATGATTC
137394 TAAAAATTAAGAAAATAT-AAAT-A
1 TAAAAATTAA-AAAATATAAAATCA
*
137417 T-AAAATAAAAAAATATAAAAATACA
1 TAAAAATTAAAAAATAT-AAAAT-CA
*
137442 TAAAAATTAAAAAGTATTAAAATTCA
1 TAAAAATTAAAAAATA-TAAAA-TCA
137468 TAAAAA
1 TAAAAA
137474 AATATAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
21 7 0.15
22 7 0.15
23 5 0.11
25 2 0.04
26 24 0.51
27 2 0.04
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (24 bp):
TAAAAATTAAAAAATATAAAATCA
Found at i:142837 original size:2 final size:2
Alignment explanation
Indices: 142830--142860 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
142820 TTTATAACTT
142830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
142861 TTAGATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:142928 original size:40 final size:40
Alignment explanation
Indices: 142884--142963 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
142874 AATTTTTTTA
*
142884 AAAATATAAATTTTGAAATTTTTATAAATATTTTGAATTT
1 AAAATATAAATTTTGAAATTTTTAAAAATATTTTGAATTT
* *** * *
142924 AAAATTTTTTTTTTGGATTTTTTAAAAATATTTTGAATTT
1 AAAATATAAATTTTGAAATTTTTAAAAATATTTTGAATTT
142964 CTTGTTTAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (40 bp):
AAAATATAAATTTTGAAATTTTTAAAAATATTTTGAATTT
Found at i:149659 original size:43 final size:44
Alignment explanation
Indices: 149585--149670 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
149575 AAAGAAAGTA
* * *
149585 AAAAAAAGGGTAAAACTTTATAGTTAGGTTAGGTTCATGAAAAG
1 AAAAAAAGGGGAAAACTTTACAGTCAGGTTAGGTTCATGAAAAG
* *
149629 AAAAAAAGGGGAAAGCTTTACAGTCA-GTTAGGTTCGTGAAAA
1 AAAAAAAGGGGAAAACTTTACAGTCAGGTTAGGTTCATGAAAA
149671 CATGAATCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 15 0.41
44 22 0.59
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.24
Consensus pattern (44 bp):
AAAAAAAGGGGAAAACTTTACAGTCAGGTTAGGTTCATGAAAAG
Found at i:153571 original size:33 final size:33
Alignment explanation
Indices: 153467--153572 Score: 88
Period size: 33 Copynumber: 3.1 Consensus size: 33
153457 TAAATACTAA
*
153467 AAAATCTACCTGAGGTTTGTGAGGCACTTAGGC
1 AAAATCTACCTGAGGTTTGTGAAGCACTTAGGC
* * ** * * *
153500 AAATTCCCTAACTACTTATATTTG-CATGAACTTAGGC
1 AAAAT--CT-AC--CTGAGGTTTGTGAAGCACTTAGGC
153537 AAAATCTACCTGAGGTTTGTGAAGCACTTAGGC
1 AAAATCTACCTGAGGTTTGTGAAGCACTTAGGC
153570 AAA
1 AAA
153573 TACTAGTCAT
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
32 7 0.13
33 17 0.32
34 2 0.04
35 4 0.08
36 2 0.04
37 14 0.26
38 7 0.13
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (33 bp):
AAAATCTACCTGAGGTTTGTGAAGCACTTAGGC
Found at i:160121 original size:30 final size:30
Alignment explanation
Indices: 160085--160153 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
160075 CCATTCTTTC
* * *
160085 GCTCAAAACTTTCATGAAGATTTCTTGGTT
1 GCTCAAAACTTGCAAGAAGATTTCTTGGAT
160115 GCTCAAAACTTGCAAGAAGATTTCTTGGAT
1 GCTCAAAACTTGCAAGAAGATTTCTTGGAT
160145 GCTCAAAAC
1 GCTCAAAAC
160154 AATGCTCGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (30 bp):
GCTCAAAACTTGCAAGAAGATTTCTTGGAT
Found at i:165650 original size:28 final size:28
Alignment explanation
Indices: 165619--165771 Score: 96
Period size: 28 Copynumber: 5.1 Consensus size: 28
165609 ATATAAAGAT
165619 TAAATTACTATTTCTATCATTTATAATA
1 TAAATTACTATTTCTATCATTTATAATA
* *
165647 TAAATTACTA-TTCTATGATTTATGATA
1 TAAATTACTATTTCTATCATTTATAATA
*** *
165674 -AAGAGCGCTCATATAT-TGATTATTTATTTAATA
1 TAA-ATTACT-AT-T-TCT-ATCATTTA--TAATA
165707 TAGAGATTAAATTACTATTTCTATCATTTATAATA
1 TA-A-A-T---T-ACTATTTCTATCATTTATAATA
*
165742 TAAATTACTATTTCTATTATTTATAATA
1 TAAATTACTATTTCTATCATTTATAATA
165770 TA
1 TA
165772 TATATTATAA
Statistics
Matches: 97, Mismatches: 12, Indels: 32
0.69 0.09 0.23
Matches are distributed among these distances:
26 2 0.02
27 18 0.19
28 34 0.35
29 1 0.01
30 2 0.02
31 8 0.08
32 1 0.01
33 5 0.05
34 2 0.02
35 10 0.10
37 8 0.08
38 2 0.02
39 2 0.02
40 2 0.02
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (28 bp):
TAAATTACTATTTCTATCATTTATAATA
Found at i:165716 original size:95 final size:96
Alignment explanation
Indices: 165584--165765 Score: 339
Period size: 95 Copynumber: 1.9 Consensus size: 96
165574 TCATAAGGAA
165584 CGCTCATATATTGATTATTTATTTAATATAAAGATTAAATTACTATTTCTATCATTTATAATATA
1 CGCTCATATATTGATTATTTATTTAATATAAAGATTAAATTACTATTTCTATCATTTATAATATA
165649 AATTACTA-TTCTATGATTTATGATAAAGAG
66 AATTACTATTTCTATGATTTATGATAAAGAG
*
165679 CGCTCATATATTGATTATTTATTTAATATAGAGATTAAATTACTATTTCTATCATTTATAATATA
1 CGCTCATATATTGATTATTTATTTAATATAAAGATTAAATTACTATTTCTATCATTTATAATATA
*
165744 AATTACTATTTCTATTATTTAT
66 AATTACTATTTCTATGATTTAT
165766 AATATATATA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
95 72 0.86
96 12 0.14
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (96 bp):
CGCTCATATATTGATTATTTATTTAATATAAAGATTAAATTACTATTTCTATCATTTATAATATA
AATTACTATTTCTATGATTTATGATAAAGAG
Found at i:166279 original size:21 final size:20
Alignment explanation
Indices: 166233--166287 Score: 101
Period size: 20 Copynumber: 2.7 Consensus size: 20
166223 AAATTTCATC
166233 TATTTTTATTGTTAAAACAT
1 TATTTTTATTGTTAAAACAT
166253 TATTTTTATTGTTAAAACAT
1 TATTTTTATTGTTAAAACAT
166273 TATTTTTATATGTTA
1 TATTTTTAT-TGTTA
166288 GCATGATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (20 bp):
TATTTTTATTGTTAAAACAT
Found at i:172939 original size:6 final size:6
Alignment explanation
Indices: 172928--172978 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
172918 TGAGTGATTG
172928 CTTGCA CTTGCA CTTGCA CTTGCA CTTGCA CTTGCA CTTGCA CTTGCA
1 CTTGCA CTTGCA CTTGCA CTTGCA CTTGCA CTTGCA CTTGCA CTTGCA
172976 CTT
1 CTT
172979 AGGCCCCAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.35
Consensus pattern (6 bp):
CTTGCA
Found at i:186166 original size:2 final size:2
Alignment explanation
Indices: 186159--186193 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
186149 ATCTAGATTT
186159 TC 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 TC T
186194 TTTGACACTA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:192294 original size:2 final size:2
Alignment explanation
Indices: 192287--192319 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
192277 TTTAAAACTA
192287 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 A
192320 ACCAATTATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:196717 original size:31 final size:30
Alignment explanation
Indices: 196657--196729 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
196647 ATAATAAAAA
*
196657 TATTATTTTTAAAAAATTAAATCAAAATTT
1 TATTATTTTTAAAAAATTAAAGCAAAATTT
**
196687 TATTATTTTTAAAAAAGTTAAAGCGTAATTT
1 TATTATTTTTAAAAAA-TTAAAGCAAAATTT
196718 TATT-TTTATTAA
1 TATTATTT-TTAA
196730 TTCATAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.50
31 19 0.50
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (30 bp):
TATTATTTTTAAAAAATTAAAGCAAAATTT
Found at i:207350 original size:28 final size:28
Alignment explanation
Indices: 207304--207363 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
207294 TTAAGATGAC
*
207304 TATATAAAAATTTTCAATAGATAAAA-AA
1 TATATAAAAATTTTAAATA-ATAAAATAA
*
207332 TATAT-AAAATTATTAAATATTAAAATAA
1 TATATAAAAATT-TTAAATAATAAAATAA
207360 TATA
1 TATA
207364 ATATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
TATATAAAAATTTTAAATAATAAAATAA
Found at i:208314 original size:25 final size:24
Alignment explanation
Indices: 208285--208331 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
208275 TTTTATATTA
208285 ATATTAATATTAAATAGAAATAATT
1 ATATTAATATTAAATA-AAATAATT
208310 ATATTAATATTAAATAAAATAA
1 ATATTAATATTAAATAAAATAA
208332 AAATCTCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATTAATATTAAATAAAATAATT
Found at i:208314 original size:31 final size:30
Alignment explanation
Indices: 208277--208335 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
208267 AATAATAATT
* *
208277 TTATATTAATATTAATATTAAATAGAAATAA
1 TTATATTAATATTAA-ATAAAATAAAAATAA
208308 TTATATTAATATTAAATAAAATAAAAAT
1 TTATATTAATATTAAATAAAATAAAAAT
208336 CTCCCACCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
TTATATTAATATTAAATAAAATAAAAATAA
Found at i:209755 original size:98 final size:100
Alignment explanation
Indices: 209638--209831 Score: 302
Period size: 98 Copynumber: 1.9 Consensus size: 100
209628 ACTAGCTAAA
* * *
209638 ATATACTACAAATATAATATATTTGTTGAGGAAGAAATGATAAACAAAGGAGATACTGATTCAC-
1 ATATAATACAAATATAATATATTTATTGAGGAAGAAATGATAAACAAAAGAGATACTGATTCACA
* * *
209702 G-TGGTGGTGATGTGTTACTAGAGAAATTGAGCAG
66 GATGATGATGATGTGTTACGAGAGAAATTGAGCAG
*
209736 ATATAATACAAATATAATATATTTATTGAGGAAGAAATGATAAACAAAAGAGATAGTGATTCACA
1 ATATAATACAAATATAATATATTTATTGAGGAAGAAATGATAAACAAAAGAGATACTGATTCACA
209801 TGATGATGATGATGTGTTACGAGAGAAATTG
66 -GATGATGATGATGTGTTACGAGAGAAATTG
209832 CGCAAACACT
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
98 60 0.70
100 1 0.01
101 25 0.29
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.29
Consensus pattern (100 bp):
ATATAATACAAATATAATATATTTATTGAGGAAGAAATGATAAACAAAAGAGATACTGATTCACA
GATGATGATGATGTGTTACGAGAGAAATTGAGCAG
Found at i:215510 original size:22 final size:22
Alignment explanation
Indices: 215482--215532 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
215472 TACAGTGGTA
215482 AAATAAAATAAAAGTAAAGTCC
1 AAATAAAATAAAAGTAAAGTCC
215504 AAATAAAATAAAAGTAAAGTCC
1 AAATAAAATAAAAGTAAAGTCC
215526 AAATAAA
1 AAATAAA
215533 CTAGACTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.18
Consensus pattern (22 bp):
AAATAAAATAAAAGTAAAGTCC
Found at i:235533 original size:67 final size:67
Alignment explanation
Indices: 235425--235559 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
235415 CAACCATATC
*
235425 CTCAATTACAACGACAATCACGATTTCTATATTCTGATTTTTCATAGTTGTTATGTATTGTAACA
1 CTCAATTACAACGACAACCACGATTTCTATATTCTGATTTTTCATAGTTGTTATGTATTGTAACA
235490 TT
66 TT
*
235492 CTCAATTACAACGACAACCACGATTTCTATATTTTGATTTTTCATAGTTGTTATGTATTGTAACA
1 CTCAATTACAACGACAACCACGATTTCTATATTCTGATTTTTCATAGTTGTTATGTATTGTAACA
235557 TT
66 TT
235559 C
1 C
235560 ACTTCAGGGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (67 bp):
CTCAATTACAACGACAACCACGATTTCTATATTCTGATTTTTCATAGTTGTTATGTATTGTAACA
TT
Found at i:236806 original size:17 final size:17
Alignment explanation
Indices: 236780--236821 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
236770 AAAAAAAAAT
*
236780 AATTATAAAAATATGAAA
1 AATTA-AAAAAGATGAAA
236798 AATTAAAAAAGATGAAA
1 AATTAAAAAAGATGAAA
*
236815 GATTAAA
1 AATTAAA
236822 GGTTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (17 bp):
AATTAAAAAAGATGAAA
Found at i:238645 original size:37 final size:38
Alignment explanation
Indices: 238587--238663 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 38
238577 CGCTAAAATA
* *
238587 AAATTGACACCCAATGTCTCATCGGTTAAA-CCGAAGT
1 AAATTGACACCCAATGCCTCATCGGATAAATCCGAAGT
** *
238624 AAATTGACACCCTGTGCCTCATCGGATAAATCCTAAGT
1 AAATTGACACCCAATGCCTCATCGGATAAATCCGAAGT
238662 AA
1 AA
238664 TAAATCGCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
37 26 0.76
38 8 0.24
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (38 bp):
AAATTGACACCCAATGCCTCATCGGATAAATCCGAAGT
Found at i:238706 original size:101 final size:101
Alignment explanation
Indices: 238530--238717 Score: 331
Period size: 101 Copynumber: 1.9 Consensus size: 101
238520 ATCGGTTTGG
238530 CACCCTGAGCCTCATCGGATAAATCCGAAGTAATAAATCGCGCCTTGCGCTAAAATAAAATTGAC
1 CACCCTGAGCCTCATCGGATAAATCCGAAGTAATAAATCGCGCCTTGCGCTAAAATAAAATTGAC
*
238595 ACCCAATGTCTCATCGGTTAAACCGAAGTAAATTGA
66 ACCCAATGTCTCATCAGTTAAACCGAAGTAAATTGA
* * *
238631 CACCCTGTGCCTCATCGGATAAATCCTAAGTAATAAATCGCGCCTTGCGCTAAAATAAAGTTGAC
1 CACCCTGAGCCTCATCGGATAAATCCGAAGTAATAAATCGCGCCTTGCGCTAAAATAAAATTGAC
*
238696 ACCCAGTGTCTCATCAGTTAAA
66 ACCCAATGTCTCATCAGTTAAA
238718 TATAAGTAAT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (101 bp):
CACCCTGAGCCTCATCGGATAAATCCGAAGTAATAAATCGCGCCTTGCGCTAAAATAAAATTGAC
ACCCAATGTCTCATCAGTTAAACCGAAGTAAATTGA
Found at i:238764 original size:101 final size:101
Alignment explanation
Indices: 238538--238747 Score: 305
Period size: 101 Copynumber: 2.1 Consensus size: 101
238528 GGCACCCTGA
*
238538 GCCTCATCGGATAAATCCGAAGTAATAAATCGCGCCTTGCGCTAAAATAAAATTGACACCCAATG
1 GCCTCATCGGATAAATCCAAAGTAATAAATCGCGCCTTGCGCTAAAATAAAATTGACACCCAATG
* * *
238603 TCTCATCGGTTAAACCGAAGTAAATTGACACCCTGT
66 TCTCATCAGTTAAACAGAAGTAAATTGACACCCAGT
* * *
238639 GCCTCATCGGATAAATCCTAAGTAATAAATCGCGCCTTGCGCTAAAATAAAGTTGACACCCAGTG
1 GCCTCATCGGATAAATCCAAAGTAATAAATCGCGCCTTGCGCTAAAATAAAATTGACACCCAATG
* * ** *
238704 TCTCATCAGTTAAATATAAGT-AATTGGTACTCAGT
66 TCTCATCAGTTAAACAGAAGTAAATTGACACCCAGT
238739 GCCTCATCG
1 GCCTCATCG
238748 ACTCATAGTC
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
100 19 0.19
101 79 0.81
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (101 bp):
GCCTCATCGGATAAATCCAAAGTAATAAATCGCGCCTTGCGCTAAAATAAAATTGACACCCAATG
TCTCATCAGTTAAACAGAAGTAAATTGACACCCAGT
Found at i:248647 original size:3 final size:3
Alignment explanation
Indices: 248639--248668 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
248629 CAAATCTAAC
248639 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
248669 TGGAAAAAGG
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:256165 original size:14 final size:14
Alignment explanation
Indices: 256114--256165 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
256104 TTTATAAAAG
*
256114 TTGTACATTTAATCT
1 TTGTACTTTTAAT-T
256129 TTGTAC-TTTAATT
1 TTGTACTTTTAATT
* *
256142 TGGTAATTTTAATT
1 TTGTACTTTTAATT
256156 TTGTACTTTT
1 TTGTACTTTT
256166 CAAATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 5 0.16
14 21 0.66
15 6 0.19
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.60
Consensus pattern (14 bp):
TTGTACTTTTAATT
Found at i:259748 original size:42 final size:42
Alignment explanation
Indices: 259699--259779 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
259689 TAAGTATAAC
259699 ACATCACAGACAGATAATGTTGGGGAGAAATTGATAAATATT
1 ACATCACAGACAGATAATGTTGGGGAGAAATTGATAAATATT
* * *
259741 ACATCACAGACGGGTAATGTTGGGGAGAATTTGATAAAT
1 ACATCACAGACAGATAATGTTGGGGAGAAATTGATAAAT
259780 CCACGTGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.26
Consensus pattern (42 bp):
ACATCACAGACAGATAATGTTGGGGAGAAATTGATAAATATT
Found at i:270673 original size:2 final size:2
Alignment explanation
Indices: 270666--270700 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
270656 ACTATCAAGA
270666 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
270701 NNNNNNNNNN
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:271755 original size:2 final size:2
Alignment explanation
Indices: 271748--271778 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
271738 TATAATTGGA
271748 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 A
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.